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Sample records for allergen microarray detects

  1. A protein allergen microarray detects specific IgE to pollen surface, cytoplasmic, and commercial allergen extracts.

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    Katinka A Vigh-Conrad

    Full Text Available BACKGROUND: Current diagnostics for allergies, such as skin prick and radioallergosorbent tests, do not allow for inexpensive, high-throughput screening of patients. Additionally, extracts used in these methods are made from washed pollen that lacks pollen surface materials that may contain allergens. METHODOLOGY/PRINCIPAL FINDINGS: We sought to develop a high-throughput assay to rapidly measure allergen-specific IgE in sera and to explore the relative allergenicity of different pollen fractions (i.e. surface, cytoplasmic, commercial extracts. To do this, we generated a protein microarray containing surface, cytoplasmic, and commercial extracts from 22 pollen species, commercial extracts from nine non-pollen allergens, and five recombinant allergenic proteins. Pollen surface and cytoplasmic fractions were prepared by extraction into organic solvents and aqueous buffers, respectively. Arrays were incubated with <25 uL of serum from 176 individuals and bound IgE was detected by indirect immunofluorescence, providing a high-throughput measurement of IgE. We demonstrated that the allergen microarray is a reproducible method to measure allergen-specific IgE in small amounts of sera. Using this tool, we demonstrated that specific IgE clusters according to the phylogeny of the allergen source. We also showed that the pollen surface, which has been largely overlooked in the past, contained potent allergens. Although, as a class, cytoplasmic fractions obtained by our pulverization/precipitation method were comparable to commercial extracts, many individual allergens showed significant differences. CONCLUSIONS/SIGNIFICANCE: These results support the hypothesis that protein microarray technology is a useful tool for both research and in the clinic. It could provide a more efficient and less painful alternative to traditionally used skin prick tests, making it economically feasible to compare allergen sensitivity of different populations, monitor individual

  2. Allergen micro-array detection of specific IgE-reactivity in Chinese allergy patients

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yi-wu; ZHONG Nan-shan; Michael D Spangfort; LI Jing; LAI Xu-xin; ZHAO De-yu; LIU Xiao-fan; LIN Xiao-ping; Birgitte Gjesing; Paola Palazzo; Adriano Mari

    2011-01-01

    Background Allergen micro-arrays are powerful tools for screening of serum IgE-reactivity.In this study allergen micro-arrays were used to identify dominating IgE-binding allergens and cross-reactivity patterns among selected Chinese allergy patients.Methods The study was conducted using patient sera from the cities of Guangzhou,Nanjing,Chengdu and Shenyang.In total 100 sera with Dermatophagoides pteronyssinus (Der p) specific IgE-levels higher than 50 kU/L were selected for testing against 103 individual allergens.Results Among 100 selected patients, 95% showed IgE-reactivity towards house-dust mite allergens Dermatophagoides farinae (Der f) 1,Der f 2 and Der p 2 and 94% were IgE positive against Der p 1,and 60% of sera contained IgE reacting against allergen Euroglyphus maynei (Eur m) 2.IgE against cat allergen,Felisdomesticus (Fel d)1,was seen in 20%.Only 2% showed specific IgE-reactivity to Der p 10,a panallergen belonging to the tropomyosin family.Serum IgE-reactivity towards other allergens was in general low.IgE-reactivity against pollen allergens showed geographic differences.Conclusions This study clearly confirms that group 1 and group 2 are major allergens of house dust mites.These selected house-dust mite allergy patients are close to being mono-sensitized.Der p 10 is not an important allergen for cross-reactivity.Specific IgE-sensitization towards pollen allergens is low in southern China compared to other regions.The prevalence of food and stinging insect allergens known to give rise to IgE-mediated cross-reactivity is 2% or less.

  3. Multiplex component-based allergen microarray in recent clinical studies.

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    Patelis, A; Borres, M P; Kober, A; Berthold, M

    2016-08-01

    During the last decades component-resolved diagnostics either as singleplex or multiplex measurements has been introduced into the field of clinical allergology, providing important information that cannot be obtained from extract-based tests. Here we review recent studies that demonstrate clinical applications of the multiplex microarray technique in the diagnosis and risk assessment of allergic patients, and its usefulness in studies of allergic diseases. The usefulness of ImmunoCAP ISAC has been validated in a wide spectrum of allergic diseases like asthma, allergic rhinoconjunctivitis, atopic dermatitis, eosinophilic esophagitis, food allergy and anaphylaxis. ISAC provides a broad picture of a patient's sensitization profile from a single test, and provides information on specific and cross-reactive sensitizations that facilitate diagnosis, risk assessment, and disease management. Furthermore, it can reveal unexpected sensitizations which may explain anaphylaxis previously categorized as idiopathic and also display for the moment clinically non-relevant sensitizations. ISAC can facilitate a better selection of relevant allergens for immunotherapy compared with extract testing. Microarray technique can visualize the allergic march and molecular spreading in the preclinical stages of allergic diseases, and may indicate that the likelihood of developing symptomatic allergy is associated with specific profiles of sensitization to allergen components. ISAC is shown to be a useful tool in routine allergy diagnostics due to its ability to improve risk assessment, to better select relevant allergens for immunotherapy as well as detecting unknown sensitization. Multiplex component testing is especially suitable for patients with complex symptomatology. PMID:27196983

  4. Soybean allergen detection methods

    DEFF Research Database (Denmark)

    Pedersen, Mona H; Holzhauser, Thomas; Bisson, Caroline;

    2008-01-01

    ) using basophils passively sensitized with patient serum and a PCR method detecting soy DNA. Eight food products were selected as model foods to test the performance of the methods. There was an overall good agreement between the methods in terms of ranks of soy content but not the quantity. The sandwich......Soybean containing products are widely consumed, thus reliable methods for detection of soy in foods are needed in order to make appropriate risk assessment studies to adequately protect soy allergic patients. Six methods were compared using eight food products with a declared content of soy...... ELISA aimed at native soy proteins had the lowest detection limit of 0.05 ppm, but only identified soy in 5/8 products, and generally in lower amounts compared to other methods. The competitive ELISA had a higher detection limit of 21 ppm, but seemed more successful in detecting processed soy. Only HR...

  5. Multiplex detection of food allergens and gluten.

    Science.gov (United States)

    Cho, Chung Y; Nowatzke, William; Oliver, Kerry; Garber, Eric A E

    2015-05-01

    To help safeguard the food supply and detect the presence of undeclared food allergens and gluten, most producers and regulatory agencies rely on commercial test kits. Most of these are ELISAs with a few being PCR-based. These methods are very sensitive and analyte specific, requiring different assays to detect each of the different food allergens. Mass spectrometry offers an alternative approach whereby multiple allergens may be detected simultaneously. However, mass spectrometry requires expensive equipment, highly trained analysts, and several years before a quantitative approach can be achieved. Using multianalyte profiling (xMAP®) technology, a commercial multiplex test kit based on the use of established antibodies was developed for the simultaneous detection of up to 14 different food allergens plus gluten. The assay simultaneously detects crustacean seafood, egg, gluten, milk, peanut, soy, and nine tree nuts (almond, Brazil nut, cashew, coconut, hazelnut, macadamia, pine nut, pistachio, and walnut). By simultaneously performing multiple tests (typically two) for each analyte, this magnetic bead-based assay offers built-in confirmatory analyses without the need for additional resources. Twenty-five of the assays were performed on buffer extracted samples, while five were conducted on samples extracted using reduced-denatured conditions. Thus, complete analysis for all 14 allergens and gluten requires only two wells of a 96-well microtiter plate. This makes it possible to include in a single analytical run up to 48 samples. All 30 bead sets in this multiplex assay detected 5 ng/mL of food allergen and gluten with responses greater than background. In addition, 26 of the bead sets displayed signal/noise ratios of five or greater. The bead-based design makes this 30-plex assay expandable to incorporate new antibodies and capture/detector methodologies by ascribing these new detectors to any of the unassigned bead sets that are commercially available. PMID

  6. Allergen Microarray Indicates Pooideae Sensitization in Brazilian Grass Pollen Allergic Patients.

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    Priscila Ferreira de Sousa Moreira

    Full Text Available Grass pollen, in particular from Lolium multiflorum is a major allergen source in temperate climate zones of Southern Brazil. The IgE sensitization profile of Brazilian grass pollen allergic patients to individual allergen molecules has not been analyzed yet.To analyze the IgE sensitization profile of a Brazilian grass pollen allergic population using individual allergen molecules.We analyzed sera from 78 grass pollen allergic patients for the presence of IgE antibodies specific for 103 purified micro-arrayed natural and recombinant allergens by chip technology. IgE-ELISA inhibition experiments with Lolium multiflorum, Phleum pratense extracts and a recombinant fusion protein consisting of Phl p 1, Phl p 2, Phl p 5 and Phl p 6 were performed to investigate cross-reactivities.Within the Brazilian grass pollen allergic patients, the most frequently recognized allergens were Phl p 1 (95%, Phl p 5 (82%, Phl p 2 (76% followed by Phl p 4 (64%, Phl p 6 (45%, Phl p 11 (18% and Phl p 12 (18%. Most patients were sensitized only to grass pollen allergens but not to allergens from other sources. A high degree of IgE cross-reactivity between Phleum pratense, Lolium multiflorum and the recombinant timothy grass fusion protein was found.Component-resolved analysis of sera from Brazilian grass pollen allergic patients reveals an IgE recognition profile compatible with a typical Pooideae sensitization. The high degree of cross-reactivity between Phleum pratense and Lolium multiflorum allergens suggests that diagnosis and immunotherapy can be achieved with timothy grass pollen allergens in the studied population.

  7. Bioanalytical methods for food allergy diagnosis, allergen detection and new allergen discovery

    OpenAIRE

    Gasilova, Natalia; Girault, Hubert H.

    2015-01-01

    For effective monitoring and prevention of the food allergy, one of the emerging health problems nowadays, existing diagnostic procedures and allergen detection techniques are constantly improved. Meanwhile, new methods are also developed, and more and more putative allergens are discovered. This review describes traditional methods and summarizes recent advances in the fast evolving field of the in vitro food allergy diagnosis, allergen detection in food products and discovery of the new all...

  8. IgE and IgG4 Epitope Mapping of Food Allergens with a Peptide Microarray Immunoassay.

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    Martínez-Botas, Javier; de la Hoz, Belén

    2016-01-01

    Peptide microarrays are a powerful tool to identify linear epitopes of food allergens in a high-throughput manner. The main advantages of the microarray-based immunoassay are the possibility to assay thousands of targets simultaneously, the requirement of a low volume of serum, the more robust statistical analysis, and the possibility to test simultaneously several immunoglobulin subclasses. Among them, the last one has a special interest in the field of food allergy, because the development of tolerance to food allergens has been associated with a decrease in IgE and an increase in IgG4 levels against linear epitopes. However, the main limitation to the clinical use of microarray is the automated analysis of the data. Recent studies mapping the linear epitopes of food allergens with peptide microarray immunoassays have identified peptide biomarkers that can be used for early diagnosis of food allergies and to predict their severity or the self-development of tolerance. Using this approach, we have worked on epitope mapping of the two most important food allergens in the Spanish population, cow's milk and chicken eggs. The final aim of these studies is to define subsets of peptides that could be used as biomarkers to improve the diagnosis and prognosis of food allergies. This chapter describes the protocol to produce microarrays using a library of overlapping peptides corresponding to the primary sequences of food allergens and data acquisition and analysis of IgE- and IgG4-binding epitopes. PMID:26490480

  9. Microarray Scanner for Fluorescence Detection

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A novel pseudo confocal microarray scanner is introduced, in which one dimension scanning is performed by a galvanometer optical scanner and a telecentric objective, another dimension scanning is performed by a stepping motor.

  10. New Trends in Food Allergens Detection: Toward Biosensing Strategies.

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    Alves, Rita C; Barroso, M Fátima; González-García, María Begoña; Oliveira, M Beatriz P P; Delerue-Matos, Cristina

    2016-10-25

    Food allergens are a real threat to sensitized individuals. Although food labeling is crucial to provide information to consumers with food allergies, accidental exposure to allergenic proteins may result from undeclared allergenic substances by means of food adulteration, fraud or uncontrolled cross-contamination. Allergens detection in foodstuffs can be a very hard task, due to their presence usually in trace amounts, together with the natural interference of the matrix. Methods for allergens analysis can be mainly divided in two large groups: the immunological assays and the DNA-based ones. Mass spectrometry has also been used as a confirmatory tool. Recently, biosensors appeared as innovative, sensitive, selective, environmentally friendly, cheaper and fast techniques (especially when automated and/or miniaturized), able to effectively replace the classical methodologies. In this review, we present the advances in the field of food allergens detection toward the biosensing strategies and discuss the challenges and future perspectives of this technology. PMID:25779935

  11. Graph based study of allergen cross-reactivity of plant lipid transfer proteins (LTPs) using microarray in a multicenter study.

    OpenAIRE

    Palacín Gómez, Aranzazu; Gomez Casado, Cristina; Rivas, Luis; Aguirre, Jacobo; Tordesillas Villuendas, Leticia; Bartra, Joan; Blanco, Carlos; Carrillo, Teresa; Cuesta-Herranz, Javier; de Frutos, Consolación; García Álvarez-Eire, Genoveva; Fernández, Francisco; Gamboa, P. M.; Muñoz, Rosa; Sánchez-Monge Laguna de Rins, Rosa

    2012-01-01

    The study of cross-reactivity in allergy is key to both understanding. the allergic response of many patients and providing them with a rational treatment In the present study, protein microarrays and a co-sensitization graph approach were used in conjunction with an allergen microarray immunoassay. This enabled us to include a wide number of proteins and a large number of patients, and to study sensitization profiles among members of the LTP family. Fourteen LTPs from the most frequent plant...

  12. Graph based study of allergen cross-reactivity of plant lipid transfer proteins (LTPs using microarray in a multicenter study.

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    Arantxa Palacín

    Full Text Available The study of cross-reactivity in allergy is key to both understanding. the allergic response of many patients and providing them with a rational treatment In the present study, protein microarrays and a co-sensitization graph approach were used in conjunction with an allergen microarray immunoassay. This enabled us to include a wide number of proteins and a large number of patients, and to study sensitization profiles among members of the LTP family. Fourteen LTPs from the most frequent plant food-induced allergies in the geographical area studied were printed into a microarray specifically designed for this research. 212 patients with fruit allergy and 117 food-tolerant pollen allergic subjects were recruited from seven regions of Spain with different pollen profiles, and their sera were tested with allergen microarray. This approach has proven itself to be a good tool to study cross-reactivity between members of LTP family, and could become a useful strategy to analyze other families of allergens.

  13. Graph based study of allergen cross-reactivity of plant lipid transfer proteins (LTPs) using microarray in a multicenter study.

    Science.gov (United States)

    Palacín, Arantxa; Gómez-Casado, Cristina; Rivas, Luis A; Aguirre, Jacobo; Tordesillas, Leticia; Bartra, Joan; Blanco, Carlos; Carrillo, Teresa; Cuesta-Herranz, Javier; de Frutos, Consolación; Alvarez-Eire, Genoveva García; Fernández, Francisco J; Gamboa, Pedro; Muñoz, Rosa; Sánchez-Monge, Rosa; Sirvent, Sofía; Torres, María J; Varela-Losada, Susana; Rodríguez, Rosalía; Parro, Victor; Blanca, Miguel; Salcedo, Gabriel; Díaz-Perales, Araceli

    2012-01-01

    The study of cross-reactivity in allergy is key to both understanding. the allergic response of many patients and providing them with a rational treatment In the present study, protein microarrays and a co-sensitization graph approach were used in conjunction with an allergen microarray immunoassay. This enabled us to include a wide number of proteins and a large number of patients, and to study sensitization profiles among members of the LTP family. Fourteen LTPs from the most frequent plant food-induced allergies in the geographical area studied were printed into a microarray specifically designed for this research. 212 patients with fruit allergy and 117 food-tolerant pollen allergic subjects were recruited from seven regions of Spain with different pollen profiles, and their sera were tested with allergen microarray. This approach has proven itself to be a good tool to study cross-reactivity between members of LTP family, and could become a useful strategy to analyze other families of allergens. PMID:23272072

  14. Microarrays for Pathogen Detection and Analysis

    OpenAIRE

    McLoughlin, Kevin S.

    2011-01-01

    DNA microarrays have emerged as a viable platform for detection of pathogenic organisms in clinical and environmental samples. These microbial detection arrays occupy a middle ground between low cost, narrowly focused assays such as multiplex PCR and more expensive, broad-spectrum technologies like high-throughput sequencing. While pathogen detection arrays have been used primarily in a research context, several groups are aggressively working to develop arrays for clinical diagnostics, food ...

  15. Allergen micro-bead array for IgE detection: a feasibility study using allergenic molecules tested on a flexible multiplex flow cytometric immunoassay.

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    Debora Pomponi

    Full Text Available BACKGROUND: Allergies represent the most prevalent non infective diseases worldwide. Approaching IgE-mediated sensitizations improved much by adopting allergenic molecules instead of extracts, and by using the micro-technology for multiplex testing. OBJECTIVE AND METHODS: To provide a proof-of-concept that a flow cytometric bead array is a feasible mean for the detection of specific IgE reactivity to allergenic molecules in a multiplex-like way. A flow cytometry Allergenic Molecule-based micro-bead Array system (ABA was set by coupling allergenic molecules with commercially available micro-beads. Allergen specific polyclonal and monoclonal antibodies, as well as samples from 167 allergic patients, characterized by means of the ISAC microarray system, were used as means to show the feasibility of the ABA. Three hundred and thirty-six sera were tested for 1 or more of the 16 selected allergens, for a total number of 1,519 tests on each of the two systems. RESULTS: Successful coupling was initially verified by detecting the binding of rabbit polyclonal IgG, mouse monoclonal, and pooled human IgE toward three allergens, namely nDer s 1, nPen m 1, and nPru p 3. The ABA assay showed to detect IgE to nAct d 1, nAct d 11, rAln g 1, nAmb a 1, nArt v 3, rBet v 1, rCor a 1, nCup a 1, nDer p 1, nDer s 1, rHev b 5, nOle e 1, rPar j 2, nPen m 1, rPhl p 1, and nPru p 3. Results obtained by ABA IgE testing were highly correlated to ISAC testing (r = 0.87, p<0.0001. No unspecific binding was recorded because of high total IgE values. CONCLUSION: The ABA assay represents a useful and flexible method for multiplex IgE detection using allergenic molecules. As also shown by our initial experiments with monoclonals and polyclonals, ABA is suitable for detecting other human and non-human immunoglobulins.

  16. Refractive index change detection based on porous silicon microarray

    Science.gov (United States)

    Chen, Weirong; Jia, Zhenhong; Li, Peng; Lv, Guodong; Lv, Xiaoyi

    2016-05-01

    By combining photolithography with the electrochemical anodization method, a microarray device of porous silicon (PS) photonic crystal was fabricated on the crystalline silicon substrate. The optical properties of the microarray were analyzed with the transfer matrix method. The relationship between refractive index and reflectivity of each array element of the microarray at 633 nm was also studied, and the array surface reflectivity changes were observed through digital imaging. By means of the reflectivity measurement method, reflectivity changes below 10-3 can be observed based on PS microarray. The results of this study can be applied to the detection of biosensor arrays.

  17. Ultrasensitive aptamer based detection of β-conglutin food allergen.

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    Svobodova, Marketa; Mairal, Teresa; Nadal, Pedro; Bermudo, M Carmen; O'Sullivan, Ciara K

    2014-12-15

    Lupine has been increasingly used in food applications due to its high nutritional value and excellent functional properties. However, there has been a response to the increasing number of severe cases of lupine allergies reported during the last decade, and as a result lupine was recently added to the list of substances requiring mandatory advisory labelling on foodstuffs sold in the European Union. In this paper we report the robust and ultrasensitive detection of the anaphylactic β-conglutin allergen using Apta-PCR achieving a detection limit of 85 pM (25 ng mL(-1)). No cross-reactivity with other conglutins or plant species potentially used in lupine containing foodstuffs was observed. This robust method provides an effective analytical tool for the detection and quantification of the toxic β-conglutin subunit present in lupine flour. PMID:25038695

  18. Microarrays for Universal Detection and Identification of Phytoplasmas

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Nyskjold, Henriette; Bertaccini, Assunta

    2013-01-01

    Detection and identification of phytoplasmas is a laborious process often involving nested PCR followed by restriction enzyme analysis and fine-resolution gel electrophoresis. To improve throughput, other methods are needed. Microarray technology offers a generic assay that can potentially detect...... and differentiate all types of phytoplasmas in one assay. The present protocol describes a microarray-based method for identification of phytoplasmas to 16Sr group level....

  19. Lack of detectable allergenicity of transgenic maize and soya samples

    OpenAIRE

    Batista, Rita; Nunes, Baltazar; Carmo, Manuela; Cardoso, Carlos; Helena, São José; Almeida, António Bugalho de; Manique, Alda; Bento, Leonor; Ricardo, Cândido Pinto; Oliveira, Maria Margarida

    2005-01-01

    Background: The safety issues regarding foods derived from genetically modified (GM) plants are central to their acceptance into the food supply. The potential allergenicity of proteins newly introduced in GM foods is a major safety concern. Objective: We sought to monitor, in potentially sensitive human populations, the allergenicity effects of 5 GM materials obtained from sources with no allergenic potential and already under commercialization in the European Union. ...

  20. Allergen Micro-Bead Array for IgE Detection: A Feasibility Study Using Allergenic Molecules Tested on a Flexible Multiplex Flow Cytometric Immunoassay

    OpenAIRE

    Debora Pomponi; Maria Livia Bernardi; Marina Liso; Paola Palazzo; Lisa Tuppo; Chiara Rafaiani; Mario Santoro; Alexis Labrada; Maria Antonietta Ciardiello; Adriano Mari; Enrico Scala

    2012-01-01

    BACKGROUND: Allergies represent the most prevalent non infective diseases worldwide. Approaching IgE-mediated sensitizations improved much by adopting allergenic molecules instead of extracts, and by using the micro-technology for multiplex testing. OBJECTIVE AND METHODS: To provide a proof-of-concept that a flow cytometric bead array is a feasible mean for the detection of specific IgE reactivity to allergenic molecules in a multiplex-like way. A flow cytometry Allergenic Molecule-based micr...

  1. Soybean flour asthma: detection of allergens by immunoblotting

    International Nuclear Information System (INIS)

    A 43-year-old woman developed asthma 6 years after beginning work in a food-processing plant in which soybean flour was used as a protein extender. Symptoms of sneezing, coughing, and wheezing would begin within minutes of exposure to soybean flour and resolve 2 hours after exposure ceased. Skin tests were positive to a soy extract prepared from the flour. Airway hyperreactivity was confirmed by a positive bronchial challenge to methacholine. Bronchial challenge with soybean flour produced an immediate increase in specific airway resistance from 5.0 to 22.7 L. cm of H2O/L/sec. There was no response to challenge with lactose. The patient's allergic response to soy-flour extract was further characterized by several immunologic methods. IgE binding to soy-flour protein by direct RAST was 5.98 times that of a normal control serum. The soy-flour extract was separated by dodecyl sulfate-polyacrylamide gel electrophoresis. Twenty-four protein bands were detected in the crude soy-flour extract. After immunoblotting and subsequent autoradiography, nine proteins with molecular weights ranging from 54,500 to 14,875 were found. Cross-reactivity studies with other legumes demonstrated apparent immunologic identity between a component in green pea extract and a soybean protein with a molecular weight of 17,000. The clinical significance of this cross-reactivity is not known. We conclude that in this case of occupational asthma to soybean flour, multiple allergens were involved. Immunoblotting may be useful in identifying the allergens involved in occupational asthma

  2. Microarrays/DNA Chips for the Detection of Waterborne Pathogens.

    Science.gov (United States)

    Vale, Filipa F

    2016-01-01

    DNA microarrays are useful for the simultaneous detection of microorganisms in water samples. Specific probes targeting waterborne pathogens are selected with bioinformatics tools, synthesized and spotted onto a DNA array. Here, the construction of a DNA chip for waterborne pathogen detection is described, including the processes of probe in silico selection, synthesis, validation, and data analysis. PMID:27460375

  3. Lipid Microarray Biosensor for Biotoxin Detection.

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Anup K.; Throckmorton, Daniel J.; Moran-Mirabal, Jose C.; Edel, Joshua B.; Meyer, Grant D.; Craighead, Harold G.

    2006-05-01

    We present the use of micron-sized lipid domains, patterned onto planar substrates and within microfluidic channels, to assay the binding of bacterial toxins via total internal reflection fluorescence microscopy (TIRFM). The lipid domains were patterned using a polymer lift-off technique and consisted of ganglioside-populated DSPC:cholesterol supported lipid bilayers (SLBs). Lipid patterns were formed on the substrates by vesicle fusion followed by polymer lift-off, which revealed micron-sized SLBs containing either ganglioside GT1b or GM1. The ganglioside-populated SLB arrays were then exposed to either Cholera toxin subunit B (CTB) or Tetanus toxin fragment C (TTC). Binding was assayed on planar substrates by TIRFM down to 1 nM concentration for CTB and 100 nM for TTC. Apparent binding constants extracted from three different models applied to the binding curves suggest that binding of a protein to a lipid-based receptor is strongly affected by the lipid composition of the SLB and by the substrate on which the bilayer is formed. Patterning of SLBs inside microfluidic channels also allowed the preparation of lipid domains with different compositions on a single device. Arrays within microfluidic channels were used to achieve segregation and selective binding from a binary mixture of the toxin fragments in one device. The binding and segregation within the microfluidic channels was assayed with epifluorescence as proof of concept. We propose that the method used for patterning the lipid microarrays on planar substrates and within microfluidic channels can be easily adapted to proteins or nucleic acids and can be used for biosensor applications and cell stimulation assays under different flow conditions. KEYWORDS. Microarray, ganglioside, polymer lift-off, cholera toxin, tetanus toxin, TIRFM, binding constant.4

  4. A microfluidic biosensor using graphene oxide and aptamer-functionalized quantum dots for peanut allergen detection.

    Science.gov (United States)

    Weng, Xuan; Neethirajan, Suresh

    2016-11-15

    The increasing prevalence of food allergies and the intake of packing foods in the past two decades urge the need for more rapid, accurate, and sensitive assays to detect potential allergens in food in order to control the allergen content. Most of the commercial analytical tools for allergen detection rely on immunoassays such as ELISA. As far as disadvantages, ELISA can be time-consuming and expensive. Biosensors appear as a suitable alternative for the detection of allergens because they are rapid, highly sensitive, selective, less expensive, environmentally friendly, and easy to handle. In this study, we developed a microfluidic system integrated with a quantum dots (Qdots) aptamer functionalized graphene oxide (GO) nano-biosensor for simple, rapid, and sensitive food allergen detection. The biosensor utilized Qdots-aptamer-GO complexes as probes to undergo conformational change upon interaction with the food allergens, resulting in fluorescence changes due to the fluorescence quenching and recovering properties of GO by adsorption and desorption of aptamer-conjugated Qdots. This one-step 'turn on' homogenous assay in a ready-to-use microfluidic chip took ~10min to achieve a quantitative detection of Ara h 1, one of the major allergens appearing in peanuts. The results suggested this system had remarkable sensitivity and selectivity. The integration of a microfluidics platform in a homemade miniaturized optical analyzer provides a promising way for the rapid, cost-effective, and accurate on-site determination of food allergens. This biosensor can also be extended to the detection of other food allergens with a selection of corresponding aptamers. PMID:27240012

  5. Detection of bacterial pathogens in environmental samples using DNA microarrays.

    Science.gov (United States)

    Call, Douglas R; Borucki, Monica K; Loge, Frank J

    2003-05-01

    Polymerase chain reaction (PCR) is an important tool for pathogen detection, but historically, it has not been possible to accurately identify PCR products without sequencing, Southern blots, or dot-blots. Microarrays can be coupled with PCR where they serve as a set of parallel dot-blots to enhance product detection and identification. Microarrays are composed of many discretely located probes on a solid substrate such as glass. Each probe is composed of a sequence that is complimentary to a pathogen-specific gene sequence. PCR is used to amplify one or more genes and the products are then hybridized to the array to identify species-specific polymorphism within one or more genes. We illustrate this type of array using 16S rDNA probes suitable for distinguishing between several salmonid pathogens. We also describe the use of microarrays for direct detection of either RNA or DNA without the aid of PCR, although the sensitivity of these systems currently limits their application for pathogen detection. Finally, microarrays can also be used to "fingerprint" bacterial isolates and they can be used to identify diagnostic markers suitable for developing new PCR-based detection assays. We illustrate this type of array for subtyping an important food-borne pathogen, Listeria monocytogenes. PMID:12654494

  6. First screening method for the simultaneous detection of seven allergens by liquid chromatography mass spectrometry.

    Science.gov (United States)

    Heick, J; Fischer, M; Pöpping, B

    2011-02-18

    The development of a multi-method for the detection of seven allergens based on liquid chromatography and triple-quadrupole tandem mass spectrometry in multiple reaction mode is described. It is based on extraction of the allergenic proteins from a food matrix, followed by enzymatic digestion with trypsin. The chosen marker peptides were implemented into one method that is capable of the simultaneous detection of milk, egg, soy, hazelnut, peanut, walnut and almond. This method has been used to detect all seven allergenic commodities from incurred reference bread material, which was baked according to a standard recipe from the baking industry. Detected concentrations ranged from 10 to 1000 μg/g, demonstrating that the mass spectrometric based method is a useful tool for allergen screening. PMID:21227428

  7. Label and Label-Free Detection Techniques for Protein Microarrays

    Directory of Open Access Journals (Sweden)

    Amir Syahir

    2015-04-01

    Full Text Available Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano‑biological events.

  8. Detection of foodborne pathogens using microarray technology

    Science.gov (United States)

    Assays based on the polymerase chain reaction (PCR) are now accepted methods for rapidly confirming the presence or absence of specific pathogens in foods and other types of samples. Conventional PCR requires the use of agarose gel electrophoresis to detect the PCR product; whereas, real-time PCR c...

  9. Microarray technology in detection of potato pathogens

    Czech Academy of Sciences Publication Activity Database

    Šíp, Miroslav; Bystřická, Dagmar; Lenz, Ondřej; Mráz, Ivan; Petrzik, Karel; Dědič, P.

    Christchurch : Lincoln Univ. Cantebury, 2003. s. 93. [International Congress of Plant Pathology/8./. 02.02.2003-07.02.2003, Christchurch] Institutional research plan: CEZ:AV0Z5051902 Keywords : plant pathology * detection of diseases Subject RIV: EE - Microbiology, Virology

  10. Universal ligation-detection-reaction microarray applied for compost microbes

    Directory of Open Access Journals (Sweden)

    Romantschuk Martin

    2008-12-01

    Full Text Available Abstract Background Composting is one of the methods utilised in recycling organic communal waste. The composting process is dependent on aerobic microbial activity and proceeds through a succession of different phases each dominated by certain microorganisms. In this study, a ligation-detection-reaction (LDR based microarray method was adapted for species-level detection of compost microbes characteristic of each stage of the composting process. LDR utilises the specificity of the ligase enzyme to covalently join two adjacently hybridised probes. A zip-oligo is attached to the 3'-end of one probe and fluorescent label to the 5'-end of the other probe. Upon ligation, the probes are combined in the same molecule and can be detected in a specific location on a universal microarray with complementary zip-oligos enabling equivalent hybridisation conditions for all probes. The method was applied to samples from Nordic composting facilities after testing and optimisation with fungal pure cultures and environmental clones. Results Probes targeted for fungi were able to detect 0.1 fmol of target ribosomal PCR product in an artificial reaction mixture containing 100 ng competing fungal ribosomal internal transcribed spacer (ITS area or herring sperm DNA. The detection level was therefore approximately 0.04% of total DNA. Clone libraries were constructed from eight compost samples. The LDR microarray results were in concordance with the clone library sequencing results. In addition a control probe was used to monitor the per-spot hybridisation efficiency on the array. Conclusion This study demonstrates that the LDR microarray method is capable of sensitive and accurate species-level detection from a complex microbial community. The method can detect key species from compost samples, making it a basis for a tool for compost process monitoring in industrial facilities.

  11. Microarray sensors for detecting airborne explosives

    OpenAIRE

    Caygill, J. S.

    2011-01-01

    Due to the enhanced level of national security currently required due to the possibility of terrorist attack, monitoring devices for trace levels of explosive materials are now of the upmost importance. One such method that offers a possible route towards the development of a system for the detection of such analytes is via an electrochemical regime, coupled to the use of disposable sensor technology. Within this study, the use of modified carbon screen-printed sensors for the ...

  12. Microarray platform for the detection of a range of plant viruses and viroids.

    Science.gov (United States)

    Adams, Ian; Harrison, Catherine; Tomlinson, Jenny; Boonham, Neil

    2015-01-01

    Diagnostic microarrays are a useful tool for the simultaneous detection of multiple targets. In this chapter we describe the use of a simple tube-based microarray platform for the detection of plant infecting viruses and viroids. PMID:25981261

  13. Current Challenges in Detecting Food Allergens by Shotgun and Targeted Proteomic Approaches: A Case Study on Traces of Peanut Allergens in Baked Cookies

    OpenAIRE

    Romina Pedreschi; Jørgen Nørgaard; Alain Maquet

    2012-01-01

    There is a need for selective and sensitive methods to detect the presence of food allergens at trace levels in highly processed food products. In this work, a combination of non-targeted and targeted proteomics approaches are used to illustrate the difficulties encountered in the detection of the major peanut allergens Ara h 1, Ara h 2 and Ara h 3 from a representative processed food matrix. Shotgun proteomics was employed for selection of the proteotypic peptides for targeted approaches via...

  14. DNA microarray technique for detecting food-borne pathogens

    Directory of Open Access Journals (Sweden)

    Xing GAO

    2012-08-01

    Full Text Available Objective To study the application of DNA microarray technique for screening and identifying multiple food-borne pathogens. Methods The oligonucleotide probes were designed by Clustal X and Oligo 6.0 at the conserved regions of specific genes of multiple food-borne pathogens, and then were validated by bioinformatic analyses. The 5' end of each probe was modified by amino-group and 10 Poly-T, and the optimized probes were synthesized and spotted on aldehyde-coated slides. The bacteria DNA template incubated with Klenow enzyme was amplified by arbitrarily primed PCR, and PCR products incorporated into Aminoallyl-dUTP were coupled with fluorescent dye. After hybridization of the purified PCR products with DNA microarray, the hybridization image and fluorescence intensity analysis was acquired by ScanArray and GenePix Pro 5.1 software. A series of detection conditions such as arbitrarily primed PCR and microarray hybridization were optimized. The specificity of this approach was evaluated by 16 different bacteria DNA, and the sensitivity and reproducibility were verified by 4 food-borne pathogens DNA. The samples of multiple bacteria DNA and simulated water samples of Shigella dysenteriae were detected. Results Nine different food-borne bacteria were successfully discriminated under the same condition. The sensitivity of genomic DNA was 102 -103pg/ μl, and the coefficient of variation (CV of the reproducibility of assay was less than 15%. The corresponding specific hybridization maps of the multiple bacteria DNA samples were obtained, and the detection limit of simulated water sample of Shigella dysenteriae was 3.54×105cfu/ml. Conclusions The DNA microarray detection system based on arbitrarily primed PCR can be employed for effective detection of multiple food-borne pathogens, and this assay may offer a new method for high-throughput platform for detecting bacteria.

  15. Protein Microarrays for Quantitative Detection of PAI-1 in Serum

    Institute of Scientific and Technical Information of China (English)

    Xu Ma; Qing-yun Zhang

    2012-01-01

    Objective:Plasminogen activator inhibitor-1 (PAl-1),one crucial component of the plasminogen activator system,is a major player in the pathogenesis of many vascular diseases as well as in cancer.High levels of PAI-1 in breast cancer tissue are associated with poor prognosis.The aim of this study is to evaluate rigorously the potential of serum PAl-1 concentration functioning as a general screening test in diagnostic or prognostic assays.Methods:A protein-microarray-based sandwich fluorescence immunoassay (FIA) was developed to detect PAl-1 in serum.Several conditions of this microarray-based FIA were optimized to establish an efficacious method.Serum specimens of 84 healthy women and 285 women with breast cancer were analyzed using the optimized FIA microarray.Results:The median serum PAl-1 level of breast cancer patients was higher than that of healthy women (109.7 ng/ml vs.63.4 ng/ml).Analysis of covariance revealed that PAl-1 levels of the two groups were significantly different (P<0.001) when controlling for an age effect on PAl-1 levels.However,PAl-1 values in TNM stage Ⅰ-Ⅳ patients respectively were not significantly different from each other.Conclusion:This microarray-based sandwich FIA holds potential for quantitative analysis of tumor markers such as PAl-1.

  16. Summary of the ACS symposium on Advances in Food Allergen Detection.

    Science.gov (United States)

    Ross, Mark M; Jackson, Lauren

    2013-06-19

    A symposium titled "Advances in Food Allergen Detection" was held at the 243rd National Meeting of the American Chemical Society (ACS) in March 2012 in San Diego, CA, and was sponsored by the ACS Division of Agricultural and Food Chemistry. The purpose of the symposium was to convene the leaders in the food allergen analysis field for presentations on, and discussions of, the state of the art, new developments, and critical challenges in the detection and quantitation of allergenic proteins in foods. Twenty-five presentations were delivered by speakers representing academic, government, and industrial institutions in 10 countries. The presentations covered all aspects of food allergens, including a historical progress review, regulatory policies, clinical practices, food-processing effects, food production equipment cross-contamination and cleaning, and the performance of several food allergen analytical strategies and technologies. This paper is intended to provide a brief summary of the presentations as well as a record of the proceedings of the symposium, which was deemed a great success in advancing food allergen analysis. PMID:23167825

  17. Allergens of Arachis hypogaea and the effect of processing on their detection by ELISA

    Directory of Open Access Journals (Sweden)

    Amjad Iqbal

    2016-02-01

    Full Text Available Food allergies are an emerging public health problem in industrialized areas of the world. They represent a considerable health problem in these areas because of the relatively high number of reported cases. Usually, food allergens are proteins or glycoproteins with a molecular mass ranging from 10 to 70 kDa. Among the food allergies, peanut is accounted to be responsible for more than 50% of the food allergy fatalities. Threshold doses for peanut allergenic reactions have been found to range from as low as 100 µg to 1 g of peanut protein, which equal to 400 µg to 4 g peanut meal. Allergens from peanut are mainly seed storage proteins that are composed of conglutin, vicilin, and glycinin families. Several peanut proteins have been identified to induce allergic reactions, particularly Ara h 1–11. This review is mainly focused on different classes of peanut allergens, the effect of thermal and chemical treatment of peanut allergens on the IgY binding and detectability of these allergens by enzyme linked immunosorbent assay (ELISA to provide knowledge for food industry.

  18. Giant magnetoresistive sensor array for sensitive and specific multiplexed food allergen detection.

    Science.gov (United States)

    Ng, Elaine; Nadeau, Kari C; Wang, Shan X

    2016-06-15

    Current common allergen detection methods, including enzyme-linked immunosorbent assays (ELISAs) and dip-stick methods, do not provide adequate levels of sensitivity and specificity for at-risk allergic patients. A method for performing highly sensitive and specific detection of multiple food allergens is thus imperative as food allergies are becoming increasingly recognized as a major healthcare concern, affecting an estimated 4% of the total population. We demonstrate first instance of sensitive and specific multiplexed detection of major peanut allergens Ara h 1 and Ara h 2, and wheat allergen Gliadin using giant magnetoresistive (GMR) sensor arrays. Commercialized ELISA kits for Ara h 1 and Ara h 2 report limits of detection (LODs) at 31.5ng/mL and 0.2ng/mL, respectively. In addition, the 96-well-based ELISA developed in-house for Gliadin was found to have a LOD of 40ng/mL. Our multiplexed GMR-based assay demonstrates the ability to perform all three assays on the same chip specifically and with sensitivities at LODs about an order of magnitude lower than those of 96-well-based ELISAs. LODs of GMR-based assays developed for Ara h 1, Ara h 2, and Gliadin were 7.0ng/mL, 0.2ng/mL, and 1.5ng/mL, respectively, with little to no cross-reactivity. These LODs are clinically important as some patients could react strongly against such low allergen levels. Given the limitations of current industrial detection technology, multiplexed GMR-based assays provide a method for highly sensitive and specific simultaneous detection of any combination of food-product allergens, thus protecting allergic patients from life-threatening events, including anaphylaxis, by unintentional consumption. PMID:26859787

  19. Sensitization rates of causative allergens for dogs with atopic dermatitis: detection of canine allergen-specific IgE

    OpenAIRE

    Kang, Min-Hee; Kim, Ha-Jung; Jang, Hye-Jin; Park, Hee-Myung

    2014-01-01

    Allergen-specific IgE serology tests became commercially available in the 1980s. Since then these tests have been widely used to diagnose and treat allergic skin diseases. However, the relationship between a positive reaction and disease occurrence has been controversial. The purpose of this study was to evaluate allergens using a serologic allergy test in dogs with atopic dermatitis (AD). Dogs clinically diagnosed with AD (n=101) were tested using an allergen-specific IgE immunoassay. Among ...

  20. Rhodamine B doped silica nanoparticle labels for protein microarray detection

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A core-shell Rhodamine B-doped SiO2 nanoparticle was synthesized and its fluorescent intensity was found to be 1000 times higher than that of individual Rhodamine B molecule. The doped nanoparticles were further conjugated with streptavidin and the resulting nanoparticles were used in the detection of reverse-phase protein microarrays, in which human IgG of various concentrations was first immobilized on aldehyde-modified glass slides and then biotinlyated goat anti human IgG as well as the labeled nanoparticles were sequentially conjugated. The calibration curve is linear over the range from 800 fg to 500 pg and the limit of detection is 100 fg, which is 8 times lower than that of streptavidin-labeled Cy3 fluorescent dyes. The dyedoped SiO2 nanoparticles show potentials for the protein array detection.

  1. Sample size for detecting differentially expressed genes in microarray experiments

    Directory of Open Access Journals (Sweden)

    Li Jiangning

    2004-11-01

    Full Text Available Abstract Background Microarray experiments are often performed with a small number of biological replicates, resulting in low statistical power for detecting differentially expressed genes and concomitant high false positive rates. While increasing sample size can increase statistical power and decrease error rates, with too many samples, valuable resources are not used efficiently. The issue of how many replicates are required in a typical experimental system needs to be addressed. Of particular interest is the difference in required sample sizes for similar experiments in inbred vs. outbred populations (e.g. mouse and rat vs. human. Results We hypothesize that if all other factors (assay protocol, microarray platform, data pre-processing were equal, fewer individuals would be needed for the same statistical power using inbred animals as opposed to unrelated human subjects, as genetic effects on gene expression will be removed in the inbred populations. We apply the same normalization algorithm and estimate the variance of gene expression for a variety of cDNA data sets (humans, inbred mice and rats comparing two conditions. Using one sample, paired sample or two independent sample t-tests, we calculate the sample sizes required to detect a 1.5-, 2-, and 4-fold changes in expression level as a function of false positive rate, power and percentage of genes that have a standard deviation below a given percentile. Conclusions Factors that affect power and sample size calculations include variability of the population, the desired detectable differences, the power to detect the differences, and an acceptable error rate. In addition, experimental design, technical variability and data pre-processing play a role in the power of the statistical tests in microarrays. We show that the number of samples required for detecting a 2-fold change with 90% probability and a p-value of 0.01 in humans is much larger than the number of samples commonly used in

  2. Microarray-based method for detection of unknown genetic modifications

    Directory of Open Access Journals (Sweden)

    Butenko Melinka A

    2007-12-01

    Full Text Available Abstract Background Due to the increased use of genetic modifications in crop improvement, there is a need to develop effective methods for the detection of both known and unknown transgene constructs in plants. We have developed a strategy for detection and characterization of unknown genetic modifications and we present a proof of concept for this method using Arabidopsis thaliana and Oryza sativa (rice. The approach relies on direct hybridization of total genomic DNA to high density microarrays designed to have probes tiled throughout a set of reference sequences. Results We show that by using arrays with 25 basepair probes covering both strands of a set of 235 vectors (2 million basepairs we can detect transgene sequences in transformed lines of A. thaliana and rice without prior knowledge about the transformation vectors or the T-DNA constructs used to generate the studied plants. Conclusion The approach should allow the user to detect the presence of transgene sequences and get sufficient information for further characterization of unknown genetic constructs in plants. The only requirements are access to a small amount of pure transgene plant material, that the genetic construct in question is above a certain size (here ≥ 140 basepairs and that parts of the construct shows some degree of sequence similarity with published genetic elements.

  3. Oligonucleotide-based microarray detection of plant viruses

    Czech Academy of Sciences Publication Activity Database

    Šíp, M.; Bystřická, Dagmar; Lenz, Ondřej; Mráz, Ivan; Piherová, L.; Kmoch, S.

    Gdansk : Faculty of Biotechnology University of Gdansk, 2005. s. 12. [Meeting COST 853 Agricultural Biomarkers for Array-Technology: WG1 Nucleic acid microarrays, WG2 Protein microarrays. 19.06.2005-21.06.2005, Gdansk] R&D Projects: GA ČR GA522/01/1105; GA MŠk OC 853.002 Keywords : biomarkers * microarrays Subject RIV: EE - Microbiology, Virology

  4. DNA Microarray Detection of Antimicrobial Resistance Genes in Bacteria Co-Cultured from Swine Feces

    Science.gov (United States)

    One factor leading to the spread of antimicrobial resistance (AR) in bacteria is the horizontal transfer of resistance genes. To study this, a DNA microarray was recently developed to detect these genes. To maximize the capability of this microarray, probes were designed and added to detect all AR g...

  5. Fabrication of oligonucleotide microarray for the detection of Japanese encephalitis virus

    Institute of Scientific and Technical Information of China (English)

    HAI YAN ZHANG; WEN LI MA; XIAO MING ZHANG; WEN LING ZHENG

    2006-01-01

    A low-density oligonucleotide microarray was used for the detection of Japanese encephalitis virus (JEV), combining with restriction display PCR labeling method. The hybridization targets were amplified from 6 plasmids containing several JEV gene fragments. Corresponding oligonucleotide probe spots were detected unambiguously. We claim that the oligonucleotide microarray technology is feasible and may have potential for clinical laboratory application.

  6. A fluorescence-based centrifugal microfluidic system for parallel detection of multiple allergens

    Science.gov (United States)

    Chen, Q. L.; Ho, H. P.; Cheung, K. L.; Kong, S. K.; Suen, Y. K.; Kwan, Y. W.; Li, W. J.; Wong, C. K.

    2010-02-01

    This paper reports a robust polymer based centrifugal microfluidic analysis system that can provide parallel detection of multiple allergens in vitro. Many commercial food products (milk, bean, pollen, etc.) may introduce allergy to people. A low-cost device for rapid detection of allergens is highly desirable. With this as the objective, we have studied the feasibility of using a rotating disk device incorporating centrifugal microfluidics for performing actuationfree and multi-analyte detection of different allergen species with minimum sample usage and fast response time. Degranulation in basophils or mast cells is an indicator to demonstrate allergic reaction. In this connection, we used acridine orange (AO) to demonstrate degranulation in KU812 human basophils. It was found that the AO was released from granules when cells were stimulated by ionomycin, thus signifying the release of histamine which accounts for allergy symptoms [1-2]. Within this rotating optical platform, major microfluidic components including sample reservoirs, reaction chambers, microchannel and flow-control compartments are integrated into a single bio-compatible polydimethylsiloxane (PDMS) substrate. The flow sequence and reaction time can be controlled precisely. Sequentially through varying the spinning speed, the disk may perform a variety of steps on sample loading, reaction and detection. Our work demonstrates the feasibility of using centrifugation as a possible immunoassay system in the future.

  7. Protein chips for detection of mite allergens using Kunitz-type protease inhibitors.

    Science.gov (United States)

    Poltronieri, Palmiro; Cimaglia, Fabio; Santino, Angelo; De Blasi, Marialuce Daniela; Krizkova-Kudlikova, Iva; Liu, Shaoyang; Wang, Yuhong; Wang, Yifen

    2010-06-01

    Stored-food and house-dust arthropods include many species of mites and beetles that affect human health. For diagnostic tests proteases such as trypsin are utilized as they are indicators of the presence of allergen contaminants in food. We recently characterized Kunitz-type protease inhibitors (KPIs) from Solanum palustre. Here we studied biotechnological applications of KPI-B1 and -B4. We manufactured a protein chip with immobilized KPI-B1 and -B4 and showed trypsin/chymotrypsin-binding specificity, indicating that the recombinant proteins have protease selectivity. We employed the protein chip to capture mite proteins belonging to the protease family with polyclonal anti-mite antibodies. The mite diagnostic chip can be useful for detecting mite allergens. PMID:20518061

  8. Rapid Detection of Food Allergens by Microfluidics ELISA-Based Optical Sensor

    Directory of Open Access Journals (Sweden)

    Xuan Weng

    2016-06-01

    Full Text Available The risks associated with the presence of hidden allergens in food have increased the need for rapid, sensitive, and reliable methods for tracing food allergens in commodities. Conventional enzyme immunosorbent assay (ELISA has usually been performed in a centralized lab, requiring considerable time and sample/reagent consumption and expensive detection instruments. In this study, a microfluidic ELISA platform combined with a custom-designed optical sensor was developed for the quantitative analysis of the proteins wheat gluten and Ara h 1. The developed microfluidic ELISA biosensor reduced the total assay time from hours (up to 3.5 h to 15–20 min and decreased sample/reagent consumption to 5–10 μL, compared to a few hundred microliters in commercial ELISA kits, with superior sensitivity. The quantitative capability of the presented biosensor is a distinctive advantage over the commercially available rapid methods such as lateral flow devices (LFD and dipstick tests. The developed microfluidic biosensor demonstrates the potential for sensitive and less-expensive on-site determination for rapidly detecting food allergens in a complex sample system.

  9. Identification of hidden allergens: detection of pistachio traces in mortadella.

    Science.gov (United States)

    Barbieri, G; Frigeri, G

    2006-12-01

    An analytical method based on the detection of specific DNA was developed and applied to mortadella samples with and without pistachio (Pistacia vera). The method is proposed for the detection of traces of pistachio deriving from previous processes or from accidental contamination, since in predisposed individuals pistachios can cause allergic reactions leading to anaphylactic shock. Three pairs of primers were identified and tested by polymerase chain reaction (PCR) on mortadella samples prepared with pistachio. Accidental contamination was also simulated. The optimized PCR was able to detect the presence of pistachio, even at low concentrations. The primers pair PSTC 1-2 is suggested for unambiguous identification of pistachio in mortadella. The limit of detection for this primers pair was 100 mg kg-1. No interference was observed from other spices or ingredients utilized in the formulation of the mortadella. The method enabled the identification of possible traces of pistachio remaining in the production plant after less than thorough washing. PMID:17118868

  10. Testing a Microarray to Detect and Monitor Toxic Microalgae in Arcachon Bay in France

    Directory of Open Access Journals (Sweden)

    Linda K. Medlin

    2013-03-01

    Full Text Available Harmful algal blooms (HABs occur worldwide, causing health problems and economic damages to fisheries and tourism. Monitoring agencies are therefore essential, yet monitoring is based only on time-consuming light microscopy, a level at which a correct identification can be limited by insufficient morphological characters. The project MIDTAL (Microarray Detection of Toxic Algae—an FP7-funded EU project—used rRNA genes (SSU and LSU as a target on microarrays to identify toxic species. Furthermore, toxins were detected with a newly developed multiplex optical Surface Plasmon Resonance biosensor (Multi SPR and compared with an enzyme-linked immunosorbent assay (ELISA. In this study, we demonstrate the latest generation of MIDTAL microarrays (version 3 and show the correlation between cell counts, detected toxin and microarray signals from field samples taken in Arcachon Bay in France in 2011. The MIDTAL microarray always detected more potentially toxic species than those detected by microscopic counts. The toxin detection was even more sensitive than both methods. Because of the universal nature of both toxin and species microarrays, they can be used to detect invasive species. Nevertheless, the MIDTAL microarray is not completely universal: first, because not all toxic species are on the chip, and second, because invasive species, such as Ostreopsis, already influence European coasts.

  11. Can subtle changes in gene expression be consistently detected with different microarray platforms?

    NARCIS (Netherlands)

    P. Pedotti; P.A.C. 't Hoen (Peter); E. Vreugdenhil (Erno); G.J. Schenk (Geert); R. Vossen (Rolf); Y. Ariyurek (Yavuz); M. de Hollander (Mattias); R. Kuiper (Rowan); G.J. van Ommen (Gert); J.T. den Dunnen (Johan); J.M. Boer (Judith); R.X. de Menezes (Renee)

    2008-01-01

    textabstractBackground: The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging bi

  12. Improved detection of allergen-specific T-cell responses in allergic contact dermatitis through the addition of 'cytokine cocktails'.

    Science.gov (United States)

    Moed, Helen; von Blomberg, Mary; Bruynzeel, Derk P; Scheper, Rik; Gibbs, Susan; Rustemeyer, Thomas

    2005-08-01

    The gold standard for the diagnosis of allergic hypersensitivity is skin patch testing with the suspected allergens. This diagnostic tool, however, has distinct disadvantages, and therefore the development of alternative or complementary in vitro tests is of great importance. In this study, we evaluate the applicability of an in vitro test method, as developed earlier for nickel allergy, to detect allergen-specific T cells in the blood of patients allergic to frequent sensitizers (chromate, cobalt, paraphenylenediamine, fragrances and chloromethyl-isothiazolinone). Peripheral blood mononuclear cells (PBMCs) of allergic patients and healthy controls were cultured in the absence or presence of allergen. Additionally, type 1 (IL-7 and IL-12) or type 2 (IL-7 and IL-4) stimulating cytokines were added; after 6-day proliferation, IFN-gamma and IL-5 secretions were determined. Without the addition of cytokines, consistent allergen-induced proliferation was observed in PBMCs of nickel-allergic patients only. By contrast, the addition of type 1 or type 2 stimulating cytokines resulted in a significantly enhanced allergen-specific proliferation for all allergens tested (sensitivity increased from 26 to 43% or 38%, respectively, P exploration of the application of this test to a broader set of allergens. PMID:16026586

  13. Soybean allergen detection methods--a comparison study

    DEFF Research Database (Denmark)

    Pedersen, M. Højgaard; Holzhauser, T.; Bisson, C.;

    2008-01-01

    Soybean containing products are widely consumed, thus reliable methods for detection of soy in foods are needed in order to make appropriate risk assessment studies to adequately protect soy allergic patients. Six methods were compared using eight food products with a declared content of soy: a...... direct sandwich ELISA based on polyclonal rabbit antibody (ab) to raw soy flakes, a commercial and an in-house competitive ELISA both based on ab to denatured, 'renatured' soy protein, an enzyme-allergosorbent test (EAST) inhibition based on two sera from soy allergic patients, histamine release (HR...

  14. Evaluation of DNA microarray for detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis isolates

    Institute of Scientific and Technical Information of China (English)

    王峰

    2013-01-01

    Objective To evaluate the performance of DNA microarray for rapid detection resistance to rifampin and isoniazid in Mycobacterium tuberculosis clinical isolates and identify suitable target sites for molecular genetic test. Methods Twenty-four clinical Mycobacterium

  15. Hybridization kinetics analysis of an oligonucleotide microarray for microRNA detection

    Institute of Scientific and Technical Information of China (English)

    Botao Zhao; Shuo Ding; Wei Li; Youxin Jin

    2011-01-01

    MicroRNA (miRNA) microarrays have been successfully used for profiling miRNA expression in many physiological processes such as development, differentiation, oncogenesis,and other disease processes. Detecting miRNA by miRNA microarray is actually based on nucleic acid hybridization between target molecules and their corresponding complementary probes. Due to the small size and high degree of similarity among miRNA sequences, the hybridization condition must be carefully optimized to get specific and reliable signals. Previously, we reported a microarray platform to detect miRNA expression. In this study, we evaluated the sensitivity and specificity of our microarray platform. After systematic analysis, we determined an optimized hybridization condition with high sensitivity and specificity for miRNA detection. Our results would be helpful for other hybridization-based miRNA detection methods, such as northern blot and nuclease protection assay.

  16. Detection bias in microarray and sequencing transcriptomic analysis identified by housekeeping genes

    OpenAIRE

    Yijuan Zhang; Oluwafemi S. Akintola; Liu, Ken J.A.; Bingyun Sun

    2015-01-01

    This work includes the original data used to discover the gene ontology bias in transcriptomic analysis conducted by microarray and high throughput sequencing (Zhang et al., 2015) [1]. In the analysis, housekeeping genes were used to examine the differential detection ability by microarray and sequencing because these genes are probably the most reliably detected. The genes included here were compiled from 15 human housekeeping gene studies. The provided tables here comprise of detailed chrom...

  17. Food allergen digestibility: The influence on allergenicity

    DEFF Research Database (Denmark)

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard

    potential exist. Resistance to digestion is therefore a test parameter included in the safety assessment of the allergenic potential of novel proteins in genetically modified foods. In recent years, the association between resistance to digestion and allergenic potential has been challenged. When reviewing......Food allergy is a major health problem in the Western countries, affecting 3-8% of the population. What makes a dietary protein a food allergen has not yet been established, though several characteristics have been proposed to be shared by the food allergens. One of the features believed to be a...... existing data from digestibility studies on known food allergens, it becomes evident that food allergens do not necessarily resist digestion. However, the choice of assay conditions, the method used for detection of residual intact protein as well as fragments hereof greatly influences the outcome. Studies...

  18. Detection by real time PCR of walnut allergen coding sequences in processed foods.

    Science.gov (United States)

    Linacero, Rosario; Ballesteros, Isabel; Sanchiz, Africa; Prieto, Nuria; Iniesto, Elisa; Martinez, Yolanda; Pedrosa, Mercedes M; Muzquiz, Mercedes; Cabanillas, Beatriz; Rovira, Mercè; Burbano, Carmen; Cuadrado, Carmen

    2016-07-01

    A quantitative real-time PCR (RT-PCR) method, employing novel primer sets designed on Jug r 1, Jug r 3, and Jug r 4 allergen-coding sequences, was set up and validated. Its specificity, sensitivity, and applicability were evaluated. The DNA extraction method based on CTAB-phenol-chloroform was best for walnut. RT-PCR allowed a specific and accurate amplification of allergen sequence, and the limit of detection was 2.5pg of walnut DNA. The method sensitivity and robustness were confirmed with spiked samples, and Jug r 3 primers detected up to 100mg/kg of raw walnut (LOD 0.01%, LOQ 0.05%). Thermal treatment combined with pressure (autoclaving) reduced yield and amplification (integrity and quality) of walnut DNA. High hydrostatic pressure (HHP) did not produce any effect on the walnut DNA amplification. This RT-PCR method showed greater sensitivity and reliability in the detection of walnut traces in commercial foodstuffs compared with ELISA assays. PMID:26920302

  19. FRET-based dimeric aptamer probe for selective and sensitive Lup an 1 allergen detection.

    Science.gov (United States)

    Mairal, T; Nadal, P; Svobodova, M; O'Sullivan, C K

    2014-04-15

    A sensitive method for the rapid and sensitive detection of the anaphylactic food allergen Lup an 1 (β-conglutin) exploiting fluorescence resonance energy transfer (FRET) has been developed. A high affinity dimeric form of a truncated 11-mer aptamer against β-conglutin was used, with each monomeric aptamer being flanked by donor/acceptor moieties. The dimeric form in the absence of target yields fluorescence emission due to the FRET from the excited fluorophore to the proximal second fluorophore. However, upon addition of β-conglutin, the specific interaction induces a change in the bi-aptameric structure resulting in an increase in fluorescence emission. The method is highly specific and sensitive, with a detection limit of 150 pM, providing an effective tool for the direct detection of the toxic β-conglutin subunit in foodstuffs in just 1 min at room temperature. PMID:24280051

  20. Microarray-Based Detection of 90 Antibiotic Resistance Genes of Gram-Positive Bacteria

    OpenAIRE

    Perreten, Vincent; Vorlet-Fawer, Lorianne; Slickers, Peter; Ehricht, Ralf; Kuhnert, Peter; Frey, Joachim

    2005-01-01

    A disposable microarray was developed for detection of up to 90 antibiotic resistance genes in gram-positive bacteria by hybridization. Each antibiotic resistance gene is represented by two specific oligonucleotides chosen from consensus sequences of gene families, except for nine genes for which only one specific oligonucleotide could be developed. A total of 137 oligonucleotides (26 to 33 nucleotides in length with similar physicochemical parameters) were spotted onto the microarray. The mi...

  1. Can subtle changes in gene expression be consistently detected with different microarray platforms?

    OpenAIRE

    Kuiper Rowan; de Hollander Mattias; Ariyurek Yavuz; Vossen Rolf HAM; Schenk Geert J; Vreugdenhil Erno; 't Hoen Peter AC; Pedotti Paola; van Ommen Gertjan JB; den Dunnen Johan T; Boer Judith M; Menezes Renée X

    2008-01-01

    Abstract Background The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle. Results Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were...

  2. Microarray Detection of Duplex and Triplex DNA Binders with DNA-Modified Gold Nanoparticles

    OpenAIRE

    Lytton-Jean, Abigail K. R.; Han, Min Su; Mirkin, Chad A.

    2007-01-01

    We have designed a chip-based assay, using microarray technology, for determining the relative binding affinities of duplex and triplex DNA binders. This assay combines the high discrimination capabilities afforded by DNA-modified Au nanoparticles with the high-throughput capabilities of DNA microarrays. The detection and screening of duplex DNA binders are important because these molecules, in many cases, are potential anticancer agents as well as toxins. Triplex DNA binders are also promisi...

  3. Direct Detection and Genotyping of KPC Carbapenemases from Urine using a new DNA Microarray Test

    OpenAIRE

    Peter, Harald; Berggrav, Kathrine; Thomas, Peter; Pfeifer, Yvonne; Witte, Wolfgang; Templeton, Kate; Bachmann, Till T

    2012-01-01

    Klebsiella pneumoniae carbapenemases (KPC) are considered a serious threat to antibiotic therapy as they confer resistance to carbapenems, which are used to treat Extended-spectrum beta-lactamase (ESBL) producing bacteria. Here, we describe the development and evaluation of a DNA microarray for detection and genotyping of KPC genes (blaKPC) within 5 hours. To test the whole assay procedure (DNA extraction + DNA microarray assay) directly from clinical specimen, we compared two commercial DNA ...

  4. Application of a New Genetic Deafness Microarray for Detecting Mutations in the Deaf in China.

    Directory of Open Access Journals (Sweden)

    Hong Wu

    Full Text Available The aim of this study was to evaluate the GoldenGate microarray as a diagnostic tool and to elucidate the contribution of the genes on this array to the development of both nonsyndromic and syndromic sensorineural hearing loss in China.We developed a microarray to detect 240 mutations underlying syndromic and nonsyndromic sensorineural hearing loss. The microarray was then used for analysis of 382 patients with nonsyndromic sensorineural hearing loss (including 15 patients with enlarged vestibular aqueduct syndrome, 21 patients with Waardenburg syndrome, and 60 unrelated controls. Subsequently, we analyzed the sensitivity, specificity, and reproducibility of this new approach after Sanger sequencing-based verification, and also determined the contribution of the genes on this array to the development of distinct hearing disorders.The sensitivity and specificity of the microarray chip were 98.73% and 98.34%, respectively. Genetic defects were identified in 61.26% of the patients with nonsyndromic sensorineural hearing loss, and 9 causative genes were identified. The molecular etiology was confirmed in 19.05% and 46.67% of the patients with Waardenburg syndrome and enlarged vestibular aqueduct syndrome, respectively.Our new mutation-based microarray comprises an accurate and comprehensive genetic tool for the detection of sensorineural hearing loss. This microarray-based detection method could serve as a first-pass screening (before next-generation-sequencing screening for deafness-causing mutations in China.

  5. Application of a New Genetic Deafness Microarray for Detecting Mutations in the Deaf in China

    Science.gov (United States)

    Wu, Hong; Feng, Yong; Jiang, Lu; Pan, Qian; Liu, Yalan; Liu, Chang; He, Chufeng; Chen, Hongsheng; Liu, Xueming; Hu, Chang; Hu, Yiqiao; Mei, Lingyun

    2016-01-01

    Objective The aim of this study was to evaluate the GoldenGate microarray as a diagnostic tool and to elucidate the contribution of the genes on this array to the development of both nonsyndromic and syndromic sensorineural hearing loss in China. Methods We developed a microarray to detect 240 mutations underlying syndromic and nonsyndromic sensorineural hearing loss. The microarray was then used for analysis of 382 patients with nonsyndromic sensorineural hearing loss (including 15 patients with enlarged vestibular aqueduct syndrome), 21 patients with Waardenburg syndrome, and 60 unrelated controls. Subsequently, we analyzed the sensitivity, specificity, and reproducibility of this new approach after Sanger sequencing-based verification, and also determined the contribution of the genes on this array to the development of distinct hearing disorders. Results The sensitivity and specificity of the microarray chip were 98.73% and 98.34%, respectively. Genetic defects were identified in 61.26% of the patients with nonsyndromic sensorineural hearing loss, and 9 causative genes were identified. The molecular etiology was confirmed in 19.05% and 46.67% of the patients with Waardenburg syndrome and enlarged vestibular aqueduct syndrome, respectively. Conclusion Our new mutation-based microarray comprises an accurate and comprehensive genetic tool for the detection of sensorineural hearing loss. This microarray-based detection method could serve as a first-pass screening (before next-generation-sequencing screening) for deafness-causing mutations in China. PMID:27018795

  6. Oligonucleotide-based microarray: A new improvement in microarray detection of plant viruses

    Czech Academy of Sciences Publication Activity Database

    Bystřická, Dagmar; Lenz, Ondřej; Mráz, Ivan; Piherová, L.; Kmoch, S.; Šíp, M.

    2005-01-01

    Roč. 128, - (2005), s. 176-182. ISSN 0166-0934 R&D Projects: GA ČR(CZ) GA522/01/1105; GA MŠk(CZ) OC 853.002 Keywords : plant viruses * detection Subject RIV: EE - Microbiology, Virology Impact factor: 1.886, year: 2005

  7. A microarray approach for simultaneous detection of multiple pathogens in food

    Science.gov (United States)

    A pathogen detection microarray was developed for simultaneous detection of the four most prominent foodborne pathogens including Escherichia coli O157:H7, Salmonella enterica, Listeria monocytogenes and Campylobacter jejuni. The approach utilized 14 species-specific gene targets to design a variety...

  8. Detection of protein microarrays by oblique-incidence reflectivity difference technique

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Biological microarrays with different proteins and different protein concentrations are detected without external labeling by an oblique-incidence reflectivity difference (OIRD) technique. The initial experiment results reveal that the intensities of OIRD signals can distinguish the different proteins and concentrations of protein. The OIRD technique promises feasible applications to life sciences for label-free and high-throughput detection.

  9. Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays.

    Science.gov (United States)

    Chao, Jie; Li, Zhenhua; Li, Jing; Peng, Hongzhen; Su, Shao; Li, Qian; Zhu, Changfeng; Zuo, Xiaolei; Song, Shiping; Wang, Lianhui; Wang, Lihua

    2016-07-15

    Microarrays of biomolecules hold great promise in the fields of genomics, proteomics, and clinical assays on account of their remarkably parallel and high-throughput assay capability. However, the fluorescence detection used in most conventional DNA microarrays is still limited by sensitivity. In this study, we have demonstrated a novel universal and highly sensitive platform for fluorescent detection of sequence specific DNA at the femtomolar level by combining dextran-coated microarrays with hybridization chain reaction (HCR) signal amplification. Three-dimensional dextran matrix was covalently coated on glass surface as the scaffold to immobilize DNA recognition probes to increase the surface binding capacity and accessibility. DNA nanowire tentacles were formed on the matrix surface for efficient signal amplification by capturing multiple fluorescent molecules in a highly ordered way. By quantifying microscopic fluorescent signals, the synergetic effects of dextran and HCR greatly improved sensitivity of DNA microarrays, with a detection limit of 10fM (1×10(5) molecules). This detection assay could recognize one-base mismatch with fluorescence signals dropped down to ~20%. This cost-effective microarray platform also worked well with samples in serum and thus shows great potential for clinical diagnosis. PMID:26922047

  10. Accurate detection of carcinoma cells by use of a cell microarray chip.

    Directory of Open Access Journals (Sweden)

    Shohei Yamamura

    Full Text Available BACKGROUND: Accurate detection and analysis of circulating tumor cells plays an important role in the diagnosis and treatment of metastatic cancer treatment. METHODS AND FINDINGS: A cell microarray chip was used to detect spiked carcinoma cells among leukocytes. The chip, with 20,944 microchambers (105 µm width and 50 µm depth, was made from polystyrene; and the formation of monolayers of leukocytes in the microchambers was observed. Cultured human T lymphoblastoid leukemia (CCRF-CEM cells were used to examine the potential of the cell microarray chip for the detection of spiked carcinoma cells. A T lymphoblastoid leukemia suspension was dispersed on the chip surface, followed by 15 min standing to allow the leukocytes to settle down into the microchambers. Approximately 29 leukocytes were found in each microchamber when about 600,000 leukocytes in total were dispersed onto a cell microarray chip. Similarly, when leukocytes isolated from human whole blood were used, approximately 89 leukocytes entered each microchamber when about 1,800,000 leukocytes in total were placed onto the cell microarray chip. After washing the chip surface, PE-labeled anti-cytokeratin monoclonal antibody and APC-labeled anti-CD326 (EpCAM monoclonal antibody solution were dispersed onto the chip surface and allowed to react for 15 min; and then a microarray scanner was employed to detect any fluorescence-positive cells within 20 min. In the experiments using spiked carcinoma cells (NCI-H1650, 0.01 to 0.0001%, accurate detection of carcinoma cells was achieved with PE-labeled anti-cytokeratin monoclonal antibody. Furthermore, verification of carcinoma cells in the microchambers was performed by double staining with the above monoclonal antibodies. CONCLUSION: The potential application of the cell microarray chip for the detection of CTCs was shown, thus demonstrating accurate detection by double staining for cytokeratin and EpCAM at the single carcinoma cell level.

  11. Signal amplification in electrochemical detection of buckwheat allergenic protein using field effect transistor biosensor by introduction of anionic surfactant

    Directory of Open Access Journals (Sweden)

    Sho Hideshima

    2016-03-01

    Full Text Available Food allergens, especially buckwheat proteins, sometimes induce anaphylactic shock in patients after ingestion. Development of a simple and rapid screening method based on a field effect transistor (FET biosensor for food allergens in food facilities or products is in demand. In this study, we achieved the FET detection of a buckwheat allergenic protein (BWp16, which is not charged enough to be electrically detected by FET biosensors, by introducing additional negative charges from anionic surfactants to the target proteins. A change in the FET characteristics reflecting surface potential caused by the adsorption of target charged proteins was observed when the target sample was coupled with the anionic surfactant (sodium dodecyl sulfate; SDS, while no significant response was detected without any surfactant treatment. It was suggested that the surfactant conjugated with the protein could be useful for the charge amplification of the target proteins. The surface plasmon resonance analysis revealed that the SDS-coupled proteins were successfully captured by the receptors immobilized on the sensing surface. Additionally, we obtained the FET responses at various concentrations of BWp16 ranging from 1 ng/mL to 10 μg/mL. These results suggest that a signal amplification method for FET biosensing is useful for allergen detection in the food industry.

  12. Comparison of six commercial ELISA kits for their specificity and sensitivity in detecting different major peanut allergens

    NARCIS (Netherlands)

    Jayasena, S.; Smits, M.; Fiechter, D.; Jong, A. de; Nordlee, J.; Baumert, J.; Taylor, S.L.; Pieters, R.H.; Koppelman, S.J.

    2015-01-01

    Six commercial peanut enzyme-linked immunosorbent assay kits were assessed for their ability to recover peanut from the standard reference material 2387 peanut butter and also for their specificity in detecting four major peanut allergens, Ara h 1, Ara h 2, Ara h 3, and Ara h 6. The percentage recov

  13. Comparison of Six Commercial ELISA Kits for Their Specificity and Sensitivity in Detecting Different Major Peanut Allergens

    NARCIS (Netherlands)

    Jayasena, Shyamali; Smits, Mieke; Fiechter, Daniëlle; Jongh, Aard de; Nordlee, Julie; Baumert, Joe; Taylor, Steve L.; Pieters, Raymond; Koppelman, Stef J.

    2015-01-01

    Author supplied: "Six commercial peanut enzyme-linked immunosorbent assay kits were assessed for their ability to recover peanut from the standard reference material 2387 peanut butter and also for their specificity in detecting four major peanut allergens, Ara h 1, Ara h 2, Ara h 3, and Ara h 6. Th

  14. Detection of the specific binding on protein microarrays by oblique-incidence reflectivity difference method

    Science.gov (United States)

    Lu, Heng; Wen, Juan; Wang, Xu; Yuan, Kun; Li, Wei; Lu, Huibin; Zhou, Yueliang; Jin, Kuijuan; Ruan, Kangcheng; Yang, Guozhen

    2010-09-01

    The specific binding between Cy5-labeled goat anti-mouse Immunoglobulin G (IgG) and mouse IgG with a concentration range from 625 to 104 µg ml - 1 has been detected successfully by the oblique-incidence reflectivity difference (OI-RD) method in each procedure of microarray fabrication. The experimental data prove that the OI-RD method can be employed not only to distinguish the different concentrations in label-free fashion but also to detect the antibody-antigen capture. In addition, the differential treatment of the OI-RD signals can decrease the negative influences of glass slide as the microarray upholder. Therefore the OI-RD technique has promising applications for the label-free and high-throughput detection of protein microarrays.

  15. Detection of the specific binding on protein microarrays by oblique-incidence reflectivity difference method

    International Nuclear Information System (INIS)

    The specific binding between Cy5-labeled goat anti-mouse Immunoglobulin G (IgG) and mouse IgG with a concentration range from 625 to 104 µg ml−1 has been detected successfully by the oblique-incidence reflectivity difference (OI-RD) method in each procedure of microarray fabrication. The experimental data prove that the OI-RD method can be employed not only to distinguish the different concentrations in label-free fashion but also to detect the antibody–antigen capture. In addition, the differential treatment of the OI-RD signals can decrease the negative influences of glass slide as the microarray upholder. Therefore the OI-RD technique has promising applications for the label-free and high-throughput detection of protein microarrays

  16. Multi-gene detection and identification of mosquito-borne RNA viruses using an oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Nathan D Grubaugh

    Full Text Available BACKGROUND: Arthropod-borne viruses are important emerging pathogens world-wide. Viruses transmitted by mosquitoes, such as dengue, yellow fever, and Japanese encephalitis viruses, infect hundreds of millions of people and animals each year. Global surveillance of these viruses in mosquito vectors using molecular based assays is critical for prevention and control of the associated diseases. Here, we report an oligonucleotide DNA microarray design, termed ArboChip5.1, for multi-gene detection and identification of mosquito-borne RNA viruses from the genera Flavivirus (family Flaviviridae, Alphavirus (Togaviridae, Orthobunyavirus (Bunyaviridae, and Phlebovirus (Bunyaviridae. METHODOLOGY/PRINCIPAL FINDINGS: The assay utilizes targeted PCR amplification of three genes from each virus genus for electrochemical detection on a portable, field-tested microarray platform. Fifty-two viruses propagated in cell-culture were used to evaluate the specificity of the PCR primer sets and the ArboChip5.1 microarray capture probes. The microarray detected all of the tested viruses and differentiated between many closely related viruses such as members of the dengue, Japanese encephalitis, and Semliki Forest virus clades. Laboratory infected mosquitoes were used to simulate field samples and to determine the limits of detection. Additionally, we identified dengue virus type 3, Japanese encephalitis virus, Tembusu virus, Culex flavivirus, and a Quang Binh-like virus from mosquitoes collected in Thailand in 2011 and 2012. CONCLUSIONS/SIGNIFICANCE: We demonstrated that the described assay can be utilized in a comprehensive field surveillance program by the broad-range amplification and specific identification of arboviruses from infected mosquitoes. Furthermore, the microarray platform can be deployed in the field and viral RNA extraction to data analysis can occur in as little as 12 h. The information derived from the ArboChip5.1 microarray can help to establish

  17. A DNA Microarray-Based Assay to Detect Dual Infection with Two Dengue Virus Serotypes

    Directory of Open Access Journals (Sweden)

    Alvaro Díaz-Badillo

    2014-04-01

    Full Text Available Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. Single-stranded DNA targets were covalently attached to glass slides and hybridised with specific labelled probes. DENV isolates and dengue samples were used to evaluate microarray performance. Our results demonstrate that the probes hybridized specifically to DENV serotypes; with no detection of unspecific signals. This finding provides evidence that specific probes can effectively identify single and double infections in DENV samples.

  18. Allergen nomenclature.

    OpenAIRE

    Marsh, D. G.; Goodfriend, L.; King, T P; Lowenstein, H.; Platts-Mills, T A

    1986-01-01

    This article presents a nomenclature system for allergens which has been officially recommended by the International Union of Immunological Societies (IUIS). The nomenclature is based on proposals of the IUIS Sub-Committee for Allergen Nomenclature and is applicable to highly purified, well-characterized allergens and to non-purified or partially purified allergenic extracts.

  19. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.

    Science.gov (United States)

    Guo, Qingsheng; Bai, Zhixiong; Liu, Yuqian; Sun, Qingjiang

    2016-03-15

    In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs. PMID:26397421

  20. Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes

    LENUS (Irish Health Repository)

    Scheler, Ott

    2011-02-28

    Abstract Background We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification) amplification, for sensitivity. Results We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal\\/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. Conclusions The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.

  1. Validation of the performance of a GMO multiplex screening assay based on microarray detection

    NARCIS (Netherlands)

    Leimanis, S.; Hamels, S.; Naze, F.; Mbongolo, G.; Sneyers, M.; Hochegger, R.; Broll, H.; Roth, L.; Dallmann, K.; Micsinai, A.; Dijk, van J.P.; Kok, E.J.

    2008-01-01

    A new screening method for the detection and identification of GMO, based on the use of multiplex PCR followed by microarray, has been developed and is presented. The technology is based on the identification of quite ubiquitous GMO genetic target elements first amplified by PCR, followed by direct

  2. Label-free DNA hybridization detection with molecular beacon immobilized in photopolymerized acrylamide gel microarray

    Science.gov (United States)

    Wang, Hong; Li, Jiong; Liu, Quanjun; Liu, Heping; Lu, Zuhong; Zhu, Jijun

    2001-10-01

    Photopolymerized acrylamide gel microarray used to immobilize the molecular beacon for label free DNA hybridization detection is described in this paper. Polyacrylamide gel microarray was prepared by UV photopolymerization of 4% acrylamide in 40% glycerol, 0.002%methylene blue, 0.012% TEMED and 0.1M phosphate buffer (PHequals7) with a Relpel-silane pretreated quartz mask. This kind of three-dimensional gel microarray provides more than 100 times great immobilization capacity. The hybridization and other processes with it resemble a homogeneous liquid phase reaction rather than a heterogeneous liquid-solid interface reaction. The specially designed molecular beacons contain a 15 base loop sequence with 5 base pair stem, a 20 base thymine as spacer, a 5'-end amino group for immobilization, a fluorescein in the middle of the sequence as the fluorophore and a 3'-end DABCYL as the quencher. Between the 5'-end amino group and the stem, the 20 base thymine is used to minimize destability caused by 5'-end immobilization. Confocal microscope was used to investigate the fluorescence intensity of gel immobilized molecular beacon probes. After hybridization we can easily distinguish complementary and noncomplementay targets with gel-immobilized molecular beacon probes. Image analysis showed that the fluorescence intensity ratio of complementary to noncomplementay probes is great than 5. The potential applications of gel-immobilized molecular beacon microarray are mutation detection, pathogenic detection, etc. in a parallel, cost saving and label-free detection way.

  3. Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning

    OpenAIRE

    Soeria-Atmadja, D.; Lundell, T.; Gustafsson, M. G.; Hammerling, U.

    2006-01-01

    The placing of novel or new-in-the-context proteins on the market, appearing in genetically modified foods, certain bio-pharmaceuticals and some household products leads to human exposure to proteins that may elicit allergic responses. Accurate methods to detect allergens are therefore necessary to ensure consumer/patient safety. We demonstrate that it is possible to reach a new level of accuracy in computational detection of allergenic proteins by presenting a novel detector, Detection based...

  4. Easy and fast detection and genotyping of high-risk human papillomavirus by dedicated DNA microarrays.

    Science.gov (United States)

    Albrecht, Valérie; Chevallier, Anne; Magnone, Virginie; Barbry, Pascal; Vandenbos, Fanny; Bongain, André; Lefebvre, Jean-Claude; Giordanengo, Valérie

    2006-11-01

    Persistent cervical high-risk human papillomavirus (HPV) infection is correlated with an increased risk of developing a high-grade cervical intraepithelial lesion. A two-step method was developed for detection and genotyping of high-risk HPV. DNA was firstly amplified by asymmetrical PCR in the presence of Cy3-labelled primers and dUTP. Labelled DNA was then genotyped using DNA microarray hybridization. The current study evaluated the technical efficacy of laboratory-designed HPV DNA microarrays for high-risk HPV genotyping on 57 malignant and non-malignant cervical smears. The approach was evaluated for a broad range of cytological samples: high-grade squamous intraepithelial lesions (HSIL), low-grade squamous intraepithelial lesions (LSIL) and atypical squamous cells of high-grade (ASC-H). High-risk HPV was also detected in six atypical squamous cells of undetermined significance (ASC-US) samples; among them only one cervical specimen was found uninfected, associated with no histological lesion. The HPV oligonucleotide DNA microarray genotyping detected 36 infections with a single high-risk HPV type and 5 multiple infections with several high-risk types. Taken together, these results demonstrate the sensitivity and specificity of the HPV DNA microarray approach. This approach could improve clinical management of patients with cervical cytological abnormalities. PMID:16879879

  5. Establishment and Application of a Visual DNA Microarray for the Detection of Food-borne Pathogens.

    Science.gov (United States)

    Li, Yongjin

    2016-01-01

    The accurate detection and identification of food-borne pathogenic microorganisms is critical for food safety nowadays. In the present work, a visual DNA microarray was established and applied to detect pathogens commonly found in food, including Salmonella enterica, Shigella flexneri, E. coli O157:H7 and Listeria monocytogenes in food samples. Multiplex PCR (mPCR) was employed to simultaneously amplify specific gene fragments, fimY for Salmonella, ipaH for Shigella, iap for L. monocytogenes and ECs2841 for E. coli O157:H7, respectively. Biotinylated PCR amplicons annealed to the microarray probes were then reacted with a streptavidin-alkaline phosphatase conjugate and nitro blue tetrazolium/5-bromo-4-chloro-3'-indolylphosphate, p-toluidine salt (NBT/BCIP); the positive results were easily visualized as blue dots formatted on the microarray surface. The performance of a DNA microarray was tested against 14 representative collection strains and mock-contamination food samples. The combination of mPCR and a visual micro-plate chip specifically and sensitively detected Salmonella enterica, Shigella flexneri, E. coli O157:H7 and Listeria monocytogenes in standard strains and food matrices with a sensitivity of ∼10(2) CFU/mL of bacterial culture. Thus, the developed method is advantageous because of its high throughput, cost-effectiveness and ease of use. PMID:26860568

  6. High Frequency of Chlamydia trachomatis Mixed Infections Detected by Microarray Assay in South American Samples

    Science.gov (United States)

    Gallo Vaulet, Lucía; Entrocassi, Carolina; Portu, Ana I.; Castro, Erica; Di Bartolomeo, Susana; Ruettger, Anke; Sachse, Konrad; Rodriguez Fermepin, Marcelo

    2016-01-01

    Chlamydia trachomatis is one of the most common sexually transmitted infections worldwide. Based on sequence variation in the ompA gene encoding the major outer membrane protein, the genotyping scheme distinguishes 17 recognized genotypes, i.e. A, B, Ba, C, D, Da, E, F, G, H, I, Ia, J, K, L1, L2, and L3. Genotyping is an important tool for epidemiological tracking of C. trachomatis infections, including the revelation of transmission pathways and association with tissue tropism and pathogenicity. Moreover, genotyping can be useful for clinicians to establish the correct treatment when LGV strains are detected. Recently a microarray assay was described that offers several advantages, such as rapidity, ease of standardization and detection of mixed infections. The aim of this study was to evaluate the performance of the DNA microarray-based assay for C. trachomatis genotyping of clinical samples already typed by PCR-RFLP from South America. The agreement between both typing techniques was 90.05% and the overall genotype distribution obtained with both techniques was similar. Detection of mixed-genotype infections was significantly higher using the microarray assay (8.4% of cases) compared to PCR-RFLP (0.5%). Among 178 samples, the microarray assay identified 10 ompA genotypes, i.e. D, Da, E, F, G, H, I, J, K and L2. The most predominant type was genotype E, followed by D and F. PMID:27082962

  7. Simultaneous Detection of Multiple Fish Pathogens Using a Naked-Eye Readable DNA Microarray

    Directory of Open Access Journals (Sweden)

    King-Jung Lin

    2012-02-01

    Full Text Available We coupled 16S rDNA PCR and DNA hybridization technology to construct a microarray for simultaneous detection and discrimination of eight fish pathogens (Aeromonas hydrophila, Edwardsiella tarda, Flavobacterium columnare, Lactococcus garvieae, Photobacterium damselae, Pseudomonas anguilliseptica, Streptococcus iniae and Vibrio anguillarum commonly encountered in aquaculture. The array comprised short oligonucleotide probes (30 mer complementary to the polymorphic regions of 16S rRNA genes for the target pathogens. Targets annealed to the microarray probes were reacted with streptavidin-conjugated alkaline phosphatase and nitro blue tetrazolium/5-bromo-4-chloro-3′-indolylphosphate, p-toluidine salt (NBT/BCIP, resulting in blue spots that are easily visualized by the naked eye. Testing was performed against a total of 168 bacterial strains, i.e., 26 representative collection strains, 81 isolates of target fish pathogens, and 61 ecologically or phylogenetically related strains. The results showed that each probe consistently identified its corresponding target strain with 100% specificity. The detection limit of the microarray was estimated to be in the range of 1 pg for genomic DNA and 103 CFU/mL for pure pathogen cultures. These high specificity and sensitivity results demonstrate the feasibility of using DNA microarrays in the diagnostic detection of fish pathogens.

  8. Simultaneous detection of multiple fish pathogens using a naked-eye readable DNA microarray.

    Science.gov (United States)

    Chang, Chin-I; Hung, Pei-Hsin; Wu, Chia-Che; Cheng, Ta Chih; Tsai, Jyh-Ming; Lin, King-Jung; Lin, Chung-Yen

    2012-01-01

    We coupled 16S rDNA PCR and DNA hybridization technology to construct a microarray for simultaneous detection and discrimination of eight fish pathogens (Aeromonas hydrophila, Edwardsiella tarda, Flavobacterium columnare, Lactococcus garvieae, Photobacterium damselae, Pseudomonas anguilliseptica, Streptococcus iniae and Vibrio anguillarum) commonly encountered in aquaculture. The array comprised short oligonucleotide probes (30 mer) complementary to the polymorphic regions of 16S rRNA genes for the target pathogens. Targets annealed to the microarray probes were reacted with streptavidin-conjugated alkaline phosphatase and nitro blue tetrazolium/5-bromo-4-chloro-3'-indolylphosphate, p-toluidine salt (NBT/BCIP), resulting in blue spots that are easily visualized by the naked eye. Testing was performed against a total of 168 bacterial strains, i.e., 26 representative collection strains, 81 isolates of target fish pathogens, and 61 ecologically or phylogenetically related strains. The results showed that each probe consistently identified its corresponding target strain with 100% specificity. The detection limit of the microarray was estimated to be in the range of 1 pg for genomic DNA and 10(3) CFU/mL for pure pathogen cultures. These high specificity and sensitivity results demonstrate the feasibility of using DNA microarrays in the diagnostic detection of fish pathogens. PMID:22736973

  9. Carbohydrate microarrays

    DEFF Research Database (Denmark)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola; Shin, Injae

    2012-01-01

    In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray-based technol......In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray......-based technology has been widely employed for rapid analysis of the glycan binding properties of lectins and antibodies, the quantitative measurements of glycan-protein interactions, detection of cells and pathogens, identification of disease-related anti-glycan antibodies for diagnosis, and fast assessment of...

  10. Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis

    OpenAIRE

    Hoffmann, Reinhard; Seidl, Thomas; Dugas, Martin

    2002-01-01

    Background Oligonucleotide microarrays measure the relative transcript abundance of thousands of mRNAs in parallel. A large number of procedures for normalization and detection of differentially expressed genes have been proposed. However, the relative impact of these methods on the detection of differentially expressed genes remains to be determined. Results We have employed four different normalization methods and all possible combinations with three different statistical algorithms for det...

  11. 12 Comprehensive Detection of Allergens in Grass Pollen Extracts by Mass Spectrometry

    OpenAIRE

    Augustin, Steffen; Mitulski, Liane; Cromwell, Oliver; Reese, Gerald; Nandy, Andreas

    2012-01-01

    Background More than 40% of type 1-allergic individuals suffer from hypersensitivity to grass pollen. Patients are treated traditionally with specific immunotherapy using pollen extracts derived from one or several different Pooideae species. While for several species the most important allergens (group 1 and group 5) have been identified, other allergens have either not been identified or sequence data are still missing. We have used mass spectrometry (MS) together with genetic and immunolog...

  12. Label-Free and High-Throughput Detection of Protein Microarrays by Oblique-Incidence Reflectivity Difference Method

    Science.gov (United States)

    Wang, Xu; Lu, Heng; Wen, Juan; Yuan, Kun; LÜ, Hui-Bin; Jin, Kui-Juan; Zhou, Yue-Liang; Yang, Guo-Zhen

    2010-10-01

    We label-free detected the biological process of preparing a microarray that includes 400 spots of mouse immunoglobulin G (IgG) as well as the specific hybridization between mouse IgG and goat anti-mouse IgG by an oblique-incidence reflectivity difference (OI-RD) method. The detection results after each process including printing, washing, blocking, and hybridization, demonstrate that the OI-RD method can trace the preparation process of a microarray and detect the specific hybridization between antigens and antibodies. OI-RD is a promising method for label-free and high-throughput detection of biological microarrays.

  13. Label-Free and High-Throughput Detection of Protein Microarrays by Oblique-Incidence Reflectivity Difference Method

    International Nuclear Information System (INIS)

    We label-free detected the biological process of preparing a microarray that includes 400 spots of mouse immunoglobulin G (IgG) as well as the specific hybridization between mouse IgG and goat anti-mouse IgG by an oblique-incidence reflectivity difference (OI-RD) method. The detection results after each process including printing, washing, blocking, and hybridization, demonstrate that the OI-RD method can trace the preparation process of a microarray and detect the specific hybridization between antigens and antibodies. OI-RD is a promising method for label-free and high-throughput detection of biological microarrays

  14. A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds

    Directory of Open Access Journals (Sweden)

    Stegall Mark D

    2007-03-01

    Full Text Available Abstract Background Microarrays provide a means to simultaneously examine the gene expression of the entire transcriptome in a single sample. Many studies have highlighted the need for novel software and statistical approaches to assess the measured gene expression. Less attention has been directed toward whether genes considered undetectable by microarray can be detected by other strategies or whether these genes can provide accurate gene expression determinations. In the kidney this is a concern for genes such as cytokines which dramatically influence the immune response but are often considered low abundance genes produced by a small number of cells. Results Using both publicly available and our own microarray datasets we analyzed the detection p-value and detection call values for 81 human kidney samples run on the U133A or U133Plus2.0 Affymetrix microarrays (Affymetrix, Santa Clara, CA. For the cytokine genes, the frequency of detection in each sample group (normal, transplant and renal cell carcinoma was examined and revealed that a majority of cytokine related genes are not detectable in human kidney by microarray. Using a subset of 29 Mayo transplant samples, a group of seven transplant-related cytokines and eight non-cytokine genes were evaluated by real-time PCR (rt-PCR. For these 15 genes we compared the impact of decreasing microarray detection frequency with the changes in gene expression observed by both microarray and rt-PCR. We found that as microarray detection frequency decreased the correlation between microarray and rt-PCR data also decreased. Conclusion We conclude that, when analyzing microarray data from human kidney samples, genes generally expressed at low abundance (i.e. cytokines should be evaluated with more sensitive approaches such as rt-PCR. In addition, our data suggest that the use of detection frequency cutoffs for inclusion or exclusion of microarray data may be appropriate when comparing microarray and rt

  15. Outdoor allergens.

    OpenAIRE

    Rogers, Christine Anne; Burge, Harriet A.

    2000-01-01

    Outdoor allergens are an important part of the exposures that lead to allergic disease. Understanding the role of outdoor allergens requires a knowledge of the nature of outdoor allergen-bearing particles, the distributions of their source, and the nature of the aerosols (particle types, sizes, dynamics of concentrations). Primary sources for outdoor allergens include vascular plants (pollen, fern spores, soy dust), and fungi (spores, hyphae). Nonvascular plants, algae, and arthropods contrib...

  16. Silicon photonic crystal microarrays for high throughput label-free detection of lung cancer cell line lysates with sensitivity and specificity

    Science.gov (United States)

    Chakravarty, Swapnajit; Lai, Wei-Cheng; Zou, Yi; Gemmill, Robert M.; Chen, Ray T.

    2013-03-01

    Detection of biomolecules on microarrays based on label-free on-chip optical biosensors is very attractive since this format avoids complex chemistries caused by steric hindrance of labels. Application areas include the detection of cancers and allergens, and food-borne pathogens to name a few. We have demonstrated photonic crystal microcavity biosensors with high sensitivity down to 1pM concentrations (67pg/ml). High sensitivities were achieved by slow light engineering which reduced the radiation loss and increased the stored energy in the photonic crystal microcavity resonance mode. Resonances with high quality factor Q~26,760 in liquid ambient, coupled with larger optical mode volumes allowed enhanced interaction with the analyte biomolecules which resulted in sensitivities down to 10 cells per micro-liter to lung cancer cell lysates. The specificity of detection was ensured by multiplexed detections from multiple photonic crystal microcavities arrayed on the arms of a multimode interference power splitter. Specific binding interactions and control experiments were performed simultaneously at the same instant of time with the same 60 microliter sample volume. Specificity is further ensured by sandwich assay methods in the multiplexed experiment. Sandwich assay based amplification increased the sensitivity further resulting in the detection of lung cancer cell lysates down to concentrations of 2 cells per micro-liter. The miniaturization enabled by photonic crystal biosensors coupled with waveguide interconnected layout thus offers the potential of high throughput proteomics with high sensitivity and specificity.

  17. Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays

    Institute of Scientific and Technical Information of China (English)

    Lian-Qun Jin; Jun-Wen Li; Sheng-Qi Wang; Fu-Huan Chao; Xin-Wei Wang; Zheng-Quan Yuan

    2005-01-01

    AIM: To detect the common intestinal pathogenic bacteria quickly and accurately.METHODS: A rapid (<3 h) experimental procedure was set up based upon the gene chip technology. Target genes were amplified and hybridized by oligonucleotide microarrays.RESULTS: One hundred and seventy strains of bacteria in pure culture belonging to 11 genera were successfully discriminated under comparatively same conditions, and a series of specific hybridization maps corresponding to each kind of bacteria were obtained. When this method was applied to 26 divided cultures, 25 (96.2%) were identified.CONCLUSION: Salmonella sp., Escherichia coli, Shigella sp., Listeria monocytogenes, Vibrio parahaemolyticus,Staphylococcus aureus, Proteus sp., Bacillus cereus,Vibrio cholerae, Enterococcus faecalis, Yersinia enterocolitica, and Campylobacter jejuni can be detected and identified by our microarrays. The accuracy, range,and discrimination power of this assay can be continually improved by adding further oligonucleotides to the arrays without any significant increase of complexity or cost.

  18. Development and inter-laboratory transfer of a decaplex polymerase chain reaction assay combined with capillary electrophoresis for the simultaneous detection of ten food allergens.

    Science.gov (United States)

    Cheng, Fang; Wu, Jiajie; Zhang, Jin; Pan, Aihu; Quan, Sheng; Zhang, Dabing; Kim, HaeYeong; Li, Xiang; Zhou, Shan; Yang, Litao

    2016-05-15

    Food allergies cause health risks to susceptible consumers and regulations on labeling of food allergen contents have been implemented in many countries and regions. To achieve timely and accurate food allergen labeling, the development of fast and effective allergen detection methods is very important. Herein, a decaplex polymerase chain reaction (PCR) assay combined with capillary electrophoresis was developed to detect simultaneously 10 common food allergens from hazelnut, pistachio, oat, sesame, peanut, cashew, barley, wheat, soybean and pecan. The absolute limit of detection (LODa) of this system is between 2 and 20 copies of haploid genome, and the relative LOD (LODr) is as low as 0.005% (w/w) in simulated food mixtures. The developed assay was subsequently applied to 20 commercial food products and verified the allergen ingredients stated on the labels. Furthermore, results using this decaplex PCR assay was successfully replicated in three other laboratories, demonstrating the repeatability and applicability of this assay in routine analysis of the 10 food allergens. PMID:26776037

  19. A novel microbial source tracking microarray for pathogen detection and fecal source identification in environmental systems.

    Science.gov (United States)

    Li, Xiang; Harwood, Valerie J; Nayak, Bina; Staley, Christopher; Sadowsky, Michael J; Weidhaas, Jennifer

    2015-06-16

    Pathogen detection and the identification of fecal contamination sources are challenging in environmental waters. Factors including pathogen diversity and ubiquity of fecal indicator bacteria hamper risk assessment and remediation of contamination sources. A custom microarray targeting pathogens (viruses, bacteria, protozoa), microbial source tracking (MST) markers, and antibiotic resistance genes was tested against DNA obtained from whole genome amplification (WGA) of RNA and DNA from sewage and animal (avian, cattle, poultry, and swine) feces. Perfect and mismatch probes established the specificity of the microarray in sewage, and fluorescence decrease of positive probes over a 1:10 dilution series demonstrated semiquantitative measurement. Pathogens, including norovirus, Campylobacter fetus, Helicobacter pylori, Salmonella enterica, and Giardia lamblia were detected in sewage, as well as MST markers and resistance genes to aminoglycosides, beta-lactams, and tetracycline. Sensitivity (percentage true positives) of MST results in sewage and animal waste samples (21-33%) was lower than specificity (83-90%, percentage of true negatives). Next generation DNA sequencing revealed two dominant bacterial families that were common to all sample types: Ruminococcaceae and Lachnospiraceae. Five dominant phyla and 15 dominant families comprised 97% and 74%, respectively, of sequences from all fecal sources. Phyla and families not represented on the microarray are possible candidates for inclusion in subsequent array designs. PMID:25970344

  20. Resequencing Pathogen Microarray (RPM) for prospective detection and identification of emergent pathogen strains and variants

    Science.gov (United States)

    Tibbetts, Clark; Lichanska, Agnieszka M.; Borsuk, Lisa A.; Weslowski, Brian; Morris, Leah M.; Lorence, Matthew C.; Schafer, Klaus O.; Campos, Joseph; Sene, Mohamadou; Myers, Christopher A.; Faix, Dennis; Blair, Patrick J.; Brown, Jason; Metzgar, David

    2010-04-01

    High-density resequencing microarrays support simultaneous detection and identification of multiple viral and bacterial pathogens. Because detection and identification using RPM is based upon multiple specimen-specific target pathogen gene sequences generated in the individual test, the test results enable both a differential diagnostic analysis and epidemiological tracking of detected pathogen strains and variants from one specimen to the next. The RPM assay enables detection and identification of pathogen sequences that share as little as 80% sequence similarity to prototype target gene sequences represented as detector tiles on the array. This capability enables the RPM to detect and identify previously unknown strains and variants of a detected pathogen, as in sentinel cases associated with an infectious disease outbreak. We illustrate this capability using assay results from testing influenza A virus vaccines configured with strains that were first defined years after the design of the RPM microarray. Results are also presented from RPM-Flu testing of three specimens independently confirmed to the positive for the 2009 Novel H1N1 outbreak strain of influenza virus.

  1. New diagnostics for melanoma detection: from artificial intelligence to RNA microarrays.

    Science.gov (United States)

    Ahlgrimm-Siess, Verena; Laimer, Martin; Arzberger, Edith; Hofmann-Wellenhof, Rainer

    2012-07-01

    Early detection of melanoma remains crucial to ensuring a favorable prognosis. Dermoscopy and total body photography are well-established noninvasive aids that increase the diagnostic accuracy of dermatologists in their daily routine, beyond that of a naked-eye examination. New noninvasive diagnostic techniques, such as reflectance confocal microscopy, multispectral digital imaging and RNA microarrays, are currently being investigated to determine their utility for melanoma detection. This review presents emerging technologies for noninvasive melanoma diagnosis, and discusses their advantages and limitations. PMID:22830402

  2. A new oligonucleotide microarray for detection of pathogenic and non-pathogenic Legionella spp.

    Directory of Open Access Journals (Sweden)

    Boyang Cao

    Full Text Available Legionella pneumophila has been recognized as the major cause of legionellosis since the discovery of the deadly disease. Legionella spp. other than L. pneumophila were later found to be responsible to many non-pneumophila infections. The non-L. pneumophila infections are likely under-detected because of a lack of effective diagnosis. In this report, we have sequenced the 16S-23S rRNA gene internal transcribed spacer (ITS of 10 Legionella species and subspecies, including L. anisa, L. bozemanii, L. dumoffii, L. fairfieldensis, L. gormanii, L. jordanis, L. maceachernii, L. micdadei, L. pneumophila subspp. fraseri and L. pneumophila subspp. pasculleii, and developed a rapid oligonucleotide microarray detection technique accordingly to identify 12 most common Legionella spp., which consist of 11 pathogenic species of L. anisa, L. bozemanii, L. dumoffii, L. gormanii, L. jordanis, L. longbeachae, L. maceachernii, L. micdadei, and L. pneumophila (including subspp. pneumophila, subspp. fraseri, and subspp. pasculleii and one non-pathogenic species, L. fairfieldensis. Twenty-nine probes that reproducibly detected multiple Legionella species with high specificity were included in the array. A total of 52 strains, including 30 target pathogens and 22 non-target bacteria, were used to verify the oligonucleotide microarray assay. The sensitivity of the detection was at 1.0 ng with genomic DNA or 13 CFU/100 mL with Legionella cultures. The microarray detected seven samples of air conditioner-condensed water with 100% accuracy, validating the technique as a promising method for applications in basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance. The phylogenetic study based on the ITS has also revealed that the non-pathogenic L. fairfieldensis is the closest to L. pneumophila than the nine other pathogenic Legionella spp.

  3. DETECTION OF ALLERGEN SPECIFIC PLASMA CELLS IN ALLERGIC PATIENTS TREATED WITH SUBCUTANEOUS IMMUNOTHERAPY

    DEFF Research Database (Denmark)

    Schmid, Johannes Martin; Dahl, Ronald; Hoffmann, Hans Jürgen

    immune response in allergic patients and results in an inhibition of the specific type 1 allergic response. This inhibition is mainly brought about by a change in the immunoglobulin response pattern from allergen specific IgE towards predominantly IgG. Seven days after vaccination with tetanus vaccine...

  4. Detection and Quantification of Grass and Olea Airborne Pollen Allergens in Outdoor Air Samples and its Correlation with Pollen Counts

    OpenAIRE

    Ferro, Raquel; Ribeiro, Rita; Martins, R. M.; Caldeira, A.T.; Caeiro, Elsa; Antunes, Célia M.; Brandao, Rui

    2010-01-01

    Detection and Quantification of Grass and Olea Airborne Pollen Allergens in Outdoor Air Samples and its Correlation with Pollen Counts R Ferro1*, R Ribeiro1*, MR Martins1,2, AT Caldeira1,3, E Caeiro6, CM Antunes1,5 & R Brandão2,4 and the HIALINE working group7 1Dep. of Chemistry, University of Evora, Portugal; 2Mediterranean Inst. Crop and Environment Sciences, Univ.Evora, Portugal; 3Centro Química, University of Évora, Portugal; 4Dep. Biology, University of Evora; 5...

  5. A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis

    Directory of Open Access Journals (Sweden)

    Ribeiro Franclim R

    2009-01-01

    Full Text Available Abstract Background The ability to detect neoplasia-specific fusion genes is important not only in cancer research, but also increasingly in clinical settings to ensure that correct diagnosis is made and the optimal treatment is chosen. However, the available methodologies to detect such fusions all have their distinct short-comings. Results We describe a novel oligonucleotide microarray strategy whereby one can screen for all known oncogenic fusion transcripts in a single experiment. To accomplish this, we combine measurements of chimeric transcript junctions with exon-wise measurements of individual fusion partners. To demonstrate the usefulness of the approach, we designed a DNA microarray containing 68,861 oligonucleotide probes that includes oligos covering all combinations of chimeric exon-exon junctions from 275 pairs of fusion genes, as well as sets of oligos internal to all the exons of the fusion partners. Using this array, proof of principle was demonstrated by detection of known fusion genes (such as TCF3:PBX1, ETV6:RUNX1, and TMPRSS2:ERG from all six positive controls consisting of leukemia cell lines and prostate cancer biopsies. Conclusion This new method bears promise of an important complement to currently used diagnostic and research tools for the detection of fusion genes in neoplastic diseases.

  6. Simultaneous detection of marine fish pathogens by using multiplex PCR and a DNA microarray.

    Science.gov (United States)

    González, Santiago F; Krug, Melissa J; Nielsen, Michael E; Santos, Ysabel; Call, Douglas R

    2004-04-01

    We coupled multiplex PCR and a DNA microarray to construct an assay suitable for the simultaneous detection of five important marine fish pathogens (Vibrio vulnificus, Listonella anguillarum, Photobacterium damselae subsp. damselae, Aeromonas salmonicida subsp. salmonicida, and Vibrio parahaemolyticus). The array was composed of nine short oligonucleotide probes (25-mer) complementary to seven chromosomal loci (cyt, rpoN, gyrB, toxR, ureC, dly, and vapA) and two plasmid-borne loci (fatA and A.sal). Nine primer sets were designed to amplify short fragments of these loci (100 to 177 bp) in a multiplex PCR. PCR products were subsequently labeled by nick translation and hybridized to the microarray. All strains of the five target species (n = 1 to 21) hybridized to at least one species-specific probe. Assay sensitivities ranged from 100% for seven probes to 83 and 67% for the two remaining probes. Multiplex PCR did not produce any nonspecific amplification products when tested against 23 related species of bacteria (n = 40 strains; 100% specificity). Using purified genomic DNA, we were able to detect PCR products with detecting PCR products. In addition, our method allowed the tentative identification of virulent strains of L. anguillarum serotype O1 based on the presence of the fatA gene (67% sensitivity and 100% specificity). This assay is a sensitive and specific tool for the simultaneous detection of multiple pathogenic bacteria that cause disease in fish and humans. PMID:15070982

  7. Development and application of an oligonucleotide microarray and real-time quantitative PCR for detection of wastewater bacterial pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dae-Young [National Water Research Institute, Environment Canada, 867 Lakeshore Road, Burlington, Ontario, L7R 4A6 (Canada)], E-mail: daeyoung.lee@ec.gc.ca; Lauder, Heather; Cruwys, Heather; Falletta, Patricia [National Water Research Institute, Environment Canada, 867 Lakeshore Road, Burlington, Ontario, L7R 4A6 (Canada); Beaudette, Lee A. [Environmental Science and Technology Centre, Environment Canada, 335 River Road South, Ottawa, Ontario, K1A 0H3 (Canada)], E-mail: lee.beaudette@ec.gc.ca

    2008-07-15

    Conventional microbial water quality test methods are well known for their technical limitations, such as lack of direct pathogen detection capacity and low throughput capability. The microarray assay has recently emerged as a promising alternative for environmental pathogen monitoring. In this study, bacterial pathogens were detected in municipal wastewater using a microarray equipped with short oligonucleotide probes targeting 16S rRNA sequences. To date, 62 probes have been designed against 38 species, 4 genera, and 1 family of pathogens. The detection sensitivity of the microarray for a waterborne pathogen Aeromonas hydrophila was determined to be approximately 1.0% of the total DNA, or approximately 10{sup 3}A. hydrophila cells per sample. The efficacy of the DNA microarray was verified in a parallel study where pathogen genes and E. coli cells were enumerated using real-time quantitative PCR (qPCR) and standard membrane filter techniques, respectively. The microarray and qPCR successfully detected multiple wastewater pathogen species at different stages of the disinfection process (i.e. secondary effluents vs. disinfected final effluents) and at two treatment plants employing different disinfection methods (i.e. chlorination vs. UV irradiation). This result demonstrates the effectiveness of the DNA microarray as a semi-quantitative, high throughput pathogen monitoring tool for municipal wastewater.

  8. Development and application of an oligonucleotide microarray and real-time quantitative PCR for detection of wastewater bacterial pathogens

    International Nuclear Information System (INIS)

    Conventional microbial water quality test methods are well known for their technical limitations, such as lack of direct pathogen detection capacity and low throughput capability. The microarray assay has recently emerged as a promising alternative for environmental pathogen monitoring. In this study, bacterial pathogens were detected in municipal wastewater using a microarray equipped with short oligonucleotide probes targeting 16S rRNA sequences. To date, 62 probes have been designed against 38 species, 4 genera, and 1 family of pathogens. The detection sensitivity of the microarray for a waterborne pathogen Aeromonas hydrophila was determined to be approximately 1.0% of the total DNA, or approximately 103A. hydrophila cells per sample. The efficacy of the DNA microarray was verified in a parallel study where pathogen genes and E. coli cells were enumerated using real-time quantitative PCR (qPCR) and standard membrane filter techniques, respectively. The microarray and qPCR successfully detected multiple wastewater pathogen species at different stages of the disinfection process (i.e. secondary effluents vs. disinfected final effluents) and at two treatment plants employing different disinfection methods (i.e. chlorination vs. UV irradiation). This result demonstrates the effectiveness of the DNA microarray as a semi-quantitative, high throughput pathogen monitoring tool for municipal wastewater

  9. Development and application of an oligonucleotide microarray and real-time quantitative PCR for detection of wastewater bacterial pathogens.

    Science.gov (United States)

    Lee, Dae-Young; Lauder, Heather; Cruwys, Heather; Falletta, Patricia; Beaudette, Lee A

    2008-07-15

    Conventional microbial water quality test methods are well known for their technical limitations, such as lack of direct pathogen detection capacity and low throughput capability. The microarray assay has recently emerged as a promising alternative for environmental pathogen monitoring. In this study, bacterial pathogens were detected in municipal wastewater using a microarray equipped with short oligonucleotide probes targeting 16S rRNA sequences. To date, 62 probes have been designed against 38 species, 4 genera, and 1 family of pathogens. The detection sensitivity of the microarray for a waterborne pathogen Aeromonas hydrophila was determined to be approximately 1.0% of the total DNA, or approximately 10(3)A. hydrophila cells per sample. The efficacy of the DNA microarray was verified in a parallel study where pathogen genes and E. coli cells were enumerated using real-time quantitative PCR (qPCR) and standard membrane filter techniques, respectively. The microarray and qPCR successfully detected multiple wastewater pathogen species at different stages of the disinfection process (i.e. secondary effluents vs. disinfected final effluents) and at two treatment plants employing different disinfection methods (i.e. chlorination vs. UV irradiation). This result demonstrates the effectiveness of the DNA microarray as a semi-quantitative, high throughput pathogen monitoring tool for municipal wastewater. PMID:18423816

  10. Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Moerman Donald G

    2008-10-01

    Full Text Available Abstract Background Microarray comparative genomic hybridization (CGH is currently one of the most powerful techniques to measure DNA copy number in large genomes. In humans, microarray CGH is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. In model organisms such as Caenorhabditis elegans (C. elegans the technique has been applied to detect mutations, primarily deletions, in strains of interest. Although various constraints on oligonucleotide properties have been suggested to minimize non-specific hybridization and improve the data quality, there have been few experimental validations for CGH experiments. For genomic regions where strict design filters would limit the coverage it would also be useful to quantify the expected loss in data quality associated with relaxed design criteria. Results We have quantified the effects of filtering various oligonucleotide properties by measuring the resolving power for detecting deletions in the human and C. elegans genomes using NimbleGen microarrays. Approximately twice as many oligonucleotides are typically required to be affected by a deletion in human DNA samples in order to achieve the same statistical confidence as one would observe for a deletion in C. elegans. Surprisingly, the ability to detect deletions strongly depends on the oligonucleotide 15-mer count, which is defined as the sum of the genomic frequency of all the constituent 15-mers within the oligonucleotide. A similarity level above 80% to non-target sequences over the length of the probe produces significant cross-hybridization. We recommend the use of a fairly large melting temperature window of up to 10°C, the elimination of repeat sequences, the elimination of homopolymers longer than 5 nucleotides, and a threshold of -1 kcal/mol on the oligonucleotide self-folding energy. We observed very little difference in data

  11. Detection of Pathogenic Vibrio spp. in Shellfish by Using Multiplex PCR and DNA Microarrays

    OpenAIRE

    Panicker, Gitika; Call, Douglas R.; Krug, Melissa J.; Bej, Asim K.

    2004-01-01

    This study describes the development of a gene-specific DNA microarray coupled with multiplex PCR for the comprehensive detection of pathogenic vibrios that are natural inhabitants of warm coastal waters and shellfish. Multiplex PCR with vvh and viuB for Vibrio vulnificus, with ompU, toxR, tcpI, and hlyA for V. cholerae, and with tlh, tdh, trh, and open reading frame 8 for V. parahaemolyticus helped to ensure that total and pathogenic strains, including subtypes of the three Vibrio spp., coul...

  12. Silicon biochips for dual label-free and fluorescence detection: Application to protein microarray development

    OpenAIRE

    Cretich M.; Reddington A.; Monroe M.; Bagnati M.; Damin F.; Sola L.; Unlu M.S.; Chiari M.

    2011-01-01

    A new silicon chip for protein microarray development, fabrication and validation is proposed. The chip is made of two areas with oxide layers of different thicknesses: an area with a 500 nm SiO2 layer dedicated to interferometric label-free detection and quantification of proteins and an area with 100 nm SiO2 providing enhanced fluorescence. The chip allows, within a single experiment performed on the same surface, label-free imaging of arrayed protein probes coupled with high sensitivity fl...

  13. Development and comparison of two assay formats for parallel detection of four biothreat pathogens by using suspension microarrays.

    Directory of Open Access Journals (Sweden)

    Ingmar Janse

    Full Text Available Microarrays provide a powerful analytical tool for the simultaneous detection of multiple pathogens. We developed diagnostic suspension microarrays for sensitive and specific detection of the biothreat pathogens Bacillus anthracis, Yersinia pestis, Francisella tularensis and Coxiella burnetii. Two assay chemistries for amplification and labeling were developed, one method using direct hybridization and the other using target-specific primer extension, combined with hybridization to universal arrays. Asymmetric PCR products for both assay chemistries were produced by using a multiplex asymmetric PCR amplifying 16 DNA signatures (16-plex. The performances of both assay chemistries were compared and their advantages and disadvantages are discussed. The developed microarrays detected multiple signature sequences and an internal control which made it possible to confidently identify the targeted pathogens and assess their virulence potential. The microarrays were highly specific and detected various strains of the targeted pathogens. Detection limits for the different pathogen signatures were similar or slightly higher compared to real-time PCR. Probit analysis showed that even a few genomic copies could be detected with 95% confidence. The microarrays detected DNA from different pathogens mixed in different ratios and from spiked or naturally contaminated samples. The assays that were developed have a potential for application in surveillance and diagnostics.

  14. Development of a high-throughput microfluidic integrated microarray for the detection of chimeric bioweapons.

    Energy Technology Data Exchange (ETDEWEB)

    Sheppod, Timothy; Satterfield, Brent; Hukari, Kyle W.; West, Jason A. A.; Hux, Gary A.

    2006-10-01

    The advancement of DNA cloning has significantly augmented the potential threat of a focused bioweapon assault, such as a terrorist attack. With current DNA cloning techniques, toxin genes from the most dangerous (but environmentally labile) bacterial or viral organism can now be selected and inserted into robust organism to produce an infinite number of deadly chimeric bioweapons. In order to neutralize such a threat, accurate detection of the expressed toxin genes, rather than classification on strain or genealogical decent of these organisms, is critical. The development of a high-throughput microarray approach will enable the detection of unknowns chimeric bioweapons. The development of a high-throughput microarray approach will enable the detection of unknown bioweapons. We have developed a unique microfluidic approach to capture and concentrate these threat genes (mRNA's) upto a 30 fold concentration. These captured oligonucleotides can then be used to synthesize in situ oligonucleotide copies (cDNA probes) of the captured genes. An integrated microfluidic architecture will enable us to control flows of reagents, perform clean-up steps and finally elute nanoliter volumes of synthesized oligonucleotides probes. The integrated approach has enabled a process where chimeric or conventional bioweapons can rapidly be identified based on their toxic function, rather than being restricted to information that may not identify the critical nature of the threat.

  15. Animal models to detect allergenicity to foods and genetically modified products: workshop summary.

    OpenAIRE

    Tryphonas, Helen; Arvanitakis, George; Vavasour, Elizabeth; Bondy, Genevieve

    2003-01-01

    Respiratory allergy and allergy to foods continue to be important health issues. There is evidence to indicate that the incidence of food allergy around the world is on the rise. Current estimates indicate that approximately 5% of young children and 1-2% of adults suffer from true food allergy (Kagan 2003). Although a large number of in vivo and in vitro tests exist for the clinical diagnosis of allergy in humans, we lack validated animal models of allergenicity. This deficiency creates serio...

  16. The influence of digestibility on the allergenicity of food allergens

    DEFF Research Database (Denmark)

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard

    2012-01-01

    potential exist. Resistance to digestion is therefore a test parameter included in the safety assessment of the allergenic potential of novel proteins in genetically modified foods. In recent years, the association between resistance to digestion and allergenic potential has been challenged. When reviewing......Food allergy is a major health problem in the Western countries, affecting 3-8% of the population. What makes a dietary protein a food allergen has not yet been established, though several characteristics have been proposed to be shared by the food allergens. One of the features believed to be a...... existing data from digestibility studies on known food allergens, it becomes evident that food allergens do not necessarily resist digestion. However, the choice of assay conditions, the method used for detection of residual intact protein as well as fragments hereof greatly influences the outcome. Studies...

  17. Direct Detection and Genotyping of Klebsiella pneumoniae Carbapenemases from Urine by Use of a New DNA Microarray Test

    OpenAIRE

    Peter, Harald; Berggrav, Kathrine; Thomas, Peter; Pfeifer, Yvonne; Witte, Wolfgang; Templeton, Kate; Bachmann, Till T

    2012-01-01

    Klebsiella pneumoniae carbapenemases (KPCs) are considered a serious threat to antibiotic therapy, as they confer resistance to carbapenems, which are used to treat extended-spectrum beta-lactamase (ESBL)-producing bacteria. Here, we describe the development and evaluation of a DNA microarray for the detection and genotyping of KPC genes (blaKPC) within a 5-h period. To test the whole assay procedure (DNA extraction plus a DNA microarray assay) directly from clinical specimens, we compared tw...

  18. Direct Detection and Genotyping of Klebsiella pneumoniae Carbapenemases from Urine by Use of a New DNA Microarray Test

    OpenAIRE

    Peter, Harald; Berggrav, Kathrine; Thomas, Peter; Pfeifer, Yvonne; Witte, Wolfgang; Templeton, Kate; Bachmann, Till T

    2012-01-01

    Klebsiella pneumoniae carbapenemases (KPC) are considered a serious threat to antibiotic therapy as they confer resistance to carbapenems, which are used to treat Extended-spectrum beta-lactamase (ESBL) producing bacteria. Here, we describe the development and evaluation of a DNA microarray for detection and genotyping of KPC genes (bla(KPC)) within 5 hours. To test the whole assay procedure (DNA extraction + DNA microarray assay) directly from clinical specimen, we compared two commercial DN...

  19. [Binding capability of lidamycin apoprotein to human breast cancer detected by tissue microarrays].

    Science.gov (United States)

    Cai, Lin; Gao, Rui-Juan; Guo, Xiao-Zhong; Li, Yi; Zhen, Yong-Su

    2010-05-01

    This study is to investigate the binding capability of lidamycin apoprotein (LDP), an enediyne-associated apoprotein of the chromoprotein antitumor antibiotic family, to human breast cancer and normal tissues, the correlation of LDP binding capability to human breast cancer tissues and the expression of tumor therapeutic targets such as VEGF and HER2. In this study, the binding capability of LDP to human breast cancer tissues was detected with tissue microarray. The correlation study of LDP binding capability to human breast tumor tissues and relevant therapeutic targets was performed on breast cancer tissue microarrays. Immunocytochemical examination was used to detect the binding capability of LDP to human breast carcinoma MCF-7 cells. As a result, tissue microarray showed that LDP staining of 73.2% (30/41) of breast cancer tissues was positive, whereas that of 48.3% (15/31) of the adjacent normal breast specimens was positive. The difference between the tumor and normal samples was significant (Chi2 = 4.63, P < 0.05). LDP immunoreactivity in breast cancer correlated significantly with the overexpression of VEGF and HER2 (P < 0.001 and < 0.01, r = 0.389 and 0.287, respectively). Determined with confocal immunofluorescent analysis, LDP showed the binding capability to mammary carcinoma MCF-7 cells. It is demonstrated that LDP can bind to human breast cancer tissues and there is significant difference between the breast cancer tissues and the corresponding normal tissues. Notably, the binding reactivity shows positive correlation with the expression of VEGF and HER2 in breast carcinoma tissues. The results imply that LDP may have a potential use as targeting drug carrier in the research and development of new anticancer therapeutics. This study may provide reference for drug combination of LDM and other therapeutic agents. PMID:20931759

  20. Detection of cancer with serum miRNAs on an oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Michael J Lodes

    Full Text Available Micro RNAs (miRNAs are a class of small, non-coding RNA species that play critical roles throughout cellular development and regulation. miRNA expression patterns taken from various tissue types often point to the cellular lineage of an individual tissue type, thereby being a more invariant hallmark of tissue type. Recent work has shown that these miRNA expression patterns can be used to classify tumor cells, and that this classification can be more accurate than the classification achieved by using messenger RNA gene expression patterns. One aspect of miRNA biogenesis that makes them particularly attractive as a biomarker is the fact that they are maintained in a protected state in serum and plasma, thus allowing the detection of miRNA expression patterns directly from serum. This study is focused on the evaluation of miRNA expression patterns in human serum for five types of human cancer, prostate, colon, ovarian, breast and lung, using a pan-human microRNA, high density microarray. This microarray platform enables the simultaneous analysis of all human microRNAs by either fluorescent or electrochemical signals, and can be easily redesigned to include newly identified miRNAs. We show that sufficient miRNAs are present in one milliliter of serum to detect miRNA expression patterns, without the need for amplification techniques. In addition, we are able to use these expression patterns to correctly discriminate between normal and cancer patient samples.

  1. Normal uniform mixture differential gene expression detection for cDNA microarrays

    Directory of Open Access Journals (Sweden)

    Raftery Adrian E

    2005-07-01

    Full Text Available Abstract Background One of the primary tasks in analysing gene expression data is finding genes that are differentially expressed in different samples. Multiple testing issues due to the thousands of tests run make some of the more popular methods for doing this problematic. Results We propose a simple method, Normal Uniform Differential Gene Expression (NUDGE detection for finding differentially expressed genes in cDNA microarrays. The method uses a simple univariate normal-uniform mixture model, in combination with new normalization methods for spread as well as mean that extend the lowess normalization of Dudoit, Yang, Callow and Speed (2002 1. It takes account of multiple testing, and gives probabilities of differential expression as part of its output. It can be applied to either single-slide or replicated experiments, and it is very fast. Three datasets are analyzed using NUDGE, and the results are compared to those given by other popular methods: unadjusted and Bonferroni-adjusted t tests, Significance Analysis of Microarrays (SAM, and Empirical Bayes for microarrays (EBarrays with both Gamma-Gamma and Lognormal-Normal models. Conclusion The method gives a high probability of differential expression to genes known/suspected a priori to be differentially expressed and a low probability to the others. In terms of known false positives and false negatives, the method outperforms all multiple-replicate methods except for the Gamma-Gamma EBarrays method to which it offers comparable results with the added advantages of greater simplicity, speed, fewer assumptions and applicability to the single replicate case. An R package called nudge to implement the methods in this paper will be made available soon at http://www.bioconductor.org.

  2. 食物致敏蛋白及其检测方法%Food allergenic proteins and its detection methods

    Institute of Scientific and Technical Information of China (English)

    王荣春; 侯爱菊; 马莺

    2012-01-01

    食物过敏是威胁人类健康的一大问题,并随着环境的恶化和新食物资源的出现而趋于严重,因此受到科研工作者,政府职能部门以及消费者的关注.本文就食物来源的致敏蛋白加以分类并对其结构特点进行了概述,同时也介绍了现阶段致敏蛋白的主要检测手段.以期对食品安全有进一步的了解和认识,从而减少因食物过敏造成的危害.%Food allergies are a major threat to human health problems. With the deterioration of the environment and the emergence of new food resources, food allergies become more severe. This attracted the attention and concerns from the scientific researchers, government departments and consumers. In this review, the classification and structural features of food allergenic proteins were summarized, and the currently main allergenic protein detection methods were introduced. And this context was aimed to further understand the knowledge of food safety, and to reduce the harm caused by food allergies.

  3. IgE ELISA using antisera derived from epsilon chain antigenic peptides detects allergen-specific IgE in allergic horses.

    Science.gov (United States)

    Kalina, Warren V; Pettigrew, Howard D; Gershwin, Laurel J

    2003-05-12

    Equine disease with an allergic etiology is common. Environmental antigens most often implicated as allergens in horses include molds, dusty hay, grass pollen, hay dust mites, and insect saliva. Although intradermal testing with allergen is a useful diagnostic tool for some species, skin testing frequently produces false positive results in horses. Allergen deprivation as a diagnostic tool is often impossible and at best it is ineffective at diagnosing the specific allergic reactivity. Synthesis of IgE after exposure to allergen is the instigator of the allergic process. While IgE exerts its effect after binding strongly to mast cell Fc receptors, the presence of free IgE in the serum can be used to quantify and determine the allergen specificity of the allergic disease. A lack of widely available reagents for detection of equine IgE has limited this approach in horses. We have used the nucleotide sequence of equine IgE to prepare a peptide-based immunogen to elicit equine epsilon chain-specific antisera. Selection of peptides was based on antigenic attributes of the deduced amino acid sequence of the equine epsilon chain. Six peptides were selected for conjugation to carrier molecules and rabbit immunization. Of these, one peptide elicited antisera that was successfully used in enzyme linked immunosorbant assay (ELISA) to screen horse serum from 64 allergic horses for allergen-specific IgE. Twenty-four of the 64 horses showed positive reactivity to one or more of the following allergens: grass, grain mill dust, mosquito, and horsefly. This study demonstrates the usefulness of peptide-based immunogens for development of antisera to rare or difficult to purify antigens such as IgE. Resultant antisera has great usefulness in diagnostic assays for equine allergy and as a research tool. PMID:12730014

  4. Development of an ELISA microarray assay for the sensitive and simultaneous detection of ten biodefense toxins.

    Energy Technology Data Exchange (ETDEWEB)

    Jenko, Kathryn; Zhang, Yanfeng; Kostenko, Yulia; Fan, Yongfeng; Garcia-Rodriguez, Consuelo; Lou, Jianlong; Marks, James D.; Varnum, Susan M.

    2014-10-21

    Plant and microbial toxins are considered bioterrorism threat agents because of their extreme toxicity and/or ease of availability. Additionally, some of these toxins are increasingly responsible for accidental food poisonings. The current study utilized an ELISA-based protein antibody microarray for the multiplexed detection of ten biothreat toxins, botulinum neurotoxins (BoNT) A, B, C, D, E, F, ricin, shiga toxins 1 and 2 (Stx), and staphylococcus enterotoxin B (SEB), in buffer and complex biological matrices. The multiplexed assay displayed a sensitivity of 1.3 pg/mL (BoNT/A, BoNT/B, SEB, Stx-1 and Stx-2), 3.3 pg/mL (BoNT/C, BoNT/E, BoNT/F) and 8.2 pg/mL (BoNT/D, ricin). All assays demonstrated high accuracy (75-120 percent recovery) and reproducibility (most coefficients of variation < 20%). Quantification curves for the ten toxins were also evaluated in clinical samples (serum, plasma, nasal fluid, saliva, stool, and urine) and environmental samples (apple juice, milk and baby food) with overall minimal matrix effects. The multiplex assays were highly specific, with little crossreactivity observed between the selected toxin antibodies. The results demonstrate a multiplex microarray that improves current immunoassay sensitivity for biological warfare agents in buffer, clinical, and environmental samples.

  5. Commercialized rapid immunoanalytical tests for determination of allergenic food proteins: an overview.

    Science.gov (United States)

    Schubert-Ullrich, Patricia; Rudolf, Judith; Ansari, Parisa; Galler, Brigitte; Führer, Manuela; Molinelli, Alexandra; Baumgartner, Sabine

    2009-09-01

    Food allergies have become an important health issue especially in industrialized countries. Undeclared allergenic ingredients or the presence of "hidden" allergens because of contamination during the food production process pose great health risks to sensitised individuals. The EU directive for food labelling lists allergenic foods that have to be declared on food products by the manufacturers. The list includes gluten-containing cereals, crustaceans, eggs, fish, peanuts, soybeans, milk, various nuts (e.g. almond, hazelnut, and walnut, etc.), celery, mustard, sesame seeds, lupin, and molluscs. Reliable methods for detection and quantification of food allergens are needed that can be applied in a fast and easy-to-use manner, are portable, and need only limited technical equipment. This review focuses on the latest developments in food allergen analysis with special emphasis on fast immunoanalytical methods such as rapid enzyme-linked immunosorbent assays (ELISA), lateral-flow immunochromatographic assays (LFA) and dipstick tests. Emerging technologies such as immunochemical microarrays and biosensors are also discussed and their application to food allergen analysis is reviewed. Finally, a comprehensive overview of rapid immunochemical test kits that are currently available commercially is given in tabular form. PMID:19308361

  6. Optimizing a custom tiling microarray for low input detection and identification of unamplified virus targets.

    Science.gov (United States)

    Yu, Christine; Wales, Samantha Q; Mammel, Mark K; Hida, Kaoru; Kulka, Michael

    2016-08-01

    Viruses are major pathogens causing foodborne illnesses and are often present at low levels in foods, thus requiring sensitive techniques for their detection in contaminated foods. The lack of efficient culture methods for many foodborne viruses and the potential for multi-species viral contamination have driven investigation toward non-amplification based methods for virus detection and identification. A custom DNA microarray (FDA_EVIR) was assessed for its sensitivity in the detection and identification of low-input virus targets, human hepatitis A virus, norovirus, and coxsackievirus, individually and in combination. Modifications to sample processing were made to accommodate low input levels of unamplified virus targets, which included addition of carrier cDNA, RNase treatment, and optimization of DNase I-mediated target fragmentation. Amplification-free detection and identification of foodborne viruses were achieved in the range of 250-500 copies of virus RNA. Alternative data analysis methods were employed to distinguish the genotypes of the viruses particularly at lower levels of target input and the single probe-based analysis approach made it possible to identify a minority species in a multi-virus complex. The oligonucleotide array is shown to be a promising platform to detect foodborne viruses at low levels close to what are anticipated in food or environmental samples. PMID:27033182

  7. Detection of hybridization of protein microarrays using an oblique-incidence reflectivity difference method

    Science.gov (United States)

    Lu, Heng; Wen, Juan; Wang, Xu; Yuan, Kun; Lu, Huibin; Zhou, Yueliang; Jin, Kui-Juan; Yang, Guozhen; Li, Wei; Ruan, Kangcheng

    2010-07-01

    Mouse-Immunoglobulin G (mouse-IgG) with different concentrations in a range from 1000 to 0.0128 μg/mL and a specific hybridization with goat anti-mouse IgG were detected successfully by using an oblique-incidence reflectivity difference (OI-RD) method. Two detection signals, consisting of an imaginary part (Im{Δp-Δs}) and a real part (Re{Δp-Δs}) of OI-RD, were obtained simultaneously. The detection results of hybridization by OI-RD were in accord with that of traditional fluorescent scans. In particular, we label-freely detected the washed mouse-IgG microarray with a series of concentrations and acquired a linear correlation between OI-RD intensities and the protein concentrations in logarithmic coordinates. The detection sensitivity of OI-RD can reach 14 fg. These experimental results suggest that the OI-RD method has potential applications in proteomics and clinical diagnosis.

  8. Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

    Directory of Open Access Journals (Sweden)

    Gravelat Fabrice

    2010-09-01

    Full Text Available Abstract Background Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes. Results First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality can be used to study a complex environment efficiently. Conclusions We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments

  9. Inability to detect significant absorption of immunoreactive soya protein in healthy adults may be relevant to its weak allergenicity

    DEFF Research Database (Denmark)

    Lund, Cecilia M; Dirks, Christina G; Pedersen, Mona H;

    2013-01-01

    soya protein. While we cannot totally exlude technical reasons, it may also reflect a true poor absorption in healthy adult volunteers. This could, in turn, be relevant to the apparently weak allergenicity of soy protein by comparison with peanut protein in allergic subjects....... protein absorption between the two foods, might explain this diversity.In the current study the amount of soya protein absorbed after soya bean ingestion in healthy adults was estimated. Ten subjects ingested 100 grams of soya beans (40 grams of soya protein) and blood was drawn before and 1, 3 and 24...... hours after administration. Serum was analysed by ELISA and histamine release (HR). In all serum samples the soya protein concentration was below quantification limit (1.6 ng/ml which corresponds to 4.8 mug or 0.12 parts per million absorbed soya protein.We could not detect any significant absorption of...

  10. Detection of microbial communities in continuous and discontinuous membrane bioreactor using high-density oligonucleotide Microarray

    Science.gov (United States)

    Duan, Liang; Song, Yonghui; Xia, Siqing; Hermanowicz, Slawomir W.

    2010-11-01

    This study compared the whole composition of microbial communities in continuous-flow (MBR) and batch-fed (discontinuous) (MSBR) aerobic membrane bioreactors using high-density universal 16S rRNA Microarray. The array includes 506,944 probes targeted to 8935 clusters in 16S rRNA gene sequences. The Microarray results showed that both MBR and MSBR had high microbial diversity. 1126 and 1002 bacterial subfamilies were detected and can separate as 37 and 32 phyla in MBR and MSBR, respectively. Proteobacteria was the predominant phylum, 703 and 597 subfamilies were found in two systems, which constituted 62.4% and 59.6% of the whole bacteria. Gamma- and Alpha-were the dominant classes in Proteobacteria. It occupied 38.1% and 26.3%, 31.2% and 39.2% for MBR and MSBR, respectively. Bacteroidetes, Firmicutes and Actinobacteria were the subdominant groups, occupying around 9.4% and 7.6%, 6.1% and 6.5%, 6.0% and 9.0% of the total bacteria in two reactors. Some bacterial groups such as Acidobacteria, Chloroflexi, Cyanobacteria, Verrucomicrobia and Spirochaetes also found more than 15 subfamilies. All the results indicated that the MBR system had more bacteria community diversity than MSBR's. Moreover, it was very interested that MBR and MSBR had almost the same bacterial composition except Enterobacteriaceae. 63 OTUs of Enterobacteriaceae were detected in MBR, while just 10 OTUs were found in MSBR. That's one of the reasons leading to the difference of the bacterial diversity between two bioreactors.

  11. A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds

    OpenAIRE

    Stegall Mark D; Park Walter D

    2007-01-01

    Abstract Background Microarrays provide a means to simultaneously examine the gene expression of the entire transcriptome in a single sample. Many studies have highlighted the need for novel software and statistical approaches to assess the measured gene expression. Less attention has been directed toward whether genes considered undetectable by microarray can be detected by other strategies or whether these genes can provide accurate gene expression determinations. In the kidney this is a co...

  12. Novel biosensor-based microarray assay for detecting rs8099917 and rs12979860 genotypes

    Institute of Scientific and Technical Information of China (English)

    Pei-Yuan Li; Xiao-Jun Zhou; Lan Yao; Xin-Hua Fang; Jiang-Nan Ren; Jia-Wu Song

    2012-01-01

    AIM:To evaluate a novel biosensor-based microarray (BBM) assay for detecting rs12979860 and rs8099917genotypes.METHODS:Four probes specific for rs8099917C/T or rs12979860G/T detection and three sets of quality control probes were designed,constructed and arrayed on an optical biosensor to develop a microarray assay.Two sets of primers were used in a one tube polymerase chain reaction (PCR) system to amplify two target fragments simultaneously.The biosensor microarray contained probes that had been sequenced to confirm that they included the rsS099917C/T or rs12979860G/T alleles of interest and could serve as the specific assay standards.In addition to rehybridization of four probes of known sequence,a total of 40 clinical samples collected from hepatitis C seropositive patients were also tested.The target fragments of all 40 samples were amplified in a 50 μL PCR system.Ten μL of each amplicon was tested by BBM assay,and another 40 μL was used for sequencing.The agreement of the results obtained by the two methods was tested statistically using the kappa coefficient.The sensitivity of the BBM assay was evaluated using serial dilutions of ten clinical blood samples containing 103-104 white cells/lμL.RESULTS:As shown by polyacrylamide gel electrophoresis,two target segments of the interleukin 28B-associated polymorphisms (SNPs) were successfully amplified in the one-tube PCR system.The lengths of the two amplified fragments were consistent with the known length of the target sequences,137 and 159bps.After hybridization of the PCR amplicons with the probes located on the BBM array,the signals of each allele of both the rs8099917 SNPs and rs12979860 SNPs were observed simultaneously and were clearly visible by the unaided eye.The signals were distinct from each other,could be interpreted visually,and accurately recorded using an ordinary digital camera.To evaluate the specificity of the assay,both the plasmids and clinical samples were applied to the microarray

  13. A microarray-based detection system for genetically modified (GM) food ingredients.

    Science.gov (United States)

    Leimanis, Serge; Hernández, Marta; Fernández, Sophie; Boyer, Francine; Burns, Malcolm; Bruderer, Shirin; Glouden, Thomas; Harris, Neil; Kaeppeli, Othmar; Philipp, Patrick; Pla, Maria; Puigdomènech, Pere; Vaitilingom, Marc; Bertheau, Yves; Remacle, José

    2006-05-01

    A multiplex DNA microarray chip was developed for simultaneous identification of nine genetically modified organisms (GMOs), five plant species and three GMO screening elements, i.e. the 35S promoter, the nos terminator and the nptII gene. The chips also include several controls, such as that for the possible presence of CaMV. The on-chip detection was performed directly with PCR amplified products. Particular emphasis was placed on the reduction of the number of PCR reactions required and on the number of primers present per amplification tube. The targets were biotin labelled and the arrays were detected using a colorimetric methodology. Specificity was provided by specific capture probes designed for each GMO and for the common screening elements. The sensitivity of the assay was tested by experiments carried out in five different laboratories. The limit of detection was lower than 0.3% GMO for all tests and in general around 0.1% for most GMOs. The chip detection system complies with the requirements of current EU regulations and other countries where thresholds are established for the labelling of GMO. PMID:16786296

  14. Microarrays, Integrated Analytical Systems

    Science.gov (United States)

    Combinatorial chemistry is used to find materials that form sensor microarrays. This book discusses the fundamentals, and then proceeds to the many applications of microarrays, from measuring gene expression (DNA microarrays) to protein-protein interactions, peptide chemistry, carbodhydrate chemistry, electrochemical detection, and microfluidics.

  15. Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen Genes in Riverine and Marine Systems.

    Science.gov (United States)

    Li, Xiang; Harwood, Valerie J; Nayak, Bina; Weidhaas, Jennifer L

    2016-03-01

    Pathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect genes for multiple pathogens and indicators of fecal pollution in freshwater, marine water, sewage-contaminated freshwater and marine water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% for Escherichia coli and human polyomavirus. Whole-genome amplification (WGA) increased gene copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such as Legionella pneumophila, Shigella flexneri, and Campylobacter fetus were detected along with genes conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker genes grouped sewage-spiked freshwater and marine samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for gene targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between gene copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance genes by the microarray in applications ranging from beach monitoring to risk assessment. PMID:26729716

  16. Allergens and Irritants

    Science.gov (United States)

    ... Environmental Agents Acrylamide Environmental Agents Acrylamide Air Pollution Environmental Agents Air Pollution Allergens & Irritants Environmental Agents Allergens & Irritants Cigarette Smoke ...

  17. Multi-faceted, multi-versatile microarray: simultaneous detection of many viruses and their expression profiles

    Directory of Open Access Journals (Sweden)

    Li Ching

    2004-05-01

    Full Text Available Abstract There are hundreds of viruses that infect different human organs and cause diseases. Some fatal emerging viral infections have become serious public health issues worldwide. Early diagnosis and subsequent treatment are therefore essential for fighting viral infections. Current diagnostic techniques frequently employ polymerase chain reaction (PCR-based methods to quickly detect the pathogenic viruses and establish the etiology of the disease or illness. However, the fast PCR method suffers from many drawbacks such as a high false-positive rate and the ability to detect only one or a few gene targets at a time. Microarray technology solves the problems of the PCR limitations and can be effectively applied to all fields of molecular medicine. Recently, a report in Retrovirology described a multi-virus DNA array that contains more than 250 open reading frames from eight human viruses including human immunodeficiency virus type 1. This array can be used to detect multiple viral co-infections in cells and in vivo. Another benefit of this kind of multi-virus array is in studying promoter activity and viral gene expression and correlating such readouts with the progression of disease and reactivation of latent infections. Thus, the virus DNA-chip development reported in Retrovirology is an important advance in diagnostic application which could be a potent clinical tool for characterizing viral co-infections in AIDS as well as other patients.

  18. Analysis of allergen detection results in children with acute bronchitis%急性支气管炎患儿血清过敏原检测分析

    Institute of Scientific and Technical Information of China (English)

    朱晓莉; 陶春妃

    2016-01-01

    Objective:To detect and analyze serum allergen of 87 children with acute bronchitis. Methods:87 patients with acute bronchitis were selected for serum allergen detection, and compared with the control group of 87 normal subjects ( no special al-lergic history). Results:For the 87 cases of children with acute bronchitis, the serum allergen test positive rate was 62. 07% (54/87);while for the control group, the serum specific allergen test positive rate was 17. 24% (15/87);and the difference was statisti-cally significant (P0. 05). The most common inhaled allergen was house dust mites/dust mites, accounting for 25. 29%, while the common ingested al-lergens were cod/lobster/scallops, crab, peanut, the proportion of 13. 79%, 18. 39% and 12. 64%, separately. Conclusions: For the children with acute bronchitis, the serum allergen detection has a higher positive detection rate, and is significant for the treatment and prevention.%目的::检测分析儿童急性支气管炎的血清过敏原。方法:将87例临床诊断为急性支气管炎患儿设为急性支气管炎组,选择87例同期健康儿童作为对照组,检测比较两组研究对象的血清过敏原。结果:急性支气管炎组患儿的血清过敏原检测阳性率为62.07%(54/87),与对照组儿童的血清特异性过敏原阳性率为17.24%(15/87)比,差异有统计学意义(P0.05);吸入性过敏原阳性率较高的为屋尘螨/粉尘螨,占比25.29%;食入性过敏原阳性率较高的是鳕鱼/龙虾/扇贝、螃蟹、花生,占比分别为13.79%、18.39%、12.64%。结论:儿童急性支气管炎血清过敏原检测具有较高的阳性检出率,对治疗和预防具有重要意义。

  19. Detection and identification of enterohemorrhagic Escherichia coli O157:H7 and Vibrio cholerae O139 using oligonucleotide microarray

    Directory of Open Access Journals (Sweden)

    Zhang Zheng

    2007-12-01

    Full Text Available Abstract Background The rapid and accurate detection and identification of the new subtype of the pathogens is crucial for diagnosis, treatment and control of the contagious disease outbreak. Here, in this study, an approach to detect and identify Escherichia coli O157:H7 and Vibrio cholerae O139 was established using oligonucleotide microarray. We coupled multiplex PCR with oligonucleotide microarray to construct an assay suitable for simultaneous identification of two subtypes of the pathogens. Results The stx1, stx2 gene and uidA gene having the specific mutant spot were chosen as the targets for Escherichia coli O157:H7, and meanwhile the ctxA, tcpA, and LPSgt gene for Vibrio cholerae O139. The oligonucleotide microarray was composed of eight probes including negative control and positive control from 16S rDNA gene. The six primers were designed to amplify target fragments in two triplex PCR, and then hybridized with oligonucleotide microarray. An internal control would be to run a PCR reaction in parallel. Multiplex PCR did not produce any non-specific amplicons when 149 related species or genera of standard bacteria were tested (100% specificity. In addition, Escherichia coli O157:H7 and Escherichia coli O157:non-H7, Vibrio cholerae O139 and Vibrio cholerae O1 had been discriminated respectively. Using recombinant plasmid and target pathogens, we were able to detect positive hybridization signals with 102 copies/μL and 103 cfu/mL per reaction. Conclusion The DNA microarray assay reported here could detect and identify Escherichia coli O157:H7 and Vibrio cholerae O139, and furthermore the subtype was distinguished. This assay was a specific and sensitive tool for simultaneous detection and identification of the new subtype of two pathogens causing diarrhea in human.

  20. Single-cell multiple gene expression analysis based on single-molecule-detection microarray assay for multi-DNA determination

    Energy Technology Data Exchange (ETDEWEB)

    Li, Lu [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Wang, Xianwei [School of Life Sciences, Shandong University, Jinan 250100 (China); Zhang, Xiaoli [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Wang, Jinxing [School of Life Sciences, Shandong University, Jinan 250100 (China); Jin, Wenrui, E-mail: jwr@sdu.edu.cn [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China)

    2015-01-07

    Highlights: • A single-molecule-detection (SMD) microarray for 10 samples is fabricated. • The based-SMD microarray assay (SMA) can determine 8 DNAs for each sample. • The limit of detection of SMA is as low as 1.3 × 10{sup −16} mol L{sup −1}. • The SMA can be applied in single-cell multiple gene expression analysis. - Abstract: We report a novel ultra-sensitive and high-selective single-molecule-detection microarray assay (SMA) for multiple DNA determination. In the SMA, a capture DNA (DNAc) microarray consisting of 10 subarrays with 9 spots for each subarray is fabricated on a silanized glass coverslip as the substrate. On the subarrays, the spot-to-spot spacing is 500 μm and each spot has a diameter of ∼300 μm. The sequence of the DNAcs on the 9 spots of a subarray is different, to determine 8 types of target DNAs (DNAts). Thus, 8 types of DNAts are captured to their complementary DNAcs at 8 spots of a subarray, respectively, and then labeled with quantum dots (QDs) attached to 8 types of detection DNAs (DNAds) with different sequences. The ninth spot is used to detect the blank value. In order to determine the same 8 types of DNAts in 10 samples, the 10 DNAc-modified subarrays on the microarray are identical. Fluorescence single-molecule images of the QD-labeled DNAts on each spot of the subarray are acquired using a home-made single-molecule microarray reader. The amounts of the DNAts are quantified by counting the bright dots from the QDs. For a microarray, 8 types of DNAts in 10 samples can be quantified in parallel. The limit of detection of the SMA for DNA determination is as low as 1.3 × 10{sup −16} mol L{sup −1}. The SMA for multi-DNA determination can also be applied in single-cell multiple gene expression analysis through quantification of complementary DNAs (cDNAs) corresponding to multiple messenger RNAs (mRNAs) in single cells. To do so, total RNA in single cells is extracted and reversely transcribed into their cDNAs. Three

  1. Single-cell multiple gene expression analysis based on single-molecule-detection microarray assay for multi-DNA determination

    International Nuclear Information System (INIS)

    Highlights: • A single-molecule-detection (SMD) microarray for 10 samples is fabricated. • The based-SMD microarray assay (SMA) can determine 8 DNAs for each sample. • The limit of detection of SMA is as low as 1.3 × 10−16 mol L−1. • The SMA can be applied in single-cell multiple gene expression analysis. - Abstract: We report a novel ultra-sensitive and high-selective single-molecule-detection microarray assay (SMA) for multiple DNA determination. In the SMA, a capture DNA (DNAc) microarray consisting of 10 subarrays with 9 spots for each subarray is fabricated on a silanized glass coverslip as the substrate. On the subarrays, the spot-to-spot spacing is 500 μm and each spot has a diameter of ∼300 μm. The sequence of the DNAcs on the 9 spots of a subarray is different, to determine 8 types of target DNAs (DNAts). Thus, 8 types of DNAts are captured to their complementary DNAcs at 8 spots of a subarray, respectively, and then labeled with quantum dots (QDs) attached to 8 types of detection DNAs (DNAds) with different sequences. The ninth spot is used to detect the blank value. In order to determine the same 8 types of DNAts in 10 samples, the 10 DNAc-modified subarrays on the microarray are identical. Fluorescence single-molecule images of the QD-labeled DNAts on each spot of the subarray are acquired using a home-made single-molecule microarray reader. The amounts of the DNAts are quantified by counting the bright dots from the QDs. For a microarray, 8 types of DNAts in 10 samples can be quantified in parallel. The limit of detection of the SMA for DNA determination is as low as 1.3 × 10−16 mol L−1. The SMA for multi-DNA determination can also be applied in single-cell multiple gene expression analysis through quantification of complementary DNAs (cDNAs) corresponding to multiple messenger RNAs (mRNAs) in single cells. To do so, total RNA in single cells is extracted and reversely transcribed into their cDNAs. Three types of c

  2. Rapid and simultaneous detection of ricin, staphylococcal enterotoxin B and saxitoxin by chemiluminescence-based microarray immunoassay

    OpenAIRE

    Szkola, A.; Linares, E. M.; Worbs, Sylvia; Dorner, Brigitte; R. Dietrich; Märtlbauer, E.; Niessner, R.; Seidel, Michael

    2014-01-01

    Simultaneous detection of small and large molecules on microarray immunoassays is a challenge that limits some applications in multiplex analysis. This is the case for biosecurity, where fast, cheap and reliable simultaneous detection of proteotoxins and small toxins is needed. Two highly relevant proteotoxins, ricin (60 kDa) and bacterial toxin staphylococcal enterotoxin B (SEB, 30 kDa) and the small phycotoxin saxitoxin (STX, 0.3 kDa) are potential biological warfare agents and require an a...

  3. Design of microarray probes for virus identification and detection of emerging viruses at the genus level

    Directory of Open Access Journals (Sweden)

    Ho Mei-Shang

    2006-04-01

    Full Text Available Abstract Background Most virus detection methods are geared towards the detection of specific single viruses or just a few known targets, and lack the capability to uncover the novel viruses that cause emerging viral infections. To address this issue, we developed a computational method that identifies the conserved viral sequences at the genus level for all viral genomes available in GenBank, and established a virus probe library. The virus probes are used not only to identify known viruses but also for discerning the genera of emerging or uncharacterized ones. Results Using the microarray approach, the identity of the virus in a test sample is determined by the signals of both genus and species-specific probes. The genera of emerging and uncharacterized viruses are determined based on hybridization of the viral sequences to the conserved probes for the existing viral genera. A detection and classification procedure to determine the identity of a virus directly from detection signals results in the rapid identification of the virus. Conclusion We have demonstrated the validity and feasibility of the above strategy with a small number of viral samples. The probe design algorithm can be applied to any publicly available viral sequence database. The strategy of using separate genus and species probe sets enables the use of a straightforward virus identity calculation directly based on the hybridization signals. Our virus identification strategy has great potential in the diagnosis of viral infections. The virus genus and specific probe database and the associated summary tables are available at http://genestamp.sinica.edu.tw/virus/index.htm.

  4. Microarray-based comparative genomic hybridization analysis in neonates with congenital anomalies: detection of chromosomal imbalances

    Directory of Open Access Journals (Sweden)

    Luiza Emy Dorfman

    2015-02-01

    Full Text Available OBJECTIVE: To identify chromosomal imbalances by whole-genome microarray-based comparative genomic hybridization (array-CGH in DNA samples of neonates with congenital anomalies of unknown cause from a birth defects monitoring program at a public maternity hospital. METHODS: A blind genomic analysis was performed retrospectively in 35 stored DNA samples of neonates born between July of 2011 and December of 2012. All potential DNA copy number variations detected (CNVs were matched with those reported in public genomic databases, and their clinical significance was evaluated. RESULTS: Out of a total of 35 samples tested, 13 genomic imbalances were detected in 12/35 cases (34.3%. In 4/35 cases (11.4%, chromosomal imbalances could be defined as pathogenic; in 5/35 (14.3% cases, DNA CNVs of uncertain clinical significance were identified; and in 4/35 cases (11.4%, normal variants were detected. Among the four cases with results considered causally related to the clinical findings, two of the four (50% showed causative alterations already associated with well-defined microdeletion syndromes. In two of the four samples (50%, the chromosomal imbalances found, although predicted as pathogenic, had not been previously associated with recognized clinical entities. CONCLUSIONS: Array-CGH analysis allowed for a higher rate of detection of chromosomal anomalies, and this determination is especially valuable in neonates with congenital anomalies of unknown etiology, or in cases in which karyotype results cannot be obtained. Moreover, although the interpretation of the results must be refined, this method is a robust and precise tool that can be used in the first-line investigation of congenital anomalies, and should be considered for prospective/retrospective analyses of DNA samples by birth defect monitoring programs.

  5. eSensor: an electrochemical detection-based DNA microarray technology enabling sample-to-answer molecular diagnostics

    Science.gov (United States)

    Liu, Robin H.; Longiaru, Mathew

    2009-05-01

    DNA microarrays are becoming a widespread tool used in life science and drug screening due to its many benefits of miniaturization and integration. Microarrays permit a highly multiplexed DNA analysis. Recently, the development of new detection methods and simplified methodologies has rapidly expanded the use of microarray technologies from predominantly gene expression analysis into the arena of diagnostics. Osmetech's eSensor® is an electrochemical detection platform based on a low-to- medium density DNA hybridization array on a cost-effective printed circuit board substrate. eSensor® has been cleared by FDA for Warfarin sensitivity test and Cystic Fibrosis Carrier Detection. Other genetic-based diagnostic and infectious disease detection tests are under development. The eSensor® platform eliminates the need for an expensive laser-based optical system and fluorescent reagents. It allows one to perform hybridization and detection in a single and small instrument without any fluidic processing and handling. Furthermore, the eSensor® platform is readily adaptable to on-chip sample-to-answer genetic analyses using microfluidics technology. The eSensor® platform provides a cost-effective solution to direct sample-to-answer genetic analysis, and thus have a potential impact in the fields of point-of-care genetic analysis, environmental testing, and biological warfare agent detection.

  6. Food Allergens: Is There a Correlation between Stability to Digestion and Allergenicity?

    Science.gov (United States)

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard

    2016-07-01

    Food allergy is a major health problem in the Western countries, affecting 3-8% of the population. It has not yet been established what makes a dietary protein a food allergen. Several characteristics have been proposed to be shared by food allergens. One of these is resistance to digestion. This paper reviews data from digestibility studies on purified food allergens and evaluates the predictive value of digestibility tests on the allergenic potential. We point out that food allergens do not necessarily resist digestion. We discuss how the choice of in vitro digestibility assay condition and the method used for detection of residual intact protein as well as fragments hereof may greatly influence the outcome as well as the interpretation of results. The finding that digests from food allergens may retain allergenicity, stresses the importance of using immunological assays for evaluating the allergenic potential of food allergen digestion products. Studies assessing the allergenicity of digestion products, by either IgE-binding, elicitation or sensitizing capacity, shows that digestion may abolish, decrease, have no effect, or even increase the allergenicity of food allergens. Therefore, the predictive value of the pepsin resistance test for assessing the allergenic potential of novel proteins can be questioned. PMID:25607526

  7. Broad respiratory virus detection in infants hospitalized for bronchiolitis by use of a multiplex RT-PCR DNA microarray system.

    Science.gov (United States)

    Huguenin, Antoine; Moutte, Lauryane; Renois, Fanny; Leveque, Nicolas; Talmud, Deborah; Abely, Michel; Nguyen, Yohan; Carrat, Fabrice; Andreoletti, Laurent

    2012-06-01

    Newly available molecular tools allow a sensitive detection of a broad panel of viruses in respiratory tract specimens. In the present study, the application of a multiplex RT-PCR DNA microarray in diagnosis and epidemiological survey of viral infections in infants hospitalized for bronchiolitis was assessed. One hundred and thirty-eight nasopharyngeal aspirates collected from October 2007 to September 2008 were tested by direct immunofluorescence and viral culture, a combination of referenced RT-PCRs and the DNA microarray. One or more viruses were detected in 96, 126 and 126 of the specimens by direct immunofluorescence and viral culture, RT-PCRs and DNA microarray, respectively (70 vs. 91 vs. 91%, P 0.1). In conclusion, the use of this DNA microarray in clinical virology practice allows rapid and accurate identification of common and uncommon viral respiratory pathogens in infants hospitalized for bronchiolitis. It should improve the clinical management, the epidemiological survey, and the prevention of the nosocomial transmission of respiratory viruses in pediatric wards. PMID:22499022

  8. 多重PCR同时检测常见8种食物过敏原%Detection of Eight Food Allergens with Multiplex PCR

    Institute of Scientific and Technical Information of China (English)

    王玮; 韩建勋; 袁飞; 吴亚君; 陈颖; 葛毅强

    2011-01-01

    依据大豆Lectin基因,小麦Gliadin基因,花生Arah3基因,腰果Ana o3基因,鱼和虾16S rRNA,牛和鸡线粒体DNA设计特异性引物序列.在单一PCR方法基础上,建立2种4重PCR方法检测8种食物过敏原的技术.该方法检测周期短,具有较好的特异性和灵敏性,可用于对食品中多种食物过敏原的检测和监控.%Eight pairs of primers were selected according to the sequence of Lectin gene from soybean, Gliadin gene from wheat, Ara h 3 gene from peanut, Ana o3 gene from cashew, 16S rRNA from shrimp and fish, mitochondrial DNA from bovine and chicken respectively, and a multiplex PCR assay for food allergen detection was established on the basis of simple PCR technique. Eight food allergens could be detected rapid, specific and sensitive with 2 multiplex PCR assays at the same time. It could be used for detection and surveillance of many allergens in food.

  9. Fungal allergens.

    OpenAIRE

    Horner, W E; Helbling, A; Salvaggio, J E; Lehrer, S B

    1995-01-01

    Airborne fungal spores occur widely and often in far greater concentrations than pollen grains. Immunoglobulin E-specific antigens (allergens) on airborne fungal spores induce type I hypersensitivity (allergic) respiratory reactions in sensitized atopic subjects, causing rhinitis and/or asthma. The prevalence of respiratory allergy to fungi is imprecisely known but is estimated at 20 to 30% of atopic (allergy-predisposed) individuals or up to 6% of the general population. Diagnosis and immuno...

  10. Microarray comparative genomic hybridization detection of chromosomal imbalances in uterine cervix carcinoma

    International Nuclear Information System (INIS)

    Chromosomal Comparative Genomic Hybridization (CGH) has been applied to all stages of cervical carcinoma progression, defining a specific pattern of chromosomal imbalances in this tumor. However, given its limited spatial resolution, chromosomal CGH has offered only general information regarding the possible genetic targets of DNA copy number changes. In order to further define specific DNA copy number changes in cervical cancer, we analyzed 20 cervical samples (3 pre-malignant lesions, 10 invasive tumors, and 7 cell lines), using the GenoSensor microarray CGH system to define particular genetic targets that suffer copy number changes. The most common DNA gains detected by array CGH in the invasive samples were located at the RBP1-RBP2 (3q21-q22) genes, the sub-telomeric clone C84C11/T3 (5ptel), D5S23 (5p15.2) and the DAB2 gene (5p13) in 58.8% of the samples. The most common losses were found at the FHIT gene (3p14.2) in 47% of the samples, followed by deletions at D8S504 (8p23.3), CTDP1-SHGC- 145820 (18qtel), KIT (4q11-q12), D1S427-FAF1 (1p32.3), D9S325 (9qtel), EIF4E (eukaryotic translation initiation factor 4E, 4q24), RB1 (13q14), and DXS7132 (Xq12) present in 5/17 (29.4%) of the samples. Our results confirm the presence of a specific pattern of chromosomal imbalances in cervical carcinoma and define specific targets that are suffering DNA copy number changes in this neoplasm

  11. Research advances of food allergen and its detection techniques%食物致敏原及其检测技术的研究进展

    Institute of Scientific and Technical Information of China (English)

    王守法; 巢强国; 葛宇; 成姗

    2011-01-01

    With the increasing incidence of food allergy,the study on which is becoming more and more important nowadays.Food allergy is becoming a highlighted problem in the field of food safety now.The characteristics and kinds of food allergens were introduced, two major technologies applied in food allergen detection were elaborated,including protein-based methods and DNA-based methods.And the trends in the development of food allergen detection and its prospect in the food safety determination were also forward commented.%近年来随着食物过敏发病率的增加,有关食物过敏的研究越来越受人们的重视,食物过敏已成为当前食品安全领域较为突出的问题.介绍了食物致敏原的性质、种类,详细论述了两类主要的食物致敏原检测技术,并对食物致敏原检测技术的发展趋势和应用前景进行了展望.

  12. Identification of hidden allergens. The case of detection of pistachio traces in mortadella.

    OpenAIRE

    Barbieri, Giampiero; Frigeri, Giorgia

    2006-01-01

    Abstract An analytical method based on the detection of specific DNAs was defined, and was applied to mortadella samples with and without pistachio (Pistacia Vera), in order to detect traces deriving from previous processes or from accidental contamination, since in predisposed individuals pistachios can cause allergic reactions leading to anaphylactic shock. Three pairs of primers were defined and tested for PCR on mortadella samples prepared with pistachio. Accidental contamin...

  13. 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.

  14. Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells

    Directory of Open Access Journals (Sweden)

    Ahmed Sharlin

    2004-07-01

    Full Text Available Abstract Background cDNA microarrays are a powerful means to screen for biologically relevant gene expression changes, but are often limited by their ability to detect small changes accurately due to "noise" from random and systematic errors. While experimental designs and statistical analysis methods have been proposed to reduce these errors, few studies have tested their accuracy and ability to identify small, but biologically important, changes. Here, we have compared two cDNA microarray experimental design methods with northern blot confirmation to reveal changes in gene expression that could contribute to the early antiproliferative effects of neuregulin on MCF10AT human breast epithelial cells. Results We performed parallel experiments on identical samples using a dye-swap design with ANOVA and an experimental design that excludes systematic biases by "correcting" experimental/control hybridization ratios with control/control hybridizations on a spot-by-spot basis. We refer to this approach as the "control correction method" (CCM. Using replicate arrays, we identified a decrease in proliferation genes and an increase in differentiation genes. Using an arbitrary cut-off of 1.7-fold and p values Conclusions We validated two experimental design paradigms for cDNA microarray experiments capable of detecting small (

  15. Detection of Genetically Modified Crops by Combination of Multiplex PCR and Low-density DNA Microarray1

    Institute of Scientific and Technical Information of China (English)

    PING-PING ZHOU; JIAN-ZHONG ZHANG; YUAN-HAI YOU; YONG-NING WU

    2008-01-01

    Objective To develop a technique for simultaneous detection of various target genes in Roundup Ready soybean by combining multiplex PCR and low-density DNA microarray.Methods Two sets of the multiplex PCR system were used to amplify the target genes in genetically modified(GM)soybean.Seventeen capture probes(PCR products)and 17 pairs of corresponding primers were designed according to the genetic characteristies of Rroundup Ready soybean(GTS40-3-2),maize (Mort810,Nk603,GA21),canola(T45,MS1/RF1),and rice(SCK)in many identified GM crops.All of the probes were categorized and identified as species-specific probes.One negative probe and one positive control probe were uscd to assess the efficiency of all reactions,and therefore eliminate any false positive and negative results.After multiplex PCR reaction,amplicons were adulterated with Cy5-dUTP and hvbridized with DNA microarray.The array was then scanned to display the specific hybridization signals of target genes.The assay was applied to the analysis of sample of ccrtified transgenic soybean (Roundup Ready GTS40-3-2)and canola(MS1/RF1). Results A combination technique of multiplex PCR and DNA microarray was successfully developed to identify multi-target genes in Roundup Ready soybean and MS1/RF1 canola with a great specificity and reliability.Reliable identification of genetic characteristics of Roundup Ready of GM soybean from genetically modified crops was achieved at 0.5% transgenic events,indicating a high sensitivity. Conclusion A combination technique of multiplex PCR and low-density DNA microarray can reliably detect and identify the genetically modified crops.

  16. Fabrication of protein microarrays for alpha fetoprotein detection by using a rapid photo-immobilization process

    Directory of Open Access Journals (Sweden)

    Sirasa Yodmongkol

    2016-03-01

    Full Text Available In this study, protein microarrays based on sandwich immunoassays are generated to quantify the amount of alpha fetoprotein (AFP in blood serum. For chip generation a mixture of capture antibody and a photoactive copolymer consisting of N,N-dimethylacrylamide (DMAA, methacryloyloxy benzophenone (MaBP, and Na-4-styrenesulfonate (SSNa was spotted onto unmodified polymethyl methacrylate (PMMA substrates. Subsequently to printing of the microarray, the polymer and protein were photochemically cross-linked and the forming, biofunctionalized hydrogels simultaneously bound to the chip surface by short UV- irradiation. The obtained biochip was incubated with AFP antigen, followed by biotinylated AFP antibody and streptavidin-Cy5 and the fluorescence signal read-out. The developed microarray biochip covers the range of AFP in serum samples such as maternal serum in the range of 5 and 100 ng/ml. The chip production process is based on a fast and simple immobilization process, which can be applied to conventional plastic surfaces. Therefore, this protein microarray production process is a promising method to fabricate biochips for AFP screening processes.

  17. Chromosomal imbalances in malignant peripheral nerve sheath tumor detected by metaphase and microarray comparative genomic hybridization.

    Science.gov (United States)

    Nakagawa, Yasuko; Yoshida, Aki; Numoto, Kunihiko; Kunisada, Toshiyuki; Wai, Daniel; Ohata, Norihide; Takeda, Ken; Kawai, Akira; Ozaki, Toshifumi

    2006-02-01

    Malignant peripheral nerve sheath tumors (MPNSTs) are highly malignant tumors affecting adolescents and adults. There have been a few reports on chromosomal aberrations of MPNSTs; however, the tumor-specific alteration remains unknown. We characterized the genomic alterations in 8 MPNSTs and 8 schwannomas by metaphase comparative genomic hybridization (CGH). In 5 of 8 MPNSTs, microarray CGH was added for more detailed analyses. Frequent gains were identified on 3q13-26, 5p13-14, and 12q11-23 and frequent losses were at 1p31, 10p, 11q24-qter, 16, and 17. Microarray CGH revealed frequent gains of EGFR, DAB2, MSH2, KCNK12, DDX15, CDK6, and LAMA3, and losses of CDH1, GLTSCR2, EGR1, CTSB, GATA3, and SULT2A1. These genes seem to be responsible for developing MPNSTs. The concordance rate between metaphase CGH and microarray CGH was 66%. Metaphase CGH was useful for identifying chromosomal alterations before applying microarray CGH. PMID:16391845

  18. Impedance Biosensing to detect food allergens, endocrine disrupting chemicals, and food pathogens

    Science.gov (United States)

    Radhakrishnan, Rajeswaran

    Electrochemical impedance biosensors can be viewed as an AC electroanalytical method for the analyte detection in the fields of biomedicine, environmental monitoring, and food and agriculture, amongst others. The most common format for AC impedance biosensing involves surface immobilization of an antibody, receptor protein, DNA strand, or other species capable of bio-recognition, and AC impedance detection of the binding event. Technological application of AC impedance biosensors has been hindered by several obstacles, including the more complex circuitry required for AC relative to DC electrochemistry, chemical and physical interference arising from non-specific adsorption, and the stability and reproducibility of protein immobilization. One focus of these PhD studies is on methods to reduce or compensate for non-specific adsorption, including sample dilution, site blocking with BSA, and the use of control electrodes onto which reference antibodies are immobilized. Examples that will be presented include impedance detection of food pathogens, such as Listeria monocytogenes, using a mouse monoclonal antibody immobilized onto an Au electrode. This yields detection limits of 5 CFU/ml and 4 CFU/ml for ideal solutions and filtered tomato extract, respectively. Control experiments with an Au electrode onto which a mouse monoclonal antibody to GAPDH is immobilized demonstrate that non-specific adsorption is insignificant for the system and methodology studied here. Control experiments with Salmonella enterica demonstrate no cross-reactivity to this food pathogen. In addition, Detection of two endocrine-disrupting chemicals (EDC), norfluoxetine and BDE-47, is reported here by impedance biosensing, with a detection limit of 8.5 and 1.3 ng/ml for norfluoxetine and BDE-47, respectively. Additional research has focused on alternative substrates and linker chemistries for protein immobilization, including the use of degenerate (highly doped) Si and bidendate thiol monolayer

  19. Detection of respiratory allergies caused by environmental chemical allergen via measures of hyper-activation and degranulation of mast cells in lungs of NC/Nga mice.

    Science.gov (United States)

    Nishino, Risako; Fukuyama, Tomoki; Watanabe, Yuko; Kurosawa, Yoshimi; Koasaka, Tadashi; Harada, Takanori

    2016-09-01

    Respiratory allergy triggered by exposure to environmental chemical allergen is a serious problem in many Asian countries and has the potential to cause severe health problems. Here, we aimed to elucidate the pathogenic mechanisms of this disease and develop an in vivo detection method for respiratory allergy induced by environmental chemical allergen. Both BALB/c and NC/Nga mice were sensitized topically for 3 weeks and were then subjected to inhalation challenge with pulverized trimellitic anhydride into particles measuring 2-μm in diameter. On the day after the final challenge, all mice were sacrificed, and IgE levels, immunocyte counts, and cytokine levels in the serum, hilar lymph nodes, and bronchoalveolar lavage fluid were measured. We also monitored the expression of genes encoding pro-inflammatory cytokines in the lung. We found that all endpoints were significantly increased in mice of both strains subjected to trimellitic anhydride inhalation as compared with the respective control groups. However, worsening of respiratory status was noted only in NC/Nga mice. Interestingly, type 2 helper T-cell reactions were significantly increased in BALB/c mice compared with that in NC/Nga mice. In contrast, the number of mast cells, levels of mast cell-related cytokine/chemokines, and production of histamine in NC/Nga mice were significantly higher than those in BALB/c mice. Thus, environmental chemical allergen induced respiratory allergy in NC/Nga mice in terms of functional and inflammatory symptoms. Furthermore, mast cells may be involved in the aggravation of airway allergic symptoms induced by environmental chemical allergens. PMID:27404449

  20. A universal oligonucleotide microarray with a minimal number of probes for the detection and identification of viroids at the genus level.

    Directory of Open Access Journals (Sweden)

    Yongjiang Zhang

    Full Text Available A major challenge in the agricultural industry is the development of techniques that can screen plant samples for viroid infection. Microarrays are promising in this regard, as their high throughput nature can potentially allow for the detection of a range of viroids in a single test. In this paper we present a microarray that can detect a wide spectrum of all 8 reported viroid genera including 37 known plant viroid species. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viroids at the genus level. The designed microarray showed a high specificity and sensitivity when tested with a set of standard virus samples. Finally, the microarray was applied to screen infected field samples, with Hop stunt viroid infection identified as the major disease causing pathogen for an infected citrus sample.

  1. Managing allergens in food

    NARCIS (Netherlands)

    Mills, C.; Wichers, H.J.; Hoffmann-Sommergruber, K.

    2007-01-01

    Controlling allergens in food is a matter of increasing importance for the food industry, especially in light of recent legislation. Effective handling of allergens depends on identifying allergenic ingredients, creating separate production lines for allergen-free products, and effective labelling t

  2. The SOLID (Signs Of LIfe Detector) instrument concept: an antibody microarray-based biosensor for life detection in astrobiology

    Science.gov (United States)

    Parro, V.; Rivas, L. A.; Rodríguez-Manfredi, J. A.; Blanco, Y.; de Diego-Castilla, G.; Cruz-Gil, P.; Moreno-Paz, M.; García-Villadangos, M.; Compostizo, C.; Herrero, P. L.

    2009-04-01

    Immunosensors have been extensively used since many years for environmental monitoring. Different technological platforms allow new biosensor designs and implementations. We have reported (Rivas et al., 2008) a shotgun approach for antibody production for biomarker detection in astrobiology and environmental monitoring, the production of 150 new polyclonal antibodies against microbial strains and environmental extracts, and the construction and validation of an antibody microarray (LDCHIP200, for "Life Detector Chip") containing 200 different antibodies. We have successfully used the LDCHIP200 for the detection of biological polymers in extreme environments in different parts of the world (e.g., a deep South African mine, Antarctica's Dry valleys, Yellowstone, Iceland, and Rio Tinto). Clustering analysis associated similar immunopatterns to samples from apparently very different environments, indicating that they indeed share similar universal biomarkers. A redundancy in the number of antibodies against different target biomarkers apart of revealing the presence of certain biomolecules, it renders a sample-specific immuno-profile, an "immnuno-fingerprint", which may constitute by itself an indirect biosignature. We will present a case study of immunoprofiling different iron-sulfur as well as phylosilicates rich samples along the Rio Tinto river banks. Based on protein microarray technology, we designed and built the concept instrument called SOLID (for "Signs Of LIfe Detector"; Parro et al., 2005; 2008a, b; http://cab.inta.es/solid) for automatic in situ analysis of soil samples and molecular biomarkers detection. A field prototype, SOLID2, was successfully tested for the analysis of grinded core samples during the 2005 "MARTE" campaign of a Mars drilling simulation experiment by a sandwich microarray immunoassay (Parro et al., 2008b). We will show the new version of the instrument (SOLID3) which is able to perform both sandwich and competitive immunoassays. SOLID3

  3. Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray

    Directory of Open Access Journals (Sweden)

    Huyen Yentram

    2008-08-01

    Full Text Available Abstract Background Genetic mapping is a powerful method to identify mutations that cause drug resistance and other phenotypic changes in the human malaria parasite Plasmodium falciparum. For efficient mapping of a target gene, it is often necessary to genotype a large number of polymorphic markers. Currently, a community effort is underway to collect single nucleotide polymorphisms (SNP from the parasite genome. Here we evaluate polymorphism detection accuracy of a high-density 'tiling' microarray with 2.56 million probes by comparing single feature polymorphisms (SFP calls from the microarray with known SNP among parasite isolates. Results We found that probe GC content, SNP position in a probe, probe coverage, and signal ratio cutoff values were important factors for accurate detection of SFP in the parasite genome. We established a set of SFP calling parameters that could predict mSFP (SFP called by multiple overlapping probes with high accuracy (≥ 94% and identified 121,087 mSFP genome-wide from five parasite isolates including 40,354 unique mSFP (excluding those from multi-gene families and ~18,000 new mSFP, producing a genetic map with an average of one unique mSFP per 570 bp. Genomic copy number variation (CNV among the parasites was also cataloged and compared. Conclusion A large number of mSFP were discovered from the P. falciparum genome using a high-density microarray, most of which were in clusters of highly polymorphic genes at chromosome ends. Our method for accurate mSFP detection and the mSFP identified will greatly facilitate large-scale studies of genome variation in the P. falciparum parasite and provide useful resources for mapping important parasite traits.

  4. Development of a DNA Microarray-Based Assay for the Detection of Sugar Beet Root Rot Pathogens.

    Science.gov (United States)

    Liebe, Sebastian; Christ, Daniela S; Ehricht, Ralf; Varrelmann, Mark

    2016-01-01

    Sugar beet root rot diseases that occur during the cropping season or in storage are accompanied by high yield losses and a severe reduction of processing quality. The vast diversity of microorganism species involved in rot development requires molecular tools allowing simultaneous identification of many different targets. Therefore, a new microarray technology (ArrayTube) was applied in this study to improve diagnosis of sugar beet root rot diseases. Based on three marker genes (internal transcribed spacer, translation elongation factor 1 alpha, and 16S ribosomal DNA), 42 well-performing probes enabled the identification of prevalent field pathogens (e.g., Aphanomyces cochlioides), storage pathogens (e.g., Botrytis cinerea), and ubiquitous spoilage fungi (e.g., Penicillium expansum). All probes were proven for specificity with pure cultures from 73 microorganism species as well as for in planta detection of their target species using inoculated sugar beet tissue. Microarray-based identification of root rot pathogens in diseased field beets was successfully confirmed by classical detection methods. The high discriminatory potential was proven by Fusarium species differentiation based on a single nucleotide polymorphism. The results demonstrate that the ArrayTube constitute an innovative tool allowing a rapid and reliable detection of plant pathogens particularly when multiple microorganism species are present. PMID:26524545

  5. Optimised padlock probe ligation and microarray detection of multiple (non-authorised GMOs in a single reaction

    Directory of Open Access Journals (Sweden)

    Schoen Cor D

    2008-12-01

    Full Text Available Abstract Background To maintain EU GMO regulations, producers of new GM crop varieties need to supply an event-specific method for the new variety. As a result methods are nowadays available for EU-authorised genetically modified organisms (GMOs, but only to a limited extent for EU-non-authorised GMOs (NAGs. In the last decade the diversity of genetically modified (GM ingredients in food and feed has increased significantly. As a result of this increase GMO laboratories currently need to apply many different methods to establish to potential presence of NAGs in raw materials and complex derived products. Results In this paper we present an innovative method for detecting (approved GMOs as well as the potential presence of NAGs in complex DNA samples containing different crop species. An optimised protocol has been developed for padlock probe ligation in combination with microarray detection (PPLMD that can easily be scaled up. Linear padlock probes targeted against GMO-events, -elements and -species have been developed that can hybridise to their genomic target DNA and are visualised using microarray hybridisation. In a tenplex PPLMD experiment, different genomic targets in Roundup-Ready soya, MON1445 cotton and Bt176 maize were detected down to at least 1%. In single experiments, the targets were detected down to 0.1%, i.e. comparable to standard qPCR. Conclusion Compared to currently available methods this is a significant step forward towards multiplex detection in complex raw materials and derived products. It is shown that the PPLMD approach is suitable for large-scale detection of GMOs in real-life samples and provides the possibility to detect and/or identify NAGs that would otherwise remain undetected.

  6. Indoor allergens in Minnesota schools and child care centers.

    Science.gov (United States)

    Tranter, Daniel C; Wobbema, Amanda Teresa; Norlien, Kathleen; Dorschner, Dale F

    2009-09-01

    Elevated concentrations of allergens in the indoor environment may cause allergic sensitization and symptoms. Occupant exposure to indoor allergens in educational facilities should and can be controlled. This study (1) assessed the presence of indoor allergens in Minnesota schools and child care centers, (2) characterized the distribution of allergens in different materials, and (3) evaluated the effect of building and maintenance interventions on allergen concentrations. Settled dust samples were collected from carpet, vinyl tile floors, and upholstered furniture in six schools and seven child care centers before and after interventions. Interventions included changes to cleaning, ventilation, entry mats, furnishings, flooring, and classroom items. The amount of total dust, culturable fungi, and indoor allergens--cockroach, dust mite, cat, and dog--were quantified in the dust samples. Cockroach and dust mite allergens were generally low and below the detection limit, but one dust mite allergen was detected in some areas. Cat and dog allergens were frequently detected at elevated levels, with half the samples above the provisional sensitization risk thresholds and a few samples above the symptom thresholds. Allergen concentrations were highest in upholstered furniture, followed by carpeting and then vinyl floor tile. Cat and dog allergens were lower after the interventions. Cat and dog allergens, but not dust mite and cockroach allergens, seem to be ubiquitous in child care and elementary schools of the U.S. Midwest. These allergens may contribute to sensitization in atopic individuals and occasionally cause symptoms in sensitized allergic individuals. Fleecy materials that are not adequately cleaned, such as upholstered furniture, appear to be the most significant allergen reservoirs. Modest environmental interventions can be implemented by building staff, which should result in lower allergen concentrations. PMID:19585331

  7. SOLID3: a multiplex antibody microarray-based optical sensor instrument for in situ life detection in planetary exploration.

    Science.gov (United States)

    Parro, Víctor; de Diego-Castilla, Graciela; Rodríguez-Manfredi, José A; Rivas, Luis A; Blanco-López, Yolanda; Sebastián, Eduardo; Romeral, Julio; Compostizo, Carlos; Herrero, Pedro L; García-Marín, Adolfo; Moreno-Paz, Mercedes; García-Villadangos, Miriam; Cruz-Gil, Patricia; Peinado, Verónica; Martín-Soler, Javier; Pérez-Mercader, Juan; Gómez-Elvira, Javier

    2011-01-01

    The search for unequivocal signs of life on other planetary bodies is one of the major challenges for astrobiology. The failure to detect organic molecules on the surface of Mars by measuring volatile compounds after sample heating, together with the new knowledge of martian soil chemistry, has prompted the astrobiological community to develop new methods and technologies. Based on protein microarray technology, we have designed and built a series of instruments called SOLID (for "Signs Of LIfe Detector") for automatic in situ detection and identification of substances or analytes from liquid and solid samples (soil, sediments, or powder). Here, we present the SOLID3 instrument, which is able to perform both sandwich and competitive immunoassays and consists of two separate functional units: a Sample Preparation Unit (SPU) for 10 different extractions by ultrasonication and a Sample Analysis Unit (SAU) for fluorescent immunoassays. The SAU consists of five different flow cells, with an antibody microarray in each one (2000 spots). It is also equipped with an exclusive optical package and a charge-coupled device (CCD) for fluorescent detection. We demonstrated the performance of SOLID3 in the detection of a broad range of molecular-sized compounds, which range from peptides and proteins to whole cells and spores, with sensitivities at 1-2 ppb (ng mL⁻¹) for biomolecules and 10⁴ to 10³ spores per milliliter. We report its application in the detection of acidophilic microorganisms in the Río Tinto Mars analogue and report the absence of substantial negative effects on the immunoassay in the presence of 50 mM perchlorate (20 times higher than that found at the Phoenix landing site). Our SOLID instrument concept is an excellent option with which to detect biomolecules because it avoids the high-temperature treatments that may destroy organic matter in the presence of martian oxidants. PMID:21294639

  8. Automated detection of regions of interest for tissue microarray experiments: an image texture analysis

    International Nuclear Information System (INIS)

    Recent research with tissue microarrays led to a rapid progress toward quantifying the expressions of large sets of biomarkers in normal and diseased tissue. However, standard procedures for sampling tissue for molecular profiling have not yet been established. This study presents a high throughput analysis of texture heterogeneity on breast tissue images for the purpose of identifying regions of interest in the tissue for molecular profiling via tissue microarray technology. Image texture of breast histology slides was described in terms of three parameters: the percentage of area occupied in an image block by chromatin (B), percentage occupied by stroma-like regions (P), and a statistical heterogeneity index H commonly used in image analysis. Texture parameters were defined and computed for each of the thousands of image blocks in our dataset using both the gray scale and color segmentation. The image blocks were then classified into three categories using the texture feature parameters in a novel statistical learning algorithm. These categories are as follows: image blocks specific to normal breast tissue, blocks specific to cancerous tissue, and those image blocks that are non-specific to normal and disease states. Gray scale and color segmentation techniques led to identification of same regions in histology slides as cancer-specific. Moreover the image blocks identified as cancer-specific belonged to those cell crowded regions in whole section image slides that were marked by two pathologists as regions of interest for further histological studies. These results indicate the high efficiency of our automated method for identifying pathologic regions of interest on histology slides. Automation of critical region identification will help minimize the inter-rater variability among different raters (pathologists) as hundreds of tumors that are used to develop an array have typically been evaluated (graded) by different pathologists. The region of interest

  9. PAX3 gene deletion detected by microarray analysis in a girl with hearing loss

    OpenAIRE

    Drozniewska, Malgorzata; Haus, Olga

    2014-01-01

    Deletions of the PAX3 gene have been rarely reported in the literature. Mutations of this gene are a common cause of Waardenburg syndrome type 1 and 3. We report a 16 year old female presenting hearing loss and normal intellectual development, without major features of Waardenburg syndrome type 1, and without family history of the syndrome. Her phenotype, however, overlaps with features of craniofacial-deafness-hand syndrome. Microarray analysis showed ~862 kb de novo deletion at 2q36.1 inclu...

  10. Significant overexpression of oligophrenin-1 in colorectal tumors detected by cDNA microarray analysis.

    Science.gov (United States)

    Pinheiro, N A; Caballero, O L; Soares, F; Reis, L F; Simpson, A J

    2001-10-22

    The human oligophrenin-1 gene is ubiquitously expressed at low levels and expressed at high levels in the developing neuroepithelium of the neural tube. Mutations in this gene have been related to the X-linked mental retardation. Using cDNA microarrays, we found evidence that oligophrenin-1 is strongly up-regulated in colorectal tumors. Semiquantitative reverse transcriptase polymerase chain reaction confirmed this finding. Thus, a well-known nervous system-associated human gene transcript may also be an important colorectal tumor marker and potential therapeutic target. PMID:11595131

  11. Authentication of food allergen quality by physicochemical and immunological methods

    DEFF Research Database (Denmark)

    Sancho, A I; Hoffmann-Sommergruber, K; Alessandri, S;

    2010-01-01

    Purified allergens are required to detect cross-contamination with other allergenic foods and to understand allergen interaction with other components of the food matrix. Pure allergens are also used for the diagnosis and treatment of food allergies. For example, serological methods are being...... developed to improve the quality of diagnosis, and to reduce the need for food challenge tests. In addition, recombinant allergens are being evaluated as candidate vaccines for safe and efficacious specific immunotherapy. Pure allergens are indispensable as reference materials for the calibration and...... standardization of methods between different laboratories and operators for risk assessment in the food industry. Therefore, there is a need for well-defined purified food allergens. In this context, a panel of 46 food allergens from plant and animal sources has been purified, from either the food sources or as...

  12. Age-Specific Gene Expression Profiles of Rhesus Monkey Ovaries Detected by Microarray Analysis.

    Science.gov (United States)

    Wei, Hengxi; Liu, Xiangjie; Yuan, Jihong; Li, Li; Zhang, Dongdong; Guo, Xinzheng; Liu, Lin; Zhang, Shouquan

    2015-01-01

    The biological function of human ovaries declines with age. To identify the potential molecular changes in ovarian aging, we performed genome-wide gene expression analysis by microarray of ovaries from young, middle-aged, and old rhesus monkeys. Microarray data was validated by quantitative real-time PCR. Results showed that a total of 503 (60 upregulated, 443 downregulated) and 84 (downregulated) genes were differentially expressed in old ovaries compared to young and middle-aged groups, respectively. No difference in gene expression was found between middle-aged and young groups. Differentially expressed genes were mainly enriched in cell and organelle, cellular and physiological process, binding, and catalytic activity. These genes were primarily associated with KEGG pathways of cell cycle, DNA replication and repair, oocyte meiosis and maturation, MAPK, TGF-beta, and p53 signaling pathway. Genes upregulated were involved in aging, defense response, oxidation reduction, and negative regulation of cellular process; genes downregulated have functions in reproduction, cell cycle, DNA and RNA process, macromolecular complex assembly, and positive regulation of macromolecule metabolic process. These findings show that monkey ovary undergoes substantial change in global transcription with age. Gene expression profiles are useful in understanding the mechanisms underlying ovarian aging and age-associated infertility in primates. PMID:26421297

  13. Effects of aspirin on metastasis-associated gene expression detected by cDNA microarray

    Institute of Scientific and Technical Information of China (English)

    Xue-qin GAO; Jin-xiang HAN; Hai-yan HUANG; Shi YAN; Chang-zheng SONG; Hai-nan HUANG

    2004-01-01

    AIM: To investigate the effect of aspirin on the metastasis-associated gene expression in 3AO ovarian cancer cells.METHODS: 3AO cells were treated with aspirin at the concentration of 1.2 mmol/L for 16 and 48 h, respectively.The total RNA was extracted with Trizol reagents and reverse transcribed with Superscript II and hybridized with cDNA microarray (containing oncogenes, tumor suppressor genes, signal transduction pathway molecules, adhesive molecules, growth factors and ESTs) fabricated in our lab. After normalization, the ratio of gene expression of aspirin treated to untreated 3AO cells being either 2 fold up higher or 0.5 fold down (lower) were defined as differential expression. Semi-quantitative RT-PCR was used to validate the microarray results. RESULTS: Among the 447 metastasis-associated genes, 4 genes were up-regulated and 14 genes were down-regulated in 3AO cells treated with aspirin for 16 h compared with untreated cells. While 24 genes were up-regulated and 10 genes were down-regulated in cells treated with aspirin for 48 h. Several up or down-regulated gene expression changes continued from 16 h to 48 h. CONCLUSION: Aspirin might exert its anti-metastasis effects on ovarian cancer by affecting metastasis-associated gene expression.

  14. Food allergen digestibility: The influence on allergenicity

    OpenAIRE

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard

    2012-01-01

    Food allergy is a major health problem in the Western countries, affecting 3-8% of the population. What makes a dietary protein a food allergen has not yet been established, though several characteristics have been proposed to be shared by the food allergens. One of the features believed to be a general characteristic is resistance to digestion. This is based on studies showing that allergenic dietary proteins in general were more resistant to digestion than dietary proteins with no proven al...

  15. Gold Nanoparticles Surface Plasmon Resonance Enhanced Signal for the Detection of Small Molecules on Split-Aptamer Microarrays (Small Molecules Detection from Split-Aptamers

    Directory of Open Access Journals (Sweden)

    Feriel Melaine

    2015-02-01

    Full Text Available The detection of small molecules by biosensors remains a challenge for diagnostics in many areas like pharmacology, environment or homeland security. The main difficulty comes from both the low molecular weight and low concentrations of most targets, which generally requires an indirect detection with an amplification or a sandwich procedure. In this study, we combine both strategies as the amplification of Surface Plasmon Resonance imaging (SPRi signal is obtained by the use of gold nanoparticles and the sequence engineering of split-aptamers, short oligonucleotides strands with strong affinity towards small targets, allows for a sandwich structure. Combining those two strategies, we obtained state-of-the-art results in the limit of detection (LOD = 50 nM with the model target adenosine. Furthermore, the SPRi detection led on aptamer microarrays paves the way for potential multi-target detections thanks to the multi-probe imaging approach.

  16. Distributional fold change test – a statistical approach for detecting differential expression in microarray experiments

    Directory of Open Access Journals (Sweden)

    Farztdinov Vadim

    2012-11-01

    Full Text Available Abstract Background Because of the large volume of data and the intrinsic variation of data intensity observed in microarray experiments, different statistical methods have been used to systematically extract biological information and to quantify the associated uncertainty. The simplest method to identify differentially expressed genes is to evaluate the ratio of average intensities in two different conditions and consider all genes that differ by more than an arbitrary cut-off value to be differentially expressed. This filtering approach is not a statistical test and there is no associated value that can indicate the level of confidence in the designation of genes as differentially expressed or not differentially expressed. At the same time the fold change by itself provide valuable information and it is important to find unambiguous ways of using this information in expression data treatment. Results A new method of finding differentially expressed genes, called distributional fold change (DFC test is introduced. The method is based on an analysis of the intensity distribution of all microarray probe sets mapped to a three dimensional feature space composed of average expression level, average difference of gene expression and total variance. The proposed method allows one to rank each feature based on the signal-to-noise ratio and to ascertain for each feature the confidence level and power for being differentially expressed. The performance of the new method was evaluated using the total and partial area under receiver operating curves and tested on 11 data sets from Gene Omnibus Database with independently verified differentially expressed genes and compared with the t-test and shrinkage t-test. Overall the DFC test performed the best – on average it had higher sensitivity and partial AUC and its elevation was most prominent in the low range of differentially expressed features, typical for formalin-fixed paraffin-embedded sample sets

  17. Characterization of the allergenic potential of proteins: an assessment of the kiwifruit allergen actinidin.

    Science.gov (United States)

    Dearman, Rebecca J; Beresford, Lorna; Foster, Emily S; McClain, Scott; Kimber, Ian

    2014-05-01

    Assessment of the potential allergenicity (IgE-inducing properties) of novel proteins is an important challenge in the overall safety assessment of foods. Resistance to digestion with pepsin is commonly measured to characterize allergenicity, although the association is not absolute. We have previously shown that specific IgE antibody production induced by systemic [intraperitoneal (i.p.)] exposure of BALB/c strain mice to a range of proteins correlates with allergenic potential for known allergens. The purpose of the present study was to explore further the utility of these approaches using the food allergen, actinidin. Recently, kiwifruit has become an important allergenic foodstuff, coincident with its increased consumption, particularly as a weaning food. The ability of the kiwifruit allergen actinidin to stimulate antibody responses has been compared with the reference allergen ovalbumin, and with the non-allergen bovine haemoglobin. Haemoglobin was rapidly digested by pepsin whereas actinidin was resistant unless subjected to prior chemical reduction (reflecting intracellular digestion conditions). Haemoglobin stimulated detectable IgG antibody production at relatively high doses (10%), but failed to provoke detectable IgE. In contrast, actinidin was both immunogenic and allergenic at relatively low doses (0.25% to 1%). Vigorous IgG and IgG1 antibody and high titre IgE antibody responses were recorded, similar to those provoked by ovalbumin. Thus, actinidin displays a marked ability to provoke IgE, consistent with allergenic potential. These data provide further encouragement that in tandem with analysis of pepsin stability, the induction of IgE after systemic exposure of BALB/c strain mice provides a useful approach for the prospective identification of protein allergens. PMID:23754484

  18. Hymenoptera allergens: from venom to "venome".

    Science.gov (United States)

    Spillner, Edzard; Blank, Simon; Jakob, Thilo

    2014-01-01

    In Western Europe, Hymenoptera venom allergy (HVA) primarily relates to venoms of the honeybee and the common yellow jacket. In contrast to other allergen sources, only a few major components of Hymenoptera venoms had been characterized until recently. Improved expression systems and proteomic detection strategies have allowed the identification and characterization of a wide range of additional allergens. The field of HVA research has moved rapidly from focusing on venom extract and single major allergens to a molecular understanding of the entire "venome" as a system of unique and characteristic components. An increasing number of such components has been identified, characterized regarding function, and assessed for allergenic potential. Moreover, advanced expression strategies for recombinant production of venom allergens allow selective modification of molecules and provide insight into different types of immunoglobulin E reactivities and sensitization patterns. The obtained information contributes to an increased diagnostic precision in HVA and may serve for monitoring, re-evaluation, and improvement of current therapeutic strategies. PMID:24616722

  19. Use of a Microarray to Detect Expression of Genes for Lignin-Degrading Enzymes in Soil Fungi

    Science.gov (United States)

    Bailey, V. L.; Smith, J. L.; Bolton, H.

    2003-12-01

    Lignin is a complex biopolymer that is degraded by fungi. Several extracellular enzymes have been implicated in degradation and include lignin peroxidases, laccases, manganese peroxidases, and glyoxal oxidases. Versions of these enzymes are produced by multiple species of fungi, and in some cases, multiple versions of a single enzyme may be produced by the same species of fungus. Previous research has indicated changes in fungal activity and diversity along a tallgrass prairie restoration chronosequence (Fermi National Lab, IL). A cDNA microarray was designed to interrogate the expression and microbial source of these lignin degrading enzymes in the chronosequence soils. We hypothesized that less diversity in gene expression would be detected in a farmed soil than in a restored prairie soil. The array had 46 oligonucleotides (15-25mer) that represent each of the enzymes listed above. Messenger RNA was extracted from 32 one-gram subsamples of the target soils then all of the extracts were pooled prior to RNA precipitation and mRNA purification. Aminoallyl modified dUTPs were incorporated during reverse transcription, after which the cDNA was labeled with Alexa-555 dye. The labeled cDNA was hybridized with the microarray for 24 hours and then imaged. Preliminary results support the hypothesis that fewer genes were expressed in the farmed soil than in the restored soil.

  20. PAX3 gene deletion detected by microarray analysis in a girl with hearing loss.

    Science.gov (United States)

    Drozniewska, Malgorzata; Haus, Olga

    2014-01-01

    Deletions of the PAX3 gene have been rarely reported in the literature. Mutations of this gene are a common cause of Waardenburg syndrome type 1 and 3. We report a 16 year old female presenting hearing loss and normal intellectual development, without major features of Waardenburg syndrome type 1, and without family history of the syndrome. Her phenotype, however, overlaps with features of craniofacial-deafness-hand syndrome. Microarray analysis showed ~862 kb de novo deletion at 2q36.1 including PAX3. The above findings suggest that the rearrangement found in our patient appeared de novo and with high probability is a cause of her phenotype. PMID:24839464

  1. Allergens in veterinary medicine

    OpenAIRE

    Mueller, R. S.; Janda, J; Jensen-Jarolim, E.; Rhyner, C; Marti, E.

    2015-01-01

    Allergic diseases in animals are increasingly gaining importance in veterinary practice and as research models. For intradermal testing and allergen immunotherapy, a good knowledge of relevant allergens for the individual species is of great importance. Currently, the knowledge about relevant veterinary allergens is based on sensitization rates identified by intradermal testing or serum testing for allergen-specific IgE; crude extracts are the basis for most evaluations. Only a few studies pr...

  2. 5岁以下有喘息症状儿童过敏原检测及临床意义%Detection of Serum Allergen in Wheezing Children Under 5 Years Old and Its Significance

    Institute of Scientific and Technical Information of China (English)

    何莉; 王健; 刘莲香

    2011-01-01

    [目的]探讨5岁以下有喘息症状儿童血清过敏原特异性IgE检测在儿童哮喘诊断中的临床意义.[方法]采用德国Mediwiss公司Allergy-screen Analytic GmbH过敏原检测系统,对73例有喘息症状的5岁以下儿童患儿进行血清吸入性和食入性过敏原特异性IgE检测,对过敏原状况进行分析.[结果]大多数5岁以下有喘息症状的儿童具有特异性体质.吸入性过敏原阳性率为19.36%,食入过敏原阳性率为10.87%.[结论]血清特异性过敏原阳性是有喘息症状的儿童发展成为生哮喘的高危因素之一.检测5岁以下有喘息症状的患儿血清吸入性和食入性过敏原特异性IgE,有利于早期识别有可能发展为哮喘的儿童.%[Objective]To explore the detection of serum inhalant and ingestive allergen specific IgE in wheezing children under 5 years old and its significance in the diagnosis of childhood asthma. [Methods]Getman Mediwiss Company Λllergy-screen Λnalytic GmbH allergen detection system was used to detect serum inhalant and ingestive allergen specific IgE in 73 wheezing children under 5 years old. The status of allergens was analyzed. [Results]Most of wheezing children under 5 years old had atopic asthmatic constitution. The positive rate of inhalant allergen and ingestive allergen was 19.36 % and 10.87%, respectively. [Conclusion] Positive serum allergen is one of the risk factors for wheezing children developing to asthma. The detection of serum inhalation and ingestive allergen specific IgE in wheezing children under 5 years old is helpful for the early identification of possible asthma children developed from wheezing.

  3. Magnetic particles functionalized with PAMAM-dendrimers and antibodies: a new system for an ELISA method able to detect Ara h3/4 peanut allergen in foods.

    Science.gov (United States)

    Speroni, Francesca; Elviri, Lisa; Careri, Maria; Mangia, Alessandro

    2010-08-01

    An innovative enzyme-linked immunosorbent assay (ELISA) format based on antibody-coated magnetic micro-particles (MPs) for the sensitive detection of Ara h3/4 allergen in food is described. The immunosupport is suspended in the incubation solutions and the MPs with the captured allergen can be easily harvested on a magnet, separated from the solutions, and washed using an easy-to-use, fast and selective approach that allows its detection and quantification. Two differently coated MPs, ProteinA-Pn-b and MP-NH(2)-PAMAM G 1.5-Pn-b immunosupports, were tested. The functionalization of the MPs with PAMAM-sodium carboxylate dendrimers elicits a major stability on the immunoglobulin activity resulting in a threefold enhancement of the analytical sensitivity for the assay with respect to a ProteinA immobilization. Validation was carried out on two different matrices: corn flakes and biscuits. In the case of MP-NH(2)-PAMAM G 1.5 -Pn-b immunosupport, limit of detection was found to be 0.2 mg peanuts/kg matrix in both matrices; the linear response range was demonstrated from 2.5 to 15 mg peanuts/kg matrix by performing statistical tests (homoscedasticity and Mandel fitting tests). Good accuracy and recovery (>80 +/- 2%) were obtained. Different food samples were tested and the results were compared with those obtained with a commercially available ELISA kit. The results obtained in this work demonstrated the applicability of the immunomagnetic ELISA methods on real samples and the possibility to perform the assay with significantly reduced reagent and sample consumption. PMID:20607526

  4. Allergens in veterinary medicine.

    Science.gov (United States)

    Mueller, R S; Janda, J; Jensen-Jarolim, E; Rhyner, C; Marti, E

    2016-01-01

    Allergic diseases in animals are increasingly gaining importance in veterinary practice and as research models. For intradermal testing and allergen immunotherapy, a good knowledge of relevant allergens for the individual species is of great importance. Currently, the knowledge about relevant veterinary allergens is based on sensitization rates identified by intradermal testing or serum testing for allergen-specific IgE; crude extracts are the basis for most evaluations. Only a few studies provide evidence about the molecular structure of (particularly) dust mite, insect and mould allergens in dogs and horses, respectively. In those species, some major allergens differ from those in humans. This position paper summarizes the current knowledge about relevant allergens in dogs, cats and horses. PMID:26280544

  5. Exposure to indoor allergens and association with allergy symptoms of employees in a work environment

    Directory of Open Access Journals (Sweden)

    Barbara Brunetto

    2009-12-01

    Full Text Available Exposure to indoor allergens is an important risk factor for sensitisation and respiratory allergy. The aim of this paper was to evaluate the levels of mite, cat and latex allergens in dust collected from an indoor workplace and to assess whether the exposure to these allergens was associated with the allergy symptoms reported by employees. Sixty dust samples were collected. Allergen concentrations were measured with antibody based ELISAs. All 144 participants compiled a questionnaire exploring possible symptoms of allergy. No association between latex allergen exposure and symptoms was found in spite of the high frequency of latex allergens. Mite allergens were detected in a minority of rooms. Cat allergen was the most important indoor allergen in the sampled workplace and exposure to this allergen could represent a risk for employees.

  6. Enhancing the Sensitivity of DNA Microarray Using Dye-Doped Silica Nanoparticles: Detection of Human Papilloma Virus

    Science.gov (United States)

    Enrichi, F.; Riccò, R.; Meneghello, A.; Pierobon, R.; Canton, G.; Cretaio, E.

    2010-10-01

    DNA microarray is a high-throughput technology used for detection and quantification of nucleic acid molecules and others of biological interest. The analysis is based on the specific hybridization between probe sequences deposited in array and a target ss-DNA amplified by PCR and functionalized by a fluorescent dye. Organic labels have well known disadvantages like photobleaching and low signal intensities, which put a limitation to the lower amount of DNA material that can be detected. Therefore for trace analysis the development of more efficient biomarkers is required. With this aim we present in this paper the synthesis and application of alternative hybrid nanosystems obtained by incorporating standard fluorescent molecules into monodisperse silica nanoparticles. Efficient application to the detection of Human Papilloma Virus is demonstrated. This virus is associated to the formation of cervical cancer, a leading cause of death by cancer for women worldwide. It is shown that the use of the novel biomarkers increases the optical signal of about one order of magnitude with respect to the free dyes or quantum dots in conventional instruments. This is due to the high number of molecules that can be accommodated into each nanoparticle, to the reduced photobleaching and to the improved environmental protection of the dyes when encapsulated in the silica matrix. The cheap and easy synthesis of these luminescent particles, the stability in water, the surface functionalizability and bio-compatibility make them very promising for present and future bio-labeling and bio-imaging applications.

  7. Identification of Escherichia coli O157 by Using a Novel Colorimetric Detection Method with DNA Microarrays

    Science.gov (United States)

    Shiga toxin-producing Escherichia coli O157:H7 is a leading cause of foodborne illness worldwide. To evaluate better methods to rapidly detect and genotype E. coli O157 strains, the present study evaluated the use of ampliPHOX, a novel colorimetric detection method based on photopolymerization, for...

  8. Multicenter Evaluation of a New DNA Microarray for Rapid Detection of Clinically Relevant bla Genes from ? -Lactam-Resistant Gram-Negative Bacteria

    OpenAIRE

    Bogaerts, P.; Hujer, A.M.; Naas, T.; de Castro, R. R.; A. Endimiani; Nordmann, P.; Glupczynski, Y.; Bonomo, R.A.

    2011-01-01

    A new commercial low-density microarray which identifies common extended-spectrum β-lactamase plasmid-mediated cephalosporinase genes, as well as carbapenemase (blaKPC and blaNDM) genes, was evaluated. We tested 207 clinical and reference/collection isolates of the Enterobacteriaceae possessing different bla genes. Overall, the sensitivity and specificity of the microarray were 100% for the detection of the plasmid-mediated blaAmpC, blaKPC, and blaNDM genes using bla gene sequencing as the re...

  9. Evaluation of the Broad-Range PCR-Electrospray Ionization Mass Spectrometry (PCR/ESI-MS System and Virus Microarrays for Virus Detection

    Directory of Open Access Journals (Sweden)

    Lanyn P. Taliaferro

    2014-04-01

    Full Text Available Advanced nucleic acid-based technologies are powerful research tools for novel virus discovery but need to be standardized for broader applications such as virus detection in biological products and clinical samples. We have used well-characterized retrovirus stocks to evaluate the limit of detection (LOD for broad-range PCR with electrospray ionization mass spectrometry (PCR/ESI-MS or PLEX-ID, RT-PCR assays, and virus microarrays. The results indicated that in the absence of background cellular nucleic acids, PLEX-ID and RT-PCR had a similar LOD for xenotropic murine retrovirus-related virus (XMRV; 3.12 particles per µL whereas sensitivity of virus detection was 10-fold greater using virus microarrays. When virus was spiked into a background of cellular nucleic acids, the LOD using PLEX-ID remained the same, whereas virus detection by RT-PCR was 10-fold less sensitive, and no virus could be detected by microarrays. Expected endogenous retrovirus (ERV sequences were detected in cell lines tested and known species-specific viral sequences were detected in bovine serum and porcine trypsin. A follow-up strategy was developed using PCR amplification, nucleotide sequencing, and bioinformatics to demonstrate that an RD114-like retrovirus sequence that was detected by PLEX-ID in canine cell lines (Madin-Darby canine kidney (MDCK and Cf2Th canine thymus was due to defective, endogenous gammaretrovirus-related sequences.

  10. Hybrid microarray based on double biomolecular markers of DNA and carbohydrate for simultaneous genotypic and phenotypic detection of cholera toxin-producing Vibrio cholerae.

    Science.gov (United States)

    Shin, Hwa Hui; Seo, Jeong Hyun; Kim, Chang Sup; Hwang, Byeong Hee; Cha, Hyung Joon

    2016-05-15

    Life-threatening diarrheal cholera is usually caused by water or food contaminated with cholera toxin-producing Vibrio cholerae. For the prevention and surveillance of cholera, it is crucial to rapidly and precisely detect and identify the etiological causes, such as V. cholerae and/or its toxin. In the present work, we propose the use of a hybrid double biomolecular marker (DBM) microarray containing 16S rRNA-based DNA capture probe to genotypically identify V. cholerae and GM1 pentasaccharide capture probe to phenotypically detect cholera toxin. We employed a simple sample preparation method to directly obtain genomic DNA and secreted cholera toxin as target materials from bacterial cells. By utilizing the constructed DBM microarray and prepared samples, V. cholerae and cholera toxin were detected successfully, selectively, and simultaneously; the DBM microarray was able to analyze the pathogenicity of the identified V. cholerae regardless of whether the bacteria produces toxin. Therefore, our proposed DBM microarray is a new effective platform for identifying bacteria and analyzing bacterial pathogenicity simultaneously. PMID:26735874

  11. HYMENOPTERA ALLERGENS: FROM VENOM TO VENOME

    OpenAIRE

    Edzard eSpillner; Simon eBlank; Thilo eJakob

    2014-01-01

    In Western Europe hymenoptera venom allergy primarily relates to venoms of the honeybee and the common yellow jacket. In contrast to other allergen sources, only a few major components of hymenoptera venoms had been characterized until recently. Improved expression systems and proteomic detection strategies have allowed the identification and characterization of a wide range of additional allergens. The field of hymenoptera venom allergy research has moved rapidly from focusing on venom extr...

  12. Detection and characterization of human pathogenic viruses circulating in community wastewater using multi target microarrays and polymerase chain reaction.

    Science.gov (United States)

    Wong, Mark V M; Hashsham, Syed A; Gulari, Erdogan; Rouillard, Jean-Marie; Aw, Tiong Gim; Rose, Joan B

    2013-12-01

    Sewage pollution remains the most significant source of human waterborne pathogens. This study describes the detection and characterization of human enteric viruses in community wastewaters using cell culture coupled with multiple target microarrays (with a total of 780 unique probes targeting 27 different groups of both DNA and RNA viruses) and polymerase chain reaction (PCR) assays. Over a 13-month sampling period, RNA viruses (astroviruses and enteroviruses) were more frequently detected compared to DNA viruses (adenoviruses, particularly type 41 and BK polyomavirus). Overall, many more viruses were shed during the winter months (December-February) compared to the summer months. Exploration of the multiple types of enteric viruses particularly in winter months identified much more significant prevalence of key viral pathogens associated with sewage pollution of the water environment than previously realized and seasonal disinfection used in some parts of the world may lead to a seeding of ambient waters. Molecular characterization of pathogenic viruses in community wastewater will improve the understanding of the potential risk of waterborne disease transmission of viral pathogens. PMID:24334840

  13. Microarrays - new possibilities for detecting biological factors hazardous for humans and animals, and for use in environmental protection.

    Science.gov (United States)

    Mirski, Tomasz; Bartoszcze, Michał; Bielawska-Drózd, Agata; Gryko, Romuald; Niemcewicz, Marcin; Kocik, Janusz; Chomiczewski, Krzysztof

    2016-03-01

    Both the known biological agents that cause infectious diseases, as well as modified (ABF-Advanced Biological Factors) or new, emerging agents pose a significant diagnostic problem using previously applied methods, both classical, as well as based on molecular biology methods. The latter, such as PCR and real-time PCR, have significant limitations, both quantitative (low capacity), and qualitative (limited number of targets). The article discusses the results of studies on using the microarray method for the identification of viruses (e.g. Orthopoxvirus group, noroviruses, influenza A and B viruses, rhino- and enteroviruses responsible for the FRI (Febrile Respiratory Illness), European bunyaviruses, and SARS-causing viruses), and bacteria (Mycobacterium spp., Yersinia spp., Campylobacter spp., Streptococcus pneumoniae, Salmonella typhi, Salmonella enterica, Staphylococcus aureus, Neisseria meningitidis, Clostridium difficile , Helicobacter pylori), including multiple antibiotic-resistant strains. The method allows for the serotyping and genotyping of bacteria, and is useful in the diagnosis of genetically modified agents. It allows the testing of thousands of genes in one experiment. In addition to diagnosis, it is applicable for gene expression studies, analysis of the function of genes, microorganisms virulence, and allows the detection of even single mutations. The possibility of its operational application in epidemiological surveillance, and in the detection of disease outbreak agents is demonstrated. PMID:27007515

  14. Detection of analyte binding to microarrays using gold nanoparticle labels and a desktop scanner

    DEFF Research Database (Denmark)

    Han, Anpan; Dufva, Martin; Belleville, Erik;

    2003-01-01

    on gold nanoparticle labeled antibodies visualized by a commercial, office desktop flatbed scanner. Scanning electron microscopy studies showed that the signal from the flatbed scanner was proportional to the surface density of the bound antibody-gold conjugates, and that the flatbed scanner could...... detect six attomoles of antibody-gold conjugates. This detection system was used in a competitive immunoassay to measure the concentration of the pesticide metabolite 2,6-dichlorobenzamide (BAM) in water samples. The results showed that the gold labeled antibodies functioned comparably with a fluorescent...... based immunoassay for detecting BAM in water. A qualitative immunoassay based on gold-labeled antibodies could determineif a water sample contained BAM above and below 60-70 ng L(-1), which is below the maximum allowed BAM concentration for drinking water (100 ng L(-1)) according to European Union...

  15. Detection of Extended-Spectrum β-Lactamase and Klebsiella pneumoniae Carbapenemase Genes Directly from Blood Cultures by Use of a Nucleic Acid Microarray

    OpenAIRE

    Fishbain, Joel T.; Sinyavskiy, Oleg; Riederer, Kathleen; Hujer, Andrea M.; Robert A Bonomo

    2012-01-01

    The growing crisis of multidrug-resistant (MDR) Gram-negative bacteria requires that current technologies permit the rapid detection of extended-spectrum β-lactamase (blaESBL) and Klebsiella pneumoniae carbapenemase (blaKPC) genes. In the present study, we assessed the performance characteristics of a commercially available nucleic acid microarray system for the detection of blaESBL and blaKPC genes directly from positive blood cultures. Using blood cultures (BCs) that contained Gram-negative...

  16. A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells

    Directory of Open Access Journals (Sweden)

    Kloster Maria

    2012-11-01

    Full Text Available Abstract Background Malignant cells in tumours of B-cell origin account for 0.1% to 98% of the total cell content, depending on disease entity. Recently, gene expression profiles (GEPs of B-cell lymphomas based on microarray technologies have contributed significantly to improved sub-classification and diagnostics. However, the varying degrees of malignant B-cell frequencies in analysed samples influence the interpretation of the GEPs. Based on emerging next-generation sequencing technologies (NGS like tag sequencing (tag-seq for GEP, it is expected that the detection of mRNA transcripts from malignant B-cells can be supplemented. This study provides a quantitative assessment and comparison of the ability of microarrays and tag-seq to detect mRNA transcripts from malignant B-cells. A model system was established by eight serial dilutions of the malignant B-cell lymphoma cell line, OCI-Ly8, into the embryonic kidney cell line, HEK293, prior to parallel analysis by exon microarrays and tag-seq. Results We identified 123 and 117 differentially expressed genes between pure OCI-Ly8 and HEK293 cells by exon microarray and tag-seq, respectively. There were thirty genes in common, and of those, most were B-cell specific. Hierarchical clustering from all dilutions based on the differentially expressed genes showed that neither technology could distinguish between samples with less than 1% malignant B-cells from non-B-cells. A novel statistical concept was developed to assess the ability to detect single genes for both technologies, and used to demonstrate an inverse proportional relationship with the sample purity. Of the 30 common genes, the detection capability of a representative set of three B-cell specific genes - CD74, HLA-DRA, and BCL6 - was analysed. It was noticed that at least 5%, 13% and 22% sample purity respectively was required for detection of the three genes by exon microarray whereas at least 2%, 4% and 51% percent sample purity of

  17. Real-time detection of DNA hybridization on microarray using a CCD-based imaging system equipped with a rotated microlens array disk.

    Science.gov (United States)

    Mogi, Takeyuki; Hatakeyama, Keiichi; Taguchi, Tomoyuki; Wake, Hitoshi; Tanaami, Takeo; Hosokawa, Masahito; Tanaka, Tsuyoshi; Matsunaga, Tadashi

    2011-01-15

    This work describes a novel charge-coupled device (CCD)-based imaging system (MB Biochip Reader™) for real-time detection of DNA hybridization to DNA microarrays. The MB Biochip Reader™ consisted of a laser light source (532 nm), a microlens array for generation of a multi-beam laser, and a CCD for 2-D signal imaging. The MB Biochip Reader™ with a rotated microlens array, allowed large-field imaging (6.2 mm × 7.6 mm with 6.45 μm resolution) with fast time-resolution at 0.2 s without speckle noise. Furthermore, real-time detection of DNA hybridization, which is sufficient to obtain accurate data from tens of thousands of array element per field, was successfully performed without the need for laser scanning. The performance of the MB Biochip Reader™ for DNA microarray imaging was similar to the commercially available photomultiplier tube (PMT)-based microarray scanner, ScanArray Lite. The system potentially could be applied toward real-time analysis in many other fluorescent techniques in addition to real-time DNA microarray analysis. PMID:20951567

  18. Microfluidic microarray systems and methods thereof

    Science.gov (United States)

    West, Jay A. A.; Hukari, Kyle W.; Hux, Gary A.

    2009-04-28

    Disclosed are systems that include a manifold in fluid communication with a microfluidic chip having a microarray, an illuminator, and a detector in optical communication with the microarray. Methods for using these systems for biological detection are also disclosed.

  19. Application of a liquid chromatography tandem mass spectrometry method for the simultaneous detection of seven allergenic foods in flour and bread and comparison of the method with commercially available ELISA test kits.

    Science.gov (United States)

    Heick, Julia; Fischer, Markus; Kerbach, Sandra; Tamm, Ulrike; Popping, Bert

    2011-01-01

    To protect the allergic consumer, analytical methods need to be capable of detecting allergens in finished products that typically contain multiple allergens. An LC/MS/MS method for simultaneous detection of seven allergens was developed and compared with commercially available ELISA kits. The detection capabilities of this novel method were demonstrated by analyzing incurred material containing milk, egg, soy, peanut, hazelnut, walnut, and almond. Bread was chosen as a model matrix. To assess the influence of baking on the method's performance, analysis was done before and after baking. The same samples were analyzed with ELISA test kits from ELISA Systems, Morinaga, Neogen, and r-Biopharm. Peanut, hazelnut, walnut, and almond could be detected with both ELISA and LC/MS/MS regardless of whether the product was baked or not. LC/MS/MS clearly showed superior detection of milk in processed matrixes compared to ELISA, which exhibited significantly lower sensitivities when analyzing the baked products. Similar results were obtained when analyzing egg; however, one kit was capable of detecting egg in the processed samples as well. PMID:21919338

  20. Development and evaluation of a DNA microarray assay for the simultaneous detection of nine harmful algal species in ship ballast and seaport waters

    Science.gov (United States)

    Chen, Xianfeng; Zhou, Qianjin; Duan, Weijun; Zhou, Chengxu; Duan, Lijun; Zhang, Huili; Sun, Aili; Yan, Xiaojun; Chen, Jiong

    2016-01-01

    Rapid, high-throughput and reliable methods are urgently required to accurately detect and monitor harmful algae, which are responsible for algal blooms, such as red and green tides. In this study, we successfully developed a multiplex PCR-based DNA microarray method capable of detecting nine harmful algal species simultaneously, namely Alexandrium tamarense, Gyrodinium instriatum, Heterosigma akashiwo, Karenia mikimotoi, Prorocentrum donghaiense, Prorocentrum minimum, Ulva compressa, Ulva ohnoi and Ulva prolifera. This method achieved a limit of detection (LOD) of 0.5 ng of genomic DNA (orders of magnitude of the deci-nanogram range) in the tested algae cultures. Altogether, 230 field samples from ship ballast waters and seaport waters were used to evaluate the DNA microarray. The clinical sensitivity and specificity of the DNA microarray assay in detecting field samples were 96.4% and 90.9%, respectively, relative to conventional morphological methods. This indicated that this high-throughput, automatic, and specific method is well suited for the detection of algae in water samples.

  1. High-throughput Microarray Detection of Vomeronasal Receptor Gene Expression in Rodents

    OpenAIRE

    FlorenciaMarcucci

    2010-01-01

    We performed comprehensive data mining to explore the vomeronasal receptor (V1R & V2R) repertoires in mouse and rat using the mm5 and rn3 genome, respectively. This bioinformatic analysis was followed by investigation of gene expression using a custom designed high-density oligonucleotide array containing all of these receptors and other selected genes of interest. This array enabled us to detect the specific expression of V1R and V2Rs which were previously identified solely based on computa...

  2. High-Throughput Microarray Detection of Vomeronasal Receptor Gene Expression in Rodents

    OpenAIRE

    Zhang, Xiaohong; Marcucci, Florencia; Firestein, Stuart

    2010-01-01

    We performed comprehensive data mining to explore the vomeronasal receptor (V1R and V2R) repertoires in mouse and rat using the mm5 and rn3 genome, respectively. This bioinformatic analysis was followed by investigation of gene expression using a custom designed high-density oligonucleotide array containing all of these receptors and other selected genes of interest. This array enabled us to detect the specific expression of V1R and V2Rs which were previously identified solely based on comput...

  3. Detection of EBV Infection and Gene Expression in Oral Cancer from Patients in Taiwan by Microarray Analysis

    Directory of Open Access Journals (Sweden)

    Ching-Yu Yen

    2009-01-01

    Full Text Available Epstein-Barr virus is known to cause nasopharyngeal carcinoma. Although oral cavity is located close to the nasal pharynx, the pathogenetic role of Epstein-Barr virus (EBV in oral cancers is unclear. This molecular epidemiology study uses EBV genomic microarray (EBV-chip to simultaneously detect the prevalent rate and viral gene expression patterns in 57 oral squamous cell carcinoma biopsies (OSCC collected from patients in Taiwan. The majority of the specimens (82.5% were EBV-positive that probably expressed coincidently the genes for EBNAs, LMP2A and 2B, and certain structural proteins. Importantly, the genes fabricated at the spots 61 (BBRF1, BBRF2, and BBRF3 and 68 (BDLF4 and BDRF1 on EBV-chip were actively expressed in a significantly greater number of OSCC exhibiting exophytic morphology or ulceration than those tissues with deep invasive lesions (P=.0265 and .0141, resp.. The results may thus provide the lead information for understanding the role of EBV in oral cancer pathogenesis.

  4. The human allergens of mesquite (Prosopis juliflora

    Directory of Open Access Journals (Sweden)

    Killian Sue

    2004-07-01

    Full Text Available Abstract Background A computerized statistical analysis of allergy skin test results correlating patient reactivities initiated our interest in the cross-reactive allergens of mesquite tree pollen. In-vitro testing with mesquite-sensitized rabbits and a variety of deciduous tree pollens revealed so many cross-reactivities that it became apparent there could be more allergens in mesquite than previously described in the world literature. Our purpose was to examine the allergens of mesquite tree pollen (Prosopis juliflora which elicit an IgE response in allergic humans so that future research could determine if these human allergens cross-react with various tree pollens in the same manner as did the mesquite antiserum from sensitized rabbits. Methods Proteins from commercial mesquite tree pollen were separated by polyacrylamide gel electrophoresis in the presence of sodium-dodecyl-sulphate. These mesquite proteins were subjected to Western blotting using pooled sera from ten mesquite-sensitive patients and goat anti-human IgE. The allergens were detected using an Amplified Opti-4-CN kit, scanned, and then interpreted by Gel-Pro software. Results Thirteen human allergens of mesquite pollen were detected in this study. Conclusion The number of allergens in this study of mesquite exceeded the number identified previously in the literature. With the increased exposure to mesquite through its use in "greening the desert", increased travel to desert areas and exposure to mesquite in cooking smoke, the possible clinical significance of these allergens and their suggested cross-reactivity with other tree pollens merit further study.

  5. High-throughput Microarray Detection of Vomeronasal Receptor Gene Expression in Rodents

    Directory of Open Access Journals (Sweden)

    Xiaohong Zhang

    2010-11-01

    Full Text Available We performed comprehensive data mining to explore the vomeronasal receptor (V1R & V2R repertoires in mouse and rat using the mm5 and rn3 genome, respectively. This bioinformatic analysis was followed by investigation of gene expression using a custom designed high-density oligonucleotide array containing all of these receptors and other selected genes of interest. This array enabled us to detect the specific expression of V1R and V2Rs which were previously identified solely based on computational prediction from gene sequence data, thereby establishing that these genes are indeed part of the vomeronasal system, especially the V2Rs. 168 V1Rs and 98 V2Rs were detected to be highly enriched in mouse vomeronasal organ (VNO, and 108 V1Rs and 87 V2Rs in rat VNO. We monitored the expression profile of mouse VR genes in other non-VNO tissues with the result that some VR genes were re-designated as VR-like genes based on their non-olfactory expression pattern. Temporal expression profiles for mouse VR genes were characterized and their patterns were classified, revealing the developmental dynamics of these so-called pheromone receptors. We found numerous patterns of temporal expression which indicate possible behavior-related functions. The uneven composition of VR genes in certain patterns suggests a functional differentiation between the two types of VR genes. We found the coherence between VR genes and transcription factors in terms of their temporal expression patterns. In situ hybridization experiments were performed to evaluate the cell number change over time for selected receptor genes.

  6. Fluorescence of atopic allergens

    NARCIS (Netherlands)

    Berrens, L.

    1967-01-01

    Purified atopic allergens have been found to emit flue fluorescence upon irradiation with ultraviolet light of 365 mμ wavelength. The maximum of fluorescence is in the region 445–490 mμ and the intensity is of the same order of magnitude for different atopic allergens. Synthetic model compounds, inc

  7. Microbial distributions detected by an oligonucleotide microarray across geochemical zones associated with methane in marine sediments from the Ulleung Basin

    Energy Technology Data Exchange (ETDEWEB)

    Briggs, Brandon R; Graw, Michael; Brodie, Eoin L; Bahk, Jang-Jun; Kim, Sung-Han; Hyun, Jung-Ho; Kim, Ji-Hoon; Torres, Marta; Colwell, Frederick S

    2013-11-01

    The biogeochemical processes that occur in marine sediments on continental margins are complex; however, from one perspective they can be considered with respect to three geochemical zones based on the presence and form of methane: sulfate–methane transition (SMTZ), gas hydrate stability zone (GHSZ), and free gas zone (FGZ). These geochemical zones may harbor distinct microbial communities that are important in biogeochemical carbon cycles. The objective of this study was to describe the microbial communities in sediments from the SMTZ, GHSZ, and FGZ using molecular ecology methods (i.e. PhyloChip microarray analysis and terminal restriction fragment length polymorphism (T-RFLP)) and examining the results in the context of non-biological parameters in the sediments. Non-metric multidimensional scaling and multi-response permutation procedures were used to determine whether microbial community compositions were significantly different in the three geochemical zones and to correlate samples with abiotic characteristics of the sediments. This analysis indicated that microbial communities from all three zones were distinct from one another and that variables such as sulfate concentration, hydrate saturation of the nearest gas hydrate layer, and depth (or unmeasured variables associated with depth e.g. temperature, pressure) were correlated to differences between the three zones. The archaeal anaerobic methanotrophs typically attributed to performing anaerobic oxidation of methane were not detected in the SMTZ; however, the marine benthic group-B, which is often found in SMTZ, was detected. Within the GHSZ, samples that were typically closer to layers that contained higher hydrate saturation had indicator sequences related to Vibrio-type taxa. These results suggest that the biogeographic patterns of microbial communities in marine sediments are distinct based on geochemical zones defined by methane.

  8. Application of high-density DNA resequencing microarray for detection and characterization of botulinum neurotoxin-producing clostridia.

    Directory of Open Access Journals (Sweden)

    Jessica Vanhomwegen

    Full Text Available BACKGROUND: Clostridium botulinum and related clostridia express extremely potent toxins known as botulinum neurotoxins (BoNTs that cause severe, potentially lethal intoxications in humans. These BoNT-producing bacteria are categorized in seven major toxinotypes (A through G and several subtypes. The high diversity in nucleotide sequence and genetic organization of the gene cluster encoding the BoNT components poses a great challenge for the screening and characterization of BoNT-producing strains. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we designed and evaluated the performances of a resequencing microarray (RMA, the PathogenId v2.0, combined with an automated data approach for the simultaneous detection and characterization of BoNT-producing clostridia. The unique design of the PathogenID v2.0 array allows the simultaneous detection and characterization of 48 sequences targeting the BoNT gene cluster components. This approach allowed successful identification and typing of representative strains of the different toxinotypes and subtypes, as well as the neurotoxin-producing C. botulinum strain in a naturally contaminated food sample. Moreover, the method allowed fine characterization of the different neurotoxin gene cluster components of all studied strains, including genomic regions exhibiting up to 24.65% divergence with the sequences tiled on the arrays. CONCLUSIONS/SIGNIFICANCE: The severity of the disease demands rapid and accurate means for performing risk assessments of BoNT-producing clostridia and for tracing potentials sources of contamination in outbreak situations. The RMA approach constitutes an essential higher echelon component in a diagnostics and surveillance pipeline. In addition, it is an important asset to characterise potential outbreak related strains, but also environment isolates, in order to obtain a better picture of the molecular epidemiology of BoNT-producing clostridia.

  9. Fabrication of Homogeneous High-Density Antibody Microarrays for Cytokine Detection

    Directory of Open Access Journals (Sweden)

    Ingeborg Hospach

    2014-12-01

    Full Text Available Cytokine proteins are known as biomarker molecules, characteristic of a disease or specific body condition. Monitoring of the cytokine pattern in body fluids can contribute to the diagnosis of diseases. Here we report on the development of an array comprised of different anti-cytokine antibodies on an activated solid support coupled with a fluorescence readout mechanism. Optimization of the array preparation was done in regard of spot homogeneity and spot size. The proinflammatory cytokines Tumor Necrosis Factor alpha (TNFα and Interleukin 6 (IL-6 were chosen as the first targets of interest. First, the solid support for covalent antibody immobilization and an adequate fluorescent label were selected. Three differently functionalized glass substrates for spotting were compared: amine and epoxy, both having a two-dimensional structure, and the NHS functionalized hydrogel (NHS-3D. The NHS-hydrogel functionalization of the substrate was best suited to antibody immobilization. Then, the optimization of plotting parameters and geometry as well as buffer media were investigated, considering the ambient analyte theory of Roger Ekins. As a first step towards real sample studies, a proof of principle of cytokine detection has been established.

  10. Optimization of Enzymatic Hydrolysis Technology for Dust Mite Group 1 Allergen and Its Allergenic Detection%粉尘螨1类变应原的酶解工艺优化及其过敏原性检测

    Institute of Scientific and Technical Information of China (English)

    李秋雨; 姜玉新; 李朝品

    2012-01-01

    目的:优化粉尘螨1类变应原proDer f 1的酶解条件及探讨酶解产物的变应原性.方法:以水解度为指标,采用正交试验考察木瓜蛋白酶和胰蛋白酶水解proDerf1蛋白的最佳工艺;采用间接酶联免疫吸附试验(ELISA)检测酶解产物的过敏原性.结果:温度是影响proDer f 1蛋白水解效果的主要因素,其中木瓜蛋白酶最佳水解条件为pH 6.5,温度60℃,水解时间4h,酶用量4 000 U·g-1;胰蛋白酶最佳水解条件为pH 8.0,温度45℃,水解时间4h,酶用量5 000 U·g-1;ELISA检测表明与proDer f 1变应原相比,木瓜蛋白酶水解产物和胰蛋白酶水解产物的过敏原性均显著减低,且胰蛋白酶水解产物的过敏原性较木瓜蛋白酶水解产物的过敏原性低.结论:优选的粉尘螨1类变应原proDer f 1蛋白的酶解工艺可行,且变应原酶解后,过敏原性有不同程度减低,尤以胰酶水解产物变化最为显著.%Objective: To optimize enzymatic hydrolysis conditions of proDer f 1, and investigate allergenicity of enzymatic hydrolysate. Method: With hydrolysis degree as index, optimum hydrolysis technology of proDer f 1 was investigated by orthogonal test using papain and trypsin; Allergenicity of enzymatic hydrolysate was tested by ELISA. Result: Temperature was main factor affecting hydrolysis effect of proDer f 1, optimal hydrolysis conditions of proDer f 1 digested by papain were as follows: pH 6. 5, temperature 60 ℃ , hydrolysis time 4 h, the amount of papain 4 000 U·g-1 ; Optimum hydrolysis conditions of trypsin was pH 8. 0, temperature 45 ℃ , hydrolysis time 4 h, the amount of enzyme 5 000 U·g-1. Compared with proDer f 1 allergen, ELISA analysis showed that allergens were reduced significantly of papain hydrolysate and trypsin hydrolysate, allergen of trypsin hydrolysate was lower than papain hydrolysate. Conclusion: Optimized enzymatic hydrolysis process of proDer f 1 protein was feasible, and after enzymatic hydrolysis of

  11. Numerical and Structural Genomic Aberrations Are Reliably Detectable in Tissue Microarrays of Formalin-Fixed Paraffin-Embedded Tumor Samples by Fluorescence In-Situ Hybridization

    OpenAIRE

    Heike Horn; Julia Bausinger; Staiger, Annette M.; Maximilian Sohn; Christopher Schmelter; Kim Gruber; Claudia Kalla; M Michaela Ott; Andreas Rosenwald; German Ott

    2014-01-01

    Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH), especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs). We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE) tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL) specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- an...

  12. FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance

    Directory of Open Access Journals (Sweden)

    Dondorp Arjen M

    2009-10-01

    Full Text Available Abstract Background A number of molecular tools have been developed to monitor the emergence and spread of anti-malarial drug resistance to Plasmodium falciparum. One of the major obstacles to the wider implementation of these tools is the absence of practical methods enabling high throughput analysis. Here a new Zip-code array is described, called FlexiChip, linked to a dedicated software program, which largely overcomes this problem. Methods Previously published microarray probes detecting single-nucleotide polymorphisms (SNP associated with parasite resistance to anti-malarial drugs (ResMalChip were adapted for a universal microarray FlexiChip format. To evaluate the overall sensitivity of the FlexiChip package (microarray + software, the results of FlexiChip were compared to ResMalChip microarray, using the same extension probes and with the same PCR products. In both cases, sequence results were used as gold standard to calculate sensitivity and specificity. FlexiChip results obtained with a set of field isolates were then compared to those assessed in an independent reference laboratory. Results The FlexiChip package gave results identical to the ResMalChip results in 92.7% of samples (kappa coefficient 0.8491, with a standard error 0.021 and had a sensitivity of 95.88% and a specificity of 97.68% compared to the sequencing as the reference method. Moreover the method performed well compared to the results obtained in the reference laboratories, with 99.7% of identical results (kappa coefficient 0.9923, S.E. 0.0523. Conclusion Microarrays could be employed to monitor P. falciparum drug resistance markers with greater cost effectiveness and the possibility for high throughput analysis. The FlexiChip package is a promising tool for use in poor resource settings of malaria endemic countries.

  13. Nonlinear multi-photon laser wave-mixing optical detection in microarrays and microchips for ultrasensitive detection and separation of biomarkers for cancer and neurodegenerative diseases

    Science.gov (United States)

    Iwabuchi, Manna; Hetu, Marcel; Maxwell, Eric; Pradel, Jean S.; Ramos, Sashary; Tong, William G.

    2015-09-01

    Multi-photon degenerate four-wave mixing is demonstrated as an ultrasensitive absorption-based optical method for detection, separation and identification of biomarker proteins in the development of early diagnostic methods for HIV- 1, cancer and neurodegenerative diseases using compact, portable microarrays and capillary- or microchip-based chemical separation systems that offer high chemical specificity levels. The wave-mixing signal has a quadratic dependence on concentration, and hence, it allows more reliable monitoring of smaller changes in analyte properties. Our wave-mixing detection sensitivity is comparable or better than those of current methods including enzyme-linked immunoassay for clinical diagnostic and screening. Detection sensitivity is excellent since the wave-mixing signal is a coherent laser-like beam that can be collected with virtually 100% collection efficiency with high S/N. Our analysis time is short (1-15 minutes) for molecular weight-based protein separation as compared to that of a conventional separation technique, e.g., sodium dodecyl sulfate-polyacrylamide gel electrophoresis. When ultrasensitive wavemixing detection is paired with high-resolution capillary- or microchip-based separation systems, biomarkers can be separated and identified at the zepto- and yocto-mole levels for a wide range of analytes. Specific analytes can be captured in a microchannel through the use of antibody-antigen interactions that provide better chemical specificity as compared to size-based separation alone. The technique can also be combined with immune-precipitation and a multichannel capillary array for high-throughput analysis of more complex protein samples. Wave mixing allows the use of chromophores and absorption-modifying tags, in addition to conventional fluorophores, for online detection of immunecomplexes related to cancer.

  14. The allergenicity of Aspergillus fumigatus conidia is influenced by growth temperature.

    Science.gov (United States)

    Low, Swee Yang; Dannemiller, Karen; Yao, Maosheng; Yamamoto, Naomichi; Peccia, Jordan

    2011-07-01

    Common indoor and outdoor environmental fungi such as Aspergillus fumigatus produce asexual spores containing a collection of proteins that can bind IgE antibodies and trigger allergic reactions. We characterized the impact of sporulation temperature on the IgE-binding capacity (allergenicity) of A. fumigatus and explored the links between variable allergenicity and temperature-dependant expression of genes encoding these allergenic proteins. A 12-fold increase in A. fumigatus allergenicity per spore was observed when sporulation temperatures were decreased from 32°C to 17°C. Per spore protein mass and Asp f 1 allergen mass also followed this trend. Functional gene expression analysis of A. fumigatus sporulating cultures by real-time reverse-transcription PCR and gene expression microarrays revealed that a greater number of genes encoding known, major allergens are more highly expressed at lower sporulation temperatures. The results of this study indicate that environmental conditions at growth significantly influence the allergenicity of this common mould through the differential production of allergenic proteins, and highlight the importance of in vivo or in vitro allergenicity measurements for understanding environmental exposure to airborne allergenic fungi. PMID:21724168

  15. What makes peanuts so allergenic?

    Directory of Open Access Journals (Sweden)

    Petersen Arnd

    2013-01-01

    Full Text Available Peanut allergy belongs to one of the most severe food allergies. So far 12 peanut allergens have been registered by the IUIS Allergen Nomenclature Subcommittee. Here, we describe the different peanut allergens and factors that contribute to allergenicity. Peanut contains several class I food allergens (especially Ara h 1, 2, 3 that are stable against heat denaturation and proteolytic digestion and represent storage proteins. These allergens are often associated with severe allergic reactions. Additionally, peanut contains class II food allergens (Ara h 5 and 8, where the IgE reactivity is caused by cross reactions to inhalant allergens. These allergens are mostly associated with mild to moderate allergic reactions. But the severity of symptoms may change by involvement of additional factors. The peanut matrix consists of about 50% of lipids, and allergen - lipid associations have been shown for several peanut allergens. Further factors influencing allergenicity depend on peanut varieties, geographical differences and alterations in food processing. Finally, the physiological function of allergens and the mechanisms, by which they interact with the immune system, are further modulating factors. Thus, the specific allergen structure, matrix, genetic variations, geographic alterations and further augmentation factors are important parameters that induce and influence allergenicity.

  16. Potential Impact of a Microarray-Based Nucleic Acid Assay for Rapid Detection of Gram-Negative Bacteria and Resistance Markers in Positive Blood Cultures

    OpenAIRE

    Mancini, Nicasio; Infurnari, Laura; Ghidoli, Nadia; Valzano, Grazia; Clementi, Nicola; Burioni, Roberto; Clementi, Massimo

    2014-01-01

    We evaluated the Verigene Gram-negative blood culture (BC-GN) test, a microarray that detects Gram-negative bacteria and several resistance genes. A total of 102 positive blood cultures were tested, and the BC-GN test correctly identified 97.9% of the isolates within its panel. Resistance genes (CTX-M, KPC, VIM, and OXA genes) were detected in 29.8% of the isolates, with positive predictive values of 95.8% (95% confidence interval [CI], 87.7% to 98.9%) in Enterobacteriaceae and 100% (95% CI, ...

  17. Chromosome Microarray.

    Science.gov (United States)

    Anderson, Sharon

    2016-01-01

    Over the last half century, knowledge about genetics, genetic testing, and its complexity has flourished. Completion of the Human Genome Project provided a foundation upon which the accuracy of genetics, genomics, and integration of bioinformatics knowledge and testing has grown exponentially. What is lagging, however, are efforts to reach and engage nurses about this rapidly changing field. The purpose of this article is to familiarize nurses with several frequently ordered genetic tests including chromosomes and fluorescence in situ hybridization followed by a comprehensive review of chromosome microarray. It shares the complexity of microarray including how testing is performed and results analyzed. A case report demonstrates how this technology is applied in clinical practice and reveals benefits and limitations of this scientific and bioinformatics genetic technology. Clinical implications for maternal-child nurses across practice levels are discussed. PMID:27276104

  18. Allergens in the Lab.

    Science.gov (United States)

    Fisher, Thomas M.

    1987-01-01

    Points out the health and legal implications related to laboratory substances that could cause allergic reactions. Presents a list of potential cosmetic allergens and irritants. Includes precautionary measures dealing with allergy situations. (ML)

  19. Allergens and thunderstorm asthma.

    Science.gov (United States)

    Nasser, Shuaib M; Pulimood, Thomas B

    2009-09-01

    Thunderstorm-related asthma is increasingly recognized in many parts of the world. This review focuses on important advances in the understanding of the mechanism of the role of allergens, in particular fungal spores such as Alternaria, in asthma epidemics associated with thunderstorms. From our observations, we have proposed that the prerequisites for this phenomenon are as follows: 1) a sensitized, atopic, asthmatic individual; 2) prior airway hyperresponsiveness before a sudden, large allergen exposure; 3) a large-scale thunderstorm with cold outflow occurring at a time and location during an allergen season in which large numbers of asthmatics are outdoors; and 4) sudden release of large amounts of respirable allergenic fragments, particularly fungal spores such as Alternaria. PMID:19671382

  20. Is aboriginal food less allergenic? Comparing IgE-reactivity of eggs from modern and ancient chicken breeds in a cohort of allergic children.

    Directory of Open Access Journals (Sweden)

    Matthias Egger

    Full Text Available BACKGROUND: Hen's egg allergy ranks among the most frequent primary food allergies in children. We aimed to investigate sensitization profiles of egg allergic patients and compare in vitro IgE reactivities of eggs from ancient chicken breeds (Araucana and Maran with those from conventional laying hen hybrids. METHODOLOGY: Egg allergic children (n = 25 were subjected to skin prick test, double blind placebo controlled food challenge, and sensitization profiles to Gal d 1-5 were determined by allergen microarray. IgE binding and biological activity of eggs from different chicken breeds were investigated by immunoblot, ELISA, and mediator release assays. PRINCIPAL FINDINGS: We found that Gal d 1 and Gal d 2 are generally major egg allergens, whereas Gal d 3-5 displayed high sensitization prevalence only in patients reacting to both, egg white and yolk. It seems that the onset of egg allergy is mediated by egg white allergens expanding to yolk sensitization in later stages of disease. Of note, egg white/yolk weight ratios were reduced in eggs from Auraucana and Maran chicken. As determined in IgE immunoblots and mass analysis, eggs from ancient chicken breeds did not differ in their protein composition. Similar IgE-binding was observed for all egg white preparations, while an elevated allergenicity was detected in egg yolk from Araucana chicken. CONCLUSION/SIGNIFICANCE: Our results on allergenicity and biological activity do not confirm the common assumption that aboriginal food might be less allergenic. Comprehensive diagnosis of egg allergy should distinguish between reactivity to hen's egg white and yolk fractions to avoid unnecessary dietary restrictions to improve life quality of the allergic child and its family.

  1. Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis

    Directory of Open Access Journals (Sweden)

    Kolquist Kathryn A

    2011-11-01

    Full Text Available Abstract Background Cytogenetic evaluation is a key component of the diagnosis and prognosis of chronic lymphocytic leukemia (CLL. We performed oligonucleotide-based comparative genomic hybridization microarray analysis on 34 samples with CLL and known abnormal karyotypes previously determined by cytogenetics and/or fluorescence in situ hybridization (FISH. Results Using a custom designed microarray that targets >1800 genes involved in hematologic disease and other malignancies, we identified additional cryptic aberrations and novel findings in 59% of cases. These included gains and losses of genes associated with cell cycle regulation, apoptosis and susceptibility loci on 3p21.31, 5q35.2q35.3, 10q23.31q23.33, 11q22.3, and 22q11.23. Conclusions Our results show that microarray analysis will detect known aberrations, including microscopic and cryptic alterations. In addition, novel genomic changes will be uncovered that may become important prognostic predictors or treatment targets for CLL in the future.

  2. HYMENOPTERA ALLERGENS: FROM VENOM TO VENOME

    Directory of Open Access Journals (Sweden)

    Edzard eSpillner

    2014-02-01

    Full Text Available In Western Europe hymenoptera venom allergy primarily relates to venoms of the honeybee and the common yellow jacket. In contrast to other allergen sources, only a few major components of hymenoptera venoms had been characterized until recently. Improved expression systems and proteomic detection strategies have allowed the identification and characterization of a wide range of additional allergens. The field of hymenoptera venom allergy research has moved rapidly from focusing on venom extract and single major allergens to a molecular understanding of the entire venome as a system of unique and characteristic components. An increasing number of such components has been identified, characterized regarding function and assessed for allergenic potential. Moreover, advanced expression strategies for recombinant production of venom allergens allow selective modification of molecules and provide insight into different types of IgE reactivities and sensitization patterns. The obtained information contributes to an increased diagnostic precision in hymenoptera venom allergy and may serve for monitoring, reevaluation and improvement of current therapeutic strategies.

  3. An Analysis and Comparison of Quality Index Using Clustering Techniques for Spot Detection in Noisy Microarray Images

    Directory of Open Access Journals (Sweden)

    An Analysis and Comparison of Quality Index Using Clustering Techniques for Spot Detection in Noisy Microarray Images

    2011-10-01

    Full Text Available In this paper, the proposed approach consists of mainly three important steps: preprocessing,gridding and segmentation of micro array images. Initially, the microarray image is preprocessedusing filtering and morphological operators and it is given for gridding to fit a grid on the imagesusing hill-climbing algorithm. Subsequently, the segmentation is carried out using the fuzzy cmeansclustering. Initially the enhanced fuzzy c-means clustering algorithm (EFCMC isimplemented to effectively clustering the image whether the image may be affected by the noisesor not. Then, the EFCM method was employed the real microarray images and noisy microarrayimages in order to investigate the efficiency of the segmentation. Finally, the segmentationefficiency of the proposed approach was compared with the various algorithms in terms of qualityindex and the obtained results ensures that the performance efficiency of the proposed algorithmwas improved in term of quality index rather than other algorithms.

  4. Mammalian lipocalin allergens--insights into their enigmatic allergenicity.

    Science.gov (United States)

    Virtanen, T; Kinnunen, T; Rytkönen-Nissinen, M

    2012-04-01

    Most of the important mammal-derived respiratory allergens, as well as a milk allergen and a few insect allergens, belong to the lipocalin protein family. As mammalian lipocalin allergens are found in dander, saliva and urine, they disperse effectively and are widely present in the indoor environments. Initially, lipocalins were characterized as transport proteins for small, principally hydrophobic molecules, but now they are known to be involved in many other biological functions. Although the amino acid identity between lipocalins is generally at the level of 20-30%, it can be considerably higher. Lipocalin allergens do not exhibit any known physicochemical, functional or structural property that would account for their allergenicity, that is, the capacity to induce T-helper type 2 immunity against them. A distinctive feature of mammalian lipocalin allergens is their poor capacity to stimulate the cellular arm of the human or murine immune system. Nevertheless, they induce IgE production in a large proportion of atopic individuals exposed to the allergen source. The poor capacity of mammalian lipocalin allergens to stimulate the cellular immune system does not appear to result from the function of regulatory T cells. Instead, the T cell epitopes of mammalian lipocalin allergens are few and those examined have proved to be suboptimal. Moreover, the frequency of mammalian lipocalin allergen-specific CD4(+) T cells is very low in the peripheral blood. Importantly, recent research suggests that the lipocalin allergen-specific T cell repertoires differ considerably between allergic and healthy subjects. These observations are compatible with our hypothesis that the way CD4(+) T-helper cells recognize the epitopes of mammalian lipocalin allergens may be implicated in their allergenicity. Indeed, as several lipocalins exhibit homologies of 40-60% over species, mammalian lipocalin allergens may be immunologically at the borderline of self and non-self, which would not

  5. An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection

    OpenAIRE

    Wang, Xingbin; Kang, Dongwan D.; Shen, Kui; Song, Chi; Lu, Shuya; Chang, Lun-Ching; Liao, Serena G.; Huo, Zhiguang; Tang, Shaowu; Ding, Ying; Kaminski, Naftali; Sibille, Etienne; Lin, Yan; Li, Jia; Tseng, George C.

    2012-01-01

    Summary: With the rapid advances and prevalence of high-throughput genomic technologies, integrating information of multiple relevant genomic studies has brought new challenges. Microarray meta-analysis has become a frequently used tool in biomedical research. Little effort, however, has been made to develop a systematic pipeline and user-friendly software. In this article, we present MetaOmics, a suite of three R packages MetaQC, MetaDE and MetaPath, for quality control, differentially expre...

  6. 无锡市哮喘儿童和过敏性鼻炎儿童吸人性过敏原检测诊断分析%The Inhalant allergens detecting for the asthma and inhalant allergens children in a certain regions

    Institute of Scientific and Technical Information of China (English)

    周静月; 任明星

    2012-01-01

    Objective To investigate the inhalant allergens detecting situation for the asthma and inhalant allergens children in our regions to provide a reference for a reasonable choice of diagnostic methods. Methods Selected 80 children with asthma and 80 children with allergic rhinitis were skin prick test (SPT) and serum specific IgE determination, analyzed the correlation of the two methods. Results The allergen SPT positive rate of the asthma group were similar to the rhinitis group (P>0.05). and the SPT diameter compared the two groups had no significant difference (P>0.05). The coincidence rate for the SPT and serum specific IgE was 97.5% in the asthma group for dust mites, so that was 98.8% in the rhinitis group that showed good agreement. Conclusion: Children with asthma and allergic rhinitis in our region were more cause by the dust mites, the skin prick test is a safe, reliable, and rapid screening and looking for allergen detection methods that should be widely applied.%目的:探讨无锡市哮喘儿童和过敏性鼻炎儿童吸入性过敏原检测诊断情况,为合理选择诊断方法提供参考.方法:选择80例哮喘患儿与80例过敏性鼻炎患儿分别进行皮肤点刺试验(SPT)与血清特异性IgE测定,分析两种方法诊断的相关性.结果:哮喘组各过敏原的SPT阳性率与鼻炎组对比都无明显差异(P>0.05).两组的SPT直径对比也无明显差异(P>0.05).哮喘组的屋尘螨过敏原SPT与血清特异性IgE符合率达97.5%,而鼻炎组为98.8%,二者一致性较好.结论:本地区哮喘儿童和过敏性鼻炎儿童的发病多为尘螨引起,皮肤点刺试验是一种安全、可靠并可迅速筛查和寻找过敏原的检测手段,值得推广应用.

  7. Simple and robust antibody microarray-based immunoassay platform for sensitive and selective detection of PSA and hK2 toward accurate diagnosis of prostate cancer

    Directory of Open Access Journals (Sweden)

    S.W. Lee

    2015-03-01

    Full Text Available This paper reports the development of an easy to use antibody microarray-based immunoassay platform for sensitive and selective duplex detection of PSA (prostate specific antigen and hK2 (human kallikrein 2. Using PDMS wells in a 3 × 9 array on epoxy-coated glass slides 27 duplex immunoassays can be performed in parallel. Automated microarraying provided fast and reproducible antibody arraying in each assay well. To achieve highly sensitive and selective detection of each biomarker, we evaluated and optimized the density of each of the immobilized capture antibodies. The assay platform showed a limit of detection (LOD of each biomarker (PSA and hK2 of less than 10 pg/mL and a dynamic range of 104–105 orders of magnitude. Neither the PSA nor the hK2 antibody array showed any cross-reaction against each others target proteins or other plasma proteins. These results emphasize the importance of density optimization of capture antibody on the surface in order to achieve a sensitive and selective multiplex immunoassay.

  8. Simultaneous and sensitive detection of six serotypes of botulinum neurotoxin using enzyme-linked immunosorbent assay-based protein antibody microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yanfeng; Lou, Jianlong; Jenko, Kathryn L.; Marks, James D.; Varnum, Susan M.

    2012-11-15

    Botulinum neurotoxins (BoNTs), produced by Clostridium botulinum, are a group of seven (A-G) immunologically distinct proteins and cause the paralytic disease botulism. These toxins are the most poisonous substances known to humans and are potential bioweapon agents. Therefore, it is necessary to develop highly sensitive assays for the detection of BoNTs in both clinical and environmental samples. In the present study, we have developed an ELISA-based protein antibody microarray for the sensitive and simultaneous detection of BoNT serotype A, B, C, D, E and F. With engineered high-affinity antibodies, the assays have sensitivities in buffer of 8 fM (1.2 pg/mL) for serotypes A and B, and 32 fM (4.9 pg/mL) for serotypes C, D, E, and F. Using clinical and environmental samples (serum and milk), the microarray is capable of detecting BoNT/A-F to the same levels as in standard buffer. Cross reactivity between assays for individual serotype was also analyzed. These simultaneous, rapid, and sensitive assays have the potential to measure botulinum toxins in a high-throughput manner in complex clinical or environmental samples.

  9. Discovery of highly conserved unique peanut and tree nut peptides by LC-MS/MS for multi-allergen detection.

    Science.gov (United States)

    Sealey-Voyksner, Jennifer; Zweigenbaum, Jerry; Voyksner, Robert

    2016-03-01

    Proteins unique to peanuts and various tree nuts have been extracted, subjected to trypsin digestion and analysis by liquid chromatography/quadrupole time-of-flight mass spectrometry, in order to find highly conserved peptides that can be used as markers to detect peanuts and tree nuts in food. The marker peptide sequences chosen were those found to be present in both native (unroasted) and thermally processed (roasted) forms of peanuts and tree nuts. Each peptide was selected by assuring its presence in food that was processed or unprocessed, its abundance for sensitivity, sequence size, and uniqueness for peanut and each specific variety of tree nut. At least two peptides were selected to represent peanut, almond, pecan, cashew, walnut, hazelnut, pine nut, Brazil nut, macadamia nut, pistachio nut, chestnut and coconut; to determine the presence of trace levels of peanut and tree nuts in food by a novel multiplexed LC-MS method. PMID:26471545

  10. Allergenic Lipid Transfer Proteins from Plant-Derived Foods Do Not Immunologically and Clinically Behave Homogeneously: The Kiwifruit LTP as a Model

    OpenAIRE

    Bernardi, Maria Livia; Giangrieco, Ivana; Camardella, Laura; Ferrara, Rosetta; Palazzo, Paola; Panico, Maria Rosaria; Crescenzo, Roberta; Carratore, Vito; Zennaro, Danila; Liso, Marina; Santoro, Mario; Zuzzi, Sara; Tamburrini, Maurizio; Ciardiello, Maria Antonietta; Mari, Adriano

    2011-01-01

    Background Food allergy is increasingly common worldwide. Tools for allergy diagnosis measuring IgE improved much since allergenic molecules and microarrays started to be used. IgE response toward allergens belonging to the same group of molecules has not been comprehensively explored using such approach yet. Objective Using the model of lipid transfer proteins (LTPs) from plants as allergens, including two new structures, we sought to define how heterogeneous is the behavior of homologous pr...

  11. Standardization of RP-HPLC methods for the detection of the major peanut allergens Ara h 1, Ara h 2 and Ara h 3

    Science.gov (United States)

    Crude peanut extract (CPE) was analyzed for three major allergens (Ara h 1, h 2, and h 3) using a C12 and a C18 column at two wavelengths (280 and 220 nm) and under different solvent conditions. HPLC profiles were compared for retention time, resolution, and peak heights. CPE samples were spiked wit...

  12. Sublingual allergen immunotherapy

    DEFF Research Database (Denmark)

    Calderón, M A; Simons, F E R; Malling, Hans-Jørgen;

    2012-01-01

    To cite this article: Calderón MA, Simons FER, Malling H-J, Lockey RF, Moingeon P, Demoly P. Sublingual allergen immunotherapy: mode of action and its relationship with the safety profile. Allergy 2012; 67: 302-311. ABSTRACT: Allergen immunotherapy reorients inappropriate immune responses in......-presenting cells (mostly Langerhans and myeloid dendritic cells) exhibit a tolerogenic phenotype, despite constant exposure to danger signals from food and microbes. This reduces the induction of pro-inflammatory immune responses leading to systemic allergic reactions. Oral tissues contain relatively few mast...... cells and eosinophils (mostly located in submucosal areas) and, in comparison with subcutaneous tissue, are less likely to give rise to anaphylactic reactions. SLIT-associated immune responses include the induction of circulating, allergen-specific Th1 and regulatory CD4+ T cells, leading to clinical...

  13. Lack of detectable allergenicity in genetically modified maize containing "Cry" proteins as compared to native maize based on in silico & in vitro analysis.

    Directory of Open Access Journals (Sweden)

    Chandni Mathur

    Full Text Available Genetically modified, (GM crops with potential allergens must be evaluated for safety and endogenous IgE binding pattern compared to native variety, prior to market release.To compare endogenous IgE binding proteins of three GM maize seeds containing Cry 1Ab,1Ac,1C transgenic proteins with non GM maize.An integrated approach of in silico & in vitro methods was employed. Cry proteins were tested for presence of allergen sequence by FASTA in allergen databases. Biochemical assays for maize extracts were performed. Specific IgE (sIgE and Immunoblot using food sensitized patients sera (n = 39 to non GM and GM maize antigens was performed.In silico approaches, confirmed for non sequence similarity of stated transgenic proteins in allergen databases. An insignificant (p> 0.05 variation in protein content between GM and non GM maize was observed. Simulated Gastric Fluid (SGF revealed reduced number of stable protein fractions in GM then non GM maize which might be due to shift of constituent protein expression. Specific IgE values from patients showed insignificant difference in non GM and GM maize extracts. Five maize sensitized cases, recognized same 7 protein fractions of 88-28 kD as IgE bindng in both GM and non-GM maize, signifying absence of variation. Four of the reported IgE binding proteins were also found to be stable by SGF.Cry proteins did not indicate any significant similarity of >35% in allergen databases. Immunoassays also did not identify appreciable differences in endogenous IgE binding in GM and non GM maize.

  14. 食品中小麦致敏成分的常规PCR检测方法的建立%A Conventional PCR for the Detection of DNA from Wheat Allergen in Food

    Institute of Scientific and Technical Information of China (English)

    柯燕娜; 葛宇; 巢强国; 王守法

    2011-01-01

    Celiac disease (CD) is a chronic inflammatory disorder of the upper small intestine caused by cereal allergens. CD patients suffer an inappropriate immune response to those cereal allergens and have to adhere to lifelong diets, exclusive of gluten to avoid serious complications. For wheat is the most important cereal allergen, a qualitative polymerase chain reaction method was developed to detect wheat DNA in a series of raw and heat processed foods in this paper. A pair of primers was designed to amplify a 185 bp fragment of the omega gliadin storage protein gene. The limit of the detection was 10.0 ng of DNA. This method can detect wheat DNA in thermally processed foods and is of high specificity, so it can be used as a method for labeling gluten-free foods. Meanwhile, it complements the immunochemical methods toward addressing food safety in CD patients.%建立了一种常规PCR方法用于检测一系列原料和加工食品中小麦致敏成分的DNA。针对小麦的ω-醇溶谷蛋白设计了一对大小为185bp的引物。检出限为10ng。该法能检测热加工食品中的小麦DNA,并具有良好的特异性,可作为食品无谷蛋白标识的检测方法。同时它弥补了免疫化学方法的不足,并为乳糜泻患者的话品安全提供保障。

  15. Mechanisms of subcutaneous allergen immunotherapy.

    Science.gov (United States)

    Soyer, Ozge U; Akdis, Mubeccel; Akdis, Cezmi A

    2011-05-01

    Allergen-specific immunotherapy (SIT) is the only curative approach in the treatment of allergic diseases defined up-to-date. Peripheral T-cell tolerance to allergens, the goal of successful allergen-SIT, is the primary mechanism in healthy immune responses to allergens. By repeated administration of increased doses of the causative allergen, allergen-SIT induces a state of immune tolerance to allergens through the constitution of T regulatory (Treg) cells, including allergen-specific interleukin (IL)-10-secreting Treg type 1 cells and CD4(+)CD25(+)Treg cells; induction of suppressive cytokines, such as IL-10 and transforming growth factor β; suppression of allergen-specific IgE and induction of IgG4 and IgA; and suppression of mast cells, basophils, eosinophils, and inflammatory dendritic cells. This review summarizes the current knowledge on the mechanisms of allergen-SIT with emphasis on the roles of Treg cells in allergen-SIT. PMID:21530813

  16. 2012-2013年包头市过敏性哮喘群体过敏原检测%Detection of the Allergen for Allergic Asthma Individuals in 2012 -2013 in Baotou

    Institute of Scientific and Technical Information of China (English)

    高扬; 唐存亮; 姚洁; 李冬梅; 杨月元; 张毅; 李水霞; 马显军; 孙丽蓉

    2014-01-01

    目的:研究集中爆发期间患者血清特异性 IgE 过敏原种类及其与非集中发作期病例过敏原间的差别。方法:对爆发发病期间的78例过敏性哮喘患者及同期74例非集中发作期患者,检查血清中的 IgE 型变应原抗体来确定过敏原,对比两类病例过敏原是否存在差别。结果:集中发作期患者血清特异性 IgE 检测中,阳性率最高的前3位变应原分别是蒿/矮豚草67例(85.9%)、苋/藜/葎草/蒲公英62例(79.4%)、柏/榆/梧/柳/杨/榛48例(61.5%);集中发作期患者苋/藜/葎草/蒲公英(10.76±26.97)IU/ mL,蒿/矮豚草(27.62±40.81)IU/ mL,柏/榆/梧/柳/杨/榛(0.44±1.253)IU/ mL,与非集中发作期患者比较差异有统计学意义( P <0.05)。结论:集中发作期患者与非集中发作期患者的过敏原种类存在差别。%Objective:To investigate the difference between the types of specific serum IgE allergen in allergic asthma pa-tients during the concentrated attack and the allergen of allergic asthma patients during non - concentrated attack. Methods:The anti - IgE allergen antibody in the serum was detected in 78 cases of allergic asthma during concentrated attack and in 74 ca-ses of allergic asthma during non - concentrated attack to decide the allergen,with a comparison made in the allergen between the two groups of allergic asthma patients. Results:The first three highest specific serum IgE allergen positive rates in those dur-ing concentrated attack were Artemisia/ short ragweed(67 cases,85. 9 % ),amaranth/ quinoa/ humulus/ Dandelion(62 cases, 79. 4 % )and Bai Yu Wu Liuyang hazel(48 cases,61. 5 % ). Amaranth/ quinoa/ humulus/ Dandelion,Artemisia/ short ragweed and Bo Yu Wu Liuyang haze were 10. 76 ± 26. 97 IU/ mL,27. 62 ± 40. 81 IU/ mL and 0. 44 ± 1. 253 IU/ mL,respectively,in the patients during concentrated attack,with significant difference from those in the patients during non - concentrated

  17. DNA microarray-based solid-phase RT-PCR for rapid detection and identification of influenza virus type A and subtypes H5 and H7

    DEFF Research Database (Denmark)

    Yi, Sun; Dhumpa, Raghuram; Bang, Dang Duong;

    2011-01-01

    article, a DNA microarray-based solid-phase polymerase chain reaction (PCR) approach has been developed for rapid detection of influenza virus type A and for simultaneous identification of pathogenic virus subtypes H5 and H7. This solid-phase RT-PCR method combined reverse-transcription amplification of......Endemic of avian influenza virus (AIV) in Asia and epizootics in some European regions have caused considerable public concern on a possible pandemic of AIV. A rapid method for virus detection and effective surveillance in wild avian, poultry production as well as in humans is required. In this...... RNA extract in the liquid phase with sequence-specific nested PCR on the solid phase. A simple ultraviolet cross-linking method was used to immobilize the DNA probes over an unmodified glass surface, which makes solid-phase PCR a convenient possibility for AIV screening. The testing of 33 avian fecal...

  18. New Cosmetic Contact Allergens

    OpenAIRE

    An Goossens

    2015-01-01

    Allergic and photo-allergic contact dermatitis, and immunologic contact urticaria are potential immune-mediated adverse effects from cosmetics. Fragrance components and preservatives are certainly the most frequently observed allergens; however, all ingredients must be considered when investigating for contact allergy.

  19. Food Processing and Allergenicity

    NARCIS (Netherlands)

    Verhoeckx, K.; Vissers, Y.; Baumert, J.L.; Faludi, R.; Fleys, M.; Flanagan, S.; Herouet-Guicheney, C.; Holzhauser, T.; Shimojo, R.; Bolt, van der Nieke; Wichers, H.J.; Kimber, I.

    2015-01-01

    Food processing can have many beneficial effects. However, processing may also alter the allergenic properties of food proteins. A wide variety of processing methods is available and their use depends largely on the food to be processed.

    In this review the impact of processing (heat and non

  20. Bleach Neutralizes Mold Allergens

    Science.gov (United States)

    Science Teacher, 2005

    2005-01-01

    Researchers at National Jewish Medical and Research Center have demonstrated that dilute bleach not only kills common household mold, but may also neutralize the mold allergens that cause most mold-related health complaints. The study, published in the Journal of Allergy and Clinical Immunology, is the first to test the effect on allergic…

  1. New Cosmetic Contact Allergens

    Directory of Open Access Journals (Sweden)

    An Goossens

    2015-02-01

    Full Text Available Allergic and photo-allergic contact dermatitis, and immunologic contact urticaria are potential immune-mediated adverse effects from cosmetics. Fragrance components and preservatives are certainly the most frequently observed allergens; however, all ingredients must be considered when investigating for contact allergy.

  2. Evaluation of a viral microarray based on simultaneous extraction and amplification of viral nucleotide acid for detecting human herpesviruses and enteroviruses.

    Directory of Open Access Journals (Sweden)

    Yi Liu

    Full Text Available In this study, a viral microarray based assay was developed to detect the human herpesviruses and enteroviruses associated with central nervous system infections, including herpes simplex virus type 1, type 2 (HSV1 and HSV2, Epstein-Barr virus (EBV, cytomegalovirus (CMV, enterovirus 71 (EV71, coxsackievirus A 16 (CA16 and B 5(CB5. The DNA polymerase gene of human herpesviruses and 5'-untranslated region of enteroviruses were selected as the targets to design primers and probes. Human herpesviruses DNA and enteroviruses RNA were extracted simultaneously by using a guanidinium thiocyanate acid buffer, and were subsequently amplified through a biotinylated asymmetry multiplex RT-PCR with the specific primer of enteroviruses. In total, 90 blood samples and 49 cerebrospinal fluids samples with suspected systemic or neurological virus infections were investigated. Out of 139 samples, 66 were identified as positive. The specificities of this multiplex RT-PCR microarray assay were over 96% but the sensitivities were various from 100% for HSV1, HSV2, EV71 and CB5, 95.83% for CMV, 80% for EBV to 71.43% for CA16 in comparison with reference standards of TaqMan qPCR/qRT-PCR. The high Kappa values (>0.90 from HSV1, HSV2, CMV, EV71 and CB5 were obtained, indicating almost perfect agreement in term of the 5 viruses detection. But lower Kappa values for EBV (0.63 and CA16 (0.74 displayed a moderate to substantial agreement. This study provides an innovation of simultaneous extraction, amplification, hybridization and detection of DNA viruses and RNA viruses with simplicity and specificity, and demonstrates a potential clinical utility for a variety of viruses' detection.

  3. Aptamer Microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Angel-Syrett, Heather; Collett, Jim; Ellington, Andrew D.

    2009-01-02

    In vitro selection can yield specific, high-affinity aptamers. We and others have devised methods for the automated selection of aptamers, and have begun to use these reagents for the construction of arrays. Arrayed aptamers have proven to be almost as sensitive as their solution phase counterparts, and when ganged together can provide both specific and general diagnostic signals for proteins and other analytes. We describe here technical details regarding the production and processing of aptamer microarrays, including blocking, washing, drying, and scanning. We will also discuss the challenges involved in developing standardized and reproducible methods for binding and quantitating protein targets. While signals from fluorescent analytes or sandwiches are typically captured, it has proven possible for immobilized aptamers to be uniquely coupled to amplification methods not available to protein reagents, thus allowing for protein-binding signals to be greatly amplified. Into the future, many of the biosensor methods described in this book can potentially be adapted to array formats, thus further expanding the utility of and applications for aptamer arrays.

  4. Comparison of two DNA microarrays for detection of plasmid-mediated antimicrobial resistance and virulence factor genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae.

    LENUS (Irish Health Repository)

    Walsh, Fiona

    2010-06-01

    A DNA microarray was developed to detect plasmid-mediated antimicrobial resistance (AR) and virulence factor (VF) genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae. The array was validated with the following bacterial species: Escherichiacoli (n=17); Klebsiellapneumoniae (n=3); Enterobacter spp. (n=6); Acinetobacter genospecies 3 (n=1); Acinetobacterbaumannii (n=1); Pseudomonasaeruginosa (n=2); and Stenotrophomonasmaltophilia (n=2). The AR gene profiles of these isolates were identified by polymerase chain reaction (PCR). The DNA microarray consisted of 155 and 133 AR and VF gene probes, respectively. Results were compared with the commercially available Identibac AMR-ve Array Tube. Hybridisation results indicated that there was excellent correlation between PCR and array results for AR and VF genes. Genes conferring resistance to each antibiotic class were identified by the DNA array. Unusual resistance genes were also identified, such as bla(SHV-5) in a bla(OXA-23)-positive carbapenem-resistant A. baumannii. The phylogenetic group of each E. coli isolate was verified by the array. These data demonstrate that it is possible to screen simultaneously for all important classes of mobile AR and VF genes in Enterobacteriaceae and non-Enterobacteriaceae whilst also assigning a correct phylogenetic group to E. coli isolates. Therefore, it is feasible to test clinical Gram-negative bacteria for all known AR genes and to provide important information regarding pathogenicity simultaneously.

  5. Sensitive and specific detection of potentially allergenic almond (Prunus dulcis) in complex food matrices by Taqman real-time polymerase chain reaction in comparison to commercially available protein-based enzyme-linked immunosorbent assay

    International Nuclear Information System (INIS)

    Currently, causative immunotherapies are lacking in food allergy. The only option to prevent allergic reactions in susceptible individuals is to strictly avoid the offending food. Thus, reliable labelling of allergenic constituents is of major importance, but can only be achieved if appropriate specific and sensitive detection techniques for foods with allergenic potential are available. Almond is an allergenic food that requires mandatory labelling on prepackaged foods and belongs to the genus Prunus. Species of this genus are phylogenetically closely related. We observed commercially available almond specific ELISA being highly cross-reactive with other foods of the Prunoideae family, resulting in a false-positive detection of up to 500,000 mg kg-1 almond. Previously published PCR methods were reported to be cross-reactive with false positive results >1200 mg kg-1. We describe the development of a novel almond specific real-time PCR, based on mutated mismatch primers and sequence specific Taqman probe detection, in comparison with two quantitative commercially available ELISA. PCR sensitivity was investigated with chocolate, chocolate coating and cookies spiked between 5 and 100,000 mg kg-1 almond. In all matrices almond was reproducibly detected by real-time PCR at the lowest spike level of 5 mg kg-1. Further, between 100 and 100,000 mg kg-1 spiked almond, the method featured good correlation between quantified copy numbers and the amount of spiked almond. Within this range a similar relation between detectable signal and amount of almond was observed for both PCR and ELISA. In contrast to ELISA the Taqman real-time PCR method was highly specific in 59 food items with negligible cross-reactivity for a very limited number of Prunoideae foods. The real-time PCR analysis of 24 retail samples was in concordance with ELISA results: 21% (n = 5) contained undeclared almond. This is the first completely disclosed real-time PCR method for a specific and potentially

  6. Sensitive and specific detection of potentially allergenic almond (Prunus dulcis) in complex food matrices by Taqman real-time polymerase chain reaction in comparison to commercially available protein-based enzyme-linked immunosorbent assay

    Energy Technology Data Exchange (ETDEWEB)

    Roeder, Martin; Vieths, Stefan [Division of Allergology, Paul-Ehrlich-Institut, Paul-Ehrlich-Strasse 51-59, 63225 Langen (Germany); Holzhauser, Thomas, E-mail: holth@pei.de [Division of Allergology, Paul-Ehrlich-Institut, Paul-Ehrlich-Strasse 51-59, 63225 Langen (Germany)

    2011-01-24

    Currently, causative immunotherapies are lacking in food allergy. The only option to prevent allergic reactions in susceptible individuals is to strictly avoid the offending food. Thus, reliable labelling of allergenic constituents is of major importance, but can only be achieved if appropriate specific and sensitive detection techniques for foods with allergenic potential are available. Almond is an allergenic food that requires mandatory labelling on prepackaged foods and belongs to the genus Prunus. Species of this genus are phylogenetically closely related. We observed commercially available almond specific ELISA being highly cross-reactive with other foods of the Prunoideae family, resulting in a false-positive detection of up to 500,000 mg kg{sup -1} almond. Previously published PCR methods were reported to be cross-reactive with false positive results >1200 mg kg{sup -1}. We describe the development of a novel almond specific real-time PCR, based on mutated mismatch primers and sequence specific Taqman probe detection, in comparison with two quantitative commercially available ELISA. PCR sensitivity was investigated with chocolate, chocolate coating and cookies spiked between 5 and 100,000 mg kg{sup -1} almond. In all matrices almond was reproducibly detected by real-time PCR at the lowest spike level of 5 mg kg{sup -1}. Further, between 100 and 100,000 mg kg{sup -1} spiked almond, the method featured good correlation between quantified copy numbers and the amount of spiked almond. Within this range a similar relation between detectable signal and amount of almond was observed for both PCR and ELISA. In contrast to ELISA the Taqman real-time PCR method was highly specific in 59 food items with negligible cross-reactivity for a very limited number of Prunoideae foods. The real-time PCR analysis of 24 retail samples was in concordance with ELISA results: 21% (n = 5) contained undeclared almond. This is the first completely disclosed real-time PCR method for a

  7. Detection of influenza A virus homo- and heterosubtype-specific memory B-cells using a novel protein microarray-based analysis tool.

    Science.gov (United States)

    Baas, Dominique C; Koopmans, Marion P; de Bruin, Erwin; ten Hulscher, Hinke I; Buisman, Anne M; Hendrikx, Lotte H; van Beek, Janko; Godeke, Gert-Jan; Reimerink, Johan; van Binnendijk, Robert S

    2013-05-01

    The emergence of the A(H1N1) 2009 pandemic influenza virus was initially seen as a major world-wide health concern since a low degree of immunity to this virus strain was anticipated. However, age-specific infection attack rates and age-specific differences in seroresponse indicate that pre-existing immunity may have played a significant role in protection especially in older age groups. This study describes the use of a protein microarray as a multiplex analysis tool for detection of influenza virus H1 strain-specific memory B-cells before and after infection with A(H1N1)pdm09. The discrimination was based on detection of specific antibodies in culture supernatants from polyclonally stimulated B-cells against recombinant influenza virus HA1 proteins representing influenza virus subtypes H1 through H9. The protein microarray proved sensitive and specific for antibody detection in culture supernatants of B-cells, and with the potential to deduce a person's history of infection with particular influenza virus variants, including A(H1N1)pdm09. Blood samples obtained from different age groups prior to the pandemic in 2009 partly showed the presence of B-cells producing antibodies binding to the closely related A(H1N1) 1918 pandemic influenza virus, and of which the magnitude increased with age. These cross-reactive antibodies were produced by single memory B-cells present in these donors, and either bind to epitopes on HA1 which are shared within different H1 strains (homosubtypic response) or shared between different subtypes (heterosubtypic response). PMID:23508915

  8. New strategies for allergen immunotherapy.

    Science.gov (United States)

    Carnés, Jerónimo; Robinson, Douglas S

    2008-06-01

    Specific allergen immunotherapy, consisting in the administration of increasing amounts of offending allergens into sensitive patients was first used nearly one hundred years ago and remains in use worldwide for treatment of allergic rhinitis and asthma. It has been recognised as the only effective treatment for type I allergic diseases when the appropriate quantities of allergens are used. The immunological mechanisms by which specific immunotherapy is effective include the modulation of T cells and the response of B-cells and is accompanied by significant decreases of specific IgE and increases in allergen specific IgG antibodies, mainly IgG4. While specific allergen injection immunotherapy is highly effective and the most common way of administration other routes such as oral or intranasal ways have been considered as and alternative to subcutaneous injections. During the last century, allergenic vaccines have been prepared using individual allergens adsorbed to different adjuvant substances. These vaccines have demonstrated efficacy and good results in different clinical trials. However, many novel approaches to allergen immunotherapy have been developed in the last years in order to increase the safety and efficacy of allergenic vaccines. In that way, different and modern vaccines have been prepared including more purified products such as depigmented allergen extracts; allergoids, consisting on big molecules of thousands of kDa, which contain all the individual allergens and show a significant decrease in severe adverse reactions; peptides or small aminoacid sequences; recombinant allergens; hypoallergenic vaccines where the IgE binding sites have been modified; or allergen-CpG fusion molecules. New presentations are under study and new treatments will be developed in the near future with the objective that the prevention of allergic disease may become a reality. The review article also discuss recent patent related to the field. PMID:19075996

  9. The influence of digestibility on the allergenicity of food allergens

    OpenAIRE

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard

    2012-01-01

    Food allergy is a major health problem in the Western countries, affecting 3-8% of the population. What makes a dietary protein a food allergen has not yet been established, though several characteristics have been proposed to be shared by the food allergens. One of the features believed to be a general characteristic is resistance to digestion. This is based on studies showing that allergenic dietary proteins in general were more resistant to digestion than dietary proteins with no proven al...

  10. Allergenicity assay of allergen from Dermatophagoides farinae in transgenic tobacco

    Institute of Scientific and Technical Information of China (English)

    TANG Mingjuan; SHEN Ye; HU Yuanlei; CAO Lei; NI Ting; ZHANG Hongyu; LIN Zhongping

    2004-01-01

    Derf2 gene for one of mite allergens in Dermatophagoides farinae has been cloned and expressed under regulation of 35S promoter in transgenic tobacco. The transcriptional analysis showed that this mite complete gene structure in genomic sequence could be spliced at prediction site. Allergenicity assay with immunological sera indicated that the extracts from the transgenic tobacco gave obvious positive IgE binding reaction with specific serum pool. This work would be of potential use in allergenicity assessment of genetically modified food.

  11. Detection of EGFR and COX-2 Expression by Immunohistochemical Method on a Tissue Microarray Section in Lung Cancer and Biological Significance

    Directory of Open Access Journals (Sweden)

    Xinyun WANG

    2010-02-01

    Full Text Available Background and objective Epidermal growth factor receptor (EGFR and cyclooxygenase-2 (COX-2, which can regulate growth, invasion and metastasis of tumor through relevant signaling pathway, have been detected in a variety of solid tumors. The aim of this study is to investigate the biological significance of EGFR and COX-2 expression in lung cancer and the relationship between them. Methods The expression of EGFR and COX-2 was detected in 89 primary lung cancer tissues, 12 premaliganant lesions, 12 lymph node metastases, and 10 normal lung tissues as the control by immunohistochemical method on a tissue microarray section. Results EGFR protein was detectable in 59.6%, 41.7%, and 66.7% of primary lung cancer tissues, premalignant lesions and lymph node metastases, respectively; COX-2 protein was detectable in 52.8%, 41.7%, and 66.7% of primary lung cancer tissues, premalignant lesions and lymph node metastases, respectively, which were significantly higher than those of the control (P 0.05. COX-2 expression was related to gross type (P < 0.05. A highly positive correlation was observed between EGFR and COX-2 expression (P < 0.01. Conclusion Overexpression of EGFR and COX-2 may play an important role in the tumorgenesis, progression and malignancy of lung cancer. Detection of EGFR and COX-2 expression might be helpful to diagnosis and prognosis of lung cancer.

  12. Hymenoptera Allergens: From Venom to “Venome”

    OpenAIRE

    Spillner, Edzard; Blank, Simon; Jakob, Thilo

    2014-01-01

    In Western Europe, Hymenoptera venom allergy (HVA) primarily relates to venoms of the honeybee and the common yellow jacket. In contrast to other allergen sources, only a few major components of Hymenoptera venoms had been characterized until recently. Improved expression systems and proteomic detection strategies have allowed the identification and characterization of a wide range of additional allergens. The field of HVA research has moved rapidly from focusing on venom extract and single m...

  13. Cosmetic Contact Allergens

    Directory of Open Access Journals (Sweden)

    An Goossens

    2016-02-01

    Full Text Available This article presents trends in the frequency of cosmetics as causal factors of allergic contact dermatitis during a 26-year period in 14,911 patients patch-tested between 1990 and 2014, and discusses the cosmetic allergens identified during the last six years (2010–2015 in 603 patients out of 3105 tested. The data were retrieved from, and evaluated with, a patient database developed in-house. The results show the increasing importance of cosmetic allergies, up to 25% of the patients tested during the last five-year period. As expected, fragrance materials, preservatives, and hair dyes were the most frequent culprits, but a great variety of other allergenic ingredients were involved as well. This underlines the need of additional and extensive patch testing with the patient’s products used and their ingredients.

  14. Clinical Impact of Laboratory Implementation of Verigene BC-GN Microarray-Based Assay for Detection of Gram-Negative Bacteria in Positive Blood Cultures.

    Science.gov (United States)

    Walker, Tamar; Dumadag, Sandrea; Lee, Christine Jiyoun; Lee, Seung Heon; Bender, Jeffrey M; Cupo Abbott, Jennifer; She, Rosemary C

    2016-07-01

    Gram-negative bacteremia is highly fatal, and hospitalizations due to sepsis have been increasing worldwide. Molecular tests that supplement Gram stain results from positive blood cultures provide specific organism information to potentially guide therapy, but more clinical data on their real-world impact are still needed. We retrospectively reviewed cases of Gram-negative bacteremia in hospitalized patients over a 6-month period before (n = 98) and over a 6-month period after (n = 97) the implementation of a microarray-based early identification and resistance marker detection system (Verigene BC-GN; Nanosphere) while antimicrobial stewardship practices remained constant. Patient demographics, time to organism identification, time to effective antimicrobial therapy, and other key clinical parameters were compared. The two groups did not differ statistically with regard to comorbid conditions, sources of bacteremia, or numbers of intensive care unit (ICU) admissions, active use of immunosuppressive therapy, neutropenia, or bacteremia due to multidrug-resistant organisms. The BC-GN panel yielded an identification in 87% of Gram-negative cultures and was accurate in 95/97 (98%) of the cases compared to results using conventional culture. Organism identifications were achieved more quickly post-microarray implementation (mean, 10.9 h versus 37.9 h; P < 0.001). Length of ICU stay, 30-day mortality, and mortality associated with multidrug-resistant organisms were significantly lower in the postintervention group (P < 0.05). More rapid implementation of effective therapy was statistically significant for postintervention cases of extended-spectrum beta-lactamase-producing organisms (P = 0.049) but not overall (P = 0.12). The Verigene BC-GN assay is a valuable addition for the early identification of Gram-negative organisms that cause bloodstream infections and can significantly impact patient care, particularly when resistance markers are detected. PMID:27098961

  15. Allergen-specific immunotherapy

    Directory of Open Access Journals (Sweden)

    Moote William

    2011-11-01

    Full Text Available Abstract Allergen-specific immunotherapy is a potentially disease-modifying therapy that is effective for the treatment of allergic rhinitis/conjunctivitis, allergic asthma and stinging insect hypersensitivity. However, despite its proven efficacy in these conditions, it is frequently underutilized in Canada. The decision to proceed with allergen-specific immunotherapy should be made on a case-by-case basis, taking into account individual patient factors such as the degree to which symptoms can be reduced by avoidance measures and pharmacological therapy, the amount and type of medication required to control symptoms, the adverse effects of pharmacological treatment, and patient preferences. Since this form of therapy carries the risk of anaphylactic reactions, it should only be prescribed by physicians who are adequately trained in the treatment of allergy. Furthermore, injections must be given under medical supervision in clinics that are equipped to manage anaphylaxis. In this article, the authors review the indications and contraindications, patient selection criteria, and the administration, safety and efficacy of allergen-specific immunotherapy.

  16. Gene expression signatures in CD34+-progenitor-derived dendritic cells exposed to the chemical contact allergen nickel sulfate

    International Nuclear Information System (INIS)

    The detection of the sensitizing potential of chemicals is of great importance to industry. A promising in vitro alternative to the currently applied animal assays for sensitization testing makes use of dendritic cells (DCs) that have the capability to process and present antigens to naive T cells and induce their proliferation. Here, we studied changes in gene expression profiles after exposing DCs to the contact allergen nickel sulfate. CD34+-progenitor-derived DCs, initiated from 3 different donors, were exposed to 60 μM nickel sulfate, during 0.5, 1, 3, 6, 12 and 24 h. cDNA microarrays were used to assess the transcriptional activity of about 11,000 genes. Significant changes in the expression of 283 genes were observed; 178 genes were up-regulated and 93 down-regulated. These genes were involved in metabolism, cell structure, immune response, transcription, signal transduction, transport, and apoptosis. No functional information was found for 74 genes. Real-time RT-PCR was used to confirm the microarray results of 12 genes. In addition, 3 DC maturation markers not present on the microarrays (DEC205, DC LAMP and CCR7) were analyzed using real-time RT-PCR and found to be up-regulated at several time points. Our data indicate that a broad range of biological processes is influenced by nickel. Some processes are clearly linked to the immune response and DC maturation, others may indicate a toxic effect of nickel

  17. Analysis of a simulated microarray dataset: Comparison of methods for data normalisation and detection of differential expression (Open Access publication

    Directory of Open Access Journals (Sweden)

    Mouzaki Daphné

    2007-11-01

    Full Text Available Abstract Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been proposed. Methods of comparing the normalised data are also abundant, and no clear consensus has yet been reached. The purpose of this paper was to compare those methods used by the EADGENE network on a very noisy simulated data set. With the a priori knowledge of which genes are differentially expressed, it is possible to compare the success of each approach quantitatively. Use of an intensity-dependent normalisation procedure was common, as was correction for multiple testing. Most variety in performance resulted from differing approaches to data quality and the use of different statistical tests. Very few of the methods used any kind of background correction. A number of approaches achieved a success rate of 95% or above, with relatively small numbers of false positives and negatives. Applying stringent spot selection criteria and elimination of data did not improve the false positive rate and greatly increased the false negative rate. However, most approaches performed well, and it is encouraging that widely available techniques can achieve such good results on a very noisy data set.

  18. Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization.

    Directory of Open Access Journals (Sweden)

    Heike Horn

    Full Text Available Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH, especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs. We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL and six malignant mesothelioma (MM samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches.

  19. The Stanford Tissue Microarray Database.

    Science.gov (United States)

    Marinelli, Robert J; Montgomery, Kelli; Liu, Chih Long; Shah, Nigam H; Prapong, Wijan; Nitzberg, Michael; Zachariah, Zachariah K; Sherlock, Gavin J; Natkunam, Yasodha; West, Robert B; van de Rijn, Matt; Brown, Patrick O; Ball, Catherine A

    2008-01-01

    The Stanford Tissue Microarray Database (TMAD; http://tma.stanford.edu) is a public resource for disseminating annotated tissue images and associated expression data. Stanford University pathologists, researchers and their collaborators worldwide use TMAD for designing, viewing, scoring and analyzing their tissue microarrays. The use of tissue microarrays allows hundreds of human tissue cores to be simultaneously probed by antibodies to detect protein abundance (Immunohistochemistry; IHC), or by labeled nucleic acids (in situ hybridization; ISH) to detect transcript abundance. TMAD archives multi-wavelength fluorescence and bright-field images of tissue microarrays for scoring and analysis. As of July 2007, TMAD contained 205 161 images archiving 349 distinct probes on 1488 tissue microarray slides. Of these, 31 306 images for 68 probes on 125 slides have been released to the public. To date, 12 publications have been based on these raw public data. TMAD incorporates the NCI Thesaurus ontology for searching tissues in the cancer domain. Image processing researchers can extract images and scores for training and testing classification algorithms. The production server uses the Apache HTTP Server, Oracle Database and Perl application code. Source code is available to interested researchers under a no-cost license. PMID:17989087

  20. Clinico-Immunological Analysis of Eggplant (Solanum melongena) Allergy Indicates Preponderance of Allergens in the Peel

    OpenAIRE

    Harish Babu, Bheemanapalli N; Yeldur P Venkatesh

    2009-01-01

    Background Eggplant (Solanum melongena L.) is known to cause food allergy in some Asian countries but detailed studies on eggplant allergy are lacking. Objective The objective is to investigate sensitization to different parts of eggplant fruit, and detection of the allergens. Methods Six eggplant-allergic subjects were assessed for sensitization to eggplant (peel/pulp, and raw/cooked) by skin prick test, allergen-specific IgE, and immunoblots. Allergens were analyzed for glycoprotein nature ...

  1. Inkjet-assisted layer-by-layer printing of quantum dot/enzyme microarrays for highly sensitive detection of organophosphorous pesticides.

    Science.gov (United States)

    Luan, Enxiao; Zheng, Zhaozhu; Li, Xinyu; Gu, Hongxi; Liu, Shaoqin

    2016-04-15

    We present a facile fabrication of layer-by-layer (LbL) microarrays of quantum dots (QDs) and acetylcholinesterase enzyme (AChE). The resulting arrays had several unique properties, such as low cost, high integration and excellent flexibility and time-saving. The presence of organophosphorous pesticides (OPs) can inhibit the AChE activity and thus changes the fluorescent intensity of QDs/AChE microscopic dot arrays. Therefore, the QDs/AChE microscopic dot arrays were used for the sensitive visual detection of OPs. Linear calibration for parathion and paraoxon was obtained in the range of 5-100 μg L(-1) under the optimized conditions with the limit of detection (LOD) of 10 μg L(-1). The arrays have been successfully used for detection of OPs in fruits and water real samples. The new array was validated by comparison with conventional high performance liquid chromatography-mass spectrometry (HPLC-MS). PMID:27016441

  2. Comparative genomic hybridization on microarray (a-CGH in constitutional and acquired mosaicism may detect as low as 8% abnormal cells

    Directory of Open Access Journals (Sweden)

    Pasquali Francesco

    2011-05-01

    Full Text Available Abstract Background The results of cytogenetic investigations on unbalanced chromosome anomalies, both constitutional and acquired, were largely improved by comparative genomic hybridization on microarray (a-CGH, but in mosaicism the ability of a-CGH to reliably detect imbalances is not yet well established. This problem of sensitivity is even more relevant in acquired mosaicism in neoplastic diseases, where cells carrying acquired imbalances coexist with normal cells, in particular when the proportion of abnormal cells may be low. We constructed a synthetic mosaicism by mixing the DNA of three patients carrying altogether seven chromosome imbalances with normal sex-matched DNA. Dilutions were prepared mimicking 5%, 6%, 7%, 8%, 10% and 15% levels of mosaicism. Oligomer-based a-CGH (244 K whole-genome system was applied on the patients' DNA and customized slides designed around the regions of imbalance were used for the synthetic mosaics. Results and conclusions The a-CGH on the synthetic mosaics proved to be able to detect as low as 8% abnormal cells in the tissue examined. Although in our experiment some regions of imbalances escaped to be revealed at this level, and were detected only at 10-15% level, it should be remarked that these ones were the smallest analyzed, and that the imbalances recurrent as clonal anomalies in cancer and leukaemia are similar in size to those revealed at 8% level.

  3. Allergens on desktop surfaces in preschools and elementary schools of urban children with asthma.

    Science.gov (United States)

    Kanchongkittiphon, W; Sheehan, W J; Friedlander, J; Chapman, M D; King, E-M; Martirosyan, K; Baxi, S N; Permaul, P; Gaffin, J M; Kopel, L; Bailey, A; Fu, C; Petty, C R; Gold, D R; Phipatanakul, W

    2014-07-01

    Desktop dust has been studied as a source of food allergen, but not as a source of potential aeroallergen exposure. Thirty-six wiped samples from desktop surfaces were collected from preschools and schools. Samples were analyzed for detectable levels of common aeroallergens including Alternaria, cockroach, dog, dust mite, cat, mouse, and rat allergens by immunoassay. Mouse allergen was the most prevalent, detectable in 97.2% of samples. Cat allergen was detectable in 80.6% of samples, and dog allergen was detectable in 77.8% of samples. Other allergens were not as prevalent. Mouse was the only allergen that was highly correlated with settled floor dust collected from the same rooms (r = 0.721, P < 0.001). This is the first study to detect aeroallergens on desktop surfaces by using moist wipes. Allergens for mouse, cat, and dog were highly detectable in wipes with mouse desktop surface levels correlating with levels in vacuumed floor dust. PMID:24750034

  4. Cosmetic Contact Allergens

    OpenAIRE

    An Goossens

    2016-01-01

    This article presents trends in the frequency of cosmetics as causal factors of allergic contact dermatitis during a 26-year period in 14,911 patients patch-tested between 1990 and 2014, and discusses the cosmetic allergens identified during the last six years (2010–2015) in 603 patients out of 3105 tested. The data were retrieved from, and evaluated with, a patient database developed in-house. The results show the increasing importance of cosmetic allergies, up to 25% of the patients tested ...

  5. Allergens from fish and egg

    DEFF Research Database (Denmark)

    Poulsen, Lars K.; Hansen, T K; Nørgaard, A;

    2001-01-01

    Allergens from fish and egg belong to some of the most frequent causes of food allergic reactions reported in the literature. Egg allergens have been described in both white and yolk, and the egg white proteins ovomucoid, ovalbumin, ovotransferrin and lysozyme have been adopted in the allergen...... nomenclature as Gal d1-d4. The most reported allergen from egg yolk seems to be alpha-livitin. In fish, the dominating allergen is the homologues of Gad c1 from cod, formerly described as protein M. A close cross-reactivity exists within different species of fish between this calcium-binding protein family......, denominated the parvalbumins. This cross-reactivity has been indicated to be of clinical relevance for several species, since patients with a positive double-blind, placebo-controlled food challenge to cod will also react with other fish species, such as herring, plaice and mackerel. In spite...

  6. Footwear dermatitis - Clinical patterns and contact allergens

    Directory of Open Access Journals (Sweden)

    Handa S

    1991-01-01

    Full Text Available Thirty patients suspected of contact dermatitis to footwear studied to evaluate various clinical presentations and possible sensitizers. ′V′ chappals and sandals were suspected alone in 12, a combination of open and closed shoes in 15 and closed shoes alone in 3 patients. Commonest affected sites were dorsa of feet and toes in 14 and dorsa of feet corresponding to the shape of footwear in 12 patients. Patch tests were done using a battery of sixteen allergens. Positive patch tests were seen in 29 patients. Rubber chemicals were the commonest allergens detected in 26 patients, dyes in 10,leather in 6, glues and neoprene cements in 4 and rubber material from suspected footwear as such in 4 patients respectively.

  7. Allergen specific responses in cord and adult blood are differentially modulated in the presence of endotoxins

    DEFF Research Database (Denmark)

    Eiwegger, T.; Mayer, E.; Pedersen, Susanne Brix; Schabussova, I.; Dehlink, E.; Bohle, B.; Barkholt, Vibeke; Szépfalusi, Zsolt

    2008-01-01

    (LPS)-free allergens were evaluated at different time-points. Fractions of contaminated BLG were generated and assayed on their immuno-stimulatory capacity. The involvement of toll-like receptor (TLR) 2 and 4 was investigated by blocking antibodies and TLR-transfected human embryonic kidney cells....... Results The proliferative response of cord blood (CB)-derived mononuclear cells towards allergen-preparations at day 3 was related to the level of LPS contamination. At day 7, proliferation was also detected in the absence of endotoxin. Cytokine production in CB was strongly affected by the content of...... endotoxin, TLR-4 dependent and not related to the allergen content. Allergen- and endotoxin-induced proliferative responses were generally significantly higher in CB than in adult blood. Conclusion Endotoxins in allergen preparations confound allergen-specific cellular responses. The impact of these...

  8. An assessment of RNA content in Prymnesium parvum, Prymnesium polylepis, cf. Chattonella sp. and Karlodinium veneficum under varying environmental conditions for calibrating an RNA microarray for species detection.

    Science.gov (United States)

    McCoy, Gary R; Kegel, Jessica U; Touzet, Nicolas; Fleming, Gerard T A; Medlin, Linda K; Raine, Robin

    2014-04-01

    Traditional methods of identification and enumeration can be somewhat ambiguous when identifying phytoplankton that requires electron microscopic examination to verify specific morphological features. Members of the genus Prymnesium (division Haptophyta), members of the Raphidophyceae and naked dinoflagellates are examples of such phytoplankton whose identification can be difficult. One alternative to traditional microscopy-based methods of identification is to use molecular protocols to detect target species. Methods that measure cellular DNA and RNA content can be used to estimate the number of cells present in a sample. This study investigated the variation of RNA yields in Prymnesium parvum, P. polylepis, cf. Chattonella sp. and Karlodinium veneficum cells grown under different light, temperature, salinity and inorganic nutrient conditions. This information was used to calibrate the signal intensity of a variety of oligonucleotide probes spotted onto the microarrays for the detection of toxic algae (MIDTAL), which is being developed to aid national monitoring agencies and to provide a faster means of identifying and quantifying harmful phytoplankton in water column samples. PMID:24392749

  9. Shared clonal cytogenetic abnormalities in aberrant mast cells and leukemic myeloid blasts detected by single nucleotide polymorphism microarray-based whole-genome scanning.

    Science.gov (United States)

    Frederiksen, John K; Shao, Lina; Bixby, Dale L; Ross, Charles W

    2016-04-01

    Systemic mastocytosis (SM) is characterized by a clonal proliferation of aberrant mast cells within extracutaneous sites. In a subset of SM cases, a second associated hematologic non-mast cell disease (AHNMD) is also present, usually of myeloid origin. Polymerase chain reaction and targeted fluorescence in situ hybridization studies have provided evidence that, in at least some cases, the aberrant mast cells are related clonally to the neoplastic cells of the AHNMD. In this work, a single nucleotide polymorphism microarray (SNP-A) was used to characterize the cytogenetics of the aberrant mast cells from a patient with acute myeloid leukemia and concomitant mast cell leukemia associated with a KIT D816A mutation. The results demonstrate the presence of shared cytogenetic abnormalities between the mast cells and myeloid blasts, as well as additional abnormalities within mast cells (copy-neutral loss of heterozygosity) not detectable by routine karyotypic analysis. To our knowledge, this work represents the first application of SNP-A whole-genome scanning to the detection of shared cytogenetic abnormalities between the two components of a case of SM-AHNMD. The findings provide additional evidence of a frequent clonal link between aberrant mast cells and cells of myeloid AHNMDs, and also highlight the importance of direct sequencing for identifying uncommon activating KIT mutations. PMID:26865278

  10. First improvements in the detection and quantification of label-free nucleic acids by laser-induced breakdown spectroscopy: Application to the deoxyribonucleic acid micro-array technology

    International Nuclear Information System (INIS)

    The accurate quantification of nucleic acids is essential in many fields of modern biology and industry, and in some cases requires the use of fluorescence labeling. Yet, in addition to standardization problems and quantification reproducibility, labeling can modify the physicochemical properties of molecules or affect their stability. To address these limitations, we have developed a novel method to detect and quantify label-free nucleic acids. This method is based on stoichiometric proportioning of phosphorus in the nucleic acid skeleton, using laser-induced breakdown spectroscopy, and a specific statistical analysis, which indicates the error probability for each measurement. The results obtained appear to be quantitative, with a limit of detection of 105 nucleotides/μm2 (i.e. 2 x 1013 phosphorus atoms/cm2). Initial micro-array analysis has given very encouraging results, which point to new ways of quantifying hybridized nucleic acids. This is essential when comparing molecules of different sequences, which is presently very difficult with fluorescence labeling

  11. Compressive Sensing DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Sheikh Mona A

    2009-01-01

    Full Text Available Compressive sensing microarrays (CSMs are DNA-based sensors that operate using group testing and compressive sensing (CS principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed.

  12. A comparative analysis of DNA barcode microarray feature size

    OpenAIRE

    Ammar, Ron; SMITH, ANDREW M.; Heisler, Lawrence E.; Giaever, Guri; Nislow, Corey

    2009-01-01

    Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density), but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platfor...

  13. GC-MS analysis of allergens in plant oils meant to cosmetics

    Directory of Open Access Journals (Sweden)

    Kaloustian Jacques

    2007-03-01

    Full Text Available Cutaneous allergy occurs mainly as a result of the use of domestic products and cosmetics. Some fragrances, present in these products, may contain compounds that are responsible for allergy (allergens. The European Council offered a Directive limiting the level of 26 allergens found in cosmetics. GC-MS technique was used to determine the retention times of 25 allergens, determine detection and quantification limits and make calibration with standard solution of each allergen in concentrations ranging from 10 to 200 mgL–1 (21 allergens and 50 to 200 mgL–1 (4 allergens. Quantification was performed by the use of 2 internal standards (tetradecane and hexadecane. Seven oils issued from plants were studied by GC-MS. For all of them, the concentration of potential allergens was lower than their minimum detectable level. The alcoholic solution of extracts issued from different samples of oil did not demonstrate the presence of any quantifiable allergen, even when was concentrated 25 times. GC-MS could be a useful technique in the identification and, if necessary, quantification of allergen in ingredients meant to cosmetics.

  14. Kiwifruit Allergy in Children: Characterization of Main Allergens and Patterns of Recognition

    Directory of Open Access Journals (Sweden)

    Ana Moreno Álvarez

    2015-10-01

    Full Text Available Kiwifruit allergy has been described mostly in the adult population, but immunoglobulin (IgE-mediated allergic reactions to kiwifruit appear to be occurring more frequently in children. To date, 13 allergens from kiwifruit have been identified. Our aim was to identify kiwifruit allergens in a kiwifruit allergic-pediatric population, describing clinical manifestations and patterns of recognition. Twenty-four children were included. Diagnosis of kiwifruit allergy was based on compatible clinical manifestations and demonstration of specific IgE by skin prick test (SPT and/or serum-specific IgE determination. SDS-PAGE and immunoblotting were performed with kiwifruit extract, and proteins of interest were further analyzed by mass spectrometry/mass spectrometry. For component-resolved in vitro diagnosis, sera of kiwifruit-allergic patients were analyzed by an allergen microarray assay. Act d 1 and Act d 2 were bound by IgE from 15 of 24 children. Two children with systemic manifestations recognized a protein of 15 kDa, homologous to Act d 5. Act d 1 was the allergen with the highest frequency of recognition on microarray chip, followed by Act d 2 and Act d 8. Kiwifruit allergic children develop systemic reactions most frequently following ingestion compared to adults. Act d 1 and Act d 2 are major allergens in the pediatric age group.

  15. Taxonomy of Allergenic Fungi.

    Science.gov (United States)

    Levetin, Estelle; Horner, W Elliott; Scott, James A

    2016-01-01

    The Kingdom Fungi contains diverse eukaryotic organisms including yeasts, molds, mushrooms, bracket fungi, plant rusts, smuts, and puffballs. Fungi have a complex metabolism that differs from animals and plants. They secrete enzymes into their surroundings and absorb the breakdown products of enzyme action. Some of these enzymes are well-known allergens. The phylogenetic relationships among fungi were unclear until recently because classification was based on the sexual state morphology. Fungi lacking an obvious sexual stage were assigned to the artificial, now-obsolete category, "Deuteromycetes" or "Fungi Imperfecti." During the last 20 years, DNA sequencing has resolved 8 fungal phyla, 3 of which contain most genera associated with important aeroallergens: Zygomycota, Ascomycota, and Basidiomycota. Advances in fungal classification have required name changes for some familiar taxa. Because of regulatory constraints, many fungal allergen extracts retain obsolete names. A major benefit from this reorganization is that specific immunoglobulin E (IgE) levels in individuals sensitized to fungi appear to closely match fungal phylogenetic relationships. This close relationship between molecular fungal systematics and IgE sensitization provides an opportunity to systematically look at cross-reactivity and permits representatives from each taxon to serve as a proxy for IgE to the group. PMID:26725152

  16. Investigating the sensitivity of a fluorescence-based microarray for the detection of fruit-tree viruses

    Czech Academy of Sciences Publication Activity Database

    Lenz, Ondřej; Petrzik, Karel; Špak, Josef

    2008-01-01

    Roč. 148, 1/2 (2008), s. 96-105. ISSN 0166-0934 R&D Projects: GA MŠk OC 853.001 Institutional research plan: CEZ:AV0Z50510513 Keywords : plant pathology * fruit-tree viruses * detection Subject RIV: EE - Microbiology, Virology Impact factor: 2.077, year: 2008

  17. Molecular probes and microarrays for the detection of toxic algae in the genera Dinophysis and Phalacroma (Dinophyta)

    OpenAIRE

    Edvardsen, Bente; Dittami, Simon M; Groben, René; Brubak, Sissel; Escalera, Laura; Francisco RODRÍGUEZ; Reguera, Beatriz; Chen, Jixin; Medlin, Linda K.

    2012-01-01

    Dinophysis and Phalacroma species containing diarrheic shellfish toxins and pectenotoxins occur in coastal temperate waters all year round and prevent the harvesting of mussels during several months each year in regions in Europe, Chile, Japan, and New Zealand. Toxicity varies among morphologically similar species, and a precise identification is needed for early warning systems. Molecular techniques using ribosomal DNA sequences offer a means to identify and detect precisely the potentially ...

  18. Asthma-associated allergen Alternaria induces STAT6 dependent epithelial FIZZ1 that promotes airway fibrosis

    OpenAIRE

    Khorram, Naseem Melissa

    2011-01-01

    Alternaria is a fungal allergen whereby sensitization to it serves as a risk factor for the development, persistence, and severity of asthma. Naïve WT C57/B6 mice received one intranasal challenge with Alternaria, Candida, or Aspergillus allergen extracts and airway eosinophil numbers analyzed 24 hours later. RNA from airway epithelial cells was processed for gene microarray analysis. Lung cells from naïve WT and collagen-1 GFP mice were incubated with rFIZZ1, stained for cell type, and analy...

  19. Molecular Characteristics of Cockroach Allergens

    Institute of Scientific and Technical Information of China (English)

    Chii-Huei Wu; Mey-Fann Lee

    2005-01-01

    Cockroaches, commonly found in urban dwellings worldwide, have long been considered vectors of various infectious diseases and cockroach allergens are one of the major etiologic risk factors for IgE-mediated allergic respiratory illness throughout the world. A high prevalence of cockroach hypersensitivity in atopic (20-55 %) and asthmatic (49-60%) populations has been documented. Cockroach allergens with molecular weights ranging from 6 to 120 kD have been identified by various standard immunochemical techniques. This article covers the characteristics of major cockroach allergens that have been purified, sequenced, cloned, and produced as recombinant proteins.

  20. Multiplexed lateral flow microarray assay for detection of citrus pathogens Xylella fastidiosa and Xanthomonas axonopodis pv citri

    Science.gov (United States)

    Cary; R. Bruce; Stubben, Christopher J.

    2011-03-22

    The invention provides highly sensitive and specific assays for the major citrus pathogens Xylella fastidiosa and Xanthomonas axonopodis, including a field deployable multiplexed assay capable of rapidly assaying for both pathogens simultaneously. The assays are directed at particular gene targets derived from pathogenic strains that specifically cause the major citrus diseases of citrus variegated chlorosis (Xylella fastidiosa 9a5c) and citrus canker (Xanthomonas axonopodis pv citri). The citrus pathogen assays of the invention offer femtomole sensitivity, excellent linear dynamic range, and rapid and specific detection.

  1. Differential detection of alternatively spliced variants of Ciz1 in normal and cancer cells using a custom exon-junction microarray

    International Nuclear Information System (INIS)

    Ciz1 promotes initiation of mammalian DNA replication and is present within nuclear matrix associated DNA replication factories. Depletion of Ciz1 from normal and cancer cells restrains entry to S phase and inhibits cell proliferation. Several alternative splicing events with putative functional consequences have been identified and reported, but many more variants are predicted to exist based on publicly available mRNAs and expressed sequence tags. Here we report the development and validation of a custom exon and exon-junction microarray focused on the human CIZ1 gene, capable of reproducible detection of differential splice-variant expression. Using a pair of paediatric cancer cell lines and a pool of eight normal lines as reference, the array identified expected and novel CIZ1 splicing events. One novel variant (delta 8-12) that encodes a predicted protein lacking key functional sites, was validated by quantitative RT-PCR and found to be over-represented in a range of other cancer cell lines, and over half of a panel of primary lung tumours. Expression of CIZ1 delta 8-12 appears to be restricted to cancer cells, and may therefore be a useful novel biomarker

  2. Prevalence of food and airborne allergens in allergic patients in Kerman

    Directory of Open Access Journals (Sweden)

    Hamed Fouladseresht

    2014-07-01

    Full Text Available Background: Detection of various environmental allergens is the major challenge in allergic diseases and the only treatment is avoiding these allergens. The aim of this study was to determine the prevalence of food and airborne allergens in allergic patients using Skin Prick Test (SPT. Methods: A cross-sectional study was done on clinically confirmed patients of atopic-dermatitis (n=54, allergenic-rhinitis (n=64 and chronic-urticaria (n=39 who referred to asthma and allergy clinic at Afzali-Pour hospital in Kerman during 2008-2010. Skin prick test was done using allergen extracts to determine the patients' sensitivity to food and airborne antigens. Results: Fifty-nine percent of patients responded to at least one allergen. Allergy to airborne and food allergens was 55.9 % and 21.7%, respectively. Chenopodiaceae (22.9% and egg white (10.2% were most prevalent airborne and food allergens. Allergy to cockroach, egg white, egg yolk and tomato was significantly higher in males than in females (P<0.05. Conclusion: The results indicated that allergy to food and airborne allergens is different depending on the nutrition and environmental conditions.

  3. Detección de alérgenos de huevo en fideos secos por método de elisa Detection of egg allergens in dried pasta using elisa method

    Directory of Open Access Journals (Sweden)

    María Julieta Binaghi

    2012-06-01

    acuerdo con los resultados obtenidos el método ELISA permitió la detección de alergenos de huevo en varias de las muestras provistas por la industria y también en algunas muestras comerciales con leyendas precautorias. Para una correcta rotulación de estos productos resultaría necesario contar con valores umbrales establecidos por la Autoridad Sanitaria Nacional.As the mandatory declaration of allergens will be soon included in the Argentine Food Code (article 235, section seven, it is necessary to implement control methodologies to detect the possible existence of allergens in commercial products. The presence of egg allergens in pasta and in products with common wheat flour and /or durum wheat semolina is possible as a result of cross contamination. The objective of this work was to evaluate, using ELISA method, the possible contamination with egg proteins in products made with common wheat flour and /or durum wheat semolina provided by a manufacturer to verify a possible contamination with egg proteins and to analyse commercial products with precautionary labels. Nineteen products made with common wheat flour and /or durum wheat semolina provided by a manufacturer and nine commercial products (dry pasta were analysed. The egg allergen was analyzed using the r-biopharm kit - ELISA. The samples were analysed in duplicates following the kit protocol. Among the samples provided by manufacturers there were products produced in line with the production of pasta with egg, with values below the quantification limit of the kit; products produced with a low percentage of milled products that could be made with egg, in which very low quantities of egg allergens were found (lower than 5 ppm, and products produced with a high percentage of milled products that could be made with egg and in which higher concentrations were obtained (higher than 5 ppm; whole dried egg. Five of the commercial samples presented concentrations that were below or similar to the quantification limit

  4. A revisit to cockroach allergens.

    Science.gov (United States)

    Sookrung, Nitat; Chaicumpa, Wanpen

    2010-01-01

    Among cockroaches (CR) that live in people's homes, two species, i.e., German CR (Blattella germanica) and American CR (Periplaneta americana) predominate in temperate and tropical areas, respectively. CR is an important source of inhalant indoor allergens that sensitize atopic subjects to (localized) type I hypersensitivity or atopy including allergic rhinitis and atopic asthma. In Thailand the predominant CR species is P. americana. CR allergens are found throughout CR infested houses; the number found in kitchens correlates with the degree of CR infestation while sensitization and reactivation of the allergic morbidity are likely to occur in the living room and bedroom. Levels of the CR allergens in homes of CR allergic Thais, measured by using locally made quantification test kits, revealed that the highest levels occur in dust samples collected from the wooden houses of urban slums and in the cool and dry season. CR allergens are proteins that may be derived from any anatomical part of the insect at any developmental stage. The allergens may be also from CR secretions, excretions, body washes or frass. The proteins may be the insect structural proteins, enzymes or hormones. They may exist as dimers/multimers and/or in different isoforms. Exposure to CR allergens in infancy leads to allergic morbidity later in life. Clinical symptoms of CR allergy are usually more severe and prolonged than those caused by other indoor allergens. The mechanisms of acute and chronic airway inflammation and airway hyper-responsiveness (AHR) have been addressed including specific IgE- and non-IgE-mediated mechanisms, i.e., role of protease-activated receptor-2 (PAR2). Participation of various allergen activated-CD4+ T cells of different sublineages, i.e., Th2, Th17, Th22, Th9, Th25, Tregs/Th3 as well as invariant NKT cells, in asthma pathogenesis have been mentioned. The diagnosis of CR allergy and the allergy intervention by CR population control are also discussed. PMID:21038777

  5. DNA Microarray Technique

    Directory of Open Access Journals (Sweden)

    Thakare SP

    2012-11-01

    Full Text Available DNA Microarray is the emerging technique in Biotechnology. The many varieties of DNA microarray or DNA chip devices and systems are described along with their methods for fabrication and their use. It also includes screening and diagnostic applications. The DNA microarray hybridization applications include the important areas of gene expression analysis and genotyping for point mutations, single nucleotide polymorphisms (SNPs, and short tandem repeats (STRs. In addition to the many molecular biological and genomic research uses, this review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes.

  6. Risk assessment of allergen metals in cosmetic products.

    Science.gov (United States)

    Sipahi, Hande; Charehsaz, Mohammad; Güngör, Zerrin; Erdem, Onur; Soykut, Buğra; Akay, Cemal; Aydin, Ahmet

    2015-01-01

    Cosmetics are one of the most common reasons for hospital referrals with allergic contact dermatitis. Because of the increased use of cosmetics within the population and an increase in allergy cases, monitoring of heavy metals, especially allergen metals, is crucial. The aim of this study was to investigate the concentration of allergen metals, nickel (Ni), cobalt (Co), and chromium (Cr), in the most commonly used cosmetic products including mascara, eyeliner, eye shadow, lipstick, and nail polish. In addition, for safety assessment of cosmetic products, margin of safety of the metals was evaluated. Forty-eight makeup products were purchased randomly from local markets and large cosmetic stores in Istanbul, Turkey, and an atomic absorption spectrometer was used for metal content determination. Risk assessment of the investigated cosmetic products was performed by calculating the systemic exposure dosage (SED) using Scientific Committee on Consumer Safety guideline. According to the results of this investigation in all the samples tested, at least two of the allergen metals, Ni and/or Co and/or Cr were detected. Moreover, 97% of the Ni-detected products, 96% of Cr- and 54% of Co-detected products, contained over 1 μg/g of this metals, which is the suggested ultimate target value for sensitive population and thereby can be considered as the possible allergen. On the basis of the results of this study, SED of the metals was negligible; however, contact dermatitis caused by cosmetics is most probably due to the allergen metal content of the products. In conclusion, to assess the safety of the finished products, postmarketing vigilance and routine monitoring of allergen metals are very important to protect public health. PMID:26753435

  7. Development and in-house validation of an allergen-specific ELISA for quantification of Bet v 4 in diagnostic and therapeutic birch allergen products.

    Science.gov (United States)

    Dehus, Oliver; Zimmer, Julia; Döring, Sascha; Führer, Frank; Hanschmann, Kay-Martin; Holzhauser, Thomas; Neske, Florian; Strecker, Daniel; Trösemeier, Jan-Hendrik; Vieths, Stefan; Kaul, Susanne

    2015-02-01

    Birch (Betula) pollen is a major cause of allergy in northern and central Europe. The allergenic potency of products for diagnosis and therapy of birch pollen allergy is adjusted nearly exclusively to the major birch pollen allergen Bet v 1. Although every fifth patient is additionally sensitized to Bet v 4, both content and variability of this minor allergen in birch allergen products remain unclear due to a lack of simple and cost-effective quantitative methods. This study aimed to develop and in-house validate the first Bet v 4-specific sandwich enzyme-linked immunosorbent assay (ELISA). Based on a murine monoclonal antibody in combination with a polyclonal rabbit antiserum, the ELISA proved to be highly sensitive, with a lower limit of quantification of 30 pg/ml Bet v 4. After confirmation of satisfactory accuracy, reproducibility, and robustness, the ELISA was utilized to quantify Bet v 4 in 30 authorized birch allergen products. The allergen was detected in all samples tested, ranging from 0.2 to 4.4 μg/ml. No significant correlation of Bet v 4 was found with the respective amount of Bet v 1. In contrast to Bet v 1, also no correlation of Bet v 4 with total protein content or total allergenic activity could be observed. Thus, it seems presently unfeasible to base birch allergen product standardization additionally on Bet v 4. In light of these results, the continuous monitoring of Bet v 4 in birch allergen products with the presented ELISA will provide a basis for the understanding of the clinical relevance of minor allergens. PMID:25572690

  8. Crystal structure of peanut (Arachis hypogaea) allergen Ara h 5

    Science.gov (United States)

    Profilins from numerous species are known to be allergens, including food allergens, such as peanut (Arachis hypogaea) allergen Ara h 5, and pollen allergens, such as birch allergen Bet v 2. Patients with pollen allergy can also cross-react to peanut. Structural characterization of allergens will al...

  9. Allergen identification in 5 grasses by means of crossed radioimmunoelectrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Diener, C.; Skibbe, K.; Jaeger, L. (Friedrich-Schiller-Universitaet, Jena (German Democratic Republic))

    1984-01-01

    Using crossed radioimmunoelectrophoresis aqueous extracts from pollen of Phleum pratense, Lolium perenne, Poa pratensis, Festuca pratensis and Alopecurus pratensis were investigated for allergen composition. Between 24 and 32 antigens were detected. Employing sera from 11 patients with well established hay fever, IgE binding could be demonstrated in 15 out of 28 antigens in Phleum pratense, 13 out of 32 in Lolium perenne, 14 out of 26 in Poa pratensis, 12 out of 24 Festuca pratensis and 12 out of 24 antigens in Alopecurus pratensis. The 11 patients showed an individual pattern of sensitization against the various pollen allergens.

  10. Research on DNA microarray chip method for detecting drug resistance of Mycobacterium tuberculosis%DNA 微阵列芯片法用于检测结核分枝杆菌耐药性的研究

    Institute of Scientific and Technical Information of China (English)

    刘亚芹; 杨振斌; 冯冬霞; 王海英

    2014-01-01

    目的:通过与传统的比例法在结核分枝杆菌耐药性检测的比较,评价 DNA 微阵列法用于检测结核分枝杆菌耐药性的可行性。方法随机抽取本院2012年1月至2013年3月从临床标本中分离培养所得的结核分枝杆菌54株,通过 DNA 微阵列法和比例法分别进行异烟肼和利福平的耐药性检测并对结果进行比较分析。结果以比例法为金标准,DNA 微阵列法对异烟肼和利福平的耐药检测结果与比例法的符合率分别为75.0%、91.0%。结论 DNA 微阵列技术适用于临床一线耐药结核分枝杆菌的快速筛查。%Objective To evaluate the feasibility of the DNA microarray method used in detecting the drug resistance of Myco-bacterium tuberculosis by comparing the traditional proportion method and the DNA microarray method for detecting the drug re-sistance of Mycobacterium tuberculosis.Methods 54 strains of Mycobacterium tuberculosis isolated from clinical specimens in our hospital from January 2012 to March 2013 were randomly extracted and their resistance to isonicotinic acid hydrazide (INH)and rifampicin(RFP)was detected by the DNA microarray method and the proportion method.The detection results were performed the comparative analysis.Results With the proportion method as the golden standard,the coincidence rates of the DNA microarray method for detecting the Mycobacterium tuberculosis resistance to INH and RFP were 75% and 91.0% respectively.Conclusion The DNA microarray technique is suitable for the rapid screening of clinical first-line drug resistant Mycobacterium tuberculosis.

  11. Mesenteric lymph node transcriptome profiles in BALB/c mice sensitized to three common food allergens

    Directory of Open Access Journals (Sweden)

    Boermans Herman J

    2011-01-01

    Full Text Available Abstract Background Food allergy is a serious health concern among infants and young children. Although immunological mechanism of food allergy is well documented, the molecular mechanism(s involved in food allergen sensitization have not been well characterized. Therefore, the present study analyzed the mesenteric lymph node (MLN transcriptome profiles of BALB/c mice in response to three common food allergens. Results Microarray analysis identified a total of 1361, 533 and 488 differentially expressed genes in response to β-lactoglobulin (BLG from cow's milk, ovalbumin (OVA from hen's egg white and peanut agglutinin (PNA sensitizations, respectively (p Conclusions Immunological profiles indicate that the allergen dosages used are sufficient to sensitize the BALB/c mice and to conduct transcriptome profiling. Microarray studies identified several differentially expressed genes in the sensitization phase of the food allergy. These findings will help to better understand the underlying molecular mechanism(s of food allergen sensitizations and may be useful in identifying the potential biomarkers of food allergy.

  12. Exploring the temporal development of childhood IgE profiles to allergen components

    Directory of Open Access Journals (Sweden)

    Önell Annica

    2012-12-01

    Full Text Available Abstract Background Children often develop allergies that may or not persist into adulthood. Although the different allergic symptoms over time have been well documented, the underlying pattern of sensitization to various proteins and subsequent allergy development is unexplored. The aim was to study the sensitization pattern to allergen components over time from infancy to adulthood in a group of infants with heredity for allergic diseases. Methods IgE profiles were monitored in a group of 67 children from 6 months to 18 years using a microarray chip (ImmunoCAP® ISAC containing 103 allergen components derived from 47 allergen sources. The chip IgE profile was compared with clinical history, skin prick test results and diagnoses (atopic dermatitis, asthma and allergic rhinoconjunctivitis at each time point for each child. Results IgE profiles were unique for each child and showed broad agreement with the results of skin prick tests and doctors’ diagnoses. In addition, close examination of the IgE profiles often revealed early indication of subsequent allergies. IgE profiles also facilitated the examination of cross-reactivity contra co-sensitization, thereby greatly enhancing the possibility for managing patients. Conclusion This explorative description indicates that sensitization pattern to allergen components differs over time as well as among allergic individuals when examined with microarray technology.

  13. Understanding Allergic Asthma from Allergen Inhalation Tests

    Directory of Open Access Journals (Sweden)

    Donald W Cockcroft

    2007-01-01

    Full Text Available The allergen challenge has evolved, in less than 150 years, from a crude tool used to document the etiology of allergen-induced disease to a well-controlled tool used today to investigate the pathophysiology and pharmacotherapy of asthma. Highlights of the authors’ involvement with the allergen challenge include confirmation of the immunoglobulin E-dependence of the late asthmatic response, importance of (nonallergic airway hyper-responsiveness as a determinant of the airway response to allergen, identification of allergen-induced increase in airway hyper-responsiveness, documentation of beta2-agonist-induced increase in airway response to allergen (including eosinophilic inflammation, advances in understanding the pathophysiology and kinetics of allergen-induced airway responses, and development of a muticentre clinical trial group devoted to using the allergen challenge for investigating promising new therapeutic strategies for asthma.

  14. Associations between baseline allergens and polysensitization

    DEFF Research Database (Denmark)

    Carlsen, B.C.; Menne, T.; Johansen, J.D.

    2008-01-01

    : Seven allergens - parabens mix, N-isopropyl-N-phenyl-p-phenylenediamine, sesquiterpene lactone mix, wool alcohols, potassium dichromate, Myroxylon pereirae, and cobalt chloride - showed statistically significant positive associations to polysensitization. Five allergens p-phenylenediamine, neomycin...

  15. The Allergen Bank: a source of extra contact allergens for the dermatologist in practice

    DEFF Research Database (Denmark)

    Andersen, Klaus Ejner; Rastogi, S C; Carlsen, L

    1996-01-01

    described. During its first 23 months 28 dermatologists asked for 2,209 allergen samples for testing of 386 patients, an average of 6 allergens per patient and 14 patients per dermatologist. A total number of 164 positive reactions have been registered, and 440 of the 540 allergens have been in use. One...... third of the positive reactions were caused by the 16 most frequently ordered allergens, which amounted to 340 allergen samples. The allergens included plant chemicals, acrylates, animal feed additives, fragrance chemicals and preservatives. Selected allergens were investigated for stability during...

  16. Microarray analysis in pulmonary hypertension.

    Science.gov (United States)

    Hoffmann, Julia; Wilhelm, Jochen; Olschewski, Andrea; Kwapiszewska, Grazyna

    2016-07-01

    Microarrays are a powerful and effective tool that allows the detection of genome-wide gene expression differences between controls and disease conditions. They have been broadly applied to investigate the pathobiology of diverse forms of pulmonary hypertension, namely group 1, including patients with idiopathic pulmonary arterial hypertension, and group 3, including pulmonary hypertension associated with chronic lung diseases such as chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. To date, numerous human microarray studies have been conducted to analyse global (lung homogenate samples), compartment-specific (laser capture microdissection), cell type-specific (isolated primary cells) and circulating cell (peripheral blood) expression profiles. Combined, they provide important information on development, progression and the end-stage disease. In the future, system biology approaches, expression of noncoding RNAs that regulate coding RNAs, and direct comparison between animal models and human disease might be of importance. PMID:27076594

  17. Cross-Reactivity of Peanut Allergens

    OpenAIRE

    Bublin, Merima; Breiteneder, Heimo

    2014-01-01

    Peanut seeds are currently widely used as source of human food ingredients in the United States of America and in European countries due to their high quality protein and oil content. This article describes the classification and molecular biology of peanut seed allergens with particular reference to their cross-reactivities. Currently, the IUIS allergen nomenclature subcommittee accepts 12 peanut allergens. Two allergens belong to the cupin and four to the prolamin superfamily, and six are d...

  18. Sensitising capacity of peptides from food allergens

    OpenAIRE

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard; Barkholt, Vibeke

    2012-01-01

    Food allergy is a major health problem in the Western countries, affecting 3-8% of the population. What makes a dietary protein a food allergen has not yet been established, though several characteristics have been proposed to be shared by food allergens. One of the features believed to be a general characteristicof food allergens is resistance to digestion. This is based on studies showing that allergenic dietary proteins in general are more resistant to digestion than dietary proteins with ...

  19. Food Production and Processing Considerations of Allergenic Food Ingredients: A Review

    Directory of Open Access Journals (Sweden)

    Pedro A. Alvarez

    2012-01-01

    Full Text Available Although most consumers show no adverse symptoms to food allergens, health consequences for sensitized individuals can be very serious. As a result, the Codex General Standard for the Labelling of Prepackaged Foods has specified a series of allergenic ingredients/substances requiring mandatory declaration when present in processed prepackaged food products. Countries adhering to international standards are required to observe this minimum of eight substances, but additional priority allergens are included in the list in some countries. Enforcement agencies have traditionally focused their effort on surveillance of prepackaged goods, but there is a growing need to apply a bottom-up approach to allergen risk management in food manufacturing starting from primary food processing operations in order to minimize the possibility of allergen contamination in finished products. The present paper aims to review food production considerations that impact allergen risk management, and it is directed mainly to food manufacturers and policy makers. Furthermore, a series of food ingredients and the allergenic fractions identified from them, as well as the current methodology used for detection of these allergenic foods, is provided.

  20. Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information

    OpenAIRE

    Tong, Joo Chuan; Lim, Shen Jean; Muh, Hon Cheng; Chew, Fook Tim; Tammi, Martti T.

    2009-01-01

    Summary: A variety of specialist databases have been developed to facilitate the study of allergens. However, these databases either contain different subsets of allergen data or are deficient in tools for assessing potential allergenicity of proteins. Here, we describe Allergen Atlas, a comprehensive repository of experimentally validated allergen sequences collected from in-house laboratory, online data submission, literature reports and all existing general-purpose and specialist databases...

  1. Emergent and unusual allergens in cosmetics.

    Science.gov (United States)

    Pascoe, David; Moreau, Linda; Sasseville, Denis

    2010-01-01

    Allergic contact dermatitis from cosmetics is a common problem that is occasionally caused by new or rare allergens. When a patient has a positive patch test to a cosmetic product but to none of the common or commercially available allergens, it is important to further patch-test this patient to the ingredients of the product. Thorough testing with the breakdown of ingredients, usually obtained through cooperation with the manufacturer, often allows identification of the culprit allergen in the cosmetic product. In this article, we discuss emerging or rare allergens discovered by this method, including nail lacquer and lipstick allergens, copolymers, shellac, alkyl glucosides, glycols, protein derivatives, idebenone, and octocrylene. PMID:20487655

  2. Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE

    Directory of Open Access Journals (Sweden)

    Ile Kristina E

    2003-07-01

    Full Text Available Abstract Background The ADGE technique is a method designed to magnify the ratios of gene expression before detection. It improves the detection sensitivity to small change of gene expression and requires small amount of starting material. However, the throughput of ADGE is low. We integrated ADGE with DNA microarray (ADGE microarray and compared it with regular microarray. Results When ADGE was integrated with DNA microarray, a quantitative relationship of a power function between detected and input ratios was found. Because of ratio magnification, ADGE microarray was better able to detect small changes in gene expression in a drug resistant model cell line system. The PCR amplification of templates and efficient labeling reduced the requirement of starting material to as little as 125 ng of total RNA for one slide hybridization and enhanced the signal intensity. Integration of ratio magnification, template amplification and efficient labeling in ADGE microarray reduced artifacts in microarray data and improved detection fidelity. The results of ADGE microarray were less variable and more reproducible than those of regular microarray. A gene expression profile generated with ADGE microarray characterized the drug resistant phenotype, particularly with reference to glutathione, proliferation and kinase pathways. Conclusion ADGE microarray magnified the ratios of differential gene expression in a power function, improved the detection sensitivity and fidelity and reduced the requirement for starting material while maintaining high throughput. ADGE microarray generated a more informative expression pattern than regular microarray.

  3. A comparative analysis of DNA barcode microarray feature size

    OpenAIRE

    Smith Andrew M; Ammar Ron; Heisler Lawrence E; Giaever Guri; Nislow Corey

    2009-01-01

    Abstract Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density), but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarra...

  4. Skin Barrier Function and Allergens

    DEFF Research Database (Denmark)

    Engebretsen, Kristiane Aasen; Thyssen, Jacob Pontoppidan

    2016-01-01

    The skin is an important barrier protecting us from mechanical insults, microorganisms, chemicals and allergens, but, importantly, also reducing water loss. A common hallmark for many dermatoses is a compromised skin barrier function, and one could suspect an elevated risk of contact sensitization...

  5. Characterisation of wheat flour allergens

    Czech Academy of Sciences Publication Activity Database

    Šotkovský, Petr; Fuchs, M.; Havranová, M.; Tučková, Ludmila

    Vienna : Basic Science in Allergology, 2006, s. 416-416. [Congress of the European Academy of Allergology and Clinical Immunology /25./. Vienna (AT), 10.06.2006-14.06.2006] R&D Projects: GA ČR GA310/05/2245 Institutional research plan: CEZ:AV0Z50200510 Keywords : wheat flour * allergen * protein Subject RIV: EE - Microbiology, Virology

  6. Allergen immunotherapy for allergic rhinoconjunctivitis

    DEFF Research Database (Denmark)

    Dhami, Sangeeta; Nurmatov, Ulugbek; Roberts, Graham;

    2016-01-01

    BACKGROUND: The European Academy of Allergy and Clinical Immunology (EAACI) is in the process of developing the EAACI Guidelines for Allergen Immunotherapy (AIT) for the Management of Allergic Rhinoconjunctivitis. We seek to critically assess the effectiveness, cost-effectiveness and safety of AI...

  7. Anaphylaxis to Insect Venom Allergens

    DEFF Research Database (Denmark)

    Ollert, Markus; Blank, Simon

    2015-01-01

    by a lack of specificity and venom immunotherapy by severe side effects and incomplete protection. In recent years, the knowledge about the molecular composition of Hymenoptera venoms has significantly increased and more and more recombinant venom allergens with advanced characteristics have become......, and to contribute to the understanding of the immunological mechanisms elicited by insect venoms....

  8. Immune response to allergens in sheep sensitized to house dust mite

    Directory of Open Access Journals (Sweden)

    Velden Joanne

    2008-10-01

    Full Text Available Abstract Background House dust mite (HDM allergens are a major cause of allergic asthma. Most studies using animal models of allergic asthma have used rodents sensitized with the 'un-natural' allergen ovalbumin. It has only recently been recognized that the use of animal models based on HDM provide a more relevant insight into the allergen-induced mechanisms that underpin human allergic disease. We have previously described a sheep model of human allergic asthma that uses Dermatophagoides pteronyssinus HDM. The present study extends our understanding of the immune effects of HDM and the allergens Der p 1 and Der p 2 in the sheep model of asthma. Methods Peripheral blood sera from non-sensitized (control sheep and sheep sensitized to HDM was collected to determine immunoglobulin (Ig reactivities to HDM, Der p 1 and Der p 2 by ELISA. Bronchoalveolar lavage (BAL fluid collected following allergen challenge was also assessed for the presence of HDM-specific antibodies. To examine the cellular immune response to HDM allergens, T cell proliferation and cutaneous responses were assessed in sensitized and control sheep. Results Strong HDM- and Der p 1-specific IgE, IgG1, IgG2 and IgA serum responses were observed in sensitized sheep, while detectable levels of HDM-specific IgG1 and IgA were seen in BAL fluid of allergen-challenged lungs. In contrast, minimal antibody reactivity was observed to Der p 2. Marked T cell proliferation and late phase cutaneous responses, accompanied by the recruitment of eosinophils, indicates the induction of a cellular and delayed-type hypersensitivity (DTH type II response by HDM and Der p 1 allergen, but not Der p 2. Conclusion This work characterizes the humoral and cellular immune effects of HDM extract and its major constituent allergens in sheep sensitized to HDM. The effects of allergen in HDM-sensitized sheep were detectable both locally and systemically, and probably mediated via enzymatic and immune actions of the

  9. Differentiating pancreatic lesions by Microarray and QPCR analysis of pancreatic juice RNAs

    NARCIS (Netherlands)

    C.D. Rogers; N. Fukushima; N. Sato; C. Shi; N. Prasad; S.R. Hustinx; H. Matsubayashi; M. Canto; J.R. Eshleman; R.H. Hruban; M. Goggins

    2006-01-01

    Background: The gene expression profile of pancreatic cancer is significantly different from that of normal pancreas. Differences in gene expression are detectable using microarrays, but microarrays have traditionally been applied to pancreatic cancer tissue obtained from surgical resection. We hypo

  10. Recent progress in allergen immunotherapy.

    Science.gov (United States)

    Nouri-Aria, Kayhan T

    2008-03-01

    The efficacy of allergen immunotherapy for the treatment of allergic rhinoconjunctivitis with or without seasonal bronchial asthma and anaphylaxis caused by the sting of the hymenoptera class of insects has been clearly demonstrated in numerous well-designed, placebo-controlled trials. Immunotherapy whether by subcutaneous injection of allergen extract or by oral/sublingual routes modifies peripheral and mucosal TH2 responses in favour of TH1 responses and augments IL-10 synthesis by TRegs both locally and by peripheral T cells. Recent researches into the cellular and molecular basis of allergic reactions have advanced our understanding of the mechanisms involved in allergic diseases. They have also helped the development of innovative approaches that are likely to further improve the control of allergic responses in the future. Novel approaches to immunotherapy that are currently being explored include the use of peptide-based allergen preparations, which do not bind IgE and therefore do not activate mast cells, but reduce both Th1 and Th2-cytokine synthesis, while increasing levels of IL-10. Alternative strategies include the use of adjuvants, such as nucleotide immunostimulatory sequences derived from bacteria CpG or monophosphoryl lipid A that potentiate Th1 responses. Blocking the effects of IgE using anti-IgE such as omalizumab, a recombinant humanized monoclonal antibody that selectively binds to IgE, has been shown to be a useful strategy in the treatment of allergic asthma and rhinitis. The combination of anti-IgE-monoclonal antibody omalizumab with allergen immunotherapy has proved beneficial for the treatment of allergic diseases, offering improved efficacy, limited adverse effects, and potential immune-modifying effects. This combination may also accelerate the rapidity by which immunotherapy induces TReg cells. If allergic diseases are due to a lack of allergen-specific TReg cells, then effective therapies should target the induction and the

  11. Assessment of glycosylation-dependent cell adhesion molecule 1 as a correlate of allergen-stimulated lymph node activation

    International Nuclear Information System (INIS)

    Early changes in gene expression have been identified by cDNA microarray technology. Analysis of draining auricular lymph node tissue sampled at 48 h following exposure to the potent contact allergen 2,4-dinitrofluorobenzene (DNFB) provided examples of up- and down-regulated genes, including onzin and guanylate binding protein 2, and glycosylation-dependent cell adhesion molecule 1 (GlyCAM-1), respectively. Allergen-induced changes in these three genes were confirmed in dose-response and kinetic analyses using Northern blotting and/or reverse transcription-polymerase chain reaction techniques. The results confirmed that these genes are robust and relatively sensitive markers of early changes provoked in the lymph node by contact allergen. Upon further investigation, it was found that altered expression of the adhesion molecule GlyCAM-1 was not restricted to treatment with DNFB. Topical sensitization of mice to a chemically unrelated contact allergen, oxazolone, was also associated with a decrease in the expression of mRNA for GlyCAM-1. Supplementary experiments revealed that changes in expression of this gene are independent of the stimulation by chemical allergens of proliferative responses by draining lymph node cells. Taken together these data indicate that the expression of GlyCAM-1 is down-regulated rapidly following epicutaneous treatment of mice with chemical allergens, but that this reduction is associated primarily with changes in lymph node cell number, or some other aspect of lymph node activation, rather than proliferation

  12. Novel allergen preparations for use in allergen-specific immunotherapy

    OpenAIRE

    Neimert Andersson, Theresa

    2008-01-01

    Allergy is a common disease in the industrialized countries, affecting approximately 25% of the population. Therefore, there is a need to find new treatment strategies to improve the quality of life for allergic individuals. Today the only treatment that gives long-lasting reduction of allergic symptoms is allergen-specific immunotherapy (SIT). However, despite successful clinical outcome, the method as it is performed today has some drawbacks such as therapy associated side...

  13. Dust and storage mites: from allergen screening to allergen control

    Czech Academy of Sciences Publication Activity Database

    Hýblová, Jana; Hubert, J.; Kudlíková, I.; Marešová, Lucie; Horn, Martin; Mareš, Michael

    Vienna : -, 2006. [EAACI 2006. Congress of the European Academy of Allergology and Clinical Immunology /25./. 10.06.2006-14.06.2006, Vienna] R&D Projects: GA AV ČR IAA400550617 Grant ostatní: MŠk(CZ) 1P04OC853.003 Institutional research plan: CEZ:AV0Z40550506 Keywords : proteases * allergen * alpha-amylases Subject RIV: CE - Biochemistry

  14. Pollen-Associated Microbiome Correlates with Pollution Parameters and the Allergenicity of Pollen

    Science.gov (United States)

    Obersteiner, Andrea; Gilles, Stefanie; Frank, Ulrike; Beck, Isabelle; Häring, Franziska; Ernst, Dietrich; Rothballer, Michael; Hartmann, Anton; Traidl-Hoffmann, Claudia; Schmid, Michael

    2016-01-01

    Pollen allergies have been rapidly increasing over the last decades. Many allergenic proteins and non-allergenic adjuvant compounds of pollen are involved in the plant defense against environmental or microbial stress. The first aim of this study was to analyze and compare the colonizing microbes on allergenic pollen. The second aim was to investigate detectable correlations between pollen microbiota and parameters of air pollution or pollen allergenicity. To reach these aims, bacterial and fungal DNA was isolated from pollen samples of timothy grass (Phleum pratense, n = 20) and birch trees (Betula pendula, n = 55). With this isolated DNA, a terminal restriction fragment length polymorphism analysis was performed. One result was that the microbial diversity on birch tree and timothy grass pollen samples (Shannon/Simpson diversity indices) was partly significantly correlated to allergenicity parameters (Bet v 1/Phl p 5, pollen-associated lipid mediators). Furthermore, the microbial diversity on birch pollen samples was correlated to on-site air pollution (nitrogen dioxide (NO2), ammonia (NH3), and ozone (O3)). What is more, a significant negative correlation was observed between the microbial diversity on birch pollen and the measured NO2 concentrations on the corresponding trees. Our results showed that the microbial composition of pollen was correlated to environmental exposure parameters alongside with a differential expression of allergen and pollen-associated lipid mediators. This might translate into altered allergenicity of pollen due to environmental and microbial stress. PMID:26910418

  15. Measurement and analysis of the common food allergens specific IgE

    Institute of Scientific and Technical Information of China (English)

    黄惠敏

    2013-01-01

    Objective To explore the positive distribution characteristics and analyse the correlation of common food allergen-specific immunoglobulin E (sIgE) with suspected food allergy in the First Affiliated Hospital of Guangzhou Medical University.Methods Using fluorescence enzyme-linked immunosorbent assay to detect the serum sIgE antibody of 854 patients,including 7 kinds of food allergens (milk,egg white,egg yolk,shrimp,crab,peanut and soybean) from July 2006 to January 2013.

  16. DNA microarray for simultaneous screening and detection of seven rickettsia%7种立克次体甄别检测基因芯片方法的建立

    Institute of Scientific and Technical Information of China (English)

    李灵云; 张英杰; 王升启; 刘琪琦

    2015-01-01

    目的:建立一种能同时检测7种立克次体的化学发光基因芯片法。方法根据NCBI公开发表的7种立克次体的序列设计引物和探针,制备立克次体甄别检测基因芯片。利用多重不对称PCR法扩增立克次体靶基因片段,标记的产物与基因芯片上的探针杂交,经清洗、化学发光显色后进行结果分析。在优化的多重PCR体系、杂交反应和化学发光检测条件下,评价芯片的特异性、灵敏度、重复性。用实时荧光PCR法与芯片法分别检测莫氏立克次体梯度稀释的核酸,比较两种方法的灵敏度。制备双盲模拟样本,进一步评价芯片方法的准确性。结果该研究共筛选出1对通用引物、4对特异性引物和1条立克次体属通用探针、9条特异性检测探针。该芯片检测质粒DNA的灵敏度为1.5×102~3×103拷贝/反应,检测模拟样本的灵敏度为103~104拷贝/μl。实时荧光PCR法与芯片法检测结果一致,实时荧光PCR法比芯片法灵敏度高10倍。双盲模拟样本检测符合率为100%。结论成功建立了可同时检测7种立克次体的化学发光基因芯片检测方法,为立克次体病的临床诊断和流行病学调查提供了一种新的高通量检测手段。%Objective To develop a chemiluminescence ( CL ) imaging DNA microarray method for simultaneous detection of seven rickettsiae.Methods Primers and probes were designed based on the specific sequence of seven rickettsia genomes.The probes were immobilized on the aldehyde modified glass surface to prepare DNA microarray for rickettsiae.The nucleic acids of the selected rickettsiae were amplified and labelled by multiplex PCR method, and then hybridized with microarray that was scanned after washing and chemiluminescence coloration, before the results were analyzed.Facilitated by the optimization of the multiplex PCR system, hybridization, and chemiluminescence imagination, we evaluated the

  17. Allergen immunotherapy in polysensitized patient.

    Science.gov (United States)

    Hrubiško, M; Špičák, V

    2016-05-01

    Specific allergen immunotherapy (AIT) is the only therapeutic method with positive impact on natural course of allergic disease - affecting clinical development (including the progression of rhinitis to asthma) and new sensitisations. The actual problem is the increasing number of patients manifesting poly-sensitivity in allergy skin tests and / or in specific IgE tests. Usually, AIT is not recommended in such individuals. The objective we are facing is that in many patients tested as poly-reactive, we have to distinguish in which cases it is a true polysensitization, and when it is due to cross-reactivity of specific IgE antibodies induced by panallergens. This may really determine when AIT may be an appropriate course of action. The article focuses on this problem in more detail, applying the long time Czech and Slovak experience with allergy testing and allergen immunotherapy. PMID:27152601

  18. Food allergens: molecular and immunological aspects, allergen databases and cross-reactivity.

    Science.gov (United States)

    Lorenz, Anne-Regine; Scheurer, Stephan; Vieths, Stefan

    2015-01-01

    The currently known food allergens are assigned to a relatively small number of protein families. Food allergens grouped into protein families share common functional and structural features that can be attributed to the allergenic potency and potential cross-reactivity of certain proteins. Molecular data, in terms of structural information, biochemical characteristics and clinical relevance for each known allergen, including isoforms and variants, are mainly compiled into four open-access databases. Allergens are designated according to defined criteria by the World Health Organization and the International Union of Immunological Societies Allergen Nomenclature Sub-committee. Food allergies are caused by primary sensitisation to the disease-eliciting food allergens (class I food allergen), or they can be elicited as a consequence of a primary sensitisation to inhalant allergens and subsequent IgE cross-reaction to homologous proteins in food (class II food allergens). Class I and class II allergens display different clinical significance in children and adults and are characterised by different molecular features. In line with this, high stability when exposed to gastrointestinal digestion and heat treatment is attributed to many class I food allergens that frequently induce severe reactions. The stability of a food allergen is determined by its molecular characteristics and can be influenced by structural (chemical) modifications due to thermal processing. Moreover, the immunogenicity and allergenicity of food allergens further depends on specific T cell and B cell epitopes. Although the T cell epitope pattern can be highly diverse for individual patients, several immuno-prominent T cell epitopes have been identified. Such conserved T cell epitopes and IgE cross-reactive B cell epitopes contribute to cross-reactivity between food allergens of the same family and to clinical cross-reactivity, similar to the birch pollen-food syndrome. PMID:26022861

  19. New routes for allergen immunotherapy

    OpenAIRE

    Johansen, Pål; von Moos, Seraina; Mohanan, Deepa; Kündig, Thomas M.; Senti, Gabriela

    2012-01-01

    IgE-mediated allergy is a highly prevalent disease in the industrialized world. Allergen-specific immunotherapy (SIT) should be the preferred treatment, as it has long lasting protective effects and can stop the progression of the disease. However, few allergic patients choose to undergo SIT, due to the long treatment time and potential allergic adverse events. Since the beneficial effects of SIT are mediated by antigen presenting cells inducing Th1, Treg and antibody responses, whereas the a...

  20. Understanding Allergic Asthma from Allergen Inhalation Tests

    OpenAIRE

    Donald W Cockcroft; Hargreave, Fredrick E; Paul M O’Byrne; Louis-Philippe Boulet

    2007-01-01

    The allergen challenge has evolved, in less than 150 years, from a crude tool used to document the etiology of allergen-induced disease to a well-controlled tool used today to investigate the pathophysiology and pharmacotherapy of asthma. Highlights of the authors’ involvement with the allergen challenge include confirmation of the immunoglobulin E-dependence of the late asthmatic response, importance of (nonallergic) airway hyper-responsiveness as a determinant of the airway response to alle...

  1. [Significance of inhaled environmental allergens].

    Science.gov (United States)

    Zochert, J

    1983-01-01

    Whereas the importance of pollen as inhalative allergens has been largely investigated and is generally known, the experience in the frequency and the role of the sensibilization with air-borne fungi is relatively limited. In 720 patients with Asthma bronchiale the degree of sensitization has been tested with various extracts of air-borne fungi of SSW Dresden (mould mixture, aspergillin, mucor, cladosporium and penicillium and alternaria). The most frequent and also the strongest reactions were found with alternaria and the smallest part of positive skin reactions with penicillium. An isolated sensitization with mould has been demonstrated in 20 per cent of the cases. In 60 per cent of the tested patients a manifest mould allergy was shown by means of the Inhalative Allergen Test, the most favourable correlation between Intracutaneous Test (ICT) and Inhalative Test (IAT) was found with alternaria (76%). A conformance between ICT and basophils degranulation test (BDT) was stated in 69% of the cases. The aim should be comparable tests with allergen extracts without irritative effects and qualitative measurements of air-borne fungi. PMID:6649704

  2. Protein microarrays for systems biology

    Institute of Scientific and Technical Information of China (English)

    Lina Yang; Shujuan Guo; Yang Li; Shumin Zhou; Shengce Tao

    2011-01-01

    Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer,diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics,proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as highthroughput, miniaturized, and capable of parallel analysis,protein microarrays have already become an important technology platform for systems biology, In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays,and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.

  3. Microarray technology and its applications

    CERN Document Server

    Müller, UR

    2006-01-01

    It presents detailed overviews of the different techniques of fabricating microarrays, of the chemistries and preparative steps involved, of the different types of microarrays, and of the instrumentation and optical issues involved.

  4. Combining Affymetrix microarray results

    Directory of Open Access Journals (Sweden)

    Doerge RW

    2005-03-01

    Full Text Available Abstract Background As the use of microarray technology becomes more prevalent it is not unusual to find several laboratories employing the same microarray technology to identify genes related to the same condition in the same species. Although the experimental specifics are similar, typically a different list of statistically significant genes result from each data analysis. Results We propose a statistically-based meta-analytic approach to microarray analysis for the purpose of systematically combining results from the different laboratories. This approach provides a more precise view of genes that are significantly related to the condition of interest while simultaneously allowing for differences between laboratories. Of particular interest is the widely used Affymetrix oligonucleotide array, the results of which are naturally suited to a meta-analysis. A simulation model based on the Affymetrix platform is developed to examine the adaptive nature of the meta-analytic approach and to illustrate the usefulness of such an approach in combining microarray results across laboratories. The approach is then applied to real data involving a mouse model for multiple sclerosis. Conclusion The quantitative estimates from the meta-analysis model tend to be closer to the "true" degree of differential expression than any single lab. Meta-analytic methods can systematically combine Affymetrix results from different laboratories to gain a clearer understanding of genes' relationships to specific conditions of interest.

  5. The establishment of a new method to detect food allergen specific IgE and its clinical application for detecting allergic diseases%食物过敏原特异性IgE检测方法的建立及临床应用

    Institute of Scientific and Technical Information of China (English)

    丁红梅; 王学谦; 赵俊芳; 吴万通; 曾昭伟

    2008-01-01

    Objective To prepare a detective membrane strip for detection of food allergen-specific IgE in serum samples and estimate its clinical application value in allergic diseases. Methods The crude extracts of the food allergens were prepared. Nitrocellulose membrane as the solid support was selected and the coating and the detecting conditions were optimized. The membrane strips were used to detect serum samples in 210 patients with allergic diseases and the results were compared with German Allergy Screentesting system. Results The optima] experimental conditions were as follows: The NC membrane was adopted as the solid support. After being spotted, the food allergens were incubated for 2 hours at room temperature, followed by 2% PVA blocking for 1 hour. After serum samples were diluted (1: 10) and incubated for 2 hours at room temperature, the concentration of anti-human IgE was 2 μg/mL Compared with the German Allergy Screen-testing system, their positive detectical coincidence was 63.6%, and negative detectical coincidence was 94. 6%. The two methods had no difference in detecting the majority of food allergens such as egg white, milk, peanut, soybean, crab and shrimp (X2 2.53, 2.40, 2.08, 2.38, 0.17,1.13, P>0.05). Conclusions The advantages of our method for detecting allergic diseases are little serum needed, multiple detective allergens, simple manipulation and low cost. This method has obvious clinical application value, which should be a new detective method for the allergic diseases with broad perspectives.%目的 研制一种能同时检测多种食物过敏原特异性IgE检测条,并探讨其在过敏性疾病诊断中的应用价值.方法 制备常见食物过敏原的提取液,以硝酸纤维素膜(NC)膜为固相载体制备过敏原检测条,并对制备条件和检测条件进行优化.用自制检测条与德国Allergy Screen过敏原检测系统对210份过敏性疾病患者血清进行对比检测分析.结果 本研究的最佳试验条件为,

  6. Differences in the presence of allergens among several types of indoor environments

    Directory of Open Access Journals (Sweden)

    Barbara Brunetto

    2009-12-01

    Full Text Available Exposure to indoor allergens can occur both at home and in public places such as schools and workplaces. To investigate and compare the presence of indoor allergens in different kind of environments (schools, offices and homes, dust samples were collected from furniture, desks, mattresses and floors with a standardized procedure. Samples were analyzed for Der p 1, Der f 1, Mite group 2 (mites and Fel d 1(cat by monoclonal antibody ELISA assay. Mite allergens were detected with low frequencies in schools and workplaces and with high frequency in homes. Fel d 1 was found with high frequency in every examined environment. Homes rather than public places can represent the environment where people can easier incur in mite allergy. All environments could be at risk for cat allergen exposure.

  7. 利用微阵列芯片技术探究脊髓损伤的分子机制★%Molecular mechanism of spinal cord injury detected using microarray technology

    Institute of Scientific and Technical Information of China (English)

    席悦

    2013-01-01

    . Two Chinese writings were also consulted. RESULTS AND CONCLUSION: The change of gene expression from acute phase to chronic phase fol owing spinal cord injury could be detected by using microarray technology which is established on molecular research, and then, the relevant signaling pathway and transcription factors could be found. This technology not only plays a guiding role in further molecular research, but also can be used to find the suitable therapeutic targets of spinal cord injury on genetic level. The research advance of pathophysiology and the gene expression after spinal cord injury by using microarray technology was reviewed in this paper. The technological innovation of experimental design and microarray detection, the improvement of data analysis methods were put forward. The power of microarrays in finding potential therapeutic targets was also evaluated.

  8. Microarray detection and qPCR screening of potential biomarkers of Folsomia candida (Collembola: Isotomidae) exposed to Bt proteins (Cry1Ab and Cry1Ac)

    International Nuclear Information System (INIS)

    The impact of Bt proteins on non-target arthropods is less understood than their effects on target organisms where the mechanism of toxic action is known. Here, we report the effects of two Bt proteins, Cry1Ab and Cry1Ac, on gene expression in the non-target collembolan, Folsomia candida. A customized microarray was used to study gene expression in F. candida specimens that were exposed to Cry1Ab and Cry1Ac. All selected transcripts were subsequently confirmed by qPCR. Eleven transcripts were finally verified, and three of them were annotated. The responses of all eleven transcripts were tested in specimens for both Cry1Ab and Cry1Ac at a series of concentrations. These transcripts were separated into two and three groups for Cry1Ab and Cry1Ac, respectively, depend on their expression levels. However, those eleven transcripts did not respond to the Bt proteins in Bt-rice residues. -- Highlights: • We examined the effects of Bt proteins on gene expression of Folsomia candida. • Eleven transcripts were up-regulated by Bt proteins (Cry1Ab and Cry1Ac). • Only three of the eleven transcripts were annotated. • The responses of 11 transcripts were tested on both Cry1Ab and Cry1Ac. • These transcripts did not respond to the Bt proteins in Bt-rice residues. -- Eleven potential molecular biomarkers of Folsomia candida to Cry1Ab and Cry1Ac were screened by microarray and qPCR analysis

  9. AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data

    OpenAIRE

    Xia Yuannan; Nguyen The V; Lu Guoqing; Fromm Michael

    2006-01-01

    Abstract Background DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amount of microarray data and make biological sense of them. Affymetrix GeneChips are widely used microarrays, where a variety of statistical algorithms have been explored and used for detecting significant genes in the experiment. These methods rely solely on the quanti...

  10. Navigating public microarray databases.

    Science.gov (United States)

    Penkett, Christopher J; Bähler, Jürg

    2004-01-01

    With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources. PMID:18629145

  11. Raman-based microarray readout: a review.

    Science.gov (United States)

    Haisch, Christoph

    2016-07-01

    For a quarter of a century, microarrays have been part of the routine analytical toolbox. Label-based fluorescence detection is still the commonest optical readout strategy. Since the 1990s, a continuously increasing number of label-based as well as label-free experiments on Raman-based microarray readout concepts have been reported. This review summarizes the possible concepts and methods and their advantages and challenges. A common label-based strategy is based on the binding of selective receptors as well as Raman reporter molecules to plasmonic nanoparticles in a sandwich immunoassay, which results in surface-enhanced Raman scattering signals of the reporter molecule. Alternatively, capture of the analytes can be performed by receptors on a microarray surface. Addition of plasmonic nanoparticles again leads to a surface-enhanced Raman scattering signal, not of a label but directly of the analyte. This approach is mostly proposed for bacteria and cell detection. However, although many promising readout strategies have been discussed in numerous publications, rarely have any of them made the step from proof of concept to a practical application, let alone routine use. Graphical Abstract Possible realization of a SERS (Surface-Enhanced Raman Scattering) system for microarray readout. PMID:26973235

  12. Multipurpose high-throughput filtering microarrays (HiFi) for DNA and protein assays.

    Science.gov (United States)

    Le Goff, Gaelle C; Desmet, Cloé; Brès, Jean-Charles; Rigal, Dominique; Blum, Loïc J; Marquette, Christophe A

    2010-12-15

    We are reporting here a low cost colorimetric device for high-throughput multiplexed blood group genotyping and allergy diagnosis, displayed as an automated 96-well microtiter plate format. A porous polymeric membrane sealed at the bottom of each well accounts for the sensor support. For each sensing unit, a 6×6 matrix of specific probes is spotted on the external surface of the membrane resulting in 5 mm(2) microarrays. Thanks to the membrane porosity, reagents dispensed into the well can be eliminated through vacuum soaking. This unusual design drastically reduces the assay background signal. The system was first validated on robust models composed of either two complementary oligonucleotide sequences or one allergen/specific rabbit IgG pair. The quality of both oligonucleotide and protein immobilisation on the membrane substrate was then demonstrated together with the capacity to use the arrayed biomolecules as probes for the quantitative detection of specific targets (respectively complementary oligonucleotide and specific antibody). On the basis of these good results, two multiplex assays were developed for crude biological samples testing, focussing on two human in vitro diagnosis applications: a hybridisation assay for multiplex blood group genotyping and a multiparametric immunoassay for allergy diagnosis. In both cases, the transfer to crude biological samples testing was successful i.e. high signal to noise ratio of the stained membranes, reproducibility and good correlation with results obtained using routine testing procedures. PMID:20663657

  13. Genomic-Wide Analysis with Microarrays in Human Oncology

    Directory of Open Access Journals (Sweden)

    Kenichi Inaoka

    2015-10-01

    Full Text Available DNA microarray technologies have advanced rapidly and had a profound impact on examining gene expression on a genomic scale in research. This review discusses the history and development of microarray and DNA chip devices, and specific microarrays are described along with their methods and applications. In particular, microarrays have detected many novel cancer-related genes by comparing cancer tissues and non-cancerous tissues in oncological research. Recently, new methods have been in development, such as the double-combination array and triple-combination array, which allow more effective analysis of gene expression and epigenetic changes. Analysis of gene expression alterations in precancerous regions compared with normal regions and array analysis in drug-resistance cancer tissues are also successfully performed. Compared with next-generation sequencing, a similar method of genome analysis, several important differences distinguish these techniques and their applications. Development of novel microarray technologies is expected to contribute to further cancer research.

  14. Proteomic analysis of major and minor allergens from isolated pollen cytoplasmic granules.

    Science.gov (United States)

    Abou Chakra, Oussama R; Sutra, Jean-Pierre; Demey Thomas, Emmanuelle; Vinh, Joëlle; Lacroix, Ghislaine; Poncet, Pascal; Sénéchal, Hélène

    2012-02-01

    Grass pollen is one of the most important vectors of aeroallergens. Under atmospheric conditions, pollen grains can release pollen cytoplasmic granules (PCGs). The allergens associated with these intrinsic subfractions induce, in laboratory animals as well as in asthmatic patients, allergic and inflammatory responses. The objectives of this study were to characterize the PCGs' intrinsic allergens and to compare them with those of pollen grains. The water-soluble proteins were extracted from pollen grains and their PCGs. IgE-binding proteins were analyzed and characterized through an allergomic strategy: 1- and 2-dimensional gel electrophoresis (1-DE and 2-DE), immunoblotting, using grass-pollen-sensitized patient sera, mass spectrometry (MS) analysis, and database searching. Several of the allergens listed in the IUIS nomenclature, Phl p 1, 4, 5, 6, and 12, were detected in pollen and PCG extracts, whereas Phl p 11 was found only in PCGs, and Phl p 2 as well as Phl p 13 were found only in pollen extract. Some other allergens not listed in the IUIS nomenclature were also characterized in both pollen and PCG extracts. Since the major grass pollen allergens were found in PCGs and because of their small size, these submicronic particles should be considered as very potent sensitizing and challenging respirable vectors of allergens. PMID:22188203

  15. Isolation and characterization of the 68 kD allergen from house dust mite Dermatophagoides pteronyssinus

    Directory of Open Access Journals (Sweden)

    KATARINA MILOVANOVIĆ

    2009-05-01

    Full Text Available House dust mites (HDM represent a major source of allergens, contributing to the increasing incidence of type I hypersensitivity disease worldwide. Over 30 different IgE-binding proteins from the HDM extract were detected. Although group 1 and 2 have been identified as major allergens, due to the safety and efficacy of allergy diagnosis and immunotherapy, there is a need to carefully evaluate the clinical relevance of other allergens present in the HDM extract. In regard to this, a high molecular mass allergen of about 68 kD was purified from the HDM extract using a combination of gel permeation chromatography and reversed-phase chromatography. The IgG and IgE reactivity of the purified protein were preserved during the purification process, as confirmed by Western blot analysis with polyclonal rabbit antibodies and dot blot analysis with a pool of sera from subjects with house dust mite allergy, respectively. In addition, the IgE reactivity was confirmed using ELISA testing with nine patient sera. The biological potency of the 68 kD allergen was confirmed by skin prick testing in five allergic subjects, suggesting that the high molecular mass allergen is a good candidate for component-resolved diagnosis of house dust mite allergy and eventual therapeutic treatment.

  16. New routes for allergen immunotherapy.

    Science.gov (United States)

    Johansen, Pål; von Moos, Seraina; Mohanan, Deepa; Kündig, Thomas M; Senti, Gabriela

    2012-10-01

    IgE-mediated allergy is a highly prevalent disease in the industrialized world. Allergen-specific immunotherapy (SIT) should be the preferred treatment, as it has long lasting protective effects and can stop the progression of the disease. However, few allergic patients choose to undergo SIT, due to the long treatment time and potential allergic adverse events. Since the beneficial effects of SIT are mediated by antigen presenting cells inducing Th1, Treg and antibody responses, whereas the adverse events are caused by mast cells and basophils, the therapeutic window of SIT may be widened by targeting tissues rich in antigen presenting cells. Lymph nodes and the epidermis contain high density of dendritic cells and low numbers of mast cells and basophils. The epidermis has the added benefit of not being vascularised thereby reducing the chances of anaphylactic shock due to leakage of allergen. Hence, both these tissues represent highly promising routes for SIT and are the focus of discussion in this review. PMID:23095873

  17. Shared probe design and existing microarray reanalysis using PICKY

    Directory of Open Access Journals (Sweden)

    Chou Hui-Hsien

    2010-04-01

    Full Text Available Abstract Background Large genomes contain families of highly similar genes that cannot be individually identified by microarray probes. This limitation is due to thermodynamic restrictions and cannot be resolved by any computational method. Since gene annotations are updated more frequently than microarrays, another common issue facing microarray users is that existing microarrays must be routinely reanalyzed to determine probes that are still useful with respect to the updated annotations. Results PICKY 2.0 can design shared probes for sets of genes that cannot be individually identified using unique probes. PICKY 2.0 uses novel algorithms to track sharable regions among genes and to strictly distinguish them from other highly similar but nontarget regions during thermodynamic comparisons. Therefore, PICKY does not sacrifice the quality of shared probes when choosing them. The latest PICKY 2.1 includes the new capability to reanalyze existing microarray probes against updated gene sets to determine probes that are still valid to use. In addition, more precise nonlinear salt effect estimates and other improvements are added, making PICKY 2.1 more versatile to microarray users. Conclusions Shared probes allow expressed gene family members to be detected; this capability is generally more desirable than not knowing anything about these genes. Shared probes also enable the design of cross-genome microarrays, which facilitate multiple species identification in environmental samples. The new nonlinear salt effect calculation significantly increases the precision of probes at a lower buffer salt concentration, and the probe reanalysis function improves existing microarray result interpretations.

  18. Allergenic Lipid Transfer Proteins from Plant-Derived Foods Do Not Immunologically and Clinically Behave Homogeneously: The Kiwifruit LTP as a Model

    Science.gov (United States)

    Camardella, Laura; Ferrara, Rosetta; Palazzo, Paola; Panico, Maria Rosaria; Crescenzo, Roberta; Carratore, Vito; Zennaro, Danila; Liso, Marina; Santoro, Mario; Zuzzi, Sara; Tamburrini, Maurizio; Ciardiello, Maria Antonietta; Mari, Adriano

    2011-01-01

    Background Food allergy is increasingly common worldwide. Tools for allergy diagnosis measuring IgE improved much since allergenic molecules and microarrays started to be used. IgE response toward allergens belonging to the same group of molecules has not been comprehensively explored using such approach yet. Objective Using the model of lipid transfer proteins (LTPs) from plants as allergens, including two new structures, we sought to define how heterogeneous is the behavior of homologous proteins. Methods Two new allergenic LTPs, Act d 10 and Act c 10, have been identified in green (Actinidia deliciosa) and gold (Actinidia chinensis) kiwifruit (KF), respectively, using clinically characterized allergic patients, and their biochemical features comparatively evaluated by means of amino acid sequence alignments. Along with other five LTPs from peach, mulberry, hazelnut, peanut, mugwort, KF LTPs, preliminary tested positive for IgE, have been immobilized on a microarray, used for IgE testing 1,003 allergic subjects. Comparative analysis has been carried out. Results Alignment of Act d 10 primary structure with the other allergenic LTPs shows amino acid identities to be in a narrow range between 40 and 55%, with a number of substitutions making the sequences quite different from each other. Although peach LTP dominates the IgE immune response in terms of prevalence, epitope recognition driven by sequence heterogeneity has been recorded to be distributed in a wide range of behaviors. KF LTPs IgE positive results were obtained in a patient subset IgE positive for the peach LTP. Anyhow, the negative results on homologous molecules allowed us to reintroduce KF in patients' diet. Conclusion The biochemical nature of allergenic molecule belonging to a group of homologous ones should not be taken as proof of immunological recognition as well. The availability of panels of homologous molecules to be tested using microarrays is valuable to address the therapeutic intervention

  19. Allergenic lipid transfer proteins from plant-derived foods do not immunologically and clinically behave homogeneously: the kiwifruit LTP as a model.

    Directory of Open Access Journals (Sweden)

    Maria Livia Bernardi

    Full Text Available BACKGROUND: Food allergy is increasingly common worldwide. Tools for allergy diagnosis measuring IgE improved much since allergenic molecules and microarrays started to be used. IgE response toward allergens belonging to the same group of molecules has not been comprehensively explored using such approach yet. OBJECTIVE: Using the model of lipid transfer proteins (LTPs from plants as allergens, including two new structures, we sought to define how heterogeneous is the behavior of homologous proteins. METHODS: Two new allergenic LTPs, Act d 10 and Act c 10, have been identified in green (Actinidia deliciosa and gold (Actinidia chinensis kiwifruit (KF, respectively, using clinically characterized allergic patients, and their biochemical features comparatively evaluated by means of amino acid sequence alignments. Along with other five LTPs from peach, mulberry, hazelnut, peanut, mugwort, KF LTPs, preliminary tested positive for IgE, have been immobilized on a microarray, used for IgE testing 1,003 allergic subjects. Comparative analysis has been carried out. RESULTS: Alignment of Act d 10 primary structure with the other allergenic LTPs shows amino acid identities to be in a narrow range between 40 and 55%, with a number of substitutions making the sequences quite different from each other. Although peach LTP dominates the IgE immune response in terms of prevalence, epitope recognition driven by sequence heterogeneity has been recorded to be distributed in a wide range of behaviors. KF LTPs IgE positive results were obtained in a patient subset IgE positive for the peach LTP. Anyhow, the negative results on homologous molecules allowed us to reintroduce KF in patients' diet. CONCLUSION: The biochemical nature of allergenic molecule belonging to a group of homologous ones should not be taken as proof of immunological recognition as well. The availability of panels of homologous molecules to be tested using microarrays is valuable to address the

  20. The use of microarrays in microbial ecology

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

  1. The hammock: a reservoir of allergens

    Directory of Open Access Journals (Sweden)

    Francisca X. M. Rego

    2011-01-01

    Full Text Available INTRODUCTION: Asthma affects approximately 10% of the world's population. Sensitization to allergens is an important risk factor, and exposure to allergens is associated with disease severity. METHODS: We performed skin tests to evaluate allergen sensitization to mites, cockroaches, cats, dogs, and molds in 73 asthmatic patients. Enzyme Linked Immunosorbent Assay was used to assay the mite and cockroach allergens found in dust from the bedding, hammocks, bedroom floors, living rooms, and kitchens of 29 patients and 14 controls. RESULTS: Fifty patients (68.5% had positive skin test responses. There were positive responses to D. pteronyssinus (52.0%, B. tropicalis (53.4%, T. putrescentiae (15.0%, E. maynei (12.3%, L. destructor (8.2%, B. germanica (20.5%, P. americana (21.9%, Felis catus (10.9%, C. herbarium (2.7%, A. alternata (4.1%, and P. notatun (1.3%. The exposure to mite and cockroach allergens was similar in the patients and the controls. The Dermatophagoides pteronyssinus Group 1 levels were highest in the beds and hammocks. The Blattella germanica Group 1 levels were highest in the kitchens, living rooms and hammocks. DISCUSSION: The positive skin tests to mites, cockroaches and cats were consistent with previous studies. D pteronyssinus was the most prevalent home dust mite, and hammocks were a source of allergens. To improve asthma prophylaxis, it is important to determine its association with mite allergen exposure in hammocks.

  2. Cellular gene expression induced by parasite antigens and allergens in neonates from parasite-infected mothers.

    Science.gov (United States)

    Soboslay, Peter T; Orlikowsky, Thorsten; Huang, Xiangsheng; Gille, Christian; Spring, Bärbel; Kocherscheidt, Lars; Agossou, Abram; Banla, Meba; Bonin, Michael; Köhler, Carsten

    2016-05-01

    Prenatal exposure to parasite antigens or allergens will influence the profile and strength of postnatal immune responses, such contact may tolerize and increase susceptibility to future infections or sensitize to environmental allergens. Exposure in utero to parasite antigens will distinctly alter cellular gene expression in newborns. Gene microarrays were applied to study gene expression in umbilical cord blood cell (UCBC) from parasite-exposed (Para-POS) and non-exposed (Para-NEG) neonates. UCBC were activated with antigens of helminth (Onchocerca volvulus), amoeba (Entamoeba histolytica) or allergens of mite (Dermatophagoides farinae). When UCBC from Para-POS and Para-NEG newborns were exposed to helminth antigens or allergens consistent differences occurred in the expression of genes encoding for MHC class I and II alleles, signal transducers of activation and transcription (STATs), cytokines, chemokines, immunoglobulin heavy and light chains, and molecules associated with immune regulation (SOCS, TLR, TGF), inflammation (TNF, CCR) and apoptosis (CASP). Expression of genes associated with innate immune responses were enhanced in Para-NEG, while in Para-POS, the expression of MHC class II and STAT genes was reduced. Within functional gene networks for cellular growth, proliferation and immune responses, Para-NEG neonates presented with significantly higher expression values than Para-POS. In Para-NEG newborns, the gene cluster and pathway analyses suggested that gene expression profiles may predispose for the development of immunological, hematological and dermatological disorders upon postnatal helminth parasite infection or allergen exposure. Thus, prenatal parasite contact will sensitize without generating aberrant inflammatory immune responses, and increased pro-inflammatory but decreased regulatory gene expression profiles will be present in those neonates lacking prenatal parasite antigen encounter. PMID:27062712

  3. Purification, characterization and allergenicity assessment of 26kDa protein, a major allergen from Cicer arietinum.

    Science.gov (United States)

    Verma, Alok Kumar; Sharma, Akanksha; Kumar, Sandeep; Gupta, Rinkesh Kumar; Kumar, Dinesh; Gupta, Kriti; Giridhar, B H; Das, Mukul; Dwivedi, Premendra D

    2016-06-01

    Chickpea (CP), a legume of the family Fabaceae, is an important nutrient-rich food providing protein, essential amino acids, vitamins, dietary fibre, and minerals. Unfortunately, several IgE-binding proteins in CP have been detected that are responsible for allergic manifestations in sensitized population. Therefore, the prevalence of CP induced allergy prompted us towards purification, characterization and allergenicity assessment of a major ∼26kDa protein from chickpea crude protein extract (CP-CPE). Purification of CP 26kDa protein was done using a combination of fractionation and anion exchange chromatography. This protein was further characterized as "Chain A, crystal structure of a plant albumin" from Cicer arietinum with Mol wt 25.8kDa by Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Further, allergenic potential of purified 25.8kDa protein was assessed using in vivo and in vitro model. Purified protein showed IgE-binding capacity with sensitized BALB/c mice and CP allergic patient's sera. Enhanced levels of specific and total IgE, MCP-1, MCPT-1, myeloperoxidase, histamine, prostaglandin D2, and cysteinyl leukotriene were found in sera of mice treated with CP ∼26kDa protein. Further, expressions of Th2 cytokines (i.e. IL-4, IL-5, IL-13), transcription factors (i.e. GATA-3, STAT-6, SOCS-3) and mast cell signaling proteins (Lyn, cFgr, Syk, PLC-γ2, PI-3K, PKC) were also found increased at mRNA and protein levels in the intestines of mice treated with CP ∼26kDa protein. In addition, enhanced release of β-hexosaminidase, histamine, cysteinyl leukotriene and prostaglandin D2 were observed in RBL2H3 cell line when treated (125μg) with CP 26kDa protein. Conclusively, in vivo and in vitro studies revealed the allergenic potential of purified CP 26kDa protein. Being a potential allergen, plant albumin may play a pivotal role in CP induced allergenicity. Current study will be helpful for better development of therapeutic approaches to

  4. Simultaneous Determination of the Main Peanut Allergens in Foods Using Disposable Amperometric Magnetic Beads-Based Immunosensing Platforms

    Directory of Open Access Journals (Sweden)

    Víctor Ruiz-Valdepeñas Montiel

    2016-06-01

    Full Text Available In this work, a novel magnetic beads (MBs-based immunosensing approach for the rapid and simultaneous determination of the main peanut allergenic proteins (Ara h 1 and Ara h 2 is reported. It involves the use of sandwich-type immunoassays using selective capture and detector antibodies and carboxylic acid-modified magnetic beads (HOOC-MBs. Amperometric detection at −0.20 V was performed using dual screen-printed carbon electrodes (SPdCEs and the H2O2/hydroquinone (HQ system. This methodology exhibits high sensitivity and selectivity for the target proteins providing detection limits of 18.0 and 0.07 ng/mL for Ara h 1 and Ara h 2, respectively, with an assay time of only 2 h. The usefulness of the approach was evaluated by detecting the endogenous content of both allergenic proteins in different food extracts as well as trace amounts of peanut allergen (0.0001% or 1.0 mg/kg in wheat flour spiked samples. The developed platform provides better Low detection limits (LODs in shorter assay times than those claimed for the allergen specific commercial ELISA kits using the same immunoreagents and quantitative information on individual food allergen levels. Moreover, the flexibility of the methodology makes it readily translate to the detection of other food-allergens.

  5. Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip

    OpenAIRE

    Carr Steven M; Flynn Sarah MC

    2007-01-01

    Abstract Background Iterative DNA "resequencing" on oligonucleotide microarrays offers a high-throughput method to measure intraspecific biodiversity, one that is especially suited to SNP-dense gene regions such as vertebrate mitochondrial (mtDNA) genomes. However, costs of single-species design and microarray fabrication are prohibitive. A cost-effective, multi-species strategy is to hybridize experimental DNAs from diverse species to a common microarray that is tiled with oligonucleotide se...

  6. Up-regulation of cell cycle arrest protein BTG2 correlates with increased overall survival in breast cancer, as detected by immunohistochemistry using tissue microarray

    International Nuclear Information System (INIS)

    Previous studies have shown that the ADIPOR1, ADORA1, BTG2 and CD46 genes differ significantly between long-term survivors of breast cancer and deceased patients, both in levels of gene expression and DNA copy numbers. The aim of this study was to characterize the expression of the corresponding proteins in breast carcinoma and to determine their correlation with clinical outcome. Protein expression was evaluated using immunohistochemistry in an independent breast cancer cohort of 144 samples represented on tissue microarrays. Fisher's exact test was used to analyze the differences in protein expression between dead and alive patients. We used Cox-regression multivariate analysis to assess whether the new markers predict the survival status of the patients better than the currently used markers. BTG2 expression was demonstrated in a significantly lower proportion of samples from dead patients compared to alive patients, both in overall expression (P = 0.026) and cell membrane specific expression (P = 0.013), whereas neither ADIPOR1, ADORA1 nor CD46 showed differential expression in the two survival groups. Furthermore, a multivariate analysis showed that a model containing BTG2 expression in combination with HER2 and Ki67 expression along with patient age performed better than a model containing the currently used prognostic markers (tumour size, nodal status, HER2 expression, hormone receptor status, histological grade, and patient age). Interestingly, BTG2 has previously been described as a tumour suppressor gene involved in cell cycle arrest and p53 signalling. We conclude that high-level BTG2 protein expression correlates with prolonged survival in patients with breast carcinoma

  7. Mechanisms of allergen-specific immunotherapy

    OpenAIRE

    Fujita Hiroyuki; Soyka Michael B; Akdis Mübeccel; Akdis Cezmi A

    2012-01-01

    Abstract Allergen-specific immunotherapy (allergen-SIT) is a potentially curative treatment approach in allergic diseases. It has been used for almost 100 years as a desensitizing therapy. The induction of peripheral T cell tolerance and promotion of the formation of regulatory T-cells are key mechanisms in allergen-SIT. Both FOXP3+CD4+CD25+ regulatory T (Treg) cells and inducible IL-10- and TGF-β-producing type 1 Treg (Tr1) cells may prevent the development of allergic diseases and play a ro...

  8. Food Allergens: Is There a Correlation between Stability to Digestion and Allergenicity?

    DEFF Research Database (Denmark)

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard

    2016-01-01

    Food allergy is a major health problem in the Western countries, affecting 3-8% of the population. It has not yet been established what makes a dietary protein a food allergen. Several characteristics have been proposed to be shared by food allergens. One of these is resistance to digestion. This....... Therefore, the predictive value of the pepsin resistance test for assessing the allergenic potential of novel proteins can be questioned....

  9. Cat allergen exposure at school : Evaluation of sampling methods and allergen avoidance strategies

    OpenAIRE

    Karlsson, Anne-Sophie

    2004-01-01

    Cat allergy is the most common allergy among school children in Sweden. Cat allergen is ubiquitous in school premises and other public places and this indirect exposure to cat may induce symptoms among cat sensitized children with asthma. The aim of the present thesis was to evaluate sampling methods and allergen avoidance strategies used in this environment. The first study evaluated a new allergen sampling method (Petri dishes) for collection of airborne settling dust. ...

  10. Immobilization Techniques for Microarray: Challenges and Applications

    Directory of Open Access Journals (Sweden)

    Satish Balasaheb Nimse

    2014-11-01

    Full Text Available The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

  11. Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines

    Directory of Open Access Journals (Sweden)

    Vincent P. Klink

    2010-01-01

    Full Text Available Background. A comparative microarray investigation was done using detection call methodology (DCM and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.

  12. 基于抗体微阵列的食源性病原体综合检测平台%Comprehensive platform for detecting foodborne diseases pathogens based on antibody microarrays

    Institute of Scientific and Technical Information of China (English)

    林荣生

    2011-01-01

    针对超低浓度食源性病原体样本检测的需要,将表面沉积铁氰酸镍薄膜的微叉指电极与生物活化的微珠相结合,设计并实现了通过测定电化学阻抗变化的抗体微阵列食源性病原体综合检测平台样件。提出了电化学阻抗等效电路,并通过电路模型分析表明,生物活化的微珠、微叉指电极之间的电容、溶液的电阻均对电化学阻抗传感单元的输出特性有显著影响。以不同浓度的病原体为样本,完成了Escherichia coli O157∶H7为目标病原体的实验研究。实验结果表明,该微抗体阵列的检出极限低至1.0pg/mL,可满足超低浓度食源性病原体的检测需要。%With the aim to solve the difficulty in detection of ultra-low level foodborne disease pathogens on the spot,a comprehensive antibody microarray platform for rapid detection of multiple foodborne disease pathogens had been designed and realized. By combination of interdigitated microelectrodes(IDMs)deposited with thin nickel hexacyanoferrate film and bioactivated microbeads,the electrochemical impedance(ECI)cell had been rendered with a good sensitivity. An equivalent circuit was proposed to analysis the effects from the parameters of the ECI cell. It was found the existence of the microbeads,capacitance between the IDMs,and resistance in the solution could influence of the impedance of the ECI cell. Witht Escherichia coli O157∶ H7 as the target pathogens,experiments were carried out with different concentration of target. The experimental results showed a good detection limitation at 1. 0pg/mL. It indicated that the antibody microarray platform was suitable for ultra-low level detection of foodborne disease pathogens.

  13. Allergen Detection among 2769 Children with Allergic Symptoms in Ningbo Area%宁波地区2769例疑似过敏性疾病患儿过敏原检测

    Institute of Scientific and Technical Information of China (English)

    刘文渊; 周江瑾

    2013-01-01

    采用免疫印迹法(immunoblotting test,IBT)对宁波市妇女儿童医院2010年10月至2011年12月疑似过敏性疾病患儿14类过敏原进行检测.共检测患儿2769例,总特异性IgE抗体(sIgE)阳性率为76.0%(2105/2769),其中,男性sIgE阳性率(80.0%,1344/1679)高于女性(69.8%,761/1 090)(P<0.05).居前3位的过敏原分别为户尘螨/粉尘螨(33.2%)、牛奶(12.6%)和真菌(12.6%).2011年4个季度户尘螨/粉尘螨的检出率分别为19.4% (79/407)、33.9% (196/564)、39.3% (222/565)和36.0% (275/763),4个季度间差异有统计学意义(P<0.05).主要的4类过敏原(户尘螨/粉尘螨、牛奶、真菌类和鸡蛋)不同年龄组间的阳性率差异均有统计学意义(P<0.05).户尘螨/粉尘螨阳性级别以3~6级为主(66.8%,613/918).%A total of 2 769 children with allergic disease were admitted from October 2010 to December in Ningbo Women & Children's Hospital.Fourteen kinds of serum specific-IgE were detected by immunoblotting method.Among the 2 769 children,the total positive rate of sIgE was 76.0%(2 105/2 769).The sIgE positive rate in males (80.0%,1 344/1 679) was significantly higher than that of females (69.8%,761/1 090)(P<0.05).The top three allergens were dust mites(33.2%),milk(12.6%) and fungi(12.6%).There were statistical differences of positive reaction to dust mites among 4 seasons (19.4%,33.9%,39.3%,36.0%)(P<0.05).Significant differences were found in the positive rates of dust mites,milk,fungi,and egg among the age groups (P<0.05).The level of dust mite specific IgE were mainly in grade 3-6(613/918,66.8%).

  14. The Reactivity and Allergenic Potential of Hazelnut Peptides

    Directory of Open Access Journals (Sweden)

    Lavinia Florina Calinoiu

    2013-11-01

    identification of allergenic proteins. This means that peptide fragments of various size, produced during the digestion of a protein can still be immunological active. As it was shown there was still reactivity between proteins and specific antibodies. The Dot Blot is a simple immunoblotting technique used to detected specific proteins in a mixture of different proteins and/or other molecules. No separation technique prior to the actual immuno-detection is necessary. Also, Dot Blot confirmed the presence of allergenic proteins made visible through the light spots on the membrane.

  15. The contrast study for detection of allergens by MORA-super Bio-physical therapy instrument and Enzyme Immunoassay%MORA-Super生物物理治疗仪与酶联免疫法检测过敏原对比分析

    Institute of Scientific and Technical Information of China (English)

    李胜兵; 吴晓燕; 李红胜

    2012-01-01

    Objective:To analyze the difference in detection of allergens by MORA - super Bio-physical therapy instrument and Enzyme Immunoassay. Methods:249 mite allergic patients were selected randomly for allergen detection by MORA - Super Bio - physical therapy instrument and enzyme immunoassay respectively ( P < 0.05 ) , then self - designed questionnaire was used to survey the feeling of respondents, finally SPSS13.0 was employed for data input and analysis. Results: The detection rate was higher surveyed by MORA - super Bio - physical therapy instrument than enzyme Immunoassay (P < 0. 05 ). MORA - super Bio - physical therapy instrument took shorter time than enzyme Immunoassay and less pain to patients. Conclusion: MORA - super Bio - physical therapy instrument can detect allergens more quickly with more security.%目的:探讨MORA-Super生物物理治疗仪过敏原检测与酶联免疫法检测过敏原的有效性.方法:按照门诊号随机抽取249名螨虫过敏的患者分别进行MORA-Super生物物理治疗仪过敏原检测与酶联免疫法过敏原检测,并采用自制调查问卷面对面的调查方式调查249名调查对象完成该检测的感受.采用SPSS13.0进行数据录入与分析.结果:MORA-Super生物物理治疗仪的过敏原检出率高于酶联免疫法过敏原检出率(P<0.05),MORA-Super生物物理治疗仪的时效性高于酶联免疫法,痛苦性低于酶联免疫法,可接受性高于酶联免疫法.结论:MORA-Super生物物理治疗仪能够更快更好地检测过敏原,并且将患者的痛苦减到最低.

  16. DNA microarray for detection of unknown virus in clinical specimens%临床标本中未知病毒基因芯片检测方法探索

    Institute of Scientific and Technical Information of China (English)

    郑夔; 王洪敏; 黄吉城; 夏文英; 洪烨; 李小波; 师永霞; 幸芦琴; 郭波旋

    2011-01-01

    Objective To develop a DNA microarray for detection of unknown virus in clinical specimens. Methods Probes for dengue virus type 1-4 were designed and synthesized, and DNA microarray of dengue virus was prepared. After viral RNA of dengue virus type 1-4 standard strains were extracted, whole genome amplification was performed by using phi29 DNA polymerase and a random primer contain tag sequence, then the genome was amplified and labeled by random PCR with a Cy3 - conjugated tag sequence primer. The fluorescein labeled amplicon were subjected to hybridization with the DNA microarray of dengue virus. Whereafter the novel method was verified by using serum samples collected from pateints with dengue fever in Guangzhou Baiyun airport entry and exit inspection and quarantine frontier port. Results Hybridization signals of dengue virus type 1-4 standard strains were significantly distinguished, and all of the related strains showed a high probe positive rate of 100%. Similarly, 3 serum samples of dengue virus from clinical patients also had significant hybridization signals with very low background noise. Dengue virus types 1, 2 and 3 carried in the 3 serum samples can be clearly identified by the high probe positive rate of 100% related to the microarray. Conclusion The innovative DNA microarray assay can be used to detect dengue virus in clinical specimens. If more specific probes for different species of pathogens are designed and appended to this new DNA microarray, it also can be expanded for unknown pathogens identification in clinical specimens.%目的 探索可用于检测临床标本中未知病毒的基因芯片技术.方法 设计合成1~4型登革病毒基因芯片探针,制备成登革病毒基因芯片.提取1~4型登革病毒标准毒株的核酸RNA,以phi29 DNA聚合酶结合带标签序列的随机引物进行全基因组扩增,再以Cy3荧光染料标记的标签序列引物进行PCR随机扩增标记,标记产物进一步用登革病毒芯片进

  17. Allergen-Specific Immunotherapy in Food Anaphylaxis

    OpenAIRE

    Kerzl, Regina; Mempel, Martin; Ring, Johannes

    2008-01-01

    Specific immunotherapy (SIT) protocols for nutritional allergens have only recently been established with a focus on oral allergy syndrome because of pollen cross-reacting antibodies. For these patients, a substantial number of studies have been published suggesting benefits from SIT. The situation in true anaphylaxis to food allergens such as peanut allergy is more complex, and therapeutic strategies are based on individual protocols rather than controlled studies. However, in defined cases,...

  18. Allergen specific immunotherapy in nasobronchial allergy.

    Directory of Open Access Journals (Sweden)

    Joshi S

    2003-12-01

    Full Text Available BACKGROUND: More than one antigen has been used for immunotherapy of allergic disorders. So far less than five antigens have been employed with variable results. AIM: To evaluate effect of multiple antigens up to six in the immunotherapy of nasobronchial allergy. SETTING AND DESIGN: Based on clinical history, symptoms present for at least 3 years with set criteria of immunomodulation for asthma and rhinitis: documented IgE mediated asthma and rhinitis, failure in allergen avoidance and moderate to severe clinical manifestations. MATERIAL AND METHODS: Five hundred cases of various allergic disorders attending allergy clinic of Bombay hospital were screened. Allergen specific immunotherapy was initiated in 131 subjects (56 -rhinitis and 75 asthma with prior consent. Patients suffering from allergic disorders secondary to diseases or drug therapy were excluded. Multiple allergen immunotherapy was given at specific intervals up to a period of one year. Allergen extracts were prepared as per standard technique. For statistical analysis "students′t test" was used. RESULTS AND CONCLUSIONS: Significant improvement in PEFR, reduction in skin sensitivity to allergens used in immunotherapy formulation and symptomatic relief without any untoward reaction show that multiple allergen immunotherapy is as effective as monoallergen immunotherapy in nasobronchial allergy.

  19. DNA Microarray-Based Diagnostics.

    Science.gov (United States)

    Marzancola, Mahsa Gharibi; Sedighi, Abootaleb; Li, Paul C H

    2016-01-01

    The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications. PMID:26614075

  20. Allergenic evaluation of Malassezia furfur crude extracts.

    Science.gov (United States)

    Gandra, R F; Melo, T A; Matsumoto, F E; Pires, M F C; Croce, J; Gambale, W; Paula, C R

    2002-01-01

    Crude extracts of the lipophilic yeast Malassezia furfur were obtained from 2, 6, 10 and 28 day old cultures. The in vitro cultivation periods corresponded, respectively, to the lag phase, middle of the log phase, end of log phase and the decline phase of the growth curve, which was based on viable cell counts obtained with a fluorescent viability test. Biochemical analyses showed that the protein and carbohydrate contents were greater in day 10 extracts. Seventy patients with different allergic manifestations and 30 healthy volunteers were skin prick tested using the extracts. Of these, thirteen (18.57%) patients gave positive responses. SDS PAGE gradient electrophoretic profiles of the preparations indicated that the 28 day extracts contained the greatest number of protein bands with molecular weights ranging mostly between 30 and 94 kDa. Immunoblots incubated with individual patient sera showed that four IgE binding M. furfur allergens of approximately 88, 61, 52 and 39 kDa were present in the 28 day extracts. The components identified could be used for detecting IgE mediated responses to M. furfur among individuals affected with different allergic conditions. PMID:12650593

  1. Display of wasp venom allergens on the cell surface of Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Poulsen Lars K

    2010-09-01

    Full Text Available Abstract Background Yeast surface display is a technique, where the proteins of interest are expressed as fusions with yeast surface proteins and thus remain attached to the yeast cell wall after expression. Our purpose was to study whether allergens expressed on the cell surface of baker's yeast Saccharomyces cerevisiae preserve their native allergenic properties and whether the yeast native surface glycoproteins interfere with IgE binding. We chose to use the major allergens from the common wasp Vespula vulgaris venom: phospholipase A1, hyaluronidase and antigen 5 as the model. Results The proteins were expressed on the surface as fusions with a-agglutinin complex protein AGA2. The expression was confirmed by fluorescent cytometry (FACS after staining the cells with antibody against a C-tag attached to the C-terminal end of the allergens. Phospholipase A1 and hyaluronidase retained their enzymatic activities. Phospholipase A1 severely inhibited the growth of the yeast cells. Antigen 5 - expressing yeast cells bound IgE antibodies from wasp venom allergic patient sera but not from control sera as demonstrated by FACS. Moreover, antigen 5 - expressing yeast cells were capable of mediating allergen-specific histamine release from human basophils. Conclusions All the three major wasp venom allergens were expressed on the yeast surface. A high-level expression, which was observed only for antigen 5, was needed for detection of IgE binding by FACS and for induction of histamine release. The non-modified S. cerevisiae cells did not cause any unspecific reaction in FACS or histamine release assay despite the expression of high-mannose oligosaccharides. In perspective the yeast surface display may be used for allergen discovery from cDNA libraries and possibly for sublingual immunotherapy as the cells can serve as good adjuvant and can be produced in large amounts at a low price.

  2. Is high pressure treatment able to modify the allergenicity of the largemouth bass allergens?

    Science.gov (United States)

    Liu, Chu-Yi; Tao, Sha; Liu, Rong; Chen, Fu-Sheng; Xue, Wen-Tong

    2012-12-01

    The aim of this paper is to study the influence of high pressure treatment on the structural changes and allergenicity of largemouth bass. We treated the allergens at 100, 200, 300 and 400 MPa for 15 min and at 300 MPa for 5, 10, 15, 20 and 30 min at 20 °C. The treated samples from largemouth bass were tested for their IgE-binding properties by combining Sodium dodecyl sulfate-Polyacrylamide gel electrophoresis (SDS-PAGE) with western blotting (WB) and enzyme-linked immunosorbent assay (ELISA). Circular dichroism analysis was performed to characterize the structural change. In summary, we can determine that the greatest structure changes were found for samples treated by 400 MPa for 15 min. High pressure treatment did change the structure, subunit composition and molecular weight of largemouth bass allergens, but it did not change the allergenicity of the allergens.

  3. Synchronously Detecting the Allergenic Ingredients of Soybean and Celery in Food by Real-time Fluorescent PCR%实时荧光 PCR 法同时检测食物中大豆和芹菜致敏原成分

    Institute of Scientific and Technical Information of China (English)

    汪永信; 程潇; 安虹; 聂磊; 张波; 刘娟娟

    2016-01-01

    Soybean and celery as food ingredients are allergen for some special groups of people. Designing the specific primers based on atp A gene of soybean and mtd gene of celery and utilizing TaqMan probes with different fluorescents, we set up a fluorescent real-time PCR method allowing the simultaneous detection of allergenic constituents of soybean and celery in food. The specificity of the method was evaluated using template DNAs from soybean or celery and other 20 species such as rice, wheat, barley, peanut, sesame, maize, murphy, tomato, walnut, pistachio, cashew nut, sunflower seeds, almond, apple, pear, strawberry, pork, beef, mutton and fish, only the specific amplifications of soybean and celery were observed. The limit of quantification was 0. 01% through sensitivity tests. In conclusion, the developed real-time PCR method is a specific, sensitive and efficacious assay for the simultaneous detection of allergenic soybean and celery in food.%大豆、芹菜等食品原料是一些特殊人群的致敏原。根据大豆 atp A 基因和芹菜 mtd 基因设计特异性引物,利用不同荧光素标记的 TaqMan 探针,建立了一种实时荧光 PCR 检测方法,可同时检测食物中大豆和芹菜致敏原成分。分别以大豆、芹菜、大米、小麦、大麦、花生、芝麻、玉米、马铃薯、蕃茄、核桃、开心果、腰果、葵花籽、杏仁、苹果、梨、草莓、猪肉、牛肉、羊肉及鱼肉等材料的基因组 DNA 作为模板,进行 PCR 扩增实验,结果发现该方法仅能特异性扩增大豆和芹菜致敏原成分。灵敏度测试结果表明大豆和芹菜成分的检出限均达0.01%。因此,本方法可以作为同时检测食品中大豆和芹菜致敏原成分的特异性方法。

  4. The distribution of dust mite allergen in the houses of patients with asthma

    International Nuclear Information System (INIS)

    Using an inhibition radioimmunoassay for the major allergen from Dermatophagoides pteronyssinus (antigen P1), we studied the distribution of this dust allergen in the houses of patients with asthma. Both bed and floor dust samples contained a wide range of antigen P1, 100 to 100,000 ng/g of fine dust, and this concentration correlated well with the number of mite bodies (r . 0.81, p less than 0.001). We were unable to detect antigen P1 in the air of undisturbed rooms. However, during domestic activity, between 1 and 30 ng were collected on a filter than sampled air for 45 min at 17 L/min. Using a cascade impactor it was shown that greater than 80% of the airborne antigen P1 was associated with particles greater than 10 mu in diameter. Some of the particles containing allergen could be identified because they formed precipitin rings when impacted onto agarose containing rabbit antimite antiserum. These particles had the physical appearance of mite feces, which are the major source of antigen P1 in mite cultures. The results suggested that natural exposure to this dust allergen allows occasional fecal particles to enter the lungs and that these particles contain very concentrated allergen

  5. Effect of high intensity ultrasound on the allergenicity of shrimp

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The tropomyosin fraction of shrimp proteins is potentially responsible for allergic reaction in individuals with genetic predisposition to allergy. However, there are no efficient and safe methods to reduce its allergenicity. High intensity ultrasound is known to change the structure of proteins. This study is aimed at assessing high intensity ultrasound's effect on the allergenicity of shrimp allergen. Shrimp and purified shrimp allergen were treated with high intensity ultrasound for 30~180 min. Extracts of treated samples were analyzed by enzyme-linked immunosorbent assay (ELISA) with pool serum of shrimp allergy patients and polyclonal anti-allergen antibodies and by immunoblotting after polyacrylamide gel electrophoresis. Shrimp treated with high intensity ultrasound showed a decrease in allergenicity measured with ELISA. A linear relationship between the immune response induced by treated shrimp allergen and the applied treatment time was observed. The decrease in allergenicity was confirmed by immunoblot assays with shrimp allergic patients serum. Allergenicity of shrimp allergen extracted from treated shrimp was higher than that of purified shrimp allergen with the same treatment time. Gel-filtration HPLC was applied for analysis of shrimp allergen after treatment with high intensity ultrasound. Some fractions were appeared with increasing treatment time. The results suggested that high intensity ultrasound could be used to reduce the allergenicity of shrimp.

  6. A measurement error model for microarray data analysis

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yiming; CHENG Jing

    2005-01-01

    Microarray technology has been widely used to analyze the gene expression levels by detecting fluorescence intensity in a high throughput fashion. However, since the measurement error produced from various sources in microarray experiments is heterogeneous and too large to be ignored, we propose here a measurement error model for microarray data processing, by which the standard deviation of the measurement error is demonstrated to be linearly increased with fluorescence intensity. A robust algorithm, which estimates the parameters of the measurement error model from a single microarray without replicated spots, is provided. The model and algorithm for estimating of the parameters from a given data set are tested on both the real data set and the simulated data set, and the result has been proven satisfactory. And, combining the measurement error model with traditional Z-test method, a full statistical model has been developed. It can significantly improve the statistical inference for identifying differentially expressed genes.

  7. Protein microarray: sensitive and effective immunodetection for drug residues

    Directory of Open Access Journals (Sweden)

    Zer Cindy

    2010-02-01

    Full Text Available Abstract Background Veterinary drugs such as clenbuterol (CL and sulfamethazine (SM2 are low molecular weight ( Results The artificial antigens were spotted on microarray slides. Standard concentrations of the compounds were added to compete with the spotted antigens for binding to the antisera to determine the IC50. Our microarray assay showed the IC50 were 39.6 ng/ml for CL and 48.8 ng/ml for SM2, while the traditional competitive indirect-ELISA (ci-ELISA showed the IC50 were 190.7 ng/ml for CL and 156.7 ng/ml for SM2. We further validated the two methods with CL fortified chicken muscle tissues, and the protein microarray assay showed 90% recovery while the ci-ELISA had 76% recovery rate. When tested with CL-fed chicken muscle tissues, the protein microarray assay had higher sensitivity (0.9 ng/g than the ci-ELISA (0.1 ng/g for detection of CL residues. Conclusions The protein microarrays showed 4.5 and 3.5 times lower IC50 than the ci-ELISA detection for CL and SM2, respectively, suggesting that immunodetection of small molecules with protein microarray is a better approach than the traditional ELISA technique.

  8. Optical diagnostics of vascular reactions triggered by weak allergens using laser speckle-contrast imaging technique

    Energy Technology Data Exchange (ETDEWEB)

    Kuznetsov, Yu L; Kalchenko, V V [Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, 76100 (Israel); Astaf' eva, N G [V.I.Razumovsky Saratov State Medical University, Saratov (Russian Federation); Meglinski, I V [N.G. Chernyshevsky Saratov State University, Saratov (Russian Federation)

    2014-08-31

    The capability of using the laser speckle contrast imaging technique with a long exposure time for visualisation of primary acute skin vascular reactions caused by a topical application of a weak contact allergen is considered. The method is shown to provide efficient and accurate detection of irritant-induced primary acute vascular reactions of skin. The presented technique possesses a high potential in everyday diagnostic practice, preclinical studies, as well as in the prognosis of skin reactions to the interaction with potentially allergenic materials. (laser biophotonics)

  9. Use of a 3-D Dispersion Model for Calculation of Distribution of Horse Allergen and Odor around Horse Facilities

    Directory of Open Access Journals (Sweden)

    Marie Haeger-Eugensson

    2014-03-01

    Full Text Available The interest in equestrian sports has increased substantially during the last decades, resulting in increased number of horse facilities around urban areas. In Sweden, new guidelines for safe distance have been decided based on the size of the horse facility (e.g., number of horses and local conditions, such as topography and meteorology. There is therefore an increasing need to estimate dispersion of horse allergens to be used, for example, in the planning processes for new residential areas in the vicinity of horse facilities. The aim of this study was to develop a method for calculating short- and long-term emissions and dispersion of horse allergen and odor around horse facilities. First, a method was developed to estimate horse allergen and odor emissions at hourly resolution based on field measurements. Secondly, these emission factors were used to calculate concentrations of horse allergen and odor by using 3-D dispersion modeling. Results from these calculations showed that horse allergens spread up to about 200 m, after which concentration levels were very low (<2 U/m3. Approximately 10% of a study-group detected the smell of manure at 60m, while the majority—80%–90%—detected smell at 60 m or shorter distance from the manure heap. Modeling enabled horse allergen exposure concentrations to be determined with good time resolution.

  10. Use of a 3-D dispersion model for calculation of distribution of horse allergen and odor around horse facilities.

    Science.gov (United States)

    Haeger-Eugensson, Marie; Ferm, Martin; Elfman, Lena

    2014-04-01

    The interest in equestrian sports has increased substantially during the last decades, resulting in increased number of horse facilities around urban areas. In Sweden, new guidelines for safe distance have been decided based on the size of the horse facility (e.g., number of horses) and local conditions, such as topography and meteorology. There is therefore an increasing need to estimate dispersion of horse allergens to be used, for example, in the planning processes for new residential areas in the vicinity of horse facilities. The aim of this study was to develop a method for calculating short- and long-term emissions and dispersion of horse allergen and odor around horse facilities. First, a method was developed to estimate horse allergen and odor emissions at hourly resolution based on field measurements. Secondly, these emission factors were used to calculate concentrations of horse allergen and odor by using 3-D dispersion modeling. Results from these calculations showed that horse allergens spread up to about 200 m, after which concentration levels were very low (<2 U/m³). Approximately 10% of a study-group detected the smell of manure at 60m, while the majority--80%-90%--detected smell at 60 m or shorter distance from the manure heap. Modeling enabled horse allergen exposure concentrations to be determined with good time resolution. PMID:24690946

  11. Gene-metabolite expression in blood can discriminate allergen-induced isolated early from dual asthmatic responses.

    Directory of Open Access Journals (Sweden)

    Amrit Singh

    Full Text Available Some asthmatic individuals undergoing allergen inhalation challenge develop an isolated early response whereas others develop a dual response (early plus late response. In the present study we have used transcriptomics (microarrays and metabolomics (mass spectrometry of peripheral blood to identify molecular patterns that can discriminate allergen-induced isolated early from dual asthmatic responses. Peripheral blood was obtained prior to (pre- and 2 hours post allergen inhalation challenge from 33 study participants. In an initial cohort of 14 participants, complete blood counts indicated significant differences in neutrophil and lymphocyte counts at pre-challenge between early and dual responders. At post-challenge, significant genes (ALOX15, FADS2 and LPCAT2 and metabolites (lysolipids were enriched in lipid metabolism pathways. Enzymes encoding for these genes are involved in membrane biogenesis and metabolism of fatty acids into pro-inflammatory and anti-inflammatory mediators. Correlation analysis indicated a strong negative correlation between ALOX15, FADS2, and IL5RA expression with 2-arachidonoylglycerophosphocholine levels in dual responders. However, measuring arachidonic acid and docosahexaenoic acid levels in a validation cohort of 19 participants indicated that the free form of DHA (nmoles/µg of protein was significantly (p = 0.03 different between early and dual responders after allergen challenge. Collectively these results may suggest an imbalance in lipid metabolism which dictates pro- (anti- inflammatory and pro-resolving mechanisms. Future studies with larger sample sizes may reveal novel mechanisms and therapeutic targets of the late phase asthmatic response.

  12. Protein Microarray On-Demand: A Novel Protein Microarray System

    OpenAIRE

    Chatterjee, Deb K.; Sitaraman, Kalavathy; Baptista, Cassio; Hartley, James; Hill, Thomas M.; David J. Munroe

    2008-01-01

    We describe a novel, simple and low-cost protein microarray strategy wherein the microarrays are generated by printing expression ready plasmid DNAs onto slides that can be converted into protein arrays on-demand. The printed expression plasmids serve dual purposes as they not only direct the synthesis of the protein of interest; they also serve to capture the newly synthesized proteins through a high affinity DNA-protein interaction. To accomplish this we have exploited the high-affinity bin...

  13. T-cell response to allergens.

    Science.gov (United States)

    Ozdemir, Cevdet; Akdis, Mübeccel; Akdis, Cezmi A

    2010-01-01

    Anaphylaxis is a life-threatening IgE-dependent type 1 hypersensitivity reaction in which multiple organ systems are involved. The existence of allergen exposure and specific IgE are the major contributors to this systemic reaction. The decision of the immune system to respond to allergens is highly dependent on factors including the type and load of allergen, behavior and type of antigen-presenting cells, innate immune response stimulating substances in the same micromilieu, the tissue of exposure, interactions between T and B lymphocytes, costimulators, and genetic propensity known as atopy. Antigen-presenting cells introduce processed allergens to T-helper lymphocytes, where a decision of developing different types of T-cell immunity is given under the influence of several cytokines, chemokines, costimulatory signals and regulatory T cells. Among Th2-type cytokines, interleukin (IL)-4 and IL-13 are responsible for class switching in B cells, which results in production of allergen-specific IgE antibodies that bind to specific receptors on mast cells and basophils. After re-exposure to the sensitized allergen, this phase is followed by activation of IgE Fc receptors on mast cells and basophils resulting in biogenic mediator releases responsible for the symptoms and signs of anaphylaxis. Since the discovery of regulatory T cells, the concepts of immune regulation have substantially changed during the last decade. Peripheral T-cell tolerance is a key immunologic mechanism in healthy immune response to self antigens and non-infectious non-self antigens. Both naturally occurring CD4+CD25+ regulatory T (Treg) cells and inducible populations of allergen-specific, IL-10-secreting Treg type 1 cells inhibit allergen-specific effector cells and have been shown to play a central role in the maintenance of peripheral homeostasis and the establishment of controlled immune responses. On the other hand, Th17 cells are characterized by their IL-17 (or IL-17A), IL-17F, IL-6

  14. Domestic cat allergen and allergic sensitisation in young children

    NARCIS (Netherlands)

    Chen, Chih-Mei; Gehring, Ulrike; Wickman, Magnus; Hoek, Gerard; Giovannangelo, Mariella; Nordling, Emma; Wijga, Alet; de Jongste, Johan; Pershagen, Goeran; Almqvist, Catarina; Kerkhof, Marjan; Bellander, Tom; Wichmann, H. -Erich; Brunekreef, Bert; Heinrich, Joachim

    2008-01-01

    Studies have presented conflicting associations between cat allergen exposure and sensitisation and atopic disease. We therefore investigated the association between the observed domestic cat allergen level and cat sensitisation in young children in four study populations from three European countri

  15. Modifications of allergenicity linked to food technologies.

    Science.gov (United States)

    Moneret-Vautrin, D A

    1998-01-01

    The prevalence of food allergies (FA) has increased over the past fifteen years. The reasons suggested are changes in dietary behaviour and the evolution of food technologies. New cases of FA have been described with chayote, rambutan, arguta, pumpkin seeds, custard apple, and with mycoproteins from Fusarium.... Additives using food proteins are at high risk: caseinates, lysozyme, cochineal red, papaïn, alpha-amylase, lactase etc. Heating can reduce allergenicity or create neo-allergens, as well as storage, inducing the synthesis of allergenic stress or PR proteins. Aeroallergens (miles, moulds) contaminate foods and can induce allergic reactions. Involuntary contamination by peanut proteins on production lines is a problem which is not yet solved. Genetically modified plants are at risk of allergenicity, requiring methodological steps of investigations: the comparison of the amino-acid sequence of the transferred protein with the sequence of known allergens, the evaluation of thermo degradability and of the denaturation by pepsin and trypsin are required, as well as the study with sera from patients allergic to the plant producing the gene. The combination of enzymatic hydrolysis, heating, or the development of genetically modified plants may offer new alternatives towards hypoallergenic foods (57 references). PMID:9503097

  16. Mechanisms of allergen-specific immunotherapy.

    Science.gov (United States)

    Fujita, Hiroyuki; Soyka, Michael B; Akdis, Mübeccel; Akdis, Cezmi A

    2012-01-01

    Allergen-specific immunotherapy (allergen-SIT) is a potentially curative treatment approach in allergic diseases. It has been used for almost 100 years as a desensitizing therapy. The induction of peripheral T cell tolerance and promotion of the formation of regulatory T-cells are key mechanisms in allergen-SIT. Both FOXP3+CD4+CD25+ regulatory T (Treg) cells and inducible IL-10- and TGF-β-producing type 1 Treg (Tr1) cells may prevent the development of allergic diseases and play a role in successful allergen-SIT and healthy immune response via several mechanisms. The mechanisms of suppression of different pro-inflammatory cells, such as eosinophils, mast cells and basophils and the development of allergen tolerance also directly or indirectly involves Treg cells. Furthermore, the formation of non-inflammatory antibodies particularly IgG4 is induced by IL-10. Knowledge of these molecular basis is crucial in the understanding the regulation of immune responses and their possible therapeutic targets in allergic diseases. PMID:22409879

  17. Mechanisms of allergen-specific immunotherapy

    Directory of Open Access Journals (Sweden)

    Fujita Hiroyuki

    2012-01-01

    Full Text Available Abstract Allergen-specific immunotherapy (allergen-SIT is a potentially curative treatment approach in allergic diseases. It has been used for almost 100 years as a desensitizing therapy. The induction of peripheral T cell tolerance and promotion of the formation of regulatory T-cells are key mechanisms in allergen-SIT. Both FOXP3+CD4+CD25+ regulatory T (Treg cells and inducible IL-10- and TGF-β-producing type 1 Treg (Tr1 cells may prevent the development of allergic diseases and play a role in successful allergen-SIT and healthy immune response via several mechanisms. The mechanisms of suppression of different pro-inflammatory cells, such as eosinophils, mast cells and basophils and the development of allergen tolerance also directly or indirectly involves Treg cells. Furthermore, the formation of non-inflammatory antibodies particularly IgG4 is induced by IL-10. Knowledge of these molecular basis is crucial in the understanding the regulation of immune responses and their possible therapeutic targets in allergic diseases.

  18. Immunological mechanisms of allergen-specific immunotherapy.

    Science.gov (United States)

    Jutel, Marek; Akdis, C A

    2011-06-01

    The studies on the mechanisms of specific immunotherapy (SIT) point out its targets that decide on the efficacy of SIT and hence might be used for its further improvement. Several mechanisms have been proposed to explain the beneficial effects of immunotherapy. The knowledge of the mechanisms underlying allergic diseases and curative treatment possibilities has experienced exciting advances over the last three decades. Studies in several clinical trials in allergen-SIT have demonstrated that the induction of a tolerant state against allergens in many ways represents a key step in the development of a healthy immune response against allergens. Several cellular and molecular mechanisms have been demonstrated: allergen-specific suppressive capacities of both inducible subsets of CD4(+) CD25(+) forkhead box P3(+) T-regulatory and IL-10-secreting type 1 T-regulatory cells increase in peripheral blood; suppression of eosinophils, mast cells, and basophils; Ab isotype change from IgE to IgG4. This review aims at the better understanding of the observed immunological changes associated with allergen SIT. PMID:21466562

  19. Analysis of Allergens in 5473 Patients with Allergic Diseases in Harbin, China

    Institute of Scientific and Technical Information of China (English)

    CHANG Man Li; SHAO Bing; LIU Yan Hong; LI Lu Lu; PEI Li Chun; WANG Bin You

    2013-01-01

    Objective To analyze the allergic status to common inhalant allergens and food allergens in clinical patients in Harbin in northeastern China and provide evidence to develop the prevention strategy of allergic disease. Methods The data were collected from 5 473 patients with clinical suspected allergic diseases seeking medical care in the Second Affiliated Hospital of Harbin Medical University. Among these patients, 2 530 (46.2%) were males aged 0-86 years, the youngest was only 1 month old and 2 579 (47.1%) were young children and teenagers. The serum specific Immunoglobulin E (sIgE) to 14 kinds of common allergens and serum total IgE were detected by using AllergyScreen test (Mediwiss Analytic GmbH, Moers, Germany). Results In 5 473 subjects the positive rate of sIgE was 33.1%(n=1 813). Cow milk (6.9%) and wheat (3.1%) were the most common food allergens, followed by house dust mite mix (12.5%) and mould mix (9.4%) and the age and gender specific differences in the positive rate were significant. For the children aged Conclusion The results from this study showed that the food allergens in Harbin had geographic characteristics, which support the viewpoint that the environment factors play an important role in the incidence of allergic diseases. Also, the detection of sIgE and total IgE are essential to identify relevant allergens for the purpose of early diagnosis, management and prevention of allergic disease.

  20. Normalization Benefits Microarray-Based Classification

    Directory of Open Access Journals (Sweden)

    Chen Yidong

    2006-01-01

    Full Text Available When using cDNA microarrays, normalization to correct labeling bias is a common preliminary step before further data analysis is applied, its objective being to reduce the variation between arrays. To date, assessment of the effectiveness of normalization has mainly been confined to the ability to detect differentially expressed genes. Since a major use of microarrays is the expression-based phenotype classification, it is important to evaluate microarray normalization procedures relative to classification. Using a model-based approach, we model the systemic-error process to generate synthetic gene-expression values with known ground truth. These synthetic expression values are subjected to typical normalization methods and passed through a set of classification rules, the objective being to carry out a systematic study of the effect of normalization on classification. Three normalization methods are considered: offset, linear regression, and Lowess regression. Seven classification rules are considered: 3-nearest neighbor, linear support vector machine, linear discriminant analysis, regular histogram, Gaussian kernel, perceptron, and multiple perceptron with majority voting. The results of the first three are presented in the paper, with the full results being given on a complementary website. The conclusion from the different experiment models considered in the study is that normalization can have a significant benefit for classification under difficult experimental conditions, with linear and Lowess regression slightly outperforming the offset method.

  1. Normalization Benefits Microarray-Based Classification

    Directory of Open Access Journals (Sweden)

    Edward R. Dougherty

    2006-08-01

    Full Text Available When using cDNA microarrays, normalization to correct labeling bias is a common preliminary step before further data analysis is applied, its objective being to reduce the variation between arrays. To date, assessment of the effectiveness of normalization has mainly been confined to the ability to detect differentially expressed genes. Since a major use of microarrays is the expression-based phenotype classification, it is important to evaluate microarray normalization procedures relative to classification. Using a model-based approach, we model the systemic-error process to generate synthetic gene-expression values with known ground truth. These synthetic expression values are subjected to typical normalization methods and passed through a set of classification rules, the objective being to carry out a systematic study of the effect of normalization on classification. Three normalization methods are considered: offset, linear regression, and Lowess regression. Seven classification rules are considered: 3-nearest neighbor, linear support vector machine, linear discriminant analysis, regular histogram, Gaussian kernel, perceptron, and multiple perceptron with majority voting. The results of the first three are presented in the paper, with the full results being given on a complementary website. The conclusion from the different experiment models considered in the study is that normalization can have a significant benefit for classification under difficult experimental conditions, with linear and Lowess regression slightly outperforming the offset method.

  2. Search for Allergens from the Pollen Proteome of Sunflower (Helianthus annuus L.: A Major Sensitizer for Respiratory Allergy Patients.

    Directory of Open Access Journals (Sweden)

    Nandini Ghosh

    Full Text Available Respiratory allergy triggered by pollen allergens is increasing at an alarming rate worldwide. Sunflower pollen is thought to be an important source of inhalant allergens. Present study aims to identify the prevalence of sunflower pollinosis among the Indian allergic population and characterizes the pollen allergens using immuno-proteomic tools.Clinico-immunological tests were performed to understand the prevalence of sensitivity towards sunflower pollen among the atopic population. Sera from selected sunflower positive patients were used as probe to detect the IgE-reactive proteins from the one and two dimensional electrophoretic separated proteome of sunflower pollen. The antigenic nature of the sugar moiety of the glycoallergens was studied by meta-periodate modification of IgE-immunoblot. Finally, these allergens were identified by mass-spectrometry.Prevalence of sunflower pollen sensitization was observed among 21% of the pollen allergic population and associated with elevated level of specific IgE and histamine in the sera of these patients. Immunoscreening of sunflower pollen proteome with patient sera detected seven IgE-reactive proteins with varying molecular weight and pI. Hierarchical clustering of 2D-immunoblot data highlighted three allergens characterized by a more frequent immuno-reactivity and increased levels of IgE antibodies in the sera of susceptible patients. These allergens were considered as the major allergens of sunflower pollen and were found to have their glycan moiety critical for inducing IgE response. Homology driven search of MS/MS data of these IgE-reactive proteins identified seven previously unreported allergens from sunflower pollen. Three major allergenic proteins were identified as two pectate lyases and a cysteine protease.Novelty of the present report is the identification of a panel of seven sunflower pollen allergens for the first time at immuno-biochemical and proteomic level, which substantiated the

  3. Microarrayed Materials for Stem Cells

    OpenAIRE

    Ying Mei

    2012-01-01

    Stem cells hold remarkable promise for applications in disease modeling, cancer therapy, and regenerative medicine. Despite the significant progress made during the last decade, designing materials to control stem cell fate remains challenging. As an alternative, materials microarray technology has received great attention because it allows for high throughput materials synthesis and screening at a reasonable cost. Here, we discuss recent developments in materials microarray technology and th...

  4. Recent advances of protein microarrays

    OpenAIRE

    Hultschig, Claus; Kreutzberger, Jürgen; Seitz, Harald; Konthur, Zoltán; Büssow, Konrad; Lehrach, Hans

    2006-01-01

    Technological innovations and novel applications have greatly advanced the field of protein microarrays. Over the past two years, different types of protein microarrays have been used for serum profiling, protein abundance determinations, and identification of proteins that bind DNA or small compounds. However, considerable development is still required to ensure common quality standards and to establish large content repertoires. Here, we summarize applications available to date and discuss ...

  5. Vaccine-associated varicella and rubella infections in severe combined immunodeficiency with isolated CD4 lymphocytopenia and mutations in IL7R detected by tandem whole exome sequencing and chromosomal microarray.

    Science.gov (United States)

    Bayer, D K; Martinez, C A; Sorte, H S; Forbes, L R; Demmler-Harrison, G J; Hanson, I C; Pearson, N M; Noroski, L M; Zaki, S R; Bellini, W J; Leduc, M S; Yang, Y; Eng, C M; Patel, A; Rodningen, O K; Muzny, D M; Gibbs, R A; Campbell, I M; Shaw, C A; Baker, M W; Zhang, V; Lupski, J R; Orange, J S; Seeborg, F O; Stray-Pedersen, A

    2014-12-01

    In areas without newborn screening for severe combined immunodeficiency (SCID), disease-defining infections may lead to diagnosis, and in some cases, may not be identified prior to the first year of life. We describe a female infant who presented with disseminated vaccine-acquired varicella (VZV) and vaccine-acquired rubella infections at 13 months of age. Immunological evaluations demonstrated neutropenia, isolated CD4 lymphocytopenia, the presence of CD8(+) T cells, poor lymphocyte proliferation, hypergammaglobulinaemia and poor specific antibody production to VZV infection and routine immunizations. A combination of whole exome sequencing and custom-designed chromosomal microarray with exon coverage of primary immunodeficiency genes detected compound heterozygous mutations (one single nucleotide variant and one intragenic copy number variant involving one exon) within the IL7R gene. Mosaicism for wild-type allele (20-30%) was detected in pretransplant blood and buccal DNA and maternal engraftment (5-10%) demonstrated in pretransplant blood DNA. This may be responsible for the patient's unusual immunological phenotype compared to classical interleukin (IL)-7Rα deficiency. Disseminated VZV was controlled with anti-viral and immune-based therapy, and umbilical cord blood stem cell transplantation was successful. Retrospectively performed T cell receptor excision circle (TREC) analyses completed on neonatal Guthrie cards identified absent TREC. This case emphasizes the danger of live viral vaccination in severe combined immunodeficiency (SCID) patients and the importance of newborn screening to identify patients prior to high-risk exposures. It also illustrates the value of aggressive pathogen identification and treatment, the influence newborn screening can have on morbidity and mortality and the significant impact of newer genomic diagnostic tools in identifying the underlying genetic aetiology for SCID patients. PMID:25046553

  6. Microarray Technology for Major Chemical Contaminants Analysis in Food: Current Status and Prospects

    OpenAIRE

    Xiaoxia Ding; Wen Zhang; Xiaofeng Hu; Qi Zhang; Peiwu Li; Zhaowei Zhang

    2012-01-01

    Chemical contaminants in food have caused serious health issues in both humans and animals. Microarray technology is an advanced technique suitable for the analysis of chemical contaminates. In particular, immuno-microarray approach is one of the most promising methods for chemical contaminants analysis. The use of microarrays for the analysis of chemical contaminants is the subject of this review. Fabrication strategies and detection methods for chemical contaminants are discussed in detail....

  7. Concentration and determinants of molds and allergens in indoor air and house dust of French dwellings.

    Science.gov (United States)

    Dallongeville, Arnaud; Le Cann, Pierre; Zmirou-Navier, Denis; Chevrier, Cécile; Costet, Nathalie; Annesi-Maesano, Isabella; Blanchard, Olivier

    2015-12-01

    Molds and allergens are common indoor biocontaminants. The aims of this study were to assess the concentrations of common molds in indoor air and floor dust and the concentrations of house dust mite, cat and dog allergens in mattress dust in French dwellings, and to assess predictors of these concentrations. A sample of 150 houses in Brittany (western France) was investigated. Airborne Cladosporium and Penicillium were detected in more than 90% of the dwellings, Aspergillus in 46% and Alternaria in only 6% of the housings. Regarding floor dust samples, Cladosporium and Penicillium were detected in 92 and 80% of the housings respectively, Aspergillus in 49% and Alternaria in 14%. House dust mite allergens Der p1 and Der f1 were detected in 90% and 77% of the mattress dust samples respectively and Can f1 and Fel d1 in 37% and 89% of the homes. Airborne and dustborne mold concentrations, although not statistically correlated (except for Aspergillus) shared most of their predictors. Multivariate linear models for mold levels, explaining up to 62% of the variability, showed an influence of the season, of the age of the dwelling, of aeration habits, presence of pets, smoking, signals of dampness, temperature and relative humidity. Allergens in the dust of the mattress were strongly related to the presence of pets and cleaning practices of bedsheets, these factors accounting for 60% of the variability. This study highlights ubiquitous contamination by molds and underlines complex interaction between outdoor and indoor sources and factors. PMID:26094801

  8. A comparative analysis of DNA barcode microarray feature size

    Directory of Open Access Journals (Sweden)

    Smith Andrew M

    2009-10-01

    Full Text Available Abstract Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density, but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO collection used for screens of pooled yeast (Saccharomyces cerevisiae deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be ALG7. Conclusion We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.

  9. AN INTELLIGENT SEGMENTATION ALGORITHM FOR MICROARRAY IMAGE PROCESSING

    Directory of Open Access Journals (Sweden)

    P.Rajkumar

    2013-06-01

    Full Text Available Microarray technology consists of an array of thousands of microscopic spots of DNA oligonucleotides attached to a solid surface. It is a very powerful technique for analyzing gene expressions as well as to explore the underlying genetic causes of many human diseases. There are numerous applications of this technology, including environmental health research, drug design and discovery, clinical diagnosis and treatment and in cancer detection. The spots, which represent genes in microarray experiment contains the quantitative information that needs to be extracted accurately. For this process, preprocessing of microarray plays an essential role and it is also influential in future steps of the analysis. The three microarray preprocessing steps include gridding, segmentation and quantification. The first step is gridding, refers to the identification of the centre coordinates of each spot. The second step is segmentation, refers to the process of separating foreground and background fluorescence intensities. Segmentation is very important step as it directly affects the accuracy of gene expression analysis in the data mining process that follows. Accurate segmentation is one of the vital steps in microarray image processing. A novel method for segmentation of microarray image is proposed which accurately segment the spots from background when compared with adaptive threshold, combined global and local thresholdand fuzzy c-means clustering methods. Experimental results show that our proposed method provides better segmentation and improved intensity values than the above existing methods.

  10. The Schistosoma mansoni tegumental-allergen-like (TAL protein family: influence of developmental expression on human IgE responses.

    Directory of Open Access Journals (Sweden)

    Colin M Fitzsimmons

    Full Text Available BACKGROUND: A human IgE response to Sm22.6 (a dominant IgE target in Schistosoma mansoni is associated with the development of partial immunity. Located inside the tegument, the molecule belongs to a family of proteins from parasitic platyhelminths, the Tegument-Allergen-Like proteins (TALs. In addition to containing dynein-light-chain domains, these TALs also contain EF-hand domains similar to those found in numerous EF-hand allergens. METHODOLOGY/PRINCIPAL FINDINGS: S. mansoni genome searches revealed 13 members (SmTAL1-13 within the species. Recent microarray data demonstrated they have a wide range of life-cycle transcriptional profiles. We expressed SmTAL1 (Sm22.6, SmTAL2, 3, 4, 5 and 13 as recombinant proteins and measured IgE and IgG4 in 200 infected males (7-60 years from a schistosomiasis endemic region in Uganda. For SmTAL1 and 3 (transcribed in schistosomula through adult-worms and adult-worms, respectively and SmTAL5 (transcribed in cercariae through adult-worms, detectable IgE responses were rare in 7-9 year olds, but increased with age. At all ages, IgE to SmTAL2 (expressed constitutively, was rare while anti-SmTAL2 IgG4 was common. Levels of IgE and IgG4 to SmTAL4 and 13 (transcribed predominantly in the cercariae/skin stage were all low. CONCLUSIONS: We have not measured SmTAL protein abundance or exposure in live parasites, but the antibody data suggests to us that, in endemic areas, there is priming and boosting of IgE to adult-worm SmTALs by occasional death of long-lived worms, desensitization to egg SmTALs through continuous exposure to dying eggs and low immunogenicity of larval SmTALs due to immunosuppression in the skin by the parasite. Of these, it is the gradual increase in IgE to the worm antigens that parallels age-dependent immunity seen in endemic areas.

  11. Citral a fragrance allergen and irritant

    DEFF Research Database (Denmark)

    Heydorn, S; Menné, T; Andersen, Klaus Ejner;

    2003-01-01

    Citral is a well known contact allergen and a contact irritant. Routine patch testing in the past may have been restricted because of possible irritant (IR) patch test responses. 586 consecutive patients, with hand eczema, were patch tested with a selection of fragrances including citral 2...... positive patch test reactions to other fragrances compared with IR reactions (n = 82) was established. The difference regarding fragrance history found between those with IR and positive reactions to citral was not significant. Citral could be an allergen and/or irritant, worthy of further more extensive...

  12. 重庆地区食物过敏原特异性IgG检测及试剂盒性能分析%Performance Analysis of the Kit and Detection of Food Allergen-specific IgG in Chongqing

    Institute of Scientific and Technical Information of China (English)

    陈忠余; 向治平; 李新; 王凌云

    2011-01-01

    目的 了解在研试剂盒对食物过敏原特异性IgG的检测性能并筛查重庆地区常见食物过敏原特异性IgG抗体.方法 以Biomerica有限公司生产的食物不耐受检测试剂盒作为标准对照,采用ELISA方法及双盲平行对照临床试验设计,分别应用在研试剂盒和标准对照试剂盒对280例变态反应性疾病患者和70例健康对照者常见食物过敏原的特异性IgG进行平行检测,并将两种检测结果进行一致性检验.结果 重庆地区,变态反应性疾病的患者中不耐受食物主要是鸡蛋,其次是虾;280例变态反应性疾病患者检测中,标准对照试剂盒阳性率为92.50%(259/280),在研试剂盒阳性率为93.57%(262/280),两者差异无统计学意义(χ2=0.571 4,P>0.05).在研试剂盒10个检测项目的敏感度、特异度分别在92.0%~96.9%,98.2%~99.7%之间,准确度达到97.7%~99.4%;10个检测项目的Kappa值均大于0.75,说明两种检测试剂盒检测性能一致性良好.结论 重庆地区与其他地区的食物不耐受情况不完全一致,应结合本地区实际情况寻找适合本地区的过敏原筛查范围及制定相应的治疗措施;在研试剂盒和标准对照试剂盒检测食物过敏原特异性IgG抗体一致性良好,该在研试剂盒适合在临床中推广应用.%Objective To investigate the detecting efficiency of an unregistered kit upon food allergen-apecific IgG and Screening the common food allergen-specific IgG in Chongqing. Methods A double blind and parallel comparative trial was conducted and enzyme linked immunosorbent assay (ELISA) was applied. The standard control kit (Allerquant IgG Food Allergy Screening ELISA Kit,produced by Biomerica Inc) and the test kit (unregistered kit) were adopted to detect food allergen-specific IgG in 280 patients with allergic disorder and 70 healthy controls. Results The first and the second most intolerant foods were egg and shrimp in allergicdisorder in Chongqiong. In allergic

  13. Multiplex Assay for Protein Profiling and Potency Measurement of German Cockroach Allergen Extracts.

    Directory of Open Access Journals (Sweden)

    Taruna Khurana

    Full Text Available German cockroach (GCr allergens induce IgE responses and may cause asthma. Commercial GCr allergen extracts are variable and existing assays may not be appropriate for determining extract composition and potency.Our aim was to develop a multiplex antibody/bead-based assay for assessment of GCr allergen extracts.Single chain fragment variable (scFv antibodies against GCr were obtained by screening libraries derived from naïve human lymphocytes and hyperimmunized chicken splenocytes and bone marrow. Selected clones were sequenced and characterized by immunoblotting. Eighteen scFv antibodies (17 chicken, 1 human coupled to polystyrene beads were used in this suspension assay; binding of targeted GCr allergens to antibody-coated beads was detected using rabbit antisera against GCr, and against specific allergens rBla g 1, rBla g 2, and rBla g 4. The assay was tested for specificity, accuracy, and precision. Extracts were also compared by IgE competition ELISA.Chicken scFv's generated eight different binding patterns to GCr proteins from 14 to 150 kDa molecular weight. Human scFv's recognized a 100 kDa GCr protein. The multiplex assay was found to be specific and reproducible with intra-assay coefficient of variation (CV of 2.64% and inter-assay CV of 10.0%. Overall potencies of various GCr extracts were calculated using mean logEC50s for eight selected scFvs. Overall potency measures were also analyzed by assessing the contributions to potency of each target.An scFv antibody-based multiplex assay has been developed capable of simultaneously measuring different proteins in a complex mixture, and to determine the potencies and compositions of allergen extracts.

  14. The current state of recombinant allergens for immunotherapy

    DEFF Research Database (Denmark)

    Pauli, Gabrielle; Malling, H-J

    2010-01-01

    Subcutaneous immunotherapy is a well documented treatment of allergic rhinitis and asthma. The majority of the disadvantages of the treatment are related to the poor quality of the natural allergen extracts which can contain varying amounts of individual allergens including allergens to which the...... patient may not be sensitized. Recombinant allergens offer a possibility to use well defined molecules with consistent pharmaceutical quality defined in mass units. The proof of concept of the clinical efficacy of recombinant allergens is based on two studies published as full articles....

  15. Food allergens of plant origin - their molecular and evolutionary relationships

    DEFF Research Database (Denmark)

    Mills, E. N. C.; Madsen, Charlotte Bernhard; Shewry, P. R.;

    2003-01-01

    usually triggered by the protein components in a food, which are also known as allergens. However, not all the proteins in an allergenic food like peanut are allergens. Why should this be? This question has been addressed by an EU-funded inter-disciplinary network of clinicians, food chemists and plant...... biochemists called Protall. From the groups considerations it is clear that, whilst the abundance of a protein in a food is one factor involved in determining its allergenic potential, this is not sufficient on its own to predict its allergenicity. Through an analysis of common properties of plant food...

  16. Mechanisms of allergen-specific immunotherapy and immune tolerance to allergens.

    Science.gov (United States)

    Akdis, Cezmi A; Akdis, Mübeccel

    2015-01-01

    Substantial progress in understanding mechanisms of immune regulation in allergy, asthma, autoimmune diseases, tumors, organ transplantation and chronic infections has led to a variety of targeted therapeutic approaches. Allergen-specific immunotherapy (AIT) has been used for 100 years as a desensitizing therapy for allergic diseases and represents the potentially curative and specific way of treatment. The mechanisms by which allergen-AIT has its mechanisms of action include the very early desensitization effects, modulation of T- and B-cell responses and related antibody isotypes as well as inhibition of migration of eosinophils, basophils and mast cells to tissues and release of their mediators. Regulatory T cells (Treg) have been identified as key regulators of immunological processes in peripheral tolerance to allergens. Skewing of allergen-specific effector T cells to a regulatory phenotype appears as a key event in the development of healthy immune response to allergens and successful outcome in AIT. Naturally occurring FoxP3(+) CD4(+)CD25(+) Treg cells and inducible type 1 Treg (Tr1) cells contribute to the control of allergen-specific immune responses in several major ways, which can be summarized as suppression of dendritic cells that support the generation of effector T cells; suppression of effector Th1, Th2 and Th17 cells; suppression of allergen-specific IgE, and induction of IgG4; suppression of mast cells, basophils and eosinophils and suppression of effector T cell migration to tissues. New strategies for immune intervention will likely include targeting of the molecular mechanisms of allergen tolerance and reciprocal regulation of effector and regulatory T cell subsets. PMID:26023323

  17. Mechanisms of allergen-specific immunotherapy and immune tolerance to allergens

    OpenAIRE

    Cezmi A Akdis; Akdis, Mübeccel

    2015-01-01

    Substantial progress in understanding mechanisms of immune regulation in allergy, asthma, autoimmune diseases, tumors, organ transplantation and chronic infections has led to a variety of targeted therapeutic approaches. Allergen-specific immunotherapy (AIT) has been used for 100 years as a desensitizing therapy for allergic diseases and represents the potentially curative and specific way of treatment. The mechanisms by which allergen-AIT has its mechanisms of action include the very early d...

  18. A Versatile Microarray Platform for Capturing Rare Cells

    Science.gov (United States)

    Brinkmann, Falko; Hirtz, Michael; Haller, Anna; Gorges, Tobias M.; Vellekoop, Michael J.; Riethdorf, Sabine; Müller, Volkmar; Pantel, Klaus; Fuchs, Harald

    2015-10-01

    Analyses of rare events occurring at extremely low frequencies in body fluids are still challenging. We established a versatile microarray-based platform able to capture single target cells from large background populations. As use case we chose the challenging application of detecting circulating tumor cells (CTCs) - about one cell in a billion normal blood cells. After incubation with an antibody cocktail, targeted cells are extracted on a microarray in a microfluidic chip. The accessibility of our platform allows for subsequent recovery of targets for further analysis. The microarray facilitates exclusion of false positive capture events by co-localization allowing for detection without fluorescent labelling. Analyzing blood samples from cancer patients with our platform reached and partly outreached gold standard performance, demonstrating feasibility for clinical application. Clinical researchers free choice of antibody cocktail without need for altered chip manufacturing or incubation protocol, allows virtual arbitrary targeting of capture species and therefore wide spread applications in biomedical sciences.

  19. Animal allergens and their presence in the environment

    Directory of Open Access Journals (Sweden)

    Eva eZahradnik

    2014-03-01

    Full Text Available Exposure to animal allergens is a major risk factor for sensitization and allergic diseases. Besides mites and cockroaches, the most important animal allergens are derived from mammals. Cat and dog allergies affect the general population; whereas, allergies to rodents or cattle is an occupational problem. Exposure to animal allergens is not limited to direct contact to animals. Based on their aerodynamic properties, mammalian allergens easily become airborne, attach to clothing and hair, and can be spread from one environment to another. For example, the major cat allergen Fel d 1 was frequently found in homes without pets and in public buildings, including schools, day care centers and hospitals. Allergen concentrations in a particular environment showed high variability depending on numerous factors.Assessment of allergen exposure levels is a stepwise process that involves dust collection, allergen quantification and data analysis. Whereas a number of different dust sampling strategies are used, ELISA assays have prevailed in the last years as the standard technique for quantification of allergen concentrations. This review focuses on allergens arising from domestic, farm and laboratory animals and describes the ubiquity of mammalian allergens in the human environment. It includes an overview of exposure assessment studies carried out in different indoor settings (homes, schools, workplaces using numerous sampling and analytical methods and summarizes significant factors influencing exposure levels. However, methodological differences among studies have contributed to the variability of the findings and make comparisons between studies difficult. Therefore, a general standardization of methods is needed and recommended.

  20. Simultaneous allergen inactivation and detoxification of castor bean cake by treatment with calcium compounds

    International Nuclear Information System (INIS)

    Ricinus communis L. is of great economic importance due to the oil extracted from its seeds. Castor oil has been used for pharmaceutical and industrial applications, as a lubricant or coating agent, as a component of plastic products, as a fungicide or in the synthesis of biodiesel fuels. After oil extraction, a castor cake with a large amount of protein is obtained. However, this by-product cannot be used as animal feed due to the presence of toxic (ricin) and allergenic (2S albumin) proteins. Here, we propose two processes for detoxification and allergen inactivation of the castor cake. In addition, we establish a biological test to detect ricin and validate these detoxification processes. In this test, Vero cells were treated with ricin, and cell death was assessed by cell counting and measurement of lactate dehydrogenase activity. The limit of detection of the Vero cell assay was 10 ng/mL using a concentration of 1.6 × 105 cells/well. Solid-state fermentation (SSF) and treatment with calcium compounds were used as cake detoxification processes. For SSF, Aspergillus niger was grown using a castor cake as a substrate, and this cake was analyzed after 24, 48, 72, and 96 h of SSF. Ricin was eliminated after 24 h of SSF treatment. The cake was treated with 4 or 8% Ca(OH)2 or CaO, and both the toxicity and the allergenic properties were entirely abolished. A by-product free of toxicity and allergens was obtained

  1. Allergen-Specific CD4(+) T Cells in Human Asthma.

    Science.gov (United States)

    Ling, Morris F; Luster, Andrew D

    2016-03-01

    In allergic asthma, aeroallergen exposure of sensitized individuals mobilizes robust innate and adaptive airway immune responses, stimulating eosinophilic airway inflammation and the activation and infiltration of allergen-specific CD4(+) T cells into the airways. Allergen-specific CD4(+) T cells are thought to be central players in the asthmatic response as they specifically recognize the allergen and initiate and orchestrate the asthmatic inflammatory response. In this article, we briefly review the role of allergen-specific CD4(+) T cells in the pathogenesis of human allergic airway inflammation in allergic individuals, discuss the use of allergen-major histocompatibility complex class II tetramers to characterize allergen-specific CD4(+) T cells, and highlight current gaps in knowledge and directions for future research pertaining to the role of allergen-specific CD4(+) T cells in human asthma. PMID:27027948

  2. Identification of wheat allergens using proteomic approach

    Czech Academy of Sciences Publication Activity Database

    Šotkovský, Petr; Hubálek, M.; Hernychová, L.; Novák, Petr; Havranová, M.; Fuchs, M.; Stulík, J.; Tučková, Ludmila

    Latina : Allergy data laboratories, 2007, s. 41-41. [International Symposium on Molecular Allergology /2./. Roma (IT), 22.04.2007-24.04.2007] R&D Projects: GA ČR GA310/05/2245 Institutional research plan: CEZ:AV0Z50200510 Keywords : wheat flour * wheat allergens * proteins Subject RIV: EE - Microbiology, Virology

  3. Kiwifruit as a food allergen source

    Directory of Open Access Journals (Sweden)

    Popović Milica

    2013-01-01

    Full Text Available Since its first appearance on the market kiwifruit has become very popular in the human diet due to its pleasant taste, low caloric value and high content of vitamin C. However, kiwifruit allergy has become a frequent cause of type I hypersensitivity in the western society. Molecular basis for kiwifruit allergy has been ascribed to up-to-now 11 identified IgE reactive molecules. They are proteins and glycoproteins with a molecular mass between 50 and 10 kDa. The major kiwifruit allergen is a cysteine protease denoted as Act d 1, which represents 50% of the soluble protein extract. Due to a difference in the abundance of protein components and biological activity, the quality of kiwifruit extracts intended for allergy diagnosis can vary in content and amount of IgE reactive molecules. In addition, the quality of allergen extracts for allergy diagnosis depends on the fruit ripening stage and storage conditions. In terms of clinical reactivity it has become evident that kiwifruit allergy is not a homogeneous disorder. Different patterns of IgE reactivity accompany several clinical subgroups that have been identified in different geographical regions. In the last decade an enormous progress has been made in isolation and characterization of kiwifruit allergens. This paper will give an overview of the structural features of kiwifruit allergens. [Projekat Ministarstva nauke Republike Srbije, br. 172049

  4. Vaccine development for allergen-specific immunotherapy based on recombinant allergens and synthetic allergen peptides: Lessons from the past and novel mechanisms of action for the future

    OpenAIRE

    Valenta, Rudolf; Campana, Raffaela; Focke-Tejkl, Margit; Niederberger, Verena

    2016-01-01

    In the past, the development of more effective, safe, convenient, broadly applicable, and easy to manufacture vaccines for allergen-specific immunotherapy (AIT) has been limited by the poor quality of natural allergen extracts. Progress made in the field of molecular allergen characterization has now made it possible to produce defined vaccines for AIT and eventually for preventive allergy vaccination based on recombinant DNA technology and synthetic peptide chemistry. Here we review the char...

  5. Environmental allergens in patients with allergic rhinitis

    International Nuclear Information System (INIS)

    Objective: to find out the common environmental allergens responsible for sensitivity in patients with allergic rhinitis. Design: Descriptive cross sectional study. Place and Duration of Study: A local allergy clinic in an urban area of Lahore during the year 2000-2001. Subjects and Methods: Eighty patients with allergic rhinitis irrespective of age and sex were studied. These cases were selected on the basis of symptoms like sneezing, itching, watery nasal discharge and eosinophilia in nasal secretions. Forty matched healthy subjects as controls were also studied. Allergy test was performed on all the subjects by skin prick test to determine sensitivity to common environmental allergens using Bencard (England) allergy kit. Results: common environmental allergens responsible for sensitivity in allergic rhinitis patients were house dust (82.5 %), house dust mites (73.7%), mixed threshing (80%), straw dust (58.7%, hay dust (63.7%), mixed feathers (45%), cat fur (57.5%), cotton flock (56.2%), tree pollens (45%) and grass pollens (48.7%). Sensitivity to these allergens was observed in significantly higher (P<0.01) percentage of allergic rhinitis patients as compared with control subjects. Sensitivity to house dust, house dust mites and cat fur was of severe degree in majority of allergic rhinitis patients. While sensitivity to mixed threshing, straw dust, hay dust and mixed feathers was of moderate to severe degree in majority of these patients. Conclusion: Skin prick tests provide an effective and definitive mean to find out sensitivity to different allergens in cases with allergic rhinitis. Based on these findings, the physician can manage these patients in better way. (author)

  6. Parallel detection of potato viruses by microarrays

    Czech Academy of Sciences Publication Activity Database

    Lenz, Ondřej; Bystřická, Dagmar; Mráz, Ivan; Petrzik, Karel; Šíp, Miroslav

    Prague : Czech University of Agriculture, 2002. s. 55. [Conference of European Foundation for Plant Pathology "Disease Resistance in Plant Pathology" /6./. 08.09.2002-14.09.2002, Prague] R&D Projects: GA ČR GA522/01/1105 Keywords : potato viruses Subject RIV: EE - Microbiology, Virology

  7. Microarrays - parallel detection of potato viruses

    Czech Academy of Sciences Publication Activity Database

    Bystřická, Dagmar; Lenz, Ondřej; Mráz, Ivan; Šíp, M.

    Nitra : SPU, 2003 - (Hudec, K.; Huszár, J.). s. 46 [Slovak and Czech Plant Protection Conference /16./. 16.09.2003-17.09.2003, Nitra] R&D Projects: GA ČR GA522/01/1105 Institutional research plan: CEZ:AV0Z5051902 Keywords : virus diseases * potatoes * plant protection Subject RIV: EE - Microbiology, Virology

  8. DNA microarray: parallel detection of potato viruses

    Czech Academy of Sciences Publication Activity Database

    Bystřická, Dagmar; Lenz, Ondřej; Mráz, Ivan; Dědič, P.; Šíp, M.

    2003-01-01

    Roč. 47, - (2003), s. 41-44. ISSN 0001-723X R&D Projects: GA ČR GA522/01/1105 Institutional research plan: CEZ:AV0Z5051902 Keywords : potato viruses, DNA Subject RIV: EE - Microbiology, Virology Impact factor: 0.683, year: 2003

  9. Phenotypic MicroRNA Microarrays

    OpenAIRE

    Veronica Soloveva; Michel Liuzzi; Jin Yeop Kim; Hi Chul Kim; Jin Yeong Heo; Yong-Jun Kwon

    2013-01-01

    Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the bio...

  10. Why are some proteins allergenic? Implications for biotechnology.

    Science.gov (United States)

    Lehrer, S B; Horner, W E; Reese, G

    1996-07-01

    In recent years, a number of agricultural crops have been developed with recombinant DNA technology. Because the transferred genes code for proteins that are ordinarily not present in these particular foods, there is concern about the potential allergenicity of these new crop varieties. Foods contain many proteins; however, only a small fraction are allergens. Although the structural properties of proteins that cause allergic reactions have not been characterized completely, known food allergens in general have molecular weights between 10 and 70 kDa, stimulate the immune response (induce the production of allergen-specific IgE), and are stable molecules that are resistant to processing, cooking, and digestion. Although any type of food is potentially allergenic, the majority of food allergies are caused by a small group of foods (cows' milk, nuts, legumes, eggs, seafood). Cross-reactivities occur within a given food group and between foods and seemingly unrelated proteins. Even though most transgenic foods are considered safe, biotechnological manipulation can affect crop allergenicity. The safety evaluation of transgenic foods is relatively easy when the allergenicity of the gene sources are known. The recombinant food can be assayed using traditional in vitro inhibition assays. Recently, reduced allergen content of biotechnologically altered rice was shown. In contrast, increased allergenicity was demonstrated in transgenic soybeans after a methionine- and cystine-rich protein from Brazil nuts, identified as a major Brazil nut allergen, was expressed in soybean to increase its content of sulfur-rich amino acids. The most difficult issue regarding transgenic food allergenicity is the effect of transfer of proteins of unknown allergenicity. The challenge is to determine whether these proteins are allergenic as there is no generally accepted, established, definitive procedure to define or predict a protein's allergenicity. Comparing the structures of the

  11. 嗜肺军团菌15种血清型基因芯片检测方法的建立%Development of a DNA Microarray for Detection and Identification of 15 Distinct O Antigen Forms of Legionella Pneumophila

    Institute of Scientific and Technical Information of China (English)

    吴冬雪; 王乃福; 黄晨; 高旗利; 关淳

    2014-01-01

    To establish a rapid, accurate detection method for 15 distinct O antigen forms of Legionella pneumophila using DNA microarray combined with multiplex PCR. The special genes of these 15 distinct O antigen forms of L. Pneumophila were as target genes for multiplex PCR respectively, then primers and captured oligonucleotide probes were hybridizes with DNA microarray, which contained specific probes of Legionella pneumophila. Scanner was used to determinant the types of bacterium. The DNA microarray assay can detect 15 distinct O antigen forms of L. Pneumophila specially. The sensitivity of the DNA microarray was 10 ng. The detection method of 15 distinct O antigen forms of Legionella pneumophila by DNA microarray was established. The detection method has better specificity, sensitivity and repeatability.%建立一种多重PCR技术结合基因芯片检测方法,实现嗜肺军团菌15种血清型的快速、准确检测。根据嗜肺军团菌15种血清型的O抗原特异性基因设计并筛选合适的引物和探针,进行多重PCR扩增,制备寡核苷酸芯片。将多重PCR扩增产物与带有特异探针的芯片杂交。用扫描仪扫描,判定嗜肺军团菌的血清型。该基因芯片可特异性的检测嗜肺军团菌的15种血清型,具有良好的特异性,芯片纯菌DNA检测灵敏度为10 ng。所建立的嗜肺军团菌15种血清型基因芯片检测方法特异性好,灵敏度高,具有较好的实用性。

  12. Exploiting fluorescence for multiplex immunoassays on protein microarrays

    International Nuclear Information System (INIS)

    Protein microarray technology is becoming the method of choice for identifying protein interaction partners, detecting specific proteins, carbohydrates and lipids, or for characterizing protein interactions and serum antibodies in a massively parallel manner. Availability of the well-established instrumentation of DNA arrays and development of new fluorescent detection instruments promoted the spread of this technique. Fluorescent detection has the advantage of high sensitivity, specificity, simplicity and wide dynamic range required by most measurements. Fluorescence through specifically designed probes and an increasing variety of detection modes offers an excellent tool for such microarray platforms. Measuring for example the level of antibodies, their isotypes and/or antigen specificity simultaneously can offer more complex and comprehensive information about the investigated biological phenomenon, especially if we take into consideration that hundreds of samples can be measured in a single assay. Not only body fluids, but also cell lysates, extracted cellular components, and intact living cells can be analyzed on protein arrays for monitoring functional responses to printed samples on the surface. As a rapidly evolving area, protein microarray technology offers a great bulk of information and new depth of knowledge. These are the features that endow protein arrays with wide applicability and robust sample analyzing capability. On the whole, protein arrays are emerging new tools not just in proteomics, but glycomics, lipidomics, and are also important for immunological research. In this review we attempt to summarize the technical aspects of planar fluorescent microarray technology along with the description of its main immunological applications. (topical review)

  13. Exploiting fluorescence for multiplex immunoassays on protein microarrays

    Science.gov (United States)

    Herbáth, Melinda; Papp, Krisztián; Balogh, Andrea; Matkó, János; Prechl, József

    2014-09-01

    Protein microarray technology is becoming the method of choice for identifying protein interaction partners, detecting specific proteins, carbohydrates and lipids, or for characterizing protein interactions and serum antibodies in a massively parallel manner. Availability of the well-established instrumentation of DNA arrays and development of new fluorescent detection instruments promoted the spread of this technique. Fluorescent detection has the advantage of high sensitivity, specificity, simplicity and wide dynamic range required by most measurements. Fluorescence through specifically designed probes and an increasing variety of detection modes offers an excellent tool for such microarray platforms. Measuring for example the level of antibodies, their isotypes and/or antigen specificity simultaneously can offer more complex and comprehensive information about the investigated biological phenomenon, especially if we take into consideration that hundreds of samples can be measured in a single assay. Not only body fluids, but also cell lysates, extracted cellular components, and intact living cells can be analyzed on protein arrays for monitoring functional responses to printed samples on the surface. As a rapidly evolving area, protein microarray technology offers a great bulk of information and new depth of knowledge. These are the features that endow protein arrays with wide applicability and robust sample analyzing capability. On the whole, protein arrays are emerging new tools not just in proteomics, but glycomics, lipidomics, and are also important for immunological research. In this review we attempt to summarize the technical aspects of planar fluorescent microarray technology along with the description of its main immunological applications.

  14. From Allergen Back to Antigen:. a Rational Approach to New Forms of Immunotherapy

    Science.gov (United States)

    Colombo, Paolo; Trapani, Antonino; Geraci, Domenico; Golino, Massimiliano; Gianguzza, Fabrizio; Bonura, Angela

    2007-12-01

    Mapping an epitope on a protein by gene fragmentation and/or point mutations is often expensive and time consuming. Analysis of a 3D model can be utilized to detect the amino acids residues which are exposed to the solvent surface and thus represent potential epitope residues. Parj1 and Parj2 are the two major allergens of the Parietaria judaica pollen belonging to the Lipid Transfer Protein family. Using their three-dimensional structures as a guide, a head to tail dimer expressing disulphide bond variants of the major allergens was generated by means of DNA recombinant technology. The hybrid was expressed in E.coli and its immunological activity studied in vivo and in vitro. Our results demonstrate that a hybrid polypeptide expressing disulphide bond variants of the major allergens of the Parietaria pollen displayed reduced allergenicity and enhanced T cell reactivity for induction of protective antibodies able to block human IgE induced during the natural course of sensitization against the Parietaria pollen.

  15. Proteomic identification of allergenic seed proteins, napin and cruciferin, from cold-pressed rapeseed oils.

    Science.gov (United States)

    Puumalainen, T J; Puustinen, A; Poikonen, S; Turjanmaa, K; Palosuo, T; Vaali, K

    2015-05-15

    In Finland and France atopic children commonly react to seeds of oilseed rape and turnip rape in skin prick tests (SPT) and open food challenges. These seeds are not as such in dietary use and therefore the routes of sensitization are unknown. Possible allergens were extracted from commercial cold-pressed and refined rapeseed oils and identified by gel-based tandem nanoflow liquid chromatography mass spectrometry (LC-MS/MS). Napin (a 2S albumin), earlier identified as a major allergen in the seeds of oilseed rape and turnip rape, and cruciferin (an 11S globulin), a new potential seed allergen, were detected in cold-pressed oils, but not in refined oils. Pooled sera from five children sensitized or allergic to oilseed rape and turnip rape seeds reacted to these proteins from cold-pressed oil preparations and individual sera from five children reacted to these proteins extracted from the seeds when examined with IgE immunoblotting. Hence cold-pressed rapeseed oil might be one possible route of sensitization for these allergens. PMID:25577095

  16. Correction: Taliaferro, L. et al. Evaluation of the Broad-Range PCR-Electrospray Ionization Mass Spectrometry (PCR/ESI-MS System and Virus Microarrays for Virus Detection. Viruses 2014, 6, 1876-1896

    Directory of Open Access Journals (Sweden)

    Lanyn P. Taliaferro

    2014-11-01

    Full Text Available We have noted some inaccuracies in Table 1 and Table 2 of our article “Evaluation of the Broad-Range PCR-Electrospray Ionization Mass Spectrometry (PCR/ESI-MS System and Virus Microarrays for Virus Detection” (Viruses 2014, 6, 1876–1896 [1].[...

  17. Is food allergen analysis flawed? Health and supply chain risks and a proposed framework to address urgent analytical needs.

    Science.gov (United States)

    Walker, M J; Burns, D T; Elliott, C T; Gowland, M H; Mills, E N Clare

    2016-01-01

    Food allergy is an increasing problem for those affected, their families or carers, the food industry and for regulators. The food supply chain is highly vulnerable to fraud involving food allergens, risking fatalities and severe reputational damage to the food industry. Many facets are being pursued to ameliorate the difficulties including better food labelling and the concept of thresholds of elicitation of allergy symptoms as risk management tools. These efforts depend to a high degree on the ability reliably to detect and quantify food allergens; yet all current analytical approaches exhibit severe deficiencies that jeopardise accurate results being produced particularly in terms of the risks of false positive and false negative reporting. If we fail to realise the promise of current risk assessment and risk management of food allergens through lack of the ability to measure food allergens reproducibly and with traceability to an international unit of measurement, the analytical community will have failed a significant societal challenge. Three distinct but interrelated areas of analytical work are urgently needed to address the substantial gaps identified: (a) a coordinated international programme for the production of properly characterised clinically relevant reference materials and calibrants for food allergen analysis; (b) an international programme to widen the scope of proteomics and genomics bioinformatics for the genera containing the major allergens to address problems in ELISA, MS and DNA methods; (c) the initiation of a coordinated international programme leading to reference methods for allergen proteins that provide results traceable to the SI. This article describes in more detail food allergy, the risks of inapplicable or flawed allergen analyses with examples and a proposed framework, including clinically relevant incurred allergen concentrations, to address the currently unmet and urgently required analytical requirements. Support for the

  18. Complementarity between microarray and immunoblot for the comparative evaluation of IgE repertoire of French and Italian cypress pollen allergic patients.

    Science.gov (United States)

    Shahali, Y; Nicaise, P; Brázdová, A; Charpin, D; Scala, E; Mari, A; Sutra, J P; Chollet-Martin, S; Sénéchal, H; Poncet, P

    2014-01-01

    Cypress pollen represents the primary cause of respiratory allergies in Mediterranean areas. Patients allergic to Cupressus sempervirens pollen (Cups) (CPA) can be discriminated on the basis of the immunoglobulin E (IgE) binding to a basic 14 kDa protein (BP14) or to high-molecular-weight (HMW) glycoproteins only. Specific IgE repertoires of two differentially exposed CPA cohorts, French and Italian, were investigated using an IgE microarray system (some known major allergens from several allergenic sources) and individual IgE immunoblotting (IB) of whole Cups pollen extract separated by SDS-PAGE (all allergens from one allergenic source: cypress pollen). The prevalence of sensitization to BP14 was higher in French (37 %) than in Italian patients (17 %) and major differences were observed in IgE reactivities to lipid transfer proteins (LTPs). Thirty percent of the Italian CPA (4 % in the French group) had specific IgE against the Parietaria pollen LTP, independently of IB subgroups. Regarding peach LTP sensitization, all Pru p 3+ Italian CPA (10 %) were in the HMW+ subgroup, while Pru p 3+ French CPA (20 %) were all included in the BP14+ subgroup. BP14 sensitization is likely a marker of Cups exposure and is, in French CPA, significantly correlated to Pru p 3 sensitization. The IgE immunoblot and microarray are complementary tools that highlight differences in the subtle sensitization profile between groups of patients in comparative studies. PMID:25152053

  19. Exploring the feasibility of next-generation sequencing and microarray data meta-analysis

    Science.gov (United States)

    Wu, Po-Yen; Phan, John H.; Wang, May D.

    2016-01-01

    Emerging next-generation sequencing (NGS) technology potentially resolves many issues that prevent widespread clinical use of gene expression microarrays. However, the number of publicly available NGS datasets is still smaller than that of microarrays. This paper explores the possibilities for combining information from both microarray and NGS gene expression datasets for the discovery of differentially expressed genes (DEGs). We evaluate several existing methods in detecting DEGs using individual datasets as well as combined NGS and microarray datasets. Results indicate that analysis of combined NGS and microarray data is feasible, but successful detection of DEGs may depend on careful selection of algorithms as well as on data normalization and pre-processing. PMID:22256102

  20. Microarray Developed on Plastic Substrates.

    Science.gov (United States)

    Bañuls, María-José; Morais, Sergi B; Tortajada-Genaro, Luis A; Maquieira, Ángel

    2016-01-01

    There is a huge potential interest to use synthetic polymers as versatile solid supports for analytical microarraying. Chemical modification of polycarbonate (PC) for covalent immobilization of probes, micro-printing of protein or nucleic acid probes, development of indirect immunoassay, and development of hybridization protocols are described and discussed. PMID:26614067

  1. [Evaluation of the total biological activity and allergenic composition of allergenic extracts].

    Science.gov (United States)

    Lombardero, M; González, R; Duffort, O; Juan, F; Ayuso, R; Ventas, P; Cortés, C; Carreira, J

    1986-01-01

    In the present study, a complete procedure is presented in order to standardize allergenic extracts, the meaning of which is the measurement of the total allergenic activity and the determination of the allergenic composition. The measurement of the biological activity comprises 2 steps: Preparation of Reference Extracts and determination of their "in vivo" activity. Evaluation of the total allergenic activity of extracts for clinical use. Reference extracts were prepared from the main allergens and their "in vivo" biological activity was determined by a quantitative skin prick test in a sample of at least 30 allergic patients. By definition, the protein concentration of Reference Extract that produces, in the allergic population, a geometric mean wheal of 75 mm.2 has an activity of 100 biological units (BUs). The determination of the biological activity of a problem extract is made by RAST inhibition. The sample is compared with the corresponding Reference Extract by this technique and, from this comparison, it is possible to quantify the activity of the problem extract in biologic units (BUs) with clinical significance. Likewise, different techniques have been used to determine the allergenic composition of extracts. These techniques comprise 2 steps: Separation of the components of the extract. Identification of the components that bind specific human IgE. The separation of the components of the extract has been carried out by isoelectric focusing (IEF) and electrophoresis in the presence of sodium dodecyl sulphate (SDS-PAGE). In order to identify the allergenic components, an immunoblotting technique has been employed. The separated components in the IEF gel or SDS-PAGE gel are transferred to a nitrocellulose sheet and later on, this membrane is overlaid with a serum pool from allergic patients and a mouse monoclonal anti-human IgE, labelled with 125I. Finally, the autoradiography of the nitrocellulose membrane is obtained. In this way it is possible to compare

  2. Uses of Dendrimers for DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Jean-Pierre Majoral

    2006-08-01

    Full Text Available Biosensors such as DNA microarrays and microchips are gaining an increasingimportance in medicinal, forensic, and environmental analyses. Such devices are based onthe detection of supramolecular interactions called hybridizations that occur betweencomplementary oligonucleotides, one linked to a solid surface (the probe, and the other oneto be analyzed (the target. This paper focuses on the improvements that hyperbranched andperfectly defined nanomolecules called dendrimers can provide to this methodology. Twomain uses of dendrimers for such purpose have been described up to now; either thedendrimer is used as linker between the solid surface and the probe oligonucleotide, or thedendrimer is used as a multilabeled entity linked to the target oligonucleotide. In the firstcase the dendrimer generally induces a higher loading of probes and an easier hybridization,due to moving away the solid phase. In the second case the high number of localized labels(generally fluorescent induces an increased sensitivity, allowing the detection of smallquantities of biological entities.

  3. First National Survey of Lead and Allergens in Housing: survey design and methods for the allergen and endotoxin components.

    Science.gov (United States)

    Vojta, Patrick J; Friedman, Warren; Marker, David A; Clickner, Robert; Rogers, John W; Viet, Susan M; Muilenberg, Michael L; Thorne, Peter S; Arbes, Samuel J; Zeldin, Darryl C

    2002-01-01

    From July 1998 to August 1999, the U.S. Department of Housing and Urban Development and the National Institute of Environmental Health Sciences conducted the first National Survey of Lead and Allergens in Housing. The purpose of the survey was to assess children's potential household exposure to lead, allergens, and bacterial endotoxins. We surveyed a sample of 831 homes, representing 96 million permanently occupied, noninstitutional housing units that permit resident children. We administered questionnaires to household members, made home observations, and took environmental samples. This article provides general background information on the survey, an overview of the survey design, and a description of the data collection and laboratory methods pertaining to the allergen and endotoxin components. We collected dust samples from a bed, the bedroom floor, a sofa or chair, the living room floor, the kitchen floor, and a basement floor and analyzed them for cockroach allergen Bla g 1, the dust mite allergens Der f 1 and Der p 1, the cat allergen Fel d 1, the dog allergen Can f 1, the rodent allergens Rat n 1 and mouse urinary protein, allergens of the fungus Alternaria alternata, and endotoxin. This article provides the essential context for subsequent reports that will describe the prevalence of allergens and endotoxin in U.S. households, their distribution by various housing characteristics, and their associations with allergic diseases such as asthma and rhinitis. PMID:12003758

  4. Reusable conductimetric array of interdigitated microelectrodes for the readout of low-density microarrays.

    Science.gov (United States)

    Mallén, Maria; Díaz-González, María; Bonilla, Diana; Salvador, Juan P; Marco, María P; Baldi, Antoni; Fernández-Sánchez, César

    2014-06-17

    Low-density protein microarrays are emerging tools in diagnostics whose deployment could be primarily limited by the cost of fluorescence detection schemes. This paper describes an electrical readout system of microarrays comprising an array of gold interdigitated microelectrodes and an array of polydimethylsiloxane microwells, which enabled multiplexed detection of up to thirty six biological events on the same substrate. Similarly to fluorescent readout counterparts, the microarray can be developed on disposable glass slide substrates. However, unlike them, the presented approach is compact and requires a simple and inexpensive instrumentation. The system makes use of urease labeled affinity reagents for developing the microarrays and is based on detection of conductivity changes taking place when ionic species are generated in solution due to the catalytic hydrolysis of urea. The use of a polydimethylsiloxane microwell array facilitates the positioning of the measurement solution on every spot of the microarray. Also, it ensures the liquid tightness and isolation from the surrounding ones during the microarray readout process, thereby avoiding evaporation and chemical cross-talk effects that were shown to affect the sensitivity and reliability of the system. The performance of the system is demonstrated by carrying out the readout of a microarray for boldenone anabolic androgenic steroid hormone. Analytical results are comparable to those obtained by fluorescent scanner detection approaches. The estimated detection limit is 4.0 ng mL(-1), this being below the threshold value set by the World Anti-Doping Agency and the European Community. PMID:24890693

  5. Effects of nasal corticosteroids on boosts of systemic allergen-specific IgE production induced by nasal allergen exposure.

    Directory of Open Access Journals (Sweden)

    Cornelia Egger

    Full Text Available Allergen exposure via the respiratory tract and in particular via the nasal mucosa boosts systemic allergen-specific IgE production. Intranasal corticosteroids (INCS represent a first line treatment of allergic rhinitis but their effects on this boost of allergen-specific IgE production are unclear.Here we aimed to determine in a double-blind, placebo-controlled study whether therapeutic doses of an INCS preparation, i.e., nasal fluticasone propionate, have effects on boosts of allergen-specific IgE following nasal allergen exposure.Subjects (n = 48 suffering from grass and birch pollen allergy were treated with daily fluticasone propionate or placebo nasal spray for four weeks. After two weeks of treatment, subjects underwent nasal provocation with either birch pollen allergen Bet v 1 or grass pollen allergen Phl p 5. Bet v 1 and Phl p 5-specific IgE, IgG1-4, IgM and IgA levels were measured in serum samples obtained at the time of provocation and one, two, four, six and eight weeks thereafter.Nasal allergen provocation induced a median increase to 141.1% of serum IgE levels to allergens used for provocation but not to control allergens 4 weeks after provocation. There were no significant differences regarding the boosts of allergen-specific IgE between INCS- and placebo-treated subjects.In conclusion, the application of fluticasone propionate had no significant effects on the boosts of systemic allergen-specific IgE production following nasal allergen exposure.http://clinicaltrials.gov/NCT00755066.

  6. Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation

    OpenAIRE

    Richard, Arianne C.; Lyons, Paul A.; Peters, James E.; Biasci, Daniele; Flint, Shaun M; James C Lee; McKinney, Eoin F; Siegel, Richard M.; Smith, Kenneth GC

    2014-01-01

    Background Although numerous investigations have compared gene expression microarray platforms, preprocessing methods and batch correction algorithms using constructed spike-in or dilution datasets, there remains a paucity of studies examining the properties of microarray data using diverse biological samples. Most microarray experiments seek to identify subtle differences between samples with variable background noise, a scenario poorly represented by constructed datasets. Thus, microarray u...

  7. Direct calibration of PICKY-designed microarrays

    Directory of Open Access Journals (Sweden)

    Ronald Pamela C

    2009-10-01

    Full Text Available Abstract Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu under the PICKY Download area. Conclusion PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.

  8. Allergen extracts for immunotherapy: to mix or not to mix?

    Science.gov (United States)

    Nony, Emmanuel; Martelet, Armelle; Jain, Karine; Moingeon, Philippe

    2016-03-01

    Allergen immunotherapy (AIT) is established as a curative treatment for allergic rhinitis, asthma, as well as insect venom allergy. AIT is based on the administration of natural allergen extracts via the subcutaneous or sublingual routes to reorient the immune system towards tolerogenic mechanisms. In this regard, since many patients are poly-allergic, mixtures of allergen extracts are often used with a potential risk to cause allergen degradation, thereby affecting treatment efficacy. Herein, we discuss the advantages and drawbacks of mixing homologous (i.e., related) or heterogeneous (i.e., unrelated) allergen extracts. We provide evidence for incompatibilities between mixes of grass pollen and house dust mite extracts containing bodies and feces, and summarize critical points to consider when mixing allergen extracts for AIT. PMID:26652799

  9. Allergen immunotherapy for birch pollen-allergic patients: recent advances.

    Science.gov (United States)

    Moingeon, Philippe; Floch, Véronique Bordas-Le; Airouche, Sabi; Baron-Bodo, Véronique; Nony, Emmanuel; Mascarell, Laurent

    2016-05-01

    As of today, allergen immunotherapy is performed with aqueous natural allergen extracts. Recombinant allergen vaccines are not yet commercially available, although they could provide patients with well-defined and highly consistent drug substances. As Bet v 1 is the major allergen involved in birch pollen allergy, with more than 95% of patients sensitized to this allergen, pharmaceutical-grade recombinant Bet v 1-based vaccines were produced and clinically tested. Herein, we compare the clinical results and modes of action of treatments based on either a birch pollen extract or recombinant Bet v 1 expressed as hypoallergenic or natural-like molecules. We also discuss the future of allergen immunotherapy with improved drugs intended for birch pollen-allergic patients suffering from rhinoconjunctivitis. PMID:27140409

  10. Allergen specific immunotherapy in nasobronchial allergy.

    OpenAIRE

    Joshi S; Tripathi D; Dhar H

    2003-01-01

    BACKGROUND: More than one antigen has been used for immunotherapy of allergic disorders. So far less than five antigens have been employed with variable results. AIM: To evaluate effect of multiple antigens up to six in the immunotherapy of nasobronchial allergy. SETTING AND DESIGN: Based on clinical history, symptoms present for at least 3 years with set criteria of immunomodulation for asthma and rhinitis: documented IgE mediated asthma and rhinitis, failure in allergen avoidance and modera...

  11. Footwear dermatitis - Clinical patterns and contact allergens

    OpenAIRE

    Handa S; Sharma S; Sharma V; Kaur S.

    1991-01-01

    Thirty patients suspected of contact dermatitis to footwear studied to evaluate various clinical presentations and possible sensitizers. ′V′ chappals and sandals were suspected alone in 12, a combination of open and closed shoes in 15 and closed shoes alone in 3 patients. Commonest affected sites were dorsa of feet and toes in 14 and dorsa of feet corresponding to the shape of footwear in 12 patients. Patch tests were done using a battery of sixteen allergens. Positive patch tes...

  12. Industrial Fungal Enzymes: An Occupational Allergen Perspective

    OpenAIRE

    Green, Brett J.; Beezhold, Donald H.

    2011-01-01

    Occupational exposure to high-molecular-weight allergens is a risk factor for the development and pathogenesis of IgE-mediated respiratory disease. In some occupational environments, workers are at an increased risk of exposure to fungal enzymes used in industrial production. Fungal enzymes have been associated with adverse health effects in the work place, in particular in baking occupations. Exposure-response relationships have been demonstrated, and atopic workers directly handling fungal ...

  13. Allergen Immunotherapy: Past, Present, and Future.

    Science.gov (United States)

    Jutel, Marek; Kosowska, Anna; Smolinska, Sylwia

    2016-05-01

    Allergen-specific immunotherapy (AIT), although in clinical use for more than a century, is still the only causal treatment of allergic diseases. The safety and efficacy of AIT has been demonstrated in a large number of clinical trials. In addition to allergy symptom reduction AIT plays an essential role in preventing new allergies and asthma and shows long-term effects after discontinuation of treatment. Ideally, it is capable of curing allergy. However, AIT is not effective in all allergic individuals and is not equally effective in the treatment of various hypersensitivities to different allergens. For many years, the route of administration and the vaccine compositions have been evolving. Still there is a strong need for research in the field of new AIT modalities to increase its effectiveness and safety. Growing evidence on immunological effects of AIT, especially new T cell subsets involved in antigen/allergen tolerance, provides novel concepts for safer and more effective vaccination. Pharmacoeconomic studies have demonstrated a clear advantage of AIT over pharmacologic therapies. PMID:26922928

  14. The Level of Sensitivity of Food Allergens

    Directory of Open Access Journals (Sweden)

    Iris Rengganis

    2011-06-01

    Full Text Available In recent years, the occurrence of allergy continues to increase rapidly both domestically and globally. World Allergy Organization (WAO revealed that 22% of the world population suffers from allergies, and this number increases every year. Food allergy is a condition caused by the reaction of IgE against substances (chemicals in food. Food allergy can interfere with brain function and body organ systems as well as affect the quality of life. The purpose of this study is to know the level of sensitivity of food allergens in the Immunology Allergy Poly RSCM in 2007. Data were collected from 208 patients who have medical records and went through skin prick tests in the Immunology Allergy Clinic RSCM in 2007. Univariate analysis was performed to describe the types of food allergens within groups of children and adults. Around 49% of the respondents were sensitive to food allergens. The types of foods that caused the most allergies for children and adults are respectively shrimp, egg white and cornstarch. Cow's milk and wheat flour are the types of food that caused most allergies for children only, whereas for adults, the food that caused the most allergies is crab.

  15. Laser direct writing of biomolecule microarrays

    Science.gov (United States)

    Serra, P.; Fernández-Pradas, J. M.; Berthet, F. X.; Colina, M.; Elvira, J.; Morenza, J. L.

    Protein-based biosensors are highly efficient tools for protein detection and identification. The production of these devices requires the manipulation of tiny amounts of protein solutions in conditions preserving their biological properties. In this work, laser induced forward transfer (LIFT) was used for spotting an array of a purified bacterial antigen in order to check the viability of this technique for the production of protein microarrays. A pulsed Nd:YAG laser beam (355 nm wavelength, 10 ns pulse duration) was used to transfer droplets of a solution containing the Treponema pallidum 17 kDa protein antigen on a glass slide. Optical microscopy showed that a regular array of micrometric droplets could be precisely and uniformly spotted onto a solid substrate. Subsequently, it was proved that LIFT deposition of a T. pallidum 17 kDa antigen onto nylon-coated glass slides preserves its antigenic reactivity and diagnostic properties. These results support that LIFT is suitable for the production of protein microarrays and pave the way for future diagnostics applications.

  16. PERUBAHAN ALERGENISITAS PROTEIN KACANG KEDELAI DAN KACANG BOGOR AKIBAT PENGOLAHAN DENGAN PANAS [Allergenicity Changes of Soybean and Bambara Groundnut Protein Due to Heat Processing

    Directory of Open Access Journals (Sweden)

    Nurheni Sri Palupi

    2015-12-01

    Full Text Available Legumes contain protein as a potential allergen. Heating process was expected to eliminate the protein allergen. The aim of this study was to assess the changes in molecular weight and allergenicty of soybean grobogan variety and bambara groundnut proteins due to heat processing, i.e. boiling, steaming, oven, and roasting protein isolate was prepared by pH adjusting. SDS-PAGE method was used to determine the profile of protein molecular weight and the alergenicity was determined by ELISA method. Protein molecular weight profile of grobogan soybean and bambara groundnut that have been boiled, steamed, ovened, and roasted for 30 minutes showed variations when compared to the unheated soybean and bambara groundnut protein isolate. The amount of protein detected was reduced compared with unheated soybean and bambara groundnut. The protein allergens in grobogan soybean had molecular weight 110.0, 98.3, 84.5, 67.4, and 60.2. The heat treatment for 30 minutes removed allergenicity as indicated by no detectable protein band in immunoblotting results and the smaller Optical Density value compared with unheated soybean. Thus, the allergenicity of soybean protein due to heat processing was minimized. Bambara groundnut had protein allergens with molecular weight 113.1, 59.8, and 25.2 kDa. Protein allergen with molecular weight 25.2 and 59.8 kDa were detected in bambara groundnut processed through boiling and steaming for 30 minutes, respectively, but ELISA result showed there were still protein allergen of bambara groundnut after the heat treatment for 30 minutes.

  17. Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip

    Directory of Open Access Journals (Sweden)

    Carr Steven M

    2007-09-01

    Full Text Available Abstract Background Iterative DNA "resequencing" on oligonucleotide microarrays offers a high-throughput method to measure intraspecific biodiversity, one that is especially suited to SNP-dense gene regions such as vertebrate mitochondrial (mtDNA genomes. However, costs of single-species design and microarray fabrication are prohibitive. A cost-effective, multi-species strategy is to hybridize experimental DNAs from diverse species to a common microarray that is tiled with oligonucleotide sets from multiple, homologous reference genomes. Such a strategy requires that cross-hybridization between the experimental DNAs and reference oligos from the different species not interfere with the accurate recovery of species-specific data. To determine the pattern and limits of such interspecific hybridization, we compared the efficiency of sequence recovery and accuracy of SNP identification by a 15,452-base human-specific microarray challenged with human, chimpanzee, gorilla, and codfish mtDNA genomes. Results In the human genome, 99.67% of the sequence was recovered with 100.0% accuracy. Accuracy of SNP identification declines log-linearly with sequence divergence from the reference, from 0.067 to 0.247 errors per SNP in the chimpanzee and gorilla genomes, respectively. Efficiency of sequence recovery declines with the increase of the number of interspecific SNPs in the 25b interval tiled by the reference oligonucleotides. In the gorilla genome, which differs from the human reference by 10%, and in which 46% of these 25b regions contain 3 or more SNP differences from the reference, only 88% of the sequence is recoverable. In the codfish genome, which differs from the reference by > 30%, less than 4% of the sequence is recoverable, in short islands ≥ 12b that are conserved between primates and fish. Conclusion Experimental DNAs bind inefficiently to homologous reference oligonucleotide sets on a re-sequencing microarray when their sequences differ by

  18. Mold allergens in respiratory allergy: from structure to therapy.

    Science.gov (United States)

    Twaroch, Teresa E; Curin, Mirela; Valenta, Rudolf; Swoboda, Ines

    2015-05-01

    Allergic reactions to fungi were described 300 years ago, but the importance of allergy to fungi has been underestimated for a long time. Allergens from fungi mainly cause respiratory and skin symptoms in sensitized patients. In this review, we will focus on fungi and fungal allergens involved in respiratory forms of allergy, such as allergic rhinitis and asthma. Fungi can act as indoor and outdoor respiratory allergen sources, and depending on climate conditions, the rates of sensitization in individuals attending allergy clinics range from 5% to 20%. Due to the poor quality of natural fungal allergen extracts, diagnosis of fungal allergy is hampered, and allergen-specific immunotherapy is rarely given. Several factors are responsible for the poor quality of natural fungal extracts, among which the influence of culture conditions on allergen contents. However, molecular cloning techniques have allowed us to isolate DNAs coding for fungal allergens and to produce a continuously growing panel of recombinant allergens for the diagnosis of fungal allergy. Moreover, technologies are now available for the preparation of recombinant and synthetic fungal allergen derivatives which can be used to develop safe vaccines for the treatment of fungal allergy. PMID:25840710

  19. Measurement of Horse Allergen (Equ cx) in Schools.

    Science.gov (United States)

    Merritt, Anne-Sophie; Emenius, Gunnel; Elfman, Lena; Smedje, Greta

    2011-01-01

    Background. The presence of horse allergen in public places is not well-known, unlike for instance cat and dog allergens, which have been studied extensively. The aim was to investigate the presence of horse allergen in schools and to what extent the influence of number of children with regular horse contact have on indoor allergen levels. Methods. Petri dishes were used to collect airborne dust samples during one week in classrooms. In some cases, vacuumed dust samples were also collected. All samples were extracted, frozen and analysed for Equ cx content shortly after sampling, and some were re-analysed six years later with a more sensitive ELISA assay. Results. Horse allergen levels were significantly higher in classrooms, in which many children had horse contact, regardless of sampling method. Allergen levels in extracts from Petri dish samples, which had been kept frozen, dropped about 53% over a six-year period. Conclusion. Horse allergen was present in classrooms and levels were higher in classrooms where many children had regular horse contact in their leisure time. This suggests that transfer of allergens takes place via contaminated clothing. Measures should be taken to minimize possible transfer and deposition of allergens in pet-free environments, such as schools. PMID:23724238

  20. The “time-window” effect of early allergen exposure on a rat asthma model

    Institute of Scientific and Technical Information of China (English)

    HU Yan; LIU Ping; LI Hai-chao; WANG Yue-dan

    2013-01-01

    Background The hygiene hypothesis has been proposed to explain the pathogenesis of asthma.Allergen exposure was shown to inhibit asthma in an animal model.But the optimal timing of allergen exposure remains unclear.This study aims to explore the time effcct of allergen exposure and the possible mechanisms.Methods Neonate Wistar rats were randomly divided into asthma group,control group and day 1,day 3,day 7,and day 14 groups.The day 1,day 3,day 7 and day 14 groups were injected with ovalbumin (OVA) subcutaneously on days 1,3,7 and 14 after birth,respectively.Six weeks later,all groups,except the control group,were sensitized and stimulated with OVA to make the asthma model.We observed the pulmonary pathologic changes,detected the regulatory T cells,and CD28 expression level in thymus and spleen by flow cytometry.Results The asthmatic inflammation in the day 1,day 3 and day 7 groups,but not the day 14 group,was alleviated.The asthma group and day 14 group had lower proportions of regulatory T cells in the thymus compared with the control group,day 1,day 3,and day 7 groups.There was no significant difference in the CD28 expression levels on the regulatory and conventional T cells among groups.But the control group and the day 1,day 3,and day 7 groups had relatively higher proportions of CD28 positive regulatory T cells in the thymus than the day 14 group and the asthma group.Conclusions There is a “time-window” for early allergen exposure.The impairment of regulatory T cells may promote the development of asthma.Allergen exposure in the “time-window” can make the thymus produce normal quantity of regulatory cells.The CD28 signal on regulatory T cells may participate in the production of regulatory T cells.

  1. Mass spectrometric analysis of electrophoretically separated allergens and proteases in grass pollen diffusates

    Directory of Open Access Journals (Sweden)

    Geczy Carolyn L

    2003-09-01

    Full Text Available Abstract Background Pollens are important triggers for allergic asthma and seasonal rhinitis, and proteases released by major allergenic pollens can injure airway epithelial cells in vitro. Disruption of mucosal epithelial integrity by proteases released by inhaled pollens could promote allergic sensitisation. Methods Pollen diffusates from Kentucky blue grass (Poa pratensis, rye grass (Lolium perenne and Bermuda grass (Cynodon dactylon were assessed for peptidase activity using a fluorogenic substrate, as well as by gelatin zymography. Following one- or two-dimensional gel electrophoresis, Coomassie-stained individual bands/spots were excised, subjected to tryptic digestion and analysed by mass spectrometry, either MALDI reflectron TOF or microcapillary liquid chromatography MS-MS. Database searches were used to identify allergens and other plant proteins in pollen diffusates. Results All pollen diffusates tested exhibited peptidase activity. Gelatin zymography revealed high Mr proteolytic activity at ~ 95,000 in all diffusates and additional proteolytic bands in rye and Bermuda grass diffusates, which appeared to be serine proteases on the basis of inhibition studies. A proteolytic band at Mr ~ 35,000 in Bermuda grass diffusate, which corresponded to an intense band detected by Western blotting using a monoclonal antibody to the timothy grass (Phleum pratense group 1 allergen Phl p 1, was identified by mass spectrometric analysis as the group 1 allergen Cyn d 1. Two-dimensional analysis similarly demonstrated proteolytic activity corresponding to protein spots identified as Cyn d 1. Conclusion One- and two-dimensional electrophoretic separation, combined with analysis by mass spectrometry, is useful for rapid determination of the identities of pollen proteins. A component of the proteolytic activity in Bermuda grass diffusate is likely to be related to the allergen Cyn d 1.

  2. Current challenges facing the assessment of the allergenic capacity of food allergens in animal models

    DEFF Research Database (Denmark)

    Bøgh, Katrine Lindholm; van Bilsen, Jolanda; Głogowski, Robert;

    2016-01-01

    of novel food proteins. There is no doubt that robust and reliable animal models for the identification and characterization of food allergens would be valuable tools for safety assessment. However, although various animal models have been proposed for this purpose, to date, none have been formally...... validated as predictive and none are currently suitable to test the allergenic potential of new foods. Here, the design of various animal models are reviewed, including among others considerations of species and strain, diet, route of administration, dose and formulation of the test protein, relevant...

  3. Peanut Allergy, Allergen Composition, and Methods of Reducing Allergenicity: A Review

    Directory of Open Access Journals (Sweden)

    Yang Zhou

    2013-01-01

    Full Text Available Peanut allergy affects 1-2% of the world's population. It is dangerous, and usually lifelong, and it greatly decreases the life quality of peanut-allergic individuals and their families. In a word, peanut allergy has become a major health concern worldwide. Thirteen peanut allergens are identified, and they are briefly introduced in this paper. Although there is no feasible solution to peanut allergy at present, many methods have shown great promise. This paper reviews methods of reducing peanut allergenicity, including physical methods (heat and pressure, PUV, chemical methods (tannic acid and magnetic beads, and biological methods (conventional breeding, irradiation breeding, genetic engineering, enzymatic treatment, and fermentation.

  4. Comparative genomics of fungal allergens and epitopes shows widespread distribution of closely related allergen and epitope orthologues

    OpenAIRE

    Fraczek Marcin; Bowyer Paul; Denning David W

    2006-01-01

    Abstract Background Allergy is a common debilitating and occasionally life threatening condition. The fungal kingdom contains a number of species that produce a wide range of well defined protein allergens although the vast majority of fungal species have unknown allergenic potential. The recent genome sequencing of a variety of fungi provides the opportunity to assess the occurrence of allergen orthologues across the fungal kingdom. Here we use comparative genomics to survey the occurrence o...

  5. Glutathione-S-Transferase: A Minor Allergen in Birch Pollen due to Limited Release from Hydrated Pollen

    OpenAIRE

    Stephan Deifl; Christian Zwicker; Eva Vejvar; Claudia Kitzmüller; Gabriele Gadermaier; Birgit Nagl; Susanne Vrtala; Peter Briza; Zlabinger, Gerhard J.; Beatrice Jahn-Schmid; Fatima Ferreira; Barbara Bohle

    2014-01-01

    Background Recently, a protein homologous to glutathione-S-transferases (GST) was detected in prominent amounts in birch pollen by proteomic profiling. As members of the GST family are relevant allergens in mites, cockroach and fungi we investigated the allergenic relevance of GST from birch (bGST). Methodology bGST was expressed in Escherichia coli, purified and characterized by mass spectrometry. Sera from 217 birch pollen-allergic patients were tested for IgE-reactivity to bGST by ELISA. T...

  6. Microarray results: how accurate are they?

    Directory of Open Access Journals (Sweden)

    Mane Shrikant

    2002-08-01

    Full Text Available Abstract Background DNA microarray technology is a powerful technique that was recently developed in order to analyze thousands of genes in a short time. Presently, microarrays, or chips, of the cDNA type and oligonucleotide type are available from several sources. The number of publications in this area is increasing exponentially. Results In this study, microarray data obtained from two different commercially available systems were critically evaluated. Our analysis revealed several inconsistencies in the data obtained from the two different microarrays. Problems encountered included inconsistent sequence fidelity of the spotted microarrays, variability of differential expression, low specificity of cDNA microarray probes, discrepancy in fold-change calculation and lack of probe specificity for different isoforms of a gene. Conclusions In view of these pitfalls, data from microarray analysis need to be interpreted cautiously.

  7. Optimisation algorithms for microarray biclustering.

    Science.gov (United States)

    Perrin, Dimitri; Duhamel, Christophe

    2013-01-01

    In providing simultaneous information on expression profiles for thousands of genes, microarray technologies have, in recent years, been largely used to investigate mechanisms of gene expression. Clustering and classification of such data can, indeed, highlight patterns and provide insight on biological processes. A common approach is to consider genes and samples of microarray datasets as nodes in a bipartite graphs, where edges are weighted e.g. based on the expression levels. In this paper, using a previously-evaluated weighting scheme, we focus on search algorithms and evaluate, in the context of biclustering, several variations of Genetic Algorithms. We also introduce a new heuristic "Propagate", which consists in recursively evaluating neighbour solutions with one more or one less active conditions. The results obtained on three well-known datasets show that, for a given weighting scheme, optimal or near-optimal solutions can be identified. PMID:24109756

  8. How Can Microarrays Unlock Asthma?

    Directory of Open Access Journals (Sweden)

    Alen Faiz

    2012-01-01

    Full Text Available Asthma is a complex disease regulated by the interplay of a large number of underlying mechanisms which contribute to the overall pathology. Despite various breakthroughs identifying genes related to asthma, our understanding of the importance of the genetic background remains limited. Although current therapies for asthma are relatively effective, subpopulations of asthmatics do not respond to these regimens. By unlocking the role of these underlying mechanisms, a source of novel and more effective treatments may be identified. In the new age of high-throughput technologies, gene-expression microarrays provide a quick and effective method of identifying novel genes and pathways, which would be impossible to discover using an individual gene screening approach. In this review we follow the history of expression microarray technologies and describe their contributions to advancing our current knowledge and understanding of asthma pathology.

  9. Phenotypic MicroRNA Microarrays

    Directory of Open Access Journals (Sweden)

    Veronica Soloveva

    2013-04-01

    Full Text Available Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the biology of selected cellular models. After reverse-transfection of microRNAs and siRNA, the cellular phenotype generated by microRNAs regulated NF-κB expression comparably to the siRNA. The ability to print microRNA molecules for reverse transfection into cells is opening up the wide horizon for the phenotypic high content screening of microRNA libraries using cellular disease models.

  10. Evaluation of a DNA microarray (Check-MDR CT102) for rapid detection of TEM, SHV, and CTX-M extended-spectrum β-lactamases and of KPC, OXA-48, VIM, IMP, and NDM-1 carbapenemases.

    OpenAIRE

    Naas, T.; Cuzon, G.; Bogaerts, P.; Glupczynski, Y.; Nordmann, P.

    2011-01-01

    The Check-MDR CT102 microarray, aimed at identifying bacteria producing extended-spectrum β-lactamase (ESBL) (SHV, TEM, and CTX-M) and carbapenemase (KPC, OXA-48, VIM, IMP, and NDM-1), was evaluated on a total of 144 Gram-negative strains expressing various β-lactamases. The sensitivity and specificity were 100% for most tested genes, suggesting that this assay allows accurate identification of common ESBL and carbapenemase producers from bacterial cultures.

  11. Calling Biomarkers in Milk Using a Protein Microarray on Your Smartphone

    OpenAIRE

    Ludwig, S.K.J.; Tokarski, Christian; Stefan N Lang; Ginkel, van, L.A.; Zhu, Hongying; Ozcan, Aydogan; Nielen, M. W. F.

    2015-01-01

    Here we present the concept of a protein microarray-based fluorescence immunoassay for multiple biomarker detection in milk extracts by an ordinary smartphone. A multiplex immunoassay was designed on a microarray chip, having built-in positive and negative quality controls. After the immunoassay procedure, the 48 microspots were labelled with Quantum Dots (QD) depending on the protein biomarker levels in the sample. QD-fluorescence was subsequently detected by the smartphone camera under UV l...

  12. Responsiveness of the major birch allergen Bet v 1 scaffold to the gastric environment: Impact on structure and allergenic activity

    DEFF Research Database (Denmark)

    Sancho, Ana I; Wangorsch, Andrea; Jensen, Bettina M;

    2011-01-01

    Four Bet v 1 homologous food allergens from celeriac (rApi g 1), apple (rMal d 1), peach (rPru p 1) and hazelnut (rCor a 1), were used to probe the structural responsiveness of the Bet v 1 scaffold to gastric digestion conditions and its impact on allergenicity.......Four Bet v 1 homologous food allergens from celeriac (rApi g 1), apple (rMal d 1), peach (rPru p 1) and hazelnut (rCor a 1), were used to probe the structural responsiveness of the Bet v 1 scaffold to gastric digestion conditions and its impact on allergenicity....

  13. The Level of Mite Dermatophagoides’ Allergens (Der-p 1 and Der-f 1 in Birjand

    Directory of Open Access Journals (Sweden)

    Mohammad Fereidouni

    2014-06-01

    Full Text Available Background: House dust mite allergens especially pyroglyphid species are among the most important indoor allergens and have an important role in development of asthma and allergies. Materials and Methods: In current study, the level of two main allergens from mites including Der-p1 and Der-f 1 in dust of 28 homes in Birjand city was measured by ELISA method. Results: All samples were negative for Der-p1. Low leverl of Der-f 1 was detected in one sample. Prevalence of asthma, rhinitis and rhinoconjunctivitis was 2%, 28% and 15% respectively. Conclusion: The results of this study suggest that House dust mites could not grow in Birjand climate.

  14. Chromosome microarrays in diagnostic testing: interpreting the genomic data.

    Science.gov (United States)

    Peters, Greg B; Pertile, Mark D

    2014-01-01

    DNA-based Chromosome MicroArrays (CMAs) are now well established as diagnostic tools in clinical genetics laboratories. Over the last decade, the primary application of CMAs has been the genome-wide detection of a particular class of mutation known as copy number variants (CNVs). Since 2010, CMA testing has been recommended as a first-tier test for detection of CNVs associated with intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies…in the post-natal setting. CNVs are now regarded as pathogenic in 14-18 % of patients referred for these (and related) disorders.Through consideration of clinical examples, and several microarray platforms, we attempt to provide an appreciation of microarray diagnostics, from the initial inspection of the microarray data, to the composing of the patient report. In CMA data interpretation, a major challenge comes from the high frequency of clinically irrelevant CNVs observed within "patient" and "normal" populations. As might be predicted, the more common and clinically insignificant CNVs tend to be the smaller ones resolution, and some miscalling of CNVs is unavoidable. In this, there is no ideal solution, but various strategies for handling noise are available. Even without solutions, consideration of these diagnostic problems per se is informative, as they afford critical insights into the biological and technical underpinnings of CNV discovery. These are indispensable to any clinician or scientist practising within the field of genome diagnostics. PMID:24870134

  15. A novel mast cell co-culture microfluidic chip for the electrochemical evaluation of food allergen.

    Science.gov (United States)

    Jiang, Hui; Jiang, Donglei; Zhu, Pei; Pi, Fuwei; Ji, Jian; Sun, Chao; Sun, Jiadi; Sun, Xiulan

    2016-09-15

    In this study a novel cell-to-cell electrochemical microfluidic chip was developed for qualitative and quantitative analysis of food allergen. Microfluidic cell culture, food allergen-induced cell morphological changes, and cell metabolism measurements were performed simultaneously using the aforementioned device. RBL-2H3 mast cells and ANA-1 macrophages have been used within a cell co-culture model to observe their allergic response when they are introduced to the antigen stimulus. Two cell cultivation microfluidic channels are located in the microfluidic chip, which is fabricated with four groups of gold electrodes, with an additional "capillary". In order to detect the allergic response, the cells were stimulated with dinitrophenylated bovine serum albumin (DNP-BSA) without anti-DNP IgE incubation. When exocytosis occurs, the cell-secreted inflammatory cytokines were measured by enzyme-linked immuno sorbent assay (ELISA) and cell impedance changes were detected using cell-based electrochemical assay. Results indicate that the real-time cell allergic response are accurately monitored by this electrochemical microfluidic chip, which provides a general example of rapidly prototyped low-cost biosensor technology for applications in both food allergen detection and investigation. PMID:27108255

  16. Subpicomolar Iron Sensing Platform Based on Functional Lipid Monolayer Microarrays.

    Science.gov (United States)

    Kenaan, Ahmad; Nguyen, Tuyen D; Dallaporta, Hervé; Raimundo, Jean-Manuel; Charrier, Anne M

    2016-04-01

    We report herein the fabrication of novel microarrays based on air-stable functional lipid monolayers over silicon using a combination of e-beam lithography and lift-off. We demonstrate these microarrays can be use as ultrasensitive platform for Kelvin probe force microscopy in sensing experiments. Specificity of the detection is given by the functional group grafted at the lipid headgroup. The arrays developed for the detection of ferric ions, Fe(3+), using a γ-pyrone derivative chelator, demonstrate subpicomolar limit of detection with high specificity. In addition, the technique takes advantage of the structure of the array with the silicon areas playing the role of reference for the measurement, and we determine critical pattern dimensions below which the probe size/shape impacts the measured results. PMID:26974586

  17. Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S; Jaing, C

    2012-03-27

    The overall goal of this project is to forensically characterize 100 unknown Burkholderia isolates in the US-Australia collaboration. We will identify genome-wide single nucleotide polymorphisms (SNPs) from B. pseudomallei and near neighbor species including B. mallei, B. thailandensis and B. oklahomensis. We will design microarray probes to detect these SNP markers and analyze 100 Burkholderia genomic DNAs extracted from environmental, clinical and near neighbor isolates from Australian collaborators on the Burkholderia SNP microarray. We will analyze the microarray genotyping results to characterize the genetic diversity of these new isolates and triage the samples for whole genome sequencing. In this interim report, we described the SNP analysis and the microarray probe design for the Burkholderia SNP microarray.

  18. Meta-analysis of incomplete microarray studies.

    Science.gov (United States)

    Zollinger, Alix; Davison, Anthony C; Goldstein, Darlene R

    2015-10-01

    Meta-analysis of microarray studies to produce an overall gene list is relatively straightforward when complete data are available. When some studies lack information-providing only a ranked list of genes, for example-it is common to reduce all studies to ranked lists prior to combining them. Since this entails a loss of information, we consider a hierarchical Bayes approach to meta-analysis using different types of information from different studies: the full data matrix, summary statistics, or ranks. The model uses an informative prior for the parameter of interest to aid the detection of differentially expressed genes. Simulations show that the new approach can give substantial power gains compared with classical meta-analysis and list aggregation methods. A meta-analysis of 11 published studies with different data types identifies genes known to be involved in ovarian cancer and shows significant enrichment. PMID:25987649

  19. Study on allergen in 1 538 eczema of children%儿童湿疹1538例过敏原分析

    Institute of Scientific and Technical Information of China (English)

    李静; 兰凤荣; 陈亚秋; 陈昱; 赵利媛; 邵平; 李卫芹; 冷峻宏

    2013-01-01

    [目的]了解过敏原在儿童湿疹发病中的比例,为防治儿童湿疹提供依据. [方法]利用生物共振治疗仪对1 538例门诊湿疹患儿进行过敏原检测. [结果]1 538例湿疹患儿中,食物过敏原检测阳性1 272例(82.70%),吸入过敏原检测阳性653例(42.46%),食物和吸入过敏原均阳性504例(32.77%).食物过敏原以谷类(1 020,66.32%)最高,其后依次是牛奶、鸡蛋、海鲜、坚果、大豆、食品添加剂、牛羊肉;吸入过敏原以屋尘(340例,22.11%)最高,其后依次是螨虫、花粉、动物皮毛、霉菌、废气、香烟、烹调油烟.不同年龄段,食物、吸入过敏原阳性结果差异均有统计学意义(P<0.05),婴儿期主要以食物过敏原为主,随着年龄增长,吸入性过敏原阳性检出率逐渐增高,食物性过敏原阳性检出率逐渐下降. [结论]对湿疹患儿进行过敏原检测,可以找出湿疹的诱发因素,为预防和治疗湿疹提供依据.%[Objective] To understand the proportion of allergen in eczema of children for providing foundation for prevention and treatment of eczema.[Method] Bioresonance technology allergy therapy was used to detect the allergen of eczema in children.[Results] A total of 1 538 children with eczema were detected,1 272(82.70%) patients,among them had positive food allergen test.653(42.46%) patients had positive inhaled allergen test.504(32.77%) patients had positive allergen test both in food test and inhaled test.Cereal(1 020,66.32 %) was the most common allergen in food allergen,followed by milk,egg,sea food,nut,bean,food preservative,beef and lamb ; Dust (340,22.11%) was the most common allergen in inhaled allergen,followed by mite,flower,animal fur,mould,waste gas,cigarettes,cooking oil fume.Among different aging groups,there were significant differences in the positive rates between food allergen group and inhaled allergen group(P<0.05).Food allergen was the main allergen in infant eczema

  20. Serological response of cattle to Brucella allergen after repeated intradermal applications of this allergen

    NARCIS (Netherlands)

    Muskens, J.A.M.; Bercovich, Z.; Damen, C.P.R.M.

    1996-01-01

    A study was conducted to determine whether an allergen that has been prepared from a mucoid strain of Brucella abortus triggers a serum antibody response that interferes with the interpretation of serologic tests results. Fifteen cattle seronegative for Brucella antigen were tested with the SDTH tes

  1. What do we know about plant food allergens?

    DEFF Research Database (Denmark)

    Jenkins, J. A.; Sancho, A. I.; Madsen, Charlotte Bernhard;

    2005-01-01

    databases has allowed their classification into families. This has shown that plant food allergens fall into four main families, with the prolamin superfamily (including the 2S albumins, nonspecific lipid transfer proteins and cc-amylase inhibitors) predominating, followed by the family of allergens related...

  2. An overview of fruit allergy and the causative allergens.

    Science.gov (United States)

    Hassan, A K G; Venkatesh, Y P

    2015-11-01

    Plant allergens, being one of the most widespread allergenic substances, are hard to avoid. Hence, their identification and characterization are of prime importance for the diagnosis and treatment of food allergy. The reported allergies to fruits mainly evoke oral allergy syndrome caused by the presence of cross-reactive IgE to certain pollens and thus, allergy to fruits has also been linked to particular pollens. Many fruit allergies are being studied for their causative allergens, and are being characterized. Some tropical or exotic fruits are responsible for region-specific allergies for which only limited information is available, and generally lack allergen characterization. From a survey of the literature on fruit allergy, it is clear that some common fruits (apple, peach, musk melon, kiwi fruit, cherry, grape, strawberry, banana, custard apple, mango and pomegranate) and their allergens appear to be at the center of current research on food allergy. The present review focuses on common fruits reported as allergenic and their identified allergens; a brief description of allergens from six rare/tropical fruits is also covered. PMID:26549334

  3. Biomarkers of Acute Respiratory Allergen Exposure: Screening For Sensitization Potential

    Science.gov (United States)

    Rationale: An in vitro assay to identify respiratory sensitizers will provide a rapid screen and reduce animal use. The study goal was to identify biomarkers that differentiate allergen versus non-allergen responses following an acute exposure. Methods: Female BALB/c mice rec...

  4. Novel developments in the mechanisms of immune tolerance to allergens.

    Science.gov (United States)

    Eiwegger, Thomas; Gruber, Saskia; Szépfalusi, Zsolt; Akdis, Cezmi A

    2012-10-01

    Allergy is the result of a disbalanced immune response to environmental innocuous antigens. Despite of accumulating data to define the pathomechanisms that take place in case of allergic diseases a detailed understanding of sequence of events that lead to the "normal" scenario of tolerance development are still under debate. Allergen-specific immunotherapy is the only causal treatment of allergic diseases. It modifies the immune response to a particular antigen to achieve tolerance against the symptom-causing allergen. This process is considered to mirror physiological peripheral tolerance induction. A number of immunological changes have been described to occur under allergen immunotherapy, including the generation of allergen-specific regulatory T cells, the induction of allergen-specific IgG4, an increase in the Th1/Th2 cytokine ratio and decreased activation and function of effector cells such as mast cells, basophils and eosinophils. PMID:23095863

  5. Aspects of food processing and its effect on allergen structure.

    Science.gov (United States)

    Paschke, Angelika

    2009-08-01

    The article summarizes current physical and chemical methods in food processing as storage, preparation, separation, isolation or purification and thermal application on the one hand as well as enzymatic treatment on the other and their impact on the properties of food proteins. Novel methods of food processing like high pressure, electric field application or irradiation and their impact on food allergens are presented. The EU project REDALL (Reduced Allergenicity of Processed Foods, Containing Animal Allergens: QLK1-CT-2002-02687) showed that by a combination of enzyme and heat treatment the allergic potential of hen's egg decreased about 100 fold. Clinical reactions do not appear anymore. An AiF-FV 12024 N project worked with fruits like mango, lychee and apple. Processed mango and lychee had no change in allergenic potential during heating while e. g. canning. Apple almost lost its allergenic potential after pasteurization in juice production. PMID:19557818

  6. New High-Performance Liquid Chromatography Coupled Mass Spectrometry Method for the Detection of Lobster and Shrimp Allergens in Food Samples via Multiple Reaction Monitoring and Multiple Reaction Monitoring Cubed.

    Science.gov (United States)

    Korte, Robin; Monneuse, Jean-Marc; Gemrot, Elodie; Metton, Isabelle; Humpf, Hans-Ulrich; Brockmeyer, Jens

    2016-08-10

    Crustacean shellfish allergy ranks among the most frequent and severe food allergies for adults, demanding rugged and sensitive analytical routine methods. The objective of this study was therefore to develop a mass spectrometric approach for the detection of contamination with shrimp and lobster, two economically important types of crustaceans, in complex food matrices. Following a biomarker approach, we identified proteotypic peptides and developed a multiple reaction monitoring (MRM) method allowing for the identification and differentiation of shrimp and lobster in the food matrix at concentrations down to 0.1%. To further enhance sensitivity, we employed the MRM-cubed (MRM(3)) mode, which allowed us to detect crustaceans down to concentrations of 25 μg/g (crustacean/food, 0.0025%). We hereby present the first mass spectrometric method for the detection of shrimp and lobster in food matrices. PMID:27391354

  7. Triethylene glycol bis(2-ethylhexanoate) - a new contact allergen identified in a spectacle frame

    DEFF Research Database (Denmark)

    Andersen, Klaus Ejner; Vestergaard, M. E.; Christensen, Lars Porskjær

    2014-01-01

    patient's spectacle frame. Materials and methods. An extract from the temple arms was analysed by gas chromatography mass spectrometry (GC-MS), and a major low molecular weight compound was detected. This compound was isolated by semi-preparative high-performance liquid chromatography and identified by GC-MS...... and nuclear magnetic resonance spectroscopy. The purified compound was diluted in ethanol, and a dilution series was prepared for patch testing. Results. Triethylene glycol bis(2-ethylhexanoate) was identified as the major compound in the extract. Patch testing of the patient proved that triethylene...... glycol bis(2-ethylhexanoate) was the causative allergen in the spectacle frame. Ten consecutive eczema patients tested as controls were negative. Conclusion. Triethylene glycol bis(2-ethylhexanoate) is a new, hitherto unreported contact allergen....

  8. Size-selective fractionation and visual mapping of allergen protein chemistry in Arachis hypogaea.

    Science.gov (United States)

    Hebling, Christine M; Ross, Mark M; Callahan, John H; McFarland, Melinda A

    2012-11-01

    Peanuts (Arachis hypogaea) in addition to milk, eggs, fish, crustaceans, wheat, tree nuts, and soybean are commonly referred to as the "big eight" foods that contribute to the majority of food allergies worldwide. Despite the severity of allergic reactions and growing prevalence in children and adults, there is no cure for peanut allergy, leaving avoidance as the primary mode of treatment. To improve analytical methods for peanut allergen detection, researchers must overcome obstacles involved in handling complex food matrices while attempting to decipher the chemistry that underlies allergen protein interactions. To address such challenges, we conducted a global proteome characterization of raw peanuts using a sophisticated GELFrEE-PAGE-LC-MS/MS platform consisting of gel-based protein fractionation followed by mass spectrometric identification. The in-solution mass-selective protein fractionation: (1) enhances the number of unique peptide identifications, (2) provides a visual map of protein isoforms, and (3) aids in the identification of disulfide-linked protein complexes. GELFrEE-PAGE-LC-MS/MS not only overcomes many of the challenges involved in the study of plant proteomics, but enriches the understanding of peanut protein chemistry, which is typically unattainable in a traditional bottom-up proteomic analysis. A global understanding of protein chemistry in Arachis hypogaea ultimately will aid the development of improved methods for allergen detection in food. PMID:23020697

  9. Construction of metastatic spinal cancer tissue microarrays

    Institute of Scientific and Technical Information of China (English)

    Yang Xinghai; Chen Huajiang; Xiao Jianru; Yuan Wen; Jia Lianshun

    2009-01-01

    Objective: To explore the construction of metastatic spinal cancer (MSC) tissue microarrays and validate its value in immunohistochemical study of MSC. Methods: Paraffin-embedded specimens from 71 MSC cases and 6 primary tumor cases were selected as donor blocks and prepared into MSC tissue microarrays by tissue array arrangement, the steps of which included location, punching, sampling, sample seeding, and re-diagnosis by hematoxylin-eosin (HE) as well as MMP-9 and MMP-14 immunohistochemical staining. Results: The MSC tissue microarrays thus constructed were intact and crackless, containing 154 complete and well arranged microarray points. None of the sectioned tissue microarrays was lost, and the results of HE staining was consistent with the primary pathologic diagnoses. Immunohistochemical staining was also good without non-specific or marginal effect. Conclusion: The MSC tissue microarrays have a high value in the immunohistochemical study of MSC.

  10. Integrated Amplification Microarrays for Infectious Disease Diagnostics

    Directory of Open Access Journals (Sweden)

    Darrell P. Chandler

    2012-11-01

    Full Text Available This overview describes microarray-based tests that combine solution-phase amplification chemistry and microarray hybridization within a single microfluidic chamber. The integrated biochemical approach improves microarray workflow for diagnostic applications by reducing the number of steps and minimizing the potential for sample or amplicon cross-contamination. Examples described herein illustrate a basic, integrated approach for DNA and RNA genomes, and a simple consumable architecture for incorporating wash steps while retaining an entirely closed system. It is anticipated that integrated microarray biochemistry will provide an opportunity to significantly reduce the complexity and cost of microarray consumables, equipment, and workflow, which in turn will enable a broader spectrum of users to exploit the intrinsic multiplexing power of microarrays for infectious disease diagnostics.

  11. Thermodynamics of competitive surface adsorption on DNA microarrays

    International Nuclear Information System (INIS)

    Gene microarrays provide a powerful functional genomics technology which permits the expression profiling of tens of thousands of genes in parallel. The basic idea of their functioning is based on the sequence specificity of probe-target interactions combined with fluorescence detection. In reality, this straightforward principle is opposed by the complexity of the experimental system due to imperfections of chip fabrication and RNA preparation, due to the non-linearity of the probe response and especially due to competitive interactions which are inherently connected with the high throughput character of the method. We theoretically analysed aspects of the hybridization of DNA oligonucleotide probes with a complex multicomponent mixture of RNA fragments, such as the effect of different interactions between nucleotide strands competing with the formation of specific duplexes, electrostatic and entropic blocking, the fragmentation of the RNA, the incomplete synthesis of the probes and 'zipping' effects in the oligonucleotide duplexes. The effective hybridization affinities of microarray probes are considerably smaller than those for bulk hybridization owing to the effects discussed, but they correlate well with the bulk data on a relative scale. In general, the hybridization isotherms of microarray probes are shown to deviate from a Langmuir-type behaviour. Nevertheless isotherms of the Langmuir or Sips type are predicted to provide a relatively simple description of the non-linear, probe-specific concentration dependence of the signal intensity of microarray probes

  12. Simultaneous allergen inactivation and detoxification of castor bean cake by treatment with calcium compounds

    Directory of Open Access Journals (Sweden)

    K.V. Fernandes

    2012-11-01

    Full Text Available Ricinus communis L. is of great economic importance due to the oil extracted from its seeds. Castor oil has been used for pharmaceutical and industrial applications, as a lubricant or coating agent, as a component of plastic products, as a fungicide or in the synthesis of biodiesel fuels. After oil extraction, a castor cake with a large amount of protein is obtained. However, this by-product cannot be used as animal feed due to the presence of toxic (ricin and allergenic (2S albumin proteins. Here, we propose two processes for detoxification and allergen inactivation of the castor cake. In addition, we establish a biological test to detect ricin and validate these detoxification processes. In this test, Vero cells were treated with ricin, and cell death was assessed by cell counting and measurement of lactate dehydrogenase activity. The limit of detection of the Vero cell assay was 10 ng/mL using a concentration of 1.6 x 10(5 cells/well. Solid-state fermentation (SSF and treatment with calcium compounds were used as cake detoxification processes. For SSF, Aspergillus niger was grown using a castor cake as a substrate, and this cake was analyzed after 24, 48, 72, and 96 h of SSF. Ricin was eliminated after 24 h of SSF treatment. The cake was treated with 4 or 8% Ca(OH2 or CaO, and both the toxicity and the allergenic properties were entirely abolished. A by-product free of toxicity and allergens was obtained.

  13. Simultaneous allergen inactivation and detoxification of castor bean cake by treatment with calcium compounds

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, K.V.; Deus-de-Oliveira, N. [Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, RJ (Brazil); Godoy, M.G. [Laboratório de Biotecnologia Microbiana, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ (Brazil); Guimarães, Z.A.S. [Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, RJ (Brazil); Nascimento, V.V. [Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, RJ (Brazil); Melo, E.J.T. de [Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, RJ (Brazil); Freire, D.M.G. [Laboratório de Biotecnologia Microbiana, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ (Brazil); Dansa-Petretski, M.; Machado, O.L.T. [Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, RJ (Brazil)

    2012-08-24

    Ricinus communis L. is of great economic importance due to the oil extracted from its seeds. Castor oil has been used for pharmaceutical and industrial applications, as a lubricant or coating agent, as a component of plastic products, as a fungicide or in the synthesis of biodiesel fuels. After oil extraction, a castor cake with a large amount of protein is obtained. However, this by-product cannot be used as animal feed due to the presence of toxic (ricin) and allergenic (2S albumin) proteins. Here, we propose two processes for detoxification and allergen inactivation of the castor cake. In addition, we establish a biological test to detect ricin and validate these detoxification processes. In this test, Vero cells were treated with ricin, and cell death was assessed by cell counting and measurement of lactate dehydrogenase activity. The limit of detection of the Vero cell assay was 10 ng/mL using a concentration of 1.6 × 10{sup 5} cells/well. Solid-state fermentation (SSF) and treatment with calcium compounds were used as cake detoxification processes. For SSF, Aspergillus niger was grown using a castor cake as a substrate, and this cake was analyzed after 24, 48, 72, and 96 h of SSF. Ricin was eliminated after 24 h of SSF treatment. The cake was treated with 4 or 8% Ca(OH){sub 2} or CaO, and both the toxicity and the allergenic properties were entirely abolished. A by-product free of toxicity and allergens was obtained.

  14. MICROARRAYS AND THEIR POTENTIAL IN MEDICINE

    Institute of Scientific and Technical Information of China (English)

    Erick Ling; Jie Xu

    2003-01-01

    Advancement in microarray technology can revolutionize many aspects of medicine. Microarrays have applications in gene expression profiling, genotyping, mutation analysis, gene identification, and pharmacology. This paper provides a brief review on the use of microarrays in studies of cancer, infectious diseases, chromosome disorders, neurological/mental disorders, and drugs, along with a prospect on its great potential in diagnosis, prognosis and the treatment of human diseases.

  15. Comprehensive comparison of six microarray technologies

    OpenAIRE

    Yauk, Carole L.; Berndt, M. Lynn; Williams, Andrew; Douglas, George R

    2004-01-01

    Microarray technology is extensively used in biological research. The applied technologies vary greatly between laboratories, and outstanding questions remain regarding the degree of correlation among approaches. Recently, there has been a drive toward ensuring high-quality microarray data by the implementation of MIAME (Minimal Information About a Microarray Experiment) guidelines and an emphasis on ensuring public-availability to all datasets. However, despite its current widespread use and...

  16. Integrating data from heterogeneous DNA microarray platforms

    OpenAIRE

    Valente, Eduardo; Rocha, Miguel

    2015-01-01

    DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set...

  17. Sensitising capacity of peptides from food allergens

    DEFF Research Database (Denmark)

    Bøgh, Katrine Lindholm

    . This PhD project aimed to investigate the sensitising potential of digestion products from the peanut allergen Ara h 1 and the cow’s milk allergen β-lactoglobulin (BLG) in a Brown Norway (BN) rat model. Further the project aimed to compare the IgE binding epitopes of intact and digested Ara h 1. This...... was done by digesting Ara h 1 and BLG in an in vitro model simulating the human gastric or gastroduodenal digestion process. Simulated gastric digestion was performed with immobilised pepsin for 120 min at pH 2.5, while simulated duodenal digestion was performed with immobilised trypsin and....... Comparison of intact and digested Ara h 1-specific IgE binding epitopes were performed by competitive immunoscreening using a random phage-displayed peptide library followed by mapping the identified IgE-binding epitope mimics on the surface of the Ara h 1 molecule. In addition to sera from the sensitised BN...

  18. Microarray Technology for Major Chemical Contaminants Analysis in Food: Current Status and Prospects

    Directory of Open Access Journals (Sweden)

    Xiaoxia Ding

    2012-07-01

    Full Text Available Chemical contaminants in food have caused serious health issues in both humans and animals. Microarray technology is an advanced technique suitable for the analysis of chemical contaminates. In particular, immuno-microarray approach is one of the most promising methods for chemical contaminants analysis. The use of microarrays for the analysis of chemical contaminants is the subject of this review. Fabrication strategies and detection methods for chemical contaminants are discussed in detail. Application to the analysis of mycotoxins, biotoxins, pesticide residues, and pharmaceutical residues is also described. Finally, future challenges and opportunities are discussed.

  19. Reduction of the Number of Major Representative Allergens: From Clinical Testing to 3-Dimensional Structures

    Directory of Open Access Journals (Sweden)

    Ying He

    2014-01-01

    Full Text Available Vast amounts of allergen sequence data have been accumulated, thus complicating the identification of specific allergenic proteins when performing diagnostic allergy tests and immunotherapy. This study aims to rank the importance/potency of the allergens so as to logically reduce the number of allergens and/or allergenic sources. Meta-analysis of 62 allergenic sources used for intradermal testing on 3,335 allergic patients demonstrated that in southern China, mite, sesame, spiny amaranth, Pseudomonas aeruginosa, and house dust account for 88.0% to 100% of the observed positive reactions to the 62 types of allergenic sources tested. The Kolmogorov-Smironov Test results of the website-obtained allergen data and allergen family featured peptides suggested that allergen research in laboratories worldwide has been conducted in parallel on many of the same species. The major allergens were reduced to 21 representative allergens, which were further divided into seven structural classes, each of which contains similar structural components. This study therefore has condensed numerous allergenic sources and major allergens into fewer major representative ones, thus allowing for the use of a smaller number of allergens when conducting comprehensive allergen testing and immunotherapy treatments.

  20. Vaccine development for allergen-specific immunotherapy based on recombinant allergens and synthetic allergen peptides: Lessons from the past and novel mechanisms of action for the future.

    Science.gov (United States)

    Valenta, Rudolf; Campana, Raffaela; Focke-Tejkl, Margit; Niederberger, Verena

    2016-02-01

    In the past, the development of more effective, safe, convenient, broadly applicable, and easy to manufacture vaccines for allergen-specific immunotherapy (AIT) has been limited by the poor quality of natural allergen extracts. Progress made in the field of molecular allergen characterization has now made it possible to produce defined vaccines for AIT and eventually for preventive allergy vaccination based on recombinant DNA technology and synthetic peptide chemistry. Here we review the characteristics of recombinant and synthetic allergy vaccines that have reached clinical evaluation and discuss how molecular vaccine approaches can make AIT more safe and effective and thus more convenient. Furthermore, we discuss how new technologies can facilitate the reproducible manufacturing of vaccines of pharmaceutical grade for inhalant, food, and venom allergens. Allergy vaccines in clinical trials based on recombinant allergens, recombinant allergen derivatives, and synthetic peptides allow us to target selectively different immune mechanisms, and certain of those show features that might make them applicable not only for therapeutic but also for prophylactic vaccination. PMID:26853127

  1. Time-Based Measurement of Personal Mite Allergen Bioaerosol Exposure over 24 Hour Periods.

    Science.gov (United States)

    Tovey, Euan R; Liu-Brennan, Damien; Garden, Frances L; Oliver, Brian G; Perzanowski, Matthew S; Marks, Guy B

    2016-01-01

    Allergic diseases such as asthma and rhinitis are common in many countries. Globally the most common allergen associated with symptoms is produced by house dust mites. Although the bed has often been cited as the main site of exposure to mite allergens, surprisingly this has not yet been directly established by measurement due to a lack of suitable methods. Here we report on the development of novel methods to determine the pattern of personal exposure to mite allergen bioaerosols over 24-hour periods and applied this in a small field study using 10 normal adults. Air was sampled using a miniature time-based air-sampler of in-house design located close to the breathing zone of the participants, co-located with a miniature time-lapse camera. Airborne particles, drawn into the sampler at 2L/min via a narrow slot, were impacted onto the peripheral surface of a disk mounted on the hour-hand of either a 12 or 24 hour clock motor. The impaction surface was either an electret cloth, or an adhesive film; both novel for these purposes. Following a review of the time-lapse images, disks were post-hoc cut into subsamples corresponding to eight predetermined categories of indoor or outdoor location, extracted and analysed for mite allergen Der p 1 by an amplified ELISA. Allergen was detected in 57.2% of the total of 353 subsamples collected during 20 days of sampling. Exposure patterns varied over time. Higher concentrations of airborne mite allergen were typically measured in samples collected from domestic locations in the day and evening. Indoor domestic Der p 1 exposures accounted for 59.5% of total exposure, whereas total in-bed-asleep exposure, which varied 80 fold between individuals, accounted overall for 9.85% of total exposure, suggesting beds are not often the main site of exposure. This study establishes the feasibility of novel methods for determining the time-geography of personal exposure to many bioaerosols and identifies new areas for future technical

  2. A microfluidic device for the automated electrical readout of low-density glass-slide microarrays.

    Science.gov (United States)

    Díaz-González, María; Salvador, J Pablo; Bonilla, Diana; Marco, M Pilar; Fernández-Sánchez, César; Baldi, Antoni

    2015-12-15

    Microarrays are a powerful platform for rapid and multiplexed analysis in a wide range of research fields. Electrical readout systems have emerged as an alternative to conventional optical methods for microarray analysis thanks to its potential advantages like low-cost, low-power and easy miniaturization of the required instrumentation. In this work an automated electrical readout system for low-cost glass-slide microarrays is described. The system enables the simultaneous conductimetric detection of up to 36 biorecognition events by incorporating an array of interdigitated electrode transducers. A polydimethylsiloxane microfluidic structure has been designed that creates microwells over the transducers and incorporates the microfluidic channels required for filling and draining them with readout and cleaning solutions, thus making the readout process fully automated. Since the capture biomolecules are not immobilized on the transducer surface this readout system is reusable, in contrast to previously reported electrochemical microarrays. A low-density microarray based on a competitive enzymatic immunoassay for atrazine detection was used to test the performance of the readout system. The electrical assay shows a detection limit of 0.22±0.03 μg L(-1) similar to that obtained with fluorescent detection and allows the direct determination of the pesticide in polluted water samples. These results proved that an electrical readout system such as the one presented in this work is a reliable and cost-effective alternative to fluorescence scanners for the analysis of low-density microarrays. PMID:26210466

  3. Effect of Formaldehyde on Asthmatic Response to Inhaled Allergen Challenge

    Science.gov (United States)

    Ezratty, Véronique; Bonay, Marcel; Neukirch, Catherine; Orset-Guillossou, Gaëlle; Dehoux, Monique; Koscielny, Serge; Cabanes, Pierre-André; Lambrozo, Jacques; Aubier, Michel

    2007-01-01

    Background Exposure to formaldehyde may lead to exacerbation of asthma. Objectives Our aim in this study was to investigate whether exposure to a low level (500 μg/m3) of formaldehyde enhances inhaled allergen responses. Methods Twelve subjects with intermittent asthma and allergy to pollen were exposed, at rest, in a double-blind crossover study to either formaldehyde or purified air for 60 min. The order of exposure to formaldehyde and air-only was randomized, and exposures were separated by 2 weeks. We also performed an allergen inhalation challenge after each exposure. Airway responsiveness to methacholine and lower airway inflammation (induced sputum) were assessed 8 hr after allergen challenge. Results The median dose of allergen producing a 15% decrease in forced expiratory volume in 1 sec (PD15FEV1) was 0.80 IR (index of reactivity) after formaldehyde exposure compared with 0.25 IR after air-only exposure (p = 0.06). Formaldehyde exposure did not affect allergen-induced increase in responsiveness to methacholine (p = 0.42). We found no formaldehyde-associated effect on the airway inflammatory response, in particular the eosinophilic inflammatory response, induced by the allergen challenge 8 hr before. Conclusion In this study, exposure to 500 μg/m3 formaldehyde had no significant deleterious effect on airway allergen responsiveness of patients with intermittent asthma; we found a trend toward a protective effect. PMID:17384766

  4. Controlling allergens in animal rooms by using curtains

    DEFF Research Database (Denmark)

    Krohn, Thomas Cæcius; Itter, Gabi; Fosse, Richard;

    2006-01-01

    The reduction and control of allergens in the animal facility is important for staff working with laboratory animals. This study was designed to evaluate the efficiency of perforated Makrolon curtains in front of racks as a method to reduce the amount of allergen in the animal room. The experimen...... the curtains and prevents its spread from the cages into the aisle. The present study shows that the use of curtains in front of the cage racks is an efficient way to prevent spread of allergens from rodent cages to the entire animal room.......The reduction and control of allergens in the animal facility is important for staff working with laboratory animals. This study was designed to evaluate the efficiency of perforated Makrolon curtains in front of racks as a method to reduce the amount of allergen in the animal room. The...... experimental situation we studied provides some information regarding allergen disposition in animal rooms but is clearly artificial and does not reflect a typical, ‘real-world’ environment in terms of preventing exposure of workers to allergens. Plastic curtains with holes were placed in front of racks, and a...

  5. Prediction of allergenic proteins and mapping of IgE epitopes in allergens

    OpenAIRE

    sprotocols

    2015-01-01

    In present era use of genetically modified proteins in foods, therapeutics and biopharmaceuticals is increasing with exponential rate. Thus it is important to predict whether a modified protein allergenic or not. In 2003, the Codex Alimentarius Commission (Codex) conveyed a panel of international food safety regulators to review the FAO/ WHO 2001 recommendations and recognized the uncertainties associated with the bioinformatics part of the guidelines. They recommended various tests for exami...

  6. Authentication of food allergen quality by physicochemical and immunological methods

    DEFF Research Database (Denmark)

    Sancho, A I; Hoffmann-Sommergruber, K; Alessandri, S;

    2010-01-01

    and standardization of methods between different laboratories and operators for risk assessment in the food industry. Therefore, there is a need for well-defined purified food allergens. In this context, a panel of 46 food allergens from plant and animal sources has been purified, from either the food sources...... or as recombinant forms, within the EU-funded EuroPrevall project. These allergens have been characterized by a battery of diagnostic tests demonstrating that they constitute an authentic, well-defined library of comparable quality. The review summarizes the applications, potentials and limitations of key...

  7. Application of microarray technology in pulmonary diseases

    OpenAIRE

    Patlakas George; Tzouvelekis Argyris; Bouros Demosthenes

    2004-01-01

    Abstract Microarrays are a powerful tool that have multiple applications both in clinical and cell biology arenas of common lung diseases. To exemplify how this tool can be useful, in this review, we will provide an overview of the application of microarray technology in research relevant to common lung diseases and present some of the future perspectives.

  8. Current challenges facing the assessment of the allergenic capacity of food allergens in animal models.

    Science.gov (United States)

    Bøgh, Katrine Lindholm; van Bilsen, Jolanda; Głogowski, Robert; López-Expósito, Iván; Bouchaud, Grégory; Blanchard, Carine; Bodinier, Marie; Smit, Joost; Pieters, Raymond; Bastiaan-Net, Shanna; de Wit, Nicole; Untersmayr, Eva; Adel-Patient, Karine; Knippels, Leon; Epstein, Michelle M; Noti, Mario; Nygaard, Unni Cecilie; Kimber, Ian; Verhoeckx, Kitty; O'Mahony, Liam

    2016-01-01

    Food allergy is a major health problem of increasing concern. The insufficiency of protein sources for human nutrition in a world with a growing population is also a significant problem. The introduction of new protein sources into the diet, such as newly developed innovative foods or foods produced using new technologies and production processes, insects, algae, duckweed, or agricultural products from third countries, creates the opportunity for development of new food allergies, and this in turn has driven the need to develop test methods capable of characterizing the allergenic potential of novel food proteins. There is no doubt that robust and reliable animal models for the identification and characterization of food allergens would be valuable tools for safety assessment. However, although various animal models have been proposed for this purpose, to date, none have been formally validated as predictive and none are currently suitable to test the allergenic potential of new foods. Here, the design of various animal models are reviewed, including among others considerations of species and strain, diet, route of administration, dose and formulation of the test protein, relevant controls and endpoints measured. PMID:27313841

  9. Identification of novel allergen in edible insect, Gryllus bimaculatus and its cross-reactivity with Macrobrachium spp. allergens.

    Science.gov (United States)

    Srinroch, Chutima; Srisomsap, Chantragan; Chokchaichamnankit, Daranee; Punyarit, Phaibul; Phiriyangkul, Pharima

    2015-10-01

    Edible insects have recently been promoted as a source of protein and have a high nutrition value. Identification of allergens and cross-reactivity between Macrobrachium spp. and the field cricket (Gryllus bimaculatus) is necessary for food safety control and to assist in the diagnosis and therapy of allergy symptoms. Denaturing polyacrylamide gel electrophoresis (SDS-PAGE) was used to separate proteins. Allergens were determined and identified by IgE-immunoblotting with pooled sera from prawn-allergic patients (n=16) and LC-MS/MS. Arginine kinase (AK) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were determined as the important allergens in muscle of Macrobrachium rosenbergii whereas, hemocyanin (HC) was identified as an allergen in Macrobrachium spp. The allergens in Macrobrachium lanchesteri were identified as AK and HC. In addition, hexamerin1B (HEX1B) was identified as a novel and specific allergen in G. bimaculatus. The important allergen in G. bimaculatus and Macrobrachium spp. is AK and was found to cross-react between both species. PMID:25872439

  10. Flow-pattern Guided Fabrication of High-density Barcode Antibody Microarray.

    Science.gov (United States)

    Ramirez, Lisa S; Wang, Jun

    2016-01-01

    Antibody microarray as a well-developed technology is currently challenged by a few other established or emerging high-throughput technologies. In this report, we renovate the antibody microarray technology by using a novel approach for manufacturing and by introducing new features. The fabrication of our high-density antibody microarray is accomplished through perpendicularly oriented flow-patterning of single stranded DNAs and subsequent conversion mediated by DNA-antibody conjugates. This protocol outlines the critical steps in flow-patterning DNA, producing and purifying DNA-antibody conjugates, and assessing the quality of the fabricated microarray. The uniformity and sensitivity are comparable with conventional microarrays, while our microarray fabrication does not require the assistance of an array printer and can be performed in most research laboratories. The other major advantage is that the size of our microarray units is 10 times smaller than that of printed arrays, offering the unique capability of analyzing functional proteins from single cells when interfacing with generic microchip designs. This barcode technology can be widely employed in biomarker detection, cell signaling studies, tissue engineering, and a variety of clinical applications. PMID:26780370

  11. Carbohydrate Microarrays in Plant Science

    DEFF Research Database (Denmark)

    Fangel, Jonatan Ulrik; Pedersen, H.L.; Vidal-Melgosa, S.;

    2012-01-01

    Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important...... industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high...... plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities....

  12. Biomarkers for Allergen Immunotherapy: A "Panoromic" View.

    Science.gov (United States)

    Moingeon, Philippe

    2016-02-01

    Biomarkers (BMKs) are biological parameters that can be measured to predict or monitor disease severity or treatment efficacy. The induction of regulatory dendritic cells (DCs) concomitantly with a downregulation of proallergic DC2s (ie, DCs supporting the differentiation of T-helper lymphocyte type 2 cells) in the blood of patients allergic to grass pollen has been correlated with the early onset of allergen immunotherapy efficacy. The combined use of omics technologies to compare biological samples from clinical responders and nonresponders is being implemented in the context of nonhypothesis-driven approaches. Such comprehensive "panoromic" strategies help identify completely novel candidate BMKs, to be subsequently validated as companion diagnostics in large-scale clinical trials. PMID:26617233

  13. Thresholds of allergenic proteins in foods

    International Nuclear Information System (INIS)

    Threshold doses or Estimated Eliciting Doses (EEDs) represent an important new field of research in food allergy. Clinicians and regulators have embraced some toxicological concepts such as LOAEL and NOAEL and applied them to an area of significant clinical uncertainty and interest. The impact of intrinsic human factors (e.g., asthma and exercise) and extrinsic event factors (e.g., season, location and especially dose of allergen) on a future allergic reaction in the community needs to be considered carefully when interpreting results of clinical and research low-dose food challenges. The ongoing cooperation of food allergy research groups in medicine, food science and government will surely deliver results of the highest importance to the wider communities of allergology, food science and technology and the increasing number of allergic consumers

  14. Seasonal dynamics of harmful algae in outer Oslofjorden monitored by microarray, qPCR, and microscopy.

    Science.gov (United States)

    Dittami, Simon M; Hostyeva, Vladyslava; Egge, Elianne Sirnæs; Kegel, Jessica U; Eikrem, Wenche; Edvardsen, Bente

    2013-10-01

    Monitoring of marine microalgae is important to predict and manage harmful algal blooms. Microarray Detection of Toxic ALgae (MIDTAL) is an FP7-funded EU project aiming to establish a multi-species microarray as a tool to aid monitoring agencies. We tested the suitability of different prototype versions of the MIDTAL microarray for the monthly monitoring of a sampling station in outer Oslofjorden during a 1-year period. Microarray data from two different versions of the MIDTAL chip were compared to results from cell counts (several species) and quantitative real-time PCR (qPCR; only Pseudochattonella spp.). While results from generation 2.5 microarrays exhibited a high number of false positive signals, generation 3.3 microarray data generally correlated with microscopy and qPCR data, with three important limitations: (1) Pseudo-nitzschia cells were not reliably detected, possibly because cells were not sufficiently retained during filtration or lysed during the extraction, and because of low sensitivity of the probes; (2) in the case of samples with high concentrations of non-target species, the sensitivity of the arrays was decreased; (3) one occurrence of Alexandrium pseudogonyaulax was not detected due to a 1-bp mismatch with the genus probe represented on the microarray. In spite of these shortcomings our data demonstrate the overall progress made and the potential of the MIDTAL array. The case of Pseudochattonella - where two morphologically similar species impossible to separate by light microscopy were distinguished - in particular, underlines the added value of molecular methods such as microarrays in routine phytoplankton monitoring. PMID:23325054

  15. Enhancing the quality metric of protein microarray image

    Institute of Scientific and Technical Information of China (English)

    王立强; 倪旭翔; 陆祖康; 郑旭峰; 李映笙

    2004-01-01

    The novel method of improving the quality metric of protein microarray image presented in this paper reduces impulse noise by using an adaptive median filter that employs the switching scheme based on local statistics characters; and achieves the impulse detection by using the difference between the standard deviation of the pixels within the filter window and the current pixel of concern. It also uses a top-hat filter to correct the background variation. In order to decrease time consumption, the top-hat filter core is cross structure. The experimental results showed that, for a protein microarray image contaminated by impulse noise and with slow background variation, the new method can significantly increase the signal-to-noise ratio, correct the trends in the background, and enhance the flatness of the background and the consistency of the signal intensity.

  16. Lanolin allergy: history, epidemiology, responsible allergens, and management.

    Science.gov (United States)

    Lee, Bailey; Warshaw, Erin

    2008-01-01

    Allergy to lanolin has been recognized by dermatologists for decades. This review summarizes the history, epidemiology, and allergenicity of lanolin and its derivatives. "The lanolin paradox" and the safety of pharmaceutical-grade lanolin products are also discussed. PMID:18413106

  17. Cross-reactions between respiratory and food allergens.

    Science.gov (United States)

    de Blay, F; Pauli, G; Bessot, J C

    1991-01-01

    Cross-reactions between inhaled and food allergens are usually attributed to pollen hypersensitivity associated with fruit and vegetable allergy. However, other allergens are involved in these types of cross-reactions. In a few cases, there is a complete similarity between the inhaled and food allergens (garlic, crustacea proteins). More frequently, partial similarity has been demonstrated: whole inhaled allergens are included in ingested substances. Moreover, immunological techniques can demonstrate common antigenic epitopes in organic substances without any apparent relationship. This has been demonstrated by RAST-inhibition and/or immunoblot techniques, using sera from patients cross-sensitized to (1) pollens and fruits or vegetables or (2) avian sera and eggs. Respiratory sensitization always seems to precede food allergy symptoms. PMID:1720408

  18. Allergenicity assessment of Allium sativum leaf agglutinin, a potential candidate protein for developing sap sucking insect resistant food crops.

    Directory of Open Access Journals (Sweden)

    Hossain Ali Mondal

    Full Text Available BACKGROUND: Mannose-binding Allium sativum leaf agglutinin (ASAL is highly antinutritional and toxic to various phloem-feeding hemipteran insects. ASAL has been expressed in a number of agriculturally important crops to develop resistance against those insects. Awareness of the safety aspect of ASAL is absolutely essential for developing ASAL transgenic plants. METHODOLOGY/PRINCIPAL FINDINGS: Following the guidelines framed by the Food and Agriculture Organization/World Health Organization, the source of the gene, its sequence homology with potent allergens, clinical tests on mammalian systems, and the pepsin resistance and thermostability of the protein were considered to address the issue. No significant homology to the ASAL sequence was detected when compared to known allergenic proteins. The ELISA of blood sera collected from known allergy patients also failed to show significant evidence of cross-reactivity. In vitro and in vivo assays both indicated the digestibility of ASAL in the presence of pepsin in a minimum time period. CONCLUSIONS/SIGNIFICANCE: With these experiments, we concluded that ASAL does not possess any apparent features of an allergen. This is the first report regarding the monitoring of the allergenicity of any mannose-binding monocot lectin having insecticidal efficacy against hemipteran insects.

  19. Cross-reactivity among non-specific lipid-transfer proteins from food and pollen allergenic sources.

    Science.gov (United States)

    Morales, María; López-Matas, M Ángeles; Moya, Raquel; Carnés, Jerónimo

    2014-12-15

    Non-specific lipid-transfer proteins (nsLTPs) are a family of pan-allergens present in foods and pollen. However, sequence homology among them is limited. The objective of this study was to evaluate the IgE-mediated cross-reactivity between nsLTPs from different sources and evaluate the allergenic properties of LTPs from peach (Pru p 3) and pellitory (Par j 1/Par j 2), major fruit and pollen allergens. Both proteins were purified and characterised. Cross-reactivity studies among nsLTPs from different foods and pollens were performed by immunoblot inhibition using sera specific to peach or pellitory pollen. Cross-reactivity with Pru p 3 was observed in hazelnut, onion, corn, peanut and apple while in pollens, none of the extracts was inhibited with Par j 1/2. In conclusion, Pru p 3 did not inhibit LTPs from most fruits. Therefore, although Pru p 3 covers the largest number of epitopes, diagnosis with only this allergen may not detect all LTP sensitivities. PMID:25038692

  20. Tumour auto-antibody screening: performance of protein microarrays using SEREX derived antigens

    International Nuclear Information System (INIS)

    The simplicity and potential of minimal invasive testing using serum from patients make auto-antibody based biomarkers a very promising tool for use in diagnostics of cancer and auto-immune disease. Although several methods exist for elucidating candidate-protein markers, immobilizing these onto membranes and generating so called macroarrays is of limited use for marker validation. Especially when several hundred samples have to be analysed, microarrays could serve as a good alternative since processing macro membranes is cumbersome and reproducibility of results is moderate. Candidate markers identified by SEREX (serological identification of antigens by recombinant expression cloning) screenings of brain and lung tumour were used for macroarray and microarray production. For microarray production recombinant proteins were expressed in E. coli by autoinduction and purified His-tag (histidine-tagged) proteins were then used for the production of protein microarrays. Protein arrays were hybridized with the serum samples from brain and lung tumour patients. Methods for the generation of microarrays were successfully established when using antigens derived from membrane-based selection. Signal patterns obtained by microarrays analysis of brain and lung tumour patients' sera were highly reproducible (R = 0.92-0.96). This provides the technical foundation for diagnostic applications on the basis of auto-antibody patterns. In this limited test set, the assay provided high reproducibility and a broad dynamic range to classify all brain and lung samples correctly. Protein microarray is an efficient means for auto-antibody-based detection when using SEREX-derived clones expressing antigenic proteins. Protein microarrays are preferred to macroarrays due to the easier handling and the high reproducibility of auto-antibody testing. Especially when using only a few microliters of patient samples protein microarrays are ideally suited for validation of auto