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 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.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.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 responses over time, and facilitate genetic studies on pollen allergy.

  2. A Pitfall to Avoid When Using an Allergen Microarray: The Incidental Detection of IgE to Unexpected Allergens. (United States)

    Incorvaia, Cristoforo; Mauro, Marina; Ridolo, Erminia; Makrì, Eleni; Montagni, Marcello; Ciprandi, Giorgio


    The introduction of new laboratory techniques to detect specific IgE antibodies against single allergen molecules rather than whole extracts represents a significant advance in allergy diagnostics. The advantages of such component-resolved diagnosis can be summarized as follows: (1) the ability to identify the truly responsible allergens in polysensitized patients, whether they be genuine (causing specific sensitization to their corresponding allergen source) or primary (the original sensitizing molecule); (2) distinguishing these allergens from simply cross-reactive components; (3) improving the appropriateness of the prescribed specific immunotherapy; and (4) identifying a risk profile for food allergens. Component-resolved diagnosis is performed using either a singleplex (1 assay per sample) platform or a multiplex (multiple assays per sample) platform. Using an immuno solid-phase allergen chip microarray that falls into the latter category--it currently tests sensitivity to 112 allergens--may lead to a pitfall: detecting IgE to unexpected allergens, such as Hymenoptera venom. In fact, testing insect venom sensitivity in individuals with no history of reactions to stings is contrary to current guidelines and presents the physician with the dilemma of how to manage this information; moreover, this may become a legal issue. Based on what is currently known about venom allergy, it remains likely that a positive sensitization test result will have no clinical significance, but the possibility of reacting to a future sting cannot be completely ruled out. Because this problem has not been previously encountered using the more common allergy tests, no indications are currently available on how to effectively manage these cases.

  3. 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


    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.

  4. A Photo-immobilized Allergen Microarray for Screening of Allergen-specific IgE

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    Kunio Ohyama


    Full Text Available We developed an in vitro system to diagnose allergy using an allergen microarray and photo-immobilization technique. Photo-immobilization is useful for preparing the allergen microarray because it does not require specific functional groups of the allergen and because any organic material can be immobilized by a radical reaction induced by photo-irradiation. To prepare the plates, allergen solutions were mixed with polymer and a bis- azidophenyl derivative, a photo-reactive cross-linker, the mixtures were micro-spotted on the plate, and the droplets were dried. The plate was irradiated with an ultraviolet lamp for immobilization. For the assay, human serum was added to the microarray plate. Allergen-specific immunoglobulin E (IgE adsorbed on the micro- spotted allergen was detected by peroxidase-conjugated anti-IgE antibody. The chemiluminescence intensities of the substrate decomposed by the peroxidase were detected with a sensitive CCD camera. All allergens were immobilized by this method and used to screen allergen-specific IgE.

  5. Sensitive detection of major food allergens in breast milk: first gateway for allergenic contact during breastfeeding. (United States)

    Pastor-Vargas, C; Maroto, A S; Díaz-Perales, A; Villaba, M; Casillas Diaz, N; Vivanco, F; Cuesta-Herranz, J


    Food allergy is recognized as a major public health issue, especially in early childhood. It has been hypothesized that early sensitization to food allergens maybe due to their ingestion as components dissolved in the milk during the breastfeeding, explaining reaction to a food, which has never been taken before. Thus, the aim of this work has been to detect the presence of the food allergens in breast milk by microarray technology. We produced a homemade microarray with antibodies produced against major food allergens. The antibody microarray was incubated with breast milk from 14 women collected from Fundación Jiménez Díaz Hospital. In this way, we demonstrated the presence of major foods allergens in breast milk. The analysis of allergens presented in breast milk could be a useful tool in allergy prevention and could provide us a key data on the role of this feeding in tolerance induction or sensitization in children.

  6. Soybean allergen detection methods

    DEFF Research Database (Denmark)

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


    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...

  7. 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.

  8. Multiplex detection of food allergens and gluten. (United States)

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


    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.

  9. An SPR based sensor for allergens detection. (United States)

    Ashley, J; Piekarska, M; Segers, C; Trinh, L; Rodgers, T; Willey, R; Tothill, I E


    A simple, sensitive and label-free optical sensor method was developed for allergens analysis using α-casein as the biomarker for cow's milk detection, to be used directly in final rinse samples of cleaning in place systems (CIP) of food manufacturers. A Surface Plasmon Resonance (SPR) sensor chip consisting of four sensing arrays enabling the measurement of samples and control binding events simultaneously on the sensor surface was employed in this work. SPR offers several advantages in terms of label free detection, real time measurements and superior sensitivity when compared to ELISA based techniques. The gold sensor chip was used to immobilise α-casein-polyclonal antibody using EDC/NHS coupling procedure. The performance of the assay and the sensor was first optimised and characterised in pure buffer conditions giving a detection limit of 58ngmL(-1) as a direct binding assay. The assay sensitivity can be further improved by using sandwich assay format and amplified with nanoparticles. However, at this stage this is not required as the detection limit achieved exceeded the required allergens detection levels of 2µgmL(-1) for α-S1-casein. The sensor demonstrated good selectivity towards the α-casein as the target analyte and adequate recoveries from CIP final rinse wash samples. The sensor would be useful tool for monitoring allergen levels after cleaning procedures, providing additional data that may better inform upon wider food allergen risk management decision(s) that are made by food manufacturer. In particular, this sensor could potentially help validate or optimise cleaning practices for a given food manufacturing process.

  10. Microarray Scanner for Fluorescence Detection

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    Wang Liqiang; Lu zukang; Li Yingsheng; Zheng Xufeng


    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.

  11. IgE and IgG4 Epitope Mapping of Food Allergens with a Peptide Microarray Immunoassay. (United States)

    Martínez-Botas, Javier; de la Hoz, Belén


    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.

  12. New Trends in Food Allergens Detection: Toward Biosensing Strategies. (United States)

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


    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.

  13. 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.

  14. Application of photonic crystal enhanced fluorescence to detection of low serum concentrations of human IgE antibodies specific for a purified cat allergen (Fel D1). (United States)

    Tan, Yafang; Halsey, John F; Tang, Tiantian; Wetering, Scott Vande; Taine, Elaine; Cleve, Mark Van; Cunningham, Brian T


    We demonstrate the detection of low concentrations of allergen-specific Immunoglobulin E (IgE) in human sera using a Photonic Crystal Enhanced Fluorescence (PCEF) microarray platform. The Photonic Crystal (PC) surface, designed to provide optical resonances for the excitation wavelength and emission wavelength of Cy5, was used to amplify the fluorescence signal intensity measured from a multiplexed allergen microarray. Surface-based sandwich immunoassays were used to detect and quantify specific IgE antibodies against a highly purified cat allergen (Fel d1). A comparison of the lowest detectable concentration of IgE measured by the PC microarray system and a commercially available clinical analyzer demonstrated that the PCEF microarray system provides higher sensitivity. The PCEF system was able to detect low concentrations of specific IgE (~0.02 kU/L), which is 5-17-fold more sensitive than the commercially available FDA-approved analyzers. In preliminary experiments using multi-allergen arrays, we demonstrate selective simultaneous detection of IgE antibodies to multiple allergens.

  15. Hazelnut Allergens: Molecular Characterization, Detection, and Clinical Relevance. (United States)

    Costa, Joana; Mafra, Isabel; Carrapatoso, Isabel; Oliveira, Maria Beatriz P P


    In last few years, special attention has been given to food-induced allergies, in which hazelnut allergy is highlighted. Hazelnut is one of the most commonly consumed tree nuts, being largely used by the food industry in a variety of processed foods. It has been regarded as a food with potential health benefits, but also as a source of allergens capable of inducing mild to severe allergic reactions in sensitized individuals. Considering the great number of reports addressing hazelnut allergens, with an estimated increasing trend, this review intends to assemble all the relevant information available so far on the following main issues: prevalence of tree nut allergy, clinical threshold levels, molecular characterization of hazelnut allergens (Cor a 1, Cor a 2, Cor a 8, Cor a 9, Cor a 10, Cor a 11, Cor a 12, Cor a 14, and Cor a TLP) and their clinical relevance, and methodologies for detection of hazelnut allergens in foods. A comprehensive overview of the current data about the molecular characterization of hazelnut allergens is presented, relating to biochemical classification and biological function with clinical importance. Recent advances in hazelnut allergen detection methodologies are summarized and compared, including all the novel protein-based and DNA-based approaches.

  16. Antibody microarrays for native toxin detection. (United States)

    Rucker, Victor C; Havenstrite, Karen L; Herr, Amy E


    We have developed antibody-based microarray techniques for the multiplexed detection of cholera toxin beta-subunit, diphtheria toxin, anthrax lethal factor and protective antigen, Staphylococcus aureus enterotoxin B, and tetanus toxin C fragment in spiked samples. Two detection schemes were investigated: (i) a direct assay in which fluorescently labeled toxins were captured directly by the antibody array and (ii) a competition assay that employed unlabeled toxins as reporters for the quantification of native toxin in solution. In the direct assay, fluorescence measured at each array element is correlated with labeled toxin concentration to yield baseline binding information (Langmuir isotherms and affinity constants). Extending from the direct assay, the competition assay yields information on the presence, identity, and concentration of toxins. A significant advantage of the competition assay over reported profiling assays is the minimal sample preparation required prior to analysis because the competition assay obviates the need to fluorescently label native proteins in the sample of interest. Sigmoidal calibration curves and detection limits were established for both assay formats. Although the sensitivity of the direct assay is superior to that of the competition assay, detection limits for unmodified toxins in the competition assay are comparable to values reported previously for sandwich-format immunoassays of antibodies arrayed on planar substrates. As a demonstration of the potential of the competition assay for unlabeled toxin detection, we conclude with a straightforward multiplexed assay for the differentiation and identification of both native S. aureus enterotoxin B and tetanus toxin C fragment in spiked dilute serum samples.

  17. Point-of-care vertical flow allergen microarray assay: proof of concept

    NARCIS (Netherlands)

    Chinnasamy, Thiruppathiraja; Segerink, Loes I.; Nystrand, Mats; Gantelius, Jesper; Andersson Svahn, Helene


    BACKGROUND: Sophisticated equipment, lengthy protocols, and skilled operators are required to perform protein microarray-based affinity assays. Consequently, novel tools are needed to bring biomarkers and biomarker panels into clinical use in different settings. Here, we describe a novel paper-based

  18. Microarrays for Universal Detection and Identification of Phytoplasmas

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Nyskjold, Henriette; Bertaccini, Assunta


    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...

  19. 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.


    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

  20. Ultrasensitive aptamer based detection of β-conglutin food allergen. (United States)

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


    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.

  1. Large scale multiplex PCR improves pathogen detection by DNA microarrays

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    Krönke Martin


    Full Text Available Abstract Background Medium density DNA microchips that carry a collection of probes for a broad spectrum of pathogens, have the potential to be powerful tools for simultaneous species identification, detection of virulence factors and antimicrobial resistance determinants. However, their widespread use in microbiological diagnostics is limited by the problem of low pathogen numbers in clinical specimens revealing relatively low amounts of pathogen DNA. Results To increase the detection power of a fluorescence-based prototype-microarray designed to identify pathogenic microorganisms involved in sepsis, we propose a large scale multiplex PCR (LSplex PCR for amplification of several dozens of gene-segments of 9 pathogenic species. This protocol employs a large set of primer pairs, potentially able to amplify 800 different gene segments that correspond to the capture probes spotted on the microarray. The LSplex protocol is shown to selectively amplify only the gene segments corresponding to the specific pathogen present in the analyte. Application of LSplex increases the microarray detection of target templates by a factor of 100 to 1000. Conclusion Our data provide a proof of principle for the improvement of detection of pathogen DNA by microarray hybridization by using LSplex PCR.

  2. VIPR: A probabilistic algorithm for analysis of microbial detection microarrays

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    Holbrook Michael R


    Full Text Available Abstract Background All infectious disease oriented clinical diagnostic assays in use today focus on detecting the presence of a single, well defined target agent or a set of agents. In recent years, microarray-based diagnostics have been developed that greatly facilitate the highly parallel detection of multiple microbes that may be present in a given clinical specimen. While several algorithms have been described for interpretation of diagnostic microarrays, none of the existing approaches is capable of incorporating training data generated from positive control samples to improve performance. Results To specifically address this issue we have developed a novel interpretive algorithm, VIPR (Viral Identification using a PRobabilistic algorithm, which uses Bayesian inference to capitalize on empirical training data to optimize detection sensitivity. To illustrate this approach, we have focused on the detection of viruses that cause hemorrhagic fever (HF using a custom HF-virus microarray. VIPR was used to analyze 110 empirical microarray hybridizations generated from 33 distinct virus species. An accuracy of 94% was achieved as measured by leave-one-out cross validation. Conclusions VIPR outperformed previously described algorithms for this dataset. The VIPR algorithm has potential to be broadly applicable to clinical diagnostic settings, wherein positive controls are typically readily available for generation of training data.

  3. Multiplex DNA detection of food allergens on a digital versatile disk. (United States)

    Tortajada-Genaro, Luis A; Santiago-Felipe, Sara; Morais, Sergi; Gabaldón, José Antonio; Puchades, Rosa; Maquieira, Ángel


    The development of a DNA microarray method on a digital versatile disk (DVD) is described for the simultaneous detection of traces of hazelnut ( Corylus avellana L.), peanut ( Arachis hypogaea ), and soybean ( Glycine max ) in foods. After DNA extraction, multiplex PCR was set up using 5'-labeled specific primers for Cor a 1, Ar h 2, and Le genes, respectively. Digoxin-labeled PCR products were detected by hybridization with 5'-biotinylated probes immobilized on a streptavidin-modified DVD surface. The reaction product attenuates the signal intensity of the laser that reached the DVD drive used as detector, correlating well with the amount of amplified sequence. Analytical performances showed a detection limit of 1 μg/g and good assay reproducibility (RSD 8%), suitable for the simultaneous detection of the three targeted allergens. The developed methodology was tested with several commercially available foodstuffs, demonstrating its applicability. The results were in good agreement, in terms of sensitivity and reproducibility, with those obtained with ELISA, PCR-gel agarose electrophoresis, and RT-PCR.

  4. Employing image processing techniques for cancer detection using microarray images. (United States)

    Dehghan Khalilabad, Nastaran; Hassanpour, Hamid


    Microarray technology is a powerful genomic tool for simultaneously studying and analyzing the behavior of thousands of genes. The analysis of images obtained from this technology plays a critical role in the detection and treatment of diseases. The aim of the current study is to develop an automated system for analyzing data from microarray images in order to detect cancerous cases. The proposed system consists of three main phases, namely image processing, data mining, and the detection of the disease. The image processing phase performs operations such as refining image rotation, gridding (locating genes) and extracting raw data from images the data mining includes normalizing the extracted data and selecting the more effective genes. Finally, via the extracted data, cancerous cell is recognized. To evaluate the performance of the proposed system, microarray database is employed which includes Breast cancer, Myeloid Leukemia and Lymphomas from the Stanford Microarray Database. The results indicate that the proposed system is able to identify the type of cancer from the data set with an accuracy of 95.45%, 94.11%, and 100%, respectively.

  5. IgE recognition patterns of profilin, PR-10, and tropomyosin panallergens tested in 3,113 allergic patients by allergen microarray-based technology.

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    Enrico Scala

    Full Text Available BACKGROUND: IgE recognition of panallergens having highly conserved sequence regions, structure, and function and shared by inhalant and food allergen sources is often observed. METHODS: We evaluated the IgE recognition profile of profilins (Bet v 2, Cyn d 12, Hel a 2, Hev b 8, Mer a 1, Ole e 2, Par j 3, Phl p 12, Pho d 2, PR-10 proteins (Aln g 1, Api g 1, Bet v 1.0101, Bet v 1.0401, Cor a 1, Dau c 1 and Mal d 1.0108 and tropomyosins (Ani s 3, Der p 10, Hel as 1, Pen i 1, Pen m 1, Per a 7 using the Immuno-Solid phase Allergen Chip (ISAC microarray system. The three panallergen groups were well represented among the allergenic molecules immobilized on the ISAC. Moreover, they are distributed in several taxonomical allergenic sources, either close or distant, and have a route of exposure being either inhalation or ingestion. RESULTS: 3,113 individuals (49.9% female were selected on the basis of their reactivity to profilins, PR-10 or tropomyosins. 1,521 (48.8% patients were reactive to profilins (77.6% Mer a 1 IgE(+, 1,420 (45.6% to PR-10 (92.5% Bet v 1 IgE(+ and 632 (20.3% to tropomyosins (68% Der p 10 IgE(+. A significant direct relationship between different representative molecules within each group of panallergens was found. 2,688 patients (86.4% recognized only one out of the three distinct groups of molecules as confirmed also by hierarchical clustering analysis. CONCLUSIONS: Unless exposed to most of the allergens in the same or related allergenic sources, a preferential IgE response to distinct panallergens has been recorded. Allergen microarray IgE testing increases our knowledge of the IgE immune response and related epidemiological features within and between homologous molecules better describing the patients' immunological phenotypes.

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

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    Romantschuk Martin


    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.

  7. DNA microarray technique for detecting food-borne pathogens

    Directory of Open Access Journals (Sweden)

    Xing GAO


    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.

  8. Advanced DNA- and Protein-based Methods for the Detection and Investigation of Food Allergens. (United States)

    Prado, M; Ortea, I; Vial, S; Rivas, J; Calo-Mata, P; Barros-Velázquez, J


    Currently, food allergies are an important health concern worldwide. The presence of undeclared allergenic ingredients or the presence of traces of allergens due to contamination during food processing poses a great health risk to sensitized individuals. Therefore, reliable analytical methods are required to detect and identify allergenic ingredients in food products. The present review addresses the recent developments regarding the application of DNA- and protein-based methods for the detection of allergenic ingredients in foods. The fitness-for-purpose of reviewed methodology will be discussed, and future trends will be highlighted. Special attention will be given to the evaluation of the potential of newly developed and promising technologies that can improve the detection and identification of allergenic ingredients in foods, such as the use of biosensors and/or nanomaterials to improve detection limits, specificity, ease of use, or to reduce the time of analysis. Such rapid food allergen test methods are required to facilitate the reliable detection of allergenic ingredients by control laboratories, to give the food industry the means to easily determine whether its product has been subjected to cross-contamination and, simultaneously, to identify how and when this cross-contamination occurred.

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

    Institute of Scientific and Technical Information of China (English)

    Xu Ma; Qing-yun Zhang


    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.

  10. A microfluidic biosensor using graphene oxide and aptamer-functionalized quantum dots for peanut allergen detection. (United States)

    Weng, Xuan; Neethirajan, Suresh


    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.

  11. Streamlining the analytical workflow for multiplex MS/MS allergen detection in processed foods. (United States)

    Pilolli, Rosa; De Angelis, Elisabetta; Monaci, Linda


    Allergenic ingredients in pre-packaged foods are regulated by EU legislation mandating their inclusion on labels. In order to protect allergic consumers, sensitive analytical methods are required for detect allergen traces in different food products. As a follow-up to our previous investigations, an optimized, sensitive, label-free LC-MS/MS method for multiplex detection of five allergenic ingredients in a processed food matrix is proposed. A cookie base was chosen as a complex food matrix and home-made cookies incurred with whole egg, skimmed milk, soy flour, ground hazelnut and ground peanut were prepared at laboratory scale. In order to improve the analytical workflow both protein extraction and purification protocols were optimized and finally a sensitive streamlined SRM based analytical method for allergens detection in incurred cookies was devised. The effect of baking on the detection of selected markers was also investigated.

  12. First screening method for the simultaneous detection of seven allergens by liquid chromatography mass spectrometry. (United States)

    Heick, J; Fischer, M; Pöpping, B


    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.

  13. Electrochemical Affinity Biosensors Based on Disposable Screen-Printed Electrodes for Detection of Food Allergens. (United States)

    Vasilescu, Alina; Nunes, Gilvanda; Hayat, Akhtar; Latif, Usman; Marty, Jean-Louis


    Food allergens are proteins from nuts and tree nuts, fish, shellfish, wheat, soy, eggs or milk which trigger severe adverse reactions in the human body, involving IgE-type antibodies. Sensitive detection of allergens in a large variety of food matrices has become increasingly important considering the emergence of functional foods and new food manufacturing technologies. For example, proteins such as casein from milk or lysozyme and ovalbumin from eggs are sometimes used as fining agents in the wine industry. Nonetheless, allergen detection in processed foods is a challenging endeavor, as allergen proteins are degraded during food processing steps involving heating or fermentation. Detection of food allergens was primarily achieved via Enzyme-Linked Immuno Assay (ELISA) or by chromatographic methods. With the advent of biosensors, electrochemical affinity-based biosensors such as those incorporating antibodies and aptamers as biorecognition elements were also reported in the literature. In this review paper, we highlight the success achieved in the design of electrochemical affinity biosensors based on disposable screen-printed electrodes towards detection of protein allergens. We will discuss the analytical figures of merit for various disposable screen-printed affinity sensors in relation to methodologies employed for immobilization of bioreceptors on transducer surface.

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

    Institute of Scientific and Technical Information of China (English)


    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.

  15. Detection and correction of probe-level artefacts on microarrays

    Directory of Open Access Journals (Sweden)

    Petri Tobias


    Full Text Available Abstract Background A recent large-scale analysis of Gene Expression Omnibus (GEO data found frequent evidence for spatial defects in a substantial fraction of Affymetrix microarrays in the GEO. Nevertheless, in contrast to quality assessment, artefact detection is not widely used in standard gene expression analysis pipelines. Furthermore, although approaches have been proposed to detect diverse types of spatial noise on arrays, the correction of these artefacts is mostly left to either summarization methods or the corresponding arrays are completely discarded. Results We show that state-of-the-art robust summarization procedures are vulnerable to artefacts on arrays and cannot appropriately correct for these. To address this problem, we present a simple approach to detect artefacts with high recall and precision, which we further improve by taking into account the spatial layout of arrays. Finally, we propose two correction methods for these artefacts that either substitute values of defective probes using probeset information or filter corrupted probes. We show that our approach can identify and correct defective probe measurements appropriately and outperforms existing tools. Conclusions While summarization is insufficient to correct for defective probes, this problem can be addressed in a straightforward way by the methods we present for identification and correction of defective probes. As these methods output CEL files with corrected probe values that serve as input to standard normalization and summarization procedures, they can be easily integrated into existing microarray analysis pipelines as an additional pre-processing step. An R package is freely available from

  16. Worldwide food allergy labeling and detection of allergens in processed foods. (United States)

    Taylor, Steve L; Baumert, Joseph L


    The labeling of allergenic foods is an important public health measure to assist food-allergic consumers in avoiding foods that can cause allergic reactions. The regulatory framework for such labeling depends upon the selection of priority allergenic foods, which vary among countries. Most countries include milk, eggs, fish, crustacean shellfish, peanuts, tree nuts, soybeans, and cereal sources of gluten on the priority allergenic foods list, as recommended by the Codex Alimentarius Commission. However, a variety of other foods appear on the priority lists of some countries but not on others. Sesame seeds, molluscan shellfish, buckwheat, and mustard are identified in two or more countries. In most countries, all ingredients derived from these priority allergen sources must also be declared on labels by source. However, exemptions exist for some ingredients in some countries but not in others. Detection methods are critical for the enforcement of allergen labeling regulations and for the investigation of allergic reactions in the community by public health officials. The development of detection methods has advanced considerably over the past several decades and will be briefly reviewed in this chapter. Because of the emphasis on labeling and the development of detection methods, the ingredient statement on packaged food labels now contains more information than ever before to assist food-allergic consumers.

  17. Specific Antibodies for the Detection of Alternaria Allergens and the Identification of Cross-Reactive Antigens in Other Fungi (United States)

    Twaroch, Teresa E.; Curin, Mirela; Sterflinger, Katja; Focke-Tejkl, Margit; Swoboda, Ines; Valenta, Rudolf


    Background The mould Alternaria alternata is an important source of respiratory allergens. A. alternata extracts show great variations regarding allergenic potency. The aim of this study was to generate antibody probes specific for important Alternaria allergens and to use them to study allergen expression, depending on different culture conditions, as well as to search for cross-reactive allergens in other mould species. Methods Synthetic peptides from antigenic regions of A. alternata allergens (Alt a 1, Alt a 2, Alt a 3, Alt a 6 and Alt a 8) were used to raise highly specific rabbit antibodies. These antibodies and IgE from allergic patients were used to detect allergens by immunoblotting in extracts of 4 A. alternata strains grown under varying culturing conditions, in commercial skin-prick extracts and in closely (Cladosporium herbarum and Aureobasidium pullulans) or distantly related (Aspergillus niger and Penicillium chrysogenum) mould species. Results There was a wide variation of expression of the individual A. Alternata allergens, depending on the strain and culture conditions, but the antibody probes allowed us to distinguish strains and culture conditions with low and high allergen expression. In the commercial skin-prick solutions, varying levels of Alt a 1 were found, but no other allergens were detectable. Alt a 1 was identified as species-specific A. Alternata allergen, whereas Alt a 3, 6- and Alt a 8-cross-reactive antigens were found in C. herbarum and/or A. pullulans. Conclusions and Clinical Relevance Peptide-specific antibodies are useful to analyze diagnostic and therapeutic mould extracts, to study the presence of A. Alternata allergens in biological samples and to search for cross-reactive allergens in other mould species. PMID:27780168

  18. Validation of quantitative and qualitative methods for detecting allergenic ingredients in processed foods in Japan. (United States)

    Sakai, Shinobu; Adachi, Reiko; Akiyama, Hiroshi; Teshima, Reiko


    A labeling system for food allergenic ingredients was established in Japan in April 2002. To monitor the labeling, the Japanese government announced official methods for detecting allergens in processed foods in November 2002. The official methods consist of quantitative screening tests using enzyme-linked immunosorbent assays (ELISAs) and qualitative confirmation tests using Western blotting or polymerase chain reactions (PCR). In addition, the Japanese government designated 10 μg protein/g food (the corresponding allergenic ingredient soluble protein weight/food weight), determined by ELISA, as the labeling threshold. To standardize the official methods, the criteria for the validation protocol were described in the official guidelines. This paper, which was presented at the Advances in Food Allergen Detection Symposium, ACS National Meeting and Expo, San Diego, CA, Spring 2012, describes the validation protocol outlined in the official Japanese guidelines, the results of interlaboratory studies for the quantitative detection method (ELISA for crustacean proteins) and the qualitative detection method (PCR for shrimp and crab DNAs), and the reliability of the detection methods.

  19. Protein microarray applications: Autoantibody detection and posttranslational modification. (United States)

    Atak, Apurva; Mukherjee, Shuvolina; Jain, Rekha; Gupta, Shabarni; Singh, Vedita Anand; Gahoi, Nikita; K P, Manubhai; Srivastava, Sanjeeva


    The discovery of DNA microarrays was a major milestone in genomics; however, it could not adequately predict the structure or dynamics of underlying protein entities, which are the ultimate effector molecules in a cell. Protein microarrays allow simultaneous study of thousands of proteins/peptides, and various advancements in array technologies have made this platform suitable for several diagnostic and functional studies. Antibody arrays enable researchers to quantify the abundance of target proteins in biological fluids and assess PTMs by using the antibodies. Protein microarrays have been used to assess protein-protein interactions, protein-ligand interactions, and autoantibody profiling in various disease conditions. Here, we summarize different microarray platforms with focus on its biological and clinical applications in autoantibody profiling and PTM studies. We also enumerate the potential of tissue microarrays to validate findings from protein arrays as well as other approaches, highlighting their significance in proteomics.

  20. A novel multiplex method for the simultaneous detection and relative quantitation of pollen allergens. (United States)

    Morales, Sonia; Castro, Antonio Jesús; Jimenez-Lopez, Jose Carlos; Florido, Fernando; Rodríguez-García, María Isabel; de Dios Alché, Juan


    Standardization of pollen protein extracts is essential in order to ensure efficiency and safety in allergy diagnosis and immunotherapy. In this paper, we have optimized a multiplex Western blotting method for the simultaneous detection of four olive pollen allergens (Ole e 1, Ole e 2, Ole e 5, and Ole e 9) on a single blot using a monoclonal antibody from mouse and three polyclonal antibodies raised in rabbit. We utilized unconjugated Fab antibody fragments for blocking rabbit primary antibodies, and fluorescence-based detection. These changes allowed an accurate and reliable comparative quantitation of these allergens among pollen-protein samples from six olive cultivars. In addition, we also tested the IgE-binding capacity of these pollen extracts by reprobing the same blot with a pool of sera from eight patients allergic to olive and detection with enzyme conjugated antibodies. A noticeable variability regarding allergen content and IgE-reactivity was found among the olive cultivars analyzed. Moreover, we could easily confirm the identity of some of the IgE-binding proteins by simply overlapping both fluorescence and chemiluminescence images. This method is versatile since it can be applied to other allergogenic plant species and extended to other allergens.

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

    Directory of Open Access Journals (Sweden)

    Linda K. Medlin


    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.

  2. Testing a Microarray to Detect and Monitor Toxic Microalgae in Arcachon Bay in France. (United States)

    Kegel, Jessica U; Del Amo, Yolanda; Costes, Laurence; Medlin, Linda K


    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.

  3. Detection of Food Allergens by Taqman Real-Time PCR Methodology. (United States)

    García, Aina; Madrid, Raquel; García, Teresa; Martín, Rosario; González, Isabel


    Real-time PCR (polymerase chain reaction) has shown to be a very effective technology for the detection of food allergens. The protocol described herein consists on a real-time PCR assay targeting the plant ITS (Internal Transcribed Spacer) region, using species-specific primers and hydrolysis probes (Taqman) dual labeled with a reporter fluorophore at the 5' end (6-carboxyfluorescein, FAM) and a quencher fluorophore at the 3' end (Blackberry, BBQ). The species-specific real-time PCR systems (primers/probe) described in this work allowed the detection of different nuts (peanut, hazelnut, pistachio, almond, cashew, macadamia, walnut and pecan), common allergens present in commercial food products, with a detection limit of 0.1 mg/kg.

  4. Immunological cross-reactivity between four distant parvalbumins-Impact on allergen detection and diagnostics. (United States)

    Sharp, Michael F; Stephen, Juan N; Kraft, Lukas; Weiss, Thomas; Kamath, Sandip D; Lopata, Andreas L


    Fish are the largest and most diverse group of vertebrates. Fish are also a part of the eight food groups that cause the majority of IgE mediated food reactions. Detection tools for fish allergens are however limited due to the great diversity of fish species, despite fish allergy and its major allergen parvalbumin being well documented. The most commonly studied fish are frequently consumed in North America and Europe. However, much less is known about fish allergens in the Australasian region although fish is widely consumed in this region. A comprehensive phylogenetic analysis was performed of known parvalbumin amino acid sequences to determine possible candidate antigens for new cross-reactive antibodies to be used to detect most fish parvalbumins. Polyclonal rabbit antibodies were raised against parvalbumins from frequently consumed barramundi (Lates calcarifer), basa (Pangasius bocourti), pilchard (Sardinops sagax) and Atlantic salmon (Salmo salar). These were evaluated for cross-reactivity against a panel of 45 fish extracts (raw, heated and canned fish). Anti-barramundi parvalbumin proved to be the most cross-reactive antibody, detecting 87.5% of the 40 species analyzed, followed by anti-pilchard and anti-basa antibody. In contrast the anti-salmon antibody was very specific and only reacted to salmonidae and a few other fish. All analyzed fish species, except mahi mahi, swordfish, yellowfin tuna and all 5 canned fish had parvalbumin detected in raw extracts. However antibody reactivity to many fish was heat liable or susceptible to denaturation, demonstrating that some parvalbumins have most likely conformational epitopes, which lose antibody reactivity after heat treatment. We have demonstrated the generation of highly cross-reactive anti-parvalbumin antibodies that could be used for the detection of allergenic fish parvalbumin in contaminated food products. This cross-reactivity study thus shows processing of fish, especially canning, can have on impact

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


    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.

  6. 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


    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.

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

    Institute of Scientific and Technical Information of China (English)



    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

  8. Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration (United States)

    Romualdi, Chiara; Trevisan, Silvia; Celegato, Barbara; Costa, Germano; Lanfranchi, Gerolamo


    The variability of results in microarray technology is in part due to the fact that independent scans of a single hybridised microarray give spot images that are not quite the same. To solve this problem and turn it to our advantage, we introduced the approach of multiple scanning and of image integration of microarrays. To this end, we have developed specific software that creates a virtual image that statistically summarises a series of consecutive scans of a microarray. We provide evidence that the use of multiple imaging (i) enhances the detection of differentially expressed genes; (ii) increases the image homogeneity; and (iii) reveals false-positive results such as differentially expressed genes that are detected by a single scan but not confirmed by successive scanning replicates. The increase in the final number of differentially expressed genes detected in a microarray experiment with this approach is remarkable; 50% more for microarrays hybridised with targets labelled by reverse transcriptase, and 200% more for microarrays developed with the tyramide signal amplification (TSA) technique. The results have been confirmed by semi-quantitative RT–PCR tests. PMID:14627839

  9. Comparison of CIM discs and CPG glass as solid supports for bioanalytical columns used in allergen detection. (United States)

    Cevdek, Ana; Franko, Mladen


    This work presents a comparison of convective interaction media (CIM) and controlled pore glass (CPG) as solid supports for immunoglobulin antibodies used in bioanalytical detection of allergens in foodstuffs. A flow-injection manifold with highly sensitive thermal lens spectrometric detection was used for this purpose. Using beta-lactoglobulin, a milk allergen, as a model analyte, CIM disc supports had a higher linear range (0.2-3.5 microg L(-1)), better reproducibility (intra-day RSD = 1%, inter-day RSD = 10%), lower consumption of reagents, and better immunocolumn stability (1 month, over 240 injections of substrate), while providing comparable LODs (0.1 microg L(-1)). Application of CIM discs as solid supports in immunocolumns for allergen detection enables fast and sensitive screening of allergens in foodstuffs with sample throughput of up to eight samples per hour.

  10. Design and application of 60mer oligonucleotide microarray in SARS coronavirus detection

    Institute of Scientific and Technical Information of China (English)


    The 60mer oligonucleotide microarray was designed and applied to detecting of SARS (severe acute respiratory syndrome) coronavirus. Thirty 60mer specific oligos were designed to cover the whole genome of the first submitted coronavirus strain, according to the sequence of TOR2 (GENEBANK Accession: AY274119). These primers were synthesized and printed into a microarray with 12×12 spots. RNAs were extracted from the throat swab and gargling fluid of SARS patients and reverse-transcripted into the double strand cDNAs. The cDNAs were prepared as restricted cDNA fragments by the restriction display (RD) technique and labeled by PCR with the Cy5-universal primer. The labeled samples were then applied to the oligo microarray for hybridization. The diagnostic capability of the microarray was evaluated after the washing and scanning steps. The scanning result showed that samples of SARS patients were hybridized with multiple SARS probes on the microarray, and there is no signal on the negative and blank controls. These results indicate that the genome of SARS coronavirus can be detected in parallel by the 60mer oligonucleotide microarray, which can improve the positive ratio of the diagnosis. The oligo microarray can also be used for monitoring the behavior of the virus genes in different stages of the disease status.

  11. Development and application of antibody microarray for white spot syndrome virus detection in shrimp

    Institute of Scientific and Technical Information of China (English)

    XU Xiaoli; SHENG Xiuzhen; ZHAN Wenbin


    Detecting white spot syndrome virus (WSSV) in shrimp in high efficiency and veracity is important for disease prevention in aquaculture.Antibody-based microarray is a novel proteomic technology that can meet the requirements.In this study,we developed an antibody microarray for WSSV-detection in a specific and parallel way at multiple samples.First,seven slides each with different modifications were characterized by atomic force microscope,and were compared in the efficiency of immobilizing proteins.Of the seven,3-dimensional structured agarose gel-modified slides were chosen appropriate for the microarray for having higher signal value and superior spot size.A purified rabbit anti-WSSV antibody was arrayed as the capture antibody of the microarray on the agarose gel-modified slides,and then the microarray slides were incubated in the tissue homogenate of sampled shrimp and the antibody-antigen complex was detected by Cy3-conjugated anti-WSSV monoclonal antibody.The results were measured by a laser chipscanner and analyzed with software.To obtain satisfied fluorescence signal intensity,optimal conditions were searched.The detection limit of the antibody microarray for WSSV is 0.62 μg/mL,with a proven long shelf life for 6 months at 4℃ or 8 months at -20℃.Furthermore,concordance between antibody microarray and traditional indirect ELISA reached 100% for WSSV detection.These results suggest that the antibody microarray could be served as an effective tool for diagnostic and epidemiological studies of WSSV.

  12. Identification of hidden allergens: detection of pistachio traces in mortadella. (United States)

    Barbieri, G; Frigeri, G


    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.

  13. Immunoblotting technique for the detection of allergens of Aspergillus fumigatus: influence of Nonidet P-40 on the sensitivity. (United States)

    Wijnands, L M; Deisz, W D; van Leusden, F M


    Immunoblotting provides a useful technique for the study of antigens, antibodies and allergens. To overcome problems regarding the loss of antigenic properties during the blotting and developing procedures, several solutions have been described. The inclusion of Nonidet P-40, recommended to increase the sensitivity of developing procedures for immunoblots, in an existing procedure for the detection of allergens of Aspergillus fumigatus, however, led to decreased sensitivity of the method.

  14. DNA-based analytical strategies for the detection of genetically modified organisms and of allergens in foods


    Hahn, Alexandra


    DNA-based methodologies have become an integral part of food and feed analysis and are commonly applied in different fields such as the analysis of genetically modified organisms (GMO) and the detection of allergens. The method development performed in this study was focussed on novel strategies meeting different demands of GMO and allergen analysis. The new ligation-dependent probe amplification (LPA) technique and the established real-time PCR technology were used to develop and to validate...

  15. Development of a new hazelnut sandwich ELISA based on detection of Cor a 9, a major hazelnut allergen


    Trashin, Stanislav; Cucu, Tatiana; Devreese, Bart; De Meulenaer, Bruno


    The emerging health problem of food-induced allergic reactions, including life-threatening anaphylaxis, presents an important challenge to the food. In the framework of the current ALLERRISK project, analytical approaches for allergen detection are evaluated and developed. Cor a 9 is a major hazelnut protein with nutrient reservoir function, and that also known as a major food allergen. Presence of Cor a 9 indicates contamination of a product with hazelnut and, consequently, potential risk of...

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

    DEFF Research Database (Denmark)

    Han, Anpan; Dufva, Martin; Belleville, Erik


    Microarray hybridization or antibody binding can be detected by many techniques, however, only a few are suitable for widespread use since many of these detection techniques rely on bulky and expensive instruments. Here, we describe the usefulness of a simple and inexpensive detection method base...

  17. A comparison of intradermal testing and detection of allergen-specific immunoglobulin E in serum by enzyme-linked immunosorbent assay in horses affected with skin hypersensitivity. (United States)

    Morgan, Erin E; Miller, William H; Wagner, Bettina


    Skin hypersensitivities (allergies) in horses are often diagnosed using clinical signs only. Intradermal testing or serological assays are diagnostic options to confirm the allergic nature of the disease and to identify the allergen(s). Our objective was to develop an allergen-specific enzyme-linked immunosorbent assay (ELISA) using a monoclonal antibody specific for horse IgE and to examine its potential for allergen detection in serum in comparison to intradermal testing. Intradermal testing with 61 allergen extracts was performed on 10 horses affected with skin hypersensitivity. Their sera were analyzed by ELISA for IgE antibodies to the same allergens. The kappa test of concordance was used for comparison of the results of both tests. Out of 61 allergen extracts, only two (Timothy and Quack) had kappa values greater than 0.60, suggesting a substantial agreement between skin testing and IgE ELISA. The statistical comparison of the remaining 59 allergens showed little or no concordance between the tests beyond chance. To identify parameters that may influence the sensitivity of the ELISA, the assay was modified to detect allergen-specific IgGb and IgG(T) in serum, and the protein content in all allergen extracts was determined by SDS-PAGE. The commercial allergen extracts revealed a high variation in detectable protein. High concentrations of allergen-specific IgG in horse serum were found to compete with IgE for binding to the plates. In conclusion, an ELISA using whole serum and crude allergen preparations provides limited diagnostic information in horses. The reliable diagnosis of allergens in equine skin hypersensitivity is essential to improve allergen-specific treatments, such as hyposensitization, or the development of allergy vaccines.

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


    Alvaro Díaz-Badillo; María de Lourdes Muñoz; Gerardo Perez-Ramirez; Victor Altuzar; Juan Burgueño; Mendoza-Alvarez, Julio G.; Martínez-Muñoz, Jorge P.; Alejandro Cisneros; Joel Navarrete-Espinosa; Feliciano Sanchez-Sinencio


    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 hybrid...

  19. Soybean allergen detection methods--a comparison study

    DEFF Research Database (Denmark)

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


    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...

  20. Detection of allergenic ingredients using real-time PCR: a case study on hazelnut (Corylus avellena) and soy (Glycine max). (United States)

    Platteau, Céline; De Loose, Marc; De Meulenaer, Bruno; Taverniers, Isabel


    Compliance with the European allergen labeling legislation (Directive 2007/68/EC) is only possible when coupled with appropriate methods to detect allergens in food. The aim of the current study was to develop new real-time PCR assays for the detection of hazelnut and soy and evaluate these assays via comparison with commercially available kits. Although the new assays were not as sensitive as the commercial qualitative assays, they proved to be more specific. Moreover, the cross-reactivity study indicated contamination of some of the food products used with either hazelnut or soy, which presents a risk for the allergic consumer. The assays were able to quantify as few as 5-15 genome copies. This unit, used to express analytical results for allergen detection by means of PCR, needs to be converted to a unit expressing the amount of allergenic ingredient in order to be informative. This study emphasizes that the use of real-time PCR for allergen quantification is complicated by the lack of appropriate reference materials for allergens.

  1. Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays. (United States)

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


    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.

  2. Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays

    Directory of Open Access Journals (Sweden)

    Hultman Jenni


    Full Text Available Abstract Background Nucleic acid detection based on ligation reaction or single nucleotide extension of ssDNA probes followed by tag microarray hybridization provides an accurate and sensitive detection tool for various diagnostic purposes. Since microarray quality is crucial for reliable detection, these methods can benefit from correcting for microarray artefacts using specifically adapted techniques. Findings Here we demonstrate the application of a per-spot hybridization control oligonucleotide probe and a novel way of computing normalization for tag array data. The method takes into account the absolute value of the detection probe signal and the variability in the control probe signal to significantly alleviate problems caused by artefacts and noise on low quality microarrays. Conclusions Diagnostic microarray platforms require experimental and computational tools to enable efficient correction of array artefacts. The techniques presented here improve the signal to noise ratio and help in determining true positives with better statistical significance and in allowing the use of arrays with poor quality that would otherwise be discarded.

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

    Institute of Scientific and Technical Information of China (English)


    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.

  4. 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.

  5. Effects of Microwave and Ultrasound Assisted Extraction on the Recovery of Soy Proteins for Soy Allergen Detection. (United States)

    Amponsah, Amma; Nayak, Balunkeswar


    The extraction of soy proteins for soy allergen detections is conventionally achieved with PBS buffer for at least 2 h at room temperature or 4 °C. This method has been reported to be inefficient due to time consumption and inadequate protein extraction resulting in false negative allergen detection and mislabeling of foods containing allergenic proteins. This study investigated the application of microwave (MAE) and ultrasound assisted extraction (UAE) techniques to extract and improve recovery of allergens from various soy matrices. Soy proteins were extracted from raw soy flour, soy protein isolate (SPI) and soy milk using MAE at 60, 70, and 100 °C for 5 and 10 min and UAE at 4 and 23 °C for extraction times of 1, 5, and 10 min with PBS, Laemmli and urea buffers. Extracts were analyzed for total proteins, protein profile, and antibody-based detection (ELISA) of soy proteins. Conventional extraction with each of the buffers was used as controls. Overall, proteins recovered from MAE and UAE samples were higher than recoveries from the controls in all soy matrices. Under all extraction conditions, Laemmli and urea buffer recovered more proteins than PBS. Electrophoresis analysis of protein showed bands around 75, 50, and 33 kDa indicating the presence of soy allergenic proteins β-conglycinin and glycinin, in all samples. Using sandwich ELISA, control and UAE extracts resulted in high soy protein detection but this reduced in MAE extracts.

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


    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.

  7. Development of a DNA-based microarray for the detection of zoonotic pathogens in rodent species. (United States)

    Giles, Timothy; Yon, Lisa; Hannant, Duncan; Barrow, Paul; Abu-Median, Abu-Bakr


    The demand for diagnostic tools that allow simultaneous screening of samples for multiple pathogens is increasing because they overcome the limitations of other methods, which can only screen for a single or a few pathogens at a time. Microarrays offer the advantages of being capable to test a large number of samples simultaneously, screening for multiple pathogen types per sample and having comparable sensitivity to existing methods such as PCR. Array design is often considered the most important process in any microarray experiment and can be the deciding factor in the success of a study. There are currently no microarrays for simultaneous detection of rodent-borne pathogens. The aim of this report is to explicate the design, development and evaluation of a microarray platform for use as a screening tool that combines ease of use and rapid identification of a number of rodent-borne pathogens of zoonotic importance. Nucleic acid was amplified by multiplex biotinylation PCR prior to hybridisation onto microarrays. The array sensitivity was comparable to standard PCR, though less sensitive than real-time PCR. The array presented here is a prototype microarray identification system for zoonotic pathogens that can infect rodent species.

  8. 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

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

    Directory of Open Access Journals (Sweden)

    Alvaro Díaz-Badillo


    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.

  10. A DNA Microarray-Based Assay to Detect Dual Infection with Two Dengue Virus Serotypes (United States)

    Díaz-Badillo, Alvaro; de Lourdes Muñoz, María; Perez-Ramirez, Gerardo; Altuzar, Victor; Burgueño, Juan; Mendoza-Alvarez, Julio G.; Martínez-Muñoz, Jorge P.; Cisneros, Alejandro; Navarrete-Espinosa, Joel; Sanchez-Sinencio, Feliciano


    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. PMID:24776933

  11. Rapid and highly sensitive detection of malaria-infected erythrocytes using a cell microarray chip.

    Directory of Open Access Journals (Sweden)

    Shouki Yatsushiro

    Full Text Available BACKGROUND: Malaria is one of the major human infectious diseases in many endemic countries. For prevention of the spread of malaria, it is necessary to develop an early, sensitive, accurate and conventional diagnosis system. METHODS AND FINDINGS: A cell microarray chip was used to detect for malaria-infected erythrocytes. The chip, with 20,944 microchambers (105 µm width and 50 µm depth, was made from polystyrene, and the formation of monolayers of erythrocytes in the microchambers was observed. Cultured Plasmodium falciparum strain 3D7 was used to examine the potential of the cell microarray chip for malaria diagnosis. An erythrocyte suspension in a nuclear staining dye, SYTO 59, was dispersed on the chip surface, followed by 10 min standing to allow the erythrocytes to settle down into the microchambers. About 130 erythrocytes were accommodated in each microchamber, there being over 2,700,000 erythrocytes in total on a chip. A microarray scanner was employed to detect any fluorescence-positive erythrocytes within 5 min, and 0.0001% parasitemia could be detected. To examine the contamination by leukocytes of purified erythrocytes from human blood, 20 µl of whole blood was mixed with 10 ml of RPMI 1640, and the mixture was passed through a leukocyte isolation filter. The eluted portion was centrifuged at 1,000×g for 2 min, and the pellet was dispersed in 1.0 ml of medium. SYTO 59 was added to the erythrocyte suspension, followed by analysis on a cell microarray chip. Similar accommodation of cells in the microchambers was observed. The number of contaminating leukocytes was less than 1 on a cell microarray chip. CONCLUSION: The potential of the cell microarray chip for the detection of malaria-infected erythrocytes was shown, it offering 10-100 times higher sensitivity than that of conventional light microscopy and easy operation in 15 min with purified erythrocytes.

  12. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms. (United States)

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


    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.

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

    LENUS (Irish Health Repository)

    Scheler, Ott


    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.

  14. Detection and analysis system for hybridization images of lab-in-a-tube microarray

    Institute of Scientific and Technical Information of China (English)

    LIU Quanjun; ZHOU Qin; BAI Yunfei; GE Qinyu; LU Zuhong


    A lab-in-a-tube microarray system is developed for sample inspection and signal detection by fabricating a flat transparent window cap of the Eppendorf tube. The oli- gonucleotide microarray is immobilized on the inner surface of the cap. A small vessel is placed in an Eppendorf tube for storing hybridization solutions. With the microarray system, the full biochemical processes, including gene fragment amplification, fluorescence labeling, hybridization, and fluorescence detection, have been performed in the sealed tube without opening the cap. The images are obtained from a fluorescence microscope and captured by a CCD, and the data are transported to a computer through the universal serial bus (USB). After noise reduction, signal intensity is determined from hybridization image and the presence of gene fragments is identified. The final data output includes sample information, process steps, and hybridization results. A lab-in- a-tube microarray system for detecting ten respiratory viruses at a single detection is designed. High detection throug- hput and accuracy have been demonstrated with the system.

  15. 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.


    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

  16. Surface-activated microtiter-plate microarray for simultaneous CRP quantification and viral antibody detection. (United States)

    Viitala, Sari M; Jääskeläinen, Anne J; Kelo, Eira; Sirola, Helena; Moilanen, Kirsi; Suni, Jukka; Vaheri, Antti; Vapalahti, Olli; Närvänen, Ale


    Microarrays are widely used in high-throughput DNA and RNA hybridization tests and recently adopted to protein and small molecule interaction studies in basic research and diagnostics. Parallel detection of serum antibodies and antigens has several potential applications in epidemiologic research, vaccine development, and in the diagnosis of allergies, autoimmunity, and infectious diseases. This study demonstrates an immobilization method for immunoassay-based microarray in conventional 96-well polystyrene plates for a serologic diagnostic method combined with quantitative C-reactive protein (CRP) assay. A synthetic peptide (HIV-1), a recombinant protein (Puumala hantavirus nucleocapsid), and purified virus preparations (Sindbis and adenoviruses) were used as antigens for virus-specific antibody detection and monoclonal anti-CRP antibody for antigen detection. The microarray was based on conventional enzyme immunoassays and densitometry from photographed results. Peptide and recombinant antigens functioned well, while whole virus antigens gave discrepant results in 1 out of 23 samples from the reference method, tested with human sera with various antibody responses. The CRP results were in concordance in the concentration range 0.5-150 mg/L with 2 commercially available CRP assays: ReaScan rapid test (R(2) = 0.9975) and Cobas 6000 analyzer (R(2) =0.9595). The results indicate that microtiter plates provide a promising platform for further development of microarrays for parallel antibody and antigen detection.

  17. Renaturation of blotted allergens increases the sensitivity of specific IgE detection. (United States)

    Muro, M D; Fernández, C; Moneo, I


    Several authors have demonstrated that renaturation is an essential step for the appropriate recognition of blotted proteins. The use of nonionic detergents has been described as a useful alternative to enhance the antigenicity in immunoblotting, although elution from proteins by detergents has been observed. To measure the influence of different factors on the sensitivity of specific IgE by immunoblotting, we used twenty human sera from atopic patients who were allergic or nonallergic to a common, reliable allergen (grass pollen mixture). The use of Nonidet-P40 was found to be a useful alternative for the renaturation of the allergens. No elution from the membrane was found when employing this detergent, even at high concentrations (3%), and its use gave better sensitivity than methanol. On the other hand, we detected that methanol possessed renaturing properties. A transfer method using diffusion instead of electric transfer gave the best results and two membranes could be obtained from each gel. Using this method, we found that after NP-40 incubation of the membrane, the use of bovine albumin could be omitted as blocking agent and that its use had even deleterious effects.

  18. Easy and fast detection and genotyping of high-risk human papillomavirus by dedicated DNA microarrays. (United States)

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


    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.

  19. Food Microbial Pathogen Detection and Analysis Using DNA Microarray Technologies


    Rasooly, Avraham; Herold, Keith E.


    Culture-based methods used for microbial detection and identification are simple to use, relatively inexpensive, and sensitive. However, culture-based methods are too time-consuming for high-throughput testing and too tedious for analysis of samples with multiple organisms and provide little clinical information regarding the pathogen (e.g., antibiotic resistance genes, virulence factors, or strain subtype). DNA-based methods, such as polymerase chain reaction (PCR), overcome some these limit...

  20. Nanoparticle probes and mid-infrared chemical imaging for DNA microarray detection. (United States)

    Mossoba, Magdi M; Al-Khaldi, Sufian F; Schoen, Brianna; Yakes, Betsy Jean


    To date most mid-infrared spectroscopic studies have been limited, due to lack of sensitivity, to the structural characterization of a single oligonucleotide probe immobilized over the entire surface of a gold-coated slide or other infrared substrate. By contrast, widely used and commercially available glass slides and a microarray spotter that prints approximately 120-μm-diameter DNA spots were employed in the present work. To our knowledge, mid-infrared chemical imaging (IRCI) in the external reflection mode has been applied in the present study for the first time to the detection of nanostructure-based DNA microarrays spotted on glass slides. Alkyl amine-modified oligonucleotide probes were immobilized on glass slides that had been prefunctionalized with succinimidyl ester groups. This molecular fluorophore-free method entailed the binding of gold-nanoparticle-streptavidin conjugates to biotinylated DNA targets. Hybridization was visualized by the silver enhancement of gold nanoparticles. The adlayer of silver, selectively bound only to hybridized spots in a microarray, formed the external reflective infrared substrate that was necessary for the detection of DNA hybridization by IRCI in the present proof-of-concept study. IRCI made it possible to discriminate between diffuse and specular external reflection modes. The promising qualitative results are presented herein, and the implications for quantitative determination of DNA microarrays are discussed.

  1. [Development of single base extension-tags microarray for the detection of food-borne pathogens]. (United States)

    Lu, Changyong; Shi, Chunlei; Zhang, Chunxiu; Chen, Jing; Shi, Xianming


    We developed single base extension-tags (SBE-tags) microarray to detect eight common food-borne pathogens, including Staphylococcus aureus, Vibrio parahaemolyticus, Listeria monocytogenes, Salmonella, Enterobacter sakazaki, Shigella, Escherichia coli O157:H7 and Campylobacter jejuni. With specific PCR primers identified and integrated for eight food-borne pathogens, target sequences were amplified and purified as template DNA of single base extension-tags reaction. The products were hybridized to microarrays and scanned for fluorescence intensity. The experiment showed a specific and simultaneous detection of eight food-borne pathogens. The system limits is 0.1 pg for a genomic DNA and 5x10(2) CFU/mL for Salmonella typhimurium cultures. The single base extension-tags assay can be used to detect food-borne pathogens rapidly and accurately with a high sensitivity, and provide an efficient way for diagnosis and control of disease caused by food-borne pathogens.

  2. Real Time PCR to detect hazelnut allergen coding sequences in processed foods. (United States)

    Iniesto, Elisa; Jiménez, Ana; Prieto, Nuria; Cabanillas, Beatriz; Burbano, Carmen; Pedrosa, Mercedes M; Rodríguez, Julia; Muzquiz, Mercedes; Crespo, Jesús F; Cuadrado, Carmen; Linacero, Rosario


    A quantitative RT-PCR method, employing novel primer sets designed on Cor a 9, Cor a 11 and Cor a 13 allergen-coding sequences has been setup and validated. Its specificity, sensitivity and applicability have been compared. The effect of processing on detectability of these hazelnut targets in complex food matrices was also studied. The DNA extraction method based on CTAB-phenol-chloroform was the best for hazelnut. RT-PCR using primers for Cor a 9, 11 and 13 allowed a specific and accurate amplification of these sequences. The limit of detection was 1 ppm of raw hazelnut. The method sensitivity and robustness were confirmed with spiked samples. Thermal treatments (roasting and autoclaving) reduced yield and amplificability of hazelnut DNA, however, high-hydrostatic pressure did not affect. Compared with an ELISA assay, this RT-PCR showed higher sensitivity to detected hazelnut traces in commercial foodstuffs. The RT-PCR method described is the most sensitive of those reported for the detection of hazelnut traces in processed foods.

  3. 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


    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.

  4. A Strategy to Optimize the Oligo-Probes for Microarray-based Detection of Viruses

    Institute of Scientific and Technical Information of China (English)


    DNA microarrays have been acknowledged to represent a promising approach for the detection of viral pathogens. However, the probes designed for current arrays could cover only part of the given viral variants, that could result in false-negative or ambiguous data. If all the variants are to be covered, the requirement for more probes would render much higher spot density and thus higher cost of the arrays. Here we have developed a new strategy for oligonucleotide probe design. Using type I human immunodeficiency virus (HIV-1) tat gene as an example, we designed the array probes and validated the optimized parameters in silico. Results show that the oligo number is significantly reduced comparing with the existing methods, while specificity and hybridization efficiency remain intact. The adoption of this method in reducing the oligo numbers could increase the detection capacity for DNA microarrays, and would significantly lower the manufacturing cost for making array chips.

  5. Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens. (United States)

    Kostić, Tanja; Sessitsch, Angela


    Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples.

  6. Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial Pathogens

    Directory of Open Access Journals (Sweden)

    Tanja Kostić


    Full Text Available Reliable and sensitive pathogen detection in clinical and environmental (including food and water samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i specificity; (ii sensitivity; (iii multiplexing potential; (iv robustness; (v speed; (vi automation potential; and (vii low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples.

  7. A method for detecting and correcting feature misidentification on expression microarrays (United States)

    Tu, I-Ping; Schaner, Marci; Diehn, Maximilian; Sikic, Branimir I; Brown, Patrick O; Botstein, David; Fero, Michael J


    Background Much of the microarray data published at Stanford is based on mouse and human arrays produced under controlled and monitored conditions at the Brown and Botstein laboratories and at the Stanford Functional Genomics Facility (SFGF). Nevertheless, as large datasets based on the Stanford Human array began to accumulate, a small but significant number of discrepancies were detected that required a serious attempt to track down the original source of error. Due to a controlled process environment, sufficient data was available to accurately track the entire process leading to up to the final expression data. In this paper, we describe our statistical methods to detect the inconsistencies in microarray data that arise from process errors, and discuss our technique to locate and fix these errors. Results To date, the Brown and Botstein laboratories and the Stanford Functional Genomics Facility have together produced 40,000 large-scale (10–50,000 feature) cDNA microarrays. By applying the heuristic described here, we have been able to check most of these arrays for misidentified features, and have been able to confidently apply fixes to the data where needed. Out of the 265 million features checked in our database, problems were detected and corrected on 1.3 million of them. Conclusion Process errors in any genome scale high throughput production regime can lead to subsequent errors in data analysis. We show the value of tracking multi-step high throughput operations by using this knowledge to detect and correct misidentified data on gene expression microarrays. PMID:15357875

  8. A method for detecting and correcting feature misidentification on expression microarrays

    Directory of Open Access Journals (Sweden)

    Brown Patrick O


    Full Text Available Abstract Background Much of the microarray data published at Stanford is based on mouse and human arrays produced under controlled and monitored conditions at the Brown and Botstein laboratories and at the Stanford Functional Genomics Facility (SFGF. Nevertheless, as large datasets based on the Stanford Human array began to accumulate, a small but significant number of discrepancies were detected that required a serious attempt to track down the original source of error. Due to a controlled process environment, sufficient data was available to accurately track the entire process leading to up to the final expression data. In this paper, we describe our statistical methods to detect the inconsistencies in microarray data that arise from process errors, and discuss our technique to locate and fix these errors. Results To date, the Brown and Botstein laboratories and the Stanford Functional Genomics Facility have together produced 40,000 large-scale (10–50,000 feature cDNA microarrays. By applying the heuristic described here, we have been able to check most of these arrays for misidentified features, and have been able to confidently apply fixes to the data where needed. Out of the 265 million features checked in our database, problems were detected and corrected on 1.3 million of them. Conclusion Process errors in any genome scale high throughput production regime can lead to subsequent errors in data analysis. We show the value of tracking multi-step high throughput operations by using this knowledge to detect and correct misidentified data on gene expression microarrays.

  9. DNA microarray-based detection of multiple pathogens: Mycoplasma spp. and Chlamydia spp. (United States)

    Schnee, Christiane; Sachse, Konrad


    Rapid detection of slow-growing or non-culturable microorganisms, such as Mycoplasma spp. and Chlamydia spp., is still a challenge to diagnosticians in the veterinary field. In addition, as epidemiological evidence on the frequency of mixed infections involving two and more bacterial species has been emerging, detection methods allowing simultaneous identification of different pathogens are required. In the present chapter, we describe DNA microarray-based procedures for the detection of 83 Mollicutes species (Mycoplasma assay) and 11 Chlamydia spp. (Chlamydia assay). The assays are suitable for use in a routine diagnostic environment, as well as in microbiological research.

  10. Genomic Imbalances in Neonates With Birth Defects: High Detection Rates by Using Chromosomal Microarray Analysis (United States)

    Lu, Xin-Yan; Phung, Mai T.; Shaw, Chad A.; Pham, Kim; Neil, Sarah E.; Patel, Ankita; Sahoo, Trilochan; Bacino, Carlos A.; Stankiewicz, Pawel; Lee Kang, Sung-Hae; Lalani, Seema; Chinault, A. Craig; Lupski, James R.; Cheung, Sau W.; Beaudet, Arthur L.


    OBJECTIVES Our aim was to determine the frequency of genomic imbalances in neonates with birth defects by using targeted array-based comparative genomic hybridization, also known as chromosomal microarray analysis. METHODS Between March 2006 and September 2007, 638 neonates with various birth defects were referred for chromosomal microarray analysis. Three consecutive chromosomal microarray analysis versions were used: bacterial artificial chromosome-based versions V5 and V6 and bacterial artificial chromosome emulated oligonucleotide-based version V6 Oligo. Each version had targeted but increasingly extensive genomic coverage and interrogated >150 disease loci with enhanced coverage in genomic rearrangement-prone pericentromeric and subtelomeric regions. RESULTS Overall, 109 (17.1%) patients were identified with clinically significant abnormalities with detection rates of 13.7%, 16.6%, and 19.9% on V5, V6, and V6 Oligo, respectively. The majority of these abnormalities would not be defined by using karyotype analysis. The clinically significant detection rates by use of chromosomal microarray analysis for various clinical indications were 66.7% for “possible chromosomal abnormality” ± “others” (other clinical indications), 33.3% for ambiguous genitalia ± others, 27.1% for dysmorphic features + multiple congenital anomalies ± others, 24.6% for dysmorphic features ± others, 21.8% for congenital heart disease ± others, 17.9% for multiple congenital anomalies ± others, and 9.5% for the patients referred for others that were different from the groups defined. In all, 16 (2.5%) patients had chromosomal aneuploidies, and 81 (12.7%) patients had segmental aneusomies including common microdeletion or microduplication syndromes and other genomic disorders. Chromosomal mosaicism was found in 12 (1.9%) neonates. CONCLUSIONS Chromosomal microarray analysis is a valuable clinical diagnostic tool that allows precise and rapid identification of genomic imbalances

  11. Detection of low-molecular weight allergens resolved on two-dimensional electrophoresis with acid-urea polyacrylamide gel. (United States)

    Kitta, Kazumi; Ohnishi-Kameyama, Mayumi; Moriyama, Tatsuya; Ogawa, Tadashi; Kawamoto, Shinichi


    Two-dimensional electrophoresis with immobilized pH gradient (IPG) followed by acetic acid/urea-polyacrylamide gel electrophoresis (AU-PAGE) was developed for the detection of low-molecular weight food allergens. Wheat proteins were used to test the applicability of AU-PAGE for the analysis of food allergens. Isoelectric focusing (IEF) for first dimension was performed with IPG pH 3-10. AU-PAGE was performed as a second-dimensional electrophoresis and high resolution was obtained, especially for proteins below 15 kDa. For immunodetection, the proteins resolved on AU gel were transferred to a polyvinylidene difluoride membrane. The assembly of semidry electroblotting for AU gel was set reversed as for sodium dodecyl sulfate (SDS)-PAGE gel. The electroblotted membrane was immunolabeled with serum from a radio-allergosorbent test-positive individual for wheat to identify allergenic proteins. Protein spots strongly recognized by the patient's serum were chosen for further analysis. Mass spectrometry analysis revealed that these proteins were alpha-amylase/trypsin inhibitors and lipid transfer protein. The system developed in this study was shown to be useful as a standard protocol for the separation of low-molecular weight proteins. Moreover, the IPG strips on which IEF was performed could be used either for SDS-PAGE or AU-PAGE by only changing equilibrating conditions, allowing for a wide range of allergen analysis.

  12. Development and Clinical Evaluation of a Highly Sensitive DNA Microarray for Detection and Genotyping of Human Papillomaviruses (United States)

    Oh, TaeJeong; Kim, ChangJin; Woo, SukKyung; Kim, TaeSeung; Jeong, DongJun; Kim, MyungSoon; Lee, Sunwoo; Cho, HyunSill; An, Sungwhan


    Human papillomavirus (HPV) has been found in cervical cancer, tonsillar cancer, and certain types of head and neck cancers. We report on a DNA microarray-based method for the simultaneous detection and typing of HPVs. The genotype spectrum discriminated by this HPV DNA microarray includes 15 high-risk HPV genotypes and 12 low-risk HPV genotypes. The HPV DNA microarray showed high degrees of specificity and reproducibility. We evaluated the performance of the HPV DNA microarray by application to three HPV-positive cell lines (HeLa, Caski, and SiHa cells) and two HPV-negative cell lines (C33A and A549 cells). The HPV DNA microarray successfully identified the known types of HPV present in the cell lines. The detection limit of the HPV DNA microarray was at least 100-fold higher than that of PCR. To assess the clinical applicability of the HPV DNA microarray, we performed the HPV genotyping assay with 73 nonmalignant and malignant samples from 39 tonsillar cancer patients. Twenty-five of the 39 (64.1%) malignant samples were positive for HPV, whereas 3 of 34 (8.8%) nonmalignant samples were positive for HPV. This result shows a preferential association of HPV with tonsillar carcinomas. The correlations of the presence of HPV with the grade of differentiation and risk factors were not significant. Our data show that the HPV DNA microarray may be useful for the diagnosis and typing of HPV in large-scale epidemiological studies. PMID:15243092

  13. Rapid Detection of rpoB Gene Mutations in Rif-resistant M.tuberculosis Isolates by Obligonucleotide Microarray

    Institute of Scientific and Technical Information of China (English)



    Objective To detect the specific mutations in rpoB gene of Mycobacterium tuberculosis by oligonucleotide microarray.Methods Four wild-type and 8 mutant probes were used to detect rifampin resistant strains.Target DNA of M.tuberculosis was amplified by PCR,hybridized and scanned.Direct sequencing was performed to verify the results of oligonuclcotide microarray.Results of the 102 rifampin-resistant strains 98 (96.1%) had mutations in the rpoB genes. Conclusion Oligonucleotide microarray with mutation-specific probes is a reliable and useful tool for the rapid and accurate diagnosis of rifampin resistance in M.tuberculosis isolates.

  14. Disposable electrochemical DNA-array for PCR amplified detection of hazelnut allergens in foodstuffs. (United States)

    Bettazzi, Francesca; Lucarelli, Fausto; Palchetti, Ilaria; Berti, Francesca; Marrazza, Giovanna; Mascini, Marco


    An electrochemical low-density DNA-array has been designed and implemented to be used in combination with polymerase chain reaction (PCR) in order to investigate the presence of hazelnut major allergens (Cor a 1.04, Cor a 1.03) in foodstuff. Unmodified PCR products were captured at the sensor interface via sandwich hybridization with surface-tethered probes and biotinylated signalling probes. The resulting biotinylated hybrids were coupled with a streptavidin-alkaline phosphatase conjugate and then exposed to a alpha-naphthyl phosphate solution. Differential pulse voltammetry was finally used to detect the alpha-naphthol signal. The detection limits for Cor a 1.03 and Cor a 1.04 were 0.3 and 0.1 nmol L(-1), respectively (R.S.D. 10%). The optimized conditions were used to test several commercially available foodstuffs, claiming to contain or not the targeted nuts. The results were compared with those obtained with classical ELISA tests.

  15. Detection of parvalbumin, a common fish allergen gene in food, by real-time polymerase chain reaction. (United States)

    Sun, Min; Liang, Chengzhu; Gao, Hongwei; Lin, Chao; Deng, Mingjun


    Fish, as one of the most common causes of IgE-mediated food hypersensitivity, has recently received increasing attention from the food industry and legislative and regulatory agencies. A real-time polymerase chain reaction assay based on TaqMan-MGB probe technology was developed for the detection of parvalbumin, a major fish allergen gene. The assay had a sensitivity up to 5 pg purified fish DNA and had no cross-reaction with other species, such as cattle, sheep, swine, chicken, shrimp, lobster, crab, squid, clam, rice, soybean, maize, and potato. The coefficient of variation for both intra- and interexperimental variability demonstrated high reproducibility and accuracy. The assay proved to be a potential tool for the detection and label management of fish allergens in food.

  16. A new oligonucleotide microarray for detection of pathogenic and non-pathogenic Legionella spp. (United States)

    Cao, Boyang; Liu, Xiangqian; Yu, Xiang; Chen, Min; Feng, Lu; Wang, Lei


    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.

  17. A universal microarray detection method for identification of multiple Phytophthora spp. using padlock probes. (United States)

    Sikora, Katarzyna; Verstappen, Els; Mendes, Odette; Schoen, Cor; Ristaino, Jean; Bonants, Peter


    The genus Phytophthora consists of many species that cause important diseases in ornamental, agronomic, and forest ecosystems worldwide. Molecular methods have been developed for detection and identification of one or several species of Phytophthora in single or multiplex reactions. In this article, we describe a padlock probe (PLP)-based multiplex method of detection and identification for many Phytophthora spp. simultaneously. A generic TaqMan polymerase chain reaction assay, which detects all known Phytophthora spp., is conducted first, followed by a species-specific PLP ligation. A 96-well-based microarray platform with colorimetric readout is used to detect and identify the different Phytophthora spp. PLPs are long oligonucleotides containing target complementary sequence regions at both their 5' and 3' ends which can be ligated on the target into a circular molecule. The ligation is point mutation specific; therefore, closely related sequences can be differentiated. This circular molecule can then be detected on a microarray. We developed 23 PLPs to economically important Phytophthora spp. based upon internal transcribed spacer-1 sequence differences between individual Phytophthora spp. Tests on genomic DNA of many Phytophthora isolates and DNA from environmental samples showed the specificity and utility of PLPs for Phytophthora diagnostics.

  18. Microarrays: molecular allergology and nanotechnology for personalised medicine (I). (United States)

    Lucas, J M


    The diagnosis of antibody-mediated allergic disorders is based on the clinical findings and the detection of allergen-specific IgE based on in vitro and in vivo techniques, together with allergen provocation tests. In vitro diagnostic techniques have progressed enormously following the introduction of the advances made in proteomics and nanotechnology--offering tools for the diagnosis and investigation of allergy at molecular level. The most advanced developments are the microarray techniques, which in genomics allowed rapid description of the human genetic code, and which now have been applied to proteomics, broadening the field for research and clinical use. Together with these technological advances, the characterisation of most of the different proteins generating specific IgE and which conform each natural allergen, as well as their purification or genetic engineering-based synthesis, have been crucial elements--offering the possibility of identifying disease-causing allergens at molecular level, establishing a component-resolved diagnosis (CRD), using them to study the natural course of the disease, and applying them to improvements in specific immunotherapy. Microarrays of allergic components offer results relating to hundreds of these allergenic components in a single test, and use a small amount of serum that can be obtained from capillary blood. The availability of new molecules will allow the development of panels including new allergenic components and sources, which will require evaluation for clinical use. The present study reviews these new developments, component-resolved diagnosis, and the development of microarray techniques as a critical element for furthering our knowledge of allergic disease.

  19. 12 Comprehensive Detection of Allergens in Grass Pollen Extracts by Mass Spectrometry



    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...

  20. Development of an oligonucleotide microarray for the detection and monitoring of marine dinoflagellates. (United States)

    Galluzzi, Luca; Cegna, Alessandra; Casabianca, Silvia; Penna, Antonella; Saunders, Nick; Magnani, Mauro


    Harmful Algal Blooms (HABs), mainly caused by dinoflagellates and diatoms, have great economic and sanitary implications. An important contribution for the comprehension of HAB phenomena and for the identification of risks related to toxic algal species is given by the monitoring programs. In the microscopy-based monitoring methods, harmful species are distinguished through their morphological characteristics. This can be time consuming and requires great taxonomic expertise due to the existence of morphologically close-related species. The high throughput, automation possibility and specificity of microarray-based detection assay, makes this technology very promising for qualitative detection of HAB species. In this study, an oligonucleotide microarray targeted to the ITS1-5.8S-ITS2 rDNA region of nine toxic dinoflagellate species/clades was designed and evaluated. Two probes (45-47 nucleotides in length) were designed for each species/clade to reduce the potential for false positives. The specificity and sensitivity of the probes were evaluated with ITS1-5.8S-ITS2 PCR amplicons obtained from 20 dinoflagellates cultured strains. Cross hybridization experiments confirmed the probe specificity; moreover, the assay showed a good sensitivity, allowing the detection of up to 2 ng of labeled PCR product. The applicability of the assay with field samples was demonstrated using net concentrated seawater samples, un-spiked or spiked with known amounts of cultured cells. Despite the general application of microarray technology for harmful algae detection is not new, a peculiar group of target species/clades has been included in this new-format assay. Moreover, novelties regarding mainly the probes and the target rDNA region have allowed sensitivity improvements in comparison to previously published studies.

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

    Directory of Open Access Journals (Sweden)

    Ribeiro Franclim R


    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.

  2. DNA-microarray for detection of harmful microorganisms in indoor environments

    Energy Technology Data Exchange (ETDEWEB)

    Kaerkkaeinen, P.; Nevalainen, A.; Rintala, H. [National Public Health Institute, Kuopio (Finland); Ritari, J.; Pitkaeranta, M.; Paulin, L.; Auvinen, P. [Helsinki Univ. (Finland)


    The composition of the microbial flora in a building strongly correlates with moisture damage, and compounds of microbial origin are suspected to cause some of the related health effects. The method for reliable detection of such microbes is therefore needed, but to date methodology has not been up to the task. DNA microarrays have turned out to be a promising approach and the aim of this project is to test and develop a DNA microarray for quick and reliable simultaneous detection of several harmful microbes in an indoor air sample. The specific detection of species is based on ligation reaction whereby two probes are joined when they match the template perfectly. The ligation products are hybridized on a universal array with specific zip code sequence. The obtained results show that the universal array coupled to LDR is a feasible approach in detecting microbial species characteristic of moisture damaged buildings. The specificity and sensitivity of the method have turned out to be good and can be developed further. (orig.)

  3. Reliability of a Tissue Microarray in Detecting Thyroid Transcription Factor-1 Protein in Lung Carcinomas

    Institute of Scientific and Technical Information of China (English)

    Xiaoyan Bai; Hong Shen


    OBJECTIVE To compare the expression of the thyroid transcription factor-1 (TTF-1) in human normal adult type Ⅱ alveolar epithelial cells,embryonic pneumocytes and cancer cells of lung carcinoma and metastatic lymph nodes using a tissue microarray (TMA) along with paired conventional full sections.and to jnvestigate the reliability of tissue microarrays in detecting protein expression in lung carcinoma.METHODS A lung carcinoma TMA including 765 cores was constructed.TTF-1 protein expression in both TMA and paired conventional full sections were detected by yhe immunohistochemical SP method using a monoclonal antibody to TTF-1.A PU (Positive Unit) of TTF-1 protein was assessed quantitatively by the Leica Q500MC image analysis system with results from the paired conventional full sections as controls.RESULTS There was no signifcance between TMA and paired conven tional full sections in TTF-1 expression in difierent nuclei of the lung tissue.CONCLUSION TTF-1 protein expression in lung carcinoma detected by TMA was highly concordanl with that of paired full sections.TMA is a reliable method in detecting protein expression.

  4. Detection of serum allergen in children and its clinical significance%儿童血清过敏原检测及其临床意义

    Institute of Scientific and Technical Information of China (English)

    林雪迟; 廖迎; 陈贤; 莫卉; 谌芳; 徐文


    目的 检测儿童血清过敏原并分析其临床意义,为儿童过敏性疾病预防和诊治提供依据. 方法 收集患者2 253例儿童血清过敏原检测结果,包括食入性过敏原及吸入性过敏原,比较不同年份、性别、年龄、过敏性疾病过敏原阳性率. 结果 2012年与2013年过敏原阳性率差异无统计学意义( P>0.05);男童与女童患儿过敏原阳性率比较、吸入性与食入性过敏原阳性率比较,差异均无统计学意义(P>0.05);吸入性与食入性过敏原阳性率均高于混合型(P1~3岁组食入性过敏原阳性率显著高于其他年龄组( P 3 ~7 岁组与 >7 ~15 岁组吸入性过敏原阳性率均显著高于≤1岁组或>1~3岁组( P0.05). No significant difference was observed in the positive rate of allergen detection between boys and girls,or between inhalant allergen and food allergen(P>0.05).The positive rate of inhalant allergen detection or food allergen detection was higher than that of mixed allergen detection(P1-3 years obtained a higher positive rate of food allergen detection compared with the children of other ages(P3-7 years and >7-15 years were obvious higher compared to that in the children aged≤1 years or >1-3 years(P<0.05).The children with asthma gained the highest positive rate of inhalant allergen detection,and the positive rate of inhalant allergen detection was higher than that of food allergen detection(P<0.05).Conclusion There is no difference in the positive rate of allergen detection between boys and girls.The positive rates of inhalant and food allergen detection both are significantly higher than that of the mixed one.The common allergen in the children younger than 3 years is food allergen,while in the children older than 3 is inhalant allergen.Asthma is the common allergic disease with the highest positive rate of inhalant allergen detection in children.

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

    Directory of Open Access Journals (Sweden)

    Moerman Donald G


    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

  6. 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.


    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.

  7. Taguchi design-based optimization of sandwich immunoassay microarrays for detecting breast cancer biomarkers. (United States)

    Luo, Wen; Pla-Roca, Mateu; Juncker, David


    Taguchi design, a statistics-based design of experiment method, is widely used for optimization of products and complex production processes in many different industries. However, its use for antibody microarray optimization has remained underappreciated. Here, we provide a brief explanation of Taguchi design and present its use for the optimization of antibody sandwich immunoassay microarray with five breast cancer biomarkers: CA15-3, CEA, HER2, MMP9, and uPA. Two successive optimization rounds with each 16 experimental trials were performed. We tested three factors (capture antibody, detection antibody, and analyte) at four different levels (concentrations) in the first round and seven factors (including buffer solution, streptavidin-Cy5 dye conjugate concentration, and incubation times for five assay steps) with two levels each in the second round; five two-factor interactions between selected pairs of factors were also tested. The optimal levels for each factor as measured by net assay signal increase were determined graphically, and the significance of each factor was analyzed statistically. The concentration of capture antibody, streptavidin-Cy5, and buffer composition were identified as the most significant factors for all assays; analyte incubation time and detection antibody concentration were significant only for MMP9 and CA15-3, respectively. Interactions between pairs of factors were identified, but were less influential compared with single factor effects. After Taguchi optimization, the assay sensitivity was improved between 7 and 68 times, depending on the analyte, reaching 640 fg/mL for uPA, and the maximal signal intensity increased between 1.8 and 3 times. These results suggest that Taguchi design is an efficient and useful approach for the rapid optimization of antibody microarrays.

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

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


    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.

  9. Identification of upper respiratory tract pathogens using electrochemical detection on an oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Michael J Lodes

    Full Text Available Bacterial and viral upper respiratory infections (URI produce highly variable clinical symptoms that cannot be used to identify the etiologic agent. Proper treatment, however, depends on correct identification of the pathogen involved as antibiotics provide little or no benefit with viral infections. Here we describe a rapid and sensitive genotyping assay and microarray for URI identification using standard amplification and hybridization techniques, with electrochemical detection (ECD on a semiconductor-based oligonucleotide microarray. The assay was developed to detect four bacterial pathogens (Bordetella pertussis, Streptococcus pyogenes, Chlamydia pneumoniae and Mycoplasma pneumoniae and 9 viral pathogens (adenovirus 4, coronavirus OC43, 229E and HK, influenza A and B, parainfluenza types 1, 2, and 3 and respiratory syncytial virus. This new platform forms the basis for a fully automated diagnostics system that is very flexible and can be customized to suit different or additional pathogens. Multiple probes on a flexible platform allow one to test probes empirically and then select highly reactive probes for further iterative evaluation. Because ECD uses an enzymatic reaction to create electrical signals that can be read directly from the array, there is no need for image analysis or for expensive and delicate optical scanning equipment. We show assay sensitivity and specificity that are excellent for a multiplexed format.

  10. Detection of allergenic compounds using an IL-4/luciferase/CNS-1 transgenic mice model. (United States)

    Bae, Chang Joon; Lee, Jae Won; Bae, Hee Sook; Shim, Sun Bo; Jee, Seung Wan; Lee, Su Hae; Lee, Chang Kyu; Hong, Jin Tae; Hwang, Dae Youn


    The interleukin-4 (IL-4) signaling cascade has been identified as a potentially important pathway in the development of allergies. The principal objective of this study was to produce novel transgenic (Tg) mice harboring the luciferase gene under the control of the human IL-4 promoter and the enhancer of IL-4 (CNS-1), in an effort to evaluate three types of allergens including a respiratory sensitizer, vaccine additives, and crude extracts of natural allergens in vivo. A new lineage of Tg mice was generated by the microinjection of pIL-4/Luc/CNS-1 constructs into a fertilized mice egg. The luciferase activity was successfully regulated by the IL-4 promoter in splenocytes cultured from IL-4/Luc/CNS-1 Tg mice. From the first five founder lines, one (#57) evidencing a profound response to ovalbumin was selected for use in evaluating the allergens. Additionally, the lungs, thymus, and lymph nodes of IL-4/Luc/CNS-1 Tg mice evidenced high luciferase activity in response to allergens such as phthalic anhydride (PA), trimellitic anhydride, ovalbumin, gelatin, Dermatophagoides pteronyssinus extracts, and Japanese cedar pollen, whereas key allergy-related indicators including ear thickness, Immunoglobulin E concentration, and the infiltration of inflammatory leukocytes in response to PA were unaltered in the Tg mice relative to the non-Tg mice. Furthermore, the expression levels of endogenous type 2 helper T cells cytokines and proinflammatory cytokines were similarly increased in these organs of IL-4/Luc/CNS-1 Tg mice in response to allergens. These results indicate that IL-4/Luc/CNS-1 Tg mice may be used as an animal model for the evaluation and prediction of the human body response to a variety of allergens originating from the environment and from certain industrial products.

  11. Use of culture, PCR analysis, and DNA microarrays for detection of Campylobacter jejuni and Campylobacter coli from chicken feces

    DEFF Research Database (Denmark)

    Keramas, Georgios; Bang, Dang Duong; Lund, Marianne


    . detection obtained with DNA microarrays were compared to those obtained by conventional culture and gel electrophoresis. By conventional culture, 60% of the samples were positive for either Campylobacter jejuni or Campylobacter coli. By PCR and capillary electrophoresis, 95% of the samples were positive...... for Campylobacter spp., whereas with DNA microarrays all samples were positive for Campylobacter spp. By application of DNA microarray analysis, the isolates in 4 samples (6%) could not be identified to the species level, whereas by PCR-capillary electrophoresis, the isolates in 12 samples (19%) remained...... unidentified. Interestingly, PCR-capillary electrophoresis analysis revealed that two (3%) of the samples were positive for both C. jejuni and C. coli, while DNA microarray analysis revealed that nine (14%) of the samples were positive for both species. Of 65 samples, 2 samples were identified to contain C...

  12. Simultaneous detection of multi-allergens in an incurred food matrix using ELISA, multiplex flow cytometry and liquid chromatography mass spectrometry (LC-MS). (United States)

    Gomaa, Ahmed; Boye, Joyce


    Food allergy is a public health concern and an important food safety issue. Food allergies affect up to 6% of infants and children and 4% of adults. The objective of this work was to determine differences in the detection of single and multiple allergens (i.e., casein, soy protein, and gluten) in an incurred food matrix before and after baking. Cookies were used as a model food system. Three methods, namely, multiplex assay (a new optimized method based on flow cytometry for multiple allergen analysis), enzyme-linked immunosorbent assay (ELISA) using commercial kits and LC-MS were used to detect allergens in the samples before and after baking. The ELISA kits performed well in detecting allergens in the raw samples with recoveries of 91-108%, 88-127% and 85-108% for casein, soy protein and gluten, respectively. Recoveries were poor for the baked cookies (67-90%, 66-95% and 66-88% for casein, soy protein and gluten, respectively). The multiplex flow cytometry assay permitted multiple allergen detection in the raw samples, with the following recoveries based on soluble protein: casein, 95-107%; soy protein, 92-97%, and gluten, 96-99%. Data for the baked cookies were as follows: casein, 84-90%; soy protein, 80-88%, and gluten, 80-90%. The LC-MS technique detected marker peptides that could be used to identify allergens in the baked food samples up to concentrations of 10 ppm for casein and soy protein, and 100 ppm for gluten. To the best of our knowledge, the current study is the first to compare ELISA, LC-MS and multiplex flow cytometry methods for the detection of multiple allergens simultaneously incurred in a model food system.

  13. A New Generation Microarray for the Simultaneous Detection and Identification of Yersinia pestis and Bacillus anthracis in Food

    Directory of Open Access Journals (Sweden)

    Noriko Goji


    Full Text Available The use of microarrays as a multiple analytic system has generated increased interest and provided a powerful analytical tool for the simultaneous detection of pathogens in a single experiment. A wide array of applications for this technology has been reported. A low density oligonucleotide microarray was generated from the genetic sequences of Y. pestis and B. anthracis and used to fabricate a microarray chip. The new generation chip, consisting of 2,240 spots in 4 quadrants with the capability of stripping/rehybridization, was designated as “Y-PESTIS/B-ANTHRACIS 4x2K Array.” The chip was tested for specificity using DNA from a panel of bacteria that may be potentially present in food. In all, 37 unique Y. pestis-specific and 83 B. anthracis-specific probes were identified. The microarray assay distinguished Y. pestis and B. anthracis from the other bacterial species tested and correctly identified the Y. pestis-specific oligonucleotide probes using DNA extracted from experimentally inoculated milk samples. Using a whole genome amplification method, the assay was able to detect as low as 1 ng genomic DNA as the start sample. The results suggest that oligonucleotide microarray can specifically detect and identify Y. pestis and B. anthracis and may be a potentially useful diagnostic tool for detecting and confirming the organisms in food during a bioterrorism event.

  14. An aptamer based on-plate microarray for high-throughput insulin detection by MALDI-TOF MS. (United States)

    Zhang, Xueyang; Zhu, Shaochun; Deng, Chunhui; Zhang, Xiangmin


    An aptamer microarray was directly fabricated on a MALDI target plate for high-throughput insulin detection. High sensitivities were observed both in standard solutions (5 ng mL(-1), 0.86 nM) and serum sample (20 ng mL(-1), 3.4 nM). This method shows great promise in the field of biomarker detection.

  15. Inter-laboratory optimization of protein extraction, separation, and fluorescent detection of endogenous rice allergens

    DEFF Research Database (Denmark)

    Satoh, Rie; Teshima, Reiko; Kitta, Kazumi


    In rice, several allergens have been identified such as the non-specific lipid transfer protein-1, the α-amylase/trypsin-inhibitors, the α-globulin, the 33 kDa glyoxalase I (Gly I), the 52-63 kDa globulin, and the granule-bound starch synthetase. The goal of the present study was to define optima...

  16. 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.


    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.

  17. Microarray-based large scale detection of single feature polymorphism in Gossypium hirsutum L.

    Indian Academy of Sciences (India)

    Anukool Srivastava; Samir V. Sawant; Satya Narayan Jena


    Microarrays offer an opportunity to explore the functional sequence polymorphism among different cultivars of many crop plants. The Affymetrix microarray expression data of five genotypes of Gossypium hirsutum L. at six different fibre developmental stages was used to identify single feature polymorphisms (SFPs). The background corrected and quantile-normalized log2 intensity values of all probes of triplicate data of each cotton variety were subjected to SFPs call by using SAM procedure in R language software. We detected a total of 37,473 SFPs among six pair genotype combinations of two superior (JKC777 and JKC725) and three inferior (JKC703, JKC737 and JKC783) using the expression data. The 224 SFPs covering 51 genes were randomly selected from the dataset of all six fibre developmental stages of JKC777 and JKC703 for validation by sequencing on a capillary sequencer. Of these 224 SFPs, 132 were found to be polymorphic and 92 monomorphic which indicate that the SFP prediction from the expression data in the present study confirmed a ∼ 58.92% of true SFPs. We further identified that most of the SFPs are associated with genes involved in fatty acid, flavonoid, auxin biosynthesis etc. indicating that these pathways significantly involved in fibre development.

  18. Microarray-Based Detection and Differentiation of Virulent and Attenuated Pseudorabies Virus

    Institute of Scientific and Technical Information of China (English)

    LIU Li-na; LIU Zheng-fei; RUAN Li; WANG Zhao-xiong; LI Ren-feng; ZHANG Song-lin; CHEN Huan-chun; HE Qi-gai


    DNA microchip used in this study was formed from miniature arrays of pseudorabies virus (PrV) gene-specific probes immobilized on a glass surface. Hybridization using DNA microchip (microarrays) was used for differentiation between virulent and attenuated PrV. The presence of four gene segments (gB, gD, gE+, and gE- ) encoding conservative glycoprotein B (gB), D (gD), and E (gE) of PrV was monitored using multiplex PCR. The amplicons were labeled with Cy5 or Cy3 dyes followed by hybridization to the gene-specific capture probes on the microchip. The presence of gD and gB, gE+ gene fragments was shown in virulent (gE+ genotype) and attenuated PrV (gE genotype), whereas gE- gene (deleted domain in gE gene) was demonstrated only in virulent, not in attenuated, virus. No cross-hybridization was observed when fluorescence labeled-PCR products of PrV were hybridized using capture probes of related viruses, such as porcine respiratory and reproductive syndrome virus (PRRSV), porcine parvovirus (PPV), Japanese encephalitis virus (JEV), and porcine circovirus type 2 (PCV-2). The assay was 10 times sensitive than gD gene-specific PCR. Overall, the results of this study suggested that the microarray might be very useful for detection and differentiation of virulent PrV from attenuated one.

  19. Human T cell priming assay: depletion of peripheral blood lymphocytes in CD25(+) cells improves the in vitro detection of weak allergen-specific T cells. (United States)

    Vocanson, Marc; Achachi, Amine; Mutez, Virginie; Cluzel-Tailhardat, Magalie; Varlet, Béatrice Le; Rozières, Aurore; Fournier, Philippe; Nicolas, Jean-François


    To develop an in vitro assay that recapitulates the key event of allergic contact dermatitis (ACD), that is the priming of effector T cells by hapten-presenting dendritic cells, and then allows for the sensitive detection of chemical allergens represents a major challenge. Classical human T cell priming assays (hTCPA) that have been developed in the past, using hapten-loaded monocyte-derived dendritic cells (MDDCs) as antigen-presenting cells and peripheral blood lymphocytes (PBLs) as responding cells, were not efficient to prime T cells to common allergens with moderate/weak sensitizing properties. Recent progress in the understanding of the effector and regulatory mechanisms of ACD have shown that T cell priming requires efficient uptake of allergens by immunogenic DCs and that it is controlled by several subsets of regulatory cells including CD25(+) Tregs. We therefore analyzed various parameters involved in allergen-specific T cell activation in vitro and showed that priming of allergen-specific T cells is hampered by several subsets of immune cells comprising CD1a(neg) DCs, CD25(+) T cells, and CD56(+) regulatory cells.CD4(+)CD25(+)FoxP3(+) Tregs prevented the in vitro T cell priming to moderate/weak allergens, and depletion of human PBLs in CD25(+) cells significantly increased specific T cell proliferation and IFN-γ secretion. CD56(+) cells exerted an additional control of T cell priming since co-depletion of both CD56(+) and CD25(+) cells improved the magnitude of chemical-specific T cell activation. Finally, CD1a(low) MDDCs were able to inhibit T cell activation obtained by allergen-pulsed CD1a(high) MDDC. Moreover, we showed that uptake by DC of allergen-encapsulated nanoparticles significantly increased their activation status and their ability to prompt specific T cell activation. Hence, by combining the different strategies, i.e., depletion of CD25(+) and CD56(+) cells, use of CD1a(high) MDDC, and nanoparticle encapsulation of allergens, it was

  20. 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


    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

  1. Detection of gene expression in an individual cell type within a cell mixture using microarray analysis.

    Directory of Open Access Journals (Sweden)

    Penelope A Bryant

    Full Text Available BACKGROUND: A central issue in the design of microarray-based analysis of global gene expression is the choice between using cells of single type and a mixture of cells. This study quantified the proportion of lipopolysaccharide (LPS induced differentially expressed monocyte genes that could be measured in peripheral blood mononuclear cells (PBMC, and determined the extent to which gene expression in the non-monocyte cell fraction diluted or obscured fold changes that could be detected in the cell mixture. METHODOLOGY/PRINCIPAL FINDINGS: Human PBMC were stimulated with LPS, and monocytes were then isolated by positive (Mono+ or negative (Mono- selection. The non-monocyte cell fraction (MonoD remaining after positive selection of monocytes was used to determine the effect of non-monocyte cells on overall expression. RNA from LPS-stimulated PBMC, Mono+, Mono- and MonoD samples was co-hybridised with unstimulated RNA for each cell type on oligonucleotide microarrays. There was a positive correlation in gene expression between PBMC and both Mono+ (0.77 and Mono- (0.61-0.67 samples. Analysis of individual genes that were differentially expressed in Mono+ and Mono- samples showed that the ability to detect expression of some genes was similar when analysing PBMC, but for others, differential expression was either not detected or changed in the opposite direction. As a result of the dilutional or obscuring effect of gene expression in non-monocyte cells, overall about half of the statistically significant LPS-induced changes in gene expression in monocytes were not detected in PBMC. However, 97% of genes with a four fold or greater change in expression in monocytes after LPS stimulation, and almost all (96-100% of the top 100 most differentially expressed monocyte genes were detected in PBMC. CONCLUSIONS/SIGNIFICANCE: The effect of non-responding cells in a mixture dilutes or obscures the detection of subtle changes in gene expression in an individual

  2. Microarrays, Integrated Analytical Systems (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.

  3. 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


    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

  4. Rapid and sensitive detection of fluoroquinolone-resistant Escherichia coli from urine samples using a genotyping DNA microarray. (United States)

    Yu, Xiaolei; Susa, Milorad; Weile, Jan; Knabbe, Cornelius; Schmid, Rolf D; Bachmann, Till T


    Urinary tract infections (UTI) are among the most common bacterial infections in humans, with Escherichia coli being the major cause of infection. Fluoroquinolone resistance of uropathogenic E. coli has increased significantly over the last decade. In this study a microarray-based assay was developed and applied, which provides a rapid, sensitive and specific detection of fluoroquinolone-resistant E. coli in urine. The capture probes were designed against previously identified and described hotspots for quinolone resistance (codons 83 and 87 of gyrA). The key goals of this development were to reduce assay time while increasing the sensitivity and specificity as compared with a pilot version of a gyrA genotyping DNA microarray. The performance of the assay was demonstrated with pure cultures of 30 E. coli isolates as well as with urine samples spiked with 6 E. coli isolates. The microarray results were confirmed by standard DNA sequencing and were in full agreement with the phenotypic antimicrobial susceptibility testing using standard methods. The DNA microarray test displayed an assay time of 3.5h, a sensitivity of 100CFU/ml, and the ability to detect fluoroquinolone-resistant E. coli in the presence of a 10-fold excess of fluoroquinolone-susceptible E. coli cells. As a consequence, we believe that this microarray-based determination of antibiotics resistance has a true potential for the application in clinical routine laboratories in the future.

  5. Detection of Sesame Allergen Traces with Two PCR Assays - The Challenge to Protect Food-Allergic Consumers

    Directory of Open Access Journals (Sweden)

    Dimitra Panagiotis Houhoula


    Full Text Available The purpose of this study was to investigate the possible presence of sesame in commercial foods normally carrying no warning for the allergen, but which may have been subjected to contamination during processing. One hundred units of widely consumed goods with high potential to contain allergenic substances deriving from nuts were analyzed, using sensitive and capable PCR (C-PCR and Real Time PCR (RT-PCR methodologies. Of the products examined, 15 (15.0% declared the presence of sesame, 36 (36.0% carried no food allergy label, 44 (44.0% were marked by the phrase “may contain traces of nuts” and 5 (5.0% carried the indication “may contain sesame traces”. The sesame-positive products detected using the C-PCR method were 15 (100%, 12 (33.3%, 14 (31.8% and 3 (60%, respectively. Using the RT-PCR technique, positive results were obtained for 15 (100%, 18 (50.0%, 18 (20.5% and 5 (100% samples, respectively. The results indicate that the PCR methods applied are highly sensitive and selective, which makes them suitable for the detection of sesame traces in food samples. In addition, they can be useful for monitoring the effectiveness of cleaning processes in the production units of the food industry.

  6. SERS-based multiple biomarker detection using a gold-patterned microarray chip (United States)

    Kim, Insup; Junejo, Inam-ur-Rehman; Lee, Moonkwon; Lee, Sangyeop; Lee, Eun Kyu; Chang, Soo-Ik; Choo, Jaebum


    We report a highly sensitive surface-enhanced Raman scattering (SERS)-based immunoassay platform for the multiplex detection of biomarkers. For this purpose, a gold-patterned microarray chip has been fabricated and used as a SERS detection template. Here, a typical sandwich immunocomplex protocol was adopted. Monoclonal antibodies were immobilized on gold patterned substrates, and then antigen solutions and polyclonal antibody-conjugated hollow gold nanospheres (HGNs) were sequentially added for the formation of sandwich immunocomplexes. Antigen biomarkers can be quantitatively assayed by monitoring the intensity change of a characteristic SERS peak of a reporter molecule adsorbed on the surfaces of HGNs. Under optimized assay conditions, the limits of detections (LODs) were determined to be 10 fg/mL for human IgG and 10-100 fg/mL for rabbit IgG. In addition, the SERS-based immunoassay technique can be applied in a wider dynamic concentration range with a good sensitivity compared to ELISA. The proposed method fulfills the current needs of high sensitivity and selectivity which are essential for the clinical diagnosis of a disease.

  7. Development of a microarray-based method to detect exposure of human basophils to IL-3. (United States)

    MacGlashan, Donald


    Human basophils are an accessible participant of the human allergic reaction. There is natural variation in various functional endpoints and in signaling molecule expression but there has been only a limited effort to place this information in the context of mRNA expression profiles. The goal of these studies was to develop gene transcript profiles associated with IL-3 exposure for use in probing basophil phenotypes. Highly purified human basophils were cultured under several conditions and the cells subsequently analyzed by microarray analysis of gene transcript expression. Basophils were cultured with or without IL-3 for 24 h and the expression profile, relative to pre-culture, analyzed for transcripts that act in a reciprocal fashion depending on the condition. A 51-gene transcript set was identified that was composed of 34 transcripts that increased with IL-3 and decreased without IL-3 and a further 17 transcripts that did the reverse. This set of transcripts was validated on two microarray chips. The changes induced by IL-3 were stable in time, with 3 day cultures generating a signature concordant with 1 day cultures. The inverted nature of the response to ±IL-3 suggested that the normal circulating basophil is balanced between a state of high and low IL-3 exposure and thus is very sensitive to changes in IL-3. For example, the basophil could detect the early generation of IL-3 that follows IgE-mediated stimulation of basophils. When this signature tool was applied to freshly isolated basophils, it was observed that the signature was similar for the same subjects' basophil sampled weeks apart. It was also shown that the 51-gene transcript was insensitive to the method of preparing purified basophils. Finally, these studies provided an estimate for the normal in vivo exposure of circulating basophils to IL-3 or IL-3-like functionality. These studies identified an IL-3 signature to probe changes in basophils occurring in vivo.

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

    Directory of Open Access Journals (Sweden)

    Zhang Zheng


    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.

  9. 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


    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.

  10. Testing and validation of high density resequencing microarray for broad range biothreat agents detection.

    Directory of Open Access Journals (Sweden)

    Tomasz A Leski

    Full Text Available Rapid and effective detection and identification of emerging microbiological threats and potential biowarfare agents is very challenging when using traditional culture-based methods. Contemporary molecular techniques, relying upon reverse transcription and/or polymerase chain reaction (RT-PCR/PCR provide a rapid and effective alternative, however, such assays are generally designed and optimized to detect only a limited number of targets, and seldom are capable of differentiation among variants of detected targets. To meet these challenges, we have designed a broad-range resequencing pathogen microarray (RPM for detection of tropical and emerging infectious agents (TEI including biothreat agents: RPM-TEI v 1.0 (RPM-TEI. The scope of the RPM-TEI assay enables detection and differential identification of 84 types of pathogens and 13 toxin genes, including most of the class A, B and C select agents as defined by the Centers for Disease Control and Prevention (CDC, Atlanta, GA. Due to the high risks associated with handling these particular target pathogens, the sensitivity validation of the RPM-TEI has been performed using an innovative approach, in which synthetic DNA fragments are used as templates for testing the assay's limit of detection (LOD. Assay specificity and sensitivity was subsequently confirmed by testing with full-length genomic nucleic acids of selected agents. The LOD for a majority of the agents detected by RPM-TEI was determined to be at least 10(4 copies per test. Our results also show that the RPM-TEI assay not only detects and identifies agents, but is also able to differentiate near neighbors of the same agent types, such as closely related strains of filoviruses of the Ebola Zaire group, or the Machupo and Lassa arenaviruses. Furthermore, each RPM-TEI assay results in specimen-specific agent gene sequence information that can be used to assess pathogenicity, mutations, and virulence markers, results that are not generally

  11. 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


    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

  12. Detection of human papillomaviruses by polymerase chain reaction and ligation reaction on universal microarray.

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    Jarmo Ritari

    Full Text Available Sensitive and specific detection of human papillomaviruses (HPV in cervical samples is a useful tool for the early diagnosis of epithelial neoplasia and anogenital lesions. Recent studies support the feasibility of HPV DNA testing instead of cytology (Pap smear as a primary test in population screening for cervical cancer. This is likely to be an option in the near future in many countries, and it would increase the efficiency of screening for cervical abnormalities. We present here a microarray test for the detection and typing of 15 most important high-risk HPV types and two low risk types. The method is based on type specific multiplex PCR amplification of the L1 viral genomic region followed by ligation detection reaction where two specific ssDNA probes, one containing a fluorescent label and the other a flanking ZipCode sequence, are joined by enzymatic ligation in the presence of the correct HPV PCR product. Human beta-globin is amplified in the same reaction to control for sample quality and adequacy. The genotyping capacity of our approach was evaluated against Linear Array test using cervical samples collected in transport medium. Altogether 14 out of 15 valid samples (93% gave concordant results between our test and Linear Array. One sample was HPV56 positive in our test and high-risk positive in Hybrid Capture 2 but remained negative in Linear Array. The preliminary results suggest that our test has accurate multiple HPV genotyping capability with the additional advantages of generic detection format, and potential for high-throughput screening.

  13. Detection of human papillomaviruses by polymerase chain reaction and ligation reaction on universal microarray. (United States)

    Ritari, Jarmo; Hultman, Jenni; Fingerroos, Rita; Tarkkanen, Jussi; Pullat, Janne; Paulin, Lars; Kivi, Niina; Auvinen, Petri; Auvinen, Eeva


    Sensitive and specific detection of human papillomaviruses (HPV) in cervical samples is a useful tool for the early diagnosis of epithelial neoplasia and anogenital lesions. Recent studies support the feasibility of HPV DNA testing instead of cytology (Pap smear) as a primary test in population screening for cervical cancer. This is likely to be an option in the near future in many countries, and it would increase the efficiency of screening for cervical abnormalities. We present here a microarray test for the detection and typing of 15 most important high-risk HPV types and two low risk types. The method is based on type specific multiplex PCR amplification of the L1 viral genomic region followed by ligation detection reaction where two specific ssDNA probes, one containing a fluorescent label and the other a flanking ZipCode sequence, are joined by enzymatic ligation in the presence of the correct HPV PCR product. Human beta-globin is amplified in the same reaction to control for sample quality and adequacy. The genotyping capacity of our approach was evaluated against Linear Array test using cervical samples collected in transport medium. Altogether 14 out of 15 valid samples (93%) gave concordant results between our test and Linear Array. One sample was HPV56 positive in our test and high-risk positive in Hybrid Capture 2 but remained negative in Linear Array. The preliminary results suggest that our test has accurate multiple HPV genotyping capability with the additional advantages of generic detection format, and potential for high-throughput screening.

  14. MS(E) based multiplex protein analysis quantified important allergenic proteins and detected relevant peptides carrying known epitopes in wheat grain extracts. (United States)

    Uvackova, Lubica; Skultety, Ludovit; Bekesova, Slavka; McClain, Scott; Hajduch, Martin


    The amount of clinically relevant, allergy-related proteins in wheat grain is still largely unknown. The application of proteomics may create a platform not only for identification and characterization, but also for quantitation of these proteins. The aim of this study was to evaluate the data-independent quantitative mass spectrometry (MS(E)) approach in combination with 76 wheat allergenic sequences downloaded from the AllergenOnline database ( ) as a starting point. Alcohol soluble extracts of gliadin and glutenin proteins were analyzed. This approach has resulted in identification and quantification of 15 allergenic protein isoforms that belong to amylase/trypsin inhibitors, γ-gliadins, and high or low molecular weight glutenins. Additionally, several peptides carrying four previously discovered epitopes of γ-gliadin B precursor have been detected. These data were validated against the UniProt database, which contained 11764 Triticeae protein sequences. The identified allergens are discussed in relation to Baker's asthma, food allergy, wheat dependent exercise induced anaphylaxis, atopic dermatitis, and celiac disease (i.e., gluten-sensitive enteropathy). In summary, the results showed that the MS(E) approach is suitable for quantitative analysis and allergens profiling in wheat varieties and/or other food matrices.

  15. 过敏性紫癜患儿血清过敏原检测应用%Application of serum allergen detection for children with allergic purpura

    Institute of Scientific and Technical Information of China (English)



    Objective To investigate clinical significance by serum allergen detection in diagnosis of children with allergic purpura. Methods A total of 120 children with allergic purpura received serum allergen detection of immune globulin E (IgE) antibody for allergen identification. Results The 120 cases had total positive rate of inhaled allergen as 54.17% (65 cases), with proportion as dermatophagoides farina > mould > tree pollen > house dust > hair and scurf of cat and dog > common ragweed artemisia, cockroach, mosquito. Their total positive rate of food allergen was 35.00% (42 cases), with proportion as peanut, soybean > shrimp, crab > pork, beef, mutton > egg > fish > milk. Conclusion Under certain circumstance, allergic purpura can be induced by various allergen. Therefore, both convention therapy and allergen detection are necessary in clinical treatment to identify allergen and restrain occurrence of allergic purpura.%目的:探究血清过敏原检测在过敏性紫癜患儿诊断中的临床意义。方法120例过敏性紫癜患儿,检测其血清中过敏原特异性免疫球蛋白 E(IgE)抗体等,并找出过敏原。结果120例患儿中,其中总吸入过敏原阳性率为54.17%(65例),过敏原占比由高到低排列为:尘粉螨>霉菌>树花粉>屋尘>猫狗毛发皮屑>普通豚草蒿属及蟑螂、蚊子;总食物过敏原阳性率为35.00%(42例),过敏原占比由高到低排列为:花生、大豆>虾、蟹>猪肉、牛肉、羊肉>蛋类>鱼>牛奶。结论多种过敏原在一定条件下均可诱发过敏性紫癜,因此,在临床治疗中既需要进行常规治疗,也应进行过敏原检测,以查找出过敏原,减少紫癜的发生。

  16. Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma

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    Orengo Christine


    Full Text Available Abstract Background RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological variation in expression have not been explored sufficiently to define the true extent of usability and limitations of such amplification techniques. Results We show that expression ratios are occasionally distorted by amplification using the Affymetrix small sample protocol version 2 due to a disproportional shift in intensity across biological samples. This occurs when a shift in one sample cannot be reflected in the other sample because the intensity would lie outside the dynamic range of the scanner. Interestingly, such distortions most commonly result in smaller ratios with the consequence of reducing the statistical significance of the ratios. This becomes more critical for less pronounced ratios where the evidence for differential expression is not strong. Indeed, statistical analysis by limma suggests that up to 87% of the genes with the largest and therefore most significant ratios (p -20 in the unamplified group have a p-value below 10e-20 in the amplified group. On the other hand, only 69% of the more moderate ratios (10e-20 -10 in the unamplified group have a p-value below 10e-10 in the amplified group. Our analysis also suggests that, overall, limma shows better overlap of genes found to be significant in the amplified and unamplified groups than the Z-scores statistics. Conclusion We conclude that microarray analysis of amplified samples performs best at detecting differences in gene expression, when these are large and when limma statistics are used.

  17. Advances in ultra-high performance liquid chromatography coupled to tandem mass spectrometry for sensitive detection of several food allergens in complex and processed foodstuffs. (United States)

    Planque, M; Arnould, T; Dieu, M; Delahaut, P; Renard, P; Gillard, N


    Sensitive detection of food allergens is affected by food processing and foodstuff complexity. It is therefore a challenge to detect cross-contamination in food production that could endanger an allergic customer's life. Here we used ultra-high performance liquid chromatography coupled to tandem mass spectrometry for simultaneous detection of traces of milk (casein, whey protein), egg (yolk, white), soybean, and peanut allergens in different complex and/or heat-processed foodstuffs. The method is based on a single protocol (extraction, trypsin digestion, and purification) applicable to the different tested foodstuffs: chocolate, ice cream, tomato sauce, and processed cookies. The determined limits of quantitation, expressed in total milk, egg, peanut, or soy proteins (and not soluble proteins) per kilogram of food, are: 0.5mg/kg for milk (detection of caseins), 5mg/kg for milk (detection of whey), 2.5mg/kg for peanut, 5mg/kg for soy, 3.4mg/kg for egg (detection of egg white), and 30.8mg/kg for egg (detection of egg yolk). The main advantage is the ability of the method to detect four major food allergens simultaneously in processed and complex matrices with very high sensitivity and specificity.

  18. Detection of potentially allergenic hazelnut (Corylus avellana) residues in food: a comparative study with DNA PCR-ELISA and protein sandwich-ELISA. (United States)

    Holzhauser, Thomas; Stephan, Oliver; Vieths, Stefan


    Allergen detection is of increasing interest for food labeling purposes. A comparative study with a commercial hazelnut-specific PCR-ELISA and a sandwich-type ELISA detecting hazelnut protein was performed to investigate to what extent immunochemical and DNA-based techniques would correlate in the detection of trace amounts of potentially allergenic hazelnut residues. Both methods were highly sensitive and allowed the detection of even hazelnut in complex food matrixes. The protein-ELISA was highly specific for hazelnut. However, some foods could lead to false-positive results at the 10 ppm level. The PCR-ELISA did not show any cross-reactions with non-hazelnut foods, thus reducing the probability of having false positives at the trace level. Forty-one commercial food products with and without hazelnut components on their labels were analyzed for the presence of hazelnut. Of the 27 products in which hazelnut components were detected, two samples were not identified by the protein-ELISA, and only one sample, namely one white chocolate having hazelnut protein, was not detected by PCR-ELISA. The good correlation of the results of PCR-ELISA and protein-ELISA suggested that both PCR-based and immunochemical techniques are suitable for reliable detection of potentially allergenic hazelnut residues in foods at the trace level.

  19. Evaluation of a field-portable DNA microarray platform and nucleic acid amplification strategies for the detection of arboviruses, arthropods, and bloodmeals. (United States)

    Grubaugh, Nathan D; Petz, Lawrence N; Melanson, Vanessa R; McMenamy, Scott S; Turell, Michael J; Long, Lewis S; Pisarcik, Sarah E; Kengluecha, Ampornpan; Jaichapor, Boonsong; O'Guinn, Monica L; Lee, John S


    Highly multiplexed assays, such as microarrays, can benefit arbovirus surveillance by allowing researchers to screen for hundreds of targets at once. We evaluated amplification strategies and the practicality of a portable DNA microarray platform to analyze virus-infected mosquitoes. The prototype microarray design used here targeted the non-structural protein 5, ribosomal RNA, and cytochrome b genes for the detection of flaviviruses, mosquitoes, and bloodmeals, respectively. We identified 13 of 14 flaviviruses from virus inoculated mosquitoes and cultured cells. Additionally, we differentiated between four mosquito genera and eight whole blood samples. The microarray platform was field evaluated in Thailand and successfully identified flaviviruses (Culex flavivirus, dengue-3, and Japanese encephalitis viruses), differentiated between mosquito genera (Aedes, Armigeres, Culex, and Mansonia), and detected mammalian bloodmeals (human and dog). We showed that the microarray platform and amplification strategies described here can be used to discern specific information on a wide variety of viruses and their vectors.


    Institute of Scientific and Technical Information of China (English)

    Xin-yun Wang; Xing-ye Wu; Zhi Yao; Yan Li; Ting Liu; Hai-yan Zheng; Cong-zhong Zhu; Cui-yun Sun; Ai-xiang Wang; Min Zhao


    Objective To investigate the expression of Survivin mRNA in lung cancer tissue microarray (TMA) by fluorescence in situ hybridization (FISH) method, and determine the role and significance of it in lung cancer genesis and progress. Methods The expression of Survivin mRNA was detected by FISH method and TMA technology. Fifty-four cases of lung cancer and 10 cases of normal lung tissue were examined. Results Survivin mRNA was expressed in 66.7% (36/54) of lung cancer; the positive ratio of lung cancer was significantly higher than that of normal lung tissue (0/10; x2= 15.238, P < 0.05). The positive ratio of Survivin mRNA was significantly higher in poor differentiated cancer (20/24, 83.3%) than moderate and well differentiated cancer (16/30, 53.3%; x2= 5.40, P <0.05). The positive ratio of Survivin mRNA was significantly higher in group with lymph node metastasis (27/32, 84.4%) than without lymph node metastasis (9/22, 40.9%; x2= 11.084, P < 0.05). The positive ratio of Survivin mRNA was significantly higher in stage Ⅲ-Ⅳ(12/13, 92.3%) than stage Ⅰ - Ⅱ (24/41, 58.5%; x2= 5.066, P < 0.05). Conclusion Survivin mRNA highly expresses in lung cancer, which is related to the progress and malignant behavior. Survivin may play a promoting role in lung cancer genesis and progress and provide a basis for estimating prognosis and treatment.

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

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    García José


    Full Text Available Abstract Background 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. Methods 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. Results 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. Conclusion 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.

  2. Comprehensive peptide marker identification for the detection of multiple nut allergens using a non-targeted LC-HRMS multi-method. (United States)

    Korte, Robin; Lepski, Silke; Brockmeyer, Jens


    Food allergies have emerged as a global problem over the last few decades; therefore, reliable and sensitive analytical methods to ensure food safety for allergic consumers are required. The application of mass spectrometry is of growing interest in this field and several procedures based on low resolution tandem mass spectrometry using single tryptic peptides as analytical targets have recently been described. However, a comprehensive survey of marker peptides for the development of multi-methods is still missing, as is a consensus guide to marker identification. In this study, we therefore report a consistent approach to the development of liquid chromatography-mass spectrometry (LC-MS) multi-screening methods for the detection of allergens in food matrices. Proteotypic peptides were identified by a shotgun proteomics approach and verified through a thorough investigation of specificity and sensitivity. On the basis of this procedure, we identified 44 suitable tryptic marker peptides from six allergenic nut species and developed the first analytical LC-MS method for the detection of trace nut contaminations in processed foods using high resolution mass spectrometry (HRMS). The analysis of spiked matrix samples gave limits of detection (LODs) below 10 μg/g for several nuts; these LODs are comparable with routinely used methods such as ELISA and PCR. Notably, the HRMS approach can be used in an untargeted fashion to identify multiple allergens also retrospectively. In conclusion, we present here the so far largest consensus set of analytical markers from nut allergens and to the best of our knowledge the first multi-allergen method based on LC-HRMS.

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

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    Song Yang


    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.

  4. Multiple detection of single nucleotide polymorphism by microarray-based resonance light scattering assay with enlarged gold nanoparticle probes. (United States)

    Gao, Jiaxue; Ma, Lan; Lei, Zhen; Wang, Zhenxin


    The mapping of specific single nucleotide polymorphisms (SNPs) in patients' genome is a critical process for the development of personalized therapy. In this work, a DNA microarray-based resonance light scattering (RLS) assay has been developed for multiplexed detection of breast cancer related SNPs with high sensitivity and selectivity. After hybridization of the desired target single-stranded DNAs (ssDNAs) with the ssDNA probes on a microarray, the polyvalent ssDNA modified 13 nm gold nanoparticles (GNPs) are employed to label the hybridization reaction through the formation of a three-stranded DNA system. The H2O2-mediated enlargement of GNPs is then used to enhance the RLS signal. The microarray-based RLS assay provides a detection limit of 10 pM (S/N = 3) for the target ssDNA and determines an allele frequency as low as 1.0% in the target ssDNA cocktail. Combined with an asymmetric PCR technique, the proposed assay shows good accuracy and sensitivity in profiling 4 SNPs related to breast cancer of three selected cell lines.

  5. Multiplexed identification of different fish species by detection of parvalbumin, a common fish allergen gene: a DNA application of multi-analyte profiling (xMAP) technology. (United States)

    Hildebrandt, Sabine


    Fish are a common cause of allergic reactions associated with food consumption, with parvalbumin being the major allergenic protein. Some fish-hypersensitive patients tolerate some fish species while being allergic to others. Reliable detection methods for allergenic fish species in foods are necessary to ensure compliance with food allergen labeling guidelines to protect fish-allergic consumers. The objective of this project was to develop a multi-analyte detection method for the presence of fish in food. Therefore, conserved parvalbumin exon sequences were utilized for the design of universal PCR primers amplifying intron DNA and small regions of exons flanking the enclosed intron from even very distantly related fish species. An assay for the identification of eight fish species was developed using xMAP technology with probes targeting species-specific parvalbumin intron regions. Additionally, a universal fish probe was designed targeting a highly conserved exon region located between the intron and the reverse primer region. The universal fish assay showed no cross-reactivity with other species, such as beef, pork, lamb, chicken, turkey, and shrimp. Importantly, with the exception of one notable case with fish in the same subfamily, species-specific detection showed no cross-reactivity with other fish species. Limits of detection for these eight species were experimentally estimated to range from 0.01% to 0.04%, with potential to increase the detection sensitivity. This report introduces a newly developed method for the multiplex identification of at least eight allergenic fish species in food, which could conceivably be extended to detect up to 100 species simultaneously in one sample.

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

    Institute of Scientific and Technical Information of China (English)



    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.

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

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    Sirasa Yodmongkol


    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.

  8. Rapid Detection of Rare Deleterious Variants by Next Generation Sequencing with Optional Microarray SNP Genotype Data. (United States)

    Watson, Christopher M; Crinnion, Laura A; Gurgel-Gianetti, Juliana; Harrison, Sally M; Daly, Catherine; Antanavicuite, Agne; Lascelles, Carolina; Markham, Alexander F; Pena, Sergio D J; Bonthron, David T; Carr, Ian M


    Autozygosity mapping is a powerful technique for the identification of rare, autosomal recessive, disease-causing genes. The ease with which this category of disease gene can be identified has greatly increased through the availability of genome-wide SNP genotyping microarrays and subsequently of exome sequencing. Although these methods have simplified the generation of experimental data, its analysis, particularly when disparate data types must be integrated, remains time consuming. Moreover, the huge volume of sequence variant data generated from next generation sequencing experiments opens up the possibility of using these data instead of microarray genotype data to identify disease loci. To allow these two types of data to be used in an integrated fashion, we have developed AgileVCFMapper, a program that performs both the mapping of disease loci by SNP genotyping and the analysis of potentially deleterious variants using exome sequence variant data, in a single step. This method does not require microarray SNP genotype data, although analysis with a combination of microarray and exome genotype data enables more precise delineation of disease loci, due to superior marker density and distribution.

  9. Food Allergens: Is There a Correlation between Stability to Digestion and Allergenicity? (United States)

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard


    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.

  10. Construction, detection and microarray analysis on the Shigella flexneri 2a sitC mutant

    Institute of Scientific and Technical Information of China (English)

    LIU; Moqing; LIU; Hong; SUN; Lilian; DONG; Jie; XUE; Ying; C


    In order to overcome the defects of difficult gene operations in Iow-copy suicide plasmid pCVD442, Gateway technology was applied in the construction process of recombinant plasmid for gene knockout in this study. With this improved knockout system, we inactivated sitC gene, which is associated with iron transport in Shigella flexneri2a strain 301, to yield the mutant,MTS. The functional detection of the mutant was performed at the level of culture medium, cell and animal experiment, respectively. The gene expression profiles were compared with DNA microarray between the mutant and the wild type under iron-restricted conditions. The results showed that MTS grew obviously less well than the wild-type strains in L broth containing 150μmol/L iron chelator DIP (2,2'-dipyridyl). Addition of iron or manganese to the cultures stimulated the growth of MTS to wild-type levels in rich culture medium. In either the experiment on the ability of intracellular multiplication and cell-to-cell spread in HeLa and U937 cell lines, or the experiment on keratoconjunctivitis in guinea pigs, MTS showed no obvious changes in virulence compared with the parental strain Sf301. When 65 μmol/L DIP was added to the cultured HeLa cells, the ability of intracellular multiplication of MTS reduced about 51.6% as compared with that of Sf301. The analysis of expression profiles under iron-limited condition showed that MTS was more sensitive for the change of iron deficiency than Sf301. There are 106 more up-regulated genes in MTS than in wild-type strains, which are involved in membrane transportation, amino acid metabolism and uncategorized function genes, while down-regulated genes are mainly involved in energy and carbohydrate metabolism. Under Iow iron conditions, the expression levels of known iron-transport associated genes generally increased. Additionally, the number of these genes and their increase amplitude in MTS are more than those in Sf301. Together, these results confirmed that Sit

  11. A regression-based differential expression detection algorithm for microarray studies with ultra-low sample size. (United States)

    Vasiliu, Daniel; Clamons, Samuel; McDonough, Molly; Rabe, Brian; Saha, Margaret


    Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly available, and possibly many more unpublished, gene expression datasets. We propose a novel variable selection algorithm for ultra-low-n microarray studies using generalized linear model-based variable selection with a penalized binomial regression algorithm called penalized Euclidean distance (PED). Our method uses PED to build a classifier on the experimental data to rank genes by importance. In place of cross-validation, which is required by most similar methods but not reliable for experiments with small sample size, we use a simulation-based approach to additively build a list of differentially expressed genes from the rank-ordered list. Our simulation-based approach maintains a low false discovery rate while maximizing the number of differentially expressed genes identified, a feature critical for downstream pathway analysis. We apply our method to microarray data from an experiment perturbing the Notch signaling pathway in Xenopus laevis embryos. This dataset was chosen because it showed very little differential expression according to limma, a powerful and widely-used method for microarray analysis. Our method was able to detect a significant number of differentially expressed genes in this dataset and suggest future directions for investigation. Our method is easily adaptable for analysis of data from RNA-seq and other global expression experiments with low sample size and high dimensionality.

  12. A regression-based differential expression detection algorithm for microarray studies with ultra-low sample size.

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    Daniel Vasiliu

    Full Text Available Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly available, and possibly many more unpublished, gene expression datasets. We propose a novel variable selection algorithm for ultra-low-n microarray studies using generalized linear model-based variable selection with a penalized binomial regression algorithm called penalized Euclidean distance (PED. Our method uses PED to build a classifier on the experimental data to rank genes by importance. In place of cross-validation, which is required by most similar methods but not reliable for experiments with small sample size, we use a simulation-based approach to additively build a list of differentially expressed genes from the rank-ordered list. Our simulation-based approach maintains a low false discovery rate while maximizing the number of differentially expressed genes identified, a feature critical for downstream pathway analysis. We apply our method to microarray data from an experiment perturbing the Notch signaling pathway in Xenopus laevis embryos. This dataset was chosen because it showed very little differential expression according to limma, a powerful and widely-used method for microarray analysis. Our method was able to detect a significant number of differentially expressed genes in this dataset and suggest future directions for investigation. Our method is easily adaptable for analysis of data from RNA-seq and other global expression experiments with low sample size and high dimensionality.

  13. In vitro selection of DNA aptamers targeting β-lactoglobulin and their integration in graphene-based biosensor for the detection of milk allergen. (United States)

    Eissa, Shimaa; Zourob, Mohammed


    Food allergy has increased rapidly in recent years affecting millions of people worldwide. With the increased consumption of packed food nowadays, a sensitive, accurate and rapid screening method for potential food allergens has become an urgent need in order to protect the sensitive consumers from life-threatening reactions. The current detection methods for food allergens are mostly based on immunoassays which are costly and times-consuming. In this work, we developed an aptamer/graphene-based electrochemical biosensor for on-step, sensitive and low cost detection of β-lactoglobulin (β-LG) milk protein, one of the most common food allergens specially in infants. The selection of DNA aptamers against the two β-LG variants A and B was successfully realised using systemic evolution of ligands by exponential enrichment (SELEX) method. Among the selected aptamers, BLG14 aptamer sequence has shown high affinity and specificity to both β-LG A and B with dissociation constants (Kds) of 82 and 80nM, respectively as calculated using fluorescence binding assays. The aptamer was then integrated in a voltammetric biosensor utilizing graphene-modified screen printed carbon electrodes. The binding is monitored by following the change in the square wave voltammetry (SWV) reduction peak signal of ferrocyanide/ferricyanide redox couple due to the removal of the negatively charged aptamers from the surface upon protein binding. This one-step "signal on" biosensor takes 20min for the sensitive and selective detection of β-LG without using any labelling or sophisticated designs. The method was also tested in spiked food sample extract achieving good recovery percentage. The integration of the novel aptamer in the graphene biosensor allows a promising way for cost-effective, rapid and sensitive on-site detection of milk allergen in food stuff.

  14. Occupational allergens

    NARCIS (Netherlands)

    Terwoert, J.


    Allergens are substances that may cause a hypersensitivity (allergy) of the immune system. After acquiring this hypersensitivity, further exposure to the same substance may result in allergic skin disease such as allergic contact dermatitis, or allergic airway disease such as allergic rhinitis or as

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


    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; 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

  16. 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


    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.

  17. 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


    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.

  18. 20万项次过敏原特异性IgE检测结果%Two Hundred Thousands Results of Allergen Specific IgE Detection

    Institute of Scientific and Technical Information of China (English)

    王瑞琦; 张宏誉


    Objective To analyze and determine the common inhalant allergens and important food allergens in clinical practice. Methods Base on the allergen-specific IgE( slgE ) results detected by ImmunoCAP system in Department of Allergy, Peking Union Medical College Hospital in the past three years, the test amount, the positive results number, and the positive rate of each allergen were calculated respectively, and the sorting analysis of positive results number was performed. Results 215 210 detection were assayed in the past 3 years, 76% of them were inhalant allergens slgE, 22% were food allergens slgE, and 2% were other allergens ( including drugs and insects et al ) slgE. There were 18 kinds of common inhalant allergens, including pteronyssinus, farinae, mugwort, Japanese hop, Altermaria alternate, white ash, mountain juniper, common ragweed, common silver birch, Cockroach ( German ), maple leaf sycamore, cocklebur, hand dander, goosefoot ( Lambs quarters ), and Aspergillus fumigatus, which contributed to 95 % of inhalant allergen sigE positive results. The important food allergens were egg, milk, peanut, soybean, shrimp, crab, grain, nut and fruit. The positive slgE results number of 27 kinds ofinhalant and 42 kinds of food allergens was less then ten in the past 3 years, and no positive result was found in some of them. Phadiatop and fx5 were the most common screening tests used in clinical practice. Conclusions The variety of allergens is great, but the common inhalant and important food allergens are limited in clinical practice. Some allergens are really rare. The common inhalant and important food allergens spectrum of China is in accord with data of foreign publications.%目的 分析临床常见吸入物过敏原和重要食物过敏原的种类.方法 依据北京协和医院变态反应科近3年来应用ImmunoCAP过敏原检测系统所做的过敏原特异性IgE(specific IgE,sIgE)检测结果,统计每种过敏原的

  19. 芝麻过敏原PCR检测方法%Establishment of PCR method for detecting sesame allergen

    Institute of Scientific and Technical Information of China (English)

    张文举; 许庆金; 邓志瑞; 陈沁


    Sesame is an important food allergen;low-level doses can cause severe allergic reactions. In this paper, PCR primers were designed based on sesame allergy protein (2S albumin) gene sequence, and conventional PCR and Real-time PCR were established and optimized. The lowest DNA content that can be detected for conventional PCR was 0. 1 ng and 0, 01 ng for real-time PCR, respectively. The specificity of the methods is good and can be widely used.%芝麻是重要的食品过敏原之一,微小剂量即可引起严重的过敏反应.针对芝麻过敏蛋白-2S白蛋白的基因序列设计PCR扩增引物,建立并优化芝麻过敏原检测的普通聚合酶链式反应(PCR)和实时荧光定量聚合酶链式反应(Realtime PCR)方法.结果表明,两种方法的最低检测限分别为0.1,0.01 ng DNA,该方法特异性良好,成本较低,具有一定的应用价值.

  20. 荧光定量PCR方法检测榛果过敏原成分%Detection of the allergen of hazelnut by real-time PCR

    Institute of Scientific and Technical Information of China (English)

    吴冬雪; 张霞; 黄晨; 刘国红; 王乃福


    目的:建立榛果过敏原成分的荧光定量PCR检测方法,并将此方法与酶联免疫吸附法(enzyme-linked immunosorbent assay, ELISA)方法进行比对实验。方法根据榛果成分oleosin特异性基因设计并筛选合适的引物和探针,优化反应体系和反应条件,建立榛果过敏原成分的荧光定量 PCR 检测方法,对荧光定量 PCR 方法与ELISA方法检测结果进行分析。结果建立的榛果过敏原成分荧光定量PCR方法特异性良好,可用于榛果过敏原成分的定量检测,但检测灵敏度低于ELISA检测方法。结论所建立的榛果过敏原成分的荧光定量PCR检测方法特异性好,灵敏度达到10 mg/kg,具有较好的实用性, ELISA检测方法灵敏度高于荧光定量PCR法,但当榛果过敏蛋白被破坏后有可能出现假阴性结果。%Objective To establish a real-time PCR method for detection of the allergen of hazelnut, and compare the method with the enzyme-linked immunosorbent assay (ELISA) method. Methods According to the oleosin gene of hazelnut, the optimized reaction system and the reaction conditions had been proposed. To establish a real-time PCR method for detection of the allergen of hazelnut, a comparative analysis of the detection results by this method and ELISA was made. Results The method was specific for hazelnut allergens, and was suitable for the detection of hazelnut allergens. But the sensitivity of this method was lower than ELISA. Conclusion The real-time PCR method for detecting the allergen of hazelnut is suitable for application, the sensitivity is up to 10 mg/kg, lower than the ELISA detection method, but a false negative result may occur in ELISA method due to the hazelnut allergic protein damaged.

  1. Carbohydrate microarrays

    DEFF Research Database (Denmark)

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


    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...

  2. 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


    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.

  3. Detection of Allergens in Children with Henoch-schonlein Purpura%过敏性紫癜患儿过敏原检测分析

    Institute of Scientific and Technical Information of China (English)

    刘静; 陆彪


    Objective To detect and analyze allergens with the common seasonal food and inhalant allergens in children with henoch - schonlein purpura ( HSP) . Methods 849 children with HSP admitted between November 2005 and November 2010 were recruited in this research. The biological resonance of the common food and inhalant allergens of 849 children were characterized using 2000 German BICOM allergy treatment system. Results ① The top five allergens based on positive rate of allergens for both foods and inhalants in children with HSP were dust mites, pod, cocoa, flowers and artemisia. ②The significant difference in food and inhalant allergens was found for both male and female ( P < 0. 05 ) . However, the female had more positive for food allergens (P =0.04)while the male had more positive for the inhalant allergens(P =0. 168). ③Food allergens had a significant higher positive rate(P <0.05) in aged 1-6 than that in aged 7-15. ④The food allergens had significantly higher positive rate in Hui ethnicity than that in Han ethnicity (P <0. 01 ). ⑤ The food and inhaled allergens shoewed the significantly seasonal difference (P <0. 01 ). The food allergens had the highest positive rate in winter while the inhalant allergens had the highest positive rate in summer. Conclusion In Ningxia, dust mites, pod, cocoa, flowers and Artemisia are the most significant allergens in children who have Henoch - Schonlein purpura. Gender, age, ethnicity, seasonal have impact on the distribution of food, and inhalant allergens.%目的 探讨宁夏地区过敏性紫癜患儿常见食物和吸入性过敏原的检出与分布特征,为过敏性紫癜的预防和治疗提供参考.方法 选取2005年11月-2010年11月我院儿科收治的过敏性紫癜患儿849例,应用生物共振治疗仪进行食物和吸入性过敏原检测.结果 ①过敏性紫癜患儿过敏原阳性率由高到低依次为粉尘螨、豆荚、可可饮料、花草混合物、艾蒿蒿属等.②男女性

  4. 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


    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.

  5. Fungal allergens.



    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...

  6. Detection and identification of Vibrio parahaemolyticus by multiplex PCR and DNA-DNA hybridization on a microarray

    Institute of Scientific and Technical Information of China (English)

    Rongzhi Wang; Jiadong Huang; Wei Zhang; Guangmei Lin; Junwei Lian; Libin Jiang; Hongcong Lin; Songfa Wang; Shihua Wang


    In this paper,we developed a rapid and accurate method for the detection of Vibrio parahaemolyticus strains,using multiplex PCR and DNA-DNA hybridization.Multiplex PCR was used to simultaneously amplify three diagnostic genes(tlh,tdh and fia)that serve as molecular markers of V.parahaemolyticus.Biotinylated PCR products were hybridized to primers immobilized on a microarray,and detected by chemiluminesce with avidin-conjugated alkaline phosphatase.With this method,forty-five samples were tested.Eight known virulent strains (tlh+/tdh+/fia+)and four known avirulent strains(tlh+/tdh-/fla+)of the V.parahaemolyttcus were successtuny aetectea,ana no non-spectnc hybridization and cross-hybridization reaction were found from fifteen closely-related strains(tin-/tdh-/fta+)or the Vibrio spp.In addition,all the other eighteen strains of non-Vibrio bacteria(tlh-/tdh-/fla-)gave negative results.The DNA microarray successfully distinguished V.parahaemolyticus from other Vibrio spp.The results demonstrated that this was an efficient and robust method for identifying virulent strains of V.parahaemolyticus.

  7. Clinical utility of chromosomal microarray analysis of DNA from buccal cells: detection of mosaicism in three patients. (United States)

    Sdano, Mallory R; Vanzo, Rena J; Martin, Megan M; Baldwin, Erin E; South, Sarah T; Rope, Alan F; Allen, William P; Kearney, Hutton


    Mosaic chromosomal abnormalities are relatively common. However, mosaicism may be missed due to multiple factors including failure to recognize clinical indications and order appropriate testing, technical limitations of diagnostic assays, or sampling tissue (s) in which mosaicism is either not present, or present at very low levels. Blood leukocytes have long been the "gold standard" sample for cytogenetic analysis; however, the culturing process for routine chromosome analysis can complicate detection of mosaicism since the normal cell line may have a growth advantage in culture, or may not be present in the cells that produce metaphases (the lymphocytes). Buccal cells are becoming increasingly utilized for clinical analyses and are proving to have many advantages. Buccal swabs allow for simple and noninvasive DNA collection. When coupled with a chromosomal microarray that contains single nucleotide polymorphic probes, analysis of buccal cells can maximize a clinician's opportunity to detect cytogenetic mosaicism. We present three cases of improved diagnosis of mosaic aberrations using buccal specimens for chromosomal microarray analysis. In each case, the aberration was either undetectable in blood or present at such a low level it likely could have gone undetected. These cases highlight the limitations of certain laboratory methodologies for identifying mosaicism. We also present practice implications for genetic counselors, including clinic workflow changes and counseling approaches based on increasing use of buccal samples.

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

    Directory of Open Access Journals (Sweden)

    Hengxi Wei


    Full Text Available 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.

  9. Detection and isolation of selected genes of interest from metagenomic libraries by a DNA microarray approach. (United States)

    Pathak, Gopal P; Gärtner, Wolfgang


    A DNA microarray-based approach is described for screening metagenomic libraries for the presence of selected genes. The protocol is exemplified for the identification of flavin-binding, blue-light-sensitive biological photoreceptors (BL), based on a homology search in already sequenced, annotated genomes. The microarray carried 149 different 54-mer oligonucleotides, derived from consensus sequences of BL photoreceptors. The array could readily identify targets carrying 4% sequence mismatch, and allowed unambiguous identification of a positive cosmid clone of as little as 10 ng against a background of 25 μg of cosmid DNA. The protocol allows screening up to 1,200 library clones in concentrations as low as ca. 20 ng, each with a ca. 40 kb insert size readily in a single batch. Calibration and control conditions are outlined. This protocol, when applied to the thermophilic fraction of a soil sample, yielded the identification and functional characterization of a novel, BL-encoding gene that showed a 58% similarity to a known, BL-encoding gene from Kineococcus radiotolerans SRS30216 (similarity values refer to the respective LOV domains).

  10. Detection of perturbation phases and developmental stages in organisms from DNA microarray time series data.

    Directory of Open Access Journals (Sweden)

    Marianne Rooman

    Full Text Available Available DNA microarray time series that record gene expression along the developmental stages of multicellular eukaryotes, or in unicellular organisms subject to external perturbations such as stress and diauxie, are analyzed. By pairwise comparison of the gene expression profiles on the basis of a translation-invariant and scale-invariant distance measure corresponding to least-rectangle regression, it is shown that peaks in the average distance values are noticeable and are localized around specific time points. These points systematically coincide with the transition points between developmental phases or just follow the external perturbations. This approach can thus be used to identify automatically, from microarray time series alone, the presence of external perturbations or the succession of developmental stages in arbitrary cell systems. Moreover, our results show that there is a striking similarity between the gene expression responses to these a priori very different phenomena. In contrast, the cell cycle does not involve a perturbation-like phase, but rather continuous gene expression remodeling. Similar analyses were conducted using three other standard distance measures, showing that the one we introduced was superior. Based on these findings, we set up an adapted clustering method that uses this distance measure and classifies the genes on the basis of their expression profiles within each developmental stage or between perturbation phases.

  11. 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


    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.

  12. Indoor determinants of dustborne allergens in Mexican homes. (United States)

    Hernández-Cadena, Leticia; Zeldin, Darryl C; Barraza-Villarreal, Albino; Sever, Michelle L; Sly, Peter D; London, Stephanie J; Escamilla-Nuñez, María Consuelo; Romieu, Isabelle


    Exposure to indoor allergens represents a significant risk factor for allergies and asthma in several parts of the world. In Mexico, few studies have evaluated indoor allergens, including cat, dog, and mouse allergens and the factors that predict their presence. This study evaluates the main environmental and household predictors of high prenatal allergen levels and multiple allergen exposures in a birth cohort from Mexico City. A cross-sectional study was conducted as part of a birth cohort study of 1094 infants recruited during pregnancy and followed until delivery. We collected dust samples in a subset of 264 homes and assessed environmental factors. Der p 1, Der f 1, dust mite group 2, Fel d 1, Can f 1, Rat n 1, Mus m 1, and Bla g 2 concentrations in dust samples were measured using immunoassays. To define detectable allergen levels, the lowest limits of detection for each allergen were taken as cutoff points. Overall allergen exposure was considered high when four or more allergens exceeded detectable levels in the same household. Logistic regression was used for predictive models. Eighty-five percent of homes had at least one allergen in dust over the detection limit, 52.1% had high exposure (four or more allergens above detectable limits), and 11.7% of homes had detectable levels for more than eight allergens. Der p 1, Der p 2, Mus m 1, and Fel d 1 were the most frequent allergens detected. Each allergen had both common and distinct predictors. The main predictors of a high multiple allergen index were the size of the home, pesticide use, mother's age, mother as homemaker, and season. Increased indoor environmental allergen exposure is mainly related to sociodemographic factors and household cleaning.

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

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

    Directory of Open Access Journals (Sweden)

    Tözeren Aydin


    Full Text Available Abstract Background 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. Methods 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. Results 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. Conclusion 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

  15. Beneficial cross-protection of allergen-specific immunotherapy on airway eosinophilia using unrelated or a partial repertoire of allergen(s) implicated in experimental feline asthma. (United States)

    Reinero, Carol; Lee-Fowler, Tekla; Chang, Chee-Hoon; Cohn, Leah; Declue, Amy


    The study hypothesis was that in experimentally asthmatic cats rush immunotherapy (RIT) using allergens not completely matched with sensitizing allergen(s) would at least partially attenuate the asthmatic phenotype and modulate the aberrant immune response. In phase I, cats sensitized to Bermuda grass allergen (BGA), house dust mite allergen (HDMA) or placebo received BGA RIT. In phase II, cats dually sensitized to BGA and HDMA received RIT using BGA, HDMA or placebo. Efficacy of RIT was assessed using percentage bronchoalveolar lavage fluid (BALF) eosinophils. Additionally, a variety of immunologic assays were performed. Eosinophilic airway inflammation significantly decreased over time in asthmatic cats given RIT using sensitizing allergen or unrelated allergen (P<0.001). In dually sensitized cats, single allergen RIT but not placebo reduced airway eosinophilia (P=0.038). Differences in allergen-specific lymphocyte proliferation, in the number of IL-10 producing cells and in the percentage T regulatory cells were detected between asthmatic cats getting RIT and controls. Cross-protection manifested by reduced airway eosinophilia was noted in cats treated with RIT allergens which did not completely match allergen used in asthma induction. However, the mechanism of immunologic tolerance may differ when improperly matched allergens to the sensitizing allergens are used in RIT.

  16. Label-free detection of gliadin food allergen mediated by real-time apta-PCR. (United States)

    Pinto, Alessandro; Polo, Pedro Nadal; Henry, Olivier; Redondo, M Carmen Bermudo; Svobodova, Marketa; O'Sullivan, Ciara K


    Celiac disease is an immune-mediated enteropathy triggered by the ingestion of gluten. The only effective treatment consists in a lifelong gluten-free diet, requiring the food industry to tightly control the gluten contents of their products. To date, several gluten quantification approaches using antibodies are available and recommended by the legal authorities, such as Codex Alimentarius. However, whilst these antibody-based tests exhibit high sensitivity and specificity, the production of antibodies inherently requires the killing of host animals and is time-consuming and relatively expensive. Aptamers are structured single-stranded nucleic acid ligands that bind with high affinity and specificity to their cognate target, and aiming for a cost-effective viable alternative to the use of antibodies. Herein, we report the systematic evolution of ligands by exponential enrichment (SELEX)-based selection of a DNA aptamer against gliadin from a combinatorial DNA library and its application in a novel detection assay. Taking into account the hydrophobic nature of the gliadin target, a microtitre plate format was exploited for SELEX, where the target was immobilised via hydrophobic interactions, thus exposing aptatopes accessible for interaction with the DNA library. Evolution was followed using surface plasmon resonance, and following eight rounds of SELEX, the enriched DNA pool was cloned, sequenced and a clear consensus motif was identified. An apta-PCR assay was developed where competition for the aptamer takes place between the surface-immobilised gliadin and gliadin in the target sample, akin to an ELISA competitive format where the more target present in the sample, the less aptamer will bind to the immobilised gliadin. Following competition, any aptamer bound to the immobilised gliadin was heat-eluted and quantitatively amplified using real-time PCR, achieving a detection limit of approx. 2 nM (100 ng mL(-1)). The specificity of the selected aptamer was

  17. Evaluation of a real-time polymerase chain reaction (PCR) assay for detection of anisakis simplex parasite as a food-borne allergen source in seafood products. (United States)

    Lopez, Itziar; Pardo, Miguel Angel


    Anisakis simplex has been recognized as an important cause of disease in humans and as a food-borne allergen source. Actually, this food-borne parasite was recently identified as an emerging food safety risk. An A. simplex -specific primer-probe system based on a real-time polymerase chain reaction (PCR) detection assay has been successfully optimized and validated with seafood samples. In addition, a DNA extraction procedure has been optimized to detect the presence of the nematode in food samples. The assay is a very reliable, specific, and sensitive methodology to detect the presence of traces of this parasite in seafood products, including highly processed samples. As a result, 13 sequences of cytochrome c oxidase II gene were obtained and scrutinized to calculate intra- and interspecific variabilities of 0 and 35-67%, respectively. Finally, an efficiency of 2.07 +/- 0.14 of the assay was calculated, and a limit of detection of 40 ppm parasite in 25 g of sample was also optimized. Actually, the presence of this parasite in several seafood products has been demonstrated, enforcing the necessity of a design for a good manufacturing practice protocol for the processing industry to minimize the presence of this parasite as a food-borne allergen source in seafood products.

  18. Managing allergens in food

    NARCIS (Netherlands)

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


    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

  19. Detection of airborne allergen (Pla a 1 in relation to Platanus pollen in Córdoba, South Spain

    Directory of Open Access Journals (Sweden)

    Purificación Alcázar


    Full Text Available Córdoba is one of the Spanish cities with the highest records of plane tree pollen grains in the air. Clinical studies have identified[i] Platanus[/i] as a major cause of pollinosis. This fact provokes an important public health problem during early spring when these trees bloom. The objective of the study is to evaluate the correlation between airborne pollen counts and Pla a 1 aeroallergen concentrations in Córdoba, to elucidate if airborne pollen can be an accurate measure that helps to explain the prevalence of allergenic symptoms. Pollen sampling was performed during 2011–2012 using a Hirst-type sampler. Daily average concentration of pollen grains (pollen grains/m 3 was obtained following the methodology proposed by the Spanish Aerobiology Network. A multi-vial cyclone was used for the aeroallergen quantification. Allergenic particles were measured by ELISA using specific antibodies Pla a 1. The trend of[i] Platanus[/i] pollen was characterized by a marked seasonality, reaching high concentrations in a short period of time. Airborne pollen and aeroallergen follow similar trends. The overlapping profile between both variables during both years shows that pollen and Pla a 1 are significantly correlated. The highest significant correlation coefficients were obtained during 2011 and for the post peak. Although some studies have found notable divergence between pollen and allergen concentrations in the air, in the case of [i]Platanus[/i] in Córdoba, similar aerobiological dynamics between pollen and Pla a 1 have been found. Allergenic activity was found only during the plane tree pollen season, showing a close relationship with daily pollen concentrations. The obtained pollen potency was similar for both years of study. The results suggest that the allergenic response in sensitive patients to plane tree pollen coincide with the presence and magnitude of airborne pollen.

  20. Multiplex Detection and Genotyping of Point Mutations Involved in Charcot-Marie-Tooth Disease Using a Hairpin Microarray-Based Assay

    Directory of Open Access Journals (Sweden)

    Yasser Baaj


    Full Text Available We previously developed a highly specific method for detecting SNPs with a microarray-based system using stem-loop probes. In this paper we demonstrate that coupling a multiplexing procedure with our microarray method is possible for the simultaneous detection and genotyping of four point mutations, in three different genes, involved in Charcot-Marie-Tooth disease. DNA from healthy individuals and patients was amplified, labeled with Cy3 by multiplex PCR; and hybridized to microarrays. Spot signal intensities were 18 to 74 times greater for perfect matches than for mismatched target sequences differing by a single nucleotide (discrimination ratio for “homozygous” DNA from healthy individuals. “Heterozygous” mutant DNA samples gave signal intensity ratios close to 1 at the positions of the mutations as expected. Genotyping by this method was therefore reliable. This system now combines the principle of highly specific genotyping based on stem-loop structure probes with the advantages of multiplex analysis.

  1. Reexploring the Possible Roles of Some Genes Associated with Nasopharyngeal Carcinoma Using Microarray-based Detection

    Institute of Scientific and Technical Information of China (English)

    Wei-Yi FANG; Xin LI; Yan-Qing DING; Kai-Tai YAO; Teng-Fei LIU; Wei-Bing XIE; Xu-Yu YANG; Shuang WANG; Cai-Ping REN; Xin DENG; Qiu-Zhen LIU; Zhong-Xi HUANG


    In gene expression profiling, nasopharyngeal carcinoma (NPC) 5-8F cells differ from 6-10B cells in terms of their high tumorigenicity and metastatic ability. Differentially expressed genes from the two cell types were analyzed by combining with MILANO (the automatic custom annotation of microarray results which is based on all the available published work in PubMed). The results showed that five genes, including CTSD, P63, CSE1L, BPAG1 and EGR1, have been studied or mentioned in published work on NPC. Subsequently, we revaluated the roles of these genes in the pathogenesis of NPC by combining the data of gene chips from NPCs versus NPs and pooled cells from 5-8F, 6-10B and CNE2 versus NPs. The results suggested that the roles of BPAG1 and EGR1 are possibly different from those reported in previous NPC studies. These five genes are likely to be involved in the proliferation, apoptosis, invasion and metastasis of NPC. A reexploration of the genes will further define their roles in the pathogenesis of NPC.

  2. Food allergen digestibility: The influence on allergenicity

    DEFF Research Database (Denmark)

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard

    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 allergenicity, leading to the conclusion, that a correlation between stability to digestion and allergenic...... 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...

  3. On-Chip Isothermal Nucleic Acid Amplification on Flow-Based Chemiluminescence Microarray Analysis Platform for the Detection of Viruses and Bacteria. (United States)

    Kunze, A; Dilcher, M; Abd El Wahed, A; Hufert, F; Niessner, R; Seidel, M


    This work presents an on-chip isothermal nucleic acid amplification test (iNAAT) for the multiplex amplification and detection of viral and bacterial DNA by a flow-based chemiluminescence microarray. In a principle study, on-chip recombinase polymerase amplification (RPA) on defined spots of a DNA microarray was used to spatially separate the amplification reaction of DNA from two viruses (Human adenovirus 41, Phi X 174) and the bacterium Enterococcus faecalis, which are relevant for water hygiene. By establishing the developed assay on the microarray analysis platform MCR 3, the automation of isothermal multiplex-amplification (39 °C, 40 min) and subsequent detection by chemiluminescence imaging was realized. Within 48 min, the microbes could be identified by the spot position on the microarray while the generated chemiluminescence signal correlated with the amount of applied microbe DNA. The limit of detection (LOD) determined for HAdV 41, Phi X 174, and E. faecalis was 35 GU/μL, 1 GU/μL, and 5 × 10(3) GU/μL (genomic units), which is comparable to the sensitivity reported for qPCR analysis, respectively. Moreover the simultaneous amplification and detection of DNA from all three microbes was possible. The presented assay shows that complex enzymatic reactions like an isothermal amplification can be performed in an easy-to-use experimental setup. Furthermore, iNAATs can be potent candidates for multipathogen detection in clinical, food, or environmental samples in routine or field monitoring approaches.

  4. Mammalian-derived respiratory allergens - implications for diagnosis and therapy of individuals allergic to furry animals. (United States)

    Nilsson, Ola B; van Hage, Marianne; Grönlund, Hans


    Furry animals cause respiratory allergies in a significant proportion of the population. A majority of all mammalian allergens are spread as airborne particles, and several have been detected in environments where furry animals are not normally kept. The repertoire of allergens from each source belongs to a restricted number of allergen families. Classification of allergen families is particularly important for the characterization of allergenicity and cross-reactivity of allergens. In fact, major mammalian allergens are taken from only three protein families, i.e. the secretoglobin, lipocalin and kallikrein families. In particular, the lipocalin superfamily harbours major allergens in all important mammalian allergen sources, and cross-reactivity between lipocalin allergens may explain cross-species sensitization between mammals. The identification of single allergen components is of importance to improve diagnosis and therapy of allergic patients using component-resolved diagnostics and allergen-specific immunotherapy (ASIT) respectively. Major disadvantages with crude allergen extracts for these applications emphasize the benefits of careful characterization of individual allergens. Furthermore, detailed knowledge of the characteristics of an allergen is crucial to formulate attenuated allergy vaccines, e.g. hypoallergens. The diverse repertoires of individual allergens from different mammalian species influence the diagnostic potential and clinical efficacy of ASIT to furry animals. As such, detailed knowledge of individual allergens is essential for adequate clinical evaluation. This review compiles current knowledge of the allergen families of mammalian species, and discusses how this information may be used for improved diagnosis and therapy of individuals allergic to mammals.

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

    DEFF Research Database (Denmark)

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


    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...

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

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


    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. Properties of tree and grass pollen allergens: reinvestigation of the linkage between solubility and allergenicity. (United States)

    Vrtala, S; Grote, M; Duchêne, M; van Ree, R; Kraft, D; Scheiner, O; Valenta, R


    In this study we reinvestigated the kinetics of allergen release from birch pollen (Betula verrucosa) and timothy grass pollen (Phleum pratense) using different protein extraction procedures, immunoblotting with specific antibodies and immune electron microscopy. Pollen allergens such as the major birch pollen allergen, Bet v I, the major timothy grass pollen allergens, Phl p I and Phl p V, group-II/III allergens from timothy grass and profilins were released rapidly and in large amounts from hydrated pollen. Within a few minutes pollen allergens could be detected in aqueous supernatants prepared from birch and grass pollen with serum IgE or specific antibodies. In parallel the allergen content in the pollen pellet fractions decreased. A nonallergenic protein such as heat shock protein 70 can be extracted in sufficient amounts only with harsh extraction procedures. Immune electron microscopy of dry and rehydrated birch pollens showed that after short hydration, the major birch pollen allergen, Bet v I, migrated into the exine and to the surface of intact pollen grains, whereas profilin, against which a lower percentage of patients is sensitized, was retained in the pollen grain. Comparing the amino acid composition and hydrophilicity of the tested allergens with a nonallergenic protein such as heat shock protein 70, no significant difference was noted. In agreement with earlier observations we conclude that the allergenic properties of proteins are rather linked to the amount and speed of solubility from airborne particles than to intrinsic properties.

  8. Microarray-based method for detecting methylation changes of p16Ink4a gene 5'-CpG islands in gastric carcinomas

    Institute of Scientific and Technical Information of China (English)

    Peng Hou; Jia-Yao Shen; Mei-Ju Ji; Nong-Yue He; Zu-Hong Lu


    AIM: Aberrant DNA methylation of CpG site is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation of the CpG sites of the tumor suppressor gene is closely associated with carcinogenesis. However, large-scale analysis of candidate genes has so far been hampered by the lack of highthroughput approach for analyzing DNA methylation. The aim of this study was to describe a microarray-based method for detecting changes of DNA methylation in cancer.METHODS: This method used bisulfite-modified DNA as a template for PCR amplification, resulting in conversion of unmethylated cytosine, but not methylated cytosine, into thymine within CpG islands of interest. Therefore, the amplified product might contain a pool of DNA fragments with altered nucleotide sequences due to differential methylation status.Nine sets of oligonucleotide probes were designed to fabricate a DNA microarray to detect the methylation changes of p16 gene CpG islands in gastric carcinomas. The results were further validated by methylation-specific PCR (MSP).RESULTS: The experimental results showed that the microarray assay could successfully detect methylation changes of p16 gene in 18 gastric tumor samples. Moreover,it could also potentially increase the frequency of detecting p16 methylation from tumor samples than MSP.CONCLUSION: Microarray assay could be applied as a useful tool for mapping methylation changes in multiple CpG loci and for generating epigenetic profiles in cancer.

  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


    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. Detection of hazelnut allergens by real time PCR assay%实时荧光PCR法检测食物中榛子过敏原成分

    Institute of Scientific and Technical Information of China (English)

    孙敏; 梁君妮; 徐彪; 高宏伟; 林超; 刘彩霞


    Hazelnut is one of the most common allergens. After experimenting on primers and probes specific to different genes of hazelnut and optimizing experimental parameters, a real time PCR assay for detecting hazelnut allergen was established. The primers and probes targeting hspl gene were proved to be preferable,which had a sensitivity up to 0.1 1ng purified DNA and had no cross-reactions with other species. This assay may provide a potential tool for food allergens supervision, which is of importance in protecting consumers' right and promoting exportation.%榛子是最常见的食品过敏原之一,选择针对榛子不同基因的引物和探针,进行验证、比对和条件优化,建立榛子过敏原的实时荧光PCR检测方法经实验比较,针对榛子热休克蛋白设计合成的引物和探针具有相对较高的灵敏性,检测限可达0.1 lng DNA,而且和常见的食物种类无交叉反应,适于榛子过敏原的检测.该方法的建立,对于加强食品过敏原的标识管理,保护消费者利益、促进进出口贸易具有重要意义.

  11. Comparison between two commercial immunoassays: Dr. Fooke ALLERG-O-LIQ versus Phadia ImmunoCA(R) System in detecting allergen-specific IgE and total IgE values

    Institute of Scientific and Technical Information of China (English)

    Baoqing Sun; Mahler Michael; Mei Jiang; Jing Li; Nanshan Zhong


    Objective: Beside patient's history and skin prick testing(SPT) the detection of specific IgE(slgE) represents an important tool of allergy diagnostics. In recent years different technologies for the detection of sIgE have been developed. The objective of this study is the comparison of the ALLERG-O-LIQ with the ImmunoCAP System using seven inhalant and four food allergens. Methods: Sera from patients were collected and tested for sIgE to inhalant(d1, d2, d5, i6, el, e5 and m3) and food allergens(fl, 12, f24, t24) by ALLERG-O-LIQ(Dr. Fooke Laboratorien GmbH) and by ImmunoCAP System(Phadia). Further, samples were also tested for total IgE in both systems. Results: Prevalence of positive test results varied between 0/20(124) and 11/20(e5) for ALLERG-O-LIQ and between 3/18(f23) and 11/20(d1/d5) for ImmunoCAP . The qualitative agreement between both methods was found between 75%(f24) and 100%(d2) depending on the allergen. Overall qualitative agreement for inhalant(n = 140), food(n = 78) and all allergens(n = 218) tested was 92.1%(kappa = 0.84), 83.3%(kappa = 0.58), 89.0%(kappa = 0.77), respectively. Sensitivity, specificity, positive predictive value (PPV), negative predictive value(NPV) and diagnostic efficiency(DE) were found at 88.2%, 95.8%, 95.2%, 89.6%, 92.1%(inhalant allergens), 62.5%, 92.6%, 78.9%, 84.7%, 83.3%(food allergens) and 81.5%, 94.4%, 91.5%, 87.5%, 89.0%(all allergens). Conclusion: Good to excellent qualitative agreement between ALLERG-O-LIQ and ImmunoCAP for the detection of specific and total IgE could be observed. The degree of agreement depended on the allergen and was higher in the group of inhalant allergens. The ALLERG-O-LIQ System represents a reliable test for the detection of specific and total IgE.

  12. Hybrid microarray based on double biomolecular markers of DNA and carbohydrate for simultaneous genotypic and phenotypic detection of cholera toxin-producing Vibrio cholerae. (United States)

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


    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.

  13. 哮喘儿童血清变应原特异性IgE检测与分布特征%Detection and distribution characteristics of serum allergen-specific IgE in children with asthma

    Institute of Scientific and Technical Information of China (English)

    吕慧; 刘建忠


    Objective: To understand the distribution characteristics of allergens in children with asthma Methods: 256 children with asthma received serum aspiratory and ingestive allergen - specific IgE detection. Results: The positive rate of aspiratory allergen - specific IgE in children with asthma was 82. 4% (211 children), 71.1% of the children had two or more than two kinds of positive allergen specific IgE; the positive rate of ingestive allergen- specific IgE in children with asthma was 17. 6% (45 children), 8.2% of the children had two or more than two kinds of positive allergen - specific IgE. Conclusion: The main allergen of children with asthma is aspiratory allergen, the most are mixed allergen sensitization, the incidences on summer and autumn increase in recent years, weeds and pollens on summer and autumn may be allergens.%目的:了解哮喘患儿过敏原分布特征.方法:256例哮喘患儿分别进行血清吸人性和食人性过敏原特异性IgE检测.结果:哮喘患儿吸入性过敏原特异性IgE阳性211例,阳性率为82.4%,71.1%为两种或两种以上过敏原特异性IgE阳性;食人性过敏原特异性IgE阳性45例,阳性率为17.6%,8.2%为两种或两种以上过敏原特异性IgE阳性.结论:哮喘患儿以吸入性过敏原为主,多数为多种过敏原混合致敏,近年夏秋季发病率升高,夏秋季杂草花粉可能为其过敏原.

  14. Allergen characteristic and clinical detection meaning of children asthma%儿童哮喘过敏原特征及其临床检测意义

    Institute of Scientific and Technical Information of China (English)



    Objective To explore allergen characteristic and clinical detection meaning of children asthma. Methods With case-control study method, 135 children with asthma and 140 healthy children through physical examination were respec-tively accepted questionnaire investigation, skin prick test and serum allergen detection. The positive rates of inhaled allergens and food allergens, family history of asthma and history of hypersensitivity disease, IgE positive rate of serum were compared be-tween the two groups. Results The positive rates of allergen such as dust mite, pollen, cat dog dander, plumery, Blattella ger-manica, milk, egg white and flesh in the asthma group were much higher than those of the control group (P<0. 05). Multiple factors analysis result showed that these factors of family history of allergy (OR=3. 662), history of asthma of first-degree relative (OR=8. 388), history of asthma of second-degree relative (OR=5. 775), allergic rhinitis history (OR=5. 569), drug allergy history (OR=7. 942) and eczema history (OR=6. 716) in the asthma group were much higher than those of the control group (P<0. 01). The positive rates of TIgE and SIgE in the asthma group were respectively 48. 1% and 65. 2%, both much higher than those of the control group (22. 9% and 27. 1%, both P<0. 01). Conclusion The influencing factors of asthma include family history of asthma, family history of allergy, eczema history, inhaled allergens and food allergens. Skin prick test and serum IgE detection play an important role in detecting allergen of children asthma.%目的:探讨儿童哮喘的过敏原特征及其临床检测意义。方法采用病例对照的研究方法,对135例哮喘患儿和140例健康体检儿童分别进行问卷调查、皮肤点刺试验、血清过敏原检测等,比较分析2组的吸入性过敏原和食物性过敏原的阳性率、哮喘既往家族史及过敏性疾病史、血清学IgE阳性率等。结果哮喘组的尘螨、花粉、猫狗皮毛

  15. Detection of Lupine (Lupinus spp. L. as a food allergen using three methods: end-point PCR, Real-Time PCR and Elisa

    Directory of Open Access Journals (Sweden)

    Ondrej Revák


    Full Text Available The aim of this work was to compare three methods for the detection and quantification of lupine as an allergen in food. The methods that were used in this work were the direct method: ELISA and the indirect methods: end-point PCR and real-time PCR. We examined the detection limit (the sensitivity with which we can detect the presence of the allergen in a sample and the reliability for performing an analysis. We used 17 samples of plant species from a processing plant for dehydrated soups production and lupine samples from lupine processing companies. Its practical use is wide and it is used mainly in the bakery industry, in the manufacture of confectionery, pasta, sauces, as a substitute for soy and also in the production of gluten-free food, because it does not contain gluten. Lupine, however, is also included in the list of 14 allergenic substances, which in accordance with the EU legislation must be listed on food labels. The high risk group, which suffers from primary sensitization or cross-reaction with peanuts, are allergic patients. In the EU, people who are allergic to peanuts range from 0.7 to 1.5%. In experiment 1, we detected the presence of lupine using primers for the detection of α- and δ-conglutine in the samples, using the end-point PCR method and the detection limit of this reaction was at the level of 100 ppm. For the vizualization of the DNA fragments, we used a 2% agarose gel and UV visualizer. In experiment 2 we detected lupine using the TaqMan real-time PCR reaction and primers for the detection of α and δ-conglutine at the level of 10 ppm of lupine in sample. The CP values of lupine using primers for the detection of α-conglutine was 24.85 ± 0.12 and the reliability equation was R2 = 0.9767. The CP lupine values using primers for the detection of δ-conglutine was 22.52 ± 0.17 and the reliability equation was R2 = 0.9925. In experiment 3, we used a sandwich ELISA method for the detection of lupine and the

  16. Detection and structural characterization of natural Ara h 7, the third peanut allergen of the 2S albumin family. (United States)

    Schmidt, Hendrik; Krause, Susanne; Gelhaus, Christoph; Petersen, Arnd; Janssen, Ottmar; Becker, Wolf-Meinhard


    In recent years, several novel relevant peanut allergens have been identified. Among those, a new member of the conglutin family was cloned by a phage display approach and initially annotated as Ara h 7.0101. Later, however, recloning of Ara h 7 revealed an alternate isoform, termed Ara h 7.0201. Because the natural Ara h 7 counterpart had not been found at the protein level in peanut extracts, the aim of the present study was to search for authentic natural Ara h 7 protein(s). To this end, enriched low molecular mass proteins (amylase/trypsin inhibitors.

  17. Immunotherapy with Allergen Peptides


    Larché Mark


    Specific allergen immunotherapy (SIT) is disease-modifying and efficacious. However, the use of whole allergen preparations is associated with frequent allergic adverse events during treatment. Many novel approaches are being designed to reduce the allergenicity of immunotherapy preparations whilst maintaining immunogenicity. One approach is the use of short synthetic peptides which representing dominant T cell epitopes of the allergen. Short peptides exhibit markedly reduced capacity to cro...

  18. Allergens in veterinary medicine



    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...

  19. A new direction for prenatal chromosome microarray testing: software-targeting for detection of clinically significant chromosome imbalance without equivocal findings

    Directory of Open Access Journals (Sweden)

    Joo Wook Ahn


    Full Text Available Purpose. To design and validate a prenatal chromosomal microarray testing strategy that moves away from size-based detection thresholds, towards a more clinically relevant analysis, providing higher resolution than G-banded chromosomes but avoiding the detection of copy number variants (CNVs of unclear prognosis that cause parental anxiety.Methods. All prenatal samples fulfilling our criteria for karyotype analysis (n = 342 were tested by chromosomal microarray and only CNVs of established deletion/duplication syndrome regions and any other CNV >3 Mb were detected and reported. A retrospective full-resolution analysis of 249 of these samples was carried out to ascertain the performance of this testing strategy.Results. Using our prenatal analysis, 23/342 (6.7% samples were found to be abnormal. Of the remaining samples, 249 were anonymized and reanalyzed at full-resolution; a further 46 CNVs were detected in 44 of these cases (17.7%. None of these additional CNVs were of clear clinical significance.Conclusion. This prenatal chromosomal microarray strategy detected all CNVs of clear prognostic value and did not miss any CNVs of clear clinical significance. This strategy avoided both the problems associated with interpreting CNVs of uncertain prognosis and the parental anxiety that are a result of such findings.

  20. 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


    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.

  1. Allergenic fragments of ryegrass (Lolium perenne) pollen allergen Lol p IV. (United States)

    Jaggi, K S; Ekramoddoullah, A K; Kisil, F T


    To facilitate studies on establishing the nature of structure/function relationships of allergens, ryegrass pollen allergen, Lol p IV, was cleaved into smaller fragments by cyanogen bromide (CNBr) and the resulting peptides were further digested with trypsin. The resulting peptides were then fractionated by high performance liquid chromatography (HPLC) on a C-18 reverse phase column. The allergenic activity of the HPLC fractions was evaluated in terms of their ability to inhibit the binding of 125I-Lol p IV to serum IgE antibodies of a grass-allergic patient. Many of these fractions inhibited the binding between the native allergen and IgE antibodies in a dose-dependent manner. The inhibitions were specific, i.e., the fractions did not inhibit the binding between 125I-Lol p I (a group-I ryegrass pollen allergen) and the IgE antibodies present in the allergic human serum. The possibility that the allergenic peptide fractions were contaminated by the native undegraded allergen, which might have accounted for the observed inhibition, was ruled out by the fact that the native allergen could not be detected by SDS-PAGE and the elution profiles of allergenically active peptides did not coincide with that of native allergen. One of the allergenic sites recognized by monoclonal antibody (Mab) 90, i.e., site A, was located in HPLC fractions 90-100 while another allergenic site B (recognized by Mab 12) appeared to be lost following the sequential digestion of Lol p IV with CNBr and trypsin.

  2. New tree nut allergens (United States)

    The 7S vicilin and 11S legumin seed storage globulins belong to the cupin protein superfamily and are major food allergens in many of the “big eight” food allergen groups. Korean pine vicilin and pecan vicilin are thus predicted to be food allergens. Recombinant vicilins were expressed in E. coli an...

  3. 4p16.3 microdeletions and microduplications detected by chromosomal microarray analysis: New insights into mechanisms and critical regions. (United States)

    Bi, Weimin; Cheung, Sau-Wai; Breman, Amy M; Bacino, Carlos A


    Deletions in the 4p16.3 region cause Wolf-Hirschhorn syndrome, a well known contiguous microdeletion syndrome with the critical region for common phenotype mapped in WHSCR2. Recently, duplications in 4p16.3 were reported in three patients with developmental delay and dysmorphic features. Through chromosomal microarray analysis, we identified 156 patients with a deletion (n = 109) or duplication (n = 47) in 4p16.3 out of approximately 60,000 patients analyzed by Baylor Miraca Genetics Laboratories. Seventy-five of the postnatally detected deletions encompassed the entire critical region, 32 (43%) of which were associated with other chromosome rearrangements, including six patients (8%) that had a duplication adjacent to the terminal deletion. Our data indicate that Wolf-Hirschhorn syndrome deletions with an adjacent duplication occur at a higher frequency than previously appreciated. Pure deletions (n = 14) or duplications (n = 15) without other copy number changes distal to or inside the WHSCR2 were identified for mapping of critical regions. Our data suggest that deletion of the segment from 0.6 to 0.9 Mb from the terminus of 4p causes a seizure phenotype and duplications of a region distal to the previously defined smallest region of overlap for 4p16.3 microduplication syndrome are associated with neurodevelopmental problems. We detected seven Wolf-Hirschhorn syndrome deletions and one 4p16.3 duplication prenatally; all of the seven are either >8 Mb in size and/or associated with large duplications. In conclusion, our study provides deeper insight into the molecular mechanisms, the critical regions and effective prenatal diagnosis for 4p16.3 deletions/ duplications. © 2016 Wiley Periodicals, Inc.

  4. 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


    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.

  5. A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of unknown microorganisms

    Directory of Open Access Journals (Sweden)

    McCormick John


    Full Text Available Abstract Background The ability to differentiate a bioterrorist attack or an accidental release of a research pathogen from a naturally occurring pandemic or disease event is crucial to the safety and security of this nation by enabling an appropriate and rapid response. It is critical in samples from an infected patient, the environment, or a laboratory to quickly and accurately identify the precise pathogen including natural or engineered variants and to classify new pathogens in relation to those that are known. Current approaches for pathogen detection rely on prior genomic sequence information. Given the enormous spectrum of genetic possibilities, a field deployable, robust technology, such as a universal (any species microarray has near-term potential to address these needs. Results A new and comprehensive sequence-independent array (Universal Bio-Signature Detection Array was designed with approximately 373,000 probes. The main feature of this array is that the probes are computationally derived and sequence independent. There is one probe for each possible 9-mer sequence, thus 49 (262,144 probes. Each genome hybridized on this array has a unique pattern of signal intensities corresponding to each of these probes. These signal intensities were used to generate an un-biased cluster analysis of signal intensity hybridization patterns that can easily distinguish species into accepted and known phylogenomic relationships. Within limits, the array is highly sensitive and is able to detect synthetically mixed pathogens. Examples of unique hybridization signal intensity patterns are presented for different Brucella species as well as relevant host species and other pathogens. These results demonstrate the utility of the UBDA array as a diagnostic tool in pathogen forensics. Conclusions This pathogen detection system is fast, accurate and can be applied to any species. Hybridization patterns are unique to a specific genome and these can be used

  6. Detection of Yersinia enterocolitica in alfalfa, mung bean, cilantro, and mamey sapote (Pouteria sapota) food matrices using DNA microarray chip hybridization. (United States)

    Siddique, Nusrat; Sharma, Devang; Al-Khaldi, Sufian F


    Four different food matrices (alfalfa, cilantro, mamey sapote, and mung bean) were contaminated with three different dilutions 10(6), 10(4), and 10(3) cfu/g of Yersinia enterocolitica. DNA was isolated from each food mix and used in chromosomal amplifications. The amplified DNA was used as templates in single PCR reactions of the four genes (virF, ail, yst, and blaA) followed by mixing the four reactions for one PCR primer extension reaction. The presence and the limit of detection of four genes in four food matrices were established by microarray hybridization. Data revealed the diversity of signal intensities. Neither the microarray chip hybridization nor the single PCR amplification could detect virF's presence located on a plasmid. Ail was detected in 10(3) cfu/g, whereas blaA and yst were detected from 10(5) to 10(6) cfu/g in all food matrices. Therefore, the ail gene could be the gene of choice in identifying Y. enterocolitica in alfalfa, cilantro, mamey, and mung bean. Other genes--blaA, yst, virF--exhibited wide variability in hybridization signals, highlighting the need of a better DNA purification step prior to DNA microarray hybridization.

  7. Standardization of RP-HPLC methods for the detection of the major peanut allergens Ara h 1, Ara h 2 and Ara h 3. (United States)

    Singh, Harmit; Cantoria, Mary Jo; Malave, Poonam; Saputra, Denny; Maleki, Soheila


    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 220nm) and under different solvent conditions. HPLC profiles were compared for retention time, resolution, and peak heights. CPE samples were spiked with pure allergens to identify the peaks corresponding to allergens. The HPLC fractions of corresponding allergens were collected and freeze-dried in order to perform SDS-PAGE and immunoblotting tests. The best method was identified the one with a shorter retention time, better resolution, and greater peak height as compared with the other methods. In general, the peak heights were greater at 220nm than at 280nm. The major disadvantage of the C12 column was the need for two sets of conditions to identify the allergens as compared to the C18 column where all three allergens could be identified in one run.

  8. Glucose transporter Glut-1 is detectable in peri-necrotic regions in many human tumor types but not normal tissues: Study using tissue microarrays. (United States)

    Airley, Rachel; Evans, Andrew; Mobasheri, Ali; Hewitt, Stephen M


    The hypoxic tumor microenvironment is associated with malignant progression and poor treatment response. The glucose transporter Glut-1 is a prognostic factor and putative hypoxia marker. So far, studies of Glut-1 in cancer have utilized conventional immunohistochemical analysis in a series of individual biopsy or surgical specimens. Tissue microarrays, however, provide a rapid, inexpensive means of profiling biomarker expression. To evaluate hypoxia markers, tissue cores must show the architectural features of hypoxia; i.e. viable tissue surrounding necrotic regions. Glut-1 may be a useful biomarker to validate tissue microarrays for use in studies of hypoxia-regulated genes in cancer. In this study, we carried out immunohistochemical detection of Glut-1 protein in many tumor and normal tissue types in a range of tissue microarrays. Glut-1 was frequently found in peri-necrotic regions, occurring in 9/34 lymphomas, 6/12 melanomas, and 5/16 glioblastomas; and in 43/54 lung, 22/84 colon, and 23/60 ovarian tumors. Expression was rare in breast (6/40) and prostate (1/57) tumors, and in normal tissue, was restricted to spleen, tongue, and CNS endothelium. In conclusion, tissue microarrays enable the observation of Glut-1 expression in peri-necrotic regions, which may be linked to hypoxia, and reflect previous studies showing differential Glut-1 expression across tumor types and non-malignant tissue.

  9. Detection of cashew allergen in food with PCR%食品中腰果过敏原成分PCR检测方法建立

    Institute of Scientific and Technical Information of China (English)

    袁飞; 陈颖; 暴书婵; 杨海荣; 赵勇胜; 吴亚君; 王斌; 邓婷婷; 黄文胜; 赵贵明


    Objective To develop a PCR method for detection of cashew allergen in food. Methods Nut DNA was extracted with alkyl trimethyl ammonium bromide( CTAB ) and magnetic microspheres. Nine pairs of primers were designed according to cashew allergenic protein gene sequences from NCBI GenBank and a pair of specific primers was screened out by amplifying results. Thirteen nut samples were determined using double PCR with the cashew-specific primer pair AnaO3 F3R3 and plant universal primer pair Plant159. The sensitivity of the PCR method was detected by DNA gradient dilution experiment and the detection of cashew allergen in food was simulated by stimulated sample experiment. Results A260/A280 of DNA extracted by CTAB method was lower than 1. 8, which meant there was protein contamination. While A260/A280 of DNA extracted by magnetic bead method was higher than 1.8, which meant the protein was cleaned. The specificity of primer pair AnaO3 F3R3 was best among the 9 primer pairs and the best anneal temperature was 55.4 ℃. Double PCR method was established to detect cashew and the other 12 kinds of nuts with primer plant 159 and AnaO3 F3R3. Only for cashew the 312bp specific band was amplified. The sensitivity of the method was 0. lpg/μl. And 0. 001% cashew allergen in food could be detected. Conclusion A PCR method for detection of cashew allergen was developed and the method can be used to detect cashew allergen effectively, rapidly, differentially, and sensitively.%目的 建立食品中腰果过敏原成分的PCR检测方法.方法 采用溴化十六烷三甲基胺(CTAB)法和磁珠法提取的坚果DNA,根据GenBank中腰果3种主要致敏蛋白AnaO1、AnaO2、AnaO3的基因序列,设计9对引物;通过扩增效果和特异性,筛选腰果最佳扩增引物对;采用腰果特异性引物对AnaO3 F3R3和植物通用引物对Plant 159,对腰果、杏仁、开心果等13种坚果成分进行双重PCR扩增,确定方法特异性;通过腰果DNA梯度稀释确定该

  10. Allergens in veterinary medicine. (United States)

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


    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.

  11. Rapid and Sensitive Multiplex Detection of Burkholderia pseudomallei-Specific Antibodies in Melioidosis Patients Based on a Protein Microarray Approach.

    Directory of Open Access Journals (Sweden)

    Christian Kohler


    Full Text Available The environmental bacterium Burkholderia pseudomallei causes the infectious disease melioidosis with a high case-fatality rate in tropical and subtropical regions. Direct pathogen detection can be difficult, and therefore an indirect serological test which might aid early diagnosis is desirable. However, current tests for antibodies against B. pseudomallei, including the reference indirect haemagglutination assay (IHA, lack sensitivity, specificity and standardization. Consequently, serological tests currently do not play a role in the diagnosis of melioidosis in endemic areas. Recently, a number of promising diagnostic antigens have been identified, but a standardized, easy-to-perform clinical laboratory test for sensitive multiplex detection of antibodies against B. pseudomallei is still lacking.In this study, we developed and validated a protein microarray which can be used in a standard 96-well format. Our array contains 20 recombinant and purified B. pseudomallei proteins, previously identified as serodiagnostic candidates in melioidosis. In total, we analyzed 196 sera and plasmas from melioidosis patients from northeast Thailand and 210 negative controls from melioidosis-endemic and non-endemic regions. Our protein array clearly discriminated between sera from melioidosis patients and controls with a specificity of 97%. Importantly, the array showed a higher sensitivity than did the IHA in melioidosis patients upon admission (cut-off IHA titer ≥1:160: IHA 57.3%, protein array: 86.7%; p = 0.0001. Testing of sera from single patients at 0, 12 and 52 weeks post-admission revealed that protein antigens induce either a short- or long-term antibody response.Our protein array provides a standardized, rapid, easy-to-perform test for the detection of B. pseudomallei-specific antibody patterns. Thus, this system has the potential to improve the serodiagnosis of melioidosis in clinical settings. Moreover, our high-throughput assay might be useful

  12. Analysis of detection of allergens in 284 chronic urticaria cases in Zhuhai City%珠海地区慢性荨麻疹284例患者过敏原检测分析

    Institute of Scientific and Technical Information of China (English)

    王晓鸿; 蒋明华; 肖佐环


    Aim To investigate significance of allergens in pathogenesis of chronic urticaria. Methods Allergens in 133 female and 151 male cases with chronic urticaria were tested in vitro,including total serum IgE,inhalational allergens and ingestive allergens. Results The positive rates of IgE in 133 female cases and 151 male case were 92.30%(120/133)and 81.46%(123/133).The common allergens detected were house dust,acarid,fish and seafood. Conclusions Both inhalational and ingestive allergens are closely related to chronic urticaria.%目的 探讨过敏原在慢性荨麻疹发病中的意义.方法 采用过敏反应体外检测系统(IVT)对284例慢性荨麻疹患者进行血清总IgE检测、吸入性过敏原和食入性过敏原检测.结果 133例女性患者血清总IgE阳性120例,阳性率为92.30%,151例男性患者血清总IgE阳性123例,阳性率81.46%,吸入性过敏原过敏原阳性的多见于屋尘、尘螨,食入性过敏原阳性的多见于鱼类、海鲜类.结论 吸入性及食入性过敏原与慢性荨麻疹的发病密切相关.

  13. 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


    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.

  14. Construction, detection and microarray analysis on Shigella dysenteriae A1 IroN, ShuA single, double mutants

    Institute of Scientific and Technical Information of China (English)

    BIN; Wen; LIU; Moqing; PENG; Junping; SUN; Lilian; XU; Xingye; ZHANG; Jinghai; JIN; Qi


    In this study, we constructed single mutants MTS-1, MTS-2 of IroN and ShuA gene and double mutant MTS of them in Shigella dysenteriae A1 strain 51197 by insert and absence. The functional detection of every mutant was performed at the level of culture medium and cell experiment. The gene expression profiles of the mutants and the wild-type strains under iron- enriched and iron-limited conditions were analyzed by the SD51197 whole genomic microarray. The results showed that all the mutants grew obviously less well than the wild-type strains in L broth appending iron chelator DIP. The addition of iron to the cultures can stimulate the growth of mutants back to wild-type levels. In either the experiments on the ability of intracellular multiplication or the cell-to-cell spread in HeLa and U937 cell lines, mutants showed no obvious change in virulence compared with the parental strain SD51197. However when DIP was added to the cultured HeLa cells, the ability of intracellular multiplication of MTS-1, MTS-2, MTS has reduced about 23.4%, 25.2%, 43.6% respectively. The analysis of expression profiles under the iron-limited condition showed that the mutants were more sensitive for the changes of iron deficiency than the wild-type strains, many genes have been altered. Up-regulated genes mainly involved genes of transcription, coenzyme metabolism, amino acid transport and metabolism, and unknown functional genes, while down-regulated genes mainly involved genes of energy and carbohydrate metabolism and unknown function genes; the expression levels of known iron-transport associated genes generally showed up-regulated. The results demonstrated that iron-transport associated genes IroN, ShuA were likely to have some effects on the virulence and growth of S. dysenteriae.

  15. Nonlinear multi-photon laser wave-mixing optical detection in microarrays and microchips for ultrasensitive detection and separation of biomarkers for cancer and neurodegenerative diseases (United States)

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


    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.

  16. Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice. (United States)

    Chan, Kaman; Kim, Charles C; Falkow, Stanley


    DNA microarrays provide an opportunity to combine the principles of signature-tagged mutagenesis (STM) with microarray technology to identify potentially important bacterial virulence genes. The scope of DNA microarrays allows for less laborious screening on a much larger scale than possible by STM alone. We have adapted a microarray-based transposon tracking strategy for use with a Salmonella enterica serovar Typhimurium cDNA microarray in order to identify genes important for survival and replication in RAW 264.7 mouse macrophage-like cells or in the spleens of BALB/cJ mice. A 50,000-CFU transposon library of S. enterica serovar Typhimurium strain SL1344 was serially passaged in cultured macrophages or intraperitoneally inoculated into BALB/cJ mice. The bacterial genomic DNA was isolated and processed for analysis on the microarray. The novel application of this approach to identify mutants unable to survive in cultured cells resulted in the identification of components of Salmonella pathogenicity island 2 (SPI2), which is known to be critical for intracellular survival and replication. In addition, array results indicated that a number of SPI1-associated genes, currently not associated with intracellular survival, are negatively selected. However, of the SPI1-associated mutants individually tested for intracellular survival, only a sirA mutant exhibited reduced numbers relative to those of wild-type bacteria. Of the mutants unable to survive in mice, significant proportions are either components of the SPI2 pathogenicity island or involved in lipopolysaccharide synthesis. This observation is in agreement with results obtained in the original S. enterica serovar Typhimurium STM screen, illustrating the utility of this approach for the high-throughput identification of virulence factors important for survival in the host.

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

    Energy Technology Data Exchange (ETDEWEB)

    Luan, Enxiao; Zheng, Zhaozhu; Li, Xinyu; Gu, Hongxi [State Key Laboratory of Urban Water Resource and Environment, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080 (China); Micro- and Nanotechnology Research Center, Harbin Institute of Technology, Harbin 150080 (China); Liu, Shaoqin, E-mail: [Micro- and Nanotechnology Research Center, Harbin Institute of Technology, Harbin 150080 (China)


    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{sup −1} under the optimized conditions with the limit of detection (LOD) of 10 μg L{sup −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). - Graphical abstract: A fluorimetric assay for high-throughput screening of organophosphorous pesticides was developed based on the CdTe QDs/AChE microarrays via inkjet-assisted LbL printing techniques. - Highlights: • The large scale microarrays of CdTe QDs and AChE were fabricated by facile inkjet-assisted LbL printing technique. • The QDs/AChE microscopic dot arrays could be used quantitatively and rapidly for the sensitively visual detection of OPs. • A detection limit of 10 μg L{sup −1} was achieved, much lower than levels specified by standard tests and other colorimetric detection methods. • The low cost, short processing time, sufficient sensitivity, good stability and ease of use make it for a facile platform for on-site screening.

  18. Analysis of a simulated microarray dataset: Comparison of methods for data normalisation and detection of differntial expression

    NARCIS (Netherlands)

    Watson, M.; Perez-Alegre, M.; Denis Baron, M.; Delmas, C.; Dovc, P.; Duval, M.; Foulley, J.L.; Garrido-Pavon, J.J.; Hulsegge, B.; Jafrezic, F.; Jiménez-Marín, A.; Lavric, M.; Lê Cao, K.A.; Marot, G.; Mouzaki, D.; Pool, M.H.; Robert-Granié, C.; San Cristobal, M.; Tosser-Klop, G.; Waddington, D.; Koning, de D.J.


    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

  19. Immunotherapy with Allergen Peptides

    Directory of Open Access Journals (Sweden)

    Larché Mark


    Full Text Available Specific allergen immunotherapy (SIT is disease-modifying and efficacious. However, the use of whole allergen preparations is associated with frequent allergic adverse events during treatment. Many novel approaches are being designed to reduce the allergenicity of immunotherapy preparations whilst maintaining immunogenicity. One approach is the use of short synthetic peptides which representing dominant T cell epitopes of the allergen. Short peptides exhibit markedly reduced capacity to cross link IgE and activate mast cells and basophils, due to lack of tertiary structure. Murine pre-clinical studies have established the feasibility of this approach and clinical studies are currently in progress in both allergic and autoimmune diseases.

  20. Food processing and allergenicity. (United States)

    Verhoeckx, Kitty C M; Vissers, Yvonne M; Baumert, Joseph L; Faludi, Roland; Feys, Marcel; Flanagan, Simon; Herouet-Guicheney, Corinne; Holzhauser, Thomas; Shimojo, Ryo; van der Bolt, Nieke; Wichers, Harry; Kimber, Ian


    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-heat treatment) on the allergenic potential of proteins, and on the antigenic (IgG-binding) and allergenic (IgE-binding) properties of proteins has been considered. A variety of allergenic foods (peanuts, tree nuts, cows' milk, hens' eggs, soy, wheat and mustard) have been reviewed. The overall conclusion drawn is that processing does not completely abolish the allergenic potential of allergens. Currently, only fermentation and hydrolysis may have potential to reduce allergenicity to such an extent that symptoms will not be elicited, while other methods might be promising but need more data. Literature on the effect of processing on allergenic potential and the ability to induce sensitisation is scarce. This is an important issue since processing may impact on the ability of proteins to cause the acquisition of allergic sensitisation, and the subject should be a focus of future research. Also, there remains a need to develop robust and integrated methods for the risk assessment of food allergenicity.

  1. Protocol for simultaneous isolation of three important banana allergens. (United States)

    Nikolic, Jasna; Mrkic, Ivan; Grozdanovic, Milica; Popovic, Milica; Petersen, Arnd; Jappe, Uta; Gavrovic-Jankulovic, Marija


    Banana fruit (Musa acuminata) has become an important food allergen source in recent years. So far, 5 IgE reactive banana proteins have been identified, and the major allergens are: Mus a 2 (a class I chitinase, 31kDa), Mus a 4 (thaumatin-like protein, 21kDa), and Mus a 5 (β-1,3-glucanase, 33kDa). Due to variations in allergen expression levels, diagnostic reagents for food allergy can be improved by using individual allergen components instead of banana allergen extracts. The purpose of this study was to optimize the purification protocol of the three major allergens present in banana fruit: Mus a 2, Mus a 4 and Mus a 5. By employing a three-step purification protocol (a combination of anion-exchange, cation-exchange and reversed-phase chromatography) three important banana allergens were obtained in sufficient yield and high purity. Characterization of the purified proteins was performed by both biochemical (2-D PAGE, mass fingerprint and N-terminal sequencing) and immunochemical (immunoblot) methods. IgE reactivity to the purified allergens was tested by employing sera of five allergic patients. The purified allergens displayed higher sensitivity in IgE detection than the routinely used extracts. The three purified allergens are good candidates for reagents in component-based diagnosis of banana allergy.

  2. Spot the difference-development of a syndrome based protein microarray for specific serological detection of multiple flavivirus infections in travelers.

    Directory of Open Access Journals (Sweden)

    Natalie B Cleton


    Full Text Available The family Flaviviridae, genus Flavivirus, holds many of the world's most prevalent arboviral diseases that are also considered the most important travel related arboviral infections. In most cases, flavivirus diagnosis in travelers is primarily based on serology as viremia is often low and typically has already been reduced to undetectable levels when symptoms set in and patients seek medical attention. Serological differentiation between flaviviruses and the false-positive results caused by vaccination and cross-reactivity among the different species, are problematic for surveillance and diagnostics of flaviviruses. Their partially overlapping geographic distribution and symptoms, combined with increase in travel, and preexisting antibodies due to flavivirus vaccinations, expand the need for rapid and reliable multiplex diagnostic tests to supplement currently used methods.We describe the development of a multiplex serological protein microarray using recombinant NS1 proteins for detection of medically important viruses within the genus Flavivirus. Sera from clinical flavivirus patients were used for primary development of the protein microarray.Results show a high IgG and IgM sensitivity and specificity for individual NS1 antigens, and limited cross reactivity, even within serocomplexes. In addition, the serology based on this array allows for discrimination between infection and vaccination response for JEV vaccine, and no cross-reactivity with TBEV and YFV vaccine induced antibodies when testing for antibodies to other flaviviruses.Based on these data, multiplex NS1-based protein microarray is a promising tool for surveillance and diagnosis of flaviviruses.

  3. Allergens of mites

    Directory of Open Access Journals (Sweden)

    Emilia Siwak


    Full Text Available Mite allergens belong to the group of inhalant allergens and represent antigenic substances which are particutlarly important in the pathogenesis of respiratory system diseases and skin diseases. The most common diseases associated with chronic exposure to these aeroallergens include: allergic rhinitis, bronchial asthma and atopic dermatitis. Mite allergens are simple proteins or glycoproteins with different molecular structures and various biochemical functions. The sensitizing capacity of these proteins is connected from their physicochemical properties. Individual allergens perform, among others, the functions of structural proteins, act as enzymes, transport lipids, bind metal ions, and are capable of glycosylation. In addition, mite allergenic proteases degrade proteins of the skin epithelium-resulting in a weakening of its natural protective barrier-and induce the immune response. The proteases also induce the release of pro-inflammatory cytokines: interleukin-4 (IL-4, interleukin 6 (IL-6, interleukin 8 (IL-8, eotaxin, and granulocyte-macrophage colony-stimulating factor-GM-CSF. The article presents the tertiary structure of major and mid-range mite allergens and their classification. Based on literature reports concerning the chemical structure of allergenic proteins, it was emphasized that the structural differences between homologous proteins with allergenic pozoproperties relate to the distribution of amino acid residues on the surface of the molecule. IgE binding affinity and the similarities and differences in the amino acid sequence of the allergens were also the basis for determining cross-reactivity of allergenic proteins. The paper shows an example of this phenomenon, describing the existence of common allergens for various mite species.

  4. 165例5岁以下有反复喘息症状儿童过敏原检测及临床意义%Detection of allergens in 165 children below 5 with wheeze and its clinical significance

    Institute of Scientific and Technical Information of China (English)

    陈晓; 张融; 徐金梅; 李婷婷; 蒋丽军


    目的 探讨血清特异性过敏原检测在5岁以下反复喘息儿童早期哮喘诊断中的价值.方法 应用酶联免疫法对165例有反复喘息症状5岁以下儿童血清测定总免疫蛋白E(IgE)和12种吸入过敏原、食入过敏原特异性IgE,将受检儿童分婴儿组(<3岁)和3~5岁组.对过敏原状况进行分析比较.结果 165例儿童总IgE阳性率为89.1%,特异性过敏原阳性率为58.8%,吸入组最高为尘螨/粉螨,食入组最高为蛋 白/蛋黄,其次为鱼、虾/蟹、肉类.食入过敏原随年龄增长有下降趋势,吸入过敏原随年龄增长有增加趋势.结论 血清特异性过敏原阳性是有喘息症状儿童发展为哮喘的高危因素之一,检测5岁以下有反复喘息症状患儿血清吸入性和食入性过敏原有利于早期识别可能发展为哮喘的儿童,为儿童哮喘的早期干预提供依据.%Objective To explore the clinical significance of serum specific allergen test in early asthma diagnosis with wheezing children under 5 years old. Methods The serai total IgE, the specific IgE of 12 types of inhalation and food allergens were detected in 165 cases of children aged below 5 with asthma using the method of enzyme linked immunosorbent assay. The children were divided into infancy group (aged<3) and 3-5 age group. Results In 165 cases, the positive ratio of total IgE was 89. 1% . The positive ratio of specific allergens was 58. 8% . The most common inhalation allergen was dust mite/acarid and the most common food allergen was egg white/yolk, followed by fish, shrimp/crab and meat. The number of inhalation allergens droped with the food of age, while the number of inhalation allergens rose. Conclusion Positive serum specific allergens is one of the highly hazardous factors which leads to childhood wheeze into asthma. Thus, the test of inhalation allergens and food allergens in serum for children with wheeze aged below 5 plays an important role in detecting the potential

  5. Serum IgE measurement and the detection of allergens for pediatric patients in Zhoushan islands%舟山海岛儿童血清过敏原检测分析

    Institute of Scientific and Technical Information of China (English)

    林鸣国; 苏亮; 姜立波; 贝国平; 颜云容


    目的 研究舟山海岛地区过敏性疾病患儿的过敏原分布特点,为临床诊断,治疗及预防提供依据.方法 采用酶免疫分析法(ELISA),对患儿的血清样本进行过敏总IgE抗体体外检测呈阳性的475例进行总结分析.结果 明确有过敏原的380例(80.00%),其中单一过敏原阳性为87例(18.32%),2种及以上过敏原阳性293例(61.68%).吸入性过敏原阳性率较高的是螨虫(38.31%)、屋尘(12.21%)、真菌组合(2.53%);食入性过敏原阳性率较高的是鱼类(6.53%)、贝类(6.11%)、豆类(4.21%).婴幼儿以食物性过敏为主,学龄儿童以吸入性过敏为主.结论 螨及鱼类是舟山海岛儿童最常见过敏原,多数患者同时存在多种过敏原.%Objective To determine the characteristics of allergens among clinical children with allergic diseases in Zhoushan islands. Methods A total of 475 children with allegic diseases were tested for serum IgE antibody by enzyme linked immune assay (ELISA) from November, 2007 to July, 2010. IgE positive specimens were tested for the identification of allergens. Results Allergens were confirmed in 80% (380/475) of serum specimens. Most of the positive specimens had at least 2 allergens (77. 1%,293/380). Single allergen was detected in 22.9% (87/380) of the positive specimens. There were more patients with inhaled allergies (74.47%, 283/380) than with food allergies (25.53%, 137/380). Among the patients with inhaled allergies, most (64.31%, 182/283) were caused by mite allergen, which was followed by house dust (20.49%, 58/283), fungi combination (4.2%, 12/283) and etc. Fish (22.63%,31/137), shellfish (21.17%, 29/137) and beans (14.6%, 20/137) were major sources for food allergy.Infants were more likely to be affected by food allergens while school-age children were majorly affected by inhaled allergens. Conclusion Multiple allergens were frequently detected in children with allergies.Food and inhaled allergens played different

  6. 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


    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

  7. Analyzing Microarray Data. (United States)

    Hung, Jui-Hung; Weng, Zhiping


    Because there is no widely used software for analyzing RNA-seq data that has a graphical user interface, this protocol provides an example of analyzing microarray data using Babelomics. This analysis entails performing quantile normalization and then detecting differentially expressed genes associated with the transgenesis of a human oncogene c-Myc in mice. Finally, hierarchical clustering is performed on the differentially expressed genes using the Cluster program, and the results are visualized using TreeView.

  8. Fluorescence of atopic allergens

    NARCIS (Netherlands)

    Berrens, L.


    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

  9. Inhaled allergen bronchoprovocation tests

    NARCIS (Netherlands)

    Diamant, Zuzana; Gauvreau, Gail M.; Cockcroft, Don W.; Boulet, Louis-Philippe; Sterk, Peter J.; Jongh, de Frans H.C.; Dahlen, Barbo; O'Byrne, Paul M.


    The allergen bronchoprovocation test is a long-standing exacerbation model of allergic asthma that can induce several clinical and pathophysiologic features of asthma in sensitized subjects. Standardized allergen challenge is primarily a research tool, and when properly conducted by qualified and ex

  10. Allergenicity attributes of different peanut market types. (United States)

    Koppelman, Stef J; Jayasena, Shyamali; Luykx, Dion; Schepens, Erik; Apostolovic, Danijela; de Jong, Govardus A H; Isleib, Thomas G; Nordlee, Julie; Baumert, Joe; Taylor, Steve L; Cheng, Hsiaopo; Maleki, Soheila


    Four different market classes of peanut (Runner, Virginia Spanish, and Valencia) are commonly consumed in Western countries, but for some consumers peanuts are a main cause of food-induced anaphylaxis. Limited information is available on the comparative allergenicity of these distinct market classes. The aim of this study was to compare allergenicity attributes of different peanut cultivars. The protein content and protein profiles were highly comparable for all tested cultivars. All cultivar samples contained the major allergens Ara h 1, Ara h 2, Ara h 3 and Ara h 6, as assessed by SDS-PAGE and RP-HPLC, although some minor differences in major allergen content were found between samples. All samples were reactive in commercial ELISAs for detection and quantification of peanut protein. IgE-binding potency differed between samples with a maximum factor of 2, indicating a highly comparable allergenicity. Based on our observations, we conclude that peanuts from the main market types consumed in Western countries are highly comparable in their allergenicity attributes, indicating that safety considerations with regard to peanut allergy are not dependent on the peanut cultivar in question.

  11. High pressure effects on allergen food proteins. (United States)

    Somkuti, Judit; Smeller, László


    There are several proteins, which can cause allergic reaction if they are inhaled or ingested. Our everyday food can also contain such proteins. Food allergy is an IgE-mediated immune disorder, a growing health problem of great public concern. High pressure is known to affect the structure of proteins; typically few hundred MPa pressure can lead to denaturation. That is why several trials have been performed to alter the structure of the allergen proteins by high pressure, in order to reduce its allergenicity. Studies have been performed both on simple protein solutions and on complex food systems. Here we review those allergens which have been investigated under or after high pressure treatment by methods capable of detecting changes in the secondary and tertiary structure of the proteins. We focus on those allergenic proteins, whose structural changes were investigated by spectroscopic methods under pressure in correlation with the observed allergenicity (IgE binding) changes. According to this criterion we selected the following allergen proteins: Mal d 1 and Mal d 3 (apple), Bos d 5 (milk), Dau c 1 (carrot), Gal d 2 (egg), Ara h 2 and Ara h 6 (peanut), and Gad m 1 (cod).

  12. Tree nut allergens. (United States)

    Roux, Kenneth H; Teuber, Suzanne S; Sathe, Shridhar K


    Allergic reactions to tree nuts can be serious and life threatening. Considerable research has been conducted in recent years in an attempt to characterize those allergens that are most responsible for allergy sensitization and triggering. Both native and recombinant nut allergens have been identified and characterized and, for some, the IgE-reactive epitopes described. Some allergens, such as lipid transfer proteins, profilins, and members of the Bet v 1-related family, represent minor constituents in tree nuts. These allergens are frequently cross-reactive with other food and pollen homologues, and are considered panallergens. Others, such as legumins, vicilins, and 2S albumins, represent major seed storage protein constituents of the nuts. The allergenic tree nuts discussed in this review include those most commonly responsible for allergic reactions such as hazelnut, walnut, cashew, and almond as well as those less frequently associated with allergies including pecan, chestnut, Brazil nut, pine nut, macadamia nut, pistachio, coconut, Nangai nut, and acorn.

  13. Sublingual allergen immunotherapy

    DEFF Research Database (Denmark)

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


    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 allergic patients. Sublingual allergen immunotherapy (SLIT) has been approved, notably in the European Union, as an effective alternative to subcutaneous allergen immunotherapy (SCIT) for allergic rhinitis patients. Compared with SCIT, SLIT has a better safety profile. This is possibly because oral antigen...... 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...

  14. Allergen Specific Immunotherapy

    Directory of Open Access Journals (Sweden)

    Şükrü Çekiç


    Full Text Available Allergen specific immunotherapy (SIT is the only treatment that can provide a cure for allergic disorders. This treatment is based on development of immune tolerance by exposure to allergen in repetitive and increasing doses. It is tertiary to avoidance of allergen and pharmacotherapy. Allergens used for immunotherapy, must be confirmed by skin prick test or specific IgE and must be applied in supervision of allergy specialists. Studies show that immunotherapy, improve asthma symptoms, decreases drug consumption, prevent development of asthma in rhinitis patients and reduce new sensitizations. Common side effects diminished with the usage of standardized allergen solutions. It is contraindicated in severe asthma. Though it is recommended to avoid immunotherapy in patients using beta blockers and ACE inhibitors, immunotherapy can be considered in mandatory situations regarding possible benefits and harms. Most common ways of administration are subcutaneous and sublingual; new methods such as epicutaneous and intralymphatic injections are currently being studied.

  15. Detection of mutations using microarrays of poly(C)10-poly(T)10 modified DNA probes immobilized on agarose films

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Petersen, Jesper; Stoltenborg, M.


    to an agarose film grafted onto unmodified glass. Microarrays of TC-tagged probes immobilized on the agarose film can be used to diagnose Mutations in the human P-globin gene, which encodes the beta-chains in hemoglobin. Although the probes differed widely regarding inciting point temperature (similar to 20...... degrees C), a single stringency wash still gave sufficiently high discrimination signals between perfect match and mismatch probes to allow robust mutation detection. In all, 270 genotypings were performed on patient materials, and no genotype was incorrectly classified. Quality control experiments...

  16. Advances in the quantification of relevant allergens in allergenic extracts. (United States)

    Batard, T; Nony, E; Hrabina, M; Chabre, H; Frati, F; Moingeon, P


    Relevant allergens are major contributors to the safety and efficacy of allergenic extracts used in allergen immunotherapy (AIT). As such, they should be accurately quantified, as recommended by the 2008 European guidelines on allergen products. Until now, the quantification of relevant allergens was mainly performed by using immunoassays (e.g. ELISA) that relying upon specific antibodies. Although antibody-based quantification is commonly used to assess the concentration of relevant allergens in allergenic extracts, results must be taken with caution in the light of the inherent limitations of such techniques. In the present study, we discuss how those limitations can be overcome by using comprehensive mass spectrometry-based techniques.

  17. 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.


    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.

  18. A B Cell Epitope Peptide Derived from the Major Grass Pollen Allergen Phl p 1 Boosts Allergen-Specific Secondary Antibody Responses without Allergen-Specific T Cell Help (United States)

    Narayanan, Meena; Freidl, Raphaela; Focke-Tejkl, Margarete; Baranyi, Ulrike; Wekerle, Thomas; Valenta, Rudolf


    More than 40% of allergic patients suffer from grass pollen allergy. Phl p 1, the major timothy grass pollen allergen, belongs to the cross-reactive group 1 grass pollen allergens that are thought to initiate allergic sensitization to grass pollen. Repeated allergen encounter boosts allergen-specific IgE production and enhances clinical sensitivity in patients. To investigate immunological mechanisms underlying the boosting of allergen-specific secondary IgE Ab responses and the allergen epitopes involved, a murine model for Phl p 1 was established. A B cell epitope–derived peptide of Phl p 1 devoid of allergen-specific T cell epitopes, as recognized by BALB/c mice, was fused to an allergen-unrelated carrier in the form of a recombinant fusion protein and used for sensitization. This fusion protein allowed the induction of allergen-specific IgE Ab responses without allergen-specific T cell help. Allergen-specific Ab responses were subsequently boosted with molecules containing the B cell epitope–derived peptide without carrier or linked to other allergen-unrelated carriers. Oligomeric peptide bound to a carrier different from that which had been used for sensitization boosted allergen-specific secondary IgE responses without a detectable allergen-specific T cell response. Our results indicate that allergen-specific secondary IgE Ab responses can be boosted by repetitive B cell epitopes without allergen-specific T cell help by cross-linking of the B cell epitope receptor. This finding has important implications for the design of new allergy vaccines. PMID:28093528

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



    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 ...

  20. The significance of allergen detection for eczema, allergic rhinitis and asthma patients%过敏原检测对湿疹、过敏性鼻炎和哮喘患者的意义

    Institute of Scientific and Technical Information of China (English)

    尧荣凤; 姜培红; 许国祥; 徐龙; 李智; 薛龙; 赵迪


    Objective To understand allergen IgE antibody distribution for different allergic diseases, in order to provide the reference for clinical prevention and treatment.Methods A total of 236 patients with allergic rhinitis, 250 patients with asthma and 275 patients with eczema were enrolled.Western blot was performed to detect the serological specific allergen IgE antibody.The allergens for allergic rhinitis, asthma and eczema were analyzed comparatively. Results The inhaled allergen detection rate was 41.66% in the 761 patients, and the ingested allergen detection rate was 8.28%.Dust mite(43.10%) was the most common allergen, and dog hair (12.22%),milk(11.43%) and house dust(10.78%) were the other 3 common allergens.The prevalence rates of dust mite(62.35%), dog hair(21.11%), house dust(18.89%) and milk (26.47%) in 11-30 years old group were higher than those in the other age groups (P 0.05).Conclusions Serum allergen detection might be conducive to identify the allergic status of patients, and provides a reliable reference to assist in the diagnosis of allergic diseases, prevent from environmental factors and make treatment plan.%目的:了解过敏原 IgE 抗体在不同过敏性疾病中的分布情况,为临床防治提供依据。方法采用免疫印迹法检测过敏性鼻炎(236例)、哮喘(250例)和湿疹(275例)患者血清过敏原特异性 IgE 抗体,同时对过敏性鼻炎、哮喘和湿疹患者的过敏原进行比较分析。结果761例患者吸入性过敏原检出率为41.66%,食入性过敏原检出率为8.28%;最常见的过敏原为户尘螨(43.10%)、狗毛皮屑(12.22%)、牛奶(11.43%)和屋尘(10.78%)。11~30岁组的户尘螨(62.35%)、狗毛皮屑(21.11%)、屋尘(18.89%)和牛奶(26.47%)阳性率明显高于其他年龄组(P <0.05)。湿疹患者蟑螂、牛奶和点青霉/分枝孢霉/烟曲霉/黑曲霉/交链孢霉的阳

  1. Allergenic Proteins in Foods and Beverages

    Directory of Open Access Journals (Sweden)

    Fernanda Cosme


    Full Text Available Food allergies can be defined as immunologically mediated hypersensitivity reactions; therefore, a food allergy is also known as food hypersensitivity. The reactions are caused by the immune system response to some food proteins. The eight most common food allergens are proteins from milk, eggs, peanuts, tree nuts, soya, wheat, fish and shellfish. However, many other foods have been identified as allergens for some people, such as certain fruits or vegetables and seeds. It is now recognized that food allergens are an important food safety issue. A food allergy occurs when the body’s immune system reacts to otherwise harmless substances in certain foods. For these reasons, one of the requirements from the European Union is that allergenic food ingredients should be labelled in order to protect allergic consumers. According to the European Federation of Allergy and Airways Diseases Patients’ Associations, about 8 % of children and 4 % of adults suffer from some type of food allergy. Food allergies often develop during infant or early childhood ages, affecting mainly the gastrointestinal tract (stomach and intestines. In some cases, the allergy may persist in adult age, for example, coeliac disease, which is an abnormal immune response to certain proteins present in gluten, a type of protein composite found in wheat and barley. Almost all allergens are proteins, and highly sensitive analytical methods have been developed to detect traces of these compounds in food, such as electrophoretic and immunological methods, enzyme-linked immunosorbent assay (ELISA and polyacrylamide gel electrophoresis. The purpose of this review is to describe the allergenic components of the most common causes of food allergies, followed by a brief discussion regarding their importance in the food industry and for consumer safety. The most important methods used to detect allergenicity in food will also be discussed.

  2. Immunoproteomic tools are used to identify masked allergens: Ole e 12, an allergenic isoflavone reductase from olive (Olea europaea) pollen. (United States)

    Castro, Lourdes; Crespo, Jesús F; Rodríguez, Julia; Rodríguez, Rosalía; Villalba, Mayte


    Proteins performing important biochemical activities in the olive tree (Olea europaea) pollen have been identified as allergens. One novel 37-kDa protein seems to be associated to the IgE-binding profile of a group of patients suffering allergy to peach and olive pollen. Three previously described olive pollen allergens exhibit very similar molecular mass. Our objective was to identify this allergen by using immunoproteomic approaches. After 2D-electrophoresis and mass spectrometry, peptide sequences from several IgE-binding spots, allowed identifying this new allergen, as well as cloning and DNA sequencing of the corresponding gene. The allergen, named Ole e 12, is a polymorphic isoflavone reductase-like protein of 308 amino acids showing 80% and 74% identity with birch and pear allergens, Bet v 6 and Pyr c 5, respectively. A prevalence of 33% in the selected population is in contrast to 4%-10% in groups of subjects suffering from pollinosis. Recombinant allergen was produced in Escherichia coli, and deeply characterised. Immunoblotting and ELISA detection as well as inhibition experiments were performed with polyclonal antisera and allergic patients' sera. The recombinant allergen retains the IgE reactivity of its natural counterpart. Close structural and immunological relationships between members of this protein family were supported by their IgG recognition in vegetable species. In summary, Ole e 12 is a minor olive pollen allergen, which gains relevance in patients allergic to peach with olive pollinosis. Proteomic approaches used to analyse this allergen provide useful tools to identify hidden allergens, relevant for several allergic populations and thus complete allergenic panels.

  3. Potential impact of a microarray-based nucleic acid assay for rapid detection of Gram-negative bacteria and resistance markers in positive blood cultures. (United States)

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


    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, 75.9% to 100%) in Pseudomonas aeruginosa and negative predictive values of 100% (95% CI, 93.9% to 100%) and 78.6% (95% CI, 51.0% to 93.6%), respectively.

  4. Allergens in the Lab. (United States)

    Fisher, Thomas M.


    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)

  5. 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.

  6. Plant food allergens--structural and functional aspects of allergenicity. (United States)

    Breiteneder, Heimo; Clare Mills, E N


    The three dominating plant food allergen groups belong to the prolamin and cupin superfamilies and to the family 10 of pathogenesis-related proteins. The prolamin superfamily comprises allergenic 2S albumins, nonspecific lipid transfer proteins and cereal alpha-amylase/trypsin inhibitors. These allergens have related structures and are stable to thermal processing and proteolysis. The cupin superfamily comprises the allergenic 7S and 11S globulin storage proteins from peanuts, soybean and tree nuts which are heat stable and can form immunogenicity enhancing aggregates. The Bet v 1 family of allergens includes tree pollinosis-associated food allergens with low stability which induce the symptoms of the oral allergy syndrome.

  7. Use of humanized rat basophilic leukemia reporter cell lines as a diagnostic tool for detection of allergen-specific IgE in allergic patients: time for a reappraisal? (United States)

    Falcone, Franco H; Alcocer, Marcos J C; Okamoto-Uchida, Yoshimi; Nakamura, Ryosuke


    The interaction between allergens and specific IgE is at the heart of the allergic response and as such lies at the center of techniques used for diagnosis of allergic sensitization. Although serological tests are available, in vivo tests such as double-blind placebo-controlled food challenges (DBPCFC) and skin prick test (SPT) associated to the patients' clinical history are still the main guides to clinicians in many practices around the world. More recently, complex protein arrays and basophil activation tests, requiring only small amounts of whole blood, have been developed and refined, but are yet to enter clinical practice. Similarly, the use of rat basophilic leukemia (RBL) cell lines for detection of allergen-specific IgE has been made possible by stable transfection of the human FcεRI α chain into this cell line more than 20 years ago, but has not found widespread acceptance among clinicians. Here, we review the perceived limitations of diagnostic applications of humanized RBL systems. Furthermore, we illustrate how the introduction of reporter genes into humanized RBL cells is able to overcome most of these limitations, and has the potential to become a new powerful tool to complement the armamentarium of allergists. A demonstration of the usefulness of humanized RBL reporter systems for elucidation of complex IgE sensitization patterns against wheat proteins and a section on the use of fluorescence-based reporter systems in combination with allergen arrays close the review.

  8. 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


    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.

  9. Parvalbumin--the major tropical fish allergen. (United States)

    Lim, Dawn Li-Chern; Neo, Keng Hwee; Yi, Fong Cheng; Chua, Kaw Yan; Goh, Denise Li-Meng; Shek, Lynette Pei-Chi; Giam, Yoke Chin; Van Bever, Hugo P S; Lee, Bee Wah


    Fish allergy is common in countries where consumption is high. Asian nations are amongst the world's largest consumers of fish but the allergen profiles of tropical fish are unknown. This study sought to evaluate the allergenicity of four commonly consumed tropical fish, the threadfin (Polynemus indicus), Indian anchovy (Stolephorus indicus), pomfret (Pampus chinensis) and tengirri (Scomberomorus guttatus). Immunoglobulin E (IgE) cross-reactivity with parvalbumin of cod fish (Gad c 1), the major fish allergen, was also studied. Detection of tropical fish and cod specific-IgE was performed by UniCap assay, and skin prick tests were also carried out. The IgE-binding components of tropical fish were identified using IgE immunoblot techniques, and cross-reactivity with Gad c 1 was assessed by ELISA inhibition and IgE immunoblot inhibition. Clinically, nine of 10 patients studied were allergic to multiple fish. All patients exhibited detectable specific-IgE to cod fish (10 of 10 skin prick test positive, eight of 10 UniCap assay positive) despite lack of previous exposure. The major allergen of the four tropical fish was the 12-kDa parvalbumin. IgE cross-reactivity of these allergens to Gad c 1 was observed to be moderate to high in the tropical fish studied. Parvalbumins are the major allergens in commonly consumed tropical fish. They are cross-reactive with each other as well as with Gad c 1. Commercial tests for cod fish appear to be sufficient for the detection of tropical fish specific-IgE.

  10. Multiplexed, rapid point of care platform to quantify allergen-specific IgE. (United States)

    Monroe, M R; Reddington, A P; Cretich, M; Chiari, M; Little, F; Ünlü, M S


    Variation of probe immobilization on microarrays hinders the ability to make high quality, assertive and statistically relevant conclusions needed in the healthcare setting. To address this problem, we have developed a calibrated, compact, inexpensive, multiplexed, dual modality point-of-care detection platform that calibrates and correlates surface probe density measured label-free to captured labeled secondary antibody, is independent of chip-to-chip variability, and improves upon existing diagnostic technology. We have identified four major technological advantages of our proposed platform: the capability to perform single spot analysis based on the fluorophore used for detection, a 10-fold gain in fluorescence signal due to optimized substrate, a calibrated, quantitative method that uses the combined fluorescent and label-free modalities to accurately measure the density of probe and bound target for a variety of systems, and a compact measurement platform offering reliable and rapid results at the doctor's office. Already, we have formulated over a 90% linear correlation between the amount of probe bound to surface and the resulting fluorescence of captured target for IgG, β-lactoglobulin, Ara h 1 peanut allergen, and Phl 5a Timothy grass allergen.

  11. Recombinant allergens for allergen-specific immunotherapy: 10 years anniversary of immunotherapy with recombinant allergens. (United States)

    Valenta, Rudolf; Linhart, B; Swoboda, I; Niederberger, V


    The broad applicability of allergen-specific immunotherapy for the treatment and eventually prevention of IgE-mediated allergy is limited by the poor quality and allergenic activity of natural allergen extracts that are used for the production of current allergy vaccines. Today, the genetic code of the most important allergens has been deciphered; recombinant allergens equalling their natural counterparts have been produced for diagnosis and immunotherapy, and a large panel of genetically modified allergens with reduced allergenic activity has been characterized to improve safety of immunotherapy and explore allergen-specific prevention strategies. Successful immunotherapy studies have been performed with recombinant allergens and hypoallergenic allergen derivatives and will lead to the registration of the first recombinant allergen-based vaccines in the near future. There is no doubt that recombinant allergen-based vaccination strategies will be generally applicable to most allergen sources, including respiratory, food and venom allergens and allow to produce safe allergy vaccines for the treatment of the most common forms of IgE-mediated allergies.


    Directory of Open Access Journals (Sweden)

    Edzard eSpillner


    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.

  13. A Cross-Reactive Human Single-Chain Antibody for Detection of Major Fish Allergens, Parvalbumins, and Identification of a Major IgE-Binding Epitope.

    Directory of Open Access Journals (Sweden)

    Merima Bublin

    Full Text Available Fish allergy is associated with moderate to severe IgE-mediated reactions to the calcium binding parvalbumins present in fish muscle. Allergy to multiple fish species is caused by parvalbumin-specific cross-reactive IgE recognizing conserved epitopes. In this study, we aimed to produce cross-reactive single chain variable fragment (scFv antibodies for the detection of parvalbumins in fish extracts and the identification of IgE epitopes. Parvalbumin-specific phage clones were isolated from the human ETH-2 phage display library by three rounds of biopanning either against cod parvalbumin or by sequential biopanning against cod (Gad m 1, carp (Cyp c 1 and rainbow trout (Onc m 1 parvalbumins. While biopanning against Gad m 1 resulted in the selection of clones specific exclusively for Gad m 1, the second approach resulted in the selection of clones cross-reacting with all three parvalbumins. Two clones, scFv-gco9 recognizing all three parvalbumins, and scFv-goo8 recognizing only Gad m 1 were expressed in the E. coli non-suppressor strain HB2151 and purified from the periplasm. scFv-gco9 showed highly selective binding to parvalbumins in processed fish products such as breaded cod sticks, fried carp and smoked trout in Western blots. In addition, the scFv-gco9-AP produced as alkaline phosphatase fusion protein, allowed a single-step detection of the parvalbumins. In competitive ELISA, scFv-gco9 was able to inhibit binding of IgE from fish allergic patients' sera to all three β-parvalbumins by up to 80%, whereas inhibition by scFv-goo8 was up to 20%. 1H/15N HSQC NMR analysis of the rGad m 1:scFv-gco9 complex showed participation of amino acid residues conserved among these three parvalbumins explaining their cross-reactivity on a molecular level. In this study, we have demonstrated an approach for the selection of cross-reactive parvalbumin-specific antibodies that can be used for allergen detection and for mapping of conserved epitopes.

  14. 皮肤点刺试验在慢性荨麻疹变应原检测中的临床应用%Clinical application of skin-prick test in chronic urticaria allergen detection

    Institute of Scientific and Technical Information of China (English)

    陈小玉; 贺春香


    目的 了解永川地区及周边县城慢性荨麻疹病人的常见致敏原,评价变应原皮肤点刺试验在慢性荨麻疹病原诊断中的价值.方法 采用国际标准方法的皮肤点刺(skin prick test,SPT)试验,对950例慢性荨麻疹病人做30种变应原(北京协和公司提供)测定,其中吸入性变应原16种,食物性变应原14种,并设阳性及阴性对照,以阳性对照为判断标准.结果 950例慢性荨麻疹病人中阳性者630例,阳性率66.3%,吸入组、食入组阳性率分别为54.2%和34.2%、.吸入组中以以尘螨、蟑螂、蒿类花粉、棉絮、狗毛、香烟居前;食入组中虾类、蟹类、辣椒、带鱼、橘子、芒果居前,吸入性变应原与慢性荨麻的相关性强于食入性变应原.结论 变应原皮肤点刺试验安全、可靠,易操作,为慢性荨麻疹病人寻找可能的变应原提供客观依据,为预防、治疗及护理起到一定的指导作用.%Objective To investigate the common allergens of patients with chronic urticaria I and evaluate the value of skin prick test in the diagnosis of chronic urticaria pathogen. Methods 950 cases of chronic urticaria patients were detected with 30 kinds of allergens (provided by Beijing Union Company) in the skin prick ((skin prick test, SPT) experiments of international standard method, including 16 inhaled allergens andH food allergens. Positive and negative controls were established, of which the positive control was taken as the criterion. Results Of the 950 cases of chronic urticaria patients,630 cases were positive, and the positive rate was 66. 3%. The positive rates of inhalation group and food group were 54. 2% and 34. 2%. In the inhalation group, dust mites, cockroaches, Artemisia pollen, cotton, dog hair and cigarette were on the top. The top factors were shrimp, crab, peppers, octopus, orange and mango. The inhalation allergens were more associated with chronic urticaria than that of ingestion allergens. Conclusion

  15. 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


    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.

  16. Detection of serum allergen specific IgE in the child with recurrent auergic purpura%过敏性紫癜患儿血清过敏原特异性IgE的检测及意义

    Institute of Scientific and Technical Information of China (English)



    Objective To investigate the role of allergen specific IgE in the child with recurrent auergic purpura,and to detect the relation between all kinds of allergen and the disease.Methods The serum specific IgE of allergen detected by ELISA in 100 cases of the child with recurrent auergic purpura.Results 81 cases of serum allergen-specific IgE were over than 50ku/L(81%).52 cases(52%)were positive reaction to more than two kinds of allergens and 29 cases(29%)were positive reaction to one kind of allergen.Several familiar aeroallergen mixed molds (19/100),dermatophagoides(12/100)and mugwort pollens(9/100).The most familiar food fish(28/100).shrimpand crab(22/100),milk(18/100).protein(11/100).Conclusion It suggests that aeroallergens,fish,shrimp and crab play an important role in the pathogenesis of repeating child anaphy lactic purpura.Mixed molds and protein foods are important pathogens to the disease.To detect the serum specific IgE could help screen allergens,and have important role to prevent disease.%目的 探讨反复发作性过敏性紫癜患儿血清过敏原特异性IgE的变化及与疾病发病的关系.方法 采用酶联免疫吸附试验检测100例反复发作性过敏性紫癜患儿的血清过敏原特异性IgE.结果 100例患儿中血清总IgE水平>50 ku/L者81例,阳性率81%,其中52例(52%)对两种以上过敏原呈阳性反应,29例(29%)对一种过敏原呈阳性反应;常见吸人性过敏原为霉菌(19/100)、尘螨(12/100)和蒿类花粉(9/100).常见的食人性过敏原为海鱼类(28/100)、虾蟹(22/100)、牛奶(18/100)、蛋白蛋黄类(11/100).结论 反复发作性过敏性紫癜的发生与吸人性和食人性过敏原都有一定的相关性,特异性IgE检测可帮助筛选过敏原,对疾病的预防具有积极意义.

  17. 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


    ABSTRACT: Soya and peanut are botanically closely related and share cross-reacting antigens, but compared to soya, peanut allergy has a higher prevalence with more severe allergic reactions. Furthermore, the threshold dose for eliciting reactions is higher for soya. A difference in undigested...... 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...

  18. Discovery of highly conserved unique peanut and tree nut peptides by LC-MS/MS for multi-allergen detection. (United States)

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


    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.

  19. Rapid one-step assays for on-site monitoring of mouse and rat urinary allergens. (United States)

    Koets, Marjo; Renström, Anne; Zahradnik, Eva; Bogdanovic, Jelena; Wouters, Inge M; van Amerongen, Aart


    Allergy to rodent proteins is common among laboratory animal workers. Sensitive methods to measure exposure to these allergens have been developed. These assays are, however, expensive, time-consuming, and require a laboratory facility and methodological expertise. A simple method to screen for allergen spread, or to test whether hygiene standards are maintained, would be useful. Lateral flow immunoassays (LFIAs) are especially suited for field settings; the tests are simple and results are visible within minutes. LFIAs were developed for detection of the rodent urinary allergens Mus m 1 and Rat n 1. Pilot studies were performed in animal facilities in three countries using both extracts from airborne dust samples and samples collected by wiping surfaces. For comparison and determination of sensitivity, the concentrations of rodent urinary allergens in the samples were also measured using enzyme immunoassays (EIAs). The LFIAs for rat and mouse urinary allergens had a detection limit of 31 pg allergen per mL in a buffer system with purified allergen standards. Results of environmental dust extracts tested in LFIAs correlated well with levels obtained using EIAs. Spread of rodent allergens, or non-adherence to hygiene around laboratory animal facilities, may aggravate rodent allergy. Using a simple, sensitive one-step assay, allergens can be detected to prevent allergen exposure. The results reveal that the rapid assays are suited for on-site demonstration of exposure to rodent allergens, and thus, useful in occupational hygiene practice.

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


    Directory of Open Access Journals (Sweden)

    M. Wardhana


    Full Text Available Background: Atopic dermatitis (AD is a chronic eczematous skin disease that develops in a patient with atopic diathesis, which is characterized by an increased liability to produce IgE antibodies for allergens mostly derived from environmental or inhalant allergens and food allergens. They are produced by cell-mediated allergic contact reactions, and recently contact sensitivity to various environmental allergens has been demonstrated in patients with AD. Atopic patients are recognized by their ability to produce large amounts of specific IgE antibodies to common substances as environmental allergens, i.e. house dust mites, grass pollens, animal danders, molds, food, etc. These antibodies can be detected by skin prick test. The aim of this study was to identify the sensitization against environmental or inhalants allergens through skin prick tests in the patients with atopic dermatitis. Material and Methods: This is a retrospective, descriptive study. We revised all medical records of patients with AD since January 2002 to December 2004 in the Out Patients Unit of Sanglah General Hospital, Bali-Indonesia. The variables studied were: gender, age, work related, diagnosis associates to AD, and prick test of environmental allergens. Results: In 3 years periods we had revised 46 of patients with AD that was done skin prick tests. The median age was 38 years (range 29-54 years, 34/46 (73.9 % of these were male and 12 (26.1 % female. Twenty nine patients presented pure AD, and 17 patients had AD with asthma and allergic rhinitis. Only 16 (34.7% of patients had no history of allergic disease. Thirsty six of 46 (78.20% of all tested AD patients had a positive skin prick tests against inhalant (aeroallergens 16 patients and food allergens 21 patients. Sixteen patients with positive of skin test include; dust mite in 12 patients, animal dander in 10 patients, grass pollen in 9 patients and cockroach in 6 patients. Conclusion: We concluded that

  2. Application of microarray and functional-based screening methods for the detection of antimicrobial resistance genes in the microbiomes of healthy humans.

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    Roderick M Card

    Full Text Available The aim of this study was to screen for the presence of antimicrobial resistance genes within the saliva and faecal microbiomes of healthy adult human volunteers from five European countries. Two non-culture based approaches were employed to obviate potential bias associated with difficult to culture members of the microbiota. In a gene target-based approach, a microarray was employed to screen for the presence of over 70 clinically important resistance genes in the saliva and faecal microbiomes. A total of 14 different resistance genes were detected encoding resistances to six antibiotic classes (aminoglycosides, β-lactams, macrolides, sulphonamides, tetracyclines and trimethoprim. The most commonly detected genes were erm(B, blaTEM, and sul2. In a functional-based approach, DNA prepared from pooled saliva samples was cloned into Escherichia coli and screened for expression of resistance to ampicillin or sulphonamide, two of the most common resistances found by array. The functional ampicillin resistance screen recovered genes encoding components of a predicted AcrRAB efflux pump. In the functional sulphonamide resistance screen, folP genes were recovered encoding mutant dihydropteroate synthase, the target of sulphonamide action. The genes recovered from the functional screens were from the chromosomes of commensal species that are opportunistically pathogenic and capable of exchanging DNA with related pathogenic species. Genes identified by microarray were not recovered in the activity-based screen, indicating that these two methods can be complementary in facilitating the identification of a range of resistance mechanisms present within the human microbiome. It also provides further evidence of the diverse reservoir of resistance mechanisms present in bacterial populations in the human gut and saliva. In future the methods described in this study can be used to monitor changes in the resistome in response to antibiotic therapy.

  3. 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


    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.

  4. Microarray-based detection and expression analysis of extracellular matrix proteins in drug‑resistant ovarian cancer cell lines. (United States)

    Januchowski, Radosław; Zawierucha, Piotr; Ruciński, Marcin; Zabel, Maciej


    Ovarian cancer is the most lethal gynecological malignancy. Multiple drug resistance (MDR) development leads to resistance of cancer cells to chemotherapy. Microarray methods can provide information regarding new candidate genes that can play a role in resistance to cytostatic drugs. Extracellular matrix (ECM) can influence drug resistance by inhibiting the penetration of the drug into cancer tissue as well as increased apoptosis resistance. In the present study, we report changes in the ECM and related gene expression pattern in methotrexate-, cisplatin-, doxorubicin-, vincristine-, topotecan- and paclitaxel-resistant variants of the W1 ovarian cancer cell line. The resistant variants of the W1 cell line were generated by stepwise selection of cells with an increasing concentration of the indicated drugs. Affymetrix GeneChip® Human Genome U219 Array Strips were used for hybridizations. Independent t-tests were used to determinate the statistical significance of results. Genes whose expression levels were higher than the assumed threshold (upregulated, >5-fold and downregulated, 20-fold. These genes were: ITGB1BP3, COL3A1, COL5A2, COL15A1, TGFBI, DCN, LUM, MATN2, POSTN and EGFL6. The expression of seven genes decreased very significantly: ITGA1, COL1A2, LAMA2, GPC3, KRT23, VIT and HMCN1. The expression pattern of ECM and related genes provided the preliminary view into the role of ECM components in cytostatic drug resistance of cancer cells. The exact role of the investigated genes in drug resistance requires further investigation.

  5. In vitro detection of contact allergens: development of an optimized protocol using human peripheral blood monocyte-derived dendritic cells. (United States)

    Reuter, Hendrik; Spieker, Jochem; Gerlach, Silke; Engels, Ursula; Pape, Wolfgang; Kolbe, Ludger; Schmucker, Robert; Wenck, Horst; Diembeck, Walter; Wittern, Klaus-Peter; Reisinger, Kerstin; Schepky, Andreas G


    Allergic contact dermatitis is a delayed T-cell mediated allergic response associated with relevant social and economic impacts. Animal experiments (e.g. the local lymph node assay) are still supplying most of the data used to assess the sensitization potential of new chemicals. However, the 7th amendment to the EU Cosmetic Directive will introduce a testing ban for cosmetic ingredients after 2013. In vitro alternative methods are thus being actively developed. Although promising results have been obtained with cell lines, their reduced functionality and inherent genomic instability led us to reinvestigate the use of peripheral blood monocyte-derived dendritic cells (PBMDCs) for the establishment of a reliable in vitro sensitization test. To solve the issues associated with the use of primary cells, the culture and exposure conditions (cytokine concentrations, incubation time, readout, pooled vs. single donors and cytotoxicity) were re-assessed and optimized. Here we propose a stable and reproducible protocol based on PBMDCs. This should allow a wider acceptance of PBMDCs as a reliable test system for the detection of human skin sensitizers and the inclusion of this protocol in an integrated testing strategy.

  6. Detection of occupational contact dermatitis allergen by using patch test%斑贴试验检测职业性接触陸皮炎变应原

    Institute of Scientific and Technical Information of China (English)

    曾碧冰; 陈明春; 李俊杰; 周敏慧; 李丹; 林绍华; 张静


    目的 探讨东莞地区职业性接触性皮炎主要致病因素,了解其常见的接触性变应原.方法 采用斑贴试验试剂盒对每例患者进行斑贴试验.结果 300例患者中有167例至少对一种物质过敏,总阳性率为55.67%,阳性率较高的几种变应原依次为:硫酸镍104例(34.67%),甲醛42例(14.00%),重铬酸钾30例(10.00%).结论 东莞地区职业性接触性皮炎主要变应原为三种化学物质,调查结果有助于临床指导该疾病的预防和治疗.%Aim To analysis the pathogens of occupational contact dermatitis in Dongguan city,and find out the common contact allergens.Methods Patch tests were performed by using RuiminTM serial allergen kit in the patients with occupational contact dermatitis.Results 300 cases of occupational contact dermatitis were patch tested, 167 cases showed positive reaction to one or more allergens, and the positive rate was 55.67%.The most familiar allergens were:nikel sulfate(104 cases,34.67%),formaldehyde(42 cases,14.00%),potassium dichromate(30 cases, 10.00%).Conclusions The main allergens of occupational contact dermatitis in Dongguan city are three kinds of chemical materials.This study is helpful to the prevention and treatment of the disease.

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

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    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.

  8. 成都地区过敏性鼻炎患者过敏原的检测分析%Detection and analysis of allergens in allergic rhinitis patients in Chengdu

    Institute of Scientific and Technical Information of China (English)

    蒋锐明; 范敏; 谢亚柳; 袁洛花; 许琴


    目的 检测成都地区过敏性鼻炎(AR)患者血清中的过敏原情况,为临床诊断和治疗过敏性鼻炎提供实验室依据.方法 过敏性鼻炎患者88例及同期就诊的非过敏性鼻炎患者30例,采用酶免疫斑点法,检测患者血清中的吸入性和食入性过敏原共20项.结果 吸入性过敏原前3位为:屋尘螨/粉尘螨组合(65.9%)、屋尘(43.2%)狗上皮(9.1%);食入性过敏原前3位为:虾和海鱼组合(13.6%)、艾蒿(11.4%)、黄豆(10.2%).30例阴性对照仅有1例检测出阳性过敏原为虾和海鱼.结论 屋尘螨/粉尘螨和虾/海鱼分别是导致成都地区AR最主要的吸入性和食入性过敏原,有意识地避免接触这些过敏原及进行特异性的免疫治疗对防治过敏性鼻炎具有积极意义.%Objective To detect allergen in serum of patients with allergic rhinitis (AR) for diagnosis and treatment.Methods Sera from 88 AR patients and 30 non-allergic rhinitis controls were collected and detected for 20 kinds of allergen by using enzyme-linked immunospot assay.Results In Chengdu city,the positve rates arrangement of top 3 of inhalant allergens are house dust mite/dermatophagoides farinae (65.9%),house dust (43.2%) and dog epithelium (9.1%),respectively and of ingested allergens are shrimp/marine fish (13.6%),artemisia argyi (11.4%) and soybean (10.2%),respectively.Only 1 of 30 controls is allergic to shrimp and marine fish.Conclusion House dust mite/dermatophagoides farinae and shrimp/marine fish are the uppermost inhalant and ingested allergens recpectively which induced AR in Chengdu city.Dection of allergen is meaningful for patients to prevent suffering from AR disease by avoiding touching these allergens consciously,and it is important for clinicians to perform specific immunotherapy on AR patients.

  9. 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


    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。

  10. Development of a new resequencing pathogen microarray based assay for detection of broad-spectrum respiratory tract viruses in patients with community-acquired pneumonia.

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    Hongwei Shen

    Full Text Available A Resequencing Pathogen Microarray (RPM is a single, highly multiplexed assay for detecting and differentiating similarly related pathogens by using closely overlapping probe sets to determine a target organism's nucleotide sequence. In this study, a new RPM (RPM-IVDC1 that consisted of 224-bp detector tiles corresponding to 9 influenza A subtypes, 11 rhinoviruses, 28 enteroviruses and 38 other respiratory viruses was developed and optimized to provide individual and simultaneous detection sensitivities ranging from 15 to 750 genomic copies for 16 common respiratory pathogens. A total of 110 consecutive patients with community-acquired pneumonia (CAP admitted to 5 district general hospitals in Beijing during a 1-year period were assessed using the new assay. Among the children (under age 5 and adult patients (above age 18, respiratory syncytial virus (RSV and rhinovirus (RV were the most common etiological agents, respectively, which is consistent with reference assays. Atypical pathogens that may cause CAP-like illness, including rubella virus, measles virus, influenza type C virus, human herpesvirus (HHV were also detected. The results show the capability of RPM-IVDC1 for the accurate detection and identification of multiple virus types, which may be of significant use in epidemic surveillance and outbreak investigations of atypical pathogens.

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

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    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.

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

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


    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.

  13. Microarray Technologies in Fungal Diagnostics. (United States)

    Rupp, Steffen


    Microarray technologies have been a major research tool in the last decades. In addition they have been introduced into several fields of diagnostics including diagnostics of infectious diseases. Microarrays are highly parallelized assay systems that initially were developed for multiparametric nucleic acid detection. From there on they rapidly developed towards a tool for the detection of all kind of biological compounds (DNA, RNA, proteins, cells, nucleic acids, carbohydrates, etc.) or their modifications (methylation, phosphorylation, etc.). The combination of closed-tube systems and lab on chip devices with microarrays further enabled a higher automation degree with a reduced contamination risk. Microarray-based diagnostic applications currently complement and may in the future replace classical methods in clinical microbiology like blood cultures, resistance determination, microscopic and metabolic analyses as well as biochemical or immunohistochemical assays. In addition, novel diagnostic markers appear, like noncoding RNAs and miRNAs providing additional room for novel nucleic acid based biomarkers. Here I focus an microarray technologies in diagnostics and as research tools, based on nucleic acid-based arrays.

  14. Recombinant house dust mite allergens



    House dust mites (HDM) are a globally important source of allergen responsible for the sensitization of more than 50% of allergic patients. Specific immunotherapy with HDM extracts is effective but allergen extracts cannot be fully standardized and severe side-effects can occur during the protracted course of treatment. The introduction of molecular biological techniques into allergy research allowed the indentification of more than 20 groups of HDM allergens. Recombinant HDM allergens can be...

  15. Detection of total and A1c-glycosylated hemoglobin in human whole blood using sandwich immunoassays on polydimethylsiloxane-based antibody microarrays. (United States)

    Chen, Huang-Han; Wu, Chih-Hsing; Tsai, Mei-Ling; Huang, Yi-Jing; Chen, Shu-Hui


    The percentage of glycosylated hemoglobin A1c (%GHbA1c) in human whole blood indicates the average plasma glucose concentration over a prolonged period of time and is used to diagnose diabetes. However, detecting GHbA1c in the whole blood using immunoassays has limited detection sensitivity due to its low percentage in total hemoglobin (tHb) and interference from various glycan moieties in the sample. We have developed a sandwich immunoassay using an antibody microarray on a polydimethylsiloxane (PDMS) substrate modified with fluorinated compounds to detect tHb and glycosylated hemoglobin A1c (GHbA1c) in human whole blood without sample pretreatment. A polyclonal antibody against hemoglobin (Hb) immobilized on PDMS is used as a common capture probe to enrich all forms of Hb followed by detection via monoclonal anti-Hb and specific monoclonal anti-GHbA1c antibodies for tHb and GHbA1c detection, respectively. This method prevents the use of glycan binding molecules and dramatically reduces the background interference, yielding a detection limit of 3.58 ng/mL for tHb and 0.20 ng/mL for GHbA1c. The fluorinated modification on PDMS is superior to the glass substrate and eliminates the need for the blocking step which is required in commercial enzyme linked immunosorbent assay (ELISA) kits. Moreover, the detection sensitivity for GHbA1c is 4-5 orders of magnitude higher, but the required sample amount is 25 times less than the commercial method. On the basis of patient sample data, a good linear correlation between %GHbA1c values determined by our method and the certified high performance liquid chromatography (HPLC) standard method is shown with R(2) > 0.98, indicating the great promise of the developed method for clinical applications.

  16. Progress with respect to research work on allergenic ingredients in cosmetics and their detection methods%化妆品中致敏成分及其检测方法研究进展

    Institute of Scientific and Technical Information of China (English)

    张银志; 田秀梅; 余雯静; 郑利; 孙秀兰; 钱和


    综述了化妆品中的致敏成分及其检测方法;主要介绍了化妆品中易引起过敏反应的过敏原的种类,包括香精、防腐剂、对苯二胺、中药提取成分以及为满足一定的使用目的而添加的功能性成分如紫外吸收剂、收敛剂等;同时针对各种致敏成分分别讨论了其相应的检测方法,主要有斑贴试验、高效液相色谱法、气相色谱法、气相色谱-质谱法;最后提出了目前在检测方法方面存在的问题和发展方向.%Allergenic ingredients in cosmetics and their detection methods were summarized. Mainly categories of materials that facilitate allergic reaction, including fragrances, preservatives, p - phenylenediamine, herbal extracts and some functional components that added for specific purposes, such as UV absorbents, astringents, et al. Meanwhile,the detection methods of various allergenic ingredients were discussed, including patch test, high performance liquid chromatography, gas chromatography, gas chromatography - mass spectrometry. Finally, existing problems in detection methods and development trends in this field were put forward.

  17. Detection of causative allergens of cosmetic allergic contact dermatitis%化妆品变应性接触性皮炎变应原检测分析

    Institute of Scientific and Technical Information of China (English)

    蔡永莲; 刘润秋; 施辛; 张静; 黎平


    Objective To make a survey on common cosmetic allergens, and to provide epidemiological data and clinical evidence for cosmetic allergy. Methods Patch test was performed by using 49cosmetic allergens from a European cosmetic series and 5 Chinese standard screening allergens on 89patients with suspected cosmetic allergic contact dermatitis. Test results were determined according to the International Contact Dermatitis Research Group (ICDRG) recommendation. Results Of the 89 patients, 61(68.5%) showed positive reactions to one or more cosmetic allergens. The most common allergens were fragrances (33.7%), followed by preservatives (30.3%), para-phenylenediamine (25.8%) and amerchol L 101(10.1%). Conclusion Fragrances, preservatives, para-phenylenediamine and amerchol L 101 are dominant causative allergens in patients with cosmetic allergic contact dermatitis.%目的 调查化妆品变应原种类,为化妆品过敏提供流行病学资料和临床依据.方法 对89例门诊疑诊化妆品变应性接触性皮炎患者采用49种欧洲化妆品系列变应原及5种中国筛查系列化妆品变应原进行斑贴试验,按国际接触性皮炎研究组推荐标准判读结果.结果 89例患者中,61例对1种或1种以上化妆品变应原过敏,阳性反应率68.5%.其中阳性率较高的有香料33.7%,防腐剂30.3%,对苯二胺25.8%,阿莫醇10.1%.结论 香料、防腐剂、对苯二胺、阿莫醇等是化妆品变应性接触性皮炎患者的主要致敏原.

  18. 花生过敏原及其检测方法研究进展%Research progress of peanut allergens and its detection methods

    Institute of Scientific and Technical Information of China (English)

    洪宇伟; 陈启; 张京顺; 任一平


    Peanut allergy represents an important food safety issue because of the potential lethal effects. The only effective treatment is to avoid eating allergen foods. However, during the process of manufacture, machining, storing, transporting and selling, foods may be unintentionally contaminated by food allergens. Therefore, it is of great significance to quantify the amount of peanut allergens in a food for preventing the anaphylaxis. Thirteen potentially important allergens of peanut have been identified to date, assigned as Ara h 1~Ara h 13, respectively. This article summarized the structural information of peanut allergens and several popular extraction methods. At the same time, various qualitative and quantitative methods to determine the peanut allergens in foods were described in detail. At last, the trend of development in establishing a specific, sensitive and accurate method was prospected.%花生过敏可导致某些人群严重的食品安全问题。过敏患者只能通过避免食用含有花生过敏原成分的食物来避免过敏。但是,食品在生产加工、储存、运输、销售过程中有可能被过敏原污染。因此,确定各类加工食品中是否含有花生过敏原成分,对于预防食用者发生花生过敏反应具有重要意义。花生中已确定的过敏原蛋白有13种(Ara h 1~Ara h 13)。本文综述了花生中过敏原蛋白的结构信息,当前流行的提取方法,以及各种定性定量的检测方法,总结了各种方法的优缺点。同时对建立一种具有特异性强、灵敏度高、定量准确的花生致敏蛋白检测方法的发展趋势进行了展望。

  19. 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


    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

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

    DEFF Research Database (Denmark)

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard


    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 allergenicity, leading to the conclusion, that a correlation between stability to digestion and allergenic...... 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...

  1. The predictive value of total serum IgE for a positive allergen specific IgE result



    Background: Measurement of total serum IgE and allergen specific IgE is often requested to assess possible allergy. As public awareness increases, so do requests for allergy assessment; unless there is a clear “allergen suspect” in the history, several allergen specific IgE requests may be made. This increases the likelihood of detecting borderline increases in allergen specific IgE of uncertain relevance, and has important cost implications for the service.

  2. Living Cell Microarrays: An Overview of Concepts

    Directory of Open Access Journals (Sweden)

    Rebecca Jonczyk


    Full Text Available Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays.

  3. Significance of allergen and serum IgE detection in the diagnosis of infants with asthmatic diseases%过敏原检测和血清IgE检测在婴幼儿喘息性疾病诊断中的意义

    Institute of Scientific and Technical Information of China (English)



    Objective:To analyze the allergies of infants with asthmatic diseases,in order to facilitate early intervention.Methods:54 infants were detected of allergen and serum IgE by automatic fluorescence immunity analyzer and skin prick test.Results:The difference between IgE detection and inhaled allergens was statistically significant,but when IgE detection compare with ingested allergens,there was no statistical significance.Conclusion:Compare with ingested allergens,the inhaled allergens are more likely to leading the high level of IgE.%目的:分析喘息性疾病的婴幼儿过敏情况,以利于早期干预。方法:用全自动荧光免疫分析仪和皮肤点刺试验对54例喘息性疾病婴幼儿进行过敏原检测和血清IgE检测。结果:血清IgE检测与吸入过敏原比较,差异有统计学意义,与食入过敏原比较,无统计学意义。结论:吸入过敏原较食入过敏原更易导致机体的高IgE水平。

  4. Allergen detection and clinical analysis of 280 children with asthma%280儿童哮喘的过敏原检测临床分析

    Institute of Scientific and Technical Information of China (English)

    王莲; 赵腾飞


    目的:了解280儿童哮喘的过敏原。方法:对280例哮喘患儿(年龄≥3岁至≤14岁),进行皮肤点刺试验,对检测结果进行分析比较。结果:随年龄增加吸入性过敏原粉屋尘螨阳性率逐渐升高。结论:280儿童哮喘的发作与过敏原关系密切,尘螨是最常见的过敏原。%Objective: To investigate allergens in 280 children with asthma.Methods: To analysis and compare Results of skin prick test in 280 asthmatic children (age ≥ 3 years old to ≤ 14 years). Results:The positive rate of inhaled allergens powder mites increased gradually with increasing age.Conclusion: 280 children with asthma and allergy close relationship, dust mites are the most common allergens.

  5. Establishment of loop-mediated isothermal amplification method for detection of milk allergen in foods%食品中牛奶过敏原成分LAMP检测方法的建立

    Institute of Scientific and Technical Information of China (English)

    程晋霞; 曾静; 马丹; 魏海燕; 张海予


    Objective The loop-mediated isothermal amplification (LAMP) detection method was established for milk allergen testing and compared with the real-time PCR detection methods. Methods The cyt-b gene of bovine was used to design LAMP primers and then establish reaction system. The spe-cificity and sensitivity of LAMP were compared with real-time PCR detection method. Results The specificity of LAMP method was tested by 9 different milk and goat milk products. The results showed that the LAMP method was highly specific to milk. No cross-reaction was founded. The detection limit of LAMP reached 0.5%in base-material addition test which was consistent with the real-time PCR method. Through 69 practical food samples testing, the LAMP results were consistent with real-time PCR results. Conclusion The LAMP detection method of milk allergen established in this study is simple, economi-cal and reliable, which can effectively reduce the detection time and apply to the detection of milk aller-gen with good application prospects.%目的:建立食品过敏原牛奶成分LAMP(loop-mediated isothermal amplification)检测方法,并与实时荧光PCR(real-time PCR)检测方法比对。方法针对牛线粒体细胞色素b(cyt-b)基因设计LAMP引物并建立反应体系,在特异性和灵敏度方面与real-time PCR检测方法比对。结果本研究建立的LAMP方法检测9份不同品牌的牛奶和羊奶及其加工制品,没有出现交叉反应,具有良好的特异性。该方法的检测灵敏度为0.5%,与real-time PCR方法检测灵敏度相当。检测了69份实际样品,检测结果与real-time PCR检测结果一致。结论本研究建立的食品过敏原牛奶成分LAMP检测方法简单经济,检测结果可靠,可有效缩短检测时间,适用于过敏原牛奶成分的检测,具有良好的应用前景。

  6. New Cosmetic Contact Allergens

    Directory of Open Access Journals (Sweden)

    An Goossens


    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.

  7. Food processing and allergenicity

    NARCIS (Netherlands)

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


    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-heat tre

  8. Bleach Neutralizes Mold Allergens (United States)

    Science Teacher, 2005


    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…

  9. 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.


    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

  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

    Energy Technology Data Exchange (ETDEWEB)

    Le Meur, Julien [Laboratoire de Cancerologie Experimentale, Commissariat a l' Energie Atomique de Fontenay-aux-Roses, Direction des Sciences du Vivant, Departement de Radiobiologie et Radiopathologie, Fontenay-aux-Roses (France); Menut, Denis [Laboratoire de Reactivite des Surfaces et des Interfaces, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Wodling, Pascal [Laboratoire d' Interaction Laser-Matiere, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Salmon, Laurent [Laboratoire de Reactivite des Surfaces et des Interfaces, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Thro, Pierre-Yves [Laboratoire d' Interaction Laser-Matiere, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Chevillard, Sylvie [Laboratoire de Cancerologie Experimentale, Commissariat a l' Energie Atomique de Fontenay-aux-Roses, Direction des Sciences du Vivant, Departement de Radiobiologie et Radiopathologie, Fontenay-aux-Roses (France); Ugolin, Nicolas [Laboratoire de Cancerologie Experimentale, Commissariat a l' Energie Atomique de Fontenay-aux-Roses, Direction des Sciences du Vivant, Departement de Radiobiologie et Radiopathologie, Fontenay-aux-Roses (France)], E-mail:


    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 10{sup 5} nucleotides/{mu}m{sup 2} (i.e. 2 x 10{sup 13} phosphorus atoms/cm{sup 2}). 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)

    Richard G. Baraniuk


    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. Allelic imbalance analysis using a single-nucleotide polymorphism microarray for the detection of bladder cancer recurrence.

    NARCIS (Netherlands)

    Coenen, M.J.H.; Ploeg, M.; Schijvenaars, M.M.V.A.P.; Cornel, E.B.; Karthaus, H.F.M.; Scheffer, H.; Witjes, J.A.M.; Franke, B.; Kiemeney, L.A.L.M.


    PURPOSE: Non-muscle-invasive bladder cancer is a frequently occurring cancer, with an extremely high recurrence risk. Recurrence detection is based on cytology and urethrocystoscopy. A previous study suggested that a single-nucleotide polymorphism (SNP) array may be effective for noninvasive detecti

  13. Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms. (United States)

    Knijnenburg, Jeroen; van der Burg, Marja; Nilsson, Philomeen; Ploos van Amstel, Hans Kristian; Tanke, Hans; Szuhai, Károly


    A strategy is presented to select, pool and spot human BAC clones on an array in such a way that each spot contains five well performing BAC clones, covering one chromosome arm. A mini-array of 240 spots was prepared representing all human chromosome arms in a 5-fold as well as some controls, and used for comparative genomic hybridization (CGH) of 10 cell lines with aneusomies frequently found in clinical cytogenetics and oncology. Spot-to-spot variation within five replicates was below 6% and all expected abnormalities were detected 100% correctly. Sensitivity was such that replacing one BAC clone in a given spot of five by a BAC clone from another chromosome, thus resulting in a change in ratio of 20%, was reproducibly detected. Incubation time of the mini-array was varied and the fluorescently labelled target DNA was diluted. Typically, aneusomies could be detected using 30 ng of non-amplified random primed labelled DNA amounts in a 4 h hybridization reaction. Potential application of these mini-arrays for genomic profiling of disseminated tumour cells or of blastomeres for preimplantation genetic diagnosis, using specially designed DNA amplification methods, are discussed.

  14. 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


    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Cary; R. Bruce (Santa Fe, NM); Stubben, Christopher J. (Los Alamos, NM)


    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.

  16. An Xq22.3 duplication detected by comparative genomic hybridization microarray (Array-CGH) defines a new locus (FGS5) for FG syndrome. (United States)

    Jehee, Fernanda Sarquis; Rosenberg, Carla; Krepischi-Santos, Ana Cristina; Kok, Fernando; Knijnenburg, Jeroen; Froyen, Guy; Vianna-Morgante, Angela M; Opitz, John M; Passos-Bueno, Maria Rita


    FG syndrome is an X-linked multiple congenital anomalies (MCA) syndrome. It has been mapped to four distinct loci FGS1-4, through linkage analysis (Xq13, Xp22.3, and Xp11.4-p11.3) and based on the breakpoints of an X chromosome inversion (Xq11:Xq28), but so far no gene has been identified. We describe a boy with FG syndrome who has an inherited duplication at band Xq22.3 detected by comparative genomic hybridization microarray (Array-CGH). These duplication maps outside all four loci described so far for FG syndrome, representing therefore a new locus, which we propose to be called FGS5. MID2, a gene closely related to MID1, which is known to be mutated in Opitz G/BBB syndrome, maps within the duplicated segment of our patient. Since FG and Opitz G/BBB syndromes share many manifestations we considered MID2 a candidate gene for FG syndrome. We also discuss the involvement of other potential genes within the duplicated segment and its relationship with clinical symptoms of our patient, as well as the laboratory abnormalities found in his mother, a carrier of the duplication.

  17. Pectate lyase pollen allergens: sensitization profiles and cross-reactivity pattern.

    Directory of Open Access Journals (Sweden)

    Ulrike Pichler

    Full Text Available Pollen released by allergenic members of the botanically unrelated families of Asteraceae and Cupressaceae represent potent elicitors of respiratory allergies in regions where these plants are present. As main allergen sources the Asteraceae species ragweed and mugwort, as well as the Cupressaceae species, cypress, mountain cedar, and Japanese cedar have been identified. The major allergens of all species belong to the pectate lyase enzyme family. Thus, we thought to investigate cross-reactivity pattern as well as sensitization capacities of pectate lyase pollen allergens in cohorts from distinct geographic regions.The clinically relevant pectate lyase pollen allergens Amb a 1, Art v 6, Cup a 1, Jun a 1, and Cry j 1 were purified from aqueous pollen extracts, and patients' sensitization pattern of cohorts from Austria, Canada, Italy, and Japan were determined by IgE ELISA and cross-inhibition experiments. Moreover, we performed microarray experiments and established a mouse model of sensitization.In ELISA and ELISA inhibition experiments specific sensitization pattern were discovered for each geographic region, which reflected the natural allergen exposure of the patients. We found significant cross-reactivity within Asteraceae and Cupressaceae pectate lyase pollen allergens, which was however limited between the orders. Animal experiments showed that immunization with Asteraceae allergens mainly induced antibodies reactive within the order, the same was observed for the Cupressaceae allergens. Cross-reactivity between orders was minimal. Moreover, Amb a 1, Art v 6, and Cry j 1 showed in general higher immunogenicity.We could cluster pectate lyase allergens in four categories, Amb a 1, Art v 6, Cup a 1/Jun a 1, and Cry j 1, respectively, at which each category has the potential to sensitize predisposed individuals. The sensitization pattern of different cohorts correlated with pollen exposure, which should be considered for future allergy

  18. Cosmetic Contact Allergens

    Directory of Open Access Journals (Sweden)

    An Goossens


    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.

  19. Use of quantum dots as mass and fluorescence labels in microarray biosensing. (United States)

    Finetti, Chiara; Plavisch, Lauren; Chiari, Marcella


    In this work, we demonstrate the efficacy of a Quantum Dot (QD) mass label strategy to enhance sensitivity in an interferometric technique called interferometric reflectance imaging sensor (IRIS). This biomass detection platform confers the advantage of absolute mass quantification and lower cost, easily implementable equipment. We discuss the advantages of this label when used in parallel with fluorescence detection. QDs represent a unique opportunity to improve sensitivity in both mass-label detection methods due to their large detectable mass, as well as in fluorescence detection, as they fluoresce without quenching. Streptavidin-conjugated QDs (SA-QDs) have been investigated as such a dual-role probe because of their large shape and mass, their 655nm emission peak for fluorescent detection platforms, and their robust insensitivity to photobleaching and quenching. In particular we explored their dual role in a microarrays immunoassay designed to detect antibodies against β-lactoglobulin, a common milk allergen. The SA-QDs formed a large detectable monolayer of 6.2ng/mm(2) in the saturation conditions, a mass signal corroborated by previous studies by Platt et al..

  20. Endonuclease-based Method for Detecting the Sequence Specific DNA Binding Protein on Double-stranded DNA Microarray

    Institute of Scientific and Technical Information of China (English)

    Yun Fei BAI; Qin Yu GE; Tong Xiang LI; Jin Ke WANG; Quan Jun LIU; Zu Hong LU


    The double-stranded DNA (dsDNA) probe contains two different protein binding sites.One is for DNA- binding proteins to be detected and the other is for a DNA restriction enzyme.The two sites were arranged together with no base interval. The working principle of the capturing dsDNA probe is described as follows: the capturing probe can be cut with the DNA restriction enzyme (such as EcoR I) to cause a sticky terminal, if the probe is not bound with a target protein, and the sticky terminal can be extended and labeled with Cy3-dUTP by DNA polymerase. When the probe is bound with a target protein, the probe is not capable to be cut by the restriction enzyme because of space obstruction. The amount of the target DNA binding proteins can be measured according to the variations of fluorescent signals of the corresponding probes.

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



    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 ...

  2. Allergen-specific immunotherapy

    Directory of Open Access Journals (Sweden)

    Moote William


    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.

  3. Genome-Wide lncRNA Microarray Profiling Identifies Novel Circulating lncRNAs for Detection of Gastric Cancer (United States)

    Zhang, Kecheng; Shi, Hongzhi; Xi, Hongqing; Wu, Xiaosong; Cui, Jianxin; Gao, Yunhe; Liang, Wenquan; Hu, Chong; Liu, Yi; Li, Jiyang; Wang, Ning; Wei, Bo; Chen, Lin


    Long non-coding RNAs (lncRNAs) can serve as blood-based biomarkers for cancer detection. To identify novel lncRNA biomarkers for gastric cancer (GC), we conducted, for the first time, genome-wide lncRNA screening analysis in two sets of samples: five paired preoperative and postoperative day 14 plasma samples from GC patients, and tissue samples from tumor and adjacent normal tissues. Candidate tumor-related lncRNAs were then quantitated and evaluated in three independent phases comprising 321 participants. The expression levels of lncRNAs were also measured in GC cell lines and the corresponding culture medium. Biomarker panels, lncRNA-based Index I and carcinoembryonic antigen (CEA)-based Index II, were constructed using logistic regression, and their diagnostic performance compared. Fagan's nomogram was plotted to facilitate clinical application. As a result, we identified five novel plasma lncRNAs (TINCR, CCAT2, AOC4P, BANCR and LINC00857), which, when combined in the lncRNA-based Index I, outperformed the CEA-based Index II (P < 0.001) and could distinguish GC patients from healthy controls with an area under the receiver-operating curve (AUC) of 0.91 (95% confidence interval (CI): 0.88-0.95). The lncRNA-based index decreased significantly by postoperative day 14 (P = 0.016), indicating its ability to monitor tumor dynamics. High values of the lncRNA-based index were correlated with tumor size (P = 0.036), depth of invasion (P = 0.025), lymphatic metastasis (P = 0.012) and more advanced tumor stages (P = 0.003). The lncRNA-based index was also able to discriminate GC patients from precancerous individuals and patients with gastrointestinal stromal tumor with AUC values of 0.82 (95% CI: 0.71-0.92) and 0.80 (95% CI: 0.68-0.91), respectively. Taken together, our findings demonstrate that this panel of five plasma lncRNAs could serve as a set of novel diagnostic biomarkers for GC detection. PMID:28042329

  4. PCR amplfication on a microarray of gel-immobilized oligonucleotides : detection of bacterial toxin- and drug-resistent genes and their mutations.

    Energy Technology Data Exchange (ETDEWEB)

    Strizhkov, B. N.; Drobyshev, A. L.; Mikhailovich, V. M.; Mirzabekov, A. D.; Biochip Technology Center; Engelhardt Inst. of Molecular Biology


    PCR amplification on a microarray of gel-immobilized primers (microchip) has been developed. One of a pair of PCR primers was immobilized inside a separate microchip polyacrylamide porous gel pad of 0.1 x 0.1 x 0.02 (or 0.04) micron in size and 0.2 (or 0.4) nL in volume. The amplification was carried out simultaneously both in solution covering the microchip array and inside gel pads. Each gel pad contained the immobilized forward primers, while the fluorescently labeled reverse primers, as well as all components of the amplification reaction, diffused into the gel pads from the solution. To increase the amplification efficiency, the forward primers were also added into the solution. The kinetics of amplification was measured in real time in parallel for all gel pads with a fluorescent microscope equipped with a charge-coupled device (CCD) camera. The accuracy of the amplification was assessed by using the melting curves obtained for the duplexes formed by the labeled amplification product and the gel-immobilized primers during the amplification process; alternatively, the duplexes were produced by hybridization of the extended immobilized primers with labeled oligonucleotide probes. The on-chip amplification was applied to detect the anthrax toxin genes and the plasmid-borne beta-lactamase gene responsible for bacterial ampicillin resistance. The allele-specific type of PCR amplification was used to identify the Shiga toxin gene and discriminate it from the Shiga-like one. The genomic mutations responsible for rifampicin resistance of the Mycobacterium tuberculosis strains were detected by the same type of PCR amplification of the rpoB gene fragment isolated from sputum of tuberculosis patients. The on-chip PCR amplification has been shown to be a rapid, inexpensive and powerful tool to test genes responsible for bacterial toxin production and drug resistance, as well as to reveal point nucleotide mutations.

  5. Japan food allergen labeling regulation--history and evaluation. (United States)

    Akiyama, Hiroshi; Imai, Takanori; Ebisawa, Motohiro


    According to a national survey of food allergy cases, the food-labeling system for specific allergenic ingredients (i.e., egg, milk, wheat, buckwheat, and peanut) in Japan was mandated under law on April 1, 2002. By Japanese law, labeling of allergens is designated as mandatory or recommended based on the number of cases of actual illness and the degree of seriousness. Mandatory labeling is enforced by the ministerial ordinance, and the ministerial notification recommends that foods containing walnut and soybean be labeled with subspecific allergenic ingredients. Additional labeling of shrimp/prawn and crab has also become mandatory since 2008. To monitor the validity of the labeling system, the Japanese government announced the official methods for detection of allergens in a November 2002 ministry notification. These official methods, including two kinds of enzyme-linked immunosorbent assay kits for screening, Western blotting analyses for egg and milk, and polymerase chain reaction analyses for wheat, buckwheat, peanut, shrimp/prawn and crab as confirmation tests, have provided a means to monitor the labeling system. To standardize the official methods, the Japanese government described the validation protocol criteria in the 2006 official guidelines. The guidelines stipulate that any food containing allergen proteins at greater than 10mg/kg must be labeled under the Law. This review covers the selection of the specific allergenic ingredients by the Japanese government, the implementation of regulatory action levels and the detection methods to support them, and the assessment of the effectiveness of this approach.

  6. 恩施土家族苗族自治州常见过敏性疾病相关过敏原检测结果分析%Outcome Analysis of Detecting the Allergens of Common Allergic Diseases in Enshi Autonomous Prefecture of Tujia and Miao Population

    Institute of Scientific and Technical Information of China (English)

    沈艳芳; 雷锐


    目的 探讨过敏性疾病患者发病与过敏原的关系,寻找该疾病常见的过敏原,为患者的脱敏治疗及预防提供依据.方法 应用德国摩拉生物共振仪对过敏性疾病(荨麻疹、湿疹、哮喘、紫癜、鼻炎)患者234例进行过敏原检测,回顾性分析常见过敏性疾病患者中各类过敏原阳性率及其分布差异.结果 过敏性疾病常见的过敏原有螨虫、环境化学、花粉、真菌、食品添加剂、动物等,食入类过敏原中阳性率最高是鱼类,湿疹阳性率为65.22%,荨麻疹为62.07%;吸入类过敏原以支气管哮喘花粉阳性率最高,为89.74%,昆虫螨虫为79.49%;接触类过敏原以鼻炎的霉菌检出率最高,为77.78%,环境化学物质为66.67%.与部分其他地区相比,恩施地区花粉、尘螨的检出率较高,与本地区植被及气候特点有一定关系.结论 摩拉生物系统可用于过敏性疾病病因的检测,过敏原种类全.大多数过敏性疾病患者能找到过敏原,且以螨虫、环境化学、花粉、真菌等为主.%Objective To explore the relationship of allergic disease onset and allergens, looking for common allergens in this kind of disease, and provide the basis for desensitization treatment and prevention for patients. Methods The German Mora ( MORA ) bio-resonance spectrometer was used in 234 cases of allergic patients ( urticaria, eczema, asthma,purpura,rhinitis ) for allergen detection. The various types of allergens positive rate in patients with common allergic diseases and the difference of the distribution were analyzed retrospectively. Results Allergic diseases' common allergens were mites, environmental chemicals, pollen,mold,food additives,fungi,animals and so on. The highest positive rate of ingested allergens was fish, the positive of eczema was 65.22% and of urticaria was 62.07% ;the highest positive rate of inhaled allergens was bronchial asthma pollen with the rate up to 89.74% ,the rate of insect mites was 79

  7. DNA Microarray Technique

    Directory of Open Access Journals (Sweden)

    Thakare SP


    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.

  8. American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities. (United States)

    Kearney, Hutton M; South, Sarah T; Wolff, Daynna J; Lamb, Allen; Hamosh, Ada; Rao, Kathleen W


    Genomic copy number microarrays have significantly increased the diagnostic yield over a karyotype for clinically significant imbalances in individuals with developmental delay, intellectual disability, multiple congenital anomalies, and autism, and they are now accepted as a first tier diagnostic test for these indications. As it is not feasible to validate microarray technology that targets the entire genome in the same manner as an assay that targets a specific gene or syndromic region, a new paradigm of validation and regulation is needed to regulate this important diagnostic technology. We suggest that these microarray platforms be evaluated and manufacturers regulated for the ability to accurately measure copy number gains or losses in DNA (analytical validation) and that the subsequent interpretation of the findings and assignment of clinical significance be determined by medical professionals with appropriate training and certification. To this end, the American College of Medical Genetics, as the professional organization of board-certified clinical laboratory geneticists, herein outlines recommendations for the design and performance expectations for clinical genomic copy number microarrays and associated software intended for use in the postnatal setting for detection of constitutional abnormalities.

  9. Microarray-based Identification of Novel Biomarkers in Asthma

    Directory of Open Access Journals (Sweden)

    Kenji Izuhara


    Full Text Available Bronchial asthma is a complicated and diverse disorder affected by genetic and environmental factors. It is widely accepted that it is a Th2-type inflammation originating in lung and caused by inhalation of ubiquitous allergens. The complicated and diverse pathogenesis of this disease yet to be clarified. Functional genomics is the analysis of whole gene expression profiling under given condition, and microarray technology is now the most powerful tool for functional genomics. Several attempts to clarify the pathogenesis of bronchial asthma have been carried out using microarray technology, providing us some novel biomarkers for diagnosis, therapeutic targets or understanding pathogenic mechanisms of bronchial asthma. In this article, we review the outcomes of these analyses by the microarray approach as applied to this disease by focusing on the identification of novel biomarkers.

  10. [The study of profile of hypersensitivity to pollen and fungal allergens in the Moscow region]. (United States)

    Akhapkina, I G; Krakhanenkova, S N; Dobronravova, E V; Shushpanova, E N


    The profile of hypersensitivity to pollen and fungal allergens is an important element of common pattern of immune diseases needed for development of effective pharmaceuticals. The purpose of the study was to analyze the rate of detection of combined forms of hypersensitivity to pollen and fungal allergens (pollen of birch, hazel, cocksfoot, wormwood, fungi A. alternata, C. herbarum, R. nigricans, P. notatum, C. albicans, A. fumigatus) in the Moscow region on the basis of data of scarification skin samples. The mono-sensibilization was established in 23.36% of all cases of hypersensitivity. At that, among leading allergens turned out A. alternata and cocksfoot pollen (6.54% and 4.67%), followed by allergens of wormwood pollen, P. notatum, R. nigricans, birch pollen and C. albicans (3.74%, 3.74%, 1.87%, 1.87% and 0.93% correspondingly). The polysensibilization was established in 51.40% of cases. Besides, the combined hypersensitivity to pollen allergens of plants (20.26%) and to pollen and fungal allergens (20.56%) occurred more frequently In the group of patients with polysensibilization predominated combined allergic reactions to pollen allergens and A. alternata allergens (36.36%). On the whole, most frequently occurred sensitization to allergens of birch, hazel, cocksfoot, wormwood and A. alternata allergen (76.14%, 69.32%, 57.95%, 55.68%, 39.77% and 56.82% correspondingly). In the Moscow region predominate combined forms of hypersensitivity to two and more pollen and fungal allergens. The polysensitization to pollen allergens and A. alternata allergen occurs more frequently.

  11. Effects of processing on the recovery of food allergens from a model dark chocolate matrix. (United States)

    Khuda, Sefat E; Jackson, Lauren S; Fu, Tong-Jen; Williams, Kristina M


    To alleviate the risk to allergic consumers, it is crucial to improve factors affecting the detection of food allergens in processed chocolate products. This study evaluated processing effects on (1) recovery of peanut, egg, and milk allergens using five different extraction buffers, and (2) identification of specific allergenic proteins from extracts of incurred chocolate using allergen-specific antibodies and human allergic sera. Immunochemical staining with polyclonal antibodies showed that the addition of detergent or reducing agent improved extraction efficiency of peanut proteins, but not of egg and milk proteins. Tempering decreased antibody binding regardless of extractant. Detection of IgE-reactive peanut, egg, and milk allergens was differentially affected by tempering and extractant. Detection problems associated with matrix and processing effects may be overcome by the choice of extraction buffer and detecting antibody.

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

    Directory of Open Access Journals (Sweden)

    Ana Moreno Álvarez


    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.

  13. Food, novel foods, and allergenicity

    NARCIS (Netherlands)

    Loveren H van; LPI


    Certain foods lead may to allergic responses in certain individuals. Main allergenic foods are Crustacea (shrimp, lobster, crab), egg, fish, milk, peanuts, soybeans, tree nuts, and wheat, and allergens are always proteins. A wide array of symptoms can result from food allergy (gastrointestinal, ski

  14. Footwear dermatitis - Clinical patterns and contact allergens

    Directory of Open Access Journals (Sweden)

    Handa S


    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.

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

    Directory of Open Access Journals (Sweden)

    Kaloustian Jacques


    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.

  16. Degradation of wheat allergen in Japanese soy sauce. (United States)

    Kobayashi, Makio; Hashimoto, Yuichiro; Taniuchi, Shoichiro; Tanabe, Soichi


    Soy sauce is a traditional fermented seasoning of East Asian countries and is available throughout the world. Wheat and soybeans are the 2 main raw materials of soy sauce, and soy sauce also contains a high concentration of salt. Since wheat allergy is considered a serious problem globally, it is significant to examine the allergenicity of soy sauce. In this study, by immunoblotting, inhibition ELISA and direct ELISA using sera from 5 children with wheat allergy, it was clearly demonstrated that wheat allergens were degraded into amino acids and peptides losing the IgE-binding ability in both salt-soluble and salt-insoluble fractions of soy sauce during fermentation. Furthermore, no wheat allergen was detected in 10 items of commercial soy sauce in Japan, by inhibition ELISA or direct ELISA using the sera of patients. In the brewing process of soy sauce, first salt-insoluble wheat allergen was solubilized to salt water during the koji stage (mold cultivation and enzyme production), and second both the resultant salt-solubilized and initially salt-soluble wheat allergens were completely degraded during the moromi stage (fermentation) by microbial proteolytic enzymes. Therefore, it was concluded that no wheat allergen is contained in soy sauce.

  17. Allergens from fish and egg

    DEFF Research Database (Denmark)

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


    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...

  18. Structural aspects of fungal allergens. (United States)

    Crameri, Reto


    Despite the increasing number of solved crystal structures of allergens, the key question why some proteins are allergenic and the vast majority is not remains unanswered. The situation is not different for fungal allergens which cover a wide variety of proteins with different chemical properties and biological functions. They cover enzymes, cell wall, secreted, and intracellular proteins which, except cross-reactive allergens, does not show any evidence for structural similarities at least at the three-dimensional level. However, from a diagnostic point of view, pure allergens biotechnologically produced by recombinant technology can provide us, in contrast to fungal extracts which are hardly producible as standardized reagents, with highly pure perfectly standardized diagnostic reagents.

  19. Identification of autoclave-resistant Anisakis simplex allergens. (United States)

    Carballeda-Sangiao, Noelia; Olivares, Fabiola; Rodriguez-Mahillo, Ana I; Careche, Mercedes; Tejada, Margarita; Moneo, Ignacio; González-Muñoz, Miguel


    Anisakis simplex is a fish parasite able to induce allergic reactions in humans infected when eating raw or undercooked fish parasitized with viable third-stage larvae. Some authors claim that exposure to nonviable Anisakis material can result in allergic symptoms in previously sensitized patients, indicating that parasite allergens are resistant to the thermal treatments of usual cooking procedures. Furthermore, some patients report symptoms after eating canned fish. The aim of this work was the analysis of parasite allergen stability in heating to 121 °C in an autoclave to simulate the thermal process applied to canned fish. Third-stage larvae were subjected to autoclaving for 20, 40, and 80 min, and parasite crude extracts were analyzed by electrophoresis, immunoblotting, and a flow-cytometric basophil activation test. Allergens resistant to autoclaving were separated by reversed-phase high-performance liquid chromatography and identified by ion trap mass spectrometry. Protein analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that autoclaving considerably reduced the number and intensity of identifiable protein bands in a time-dependent manner. Several allergens were detected by immunoblotting with a pool of A. simplex allergic patients' sera after autoclaving. Allergens of 9 and 14 kDa resistant to autoclaving were identified as Ani s 4 and Ani s 1 allergens, respectively. Functional analysis showed that allergens retain their capacity to activate basophils even after autoclaving for 80 min. In conclusion, some relevant A. simplex allergens retain their capacity to bind immunoglobulin E and activate basophils after being subjected to autoclaving, which is a method equivalent to that used in industrial canning processes.

  20. 南阳市慢性过敏性鼻炎患者过敏原检测结果分析%Analysis of Allergen Detection Results in Patients With Chronic Allergic Rhinitis in Nanyang City

    Institute of Scientific and Technical Information of China (English)



    Objective To understand the types and distribution of allergens in patients with chronic allergic rhinitis in nanyang, and to provide reliable evidence for the prevention and treatment of this disease.Methods ELISA method was used for the determination of serum total IgE and specific IgE in patients with chronic allergic rhinitis, and the comparative analysis was carried out.Results Patients with chronic allergic rhinitis in total IgE positive rate of 100%, the 2 cases of specific allergen test negative, specific allergen detection results for dermatophagoides pteronyssinus 113 cases of the positive (37.7%), house dust was positive in 90 cases (30.0%), trees (oak, elm, sycamore, willow, cottonwood yang) was positive in 54 cases (18.0%). Conclusion Nanyang city cause chronic allergic rhinitis allergic principle mainly in household dust mites, house dust, trees (oak, elm, sycamore, willow, cottonwood yang).%目的 了解南阳市慢性过敏性鼻炎患者过敏原的种类及分布,为本病预防和治疗提供可靠依据.方法 采用ELISA法对慢性过敏性鼻炎患者的血清总IgE和特异性IgE进行半定量测定,并进行对比分析.结果 慢性过敏性鼻炎患者中总IgE阳性率100%,其中2例特异性过敏原检测阴性,特异性过敏原检测结果 为:户尘螨阳性113例(37.7%),屋尘阳性90例(30.0%),树木(栎树、榆树、梧桐、柳树、三角叶杨)阳性54例(18.0%).结论 南阳市引起慢性过敏性鼻炎的过敏原主要是户尘螨,屋尘,树木(栎树、榆树、梧桐、柳树、三角叶杨).

  1. Absolute quantification of allergens from complex mixtures: a new sensitive tool for standardization of allergen extracts for specific immunotherapy. (United States)

    Seppälä, Ulla; Dauly, Claire; Robinson, Sarah; Hornshaw, Martin; Larsen, Jørgen Nedergaard; Ipsen, Henrik


    Products for specific diagnosis and immunotherapy of IgE-mediated allergies are currently based on natural extracts. Quantification of major allergen content is an important aspect of standardization as important allergens particularly impact vaccine potency. The aim of the study was to develop a mass spectrometry (MS) based assay for absolute quantification of Timothy (Phleum pratense) pollen allergens Phl p 1 and Phl p 5 in P. pratense extract. High-resolution and accurate mass (HRAM) MS was selected for its ability to detect peptides with high selectivity and mass accuracy (extract. Robustness and linearity of the method was demonstrated with intra day precision ≤ 5% (n = 3). Phl p 1b was shown to be 5 times less abundant than its variant Phl p 1a and Phl p 5b was shown to be 9 times more abundant than the Phl p 5a. The present study shows that allergen, and/or isoallergen specific, surrogate signature peptides analyzed with HRAM MS is a sensitive and accurate tool for identification and quantification of allergens from complex allergen sources.

  2. Molecular and immunological characterization of the first allergenic lipocalin in hamster: the major allergen from Siberian hamster (Phodopus sungorus). (United States)

    Torres, José Alberto; de Las Heras, Manuel; Maroto, Aroa Sanz; Vivanco, Fernando; Sastre, Joaquín; Pastor-Vargas, Carlos


    The most frequent pet allergy is to cat and dog, but in recent years, it has become increasingly popular to have other pets, and the risk of exposure to new allergens is more prevalent. The list of new pets includes hamsters, and one of the most popular hamsters is the Siberian hamster (Phodopus sungorus). The aim of this study was the characterization and cloning of the major allergen from this hamster. The study of its allergenicity and cross-reactivity could improve the specific diagnosis and treatment for hamster-allergic patients. Thirteen Siberian hamster-allergic patients were recruited at the outpatient clinic. Protein extracts were prepared from the hair, urine, and salivary glands of four hamster species (European, golden, Siberian, and Roborovski). IgE-binding proteins were detected by immunoblotting and identified by mass spectrometry. The recombinant protein was produced in Escherichia coli and then purified by metal chelate affinity chromatography. The allergenic properties of the recombinant protein were tested by ELISA and immunoblotting, and biological activity was tested according to capacity for basophil activation. Three IgE-binding proteins were identified in extracts obtained from Siberian hamster hair, urine, and salivary glands. All proteins corresponded to the same protein, which was identified as a lipocalin. This lipocalin had no cross-reactivity with common and golden hamsters. The recombinant allergen was cloned and purified, showing similar IgE reactivity in vitro to Siberian hamster protein extracts. Also, the recombinant allergen was capable of producing biological activation in vivo. The major Siberian hamster allergen was cloned, and allergenic properties were characterized, providing a new tool for specific diagnosis of allergy to Siberian hamster.

  3. Label-free Protein Detection Based on the Heat-Transfer Method--A Case Study with the Peanut Allergen Ara h 1 and Aptamer-Based Synthetic Receptors. (United States)

    Peeters, Marloes; van Grinsven, Bart; Cleij, Thomas J; Jiménez-Monroy, Kathia Lorena; Cornelis, Peter; Pérez-Ruiz, Elena; Wackers, Gideon; Thoelen, Ronald; De Ceuninck, Ward; Lammertyn, Jeroen; Wagner, Patrick


    Aptamers are an emerging class of molecules that, because of the development of the systematic evolution of ligands by exponential enrichment (SELEX) process, can recognize virtually every target ranging from ions, to proteins, and even whole cells. Although there are many techniques capable of detecting template molecules with aptamer-based systems with high specificity and selectivity, they lack the possibility of integrating them into a compact and portable biosensor setup. Therefore, we will present the heat-transfer method (HTM) as an interesting alternative because this offers detection in a fast and low-cost manner and has the possibility of performing experiments with a fully integrated device. This concept has been demonstrated for a variety of applications including DNA mutation analysis and screening of cancer cells. To the best our knowledge, this is the first report on HTM-based detection of proteins, in this case specifically with aptamer-type receptors. For proof-of-principle purposes, measurements will be performed with the peanut allergen Ara h 1 and results indicate detection limits in the lower nanomolar regime in buffer liquid. As a first proof-of-application, spiked Ara h 1 solutions will be studied in a food matrix of dissolved peanut butter. Reference experiments with the quartz-crystal microbalance will allow for an estimate of the areal density of aptamer molecules on the sensor-chip surface.

  4. Review: DNA microarray technology and drug development

    Directory of Open Access Journals (Sweden)

    Sana Khan


    Full Text Available On the contrary to slow and non specific traditional drug discovery methods, DNA microarray technology could accelerate the identification of potential drugs for treating diseases like cancer, AIDS and provide fruitful results in the drug discovery. The technique provides efficient automation and maximum flexibility to the researchers and can test thousand compounds at a time. Scientists find DNA microarray useful in disease diagnosis, monitoring desired and adverse outcomes of therapeutic interventions, as well as, in the selection, assessment and quality con-trol of the potential drugs. In the current scenario, where new pathogens are expected every year, DNA microarray promises as an efficient technology to detect new organisms in a short time. Classification of carcinomas at the molecular level and prediction of how various types of tumor respond to different therapeutic agents can be made possible with the use of microarray analysis. Also, microarray technique can prove instrumental in personalized medicines development by providing microarray data of a patient which could be used for identifying diseases, treatment specific to individual and trailing disease prognosis. Microarray analysis could be beneficial in the area of molecular medicines for analysis of genetic variations and functions of genes in normal individuals and diseased conditions. The technique can give satisfactory results in single nucleotide polymorphism (SNP analysis and pharmacogenomics studies. The challenges that arise with the technology are high degree of variability with data obtained, frequent up gradation of methods and machines and lack of trained manpower. Despite this, DNA micro-array promises to be the next generation sequencer which could explain how organisms evolve and adapt looking at the whole genome. In a nutshell, Microarray technology makes it possible for molecular biologists to analyze simultaneously thousands of DNA samples and monitor their

  5. Microarray Analysis in Glioblastomas (United States)

    Bhawe, Kaumudi M.; Aghi, Manish K.


    Microarray analysis in glioblastomas is done using either cell lines or patient samples as starting material. A survey of the current literature points to transcript-based microarrays and immunohistochemistry (IHC)-based tissue microarrays as being the preferred methods of choice in cancers of neurological origin. Microarray analysis may be carried out for various purposes including the following: To correlate gene expression signatures of glioblastoma cell lines or tumors with response to chemotherapy (DeLay et al., Clin Cancer Res 18(10):2930–2942, 2012)To correlate gene expression patterns with biological features like proliferation or invasiveness of the glioblastoma cells (Jiang et al., PLoS One 8(6):e66008, 2013)To discover new tumor classificatory systems based on gene expression signature, and to correlate therapeutic response and prognosis with these signatures (Huse et al., Annu Rev Med 64(1):59–70, 2013; Verhaak et al., Cancer Cell 17(1):98–110, 2010) While investigators can sometimes use archived tumor gene expression data available from repositories such as the NCBI Gene Expression Omnibus to answer their questions, new arrays must often be run to adequately answer specific questions. Here, we provide a detailed description of microarray methodologies, how to select the appropriate methodology for a given question, and analytical strategies that can be used. Experimental methodology for protein microarrays is outside the scope of this chapter, but basic sample preparation techniques for transcript-based microarrays are included here. PMID:26113463

  6. Recombinant allergens for pollen immunotherapy. (United States)

    Wallner, Michael; Pichler, Ulrike; Ferreira, Fatima


    Specific immunotherapy (IT) represents the only potentially curative therapeutic intervention of allergic diseases capable of suppressing allergy-associated symptoms not only during treatment, but also after its cessation. Presently, IT is performed with allergen extracts, which represent a heterogeneous mixture of allergenic, as well as nonallergenic, compounds of a given allergen source. To overcome many of the problems associated with extract-based IT, strategies based on the use of recombinant allergens or derivatives thereof have been developed. This review focuses on recombinant technologies to produce allergy therapeuticals, especially for allergies caused by tree, grass and weed pollen, as they are among the most prevalent allergic disorders affecting the population of industrialized societies. The reduction of IgE-binding of recombinant allergen derivatives appears to be mandatory to increase the safety profile of vaccine candidates. Moreover, increased immunogenicity is expected to reduce the dosage regimes of the presently cumbersome treatment. In this regard, it has been convincingly demonstrated in animal models that hypoallergenic molecules can be engineered to harbor inherent antiallergenic immunologic properties. Thus, strategies to modulate the allergenic and immunogenic properties of recombinant allergens will be discussed in detail. In recent years, several successful clinical studies using recombinant wild-type or hypoallergens as active ingredients have been published and, currently, novel treatment forms with higher safety and efficacy profiles are under investigation in clinical trials. These recent developments are summarized and discussed.

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

    DEFF Research Database (Denmark)

    Yuan, Yiyang; Krogh, Paul Henning; Bai, Xue


    . 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...

  8. 50 The Allergic March Resolved at Allergen Component Level (United States)

    Melioli, Giovanni; Marcomini, Laura; Agazzi, Alessia; Bazurro, Gyada; Rossi, Lucilla; Tosca, Mariangela; Minale, Paola; Rossi, Renato; Passalacqua, Giovanni; Canonica, Giorgio Walter


    Background The allergic march is well known at the level of pattern of sensitisation, but there is no information of its evolution in term of sensitzation to single allergenic molecules. We investigated the evolution of the IgE repertoire by means of a microarray allergen assay. Methods Serum samples from allergic patients of a wide age range were analyzed by a micorarray chip, which allow to identify in a single assay the presence of specific IgE towards 103 allergenic molecules. Total IgE were also evaluated as an internal control. Patients were stratified in 6 groups according to their age (0–2; 3–5; 6–9; 10–13; 14–17 and >17 years). Results Samples from 609 patients were analysed. The behaviour of total IgE according to age strictly paralleled that of the sum of specific IgE. Food-related components were the more frequently recognized in the first ages, whereas specific IgE to plant allergens appeared later. Nonetheless, mite-specific IgE were the most represented in all age classes. Specific IgE against cross-reacting allergens were virtually absent in the first years and tended to appear after the age of 6. Conclusions The molecular pattern of allergen recognition according to age well reflects the clinical characteristics of the allergic march.

  9. Analysis of regulated suspected allergens in waters. (United States)

    Becerril, Elias; Lamas, J Pablo; Sanchez-Prado, Lucia; Llompart, Maria; Lores, Marta; Garcia-Jares, Carmen


    Fragrance suspected allergens including those regulated by the EU Directive 76/768/EEC have been determined in different types of waters using solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS). The procedure was based on headspace sampling (HS-SPME) using polydimethylsiloxane/divinylbenzene (PDMS/DVB) fibers and has been optimized by an experimental design approach. The method performance has been studied showing good linearity (R ≥ 0.994) as well as good intra-day and inter-day precision (RSD ≤ 12%). Detection limits (S/N=3) ranged from 0.001 to 0.3 ng mL(-1). Reliability was demonstrated through the quantitative recoveries of the compounds in real water samples, including baby bathwaters, swimming pool waters, and wastewaters. The absence of matrix effects allowed quantification of the compounds by external aqueous calibration. The analysis of 35 samples of different types of waters showed the presence of suspected allergens in all the analyzed samples. All targets were found in the samples, with the exception of methyl eugenol and amyl cinnamic alcohol. Highest concentrations of suspected allergens were present in baby bathwaters, containing from 5 to 15 of the compounds at concentrations ranging from few pg mL(-1) to several hundreds of ng mL(-1).

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

    Directory of Open Access Journals (Sweden)

    Hamed Fouladseresht


    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.

  11. Molecular Characteristics of Cockroach Allergens

    Institute of Scientific and Technical Information of China (English)

    Chii-Huei Wu; Mey-Fann Lee


    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.

  12. Large particulate allergens can elicit mast cell-mediated anaphylaxis without exit from blood vessels as efficiently as do small soluble allergens. (United States)

    LiHua, Li; Yoshikawa, Soichiro; Ohta, Takuya; Horiguchi, Kayo; Kawano, Yohei; Ohtsu, Hiroshi; Yamanishi, Yoshinori; Karasuyama, Hajime


    Anaphylaxis is a rapid-onset, life-threatening allergic reaction in that IgE, mast cells and histamine are commonly involved. It can be experimentally induced in IgE-sensitized animals by intravenous injection of corresponding allergens, and the sign of anaphylactic reaction can be detected within minutes after allergen challenge. However, it remains puzzling why the anaphylactic reaction can be initiated in vivo so quickly, considering that allergens are delivered into the blood circulation while mast cells reside within peripheral tissues but not in the blood circulation. To address this issue, we compared two different forms of the same allergen, small soluble and large particulate ones, in their ability to induce anaphylaxis in IgE-sensitized mice. In contrast to our expectation, particulate allergens could induce anaphylaxis as quickly and efficiently as did soluble allergens, even though they remained inside of blood vessels. In vivo imaging analysis suggested the direct interaction of intravascular particulate allergens and perivascular mast cells across the capillary wall. Taken together with previous report that perivascular mast cells can capture IgE in the blood circulation by extending cell processes across the vessel wall, our findings imply that blood-circulating allergens, regardless of their size, can stimulate mast cells without exit from blood vessels, by means of cross-linking IgE on mast cell processes inserted into the vessel lumen, and hence initiate anaphylactic reaction so quickly.

  13. 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


    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

  14. Improving the extraction of Ara h 6 (a peanut allergen) from a chocolate-based matrix for immunosensing detection: Influence of time, temperature and additives. (United States)

    Alves, Rita C; Pimentel, Filipa B; Nouws, Henri P A; Silva, Túlio H B; Oliveira, M Beatriz P P; Delerue-Matos, Cristina


    The extraction of Ara h 6 (a peanut allergen) from a complex chocolate-based food matrix was optimized by testing different temperatures, extraction times, and the influence of additives (NaCl and skimmed milk powder) in a total of 36 different conditions. Analyses were carried out using an electrochemical immunosensor. Three conditions were selected since they allowed the extraction of the highest levels of Ara h 6. These extractions were performed using 2g of sample and 20ml of Tris-HNO3 (pH=8) containing: a) 0.1M NaCl and 2g of skimmed milk powder at 21°C for 60min; b) 1M NaCl and 1g of skimmed milk powder at 21°C for 60min; and c) 2g of skimmed milk powder at 60°C for 60min. Recoveries were similar or higher than 94.7%. This work highlights the importance to adjust extraction procedures regarding the target analyte and food matrix components.

  15. A murine monoclonal anti-idiotypic antibody detects a common idiotope on human, mouse and rabbit antibodies to allergen Lol p IV. (United States)

    Zhou, E M; Dzuba-Fischer, J M; Rector, E S; Sehon, A H; Kisil, F T


    A syngeneic mouse monoclonal anti-idiotypic antibody (anti-Id), designated as B1/1, was generated against a monoclonal antibody (MoAb 91) specific for Ryegrass pollen allergen Lol p IV. This anti-Id recognized an idiotope (Id) that was also present on other monoclonal antibodies with the same specificity as MoAb 91. Observations that (i) the anti-Id inhibited the binding of MoAb 91 to Lol p IV and (ii) the Id-anti-Id interaction could be inhibited by Lol p IV indicated that the Id was located within or near the antigen combining site. These properties served to characterize B1/1 as an internal image anti-Id. Evidence that an immune response in different species to Lol p IV elicits the formation of antibodies which express a common Id was provided by the observations that (i) the Id-anti-Id interactions could be inhibited by mouse, human and rabbit antisera to Lol p IV and (ii) the binding of these antisera to Lol p IV could be inhibited by the anti-Id. Interestingly, the internal image anti-Id B1/1 also recognized an Id on a monoclonal antibody which was directed to an epitope of Lol p IV, different from that recognized by MoAb 91.

  16. Microarray Genomic Systems Development (United States)


    proteins, and lipids were pelleted at 10,000 x g for 5 minutes, and the supernatant was collected. DNA pellet was precipitated from the DNAzol by...For hybridization to the microarray, 3.5 ml of hybridization buffer, made with 10% (w/v) Dextran sulphate (EMD Chemicals, Gibbstown, NJ), 1 M...microarray system. Genome Biology, 3(9): 1-16. DRDC Suffield CR 2009-145 15 List of symbols/abbreviations/acronyms/initialisms APS Ammonium

  17. [Value of the microarray for the study of Laboratory Animal Allergy (LAA)]. (United States)

    D'Ovidio, Maria Concetta; Martini, Agnese; Melis, Paola; Signorini, Stefano


    Since 1989, the National Institute for Occupational Safety and Health (NIOSH) considers the Laboratory Animal Allergy - LAA a risk for workers and in 1998 the LAA has been recognized as occupational risk in the USA. Rat and mouse are the most source of allergens, not so much for the higher power of allergy respect to the other animals, but because represent the more utilized species in the research. Most of the allergens are members of the lipocalin superfamily, small extracellular proteins represented by at least 50 proteins that mainly bind or carry small hydrophobic molecules. The recent and innovative molecular techniques, as the microarray, have allow the characterization of numerous allergens. The protein microarray gives the possibility to study of IgE profile for each individual, simultaneos analysis of a wide number of parameters concerning the allergy, giving new diagnostic and therapeutic opportunities for the allergies. In the study of occupational allergy--as LAA--the protein microarray could improve: the identification and characterization of new allergens; the individuation of susceptible workers; the study of immunological responses in exposed workers; the strategies of prevention and protection; the environmental and housing conditions. The participation, formation and information of the workers could improve the behavioural and occupational practices, the use of personal and collective protective devices in order to reduce the exposure to LAA in occupational context.

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

    DEFF Research Database (Denmark)

    Bøgh, Katrine Lindholm; Madsen, Charlotte Bernhard


    . 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...... 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...

  19. 过敏原检测对小儿毛细支气管炎的临床意义探讨%clinical significance discussion of allergen detection to infantile capillary bronchitis

    Institute of Scientific and Technical Information of China (English)

    彭俊云; 吴赞开; 陆国伟; 李裕昌


    目的:探讨研究过敏原检测,对于小儿毛细支气管炎的临床意义。方法:选取我院儿科确诊的21例毛细支气管炎患儿作为观察组,同期住院的其他患儿21例作为对照组,均进行血清特异性IgE检测。通过两组患儿的血清特异性IgE水平以及随访3个月后的喘息发生率比较两组检测结果的意义。结果:观察组患儿血清特异性IgE水平显著高于对照组(P<0.05),随访3个月后观察组患儿喘息发生率高于对照组,差异有显著性(P<0.05)。结论:对毛细支气管炎患儿进行过敏原检测,可有效预测病情的严重程度和转归,有利于避开相关的触发因素,预防反复喘息发作甚至哮喘发生。%Objective:to explore the allergen detection, for the clinical significance of children capillary bronchitis. Selection. Methods:our hospital pediatric diagnosis of 21 cases of capillary bronchitis patients as observation group, other children in 21 cases as control group, both detection of serum specific IgE. Through two groups of children with serum specific IgE levels and followed up for 3 months after the incidence of breathing is the meaning of two groups of test results.Results:the observation group had a significantly higher serum specific IgE levels in children with the control group (P<0.05), the observation group were followed up for 3 months after children breathing rate is higher than the control group, with significant difference (P<0.05). Conclusions:children with capillary bronchitis is used to detect the allergen, which can effectively predict the severity of the illness, and outcome, to avoid trigger factors and prevention of recurrent wheeze and asthma.

  20. Pollen Allergens for Molecular Diagnosis. (United States)

    Pablos, Isabel; Wildner, Sabrina; Asam, Claudia; Wallner, Michael; Gadermaier, Gabriele


    Pollen allergens are one of the main causes of type I allergies affecting up to 30% of the population in industrialized countries. Climatic changes affect the duration and intensity of pollen seasons and may together with pollution contribute to increased incidences of respiratory allergy and asthma. Allergenic grasses, trees, and weeds often present similar habitats and flowering periods compromising clinical anamnesis. Molecule-based approaches enable distinction between genuine sensitization and clinically mostly irrelevant IgE cross-reactivity due to, e. g., panallergens or carbohydrate determinants. In addition, sensitivity as well as specificity can be improved and lead to identification of the primary sensitizing source which is particularly beneficial regarding polysensitized patients. This review gives an overview on relevant pollen allergens and their usefulness in daily practice. Appropriate allergy diagnosis is directly influencing decisions for therapeutic interventions, and thus, reliable biomarkers are pivotal when considering allergen immunotherapy in the context of precision medicine.

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

    Directory of Open Access Journals (Sweden)

    Ile Kristina E


    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.

  2. Biochemical and immunological characterization of recombinant allergen Lol p 1. (United States)

    Tamborini, E; Faccini, S; Lidholm, J; Svensson, M; Brandazza, A; Longhi, R; Groenlund, H; Sidoli, A; Arosio, P


    Pollen from perennial rye grass (Lolium perenne), a major cause of type-I allergy worldwide, contains a complex mixture of allergenic proteins among which Lol p 1 is one of the most important. We describe the expression, purification and characterization of a recombinant Lol p 1 overproduced in Escherichia coli. The recombinant allergen, expressed in high yields and purified in milligram amounts, bound to specific IgE antibodies from human sera, induced histamine release from sensitized human basophils, and elicited rabbit antisera that recognize specifically recombinant Lol p 1 and natural Lol p 1 of pollen extract. Recombinant Lol p 1 was used to develop ImmunoCAP assays for analysis of 150 sera that were Radioallergosorbent test positive to L. perenne pollen. In 130 of them (87%) the assay detected a significant level of IgE antibodies to Lol p 1, reaching on average 37% of the level obtained with a test for IgE to the whole grass pollen extract. To map epitopes on Lol p 1, we produced three deletion mutants [des-(116-240)-Lol p 1, des-(1-88)-Lol p 1 and des-(133-189)-Lol p 1], which were efficiently expressed in bacteria. These all showed a strong reactivity with the specific rabbit IgG antibodies, but lacked most or all the allergenic properties of recombinant Lol p 1. A study of the antigenic structure of Lol p 1 was performed using the three deletion mutants and a set of 17-18-residue overlapping synthetic peptides covering the whole allergen sequence. The results indicate that human IgE and rabbit IgG antibodies bind to distinct regions of Lol p 1, and that at least some important IgE epitopes are mainly conformational. The findings suggest that recombinant allergens constitute useful reagents for further development of serological diagnosis of allergy, and that it should be possible to produce immunogenic fragments of allergenic proteins without allergenic properties.

  3. Screening for Compositae sensitization with pure allergens: implications of molecular structure, strength of reaction, and time of testing

    DEFF Research Database (Denmark)

    Paulsen, Evy; Andersen, Klaus Ejner


    The sesquiterpene lactone (SL) mix is the only commercial Compositae allergy screening agent that consists of pure allergens; its detection rate is lower than that of Compositae plant extracts.......The sesquiterpene lactone (SL) mix is the only commercial Compositae allergy screening agent that consists of pure allergens; its detection rate is lower than that of Compositae plant extracts....

  4. 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


    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

  5. Risk assessment of allergen metals in cosmetic products. (United States)

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


    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.

  6. Fish allergens at a glance: Variable allergenicity of parvalbumins, the major fish allergens


    Annette eKuehn; Ines eSwoboda; Karthik eArumugam; Christiane eHilger; François eHentges


    Fish is a common trigger of severe, food-allergic reactions. Only a limited number of proteins induce specific IgE-mediated immune reactions. The major fish allergens are the parvalbumins. They are members of the calcium-binding EF-hand protein family characterized by a conserved protein structure. They represent highly cross-reactive allergens for patients with specific IgE to conserved epitopes. These patients might experience clinical reactions with various fish species. On the other hand,...

  7. Fish Allergens at a Glance: Variable Allergenicity of Parvalbumins, the Major Fish Allergens


    Kuehn, Annette; Swoboda, Ines; Arumugam, Karthik; Hilger, Christiane; Hentges, François


    Fish is a common trigger of severe, food-allergic reactions. Only a limited number of proteins induce specific IgE-mediated immune reactions. The major fish allergens are the parvalbumins. They are members of the calcium-binding EF-hand protein family characterized by a conserved protein structure. They represent highly cross-reactive allergens for patients with specific IgE to conserved epitopes. These patients might experience clinical reactions with various fish species. On the other hand,...

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

    Directory of Open Access Journals (Sweden)

    Önell Annica


    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.

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

  10. Novel in silico technology in combination with microarrays: a state-of-the-art technology for allergy diagnosis and management? (United States)

    Melioli, Giovanni; Passalacqua, Giovanni; Canonica, Giorgio W


    'Allergen microarrays, in poly-sensitized allergic patients, represent a real value added in the accurate IgE profiling and in the identification of allergen(s) to administer for an effective allergen immunotherapy.' Allergen microarrays (AMA) were developed in the early 2000s to improve the diagnostic pathway of patients with allergic reactions. Nowadays, AMA are constituted by more than 100 different components (either purified or recombinant), representing genuine and cross-reacting molecules from plants and animals. The cost of the procedure had suggested its use as third-level diagnostics (following in vivo- and in vitro-specific IgE tests) in poly-sensitized patients. The complexity of the interpretation had inspired the development of in silico technologies to help clinicians in their work. Both machine learning techniques and expert systems are now available. In particular, an expert system that has been recently developed not only identifies positive and negative components but also lists dangerous components and classifies patients based on their potential responsiveness to allergen immunotherapy, on the basis of published algorithms. For these characteristics, AMA represents the state-of-the-art technology for allergy diagnosis in poly-sensitized patients.

  11. 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))


    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.

  12. Information provision for allergic consumers - where are we going with food allergen labelling?

    DEFF Research Database (Denmark)

    Mills, E.N.C.; Valovirta, E.; Madsen, Charlotte Bernhard


    As the current treatment for food allergy involves dietary exclusion of the problem food, information for food-allergic consumers provided on food labels about the nature of allergenic ingredients is important to the management of their condition. The members of an EU-funded networking project...... directive on food labelling, its relevance to food-allergic consumers and the problems that might arise if precautionary labelling becomes more widespread in response to concerns regarding inadvertent allergen contamination in foods. International efforts to define threshold levels of allergens able...... to trigger a reaction coupled with validated allergen detection methods are essential if the food industry is to implement effective hazard control procedures and address the problems of cross-contact allergens without devaluing the information provided to consumers on food labels....

  13. Detection of Eleven Pathogenic Bacterium Using DNA Microarray Combined With Multiplex PCR%多重PCR结合基因芯片技术检测11种致病菌方法的建立

    Institute of Scientific and Technical Information of China (English)

    贺晨; 孙鸿燕; 邵丽筠; 刘金华; 张春秀; 刘娅


    Objective To establish a rapid ,accurate detection method for 11 kinds of pathogenic bacteria using DNA microarray combined with multiplex PCR .Methods The special genes of these Bacterium including Shigella, Listeria monocytogenes ,Escherichi-a coli O157, Staphylococcus aureus , Bacillus cereus , Campylobacter jejuni, Proteusbacillus vulgaris , C . perfringens , Vibiro para-haemolyticus ,Salmonella typhi ,Salmonella enteritidis were as target genes for multiplex PCR respectively ,then primers and captured oligonucleotide probes were designed and synthesized .After multiplex PCR system and hybridization reaction were optimized ,the multr-plex PCR products were hybridizes with DNA microarray ,which contained specific probes of eleven pathogenic bacterium .Scanner was used to determinant the types of bacterium .Results The DNA microarray assay can detect 11 kinds of pathogenic bacterium specially .The sensitivity of the DNA may reach 2?0-3 ng .Conclusion To detect 11 kinds of pathogenic bacteria using DNA microarray combined with multiplex PCR is specific ,sensiu've ,practical.%目的 建立一种运用多重PCR方法结合基因芯片技术快速、准确检测11种常见致病菌的方法.方法 筛选志贺氏菌、肠炎沙门氏菌、伤寒沙门氏菌、大肠杆菌O157、副溶血性弧菌、普通变形杆菌、蜡样芽孢杆菌、金黄色葡萄球菌、单核细胞增生李斯特菌、产气荚膜梭菌、空肠弯曲菌的特异基因作为目的 基因.设计相应的引物及探针,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11种特异探针的基因芯片杂交.用扫描仪扫描,判定细菌种类.结果 该基因芯片可特异性地检测11种致病菌,具有良好的特异性,基因组DNA检测灵敏度可达2×10-3ng.结论 多重PCR结合基因芯片技术检测11种不同致病菌的方法特异性好,灵敏度高,具有较好的实用性.

  14. Maize microarray annotation database

    Directory of Open Access Journals (Sweden)

    Berger Dave K


    Full Text Available Abstract Background Microarray technology has matured over the past fifteen years into a cost-effective solution with established data analysis protocols for global gene expression profiling. The Agilent-016047 maize 44 K microarray was custom-designed from EST sequences, but only reporter sequences with EST accession numbers are publicly available. The following information is lacking: (a reporter - gene model match, (b number of reporters per gene model, (c potential for cross hybridization, (d sense/antisense orientation of reporters, (e position of reporter on B73 genome sequence (for eQTL studies, and (f functional annotations of genes represented by reporters. To address this, we developed a strategy to annotate the Agilent-016047 maize microarray, and built a publicly accessible annotation database. Description Genomic annotation of the 42,034 reporters on the Agilent-016047 maize microarray was based on BLASTN results of the 60-mer reporter sequences and their corresponding ESTs against the maize B73 RefGen v2 "Working Gene Set" (WGS predicted transcripts and the genome sequence. The agreement between the EST, WGS transcript and gDNA BLASTN results were used to assign the reporters into six genomic annotation groups. These annotation groups were: (i "annotation by sense gene model" (23,668 reporters, (ii "annotation by antisense gene model" (4,330; (iii "annotation by gDNA" without a WGS transcript hit (1,549; (iv "annotation by EST", in which case the EST from which the reporter was designed, but not the reporter itself, has a WGS transcript hit (3,390; (v "ambiguous annotation" (2,608; and (vi "inconclusive annotation" (6,489. Functional annotations of reporters were obtained by BLASTX and Blast2GO analysis of corresponding WGS transcripts against GenBank. The annotations are available in the Maize Microarray Annotation Database, as well as through a GBrowse annotation file that can be uploaded to

  15. 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


    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

  16. Recombinant allergens: what does the future hold? (United States)

    Valenta, Rudolf; Niespodziana, Katarzyna; Focke-Tejkl, Margit; Marth, Katharina; Huber, Hans; Neubauer, Angela; Niederberger, Verena


    This year we are celebrating not only the centenary of allergen-specific immunotherapy but also the 10-year anniversary of the first administration of recombinant allergen-based vaccines to allergic patients. By using recombinant DNA technology, defined and safe allergy vaccines can be produced that allow us to overcome many, if not all, of the problems associated with the use of natural allergen extracts, such as insufficient quality, allergenic activity, and poor immunogenicity. Here we provide an update of clinical studies with recombinant allergen-based vaccines, showing that some of these vaccines have undergone successful clinical evaluation up to phase III studies. Furthermore, we introduce a strategy for allergen-specific immunotherapy based on recombinant fusion proteins consisting of viral carrier proteins and allergen-derived peptides without allergenic activity, which holds the promise of being free of side effects and eventually being useful for prophylactic vaccination.

  17. Understanding allergic asthma from allergen inhalation tests (United States)

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


    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. PMID:17948142

  18. Associations between baseline allergens and polysensitization

    DEFF Research Database (Denmark)

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


    : 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...

  19. Intra and inter-laboratory reproducibility of a monoclonal antibody cocktail based ELISA for detection of allergen specific IgE in dogs: proficiency monitoring of macELISA in six laboratories. (United States)

    Lee, Kenneth W; Blankenship, Karen D; McCurry, Zachary M; McKinney, Brennan; Ruffner, Rick; Esch, Robert E; Tambone, Cecilia; Faas, Rebecca; Hermes, Darren; Brazis, Pilar; Drouet, Laurent


    The purpose of this study was to evaluate the reproducibility of results yielded using a monoclonal antibody based ELISA for detection of allergen specific IgE when run in six separate affiliated laboratories. On two separate occasions, duplicate samples of 15 different sera pools were independently evaluated by each laboratory in a single blinded fashion. The average intra-assay variance among reactive assay calibrators in all laboratories was 6.2% (range 2.6-18.2%), while the average intra-laboratory inter-assay variance was 12.1% (range 8.0-17.1%). The overall inter-assay inter-laboratory variance was consistent among laboratories and averaged 15.6% (range 15.1-16.6%). All laboratories yielded similar profiles and magnitudes of responses for replicate unknown samples; dose-response profiles observed in each of the laboratories were indistinguishable. Considering positive/negative results, inter-assay inter-laboratory concordance of results exceeded 95%. Correlation of OD values between and among all laboratories was strong (r>0.9, plaboratory, but between laboratories using the same monoclonal-based ELISA.

  20. [Evaluation of allergen-specific IgE antibodies by a newly developed mast allergy system]. (United States)

    Nakagawa, T; Iwasaki, E; Baba, M; Matsushita, T; Baba, S; Ito, K; Miyamoto, T


    MAST, which stand for multiple antigen simultaneous test, uses enzyme-linked anti-human IgE and chemiluminogenic substate to determine IgE. This system is characterized by simultaneous analysis of multiple allergen items, up to 35, together with total IgE determination. We evaluated usefulness of this MAST system using 191 serum samples obtained from patients with bronchial asthma, allergic rhinitis and/or atopic dermatitis. It was found that there were statistically significant correlations between IgE antibody quantification by MAST and RAST in 24 out of 35 allergen items, with correlation coefficients more than r = 0.60. These included Dermatophagoides farinae and pteronyssinus, Japanese cedar pollen, orchard grass, Alternaria, Candida as inhalant allergens; egg white, milk, soybeans, wheat and rice as food allergens. It was also evaluated how many allergen-specific IgE antibodies could be detected in one serum sample. More than six allergen-specific IgE antibodies were simultaneously detected in 33% of 191 cases, indicating the importance of multiple-allergen analysis. These results indicate the clinical usefulness of the MAST allergy system in detecting IgE antibodies in allergic subjects.

  1. Dermatophagoides farinae Allergens Diversity Identification by Proteomics*



    The most important indoor allergens for humans are house dust mites (HDM). Fourteen Dermatophagoides farinae allergens (Der f 1–3, 6, 7, 10, 11, 13–18, and 22) are reported although more than 30 allergens have been estimated in D. farinae. Seventeen allergens belonging to 12 different groups were identified by a procedure of proteomics combined with two-dimensional immunoblotting from D. farina extracts. Their sequences were determined by Edman degradation, mass spectrometry analysis, and cDN...

  2. Chemical and Biological Properties of Food Allergens

    NARCIS (Netherlands)

    Jedrychowski, L.; Wichers, H.J.


    This book provides epidemiological data on food allergens and information on the incidence of food allergies. It discusses the link between hypersensitivity and immune system health and covers methods used for assays on allergenic components, animal models for allergen analysis, and clinical methods

  3. Prominent feature selection of microarray data

    Institute of Scientific and Technical Information of China (English)

    Yihui Liu


    For wavelet transform, a set of orthogonal wavelet basis aims to detect the localized changing features contained in microarray data. In this research, we investigate the performance of the selected wavelet features based on wavelet detail coefficients at the second level and the third level. The genetic algorithm is performed to optimize wavelet detail coefficients to select the best discriminant features. Exper-iments are carried out on four microarray datasets to evaluate the performance of classification. Experimental results prove that wavelet features optimized from detail coefficients efficiently characterize the differences between normal tissues and cancer tissues.

  4. Diagnostic and analytical applications of protein microarrays

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Christensen, C.B.V.


    -linked immunosorbent assay, mass spectrometry or high-performance liquid chromatography-based assays. However, for protein and antibody arrays to be successfully introduced into diagnostics, the biochemistry of immunomicroarrays must be better characterized and simplified, they must be validated in a clinical setting...... years. A genome-scale protein microarray has been demonstrated for identifying protein-protein interactions as well as for rapid identification of protein binding to a particular drug. Furthermore, protein microarrays have been shown as an efficient tool in cancer profiling, detection of bacteria...

  5. Protein microarrays for systems biology

    Institute of Scientific and Technical Information of China (English)

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


    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.

  6. Microarray Applications in Cancer Research (United States)

    Kim, Il-Jin; Kang, Hio Chung


    DNA microarray technology permits simultaneous analysis of thousands of DNA sequences for genomic research and diagnostics applications. Microarray technology represents the most recent and exciting advance in the application of hybridization-based technology for biological sciences analysis. This review focuses on the classification (oligonucleotide vs. cDNA) and application (mutation-genotyping vs. gene expression) of microarrays. Oligonucleotide microarrays can be used both in mutation-genotyping and gene expression analysis, while cDNA microarrays can only be used in gene expression analysis. We review microarray mutation analysis, including examining the use of three oligonucleotide microarrays developed in our laboratory to determine mutations in RET, β-catenin and K-ras genes. We also discuss the use of the Affymetrix GeneChip in mutation analysis. We review microarray gene expression analysis, including the classifying of such studies into four categories: class comparison, class prediction, class discovery and identification of biomarkers. PMID:20368836

  7. Multi-allergen Quantitation and the Impact of Thermal Treatment in Industry-Processed Baked Goods by ELISA and Liquid Chromatography-Tandem Mass Spectrometry. (United States)

    Parker, Christine H; Khuda, Sefat E; Pereira, Marion; Ross, Mark M; Fu, Tong-Jen; Fan, Xuebin; Wu, Yan; Williams, Kristina M; DeVries, Jonathan; Pulvermacher, Brian; Bedford, Binaifer; Zhang, Xi; Jackson, Lauren S


    Undeclared food allergens account for 30-40% of food recalls in the United States. Compliance with ingredient labeling regulations and the implementation of effective manufacturing allergen control plans require the use of reliable methods for allergen detection and quantitation in complex food products. The objectives of this work were to (1) produce industry-processed model foods incurred with egg, milk, and peanut allergens, (2) compare analytical method performance for allergen quantitation in thermally processed bakery products, and (3) determine the effects of thermal treatment on allergen detection. Control and allergen-incurred cereal bars and muffins were formulated in a pilot-scale industry processing facility. Quantitation of egg, milk, and peanut in incurred baked goods was compared at various processing stages using commercial enzyme-linked immunosorbent assay (ELISA) kits and a novel multi-allergen liquid chromatography (LC)-tandem mass spectrometry (MS/MS) multiple-reaction monitoring (MRM) method. Thermal processing was determined to negatively affect the recovery and quantitation of egg, milk, and peanut to different extents depending on the allergen, matrix, and analytical test method. The Morinaga ELISA and LC-MS/MS quantitative methods reported the highest recovery across all monitored allergens, whereas the ELISA Systems, Neogen BioKits, Neogen Veratox, and R-Biopharm ELISA Kits underperformed in the determination of allergen content of industry-processed bakery products.

  8. 基于16S和23S rDNA基因芯片检测和鉴定七种临床常见病原菌%Detection and identification of seven clinical common pathogenic bacteria by oligonucleotide microarray

    Institute of Scientific and Technical Information of China (English)

    邢建明; 张甦; 张红河; 沈翠芬; 毕丹; 李刚; 姚丽惠


    Objective Using 16S rDNA and 23S rDNA genes as the target sequences to develop a system based on oligonucleotide microarray and to detect the seven clinical pathogenic bacteria, commonly seen. Methods Double polymerase chain reaction(PCR) was applied to amplify the segments of 16S rDNA and 23S rDNA genes of the target bacteria. An oligonucleotide microarray was constructed to simultaneously detect EHEC O157:H7, Vibrio parahaemolyticus , Saimonella sp., Vibrio cholerae ,Listeria monocytogenes, Campylobacter jejuni and Shigella sp. Specificity, sensitivity and reproducibility of the microarray during detection were checked. And then microarray was used to detect the microbes in stool specimens of 81 patients with diarrhea and vomiting. Results The double PCR method could simultaneously amplify the target sequences of 16S rDNA and 23S rDNA genes of the seven pathogens. The sensitivity of the developed oligonueleotide microarray could reach 103 cfu/ml but no positive results were presented for non-targeted bacteria. The coefficients of differentiation in one lot or among different lots of the microarray slices were 3.89%-5.81%. The positive detection rate of the stool specimens by oligonucleotide microarray was 39.5 % (32/81), with a coincidence of 96.3 % (78/81) for the patients and another coincidence of 96.8% (31/32) for bacterial genus or species identification, when comparing to the results by routine bacteriological examinations. Conclusion The established assay in this study based on oligonucleotide microarray to detect the seven pathogenic bacteria has many advantages such as convenient,rapid, accurate, stable and high flux, which is suitable for clinical specimen examination and epidemiological field investigation.%目的 以细菌16S rDNA和23S rDNA基因为靶序列建立可检测临床七种常见病原菌寡核苷酸芯片系统.方法 采用双重PCR扩增标本中靶细菌16S和23S rDNA基因片段.构建能同时检测肠出血性大肠埃希菌O157:H7

  9. Fish allergens at a glance: variable allergenicity of parvalbumins, the major fish allergens. (United States)

    Kuehn, Annette; Swoboda, Ines; Arumugam, Karthik; Hilger, Christiane; Hentges, François


    Fish is a common trigger of severe, food-allergic reactions. Only a limited number of proteins induce specific IgE-mediated immune reactions. The major fish allergens are the parvalbumins. They are members of the calcium-binding EF-hand protein family characterized by a conserved protein structure. They represent highly cross-reactive allergens for patients with specific IgE to conserved epitopes. These patients might experience clinical reactions with various fish species. On the other hand, some individuals have IgE antibodies directed against unique, species-specific parvalbumin epitopes, and these patients show clinical symptoms only with certain fish species. Furthermore, different parvalbumin isoforms and isoallergens are present in the same fish and might display variable allergenicity. This was shown for salmon homologs, where only a single parvalbumin (beta-1) isoform was identified as allergen in specific patients. In addition to the parvalbumins, several other fish proteins, enolases, aldolases, and fish gelatin, seem to be important allergens. New clinical and molecular insights advanced the knowledge and understanding of fish allergy in the last years. These findings were useful for the advancement of the IgE-based diagnosis and also for the management of fish allergies consisting of advice and treatment of fish-allergic patients.

  10. Fish allergens at a glance: Variable allergenicity of parvalbumins, the major fish allergens

    Directory of Open Access Journals (Sweden)

    Annette eKuehn


    Full Text Available Fish is a common trigger of severe, food-allergic reactions. Only a limited number of proteins induce specific IgE-mediated immune reactions. The major fish allergens are the parvalbumins. They are members of the calcium-binding EF-hand protein family characterized by a conserved protein structure. They represent highly cross-reactive allergens for patients with specific IgE to conserved epitopes. These patients might experience clinical reactions with various fish species. On the other hand, some individuals have IgE antibodies directed against unique, species-specific parvalbumin epitopes, and these patients show clinical symptoms only with certain fish species. Furthermore, different parvalbumin isoforms and isoallergens are present in the same fish and might display variable allergenicity. This was shown for salmon homologs, where only a single parvalbumin (beta-1 isoform was identified as allergen in specific patients. In addition to the parvalbumins, several other fish proteins, enolases, aldolases and fish gelatin, seem to be important allergens.New clinical and molecular insights advanced the knowledge and understanding of fish allergy in the last years. These findings will be useful for the advancement of the IgE-based diagnosis but also for the management of fish allergies consisting of advice and treatment of fish-allergic patients.

  11. Detection of influenza viruses/avian influenza viruses and identification of virulence using a microarray%流感/禽流感病毒及其致病力鉴别的基因芯片技术研究

    Institute of Scientific and Technical Information of China (English)

    贾菲; 高荣保; 王敏; 郭元吉; 温乐英; 张烨; 成艳辉; 舒跃龙; 刘宏生


    目的 建立流感/禽流感病毒及其致病力鉴别的基因芯片检测技术.方法 以血凝素(HA)、神经氨酸酶(NA)、核蛋白(NP)基冈作为靶片段,设计病毒检测和致病力特异性鉴别探针,建立基因芯片鉴别检测技术,采用单引物扩增法(SPA)处理样本核酸,分别对此芯片进行特异性、敏感性和符合率评价.结果 此芯片能够特异性的检测H1N1、H3N2、B型流感病毒及H5N1、H9N2禽流感病毒,敏感性分别为8HAU、16HAU、32HAU及8HAU、8HAU.致病力鉴别探针敏感性为32HAU.同RT-PCR方法比较,检测灵敏度为83.9%.结论 建立的常见流感病毒检测基因芯片特异性高、敏感性高、灵敏度高,更能够对致病力进行有效甄别,可作为临床诊断、传染病防控等方面的有益补充.%Objective To establish the DNA microarray to detect influenza viruses and avian influenza viruses,and identify their vindence. Methods Hemagglutinin(HA) ,neuramidinase(NA) and nuclooprotein(NP) genes were chosen simultaneously as targets for designing a microarray used for detection of viruses and identification virulence. The nucleic acid were amplified by single primer amplication (SPA). And then its specificity,seusitivity and reproducibility were evaluated. Results The microarray was able to specially detect H1N1 ,H3N2,B influenza viruses and H5N1,H9N2 avian influenza viruses. Their limits were 8HAU,16HAU,32HAU,and 8HAU,8HAU respectively .The limit for virulence was 32HAU. When samples were analyzed by both RT-PCR and microarray in parallel,the results agreed in 83.9% (47/56).Conclusion The microarray can detect and distinguish five tested viruses,and especially identify virulence. It not only supplies an assistant tool for clinical diagnosis and control of infectious disease,but also is valuable for controlling and preventing outbreak of avian influerza epidemic.

  12. Chemiluminescence microarrays in analytical chemistry: a critical review. (United States)

    Seidel, Michael; Niessner, Reinhard


    Multi-analyte immunoassays on microarrays and on multiplex DNA microarrays have been described for quantitative analysis of small organic molecules (e.g., antibiotics, drugs of abuse, small molecule toxins), proteins (e.g., antibodies or protein toxins), and microorganisms, viruses, and eukaryotic cells. In analytical chemistry, multi-analyte detection by use of analytical microarrays has become an innovative research topic because of the possibility of generating several sets of quantitative data for different analyte classes in a short time. Chemiluminescence (CL) microarrays are powerful tools for rapid multiplex analysis of complex matrices. A wide range of applications for CL microarrays is described in the literature dealing with analytical microarrays. The motivation for this review is to summarize the current state of CL-based analytical microarrays. Combining analysis of different compound classes on CL microarrays reduces analysis time, cost of reagents, and use of laboratory space. Applications are discussed, with examples from food safety, water safety, environmental monitoring, diagnostics, forensics, toxicology, and biosecurity. The potential and limitations of research on multiplex analysis by use of CL microarrays are discussed in this review.

  13. Fish allergy and fish allergens

    DEFF Research Database (Denmark)

    Kuehn, A; Hilger, Christiane; Ollert, Markus


    Fish is one of the main elicitors for food allergies. For a long time, the clinical picture of fish allergy was reduced to the following features. First, fish-allergic patients suffer from a high IgE cross-reactivity among fishes so that they have to avoid all species. Second, clinically relevant...... review gives an overview on the clinical characteristics of fish allergy and the molecular properties of relevant fish allergens. The advancement of the IgE-based diagnosis using a panel of well-defined fish allergens from different species is in the focus of the discussion. © 2016 Dustri-Verlag Dr. Karl...

  14. Comparative and Evolutionary Analysis of Grass Pollen Allergens Using Brachypodium distachyon as a Model System (United States)

    Sharma, Akanksha; Sharma, Niharika; Bhalla, Prem; Singh, Mohan


    Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc) for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their functional

  15. "Harshlighting" small blemishes on microarrays

    Directory of Open Access Journals (Sweden)

    Wittkowski Knut M


    Full Text Available Abstract Background Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs. Results We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes. Conclusion Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method provides investigators with a novel robust approach to improve the sensitivity of microarray analyses. By utilizing topological information to identify and mask blemishes prior to model based analyses, the method prevents artefacts from confounding the process of background correction, normalization, and summarization.

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

    Directory of Open Access Journals (Sweden)

    Velden Joanne


    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

  17. Review: DNA Microarray Technology and Drug Development

    Directory of Open Access Journals (Sweden)

    Sushma Drabu


    Full Text Available

    On the contrary to slow and non specific traditional drug discovery methods, DNA microarray technology could
    accelerate the identification of potential drugs for treating diseases like cancer, AIDS and provide fruitful results in
    the drug discovery. The technique provides efficient automation and maximum flexibility to the researchers and
    can test thousand compounds at a time. Scientists find DNA microarray useful in disease diagnosis, monitoring
    desired and adverse outcomes of therapeutic interventions, as well as, in the selection, assessment and quality control
    of the potential drugs. In the current scenario, where new pathogens are expected every year, DNA microarray
    promises as an efficient technology to detect new organisms in a short time. Classification of carcinomas at the
    molecular level and prediction of how various types of tumor respond to different therapeutic agents can be made
    possible with the use of microarray analysis. Also, microarray technique can prove instrumental in personalized
    medicines development by providing microarray data of a patient which could be used for identifying diseases,
    treatment specific to individual and trailing disease prognosis. Microarray analysis could be beneficial in the area
    of molecular medicines for analysis of genetic variations and functions of genes in normal individuals and diseased
    conditions. The technique can give satisfactory results in single nucleotide polymorphism (SNP analysis and
    pharmacogenomics studies. The challenges that arise with the technology are high degree of variability with data
    obtained, frequent up gradation of methods and machines and lack of trained manpower. Despite this, DNA microarray
    promises to be the next generation sequencer which could explain how organisms evolve and adapt looking
    at the whole

  18. Dermatophagoides farinae allergens diversity identification by proteomics. (United States)

    An, Su; Chen, Lingling; Long, Chengbo; Liu, Xiaoyu; Xu, Xuemei; Lu, Xingre; Rong, Mingqiang; Liu, Zhigang; Lai, Ren


    The most important indoor allergens for humans are house dust mites (HDM). Fourteen Dermatophagoides farinae allergens (Der f 1-3, 6, 7, 10, 11, 13-18, and 22) are reported although more than 30 allergens have been estimated in D. farinae. Seventeen allergens belonging to 12 different groups were identified by a procedure of proteomics combined with two-dimensional immunoblotting from D. farina extracts. Their sequences were determined by Edman degradation, mass spectrometry analysis, and cDNA cloning. Their allergenicities were assayed by enzyme-linked immunosorbent assay inhibition tests, immunoblots, basophil activation test, and skin prick tests. Eight of them are the first report as D. farinae allergens. The procedure of using a proteomic approach combined with a purely discovery approach using sera of patients with broad IgE reactivity profiles to mite allergens was an effective method to investigate a more complete repertoire of D. farinae allergens. The identification of eight new D. farinae allergens will be helpful for HDM allergy diagnosis and therapy, especially for patients without response for HDM major allergens. In addition, the current work significantly extendedthe repertoire of D. farinae allergens.

  19. 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


    The Allergen Bank was established to give dermatologists easy access to special test materials in order to make early diagnoses of special cases of allergic contact dermatitis. The Allergen Bank comprises a computer system to register several hundred contact allergens in appropriate patch test...... concentrations available at the allergy laboratory and the patch test results. At the request of dermatologists in practice for Allergen Bank may supply special contact allergens for aimed patch testing of contact dermatitis patients. The organization of the Allergen Bank and the procedure of its use...... are 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...

  20. Market analysis of food products for detection of allergenic walnut (Juglans regia) and pecan (Carya illinoinensis) by real-time PCR. (United States)

    López-Calleja, Inés María; de la Cruz, Silvia; González, Isabel; García, Teresa; Martín, Rosario


    Two real-time polymerase chain reaction (PCR)-based assays for detection of walnut (Juglans regia) and pecan (Carya illinoinensis) traces in a wide range of processed foods are described here. The method consists on a real-time PCR assay targeting the ITS1 region, using a nuclease (TaqMan) probe labeled with FAM and BBQ. The method was positive for walnut and pecan respectively, and negative for all other heterologous plants and animals tested. Using a series of model samples with defined raw walnut in wheat flour and heat-treated walnut in wheat flour with a range of concentrations of 0.1-100,000 mg kg(-1), a practical detection limit of 0.1 mg kg(-1) of walnut content was estimated. Identical binary mixtures were done for pecan, reaching the same limit of detection of 0.1 mg kg(-1). The assay was successfully trialed on a total of 232 commercial foodstuffs.

  1. [Soybean allergens and hypoallergenic germplasm enhancement]. (United States)

    Fang, Xu-Qian; Zhu, You-Lin; Qiu, Li-Juan


    Food allergy is a public sanitary problem which has received attention worldwide. It is becoming an increasingly interesting problem to decrease the concentration of allergens for improvement of the food security. Soybean allergens in seeds are composing of storage proteins, structure proteins, and disease-related proteins. Among them, Gly m Bd 28K, Gly m Bd 30K and Gly m Bd 60K are the major allergens located in 7S conglycinin fragments. By recognizing allergens' physicochemical property, hypersensitivity and gene structure, certain progresses had been made to reduce the concentration of allergens in soybean through food processing, traditional breeding and genetic engineering. The paper reviewed the sorts and characters of soybean allergens, the physicochemical property of the three immunodominant allergens and their gene structures. Progress in developing hypoallergenic cultivars was also discussed.

  2. New insights into ragweed pollen allergens. (United States)

    Bordas-Le Floch, Véronique; Groeme, Rachel; Chabre, Henri; Baron-Bodo, Véronique; Nony, Emmanuel; Mascarell, Laurent; Moingeon, Philippe


    Pollen allergens from short ragweed (Ambrosia artemisiifolia) cause severe respiratory allergies in North America and Europe. To date, ten short ragweed pollen allergens belonging to eight protein families, including the recently discovered novel major allergen Amb a 11, have been recorded in the International Union of Immunological Societies (IUIS) allergen database. With evidence that other components may further contribute to short ragweed pollen allergenicity, a better understanding of the allergen repertoire is a requisite for the design of proper diagnostic tools and efficient immunotherapies. This review provides an update on both known as well as novel candidate allergens from short ragweed pollen, identified through a comprehensive characterization of the ragweed pollen transcriptome and proteome.

  3. Undetected sex chromosome aneuploidy by chromosomal microarray. (United States)

    Markus-Bustani, Keren; Yaron, Yuval; Goldstein, Myriam; Orr-Urtreger, Avi; Ben-Shachar, Shay


    We report on a case of a female fetus found to be mosaic for Turner syndrome (45,X) and trisomy X (47,XXX). Chromosomal microarray analysis (CMA) failed to detect the aneuploidy because of a normal average dosage of the X chromosome. This case represents an unusual instance in which CMA may not detect chromosomal aberrations. Such a possibility should be taken into consideration in similar cases where CMA is used in a clinical setting.

  4. 基因芯片方法检测6种动物源性人兽共患病病原%Detection of six animal original zoonosis pathogens by microarray

    Institute of Scientific and Technical Information of China (English)

    王振全; 罗宝正; 薄清如; 徐海聂; 沙才华; 廖秀云; 陈伟生


    To establish a microarray for detections of avian influenza virus serotype H5, rabies virus, Streptococcus suis type 2, Bacillus anthracis, Salmonella and Escherichia coli 0157, the specific primers and probes were designed and synthesized based on the gene sequences of the 6 animal organized pathogens in GenBank. The microarray chip was prepared by spotting probes on matrix, and then hybridized with the PCR products. The results showed that no nonspecific reaction existed in specificity test and the limited detections was 1.38 × 10-5 pg/μL to 151 pg/μL PCR products from the pathogens. A total of 930 clinical samples were tested by the microarray, the results showed that the PCR assay was in accordance completely with real-time PCR detection.%为了建立可同时检测H5亚型禽流感病毒、狂犬病病毒、猪链球菌2型、炭疽芽孢杆菌、沙门氏菌、大肠杆菌O157的基因芯片检测方法,本实验根据GenBank中上述6种病原的基因序列,设计并合成了特异性的引物和探针.采用点样法制备杂交芯片,将上述病原扩增产物混合后与芯片杂交.杂交结果显示,针对本试验中6种人兽共患传染病所设计的寡核苷酸探针可特异性识别靶基因,与其他常见病原体之间没有交叉反应.检测的灵敏度在1.38×10-5pg/μL~151 pg/μL之间.将建立的基因芯片检测方法对临床样品进行检测,结果与荧光PCR方法一致.

  5. Allergen immunotherapy for allergic rhinoconjunctivitis

    DEFF Research Database (Denmark)

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


    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 AIT...

  6. Microarrays for rapid identification of plant viruses. (United States)

    Boonham, Neil; Tomlinson, Jenny; Mumford, Rick


    Many factors affect the development and application of diagnostic techniques. Plant viruses are an inherently diverse group that, unlike cellular pathogens, possess no nucleotide sequence type (e.g., ribosomal RNA sequences) in common. Detection of plant viruses is becoming more challenging as globalization of trade, particularly in ornamentals, and the potential effects of climate change enhance the movement of viruses and their vectors, transforming the diagnostic landscape. Techniques for assessing seed, other propagation materials and field samples for the presence of specific viruses include biological indexing, electron microscopy, antibody-based detection, including enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), and microarray detection. Of these, microarray detection provides the greatest capability for parallel yet specific testing, and can be used to detect individual, or combinations of viruses and, using current approaches, to do so with a sensitivity comparable to ELISA. Methods based on PCR provide the greatest sensitivity among the listed techniques but are limited in parallel detection capability even in "multiplexed" applications. Various aspects of microarray technology, including probe development, array fabrication, assay target preparation, hybridization, washing, scanning, and interpretation are presented and discussed, for both current and developing technology.

  7. Bioinformatic analysis for allergenicity assessment of Bacillus thuringiensis Cry proteins expressed in insect-resistant food crops. (United States)

    Randhawa, Gurinder Jit; Singh, Monika; Grover, Monendra


    The novel proteins introduced into the genetically modified (GM) crops need to be evaluated for the potential allergenicity before their introduction into the food chain to address the safety concerns of consumers. At present, there is no single definitive test that can be relied upon to predict allergic response in humans to a new protein; hence a composite approach to allergic response prediction is described in this study. The present study reports on the evaluation of the Cry proteins, encoded by cry1Ac, cry1Ab, cry2Ab, cry1Ca, cry1Fa/cry1Ca hybrid, being expressed in Bt food crops that are under field trials in India, for potential allergenic cross-reactivity using bioinformatics search tools. The sequence identity of amino acids was analyzed using FASTA3 of AllergenOnline version 10.0 and BLASTX of NCBI Entrez to identify any potential sequence matches to allergen proteins. As a step further in the detection of allergens, an independent database of domains in the allergens available in the AllergenOnline database was also developed. The results indicated no significant alignment and similarity of Cry proteins at domain level with any of the known allergens revealing that there is no potential risk of allergenic cross-reactivity.

  8. Allergen detection result analysis of 1062 patients with chronic urticaria in Anhui province%安徽省1062例慢性荨麻疹过敏原检测结果分析

    Institute of Scientific and Technical Information of China (English)

    周海林; 胡白; 蒋法兴; 廖理超; 姚秀华


    目的 了解安徽省慢性荨麻疹患者的食入性与吸入性过敏原情况,为该病的预防和治疗提供依据.方法 采用酶联免疫分析法,对1062例慢性荨麻疹患者进行吸入性过敏原和食入性过敏原特异性lgE抗体检测.结果 1062例慢性荨麻疹患者过敏原阳性检出率为48.78%(518例),吸入组过敏原的阳性率明显高于食入组,其中粉螨、尘螨 (34.56%)、屋尘(10.73%)为主要过敏原.结论 安徽省慢性荨麻疹患者吸入性过敏原的检出率明显高于食入性,过敏原以尘螨、粉螨和屋尘多见,找出致病因素对临床治疗慢性荨麻疹有较好的指导意义.%Objective To investigate Anhui province patients with chronic urticaria in ingestion and inhalation allergen conditions respectively, in order to provide evidence for prevention and treatment. Methods Enzyme immunoassay method was used to test 1 062 patients with chronic urticaria in allergen-specific lgE antibodies. Results The testing results of 1 062 cases showed that the total of the positive reaction rates reached 48. 78% (518 positive cases). Inhalation allergen positive rate was significantly higher than that of ingestion allergen group. The positive reaction rates of the mites and the house dust reached 34. 56% and 10. 37% respectively, which were the first and the second in the allergens tested. Conclusion Both ingestion allergens and inhalation allergens are contributing causes to chronic urticaria. The mites and the house dust were perhaps the ordinary pathogenic allergens for the patients with chronic urticaria in Anhui province. Identifying the causative factors is of instructive significance for the clinical treatment of chronic urticaria.

  9. Validation and comparison of two commercial ELISA kits and three in-house developed real-time PCR assays for the detection of potentially allergenic mustard in food. (United States)

    Palle-Reisch, Monika; Hochegger, Rupert; Štumr, Stepan; Korycanova, Kveta; Cichna-Markl, Margit


    The study compares the applicability of two commercial mustard ELISA kits (Mustard ELISA Kit-specific and Mustard ELISA Kit-total) and three in-house developed real-time PCR assays (singleplex assay for white mustard, singleplex assay for black/brown mustard and duplex assay for the detection of white, black and brown mustard). Analyses of raw and brewed model sausages containing white and black/brown mustard in the range from 1 to 50 ppm indicate that both ELISAs and the three real-time PCR assays allow the detection of traces of mustard in raw and in brewed sausages. The ELISAs were found to be more sensitive than the real-time PCR assays. When the ELISAs and real-time PCR assays were applied to the analysis of 15 commercial foodstuffs differing in their labelling concerning mustard, in one sample mustard was detected with both ELISAs and the three real-time PCR assays although mustard was not indicated on the food ingredient list.

  10. Hybridization and Selective Release of DNA Microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J; Benett, W; Mukerjee, E; Dzenitis, J; Wheeler, E K


    DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy


    Institute of Scientific and Technical Information of China (English)

    林芳辉; 梁锋; 韩景辉; 符生苗


    [Objective] Through the detection on serum total IgE content and allergens specificity IgE 132 of 132 cases of cough variant asthma and other 56 cases of chronic cough {control group) , to investigate the application value of serum total IgE content ami specific allergen in clinical diagnosis, treatment and prevention of cough variant asthma. [Methods] Used I-niled Slates DX1800 beckman chemiluminescence to detect total IgE content, used Gentian ormond imprinting method to detect 20 kinds of allergens specificity IgE. [Resiltts] The positive rale of CVA total IgE was 87.1%. Specific IgE of 78.8%. The total IgE in the control group was 8.9% , positive rate of specificity IgE of 7.1%. CVA inhaled allergens were highest, der-malophagoides pUfronyssinus/dermalopbagoides farinue, mould combination, house dust were 55.3%, 43.2%, 38.95%; higher food allergen was the sea (water) products, among them, shrimp was the highest, about 17.4%. [Conclusion] CVA is the reactive disease that IgE mediated, allergen is the main pathogenic factor. Detection on serum total IgE and allergens specificity IgE has effect in helping diagnosing suspected cough variant asthma disease, l>ut also has significance in the treatment and pre-venlion.%[目的]通过对132例咳嗽变异性哮喘患儿和56例其他慢性咳嗽疾病患儿(对照组)的血清总IgE含量及过敏原特异性IgE的检测,探讨血清总IgE含量及过敏原特异性IgE检测在临床诊治及预防咳嗽变异性哮喘的应用价值.[方法]用美国贝克曼化学发光DX1800检测总IgE含量,使用德国欧蒙印迹法检测20种过敏原特异性IgE.[结果]CVA总IgE阳性率87.1%,特异性IgE阳性率78.8%.对照组总IgE阳性率8.9%,特异性IgE阳性率7.1%.CVA吸入性过敏原阳性率最高,主要是屋尘螨/粉尘螨、霉菌组合、屋尘,分别是55.3%、43.2%、38.95%;食入性过敏原阳性率较高的主要是海(水)产品,其中以虾最高,为17A%.[结论]说明CVA是特异性Ig

  12. The identification of allergen proteins in sugar beet (Beta vulgaris pollen causing occupational allergy in greenhouses

    Directory of Open Access Journals (Sweden)

    Blomqvist Anna


    Full Text Available Abstract Background During production of sugar beet (Beta vulgaris seeds in greenhouses, workers frequently develop allergic symptoms. The aim of this study was to identify and characterize possible allergens in sugar beet pollen. Methods Sera from individuals at a local sugar beet seed producing company, having positive SPT and specific IgE to sugar beet pollen extract, were used for immunoblotting. Proteins in sugar beet pollen extracts were separated by 1- and 2-dimensional electrophoresis, and IgE-reactive proteins analyzed by liquid chromatography tandem mass spectrometry. Results A 14 kDa protein was identified as an allergen, since IgE-binding was inhibited by the well-characterized allergen Che a 2, profilin, from the related species Chenopodium album. The presence of 17 kDa and 14 kDa protein homologues to both the allergens Che a 1 and Che a 2 were detected in an extract from sugar beet pollen, and partial amino acid sequences were determined, using inclusion lists for tandem mass spectrometry based on homologous sequences. Conclusion Two occupational allergens were identified in sugar beet pollen showing sequence similarity with Chenopodium allergens. Sequence data were obtained by mass spectrometry (70 and 25%, respectively for Beta v 1 and Beta v 2, and can be used for cloning and recombinant expression of the allergens. As for treatment of Chenopodium pollinosis, immunotherapy with sugar beet pollen extracts may be feasible.

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

    Institute of Scientific and Technical Information of China (English)



    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.

  14. 食品中鲍鱼过敏源基因成分的检测%Detection of allergen gene of abalone in food

    Institute of Scientific and Technical Information of China (English)

    徐杨; 孙瑶; 杜影; 战晓微; 郑秋月


    Objective To establish a real-time fluorescent PCR method for detection of abalone gene anaphylactogen in food. Methods Genomic DNA of abalone muscle tissue was extracted by proteinase K digestion method. Specific primers and the probe were designed based on 16S rRNA genes of abalone. After PCR reaction system and conditions were optimized, the rapid real-time PCR detection method of abalone anaphylactogen was developed. The seafood including squid, sea cucumber and so on, was tested for specificity. The samples that contained abalone-derived components of 100%,10%,1%,0.1%,0.01%,and 0.001%respectively were made by blend method for sensitivity test. Results It was of high specificity by testing non abalone products, and the sensitivity test showed that the lowest amount of detecting was 0.01%. Conclusion The detection method of allergic abalone gene anaphylactogen with high specificity and sensitivity was established in this research.%目的:本文建立食品中鲍鱼过敏源基因成分实时荧光PCR检测方法。方法采用蛋白酶K消化法提取鲍鱼肌肉组织中基因组DNA,针对鲍鱼管家基因16S rRNA基因设计特异性引物和探针,确定实时荧光PCR反应体系和反应条件,建立了鲍鱼过敏源基因成分实时荧光 PCR 快速检测方法。选用鱿鱼、海参等海产品进行特异性试验;采用添加方法制备灵敏度试验样品,分别制备了鲍鱼过敏源基因成分含量分别为100%、10%、1%、0.1%、0.01%、0.001%的样品。结果对非鲍鱼类食品进行检测,结果显示出良好的特异性;灵敏度试验表明,本文建立方法的最低检测下限为0.01%。结论本文建立了特异性好,灵敏度高的鲍鱼过敏源基因成分检测方法。

  15. Impact of thermal processing on legume allergens. (United States)

    Verma, Alok Kumar; Kumar, Sandeep; Das, Mukul; Dwivedi, Premendra D


    Food induced allergic manifestations are reported from several parts of the world. Food proteins exert their allergenic potential by absorption through the gastrointestinal tract and can even induce life threatening anaphylaxis reactions. Among all food allergens, legume allergens play an important role in induction of allergy because legumes are a major source of protein for vegetarians. Most of the legumes are cooked either by boiling, roasting or frying before consumption, which can be considered a form of thermal treatment. Thermal processing may also include autoclaving, microwave heating, blanching, pasteurization, canning, or steaming. Thermal processing of legumes may reduce, eliminate or enhance the allergenic potential of a respective legume. In most of the cases, minimization of allergenic potential on thermal treatment has generally been reported. Thus, thermal processing can be considered an important tool by indirectly prevent allergenicity in susceptible individuals, thereby reducing treatment costs and reducing industry/office/school absence in case of working population/school going children. The present review attempts to explore various possibilities of reducing or eliminating allergenicity of leguminous food using different methods of thermal processing. Further, this review summarizes different methods of food processing, major legumes and their predominant allergenic proteins, thermal treatment and its relation with antigenicity, effect of thermal processing on legume allergens; also suggests a path that may be taken for future research to reduce the allergenicity using conventional/nonconventional methods.

  16. Case of 7p22.1 Microduplication Detected by Whole Genome Microarray (REVEAL in Workup of Child Diagnosed with Autism

    Directory of Open Access Journals (Sweden)

    Veronica Goitia


    Full Text Available Introduction. More than 60 cases of 7p22 duplications and deletions have been reported with over 16 of them occurring without concomitant chromosomal abnormalities. Patient and Methods. We report a 29-month-old male diagnosed with autism. Whole genome chromosome SNP microarray (REVEAL demonstrated a 1.3 Mb interstitial duplication of 7p22.1 ->p22.1 arr 7p22.1 (5,436,367–6,762,394, the second smallest interstitial 7p duplication reported to date. This interval included 14 OMIM annotated genes (FBXL18, ACTB, FSCN1, RNF216, OCM, EIF2AK1, AIMP2, PMS2, CYTH3, RAC1, DAGLB, KDELR2, GRID2IP, and ZNF12. Results. Our patient presented features similar to previously reported cases with 7p22 duplication, including brachycephaly, prominent ears, cryptorchidism, speech delay, poor eye contact, and outburst of aggressive behavior with autism-like features. Among the genes located in the duplicated segment, ACTB gene has been proposed as a candidate gene for the alteration of craniofacial development. Overexpression of RNF216L has been linked to autism. FSCN1 may play a role in neurodevelopmental disease. Conclusion. Characterization of a possible 7p22.1 Duplication Syndrome has yet to be made. Recognition of the clinical spectrum in patients with a smaller duplication of 7p should prove valuable for determining the minimal critical region, helping delineate a better prediction of outcome and genetic counseling

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

    Yuan, Yiyang; Krogh, Paul Henning; Bai, Xue; Roelofs, Dick; Chen, Fajun; Zhu-Salzman, Keyan; Liang, Yuyong; Sun, Yucheng; Ge, Feng


    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.


    Institute of Scientific and Technical Information of China (English)

    WANG Xin-yun; LIU Ting; LI Yan; ZHAO Feng-yun; SUN Cui-yun; WANG Ai-xiang


    Objective: The aim of this study was to investigate the MRP-1/CD9mRNA expression in lung cancer and normal lung tissues and the relationship between its expression and pathologic grades, clinical stages, metastasis and prognosis.Methods: To observe MRP-1/C9mRNA expression, tissue microarray (TMA) containing 54 lung cancers and 10 normal lung tissues was prepared and Fluorescence in situ hybridization was used. Results: The positive rate of MRP-1/CD9 expression was 48.1% in lung cancer, lower than that of normal lung tissues. The statistical difference was significant (P<0.05). Its protein expression had no relationship with the patients' ages, sex and the macroscopic type of tumor, but had relationships with the histological type, clinical stage, differentiated degree and metastasis. The expression in non-small cell lung cancer (NSCLC) was higher than that in small cell lung cancer (SCLC); in well-moderately differentiated group was higher than that in poorly differentiated group; Earlier period group (Ⅰ+Ⅱ) was higher than in later period group (Ⅲ+Ⅳ); and in group without lymphoid metastasis was higher than in patients with lymphoid metastasis. Conclusion: The progression of the lung cancer maybe related with the descended MRP-1/Cd9 expression, which may be useful in evaluating the prognosis of cancer patients.

  19. 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.


    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

  20. The involvement of thaumatin-like proteins in plant food cross-reactivity: a multicenter study using a specific protein microarray.

    Directory of Open Access Journals (Sweden)

    Arantxa Palacín

    Full Text Available Cross-reactivity of plant foods is an important phenomenon in allergy, with geographical variations with respect to the number and prevalence of the allergens involved in this process, whose complexity requires detailed studies. We have addressed the role of thaumatin-like proteins (TLPs in cross-reactivity between fruit and pollen allergies. A representative panel of 16 purified TLPs was printed onto an allergen microarray. The proteins selected belonged to the sources most frequently associated with peach allergy in representative regions of Spain. Sera from two groups of well characterized patients, one with allergy to Rosaceae fruit (FAG and another against pollens but tolerant to food-plant allergens (PAG, were obtained from seven geographical areas with different environmental pollen profiles. Cross-reactivity between members of this family was demonstrated by inhibition assays. Only 6 out of 16 purified TLPs showed noticeable allergenic activity in the studied populations. Pru p 2.0201, the peach TLP (41%, chestnut TLP (24% and plane pollen TLP (22% proved to be allergens of probable relevance to fruit allergy, being mainly associated with pollen sensitization, and strongly linked to specific geographical areas such as Barcelona, Bilbao, the Canary Islands and Madrid. The patients exhibited >50% positive response to Pru p 2.0201 and to chestnut TLP in these specific areas. Therefore, their recognition patterns were associated with the geographical area, suggesting a role for pollen in the sensitization of these allergens. Finally, the co-sensitizations of patients considering pairs of TLP allergens were analyzed by using the co-sensitization graph associated with an allergen microarray immunoassay. Our data indicate that TLPs are significant allergens in plant food allergy and should be considered when diagnosing and treating pollen-food allergy.

  1. The Involvement of Thaumatin-Like Proteins in Plant Food Cross-Reactivity: A Multicenter Study Using a Specific Protein Microarray (United States)

    Palacín, Arantxa; Rivas, Luis A.; Gómez-Casado, Cristina; Aguirre, Jacobo; Tordesillas, Leticia; Bartra, Joan; Blanco, Carlos; Carrillo, Teresa; Cuesta-Herranz, Javier; Bonny, José A. Cumplido; Flores, Enrique; García-Alvarez-Eire, Mar G.; García-Nuñez, Ignacio; Fernández, Francisco J.; Gamboa, Pedro; Muñoz, Rosa; Sánchez-Monge, Rosa; Torres, Maria; Losada, Susana Varela; Villalba, Mayte; Vega, Francisco; Parro, Victor; Blanca, Miguel; Salcedo, Gabriel; Díaz-Perales, Araceli


    Cross-reactivity of plant foods is an important phenomenon in allergy, with geographical variations with respect to the number and prevalence of the allergens involved in this process, whose complexity requires detailed studies. We have addressed the role of thaumatin-like proteins (TLPs) in cross-reactivity between fruit and pollen allergies. A representative panel of 16 purified TLPs was printed onto an allergen microarray. The proteins selected belonged to the sources most frequently associated with peach allergy in representative regions of Spain. Sera from two groups of well characterized patients, one with allergy to Rosaceae fruit (FAG) and another against pollens but tolerant to food-plant allergens (PAG), were obtained from seven geographical areas with different environmental pollen profiles. Cross-reactivity between members of this family was demonstrated by inhibition assays. Only 6 out of 16 purified TLPs showed noticeable allergenic activity in the studied populations. Pru p 2.0201, the peach TLP (41%), chestnut TLP (24%) and plane pollen TLP (22%) proved to be allergens of probable relevance to fruit allergy, being mainly associated with pollen sensitization, and strongly linked to specific geographical areas such as Barcelona, Bilbao, the Canary Islands and Madrid. The patients exhibited >50% positive response to Pru p 2.0201 and to chestnut TLP in these specific areas. Therefore, their recognition patterns were associated with the geographical area, suggesting a role for pollen in the sensitization of these allergens. Finally, the co-sensitizations of patients considering pairs of TLP allergens were analyzed by using the co-sensitization graph associated with an allergen microarray immunoassay. Our data indicate that TLPs are significant allergens in plant food allergy and should be considered when diagnosing and treating pollen-food allergy. PMID:22970164

  2. Cat (Fel d 1) and dog (Can f 1) allergen levels in cars, dwellings and schools. (United States)

    Niesler, A; Ścigała, G; Łudzeń-Izbińska, B

    Pets are an important source of indoor allergens. The aim of the study was to compare cat and dog allergen levels in cars, schools and homes. The study was carried out in 17 cars, 14 classrooms and 19 dwellings located in the highly industrialized and urbanized region of Poland. Dust and air samples were analyzed for Fel d 1 and Can f 1 using a double monoclonal ELISA assay. The highest amounts of cat and dog allergens (Fel d 1: 1169 μg/g; Can f 1: 277 μg/g) were found in dwellings with pets. Allergen concentrations were correlated with the number of animals kept at home. Although concentrations on automobile seats were lower, Fel d 1 levels exceeded 8 μg/g in 23.5 % of cars and high levels of Can f 1 (>10 μg/g) were found in 17.6 % of cars. The study revealed that cars of pet owners may be reservoirs of cat and dog allergens even when animals are not transported in them. In schools, concentrations of pet allergens did not reach high levels, but the moderate levels of Fel d 1 (≥1-8 μg/g) and Can f 1 (≥2-10 μg/g) were detected in 42.9 and 7.1 % of the investigated classrooms. Concentrations of cat and dog allergen in schools were higher than in homes without pets. While airborne Fel d 1 and Can f 1 levels were found low, residential allergen concentrations in settled dust and air were correlated. The study results suggest that classrooms and cars of pet owners may be important sites of exposure to cat and dog allergens, though the highest concentrations of Fel d 1 and Can f 1 are found in homes of pet owners.

  3. Allergenicity and allergens of amphipods found in nori (dried laver). (United States)

    Motoyama, Kanna; Hamada, Yuki; Nagashima, Yuji; Shiomi, Kazuo


    Gammaridean and caprellid amphipods, crustaceans of the order Amphipoda, inhabit laver culture platforms and, hence, are occasionally found in nori (dried laver) sheets. Amphipods mixed in nori may cause allergic reactions in sensitized patients, as is the case with other crustaceans, such as shrimp and crab, members of the order Decapoda. In this study, dried samples of amphipods (unidentified) found in nori and fresh samples of gammaridean amphipod (Gammarus sp., not accurately identified) and caprellid amphipod (Caprella equilibra) were examined for allergenicity and allergens using two species of decapods (black tiger prawn and spiny lobster) as references. When analyzed by ELISA, sera from crustacean-allergic patients reacted to extracts from amphipod samples, although less potently than to the extracts from decapods. In IgE-immunoblotting, a 37-kDa protein was found to be the major allergen in amphipods. Based on the molecular mass and the cross-reactivity with decapod tropomyosin evidenced by inhibition ELISA and inhibition immunoblotting, the 37-kDa protein was identified as amphipod tropomyosin.

  4. Food allergens: molecular and immunological aspects, allergen databases and cross-reactivity. (United States)

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


    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.

  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


    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. Sensitising capacity of peptides from food allergens

    DEFF Research Database (Denmark)

    Bøgh, Katrine Lindholm

    to be a general characteristic of 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 no proven allergenicity, concluding that a correlation between stability to digestion and allergenic......, MALDI-TOF mass spectrometry, amino acid analysis and GPC. To study the sensitising capacity groups of BN rats were immunised with the intact allergen or digestion products hereof by i.p. immunisation and specific antibody responses were examined by ELISAs, RBL-assay or avidity measurements. Comparison...... of aggregates is suggested by the epitope mapping study, where survival of conformational epitopes is demonstrated. This together with the findings, that fractionation of digestion products leads to a loss of the sensitising potential, reveals that the allergenicity had to be more than simply a result...

  7. Novel liquid chromatography-mass spectrometry method for sensitive determination of the mustard allergen Sin a 1 in food. (United States)

    Posada-Ayala, Maria; Alvarez-Llamas, Gloria; Maroto, Aroa S; Maes, Xavier; Muñoz-Garcia, Esther; Villalba, Mayte; Rodríguez, Rosalía; Perez-Gordo, Marina; Vivanco, Fernando; Pastor-Vargas, Carlos; Cuesta-Herranz, Javier


    Mustard is a condiment added to a variety of foodstuffs and a frequent cause of food allergy. A new strategy for the detection of mustard allergen in food products is presented. The methodology is based on liquid chromatography analysis coupled to mass spectrometry. Mustard allergen Sin a 1 was purified from yellow mustard seeds. Sin a 1 was detected with a total of five peptides showing a linear response (lowest LOD was 5ng). Sin a 1 was detected in mustard sauces and salty biscuit (19±3mg/kg) where mustard content is not specified. Sin a 1, used as an internal standard, allowed quantification of this mustard allergen in foods. A novel LC/MS/MS SRM-based method has been developed to detect and quantify the presence of mustard. This method could help to detect mustard allergen Sin a 1 in processed foods and protect mustard-allergic consumers.

  8. Characterization of Allergen Exposure in Homes (United States)


    dust mixture.6 Dust mite allergens have been associated causatively with asthma, atopic dermatitis , and rhini- tis. 7 Studies from several countries...Asthma: A Controlled Trial. The Lancet 1976; ***:333-335. 10. Tuft L. Importance of Inhalant Allergens in Atopic Dermatitis . The Journal of Investigative...Monoclonal Antibodies to the Major Feline Allergen Fel d 1. 1I. Single Step Affinity Purification of Fel d 1, N-Terminal Sequence Analysis, and Development of

  9. Legumin allergens from peanuts and soybeans: Effects of denaturation and aggregation on allergenicity

    NARCIS (Netherlands)

    Boxtel, E.L. van; Broek, L.A.M. van den; Koppelman, S.J.; Gruppen, H.


    Legumin proteins Ara h 3 from peanuts and glycinin from soybeans are increasingly described as important allergens. The stability of an allergen's IgE binding capacity towards heating and digestion is considered an important characteristic for food allergens. We investigated the effects of heating a

  10. Legumin allergens from peanuts and soybeans : Effects of denaturation and aggregation on allergenicity

    NARCIS (Netherlands)

    Boxtel, van E.L.; Broek, van den L.A.M.; Koppelman, S.J.; Gruppen, H.


    Legumin proteins Ara h 3 from peanuts and glycinin from soybeans are increasingly described as important allergens. The stability of an allergen's IgE binding capacity towards heating and digestion is considered an important characteristic for food allergens. We investigated the effects of heating a

  11. Peanut Allergens Attached With p-Aminobenzamidine Are More Resistant to Digestion than Native Allergens (United States)

    Undigested foods are excreted rather than absorbed and therefore, peanut allergens, if undigested, may not cause an allergic reaction in peanut-allergic individuals. Our objective was to make peanut allergens more resistant to digestion by preparing allergen conjugates and demonstrating that the con...

  12. Effective Allergen Management : Precautionary (may contain) allergen labeling; when to apply?

    NARCIS (Netherlands)

    Zandvoort. M.M.J. van


    When do you label food products as having been possibly cross contaminated by allergens? TNO can help you to develop a quantitative risk management guidance for food allergens, based on a unique method that quantifies the risk of food allergen traces in products and validated data on thresholds. Thi

  13. Immobilization Techniques for Microarray: Challenges and Applications

    Directory of Open Access Journals (Sweden)

    Satish Balasaheb Nimse


    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.

  14. Indoor allergens: identification and quantification

    Energy Technology Data Exchange (ETDEWEB)

    Reed, C.E.; Swanson, M.C.


    A large number of allergens occur in the air of the home and many work sites. Almost any organic dust or volatile chemical reactive with proteins can cause allergic respiratory disease: allergic rhinitis, asthma, and hypersensitivity pneumonitis (extrinsic allergic alveolitis). If the exposure continues several years after the disease begins there may be permanent disability, so recognition and control of exposure are important. Techniques now exist to sample the particulate antigens suspended in the air and assay them by sensitive immunochemical methods.

  15. Mesoscale atmospheric transport of ragweed pollen allergens from infected to uninfected areas (United States)

    Grewling, Ł.; Bogawski, P.; Jenerowicz, D.; Czarnecka-Operacz, M.; Šikoparija, B.; Skjøth, C. A.; Smith, M.


    Allergenic ragweed ( Ambrosia spp.) pollen grains, after being released from anthers, can be dispersed by air masses far from their source. However, the action of air temperature, humidity and solar radiation on pollen grains in the atmosphere could impact on the ability of long distance transported (LDT) pollen to maintain allergenic potency. Here, we report that the major allergen of Ambrosia artemisiifolia pollen (Amb a 1) collected in ambient air during episodes of LDT still have immunoreactive properties. The amount of Amb a 1 found in LDT ragweed pollen grains was not constant and varied between episodes. In addition to allergens in pollen sized particles, we detected reactive Amb a 1 in subpollen sized respirable particles. These findings suggest that ragweed pollen grains have the potential to cause allergic reactions, not only in the heavily infested areas but, due to LDT episodes, also in the regions unaffected by ragweed populations.

  16. Transcriptome-Based Examination of Putative Pollen Allergens of Rice(Oryza sativa ssp.japonica)

    Institute of Scientific and Technical Information of China (English)

    Scott D.Russell; Prem L Bhalla; Mohan B.Singh


    Pollen allergens are among the most abundantly transcribed and translated products in the Iife history of plants,and particularly grasses.To identify different pollen allergens in rice,putative allergens were identified in the rice genome and their expression characterized using the Affymetrix 57K rice GeneChip microarray.Among the most abundant pollen-specific candidate transcripts were Ory s 1 beta-expansin.Ory s 2,Ory s 7 EFhand,Ory s 11,Ory s 12 profilin A,Ory s 23,glycosyl hydrolase family 28(polygalacturonase).and FAD binding proteins.Highly expressed pollen proteins are frequently present in multiple copy numbers,sometimes with mirror images Iocated on nearby regions of the opposite DNA strand.Many of these are intronless and inserted as copies that retain nearly exact copies of their regulatory elements.Ory s 23 reflects low variability and high copy number,suggesting recent gene amplification.Some copies contain pseudogenes,which may reflect their origin through activity of retrotransposition;some putative allergenic sequences bear fusion products with repeat sequences of transposable elements(LTRs).The abundance of nearby repetitive sequences,activation of transposable elements.and high production of mRNA transcripts appear to coincide in pollen and may contribute to a syndrome in which highly transcribed proteins may be copied and inserted with streamlined features for translation,including grouping and removaI of introns.

  17. Recombinant expression systems for allergen vaccines. (United States)

    Singh, Mohan B; Bhalla, Prem L


    Allergen immunotherapy of future is likely to be based on allergy vaccines that contain engineered allergens modified to abolish or substantially reduce their IgE-binding activity in order to remove the risk of unwanted anaphylactic responses. The development of efficient systems for the production of recombinant allergens in sufficient quantities is requirement for establishing use of engineered allergens as components of allergy vaccines. This review outlines relative advantages and disadvantages of various heterologous systems for production of recombinant allergens. Microbial systems are most convenient and cost effective platforms for the production of recombinant allergens. However, lack of post-translational processing implies that some allergens have to be expressed in eukaryotic systems for proper folding and post-translational modifications such as glycosylation. Yeast systems can yield high levels of recombinant allergens but often are associated with hyper- glycosylation problems. Mammalian cell culture systems offer suitable post -translational modifications but are nearly hundred fold more expensive than microbial systems. The use of plants as bio-factories for production of recombinant allergens is emerging as a very attractive option as plants-based production system offer several advantages over other expression systems such as post translational processing of proteins, low production costs, scale up ability and enhanced safety due to absence of animal or human pathogens.

  18. Towards standardization of microarray-based genotyping of Salmonella

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Grønlund, Hugo Ahlm; Riber, Leise


    Genotyping is becoming an increasingly important tool to improve risk assessments of Salmonella. DNA microarray technology is a promising diagnostic tool that can provide high resolution genomic profile of many genes simultaneously. However, standardization of DNA microarray analysis is needed...... of Salmonella at two different laboratories. The low-density array contained 281 of 57-60-mer oligonucleotide probes for detecting a wide range of specific genomic markers associated with antibiotic resistance, cell envelope structures, mobile genetic elements and pathogenicity. Several test parameters...... for a decentralized and simple-to-implement DNA microarray as part of a pan-European source-attribution model for risk assessment of Salmonella....

  19. 应用基因芯片技术检测肉及肉制品中5种致病菌%Rapid Detection of Five Pathogens in Meat and Meat Products by DNA Microarray

    Institute of Scientific and Technical Information of China (English)

    祝儒刚; 李拖平; 宋立峰


    建立一种运用多重聚合酶链式反应(PCR)结合基因芯片技术检测大肠埃希氏菌、沙门氏菌、金黄色葡萄球菌、志贺氏菌和单核细胞增生李斯特菌5种食源性致病菌的快速、准确、灵敏的方法。分别选取编码大肠埃希氏菌的slt基因、沙门氏菌invA基因、金黄色葡萄球菌nuc基因、志贺氏菌jpd日基因和单核细胞增生李斯特菌inlA基因,并以细菌16SrDNA基因作为阳性对照,设计引物和探针,进行多重PCR扩增,产物与含特异性探针的芯片杂交。结果表明:该基因芯片可同时特异性地检测5种致病菌,多重PCR检测灵敏度为20pg,而DNA芯片检测灵敏度可达2pg;用所制备的基因芯片检测实际肉及肉制品样品,准确率高于传统培养法。所建立的基因芯片检测方法特异性好、灵敏度高,可为食源性致病菌的检测提供理想手段。%A rapid, accurate and sensitive method for simultaneous detection of Escherichia coli, Salmonella spp, Staphylo- coccus aureus, Shigella dysenteriae and Listeria monocytogenes was developed by using DNA microarray coupled with multiplex PCR. Six pairs of primers and oligo-nucleotide probes were designed and synthesized by using the Sit gene ofEscherichia coli, the invA gene of Salmonella spp, the nuc gene of Staphylococcus aureus, the ipaH gene of Shigella dysenteriae and the inlA gene of Listeria monocytogenes as target genes, and 16S rDNA of bacteria as positive control. The multiplex PCR products were hybridized with DNA microarray containing specific probes for five food-borne pathogenic microorganisms. DNA microarray could allow simultaneous detection of five specific pathogens with de, tection limit of 2 pg, which was more sensitive than multiplex PCR with detection limit of 20 pg. Similarly, the application of DNA microarrary in the detection of actual meat and meat products revealed higher accuracy than traditional culture method. Therefore

  20. Variability of Corylus avellana, L. CorA and profilin pollen allergens expression. (United States)

    Ražná, Katarína; Bežo, Milan; Nikolaieva, Natalia; Garkava, Katerina; Brindza, Ján; Ziarovská, Jana


    Corylus avellana is the source of inhalant allergies induced by hazel pollen as well as food allergies induced after ingestion of hazelnuts. In this study, real-time PCR approach was used to analyse expression of hazel pollen allergens on the molecular level. Relative quantity of hazelnut allergens Corylus avellana, L. CorA and Corylus avellana, L. pollen profiling in samples from different Ukraine areas were determining and comparing. Differences among the levels of both analysed allergen transcripts were found for hazel CorA and profillin. In both cases, the expression within the urbanized growth conditions was higher when compared to the sample from village area. The average expression for CorA was 0.84 times higher than for profilin and the results are very variable depending on the place of growth. Expression levels here were within the range of 2.957 up to the 52.936. Profilin expression was the highest in the sample from the polluted place of growth-cement plant area with the value of 52 times higher when compared to the sample from the village area. In this study, comparison of expression levels of hazel CorA and profiling pollen allergens was performed for the first time. Real-time PCR assay developed in this study proved the sensitivity for detection of the changes of the hazel pollen allergens expression levels and could benefit labs by fast and reproducible detection method of these allergens.

  1. Antibody reactivity to the major fish allergen parvalbumin is determined by isoforms and impact of thermal processing. (United States)

    Saptarshi, Shruti R; Sharp, Michael F; Kamath, Sandip D; Lopata, Andreas L


    The EF-hand calcium binding protein, parvalbumin, is a major fish allergen. Detection of this allergen is often difficult due to its structural diversity among various fish species. The aim of this study was to evaluate the cross-reactivity of parvalbumin in a comprehensive range of bony and cartilaginous fish, from the Asia-Pacific region, and conduct a molecular analysis of this highly allergenic protein. Using the monoclonal anti-parvalbumin antibody PARV-19, we demonstrated the presence of monomeric and oligomeric parvalbumin in all fish analysed, except for gummy shark a cartilaginous fish. Heat processing of this allergen greatly affected its antibody reactivity. While heating caused a reduction in antibody reactivity to multimeric forms of parvalbumins for most bony fish, a complete loss of reactivity was observed for cartilaginous fish. Molecular analysis demonstrated that parvalbumin cross-reactivity, among fish species, is due to the molecular phylogenetic association of this major fish allergen.

  2. Relationship between Serum Specific IgE and Allergen Skin Test in Allergic Patients of Wuhan Area

    Institute of Scientific and Technical Information of China (English)


    In order to study the relationship between serum specific IgE (sIgE) and allergen skin test, allergen skin tests and detections of sIgE in 220 allergic patients of Wuhan area were analyzed.The coherent rate of the two methods was beyond 70 % (P<0.01). It was concluded that the in vitro and in vivo detection methods of allergens have a high coherence and can be used as the effective ways to diagnose the allergic diseases in clinical practice.

  3. 江门市荨麻疹患者血清总IgE及过敏原体外检测分析%Detection in vitro of serum total IgE and allergen-specific IgE in urticaria patients in Jiangmen City

    Institute of Scientific and Technical Information of China (English)

    张焕梅; 吴志周; 柯建良


    目的 探讨江门市荨麻疹患者血清总IgE及常见过敏原特异性IgE的分布.方法 采用欧蒙印迹法对162例荨麻疹患者进行血清体外检测.结果 162例患者中154例总IgE阳性,男、女患者阳性率比较差异无统计学意义(P>0.05),其中特异性IgE阳性率最高的为屋尘,其次为动物毛发组合.结论 过敏原总IgE血清体外检测阳性率高,常见过敏原的检出为慢性荨麻疹患者的诊治提供一定帮助.%Objective To study the distribution of serum total IgE and allergen-specific IgE in urticaria patients of Jiangmen. Method The 162 patients were detected by EUR0L1NE atopy. Results Among the 162 patients studied, 154 patients responded positively to the total IgE,positive rates of the total IgE in the male and female cases showed no significant difference (P>0.05),the house dust was the commonest allergen and next was the animal hairs. Conclusion The results of detection of common allergens provided a significant basis for diagnosis and treatment of the patients.

  4. Non-instrumented DNA isolation, amplification and microarray-based hybridization for a rapid on-site detection of devastating Phytophthora kernoviae. (United States)

    Schwenkbier, Lydia; Pollok, Sibyll; Rudloff, Anne; Sailer, Sebastian; Cialla-May, Dana; Weber, Karina; Popp, Jürgen


    A rapid and simple instrument-free detection system was developed for the identification of the plant pathogen Phytophthora kernoviae (P. kernoviae). The on-site operable analysis steps include magnetic particle based DNA isolation, helicase-dependent amplification (HDA) and chip-based DNA hybridization. The isothermal approach enabled the convenient amplification of the yeast GTP-binding protein (Ypt1) target gene in a miniaturized HDA-zeolite-heater (HZH) by an exothermic reaction. The amplicon detection on the chip was performed under room temperature conditions – either by successive hybridization and enzyme binding or by a combined step. A positive signal is displayed by enzymatically generated silver nanoparticle deposits, which serve as robust endpoint signals allowing an immediate visual readout. The hybridization assay enabled the reliable detection of 10 pg μL(-1) target DNA. This is the first report of an entirely electricity-free, field applicable detection approach for devastating Phytophthora species, exemplarily shown for P. kernoviae.

  5. DNA Microarray-Based Diagnostics. (United States)

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


    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.

  6. Influence of Ultrasonic Treatment on the Allergenic Properties of Shrimp (Penaeus vannamei ) Allergen

    Institute of Scientific and Technical Information of China (English)

    LI Zhenxing; LIN Hong; CAO Limin


    The present study was undertaken to determine whether high intensity ultrasound could reduce the allergic properties of shrimp allergens. Reducing the allergenic properties of these allergens will be beneficial to allergic individuals. Samples of shrimp protein extract and shrimp muscle were treated by high-intensity ultrasound with water bathing at 0 ℃ or 50 ℃for different time periods. The treated and untreated samples were then analyzed by SDS-PAGE, Western blots and competitive inhibition ELISA (Ci-ELISA) to determine the shrimp allergenicity. The results show that high-intensity ultrasound has no effect on allergenicity when the extracts were treated at 0 ℃. However, a significant decrease was observed in the level of the major shrimp allergen, Pen a 1, when the samples were treated at 50 ℃. In the determination of allergenicity with CiELISA, a reduction in IgE binding was also observed.

  7. The allergenic significance of certain fungi rarely reported as allergens. (United States)

    Giannini, E H; Northey, W T; Leathers, C R


    The allergenic significance of seven different species of fungi was investigated. Included were Chlorophyllum molybdites, Podaxis pistillaris, Stemonitis ferruginea, Lycogala epidendrum, Fuligo septica, Ustilago maydis and Puccinia cynodontis. All of these fungi have wide distribution patterns and aerially disseminated spores but, because of their unique growth characteristics, are usually not reported in atmospheric fungal surveys. Seventy-eight patients were treated for dermal sensitivity to extracts of the organisms after the spores were extracted in 50% glycerinated Coca's solution. The results represent a six-month test period. Forty-four patients, representing 56% of the total number tested, demonstrated dermal reactivity toward one or more of the extracts.

  8. Rapid and quantitative quality control of microarrays using cationic nanoparticles. (United States)

    Sun, Ye; Fan, Wenhua; McCann, Michael P; Golovlev, Val


    The fabrication quality of microarrays significantly influences the accuracy and reproducibility of microarray experiments. In this report, we present a simple and fast quality control (QC) method for spotted oligonucleotide and cDNA microarrays. It employs a nonspecific electrostatic interaction of colloidal gold nanoparticles with the chemical groups of DNA molecules and other biomolecules immobilized on the microarray surface that bear positive or negative charges. An inexpensive flatbed scanner is used to visualize and quantify the binding of cationic gold particles to the anionic DNA probes on the microarray surface. An image analysis software was designed to assess the various parameters of the array spots including spot intensity, shape and array homogeneity, calculate the overall array quality score, and save the detailed array quality report in an Excel file. The gold staining technique is fast and sensitive. It can be completed in 10 min and detect less than 1% of the probe amount commonly recommended for microarrays. Compared to the current microarray QC method that utilizes the hybridization of probes with short random sequence oligonucleotides labeled with fluorophore, our gold staining method requires less time for the analysis, reduces the reagent cost, and eliminates the need for the expensive laser scanner.

  9. eSensor®: A Microarray Technology Based on Electrochemical Detection of Nucleic Acids and Its Application to Cystic Fibrosis Carrier Screening (United States)

    Reed, Michael R.; Coty, William A.

    We have developed a test for identification of carriers for cystic fibrosis using the eSensor® DNA detection technology. Oligonucleotide probes are deposited within self-assembled monolayers on gold electrodes arrayed upon printed circuit boards. These probes allow sequence-specific capture of amplicons containing a panel of mutation sites associated with cystic fibrosis. DNA targets are detected and mutations genotyped using a “sandwich” assay methodology employing electrochemical detection of ferrocene-labeled oligonucleotides for discrimination of carrier and non-carrier alleles. Performance of the cystic fibrosis application demonstrates sufficient accuracy and reliability for clinical diagnostic use, and the procedure can be performed by trained medical technologists available in the hospital laboratory.

  10. Profilins: Mimickers of Allergy or Relevant Allergens?

    NARCIS (Netherlands)

    A. Santos; R. van Ree


    Profilins are ubiquitous proteins, present in all eukaryotic cells and identified as allergens in pollen, latex and plant foods. The highly conserved structure justifies the cross-reactive nature of IgE antibodies against plant profilins and their designation as pan-allergens. Primary sensitization

  11. 21 CFR 680.1 - Allergenic Products. (United States)


    ... ADDITIONAL STANDARDS FOR MISCELLANEOUS PRODUCTS § 680.1 Allergenic Products. (a) Definition. Allergenic... (b). (ii) Mold cultures shall be free of contaminating materials (including microorganisms) prior to... individual, that will ensure the identity of the seed culture, prescribe adequate processing of the mold,...

  12. New structural information on food allergens (abstract) (United States)

    A small number of protein families are responsible for food allergies suffered by the majority of allergy patients. What properties of these proteins make them allergens is not clear at present. Reliable methods for allergen prediction and mitigation are lacking. Most the immediate type of food alle...

  13. 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

  14. 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;


    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 a...

  15. Rapid detection of Gram-negative bacteria and their drug resistance genes from positive blood cultures using an automated microarray assay. (United States)

    Han, Eunhee; Park, Dong-Jin; Kim, Yukyoung; Yu, Jin Kyung; Park, Kang Gyun; Park, Yeon-Joon


    We evaluated the performance of the Verigene Gram-negative blood culture (BC-GN) assay (CE-IVD version) for identification of Gram-negative (GN) bacteria and detection of resistance genes. A total of 163 GN organisms (72 characterized strains and 91 clinical isolates from 86 patients) were tested; among the clinical isolates, 86 (94.5%) isolates were included in the BC-GN panel. For identification, the agreement was 98.6% (146/148, 95% confidence interval [CI], 92.1-100) and 70% (7/10, 95% CI, 53.5-100) for monomicrobial and polymicrobial cultures, respectively. Of the 48 resistance genes harbored by 43 characterized strains, all were correctly detected. Of the 19 clinical isolates harboring resistance genes, 1 CTX-M-producing Escherichia coli isolated in polymicrobial culture was not detected. Overall, BC-GN assay provides acceptable accuracy for rapid identification of Gram-negative bacteria and detection of resistance genes, compared with routine laboratory methods despite that it has limitations in the number of genus/species and resistance gene included in the panel and it shows lower sensitivity in polymicrobial cultures.

  16. Apoptosis detected by tissue microarray in cervical squamous epithelial lesions%组织芯片技术检测宫颈鳞状上皮病变中细胞凋亡

    Institute of Scientific and Technical Information of China (English)

    林静; 乐江华; 寥芝玲


    Objective: To study the condition and significance of apoptosis in cervical squamous epithelial lesions. Methods: 53 cervical specimens were selected from the hospital from January 2008 to October 2009 to prepare tissue microarray, including 9 normal specimens, 32 specimens of CIN and 12 specimens of cervical squamous cell carcinoma; TUNEL method was used to detect apoptosis. Results; The positive rates of apoptosis were 0% (0/9) in normal cervix group, 15. 62% (5/32) in CIN group, 66. 67% (8/12) in squamous cell carcinoma group; there was significant difference among the three groups (P <0. 01) . Conclusion: The phenomenon of apoptosis becomes clear with the aggravation of cervical squamous epithelial lesions, TUNEL technique has the advantages of high quality, high efficiency and reliability for tissue microarray detection.%目的:研究宫颈鳞状上皮病变中细胞凋亡的情况及其意义.方法:选择2008年1月~2009年10月桂林医学院附属医院53例宫颈组织制成组织芯片,其中正常9例,CIN 32例,鳞状细胞癌12例;应用TUNEL法检测细胞凋亡情况.结果:凋亡阳性率依次为:正常组0% (0/9),CIN组15.62% (5/32),鳞状细胞癌66.67%(8/12);正常组、CIN组与癌症组凋亡阳性率比较差异有统计学意义(P<0.01).结论:细胞凋亡现象随着宫颈鳞状上皮病变的发展逐渐明显,应用TUNEL法检测宫颈组织芯片,具有优质、高效、结果可靠的特点.

  17. Plasmonically amplified fluorescence bioassay with microarray format (United States)

    Gogalic, S.; Hageneder, S.; Ctortecka, C.; Bauch, M.; Khan, I.; Preininger, Claudia; Sauer, U.; Dostalek, J.


    Plasmonic amplification of fluorescence signal in bioassays with microarray detection format is reported. A crossed relief diffraction grating was designed to couple an excitation laser beam to surface plasmons at the wavelength overlapping with the absorption and emission bands of fluorophore Dy647 that was used as a label. The surface of periodically corrugated sensor chip was coated with surface plasmon-supporting gold layer and a thin SU8 polymer film carrying epoxy groups. These groups were employed for the covalent immobilization of capture antibodies at arrays of spots. The plasmonic amplification of fluorescence signal on the developed microarray chip was tested by using interleukin 8 sandwich immunoassay. The readout was performed ex situ after drying the chip by using a commercial scanner with high numerical aperture collecting lens. Obtained results reveal the enhancement of fluorescence signal by a factor of 5 when compared to a regular glass chip.

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

    Directory of Open Access Journals (Sweden)



    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.

  19. From allergen genes to allergy vaccines. (United States)

    Valenta, Rudolf; Ferreira, Fatima; Focke-Tejkl, Margarete; Linhart, Birgit; Niederberger, Verena; Swoboda, Ines; Vrtala, Susanne


    IgE-mediated allergy is a hypersensitivity disease affecting more than 25% of the population. The structures of the most common allergens have been revealed through molecular cloning technology in the past two decades. On the basis of this knowledge of the sequences and three-dimensional structures of culprit allergens, investigators can now analyze the immune recognition of allergens and the mechanisms of allergic inflammation in allergic patients. Allergy vaccines have been constructed that are able to selectively target the aberrant immune responses in allergic patients via different pathways of the immune system. Here we review various types of allergy vaccines that have been developed based on allergen structures, results from their clinical application in allergic patients, and future strategies for allergen-specific immunotherapy and allergy prophylaxis.

  20. Expression of the major mugwort pollen allergen Art v 1 in tobacco plants and cell cultures: problems and perspectives for allergen production in plants. (United States)

    Siegert, Marc; Pertl-Obermeyer, Heidi; Gadermaier, Gabriele; Ferreira, Fatima; Obermeyer, Gerhard


    An economic and cheap production of large amounts of recombinant allergenic proteins might become a prerequisite for the common use of microarray-based diagnostic allergy assays which allow a component-specific diagnosis. A molecular pharming strategy was applied to express the major allergen of Artemisia vulgaris pollen, Art v 1, in tobacco plants and tobacco cell cultures. The original Art v 1 with its endogenous signal peptide which directs Art v 1 to the secretory pathway, was expressed in transiently transformed tobacco leaves but was lost in stable transformed tobacco plants during the alternation of generations. Using a light-regulated promoter and "hiding" the recombinant Art v 1 in the ER succeeded in expression of Art v 1 over three generations of tobacco plants and in cell cultures generated from stable transformed plants. However, the amounts of the recombinant allergen were sufficient for analysis but not high enough to allow an economic production. Although molecular pharming has been shown to work well for the production of non-plant therapeutic proteins, it might be less efficient for closely related plant proteins.

  1. Aeroallergen analyses and their clinical relevance. I. Immunochemical quantification of allergens by RAST-inhibition, Mab-ELISA, basophil histamine release, and counter current immuno electrophoresis. (United States)

    Johnsen, C R; Abrahamsen, L; Stahl Skov, P; Johansen, N; Poulsen, L K


    The aim was to compare IgE and IgG4 RAST-inhibition assay (RI), monoclonal antibody ELISA (Mab-ELISA), counter current immuno electrophoresis (CCIE) and histamine release from basophil leukocytes (HR) for allergen quantification with special reference to aeroallergen detection. As components of indoor aeroallergens, cat, dog, and Derm. pter. allergen extracts were selected for the experiments. To evaluate unspecific interference, these allergens were compared mutually and with Cladosporium herbarum. Allergen extracts in varying dilutions were mixed with crushed glass fibre filter materials, eluted, recovered by centrifugation, and allergen concentration quantified by the assays. Equal sensitivity was found for both IgE- and IgG4-RI assaying cat allergen (in the range 5-50 SQ-U/ml) and dog allergen (in the range 10(2)-10(3) SQ-U/ml). The IgG4-RI assaying Derm. pter. was more sensitive (50 SQ-U/ml) than IgE-RI (2*10(3) SQ-U/ml). The ranges of allergen detection limits for the Mab-ELISA were equal for cat and Derm. pter. (10-10(2) SQ-U/ml). The range of allergen detection limits for CCIE, assaying dog were 10(4)-10(5) SQ-U/ml. The ranges of allergen detection limits for HR were equal for cat and Derm. pter. (10-10(2) SQ-U/ml), and 10(2)-10(3) SQ-U/ML for dog. Because of cross-reactivity, a minor degree of interference was observed in the IgE-RI and the HR test for the highest concentration of cat and dog allergens.

  2. 成都地区859例慢性荨麻疹患者过敏原检测结果分析%Detection and analysis of allergens in 859 patients with chronic urticaria in Chengdu

    Institute of Scientific and Technical Information of China (English)

    宋黎; 叶俊儒; 陆茂; 唐懿; 刘彦麟


    Objective To analyze the allergens and sex ,age distribution of chronic urticaria in Chengdu .Methods Totally 859 patients with chronic urticaria were tested with 13 kinds inhaled allergens and 15 kinds of food allergens by skin prick test .Re‐sults The top 5 allergens were:dermatophagoides farinae、dermatophagoides pteronyssinus ,cockroach ,shrimp and sea‐crab .The positive rate of dermatophagoides farinae was 58 .7% ,dermatophagoides pteronyssinus which was 55 .1% took second place .No difference was found between sex ,more inhaled allergens were found positive than food allergens in both sex groups .The positive rate was higher in people younger than 60 .Conclusion Dermatophagoides farinae ,dermatophagoides pteronyssinus ,cockroach , shrimp and sea‐crab are the commonest allergens in Chengdu .The skin prick test is important in the individualized treatment of chronic urticaria and health education .It may also be helpful in the management of chronic allergic skin diseases .%目的:分析成都地区慢性荨麻疹的常见过敏原及其性别、年龄分布。方法采用变应原点刺液(商品名:阿罗格)对859例慢性荨麻疹患者实施13种吸入物及15种食物过敏原皮肤点刺试验。结果皮试阳性率最高的前5位变应原依次是:粉尘螨、屋尘螨、蟑螂、小虾和蟹肉。其中粉尘螨阳性率最高,为58.7%,屋尘螨次之,为55.1%。不同性别变应原阳性率差异无统计学意义,男女两组吸入组变应原阳性率明显高于食物组。儿童、青中年人群变应原阳性率更高。结论粉尘螨、屋尘螨、蟑螂、小虾和蟹肉等是成都地区慢性荨麻疹的主要过敏原。皮肤点刺试验可以明确过敏原,对于慢性荨麻疹的个体化治疗及健康教育起重要作用,并为该地区慢性病管理提供合理数据。

  3. Evaluation of a Field-Portable DNA Microarray Platform and Nucleic Acid Amplification Strategies for the Detection of Arboviruses, Arthropods, and Bloodmeals (United States)


    successfully identified flaviviruses (Culex flavivirus, dengue-3, and Japanese encephalitis viruses), differen- tiated between mosquito genera ( Aedes , Armigeres...detection and confirmation of arthropod- borne pathogens by surveillance programs or preventive med- icine units, ruggedized and miniaturized equipment...Mosquito-derived virus Detected† Mosquito species Detected† CYV (ROK144) + NT NT DENV-1 (HAW) + NT NT DENV-2 (S16803) + NT NT DENV-3 (Thai87) + Aedes

  4. Quantum-dot-based suspension microarray for multiplex detection of lung cancer markers: preclinical validation and comparison with the Luminex xMAP® system (United States)

    Bilan, Regina; Ametzazurra, Amagoia; Brazhnik, Kristina; Escorza, Sergio; Fernández, David; Uríbarri, María; Nabiev, Igor; Sukhanova, Alyona


    A novel suspension multiplex immunoassay for the simultaneous specific detection of lung cancer markers in bronchoalveolar lavage fluid (BALF) clinical samples based on fluorescent microspheres having different size and spectrally encoded with quantum dots (QDEM) was developed. The designed suspension immunoassay was validated for the quantitative detection of three lung cancer markers in BALF samples from 42 lung cancer patients and 10 control subjects. Tumor markers were detected through simultaneous formation of specific immune complexes consisting of a capture molecule, the target antigen, and biotinylated recognition molecule on the surface of the different QDEM in a mixture. The immune complexes were visualized by fluorescently labeled streptavidin and simultaneously analyzed using a flow cytometer. Preclinical validation of the immunoassay was performed and results were compared with those obtained using an alternative 3-plex immunoassay based on Luminex xMAP® technology, developed on classical organic fluorophores. The comparison showed that the QDEM and xMAP® assays yielded almost identical results, with clear discrimination between control and clinical samples. Thus, developed QDEM technology can become a good alternative to xMAP® assays permitting analysis of multiple protein biomarkers using conventional flow cytometers. PMID:28300171

  5. Quantum-dot-based suspension microarray for multiplex detection of lung cancer markers: preclinical validation and comparison with the Luminex xMAP® system (United States)

    Bilan, Regina; Ametzazurra, Amagoia; Brazhnik, Kristina; Escorza, Sergio; Fernández, David; Uríbarri, María; Nabiev, Igor; Sukhanova, Alyona


    A novel suspension multiplex immunoassay for the simultaneous specific detection of lung cancer markers in bronchoalveolar lavage fluid (BALF) clinical samples based on fluorescent microspheres having different size and spectrally encoded with quantum dots (QDEM) was developed. The designed suspension immunoassay was validated for the quantitative detection of three lung cancer markers in BALF samples from 42 lung cancer patients and 10 control subjects. Tumor markers were detected through simultaneous formation of specific immune complexes consisting of a capture molecule, the target antigen, and biotinylated recognition molecule on the surface of the different QDEM in a mixture. The immune complexes were visualized by fluorescently labeled streptavidin and simultaneously analyzed using a flow cytometer. Preclinical validation of the immunoassay was performed and results were compared with those obtained using an alternative 3-plex immunoassay based on Luminex xMAP® technology, developed on classical organic fluorophores. The comparison showed that the QDEM and xMAP® assays yielded almost identical results, with clear discrimination between control and clinical samples. Thus, developed QDEM technology can become a good alternative to xMAP® assays permitting analysis of multiple protein biomarkers using conventional flow cytometers.

  6. Identification of six potential markers for the detection of circulating canine mammary tumour cells in the peripheral blood identified by microarray analysis. (United States)

    da Costa, A; Lenze, D; Hummel, M; Kohn, B; Gruber, A D; Klopfleisch, R


    The presence of circulating tumour cells (CTCs) in the peripheral blood is a prognostic factor for survival of human breast cancer patients. CTCs in the peripheral blood of dogs with mammary tumours have not been reported definitively. The present pilot study identifies mRNA markers for CTCs by comparing the transcriptome of canine mammary carcinoma cell lines CMM26 and CMM115 and peripheral blood leucocytes (PBLs). Genes with a 200-fold or higher mRNA expression in carcinoma cell lines were tested for specificity and sensitivity to detect CTCs using reverse transcriptase polymerase chain reaction (PCR). Six mRNA markers, AGR2, ATP8B1, CRYAB, F3 IRX3 and SLC1A1 were expressed in cell lines, but not PBL. All PCRs were able to detect one carcinoma cell admixed in 10(6) or more PBLs. The six mRNA markers may be suitable for detection of canine mammary CTCs and allow the analysis of their spatiotemporal distribution in dogs with mammary tumours.

  7. Indoor Dust Allergen Levels in the Homes of Patients with Childhood Asthma: An Experience From Southwestern Iran

    Directory of Open Access Journals (Sweden)

    Mozhgan Moghtaderi


    Full Text Available Exposure to indoor allergens plays an important role in the etiology of asthma. This study was designed to quantify indoor allergens from homes of families that had at least one case of childhood asthma at home in a southwestern city of Iran. The relationship between the indoor allergen levels and home characteristics was also investigated. Dust samples were collected from the bedrooms and the kitchens of 35 homes where children with persistent asthma were living. The levels of indoor allergens were measured by enzyme linked immunosorbent assay (ELISA. Detectable amounts of mite, mouse and cockroach allergens were found in all evaluated places. None of our patients were exposed to a threshold concentration of indoor allergen for sensitizing at home. Regarding of mite allergens, the levels of Der f1 were significantly higher than Der p1 and a direct correlation was observed between living in an apartment and Der f1 levels. Moreover, Fel d1 (cat and Bla g1 (cockroach allergens were found in the children’s bedrooms more frequently than those in the kitchens. In this study, direct associations were obtained between Bla g1 allergen and the duration of occupancy and between Fel d1 and average home size. A total of 34.2% of the patients showed positive skin reactions to at least one of the tested allergens as 17.1% of them showed reactivity to D. pteronyssinus. Proper controlling of cockroaches and mice by public health officials would be a practical approach to avoid inducing asthma or worsening the symptoms.

  8. Fluorescence Lifetime Imaging of Quantum Dot Labeled DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Jonathan G. Terry


    Full Text Available Quantum dot (QD labeling combined with fluorescence lifetime imaging microscopy is proposed as a powerful transduction technique for the detection of DNA hybridization events. Fluorescence lifetime analysis of DNA microarray spots of hybridized QD labeled target indicated a characteristic lifetime value of 18.8 ns, compared to 13.3 ns obtained for spots of free QD solution, revealing that QD labels are sensitive to the spot microenvironment. Additionally, time gated detection was shown to improve the microarray image contrast ratio by 1.8, achieving femtomolar target sensitivity. Finally, lifetime multiplexing based on Qdot525 and Alexa430 was demonstrated using a single excitation-detection readout channel.

  9. Effects of NO2 and ozone on pollen allergenicity

    Directory of Open Access Journals (Sweden)

    Ulrike eFrank


    Full Text Available This mini-review summarizes the available data of the air pollutants NO2 and ozone on allergenic pollen from different plant species, focusing on potentially allergenic components of the pollen, such as allergen content, protein release, IgE-binding or protein modification. Various in vivo and in vitro studies on allergenic pollen are shown and discussed.

  10. DNA Microarray Characterization of Pathogens Associated with Sexually Transmitted Diseases. (United States)

    Cao, Boyang; Wang, Suwei; Tian, Zhenyang; Hu, Pinliang; Feng, Lu; Wang, Lei


    This study established a multiplex PCR-based microarray to detect simultaneously a diverse panel of 17 sexually transmitted diseases (STDs)-associated pathogens including Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma, Herpes simplex virus (HSV) types 1 and 2, and Human papillomavirus (HPV) types 6, 11, 16, 18, 31, 33, 35, 39, 54 and 58. The target genes are 16S rRNA gene for N. gonorrhoeae, M. genitalium, M. hominism, and Ureaplasma, the major outer membrane protein gene (ompA) for C. trachomatis, the glycoprotein B gene (gB) for HSV; and the L1 gene for HPV. A total of 34 probes were selected for the microarray including 31 specific probes, one as positive control, one as negative control, and one as positional control probe for printing reference. The microarray is specific as the commensal and pathogenic microbes (and closely related organisms) in the genitourinary tract did not cross-react with the microarray probes. The microarray is 10 times more sensitive than that of the multiplex PCR. Among the 158 suspected HPV specimens examined, the microarray showed that 49 samples contained HPV, 21 samples contained Ureaplasma, 15 contained M. hominis, four contained C. trachomatis, and one contained N. gonorrhoeae. This work reports the development of the first high through-put detection system that identifies common pathogens associated with STDs from clinical samples, and paves the way for establishing a time-saving, accurate and high-throughput diagnostic tool for STDs.

  11. Optimized light-directed synthesis of aptamer microarrays. (United States)

    Franssen-van Hal, Nicole L W; van der Putte, Pepijn; Hellmuth, Klaus; Matysiak, Stefan; Kretschy, Nicole; Somoza, Mark M


    Aptamer microarrays are a promising high-throughput method for ultrasensitive detection of multiple analytes, but although much is known about the optimal synthesis of oligonucleotide microarrays used in hybridization-based genomics applications, the bioaffinity interactions between aptamers and their targets is qualitatively different and requires significant changes to synthesis parameters. Focusing on streptavidin-binding DNA aptamers, we employed light-directed in situ synthesis of microarrays to analyze the effects of sequence fidelity, linker length, surface probe density, and substrate functionalization on detection sensitivity. Direct comparison with oligonucleotide hybridization experiments indicates that aptamer microarrays are significantly more sensitive to sequence fidelity and substrate functionalization and have different optimal linker length and surface probe density requirements. Whereas microarray hybridization probes generate maximum signal with multiple deletions, aptamer sequences with the same deletion rate result in a 3-fold binding signal reduction compared with the same sequences synthesized for maximized sequence fidelity. The highest hybridization signal was obtained with dT 5mer linkers, and the highest aptamer signal was obtained with dT 11mers, with shorter aptamer linkers significantly reducing the binding signal. The probe hybridization signal was found to be more sensitive to molecular crowding, whereas the aptamer probe signal does not appear to be constrained within the density of functional surface groups commonly used to synthesize microarrays.

  12. Carbohydrate Microarrays in Plant Science

    DEFF Research Database (Denmark)

    Fangel, Jonatan Ulrik; Pedersen, H.L.; Vidal-Melgosa, S.


    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......-throughput analysis of nucleotides, proteins, and increasingly carbohydrates. Using microarrays, the abundance of and interactions between hundreds and thousands of molecules can be assessed simultaneously using very small amounts of analytes. Here we show that carbohydrate microarrays are multifunctional tools...... for 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....

  13. Transfection microarray and the applications. (United States)

    Miyake, Masato; Yoshikawa, Tomohiro; Fujita, Satoshi; Miyake, Jun


    Microarray transfection has been extensively studied for high-throughput functional analysis of mammalian cells. However, control of efficiency and reproducibility are the critical issues for practical use. By using solid-phase transfection accelerators and nano-scaffold, we provide a highly efficient and reproducible microarray-transfection device, "transfection microarray". The device would be applied to the limited number of available primary cells and stem cells not only for large-scale functional analysis but also reporter-based time-lapse cellular event analysis.

  14. 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


    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.

  15. Detection of fungal DNA in peritoneal fluids by a PCR DNA low-density microarray system and quantitation of serum (1-3)-β-D-glucan in the diagnosis of peritoneal candidiasis. (United States)

    Corrales, Isabel; Giménez, Estela; Aguilar, Gerardo; Delgado, Carlos; Puig, Jaime; Izquierdo, Ana; Belda, Javier; Navarro, David


    Microbiological documentation of peritoneal candidiasis (PC) is hampered by the low numbers of yeasts observable by direct microscopic examination and recoverable by culture methods. The performance of a polymerase chain reaction (PCR) DNA Low-Density Microarray System (CLART STIs B) was compared to that of BACTEC FX automated culture method for the detection of Candida spp. in 161 peritoneal fluids (PF) from patients with peritonitis. The clinical utility of (1-3)-β-d-glucan (BDG) antigenemia in the diagnosis of PC was evaluated in 42 of these patients. The overall agreement between the PCR assay and the culture method was good (κ = 0.790), and their sensitivities were 93.5% and 74.19%, respectively. Serum BDG levels in patients with Candida spp. in PFs (median, 200.3 pg/mL; Range, 22.0-523.4 pg/mL) was significantly higher (P = 0.002) than those found in patients without the yeast (median, 25.3 pg/mL; Range, 0-523.4 pg/mL). Our study demonstrates the potential clinical utility of molecular methods and the measurement of serum BDG levels for the diagnosis of PC.

  16. Regenerable immuno-biochip for screening ochratoxin A in green coffee extract using an automated microarray chip reader with chemiluminescence detection. (United States)

    Sauceda-Friebe, Jimena C; Karsunke, Xaver Y Z; Vazac, Susanna; Biselli, Scarlett; Niessner, Reinhard; Knopp, Dietmar


    Ochratoxin A (OTA) can contaminate foodstuffs in the ppb to ppm range and once formed, it is difficult to remove. Because of its toxicity and potential risks to human health, the need exists for rapid, efficient detection methods that comply with legal maximum residual limits. In this work we have synthesized an OTA conjugate functionalized with a water-soluble peptide for covalent immobilization on a glass biochip by means of contact spotting. The chip was used for OTA determination with an indirect competitive immunoassay format with flow-through reagent addition and chemiluminescence detection, carried out with the stand-alone automated Munich Chip Reader 3 (MCR 3) platform. A buffer model and real green coffee extracts were used for this purpose. At the present, covalent conjugate immobilization allowed for at least 20 assay-regeneration cycles of the biochip surface. The total analysis time for a single sample, including measurement and surface regeneration, was 12 min and the LOQ of OTA in green coffee extract was 0.3 μg L(-1) which corresponds to 7 μg kg(-1).

  17. The Level of Mite Dermatophagoides’ Allergens (Der-p 1 and Der-f 1) in Birjand


    Mohammad Fereidouni; Farkhondeh Fereidouni; Mehrasa Hadian; Zahra Asghari; S. Masood Zojaji


    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 an...

  18. The detection of inhalant allergens for children with asthma and the analysis of clinical features%哮喘患儿吸入性过敏原检测及其临床特征分析

    Institute of Scientific and Technical Information of China (English)

    成胜权; 强欢; 罗建峰; 丁翠玲; 丁亚楠


    Objective This study is aimed to investigate the type and distribution features of allergens inhaled by asthma children as well as their relationship with the age and gender of patients, to provide theoretical basis for the clinical diagnosis, treatment, and prevention of asthma in children. Method 13 types of standardized allergen skin prick liquid, provided by the Danish ALK-ABELL company, were used for inhaled allergen skin prick test (SPT) in 653 cases of children with asthma, treated in the pediatric clinic from July 2008 to July 2013. The patients were divided into three groups by age, <4 years old, 4-7 years old, and 7 -14 years old. The SPT-positive rate and changes of allergens species were compared among these three groups of patients. Result (1)Of the 653 patients,409(62.6%)cases were SPT-positive. The most prevalent inhalant allergens were: Dermatophagns farina in 266 cases(40.7%) , Dermatophagoides pteronyss inus in 265 cases (40.6%), tropical mite in 162 cases (24.8%), cat dander in 91 cases (13.9%), mugwort in 89 cases (13.6%);(2)The SPT-positive rate in males(299 in 455 cases; 65.7%) was greater than that in females (110 in 198 cases; 55.6%; P<0.05)The top 5 allergens were different between males and females. For males, they are house dust mites, dust mites, tropical mites, mugwort, and dog hair allergens, respectively. And for females, the top five allergens were dust mites, house dust mites, tropical mites, mugwort, and cat hair, respectively. (3)For <4 years old patients, the female's SPT-positive rate was higher than male's whereas male's SPT-positive rate was higher than females in groups of 4-7 years old and 7-14 years old. (4) SPT-positive male children is easier than SPT-positive female children with asthma to inhale three or more kinds of allergens(62.6% in male vs. 50.9% in female; P<0.05). Conclusion There are differences of gender and age in common inhalant allergens for children with asthma The top four common allergens were

  19. Microtiter plate-based antibody microarrays for bacteria and toxins (United States)

    Research has focused on the development of rapid biosensor-based, high-throughput, and multiplexed detection of pathogenic bacteria in foods. Specifically, antibody microarrays in 96-well microtiter plates have been generated for the purpose of selective detection of Shiga toxin-producing E. coli (...

  20. Will genetically modified foods be allergenic? (United States)

    Taylor, S L; Hefle, S L


    Foods produced through agricultural biotechnology, including such staples as corn, soybeans, canola, and potatoes, are already reaching the consumer marketplace. Agricultural biotechnology offers the promise to produce crops with improved agronomic characteristics (eg, insect resistance, herbicide tolerance, disease resistance, and climatic tolerance) and enhanced consumer benefits (eg, better taste and texture, longer shelf life, and more nutritious). Certainly, the products of agricultural biotechnology should be subjected to a careful and complete safety assessment before commercialization. Because the genetic modification ultimately results in the introduction of new proteins into the food plant, the safety, including the potential allergenicity, of the newly introduced proteins must be assessed. Although most allergens are proteins, only a few of the many proteins found in foods are allergenic under the typical circumstances of exposure. The potential allergenicity of the introduced proteins can be evaluated by focusing on the source of the gene, the sequence homology of the newly introduced protein to known allergens, the expression level of the novel protein in the modified crop, the functional classification of the novel protein, the reactivity of the novel protein with IgE from the serum of individuals with known allergies to the source of the transferred genetic material, and various physicochemical properties of the newly introduced protein, such as heat stability and digestive stability. Few products of agricultural biotechnology (and none of the current products) will involve the transfer of genes from known allergenic sources. Applying such criteria provides reasonable assurance that the newly introduced protein has limited capability to become an allergen.

  1. The hammock: a reservoir of allergens

    Directory of Open Access Journals (Sweden)

    Francisca X. M. Rego


    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. Chicken sperm transcriptome profiling by microarray analysis. (United States)

    Singh, R P; Shafeeque, C M; Sharma, S K; Singh, R; Mohan, J; Sastry, K V H; Saxena, V K; Azeez, P A


    It has been confirmed that mammalian sperm contain thousands of functional RNAs, and some of them have vital roles in fertilization and early embryonic development. Therefore, we attempted to characterize transcriptome of the sperm of fertile chickens using microarray analysis. Spermatozoal RNA was pooled from 10 fertile males and used for RNA preparation. Prior to performing the microarray, RNA quality was assessed using a bioanalyzer, and gDNA and somatic cell RNA contamination was assessed by CD4 and PTPRC gene amplification. The chicken sperm transcriptome was cross-examined by analysing sperm and testes RNA on a 4 × 44K chicken array, and results were verified by RT-PCR. Microarray analysis identified 21,639 predominantly nuclear-encoded transcripts in chicken sperm. The majority (66.55%) of the sperm transcripts were shared with the testes, while surprisingly, 33.45% transcripts were detected (raw signal intensity greater than 50) only in the sperm and not in the testes. The greatest proportion of up-regulated transcripts were responsible for signal transduction (63.20%) followed by embryonic development (56.76%) and cell structure (56.25%). Of the 20 most abundant transcripts, 18 remain uncharacterized, whereas the least abundant genes were mostly associated with the ribosome. These findings lay a foundation for more detailed investigations on sperm RNAs in chickens to identify sperm-based biomarkers for fertility.

  3. Allergen source materials: state-of-the-art. (United States)

    Esch, Robert E


    A variety of positive outcomes can be realized from validation and risk management activities (see Table 4). They are dependent on the participation of multiple functional groups including the quality unit, regulatory and legal affairs, engineering and production operations, research and development, and sales and marketing. Quality risk management is receiving increased attention in the area of public health, pharmacovigilance, and pharmaceutical manufacturing. Recent examples of its regulatory use in our industry include the assessment of the potential risks of transmissible spongiform encephalopathies (TSE) agents through contaminated products], the risks of precipitates in allergenic extracts, and the revision of the potency limits for standardized dust mite and grass allergen vaccines. Its application to allergen source material process validation activities allowed for a practical strategy, especially in a complex manufacturing environment involving hundreds of products with multiple intended uses. In addition, the use of tools such as FMEA was useful in evaluating proposed changes made to manufacturing procedures and product specifications, new regulatory actions, and customer feedback or complaints. The success of such a quality assurance programs will ultimately be reflected in the elimination or reduction of product failures, improvement in the detection and prediction of potential product failures, and increased confidence in product quality.

  4. IgE reactivity to hen egg white allergens in dogs with cutaneous adverse food reactions. (United States)

    Shimakura, Hidekatsu; Uchiyama, Jumpei; Saito, Taku; Miyaji, Kazuki; Fujimura, Masato; Masuda, Kenichi; Okamoto, Noriaki; DeBoer, Douglas J; Sakaguchi, Masahiro


    Dogs with cutaneous adverse food reactions (CAFR) often have specific IgE to food allergens. Egg white, which is majorly composed of ovomucoid, ovalbumin, ovotransferrin, and lysozyme, is a food allergen in dogs. Information of the IgE reactivity to purified egg white allergens supports accurate diagnosis and efficiency treatment in humans. However, to the best of our knowledge, there have been no studies on the IgE reactivity to purified egg white allergens in dogs. Here, we investigated the IgE reactivity to crude and purified allergens of hen egg white in dogs with CAFR. First, when we examined serum samples from 82 dogs with CAFR for specific IgE to crude egg white by ELISA, 9.8% (8/82) of the dogs with CAFR showed the IgE reactivity to crude egg white. We then used sera from the eight dogs with positive IgE reactivity to crude egg white to examine the IgE reactivity to four purified allergens, ovomucoid, ovalbumin, ovotransferrin, and lysozyme, by ELISA. We found that 75% (6/8) of the dogs showed IgE reactivity to both ovomucoid and ovalbumin, and that 37.5% (3/8) of the dogs showed IgE reactivity to ovotransferrin. None (0/8) showed IgE reactivity to lysozyme. Moreover, validating these results, the immunoblot analyses were performed using the sera of the three dogs showing the highest IgE reactivity to crude egg white. Both anti-ovomucoid and anti-ovalbumin IgE were detected in the sera of these dogs, while anti-ovotransferrin IgE was not detected. Considering these, ovomucoid and ovalbumin appears to be the major egg white allergens in dogs with CAFR.

  5. A histamine release assay to identify sensitization to Culicoides allergens in horses with skin hypersensitivity. (United States)

    Wagner, Bettina; Childs, Bronwen A; Erb, Hollis N


    Skin hypersensitivity is an allergic disease induced in horses by allergens of Culicoides midges. The condition is typically diagnosed by clinical signs and in some horses in combination with allergy testing such as intradermal skin testing or serological allergen-specific IgE determination. Here, we describe an alternative method for allergy testing: a histamine release assay (HRA) that combines the functional aspects of skin testing with the convenience of submitting a blood sample. The assay is based on the principle that crosslinking of allergen-specific IgE bound via high-affinity IgE receptors to the surfaces of mast cells and basophils induces the release of inflammatory mediators. One of these mediators is histamine. The histamine was then detected by a colorimetric enzyme-linked immunosorbent assay. The histamine assay was used to test 33 horses with skin hypersensitivity and 20 clinically healthy control animals for histamine release from their peripheral blood basophils after stimulation with Culicoides allergen extract or monoclonal anti-IgE antibody. An increased histamine release was observed in the horses with skin hypersensitivity compared to the control group after allergen-specific stimulation with Culicoides extract (p=0.023). In contrast, stimulation with anti-IgE induced similar amounts of released histamine in both groups (p=0.46). For further evaluation of the HRA, we prepared a receiver operating-characteristic (ROC) curve and performed a likelihood-ratio analysis for assay interpretation. Our results suggested that the assay is a valuable diagnostic tool to identify sensitization to Culicoides allergens in horses. Because some of the clinically healthy horses also showed sensitization to Culicoides extract, the assay cannot be used to distinguish allergic from non-allergic animals. The observation that sensitization is sometimes detectable in non-affected animals suggested that clinically healthy horses use immune mechanisms to control the

  6. Characterization and standardization of allergen extracts. (United States)

    Løwenstein, Henning


    This paper summarizes the development of the extraction and characterization of allergens responsible for the induction of immunoglobulin (lg) E-induced allergies from the beginning of the 20th century, including the nomenclature of allergens. The majority of papers characterizing allergens and allergen extracts state that the lack of standardization of allergen extracts is the reason for the paper, and so it has been for more than 100 years. A natural part of that process might be the isolation of an allergen molecule and this starts the speculation of 'what makes that allergen an allergen?' To achieve the perfect standardization is a desirable end that is still awaited. So far none of these problems have been finally solved. I started in allergy shortly after the discovery of IgE in 1967. Since that time the history as I remember it is based on the literature, my interpretation of it, and of course may be a little biased due to personal prejudice! The history of the last 10-15 years has still not matured and it might be a little early to draw conclusions. However, at the end of this chapter I do dare to make a few conclusions after having followed the development in this field for 40 years. As this is history it is not meant to be either comprehensive or technically and scientifically precise in all aspects, but rather draws on some thoughts as to what in my mind have been important developments until now. Specific techniques are only mentioned by name and not intended to be discussed in depth. This activity has, however, pushed me to reflect on my hopes and speculations at the time of my introduction to the field of allergen chemistry. To my surprise I realize that far more than I ever expected at that time has been fulfilled. It has been extremely exciting to be a part of that development.

  7. 变应性鼻炎患者伴发食物变应原致敏的特异性抗体检测分析%Detection and analysis of specific antibodies of food allergens in patients with allergic rhinitis

    Institute of Scientific and Technical Information of China (English)

    王俊阁; 陈钢; 俞琳琳; 李婉英; 盖建青; 闫新宇; 吴慧莉


    [ABSTRACT]OBJECTIVETo investigate the relationship between food allergen specific IgE, IgG and allergic rhinitis, and to explore the significance of food allergen in the diagnosis and prevention of allergic rhinitis.METHODSTen kinds of food specific IgE were detected by Western blot and 14 kinds of food specific IgG were detected by ELISA in 2860 allergic rhinitis patients. The positive results of specific IgE and specific IgG were retrospectively analyzed.RESULTSThere was no difference in positive rate of allergen in patients with different gender. Total positive rate of food specific IgE was 68.5%. The specific IgE positive rate of crab was 31.5%, shrimp 27.6%, milk 21.3%, fish assemblages 19.2%, freshwater fish assemblages 18.3% and soybean 17.2%. With the growth of age, the specific IgE positive rate of peanut increased, but eggs decreased. The total positive rate of food allergen specific IgG was 81.5%. The specific IgG positive rate of egg was 59.4%, milk 38.2%, codfish 32.6%, soybean 22.8%, rice 19% and shrimp 12.7%. With the growth of age, the specific IgG positive rate of crab increased. Specific IgE and IgG of soybean, milk, crab, shrimp and fish were correlated well.CONCLUSIONThe detection of specific food allergen antibodies is helpful for the diagnosis of allergic rhinitis.%目的:研究食物变应原特异性IgE(specific IgE,sIgE)、sIgG与变应性鼻炎的关系,探讨食物变应原在变应性鼻炎诊断和预防中的意义。方法对2860例变应性鼻炎患者采用免疫印迹法检测10种食物sIgE和ELISA法检测14种食物sIgG阳性结果进行回顾性分析。结果变应原阳性率在不同性别患者间无差别。食物sIgE总阳性率为68.5%,依次为螃蟹(31.5%)、虾(27.6%)、牛奶(21.3%)、海鱼组合(19.2%)、淡水鱼组合(18.3%)、大豆(17.2%),其中花生随年龄增长,阳性率增加,鸡蛋则降低。食物变应原sIgG总阳性率81.5%,以鸡蛋(59.4%

  8. An effective method for network module extraction from microarray data

    Directory of Open Access Journals (Sweden)

    Mahanta Priyakshi


    Full Text Available Abstract Background The development of high-throughput Microarray technologies has provided various opportunities to systematically characterize diverse types of computational biological networks. Co-expression network have become popular in the analysis of microarray data, such as for detecting functional gene modules. Results This paper presents a method to build a co-expression network (CEN and to detect network modules from the built network. We use an effective gene expression similarity measure called NMRS (Normalized mean residue similarity to construct the CEN. We have tested our method on five publicly available benchmark microarray datasets. The network modules extracted by our algorithm have been biologically validated in terms of Q value and p value. Conclusions Our results show that the technique is capable of detecting biologically significant network modules from the co-expression network. Biologist can use this technique to find groups of genes with similar functionality based on their expression information.

  9. Quantification of Anisakis simplex allergens in fresh, long-term frozen, and cooked fish muscle. (United States)

    Rodríguez-Mahillo, Ana Isabel; González-Muñoz, Miguel; de las Heras, Cristina; Tejada, Margarita; Moneo, Ignacio


    Fish-borne parasitic zoonoses such as Anisakiasis were once limited to people living in countries where raw or undercooked fish is traditionally consumed. Nowadays, several factors, such as the growing international markets, the improved transportation systems, the population movements, and the expansion of ethnic ways of cooking in developed countries, have increased the population exposed to these parasites. Improved diagnosis technology and a better knowledge of the symptoms by clinicians have increased the Anisakiasis cases worldwide. Dietary recommendations to Anisakis-sensitized patients include the consumption of frozen or well-cooked fish, but these probably do not defend sensitized patients from allergen exposure. The aim of our work was to develop a sensitive and specific method to detect and quantify Anisakis simplex allergens in fish muscle and its derivatives. Protein extraction was made in saline buffer followed by preparation under acid conditions. A. simplex antigens were detected by IgG immunoblot and quantified by dot blot. The allergenic properties of the extracts were assessed by IgE immunoblotting and basophil activation test. We were able to detect less than 1 ppm of A. simplex antigens, among them the allergen Ani s 4, in fish muscle with no cross-reactions and with a recovery rate of 82.5%. A. simplex antigens were detected in hakes and anchovies but not in sardines, red mullets, or shellfish. We detected A. simplex allergens in cooked hakes and also in hake stock. We proved that A. simplex allergens are preserved in long-term frozen storage (-20 degrees C +/- 2 degrees C for 11 months) of parasitized hakes. Basophil activation tests have proven the capability of the A. simplex-positive fish extracts to induce allergic symptoms.

  10. Contact Dermatitis, Patch Testing, and Allergen Avoidance. (United States)

    Burkemper, Nicole M


    In patients presenting with a complaint of rash, contact dermatitis is often the underlying diagnosis making it an entity with which health care providers should be familiar. Contact dermatitis can be divided into irritant contact dermatitis and allergic contact dermatitis. In a patient suspected of having allergic contact dermatitis, patch testing can be done to identify specific allergens. Education focused on allergen avoidance and safe products is an integral part of treatment for the contact dermatitis patient. Knowledge of the most common allergens is helpful for clinicians to be able to provide this education.