WorldWideScience

Sample records for rapid fungi detection

  1. ETV Tech Brief: Rapid Fungi and Bacteria Detection Technologies

    Science.gov (United States)

    Technical brief that summarizes the results for Mycometer, Inc. Mycometer®-test and Bactiquant®-test, which are rapid detection technologies for fungi and bacteria. The brief summarizes the results of the verification report and statement.

  2. Rapid identification and detection of pathogenic Fungi by padlock probes

    NARCIS (Netherlands)

    Tsui, C.K.M.; Wang, B.; Schoen, C.D.; Hamelin, R.C.

    2013-01-01

    Fungi are important pathogens of human diseases, as well as to agricultural crop and trees. Molecular diagnostics can detect diseases early, and improve identification accuracy and follow-up disease management. The use of padlock probe is effective to facilitate these detections and pathogen

  3. Plasmonic gold nanoparticles for detection of fungi and human cutaneous fungal infections.

    Science.gov (United States)

    Sojinrin, Tobiloba; Conde, João; Liu, Kangze; Curtin, James; Byrne, Hugh J; Cui, Daxiang; Tian, Furong

    2017-07-01

    Fungi, which are common in the environment, can cause a multitude of diseases. Warm, humid conditions allow fungi to grow and infect humans via the respiratory, digestive and reproductive tracts, genital area and other bodily interfaces. Fungi can be detected directly by microscopy, using the potassium hydroxide test, which is the gold standard and most popular method for fungal screening. However, this test requires trained personnel operating specialist equipment, including a fluorescent microscope and culture facilities. As most acutely infected patients seek medical attention within the first few days of symptoms, the optimal diagnostic test would be rapid and self-diagnostic simplifying and improving the therapeutic outcome. In suspensions of gold nanoparticles, Aspergillus niger can cause a colour change from red to blue within 2 min, as a result of changes in nanoparticle shape. A similar colour change was observed in the supernatant of samples of human toenails dispersed in water. Scanning electron microscopy, UV/Vis and Raman spectroscopy were employed to monitor the changes in morphology and surface plasmon resonance of the nanoparticles. The correlation of colour change with the fungal infection was analysed using the absorbance ratio at 520 nm/620 nm. We found a decrease in the ratio when the fungi concentration increased from 1 to 16 CFU/mL, with a detection limit of 10 CFU/mL. The test had an 80% sensitivity and a 95% specificity value for the diagnosis of athlete's foot in human patients. This plasmonic gold nanoparticle-based system for detection of fungal infections measures the change in shape of gold nanoparticles and generates coloured solutions with distinct tonality. Our application has the potential to contribute to self-diagnosis and hygiene control in laboratories/hospitals with fewer resources, just using the naked eye. Graphical abstract Colorimetric method for fungi detection with gold nano particles.

  4. Detection of species diversity of arbuscular mycorrhizal fungi (AMF ...

    African Journals Online (AJOL)

    Arbuscular-mycorhizal fungi (AMF) from melon plants grown in Van province, were studied by nested-PCR method to establish colonization ratio of related fungi in plants and to detect the fungi at species level. From 10 different locations, a total of 100 soil samples were taken from rhizosphere area of melon plants.

  5. Early detection of fungi damage in citrus using NIR spectroscopy

    Science.gov (United States)

    Blasco, Jose; Ortiz, Coral; Sabater, Maria D.; Molto, Enrique

    2000-12-01

    Early detection of defects and diseases in fruit helps to correctly classify them and make more adequate decisions about the destination of the product: internal market, export or industry. An early fungi infection detection is especially important because a few infected fruits can disseminate the infection to a whole batch, causing great economic losses and affecting to further exports. Ensure products with excellent quality and absolute absence of fungi infections is particularly important in those batches for long conservation or to be exported. The main objective of this work is to detect the fungi infections before they can be visible. Near Infrared spectroscopy has been employed in this work, because it is a non-destructive technique and can be easily implemented on line due to the high speed and simplicity of the process.

  6. 9 CFR 113.25 - Culture media for detection of bacteria and fungi.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Culture media for detection of bacteria and fungi. 113.25 Section 113.25 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION... STANDARD REQUIREMENTS Standard Procedures § 113.25 Culture media for detection of bacteria and fungi. (a...

  7. 9 CFR 113.26 - Detection of viable bacteria and fungi except in live vaccine.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Detection of viable bacteria and fungi... VECTORS STANDARD REQUIREMENTS Standard Procedures § 113.26 Detection of viable bacteria and fungi except... required to be free of viable bacteria and fungi, they shall also be tested as prescribed in this section...

  8. Comparison of media for detection of fungi on spacecraft

    Science.gov (United States)

    Herring, C. M.; Brandsberg, J. W.; Oxborrow, G. S.; Puleo, J. R.

    1974-01-01

    Five media, including Trypticase soy agar (TSA; BBL) pour plates, spread plates of TSA, Mycophil agar with chloromycetin, Mycophil agar with chloromycetin and Actidione, and cornmeal agar with chloromycetin were quantitatively and qualitatively compared for the detection of fungi on spacecraft. Cornmeal agar with chloromycetin yielded the highest number of fungal colonies, although not always significantly higher than Mycophil agar with chloromycetin or TSA spread plates. Cornmeal agar with chloromycetin also gave the best qualitative representation of fungi on the spacecraft, recovering 68% of the genera found from all media. This medium yielded 10 times the number of fungal colonies and 3 times the number of genera found on TSA pour plates as currently used for spacecraft assay.

  9. Strigolactones Stimulate Arbuscular Mycorrhizal Fungi by Activating Mitochondria

    Science.gov (United States)

    Besserer, Arnaud; Puech-Pagès, Virginie; Kiefer, Patrick; Gomez-Roldan, Victoria; Jauneau, Alain; Roy, Sébastien; Portais, Jean-Charles; Roux, Christophe; Bécard, Guillaume

    2006-01-01

    The association of arbuscular mycorrhizal (AM) fungi with plant roots is the oldest and ecologically most important symbiotic relationship between higher plants and microorganisms, yet the mechanism by which these fungi detect the presence of a plant host is poorly understood. Previous studies have shown that roots secrete a branching factor (BF) that strongly stimulates branching of hyphae during germination of the spores of AM fungi. In the BF of Lotus, a strigolactone was found to be the active molecule. Strigolactones are known as germination stimulants of the parasitic plants Striga and Orobanche. In this paper, we show that the BF of a monocotyledonous plant, Sorghum, also contains a strigolactone. Strigolactones strongly and rapidly stimulated cell proliferation of the AM fungus Gigaspora rosea at concentrations as low as 10 −13 M. This effect was not found with other sesquiterperne lactones known as germination stimulants of parasitic weeds. Within 1 h of treatment, the density of mitochondria in the fungal cells increased, and their shape and movement changed dramatically. Strigolactones stimulated spore germination of two other phylogenetically distant AM fungi, Glomus intraradices and Gl. claroideum. This was also associated with a rapid increase of mitochondrial density and respiration as shown with Gl. intraradices. We conclude that strigolactones are important rhizospheric plant signals involved in stimulating both the pre-symbiotic growth of AM fungi and the germination of parasitic plants. PMID:16787107

  10. Strigolactones stimulate arbuscular mycorrhizal fungi by activating mitochondria.

    Directory of Open Access Journals (Sweden)

    Arnaud Besserer

    2006-07-01

    Full Text Available The association of arbuscular mycorrhizal (AM fungi with plant roots is the oldest and ecologically most important symbiotic relationship between higher plants and microorganisms, yet the mechanism by which these fungi detect the presence of a plant host is poorly understood. Previous studies have shown that roots secrete a branching factor (BF that strongly stimulates branching of hyphae during germination of the spores of AM fungi. In the BF of Lotus, a strigolactone was found to be the active molecule. Strigolactones are known as germination stimulants of the parasitic plants Striga and Orobanche. In this paper, we show that the BF of a monocotyledonous plant, Sorghum, also contains a strigolactone. Strigolactones strongly and rapidly stimulated cell proliferation of the AM fungus Gigaspora rosea at concentrations as low as 10(-13 M. This effect was not found with other sesquiterperne lactones known as germination stimulants of parasitic weeds. Within 1 h of treatment, the density of mitochondria in the fungal cells increased, and their shape and movement changed dramatically. Strigolactones stimulated spore germination of two other phylogenetically distant AM fungi, Glomus intraradices and Gl. claroideum. This was also associated with a rapid increase of mitochondrial density and respiration as shown with Gl. intraradices. We conclude that strigolactones are important rhizospheric plant signals involved in stimulating both the pre-symbiotic growth of AM fungi and the germination of parasitic plants.

  11. Taxon-specific PCR primers to detect two inconspicuous arbuscular mycorrhizal fungi from temperate agricultural grassland

    NARCIS (Netherlands)

    Gamper, H.A.; Leuchtmann, A.

    2007-01-01

    Taxon-specific polymerase chain reaction (PCR) primers enable detection of arbuscular mycorrhizal fungi (AMF, Glomeromycota) in plant roots where the fungi lack discriminative morphological and biochemical characters. We designed and validated pairs of new PCR primers targeted to the flanking

  12. Design of a species-specific PCR method for the detection of the heat-resistant fungi Talaromyces macrosporus and Talaromyces trachyspermus.

    Science.gov (United States)

    Yamashita, S; Nakagawa, H; Sakaguchi, T; Arima, T-H; Kikoku, Y

    2018-01-01

    Heat-resistant fungi occur sporadically and are a continuing problem for the food and beverage industry. The genus Talaromyces, as a typical fungus, is capable of producing the heat-resistant ascospores responsible for the spoilage of processed food products. Isocitrate lyase, a signature enzyme of the glyoxylate cycle, is required for the metabolism of non-fermentable carbon compounds, like acetate and ethanol. Here, species-specific primer sets for detection and identification of DNA derived from Talaromyces macrosporus and Talaromyces trachyspermus were designed based on the nucleotide sequences of their isocitrate lyase genes. Polymerase chain reaction (PCR) using a species-specific primer set amplified products specific to T. macrosporus and T. trachyspermus. Other fungal species, such as Byssochlamys fulva and Hamigera striata, which cause food spoilage, were not detected using the Talaromyces-specific primer sets. The detection limit for each species-specific primer set was determined as being 50 pg of template DNA, without using a nested PCR method. The specificity of each species-specific primer set was maintained in the presence of 1,000-fold amounts of genomic DNA from other fungi. The method also detected fungal DNA extracted from blueberry inoculated with T. macrosporus. This PCR method provides a quick, simple, powerful and reliable way to detect T. macrosporus and T. trachyspermus. Polymerase chain reaction (PCR)-based detection is rapid, convenient and sensitive compared with traditional methods of detecting heat-resistant fungi. In this study, a PCR-based method was developed for the detection and identification of amplification products from Talaromyces macrosporus and Talaromyces trachyspermus using primer sets that target the isocitrate lyase gene. This method could be used for the on-site detection of T. macrosporus and T. trachyspermus in the near future, and will be helpful in the safety control of raw materials and in food and beverage

  13. Rapid deployment intrusion detection system

    International Nuclear Information System (INIS)

    Graham, R.H.

    1997-01-01

    A rapidly deployable security system is one that provides intrusion detection, assessment, communications, and annunciation capabilities; is easy to install and configure; can be rapidly deployed, and is reusable. A rapidly deployable intrusion detection system (RADIDS) has many potential applications within the DOE Complex: back-up protection for failed zones in a perimeter intrusion detection and assessment system, intrusion detection and assessment capabilities in temporary locations, protection of assets during Complex reconfiguration, and protection in hazardous locations, protection of assets during Complex reconfiguration, and protection in hazardous locations. Many DOE user-need documents have indicated an interest in a rapidly deployable intrusion detection system. The purpose of the RADIDS project is to design, develop, and implement such a system. 2 figs

  14. Addition of Carbon to the Culture Medium Improves the Detection Efficiency of Aflatoxin Synthetic Fungi

    Directory of Open Access Journals (Sweden)

    Tadahiro Suzuki

    2016-11-01

    Full Text Available Aflatoxin (AF is a harmful secondary metabolite that is synthesized by the Aspergillus species. Although AF detection techniques have been developed, techniques for detection of AF synthetic fungi are still required. Techniques such as plate culture methods are continually being modified for this purpose. However, plate culture methods require refinement because they suffer from several issues. In this study, activated charcoal powder (carbon was added to a culture medium containing cyclodextrin (CD to enhance the contrast of fluorescence and improve the detection efficiency for AF synthetic fungi. Two culture media, potato dextrose agar and yeast extract sucrose agar, were investigated using both plate and liquid cultures. The final concentrations of CD and carbon in the media were 3 mg/mL and 0.3 mg/mL, respectively. Addition of carbon improved the visibility of fluorescence by attenuating approximately 30% of light scattering. Several fungi that could not be detected with only CD in the medium were detected with carbon addition. The carbon also facilitated fungal growth in the potato dextrose liquid medium. The results suggest that addition of carbon to media can enhance the observation of AF-derived fluorescence.

  15. Use of Selective Fungal Culture Media Increases Rates of Detection of Fungi in the Respiratory Tract of Cystic Fibrosis Patients.

    Science.gov (United States)

    Hong, Gina; Miller, Heather B; Allgood, Sarah; Lee, Richard; Lechtzin, Noah; Zhang, Sean X

    2017-04-01

    The prevalence of fungi in the respiratory tracts of cystic fibrosis (CF) patients has risen. However, fungal surveillance is not routinely performed in most clinical centers in the United States, which may lead to an underestimation of the true prevalence of the problem. We conducted a prospective study comparing the rates of detection for clinically important fungi (CIF), defined as Aspergillus , Scedosporium , and Trichosporon species and Exophiala dermatitidis , in CF sputa using standard bacterial and selective fungal culture media, including Sabouraud dextrose agar with gentamicin (SDA), inhibitory mold agar (IMA), and brain heart infusion (BHI) agar with chloramphenicol and gentamicin. We described the prevalence of these fungi in an adult CF population. A total of 487 CF respiratory samples were collected from 211 unique participants. CIF were detected in 184 (37.8%) samples. Only 26.1% of CIF-positive samples were detected in bacterial culture medium, whereas greater rates of detection for fungi were found in IMA (65.8%; P culture media and longer incubation periods yielded higher rates of detection for CIF in CF sputum samples compared with that detected in bacterial culture medium, resulting in an underdetection of fungi by bacterial culture alone. The prevalence of fungi in CF may be better estimated by using selective fungal culture media, and this may translate to important clinical decisions. Copyright © 2017 American Society for Microbiology.

  16. Rapid extraction of genomic DNA from medically important yeasts and filamentous fungi by high-speed cell disruption.

    Science.gov (United States)

    Müller, F M; Werner, K E; Kasai, M; Francesconi, A; Chanock, S J; Walsh, T J

    1998-06-01

    Current methods of DNA extraction from different fungal pathogens are often time-consuming and require the use of toxic chemicals. DNA isolation from some fungal organisms is difficult due to cell walls or capsules that are not readily susceptible to lysis. We therefore investigated a new and rapid DNA isolation method using high-speed cell disruption (HSCD) incorporating chaotropic reagents and lysing matrices in comparison to standard phenol-chloroform (PC) extraction protocols for isolation of DNA from three medically important yeasts (Candida albicans, Cryptococcus neoformans, and Trichosporon beigelii) and two filamentous fungi (Aspergillus fumigatus and Fusarium solani). Additional extractions by HSCD were performed on Saccharomyces cerevisiae, Pseudallescheria boydii, and Rhizopus arrhizus. Two different inocula (10(8) and 10(7) CFU) were compared for optimization of obtained yields. The entire extraction procedure was performed on as many as 12 samples within 1 h compared to 6 h for PC extraction. In comparison to the PC procedure, HSCD DNA extraction demonstrated significantly greater yields for 10(8) CFU of C. albicans, T. beigelii, A. fumigatus, and F. solani (P extraction and PC extraction. For 10(7) CFU of T. beigelii, PC extraction resulted in a greater yield than did HSCD (P fungi than for yeasts by the HSCD extraction procedure (P extraction procedure, differences were not significant. For all eight organisms, the rapid extraction procedure resulted in good yield, integrity, and quality of DNA as demonstrated by restriction fragment length polymorphism, PCR, and random amplified polymorphic DNA. We conclude that mechanical disruption of fungal cells by HSCD is a safe, rapid, and efficient procedure for extracting genomic DNA from medically important yeasts and especially from filamentous fungi.

  17. Identification of aflatoxigenic fungi using polymerase chain reaction-based assay

    Directory of Open Access Journals (Sweden)

    Šošo Vladislava M.

    2014-01-01

    Full Text Available As the aflatoxins represent a health-risk for humans because of their proven carcinogenicity, food-borne fungi that produce them as secondary metabolites, mainly Aspergillus flavus and Aspergillus parasiticus, have to be isolated and identified. The best argument for identifying problem fungi is that it indicates control points within the food system as part of a hazard analysis critical control point (HACCP approach. This assumes there is a close link between fungus and toxin. Conventional methods for isolation and identification of fungi are time consuming and require admirably dedicated taxonomists. Hence, it is imperative to develop methodologies that are relatively rapid, highly specific and as an alternative to the existing methods. The polymerase chain reaction (PCR facilitates the in vitro amplification of the target sequence. The main advantages of PCR is that organisms need not be cultured, at least not for a long time, prior to their detection, target DNA can be detected even in a complex mixture, no radioactive probes are required, it is rapid, sensitive and highly versatile. The gene afl-2 has been isolated and shown to regulate aflatoxin biosynthesis in A. flavus. Also, the PCR reaction was targeted against aflatoxin synthesis regulatory gene (aflR1 since these genes are nearly identical in A. flavus and A. parasiticus in order to indicate the possibility of detection of both the species with the same PCR system (primers/reaction. [Projekat Ministarstva nauke Republike Srbije, br. III46009

  18. DNA extraction method for PCR in mycorrhizal fungi.

    Science.gov (United States)

    Manian, S; Sreenivasaprasad, S; Mills, P R

    2001-10-01

    To develop a simple and rapid DNA extraction protocol for PCR in mycorrhizal fungi. The protocol combines the application of rapid freezing and boiling cycles and passage of the extracts through DNA purification columns. PCR amplifiable DNA was obtained from a number of endo- and ecto-mycorrhizal fungi using minute quantities of spores and mycelium, respectively. DNA extracted following the method, was used to successfully amplify regions of interest from high as well as low copy number genes. The amplicons were suitable for further downstream applications such as sequencing and PCR-RFLPs. The protocol described is simple, short and facilitates rapid isolation of PCR amplifiable genomic DNA from a large number of fungal isolates in a single day. The method requires only minute quantities of starting material and is suitable for mycorrhizal fungi as well as a range of other fungi.

  19. Detection of airborne psychrotrophic bacteria and fungi in food storage refrigerators

    Directory of Open Access Journals (Sweden)

    Sema Sandikci Altunatmaz

    2012-12-01

    Full Text Available The purpose of this study was to determine the microbiological air quality (psychrotrophic bacteria and airborne fungi and distribution of fungi in different types of ready-to-eat (RTE food-storage refrigerators (n=48 at selected retail stores in the city of Edirne, Turkey. Refrigerators were categorized according to the type of RTE food-storage: meat products, vegetables, desserts, or a mix of food types. Microbiological quality of air samples was evaluated by using a Mas-100 Eco Air Sampler. Four refrigerators (all containing meat products, 8.3% produced air samples with undetectable microorganisms. The highest detected mean value of airborne psychrotrophic bacteria and fungi was 82.3 CFU/m³ and 54.6 CFU/m³, respectively and were found in mixed-food refrigerators. The dominant airborne fungal genera found were Penicillium (29.0%, Aspergillus (12.0%, Mucor (9%, Cladosporium (8%, Botyrtis (7%, and Acremonium (6%. By definition, RTE food does not undergo a final treatment to ensure its safety prior to consumption. Therefore, ensuring a clean storage environment for these foods is important to prevent food-borne disease and other health risks.

  20. Acridine Orange Indicates Early Oxidation of Wood Cell Walls by Fungi

    Science.gov (United States)

    Carl J. Houtman; Peter Kitin; Jon C. D. Houtman; Kenneth E. Hammel; Christopher G. Hunt

    2016-01-01

    Colonization of wood blocks by brown and white rot fungi rapidly resulted in detectable wood oxidation, as shown by a reduced phloroglucinol response, a loss of autofluorescence, and acridine orange (AO) staining. This last approach is shown to provide a novel method for identifying wood oxidation. When lignin was mildly oxidized, the association between AO and lignin...

  1. Method for rapid detection and identification of chaetomium and evaluation of resistance to peracetic acid.

    Science.gov (United States)

    Nakayama, Motokazu; Hosoya, Kouichi; Tomiyama, Daisuke; Tsugukuni, Takashi; Matsuzawa, Tetsuhiro; Imanishi, Yumi; Yaguchi, Takashi

    2013-06-01

    In the beverage industry, peracetic acid has been increasingly used as a disinfectant for the filling machinery and environment due to merits of leaving no residue, it is safe for humans, and its antiseptic effect against fungi and endospores of bacteria. Recently, Chaetomium globosum and Chaetomium funicola were reported resistant to peracetic acid; however, little is known concerning the detail of peracetic acid resistance. Therefore, we assessed the peracetic acid resistance of the species of Chaetomium and related genera under identical conditions and made a thorough observation of the microstructure of their ascospores by transmission electron microscopy. The results of analyses revealed that C. globosum and C. funicola showed the high resistance to peracetic acid (a 1-D antiseptic effect after 900 s and 3-D antiseptic effect after 900 s) and had thick cell walls of ascospores that can impede the action mechanism of peracetic acid. We also developed specific primers to detect the C. globosum clade and identify C. funicola by using PCR to amplify the β-tubulin gene. PCR with the primer sets designed for C. globosum (Chae 4F/4R) and C. funicola (Cfu 2F/2R) amplified PCR products specific for the C. globosum clade and C. funicola, respectively. PCR with these two primer sets did not detect other fungi involved in food spoilage and environmental contamination. This detection and identification method is rapid and simple, with extremely high specificity.

  2. Bioconversion of dieldrin by wood-rotting fungi and metabolite detection.

    Science.gov (United States)

    Kamei, Ichiro; Takagi, Kazuhiro; Kondo, Ryuichiro

    2010-08-01

    Dieldrin is one of the most persistent organochlorine pesticides, listed as one of the 12 persistent organic pollutants in the Stockholm Convention. Although microbial degradation is an effective way to remediate environmental pollutants, reports on aerobic microbial degradation of dieldrin are limited. Wood-rotting fungi can degrade a wide spectrum of recalcitrant organopollutants, and an attempt has been made to select wood-rotting fungi that can degrade dieldrin, and to identify the metabolite. Thirty-four isolates of wood-rotting fungi were investigated for their ability to degrade dieldrin. Strain YK543 degraded 39.1 +/- 8.8% of dieldrin during 30 days of incubation. Phylogenetic analysis demonstrated that strain YK543 was closely related to the fungus Phlebia brevispora Nakasone TMIC33929, which has been reported as a fungus that can degrade chlorinated dioxins and polychlorinated biphenyls. 9-Hydroxydieldrin was detected as a metabolite in the cultures of strain YK543. It is important to select the microorganisms that degrade organic pollutants, and to identify the metabolic pathway for the development of bioremediation methods. Strain YK543 was selected as a fungus capable of degrading dieldrin. The metabolic pathway includes 9-hydroxylation reported in rat's metabolism catalysed by liver microsomal monooxygenase. This is the first report of transformation of dieldrin to 9-hydroxydieldrin by a microorganism. Copyright (c) 2010 Society of Chemical Industry.

  3. Nematode-Trapping Fungi.

    Science.gov (United States)

    Jiang, Xiangzhi; Xiang, Meichun; Liu, Xingzhong

    2017-01-01

    Nematode-trapping fungi are a unique and intriguing group of carnivorous microorganisms that can trap and digest nematodes by means of specialized trapping structures. They can develop diverse trapping devices, such as adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and nonconstricting rings. Nematode-trapping fungi have been found in all regions of the world, from the tropics to Antarctica, from terrestrial to aquatic ecosystems. They play an important ecological role in regulating nematode dynamics in soil. Molecular phylogenetic studies have shown that the majority of nematode-trapping fungi belong to a monophyletic group in the order Orbiliales (Ascomycota). Nematode-trapping fungi serve as an excellent model system for understanding fungal evolution and interaction between fungi and nematodes. With the development of molecular techniques and genome sequencing, their evolutionary origins and divergence, and the mechanisms underlying fungus-nematode interactions have been well studied. In recent decades, an increasing concern about the environmental hazards of using chemical nematicides has led to the application of these biological control agents as a rapidly developing component of crop protection.

  4. Impedimetric method for physiologically characterisation of fungi

    DEFF Research Database (Denmark)

    Nielsen, Per Væggemose; Petersen, Karina

    1998-01-01

    Fungi are playing an important role in the food and pharmaceutical industry today, both as starter cultures, fermentation organisms, and as contaminants. Characterisation of fungal growth is normally time consuming as it includes measurements and study on a wide range of media at different...... temperatures, pH, water activity and atmosphere composition. Nevertheless is it important information in ecophysiological studies, where the growth potential by fungi are related to composition and storage of food. It is therefore of great interest to device a rapid method for characterisation of fungi.......The objective was to determine the growth phases of various fungi using an impedimetric method and compare this with traditional methods using agar plates, in order to determine if this rapid method can replace the traditional method.The method is based on impedimetric assessment of growth on the Bactometer 128...

  5. Rapid methods for detection of bacteria

    DEFF Research Database (Denmark)

    Corfitzen, Charlotte B.; Andersen, B.Ø.; Miller, M.

    2006-01-01

    Traditional methods for detection of bacteria in drinking water e.g. Heterotrophic Plate Counts (HPC) or Most Probable Number (MNP) take 48-72 hours to give the result. New rapid methods for detection of bacteria are needed to protect the consumers against contaminations. Two rapid methods...

  6. Advances in Genomics of Entomopathogenic Fungi.

    Science.gov (United States)

    Wang, J B; St Leger, R J; Wang, C

    2016-01-01

    Fungi are the commonest pathogens of insects and crucial regulators of insect populations. The rapid advance of genome technologies has revolutionized our understanding of entomopathogenic fungi with multiple Metarhizium spp. sequenced, as well as Beauveria bassiana, Cordyceps militaris, and Ophiocordyceps sinensis among others. Phylogenomic analysis suggests that the ancestors of many of these fungi were plant endophytes or pathogens, with entomopathogenicity being an acquired characteristic. These fungi now occupy a wide range of habitats and hosts, and their genomes have provided a wealth of information on the evolution of virulence-related characteristics, as well as the protein families and genomic structure associated with ecological and econutritional heterogeneity, genome evolution, and host range diversification. In particular, their evolutionary transition from plant pathogens or endophytes to insect pathogens provides a novel perspective on how new functional mechanisms important for host switching and virulence are acquired. Importantly, genomic resources have helped make entomopathogenic fungi ideal model systems for answering basic questions in parasitology, entomology, and speciation. At the same time, identifying the selective forces that act upon entomopathogen fitness traits could underpin both the development of new mycoinsecticides and further our understanding of the natural roles of these fungi in nature. These roles frequently include mutualistic relationships with plants. Genomics has also facilitated the rapid identification of genes encoding biologically useful molecules, with implications for the development of pharmaceuticals and the use of these fungi as bioreactors. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Species-specific optical genosensors for the detection of mycotoxigenic Fusarium fungi in food samples

    International Nuclear Information System (INIS)

    Peltomaa, Riikka; Vaghini, Silvia; Patiño, Belén; Benito-Peña, Elena; Moreno-Bondi, María C.

    2016-01-01

    Plant-pathogenic Fusarium species, Fusarium verticillioides and Fusarium proliferatum, are the major producers of fumonisins which are one of the most common mycotoxins found in maize. Herein, we report the development of specific and sensitive genosensors for detecting these two closely related Fusarium species in food samples. The sensors are based on species-specific capture and detection probes, which bind to the intergenic spacer region of rDNA (IGS). Oligonucleotide functionalized magnetic microbeads are used to capture the target DNA which is then detected using biotinylated detection probes and a streptavidin-coupled label. The developed genosensors had detection limits of 1.8 pM and 3.0 pM for F. proliferatum and F. verticillioides, respectively, using synthetic DNA targets. Furthermore, the biosensors were used to analyze natural fungal contamination of commercial maize samples. After amplification of the genomic DNA the sensors detected the presence of the fungi, in accordance with previous results obtained with PCR. No cross-reactivity between F. verticillioides and F. proliferatum, or other fungi species tested, was observed. The developed biosensors can provide a valuable tool to evaluate the potential for mycotoxin contamination in conditions where detection of mycotoxins directly is challenging. - Highlights: • Optical genosensors detect fumonisin producing Fusarium species in maize samples. • Oligonucleotide probes designed on the intergenic spacer region of rDNA can distinguish between closely related species. • Sandwich hybridization assay with magnetic microbeads allows species-specific detection of Fusarium spp. directly from PCR.

  8. Species-specific optical genosensors for the detection of mycotoxigenic Fusarium fungi in food samples

    Energy Technology Data Exchange (ETDEWEB)

    Peltomaa, Riikka; Vaghini, Silvia [Department of Analytical Chemistry, Faculty of Chemistry, Complutense University, Ciudad Universitaria s/n, Madrid 28040 (Spain); Patiño, Belén [Department of Microbiology III, Faculty of Biology, Complutense University, Ciudad Universitaria s/n, Madrid 28040 (Spain); Benito-Peña, Elena, E-mail: elenabp@ucm.es [Department of Analytical Chemistry, Faculty of Chemistry, Complutense University, Ciudad Universitaria s/n, Madrid 28040 (Spain); Moreno-Bondi, María C., E-mail: mcmbondi@ucm.es [Department of Analytical Chemistry, Faculty of Chemistry, Complutense University, Ciudad Universitaria s/n, Madrid 28040 (Spain)

    2016-09-07

    Plant-pathogenic Fusarium species, Fusarium verticillioides and Fusarium proliferatum, are the major producers of fumonisins which are one of the most common mycotoxins found in maize. Herein, we report the development of specific and sensitive genosensors for detecting these two closely related Fusarium species in food samples. The sensors are based on species-specific capture and detection probes, which bind to the intergenic spacer region of rDNA (IGS). Oligonucleotide functionalized magnetic microbeads are used to capture the target DNA which is then detected using biotinylated detection probes and a streptavidin-coupled label. The developed genosensors had detection limits of 1.8 pM and 3.0 pM for F. proliferatum and F. verticillioides, respectively, using synthetic DNA targets. Furthermore, the biosensors were used to analyze natural fungal contamination of commercial maize samples. After amplification of the genomic DNA the sensors detected the presence of the fungi, in accordance with previous results obtained with PCR. No cross-reactivity between F. verticillioides and F. proliferatum, or other fungi species tested, was observed. The developed biosensors can provide a valuable tool to evaluate the potential for mycotoxin contamination in conditions where detection of mycotoxins directly is challenging. - Highlights: • Optical genosensors detect fumonisin producing Fusarium species in maize samples. • Oligonucleotide probes designed on the intergenic spacer region of rDNA can distinguish between closely related species. • Sandwich hybridization assay with magnetic microbeads allows species-specific detection of Fusarium spp. directly from PCR.

  9. Molecular identification of fungi trichothecens producing in seeds madder and detection of their nivalenol gene synthesis using PCR

    Directory of Open Access Journals (Sweden)

    Seyyed Alireza Esmailzadeh Hosseini

    2018-01-01

    Full Text Available Madder is one of the most important crops that used for medical and industrial applications and is widely cultivated in Yazd province. During 2012, sampling was done form seeds madder in important areas planted in Yazd province, including Bafq and Ardakan. After culturing and purification of fungal isolates in PDA and CLA media, additional identification was performed by PCR with specific primers for each species. Detection of fungi mycotoxins producing potential such as Nivalenol (NIV using Tri13 primers was done. High-performance liquid chromatography (HPLC was used to confirm the produce NIV mycotoxins potential in Fusarium species. 249 fungal strains were isolated from madder seed belonging to 6 genera of fungi including Fusarium spp., Aspergillus spp., Penicillium spp., Alternaria spp., Rhizoctonia solani and Rhizpous spp., that Fusarium isolates with 71 percent was the most frequency among fungi isolated. Among Fusarium fungi isolated, F. solani (55 isolates and F. oxysporum (41 isolates were the most frequency. F. poae, F. semitectum and F. equiseti ability to produce mycotoxins such as Nivalenol (NIV that are harmful to human health and animals as well as effect on the quantity and quality of madder color production. Tri13 gene involved in production NIV was detected in three Fusarium species that all isolates produce NIV. The results of HPLC showed that all studied Fusarium fungi, have the potential to produce NIV mycotoxins. The results of this study showed that fungi associated with seeds madder are able to produce trichothecene mycotoxins that they can be dangerous for consumers. Given that, this is the first report of fungi mycotoxins producing on seeds madder in Yazd province, thus should be measures to control and reduce fungal agents in these products.

  10. Fourier Transform Infrared Radiation Spectroscopy Applied for Wood Rot Decay and Mould Fungi Growth Detection

    Directory of Open Access Journals (Sweden)

    Bjørn Petter Jelle

    2012-01-01

    Full Text Available Material characterization may be carried out by the attenuated total reflectance (ATR Fourier transform infrared (FTIR radiation spectroscopical technique, which represents a powerful experimental tool. The ATR technique may be applied on both solid state materials, liquids, and gases with none or only minor sample preparations, also including materials which are nontransparent to IR radiation. This facilitation is made possible by pressing the sample directly onto various crystals, for example, diamond, with high refractive indices, in a special reflectance setup. Thus ATR saves time and enables the study of materials in a pristine condition, that is, the comprehensive sample preparation by pressing thin KBr pellets in traditional FTIR transmittance spectroscopy is hence avoided. Materials and their ageing processes, both ageing by natural and accelerated climate exposure, decomposition and formation of chemical bonds and products, may be studied in an ATR-FTIR analysis. In this work, the ATR-FTIR technique is utilized to detect wood rot decay and mould fungi growth on various building material substrates. An experimental challenge and aim is to be able to detect the wood rot decay and mould fungi growth at early stages when it is barely visible to the naked eye. Another goal is to be able to distinguish between various species of fungi and wood rot.

  11. Detection of fungi colony growth on bones by dynamic speckle

    Science.gov (United States)

    Vincitorio, F. M.; Budini, N.; Mulone, C.; Spector, M.; Freyre, C.; López Díaz, A. J.; Ramil, A.

    2013-11-01

    In this work we have studied the dynamic speckle patterns of mucor fungi colonies, which were inoculated on different samples. We were interested in analyzing the development of fungi colonies in bones, since during the last two years, a series of infections by mucor fungi have been reported on patients from different hospitals in Argentina. Coincidentally, all of these infections appeared on patients that were subjected to a surgical intervention for implantation of a titanium prosthesis. Apparently, the reason of the infection was a deficient sterilization process in conjunction with an accidental contamination. We observed that fungi growth, activity and death can be distinguished by means of the dynamic speckle technique.

  12. Thermophilic Fungi to Dominate Aflatoxigenic/Mycotoxigenic Fungi on Food under Global Warming.

    Science.gov (United States)

    Paterson, Robert Russell M; Lima, Nelson

    2017-02-17

    Certain filamentous fungi produce mycotoxins that contaminate food. Mycotoxin contamination of crops is highly influenced by environmental conditions and is already affected by global warming, where there is a succession of mycotoxigenic fungi towards those that have higher optimal growth temperatures. Aflatoxigenic fungi are at the highest limit of temperature although predicted increases in temperature are beyond that constraint. The present paper discusses what will succeed these fungi and represents the first such consideration. Aflatoxins are the most important mycotoxins and are common in tropical produce, much of which is exported to temperate regions. Hot countries may produce safer food under climate change because aflatoxigenic fungi will be inhibited. The same situation will occur in previously temperate regions where these fungi have recently appeared, although decades later. Existing thermotolerant and thermophilic fungi (TTF) will dominate, in contrast to the conventional mycotoxigenic fungi adapting or mutating, as it will be quicker. TTF produce a range of secondary metabolites, or potential mycotoxins and patulin which may become a new threat. In addition, Aspergillus fumigatus will appear more frequently, a serious human pathogen, because it is (a) thermotolerant and (b) present on crops: hence this is an even greater problem. An incubation temperature of 41 °C needs employing forthwith to detect TTF. Finally, TTF in crops requires study because of the potential for diseases in humans and animals under climate change.

  13. New strategy for rapid diagnosis and characterization of fungal infections: the example of corneal scrapings.

    Directory of Open Access Journals (Sweden)

    Pablo Goldschmidt

    Full Text Available PURPOSE: The prognosis of people infected with Fungi especially immunocompromised depends on rapid and accurate diagnosis to capitalize on time administration of specific treatments. However, cultures produce false negative results and nucleic-acid amplification techniques require complex post-amplification procedures to differentiate relevant fungal types. The objective of this work was to develop a new diagnostic strategy based on real-time polymerase-chain reaction high-resolution melting analysis (PCR-HRM that a detects yeasts and filamentous Fungi, b differentiates yeasts from filamentous Fungi, and c discriminates among relevant species of yeasts. METHODS: PCR-HRM detection limits and specificity were assessed with a isolated strains; b human blood samples experimentally infected with Fungi; c blood experimentally infected with other infectious agents; d corneal scrapings from patients with suspected fungal keratitis (culture positive and negative and e scrapings from patients with suspected bacterial, viral or Acanthamoeba infections. The DNAs were extracted and mixed with primers diluted in the MeltDoctor® HRM Master Mix in 2 tubes, the first for yeasts, containing the forward primer CandUn (5'CATGCCTGTTTGAGCGTC and the reverse primer FungUn (5'TCCTCCGCTT ATTGATATGCT and the second for filamentous Fungi, containing the forward primer FilamUn (5'TGCCTGTCCGAGCGTCAT and FungUn. Molecular probes were not necessary. The yields of DNA extraction and the PCR inhibitors were systematically monitored. RESULTS: PCR-HRM detected 0.1 Colony Forming Units (CFU/µl of yeasts and filamentous Fungi, differentiated filamentous Fungi from yeasts and discriminated among relevant species of yeasts. PCR-HRM performances were higher than haemoculture and sensitivity and specificity was 100% for culture positive samples, detecting and characterizing Fungi in 7 out 10 culture negative suspected fungal keratitis. CONCLUSIONS: PCR-HRM appears as a new, sensitive

  14. A multiplex PCR-based method for the detection and early identification of wood rotting fungi in standing trees.

    Science.gov (United States)

    Guglielmo, F; Bergemann, S E; Gonthier, P; Nicolotti, G; Garbelotto, M

    2007-11-01

    The goal of this research was the development of a PCR-based assay to identify important decay fungi from wood of hardwood tree species in northern temperate regions. Eleven taxon-specific primers were designed for PCR amplification of either nuclear or mitochondrial ribosomal DNA regions of Armillaria spp., Ganoderma spp., Hericium spp., Hypoxylon thouarsianum var. thouarsianum, Inonotus/Phellinus-group, Laetiporus spp., Perenniporia fraxinea, Pleurotus spp., Schizophyllum spp., Stereum spp. and Trametes spp. Multiplex PCR reactions were developed and optimized to detect fungal DNA and identify each taxon with a sensitivity of at least 1 pg of target DNA in the template. This assay correctly identified the agents of decay in 82% of tested wood samples. The development and optimization of multiplex PCRs allowed for reliable identification of wood rotting fungi directly from wood. Early detection of wood decay fungi is crucial for assessment of tree stability in urban landscapes. Furthermore, this method may prove useful for prediction of the severity and the evolution of decay in standing trees.

  15. Thermophilic Fungi to Dominate Aflatoxigenic/Mycotoxigenic Fungi on Food under Global Warming

    Directory of Open Access Journals (Sweden)

    Robert Russell M. Paterson

    2017-02-01

    Full Text Available Certain filamentous fungi produce mycotoxins that contaminate food. Mycotoxin contamination of crops is highly influenced by environmental conditions and is already affected by global warming, where there is a succession of mycotoxigenic fungi towards those that have higher optimal growth temperatures. Aflatoxigenic fungi are at the highest limit of temperature although predicted increases in temperature are beyond that constraint. The present paper discusses what will succeed these fungi and represents the first such consideration. Aflatoxins are the most important mycotoxins and are common in tropical produce, much of which is exported to temperate regions. Hot countries may produce safer food under climate change because aflatoxigenic fungi will be inhibited. The same situation will occur in previously temperate regions where these fungi have recently appeared, although decades later. Existing thermotolerant and thermophilic fungi (TTF will dominate, in contrast to the conventional mycotoxigenic fungi adapting or mutating, as it will be quicker. TTF produce a range of secondary metabolites, or potential mycotoxins and patulin which may become a new threat. In addition, Aspergillus fumigatus will appear more frequently, a serious human pathogen, because it is (a thermotolerant and (b present on crops: hence this is an even greater problem. An incubation temperature of 41 °C needs employing forthwith to detect TTF. Finally, TTF in crops requires study because of the potential for diseases in humans and animals under climate change.

  16. Phylogenetic diversity of culturable endophytic fungi in Dongxiang wild rice (Oryza rufipogon Griff), detection of polyketide synthase gene and their antagonistic activity analysis.

    Science.gov (United States)

    Wang, Ya; Gao, Bo Liang; Li, Xi Xi; Zhang, Zhi Bin; Yan, Ri Ming; Yang, Hui Lin; Zhu, Du

    2015-11-01

    The biodiversity of plant endophytic fungi is enormous, numerous competent endophytic fungi are capable of providing different forms of fitness benefits to host plants and also could produce a wide array of bioactive natural products, which make them a largely unexplored source of novel compounds with potential bioactivity. In this study, we provided a first insights into revealing the diversity of culturable endophytic fungi in Dongxiang wild rice (Oryza rufipogon Griff.) from China using rDNA-ITS phylogenetic analysis. Here, the potential of fungi in producing bioactive natural products was estimated based on the beta-ketosynthase detected in the polyketide synthase (PKS) gene cluster and on the bioassay of antagonistic activity against two rice phytopathogens Thanatephorus cucumeris and Xanthomonas oryzae. A total of 229 endophytic fungal strains were validated in 19 genera. Among the 24 representative strains, 13 strains displayedantagonistic activity against the phytopathogens. Furthermore, PKS genes were detected in 9 strains, indicating their potential for synthesising PKS compounds. Our study confirms the phylogenetic diversity of endophytic fungi in O. rufipogon G. and highlights that endophytic fungi are not only promising resources of biocontrol agents against phytopathogens of rice plants, but also of bioactive natural products and defensive secondary metabolites. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  17. Phylogenetic congruence between subtropical trees and their associated fungi

    NARCIS (Netherlands)

    Liu, Xubing; Liang, Minxia; Etienne, Rampal S.; Gilbert, Gregory S; Yu, Shixiao

    2016-01-01

    Recent studies have detected phylogenetic signals in pathogen-host networks for both soil-borne and leaf-infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi

  18. Nanomaterial-enabled Rapid Detection of Water Contaminants.

    Science.gov (United States)

    Mao, Shun; Chang, Jingbo; Zhou, Guihua; Chen, Junhong

    2015-10-28

    Water contaminants, e.g., inorganic chemicals and microorganisms, are critical metrics for water quality monitoring and have significant impacts on human health and plants/organisms living in water. The scope and focus of this review is nanomaterial-based optical, electronic, and electrochemical sensors for rapid detection of water contaminants, e.g., heavy metals, anions, and bacteria. These contaminants are commonly found in different water systems. The importance of water quality monitoring and control demands significant advancement in the detection of contaminants in water because current sensing technologies for water contaminants have limitations. The advantages of nanomaterial-based sensing technologies are highlighted and recent progress on nanomaterial-based sensors for rapid water contaminant detection is discussed. An outlook for future research into this rapidly growing field is also provided. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Eukaryote-Made Thermostable DNA Polymerase Enables Rapid PCR-Based Detection of Mycoplasma, Ureaplasma and Other Bacteria in the Amniotic Fluid of Preterm Labor Cases.

    Science.gov (United States)

    Ueno, Tomohiro; Niimi, Hideki; Yoneda, Noriko; Yoneda, Satoshi; Mori, Masashi; Tabata, Homare; Minami, Hiroshi; Saito, Shigeru; Kitajima, Isao

    2015-01-01

    Intra-amniotic infection has long been recognized as the leading cause of preterm delivery. Microbial culture is the gold standard for the detection of intra-amniotic infection, but several days are required, and many bacterial species in the amniotic fluid are difficult to cultivate. We developed a novel nested-PCR-based assay for detecting Mycoplasma, Ureaplasma, other bacteria and fungi in amniotic fluid samples within three hours of sample collection. To detect prokaryotes, eukaryote-made thermostable DNA polymerase, which is free from bacterial DNA contamination, is used in combination with bacterial universal primers. In contrast, to detect eukaryotes, conventional bacterially-made thermostable DNA polymerase is used in combination with fungal universal primers. To assess the validity of the PCR assay, we compared the PCR and conventional culture results using 300 amniotic fluid samples. Based on the detection level (positive and negative), 93.3% (280/300) of Mycoplasma, 94.3% (283/300) of Ureaplasma, 89.3% (268/300) of other bacteria and 99.7% (299/300) of fungi matched the culture results. Meanwhile, concerning the detection of bacteria other than Mycoplasma and Ureaplasma, 228 samples were negative according to the PCR method, 98.2% (224/228) of which were also negative based on the culture method. Employing the devised primer sets, mixed amniotic fluid infections of Mycoplasma, Ureaplasma and/or other bacteria could be clearly distinguished. In addition, we also attempted to compare the relative abundance in 28 amniotic fluid samples with mixed infection, and judged dominance by comparing the Ct values of quantitative real-time PCR. We developed a novel PCR assay for the rapid detection of Mycoplasma, Ureaplasma, other bacteria and fungi in amniotic fluid samples. This assay can also be applied to accurately diagnose the absence of bacteria in samples. We believe that this assay will positively contribute to the treatment of intra-amniotic infection and

  20. Human exposure to airborne fungi from genera used as biocontrol agents in plant production.

    Science.gov (United States)

    Madsen, Anne Mette; Hansen, Vinni Mona; Meyling, Nicolai Vitt; Eilenberg, Jørgen

    2007-01-01

    The fungi Trichoderma harzianum, T. polysporum, T. viride, Paeciliomyces fumosoroseus, P. lilacinus, Verticillium/lecanicillium lecanii, Ulocladium oudemansii, U. atrum and Beauveria bassiana are used or considered to be used for biocontrol of pests and plant diseases. Human exposure to these fungi in environments where they may naturally occur or are used as biocontrol agents has not been directly investigated to date. This review aims to provide an overview of the current knowledge of human exposure to fungi from the relevant genera. The subject of fungal taxonomy due to the rapid development of this issue is also discussed. B. bassiana, V. lecanii, T. harzianum, T. polysporum, P. lilacinus and U. oudemansii were infrequently present in the air and thus people in general seem to be seldom exposed to these fungi. However, when V. lecanii was present, high concentrations were measured. Fungi from the genera Trichoderma, Paecilomyces and Ulocladium were rarely identified to the species level and sometimes high concentrations were reported. T. viride and U. atrum were detected frequently in different environments and sometimes with a high frequency of presence in samples. Thus, people seem to be frequently exposed to these fungi. Sequence data have led to recent revisions of fungal taxonomy, and in future studies it is important to specify the taxonomy used for identification, thus making comparisons possible.

  1. A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae

    OpenAIRE

    Farkhondeh Saba; Moslem Papizadeh; Javad Khansha; Mahshid Sedghi; Mehrnoosh Rasooli; Mohammad Ali Amoozegar; Mohammad Reza Soudi; Seyed Abolhassan Shahzadeh Fazeli

    2016-01-01

    Background:  Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR). Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Me...

  2. Development of Loop-Mediated Isothermal Amplification (LAMP) assay for rapid detection of Fusarium oxysporum f. sp. ciceris - wilt pathogen of chickpea.

    Science.gov (United States)

    Ghosh, Raju; Nagavardhini, Avuthu; Sengupta, Anindita; Sharma, Mamta

    2015-02-11

    Fusarium oxysporum f. sp. ciceris (Foc), the causal agent of Fusarium wilt is a devastating pathogen of chickpea. In chickpea, various soil borne pathogens produce (s) similar symptoms, therefore cannot be distinguished easily at field level. There is real need for a rapid, inexpensive, and easy to operate and maintain genotyping tool to facilitate accurate disease diagnosis and surveillance for better management of Fusarium wilt outbreaks. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay targeting the elongation factor 1 alpha gene sequence for visual detection of Foc. The LAMP reaction was optimal at 63°C for 60 min. When hydroxynaphthol blue (HNB) was added before amplification, samples with Foc DNA developed a characteristic sky blue colour but those without DNA or with the DNA of six other plant pathogenic fungi did not. Results obtained with LAMP and HNB were confirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for Foc was 10 fg of genomic DNA per reaction, while that of conventional PCR was 100 pg. In conclusion, it was found that a LAMP assay combined with HNB is simple, rapid, sensitive, and specific. The LAMP assay does not require specialized equipment, hence can be used in the field for the rapid detection of Foc. This is the first report of the use of LAMP assay for the detection of Foc. The presented LAMP method provides a specific, sensitive and rapid diagnostic tool for the distinction of Foc, with the potential to be standardized as a detection method for Foc in endemic areas and will be very useful for monitoring the disease complex in the field further suggesting the management strategies.

  3. Rapid detection of bacterial contamination in cell or tissue cultures based on Raman spectroscopy

    Science.gov (United States)

    Bolwien, Carsten; Sulz, Gerd; Becker, Sebastian; Thielecke, Hagen; Mertsching, Heike; Koch, Steffen

    2008-02-01

    Monitoring the sterility of cell or tissue cultures is an essential task, particularly in the fields of regenerative medicine and tissue engineering when implanting cells into the human body. We present a system based on a commercially available microscope equipped with a microfluidic cell that prepares the particles found in the solution for analysis, a Raman-spectrometer attachment optimized for non-destructive, rapid recording of Raman spectra, and a data acquisition and analysis tool for identification of the particles. In contrast to conventional sterility testing in which samples are incubated over weeks, our system is able to analyze milliliters of supernatant or cell suspension within hours by filtering relevant particles and placing them on a Raman-friendly substrate in the microfluidic cell. Identification of critical particles via microscopic imaging and subsequent image analysis is carried out before micro-Raman analysis of those particles is then carried out with an excitation wavelength of 785 nm. The potential of this setup is demonstrated by results of artificial contamination of samples with a pool of bacteria, fungi, and spores: single-channel spectra of the critical particles are automatically baseline-corrected without using background data and classified via hierarchical cluster analysis, showing great promise for accurate and rapid detection and identification of contaminants.

  4. Rapid enumeration of low numbers of moulds in tea based drinks using an automated system.

    Science.gov (United States)

    Tanaka, Kouichi; Yamaguchi, Nobuyasu; Baba, Takashi; Amano, Norihide; Nasu, Masao

    2011-01-31

    Aseptically prepared cold drinks based on tea have become popular worldwide. Contamination of these drinks with harmful microbes is a potential health problem because such drinks are kept free from preservatives to maximize aroma and flavour. Heat-tolerant conidia and ascospores of fungi can survive pasteurization, and need to be detected as quickly as possible. We were able to rapidly and accurately detect low numbers of conidia and ascospores in tea-based drinks using fluorescent staining followed by an automated counting system. Conidia or ascospores were inoculated into green tea and oolong tea, and samples were immediately filtered through nitrocellulose membranes (pore size: 0.8 μm) to concentrate fungal propagules. These were transferred onto potato dextrose agar and incubated for 23 h at 28 °C. Fungi germinating on the membranes were fluorescently stained for 30 min. The stained mycelia were counted selectively within 90s using an automated counting system (MGS-10LD; Chuo Electric Works, Osaka, Japan). Very low numbers (1 CFU/100ml) of conidia or ascospores could be rapidly counted, in contrast to traditional labour intensive techniques. All tested mould strains were detected within 24h while conventional plate counting required 72 h for colony enumeration. Counts of slow-growing fungi (Cladosporium cladosporioides) obtained by automated counting and by conventional plate counting were close (r(2) = 0.986). Our combination of methods enables counting of both fast- and slow-growing fungi, and should be useful for microbiological quality control of tea-based and also other drinks. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Filamentous Fungi.

    Science.gov (United States)

    Powers-Fletcher, Margaret V; Kendall, Brian A; Griffin, Allen T; Hanson, Kimberly E

    2016-06-01

    Filamentous mycoses are often associated with significant morbidity and mortality. Prompt diagnosis and aggressive treatment are essential for good clinical outcomes in immunocompromised patients. The host immune response plays an essential role in determining the course of exposure to potential fungal pathogens. Depending on the effectiveness of immune response and the burden of organism exposure, fungi can either be cleared or infection can occur and progress to a potentially fatal invasive disease. Nonspecific cellular immunity (i.e., neutrophils, natural killer [NK] cells, and macrophages) combined with T-cell responses are the main immunologic mechanisms of protection. The most common potential mold pathogens include certain hyaline hyphomycetes, endemic fungi, the Mucorales, and some dematiaceous fungi. Laboratory diagnostics aimed at detecting and differentiating these organisms are crucial to helping clinicians make informed decisions about treatment. The purpose of this chapter is to provide an overview of the medically important fungal pathogens, as well as to discuss the patient characteristics, antifungal-therapy considerations, and laboratory tests used in current clinical practice for the immunocompromised host.

  6. Rapid Detection Strategies for the Global Threat of Zika Virus: Current State, New Hypotheses and Limitations

    Directory of Open Access Journals (Sweden)

    Shruti Shukla

    2016-10-01

    Full Text Available The current scenario regarding the widespread Zika virus (ZIKV has resulted in numerous diagnostic studies, specifically in South America and in locations where there is frequent entry of travelers returning from ZIKV-affected areas, including pregnant women with or without clinical symptoms of ZIKV infection. The World Health Organization, WHO, announced that millions of cases of ZIKV are likely to occur in the United States of America in the near future. This situation has created an alarming public health emergency of international concern requiring the detection of this life-threatening viral candidate due to increased cases of newborn microcephaly associated with ZIKV infection. Hence, this review reports possible methods and strategies for the fast and reliable detection of ZIKV with particular emphasis on current updates, knowledge and new hypotheses that might be helpful for medical professionals in poor and developing countries that urgently need to address this problem. In particular, we emphasize liposome-based biosensors. Although these biosensors are currently among the less popular tools for human disease detection, they have become useful tools for the screening and detection of pathogenic bacteria, fungi and viruses because of their versatile advantageous features compared to other sensing devices. This review summarizes the currently available methods employed for the rapid detection of ZIKV and suggests an innovative approach involving the application of a liposome-based hypothesis for the development of new strategies for ZIKV detection and their use as effective biomedicinal tools.

  7. Evaluating the use of dedicated swab for rapid antigen detection ...

    African Journals Online (AJOL)

    Evaluating the use of dedicated swab for rapid antigen detection testing in group a ... African Journal of Clinical and Experimental Microbiology ... Several generations of rapid antigen detection tests (RADTs) have been developed to facilitate ...

  8. The use of real-time polymerase chain reaction for rapid diagnosis of skeletal tuberculosis.

    Science.gov (United States)

    Kobayashi, Naomi; Fraser, Thomas G; Bauer, Thomas W; Joyce, Michael J; Hall, Gerri S; Tuohy, Marion J; Procop, Gary W

    2006-07-01

    We identified Mycobacterium tuberculosis DNA using real-time polymerase chain reaction on a specimen from an osteolytic lesion of a femoral condyle, in which the frozen section demonstrated granulomas. The process was much more rapid than is possible with culture. The rapid detection of M tuberculosis and the concomitant exclusion of granulomatous disease caused by nontuberculous mycobacteria or systemic fungi are necessary to appropriately treat skeletal tuberculosis. The detection and identification of M tuberculosis by culture may require several weeks using traditional methods. The real-time polymerase chain reaction method used has been shown to be rapid and reliable, and is able to detect and differentiate both tuberculous and nontuberculous mycobacteria. Real-time polymerase chain reaction may become a diagnostic standard for the evaluation of clinical specimens for the presence of mycobacteria; this case demonstrates the potential utility of this assay for the rapid diagnosis of skeletal tuberculosis.

  9. Soil fungi as indicators of pesticide soil pollution

    Directory of Open Access Journals (Sweden)

    Mandić Leka

    2005-01-01

    Full Text Available Soil fungi, with their pronounced enzymic activity and high osmotic potential, represent a significant indicator of negative effects of different pesticides on the agroecosystem as a whole. In that respect, a trial was set up on the alluvium soil type with the aim to investigate the effect of different herbicides (Simazine, Napropamid, Paraquat, fungicides (Captan and Mancozeb and insecticides (Fenitrothion and Dimethoate on a number of soil fungi under apple trees. The number of soil fungi was determined during four growing seasons by an indirect method of dilution addition on the Czapek agar. The study results indicate that the fungi belong to the group of microorganisms that, after an initial sensible response to the presence of pesticides in the soil, very rapidly establish normal metabolism enabling them even to increase their number. The fungicides and insecticides applied were found to be particularly effective in that respect.

  10. Rapid assessment of assignments using plagiarism detection software.

    Science.gov (United States)

    Bischoff, Whitney R; Abrego, Patricia C

    2011-01-01

    Faculty members most often use plagiarism detection software to detect portions of students' written work that have been copied and/or not attributed to their authors. The rise in plagiarism has led to a parallel rise in software products designed to detect plagiarism. Some of these products are configurable for rapid assessment and teaching, as well as for plagiarism detection.

  11. Rapid detection of small oscillation faults via deterministic learning.

    Science.gov (United States)

    Wang, Cong; Chen, Tianrui

    2011-08-01

    Detection of small faults is one of the most important and challenging tasks in the area of fault diagnosis. In this paper, we present an approach for the rapid detection of small oscillation faults based on a recently proposed deterministic learning (DL) theory. The approach consists of two phases: the training phase and the test phase. In the training phase, the system dynamics underlying normal and fault oscillations are locally accurately approximated through DL. The obtained knowledge of system dynamics is stored in constant radial basis function (RBF) networks. In the diagnosis phase, rapid detection is implemented. Specially, a bank of estimators are constructed using the constant RBF neural networks to represent the training normal and fault modes. By comparing the set of estimators with the test monitored system, a set of residuals are generated, and the average L(1) norms of the residuals are taken as the measure of the differences between the dynamics of the monitored system and the dynamics of the training normal mode and oscillation faults. The occurrence of a test oscillation fault can be rapidly detected according to the smallest residual principle. A rigorous analysis of the performance of the detection scheme is also given. The novelty of the paper lies in that the modeling uncertainty and nonlinear fault functions are accurately approximated and then the knowledge is utilized to achieve rapid detection of small oscillation faults. Simulation studies are included to demonstrate the effectiveness of the approach.

  12. Isolation of Cryptococcus neoformans and other opportunistic fungi from pigeon droppings.

    Science.gov (United States)

    Soltani, Maryam; Bayat, Mansour; Hashemi, Seyed J; Zia, Mohammadali; Pestechian, Nader

    2013-01-01

    Invasive fungal infections cause considerable morbidity and mortality in immunocompromised hosts. Pigeon droppings could especially be a potential carrier in the spread of pathogenic yeasts and mold fungi into the environment. The objective of this study was to isolation of Cryptococcus neoformans and other opportunistic fungi from pigeon droppings. One hundred twenty samples of pigeon droppings were suspended 1:10 in saline solution and then cultured. Identification of C. neoformans was performed on bird seed agar, presence of a capsule on India ink preparation, urease production on urea agar medium and RapID yeast plus system. The identification of candida species was based on micro-morphological analysis on corn meal-Tween 80 agar, RapID yeast plus system and growth in CHROMagar candida. The identification of other fungi was based on macromorphologic, microscopic, biochemical and physiological characteristics. The highest frequency of yeasts and mold fungi were observed in Candida albicans 6.6% and Penicillium spp. 25%. The frequency rate of C. neoformans isolation was 2.5%. Several types of fungi are present in pigeon droppings that can spread in environment and transmit to children and elderly as well as immunocompromised patients who are at increased risk of contracting opportunistic diseases.

  13. Isolation of Cryptococcus neoformans and other opportunistic fungi from pigeon droppings

    Directory of Open Access Journals (Sweden)

    Maryam Soltani

    2013-01-01

    Full Text Available Background: Invasive fungal infections cause considerable morbidity and mortality in immunocompromised hosts. Pigeon droppings could especially be a potential carrier in the spread of pathogenic yeasts and mold fungi into the environment. The objective of this study was to isolation of Cryptococcus neoformans and other opportunistic fungi from pigeon droppings. Materials and Methods: One hundred twenty samples of pigeon droppings were suspended 1:10 in saline solution and then cultured. Identification of C. neoformans was performed on bird seed agar, presence of a capsule on India ink preparation, urease production on urea agar medium and RapID yeast plus system. The identification of candida species was based on micro-morphological analysis on corn meal-Tween 80 agar, RapID yeast plus system and growth in CHROMagar candida. The identification of other fungi was based on macromorphologic, microscopic, biochemical and physiological characteristics. Results: The highest frequency of yeasts and mold fungi were observed in Candida albicans 6.6% and Penicillium spp. 25%. The frequency rate of C. neoformans isolation was 2.5%. Conclusion: Several types of fungi are present in pigeon droppings that can spread in environment and transmit to children and elderly as well as immunocompromised patients who are at increased risk of contracting opportunistic diseases.

  14. Safety evaluation of filamentous fungi isolated from industrial doenjang koji.

    Science.gov (United States)

    Lee, Jin Hee; Jo, Eun Hye; Hong, Eun Jin; Kim, Kyung Min; Lee, Inhyung

    2014-10-01

    A few starters have been developed and used for doenjang fermentation but often without safety evaluation. Filamentous fungi were isolated from industrial doenjang koji, and their potential for mycotoxin production was evaluated. Two fungi were isolated; one was more dominantly present (90%). Both greenish (SNU-G) and whitish (SNU-W) fungi showed 97% and 95% internal transcribed spacer sequence identities to Aspergillus oryzae/flavus, respectively. However, the SmaI digestion pattern of their genomic DNA suggested that both belong to A. oryzae. Moreover, both fungi had morphological characteristics similar to that of A. oryzae. SNU-G and SNU-W did not form sclerotia, which is a typical characteristic of A. oryzae. Therefore, both fungi were identified to be A. oryzae. In aflatoxin gene cluster analysis, both fungi had norB-cypA genes similar to that of A. oryzae. Consistent with this, aflatoxins were not detected in SNU-G and SNU-W using ammonia vapor, TLC, and HPLC analyses. Both fungi seemed to have a whole cyclopiazonic acid (CPA) gene cluster based on PCR of the maoA, dmaT, and pks-nrps genes, which are key genes for CPA biosynthesis. However, CPA was not detected in TLC and HPLC analyses. Therefore, both fungi seem to be safe to use as doenjang koji starters and may be suitable fungal candidates for further development of starters for traditional doenjang fermentation.

  15. Cross-reactivity among antigens of different air-borne fungi detected by ELISA using five monoclonal antibodies against Penicillium notatum.

    Science.gov (United States)

    Shen, H D; Lin, W L; Chen, R J; Han, S H

    1990-10-01

    Cross-reactivity among antigens of 12 genera of air-borne fungi, 13 species of Penicillium, and 5 species of Aspergillus was studied by ELISA using five monoclonal antibodies (MoAbs) against Penicillium notatum. Epitopes recognized by all the five MoAbs were susceptible to treatment of mild periodate oxidation and may therefore be associated with carbohydrates. Furthermore, our results showed that there is cross-reactivity among antigens of Penicillium, Aspergillus, and Eurotium species. By using these MoAbs, cross reactivity was not detected between antigens of Penicillium notatum and antigens of Fusarium solani, Alternaria porri, Cladosporium cladosporoides, Curvularia species, Nigrospora species, Aureobasidium pullulans, Wallemia species, Rhizopus arrhizus, and Candida albicans. Cross-reactivity among antigens of 11 species of Penicillium and 5 species of Aspergillus could be detected by ELISA using one of the five MoAbs (MoAb P15). The fact that there may be cross-reactivity among antigens of closely related fungi species should be considered in the diagnosis and treatment of mold allergic diseases.

  16. 9 CFR 113.27 - Detection of extraneous viable bacteria and fungi in live vaccines.

    Science.gov (United States)

    2010-01-01

    ... bacteria and fungi in live vaccines. 113.27 Section 113.27 Animals and Animal Products ANIMAL AND PLANT... bacteria and fungi in live vaccines. Unless otherwise specified by the Administrator or elsewhere exempted... Seed Bacteria shall be tested for extraneous viable bacteria and fungi as prescribed in this section. A...

  17. Detection of fungi from rice black bug Paraeucosmetus pallicornis Dallas (Hemiptera: Lygaeidae) and inhibition with crude extract of Calatropis gigantea (Asclepiadaceae)

    Science.gov (United States)

    Sjam, S.; Surapati, U.; Adiwena; Syatri, A.; Dewi, V. S.; Rosmana, A.

    2018-05-01

    Rice black bug (P. palicornis) is one of the pests that attack the rice plants in the generative phase that causes the rice easily destroyed when milled and tasted bitter after cooking hence reduces the quality and quantity of rice. The bitter taste in rice may be due to the fungus associated with rice black bug. The aimed of this research was to detect the associated fungi with rice black bug P. pallicornis using some sterilization methods and inhibition with of leaf crude extract of C. gigatea. Detection of fungi from P. pallicornis was conducted using three sterilization methods and control (without sterilization) namely: (1) sterilization with aquades + alcohol 70% (5, 10, 15 and 20 times dipping) + aquades; (2) aquades + alcohol 70% (10 and 20 times dipping); (3) Aquades + alcohol 90 %+ NaCl 0.5 % +alcohol 90 % + aquades. Inhibition of fungi from P. pallicornis with crude extract of C. gigantea obtained by maceration method and then made some concentration to see the effect of its inhibition on the fungi associated with the P. pallicornis. The results showed that without sterilization, four microbe were obtained: Gliocladium sp., Aspergillus sp., black hyphae fungus and white hyphae fungus, sterilization method of Aquades + alcohol 70% with 5 times dipping in alcohol obtained Gliocladium sp., 10 and 20 times dipping found Aspergillus sp. and Gliocladium sp and 15 times dipping found Aspergillus sp. Sterilization with 10 and 20 times dipping in alcohol 70% then washing 2 times with aquades found Gliogladium sp. and Aspergillus sp. Sterilization with Aquades + alcohol 90 % + NaCl 0.5% + alcohol 90% + aquades found Gliocladium sp. Crude extract of C. gigantea had the potential to inhibit fungi Aspergillus sp. and Gliocladium sp. from rice black bug.

  18. Rapid Magnetic Nanobiosensor for the detection of Serratia marcescen

    Science.gov (United States)

    Aljabali, Alaa A. A.; Hussein, Emad; Aljumaili, Omar; Zoubi, Mazhar Al; Altrad, Bahaa; Albatayneh, Khaled; Al-razaq, Mutaz A. Abd

    2018-02-01

    The development of rapid, sensitive, accurate and reliable bacterial detection methods are of keen interest to ensure food safety and hospital security. Therefore, the development of a fast, specific, low-cost and trusted methods is in high demand. Magnetic nanoparticles with their unique material properties have been utilized as a tool for pathogen detection. Here, we present a novel iron oxide nanoparticles labeled with specific targeting antibodies to improve specificity and extend the use of nanoparticles as nanosensors. The results indicated that antibody labeled iron oxide platform that binds specifically to Serriata marcescenst in a straightforward method is very specific and sensitive. The system is capable of rapid and specific detection of various clinically relevant bacterial species, with sensitivity down to single bacteria. The generic platform could be used to identify pathogens for a variety of applications rapidly.

  19. Rapid detection, characterization, and enumeration of foodborne pathogens.

    Science.gov (United States)

    Hoorfar, J

    2011-11-01

    As food safety management further develops, microbiological testing will continue to play an important role in assessing whether Food Safety Objectives are achieved. However, traditional microbiological culture-based methods are limited, particularly in their ability to provide timely data. The present review discusses the reasons for the increasing interest in rapid methods, current developments in the field, the research needs, and the future trends. The advent of biotechnology has introduced new technologies that led to the emergence of rapid diagnostic methods and altered food testing practices. Rapid methods are comprised of many different detection technologies, including specialized enzyme substrates, antibodies and DNA, ranging from simple differential plating media to the use of sophisticated instruments. The use of non-invasive sampling techniques for live animals especially came into focus with the 1990s outbreak of bovine spongiform encephalopathy that was linked to the human outbreak of Creutzfeldt Jakob's Disease. Serology is still an important tool in preventing foodborne pathogens to enter the human food supply through meat and milk from animals. One of the primary uses of rapid methods is for fast screening of large number of samples, where most of them are expected to be test-negative, leading to faster product release for sale. This has been the main strength of rapid methods such as real-time Polymerase Chain Reaction (PCR). Enrichment PCR, where a primary culture broth is tested in PCR, is the most common approach in rapid testing. Recent reports show that it is possible both to enrich a sample and enumerate by pathogen-specific real-time PCR, if the enrichment time is short. This can be especially useful in situations where food producers ask for the level of pathogen in a contaminated product. Another key issue is automation, where the key drivers are miniaturization and multiple testing, which mean that not only one instrument is flexible

  20. dianthiBiological aspects of one fungi Rhizoctoniaand its in vitrointeraction withFusarium oxysporum f. sp.dianthi

    Directory of Open Access Journals (Sweden)

    Marina A. Correa de Restrepo

    2002-01-01

    Full Text Available ABSTRACTGrowth in different culture media and temperature as well as its antagonic roleagainst Fusarium oxysporumSchlencht f. sp. dianthi(Prill & Del Snyder & Hansen, werestudied on an isolated of the fungi Theobroma grandiflorum(Spreng K. Schum. Lowgrowth and the presence of abundat moniloid cells were detected when the fungi wascultured in PDA in microculture, with natural light and at 20ºC. Higher temperatures(27ºC and 30ºC increased growh rate. When cultured at 20ºC, in darkness, similarresults as those recorded at 30ºC in natural light were found. After a month sclerotiagrotwh was present. Culture in AMS in Petri dishes, with natural light at 20ºC showedgrowth in patches which suggests phenotype variability. Poor growth was recordedwhen cultured in AAg. Our results showed that rapid and vigorous growth isobtanined when the fungi is cultured in PDA at 30ºC in darkness producing conidiaand sclerotia. T. grandiflorumalso has an antagonic role against F.oxysporumsp. dianthi,growing faster and inihibitingits growth.

  1. Phylogenetic congruence between subtropical trees and their associated fungi.

    Science.gov (United States)

    Liu, Xubing; Liang, Minxia; Etienne, Rampal S; Gilbert, Gregory S; Yu, Shixiao

    2016-12-01

    Recent studies have detected phylogenetic signals in pathogen-host networks for both soil-borne and leaf-infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next-generation high-throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK , rbcL , atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host-fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant-fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant-fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.

  2. Heterologous gene expression in filamentous fungi.

    Science.gov (United States)

    Su, Xiaoyun; Schmitz, George; Zhang, Meiling; Mackie, Roderick I; Cann, Isaac K O

    2012-01-01

    Filamentous fungi are critical to production of many commercial enzymes and organic compounds. Fungal-based systems have several advantages over bacterial-based systems for protein production because high-level secretion of enzymes is a common trait of their decomposer lifestyle. Furthermore, in the large-scale production of recombinant proteins of eukaryotic origin, the filamentous fungi become the vehicle of choice due to critical processes shared in gene expression with other eukaryotic organisms. The complexity and relative dearth of understanding of the physiology of filamentous fungi, compared to bacteria, have hindered rapid development of these organisms as highly efficient factories for the production of heterologous proteins. In this review, we highlight several of the known benefits and challenges in using filamentous fungi (particularly Aspergillus spp., Trichoderma reesei, and Neurospora crassa) for the production of proteins, especially heterologous, nonfungal enzymes. We review various techniques commonly employed in recombinant protein production in the filamentous fungi, including transformation methods, selection of gene regulatory elements such as promoters, protein secretion factors such as the signal peptide, and optimization of coding sequence. We provide insights into current models of host genomic defenses such as repeat-induced point mutation and quelling. Furthermore, we examine the regulatory effects of transcript sequences, including introns and untranslated regions, pre-mRNA (messenger RNA) processing, transcript transport, and mRNA stability. We anticipate that this review will become a resource for researchers who aim at advancing the use of these fascinating organisms as protein production factories, for both academic and industrial purposes, and also for scientists with general interest in the biology of the filamentous fungi. Copyright © 2012 Elsevier Inc. All rights reserved.

  3. Individual differences in detecting rapidly presented fearful faces.

    Directory of Open Access Journals (Sweden)

    Dandan Zhang

    Full Text Available Rapid detection of evolutionarily relevant threats (e.g., fearful faces is important for human survival. The ability to rapidly detect fearful faces exhibits high variability across individuals. The present study aimed to investigate the relationship between behavioral detection ability and brain activity, using both event-related potential (ERP and event-related oscillation (ERO measurements. Faces with fearful or neutral facial expressions were presented for 17 ms or 200 ms in a backward masking paradigm. Forty-two participants were required to discriminate facial expressions of the masked faces. The behavioral sensitivity index d' showed that the detection ability to rapidly presented and masked fearful faces varied across participants. The ANOVA analyses showed that the facial expression, hemisphere, and presentation duration affected the grand-mean ERP (N1, P1, and N170 and ERO (below 20 Hz and lasted from 100 ms to 250 ms post-stimulus, mainly in theta band brain activity. More importantly, the overall detection ability of 42 subjects was significantly correlated with the emotion effect (i.e., fearful vs. neutral on ERP (r = 0.403 and ERO (r = 0.552 measurements. A higher d' value was corresponding to a larger size of the emotional effect (i.e., fearful--neutral of N170 amplitude and a larger size of the emotional effect of the specific ERO spectral power at the right hemisphere. The present results suggested a close link between behavioral detection ability and the N170 amplitude as well as the ERO spectral power below 20 Hz in individuals. The emotional effect size between fearful and neutral faces in brain activity may reflect the level of conscious awareness of fearful faces.

  4. Aerobiology of the built environment: Synergy between Legionella and fungi.

    Science.gov (United States)

    Alum, Absar; Isaacs, Galahad Zachariah

    2016-09-02

    The modern built environment (BE) design creates unique ecological niches ideal for the survival and mutual interaction of microbial communities. This investigation focused on the synergistic relations between Legionella and the fungal species commonly found in BEs and the impact of these synergistic relationships on the survival and transmission of Legionella. A field study was conducted to identify the types and concentrations of fungi in BEs. The fungal isolates purified from BEs were cocultured with Legionella to study their synergistic association. Cocultured Legionella cells were aerosolized in an air-tight chamber to evaluate the efficacy of ultraviolet (UV) to inactivate these cells. Aspergillus, Alternaria, and Cladosporium were the most common fungi detected in samples that tested positive for Legionella. After coculturing, Legionella cells were detected inside fungal hyphae. The microscopic observations of Legionella internalization in fungal hyphae were confirmed by molecular analyses. UV disinfection of the aerosolized Legionella cells that were cocultured with fungi indicated that fungal spores and propagules act as a shield against UV radiation. The shield effect of fungal spores on Legionella cells was quantified at >2.5 log10. This study provides the first evidence, to our knowledge, of Legionella cell presence inside fungi detected in an indoor environment. This symbiotic relationship with fungi results in longer survival of Legionella under ambient conditions and provides protection against UV rays. Copyright © 2016. Published by Elsevier Inc.

  5. Amperometric immunosensor for rapid detection of Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Hiraiwa, Morgan; Lee, Hyun-Boo; Inoue, Shinnosuke; Chung, Jae-Hyun; Kim, Jong-Hoon; Becker, Annie L; Weigel, Kris M; Cangelosi, Gerard A; Lee, Kyong-Hoon

    2015-01-01

    Tuberculosis (TB) has been a major public health problem, which can be better controlled by using accurate and rapid diagnosis in low-resource settings. A simple, portable, and sensitive detection method is required for point-of-care (POC) settings. This paper studies an amperometric biosensor using a microtip immunoassay for a rapid and low-cost detection of Mycobacterium tuberculosis (MTB) in sputum. MTB in sputum is specifically captured on the functionalized microtip surface and detected by electric current. According to the numerical study, the current signal on the microtip surface is linearly changed with increasing immersion depth. Using a reference microtip, the immersion depth is compensated for a sensing microtip. On the microtip surface, target bacteria are concentrated and organized by a coffee-ring effect, which amplifies the electric current. To enhance the signal-to-noise ratio, both the sample processing and rinsing steps are presented with the use of deionized water as a medium for the amperometric measurement. When applied to cultured MTB cells spiked into human sputum, the detection limit was 100 CFU mL −1 , comparable to a more labor-intensive fluorescence detection method reported previously. (paper)

  6. Amperometric immunosensor for rapid detection of Mycobacterium tuberculosis

    Science.gov (United States)

    Hiraiwa, Morgan; Kim, Jong-Hoon; Lee, Hyun-Boo; Inoue, Shinnosuke; Becker, Annie L.; Weigel, Kris M.; Cangelosi, Gerard A.; Lee, Kyong-Hoon; Chung, Jae-Hyun

    2015-05-01

    Tuberculosis (TB) has been a major public health problem, which can be better controlled by using accurate and rapid diagnosis in low-resource settings. A simple, portable, and sensitive detection method is required for point-of-care (POC) settings. This paper studies an amperometric biosensor using a microtip immunoassay for a rapid and low-cost detection of Mycobacterium tuberculosis (MTB) in sputum. MTB in sputum is specifically captured on the functionalized microtip surface and detected by electric current. According to the numerical study, the current signal on the microtip surface is linearly changed with increasing immersion depth. Using a reference microtip, the immersion depth is compensated for a sensing microtip. On the microtip surface, target bacteria are concentrated and organized by a coffee-ring effect, which amplifies the electric current. To enhance the signal-to-noise ratio, both the sample processing and rinsing steps are presented with the use of deionized water as a medium for the amperometric measurement. When applied to cultured MTB cells spiked into human sputum, the detection limit was 100 CFU mL-1, comparable to a more labor-intensive fluorescence detection method reported previously.

  7. Rapid detection of EBOLA VP40 in microchip immunofiltration assay

    Science.gov (United States)

    Miethe, Peter; Gary, Dominik; Hlawatsch, Nadine; Gad, Anne-Marie

    2015-05-01

    In the spring of 2014, the Ebola virus (EBOV) strain Zaire caused a dramatic outbreak in several regions of West Africa. The RT-PCR and antigen capture diagnostic proved to be effective for detecting EBOV in blood and serum. In this paper, we present data of a rapid antigen capture test for the detection of VP40. The test was performed in a microfluidic chip for immunofiltration analysis. The chip integrates all necessary assay components. The analytical sensitivity of the rapid test was 8 ng/ml for recombinant VP40. In serum and whole blood samples spiked with virus culture material, the detection limit was 2.2 x 102 PFU/ml. The performance data of the rapid test (15 min) are comparable to that of the VP40 laboratory ELISA.

  8. Massive gene swamping among cheese-making Penicillium fungi

    Directory of Open Access Journals (Sweden)

    Jeanne Ropars

    2015-03-01

    Full Text Available Horizontal gene transfers (HGT, i.e., the transmission of genetic material between species not directly attributable to meiotic gene exchange, have long been acknowledged as a major driver of prokaryotic evolution and is increasingly recognized as an important source of adaptation in eukaryotes. In fungi in particular, many convincing examples of HGT have been reported to confer selective advantages on the recipient fungal host, either promoting fungal pathogenicity on plants or increasing their toxicity by the acquisition of secondary metabolic clusters, resulting in adaptation to new niches and in some cases eventually even in speciation. These horizontal gene transfers involve single genes, complete metabolic pathways or even entire chromosomes. A recent study has uncovered multiple recent horizontal transfers of a 575 kb genomic island in cheese Penicillium fungi, representing ca. 2% of the Penicillium roqueforti’s genome, that may confer selective advantage in the competing cheese environment where bacteria and fungi occur. Novel phylogenomic methods are being developed, revealing massive HGT among fungi. Altogether, these recent studies indicate that HGT is a crucial mechanism of rapid adaptation, even among eukaryotes.

  9. Microbial and 'de novo' transformation of dicarboxylic acids by three airborne fungi

    International Nuclear Information System (INIS)

    Cote, Valerie; Kos, Gregor; Mortazavi, Roya; Ariya, Parisa A.

    2008-01-01

    Micro-organisms and organic compounds of biogenic or anthropogenic origins are important constituents of atmospheric aerosols, which are involved in atmospheric processes and climate change. In order to investigate the role of fungi and their metabolisation activity, we collected airborne fungi using a biosampler in an urban location of Montreal, Quebec, Canada (45 o 28' N, 73 o 45' E). After isolation on Sabouraud dextrose agar, we exposed isolated colonies to dicarboxylic acids (C 2 -C 7 ), a major group of organic aerosols and monitored their growth. Depending on the acid, total fungi numbers varied from 35 (oxalic acid) to 180 CFU/mL (glutaric acid). Transformation kinetics of malonic acid, presumably the most abundant dicarboxylic acid, at concentrations of 0.25 and 1.00 mM for isolated airborne fungi belonging to the genera Aspergillus, Penicillium, Eupenicillium, and Thysanophora with the fastest transformation rate are presented. The initial concentration was halved within 4.5 and 11.4 days. Other collected fungi did not show a significant degradation and the malonic acid concentration remained unchanged (0.25 and 1.00 mM) within 20 days. Degradation of acid with formation of metabolites was followed using high performance liquid chromatography-ultraviolet detection (HPLC/UV) and gas chromatography-mass spectrometry (GC/MS), as well as monitoring of 13 C labelled malonic acid degradation with solid-state nuclear magnetic resonance spectroscopy (NMR). Using GC/MS we identified two processes driving chemical modifications of organic aerosol solutions: (I) formation of metabolites within several days, and (II) rapid release (≤ 2 min) of organic molecules from fungal species upon the insertion of taxa in organic aerosol solutions. Metabolites included aromatic compounds and alcohols (e.g. trimethylbenzene and butanol). Potential atmospheric implications of our results are discussed

  10. In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections.

    Science.gov (United States)

    Ellison, Mitchell A; McMahon, Michael B; Bonde, Morris R; Palmer, Cristi L; Luster, Douglas G

    2016-01-01

    Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here. To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues. This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.

  11. Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil.

    Science.gov (United States)

    Blazewicz, Steven J; Schwartz, Egbert; Firestone, Mary K

    2014-05-01

    The rapid increase in microbial activity that occurs when a dry soil is rewetted has been well documented and is of great interest due to implications of changing precipitation patterns on soil C dynamics. Several studies have shown minor net changes in microbial population diversity or abundance following wet-up, but the gross population dynamics of bacteria and fungi resulting from soil wet-up are virtually unknown. Here we applied DNA stable isotope probing with H218O coupled with quantitative PCR to characterize new growth, survival, and mortality of bacteria and fungi following the rewetting of a seasonally dried California annual grassland soil. Microbial activity, as determined by CO2 production, increased significantly within three hours of wet-up, yet new growth was not detected until after three hours, suggesting a pulse of nongrowth activity immediately following wet-up, likely due to osmo-regulation and resuscitation from dormancy in response to the rapid change in water potential. Total microbial abundance revealed little change throughout the seven-day post-wet incubation, but there was substantial turnover of both bacterial and fungal populations (49% and 52%, respectively). New growth was linear between 24 and 168 hours for both bacteria and fungi, with average growth rates of 2.3 x 10(8) bacterial 16S rRNA gene copies x [g dry mass](-1) x h(-1) and 4.3 x 10(7) fungal ITS copies x [g dry mass](-1) x h(-1). While bacteria and fungi differed in their mortality and survival characteristics during the seven-day incubation, mortality that occurred within the first three hours was similar, with 25% and 27% of bacterial and fungal gene copies disappearing from the pre-wet community, respectively. The rapid disappearance of gene copies indicates that cell death, occurring either during the extreme dry down period (preceding five months) or during the rapid change in water potential due to wet-up, generates a significant pool of available C that likely

  12. Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and Their Host Orchid.

    Science.gov (United States)

    Shimura, Hanako; Masuta, Chikara; Koda, Yasunori

    2018-01-01

    In nature, mycorrhizal association with soilborne fungi is indispensable for orchid families. Fungal structures from compatible endo-mycorrhizal fungi in orchid cells are digested in cells to be supplied to orchids as nutrition. Because orchid seeds lack the reserves for germination, they keep receiving nutrition through mycorrhizal formation from seed germination until shoots develop (leaves) and become photoautotrophic. Seeds of all orchid species surely geminate with the help of their own fungal partners, and this specific partnership has been acquired for a long evolutional history between orchids and fungi.We have studied the interactions between orchids and mycorrhizal fungi and recently conducted transcriptome analyses (RNAseq) by a next-generation sequencing (NGS) approach. It is possible that orchid RNA isolated form naturally grown plants is contaminated with RNAs derived from mycorrhizal fungi in the orchid cells. To avoid such contamination, we here prepared aseptically germinated orchid plants (i.e., fungus-free plants) together with a pure-cultured fungal isolate and field-growing orchid samples. In the cDNA library prepared from orchid and fungal tissues, we found that partitivirus-like sequences were common in an orchid and its mycorrhizal fungus. These partitivirus-like sequences were closely related by a phylogenetic analysis, suggesting that transmission of an ancestor virus between the two organisms occurred through the specific relation of the orchid and its associated fungus.

  13. Luciferase-Zinc-Finger System for the Rapid Detection of Pathogenic Bacteria.

    Science.gov (United States)

    Shi, Chu; Xu, Qing; Ge, Yue; Jiang, Ling; Huang, He

    2017-08-09

    Rapid and reliable detection of pathogenic bacteria is crucial for food safety control. Here, we present a novel luciferase-zinc finger system for the detection of pathogens that offers rapid and specific profiling. The system, which uses a zinc-finger protein domain to probe zinc finger recognition sites, was designed to bind the amplified conserved regions of 16S rDNA, and the obtained products were detected using a modified luciferase. The luciferase-zinc finger system not only maintained luciferase activity but also allowed the specific detection of different bacterial species, with a sensitivity as low as 10 copies and a linear range from 10 to 10 4 copies per microliter of the specific PCR product. Moreover, the system is robust and rapid, enabling the simultaneous detection of 6 species of bacteria in artificially contaminated samples with excellent accuracy. Thus, we envision that our luciferase-zinc finger system will have far-reaching applications.

  14. Rapid detection of the positive side reactions in vanadium flow batteries

    International Nuclear Information System (INIS)

    Liu, Le; Li, Zhaohua; Xi, Jingyu; Zhou, Haipeng; Wu, Zenghua; Qiu, Xinping

    2017-01-01

    Highlights: • A method for rapid measurement of the positive side reactions in VFB is presented. • The SOC of positive electrolytes can be detected with resolution of 0.002%. • Side reaction ratios at different charge currents, flow rates are obtained. - Abstract: We present an optical detection method for rapid measurement of the positive side reactions in vanadium flow batteries (VFB). By measuring the transmittance of the positive electrolytes in VFB, the states of charge (SOC) of the positive electrolytes can be detected at very high resolution (better than 0.002% in the SOC range from 98% to 100%), due to the nonlinear transmittance spectra caused by the interactions between V(IV) and V(V) ions. The intensity of the positive side reactions of a VFB can be rapidly measured by a few steps, attributing to the fact that the positive side reactions occur only during the high voltage charging process. The ratios of the positive side reactions at different charge currents and different flow rates are obtained while causing no damage to the battery. This optical detection method can rapidly determine the optimal parameters of the VFB system, providing new means for studying the electrochemical reactions in the VFB system and rapid test in industrial production of VFBs.

  15. Rapid Aminoglycoside NP Test for Rapid Detection of Multiple Aminoglycoside Resistance in Enterobacteriaceae.

    Science.gov (United States)

    Nordmann, Patrice; Jayol, Aurélie; Dobias, Jan; Poirel, Laurent

    2017-04-01

    The rapid aminoglycoside NP (Nordmann/Poirel) test was developed to rapidly identify multiple aminoglycoside (AG) resistance in Enterobacteriaceae It is based on the detection of the glucose metabolism related to enterobacterial growth in the presence of a defined concentration of amikacin plus gentamicin. Formation of acid metabolites was evidenced by a color change (orange to yellow) of the red phenol pH indicator. The rapid aminoglycoside NP test was evaluated by using bacterial colonies of 18 AG-resistant isolates producing 16S rRNA methylases, 20 AG-resistant isolates expressing AG-modifying enzymes (acetyl-, adenyl-, and phosphotransferases), and 10 isolates susceptible to AG. Its sensitivity and specificity were 100% and 97%, respectively, compared to the broth dilution method, which was taken as the gold standard for determining aminoglycoside resistance. The test is inexpensive, rapid (<2 h), and implementable worldwide. Copyright © 2017 American Society for Microbiology.

  16. Rapid Detection of the Varicella Zoster Virus

    Science.gov (United States)

    Lewis, Michelle P.; Harding, Robert

    2011-01-01

    1.Technology Description-Researchers discovered that when the Varicella Zoster Virus (VZV) reactivates from latency in the body, the virus is consistently present in saliva before the appearance of skin lesions. A small saliva sample is mixed with a specialized reagent in a test kit. If the virus is present in the saliva sample, the mixture turns a red color. The sensitivity and specificity emanates from an antibody-antigen reaction. This technology is a rapid, non-invasive, point of-of-care testing kit for detecting the virus from a saliva sample. The device is easy to use and can be used in clinics and in remote locations to quickly detect VZV and begin treatment with antiviral drugs. 2.Market Opportunity- RST Bioscience will be the first and only company to market a rapid, same day test kit for the detection of VZV in saliva. The RST detection test kit will have several advantages over existing, competitive technology. The test kit is self contained and laboratory equipment is not required for analysis of the sample. Only a single saliva sample is required to be taken instead of blood or cerebral spinal fluid. The test kit is portable, sterile and disposable after use. RST detection test kits require no electrical power or expensive storage equipment and can be used in remote locations. 3.Market Analysis- According to the CDC, it is estimated that 1 million cases of shingles occur each year in the U.S. with more than half over the age of sixty. There is a high demand for rapid diagnostics by the public. The point-of-care testing (POCT) market is growing faster than other segments of in vitro diagnostics. According to a July 2007 InteLab Corporation industry report the overall market for POCT was forecast to increase from $10.3 billion in 2005 to $18.7 billion by 2011. The market value of this test kit has not been determined. 4.Competition- The VZV vaccine prevents 50% of cases and reduces neuralgia by 66%. The most popular test detects VZV-specific IgM antibody

  17. An integrated micro-chip for rapid detection of magnetic particles

    KAUST Repository

    Gooneratne, Chinthaka P.; Liang, Cai; Giouroudi, Ioanna; Kosel, Jü rgen

    2012-01-01

    This paper proposes an integrated micro-chip for the manipulation and detection of magnetic particles (MPs). A conducting ring structure is used to manipulate MPs toward giant magnetoresistance(GMR) sensing elements for rapid detection

  18. Lab-on-a-chip for rapid electrochemical detection of nerve agent Sarin

    DEFF Research Database (Denmark)

    Tan, Hsih-Yin; Loke, Weng Keong; Nguyen, Nam-Trung

    2014-01-01

    This paper reports a lab-on-a-chip for the detection of Sarin nerve agent based on rapid electrochemical detection. The chemical warfare agent Sarin (C4H10FO2P, O-isopropyl methylphosphonofluoridate) is a highly toxic organophosphate that induces rapid respiratory depression, seizures and death...

  19. Advances in developing rapid, reliable and portable detection systems for alcohol.

    Science.gov (United States)

    Thungon, Phurpa Dema; Kakoti, Ankana; Ngashangva, Lightson; Goswami, Pranab

    2017-11-15

    Development of portable, reliable, sensitive, simple, and inexpensive detection system for alcohol has been an instinctive demand not only in traditional brewing, pharmaceutical, food and clinical industries but also in rapidly growing alcohol based fuel industries. Highly sensitive, selective, and reliable alcohol detections are currently amenable typically through the sophisticated instrument based analyses confined mostly to the state-of-art analytical laboratory facilities. With the growing demand of rapid and reliable alcohol detection systems, an all-round attempt has been made over the past decade encompassing various disciplines from basic and engineering sciences. Of late, the research for developing small-scale portable alcohol detection system has been accelerated with the advent of emerging miniaturization techniques, advanced materials and sensing platforms such as lab-on-chip, lab-on-CD, lab-on-paper etc. With these new inter-disciplinary approaches along with the support from the parallel knowledge growth on rapid detection systems being pursued for various targets, the progress on translating the proof-of-concepts to commercially viable and environment friendly portable alcohol detection systems is gaining pace. Here, we summarize the progress made over the years on the alcohol detection systems, with a focus on recent advancement towards developing portable, simple and efficient alcohol sensors. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Research advance in rapid detection of foodborne Staphylococcus aureus

    OpenAIRE

    Xihong Zhao; Caijiao Wei; Junliang Zhong; Shiwei Jin

    2016-01-01

    Staphylococcus aureus is a gram-positive, coccus-shaped facultative anaerobe and a member of the Staphylococcaceae family. In recent years, alimentary toxicosis caused by S. aureus is a very serious problem worldwide, which constitutes a great threat to public health. In this review, we tried to summarize the conventional methods and newly developed rapid detection techniques of S. aureus (traditional detection method, biochemical detection, immunology method, molecular biology, and biosensor...

  1. Synergism between hydrogen peroxide and seventeen acids against five agri-food-borne fungi and one yeast strain.

    Science.gov (United States)

    Martin, H; Maris, P

    2012-12-01

    The objective of this study was to evaluate fungicidal efficacy of hydrogen peroxide administered in combination with 17 mineral and organic acids authorized for use in the food industry. The assays were performed on a 96-well microplate using a microdilution technique based on the checkerboard titration method. The six selected strains (one yeast and five fungi) were reference strains and strains representative of contaminating fungi found in the food industry. Each synergistic hydrogen peroxide/acid combination found after fifteen minutes contact time at 20 °C in distilled water was then tested in conditions simulating four different use conditions. Twelve combinations were synergistic in distilled water, eleven of these remained synergistic with one or more of the four mineral and organic interfering substances selected. Hydrogen peroxide/formic acid combination remained effective against four strains and was never antagonistic against the other two fungi. Combinations with propionic acid and acetic acid stayed synergistic against two strains. Those with oxalic acid and lactic acid kept their synergism only against Candida albicans. No synergism was detected against Penicillium cyclopium. Synergistic combinations of disinfectants were revealed, among them the promising hydrogen peroxide/formic acid combination. A rapid screening method developed in our laboratory for bacteria was adapted to fungi and used to reveal the synergistic potential of disinfectants and/or sanitizers combinations. © 2012 The Society for Applied Microbiology.

  2. Metal-chelating compounds produced by ectomycorrhizal fungi collected from pine plantations.

    Science.gov (United States)

    Machuca, A; Pereira, G; Aguiar, A; Milagres, A M F

    2007-01-01

    To investigate the in vitro production of metal-chelating compounds by ectomycorrhizal fungi collected from pine plantations in southern Chile. Scleroderma verrucosum, Suillus luteus and two isolates of Rhizopogon luteolus were grown in solid and liquid modified Melin-Norkans (MMN) media with and without iron addition and the production of iron-chelating compounds was determined by Chrome Azurol S (CAS) assay. The presence of hydroxamate and catecholate-type compounds and organic acids was also investigated in liquid medium. All isolates produced iron-chelating compounds as detected by CAS assay, and catecholates, hydroxamates as well as oxalic, citric and succinic acids were also detected in all fungal cultures. Scleroderma verrucosum produced the greatest amounts of catecholates and hydroxamates whereas the highest amounts of organic acids were detected in S. luteus. Nevertheless, the highest catecholate, hydroxamate and organic acid concentrations did not correlate with the highest CAS reaction which was observed in R. luteolus (Yum isolate). Ectomycorrhizal fungi produced a variety of metal-chelating compounds when grown in liquid MMN medium. However, the addition of iron to all fungi cultures reduced the CAS reaction, hydroxamate and organic acid concentrations. Catecholate production was affected differently by iron, depending on the fungal isolate. The ectomycorrhizal fungi described in this study have never been reported to produce metal-chelating compound production. Moreover, apart from some wood-rotting fungi, this is the first evidence of the presence of catecholates in R. luteolus, S. luteus and S. verrucosum cultures.

  3. Accelerated detection of brown-rot decay : comparison of soil block test, chemical analysis, mechanical properties, and immunodetection

    Science.gov (United States)

    C. A. Clausen; S. N. Kartal

    2003-01-01

    Early detection of wood decay is critical because decay fungi can cause rapid structural failure. The objective of this study was to compare the sensitivity of different methods purported to detect brown-rot decay in the early stages of development. The immunodiagnostic wood decay (IWD)test, soil block test/cake pan test, mechanical property tests, and chemical...

  4. Development and evaluation of a novel and rapid detection assay for Botrytis cinerea based on loop-mediated isothermal amplification.

    Directory of Open Access Journals (Sweden)

    Ya-Bing Duan

    Full Text Available Botrytis cinerea is a devastating plant pathogen that causes grey mould disease. In this study, we developed a visual detection method of B. cinerea based on the Bcos5 sequence using loop-mediated isothermal amplification (LAMP with hydroxynaphthol blue dye (HNB. The LAMP reaction was optimal at 63 °C for 45 min. When HNB was added prior to amplification, samples with B. cinerea DNA developed a characteristic sky blue color after the reaction but those without DNA or with DNA of other plant pathogenic fungi did not. Results of HNB staining method were reconfirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for B. cinerea was 10(-3 ng µL(-1 of genomic DNA per reaction, which was 10-fold more sensitive than conventional PCR (10(-2 ng µL(-1. Detection of the LAMP assay for inoculum of B. cinerea was possible in the inoculated tomato and strawberry petals. In the 191 diseased samples, 180 (94.2% were confirmed as positive by LAMP, 172 (90.1% positive by the tissue separation, while 147 (77.0% positive by PCR. Because the LAMP assay performed well in aspects of sensitivity, specificity, repeatability, reliability, and visibility, it is suitable for rapid detection of B. cinerea in infected plant materials prior to storage and during transportation, such as cut flowers, fruits and vegetables.

  5. Application of molecular genetic methods for identification of wood-decaying fungi in wood constructions

    OpenAIRE

    Elena Bobeková; Michal Tomšovský; Petr Horáček

    2008-01-01

    The aim of the paper is to evaluate the utilization of molecular biology methods for detection of wood decaying fungi directly from decomposed wood using a commercial DNA extraction kit developed for soil substrates (PowerSoil™ DNA isolation kit). The experiment based on dry rot fungus (Serpula lacrymans) detection from inoculated wooden pieces under laboratory conditions was followed by field detection of wood-decaying fungi from wood structures on building constructions. Fungal DNA was ide...

  6. Communities of fungi in decomposed wood of oak and pine

    Directory of Open Access Journals (Sweden)

    Kwaśna Hanna

    2016-09-01

    Full Text Available The abundance and diversity of wood decomposing fungi were investigated by isolating and cultivating filamentous fungi from wood and by detection of fruit bodies of ascomycetous and basidiomycetous fungi. The objective was to study the impact of forest management on fungi in 100-year-old oak and 87-year-old Scots pine forests in Northern Poland. Fungi were found on coarse woody debris of decayed stumps and fallen logs, boughs and branches in each of the three (managed and unmanaged examined stands. In total, 226 species of Oomycota and fungi were recorded. Oak wood was colonized by one species of Oomycota and 141 species of fungi including Zygomycota (19 species, Ascomycota (103 species and Basidiomycota (19 species. Scots pine wood was also colonized by one species of Oomycota and 138 species of fungi including Zygomycota (19 species, Ascomycota (90 species and Basidiomycota (29 species. In the first, second and third stages of decomposition, the oak wood was colonized by 101, 89 and 56 species of fungi respectively and pine wood was colonized by 82, 103 and 47 species respectively. Eighty three of the observed species (37% occurred on both types of wood, while the other species displayed nutritional preferences. A decrease in the number of species with advancing decay indicates the necessity for a continuous supply of dead wood to the forest ecosystem.

  7. Rapid Methods for the Detection of Foodborne Bacterial Pathogens: Principles, Applications, Advantages and Limitations

    Directory of Open Access Journals (Sweden)

    Law eJodi Woan-Fei

    2015-01-01

    Full Text Available The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR, multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA, loop-mediated isothermal amplification (LAMP and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.

  8. Rapid detection, characterization, and enumeration of foodborne pathogens

    DEFF Research Database (Denmark)

    Hoorfar, Jeffrey

    2011-01-01

    . The present review discusses the reasons for the increasing interest in rapid methods; current developments in the field, the research needs, and the future trends. The advent of biotechnology has introduced new technologies that led to the emergence of rapid diagnostic methods and altered food testing...... of rapid methods is for fast screening of large number of samples, where most of them are expected to be test-negative, leading to faster product release for sale. This has been the main strength of rapid methods such as real-time Polymerase Chain Reaction (PCR). Enrichment PCR, where a primary culture...... of pathogen in a contaminated product. Another key issue is automation, where the key drivers are miniaturization and multiple testing, which mean that not only one instrument is flexible enough to test for many pathogens but also many pathogens can be detected with one test. The review is mainly based...

  9. Pathogenic Fungi Transmitted Through Cucumber Seeds and Safely Elimination by Application of Peppermint Extract and Oil

    Directory of Open Access Journals (Sweden)

    Eman S.H. FARRAG

    2012-08-01

    Full Text Available Diseases induced by Fusarium, like damping-off and wilt on cucumber, are serious problems around the world. Samples of cucumber seeds were collected from commercial markets in Egypt and tested for seed-borne fungi. In order to detect the maximum number of internal and external seed-borne fungi, agar plate examination of disinfected and non-disinfected seeds were used. Two species of Fusarium were the most frequent and predominant fungi. Facultative parasites of the genera Alternaria, Rhizoctonia, Helminthosporium and Penicillium were also found. A total 33 isolates of Fusarium spp. were obtained using Komadas selective medium. Fusarium oxysporum and F. solani were highly frequent. Pathogenicity test indicated that, F. oxysporum isolate (Fem8 was the main causal organism of pre- and post-emergence damping off. Furthermore, it occurred in all seed parts tested. Some infected seeds germinate, but they were either rapidly overgrown by F. oxysporum or they developed into a diseased seedling. The water extract of garlic, peppermint and rheum completely inhibited the conidiospore germination and mycelial growth of F. oxysporum at tested conc. 3, 2 and 3%, respectively. Soaked seeds in 2% peppermint extract and evaporated seeds by vapor of peppermint oil caused a highly reduction in the infection and reduced transmission of the referred fungi from seeds to the growing seedlings. The vigor of cucumber seedlings raised from the treated seeds was better than that developed from untreated ones.

  10. Pathogenic Fungi Transmitted Through Cucumber Seeds and Safely Elimination by Application of Peppermint Extract and Oil

    Directory of Open Access Journals (Sweden)

    Eman S.H. FARRAG

    2012-08-01

    Full Text Available Diseases induced by Fusarium, like damping-off and wilt on cucumber, are serious problems around the world. Samples of cucumber seeds were collected from commercial markets in Egypt and tested for seed-borne fungi. In order to detect the maximum number of internal and external seed-borne fungi, agar plate examination of disinfected and non-disinfected seeds were used. Two species of Fusarium were the most frequent and predominant fungi. Facultative parasites of the genera Alternaria, Rhizoctonia, Helminthosporium and Penicillium were also found. A total 33 isolates of Fusarium spp. were obtained using Komada�s selective medium. Fusarium oxysporum and F. solani were highly frequent. Pathogenicity test indicated that, F. oxysporum isolate (Fem8 was the main causal organism of pre- and post-emergence damping off. Furthermore, it occurred in all seed parts tested. Some infected seeds germinate, but they were either rapidly overgrown by F. oxysporum or they developed into a diseased seedling. The water extract of garlic, peppermint and rheum completely inhibited the conidiospore germination and mycelial growth of F. oxysporum at tested conc. 3, 2 and 3%, respectively. Soaked seeds in 2% peppermint extract and evaporated seeds by vapor of peppermint oil caused a highly reduction in the infection and reduced transmission of the referred fungi from seeds to the growing seedlings. The vigor of cucumber seedlings raised from the treated seeds was better than that developed from untreated ones.

  11. Research advance in rapid detection of foodborne Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    Xihong Zhao

    2016-09-01

    Full Text Available Staphylococcus aureus is a gram-positive, coccus-shaped facultative anaerobe and a member of the Staphylococcaceae family. In recent years, alimentary toxicosis caused by S. aureus is a very serious problem worldwide, which constitutes a great threat to public health. In this review, we tried to summarize the conventional methods and newly developed rapid detection techniques of S. aureus (traditional detection method, biochemical detection, immunology method, molecular biology, and biosensor method for their principles, advantages, disadvantages, and applications. Furthermore, the future perspectives of S. aureus detection methods were forecasted at last.

  12. Fungi and fungi-like Oomycetes isolated from affected leaves of rhododendron

    Directory of Open Access Journals (Sweden)

    Maria Kowalik

    2013-12-01

    Full Text Available The aim of the work is to identify fungi and fungi-like Oomycetes occurring on affected leaves of rhododendron Rhododendron L. Mycological analyses were carried out on 200 leaves collected from green areas of Kraków from May till September 2005. Isolated fungi-like Oomycetes belonged to 67 taxa. The most frequently found fungi included: Alternaria alternata, Aspergillus niger, Botrytis cinerea, Coelophoma empetri, Nigrospora sphaerica, Pestalotia sydowiana, Phialophora cyclaminis, Phomopsis archeri, Septoria azalea and Sordaria fimicola. Among fungi-like organisms Phytophthora cinnamomi and P. citricola were isolated.

  13. Rapid In-Place Composite Rotor Damage Detection, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Luna Innovations is proposing to further develop the Rapid In-Place Composite Rotor Damage Detection (RIPCoRDD) System for determining and tracking the structural...

  14. Rapid In-Place Composite Rotor Damage Detection, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Luna Innovations is proposing to develop the Rapid In-Place Composite Rotor Damage Detection (RIPCoRDD) for determining and tracking the structural health of...

  15. Rapid Detection of Biological and Chemical Threat Agents Using Physical Chemistry, Active Detection, and Computational Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Myung; Dong, Li; Fu, Rong; Liotta, Lance; Narayanan, Aarthi; Petricoin, Emanuel; Ross, Mark; Russo, Paul; Zhou, Weidong; Luchini, Alessandra; Manes, Nathan; Chertow, Jessica; Han, Suhua; Kidd, Jessica; Senina, Svetlana; Groves, Stephanie

    2007-01-01

    Basic technologies have been successfully developed within this project: rapid collection of aerosols and a rapid ultra-sensitive immunoassay technique. Water-soluble, humidity-resistant polyacrylamide nano-filters were shown to (1) capture aerosol particles as small as 20 nm, (2) work in humid air and (3) completely liberate their captured particles in an aqueous solution compatible with the immunoassay technique. The immunoassay technology developed within this project combines electrophoretic capture with magnetic bead detection. It allows detection of as few as 150-600 analyte molecules or viruses in only three minutes, something no other known method can duplicate. The technology can be used in a variety of applications where speed of analysis and/or extremely low detection limits are of great importance: in rapid analysis of donor blood for hepatitis, HIV and other blood-borne infections in emergency blood transfusions, in trace analysis of pollutants, or in search of biomarkers in biological fluids. Combined in a single device, the water-soluble filter and ultra-sensitive immunoassay technique may solve the problem of early warning type detection of aerosolized pathogens. These two technologies are protected with five patent applications and are ready for commercialization.

  16. Back to basics: an evaluation of NaOH and alternative rapid DNA extraction protocols for DNA barcoding, genotyping, and disease diagnostics from fungal and oomycete samples.

    Science.gov (United States)

    Osmundson, Todd W; Eyre, Catherine A; Hayden, Katherine M; Dhillon, Jaskirn; Garbelotto, Matteo M

    2013-01-01

    The ubiquity, high diversity and often-cryptic manifestations of fungi and oomycetes frequently necessitate molecular tools for detecting and identifying them in the environment. In applications including DNA barcoding, pathogen detection from plant samples, and genotyping for population genetics and epidemiology, rapid and dependable DNA extraction methods scalable from one to hundreds of samples are desirable. We evaluated several rapid extraction methods (NaOH, Rapid one-step extraction (ROSE), Chelex 100, proteinase K) for their ability to obtain DNA of quantity and quality suitable for the following applications: PCR amplification of the multicopy barcoding locus ITS1/5.8S/ITS2 from various fungal cultures and sporocarps; single-copy microsatellite amplification from cultures of the phytopathogenic oomycete Phytophthora ramorum; probe-based P. ramorum detection from leaves. Several methods were effective for most of the applications, with NaOH extraction favored in terms of success rate, cost, speed and simplicity. Frozen dilutions of ROSE and NaOH extracts maintained PCR viability for over 32 months. DNA from rapid extractions performed poorly compared to CTAB/phenol-chloroform extracts for TaqMan diagnostics from tanoak leaves, suggesting that incomplete removal of PCR inhibitors is an issue for sensitive diagnostic procedures, especially from plants with recalcitrant leaf chemistry. NaOH extracts exhibited lower yield and size than CTAB/phenol-chloroform extracts; however, NaOH extraction facilitated obtaining clean sequence data from sporocarps contaminated by other fungi, perhaps due to dilution resulting from low DNA yield. We conclude that conventional extractions are often unnecessary for routine DNA sequencing or genotyping of fungi and oomycetes, and recommend simpler strategies where source materials and intended applications warrant such use. © 2012 Blackwell Publishing Ltd.

  17. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

    Directory of Open Access Journals (Sweden)

    Evelina Y. Basenko

    2018-03-01

    Full Text Available FungiDB (fungidb.org is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic and nonpathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, Aspergillus Genome Database (AspGD, The Broad Institute, Joint Genome Institute (JGI, Ensembl, and other sources. FungiDB offers a user-friendly web interface with embedded bioinformatics tools that support custom in silico experiments that leverage FungiDB-integrated data. In addition, a Galaxy-based workspace enables users to generate custom pipelines for large-scale data analysis (e.g., RNA-Seq, variant calling, etc.. This review provides an introduction to the FungiDB resources and focuses on available features, tools, and queries and how they can be used to mine data across a diverse range of integrated FungiDB datasets and records.

  18. Radiometric method for the rapid detection of Leptospira organisms

    International Nuclear Information System (INIS)

    Manca, N.; Verardi, R.; Colombrita, D.; Ravizzola, G.; Savoldi, E.; Turano, A.

    1986-01-01

    A rapid and sensitive radiometric method for detection of Leptospira interrogans serovar pomona and Leptospira interrogans serovar copenhageni is described. Stuart's medium and Middlebrook TB (12A) medium supplemented with bovine serum albumin, catalase, and casein hydrolysate and labeled with 14 C-fatty acids were used. The radioactivity was measured in a BACTEC 460. With this system, Leptospira organisms were detected in human blood in 2 to 5 days, a notably shorter time period than that required for the majority of detection techniques

  19. ECOTOXICITY AND PHYTOTOXICITY OF PLANT PROTECTION PRODUCTS TO RHIZOSPHERE FUNGI AND WINTER WHEAT SEEDLINGS

    Directory of Open Access Journals (Sweden)

    Anna Daria Stasiulewicz-Paluch

    2015-11-01

    Full Text Available Registration of plant protection products involves the analysis of their effects on soil microorganisms. The residues of plant protection products penetrate the soil, but their impact on fungi remains scarcely researched. In this study, the influence of selected plant protection products on the abundance of rhizosphere-dwelling fungi and the growth of winter wheat seedlings was evaluated under greenhouse conditions. The analysed plant protection products had an inhibitory effect on the growth of filamentous fungi in the rhizosphere, whereas yeasts were resistant to those products applied to soil. Tebuconazole exerted the strongest suppressive effect on the growth of filamentous fungi, and propiconazole was characterized by the greatest phytotoxic activity against winter wheat seedlings. Azoxystrobin had the weakest ecotoxic and phytotoxic effects, and its application to soil usually led to a rapid increase in the counts of fungi of the genus Acremonium.

  20. Culturable fungi in potting soils and compost.

    Science.gov (United States)

    Haas, Doris; Lesch, Susanne; Buzina, Walter; Galler, Herbert; Gutschi, Anna Maria; Habib, Juliana; Pfeifer, Bettina; Luxner, Josefa; Reinthaler, Franz F

    2016-11-01

    In the present study the spectrum and the incidence of fungi in potting soils and compost was investigated. Since soil is one of the most important biotopes for fungi, relatively high concentrations of fungal propagules are to be expected. For detection of fungi, samples of commercial soils, compost and soils from potted plants (both surface and sub-surface) were suspended and plated onto several mycological media. The resulting colonies were evaluated qualitatively and quantitatively. The results from the different sampling series vary, but concentrations on the surface of potted plants and in commercial soils are increased tenfold compared to compost and sub-surface soils. Median values range from 9.5 × 10(4) colony forming units (CFU)/g to 5.5 × 10(5) CFU/g. The spectrum of fungi also varies in the soils. However, all sampling series show high proportion of Aspergillus and Penicillium species, including potentially pathogenic species such as Aspergillus fumigatus. Cladosporium, a genus dominant in the ambient air, was found preferably in samples which were in contact with the air. The results show that potentially pathogenic fungi are present in soils. Immunocompromised individuals should avoid handling soils or potted plants in their immediate vicinity. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. Molecular detection of toxigenic potential of fungi in peanut samples collected in retail shops in Maringá/PR, Brazil

    Directory of Open Access Journals (Sweden)

    Alessandra Valéria de Oliveira

    2015-02-01

    Full Text Available Many foods are susceptible to fungal contamination. Grains, such as peanuts, are commonly affected, with consequences including compromised integrity and infeasibility for human and animal consumption. Furthermore, some fungi may pose a health risk, largely due the production of mycotoxins. Among these, aflatoxins produced by Aspergillus flavus and A. parasiticus produce various carcinogenic, teratogenic, immunosuppressive, hepatotoxic and nephrotoxic effects. Molecular techniques have been used to identify and distinguish fungal species in foods. The objective of this study was molecular detection of Aspergillus species in peanut samples collected in stores in Maringá-PR, by amplification of fungal genetic material with specific primers for the intergenic spacer aflR-aflJ and later cutting with restriction enzymes. Of the 50 peanut samples analyzed, 27 were positive for the intergenic spacer aflR-aflJ, seven of which were identified as Aspergillus flavus. Our results demonstrate that peanuts sold in retail stores in this region have potential for contamination with toxigenic fungi.

  2. Radiometric method for the rapid detection of Leptospira organisms

    Energy Technology Data Exchange (ETDEWEB)

    Manca, N.; Verardi, R.; Colombrita, D.; Ravizzola, G.; Savoldi, E.; Turano, A.

    1986-02-01

    A rapid and sensitive radiometric method for detection of Leptospira interrogans serovar pomona and Leptospira interrogans serovar copenhageni is described. Stuart's medium and Middlebrook TB (12A) medium supplemented with bovine serum albumin, catalase, and casein hydrolysate and labeled with /sup 14/C-fatty acids were used. The radioactivity was measured in a BACTEC 460. With this system, Leptospira organisms were detected in human blood in 2 to 5 days, a notably shorter time period than that required for the majority of detection techniques.

  3. Fungi with multifunctional lifestyles: endophytic insect pathogenic fungi.

    Science.gov (United States)

    Barelli, Larissa; Moonjely, Soumya; Behie, Scott W; Bidochka, Michael J

    2016-04-01

    This review examines the symbiotic, evolutionary, proteomic and genetic basis for a group of fungi that occupy a specialized niche as insect pathogens as well as endophytes. We focus primarily on species in the genera Metarhizium and Beauveria, traditionally recognized as insect pathogenic fungi but are also found as plant symbionts. Phylogenetic evidence suggests that these fungi are more closely related to grass endophytes and diverged from that lineage ca. 100 MYA. We explore how the dual life cycles of these fungi as insect pathogens and endophytes are coupled. We discuss the evolution of insect pathogenesis while maintaining an endophytic lifestyle and provide examples of genes that may be involved in the transition toward insect pathogenicity. That is, some genes for insect pathogenesis may have been co-opted from genes involved in endophytic colonization. Other genes may be multifunctional and serve in both lifestyle capacities. We suggest that their evolution as insect pathogens allowed them to effectively barter a specialized nitrogen source (i.e. insects) with host plants for photosynthate. These ubiquitous fungi may play an important role as plant growth promoters and have a potential reservoir of secondary metabolites.

  4. In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections

    Science.gov (United States)

    Rust fungi infect a wide range of plant species making them of particular interest to plant pathologists. In order to study the interactions between these important pathogenic fungi and their host plants it is useful to be able to differentiate fungal tissue from plant tissue. This can be accomplish...

  5. Chemical ecology of fungi.

    Science.gov (United States)

    Spiteller, Peter

    2015-07-01

    Fungi are widespread in nature and have conquered nearly every ecological niche. Fungi occur not only in terrestrial but also in freshwater and marine environments. Moreover, fungi are known as a rich source of secondary metabolites. Despite these facts, the ecological role of many of these metabolites is still unknown and the chemical ecology of fungi has not been investigated systematically so far. This review intends to present examples of the various chemical interactions of fungi with other fungi, plants, bacteria and animals and to give an overview of the current knowledge of fungal chemical ecology.

  6. Validation of the Applied Biosystems RapidFinder Shiga Toxin-Producing E. coli (STEC) Detection Workflow.

    Science.gov (United States)

    Cloke, Jonathan; Matheny, Sharon; Swimley, Michelle; Tebbs, Robert; Burrell, Angelia; Flannery, Jonathan; Bastin, Benjamin; Bird, Patrick; Benzinger, M Joseph; Crowley, Erin; Agin, James; Goins, David; Salfinger, Yvonne; Brodsky, Michael; Fernandez, Maria Cristina

    2016-11-01

    The Applied Biosystems™ RapidFinder™ STEC Detection Workflow (Thermo Fisher Scientific) is a complete protocol for the rapid qualitative detection of Escherichia coli (E. coli) O157:H7 and the "Big 6" non-O157 Shiga-like toxin-producing E. coli (STEC) serotypes (defined as serogroups: O26, O45, O103, O111, O121, and O145). The RapidFinder STEC Detection Workflow makes use of either the automated preparation of PCR-ready DNA using the Applied Biosystems PrepSEQ™ Nucleic Acid Extraction Kit in conjunction with the Applied Biosystems MagMAX™ Express 96-well magnetic particle processor or the Applied Biosystems PrepSEQ Rapid Spin kit for manual preparation of PCR-ready DNA. Two separate assays comprise the RapidFinder STEC Detection Workflow, the Applied Biosystems RapidFinder STEC Screening Assay and the Applied Biosystems RapidFinder STEC Confirmation Assay. The RapidFinder STEC Screening Assay includes primers and probes to detect the presence of stx1 (Shiga toxin 1), stx2 (Shiga toxin 2), eae (intimin), and E. coli O157 gene targets. The RapidFinder STEC Confirmation Assay includes primers and probes for the "Big 6" non-O157 STEC and E. coli O157:H7. The use of these two assays in tandem allows a user to detect accurately the presence of the "Big 6" STECs and E. coli O157:H7. The performance of the RapidFinder STEC Detection Workflow was evaluated in a method comparison study, in inclusivity and exclusivity studies, and in a robustness evaluation. The assays were compared to the U.S. Department of Agriculture (USDA), Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook (MLG) 5.09: Detection, Isolation and Identification of Escherichia coli O157:H7 from Meat Products and Carcass and Environmental Sponges for raw ground beef (73% lean) and USDA/FSIS-MLG 5B.05: Detection, Isolation and Identification of Escherichia coli non-O157:H7 from Meat Products and Carcass and Environmental Sponges for raw beef trim. No statistically significant

  7. Use of Tethered Enzymes as a Platform Technology for Rapid Analyte Detection.

    Directory of Open Access Journals (Sweden)

    Roy Cohen

    Full Text Available Rapid diagnosis for time-sensitive illnesses such as stroke, cardiac arrest, and septic shock is essential for successful treatment. Much attention has therefore focused on new strategies for rapid and objective diagnosis, such as Point-of-Care Tests (PoCT for blood biomarkers. Here we use a biomimicry-based approach to demonstrate a new diagnostic platform, based on enzymes tethered to nanoparticles (NPs. As proof of principle, we use oriented immobilization of pyruvate kinase (PK and luciferase (Luc on silica NPs to achieve rapid and sensitive detection of neuron-specific enolase (NSE, a clinically relevant biomarker for multiple diseases ranging from acute brain injuries to lung cancer. We hypothesize that an approach capitalizing on the speed and catalytic nature of enzymatic reactions would enable fast and sensitive biomarker detection, suitable for PoCT devices.We performed in-vitro, animal model, and human subject studies. First, the efficiency of coupled enzyme activities when tethered to NPs versus when in solution was tested, demonstrating a highly sensitive and rapid detection of physiological and pathological concentrations of NSE. Next, in rat stroke models the enzyme-based assay was able in minutes to show a statistically significant increase in NSE levels in samples taken 1 hour before and 0, 1, 3 and 6 hours after occlusion of the distal middle cerebral artery. Finally, using the tethered enzyme assay for detection of NSE in samples from 20 geriatric human patients, we show that our data match well (r = 0.815 with the current gold standard for biomarker detection, ELISA-with a major difference being that we achieve detection in 10 minutes as opposed to the several hours required for traditional ELISA.Oriented enzyme immobilization conferred more efficient coupled activity, and thus higher assay sensitivity, than non-tethered enzymes. Together, our findings provide proof of concept for using oriented immobilization of active

  8. Biocontrol and Rapid Detection of Food-borne Pathogens Using Bacteriophages and Endolysins

    Directory of Open Access Journals (Sweden)

    Jaewoo eBai

    2016-04-01

    Full Text Available Bacteriophages have been suggested as natural food preservatives as well as rapid detection materials for food-borne pathogens in various foods. Since Listeria monocytogenes-targeting phage cocktail (ListShield was approved for applications in foods, numerous phages have been screened and experimentally characterized for phage applications in foods. A single phage and phage cocktail treatments to various foods contaminated with food-borne pathogens including E. coli O157:H7, Salmonella enterica, Campylobacter jejuni, Listeria monocytogenes, Staphylococcus aureus, Cronobacter sakazakii, and Vibrio spp. revealed that they have great potential to control various food-borne pathogens and may be alternative for conventional food preservatives. In addition, phage-derived endolysins with high host specificity and host lysis activities may be preferred to food applications rather than phages. For rapid detection of food-borne pathogens, cell-wall binding domains (CBDs from endolysins have been suggested due to their high host-specific binding. Fluorescence-tagged CBDs have been successfully evaluated and suggested to be alternative materials of expensive antibodies for various detection applications. Most recently, reporter phage systems have been developed and tested to confirm their usability and accuracy for specific detection. These systems revealed some advantages like rapid detection of only viable pathogenic cells without interference by food components in a very short reaction time, suggesting that these systems may be suitable for monitoring of pathogens in foods. Consequently, phage is the next-generation biocontrol agent as well as rapid detection tool to confirm and even identify the food-borne pathogens present in various foods.

  9. Aflatoxigenic Fungi and Aflatoxins in Portuguese Almonds

    Science.gov (United States)

    Rodrigues, P.; Venâncio, A.; Lima, N.

    2012-01-01

    Aflatoxin contamination of nuts is an increasing concern to the consumer's health. Portugal is a big producer of almonds, but there is no scientific knowledge on the safety of those nuts, in terms of mycotoxins. The aim of this paper was to study the incidence of aflatoxigenic fungi and aflatoxin contamination of 21 samples of Portuguese almonds, and its evolution throughout the various stages of production. All fungi belonging to Aspergillus section Flavi were identified and tested for their aflatoxigenic ability. Almond samples were tested for aflatoxin contamination by HPLC-fluorescence. In total, 352 fungi belonging to Aspergillus section Flavi were isolated from Portuguese almonds: 127 were identified as A. flavus (of which 28% produced aflatoxins B), 196 as typical or atypical A. parasiticus (all producing aflatoxins B and G), and 29 as A. tamarii (all nonaflatoxigenic). Aflatoxins were detected in only one sample at 4.97 μg/kg. PMID:22666128

  10. Aflatoxigenic Fungi and Aflatoxins in Portuguese Almonds

    Directory of Open Access Journals (Sweden)

    P. Rodrigues

    2012-01-01

    Full Text Available Aflatoxin contamination of nuts is an increasing concern to the consumer’s health. Portugal is a big producer of almonds, but there is no scientific knowledge on the safety of those nuts, in terms of mycotoxins. The aim of this paper was to study the incidence of aflatoxigenic fungi and aflatoxin contamination of 21 samples of Portuguese almonds, and its evolution throughout the various stages of production. All fungi belonging to Aspergillus section Flavi were identified and tested for their aflatoxigenic ability. Almond samples were tested for aflatoxin contamination by HPLC-fluorescence. In total, 352 fungi belonging to Aspergillus section Flavi were isolated from Portuguese almonds: 127 were identified as A. flavus (of which 28% produced aflatoxins B, 196 as typical or atypical A. parasiticus (all producing aflatoxins B and G, and 29 as A. tamarii (all nonaflatoxigenic. Aflatoxins were detected in only one sample at 4.97 μg/kg.

  11. Rapid Monitoring of Bacteria and Fungi aboard the International Space Station (ISS)

    Science.gov (United States)

    Gunter, D.; Flores, G.; Effinger, M.; Maule, J.; Wainwright, N.; Steele, A.; Damon, M.; Wells, M.; Williams, S.; Morris, H.; hide

    2009-01-01

    Microorganisms within spacecraft have traditionally been monitored with culture-based techniques. These techniques involve growth of environmental samples (cabin water, air or surfaces) on agar-type media for several days, followed by visualization of resulting colonies or return of samples to Earth for ground-based analysis. Data obtained over the past 4 decades have enhanced our understanding of the microbial ecology within space stations. However, the approach has been limited by the following factors: i) Many microorganisms (estimated > 95%) in the environment cannot grow on conventional growth media; ii) Significant time lags (3-5 days for incubation and up to several months to return samples to ground); iii) Condensation in contact slides hinders colony counting by crew; and iv) Growth of potentially harmful microorganisms, which must then be disposed of safely. This report describes the operation of a new culture-independent technique onboard the ISS for rapid analysis (within minutes) of endotoxin and beta-1, 3-glucan, found in the cell walls of gramnegative bacteria and fungi, respectively. The technique involves analysis of environmental samples with the Limulus Amebocyte Lysate (LAL) assay in a handheld device, known as the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS). LOCADPTS was launched to the ISS in December 2006, and here we present data obtained from Mach 2007 until the present day. These data include a comparative study between LOCADPTS analysis and existing culture-based methods; and an exploratory survey of surface endotoxin and beta-1, 3-glucan throughout the ISS. While a general correlation between LOCAD-PTS and traditional culture-based methods should not be expected, we will suggest new requirements for microbial monitoring based upon culture-independent parameters measured by LOCAD-PTS.

  12. Use of DNA sequencing to detect pathogenic, saprotrophic, and stain fungi in sapwood of declining red pine (Pinus resinosa) in the Upper Midwest

    Science.gov (United States)

    M.T. Banik; D.L. Lindner; J. Juzwik; J.A. Glaeser

    2013-01-01

    An inexpensive kit was developed to collect wood samples for molecular detection of pathogenic, saprotrophic and stain fungi in declining Pinus resinosa in the Upper Midwest. The kit contained materials for "clean" collection of sapwood drill shavings, which were then subjected to PCR of the rDNA ITS region with fungal-specific primers,...

  13. Exposure to airborne fungi during sorting of recyclable plastics in waste treatment facilities

    Directory of Open Access Journals (Sweden)

    Kristýna Černá

    2017-02-01

    Full Text Available Background: In working environment of waste treatment facilities, employees are exposed to high concentrations of airborne microorganisms. Fungi constitute an essential part of them. This study aims at evaluating the diurnal variation in concentrations and species composition of the fungal contamination in 2 plastic waste sorting facilities in different seasons. Material and Methods: Air samples from the 2 sorting facilities were collected through the membrane filters method on 4 different types of cultivation media. Isolated fungi were classified to genera or species by using a light microscopy. Results: Overall, the highest concentrations of airborne fungi were recorded in summer (9.1×103–9.0×105 colony-forming units (CFU/m3, while the lowest ones in winter (2.7×103–2.9×105 CFU/m3. The concentration increased from the beginning of the work shift and reached a plateau after 6–7 h of the sorting. The most frequently isolated airborne fungi were those of the genera Penicillium and Aspergillus. The turnover of fungal species between seasons was relatively high as well as changes in the number of detected species, but potentially toxigenic and allergenic fungi were detected in both facilities during all seasons. Conclusions: Generally, high concentrations of airborne fungi were detected in the working environment of plastic waste sorting facilities, which raises the question of health risk taken by the employees. Based on our results, the use of protective equipment by employees is recommended and preventive measures should be introduced into the working environment of waste sorting facilities to reduce health risk for employees. Med Pr 2017;68(1:1–9

  14. Detection of phytohormones in temperate forest fungi predicts consistent abscisic acid production and a common pathway for cytokinin biosynthesis.

    Science.gov (United States)

    Morrison, Erin N; Knowles, Sarah; Hayward, Allison; Thorn, R Greg; Saville, Barry J; Emery, R J N

    2015-01-01

    The phytohormones, abscisic acid and cytokinin, once were thought to be present uniquely in plants, but increasing evidence suggests that these hormones are present in a wide variety of organisms. Few studies have examined fungi for the presence of these "plant" hormones or addressed whether their levels differ based on the nutrition mode of the fungus. This study examined 20 temperate forest fungi of differing nutritional modes (ectomycorrhizal, wood-rotting, saprotrophic). Abscisic acid and cytokinin were present in all fungi sampled; this indicated that the sampled fungi have the capacity to synthesize these two classes of phytohormones. Of the 27 cytokinins analyzed by HPLC-ESI MS/MS, seven were present in all fungi sampled. This suggested the existence of a common cytokinin metabolic pathway in fungi that does not vary among different nutritional modes. Predictions regarding the source of isopentenyl, cis-zeatin and methylthiol CK production stemming from the tRNA degradation pathway among fungi are discussed. © 2015 by The Mycological Society of America.

  15. Rapid Detection and Characterization of Emerging Foreign Animal Disease Pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-11-18

    To best safeguard human and animal health requires early detection and characterization of disease events. This must include effective surveillance for emerging infectious diseases. Both deliberate and natural outbreaks have enormous economic and public health impacts, and can present serious threats to national security. In this project, we developed novel next generation detection technologies to protect the agricultural economy and biosecurity. The first technology is a multiplexed assay to simultaneously detection 10 swine viral and bacterial pathogens. The second one is the Lawrence Livermore Microbial Detection Array (LLMDA) which can detect more than 10,000 microbial species including 4219 viruses, 5367 bacteria, 265 fungi, 117 protozoa and 293 archaea. We analyzed a series of swine clinical samples from past disease events to demonstrate the utility of the assays for faster and cheaper detection of emerging and foreign animal disease pathogens, and their utility as s routine diagnosis and surveillance tool. A second goal of the study is to better understand mechanisms of African swine fever virus (ASFV) infection in pigs to aid the development of countermeasures and diagnostics. There is no vaccine available for ASF. ASF outbreak is on the rise on several European countries. Though ASF is not currently in the U.S., a potential outbreak in the U.S. would be detrimental to the swine industry and the US agricultural economy. We pursued a genome-wide approach to characterize the pig immune responses after ASFV infection. We used RNA sequencing and bioinformatics methods to identify genes and pathways that are affected during ASF infection. We have identified a list of most differentially expressed genes that are in the immune response pathways.

  16. Using molecular techniques for rapid detection of Salmonella ...

    African Journals Online (AJOL)

    PRECIOUS

    2010-02-01

    Feb 1, 2010 ... A total of 152 samples of chicken and chicken products ... detection of Salmonella species in the collected field samples ... that 16 million new cases of typhoid fever occur each ... vative methods for the rapid identification of Salmonella ... saved for the PCR-Non Selective test (PCR-NS) and 1 ml of the.

  17. Indigenous people's detection of rapid ecological change.

    Science.gov (United States)

    Aswani, Shankar; Lauer, Matthew

    2014-06-01

    When sudden catastrophic events occur, it becomes critical for coastal communities to detect and respond to environmental transformations because failure to do so may undermine overall ecosystem resilience and threaten people's livelihoods. We therefore asked how capable of detecting rapid ecological change following massive environmental disruptions local, indigenous people are. We assessed the direction and periodicity of experimental learning of people in the Western Solomon Islands after a tsunami in 2007. We compared the results of marine science surveys with local ecological knowledge of the benthos across 3 affected villages and 3 periods before and after the tsunami. We sought to determine how people recognize biophysical changes in the environment before and after catastrophic events such as earthquakes and tsunamis and whether people have the ability to detect ecological changes over short time scales or need longer time scales to recognize changes. Indigenous people were able to detect changes in the benthos over time. Detection levels differed between marine science surveys and local ecological knowledge sources over time, but overall patterns of statistically significant detection of change were evident for various habitats. Our findings have implications for marine conservation, coastal management policies, and disaster-relief efforts because when people are able to detect ecological changes, this, in turn, affects how they exploit and manage their marine resources. © 2014 Society for Conservation Biology.

  18. Rapid detection of Avian Influenza Virus - Towards point of care diagnosis

    DEFF Research Database (Denmark)

    Dhumpa, Raghuram

    barcode and fluorescent beads were also developed for rapid detection and identification of the AIV. In both methods, the detection involved sandwiching of the target AIV between monoclonal antibodies for nucleoproteins and for matrix proteins. In the fluorescent DNA barcode-based immunoassay, fluorophore...

  19. Enrichment of arbuscular mycorrhizal fungi in a contaminated soil after rehabilitation.

    Science.gov (United States)

    Lopes Leal, Patrícia; Varón-López, Maryeimy; Gonçalves de Oliveira Prado, Isabelle; Valentim Dos Santos, Jessé; Fonsêca Sousa Soares, Cláudio Roberto; Siqueira, José Oswaldo; de Souza Moreira, Fatima Maria

    Spore counts, species composition and richness of arbuscular mycorrhizal fungi, and soil glomalin contents were evaluated in a soil contaminated with Zn, Cu, Cd and Pb after rehabilitation by partial replacement of the contaminated soil with non-contaminated soil, and by Eucalyptus camaldulensis planting with and without Brachiaria decumbens sowing. These rehabilitation procedures were compared with soils from contaminated non-rehabilitated area and non-contaminated adjacent soils. Arbuscular mycorrhizal fungi communities attributes were assessed by direct field sampling, trap culture technique, and by glomalin contents estimate. Arbuscular mycorrhizal fungi was markedly favored by rehabilitation, and a total of 15 arbuscular mycorrhizal fungi morphotypes were detected in the studied area. Species from the Glomus and Acaulospora genera were the most common mycorrhizal fungi. Number of spores was increased by as much as 300-fold, and species richness almost doubled in areas rehabilitated by planting Eucalyptus in rows and sowing B. decumbens in inter-rows. Contents of heavy metals in the soil were negatively correlated with both species richness and glomalin contents. Introduction of B. decumbens together with Eucalyptus causes enrichment of arbuscular mycorrhizal fungi species and a more balanced community of arbuscular mycorrhizal fungi spores in contaminated soil. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  20. Use of rapid-scan EPR to improve detection sensitivity for spin-trapped radicals.

    Science.gov (United States)

    Mitchell, Deborah G; Rosen, Gerald M; Tseitlin, Mark; Symmes, Breanna; Eaton, Sandra S; Eaton, Gareth R

    2013-07-16

    The short lifetime of superoxide and the low rates of formation expected in vivo make detection by standard continuous wave (CW) electron paramagnetic resonance (EPR) challenging. The new rapid-scan EPR method offers improved sensitivity for these types of samples. In rapid-scan EPR, the magnetic field is scanned through resonance in a time that is short relative to electron spin relaxation times, and data are processed to obtain the absorption spectrum. To validate the application of rapid-scan EPR to spin trapping, superoxide was generated by the reaction of xanthine oxidase and hypoxanthine with rates of 0.1-6.0 μM/min and trapped with 5-tert-butoxycarbonyl-5-methyl-1-pyrroline-N-oxide (BMPO). Spin trapping with BMPO to form the BMPO-OOH adduct converts the very short-lived superoxide radical into a more stable spin adduct. There is good agreement between the hyperfine splitting parameters obtained for BMPO-OOH by CW and rapid-scan EPR. For the same signal acquisition time, the signal/noise ratio is >40 times higher for rapid-scan than for CW EPR. Rapid-scan EPR can detect superoxide produced by Enterococcus faecalis at rates that are too low for detection by CW EPR. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  1. Control of grapevine wood fungi in commercial nurseries

    Directory of Open Access Journals (Sweden)

    C. Rego

    2009-05-01

    Full Text Available Previous surveys conducted in commercial nurseries found that different wood fungi, namely Cylindrocarpon spp., Botryosphaeriaceae, Phomopsis viticola and Phaeomoniella chlamydospora infect grapevine cuttings. Two field trials were carried out to evaluate the effectiveness of cyprodinil + fludioxonil, pyraclostrobin + metiram, fludioxonil and cyprodinil to prevent or reduce natural infections caused by such fungi. Rootstock and scion cuttings were soaked in fungicidal suspensions for 50 min prior to grafting. After callusing, the grafted cuttings were planted in two commercial field nurseries with and without a previous history of grapevine cultivation. After nine months in the nursery, the plants were uprooted and analysed for the incidence and severity of the wood fungi. Plants uprooted from the field without a previous history of grapevine cultivation were generally less strongly infected by wood fungi. Under this condition, only the mixture cyprodinil + fludioxonil simultaneously reduced the incidence of Cylindrocarpon and Botryosphaeriaceae fungi, as well as the severity of Cylindrocarpon infections. Treatments did not produce significant differences in the incidence and severity of P. viticola, and Pa. chlamydospora. For plants grown in the field with a grapevine history, all fungicides except cyprodinil significantly reduced the incidence and severity of Cylindrocarpon fungi. Also, the incidence and severity of Botryosphaeriaceae pathogens were significantly decreased both by cyprodinil + fludioxonil and by cyprodinil. No significant differences were noticed for P. viticola incidence and severity, and Pa. chlamydospora was not detected again. These results suggest that the practice of soaking grapevine cuttings in selected fungicides prior to grafting significantly reduces Cylindrocarpon spp. and Botryosphaeriaceae infections, thus improving the quality of planting material.

  2. Root-Associated Fungi Shared Between Arbuscular Mycorrhizal and Ectomycorrhizal Conifers in a Temperate Forest.

    Science.gov (United States)

    Toju, Hirokazu; Sato, Hirotoshi

    2018-01-01

    Arbuscular mycorrhizal and ectomycorrhizal symbioses are among the most important drivers of terrestrial ecosystem dynamics. Historically, the two types of symbioses have been investigated separately because arbuscular mycorrhizal and ectomycorrhizal plant species are considered to host discrete sets of fungal symbionts (i.e., arbuscular mycorrhizal and ectomycorrhizal fungi, respectively). Nonetheless, recent studies based on high-throughput DNA sequencing technologies have suggested that diverse non-mycorrhizal fungi (e.g., endophytic fungi) with broad host ranges play roles in relationships between arbuscular mycorrhizal and ectomycorrhizal plant species in forest ecosystems. By analyzing an Illumina sequencing dataset of root-associated fungi in a temperate forest in Japan, we statistically examined whether co-occurring arbuscular mycorrhizal ( Chamaecyparis obtusa ) and ectomycorrhizal ( Pinus densiflora ) plant species could share non-mycorrhizal fungal communities. Among the 919 fungal operational taxonomic units (OTUs) detected, OTUs in various taxonomic lineages were statistically designated as "generalists," which associated commonly with both coniferous species. The list of the generalists included fungi in the genera Meliniomyces, Oidiodendron, Cladophialophora, Rhizodermea, Penicillium , and Mortierella . Meanwhile, our statistical analysis also detected fungi preferentially associated with Chamaecyparis (e.g., Pezicula ) or Pinus (e.g., Neolecta ). Overall, this study provides a basis for future studies on how arbuscular mycorrhizal and ectomycorrhizal plant species interactively drive community- or ecosystem-scale processes. The physiological functions of the fungi highlighted in our host-preference analysis deserve intensive investigations for understanding their roles in plant endosphere and rhizosphere.

  3. Rapid Detection of Salmonella enterica in Food Using a Compact Disc-Shaped Device

    Directory of Open Access Journals (Sweden)

    Shunsuke Furutani

    2016-01-01

    Full Text Available Rapid detection of food-borne pathogens is essential to public health and the food industry. Although the conventional culture method is highly sensitive, it takes at least a few days to detect food-borne pathogens. Even though polymerase chain reaction (PCR can detect food-borne pathogens in a few hours, it is more expensive and unsatisfactorily sensitive relative to the culture method. We have developed a method to rapidly detect Salmonella enterica by using a compact disc (CD-shaped device that can reduce reagent consumption in conventional PCR. The detection method, which combines culture and PCR, is more rapid than the conventional culture method and is more sensitive and cheaper than PCR. In this study, we also examined a sample preparation method that involved collecting bacterial cells from food. The bacteria collected from chicken meat spiked with S. enterica were mixed with PCR reagents, and PCR was performed on the device. At a low concentration of S. enterica, the collected S. enterica was cultured before PCR for sensitive detection. After cultivation for 4 h, S. enterica at 1.7 × 104 colony-forming units (CFUs·g−1 was detected within 8 h, which included the time needed for sample preparation and detection. Furthermore, the detection of 30 CFUs·g−1 of S. enterica was possible within 12 h including 8 h for cultivation.

  4. Exposure to airborne fungi during sorting of recyclable plastics in waste treatment facilities.

    Science.gov (United States)

    Černá, Kristýna; Wittlingerová, Zdeňka; Zimová, Magdaléna; Janovský, Zdeněk

    2017-02-28

    In working environment of waste treatment facilities, employees are exposed to high concentrations of airborne microorganisms. Fungi constitute an essential part of them. This study aims at evaluating the diurnal variation in concentrations and species composition of the fungal contamination in 2 plastic waste sorting facilities in different seasons. Air samples from the 2 sorting facilities were collected through the membrane filters method on 4 different types of cultivation media. Isolated fungi were classified to genera or species by using a light microscopy. Overall, the highest concentrations of airborne fungi were recorded in summer (9.1×103-9.0×105 colony-forming units (CFU)/m3), while the lowest ones in winter (2.7×103-2.9×105 CFU/m3). The concentration increased from the beginning of the work shift and reached a plateau after 6-7 h of the sorting. The most frequently isolated airborne fungi were those of the genera Penicillium and Aspergillus. The turnover of fungal species between seasons was relatively high as well as changes in the number of detected species, but potentially toxigenic and allergenic fungi were detected in both facilities during all seasons. Generally, high concentrations of airborne fungi were detected in the working environment of plastic waste sorting facilities, which raises the question of health risk taken by the employees. Based on our results, the use of protective equipment by employees is recommended and preventive measures should be introduced into the working environment of waste sorting facilities to reduce health risk for employees. Med Pr 2017;68(1):1-9. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

  5. Use of Tethered Enzymes as a Platform Technology for Rapid Analyte Detection

    Science.gov (United States)

    Cohen, Roy; Lata, James P.; Lee, Yurim; Hernández, Jean C. Cruz; Nishimura, Nozomi; Schaffer, Chris B.; Mukai, Chinatsu; Nelson, Jacquelyn L.; Brangman, Sharon A.; Agrawal, Yash; Travis, Alexander J.

    2015-01-01

    Background Rapid diagnosis for time-sensitive illnesses such as stroke, cardiac arrest, and septic shock is essential for successful treatment. Much attention has therefore focused on new strategies for rapid and objective diagnosis, such as Point-of-Care Tests (PoCT) for blood biomarkers. Here we use a biomimicry-based approach to demonstrate a new diagnostic platform, based on enzymes tethered to nanoparticles (NPs). As proof of principle, we use oriented immobilization of pyruvate kinase (PK) and luciferase (Luc) on silica NPs to achieve rapid and sensitive detection of neuron-specific enolase (NSE), a clinically relevant biomarker for multiple diseases ranging from acute brain injuries to lung cancer. We hypothesize that an approach capitalizing on the speed and catalytic nature of enzymatic reactions would enable fast and sensitive biomarker detection, suitable for PoCT devices. Methods and findings We performed in-vitro, animal model, and human subject studies. First, the efficiency of coupled enzyme activities when tethered to NPs versus when in solution was tested, demonstrating a highly sensitive and rapid detection of physiological and pathological concentrations of NSE. Next, in rat stroke models the enzyme-based assay was able in minutes to show a statistically significant increase in NSE levels in samples taken 1 hour before and 0, 1, 3 and 6 hours after occlusion of the distal middle cerebral artery. Finally, using the tethered enzyme assay for detection of NSE in samples from 20 geriatric human patients, we show that our data match well (r = 0.815) with the current gold standard for biomarker detection, ELISA—with a major difference being that we achieve detection in 10 minutes as opposed to the several hours required for traditional ELISA. Conclusions Oriented enzyme immobilization conferred more efficient coupled activity, and thus higher assay sensitivity, than non-tethered enzymes. Together, our findings provide proof of concept for using

  6. Modified DNA extraction for rapid PCR detection of methicillin-resistant staphylococci

    International Nuclear Information System (INIS)

    Japoni, A.; Alborzi, A.; Rasouli, M.; Pourabbas, B.

    2004-01-01

    Nosocomial infection caused by methicillin-resistant staphylococci poses a serious problem in many countries. The aim of this study was to rapidly and reliably detect methicillin-resistant-staphylococci in order to suggest appropriate therapy. The presence or absence of the methicillin-resistance gene in 115 clinical isolates of staphylococcus aureus and 50 isolates of coagulase negative staphylococci was examined by normal PCR. DNA extraction for PCR performance was then modified by omission of achromopeptadiase and proteinase K digestion, phenol/chloroform extraction and ethanol precipitation. All isolates with Mic>8 μ g/ml showed positive PCR. No differences in PCR detection have been observed when normal and modified DNA extractions have been performed. Our modified DNA extraction can quickly detect methicillin-resistant staphylococci by PCR. The advantage of rapid DNA extraction extends to both reduction of time and cost of PCR performance. This modified DNA extraction is suitable for different PCR detection, when staphylococci are the subject of DNA analysis

  7. Rapid and specific detection of Asian- and African-lineage Zika viruses.

    Science.gov (United States)

    Chotiwan, Nunya; Brewster, Connie D; Magalhaes, Tereza; Weger-Lucarelli, James; Duggal, Nisha K; Rückert, Claudia; Nguyen, Chilinh; Garcia Luna, Selene M; Fauver, Joseph R; Andre, Barb; Gray, Meg; Black, William C; Kading, Rebekah C; Ebel, Gregory D; Kuan, Guillermina; Balmaseda, Angel; Jaenisch, Thomas; Marques, Ernesto T A; Brault, Aaron C; Harris, Eva; Foy, Brian D; Quackenbush, Sandra L; Perera, Rushika; Rovnak, Joel

    2017-05-03

    Understanding the dynamics of Zika virus transmission and formulating rational strategies for its control require precise diagnostic tools that are also appropriate for resource-poor environments. We have developed a rapid and sensitive loop-mediated isothermal amplification (LAMP) assay that distinguishes Zika viruses of Asian and African lineages. The assay does not detect chikungunya virus or flaviviruses such as dengue, yellow fever, or West Nile viruses. The assay conditions allowed direct detection of Zika virus RNA in cultured infected cells; in mosquitoes; in virus-spiked samples of human blood, plasma, saliva, urine, and semen; and in infected patient serum, plasma, and semen samples without the need for RNA isolation or reverse transcription. The assay offers rapid, specific, sensitive, and inexpensive detection of the Asian-lineage Zika virus strain that is currently circulating in the Western hemisphere, and can also detect the African-lineage Zika virus strain using separate, specific primers. Copyright © 2017, American Association for the Advancement of Science.

  8. Rapid and specific detection of Asian- and African-lineage Zika viruses

    Science.gov (United States)

    Chotiwan, Nunya; Brewster, Connie D.; Magalhaes, Tereza; Weger-Lucarelli, James; Duggal, Nisha K.; Rückert, Claudia; Nguyen, Chilinh; Garcia Luna, Selene M.; Fauver, Joseph R.; Andre, Barb; Gray, Meg; Black, William C.; Kading, Rebekah C.; Ebel, Gregory D.; Kuan, Guillermina; Balmaseda, Angel; Jaenisch, Thomas; Marques, Ernesto T. A.; Brault, Aaron C.; Harris, Eva; Foy, Brian D.; Quackenbush, Sandra L.; Perera, Rushika; Rovnak, Joel

    2017-01-01

    Understanding the dynamics of Zika virus transmission and formulating rational strategies for its control require precise diagnostic tools that are also appropriate for resource-poor environments. We have developed a rapid and sensitive loop-mediated isothermal amplification (LAMP) assay that distinguishes Zika viruses of Asian and African lineages. The assay does not detect chikungunya virus or flaviviruses such as dengue, yellow fever, or West Nile viruses. The assay conditions allowed direct detection of Zika virus RNA in cultured infected cells; in mosquitoes; in virus-spiked samples of human blood, plasma, saliva, urine, and semen; and in infected patient serum, plasma, and semen samples without the need for RNA isolation or reverse transcription. The assay offers rapid, specific, sensitive, and inexpensive detection of the Asian-lineage Zika virus strain that is currently circulating in the Western hemisphere, and can also detect the African-lineage Zika virus strain using separate, specific primers. PMID:28469032

  9. Application of molecular genetic methods for identification of wood-decaying fungi in wood constructions

    Directory of Open Access Journals (Sweden)

    Elena Bobeková

    2008-01-01

    Full Text Available The aim of the paper is to evaluate the utilization of molecular biology methods for detection of wood decaying fungi directly from decomposed wood using a commercial DNA extraction kit developed for soil substrates (PowerSoil™ DNA isolation kit. The experiment based on dry rot fungus (Serpula lacrymans detection from inoculated wooden pieces under laboratory conditions was followed by field detection of wood-decaying fungi from wood structures on building constructions. Fungal DNA was identified using the PCR–based methods including species-specific PCR and sequencing of amplified ITS region of ribosomal DNA.

  10. Fungal conservation: Protected species of fungi in South Serbia region

    Directory of Open Access Journals (Sweden)

    Sadiković, D.

    2013-12-01

    Full Text Available Protection and conservation of fungi has only recently became an issue of concern. Main motives for increased attention are uncontrolled, mass collecting of edible wild mushrooms and environmental pollution which leads to the rapid decline of their natural habitats, some of which are rich with rare and endangered species. By Serbian Nature Conservation Law 2010. there are 38 strictly protected fungal species of which 17 species are recorded in this paper. 11 of those recorded species are on European and/or National Red List of endangered fungal species. All investigated territories were in South Serbia region. This study is a contribution to conservation of protected and threatened fungi and their respective habitats in Serbia.

  11. Rapid antemortem detection of CWD prions in deer saliva.

    Directory of Open Access Journals (Sweden)

    Davin M Henderson

    Full Text Available Chronic wasting disease (CWD is an efficiently transmitted prion disease of cervids, now identified in 22 United States, 2 Canadian provinces and Korea. One hallmark of CWD is the shedding of infectious prions in saliva, as demonstrated by bioassay in deer. It is also clear that the concentration of prions in saliva, blood, urine and feces is much lower than in the nervous system or lymphoid tissues. Rapid in vitro detection of CWD (and other prions in body fluids and excreta has been problematic due to the sensitivity limits of direct assays (western blotting, ELISA and the presence of inhibitors in these complex biological materials that hamper detection. Here we use real-time quaking induced conversion (RT-QuIC to demonstrate CWD prions in both diluted and prion-enriched saliva samples from asymptomatic and symptomatic white-tailed deer. CWD prions were detected in 14 of 24 (58.3% diluted saliva samples from CWD-exposed white-tailed deer, including 9 of 14 asymptomatic animals (64.2%. In addition, a phosphotungstic acid enrichment enhanced the RT-QuIC assay sensitivity, enabling detection in 19 of 24 (79.1% of the above saliva samples. Bioassay in Tg[CerPrP] mice confirmed the presence of infectious prions in 2 of 2 RT-QuIC-positive saliva samples so examined. The modified RT-QuIC analysis described represents a non-invasive, rapid ante-mortem detection of prions in complex biologic fluids, excreta, or environmental samples as well as a tool for exploring prion trafficking, peripheralization, and dissemination.

  12. ASYMMETRIC SULFOXIDATION OF ALBENDAZOLE TO RICOBENDAZOLE BY FUNGI: EFFECT OF pH

    Directory of Open Access Journals (Sweden)

    Thiago Barth

    2015-08-01

    Full Text Available Albendazole (ABZ is an anthelmintic drug used for the treatment of infectious diseases in veterinary and human medicine. This drug is a prochiral drug that after administration, is rapidly oxidized in the pharmacologically active sulfoxide metabolite, which is also known as ricobendazole (ABZSOX. ABZSOX has a stereogenic center and possibly two enantiomers, (+-ABZSOX and (--ABZSOX. In the present work, we investigate the pH effect on the asymmetric stereoselective sulfoxidation of ABZ into ABZSOX by employing the fungi Nigrospora sphaerica, Papulaspora immera Hotson, and Mucor rouxii. The results show a possibility of obtaining the pure enantiomers of the ricobendazole drug using fungi as biocatalytic agents. The three fungi showed a high degree of enantioselectivity expressed by enantiomeric excess. In addition, M. rouxii can be used as an alternative to obtain the (+-ABZSOX enantiomer (ee 89.8%.

  13. Multifunctional Nanotechnology-Enabled Sensors for Rapid Capture and Detection of Pathogens.

    Science.gov (United States)

    Mustafa, Fatima; Hassan, Rabeay Y A; Andreescu, Silvana

    2017-09-15

    Nanomaterial-based sensing approaches that incorporate different types of nanoparticles (NPs) and nanostructures in conjunction with natural or synthetic receptors as molecular recognition elements provide opportunities for the design of sensitive and selective assays for rapid detection of contaminants. This review summarizes recent advancements over the past ten years in the development of nanotechnology-enabled sensors and systems for capture and detection of pathogens. The most common types of nanostructures and NPs, their modification with receptor molecules and integration to produce viable sensing systems with biorecognition, amplification and signal readout are discussed. Examples of all-in-one systems that combine multifunctional properties for capture, separation, inactivation and detection are also provided. Current trends in the development of low-cost instrumentation for rapid assessment of food contamination are discussed as well as challenges for practical implementation and directions for future research.

  14. The application of automatic chemiluminescence machine in rapid immune detection

    International Nuclear Information System (INIS)

    Lin Aizhen; Li Xuanwei; Chen Binhong; Li Zhenqian; Chen Zhaoxuan

    2004-01-01

    Objective: To provide high-quality, rapid and dependable result for clinical practice, and give satisfactory service to patients of different economical status by supplementation with other labeling immune examination. With an innovative attitude, we carried out efficient technical reform on ACS180 automatic chemiluminescence machine, making it possible for patients to complete the whole process including examination, check-out, diagnosis and getting drugs. The reported will be issued within an hour, thus a rapid immune detection service was established in out-patients department. Methods: 1. ACS-180 automatic chemiluminescence machine is used based on the principle of chemiluminescence immune methods. 2. The reagents are provided by Ciba-Comig Company of USA, composed of anti acridinium ester antibody of liquid phase and particulate antigen of solid phase wrapped in magnetic powder. 3. Calibration and quality control: high and low concentration are set for each calibration fluid with attached standard curve. Product for quality controlling includes three concentration of low, moderate and high. Results: 1. rapid machine detection for sample: serum is replaced with plasma coagulated by heparin, and comparison among series of methods using serum or plasma suggest no significant difference exists. 2. The problem about fasting detection: chemiluminescence machine measure optical density directly, with the results hardly being influenced by turbidity. But attention should be paid to the treatment of lipid turbid samples. 3. Other innovations: (1) direct placement of sample tube on machine: a cushion is placed on sample plate to transfer sample to machine directly after centrifugation, saving time and reducing the accident in sample transference. (2) for HCG quantification in blood and urine, 'gold criteria' is used firstly in screening to determine approximately the dilution range, with an advantage of saving time and reagent as well as accuracy. (3) we design a

  15. Enzymatic activity of fungi isolated from crops

    Directory of Open Access Journals (Sweden)

    Wioletta A. Żukiewicz-Sobczak

    2016-12-01

    Full Text Available Aim: To detect and assess the activity of extracellular hydrolytic enzymes and to find differences in enzymograms between fungi isolated from wheat and rye samples and grown on Czapek-Dox Broth and Sabouraud Dextrose Broth enriched with cereal (wheat or rye. Isolated strains were also classified in the scale of biosafety levels (BSL. Material and methods: The study used 23 strains of fungi cultured from samples of wheat and rye (grain, grain dust obtained during threshing and soil collected in the Lublin region (eastern Poland. API ZYM test (bioMérieux was carried out according to the manufacturer’s instructions. Classification of BSL (Biosafety levels was based on the current literature. Results : High enzymatic activity was found in strains cultured in media containing 1% of wheat grain ( Bipolaris holmi, Penicillium decumbens and with an addition of 1% of rye grain ( Cladosporium herbarum, Aspergillus versicolor, Alternaria alternata . The total number of enzymes varied depending on the type of media, and in most cases it was higher in the culture where an addition of cereal grains was used. Conclusions : Isolated strains of fungi reveal differences in the profiles of the enzyme assay. It can be assumed that the substrate enriched in grains stimulate the higher activity of mold enzymes. Key words: enzymatic activity, mold fungi, zymogram, biohazards.

  16. Pyrene degradation by yeasts and filamentous fungi.

    Science.gov (United States)

    Romero, M Cristina; Salvioli, Mónica L; Cazau, M Cecilia; Arambarri, A M

    2002-01-01

    The saprotrophic soil fungi Fusarium solani (Mart.) Sacc., Cylindrocarpon didymum (Hartig) Wollenw, Penicillium variabile Sopp. and the yeasts Rhodotorula glutinis (Fresenius) Harrison and Rhodotorula minuta (Saito) Harrison were cultured in mineral medium with pyrene. The remaining pyrene concentrations were periodically determined during 20 incubation days, using HPLC. To assess the metabolism of pyrene degradation we added 0.1 microCi of [4,5,9,10] 14C-pyrene to each fungi culture and measured the radioactivity in the volatile organic substances, extractable, aqueous phase, biomass and 14CO2 fractions. The assays demonstrated that F. solani and R. glutinis metabolized pyrene as a sole source of carbon. Differences in their activities at the beginning of the cultures disappeared by the end of the experiment, when 32 and 37% of the original pyrene concentration was detected, for the soil fungi and yeasts, respectively. Among the filamentous fungi, F. solani was highly active and oxidized pyrene; moreover, small but significant degradation rates were observed in C. didymum and P. variahile cultures. An increase in the 14CO2 evolution was observed at the 17th day with cosubstrate. R. glutinis and R. minuta cultures showed similar ability to biotransform pyrene, and that 35% of the initial concentration was consumed at the end of the assay. The same results were obtained in the experiments with or without glucose as cosubstrate.

  17. A duplex endpoint PCR assay for rapid detection and differentiation of Leptospira strains.

    Science.gov (United States)

    Benacer, Douadi; Zain, Siti Nursheena Mohd; Lewis, John W; Khalid, Mohd Khairul Nizam Mohd; Thong, Kwai Lin

    2017-01-01

    This study aimed to develop a duplex endpoint PCR assay for rapid detection and differentiation of Leptospira strains. Primers were designed to target the rrs (LG1/LG2) and ligB (LP1/LP2) genes to confirm the presence of the Leptospira genus and the pathogenic species, respectively. The assay showed 100% specificity against 17 Leptospira strains with a limit of detection of 23.1pg/µl of leptospiral DNA and sensitivity of 103 leptospires/ml in both spiked urine and water. Our duplex endpoint PCR assay is suitable for rapid early detection of Leptospira with high sensitivity and specificity.

  18. Rapid-scan Fourier-transform coherent anti-Stokes Raman scattering spectroscopy with heterodyne detection.

    Science.gov (United States)

    Hiramatsu, Kotaro; Luo, Yizhi; Ideguchi, Takuro; Goda, Keisuke

    2017-11-01

    High-speed Raman spectroscopy has become increasingly important for analyzing chemical dynamics in real time. To address the need, rapid-scan Fourier-transform coherent anti-Stokes Raman scattering (FT-CARS) spectroscopy has been developed to realize broadband CARS measurements at a scan rate of more than 20,000 scans/s. However, the detection sensitivity of FT-CARS spectroscopy is inherently low due to the limited number of photons detected during each scan. In this Letter, we show our experimental demonstration of enhanced sensitivity in rapid-scan FT-CARS spectroscopy by heterodyne detection. Specifically, we implemented heterodyne detection by superposing the CARS electric field with an external local oscillator (LO) for their interference. The CARS signal was amplified by simply increasing the power of the LO without the need for increasing the incident power onto the sample. Consequently, we achieved enhancement in signal intensity and the signal-to-noise ratio by factors of 39 and 5, respectively, compared to FT-CARS spectroscopy with homodyne detection. The sensitivity-improved rapid-scan FT-CARS spectroscopy is expected to enable the sensitive real-time observation of chemical dynamics in a broad range of settings, such as combustion engines and live biological cells.

  19. Use of HPLC for the detection of iron chelators in cultures of bacteria, fungi, and algae

    International Nuclear Information System (INIS)

    Boyer, G.L.; Speirs, R.J.; Morse, P.D.

    1990-01-01

    Iron is essential for the growth of living cells. To meet biochemical needs, microorganisms, including algae, produce high affinity chelators termed siderophores. These compounds solubilize Fe and increase its bioavailability. We have developed a new method to study siderophore formation in cultured and natural environments. Based on the fact siderophores tightly bind 55-Fe, the radioactive complexes can be separated by HPLC using an inert PRP-1 column and detected by scintillation counting. This method cleanly resolves several known siderophores, including ferrichrome A, ferrichrome, desferal, and rhodotorulic acid. The optimization of the method and its use for analysis of siderophore formation in bacteria (E. coli, and Bacillus megaterium), fungi (Ustilago sphaerogena), and cyanobacteria (Anabaena flos-aqua UTEX 1444 and Anabaena sp. ATCC 27898) will be presented

  20. Flexible gateway constructs for functional analyses of genes in plant pathogenic fungi

    NARCIS (Netherlands)

    Mehrabi, Rahim; Mirzadi Gohari, Amir; Silva, da Gilvan Ferreira; Steinberg, Gero; Kema, Gert H.J.; Wit, de Pierre J.G.M.

    2015-01-01

    Genetic manipulation of fungi requires quick, low-cost, efficient, high-throughput and molecular tools. In this paper, we report 22 entry constructs as new molecular tools based on the Gateway technology facilitating rapid construction of binary vectors that can be used for functional analysis of

  1. Rapid detection of urinary polyomavirus BK by heterodyne-based surface plasmon resonance biosensor

    Science.gov (United States)

    Su, Li-Chen; Tian, Ya-Chung; Chang, Ying-Feng; Chou, Chien; Lai, Chao-Sung

    2014-01-01

    In renal transplant patients, immunosuppressive therapy may result in the reactivation of polyomavirus BK (BKV), leading to polyomavirus-associated nephropathy (PVAN), which inevitably causes allograft failure. Since the treatment outcomes of PVAN remain unsatisfactory, early identification and continuous monitoring of BKV reactivation and reduction of immunosuppressants are essential to prevent PVAN development. The present study demonstrated that the developed dual-channel heterodyne-based surface plasmon resonance (SPR) biosensor is applicable for the rapid detection of urinary BKV. The use of a symmetrical reference channel integrated with the poly(ethylene glycol)-based low-fouling self-assembled monolayer to reduce the environmental variations and the nonspecific noise was proven to enhance the sensitivity in urinary BKV detection. Experimentally, the detection limit of the biosensor for BKV detection was estimated to be around 8500 copies/mL. In addition, urine samples from five renal transplant patients were tested to rapidly distinguish PVAN-positive and PVAN-negative renal transplant patients. By virtue of its simplicity, rapidity, and applicability, the SPR biosensor is a remarkable potential to be used for continuous clinical monitoring of BKV reactivation.

  2. A biosensor platform for rapid detection of E. coli in drinking water.

    Science.gov (United States)

    Hesari, Nikou; Alum, Absar; Elzein, Mohamad; Abbaszadegan, Morteza

    2016-02-01

    There remains a need for rapid, specific and sensitive assays for the detection of bacterial indicators for water quality monitoring. In this study, a strategy for rapid detection of Escherichia coli in drinking water has been developed. This strategy is based on the use of the substrate 4-methylumbelliferyl-β-d-glucuronide (MUG), which is hydrolyzed rapidly by the action of E. coli β-d-glucuronidase (GUD) enzyme to yield a fluorogenic 4-methylumbelliferone (4-MU) product that can be quantified and related to the number of E. coli cells present in water samples. In this study, the detection time required for the biosensor response ranged between 20 and 120 min, depending on the number of bacteria in the sample. This approach does not need extensive sample processing with a rapid detection capability. The specificity of the MUG substrate was examined in both, pure cultures of non-target bacterial genera such as Klebsiella, Salmonella, Enterobacter and Bacillus. Non-target substrates that included 4-methylumbelliferyl-β-d-galactopyranoside (MUGal) and l-leucine β-naphthylamide aminopeptidase (LLβ-N) were also investigated to identify nonspecific patterns of enzymatic activities in E. coli. GUD activity was found to be specific for E. coli and no further enzymatic activity was detected by other species. In addition, fluorescence assays were performed for the detection of E. coli to generate standard curves; and the sensitivity of the GUD enzymatic response was measured and repeatedly determined to be less than 10 E. coli cells in a reaction vial. The applicability of the method was tested by performing multiple fluorescence assays under pure and mixed bacterial flora in environmental samples. The results of this study showed that the fluorescence signals generated in samples using specific substrate molecules can be utilized to develop a bio-sensing platform for the detection of E. coli in drinking water. Furthermore, this system can be applied independently or

  3. Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi.

    Science.gov (United States)

    Nerva, L; Ciuffo, M; Vallino, M; Margaria, P; Varese, G C; Gnavi, G; Turina, M

    2016-07-02

    The number of reported mycoviruses is increasing exponentially due to the current ability to detect mycoviruses using next-generation sequencing (NGS) approaches, with a large number of viral genomes built in-silico using data from fungal transcriptome projects. We decided to screen a collection of fungi originating from a specific marine environment (associated with the seagrass Posidonia oceanica) for the presence of mycoviruses: our findings reveal a wealth of diversity among these symbionts and this complexity will require further studies to address their specific role in this ecological niche. In specific, we identified twelve new virus species belonging to nine distinct lineages: they are members of megabirnavirus, totivirus, chrysovirus, partitivirus and five still undefined clades. We showed evidence of an endogenized virus ORF, and evidence of accumulation of dsRNA from metaviridae retroviral elements. We applied different techniques for detecting the presence of mycoviruses including (i) dsRNA extraction and cDNA cloning, (ii) small and total RNA sequencing through NGS techniques, (iii) rolling circle amplification (RCA) and total DNA extraction analyses, (iv) virus purifications and electron microscopy. We tried also to critically evaluate the intrinsic value and limitations of each of these techniques. Based on the samples we could compare directly, RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses. To our knowledge this is the first report on the virome of fungi isolated from marine environment. The GenBank/eMBL/DDBJ accession numbers of the sequences reported in this paper are: KT601099-KT601110; KT601114-KT601120; KT592305; KT950836-KT950841. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Fusarium and other opportunistic hyaline fungi

    Science.gov (United States)

    This chapter focuses on those fungi that grow in tissue in the form of hyaline or lightly colored septate hyphae. These fungi include Fusarium and other hyaline fungi. Disease caused by hyaline fungi is referred to as hyalohyphomycosis. Hyaline fungi described in this chapter include the anamorphic,...

  5. Rhizosphere Colonization and Control of Meloidogyne spp. by Nematode-trapping Fungi

    Science.gov (United States)

    Persson, Christina; Jansson, Hans-Börje

    1999-01-01

    The ability of nematode-trapping fungi to colonize the rhizosphere of crop plants has been suggested to be an important factor in biological control of root-infecting nematodes. In this study, rhizosphere colonization was evaluated for 38 isolates of nematode-trapping fungi representing 11 species. In an initial screen, Arthrobotrys dactyloides, A. superba, and Monacrosporium ellipsosporum were most frequently detected in the tomato rhizosphere. In subsequent pot experiments these fungi and the non-root colonizing M. geophyropagum were introduced to soil in a sodium alginate matrix, and further tested both for establishment in the tomato rhizosphere and suppression of root-knot nematodes. The knob-forming M. ellipsosporum showed a high capacity to colonize the rhizosphere both in the initial screen and the pot experiments, with more than twice as many fungal propagules in the rhizosphere as in the root-free soil. However, neither this fungus nor the other nematode-trapping fungi tested reduced nematode damage to tomato plants. PMID:19270886

  6. Controlled rate cooling of fungi using a stirling cycle freezer.

    Science.gov (United States)

    Ryan, Matthew J; Kasulyte-Creasey, Daiva; Kermode, Anthony; San, Shwe Phue; Buddie, Alan G

    2014-01-01

    The use of a Stirling cycle freezer for cryopreservation is considered to have significant advantages over traditional methodologies including N2 free operation, application of low cooling rates, reduction of sample contamination risks and control of ice nucleation. The study assesses the suitability of an 'N2-free' Stirling Cycle controlled rate freezer for fungi cryopreservation. In total, 77 fungi representing a broad taxonomic coverage were cooled using the N2 free cooler following a cooling rate of -1 degrees C min(-1). Of these, 15 strains were also cryopreserved using a traditional 'N2 gas chamber' controlled rate cooler and a comparison of culture morphology and genomic stability against non-cryopreserved starter cultures was undertaken. In total of 75 fungi survived cryopreservation, only a recalcitrant Basidiomycete and filamentous Chromist failed to survive. No changes were detected in genomic profile after preservation, suggesting that genomic function is not adversely compromised as a result of using 'N2 free' cooling. The results demonstrate the potential of 'N2-free' cooling for the routine cryopreservation of fungi in Biological Resource Centres.

  7. Endophytic Fungi Isolated from Coleus amboinicus Lour Exhibited Antimicrobial Activity.

    Science.gov (United States)

    Astuti, Puji; Sudarsono, Sudarsono; Nisak, Khoirun; Nugroho, Giri Wisnu

    2014-12-01

    Coleus amboinicus is a medicinal plant traditionally used to treat various diseases such as throat infection, cough and fever, diarrhea, nasal congestion and digestive problems. The plant was explored for endophytic fungi producing antimicrobial agents. Screening for endophytic fungi producing antimicrobial agents was conducted using agar plug method and antimicrobial activity of promising ethyl acetate extracts was determined by disc diffusion assay. Thin layer chromatography (TLC) - bioautography was performed to localize the bioactive components within the extract. TLC visualization detection reagents were used to preliminary analyze phytochemical groups of the bioactive compounds. Three endophytic fungi were obtained, two of them showed promising potential. Agar diffusion method showed that endophytic fungi CAL-2 exhibited antimicrobial activity against P. aeruginosa, B. subtilis, S. aureus and S. thypi, whilst CAS-1 inhibited the growth of B. subtilis. TLC bioautography of ethyl acetate extract of CAL-2 revealed at least three bands exhibited antimicrobial activity and at least two bands showed inhibition of B. subtilis growth. Preliminary analysis of the crude extracts suggests that bioactive compounds within CAL-2 extract are terpenoids, phenolics and phenyl propanoid compounds whilst the antimicrobial agents within CAS-1 extract are terpenoids, propylpropanoids, alkaloids or heterocyclic nitrogen compounds. These data suggest the potential of endophytic fungi of C. amboinicus as source for antimicrobial agents.

  8. Responses of mycorrhizal fungi and other rootassociated fungi to climate change

    DEFF Research Database (Denmark)

    Merrild, Marie Porret

    Climate change is expected to affect many terrestrial ecosystem processes. Mycorrhizal fungi are important to soil carbon (C) and nutrient cycling thus changes in abundance of mycorrhizal fungi could alter ecosystem functioning. The aim of the present thesis was therefore to investigate responses...... of mycorrhizal fungi to climate change in a seasonal and long-term perspective. Effects of elevated CO2 (510 ppm), night-time warming and extended summer drought were investigated in the long-term field experiment CLIMAITE located in a Danish semi-natural heathland. Mycorrhizal colonization was investigated...... levels. Colonization by arbuscular mycorrhizal (AM) fungi increased under elevated CO2 and warming in spring while ericoid mycorrhiza (ErM) colonisation decreased in response to drought and warming. Increased AM colonization correlated with higher phosphorus and nitrogen root pools. Dark septate...

  9. Rapid Detection Technology for Pesticides Residues Based on Microelectrodes Impedance Immunosensor

    Directory of Open Access Journals (Sweden)

    Wen Ping Zhao

    2014-09-01

    Full Text Available Compared with conventional methods, electrochemical immunosensors have many advantages, such as low cost, high sensitivity, and rapid detection, and has certain prospects for realizing real-time-monitoring. In this paper, a design of portable pesticide residues detection instrument was presented based on an electrochemical impedance immunosensor. Firstly, we studied on an impedance immunosensor based on interdigitated array microelectrode (IDAM coupled with magnetic nanobeads-antibody conjugates (MNAC for the pesticide detection. Magnetic nanobeads (diameter 150 nm coated with anti-carbofuran antibodies were used for further amplification of the binding reaction between antibody and hapten (carbofuran. Secondly, in order to develop a portable pesticide residue apparatus, we designed the impedance detection electric circuit. Main work included designing and constructing of the system circuit, designing and debugging of the system software and so on. Thirdly, the apparatus was used for the standard pesticides solutions testing combined with immunosensor to test the reliability and stability. The pesticide added standard recovery was more than 70 % and the impedance test error was less than 5 %. The results showed that the proposed instrument had a good consistence compared with the traditional analytical methods. Thus, it would be a promising rapid detection instrument for pesticide residues in agricultural products.

  10. RNA aptasensor for rapid detection of natively folded type A botulinum neurotoxin.

    Science.gov (United States)

    Janardhanan, Pavithra; Mello, Charlene M; Singh, Bal Ram; Lou, Jianlong; Marks, James D; Cai, Shuowei

    2013-12-15

    A surface plasmon resonance based RNA aptasensor for rapid detection of natively folded type A botulinum neurotoxin is reported. Using detoxified recombinant type A botulinum neurotoxin as the surrogate, the aptasensor detects active toxin within 90 min. The detection limit of the aptasensor in phosphate buffered saline, carrot juice, and fat free milk is 5.8 ng/ml, 20.3 ng/ml and 23.4 ng/ml, respectively, while that in 5-fold diluted human serum is 22.5 ng/ml. Recovery of toxin from disparate sample matrices are within 91-116%. Most significant is the ability of this aptasensor to effectively differentiate the natively folded toxin from denatured, inactive toxin, which is important for homeland security surveillance and threat assessment. The aptasensor is stable for more than 30 days and over 400 injections/regeneration cycles. Such an aptasensor holds great promise for rapid detection of active botulinum neurotoxin for field surveillance due to its robustness, stability and reusability. © 2013 Elsevier B.V. All rights reserved.

  11. Growth and nutrition of eucalyptus clones seedlings inoculated with mycorrhizal fungi

    Directory of Open Access Journals (Sweden)

    Francisco de Sousa Lima

    2014-06-01

    Full Text Available Eucalyptus is one of the most planted forest species, in Brazil, due to its rapid growth and high economic yield. Arbuscular mycorrhizal fungi improve the seedlings nutritional and phytosanitary status, besides increasing their resistance to biotic and abiotic stress. This study aimed to evaluate the effect of inoculation with arbuscular mycorrhizal fungi species on the growth and nutrition of different eucalyptus clones seedlings. The experiment was conducted under greenhouse conditions, in a randomized blocks design and a 5x5 factorial scheme (five fungal species and five eucalyptus clones, with five replications. In general, the mycorrhizal symbiosis significantly increased the growth and nutrition of eucalyptus seedlings, when compared to the non-inoculated seedlings. The most efficient interaction occured between the 2361 clone and the Entrophospora infrequens fungus, with increases of 107.3% and 120.6%, for the shoot and root dry biomass yield, and 107.7%, 94.1% and 103.3%, respectively for the accumulation of N, P and K in the seedlings shoots. All the fungal species studied showed a high absolute compatibility index with eucalyptus clones. The Glomus manihots and E. infrequens fungi presented a higher functional compatibility index with the clones tested. The 5204 clone showed 75% of compatibility with the fungi evaluated.

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

    Directory of Open Access Journals (Sweden)

    Xuan Weng

    2016-06-01

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

  13. Rapid and real-time detection technologies for emerging viruses of ...

    Indian Academy of Sciences (India)

    2008-10-17

    Oct 17, 2008 ... The development of technologies with rapid and sensitive detection capabilities and increased throughput have become crucial for responding to greater number threats posed by emerging and re-emerging viruses in the recent past. The conventional identification methods require time-consuming culturing ...

  14. Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment.

    Directory of Open Access Journals (Sweden)

    Serena Dollive

    Full Text Available Antibiotic use in humans has been associated with outgrowth of fungi. Here we used a murine model to investigate the gut microbiome over 76 days of treatment with vancomycin, ampicillin, neomycin, and metronidazole and subsequent recovery. Mouse stool was studied as a surrogate for the microbiota of the lower gastrointestinal tract. The abundance of fungi and bacteria was measured using quantitative PCR, and the proportional composition of the communities quantified using 454/Roche pyrosequencing of rRNA gene tags. Prior to treatment, bacteria outnumbered fungi by >3 orders of magnitude. Upon antibiotic treatment, bacteria dropped in abundance >3 orders of magnitude, so that the predominant 16S sequences detected became transients derived from food. Upon cessation of treatment, bacterial communities mostly returned to their previous numbers and types after 8 weeks, though communities remained detectably different from untreated controls. Fungal communities varied substantially over time, even in the untreated controls. Separate cages within the same treatment group showed radical differences, but mice within a cage generally behaved similarly. Fungi increased ∼40-fold in abundance upon antibiotic treatment but declined back to their original abundance after cessation of treatment. At the last time point, Candida remained more abundant than prior to treatment. These data show that 1 gut fungal populations change radically during normal mouse husbandry, 2 fungi grow out in the gut upon suppression of bacterial communities with antibiotics, and 3 perturbations due to antibiotics persist long term in both the fungal and bacterial microbiota.

  15. Rapid Change Detection Algorithm for Disaster Management

    Science.gov (United States)

    Michel, U.; Thunig, H.; Ehlers, M.; Reinartz, P.

    2012-07-01

    This paper focuses on change detection applications in areas where catastrophic events took place which resulted in rapid destruction especially of manmade objects. Standard methods for automated change detection prove not to be sufficient; therefore a new method was developed and tested. The presented method allows a fast detection and visualization of change in areas of crisis or catastrophes. While often new methods of remote sensing are developed without user oriented aspects, organizations and authorities are not able to use these methods because of absence of remote sensing know how. Therefore a semi-automated procedure was developed. Within a transferable framework, the developed algorithm can be implemented for a set of remote sensing data among different investigation areas. Several case studies are the base for the retrieved results. Within a coarse dividing into statistical parts and the segmentation in meaningful objects, the framework is able to deal with different types of change. By means of an elaborated Temporal Change Index (TCI) only panchromatic datasets are used to extract areas which are destroyed, areas which were not affected and in addition areas where rebuilding has already started.

  16. Rapid and Sensitive Detection of BLAD in Cattle Population

    Directory of Open Access Journals (Sweden)

    Daniela Elena Ilie

    2014-05-01

    Full Text Available Bovine leukocyte adhesion deficiency (BLAD is an autosomal recessive disorder with negative impact on dairy cattle breeding. The molecular basis of BLAD is a single point mutation (A→G, resulting in a single amino acid substitution (aspartic acid → glycine at amino acid 128 in the adhesion molecule CD18. The object of this study was to establish a fast and sensitive molecular genotyping assay to detect BLAD carriers using high-resolution melting (HRM curve analysis. We tested animals with known genotypes for BLAD that were previously confirmed by PCR-RFLP method, and then examined the sensitivity of mutation detection using PCR followed by HRM curve analysis. BLAD carriers were readily detectable using HRM assay. Thus, the PCR-HRM genotyping method is a rapid, easily interpretable, reliable and cost-effective assay for BLAD mutant allele detection. This assay can be useful in cattle genotyping and genetic selection.

  17. An integrated micro-chip for rapid detection of magnetic particles

    KAUST Repository

    Gooneratne, Chinthaka P.

    2012-03-09

    This paper proposes an integrated micro-chip for the manipulation and detection of magnetic particles (MPs). A conducting ring structure is used to manipulate MPs toward giant magnetoresistance(GMR) sensing elements for rapid detection. The GMRsensor is fabricated in a horseshoe shape in order to detect the majority of MPs that are trapped around the conducting structure. The GMR sensing elements are connected in a Wheatstone bridge circuit topology for optimum noise suppression. Full fabrication details of the micro-chip, characterization of the GMRsensors, and experimental results with MPs are presented in this paper. Experimental results showed that the micro-chip can detect MPs from low concentration samples after they were guided toward the GMRsensors by applying current to the conducting ring structure.

  18. [Rapid test for detection of susceptibility to cefotaxime in Enterobacteriaceae].

    Science.gov (United States)

    Jiménez-Guerra, Gemma; Hoyos-Mallecot, Yannik; Rodríguez-Granger, Javier; Navarro-Marí, José María; Gutiérrez-Fernández, José

    In this work an "in house" rapid test based on the change in pH that is due to hydrolysis for detecting Enterobacteriaceae susceptible to cefotaxime is evaluated. The strains of Enterobacteriaceae from 1947 urine cultures were assessed using MicroScan panels and the "in house" test. This rapid test includes red phenol solution and cefotaxime. Using MicroScan panels, 499 Enterobacteriaceae isolates were evaluated, which included 27 isolates of Escherichia coli producing extended-spectrum beta-lactamases (ESBL), 16 isolates of Klebsiella pneumoniae ESBL and 1 isolate of Klebsiella oxytoca ESBL. The "in house" test offers the following values: sensitivity 98% and specificity 97%, with negative predictive value 100% and positive predictive value 78%. The "in house" test based on the change of pH is useful in our area for detecting presumptively cefotaxime-resistant Enterobacteriaceae strains. Copyright © 2016 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

  19. Effects of aluminum and manganese on the growth of ectomycorrhizal fungi.

    Science.gov (United States)

    Thompson, G W; Medve, R J

    1984-09-01

    Cenococcum graniforme, Suillus luteus, Thelephora terrestris, and three isolates of Pisolithus tinctorius were cultured on modified Melin-Norkrans medium at pH 3.4 and adjusted to 0 to 500 ppm (0 to 500 mug/ml) of aluminum or manganese sulfate. Except for T. terrestris, which was intolerant of aluminum at 150 and 250 to 500 ppm, and P. tinctorius isolate 250, which was intolerant of aluminum at 450 ppm, all fungi showed some growth at all concentrations of aluminum. S. luteus was the most tolerant to aluminum. Manganese was less fungitoxic than aluminum, with all fungi showing at least 65% growth at 500 ppm as compared with the control. C. graniforme was not inhibited at any concentration of manganese, and S. luteus was only affected at 500 ppm. P. tinctorius isolate 230 showed no significant variation in growth when subjected to various concentrations of three forms of manganese salts. Significant differences in growth were detected in response to three aluminum salts, but no detectable pattern was apparent. Genotypic responses to aluminum and manganese were evident for P. tinctorius. Isolates 210 and 230 were more tolerant to manganese than was isolate 250. Aluminum tolerance was in the order of isolate 230 > 210 > 250. Results of in vitro studies concerning tolerance responses of ectomycorrhizal fungi to aluminum and manganese were not consistent with field observations of the successional sequence of these fungi on acid coal spoils.

  20. Effects of aluminum and manganese on the growth of ectomycorrhizal fungi

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, G.W.; Medve, R.J.

    1984-09-01

    Cenococcum graniforme, Suillus luteus, Thelephora terrestris, and three isolates of Pisolithus tinctorius were cultured on modified Melin-Norkrans medium at pH 3.4 and adjusted to 0 to 500 ppm (0 to 500 ..mu..g/ml) of aluminum or manganese sulfate. Except for T. terrestris, which was intolerant of aluminum at 150 and 250 to 500 ppm, and P. tinctorius isolate 250, which was intolerant of aluminum at 450 ppm, all fungi showed some growth at all concentrations of aluminum. S. luteus was the most tolerant to aluminum. Manganese was less fungitoxic than aluminum, with all fungi showing at least 65% growth at 500 ppm as compared with the control. C graniforme was not inhibited at any concentration of manganese, and S. luteus was only affected at 500 ppm. P. tinctorius isolate 230 showed no significant variation in growth when subjected to various concentrations of three forms of manganese salts. Significant differences in growth were detected in response to three aluminum salts, but no detectable pattern was apparent. Genotypic responses to aluminum and manganese were evident for P. tinctorius. Isolates 210 and 230 were more tolerant to manganese than was isolate 250. Aluminum tolerance was in the order of isolate 230 > 210 > 250. Results of in vitro studies concerning tolerance responses of ectomycorrhizal fungi to aluminum and manganese were not consistent with field observations of the successional sequence of these fungi on acid coal spoils. 43 references, 3 tables.

  1. Genome-Enhanced Detection and Identification (GEDI of plant pathogens

    Directory of Open Access Journals (Sweden)

    Nicolas Feau

    2018-02-01

    Full Text Available Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1 selection and genome sequencing of phylogenetically related taxa, (2 identification of clusters of orthologous genes, (3 elimination of false positives by filtering, and (4 assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota, Dothideomycetes (Fungi, Ascomycota and Pucciniales (Fungi, Basidiomycota. Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.

  2. A method for detecting fungal contaminants in wall cavities.

    Science.gov (United States)

    Spurgeon, Joe C

    2003-01-01

    This article describes a practical method for detecting the presence of both fungal spores and culturable fungi in wall cavities. Culturable fungi were collected in 25 mm cassettes containing 0.8 microm mixed cellulose ester filters using aggressive sampling conditions. Both culturable fungi and fungal spores were collected in modified slotted-disk cassettes. The sample volume was 4 L. The filters were examined microscopically and dilution plated onto multiple culture media. Collecting airborne samples in filter cassettes was an effective method for assessing wall cavities for fungal contaminants, especially because this method allowed the sample to be analyzed by both microscopy and culture media. Assessment criteria were developed that allowed the sample results to be used to classify wall cavities as either uncontaminated or contaminated. As a criterion, wall cavities with concentrations of culturable fungi below the limit of detection (LOD) were classified as uncontaminated, whereas those cavities with detectable concentrations of culturable fungi were classified as contaminated. A total of 150 wall cavities was sampled as part of a field project. The concentrations of culturable fungi were below the LOD in 34% of the samples, whereas Aspergillus and/or Penicillium were the only fungal genera detected in 69% of the samples in which culturable fungi were detected. Spore counting resulted in the detection of Stachybotrys-like spores in 25% of the samples that were analyzed, whereas Stachybotrys chartarum colonies were only detected on 2% of malt extract agar plates and on 6% of corn meal agar plates.

  3. Fungi in space--literature survey on fungi used for space research.

    Science.gov (United States)

    Kern, V D; Hock, B

    1993-09-01

    A complete review of the scientific literature on experiments involving fungi in space is presented. This review begins with balloon experiments around 1935 which carried fungal spores, rocket experiments in the 1950's and 60's, satellite and moon expeditions, long-time orbit experiments and Spacelab missions in the 1980's and 90's. All these missions were aimed at examining the influence of cosmic radiation and weightlessness on genetic, physiological, and morphogenetic processes. During the 2nd German Spacelab mission (D-2, April/May 1993), the experiment FUNGI provided the facilities to cultivate higher basidiomycetes over a period of 10 d in orbit, document gravimorphogenesis and chemically fix fruiting bodies under weightlessness for subsequent ultrastructural analysis. This review shows the necessity of space travel for research on the graviperception of higher fungi and demonstrates the novelty of the experiment FUNGI performed within the framework of the D-2 mission.

  4. Diurnal patterns of productivity of arbuscular mycorrhizal fungi revealed with the Soil Ecosystem Observatory.

    Science.gov (United States)

    Hernandez, Rebecca R; Allen, Michael F

    2013-10-01

    Arbuscular mycorrhizal (AM) fungi are the most abundant plant symbiont and a major pathway of carbon sequestration in soils. However, their basic biology, including their activity throughout a 24-h day : night cycle, remains unknown. We employed the in situ Soil Ecosystem Observatory to quantify the rates of diurnal growth, dieback and net productivity of extra-radical AM fungi. AM fungal hyphae showed significantly different rates of growth and dieback over a period of 24 h and paralleled the circadian-driven photosynthetic oscillations observed in plants. The greatest rates (and incidences) of growth and dieback occurred between noon and 18:00 h. Growth and dieback events often occurred simultaneously and were tightly coupled with soil temperature and moisture, suggesting a rapid acclimation of the external phase of AM fungi to the immediate environment. Changes in the environmental conditions and variability of the mycorrhizosphere may alter the diurnal patterns of productivity of AM fungi, thereby modifying soil carbon sequestration, nutrient cycling and host plant success. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  5. Endophytic Fungi Isolated from Coleus amboinicus Lour Exhibited Antimicrobial Activity

    Directory of Open Access Journals (Sweden)

    Puji Astuti

    2014-12-01

    Full Text Available Purpose: Coleus amboinicus is a medicinal plant traditionally used to treat various diseases such as throat infection, cough and fever, diarrhea, nasal congestion and digestive problems. The plant was explored for endophytic fungi producing antimicrobial agents. Methods: Screening for endophytic fungi producing antimicrobial agents was conducted using agar plug method and antimicrobial activity of promising ethyl acetate extracts was determined by disc diffusion assay. Thin layer chromatography (TLC - bioautography was performed to localize the bioactive components within the extract. TLC visualization detection reagents were used to preliminary analyze phytochemical groups of the bioactive compounds. Results: Three endophytic fungi were obtained, two of them showed promising potential. Agar diffusion method showed that endophytic fungi CAL-2 exhibited antimicrobial activity against P. aeruginosa, B. subtilis, S. aureus and S. thypi, whilst CAS-1 inhibited the growth of B. subtilis. TLC bioautography of ethyl acetate extract of CAL-2 revealed at least three bands exhibited antimicrobial activity and at least two bands showed inhibition of B. subtilis growth. Preliminary analysis of the crude extracts suggests that bioactive compounds within CAL-2 extract are terpenoids, phenolics and phenyl propanoid compounds whilst the antimicrobial agents within CAS-1 extract are terpenoids, propylpropanoids, alkaloids or heterocyclic nitrogen compounds. Conclusion: These data suggest the potential of endophytic fungi of C. amboinicus as source for antimicrobial agents.

  6. Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi.

    Science.gov (United States)

    Solomon, Kevin V; Henske, John K; Theodorou, Michael K; O'Malley, Michelle A

    2016-04-01

    Cell storage and DNA isolation are essential to developing an expanded suite of microorganisms for biotechnology. However, many features of non-model microbes, such as an anaerobic lifestyle and rigid cell wall, present formidable challenges to creating strain repositories and extracting high quality genomic DNA. Here, we establish accessible, high efficiency, and robust techniques to store lignocellulolytic anaerobic gut fungi long term without specialized equipment. Using glycerol as a cryoprotectant, gut fungal isolates were preserved for a minimum of 23 months at -80 °C. Unlike previously reported approaches, this improved protocol is non-toxic and rapid, with samples surviving twice as long with negligible growth impact. Genomic DNA extraction for these isolates was optimized to yield samples compatible with next generation sequencing platforms (e.g. Illumina, PacBio). Popular DNA isolation kits and precipitation protocols yielded preps that were unsuitable for sequencing due to carbohydrate contaminants from the chitin-rich cell wall and extensive energy reserves of gut fungi. To address this, we identified a proprietary method optimized for hardy plant samples that rapidly yielded DNA fragments in excess of 10 kb with minimal RNA, protein or carbohydrate contamination. Collectively, these techniques serve as fundamental tools to manipulate powerful biomass-degrading gut fungi and improve their accessibility among researchers. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Application of a rapid screening method to detect irradiated meat in Brazil

    International Nuclear Information System (INIS)

    Villavicencio, A.L.C.H.; Delincee, H.

    1998-01-01

    Complete text of publication follows. Based on the enormous potential for food irradiation in Brazil, and to ensure free consumer choice, there is a need to find a convenient and rapid method for detection of irradiated food. Since treatment with ionizing radiation causes DNA fragmentation, the analysis of DNA damage might be promising. In fact, DNA fragmentation measured in single cells by agarose gel electrophoresis - DNA Comet Assay - has shown to offer great potential as a rapid tool to detect whether a wide variety of foodstuffs has been radiation processed. However, more work is needed to exploit the full potential of this promising technique. In this paper, the DNA Comet Assay was used to identify exotic meat (boar, jacare and capybara), irradiated with 60 Co gamma-rays. The applied radiation doses were 0, 1.5, 3.0 and 4.5 kGy. Analysis of the DNA migration enable a rapid identification of the radiation treatment

  8. It’s a Jungle Out There! Abiotic and Biotic Factors That Affect Efficacy and Persistence of the Entomopathogenic Fungi

    Science.gov (United States)

    One might conclude the soil is a more congenial arena for using entomopathogenic fungi (EPF) than the phylloplane. No ultraviolet light, no rainfall washing conidia from foliage, no rapid attenuation of conidial deposits by rapid plant canopy expansion. The soil is cool, damp and dark – perfect fo...

  9. Rapid antigen detection test for respiratory syncytial virus diagnosis as a diagnostic tool.

    Science.gov (United States)

    Mesquita, Flávio da Silva; Oliveira, Danielle Bruna Leal de; Crema, Daniela; Pinez, Célia Miranda Nunes; Colmanetti, Thaís Cristina; Thomazelli, Luciano Matsumia; Gilio, Alfredo Elias; Vieira, Sandra Elisabeth; Martinez, Marina Baquerizo; Botosso, Viviane Fongaro; Durigon, Edison Luiz

    The aim of this study was to evaluate the QuickVue ® RSV Test Kit (QUIDEL Corp, CA, USA) as a screening tool for respiratory syncytial virus in children with acute respiratory disease in comparison with the indirect immunofluorescence assay as gold standard. In Brazil, rapid antigen detection tests for respiratory syncytial virus are not routinely utilized as a diagnostic tool, except for the diagnosis of dengue and influenza. The authors retrospectively analyzed 486 nasopharyngeal aspirate samples from children under age 5 with acute respiratory infection, between December 2013 and August 2014, the samples were analyzed by indirect immunofluorescence assay and QuickVue ® RSV Test kit. Samples with discordant results were analyzed by real time PCR and nucleotide sequencing. From 313 positive samples by immunofluorescence assays, 282 (90%) were also positive by the rapid antigen detection test, two were positive only by rapid antigen detection test, 33 were positive only by immunofluorescence assays, and 171 were positive by both methods. The 35 samples with discordant results were analyzed by real time PCR; the two samples positive only by rapid antigen detection test and the five positive only by immunofluorescence assays were also positive by real time PCR. There was no relation between the negativity by QuickVue ® RSV Test and viral load or specific strain. The QuickVue ® RSV Test showed sensitivity of 90%, specificity of 98.8%, predictive positive value of 99.3%, and negative predictive value of 94.6%, with accuracy of 93.2% and agreement κ index of 0.85 in comparison to immunofluorescence assay. This study demonstrated that the QuickVue ® RSV Test Kit can be effective in early detection of Respiratory syncytial virus in nasopharyngeal aspirate and is reliable for use as a diagnostic tool in pediatrics. Copyright © 2016 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

  10. Rapid antigen detection test for respiratory syncytial virus diagnosis as a diagnostic tool,

    Directory of Open Access Journals (Sweden)

    Flávio da Silva Mesquita

    Full Text Available Abstract Objective: The aim of this study was to evaluate the QuickVue® RSV Test Kit (QUIDEL Corp, CA, USA as a screening tool for respiratory syncytial virus in children with acute respiratory disease in comparison with the indirect immunofluorescence assay as gold standard. In Brazil, rapid antigen detection tests for respiratory syncytial virus are not routinely utilized as a diagnostic tool, except for the diagnosis of dengue and influenza. Methods: The authors retrospectively analyzed 486 nasopharyngeal aspirate samples from children under age 5 with acute respiratory infection, between December 2013 and August 2014, the samples were analyzed by indirect immunofluorescence assay and QuickVue® RSV Test kit. Samples with discordant results were analyzed by real time PCR and nucleotide sequencing. Results: From 313 positive samples by immunofluorescence assays, 282 (90% were also positive by the rapid antigen detection test, two were positive only by rapid antigen detection test, 33 were positive only by immunofluorescence assays, and 171 were positive by both methods. The 35 samples with discordant results were analyzed by real time PCR; the two samples positive only by rapid antigen detection test and the five positive only by immunofluorescence assays were also positive by real time PCR. There was no relation between the negativity by QuickVue® RSV Test and viral load or specific strain. The QuickVue® RSV Test showed sensitivity of 90%, specificity of 98.8%, predictive positive value of 99.3%, and negative predictive value of 94.6%, with accuracy of 93.2% and agreement κ index of 0.85 in comparison to immunofluorescence assay. Conclusions: This study demonstrated that the QuickVue® RSV Test Kit can be effective in early detection of Respiratory syncytial virus in nasopharyngeal aspirate and is reliable for use as a diagnostic tool in pediatrics.

  11. Fungi in a heavy metal precipitating stream in the Mansfeld mining district, Germany

    International Nuclear Information System (INIS)

    Ehrman, James M.; Baerlocher, Felix; Wennrich, Rainer; Krauss, Gerd-Joachim; Krauss, Gudrun

    2008-01-01

    Fungal growth on alder leaves was studied in two heavy metal polluted streams in central Germany. The aim of the study was to examine previously observed differences in leaf decomposition rates, heavy metal precipitation and fungal involvement in these processes at the microscopic level. Ergosterol analyses indicated that neither habitat was optimal for fungi, but leaves exposed at the less polluted site (H8) decomposed rapidly and were colonized externally and internally by fungi and other microorganisms. Leaves exposed at the more polluted site (H4) decomposed very slowly and fungal colonization was restricted to external surfaces. An amorphous organic layer, deposited within 24 h of exposure, quickly became covered with a pale blue-green crystalline deposit (zincowoodwardite) with significant amounts of Al, S, Cu and Zn, determined by energy dispersive X-ray spectroscopy (EDS). Scanning electron microscopy (SEM) analysis of the precipitate revealed a branching arrangement of the precipitated particles caused by the presence of fungal hyphae growing on the surface. Hyphae that were not disturbed by handling were usually completely encased in the precipitate, but hyphae did not contain EDS-detectable amounts of precipitate metals. Elemental analysis using inductively coupled plasma (ICP) atomic emission spectrometry and ICP mass spectrometry revealed continuing accumulation of Zn, Cu and several other metals/metalloids on and in leaves. The formation of metal precipitates on various artificial substrates at site H4 was much reduced compared to leaves, which we attribute to the absence of fungal colonization on the artificial substrates. We could not determine whether fungi accelerate the precipitation of heavy metals at site H4, but mycelial growth on leaves continues to create new surfaces and therefore thicker layers of precipitate on leaves compared to artificial substrates

  12. Fungi in a heavy metal precipitating stream in the Mansfeld mining district, Germany

    Energy Technology Data Exchange (ETDEWEB)

    Ehrman, James M. [Department of Biology, Mount Allison University, 63B York St., Sackville, NB, E4L 1G7 (Canada)], E-mail: jehrman@mta.ca; Baerlocher, Felix [Department of Biology, Mount Allison University, 63B York St., Sackville, NB, E4L 1G7 (Canada); Wennrich, Rainer [Helmholtz Centre for Environmental Research- UFZ, Department of Analytical Chemistry, Permoserstr. 15, 04318 Leipzig (Germany); Krauss, Gerd-Joachim [Martin-Luther-University, Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Div. Ecological and Plant Biochemistry, Kurt-Mothes-Str. 3, 06120 Halle/Saale (Germany); Krauss, Gudrun [Helmholtz Centre for Environmental Research- UFZ, Department of Environmental Microbiology, Theodor-Lieser-Str. 4, 06120 Halle/Saale (Germany)

    2008-01-25

    Fungal growth on alder leaves was studied in two heavy metal polluted streams in central Germany. The aim of the study was to examine previously observed differences in leaf decomposition rates, heavy metal precipitation and fungal involvement in these processes at the microscopic level. Ergosterol analyses indicated that neither habitat was optimal for fungi, but leaves exposed at the less polluted site (H8) decomposed rapidly and were colonized externally and internally by fungi and other microorganisms. Leaves exposed at the more polluted site (H4) decomposed very slowly and fungal colonization was restricted to external surfaces. An amorphous organic layer, deposited within 24 h of exposure, quickly became covered with a pale blue-green crystalline deposit (zincowoodwardite) with significant amounts of Al, S, Cu and Zn, determined by energy dispersive X-ray spectroscopy (EDS). Scanning electron microscopy (SEM) analysis of the precipitate revealed a branching arrangement of the precipitated particles caused by the presence of fungal hyphae growing on the surface. Hyphae that were not disturbed by handling were usually completely encased in the precipitate, but hyphae did not contain EDS-detectable amounts of precipitate metals. Elemental analysis using inductively coupled plasma (ICP) atomic emission spectrometry and ICP mass spectrometry revealed continuing accumulation of Zn, Cu and several other metals/metalloids on and in leaves. The formation of metal precipitates on various artificial substrates at site H4 was much reduced compared to leaves, which we attribute to the absence of fungal colonization on the artificial substrates. We could not determine whether fungi accelerate the precipitation of heavy metals at site H4, but mycelial growth on leaves continues to create new surfaces and therefore thicker layers of precipitate on leaves compared to artificial substrates.

  13. Philatelic Mycology: Families of Fungi

    NARCIS (Netherlands)

    Marasas, W.F.O.; Marasas, H.M.; Wingfield, M.J.; Crous, P.W.

    2014-01-01

    Philately, the study of postage stamps, and mycology, the study of fungi, are seldom connected by those that practice these very different activities. When associated, philatelic mycology would be considered as the study of fungi on stamps. The Fungi touch every aspect of our daily lives, most

  14. The diversity and distribution of fungi on residential surfaces.

    Directory of Open Access Journals (Sweden)

    Rachel I Adams

    Full Text Available The predominant hypothesis regarding the composition of microbial assemblages in indoor environments is that fungal assemblages are structured by outdoor air with a moderate contribution by surface growth, whereas indoor bacterial assemblages represent a mixture of bacteria entered from outdoor air, shed by building inhabitants, and grown on surfaces. To test the fungal aspect of this hypothesis, we sampled fungi from three surface types likely to support growth and therefore possible contributors of fungi to indoor air: drains in kitchens and bathrooms, sills beneath condensation-prone windows, and skin of human inhabitants. Sampling was done in replicated units of a university-housing complex without reported mold problems, and sequences were analyzed using both QIIME and the new UPARSE approach to OTU-binning, to the same result. Surfaces demonstrated a mycological profile similar to that of outdoor air from the same locality, and assemblages clustered by surface type. "Weedy" genera typical of indoor air, such as Cladosporium and Cryptococcus, were abundant on sills, as were a diverse set of fungi of likely outdoor origin. Drains supported more depauperate assemblages than the other surfaces and contained thermotolerant genera such as Exophiala, Candida, and Fusarium. Most surprising was the composition detected on residents' foreheads. In addition to harboring Malassezia, a known human commensal, skin also possessed a surprising richness of non-resident fungi, including plant pathogens such as ergot (Claviceps purperea. Overall, fungal richness across indoor surfaces was high, but based on known autecologies, most of these fungi were unlikely to be growing on surfaces. We conclude that while some endogenous fungal growth on typical household surfaces does occur, particularly on drains and skin, all residential surfaces appear - to varying degrees - to be passive collectors of airborne fungi of putative outdoor origin, a view of the origins

  15. Application of ATR-FTIR Spectroscopy to Compare the Cell Materials of Wood Decay Fungi with Wood Mould Fungi

    Directory of Open Access Journals (Sweden)

    Barun Shankar Gupta

    2015-01-01

    Full Text Available Wood fungi create vast damage among standing trees and all types of wood materials. The objectives of this study are to (a characterize the cell materials of two major wood decay fungi (Basidiomycota, namely, Trametes versicolor and Postia placenta, and (b compare the cell materials of decay fungi with four wood mould fungi (Ascomycota, namely, Aureobasidium pullulans, Alternaria alternata, Cladosporium cladosporioides, and Ulocladium atrum. Fourier transform infrared (FTIR spectroscopy is used to characterize the microbial cellular materials. The results showed that the IR bands for the fatty acid at ∼2900 cm−1 were different for the two-decay-fungi genre. Postia placenta shows more absorbance peaks at the fatty acid region. Band ratio indices for amide I and amide II from protein amino acids were higher for the mould fungi (Ascomycota than the decay fungi (Basidiomycota. Similarly, the band ratio index calculated for the protein end methyl group was found to be higher for the mould fungi than the decay fungi. Mould fungi along with the decay fungi demonstrated a positive correlation (R2=0.75 between amide I and amide II indices. The three-component multivariate, principal component analysis showed a strong correlation of amide and protein band indices.

  16. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

    Directory of Open Access Journals (Sweden)

    Corinne Rancurel

    2017-09-01

    Full Text Available Horizontal gene transfer (HGT is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI protein library. The user defines recipient (e.g., Metazoa and donor (e.g., bacteria, fungi branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.

  17. [Survey on fungi contamination and natural occurrence of mycotoxins in 94 corn feed ingredients collected from China].

    Science.gov (United States)

    Han, X M; Zhang, H Y; Zhang, J; Xu, W J; Liu, D; Jiang, T; Xu, J; Li, F Q

    2016-10-06

    Objective: To investigate fungi contamination and the natural occurrence of mycotoxins in corn feed ingredients collected from China. Methods: A total of 94 corn feed ingredient samples were collected from 8 Chinese provinces(i.e., Anhui, Hebei, Heilongjiang, Jilin, Jiangsu, Liaoning, Inner Mongolia, and Shandong)in February 2014. A tandem ultra-performance liquid chromatographymass spectrometry method was used for simultaneous detection of twelve kinds of mycotoxins, including aflatoxin(AF), type A and type B tricothecenes, and zearalenone(ZEN). Contaminated fungi were also identified and counted. Results: AF was detected in 36.2%(34/94)of samples; the concentration of AFB 1 was the highest in the four AFs with the range: 0.3~181.3 μg/kg; and then followed by AFB 2 (range: 1.0-74.3 μg/kg). There were 7 samples(7.5%)with AFB 1 concentrations higher than the tolerance limit of 50 μg/kg. The concentration of type A tricothecenes in all samples was lower(0.1-10.5 μg/kg). DON had the most serious contamination than other kind of type B tricothecenes(range: 0.7-606.6 μg/kg; median: 66.3 μg/kg). The DON concentration in all samples was below the tolerance limit of 1 000 μg/kg. ZEN was detected in 76.6%(72/ 94)of samples(median: 36.9 μg/kg), with 3 samples having ZEN concentrations higher than the tolerance limit of 500 μg/kg. The survey on fungi contamination showed that all samples were contaminated by fungi(range: 5.0-1.4×10 5 CFU/g). There were 18 and 3 samples with quantities of fungi higher than the tolerance and forbidden limits, respectively. The Aspergillus , Penicillium , Fusarium , Trichoderma and Mucor genuses were the predominant fungi in corn feed ingredients, with detection rates of 71.3%(67), 60.6%(57), 71.3%(67), 27.7%(26), and 24.5%(23), respectively. The detection rate of Fusarium moniliforme , 73.4%(69/94)was higher than that of Aspergillus flavus , 41.5%(39/94). Conclusion: In this survey, the corn feed ingredients were not seriously

  18. Microfluidic devices for sample preparation and rapid detection of foodborne pathogens.

    Science.gov (United States)

    Kant, Krishna; Shahbazi, Mohammad-Ali; Dave, Vivek Priy; Ngo, Tien Anh; Chidambara, Vinayaka Aaydha; Than, Linh Quyen; Bang, Dang Duong; Wolff, Anders

    2018-03-10

    Rapid detection of foodborne pathogens at an early stage is imperative for preventing the outbreak of foodborne diseases, known as serious threats to human health. Conventional bacterial culturing methods for foodborne pathogen detection are time consuming, laborious, and with poor pathogen diagnosis competences. This has prompted researchers to call the current status of detection approaches into question and leverage new technologies for superior pathogen sensing outcomes. Novel strategies mainly rely on incorporating all the steps from sample preparation to detection in miniaturized devices for online monitoring of pathogens with high accuracy and sensitivity in a time-saving and cost effective manner. Lab on chip is a blooming area in diagnosis, which exploits different mechanical and biological techniques to detect very low concentrations of pathogens in food samples. This is achieved through streamlining the sample handling and concentrating procedures, which will subsequently reduce human errors and enhance the accuracy of the sensing methods. Integration of sample preparation techniques into these devices can effectively minimize the impact of complex food matrix on pathogen diagnosis and improve the limit of detections. Integration of pathogen capturing bio-receptors on microfluidic devices is a crucial step, which can facilitate recognition abilities in harsh chemical and physical conditions, offering a great commercial benefit to the food-manufacturing sector. This article reviews recent advances in current state-of-the-art of sample preparation and concentration from food matrices with focus on bacterial capturing methods and sensing technologies, along with their advantages and limitations when integrated into microfluidic devices for online rapid detection of pathogens in foods and food production line. Copyright © 2018. Published by Elsevier Inc.

  19. Biotechnology of marine fungi

    Digital Repository Service at National Institute of Oceanography (India)

    Damare, S.R.; Singh, P.; Raghukumar, S.

    Filamentous fungi are the most widely used eukaryotes in industrial and pharmaceutical applications. Their biotechnological uses include the production of enzymes, vitamins, polysaccharides, pigments, lipids and others. Marine fungi are a still...

  20. Portable microfluidic raman system for rapid, label-free early disease signature detection

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Meiye [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Davis, Ryan Wesley [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Hatch, Anson [Sandia National Laboratories (SNL-CA), Livermore, CA (United States)

    2015-09-01

    In the early stages of infection, patients develop non-specific or no symptoms at all. While waiting for identification of the infectious agent, precious window of opportunity for early intervention is lost. The standard diagnostics require affinity reagents and sufficient pathogen titers to reach the limit of detection. In the event of a disease outbreak, triaging the at-risk population rapidly and reliably for quarantine and countermeasure is more important than the identification of the pathogen by name. To expand Sandia's portfolio of Biological threat management capabilities, we will utilize Raman spectrometry to analyze immune subsets in whole blood to rapidly distinguish infected from non-infected, and bacterial from viral infection, for the purpose of triage during an emergency outbreak. The goal of this one year LDRD is to determine whether Raman spectroscopy can provide label-free detection of early disease signatures, and define a miniaturized Raman detection system meeting requirements for low- resource settings.

  1. Rapid single cell detection of Staphylococcus aureus by aptamer-conjugated gold nanoparticles.

    Science.gov (United States)

    Chang, Yi-Chung; Yang, Chia-Ying; Sun, Ruei-Lin; Cheng, Yi-Feng; Kao, Wei-Chen; Yang, Pan-Chyr

    2013-01-01

    Staphylococcus aureus is one of the most important human pathogens, causing more than 500,000 infections in the United States each year. Traditional methods for bacterial culture and identification take several days, wasting precious time for patients who are suffering severe bacterial infections. Numerous nucleic acid-based detection methods have been introduced to address this deficiency; however, the costs and requirement for expensive equipment may limit the widespread use of such technologies. Thus, there is an unmet demand of new platform technology to improve the bacterial detection and identification in clinical practice. In this study, we developed a rapid, ultra-sensitive, low cost, and non-polymerase chain reaction (PCR)-based method for bacterial identification. Using this method, which measures the resonance light-scattering signal of aptamer-conjugated gold nanoparticles, we successfully detected single S. aureus cell within 1.5 hours. This new platform technology may have potential to develop a rapid and sensitive bacterial testing at point-of-care.

  2. Detection of gonococcal infection : pros and cons of a rapid test.

    Science.gov (United States)

    Vickerman, Peter; Peeling, Rosanna W; Watts, Charlotte; Mabey, David

    2005-01-01

    WHO estimates that 62 million cases of gonorrhea occur annually worldwide. Untreated infection can cause serious long-term complications, especially in women. In addition, Neisseria gonorrheae infection can facilitate HIV transmission, and babies born to infected mothers are at risk of ocular infection, which can lead to blindness. Where diagnostic facilities are lacking, gonorrhea can be treated syndromically. However, this inevitably leads to over-treatment, especially in women in whom the syndrome of vaginal discharge may be due not to N. gonorrheae infection but to several other more prevalent conditions. Over-treatment is a major concern because of widespread N. gonorrheae antibiotic resistance. Moreover, a high proportion of gonorrhea cases are asymptomatic and so do not present for syndromic management. Such cases will only be detected by screening tests. The gold standard test for the detection of N. gonorrheae is culture, which has high sensitivity and specificity. However, it requires well trained staff and its performance is affected by specimen transport conditions. Other options include microscopy and tests that detect gonococcal antigen or nucleic acid. Nucleic acid amplification tests (NAATs) have higher sensitivity and can be used on non-invasive samples (urine). However, they can cross-react with other Neisseria species and are expensive, requiring highly trained staff and sophisticated equipment. In settings where patients are asked to return for laboratory results, some infected patients never receive treatment as they fail to return for their test results. This reduction in treatment, and the possible onward transmission of N. gonorrheae during any delay in treatment, means that a rapid test of lower sensitivity may be more effective if it results in patients being treated at the initial visit. Indeed, even with the low sensitivity of currently available rapid tests (50-70%), modeling shows that they can outperform gold standard tests in

  3. [Isolation of endophytic fungi from medicinal plant Brucea javanica and their microbial inhibition activity].

    Science.gov (United States)

    Liang, Zi-Ning; Zhu, Hua; Lai, Kai-Ping; Chen, Long

    2014-04-01

    To isolate and identify endophytic fungi from Brucea javanica, and to detect the antimicrobial activity of these strains. Endophytic fungi were isolated by tissue inoculation culture and identified by conventional morphological characteristic method. Seven kinds of pathogenic fungi and three kinds of bacteria were used as targeting microbes to test microbial inhibition activities by agar plate antagonistic action and modified agar gel diffusion methods, respectively. A total of 83 endophytic fungi strains were isolated from the root, stem, leaf and fruit of Brucea javanica. 34 strains were obtained from the stem, 32 strains were obtained from the leaf, 15 strains were isolated from the root and 2 strains came from the fruit. These 73 strains which had been identified attribute to 5 orders, 6 families and 12 genera. For the isolated strains, 14 strains had antifungal activities against at least one pathogenic fungi, 9 strains showed antibacterial activities against one or more bacteria. Especially, the strain YJ-17 which belonged to Phomopsis genus showed the best inhibitory effect on the targeting microbes. The endophytic fungi from Brucea javanica show diversity and microbial inhibition activity, and are worthy for further study on plant disease controlling.

  4. Protein patterns of black fungi under simulated Mars-like conditions.

    Science.gov (United States)

    Zakharova, Kristina; Marzban, Gorji; de Vera, Jean-Pierre; Lorek, Andreas; Sterflinger, Katja

    2014-05-29

    Two species of microcolonial fungi - Cryomyces antarcticus and Knufia perforans - and a species of black yeasts-Exophiala jeanselmei - were exposed to thermo-physical Mars-like conditions in the simulation chamber of the German Aerospace Center. In this study the alterations at the protein expression level from various fungi species under Mars-like conditions were analyzed for the first time using 2D gel electrophoresis. Despite of the expectations, the fungi did not express any additional proteins under Mars simulation that could be interpreted as stress induced HSPs. However, up-regulation of some proteins and significant decreasing of protein number were detected within the first 24 hours of the treatment. After 4 and 7 days of the experiment protein spot number was increased again and the protein patterns resemble the protein patterns of biomass from normal conditions. It indicates the recovery of the metabolic activity under Martian environmental conditions after one week of exposure.

  5. Rapid visual and spectrophotometric nitrite detection by cyclometalated ruthenium complex.

    Science.gov (United States)

    Lo, Hoi-Shing; Lo, Ka-Wai; Yeung, Chi-Fung; Wong, Chun-Yuen

    2017-10-16

    Quantitative determination of nitrite ion (NO 2 - ) is of great importance in environmental and clinical investigations. A rapid visual and spectrophotometric assay for NO 2 - detection was developed based on a newly designed ruthenium complex, [Ru(npy)([9]aneS3)(CO)](ClO 4 ) (denoted as RuNPY; npy = 2-(1-naphthyl)pyridine, [9]aneS3 = 1,4,7-trithiacyclononane). This complex traps NO + produced in acidified NO 2 - solution, and yields observable color change within 1 min at room temperature. The assay features excellent dynamic range (1-840 μmol L -1 ) and high selectivity, and its limit of detection (0.39 μmol L -1 ) is also well below the guideline values for drinking water recommended by WHO and U.S. EPA. Practical use of this assay in tap water and human urine was successfully demonstrated. Overall, the rapidity and selectivity of this assay overcome the problems suffered by the commonly used modified Griess assays for nitrite determination. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. A rapid Salmonella detection method involving thermophilic helicase-dependent amplification and a lateral flow assay.

    Science.gov (United States)

    Du, Xin-Jun; Zhou, Tian-Jiao; Li, Ping; Wang, Shuo

    2017-08-01

    Salmonella is a major foodborne pathogen that is widespread in the environment and can cause serious human and animal disease. Since conventional culture methods to detect Salmonella are time-consuming and laborious, rapid and accurate techniques to detect this pathogen are critically important for food safety and diagnosing foodborne illness. In this study, we developed a rapid, simple and portable Salmonella detection strategy that combines thermophilic helicase-dependent amplification (tHDA) with a lateral flow assay to provide a detection result based on visual signals within 90 min. Performance analyses indicated that the method had detection limits for DNA and pure cultured bacteria of 73.4-80.7 fg and 35-40 CFU, respectively. Specificity analyses showed no cross reactions with Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Enterobacter aerogenes, Shigella and Campylobacter jejuni. The results for detection in real food samples showed that 1.3-1.9 CFU/g or 1.3-1.9 CFU/mL of Salmonella in contaminated chicken products and infant nutritional cereal could be detected after 2 h of enrichment. The same amount of Salmonella in contaminated milk could be detected after 4 h of enrichment. This tHDA-strip can be used for the rapid detection of Salmonella in food samples and is particularly suitable for use in areas with limited equipment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. A novel kit for rapid detection of Vibrio cholerae O1.

    OpenAIRE

    Hasan, J A; Huq, A; Tamplin, M L; Siebeling, R J; Colwell, R R

    1994-01-01

    We report on the development and testing of a novel, rapid, colorimetric immunodiagnostic kit, Cholera SMART, for direct detection of the presence of Vibrio cholerae O1 in clinical specimens. Unlike conventional culture methods requiring several days to complete, the Cholera SMART kit can be used directly in the field by untrained or minimally skilled personnel to detect V. cholerae O1 in less than 15 min, without cumbersome laboratory equipment. A total of 120 clinical and environmental bact...

  8. Exposure level and distribution characteristics of airborne bacteria and fungi in Seoul metropolitan subway stations.

    Science.gov (United States)

    Kim, Ki Youn; Kim, Yoon Shin; Kim, Daekeun; Kim, Hyeon Tae

    2011-01-01

    The exposure level and distribution characteristics of airborne bacteria and fungi were assessed in the workers' activity areas (station office, bedroom, ticket office and driver's seat) and passengers' activity areas (station precinct, inside the passenger carriage, and platform) of the Seoul metropolitan subway. Among investigated areas, the levels of airborne bacteria and fungi in the workers' bedroom and station precincts were relatively high. No significant difference was found in the concentration of airborne bacteria and fungi between the underground and above ground activity areas of the subway. The genera identified in all subway activity areas with a 5% or greater detection rate were Staphylococcus, Micrococcus, Bacillus and Corynebacterium for airborne bacteria and Penicillium, Cladosporium, Chrysosporium, Aspergillus for airborne fungi. Staphylococcus and Micrococcus comprised over 50% of the total airborne bacteria and Penicillium and Cladosporium comprised over 60% of the total airborne fungi, thus these four genera are the predominant genera in the subway station.

  9. Immunomagnetic nanoparticle based quantitative PCR for rapid detection of Salmonella

    International Nuclear Information System (INIS)

    Bakthavathsalam, Padmavathy; Rajendran, Vinoth Kumar; Saran, Uttara; Chatterjee, Suvro; Ali, Baquir Mohammed Jaffar

    2013-01-01

    We have developed a rapid and sensitive method for immunomagnetic separation (IMS) of Salmonella along with their real time detection via PCR. Silica-coated magnetic nanoparticles were functionalized with carboxy groups to which anti-Salmonella antibody raised against heat-inactivated whole cells of Salmonella were covalently attached. The immuno-captured target cells were detected in beverages like milk and lemon juice by multiplex PCR and real time PCR with a detection limit of 10 4 cfu.mL −1 and 10 3 cfu.mL −1 , respectively. We demonstrate that IMS can be used for selective concentration of target bacteria from beverages for subsequent use in PCR detection. PCR also enables differentiation of Salmonella typhi and Salmonella paratyphi A using a set of four specific primers. In addition, IMS—PCR can be used as a screening tool in the food and beverage industry for the detection of Salmonella within 3–4 h which compares favorably to the time of several days that is needed in case of conventional detection based on culture and biochemical methods. (author)

  10. Natural substrata for corticioid fungi

    Directory of Open Access Journals (Sweden)

    Eugene O. Yurchenko

    2013-12-01

    Full Text Available The paper reviews the types of substrata inhabited by non-poroid resupinate Homobasidiomycetes in situ in global scale with both examples from literature sources and from observations on Belarus corticioid fungi biota. The groups of organic world colonized by corticioid basidiomata and vegetative mycelium are arboreous, semi-arboreous, and herbaceous vascular plants, Bryophyta, epiphytic coccoid algae, lichenized and non-lichenized fungi, and occasionally myxomycetes and invertebrates. The fungi occur on living, dying, and dead on all decay stages parts of organisms. Besides, the fungi are known on soil, humus, stones, artificial inorganic and synthetic materials and dung.

  11. Rapid on-site detection of Acidovorax avenae subsp. citrulli by gold-labeled DNA strip sensor.

    Science.gov (United States)

    Zhao, Wenjun; Lu, Jie; Ma, Wenwei; Xu, Chuanlai; Kuang, Hua; Zhu, Shuifang

    2011-06-15

    Acidovorax avenae subsp. citrulli (AAC) is one of the most harmful diseases in cucurbit production. A rapid and sensitive DNA strip sensor was constructed based on gold nanoparticle-labeled oligonucleotide probes for the detection of AAC. Both the qualitative and semi-quantitative detections of target DNA were successfully achieved using the developed DNA strip sensor. The qualitative limit of detection (LOD) of the strip sensor was determined as 4 nM. The LOD for the semi-quantitative detection was calculated to be 0.48 nM in the range of 0-10 nM. The genomic DNA was detected directly using the DNA strip sensor without any further treatment. This DNA strip sensor is a potentially useful tool for rapid on-site DNA screening. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Thermophilic Fungi: Their Physiology and Enzymes†

    Science.gov (United States)

    Maheshwari, Ramesh; Bharadwaj, Girish; Bhat, Mahalingeshwara K.

    2000-01-01

    Thermophilic fungi are a small assemblage in mycota that have a minimum temperature of growth at or above 20°C and a maximum temperature of growth extending up to 60 to 62°C. As the only representatives of eukaryotic organisms that can grow at temperatures above 45°C, the thermophilic fungi are valuable experimental systems for investigations of mechanisms that allow growth at moderately high temperature yet limit their growth beyond 60 to 62°C. Although widespread in terrestrial habitats, they have remained underexplored compared to thermophilic species of eubacteria and archaea. However, thermophilic fungi are potential sources of enzymes with scientific and commercial interests. This review, for the first time, compiles information on the physiology and enzymes of thermophilic fungi. Thermophilic fungi can be grown in minimal media with metabolic rates and growth yields comparable to those of mesophilic fungi. Studies of their growth kinetics, respiration, mixed-substrate utilization, nutrient uptake, and protein breakdown rate have provided some basic information not only on thermophilic fungi but also on filamentous fungi in general. Some species have the ability to grow at ambient temperatures if cultures are initiated with germinated spores or mycelial inoculum or if a nutritionally rich medium is used. Thermophilic fungi have a powerful ability to degrade polysaccharide constituents of biomass. The properties of their enzymes show differences not only among species but also among strains of the same species. Their extracellular enzymes display temperature optima for activity that are close to or above the optimum temperature for the growth of organism and, in general, are more heat stable than those of the mesophilic fungi. Some extracellular enzymes from thermophilic fungi are being produced commercially, and a few others have commercial prospects. Genes of thermophilic fungi encoding lipase, protease, xylanase, and cellulase have been cloned and

  13. Aptasensors for rapid detection of Escherichia coli O157:H7 and Salmonella typhimurium

    Science.gov (United States)

    Wu, Wen-he; Li, Min; Wang, Yue; Ouyang, Hou-xian; Wang, Lin; Li, Ci-xiu; Cao, Yu-chen; Meng, Qing-he; Lu, Jian-xin

    2012-11-01

    Herein we reported the development of aptamer-based biosensors (aptasensors) based on label-free aptamers and gold nanoparticles (AuNPs) for detection of Escherichia coli ( E. coli) O157:H7 and Salmonella typhimurium. Target bacteria binding aptamers are adsorbed on the surface of unmodified AuNPs to capture target bacteria, and the detection was accomplished by target bacteria-induced aggregation of the aptasensor which is associated as red-to-purple color change upon high-salt conditions. By employing anti- E. coli O157:H7 aptamer and anti- S. typhimurium aptamer, we developed a convenient and rapid approach that could selectively detect bacteria without specialized instrumentation and pretreatment steps such as cell lysis. The aptasensor could detect as low as 105colony-forming units (CFU)/ml target bacteria within 20 min or less and its specificity was 100%. This novel method has a great potential application in rapid detection of bacteria in the near future.

  14. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  15. Quantum Dot-Fullerene Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection.

    Science.gov (United States)

    Liu, Ye; Kannegulla, Akash; Wu, Bo; Cheng, Li-Jing

    2018-05-15

    Spherical fullerene (C 60 ) can quench the fluorescence of a quantum dot (QD) through energy transfer and charge transfer processes, with the quenching efficiency regulated by the number of proximate C 60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C 60 -labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C 60 based MBs carried by magnetic nanoparticles (MNPs). The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance 3-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (< 10 min) with a small sample volume (1-10 µl). The high signal-to-noise ratio produced by the QD-C 60 pairs and magnetic concentration yielded a detection limit of 100 fM (~106 target DNA copies for a 10 µl analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.

  16. Flow cytometry for rapid detection of Salmonella spp. in seed sprouts

    Directory of Open Access Journals (Sweden)

    Bledar Bisha

    2014-12-01

    Full Text Available Seed sprouts (alfalfa, mung bean, radish, etc. have been implicated in several recent national and international outbreaks of salmonellosis. Conditions used for sprouting are also conducive to the growth of Salmonella. As a result, this pathogen can quickly grow to very high cell densities during sprouting without any detectable organoleptic impact. Seed sprouts typically also support heavy growth (~108 CFU g−1 of a heterogeneous microbiota consisting of various bacterial, yeast, and mold species, often dominated by non-pathogenic members of the family Enterobacteriaceae. This heavy background may present challenges to the detection of Salmonella, especially if this pathogen is present in relatively low numbers. We combined DNA-based fluorescence in situ hybridization (FISH with flow cytometry (FCM for the rapid molecular detection of Salmonella enterica ser. Typhimurium in artificially contaminated alfalfa and other seed sprouts. Components of the assay included a set of cooperatively binding probes, a chemical blocking treatment intended to reduce non-specific background, and sample concentration via tangential flow filtration (TFF. We were able to detect S. Typhimurium in sprout wash at levels as low as 103 CFU ml−1 sprout wash (104 CFU g−1 sprouts against high microbial backgrounds (~108 CFU g−1 sprouts. Hybridization times were typically 30 min, with additional washing, but we ultimately found that S. Typhimurium could be readily detected using hybridization times as short as 2 min, without a wash step. These results clearly demonstrate the potential of combined DNA-FISH and FCM for rapid detection of Salmonella in this challenging food matrix and provide industry with a useful tool for compliance with sprout production standards proposed in the Food Safety Modernization Act (FSMA.

  17. Fight Fungi with Fungi: Antifungal Properties of the Amphibian Mycobiome

    Directory of Open Access Journals (Sweden)

    Patrick J. Kearns

    2017-12-01

    Full Text Available Emerging infectious diseases caused by fungal taxa are increasing and are placing a substantial burden on economies and ecosystems worldwide. Of the emerging fungal diseases, chytridomycosis caused by the fungus Batrachochytrium dendrobatidis (hereafter Bd is linked to global amphibian declines. Amphibians have innate immunity, as well as additional resistance through cutaneous microbial communities. Despite the targeting of bacteria as potential probiotics, the role of fungi in the protection against Bd infection in unknown. We used a four-part approach, including high-throughput sequencing of bacterial and fungal communities, cultivation of fungi, Bd challenge assays, and experimental additions of probiotic to Midwife Toads (Altyes obstetricans, to examine the overlapping roles of bacterial and fungal microbiota in pathogen defense in captive bred poison arrow frogs (Dendrobates sp.. Our results revealed that cutaneous fungal taxa differed from environmental microbiota across three species and a subspecies of Dendrobates spp. frogs. Cultivation of host-associated and environmental fungi realved numerous taxa with the ability to inhibit or facilitate the growth of Bd. The abundance of cutaneous fungi contributed more to Bd defense (~45% of the fungal community, than did bacteria (~10% and frog species harbored distinct inhibitory communities that were distinct from the environment. Further, we demonstrated that a fungal probiotic therapy did not induce an endocrine-immune reaction, in contrast to bacterial probiotics that stressed amphibian hosts and suppressed antimicrobial peptide responses, limiting their long-term colonization potential. Our results suggest that probiotic strategies against amphibian fungal pathogens should, in addition to bacterial probiotics, focus on host-associated and environmental fungi such as Penicillium and members of the families Chaetomiaceae and Lasiosphaeriaceae.

  18. Importance of nuclear technology in the conservation and production of nutritional fungi

    International Nuclear Information System (INIS)

    Sajet, A.S.

    2008-01-01

    The shortfall in food and field crops due to bad weather and the incidence of insects and microbes during harvesting, handling and storage under non-suitable conditions, called the attention of researchers to try to minimize the damage happening and by various means, whether to develop sources of new food, such as producing nutritional fungi, or by following non-traditional methods of anti-microbes and insects such as the use of radiation as a safe and successful way to save the food without any toxic effects. Permits have been issued for food irradiation by many international organizations including IAEA, World Health Organization and FAO. Nutritional fungi is one of the food sources used as food fit for human consumption in various countries around the world due to their importance which includes many aspects: the nutritional and health value; medical significance; environmental importance and industrial importance. Nuclear technology has contributed in many of the developments in the production and conservation of nutritional fungi, notably, biological studies of nutritional fungi, production technology of fungus, the role of radiation in the preparation and improvement of the nutritional media, improvement of the fungus strains, the use of radiation in the conservation of nutritional fungi and the detection of irradiated nutritional fungus.

  19. Identifying and naming plant-pathogenic fungi: past, present, and future.

    Science.gov (United States)

    Crous, Pedro W; Hawksworth, David L; Wingfield, Michael J

    2015-01-01

    Scientific names are crucial in communicating knowledge about fungi. In plant pathology, they link information regarding the biology, host range, distribution, and potential risk. Our understanding of fungal biodiversity and fungal systematics has undergone an exponential leap, incorporating genomics, web-based systems, and DNA data for rapid identification to link species to metadata. The impact of our ability to recognize hitherto unknown organisms on plant pathology and trade is enormous and continues to grow. Major challenges for phytomycology are intertwined with the Genera of Fungi project, which adds DNA barcodes to known biodiversity and corrects the application of old, established names via epi- or neotypification. Implementing the one fungus-one name system and linking names to validated type specimens, cultures, and reference sequences will provide the foundation on which the future of plant pathology and the communication of names of plant pathogens will rest.

  20. Early Detection Rapid Response Program Targets New Noxious Weed Species in Washington State

    Science.gov (United States)

    Andreas, Jennifer E.; Halpern, Alison D.; DesCamp, Wendy C.; Miller, Timothy W.

    2015-01-01

    Early detection, rapid response is a critical component of invasive plant management. It can be challenging, however, to detect new invaders before they become established if landowners cannot identify species of concern. In order to increase awareness, eye-catching postcards were developed in Washington State as part of a noxious weed educational…

  1. Marine fungi: A critique

    Digital Repository Service at National Institute of Oceanography (India)

    Raghukumar, S.; Raghukumar, C.

    in the sea have been ignored to a large extent. However, several instances of terrestrial species of fungi, active in marine environment have been reported. The arguments to support the view that terrestrial species of fungi by virtue of their physiological...

  2. Toxicity of organic and inorganic nanoparticles to four species of white-rot fungi

    International Nuclear Information System (INIS)

    Galindo, T.P.S.; Pereira, R.; Freitas, A.C.; Santos-Rocha, T.A.P.; Rasteiro, M.G.; Antunes, F.; Rodrigues, D.; Soares, A.M.V.M.; Gonçalves, F.

    2013-01-01

    The rapid development of nanoparticles (NP) for industrial applications and large-volume manufacturing, with its subsequent release into the environment, raised the need to understand and characterize the potential effects of NP to biota. Accordingly, this work aimed to assess sublethal effects of five NP to the white-rot fungi species Trametes versicolor, Lentinus sajor caju, Pleurotus ostreatus, and Phanerochaete chrysosporium. Each species was exposed to serial dilutions of the following NP: organic-vesicles of SDS/DDAB and of Mo/NaO; gold-NP, quantum dot CdSe/ZnS, and Fe/Co. Fungi growth rate was monitored every day, and at the end of assay the mycelium from each replicate was collected to evaluate possible changes in its chemical composition. For all NP-suspensions the following parameters were characterized: hydrodynamic diameter, surface charge, aggregation index, zeta potential, and conductivity. All tested NP tended to aggregate when suspended in aqueous media. The obtained results showed that gold-NP, CdSe/ZnS, Mo/NaO, and SDS/DDAB significantly inhibited the growth of fungi with effects on the mycelium chemical composition. Among the tested NP, gold-NP and CdSe/ZnS were the ones exerting a higher effect on the four fungi. Finally to our knowledge, this is the first study reporting that different types of NP induce changes in the chemical composition of fungi mycelium. - Highlights: • Nanoparticles (NP) tend to aggregate when in aqueous suspensions. • Chemical composition revealed to be very important in the ecotoxicity of NP. • Observed effects suggested diversified modes of action of different NP. • White-rot fungi species exhibit great differences in their sensitivity to NP

  3. Toxicity of organic and inorganic nanoparticles to four species of white-rot fungi

    Energy Technology Data Exchange (ETDEWEB)

    Galindo, T.P.S., E-mail: pgalindo@ua.pt [CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); Pereira, R. [CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 4169-007 Porto (Portugal); Freitas, A.C.; Santos-Rocha, T.A.P. [CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); ISEIT, Instituto Piaget Viseu, Estrada do Alto do Gaio, Lordosa, 3515-776 Viseu (Portugal); Rasteiro, M.G.; Antunes, F. [Department of Chemical Engineering, University of Coimbra, 3030-290 Coimbra (Portugal); Rodrigues, D. [CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); ISEIT, Instituto Piaget Viseu, Estrada do Alto do Gaio, Lordosa, 3515-776 Viseu (Portugal); Soares, A.M.V.M.; Gonçalves, F. [CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); and others

    2013-08-01

    The rapid development of nanoparticles (NP) for industrial applications and large-volume manufacturing, with its subsequent release into the environment, raised the need to understand and characterize the potential effects of NP to biota. Accordingly, this work aimed to assess sublethal effects of five NP to the white-rot fungi species Trametes versicolor, Lentinus sajor caju, Pleurotus ostreatus, and Phanerochaete chrysosporium. Each species was exposed to serial dilutions of the following NP: organic-vesicles of SDS/DDAB and of Mo/NaO; gold-NP, quantum dot CdSe/ZnS, and Fe/Co. Fungi growth rate was monitored every day, and at the end of assay the mycelium from each replicate was collected to evaluate possible changes in its chemical composition. For all NP-suspensions the following parameters were characterized: hydrodynamic diameter, surface charge, aggregation index, zeta potential, and conductivity. All tested NP tended to aggregate when suspended in aqueous media. The obtained results showed that gold-NP, CdSe/ZnS, Mo/NaO, and SDS/DDAB significantly inhibited the growth of fungi with effects on the mycelium chemical composition. Among the tested NP, gold-NP and CdSe/ZnS were the ones exerting a higher effect on the four fungi. Finally to our knowledge, this is the first study reporting that different types of NP induce changes in the chemical composition of fungi mycelium. - Highlights: • Nanoparticles (NP) tend to aggregate when in aqueous suspensions. • Chemical composition revealed to be very important in the ecotoxicity of NP. • Observed effects suggested diversified modes of action of different NP. • White-rot fungi species exhibit great differences in their sensitivity to NP.

  4. Screen-printed fluorescent sensors for rapid and sensitive anthrax biomarker detection

    International Nuclear Information System (INIS)

    Lee, Inkyu; Oh, Wan-Kyu; Jang, Jyongsik

    2013-01-01

    Highlights: •We fabricated flexible anthrax sensors with a simple screen-printing method. •The sensors selectively detected B. anthracis biomarker. •The sensors provide the visible alarm against anthrax attack. -- Abstract: Since the 2001 anthrax attacks, efforts have focused on the development of an anthrax detector with rapid response and high selectivity and sensitivity. Here, we demonstrate a fluorescence sensor for detecting anthrax biomarker with high sensitivity and selectivity using a screen-printing method. A lanthanide–ethylenediamine tetraacetic acid complex was printed on a flexible polyethersulfone film. Screen-printing deposition of fluorescent detecting moieties produced fluorescent patterns that acted as a visual alarm against anthrax

  5. The cultivation bias: different communities of arbuscular mycorrhizal fungi detected in roots from the field, from bait plants transplanted to the field, and from a greenhouse trap experiment.

    Science.gov (United States)

    Sýkorová, Zuzana; Ineichen, Kurt; Wiemken, Andres; Redecker, Dirk

    2007-12-01

    The community composition of arbuscular mycorrhizal fungi (AMF) was investigated in roots of four different plant species (Inula salicina, Medicago sativa, Origanum vulgare, and Bromus erectus) sampled in (1) a plant species-rich calcareous grassland, (2) a bait plant bioassay conducted directly in that grassland, and (3) a greenhouse trap experiment using soil and a transplanted whole plant from that grassland as inoculum. Roots were analyzed by AMF-specific nested polymerase chain reaction, restriction fragment length polymorphism screening, and sequence analyses of rDNA small subunit and internal transcribed spacer regions. The AMF sequences were analyzed phylogenetically and used to define monophyletic phylotypes. Overall, 16 phylotypes from several lineages of AMF were detected. The community composition was strongly influenced by the experimental approach, with additional influence of cultivation duration, substrate, and host plant species in some experiments. Some fungal phylotypes, e.g., GLOM-A3 (Glomus mosseae) and several members of Glomus group B, appeared predominantly in the greenhouse experiment or in bait plants. Thus, these phylotypes can be considered r strategists, rapidly colonizing uncolonized ruderal habitats in early successional stages of the fungal community. In the greenhouse experiment, for instance, G. mosseae was abundant after 3 months, but could not be detected anymore after 10 months. In contrast, other phylotypes as GLOM-A17 (G. badium) and GLOM-A16 were detected almost exclusively in roots sampled from plants naturally growing in the grassland or from bait plants exposed in the field, indicating that they preferentially occur in late successional stages of fungal communities and thus represent the K strategy. The only phylotype found with high frequency in all three experimental approaches was GLOM A-1 (G. intraradices), which is known to be a generalist. These results indicate that, in greenhouse trap experiments, it is difficult

  6. Predominant mycotoxins, mycotoxigenic fungi and climate change related to wine.

    Science.gov (United States)

    Paterson, R Russell M; Venâncio, Armando; Lima, Nelson; Guilloux-Bénatier, Michèle; Rousseaux, Sandrine

    2018-01-01

    Wine is a significant contributor to the economies of many countries. However, the commodity can become contaminated with mycotoxins produced by certain fungi. Most information on mycotoxins in wine is from Spain, Italy and France. Grapes can be infected by mycotoxigenic fungi, of which Aspergillus carbonarius producing ochratoxin A (OTA) is of highest concern. Climate is the most important factor in determining contamination once the fungi are established, with high temperatures being a major factor for OTA contamination: OTA in wine is at higher concentrations in warmer southern Europe than northern. Contamination by fumonisins is a particular concern, related to Aspergillus niger producing these compounds and the fungus being isolated frequently from grapes. Aflatoxins can be present in wine, but patulin is seldom detected. Alternaria mycotoxins (e.g. alternariol) have been frequently observed. There are indications that T-2 toxin may be common. Also, the combined effects of mycotoxins in wine require consideration. No other mycotoxins are currently of concern. Accurate fungal identifications and mycotoxin detection from the fungi are important and a consideration of practical methods are required. There is a diversity of wines that can be contaminated (e.g. red, white, sweet, dry and fortified). The occurrence of OTA is higher in red and sweet than white wines. Steps to control mycotoxins in wine involve good agriculture practices. The effect of climate change on vines and mycotoxins in wine needs urgent consideration by well-constructed modelling studies and expert interpretation of existing data. Reliable models of the effect of climate change on vines is a priority: the health of vines affects mycotoxin contamination. A modelling study of OTA in grapes at higher temperatures over 100years is required. Progress has been made in reducing OTA in wine. The other mycotoxins require consideration and the effects of climate change will become crucial. Copyright

  7. Autophagy in plant pathogenic fungi.

    Science.gov (United States)

    Liu, Xiao-Hong; Xu, Fei; Snyder, John Hugh; Shi, Huan-Bin; Lu, Jian-Ping; Lin, Fu-Cheng

    2016-09-01

    Autophagy is a conserved cellular process that degrades cytoplasmic constituents in vacuoles. Plant pathogenic fungi develop special infection structures and/or secrete a range of enzymes to invade their plant hosts. It has been demonstrated that monitoring autophagy processes can be extremely useful in visualizing the sequence of events leading to pathogenicity of plant pathogenic fungi. In this review, we introduce the molecular mechanisms involved in autophagy. In addition, we explore the relationship between autophagy and pathogenicity in plant pathogenic fungi. Finally, we discuss the various experimental strategies available for use in the study of autophagy in plant pathogenic fungi. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Proteomics of Filamentous Fungi

    NARCIS (Netherlands)

    Passel, van M.W.J.; Schaap, P.J.; Graaff, de L.H.

    2013-01-01

    Filamentous fungi, such as Aspergillus niger and Aspergillus oryzae traditionally have had an important role in providing enzymes and enzyme cocktails that are used in food industry. In recent years the genome sequences of many filamentous fungi have become available. This combined with

  9. Establishment of vesicular-arbuscular mycorrhizal fungi and other microorganisms on a beach replenishment site in Florida.

    Science.gov (United States)

    Sylvia, D M; Will, M E

    1988-02-01

    Beach replenishment is a widely used method of controlling coastal erosion. To reduce erosional losses from wind, beach grasses are often planted on the replenishment sands. However, there is little information on the microbial populations in this material that may affect plant establishment and growth. The objectives of this research were to document changes in the populations of vesicular-arbuscular mycorrhizal (VAM) fungi and other soil microorganisms in replenishment materials and to determine whether roots of transplanted beach grasses become colonized by beneficial microbes. The study was conducted over a 2-year period on a replenishment project in northeastern Florida. Three sampling locations were established at 1-km intervals along the beach. Each location consisted of three plots: an established dune, replenishment sand planted with Uniola paniculata and Panicum sp., and replenishment sand left unplanted. Fungal and bacterial populations increased rapidly in the rhizosphere of beach grasses in the planted plots. However, no bacteria were recovered that could fix significant amounts of N(2). The VAM fungi established slowly on the transplanted grasses. Even after two growing seasons, levels of root colonization and sporulation were significantly below those found in the established dune. There was a shift in the dominant VAM fungi found in the planted zone with respect to those in the established dunes. The most abundant species recovered from the established dunes were Glomus deserticola, followed by Acaulospora scrobiculata and Scutellospora weresubiae. The VAM fungi that colonized the planted zone most rapidly were Glomus globiferum, followed by G. deserticola and Glomus aggregatum.

  10. RAPID DETECTION OF PNEUMOCOCCAL ANTIGEN IN PLEURAL FLUID OF PATIENTS WITH COMMUNITY ACQUIRED PNEUMONIA

    NARCIS (Netherlands)

    BOERSMA, WG; LOWENBERG, A; HOLLOWAY, Y; KUTTSCHRUTTER, H; SNIJDER, JAM; KOETER, GH

    Background Detection of pneumococcal antigen may help to increase the rate of diagnosis of pneumococcal pneumonia. This study was designed to determine the value of rapid detection of pneumococcal antigen in pleural fluid from patients with community acquired pneumonia. Methods Thoracentesis was

  11. Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants

    OpenAIRE

    Zhou, Xiaofan; Lin, Zhenguo; Ma, Hong

    2010-01-01

    Background Gene duplication is considered a major driving force for evolution of genetic novelty, thereby facilitating functional divergence and organismal diversity, including the process of speciation. Animals, fungi and plants are major eukaryotic kingdoms and the divergences between them are some of the most significant evolutionary events. Although gene duplications in each lineage have been studied extensively in various contexts, the extent of gene duplication prior to the split of pla...

  12. MALDI-TOF mass spectrometry in the clinical mycology laboratory: identification of fungi and beyond.

    Science.gov (United States)

    Posteraro, Brunella; De Carolis, Elena; Vella, Antonietta; Sanguinetti, Maurizio

    2013-04-01

    MALDI-TOF mass spectrometry (MS) is becoming essential in most clinical microbiology laboratories throughout the world. Its successful use is mainly attributable to the low operational costs, the universality and flexibility of detection, as well as the specificity and speed of analysis. Based on characteristic protein spectra obtained from intact cells - by means of simple, rapid and reproducible preanalytical and analytical protocols - MALDI-TOF MS allows a highly discriminatory identification of yeasts and filamentous fungi starting from colonies. Whenever used early, direct identification of yeasts from positive blood cultures has the potential to greatly shorten turnaround times and to improve laboratory diagnosis of fungemia. More recently, but still at an infancy stage, MALDI-TOF MS is used to perform strain typing and to determine antifungal drug susceptibility. In this article, the authors discuss how the MALDI-TOF MS technology is destined to become a powerful tool for routine mycological diagnostics.

  13. Assessing the potential effects of fungicides on nontarget gut fungi (trichomycetes) and their associated larval black fly hosts

    Science.gov (United States)

    Wilson, Emma R.; Smalling, Kelly L.; Reilly, Timothy J.; Gray, Elmer; Bond, Laura; Steele, Lance; Kandel, Prasanna; Chamberlin, Alison; Gause, Justin; Reynolds, Nicole; Robertson, Ian; Novak, Stephen; Feris, Kevin; White, Merlin M.

    2014-01-01

    Fungicides are moderately hydrophobic and have been detected in water and sediment, particularly in agricultural watersheds, but typically are not included in routine water quality monitoring efforts. This is despite their widespread use and frequent application to combat fungal pathogens. Although the efficacy of these compounds on fungal pathogens is well documented, little is known about their effects on nontarget fungi. This pilot study, a field survey in southwestern Idaho from April to December 2010 on four streams with varying pesticide inputs (two agricultural and two reference sites), was conducted to assess nontarget impact of fungicides on gut fungi, or trichomycetes. Tissues of larval black flies (Diptera: Simuliidae), hosts of gut fungi, were analyzed for pesticide accumulation. Fungicides were detected in hosts from streams within agricultural watersheds but were not detected in hosts from reference streams. Gut fungi from agricultural sites exhibited decreased percent infestation, density and sporulation within the gut, and black fly tissues had elevated pesticide concentrations. Differences observed between the sites demonstrate a potential effect on this symbiotic system. Future research is needed to parse out the details of the complex biotic and abiotic relationships; however, these preliminary results indicate that impacts to nontarget organisms could have far-reaching consequences within aquatic ecosystems.

  14. Fat Content Modulates Rapid Detection of Food: A Visual Search Study Using Fast Food and Japanese Diet

    Directory of Open Access Journals (Sweden)

    Reiko Sawada

    2017-06-01

    Full Text Available Rapid detection of food is crucial for the survival of organisms. However, previous visual search studies have reported discrepant results regarding the detection speeds for food vs. non-food items; some experiments showed faster detection of food than non-food, whereas others reported null findings concerning any speed advantage for the detection of food vs. non-food. Moreover, although some previous studies showed that fat content can affect visual attention for food, the effect of fat content on the detection of food remains unclear. To investigate these issues, we measured reaction times (RTs during a visual search task in which participants with normal weight detected high-fat food (i.e., fast food, low-fat food (i.e., Japanese diet, and non-food (i.e., kitchen utensils targets within crowds of non-food distractors (i.e., cars. Results showed that RTs for food targets were shorter than those for non-food targets. Moreover, the RTs for high-fat food were shorter than those for low-fat food. These results suggest that food is more rapidly detected than non-food within the environment and that a higher fat content in food facilitates rapid detection.

  15. Fat Content Modulates Rapid Detection of Food: A Visual Search Study Using Fast Food and Japanese Diet.

    Science.gov (United States)

    Sawada, Reiko; Sato, Wataru; Toichi, Motomi; Fushiki, Tohru

    2017-01-01

    Rapid detection of food is crucial for the survival of organisms. However, previous visual search studies have reported discrepant results regarding the detection speeds for food vs. non-food items; some experiments showed faster detection of food than non-food, whereas others reported null findings concerning any speed advantage for the detection of food vs. non-food. Moreover, although some previous studies showed that fat content can affect visual attention for food, the effect of fat content on the detection of food remains unclear. To investigate these issues, we measured reaction times (RTs) during a visual search task in which participants with normal weight detected high-fat food (i.e., fast food), low-fat food (i.e., Japanese diet), and non-food (i.e., kitchen utensils) targets within crowds of non-food distractors (i.e., cars). Results showed that RTs for food targets were shorter than those for non-food targets. Moreover, the RTs for high-fat food were shorter than those for low-fat food. These results suggest that food is more rapidly detected than non-food within the environment and that a higher fat content in food facilitates rapid detection.

  16. Fat Content Modulates Rapid Detection of Food: A Visual Search Study Using Fast Food and Japanese Diet

    Science.gov (United States)

    Sawada, Reiko; Sato, Wataru; Toichi, Motomi; Fushiki, Tohru

    2017-01-01

    Rapid detection of food is crucial for the survival of organisms. However, previous visual search studies have reported discrepant results regarding the detection speeds for food vs. non-food items; some experiments showed faster detection of food than non-food, whereas others reported null findings concerning any speed advantage for the detection of food vs. non-food. Moreover, although some previous studies showed that fat content can affect visual attention for food, the effect of fat content on the detection of food remains unclear. To investigate these issues, we measured reaction times (RTs) during a visual search task in which participants with normal weight detected high-fat food (i.e., fast food), low-fat food (i.e., Japanese diet), and non-food (i.e., kitchen utensils) targets within crowds of non-food distractors (i.e., cars). Results showed that RTs for food targets were shorter than those for non-food targets. Moreover, the RTs for high-fat food were shorter than those for low-fat food. These results suggest that food is more rapidly detected than non-food within the environment and that a higher fat content in food facilitates rapid detection. PMID:28690568

  17. Lectins in human pathogenic fungi.

    Science.gov (United States)

    Gallegos, Belém; Martínez, Ruth; Pérez, Laura; Del Socorro Pina, María; Perez, Eduardo; Hernández, Pedro

    2014-01-01

    Lectins are carbohydrate-binding proteins widely distributed in nature. They constitute a highly diverse group of proteins consisting of many different protein families that are, in general, structurally unrelated. In the last few years, mushroom and other fungal lectins have attracted wide attention due to their antitumour, antiproliferative and immunomodulatory activities. The present mini-review provides concise information about recent developments in understanding lectins from human pathogenic fungi. A bibliographic search was performed in the Science Direct and PubMed databases, using the following keywords "lectin", "fungi", "human" and "pathogenic". Lectins present in fungi have been classified; however, the role played by lectins derived from human pathogenic fungi in infectious processes remains uncertain; thus, this is a scientific field requiring more research. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  18. Towards global patterns in the diversity and community structure of ectomycorrhizal fungi

    DEFF Research Database (Denmark)

    Tedersoo, Leho; Bahram, Mohammad; Toots, Märt

    2012-01-01

    Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi—microbial symbionts that play key roles in plant...... nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting...... with latitudinal patterns of macro-organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM...

  19. Highly sensitive quantitative PCR for the detection and differentiation of Pseudogymnoascus destructans and other Pseudogymnoascus species.

    Science.gov (United States)

    Shuey, Megan M; Drees, Kevin P; Lindner, Daniel L; Keim, Paul; Foster, Jeffrey T

    2014-03-01

    White-nose syndrome is a fungal disease that has decimated bat populations across eastern North America. Identification of the etiologic agent, Pseudogymnoascus destructans (formerly Geomyces destructans), in environmental samples is essential to proposed management plans. A major challenge is the presence of closely related species, which are ubiquitous in many soils and cave sediments and often present in high abundance. We present a dual-probe real-time quantitative PCR assay capable of detecting and differentiating P. destructans from closely related fungi in environmental samples from North America. The assay, based on a single nucleotide polymorphism (SNP) specific to P. destructans, is capable of rapid low-level detection from various sampling media, including sediment, fecal samples, wing biopsy specimens, and skin swabs. This method is a highly sensitive, high-throughput method for identifying P. destructans, other Pseudogymnoascus spp., and Geomyces spp. in the environment, providing a fundamental component of research and risk assessment for addressing this disease, as well as other ecological and mycological work on related fungi.

  20. Bioconjugated fluorescent silica nanoparticles for the rapid detection of Entamoeba histolytica.

    Science.gov (United States)

    Hemadi, Ahmad; Ekrami, Alireza; Oormazdi, Hormozd; Meamar, Ahmad Reza; Akhlaghi, Lame; Samarbaf-Zadeh, Ali Reza; Razmjou, Elham

    2015-05-01

    Rapid detection of Entamoeba histolytica based on fluorescent silica nanoparticle (FSNP) indirect immunofluorescence microscopy was evaluated. Silica nanoparticles were synthesized using Stöber's method, with their surface activated to covalently bind to, and immobilize, protein A. For biolabeling, FSNP was added to conjugated E. histolytica trophozoites with monoclonal anti-E. histolytica IgG1 for microscopic observation of fluorescence. Fluorescent silica nanoparticle sensitivity was determined with axenically cultured E. histolytica serially diluted to seven concentrations. Specificity was evaluated using other intestinal protozoa. Fluorescent silica nanoparticles detected E. histolytica at the lowest tested concentration with no cross-reaction with Entamoeba dispar, Entamoeba moshkovskii, Blastocystis sp., or Giardia lamblia. Visualization of E. histolytica trophozoites with anti-E. histolytica antibody labeled with fluorescein isothiocyanate (FITC) was compared with that using anti-E. histolytica antibody bioconjugated FSNP. Although FITC and FSNP produced similar results, the amount of specific antibody required for FITC to induce fluorescence of similar intensity was fivefold that for FSNP. Fluorescent silica nanoparticles delivered a rapid, simple, cost-effective, and highly sensitive and specific method of detecting E. histolytica. Further study is needed before introducing FSNP for laboratory diagnosis of amoebiasis. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. [Development and evaluation of a rapid PCR detection kit for Ophiocordyceps sinensis].

    Science.gov (United States)

    Hou, Fei-Xia; Cao, Jing; Wang, Sha-Sha; Wang, Xi; Yuan, Yuan; Peng, Cheng; Wan, De-Guang; Guo, Jin-Lin

    2017-03-01

    Ophiocordyceps sinensis is a valuable traditional Chinese medicine. Due to resource shortage, expensive price and huge market demand, there are many adulterants of O. sinensis in markets. Therefore, it is necessary to establish a rapid and effective method for distinguishing O. sinensis. Based on the species-specific PCR of O. sinensis, this study developed a detection kit by optimizing the components and evaluated the specificity, detection limit, repeatability and shelf life of the kit. The results showed that when the quality of O. sinensis accounted for more than 1/200 of that mixture, it could be detected successfully. Moreover, only O. sinensis could be amplified and glowed bright green fluorescence under ultraviolet light. The kit was still in effect when it was placed at 37 ℃ for three days, which indicated that it was stable and effective for one year stored in 4 ℃. The kit in the same batch under different operation conditions, and in different batch under the same operation conditions gave the same result and accuracy, which showed good repeatability of the kit. It is simple, rapid and accurate to distinguish O. sinensis from its adulterants using the kit, and lays the foundation for commercialization of traditional Chinese medicine fast detection kit. Copyright© by the Chinese Pharmaceutical Association.

  2. Highly sensitive multianalyte immunochromatographic test strip for rapid chemiluminescent detection of ractopamine and salbutamol

    International Nuclear Information System (INIS)

    Gao, Hongfei; Han, Jing; Yang, Shijia; Wang, Zhenxing; Wang, Lin; Fu, Zhifeng

    2014-01-01

    Graphical abstract: A multianalyte immunochromatographic test strip was developed for the rapid detection of two β 2 -agonists. Due to the application of chemiluminescent detection, this quantitative method shows much higher sensitivity. - Highlights: • An immunochromatographic test strip was developed for detection of multiple β 2 -agonists. • The whole assay process can be completed within 20 min. • The proposed method shows much higher sensitivity due to the application of CL detection. • It is a portable analytical tool suitable for field analysis and rapid screening. - Abstract: A novel immunochromatographic assay (ICA) was proposed for rapid and multiple assay of β 2 -agonists, by utilizing ractopamine (RAC) and salbutamol (SAL) as the models. Owing to the introduction of chemiluminescent (CL) approach, the proposed protocol shows much higher sensitivity. In this work, the described ICA was based on a competitive format, and horseradish peroxidase-tagged antibodies were used as highly sensitive CL probes. Quantitative analysis of β 2 -agonists was achieved by recording the CL signals of the probes captured on the two test zones of the nitrocellulose membrane. Under the optimum conditions, RAC and SAL could be detected within the linear ranges of 0.50–40 and 0.10–50 ng mL −1 , with the detection limits of 0.20 and 0.040 ng mL −1 (S/N = 3), respectively. The whole process for multianalyte immunoassay of RAC and SAL can be completed within 20 min. Furthermore, the test strip was validated with spiked swine urine samples and the results showed that this method was reliable in measuring β 2 -agonists in swine urine. This CL-based multianalyte test strip shows a series of advantages such as high sensitivity, ideal selectivity, simple manipulation, high assay efficiency and low cost. Thus, it opens up new pathway for rapid screening and field analysis, and shows a promising prospect in food safety

  3. Highly sensitive multianalyte immunochromatographic test strip for rapid chemiluminescent detection of ractopamine and salbutamol

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Hongfei; Han, Jing; Yang, Shijia; Wang, Zhenxing; Wang, Lin; Fu, Zhifeng, E-mail: fuzf@swu.edu.cn

    2014-08-11

    Graphical abstract: A multianalyte immunochromatographic test strip was developed for the rapid detection of two β{sub 2}-agonists. Due to the application of chemiluminescent detection, this quantitative method shows much higher sensitivity. - Highlights: • An immunochromatographic test strip was developed for detection of multiple β{sub 2}-agonists. • The whole assay process can be completed within 20 min. • The proposed method shows much higher sensitivity due to the application of CL detection. • It is a portable analytical tool suitable for field analysis and rapid screening. - Abstract: A novel immunochromatographic assay (ICA) was proposed for rapid and multiple assay of β{sub 2}-agonists, by utilizing ractopamine (RAC) and salbutamol (SAL) as the models. Owing to the introduction of chemiluminescent (CL) approach, the proposed protocol shows much higher sensitivity. In this work, the described ICA was based on a competitive format, and horseradish peroxidase-tagged antibodies were used as highly sensitive CL probes. Quantitative analysis of β{sub 2}-agonists was achieved by recording the CL signals of the probes captured on the two test zones of the nitrocellulose membrane. Under the optimum conditions, RAC and SAL could be detected within the linear ranges of 0.50–40 and 0.10–50 ng mL{sup −1}, with the detection limits of 0.20 and 0.040 ng mL{sup −1} (S/N = 3), respectively. The whole process for multianalyte immunoassay of RAC and SAL can be completed within 20 min. Furthermore, the test strip was validated with spiked swine urine samples and the results showed that this method was reliable in measuring β{sub 2}-agonists in swine urine. This CL-based multianalyte test strip shows a series of advantages such as high sensitivity, ideal selectivity, simple manipulation, high assay efficiency and low cost. Thus, it opens up new pathway for rapid screening and field analysis, and shows a promising prospect in food safety.

  4. Microfluidic devices for sample preparation and rapid detection of foodborne pathogens

    DEFF Research Database (Denmark)

    Kant, Krishna; Shahbazi, Mohammad-Ali; Dave, Vivek Priy

    2018-01-01

    and improve the limit of detections. Integration of pathogen capturing bio-receptors on microfluidic devices is a crucial step, which can facilitate recognition abilities in harsh chemical and physical conditions, offering a great commercial benefit to the food-manufacturing sector. This article reviews...... diagnosis competences. This has prompted researchers to call the current status of detection approaches into question and leverage new technologies for superior pathogen sensing outcomes. Novel strategies mainly rely on incorporating all the steps from sample preparation to detection in miniaturized devices...... recent advances in current state-of-the-art of sample preparation and concentration from food matrices with focus on bacterial capturing methods and sensing technologies, along with their advantages and limitations when integrated into microfluidic devices for online rapid detection of pathogens in foods...

  5. Modelling the sporulation of some fungi associated with cheese, at different temperature and water activity regimes.

    Science.gov (United States)

    Camardo Leggieri, Marco; Decontardi, Simone; Battilani, Paola

    2018-08-02

    The objectives of this study were to determine, in-vitro, the influence of temperature (T; 10-30 °C, step 5°), water activity (a w , 0.83-0.99; step 0.04) and time on sporulation (SPO) of some cheese-related fungi belonging to Penicillium spp. and A. versicolor. Overall, sporulation started rapidly (8 h in optimal conditions); it was significantly influenced by T and a w and the fungi studied were clearly distinguished based on their thermo-hydro adaptation. Boundary conditions for sporulation were defined for all the fungi considered and the sporulation rate was successfully modelled, especially based on T and time regimes. Penicillium crustosum, P. nordicum and P. verrucosum showed optimum for SPO at T between 20 and 25 °C and their sporulation continued up to a w  = 0.87 (a w  = 0.83 for P. nordicum). They resulted the fungi best adapted to the environmental conditions of ripening grana cheese storehouses; therefore, it is expected they dominate on the grana cheese surface. Studies on cheese are necessary to validate these results obtained on artificial media and without fungi co-occurrence. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential.

    Science.gov (United States)

    Gruninger, Robert J; Puniya, Anil K; Callaghan, Tony M; Edwards, Joan E; Youssef, Noha; Dagar, Sumit S; Fliegerova, Katerina; Griffith, Gareth W; Forster, Robert; Tsang, Adrian; McAllister, Tim; Elshahed, Mostafa S

    2014-10-01

    Anaerobic fungi (phylum Neocallimastigomycota) inhabit the gastrointestinal tract of mammalian herbivores, where they play an important role in the degradation of plant material. The Neocallimastigomycota represent the earliest diverging lineage of the zoosporic fungi; however, understanding of the relationships of the different taxa (both genera and species) within this phylum is in need of revision. Issues exist with the current approaches used for their identification and classification, and recent evidence suggests the presence of several novel taxa (potential candidate genera) that remain to be characterised. The life cycle and role of anaerobic fungi has been well characterised in the rumen, but not elsewhere in the ruminant alimentary tract. Greater understanding of the 'resistant' phase(s) of their life cycle is needed, as is study of their role and significance in other herbivores. Biotechnological application of anaerobic fungi, and their highly active cellulolytic and hemi-cellulolytic enzymes, has been a rapidly increasing area of research and development in the last decade. The move towards understanding of anaerobic fungi using -omics based (genomic, transcriptomic and proteomic) approaches is starting to yield valuable insights into the unique cellular processes, evolutionary history, metabolic capabilities and adaptations that exist within the Neocallimastigomycota. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  7. [Indiscriminate use of Latin name for natural Cordyceps sinensis insect-fungi complex and multiple Ophiocordyceps sinensis fungi].

    Science.gov (United States)

    Yao, Yi-Sang; Zhu, Jia-Shi

    2016-04-01

    Natural Cordyceps sinensis(Dongchongxiacao) is an insect-fungi complex containing multiple Ophiocordyceps sinensis(≡Cordyceps sinensis) fungi and dead body of larva of the family of Hepialidae. But natural C. sinensis and O. sinensis fungi use the same Latin name, resulting in uncertainty of the specific meaning, even disturbing the formulation and implementation of governmental policies and regulations, and influencing consumer psychology onthe market. This paper reviews the history and current status of the indiscriminate use of the Latin name O. sinensis for both the natural insect-fungi complex C. sinensis and O. sinensis fungi and lists the rename suggetions. Some scholars suggested using the term O. sinensis for the fungi and renaming the natural C. sinensis "Chinese cordyceps". Others suggested renaming the natural C. sinensis "Ophiocordyceps & Hepialidae". Both suggestions have not reached general consensus due to various academic concerns. This paper also reviews the exacerbation of the academic uncertainties when forcing implementing the 2011 Amsterdam Declaration "One Fungus=One Name" under the academic debate. Joint efforts of mycological, zoological and botany-TCM taxonomists and properly initiating the dispute systems offered by International Mycology Association may solve the debate on the indiscriminate use of the Latin name O.sinensis for the natural insect-fungi complex,the teleomorph and anamorph(s) of O. sinensis fungi. Copyright© by the Chinese Pharmaceutical Association.

  8. [Contribution of fungi to soil nitrous oxide emission and their research methods: a review].

    Science.gov (United States)

    Huang, Ying; Long, Xi-En

    2014-04-01

    Nitrous oxide is an important greenhouse gas. Soil is one major emission source of N2O, which is a by-product of microorganisms-driven nitrification and denitrification processes. Extensive research has demonstrated archaea and bacteria are the predominant contributors in nitrification and denitrification. However, fungi may play a predominant role in the N transformation in a certain soil ecosystem. The fungal contribution to N2O production has been rarely investigated. Here, we reviewed the mechanism of N2O production by soil fungi. The mechanisms of denitrification, autotrophic and heterotrophic nitrification and their key microbes and functional genes were described, respectively. We discriminated the differences in denitrification between bacteria and fungi and discussed the methods being used to determine the contribution of fungi to soil N2O emission, including selective inhibitors, 15N stable isotope probing, isolation and pure culturing and uncultured molecular detection methods. The existing problems and research prospects were also presented.

  9. How to know unknown fungi: the role of a herbarium.

    Science.gov (United States)

    Brock, Patrick M; Döring, Heidi; Bidartondo, Martin I

    2009-01-01

    The development of a universal approach to the identification of fungi from the environment is impeded by the limited number and narrow phylogenetic range of the named internal transcribed spacer DNA sequences available on GenBank. The goal here was to assess the potential impact of systematic DNA sequencing from a fungal herbarium collection. DNA sequences were generated from a diverse set of 279 specimens deposited at the fungal herbarium of the Royal Botanic Gardens at Kew (UK) and bioinformatic analyses were used to study their overlap with the public database. It is estimated that c. 70% of the herbarium taxonomic diversity is not yet represented in GenBank and that a further c. 10% of our sequences match solely to 'environmental samples' or fungi otherwise unidentified. Here it is shown that the unsampled diversity residing in fungal herbaria can substantially enlarge the coverage of GenBank's fully identified sequence pool to ameliorate the problem of environmental unknowns and to aid in the detection of truly novel fungi by molecular data.

  10. A recombinase polymerase amplification assay for rapid detection of Crimean-Congo Haemorrhagic fever Virus infection.

    Directory of Open Access Journals (Sweden)

    Laura C Bonney

    2017-10-01

    Full Text Available Crimean-Congo Haemorrhagic fever Virus (CCHFV is a rapidly emerging vector-borne pathogen and the cause of a virulent haemorrhagic fever affecting large parts of Europe, Africa, the Middle East and Asia.An isothermal recombinase polymerase amplification (RPA assay was successfully developed for molecular detection of CCHFV. The assay showed rapid (under 10 minutes detection of viral extracts/synthetic virus RNA of all 7 S-segment clades of CCHFV, with high target specificity. The assay was shown to tolerate the presence of inhibitors in crude preparations of mock field samples, indicating that this assay may be suitable for use in the field with minimal sample preparation. The CCHFV RPA was successfully used to screen and detect CCHFV positives from a panel of clinical samples from Tajikistan.The assay is a rapid, isothermal, simple-to-perform molecular diagnostic, which can be performed on a light, portable real-time detection device. It is ideally placed therefore for use as a field-diagnostic or in-low resource laboratories, for monitoring of CCHF outbreaks at the point-of-need, such as in remote rural regions in affected countries.

  11. Rapid Detection of Herpes Viruses for Clinical Applications

    Science.gov (United States)

    Pierson, Duane; Mehta, Satish

    2013-01-01

    There are eight herpes viruses that infect humans, causing a wide range of diseases resulting in considerable morbidity and associated costs. Varicella zoster virus (VZV) is a human herpes virus that causes chickenpox in children and shingles in adults. Approximately 1,000,000 new cases of shingles occur each year; post-herpetic neuralgia (PHN) follows shingles in 100,000 to 200,000 people annually. PHN is characterized by debilitating, nearly unbearable pain for weeks, months, and even years. The onset of shingles is characterized by pain, followed by the zoster rash, leading to blisters and severe pain. The problem is that in the early stages, shingles can be difficult to diagnose; chickenpox in adults can be equally difficult to diagnose. As a result, both diseases can be misdiagnosed (false positive/negative). A molecular assay has been adapted for use in diagnosing VZV diseases. The polymerase chain reaction (PCR) assay is a non-invasive, rapid, sensitive, and highly specific method for VZV DNA detection. It provides unequivocal results and can effectively end misdiagnoses. This is an approximately two-hour assay that allows unequivocal diagnosis and rapid antiviral drug intervention. It has been demonstrated that rapid intervention can prevent full development of the disease, resulting in reduced likelihood of PHN. The technology was extended to shingles patients and demonstrated that VZV is shed in saliva and blood of all shingles patients. The amount of VZV in saliva parallels the medical outcome.

  12. Rapid detection of cancer related DNA nanoparticulate biomarkers and nanoparticles in whole blood

    Science.gov (United States)

    Heller, Michael J.; Krishnan, Raj; Sonnenberg, Avery

    2010-08-01

    The ability to rapidly detect cell free circulating (cfc) DNA, cfc-RNA, exosomes and other nanoparticulate disease biomarkers as well as drug delivery nanoparticles directly in blood is a major challenge for nanomedicine. We now show that microarray and new high voltage dielectrophoretic (DEP) devices can be used to rapidly isolate and detect cfc-DNA nanoparticulates and nanoparticles directly from whole blood and other high conductance samples (plasma, serum, urine, etc.). At DEP frequencies of 5kHz-10kHz both fluorescent-stained high molecular weight (hmw) DNA, cfc-DNA and fluorescent nanoparticles separate from the blood and become highly concentrated at specific DEP highfield regions over the microelectrodes, while blood cells move to the DEP low field-regions. The blood cells can then be removed by a simple fluidic wash while the DNA and nanoparticles remain highly concentrated. The hmw-DNA could be detected at a level of <260ng/ml and the nanoparticles at <9.5 x 109 particles/ml, detection levels that are well within the range for viable clinical diagnostics and drug nanoparticle monitoring. Disease specific cfc-DNA materials could also be detected directly in blood from patients with Chronic Lymphocytic Leukemia (CLL) and confirmed by PCR genotyping analysis.

  13. Rapid Detection of Enterobacter Sakazakii in milk Powder using amino modified chitosan immunomagnetic beads.

    Science.gov (United States)

    Zhu, Yinglian; Wang, Dongfeng

    2016-12-01

    Chitosan immunomagnetic beads (CIBs) were first prepared through converting hydroxyl groups of natural polymer material-chitosan into amino groups using epichlorohydrin and ethylenediamine as modification agent and then coupling with polyclonal antibodies of Enterobacter sakazakii using glutaraldehyde as cross-linking agent. The beads before coupling with antibodies were characterized by magnetic property measurement, FTIR, SEM and XRD technologies. In the assay a natural polysaccharide-chitosan, which has good biological and chemical properties such as non-toxicity, biocompatibility and high chemical reactivity was first used for synthesis of immunomagnetic beads. The detection method first established in this paper that combined the beads with chromogenic medium together to rapid detect E. sakazakii in milk powder could greatly improve the detection specificity and working efficiency. The beads exhibited a maximum capturing capacity of 1×10 6 cfu/g with the detection sensitivity of 4cfu/g. The results demonstrate that the assay is a straightforward, specific and sensitive alternative for rapid detection of E.sakazakii in food matrix. The total analysis time was as little as about 25h, which greatly shorten the detection time. The method can provides new ideas not only to preparation technique of immunomagnetic beads but to imunne detection technique in food safety. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Rapid detection of acetamiprid in foods using surface-enhanced Raman spectroscopy (SERS).

    Science.gov (United States)

    Wijaya, Wisiani; Pang, Shintaro; Labuza, Theodore P; He, Lili

    2014-04-01

    Acetamiprid is a neonicotinoid pesticide that is commonly used in modern farming. Acetamiprid residue in food commodities can be a potential harm to human and has been implicated in the honey bee hive die off crisis. In this study, we developed rapid, simple, and sensitive methods to detect acetamiprid in apple juice and on apple surfaces using surface-enhanced Raman spectroscopy (SERS). No pretreatment of apple juice sample was performed. A simple surface swab method was used to recover acetamiprid from the apple surface. Samples were incubated with silver dendrites for several minutes and SERS spectra were taken directly from the silver surface. Detection of a set of 5 apple juice samples can be done within 10 min. The swab-SERS method took 15 min for a set of 5 samples. Resulting spectral data were analyzed using principal component analysis. The highest acetamiprid peak at 634 cm(-1) was used to detect and quantify the amount of acetamiprid spiked in 1:1 water-methanol solvent, apple juice, and on apple surface. The SERS method was able to successfully detect acetamiprid at 0.5 μg/mL (0.5 ppm) in solvent, 3 μg/mL (3 ppm) in apple juice, and 0.125 μg/cm(2) on apple surfaces. The SERS methods provide simple, rapid, and sensitive ways to detect acetamiprid in beverages and on the surfaces of thick skinned fruits and vegetables. © 2014 Institute of Food Technologists®

  15. Fungi as a Source of Food.

    Science.gov (United States)

    Dupont, Joëlle; Dequin, Sylvie; Giraud, Tatiana; Le Tacon, François; Marsit, Souhir; Ropars, Jeanne; Richard, Franck; Selosse, Marc-André

    2017-06-01

    In this article, we review some of the best-studied fungi used as food sources, in particular, the cheese fungi, the truffles, and the fungi used for drink fermentation such as beer, wine, and sake. We discuss their history of consumption by humans and the genomic mechanisms of adaptation during artificial selection.

  16. A nationwide web-based automated system for early outbreak detection and rapid response in China

    Directory of Open Access Journals (Sweden)

    Yilan Liao

    2011-03-01

    Full Text Available Timely reporting, effective analyses and rapid distribution of surveillance data can assist in detecting the aberration of disease occurrence and further facilitate a timely response. In China, a new nationwide web-based automated system for outbreak detection and rapid response was developed in 2008. The China Infectious Disease Automated-alert and Response System (CIDARS was developed by the Chinese Center for Disease Control and Prevention based on the surveillance data from the existing electronic National Notifiable Infectious Diseases Reporting Information System (NIDRIS started in 2004. NIDRIS greatly improved the timeliness and completeness of data reporting with real time reporting information via the Internet. CIDARS further facilitates the data analysis, aberration detection, signal dissemination, signal response and information communication needed by public health departments across the country. In CIDARS, three aberration detection methods are used to detect the unusual occurrence of 28 notifiable infectious diseases at the county level and to transmit that information either in real-time or on a daily basis. The Internet, computers and mobile phones are used to accomplish rapid signal generation and dissemination, timely reporting and reviewing of the signal response results. CIDARS has been used nationwide since 2008; all Centers for Disease Control and Prevention (CDC in China at the county, prefecture, provincial and national levels are involved in the system. It assists with early outbreak detection at the local level and prompts reporting of unusual disease occurrences or potential outbreaks to CDCs throughout the country.

  17. Fungi found in Mediterranean and North Sea sponges: how specific are they?

    Directory of Open Access Journals (Sweden)

    Mohd Azrul Naim

    2017-09-01

    Full Text Available Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales, representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point in the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.

  18. Comparing rapid methods for detecting Listeria in seafood and environmental samples using the most probably number (MPN) technique.

    Science.gov (United States)

    Cruz, Cristina D; Win, Jessicah K; Chantarachoti, Jiraporn; Mutukumira, Anthony N; Fletcher, Graham C

    2012-02-15

    The standard Bacteriological Analytical Manual (BAM) protocol for detecting Listeria in food and on environmental surfaces takes about 96 h. Some studies indicate that rapid methods, which produce results within 48 h, may be as sensitive and accurate as the culture protocol. As they only give presence/absence results, it can be difficult to compare the accuracy of results generated. We used the Most Probable Number (MPN) technique to evaluate the performance and detection limits of six rapid kits for detecting Listeria in seafood and on an environmental surface compared with the standard protocol. Three seafood products and an environmental surface were inoculated with similar known cell concentrations of Listeria and analyzed according to the manufacturers' instructions. The MPN was estimated using the MPN-BAM spreadsheet. For the seafood products no differences were observed among the rapid kits and efficiency was similar to the BAM method. On the environmental surface the BAM protocol had a higher recovery rate (sensitivity) than any of the rapid kits tested. Clearview™, Reveal®, TECRA® and VIDAS® LDUO detected the cells but only at high concentrations (>10(2) CFU/10 cm(2)). Two kits (VIP™ and Petrifilm™) failed to detect 10(4) CFU/10 cm(2). The MPN method was a useful tool for comparing the results generated by these presence/absence test kits. There remains a need to develop a rapid and sensitive method for detecting Listeria in environmental samples that performs as well as the BAM protocol, since none of the rapid tests used in this study achieved a satisfactory result. Copyright © 2011 Elsevier B.V. All rights reserved.

  19. Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing

    Directory of Open Access Journals (Sweden)

    Ellis David

    2009-08-01

    assay described here is a simple, robust and rapid (2 h method for the detection of ERG11 polymorphisms. It showed excellent concordance with ERG11 sequencing and is a potentially valuable tool to track the emergence and spread of azole-resistant C. albicans and to study the epidemiology of ERG11 mutations. The RCA method is applicable to the study of azole resistance in other fungi.

  20. Metal stress induces programmed cell death in aquatic fungi

    International Nuclear Information System (INIS)

    Azevedo, Maria-Manuel; Almeida, Bruno; Ludovico, Paula; Cassio, Fernanda

    2009-01-01

    Aquatic hyphomycetes are a group of fungi that play a key role in organic matter turnover in both clean and metal-polluted streams. We examined the ability of Cu or Zn to induce programmed cell death (PCD) in three aquatic hyphomycete species through the evaluation of typical apoptotic markers, namely reactive oxygen species (ROS) accumulation, caspase-like activity, nuclear morphological alterations, and the occurrence of DNA strand breaks assessed by TUNEL assay. The exposure to both metals induced apoptotic events in all tested aquatic fungi. The most tolerant fungi either to Zn (Varicosporium elodeae) or Cu (Heliscussubmersus) exhibited higher levels of PCD markers, suggesting that PCD processes might be linked to fungal resistance/tolerance to metal stress. Moreover, different patterns of apoptotic markers were found, namely a PCD process independent of ROS accumulation in V. elodeae exposed to Cu, or independent of caspase-like activity in Flagellospora curta exposed to Zn, or even without the occurrence of DNA strand breaks in F. curta exposed to Cu. This suggests that a multiplicity of PCD pathways might be operating in aquatic hyphomycetes. The occurrence of a tightly regulated cell death pathway, such as PCD, in aquatic hyphomycetes under metal stress might be a part of the mechanisms underlying fungal acclimation in metal-polluted streams, because it would allow the rapid removal of unwanted or damaged cells sparing nutrients and space for the fittest ones.

  1. Amperometric biosensor based on a single antibody of dual function for rapid detection of Streptococcus agalactiae.

    Science.gov (United States)

    Vásquez, Gersson; Rey, Alba; Rivera, Camilo; Iregui, Carlos; Orozco, Jahir

    2017-01-15

    Pathogenic bacteria are responsible for several diseases in humans and in a variety of hosts. Detection of pathogenic bacteria is imperative to avoid and/or fight their potential harmful effects. This work reports on the first amperometric biosensor for the rapid detection of Streptococcus agalactiae (S. agalactiae). The biosensor relies on a single biotinylated antibody that immobilizes the bacteria on a screen-printed carbon electrode while is further linked to a streptavidin-conjugated HRP reporter. The biotinylated antibody provides selectivity to the biosensor whereas serves as an anchoring point to the reporter for further amplification of the electrochemical signal. The resultant immunosensor is simple, responds rapidly, and allows for the selective and highly sensitive quantification of S. agalactiae cells in a concentration range of 10 1 -10 7 CFUml -1 , with a detection limit of 10CFUml -1 . The approach not only enables a rapid detection and quantification of S. agalactiae in environmental samples but also opens up new opportunities for the simple fabrication of electrochemical immunosensors for different target pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Fungi

    DEFF Research Database (Denmark)

    Hajek, Ann E.; Meyling, Nicolai Vitt

    2018-01-01

    been the focus of most ecological research. Some taxa of invertebrate pathogenic fungi have evolved adaptations for utilizing living plants as substrates, and these lifestyles have recently received increased attention from researchers following the initial documentations of such plant associations...

  3. Rapid detection of fungal keratitis with DNA-stabilizing FTA filter paper.

    Science.gov (United States)

    Menassa, Nardine; Bosshard, Philipp P; Kaufmann, Claude; Grimm, Christian; Auffarth, Gerd U; Thiel, Michael A

    2010-04-01

    Purpose. Polymerase chain reaction (PCR) is increasingly important for the rapid detection of fungal keratitis. However, techniques of specimen collection and DNA extraction before PCR may interfere with test sensitivity. The purpose of this study was to investigate the use of DNA-stabilizing FTA filter paper (Indicating FTA filter paper; Whatman International, Ltd., Maidstone, UK) for specimen collection without DNA extraction in a single-step, nonnested PCR for fungal keratitis. Methods. Specimens were collected from ocular surfaces with FTA filter discs, which automatically lyse collected cells and stabilize nucleic acids. Filter discs were directly used in single-step PCR reactions to detect fungal DNA. Test sensitivity was evaluated with serial dilutions of Candida albicans, Fusarium oxysporum, and Aspergillus fumigatus cultures. Test specificity was analyzed by comparing 196 and 155 healthy individuals from Switzerland and Egypt, respectively, with 15 patients with a diagnosis of microbial keratitis. Results. PCR with filter discs detected 3 C. albicans, 25 F. oxysporum, and 125 A. fumigatus organisms. In healthy volunteers, fungal PCR was positive in 1.0% and 8.4% of eyes from Switzerland and Egypt, respectively. Fungal PCR remained negative in 10 cases of culture-proven bacterial keratitis, became positive in 4 cases of fungal keratitis, but missed 1 case of culture-proven A. fumigatus keratitis. Conclusions. FTA filter paper for specimen collection together with direct PCR is a promising method of detecting fungal keratitis. The analytical sensitivity is high without the need for a semi-nested or nested second PCR, the clinical specificity is 91.7% to 99.0%, and the method is rapid and inexpensive.

  4. Infrared camera - specially developed for professional building inspection - with dew point detection tracing out fungi formation; Infrarotkamera - speziell entwickelt fuer die professionelle Gebaeudeinspektion - mit Taupunktermittlungsfunktion zum schnellen Auffinden von Gefahrbereichen fuer Schimmelbildung

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    2004-07-01

    Besides the positive effect of energy saving the aspect of fungi formation has also to be respected. Fungi is not only responseable for health diseases but can also damage building materials. Examples are shown and how they can be detect by an infrared monitoring camera. (GL) [German] Die Waermeschutzverordnung und das daraus hervorgegangene Energieeinspargesetz haben weitreichende Folgen fuer Architekten, Bauingenieure, Instandhalter und Sanierer: Zeitgemaesse Gebaeude werden immer dichter, Luftzirkulation und damit der Feuchtigkeitsaustausch werden weitgehend unterbunden. Neben dem positiven Effekt der Energieersparnis ergibt sich dadurch leider oft auch ein Problem durch Schimmelbildung. Dabei ist zu bedenken, dass Schimmelpilz nicht nur gesundheitsgefaehrend ist, sondern oft auch die Bausubstanz signifikant schaedigen kann. (orig.)

  5. Differential Utilization of Carbon Substrates by Bacteria and Fungi in Tundra Soil

    DEFF Research Database (Denmark)

    Rinnan, Riikka; Bååth, Erland

    2009-01-01

    Little is known about the contribution of bacteria and fungi to decomposition of different carbon compounds in arctic soils, which are an important carbon store and possibly vulnerable to climate warming. Soil samples from a subarctic tundra heath were incubated with 13C-labeled glucose, acetic...... at concentrations low enough not to affect the total amount of PLFA. The label of glucose and acetic acid was rapidly incorporated into the PLFA in a pattern largely corresponding to the fatty acid concentration profile, while glycine and especially starch were mainly taken up by bacteria and not fungi, showing......, the allocation decreased over time, indicating use of the storage products, whereas for vanillin incorporation into fungal NLFA increased during the incubation. In addition to providing information on functioning of the microbial communities in an arctic soil, our study showed that the combination of PLFA...

  6. Identification of ochratoxin A producing fungi associated with fresh and dry liquorice.

    Directory of Open Access Journals (Sweden)

    Amanda Juan Chen

    Full Text Available The presence of fungi on liquorice could contaminate the crop and result in elevated levels of mycotoxin. In this study, the mycobiota associated with fresh and dry liquorice was investigated in 3 producing regions of China. Potential toxigenic fungi were tested for ochratoxin A (OTA and aflatoxin B1 (AFB1 production using liquid chromatography/mass spectrometry/mass spectrometry. Based on a polyphasic approach using morphological characters, β-tubulin and RNA polymerase II second largest subunit gene phylogeny, a total of 9 genera consisting of 22 fungal species were identified, including two new Penicillium species (Penicillium glycyrrhizacola sp. nov. and Penicillium xingjiangense sp. nov.. The similarity of fungal communities associated with fresh and dry liquorice was low. Nineteen species belonging to 8 genera were detected from fresh liquorice with populations affiliated with P. glycyrrhizacola, P. chrysogenum and Aspergillus insuetus comprising the majority (78.74%, 33.33% and 47.06% of total of the community from Gansu, Ningxia and Xinjiang samples, respectively. In contrast, ten species belonging to 4 genera were detected from dry liquorice with populations affiliated with P. chrysogenum, P. crustosum and Aspergillus terreus comprising the majority (64.00%, 52.38% and 90.91% of total of the community from Gansu, Ningxia and Xinjiang samples, respectively. Subsequent LC/MS/MS analysis indicated that 5 fungal species were able to synthesize OTA in vitro including P. chrysogenum, P. glycyrrhizacola, P. polonicum, Aspergillus ochraceus and A. westerdijkiae, the OTA concentration varied from 12.99 to 39.03 µg/kg. AFB1 was absent in all tested strains. These results demonstrate the presence of OTA producing fungi on fresh liquorice and suggest that these fungi could survive on dry liquorice after traditional sun drying. Penicillium chrysogenum derived from surrounding environments is likely to be a stable contributor to high OTA level in

  7. Rapid detection and quantification of haptophyte alkenones by Fourier transform infrared spectroscopy (FTIR)

    Czech Academy of Sciences Publication Activity Database

    Pelusi, A.; Hanawa, Y.; Araie, H.; Suzuki, I.; Giordano, Mario; Shiraiwa, I.

    2016-01-01

    Roč. 19, NOVEMBER 2016 (2016), s. 48-56 ISSN 2211-9264 Institutional support: RVO:61388971 Keywords : Rapid detection * haptophyte alkenones * Fourier spectroscopy Subject RIV: EE - Microbiology, Virology Impact factor: 3.994, year: 2016

  8. Development of selective media for the isolation of yeasts and filamentous fungi from the sputum of adult patients with cystic fibrosis (CF).

    Science.gov (United States)

    Nagano, Yuriko; Millar, B Cherie; Goldsmith, Colin E; Walker, James M; Elborn, J Stuart; Rendall, Jackie; Moore, John E

    2008-11-01

    Yeasts and filamentous fungi are beginning to emerge as significant microbial pathogens in patients with cystic fibrosis (CF), particularly in relation to allergic-type responses, as seen in patients with allergic bronchopulmonary aspergillosis (ABPA), Aspergillus bronchitis and in invasive fungal disease in lung transplant patients. Four fungal media were compared in this study, including Sabouraud Dextrose Agar (SDA) and Medium B, with and without the addition of selective antibiotics, where antibiotic-supplemented media were designated with (+). These media were compared for their ability to suppress contaminating, mainly Gram-ve pathogens, in CF sputa (Pseudomonas aeruginosa, Burkholderia cepacia complex [BCC] organisms) and to enhance the growth of fungi present in CF sputum. Medium B consisted of glucose (16.7 g/l), agar (20 g/l), yeast extract (30 g/l) and peptone (6.8 g/l) at pH 6.3 and both SDA(+) and Medium B(+) were supplemented with cotrimethoxazole, 128 mg/l; chloramphenicol, 50 mg/l; ceftazidime, 32 mg/l; colistin, 24 mg/l). Employment of SDA(+) or Medium B(+) allowed an increase in specificity in the detection of yeasts and moulds, by 42.8% and 39.3%, respectively, over SDA when used solely. SDA(+) had a greater ability than Medium B(+) to suppress bacterial growth from predominantly Gram-ve co-colonisers. This is a significant benefit when attempting to detect and isolate fungi from the sputum of CF patients, as it largely suppressed any bacterial growth, with the exception of the BCC organisms, thus allowing for an increased opportunity to detect target fungal organisms in sputum and represented a significant improvement over the commercial medium (SDA), which is currently used. Overall, both novel selective media were superior in their ability to suppress bacteria in comparison with the commercially available SDA medium, which is routinely employed in most clinical microbiology diagnostic laboratories presently. Alternatively, Medium B(+) had a

  9. Rapid and sensitive detection of ketamine in blood using novel fluorescence genosensor.

    Science.gov (United States)

    Ding, Yanjun; Li, Xingmei; Guo, Yadong; Yan, Jie; Ling, Jiang; Li, Weichen; Lan, Lingmei; Chang, Yunfeng; Cai, Jifeng; Zha, Lagabaiyla

    2017-12-01

    In recent years, drug abuse has been considered as a most challenging social problem that aroused public attention. Ketamine has increased in unregulated use as a 'recreational drug' in teenagers. However, there is no suitable and maneuverable detection method for ketamine in situ at the moment. Fluorescence sensor technique, with predominant recognition and simple operation, is a good potential application in drug detection. Here, we first reported a highly sensitive and selective fluorescence genosensor for rapid detection of ketamine based on DNA-templated silver nanoclusters (DNA-AgNCs) probes, in which the DNA sequence could specially recognize ketamine with high affinity. Parameters affecting detection efficiency were investigated and optimized. Under optimum conditions, the as-prepared genosensor can allow for the determination of ketamine in the concentration range of 0.0001-20 μg/mL with two linear equations: one is y = 2.84x-7.139 (R 2 = 0.987) for 0.0001-0.1 μg/mL, and the other is y = 1.87x-0.091 (R 2 = 0.962) for 0.1-20 μg/mL, and the estimated detection limit of ketamine is 0.06 ng/mL. Moreover, the feasibility of this proposed method was also demonstrated by analyzing forensic blood samples. Compared with official gas chromatography/mass spectrometry (GC/MS), this fluorescence genosensor is simple, rapid, and accurate for quantitative determination of ketamine in blood for pharmaceutical and forensic analysis. Overall, it is the first report on a fluorescence genosensor for detecting ketamine directly in blood. This research may provide a new insight for the analyst to band fluorescence genosensor technology together with drug monitoring in the battle against drug abuse and forensic examination. Graphical abstract High selectively detection of ketamine using a novel fluorescence genosensor based on DNA-AgNCs probe.

  10. Higher marine fungi from mangroves (Manglicolous fungi)

    Digital Repository Service at National Institute of Oceanography (India)

    ChinnaRaj, S.

    of higher marine fungi which included 23 Ascomycetes, 2 Basidiomycetes and 17 Deuteromycetes (Kohlmeyer and Kohlmeyer, 1979). Hyde (1990a) listed 120 species from 29 mangroves from all over the World this includes 87 Ascomycetes, 2 Basidiomycetes and 31...

  11. Development of an immunochromatographic assay for the rapid detection of bromoxynil in water

    International Nuclear Information System (INIS)

    Zhu Jiang; Chen Wenchao; Lu Yitong; Cheng Guohua

    2008-01-01

    A rapid immunochromatographic one-step strip test was developed to specifically determine bromoxynil in surface and drinking water by competitive inhibition with the nano colloidal gold-conjugated monoclonal antibody (mAb). Bromoxynil standard samples of 0.01-10 mg L -1 in water were tested by this method and the visual limit was 0.06 mg L -1 . The assay only required 5 min and one-step by dispensing a drop of sample solution onto a strip. Parallel analysis of water samples with bromoxynil showed comparable results from one-step strip test and ELISA. Therefore, the one-step strip test is very useful as a screening method for qualitative detection of bromoxynil in water. - One-step strip test is a rapid method for qualitative detection of bromoxynil residues in water

  12. The pathogenic fungi in mushroom cultivation of Agaricus bisporus (Lange.) Imbach.

    OpenAIRE

    Agata Tekiela

    2012-01-01

    The research was conducted in a mushroom growing facility located near Rzeszów, consisting of three production cycles. The number and composition of microorganisms which accompany the mushroom cultivation depended on the healthiness of: the compost, casing and spawn of Agaricus bisporus. The presence of pathogenic fungi in the cultivation halls at the beginning of the production cycle is a serious threat to the cultivation of common mushroom because their rapid development shortens the span o...

  13. Rapid multiplex detection of 10 foodborne pathogens with an up-converting phosphor technology-based 10-channel lateral flow assay

    Science.gov (United States)

    Zhao, Yong; Wang, Haoran; Zhang, Pingping; Sun, Chongyun; Wang, Xiaochen; Wang, Xinrui; Yang, Ruifu; Wang, Chengbin; Zhou, Lei

    2016-01-01

    The rapid high-throughput detection of foodborne pathogens is essential in controlling food safety. In this study, a 10-channel up-converting phosphor technology-based lateral flow (TC-UPT-LF) assay was established for the rapid and simultaneous detection of 10 epidemic foodborne pathogens. Ten different single-target UPT-LF strips were developed and integrated into one TC-UPT-LF disc with optimization. Without enrichment the TC-UPT-LF assay had a detection sensitivity of 104 CFU mL−1 or 105 CFU mL−1 for each pathogen, and after sample enrichment it was 10 CFU/0.6 mg. The assay also showed good linearity, allowing quantitative detection, with a linear fitting coefficient of determination (R2) of 0.916–0.998. The 10 detection channels did not cross-react, so multiple targets could be specifically detected. When 279 real food samples were tested, the assay was highly consistent (100%) with culture-based methods. The results for 110 food samples artificially contaminated with single or multiple targets showed a high detection rate (≥80%) for most target bacteria. Overall, the TC-UPT-LF assay allows the rapid, quantitative, and simultaneous detection of 10 kinds of foodborne pathogens within 20 min, and is especially suitable for the rapid detection and surveillance of foodborne pathogens in food and water. PMID:26884128

  14. Underground resource allocation between individual networks of mycorrhizal fungi

    DEFF Research Database (Denmark)

    Mikkelsen, Bolette Lind; Rosendahl, Søren; Jakobsen, Iver

    2008-01-01

    * Fusions between individual mycelia of arbuscular mycorrhizal (AM) fungi have been observed in two-dimensional systems but never in soil systems. Here, phosphorus ((32)P) labelling was used to demonstrate nutrient transfer between individual mycelia and to investigate the possible role...... of G. mosseae overlapped. The transfer probably occurred via anastomoses between the mycelia as no transfer of (32)P was detected between the mycelia of different fungi at the second harvest. * The indicated ability of AM fungal mycelia to anastomose in soil has implications for the formation of large...... of anastomosis. * Trifolium subterraneum colonized by Glomus mosseae were grown in root-retaining mesh bags, which were placed 20 cm apart. The mycelium of one plant, the donor, had access to (32)P-labelled soil placed adjacent to the mesh bag. Transfer of (32)P from the donor mycelium to the receiver plant...

  15. A Portable Impedance Immunosensing System for Rapid Detection of Salmonella Typhimurium.

    Science.gov (United States)

    Wen, Tao; Wang, Ronghui; Sotero, America; Li, Yanbin

    2017-08-28

    Salmonella Typhimurium is one of the most dangerous foodborne pathogens and poses a significant threat to human health. The objective of this study was to develop a portable impedance immunosensing system for rapid and sensitive detection of S . Typhimurium in poultry. The developed portable impedance immunosensing system consisted of a gold interdigitated array microelectrode (IDAM), a signal acquisitive interface and a laptop computer with LabVIEW software. The IDAM was first functionalized with 16-Mercaptohexadecanoic acid, and streptavidin was immobilized onto the electrode surface through covalent bonding. Then, biotin-labelled S . Typhimurium -antibody was immobilized onto the IDAM surface. Samples were dropped on the surface of the IDAM and the S . Typhimurium cells in the samples were captured by the antibody on the IDAM. This resulted in impedance changes that were measured and displayed with the LabVIEW software. An equivalent circuit of the immunosensor demonstrated that the largest change in impedance was due to the electron-transfer resistance. The equivalent circuit showed an increase of 35% for the electron-transfer resistance value compared to the negative control. The calibration result indicated that the portable impedance immunosensing system could be used to measure the standard impedance elements, and it had a maximum error of measurement of approximately 13%. For pure culture detection, the system had a linear relationship between the impedance change and the logarithmic value of S . Typhimurium cells ranging from 76 to 7.6 × 10⁶ CFU (colony-forming unit) (50 μL) -1 . The immunosensor also had a correlation coefficient of 0.98, and a high specificity for detection of S . Typhimurium cells with a limit of detection (LOD) of 10² CFU (50 μL) -1 . The detection time from the moment a sample was introduced to the display of the results was 1 h. To conclude, the portable impedance immunosensing system for detection of S . Typhimurium achieved

  16. A Portable Impedance Immunosensing System for Rapid Detection of Salmonella Typhimurium

    Directory of Open Access Journals (Sweden)

    Tao Wen

    2017-08-01

    Full Text Available Salmonella Typhimurium is one of the most dangerous foodborne pathogens and poses a significant threat to human health. The objective of this study was to develop a portable impedance immunosensing system for rapid and sensitive detection of S. Typhimurium in poultry. The developed portable impedance immunosensing system consisted of a gold interdigitated array microelectrode (IDAM, a signal acquisitive interface and a laptop computer with LabVIEW software. The IDAM was first functionalized with 16-Mercaptohexadecanoic acid, and streptavidin was immobilized onto the electrode surface through covalent bonding. Then, biotin-labelled S. Typhimurium-antibody was immobilized onto the IDAM surface. Samples were dropped on the surface of the IDAM and the S. Typhimurium cells in the samples were captured by the antibody on the IDAM. This resulted in impedance changes that were measured and displayed with the LabVIEW software. An equivalent circuit of the immunosensor demonstrated that the largest change in impedance was due to the electron-transfer resistance. The equivalent circuit showed an increase of 35% for the electron-transfer resistance value compared to the negative control. The calibration result indicated that the portable impedance immunosensing system could be used to measure the standard impedance elements, and it had a maximum error of measurement of approximately 13%. For pure culture detection, the system had a linear relationship between the impedance change and the logarithmic value of S. Typhimurium cells ranging from 76 to 7.6 × 106 CFU (colony-forming unit (50 μL−1. The immunosensor also had a correlation coefficient of 0.98, and a high specificity for detection of S. Typhimurium cells with a limit of detection (LOD of 102 CFU (50 μL−1. The detection time from the moment a sample was introduced to the display of the results was 1 h. To conclude, the portable impedance immunosensing system for detection of S. Typhimurium

  17. Simultaneous determination of four aflatoxins and ochratoxin A in ginger after inoculation with fungi by ultra-fast liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Yang, Ying; Wen, Jing; Kong, Weijun; Liu, Qiutao; Luo, Hongli; Wang, Jian; Yang, Meihua

    2016-09-01

    Aflatoxins (AFs) and ochratoxin A (OTA) have been detected frequently in food, agricultural products and traditional Chinese medicines, and their presence poses serious health and economic problems worldwide. Ginger can easily be polluted with mycotoxins. In this study, ginger samples were cultivated for 15 days after inoculation with fungi and were prepared based on ultrasound-assisted solid-liquid extraction using methanol/water followed by immunoaffinity column clean-up and analysed by ultra-fast liquid chromatography-tandem mass spectrometry (UFLC-MS/MS) for AFs and OTA. The limits of detection and quantification of AFs and OTA were 0.04-0.30 µg mL(-1) and 0.125-1.0 µg mL(-1) , respectively. The recoveries were 82.0-100.2%. After 15 days' cultivation, no macroscopic mildew was found in ginger. But, the content of AFB1 expressed an increasing trend in ginger, peel [less than the limit of quantification (LOQ)] to the innermost layer (51.86 µ mL(-1) ), AFB2 was only detected in the innermost layer at the level of 0.87 µ mL(-1) . A small amount (fungi were inoculated on the surface of ginger. The developed method was successfully applied to analyse five mycotoxins, and has many advantages including rapid determination and high sensitivity. Meanwhile, in practice, more attention should be paid to the safety and quality of ginger. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  18. Enumeration of fungi in barley

    CSIR Research Space (South Africa)

    Rabie, CJ

    1997-04-01

    Full Text Available Estimation of fungal contamination of barley grain is important as certain fungi can proliferate during the malting process. The following factors which may affect the enumeration of fungi were evaluated: dilution versus direct plating, pre...

  19. A parylene-based dual channel microelectrophoresis system for rapid mutation detection via heteroduplex analysis

    NARCIS (Netherlands)

    Sukas, S.; Erson, Ayse Elif; Sert, Cuneyt; Kulah, Haluk

    2008-01-01

    A new dual channel micro-electrophoresis system for rapid mutation detection based on heteroduplex analysis was designed and implemented. Mutation detection was successfully achieved in a total separation length of 250 μm in less than 3 min for a 590 bp DNA sample harboring a 3 bp mutation causing

  20. Rapid detection of Brucella spp. using loop-mediated isothermal amplification (LAMP).

    Science.gov (United States)

    Chen, Shouyi; Li, Xunde; Li, Juntao; Atwill, Edward R

    2013-01-01

    Brucella spp. are facultative intracellular bacteria that cause zoonotic disease of brucellosis worldwide. Livestock that are most vulnerable to brucellosis include cattle, goats, and pigs. Brucella spp. cause serious health problems to humans and animals and economic losses to the livestock industry. Traditional methods for detection of Brucella spp. take 48-72 h (Kumar et al., J Commun Dis 29:131-137, 1997; Barrouin-Melo et al., Res Vet Sci 83:340-346, 2007) that do not meet the food industry's need of rapid detection. Therefore, there is an urgent need of fast, specific, sensitive, and inexpensive method for diagnosing of Brucella spp. Loop-mediated isothermal amplification (LAMP) is a method to amplify nucleic acid at constant temperatures. Amplification can be detected by visual detection, fluorescent stain, turbidity, and electrophoresis. We targeted at the Brucella-specific gene omp25 and designed LAMP primers for detection of Brucella spp. Amplification of DNA with Bst DNA polymerase can be completed at 65 °C in 60 min. Amplified products can be detected by SYBR Green I stain and 2.0% agarose gel electrophoresis. The LAMP method is feasible for detection of Brucella spp. from blood and milk samples.

  1. Rapid detection and identification of Bacillus anthracis in food using pyrosequencing technology.

    Science.gov (United States)

    Amoako, Kingsley K; Janzen, Timothy W; Shields, Michael J; Hahn, Kristen R; Thomas, Matthew C; Goji, Noriko

    2013-08-01

    The development of advanced methodologies for the detection of Bacillus anthracis has been evolving rapidly since the release of the anthrax spores in the mail in 2001. Recent advances in detection and identification techniques could prove to be an essential component in the defense against biological attacks. Sequence based such as pyrosequencing, which has the capability to determine short DNA stretches in real-time using biotinylated PCR amplicons, has potential biodefense applications. Using markers from the virulence plasmids (pXO1 and pXO2) and chromosomal regions, we have demonstrated the power of this technology in the rapid, specific and sensitive detection of B. anthracis spores in food matrices including milk, juice, bottled water, and processed meat. The combined use of immunomagnetic separation and pyrosequencing showed positive detection when liquid foods (bottled water, milk, juice), and processed meat were experimentally inoculated with 6CFU/mL and 6CFU/g, respectively, without an enrichment step. Pyrosequencing is completed in about 60min (following PCR amplification) and yields accurate and reliable results with an added layer of confidence. The entire assay (from sample preparation to sequencing information) can be completed in about 7.5h. A typical run on food samples yielded 67-80bp reads with 94-100% identity to the expected sequence. This sequence based approach is a novel application for the detection of anthrax spores in food with potential application in foodborne bioterrorism response and biodefense involving the use of anthrax spores. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

  2. Development of Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid Detection of Cannabis sativa.

    Science.gov (United States)

    Kitamura, Masashi; Aragane, Masako; Nakamura, Kou; Watanabe, Kazuhito; Sasaki, Yohei

    2016-07-01

    In many parts of the world, the possession and cultivation of Cannabis sativa L. are restricted by law. As chemical or morphological analyses cannot identify the plant in some cases, a simple yet accurate DNA-based method for identifying C. sativa is desired. We have developed a loop-mediated isothermal amplification (LAMP) assay for the rapid identification of C. sativa. By optimizing the conditions for the LAMP reaction that targets a highly conserved region of tetrahydrocannabinolic acid (THCA) synthase gene, C. sativa was identified within 50 min at 60-66°C. The detection limit was the same as or higher than that of conventional PCR. The LAMP assay detected all 21 specimens of C. sativa, showing high specificity. Using a simple protocol, the identification of C. sativa could be accomplished within 90 min from sample treatment to detection without use of special equipment. A rapid, sensitive, highly specific, and convenient method for detecting and identifying C. sativa has been developed and is applicable to forensic investigations and industrial quality control.

  3. A rapid and simple method of detection of Blepharisma japonicum using PCR and immobilisation on FTA paper

    Science.gov (United States)

    Hide, Geoff; Hughes, Jacqueline M; McNuff, Robert

    2003-01-01

    Background The rapid expansion in the availability of genome and DNA sequence information has opened up new possibilities for the development of methods for detecting free-living protozoa in environmental samples. The protozoan Blepharisma japonicum was used to investigate a rapid and simple detection system based on polymerase chain reaction amplification (PCR) from organisms immobilised on FTA paper. Results Using primers designed from the α-tubulin genes of Blepharisma, specific and sensitive detection to the equivalent of a single Blepharisma cell could be achieved. Similar detection levels were found using water samples, containing Blepharisma, which were dried onto Whatman FTA paper. Conclusion This system has potential as a sensitive convenient detection system for Blepharisma and could be applied to other protozoan organisms. PMID:14516472

  4. Molecular and phenotypic characterization of anamorphic fungi

    OpenAIRE

    Madrid Lorca, Hugo

    2011-01-01

    Anamorphic fungi (those reproducing asexually) are a big part of kingdom Fungi. Most of them occur as saprobes in nature, but numerous species are pathogenic to plants and animals including man. With the aim of contributing to the knowledge of the diversity and distribution of anamorphic fungi, we performed a phenotypic and molecular characterization of environmental and clinical isolates of these fungi. Based on a polyphasic taxonomy approach which included morphology, physiology and DNA seq...

  5. Rapid and label-free bioanalytical method of alpha fetoprotein detection using LSPR chip

    Science.gov (United States)

    Kim, Dongjoo; Kim, Jinwoon; Kwak, Cheol Hwan; Heo, Nam Su; Oh, Seo Yeong; Lee, Hoomin; Lee, Go-Woon; Vilian, A. T. Ezhil; Han, Young-Kyu; Kim, Woo-Sik; Kim, Gi-bum; Kwon, Soonjo; Huh, Yun Suk

    2017-07-01

    Alpha fetoprotein (AFP) is a cancer marker, particularly for hepatocellular carcinoma. Normal levels of AFP are less than 20 ng/mL; however, its levels can reach more than 400 ng/mL in patients with HCC. Enzyme linked immunosorbent assay (ELISA) and radioimmunoassay (RIA) have been employed for clinical diagnosis of AFP; however, these methods are time consuming and labor intensive. In this study, we developed a localized surface plasmon resonance (LSPR) based biosensor for simple and rapid detection of AFP. This biosensor consists of a UV-Vis spectrometer, a cuvette cell, and a biosensor chip nanopatterned with gold nanoparticles (AuNPs). In our LSPR biosensor, binding of AFP to the surface of the sensor chip led to an increasing magnitude of the LSPR signals, which was measured by an ultraviolet-visible (UV-Vis) spectrometer. Our LSPR biosensor showed sufficient detectability of AFP at concentrations of 1 ng/mL to 1 μg/mL. Moreover, the overall procedure for detection of AFP was completed within 20 min. This biosensor could also be utilized for a point of care test (POCT) by employing a portable UV-Vis spectrometer. Owing to the simplicity and rapidity of the detection process, our LSPR biosensor is expected to replace traditional diagnostic methods for the early detection of diseases.

  6. Some mycogenous fungi from Poland

    Directory of Open Access Journals (Sweden)

    Andrzej Chlebicki

    2014-08-01

    Full Text Available In the present paper the results of earlier studies on mycogenous fungi which were gathered occasionally are summarized. Fifieen specres. previously Pyrenomycetes s.l., have been found growing on other fungi Immothia hypoxylon and Lophiostoma polyporicola are new species to the Polish mycoflora. Sphaeronaemella Kulczyńskiana described by K. R o u p p e r t (1912 is considered to be Eleuteromyces subultus. Relatively high number of fungi inhabiting stromata of Diatrypella favacea is probably connected with its early colonization of the Polish area.

  7. Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification.

    Directory of Open Access Journals (Sweden)

    David S Boyle

    Full Text Available Improved access to effective tests for diagnosing tuberculosis (TB has been designated a public health priority by the World Health Organisation. In high burden TB countries nucleic acid based TB tests have been restricted to centralised laboratories and specialised research settings. Requirements such as a constant electrical supply, air conditioning and skilled, computer literate operators prevent implementation of such tests in many settings. Isothermal DNA amplification technologies permit the use of simpler, less energy intensive detection platforms more suited to low resource settings that allow the accurate diagnosis of a disease within a short timeframe. Recombinase Polymerase Amplification (RPA is a rapid, low temperature isothermal DNA amplification reaction. We report here RPA-based detection of Mycobacterium tuberculosis complex (MTC DNA in <20 minutes at 39 °C. Assays for two MTC specific targets were investigated, IS6110 and IS1081. When testing purified MTC genomic DNA, limits of detection of 6.25 fg (IS6110 and 20 fg (IS1081were consistently achieved. When testing a convenience sample of pulmonary specimens from suspected TB patients, RPA demonstrated superior accuracy to indirect fluorescence microscopy. Compared to culture, sensitivities for the IS1081 RPA and microscopy were 91.4% (95%CI: 85, 97.9 and 86.1% (95%CI: 78.1, 94.1 respectively (n = 71. Specificities were 100% and 88.6% (95% CI: 80.8, 96.1 respectively. For the IS6110 RPA and microscopy sensitivities of 87.5% (95%CI: 81.7, 93.2 and 70.8% (95%CI: 62.9, 78.7 were obtained (n = 90. Specificities were 95.4 (95% CI: 92.3,98.1 and 88% (95% CI: 83.6, 92.4 respectively. The superior specificity of RPA for detecting tuberculosis was due to the reduced ability of fluorescence microscopy to distinguish Mtb complex from other acid fast bacteria. The rapid nature of the RPA assay and its low energy requirement compared to other amplification technologies suggest RPA-based TB

  8. [Research on rapid and quantitative detection method for organophosphorus pesticide residue].

    Science.gov (United States)

    Sun, Yuan-Xin; Chen, Bing-Tai; Yi, Sen; Sun, Ming

    2014-05-01

    The methods of physical-chemical inspection is adopted in the traditional pesticide residue detection, which require a lot of pretreatment processes, are time-consuming and complicated. In the present study, the authors take chlorpyrifos applied widely in the present agricultural field as the research object and propose a rapid and quantitative detection method for organophosphorus pesticide residues. At first, according to the chemical characteristics of chlorpyrifos and comprehensive chromogenic effect of several colorimetric reagents and secondary pollution, the pretreatment of the scheme of chromogenic reaction of chlorpyrifos with resorcin in a weak alkaline environment was determined. Secondly, by analyzing Uv-Vis spectrum data of chlorpyrifos samples whose content were between 0. 5 and 400 mg kg-1, it was confirmed that the characteristic information after the color reaction mainly was concentrated among 360 approximately 400 nm. Thirdly, the full spectrum forecasting model was established based on the partial least squares, whose correlation coefficient of calibration was 0. 999 6, correlation coefficient of prediction reached 0. 995 6, standard deviation of calibration (RMSEC) was 2. 814 7 mg kg-1, and standard deviation of verification (RMSEP) was 8. 012 4 mg kg-1. Fourthly, the wavelengths whose center wavelength is 400 nm was extracted as characteristic region to build a forecasting model, whose correlation coefficient of calibration was 0. 999 6, correlation coefficient of prediction reached 0. 999 3, standard deviation of calibration (RMSEC) was 2. 566 7 mg kg-1 , standard deviation of verification (RMSEP) was 4. 886 6 mg kg-1, respectively. At last, by analyzing the near infrared spectrum data of chlorpyrifos samples with contents between 0. 5 and 16 mg kg-1, the authors found that although the characteristics of the chromogenic functional group are not obvious, the change of absorption peaks of resorcin itself in the neighborhood of 5 200 cm

  9. Development and Evaluation of a Rapid Antigen Detection and Serotyping Lateral Flow Antigen Detection System for Foot-and-Mouth Disease Virus.

    Directory of Open Access Journals (Sweden)

    Kazuki Morioka

    Full Text Available We developed a lateral flow strip using monoclonal antibodies (MAbs which allows for rapid antigen detection and serotyping of foot-and-mouth disease virus (FMDV. This FMDV serotyping strip was able to detect all 7 serotypes and distinguish serotypes O, A, C and Asia1. Its sensitivities ranged from 10(3 to 10(4 of a 50% tissue culture infectious dose of each FMDV stain; this is equal to those of the commercial product Svanodip (Boehringer Ingelheim Svanova, Uppsala, Sweden, which can detect all seven serotypes of FMDV, but does not distinguish them. Our evaluation of the FMDV serotyping strip using a total of 118 clinical samples (vesicular fluids, vesicular epithelial emulsions and oral and/or nasal swabs showed highly sensitive antigen detection and accuracy in serotyping in accordance with ELISA or RT-PCR. To the best of our knowledge, this is the first report on any FMDV serotyping strip that provides both rapid antigen detection and serotyping of FMDV at the same time on one strip without extra devices. This method will be useful in both FMD-free countries and FMD-infected countries, especially where laboratory diagnosis cannot be carried out.

  10. Impact of the rapid antigen detection test in diagnosis and treatment of acute pharyngotonsillitis in a pediatric emergency room.

    Science.gov (United States)

    Cardoso, Débora Morais; Gilio, Alfredo Elias; Hsin, Shieh Huei; Machado, Beatriz Marcondes; de Paulis, Milena; Lotufo, João Paulo B; Martinez, Marina Baquerizo; Grisi, Sandra Josefina E

    2013-01-01

    To evaluate the impact of the routine use of rapid antigen detection test in the diagnosis and treatment of acute pharyngotonsillitis in children. This is a prospective and observational study, with a protocol compliance design established at the Emergency Unit of the University Hospital of Universidade de São Paulo for the care of children and adolescents diagnosed with acute pharyngitis. 650 children and adolescents were enrolled. Based on clinical findings, antibiotics would be prescribed for 389 patients (59.8%); using the rapid antigen detection test, they were prescribed for 286 patients (44.0%). Among the 261 children who would not have received antibiotics based on the clinical evaluation, 111 (42.5%) had positive rapid antigen detection test. The diagnosis based only on clinical evaluation showed 61.1% sensitivity, 47.7% specificity, 44.9% positive predictive value, and 57.5% negative predictive value. The clinical diagnosis of streptococcal pharyngotonsillitis had low sensitivity and specificity. The routine use of rapid antigen detection test led to the reduction of antibiotic use and the identification of a risk group for complications of streptococcal infection, since 42.5% positive rapid antigen detection test patients would not have received antibiotics based only on clinical diagnosis.

  11. Development of Rapid Detection and Genetic Characterization of Salmonella in Poultry Breeder Feeds

    Science.gov (United States)

    Jarquin, Robin; Hanning, Irene; Ahn, Soohyoun; Ricke, Steven C.

    2009-01-01

    Salmonella is a leading cause of foodborne illness in the United States, with poultry and poultry products being a primary source of infection to humans. Poultry may carry some Salmonella serovars without any signs or symptoms of disease and without causing any adverse effects to the health of the bird. Salmonella may be introduced to a flock by multiple environmental sources, but poultry feed is suspected to be a leading source. Detecting Salmonella in feed can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. Numerous detection methodologies have been examined over the years for quantifying Salmonella in feeds and many have proven to be effective for Salmonella isolation and detection in a variety of feeds. However, given the potential need for increased detection sensitivity, molecular detection technologies may the best candidate for developing rapid sensitive methods for identifying small numbers of Salmonella in the background of large volumes of feed. Several studies have been done using polymerase chain reaction (PCR) assays and commercial kits to detect Salmonella spp. in a wide variety of feed sources. In addition, DNA array technology has recently been utilized to track the dissemination of a specific Salmonella serotype in feed mills. This review will discuss the processing of feeds and potential points in the process that may introduce Salmonella contamination to the feed. Detection methods currently used and the need for advances in these methods also will be discussed. Finally, implementation of rapid detection for optimizing control methods to prevent and remove any Salmonella contamination of feeds will be considered. PMID:22346699

  12. Development of Rapid Detection and Genetic Characterization of Salmonella in Poultry Breeder Feeds

    Directory of Open Access Journals (Sweden)

    Steven C. Ricke

    2009-07-01

    Full Text Available Salmonella is a leading cause of foodborne illness in the United States, with poultry and poultry products being a primary source of infection to humans. Poultry may carry some Salmonella serovars without any signs or symptoms of disease and without causing any adverse effects to the health of the bird. Salmonella may be introduced to a flock by multiple environmental sources, but poultry feed is suspected to be a leading source. Detecting Salmonella in feed can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. Numerous detection methodologies have been examined over the years for quantifying Salmonella in feeds and many have proven to be effective for Salmonella isolation and detection in a variety of feeds. However, given the potential need for increased detection sensitivity, molecular detection technologies may the best candidate for developing rapid sensitive methods for identifying small numbers of Salmonella in the background of large volumes of feed. Several studies have been done using polymerase chain reaction (PCR assays and commercial kits to detect Salmonella spp. in a wide variety of feed sources. In addition, DNA array technology has recently been utilized to track the dissemination of a specific Salmonella serotype in feed mills. This review will discuss the processing of feeds and potential points in the process that may introduce Salmonella contamination to the feed. Detection methods currently used and the need for advances in these methods also will be discussed. Finally, implementation of rapid detection for optimizing control methods to prevent and remove any Salmonella contamination of feeds will be considered.

  13. Rapid, portable detection of endocrine disrupting chemicals through ligand-nuclear hormone receptor interactions.

    Science.gov (United States)

    Hunt, J Porter; Schinn, Song-Min; Jones, Matthew D; Bundy, Bradley C

    2017-12-04

    Endocrine disrupting chemicals (EDC) are structurally diverse compounds that can interact with nuclear hormone receptors, posing significant risk to human and ecological health. Unfortunately, many conventional biosensors have been too structure-specific, labor-intensive or laboratory-oriented to detect broad ranges of EDC effectively. Recently, several technological advances are providing more rapid, portable, and affordable detection of endocrine-disrupting activity through ligand-nuclear hormone receptor interactions. Here, we overview these recent advances applied to EDC biosensors - including cell lyophilization, cell immobilization, cell-free systems, smartphone-based signal detection, and improved competitive binding assays.

  14. Detecting and Remembering Simultaneous Pictures in a Rapid Serial Visual Presentation

    Science.gov (United States)

    Potter, Mary C.; Fox, Laura F.

    2009-01-01

    Viewers can easily spot a target picture in a rapid serial visual presentation (RSVP), but can they do so if more than 1 picture is presented simultaneously? Up to 4 pictures were presented on each RSVP frame, for 240 to 720 ms/frame. In a detection task, the target was verbally specified before each trial (e.g., "man with violin"); in a…

  15. Application of a rapid screening method to detect irradiated meat in Brazil

    International Nuclear Information System (INIS)

    Villavicencio, A.L.C.H.; Mancini-Filho, J.; Delincee, H.

    2000-01-01

    Based on the enormous potential for food irradiation in Brazil, and to ensure free consumer choice, there is a need to find a convenient and rapid method for detection of irradiated food. Since treatment with ionising radiation causes DNA fragmentation, the analysis of DNA damage might be promising. In this paper, the DNA Comet Assay was used to identify exotic meat (boar, jacare and capybara), irradiated with 60 Co gamma rays. The applied radiation doses were 0, 1.5, 3.0 and 4.5 kGy. Analysis of the DNA migration enabled a rapid identification of the radiation treatment

  16. In vitro susceptibility of filamentous fungi to copper nanoparticles assessed by rapid XTT colorimetry and agar dilution method.

    Science.gov (United States)

    Ghasemian, E; Naghoni, A; Tabaraie, B; Tabaraie, T

    2012-12-01

    Metal nanoparticles and their uses in various aspects have recently drawn a great deal of attention. One of the major applications is that it can be used as an antimicrobial agent. They can be considered in approaches targeted to decrease the harms caused by microorganisms, specifically fungi, threatening the medical and industrial areas. The aim of this study was to investigate the antifungal activity of synthesized copper nanoparticles (CuNPs) against four filamentous fungi including Alternaria alternata, Aspergillus flavus, Fusarium solani, and Penicillium chrysogenum. Zerovalent copper nanoparticles of mean size 8nm were synthesized by inert gas condensation (IGC) method. The antifungal activity of these synthesized copper nanoparticles was measured against selected fungi by using two different techniques including agar dilution method and XTT reduction assay. The minimal inhibitory concentrations (MICs) for copper nanoparticles by agar dilution method were less or equal to 40mg/L for P. chrysogenum, less or equal to 60mg/L for A. alternata, less or equal to 60mg/L for F. solani, and less or equal to 80mg/L for A. flavus. And also MICs obtained by XTT reduction assay ranged from 40 to 80mg/L. Our data demonstrated that the copper nanoparticles inhibited fungal growth, but the fungal sensitivity to copper nanoparticles varies depending on the fungal species. Therefore, it is advisable that the minimal inhibitory concentrations (MICs) be examined before using these compounds. It is hoped that, in future, copper nanoparticles could replace some antifungal agents, making them applicable to many different medical devices and antimicrobial control system. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  17. Airstream Fractionation of Vesicular-Arbuscular Mycorrhizal Fungi: Concentration and Enumeration of Propagules

    OpenAIRE

    Tommerup, Inez C.

    1982-01-01

    Spores and fragments of vesicular-arbuscular mycorrhizal fungi in dry soils were concentrated up to 100-fold when the soils were partitioned by fluidization and elutriation with a series of upward airstreams at progressively increasing velocities. The propagules were transported with the finer soil particles according to their equivalent spherical diameters. The system was used to predict the transport of propagules by wind. Concentrated propagules were rapidly separated from the soil particl...

  18. A Rapid, Onsite, Ultrasensitive Melamine Quantitation Method for Protein Beverages Using Time-Resolved Fluorescence Detection Paper.

    Science.gov (United States)

    Li, Guanghua; Wang, Du; Zhou, Aijun; Sun, Yimin; Zhang, Qi; Poapolathep, Amnart; Zhang, Li; Fan, Zhiyong; Zhang, Zhaowei; Li, Peiwu

    2018-05-02

    To ensure protein beverage safety and prevent illegal melamine use to artificially increase protein content, a rapid, onsite, ultrasensitive detection method for melamine must be developed because melamine is detrimental to human health and life. Herein, an ultrasensitive time-resolved fluorescence detection paper (TFDP) was developed to detect melamine in protein beverages within 15 min using a one-step sample preparation. The lower limits of detection were 0.89, 0.94, and 1.05 ng/mL, and the linear ranges were 2.67-150, 2.82-150, and 3.15-150 ng/mL (R2>0.982) for peanut, walnut, and coconut beverages, respectively. The recovery rates were 85.86-110.60% with a coefficient of variation beverage samples, the TFDP and ultra-performance liquid chromatography-tandem mass spectrometer (UPLC-MS/MS) results were consistent. This method is a promising alternative for rapid, onsite detection of melamine in beverages.

  19. Identification of Contaminated Cells with Viruses, Bacteria, or Fungi by Fourier Transform Infrared Microspectroscopy

    Directory of Open Access Journals (Sweden)

    V. Erukhimovitch

    2013-01-01

    Full Text Available Fourier transform infrared microspectroscopy (FTIR-M can detect small molecular changes in cells and therefore was previously applied for the identification of different biological samples. In the present study, FTIR spectroscopy was used for the identification and discrimination of Vero cells infected with herpes viruses or contaminated with bacteria or fungi in cell culture. Vero cells in culture were infected herpes simplex virus type 1 (HSV-1 or contaminated with E. coli bacteria or Candida albicans fungi and analyzed by FTIR microscopy at 24 h postinfection/contamination. Specific different spectral changes were observed according to the infecting or contaminating agent. For instance, both pure fungi and cell culture contaminated with this fungi showed specific peaks at 1030 cm−1 and at 1373 cm−1 regions, while pure E. coli and cell culture contaminated with this bacteria showed a specific and unique peak at 1657 cm−1. These results support the potential of developing FTIR microspectroscopy as a simple, reagent free method for identification and discrimination between different tissue infection or contamination with various pathogens.

  20. DNA quantification of basidiomycetous fungi during storage of logging residues

    Directory of Open Access Journals (Sweden)

    Isabella Børja

    2015-04-01

    Full Text Available The demand for bioenergy caused an increased use of logging residues, branches and treetops that were previously left on the ground after harvesting. Residues are stored outdoors in piles and it is unclear to what extent fungi transform this material. Our objective was to quantify the amount of wood degrading fungi during storage using quantitative real-time PCR (qPCR to detect basidiomycetous DNA in logging residues, a novel approach in this field. We found that the qPCR method was accurate in quantifying the fungal DNA during storage. As the moisture content of the piled logging residues decreased during the storage period, the fungal DNA content also decreased. Scots pine residues contained more fungal DNA than residues from Norway spruce. Loose piles had generally more fungal DNA than bundled ones.

  1. Fungi treated with small chemicals exhibit increased antimicrobial activity against facultative bacterial and yeast pathogens.

    Science.gov (United States)

    Zutz, Christoph; Bandian, Dragana; Neumayer, Bernhard; Speringer, Franz; Gorfer, Markus; Wagner, Martin; Strauss, Joseph; Rychli, Kathrin

    2014-01-01

    For decades, fungi have been the main source for the discovery of novel antimicrobial drugs. Recent sequencing efforts revealed a still high number of so far unknown "cryptic" secondary metabolites. The production of these metabolites is presumably epigenetically silenced under standard laboratory conditions. In this study, we investigated the effect of six small mass chemicals, of which some are known to act as epigenetic modulators, on the production of antimicrobial compounds in 54 spore forming fungi. The antimicrobial effect of fungal samples was tested against clinically facultative pathogens and multiresistant clinical isolates. In total, 30 samples of treated fungi belonging to six different genera reduced significantly growth of different test organisms compared to the untreated fungal sample (growth log reduction 0.3-4.3). For instance, the pellet of Penicillium restrictum grown in the presence of butyrate revealed significant higher antimicrobial activity against Staphylococcus (S.) aureus and multiresistant S. aureus strains and displayed no cytotoxicity against human cells, thus making it an ideal candidate for antimicrobial compound discovery. Our study shows that every presumable fungus, even well described fungi, has the potential to produce novel antimicrobial compounds and that our approach is capable of rapidly filling the pipeline for yet undiscovered antimicrobial substances.

  2. A rapid PCR-based approach for molecular identification of filamentous fungi.

    Science.gov (United States)

    Chen, Yuanyuan; Prior, Bernard A; Shi, Guiyang; Wang, Zhengxiang

    2011-08-01

    In this study, a novel rapid and efficient DNA extraction method based on alkaline lysis, which can deal with a large number of filamentous fungal isolates in the same batch, was established. The filamentous fungal genomic DNA required only 20 min to prepare and can be directly used as a template for PCR amplification. The amplified internal transcribed spacer regions were easy to identify by analysis. The extracted DNA also can be used to amplify other protein-coding genes for fungal identification. This method can be used for rapid systematic identification of filamentous fungal isolates.

  3. Computer aided detection of suspicious regions on digital mammograms : rapid segmentation and feature extraction

    Energy Technology Data Exchange (ETDEWEB)

    Ruggiero, C; Giacomini, M; Sacile, R [DIST - Department of Communication Computer and System Sciences, University of Genova, Via Opera Pia 13, 16145 Genova (Italy); Rosselli Del Turco, M [Centro per lo studio e la prevenzione oncologica, Firenze (Italy)

    1999-12-31

    A method is presented for rapid detection of suspicious regions which consists of two steps. The first step is segmentation based on texture analysis consisting of : histogram equalization, Laws filtering for texture analysis, Gaussian blur and median filtering to enhance differences between tissues in different respects, histogram thresholding to obtain a binary image, logical masking in order to detect regions to be discarded from the analysis, edge detection. This method has been tested on 60 images, obtaining 93% successful detection of suspicious regions. (authors) 4 refs, 9 figs, 1 tabs.

  4. Rapid determination of ampicillin in bovine milk by liquid chromatography with fluorescence detection

    Energy Technology Data Exchange (ETDEWEB)

    Ang, C.Y.W.; Luo, Wenhong [National Center for Toxicological Research, Jefferson, AR (United States)

    1997-01-01

    A rapid and sensitive liquid chromatographic (LC) method was developed for the determination of ampicillin residues in raw bovine milk, processed skim milk, and pasteurized, homogenized whole milk with vitamin D. Milk samples were deproteinized with trichloroacetic acid (TCA) and acetonictrile. After centrifugation, the clear supernatant was reacted with formaldehyde and TCA under heat. The major fluorescent derivative of ampicillin was then determined by reversed-phase LC with fluorescence detection. Average recoveries of ampicillin fortified at 5, 10, and 20 ppb (ng/mL) were all >85% with coefficients of variation <10%. Limits of detection ranged from 0.31 to 0.51 ppb and limits of quantitation, from 0.66 to 1.2 ppb. After appropriate validation, this method should be suitable for rapid analysis of milk for ampicillin residues at the tolerance level of 10 ppb. 16 refs., 4 figs., 3 tabs.

  5. Microbiological evaluation of a new growth-based approach for rapid detection of methicillin-resistant Staphylococcus aureus

    NARCIS (Netherlands)

    von Eiff, Christof; Maas, Dominik; Sander, Gunnar; Friedrich, Alexander W; Peters, Georg; Becker, Karsten

    OBJECTIVES: Recently, a rapid screening tool for methicillin-resistant Staphylococcus aureus (MRSA) has been introduced that applies a novel detection technology allowing the rapid presence or absence of MRSA to be determined from an enrichment broth after only a few hours of incubation. To evaluate

  6. The modular nature of dendritic cell responses to commensal and pathogenic fungi.

    Directory of Open Access Journals (Sweden)

    Lisa Rizzetto

    Full Text Available The type of adaptive immune response following host-fungi interaction is largely determined at the level of the antigen-presenting cells, and in particular by dendritic cells (DCs. The extent to which transcriptional regulatory events determine the decision making process in DCs is still an open question. By applying the highly structured DC-ATLAS pathways to analyze DC responses, we classified the various stimuli by revealing the modular nature of the different transcriptional programs governing the recognition of either pathogenic or commensal fungi. Through comparison of the network parts affected by DC stimulation with fungal cells and purified single agonists, we could determine the contribution of each receptor during the recognition process. We observed that initial recognition of a fungus creates a temporal window during which the simultaneous recruitment of cell surface receptors can intensify, complement and sustain the DC activation process. The breakdown of the response to whole live cells, through the purified components, showed how the response to invading fungi uses a set of specific modules. We find that at the start of fungal recognition, DCs rapidly initiate the activation process. Ligand recognition is further enhanced by over-expression of the receptor genes, with a significant correspondence between gene expression and protein levels and function. Then a marked decrease in the receptor levels follows, suggesting that at this moment the DC commits to a specific fate. Overall our pathway based studies show that the temporal window of the fungal recognition process depends on the availability of ligands and is different for pathogens and commensals. Modular analysis of receptor and signalling-adaptor expression changes, in the early phase of pathogen recognition, is a valuable tool for rapid and efficient dissection of the pathogen derived components that determine the phenotype of the DC and thereby the type of immune response

  7. Genetically Engineering Entomopathogenic Fungi.

    Science.gov (United States)

    Zhao, H; Lovett, B; Fang, W

    2016-01-01

    Entomopathogenic fungi have been developed as environmentally friendly alternatives to chemical insecticides in biocontrol programs for agricultural pests and vectors of disease. However, mycoinsecticides currently have a small market share due to low virulence and inconsistencies in their performance. Genetic engineering has made it possible to significantly improve the virulence of fungi and their tolerance to adverse conditions. Virulence enhancement has been achieved by engineering fungi to express insect proteins and insecticidal proteins/peptides from insect predators and other insect pathogens, or by overexpressing the pathogen's own genes. Importantly, protein engineering can be used to mix and match functional domains from diverse genes sourced from entomopathogenic fungi and other organisms, producing insecticidal proteins with novel characteristics. Fungal tolerance to abiotic stresses, especially UV radiation, has been greatly improved by introducing into entomopathogens a photoreactivation system from an archaean and pigment synthesis pathways from nonentomopathogenic fungi. Conversely, gene knockout strategies have produced strains with reduced ecological fitness as recipients for genetic engineering to improve virulence; the resulting strains are hypervirulent, but will not persist in the environment. Coupled with their natural insect specificity, safety concerns can also be mitigated by using safe effector proteins with selection marker genes removed after transformation. With the increasing public concern over the continued use of synthetic chemical insecticides and growing public acceptance of genetically modified organisms, new types of biological insecticides produced by genetic engineering offer a range of environmentally friendly options for cost-effective control of insect pests. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Fungi isolated in school buildings

    Directory of Open Access Journals (Sweden)

    Elżbieta Ejdys

    2013-12-01

    Full Text Available The aim of the study was to determine the species composition of fungi occurring on wall surfaces and in the air in school buildings. Fungi isolated from the air using the sedimentation method and from the walls using the surface swab technique constituted the study material. Types of finish materials on wall surfaces were identified and used in the analysis. Samples were collected in selected areas in two schools: classrooms, corridors, men's toilets and women's toilets, cloakrooms, sports changing rooms and shower. Examinations were conducted in May 2005 after the heating season was over. Fungi were incubated on Czapek-Dox medium at three parallel temperatures: 25, 37 and 40°C, for at least three weeks. A total of 379 isolates of fungi belonging to 32 genera of moulds, yeasts and yeast-like fungi were obtained from 321 samples in the school environment. The following genera were isolated most frequently: Aspergillus, Penicillium and Cladosporium. Of the 72 determined species, Cladosporium herbarum, Aspergillus fumigatus and Penicillium chrysogenum occurred most frequently in the school buildings. Wall surfaces were characterised by an increased prevalence of mycobiota in comparison with the air in the buildings, with a slightly greater species diversity. A certain species specificity for rough and smooth wall surfaces was demonstrated. Fungi of the genera Cladosporium and Emericella with large spores adhered better to smooth surfaces while those of the genus Aspergillus with smaller conidia adhered better to rough surfaces. The application of three incubation temperatures helped provide a fuller picture of the mycobiota in the school environment.

  9. The pathogenic fungi in mushroom cultivation of Agaricus bisporus (Lange. Imbach.

    Directory of Open Access Journals (Sweden)

    Agata Tekiela

    2012-12-01

    Full Text Available The research was conducted in a mushroom growing facility located near Rzeszów, consisting of three production cycles. The number and composition of microorganisms which accompany the mushroom cultivation depended on the healthiness of: the compost, casing and spawn of Agaricus bisporus. The presence of pathogenic fungi in the cultivation halls at the beginning of the production cycle is a serious threat to the cultivation of common mushroom because their rapid development shortens the span of fruiting body harvests.

  10. Screening Senyawa Metabolit Sekunder Pada Fungi Laut Emericella Nidulans

    Directory of Open Access Journals (Sweden)

    Irah Namirah

    2016-01-01

    Full Text Available Abstract: Investigation bioactive secondary metabolite previously, Research Center for Marine and Fisheries Product Processing and Biotechnology found anticancer properties to Emericella nidulans marine fungi strain MFW39 isolated from ascidia Aplidium longithorax collected from Wakatobi Marine National Park. Emestrin was a compound with an ETP (epipolithiodioxopiperazine group that found in Emericella nidulans marine fungi have cytotoxicity properties. Emestrin show cytotoxic activity to breast cancer cell line [T47D], cancer cervic cell line [HeLa], colon cancer cell line [WiDr] and liver cancer cell line (HepG2. The aim of the research to investigated other derivative of emestrin compound. The screening with UPLC (Ultra Performance Liquid Chromatography mass analysis q-TOF/MS (quadrupole-Time of Flight/Mass spectra positif mode (ES+.. Monoisotopic ion Derivative compound of emestrin that detected from (ES+ UPLC-ESI-qTOF-MS spectrum are emestrin B, emestrin C. Another compound that detected are cytochalasin B dan C.Keywords: Emericella nidulans, Emestrin, Emestrin derivative, UPLC- q-TOF/MS spectrum Abstrak: Pada penelitian pencarian metabolit sekunder bioaktif sebelumnya, Balai Besar Riset Pengolahan Produk dan Bioteknologi Kelautan dan Perikanan menemukan fungi Emericella nidulans strain MFW39 yang diisolasi dari ascidia Aplidium longithorax dari Taman Nasional Laut Wakatobi, Sulawesi tenggara memiliki aktivitas sitotoksik terhadap beberapa sel kanker, diantaranya sel turunan kanker payudara (T47D, liver (HepG2, kanker usus (C28 dan serviks (HeLa. Senyawa yang berkontribusi terhadap sifat sitotoksik adalah senyawa emestrin yang memiliki gugus ETP (epipolithiodioxopiperazine. Hasil isolasi dan karakterisasi senyawa bioaktif yang ditemukan pada fungi Emericella nidulans strain MFW39 adalah senyawa emestrin. Penelitian ini bertujuan mencari derivat senyawa emestrin lain. Proses screening dilakukan dengan mencari puncak monoisotopik senyawa

  11. Identifikasi Cendawan Endofit Menggunakan Teknik Polymerase Chain Reaction (Detection of Endophytic Fungi Using Polymerase Chain Reaction Technique

    Directory of Open Access Journals (Sweden)

    Tuti Susanti Legiastuti

    2013-04-01

    Full Text Available Yellow leaf curl disease, caused by a member of Begomovirus (Geminiviridae, is one of important diseases of chilli pepper in Indonesia. Exploration of endophytic fungi was initiated in order to find biological control agents for an alternative control strategies of this disease. Isolates of endophytic fungi were collected from chilli pepper growing area in Sleman, Yogyakarta and further identification using molecular technique involving polymerase chain reaction (PCR and DNA sequencing was performed. DNA fragments of ±500 bp were successfully amplified from 10 fungal isolates by PCR using primer pair ITS1/ITS4, but only 8 DNA sequences was obtained for further genetic analysis. Based on BLASTN analysis the endophytic fungi were identified as having the highest similarity with Pleosporaceae sp. (98% for H1 isolate, Cercospora nicotianae (100% for H5 isolate, ercospora piaropi (98% for H11 isolate, Guignardia mangiferae (99% for H16 isolate, Geomyces pannorum 95% for H17 isolate, Diaporthe phaseoloru (99% for H18 isolate, Dothideomycete sp. (100% for K3 isolate, and Alternaria longissima (99% for K10 isolate. Key words: Begomovirus, chillipepper, DNA sequencing, polymerase chain reaction

  12. Human anti-HIV IgM detection by the OraQuick ADVANCE® Rapid HIV 1/2 Antibody Test.

    Science.gov (United States)

    Guillon, Geraldine; Yearwood, Graham; Snipes, Casey; Boschi, Daniel; Reed, Michael R

    2018-01-01

    The Centers for Disease Control and Prevention (CDC) and many public health jurisdictions continue to advocate for the most sensitive rapid HIV test that is available. Currently, the recommendation is to utilize tests that can detect HIV infection biomarkers within 30 days of infection, when initial immune responses are mounted. The infected patient's IgM response is often used to detect acute infection within a 20-25 days window after infection. This requirement applies to lab-based testing with automated analyzers and rapid, point of care (POC) testing used for screening in a non-clinical setting. A recent study has demonstrated that POC tests using a Protein A-based detection system can detect samples with predominantly HIV-1 IgM reactivity (Moshgabadi et al., 2015). The OraQuick ADVANCE ® Rapid HIV-1/2 Antibody Test (OraQuick ADVANCE ®) also uses Protein A as the detection protein in the antibody-binding colloidal gold conjugate, so it is expected that the OraQuick ADVANCE ® Test will also detect samples with predominantly IgM reactivity. This report definitively demonstrates that the OraQuick ADVANCE ® Test can detect IgM antibodies during an acute infection window period of approximately 20-25 days after infection, and is therefore suitable for use in testing environments requiring adherence to current CDC recommendations.

  13. Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Common Strains of Escherichia coli▿

    Science.gov (United States)

    Hill, Joshua; Beriwal, Shilpa; Chandra, Ishwad; Paul, Vinod K.; Kapil, Aarti; Singh, Tripti; Wadowsky, Robert M.; Singh, Vinita; Goyal, Ankur; Jahnukainen, Timo; Johnson, James R.; Tarr, Phillip I.; Vats, Abhay

    2008-01-01

    We developed a highly sensitive and specific LAMP assay for Escherichia coli. It does not require DNA extraction and can detect as few as 10 copies. It detected all 36 of 36 E. coli isolates and all 22 urine samples (out of 89 samples tested) that had E. coli. This assay is rapid, low in cost, and simple to perform. PMID:18550738

  14. Loop-mediated isothermal amplification assay for rapid detection of common strains of Escherichia coli.

    Science.gov (United States)

    Hill, Joshua; Beriwal, Shilpa; Chandra, Ishwad; Paul, Vinod K; Kapil, Aarti; Singh, Tripti; Wadowsky, Robert M; Singh, Vinita; Goyal, Ankur; Jahnukainen, Timo; Johnson, James R; Tarr, Phillip I; Vats, Abhay

    2008-08-01

    We developed a highly sensitive and specific LAMP assay for Escherichia coli. It does not require DNA extraction and can detect as few as 10 copies. It detected all 36 of 36 E. coli isolates and all 22 urine samples (out of 89 samples tested) that had E. coli. This assay is rapid, low in cost, and simple to perform.

  15. Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi.

    Science.gov (United States)

    Ropars, Jeanne; Rodríguez de la Vega, Ricardo C; López-Villavicencio, Manuela; Gouzy, Jérôme; Sallet, Erika; Dumas, Émilie; Lacoste, Sandrine; Debuchy, Robert; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana

    2015-10-05

    Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [1-5]. Few studies have focused on the domestication of fungi, with notable exceptions [6-11], despite their importance to bioindustry [12] and to a general understanding of adaptation in eukaryotes [5]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making-P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [13-15]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. Rapid method for Detection of Irradiation Mango Fruits

    International Nuclear Information System (INIS)

    El Salhy, F.T.

    2011-01-01

    To detect mango fruits which have been exposed to low doses of gamma rays (0.5-3.0 kGy), three recommended methods by European Committee for Standardization (EN 1784:1996, EN 1785:1996 and EN 1787:2000) were used to study the possibility for identification of irradiated mango fruits (Ewais variety). Fresh mangoes were irradiated to different doses (0.5, 0.75, 1.0 and 3.0 kGy). The first method for determining the volatile hydrocarbons (VHC) was carried out by using florisil column then identified by gas chromatography and mass spectrometry (GC-MS). The major VHCs were C14:1, C15:0 and C17:1 at different doses which increased linearly with increasing doses either at low or high doses. The second one for determining the 2-alkyl cyclobutanone (2-DCB) was carried out using florisil chromatography method activated with 20% for separation and identified by GC-MS. 2-DCB bio marker specific for irradiated food proved its presence at the applied doses from 0.75-3.0 kGy but not at 0.5 kGy. All the mentioned compounds could not detected in non-irradiated samples, which mean that these radiolytic products (VHC and 2-DCB) can be used as a detection markers for irradiated mangoes even at low doses. The third one (EN 1787:2000) was conducted by electron spin resonance (ESR) on dried petioles of mangoes. The results proved that ESR was more sensitive for all applied doses.It could be concluded that using the three methods can be succeeded for detection of irradiated mangoes but the rapid one even at low doses with high accuracy was ESR.

  17. A PCA-based hyperspectral approach to detect infections by mycophilic fungi on dried porcini mushrooms (boletus edulis and allied species).

    Science.gov (United States)

    Bagnasco, Lucia; Zotti, Mirca; Sitta, Nicola; Oliveri, Paolo

    2015-11-01

    Mycophilic fungi of anamorphic genus Sepedonium (telomorphs in Hypomyces, Hypocreales, Ascomycota) infect and parasitize sporomata of boletes. The obligated hosts such as Boletus edulis and allied species (known as "porcini mushrooms") are among the most valued and prized edible wild mushrooms in the world. Sepedonium infections have a great morphological variability: at the initial state, contaminated mushrooms present a white coating covering tubes and pores; at the final state, Sepedonium forms a deep and thick hyphal layer that eventually leads to the total necrosis of the host. Up to date, Sepedonium infections in porcini mushrooms have been evaluated only through macroscopic and microscopic visual analysis. In this study, in order to implement the infection evaluation as a routine methodology for industrial purposes, the potential application of Hyperspectral Imaging (HSI) and Principal Component Analysis (PCA) for detection of Sepedonium presence on sliced and dried B. edulis and allied species was investigated. Hyperspectral images were obtained using a pushbroom line-scanning HSI instrument, operating in the wavelength range between 400 and 1000 nm with 5 nm resolution. PCA was applied on normal and contaminated samples. To reduce the spectral variability caused by factors unrelated to Sepedonium infection, such as scattering effects and differences in sample height, different spectral pre-treatments were applied. A supervised rule was then developed to assign spectra recorded on new test samples to each of the two classes, based on the PC scores. This allowed to visualize directly - within false-color images of test samples - which points of the samples were contaminated. The results achieved may lead to the development of a non-destructive monitoring system for a rapid on-line screening of contaminated mushrooms. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Rapid detection of pandemic influenza in the presence of seasonal influenza

    Science.gov (United States)

    2010-01-01

    Background Key to the control of pandemic influenza are surveillance systems that raise alarms rapidly and sensitively. In addition, they must minimise false alarms during a normal influenza season. We develop a method that uses historical syndromic influenza data from the existing surveillance system 'SERVIS' (Scottish Enhanced Respiratory Virus Infection Surveillance) for influenza-like illness (ILI) in Scotland. Methods We develop an algorithm based on the weekly case ratio (WCR) of reported ILI cases to generate an alarm for pandemic influenza. From the seasonal influenza data from 13 Scottish health boards, we estimate the joint probability distribution of the country-level WCR and the number of health boards showing synchronous increases in reported influenza cases over the previous week. Pandemic cases are sampled with various case reporting rates from simulated pandemic influenza infections and overlaid with seasonal SERVIS data from 2001 to 2007. Using this combined time series we test our method for speed of detection, sensitivity and specificity. Also, the 2008-09 SERVIS ILI cases are used for testing detection performances of the three methods with a real pandemic data. Results We compare our method, based on our simulation study, to the moving-average Cumulative Sums (Mov-Avg Cusum) and ILI rate threshold methods and find it to be more sensitive and rapid. For 1% case reporting and detection specificity of 95%, our method is 100% sensitive and has median detection time (MDT) of 4 weeks while the Mov-Avg Cusum and ILI rate threshold methods are, respectively, 97% and 100% sensitive with MDT of 5 weeks. At 99% specificity, our method remains 100% sensitive with MDT of 5 weeks. Although the threshold method maintains its sensitivity of 100% with MDT of 5 weeks, sensitivity of Mov-Avg Cusum declines to 92% with increased MDT of 6 weeks. For a two-fold decrease in the case reporting rate (0.5%) and 99% specificity, the WCR and threshold methods

  19. Comparative study of cellulolytic activity of three rumen fungi on different substrates

    Directory of Open Access Journals (Sweden)

    Atanasova-Pančevska Natalija

    2011-01-01

    Full Text Available Anaerobic chytridiomycete fungi are found in the gastrointestinal tracts of many domesticated ruminant and nonruminant herbivores and of a wide variety of wild herbivorous mammals. They produce high levels of cellulases and hemicellulases; these enzymes are regulated by substrate (especially soluble sugars available to the organisms. The aim of this paper was to do a comparative study of cellulolytic activity of three rumen fungi on carboxymethyl cellulose and Avicel. The capacity of enzymes was determined by monitoring the growth on carboxymethyl cellulose (CMC and Avicel. Enzyme activity was detected extracellularly in culture supernatants after vegetative growth. All of the isolates degraded CMC and avicel, and exhibited cellulolytic activities (carboxymethyl cellulose-(CMC-ase and avicelase.

  20. Rapid molecular assays for the detection of yellow fever virus in low-resource settings.

    Science.gov (United States)

    Escadafal, Camille; Faye, Oumar; Sall, Amadou Alpha; Faye, Ousmane; Weidmann, Manfred; Strohmeier, Oliver; von Stetten, Felix; Drexler, Josef; Eberhard, Michael; Niedrig, Matthias; Patel, Pranav

    2014-03-01

    Yellow fever (YF) is an acute viral hemorrhagic disease transmitted by Aedes mosquitoes. The causative agent, the yellow fever virus (YFV), is found in tropical and subtropical areas of South America and Africa. Although a vaccine is available since the 1930s, YF still causes thousands of deaths and several outbreaks have recently occurred in Africa. Therefore, rapid and reliable diagnostic methods easy to perform in low-resources settings could have a major impact on early detection of outbreaks and implementation of appropriate response strategies such as vaccination and/or vector control. The aim of this study was to develop a YFV nucleic acid detection method applicable in outbreak investigations and surveillance studies in low-resource and field settings. The method should be simple, robust, rapid and reliable. Therefore, we adopted an isothermal approach and developed a recombinase polymerase amplification (RPA) assay which can be performed with a small portable instrument and easy-to-use lyophilized reagents. The assay was developed in three different formats (real-time with or without microfluidic semi-automated system and lateral-flow assay) to evaluate their application for different purposes. Analytical specificity and sensitivity were evaluated with a wide panel of viruses and serial dilutions of YFV RNA. Mosquito pools and spiked human plasma samples were also tested for assay validation. Finally, real-time RPA in portable format was tested under field conditions in Senegal. The assay was able to detect 20 different YFV strains and demonstrated no cross-reactions with closely related viruses. The RPA assay proved to be a robust, portable method with a low detection limit (<21 genome equivalent copies per reaction) and rapid processing time (<20 min). Results from real-time RPA field testing were comparable to results obtained in the laboratory, thus confirming our method is suitable for YFV detection in low-resource settings.

  1. Rapid molecular assays for the detection of yellow fever virus in low-resource settings.

    Directory of Open Access Journals (Sweden)

    Camille Escadafal

    2014-03-01

    Full Text Available BACKGROUND: Yellow fever (YF is an acute viral hemorrhagic disease transmitted by Aedes mosquitoes. The causative agent, the yellow fever virus (YFV, is found in tropical and subtropical areas of South America and Africa. Although a vaccine is available since the 1930s, YF still causes thousands of deaths and several outbreaks have recently occurred in Africa. Therefore, rapid and reliable diagnostic methods easy to perform in low-resources settings could have a major impact on early detection of outbreaks and implementation of appropriate response strategies such as vaccination and/or vector control. METHODOLOGY: The aim of this study was to develop a YFV nucleic acid detection method applicable in outbreak investigations and surveillance studies in low-resource and field settings. The method should be simple, robust, rapid and reliable. Therefore, we adopted an isothermal approach and developed a recombinase polymerase amplification (RPA assay which can be performed with a small portable instrument and easy-to-use lyophilized reagents. The assay was developed in three different formats (real-time with or without microfluidic semi-automated system and lateral-flow assay to evaluate their application for different purposes. Analytical specificity and sensitivity were evaluated with a wide panel of viruses and serial dilutions of YFV RNA. Mosquito pools and spiked human plasma samples were also tested for assay validation. Finally, real-time RPA in portable format was tested under field conditions in Senegal. CONCLUSION/SIGNIFICANCE: The assay was able to detect 20 different YFV strains and demonstrated no cross-reactions with closely related viruses. The RPA assay proved to be a robust, portable method with a low detection limit (<21 genome equivalent copies per reaction and rapid processing time (<20 min. Results from real-time RPA field testing were comparable to results obtained in the laboratory, thus confirming our method is suitable for

  2. A technique to detect periodic and non-periodic ultra-rapid flux time variations with standard radio-astronomical data

    Science.gov (United States)

    Borra, Ermanno F.; Romney, Jonathan D.; Trottier, Eric

    2018-06-01

    We demonstrate that extremely rapid and weak periodic and non-periodic signals can easily be detected by using the autocorrelation of intensity as a function of time. We use standard radio-astronomical observations that have artificial periodic and non-periodic signals generated by the electronics of terrestrial origin. The autocorrelation detects weak signals that have small amplitudes because it averages over long integration times. Another advantage is that it allows a direct visualization of the shape of the signals, while it is difficult to see the shape with a Fourier transform. Although Fourier transforms can also detect periodic signals, a novelty of this work is that we demonstrate another major advantage of the autocorrelation, that it can detect non-periodic signals while the Fourier transform cannot. Another major novelty of our work is that we use electric fields taken in a standard format with standard instrumentation at a radio observatory and therefore no specialized instrumentation is needed. Because the electric fields are sampled every 15.625 ns, they therefore allow detection of very rapid time variations. Notwithstanding the long integration times, the autocorrelation detects very rapid intensity variations as a function of time. The autocorrelation could also detect messages from Extraterrestrial Intelligence as non-periodic signals.

  3. Occurrence of keratinophilic fungi on Indian birds.

    Science.gov (United States)

    Dixit, A K; Kushwaha, R K

    1991-01-01

    Keratinophilic fungi were isolated from feathers of most common Indian birds, viz. domestic chicken (Gallus domesticus), domestic pigeon (Columba livia), house sparrow (Passer domesticus), house crow (Corvus splendens), duck (Anas sp.), rose-ringed parakeet (Psittacula krameri). Out of 87 birds, 58 yielded 4 keratinophilic fungal genera representing 13 fungal species and one sterile mycelium. The isolated fungi were cultured on Sabouraud's dextrose agar at 28 +/- 2 degrees C. Chrysosporium species were isolated on most of the birds. Chrysosporium lucknowense and Chrysosporium tropicum were the most common fungal species associated with these Indian birds. Maximum occurrence of fungi (47%) was recorded on domestic chickens and the least number of keratinophilic fungi was isolated from the domestic pigeon and duck. The average number of fungi per bird was found to be the 0.44.

  4. Correlation between organic acid exudation and metal uptake by ectomycorrhizal fungi grown on pond ash in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Ray, P.; Adholeya, A. [Energy & Resources Institute, New Delhi (India). India Habitat Centre

    2009-04-15

    Experiments were conducted to investigate the effect of coal ash on organic acid exudation and subsequent metal uptake by ectomycorrhizal fungi. Four isolates of ectomycorrhizal fungi namely, Pisolithus tinctorius (EM-1293 and EM-1299), Scleroderma verucosum (EM-1283) and Scleroderma cepa (EM-1233) were grown on pond ash moistened with Modified Melin-Norkans medium in vitro. Exudation of formic acid, malic acid and succinic acid by these fungi were detected by HPLC. Mycelial accumulation of Al, As, Cd, Cr, Ni and Pb by these fungi was assayed by atomic absorption spectrophotometer. Relationship between organic acid exudation and metal uptake was determined using classical multivariate linear regression model. Correlation between organic acid exudation and metal uptake could be substantiated when several metals are considered collectively. The finding supports the widespread role of low molecular weight organic acid as a function of tolerance, when exposed to metals in vitro.

  5. A Survey of occurrence of toxogenic fungi and mycotoxins in pig feed samples-Use in evaluation of risk assessment

    Directory of Open Access Journals (Sweden)

    Dragan Milicevic

    Full Text Available In order to assess of risk assessment, the aim of this paper was to provide good and detailed insight into the level of contamination of complete feedmixes intended for fattening swine from mycotoxin-producing fungi and mycotoxins (n=18. Isolation and quantitative enumeration of fungal propagules were done on solid media using the standard microbiological procedure. These plates were incubated the number of colonies was determined and thent on the basis of characteristic colonies and microscopic analysis was performed to identify genera and species of moulds. Isolates identified as Aspergillus and Penicillium species were subjected to molecular characterization of the presence of genes responsible for the synthesis of OTA (polyketide synthase gene-PKS. Total fungal counts (CFU/g ranged from 0,5x105 do 4x106. From a total samples analysed, seven samples had fungal counts higher than the limit established by Serbian regulations (3x105. During a mycological analysis of complete feedmixes intended for fattening swine, a total of six genera and 14 species of moulds were identified of which the most frequent one was of the genus Penicillium (94,4% while the moulds from Fusarium genere isolated in 55,5% and Paecilomyces in 44,4% of the samples from investigated localities. Other fungi from the genera Aspergillus (22%, Mycor (11,1% and Alternaria (5,5% were represented in a less amount. Polymerase chain reaction (PCR is a set of 18 isolates of the DNA belonging to families Penicillium and Aspergillus. The sequences of PCR reaction products in three samples were compared with nucleotide sequences of genes for poliketid synthase (PKS from Penicillium species and found that the samples possess PKS sequence. The traditional methods for identification of ochratoxin-producing fungi are time-consuming and labor-intensive. Rapid and specific detection of ochratoxinproducing fungi is important for ensuring microbiological quality and safety of feed and food

  6. Phylogenetic diversity of stress signalling pathways in fungi

    Directory of Open Access Journals (Sweden)

    Stansfield Ian

    2009-02-01

    Full Text Available Abstract Background Microbes must sense environmental stresses, transduce these signals and mount protective responses to survive in hostile environments. In this study we have tested the hypothesis that fungal stress signalling pathways have evolved rapidly in a niche-specific fashion that is independent of phylogeny. To test this hypothesis we have compared the conservation of stress signalling molecules in diverse fungal species with their stress resistance. These fungi, which include ascomycetes, basidiomycetes and microsporidia, occupy highly divergent niches from saline environments to plant or mammalian hosts. Results The fungi displayed significant variation in their resistance to osmotic (NaCl and sorbitol, oxidative (H2O2 and menadione and cell wall stresses (Calcofluor White and Congo Red. There was no strict correlation between fungal phylogeny and stress resistance. Rather, the human pathogens tended to be more resistant to all three types of stress, an exception being the sensitivity of Candida albicans to the cell wall stress, Calcofluor White. In contrast, the plant pathogens were relatively sensitive to oxidative stress. The degree of conservation of osmotic, oxidative and cell wall stress signalling pathways amongst the eighteen fungal species was examined. Putative orthologues of functionally defined signalling components in Saccharomyces cerevisiae were identified by performing reciprocal BLASTP searches, and the percent amino acid identities of these orthologues recorded. This revealed that in general, central components of the osmotic, oxidative and cell wall stress signalling pathways are relatively well conserved, whereas the sensors lying upstream and transcriptional regulators lying downstream of these modules have diverged significantly. There was no obvious correlation between the degree of conservation of stress signalling pathways and the resistance of a particular fungus to the corresponding stress. Conclusion Our

  7. Bienzymatic Biosensor for Rapid Detection of Aspartame by Flow Injection Analysis

    Directory of Open Access Journals (Sweden)

    Maria-Cristina Radulescu

    2014-01-01

    Full Text Available A rapid, simple and stable biosensor for aspartame detection was developed. Alcohol oxidase (AOX, carboxyl esterase (CaE and bovine serum albumin (BSA were immobilised with glutaraldehyde (GA onto screen-printed electrodes modified with cobalt-phthalocyanine (CoPC. The biosensor response was fast. The sample throughput using a flow injection analysis (FIA system was 40 h−1 with an RSD of 2.7%. The detection limits for both batch and FIA measurements were 0.1 µM for methanol and 0.2 µM for aspartame, respectively. The enzymatic biosensor was successfully applied for aspartame determination in different sample matrices/commercial products (liquid and solid samples without any pre-treatment step prior to measurement.

  8. Bienzymatic biosensor for rapid detection of aspartame by flow injection analysis.

    Science.gov (United States)

    Radulescu, Maria-Cristina; Bucur, Bogdan; Bucur, Madalina-Petruta; Radu, Gabriel Lucian

    2014-01-09

    A rapid, simple and stable biosensor for aspartame detection was developed. Alcohol oxidase (AOX), carboxyl esterase (CaE) and bovine serum albumin (BSA) were immobilised with glutaraldehyde (GA) onto screen-printed electrodes modified with cobalt-phthalocyanine (CoPC). The biosensor response was fast. The sample throughput using a flow injection analysis (FIA) system was 40 h⁻¹ with an RSD of 2.7%. The detection limits for both batch and FIA measurements were 0.1 µM for methanol and 0.2 µM for aspartame, respectively. The enzymatic biosensor was successfully applied for aspartame determination in different sample matrices/commercial products (liquid and solid samples) without any pre-treatment step prior to measurement.

  9. Lab on a chip sensor for rapid detection and antibiotic resistance determination of Staphylococcus aureus.

    Science.gov (United States)

    Abeyrathne, Chathurika D; Huynh, Duc H; Mcintire, Thomas W; Nguyen, Thanh C; Nasr, Babak; Zantomio, Daniela; Chana, Gursharan; Abbott, Iain; Choong, Peter; Catton, Mike; Skafidas, Efstratios

    2016-03-21

    The Gram-positive bacterium, Staphylococcus aureus (S. aureus), is a major pathogen responsible for a variety of infectious diseases ranging from cellulitis to more serious conditions such as septic arthritis and septicaemia. Timely treatment with appropriate antibiotic therapy is essential to ensure clinical defervescence and to prevent further complications such as infective endocarditis or organ impairment due to septic shock. To date, initial antibiotic choice is empirical, using a "best guess" of likely organism and sensitivity- an approach adopted due to the lack of rapid identification methods for bacteria. Current culture based methods take up to 5 days to identify the causative bacterial pathogen and its antibiotic sensitivity. This paper provides proof of concept for a biosensor, based on interdigitated electrodes, to detect the presence of S. aureus and ascertain its sensitivity to flucloxacillin rapidly (within 2 hours) in a cost effective manner. The proposed method is label-free and uses non-faradic measurements. This is the first study to successfully employ interdigitated electrodes for the rapid detection of antibiotic resistance. The method described has important potential outcomes of faster definitive antibiotic treatment and more rapid clinical response to treatment.

  10. Rapid colorimetric sensing platform for the detection of Listeria monocytogenes foodborne pathogen.

    Science.gov (United States)

    Alhogail, Sahar; Suaifan, Ghadeer A R Y; Zourob, Mohammed

    2016-12-15

    Listeria monocytogenes is a serious cause of human foodborne infections worldwide, which needs spending billions of dollars for inspection of bacterial contamination in food every year. Therefore, there is an urgent need for rapid, in-field and cost effective detection techniques. In this study, rapid, low-cost and simple colorimetric assay was developed using magnetic nanoparticles for the detection of listeria bacteria. The protease from the listeria bacteria was detected using D-amino acid substrate. D-amino acid substrate was linked to the carboxylic acid on the magnetic nanoparticles using EDC/NHS chemistry. The cysteine residue at the C-terminal of the substrate was used for the self-assembled monolayer formation on the gold sensor surface, which in turn the black magnetic nanobeads will mask the golden color. The color will change from black to golden color upon the cleavage of the specific peptide sequence by the Listeria protease. The sensor was tested with serial dilutions of Listeria bacteria. It was found that the appearance of the gold surface area is proportional to the bacterial concentrations in CFU/ml. The lowest detection limit of the developed sensor for Listeria was found to be 2.17×10(2) colony forming unit/ml (CFU/ml). The specificity of the biosensor was tested against four different foodborne associated bacteria (Escherichia coli, Salmonella, Shigella flexnerii and Staphylococcus aureus). Finally, the sensor was tested with artificially spiked whole milk and ground meat spiked with listeria. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Rapid Newcastle Disease Virus Detection Based on Loop-Mediated Isothermal Amplification and Optomagnetic Readout

    DEFF Research Database (Denmark)

    Tian, Bo; Ma, Jing; Zardán Gómez de la Torre, Teresa

    2016-01-01

    Rapid and sensitive diagnostic methods based on isothermal amplification are ideal substitutes for PCR in out-of-lab settings. However, there are bottlenecks in terms of establishing low-cost and user-friendly readout methods for isothermal amplification schemes. Combining the high amplification...... efficiency of loop-mediated isothermal amplification (LAMP) with an optomagnetic nanoparticle-based readout system, we demonstrate ultrasensitive and rapid detection of Newcastle disease virus RNA. Biotinylated amplicons of LAMP and reverse transcription LAMP (RT-LAMP) bind to streptavidin-coated magnetic...... nanoparticles (MNPs) resulting in a dramatical increase in the hydrodynamic size of the MNPs. This increase was measured by an optomagnetic readout system and provided quantitative information on the amount of LAMP target sequence. Our assay resulted in a limit of detection of 10 aM of target sequence...

  12. Plasmonic Nanobubbles Rapidly Detect and Destroy Drug-Resistant Tumors

    Science.gov (United States)

    Lukianova-Hleb, Ekaterina Y.; Ren, Xiaoyang; Townley, Debra; Wu, Xiangwei; Kupferman, Michael E.; Lapotko, Dmitri O.

    2012-01-01

    The resistance of residual cancer cells after oncological resection to adjuvant chemoradiotherapies results in both high recurrence rates and high non-specific tissue toxicity, thus preventing the successful treatment of such cancers as head and neck squamous cell carcinoma (HNSCC). The patients' survival rate and quality of life therefore depend upon the efficacy, selectivity and low non-specific toxicity of the adjuvant treatment. We report a novel, theranostic in vivo technology that unites both the acoustic diagnostics and guided intracellular delivery of anti-tumor drug (liposome-encapsulated doxorubicin, Doxil) in one rapid process, namely a pulsed laser-activated plasmonic nanobubble (PNB). HNSCC-bearing mice were treated with gold nanoparticle conjugates, Doxil, and single near-infrared laser pulses of low energy. Tumor-specific clusters of gold nanoparticles (solid gold spheres) converted the optical pulses into localized PNBs. The acoustic signals of the PNB detected the tumor with high specificity and sensitivity. The mechanical impact of the PNB, co-localized with Doxil liposomes, selectively ejected the drug into the cytoplasm of cancer cells. Cancer cell-specific generation of PNBs and their intracellular co-localization with Doxil improved the in vivo therapeutic efficacy from 5-7% for administration of only Doxil or PNBs alone to 90% thus demonstrating the synergistic therapeutic effect of the PNB-based intracellular drug release. This mechanism also reduced the non-specific toxicity of Doxil below a detectable level and the treatment time to less than one minute. Thus PNBs combine highly sensitive diagnosis, overcome drug resistance and minimize non-specific toxicity in a single rapid theranostic procedure for intra-operative treatment. PMID:23139725

  13. A Rapid Detection Method of Brucella with Quantum Dots and Magnetic Beads Conjugated with Different Polyclonal Antibodies

    Science.gov (United States)

    Song, Dandan; Qu, Xiaofeng; Liu, Yushen; Li, Li; Yin, Dehui; Li, Juan; Xu, Kun; Xie, Renguo; Zhai, Yue; Zhang, Huiwen; Bao, Hao; Zhao, Chao; Wang, Juan; Song, Xiuling; Song, Wenzhi

    2017-03-01

    Brucella spp. are facultative intracellular bacteria that cause zoonotic disease of brucellosis worldwide. Traditional methods for detection of Brucella spp. take 48-72 h that does not meet the need of rapid detection. Herein, a new rapid detection method of Brucella was developed based on polyclonal antibody-conjugating quantum dots and antibody-modified magnetic beads. First, polyclonal antibodies IgG and IgY were prepared and then the antibody conjugated with quantum dots (QDs) and immunomagnetic beads (IMB), respectively, which were activated by N-(3-dimethylaminopropyl)- N'-ethylcar-bodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) to form probes. We used the IMB probe to separate the Brucella and labeled by the QD probe, and then detected the fluorescence intensity with a fluorescence spectrometer. The detection method takes 105 min with a limit of detection of 103 CFU/mL and ranges from 10 to 105 CFU/mL ( R 2 = 0.9983), and it can be well used in real samples.

  14. Rapid and robust detection methods for poison and microbial contamination.

    Science.gov (United States)

    Hoehl, Melanie M; Lu, Peter J; Sims, Peter A; Slocum, Alexander H

    2012-06-27

    Real-time on-site monitoring of analytes is currently in high demand for food contamination, water, medicines, and ingestible household products that were never tested appropriately. Here we introduce chemical methods for the rapid quantification of a wide range of chemical and microbial contaminations using a simple instrument. Within the testing procedure, we used a multichannel, multisample, UV-vis spectrophotometer/fluorometer that employs two frequencies of light simultaneously to interrogate the sample. We present new enzyme- and dye-based methods to detect (di)ethylene glycol in consumables above 0.1 wt % without interference and alcohols above 1 ppb. Using DNA intercalating dyes, we can detect a range of pathogens ( E. coli , Salmonella , V. Cholera, and a model for Malaria) in water, foods, and blood without background signal. We achieved universal scaling independent of pathogen size above 10(4) CFU/mL by taking advantage of the simultaneous measurement at multiple wavelengths. We can detect contaminants directly, without separation, purification, concentration, or incubation. Our chemistry is stable to ± 1% for >3 weeks without refrigeration, and measurements require <5 min.

  15. Rapid detection and subtyping of human influenza A viruses and reassortants by pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Yi-Mo Deng

    Full Text Available BACKGROUND: Given the continuing co-circulation of the 2009 H1N1 pandemic influenza A viruses with seasonal H3N2 viruses, rapid and reliable detection of newly emerging influenza reassortant viruses is important to enhance our influenza surveillance. METHODOLOGY/PRINCIPAL FINDINGS: A novel pyrosequencing assay was developed for the rapid identification and subtyping of potential human influenza A virus reassortants based on all eight gene segments of the virus. Except for HA and NA genes, one universal set of primers was used to amplify and subtype each of the six internal genes. With this method, all eight gene segments of 57 laboratory isolates and 17 original specimens of seasonal H1N1, H3N2 and 2009 H1N1 pandemic viruses were correctly matched with their corresponding subtypes. In addition, this method was shown to be capable of detecting reassortant viruses by correctly identifying the source of all 8 gene segments from three vaccine production reassortant viruses and three H1N2 viruses. CONCLUSIONS/SIGNIFICANCE: In summary, this pyrosequencing assay is a sensitive and specific procedure for screening large numbers of viruses for reassortment events amongst the commonly circulating human influenza A viruses, which is more rapid and cheaper than using conventional sequencing approaches.

  16. Rapid detection and subtyping of human influenza A viruses and reassortants by pyrosequencing.

    Science.gov (United States)

    Deng, Yi-Mo; Caldwell, Natalie; Barr, Ian G

    2011-01-01

    Given the continuing co-circulation of the 2009 H1N1 pandemic influenza A viruses with seasonal H3N2 viruses, rapid and reliable detection of newly emerging influenza reassortant viruses is important to enhance our influenza surveillance. A novel pyrosequencing assay was developed for the rapid identification and subtyping of potential human influenza A virus reassortants based on all eight gene segments of the virus. Except for HA and NA genes, one universal set of primers was used to amplify and subtype each of the six internal genes. With this method, all eight gene segments of 57 laboratory isolates and 17 original specimens of seasonal H1N1, H3N2 and 2009 H1N1 pandemic viruses were correctly matched with their corresponding subtypes. In addition, this method was shown to be capable of detecting reassortant viruses by correctly identifying the source of all 8 gene segments from three vaccine production reassortant viruses and three H1N2 viruses. In summary, this pyrosequencing assay is a sensitive and specific procedure for screening large numbers of viruses for reassortment events amongst the commonly circulating human influenza A viruses, which is more rapid and cheaper than using conventional sequencing approaches.

  17. Spatial Segregation and Aggregation of Ectomycorrhizal and Root-Endophytic Fungi in the Seedlings of Two Quercus Species

    Science.gov (United States)

    Yamamoto, Satoshi; Sato, Hirotoshi; Tanabe, Akifumi S.; Hidaka, Amane; Kadowaki, Kohmei; Toju, Hirokazu

    2014-01-01

    Diverse clades of mycorrhizal and endophytic fungi are potentially involved in competitive or facilitative interactions within host-plant roots. We investigated the potential consequences of these ecological interactions on the assembly process of root-associated fungi by examining the co-occurrence of pairs of fungi in host-plant individuals. Based on massively-parallel pyrosequencing, we analyzed the root-associated fungal community composition for each of the 249 Quercus serrata and 188 Quercus glauca seedlings sampled in a warm-temperate secondary forest in Japan. Pairs of fungi that co-occurred more or less often than expected by chance were identified based on randomization tests. The pyrosequencing analysis revealed that not only ectomycorrhizal fungi but also endophytic fungi were common in the root-associated fungal community. Intriguingly, specific pairs of these ectomycorrhizal and endophytic fungi showed spatially aggregated patterns, suggesting the existence of facilitative interactions between fungi in different functional groups. Due to the large number of fungal pairs examined, many of the observed aggregated/segregated patterns with very low P values (e.g., fungi could influence each other through interspecific competitive/facilitative interactions in root. To test the potential of host-plants' control of fungus–fungus ecological interactions in roots, we further examined whether the aggregated/segregated patterns could vary depending on the identity of host plant species. Potentially due to the physiological properties shared between the congeneric host plant species, the sign of hosts' control was not detected in the present study. The pyrosequencing-based randomization analyses shown in this study provide a platform of the high-throughput investigation of fungus–fungus interactions in plant root systems. PMID:24801150

  18. Rapid islanding detection using multi-level inverter for grid-interactive PV system

    International Nuclear Information System (INIS)

    Tsang, K.M.; Chan, W.L.

    2014-01-01

    Graphical abstract: - Highlights: • Novel reference signal is used to form an islanding detection scheme for PV system. • Supply fixed magnitude sinusoidal signal even if utility grid is disconnected. • Seamless transfer between grid-connected and stand-alone modes is possible. - Abstract: A novel reference signal generator is combined with a multi-level inverter to form a rapid islanding detection scheme for grid-interactive PV system. The reference signal generator can easily be synchronized with the utility grid signal and produced a fixed magnitude and very low total harmonic distortion (THD) sinusoidal signal which is in phase with the utility grid signal. Unlike conventional phase-locked loop (PLL) circuitry, the reference signal generator can also provide a fixed magnitude sinusoidal signal even if the utility grid is disconnected and automatically re-synchronous with the grid rapidly. Consequently, seamless transfer between grid-connected and stand-alone modes could easily be achieved if anti-islanding protection is not required. If a saturation element is applied to the raw reference signal followed by the synthesis of the truncated signal using a multi-level inverter, the distinct flat-top feature of the synthesized signal can quickly and easily be identified if the network is in islanding mode at the point of common coupling. Experimental results are included to demonstrate the effectiveness of the proposed detection scheme

  19. Rapid Isolation and Molecular Detection of Streptomycin-Producing Streptomycetes

    Directory of Open Access Journals (Sweden)

    M Motovali-bashi

    2006-07-01

    Full Text Available Introduction: Streptomyces species are mycelial, aerobic gram-positive bacteria that are isolated from soil and produce a diverse range of antibiotics. Streptomyces griseus produces the antibiotic, streptomycin and forms spores even in a liquid culture. The gene cluster for the production of Streptomycin antibiotic contains strR gene that encodes StrR, a pathway-specific regulator. Then, this pathway-specific regulator induces transcription of other streptomycin production genes in the gene cluster. The overall aim of this work was rapid isolation and molecular detection of streptomycin-producing Streptomycetes, especially S. griseus, from Iranian soils in order to manipulate them for increased production of streptomycin. Methods: This research used new initiative half-specific medium for isolation of Streptomycetes from natural environments, called FZmsn. The fifty colonies of Streptomyces strains grown on the surface of FZmsn medium isolated from environmental samples were defined on the basis of their morphological characteristics and light microscope studies. A set of primers was designed to detect strR by OLIGO software. Results: In colony-PCR reactions followed by gel electrophoresis, 6 colonies from Streptomyces strains colonies were detected as S. griseus colonies. Conclusion: These native Streptomyces strains will be used for genetic manipulation of S. griseus in order to increase production levels of streptomycin.

  20. Rapid detection of human fecal Eubacterium species and related genera by nested PCR method.

    Science.gov (United States)

    Kageyama, A; Benno, Y

    2001-01-01

    PCR procedures based on 16S rDNA gene sequence specific for seven Eubacterium spp. and Eggerthella lenta that predominate in the human intestinal tract were developed, and used for direct detection of these species in seven human feces samples. Three species of Eggerthella lenta, Eubacterium rectale, and Eubacterium eligens were detected from seven fecal samples. Eubacterium biforme was detected from six samples. It was reported that E. rectale, E. eligens, and E. biforme were difficult to detect by traditional culture method, but the nested PCR method is available for the detection of these species. This result shows that the nested PCR method utilizing a universal primer pair, followed by amplification with species-specific primers, would allow rapid detection of Eubacterium species in human feces.

  1. A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae

    Directory of Open Access Journals (Sweden)

    Farkhondeh Saba

    2017-01-01

    Full Text Available Background:  Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR. Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Methods:  According to our results, amplification of various genomic regions including SSU, LSU, ITS, β-tubulin, actin, RPB2, and EF-1 resulted in a reproducible and efficient DNA extraction from a wide range of microorganisms yielding adequate pure genomic material for reproducible PCR-amplifications. Results:   This method relies on a temporary shock of increased concentrations of detergent which can be applied concomitant with multiple freeze-thaws to yield sufficient amount of DNA for PCR amplification of multiple or single fragments(s of the genome. As an advantage, the recipe seems very flexible, thus, various optional steps can be included depending on the samples used.Conclusion:   Having the needed flexibility in each step, this protocol is applicable on a very wide range of samples. Hence, various steps can be included depending on the desired quantity and quality.

  2. A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae

    Directory of Open Access Journals (Sweden)

    Farkhondeh Saba

    2016-09-01

    Full Text Available Background:  Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR. Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Methods:  According to our results, amplification of various genomic regions including SSU, LSU, ITS, β-tubulin, actin, RPB2, and EF-1 resulted in a reproducible and efficient DNA extraction from a wide range of microorganisms yielding adequate pure genomic material for reproducible PCR-amplifications. Results:   This method relies on a temporary shock of increased concentrations of detergent which can be applied concomitant with multiple freeze-thaws to yield sufficient amount of DNA for PCR amplification of multiple or single fragments(s of the genome. As an advantage, the recipe seems very flexible, thus, various optional steps can be included depending on the samples used.Conclusion:   Having the needed flexibility in each step, this protocol is applicable on a very wide range of samples. Hence, various steps can be included depending on the desired quantity and quality.

  3. Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak.

    Science.gov (United States)

    Pec, Gregory J; Karst, Justine; Taylor, D Lee; Cigan, Paul W; Erbilgin, Nadir; Cooke, Janice E K; Simard, Suzanne W; Cahill, James F

    2017-01-01

    Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  4. Rapid Detection of Salmonella in Food and Beverage Samples by Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Radji, M.

    2010-01-01

    Full Text Available Polymerase chain reaction (PCR assay had been used to detect Salmonella in food and beverage samples using suitable primers which are based on specific invA gene of Salmonella. Twenty nine samples were collected from street food counters and some canteens in Margonda Street, Depok, West Java, Indonesia. It was found that five of twenty nine samples were detected to contain Salmonella and showed the presence of the amplified product of the size 244 bp. The method of PCR demonstrated the specificity of invA primers for detection of Salmonella as confirmed by biochemical and serological assay. The results of this study revealed that PCR was a rapid and useful tool for detection of Salmonella in food and beverage samples.

  5. Original Article. Evaluation of Rapid Detection of Nasopharyngeal Colonization with MRSA by Real-Time PCR

    Directory of Open Access Journals (Sweden)

    Kang Feng-feng

    2012-03-01

    Full Text Available Objective To investigate the clinical application of Real-Time PCR for rapid detection of methicillin-resistant Staphylococcus aureus (MRSA directly from nasopharyngeal swab specimens.

  6. Rapid detection of MERS coronavirus-like viruses in bats: pote1ntial for tracking MERS coronavirus transmission and animal origin.

    Science.gov (United States)

    Woo, Patrick C Y; Lau, Susanna K P; Chen, Yixin; Wong, Emily Y M; Chan, Kwok-Hung; Chen, Honglin; Zhang, Libiao; Xia, Ningshao; Yuen, Kwok-Yung

    2018-03-07

    Recently, we developed a monoclonal antibody-based rapid nucleocapsid protein detection assay for diagnosis of MERS coronavirus (MERS-CoV) in humans and dromedary camels. In this study, we examined the usefulness of this assay to detect other lineage C betacoronaviruses closely related to MERS-CoV in bats. The rapid MERS-CoV nucleocapsid protein detection assay was tested positive in 24 (88.9%) of 27 Tylonycteris bat CoV HKU4 (Ty-BatCoV-HKU4) RNA-positive alimentary samples of Tylonycteris pachypus and 4 (19.0%) of 21 Pipistrellus bat CoV HKU5 (Pi-BatCoV-HKU5) RNA-positive alimentary samples of Pipistrellus abramus. There was significantly more Ty-BatCoV-HKU4 RNA-positive alimentary samples than Pi-BatCoV-HKU5 RNA-positive alimentary samples that were tested positive by the rapid MERS-CoV nucleocapsid protein detection assay (P < 0.001 by Chi-square test). The rapid assay was tested negative in all 51 alimentary samples RNA-positive for alphacoronaviruses (Rhinolophus bat CoV HKU2, Myotis bat CoV HKU6, Miniopterus bat CoV HKU8 and Hipposideros batCoV HKU10) and 32 alimentary samples positive for lineage B (SARS-related Rhinolophus bat CoV HKU3) and lineage D (Rousettus bat CoV HKU9) betacoronaviruses. No significant difference was observed between the viral loads of Ty-BatCoV-HKU4/Pi-BatCoV-HKU5 RNA-positive alimentary samples that were tested positive and negative by the rapid test (Mann-Witney U test). The rapid MERS-CoV nucleocapsid protein detection assay is able to rapidly detect lineage C betacoronaviruses in bats. It detected significantly more Ty-BatCoV-HKU4 than Pi-BatCoV-HKU5 because MERS-CoV is more closely related to Ty-BatCoV-HKU4 than Pi-BatCoV-HKU5. This assay will facilitate rapid on-site mass screening of animal samples for ancestors of MERS-CoV and tracking transmission in the related bat species.

  7. A real-time loop-mediated isothermal amplification assay for rapid detection of Shigella species.

    Science.gov (United States)

    Liew, P S; Teh, C S J; Lau, Y L; Thong, K L

    2014-12-01

    Shigellosis is a foodborne illness caused by the genus Shigella and is an important global health issue. The development of effective techniques for rapid detection of this pathogen is essential for breaking the chain of transmission. Therefore, we have developed a novel loop-mediated isothermal amplification (LAMP) assay targeting the invasion plasmid antigen H (ipaH) gene to rapidly detect Shigella species. This assay could be performed in 90 min at an optimal temperature of 64ºC, with endpoint results visualized directly. Notably, the method was found to be more sensitive than conventional PCR. Indeed, the detection limit for the LAMP assay on pure bacterial cultures was 5.9 x 10(5) CFU/ml, while PCR displayed a limit of 5.9 x 10(7) CFU/ml. In spiked lettuce samples, the sensitivity of the LAMP assay was 3.6 x 10(4) CFU/g, whereas PCR was 3.6 x 10(5) CFU/g. Overall, the assay accurately identified 32 Shigella spp. with one enteroinvasive Escherichia coli displaying positive reaction while the remaining 32 non-Shigella strains tested were negative.

  8. Rapid and label-free detection of protein a by aptamer-tethered porous silicon nanostructures.

    Science.gov (United States)

    Urmann, Katharina; Reich, Peggy; Walter, Johanna-Gabriela; Beckmann, Dieter; Segal, Ester; Scheper, Thomas

    2017-09-10

    Protein A, which is secreted by and displayed on the cell membrane of Staphylococcus aureus is an important biomarker for S. aureus. Thus, its rapid and specific detection may facilitate the pathogen identification and initiation of proper treatment. Herein, we present a simple, label-free and rapid optical biosensor enabling specific detection of protein A. Protein A-binding aptamer serves as the capture probe and is immobilized onto a nanostructured porous silicon thin film, which serves as the optical transducer element. We demonstrate high sensitivity of the biosensor with a linear detection range between 8 and 23μM. The apparent dissociation constant was determined as 13.98μM and the LoD is 3.17μM. Harnessing the affinity between protein A and antibodies, a sandwich assay format was developed to amplify the optical signal associated with protein A capture by the aptamer. Using this approach, we increase the sensitivity of the biosensor, resulting in a three times lower LoD. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Filamentous Growth in Eremothecium Fungi

    DEFF Research Database (Denmark)

    Oskarsson, Therese

    , this thesis deals with some of the aspects of hyphal growth, which is an important virulence factor for pathogenic fungi infecting both humans and plants. Hyphal establishment through continuous polar growth is a complex process, requiring the careful coordination of a large subset of proteins involved......-regulatory activity of AgGts1, the protein could have additional actin organizing properties. In the second and third part, this thesis addresses the use of A. gossypii and its relative E. cymbalariae as model organisms for filamentous growth. A series of assays analyzed the capability of Eremothecium genus fungi...... of molecular tools for E. cymbalariae to enable a faster and more efficient approach for genetic comparisons between Eremothecium genus fungi....

  10. Rapid capacitive detection of femtomolar levels of bisphenol A using an aptamer-modified disposable microelectrode array

    International Nuclear Information System (INIS)

    Cui, Haochen; Wu, Jayne; Eda, Shigetoshi; Chen, Jiangang; Chen, Wei; Zheng, Lei

    2015-01-01

    A label-free and single-step method is reported for rapid and highly sensitive detection of bisphenol A (BPA) in aqueous samples. It utilizes an aptamer acting as a probe molecule immobilized on a commercially available array of interdigitated aluminum microelectrodes. BPA was quantified by measuring the interfacial capacitance change rate caused by the specific binding between bisphenol A and the immobilized aptamer. The AC signal also induces an AC electrokinetic effect to generate microfluidic motion for enhanced binding. The capacitive aptasensor achieves a limit of detection as low as 10 fM(2.8 fg ⋅ mL −1 ) with a 20 s response time. The method is inexpensive, highly sensitive, rapid and therefore provides a promising technology for on-site detection of BPA in food and water samples. (author)

  11. Heteroresistance and fungi.

    Science.gov (United States)

    Ferreira, Gabriella F; Santos, Daniel A

    2017-09-01

    The concept of heteroresistance refers to the heterogeneous susceptibility to an antimicrobial drug in a microorganism population, meaning that some clones may be resistant and others are susceptible. This phenomenon has been widely studied in bacteria, but little attention has been given to its expression in fungi. We review the available literature on heteroresistance in fungi and invite the reader to recognise this phenomenon as a fungal mechanism to adapt to environmental stress, which may interfere both in resistance and virulence. Finally, heteroresistance may explain the treatment failures to eradicate mycosis in some patients treated with a seemingly appropriate antifungal. © 2017 Blackwell Verlag GmbH.

  12. Rapid detection of TiO2 (E171) in table sugar using Raman spectroscopy.

    Science.gov (United States)

    Tan, Chen; Zhao, Bin; Zhang, Zhiyun; He, Lili

    2017-02-01

    The potential toxic effects of titanium dioxide (TiO 2 ) to humans remain debatable despite its broad application as a food additive. Thus, confirmation of the existence of TiO 2 particles in food matrices and subsequently quantifying them are becoming increasingly critical. This study developed a facile, rapid (E171) from food products (e.g., table sugar) by Raman spectroscopy. To detect TiO 2 particles from sugar solution, sequential centrifugation and washing procedures were effectively applied to separate and recover 97% of TiO 2 particles from the sugar solution. The peak intensity of TiO 2 sensitively responded to the concentration of TiO 2 with a limit of detection (LOD) of 0.073 mg kg -1 . In the case of sugar granules, a mapping technique was applied to directly estimate the level of TiO 2 , which can be potentially used for rapid online monitoring. The plot of averaged intensity to TiO 2 concentration in the sugar granules exhibited a good linear relationship in the wide range of 5-2000 mg kg -1 , with an LOD of 8.46 mg kg -1 . Additionally, we applied Raman spectroscopy to prove the presence of TiO 2 in sugar-coated doughnuts. This study begins to fill in the analytical gaps that exist regarding the rapid detection and quantification of TiO 2 in food, which facilitate the risk assessment of TiO 2 through food exposure.

  13. Rapid Discovery and Functional Characterization of Terpene Synthases from Four Endophytic Xylariaceae.

    Directory of Open Access Journals (Sweden)

    Weihua Wu

    Full Text Available Endophytic fungi are ubiquitous plant endosymbionts that establish complex and poorly understood relationships with their host organisms. Many endophytic fungi are known to produce a wide spectrum of volatile organic compounds (VOCs with potential energy applications, which have been described as "mycodiesel". Many of these mycodiesel hydrocarbons are terpenes, a chemically diverse class of compounds produced by many plants, fungi, and bacteria. Due to their high energy densities, terpenes, such as pinene and bisabolene, are actively being investigated as potential "drop-in" biofuels for replacing diesel and aviation fuel. In this study, we rapidly discovered and characterized 26 terpene synthases (TPSs derived from four endophytic fungi known to produce mycodiesel hydrocarbons. The TPS genes were expressed in an E. coli strain harboring a heterologous mevalonate pathway designed to enhance terpene production, and their product profiles were determined using Solid Phase Micro-Extraction (SPME and GC-MS. Out of the 26 TPS's profiled, 12 TPS's were functional, with the majority of them exhibiting both monoterpene and sesquiterpene synthase activity.

  14. Rapid eye movement sleep behavior disorder as an outlier detection problem

    DEFF Research Database (Denmark)

    Kempfner, Jacob; Sørensen, Gertrud Laura; Nikolic, M.

    2014-01-01

    OBJECTIVE: Idiopathic rapid eye movement (REM) sleep behavior disorder is a strong early marker of Parkinson's disease and is characterized by REM sleep without atonia and/or dream enactment. Because these measures are subject to individual interpretation, there is consequently need...... for quantitative methods to establish objective criteria. This study proposes a semiautomatic algorithm for the early detection of Parkinson's disease. This is achieved by distinguishing between normal REM sleep and REM sleep without atonia by considering muscle activity as an outlier detection problem. METHODS......: Sixteen healthy control subjects, 16 subjects with idiopathic REM sleep behavior disorder, and 16 subjects with periodic limb movement disorder were enrolled. Different combinations of five surface electromyographic channels, including the EOG, were tested. A muscle activity score was automatically...

  15. Rapid detection of pandemic influenza in the presence of seasonal influenza

    Directory of Open Access Journals (Sweden)

    Robertson Chris

    2010-11-01

    Full Text Available Abstract Background Key to the control of pandemic influenza are surveillance systems that raise alarms rapidly and sensitively. In addition, they must minimise false alarms during a normal influenza season. We develop a method that uses historical syndromic influenza data from the existing surveillance system 'SERVIS' (Scottish Enhanced Respiratory Virus Infection Surveillance for influenza-like illness (ILI in Scotland. Methods We develop an algorithm based on the weekly case ratio (WCR of reported ILI cases to generate an alarm for pandemic influenza. From the seasonal influenza data from 13 Scottish health boards, we estimate the joint probability distribution of the country-level WCR and the number of health boards showing synchronous increases in reported influenza cases over the previous week. Pandemic cases are sampled with various case reporting rates from simulated pandemic influenza infections and overlaid with seasonal SERVIS data from 2001 to 2007. Using this combined time series we test our method for speed of detection, sensitivity and specificity. Also, the 2008-09 SERVIS ILI cases are used for testing detection performances of the three methods with a real pandemic data. Results We compare our method, based on our simulation study, to the moving-average Cumulative Sums (Mov-Avg Cusum and ILI rate threshold methods and find it to be more sensitive and rapid. For 1% case reporting and detection specificity of 95%, our method is 100% sensitive and has median detection time (MDT of 4 weeks while the Mov-Avg Cusum and ILI rate threshold methods are, respectively, 97% and 100% sensitive with MDT of 5 weeks. At 99% specificity, our method remains 100% sensitive with MDT of 5 weeks. Although the threshold method maintains its sensitivity of 100% with MDT of 5 weeks, sensitivity of Mov-Avg Cusum declines to 92% with increased MDT of 6 weeks. For a two-fold decrease in the case reporting rate (0.5% and 99% specificity, the WCR and

  16. Mini-column assay for rapid detection of malachite green in fish.

    Science.gov (United States)

    Shalaby, Ali R; Emam, Wafaa H; Anwar, Mervat M

    2017-07-01

    A simple, rapid and economical mini-column method for detecting malachite green (MG) residue in fish was developed. The method used a column with 2mm ID that was tightly packed with silica gel followed by alumina. Detection of MG was performed by viewing the developed mini-column at visible light by naked eye; where MG was seen as compact green band at the confluence of the silica gel layer with alumina layer. The limit of detection of the assay was 2ng which conform the minimum required performance limit (MRPL). Evaluation utility of the method indicated that all blank and spiked samples at levels below MRPL were assessed as accepted. The intensity of the green band increased whenever MG level in the extract increased; indicated that suggested mini-column technique could be used for semi-quantitative determination of MG in fish samples. The method can be used to select the questionable samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Facile preparation of a DNA sensor for rapid herpes virus detection

    Energy Technology Data Exchange (ETDEWEB)

    Tam, Phuong Dinh, E-mail: tampd-hast@mail.hut.edu.vn [Hanoi Advanced School of Science and Technology, Hanoi University of Technology (Viet Nam); Tuan, Mai Anh, E-mail: tuanma-itims@mail.hut.edu.vn [International Training Institute for Materials Science, Hanoi University of Technology (Viet Nam); Huy, Tran Quang [National Institute of Hygiene and Epidemiology (NIHE), 01 Yersin, Hai Ba Trung District, Hanoi (Viet Nam); Le, Anh-Tuan [Hanoi Advanced School of Science and Technology, Hanoi University of Technology (Viet Nam); Hieu, Nguyen Van, E-mail: hieu@itims.edu.vn [International Training Institute for Materials Science, Hanoi University of Technology (Viet Nam)

    2010-10-12

    In this paper, a simple DNA sensor platform was developed for rapid herpes virus detection in real samples. The deoxyribonucleic acid (DNA) sequences of the herpes simplex virus (DNA probe) were directly immobilized on the surface of interdigitated electrodes by electrochemical polymerization along with pyrrole monomers. The potential was scanned from - 0.7 to + 0.6 V, and the scanning rate was 100 mV/s. Fourier transform infrared spectroscopy was employed to verify specific DNA sequence binding and the conducting polymer. The morphology of the conducting polymer doped with DNA strands was characterized using a field emission scanning electron microscope. As-obtained DNA sensor was used to detect the herpes virus DNA in the real samples. The results show that the current DNA sensors detected the lowest DNA concentration of 2 nM. This sensitivity appears to be better than that of the DNA sensors prepared by immobilization of the DNA probe on the 3-aminopropyl-triethoxy-silance (APTS) membrane.

  18. Facile preparation of a DNA sensor for rapid herpes virus detection

    International Nuclear Information System (INIS)

    Tam, Phuong Dinh; Tuan, Mai Anh; Huy, Tran Quang; Le, Anh-Tuan; Hieu, Nguyen Van

    2010-01-01

    In this paper, a simple DNA sensor platform was developed for rapid herpes virus detection in real samples. The deoxyribonucleic acid (DNA) sequences of the herpes simplex virus (DNA probe) were directly immobilized on the surface of interdigitated electrodes by electrochemical polymerization along with pyrrole monomers. The potential was scanned from - 0.7 to + 0.6 V, and the scanning rate was 100 mV/s. Fourier transform infrared spectroscopy was employed to verify specific DNA sequence binding and the conducting polymer. The morphology of the conducting polymer doped with DNA strands was characterized using a field emission scanning electron microscope. As-obtained DNA sensor was used to detect the herpes virus DNA in the real samples. The results show that the current DNA sensors detected the lowest DNA concentration of 2 nM. This sensitivity appears to be better than that of the DNA sensors prepared by immobilization of the DNA probe on the 3-aminopropyl-triethoxy-silance (APTS) membrane.

  19. A reassessment of the risk of rust fungi developing resistance to fungicides.

    Science.gov (United States)

    Oliver, Richard P

    2014-11-01

    Rust fungi are major pathogens of many annual and perennial crops. Crop protection is largely based on genetic and chemical control. Fungicide resistance is a significant issue that has affected many crop pathogens. Some pathogens have rapidly developed resistance and hence are regarded as high-risk species. Rust fungi have been classified as being low risk, in spite of sharing many relevant features with high-risk pathogens. An examination of the evidence suggests that rust fungi may be wrongly classified as low risk. Of the nine classes of fungicide to which resistance has developed, six are inactive against rusts. The three remaining classes are quinone outside inhibitors (QoIs), demethylation inhibitors (DMIs) and succinate dehydrogenase inhibitors (SDHIs). QoIs have been protected by a recently discovered intron that renders resistant mutants unviable. Low levels of resistance have developed to DMIs, but with limited field significance. Older SDHI fungicides were inactive against rusts. Some of the SDHIs introduced since 2003 are active against rusts, so it may be that insufficient time has elapsed for resistance to develop, especially as SDHIs are generally sold in mixtures with other actives. It would therefore seem prudent to increase the level of vigilance for possible cases of resistance to established and new fungicides in rusts. © 2014 Society of Chemical Industry.

  20. Automated and unbiased classification of chemical profiles from fungi using high performance liquid chromatography

    DEFF Research Database (Denmark)

    Hansen, Michael Edberg; Andersen, Birgitte; Smedsgaard, Jørn

    2005-01-01

    In this paper we present a method for unbiased/unsupervised classification and identification of closely related fungi, using chemical analysis of secondary metabolite profiles created by HPLC with UV diode array detection. For two chromatographic data matrices a vector of locally aligned full sp...

  1. Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions.

    Science.gov (United States)

    Mello, Antonietta; Balestrini, Raffaella

    2018-01-01

    The roots of most terrestrial plants are colonized by mycorrhizal fungi. They play a key role in terrestrial environments influencing soil structure and ecosystem functionality. Around them a peculiar region, the mycorrhizosphere, develops. This is a very dynamic environment where plants, soil and microorganisms interact. Interest in this fascinating environment has increased over the years. For a long period the knowledge of the microbial populations in the rhizosphere has been limited, because they have always been studied by traditional culture-based techniques. These methods, which only allow the study of cultured microorganisms, do not allow the characterization of most organisms existing in nature. The introduction in the last few years of methodologies that are independent of culture techniques has bypassed this limitation. This together with the development of high-throughput molecular tools has given new insights into the biology, evolution, and biodiversity of mycorrhizal associations, as well as, the molecular dialog between plants and fungi. The genomes of many mycorrhizal fungal species have been sequenced so far allowing to better understanding the lifestyle of these fungi, their sexual reproduction modalities and metabolic functions. The possibility to detect the mycelium and the mycorrhizae of heterothallic fungi has also allowed to follow the spatial and temporal distributional patterns of strains of different mating types. On the other hand, the availability of the genome sequencing from several mycorrhizal fungi with a different lifestyle, or belonging to different groups, allowed to verify the common feature of the mycorrhizal symbiosis as well as the differences on how different mycorrhizal species interact and dialog with the plant. Here, we will consider the aspects described before, mainly focusing on ectomycorrhizal fungi and their interactions with plants and other soil microorganisms.

  2. Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions

    Directory of Open Access Journals (Sweden)

    Antonietta Mello

    2018-02-01

    Full Text Available The roots of most terrestrial plants are colonized by mycorrhizal fungi. They play a key role in terrestrial environments influencing soil structure and ecosystem functionality. Around them a peculiar region, the mycorrhizosphere, develops. This is a very dynamic environment where plants, soil and microorganisms interact. Interest in this fascinating environment has increased over the years. For a long period the knowledge of the microbial populations in the rhizosphere has been limited, because they have always been studied by traditional culture-based techniques. These methods, which only allow the study of cultured microorganisms, do not allow the characterization of most organisms existing in nature. The introduction in the last few years of methodologies that are independent of culture techniques has bypassed this limitation. This together with the development of high-throughput molecular tools has given new insights into the biology, evolution, and biodiversity of mycorrhizal associations, as well as, the molecular dialog between plants and fungi. The genomes of many mycorrhizal fungal species have been sequenced so far allowing to better understanding the lifestyle of these fungi, their sexual reproduction modalities and metabolic functions. The possibility to detect the mycelium and the mycorrhizae of heterothallic fungi has also allowed to follow the spatial and temporal distributional patterns of strains of different mating types. On the other hand, the availability of the genome sequencing from several mycorrhizal fungi with a different lifestyle, or belonging to different groups, allowed to verify the common feature of the mycorrhizal symbiosis as well as the differences on how different mycorrhizal species interact and dialog with the plant. Here, we will consider the aspects described before, mainly focusing on ectomycorrhizal fungi and their interactions with plants and other soil microorganisms.

  3. Studies on certain aspects of seed-borne fungi. VI. Fungi associated with different cultivars of wheat (Triticum aestivum L.)

    OpenAIRE

    K. K. Pandey

    2014-01-01

    Fungi associated with eight cultivars of wheat have been investigated. Twenty seven species were isolated from external and internal surface of all the wheat (Triticum aestivum L.) cultivars respectively. Out of five dominant and subdominant fungi anly Aspergillus terreus and Alternaria tenuis were able to colonize internally. The culture filtrates of test fungi reduced the germination of all wheat varieties up to different degrees.

  4. Spatial segregation and aggregation of ectomycorrhizal and root-endophytic fungi in the seedlings of two Quercus species.

    Directory of Open Access Journals (Sweden)

    Satoshi Yamamoto

    Full Text Available Diverse clades of mycorrhizal and endophytic fungi are potentially involved in competitive or facilitative interactions within host-plant roots. We investigated the potential consequences of these ecological interactions on the assembly process of root-associated fungi by examining the co-occurrence of pairs of fungi in host-plant individuals. Based on massively-parallel pyrosequencing, we analyzed the root-associated fungal community composition for each of the 249 Quercus serrata and 188 Quercus glauca seedlings sampled in a warm-temperate secondary forest in Japan. Pairs of fungi that co-occurred more or less often than expected by chance were identified based on randomization tests. The pyrosequencing analysis revealed that not only ectomycorrhizal fungi but also endophytic fungi were common in the root-associated fungal community. Intriguingly, specific pairs of these ectomycorrhizal and endophytic fungi showed spatially aggregated patterns, suggesting the existence of facilitative interactions between fungi in different functional groups. Due to the large number of fungal pairs examined, many of the observed aggregated/segregated patterns with very low P values (e.g., < 0.005 turned non-significant after the application of a multiple comparison method. However, our overall results imply that the community structures of ectomycorrhizal and endophytic fungi could influence each other through interspecific competitive/facilitative interactions in root. To test the potential of host-plants' control of fungus-fungus ecological interactions in roots, we further examined whether the aggregated/segregated patterns could vary depending on the identity of host plant species. Potentially due to the physiological properties shared between the congeneric host plant species, the sign of hosts' control was not detected in the present study. The pyrosequencing-based randomization analyses shown in this study provide a platform of the high

  5. Potential Antiviral Agents from Marine Fungi: An Overview

    Directory of Open Access Journals (Sweden)

    Soheil Zorofchian Moghadamtousi

    2015-07-01

    Full Text Available Biodiversity of the marine world is only partially subjected to detailed scientific scrutiny in comparison to terrestrial life. Life in the marine world depends heavily on marine fungi scavenging the oceans of lifeless plants and animals and entering them into the nutrient cycle by. Approximately 150 to 200 new compounds, including alkaloids, sesquiterpenes, polyketides, and aromatic compounds, are identified from marine fungi annually. In recent years, numerous investigations demonstrated the tremendous potential of marine fungi as a promising source to develop new antivirals against different important viruses, including herpes simplex viruses, the human immunodeficiency virus, and the influenza virus. Various genera of marine fungi such as Aspergillus, Penicillium, Cladosporium, and Fusarium were subjected to compound isolation and antiviral studies, which led to an illustration of the strong antiviral activity of a variety of marine fungi-derived compounds. The present review strives to summarize all available knowledge on active compounds isolated from marine fungi with antiviral activity.

  6. Marine Fungi: A Source of Potential Anticancer Compounds

    Directory of Open Access Journals (Sweden)

    Sunil K. Deshmukh

    2018-01-01

    Full Text Available Metabolites from marine fungi have hogged the limelight in drug discovery because of their promise as therapeutic agents. A number of metabolites related to marine fungi have been discovered from various sources which are known to possess a range of activities as antibacterial, antiviral and anticancer agents. Although, over a thousand marine fungi based metabolites have already been reported, none of them have reached the market yet which could partly be related to non-comprehensive screening approaches and lack of sustained lead optimization. The origin of these marine fungal metabolites is varied as their habitats have been reported from various sources such as sponge, algae, mangrove derived fungi, and fungi from bottom sediments. The importance of these natural compounds is based on their cytotoxicity and related activities that emanate from the diversity in their chemical structures and functional groups present on them. This review covers the majority of anticancer compounds isolated from marine fungi during 2012–2016 against specific cancer cell lines.

  7. Thermophilic fungi in the new age of fungal taxonomy.

    Science.gov (United States)

    de Oliveira, Tássio Brito; Gomes, Eleni; Rodrigues, Andre

    2015-01-01

    Thermophilic fungi are of wide interest due to their potential to produce heat-tolerant enzymes for biotechnological processes. However, the taxonomy of such organisms remains obscure, especially given new developments in the nomenclature of fungi. Here, we examine the taxonomy of the thermophilic fungi most commonly used in industry in light of the recent taxonomic changes following the adoption of the International Code of Nomenclature for Algae, Fungi and Plants and also based on the movement One Fungus = One Name. Despite the widespread use of these fungi in applied research, several thermotolerant fungi still remain classified as thermophiles. Furthermore, we found that while some thermophilic fungi have had their genomes sequenced, many taxa still do not have barcode sequences of reference strains available in public databases. This lack of basic information is a limiting factor for the species identification of thermophilic fungi and for metagenomic studies in this field. Based on next-generation sequencing, such studies generate large amounts of data, which may reveal new species of thermophilic fungi in different substrates (composting systems, geothermal areas, piles of plant material). As discussed in this study, there are intrinsic problems associated with this method, considering the actual state of the taxonomy of thermophilic fungi. To overcome such difficulties, the taxonomic classification of this group should move towards standardizing the commonly used species names in industry and to assess the possibility of including new systems for describing species based on environmental sequences.

  8. Rapid detection of methicillin-resistant Staphylococcus aureus directly from clinical samples: methods, effectiveness and cost considerations

    Directory of Open Access Journals (Sweden)

    Stürenburg, Enno

    2009-07-01

    Full Text Available Methicillin-resistant Staphylococcus aureus (MRSA isolates is a serious public health problem whose ever-increasing rate is commensurate with the pressure it is exerting on the healthcare system. At present, more than 20% of clinical S. aureus isolates in German hospitals are methicillin resistant. Strategies from low-prevalence countries show that this development is not necessarily inevitable. In the Scandinavian countries and the Netherlands, thanks to a rigorous prevention programme, MRSA prevalence has been kept at an acceptably low level (<1–3%. Central to these ‘search and destroy’ control strategies is an admission screening using several MRSA swabs taken from mucocutaneous colonisation sites of high-risk patients (‘MRSA surveillance’. It has also been reported that the speed with which MRSA carriage is detected has an important role to play, as it is a key component of any effective strategy to prevent the pathogen from spreading. Since MRSA culturing involves a 2–3 day delay before the final results are available, rapid detection techniques (commonly referred to as ‘MRSA rapid tests’ using PCR methods and, most recently, rapid culturing methods have been developed. The implementation of rapid tests reduces the time of detection of MRSA carriers from 48–72 to 2–5 h. Clinical evaluation data have shown that MRSA can thus be detected with very high sensitivity. Specificity however is sometimes impaired due to false-positive PCR signals occurring in mixed flora specimens. In order to rule out any false-positive PCR results, a culture screen must always be carried out simultaneously.The data provide preliminary evidence that a PCR assay can reduce nosocomial MRSA transmission in high-risk patients or high-risk areas, whereas an approach that screens all patients admitted to the hospital is probably not effective. Information concerning the cost-effectiveness of rapid MRSA tests is still sparse and thus the issue remains

  9. Heterologous expression of cellobiohydrolases in filamentous fungi

    DEFF Research Database (Denmark)

    Zoglowek, Marta; Lübeck, Peter S.; Ahring, Birgitte K.

    2015-01-01

    Cellobiohydrolases are among the most important enzymes functioning in the hydrolysis of crystalline cellulose, significantly contributing to the efficient biorefining of recalcitrant lignocellulosic biomass into biofuels and bio-based products. Filamentous fungi are recognized as both well...... into valuable products. However, due to low cellobiohydrolase activities, certain fungi might be deficient with regard to enzymes of value for cellulose conversion, and improving cellobiohydrolase expression in filamentous fungi has proven to be challenging. In this review, we examine the effects of altering...... promoters, signal peptides, culture conditions and host post-translational modifications. For heterologous cellobiohydrolase production in filamentous fungi to become an industrially feasible process, the construction of site-integrating plasmids, development of protease-deficient strains and glycosylation...

  10. Distribution of ectomycorrhizal and pathogenic fungi in soil along a vegetational change from Japanese black pine (Pinus thunbergii) to black locust (Robinia pseudoacacia).

    Science.gov (United States)

    Taniguchi, Takeshi; Kataoka, Ryota; Tamai, Shigenobu; Yamanaka, Norikazu; Futai, Kazuyoshi

    2009-04-01

    The nitrogen-fixing tree black locust (Robinia pseudoacacia L.) seems to affect ectomycorrhizal (ECM) colonization and disease severity of Japanese black pine (Pinus thunbergii Parl.) seedlings. We examined the effect of black locust on the distribution of ECM and pathogenic fungi in soil. DNA was extracted from soil at depths of 0-5 and 5-10 cm, collected from the border between a Japanese black pine- and a black locust-dominated forest, and the distribution of these fungi was investigated by denaturing gradient gel electrophoresis. The effect of soil nutrition and pH on fungal distribution was also examined. Tomentella sp. 1 and Tomentella sp. 2 were not detected from some subplots in the Japanese black pine-dominated forest. Ectomycorrhizas formed by Tomentella spp. were dominant in black locust-dominated subplots and very little in the Japanese black pine-dominated forest. Therefore, the distribution may be influenced by the distribution of inoculum potential, although we could not detect significant relationships between the distribution of Tomentella spp. on pine seedlings and in soils. The other ECM fungi were detected in soils in subplots where the ECM fungi was not detected on pine seedlings, and there was no significant correlation between the distribution of the ECM fungi on pine seedlings and in soils. Therefore, inoculum potential seemed to not always influence the ECM community on roots. The distribution of Lactarius quieticolor and Tomentella sp. 2 in soil at a depth of 0-5 cm positively correlated with soil phosphate (soil P) and that of Tomentella sp. 2 also positively correlated with soil nitrogen (soil N). These results suggest the possibility that the distribution of inoculum potential of the ECM fungi was affected by soil N and soil P. Although the mortality of the pine seedlings was higher in the black locust-dominated area than in the Japanese black pine-dominated area, a pathogenic fungus of pine seedlings, Cylindrocladium pacificum, was

  11. Distinguishing ectomycorrhizal and saprophytic fungi using carbon and nitrogen isotopic compositions

    Directory of Open Access Journals (Sweden)

    Weiguo Hou

    2012-05-01

    Full Text Available Ectomycorrhizal fungi, a group of widespread symbiotic fungi with plant, obtain carbon source from trees and improve plant mineral nutrient uptake with their widespread hyphal network. Ectomycorrhizal fungi can be used as inoculants to improve the survival rates of plantation. Saprophytic fungi use the nutrition from the debris of plant or animals, and it is difficult to distinguish the saprophytic and ectomycorrhizal fungi by morphological and anatomic methods. In this research, the differences of stable carbon and nitrogen isotopic compositions of these fungi were analyzed. The results showed that the abundances of 13C of were higher than those of ectomycorrhizal fungi and the abundances of 15N of saprophytic fungi were lower than those of ectomycorrhizal fungi. Such differences of stable carbon and nitrogen isotopic compositions between ectomycorrhizal fungi and saprophytic fungi can be ascribed to their different nutrition sources and ecological functions. These results collectively indicate that stable carbon and nitrogen isotopic compositions are an effective proxy for distinguishing between ectomycorrhizal and saprophytic fungi.

  12. Common wood decay fungi found in the Caribbean Basin

    Science.gov (United States)

    D. Jean. Lodge

    2016-01-01

    There are hundreds of wood-decay fungi in the Caribbean Basin, but relatively few of these are likely to grow on manmade structures built of wood or wood-composites. The wood-decay fungi of greatest concern are those that cause brown-rot, and especially brown-rot fungi that are resistant to copper-based wood preservatives. Some fungi that grow in the Caribbean and...

  13. Rapid and sensitive detection of malachite green in aquaculture water by electrochemical preconcentration and surface-enhanced Raman scattering.

    Science.gov (United States)

    Xu, Kai-Xuan; Guo, Mei-Hong; Huang, Yu-Ping; Li, Xiao-Dong; Sun, Jian-Jun

    2018-04-01

    A highly sensitive and rapid method of in-situ surface-enhanced Raman spectroscopy (SERS) combining with electrochemical preconcentration (EP) in detecting malachite green (MG) in aquaculture water was established. Ag nanoparticles (AgNPs) were synthesized and spread onto the surface of gold electrodes after centrifuging to produce SERS-active substrates. After optimizing the pH values, preconcentration potentials and times, in-situ EP-SERS detection was carried out. A sensitive and rapid analysis of the low-concentration MG was accomplished within 200s and the limit of detection was 2.4 × 10 -16 M. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Genome Studies on Nematophagous and Entomogenous Fungi in China

    Science.gov (United States)

    Zhang, Weiwei; Cheng, Xiaoli; Liu, Xingzhong; Xiang, Meichun

    2016-01-01

    The nematophagous and entomogenous fungi are natural enemies of nematodes and insects and have been utilized by humans to control agricultural and forestry pests. Some of these fungi have been or are being developed as biological control agents in China and worldwide. Several important nematophagous and entomogenous fungi, including nematode-trapping fungi (Arthrobotrys oligospora and Drechslerella stenobrocha), nematode endoparasite (Hirsutella minnesotensis), insect pathogens (Beauveria bassiana and Metarhizium spp.) and Chinese medicinal fungi (Ophiocordyceps sinensis and Cordyceps militaris), have been genome sequenced and extensively analyzed in China. The biology, evolution, and pharmaceutical application of these fungi and their interacting with host nematodes and insects revealed by genomes, comparing genomes coupled with transcriptomes are summarized and reviewed in this paper. PMID:29376926

  15. Fossil evidence of the zygomycetous fungi

    NARCIS (Netherlands)

    Krings, M.; Taylor, T.N.; Dotzler, N.

    2013-01-01

    Molecular clock data indicate that the first zygomycetous fungi occurred on Earth during the Precambrian, however, fossil evidence of these organisms has been slow to accumulate. In this paper, the fossil record of the zygomycetous fungi is compiled, with a focus on structurally preserved

  16. Epiphitic microbiote and fungi contaminats from in vitro establishment of guajaba (Psidium guajava L.

    Directory of Open Access Journals (Sweden)

    Mayra Acosta-Suárez

    2002-04-01

    Full Text Available The studying of contaminats micobiote on guajaba (Psidium guajava L. could help for creating schedule treatment of donator plants and its explants to eliminate or prevent the fungi contamination during guajaba micropropagation. The present work were focused on: qualitative evaluation of epiphytic micobiote from explants of Enana Roja cubana EEA 18-40 plants (treated and not treated with fungicide, to isolate, characterize and identify the filamentous fungi from in vitro establishment of nodal segments. For the filamentous identification was used the wet chamber method and preparations were observed in optic microscopic. PDA Petri dishes were used to cultivate the filamentous fungi at 28ºC and dark during 7 to 14 days. The cultural and morphological characteristics were used to identifying each isolate. Nine filamentous fungi genera were identify on donator plants without any fungicide application, the principal genera’s were: Alternaria, Aspergillus, Cladosporium, Colletotrichum, Curvularia, Fusarium, Nigrospora, Penicillium and Trichoderma. The application of Mancozeb 80 PH (7.5g.l-1 and Benomyl 50 PH (4g.l-1 was not effective on epiphytic contaminants micobiote elimination. All these genera’s with the exception of Nigrospora were detected during the establishment of nodal segments. However the disinfection with hypochlorite at 3% for 10 minutes and HgCl2 solution at 0.05% and 0.1% could reduced the 50% of al contaminates genera’s. Key words: micropropagation, microbiote contamination,filamentous fungi, surface dessinfectants.

  17. Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay.

    Science.gov (United States)

    Zhou, Dinggang; Wang, Chunfeng; Li, Zhu; Chen, Yun; Gao, Shiwu; Guo, Jinlong; Lu, Wenying; Su, Yachun; Xu, Liping; Que, Youxiong

    2016-01-01

    Genetic engineering offers an attractive alternative in sugarcane breeding for increasing cane and sugar yields as well as disease and insect resistance. Bar transgenic sugarcane employing the herbicide tolerance is a useful agronomical trait in weed control. In this study, a loop-mediated isothermal amplification (LAMP) assay for rapid detection of the bar gene in transgenic sugarcane has been developed and evaluated. A set of six primers was designed for LAMP-based amplification of the bar gene. The LAMP reaction conditions were optimized as follows: 5.25 mM of Mg(2+), 6:1 ratio of inner vs. outer primer, and 6.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. The detection limit of the recombinant plasmid 1Ac0229 was as low as 10 copies in the developed LAMP, which was 10-fold higher sensitive than that of conventional PCR. In 100 putative transgenic lines, the bar gene was detected in 100/100 cases (100%) by LAMP and 97/100 cases (97%) by conventional PCR, respectively. In conclusion, the developed LAMP assay is visual, rapid, sensitive, reliable, and cost-effective for detection of the bar specific transgenic sugarcane.

  18. Detection of bar transgenic sugarcane with a rapid and visual loop-mediated isothermal amplification assay

    Directory of Open Access Journals (Sweden)

    Dinggang eZhou

    2016-03-01

    Full Text Available Genetic engineering offers an attractive alternative in sugarcane breeding for increasing cane and sugar yields as well as disease and insect resistance. Bar transgenic sugarcane employing the herbicide tolerance is a useful agronomical trait in weed control. In this study, a loop-mediated isothermal amplification (LAMP assay for rapid detection of the bar gene in transgenic sugarcane has been developed and evaluated. A set of six primers was designed for LAMP-based amplification of the bar gene. The LAMP reaction conditions were optimized as follows: 5.25 mM of Mg2+, 6:1 ratio of inner vs outer primer, and 6.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. The detection limit of the recombinant plasmid 1Ac0229 was as low as 10 copies in the developed LAMP, which was ten-fold higher sensitive than that of conventional PCR. In 100 putative transgenic lines, the bar gene was detected in 100/100 cases (100% by LAMP and 97/100 cases (97% by conventional PCR, respectively. In conclusion, the developed LAMP assay is visual, rapid, sensitive, reliable and cost-effective for detection of the bar specific transgenic sugarcane.

  19. Foliar fungi of Scots pine (Pinus sylvestris)

    OpenAIRE

    Millberg, Hanna

    2015-01-01

    Scots pine (Pinus sylvestris) is an ecologically and economically important tree species in Fennoscandia. Scots pine needles host a variety of fungi, some with the potential to profoundly influence their host. These fungi can have beneficial or detrimental effects with important implications for both forest health and primary production. In this thesis, the foliar fungi of Scots pine needles were investigated with the aim of exploring spatial and temporal patterns, and development with needle...

  20. Fungi and mycotoxins: Food contaminants

    Directory of Open Access Journals (Sweden)

    Kocić-Tanackov Sunčica D.

    2013-01-01

    Full Text Available The growth of fungi on food causes physical and chemical changes which, further affect negatively the sensory and nutritive quality of food. Species from genera: Aspergillus, Penicillium, Fusarium, Alternariа, Cladosporium, Mucor, Rhizopus, Eurotium and Emericella are usually found. Some of them are potentially dangerous for humans and animals, due to possible synthesis and excretion of toxic secondary metabolites - mycotoxins into the food. Their toxic syndroms in animals and humans are known as mycotoxicoses. The pathologic changes can be observed in parenhimatic organs, and in bones and central nervous system also. Specific conditions are necessary for mycotoxin producing fungi to synthetize sufficient quantities of these compounds for demonstration of biologic effects. The main biochemical paths in the formation of mycotoxins include the polyketide (aflatoxins, sterigmatocystin, zearalenone, citrinine, patulin, terpenic (trichothecenes, aminoacid (glicotoxins, ergotamines, sporidesmin, malformin C, and carbonic acids path (rubratoxins. Aflatoxins are the most toxigenic metabolites of fungi, produced mostly by Aspergillus flavus and A. parasiticus species. Aflatoxins appear more frequently in food in the tropic and subtropic regions, while the food in Europe is more exposed to also very toxic ochratoxin A producing fungi (A. ochraceus and some Penicillium species. The agricultural products can be contaminated by fungi both before and after the harvest. The primary mycotoxicoses in humans are the result of direct intake of vegetable products contaminated by mycotoxins, while the secondary mycotoxicoses are caused by products of animal origin. The risk of the presence of fungi and mycotoxin in food is increasing, having in mind that some of them are highly thermoresistent, and the temperatures of usual food sterilization is not sufficient for their termination. The paper presents the review of most important mycotoxins, their biologic effects

  1. The effect of Mirabilis jalapa leaves biopesticide treatment on the mycelium growth of entomopathogenic fungi Beauveria bassiana inside the larvae body Crocidolomia binotalis

    Science.gov (United States)

    Pramita, Mia; Anggraeni, Tjandra

    2015-09-01

    Pest control with biological method (biopesticide and entomopathogenic fungi) is an alternative program to reduce application of chemical insecticide. Biopesticide of Mirabilis jalapa leaves has been discovered rich in secondary metabolites which has antifeedant activity that can provide physiological interference in insect larvae and the generation numbers[1]. Entomopathogenic fungi Beauveria bassiana has potential to control pest populations[2]. The growth of mycelium B. bassiana may interfere metabolism process inside the host body. Otherwise, B. bassiana produce toxins such as beauvericin that can increase mortality of pest. Combination of M. jalapa and B. bassiana reduce LT50 on C. binotalis larvae[3]. Thus, this study aims to determine influence of provision of biopesticide M. jalapa leaves on growth of mycelium entomopathogenic fungi B. bassiana inside larvae body C. binotalis and to detect the presence of beauvericin in vivo. Third instar larvae of C. binotalis were divided into a control, fungal and combination group. The combination group was given biopesticide and fungi. The concentration of biopesticide was 0.8% (w/v) and concentration of fungi spores was 107 spores/ml. Spores (vol. 5µl) done topically to larvae in interval 6 hours after treatment of biopesticide on non-pesticide cabbage leaves. Afterwards, histological observations performed at 24, 48, 72, 96 hours after treatment. The result show of emergence hyphae and mycelium growth inside lumen of larvae midgut on combination group faster than fungal group. This is thought to be caused by the influence of secondary metabolites of biopesticide M. jalapa leaves. In addition, beauviricin is detectable both of fungal and combination group. Thus, it can be concluded that treatment of biopesticide from M. jalapa leaves can accelerate on growth of mycelium entomopathogenic fungi B. bassiana inside the larvae body C. binotalis and toxic of B. bassiana such as beauvericin was detected on fungal and

  2. Long-term cryopreservation of non-spore-forming fungi in Microbank™ beads for plant pathological investigations.

    Science.gov (United States)

    Lakshman, Dilip K; Singh, Vimla; Camacho, Manuel E

    2018-05-01

    Long-term preservation of experimental fungi without genetic, morphological, and pathogenic changes is of paramount importance in mycological and plant pathological investigations. Several cryogenic and non-cryogenic methods are available for the preservation of fungi, but the methods can be cumbersome, hazardous, expensive, and often not suitable for long-term storage of non-spore-forming (sterile) fungi. A method of preservation of spore-forming fungi in commercially available porous beads (Micrbank™) under cryogenic condition was successfully tested for three non-spore-forming basidiomycetes genera: Rhizoctonia solani (teleomorph: Thanatephorus cucumeris) (n = 19), Ceratobasidium species (n = 1), and Waitea circinata (n = 3), and a non-spore forming ascomycetes, Sclerotinia sclerotiorum (n = 1). For comparison, spore-forming ascomycetous fungi, Alternaria alternata (n = 1), Bauveria basiana (n = 2), Botrytis cinerea (n = 1), Fusarium oxysporum f.sp. gladiolii (n = 1), Trichoderma spp. (n = 3), and Thielaviopsis basicola (n = 2) were also cryopreserved in Microbank beads. Viable fungal isolates of all test species were retrieved after five years of storage at -80 °C, which was longer than the viabilities of the corresponding isolates cryopreserved in agar plugs or colonized wheat seeds. Fungi revived from the Microbank beads maintained identical morphology and cultural characteristics of the parent isolates. Randomly selected Rhizoctonia isolates revived from the Microbank beads maintained respective pathological properties of the parent isolates; also, no mutation was detected in the internal transcribed spacer (ITS) ribosomal DNA when compared with respective cultures maintained at ambient temperature. This finding demonstrated the utility of cryopreservation in Microbank beads as a convenient alternative to conventional long-term preservation of a wide group of fungal cultures for plant pathological investigations

  3. Antibacterial activity of marine-derived fungi

    DEFF Research Database (Denmark)

    Christophersen, Carsten; Crescente, Oscar; Frisvad, Jens Christian

    1998-01-01

    A total of 227 marine isolates of ubiqituous fungi were cultivated on different media and the secondary metabolite content of the extracts (ethyl acetate/chlorofonn/methanol 3 : 2 : 1) characterized by HPLC. The fungi were secured from animals, plants and sediments of Venezuelan waters (0-10 m...

  4. Changes in fungi and mycotoxins in pearl millet under controlled storage conditions.

    Science.gov (United States)

    Jurjevic, Zeljko; Wilson, Jeffrey P; Wilson, David M; Casper, Howard H

    2007-11-01

    Pearl millet is increasingly being grown as a premium-value grain for the recreational wildlife and poultry industries in the southern US. We conducted three experiments to assess grain mold development in storage conditions typically encountered in the region of production. Variables included production year, temperature, relative humidity, atmosphere, and grain moisture content. In the first experiment, grain was stored for 9 weeks at 20 or 25 degrees C and maintained at 86% or 91% relative humidity (r.h.). In the second experiment, grain was stored for 9 weeks at 20 or 25 degrees C in either air (aerobic) or N2 (anaerobic), and maintained at 100% r.h. In the third experiment, high-moisture grain was stored for 3 weeks at 20 or 25 degrees C and maintained at 100% r.h. Grain was sampled at weekly intervals and plated to determine changes in fungal frequency. Fungi isolated included Fusarium chlamydosporum (19% of grain), Curvularia spp. (14%), F. semitectum (16%), Alternaria spp. (9%), Aspergillus flavus (8%), "Helminthosporium"-type spp. (6%), and F. moniliforme sensu lato (3%). Year of grain production significantly affected isolation frequency of fungi. Isolation frequencies from low-moisture grain were rarely affected by temperature, relative humidity, or atmosphere treatments, but was affected by storage duration for some fungi. Changes in isolation of toxigenic fungi occurred in high-moisture grain. Isolation frequency of F. chlamydosporum increased in grain stored at 86% and 91% r.h. Incidence of A. flavus increased in high-moisture grain treatments, particularly at 25 degrees C. Incidence of deoxynivalenol was not affected by storage treatment. Low concentrations of nivalenol were detected in most grain incubated at 100% r.h. Zearalenone was detected only when grain moisture content was 20-22%. Aflatoxin contamination averaged 174 ng g(-1) over all treatments, and increased up to 798 ng g(-1) in high-moisture grain at stored at 25 degrees C.

  5. Potassium, rubidium and caesium in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Johanson, K.J.; Nikolova, I. [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Forest Mycology and Pathology; Vinichuk, M. [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Soil Sciences

    2005-09-15

    Samples of mushrooms and soil were collected in a forest ecosystem close to Nuclear Power Plant at Forsmark, Sweden. The soil were fractionated in bulk soil, rhizosphere, soil-root interface and fungal mycelium and the concentration of K, Rb and Cs were determined. The K concentration increased from 605 mg/kg in bulk soil to 2,750 mg/kg in mycelium and 39,500 in fruitbodies of fungi. The corresponding values for Rb was 2.5 mg/kg in bulk soil and 191 mg/kg in fruitbodies of fungi. For Cs the corresponding values were 0.21 mg/kg for bulk soil and 3.9 mg/kg in fruitbodies. In fruitbodies of fungi good correlation was found between the concentration of K and Rb or of Rb and Cs, but not between K and Cs. Yoshida found similar correlation and concluded that the mechanism of Cs uptake by fungi may be different from that of K.

  6. A rapid qualitative assay for detection of Clostridium perfringens in canned food products.

    Science.gov (United States)

    Dave, Gayatri Ashwinkumar

    2017-01-01

    Clostridium perfringens (MTCC 1349) is a Gram-positive, anaerobic, endospore forming, and rod-shaped bacterium. This bacterium produces a variety of toxins under strict anaerobic environment. C. perfringens can grow at temperatures ranging between 20°C and 50°C. It is the major causetive agent for gas gangrene, cellulitis, septicemia, necrotic enteritis and food poisoning, which are common toxin induced conditions noted in human and animals. C. perfringens can produce produce four major types of toxins that are used for the classification of strains, classified under type A-E. Across the globe many countries, including the United States, are affected by C. perfringens food poisonings where it is ranked as one of the most common causes of food borne infections. To date, no direct one step assay for the detection of C. perfringens has been developed and only few methods are known for accurate detection of C. perfringens. Long detection and incubation time is the major consideration of these reporter assays. The prensent study proposes a rapid and reliable colorimetric assay for the detection of C. perfringens. In principale, this assay detects the para nitrophenyl (yellow colour end product) liberated due to the hydrolysis of paranitrophenyl phosphetidyl choline (PNPC) through phospholipase C (lecithinase). Constitutive secretion of phospholipase C is a charactristic feature of C. perfringens. This assay detects the presence of the extracellular lecithinse through the PNPC impragnated impregnated probe. The probe is impregnated with peranitrophenyl phosphotidyl choline ester, which is colourless substrate used by lecithinase. The designed assay is specific towards PNPC and detectes very small quantites of lecithinase under conditions used. The reaction is substrate specific, no cross reaction was observed upon incubation with other substrates. In addition, this assay gave negative results with other clostridium strains, no cross reactions were observed with other

  7. A simple, rapid, cost-effective and sensitive method for detection of Salmonella in environmental and pecan samples.

    Science.gov (United States)

    Dobhal, S; Zhang, G; Rohla, C; Smith, M W; Ma, L M

    2014-10-01

    PCR is widely used in the routine detection of foodborne human pathogens; however, challenges remain in overcoming PCR inhibitors present in some sample matrices. The objective of this study was to develop a simple, sensitive, cost-effective and rapid method for processing large numbers of environmental and pecan samples for Salmonella detection. This study was also aimed at validation of a new protocol for the detection of Salmonella from in-shell pecans. Different DNA template preparation methods, including direct boiling, prespin, multiple washing and commercial DNA extraction kits, were evaluated with pure cultures of Salmonella Typhimurium and with enriched soil, cattle feces and in-shell pecan each spiked individually with Salmonella Typhimurium. PCR detection of Salmonella was conducted using invA and 16S rRNA gene (internal amplification control) specific primers. The effect of amplification facilitators, including bovine serum albumin (BSA), polyvinylpyrrolidone (PVP), polyethylene glycol (PEG) and gelatin on PCR sensitivity, was also evaluated. Conducting a prespin of sample matrices in combination with the addition of 0·4% (w/v) BSA and 1% (w/v) PVP in PCR mix was the simplest, most rapid, cost-effective and sensitive method for PCR detection of Salmonella, with up to 40 CFU Salmonella per reaction detectable in the presence of over 10(9 ) CFU ml(-1) of background micro-organisms from enriched feces soil or pecan samples. The developed method is rapid, cost-effective and sensitive for detection of Salmonella from different matrices. This study provides a method with broad applicability for PCR detection of Salmonella in complex sample matrices. This method has a potential for its application in different research arenas and diagnostic laboratories. © 2014 The Society for Applied Microbiology.

  8. Community structure of ectomycorrhizal fungi in Swedish boreal forests

    Energy Technology Data Exchange (ETDEWEB)

    Jonsson, Lena [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Forest Mycology and Pathology

    1998-12-31

    The main aim of this work has been to elucidate the species composition and community structure of ectomycorrhizal fungi associated with mature trees and naturally regenerated seedlings in natural boreal forests in Sweden. Further, the effects of disturbances, such as wildfire and nitrogen inputs, were studied. Sporocarp surveys, morphological stratification and DNA-based analyses of mycorrhizas were used to describe the mycorrhizal fungal communities. In addition, a reference database useful for identifying individual mycorrhizas was developed based on analyses of sporocarp tissue. Overall, the species richness of ectomycorrhizal fungi was at least 30 to 40 times higher than that of their host trees. Naturally regenerated seedlings were colonized by the ectomycorrhizal fungal species present in the mycelial network of the old trees, indicating that the species composition will remain about the same provided that the host does not disappear. Wildfire, disturbing the fungal continuum, caused a shift in the frequencies of ectomycorrhizal fungi rather than a change in species composition. Nitrogen addition did not have any detectable effect on the abundance or species richness of mycorrhizas, but led to a decrease in sporocarp production. In all the studies, there was little resemblance between the species composition of sporocarps and that of mycorrhizas. The ITS-RFLP reference database was very useful in identifying single mycorrhizas, and proved to be a powerful tool for species identification of unknown mycorrhizas 76 refs, 2 figs, 2 tabs

  9. BIOMODIFICATION OF KENAF USING WHITE ROT FUNGI

    OpenAIRE

    Rasmina Halis,; Hui Rus Tan,; Zaidon Ashaari,; Rozi Mohamed

    2012-01-01

    White rot fungi can be used as a pretreatment of biomass to degrade lignin. It also alters the structure of the lignocellulosic matter, thus increasing its accessibility to enzymes able to convert polysaccharides into simple sugars. This study compares the ability of two species of white rot fungi, Pycnoporous sanguineus and Oxyporus latemarginatus FRIM 31, to degrade lignin in kenaf chips. The white rot fungi were originally isolated from the tropical forest in Malaysia. Kenaf chips were fir...

  10. Airborne fungi in an intensive care unit

    Directory of Open Access Journals (Sweden)

    C. L. Gonçalves

    2017-07-01

    Full Text Available Abstract The presence of airborne fungi in Intensive Care Unit (ICUs is associated with increased nosocomial infections. The aim of this study was the isolation and identification of airborne fungi presented in an ICU from the University Hospital of Pelotas – RS, with the attempt to know the place’s environmental microbiota. 40 Petri plates with Sabouraud Dextrose Agar were exposed to an environment of an ICU, where samples were collected in strategic places during morning and afternoon periods for ten days. Seven fungi genera were identified: Penicillium spp. (15.18%, genus with the higher frequency, followed by Aspergillus spp., Cladosporium spp., Fusarium spp., Paecelomyces spp., Curvularia spp., Alternaria spp., Zygomycetes and sterile mycelium. The most predominant fungi genus were Aspergillus spp. (13.92% in the morning and Cladosporium spp. (13.92% in the afternoon. Due to their involvement in different diseases, the identified fungi genera can be classified as potential pathogens of inpatients. These results reinforce the need of monitoring the environmental microorganisms with high frequency and efficiently in health institutions.

  11. Development of a nested-PCR assay for the rapid detection of Pilidiella granati in pomegranate fruit

    Science.gov (United States)

    Yang, Xue; Hameed, Uzma; Zhang, Ai-Fang; Zang, Hao-Yu; Gu, Chun-Yan; Chen, Yu; Xu, Yi-Liu

    2017-01-01

    Pilidiella granati, a causal agent of twig blight and crown rot of pomegranate, is an emerging threat that may cause severe risk to the pomegranate industry in the future. Development of a rapid assay for the timely and accurate detection of P. granati will be helpful in the active surveillance and management of the disease caused by this pathogen. In this study, a nested PCR method was established for the detection of P. granati. Comparative analysis of genetic diversity within 5.8S rDNA internal transcribed spacer (ITS) sequences of P. granati and 21 other selected fungal species was performed to design species-specific primers (S1 and S2). This primer pair successfully amplified a 450 bp product exclusively from the genomic DNA of P. granati. The developed method can detect 10 pg genomic DNA of the pathogen in about 6 h. This technique was successfully applied to detect the natural infection of P. granati in the pomegranate fruit. The designed protocol is rapid and precise with a high degree of sensitivity. PMID:28106107

  12. Surface-bound phosphatase activity in living hyphae of ectomycorrhizal fungi of Nothofagus obliqua.

    Science.gov (United States)

    Alvarez, Maricel; Godoy, Roberto; Heyser, Wolfgang; Härtel, Steffen

    2004-01-01

    We determined the location and the activity of surface-bound phosphomonoesterase (SBP) of five ectomycorrhizal (EM) fungi of Nothofagus oblique. EM fungal mycelium of Paxillus involutus, Austropaxillus boletinoides, Descolea antartica, Cenococcum geophilum and Pisolithus tinctorius was grown in media with varying concentrations of dissolved phosphorus. SBP activity was detected at different pH values (3-7) under each growth regimen. SBP activity was assessed using a colorimetric method based on the hydrolysis of p-nitrophenyl phosphate (pNPP) to p-nitrophenol phosphate (pNP) + P. A new technique involving confocal laser-scanning microscopy (LSM) was used to locate and quantify SBP activity on the hyphal surface. EM fungi showed two fundamentally different patterns of SBP activity in relation to varying environmental conditions (P-concentrations and pH). In the cases of D. antartica, A. boletinoides and C. geophilum, changes in SBP activity were induced primarily by changes in the number of SBP-active centers on the hyphae. In the cases of P. tinctorius and P. involutus, the number of SBP-active centers per μm hyphal length changed much less than the intensity of the SBP-active centers on the hyphae. Our findings not only contribute to the discussion about the role of SBP-active centers in EM fungi but also introduce LSM as a valuable method for studying EM fungi.

  13. Rapid detection of undesired cosmetic ingredients by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

    Science.gov (United States)

    Ouyang, Jie; An, Dongli; Chen, Tengteng; Lin, Zhiwei

    2017-10-01

    In recent years, cosmetic industry profits soared due to the widespread use of cosmetics, which resulted in illicit manufacturers and products of poor quality. Therefore, the rapid and accurate detection of the composition of cosmetics has become crucial. At present, numerous methods, such as gas chromatography and liquid chromatography-mass spectrometry, were available for the analysis of cosmetic ingredients. However, these methods present several limitations, such as failure to perform comprehensive and rapid analysis of the samples. Compared with other techniques, matrix-assisted laser desorption ionization time-of-flight mass spectrometry offered the advantages of wide detection range, fast speed and high accuracy. In this article, we briefly summarized how to select a suitable matrix and adjust the appropriate laser energy. We also discussed the rapid identification of undesired ingredients, focusing on antibiotics and hormones in cosmetics.

  14. Deep Subseafloor Fungi as an Untapped Reservoir of Amphipathic Antimicrobial Compounds.

    Science.gov (United States)

    Navarri, Marion; Jégou, Camille; Meslet-Cladière, Laurence; Brillet, Benjamin; Barbier, Georges; Burgaud, Gaëtan; Fleury, Yannick

    2016-03-10

    The evolving global threat of antimicrobial resistance requires a deep renewal of the antibiotic arsenal including the isolation and characterization of new drugs. Underexplored marine ecosystems may represent an untapped reservoir of novel bioactive molecules. Deep-sea fungi isolated from a record-depth sediment core of almost 2000 m below the seafloor were investigated for antimicrobial activities. This antimicrobial screening, using 16 microbial targets, revealed 33% of filamentous fungi synthesizing bioactive compounds with activities against pathogenic bacteria and fungi. Interestingly, occurrence of antimicrobial producing isolates was well correlated with the complexity of the habitat (in term of microbial richness), as higher antimicrobial activities were obtained at specific layers of the sediment core. It clearly highlights complex deep-sea habitats as chemical battlefields where synthesis of numerous bioactive compounds appears critical for microbial competition. The six most promising deep subseafloor fungal isolates were selected for the production and extraction of bioactive compounds. Depending on the fungal isolates, antimicrobial compounds were only biosynthesized in semi-liquid or solid-state conditions as no antimicrobial activities were ever detected using liquid fermentation. An exception was made for one fungal isolate, and the extraction procedure designed to extract amphipathic compounds was successful and highlighted the amphiphilic profile of the bioactive metabolites.

  15. Loop-Mediated Isothermal Amplification Assay Targeting the MOMP Gene for Rapid Detection of Chlamydia psittaci Abortus Strain

    Directory of Open Access Journals (Sweden)

    Guo-Zhen Lin, Fu-Ying Zheng, Ji-Zhang Zhou, Guang-Hua Wang, Xiao-An Cao, Xiao-Wei Gong and Chang-Qing Qiu*

    2012-05-01

    Full Text Available For rapid detection of the Chlamydia psittaci abortus strain, a loop-mediated isothermal amplification (LAMP assay was developed and evaluated in this study. The primers for the LAMP assay were designed on the basis of the main outer membrane protein (MOMP gene sequence of C. psittaci. Analysis showed that the assay could detect the abortus strain of C. psittaci with adequate specificity. The sensitivity of the test was the same as that of the nested-conventional PCR and higher than that of chick embryo isolation. Testing of 153 samples indicated that the LAMP assay could detect the genome of the C. psittaci abortus strain effectively in clinical samples. This assay is a useful tool for rapid diagnosis of C. psittaci infection in sheep, swine and cattle.

  16. Simplified and rapid method for extraction of ergosterol from natural samples and detection with quantitative and semi-quantitative methods using thin-layer chromatography

    OpenAIRE

    Larsen, Cand.scient Thomas; Ravn, Senior scientist Helle; Axelsen, Senior Scientist Jørgen

    2004-01-01

    A new and simplified method for extraction of ergosterol (ergoste-5,7,22-trien-3-beta-ol) from fungi in soil and litter was developed using pre-soaking extraction and paraffin oil for recovery. Recoveries of ergosterol were in the range of 94 - 100% depending on the solvent to oil ratio. Extraction efficiencies equal to heat-assisted extraction treatments were obtained with pre-soaked extraction. Ergosterol was detected with thin-layer chromatography (TLC) using fluorodensitometry with a quan...

  17. Rapid detection of Ganoderma-infected oil palms by microwave ergosterol extraction with HPLC and TLC.

    Science.gov (United States)

    Muniroh, M S; Sariah, M; Zainal Abidin, M A; Lima, N; Paterson, R R M

    2014-05-01

    Detection of basal stem rot (BSR) by Ganoderma of oil palms was based on foliar symptoms and production of basidiomata. Enzyme-Linked Immunosorbent Assays-Polyclonal Antibody (ELISA-PAB) and PCR have been proposed as early detection methods for the disease. These techniques are complex, time consuming and have accuracy limitations. An ergosterol method was developed which correlated well with the degree of infection in oil palms, including samples growing in plantations. However, the method was capable of being optimised. This current study was designed to develop a simpler, more rapid and efficient ergosterol method with utility in the field that involved the use of microwave extraction. The optimised procedure involved extracting a small amount of Ganoderma, or Ganoderma-infected oil palm suspended in low volumes of solvent followed by irradiation in a conventional microwave oven at 70°C and medium high power for 30s, resulting in simultaneous extraction and saponification. Ergosterol was detected by thin layer chromatography (TLC) and quantified using high performance liquid chromatography with diode array detection. The TLC method was novel and provided a simple, inexpensive method with utility in the field. The new method was particularly effective at extracting high yields of ergosterol from infected oil palm and enables rapid analysis of field samples on site, allowing infected oil palms to be treated or culled very rapidly. Some limitations of the method are discussed herein. The procedures lend themselves to controlling the disease more effectively and allowing more effective use of land currently employed to grow oil palms, thereby reducing pressure to develop new plantations. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Rapid detection of SMARCB1 sequence variation using high resolution melting

    Directory of Open Access Journals (Sweden)

    Ashley David M

    2009-12-01

    Full Text Available Abstract Background Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM, for detecting sequence variations in SMARCB1. Methods Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. Results The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4% showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA. A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. Conclusions This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to

  19. Rapid detection of SMARCB1 sequence variation using high resolution melting

    International Nuclear Information System (INIS)

    Dagar, Vinod; Chow, Chung-Wo; Ashley, David M; Algar, Elizabeth M

    2009-01-01

    Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM), for detecting sequence variations in SMARCB1. Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4%) showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA). A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to facilitate whole gene mutation screening

  20. Development of Colloidal Gold-Based Immunochromatographic Assay for Rapid Detection of Goose Parvovirus

    Directory of Open Access Journals (Sweden)

    Xianglong Yu

    2018-05-01

    Full Text Available Goose parvovirus (GPV remains as a worldwide problem in goose industry. For this reason, it is necessary to develop a new diagnostic approach that is easier and faster than conventional tests. A rapid immunochromatographic assay based on antibody colloidal gold nanoparticles specific to GPV was developed for the detection of GPV in goose allantoic fluid and supernatant of tissue homogenate. The monoclonal antibodies (Mab was produced by immunizing the BALB/c mice with purified GPV suspension, and the polyclonal antibody (pAb was produced by immunizing the rabbits with recombinant VP3 protein. The colloidal gold was prepared by the reduction of gold salt with sodium citrate coupled with Mab against GPV. The optimal concentrations of the coating antibody and capture antibody were determined to be 1.6 mg/ml and 9 μg/ml. With visual observation, the lower limit was found to be around 1.2 μg/ml. Common diseases of goose were tested to evaluate the specificity of the immune colloidal gold (ICG strip, and no cross-reaction was observed. The clinical detection was examined by carrying out the ICG strip test with 92 samples and comparing the results of these tests with those obtained via agar diffusion test and polymerase chain reaction (PCR test. Therefore, the ICG strip test was a sufficiently sensitive and accurate detection method for a rapid screening of GPV.

  1. Black yeast-like fungi in skin and nail

    DEFF Research Database (Denmark)

    Saunte, D M; Tarazooie, B; Arendrup, M C

    2011-01-01

    Black yeast-like fungi are rarely reported from superficial infections. We noticed a consistent prevalence of these organisms as single isolations from mycological routine specimens. To investigate the prevalence of black yeast-like fungi in skin, hair and nail specimens and to discuss...... the probability of these species to be involved in disease. Slow-growing black yeast-like fungi in routine specimens were prospectively collected and identified. A questionnaire regarding patient information was sent to physicians regarding black yeast-like fungus positive patients. A total of 20 746...... dermatological specimens were examined by culture. Black yeast-like fungi accounted for 2.2% (n = 108) of the positive cultures. Only 31.0% of the samples, culture positive for black yeast-like fungi were direct microscopy positive when compared with overall 68.8% of the culture positive specimens. The most...

  2. Rapid and early detection of salmonella serotypes with hyperspectral microscope and multivariate data analysis

    Science.gov (United States)

    This study was designed to evaluate hyperspectral microscope images for early and rapid detection of Salmonella serotypes: S. Enteritidis, S. Heidelberg, S. Infantis, S. Kentucky, and S. Typhimurium at incubation times of 6, 8, 10, 12, and 24 hours. Images were collected by an acousto-optical tunab...

  3. Identification of Toxigenic Fungi And its Respective Toxins in Dark Raisins Commercialized in Votuporanga- SP

    Directory of Open Access Journals (Sweden)

    Ana Fernandes Santos

    2015-06-01

    presence of A. niger and Penicillium spp were detected, the first ones being producers of ocratoxina and A. flavus, the producer of aflatoxina. Therefore the research showed the contamination by toxigenic fungi in the collected samples in 82% of the evaluated establishments.

  4. Rapid surface enhanced Raman scattering detection method for chloramphenicol residues

    Science.gov (United States)

    Ji, Wei; Yao, Weirong

    2015-06-01

    Chloramphenicol (CAP) is a widely used amide alcohol antibiotics, which has been banned from using in food producing animals in many countries. In this study, surface enhanced Raman scattering (SERS) coupled with gold colloidal nanoparticles was used for the rapid analysis of CAP. Density functional theory (DFT) calculations were conducted with Gaussian 03 at the B3LYP level using the 3-21G(d) and 6-31G(d) basis sets to analyze the assignment of vibrations. Affirmatively, the theoretical Raman spectrum of CAP was in complete agreement with the experimental spectrum. They both exhibited three strong peaks characteristic of CAP at 1104 cm-1, 1344 cm-1, 1596 cm-1, which were used for rapid qualitative analysis of CAP residues in food samples. The use of SERS as a method for the measurements of CAP was explored by comparing use of different solvents, gold colloidal nanoparticles concentration and absorption time. The method of the detection limit was determined as 0.1 μg/mL using optimum conditions. The Raman peak at 1344 cm-1 was used as the index for quantitative analysis of CAP in food samples, with a linear correlation of R2 = 0.9802. Quantitative analysis of CAP residues in foods revealed that the SERS technique with gold colloidal nanoparticles was sensitive and of a good stability and linear correlation, and suited for rapid analysis of CAP residue in a variety of food samples.

  5. One Step Construction of Agrobacterium Recombination-ready-plasmids (OSCAR), an efficient and robust tool for ATMT based gene deletion construction in fungi

    Science.gov (United States)

    Increasing availability of genomic data and sophistication of analytical methodology in fungi has elevated the need for functional genomics tools in these organisms. Previously we reported a method called DelsGate for rapid preparation of deletion constructs for protoplast-mediated fungal transforma...

  6. Proposals to clarify and enhance the naming of fungi under the International Code of Nomenclature for algae, fungi, and plants.

    Science.gov (United States)

    Hawksworth, David L

    2015-06-01

    Twenty-three proposals to modify the International Code of Nomenclature for algae, fungi, and plants adopted in 2011 with respect to the provisions for fungi are made, in accordance with the wishes of mycologists expressed at the 10(th) International Mycological Congress in Bangkok in 2014, and with the support of the International Commission on the Taxonomy of Fungi (ICTF), the votes of which are presented here. The proposals relate to: conditions for epitypification, registration of later typifications, protected lists of names, removal of exemptions for lichen-forming fungi, provision of a diagnosis when describing a new taxon, citation of sanctioned names, avoiding homonyms in other kingdoms, ending preference for sexually typified names, and treatment of conspecific names with the same epithet. These proposals are also being published in Taxon, will be considered by the Nomenclature Committee for Fungi and General Committee on Nomenclature, and voted on at the 19(th) International Botanical Congress in Shenzhen, China, in 2017.

  7. Fungi that Infect Humans.

    Science.gov (United States)

    Köhler, Julia R; Hube, Bernhard; Puccia, Rosana; Casadevall, Arturo; Perfect, John R

    2017-06-01

    Fungi must meet four criteria to infect humans: growth at human body temperatures, circumvention or penetration of surface barriers, lysis and absorption of tissue, and resistance to immune defenses, including elevated body temperatures. Morphogenesis between small round, detachable cells and long, connected cells is the mechanism by which fungi solve problems of locomotion around or through host barriers. Secretion of lytic enzymes, and uptake systems for the released nutrients, are necessary if a fungus is to nutritionally utilize human tissue. Last, the potent human immune system evolved in the interaction with potential fungal pathogens, so few fungi meet all four conditions for a healthy human host. Paradoxically, the advances of modern medicine have made millions of people newly susceptible to fungal infections by disrupting immune defenses. This article explores how different members of four fungal phyla use different strategies to fulfill the four criteria to infect humans: the Entomophthorales, the Mucorales, the Ascomycota, and the Basidiomycota. Unique traits confer human pathogenic potential on various important members of these phyla: pathogenic Onygenales comprising thermal dimorphs such as Histoplasma and Coccidioides ; the Cryptococcus spp. that infect immunocompromised as well as healthy humans; and important pathogens of immunocompromised patients- Candida , Pneumocystis , and Aspergillus spp. Also discussed are agents of neglected tropical diseases important in global health such as mycetoma and paracoccidiomycosis and common pathogens rarely implicated in serious illness such as dermatophytes. Commensalism is considered, as well as parasitism, in shaping genomes and physiological systems of hosts and fungi during evolution.

  8. Richness of endophytic fungi isolated from Opuntia ficus-indica Mill. (Cactaceae) and preliminary screening for enzyme production.

    Science.gov (United States)

    Bezerra, J D P; Santos, M G S; Svedese, V M; Lima, D M M; Fernandes, M J S; Paiva, L M; Souza-Motta, C M

    2012-05-01

    Opuntia ficus-indica Mill. (forage cactus) is farmed with relative success in the semi-arid region of the Brazilian northeast for commercial purposes, particularly as forage and food. Endophytic microorganisms are those that can be isolated inside plant tissues and can be a new source to production of enzymes with different potentialities. The objective of this study was to describe the richness of endophytic fungi from O. ficus-indica and to detect the capacity of these species to produce extracellular hydrolytic enzymes. Forty-four endophytic fungi species were isolated. Among them, the most commonly found were Cladosporium cladosporioides (20.43%) and C. sphaerospermum (15.99%). Acremonium terricola, Monodictys castaneae, Penicillium glandicola, Phoma tropica and Tetraploa aristata are being reported for the first time as endophytic fungi for Brazil. The majority of isolated fungi exhibited enzymatic potential. Aspergillus japonicus and P. glandicola presented pectinolytic activity. Xylaria sp. was the most important among the other 14 species with positive cellulase activity. All 24 isolates analysed were xylanase-positive. Protease was best produced by isolate PF103. The results indicate that there is a significant richness of endophytic fungi in O. ficus-indica, and that these isolates indicate promising potential for deployment in biotechnological processes involving production of pectinases, cellulases, xylanases and proteases.

  9. Rapid-viability PCR method for detection of live, virulent Bacillus anthracis in environmental samples.

    Science.gov (United States)

    Létant, Sonia E; Murphy, Gloria A; Alfaro, Teneile M; Avila, Julie R; Kane, Staci R; Raber, Ellen; Bunt, Thomas M; Shah, Sanjiv R

    2011-09-01

    In the event of a biothreat agent release, hundreds of samples would need to be rapidly processed to characterize the extent of contamination and determine the efficacy of remediation activities. Current biological agent identification and viability determination methods are both labor- and time-intensive such that turnaround time for confirmed results is typically several days. In order to alleviate this issue, automated, high-throughput sample processing methods were developed in which real-time PCR analysis is conducted on samples before and after incubation. The method, referred to as rapid-viability (RV)-PCR, uses the change in cycle threshold after incubation to detect the presence of live organisms. In this article, we report a novel RV-PCR method for detection of live, virulent Bacillus anthracis, in which the incubation time was reduced from 14 h to 9 h, bringing the total turnaround time for results below 15 h. The method incorporates a magnetic bead-based DNA extraction and purification step prior to PCR analysis, as well as specific real-time PCR assays for the B. anthracis chromosome and pXO1 and pXO2 plasmids. A single laboratory verification of the optimized method applied to the detection of virulent B. anthracis in environmental samples was conducted and showed a detection level of 10 to 99 CFU/sample with both manual and automated RV-PCR methods in the presence of various challenges. Experiments exploring the relationship between the incubation time and the limit of detection suggest that the method could be further shortened by an additional 2 to 3 h for relatively clean samples.

  10. Rapid and sensitive detection of Didymella bryoniae by visual loop-mediated isothermal amplification assay

    Directory of Open Access Journals (Sweden)

    Xiefeng Yao

    2016-08-01

    Full Text Available Didymella bryoniae is a pathogenic fungus that causes gummy stem blight (GSB in Cucurbitaceae crops (e.g. cantaloupe, muskmelon, cucumber, and watermelon. GSB produces lesions on the stems and leaves, and can also be spread by seeds. Here, we developed a rapid, visual, and sensitive loop-mediated amplification (LAMP assay for D. bryoniae detection based on sequence-characterized amplified regions (GenBank accession nos GQ872461 and GQ872462 common to the two random amplification of polymorphic DNA group genotypes (RGI and RGII of D. bryoniae; ideal conditions for detection were optimized for completion in 45 min at 63°C. The sensitivity and specificity of the LAMP assay were further analyzed in comparison with those of a conventional polymerase chain reaction (PCR. The sensitivity of the LAMP assay was 1000-fold higher than that of conventional PCR with a detection limit of 0.1 fg μL−1 of targeted DNA. The LAMP assay could be accomplished in about 45 min, with the results visible to the naked eye. The assay showed high specificity in discriminating all D. bryoniae isolates from seven other fungal pathogens that occur in Cucurbitaceae crops. The LAMP assay also detected D. bryoniae infection in young muskmelon leaves with suspected early symptoms of GSB disease. Hence, the technique has great potential for developing rapid and sensitive visual detection methods for the D. bryoniae pathogen in crops and seeds. This method has potential application in early prediction of disease and reducing the risk of epidemics.

  11. Bioremediation of treated wood with fungi

    Science.gov (United States)

    Barbara L. Illman; Vina W. Yang

    2006-01-01

    The authors have developed technologies for fungal bioremediation of waste wood treated with oilborne or metal-based preservatives. The technologies are based on specially formulated inoculum of wood-decay fungi, obtained through strain selection to obtain preservative-tolerant fungi. This waste management approach provides a product with reduced wood volume and the...

  12. [Heavy metal pollution ecology of macro-fungi: research advances and expectation].

    Science.gov (United States)

    Zhou, Qi-xing; An, Xin-long; Wei, Shu-he

    2008-08-01

    Macro-fungi are the main component of biosphere and one of the ecological resources, and play very important roles in matter cycling and in maintaining ecological balances. This paper summarized and reviewed the research advances in the eco-toxicological effects of heavy metals on macro-fungi, the bioaccumulation function of macro-fungi on heavy metals, the ecological adaptation mechanisms of macro-fungi to heavy metal pollution, the role of macro-fungi as a bio-indicator of heavy metal pollution, and the potential of macro-fungi in the ecological remediation of contaminated environment. To strengthen the researches on the heavy metal pollution ecology of macro-fungi would be of practical significance in the reasonable utilization of macro-fungi resources and in the ecological remediation of contaminated environment.

  13. Rapid Reagentless Detection of M. tuberculosis H37Ra in Respiratory Effluents

    International Nuclear Information System (INIS)

    Adams, K.L.; Steele, P.T.; Bogan, M.J.; Sadler, N.M.; Martin, S.; Martin, A.N.; Frank, M.

    2008-01-01

    Two similar mycobacteria, Mycobacteria tuberculosis H37Ra and Mycobacteria smegmatis are rapidly detected and identified within samples containing a complex background of respiratory effluents using Single Particle Aerosol Mass Spectrometry (SPAMS). M. tuberculosis H37Ra (TBa), an avirulent strain, is used as a surrogate for virulent tuberculosis (TBv); M. smegmatis (MSm) is utilized as a near neighbor confounder for TBa. Bovine lung surfactant and human exhaled breath condensate are used as first-order surrogates for infected human lung expirations from patients with pulmonary tuberculosis. This simulated background sputum is mixed with TBa or MSm and nebulized to produce conglomerate aerosol particles, single particles that contain a bacterium embedded within a background respiratory matrix. Mass spectra of single conglomerate particles exhibit ions associated with both respiratory effluents and mycobacteria. Spectral features distinguishing TBa from MSm in pure and conglomerate particles are shown. SPAMS pattern matching alarm algorithms are able to distinguish TBa containing particles from background matrix and MSm for >50% of the test particles, which is sufficient to enable a high probability of detection and a low false alarm rate if an adequate number of such particles are present. These results indicate the potential usefulness of SPAMS for rapid, reagentless tuberculosis screening

  14. Rapid Reagentless Detection of M. tuberculosis H37Ra in Respiratory Effluents

    Energy Technology Data Exchange (ETDEWEB)

    Adams, K L; Steele, P T; Bogan, M J; Sadler, N M; Martin, S; Martin, A N; Frank, M

    2008-01-29

    Two similar mycobacteria, Mycobacteria tuberculosis H37Ra and Mycobacteria smegmatis are rapidly detected and identified within samples containing a complex background of respiratory effluents using Single Particle Aerosol Mass Spectrometry (SPAMS). M. tuberculosis H37Ra (TBa), an avirulent strain, is used as a surrogate for virulent tuberculosis (TBv); M. smegmatis (MSm) is utilized as a near neighbor confounder for TBa. Bovine lung surfactant and human exhaled breath condensate are used as first-order surrogates for infected human lung expirations from patients with pulmonary tuberculosis. This simulated background sputum is mixed with TBa or MSm and nebulized to produce conglomerate aerosol particles, single particles that contain a bacterium embedded within a background respiratory matrix. Mass spectra of single conglomerate particles exhibit ions associated with both respiratory effluents and mycobacteria. Spectral features distinguishing TBa from MSm in pure and conglomerate particles are shown. SPAMS pattern matching alarm algorithms are able to distinguish TBa containing particles from background matrix and MSm for >50% of the test particles, which is sufficient to enable a high probability of detection and a low false alarm rate if an adequate number of such particles are present. These results indicate the potential usefulness of SPAMS for rapid, reagentless tuberculosis screening.

  15. A magnetic particles-based chemiluminescence enzyme immunoassay for rapid detection of ovalbumin.

    Science.gov (United States)

    Feng, Xiao-Li; Ren, Hong-Lin; Li, Yan-Song; Hu, Pan; Zhou, Yu; Liu, Zeng-Shan; Yan, Dong-Ming; Hui, Qi; Liu, Dong; Lin, Chao; Liu, Nan-Nan; Liu, Yan-Yan; Lu, Shi-Ying

    2014-08-15

    Egg allergy is an important public health and safety concern, so quantification and administration of food or vaccines containing ovalbumin (OVA) are urgently needed. This study aimed to establish a rapid and sensitive magnetic particles-chemiluminescence enzyme immunoassay (MPs-CLEIA) for the determination of OVA. The proposed method was developed on the basis of a double antibodies sandwich immunoreaction and luminol-H2O2 chemiluminescence system. The MPs served as both the solid phase and separator, the anti-OVA MPs-coated polyclonal antibodies (pAbs) were used as capturing antibody, and the horseradish peroxidase (HRP)-labeled monoclonal antibody (mAb) was taken as detecting antibody. The parameters of the method were evaluated and optimized. The established MPs-CLEIA method had a linear range from 0.31 to 100ng/ml with a detection limit of 0.24ng/ml. The assays showed low reactivities and less than 5% of intraassay and interassay coefficients of variation (CVs), and the average recoveries were between 92 and 97%. Furthermore, the developed method was applied in real samples analysis successfully, and the correlation coefficient with the commercially available OVA kit was 0.9976. Moreover, it was more rapid and sensitive compared with the other methods for testing OVA. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Automatic RST-based system for a rapid detection of man-made disasters

    Science.gov (United States)

    Tramutoli, Valerio; Corrado, Rosita; Filizzola, Carolina; Livia Grimaldi, Caterina Sara; Mazzeo, Giuseppe; Marchese, Francesco; Pergola, Nicola

    2010-05-01

    Man-made disasters may cause injuries to citizens and damages to critical infrastructures. When it is not possible to prevent or foresee such disasters it is hoped at least to rapidly detect the accident in order to intervene as soon as possible to minimize damages. In this context, the combination of a Robust Satellite Technique (RST), able to identify for sure actual (i.e. no false alarm) accidents, and satellite sensors with high temporal resolution seems to assure both a reliable and a timely detection of abrupt Thermal Infrared (TIR) transients related to dangerous explosions. A processing chain, based on the RST approach, has been developed in the framework of the GMOSS and G-MOSAIC projects by DIFA-UNIBAS team, suitable for automatically identify on MSG-SEVIRI images harmful events. Maps of thermal anomalies are generated every 15 minutes (i.e. SEVIRI temporal repetition rate) over a selected area together with kml files (containing information on latitude and longitude of "thermally" anomalous SEVIRI pixel centre, time of image acquisition, relative intensity of anomalies, etc.) for a rapid visualization of the accident position even on Google Earth. Results achieved in the cases of gas pipelines recently exploded or attacked in Russia and in Iraq will be presented in this work.

  17. Partnerships Between Ambrosia Beetles and Fungi: Lineage-Specific Promiscuity Among Vectors of the Laurel Wilt Pathogen, Raffaelea lauricola.

    Science.gov (United States)

    Saucedo-Carabez, J R; Ploetz, Randy C; Konkol, J L; Carrillo, D; Gazis, R

    2018-04-20

    Nutritional mutualisms that ambrosia beetles have with fungi are poorly understood. Although these interactions were initially thought to be specific associations with a primary symbiont, there is increasing evidence that some of these fungi are associated with, and move among, multiple beetle partners. We examined culturable fungi recovered from mycangia of ambrosia beetles associated with trees of Persea humilis (silk bay, one site) and P. americana (avocado, six commercial orchards) that were affected by laurel wilt, an invasive disease caused by a symbiont, Raffaelea lauricola, of an Asian ambrosia beetle, Xyleborus glabratus. Fungi were isolated from 20 adult females of X. glabratus from silk bay and 70 each of Xyleborus affinis, Xyleborus bispinatus, Xyleborus volvulus, Xyleborinus saxesenii, and Xylosandrus crassiusculus from avocado. With partial sequences of ribosomal (LSU and SSU) and nuclear (β-tubulin) genes, one to several operational taxonomic units (OTUs) of fungi were identified in assayed individuals. Distinct populations of fungi were recovered from each of the examined beetle species. Raffaelea lauricola was present in all beetles except X. saxesenii and X. crassiusculus, and Raffaelea spp. predominated in Xyleborus spp. Raffaelea arxii, R. subalba, and R. subfusca were present in more than a single species of Xyleborus, and R. arxii was the most abundant symbiont in both X. affinis and X. volvulus. Raffaelea aguacate was detected for the first time in an ambrosia beetle (X. bispinatus). Yeasts (Ascomycota, Saccharomycotina) were found consistently in the mycangia of the examined beetles, and distinct, putatively co-adapted populations of these fungi were associated with each beetle species. Greater understandings are needed for how mycangia in ambrosia beetles interact with fungi, including yeasts which play currently underresearched roles in these insects.

  18. Development of a loop-mediated Isothermal amplification assay for sensitive and rapid detection of Vibrio parahaemolyticus

    Directory of Open Access Journals (Sweden)

    Kawahara Ryuji

    2008-09-01

    Full Text Available Abstract Background Vibrio parahaemolyticus is a marine seafood-borne pathogen causing gastrointestinal disorders in humans. Thermostable direct hemolysin (TDH and TDH-related hemolysin (TRH are known as major virulence determinants of V. parahaemolyticus. Most V. parahaemolyticus isolates from the environment do not produce TDH or TRH. Total V. parahaemolyticus has been used as an indicator for control of seafood contamination toward prevention of infection. Detection of total V. parahaemolyticus using conventional culture- and biochemical-based assays is time-consuming and laborious, requiring more than three days. Thus, we developed a novel and highly specific loop-mediated isothermal amplification (LAMP assay for the sensitive and rapid detection of Vibrio parahaemolyticus. Results The assay provided markedly more sensitive and rapid detection of V. parahaemolyticus strains than conventional biochemical and PCR assays. The assay correctly identified 143 V. parahaemolyticus strains, but did not detect 33 non-parahaemolyticus Vibrio and 56 non-Vibrio strains. Sensitivity of the LAMP assay for direct detection of V. parahaemolyticus in pure cultures and in spiked shrimp samples was 5.3 × 102 CFU per ml/g (2.0 CFU per reaction. The sensitivity of the LAMP assay was 10-fold more sensitive than that of the conventional PCR assay. The LAMP assay was markedly faster, requiring for amplification 13–22 min in a single colony on TCBS agar from each of 143 V. parahaemolyticus strains and less than 35 min in spiked shrimp samples. The LAMP assay for detection of V. parahaemolyticus required less than 40 min in a single colony on thiosulfate citrate bile salt sucrose (TCBS agar and 60 min in spiked shrimp samples from the beginning of DNA extraction to final determination. Conclusion The LAMP assay is a sensitive, rapid and simple tool for the detection of V. parahaemolyticus and will facilitate the surveillance for control of contamination of V

  19. Isolation and Identification of Spoilage Fungi Associated With Rice ...

    African Journals Online (AJOL)

    The spoilage fungi isolated were Aspergillus species, Rhizopus, Penicilluim, Fusarium, Eurotium, Mucor, Geotrichum, Alternaria, Cladosporium and Actinomyces species. The predominant spoilage fungi in the grains were Aspergillus species. The populations of some spoilage fungi isolated from the grains were not high ...

  20. Development of molecular tools for rapid detection and quantification of indoor airborne molds to assess their impact on public health

    OpenAIRE

    Libert, Xavier

    2017-01-01

    Currently, contamination of the indoor environment by fungi is suggested to be a public health problem, although scientific evidence on the causal link is still limited. The monitoring of indoor airborne fungal contamination is a common tool to help understanding the link between fungi in houses and respiratory problems. Classical monitoring methods, based on cultivation and microscopic identification, have some limitations. For example, uncultivable or dead fungi (“unknown” fraction) cannot ...

  1. Rapid detection of polyethylene glycol sonolysis upon functionalization of carbon nanomaterials.

    Science.gov (United States)

    Murali, Vasanth S; Wang, Ruhung; Mikoryak, Carole A; Pantano, Paul; Draper, Rockford

    2015-09-01

    Polyethylene glycol (PEG) and related polymers are often used in the functionalization of carbon nanomaterials in procedures that involve sonication. However, PEG is very sensitive to sonolytic degradation and PEG degradation products can be toxic to mammalian cells. Thus, it is imperative to assess potential PEG degradation to ensure that the final material does not contain undocumented contaminants that can introduce artifacts into experimental results. Described here is a simple and inexpensive polyacrylamide gel electrophoresis method to detect the sonolytic degradation of PEG. The method was used to monitor the integrity of PEG phospholipid constructs and branched chain PEGs after different sonication times. This approach not only helps detect degraded PEG, but should also facilitate rapid screening of sonication parameters to find optimal conditions that minimize PEG damage. © 2015 by the Society for Experimental Biology and Medicine.

  2. Fat Content Modulates Rapid Detection of Food: A Visual Search Study Using Fast Food and Japanese Diet

    OpenAIRE

    Sawada, Reiko; Sato, Wataru; Toichi, Motomi; Fushiki, Tohru

    2017-01-01

    Rapid detection of food is crucial for the survival of organisms. However, previous visual search studies have reported discrepant results regarding the detection speeds for food vs. non-food items; some experiments showed faster detection of food than non-food, whereas others reported null findings concerning any speed advantage for the detection of food vs. non-food. Moreover, although some previous studies showed that fat content can affect visual attention for food, the effect of fat cont...

  3. [Distribution of airborne fungi, particulate matter and carbon dioxide in Seoul metropolitan subway stations].

    Science.gov (United States)

    Kim, Ki Youn; Park, Jae Beom; Kim, Chi Nyon; Lee, Kyung Jong

    2006-07-01

    The aims of this study were to examine the level of airborne fungi and environmental factors in Seoul metropolitan subway stations and to provide fundamental data to protect the health of subway workers and passengers. The field survey was performed from November in 2004 to February in 2005. A total 22 subway stations located at Seoul subway lines 1-4 were randomly selected. The measurement points were subway workers' activity areas (station office, bedroom, ticket office and driver's seat) and the passengers' activity areas (station precincts, inside train and platform). Air sampling for collecting airborne fungi was carried out using a one-stage cascade impactor. The PM and CO2 were measured using an electronic direct recorder and detecting tube, respectively. In the activity areas of the subway workers and passengers, the mean concentrations of airborne fungi were relatively higher in the workers' bedroom and station precinct whereas the concentration of particulate matter, PM10 and PM2.5, were relatively higher in the platform, inside the train and driver's seat than in the other activity areas. There was no significant difference in the concentration of airborne fungi between the underground and ground activity areas of the subway. The mean PM10 and PM2.5 concentration in the platform located at underground was significantly higher than that of the ground (psubway line 1-4 were not serious enough to cause respiratory disease in subway workers and passengers. This indicates that there is little correlation between airborne fungi and particulate matter.

  4. Comet assay for rapid detection of base damage in foods

    International Nuclear Information System (INIS)

    Al-Zubaidi, I. A.; Abdullah, T. S.; Qasim, S. R.

    2012-12-01

    Single cell gel electrophoresis (SCGE) or comet assay technique a sensitive, reliable and rapid method for DNA double and single strand break, alkali- labile site and delayed repair site detection in individual cells. In recent years, this method has been widely used for studies of DNA repair, genetic toxicology, and environmental biomontoring, however, this technique serves as an important tool for detection of DNA damage in living organism and is increasing being used in genetic testing of industrial chemicals, environmental agent's contaminations. This research paper helps to evaluate the oxidant agent's effects of exposure to organic pollutants by using comet assay techniques. This study used five samples of each food sample (Meat, Chicken, Rice, Fruits, Vegetables and Tea) to evaluate the genotoxic effects of exposure, to environmental agent's pollutants. The experimental data suggest that the DNA damage parameters ( Tail length, Tail width 1 ) were found higher value in exposed population when compared with the ratio of the length to width that cells exhibiting no migration having a ratio of 1. The percentage and distribution of cells in exposed population of cells also increases with the increase in values. This study demonstrates that, using sensitive techniques, it is possible to detect environmental agent's risks at an early stage. (Author)

  5. The Utilization of Fungi and Their Products to Increase Livestock Production

    OpenAIRE

    Riza Zainuddin Ahmad

    2011-01-01

    Fungi as part of eukaryotic organisms play an important role for livestock. Some fungi are detrimental because they cause animal diseases, and some fungi are beneficial because they can improve animal productivity. The use of fungi that benefit from starting he has done as agents of biological control and to be as probiotics.Within the fungi, the use of simple technologies to high level degree for the benefit of cattle is developed. This paper describes some fungi that are beneficial and dire...

  6. Whole-bacterium SELEX of DNA aptamers for rapid detection of E.coli O157:H7 using a QCM sensor.

    Science.gov (United States)

    Yu, Xiaofan; Chen, Fang; Wang, Ronghui; Li, Yanbin

    2018-01-20

    The rapid detection of foodborne pathogens is critical to ensure food safety. The objective of this study is to select aptamers specifically bound to Escherichia coli O157:H7 using the whole-bacterium SELEX (Systematic Evolution of Ligands by Exponential Enrichment) and apply the selected aptamer to a QCM (quartz crystal microbalance) sensor for rapid and sensitive detection of target bacteria. A total of 19 rounds of selection against live E. coli O157:H7 and 6 rounds of counter selection against a mixture of Staphylococcus aureus, Listeria monocytogenes, and Salmonella Typhimurium, were performed. The aptamer pool from the last round was cloned and sequenced. One sequence S1 that appeared 16 times was characterized and a dissociation constant (K d ) of 10.30nM was obtained. Subsequently, a QCM aptasensor was developed for the rapid detection of E. coli O157:H7. The limit of detection (LOD) and the detection time of the aptasensor was determined to be 1.46×10 3 CFU/ml and 50min, respectively. This study demonstrated that the ssDNA aptamer selected by the whole-bacterium SELEX possessed higher sensitivity than previous work and the potential use of the constructed QCM aptasensor in rapid screening of foodborne pathogens. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Maarja Unduski 'Fungi'

    Index Scriptorium Estoniae

    1999-01-01

    24. nov.-st Linnagaleriis Tallinnas Maarja Unduski kolmas isiknäitus 'Fungi'. Eksponeeritud hiigelseened ja rida värviliste lehtedega ramatuid, mille kaante valmistamisel on autor esmakordselt kasutanud ka lõuendit ja paberreljeefi.

  8. Rapid and sensitive detection of Yersinia pestis using amplification of plague diagnostic bacteriophages monitored by real-time PCR.

    Directory of Open Access Journals (Sweden)

    Kirill V Sergueev

    Full Text Available BACKGROUND: Yersinia pestis, the agent of plague, has caused many millions of human deaths and still poses a serious threat to global public health. Timely and reliable detection of such a dangerous pathogen is of critical importance. Lysis by specific bacteriophages remains an essential method of Y. pestis detection and plague diagnostics. METHODOLOGY/PRINCIPAL FINDINGS: The objective of this work was to develop an alternative to conventional phage lysis tests--a rapid and highly sensitive method of indirect detection of live Y. pestis cells based on quantitative real-time PCR (qPCR monitoring of amplification of reporter Y. pestis-specific bacteriophages. Plague diagnostic phages phiA1122 and L-413C were shown to be highly effective diagnostic tools for the detection and identification of Y. pestis by using qPCR with primers specific for phage DNA. The template DNA extraction step that usually precedes qPCR was omitted. phiA1122-specific qPCR enabled the detection of an initial bacterial concentration of 10(3 CFU/ml (equivalent to as few as one Y. pestis cell per 1-microl sample in four hours. L-413C-mediated detection of Y. pestis was less sensitive (up to 100 bacteria per sample but more specific, and thus we propose parallel qPCR for the two phages as a rapid and reliable method of Y. pestis identification. Importantly, phiA1122 propagated in simulated clinical blood specimens containing EDTA and its titer rise was detected by both a standard plating test and qPCR. CONCLUSIONS/SIGNIFICANCE: Thus, we developed a novel assay for detection and identification of Y. pestis using amplification of specific phages monitored by qPCR. The method is simple, rapid, highly sensitive, and specific and allows the detection of only live bacteria.

  9. TaqMan MGB probe fluorescence real-time quantitative PCR for rapid detection of Chinese Sacbrood virus.

    Directory of Open Access Journals (Sweden)

    Ma Mingxiao

    Full Text Available Sacbrood virus (SBV is a picorna-like virus that affects honey bees (Apis mellifera and results in the death of the larvae. Several procedures are available to detect Chinese SBV (CSBV in clinical samples, but not to estimate the level of CSBV infection. The aim of this study was develop an assay for rapid detection and quantification of this virus. Primers and probes were designed that were specific for CSBV structural protein genes. A TaqMan minor groove binder (MGB probe-based, fluorescence real-time quantitative PCR was established. The specificity, sensitivity and stability of the assay were assessed; specificity was high and there were no cross-reactivity with healthy larvae or other bee viruses. The assay was applied to detect CSBV in 37 clinical samples and its efficiency was compared with clinical diagnosis, electron microscopy observation, and conventional RT-PCR. The TaqMan MGB-based probe fluorescence real-time quantitative PCR for CSBV was more sensitive than other methods tested. This assay was a reliable, fast, and sensitive method that was used successfully to detect CSBV in clinical samples. The technology can provide a useful tool for rapid detection of CSBV. This study has established a useful protocol for CSBV testing, epidemiological investigation, and development of animal models.

  10. Real-time PCR-based method for the rapid detection of extended RAS mutations using bridged nucleic acids in colorectal cancer.

    Science.gov (United States)

    Iida, Takao; Mizuno, Yukie; Kaizaki, Yasuharu

    2017-10-27

    Mutations in RAS and BRAF are predictors of the efficacy of anti-epidermal growth factor receptor (EGFR) therapy in patients with metastatic colorectal cancer (mCRC). Therefore, simple, rapid, cost-effective methods to detect these mutations in the clinical setting are greatly needed. In the present study, we evaluated BNA Real-time PCR Mutation Detection Kit Extended RAS (BNA Real-time PCR), a real-time PCR method that uses bridged nucleic acid clamping technology to rapidly detect mutations in RAS exons 2-4 and BRAF exon 15. Genomic DNA was extracted from 54 formalin-fixed paraffin-embedded (FFPE) tissue samples obtained from mCRC patients. Among the 54 FFPE samples, BNA Real-time PCR detected 21 RAS mutations (38.9%) and 5 BRAF mutations (9.3%), and the reference assay (KRAS Mutation Detection Kit and MEBGEN™ RASKET KIT) detected 22 RAS mutations (40.7%). The concordance rate of detected RAS mutations between the BNA Real-time PCR assay and the reference assays was 98.2% (53/54). The BNA Real-time PCR assay proved to be a more simple, rapid, and cost-effective method for detecting KRAS and RAS mutations compared with existing assays. These findings suggest that BNA Real-time PCR is a valuable tool for predicting the efficacy of early anti-EGFR therapy in mCRC patients. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Highly sensitive and rapid bacteria detection using molecular beacon-Au nanoparticles hybrid nanoprobes.

    Science.gov (United States)

    Cao, Jing; Feng, Chao; Liu, Yan; Wang, Shouyu; Liu, Fei

    2014-07-15

    Since many diseases are caused by pathogenic bacterial infections, accurate and rapid detection of pathogenic bacteria is in urgent need to timely apply appropriate treatments and to reduce economic costs. To end this, we designed molecular beacon-Au nanoparticle hybrid nanoprobes to improve the bacterial detection efficiency and sensitivity. Here, we show that the designed molecular beacon modified Au nanoparticles could specifically recognize synthetic DNAs targets and can readily detect targets in clinical samples. Moreover, the hybrid nanoprobes can recognize Escherichia coli within an hour at a concentration of 10(2) cfu/ml, which is 1000-folds sensitive than using molecular beacon directly. Our results show that the molecular beacon-Au nanoparticle hybrid nanoprobes have great potential in medical and biological applications. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Evaluation of a rapid immunodiagnostic test kit for detection of African lyssaviruses from brain material

    Directory of Open Access Journals (Sweden)

    W. Markotter

    2009-09-01

    Full Text Available Rapid immunodiagnostic test kit was evaluated against a selection of isolates of lyssavirus genotypes occurring in Africa. The test was carried out in parallel comparison with the fluorescent antibody test (FAT and isolates representing previously established phylogenetic groups from each genotype were included. The specificity of the rapid immunodiagnostic test compared favourably with the FAT and was found to detect all representatives of genotypes 1, 2, 3 and 4 in brain samples of either field cases or suckling mouse brain inoculates.

  13. Rapid detection of fungal alpha-amylase in the work environment with a lateral flow immunoassay

    NARCIS (Netherlands)

    Bogdanovic, J.; Koets, M.; Sander, I.; Wouters, I.; Meijster, T.; Heederik, D.J.J.; Amerongen, van A.; Doekes, G.

    2006-01-01

    Background Occupational allergen exposure assessment usually requires airborne dust sampling at the worksite followed by dust extraction and enzyme immunoassay (EIA) analysis at the laboratory. Use of semiquantitative lateral flow immunoassays (LFIAs) may allow a more rapid detection procedure with

  14. A C. elegans-based foam for rapid on-site detection of residual live virus.

    Energy Technology Data Exchange (ETDEWEB)

    Negrete, Oscar A.; Branda, Catherine; Hardesty, Jasper O. E. (Sandia National Laboratories, Albuquerque, NM); Tucker, Mark David (Sandia National Laboratories, Albuquerque, NM); Kaiser, Julia N. (Global Product Management, Hilden, Germany); Kozina, Carol L.; Chirica, Gabriela S.

    2012-02-01

    In the response to and recovery from a critical homeland security event involving deliberate or accidental release of biological agents, initial decontamination efforts are necessarily followed by tests for the presence of residual live virus or bacteria. Such 'clearance sampling' should be rapid and accurate, to inform decision makers as they take appropriate action to ensure the safety of the public and of operational personnel. However, the current protocol for clearance sampling is extremely time-intensive and costly, and requires significant amounts of laboratory space and capacity. Detection of residual live virus is particularly problematic and time-consuming, as it requires evaluation of replication potential within a eukaryotic host such as chicken embryos. The intention of this project was to develop a new method for clearance sampling, by leveraging Sandia's expertise in the biological and material sciences in order to create a C. elegans-based foam that could be applied directly to the entire contaminated area for quick and accurate detection of any and all residual live virus by means of a fluorescent signal. Such a novel technology for rapid, on-site detection of live virus would greatly interest the DHS, DoD, and EPA, and hold broad commercial potential, especially with regard to the transportation industry.

  15. Compatibility and incompatibility in hyphal anastomosis of arbuscular mycorrhizal fungi

    Directory of Open Access Journals (Sweden)

    Candido Barreto de Novais

    Full Text Available ABSTRACT: Arbuscular mycorrhizal fungi (AMF, which live in symbiosis with 80 % of plants, are not able to grow when separated from their hosts. Spore germination is not host-regulated and germling growth is shortly arrested in the absence of host roots. Germling survival chances may be increased by hyphal fusions (anastomoses, which allow access to nutrients flowing in the extraradical mycelium (ERM. Perfect anastomoses, occurring with high frequency among germlings and the ERM of the same isolate, show protoplasm continuity and disappearance of hyphal walls. A low frequency of perfect fusions has been detected among co-specific genetically different isolates, although fungal nuclei have been consistently detected in all perfect fusions, suggesting active nuclear migration. When plants of different taxa establish symbioses with the same AMF species, anastomoses between ERM spreading from single root systems establish a common mycelium, which is an essential element to plant nutrition and communication. The interaction among mycelia produced by different isolates may also lead to pre-fusion incompatibility which hinders anastomosis formation, or to incompatibility after fusion, which separates the hyphal compartments. Results reported here, obtained by analyses of hyphal compatibility/incompatibility in AMF, suggest that anastomosis formation and establishment of protoplasm flow, fundamental to the maintenance of mycelial physiological and genetic continuity, may affect the fitness of these ecologically important biotrophic fungi.

  16. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.

    Directory of Open Access Journals (Sweden)

    Christian Hoffmann

    Full Text Available Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.

  17. Studies of separation and purification of fungi for uranium-leaching

    International Nuclear Information System (INIS)

    Wang Yongdong; Li Guangyue; Shi Wenge; Hu Nan; Pan Wenjun; Zhou Zhixiang; Deng Qinwen; Ding Dexin

    2010-01-01

    To obtain purified fungi for uranium-leaching, fungi in uranium ores were separated using Dox(-), SDA, PDA and Dox(+) medium, then spores were picked from the plates for fungi purification. Four strains of fungi were acquired and one of them is aspergillus niger,others are Penicillium. The results demonstrate that a large number of fungi species exist in uranium ores, and some of them have the ability of producing organic acid, in addition,they have high growing velocity with the potential of being applied to uranium leaching. (authors)

  18. In vivo interactions of entomopathogenic fungi, Beauveria spp. and Metarhizium anisopliae with selected opportunistic soil fungi of sugarcane ecosystem.

    Science.gov (United States)

    Geetha, N; Preseetha, M; Hari, K; Santhalakshmi, G; Bai, K Subadra

    2012-07-01

    In the present study, the interactions of entomopathogenic fungi viz., Beauveria bassiana, Beauveria brongniartii and Metarhizium anisopliae among themselves and three other opportunistic soil fungi from the sugarcane ecosystem namely, Fusarium saachari, Aspergillus sp. and Penecillium sp. were assayed in vivo against Galleria mellonella larvae. The tested fungi were co-applied on IV instar G. mellonella @ 1 x 10(7) ml(-1), in combinations of two, at the interval of 24 hrs either preceding or succeeding each otherto assess their efficacy and sporulation rates. Results showed that often mortality rates did not correspond to the spore harvest of the mortality agent and presence of other fungus may be antagonistic. The efficacy of B. bassiana (90%) and B. brongniartii (100%) was not enhanced further but was negatively affected in most combinations with other fungi. In case of M. anisopliae compatibility was higher, resulting in higher mortality by application of B. bassiana before (100%) or after (83.3%) M. anisopliae than when it was applied alone (70%). During sporulation, B. bassiana faced the most intense competition from M. anisopliae (2.75 x 10(6) larva(-1)) and enhancement due to F sacchari irrespective of sequence of application. In case of B. brongniartii, sporulation was lowest in the combination of B. brongniartiipreceding M. anisopliae (1.83 x10(6) larva(-1)) and B. brongniartii succeeding B. bassiana (1.58 x 10(6) larva(-1)). Of all fungi tested, except F sacchari (65.33 x 10(6) larva(-1)) all the other species affected sporulation of M. ansiopliae with the least in treatment of B. bassiana application following M. anisopliae. Similar kind of interaction was observed during sporulation of soil fungi when combined with entomopathogenic fungi, though individually they could not cause mortality of larvae.

  19. Comparative genome analysis of Basidiomycete fungi

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Salamov, Asaf; Henrissat, Bernard; Nagy, Laszlo; Brown, Daren; Held, Benjamin; Baker, Scott; Blanchette, Robert; Boussau, Bastien; Doty, Sharon L.; Fagnan, Kirsten; Floudas, Dimitris; Levasseur, Anthony; Manning, Gerard; Martin, Francis; Morin, Emmanuelle; Otillar, Robert; Pisabarro, Antonio; Walton, Jonathan; Wolfe, Ken; Hibbett, David; Grigoriev, Igor

    2013-08-07

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism. Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may be inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.

  20. The Utilization of Fungi and Their Products to Increase Livestock Production

    Directory of Open Access Journals (Sweden)

    Riza Zainuddin Ahmad

    2011-06-01

    Full Text Available Fungi as part of eukaryotic organisms play an important role for livestock. Some fungi are detrimental because they cause animal diseases, and some fungi are beneficial because they can improve animal productivity. The use of fungi that benefit from starting he has done as agents of biological control and to be as probiotics.Within the fungi, the use of simple technologies to high level degree for the benefit of cattle is developed. This paper describes some fungi that are beneficial and direction and suggestion to develop research on veterinary micology in Indonesia.

  1. Rapid detection of food pathogens using RNA aptamers-immobilized slide.

    Science.gov (United States)

    Maeng, Jin-Soo; Kim, Namsoo; Kim, Chong-Tai; Han, Seung Ryul; Lee, Young Ju; Lee, Seong-Wook; Lee, Myung-Hyun; Cho, Yong-Jin

    2012-07-01

    The purpose of this study was to develop a simple and rapid detection system for foodborne bacteria, which consisted of an optical microscope and its slide chip with artificial antibodies, or RNA aptamers. From an RNA pool, three each RNA aptamers were built by the method of SELEX (systematic evolution of ligands by exponential enrichment) for components of cell wall, LPS (lipopolysaccharide) from E. coli O157:H7, teichoic acid from Staphylococcus aureus and a cell membrane protein of OmpC from Salmonella typhimurium, respectively. These aptamers were hybridized with thiol-conjugated 16 dT-linker molecules in order to be immobilized on silver surface which was, in advance, fabricated on glass slide, using a spin-coating method. To confirm that each aptamers retained its specific binding activities to their antigenic live bacteria, microscopic view of bound cells immobilized on silver film were observed. Furthermore, we observed the fluorescence-emitting bacteria-aptamer complex immobilized on silver film after adding RNA aptamers hybridized with fluorophore, FAM-conjugated 16 dT-linker molecules. As a result, the RNA aptamers-immobilized slide system developed in this study was a useful new tool to rapidly monitor individual food pathogens.

  2. Product ion filtering with rapid polarity switching for the detection of all fumonisins and AAL-toxins.

    Science.gov (United States)

    Renaud, Justin B; Kelman, Megan J; Qi, Tianyu F; Seifert, Keith A; Sumarah, Mark W

    2015-11-30

    Fumonisins and AAL-toxins are structurally similar mycotoxins that contaminate agricultural crops and foodstuffs. Traditional analytical screening methods are designed to target the known compounds for which standards are available but there is clear evidence that many other derivatives exist and could be toxic. A fast, semi-targeted method for the detection of all known fumonisins, AAL-toxins and related emerging toxins is required. Strains of Fusarium verticillioides, Alternaria arborescens and Aspergillus welwitschiae were grown on their associated crops (maize, tomatoes, and grapes, respectively). Extracts were first analyzed in negative mode using product ion filtering to detect the tricarballylic ester product ion that is common to fumonisins and AAL-toxins (m/z 157.0142). During the same liquid chromatography (LC) run, rapid polarity switching was then used to collect positive mode tandem mass spectrometric (MS(2) ) data for characterization of the detected compounds. Fumonisin B1 , B2 , B3 and B4 were detected on Fusarium contaminated maize, AAL-toxins TA, TB, TD, TE were detected on Alternaria inoculated tomatoes and fumonisin B2 , B4 and B6 on Aspergillus contaminated grapes. Additionally, over 100 structurally related compounds possessing a tricarballylic ester were detected from the mould inoculated plant material. These included a hydroxyl-FB1 from F. verticillioides inoculated maize, keto derivatives of AAL-toxins from A. arborescens inoculated tomatoes, and two previously unreported classes of non-aminated fumonisins from Asp. welwitschiae contaminated grapes. A semi-targeted method for the detection of all fumonisins and AAL-toxins in foodstuffs was developed. The use of the distinctive tricarballylic ester product anion for detection combined with rapid polarity switching and positive mode MS(2) is an effective strategy for differentiating between known isomers such as FB1 and FB6 . This analytical tool is also effective for the identification of

  3. The geographical distribution of tremellaceous fungi in Poland

    Directory of Open Access Journals (Sweden)

    Władysław Wojewoda

    2014-11-01

    Full Text Available The geographical distribution of the Polish tremellaceous fungi is discussed in this paper. The list of localities and the maps of the distribution of 60 Polish species (45 of Tremellales, 13 of Auriculariales and 2 of Septobasidiales are given. The author distinguishes several geographical elements, and describes the vertical distribution of these fungi. This paper is a supplement to "Fungi (Mycota", vol. 8, Polish Flora (Wojewoda 1977.

  4. Genetic diversity patterns of arbuscular mycorrhizal fungi associated with the mycoheterotroph Arachnitis uniflora Phil. (Corsiaceae).

    Science.gov (United States)

    Renny, Mauricio; Acosta, M Cristina; Cofré, Noelia; Domínguez, Laura S; Bidartondo, Martin I; Sérsic, Alicia N

    2017-06-01

    Arachnitis uniflora is a mycoheterotrophic plant that exploits arbuscular mycorrhizal fungi of neighbouring plants. We tested A. uniflora 's specificity towards fungi across its large latitudinal range, as well as the role of historical events and current environmental, geographical and altitudinal variables on fungal genetic diversity. Arachnitis uniflora mycorrhizas were sampled at 25 sites. Fungal phylogenetic relationships were reconstructed, genetic diversity was calculated and the main divergent lineages were dated. Phylogeographical analysis was performed with the main fungal clade. Fungal diversity correlations with environmental factors were investigated. Glomeraceae fungi dominated, with a main clade that likely originated in the Upper Cretaceous and diversified in the Miocene. Two other arbuscular mycorrhizal fungal families not previously known to be targeted by A. uniflora were detected rarely and appear to be facultative associations. High genetic diversity, found in Bolivia and both northern and southern Patagonia, was correlated with temperature, rainfall and soil features. Fungal genetic diversity and its distribution can be explained by the ancient evolutionary history of the target fungi and by micro-scale environmental conditions with a geographical mosaic pattern. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  5. Diversity and persistence of ectomycorrhizal fungi and their effect on nursery-inoculated Pinus pinaster in a post-fire plantation in Northern Portugal.

    Science.gov (United States)

    Franco, Albina R; Sousa, Nadine R; Ramos, Miguel A; Oliveira, Rui S; Castro, Paula M L

    2014-11-01

    Ectomycorrhizal fungi (ECMF) play an important role in forest ecosystems, often mitigating stress factors and increasing seedling performance. The aim of this study was to investigate the effects of a nursery inoculation on Pinus pinaster growth and on the fungal communities established when reforesting burned areas. Inoculated P. pinaster saplings showed 1.5-fold higher stem height than the non-inoculated controls after a 5 year growth period, suggesting that fungal inoculation could potentiate tree growth in the field. Ordination analysis revealed the presence of different ECMF communities on both plots. Among the nursery-inoculated fungi, Laccaria sp., Rhizopogon sp., Suillus bovinus and Pisolithus sp. were detected on inoculated Pinus saplings on both sampling periods, indicating that they persisted after field establishment. Other fungi were also detected in the inoculated plants. Phialocephala sp. was found on the first assessment, while Terfezia sp. was detected on both sampling periods. Laccaria sp. and Rhizopogon sp. were identified in the control saplings, belonging however to different species than those found in the inoculated plot. Inocybe sp., Thelephora sp. and Paxillus involutus were present on both sampling periods in the non-inoculated plots. The results suggest that ECMF inoculation at nursery stage can benefit plant growth after transplantation to a post-fire site and that the inoculated fungi can persist in the field. This approach has great potential as a biotechnological tool to aid in the reforestation of burned areas.

  6. Fungi associated with free-living soil nematodes in Turkey

    Directory of Open Access Journals (Sweden)

    Karabörklü Salih

    2015-01-01

    Full Text Available Free-living soil nematodes have successfully adapted world-wide to nearly all soil types from the highest to the lowest of elevations. In the current study, nematodes were isolated from soil samples and fungi associated with these free-living soil nematodes were determined. Large subunit (LSU rDNAs of nematode-associated fungi were amplified and sequenced to construct phylogenetic trees. Nematode-associated fungi were observed in six nematode strains belonging to Acrobeloides, Steinernema and Cephalobus genera in different habitats. Malassezia and Cladosporium fungal strains indicated an association with Acrobeloides and Cephalobus nematodes, while Alternaria strains demonstrated an association with the Steinernema strain. Interactions between fungi and free-living nematodes in soil are discussed. We suggest that nematodes act as vectors for fungi.

  7. Preliminary Results of a Multicentre Study of the UBC Rapid Test for Detection of Urinary Bladder Cancer.

    Science.gov (United States)

    Ecke, Thorsten H; Arndt, Christian; Stephan, Carsten; Hallmann, Steffen; Lux, Oliver; Otto, Thomas; Ruttloff, Jürgen; Gerullis, Holger

    2015-05-01

    UBC Rapid is a test detecting fragments of cytokeratins 8 and 18 in urine. These are cytokeratins frequently overexpressed in tumor cells. We present the first results of a multi-centre study using UBC Rapid in patients with bladder cancer and healthy controls. Clinical urine samples from 92 patients with tumors of the urinary bladder (45 low-grade and 47 high-grade tumors) and from 33 healthy controls were used. Urine samples were analyzed by the UBC Rapid point-of-care (POC) system and evaluated both visually and quantitatively using a concile Omega 100 POC reader. For visual evaluation, different thresholds of band intensity for considering a test as positive were applied. Sensitivities and specificities were calculated by contingency analyses. We found that pathological concentrations by UBC Rapid are detectable in urine of patients with bladder cancer. The calculated diagnostic sensitivity of UBC Rapid in urine was 68.1% for high-grade, but only 46.2% for low-grade tumors. The specificity was 90.9%. The area under the curve (AUC) after receiver-operated curve (ROC) analysis was 0.733. Pathological levels of UBC Rapid in urine are higher in patients with bladder cancer in comparison to the control group (pbladder cancer and controls. Further studies with a greater number of patients will show how valuable these results are. Copyright© 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  8. Detection and monitoring of human bocavirus 1 infection by a new rapid antigen test

    Directory of Open Access Journals (Sweden)

    A.H.L. Bruning

    2016-05-01

    Full Text Available Clinically relevant diagnosis of human bocavirus 1 (HBoV1 is challenging, as the virus is frequently detected in asymptomatic patients, and cofindings with other respiratory viruses are common. The clinical value of current diagnostic methods, such as PCR, is therefore low, and alternative diagnostic strategies are needed. We describe for the first time the use of an antigen detection assay for the rapid identification of HBoV1 in a paediatric patient with respiratory tract infection symptoms. We estimate the duration of active HBoV1 infection to be 6 days.

  9. A nanoparticle label/immunochromatographic electrochemical biosensor for rapid and sensitive detection of prostate-specific antigen

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Ying-Ying; Wang, Jun; Liu, Guodong; Wu, Hong; Wai, Chien M.; Lin, Yuehe

    2008-06-15

    We present a nanoparticle (NP) label/immunochromatographic electrochemical biosensor (IEB) for rapid and sensitive detection of prostate-specific antigen (PSA) in human serum. This IEB integrates the immunochromatographic strip with the electrochemical detector for transducing quantitative signals. The NP label, made of CdSe@ZnS, serves as a signal-amplifier vehicle. A sandwich immunoreaction was performed on the immunochromatographic strip. The captured NP labels in the test zone were determined by highly sensitive stripping voltammetric measurement of the dissolved metallic component (cadmium) with a disposable-screen-printed electrode, which is embedded underneath the membrane of the test zone. Experimental parameters (e.g., immunoreaction time, the amount of anti-PSA-NP conjugations applied) and electrochemical detection conditions (e.g., preconcentration potential and time) were optimized using this biosensor for PSA detection. The analytical performance of this biosensor was evaluated with serum PSA samples according to the “figure-of-merits” (e.g., dynamic range, reproducibility, and detection limit). The results were validated with enzyme-linked immunosorbent assay (ELISA) and show high consistency. It is found that this biosensor is very sensitive with the detection limit of 0.02 ng/mL PSA and is quite reproducible. This method is rapid, clinically accurate, and less expensive than other diagnosis tools for PSA; therefore, this IEB coupled with a portable electrochemical analyzer shows great promise for simple, sensitive, quantitative point-of-care testing of disease-related protein biomarkers.

  10. Rapid DNA haplotyping using a multiplex heteroduplex approach: Application to Duchenne muscula dystrophy carrier detection

    Energy Technology Data Exchange (ETDEWEB)

    Prior, T.W.; Wenger, G.D.; Moore, J. [Ohio State Univ., Columbus, OH (United States)] [and others

    1994-09-01

    A new strategy has been developed for rapid haplotype analysis. It is based on an initial multiplex amplification of several polymorphic sites, followed by heteroduplex detection. Heteroduplexes formed between two different alleles are detected because they migrate differently than the corresponding homoduplexes in Hydrolink-MDE gel. The method is simple, rapid, does not depend on specific sequences such as restriction enzyme sites or CA boxes and does not require the use of isotope. This approach has been tested using 12 commonly occurring polymorphisms spanning the dystrophin gene as a model. We describe the use of the method to assign the carrier status of females in Duchenne muscular dystrophy (DMD) pedigrees. As a result of expanding the number of detectable polymorphisms throughout the dystrophin gene, we show how the method can easily be combined with dinucleotide analysis to improve the accuracy of carrier detection in the nondeletion cases. The technique is also shown to be used as an effective screen for improving carrier detection in several families with deletions. The finding of heterozygosity within the deletion identifies the at-risk female as a noncarrier. Using this method, we have identified and incorporated 3 new dystrophin polymorphisms (one of which in exon 16 is unique to African Americans). The method may be used other genetic diseases when mutations are unknown, or there are few dinucleotide markers in the gene proximity, or for the identification of haplotype backgrounds of mutant alleles.

  11. High resolution melting analysis: a rapid and accurate method to detect CALR mutations.

    Directory of Open Access Journals (Sweden)

    Cristina Bilbao-Sieyro

    Full Text Available The recent discovery of CALR mutations in essential thrombocythemia (ET and primary myelofibrosis (PMF patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN. We tested the feasibility of high-resolution melting (HRM as a screening method for rapid detection of CALR mutations.CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET.Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34, 14% of persistent thrombocytosis suggestive of MPN (3/21 and none of the secondary thrombocytosis (0/98. Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%.This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations.

  12. An empirical investigation of the possibility of adaptability of arbuscular mycorrhizal fungi to new hosts.

    Science.gov (United States)

    Koyama, Akihiro; Pietrangelo, Olivia; Sanderson, Laura; Antunes, Pedro M

    2017-08-01

    Little is known about the adaptive capacity of arbuscular mycorrhizal (AM) fungi to novel hosts. Here we assessed the possibility of two heterospecific AM fungal isolates to adaptively change, in terms of host biomass response, as a function of host plant identity, over the course of a growing season. First, we produced pure inocula of Rhizophagus clarus and Rhizophagus intraradices, each starting from a single spore. Second, we "trained" each isolate individually in a community with two plants, sudangrass (Sorgum bicolour subsp. drummondii) and leek (Aliium ampeloprasum var. porrum), using a dual-compartment system to allow the establishment of a common mycorrhizal network between the two hosts. Third, we conducted a greenhouse experiment to reciprocally test each "trained" clone, obtained from each compartment, either with the same (home), or the other host (away) under two contrasting phosphorus levels. Overall, results did not support adaptive responses of the AM fungi to their hosts (i.e., greater host biomass under "home" relative to "away" conditions), but the opposite (i.e., greater host biomass under "away" relative to "home" conditions) was more frequently observed. These changes in AM fungal symbiotic functioning open the possibility for relatively rapid genetic change of arbuscular mycorrhizal fungi in response to new hosts, which represents one step forward from in vitro experiments.

  13. Prevention and Control of Fungi Contaminated Stored Pistachio Nuts Imported to Saudi Arabia

    Energy Technology Data Exchange (ETDEWEB)

    Nawar, Lubna Saleh [Dept. of Biology, Faculty of Science, King Abdulaziz Univ., Jeddah (Saudi Arabia)

    2008-07-01

    To evaluate the contamination risk of the improper storage of pistachio nuts was studied in the major location of Saudi Arabia by studying the fungi associated with non and salted pistachio nuts. The infection with Aspergillus flavus and A. niger and treatment of this infection with some abiotic factors , salting and fumigation with acetic acid on the invasion and colonization were also stu ded. High percentage infection (100%) were found in salted pistachio of Maidenhead , while low infection (68.75%) was found in non salted pistachio of Jihad. Referring to the total fungal counts (9845.5 and 5681.8 CFU/g nuts) were detected on malt extract yeast agar and rose bengal agar media respectively. Aspergillus niger and A. flavus were found common in all pistachio samples collected from the three locations on the two media used. The both fungi were grew at temperatures between 20 and 35 degree C, also as the relative humidity increased the fungal growth increased reached its maximum at 100% RH. Sodium chloride at 20 and 25 % completely stopped the linear of the both fungi on malt yeast extract agar medium. Application of nuts with sodium chloride was found to increased the resistance of pistachio nut to invasion and colonization by the fungi during storage. Also, the resistance to invasion was increased by increasing the doses of fumigation with acetic acid applied to the pistachio nuts reached 0% infection at the higher dose of acetic acid (60%). (author)

  14. Prevention and Control of Fungi Contaminated Stored Pistachio Nuts Imported to Saudi Arabia

    International Nuclear Information System (INIS)

    Nawar, Lubna Saleh

    2008-01-01

    To evaluate the contamination risk of the improper storage of pistachio nuts was studied in the major location of Saudi Arabia by studying the fungi associated with non and salted pistachio nuts. The infection with Aspergillus flavus and A. niger and treatment of this infection with some abiotic factors , salting and fumigation with acetic acid on the invasion and colonization were also stu ded. High percentage infection (100%) were found in salted pistachio of Maidenhead , while low infection (68.75%) was found in non salted pistachio of Jihad. Referring to the total fungal counts (9845.5 and 5681.8 CFU/g nuts) were detected on malt extract yeast agar and rose bengal agar media respectively. Aspergillus niger and A. flavus were found common in all pistachio samples collected from the three locations on the two media used. The both fungi were grew at temperatures between 20 and 35 degree C, also as the relative humidity increased the fungal growth increased reached its maximum at 100% RH. Sodium chloride at 20 and 25 % completely stopped the linear of the both fungi on malt yeast extract agar medium. Application of nuts with sodium chloride was found to increased the resistance of pistachio nut to invasion and colonization by the fungi during storage. Also, the resistance to invasion was increased by increasing the doses of fumigation with acetic acid applied to the pistachio nuts reached 0% infection at the higher dose of acetic acid (60%). (author)

  15. Rapid antibiotic efficacy screening with aluminum oxide nanoporous membrane filter-chip and optical detection system.

    Science.gov (United States)

    Tsou, Pei-Hsiang; Sreenivasappa, Harini; Hong, Sungmin; Yasuike, Masayuki; Miyamoto, Hiroshi; Nakano, Keiyo; Misawa, Takeyuki; Kameoka, Jun

    2010-09-15

    We have developed a filter-chip and optical detection system for rapid antibiotic efficacy screening. The filter-chip consisted of a 1-mL reservoir and an anodic aluminum oxide (AAO) nanoporous membrane. Sample solution with liquid growth media, bacteria, and antibiotics was incubated in the reservoir for a specific period of time. The number of live bacteria on the surface of membrane was counted after the incubation with antibiotics and filtration. Using this biosensing system, we have demonstrated a 1-h antibiotic screening for patients' clinical samples, significantly faster than the conventional antibiotic susceptibility tests that typically take more than 24h. This rapid screening nature makes the filter-chip and detection system ideal for tailoring antibiotic treatment to individual patients by reducing the microbial antibiotic resistance, and improving the survival rate for patients suffering from postoperative infections. Published by Elsevier B.V.

  16. Effect of gamma irradiation on fungi in stored rice

    International Nuclear Information System (INIS)

    Zainal Abidin Mior Ahmad.

    1987-01-01

    The objective of this study is to examine the effect of different doses of gamma irradiation on fungi infecting rice stored in various packaging materials. The agar plate test method was used. It was observed that the percentage of fungi did not appear to decrease with the increase of irradiation up to 2 kGy and also no indication of any significant reduction in percentage of fungi isolated with increasing time of storage at all levels of radiation treatment. The majority of the fungi isolated were Aspergillus and Penicillium species. (A.J.)

  17. Rapid and Sensitive Detection of Bacteria Response to Antibiotics Using Nanoporous Membrane and Graphene Quantum Dot (GQDs-Based Electrochemical Biosensors

    Directory of Open Access Journals (Sweden)

    Weiwei Ye

    2017-05-01

    Full Text Available The wide abuse of antibiotics has accelerated bacterial multiresistance, which means there is a need to develop tools for rapid detection and characterization of bacterial response to antibiotics in the management of infections. In the study, an electrochemical biosensor based on nanoporous alumina membrane and graphene quantum dots (GQDs was developed for bacterial response to antibiotics detection. Anti-Salmonella antibody was conjugated with amino-modified GQDs by glutaraldehyde and immobilized on silanized nanoporous alumina membranes for Salmonella bacteria capture. The impedance signals across nanoporous membranes could monitor the capture of bacteria on nanoporous membranes as well as bacterial response to antibiotics. This nanoporous membrane and GQD-based electrochemical biosensor achieved rapid detection of bacterial response to antibiotics within 30 min, and the detection limit could reach the pM level. It was capable of investigating the response of bacteria exposed to antibiotics much more rapidly and conveniently than traditional tools. The capability of studying the dynamic effects of antibiotics on bacteria has potential applications in the field of monitoring disease therapy, detecting comprehensive food safety hazards and even life in hostile environment.

  18. Nematophagous fungi from decomposing cattle faeces in Argentina.

    Science.gov (United States)

    Saumell, Carlos Alfredo; Fernández, Alicia Silvina; Fusé, Luis Alberto; Rodríguez, Manuela; Sagüés, María Federica; Iglesias, Lucía Emilia

    2015-01-01

    Biological control of gastrointestinal nematodes of ruminants by use of nematophagous fungi would become part of any livestock parasite integral control system. Identifying autochthonous species that could then be selected for mass production is an important phase in the practical use of biological control. To search for nematophagous fungi with potential use as biological control agents against gastrointestinal nematodes in Argentina. Decomposing cattle faeces sampled in different locations were incubated in water agar 2% with Panagrellus sp. The developed nematophagous fungi were transferred to new water agar 2% plates and then to corn meal agar plates in order to carry out their identification. Fungal diversity and richness were also assessed. Seventeen species from nine genera of nematophagous fungi were found. Twelve species were nematode-trapping fungi and three species plus two fungi identified to genus level corresponded to endoparasitic fungi. Arthrobotrys conoides, Arthrobotrys oligospora, Duddingtonia flagrans, Monacrosporium doedycoides, Arthrobotrys robusta and Drechmeria coniospora were the most frequently isolated species overall in the whole study (6.6%, 5.7%, 5.7%, 5.7%, 4.7% and 4.7%, respectively) although other species were more frequently recorded at local levels such as Arthrobotrys pyriformis (18.8%). Only A. conoides has been previously isolated from ruminant faecal samples in Argentina. Five nematode-trapping fungal species are mentioned for the first time in the Americas D. flagrans and A. conoides, both identified in the present study, are among the most promising ones as biological control agents against gastrointestinal nematodes of ruminants. Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  19. Aquatic fungi in the Lake Sejny complex

    OpenAIRE

    Bazyli Czeczuga

    2014-01-01

    The mycoflora of the Lake Sejny complex was studied. Samples of water were collected in 1990-1991 for hydrochemical analysis and determination of fungi species. In total 69 species of fungi reported for the first time from Poland (Myzocylium vermicolum, Angulospora aquatica, Zoophthora rhizospora).

  20. Interactions between biochar and mycorrhizal fungi in a water-stressed agricultural soil.

    Science.gov (United States)

    Mickan, Bede S; Abbott, Lynette K; Stefanova, Katia; Solaiman, Zakaria M

    2016-08-01

    Biochar may alleviate plant water stress in association with arbuscular mycorrhizal (AM) fungi but research has not been conclusive. Therefore, a glasshouse experiment was conducted to understand how interactions between AM fungi and plants respond to biochar application under water-stressed conditions. A twin chamber pot system was used to determine whether a woody biochar increased root colonisation by a natural AM fungal population in a pasture soil ('field' chamber) and whether this was associated with increased growth of extraradical AM fungal hyphae detected by plants growing in an adjacent ('bait') chamber containing irradiated soil. The two chambers were separated by a mesh that excluded roots. Subterranean clover was grown with and without water stress and harvested after 35, 49 and 63 days from each chamber. When biochar was applied to the field chamber under water-stressed conditions, shoot mass increased in parallel with mycorrhizal colonisation, extraradical hyphal length and shoot phosphorus concentration. AM fungal colonisation of roots in the bait chamber indicated an increase in extraradical mycorrhizal hyphae in the field chamber. Biochar had little effect on AM fungi or plant growth under well-watered conditions. The biochar-induced increase in mycorrhizal colonisation was associated with increased growth of extraradical AM fungal hyphae in the pasture soil under water-stressed conditions.

  1. Fungi in carpeting and furniture dust.

    Science.gov (United States)

    Schober, G

    1991-11-01

    The qualitative and quantitative species composition of fungi in carpets and upholstered furniture dust found in the living-rooms of nine Dutch dwellings was examined in a pilot study. Numbers of spores of xerophilic fungi did not differ in dust removed from carpeting and upholstery. Spores of hydrophilic species were found to be more predominant on floors (P less than 0.05), whereas meso-hygrophilic spores, largely dominated by allergologically relevant Penicillium species, were significantly more abundant in dust taken from regularly used furniture (P less than 0.05). Our results indicate that growth conditions for fungi in the micro-habitats of furniture differ from those in carpeting. No statistically significant differences in number of viable spores have been found in samples taken from ground-floor level compared with those taken from 1st to 3rd floor level of dwellings. From this study, the need for a micro-topographic analysis of the fungal flora in the human environment has become apparent. Efficient allergological home sanitation in dwellings of allergic patients requires detailed data about the colonization of the various micro-habitats by allergenic fungi.

  2. Fungi colonizing dead leaves of herbs

    Directory of Open Access Journals (Sweden)

    Maria Kowalik

    2013-04-01

    Full Text Available The material was collected from the Botanical Garden and the Collegium Medicum Medicinal Plant Garden of the Jagiellonian University in Krakow. The investigated species were: lemon balm (Mellisa officinalis L., common lavender (Lavendula angustifolia Mill., horsemint (Mentha longifolia L., sage (Salvia officinalis L., sweet basil (Ocimum basilicum L., and wild marjoram (Origanum vulgare L.. The aim of the investigation was to identify fungi causing the death of leaf tissues of herbs from the mint family Lamiaceae. In mycological investigations, 180 fragments of each plant leaves (1,080 dead leaf fragments in total were placed in a 2% PDA medium. Over 970 colonies of fungi belonging to 48 species were isolated from the dead leaf tissues of the six herb species. Alternaria alternata (toxin-producing, Epicoccum nigrum and Sordaria fimicola were the most frequently isolated. The largest numbers of colonies and species of fungi were isolated from horsemint, while the lowest numbers were from wild marjoram leaves. It was shown that the death of leaves of selected herb species from the Lamiaceae family was caused by various fungi. The results of the mycological analysis confirmed the diversity of species colonizing the leaves of the herbs.

  3. Sensitivity of Canola Seeds Associated Fungi to Gamma Rays During Storage

    International Nuclear Information System (INIS)

    Botros, H.W.

    2011-01-01

    The present study was carried out to investigate the possibility of using the gamma radiation to elongate the storage periods of canola seeds (Brassica naps L.). In this respect, canola seeds were irradiated at doses of 0.5, 1.5, 2.5, 3.5, 5.0 and 7.5 kGy gamma rays and stored at room temperature for periods 0, 3, 6, 9 and 12 months. The isolated fungi from non-irradiated post-harvest canola seeds included different species identified as Aspergillus flavus, A. niger, A. condidus, A. fumigatus, A. ochraceus, A. parasiticus, Fusarium oxysporium, F. moniliforme, Penicillium expansum, P. crysogenum, Alternaria brassicae, A. raphani and Trichoderma spp. It was noticed that the predominant species were A. ochraceus, A. flavus, A. niger and F. oxysporium at percentages 16.18, 14.73, 11.00 and 10.53%, respectively. The effective gamma irradiation on the predominant fungi (the sub-lethal dose) was 3.5 kGy for A. ochraceus and 5.0 kGy for F. oxysporium and F. moniliforme. Increasing the irradiated dose up to 7.5 kGy decreased significantly the growth of most isolated fungi. The data also showed that there was a decrease in the total fungal count in stored seeds under the effect of gamma rays for 12 months storage. Also, mycotoxins at the stored seeds were not detected after 12 months storage

  4. Calcium homeostasis and signaling in fungi and their relevance for pathogenicity of yeasts and filamentous fungi

    Directory of Open Access Journals (Sweden)

    Renata Tisi

    2016-09-01

    Full Text Available Though fungi show peculiarities in the purposes and specific traits of calcium signaling pathways, the general scheme and the most important players are well conserved if compared to higher eukaryotes. This provides a powerful opportunity either to investigate shared features using yeast as a model or to exploit fungal specificities as potential targets for antifungal therapies. The sequenced genomes from yeast Saccharomyces cerevisiae, Schizosaccharomyces pombe and the filamentous fungus Neurospora crassa were already published more than ten years ago. More recently the genome sequences of filamentous fungi of Aspergillus genus, some of which threatening pathogens, and dimorphic fungi Ustilago maydis were published, giving the chance to identify several proteins involved in calcium signaling based on their homology to yeast or mammalian counterparts. Nonetheless, unidentified calcium transporters are still present in these organisms which await to be molecularly characterized. Despite the relative simplicity in yeast calcium machinery and the availability of sophisticated molecular tools, in the last years, a number of new actors have been identified, albeit not yet fully characterized. This review will try to describe the state of the art in calcium channels and calcium signaling knowledge in yeast, with particular attention to the relevance of this knowledge with respect to pathological fungi.

  5. Rapid detection of Listeria monocytogenes in foods, by a combination of PCR and DNA probe.

    Science.gov (United States)

    Ingianni, A; Floris, M; Palomba, P; Madeddu, M A; Quartuccio, M; Pompei, R

    2001-10-01

    Listeria monocytogenes is a frequent contaminant of water and foods. Its rapid detection is needed before some foods can be prepared for marketing. In this work L. monocytogenes has been searched for in foods, by a combination of polymerase chain reaction (PCR) and a DNA probe. Both PCR and the probe were prepared for recognizing a specific region of the internalin gene, which is responsible for the production of one of the most important pathogenic factors of Listeria. The combined use of PCR and the DNA probe was used for the detection of L. monocytogenes in over 180 environmental and food samples. Several detection methods were compared in this study, namely conventional culture methods; direct PCR; PCR after an enrichment step; a DNA probe alone; a DNA probe after enrichment and another commercially available gene-probe. Finally PCR and the DNA probe were used in series on all the samples collected. When the DNA probe was associated with the PCR, specific and accurate detection of listeria in the samples could be obtained in about a working-day. The present molecular method showed some advantages in terms of rapidity and specificity in comparison to the other aforementioned tests. In addition, it resulted as being easy to handle, even for non-specialized personnel in small diagnostic microbiology laboratories. Copyright 2001 Academic Press.

  6. Oligo-DNA custom macroarray for monitoring major pathogenic and non-pathogenic fungi and bacteria in the phyllosphere of apple trees.

    Science.gov (United States)

    He, Ying-Hong; Isono, Sayaka; Shibuya, Makoto; Tsuji, Masaharu; Adkar Purushothama, Charith-Raj; Tanaka, Kazuaki; Sano, Teruo

    2012-01-01

    To monitor the richness in microbial inhabitants in the phyllosphere of apple trees cultivated under various cultural and environmental conditions, we developed an oligo-DNA macroarray for major pathogenic and non-pathogenic fungi and bacteria inhabiting the phyllosphere of apple trees. First, we isolated culturable fungi and bacteria from apple orchards by an agar-plate culture method, and detected 32 fungal and 34 bacterial species. Alternaria, Aureobasidium, Cladosporium, Rhodotorula, Cystofilobasidium, and Epicoccum genera were predominant among the fungi, and Bacillus, Pseudomonas, Sphingomonas, Methylobacterium, and Pantoea genera were predominant among the bacteria. Based on the data, we selected 29 major non-pathogenic and 12 phytopathogenic fungi and bacteria as the targets of macroarray. Forty-one species-specific 40-base pair long oligo-DNA sequences were selected from the nucleotide sequences of rDNA-internal transcribed spacer region for fungi and 16S rDNA for bacteria. The oligo-DNAs were fixed on nylon membrane and hybridized with digoxigenin-labeled cRNA probes prepared for each species. All arrays except those for Alternaria, Bacillus, and their related species, were specifically hybridized. The array was sensitive enough to detect 10(3) CFU for Aureobasidium pullulans and Bacillus cereus. Nucleotide sequencing of 100 each of independent fungal rDNA-ITS and bacterial 16S-rDNA sequences from apple tree was in agreement with the macroarray data obtained using the same sample. Finally, we analyzed the richness in the microbial inhabitants in the samples collected from apple trees in four orchards. Major apple pathogens that cause scab, Alternaria blotch, and Marssonina blotch were detected along with several non-phytopathogenic fungal and bacterial inhabitants. The macroarray technique presented here is a strong tool to monitor the major microbial species and the community structures in the phyllosphere of apple trees and identify key species

  7. Oligo-DNA custom macroarray for monitoring major pathogenic and non-pathogenic fungi and bacteria in the phyllosphere of apple trees.

    Directory of Open Access Journals (Sweden)

    Ying-Hong He

    Full Text Available BACKGROUND: To monitor the richness in microbial inhabitants in the phyllosphere of apple trees cultivated under various cultural and environmental conditions, we developed an oligo-DNA macroarray for major pathogenic and non-pathogenic fungi and bacteria inhabiting the phyllosphere of apple trees. METHODS AND FINDINGS: First, we isolated culturable fungi and bacteria from apple orchards by an agar-plate culture method, and detected 32 fungal and 34 bacterial species. Alternaria, Aureobasidium, Cladosporium, Rhodotorula, Cystofilobasidium, and Epicoccum genera were predominant among the fungi, and Bacillus, Pseudomonas, Sphingomonas, Methylobacterium, and Pantoea genera were predominant among the bacteria. Based on the data, we selected 29 major non-pathogenic and 12 phytopathogenic fungi and bacteria as the targets of macroarray. Forty-one species-specific 40-base pair long oligo-DNA sequences were selected from the nucleotide sequences of rDNA-internal transcribed spacer region for fungi and 16S rDNA for bacteria. The oligo-DNAs were fixed on nylon membrane and hybridized with digoxigenin-labeled cRNA probes prepared for each species. All arrays except those for Alternaria, Bacillus, and their related species, were specifically hybridized. The array was sensitive enough to detect 10(3 CFU for Aureobasidium pullulans and Bacillus cereus. Nucleotide sequencing of 100 each of independent fungal rDNA-ITS and bacterial 16S-rDNA sequences from apple tree was in agreement with the macroarray data obtained using the same sample. Finally, we analyzed the richness in the microbial inhabitants in the samples collected from apple trees in four orchards. Major apple pathogens that cause scab, Alternaria blotch, and Marssonina blotch were detected along with several non-phytopathogenic fungal and bacterial inhabitants. CONCLUSIONS: The macroarray technique presented here is a strong tool to monitor the major microbial species and the community structures in

  8. Combining magnetic nanoparticle with biotinylated nanobodies for rapid and sensitive detection of influenza H3N2

    Science.gov (United States)

    Zhu, Min; Hu, Yonghong; Li, Guirong; Ou, Weijun; Mao, Panyong; Xin, Shaojie; Wan, Yakun

    2014-09-01

    Our objective is to develop a rapid and sensitive assay based on magnetic beads to detect the concentration of influenza H3N2. The possibility of using variable domain heavy-chain antibodies (nanobody) as diagnostic tools for influenza H3N2 was investigated. A healthy camel was immunized with inactivated influenza H3N2. A nanobody library of 8 × 108 clones was constructed and phage displayed. After three successive biopanning steps, H3N2-specific nanobodies were successfully isolated, expressed in Escherichia coli, and purified. Sequence analysis of the nanobodies revealed that we possessed four classes of nanobodies against H3N2. Two nanobodies were further used to prepare our rapid diagnostic kit. Biotinylated nanobody was effectively immobilized onto the surface of streptavidin magnetic beads. The modified magnetic beads with nanobody capture specifically influenza H3N2 and can still be recognized by nanobodies conjugated to horseradish peroxidase (HRP) conjugates. Under optimized conditions, the present immunoassay exhibited a relatively high sensitive detection with a limit of 50 ng/mL. In conclusion, by combining magnetic beads with specific nanobodies, this assay provides a promising influenza detection assay to develop a potential rapid, sensitive, and low-cost diagnostic tool to screen for influenza infections.

  9. Rapid Detection of Human Immunodeficiency Virus Types 1 and 2 by Use of an Improved Piezoelectric Biosensor

    Science.gov (United States)

    Severns, Virginia; Branch, Darren W.; Edwards, Thayne L.; Larson, Richard S.

    2013-01-01

    Disasters can create situations in which blood donations can save lives. However, in emergency situations and when resources are depleted, on-site blood donations require the rapid and accurate detection of blood-borne pathogens, including human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2). Techniques such as PCR and antibody capture by an enzyme-linked immunosorbent assay (ELISA) for HIV-1 and HIV-2 are precise but time-consuming and require sophisticated equipment that is not compatible with emergency point-of-care requirements. We describe here a prototype biosensor based on piezoelectric materials functionalized with specific antibodies against HIV-1 and HIV-2. We show the rapid and accurate detection of HIV-1 and HIV-2 in both simple and complex solutions, including human serum, and in the presence of a cross-confounding virus. We report detection limits of 12 50% tissue culture infective doses (TCID50s) for HIV-1 and 87 TCID50s for HIV-2. The accuracy, precision of measurements, and operation of the prototype biosensor compared favorably to those for nucleic acid amplification. We conclude that the biosensor has significant promise as a successful point-of-care diagnostic device for use in emergency field applications requiring rapid and reliable testing for blood-borne pathogens. PMID:23515541

  10. Communities, populations and individuals of arbuscular mycorrhizal fungi

    DEFF Research Database (Denmark)

    Rosendahl, Søren

    2008-01-01

    Arbuscular mycorrhizal fungi in the phylum Glomeromycota are found globally in most vegetation types, where they form a mutualistic symbiosis with plant roots. Despite their wide distribution, only relatively few species are described. The taxonomy is based on morphological characters...... of the asexual resting spores, but molecular approaches to community ecology have revealed a considerable unknown diversity from colonized roots. Although the lack of genetic recombination is not unique in the fungal kingdom, arbuscular mycorrhizal fungi are probably ancient asexuals. The long asexual evolution...... of the fungi has resulted in considerable genetic diversity within morphologically recognizable species, and challenges our concepts of individuals and populations. This review critically examines the concepts of species, communities, populations and individuals of arbuscular mycorrhizal fungi....

  11. Aquatic fungi in the Lake Sejny complex

    Directory of Open Access Journals (Sweden)

    Bazyli Czeczuga

    2014-08-01

    Full Text Available The mycoflora of the Lake Sejny complex was studied. Samples of water were collected in 1990-1991 for hydrochemical analysis and determination of fungi species. In total 69 species of fungi reported for the first time from Poland (Myzocylium vermicolum, Angulospora aquatica, Zoophthora rhizospora.

  12. Interagency partnering for weed prevention--progress on development of a National Early Detection and Rapid Response System for Invasive Plants in the United States

    Science.gov (United States)

    Westbrooks, R.; Westbrooks, R.

    2011-01-01

    Over the past 50 years, experience has shown that interagency groups provide an effective forum for addressing various invasive species issues and challenges on multiple land units. However, more importantly, they can also provide a coordinated framework for early detection, reporting, identification and vouchering, rapid assessment, and rapid response to new and emerging invasive plants in the United States. Interagency collaboration maximizes the use of available expertise, resources, and authority for promoting early detection and rapid response (EDRR) as the preferred management option for addressing new and emerging invasive plants. Currently, an interagency effort is underway to develop a National EDRR System for Invasive Plants in the United States. The proposed system will include structural and informational elements. Structural elements of the system include a network of interagency partner groups to facilitate early detection and rapid response to new invasive plants, including the Federal Interagency Committee for the Management of Noxious and Exotic Weeds (FICMNEW), State Invasive Species Councils, State Early Detection and Rapid Response Coordinating Committees, State Volunteer Detection and Reporting Networks, Invasive Plant Task Forces, and Cooperative Weed Management Areas. Informational elements and products being developed include Regional Invasive Plant Atlases, and EDRR Guidelines for EDRR Volunteer Network Training, Rapid Assessment and Rapid Response, and Criteria for Selection of EDRR Species. System science and technical support elements which are provided by cooperating state and federal scientists, include EDRR guidelines, training curriculum for EDRR volunteers and agency field personnel, plant identification and vouchering, rapid assessments, as well as predictive modeling and ecological range studies for invasive plant species.

  13. [Keratinophilic fungi in soils of parks of Corrientes city, Argentina].

    Science.gov (United States)

    Sarmiento, María Mercedes; Mangiaterra, Magdalena; Bojanich, María Viviana; Basualdo, Juan Ángel; Giusiano, Gustavo

    2016-01-01

    The soil is a natural reservoir of keratinophilic fungi, which are a small but important group of filamentous fungi, some of which typically develop on keratinized tissues of living animals. There are numerous species of saprophytic fungi with recognized keratinophilic abilities, and several studies have been undertaken in order to link their presence to possible human disease. To know the biota of geophilic fungi in general and of keratinophilic fungi particularly in soils from two public parks. Soil samples from two public parks of Corrientes city, Argentina, were studied during two seasons, using the hook technique and serial dilutions for fungal isolation. Using the hook technique, 170 isolates were classified into 17 genera and 21 species, among which it is worth mentioning the presence of Microsporum canis. Shannon index for keratinophilic fungi in autumn was 2.27, and 1.92 in spring. By means of the serial dilutions technique, 278 fungi isolated were identified into 33 genera and 71 species. Shannon index in autumn was 3.9, and 3.5 in spring. The soils studied have particularly favorable conditions for the survival of pathogens and opportunistic geophilic fungi for humans and animals. Copyright © 2014 Asociación Española de Micología. Published by Elsevier Espana. All rights reserved.

  14. Comparison of the lysis-centrifugation and agitated biphasic blood culture systems for detection of fungemia.

    Science.gov (United States)

    Murray, P R

    1991-01-01

    Although the detection of fungemia has been improved by the use of vented or biphasic blood culture bottles, the best recovery and earliest detection have been reported in the Isolator lysis-centrifugation system. It was recently demonstrated that improved detection of both bacteria and fungi was accomplished by mechanically agitating blood culture bottles for the first 24 h of incubation. In this study the detection of fungemia by use of the Isolator system was compared with that of an agitated biphasic system. A total of 182 fungi were isolated from blood specimens inoculated into both culture systems. No difference in the overall recovery of fungi or individual species of yeasts was observed between the two systems. However, all seven isolates of Histoplasma capsulatum were recovered in the Isolator system only. The time required to detect fungemia with each of the two systems was also compared. No statistically significant difference was observed. From the data collected during this 18-month study, it can be concluded that the overall recovery and time of detection of yeasts are equivalent in the lysis-centrifugation system and the agitated biphasic blood culture system. The lysis-centrifugation system is still superior for the detection of filamentous fungi such as H. capsulatum. PMID:1993772

  15. Diversity of endophytic fungi in Glycine max.

    Science.gov (United States)

    Fernandes, Elio Gomes; Pereira, Olinto Liparini; da Silva, Cynthia Cânedo; Bento, Claudia Braga Pereira; de Queiroz, Marisa Vieira

    2015-12-01

    Endophytic fungi are microorganisms that live within plant tissues without causing disease during part of their life cycle. With the isolation and identification of these fungi, new species are being discovered, and ecological relationships with their hosts have also been studied. In Glycine max, limited studies have investigated the isolation and distribution of endophytic fungi throughout leaves and roots. The distribution of these fungi in various plant organs differs in diversity and abundance, even when analyzed using molecular techniques that can evaluate fungal communities in different parts of the plants, such as denaturing gradient gel electrophoresis (DGGE). Our results show there is greater species richness of culturable endophytic filamentous fungi in the leaves G. max as compared to roots. Additionally, the leaves had high values for diversity indices, i.e. Simpsons, Shannon and Equitability. Conversely, dominance index was higher in roots as compared to leaves. The fungi Ampelomyces sp., Cladosporium cladosporioides, Colletotrichum gloeosporioides, Diaporthe helianthi, Guignardia mangiferae and Phoma sp. were more frequently isolated from the leaves, whereas the fungi Fusarium oxysporum, Fusarium solani and Fusarium sp. were prevalent in the roots. However, by evaluating the two communities by DGGE, we concluded that the species richness was higher in the roots than in the leaves. UPGMA analysis showed consistent clustering of isolates; however, the fungus Leptospora rubella, which belongs to the order Dothideales, was grouped among species of the order Pleosporales. The presence of endophytic Fusarium species in G. max roots is unsurprising, since Fusarium spp. isolates have been previously described as endophyte in other reports. However, it remains to be determined whether the G. max Fusarium endophytes are latent pathogens or non-pathogenic forms that benefit the plant. This study provides a broader knowledge of the distribution of the fungal

  16. Transcriptomes of Arbuscular Mycorrhizal Fungi and Litchi Host Interaction after Tree Girdling.

    Science.gov (United States)

    Shu, Bo; Li, Weicai; Liu, Liqin; Wei, Yongzan; Shi, Shengyou

    2016-01-01

    Trunk girdling can increase carbohydrate content above the girdling site and is an important strategy for inhibiting new shoot growth to promote flowering in cultivated litchi (Litchi chinensis Sonn.). However, girdling inhibits carbohydrate transport to the root in nearly all of the fruit development periods and consequently decreases root absorption. The mechanism through which carbohydrates regulate root development in arbuscular mycorrhiza (AM) remains largely unknown. Carbohydrate content, AM colonization, and transcriptome in the roots were analyzed to elucidate the interaction between host litchi and AM fungi when carbohydrate content decreases. Girdling decreased glucose, fructose, sucrose, quebrachitol, and starch contents in the litchi mycorrhizal roots, thereby reducing AM colonization. RNA-seq achieved approximately 60 million reads of each sample, with an average length of reads reaching 100 bp. Assembly of all the reads of the 30 samples produced 671,316 transcripts and 381,429 unigenes, with average lengths of 780 and 643 bp, respectively. Litchi (54,100 unigenes) and AM fungi unigenes (33,120 unigenes) were achieved through sequence annotation during decreased carbohydrate content. Analysis of differentially expressed genes (DEG) showed that flavonoids, alpha-linolenic acid, and linoleic acid are the main factors that regulate AM colonization in litchi. However, flavonoids may play a role in detecting the stage at which carbohydrate content decreases; alpha-linolenic acid or linoleic acid may affect AM formation under the adaptation process. Litchi trees stimulated the expression of defense-related genes and downregulated symbiosis signal-transduction genes to inhibit new AM colonization. Moreover, transcription factors of the AP2, ERF, Myb, WRKY, bHLH families, and lectin genes altered maintenance of litchi mycorrhizal roots in the post-symbiotic stage for carbohydrate starvation. Similar to those of the litchi host, the E3 ubiquitin ligase complex

  17. Rapid Detection of Bacillus anthracis Spores Using Immunomagnetic Separation and Amperometry

    Directory of Open Access Journals (Sweden)

    David F. Waller

    2016-12-01

    Full Text Available Portable detection and quantitation methods for Bacillus anthracis (anthrax spores in pure culture or in environmental samples are lacking. Here, an amperometric immunoassay has been developed utilizing immunomagnetic separation to capture the spores and remove potential interferents from test samples followed by amperometric measurement on a field-portable instrument. Antibody-conjugated magnetic beads and antibody-conjugated glucose oxidase were used in a sandwich format for the capture and detection of target spores. Glucose oxidase activity of spore pellets was measured indirectly via amperometry by applying a bias voltage after incubation with glucose, horseradish peroxidase, and the electron mediator 2,2′-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid. Target capture was mediated by polyclonal antisera, whereas monoclonal antibodies were used for signal generation. This strategy maximized sensitivity (500 target spores, 5000 cfu/mL, while also providing a good specificity for Bacillus anthracis spores. Minimal signal deviation occurs in the presence of environmental interferents including soil and modified pH conditions, demonstrating the strengths of immunomagnetic separation. The simultaneous incubation of capture and detection antibodies and rapid substrate development (5 min result in short sample-to-signal times (less than an hour. With attributes comparable or exceeding that of ELISA and LFDs, amperometry is a low-cost, low-weight, and practical method for detecting anthrax spores in the field.

  18. Deep-sea fungi

    Digital Repository Service at National Institute of Oceanography (India)

    Raghukumar, C; Damare, S.R.

    significant in terms of carbon sequestration (5, 8). In light of this, the diversity, abundance, and role of fungi in deep-sea sediments may form an important link in the global C biogeochemistry. This review focuses on issues related to collection...

  19. Rapid and reliable detection and identification of GM events using multiplex PCR coupled with oligonucleotide microarray.

    Science.gov (United States)

    Xu, Xiaodan; Li, Yingcong; Zhao, Heng; Wen, Si-yuan; Wang, Sheng-qi; Huang, Jian; Huang, Kun-lun; Luo, Yun-bo

    2005-05-18

    To devise a rapid and reliable method for the detection and identification of genetically modified (GM) events, we developed a multiplex polymerase chain reaction (PCR) coupled with a DNA microarray system simultaneously aiming at many targets in a single reaction. The system included probes for screening gene, species reference gene, specific gene, construct-specific gene, event-specific gene, and internal and negative control genes. 18S rRNA was combined with species reference genes as internal controls to assess the efficiency of all reactions and to eliminate false negatives. Two sets of the multiplex PCR system were used to amplify four and five targets, respectively. Eight different structure genes could be detected and identified simultaneously for Roundup Ready soybean in a single microarray. The microarray specificity was validated by its ability to discriminate two GM maizes Bt176 and Bt11. The advantages of this method are its high specificity and greatly reduced false-positives and -negatives. The multiplex PCR coupled with microarray technology presented here is a rapid and reliable tool for the simultaneous detection of GM organism ingredients.

  20. Development of rapid detection system on BEPC Ⅱ magnet power supply

    International Nuclear Information System (INIS)

    Chen Suying; Zhan Mingchuan; Long Fengli; Ye Weidong

    2014-01-01

    To quickly find the causes of the accelerator unstable or lost beam caused by magnet power supply in Beijing Electron Positron Collider (BEPC Ⅱ) running, the rapid detection system for magnet power supply was developed. The stability of the system in 8 h is about 0.005%, and it can acquire over nearly 500 sets of magnet power supply current values most quickly in 0.33 ms. All data were written to the MySQL database in real time, so as to be able to quickly troubleshoot magnet power supply problem through historical data analysis and comparison. (authors)

  1. Alkali metals in fungi of forest soil

    International Nuclear Information System (INIS)

    Vinichuk, M.; Taylor, A.; Rosen, K.; Nikolova, I.; Johanson, K.J.

    2009-01-01

    The high affinity of forest soil fungi for alkali metals such as potassium, rubidium, caesium as well as radiocaesium is shown and discussed. Good positive correlation was found between K: Rb concentration ratios in soil and in fungi, when correlation between K: Cs concentration ratios was less pronounced. (LN)

  2. Community composition of root-associated fungi in a Quercus-dominated temperate forest: “codominance” of mycorrhizal and root-endophytic fungi

    Science.gov (United States)

    Toju, Hirokazu; Yamamoto, Satoshi; Sato, Hirotoshi; Tanabe, Akifumi S; Gilbert, Gregory S; Kadowaki, Kohmei

    2013-01-01

    In terrestrial ecosystems, plant roots are colonized by various clades of mycorrhizal and endophytic fungi. Focused on the root systems of an oak-dominated temperate forest in Japan, we used 454 pyrosequencing to explore how phylogenetically diverse fungi constitute an ecological community of multiple ecotypes. In total, 345 operational taxonomic units (OTUs) of fungi were found from 159 terminal-root samples from 12 plant species occurring in the forest. Due to the dominance of an oak species (Quercus serrata), diverse ectomycorrhizal clades such as Russula, Lactarius, Cortinarius, Tomentella, Amanita, Boletus, and Cenococcum were observed. Unexpectedly, the root-associated fungal community was dominated by root-endophytic ascomycetes in Helotiales, Chaetothyriales, and Rhytismatales. Overall, 55.3% of root samples were colonized by both the commonly observed ascomycetes and ectomycorrhizal fungi; 75.0% of the root samples of the dominant Q. serrata were so cocolonized. Overall, this study revealed that root-associated fungal communities of oak-dominated temperate forests were dominated not only by ectomycorrhizal fungi but also by diverse root endophytes and that potential ecological interactions between the two ecotypes may be important to understand the complex assembly processes of belowground fungal communities. PMID:23762515

  3. Secondary metabolites of Antarctic fungi antagonistic to aquatic pathogenic bacteria

    Directory of Open Access Journals (Sweden)

    Zhao Huibin

    2018-03-01

    Full Text Available Polar microbial derived antibiotics have potential as alternatives to traditional antibiotics in treating fish against pathogenic bacteria. In this paper, 23 strains of polar fungi were fermented to detect bacteriostatic products on three aquatic pathogenic bacteria, subsequently the active fungus was identified. It was indicated that secondary metabolites of 23 strains weredistinct; of these, the extract of strain B-7 (belonging to Bjerkandera according to molecular identification demonstrated a strong antibacterial activity to Streptococcus agalactiae, Vibrio anguillarum and Aeromonas hydrophila ATCC7966 by Kirby-Bauerpaper strip method. During one fermentation cycle, the pH curve of the fermentation liquor became lowest (4.0 on the 4th day and rose back to 7.6 finally after 5 days, The residual sugar curve was decreased before stablising on the 6th day. It is presumed that a large amount of alkaline secondary metabolites might have been produced during fermentation. This study focuses on antagonism between aquatic pathogenic bacteria and fermentation metabolites from Antarctic fungi for the first time, which may provide data on research of antibiotics against aquatic pathogenic bacteria.

  4. Genus- and species-level identification of dermatophyte fungi by surface-enhanced Raman spectroscopy

    Science.gov (United States)

    Witkowska, Evelin; Jagielski, Tomasz; Kamińska, Agnieszka

    2018-03-01

    This paper demonstrates that surface-enhanced Raman spectroscopy (SERS) coupled with principal component analysis (PCA) can serve as a fast and reliable technique for detection and identification of dermatophyte fungi at both genus and species level. Dermatophyte infections are the most common mycotic diseases worldwide, affecting a quarter of the human population. Currently, there is no optimal method for detection and identification of fungal diseases, as each has certain limitations. Here, for the first time, we have achieved with a high accuracy, differentiation of dermatophytes representing three major genera, i.e. Trichophyton, Microsporum, and Epidermophyton. Two first principal components (PC), namely PC-1 and PC-2, gave together 97% of total variance. Additionally, species-level identification within the Trichophyton genus has been performed. PC-1 and PC-2, which are the most diagnostically significant, explain 98% of the variance in the data obtained from spectra of: Trichophyton rubrum, Trichophyton menatgrophytes, Trichophyton interdigitale and Trichophyton tonsurans. This study offers a new diagnostic approach for the identification of dermatophytes. Being fast, reliable and cost-effective, it has the potential to be incorporated in the clinical practice to improve diagnostics of medically important fungi.

  5. LAMP-based group specific detection of aflatoxin producers within Aspergillus section Flavi in food raw materials, spices, and dried fruit using neutral red for visible-light signal detection.

    Science.gov (United States)

    Niessen, Ludwig; Bechtner, Julia; Fodil, Sihem; Taniwaki, Marta H; Vogel, Rudi F

    2018-02-02

    Aflatoxins can be produced by 21 species within sections Flavi (16 species), Ochraceorosei (2), and Nidulantes (3) of the fungal genus Aspergillus. They pose risks to human and animal health due to high toxicity and carcinogenicity. Detecting aflatoxin producers can help to assess toxicological risks associated with contaminated commodities. Species specific molecular assays (PCR and LAMP) are available for detection of major producers, but fail to detect species of minor importance. To enable rapid and sensitive detection of several aflatoxin producing species in a single analysis, a nor1 gene-specific LAMP assay was developed. Specificity testing showed that among 128 fungal species from 28 genera, 15 aflatoxigenic species in section Flavi were detected, including synonyms of A. flavus and A. parasiticus. No cross reactions were found with other tested species. The detection limit of the assay was 9.03pg of A. parasiticus genomic DNA per reaction. Visual detection of positive LAMP reactions under daylight conditions was facilitated using neutral red to allow unambiguous distinction between positive and negative assay results. Application of the assay to the detection of A. parasiticus conidia revealed a detection limit of 211 conidia per reaction after minimal sample preparation. The usefulness of the assay was demonstrated in the analysis of aflatoxinogenic species in samples of rice, nuts, raisins, dried figs, as well as powdered spices. Comparison of LAMP results with presence/absence of aflatoxins and aflatoxin producing fungi in 50 rice samples showed good correlation between these parameters. Our study suggests that the developed LAMP assay is a rapid, sensitive and user-friendly tool for surveillance and quality control in our food industry. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. A novel kit for rapid detection of Vibrio cholerae O1.

    Science.gov (United States)

    Hasan, J A; Huq, A; Tamplin, M L; Siebeling, R J; Colwell, R R

    1994-01-01

    We report on the development and testing of a novel, rapid, colorimetric immunodiagnostic kit, Cholera SMART, for direct detection of the presence of Vibrio cholerae O1 in clinical specimens. Unlike conventional culture methods requiring several days to complete, the Cholera SMART kit can be used directly in the field by untrained or minimally skilled personnel to detect V. cholerae O1 in less than 15 min, without cumbersome laboratory equipment. A total of 120 clinical and environmental bacterial strains, including both O1 and non-O1 serotypes of V. cholerae isolated from samples collected from a variety of geographical regions, were tested, and positive reactions were observed only with V. cholerae O1. Also, results of a field trial in Bangladesh, employing Cholera SMART, showed 100% specificity and 96% sensitivity compared with conventional culture methods. Another field trial, in Mexico, showed that Cholera SMART was 100% in agreement with a recently described coagglutination test when 108 stool specimens were tested.

  7. Degradation of terbuthylazine, difenoconazole and pendimethalin pesticides by selected fungi cultures.

    Science.gov (United States)

    Pinto, A P; Serrano, C; Pires, T; Mestrinho, E; Dias, L; Teixeira, D Martins; Caldeira, A T

    2012-10-01

    Contamination of waters by xenobiotic compounds such as pesticides presents a serious environmental problem with substantial levels of pesticides now contaminating European water resources. The aim of this work was to evaluate the ability of the fungi Fusarium oxysporum, Aspergillus oryzae, Lentinula edodes, Penicillium brevicompactum and Lecanicillium saksenae, for the biodegradation of the pesticides terbuthylazine, difenoconazole and pendimethalin in batch liquid cultures. These pesticides are common soil and water contaminants and terbuthylazine is considered the most persistent triazine herbicide in surface environments. P. brevicompactum and L. saksenae were achieved by enrichment, isolation and screening of fungi capable to metabolize the pesticides studied. The isolates were obtained from two pesticide-primed materials (soil and biomixture). Despite the relatively high persistence of terbuthylazine, the results obtained in this work showed that the fungi species studied have a high capability of biotransformation of this xenobiotic, comparatively the results obtained in other similar studies. The highest removal percentage of terbuthylazine from liquid medium was achieved with A. oryzae (~80%), although the major biodegradation has been reached with P. brevicompactum. The higher ability of P. brevicompactum to metabolize terbuthylazine was presumably acquired through chronic exposure to contamination with the herbicide. L. saksenae could remove 99.5% of the available pendimethalin in batch liquid cultures. L. edodes proved to be a fungus with a high potential for biodegradation of pesticides, especially difenoconazole and pendimethalin. Furthermore, the metabolite desethyl-terbuthylazine was detected in L. edodes liquid culture medium, indicating terbuthylazine biodegradation by this fungus. The fungi strains investigated could prove to be valuable as active pesticide-degrading microorganisms, increasing the efficiency of biopurification systems containing

  8. Direct, Specific and Rapid Detection of Staphylococcal Proteins and Exotoxins Using a Multiplex Antibody Microarray.

    Directory of Open Access Journals (Sweden)

    Bettina Stieber

    Full Text Available S. aureus is a pathogen in humans and animals that harbors a wide variety of virulence factors and resistance genes. This bacterium can cause a wide range of mild to life-threatening diseases. In the latter case, fast diagnostic procedures are important. In routine diagnostic laboratories, several genotypic and phenotypic methods are available to identify S. aureus strains and determine their resistances. However, there is a demand for multiplex routine diagnostic tests to directly detect staphylococcal toxins and proteins.In this study, an antibody microarray based assay was established and validated for the rapid detection of staphylococcal markers and exotoxins. The following targets were included: staphylococcal protein A, penicillin binding protein 2a, alpha- and beta-hemolysins, Panton Valentine leukocidin, toxic shock syndrome toxin, enterotoxins A and B as well as staphylokinase. All were detected simultaneously within a single experiment, starting from a clonal culture on standard media. The detection of bound proteins was performed using a new fluorescence reading device for microarrays.110 reference strains and clinical isolates were analyzed using this assay, with a DNA microarray for genotypic characterization performed in parallel. The results showed a general high concordance of genotypic and phenotypic data. However, genotypic analysis found the hla gene present in all S. aureus isolates but its expression under given conditions depended on the clonal complex affiliation of the actual isolate.The multiplex antibody assay described herein allowed a rapid and reliable detection of clinically relevant staphylococcal toxins as well as resistance- and species-specific markers.

  9. Rapid Electrochemical Detection and Identification of Microbiological and Chemical Contaminants for Manned Spaceflight Project

    Science.gov (United States)

    Pierson, Duane; Botkin, Douglas; Gazda, Daniel

    2014-01-01

    Microbial control in the spacecraft environment is a daunting task, especially in the presence of human crew members. Currently, assessing the potential crew health risk associated with a microbial contamination event requires return of representative environmental samples that are analyzed in a ground-based laboratory. It is therefore not currently possible to quickly identify microbes during spaceflight. This project addresses the unmet need for spaceflight-compatible microbial identification technology. The electrochemical detection and identification platform is expected to provide a sensitive, specific, and rapid sample-to-answer capability for in-flight microbial monitoring that can distinguish between related microorganisms (pathogens and non-pathogens) as well as chemical contaminants. This will dramatically enhance our ability to monitor the spacecraft environment and the health risk to the crew. Further, the project is expected to eliminate the need for sample return while significantly reducing crew time required for detection of multiple targets. Initial work will focus on the optimization of bacterial detection and identification. The platform is designed to release nucleic acids (DNA and RNA) from microorganisms without the use of harmful chemicals. Bacterial DNA or RNA is captured by bacteria-specific probe molecules that are bound to a microelectrode, and that capture event can generate a small change in the electrical current (Lam, et al. 2012. Anal. Chem. 84(1): 21-5.). This current is measured, and a determination is made whether a given microbe is present in the sample analyzed. Chemical detection can be accomplished by directly applying a sample to the microelectrode and measuring the resulting current change. This rapid microbial and chemical detection device is designed to be a low-cost, low-power platform anticipated to be operated independently of an external power source, characteristics optimal for manned spaceflight and areas where power

  10. Comparison of rapid diagnostic tests to detect Mycobacterium avium subsp. paratuberculosis disseminated infection in bovine liver.

    Science.gov (United States)

    Zarei, Mehdi; Ghorbanpour, Masoud; Tajbakhsh, Samaneh; Mosavari, Nader

    2017-08-01

    Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, a chronic enteritis in cattle and other domestic and wild ruminants. The presence of MAP in tissues other than intestines and associated lymph nodes, such as meat and liver, is a potential public health concern. In the present study, the relationship between the results of rapid diagnostic tests of the Johne's disease, such as serum ELISA, rectal scraping PCR, and acid-fast staining, and the presence of MAP in liver was evaluated. Blood, liver, and rectal scraping samples were collected from 200 slaughtered cattle with unknown Johne's disease status. ELISA was performed to determine the MAP antibody activity in the serum. Acid-fast staining was performed on rectal scraping samples, and PCR was performed on rectal scraping and liver samples. PCR-positive liver samples were used for mycobacterial culture. Overall, the results of this study demonstrated that MAP can be detected and cultured from liver of slaughtered cattle and rapid diagnostic tests of Johne's disease have limited value in detecting cattle with MAP infection in liver. These findings show that the presence of MAP in liver tissue may occur in cows with negative results for rapid diagnostic tests and vice versa. Hence, liver might represent another possible risk of human exposure to MAP. Given concerns about a potential zoonotic role for MAP, these results show the necessity to find new methods for detecting cattle with MAP disseminated infection.

  11. Rapid, enhanced detection of Salmonella Typhimurium on fresh spinach leaves using micron-scale, phage-coated magnetoelastic biosensors

    Science.gov (United States)

    Horikawa, Shin; Vaglenov, Kiril A.; Gerken, Dana M.; Chai, Yating; Park, Mi-Kyung; Li, Suiqiong; Petrenko, Valery A.; Chin, Bryan A.

    2012-05-01

    In order to cost-effectively and rapidly detect bacterial food contamination in the field, the potential usefulness of phage-coated magnetoelastic (ME) biosensors has been recently reported. These biosensors are freestanding, mass-sensitive biosensors that can be easily batch-fabricated, thereby reducing the fabrication cost per sensor to a fraction of a cent. In addition, the biosensors can be directly placed on fresh produce surfaces and used to rapidly monitor possible bacterial food contamination without any preceding sample preparation. Previous investigations showed that the limit of detection (LOD) with millimeter-scale ME biosensors was fairly low for fresh produce with smooth surfaces (e.g., tomatoes and shell eggs). However, the LOD is anticipated to be dependent on the size of the biosensors as well as the topography of produce surfaces of interest. This paper presents an investigation into the use of micron-scale, phage-coated ME biosensors for the enhanced detection of Salmonella Typhimurium on fresh spinach leaves.

  12. Molecular diversity of fungi from marine oxygen-deficient environments (ODEs)

    Digital Repository Service at National Institute of Oceanography (India)

    Manohar, C.S.; Forster, D.; Kauff, F.; Stoeck, T.

    . Sparrow Jr F K (1936) Biological observations of the marine fungi of woods hole waters. Biol Bull 70: 236-263. States JS & Christensen M (2001) Fungi Associated with Biological Soil Crusts in Desert Grasslands of Utah and Wyoming. Mycologia 93: 432... version: Biology of marine fungi. Ed. by: Raghukumar, C. (Prog. Mol. Subcellular Biol). Springer, vol.53 (Chap 10); 2012; 189-208 Chapter # 10 Molecular diversity of fungi from marine oxygen-deficient environments (ODEs) Cathrine S. Jebaraj 1...

  13. Promising carbons for supercapacitors derived from fungi

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Hui; Wang, Xiaolei; Yang, Fan; Yang, Xiurong [State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (China)

    2011-06-24

    Activated carbons with promising performance in capacitors are produced from fungi via a hydrothermal assistant pyrolysis approach. This study introduces a facile strategy to discover carbonaceous materials and triggers interest in exploring fungi for material science applications. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  14. Freeze-drying of filamentous fungi and yeasts

    NARCIS (Netherlands)

    Tan, C.S.

    2011-01-01

    The aim of this thesis was to optimize the freeze-drying protocol for fungi in general and for those genera that do not survive this preservation method, in particular. To this end, the influence of the cooling rate, the lyoprotectant and the drying process itself was examined. Since most fungi

  15. Rapid Molecular detection of citrus brown spot disease using ACT gene in Alternaria alternata

    Directory of Open Access Journals (Sweden)

    Hamid Moghimi

    2017-06-01

    Full Text Available Introduction:Using rapid detection methods is important for detection of plant pathogens and also prevention through spreading pests in agriculture. Citrus brown spot disease caused by pathogenic isolates of Alternaria alternata is a common disease in Iran. Materials and methods: In this study, for the first time a PCR based molecular method was used for rapid diagnosis of brown spot disease. Nine isolates of A. Alternata were isolated in PDA medium from different citrus gardens. The plant pathogenic activity was examined in tangerine leaves for isolates. Results showed that these isolates are the agents of brown spot disease. PCR amplification of specific ACT-toxin gene was performed for DNA extracted from A. alternata isolates, with 11 different fungal isolates as negative controls and 5 DNA samples extracted from soil. Results: Results showed that A. alternata, the causal agent of brown spot disease, can be carefully distinguished from other pathogenic agents by performing PCR amplification with specific primers for ACT toxin gene. Also, the results from Nested-PCR method confirmed the primary reaction and the specificity of A. alternata for brown spot disease. PCR results to control samples of the other standard fungal isolates, showed no amplification band. In addition, PCR with the DNA extracted from contaminated soils confirmed the presence of ACT toxin gene. Discussion and conclusion: Molecular procedure presented here can be used in rapid identification and prevention of brown spot infection in citrus gardens all over the country.

  16. Fun with Fungi.

    Science.gov (United States)

    McLure, John W.

    1993-01-01

    Describes hands-on activities with fungi that may provoke the curiosity of early adolescents and increase their enjoyment and understanding of a vast, important portion of botany. Some of the activities may be conducted during the winter months when most fieldwork ceases. (PR)

  17. A Rapid and Simple Real-Time PCR Assay for Detecting Foodborne Pathogenic Bacteria in Human Feces.

    Science.gov (United States)

    Hanabara, Yutaro; Ueda, Yutaka

    2016-11-22

    A rapid, simple method for detecting foodborne pathogenic bacteria in human feces is greatly needed. Here, we examined the efficacy of a method that employs a combination of a commercial PCR master mix, which is insensitive to PCR inhibitors, and a DNA extraction method which used sodium dodecyl benzene sulfonate (SDBS), and Tween 20 to counteract the inhibitory effects of SDBS on the PCR assay. This method could detect the target genes (stx1 and stx2 of enterohemorrhagic Escherichia coli, invA of Salmonella Enteritidis, tdh of Vibrio parahaemolyticus, gyrA of Campylobacter jejuni, ceuE of Campylobacter coli, SEA of Staphylococcus aureus, ces of Bacillus cereus, and cpe of Clostridium perfringens) in a fecal suspension containing 1.0 × 10 1 to 1.0 × 10 3 CFU/ml. Furthermore, the assay was neither inhibited nor influenced by individual differences among the fecal samples of 10 subjects or fecal concentration (40-160 mg/ml in the fecal suspension). When we attempted to detect the genes of pathogenic bacteria in 4 actual clinical cases, we found that this method was more sensitive than standard culture method. These results showed that this assay is a rapid, simple detection method for foodborne pathogenic bacteria in human feces.

  18. Endophytic fungi producing of esterases: evaluation in vitro of the enzymatic activity using pH indicator

    Directory of Open Access Journals (Sweden)

    Helen Cristina Fávero Lisboa

    2013-09-01

    Full Text Available A sensitive and efficient colorimetric method was optimized for detection of esterase enzymes produced by endophytic fungi for development of High-Throughput Screening (HTS. The fungi were isolated and obtained previously from plant species of Cerrado and Atlantic Forest located in areas of environmental preservation in the State of Sao Paulo / Brazil, as part of the project "Chemical and biological prospecting endophytic fungi associated to plant species of Cerrado and Atlantic Forest". The compounds ethyl butyrate, ethyl acetate and methyl propionate were used as standards esters which were hydrolyzed by extracellular enzyme from endophytic fungi (EC. 3.1.1.1 -carboxylesterases for production of carboxylic acids. Thus, the reduction of the pH increases the protonated indicator concentration (bromothymol blue, changing the color of the reaction medium (from blue to yellow, that can be observed and measured by spectrophotometry at 616 nm. The methodology with acid-base indicator was performed on 13 microorganisms, aiming Periconia atropurpurea asapotential source of esterase for biotransformation of short chain esters. The results also evidenced that this methodology showed to be efficient, fast, cheap, having low consumption of reagents and easy development, and can be applied to screen carboxylic-ester hydrolases in a large number of microorganisms.

  19. Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

    Science.gov (United States)

    Stevenson, Lindsay G; Drake, Steven K; Murray, Patrick R

    2010-02-01

    Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid, accurate method for identifying bacteria and fungi recovered on agar culture media. We report herein a method for the direct identification of bacteria in positive blood culture broths by MALDI-TOF mass spectrometry. A total of 212 positive cultures were examined, representing 32 genera and 60 species or groups. The identification of bacterial isolates by MALDI-TOF mass spectrometry was compared with biochemical testing, and discrepancies were resolved by gene sequencing. No identification (spectral score of blood culture broth. Of the bacteria with a spectral score of > or = 1.7, 162 (95.3%) of 170 isolates were correctly identified. All 8 isolates of Streptococcus mitis were misidentified as being Streptococcus pneumoniae isolates. This method provides a rapid, accurate, definitive identification of bacteria within 1 h of detection in positive blood cultures with the caveat that the identification of S. pneumoniae would have to be confirmed by an alternative test.

  20. Susceptibility of ectomycorrhizal fungi to soil heating.

    Science.gov (United States)

    Kipfer, Tabea; Egli, Simon; Ghazoul, Jaboury; Moser, Barbara; Wohlgemuth, Thomas

    2010-01-01

    Ectomycorrhizal (EcM) fungi are an important biotic factor for successful tree recruitment because they enhance plant growth and alleviate drought stress of their hosts. Thus, EcM propagules are expected to be a key factor for forest regeneration after major disturbance events such as stand-replacing forest fires. Yet the susceptibility of soil-borne EcM fungi to heat is unclear. In this study, we investigated the heat tolerance of EcM fungi of Scots pine (Pinus sylvestris L., Pinaceae). Soil samples of three soil depths were heated to the temperature of 45, 60 and 70 °C, respectively, and surviving EcM fungi were assessed by a bioassay using Scots pine as an experimental host plant. EcM species were identified by a combination of morphotyping and sequencing of the ITS region. We found that mean number of species per sample was reduced by the 60 and 70 °C treatment, but not by the 45 °C treatment. Species composition changed due to heat. While some EcM fungi species did not survive heating, the majority of species was also found in the heated samples. The most frequent species in the heat treatment were Rhizopogon roseolus, Cenococcum geophilum and several unidentified species. Copyright © 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  1. Rapid detection of chlorpyrifos pesticide residue concentration in agro-product using Raman spectroscopy

    Science.gov (United States)

    Dhakal, Sagar; Peng, Yankun; Li, Yongyu; Chao, Kuanglin; Qin, Jianwei; Zhang, Leilei; Xu, Tianfeng

    2014-05-01

    Different chemicals are sprayed in fruits and vegetables before and after harvest for better yield and longer shelf-life of crops. Cases of pesticide poisoning to human health are regularly reported due to excessive application of such chemicals for greater economic benefit. Different analytical technologies exist to detect trace amount of pesticides in fruits and vegetables, but are expensive, sample destructive, and require longer processing time. This study explores the application of Raman spectroscopy for rapid and non-destructive detection of pesticide residue in agricultural products. Raman spectroscopy with laser module of 785 nm was used to collect Raman spectral information from the surface of Gala apples contaminated with different concentrations of commercially available organophosphorous (48% chlorpyrifos) pesticide. Apples within 15 days of harvest from same orchard were used in this study. The Raman spectral signal was processed by Savitzky-Golay (SG) filter for noise removal, Multiplicative Scatter Correction (MSC) for drift removal and finally polynomial fitting was used to eliminate the fluorescence background. The Raman spectral peak at 677 cm-1 was recognized as Raman fingerprint of chlorpyrifos. Presence of Raman peak at 677 cm-1 after fluorescence background removal was used to develop classification model (presence and absence of pesticide). The peak intensity was correlated with actual pesticide concentration obtained using Gas Chromatography and MLR prediction model was developed with correlation coefficient of calibration and validation of 0.86 and 0.81 respectively. Result shows that Raman spectroscopy is a promising tool for rapid, real-time and non-destructive detection of pesticide residue in agro-products.

  2. [Soil propagule bank of ectomycorrhizal fungi in natural forest of Pinus bungeana].

    Science.gov (United States)

    Zhao, Nan Xing; Han, Qi Sheng; Huang, Jian

    2017-12-01

    To conserve and restore the forest of Pinu bungeana, we investigated the soil propagule bank of ectomycorrhizal (ECM) fungi in a severely disturbed natural forest of P. bungeana in Shaanxi Province, China. We used a seedling-bioassay method to bait the ECM fungal propagules in the soils collected from the forest site. ECM was identified by combining morph typing with ITS-PCR-sequencing. We obtained 73 unique sequences from the ECM associated with P. bungeana seedlings, and assigned them into 12 ECM fungal OTUs at the threshold of 97% based on the sequence similarity. Rarefaction curve displayed almost all ECM fungi in the propagule bank were detected. The most frequent OTU (80%) showed poor similarity (75%) with existing sequences in the online database, which suggested it might be a new species. Cenococcum geophilum, Tomentella sp., Tuber sp. were common species in the propagule bank. Although C. geophilum and Tomentella sp. were frequently detected in other soil propagule banks of pine forest, the most frequent OTU was not assigned to known genus or family, which indicated the host-specif of ECM propagule banks associa-ted with P. bungeana. This result confirmed the importance of the special ECM propagule banks associated with P. bungeana for natural forest restoration.

  3. Selective effects of two systemic fungicides on soil fungi.

    Science.gov (United States)

    Abdel-Fattah, H M; Abdel-Kader, M I; Hamida, S

    1982-08-20

    BAS 317 00F was not toxic to the total count of fungi after 2 days but was regularly significantly toxic at the three doses after 5, 20 and 40 days and toxic at the low and the high doses after 80 days. In the agar medium, it was toxic to the counts of total fungi. Aspergillus, A. terreus, Rhizopus oryzae and Mucor racemosus at the high dose. Only the mycelial growth of Trichoderma viride which was significantly inhibited by the three doses when this fungicide was added to the liquid medium. Polyram-Combi induced two effects on the total population of soil fungi. One inhibitory and this was demonstrated almost regularly after 2, 10 and 40 days and the other stimulatory after 80 days of treatment with the low and the high doses. In the agar medium, this fungicide was very toxic to total fungi and to almost all fungal genera and species at the three doses. Several fungi could survive the high dose. In liquid medium, the test fungi showed variable degree of sensitivity and the most sensitive was Gliocladium roseum which was completely eradicated by the three doses.

  4. Fluorescent QDs-polystyrene composite nanospheres for highly efficient and rapid protein antigen detection

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Changhua; Mao, Mao [Henan University, Key Laboratory for Special Functional Materials of the Ministry of Education (China); Yuan, Hang [Tsinghua University, Life Science Division, Graduate School at Shenzhen (China); Shen, Huaibin [Henan University, Key Laboratory for Special Functional Materials of the Ministry of Education (China); Wu, Feng; Ma, Lan, E-mail: malan@sz.tsinghua.edu.cn [Tsinghua University, Life Science Division, Graduate School at Shenzhen (China); Li, Lin Song, E-mail: lsli@henu.edu.cn [Henan University, Key Laboratory for Special Functional Materials of the Ministry of Education (China)

    2013-09-15

    In this paper, high-quality carboxyl-functionalized fluorescent (red, green, and blue emitting) nanospheres (46-103 nm) consisting of hydrophobic quantum dots (QDs) and polystyrene were prepared by a miniemulsion polymerization approach. This miniemulsion polymerization approach induced a homogeneous distribution and high aqueous-phase transport efficiency of fluorescent QDs in composite nanospheres, which proved the success of our encoding QDs strategy. The obtained fluorescent nanospheres exhibited high stability in aqueous solution under a wide range of pH, different salt concentrations, PBS buffer, and thermal treatment at 80 Degree-Sign C. Based on the red emitting composite nanosphere, we performed fluorescent lateral flow immunoassay (LFIA) strips for high-sensitivity and rapid alpha-fetal protein detection. The detection limit reached 0.1 ng/mL, which was 200 times higher than commercial colloidal gold-labeled LFIA strips, and it reached similar detection level in enzyme-linked immunosorbent assay kit.

  5. Rapid, highly sensitive detection of Gram-negative bacteria with lipopolysaccharide based disposable aptasensor.

    Science.gov (United States)

    Zhang, Jian; Oueslati, Rania; Cheng, Cheng; Zhao, Ling; Chen, Jiangang; Almeida, Raul; Wu, Jayne

    2018-07-30

    Gram-negative bacteria are one of the most common microorganisms in the environment. Their differential detection and recognition from Gram-positive bacteria has been attracting much attention over the years. Using Escherichia coli (E. coli) as a model, we demonstrated on-site detection of Gram-negative bacteria by an AC electrokinetics-based capacitive sensing method using commercial microelectrodes functionalized with an aptamer specific to lipopolysaccharides. Dielectrophoresis effect was utilized to enrich viable bacteria to the microelectrodes rapidly, achieving a detection limit of 10 2 cells/mL within a 30 s' response time. The sensor showed a negligible response to Staphylococcus aureus (S. aureus), a Gram-positive species. The developed sensor showed significant advantages in sensitivity, selectivity, cost, operation simplicity, and response time. Therefore, this sensing method has shown great application potential for environmental monitoring, food safety, and real-time diagnosis. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. Composition of arbuscular mycorrhizal fungi associated with cassava

    African Journals Online (AJOL)

    SARAH

    2016-02-29

    Feb 29, 2016 ... Objectives: Arbuscular mycorrhizal fungi (AMF) form root symbiotic relationships with higher plants, but .... including growth habit of stem, stem colour, outer and inner root ..... of AM fungi to colonize roots, breaking down their.

  7. Aflatoxins Associated with Storage Fungi in Fish Feed

    African Journals Online (AJOL)

    Timothy Ademakinwa

    This study investigates storage fungi and aflatoxin in fish feed stored under three different ... secondary metabolites of fungi which are formed ... Department of Marine Sciences, Faculty of ... antibiotic is to inhibit the growth of any bacterial.

  8. Rapid direct identification of Cryptococcus neoformans from pigeon droppings by nested PCR using CNLAC1 gene.

    Science.gov (United States)

    Chae, H S; Park, G N; Kim, S H; Jo, H J; Kim, J T; Jeoung, H Y; An, D J; Kim, N H; Shin, B W; Kang, Y I; Chang, K S

    2012-08-01

    Isolation and identification of Cryptococcus neoformans and pathogenic yeast-like fungi from pigeon droppings has been taken for a long time and requires various nutrients for its growth. In this study, we attempted to establish a rapid direct identification method of Cr. neoformans from pigeon dropping samples by nested-PCR using internal transcribed spacer (ITS) CAP64 and CNLAC1 genes, polysaccharide capsule gene and laccase-associated gene to produce melanin pigment, respectively, which are common genes of yeasts. The ITS and CAP64 genes were amplified in all pathogenic yeasts, but CNLAC1 was amplified only in Cr. neoformans. The ITS gene was useful for yeast genotyping depending on nucleotide sequence. Homology of CAP64 genes among the yeasts were very high. The specificity of PCR using CNLAC1 was demonstrated in Cr. neoformans environmental strains but not in other yeast-like fungi. The CNLAC1 gene was detected in 5 serotypes of Cr. neoformans. The nested-PCR amplified up to 10(-11) μg of the genomic DNA and showed high sensitivity. All pigeon droppings among 31 Cr. neoformans-positive samples were positive and all pigeon droppings among 348 Cr. neoformans-negative samples were negative by the direct nested-PCR. In addition, after primary enrichment of pigeon droppings in Sabouraud dextrose broth, all Cr. neoformans-negative samples were negative by the nested-PCR, which showed high specificity. The nested-PCR showed high sensitivity without culture of pigeon droppings. Nested-PCR using CNLAC1 provides a rapid and reliable molecular diagnostic method to overcome weak points such as long culture time of many conventional methods.

  9. A novel electrochemical sensing strategy for rapid and ultrasensitive detection of Salmonella by rolling circle amplification and DNA–AuNPs probe

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Dan; Yan, Yurong; Lei, Pinhua; Shen, Bo [Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016 (China); Cheng, Wei [Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016 (China); The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Ju, Huangxian [Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016 (China); State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210093 (China); Ding, Shijia, E-mail: dingshijia@163.com [Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016 (China)

    2014-10-10

    A novel electrochemical sensing strategy was developed for ultrasensitive and rapid detection of Salmonella by combining the rolling circle amplification with DNA–AuNPs probe. - Highlights: • This paper presented a novel sensing strategy for the rapid and ultrasensitive detection for Salmonella. • Combination of rolling circle amplification and DNA–AuNPs probe is the first time for Salmonella electrochemical detection. • The method displayed excellent sensitivity and specificity for detection of Salmonella. • The fabricated biosensor was successfully applied to detect Salmonella in milk samples. - Abstract: A novel electrochemical sensing strategy was developed for ultrasensitive and rapid detection of Salmonella by combining the rolling circle amplification with DNA–AuNPs probe. The target DNA could be specifically captured by probe 1 on the sensing interface. Then the circularization mixture was added to form a typical sandwich structure. In the presence of dNTPs and phi29 DNA polymerase, the RCA was initiated to produce micrometer-long single-strand DNA. Finally, the detection probe (DNA–AuNPs) could recognize RCA product to produce enzymatic electrochemical signal. Under optimal conditions, the calibration curve of synthetic target DNA had good linearity from 10 aM to 10 pM with a detection limit of 6.76 aM (S/N = 3). The developed method had been successfully applied to detect Salmonella as low as 6 CFU mL{sup −1} in real milk sample. This proposed strategy showed great potential for clinical diagnosis, food safety and environmental monitoring.

  10. A novel electrochemical sensing strategy for rapid and ultrasensitive detection of Salmonella by rolling circle amplification and DNA–AuNPs probe

    International Nuclear Information System (INIS)

    Zhu, Dan; Yan, Yurong; Lei, Pinhua; Shen, Bo; Cheng, Wei; Ju, Huangxian; Ding, Shijia

    2014-01-01

    A novel electrochemical sensing strategy was developed for ultrasensitive and rapid detection of Salmonella by combining the rolling circle amplification with DNA–AuNPs probe. - Highlights: • This paper presented a novel sensing strategy for the rapid and ultrasensitive detection for Salmonella. • Combination of rolling circle amplification and DNA–AuNPs probe is the first time for Salmonella electrochemical detection. • The method displayed excellent sensitivity and specificity for detection of Salmonella. • The fabricated biosensor was successfully applied to detect Salmonella in milk samples. - Abstract: A novel electrochemical sensing strategy was developed for ultrasensitive and rapid detection of Salmonella by combining the rolling circle amplification with DNA–AuNPs probe. The target DNA could be specifically captured by probe 1 on the sensing interface. Then the circularization mixture was added to form a typical sandwich structure. In the presence of dNTPs and phi29 DNA polymerase, the RCA was initiated to produce micrometer-long single-strand DNA. Finally, the detection probe (DNA–AuNPs) could recognize RCA product to produce enzymatic electrochemical signal. Under optimal conditions, the calibration curve of synthetic target DNA had good linearity from 10 aM to 10 pM with a detection limit of 6.76 aM (S/N = 3). The developed method had been successfully applied to detect Salmonella as low as 6 CFU mL −1 in real milk sample. This proposed strategy showed great potential for clinical diagnosis, food safety and environmental monitoring

  11. Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons.

    Science.gov (United States)

    Toju, Hirokazu; Kishida, Osamu; Katayama, Noboru; Takagi, Kentaro

    2016-01-01

    Fungi in soil play pivotal roles in nutrient cycling, pest controls, and plant community succession in terrestrial ecosystems. Despite the ecosystem functions provided by soil fungi, our knowledge of the assembly processes of belowground fungi has been limited. In particular, we still have limited knowledge of how diverse functional groups of fungi interact with each other in facilitative and competitive ways in soil. Based on the high-throughput sequencing data of fungi in a cool-temperate forest in northern Japan, we analyzed how taxonomically and functionally diverse fungi showed correlated fine-scale distributions in soil. By uncovering pairs of fungi that frequently co-occurred in the same soil samples, networks depicting fine-scale co-occurrences of fungi were inferred at the O (organic matter) and A (surface soil) horizons. The results then led to the working hypothesis that mycorrhizal, endophytic, saprotrophic, and pathogenic fungi could form compartmentalized (modular) networks of facilitative, antagonistic, and/or competitive interactions in belowground ecosystems. Overall, this study provides a research basis for further understanding how interspecific interactions, along with sharing of niches among fungi, drive the dynamics of poorly explored biospheres in soil.

  12. Rapid Detection of Microorganisms Based on Active and Passive Modes of QCM

    Directory of Open Access Journals (Sweden)

    Zdeněk Farka

    2014-12-01

    Full Text Available Label-free immunosensors are well suited for detection of microorganisms because of their fast response and reasonable sensitivity comparable to infection doses of common pathogens. Active (lever oscillator and frequency counter and passive (impedance analyzer modes of quartz crystal microbalance (QCM were used and compared for rapid detection of three strains of E. coli. Different approaches for antibody immobilization were compared, the immobilization of reduced antibody using Sulfo‑SMCC was most effective achieving the limit of detection (LOD 8 × 104 CFU·mL−1 in 10 min. For the passive mode, software evaluating impedance characteristics in real-time was developed and used. Almost the same results were achieved using both active and passive modes confirming that the sensor properties are not limited by the frequency evaluation method but mainly by affinity of the antibody. Furthermore, reference measurements were done using surface plasmon resonance. Effect of condition of cells on signal was observed showing that cells ruptured by ultrasonication provided slightly higher signal changes than intact microbes.

  13. Genera of phytopathogenic fungi: GOPHY 1

    Directory of Open Access Journals (Sweden)

    Y. Marin-Felix

    2017-03-01

    Full Text Available Genera of Phytopathogenic Fungi (GOPHY is introduced as a new series of publications in order to provide a stable platform for the taxonomy of phytopathogenic fungi. This first paper focuses on 21 genera of phytopathogenic fungi: Bipolaris, Boeremia, Calonectria, Ceratocystis, Cladosporium, Colletotrichum, Coniella, Curvularia, Monilinia, Neofabraea, Neofusicoccum, Pilidium, Pleiochaeta, Plenodomus, Protostegia, Pseudopyricularia, Puccinia, Saccharata, Thyrostroma, Venturia and Wilsonomyces. For each genus, a morphological description and information about its pathology, distribution, hosts and disease symptoms are provided. In addition, this information is linked to primary and secondary DNA barcodes of the presently accepted species, and relevant literature. Moreover, several novelties are introduced, i.e. new genera, species and combinations, and neo-, lecto- and epitypes designated to provide a stable taxonomy. This first paper includes one new genus, 26 new species, ten new combinations, and four typifications of older names.

  14. Comparative Genome Analysis of Basidiomycete Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Salamov, Asaf; Morin, Emmanuelle; Nagy, Laszlo; Manning, Gerard; Baker, Scott; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Hibbett, David; Martin, Francis; Grigoriev, Igor

    2012-03-19

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, symbionts, and plant and animal pathogens. To better understand the diversity of phenotypes in basidiomycetes, we performed a comparative analysis of 35 basidiomycete fungi spanning the diversity of the phylum. Phylogenetic patterns of lignocellulose degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay. Patterns of secondary metabolic enzymes give additional insight into the broad array of phenotypes found in the basidiomycetes. We suggest that the profile of an organism in lignocellulose-targeting genes can be used to predict its nutritional mode, and predict Dacryopinax sp. as a brown rot; Botryobasidium botryosum and Jaapia argillacea as white rots.

  15. Biology of flower-infecting fungi.

    Science.gov (United States)

    Ngugi, Henry K; Scherm, Harald

    2006-01-01

    The ability to infect host flowers offers important ecological benefits to plant-parasitic fungi; not surprisingly, therefore, numerous fungal species from a wide range of taxonomic groups have adopted a life style that involves flower infection. Although flower-infecting fungi are very diverse, they can be classified readily into three major groups: opportunistic, unspecialized pathogens causing necrotic symptoms such as blossom blights (group 1), and specialist flower pathogens which infect inflorescences either through the gynoecium (group 2) or systemically through the apical meristem (group 3). This three-tier system is supported by life history attributes such as host range, mode of spore transmission, degree of host sterilization as a result of infection, and whether or not the fungus undergoes an obligate sexual cycle, produces resting spores in affected inflorescences, and is r- or K-selected. Across the three groups, the flower as an infection court poses important challenges for disease management. Ecologically and evolutionarily, terms and concepts borrowed from the study of venereal (sexually transmitted) diseases of animals do not adequately capture the range of strategies employed by fungi that infect flowers.

  16. Fusarium toxins and fungi associated with handling of grain on eight Finnish farms

    Science.gov (United States)

    Lappalainen, Sanna; Nikulin, Marjo; Berg, Seija; Parikka, Päivi; Hintikka, Eeva-Liisa; Pasanen, Anna-Liisa

    Farmers' exposure to airborne dust, fungi and possibly also to Fusarium toxins during the drying and milling of grain and feeding of cattle was studied on eight Finnish farms. Airborne viable and total spores were collected on polycarbonate filters. Spore concentrations and fungal flora were determined by cultivation and epifluorescence microscope counting. Eighteen airborne dust samples were taken on glass-fiber filters with a high-volume sampler, and biological toxicity was tested from those samples. In toxic dust samples, Fusarium toxins were analyzed with a gas chromatography-mass spectroscopy. Fungi and Fusarium toxins were also analyzed in ten grain samples collected from the farms during the air sampling. Yeasts, as well as species of Cladosporium, Penicillium, Aspergillus, Absidia and Fusarium occurred in the air at all three stages of grain handling. Airborne spore concentrations ranged from 103 to 10 6 cfu m -3 for viable fungi and from 10 5 to 10 7 spores m -3 for total spores; airborne dust concentrations varied from 0.04 to 81.1 mg m -3. Low deoxynivalenol concentrations (3 and 20 ng m -3) were found in two air samples collected during milling. Fusarium spp. were identified in eight grain samples, and DON concentrations of 0.004-11 mg kg -1 were detected in all samples analyzed. Although any conclusion on Finnish farmers' exposure to mycotoxins cannot be done on the basis of this small data, it can be assumed that toxigenic fungi and Fusarium toxins may occur in the air and inhalation exposure of farmers to Fusarium toxins is possible in agricultural environment.

  17. Community assembly and coexistence in communities of arbuscular mycorrhizal fungi.

    Science.gov (United States)

    Vályi, Kriszta; Mardhiah, Ulfah; Rillig, Matthias C; Hempel, Stefan

    2016-10-01

    Arbuscular mycorrhizal fungi are asexual, obligately symbiotic fungi with unique morphology and genomic structure, which occupy a dual niche, that is, the soil and the host root. Consequently, the direct adoption of models for community assembly developed for other organism groups is not evident. In this paper we adapted modern coexistence and assembly theory to arbuscular mycorrhizal fungi. We review research on the elements of community assembly and coexistence of arbuscular mycorrhizal fungi, highlighting recent studies using molecular methods. By addressing several points from the individual to the community level where the application of modern community ecology terms runs into problems when arbuscular mycorrhizal fungi are concerned, we aim to account for these special circumstances from a mycocentric point of view. We suggest that hierarchical spatial structure of arbuscular mycorrhizal fungal communities should be explicitly taken into account in future studies. The conceptual framework we develop here for arbuscular mycorrhizal fungi is also adaptable for other host-associated microbial communities.

  18. First record of entomopathogenic fungi on autumn leaf Caterpillar (Doleschallia bisaltide)

    Science.gov (United States)

    Dayanti, A. K.; Sholahuddin; Yunus, A.; Subositi, D.

    2018-03-01

    Caricature plant is one of the medicinal plants in Indonesia to cure hemorrhoids, menstruation, and others. The cultivation constraints of caricature plant is autumn leaf caterpillars (Doleschallia bisaltide). Utilization of synthetic insecticides is not allowed to avoid bioaccumulation of chemical residues. Entomopathogenic fungi is an alternative way to control D. bisaltide. The objective of the research was to obtain isolates of entomopathogenic fungi of D. bisaltide. The research conducted by two steps, which were exsploration of infecfted D. bisaltide. The second step was identification of the fungi. Exploration results of 16 pupae of D. Bisaltide were infected by fungi. Identification done by classify the mcroscopic and microscopic fungi isolate characteristic. One from five fungal isolates were entomopathogenic fungi from Verticillium genera.

  19. Some Orchid Species Fungi Isolated by Different Methods

    Directory of Open Access Journals (Sweden)

    Arzu ÇIĞ

    2014-03-01

    Full Text Available Due to their very small seeds that do not contain endosperm, many terrestrial orchid species require the presence of fungi in order to germinate and maintain their lives; and symbiotic culture studies are being carried out on this topic. For the purpose of determining the orchid species on which the fungus to be used as inoculants in the symbiotic culture will be effective, fungi isolated through several isolation methods are cultured with orchid species. In this study a total of four different isolation methods were applied as one on the tubers and rhizomes and three on the soil of eleven orchid species from the Anacamptis, Cephalanthera, Dactylorhiza and Orchis genera. Three different culture media were used in the methods. At the end of the study Alternaria, Aspergillus, Fusarium, Macrophomina, Rhizoctonia, Trichoderma and Verticillium fungi were isolated. In the study that was conducted with the aimed to isolate particularly Rhizoctania spp. fungi, the fungi was isolated from the tubers of Dactylorhiza umbrosa and Orchis palustris species and the soil of the Orchis simia species. Fusarium and Aspergillus species were isolated the most in all implemented methods and from all species.

  20. Rapid detection and identification of four major Schistosoma species by high-resolution melt (HRM) analysis.

    Science.gov (United States)

    Li, Juan; Zhao, Guang-Hui; Lin, RuiQing; Blair, David; Sugiyama, Hiromu; Zhu, Xing-Quan

    2015-11-01

    Schistosomiasis, caused by blood flukes belonging to several species of the genus Schistosoma, is a serious and widespread parasitic disease. Accurate and rapid differentiation of these etiological agents of animal and human schistosomiasis to species level can be difficult. We report a real-time PCR assay coupled with a high-resolution melt (HRM) assay targeting a portion of the nuclear 18S rDNA to detect, identify, and distinguish between four major blood fluke species (Schistosoma japonicum, Schistosoma mansoni, Schistosoma haematobium, and Schistosoma mekongi). Using this system, the Schistosoma spp. was accurately identified and could also be distinguished from all other trematode species with which they were compared. As little as 10(-5) ng genomic DNA from a Schistosoma sp. could be detected. This process is inexpensive, easy, and can be completed within 3 h. Examination of 21 representative Schistosoma samples from 15 geographical localities in seven endemic countries validated the value of the HRM detection assay and proved its reliability. The melting curves were characterized by peaks of 83.65 °C for S. japonicum and S. mekongi, 85.65 °C for S. mansoni, and 85.85 °C for S. haematobium. The present study developed a real-time PCR coupled with HRM analysis assay for detection and differential identification of S. mansoni, S. haematobium, S. japonicum, and S. mekongi. This method is rapid, sensitive, and inexpensive. It has important implications for epidemiological studies of Schistosoma.