WorldWideScience

Sample records for fungal regulatory evolution

  1. The evolution of fungal epiphytes

    NARCIS (Netherlands)

    Hongsanan, S.; Sánchez-Ramírez, S.; Crous, P.W.; Ariyawansa, H.A.; Zhao, R.L.; Hyde, K.D.

    2016-01-01

    Fungal epiphytes are a polyphyletic group found on the surface of plants, particularly on leaves, with a worldwide distribution. They belong in the phylum Ascomycota, which contains the largest known number of fungal genera. There has been little research dating the origins of the common ancestors o

  2. Divergent and Convergent Evolution of Fungal Pathogenicity.

    Science.gov (United States)

    Shang, Yanfang; Xiao, Guohua; Zheng, Peng; Cen, Kai; Zhan, Shuai; Wang, Chengshu

    2016-05-12

    Fungal pathogens of plants and animals have multifarious effects; they cause devastating damages to agricultures, lead to life-threatening diseases in humans, or induce beneficial effects by reducing insect pest populations. Many virulence factors have been determined in different fungal pathogens; however, the molecular determinants contributing to fungal host selection and adaptation are largely unknown. In this study, we sequenced the genomes of seven ascomycete insect pathogens and performed the genome-wide analyses of 33 species of filamentous ascomycete pathogenic fungi that infect insects (12 species), plants (12), and humans (9). Our results revealed that the genomes of plant pathogens encode more proteins and protein families than the insect and human pathogens. Unexpectedly, more common orthologous protein groups are shared between the insect and plant pathogens than between the two animal group pathogens. We also found that the pathogenicity of host-adapted fungi evolved multiple times, and that both divergent and convergent evolutions occurred during pathogen-host cospeciation thus resulting in protein families with similar features in each fungal group. However, the role of phylogenetic relatedness on the evolution of protein families and therefore pathotype formation could not be ruled out due to the effect of common ancestry. The evolutionary correlation analyses led to the identification of different protein families that correlated with alternate pathotypes. Particularly, the effector-like proteins identified in plant and animal pathogens were strongly linked to fungal host adaptation, suggesting the existence of similar gene-for-gene relationships in fungus-animal interactions that has not been established before. These results well advance our understanding of the evolution of fungal pathogenicity and the factors that contribute to fungal pathotype formation. © The Author 2016. Published by Oxford University Press on behalf of the Society for

  3. Fungal Systematics and Evolution: FUSE 1

    NARCIS (Netherlands)

    Crous, Pedro W; Schumacher, René K; Wingfield, Michael J; Lombard, Lorenzo; Giraldo, Alejandra; Christensen, Martha; Gardiennet, Alain; Nakashima, Chiharu; Pereira, Olinto L; Smith, Alexander J; Groenewald, Johannes Z

    2015-01-01

    Fungal Systematics and Evolution (FUSE) is introduced as a new series to expedite the publication of issues relating to the epitypification of formerly described species, report new sexual-asexual connections, the merging of sexual and asexual gen¬era following the end of dual nomenclature, and to

  4. Evolution and genome architecture in fungal plant pathogens.

    Science.gov (United States)

    Möller, Mareike; Stukenbrock, Eva H

    2017-08-07

    The fungal kingdom comprises some of the most devastating plant pathogens. Sequencing the genomes of fungal pathogens has shown a remarkable variability in genome size and architecture. Population genomic data enable us to understand the mechanisms and the history of changes in genome size and adaptive evolution in plant pathogens. Although transposable elements predominantly have negative effects on their host, fungal pathogens provide prominent examples of advantageous associations between rapidly evolving transposable elements and virulence genes that cause variation in virulence phenotypes. By providing homogeneous environments at large regional scales, managed ecosystems, such as modern agriculture, can be conducive for the rapid evolution and dispersal of pathogens. In this Review, we summarize key examples from fungal plant pathogen genomics and discuss evolutionary processes in pathogenic fungi in the context of molecular evolution, population genomics and agriculture.

  5. Evolution of Fungal enzymes in the attine ant symbiosis

    DEFF Research Database (Denmark)

    de Fine Licht, Henrik Hjarvard; Schiøtt, Morten; Boomsma, Jacobus Jan

    The attine ant symbiosis is characterized by ancient but varying degrees of diffuse co-evolution between the ants and their fungal cultivars. Domesticated fungi became dependent on vertical transmission by queens and the ant colonies came to rely on their symbiotic fungus for food and thus......, indirectly, on fungal enzymes to break down the plant material brought in by the ants as fungal substrate. The more than 210 extant fungus-growing ant species differ considerably in colony size, social complexity and substrate-use. Only the derived leaf-cutting ants are specialized on using fresh leaves...... enzyme activity across ant genera could indeed be partially explained by substrate differences. This implies that fungal enzyme activity has likely coevolved with the genus- or species-specific substrates that the ants use to manure their fungus garden. Plant decomposing enzymes are thus not only...

  6. Genetic Regulatory Networks in Embryogenesis and Evolution

    Science.gov (United States)

    1998-01-01

    The article introduces a series of papers that were originally presented at a workshop titled Genetic Regulatory Network in Embryogenesis and Evaluation. Contents include the following: evolution of cleavage programs in relationship to axial specification and body plan evolution, changes in cell lineage specification elucidate evolutionary relations in spiralia, axial patterning in the leech: developmental mechanisms and evolutionary implications, hox genes in arthropod development and evolution, heterochronic genes in development and evolution, a common theme for LIM homeobox gene function across phylogeny, and mechanisms of specification in ascidian embryos.

  7. Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts.

    Science.gov (United States)

    Nagy, László G; Ohm, Robin A; Kovács, Gábor M; Floudas, Dimitrios; Riley, Robert; Gácser, Attila; Sipiczki, Mátyás; Davis, John M; Doty, Sharon L; de Hoog, G Sybren; Lang, B Franz; Spatafora, Joseph W; Martin, Francis M; Grigoriev, Igor V; Hibbett, David S

    2014-07-18

    Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the potential to develop yeast forms arose early in fungal evolution and became dominant independently in multiple clades, most likely via parallel diversification of Zn-cluster transcription factors, a fungal-specific family involved in regulating yeast-filamentous switches. Our results imply that convergent evolution can happen by the repeated deployment of a conserved genetic toolkit for the same function in distinct clades via regulatory evolution. We suggest that this mechanism might be a common source of evolutionary convergence even at large time scales.

  8. Evolution of evolvability in gene regulatory networks.

    Directory of Open Access Journals (Sweden)

    Anton Crombach

    Full Text Available Gene regulatory networks are perhaps the most important organizational level in the cell where signals from the cell state and the outside environment are integrated in terms of activation and inhibition of genes. For the last decade, the study of such networks has been fueled by large-scale experiments and renewed attention from the theoretical field. Different models have been proposed to, for instance, investigate expression dynamics, explain the network topology we observe in bacteria and yeast, and for the analysis of evolvability and robustness of such networks. Yet how these gene regulatory networks evolve and become evolvable remains an open question. An individual-oriented evolutionary model is used to shed light on this matter. Each individual has a genome from which its gene regulatory network is derived. Mutations, such as gene duplications and deletions, alter the genome, while the resulting network determines the gene expression pattern and hence fitness. With this protocol we let a population of individuals evolve under Darwinian selection in an environment that changes through time. Our work demonstrates that long-term evolution of complex gene regulatory networks in a changing environment can lead to a striking increase in the efficiency of generating beneficial mutations. We show that the population evolves towards genotype-phenotype mappings that allow for an orchestrated network-wide change in the gene expression pattern, requiring only a few specific gene indels. The genes involved are hubs of the networks, or directly influencing the hubs. Moreover, throughout the evolutionary trajectory the networks maintain their mutational robustness. In other words, evolution in an alternating environment leads to a network that is sensitive to a small class of beneficial mutations, while the majority of mutations remain neutral: an example of evolution of evolvability.

  9. The Evolution of Sex: a Perspective from the Fungal Kingdom

    Science.gov (United States)

    Lee, Soo Chan; Ni, Min; Li, Wenjun; Shertz, Cecelia; Heitman, Joseph

    2010-01-01

    Summary: Sex is shrouded in mystery. Not only does it preferentially occur in the dark for both fungi and many animals, but evolutionary biologists continue to debate its benefits given costs in light of its pervasive nature. Experimental studies of the benefits and costs of sexual reproduction with fungi as model systems have begun to provide evidence that the balance between sexual and asexual reproduction shifts in response to selective pressures. Given their unique evolutionary history as opisthokonts, along with metazoans, fungi serve as exceptional models for the evolution of sex and sex-determining regions of the genome (the mating type locus) and for transitions that commonly occur between outcrossing/self-sterile and inbreeding/self-fertile modes of reproduction. We review here the state of the understanding of sex and its evolution in the fungal kingdom and also areas where the field has contributed and will continue to contribute to illuminating general principles and paradigms of sexual reproduction. PMID:20508251

  10. From elements to modules: regulatory evolution in Ascomycota fungi

    OpenAIRE

    Wohlbach, Dana J.; Thompson, Dawn Anne; Audrey P Gasch; Regev, Aviv

    2009-01-01

    Regulatory divergence is likely a major driving force in evolution. Comparative transcriptomics provides a new glimpse into the evolution of gene regulation. Ascomycota fungi are uniquely suited among eukaryotes for studies of regulatory evolution, because of broad phylogenetic scope, many sequenced genomes, and facility of genomic analysis. Here we review the substantial divergence in gene expression in Ascomycota and how this is reconciled with the modular organization of transcriptional ne...

  11. Evolution of the chitin synthase gene family correlates with fungal morphogenesis and adaption to ecological niches

    Science.gov (United States)

    Liu, Ran; Xu, Chuan; Zhang, Qiangqiang; Wang, Shiyi; Fang, Weiguo

    2017-01-01

    The fungal kingdom potentially has the most complex chitin synthase (CHS) gene family, but evolution of the fungal CHS gene family and its diversification to fulfill multiple functions remain to be elucidated. Here, we identified the full complement of CHSs from 231 fungal species. Using the largest dataset to date, we characterized the evolution of the fungal CHS gene family using phylogenetic and domain structure analysis. Gene duplication, domain recombination and accretion are major mechanisms underlying the diversification of the fungal CHS gene family, producing at least 7 CHS classes. Contraction of the CHS gene family is morphology-specific, with significant loss in unicellular fungi, whereas family expansion is lineage-specific with obvious expansion in early-diverging fungi. ClassV and ClassVII CHSs with the same domain structure were produced by the recruitment of domains PF00063 and PF08766 and subsequent duplications. Comparative analysis of their functions in multiple fungal species shows that the emergence of ClassV and ClassVII CHSs is important for the morphogenesis of filamentous fungi, development of pathogenicity in pathogenic fungi, and heat stress tolerance in Pezizomycotina fungi. This work reveals the evolution of the fungal CHS gene family, and its correlation with fungal morphogenesis and adaptation to ecological niches. PMID:28300148

  12. Regulatory Evolution and Theoretical Arguments in Evolutionary Biology

    Science.gov (United States)

    Ioannidis, Stavros

    2013-01-01

    The "cis"-regulatory hypothesis is one of the most important claims of evolutionary developmental biology. In this paper I examine the theoretical argument for "cis"-regulatory evolution and its role within evolutionary theorizing. I show that, although the argument has some weaknesses, it acts as a useful example for the importance of current…

  13. Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells

    Directory of Open Access Journals (Sweden)

    Guthke Reinhard

    2010-11-01

    Full Text Available Abstract Background Reverse engineering of gene regulatory networks can be used to predict regulatory interactions of an organism faced with environmental changes, but can prove problematic, especially when focusing on complicated multi-factorial processes. Candida albicans is a major human fungal pathogen. During the infection process, this fungus is able to adapt to conditions of very low iron availability. Such adaptation is an important virulence attribute of virtually all pathogenic microbes. Understanding the regulation of iron acquisition genes will extend our knowledge of the complex regulatory changes during the infection process and might identify new potential drug targets. Thus, there is a need for efficient modelling approaches predicting key regulatory events of iron acquisition genes during the infection process. Results This study deals with the regulation of C. albicans iron uptake genes during adhesion to and invasion into human oral epithelial cells. A reverse engineering strategy is presented, which is able to infer regulatory networks on the basis of gene expression data, making use of relevant selection criteria such as sparseness and robustness. An exhaustive use of available knowledge from different data sources improved the network prediction. The predicted regulatory network proposes a number of new target genes for the transcriptional regulators Rim101, Hap3, Sef1 and Tup1. Furthermore, the molecular mode of action for Tup1 is clarified. Finally, regulatory interactions between the transcription factors themselves are proposed. This study presents a model describing how C. albicans may regulate iron acquisition during contact with and invasion of human oral epithelial cells. There is evidence that some of the proposed regulatory interactions might also occur during oral infection. Conclusions This study focuses on a typical problem in Systems Biology where an interesting biological phenomenon is studied using a small

  14. Evolution of cichlid vision via trans-regulatory divergence

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    O’Quin Kelly E

    2012-12-01

    Full Text Available Abstract Background Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within the opsin genes, recent research has shown that opsin regulatory mutations can also tune photoreceptor sensitivity and color vision. Visual sensitivity in African cichlid fishes varies as a result of the differential expression of seven opsin genes. We crossed cichlid species that express different opsin gene sets and scanned their genome for expression Quantitative Trait Loci (eQTL responsible for these differences. Our results shed light on the role that different structural, cis-, and trans-regulatory mutations play in the evolution of color vision. Results We identified 11 eQTL that contribute to the divergent expression of five opsin genes. On three linkage groups, several eQTL formed regulatory “hotspots” associated with the expression of multiple opsins. Importantly, however, the majority of the eQTL we identified (8/11 or 73% occur on linkage groups located trans to the opsin genes, suggesting that cichlid color vision has evolved primarily via trans-regulatory divergence. By modeling the impact of just two of these trans-regulatory eQTL, we show that opsin regulatory mutations can alter cichlid photoreceptor sensitivity and color vision at least as much as opsin structural mutations can. Conclusions Combined with previous work, we demonstrate that the evolution of cichlid color vision results from the interplay of structural, cis-, and especially trans-regulatory loci. Although there are numerous examples of structural and cis-regulatory mutations that contribute to phenotypic evolution, our results suggest that trans-regulatory mutations could contribute to phenotypic divergence more commonly than previously expected, especially in systems like color vision, where compensatory changes in the

  15. The regulatory mechanism of fungal elicitor-induced secondary metabolite biosynthesis in medical plants.

    Science.gov (United States)

    Zhai, Xin; Jia, Min; Chen, Ling; Zheng, Cheng-Jian; Rahman, Khalid; Han, Ting; Qin, Lu-Ping

    2017-03-01

    A wide range of external stress stimuli trigger plant cells to undergo complex network of reactions that ultimately lead to the synthesis and accumulation of secondary metabolites. Accumulation of such metabolites often occurs in plants subjected to stresses including various elicitors or signal molecules. Throughout evolution, endophytic fungi, an important constituent in the environment of medicinal plants, have known to form long-term stable and mutually beneficial symbiosis with medicinal plants. The endophytic fungal elicitor can rapidly and specifically induce the expression of specific genes in medicinal plants which can result in the activation of a series of specific secondary metabolic pathways resulting in the significant accumulation of active ingredients. Here we summarize the progress made on the mechanisms of fungal elicitor including elicitor signal recognition, signal transduction, gene expression and activation of the key enzymes and its application. This review provides guidance on studies which may be conducted to promote the efficient synthesis and accumulation of active ingredients by the endogenous fungal elicitor in medicinal plant cells, and provides new ideas and methods of studying the regulation of secondary metabolism in medicinal plants.

  16. Bioattractors: dynamical systems theory and the evolution of regulatory processes.

    Science.gov (United States)

    Jaeger, Johannes; Monk, Nick

    2014-06-01

    In this paper, we illustrate how dynamical systems theory can provide a unifying conceptual framework for evolution of biological regulatory systems. Our argument is that the genotype-phenotype map can be characterized by the phase portrait of the underlying regulatory process. The features of this portrait--such as attractors with associated basins and their bifurcations--define the regulatory and evolutionary potential of a system. We show how the geometric analysis of phase space connects Waddington's epigenetic landscape to recent computational approaches for the study of robustness and evolvability in network evolution. We discuss how the geometry of phase space determines the probability of possible phenotypic transitions. Finally, we demonstrate how the active, self-organizing role of the environment in phenotypic evolution can be understood in terms of dynamical systems concepts. This approach yields mechanistic explanations that go beyond insights based on the simulation of evolving regulatory networks alone. Its predictions can now be tested by studying specific, experimentally tractable regulatory systems using the tools of modern systems biology. A systematic exploration of such systems will enable us to understand better the nature and origin of the phenotypic variability, which provides the substrate for evolution by natural selection.

  17. Abundant raw material for cis-regulatory evolution in humans

    Science.gov (United States)

    Rockman, Matthew V.; Wray, Gregory A.

    2002-01-01

    Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (human phenotypic variation.

  18. Abundant raw material for cis-regulatory evolution in humans

    Science.gov (United States)

    Rockman, Matthew V.; Wray, Gregory A.

    2002-01-01

    Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (human phenotypic variation.

  19. (R)evolution of complex regulatory systems

    DEFF Research Database (Denmark)

    Linding, Rune

    2010-01-01

    Signaling systems are exciting to study precisely because they are some of the most complex and dynamical systems that we know. The cell needs operational freedom and, thus, many motif-domain interactions might not be "hard-wired" through evolution, but instead may be like the Linux operating...

  20. The role of cis regulatory evolution in maize domestication.

    Science.gov (United States)

    Lemmon, Zachary H; Bukowski, Robert; Sun, Qi; Doebley, John F

    2014-11-01

    Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes) show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues.

  1. The Role of cis Regulatory Evolution in Maize Domestication

    Science.gov (United States)

    Lemmon, Zachary H.; Bukowski, Robert; Sun, Qi; Doebley, John F.

    2014-01-01

    Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes) show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues. PMID:25375861

  2. The role of cis regulatory evolution in maize domestication.

    Directory of Open Access Journals (Sweden)

    Zachary H Lemmon

    2014-11-01

    Full Text Available Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem. Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues.

  3. The role of cis regulatory evolution in maize domestication.

    Directory of Open Access Journals (Sweden)

    Zachary H Lemmon

    2014-11-01

    Full Text Available Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem. Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues.

  4. Stepwise Functional Evolution in a Fungal Sugar Transporter Family.

    Science.gov (United States)

    Gonçalves, Carla; Coelho, Marco A; Salema-Oom, Madalena; Gonçalves, Paula

    2016-02-01

    Sugar transport is of the utmost importance for most cells and is central to a wide range of applied fields. However, despite the straightforward in silico assignment of many novel transporters, including sugar porters, to existing families, their exact biological role and evolutionary trajectory often remain unclear, mainly because biochemical characterization of membrane proteins is inherently challenging, but also owing to their uncommonly turbulent evolutionary histories. In addition, many important shifts in membrane carrier function are apparently ancient, which further limits our ability to reconstruct evolutionary trajectories in a reliable manner. Here, we circumvented some of these obstacles by examining the relatively recent emergence of a unique family of fungal sugar facilitators, related to drug antiporters. The former transporters, named Ffz, were previously shown to be required for fructophilic metabolism in yeasts. We first exploited the wealth of fungal genomic data available to define a comprehensive but well-delimited family of Ffz-like transporters, showing that they are only present in Dikarya. Subsequently, a combination of phylogenetic analyses and in vivo functional characterization was used to retrace important changes in function, while highlighting the evolutionary events that are most likely to have determined extant distribution of the gene, such as horizontal gene transfers (HGTs). One such HGT event is proposed to have set the stage for the onset of fructophilic metabolism in yeasts, a trait that according to our results may be the metabolic hallmark of close to 100 yeast species that thrive in sugar rich environments.

  5. Evolution of fungal population and mycotoxins in sorghum silage.

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    Del Palacio, Agustina; Mionetto, Ana; Bettucci, Lina; Pan, Dinorah

    2016-12-01

    Silage, one of the most important feed sources for cattle, is vulnerable to contamination by spoilage moulds and mycotoxins because ensilage materials are excellent substrates for fungal growth. The aim of this study was to identify the mycobiota of sorghum silages, to determine the presence of aflatoxins and fumonisins, and to correlate these results with physical parameters of the silage. A total of 275 samples of sorghum were collected from dairy farms in the south-west region of Uruguay were silage practices are developed. The presence of fungi was observed in all of the sorghum samples with values varying from 0.2 × 10(4) to 4085 × 10(4) UFC g(-1). Significant difference were detected in the total number of fungi during the storage period; at six months there is a high risk of fungal spoilage. The most frequent genera isolated from sorghum samples were Penicillium (70%), Aspergillus (65%), Absidia (40%), Fusarium (35%), Paecilomyces (35%) and Alternaria, Cladosporium, Gliocadium and Mucor (30%). The toxigenic species most frequently found were Penicillium citrinum, Aspergillus flavus and Fusarium nygamai. Only two samples were contaminated by AFB1 with levels of 1 and 14 µg kg(-1). Fumonisin was detected in 40% of freshly harvest samples with levels ranged from 533 µg kg(-1) to 933 µg kg(-1). The use of silo bags seems to be an effective tool to store sorghum. However, the presence of toxigenic fungi show that regular screening for mycotoxins levels in silages must be performed to avoid the exposure of animals to contaminated feed and the introduction of these compounds into the food chain.

  6. Recruitment of a hedgehog regulatory circuit in butterfly eyespot evolution.

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    Keys, D N; Lewis, D L; Selegue, J E; Pearson, B J; Goodrich, L V; Johnson, R L; Gates, J; Scott, M P; Carroll, S B

    1999-01-22

    The origin of new morphological characters is a long-standing problem in evolutionary biology. Novelties arise through changes in development, but the nature of these changes is largely unknown. In butterflies, eyespots have evolved as new pattern elements that develop from special organizers called foci. Formation of these foci is associated with novel expression patterns of the Hedgehog signaling protein, its receptor Patched, the transcription factor Cubitus interruptus, and the engrailed target gene that break the conserved compartmental restrictions on this regulatory circuit in insect wings. Redeployment of preexisting regulatory circuits may be a general mechanism underlying the evolution of novelties.

  7. General trends in the evolution of prokaryotic transcriptional regulatory networks.

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    Madan Babu, M; Balaji, S; Aravind, L

    2007-01-01

    Gene expression in organisms is controlled by regulatory proteins termed transcription factors, which recognize and bind to specific nucleotide sequences. Over the years, considerable information has accumulated on the regulatory interactions between transcription factors and their target genes in various model prokaryotes, such as Escherichia coli and Bacillus subtilis. This has allowed the representation of this information in the form of a directed graph, which is commonly referred to as the transcriptional regulatory network. The network representation provides us with an excellent conceptual framework to understand the structure of the transcriptional regulation, both at local and global levels of organization. Several studies suggest that the transcriptional network inferred from model organisms may be approximated by a scale-free topology, which in turn implies the presence of a relatively small group of highly connected regulators (hubs or global regulators). While the graph theoretical principles have been applied to infer various properties of such networks, there have been few studies that have actually investigated the evolution of the transcriptional regulatory networks across diverse organisms. Using recently developed computational methods that exploit various evolutionary principles, we have attempted to reconstruct and compare these networks across a wide-range of prokaryotes. This has provided several insights on the modification and diversification of network structures of various organisms in course of evolution. Firstly, we observed that target genes show a much higher level of conservation than their transcriptional regulators. This in turn suggested that the same set of functions could be differently controlled across diverse organisms, contributing significantly to their adaptive radiations. In particular, at the local level of network structure, organism-specific optimization of the transcription network has evolved primarily via tinkering

  8. Evolution of anterior Hox regulatory elements among chordates

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    Natale Alfonso

    2011-11-01

    Full Text Available Abstract Background The Hox family of transcription factors has a fundamental role in segmentation pathways and axial patterning of embryonic development and their clustered organization is linked with the regulatory mechanisms governing their coordinated expression along embryonic axes. Among chordates, of particular interest are the Hox paralogous genes in groups 1-4 since their expression is coupled to the control of regional identity in the anterior nervous system, where the highest structural diversity is observed. Results To investigate the degree of conservation in cis-regulatory components that form the basis of Hox expression in the anterior nervous system, we have used assays for transcriptional activity in ascidians and vertebrates to compare and contrast regulatory potential. We identified four regulatory sequences located near the CiHox1, CiHox2 and CiHox4 genes of the ascidian Ciona intestinalis which direct neural specific domains of expression. Using functional assays in Ciona and vertebrate embryos in combination with sequence analyses of enhancer fragments located in similar positions adjacent to Hox paralogy group genes, we compared the activity of these four Ciona cis-elements with a series of neural specific enhancers from the amphioxus Hox1-3 genes and from mouse Hox paralogous groups 1-4. Conclusions This analysis revealed that Kreisler and Krox20 dependent enhancers critical in segmental regulation of the hindbrain appear to be specific for the vertebrate lineage. In contrast, neural enhancers that function as Hox response elements through the action of Hox/Pbx binding motifs have been conserved during chordate evolution. The functional assays reveal that these Hox response cis-elements are recognized by the regulatory components of different and extant species. Together, our results indicate that during chordate evolution, cis-elements dependent upon Hox/Pbx regulatory complexes, are responsible for key aspects of

  9. Parallel evolution of chordate cis-regulatory code for development.

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    Laura Doglio

    2013-11-01

    Full Text Available Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs, yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations.

  10. Evolution of communication protocols using an artificial regulatory network.

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    Mitchener, W Garrett

    2014-01-01

    I describe the Utrecht Machine (UM), a discrete artificial regulatory network designed for studying how evolution discovers biochemical computation mechanisms. The corresponding binary genome format is compatible with gene deletion, duplication, and recombination. In the simulation presented here, an agent consisting of two UMs, a sender and a receiver, must encode, transmit, and decode a binary word over time using the narrow communication channel between them. This communication problem has chicken-and-egg structure in that a sending mechanism is useless without a corresponding receiving mechanism. An in-depth case study reveals that a coincidence creates a minimal partial solution, from which a sequence of partial sending and receiving mechanisms evolve. Gene duplications contribute by enlarging the regulatory network. Analysis of 60,000 sample runs under a variety of parameter settings confirms that crossover accelerates evolution, that stronger selection tends to find clumsier solutions and finds them more slowly, and that there is implicit selection for robust mechanisms and genomes at the codon level. Typical solutions associate each input bit with an activation speed and combine them almost additively. The parents of breakthrough organisms sometimes have lower fitness scores than others in the population, indicating that populations can cross valleys in the fitness landscape via outlying members. The simulation exhibits back mutations and population-level memory effects not accounted for in traditional population genetics models. All together, these phenomena suggest that new evolutionary models are needed that incorporate regulatory network structure.

  11. The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

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    Stefanie Traeger

    Full Text Available Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and ~13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721 was used to complement the S. macrospora

  12. Comparative Evolution of Morphological Regulatory Functions in Candida Species

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    Lackey, Erika; Vipulanandan, Geethanjali; Childers, Delma S.

    2013-01-01

    Morphological transitions play an important role in virulence and virulence-related processes in a wide variety of pathogenic fungi, including the most commonly isolated human fungal pathogen Candida albicans. While environmental signals, transcriptional regulators, and target genes associated with C. albicans morphogenesis are well-characterized, considerably little is known about morphological regulatory mechanisms and the extent to which they are evolutionarily conserved in less pathogenic and less filamentous non-albicans Candida species (NACS). We have identified specific optimal filament-inducing conditions for three NACS (C. tropicalis, C. parapsilosis, and C. guilliermondii), which are very limited, suggesting that these species may be adapted for niche-specific filamentation in the host. Only a subset of evolutionarily conserved C. albicans filament-specific target genes were induced upon filamentation in C. tropicalis, C. parapsilosis, and C. guilliermondii. One of the genes showing conserved expression was UME6, a key filament-specific regulator of C. albicans hyphal development. Constitutive high-level expression of UME6 was sufficient to drive increased filamentation as well as biofilm formation and partly restore conserved filament-specific gene expression in both C. tropicalis and C. parapsilosis, suggesting that evolutionary differences in filamentation ability among pathogenic Candida species may be partially attributed to alterations in the expression level of a conserved filamentous growth machinery. In contrast to UME6, NRG1, an important repressor of C. albicans filamentation, showed only a partly conserved role in controlling NACS filamentation. Overall, our results suggest that C. albicans morphological regulatory functions are partially conserved in NACS and have evolved to respond to more specific sets of host environmental cues. PMID:23913541

  13. Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms.

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    Fraser, James A; Diezmann, Stephanie; Subaran, Ryan L; Allen, Andria; Lengeler, Klaus B; Dietrich, Fred S; Heitman, Joseph

    2004-12-01

    Sexual identity is governed by sex chromosomes in plants and animals, and by mating type (MAT) loci in fungi. Comparative analysis of the MAT locus from a species cluster of the human fungal pathogen Cryptococcus revealed sequential evolutionary events that fashioned this large, highly unusual region. We hypothesize that MAT evolved via four main steps, beginning with acquisition of genes into two unlinked sex-determining regions, forming independent gene clusters that then fused via chromosomal translocation. A transitional tripolar intermediate state then converted to a bipolar system via gene conversion or recombination between the linked and unlinked sex-determining regions. MAT was subsequently subjected to intra- and interallelic gene conversion and inversions that suppress recombination. These events resemble those that shaped mammalian sex chromosomes, illustrating convergent evolution in sex-determining structures in the animal and fungal kingdoms.

  14. Phase transitions in the evolution of gene regulatory networks

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    Skanata, Antun; Kussell, Edo

    The role of gene regulatory networks is to respond to environmental conditions and optimize growth of the cell. A typical example is found in bacteria, where metabolic genes are activated in response to nutrient availability, and are subsequently turned off to conserve energy when their specific substrates are depleted. However, in fluctuating environmental conditions, regulatory networks could experience strong evolutionary pressures not only to turn the right genes on and off, but also to respond optimally under a wide spectrum of fluctuation timescales. The outcome of evolution is predicted by the long-term growth rate, which differentiates between optimal strategies. Here we present an analytic computation of the long-term growth rate in randomly fluctuating environments, by using mean-field and higher order expansion in the environmental history. We find that optimal strategies correspond to distinct regions in the phase space of fluctuations, separated by first and second order phase transitions. The statistics of environmental randomness are shown to dictate the possible evolutionary modes, which either change the structure of the regulatory network abruptly, or gradually modify and tune the interactions between its components.

  15. Changes in Cis-regulatory Elements during Morphological Evolution

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    Yu-Lee Paul

    2012-10-01

    Full Text Available How have animals evolved new body designs (morphological evolution? This requires explanations both for simple morphological changes, such as differences in pigmentation and hair patterns between different Drosophila populations and species, and also for more complex changes, such as differences in the forelimbs of mice and bats, and the necks of amphibians and reptiles. The genetic changes and pathways involved in these evolutionary steps require identification. Many, though not all, of these events occur by changes in cis-regulatory (enhancer elements within developmental genes. Enhancers are modular, each affecting expression in only one or a few tissues. Therefore it is possible to add, remove or alter an enhancer without producing changes in multiple tissues, and thereby avoid widespread (pleiotropic deleterious effects. Ideally, for a given step in morphological evolution it is necessary to identify (i the change in phenotype, (ii the changes in gene expression, (iii the DNA region, enhancer or otherwise, affected, (iv the mutation involved, (v the nature of the transcription or other factors that bind to this site. In practice these data are incomplete for most of the published studies upon morphological evolution. Here, the investigations are categorized according to how far these analyses have proceeded.

  16. Vertical evolution and intragenic spread of lichen-fungal group I introns.

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    Bhattacharya, Debashish; Friedl, Thomas; Helms, Gert

    2002-07-01

    One family within the Euascomycetes (Ascomycota), the lichen-forming Physciaceae, is particularly rich in nuclear ribosomal [r]DNA group I introns. We used phylogenetic analyses of group I introns and lichen-fungal host cells to address four questions about group I intron evolution in lichens, and generally in all eukaryotes: 1) Is intron spread in the lichens associated with the intimate association of the fungal and photosynthetic cells that make up the lichen thallus? 2) Are the multiple group I introns in the lichen-fungi of independent origins, or have existing introns spread into novel sites in the rDNA? 3) If introns have moved to novel sites, then does the exon context of these sites provide insights into the mechanism of intron spread? and 4) What is the pattern of intron loss in the small subunit rDNA gene of lichen-fungi? Our analyses show that group I introns in the lichen-fungi and in the lichen-algae (and lichenized cyanobacteria) do not share a close evolutionary relationship, suggesting that these introns do not move between the symbionts. Many group I introns appear to have originated in the common ancestor of the Lecanorales, whereas others have spread within this lineage (particularly in the Physciaceae) putatively through reverse-splicing into novel rRNA sites. We suggest that the evolutionary history of most lichen-fungal group I introns is characterized by rare gains followed by extensive losses in descendants, resulting in a sporadic intron distribution. Detailed phylogenetic analyses of the introns and host cells are required, therefore, to distinguish this scenario from the alternative hypothesis of widespread and independent intron gains in the different lichen-fungal lineages.

  17. Regulatory Divergence among Beta-Keratin Genes during Bird Evolution.

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    Bhattacharjee, Maloyjo Joyraj; Yu, Chun-Ping; Lin, Jinn-Jy; Ng, Chen Siang; Wang, Tzi-Yuan; Lin, Hsin-Hung; Li, Wen-Hsiung

    2016-11-01

    Feathers, which are mainly composed of α- and β-keratins, are highly diversified, largely owing to duplication and diversification of β-keratin genes during bird evolution. However, little is known about the regulatory changes that contributed to the expressional diversification of β-keratin genes. To address this issue, we studied transcriptomes from five different parts of chicken contour and flight feathers. From these transcriptomes we inferred β-keratin enriched co-expression modules of genes and predicted transcription factors (TFs) of β-keratin genes. In total, we predicted 262 TF-target gene relationships in which 56 TFs regulate 91 β-keratin genes; we validated 14 of them by in vitro tests. A dual criterion of TF enrichment and "TF-target gene" expression correlation identified 26 TFs as the major regulators of β-keratin genes. According to our predictions, the ancestral scale and claw β-keratin genes have common and unique regulators, whereas most feather β-keratin genes show chromosome-wise regulation, distinct from scale and claw β-keratin genes. Thus, after expansion from the β-keratin gene on Chr7 to other chromosomes, which still shares a TF with scale and claw β-keratin genes, most feather β-keratin genes have recruited distinct or chromosome-specific regulators. Moreover, our data showed correlated gene expression profiles, positive or negative, between predicted TFs and their target genes over the five studied feather regions. Therefore, regulatory divergences among feather β-keratin genes have contributed to structural differences among different parts of feathers. Our study sheds light on how feather β-keratin genes have diverged in regulation from scale and claw β-keratin genes and among themselves. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Evolution of the CNS myelin gene regulatory program.

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    Li, Huiliang; Richardson, William D

    2016-06-15

    Myelin is a specialized subcellular structure that evolved uniquely in vertebrates. A myelinated axon conducts action potentials many times faster than an unmyelinated axon of the same diameter; for the same conduction speed, the unmyelinated axon would need a much larger diameter and volume than its myelinated counterpart. Hence myelin speeds information transfer and saves space, allowing the evolution of a powerful yet portable brain. Myelination in the central nervous system (CNS) is controlled by a gene regulatory program that features a number of master transcriptional regulators including Olig1, Olig2 and Myrf. Olig family genes evolved from a single ancestral gene in non-chordates. Olig2, which executes multiple functions with regard to oligodendrocyte identity and development in vertebrates, might have evolved functional versatility through post-translational modification, especially phosphorylation, as illustrated by its evolutionarily conserved serine/threonine phospho-acceptor sites and its accumulation of serine residues during more recent stages of vertebrate evolution. Olig1, derived from a duplicated copy of Olig2 in early bony fish, is involved in oligodendrocyte development and is critical to remyelination in bony vertebrates, but is lost in birds. The origin of Myrf orthologs might be the result of DNA integration between an invading phage or bacterium and an early protist, producing a fusion protein capable of self-cleavage and DNA binding. Myrf seems to have adopted new functions in early vertebrates - initiation of the CNS myelination program as well as the maintenance of mature oligodendrocyte identity and myelin structure - by developing new ways to interact with DNA motifs specific to myelin genes. This article is part of a Special Issue entitled SI: Myelin Evolution.

  19. Pleiotropy constrains the evolution of protein but not regulatory sequences in a transcription regulatory network influencing complex social behaviours

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    Daria eMolodtsova

    2014-12-01

    Full Text Available It is increasingly apparent that genes and networks that influence complex behaviour are evolutionary conserved, which is paradoxical considering that behaviour is labile over evolutionary timescales. How does adaptive change in behaviour arise if behaviour is controlled by conserved, pleiotropic, and likely evolutionary constrained genes? Pleiotropy and connectedness are known to constrain the general rate of protein evolution, prompting some to suggest that the evolution of complex traits, including behaviour, is fuelled by regulatory sequence evolution. However, we seldom have data on the strength of selection on mutations in coding and regulatory sequences, and this hinders our ability to study how pleiotropy influences coding and regulatory sequence evolution. Here we use population genomics to estimate the strength of selection on coding and regulatory mutations for a transcriptional regulatory network that influences complex behaviour of honey bees. We found that replacement mutations in highly connected transcription factors and target genes experience significantly stronger negative selection relative to weakly connected transcription factors and targets. Adaptively evolving proteins were significantly more likely to reside at the periphery of the regulatory network, while proteins with signs of negative selection were near the core of the network. Interestingly, connectedness and network structure had minimal influence on the strength of selection on putative regulatory sequences for both transcription factors and their targets. Our study indicates that adaptive evolution of complex behaviour can arise because of positive selection on protein-coding mutations in peripheral genes, and on regulatory sequence mutations in both transcription factors and their targets throughout the network.

  20. The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat

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    Clémence Plissonneau

    2016-10-01

    Full Text Available Fungal plant pathogens rapidly evolve virulence on resistant hosts through mutations in genes encoding proteins that modulate the host immune responses. The mutational spectrum likely includes chromosomal rearrangements responsible for gains or losses of entire genes. However, the mechanisms creating adaptive structural variation in fungal pathogen populations are poorly understood. We used complete genome assemblies to quantify structural variants segregating in the highly polymorphic fungal wheat pathogen Zymoseptoria tritici. The genetic basis of virulence in Z. tritici is complex, and populations harbor significant genetic variation for virulence; hence, we aimed to identify whether structural variation led to functional differences. We combined single-molecule real-time sequencing, genetic maps, and transcriptomics data to generate a fully assembled and annotated genome of the highly virulent field isolate 3D7. Comparative genomics analyses against the complete reference genome IPO323 identified large chromosomal inversions and the complete gain or loss of transposable-element clusters, explaining the extensive chromosomal-length polymorphisms found in this species. Both the 3D7 and IPO323 genomes harbored long tracts of sequences exclusive to one of the two genomes. These orphan regions contained 296 genes unique to the 3D7 genome and not previously known for this species. These orphan genes tended to be organized in clusters and showed evidence of mutational decay. Moreover, the orphan genes were enriched in genes encoding putative effectors and included a gene that is one of the most upregulated putative effector genes during wheat infection. Our study showed that this pathogen species harbored extensive chromosomal structure polymorphism that may drive the evolution of virulence.

  1. The Evolution of the Secreted Regulatory Protein Progranulin.

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    Roger G E Palfree

    Full Text Available Progranulin is a secreted growth factor that is active in tumorigenesis, wound repair, and inflammation. Haploinsufficiency of the human progranulin gene, GRN, causes frontotemporal dementia. Progranulins are composed of chains of cysteine-rich granulin modules. Modules may be released from progranulin by proteolysis as 6kDa granulin polypeptides. Both intact progranulin and some of the granulin polypeptides are biologically active. The granulin module occurs in certain plant proteases and progranulins are present in early diverging metazoan clades such as the sponges, indicating their ancient evolutionary origin. There is only one Grn gene in mammalian genomes. More gene-rich Grn families occur in teleost fish with between 3 and 6 members per species including short-form Grns that have no tetrapod counterparts. Our goals are to elucidate progranulin and granulin module evolution by investigating (i: the origins of metazoan progranulins (ii: the evolutionary relationships between the single Grn of tetrapods and the multiple Grn genes of fish (iii: the evolution of granulin module architectures of vertebrate progranulins (iv: the conservation of mammalian granulin polypeptide sequences and how the conserved granulin amino acid sequences map to the known three dimensional structures of granulin modules. We report that progranulin-like proteins are present in unicellular eukaryotes that are closely related to metazoa suggesting that progranulin is among the earliest extracellular regulatory proteins still employed by multicellular animals. From the genomes of the elephant shark and coelacanth we identified contemporary representatives of a precursor for short-from Grn genes of ray-finned fish that is lost in tetrapods. In vertebrate Grns pathways of exon duplication resulted in a conserved module architecture at the amino-terminus that is frequently accompanied by an unusual pattern of tandem nearly identical module repeats near the carboxyl

  2. New fungal defensin-like peptides provide evidence for fold change of proteins in evolution

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    Wu, Yucheng; Gao, Bin

    2016-01-01

    Defensins containing a consensus cystine framework, Cys[1]…Cys[2]X3Cys[3]…Cys[4]… Cys[5]X1Cys[6] (X, any amino acid except Cys; …, variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming the cysteine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys[2]X3Cys[3]/Cys[5]X1Cys[6], are key determinants of fold formation. By using a computational genomics approach, we identified a large superfamily of fungal defensin-like peptides (fDLPs) in the phytopathogenic fungal genus – Zymoseptoria, which includes 132 structurally typical and 63 atypical members. These atypical fDLPs exhibit an altered cystine framework and accompanying fold change associated with their secondary structure elements and disulfide bridge patterns, as identified by protein structure modelling. Despite this, they definitely are homologous with the typical fDLPs in view of their precise gene structure conservation and identical precursor organization. Sequence and structural analyses combined with functional data suggest that most of Zymoseptoria fDLPs might have lost their antimicrobial activity. The present study provides a clear example of fold change in the evolution of proteins and is valuable in establishing remote homology among peptide superfamily members with different folds. PMID:27913751

  3. Evolution of Fungal U3 snoRNAs: Structural Variation and Introns

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    Sebastian Canzler

    2017-01-01

    Full Text Available The U3 small nucleolar RNA (snoRNA is an essential player in the initial steps of ribosomal RNA biogenesis which is ubiquitously present in Eukarya. It is exceptional among the small nucleolar RNAs in its size, the presence of multiple conserved sequence boxes, a highly conserved secondary structure core, its biogenesis as an independent gene transcribed by polymerase III, and its involvement in pre-rRNA cleavage rather than chemical modification. Fungal U3 snoRNAs share many features with their sisters from other eukaryotic kingdoms but differ from them in particular in their 5’ regions, which in fungi has a distinctive consensus structure and often harbours introns. Here we report on a comprehensive homology search and detailed analysis of the evolution of sequence and secondary structure features covering the entire kingdom Fungi.

  4. Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework.

    Science.gov (United States)

    Maeso, Ignacio; Tena, Juan J

    2016-09-01

    Cis-regulatory changes are arguably the primary evolutionary source of animal morphological diversity. With the recent explosion of genome-wide comparisons of the cis-regulatory content in different animal species is now possible to infer general principles underlying enhancer evolution. However, these studies have also revealed numerous discrepancies and paradoxes, suggesting that the mechanistic causes and modes of cis-regulatory evolution are still not well understood and are probably much more complex than generally appreciated. Here, we argue that the mutational mechanisms and genomic regions generating new regulatory activities must comply with the constraints imposed by the molecular properties of cis-regulatory elements (CREs) and the organizational features of long-range chromatin interactions. Accordingly, we propose a new integrative evolutionary framework for cis-regulatory evolution based on two major premises for the origin of novel enhancer activity: (i) an accessible chromatin environment and (ii) compatibility with the 3D structure and interactions of pre-existing CREs. Mechanisms and DNA sequences not fulfilling these premises, will be less likely to have a measurable impact on gene expression and as such, will have a minor contribution to the evolution of gene regulation. Finally, we discuss current comparative cis-regulatory data under the light of this new evolutionary model, and propose that the two most prominent mechanisms for the evolution of cis-regulatory changes are the overprinting of ancestral CREs and the exaptation of transposable elements.

  5. How do fungal partners affect the evolution and habitat preferences of mycoheterotrophic plants? A case study in Gastrodia.

    Science.gov (United States)

    Kinoshita, Akihiko; Ogura-Tsujita, Yuki; Umata, Hidetaka; Sato, Hiroki; Hashimoto, Toshimasa; Yukawa, Tomohisa

    2016-02-01

    Since mycoheterotrophic plants (MHPs) completely depend on their mycorrhizal fungi for carbon, selection of fungal partners has an important role in the speciation of MHPs. However, the causes and mechanisms of mycobiont changes during speciation are not clear. We tested fungal partner shifts and changes in mycorrhizal specificity during speciation of three closely related MHPs-Gastrodia confusa (Gc), G. pubilabiata (Gp), and G. nipponica (Gn) (Orchidaceae)-and correlations between these changes and the vegetation types where each species grows. We investigated the diversity of mycobionts of the three species by sequencing nrDNA ITS, and the sequence data were subjected to test changes in fungal specificity and fungal partner shifts among the three species. Furthermore, we conducted multivariate analysis to test for differences in mycobiont communities of vegetation types where each species grows. Two saprobic Basidiomycota, Marasmiaceae and Mycenaceae, were dominant fungal partners of the three species, and Gn was simultaneously associated with the ectomycorrhizal Russulaceae and Sebacinaceae. Although mycobiont composition differed among the three species, they also sometimes shared identical fungal species. Multivariate analysis revealed that mycobiont communities of the three species in bamboo thickets differed significantly from those in other vegetation types. Fungal partner shifts are not necessarily associated with the evolution of MHPs, and fungal specificity of Gc and Gp was significantly higher than that of Gn, implying that the specificity fluctuates during speciation. Further, Gc exclusively inhabits bamboo thickets, which suggests that adaptation to particular fungi specific to bamboo thickets triggered speciation of this species. © 2016 Botanical Society of America.

  6. Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts

    NARCIS (Netherlands)

    Nagy, L.G.; Ohm, R.A.; Kovács, G.M.; Floudas, D.; Riley, R.; Gácser, A.; Sipiczki, M.; Davis, J.M.; Doty, S.L.; de Hoog, G.S.; Lang, B.F.; Spatafora, J.W.; Martin, F.M.; Grigoriev, I.V.; Hibbett, D.S.

    2014-01-01

    Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the

  7. Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts

    NARCIS (Netherlands)

    Nagy, László G; Ohm, Robin A; Kovács, Gábor M; Floudas, Dimitrios; Riley, Robert; Gácser, Attila; Sipiczki, Mátyás; Davis, John M; Doty, Sharon L; de Hoog, G Sybren; Lang, B Franz; Spatafora, Joseph W; Martin, Francis M; Grigoriev, Igor V; Hibbett, David S

    Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the

  8. Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution

    Science.gov (United States)

    Plissonneau, Clémence; Benevenuto, Juliana; Mohd-Assaad, Norfarhan; Fouché, Simone; Hartmann, Fanny E.; Croll, Daniel

    2017-01-01

    Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution. PMID:28217138

  9. Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

    NARCIS (Netherlands)

    Vermunt, Marit W; Tan, Sander C; Castelijns, Bas; Geeven, Geert; Reinink, Peter; de Bruijn, Ewart; Kondova, Ivanela; Persengiev, Stephan; Bontrop, Ronald; Cuppen, Edwin; de Laat, Wouter; Creyghton, Menno P

    Although genome sequencing has identified numerous noncoding alterations between primate species, which of those are regulatory and potentially relevant to the evolution of the human brain is unclear. Here we annotated cis-regulatory elements (CREs) in the human, rhesus macaque and chimpanzee

  10. Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

    NARCIS (Netherlands)

    Vermunt, Marit W.; Tan, Sander C.; Castelijns, Bas; Geeven, Geert; Reinink, Peter; de Bruijn, Ewart; Kondova, Ivanela; Persengiev, Stephan; Bontrop, Ronald; Cuppen, Edwin|info:eu-repo/dai/nl/183050487; de laat, Wouter|info:eu-repo/dai/nl/169934497; Creyghton, Menno P.

    2016-01-01

    Although genome sequencing has identified numerous noncoding alterations between primate species, which of those are regulatory and potentially relevant to the evolution of the human brain is unclear. Here we annotated cis-regulatory elements (CREs) in the human, rhesus macaque and chimpanzee genome

  11. Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.

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    Marco Galardini

    2015-09-01

    Full Text Available Reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. Recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. The evolution of such networks within and outside the species boundary is however still obscure. Sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a significant knowledge of its transcription factors (TF. Each replicon has a specific functional and evolutionary mark; which might also emerge from the analysis of their regulatory signatures. Here we have studied the plasticity of the regulatory network within and outside the S. meliloti species, looking for the presence of 41 TFs binding motifs in 51 strains and 5 related rhizobial species. We have detected a preference of several TFs for one of the three replicons, and the function of regulated genes was found to be in accordance with the overall replicon functional signature: house-keeping functions for the chromosome, metabolism for the chromid, symbiosis for the megaplasmid. This therefore suggests a replicon-specific wiring of the regulatory network in the S. meliloti species. At the same time a significant part of the predicted regulatory network is shared between the chromosome and the chromid, thus adding an additional layer by which the chromid integrates itself in the core genome. Furthermore, the regulatory network distance was found to be correlated with both promoter regions and accessory genome evolution inside the species, indicating that both pangenome compartments are involved in the regulatory network evolution. We also observed that genes which are not included in the species regulatory network are more likely to belong to the accessory genome, indicating that regulatory interactions should also be considered to predict gene conservation in

  12. Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.

    Science.gov (United States)

    Galardini, Marco; Brilli, Matteo; Spini, Giulia; Rossi, Matteo; Roncaglia, Bianca; Bani, Alessia; Chiancianesi, Manuela; Moretto, Marco; Engelen, Kristof; Bacci, Giovanni; Pini, Francesco; Biondi, Emanuele G; Bazzicalupo, Marco; Mengoni, Alessio

    2015-09-01

    Reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. Recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. The evolution of such networks within and outside the species boundary is however still obscure. Sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a significant knowledge of its transcription factors (TF). Each replicon has a specific functional and evolutionary mark; which might also emerge from the analysis of their regulatory signatures. Here we have studied the plasticity of the regulatory network within and outside the S. meliloti species, looking for the presence of 41 TFs binding motifs in 51 strains and 5 related rhizobial species. We have detected a preference of several TFs for one of the three replicons, and the function of regulated genes was found to be in accordance with the overall replicon functional signature: house-keeping functions for the chromosome, metabolism for the chromid, symbiosis for the megaplasmid. This therefore suggests a replicon-specific wiring of the regulatory network in the S. meliloti species. At the same time a significant part of the predicted regulatory network is shared between the chromosome and the chromid, thus adding an additional layer by which the chromid integrates itself in the core genome. Furthermore, the regulatory network distance was found to be correlated with both promoter regions and accessory genome evolution inside the species, indicating that both pangenome compartments are involved in the regulatory network evolution. We also observed that genes which are not included in the species regulatory network are more likely to belong to the accessory genome, indicating that regulatory interactions should also be considered to predict gene conservation in bacterial

  13. Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome.

    Science.gov (United States)

    Dong, Xinran; Wang, Xiao; Zhang, Feng; Tian, Weidong

    2016-10-01

    Accelerated evolution of regulatory sequence can alter the expression pattern of target genes, and cause phenotypic changes. In this study, we used DNase I hypersensitive sites (DHSs) to annotate putative regulatory sequences in the human genome, and conducted a genome-wide analysis of the effects of accelerated evolution on regulatory sequences. Working under the assumption that local ancient repeat elements of DHSs are under neutral evolution, we discovered that ∼0.44% of DHSs are under accelerated evolution (ace-DHSs). We found that ace-DHSs tend to be more active than background DHSs, and are strongly associated with epigenetic marks of active transcription. The target genes of ace-DHSs are significantly enriched in neuron-related functions, and their expression levels are positively selected in the human brain. Thus, these lines of evidences strongly suggest that accelerated evolution on regulatory sequences plays important role in the evolution of human-specific phenotypes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  14. ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera.

    Science.gov (United States)

    Lewis, James J; van der Burg, Karin R L; Mazo-Vargas, Anyi; Reed, Robert D

    2016-09-13

    Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq) annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution.

  15. [Role of genes and their cis-regulatory elements during animal morphological evolution].

    Science.gov (United States)

    Sun, Boyuan; Tu, Jianbo; Li, Ying; Yang, Mingyao

    2014-06-01

    Cis-regulatory hypothesis is one of the most important theories in evolutionary developmental biology (evo-devo), which claims that evolution of cis-regulatory elements (CREs) plays a key role during evolution of morphology. However, an increasing number of experimental results show that cis-regulatory hypothesis alone is not far enough to explain the complexity of evo-devo processes. Other modifications, including mutations of protein coding, gene and genome duplications, and flexibility of homeodomains and CREs, also cause the morphological changes in animals. In this review, we retrospect the recent results of evolution of CREs and genes associated with CREs and discuss new methods and trends for research in evo-devo.

  16. Rapid evolution of cis-regulatory sequences via local point mutations

    Science.gov (United States)

    Stone, J. R.; Wray, G. A.

    2001-01-01

    Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.

  17. Extended evolution: A conceptual framework for integrating regulatory networks and niche construction.

    Science.gov (United States)

    Laubichler, Manfred D; Renn, Jürgen

    2015-11-01

    This paper introduces a conceptual framework for the evolution of complex systems based on the integration of regulatory network and niche construction theories. It is designed to apply equally to cases of biological, social and cultural evolution. Within the conceptual framework we focus especially on the transformation of complex networks through the linked processes of externalization and internalization of causal factors between regulatory networks and their corresponding niches and argue that these are an important part of evolutionary explanations. This conceptual framework extends previous evolutionary models and focuses on several challenges, such as the path-dependent nature of evolutionary change, the dynamics of evolutionary innovation and the expansion of inheritance systems.

  18. Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria

    Directory of Open Access Journals (Sweden)

    Vasconcelos Ana

    2008-03-01

    Full Text Available Abstract Background In the past years, several studies begun to unravel the structure, dynamical properties, and evolution of transcriptional regulatory networks. However, even those comparative studies that focus on a group of closely related organisms are limited by the rather scarce knowledge on regulatory interactions outside a few model organisms, such as E. coli among the prokaryotes. Results In this paper we used the information annotated in Tractor_DB (a database of regulatory networks in gamma-proteobacteria to calculate a normalized Site Orthology Score (SOS that quantifies the conservation of a regulatory link across thirty genomes of this subclass. Then we used this SOS to assess how regulatory connections have evolved in this group, and how the variation of basic regulatory connection is reflected on the structure of the chromosome. We found that individual regulatory interactions shift between different organisms, a process that may be described as rewiring the network. At this evolutionary scale (the gamma-proteobacteria subclass this rewiring process may be an important source of variation of regulatory incoming interactions for individual networks. We also noticed that the regulatory links that form feed forward motifs are conserved in a better correlated manner than triads of random regulatory interactions or pairs of co-regulated genes. Furthermore, the rewiring process that takes place at the most basic level of the regulatory network may be linked to rearrangements of genetic material within bacterial chromosomes, which change the structure of Transcription Units and therefore the regulatory connections between Transcription Factors and structural genes. Conclusion The rearrangements that occur in bacterial chromosomes-mostly inversion or horizontal gene transfer events – are important sources of variation of gene regulation at this evolutionary scale.

  19. Evolution of the mammalian embryonic pluripotency gene regulatory network

    Science.gov (United States)

    Fernandez-Tresguerres, Beatriz; Cañon, Susana; Rayon, Teresa; Pernaute, Barbara; Crespo, Miguel; Torroja, Carlos; Manzanares, Miguel

    2010-01-01

    Embryonic pluripotency in the mouse is established and maintained by a gene-regulatory network under the control of a core set of transcription factors that include octamer-binding protein 4 (Oct4; official name POU domain, class 5, transcription factor 1, Pou5f1), sex-determining region Y (SRY)-box containing gene 2 (Sox2), and homeobox protein Nanog. Although this network is largely conserved in eutherian mammals, very little information is available regarding its evolutionary conservation in other vertebrates. We have compared the embryonic pluripotency networks in mouse and chick by means of expression analysis in the pregastrulation chicken embryo, genomic comparisons, and functional assays of pluripotency-related regulatory elements in ES cells and blastocysts. We find that multiple components of the network are either novel to mammals or have acquired novel expression domains in early developmental stages of the mouse. We also find that the downstream action of the mouse core pluripotency factors is mediated largely by genomic sequence elements nonconserved with chick. In the case of Sox2 and Fgf4, we find that elements driving expression in embryonic pluripotent cells have evolved by a small number of nucleotide changes that create novel binding sites for core factors. Our results show that the network in charge of embryonic pluripotency is an evolutionary novelty of mammals that is related to the comparatively extended period during which mammalian embryonic cells need to be maintained in an undetermined state before engaging in early differentiation events. PMID:21048080

  20. Deconvoluting lung evolution: from phenotypes to gene regulatory networks

    DEFF Research Database (Denmark)

    Torday, J.S.; Rehan, V.K.; Hicks, J.W.

    2007-01-01

    Speakers in this symposium presented examples of respiratory regulation that broadly illustrate principles of evolution from whole organ to genes. The swim bladder and lungs of aquatic and terrestrial organisms arose independently from a common primordial "respiratory pharynx" but not from each...... other. Pathways of lung evolution are similar between crocodiles and birds but a low compliance of mammalian lung may have driven the development of the diaphragm to permit lung inflation during inspiration. To meet the high oxygen demands of flight, bird lungs have evolved separate gas exchange...... diffusing capacities than required by their oxygen consumption. The "primitive" central admixture of oxygenated and deoxygenated blood in the incompletely divided reptilian heart is actually co-regulated with other autonomic cardiopulmonary responses to provide flexible control of arterial oxygen tension...

  1. Evolution of nuclear security regulatory activities in Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Mello, Luiz A. de; Monteiro Filho, Joselio S.; Belem, Lilia M.J.; Torres, Luiz F.B. [Comissao Nacional de Energia Nuclear (CNEN), Rio de Janeiro, RJ (Brazil). Diretoria de Radioprotecao e Segurania Nuclear. Coordenacao de Salvaguardas e Protecao Fisica], e-mail: gpf@cnen.gov.br

    2009-07-01

    The changing of the world scenario in the last 15 years has increased worldwide the concerns about overall security and, as a consequence, about the nuclear and radioactive material as well as their associated facilities. Considering the new situation, in February 2004, the Brazilian National Nuclear Energy Commission (CNEN), decided to create the Nuclear Security Office. This Office is under the Coordination of Nuclear Safeguards and Security, in the Directorate for Safety, Security and Safeguards (Regulatory Directorate). Before that, security regulation issues were dealt in a decentralized manner, within that Directorate, by different licensing groups in specific areas (power reactors, fuel cycle facilities, radioactive facilities, transport of nuclear material, etc.). This decision was made in order to allow a coordinated approach on the subject, to strengthen the regulation in nuclear/radioactive security, and to provide support to management in the definition of institutional security policies. The CNEN Security Office develops its work based in the CNEN Physical Protection Regulation for Nuclear Operational Units - NE-2.01, 1996, the Convention on the Physical Protection of Nuclear Material and the IAEA Nuclear Security Series . This paper aims at presenting the activities developed and the achievements obtained by this new CNEN office, as well as identifying the issues and directions for future efforts. (author)

  2. Experimental evolution of defense against a competitive mold confers reduced sensitivity to fungal toxins but no increased resistance in Drosophila larvae

    Directory of Open Access Journals (Sweden)

    Trienens Monika

    2011-07-01

    Full Text Available Abstract Background Fungal secondary metabolites have been suggested to function as chemical defenses against insect antagonists, i.e. predators and competitors. Because insects and fungi often compete for dead organic material, insects may achieve protection against fungi by reducing sensitivity to fungal chemicals. This, in turn, may lead to increased resistance allowing insects better to suppress the spread of antagonistic but non-pathogenic microbes in their habitat. However, it remains controversial whether fungal toxins serve as a chemical shield that selects for insects that are less sensitive to toxins, and hence favors the evolution of insect resistance against microbial competitors. Results To examine the relationship between the ability to survive competition with toxic fungi, sensitivity to fungal toxins and resistance, we created fungal-selected (FS replicated insect lines by exposing Drosophila melanogaster larvae to the fungal competitor Aspergillus nidulans over 26 insect generations. Compared to unselected control lines (UC, larvae from the FS lines had higher survival rates in the presence of A. nidulans indicating selection for increased protection against the fungal antagonist. In line with our expectation, FS lines were less susceptible to the A. nidulans mycotoxin Sterigmatocystin. Of particular interest is that evolved protection against A. nidulans and Sterigmatocytin was not correlated with increased insect survival in the presence of other fungi and mycotoxins. We found no evidence that FS lines were better at suppressing the expansion of fungal colonies but observed a trend towards a less detrimental effect of FS larvae on fungal growth. Conclusion Antagonistic but non-pathogenic fungi favor insect variants better protected against the fungal chemical arsenal. This highlights the often proposed but experimentally underexplored importance of secondary metabolites in driving animal-fungus interactions. Instead of

  3. Evolution of regulatory networks towards adaptability and stability in a changing environment

    Science.gov (United States)

    Lee, Deok-Sun

    2014-11-01

    Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which evolve by selectively rewiring links towards enhancing adaptability to a changing environment and stability against dynamical perturbations. We find that sparse and heterogeneous connectivity patterns emerge, which show qualitative agreement with real transcriptional regulatory networks and metabolic networks. The characteristic scaling behavior of stability reflects the balance between robustness and flexibility. The scaling of fluctuation in the perturbation spread shows a dynamic crossover, which is analyzed by investigating separately the stochasticity of internal dynamics and the network structure differences depending on the evolution pathways. Our study delineates how the ambivalent pressure of evolution shapes biological networks, which can be helpful for studying general complex systems interacting with environments.

  4. PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.

    Directory of Open Access Journals (Sweden)

    Stéphane Mahé

    Full Text Available BACKGROUND: In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation. METHODS AND PRINCIPAL FINDINGS: To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ~20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples. CONCLUSION: PHYMYCO-DB offers the tools necessary to: (i extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii extract already performed alignments, to act as 'reference alignments', (iii launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/.

  5. PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution

    Science.gov (United States)

    Mahé, Stéphane; Duhamel, Marie; Le Calvez, Thomas; Guillot, Laetitia; Sarbu, Ludmila; Bretaudeau, Anthony; Collin, Olivier; Dufresne, Alexis; Kiers, E. Toby; Vandenkoornhuyse, Philippe

    2012-01-01

    Background In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation. Methods and Principal Findings To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ∼20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples. Conclusion PHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as ‘reference alignments’, (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/. PMID:23028445

  6. The evolution of lineage-specific regulatory activities in the human embryonic limb.

    Science.gov (United States)

    Cotney, Justin; Leng, Jing; Yin, Jun; Reilly, Steven K; DeMare, Laura E; Emera, Deena; Ayoub, Albert E; Rakic, Pasko; Noonan, James P

    2013-07-03

    The evolution of human anatomical features likely involved changes in gene regulation during development. However, the nature and extent of human-specific developmental regulatory functions remain unknown. We obtained a genome-wide view of cis-regulatory evolution in human embryonic tissues by comparing the histone modification H3K27ac, which provides a quantitative readout of promoter and enhancer activity, during human, rhesus, and mouse limb development. Based on increased H3K27ac, we find that 13% of promoters and 11% of enhancers have gained activity on the human lineage since the human-rhesus divergence. These gains largely arose by modification of ancestral regulatory activities in the limb or potential co-option from other tissues and are likely to have heterogeneous genetic causes. Most enhancers that exhibit gain of activity in humans originated in mammals. Gains at promoters and enhancers in the human limb are associated with increased gene expression, suggesting they include molecular drivers of human morphological evolution.

  7. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

    Science.gov (United States)

    He, Xin; Ling, Xu; Sinha, Saurabh

    2009-03-01

    Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs) and understanding their evolution. The comparison requires reliable sequence alignment, which remains a challenging task for less conserved noncoding sequences. Furthermore, the existing models of DNA sequence evolution generally do not explicitly treat the special properties of CRM sequences. To address these limitations, we propose a model of CRM evolution that captures different modes of evolution of functional transcription factor binding sites (TFBSs) and the background sequences. A particularly novel aspect of our work is a probabilistic model of gains and losses of TFBSs, a process being recognized as an important part of regulatory sequence evolution. We present a computational framework that uses this model to solve the problems of CRM alignment and prediction. Our alignment method is similar to existing methods of statistical alignment but uses the conserved binding sites to improve alignment. Our CRM prediction method deals with the inherent uncertainties of binding site annotations and sequence alignment in a probabilistic framework. In simulated as well as real data, we demonstrate that our program is able to improve both alignment and prediction of CRM sequences over several state-of-the-art methods. Finally, we used alignments produced by our program to study binding site conservation in genome-wide binding data of key transcription factors in the Drosophila blastoderm, with two intriguing results: (i) the factor-bound sequences are under strong evolutionary constraints even if their neighboring genes are not expressed in the blastoderm and (ii) binding sites in distal bound sequences (relative to transcription start sites) tend to be more conserved than those in proximal regions. Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis), ready to be applied in a broad biological context.

  8. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

    Directory of Open Access Journals (Sweden)

    Xin He

    2009-03-01

    Full Text Available Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs and understanding their evolution. The comparison requires reliable sequence alignment, which remains a challenging task for less conserved noncoding sequences. Furthermore, the existing models of DNA sequence evolution generally do not explicitly treat the special properties of CRM sequences. To address these limitations, we propose a model of CRM evolution that captures different modes of evolution of functional transcription factor binding sites (TFBSs and the background sequences. A particularly novel aspect of our work is a probabilistic model of gains and losses of TFBSs, a process being recognized as an important part of regulatory sequence evolution. We present a computational framework that uses this model to solve the problems of CRM alignment and prediction. Our alignment method is similar to existing methods of statistical alignment but uses the conserved binding sites to improve alignment. Our CRM prediction method deals with the inherent uncertainties of binding site annotations and sequence alignment in a probabilistic framework. In simulated as well as real data, we demonstrate that our program is able to improve both alignment and prediction of CRM sequences over several state-of-the-art methods. Finally, we used alignments produced by our program to study binding site conservation in genome-wide binding data of key transcription factors in the Drosophila blastoderm, with two intriguing results: (i the factor-bound sequences are under strong evolutionary constraints even if their neighboring genes are not expressed in the blastoderm and (ii binding sites in distal bound sequences (relative to transcription start sites tend to be more conserved than those in proximal regions. Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis, ready to be applied in a broad biological context.

  9. Breakage-fusion-bridge cycles and large insertions contribute to the rapid evolution of accessory chromosomes in a fungal pathogen.

    Directory of Open Access Journals (Sweden)

    Daniel Croll

    2013-06-01

    Full Text Available Chromosomal rearrangements are a major driver of eukaryotic genome evolution, affecting speciation, pathogenicity and cancer progression. Changes in chromosome structure are often initiated by mis-repair of double-strand breaks in the DNA. Mis-repair is particularly likely when telomeres are lost or when dispersed repeats misalign during crossing-over. Fungi carry highly polymorphic chromosomal complements showing substantial variation in chromosome length and number. The mechanisms driving chromosome polymorphism in fungi are poorly understood. We aimed to identify mechanisms of chromosomal rearrangements in the fungal wheat pathogen Zymoseptoria tritici. We combined population genomic resequencing and chromosomal segment PCR assays with electrophoretic karyotyping and resequencing of parents and offspring from experimental crosses to show that this pathogen harbors a highly diverse complement of accessory chromosomes that exhibits strong global geographic differentiation in numbers and lengths of chromosomes. Homologous chromosomes carried highly differentiated gene contents due to numerous insertions and deletions. The largest accessory chromosome recently doubled in length through insertions totaling 380 kb. Based on comparative genomics, we identified the precise breakpoint locations of these insertions. Nondisjunction during meiosis led to chromosome losses in progeny of three different crosses. We showed that a new accessory chromosome emerged in two viable offspring through a fusion between sister chromatids. Such chromosome fusion is likely to initiate a breakage-fusion-bridge (BFB cycle that can rapidly degenerate chromosomal structure. We suggest that the accessory chromosomes of Z. tritici originated mainly from ancient core chromosomes through a degeneration process that included BFB cycles, nondisjunction and mutational decay of duplicated sequences. The rapidly evolving accessory chromosome complement may serve as a cradle for

  10. Breakage-fusion-bridge cycles and large insertions contribute to the rapid evolution of accessory chromosomes in a fungal pathogen.

    Science.gov (United States)

    Croll, Daniel; Zala, Marcello; McDonald, Bruce A

    2013-06-01

    Chromosomal rearrangements are a major driver of eukaryotic genome evolution, affecting speciation, pathogenicity and cancer progression. Changes in chromosome structure are often initiated by mis-repair of double-strand breaks in the DNA. Mis-repair is particularly likely when telomeres are lost or when dispersed repeats misalign during crossing-over. Fungi carry highly polymorphic chromosomal complements showing substantial variation in chromosome length and number. The mechanisms driving chromosome polymorphism in fungi are poorly understood. We aimed to identify mechanisms of chromosomal rearrangements in the fungal wheat pathogen Zymoseptoria tritici. We combined population genomic resequencing and chromosomal segment PCR assays with electrophoretic karyotyping and resequencing of parents and offspring from experimental crosses to show that this pathogen harbors a highly diverse complement of accessory chromosomes that exhibits strong global geographic differentiation in numbers and lengths of chromosomes. Homologous chromosomes carried highly differentiated gene contents due to numerous insertions and deletions. The largest accessory chromosome recently doubled in length through insertions totaling 380 kb. Based on comparative genomics, we identified the precise breakpoint locations of these insertions. Nondisjunction during meiosis led to chromosome losses in progeny of three different crosses. We showed that a new accessory chromosome emerged in two viable offspring through a fusion between sister chromatids. Such chromosome fusion is likely to initiate a breakage-fusion-bridge (BFB) cycle that can rapidly degenerate chromosomal structure. We suggest that the accessory chromosomes of Z. tritici originated mainly from ancient core chromosomes through a degeneration process that included BFB cycles, nondisjunction and mutational decay of duplicated sequences. The rapidly evolving accessory chromosome complement may serve as a cradle for adaptive evolution in

  11. Developmental evolution in social insects: regulatory networks from genes to societies.

    Science.gov (United States)

    Linksvayer, Timothy A; Fewell, Jennifer H; Gadau, Jürgen; Laubichler, Manfred D

    2012-05-01

    The evolution and development of complex phenotypes in social insect colonies, such as queen-worker dimorphism or division of labor, can, in our opinion, only be fully understood within an expanded mechanistic framework of Developmental Evolution. Conversely, social insects offer a fertile research area in which fundamental questions of Developmental Evolution can be addressed empirically. We review the concept of gene regulatory networks (GRNs) that aims to fully describe the battery of interacting genomic modules that are differentially expressed during the development of individual organisms. We discuss how distinct types of network models have been used to study different levels of biological organization in social insects, from GRNs to social networks. We propose that these hierarchical networks spanning different organizational levels from genes to societies should be integrated and incorporated into full GRN models to elucidate the evolutionary and developmental mechanisms underlying social insect phenotypes. Finally, we discuss prospects and approaches to achieve such an integration.

  12. Investigating the Ustilago maydis/Zea mays pathosystem: transcriptional responses and novel functional aspects of a fungal calcineurin regulatory B subunit.

    Science.gov (United States)

    Donaldson, Michael E; Meng, Shaowu; Gagarinova, Alla; Babu, Mohan; Lambie, Scott C; Swiadek, Alexander A; Saville, Barry J

    2013-01-01

    The sustainable control of basidiomycete biotrophic plant pathogenesis requires an understanding of host responses to infection, as well as the identification and functional analysis of fungal genes involved in disease development. The creation and analysis of a suppressive subtractive hybridization (SSH) cDNA library from Ustilago maydis-infected Zea mays seedlings enabled the identification of fungal and plant genes expressed during disease development, and uncovered new insights into the interactions of this model system. Candidate U. maydis pathogenesis genes were identified by using the current SSH cDNA library analysis, and by knowledge generated from previous cDNA microarray and comparative genomic analyses. These identifications were supported by the independent determination of transcript level changes in different cell-types and during pathogenic development. The basidiomycete specific um01632, the highly in planta expressed um03046 (zig1), and the calcineurin regulatory B subunit (um10226, cnb1), were chosen for deletion experiments. um01632 and zig1 mutants showed no difference in morphology and did not have a statistically significant impact on pathogenesis. cnb1 mutants had a distinct cell division phenotype and reduced virulence in seedling assays. Infections with reciprocal wild-type×Δcnb1 haploid strain crosses revealed that the wild-type allele was unable to fully compensate for the lack of a second cnb1 allele. This haploinsufficiency was undetected in other fungal cnb1 mutational analyses. The reported data improves U. maydis genome annotation and expands on the current understanding of pathogenesis genes in this model basidiomycete.

  13. ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera

    Directory of Open Access Journals (Sweden)

    James J. Lewis

    2016-09-01

    Full Text Available Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution.

  14. Evolution of gene regulatory network architectures: examples of subcircuit conservation and plasticity between classes of echinoderms.

    Science.gov (United States)

    Hinman, Veronica F; Yankura, Kristen A; McCauley, Brenna S

    2009-04-01

    Developmental gene regulatory networks (GRNs) explain how regulatory states are established in particular cells during development and how these states then determine the final form of the embryo. Evolutionary changes to the sequence of the genome will direct reorganization of GRN architectures, which in turn will lead to the alteration of developmental programs. A comparison of GRN architectures must consequently reveal the molecular basis for the evolution of developmental programs among different organisms. This review highlights some of the important findings that have emerged from the most extensive direct comparison of GRN architectures to date. Comparison of the orthologous GRNs for endomesodermal specification in the sea urchin and sea star, provides examples of several discrete, functional GRN subcircuits and shows that they are subject to diverse selective pressures. This demonstrates that different regulatory linkages may be more or less amenable to evolutionary change. One of the more surprising findings from this comparison is that GRN-level functions may be maintained while the factors performing the functions have changed, suggesting that GRNs have a high capacity for compensatory changes involving transcription factor binding to cis regulatory modules.

  15. Fungal Sinusitis

    Science.gov (United States)

    ... Marketplace Find an ENT Doctor Near You Fungal Sinusitis Fungal Sinusitis Patient Health Information News media interested ... sinusitis results. There Are Four Types Of Fungal Sinusitis: Mycetoma Fungal Sinusitis produces clumps of spores, a " ...

  16. Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.

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    Yan, Koon-Kiu; Fang, Gang; Bhardwaj, Nitin; Alexander, Roger P; Gerstein, Mark

    2010-05-18

    The genome has often been called the operating system (OS) for a living organism. A computer OS is described by a regulatory control network termed the call graph, which is analogous to the transcriptional regulatory network in a cell. To apply our firsthand knowledge of the architecture of software systems to understand cellular design principles, we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology and evolution. We show that both networks have a fundamentally hierarchical layout, but there is a key difference: The transcriptional regulatory network possesses a few global regulators at the top and many targets at the bottom; conversely, the call graph has many regulators controlling a small set of generic functions. This top-heavy organization leads to highly overlapping functional modules in the call graph, in contrast to the relatively independent modules in the regulatory network. We further develop a way to measure evolutionary rates comparably between the two networks and explain this difference in terms of network evolution. The process of biological evolution via random mutation and subsequent selection tightly constrains the evolution of regulatory network hubs. The call graph, however, exhibits rapid evolution of its highly connected generic components, made possible by designers' continual fine-tuning. These findings stem from the design principles of the two systems: robustness for biological systems and cost effectiveness (reuse) for software systems.

  17. Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution.

    Science.gov (United States)

    Mendizabal, Isabel; Shi, Lei; Keller, Thomas E; Konopka, Genevieve; Preuss, Todd M; Hsieh, Tzung-Fu; Hu, Enzhi; Zhang, Zhe; Su, Bing; Yi, Soojin V

    2016-11-01

    How do epigenetic modifications change across species and how do these modifications affect evolution? These are fundamental questions at the forefront of our evolutionary epigenomic understanding. Our previous work investigated human and chimpanzee brain methylomes, but it was limited by the lack of outgroup data which is critical for comparative (epi)genomic studies. Here, we compared whole genome DNA methylation maps from brains of humans, chimpanzees and also rhesus macaques (outgroup) to elucidate DNA methylation changes during human brain evolution. Moreover, we validated that our approach is highly robust by further examining 38 human-specific DMRs using targeted deep genomic and bisulfite sequencing in an independent panel of 37 individuals from five primate species. Our unbiased genome-scan identified human brain differentially methylated regions (DMRs), irrespective of their associations with annotated genes. Remarkably, over half of the newly identified DMRs locate in intergenic regions or gene bodies. Nevertheless, their regulatory potential is on par with those of promoter DMRs. An intriguing observation is that DMRs are enriched in active chromatin loops, suggesting human-specific evolutionary remodeling at a higher-order chromatin structure. These findings indicate that there is substantial reprogramming of epigenomic landscapes during human brain evolution involving noncoding regions. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks.

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    Mario Pujato

    Full Text Available Gene regulatory networks show robustness to perturbations. Previous works identified robustness as an emergent property of gene network evolution but the underlying molecular mechanisms are poorly understood. We used a multi-tier modeling approach that integrates molecular sequence and structure information with network architecture and population dynamics. Structural models of transcription factor-DNA complexes are used to estimate relative binding specificities. In this model, mutations in the DNA cause changes on two levels: (a at the sequence level in individual binding sites (modulating binding specificity, and (b at the network level (creating and destroying binding sites. We used this model to dissect the underlying mechanisms responsible for the evolution of robustness in gene regulatory networks. Results suggest that in sparse architectures (represented by short promoters, a mixture of local-sequence and network-architecture level changes are exploited. At the local-sequence level, robustness evolves by decreasing the probabilities of both the destruction of existent and generation of new binding sites. Meanwhile, in highly interconnected architectures (represented by long promoters, robustness evolves almost entirely via network level changes, deleting and creating binding sites that modify the network architecture.

  19. Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4.

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    Hanikenne, Marc; Talke, Ina N; Haydon, Michael J; Lanz, Christa; Nolte, Andrea; Motte, Patrick; Kroymann, Juergen; Weigel, Detlef; Krämer, Ute

    2008-05-15

    Little is known about the types of mutations underlying the evolution of species-specific traits. The metal hyperaccumulator Arabidopsis halleri has the rare ability to colonize heavy-metal-polluted soils, and, as an extremophile sister species of Arabidopsis thaliana, it is a powerful model for research on adaptation. A. halleri naturally accumulates and tolerates leaf concentrations as high as 2.2% zinc and 0.28% cadmium in dry biomass. On the basis of transcriptomics studies, metal hyperaccumulation in A. halleri has been associated with more than 30 candidate genes that are expressed at higher levels in A. halleri than in A. thaliana. Some of these genes have been genetically mapped to broad chromosomal segments of between 4 and 24 cM co-segregating with Zn and Cd hypertolerance. However, the in planta loss-of-function approaches required to demonstrate the contribution of a given candidate gene to metal hyperaccumulation or hypertolerance have not been pursued to date. Using RNA interference to downregulate HMA4 (HEAVY METAL ATPASE 4) expression, we show here that Zn hyperaccumulation and full hypertolerance to Cd and Zn in A. halleri depend on the metal pump HMA4. Contrary to a postulated global trans regulatory factor governing high expression of numerous metal hyperaccumulation genes, we demonstrate that enhanced expression of HMA4 in A. halleri is attributable to a combination of modified cis-regulatory sequences and copy number expansion, in comparison to A. thaliana. Transfer of an A. halleri HMA4 gene to A. thaliana recapitulates Zn partitioning into xylem vessels and the constitutive transcriptional upregulation of Zn deficiency response genes characteristic of Zn hyperaccumulators. Our results demonstrate the importance of cis-regulatory mutations and gene copy number expansion in the evolution of a complex naturally selected extreme trait. The elucidation of a natural strategy for metal hyperaccumulation enables the rational design of technologies

  20. Developmental gene regulatory network evolution: insights from comparative studies in echinoderms.

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    Hinman, Veronica F; Cheatle Jarvela, Alys M

    2014-03-01

    One of the central concerns of Evolutionary Developmental biology is to understand how the specification of cell types can change during evolution. In the last decade, developmental biology has progressed toward a systems level understanding of cell specification processes. In particular, the focus has been on determining the regulatory interactions of the repertoire of genes that make up gene regulatory networks (GRNs). Echinoderms provide an extraordinary model system for determining how GRNs evolve. This review highlights the comparative GRN analyses arising from the echinoderm system. This work shows that certain types of GRN subcircuits or motifs, i.e., those involving positive feedback, tend to be conserved and may provide a constraint on development. This conservation may be due to a required arrangement of transcription factor binding sites in cis regulatory modules. The review will also discuss ways in which novelty may arise, in particular through the co-option of regulatory genes and subcircuits. The development of the sea urchin larval skeleton, a novel feature that arose in echinoderms, has provided a model for study of co-option mechanisms. Finally, the types of GRNs that can permit the great diversity in the patterns of ciliary bands and their associated neurons found among these taxa are discussed. The availability of genomic resources is rapidly expanding for echinoderms, including genome sequences not only for multiple species of sea urchins but also a species of sea star, sea cucumber, and brittle star. This will enable echinoderms to become a particularly powerful system for understanding how developmental GRNs evolve.

  1. Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis.

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    Michalis Barkoulas

    2016-09-01

    Full Text Available Patterning of C. elegans vulval cell fates relies on inductive signaling. In this induction event, a single cell, the gonadal anchor cell, secretes LIN-3/EGF and induces three out of six competent precursor cells to acquire a vulval fate. We previously showed that this developmental system is robust to a four-fold variation in lin-3/EGF genetic dose. Here using single-molecule FISH, we find that the mean level of expression of lin-3 in the anchor cell is remarkably conserved. No change in lin-3 expression level could be detected among C. elegans wild isolates and only a low level of change-less than 30%-in the Caenorhabditis genus and in Oscheius tipulae. In C. elegans, lin-3 expression in the anchor cell is known to require three transcription factor binding sites, specifically two E-boxes and a nuclear-hormone-receptor (NHR binding site. Mutation of any of these three elements in C. elegans results in a dramatic decrease in lin-3 expression. Yet only a single E-box is found in the Drosophilae supergroup of Caenorhabditis species, including C. angaria, while the NHR-binding site likely only evolved at the base of the Elegans group. We find that a transgene from C. angaria bearing a single E-box is sufficient for normal expression in C. elegans. Even a short 58 bp cis-regulatory fragment from C. angaria with this single E-box is able to replace the three transcription factor binding sites at the endogenous C. elegans lin-3 locus, resulting in the wild-type expression level. Thus, regulatory evolution occurring in cis within a 58 bp lin-3 fragment, results in a strict requirement for the NHR binding site and a second E-box in C. elegans. This single-cell, single-molecule, quantitative and functional evo-devo study demonstrates that conserved expression levels can hide extensive change in cis-regulatory site requirements and highlights the evolution of new cis-regulatory elements required for cell-specific gene expression.

  2. Evolution and diversity of a fungal self/nonself recognition locus.

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    Charles Hall

    Full Text Available BACKGROUND: Self/nonself discrimination is an essential feature for pathogen recognition and graft rejection and is a ubiquitous phenomenon in many organisms. Filamentous fungi, such as Neurospora crassa, provide a model for analyses of population genetics/evolution of self/nonself recognition loci due to their haploid nature, small genomes and excellent genetic/genomic resources. In N. crassa, nonself discrimination during vegetative growth is determined by 11 heterokaryon incompatibility (het loci. Cell fusion between strains that differ in allelic specificity at any of these het loci triggers a rapid programmed cell death response. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we evaluated the evolution, population genetics and selective mechanisms operating at a nonself recognition complex consisting of two closely linked loci, het-c (NCU03493 and pin-c (NCU03494. The genomic position of pin-c next to het-c is unique to Neurospora/Sordaria species, and originated by gene duplication after divergence from other species within the Sordariaceae. The het-c pin-c alleles in N. crassa are in severe linkage disequilibrium and consist of three haplotypes, het-c1/pin-c1, het-c2/pin-c2 and het-c3/pin-c3, which are equally frequent in population samples and exhibit trans-species polymorphisms. The absence of recombinant haplotypes is correlated with divergence of the het-c/pin-c intergenic sequence. Tests for positive and balancing selection at het-c and pin-c support the conclusion that both of these loci are under non-neutral balancing selection; other regions of both genes appear to be under positive selection. Our data show that the het-c2/pin-c2 haplotype emerged by a recombination event between the het-c1/pin-c1 and het-c3/pin-c3 approximately 3-12 million years ago. CONCLUSIONS/SIGNIFICANCE: These results support models by which loci that confer nonself discrimination form by the association of polymorphic genes with genes containing HET

  3. Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan

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    Guerreiro, Isabel; Gitto, Sandra; Novoa, Ana; Codourey, Julien; Nguyen Huynh, Thi Hanh; Gonzalez, Federico; Milinkovitch, Michel C; Mallo, Moises; Duboule, Denis

    2016-01-01

    Within land vertebrate species, snakes display extreme variations in their body plan, characterized by the absence of limbs and an elongated morphology. Such a particular interpretation of the basic vertebrate body architecture has often been associated with changes in the function or regulation of Hox genes. Here, we use an interspecies comparative approach to investigate different regulatory aspects at the snake HoxD locus. We report that, unlike in other vertebrates, snake mesoderm-specific enhancers are mostly located within the HoxD cluster itself rather than outside. In addition, despite both the absence of limbs and an altered Hoxd gene regulation in external genitalia, the limb-associated bimodal HoxD chromatin structure is maintained at the snake locus. Finally, we show that snake and mouse orthologous enhancer sequences can display distinct expression specificities. These results show that vertebrate morphological evolution likely involved extensive reorganisation at Hox loci, yet within a generally conserved regulatory framework. DOI: http://dx.doi.org/10.7554/eLife.16087.001 PMID:27476854

  4. Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

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    Vincent J. Lynch

    2015-02-01

    Full Text Available A major challenge in biology is determining how evolutionarily novel characters originate; however, mechanistic explanations for the origin of new characters are almost completely unknown. The evolution of pregnancy is an excellent system in which to study the origin of novelties because mammals preserve stages in the transition from egg laying to live birth. To determine the molecular bases of this transition, we characterized the pregnant/gravid uterine transcriptome from tetrapods to trace the evolutionary history of uterine gene expression. We show that thousands of genes evolved endometrial expression during the origins of mammalian pregnancy, including genes that mediate maternal-fetal communication and immunotolerance. Furthermore, thousands of cis-regulatory elements that mediate decidualization and cell-type identity in decidualized stromal cells are derived from ancient mammalian transposable elements (TEs. Our results indicate that one of the defining mammalian novelties evolved from DNA sequences derived from ancient mammalian TEs co-opted into hormone-responsive regulatory elements distributed throughout the genome.

  5. Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens.

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    Glinsky, Gennadi V

    2016-09-19

    Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8-10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of

  6. Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

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    van Helden Jacques

    2008-01-01

    Full Text Available Abstract Background The detection of conserved motifs in promoters of orthologous genes (phylogenetic footprints has become a common strategy to predict cis-acting regulatory elements. Several software tools are routinely used to raise hypotheses about regulation. However, these tools are generally used as black boxes, with default parameters. A systematic evaluation of optimal parameters for a footprint discovery strategy can bring a sizeable improvement to the predictions. Results We evaluate the performances of a footprint discovery approach based on the detection of over-represented spaced motifs. This method is particularly suitable for (but not restricted to Bacteria, since such motifs are typically bound by factors containing a Helix-Turn-Helix domain. We evaluated footprint discovery in 368 Escherichia coli K12 genes with annotated sites, under 40 different combinations of parameters (taxonomical level, background model, organism-specific filtering, operon inference. Motifs are assessed both at the levels of correctness and significance. We further report a detailed analysis of 181 bacterial orthologs of the LexA repressor. Distinct motifs are detected at various taxonomical levels, including the 7 previously characterized taxon-specific motifs. In addition, we highlight a significantly stronger conservation of half-motifs in Actinobacteria, relative to Firmicutes, suggesting an intermediate state in specificity switching between the two Gram-positive phyla, and thereby revealing the on-going evolution of LexA auto-regulation. Conclusion The footprint discovery method proposed here shows excellent results with E. coli and can readily be extended to predict cis-acting regulatory signals and propose testable hypotheses in bacterial genomes for which nothing is known about regulation.

  7. Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms

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    Jennings Charlotte K

    2010-11-01

    Full Text Available Abstract Background Conservation of orthologous regulatory gene expression domains, especially along the neuroectodermal anterior-posterior axis, in animals as disparate as flies and vertebrates suggests that common patterning mechanisms have been conserved since the base of Bilateria. The homology of axial patterning is far less clear for the many marine animals that undergo a radical transformation in body plan during metamorphosis. The embryos of these animals are microscopic, feeding within the plankton until they metamorphose into their adult forms. Results We describe here the localization of 14 transcription factors within the ectoderm during early embryogenesis in Patiria miniata, a sea star with an indirectly developing planktonic bipinnaria larva. We find that the animal-vegetal axis of this very simple embryo is surprisingly well patterned. Furthermore, the patterning that we observe throughout the ectoderm generally corresponds to that of "head/anterior brain" patterning known for hemichordates and vertebrates, which share a common ancestor with the sea star. While we suggest here that aspects of head/anterior brain patterning are generally conserved, we show that another suite of genes involved in retinal determination is absent from the ectoderm of these echinoderms and instead operates within the mesoderm. Conclusions Our findings therefore extend, for the first time, evidence of a conserved axial pattering to echinoderm embryos exhibiting maximal indirect development. The dissociation of head/anterior brain patterning from "retinal specification" in echinoderm blastulae might reflect modular changes to a developmental gene regulatory network within the ectoderm that facilitates the evolution of these microscopic larvae.

  8. Unstable microsatellite repeats facilitate rapid evolution of coding and regulatory sequences.

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    Jansen, A; Gemayel, R; Verstrepen, K J

    2012-01-01

    Tandem repeats are intrinsically highly variable sequences since repeat units are often lost or gained during replication or following unequal recombination events. Because of their low complexity and their instability, these repeats, which are also called satellite repeats, are often considered to be useless 'junk' DNA. However, recent findings show that tandem repeats are frequently found within promoters of stress-induced genes and within the coding regions of genes encoding cell-surface and regulatory proteins. Interestingly, frequent changes in these repeats often confer phenotypic variability. Examples include variation in the microbial cell surface, rapid tuning of internal molecular clocks in flies, and enhanced morphological plasticity in mammals. This suggests that instead of being useless junk DNA, some variable tandem repeats are useful functional elements that confer 'evolvability', facilitating swift evolution and rapid adaptation to changing environments. Since changes in repeats are frequent and reversible, repeats provide a unique type of mutation that bridges the gap between rare genetic mutations, such as single nucleotide polymorphisms, and highly unstable but reversible epigenetic inheritance.

  9. Genetic bases of fungal white rot wood decay predicted by phylogenomic analysis of correlated gene-phenotype evolution

    Science.gov (United States)

    László G. Nagy; Robert Riley; Philip J. Bergmann; Krisztina Krizsán; Francis M. Martin; Igor V. Grigoriev; Dan Cullen; David S. Hibbett

    2016-01-01

    Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR...

  10. Fungal arthritis

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    ... this page: //medlineplus.gov/ency/article/000444.htm Fungal arthritis To use the sharing features on this page, please enable JavaScript. Fungal arthritis is swelling and irritation (inflammation) of a joint ...

  11. Fungal Meningitis

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    ... Schedules Preteen & Teen Vaccines Meningococcal Disease Sepsis Fungal Meningitis Language: English Español (Spanish) Recommend on Facebook Tweet ... the brain or spinal cord. Investigation of Fungal Meningitis, 2012 In September 2012, the Centers for Disease ...

  12. Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria

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    Babujee Lavanya

    2012-03-01

    Full Text Available Abstract Background Dickeya dadantii and Pectobacterium atrosepticum are phytopathogenic enterobacteria capable of facultative anaerobic growth in a wide range of O2 concentrations found in plant and natural environments. The transcriptional response to O2 remains under-explored for these and other phytopathogenic enterobacteria although it has been well characterized for animal-associated genera including Escherichia coli and Salmonella enterica. Knowledge of the extent of conservation of the transcriptional response across orthologous genes in more distantly related species is useful to identify rates and patterns of regulon evolution. Evolutionary events such as loss and acquisition of genes by lateral transfer events along each evolutionary branch results in lineage-specific genes, some of which may have been subsequently incorporated into the O2-responsive stimulon. Here we present a comparison of transcriptional profiles measured using densely tiled oligonucleotide arrays for two phytopathogens, Dickeya dadantii 3937 and Pectobacterium atrosepticum SCRI1043, grown to mid-log phase in MOPS minimal medium (0.1% glucose with and without O2. Results More than 7% of the genes of each phytopathogen are differentially expressed with greater than 3-fold changes under anaerobic conditions. In addition to anaerobic metabolism genes, the O2 responsive stimulon includes a variety of virulence and pathogenicity-genes. Few of these genes overlap with orthologous genes in the anaerobic stimulon of E. coli. We define these as the conserved core, in which the transcriptional pattern as well as genetic architecture are well preserved. This conserved core includes previously described anaerobic metabolic pathways such as fermentation. Other components of the anaerobic stimulon show variation in genetic content, genome architecture and regulation. Notably formate metabolism, nitrate/nitrite metabolism, and fermentative butanediol production, differ between E

  13. In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression.

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    Zagrijchuk, Elizaveta A; Sabirov, Marat A; Holloway, David M; Spirov, Alexander V

    2014-04-01

    Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes.

  14. In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression

    Science.gov (United States)

    Zagrijchuk, Elizaveta A.; Sabirov, Marat A.; Holloway, David M.; Spirov, Alexander V.

    2014-01-01

    Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes. PMID:24712536

  15. Global characterization of interferon regulatory factor (IRF genes in vertebrates: Glimpse of the diversification in evolution

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    Xu Zhen

    2010-05-01

    Full Text Available Abstract Background Interferon regulatory factors (IRFs, which can be identified based on a unique helix-turn-helix DNA-binding domain (DBD are a large family of transcription factors involved in host immune response, haemotopoietic differentiation and immunomodulation. Despite the identification of ten IRF family members in mammals, and some recent effort to identify these members in fish, relatively little is known in the composition of these members in other classes of vertebrates, and the evolution and probably the origin of the IRF family have not been investigated in vertebrates. Results Genome data mining has been performed to identify any possible IRF family members in human, mouse, dog, chicken, anole lizard, frog, and some teleost fish, mainly zebrafish and stickleback, and also in non-vertebrate deuterostomes including the hemichordate, cephalochordate, urochordate and echinoderm. In vertebrates, all ten IRF family members, i.e. IRF-1 to IRF-10 were identified, with two genes of IRF-4 and IRF-6 identified in fish and frog, respectively, except that in zebrafish exist three IRF-4 genes. Surprisingly, an additional member in the IRF family, IRF-11 was found in teleost fish. A range of two to ten IRF-like genes were detected in the non-vertebrate deuterostomes, and they had little similarity to those IRF family members in vertebrates as revealed in genomic structure and in phylogenetic analysis. However, the ten IRF family members, IRF-1 to IRF-10 showed certain degrees of conservation in terms of genomic structure and gene synteny. In particular, IRF-1, IRF-2, IRF-6, IRF-8 are quite conserved in their genomic structure in all vertebrates, and to a less degree, some IRF family members, such as IRF-5 and IRF-9 are comparable in the structure. Synteny analysis revealed that the gene loci for the ten IRF family members in vertebrates were also quite conservative, but in zebrafish conserved genes were distributed in a much longer distance in

  16. Global characterization of interferon regulatory factor (IRF) genes in vertebrates: glimpse of the diversification in evolution.

    Science.gov (United States)

    Huang, Bei; Qi, Zhi T; Xu, Zhen; Nie, Pin

    2010-05-05

    Interferon regulatory factors (IRFs), which can be identified based on a unique helix-turn-helix DNA-binding domain (DBD) are a large family of transcription factors involved in host immune response, haemotopoietic differentiation and immunomodulation. Despite the identification of ten IRF family members in mammals, and some recent effort to identify these members in fish, relatively little is known in the composition of these members in other classes of vertebrates, and the evolution and probably the origin of the IRF family have not been investigated in vertebrates. Genome data mining has been performed to identify any possible IRF family members in human, mouse, dog, chicken, anole lizard, frog, and some teleost fish, mainly zebrafish and stickleback, and also in non-vertebrate deuterostomes including the hemichordate, cephalochordate, urochordate and echinoderm. In vertebrates, all ten IRF family members, i.e. IRF-1 to IRF-10 were identified, with two genes of IRF-4 and IRF-6 identified in fish and frog, respectively, except that in zebrafish exist three IRF-4 genes. Surprisingly, an additional member in the IRF family, IRF-11 was found in teleost fish. A range of two to ten IRF-like genes were detected in the non-vertebrate deuterostomes, and they had little similarity to those IRF family members in vertebrates as revealed in genomic structure and in phylogenetic analysis. However, the ten IRF family members, IRF-1 to IRF-10 showed certain degrees of conservation in terms of genomic structure and gene synteny. In particular, IRF-1, IRF-2, IRF-6, IRF-8 are quite conserved in their genomic structure in all vertebrates, and to a less degree, some IRF family members, such as IRF-5 and IRF-9 are comparable in the structure. Synteny analysis revealed that the gene loci for the ten IRF family members in vertebrates were also quite conservative, but in zebrafish conserved genes were distributed in a much longer distance in chromosomes. Furthermore, all ten different

  17. Evolution of Chemical Diversity in a Group of Non-Reduced Polyketide Gene Clusters: Using Phylogenetics to Inform the Search for Novel Fungal Natural Products

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    Kurt Throckmorton

    2015-09-01

    Full Text Available Fungal polyketides are a diverse class of natural products, or secondary metabolites (SMs, with a wide range of bioactivities often associated with toxicity. Here, we focus on a group of non-reducing polyketide synthases (NR-PKSs in the fungal phylum Ascomycota that lack a thioesterase domain for product release, group V. Although widespread in ascomycete taxa, this group of NR-PKSs is notably absent in the mycotoxigenic genus Fusarium and, surprisingly, found in genera not known for their secondary metabolite production (e.g., the mycorrhizal genus Oidiodendron, the powdery mildew genus Blumeria, and the causative agent of white-nose syndrome in bats, Pseudogymnoascus destructans. This group of NR-PKSs, in association with the other enzymes encoded by their gene clusters, produces a variety of different chemical classes including naphthacenediones, anthraquinones, benzophenones, grisandienes, and diphenyl ethers. We discuss the modification of and transitions between these chemical classes, the requisite enzymes, and the evolution of the SM gene clusters that encode them. Integrating this information, we predict the likely products of related but uncharacterized SM clusters, and we speculate upon the utility of these classes of SMs as virulence factors or chemical defenses to various plant, animal, and insect pathogens, as well as mutualistic fungi.

  18. Causality Assessment in Premarketing Drug Clinical Trials: Regulatory Evolution in the USA and Ongoing Concerns.

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    Goldman, Stephen A

    2016-10-01

    Since 1993, how to assess the causality of serious adverse events in premarketing drug clinical trials has undergone sustained regulatory evolution in the USA. In that year, an investigational drug study for chronic hepatitis B virus infection was emergently stopped after a patient suddenly exhibited hepatic failure and lactic acidosis, which later developed, along with pancreatitis and peripheral neuropathy, in several others after drug discontinuation. Five patients eventually died, including three despite emergency liver transplantation. The drug's multisystem toxicity was not predicted by preclinical animal studies, with grave injury to human mitochondria subsequently implicated. A concerned US Food and Drug Administration (FDA) created a task force whose findings would have a lasting impact on the agency's thinking. In 1994, the FDA proposed to amend its investigational new drug reporting requirements largely based on task force recommendations for ways to enhance the likelihood that sponsors and investigators would consider investigational agents as a possible cause of serious adverse events mimicking the underlying disease or concomitant drug toxicity. Then, in its 1997 final rule for expedited safety reporting requirements for drugs and biologics, the FDA advised sponsors that such reporting of serious, unexpected clinical trial cases would be expected when "there is a reasonable suspected causal relationship between the investigational product and the adverse event (i.e., the causal relationship cannot be ruled out)." This last clause was codified into the suspected adverse drug reaction definition in the FDA's 2003 safety reporting requirements for drugs and biologics proposed rule. The negatively received suspected adverse drug reaction and proposed causality standard were not adopted in the FDA's 2010 finalized investigational new drug safety reporting regulations, the agency stating that "'reasonable possibility' means there is evidence to suggest a

  19. Evolution of habitat preference and nutrition mode in a cosmopolitan fungal genus with evidence of interkingdom host jumps and major shifts in ecology.

    Science.gov (United States)

    Chaverri, Priscila; Samuels, Gary J

    2013-10-01

    Host jumps by microbial symbionts are often associated with bursts of species diversification driven by the exploitation of new adaptive zones. The objective of this study was to infer the evolution of habitat preference (decaying plants, soil, living fungi, and living plants), and nutrition mode (saprotrophy and mycoparasitism) in the fungal genus Trichoderma to elucidate possible interkingdom host jumps and shifts in ecology. Host and ecological role shifts were inferred by phylogenetic analyses and ancestral character reconstructions. The results support several interkingdom host jumps and also show that the preference for a particular habitat was gained or lost multiple times. Diversification analysis revealed that mycoparasitism is associated with accelerated speciation rates, which then suggests that this trait may be linked to the high number of species in Trichoderma. In this study it was also possible to infer the cryptic roles that endophytes or soil inhabitants play in their hosts by evaluating their closest relatives and determining their most recent ancestors. Findings from this study may have implications for understanding certain evolutionary processes such as species radiations in some hyperdiverse groups of fungi, and for more applied fields such as the discovery and development of novel biological control strategies. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  20. [Fungal keratitis].

    Science.gov (United States)

    Bourcier, T; Sauer, A; Letscher-Bru, V; Candolfi, E

    2011-10-01

    Fungal keratitis (keratomycosis) is a rare but severe cause of infectious keratitis. Its incidence is constant, due to steroids or immunosuppressive treatments and contact lenses. Pathogens often invade corneas with chronic diseases of the ocular surface but fungal keratitis is also observed following injuries with plant foreign objects. The poor prognosis of these infections is related both to fungal virulence, decreased host defense, as well as delays in diagnosis. However, new antimycotic treatments allow better management and prognosis.

  1. N-termini of fungal CSL transcription factors are disordered, enriched in regulatory motifs and inhibit DNA binding in fission yeast.

    Directory of Open Access Journals (Sweden)

    Martin Převorovský

    Full Text Available BACKGROUND: CSL (CBF1/RBP-Jκ/Suppressor of Hairless/LAG-1 transcription factors are the effector components of the Notch receptor signalling pathway, which is critical for metazoan development. The metazoan CSL proteins (class M can also function in a Notch-independent manner. Recently, two novel classes of CSL proteins, designated F1 and F2, have been identified in fungi. The role of the fungal CSL proteins is unclear, because the Notch pathway is not present in fungi. In fission yeast, the Cbf11 and Cbf12 CSL paralogs play antagonistic roles in cell adhesion and the coordination of cell and nuclear division. Unusually long N-terminal extensions are typical for fungal and invertebrate CSL family members. In this study, we investigate the functional significance of these extended N-termini of CSL proteins. METHODOLOGY/PRINCIPAL FINDINGS: We identify 15 novel CSL family members from 7 fungal species and conduct bioinformatic analyses of a combined dataset containing 34 fungal and 11 metazoan CSL protein sequences. We show that the long, non-conserved N-terminal tails of fungal CSL proteins are likely disordered and enriched in phosphorylation sites and PEST motifs. In a case study of Cbf12 (class F2, we provide experimental evidence that the protein is proteolytically processed and that the N-terminus inhibits the Cbf12-dependent DNA binding activity in an electrophoretic mobility shift assay. CONCLUSIONS/SIGNIFICANCE: This study provides insight into the characteristics of the long N-terminal tails of fungal CSL proteins that may be crucial for controlling DNA-binding and CSL function. We propose that the regulation of DNA binding by Cbf12 via its N-terminal region represents an important means by which fission yeast strikes a balance between the class F1 and class F2 paralog activities. This mode of regulation might be shared with other CSL-positive fungi, some of which are relevant to human disease and biotechnology.

  2. Developmental gene regulatory network architecture across 500 million years of echinoderm evolution

    Science.gov (United States)

    Hinman, Veronica F.; Nguyen, Albert T.; Cameron, R. Andrew; Davidson, Eric H.

    2003-01-01

    Evolutionary change in morphological features must depend on architectural reorganization of developmental gene regulatory networks (GRNs), just as true conservation of morphological features must imply retention of ancestral developmental GRN features. Key elements of the provisional GRN for embryonic endomesoderm development in the sea urchin are here compared with those operating in embryos of a distantly related echinoderm, a starfish. These animals diverged from their common ancestor 520-480 million years ago. Their endomesodermal fate maps are similar, except that sea urchins generate a skeletogenic cell lineage that produces a prominent skeleton lacking entirely in starfish larvae. A relevant set of regulatory genes was isolated from the starfish Asterina miniata, their expression patterns determined, and effects on the other genes of perturbing the expression of each were demonstrated. A three-gene feedback loop that is a fundamental feature of the sea urchin GRN for endoderm specification is found in almost identical form in the starfish: a detailed element of GRN architecture has been retained since the Cambrian Period in both echinoderm lineages. The significance of this retention is highlighted by the observation of numerous specific differences in the GRN connections as well. A regulatory gene used to drive skeletogenesis in the sea urchin is used entirely differently in the starfish, where it responds to endomesodermal inputs that do not affect it in the sea urchin embryo. Evolutionary changes in the GRNs since divergence are limited sharply to certain cis-regulatory elements, whereas others have persisted unaltered.

  3. Fungal rhinosinusitis.

    Science.gov (United States)

    Netkovski, J; Shirgoska, B

    2012-01-01

    Fungi are a major part of the ecosystem. In fact, over 250 fungal species have been reported to produce human infections. More than ever, fungal diseases have emerged as major challenges for physicians and clinical microbiologists. The aim of this study was to summarize the diagnostic procedures and endoscopic surgical treatment of patients with fungal rhinosinusitis. Eleven patients, i.e. 10% of all cases with chronic inflammation of paranasal sinuses, were diagnosed with fungal rhinosinusitis. Ten of them were patients with a noninvasive form, fungus ball, while only one patient was classified in the group of chronic invasive fungal rhinosinusitis which was accompanied with diabetes mellitus. All patients underwent nasal endoscopic examination, skin allergy test and had preoperative computed tomography (CT) scans of the sinuses in axial and coronal plane. Functional endoscopic sinus surgery was performed in 10 patients with fungus ball, while a combined approach, endoscopic and external, was done in the immunocompromised patient with the chronic invasive form of fungal rhinosinusitis. Most cases (9/11) had unilateral infection. In 9 cases infection was restricted to a single sinus, and here the maxillary sinus was most commonly affected (8/9) with infections in other patients being restricted to the sphenoid sinus (1/9). Two patients had infections affecting two or more sinuses. In patients with an invasive form of the fungal disease there was involvement of the periorbital and orbital tissues. In patients with fungus ball the mycelia masses were completely removed from the sinus cavities. Long-term outcome was positive in all the operated patients and no recurrence was detected. The most frequent fungal agent that caused rhinosinusitis was Aspergillus. Mucor was identified in the patient with the invasive form. Endoscopic examination of the nasal cavity and CT scanning of paranasal sinuses followed by endoscopic sinus surgery were represented as valuable

  4. Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host.

    Science.gov (United States)

    Lê Van, Amandine; Gladieux, Pierre; Lemaire, Christophe; Cornille, Amandine; Giraud, Tatiana; Durel, Charles-Eric; Caffier, Valérie; Le Cam, Bruno

    2012-11-01

    Understanding how pathogens emerge is essential to bring disease-causing agents under durable human control. Here, we used cross-pathogenicity tests to investigate the changes in life-history traits of the fungal pathogen Venturia inaequalis associated with host-tracking during the domestication of apple and subsequent host-range expansion on the wild European crabapple (Malus sylvestris). Pathogenicity of 40 isolates collected in wild and domesticated ecosystems was assessed on the domesticated apple, its Central Asian main progenitor (M. sieversii) and M. sylvestris. Isolates from wild habitats in the centre of origin of the crop were not pathogenic on the domesticated apple and less aggressive than other isolates on their host of origin. Isolates from the agro-ecosystem in Central Asia infected a higher proportion of plants with higher aggressiveness, on both the domesticated host and its progenitor. Isolates from the European crabapple were still able to cause disease on other species but were less aggressive and less frequently virulent on these hosts than their endemic populations. Our results suggest that the domestication of apple was associated with the acquisition of virulence in the pathogen following host-tracking. The spread of the disease in the agro-ecosystem would also have been accompanied by an increase in overall pathogenicity.

  5. Evolution of Transcriptional Regulatory Networks in Pseudomonas aeruginosa During Long Time Growth in Human Hosts

    DEFF Research Database (Denmark)

    Andresen, Eva Kammer

    ) as a natural model system, the work has focused on characterising a number of mutations in global regulators that are known to provide an adaptive advantage in this specific environment. The aim has been to provide a molecular explanation of the effects of the specific mutations in relation to regulatory...... network remodelling, and to provide insight into the extent of epistasis and evolutionary dynamics of these systems. The two studies presented in this thesis specifically deal with single amino acid substitutions or deletions in the sigma factors RpoD, AlgT, and RpoN. Through in vitro techniques, we...... characterised the direct molecular effects of the sigma factors’ abilities to interact with DNA and the core RNA polymerase (RNAP). By combining this approach with in vivo transcription profile data, Chromatin Immunoprecipitation-sequencing (ChIP-seq) data and artificial regulatory network modifications...

  6. Fungal allergens.

    OpenAIRE

    1995-01-01

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

  7. Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution.

    Directory of Open Access Journals (Sweden)

    Jingjing Li

    Full Text Available MicroRNA (miRNA-mediated gene regulation is of critical functional importance in animals and is thought to be largely constrained during evolution. However, little is known regarding evolutionary changes of the miRNA network and their role in human evolution. Here we show that a number of miRNA binding sites display high levels of population differentiation in humans and thus are likely targets of local adaptation. In a subset we demonstrate that allelic differences modulate miRNA regulation in mammalian cells, including an interaction between miR-155 and TYRP1, an important melanosomal enzyme associated with human pigmentary differences. We identify alternate alleles of TYRP1 that induce or disrupt miR-155 regulation and demonstrate that these alleles are selected with different modes among human populations, causing a strong negative correlation between the frequency of miR-155 regulation of TYRP1 in human populations and their latitude of residence. We propose that local adaptation of microRNA regulation acts as a rheostat to optimize TYRP1 expression in response to differential UV radiation. Our findings illustrate the evolutionary plasticity of the microRNA regulatory network in recent human evolution.

  8. Tissue Specificity and Sex-Specific Regulatory Variation Permit the Evolution of Sex-Biased Gene Expression.

    Science.gov (United States)

    Dean, Rebecca; Mank, Judith E

    2016-09-01

    Genetic correlations between males and females are often thought to constrain the evolution of sexual dimorphism. However, sexually dimorphic traits and the underlying sexually dimorphic gene expression patterns are often rapidly evolving. We explore this apparent paradox by measuring the genetic correlation in gene expression between males and females (Cmf) across broad evolutionary timescales, using two RNA-sequencing data sets spanning multiple populations and multiple species. We find that unbiased genes have higher Cmf than sex-biased genes, consistent with intersexual genetic correlations constraining the evolution of sexual dimorphism. However, we found that highly sex-biased genes (both male and female biased) also had higher tissue specificity, and unbiased genes had greater expression breadth, suggesting that pleiotropy may constrain the breakdown of intersexual genetic correlations. Finally, we show that genes with high Cmf showed some degree of sex-specific changes in gene expression in males and females. Together, our results suggest that genetic correlations between males and females may be less important in constraining the evolution of sex-biased gene expression than pleiotropy. Sex-specific regulatory variation and tissue specificity may resolve the paradox of widespread sex bias within a largely shared genome.

  9. Evolution of UCP1 Transcriptional Regulatory Elements Across the Mammalian Phylogeny

    Directory of Open Access Journals (Sweden)

    Michael J. Gaudry

    2017-09-01

    Full Text Available Uncoupling protein 1 (UCP1 permits non-shivering thermogenesis (NST when highly expressed in brown adipose tissue (BAT mitochondria. Exclusive to placental mammals, BAT has commonly been regarded to be advantageous for thermoregulation in hibernators, small-bodied species, and the neonates of larger species. While numerous regulatory control motifs associated with UCP1 transcription have been proposed for murid rodents, it remains unclear whether these are conserved across the eutherian mammal phylogeny and hence essential for UCP1 expression. To address this shortcoming, we conducted a broad comparative survey of putative UCP1 transcriptional regulatory elements in 139 mammals (135 eutherians. We find no evidence for presence of a UCP1 enhancer in monotremes and marsupials, supporting the hypothesis that this control region evolved in a stem eutherian ancestor. We additionally reveal that several putative promoter elements (e.g., CRE-4, CCAAT identified in murid rodents are not conserved among BAT-expressing eutherians, and together with the putative regulatory region (PRR and CpG island do not appear to be crucial for UCP1 expression. The specificity and importance of the upTRE, dnTRE, URE1, CRE-2, RARE-2, NBRE, BRE-1, and BRE-2 enhancer elements first described from rats and mice are moreover uncertain as these motifs differ substantially—but generally remain highly conserved—in other BAT-expressing eutherians. Other UCP1 enhancer motifs (CRE-3, PPRE, and RARE-3 as well as the TATA box are also highly conserved in nearly all eutherian lineages with an intact UCP1. While these transcriptional regulatory motifs are generally also maintained in species where this gene is pseudogenized, the loss or degeneration of key basal promoter (e.g., TATA box and enhancer elements in other UCP1-lacking lineages make it unlikely that the enhancer region is pleiotropic (i.e., co-regulates additional genes. Importantly, differential losses of (or mutations

  10. Evolution of cold-tolerant fungal symbionts permits winter fungiculture by leafcutter ants at the northern frontier of a tropical ant-fungus symbiosis.

    Science.gov (United States)

    Mueller, Ulrich G; Mikheyev, Alexander S; Hong, Eunki; Sen, Ruchira; Warren, Dan L; Solomon, Scott E; Ishak, Heather D; Cooper, Mike; Miller, Jessica L; Shaffer, Kimberly A; Juenger, Thomas E

    2011-03-08

    The obligate mutualism between leafcutter ants and their Attamyces fungi originated 8 to 12 million years ago in the tropics, but extends today also into temperate regions in South and North America. The northernmost leafcutter ant Atta texana sustains fungiculture during winter temperatures that would harm the cold-sensitive Attamyces cultivars of tropical leafcutter ants. Cold-tolerance of Attamyces cultivars increases with winter harshness along a south-to-north temperature gradient across the range of A. texana, indicating selection for cold-tolerant Attamyces variants along the temperature cline. Ecological niche modeling corroborates winter temperature as a key range-limiting factor impeding northward expansion of A. texana. The northernmost A. texana populations are able to sustain fungiculture throughout winter because of their cold-adapted fungi and because of seasonal, vertical garden relocation (maintaining gardens deep in the ground in winter to protect them from extreme cold, then moving gardens to warmer, shallow depths in spring). Although the origin of leafcutter fungiculture was an evolutionary breakthrough that revolutionized the food niche of tropical fungus-growing ants, the original adaptations of this host-microbe symbiosis to tropical temperatures and the dependence on cold-sensitive fungal symbionts eventually constrained expansion into temperate habitats. Evolution of cold-tolerant fungi within the symbiosis relaxed constraints on winter fungiculture at the northern frontier of the leafcutter ant distribution, thereby expanding the ecological niche of an obligate host-microbe symbiosis.

  11. Transcriptional network structure has little effect on the rate of regulatory evolution in yeast.

    Science.gov (United States)

    Kopp, Artyom; McIntyre, Lauren M

    2012-08-01

    Studies in evolutionary developmental biology suggest that the structure of genetic pathways may bias the fixation of natural variation toward particular nodes in these pathways. In an attempt to test this trend genome wide, we integrated several previously published data sets to examine whether the position of genes in the whole-genome transcriptional network of Saccharomyces cerevisiae is associated with the amount of cis-regulatory expression divergence between S. cerevisiae and its sibling species Saccharomyces paradoxus. We find little evidence for an association between connectivity and divergence in the global network that combines data from multiple conditions. However, relationships between connectivity and divergence are apparent in some of the smaller subnetworks. Despite a slight tendency for genes with more transcriptional interactions to show greater divergence, these differences explain no more than a small fraction of variation in evolutionary rates. These results suggest that the systems biology focus on large interactomes may miss some critical details of local interactions. More detailed experimental analysis will be needed to define the genetic pathways that control specific phenotypic traits and quantify the rate of regulatory changes at different points in these pathways.

  12. Evolution in performance assessment modeling as a result of regulatory review

    Energy Technology Data Exchange (ETDEWEB)

    Rowat, J.H.; Dolinar, G.M.; Stephens, M.E. [AECL Chalk River Labs., Ontario (Canada)] [and others

    1995-12-31

    AECL is planning to build the IRUS (Intrusion Resistant Underground Structure) facility for near-surface disposal of LLRW. The PSAR (preliminary safety assessment report) was subject to an initial regulatory review during mid-1992. The regulatory authority provided comments on many aspects of the safety assessment documentation including a number of questions on specific PA (Performance Assessment) modelling assumptions. As a result of these comments as well as a separate detailed review of the IRUS disposal concept, changes were made to the conceptual and mathematical models. The original disposal concept included a non-sorbing vault backfill, with a strong reliance on the wasteform as a barrier. This concept was altered to decrease reliance on the wasteform by replacing the original backfill with a sand/clinoptilolite mix, which is a better sorber of metal cations. This change lead to changes in the PA models which in turn altered the safety case for the facility. This, and other changes that impacted performance assessment modelling are the subject of this paper.

  13. A comparative analysis of the evolution, expression, and cis-regulatory element of polygalacturonase genes in grasses and dicots.

    Science.gov (United States)

    Liang, Ying; Yu, Youjian; Cui, Jinlong; Lyu, Meiling; Xu, Liai; Cao, Jiashu

    2016-11-01

    Cell walls are a distinguishing characteristic of plants essential to their survival. The pectin content of primary cell walls in grasses and dicots is distinctly different. Polygalacturonases (PGs) can degrade pectins and participate in multiple developmental processes of plants. This study comprehensively compared the evolution, expression, and cis-regulatory element of PGs in grasses and dicots. A total of 577 PGs identified from five grasses and five dicots fell into seven clades. Evolutionary analysis demonstrated the distinct differences between grasses and dicots in patterns of gene duplication and loss, and evolutionary rates. Grasses generally contained much fewer clade C and F members than dicots. We found that this disparity was the result of less duplication and more gene losses in grasses. More duplications occurred in clades D and E, and expression analysis showed that most of clade E members were expressed ubiquitously at a high overall level and clade D members were closely related to male reproduction in both grasses and dicots, suggesting their biological functions were highly conserved across species. In addition to the general role in reproductive development, PGs of clades C and F specifically played roles in root development in dicots, shedding light on organ differentiation between the two groups of plants. A regulatory element analysis of clade C and F members implied that possible functions of PGs in specific biological responses contributed to their expansion and preservation. This work can improve the knowledge of PGs in plants generally and in grasses specifically and is beneficial to functional studies.

  14. Fungal nail infection

    Science.gov (United States)

    Nails - fungal infection; Onychomycosis; Infection - fungal - nails; Tinea unguium ... hair, nails, and outer skin layers. Common fungal infections include: Athlete's foot Jock itch Ringworm on the ...

  15. Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4

    OpenAIRE

    Hanikenne, Marc; Talke, Ina N.; Haydon, Michael J.; Lanz, Christa; Nolte, Andrea; Motte, Patrick; Kroymann, Juergen; Weigel, Detlef; Krämer, Ute

    2008-01-01

    Little is known about the types of mutations underlying the evolution of species-specific traits. The metal hyperaccumulator Arabidopsis halleri has the rare ability to colonize heavy-metal-polluted soils, and, as an extremophile sister species of Arabidopsis thaliana, it is a powerful model for research on adaptation. A. halleri naturally accumulates and tolerates leaf concentrations as high as 2.2% zinc and 0.28% cadmium in dry biomass. On the basis of transcriptomics studies, metal hyperac...

  16. Fungal keratitis

    Directory of Open Access Journals (Sweden)

    Sonal S Tuli

    2011-02-01

    Full Text Available Sonal S TuliUniversity of Florida, Gainesville, FL, USA  Clinical question: What is the most appropriate management of fungal keratitis?Results: Traditionally, topical Natamycin is the most commonly used medication for filamentous fungi while Amphotericin B is most commonly used for yeast. Voriconazole is rapidly becoming the drug of choice for all fungal keratitis because of its wide spectrum of coverage and increased penetration into the cornea.Implementation: Repeated debridement of the ulcer is recommended for the penetration of topical medications. While small, peripheral ulcers may be treated in the community, larger or central ulcers, especially if associated with signs suggestive of anterior chamber penetration should be referred to a tertiary center. Prolonged therapy for approximately four weeks is usually necessary.Keywords: fungal keratitis, keratomycosis, antifungal medications, debridement

  17. THE INDIAN PHARMACEUTICAL INDUSTRY; EVOLUTION OF REGULATORY SYSTEM AND PRESENT SCENARIO

    Directory of Open Access Journals (Sweden)

    Sarda Rohit R.

    2012-06-01

    Full Text Available Indian pharmaceutical industry evolved in true sense only after independence. Government provided the impetus to growth with the establishment of few public sector units. Healthcare facilities in India are still below standard as compared to most developed nations. Indian government is stringent on price control of Pharmaceuticals and this becomes a major hurdle for global players to enter in India but Indian patent act and new drug policy has bought a new dimension to Indian Pharmaceutical Industry. Some of the Indo-global industries like Cipla, Ranbaxy and Dr .Reddy’s are showing rapid and consistent growth with their impact worldwide. India is also turning out to be a prime destination for clinical trials. Industry today is governed by wide range of regulations and different regulatory bodies. Current article focuses on all these aspects along with regulations for new drugs, medical devices, imports etc.

  18. Adaptive evolution of the Streptococcus pyogenes regulatory aldolase LacD.1.

    Science.gov (United States)

    Cusumano, Zachary; Caparon, Michael

    2013-03-01

    In the human-pathogenic bacterium Streptococcus pyogenes, the tagatose bisphosphate aldolase LacD.1 likely originated through a gene duplication event and was adapted to a role as a metabolic sensor for regulation of virulence gene transcription. Although LacD.1 retains enzymatic activity, its ancestral metabolic function resides in the LacD.2 aldolase, which is required for the catabolism of galactose. In this study, we compared these paralogous proteins to identify characteristics correlated with divergence and novel function. Surprisingly, despite the fact that these proteins have identical active sites and 82% similarity in amino acid sequence, LacD.1 was less efficient at cleaving both fructose and tagatose bisphosphates. Analysis of kinetic properties revealed that LacD.1's adaptation was associated with a decrease in k(cat) and an increase in K(m). Construction and analysis of enzyme chimeras indicated that non-active-site residues previously associated with the variable activities of human aldolase isoenzymes modulated LacD.1's affinity for substrate. Mutant LacD.1 proteins engineered to have LacD.2-like levels of enzymatic efficiency lost the ability to function as regulators, suggesting that an alteration in efficiency was required for adaptation. In competition under growth conditions that mimic a deep-tissue environment, LacD.1 conferred a significant gain in fitness that was associated with its regulatory activity. Taken together, these data suggest that LacD.1's adaptation represents a form of neofunctionalization in which duplication facilitated the gain of regulatory function important for growth in tissue and pathogenesis.

  19. Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

    Science.gov (United States)

    McNally, Alan; Oren, Yaara; Kelly, Darren; Sreecharan, Tristan; Vehkala, Minna; Välimäki, Niko; Prentice, Michael B.; Ashour, Amgad; Avram, Oren; Pupko, Tal; Literak, Ivan; Guenther, Sebastian; Schaufler, Katharina; Wieler, Lothar H.; Zhiyong, Zong; Sheppard, Samuel K.; Corander, Jukka

    2016-01-01

    The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements. PMID:27618184

  20. Functional evolution of the p53 regulatory network through its target response elements

    Science.gov (United States)

    Jegga, Anil G.; Inga, Alberto; Menendez, Daniel; Aronow, Bruce J.; Resnick, Michael A.

    2008-01-01

    Transcriptional network evolution is central to the development of complex biological systems. Networks can evolve through variation of master regulators and/or by changes in regulation of genes within networks. To gain insight into meaningful evolutionary differences in large networks, it is essential to address the functional consequences of sequence differences in response elements (REs) targeted by transcription factors. Using a combination of custom bioinformatics and multispecies alignment of promoter regions, we investigated the functional evolution of REs in terms of responsiveness to the sequence-specific transcription factor p53, a tumor suppressor and master regulator of stress responses. We identified REs orthologous to known p53 targets in human and rodent cells or alternatively REs related to the established p53 consensus. The orthologous REs were assigned p53 transactivation capabilities based on rules determined from model systems, and a functional heat map was developed to visually summarize conservation of sequence and relative level of responsiveness to p53 for 47 REs in 14 species. Individual REs exhibited marked differences in transactivation potentials and widespread evolutionary turnover. Functional differences were often not predicted from consensus sequence evaluations. Of the established human p53 REs analyzed, 91% had sequence conservation in at least one nonprimate species compared with 67.5% for functional conservation. Surprisingly, there was almost no conservation of functional REs for genes involved in DNA metabolism or repair between humans and rodents, suggesting important differences in p53 stress responses and cancer development. PMID:18187580

  1. Fungal prions.

    Science.gov (United States)

    Staniforth, Gemma L; Tuite, Mick F

    2012-01-01

    For both mammalian and fungal prion proteins, conformational templating drives the phenomenon of protein-only infectivity. The conformational conversion of a protein to its transmissible prion state is associated with changes to host cellular physiology. In mammals, this change is synonymous with disease, whereas in fungi no notable detrimental effect on the host is typically observed. Instead, fungal prions can serve as epigenetic regulators of inheritance in the form of partial loss-of-function phenotypes. In the presence of environmental challenges, the prion state [PRION(+)], with its resource for phenotypic plasticity, can be associated with a growth advantage. The growing number of yeast proteins that can switch to a heritable [PRION(+)] form represents diverse and metabolically penetrating cellular functions, suggesting that the [PRION(+)] state in yeast is a functional one, albeit rarely found in nature. In this chapter, we introduce the biochemical and genetic properties of fungal prions, many of which are shared by the mammalian prion protein PrP, and then outline the major contributions that studies on fungal prions have made to prion biology.

  2. Fungal Entomopathogens

    Science.gov (United States)

    Fungal entomopathogens are important biological control agents worldwide and have been the subject of intense research for more than100 years. They exhibit both sexual and asexual reproduction and produce different types of infective propagules. Their mode of action against insects involves attachme...

  3. Dominance hierarchy arising from the evolution of a complex small RNA regulatory network.

    Science.gov (United States)

    Durand, Eléonore; Méheust, Raphaël; Soucaze, Marion; Goubet, Pauline M; Gallina, Sophie; Poux, Céline; Fobis-Loisy, Isabelle; Guillon, Eline; Gaude, Thierry; Sarazin, Alexis; Figeac, Martin; Prat, Elisa; Marande, William; Bergès, Hélène; Vekemans, Xavier; Billiard, Sylvain; Castric, Vincent

    2014-12-05

    The prevention of fertilization through self-pollination (or pollination by a close relative) in the Brassicaceae plant family is determined by the genotype of the plant at the self-incompatibility locus (S locus). The many alleles at this locus exhibit a dominance hierarchy that determines which of the two allelic specificities of a heterozygous genotype is expressed at the phenotypic level. Here, we uncover the evolution of how at least 17 small RNA (sRNA)-producing loci and their multiple target sites collectively control the dominance hierarchy among alleles within the gene controlling the pollen S-locus phenotype in a self-incompatible Arabidopsis species. Selection has created a dynamic repertoire of sRNA-target interactions by jointly acting on sRNA genes and their target sites, which has resulted in a complex system of regulation among alleles. Copyright © 2014, American Association for the Advancement of Science.

  4. Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis.

    Science.gov (United States)

    Cao, Chensi; Xu, Jiajia; Zheng, Guangyong; Zhu, Xin-Guang

    2016-03-08

    C4 photosynthesis evolved from C3 photosynthesis and has higher light, water, and nitrogen use efficiencies. Several C4 photosynthesis genes show cell-specific expression patterns, which are required for these high resource-use efficiencies. However, the mechanisms underlying the evolution of cis-regulatory elements that control these cell-specific expression patterns remain elusive. In the present study, we tested the hypothesis that the cis-regulatory motifs related to C4 photosynthesis genes were recruited from non-photosynthetic genes and further examined potential mechanisms facilitating this recruitment. We examined 65 predicted bundle sheath cell-specific motifs, 17 experimentally validated cell-specific cis-regulatory elements, and 1,034 motifs derived from gene regulatory networks. Approximately 7, 5, and 1,000 of these three categories of motifs, respectively, were apparently recruited during the evolution of C4 photosynthesis. In addition, we checked 1) the distance between the acceptors and the donors of potentially recruited motifs in a chromosome, and 2) whether the potentially recruited motifs reside within the overlapping region of transposable elements and the promoter of donor genes. The results showed that 7, 4, and 658 of the potentially recruited motifs might have moved via the transposable elements. Furthermore, the potentially recruited motifs showed higher binding affinity to transcription factors compared to randomly generated sequences of the same length as the motifs. This study provides molecular evidence supporting the hypothesis that transposon-driven recruitment of pre-existing cis-regulatory elements from non-photosynthetic genes into photosynthetic genes plays an important role during C4 evolution. The findings of the present study coincide with the observed repetitive emergence of C4 during evolution.

  5. History of knowledge and evolution of occupational health and regulatory aspects of asbestos exposure science: 1900-1975.

    Science.gov (United States)

    Barlow, Christy A; Sahmel, Jennifer; Paustenbach, Dennis J; Henshaw, John L

    2017-04-01

    The understanding by industrial hygienists of the hazards of asbestos and appropriate ways to characterize and control exposure has evolved over the years. Here, a detailed analysis of the evolution of industrial hygiene practices regarding asbestos and its health risks, from the early 1900s until the advent of the national occupational health and safety regulatory structure currently in place in the US (early-to-mid 1970s) is presented. While industrial hygienists recognized in the early 1900s that chronic and high-level exposures to airborne concentrations of asbestos could pose a serious health hazard, it was not until the mid-1950s that the carcinogenic nature of asbestos began to be characterized and widespread concern followed. With the introduction of the membrane filter sampling method in the late 1960s and early 1970s, asbestos sampling and exposure assessment capabilities advanced to a degree which allowed industrial hygienists to more precisely characterize the exposure-response relationship. The ability of industrial hygienists, analytical chemists, toxicologists, and physicians to more accurately define this relationship was instrumental to the scientific community's ability to establish Occupational Exposure Levels (OELs) for asbestos. These early developments set the stage for decades of additional study on asbestos exposure potential and risk of disease. This was followed by the application of engineering controls and improved respiratory protection which, over the years, saved thousands of lives. This paper represents a state-of-the-art review of the knowledge of asbestos within the industrial hygiene community from about 1900 to 1975.

  6. The Cryptosporidium parvum ApiAP2 gene family: insights into the evolution of apicomplexan AP2 regulatory systems.

    Science.gov (United States)

    Oberstaller, Jenna; Pumpalova, Yoanna; Schieler, Ariel; Llinás, Manuel; Kissinger, Jessica C

    2014-07-01

    We provide the first comprehensive analysis of any transcription factor family in Cryptosporidium, a basal-branching apicomplexan that is the second leading cause of infant diarrhea globally. AP2 domain-containing proteins have evolved to be the major regulatory family in the phylum to the exclusion of canonical regulators. We show that apicomplexan and perkinsid AP2 domains cluster distinctly from other chromalveolate AP2s. Protein-binding specificity assays of C. parvum AP2 domains combined with motif conservation upstream of co-regulated gene clusters allowed the construction of putative AP2 regulons across the in vitro life cycle. Orthologous Apicomplexan AP2 (ApiAP2) expression has been rearranged relative to the malaria parasite P. falciparum, suggesting ApiAP2 network rewiring during evolution. C. hominis orthologs of putative C. parvum ApiAP2 proteins and target genes show greater than average variation. C. parvum AP2 domains display reduced binding diversity relative to P. falciparum, with multiple domains binding the 5'-TGCAT-3', 5'-CACACA-3' and G-box motifs (5'-G[T/C]GGGG-3'). Many overrepresented motifs in C. parvum upstream regions are not AP2 binding motifs. We propose that C. parvum is less reliant on ApiAP2 regulators in part because it utilizes E2F/DP1 transcription factors. C. parvum may provide clues to the ancestral state of apicomplexan transcriptional regulation, pre-AP2 domination. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation

    Directory of Open Access Journals (Sweden)

    Hogeweg Paulien

    2009-07-01

    Full Text Available Abstract Background Sexual reproduction has classically been considered as a barrier to the buildup of discrete phenotypic differentiation. This notion has been confirmed by models of sympatric speciation in which a fixed genetic architecture and a linear genotype phenotype mapping were assumed. In this paper we study the influence of a flexible genetic architecture and non-linear genotype phenotype map on differentiation under sexual reproduction. We use an individual based model in which organisms have a genome containing genes and transcription factor binding sites. Mutations involve single genes or binding sites or stretches of genome. The genome codes for a regulatory network that determines the gene expression pattern and hence the phenotype of the organism, resulting in a non-linear genotype phenotype map. The organisms compete in a multi-niche environment, imposing selection for phenotypic differentiation. Results We find as a generic outcome the evolution of discrete clusters of organisms adapted to different niches, despite random mating. Organisms from different clusters are distinct on the genotypic, the network and the phenotypic level. However, the genome and network differences are constrained to a subset of the genome locations, a process we call genotypic canalization. We demonstrate how this canalization leads to an increased robustness to recombination and increasing hybrid fitness. Finally, in case of assortative mating, we explain how this canalization increases the effectiveness of assortativeness. Conclusion We conclude that in case of a flexible genetic architecture and a non-linear genotype phenotype mapping, sexual reproduction does not constrain phenotypic differentiation, but instead constrains the genotypic differences underlying it. We hypothesize that, as genotypic canalization enables differentiation despite random mating and increases the effectiveness of assortative mating, sympatric speciation is more likely

  8. Fungal Eye Infections

    Science.gov (United States)

    ... Treatment & Outcomes Statistics More Resources Fungal Nail Infections Histoplasmosis Definition Symptoms People at Risk & Prevention Sources Diagnosis & ... CDC at Work Global Fungal Diseases Cryptococcal Meningitis Histoplasmosis ... Resistance Resources Laboratory Submission Information Reportable Fungal ...

  9. Creation of cis-regulatory elements during sea urchin evolution by co-option and optimization of a repetitive sequence adjacent to the spec2a gene.

    Science.gov (United States)

    Dayal, Sandeep; Kiyama, Takae; Villinski, Jeffrey T; Zhang, Ning; Liang, Shuguang; Klein, William H

    2004-09-15

    The creation, preservation, and degeneration of cis-regulatory elements controlling developmental gene expression are fundamental genome-level evolutionary processes about which little is known. Here, we identify critical differences in cis-regulatory elements controlling the expression of the sea urchin aboral ectoderm-specific spec genes. We found multiple copies of a repetitive sequence element termed RSR in genomes of species within the Strongylocentrotidae family, but RSRs were not detected in genomes of species outside Strongylocentrotidae. spec genes in Strongylocentrotus purpuratus are invariably associated with RSRs, and the spec2a RSR functioned as a transcriptional enhancer and displayed greater activity than did spec1 or spec2c RSRs. Single-base pair differences at two cis-regulatory elements within the spec2a RSR increased the binding affinities of four transcription factors, SpCCAAT-binding factor at one element and SpOtx, SpGoosecoid, and SpGATA-E at another. The cis-regulatory elements to which these four factors bound were recent evolutionary acquisitions that acted to either activate or repress transcription, depending on the cell type. These elements were found in the spec2a RSR ortholog in Strongylocentrotus pallidus but not in RSR orthologs of Strongylocentrotus droebachiensis or Hemicentrotus pulcherrimus. Our results indicated that a dynamic pattern of cis-regulatory element evolution exists for spec genes despite their conserved aboral ectoderm expression.

  10. The evolution of combinatorial gene regulation in fungi.

    OpenAIRE

    Tuch, Brian B.; Galgoczy, David J.; Hernday, Aaron D.; Hao Li; Johnson, Alexander D.

    2008-01-01

    It is widely suspected that gene regulatory networks are highly plastic. The rapid turnover of transcription factor binding sites has been predicted on theoretical grounds and has been experimentally demonstrated in closely related species. We combined experimental approaches with comparative genomics to focus on the role of combinatorial control in the evolution of a large transcriptional circuit in the fungal lineage. Our study centers on Mcm1, a transcriptional regulator that, in combinati...

  11. Analyses of fugu hoxa2 genes provide evidence for subfunctionalization of neural crest cell and rhombomere cis-regulatory modules during vertebrate evolution.

    Science.gov (United States)

    McEllin, Jennifer A; Alexander, Tara B; Tümpel, Stefan; Wiedemann, Leanne M; Krumlauf, Robb

    2016-01-15

    Hoxa2 gene is a primary player in regulation of craniofacial programs of head development in vertebrates. Here we investigate the evolution of a Hoxa2 neural crest enhancer identified originally in mouse by comparing and contrasting the fugu hoxa2a and hoxa2b genes with their orthologous teleost and mammalian sequences. Using sequence analyses in combination with transgenic regulatory assays in zebrafish and mouse embryos we demonstrate subfunctionalization of regulatory activity for expression in hindbrain segments and neural crest cells between these two fugu co-orthologs. hoxa2a regulatory sequences have retained the ability to mediate expression in neural crest cells while those of hoxa2b include cis-elements that direct expression in rhombomeres. Functional dissection of the neural crest regulatory potential of the fugu hoxa2a and hoxa2b genes identify the previously unknown cis-element NC5, which is implicated in generating the differential activity of the enhancers from these genes. The NC5 region plays a similar role in the ability of this enhancer to mediate reporter expression in mice, suggesting it is a conserved component involved in control of neural crest expression of Hoxa2 in vertebrate craniofacial development.

  12. Expression patterns of developmental regulatory genes show comparable divisions in the telencephalon of Xenopus and mouse: insights into the evolution of the forebrain.

    Science.gov (United States)

    Medina, Loreta; Brox, Aurora; Legaz, Isabel; García-López, Margarita; Puelles, Luis

    2005-09-15

    In this study, we review data on the existence of comparable divisions and subdivisions in the telencephalon of different groups of tetrapods based on expression of some developmental regulatory genes, having a particular focus in the comparison of the anuran amphibian Xenopus and the mouse. The available data on Xenopus, mouse, chick and turtle indicate that apparently all tetrapod groups possess the same molecularly distinct divisions and subdivisions in the telencephalon. This basic organization was likely present in the telencephalon of stem tetrapods. Each division/subdivision is characterized by expression of a unique combination of developmental regulatory genes, and appears to represent a self-regulated and topologically constant histogenetic brain compartment that gives rise to specific groups of cells. This interpretation has an important consequence for searching homologies, since a basic condition for cell groups in different vertebrates to be considered homologous is that they originate in the same compartment. However, evolution may allow individual cell groups derived from comparable (field homologous) subdivisions to be either similar or dissimilar across the vertebrate groups, giving rise to several possible scenarios of evolution, which include both the evolutionary conservation of similar (homologous) cells or the production of novel cell groups. Finally, available data in the lamprey, a jawless fish, suggest that not all telencephalic subdivisions were present at the origin of vertebrates, raising important questions about their evolution.

  13. From road to lab to math: the co-evolution of technological, regulatory, and organizational innovations for automotive crash testing.

    Science.gov (United States)

    Leonardi, Paul M

    2010-04-01

    Today, in the midst of economic crisis, senior executives at US automakers and influential industry analysts frequently reflect on the progression that safety testing has taken from the crude trials done on the road, to controlled laboratory experiments, and to today's complex math-based simulation models. They use stories of this seemingly linear and natural sequence to justify further investment in simulation technologies. The analysis presented in this paper shows that change in the structures of automakers' organizations co-evolved with regulations specifying who was at fault in vehicle impacts, how vehicles should be built to withstand the force of an impact, and how testing should be done to assure that vehicles met those requirements. Changes in the regulatory environment were bolstered by new theories about crash test dynamics and changing technologies with which to test those theories. Thus, as new technological and regulatory innovations co-evolved with innovations in organizational structuring, ideas about how to best conduct crash tests shifted and catalyzed new cycles of technological, regulatory, and organizational innovation. However, this co-evolutionary story tells us that the move from road to lab to math was not natural or linear as today's managerial rhetoric would have us believe. Rather, the logic of math-based simulation was the result of technological, regulatory and organizational changes that created an industry-wide ideology that supported the move toward math while making it appear natural within the shifting structure of the industry.

  14. More than 400 million years of evolution and some plants still can't make it on their own: Plant stress tolerance via fungal symbiosis

    Science.gov (United States)

    Rodriguez, R.; Redman, R.

    2008-01-01

    All plants in natural ecosystems are thought to be symbiotic with mycorrhizal and/or endophytic fungi. Collectively, these fungi express different symbiotic lifestyles ranging from parasitism to mutualism. Analysis of Colletotrichum species indicates that individual isolates can express either parasitic or mutualistic lifestyles depending on the host genotype colonized. The endophyte colonization pattern and lifestyle expression indicate that plants can be discerned as either disease, non-disease, or non-hosts. Fitness benefits conferred by fungi expressing mutualistic lifestyles include biotic and abiotic stress tolerance, growth enhancement, and increased reproductive success. Analysis of plant-endophyte associations in high stress habitats revealed that at least some fungal endophytes confer habitat-specific stress tolerance to host plants. Without the habitat-adapted fungal endophytes, the plants are unable to survive in their native habitats. Moreover, the endophytes have a broad host range encompassing both monocots and eudicots, and confer habitat-specific stress tolerance to both plant groups. ?? The Author [2008]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved.

  15. Entomopathogenic fungal endophytes

    Science.gov (United States)

    Fungal endophytes are quite common in nature and some of them have been shown to have adverse effects against insects, nematodes, and plant pathogens. An introduction to fungal endophytes will be presented, followed by a discussion of research aimed at introducing Beauveria bassiana as a fungal endo...

  16. A novel N-terminal motif is responsible for the evolution of neural crest-specific gene-regulatory activity in vertebrate FoxD3.

    Science.gov (United States)

    Ono, Hiroki; Kozmik, Zbynek; Yu, Jr-Kai; Wada, Hiroshi

    2014-01-15

    The neural crest is unique to vertebrates and has allowed the evolution of their complicated craniofacial structures. During vertebrate evolution, the acquisition of the neural crest must have been accompanied by the emergence of a new gene regulatory network (GRN). Here, to investigate the role of protein evolution in the emergence of the neural crest GRN, we examined the neural crest cell (NCC) differentiation-inducing activity of chordate FoxD genes. Amphioxus and vertebrate (Xenopus) FoxD proteins both exhibited transcriptional repressor activity in Gal4 transactivation assays and bound to similar DNA sequences in vitro. However, whereas vertebrate FoxD3 genes induced the differentiation of ectopic NCCs when overexpressed in chick neural tube, neither amphioxus FoxD nor any other vertebrate FoxD paralogs exhibited this activity. Experiments using chimeric proteins showed that the N-terminal portion of the vertebrate FoxD3 protein is critical to its NCC differentiation-inducing activity. Furthermore, replacement of the N-terminus of amphioxus FoxD with a 39-amino-acid segment from zebrafish FoxD3 conferred neural crest-inducing activity on amphioxus FoxD or zebrafish FoxD1. Therefore, fixation of this N-terminal amino acid sequence may have been crucial in the evolutionary recruitment of FoxD3 to the vertebrate neural crest GRN. © 2013 Published by Elsevier Inc.

  17. Fungal infection in organ transplant patients

    Institute of Scientific and Technical Information of China (English)

    洪微; 温海; 廖万清

    2003-01-01

    Purpose To review the characteristics and evolution of the fungal spectrum, and the risk factors causing fungal infection, and to make progress in diagnosing fungal infection after organ transplantation.Data sources An English-language literature search (MEDLINE 1990-2000) and bibliographic review of textbooks and review articles.Study selection Twenty-three articles were selected from the literature that specifically addressed the stated purpose.Results Fungal infections in organ transplant patients were generally divided into two types: ① disseminated primary or reactivation infection with one of the geographically restricted systemic mycoses; ② opportunistic infection by fungal species that rarely cause invasive infection in normal hosts. The risk factors of fungal infection after a transplant can be evaluated and predicted according to the organ recipient ’s conditions before, during and after the transplant. Progress in early diagnostic methods during the past 10 years has mainly revolved around two aspects, culture and non-culture. Conclusions It is important to undertake a systemic evaluation on the condition of the organ recipient before, during and after a transplant; should any risk factor for fungal infection be suspected, diagnosis should be made as early as possible by employing mycological techniques including culture and non-culture methods.

  18. The crucial role of the Pls1 tetraspanin during ascospore germination in Podospora anserina provides an example of the convergent evolution of morphogenetic processes in fungal plant pathogens and saprobes.

    Science.gov (United States)

    Lambou, Karine; Malagnac, Fabienne; Barbisan, Crystel; Tharreau, Didier; Lebrun, Marc-Henri; Silar, Philippe

    2008-10-01

    Pls1 tetraspanins were shown for some pathogenic fungi to be essential for appressorium-mediated penetration into their host plants. We show here that Podospora anserina, a saprobic fungus lacking appressorium, contains PaPls1, a gene orthologous to known PLS1 genes. Inactivation of PaPls1 demonstrates that this gene is specifically required for the germination of ascospores in P. anserina. These ascospores are heavily melanized cells that germinate under inducing conditions through a specific pore. On the contrary, MgPLS1, which fully complements a DeltaPaPls1 ascospore germination defect, has no role in the germination of Magnaporthe grisea nonmelanized ascospores but is required for the formation of the penetration peg at the pore of its melanized appressorium. P. anserina mutants with mutation of PaNox2, which encodes the NADPH oxidase of the NOX2 family, display the same ascospore-specific germination defect as the DeltaPaPls1 mutant. Both mutant phenotypes are suppressed by the inhibition of melanin biosynthesis, suggesting that they are involved in the same cellular process required for the germination of P. anserina melanized ascospores. The analysis of the distribution of PLS1 and NOX2 genes in fungal genomes shows that they are either both present or both absent. These results indicate that the germination of P. anserina ascospores and the formation of the M. grisea appressorium penetration peg use the same molecular machinery that includes Pls1 and Nox2. This machinery is specifically required for the emergence of polarized hyphae from reinforced structures such as appressoria and ascospores. Its recurrent recruitment during fungal evolution may account for some of the morphogenetic convergence observed in fungi.

  19. Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline.

    Directory of Open Access Journals (Sweden)

    Emily L Landeen

    2016-07-01

    Full Text Available The evolution of heteromorphic sex chromosomes has repeatedly resulted in the evolution of sex chromosome-specific forms of regulation, including sex chromosome dosage compensation in the soma and meiotic sex chromosome inactivation in the germline. In the male germline of Drosophila melanogaster, a novel but poorly understood form of sex chromosome-specific transcriptional regulation occurs that is distinct from canonical sex chromosome dosage compensation or meiotic inactivation. Previous work shows that expression of reporter genes driven by testis-specific promoters is considerably lower-approximately 3-fold or more-for transgenes inserted into X chromosome versus autosome locations. Here we characterize this transcriptional suppression of X-linked genes in the male germline and its evolutionary consequences. Using transgenes and transpositions, we show that most endogenous X-linked genes, not just testis-specific ones, are transcriptionally suppressed several-fold specifically in the Drosophila male germline. In wild-type testes, this sex chromosome-wide transcriptional suppression is generally undetectable, being effectively compensated by the gene-by-gene evolutionary recruitment of strong promoters on the X chromosome. We identify and experimentally validate a promoter element sequence motif that is enriched upstream of the transcription start sites of hundreds of testis-expressed genes; evolutionarily conserved across species; associated with strong gene expression levels in testes; and overrepresented on the X chromosome. These findings show that the expression of X-linked genes in the Drosophila testes reflects a balance between chromosome-wide epigenetic transcriptional suppression and long-term compensatory adaptation by sex-linked genes. Our results have broad implications for the evolution of gene expression in the Drosophila male germline and for genome evolution.

  20. Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline.

    Science.gov (United States)

    Landeen, Emily L; Muirhead, Christina A; Wright, Lori; Meiklejohn, Colin D; Presgraves, Daven C

    2016-07-01

    The evolution of heteromorphic sex chromosomes has repeatedly resulted in the evolution of sex chromosome-specific forms of regulation, including sex chromosome dosage compensation in the soma and meiotic sex chromosome inactivation in the germline. In the male germline of Drosophila melanogaster, a novel but poorly understood form of sex chromosome-specific transcriptional regulation occurs that is distinct from canonical sex chromosome dosage compensation or meiotic inactivation. Previous work shows that expression of reporter genes driven by testis-specific promoters is considerably lower-approximately 3-fold or more-for transgenes inserted into X chromosome versus autosome locations. Here we characterize this transcriptional suppression of X-linked genes in the male germline and its evolutionary consequences. Using transgenes and transpositions, we show that most endogenous X-linked genes, not just testis-specific ones, are transcriptionally suppressed several-fold specifically in the Drosophila male germline. In wild-type testes, this sex chromosome-wide transcriptional suppression is generally undetectable, being effectively compensated by the gene-by-gene evolutionary recruitment of strong promoters on the X chromosome. We identify and experimentally validate a promoter element sequence motif that is enriched upstream of the transcription start sites of hundreds of testis-expressed genes; evolutionarily conserved across species; associated with strong gene expression levels in testes; and overrepresented on the X chromosome. These findings show that the expression of X-linked genes in the Drosophila testes reflects a balance between chromosome-wide epigenetic transcriptional suppression and long-term compensatory adaptation by sex-linked genes. Our results have broad implications for the evolution of gene expression in the Drosophila male germline and for genome evolution.

  1. Plant Fungal Pathogens: Methods and Protocols

    NARCIS (Netherlands)

    Bolton, M.D.; Thomma, B.P.H.J.

    2012-01-01

    Over the course of evolution, fungi have adapted to occupy specific niches, from symbiotically inhabiting the flora of the intestinal tract of mammals to saprophytic growth on leaf litter resting on the forest floor. In Plant Fungal Pathogens: Methods and Protocols, expert researchers in the field d

  2. Major regulatory factors in the evolution of development: the roles of goosecoid and Msx in the evolution of the direct-developing sea urchin Heliocidaris erythrogramma.

    Science.gov (United States)

    Wilson, Keen A; Andrews, Mary E; Rudolf Turner, F; Raff, Rudolf A

    2005-01-01

    The transcription factors Gsc and Msx are expressed in the oral ectoderm of the indirect-developing sea urchin Heliocidaris tuberculata. Their patterns of expression are highly modified in the direct developer Heliocidaris erythrogramma, which lacks an oral ectoderm. We here test the hypothesis that they are large effect genes responsible for the loss of the oral ectoderm module in the direct-developing larva of H. erythrogramma as well as for the restoration of an overt oral ectoderm in H.e. xH.t. hybrids. We undertook misexpression/overexpression and knockdown assays in the two species and in hybrids by mRNA injection. The results indicate that dramatic changes of function of these transcription factors has occurred. One of these genes, Gsc, has the ability when misexpressed to partially restore oral ectoderm in H. erythrogramma. On the other hand, Msx has lost any oral function and instead has a role in mesoderm proliferation and patterning. In addition, we found that the H. tuberculataGsc is up regulated in H.e. xH.t. hybrids, showing a preferential use of the indirect developing parental gene in the development of the hybrid. We suggest that Gsc qualifies as a gene of large evolutionary effect and is partially responsible for the evolution of direct development of H. erythrogramma. We discuss these results in light of modularity and genetic networks in development, as well as in their implications for the rapid evolution of large morphological changes in development.

  3. Freshwater Fungal Infections

    Directory of Open Access Journals (Sweden)

    Dennis J. Baumgardner

    2017-01-01

    Full Text Available Fungal infections as a result of freshwater exposure or trauma are fortunately rare. Etiologic agents are varied, but commonly include filamentous fungi and Candida. This narrative review describes various sources of potential freshwater fungal exposure and the diseases that may result, including fungal keratitis, acute otitis externa and tinea pedis, as well as rare deep soft tissue or bone infections and pulmonary or central nervous system infections following traumatic freshwater exposure during natural disasters or near-drowning episodes. Fungal etiology should be suspected in appropriate scenarios when bacterial cultures or molecular tests are normal or when the infection worsens or fails to resolve with appropriate antibacterial therapy.

  4. Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters.

    Science.gov (United States)

    Zanni, Vanessa; Eymery, Angéline; Coiffet, Michael; Zytnicki, Matthias; Luyten, Isabelle; Quesneville, Hadi; Vaury, Chantal; Jensen, Silke

    2013-12-03

    Most of our understanding of Drosophila heterochromatin structure and evolution has come from the annotation of heterochromatin from the isogenic y; cn bw sp strain. However, almost nothing is known about the heterochromatin's structural dynamics and evolution. Here, we focus on a 180-kb heterochromatic locus producing Piwi-interacting RNAs (piRNA cluster), the flamenco (flam) locus, known to be responsible for the control of at least three transposable elements (TEs). We report its detailed structure in three different Drosophila lines chosen according to their capacity to repress or not to repress the expression of two retrotransposons named ZAM and Idefix, and we show that they display high structural diversity. Numerous rearrangements due to homologous and nonhomologous recombination, deletions and segmental duplications, and loss and gain of TEs are diverse sources of active genomic variation at this locus. Notably, we evidence a correlation between the presence of ZAM and Idefix in this piRNA cluster and their silencing. They are absent from flam in the strain where they are derepressed. We show that, unexpectedly, more than half of the flam locus results from recent TE insertions and that most of the elements concerned are prone to horizontal transfer between species of the melanogaster subgroup. We build a model showing how such high and constant dynamics of a piRNA master locus open the way to continual emergence of new patterns of piRNA biogenesis leading to changes in the level of transposition control.

  5. Patterns of fungal diversity and composition along a salinity gradient

    Science.gov (United States)

    Mohamed, Devon J; Martiny, Jennifer BH

    2011-01-01

    Estuarine salinity gradients are known to influence plant, bacterial and archaeal community structure. We sequenced 18S rRNA genes to investigate patterns in sediment fungal diversity (richness and evenness of taxa) and composition (taxonomic and phylogenetic) along an estuarine salinity gradient. We sampled three marshes—a salt, brackish and freshwater marsh—in Rhode Island. To compare the relative effect of the salinity gradient with that of plants, we sampled fungi in plots with Spartina patens and in plots from which plants were removed 2 years prior to sampling. The fungal sediment community was unique compared with previously sampled fungal communities; we detected more Ascomycota (78%), fewer Basidiomycota (6%) and more fungi from basal lineages (16%) (Chytridiomycota, Glomeromycota and four additional groups) than typically found in soil. Across marshes, fungal composition changed substantially, whereas fungal diversity differed only at the finest level of genetic resolution, and was highest in the intermediate, brackish marsh. In contrast, the presence of plants had a highly significant effect on fungal diversity at all levels of genetic resolution, but less of an effect on fungal composition. These results suggest that salinity (or other covarying parameters) selects for a distinctive fungal composition, and plants provide additional niches upon which taxa within these communities can specialize and coexist. Given the number of sequences from basal fungal lineages, the study also suggests that further sampling of estuarine sediments may help in understanding early fungal evolution. PMID:20882058

  6. Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1.

    Directory of Open Access Journals (Sweden)

    Zabrina L Brumme

    2007-07-01

    Full Text Available Despite the formidable mutational capacity and sequence diversity of HIV-1, evidence suggests that viral evolution in response to specific selective pressures follows generally predictable mutational pathways. Population-based analyses of clinically derived HIV sequences may be used to identify immune escape mutations in viral genes; however, prior attempts to identify such mutations have been complicated by the inability to discriminate active immune selection from virus founder effects. Furthermore, the association between mutations arising under in vivo immune selection and disease progression for highly variable pathogens such as HIV-1 remains incompletely understood. We applied a viral lineage-corrected analytical method to investigate HLA class I-associated sequence imprinting in HIV protease, reverse transcriptase (RT, Vpr, and Nef in a large cohort of chronically infected, antiretrovirally naïve individuals. A total of 478 unique HLA-associated polymorphisms were observed and organized into a series of "escape maps," which identify known and putative cytotoxic T lymphocyte (CTL epitopes under selection pressure in vivo. Our data indicate that pathways to immune escape are predictable based on host HLA class I profile, and that epitope anchor residues are not the preferred sites of CTL escape. Results reveal differential contributions of immune imprinting to viral gene diversity, with Nef exhibiting far greater evidence for HLA class I-mediated selection compared to other genes. Moreover, these data reveal a significant, dose-dependent inverse correlation between HLA-associated polymorphisms and HIV disease stage as estimated by CD4(+ T cell count. Identification of specific sites and patterns of HLA-associated polymorphisms across HIV protease, RT, Vpr, and Nef illuminates regions of the genes encoding these products under active immune selection pressure in vivo. The high density of HLA-associated polymorphisms in Nef compared to other

  7. Regulation of the fungal secretome.

    Science.gov (United States)

    McCotter, Sean W; Horianopoulos, Linda C; Kronstad, James W

    2016-08-01

    The ability of countless representatives of the Kingdom Fungi to adapt to and proliferate in diverse environments is facilitated by regulation of their secretomes to respond to changes in environmental conditions and to mediate interactions with other organisms. Secretome changes often fulfill common functions of nutrient acquisition, facilitation of host/symbiont interactions, cell wall modification, and optimization of the enzyme suite to adapt to new environmental resources. In this review, we expand on our recent work on signaling and the secretome in the pathogenic fungus Cryptococcus neoformans to consider a range of selected examples of regulation of fungal secretomes. These examples include the impact of carbon source and aspects of the response to plant and animal hosts. Additionally, the influence of key protein kinases (e.g., Pka1, Snf1) and transcription factors (e.g., Rim101/PacC) is highlighted to illustrate some underlying regulatory factors influencing the secretome. Although there is a wealth of information about fungal secretomes from both experimentation and genome sequence mining, there are also major gaps in our knowledge about the complete composition of fungal secretomes and mechanisms of dynamic change. For example, a more comprehensive understanding of the composition and regulation of the secretome will require consideration of the emerging roles of unconventional secretion and extracellular vesicles in delivering proteins outside the cell. Overall, changes in the secretome are well documented in diverse fungi and the underlying mechanisms are currently under investigation; however, there remain unknown steps in the regulation of secretory pathways and gaps in understanding the regulation of unconventional secretion, which warrant further research.

  8. Evolutionary and structural diversity of fungal laccases.

    Science.gov (United States)

    Valderrama, Brenda; Oliver, Patricia; Medrano-Soto, Arturo; Vazquez-Duhalt, Rafael

    2003-01-01

    Fungal laccases have been extensively exploited for industrial purposes and there is a wealth of information available regarding their reaction mechanism, biological role and several molecular aspects, including cloning, heterologous expression and transcriptional analyses. Here we present the reconstruction of the fungal laccase loci evolution inferred from the comparative analysis of 48 different sequences. The topology of the phylogenetic trees indicate that a single monophyletic branch exists for fungal laccases and that laccase isozyme genes may have evolved independently, possibly through duplication-divergence events. Laccases are copper-containing enzymes generally identified by the utilization of substituted p-diphenol substrates. Interestingly, our approach permitted the assignment of two copper-containing oxidases, preliminarily catalogued as laccases, to a different evolutionary group, distantly related to the main branch of bona fide laccases.

  9. The Case of the Missing Ancient Fungal Polyploids.

    Science.gov (United States)

    Campbell, Matthew A; Ganley, Austen R D; Gabaldón, Toni; Cox, Murray P

    2016-12-01

    Polyploidy-the increase in the number of whole chromosome sets-is an important evolutionary force in eukaryotes. Polyploidy is well recognized throughout the evolutionary history of plants and animals, where several ancient events have been hypothesized to be drivers of major evolutionary radiations. However, fungi provide a striking contrast: while numerous recent polyploids have been documented, ancient fungal polyploidy is virtually unknown. We present a survey of known fungal polyploids that confirms the absence of ancient fungal polyploidy events. Three hypotheses may explain this finding. First, ancient fungal polyploids are indeed rare, with unique aspects of fungal biology providing similar benefits without genome duplication. Second, fungal polyploids are not successful in the long term, leading to few extant species derived from ancient polyploidy events. Third, ancient fungal polyploids are difficult to detect, causing the real contribution of polyploidy to fungal evolution to be underappreciated. We consider each of these hypotheses in turn and propose that failure to detect ancient events is the most likely reason for the lack of observed ancient fungal polyploids. We examine whether existing data can provide evidence for previously unrecognized ancient fungal polyploidy events but discover that current resources are too limited. We contend that establishing whether unrecognized ancient fungal polyploidy events exist is important to ascertain whether polyploidy has played a key role in the evolution of the extensive complexity and diversity observed in fungi today and, thus, whether polyploidy is a driver of evolutionary diversifications across eukaryotes. Therefore, we conclude by suggesting ways to test the hypothesis that there are unrecognized polyploidy events in the deep evolutionary history of the fungi.

  10. Phylogenetic Distribution of Fungal Sterols

    Science.gov (United States)

    Weete, John D.; Abril, Maritza; Blackwell, Meredith

    2010-01-01

    Background Ergosterol has been considered the “fungal sterol” for almost 125 years; however, additional sterol data superimposed on a recent molecular phylogeny of kingdom Fungi reveals a different and more complex situation. Methodology/Principal Findings The interpretation of sterol distribution data in a modern phylogenetic context indicates that there is a clear trend from cholesterol and other Δ5 sterols in the earliest diverging fungal species to ergosterol in later diverging fungi. There are, however, deviations from this pattern in certain clades. Sterols of the diverse zoosporic and zygosporic forms exhibit structural diversity with cholesterol and 24-ethyl -Δ5 sterols in zoosporic taxa, and 24-methyl sterols in zygosporic fungi. For example, each of the three monophyletic lineages of zygosporic fungi has distinctive major sterols, ergosterol in Mucorales, 22-dihydroergosterol in Dimargaritales, Harpellales, and Kickxellales (DHK clade), and 24-methyl cholesterol in Entomophthorales. Other departures from ergosterol as the dominant sterol include: 24-ethyl cholesterol in Glomeromycota, 24-ethyl cholest-7-enol and 24-ethyl-cholesta-7,24(28)-dienol in rust fungi, brassicasterol in Taphrinales and hypogeous pezizalean species, and cholesterol in Pneumocystis. Conclusions/Significance Five dominant end products of sterol biosynthesis (cholesterol, ergosterol, 24-methyl cholesterol, 24-ethyl cholesterol, brassicasterol), and intermediates in the formation of 24-ethyl cholesterol, are major sterols in 175 species of Fungi. Although most fungi in the most speciose clades have ergosterol as a major sterol, sterols are more varied than currently understood, and their distribution supports certain clades of Fungi in current fungal phylogenies. In addition to the intellectual importance of understanding evolution of sterol synthesis in fungi, there is practical importance because certain antifungal drugs (e.g., azoles) target reactions in the synthesis of

  11. Phylogenetic distribution of fungal sterols.

    Directory of Open Access Journals (Sweden)

    John D Weete

    Full Text Available BACKGROUND: Ergosterol has been considered the "fungal sterol" for almost 125 years; however, additional sterol data superimposed on a recent molecular phylogeny of kingdom Fungi reveals a different and more complex situation. METHODOLOGY/PRINCIPAL FINDINGS: The interpretation of sterol distribution data in a modern phylogenetic context indicates that there is a clear trend from cholesterol and other Delta(5 sterols in the earliest diverging fungal species to ergosterol in later diverging fungi. There are, however, deviations from this pattern in certain clades. Sterols of the diverse zoosporic and zygosporic forms exhibit structural diversity with cholesterol and 24-ethyl -Delta(5 sterols in zoosporic taxa, and 24-methyl sterols in zygosporic fungi. For example, each of the three monophyletic lineages of zygosporic fungi has distinctive major sterols, ergosterol in Mucorales, 22-dihydroergosterol in Dimargaritales, Harpellales, and Kickxellales (DHK clade, and 24-methyl cholesterol in Entomophthorales. Other departures from ergosterol as the dominant sterol include: 24-ethyl cholesterol in Glomeromycota, 24-ethyl cholest-7-enol and 24-ethyl-cholesta-7,24(28-dienol in rust fungi, brassicasterol in Taphrinales and hypogeous pezizalean species, and cholesterol in Pneumocystis. CONCLUSIONS/SIGNIFICANCE: Five dominant end products of sterol biosynthesis (cholesterol, ergosterol, 24-methyl cholesterol, 24-ethyl cholesterol, brassicasterol, and intermediates in the formation of 24-ethyl cholesterol, are major sterols in 175 species of Fungi. Although most fungi in the most speciose clades have ergosterol as a major sterol, sterols are more varied than currently understood, and their distribution supports certain clades of Fungi in current fungal phylogenies. In addition to the intellectual importance of understanding evolution of sterol synthesis in fungi, there is practical importance because certain antifungal drugs (e.g., azoles target reactions in

  12. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  13. Fungal DNA barcoding.

    Science.gov (United States)

    Xu, Jianping

    2016-11-01

    Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.

  14. Fungal arthritis and osteomyelitis.

    Science.gov (United States)

    Kohli, Rakhi; Hadley, Susan

    2005-12-01

    Fungal arthritis and osteomyelitis are uncommon diseases and generally present in an indolent fashion. The incidence of fungal bone and joint dis-ease is increasing with an increase in the prevalence of factors predisposing to invasive fungal disease, such as the use of central venous catheters, broad spectrum antibiotics, immunosuppression, and abdominal surgery. Definitive diagnosis relies on bone or synovial culture or biopsy. Successful management has traditionally consisted of amphotericin B in combination with surgical debridement. Given the rarity of this disease, treatment is not well defined, but reports of success with the use of azole antifungal agents, including itraconazole, fluconazole, voriconazole, and posaconazole, are promising.

  15. Asexual reproduction induces a rapid and permanent loss of sexual reproduction capacity in the rice fungal pathogen Magnaporthe oryzae: results of in vitro experimental evolution assays

    Directory of Open Access Journals (Sweden)

    Saleh Dounia

    2012-03-01

    Full Text Available Abstract Background Sexual reproduction is common in eukaryotic microorganisms, with few species reproducing exclusively asexually. However, in some organisms, such as fungi, asexual reproduction alternates with episodic sexual reproduction events. Fungi are thus appropriate organisms for studies of the reasons for the selection of sexuality or clonality and of the mechanisms underlying this selection. Magnaporthe oryzae, an Ascomycete causing blast disease on rice, reproduces mostly asexually in natura. Sexual reproduction is possible in vitro and requires (i two strains of opposite mating types including (ii at least one female-fertile strain (i.e. a strain able to produce perithecia, the female organs in which meiosis occurs. Female-fertile strains are found only in limited areas of Asia, in which evidence for contemporary recombination has recently been obtained. We induced the forced evolution of four Chinese female-fertile strains in vitro by the weekly transfer of asexual spores (conidia between Petri dishes. We aimed to determine whether female fertility was rapidly lost in the absence of sexual reproduction and whether this loss was controlled genetically or epigenetically. Results All the strains became female-sterile after 10 to 19 rounds of selection under asexual conditions. As no single-spore isolation was carried out, the observed decrease in the production of perithecia reflected the emergence and the invasion of female-sterile mutants. The female-sterile phenotype segregated in the offspring of crosses between female-sterile evolved strains and female-fertile wild-type strains. This segregation was maintained in the second generation in backcrosses. Female-sterile evolved strains were subjected to several stresses, but none induced the restoration of female fertility. This loss of fertility was therefore probably due to genetic rather than epigenetic mechanisms. In competition experiments, female-sterile mutants produced similar

  16. Insect pathology and fungal entomopathogens

    Science.gov (United States)

    Fungi that occur inside asymptomatic plant tissues are known as fungal endophytes. Different genera of fungal entomopathogens have been reported as naturally occurring fungal endophytes, and it has been shown that it is possible to inoculate plants with fungal entomopathogens, making them endophytic...

  17. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi 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 50 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

  18. Regulatory agencies and regulatory risk

    OpenAIRE

    Knieps, Günter; Weiß, Hans-Jörg

    2007-01-01

    The aim of this paper is to show that regulatory risk is due to the discretionary behaviour of regulatory agencies, caused by a too extensive regulatory mandate provided by the legislator. The normative point of reference and a behavioural model of regulatory agencies based on the positive theory of regulation are presented. Regulatory risk with regard to the future behaviour of regulatory agencies is modelled as the consequence of the ex ante uncertainty about the relative influence of inter...

  19. [Pathogenesis of invasive fungal infections].

    Science.gov (United States)

    Garcia-Vidal, Carolina; Carratalà, Jordi

    2012-03-01

    Invasive fungal infections remain a life-threatening disease. The development of invasive fungal disease is dependent on multiple factors, such us colonization and efficient host immune response. We aimed to review the pathogenesis of invasive fungal infections, in particular, those caused by Candida and Aspergillus. For this we propose, to describe the fungal characteristics, to detail the host defence mechanisms against fungus and to analyse the host risk factors for invasive fungal infection.

  20. Fungal endocarditis: current challenges.

    Science.gov (United States)

    Tattevin, Pierre; Revest, Matthieu; Lefort, Agnès; Michelet, Christian; Lortholary, Olivier

    2014-10-01

    Whilst it used to affect mostly intravenous drug users and patients who underwent valvular surgery with suboptimal infection control procedures, fungal endocarditis is now mostly observed in patients with severe immunodeficiency (onco-haematology), in association with chronic central venous access and broad-spectrum antibiotic use. The incidence of fungal endocarditis has probably decreased in most developed countries with access to harm-reduction policies (i.e. needle exchange programmes) and with improved infection control procedures during cardiac surgery. Use of specific blood culture bottles for diagnosis of fungal endocarditis has decreased due to optimisation of media and automated culture systems. Meanwhile, the advent of rapid techniques, including fungal antigen detection (galactomannan, mannan/anti-mannan antibodies and β-1,3-d-glucans) and PCR (e.g. universal fungal PCR targeting 18S rRNA genes), shall improve sensitivity and reduce diagnostics delays, although limited data are available on their use for the diagnosis of fungal endocarditis. New antifungal agents available since the early 2000s may represent dramatic improvement for fungal endocarditis: (i) a new class, the echinocandins, has the potential to improve the management of Candida endocarditis owing to its fungicidal effect on yeasts as well as tolerability of increased dosages; and (ii) improved survival in patients with invasive aspergillosis with voriconazole compared with amphotericin B, and this may apply to Aspergillus sp. endocarditis as well, although its prognosis remains dismal. These achievements may allow selected patients to be cured with prolonged medical treatment alone when surgery is considered too risky.

  1. Immune response to fungal infections.

    Science.gov (United States)

    Blanco, Jose L; Garcia, Marta E

    2008-09-15

    The immune mechanisms of defence against fungal infections are numerous, and range from protective mechanisms that were present early in evolution (innate immunity) to sophisticated adaptive mechanisms that are induced specifically during infection and disease (adaptive immunity). The first-line innate mechanism is the presence of physical barriers in the form of skin and mucous membranes, which is complemented by cell membranes, cellular receptors and humoral factors. There has been a debate about the relative contribution of humoral and cellular immunity to host defence against fungal infections. For a long time it was considered that cell-mediated immunity (CMI) was important, but humoral immunity had little or no role. However, it is accepted now that CMI is the main mechanism of defence, but that certain types of antibody response are protective. In general, Th1-type CMI is required for clearance of a fungal infection, while Th2 immunity usually results in susceptibility to infection. Aspergillosis, which is a disease caused by the fungus Aspergillus, has been the subject of many studies, including details of the immune response. Attempts to relate aspergillosis to some form of immunosuppression in animals, as is the case with humans, have not been successful to date. The defence against Aspergillus is based on recognition of the pathogen, a rapidly deployed and highly effective innate effector phase, and a delayed but robust adaptive effector phase. Candida albicans, part of the normal microbial flora associated with mucous surfaces, can be present as congenital candidiasis or as acquired defects of cell-mediated immunity. Resistance to this yeast is associated with Th1 CMI, whereas Th2 immunity is associated with susceptibility to systemic infection. Dermatophytes produce skin alterations in humans and other animals, and the essential role of the CMI response is to destroy the fungi and produce an immunoprotective status against re-infection. The resolution

  2. Fungal Systematics and Evolution: FUSE 2

    NARCIS (Netherlands)

    Hernández-Restrepo, Margarita; Schumacher, René K.; Wingfield, Michael J.; Ahmad, Ishtiaq; Cai, Lei; Duong, Tuan A.; Edwards, Jacqueline; Gené, Josepa; Groenewald, Johannes Z.; Jabeen, Sana; Nasir Khalid, Abdul; Lombard, Lorenzo; Madrid, Hugo; Marin-Felix, Yasmina; Marincowitz, Seonju; Miller, Andrew N.; Rajeshkumar, Kunhiraman C.; Rashid, Abdul; Sarwar, Samina; Stchigel, Alberto M.; Taylor, Paul W.J.; Zhou, Nan; Crous, Pedro W.

    2016-01-01

    The present study introduces two new genera, 14 new species, five new combinations and 12 interesting host and/or geographical records. A majority of the fungi are Ascomycetes, but the study also includes a Basidiomycete, Xerocomellus fulvus described from Pakistan. Under single name nomenclature Ze

  3. Allergic Fungal Rhinosinusitis.

    Science.gov (United States)

    Hoyt, Alice E W; Borish, Larry; Gurrola, José; Payne, Spencer

    2016-01-01

    This article reviews the history of allergic fungal rhinosinusitis and the clinical, pathologic, and radiographic criteria necessary to establish its diagnosis and differentiate this disease from other types of chronic rhinosinusitis. Allergic fungal rhinosinusitis is a noninvasive fungal form of sinus inflammation characterized by an often times unilateral, expansile process in which the typical allergic "peanut-butter-like" mucin contributes to the formation of nasal polyps, hyposmia/anosmia, and structural changes of the face. IgE sensitization to fungi is a necessary, but not sufficient, pathophysiologic component of the disease process that is also defined by microscopic visualization of mucin-containing fungus and characteristic radiological imaging. This article expounds on these details and others including the key clinical and scientific distinctions of this diagnosis, the pathophysiologic mechanisms beyond IgE-mediated hypersensitivity that must be at play, and areas of current and future research.

  4. 50-plus years of fungal viruses

    Energy Technology Data Exchange (ETDEWEB)

    Ghabrial, Said A., E-mail: saghab00@email.uky.edu [Plant Pathology Department, University of Kentucky, Lexington, KY (United States); Castón, José R. [Department of Structure of Macromolecules, Centro Nacional Biotecnologıa/CSIC, Campus de Cantoblanco, Madrid (Spain); Jiang, Daohong [State Key Lab of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province (China); Nibert, Max L. [Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA (United States); Suzuki, Nobuhiro [Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama (Japan)

    2015-05-15

    Mycoviruses are widespread in all major taxa of fungi. They are transmitted intracellularly during cell division, sporogenesis, and/or cell-to-cell fusion (hyphal anastomosis), and thus their life cycles generally lack an extracellular phase. Their natural host ranges are limited to individuals within the same or closely related vegetative compatibility groups, although recent advances have established expanded experimental host ranges for some mycoviruses. Most known mycoviruses have dsRNA genomes packaged in isometric particles, but an increasing number of positive- or negative-strand ssRNA and ssDNA viruses have been isolated and characterized. Although many mycoviruses do not have marked effects on their hosts, those that reduce the virulence of their phytopathogenic fungal hosts are of considerable interest for development of novel biocontrol strategies. Mycoviruses that infect endophytic fungi and those that encode killer toxins are also of special interest. Structural analyses of mycoviruses have promoted better understanding of virus assembly, function, and evolution. - Highlights: • Historical perspective of fungal virus research. • Description, classification and diversity of fungal virus families. • Structural features of fungal virus particles. • Hypovirulence and exploitation of mycoviruses in biological control of plant pathogenic fungi.

  5. Fungal Wound Infection

    Centers for Disease Control (CDC) Podcasts

    2016-01-28

    Dr. David Tribble, acting director of the infectious disease clinical research program at Uniformed Services University of the Health Sciences, discusses fungal wound infections after combat trauma.  Created: 1/28/2016 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 1/28/2016.

  6. Fungal pathogens of Proteaceae

    NARCIS (Netherlands)

    Crous, P.W.; Summerell, B.A.; Swart, L.; Denman, S.; Taylor, J.E.; Bezuidenhout, C.M.; Palm, M.E.; Marincowitz, S.; Groenewald, J.Z.

    2011-01-01

    Species of Leucadendron, Leucospermum and Protea (Proteaceae) are in high demand for the international floriculture market due to their brightly coloured and textured flowers or bracts. Fungal pathogens, however, create a serious problem in cultivating flawless blooms. The aim of the present study

  7. Fungal pathogens of Proteaceae

    NARCIS (Netherlands)

    Crous, P.W.; Summerell, B.A.; Swart, L.; Denman, S.; Taylor, J.E.; Bezuidenhout, C.M.; Palm, M.E.; Marincowitz, S.; Groenewald, J.Z.

    2012-01-01

    Species of Leucadendron, Leucospermum and Protea (Proteaceae) are in high demand for the international floriculture market due to their brightly coloured and textured flowers or bracts. Fungal pathogens, however, create a serious problem in cultivating flawless blooms. The aim of the present study

  8. The vertebrate Hox gene regulatory network for hindbrain segmentation: Evolution and diversification: Coupling of a Hox gene regulatory network to hindbrain segmentation is an ancient trait originating at the base of vertebrates.

    Science.gov (United States)

    Parker, Hugo J; Bronner, Marianne E; Krumlauf, Robb

    2016-06-01

    Hindbrain development is orchestrated by a vertebrate gene regulatory network that generates segmental patterning along the anterior-posterior axis via Hox genes. Here, we review analyses of vertebrate and invertebrate chordate models that inform upon the evolutionary origin and diversification of this network. Evidence from the sea lamprey reveals that the hindbrain regulatory network generates rhombomeric compartments with segmental Hox expression and an underlying Hox code. We infer that this basal feature was present in ancestral vertebrates and, as an evolutionarily constrained developmental state, is fundamentally important for patterning of the vertebrate hindbrain across diverse lineages. Despite the common ground plan, vertebrates exhibit neuroanatomical diversity in lineage-specific patterns, with different vertebrates revealing variations of Hox expression in the hindbrain that could underlie this diversification. Invertebrate chordates lack hindbrain segmentation but exhibit some conserved aspects of this network, with retinoic acid signaling playing a role in establishing nested domains of Hox expression. © 2016 WILEY Periodicals, Inc.

  9. 我国三网融合管制政策演进路径探析%Evolution Path of Regulatory Policy of Tri-networks Convergence in China

    Institute of Scientific and Technical Information of China (English)

    严奇春; 和金生

    2012-01-01

    Tri-networks convergence, affected greatly by the effective government regulation, is an important step in achieving the strategy of the next -generation information technology industry. At the same time, some testing activities about tri -networks convergence have begun in our country. It is worthy study to explore some theoretical and practical experience and constitute corresponding regulatory policy about tri-networks convergence, in line with our current conditions, for the sake of promoting and facilitating triple play effectively. Therefore, this paper makes some recommendations about the regulatory policies with an evolution path of three-stage, from regulatory by industry, regulatory by functions to integration regulatory, combining some industries fusion theories, the successfully foreign experience in the regulation of the of tri-networks convergence and our conditions.%三网融合是实现新一代信息技术产业战略的重要一步,而政府的有效管制对其发展影响甚大,所以针对我国目前已经开始试点的三网融合,如何从理论上和实践上探索经验,制定符合我国国情的管制政策,有效地推进和促进三网融合,就值得研究.为此,本文结合相关产业融合理论,并借鉴国外三网融合成功的管制经验,结合我国实际,提出分业监管、分段监管和融合监管三阶段演进的管制政策建议.

  10. [Clinically documented fungal infections].

    Science.gov (United States)

    Kakeya, Hiroshi; Kohno, Shigeru

    2008-12-01

    Proven fungal infections are diagnosed by histological/microbiological evidence of fungi at the site of infection and positive blood culture (fungemia). However, invasive diagnosing examinations are not always applied for all of immunocompromised patients. Clinically documented invasive fungal infections are diagnosed by typical radiological findings such as halo sign on chest CT plus positive serological/molecular evidence of fungi. Serological tests of Aspergillus galactomannan antigen and beta-glucan for aspergillosis and cryptococcal glucuronoxylomannan antigen for cryptococcosis are useful. Hence, none of reliable serological tests for zygomycosis are available so far. In this article, risk factors, sign and symptoms, and diagnostic methods for clinically documented cases of invasive aspergillosis, pulmonary cryptococcosis, and zygomycosis with diabates, are reviewed.

  11. An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns.

    Directory of Open Access Journals (Sweden)

    Murray P Cox

    2014-03-01

    Full Text Available Polyploidy, a state in which the chromosome complement has undergone an increase, is a major force in evolution. Understanding the consequences of polyploidy has received much attention, and allopolyploids, which result from the union of two different parental genomes, are of particular interest because they must overcome a suite of biological responses to this merger, known as "genome shock." A key question is what happens to gene expression of the two gene copies following allopolyploidization, but until recently the tools to answer this question on a genome-wide basis were lacking. Here we utilize high throughput transcriptome sequencing to produce the first genome-wide picture of gene expression response to allopolyploidy in fungi. A novel pipeline for assigning sequence reads to the gene copies was used to quantify their expression in a fungal allopolyploid. We find that the transcriptional response to allopolyploidy is predominantly conservative: both copies of most genes are retained; over half the genes inherit parental gene expression patterns; and parental differential expression is often lost in the allopolyploid. Strikingly, the patterns of gene expression change are highly concordant with the genome-wide expression results of a cotton allopolyploid. The very different nature of these two allopolyploids implies a conserved, eukaryote-wide transcriptional response to genome merger. We provide evidence that the transcriptional responses we observe are mostly driven by intrinsic differences between the regulatory systems in the parent species, and from this propose a mechanistic model in which the cross-kingdom conservation in transcriptional response reflects conservation of the mutational processes underlying eukaryotic gene regulatory evolution. This work provides a platform to develop a universal understanding of gene expression response to allopolyploidy and suggests that allopolyploids are an exceptional system to investigate gene

  12. A Disequilibrium Analysis of Evolution of Financial Regulatory System in China and its Policy Meaning%我国金融监管制度演进的非均衡分析及其政策含义

    Institute of Scientific and Technical Information of China (English)

    仲伟周; 任炳群; 张金城

    2012-01-01

    我国金融监管制度在变迁过程中,存在金融创新与市场约束等市场监管制度供给不足和市场准入、业务运营及市场退出等行政监管制度供给过剩的问题。我国金融监管制度是控制性金融监管制度,而需求主导型变迁尚未形成,政府主导型强制性制度变迁模式易引致金融监管制度供需的非均衡。要实现金融监管制度供给、需求的均衡,仅从供给和需求的单方面改进无法实现,这就必须寻求第三条道路:既要有供给的适当超前性,也要满足市场监管的需求,走供给拉动和需求推动的金融监管演进路径。%In the process of changes of financial regulatory system in China, there exist prob- lems of supply shortage of financial innovation and market constraints and supply surplus of such administrative regulatory system problems as market access, business operations and market with- drawal. In China, financial regulatory system is controlled financial regulatory system, and de- mand-oriented transformation has not been formed. Mandatory government-oriented model of insti- tutional change can easily cause supply and demand non-equilibrium of financial regulatory system. To achieve a supply and demand balance of financial regulatory system, it can not be achieved sim- ply by the improvement of supply and demand. We must find a third way, which not only has an appropriate and advanced supply, but also can meet the needs of market supervision, taking the path of financial regulatory evolution that promoting the supply and demand.

  13. Fungal osteomyelitis and septic arthritis.

    Science.gov (United States)

    Bariteau, Jason T; Waryasz, Gregory R; McDonnell, Matthew; Fischer, Staci A; Hayda, Roman A; Born, Christopher T

    2014-06-01

    Management of fungal osteomyelitis and fungal septic arthritis is challenging, especially in the setting of immunodeficiency and conditions that require immunosuppression. Because fungal osteomyelitis and fungal septic arthritis are rare conditions, study of their pathophysiology and treatment has been limited. In the literature, evidence-based treatment is lacking and, historically, outcomes have been poor. The most common offending organisms are Candida and Aspergillus, which are widely distributed in humans and soil. However, some fungal pathogens, such as Histoplasma, Blastomyces, Coccidioides, Cryptococcus, and Sporothrix, have more focal areas of endemicity. Fungal bone and joint infections result from direct inoculation, contiguous infection spread, or hematogenous seeding of organisms. These infections may be difficult to diagnose and eradicate, especially in the setting of total joint arthroplasty. Although there is no clear consensus on treatment, guidelines are available for management of many of these pathogens.

  14. Fungal biodiversity to biotechnology.

    Science.gov (United States)

    Chambergo, Felipe S; Valencia, Estela Y

    2016-03-01

    Fungal habitats include soil, water, and extreme environments. With around 100,000 fungus species already described, it is estimated that 5.1 million fungus species exist on our planet, making fungi one of the largest and most diverse kingdoms of eukaryotes. Fungi show remarkable metabolic features due to a sophisticated genomic network and are important for the production of biotechnological compounds that greatly impact our society in many ways. In this review, we present the current state of knowledge on fungal biodiversity, with special emphasis on filamentous fungi and the most recent discoveries in the field of identification and production of biotechnological compounds. More than 250 fungus species have been studied to produce these biotechnological compounds. This review focuses on three of the branches generally accepted in biotechnological applications, which have been identified by a color code: red, green, and white for pharmaceutical, agricultural, and industrial biotechnology, respectively. We also discuss future prospects for the use of filamentous fungi in biotechnology application.

  15. The 5S rDNA gene family in mollusks: characterization of transcriptional regulatory regions, prediction of secondary structures, and long-term evolution, with special attention to Mytilidae mussels.

    Science.gov (United States)

    Vizoso, Miguel; Vierna, Joaquín; González-Tizón, Ana M; Martínez-Lage, Andrés

    2011-01-01

    Several reports on the characterization of 5S ribosomal DNA (5S rDNA) in various animal groups have been published to date, but there is a lack of studies analyzing this gene family in a much broader context. Here, we have studied 5S rDNA variation in several molluskan species, including bivalves, gastropods, and cephalopods. The degree of conservation of transcriptional regulatory regions was analyzed in these lineages, revealing a conserved TATA-like box in the upstream region. The evolution of the 120 bp coding region (5S) was also studied, suggesting the occurrence of paralogue groups in razor clams, clams, and cockles. In addition, 5S rDNA sequences from 11 species and 7 genus of Mytilidae Rafinesque, 1815 mussels were sampled and studied in detail. Four different 5S rDNA types, based on the nontranscribed spacer region were identified. The phylogenetic analyses performed within each type showed a between-species gene clustering pattern, suggesting ancestral polymorphism. Moreover, some putative pseudogenized 5S copies were also identified. Our report, together with previous studies that found high degree of intragenomic divergence in bivalve species, suggests that birth-and-death evolution may be the main force driving the evolution of 5S rDNA in these animals, even at the genus level.

  16. Managing acute invasive fungal sinusitis.

    Science.gov (United States)

    Dwyhalo, Kristina M; Donald, Carrlene; Mendez, Anthony; Hoxworth, Joseph

    2016-01-01

    Acute invasive fungal sinusitis is the most aggressive form of fungal sinusitis and can be fatal, especially in patients who are immunosuppressed. Early diagnosis and intervention are crucial and potentially lifesaving, so primary care providers must maintain a high index of suspicion for this disease. Patients may need to be admitted to the hospital for IV antifungal therapy and surgical debridement.

  17. Current management of fungal infections.

    NARCIS (Netherlands)

    Meis, J.F.G.M.; Verweij, P.E.

    2001-01-01

    The management of superficial fungal infections differs significantly from the management of systemic fungal infections. Most superficial infections are treated with topical antifungal agents, the choice of agent being determined by the site and extent of the infection and by the causative organism,

  18. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific.

    Directory of Open Access Journals (Sweden)

    Tao Zhang

    Full Text Available This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs. Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems.

  19. Fungal rhinosinusitis with atypical presentation - a report of two cases

    Institute of Scientific and Technical Information of China (English)

    Rafael da Costa Monsanto; Rodrigo Silva Orem; Fernanda Resende e Silva; Fabio Hiroshi Okuyama; Fabio Tadeu Moura Lorenzetti

    2015-01-01

    Rhinosinusitis affects approximately 20% of the population, and the chronic rhinosinusitis represents over 90% of all cases of rhinosinusitis. The correct diagnosis is important for proper treatment and to predict its evolution. This study presents two cases of atypical frontal sinus disease, which the follow-up revealed a diagnosis of fungal rhinosinusitis. The present study aims to describe the cases of two patients with atypical lesions on the left frontal sinus; the treatment options, surgical approach, results, diagnosis and follow-up are further discussed. A significant increase in the reported cases of fungal rhinosinusitis has been seen in the last two decades, justified by the use of broad-spectrum antibiotics and steroids, as well as the increased number of immunocompromised individuals. This study reports the cases of two patients with a type of fungal rhinosinusitis named "fungal ball", characterized by a tangle of hyphae in the sinuses without tissue invasion. The treatment included surgical removal of the fungal infectious process with aeration of the affected sinus, and the procedure was successfully performed in our patients.

  20. Regulatory Anatomy

    DEFF Research Database (Denmark)

    Hoeyer, Klaus

    2015-01-01

    This article proposes the term “safety logics” to understand attempts within the European Union (EU) to harmonize member state legislation to ensure a safe and stable supply of human biological material for transplants and transfusions. With safety logics, I refer to assemblages of discourses, le...... they arise. In short, I expose the regulatory anatomy of the policy landscape....

  1. Hospitalized Patients and Fungal Infections

    Science.gov (United States)

    ... These types of infections are called healthcare-associated infections (HAIs). Hospital staff and healthcare providers do everything they can ... IV tube) can increase your risk for fungal infection. During your hospital stay you may need a central venous catheter, ...

  2. Fungal Entomopathogens in the Rhizosphere

    Science.gov (United States)

    Entomopathogenic fungi are found in a wide variety of fungal groups. The order Hypocreales contains the largest number of entomogenous fungi, including two of the most widely studied, Beauveria bassiana (Balsamo) Vuillemin (Hypocreales: Clavicipitaceae) and Metarhizium anisopliae (Metchnikoff) Sorok...

  3. Fungal genomics beyond Saccharomyces cerevisiae?

    DEFF Research Database (Denmark)

    Hofmann, Gerald; Mcintyre, Mhairi; Nielsen, Jens

    2003-01-01

    Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious that the a......Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious...... that the application of the existing methods of genome, transcriptome, proteome and metabolome analysis to other fungi has enormous potential, especially for the production of food and food ingredients. The developments in the past year demonstrate that we have only just started to exploit this potential....

  4. Fungal microbiota dysbiosis in IBD

    Science.gov (United States)

    Sokol, Harry; Leducq, Valentin; Aschard, Hugues; Pham, Hang-Phuong; Jegou, Sarah; Landman, Cecilia; Cohen, David; Liguori, Giuseppina; Bourrier, Anne; Nion-Larmurier, Isabelle; Cosnes, Jacques; Seksik, Philippe; Langella, Philippe; Skurnik, David; Richard, Mathias L; Beaugerie, Laurent

    2017-01-01

    Objective The bacterial intestinal microbiota plays major roles in human physiology and IBDs. Although some data suggest a role of the fungal microbiota in IBD pathogenesis, the available data are scarce. The aim of our study was to characterise the faecal fungal microbiota in patients with IBD. Design Bacterial and fungal composition of the faecal microbiota of 235 patients with IBD and 38 healthy subjects (HS) was determined using 16S and ITS2 sequencing, respectively. The obtained sequences were analysed using the Qiime pipeline to assess composition and diversity. Bacterial and fungal taxa associated with clinical parameters were identified using multivariate association with linear models. Correlation between bacterial and fungal microbiota was investigated using Spearman's test and distance correlation. Results We observed that fungal microbiota is skewed in IBD, with an increased Basidiomycota/Ascomycota ratio, a decreased proportion of Saccharomyces cerevisiae and an increased proportion of Candida albicans compared with HS. We also identified disease-specific alterations in diversity, indicating that a Crohn's disease-specific gut environment may favour fungi at the expense of bacteria. The concomitant analysis of bacterial and fungal microbiota showed a dense and homogenous correlation network in HS but a dramatically unbalanced network in IBD, suggesting the existence of disease-specific inter-kingdom alterations. Conclusions Besides bacterial dysbiosis, our study identifies a distinct fungal microbiota dysbiosis in IBD characterised by alterations in biodiversity and composition. Moreover, we unravel here disease-specific inter-kingdom network alterations in IBD, suggesting that, beyond bacteria, fungi might also play a role in IBD pathogenesis. PMID:26843508

  5. Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide

    OpenAIRE

    2010-01-01

    Specific regulatory nascent chains establish direct interactions with the ribosomal tunnel, leading to translational stalling. Despite a wealth of biochemical data, structural insight into the mechanism of translational stalling in eukaryotes is still lacking. Here we use cryo-electron microscopy to visualize eukaryotic ribosomes stalled during the translation of two diverse regulatory peptides: the fungal arginine attenuator peptide (AAP) and the human cytomegalovirus (hCMV) gp48 upstream op...

  6. Mixed chimerism evolution is associated with T regulatory type 1 (Tr1) cells in a β-thalassemic patient after haploidentical haematopoietic stem cell transplantation

    Science.gov (United States)

    Andreani, Marco; Gianolini, Monica Emma; Testi, Manuela; Battarra, MariaRosa; Tiziana, Galluccio; Morrone, Aldo; Sodani, Pietro; Lucarelli, Guido; Roncarolo, Maria-Grazia; Gregori, Silvia

    2014-01-01

    In a cohort of β-Thalassemia (β-Thal) transplanted with haploidentical-HSCT we identified one transplanted patient characterized by persistent mixed chimerism (PMC) for several months after HSCT. In this unique β-Thal patient we assessed the donor engraftment overtime after transplantation, the potential loss of the non-shared HLA haplotype, and the presence of CD49b+LAG-3+ T regulatory type 1 (Tr1) cells, previously demonstrated to be associated with PMC after HLA-related HSCT for β-Thal. The majority of the patient's erythrocytes were of donor origin, whereas T cells were initially mostly derived from the recipient, no HLA loss, but an increased frequency of circulating Tr1 cells were observed. For the first time, we showed that when the proportion of residual donor cells decreases, the frequency of CD49b+LAG-3+ Tr1 cells declines, reaching the levels present in healthy subjects. These findings confirm previous results obtained in transplant related settings for β-Thal, and supported the central role of Tr1 cells in promoting and maintaining PMC after allo-HSCT. PMID:26650878

  7. Fungal-Fungal Interactions in Leaf-Cutting Ant Agriculture

    Directory of Open Access Journals (Sweden)

    Sunshine A. Van Bael

    2011-01-01

    Full Text Available Many organisms participate in symbiotic relationships with other organisms, yet studies of symbioses typically have focused on the reciprocal costs and benefits within a particular host-symbiont pair. Recent studies indicate that many ecological interactions involve alliances of symbionts acting together as mutualistic consortia against other consortia. Such interacting consortia are likely to be widespread in nature, even if the interactions often occur in a cryptic fashion. Little theory and empirical data exist concerning how these complex interactions shape ecological outcomes in nature. Here, we review recent work on fungal-fungal interactions between two consortia: (i leaf-cutting ants and their symbiotic fungi (the latter grown as a food crop by the former and (ii tropical plants and their foliar endophytes (the cryptic symbiotic fungi within leaves of the former. Plant characteristics (e.g., secondary compounds or leaf physical properties of leaves are involved in leaf-cutting ant preferences, and a synthesis of published information suggests that these plant traits could be modified by fungal presence. We discuss potential mechanisms for how fungal-fungal interactions proceed in the leaf-cutting ant agriculture and suggest themes for future research.

  8. Speciation in fungal and oomycete plant pathogens.

    Science.gov (United States)

    Restrepo, Silvia; Tabima, Javier F; Mideros, Maria F; Grünwald, Niklaus J; Matute, Daniel R

    2014-01-01

    The process of speciation, by definition, involves evolution of one or more reproductive isolating mechanisms that split a single species into two that can no longer interbreed. Determination of which processes are responsible for speciation is important yet challenging. Several studies have proposed that speciation in pathogens is heavily influenced by host-pathogen dynamics and that traits that mediate such interactions (e.g., host mobility, reproductive mode of the pathogen, complexity of the life cycle, and host specificity) must lead to reproductive isolation and ultimately affect speciation rates. In this review, we summarize the main evolutionary processes that lead to speciation of fungal and oomycete plant pathogens and provide an outline of how speciation can be studied rigorously, including novel genetic/genomic developments.

  9. 50-plus years of fungal viruses.

    Science.gov (United States)

    Ghabrial, Said A; Castón, José R; Jiang, Daohong; Nibert, Max L; Suzuki, Nobuhiro

    2015-05-01

    Mycoviruses are widespread in all major taxa of fungi. They are transmitted intracellularly during cell division, sporogenesis, and/or cell-to-cell fusion (hyphal anastomosis), and thus their life cycles generally lack an extracellular phase. Their natural host ranges are limited to individuals within the same or closely related vegetative compatibility groups, although recent advances have established expanded experimental host ranges for some mycoviruses. Most known mycoviruses have dsRNA genomes packaged in isometric particles, but an increasing number of positive- or negative-strand ssRNA and ssDNA viruses have been isolated and characterized. Although many mycoviruses do not have marked effects on their hosts, those that reduce the virulence of their phytopathogenic fungal hosts are of considerable interest for development of novel biocontrol strategies. Mycoviruses that infect endophytic fungi and those that encode killer toxins are also of special interest. Structural analyses of mycoviruses have promoted better understanding of virus assembly, function, and evolution.

  10. Serious fungal infections in Ecuador.

    Science.gov (United States)

    Zurita, J; Denning, D W; Paz-Y-Miño, A; Solís, M B; Arias, L M

    2017-06-01

    There is a dearth of data from Ecuador on the burden of life-threatening fungal disease entities; therefore, we estimated the burden of serious fungal infections in Ecuador based on the populations at risk and available epidemiological databases and publications. A full literature search was done to identify all epidemiology papers reporting fungal infection rates. WHO, ONU-AIDS, Index Mundi, Global Asthma Report, Globocan, and national data [Instituto Nacional de Estadística y Censos (INEC), Ministerio de Salud Pública (MSP), Sociedad de Lucha Contra el Cáncer (SOLCA), Instituto Nacional de Donación y Trasplante de Órganos, Tejidos y Células (INDOT)] were reviewed. When no data existed, risk populations were used to estimate frequencies of fungal infections, using previously described methodology by LIFE. Ecuador has a variety of climates from the cold of the Andes through temperate to humid hot weather at the coast and in the Amazon basin. Ecuador has a population of 15,223,680 people and an average life expectancy of 76 years. The median estimate of the human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS) population at risk for fungal disease (<200 CD4 cell counts) is ∼10,000, with a rate of 11.1% (1100) of histoplasma, 7% (700) of cryptococcal meningitis, and 11% (1070) of Pneumocystis pneumonia. The burden of candidemia is 1037. Recurrent Candida vaginitis (≥4 episodes per year) affects 307,593 women aged 15-50 years. Chronic pulmonary aspergillosis probably affects ∼476 patients following tuberculosis (TB). Invasive aspergillosis is estimated to affect 748 patients (∼5.5/100,000). In addition, allergic bronchopulmonary aspergillosis (ABPA) in asthma and severe asthma with fungal sensitization (SAFS) were estimated to affect 26,642 and 45,013 people, respectively. Our estimates indicate that 433,856 (3%) of the population in Ecuador is affected by serious fungal infection.

  11. Evolution of hepatic glucose metabolism: liver-specific glucokinase deficiency explained by parallel loss of the gene for glucokinase regulatory protein (GCKR.

    Directory of Open Access Journals (Sweden)

    Zhao Yang Wang

    Full Text Available BACKGROUND: Glucokinase (GCK plays an important role in the regulation of carbohydrate metabolism. In the liver, phosphorylation of glucose to glucose-6-phosphate by GCK is the first step for both glycolysis and glycogen synthesis. However, some vertebrate species are deficient in GCK activity in the liver, despite containing GCK genes that appear to be compatible with function in their genomes. Glucokinase regulatory protein (GCKR is the most important post-transcriptional regulator of GCK in the liver; it participates in the modulation of GCK activity and location depending upon changes in glucose levels. In experimental models, loss of GCKR has been shown to associate with reduced hepatic GCK protein levels and activity. METHODOLOGY/PRINCIPAL FINDINGS: GCKR genes and GCKR-like sequences were identified in the genomes of all vertebrate species with available genome sequences. The coding sequences of GCKR and GCKR-like genes were identified and aligned; base changes likely to disrupt coding potential or splicing were also identified. CONCLUSIONS/SIGNIFICANCE: GCKR genes could not be found in the genomes of 9 vertebrate species, including all birds. In addition, in multiple mammalian genomes, whereas GCKR-like gene sequences could be identified, these genes could not predict a functional protein. Vertebrate species that were previously reported to be deficient in hepatic GCK activity were found to have deleted (birds and lizard or mutated (mammals GCKR genes. Our results suggest that mutation of the GCKR gene leads to hepatic GCK deficiency due to the loss of the stabilizing effect of GCKR.

  12. Fungal farming in a non-social beetle.

    Directory of Open Access Journals (Sweden)

    Wataru Toki

    evolution of fungal farming in a non-social insect.

  13. Microbiological diagnostics of fungal infections

    Directory of Open Access Journals (Sweden)

    Corrado Girmenia

    2013-07-01

    Full Text Available Laboratory tests for the detection of fungal infections are easy to perform. The main obstacle to a correct diagnosis is the correlation between the laboratory findings and the clinical diagnosis. Among pediatric patients, the most common fungal pathogen is Candida. The detection of fungal colonization may be performed through the use of chromogenic culture media, which allows also the identification of Candida subspecies, from which pathogenicity depends. In neonatology, thistest often drives the decision to begin a empiric therapy; in this regard, a close cooperation between microbiologists and clinicians is highly recommended. Blood culture, if positive, is a strong confirmation of fungal infection; however, its low sensitivity results in a high percentage of false negatives, thus decreasing its reliability. Molecular diagnostics is still under evaluation, whereas the detection of some fungal antigens, such as β-D-glucan, galactomannan, mannoprotein, and cryptococcal antigen in the serum is used for adults, but still under evaluations for pediatric patients.http://dx.doi.org/10.7175/rhc.v4i1S.862

  14. Fungal artificial chromosomes for mining of the fungal secondary metabolome

    OpenAIRE

    2015-01-01

    Background With thousands of fungal genomes being sequenced, each genome containing up to 70 secondary metabolite (SM) clusters 30–80 kb in size, breakthrough techniques are needed to characterize this SM wealth. Results Here we describe a novel system-level methodology for unbiased cloning of intact large SM clusters from a single fungal genome for one-step transformation and expression in a model host. All 56 intact SM clusters from Aspergillus terreus were individually captured in self-rep...

  15. The Political Economy of Regulatory Change

    DEFF Research Database (Denmark)

    Buch-Hansen, Hubert

    2012-01-01

    This article aims to explain the broader evolution of British merger control. To this end it outlines a novel critical political economy perspective on regulation and regulatory change which differs from established political economy approaches, such as the regulatory capitalism/state perspectives......, in three main ways: it places regulatory ideas at the heart of the analysis, it differentiates between different degrees of regulatory change, and it links regulatory change in delineated issue areas with changing power balances between fractions of capital and labor. The application of this perspective...... to the analysis of the evolution of British merger control provides some important new insights, most notably that the content, form, and scope of merger control in Britain have been deeply transformed in accordance with neoliberal ideas since the 1980s and that this process, which was part of a broader...

  16. Fungal secondary metabolites as modulators of interactions with insects and other arthropods.

    Science.gov (United States)

    Rohlfs, Marko; Churchill, Alice C L

    2011-01-01

    Fungi share a diverse co-evolutionary history with animals, especially arthropods. In this review, we focus on the role of secondary metabolism in driving antagonistic arthropod-fungus interactions, i.e., where fungi serve as a food source to fungal grazers, compete with saprophagous insects, and attack insects as hosts for growth and reproduction. Although a wealth of studies on animal-fungus interactions point to a crucial role of secondary metabolites in deterring animal feeding and resisting immune defense strategies, causal evidence often remains to be provided. Moreover, it still remains an unresolved puzzle as to what extent the tight regulatory control of secondary metabolite formation in some model fungi represents an evolved chemical defense system favored by selective pressure through animal antagonists. Given these gaps in knowledge, we highlight some co-evolutionary aspects of secondary metabolism, such as induced response, volatile signaling, and experimental evolution, which may help in deciphering the ecological importance and evolutionary history of secondary metabolite production in fungi.

  17. Duplication of AP1 within the Spinacia oleracea L. AP1/FUL clade is followed by rapid amino acid and regulatory evolution.

    Science.gov (United States)

    Sather, D Noah; Golenberg, Edward M

    2009-02-01

    The AP1/FUL clade of MADS box genes have undergone multiple duplication events among angiosperm species. While initially identified as having floral meristem identity and floral organ identity function in Arabidopsis, the role of AP1 homologs does not appear to be universally conserved even among eudicots. In comparison, the role of FRUITFULL has not been extensively explored in non-model species. We report on the isolation of three AP1/FUL genes from cultivated spinach, Spinacia oleracea L. Two genes, designated SpAPETALA1-1 (SpAP1-1) and SpAPETALA1-2 (SpAP1-2), cluster as paralogous genes within the Caryophyllales AP1 clade. They are highly differentiated in the 3', carboxyl-end encoding region of the gene following the third amphipathic alpha-helix region, while still retaining some elements of a signature AP1 carboxyl motifs. In situ hybridization studies also demonstrate that the two paralogs have evolved different temporal and spatial expression patterns, and that neither gene is expressed in the developing sepal whorl, suggesting that the AP1 floral organ identity function is not conserved in spinach. The spinach FRUITFULL homolog, SpFRUITFULL (SpFUL), has retained the conserved motif and groups with Caryophyllales FRUITFULL homologs. SpFUL is expressed in leaf as well as in floral tissue, and shows strong expression late in flower development, particularly in the tapetal layer in males, and in the endothecium layer and stigma, in the females. The combined evidence of high rates of non-synonymous substitutions and differential expression patterns supports a scenario in which the AP1 homologs in the spinach AP1/FUL gene family have experienced rapid evolution following duplication.

  18. Fungal infection following renal transplantation.

    Science.gov (United States)

    Gallis, H A; Berman, R A; Cate, T R; Hamilton, J D; Gunnells, J C; Stickel, D L

    1975-09-01

    Twenty-seven deep fungal infections developed in 22 of 171 patients following renal transplantation. These infections included cryptococcosis (ten), nocardiosis (seven), candidiasis (four), aspergillosis (two), phycomycosis (two), chromomycosis (one), and subcutaneous infection with Phialophora gougeroti (one). Twelve infections occurred in living-related and ten in cadaveric recipients. Nineteen of the 22 patients were male. Infections occurred from 0 to 61 months after transplantation. Complicating non-fungal infections were present concomitantly in 15 patients. Thirteen patients died, eight probably as a result of fungal infection. Appropriate diagnostic procedures yielded a diagnosis in 20 of 27 infections, and therapy was begun in 18 patients. Serologic, culture, and biopsy procedures useful in making rapid diagnoses are advocated in the hope of increasing survival.

  19. The Fungal Defensin Family Enlarged

    Directory of Open Access Journals (Sweden)

    Jiajia Wu

    2014-08-01

    Full Text Available Fungi are an emerging source of peptide antibiotics. With the availability of a large number of model fungal genome sequences, we can expect that more and more fungal defensin-like peptides (fDLPs will be discovered by sequence similarity search. Here, we report a total of 69 new fDLPs encoded by 63 genes, in which a group of fDLPs derived from dermatophytes are defined as a new family (fDEF8 according to sequence and phylogenetic analyses. In the oleaginous fungus Mortierella alpine, fDLPs have undergone extensive gene expansion. Our work further enlarges the fungal defensin family and will help characterize new peptide antibiotics with therapeutic potential.

  20. Molecular evolution of cyclin proteins in animals and fungi

    Directory of Open Access Journals (Sweden)

    Afonnikov Dmitry A

    2011-07-01

    Full Text Available Abstract Background The passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which differ considerably in primary structure from one eukaryotic organism to another. Despite these lines of evidence, the relationship between the evolution of cyclins and their function is an open issue. Here we present the results of our study on the molecular evolution of A-, B-, D-, E-type cyclin proteins in animals and fungi. Results We constructed phylogenetic trees for these proteins, their ancestral sequences and analyzed patterns of amino acid replacements. The analysis of infrequently fixed atypical amino acid replacements in cyclins evidenced that accelerated evolution proceeded predominantly during paralog duplication or after it in animals and fungi and that it was related to aromorphic changes in animals. It was shown also that evolutionary flexibility of cyclin function may be provided by consequential reorganization of regions on protein surface remote from CDK binding sites in animal and fungal cyclins and by functional differentiation of paralogous cyclins formed in animal evolution. Conclusions The results suggested that changes in the number and/or nature of cyclin-binding proteins may underlie the evolutionary role of the alterations in the molecular structure of cyclins and their involvement in diverse molecular-genetic events.

  1. Fungal laryngitis in immunocompetent patients.

    Science.gov (United States)

    Ravikumar, A; Prasanna Kumar, S; Somu, L; Sudhir, B

    2014-01-01

    The diagnosis of fungal laryngitis is often overlooked in immunocompetent patients because it is commonly considered a disease of the immunocompromised. Further confusion is caused by clinical and histological similarity to more common conditions like Leukoplakia. Demonstration of hyperkeratosis particularly if associated with intraepithelial neutrophils on biopsy should trigger a search for fungus using specialized stains. These patients usually present with hoarseness of voice. Pain is present inconsistently along with dysphagia and odynophagia. We present three cases of fungal laryngitis in immunocompetent patients out of which one underwent microlaryngeal surgery with excision biopsy. All these patients responded well with oral antifungal therapy.

  2. CFGP: a web-based, comparative fungal genomics platform.

    Science.gov (United States)

    Park, Jongsun; Park, Bongsoo; Jung, Kyongyong; Jang, Suwang; Yu, Kwangyul; Choi, Jaeyoung; Kong, Sunghyung; Park, Jaejin; Kim, Seryun; Kim, Hyojeong; Kim, Soonok; Kim, Jihyun F; Blair, Jaime E; Lee, Kwangwon; Kang, Seogchan; Lee, Yong-Hwan

    2008-01-01

    Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the 'fill-in-the-form-and-press-SUBMIT' user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI.

  3. Protective immune responses to fungal infections.

    Science.gov (United States)

    Rivera, A

    2014-09-01

    The incidence of fungal infections has been on the rise over several decades. Fungal infections threaten animals, plants and humans alike and are thus of significant concern to scientists across disciplines. Over the last decade, significant advances on fungal immunology have lead to a better understanding of important mechanisms of host protection against fungi. In this article, I review recent advances of relevant mechanisms of immune-mediated protection to fungal infections.

  4. Imaging fungal infections in children

    NARCIS (Netherlands)

    Ankrah, Alfred O.; Sathekge, Mike M; Dierckx, Rudi A.J.O.; Glaudemans, Andor W.J.M.

    2016-01-01

    Fungal infections in children rarely occur, but continue to have a high morbidity and mortality despite the development of newer antifungal agents. It is essential for these infections to be diagnosed at the earliest possible stage so appropriate treatment can be initiated promptly. The addition of

  5. Microbiology of systemic fungal infections

    Directory of Open Access Journals (Sweden)

    Chakrabarti A

    2005-01-01

    Full Text Available The increased incidence of systemic fungal infections in the past two decades has been overwhelming. Earlier, it was pathogenic dimorphic fungi, which were known to cause systemic infections. However, starting from the 1960s, opportunistic fungi started causing more number of infections, especially in the immunocompromised host. More recently, newer and less common fungal agents are being increasingly associated with infection in immunosuppressed hosts. Amongst dimorphic fungi, infections due to Histoplasma capsulatum and Penicillium marneffei are increasingly reported in patients with AIDS in India. H. capsulatum is found country wide, but P. marneffei remains restricted to Manipur state. Although both varieties of C. neoformans , C. neoformans var. neoformans (serotypes A & D, and C. neoformans var. gattii (serotypes B & C are reported in India, most of the cases reported are of serotype A. Increased incidence of cryptococcosis is reported from all centers with the emergence of AIDS. Systemic infection due to species under Candida , Aspergillus and zygomycetes is widely prevalent in nosocomial setting, and outbreaks due to unusual fungi are reported occasionally from tertiary care centers. This global change in systemic fungal infections has emphasized the need to develop good diagnostic mycology laboratories in this country and to recognize this increasingly large group of potential fungal pathogens.

  6. Fungal endophyte diversity in Sarracenia

    Science.gov (United States)

    Fungal endophytes were isolated from four species of the carnivorous pitcher plant genus Sarracenia: S. minor, S. oreophila, S. purpurea, and S. psittacina. Twelve taxa of fungi, eight within the Ascomycota and four within the Basidiomycota, were identified based on PCR amplification and sequencing ...

  7. (Post-)genomics approaches in fungal research

    NARCIS (Netherlands)

    Aguilar-Pontes, María Victoria; de Vries, Ronald P; Zhou, M.; van den Brink, J.

    2014-01-01

    To date, hundreds of fungal genomes have been sequenced and many more are in progress. This wealth of genomic information has provided new directions to study fungal biodiversity. However, to further dissect and understand the complicated biological mechanisms involved in fungal life styles, functio

  8. Fungal Mimicry of a Mammalian Aminopeptidase Disables Innate Immunity and Promotes Pathogenicity.

    Science.gov (United States)

    Sterkel, Alana K; Lorenzini, Jenna L; Fites, J Scott; Subramanian Vignesh, Kavitha; Sullivan, Thomas D; Wuthrich, Marcel; Brandhorst, Tristan; Hernandez-Santos, Nydiaris; Deepe, George S; Klein, Bruce S

    2016-03-09

    Systemic fungal infections trigger marked immune-regulatory disturbances, but the mechanisms are poorly understood. We report that the pathogenic yeast of Blastomyces dermatitidis elaborates dipeptidyl-peptidase IVA (DppIVA), a close mimic of the mammalian ectopeptidase CD26, which modulates critical aspects of hematopoiesis. We show that, like the mammalian enzyme, fungal DppIVA cleaved C-C chemokines and GM-CSF. Yeast producing DppIVA crippled the recruitment and differentiation of monocytes and prevented phagocyte activation and ROS production. Silencing fungal DppIVA gene expression curtailed virulence and restored recruitment of CCR2(+) monocytes, generation of TipDC, and phagocyte killing of yeast. Pharmacological blockade of DppIVA restored leukocyte effector functions and stemmed infection, while addition of recombinant DppIVA to gene-silenced yeast enabled them to evade leukocyte defense. Thus, fungal DppIVA mediates immune-regulatory disturbances that underlie invasive fungal disease. These findings reveal a form of molecular piracy by a broadly conserved aminopeptidase during disease pathogenesis.

  9. Subseafloor basalts as fungal habitats

    Science.gov (United States)

    Ivarsson, M.

    2012-09-01

    The oceanic crust is believed to host the largest potential habitat for microbial life on Earth, yet, still we lack substantial information about the abundance, diversity, and consequence of its biosphere. The last two decades have involved major research accomplishments within this field and a change in view of the ocean crust and its potential to harbour life. Here fossilised fungal colonies in subseafloor basalts are reported from three different seamounts in the Pacific Ocean. The fungal colonies consist of various characteristic structures interpreted as fungal hyphae, fruit bodies and spores. The fungal hyphae are well preserved with morphological characteristics such as hyphal walls, septa, thallic conidiogenesis, and hyphal tips with hyphal vesicles within. The fruit bodies consist of large (∼50-200 µm in diameter) body-like structures with a defined outer membrane and an interior filled with calcite. The fruit bodies have at some stage been emptied of their contents of spores and filled by carbonate-forming fluids. A few fruit bodies not filled by calcite and with spores still within support this interpretation. Spore-like structures (ranging from a few µm to ∼20 µm in diameter) are also observed outside of the fruit bodies and in some cases concentrated to openings in the membrane of the fruit bodies. The hyphae, fruit bodies and spores are all closely associated with a crust lining the vein walls that probably represent a mineralized biofilm. The results support a fungal presence in deep subseafloor basalts and indicate that such habitats were vital between ∼81 and 48 Ma.

  10. The Chemical Basis of Fungal Bioluminescence.

    Science.gov (United States)

    Purtov, Konstantin V; Petushkov, Valentin N; Baranov, Mikhail S; Mineev, Konstantin S; Rodionova, Natalja S; Kaskova, Zinaida M; Tsarkova, Aleksandra S; Petunin, Alexei I; Bondar, Vladimir S; Rodicheva, Emma K; Medvedeva, Svetlana E; Oba, Yuichi; Oba, Yumiko; Arseniev, Alexander S; Lukyanov, Sergey; Gitelson, Josef I; Yampolsky, Ilia V

    2015-07-06

    Many species of fungi naturally produce light, a phenomenon known as bioluminescence, however, the fungal substrates used in the chemical reactions that produce light have not been reported. We identified the fungal compound luciferin 3-hydroxyhispidin, which is biosynthesized by oxidation of the precursor hispidin, a known fungal and plant secondary metabolite. The fungal luciferin does not share structural similarity with the other eight known luciferins. Furthermore, it was shown that 3-hydroxyhispidin leads to bioluminescence in extracts from four diverse genera of luminous fungi, thus suggesting a common biochemical mechanism for fungal bioluminescence.

  11. Fungal rhinosinusitis: what every allergist should know.

    Science.gov (United States)

    Callejas, C A; Douglas, R G

    2013-08-01

    The interaction between fungi and the sinonasal tract results in a diverse range of diseases with an equally broad spectrum of clinical severity. The classification of these interactions has become complex, and this review seeks to rationalize and simplify the approach to fungal diseases of the nose and paranasal sinuses. These conditions may be discussed under two major headings: non-invasive disease (localized fungal colonization, fungal ball and allergic fungal rhinosinusitis) and invasive disease (acute invasive rhinosinusitis, chronic invasive rhinosinusitis and granulomatous invasive rhinosinusitis). A diagnosis of fungal rhinosinusitis is established by combining findings on history, clinical examination, laboratory testing, imaging and histopathology. The immunocompetence of the patient is of great importance, as invasive fungal rhinosinusitis is uncommon in immunocompetent patients. With the exception of localized fungal colonization, treatment of all forms of fungal rhinosinusitis relies heavily on surgery. Systemic antifungal agents are a fundamental component in the treatment of invasive forms, but are not indicated for the treatment of the non-invasive forms. Antifungal drugs may have a role as adjuvant therapy in allergic fungal rhinosinusitis, but evidence is poor to support recommendations. Randomized controlled trials need to be performed to confirm the benefit of immunotherapy in the treatment of allergic fungal rhinosinusitis. In this article, we will summarize the current literature, addressing the controversies regarding the diagnosis and management of fungal rhinosinusitis, and focussing on those aspects which are important for clinical immunologists and allergists.

  12. Induced fungal resistance to insect grazing: reciprocal fitness consequences and fungal gene expression in the Drosophila-Aspergillus model system.

    Directory of Open Access Journals (Sweden)

    Silvia Caballero Ortiz

    fungivore-rich habitats. Induced fungal defence responses thus need to be included if we wish to have a complete conception of animal-fungus co-evolution, fungal gene regulation, and multitrophic interactions.

  13. The dynamic organization of fungal acetyl-CoA carboxylase

    Science.gov (United States)

    Hunkeler, Moritz; Stuttfeld, Edward; Hagmann, Anna; Imseng, Stefan; Maier, Timm

    2016-04-01

    Acetyl-CoA carboxylases (ACCs) catalyse the committed step in fatty-acid biosynthesis: the ATP-dependent carboxylation of acetyl-CoA to malonyl-CoA. They are important regulatory hubs for metabolic control and relevant drug targets for the treatment of the metabolic syndrome and cancer. Eukaryotic ACCs are single-chain multienzymes characterized by a large, non-catalytic central domain (CD), whose role in ACC regulation remains poorly characterized. Here we report the crystal structure of the yeast ACC CD, revealing a unique four-domain organization. A regulatory loop, which is phosphorylated at the key functional phosphorylation site of fungal ACC, wedges into a crevice between two domains of CD. Combining the yeast CD structure with intermediate and low-resolution data of larger fragments up to intact ACCs provides a comprehensive characterization of the dynamic fungal ACC architecture. In contrast to related carboxylases, large-scale conformational changes are required for substrate turnover, and are mediated by the CD under phosphorylation control.

  14. Fungal keratitis in Lattice dystrophy

    Directory of Open Access Journals (Sweden)

    Chatterjee Samrat

    2010-01-01

    Full Text Available We report a case of fungal keratitis occurring in a patient with lattice dystrophy. A 57-year-old farmer presented with a corneal ulcer following probable entry of paddy husk in the right eye, of one month duration. Corneal scraping revealed pigmented fungal filaments while culture grew Alternaria alternata. Treatment with 5% natamycin eye drops and 1% atropine healed the infection in four weeks. We would like to draw attention to the fact that the cornea in lattice dystrophy is prone to frequent erosions and is a compromised epithelial barrier to invasion by microorganisms. Patients must be made aware of this fact and should seek attention at the earliest following any trivial trauma. Management of minor corneal abrasions in them should be directed at healing the epithelium with adequate lubricants and preventing infection with topical antibiotic prophylaxis.

  15. Structural aspects of fungal allergens.

    Science.gov (United States)

    Crameri, Reto

    2015-03-01

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

  16. Fungal metabolites with anticancer activity.

    Science.gov (United States)

    Evidente, Antonio; Kornienko, Alexander; Cimmino, Alessio; Andolfi, Anna; Lefranc, Florence; Mathieu, Véronique; Kiss, Robert

    2014-05-01

    Covering: 1964 to 2013. Natural products from bacteria and plants have played a leading role in cancer drug discovery resulting in a large number of clinically useful agents. In contrast, the investigations of fungal metabolites and their derivatives have not led to a clinical cancer drug in spite of significant research efforts revealing a large number of fungi-derived natural products with promising anticancer activity. Many of these natural products have displayed notable in vitro growth-inhibitory properties in human cancer cell lines and select compounds have been demonstrated to provide therapeutic benefits in mouse models of human cancer. Many of these compounds are expected to enter human clinical trials in the near future. The present review discusses the reported sources, structures and biochemical studies aimed at the elucidation of the anticancer potential of these promising fungal metabolites.

  17. Nattrassia mangiferae causing fungal keratitis

    Directory of Open Access Journals (Sweden)

    Kindo A

    2010-01-01

    Full Text Available We report a case of fungal keratitis caused by the coelomycetous fungus Nattrassia mangiferae in a 70 year old gentleman, agriculturist by occupation, with a history of injury to his right eye. The scraping showed narrow septate fungal hyphae on a KOH mount, isolation of a fast growing black mould, which demonstrated hyphae and arthroconidia of varying widths typical of the Scytalidium synanamorph (S. dimidiatum. The formation of the pycnidia, which at maturity, expressed conidia. The patient was started on topical itraconazole one hourly and topical atropine thrice a day. The patient was lost to follow up hence we are not able to comment on the final outcome of the patient.

  18. Fungal contaminants in cytopathology specimens

    Directory of Open Access Journals (Sweden)

    Prashant Sharma

    2014-02-01

    Full Text Available A pseudo-epidemic of environmental fungi, most likely by Fusarium spp., leading to inappropriate investigations for disseminated systemic mycosis is described. Subtle diagnostic clues, including the specimens affected, the nature of the host response, and the type of fungal elements noted helped to determine the nature of contaminants. The potential pitfall can be avoided by the knowledge of pertinent disease biology, prompt consultation for infectious diseases, and investigations of the potential environmental sources followed by source control.

  19. Systems biology of fungal infection

    Directory of Open Access Journals (Sweden)

    Fabian eHorn

    2012-04-01

    Full Text Available Elucidation of pathogenicity mechanisms of the most important human pathogenic fungi, Aspergillus fumigatus and Candida albicans, has gained great interest in the light of the steadily increasing number of cases of invasive fungal infections.A key feature of these infections is the interaction of the different fungal morphotypes with epithelial and immune effector cells in the human host. Because of the high level of complexity, it is necessary to describe and understand invasive fungal infection by taking a systems biological approach, i.e., by a comprehensive quantitative analysis of the non-linear and selective interactions of a large number of functionally diverse, and frequently multifunctional, sets of elements, e.g., genes, proteins, metabolites, which produce coherent and emergent behaviours in time and space. The recent advances in systems biology will now make it possible to uncover the structure and dynamics of molecular and cellular cause-effect relationships within these pathogenic interactions.We review current efforts to integrate omics and image-based data of host-pathogen interactions into network and spatio-temporal models. The modelling will help to elucidate pathogenicity mechanisms and to identify diagnostic biomarkers and potential drug targets for therapy and could thus pave the way for novel intervention strategies based on novel antifungal drugs and cell therapy.

  20. Fungal genome resources at NCBI.

    Science.gov (United States)

    Robbertse, B; Tatusova, T

    2011-09-01

    The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.

  1. Allergen Immunotherapy in an HIV+ Patient with Allergic Fungal Rhinosinusitis

    OpenAIRE

    2015-01-01

    Patients with HIV/AIDS can present with multiple types of fungal rhinosinusitis, fungal balls, granulomatous invasive fungal rhinosinusitis, acute or chronic invasive fungal rhinosinusitis, or allergic fungal rhinosinusitis (AFRS). Given the variable spectrum of immune status and susceptibility to severe infection from opportunistic pathogens it is extremely important that clinicians distinguish aggressive fungal invasive fungal disease from the much milder forms such as AFRS. Here we descr...

  2. Adaptive Dynamics of Regulatory Networks: Size Matters

    Directory of Open Access Journals (Sweden)

    2009-03-01

    Full Text Available To accomplish adaptability, all living organisms are constructed of regulatory networks on different levels which are capable to differentially respond to a variety of environmental inputs. Structure of regulatory networks determines their phenotypical plasticity, that is, the degree of detail and appropriateness of regulatory replies to environmental or developmental challenges. This regulatory network structure is encoded within the genotype. Our conceptual simulation study investigates how network structure constrains the evolution of networks and their adaptive abilities. The focus is on the structural parameter network size. We show that small regulatory networks adapt fast, but not as good as larger networks in the longer perspective. Selection leads to an optimal network size dependent on heterogeneity of the environment and time pressure of adaptation. Optimal mutation rates are higher for smaller networks. We put special emphasis on discussing our simulation results on the background of functional observations from experimental and evolutionary biology.

  3. Adaptive Dynamics of Regulatory Networks: Size Matters

    Directory of Open Access Journals (Sweden)

    Martinetz Thomas

    2009-01-01

    Full Text Available To accomplish adaptability, all living organisms are constructed of regulatory networks on different levels which are capable to differentially respond to a variety of environmental inputs. Structure of regulatory networks determines their phenotypical plasticity, that is, the degree of detail and appropriateness of regulatory replies to environmental or developmental challenges. This regulatory network structure is encoded within the genotype. Our conceptual simulation study investigates how network structure constrains the evolution of networks and their adaptive abilities. The focus is on the structural parameter network size. We show that small regulatory networks adapt fast, but not as good as larger networks in the longer perspective. Selection leads to an optimal network size dependent on heterogeneity of the environment and time pressure of adaptation. Optimal mutation rates are higher for smaller networks. We put special emphasis on discussing our simulation results on the background of functional observations from experimental and evolutionary biology.

  4. Invasive fungal infections after natural disasters.

    Science.gov (United States)

    Benedict, Kaitlin; Park, Benjamin J

    2014-03-01

    The link between natural disasters and subsequent fungal infections in disaster-affected persons has been increasingly recognized. Fungal respiratory conditions associated with disasters include coccidioidomycosis, and fungi are among several organisms that can cause near-drowning pneumonia. Wound contamination with organic matter can lead to post-disaster skin and soft tissue fungal infections, notably mucormycosis. The role of climate change in the environmental growth, distribution, and dispersal mechanisms of pathogenic fungi is not fully understood; however, ongoing climate change could lead to increased disaster-associated fungal infections. Fungal infections are an often-overlooked clinical and public health issue, and increased awareness by health care providers, public health professionals, and community members regarding disaster-associated fungal infections is needed.

  5. Fungal biology: compiling genomes and exploiting them

    Energy Technology Data Exchange (ETDEWEB)

    Labbe, Jessy L [ORNL; Uehling, Jessie K [ORNL; Payen, Thibaut [INRA; Plett, Jonathan [University of Western Sydney, Australia

    2014-01-01

    The last 10 years have seen the cost of sequencing complete genomes decrease at an incredible speed. This has led to an increase in the number of genomes sequenced in all the fungal tree of life as well as a wide variety of plant genomes. The increase in sequencing has permitted us to study the evolution of organisms on a genomic scale. A number of talks during the conference discussed the importance of transposable elements (TEs) that are present in almost all species of fungi. These TEs represent an especially large percentage of genomic space in fungi that interact with plants. Thierry Rouxel (INRA, Nancy, France) showed the link between speciation in the Leptosphaeria complex and the expansion of TE families. For example in the Leptosphaeria complex, one species associated with oilseed rape has experienced a recent and massive burst of movement by a few TE families. The alterations caused by these TEs took place in discrete regions of the genome leading to shuffling of the genomic landscape and the appearance of genes specific to the species, such as effectors useful for the interactions with a particular plant (Rouxel et al., 2011). Other presentations showed the importance of TEs in affecting genome organization. For example, in Amanita different species appear to have been invaded by different TE families (Veneault-Fourrey & Martin, 2011).

  6. Prevalence and clinical profile of fungal rhinosinusitis

    OpenAIRE

    2016-01-01

    Background: There are only a few landmark studies from the Indian subcontinent on fungal rhinosinusitis. The lack of awareness among clinicians regarding the varying clinical presentations of fungal rhinosinusitis prompted us to undertake this study. Objective: To determine the prevalence, etiologic basis, clinical features, radiologic features, and microscopic features of fungal rhinosinusitis, and to evaluate the various treatment modalities available. Methods: This was a prospective study ...

  7. Reconstructing fungal natural product biosynthetic pathways.

    Science.gov (United States)

    Lazarus, C M; Williams, K; Bailey, A M

    2014-10-01

    Large scale fungal genome sequencing has revealed a multitude of potential natural product biosynthetic pathways that remain uncharted. Here we describe some of the methods that have been used to explore them via heterologous gene expression. We focus on filamentous fungal hosts and discuss the technological challenges and successes behind the reconstruction of fungal natural product pathways. Optimised, efficient heterologous expression of reconstructed biosynthetic pathways promises progress in the discovery of novel compounds that could be utilised by the pharmaceutical and agrochemical industries.

  8. Fungal Endocarditis: Update on Diagnosis and Management.

    Science.gov (United States)

    Pasha, Ahmed Khurshid; Lee, Justin Z; Low, See-Wei; Desai, Hem; Lee, Kwan S; Al Mohajer, Mayar

    2016-10-01

    Fungal endocarditis is an extremely debilitating disease associated with high morbidity and mortality. Candida spp. are the most common isolated organisms in fungal endocarditis. It is most prevalent in patients who are immunosuppressed and intravenous drug users. Most patients present with constitutional symptoms, which are indistinguishable from bacterial endocarditis, hence a high index of suspicion is required for pursuing diagnosis. Diagnosis of fungal endocarditis can be very challenging: most of the time, blood cultures are negative or take a long time to yield growth. Fungal endocarditis mandates an aggressive treatment strategy. A medical and surgical combined approach is the cornerstone of therapy. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. [Response of arbuscular mycorrhizal fungal lipid metabolism to symbiotic signals in mycorrhiza].

    Science.gov (United States)

    Tian, Lei; Li, Yuanjing; Tian, Chunjie

    2016-01-04

    Arbuscular mycorrhizal (AM) fungi play an important role in energy flow and nutrient cycling, besides their wide distribution in the cosystem. With a long co-evolution, AM fungi and host plant have formed a symbiotic relationship, and fungal lipid metabolism may be the key point to find the symbiotic mechanism in arbusculart mycorrhiza. Here, we reviewed the most recent progress on the interaction between AM fungal lipid metabolism and symbiotic signaling networks, especially the response of AM fungal lipid metabolism to symbiotic signals. Furthermore, we discussed the response of AM fungal lipid storage and release to symbiotic or non-symbiotic status, and the correlation between fungal lipid metabolism and nutrient transfer in mycorrhiza. In addition, we explored the feedback of the lipolysis process to molecular signals during the establishment of symbiosis, and the corresponding material conversion and energy metabolism besides the crosstalk of fungal lipid metabolism and signaling networks. This review will help understand symbiotic mechanism of arbuscular mycorrhiza fungi and further application in ecosystem.

  10. 5.5.Fungal disease

    Institute of Scientific and Technical Information of China (English)

    1993-01-01

    930234 Penicilliosis marneffei report of a caseand review of literatures.KANG Xiaoming (康晓明),et al.Nanjing Army General Hosp,210002.Chin J Tuberc & Respir Dis 1992;15(6):336—338.Penicilliosis marneffei is a rare deep fungal in-fection.Southeast Asia is the endemic area.Inthe literatures before 1990,29 cases were re-ported and most of them were diagnosed patho-logically from autopsy.Since 1989 there havebeen more reports of P.marneffei in the HIV in-fected individuals or graft recipient,so far as

  11. Diagnosis of invasive fungal infections

    Directory of Open Access Journals (Sweden)

    Anna Maria Barbui

    2013-01-01

    Full Text Available A proper diagnostic strategy of invasive fungal infections (IFI is a very important component in the management of infectious complications in hematological patients. A good diagnostic approach should be adapted to the patient in relation to the underlying disease, stage of disease, localization of infection and immune status. None of the diagnostic markers can be entirely adopted for medical decision making, and sometimes it’s useful to use the combination of several microbiological tests.The diagnosis of IFI must therefore have a multidisciplinary approach that includes clinical suspicion, microbiological results and radiological evidence.

  12. Optimal Fungal Space Searching Algorithms.

    Science.gov (United States)

    Asenova, Elitsa; Lin, Hsin-Yu; Fu, Eileen; Nicolau, Dan V; Nicolau, Dan V

    2016-10-01

    Previous experiments have shown that fungi use an efficient natural algorithm for searching the space available for their growth in micro-confined networks, e.g., mazes. This natural "master" algorithm, which comprises two "slave" sub-algorithms, i.e., collision-induced branching and directional memory, has been shown to be more efficient than alternatives, with one, or the other, or both sub-algorithms turned off. In contrast, the present contribution compares the performance of the fungal natural algorithm against several standard artificial homologues. It was found that the space-searching fungal algorithm consistently outperforms uninformed algorithms, such as Depth-First-Search (DFS). Furthermore, while the natural algorithm is inferior to informed ones, such as A*, this under-performance does not importantly increase with the increase of the size of the maze. These findings suggest that a systematic effort of harvesting the natural space searching algorithms used by microorganisms is warranted and possibly overdue. These natural algorithms, if efficient, can be reverse-engineered for graph and tree search strategies.

  13. Fungal infections of the orbit

    Directory of Open Access Journals (Sweden)

    Bipasha Mukherjee

    2016-01-01

    Full Text Available Fungal infections of the orbit can lead to grave complications. Although the primary site of inoculation of the infective organism is frequently the sinuses, the patients can initially present to the ophthalmologist with ocular signs and symptoms. Due to its varied and nonspecific clinical features, especially in the early stages, patients are frequently misdiagnosed and even treated with steroids which worsen the situation leading to dire consequences. Ophthalmologists should be familiar with the clinical spectrum of disease and the variable presentation of this infection, as early diagnosis and rapid institution of appropriate therapy are crucial elements in the management of this invasive sino-orbital infection. In this review, relevant clinical, microbiological, and imaging findings are discussed along with the current consensus on local and systemic management. We review the recent literature and provide a comprehensive analysis. In the immunocompromised, as well as in healthy patients, a high index of suspicion must be maintained as delay in diagnosis of fungal pathology may lead to disfiguring morbidity or even mortality. Obtaining adequate diagnostic material for pathological and microbiological examination is critical. Newer methods of therapy, particularly oral voriconazole and topical amphotericin B, may be beneficial in selected patients.

  14. A novel class of fungal lipoxygenases

    NARCIS (Netherlands)

    Heshof, R.; Jylhä, S.; Haarmann, T.; Jørgensen, A.L.W.; Dalsgaard, T.K.; Graaff, de L.H.

    2014-01-01

    Lipoxygenases (LOXs) are well-studied enzymes in plants and mammals. However, fungal LOXs are less studied. In this study, we have compared fungal LOX protein sequences to all known characterized LOXs. For this, a script was written using Shell commands to extract sequences from the NCBI database an

  15. European gas market liberalisation: are regulatory regimes moving towards convergence?

    NARCIS (Netherlands)

    Haase, N.

    2008-01-01

    This study has assessed the evolution of regulatory regimes in European gas markets on the basis of panel data from the old member states (EU15) for the period between 2000 and 2005. The methodology used enabled us to assess whether regulatory regimes are converging. In this context, an index has

  16. Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation

    OpenAIRE

    Hogues, Hervé; Lavoie, Hugo; Sellam, Adnane; Mangos, Maria; Roemer, Terry; Purisima, Enrico; Nantel, André; Whiteway, Malcolm

    2008-01-01

    Coordinated ribosomal protein (RP) gene expression is crucial for cellular viability, but the transcriptional network controlling this regulon has only been well characterized in the yeast Saccharomyces cerevisiae. We have used whole-genome transcriptional and location profiling to establish that, in Candida albicans, the RP regulon is controlled by the Myb domain protein Tbf1 working in conjunction with Cbf1. These two factors bind both the promoters of RP genes and the rDNA locus; Tbf1 acti...

  17. On the ecology and evolution of fungal senescence

    NARCIS (Netherlands)

    Maas, M.F.P.M.

    2005-01-01

    Aging evolves in the shadow of natural selection: Since the efficiency of natural selection declines with age, organisms will over the course of generations accumulate intrinsic, genetic factors that have a negative effect only late in life. This is generally known as the 'mutation accumulation' the

  18. Allergic fungal sinusitis causing nasolacrimal duct obstruction.

    Science.gov (United States)

    Kim, Charles; Kacker, Ashutosh; Chee, Ru-Ik; Lelli, Gary J

    2013-04-01

    Allergic fungal sinusitis is thought to represent a chronic autoimmune reaction directed against fungal elements within the sinuses, and is commonly seen in individuals with a history of chronic sinusitis that is refractory to medical therapy. The authors present a case of allergic fungal sinusitis involving the lacrimal drainage system. A 54-year-old woman initially presented with recurrent erythema and induration of the left nasolacrimal sac due to dacryocystitis, which was unresponsive to treatment with topical and systemic antibiotics. Radiological evaluation demonstrated the presence of multiple soft tissue masses along the medial canthi. During subsequent endoscopic dacryocystorhinostomy, significant amounts of allergic mucin were found within the sinuses and marked eosinophilia was present within tissue obtained from the lacrimal sac, findings highly suggestive of allergic fungal sinusitis. A diagnosis of allergic fungal sinusitis should be considered in patients presenting with epiphora in the appropriate clinical context. However, involvement of the lacrimal drainage system is an exceedingly unusual presentation.

  19. Histone Acetylation in Fungal Pathogens of Plants

    Directory of Open Access Journals (Sweden)

    Junhyun Jeon

    2014-03-01

    Full Text Available Acetylation of histone lysine residues occurs in different organisms ranging from yeast to plants and mammals for the regulation of diverse cellular processes. With the identification of enzymes that create or reverse this modification, our understanding on histone acetylation has expanded at an amazing pace during the last two decades. In fungal pathogens of plants, however, the importance of such modification has only just begun to be appreciated in the recent years and there is a dearth of information on how histone acetylation is implicated in fungal pathogenesis. This review covers the current status of research related to histone acetylation in plant pathogenic fungi and considers relevant findings in the interaction between fungal pathogens and host plants. We first describe the families of histone acetyltransferases and deacetylases. Then we provide the cases where histone acetylation was investigated in the context of fungal pathogenesis. Finally, future directions and perspectives in epigenetics of fungal pathogenesis are discussed.

  20. Fungal Adaptations to Mutualistic Life with Ants

    DEFF Research Database (Denmark)

    Kooij, Pepijn Wilhelmus

    . However, in rare occasions fungal symbionts might come into contact with symbionts from other colonies. I showed that in both leaf-cutting ant genera incompatibility reactions between fungal strains can avoid intermixing of different strains, and that these reactions strengthen when genetic distance...... successful. To understand the evolutionary development of domestication of the fungus over the phylogeny of the Attine ants, I compared the average number of nuclei per cell for the fungal symbionts, for each of the different groups of fungus-growing ants. I found that the fungal symbionts of the paleo...... is increased. This pattern, however, becomes distorted when fungal symbionts are contested across ant genera. The most important mechanism in the succession of this mutualism of leaf-cutting ants is the controlled degradation of plant material. I show that in the area of Gamboa, Panama, the two leaf...

  1. Soil fungal community responses to global changes

    DEFF Research Database (Denmark)

    Haugwitz, Merian Skouw

    Global change will affect the functioning and structure of terrestrial ecosystems and since soil fungi are key players in organic matter decomposition and nutrient turnover, shifts in fungal community composition might have a strong impact on soil functioning. The main focus of this thesis...... and nutrient availability and storage. By combining molecular methods such as 454 pyrosequencing and quantitative PCR of fungal ITS amplicons with analyses of soil enzymes, nutrient pools of carbon, nitrogen and phosphorus we were able to characterize soil fungal communities as well as their impact on nutrient...... was therefore to investigate the impact of global environmental changes on soil fungal communities in a temperate and subartic heath ecosystem. The objective was further to determine global change effects on major functional groups of fungi and analyze the influence of fungal community changes on soil carbon...

  2. Chapter 8: Invasive fungal rhinosinusitis.

    Science.gov (United States)

    Duggal, Praveen; Wise, Sarah K

    2013-01-01

    Invasive fungal rhinosinusitis (IFRS) is a disease of the paranasal sinuses and nasal cavity that typically affects immunocompromised patients in the acute fulminant form. Early symptoms can often mimic rhinosinusitis, while late symptoms can cause significant morbidity and mortality. Swelling and mucosal thickening can quickly progress to pale or necrotic tissue in the nasal cavity and sinuses, and the disease can rapidly spread and invade the palate, orbit, cavernous sinus, cranial nerves, skull base, carotid artery, and brain. IFRS can be life threatening if left undiagnosed or untreated. While the acute fulminant form of IFRS is the most rapidly progressive and destructive, granulomatous and chronic forms also exist. Diagnosis of IFRS often mandates imaging studies in conjunction with clinical, endoscopic, and histopathological examination. Treatment of IFRS consists of reversing the underlying immunosuppression, antifungal therapy, and aggressive surgical debridement. With early diagnosis and treatment, IFRS can be treated and increase patient survival.

  3. Scabies, lice, and fungal infections.

    Science.gov (United States)

    Taplin, D; Meinking, T L

    1989-09-01

    Scabies and pediculosis capitis are frequent and often unrecognized causes of multiple streptococcal and staphylococcal pyodermas. Permethrin 1 per cent creme rinse (NIX) for head lice, and permethrin 5 per cent topical cream for scabies are new, highly effective, safe, and cosmetically elegant treatments which have shown superiority over older remedies. In populations in which pediculosis and scabies have resisted traditional lindane therapy, patients promptly responded to these permethrin products. Scabies in nursing homes is a persistent and expanding problem which demands a high level of diagnostic suspicion and an integrated approach to management. For fungal infections, several new broad-spectrum oral and topical agents have been introduced. Their successful use is enhanced by appropriate diagnostic tests which can be performed in the office setting. Recommendations and references are given to assist the physician in diagnosis and choice of therapy.

  4. Innate Defense against Fungal Pathogens.

    Science.gov (United States)

    Drummond, Rebecca A; Gaffen, Sarah L; Hise, Amy G; Brown, Gordon D

    2014-11-10

    Human fungal infections have been on the rise in recent years and proved increasingly difficult to treat as a result of the lack of diagnostics, effective antifungal therapies, and vaccines. Most pathogenic fungi do not cause disease unless there is a disturbance in immune homeostasis, which can be caused by modern medical interventions, disease-induced immunosuppression, and naturally occurring human mutations. The innate immune system is well equipped to recognize and destroy pathogenic fungi through specialized cells expressing a broad range of pattern recognition receptors (PRRs). This review will outline the cells and PRRs required for effective antifungal immunity, with a special focus on the major antifungal cytokine IL-17 and recently characterized antifungal inflammasomes.

  5. Fungal and mycotoxin assessment of dried edible mushroom in Nigeria.

    Science.gov (United States)

    Ezekiel, C N; Sulyok, M; Frisvad, J C; Somorin, Y M; Warth, B; Houbraken, J; Samson, R A; Krska, R; Odebode, A C

    2013-04-01

    In order to determine whether dried mushrooms are a foodstuff that may be less susceptible to infection by toxigenic molds and consequently to mycotoxin contamination, 34 dried market samples were analyzed. Fungal population was determined in the samples by conventional mycological techniques and molecular studies, while the spectrum of microbial metabolites including mycotoxins was analyzed by a liquid chromatography tandem mass spectrometric method covering 320 metabolites. Molds such as Fusarium, Penicillium, Trichoderma and aflatoxigenic species of Aspergillus (Aspergillus flavus and Aspergillus parvisclerotigenus) were recovered from all samples at varying levels. None of the mycotoxins addressed by regulatory limits in the EU was positively identified in the samples. However, 26 other fungal metabolites occurred at sub- to medium μg/kg levels in the samples, including aflatoxin/sterigmatocystin bio-precursors, bis-anthraquinone derivatives from Talaromyces islandicus, emerging toxins (e.g. enniatins) and other Fusarium metabolites, and clavine alkaloids. Although little is known on the toxicology of these substances, the absence of aflatoxins and other primary mycotoxins suggests that dried mushrooms may represent a relatively safe type of food in view of mycotoxin contamination.

  6. New insights into 1-aminocyclopropane-1-carboxylate (ACC deaminase phylogeny, evolution and ecological significance.

    Directory of Open Access Journals (Sweden)

    Francisco X Nascimento

    Full Text Available The main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (ACC deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth-promoting microorganisms. The ACC deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis was conducted. Strain habitat, origin and ACC deaminase activity were taken into account when analyzing the results. In order to unveil ACC deaminase origin, evolution and relationships with other closely related pyridoxal phosphate (PLP dependent enzymes a phylogenetic analysis was also performed. The data obtained show that ACC deaminase is mostly prevalent in some Bacteria, Fungi and members of Stramenopiles. Contrary to previous reports, we show that ACC deaminase genes are predominantly vertically inherited in various bacterial and fungal classes. Still, results suggest a considerable degree of horizontal gene transfer events, including interkingdom transfer events. A model for ACC deaminase origin and evolution is also proposed. This study also confirms the previous reports suggesting that the Lrp-like regulatory protein AcdR is a common mechanism regulating ACC deaminase expression in Proteobacteria, however, we also show that other regulatory mechanisms may be present in some Proteobacteria and other bacterial phyla. In this study we provide a more complete view of the role for ACC deaminase than was previously available. The results show that ACC deaminase may not only be related to plant growth promotion abilities, but may also play multiple roles in microorganism's developmental processes. Hence, exploring the origin and functioning of this enzyme may be the key in a variety of important agricultural and biotechnological applications.

  7. A novel class of fungal lipoxygenases.

    Science.gov (United States)

    Heshof, Ruud; Jylhä, Sirpa; Haarmann, Thomas; Jørgensen, Ann Louise Worsøe; Dalsgaard, Trine Kastrup; de Graaff, Leo H

    2014-02-01

    Lipoxygenases (LOXs) are well-studied enzymes in plants and mammals. However, fungal LOXs are less studied. In this study, we have compared fungal LOX protein sequences to all known characterized LOXs. For this, a script was written using Shell commands to extract sequences from the NCBI database and to align the sequences obtained using Multiple Sequence Comparison by Log-Expectation. We constructed a phylogenetic tree with the use of Quicktree to visualize the relation of fungal LOXs towards other LOXs. These sequences were analyzed with respect to the signal sequence, C-terminal amino acid, the stereochemistry of the formed oxylipin, and the metal ion cofactor usage. This study shows fungal LOXs are divided into two groups, the Ile- and the Val-groups. The Ile-group has a conserved WRYAK sequence that appears to be characteristic for fungal LOXs and has as a C-terminal amino acid Ile. The Val-group has a highly conserved WL-L/F-AK sequence that is also found in LOXs of plant and animal origin. We found that fungal LOXs with this conserved sequence have a Val at the C-terminus in contrast to other LOXs of fungal origin. Also, these LOXs have signal sequences implying these LOXs will be expressed extracellularly. Our results show that in this group, in addition to the Gaeumannomyces graminis and the Magnaporthe salvinii LOXs, the Aspergillus fumigatus LOX uses manganese as a cofactor.

  8. Fungal genome sequencing: basic biology to biotechnology.

    Science.gov (United States)

    Sharma, Krishna Kant

    2016-08-01

    The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research.

  9. Isolated secondary fungal infections of pleural cavity

    Directory of Open Access Journals (Sweden)

    Makbule Ergin

    2013-12-01

    Full Text Available Objectives: Pleural fungal infections are rare, but the incidence has been increasing with immunosuppressant diseases and use of immunosuppressive medications. In this report, we present 6 patients with pleural effusions that have been determined fungal infection. Methods: The medical records of patients with followed and treated due to fungal infection of the pleural were retrospectively reviewed. Result: The 6 cases whom was 58 of the value median for age were treated as surgical and medical due to fungal infection of the pleural cavity. Dyspnea, cough and chest pain were the most common symptoms. Fever, night sweats and expectoration are relatively rare. In 4 patients, the infections of pleural cavity developed on the bases of rheumatoid arthritis, tuberculosis, pleural mesothelioma and esophagopleural fistula. In two patients had isolated fungal infections. Cultural positivity was seen in 5 patients. Fungal hyphae were determined by cytopathology in all of the patients. As a surgical procedure, all of the patients underwent decortication or pleural biopsy and pleural irrigation. In all patients, antifungal agents were added to surgical procedures. Full recovery of infection was seen in 5 patients. One patient died. Conclusion: In immunosuppressive patients, the incidence of pleural effusions due to or associated with fungal infections are more common. Addition to culture of pleural fluid, histopathological evaluation of pleura will aid diagnosis. J Clin Exp Invest 2013; 4 (4: 443-446

  10. Fungal symbionts alter plant drought response.

    Science.gov (United States)

    Worchel, Elise R; Giauque, Hannah E; Kivlin, Stephanie N

    2013-04-01

    Grassland productivity is often primarily limited by water availability, and therefore, grasslands may be especially sensitive to climate change. Fungal symbionts can mediate plant drought response by enhancing drought tolerance and avoidance, but these effects have not been quantified across grass species. We performed a factorial meta-analysis of previously published studies to determine how arbuscular mycorrhizal (AM) fungi and endophytic fungal symbionts affect growth of grasses under drought. We then examined how the effect of fungal symbionts on plant growth was influenced by biotic (plant photosynthetic pathway) and abiotic (level of drought) factors. We also measured the phylogenetic signal of fungal symbionts on grass growth under control and drought conditions. Under drought conditions, grasses colonized by AM fungi grew larger than those without mycorrhizal symbionts. The increased growth of grasses conferred from fungal symbionts was greatest at the lowest soil moisture levels. Furthermore, under both drought and control conditions, C3 grasses colonized by AM fungi grew larger than C3 grasses without symbionts, but the biomass of C4 grasses was not affected by AM fungi. Endophytes did not increase plant biomass overall under any treatment. However, there was a phylogenetically conserved increase in plant biomass in grasses colonized by endophytes. Grasses and their fungal symbionts seem to interact within a context-dependent symbiosis, varying with biotic and abiotic conditions. Because plant-fungal symbioses significantly alter plant drought response, including these responses could improve our ability to predict grassland functioning under global change.

  11. Invasive fungal infections in renal transplant recipients.

    Science.gov (United States)

    Badiee, Parisa; Alborzi, Abdolvahab

    2011-12-01

    Invasive fungal infections are a significant and often lethal problem in transplant patients. Infections caused by geographically limited endemic fungi are infrequent, and Aspergillus species, Mucorales species, Candida species, and Cryptococcus neoformans are the opportunistic fungi responsible for most such infections. The symptoms of systemic fungal infections are nonspecific, particularly in their early stages. The high rates of mortality and graft loss owing to fungal infections render early diagnosis and treatment imperative in immunosuppressed patients. Current methods for the diagnosis of systemic fungal infections include imaging procedures, endoscopic methods and biopsies, microscopic and culture techniques, antibody and antigen-based serologic testing, and the detection (via polymerase chain reaction) of fungal deoxyribonucleic acid in blood or bronchoalveolar lavage fluid, as well as the careful analysis of signs and symptoms. Antifungal therapy should be initiated early in patients with a suspected fungal infection (even before laboratory findings have confirmed that diagnosis) and should be administered with appropriate adjustment of immunosuppressive regimens. To manage fungal infections in patients with renal failure, optimizing the pharmacokinetics of antifungal drugs to reduce the risk of nephrotoxicity is crucial.

  12. Clash of kingdoms or why Drosophila larvae positively respond to fungal competitors

    Directory of Open Access Journals (Sweden)

    Rohlfs Marko

    2005-01-01

    Full Text Available Abstract Background Competition with filamentous fungi has been demonstrated to be an important cause of mortality for the vast group of insects that depend on ephemeral resources (e.g. fruit, dung, carrion. Recent data suggest that the well-known aggregation of Drosophila larvae across decaying fruit yields a competitive advantage over mould, by which the larvae achieve a higher survival probability in larger groups compared with smaller ones. Feeding and locomotor behaviour of larger larval groups is assumed to cause disruption of fungal hyphae, leading to suppression of fungal growth, which in turn improves the chances of larval survival to the adult stage. Given the relationship between larval density, mould suppression and larval survival, the present study has tested whether fungal-infected food patches elicit communal foraging behaviour on mould-infected sites by which larvae might hamper mould growth more efficiently. Results Based on laboratory experiments in which Drosophila larvae were offered the choice between fungal-infected and uninfected food patches, larvae significantly aggregated on patches containing young fungal colonies. Grouping behaviour was also visible when larvae were offered only fungal-infected or only uninfected patches; however, larval aggregation was less strong under these conditions than in a heterogeneous environment (infected and uninfected patches. Conclusion Because filamentous fungi can be deadly competitors for insect larvae on ephemeral resources, social attraction of Drosophila larvae to fungal-infected sites leading to suppression of mould growth may reflect an adaptive behavioural response that increases insect larval fitness and can thus be discussed as an anti-competitor behaviour. These observations support the hypothesis that adverse environmental conditions operate in favour of social behaviour. In a search for the underlying mechanisms of communal behaviour in Drosophila, this study highlights

  13. Clash of kingdoms or why Drosophila larvae positively respond to fungal competitors.

    Science.gov (United States)

    Rohlfs, Marko

    2005-01-27

    BACKGROUND: Competition with filamentous fungi has been demonstrated to be an important cause of mortality for the vast group of insects that depend on ephemeral resources (e.g. fruit, dung, carrion). Recent data suggest that the well-known aggregation of Drosophila larvae across decaying fruit yields a competitive advantage over mould, by which the larvae achieve a higher survival probability in larger groups compared with smaller ones. Feeding and locomotor behaviour of larger larval groups is assumed to cause disruption of fungal hyphae, leading to suppression of fungal growth, which in turn improves the chances of larval survival to the adult stage. Given the relationship between larval density, mould suppression and larval survival, the present study has tested whether fungal-infected food patches elicit communal foraging behaviour on mould-infected sites by which larvae might hamper mould growth more efficiently. RESULTS: Based on laboratory experiments in which Drosophila larvae were offered the choice between fungal-infected and uninfected food patches, larvae significantly aggregated on patches containing young fungal colonies. Grouping behaviour was also visible when larvae were offered only fungal-infected or only uninfected patches; however, larval aggregation was less strong under these conditions than in a heterogeneous environment (infected and uninfected patches). CONCLUSION: Because filamentous fungi can be deadly competitors for insect larvae on ephemeral resources, social attraction of Drosophila larvae to fungal-infected sites leading to suppression of mould growth may reflect an adaptive behavioural response that increases insect larval fitness and can thus be discussed as an anti-competitor behaviour. These observations support the hypothesis that adverse environmental conditions operate in favour of social behaviour. In a search for the underlying mechanisms of communal behaviour in Drosophila, this study highlights the necessity of

  14. The prominent role of fungi and fungal enzymes in the ant-fungus biomass conversion symbiosis.

    Science.gov (United States)

    Lange, L; Grell, M N

    2014-06-01

    Molecular studies have added significantly to understanding of the role of fungi and fungal enzymes in the efficient biomass conversion, which takes place in the fungus garden of leaf-cutting ants. It is now clear that the fungal symbiont expresses the full spectrum of genes for degrading cellulose and other plant cell wall polysaccharides. Since the start of the genomics era, numerous interesting studies have especially focused on evolutionary, molecular, and organismal aspects of the biological and biochemical functions of the symbiosis between leaf-cutting ants (Atta spp. and Acromyrmex spp.) and their fungal symbiont Leucoagaricus gongylophorus. Macroscopic observations of the fungus-farming ant colony inherently depict the ants as the leading part of the symbiosis (the myrmicocentric approach, overshadowing the mycocentric aspects). However, at the molecular level, it is fungal enzymes that enable the ants to access the nutrition embedded in recalcitrant plant biomass. Our hypothesis is that the evolutionary events that established fungus-farming practice were predisposed by a fascinating fungal evolution toward increasing attractiveness to ants. This resulted in the ants allowing the fungus to grow in the nests and began to supply plant materials for more fungal growth. Molecular studies also confirm that specialized fungal structures, the gongylidia, with high levels of proteins and rich blend of enzymes, are essential for symbiosis. Harvested and used as ant feed, the gongylidia are the key factor for sustaining the highly complex leaf-cutting ant colony. This microbial upgrade of fresh leaves to protein-enriched animal feed can serve as inspiration for modern biorefinery technology.

  15. Fungal glycans and the innate immune recognition

    Directory of Open Access Journals (Sweden)

    Rodrigo Tinoco Figueiredo

    2014-10-01

    Full Text Available Polysaccharides such as α- and β-glucans, chitin and glycoproteins extensively modified with both N- and O-linked carbohydrates are the major components of fungal surfaces. The fungal cell wall is an excellent target for the action of antifungal agents, since most of its components are absent from mammalian cells. Recognition of these carbohydrate-containing molecules by the innate immune system triggers inflammatory responses and activation of microbicidal mechanisms by leukocytes. This review will discuss the structure of surface fungal glycoconjugates and polysaccharides and their recognition by innate immune receptors.

  16. Fungal Mating Pheromones: Choreographing the Dating Game

    Science.gov (United States)

    Jones, Stephen K.; Bennett, Richard J.

    2011-01-01

    Pheromones are ubiquitous from bacteria to mammals - a testament to their importance in regulating inter-cellular communication. In fungal species, they play a critical role in choreographing interactions between mating partners during the program of sexual reproduction. Here, we describe how fungal pheromones are synthesized, their interactions with G protein-coupled receptors, and the signals propagated by this interaction, using Saccharomyces cerevisiae as a reference point. Divergence from this model system is compared amongst the ascomycetes and basidiomycetes, which reveals the wealth of information that has been gleaned from studying pheromone-driven processes across a wide spectrum of the fungal kingdom. PMID:21496492

  17. Fungal colonization of air-conditioning systems

    Directory of Open Access Journals (Sweden)

    Ljaljević-Grbić Milica

    2008-01-01

    Full Text Available Fungi have been implicated as quantitatively the most important bioaerosol component of indoor air associated with contaminated air-conditioning systems. rarely, indoor fungi may cause human infections, but more commonly allergenic responses ranging from pneumonitis to asthma-like symptoms. From all air conditioner filters analyzed, 16 fungal taxa were isolated and identified. Aspergillus fumigatus causes more lethal infections worldwide than any other mold. Air-conditioning filters that adsorb moisture and volatile organics appear to provide suitable substrates for fungal colonization. It is important to stress that fungal colonization of air-conditioning systems should not be ignored, especially in hospital environments.

  18. Fungal mating pheromones: choreographing the dating game.

    Science.gov (United States)

    Jones, Stephen K; Bennett, Richard J

    2011-07-01

    Pheromones are ubiquitous from bacteria to mammals - a testament to their importance in regulating inter-cellular communication. In fungal species, they play a critical role in choreographing interactions between mating partners during the program of sexual reproduction. Here, we describe how fungal pheromones are synthesized, their interactions with G protein-coupled receptors, and the signals propagated by this interaction, using Saccharomyces cerevisiae as a reference point. Divergence from this model system is compared amongst the ascomycetes and basidiomycetes, which reveals the wealth of information that has been gleaned from studying pheromone-driven processes across a wide spectrum of the fungal kingdom.

  19. Fungal rhinosinusitis with atypical presentation – a report of two cases

    Directory of Open Access Journals (Sweden)

    Rafael da Costa Monsanto

    2015-05-01

    Full Text Available Rhinosinusitis affects approximately 20% of the population, and the chronic rhinosinusitis represents over 90% of all cases of rhinosinusitis. The correct diagnosis is important for proper treatment and to predict its evolution. This study presents two cases of atypical frontal sinus disease, which the follow-up revealed a diagnosis of fungal rhinosinusitis. The present study aims to describe the cases of two patients with atypical lesions on the left frontal sinus; the treatment options, surgical approach, results, diagnosis and follow-up are further discussed. A significant increase in the reported cases of fungal rhinosinusitis has been seen in the last two decades, justified by the use of broad-spectrum antibiotics and steroids, as well as the increased number of immunocompromised individuals. This study reports the cases of two patients with a type of fungal rhinosinusitis named "fungal ball", characterized by a tangle of hyphae in the sinuses without tissue invasion. The treatment included surgical removal of the fungal infectious process with aeration of the affected sinus, and the procedure was successfully performed in our patients.

  20. Expanding Fungal Diets Through Synthetic Algal-Fungal Mutualism

    Science.gov (United States)

    Sharma, Alaisha; Galazka, Jonathan (Editor)

    2015-01-01

    Fungi can synthesize numerous molecules with important properties, and could be valuable production platforms for space exploration and colonization. However, as heterotrophs, fungi require reduced carbon. This limits their efficiency in locations such as Mars, where reduced carbon is scarce. We propose a system to induce mutualistic symbiosis between the green algae Chlamydomonas reinhardtii and the filamentous fungi Neurospora crassa. This arrangement would mimic natural algal-fungal relationships found in lichens, but have added advantages including increased growth rate and genetic tractability. N. crassa would metabolize citrate (C6H5O7 (sup -3)) and release carbon dioxide (CO2) that C. reinhardtii would assimilate into organic sugars during photosynthesis. C. reinhardtii would metabolize nitrate (NO3-) and release ammonia (NH3) as a nitrogen source for N. crassa. A N. crassa mutant incapable of reducing nitrate will be used to force this interaction. This system eliminates the need to directly supply its participants with carbon dioxide and ammonia. Furthermore, the release of oxygen by C. reinhardtii via photosynthesis would enable N. crassa to respire. We hope to eventually create a system closer to lichen, in which the algae transfers not only nitrogen but reduced carbon, as organic sugars, to the fungus for growth and production of valuable compounds.

  1. The Evolution of the International Financial Regulatory Pattern and Its Enlightenment to China%国际金融监管格局变迁及对我国的启示

    Institute of Scientific and Technical Information of China (English)

    易娟

    2014-01-01

    The financial regulatory structure and organization mode is one of the hot theoretical topics in recent 20 years. The pa-per investigates the changes of the international financial regulatory pattern since the end of last century, comparatively studies the fi-nancial regulatory reform process of major developed economies such as Britain and the United States, and then puts forward sugges-tions on perfecting China’s financial regulatory framework based on the present situation of the financial regulation.%金融监管结构和组织模式是近20年理论界和监管当局最为关注的热点问题之一。本文从国际金融监管格局的变迁入手,对比研究了英美两国金融监管体制改革的路径,结合我国金融监管现状,提出完善我国金融监管框架的建议。

  2. PNNL Fungal Biotechnology Core DOE-OBP Project

    Energy Technology Data Exchange (ETDEWEB)

    Baker, Scott E.; Bruno, Kenneth S.; Butcher, Mark G.; Collett, James R.; Culley, David E.; Dai, Ziyu; Magnuson, Jon K.; Panisko, Ellen A.

    2009-11-30

    In 2009, we continued to address barriers to fungal fermentation in the primary areas of morphology control, genomics, proteomics, fungal hyperproductivity, biomass-to-products via fungal based consolidated bioprocesses, and filamentous fungal ethanol. “Alternative renewable fuels from fungi” was added as a new subtask. Plans were also made to launch a new advanced strain development subtask in FY2010.

  3. 7 CFR 201.58d - Fungal endophyte test.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Fungal endophyte test. 201.58d Section 201.58d... REGULATIONS Examinations in the Administration of the Act § 201.58d Fungal endophyte test. A fungal endophyte test may be used to determine the amount of fungal endophyte (Acremonium spp.) in certain grasses....

  4. Organ Transplant Patients and Fungal Infections

    Science.gov (United States)

    ... M, Practice ASTIDCo. Endemic fungal infections in solid organ transplantation. American Journal of Transplantation 2013;13 Suppl 4: ... Michaels MG. Strategies for safe living after solid organ transplantation. American Journal of Transplantation 2013;13 Suppl 4: ...

  5. HIV/AIDS and Fungal Infections

    Science.gov (United States)

    ... Environmental Diseases Mycotic Diseases Branch People living with HIV/AIDS Recommend on Facebook Tweet Share Compartir As ... Page Preventing fungal infections in people living with HIV/AIDS Fungi are difficult to avoid because they ...

  6. Foreword: Special issue on fungal grapevine diseases

    Science.gov (United States)

    An impressively large proportion of fungicides applied in European, North American and Australian agriculture has been used to manage grapevine powdery mildew (Erysiphe necator), grapevine downy mildew (Plasmopara viticola), and botrytis bunch rot (Botrytis cinerea). These fungal and oomycetous plan...

  7. Soil fungal community responses to global changes

    DEFF Research Database (Denmark)

    Haugwitz, Merian Skouw

    Global change will affect the functioning and structure of terrestrial ecosystems and since soil fungi are key players in organic matter decomposition and nutrient turnover, shifts in fungal community composition might have a strong impact on soil functioning. The main focus of this thesis...... composition of fungi, but the effects were generally limited to the litter layer and the uppermost humus layer (0-5 cm), which was unexpected considering the ecosystem had been manipulated for 18 years. Taken together the global change experiments altered the soil fungal communities and thereby highlight...... was therefore to investigate the impact of global environmental changes on soil fungal communities in a temperate and subartic heath ecosystem. The objective was further to determine global change effects on major functional groups of fungi and analyze the influence of fungal community changes on soil carbon...

  8. postharvest fungal deterioration of tomato (lycopersicum esculentum ...

    African Journals Online (AJOL)

    Dr A.B.Ahmed

    the effect of some fungal species on the nutritional worth of tomatoes .... flask and then boiled for another 30minutes under the cold-finger condenser rotating the ..... mycotoxicoses, liver damage, suppression of the immune system and death ...

  9. (Post-)genomics approaches in fungal research.

    Science.gov (United States)

    Aguilar-Pontes, María Victoria; de Vries, Ronald P; Zhou, Miaomiao

    2014-11-01

    To date, hundreds of fungal genomes have been sequenced and many more are in progress. This wealth of genomic information has provided new directions to study fungal biodiversity. However, to further dissect and understand the complicated biological mechanisms involved in fungal life styles, functional studies beyond genomes are required. Thanks to the developments of current -omics techniques, it is possible to produce large amounts of fungal functional data in a high-throughput fashion (e.g. transcriptome, proteome, etc.). The increasing ease of creating -omics data has also created a major challenge for downstream data handling and analysis. Numerous databases, tools and software have been created to meet this challenge. Facing such a richness of techniques and information, hereby we provide a brief roadmap on current wet-lab and bioinformatics approaches to study functional genomics in fungi.

  10. The structure and function of fungal cells

    Science.gov (United States)

    Nozawa, Y.

    1984-01-01

    The structure and function of fungal cell walls were studied with particular emphasis on dermatophytes. Extraction, isolation, analysis, and observation of the cell wall structure and function were performed. The structure is described microscopically and chemically.

  11. Fungal contaminants observed during micropropagation of Lilium ...

    African Journals Online (AJOL)

    Micropropagation is a rapid propagation technique, but the greatest problem is contamination with fungi and bacteria. ... Fungal contaminants formed during the culture were determined. ... Bulb scales rinsed in water were surface sterilized, then solutions containing chemotherapeutic substances (Benomyl, ... Article Metrics.

  12. Fungal rhino sinusitisin in tehran, iran

    NARCIS (Netherlands)

    Nazeri, M.; Hashemi, S.J.; Ardehali, M.; Rezaei, S.; Seyedmousavi, S.; Zareei, M.; Hosseinjani, E.

    2015-01-01

    BACKGROUND: Fungal rhino sinusitis (FRS) is an important infection of para nasal sinuses, which encompasses two main categories; invasive and noninvasive forms according to histopathological findings. Aspergillus spp are the most common species isolated from noninvasive form, while Mucorales are

  13. Air Contamination With Fungals In Museum

    Science.gov (United States)

    Scarlat, Iuliana; Haiducu, Maria; Stepa, Raluca

    2015-07-01

    The aim of the studies was to determine the level and kind of fungal contamination of air in museum, deposits patrimony, restoration and conservation laboratories and their effects on health of workers. Microbiological air purity was measured with a SAS-100 Surface Air System impactor. The fungal contamination was observed in all 54 rooms where we made determinations. The highest levels of fungal were recorded at rooms with hygroscopic patrimony objects, eg carpets, chairs, upholstered chairs, books etc. The most species identified included under common allergens: Aspergillus, Penicillium, and Mucor. There fungal species belonging to the genus identified in this study, can trigger serious diseases museum workers, such as for example Aspergillus fumigatus, known allergies and toxic effects that may occur. In some places of the museum, occupational exposure limit values to fungi present in the air in the work environment, recommended by the specialized literature, have been overcome.

  14. Zoosporic fungal parasites of marine biota

    Digital Repository Service at National Institute of Oceanography (India)

    RaghuKumar, C.

    laboratory media. In such instances, a detailed and careful examination of the disease symptoms and the endobiotic fungal parasites is to be recorded. Maintaining dual culture of the healthy and infected host also helps to fulfill these postulates partially....

  15. Spontaneous course of an untreated fungal spondylitis

    Energy Technology Data Exchange (ETDEWEB)

    Wittig, C.; Mueller, R.T.; Konermann, H.

    1989-06-09

    After 29 known cases in the world, we report another case of fungal spondylitis being not yet treated. Within four months with increasing clinical complaints and without neurological defects the disease led to a complete involvement of two vertebras and their partial resorption. An early radiologic hint in fungal spondylitis is possible, a sure diagnosis, however, depends on puncture. Pathogenetic aspects and the importance of a new method to identify candida infection in blood-sample are discussed. (orig.).

  16. Fungal Endophthalmitis Associated with Compounded Products

    OpenAIRE

    Mikosz, Christina A.; Rachel M. Smith; Kim, Moon; Tyson, Clara; Lee, Ellen H.; Adams, Eleanor; Straif-Bourgeois, Susanne; Sowadsky, Rick; Arroyo, Shannon; Grant-Greene, Yoran; Duran, Julie; Vasquez, Yvonne; Robinson, Byron F.; Harris, Julie R.; Lockhart, Shawn R.

    2014-01-01

    Fungal endophthalmitis is a rare but serious infection. In March 2012, several cases of probable and laboratory-confirmed fungal endophthalmitis occurring after invasive ocular procedures were reported nationwide. We identified 47 cases in 9 states: 21 patients had been exposed to the intraocular dye Brilliant Blue G (BBG) during retinal surgery, and the other 26 had received an intravitreal injection containing triamcinolone acetonide. Both drugs were produced by Franck’s Compounding Lab (Oc...

  17. Prospects for the development of fungal vaccines.

    OpenAIRE

    Deepe, G S

    1997-01-01

    In an era that emphasizes the term "cost-effective," vaccines are the ideal solution to preventing disease at a relatively low cost to society. Much of the previous emphasis has been on childhood scourges such as measles, mumps, rubella, poliomyelitis, and Haemophilus influenzae type b. The concept of vaccines for fungal diseases has had less impact because of the perceived limited problem. However, fungal diseases have become increasingly appreciated as serious medical problems that require ...

  18. Fungal infections of the oral mucosa

    OpenAIRE

    P Anitha Krishnan

    2012-01-01

    Fungal infections in humans occur as a result of defects in the immune system. An increasing emergence in oral Candidal and non-Candidal fungal infections is evident in the past decade owing to the rise in the immunodeficient and immunocompromised population globally. Oral Candidal infection usually involves a compromised host and the compromise may be local or systemic. Local compromising factors include decreased salivation, poor oral hygiene, wearing dentures among others while systemic fa...

  19. Association of fungal sepsis and galactosemia.

    Science.gov (United States)

    Verma, Sanjay; Bharti, Bhavneet; Inusha, P

    2010-06-01

    Galactosemia is one of the rare inborn errors of metabolism, which if detected early can be treated effectively. Galactosemic infants have a significant increased risk of developing sepsis. E. coli sepsis is a known entity, and also an important cause of early mortality in these children. But fungal sepsis in these patients is rarely reported. Here is a case of 45 day-old child who presented with fungal sepsis, which on investigation turned out to be galactosemia.

  20. Fungal Mating Pheromones: Choreographing the Dating Game

    OpenAIRE

    2011-01-01

    Pheromones are ubiquitous from bacteria to mammals - a testament to their importance in regulating inter-cellular communication. In fungal species, they play a critical role in choreographing interactions between mating partners during the program of sexual reproduction. Here, we describe how fungal pheromones are synthesized, their interactions with G protein-coupled receptors, and the signals propagated by this interaction, using Saccharomyces cerevisiae as a reference point. Divergence fro...

  1. Fungal allelochemicals in insect pest management.

    Science.gov (United States)

    Holighaus, Gerrit; Rohlfs, Marko

    2016-07-01

    Interactions between insects and fungi are widespread, and important mediators of these interactions are fungal chemicals that can therefore be considered as allelochemicals. Numerous studies suggest that fungal chemicals can affect insects in many different ways. Here, we apply the terminology established by insect-plant ecologists for categorizing the effect of fungal allelochemicals on insects and for evaluating the application potential of these chemicals in insect pest management. Our literature survey shows that fungal volatile and non-volatile chemicals have an enormous potential to influence insect behavior and fitness. Many of them still remain to be discovered, but some recent examples of repellents and toxins could open up new ways for developing safe insect control strategies. However, we also identified shortcomings in our understanding of the chemical ecology of insect-fungus interactions and the way they have been investigated. In particular, the mode-of-action of fungal allelochemicals has often not been appropriately designated or examined, and the way in which induction by insects affects fungal chemical diversity is poorly understood. This review should raise awareness that in-depth ecological studies of insect-fungus interactions can reveal novel allelochemicals of particular benefit for the development of innovative insect pest management strategies.

  2. Burden of fungal infections in Senegal.

    Science.gov (United States)

    Badiane, Aida S; Ndiaye, Daouda; Denning, David W

    2015-10-01

    Senegal has a high rate of tuberculosis and a low HIV seropositivity rate and aspergilloma, life-threatening fungal infections, dermatophytosis and mycetoma have been reported in this study. All published epidemiology papers reporting fungal infection rates from Senegal were identified. Where no data existed, we used specific populations at risk and fungal infection frequencies in each to estimate national incidence or prevalence. The results show that tinea capitis is common being found in 25% of children, ~1.5 million. About 191,000 Senegalese women get recurrent vaginal thrush, ≥4 times annually. We estimate 685 incident cases of chronic pulmonary aspergillosis (CPA) following TB and prevalence of 2160 cases. Asthma prevalence in adults varies from 3.2% to 8.2% (mean 5%); 9976 adults have allergic bronchopulmonary aspergillosis (ABPA) and 13,168 have severe asthma with fungal sensitisation (SAFS). Of the 59,000 estimated HIV-positive patients, 366 develop cryptococcal meningitis; 1149 develop Pneumocystis pneumonia and 1946 develop oesophageal candidiasis, in which oral candidiasis (53%) and dermatophytosis (16%) are common. Since 2008-2010, 113 cases of mycetoma were diagnosed. In conclusion, we estimate that 1,743,507 (12.5%) people in Senegal suffer from a fungal infection, excluding oral candidiasis, fungal keratitis, invasive candidiasis or aspergillosis. Diagnostic and treatment deficiencies should be rectified to allow epidemiological studies.

  3. Structure and biological functions of fungal cerebrosides

    Directory of Open Access Journals (Sweden)

    Barreto-Bergter Eliana

    2004-01-01

    Full Text Available Ceramide monohexosides (CMHs, cerebrosides are glycosphingolipids composed of a hydrophobic ceramide linked to one sugar unit. In fungal cells, CMHs are very conserved molecules consisting of a ceramide moiety containing 9-methyl-4,8-sphingadienine in amidic linkage to 2-hydroxyoctadecanoic or 2-hydroxyhexadecanoic acids, and a carbohydrate portion consisting of one residue of glucose or galactose. 9-Methyl 4,8-sphingadienine-containing ceramides are usually glycosylated to form fungal cerebrosides, but the recent description of a ceramide dihexoside (CDH presenting phytosphingosine in Magnaporthe grisea suggests the existence of alternative pathways of ceramide glycosylation in fungal cells. Along with their unique structural characteristics, fungal CMHs have a peculiar subcellular distribution and striking biological properties. In Pseudallescheria boydii, Candida albicans, Cryptococcus neoformans, Aspergillus nidulans, A. fumigatus, and Schizophyllum commune, CMHs are apparently involved in morphological transitions and fungal growth. The elucidation of structural and functional aspects of fungal cerebrosides may therefore contribute to the design of new antifungal agents inhibiting growth and differentiation of pathogenic species.

  4. Fungal Keratitis - Improving Diagnostics by Confocal Microscopy

    Directory of Open Access Journals (Sweden)

    Esben Nielsen

    2013-12-01

    Full Text Available Purpose: Introducing a simple image grading system to support the interpretation of in vivo confocal microscopy (IVCM images in filamentous fungal keratitis. Setting: Clinical and confocal studies took place at the Department of Ophthalmology, Aarhus University Hospital, Denmark. Histopathological analysis was performed at the Eye Pathology Institute, Department of Neuroscience and Pharmacology, University of Copenhagen, Denmark. Methods: A recent series of consecutive patients with filamentous fungal keratitis is presented to demonstrate the results from in-house IVCM. Based upon our experience with IVCM and previously published images, we composed a grading system for interpreting IVCM images of filamentous fungal keratitis. Results: A recent case series of filamentous fungal keratitis from 2011 to 2012 was examined. There were 3 male and 3 female patients. Mean age was 44.5 years (range 12-69, 6 out of 17 (35% cultures were positive and a total of 6/7 (86% IVCM scans were positive. Three different categories of IVCM results for the grading of diagnostic certainty were formed. Conclusion: IVCM is a valuable tool for diagnosing filamentous fungal keratitis. In order to improve the reliability of IVCM, we suggest implementing a simple and clinically applicable grading system for aiding the interpretation of IVCM images of filamentous fungal keratitis.

  5. Genome-wide fungal stress responsive miRNA expression in wheat.

    Science.gov (United States)

    Inal, Behçet; Türktaş, Mine; Eren, Hakan; Ilhan, Emre; Okay, Sezer; Atak, Mehmet; Erayman, Mustafa; Unver, Turgay

    2014-12-01

    MicroRNAs (miRNAs) are small non-coding class of RNAs. They were identified in many plants with their diverse regulatory roles in several cellular and metabolic processes. A number of miRNAs were involved in biotic and abiotic stress responses. Here, fungal stress responsive wheat miRNAs were analyzed by using miRNA-microarray strategy. Two different fungi (Fusarium culmorum and Bipolaris sorokiniana) were inoculated on resistant and sensitive wheat cultivars. A total of 87 differentially regulated miRNAs were detected in the 8 × 15 K array including all of the available plant miRNAs. Using bioinformatics tools, the target transcripts of responsive miRNAs were predicted, and related biological processes and mechanisms were assessed. A number of the miRNAs such as miR2592s, miR869.1, miR169b were highly differentially regulated showing more than 200-fold change upon fungal-inoculation. Some of the miRNAs were identified as fungal-inoculation responsive for the first time. The analyses showed that some of the differentially regulated miRNAs targeted resistance-related genes such as LRR, glucuronosyl transferase, peroxidase and Pto kinase. The comparison of the two miRNA-microarray analyses indicated that fungal-responsive wheat miRNAs were differentially regulated in pathogen- and cultivar-specific manners.

  6. Engineering and Applications of fungal laccases for organic synthesis

    Directory of Open Access Journals (Sweden)

    Ballesteros Antonio

    2008-11-01

    Full Text Available Abstract Laccases are multi-copper containing oxidases (EC 1.10.3.2, widely distributed in fungi, higher plants and bacteria. Laccase catalyses the oxidation of phenols, polyphenols and anilines by one-electron abstraction, with the concomitant reduction of oxygen to water in a four-electron transfer process. In the presence of small redox mediators, laccase offers a broader repertory of oxidations including non-phenolic substrates. Hence, fungal laccases are considered as ideal green catalysts of great biotechnological impact due to their few requirements (they only require air, and they produce water as the only by-product and their broad substrate specificity, including direct bioelectrocatalysis. Thus, laccases and/or laccase-mediator systems find potential applications in bioremediation, paper pulp bleaching, finishing of textiles, bio-fuel cells and more. Significantly, laccases can be used in organic synthesis, as they can perform exquisite transformations ranging from the oxidation of functional groups to the heteromolecular coupling for production of new antibiotics derivatives, or the catalysis of key steps in the synthesis of complex natural products. In this review, the application of fungal laccases and their engineering by rational design and directed evolution for organic synthesis purposes are discussed.

  7. Production of Dissolved Organic Matter During Fungal Wood Rot Decay

    Science.gov (United States)

    Filley, T. R.; Jellison, J.; Goodell, B.; Kelley, S.; Davis, M.

    2002-12-01

    Dissolved organic matter mediates numerous biogeochemical processes in soil systems impacting subsurface microbial activity, redox chemistry, soil structure, and carbon and nitrogen sequestration. The structure and chemistry of DOM is a function of the inherited chemistry of the source material, the type of microbial action that has occurred, and selective interaction with mineral substrates. The type of fungal decomposition imparted to woody tissue is a major factor in determining the nature of DOM in forest soils. In order to investigate the relationship between fungal decomposition and the nature of DOM in coniferous forest soils we conducted 32-week inoculation studies on spruce sapwood with basidiomycete brown-rot wood decay fungi where leachable dissolved and colloidal organic matter was separated from decayed residue. A detailed examination of the organic fractions was conducted using 13C-labeled tetramethylammonium hydroxide thermochemolysis, solid-state 13C-NMR, and electrospray mass spectrometry. The progressive stages of microbial decay (cellulolytic and ligninolytic) were manifested in the chemical composition of the DOM which showed an evolution from a composition initially polysaccharide rich to one dominated by mildly oxidized and demethylated lignin. Upon removal of all polysaccharides at 16 weeks the DOM (up to 10% by weight of the original tissue) looked chemically distinct from the degraded residue

  8. Hypopyon in patients with fungal keratitis

    Institute of Scientific and Technical Information of China (English)

    XU Ling-juan; SONG Xiu-sheng; ZHAO Jing; SUN Shi-ying; XIE Li-xin

    2012-01-01

    Background Hypopyon is common in eyes with fungal keratitis.The evaluation of the clinical features,culture results and the risk factors for hypopyon and of the possible correlation between hypopyon and the treatment outcome could be helpful for making treatment decisions.Methods The medical records of 1066 inpatients (1069 eyes) with fungal keratitis seen at the Shandong Eye Institute from January 2000 to December 2009 were reviewed retrospectively for demographic features,risk factors,clinical characteristics,laboratory findings and treatment outcomes.The incidence of hypopyon,the fungal culture positivity for hypopyon,risk factors for hypopyon and the effect of hypopyon on the treatment and prognosis were determined.Results We identified 1069 eyes with fungal keratitis.Of the 850 fungal culture-positive eyes,the Fusarium species was the most frequent (73.6%),followed by Altemaria (10.0%) and Aspergillus (9.0%).Upon admission,562 (52.6%)eyes with hypopyon were identified.The hypopyon of 66 eyes was evaluated via fungal culturing,and 31 eyes (47.0%)were positive.A total of 194 eyes had ocular hypertension,and 172 (88.7%) of these eyes had hypopyon (P <0.001).Risk factors for incident hypopyon included long duration of symptoms (P <0.001),large lesion size (P <0.001) and infection caused by the Fusarium and Aspergillus species (P <0.001).The positivity of fungal culture for hypopyon was associated with duration of symptoms and lesion size.Surgical intervention was more common in cases with hypopyon (P <0.001).Hypopyon was a risk factor for the recurrence of fungal keratitis after corneal transplantation (P=0.002).Conclusions Hypopyon is common in patients with severe fungal keratitis and can cause ocular hypertension.About half of the hypopyon cases were positive based on fungal culture.Long duration of symptoms,large lesion size and infection with the Fusarium and Aspergillus species were risk factors for hypopyon.The presence of hypopyon

  9. Novel Regulatory Mechanisms of Pathogenicity and Virulence to Combat MDR in Candida albicans

    Directory of Open Access Journals (Sweden)

    Saif Hameed

    2013-01-01

    Full Text Available Continuous deployment of antifungals in treating infections caused by dimorphic opportunistic pathogen Candida albicans has led to the emergence of drug resistance resulting in cross-resistance to many unrelated drugs, a phenomenon termed multidrug resistance (MDR. Despite the current understanding of major factors which contribute to MDR mechanisms, there are many lines of evidence suggesting that it is a complex interplay of multiple factors which may be contributed by still unknown mechanisms. Coincidentally with the increased usage of antifungal drugs, the number of reports for antifungal drug resistance has also increased which further highlights the need for understanding novel molecular mechanisms which can be explored to combat MDR, namely, ROS, iron, hypoxia, lipids, morphogenesis, and transcriptional and signaling networks. Considering the worrying evolution of MDR and significance of C. albicans being the most prevalent human fungal pathogen, this review summarizes these new regulatory mechanisms which could be exploited to prevent MDR development in C. albicans as established from recent studies.

  10. Biogeography in the air: fungal diversity over land and oceans

    Directory of Open Access Journals (Sweden)

    J. Fröhlich-Nowoisky

    2011-07-01

    Full Text Available Biogenic aerosols are relevant for the Earth system, climate, and public health on local, regional, and global scales. Up to now, however, little is known about the diversity and biogeography of airborne microorganisms. We present the first DNA-based analysis of airborne fungi on global scales, showing pronounced geographic patterns and boundaries. In particular we found that the ratio of species richness between Basidiomycota and Ascomycota is much higher in continental air than in marine air. This may be an important difference between the "blue ocean" and "green ocean" regimes in the formation of clouds and precipitation, for which fungal spores can act as nuclei. Our findings also suggest that air flow patterns and the global atmospheric circulation are important for the evolution of microbial ecology and for the understanding of global changes in biodiversity.

  11. Etiological Analysis of Fungal Keratitis and Rapid Identification of Predominant Fungal Pathogens.

    Science.gov (United States)

    He, Dan; Hao, Jilong; Gao, Song; Wan, Xue; Wang, Wanting; Shan, Qiushi; Wang, Li

    2016-02-01

    Fungal keratitis is a worldwide-distributed refractory and potentially blinding ocular infection caused by various fungi. It is necessary to investigate the etiological and epidemiological characteristics of this disease and establish a rapid and specific pathogenic identification method. Here, we isolated and identified fungal pathogens of 275 patients with presumed fungal keratitis from Jilin Province, China, and conducted statistical analyses of epidemiological information. The positive rate of fungal culture was 72.0 %. Fusarium sp. was the most common genus among 210 fungal isolates. The predominant species were Fusarium solani, Aspergillus fumigatus, and Candida glabrata, which accounted for over 50 % of the isolated organisms. Corneal trauma and previous use of drugs were the most important predisposing factors. In addition, a multiplex polymerase chain reaction (PCR) was designed with species-specific primers of the three species that could identify them with amplicons of approximately 330 bp from F. solani, 275 bp from A. fumigatus, and 230 bp from C. glabrata. Additionally, PCR with fungal universal primers and multiplex PCR were performed using DNA prepared by an improved DNA extraction method from corneal scrapings. With this method, fungal pathogens from corneal scrapings could be specifically and rapidly identified within 8 h. The culture-independent rapid identification of corneal scrapings may have great significance for the early diagnosis and treatment of fungal keratitis.

  12. Interaction between the endophytic fungus Epichloe bromicola and the grass bromus erectus: effects of endophyte infection, fungal concentration and environment on grass growth and flowering

    Science.gov (United States)

    Groppe; Steinger; Sanders; Schmid; Wiemken; Boller

    1999-11-01

    Epichloe bromicola is an endophytic fungal species that systemically and perennially colonizes intercellular spaces of leaf blades, leaf sheaths and culms of Bromus grass species. E. bromicola causes choke disease in B. erectus, suppressing maturation of most, if not all, host inflorescences. In an investigation of the interaction between fungus and host, we used a quantitative polymerase chain reaction technique to estimate the amount of fungal DNA, and thereby fungal concentration, in host plants. Fungal concentration was directly correlated with vegetative vigour of the plant, as measured by longest leaf length, number of tillers and vegetative above-ground biomass, suggesting that, during vegetative growth, the endophytic fungus is most beneficial for the plant when present in high concentrations. In contrast, the reproduction of the plant, as measured by the number of functional inflorescences, was inversely correlated with fungal concentration: the majority of infected plants, and all that were associated with high concentrations of fungi, were diseased. Thus, the benefit of endophyte infection for the plant is coupled with the disadvantages of infertility. Fungal concentration was shown to be at least in part genetically determined because fungal concentration differed significantly in different plant-endophyte genotype combinations (symbiotum). In a field experiment with normal and CO2-enriched environments, elevated CO2 levels favoured fungal reproductive vigour over host reproductive vigour, suggesting that these plant endophytes would be at a selective advantage in a corresponding environmental-change scenario. We conclude that a dynamic and complex relationship between fungal endophyte infection, fungal concentration, genotype and environment affects growth and fecundity of B. erectus and should contribute to the evolution of these plant-fungal interactions.

  13. Enhancer evolution across 20 mammalian species

    DEFF Research Database (Denmark)

    Villar, Diego; Berthelot, Camille; Aldridge, Sarah;

    2015-01-01

    The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders...... by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements....... These results provide important insight into the functional genetics underpinning mammalian regulatory evolution....

  14. Evolutionary rewiring of bacterial regulatory networks

    Directory of Open Access Journals (Sweden)

    Tiffany B. Taylor

    2015-07-01

    Full Text Available Bacteria have evolved complex regulatory networks that enable integration of multiple intracellular and extracellular signals to coordinate responses to environmental changes. However, our knowledge of how regulatory systems function and evolve is still relatively limited. There is often extensive homology between components of different networks, due to past cycles of gene duplication, divergence, and horizontal gene transfer, raising the possibility of cross-talk or redundancy. Consequently, evolutionary resilience is built into gene networks – homology between regulators can potentially allow rapid rescue of lost regulatory function across distant regions of the genome. In our recent study [Taylor, et al. Science (2015, 347(6225] we find that mutations that facilitate cross-talk between pathways can contribute to gene network evolution, but that such mutations come with severe pleiotropic costs. Arising from this work are a number of questions surrounding how this phenomenon occurs.

  15. Bacterial and Fungal Pattern Recognition Receptors in Homologous Innate Signaling Pathways of Insects and Mammals

    Directory of Open Access Journals (Sweden)

    Bethany A Stokes

    2015-01-01

    Full Text Available In response to bacterial and fungal infections in insects and mammals, distinct families of innate immune pattern recognition receptors initiate highly complex intracellular signaling cascades. Those cascades induce a variety of immune functions that restrain the spread of microbes in the host. Insect and mammalian innate immune receptors include molecules that recognize conserved microbial molecular patterns. Innate immune recognition leads to the recruitment of adaptor molecules forming multi-protein complexes that include kinases, transcription factors and other regulatory molecules. Innate immune signaling cascades induce the expression of genes encoding antimicrobial peptides and other key factors that mount and regulate the immune response against microbial challenge. In this review, we summarize our current understanding of the bacterial and fungal pattern recognition receptors for homologous innate signaling pathways of insects and mammals in an effort to provide a framework for future studies.

  16. Regulatory mechanisms link phenotypic plasticity to evolvability.

    Science.gov (United States)

    van Gestel, Jordi; Weissing, Franz J

    2016-04-18

    Organisms have a remarkable capacity to respond to environmental change. They can either respond directly, by means of phenotypic plasticity, or they can slowly adapt through evolution. Yet, how phenotypic plasticity links to evolutionary adaptability is largely unknown. Current studies of plasticity tend to adopt a phenomenological reaction norm (RN) approach, which neglects the mechanisms underlying plasticity. Focusing on a concrete question - the optimal timing of bacterial sporulation - we here also consider a mechanistic approach, the evolution of a gene regulatory network (GRN) underlying plasticity. Using individual-based simulations, we compare the RN and GRN approach and find a number of striking differences. Most importantly, the GRN model results in a much higher diversity of responsive strategies than the RN model. We show that each of the evolved strategies is pre-adapted to a unique set of unseen environmental conditions. The regulatory mechanisms that control plasticity therefore critically link phenotypic plasticity to the adaptive potential of biological populations.

  17. Adaptation by Plasticity of Genetic Regulatory Networks

    Science.gov (United States)

    Brenner, Naama

    2007-03-01

    Genetic regulatory networks have an essential role in adaptation and evolution of cell populations. This role is strongly related to their dynamic properties over intermediate-to-long time scales. We have used the budding yeast as a model Eukaryote to study the long-term dynamics of the genetic regulatory system and its significance in evolution. A continuous cell growth technique (chemostat) allows us to monitor these systems over long times under controlled condition, enabling a quantitative characterization of dynamics: steady states and their stability, transients and relaxation. First, we have demonstrated adaptive dynamics in the GAL system, a classic model for a Eukaryotic genetic switch, induced and repressed by different carbon sources in the environment. We found that both induction and repression are only transient responses; over several generations, the system converges to a single robust steady state, independent of external conditions. Second, we explored the functional significance of such plasticity of the genetic regulatory network in evolution. We used genetic engineering to mimic the natural process of gene recruitment, placing the gene HIS3 under the regulation of the GAL system. Such genetic rewiring events are important in the evolution of gene regulation, but little is known about the physiological processes supporting them and the dynamics of their assimilation in a cell population. We have shown that cells carrying the rewired genome adapted to a demanding change of environment and stabilized a population, maintaining the adaptive state for hundreds of generations. Using genome-wide expression arrays we showed that underlying the observed adaptation is a global transcriptional programming that allowed tuning expression of the recruited gene to demands. Our results suggest that non-specific properties reflecting the natural plasticity of the regulatory network support adaptation of cells to novel challenges and enhance their evolvability.

  18. Burden of serious fungal infections in Belgium.

    Science.gov (United States)

    Lagrou, Katrien; Maertens, Johan; Van Even, Ellen; Denning, David W

    2015-10-01

    We aimed to estimate the total number of serious fungal infections occurring yearly in Belgium. The number of cryptococcal infections was retrieved from the National Reference Center for Mycosis. Populations at risk and fungal infections frequencies in these populations were used to estimate incidence or prevalence of other fungal infections. The Belgian population consists of 11.10 million people. Cryptococcal meningitis is rare. In all, 15 of the 1227 newly diagnosed HIV/AIDS cases presented with Pneumocystis jirovecii pneumonia. This accounts for ±14% of total PCP cases (n = 120). The incidence of candidaemia is estimated as 5/100,000 resulting in 555 cases and 213 deaths. A total number of 675 invasive aspergillosis cases and ≥169 deaths attributed to this infection were calculated. Chronic pulmonary aspergillosis is estimated to be prevalent in 662 cases. Allergic bronchopulmonary aspergillosis cases were estimated to be 23,119 applying a 2.5% and 15% rate in adult asthma and cystic fibrosis patients respectively. Severe asthma with fungal sensitisation cases was estimated to be 30,402. There were 174,760 women with recurrent Candida vaginitis assuming a 6% rate in women aged between 15 and 50. Approximately 233,000 people of the Belgian population (2.1%) are estimated to suffer from a fungal infection on a yearly basis.

  19. Burden of fungal infections in Algeria.

    Science.gov (United States)

    Chekiri-Talbi, M; Denning, D W

    2017-02-21

    We report for the first time in Algeria and provide burden estimates. We searched for existing data and estimated the incidence and prevalence of fungal diseases based on the population at risk and available epidemiological data. Demographic data were derived from the National Office of Statistics (Office National des Statistiques: ONS), World Health Organization (WHO), The Joint Nations Programme on HIV/AIDS (UNAIDS) and national published reports. When no data existed, risk populations were used to estimate frequencies of fungal infections, using previously described methodology. Algeria has 40.4 million inhabitants, and probably at least 568,900 (1.41%) of Algerians have a serious fungal infection each year. Recurrent vulvovaginal candidiasis (485,000) and fungal asthma (72,000) are probably the commonest problems, as there are over 1 million adult asthmatics. Candidaemia is estimated in 2,020 people, invasive aspergillosis in 2,865 people, and intra-abdominal candidiasis in 303 people; these are the most common life-threatening problems. AIDS is uncommon, but cancer is not (45,000 new cases of cancer including 1,500 in children), nor is COPD (an estimated 317,762 patients, of whom 20.3% are admitted to hospital each year). A focus on improving the diagnosis and epidemiological data related to fungal infection is necessary in Algeria.

  20. Fungal infections in severe acute pancreatitis.

    Science.gov (United States)

    Kochhar, Rakesh; Noor, Mohd Talha; Wig, Jaidev

    2011-06-01

    Severe acute pancreatitis (SAP) is associated with significant morbidity and mortality. The majority of deaths related to SAP are the result of infectious complications. Although bacterial infections are most commonly encountered, fungal infections are increasingly being recognized. Candida is the most common fungal infection. The occurrence of fungal infection in patients with acute pancreatitis adversely affects the clinical course, leading to a higher incidence of systemic complications, and possibly mortality as well. Important risk factors for fungal infection in patients with acute pancreatitis include broad-spectrum antibiotics, prolonged hospitalization and surgical/endoscopic interventions, use of total parenteral nutrition, and mechanical ventilation. Patients with higher severity of pancreatitis are at a greater risk. The pathogenesis of fungal infection in patients with acute pancreatitis is multifactorial. Translocation of microorganisms across the gut epithelium, lymphocyte dysfunction, and the virulence of the invading microorganisms play important roles. Histological demonstration of fungi remains the gold standard of diagnosis, but a positive biopsy is rarely obtained. The role of biomarkers in the diagnosis is being investigated. As early diagnosis and treatment can lead to improved outcome, a high index of suspicion is required for prompt diagnosis. Limiting the use of broad-spectrum antibiotics, early introduction of enteral nutrition, and timely change of vascular catheters are important preventive strategies. The role of antifungal prophylaxis remains controversial. Surgical necrosectomy with antifungal therapy is the most widely used treatment approach. Clinical trials on antifungal prophylaxis are needed, and indications for surgical intervention need to be clearly defined.

  1. Fueling the Future with Fungal Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2014-10-27

    Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 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 will lead 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.

  2. Fungal endophytes: modifiers of plant disease.

    Science.gov (United States)

    Busby, Posy E; Ridout, Mary; Newcombe, George

    2016-04-01

    Many recent studies have demonstrated that non-pathogenic fungi within plant microbiomes, i.e., endophytes ("endo" = within, "phyte" = plant), can significantly modify the expression of host plant disease. The rapid pace of advancement in endophyte ecology warrants a pause to synthesize our understanding of endophyte disease modification and to discuss future research directions. We reviewed recent literature on fungal endophyte disease modification, and here report on several emergent themes: (1) Fungal endophyte effects on plant disease span the full spectrum from pathogen antagonism to pathogen facilitation, with pathogen antagonism most commonly reported. (2) Agricultural plant pathosystems are the focus of research on endophyte disease modification. (3) A taxonomically diverse group of fungal endophytes can influence plant disease severity. And (4) Fungal endophyte effects on plant disease severity are context-dependent. Our review highlights the importance of fungal endophytes for plant disease across a broad range of plant pathosystems, yet simultaneously reveals that complexity within plant microbiomes presents a significant challenge to disentangling the biotic environmental factors affecting plant disease severity. Manipulative studies integrating eco-evolutionary approaches with emerging molecular tools will be poised to elucidate the functional importance of endophytes in natural plant pathosystems that are fundamental to biodiversity and conservation.

  3. [Pulmonary fungal infection in patients with AIDS].

    Science.gov (United States)

    Denis, B; Lortholary, O

    2013-10-01

    Fungal infections are the most common opportunistic infections (OI) occurring during the course of HIV infection, though their incidence has decreased dramatically with the introduction of highly active antiretroviral therapy (cART). Most cases occur in untreated patients, noncompliant patients or patients whose multiple antiretroviral regimens have failed and they are a good marker of the severity of cellular immunodepression. Pneumocystis jiroveci pneumonia is the second most frequent OI in France and cryptococcosis remains a major problem in the Southern Hemisphere. With the increase in travel, imported endemic fungal infection can occur and may mimic other infections, notably tuberculosis. Fungal infections often have a pulmonary presentation but an exhaustive search for dissemination should be made in patients infected with HIV, at least those at an advanced stage of immune deficiency. Introduction of cART in combination with anti-fungal treatment depends on the risk of AIDS progression and on the risk of cumulative toxicity and the immune reconstitution inflammatory syndrome (IRIS) if introduced too early. Fungal infections in HIV infected patients remain a problem in the cART era. IRIS can complicate the management and requires an optimised treatment regime. Copyright © 2013. Published by Elsevier Masson SAS.

  4. Fungal keratitis associated with ocular rosacea.

    Science.gov (United States)

    Jain, Vandana; Shome, Debraj; Sajnani, Manoj; Natarajan, Sundaram

    2010-06-01

    In order to report fungal keratitis in patients of ocular rosacea, a retrospective review of all cases of fungal keratitis was undertaken. Cases in which ocular rosacea coexisted were identified and included in the study. The clinical course of patients thus identified was studied from the medical records and outcomes were evaluated. A total of three cases of fungal keratitis with coexisting ocular rosacea were identified. All three patients were known cases of acne rosacea with an intermittent, irregular treatment for the same. Previous history of contact lens use, ocular surgery or trauma was not present in any of the cases. Microbiological evaluation revealed Aspergillus flavus as the causative organism in two patients and an unidentified hyaline fungus in the third. Patients received simultaneous therapy for fungal keratitis and ocular rosacea. The ocular surface completely stabilized and the infiltrate resolved in all three cases. The chronic ocular surface changes and induced inflammation in ocular rosacea, along with the instillation of topical steroids for therapy, may create an environmental milieu favorable for fungal keratitis. Microbiological evaluation should be considered, even in cases of suspected sterile keratitis, prior to treatment with topical steroids, so as to prevent the possible worsening of an associated infective corneal condition.

  5. Fungal Involvement in Patients with Paranasal Sinusitis

    Directory of Open Access Journals (Sweden)

    P Kordbacheh

    2004-08-01

    Full Text Available Fungal involvement of the paranasal sinuses is frequently observed in the immunocompromised host and it can become lifethreatening if it is not diagnosed. Definitive diagnosis is made by tissue biopsy and culture. In this study biopsy materials of maxillary, ethmoidal and frontal sinuses of 60 patients with clinical manifestation of sinusitis and no response to medical therapy were assessed by mycological and pathological methods for the presence of fungi. Invasive fungal sinusitis was diagnosed in 3 patients and etiologic agents were Candida albicans, Rhizopus sp. and Aspergillus fumigatus. Predisposing factors in these patients were leukemia, diabetes mellitus and previous sinus and polyp surgery, respectively. Allergic fungal sinusitis also was seen in one patient and Alternaria sp. isolated from the biopsy material. Only the patient with allergic form of disease survived but all the patients with invasive form of fungal infection were expired. This clearly underscores the need of early recognition of fungal sinusitis in at risk population in order to start urgent treatment. In this study Nocardia asteroids also was isolated from the biopsy sample in a patient with sinunasal adenocarcinoma.

  6. Modelling combat strategies in fungal mycelia.

    Science.gov (United States)

    Boswell, Graeme P

    2012-07-07

    Fungal mycelia have a well-established role in nutrient cycling and are widely used as agents in biological control and in the remediation of polluted landscapes. Competition and combat between different fungal communities is common in these contexts and its outcome impacts on local biodiversity and the success of such biotechnological applications. In this investigation a mathematical model representing mycelia as a system of partial differential equations is used to simulate combat between two fungal colonies growing into a nutrient-free domain. The resultant equations are integrated numerically and the model simulates well-established outcomes of combat between fungal communities. The outcome of pairwise combat is shown to depend on numerous factors including the suppression of advancing hyphae in rivals, the degradation of a rival's established biomass and the utilization and redistribution of available nutrient resources. It is demonstrated how non-transitive hierarchies in fungal communities can be established through switching mechanisms, mirroring observations reported in experimental studies, and how specialized defensive structures can emerge through changes in the redistribution of internal resources.

  7. Phylogenetic analysis of fungal ABC transporters

    Directory of Open Access Journals (Sweden)

    Driessen Arnold JM

    2010-03-01

    Full Text Available Abstract Background The superfamily of ABC proteins is among the largest known in nature. Its members are mainly, but not exclusively, involved in the transport of a broad range of substrates across biological membranes. Many contribute to multidrug resistance in microbial pathogens and cancer cells. The diversity of ABC proteins in fungi is comparable with those in multicellular animals, but so far fungal ABC proteins have barely been studied. Results We performed a phylogenetic analysis of the ABC proteins extracted from the genomes of 27 fungal species from 18 orders representing 5 fungal phyla thereby covering the most important groups. Our analysis demonstrated that some of the subfamilies of ABC proteins remained highly conserved in fungi, while others have undergone a remarkable group-specific diversification. Members of the various fungal phyla also differed significantly in the number of ABC proteins found in their genomes, which is especially reduced in the yeast S. cerevisiae and S. pombe. Conclusions Data obtained during our analysis should contribute to a better understanding of the diversity of the fungal ABC proteins and provide important clues about their possible biological functions.

  8. Fungal Genomics for Energy and Environment

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2013-03-11

    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). One of its projects, 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) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 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.

  9. Prospects for the development of fungal vaccines.

    Science.gov (United States)

    Deepe, G S

    1997-10-01

    In an era that emphasizes the term "cost-effective," vaccines are the ideal solution to preventing disease at a relatively low cost to society. Much of the previous emphasis has been on childhood scourges such as measles, mumps, rubella, poliomyelitis, and Haemophilus influenzae type b. The concept of vaccines for fungal diseases has had less impact because of the perceived limited problem. However, fungal diseases have become increasingly appreciated as serious medical problems that require recognition and aggressive management. The escalation in the incidence and prevalence of infection has prompted a renewed interest in vaccine development. Herein, I discuss the most recent developments in the search for vaccines to combat fungal infections. Investigators have discovered several inert substances from various fungi that can mediate protection in animal models. The next challenge will be to find the suitable mode of delivery for these immunogens.

  10. EPICHLOE SPECIES: fungal symbionts of grasses.

    Science.gov (United States)

    Schardl, C L

    1996-01-01

    Epichloë species and their asexual descendants (Acremonium endophytes) are fungal symbionts of C3 grasses that span the symbiotic continuum from antagonism to mutualism depending on the relative importance, respectively, of horizontal transmission of sexual spores versus vertical clonal transmission in healthy grass seeds. At least seven sexual Epichloë species are identifiable by mating tests, and many asexual genotypes are interspecific hybrids. Benefits conferred by the symbionts on host plants include protection from biotic factors and abiotic stresses such as drought. Four classes of beneficial alkaloids are associated with the symbionts: ergot alkaloids, indolediterpenes (lolitrems), peramine, and saturated aminopyrrolizidines (lolines). These alkaloids protect host plants from insect and vertebrate herbivores, including livestock. Genetic engineering of the fungal symbionts as more suitable biological protectants for forage grasses requires identification of fungal genes for alkaloid biosynthesis, and DNA-mediated transformation of the fungi.

  11. Marsupialized fungal mycetoma masquerading as conjunctival melanoma.

    Science.gov (United States)

    Sayyad, Fouad E; Karp, Carol L; Wong, James R; Weiss, Matthew J; Bermudez-Magner, J Antonio; Dubovy, Sander

    2014-07-01

    To report a case of a fungal mass misdiagnosed as a pigmented conjunctival melanoma. Case report. A 38-year-old woman was referred for a pigmented conjunctival lesion that was diagnosed as a melanoma. She had a history of a scleral buckle in that eye for retinal detachment 2 years before presentation. Slit-lamp examination revealed a pigmented mass from the 11- to 2-o'clock position. This was noted to be imbricated within the invagination of a conjunctival fold from the previous surgery. The mass was removed, cultured, and confirmed to be a fungal infection from Scytalidium sp. Scleral buckles can cause folds in the conjunctiva, which can be foci for fungal infection.

  12. Immunological Consequences of Intestinal Fungal Dysbiosis.

    Science.gov (United States)

    Wheeler, Matthew L; Limon, Jose J; Bar, Agnieszka S; Leal, Christian A; Gargus, Matthew; Tang, Jie; Brown, Jordan; Funari, Vincent A; Wang, Hanlin L; Crother, Timothy R; Arditi, Moshe; Underhill, David M; Iliev, Iliyan D

    2016-06-08

    Compared to bacteria, the role of fungi within the intestinal microbiota is poorly understood. In this study we investigated whether the presence of a "healthy" fungal community in the gut is important for modulating immune function. Prolonged oral treatment of mice with antifungal drugs resulted in increased disease severity in acute and chronic models of colitis, and also exacerbated the development of allergic airway disease. Microbiota profiling revealed restructuring of fungal and bacterial communities. Specifically, representation of Candida spp. was reduced, while Aspergillus, Wallemia, and Epicoccum spp. were increased. Oral supplementation with a mixture of three fungi found to expand during antifungal treatment (Aspergillus amstelodami, Epicoccum nigrum, and Wallemia sebi) was sufficient to recapitulate the exacerbating effects of antifungal drugs on allergic airway disease. Taken together, these results indicate that disruption of commensal fungal populations can influence local and peripheral immune responses and enhance relevant disease states.

  13. Overview: fungal infections in the transplant patient.

    Science.gov (United States)

    Fishman, J A

    2002-01-01

    Fungal infection remains a major hurdle in solid organ transplantation. A variety of new antifungal agents have become available and new diagnostic tools are in development. This conference was convened to review current approaches to the prevention and treatment of fungal infection in transplantation. Among the keys to successful management of fungal infection are identification of patients at risk for infection (stratification), eradication or control of established infection in advance of transplantation, the demonstration of cure by radiologic and histopathologic means, and the use of surgical debridement, reduction in immune suppression, and fungicidal therapies whenever possible. The absence of sensitive diagnostic tools and standardization of antifungal susceptibility testing for the filamentous fungi are identified as major impediments to care in this area.

  14. [Fungal infections in children with malignant disease].

    Science.gov (United States)

    Michel, G

    2011-05-01

    Intensified chemotherapy and hematopoietic stem cell transplantation result in severe and prolonged granulocytopenia with an increased risk of invasive fungal infections. The major fungal species that cause serious infections in cancer patients are Candida species and Aspergillus species. The main features of Candida infection in this context are oropharyngeal candidiasis and Candida esophagitis, chronic disseminated candidiasis, also known as hepatosplenic candidiasis, and candidemia. Aspergillus can cause severe lung infection but also sinusal or CNS infection. Because invasive fungal infections are severe and often life-threatening, preventive and empirical managements have become standard practice. An increasing number of antifungal drugs is now available, notably lipid formulations of amphotericin B (liposomal amphotericin B), new azoles with broad spectrum of activity and echinocandin.

  15. Regulatory guidance document

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-05-01

    The Office of Civilian Radioactive Waste Management (OCRWM) Program Management System Manual requires preparation of the OCRWM Regulatory Guidance Document (RGD) that addresses licensing, environmental compliance, and safety and health compliance. The document provides: regulatory compliance policy; guidance to OCRWM organizational elements to ensure a consistent approach when complying with regulatory requirements; strategies to achieve policy objectives; organizational responsibilities for regulatory compliance; guidance with regard to Program compliance oversight; and guidance on the contents of a project-level Regulatory Compliance Plan. The scope of the RGD includes site suitability evaluation, licensing, environmental compliance, and safety and health compliance, in accordance with the direction provided by Section 4.6.3 of the PMS Manual. Site suitability evaluation and regulatory compliance during site characterization are significant activities, particularly with regard to the YW MSA. OCRWM`s evaluation of whether the Yucca Mountain site is suitable for repository development must precede its submittal of a license application to the Nuclear Regulatory Commission (NRC). Accordingly, site suitability evaluation is discussed in Chapter 4, and the general statements of policy regarding site suitability evaluation are discussed in Section 2.1. Although much of the data and analyses may initially be similar, the licensing process is discussed separately in Chapter 5. Environmental compliance is discussed in Chapter 6. Safety and Health compliance is discussed in Chapter 7.

  16. Fungal infections in burns: Diagnosis and management

    Directory of Open Access Journals (Sweden)

    Capoor Malini

    2010-10-01

    Full Text Available Burn wound infection (BWI is a major public health problem and the most devastating form of trauma worldwide. Fungi cause BWI as part of monomicrobial or polymicrobial infection, fungaemia, rare aggressive soft tissue infection and as opportunistic infections. The risk factors for acquiring fungal infection in burns include age of burns, total burn size, body surface area (BSA (30-60%, full thickness burns, inhalational injury, prolonged hospital stay, late surgical excision, open dressing, artificial dermis, central venous catheters, antibiotics, steroid treatment, long-term artificial ventilation, fungal wound colonisation (FWC, hyperglycaemic episodes and other immunosuppressive disorders. Most of the fungal infections are missed owing to lack of clinical awareness and similar presentation as bacterial infection coupled with paucity of mycology laboratories. Expedient diagnosis and treatment of these mycoses can be life-saving as the mortality is otherwise very high. Emergence of resistance in non-albicans Candida spp., unusual yeasts and moulds in fungal BWI, leaves very few fungi susceptible to antifungal drugs, leaving many patients susceptible. There is a need to speciate fungi as far as the topical and systemic antifungal is concerned. Deep tissue biopsy and other relevant samples are processed by standard mycological procedures using direct microscopy, culture and histopathological examination. Patients with FWC should be treated by aggressive surgical debridement and, in the case of fungal wound infection (FWI, in addition to surgical debridement, an intravenous antifungal drug, most commonly amphotericin B or caspofungin, is prescribed followed by de-escalating with voriconazole or itraconazole, or fluconazole depending upon the species or antifungal susceptibility, if available. The propensity for fungal infection increases, the longer the wound is present. Therefore, the development of products to close the wound more rapidly

  17. Identification & Characterization of Fungal Ice Nucleation Proteins

    Science.gov (United States)

    Scheel, Jan Frederik; Kunert, Anna Theresa; Kampf, Christopher Johannes; Mauri, Sergio; Weidner, Tobias; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

    2016-04-01

    Freezing of water at relatively warm subfreezing temperatures is dependent on ice nucleation catalysis facilitated by ice nuclei (IN). These IN can be of various origins and although extensive research was done and progress was achieved, the nature and mechanisms leading to an effective IN are to date still poorly understood. Some of the most important processes of our geosphere like the water cycle are highly dependent on effective ice nucleation at temperatures between -2°C - -8°C, a temperature range which is almost exclusively covered by biological IN (BioIN). BioIN are usually macromolecular structures of biological polymers. Sugars as well as proteins have been reported to serve as IN and the best characterized BioIN are ice nucleation proteins (IN-P) from gram negative bacteria. Fungal strains from Fusarium spp. were described to be effective IN at subfreezing temperatures up to -2°C already 25 years ago and more and more fungal species are described to serve as efficient IN. Fungal IN are also thought to be proteins or at least contain a proteinaceous compound, but to date the fungal IN-P primary structure as well as their coding genetic elements of all IN active fungi are unknown. The aim of this study is a.) to identify the proteins and their coding genetic elements from IN active fungi (F. acuminatum, F. avenaceum, M. alpina) and b.) to characterize the mechanisms by which fungal IN serve as effective IN. We designed an interdisciplinary approach using biological, analytical and physical methods to identify fungal IN-P and describe their biological, chemical, and physical properties.

  18. Fractal dimension based corneal fungal infection diagnosis

    Science.gov (United States)

    Balasubramanian, Madhusudhanan; Perkins, A. Louise; Beuerman, Roger W.; Iyengar, S. Sitharama

    2006-08-01

    We present a fractal measure based pattern classification algorithm for automatic feature extraction and identification of fungus associated with an infection of the cornea of the eye. A white-light confocal microscope image of suspected fungus exhibited locally linear and branching structures. The pixel intensity variation across the width of a fungal element was gaussian. Linear features were extracted using a set of 2D directional matched gaussian-filters. Portions of fungus profiles that were not in the same focal plane appeared relatively blurred. We use gaussian filters of standard deviation slightly larger than the width of a fungus to reduce discontinuities. Cell nuclei of cornea and nerves also exhibited locally linear structure. Cell nuclei were excluded by their relatively shorter lengths. Nerves in the cornea exhibited less branching compared with the fungus. Fractal dimensions of the locally linear features were computed using a box-counting method. A set of corneal images with fungal infection was used to generate class-conditional fractal measure distributions of fungus and nerves. The a priori class-conditional densities were built using an adaptive-mixtures method to reflect the true nature of the feature distributions and improve the classification accuracy. A maximum-likelihood classifier was used to classify the linear features extracted from test corneal images as 'normal' or 'with fungal infiltrates', using the a priori fractal measure distributions. We demonstrate the algorithm on the corneal images with culture-positive fungal infiltrates. The algorithm is fully automatic and will help diagnose fungal keratitis by generating a diagnostic mask of locations of the fungal infiltrates.

  19. Radiation and the regulatory landscape of neo2-Darwinism.

    Science.gov (United States)

    Rollo, C David

    2006-05-11

    Several recently revealed features of eukaryotic genomes were not predicted by earlier evolutionary paradigms, including the relatively small number of genes, the very large amounts of non-functional code and its quarantine in heterochromatin, the remarkable conservation of many functionally important genes across relatively enormous phylogenetic distances, and the prevalence of extra-genomic information associated with chromatin structure and histone proteins. All of these emphasize a paramount role for regulatory evolution, which is further reinforced by recent perspectives highlighting even higher-order regulation governing epigenetics and development (EVO-DEVO). Modern neo2-Darwinism, with its emphasis on regulatory mechanisms and regulatory evolution provides new vision for understanding radiation biology, particularly because free radicals and redox states are central to many regulatory mechanisms and free radicals generated by radiation mimic and amplify endogenous signalling. This paper explores some of these aspects and their implications for low-dose radiation biology.

  20. Phylogeny based discovery of regulatory elements

    Directory of Open Access Journals (Sweden)

    Cohen Barak A

    2006-05-01

    Full Text Available Abstract Background Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advantage of an explicit model for the constrained evolution of functional DNA sequences. Results We developed a probabilistic framework that combines an HKY85 model, which assigns probabilities to different base substitutions between species, and weight matrix models of transcription factor binding sites, which describe the probabilities of observing particular nucleotides at specific positions in the binding site. The method incorporates the phylogenies of the species under consideration and takes into account the position specific variation of transcription factor binding sites. Using our framework we assessed the suitability of alignments of genomic sequences from commonly used species as substrates for comparative genomic approaches to regulatory motif finding. We then applied this technique to Saccharomyces cerevisiae and related species by examining all possible six base pair DNA sequences (hexamers and identifying sequences that are conserved in a significant number of promoters. By combining similar conserved hexamers we reconstructed known cis-regulatory motifs and made predictions of previously unidentified motifs. We tested one prediction experimentally, finding it to be a regulatory element involved in the transcriptional response to glucose. Conclusion The experimental validation of a regulatory element prediction missed by other large-scale motif finding studies demonstrates that our approach is a useful addition to the current suite of tools for finding regulatory motifs.

  1. Fungal infections of the lung in children

    Energy Technology Data Exchange (ETDEWEB)

    Toma, Paolo; Colafati, Giovanna Stefania; D' Andrea, Maria Luisa [IRCCS Bambino Gesu Children' s Hospital, Department of Imaging, Rome (Italy); Bertaina, Alice; Mastronuzzi, Angela [IRCCS Bambino Gesu Children' s Hospital, Department of Pediatric Hematology/Oncology and Transfusion Medicine, Rome (Italy); Castagnola, Elio [IRCCS Istituto Giannina Gaslini, Department of Infective Diseases, Genoa (Italy); Finocchi, Andrea [IRCCS Bambino Gesu Children' s Hospital, Department of Pediatrics, Rome (Italy); Lucidi, Vincenzina [IRCCS Bambino Gesu Children' s Hospital, Cystic Fibrosis Center, Rome (Italy); Granata, Claudio [IRCCS Istituto Giannina Gaslini, Department of Pediatric Radiology, Genoa (Italy)

    2016-12-15

    Fungal infections of the lungs are relatively common and potentially life-threatening conditions in immunocompromised children. The role of imaging in children with lung mycosis is to delineate the extension of pulmonary involvement, to assess response to therapy, and to monitor for adverse sequelae such as bronchiectasis and cavitation. The aim of this paper is to show imaging findings in a series of patients with fungal pneumonia from two tertiary children's hospitals, to discuss differential diagnoses and to show how imaging findings can vary depending on the host immune response. (orig.)

  2. Tropospheric ozone as a fungal elicitor

    Indian Academy of Sciences (India)

    Paolo Zuccarini

    2009-03-01

    Tropospheric ozone has been proven to trigger biochemical plant responses that are similar to the ones induced by an attack of fungal pathogens, i.e. it resembles fungal elicitors. This suggests that ozone can represent a valid tool for the study of stress responses and induction of resistance to pathogens. This review provides an overview of the implications of such a phenomenon for basic and applied research. After an introduction about the environmental implications of tropospheric ozone and plant responses to biotic stresses, the biochemistry of ozone stress is analysed, pointing out its similarities with plant responses to pathogens and its possible applications.

  3. Fungal outbreak in a show cave.

    Science.gov (United States)

    Jurado, V; Porca, E; Cuezva, S; Fernandez-Cortes, A; Sanchez-Moral, S; Saiz-Jimenez, C

    2010-08-01

    Castañar de Ibor Cave (Spain) was discovered in 1967 and declared a Natural Monument in 1997. In 2003 the cave was opened to public visits. Despite of extensive control, on 26 August 2008 the cave walls and sediments appeared colonized by long, white fungal mycelia. This event was the result of an accidental input of detritus on the afternoon of 24 August 2008. We report here a fungal outbreak initiated by Mucor circinelloides and Fusarium solani and the methods used to control it.

  4. Fungal and bacterial killing by neutrophils.

    Science.gov (United States)

    Ermert, David; Zychlinsky, Arturo; Urban, Constantin

    2009-01-01

    Neutrophils are professional phagocytes of the innate immune system that are essential to control bacterial and fungal infections. These cells engulf and kill invading microbes. Additionally, activated neutrophils are able to release neutrophil extracellular traps (NETs). These fibers consist of chromatin decorated with antimicrobial proteins to trap and kill microbes. Appropriate quantitative methods are required to understand the nature of interactions of neutrophils with pathogens. Here we present assays to measure killing mediated by phagocytosis, by NETs, by a combination of both, and by granular extract. As examples, we use Candida albicans for fungal and Shigella flexneri for bacterial pathogens.

  5. Negative fitness consequences and transmission dynamics of a heritable fungal symbiont of a parasitic wasp.

    Science.gov (United States)

    Gibson, Cara M; Hunter, Martha S

    2009-05-01

    Heritable bacterial symbionts are widespread in insects and can have many important effects on host ecology and fitness. Fungal symbionts are also important in shaping their hosts' behavior, interactions, and evolution, but they have been largely overlooked. Experimental tests to determine the relevance of fungal symbionts to their insect hosts are currently extremely rare, and to our knowledge, there have been no such tests for strictly predacious insects. We investigated the fitness consequences for a parasitic wasp (Comperia merceti) of an inherited fungal symbiont in the Saccharomycotina (Ascomycota) that was long presumed to be a mutualist. In comparisons of wasp lines with and without this symbiont, we found no evidence of mutualism. Instead, there were significant fitness costs to the wasps in the presence of the yeast; infected wasps attacked fewer hosts and had longer development times. We also examined the relative competitive abilities of the larval progeny of infected and uninfected mothers, as well as horizontal transmission of the fungal symbiont among larval wasps that shared a single host cockroach egg case. We found no difference in larval competitive ability when larvae whose infection status differed shared a single host. We did find high rates of horizontal transmission of the fungus, and we suggest that this transmission is likely responsible for the maintenance of this infection in wasp populations.

  6. Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica.

    Science.gov (United States)

    Godinho, Valéria M; Gonçalves, Vívian N; Santiago, Iara F; Figueredo, Hebert M; Vitoreli, Gislaine A; Schaefer, Carlos E G R; Barbosa, Emerson C; Oliveira, Jaquelline G; Alves, Tânia M A; Zani, Carlos L; Junior, Policarpo A S; Murta, Silvane M F; Romanha, Alvaro J; Kroon, Erna Geessien; Cantrell, Charles L; Wedge, David E; Duke, Stephen O; Ali, Abbas; Rosa, Carlos A; Rosa, Luiz H

    2015-05-01

    We surveyed the diversity and capability of producing bioactive compounds from a cultivable fungal community isolated from oligotrophic soil of continental Antarctica. A total of 115 fungal isolates were obtained and identified in 11 taxa of Aspergillus, Debaryomyces, Cladosporium, Pseudogymnoascus, Penicillium and Hypocreales. The fungal community showed low diversity and richness, and high dominance indices. The extracts of Aspergillus sydowii, Penicillium allii-sativi, Penicillium brevicompactum, Penicillium chrysogenum and Penicillium rubens possess antiviral, antibacterial, antifungal, antitumoral, herbicidal and antiprotozoal activities. Bioactive extracts were examined using (1)H NMR spectroscopy and detected the presence of secondary metabolites with chemical shifts. Our results show that the fungi present in cold-oligotrophic soil from Antarctica included few dominant species, which may have important implications for understanding eukaryotic survival in cold-arid oligotrophic soils. We hypothesize that detailed further investigations may provide a greater understanding of the evolution of Antarctic fungi and their relationships with other organisms described in that region. Additionally, different wild pristine bioactive fungal isolates found in continental Antarctic soil may represent a unique source to discover prototype molecules for use in drug and biopesticide discovery studies.

  7. Strong fungal specificity and selectivity for algal symbionts in Florida scrub Cladonia lichens.

    Science.gov (United States)

    Yahr, Rebecca; Vilgalys, Rytas; Depriest, Paula T

    2004-11-01

    Symbiosis is a major theme in the history of life and can be an important force driving evolution. However, across symbioses, it is difficult to tease apart the mechanisms that structure the interactions among potential partners. We used genetic similarity and frequency-based methods to qualitatively and quantitatively examine the patterns of association among several co-occurring Cladonia lichen fungi and their algal photobionts in six disjunct Florida scrub sites. The patterns of association were described by the degree of specificity, i.e. the phylogenetic range of associated partners, and of selectivity, i.e. the frequency of association among partners. Six fungal species associated with only one algal internal transcribed spacer clade, with the remaining two fungi being associated with two algal clades. In all cases, the fungi associated in unequal frequencies with the observed algal photobiont genotypes within those clades--suggesting that both specificity and selectivity were higher than expected. Fungal species can be grouped into three significantly different specificity classes: photobiont specialists, intermediates and generalists. In contrast to the pronounced specificity for photobionts among fungal species, the different Florida scrub sites do not harbour distinct photobiont pools, and differential photobiont availability cannot explain the patterning of lichen associations at this spatial scale. Therefore, we conclude that fungal specificity and selectivity for algal photobionts are major factors in determining the local composition of symbiotic partnerships.

  8. Development of anti β glucan aptamers for use as radiopharmaceutical in the identification of fungal Infections

    Energy Technology Data Exchange (ETDEWEB)

    Lacerda, Camila Maria de Sousa; Reis, Mariana Flister; Correa, Cristiane Rodrigues; Andrade, Antero S.R., E-mail: cmsl@cdtn.br, E-mail: antero@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEM-MG), Belo Horizonte, MG (Brazil)

    2013-07-01

    Invasive fungal infections caused by Candida albicans, are recognized as a major cause of morbidity and mortality in immuno compromised individuals. Patients may not show obvious clinical signs or symptoms, making it difficult to detect its origin or new focus that developed through hematogenous spread. Nuclear medicine could contribute to an early diagnosis of fungal infections, since specific markers are available. The aim of this study was to develop, through SELEX technique (Systematic Evolution of Ligands by Exponential Enrichment), aptamers for beta glucan for subsequent labeling with {sup 99}mTc and evaluation of this radiopharmaceutical in the diagnosis of invasive fungal infections, scintigraphy. To obtain aptamers were performed 15 cycles of SELEX technique, using centrifugation as separation method of oligonuclotideos linked to the beta-glucan is not connected. The DNA bands were observed in all 15 cycles. The oligonucleotides obtained after cycles were cloned using the standard protocol kit-Topo TA vector (Invitrogen), and subjected to sequencing Megabase. Three aptamers for yeast cells were selected for this study. Further, other studies should be performed to assess the specificity and affinity thereof for later use in the diagnosis of fungal infections. (author)

  9. Biomass conversion in the fungal garden of the leaf-cutter ant Acromyrmex echinatior

    DEFF Research Database (Denmark)

    Grell, Morten Nedergaard; Nygaard, Sanne; Linde, Tore

    2011-01-01

    It has been demonstrated that fungal enzymes play a significant role in the fungal garden conversion of the fresh-cut leaves into accessible food for the ant larvae (Schiøtt et al. 2008, BMC Microbiol, 8:40; Licht et al. 2010, Evolution 64: 2055-2069). However, so far specific documentation...... of conversion of also the cellulose fibers itself has been scarce. In the current study, we have taken an experimental approach allowing us to discover which genes are specifically expressed in the upper, middle, and bottom layers of the fungal garden. Using the DeepSAGE technique (Nielsen et al. 2006, Nucleic...... Acids Res 34:e133) short cDNA tags of the mRNA molecules produced in each of the fungal garden layers were achieved. Subtractive comparisons were made, identifying the genes at least 2x over-expressed in the bottom layer compared to the upper layer. Extended sequence of the selected genes were acquired...

  10. New regulatory framework for wastewater quality control in Mexico.

    Science.gov (United States)

    Saade Hazin, L

    2000-01-01

    This paper analyses the new regulatory framework for wastewater quality control developed in Mexico. It provides a description of the Mexican government strategies for water pollution control. The discussion focuses on the policy instruments used, their evolution and the main difficulties encountered in their implementation. The new regulatory framework is discussed highlighting some of the economic implications of the reforms. The paper concludes that proper institutional development and monitoring are essential factors for the success of any policy instrument for wastewater quality control.

  11. Evolution of the holozoan ribosome biogenesis regulon

    Science.gov (United States)

    Brown, Seth J; Cole, Michael D; Erives, Albert J

    2008-01-01

    Background The ribosome biogenesis (RiBi) genes encode a highly-conserved eukaryotic set of nucleolar proteins involved in rRNA transcription, assembly, processing, and export from the nucleus. While the mode of regulation of this suite of genes has been studied in the yeast, Saccharomyces cerevisiae, how this gene set is coordinately regulated in the larger and more complex metazoan genomes is not understood. Results Here we present genome-wide analyses indicating that a distinct mode of RiBi regulation co-evolved with the E(CG)-binding, Myc:Max bHLH heterodimer complex in a stem-holozoan, the ancestor of both Metazoa and Choanoflagellata, the protozoan group most closely related to animals. These results show that this mode of regulation, characterized by an E(CG)-bearing core-promoter, is specific to almost all of the known genes involved in ribosome biogenesis in these genomes. Interestingly, this holozoan RiBi promoter signature is absent in nematode genomes, which have not only secondarily lost Myc but are marked by invariant cell lineages typically producing small body plans of 1000 somatic cells. Furthermore, a detailed analysis of 10 fungal genomes shows that this holozoan signature in RiBi genes is not found in hemiascomycete fungi, which evolved their own unique regulatory signature for the RiBi regulon. Conclusion These results indicate that a Myc regulon, which is activated in proliferating cells during normal development as well as during tumor progression, has primordial roots in the evolution of an inducible growth regime in a protozoan ancestor of animals. Furthermore, by comparing divergent bHLH repertoires, we conclude that regulation by Myc but not by other bHLH genes is responsible for the evolutionary maintenance of E(CG) sites across the RiBi suite of genes. PMID:18816399

  12. Evolution of the holozoan ribosome biogenesis regulon

    Directory of Open Access Journals (Sweden)

    Cole Michael D

    2008-09-01

    Full Text Available Abstract Background The ribosome biogenesis (RiBi genes encode a highly-conserved eukaryotic set of nucleolar proteins involved in rRNA transcription, assembly, processing, and export from the nucleus. While the mode of regulation of this suite of genes has been studied in the yeast, Saccharomyces cerevisiae, how this gene set is coordinately regulated in the larger and more complex metazoan genomes is not understood. Results Here we present genome-wide analyses indicating that a distinct mode of RiBi regulation co-evolved with the E(CG-binding, Myc:Max bHLH heterodimer complex in a stem-holozoan, the ancestor of both Metazoa and Choanoflagellata, the protozoan group most closely related to animals. These results show that this mode of regulation, characterized by an E(CG-bearing core-promoter, is specific to almost all of the known genes involved in ribosome biogenesis in these genomes. Interestingly, this holozoan RiBi promoter signature is absent in nematode genomes, which have not only secondarily lost Myc but are marked by invariant cell lineages typically producing small body plans of 1000 somatic cells. Furthermore, a detailed analysis of 10 fungal genomes shows that this holozoan signature in RiBi genes is not found in hemiascomycete fungi, which evolved their own unique regulatory signature for the RiBi regulon. Conclusion These results indicate that a Myc regulon, which is activated in proliferating cells during normal development as well as during tumor progression, has primordial roots in the evolution of an inducible growth regime in a protozoan ancestor of animals. Furthermore, by comparing divergent bHLH repertoires, we conclude that regulation by Myc but not by other bHLH genes is responsible for the evolutionary maintenance of E(CG sites across the RiBi suite of genes.

  13. MycoCosm, an Integrated Fungal Genomics Resource

    Energy Technology Data Exchange (ETDEWEB)

    Shabalov, Igor; Grigoriev, Igor

    2012-03-16

    MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/month or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.

  14. evaluation of indigenous fungal isolates and metarhizium anisopliae ...

    African Journals Online (AJOL)

    preferred customer

    native fungal isolates against the lesser wax moth and assessing non target effect of one isolate of. Beauveria (IITA 18) and five ... widely distributed and devastating insect pest to ..... Non-Target. Invertebrates of Fungal Biocontrol Agents, PP.

  15. Staurosporine Induces Filamentation in the Human Fungal Pathogen Candida albicans via Signaling through Cyr1 and Protein Kinase A

    Science.gov (United States)

    Xie, Jinglin L.; O’Meara, Teresa R.; Polvi, Elizabeth J.; Robbins, Nicole

    2017-01-01

    ABSTRACT Protein kinases are key regulators of signal transduction pathways that participate in diverse cellular processes. In fungal pathogens, kinases regulate signaling pathways that govern drug resistance, stress adaptation, and pathogenesis. The impact of kinases on the fungal regulatory circuitry has recently garnered considerable attention in the opportunistic fungal pathogen Candida albicans, which is a leading cause of human morbidity and mortality. Complex regulatory circuitry governs the C. albicans morphogenetic transition between yeast and filamentous growth, which is a key virulence trait. Here, we report that staurosporine, a promiscuous kinase inhibitor that abrogates fungal drug resistance, also influences C. albicans morphogenesis by inducing filamentation in the absence of any other inducing cue. We further establish that staurosporine exerts its effect via the adenylyl cyclase Cyr1 and the cyclic AMP (cAMP)-dependent protein kinase A (PKA). Strikingly, filamentation induced by staurosporine does not require the known upstream regulators of Cyr1, Ras1 or Pkc1, or effectors downstream of PKA, including Efg1. We further demonstrate that Cyr1 is capable of activating PKA to enable filamentation in response to staurosporine through a mechanism that does not require degradation of the transcriptional repressor Nrg1. We establish that staurosporine-induced filamentation is accompanied by a defect in septin ring formation, implicating cell cycle kinases as potential staurosporine targets underpinning this cellular response. Thus, we establish staurosporine as a chemical probe to elucidate the architecture of cellular signaling governing fungal morphogenesis and highlight the existence of novel circuitry through which the Cyr1 and PKA govern a key virulence trait. IMPORTANCE The impact of fungal pathogens on human health is devastating. One of the most pervasive fungal pathogens is Candida albicans, which kills ~40% of people suffering from bloodstream

  16. Regulatory T cell memory

    Science.gov (United States)

    Rosenblum, Michael D.; Way, Sing Sing; Abbas, Abul K.

    2016-01-01

    Memory for antigen is a defining feature of adaptive immunity. Antigen-specific lymphocyte populations show an increase in number and function after antigen encounter and more rapidly re-expand upon subsequent antigen exposure. Studies of immune memory have primarily focused on effector B cells and T cells with microbial specificity, using prime challenge models of infection. However, recent work has also identified persistently expanded populations of antigen-specific regulatory T cells that protect against aberrant immune responses. In this Review, we consider the parallels between memory effector T cells and memory regulatory T cells, along with the functional implications of regulatory memory in autoimmunity, antimicrobial host defence and maternal fetal tolerance. In addition, we discuss emerging evidence for regulatory T cell memory in humans and key unanswered questions in this rapidly evolving field. PMID:26688349

  17. NRC regulatory initiatives

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, T.C. [Nuclear Regulatory Commission (United States)

    1989-11-01

    The US Nuclear Regulatory Commission (NRC) is addressing several low-level waste disposal issues that will be important to waste generators and to States and Compacts developing new disposal capacity. These issues include Greater-Than-Class C (GTCC) waste, mixed waste, below regulatory concern (BRC) waste, and the low-level waste data base. This paper discusses these issues and their current status.

  18. Modulation of host-cell MAPkinase signaling during fungal infection

    OpenAIRE

    2015-01-01

    Fungal infections contribute substantially to human suffering and mortality. The interaction between fungal pathogens and their host involves the invasion and penetration of the surface epithelium, activation of cells of the innate immune system and the generation of an effective response to block infection. Numerous host-cell signaling pathways are activated during fungal infection. This review will focus on the main fungal pathogens Aspergillus fumigatus, Candida albicans and Cryptococcus n...

  19. Fungal keratitis - improving diagnostics by confocal microscopy

    DEFF Research Database (Denmark)

    Nielsen, Esben; Heegaard, S; Prause, J U;

    2013-01-01

    -69), 6 out of 17 (35%) cultures were positive and a total of 6/7 (86%) IVCM scans were positive. Three different categories of IVCM results for the grading of diagnostic certainty were formed. Conclusion: IVCM is a valuable tool for diagnosing filamentous fungal keratitis. In order to improve...

  20. Fungal infections in corn picker hand injury

    Directory of Open Access Journals (Sweden)

    Obradović-Tomašev Milana

    2016-01-01

    Full Text Available Introduction. Hand injuries caused by corn pickers are relatively rare but in most cases extensive, with massive tissue destruction. Severe wounds sustained during agricultural work are contaminated, with high incidence of infection. Objective. The aim of the study was to determine the frequency and type of fungal infection in corn picker injuries and their impact on the course and outcome of treatment. Methods. Corn picker hand injuries for the period 2006-2012 were analyzed. After setting up clinical suspicion, direct examination of repeated swabs and histopathological analysis of biopsy material were done in order to detect fungi. Results. From the total number of 60 patients, there was a fungal infection in nine of them (which makes 15% of the total number of patients. Aspergillus spp. was isolated in seven patients, Candida spp. in three, and Mucor spp. in one patient. None of the patients had increased risk factors for developing a fungal infection. In most cases, there was loss of graft and tissue necrosis in previously normally looking wound, after seven or more days. All patients were treated with repeated surgical debridement and concomitant parenteral and topical application of appropriate antifungal agents. There was no need for reamputation in any patient. Conclusion. A high degree of suspicion and a multidisciplinary approach are needed for early diagnosis of fungal infection. Confirmation of diagnosis and the initiation of surgical and appropriate antifungal therapy are essential for a successful outcome.

  1. Fungal peritonitis in children on peritoneal dialysis.

    NARCIS (Netherlands)

    Raaijmakers, R.; Schroder, C.; Monnens, L.A.H.; Cornelissen, E.A.M.; Warris, A.

    2007-01-01

    Fungal peritonitis is a rare but serious complication in children on peritoneal dialysis (PD). In this study, risk factors were evaluated, and therapeutic measures were reviewed. A retrospective, multi-centre study was performed in 159 Dutch paediatric PD patients, between 1980 and 2005 (3,573 month

  2. FUNGAL ASSOCIATION WITH SESSILE MARINE INVERTEBRATES

    Directory of Open Access Journals (Sweden)

    Oded eYarden

    2014-05-01

    Full Text Available The presence and association of fungi with sessile marine animals such as coral and sponges has been well established, yet information on the extent of diversity of the associated fungi is still in its infancy. Culture- as well as metagenomic- and transcriptomic-based analyses have shown that fungal presence in association with these animals can be dynamic and can include core residents as well as shifts in fungal communities. Evidence for detrimental and beneficial interactions between fungi and their marine hosts is accumulating and current challenges include the elucidation of the chemical and cellular crosstalk between fungi and their associates within the holobionts. The ecological function of fungi in association with sessile marine animals is complex and is founded on a combination of factors such as fungal origin, host health, environmental conditions and the presence of other resident or invasive microorganisms in the host. Based on evidence from the much more studied terrestrial systems, the evaluation of marine animal-fungal symbioses under varying environmental conditions may well prove to be critical in predicting ecosystem response to global change, including effects on the health of sessile marine animals.

  3. Meeting report : fungal its workshop (october 2012)

    NARCIS (Netherlands)

    Bates, Scott T; Ahrendt, Steven; Bik, Holly M; Bruns, Thomas D; Caporaso, J Gregory; Cole, James; Dwan, Michael; Fierer, Noah; Gu, Dai; Houston, Shawn; Knight, Rob; Leff, Jon; Lewis, Christopher; Maestre, Juan P; McDonald, Daniel; Nilsson, R Henrik; Porras-Alfaro, Andrea; Robert, Vincent; Schoch, Conrad; Scott, James; Taylor, D Lee; Parfrey, Laura Wegener; Stajich, Jason E

    2013-01-01

    This report summarizes a meeting held in Boulder, CO USA (19-20 October 2012) on fungal community analyses using ultra-high-throughput sequencing of the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA (rRNA) genes. The meeting was organized as a two-day workshop, with the prima

  4. Grass fungal endophytes and uses thereof

    Energy Technology Data Exchange (ETDEWEB)

    Craven, Kelly

    2015-03-10

    The invention provides isolated fungal endophytes and synthetic combinations thereof with host grass plants. Methods for inoculating grass plant with the endophytes, for propagating the grass-endophyte combinations, and for producing feeds and biofuels from grass-endophyte combinations are also provided.

  5. Pre- and postharvest fungal apple diseases

    Science.gov (United States)

    The domesticated apple (Malus domestica) is the most significant pome fruit grown and consumed worldwide. China is the largest producer followed by the United States on a global scale. However, fungal plant pathogens cause significant economic losses in the field and in storage which negatively impa...

  6. Packaging conditions hindering fungal growth on cheese

    DEFF Research Database (Denmark)

    Nielsen, Per Væggemose; Haasum, Iben

    1997-01-01

    Fungal contamination is one of the most important quality deteriorating factors on cheese. During the last 5 years we have studied in detail the underlying factors controlling these unwanted processes in a collaborative project financed by the Danish Dairy Board and the Ministry of Agriculture...

  7. Genetics of fungal resistance to systemic fungicides

    NARCIS (Netherlands)

    Tuyl, van J.M.

    1977-01-01

    Since the introduction of the systemic fungicides, fungicide resistance has become a serious problem in plant disease control. This study was carried out in order to contribute to the knowledge about the genetics of fungal resistance to fungicides both from a practical and a fundamental point of vie

  8. Pulmonary fungal infections after bone marrow transplantation

    Energy Technology Data Exchange (ETDEWEB)

    Allan, B.T.; Patton, D.; Ramsey, N.K.C.; Day, D.L.

    1988-02-01

    Of 319 pediatric patients treated with bone marrow transplantation (BMT) during a 10-year period, 27 developed pulmonary fungal infections (PFI). Only 2 patients (7%) survived. Twenty-three patients (85%) had been treated with systemic anti-fungal therapy immediately before or at the time of diagnosis. Nineteen patients (70%) were neutropenic, and 4 of the 8 patients who were not neutropenic were being treated with systemic steroids for graft vs. host disease (GVHD). Seven patients (26%) died within 7 days of diagnosis. The diagnosis was made ante-mortem in 9 patients (33%). Radiographic abnormalities were variable. At the onset of chest X-ray (CXR) change, the pulmonary infiltrates were unilateral in 14 patients (52%) and, at diagnosis, bilateral in 18 (66%). At diagnosis the infiltrates were interstitial in 3 patients (11%), alveolar in 20 (74%) and mixed in 4 (15%). Six patients (22%) developed cavitary lesions. The infecting agents were Aspergillus in 21 patients (78%), Candida in 7 (26%), Mucormycosis in 3 (11%), and Fusarium in 1 (4%). Five patients (19%) had mixed fungal infections and 7 (26%) had concurrent cytomegalovirus (CMV) pulmonary infections. Although the radiographic changes are often nonspecific in PFI, alveolar or nodular infiltrates in neutropenic patients or in those being treated for GVHD should strongly suggest a fungal etiology.

  9. A biotechnology perspective of fungal proteases

    Directory of Open Access Journals (Sweden)

    Paula Monteiro de Souza

    2015-06-01

    Full Text Available Proteases hydrolyze the peptide bonds of proteins into peptides and amino acids, being found in all living organisms, and are essential for cell growth and differentiation. Proteolytic enzymes have potential application in a wide number of industrial processes such as food, laundry detergent and pharmaceutical. Proteases from microbial sources have dominated applications in industrial sectors. Fungal proteases are used for hydrolyzing protein and other components of soy beans and wheat in soy sauce production. Proteases can be produced in large quantities in a short time by established methods of fermentation. The parameters such as variation in C/N ratio, presence of some sugars, besides several other physical factors are important in the development of fermentation process. Proteases of fungal origin can be produced cost effectively, have an advantage faster production, the ease with which the enzymes can be modified and mycelium can be easily removed by filtration. The production of proteases has been carried out using submerged fermentation, but conditions in solid state fermentation lead to several potential advantages for the production of fungal enzymes. This review focuses on the production of fungal proteases, their distribution, structural-functional aspects, physical and chemical parameters, and the use of these enzymes in industrial applications.

  10. Fungal infections of the oral mucosa.

    Science.gov (United States)

    Krishnan, P Anitha

    2012-01-01

    Fungal infections in humans occur as a result of defects in the immune system. An increasing emergence in oral Candidal and non-Candidal fungal infections is evident in the past decade owing to the rise in the immunodeficient and immunocompromised population globally. Oral Candidal infection usually involves a compromised host and the compromise may be local or systemic. Local compromising factors include decreased salivation, poor oral hygiene, wearing dentures among others while systemic factors include diabetes mellitus, nutritional deficiency, HIV infection/AIDS and others. Oral candidiasis is generally a localized infection and rarely appears as a systemic fungal disease whereas oral non-Candidal fungal infections are usually signs of disseminated disease. Some of the non-Candidal fungi that were once considered exotic and geographically restricted are now seen worldwide, beyond their natural habitat, probably attributed to globalization and travels. Currently infections from these fungi are more prevalent than before and they may present either as primary oral lesions or as oral manifestations of systemic mycoses. This review discusses the various predisposing factors, clinical presentations, clinical differential diagnosis, diagnosis and management of oral candidiasis, as well as briefly highlights upon a few of the more exotic non-Candidal fungi that infect the oral mucosa.

  11. Fungal peritonitis in children on peritoneal dialysis.

    NARCIS (Netherlands)

    Raaijmakers, R.; Schroder, C.; Monnens, L.A.H.; Cornelissen, E.A.M.; Warris, A.

    2007-01-01

    Fungal peritonitis is a rare but serious complication in children on peritoneal dialysis (PD). In this study, risk factors were evaluated, and therapeutic measures were reviewed. A retrospective, multi-centre study was performed in 159 Dutch paediatric PD patients, between 1980 and 2005 (3,573 month

  12. Invasive fungal infections in acute leukemia.

    Science.gov (United States)

    Bhatt, Vijaya R; Viola, George M; Ferrajoli, Alessandra

    2011-08-01

    Invasive fungal infection (IFI) is among the leading causes for morbidity, mortality, and economic burden for patients with acute leukemia. In the past few decades, the incidence of IFI has increased dramatically. The certainty of diagnosis of IFI is based on host factors, clinical evidence, and microbiological examination. Advancement in molecular diagnostic modalities (e.g. non-culture-based serum biomarkers such as β-glucan or galactomannan assays) and high-resolution radiological imaging has improved our diagnostic approach. The early use of these diagnostic tests assists in the early initiation of preemptive therapy. Nonetheless, the complexity of IFI in patients with leukemia and the limitations of these diagnostic tools still mandate astute clinical acumen. Its management has been further complicated by the increasing frequency of infection by non-Aspergillus molds (e.g. zygomycosis) and the emergence of drug-resistant fungal pathogens. In addition, even though the antifungal armamentarium has expanded rapidly in the past few decades, the associated mortality remains high. The decision to initiate antifungal treatment and the choice of anti-fungal therapy requires careful consideration of several factors (e.g. risk stratification, local fungal epidemiologic patterns, concomitant comorbidities, drug-drug interactions, prior history of antifungal use, overall cost, and the pharmacologic profile of the antifungal agents). In order to optimize our diagnostic and therapeutic management of IFI in patients with acute leukemia, further basic research and clinical trials are desperately needed.

  13. Fungal biology and agriculture: revisiting the field

    Science.gov (United States)

    Yarden, O.; Ebbole, D.J.; Freeman, S.; Rodriguez, R.J.; Dickman, M. B.

    2003-01-01

    Plant pathology has made significant progress over the years, a process that involved overcoming a variety of conceptual and technological hurdles. Descriptive mycology and the advent of chemical plant-disease management have been followed by biochemical and physiological studies of fungi and their hosts. The later establishment of biochemical genetics along with the introduction of DNA-mediated transformation have set the stage for dissection of gene function and advances in our understanding of fungal cell biology and plant-fungus interactions. Currently, with the advent of high-throughput technologies, we have the capacity to acquire vast data sets that have direct relevance to the numerous subdisciplines within fungal biology and pathology. These data provide unique opportunities for basic research and for engineering solutions to important agricultural problems. However, we also are faced with the challenge of data organization and mining to analyze the relationships between fungal and plant genomes and to elucidate the physiological function of pertinent DNA sequences. We present our perspective of fungal biology and agriculture, including administrative and political challenges to plant protection research.

  14. Fungal biology and agriculture: revisiting the field.

    Science.gov (United States)

    Yarden, O; Ebbole, D J; Freeman, S; Rodriguez, R J; Dickman, M B

    2003-10-01

    Plant pathology has made significant progress over the years, a process that involved overcoming a variety of conceptual and technological hurdles. Descriptive mycology and the advent of chemical plant-disease management have been followed by biochemical and physiological studies of fungi and their hosts. The later establishment of biochemical genetics along with the introduction of DNA-mediated transformation have set the stage for dissection of gene function and advances in our understanding of fungal cell biology and plant-fungus interactions. Currently, with the advent of high-throughput technologies, we have the capacity to acquire vast data sets that have direct relevance to the numerous subdisciplines within fungal biology and pathology. These data provide unique opportunities for basic research and for engineering solutions to important agricultural problems. However, we also are faced with the challenge of data organization and mining to analyze the relationships between fungal and plant genomes and to elucidate the physiological function of pertinent DNA sequences. We present our perspective of fungal biology and agriculture, including administrative and political challenges to plant protection research.

  15. Fungal Bioconversion of Lignocellulosic Residues; Opportunities & Perspectives

    Directory of Open Access Journals (Sweden)

    Mehdi Dashtban, Heidi Schraft, Wensheng Qin

    2009-01-01

    Full Text Available The development of alternative energy technology is critically important because of the rising prices of crude oil, security issues regarding the oil supply, and environmental issues such as global warming and air pollution. Bioconversion of biomass has significant advantages over other alternative energy strategies because biomass is the most abundant and also the most renewable biomaterial on our planet. Bioconversion of lignocellulosic residues is initiated primarily by microorganisms such as fungi and bacteria which are capable of degrading lignocellulolytic materials. Fungi such as Trichoderma reesei and Aspergillus niger produce large amounts of extracellular cellulolytic enzymes, whereas bacterial and a few anaerobic fungal strains mostly produce cellulolytic enzymes in a complex called cellulosome, which is associated with the cell wall. In filamentous fungi, cellulolytic enzymes including endoglucanases, cellobiohydrolases (exoglucanases and β-glucosidases work efficiently on cellulolytic residues in a synergistic manner. In addition to cellulolytic/hemicellulolytic activities, higher fungi such as basidiomycetes (e.g. Phanerochaete chrysosporium have unique oxidative systems which together with ligninolytic enzymes are responsible for lignocellulose degradation. This review gives an overview of different fungal lignocellulolytic enzymatic systems including extracellular and cellulosome-associated in aerobic and anaerobic fungi, respectively. In addition, oxidative lignocellulose-degradation mechanisms of higher fungi are discussed. Moreover, this paper reviews the current status of the technology for bioconversion of biomass by fungi, with focus on mutagenesis, co-culturing and heterologous gene expression attempts to improve fungal lignocellulolytic activities to create robust fungal strains.

  16. The Amsterdam Declaration on Fungal Nomenclature

    NARCIS (Netherlands)

    Hawksworth, D.L.; Crous, P.W.; Redhead, S.A.; Reynolds, D.R.; Samson, R.A.; Seifert, K.A.; Taylor, J.E.; Wingfield, M.J.; Abaci, Ö.; Aime, C.; Asan, A.; Bai, F.H.; de Beer, Z.W.; Begerow, D.; Berikten, D.; Boekhout, T.; Buchanan, P.K.; Burgess, T.I.; Buzina, W.; Cai, L.; Cannon, P.F.; Crane, J.L.; Damm, U.; Daniel, H.M.; van Diepeningen, A.D.; Druzhinina, I.; Dyer, P.S.; Eberhardt, U.; Fell, J.W.; Frisvad, J.C.; Geiser, D.M.; Geml, J.; Glienke, C.; Gräfenhan, T.; Groenewald, J.Z.; Groenewald, M.; de Gruyter, J.; Guého-Kellermann, E.; Guo, L-D.; Hibbett, D.S.; Hong, S.B.; de Hoog, G.S.; Houbraken, J.; Huhndorf, S.M.; Hyde, K.D.; Ismail, A.; Johnston, P.R.; Kadaifciler, D.G.; Kirk, P.M.; Kõljalg, U.; Kurtzman, C.P.; Lagneau, P-E.; Lévesque, C.A.; Liu, X.S.; Lombard, L.; Meyer, W.; Miller, A.N.; Minter, D.W.; Najafzadeh, M.J.; Norvell, L.L.; Ozerskaya, S.M.; Öziç, R.; Pennycook, S.R.; Peterson, S.W.; Pettersson, O.V.; Quaedvlieg, W.; Robert, V.; Ruibal, C.; Schnürer, J.; Schroers, H.J.; Shivas, R.G.; Slippers, B.; Spierenburg, H.; Takashima, M.; Taşkın, E.; Thines, M.; Thrane, U.; Uztan, A.H.; van Raak, M.; Varga, J.; Vasco, A.; Verkley, G.J.M.; Videira, S.I.R.; de Vries, R.P.; Weir, B.S.; Yilmaz, N.; Yurkov, A.; Zhang, N.

    2011-01-01

    The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current

  17. Fungal cultivation on glass-beads

    DEFF Research Database (Denmark)

    Droce, Aida; Sørensen, Jens Laurids; Giese, Henriette

    Transcription of various bioactive compounds and enzymes are dependent on fungal cultivation method. In this study we cultivate Fusarium graminearum and Fusarium solani on glass-beads with liquid media in petri dishes as an easy and inexpensive cultivation method, that resembles in secondary...

  18. Habitat filters in fungal endophyte community assembly

    Science.gov (United States)

    Fungal endophytes can influence host health, and more broadly, can instigate trophic cascades with effects scaling to the ecosystem level. Despite this, biotic mechanisms of endophyte community assembly are largely unknown. We used maize to investigate three potential habitat filters in endophyte co...

  19. Standard methods for fungal brood disease research

    DEFF Research Database (Denmark)

    Jensen, Annette Bruun; Aronstein, Kathrine; Manuel Flores, Jose;

    2013-01-01

    Chalkbrood and stonebrood are two fungal diseases associated with honey bee brood. Chalkbrood, caused by Ascosphaera apis, is a common and widespread disease that can result in severe reduction of emerging worker bees and thus overall colony productivity. Stonebrood is caused by Aspergillus spp. ...

  20. Metabolic priming by a secreted fungal effector.

    Science.gov (United States)

    Djamei, Armin; Schipper, Kerstin; Rabe, Franziska; Ghosh, Anupama; Vincon, Volker; Kahnt, Jörg; Osorio, Sonia; Tohge, Takayuki; Fernie, Alisdair R; Feussner, Ivo; Feussner, Kirstin; Meinicke, Peter; Stierhof, York-Dieter; Schwarz, Heinz; Macek, Boris; Mann, Matthias; Kahmann, Regine

    2011-10-05

    Maize smut caused by the fungus Ustilago maydis is a widespread disease characterized by the development of large plant tumours. U. maydis is a biotrophic pathogen that requires living plant tissue for its development and establishes an intimate interaction zone between fungal hyphae and the plant plasma membrane. U. maydis actively suppresses plant defence responses by secreted protein effectors. Its effector repertoire comprises at least 386 genes mostly encoding proteins of unknown function and expressed exclusively during the biotrophic stage. The U. maydis secretome also contains about 150 proteins with probable roles in fungal nutrition, fungal cell wall modification and host penetration as well as proteins unlikely to act in the fungal-host interface like a chorismate mutase. Chorismate mutases are key enzymes of the shikimate pathway and catalyse the conversion of chorismate to prephenate, the precursor for tyrosine and phenylalanine synthesis. Root-knot nematodes inject a secreted chorismate mutase into plant cells likely to affect development. Here we show that the chorismate mutase Cmu1 secreted by U. maydis is a virulence factor. The enzyme is taken up by plant cells, can spread to neighbouring cells and changes the metabolic status of these cells through metabolic priming. Secreted chorismate mutases are found in many plant-associated microbes and might serve as general tools for host manipulation.

  1. Meeting report : fungal its workshop (october 2012)

    NARCIS (Netherlands)

    Bates, Scott T; Ahrendt, Steven; Bik, Holly M; Bruns, Thomas D; Caporaso, J Gregory; Cole, James; Dwan, Michael; Fierer, Noah; Gu, Dai; Houston, Shawn; Knight, Rob; Leff, Jon; Lewis, Christopher; Maestre, Juan P; McDonald, Daniel; Nilsson, R Henrik; Porras-Alfaro, Andrea; Robert, Vincent; Schoch, Conrad; Scott, James; Taylor, D Lee; Parfrey, Laura Wegener; Stajich, Jason E

    2013-01-01

    This report summarizes a meeting held in Boulder, CO USA (19-20 October 2012) on fungal community analyses using ultra-high-throughput sequencing of the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA (rRNA) genes. The meeting was organized as a two-day workshop, with the

  2. Thigmo Responses: The Fungal Sense of Touch.

    Science.gov (United States)

    Almeida, Mariana Cruz; Brand, Alexandra C

    2017-04-01

    The growth and development of most fungi take place on a two-dimensional surface or within a three-dimensional matrix. The fungal sense of touch is therefore critical for fungi in the interpretation of their environment and often signals the switch to a new developmental state. Contact sensing, or thigmo-based responses, include thigmo differentiation, such as the induction of invasion structures by plant pathogens in response to topography; thigmonasty, where contact with a motile prey rapidly triggers its capture; and thigmotropism, where the direction of hyphal growth is guided by physical features in the environment. Like plants and some bacteria, fungi grow as walled cells. Despite the well-demonstrated importance of thigmo responses in numerous stages of fungal growth and development, it is not known how fungal cells sense contact through the relatively rigid structure of the cell wall. However, while sensing mechanisms at the molecular level are not entirely understood, the downstream signaling pathways that are activated by contact sensing are being elucidated. In the majority of cases, the response to contact is complemented by chemical cues and both are required, either sequentially or simultaneously, to elicit normal developmental responses. The importance of a sense of touch in the lifestyles and development of diverse fungi is highlighted in this review, and the candidate molecular mechanisms that may be involved in fungal contact sensing are discussed.

  3. October 2012 Multistate Fungal Meningitis Outbreak

    Centers for Disease Control (CDC) Podcasts

    2012-10-17

    This podcast gives an overview of the October 2012 multistate fungal meningitis outbreak, including symptoms to watch for and a website for up-to-date information.  Created: 10/17/2012 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 10/17/2012.

  4. Modelling Fungal Fermentations for Enzyme Production

    DEFF Research Database (Denmark)

    Albæk, Mads Orla; Gernaey, Krist; Hansen, Morten S.

    We have developed a process model of fungal fed-batch fermentations for enzyme production. In these processes, oxygen transfer rate is limiting and controls the substrate feeding rate. The model has been shown to describe cultivations of both Aspergillus oryzae and Trichoderma reesei strains in 550...

  5. Fungal endophytes of sorghum in Burkina Faso

    DEFF Research Database (Denmark)

    Zida, E P; Thio, I G; Néya, B J

    2014-01-01

    A survey was conducted to assess the natural occurrence and distribution of fungal endophytes in sorghum in relation to plant performance in two distinct agro-ecological zones in Burkina Faso. Sorghum farm-saved seeds were sown in 48 farmers’ fields in Sahelian and North Sudanian zones to produce...

  6. The Amsterdam Declaration on Fungal Nomenclature

    NARCIS (Netherlands)

    Hawksworth, D.L.; Crous, P.W.; Redhead, S.A.; Reynolds, D.R.; Samson, R.A.; Seifert, K.A.; Taylor, J.E.; Wingfield, M.J.; Abaci, Ö.; Aime, C.; Asan, A.; Bai, F.H.; de Beer, Z.W.; Begerow, D.; Berikten, D.; Boekhout, T.; Buchanan, P.K.; Burgess, T.I.; Buzina, W.; Cai, L.; Cannon, P.F.; Crane, J.L.; Damm, U.; Daniel, H.M.; van Diepeningen, A.D.; Druzhinina, I.; Dyer, P.S.; Eberhardt, U.; Fell, J.W.; Frisvad, J.C.; Geiser, D.M.; Geml, J.; Glienke, C.; Gräfenhan, T.; Groenewald, J.Z.; Groenewald, M.; de Gruyter, J.; Guého-Kellermann, E.; Guo, L-D.; Hibbett, D.S.; Hong, S.B.; de Hoog, G.S.; Houbraken, J.; Huhndorf, S.M.; Hyde, K.D.; Ismail, A.; Johnston, P.R.; Kadaifciler, D.G.; Kirk, P.M.; Kõljalg, U.; Kurtzman, C.P.; Lagneau, P-E.; Lévesque, C.A.; Liu, X.S.; Lombard, L.; Meyer, W.; Miller, A.N.; Minter, D.W.; Najafzadeh, M.J.; Norvell, L.L.; Ozerskaya, S.M.; Öziç, R.; Pennycook, S.R.; Peterson, S.W.; Pettersson, O.V.; Quaedvlieg, W.; Robert, V.; Ruibal, C.; Schnürer, J.; Schroers, H.J.; Shivas, R.G.; Slippers, B.; Spierenburg, H.; Takashima, M.; Taşkın, E.; Thines, M.; Thrane, U.; Uztan, A.H.; van Raak, M.; Varga, J.; Vasco, A.; Verkley, G.J.M.; Videira, S.I.R.; de Vries, R.P.; Weir, B.S.; Yilmaz, N.; Yurkov, A.; Zhang, N.

    2011-01-01

    The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current

  7. Invasive fungal rhinosinusitis in adult patients: Our experience in diagnosis and management.

    Science.gov (United States)

    Pagella, Fabio; De Bernardi, Francesca; Dalla Gasperina, Daniela; Pusateri, Alessandro; Matti, Elina; Avato, Irene; Cavanna, Caterina; Zappasodi, Patrizia; Bignami, Maurizio; Bernardini, Elena; Grossi, Paolo Antonio; Castelnuovo, Paolo

    2016-04-01

    This paper describes our experience in the management of acute and chronic invasive fungal rhinosinusitis (IFRS) in adults. Medical files of all patients aged >18 years treated in our institutions for IFRS from 2002 to 2013 were retrospectively reviewed. A total of 18 cases (10 acute and 8 chronic) were recorded. In acute form, haematological malignancies represented the principal comorbidity (100%), while in chronic form this was diabetes mellitus (87.5%). All patients received systemic antifungal agents. Endoscopic sinus surgery was performed in 16/18 patients (88.9%). Among patients with an acute IFRS, 4/10 died of fungal infection (40%), on the other side 2/8 patients with chronic IFRS died of the evolution of the mycosis (25%). Acute and chronic IFRS are different entities: in acute form, prognosis is poor, so therapy should be promptly performed, although host immune status and evolution of the haematological disease are key factors for the outcome. In chronic form, a wide surgical excision of the disease is recommended in order to obtain a complete removal of fungal infection. In both forms, early clinical findings are non-specific and ambiguous, so diagnosis depends on a high index of suspicion, taking into account predisposing factors. Copyright © 2016 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

  8. Non-transcriptional regulatory processes shape transcriptional network dynamics.

    Science.gov (United States)

    Ray, J Christian J; Tabor, Jeffrey J; Igoshin, Oleg A

    2011-10-11

    Information about the extra- or intracellular environment is often captured as biochemical signals that propagate through regulatory networks. These signals eventually drive phenotypic changes, typically by altering gene expression programmes in the cell. Reconstruction of transcriptional regulatory networks has given a compelling picture of bacterial physiology, but transcriptional network maps alone often fail to describe phenotypes. Cellular response dynamics are ultimately determined by interactions between transcriptional and non-transcriptional networks, with dramatic implications for physiology and evolution. Here, we provide an overview of non-transcriptional interactions that can affect the performance of natural and synthetic bacterial regulatory networks.

  9. Analysis of institutional evolution of regulatory activity in the Brazilian electric sector: 1920-1997; Analise da evolucao institucional da atividade de regulacao no setor eletrico brasileiro: 1920-1997

    Energy Technology Data Exchange (ETDEWEB)

    Tavares, Mauricio Lopes; Ferreira, Elnatan Chagas; Dias, Jose Antonio Siqueira [Universidade Estadual de Campinas (DEMIC/FEEC/UNICAMP), SP (Brazil). Fac. de Engenharia Eletrica e de Computacao. Dept. de Eletronica e Microeletronica], Email: siqueira@demic.fee.unicamp.br

    2006-07-01

    An analysis of the institutional evolution of the governmental organizations which were responsible for the regulation of the electrical energy sector in Brazil (before the establishment of the ANEEL) is presented . Taking into account the various levels of subordination and independence in their actuation, the different missions and powers given to these agencies regarding the inspection, controlling, planning and regulating the industry, are compared and discussed. The conducted analysis is essentially formal, based on the legal instruments which defined and established the creation of those agencies. (author)

  10. Nitrogen regulation of fungal secondary metabolism in fungi

    Directory of Open Access Journals (Sweden)

    Bettina eTudzynski

    2014-11-01

    Full Text Available Fungi occupy diverse environments where they are constantly challenged by stressors such as extreme pH, temperature, UV exposure and nutrient deprivation. Nitrogen is an essential requirement for growth, and the ability to metabolize a wide variety of nitrogen sources enable fungi to colonize different environmental niches and survive nutrient limitations. Favored nitrogen sources, particularly ammonium and glutamine, are used preferentially, while the expression of genes required for the use of various secondary nitrogen sources is subject to a regulatory mechanism called nitrogen metabolite repression. Studies on gene regulation in response to nitrogen availability were carried out first in Saccharomyces cerevisiae, Aspergillus nidulans, and Neurospora crassa. These studies revealed that fungi respond to changes in nitrogen availability with physiological and morphological alterations and activation of differentiation processes. In all fungal species studied, the major GATA transcription factor AreA and its co-repressor Nmr are central players of the nitrogen regulatory network. In addition to growth and development, the quality and quantity of nitrogen also affects the formation of a broad range of secondary metabolites (SMs. Recent studies, mainly on species of the genus Fusarium, revealed that AreA does not only regulate a large set of nitrogen catabolic genes, but can also be involved in regulating production of SMs. Furthermore, several other regulators, e.g. a second GATA transcription factor, AreB, that was proposed to negatively control nitrogen catabolic genes by competing with AreA for binding to GATA elements, was shown to act as activator of some nitrogen-repressed as well as nitrogen-induced SM gene clusters. This review highlights our latest understanding of canonical (AreA-dependent and non-canonical nitrogen regulation mechanisms by which fungi may regulate biosynthesis of certain SMs in response to nitrogen availability.

  11. Estimated burden of fungal infections in Kenya.

    Science.gov (United States)

    Guto, John Abuga; Bii, Christine C; Denning, David W

    2016-08-31

    Kenya is a developing country with a high rate of tuberculosis (TB) and a moderate HIV infection burden. No estimate of the burden of fungal diseases in Kenya is published. We used specific populations at risk and fungal infection frequencies from the literature to estimate national incidence or prevalence of serious fungal infections. Used sources were: 2010 WHO TB statistics, Kenya Acquired Immunodeficiency Syndrome (AIDS) Epidemic Update 2012, Kenya Facts and figures 2012, Kenya Demographic and Health Survey 2008-2009. Of Kenya's population of ~40 million, 43% are under 15 years old and approximately 594,660 Kenyan women get >4 episodes Candida vulvovaginitis annually (2,988/100,000). The HIV/AIDS population at risk of opportunistic infections (OI) is 480,000 and the OI estimates include 306,000 patients with oral thrush (768/100,000), 114,000 with oesophageal candidiasis (286/100,000), 11,900 with cryptococcal meningitis (29/100,000) and 17,000 patients with Pneumocystis pneumonia (42/100,000). Chronic pulmonary aspergillosis following TB has a prevalence of 10,848 cases (32/100,000). The adult asthma prevalence is 3.1% and assuming 2.5% have allergic bronchopulmonary aspergillosis then 17,696 (44/100,000) are affected.  Invasive aspergillosis, candidaemia and Candida peritonitis are probably uncommon. Tinea capitis infects 9.6% of children in Kenya, while fungal keratitis and otomycoses are difficult to estimate. At any one time, about 7% of the Kenyan population suffers from a significant fungal infection, with recurrent vaginitis and tinea capitis accounting for 82% of the infections. These estimates require further epidemiological studies for validation.

  12. Evaluating the impact of a fungal-origin chitosan preparation on Brettanomyces bruxellensis in the context of wine aging

    Directory of Open Access Journals (Sweden)

    Tiziana Nardi

    2014-12-01

    Full Text Available Brettanomyces bruxellensis and the consequences of its development in wines are a continuous threat for wine quality. In this context, chitosan of fungal origin was introduced as a new tool to control B. bruxellensis in the context of winemaking. Recent studies have showed the impact of a fungal origin chitosan application on wines contaminated with B. bruxellensis, leading to the elimination of B. bruxellensis cells. In these studies, the chitosan preparation was added, the wine racked off after 10 days and the efficiency of the treatment was evaluated in a short delay after the treatment. This study focused on the evaluation of the impact of different addition protocols of an enological chitosan preparation on B. bruxellensis population evolution and volatile phenols content along the aging, up to 9 months. The results confirm the interest of fungal origin chitosan as a preventive tool to control B. bruxellensis in the context of wine aging.

  13. Ionizing radiation sources: very diversified means, multiple applications and a changing regulatory environment. Conference proceedings; Les sources de rayonnements ionisants: des moyens tres diversifies, des applications multiples et une reglementation en evolution. Recueil des presentations

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2011-11-15

    This document brings together the available presentations given at the conference organised by the French society of radiation protection about ionizing radiation source means, applications and regulatory environment. Twenty eight presentations (slides) are compiled in this document and deal with: 1 - Overview of sources - some quantitative data from the national inventory of ionizing radiation sources (Yann Billarand, IRSN); 2 - Overview of sources (Jerome Fradin, ASN); 3 - Regulatory framework (Sylvie Rodde, ASN); 4 - Alternatives to Iridium radiography - the case of pressure devices at the manufacturing stage (Henri Walaszek, Cetim; Bruno Kowalski, Welding Institute); 5 - Dosimetric stakes of medical scanner examinations (Jean-Louis Greffe, Charleroi hospital of Medical University); 6 - The removal of ionic smoke detectors (Bruno Charpentier, ASN); 7 - Joint-activity and reciprocal liabilities - Organisation of labour risk prevention in case of companies joint-activity (Paulo Pinto, DGT); 8 - Consideration of gamma-graphic testing in the organization of a unit outage activities (Jean-Gabriel Leonard, EDF); 9 - Radiological risk control at a closed and independent work field (Stephane Sartelet, Areva); 10 - Incidents and accidents status and typology (Pascale Scanff, IRSN); 11 - Regional overview of radiation protection significant events (Philippe Menechal, ASN); 12 - Incident leading to a tritium contamination in and urban area - consequences and experience feedback (Laurence Fusil, CEA); 13 - Experience feedback - loss of sealing of a calibration source (Philippe Mougnard, Areva); 14 - Blocking incident of a {sup 60}Co source (Bruno Delille, Salvarem); 15 - Triggering of gantry's alarm: status of findings (Philippe Prat, Syctom); 16 - Non-medical electric devices: regulatory changes (Sophie Dagois, IRSN; Jerome Fradin, ASN); 17 - Evaluation of the dose equivalent rate in pulsed fields: method proposed by the IRSN and implementation test (Laurent Donadille

  14. Fungal and Bacterial Pigments: Secondary Metabolites with Wide Applications

    Directory of Open Access Journals (Sweden)

    Manik Prabhu Narsing Rao

    2017-06-01

    Full Text Available The demand for natural colors is increasing day by day due to harmful effects of some synthetic dyes. Bacterial and fungal pigments provide a readily available alternative source of naturally derived pigments. In contrast to other natural pigments, they have enormous advantages including rapid growth, easy processing, and independence of weather conditions. Apart from colorant, bacterial and fungal pigments possess many biological properties such as antioxidant, antimicrobial and anticancer activity. This review outlines different types of pigments. It lists some bacterial and fungal pigments and current bacterial and fungal pigment status and challenges. It also focuses on possible fungal and bacterial pigment applications.

  15. Recent Advances in Fungal Hydrophobin Towards Using in Industry.

    Science.gov (United States)

    Khalesi, Mohammadreza; Gebruers, Kurt; Derdelinckx, Guy

    2015-08-01

    Fungal hydrophobin is a family of low molecular weight proteins consisting of four disulfide bridges and an extraordinary hydrophobic patch. The hydrophobic patch of hydrophobins and the molecules of gaseous CO2 may interact together and form the stable CO2-nanobubbles covered by an elastic membrane in carbonated beverages. The nanobubbles provide the required energy to provoke primary gushing. Due to the hydrophobicity of hydrophobin, this protein is used as a biosurfactant, foaming agent or encapsulating agent in food products and medicine formulations. Increasing demands for using of hydrophobins led to a challenge regarding production and purification of this product. However, the main issue to use hydrophobin in the industry is the regulatory affairs: yet there is no approved legislation for using hydrophobin in food and beverages. To comply with the legislation, establishing a consistent method for obtaining pure hydrophobins is necessary. Currently, few research teams in Europe are focusing on different aspects of hydrophobins. In this paper, an up-to-date collection of highlights from those special groups about the bio-chemical and physicochemical characteristics of hydrophobins have been studied. The recent advances of those groups concerning the production and purification, positive applications and negative function of hydrophobin are also summarised.

  16. Experimental evolution in fungi: An untapped resource.

    Science.gov (United States)

    Fisher, Kaitlin J; Lang, Gregory I

    2016-09-01

    Historically, evolutionary biology has been considered an observational science. Examining populations and inferring evolutionary histories mold evolutionary theories. In contrast, laboratory evolution experiments make use of the amenability of traditional model organisms to study fundamental processes underlying evolution in real time in simple, but well-controlled, environments. With advances in high-throughput biology and next generation sequencing, it is now possible to propagate hundreds of parallel populations over thousands of generations and to quantify precisely the frequencies of various mutations over time. Experimental evolution combines the ability to simultaneously monitor replicate populations with the power to vary individual parameters to test specific evolutionary hypotheses, something that is impractical or infeasible in natural populations. Many labs are now conducting laboratory evolution experiments in nearly all model systems including viruses, bacteria, yeast, nematodes, and fruit flies. Among these systems, fungi occupy a unique niche: with a short generation time, small compact genomes, and sexual cycles, fungi are a particularly valuable and largely untapped resource for propelling future growth in the field of experimental evolution. Here, we describe the current state of fungal experimental evolution and why fungi are uniquely positioned to answer many of the outstanding questions in the field. We also review which fungal species are most well suited for experimental evolution.

  17. Different types of fungal sinusitis occurring concurrently: implications for therapy.

    Science.gov (United States)

    Rupa, V; Thomas, Meera

    2013-02-01

    The purpose of this study is to describe the clinical and histopathological features, management and outcome of a series of patients with simultaneous occurrence of invasive and non-invasive fungal sinusitis (mixed fungal sinusitis). The histopathological records of patients with fungal sinusitis seen over the last 6 years were reviewed. The clinical, histopathological, treatment and follow up details of all cases with mixed fungal sinusitis were noted. Six cases of mixed fungal sinusitis with concurrent occurrence of chronic granulomatous fungal sinusitis and allergic fungal sinusitis (AFS) were seen during the study period. Most (83.3 %) had bilateral disease. All patients had undergone prior endoscopic sinus surgery at least once within the previous 2 years. Histopathological features showed predominance of invasive disease in half the patients. Except for one patient who did not report for follow up, all patients with predominant chronic granulomatous fungal sinusitis received systemic antifungal therapy and inhaled steroids. Those with predominant features of AFS received oral and inhaled steroids. Five patients with mixed fungal sinusitis who had follow up ranging from 6 months to 5 years were disease free following treatment. Mixed fungal sinusitis should be recognized by the surgeon and pathologist as a separate category of fungal sinusitis whose treatment depends on accurate histological diagnosis. A good outcome may be expected with appropriate therapy.

  18. Fungal atopy in adult cystic fibrosis.

    LENUS (Irish Health Repository)

    Henry, M

    2012-02-03

    This study set out to estimate the prevalence of atopy to a variety of common ubiquitous fungi, including A. fumigatus, in cystic fibrosis (CF), and to evaluate the investigations by which the diagnosis was made. Particular attention was paid to the usefulness of skin testing and immunoassays in detecting which patients had simple fungal atopy, and which patients were at high risk of developing allergic bronchopulmonary mycoses. This cross-sectional study included 21 adult CF patients and 20 matched controls. Serum samples were taken for the measurement of total serum IgE and specific serum IgE to nine common fungi. Immediate hypersensitivity skin prick testing to each of the fungi was also performed. Simple fungal atopy was described in subjects fulfilling the following criteria: total serum IgE > 100 KU l(-1) with specific radioimmunoassay > or = grade 1 to at least one fungus and a positive skin prick test (SPT) > or = 3 mm to the same fungus. \\'High risk\\' for developing allergic bronchopulmonary mycosis (ABPM) was described in subjects fulfilling the following criteria: total serum IgE > 200 KU l(-1) with specific radioimmunoassay > or = grade 2 to at least one fungus and a positive skin prick test (SPT) > or = 6 mm to the same fungus. The adult CF group had a significantly higher total SPT score (P=0.005) and mean total serum IgE (P<0.05) than controls. Forty-three percent of CF patients fulfilled the criteria for fungal atopy to at least a single fungus. Over half this group had an atopic tendency to more than one fungus. Nineteen percent of the CF group were at least \\'high risk\\' of developing ABPM. Skin prick testing is a better marker of fungal atopy and a better predictor of those adult CF patients at higher risk of developing ABPM than specific radioimmunoassay serum testing. There is a high prevalence of fungal atopy in the adult CF population. Total serum IgE and skin prick testing are good predictors of fungal atopy and help predict those at

  19. Indicators of airborne fungal concentrations in urban homes: understanding the conditions that affect indoor fungal exposures.

    Science.gov (United States)

    Crawford, Judith A; Rosenbaum, Paula F; Anagnost, Susan E; Hunt, Andrew; Abraham, Jerrold L

    2015-06-01

    Indoor fungal exposure can compromise respiratory health. Low-income urban areas are of concern because of high asthma and allergy rates and housing disrepair. Understanding the conditions that affect indoor fungal exposures is important for assessing health risks and for developing mitigation strategies. We examined the types and concentrations of airborne fungi inside and outside of homes in low-income areas of Syracuse, NY as well as the effect of snow cover on fungal levels. At 103 homes, air samples for viable fungi were collected, occupants were interviewed and homes were inspected for visible mold, musty odors, water problems and other factors. Multivariable logistic regression was used to relate high fungal levels to home conditions. Predominant indoor fungi included Cladosporium, Penicillium, Aspergillus, Alternaria and hyaline unknowns. Basidiomycetes and an uncommon genus Acrodontium were also found frequently due to analysis methods developed for this project. With snow cover, outdoor total fungal levels were depressed and indoor concentrations were three times higher than outdoor on average with a maximum of 29 times higher. Visible mold was related to elevated levels of Penicillium (OR 4.11 95% CI 1.37-14.0) and bacteria (OR 3.79 95% CI 1.41-11.2). Musty, moldy odors were associated with elevated concentrations of total fungi (OR 3.48 95% CI 1.13-11.6) and basidiomycetes. Cockroaches, an indicator of moisture, were associated with elevated levels of Penicillium (OR 3.66 95% CI 1.16-13.1) and Aspergillus (OR 4.36 95% CI 1.60-13.4). Increasing relative humidity was associated with higher concentrations of Penicillium, yeasts and basidiomycetes. Visible mold, musty odors, indoor humidity and cockroaches are modifiable factors that were important determinants of indoor fungal exposures. Indoor air investigators should interpret indoor:outdoor fungal ratios cautiously when snow cover is present.

  20. Rationales for regulatory activity

    Energy Technology Data Exchange (ETDEWEB)

    Perhac, R.M. [Univ. of Tennessee, Knoxville, TN (United States)

    1997-02-01

    The author provides an outline which touches on the types of concerns about risk evaluation which are addressed in the process of establishing regulatory guides. Broadly he says regulatory activity serves three broad constituents: (1) Paternalism (private risk); (2) Promotion of social welfare (public risks); (3) Protection of individual rights (public risks). He then discusses some of the major issues encountered in reaching a decision on what is an acceptable level of risk within each of these areas, and how one establishes such a level.

  1. Personal and population genomics of human regulatory variation.

    Science.gov (United States)

    Vernot, Benjamin; Stergachis, Andrew B; Maurano, Matthew T; Vierstra, Jeff; Neph, Shane; Thurman, Robert E; Stamatoyannopoulos, John A; Akey, Joshua M

    2012-09-01

    The characteristics and evolutionary forces acting on regulatory variation in humans remains elusive because of the difficulty in defining functionally important noncoding DNA. Here, we combine genome-scale maps of regulatory DNA marked by DNase I hypersensitive sites (DHSs) from 138 cell and tissue types with whole-genome sequences of 53 geographically diverse individuals in order to better delimit the patterns of regulatory variation in humans. We estimate that individuals likely harbor many more functionally important variants in regulatory DNA compared with protein-coding regions, although they are likely to have, on average, smaller effect sizes. Moreover, we demonstrate that there is significant heterogeneity in the level of functional constraint in regulatory DNA among different cell types. We also find marked variability in functional constraint among transcription factor motifs in regulatory DNA, with sequence motifs for major developmental regulators, such as HOX proteins, exhibiting levels of constraint comparable to protein-coding regions. Finally, we perform a genome-wide scan of recent positive selection and identify hundreds of novel substrates of adaptive regulatory evolution that are enriched for biologically interesting pathways such as melanogenesis and adipocytokine signaling. These data and results provide new insights into patterns of regulatory variation in individuals and populations and demonstrate that a large proportion of functionally important variation lies beyond the exome.

  2. Fungal enzymes in the attine ant symbiosis

    DEFF Research Database (Denmark)

    de Fine Licht, Henrik Hjarvard; Schiøtt, Morten; Boomsma, Jacobus Jan

    the more basal attine genera use substrates such as flowers, plant debris, small twigs, insect feces and insect carcasses. This diverse array of fungal substrates across the attine lineage implies that the symbiotic fungus needs different enzymes to break down the plant material that the ants provide...... or different efficiencies of enzyme function. Fungal enzymes that degrade plant cell walls may have functionally co-evolved with the ants in this scenario. We explore this hypothesis with direct measurements of enzyme activity in fungus gardens in 12 species across 8 genera spanning the entire phylogeny...... and diversity of life-styles within the attine clade. We find significant differences in enzyme activity between different genera and life-styles of the ants. How these findings relate to attine ant coevolution and crop optimization are discussed....

  3. Fungal natural products targeting chronic lymphocytic leukemia

    DEFF Research Database (Denmark)

    Bladt, Tanja Thorskov; Kildgaard, Sara; Knudsen, Peter Boldsen

    2012-01-01

    Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults from the western world. No curative treatments of CLL are presently known so the treatment strategy today is primarily to prolong patient survival,1 why we have initiated new activities towards discovery of novel compounds...... with potential tumor specificity. Our starting point is a diverse fungal collection of thousands of Penicillium and Aspergillus species. These fungi have proven to be a very rich source of various bioactive compounds and yet our dereplication investigations have demonstrated that there are still numerous unknown...... compounds to be identified within these species. Until now we have found that 11 out of 289 fungal extracts are active against CLL cells. Using our established chemotaxonomic discovery approach we have dereplicated and fractionated these extracts to track the activity into single fractions/compounds.2...

  4. Nail Histomycology, Onychochromobiology, and Fungal Thigmatropism

    Directory of Open Access Journals (Sweden)

    Gérald E. Piérard

    2016-09-01

    Full Text Available Background: Thigmotropism is a biologic feature coping with the directional growth of cells following topographical guidance cues. This mechanism is involved in the invasive phase of pathogen and opportunistic fungi. It was shown experimentally with fungal hyphae of both dermatophytes and nondermatophyte molds, as well as with the mycelial phase of the dimorphic yeast Candida albicans. Objective: To revisit histomycology in onychomycoses of a diversity of fungal origins. Method: Histopathological section of nails plates were oriented parallel to the nail direction of growth. Result: Thigmotropism in part explains the patterns of orientations and shapes of fungi invading nail plates. It is probably influenced by onychochronobiology (speed of growth of the affected nails, and it governs various clinical presentations of onychomycoses.

  5. Standard methods for fungal brood disease research

    DEFF Research Database (Denmark)

    Jensen, Annette Bruun; Aronstein, Kathrine; Manuel Flores, Jose

    2013-01-01

    Chalkbrood and stonebrood are two fungal diseases associated with honey bee brood. Chalkbrood, caused by Ascosphaera apis, is a common and widespread disease that can result in severe reduction of emerging worker bees and thus overall colony productivity. Stonebrood is caused by Aspergillus spp. ...... interactions. We give guidelines on the preferred methods used in current research and the application of molecular techniques. We have added photographs, drawings and illustrations to assist bee-extension personnel and bee scientists in the control of these two diseases....... tissues upon inhalation by humans. In the current chapter we describe the honey bee disease symptoms of these fungal pathogens. In addition, we provide research methodologies and protocols for isolating and culturing, in vivo and in vitro assays that are commonly used to study these host pathogen...

  6. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence.

    Science.gov (United States)

    Wittkopp, Patricia J; Kalay, Gizem

    2011-12-06

    Cis-regulatory sequences, such as enhancers and promoters, control development and physiology by regulating gene expression. Mutations that affect the function of these sequences contribute to phenotypic diversity within and between species. With many case studies implicating divergent cis-regulatory activity in phenotypic evolution, researchers have recently begun to elucidate the genetic and molecular mechanisms that are responsible for cis-regulatory divergence. Approaches include detailed functional analysis of individual cis-regulatory elements and comparing mechanisms of gene regulation among species using the latest genomic tools. Despite the limited number of mechanistic studies published to date, this work shows how cis-regulatory activity can diverge and how studies of cis-regulatory divergence can address long-standing questions about the genetic mechanisms of phenotypic evolution.

  7. Molecular Identification of Human Fungal Pathogens

    Science.gov (United States)

    2011-03-01

    no pigment seen on the hyphal walls on hematoxylin-eosin or melan A staining. The biopsy specimen was sent for bacterial and fungal cul- tures, but the...aim was to design universal primers and then develop a PCR mix, which would be able to reliably amplify template from any specimen, even pigmented ...which if accepted, will result in thirty journal publications. There was also one book chapter published. II. Seventeen abstracts have been

  8. Cunninghamella echinulata causing fatally invasive fungal sinusitis.

    Science.gov (United States)

    LeBlanc, Robert E; Meriden, Zina; Sutton, Deanna A; Thompson, Elizabeth H; Neofytos, Dionissios; Zhang, Sean X

    2013-08-01

    We report a fatal case of invasive fungal sinusitis caused by Cunninghamella echinulata in a febrile, neutropenic 15-year-old male with relapsing acute leukemia. The isolate was recovered from a nasal biopsy from the right middle meatus, and microscopic examination of the tissue revealed angioinvasion and necrosis. Human infection caused by this organism has not been well documented; however, this report alerts us to its life-threatening potential.

  9. Fungal Biodiversity in the Alpine Tarfala Valley

    Directory of Open Access Journals (Sweden)

    Claudia Coleine

    2015-10-01

    Full Text Available Biological soil crusts (BSCs are distributed worldwide in all semiarid and arid lands, where they play a determinant role in element cycling and soil development. Although much work has concentrated on BSC microbial communities, free-living fungi have been hitherto largely overlooked. The aim of this study was to examine the fungal biodiversity, by cultural-dependent and cultural-independent approaches, in thirteen samples of Arctic BSCs collected at different sites in the Alpine Tarfala Valley, located on the slopes of Kebnekaise, the highest mountain in northern Scandinavia. Isolated fungi were identified by both microscopic observation and molecular approaches. Data revealed that the fungal assemblage composition was homogeneous among the BSCs analyzed, with low biodiversity and the presence of a few dominant species; the majority of fungi isolated belonged to the Ascomycota, and Cryptococcus gilvescens and Pezoloma ericae were the most frequently-recorded species. Ecological considerations for the species involved and the implication of our findings for future fungal research in BSCs are put forward.

  10. Fungal Biodiversity in the Alpine Tarfala Valley.

    Science.gov (United States)

    Coleine, Claudia; Selbmann, Laura; Ventura, Stefano; D'Acqui, Luigi Paolo; Onofri, Silvano; Zucconi, Laura

    2015-10-10

    Biological soil crusts (BSCs) are distributed worldwide in all semiarid and arid lands, where they play a determinant role in element cycling and soil development. Although much work has concentrated on BSC microbial communities, free-living fungi have been hitherto largely overlooked. The aim of this study was to examine the fungal biodiversity, by cultural-dependent and cultural-independent approaches, in thirteen samples of Arctic BSCs collected at different sites in the Alpine Tarfala Valley, located on the slopes of Kebnekaise, the highest mountain in northern Scandinavia. Isolated fungi were identified by both microscopic observation and molecular approaches. Data revealed that the fungal assemblage composition was homogeneous among the BSCs analyzed, with low biodiversity and the presence of a few dominant species; the majority of fungi isolated belonged to the Ascomycota, and Cryptococcus gilvescens and Pezoloma ericae were the most frequently-recorded species. Ecological considerations for the species involved and the implication of our findings for future fungal research in BSCs are put forward.

  11. Sebacinales everywhere: previously overlooked ubiquitous fungal endophytes.

    Science.gov (United States)

    Weiss, Michael; Sýkorová, Zuzana; Garnica, Sigisfredo; Riess, Kai; Martos, Florent; Krause, Cornelia; Oberwinkler, Franz; Bauer, Robert; Redecker, Dirk

    2011-02-15

    Inconspicuous basidiomycetes from the order Sebacinales are known to be involved in a puzzling variety of mutualistic plant-fungal symbioses (mycorrhizae), which presumably involve transport of mineral nutrients. Recently a few members of this fungal order not fitting this definition and commonly referred to as 'endophytes' have raised considerable interest by their ability to enhance plant growth and to increase resistance of their host plants against abiotic stress factors and fungal pathogens. Using DNA-based detection and electron microscopy, we show that Sebacinales are not only extremely versatile in their mycorrhizal associations, but are also almost universally present as symptomless endophytes. They occurred in field specimens of bryophytes, pteridophytes and all families of herbaceous angiosperms we investigated, including liverworts, wheat, maize, and the non-mycorrhizal model plant Arabidopsis thaliana. They were present in all habitats we studied on four continents. We even detected these fungi in herbarium specimens originating from pioneering field trips to North Africa in the 1830s/40s. No geographical or host patterns were detected. Our data suggest that the multitude of mycorrhizal interactions in Sebacinales may have arisen from an ancestral endophytic habit by specialization. Considering their proven beneficial influence on plant growth and their ubiquity, endophytic Sebacinales may be a previously unrecognized universal hidden force in plant ecosystems.

  12. Sebacinales everywhere: previously overlooked ubiquitous fungal endophytes.

    Directory of Open Access Journals (Sweden)

    Michael Weiss

    Full Text Available Inconspicuous basidiomycetes from the order Sebacinales are known to be involved in a puzzling variety of mutualistic plant-fungal symbioses (mycorrhizae, which presumably involve transport of mineral nutrients. Recently a few members of this fungal order not fitting this definition and commonly referred to as 'endophytes' have raised considerable interest by their ability to enhance plant growth and to increase resistance of their host plants against abiotic stress factors and fungal pathogens. Using DNA-based detection and electron microscopy, we show that Sebacinales are not only extremely versatile in their mycorrhizal associations, but are also almost universally present as symptomless endophytes. They occurred in field specimens of bryophytes, pteridophytes and all families of herbaceous angiosperms we investigated, including liverworts, wheat, maize, and the non-mycorrhizal model plant Arabidopsis thaliana. They were present in all habitats we studied on four continents. We even detected these fungi in herbarium specimens originating from pioneering field trips to North Africa in the 1830s/40s. No geographical or host patterns were detected. Our data suggest that the multitude of mycorrhizal interactions in Sebacinales may have arisen from an ancestral endophytic habit by specialization. Considering their proven beneficial influence on plant growth and their ubiquity, endophytic Sebacinales may be a previously unrecognized universal hidden force in plant ecosystems.

  13. Functional analysis of fungal polyketide biosynthesis genes.

    Science.gov (United States)

    Fujii, Isao

    2010-05-01

    Fungal polyketides have huge structural diversity from simple aromatics to highly modified complex reduced-type compounds. Despite such diversty, single modular iterative type I polyketide synthases (iPKSs) are responsible for their carbon skeleton construction. Using heterologous expression systems, we have studied on ATX, a 6-methylsalicylic acid synthase from Aspergillus terreus as a model iPKS. In addition, iPKS functions involved in fungal spore pigment biosynthesis were analyzed together with polyketide-shortening enzymes that convert products of PKSs to shorter ketides by hydrolytic C-C bond cleavage. In our studies on reducing-type iPKSs, we cloned and expressed PKS genes, pksN, pksF, pksK and sol1 from Alternaria solani. The sol gene cluster was found to be involved in solanapyrone biosynthesis and sol5 was identified to encode solanapyrone synthase, a Diels-Alder enzyme. Our fungal PKS studies were further extended to identify the function of PKS-nonribosomal peptide synthase involved in cyclopiazonic acid biosynthesis.

  14. Sublingual Immunotherapy for Allergic Fungal Sinusitis.

    Science.gov (United States)

    Melzer, Jonathan M; Driskill, Brent R; Clenney, Timothy L; Gessler, Eric M

    2015-10-01

    Allergic fungal sinusitis (AFS) is a condition that has an allergic basis caused by exposure to fungi in the sinonasal tract leading to chronic inflammation. Despite standard treatment modalities, which typically include surgery and medical management of allergies, patients still have a high rate of recurrence. Subcutaneous immunotherapy (SCIT) has been used as adjuvant treatment for AFS. Evidence exists to support the use of sublingual immunotherapy (SLIT) as a safe and efficacious method of treating allergies, but no studies have assessed the utility of SLIT in the management of allergic fungal sinusitis. A record review of cases of AFS that are currently or previously treated with sublingual immunotherapy from 2007 to 2011 was performed. Parameters of interest included serum IgE levels, changes in symptoms, Lund-McKay scores, decreased sensitization to fungal allergens associated with AFS, and serum IgE levels. Ten patients with diagnosed AFS were treated with SLIT. No adverse effects related to the use of SLIT therapy were identified. Decreases in subjective complaints, exam findings, Lund-McKay scores, and serum IgE levels were observed. Thus, sublingual immunotherapy appears to be a safe adjunct to the management of AFS that may improve patient outcomes.

  15. Prediction of regulatory elements

    DEFF Research Database (Denmark)

    Sandelin, Albin

    2008-01-01

    Finding the regulatory mechanisms responsible for gene expression remains one of the most important challenges for biomedical research. A major focus in cellular biology is to find functional transcription factor binding sites (TFBS) responsible for the regulation of a downstream gene. As wet-lab...

  16. A link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Cryptococcus neoformans.

    Directory of Open Access Journals (Sweden)

    Cheryl D Chun

    2007-02-01

    Full Text Available Fungal pathogens of humans require molecular oxygen for several essential biochemical reactions, yet virtually nothing is known about how they adapt to the relatively hypoxic environment of infected tissues. We isolated mutants defective in growth under hypoxic conditions, but normal for growth in normoxic conditions, in Cryptococcus neoformans, the most common cause of fungal meningitis. Two regulatory pathways were identified: one homologous to the mammalian sterol-response element binding protein (SREBP cholesterol biosynthesis regulatory pathway, and the other a two-component-like pathway involving a fungal-specific hybrid histidine kinase family member, Tco1. We show that cleavage of the SREBP precursor homolog Sre1-which is predicted to release its DNA-binding domain from the membrane-occurs in response to hypoxia, and that Sre1 is required for hypoxic induction of genes encoding for oxygen-dependent enzymes involved in ergosterol synthesis. Importantly, mutants in either the SREBP pathway or the Tco1 pathway display defects in their ability to proliferate in host tissues and to cause disease in infected mice, linking for the first time to our knowledge hypoxic adaptation and pathogenesis by a eukaryotic aerobe. SREBP pathway mutants were found to be a hundred times more sensitive than wild-type to fluconazole, a widely used antifungal agent that inhibits ergosterol synthesis, suggesting that inhibitors of SREBP processing could substantially enhance the potency of current therapies.

  17. Regulatory cross talk and microbial induction of fungal secondary metabolite gene clusters.

    Science.gov (United States)

    Nützmann, Hans-Wilhelm; Schroeckh, Volker; Brakhage, Axel A

    2012-01-01

    Filamentous fungi are well-known producers of a wealth of secondary metabolites with various biological activities. Many of these compounds such as penicillin, cyclosporine, or lovastatin are of great importance for human health. Genome sequences of filamentous fungi revealed that the encoded potential to produce secondary metabolites is much higher than the actual number of compounds produced during cultivation in the laboratory. This finding encouraged research groups to develop new methods to exploit the silent reservoir of secondary metabolites. In this chapter, we present three successful strategies to induce the expression of secondary metabolite gene clusters. They are based on the manipulation of the molecular processes controlling the biosynthesis of secondary metabolites and the simulation of stimulating environmental conditions leading to altered metabolic profiles. The presented methods were successfully applied to identify novel metabolites. They can be also used to significantly increase product yields.

  18. Orphan drugs: the regulatory environment.

    Science.gov (United States)

    Franco, Pedro

    2013-02-01

    The definition of a rare disease is not universal and depends on the legislation and policies adopted by each region or country. The main objective of this article is to describe and discuss the legal framework and the regulatory environment of orphan drugs worldwide. Some reflections and discussions on the need for specific orphan drug legislation or policies are described at length. Furthermore, some aspects of the history of each region in respect of the orphan drug legislation evolution are outlined. This article describes and compares the orphan drug legislation or policies of the following countries or regions: United Sates of America (US), European Union (EU), Japan, Australia, Singapore, Taiwan and Canada. The incentives described in the orphan drug legislations or policies, the criteria for designation of orphan status and the authorisation process of an orphan drug are also described and compared. The legislations and policies are to some extent similar but not the same. It is important to understand the main differences among all available legislative systems to improve the international collaboration in the field of orphan drugs and rare diseases.

  19. Nuclear Regulatory Commission information digest

    Energy Technology Data Exchange (ETDEWEB)

    None,

    1990-03-01

    The Nuclear Regulatory Commission information digest provides summary information regarding the US Nuclear Regulatory Commission, its regulatory responsibilities, and areas licensed by the commission. This is an annual publication for the general use of the NRC Staff and is available to the public. The digest is divided into two parts: the first presents an overview of the US Nuclear Regulatory Commission and the second provides data on NRC commercial nuclear reactor licensees and commercial nuclear power reactors worldwide.

  20. Resource competition between two fungal parasites in subterranean termites

    Science.gov (United States)

    Chouvenc, Thomas; Efstathion, Caroline A.; Elliott, Monica L.; Su, Nan-Yao

    2012-11-01

    Subterranean termites live in large groups in underground nests where the pathogenic pressure of the soil environment has led to the evolution of a complex interaction among individual and social immune mechanisms in the colonies. However, groups of termites under stress can show increased susceptibility to opportunistic parasites. In this study, an isolate of Aspergillus nomius Kurtzman, Horn & Hessltine was obtained from a collapsed termite laboratory colony. We determined that it was primarily a saprophyte and, secondarily, a facultative parasite if the termite immunity is undergoing a form of stress. This was determined by stressing individuals of the Formosan subterranean termite Coptotermes formosanus Shiraki via a co-exposure to the virulent fungal parasite Metarhizium anisopliae (Metch.) Sorokin. We also examined the dynamics of a mixed infection of A. nomius and M. anisopliae in a single termite host. The virulent parasite M. anisopliae debilitated the termite immune system, but the facultative, fast growing parasite A. nomius dominated the mixed infection process. The resource utilization strategy of A. nomius during the infection resulted in successful conidia production, while the chance for M. anisopliae to complete its life cycle was reduced. Our results also suggest that the occurrence of opportunistic parasites such as A. nomius in collapsing termite laboratory colonies is the consequence of a previous stress, not the cause of the stress.

  1. Data on litter quality of host grass plants with and without fungal endophytes

    Directory of Open Access Journals (Sweden)

    P.E. Gundel

    2016-06-01

    Full Text Available Certain Pooideae species form persistent symbiosis with fungal endophytes of Epichloë genus. Although endophytes are known to impact the ecology and evolution of host species, their effects on parameters related with quality of plant biomass has been elusive. This article provides information about parameters related with the quality of plant litter biomass of two important grass species (Schedonorus phoenix and Schedonorus pratensis affected by the symbiosis with fungal endophytes (Epichloë coenophiala and Epichloë uncinata, respectively. Four population origins of S. phoenix and one of S. pratensis were included. Mineral, biochemical and structural parameters were obtained from three samples per factors combination [species (and population origin×endophyte]. This data can be potentially used in other studies which, by means of ‘data reanalyzing’ or meta-analysis, attempt to find generalizations about endophyte effects on host plant litter biomass. The present data is associated with the research article “Role of foliar fungal endophytes on litter decomposition among species and population origins” (Gundel et al., In preparation [1].

  2. Data on litter quality of host grass plants with and without fungal endophytes

    Science.gov (United States)

    Gundel, P.E.; Helander, M.; Garibaldi, L.A.; Vázquez-de-Aldana, B.R.; Zabalgogeazcoa, I.; Saikkonen, K.

    2016-01-01

    Certain Pooideae species form persistent symbiosis with fungal endophytes of Epichloë genus. Although endophytes are known to impact the ecology and evolution of host species, their effects on parameters related with quality of plant biomass has been elusive. This article provides information about parameters related with the quality of plant litter biomass of two important grass species (Schedonorus phoenix and Schedonorus pratensis) affected by the symbiosis with fungal endophytes (Epichloë coenophiala and Epichloë uncinata, respectively). Four population origins of S. phoenix and one of S. pratensis were included. Mineral, biochemical and structural parameters were obtained from three samples per factors combination [species (and population origin)×endophyte]. This data can be potentially used in other studies which, by means of ‘data reanalyzing’ or meta-analysis, attempt to find generalizations about endophyte effects on host plant litter biomass. The present data is associated with the research article “Role of foliar fungal endophytes on litter decomposition among species and population origins” (Gundel et al., In preparation) [1]. PMID:27182541

  3. Discovery of novel intermediate forms redefines the fungal tree of life.

    Science.gov (United States)

    Jones, Meredith D M; Forn, Irene; Gadelha, Catarina; Egan, Martin J; Bass, David; Massana, Ramon; Richards, Thomas A

    2011-05-11

    Fungi are the principal degraders of biomass in terrestrial ecosystems and establish important interactions with plants and animals. However, our current understanding of fungal evolutionary diversity is incomplete and is based upon species amenable to growth in culture. These culturable fungi are typically yeast or filamentous forms, bound by a rigid cell wall rich in chitin. Evolution of this body plan was thought critical for the success of the Fungi, enabling them to adapt to heterogeneous habitats and live by osmotrophy: extracellular digestion followed by nutrient uptake. Here we investigate the ecology and cell biology of a previously undescribed and highly diverse form of eukaryotic life that branches with the Fungi, using environmental DNA analyses combined with fluorescent detection via DNA probes. This clade is present in numerous ecosystems including soil, freshwater and aquatic sediments. Phylogenetic analyses using multiple ribosomal RNA genes place this clade with Rozella, the putative primary branch of the fungal kingdom. Tyramide signal amplification coupled with group-specific fluorescence in situ hybridization reveals that the target cells are small eukaryotes of 3-5 μm in length, capable of forming a microtubule-based flagellum. Co-staining with cell wall markers demonstrates that representatives from the clade do not produce a chitin-rich cell wall during any of the life cycle stages observed and therefore do not conform to the standard fungal body plan. We name this highly diverse clade the cryptomycota in anticipation of formal classification.

  4. Sensitization to fungal allergens: Resolved and unresolved issues

    Directory of Open Access Journals (Sweden)

    Yuma Fukutomi

    2015-10-01

    Despite its importance in the management of allergic diseases, precise recognition of species-specific IgE sensitization to fungal allergens is often challenging because the majority of fungal extracts exhibit broad cross-reactivity with taxonomically unrelated fungi. Recent progress in gene technology has contributed to the identification of specific and cross-reactive allergen components from different fungal sources. However, data demonstrating the clinical relevance of IgE reactivity to these allergen components are still insufficient.

  5. Fungal symbionts of grasses: evolutionary insights and agricultural potential.

    Science.gov (United States)

    Scott, B; Schardl, C

    1993-08-01

    Some filamentous fungal endophytes confer on their grass hosts important biological properties including resistance to grazing herbivores and resistance to nematodes and some fungal pathogens, as well as drought tolerance and greater field persistence. The production of alkaloids toxic to grazing animals is an undesirable aspect of the association in agronomic situations. Consequently, genetic strategies are being pursued to manipulate fungal endophytes and their hosts for agricultural benefit.

  6. ChIP-seq and in vivo transcriptome analyses of the Aspergillus fumigatus SREBP SrbA reveals a new regulator of the fungal hypoxia response and virulence.

    Directory of Open Access Journals (Sweden)

    Dawoon Chung

    2014-11-01

    Full Text Available The Aspergillus fumigatus sterol regulatory element binding protein (SREBP SrbA belongs to the basic Helix-Loop-Helix (bHLH family of transcription factors and is crucial for antifungal drug resistance and virulence. The latter phenotype is especially striking, as loss of SrbA results in complete loss of virulence in murine models of invasive pulmonary aspergillosis (IPA. How fungal SREBPs mediate fungal virulence is unknown, though it has been suggested that lack of growth in hypoxic conditions accounts for the attenuated virulence. To further understand the role of SrbA in fungal infection site pathobiology, chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq was used to identify genes under direct SrbA transcriptional regulation in hypoxia. These results confirmed the direct regulation of ergosterol biosynthesis and iron uptake by SrbA in hypoxia and revealed new roles for SrbA in nitrate assimilation and heme biosynthesis. Moreover, functional characterization of an SrbA target gene with sequence similarity to SrbA identified a new transcriptional regulator of the fungal hypoxia response and virulence, SrbB. SrbB co-regulates genes involved in heme biosynthesis and demethylation of C4-sterols with SrbA in hypoxic conditions. However, SrbB also has regulatory functions independent of SrbA including regulation of carbohydrate metabolism. Loss of SrbB markedly attenuates A. fumigatus virulence, and loss of both SREBPs further reduces in vivo fungal growth. These data suggest that both A. fumigatus SREBPs are critical for hypoxia adaptation and virulence and reveal new insights into SREBPs' complex role in infection site adaptation and fungal virulence.

  7. Fungal community dynamics and driving factors during agricultural waste composting.

    Science.gov (United States)

    Yu, Man; Zhang, Jiachao; Xu, Yuxin; Xiao, Hua; An, Wenhao; Xi, Hui; Xue, Zhiyong; Huang, Hongli; Chen, Xiaoyang; Shen, Alin

    2015-12-01

    This study was conducted to identify the driving factors behind fungal community dynamics during agricultural waste composting. Fungal community abundance and structure were determined by quantitative PCR and denaturing gradient gel electrophoresis analysis combined with DNA sequencing. The effects of physico-chemical parameters on fungal community abundance and structure were evaluated by least significant difference tests and redundancy analysis. The results showed that Cladosporium bruhnei, Hanseniaspora uvarum, Scytalidium thermophilum, Tilletiopsis penniseti, and Coprinopsis altramentaria were prominent during the composting process. The greatest variation in the distribution of fungal community structure was statistically explained by pile temperature and total organic carbon (TOC) (P composting.

  8. [Diagnosis and treatment of fungal ball rhino-sinusitis].

    Science.gov (United States)

    Nie, Jun; Liu, Fenfang; Zhang, Hanwu; Li, Li

    2013-07-01

    To explore the diagnosis and treatment of the fungal ball rhino-sinusitis. The clinical data of 128 cases with the fungal ball rhino-sinusitis in our hospital between September 2005 and January 2012 were retrospectively analyzed. All patients were accepted nasal endoscopic surgery and followed up after surgery. The diagnosis were confirmed by postoperative pathological examination. The sinus of all patients epithelialized after the surgery from fourth to ninth weeks, one case recurred eight months later. Sinus CT scan and nasal endoscopy were very important to the diagnosis of the fungal ball rhino-sinusitis, and nasal endoscopic surgery is the most important treatment method to fungal ball rhino-sinusitis.

  9. Immunology of fungal infections: lessons learned from animal models.

    Science.gov (United States)

    Steele, Chad; Wormley, Floyd L

    2012-08-01

    The continuing AIDS epidemic coupled with increased usage of immunosuppressive drugs to prevent organ rejection or treat autoimmune diseases has resulted in an increase in individuals at risk for acquiring fungal diseases. These concerns highlight the need to elucidate mechanisms of inducing protective immune responses against fungal pathogens. Consequently, several experimental models of human mycoses have been developed to study these diseases. The availability of transgenic animal models allows for in-depth analysis of specific components, receptors, and signaling pathways that elicit protection against fungal diseases. This review focuses on recent advances in our understanding of immune responses to fungal infections gained using animal models.

  10. Fungal biogeography. Global diversity and geography of soil fungi.

    Science.gov (United States)

    Tedersoo, Leho; Bahram, Mohammad; Põlme, Sergei; Kõljalg, Urmas; Yorou, Nourou S; Wijesundera, Ravi; Villarreal Ruiz, Luis; Vasco-Palacios, Aída M; Thu, Pham Quang; Suija, Ave; Smith, Matthew E; Sharp, Cathy; Saluveer, Erki; Saitta, Alessandro; Rosas, Miguel; Riit, Taavi; Ratkowsky, David; Pritsch, Karin; Põldmaa, Kadri; Piepenbring, Meike; Phosri, Cherdchai; Peterson, Marko; Parts, Kaarin; Pärtel, Kadri; Otsing, Eveli; Nouhra, Eduardo; Njouonkou, André L; Nilsson, R Henrik; Morgado, Luis N; Mayor, Jordan; May, Tom W; Majuakim, Luiza; Lodge, D Jean; Lee, Su See; Larsson, Karl-Henrik; Kohout, Petr; Hosaka, Kentaro; Hiiesalu, Indrek; Henkel, Terry W; Harend, Helery; Guo, Liang-dong; Greslebin, Alina; Grelet, Gwen; Geml, Jozsef; Gates, Genevieve; Dunstan, William; Dunk, Chris; Drenkhan, Rein; Dearnaley, John; De Kesel, André; Dang, Tan; Chen, Xin; Buegger, Franz; Brearley, Francis Q; Bonito, Gregory; Anslan, Sten; Abell, Sandra; Abarenkov, Kessy

    2014-11-28

    Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.

  11. Hastening the regulatory process

    Energy Technology Data Exchange (ETDEWEB)

    Stringham, G. [Canadian Association of Petroleum Producers, Calgary, AB (Canada)

    2001-07-01

    The state of the Canadian oil industry was discussed during this power point presentation with particular emphasis on its production, exports, drilling, industry revenues and capital investment levels. The proposed projects in each of northern Alberta's oil sands deposits, the Athabasca, Peace River and Cold Lake were were announced, along with the inventory of major Alberta projects and the projection of oil sands capital investment. Since 1998, $9 billion has been invested and a further $33 billion has been announced for new or expanded oil sands projects. The year 2000 estimates for Canadian crude oil and natural gas production are 2.3 million barrels per day and 6.3 trillion cubic feet per year respectively. This represented a record year for production of both crude oil and natural gas. In 2000, more than 15,500 wells were drilled in Canada. A graph depicting Canadian crude oil supply forecasted a steady increase in supply from year 2000 to 2010. The Canadian Association of Petroleum Producers (CAPP) completed a review of the Alberta Energy and Utilities Board regulatory and enforcement processes. Both industry and government efforts are focusing on eliminating regulatory overlap and duplication. Some of the main areas of interest for exploration, drilling, production and pipeline facilities include the examination of regulatory processes for environmentally sensitive areas, rural municipalities with planning bylaws, aboriginal lands and additional fees. 8 figs.

  12. Fungal cell gigantism during mammalian infection.

    Directory of Open Access Journals (Sweden)

    Oscar Zaragoza

    2010-06-01

    Full Text Available The interaction between fungal pathogens with the host frequently results in morphological changes, such as hyphae formation. The encapsulated pathogenic fungus Cryptococcus neoformans is not considered a dimorphic fungus, and is predominantly found in host tissues as round yeast cells. However, there is a specific morphological change associated with cryptococcal infection that involves an increase in capsule volume. We now report another morphological change whereby gigantic cells are formed in tissue. The paper reports the phenotypic characterization of giant cells isolated from infected mice and the cellular changes associated with giant cell formation. C. neoformans infection in mice resulted in the appearance of giant cells with cell bodies up to 30 microm in diameter and capsules resistant to stripping with gamma-radiation and organic solvents. The proportion of giant cells ranged from 10 to 80% of the total lung fungal burden, depending on infection time, individual mice, and correlated with the type of immune response. When placed on agar, giant cells budded to produce small daughter cells that traversed the capsule of the mother cell at the speed of 20-50 m/h. Giant cells with dimensions that approximated those in vivo were observed in vitro after prolonged culture in minimal media, and were the oldest in the culture, suggesting that giant cell formation is an aging-dependent phenomenon. Giant cells recovered from mice displayed polyploidy, suggesting a mechanism by which gigantism results from cell cycle progression without cell fission. Giant cell formation was dependent on cAMP, but not on Ras1. Real-time imaging showed that giant cells were engaged, but not engulfed by phagocytic cells. We describe a remarkable new strategy for C. neoformans to evade the immune response by enlarging cell size, and suggest that gigantism results from replication without fission, a phenomenon that may also occur with other fungal pathogens.

  13. Fungal cell gigantism during mammalian infection.

    Science.gov (United States)

    Zaragoza, Oscar; García-Rodas, Rocío; Nosanchuk, Joshua D; Cuenca-Estrella, Manuel; Rodríguez-Tudela, Juan Luis; Casadevall, Arturo

    2010-01-01

    The interaction between fungal pathogens with the host frequently results in morphological changes, such as hyphae formation. The encapsulated pathogenic fungus Cryptococcus neoformans is not considered a dimorphic fungus, and is predominantly found in host tissues as round yeast cells. However, there is a specific morphological change associated with cryptococcal infection that involves an increase in capsule volume. We now report another morphological change whereby gigantic cells are formed in tissue. The paper reports the phenotypic characterization of giant cells isolated from infected mice and the cellular changes associated with giant cell formation. C. neoformans infection in mice resulted in the appearance of giant cells with cell bodies up to 30 microm in diameter and capsules resistant to stripping with gamma-radiation and organic solvents. The proportion of giant cells ranged from 10 to 80% of the total lung fungal burden, depending on infection time, individual mice, and correlated with the type of immune response. When placed on agar, giant cells budded to produce small daughter cells that traversed the capsule of the mother cell at the speed of 20-50 m/h. Giant cells with dimensions that approximated those in vivo were observed in vitro after prolonged culture in minimal media, and were the oldest in the culture, suggesting that giant cell formation is an aging-dependent phenomenon. Giant cells recovered from mice displayed polyploidy, suggesting a mechanism by which gigantism results from cell cycle progression without cell fission. Giant cell formation was dependent on cAMP, but not on Ras1. Real-time imaging showed that giant cells were engaged, but not engulfed by phagocytic cells. We describe a remarkable new strategy for C. neoformans to evade the immune response by enlarging cell size, and suggest that gigantism results from replication without fission, a phenomenon that may also occur with other fungal pathogens.

  14. Bacterial and fungal markers in tobacco smoke

    Energy Technology Data Exchange (ETDEWEB)

    Szponar, B., E-mail: szponar@iitd.pan.wroc.pl [Lund University, Dept. of Laboratory Medicine, Soelvegatan 23, 223 62 Lund (Sweden); Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw (Poland); Pehrson, C.; Larsson, L. [Lund University, Dept. of Laboratory Medicine, Soelvegatan 23, 223 62 Lund (Sweden)

    2012-11-01

    Previous research has demonstrated that cigarette smoke contains bacterial and fungal components including lipopolysaccharide (LPS) and ergosterol. In the present study we used gas chromatography-mass spectrometry to analyze tobacco as well as mainstream and second hand smoke for 3-hydroxy fatty acids (3-OH FAs) of 10 to 18 carbon chain lengths, used as LPS markers, and ergosterol, used as a marker of fungal biomass. The air concentrations of LPS were 0.0017 nmol/m{sup 3} (N = 5) and 0.0007/m{sup 3} (N = 6) in the smoking vs. non-smoking rooms (p = 0.0559) of the studied private houses, and 0.0231 nmol/m{sup 3} (N = 5) vs. 0.0006 nmol/m{sup 3} (N = 5) (p = 0.0173), respectively, at the worksite. The air concentrations of ergosterol were also significantly higher in rooms with ongoing smoking than in rooms without smoking. A positive correlation was found between LPS and ergosterol in rooms with smoking but not in rooms without smoking. 3-OH C14:0 was the main 3-OH FA, followed by 3-OH C12:0, both in mainstream and second hand smoke and in phenol:water smoke extracts prepared in order to purify the LPS. The Limulus activity of the phenolic phase of tobacco was 3900 endotoxin units (EU)/cigarette; the corresponding amount of the smoke, collected on filters from 8 puffs, was 4 EU/cigarette. Tobacco smoking has been associated with a range of inflammatory airway conditions including COPD, asthma, bronchitis, alveolar hypersensitivity etc. Significant levels of LPS and ergosterol were identified in tobacco smoke and these observations support the hypothesis that microbial components of tobacco smoke contribute to inflammation and airway disease. -- Highlights: Black-Right-Pointing-Pointer Air concentration of bacterial and fungal markers is significantly higher in rooms with ongoing smoking than without smoking. Black-Right-Pointing-Pointer Bacterial LPS correlates with fungal marker in rooms with ongoing smoking but not without smoking. Black-Right-Pointing-Pointer LPS

  15. Fungal infections of Adonis vernalis L. fruits

    Directory of Open Access Journals (Sweden)

    Ljaljević-Grbić Milica V.

    2005-01-01

    Full Text Available Yellow pheasant´s Eye is a herbaceous plant from dry ressy areas. Owing to habitat destruction and over- collection for ornamental and medical purposes A. vernalis L. has became scarce in central and south Europe. The reasons for A. vernalis threatened are manyfold. The low seeds germination rate is significant. According to our investigation the main cause of fruit destruction is fungal infection. From the surface of the fruits, collected in Deliblato Sands, the following micromycetes has been isolated and determinated: Fusarium solani (Mart Sacc., Fusarium sporotrichioides Sherb., Alternaria sp. and Drechslera sp. Histologycal analysis showed the presence of conidiomata and conidia Phoma sp. in the seeds.

  16. Fungal Adaptations to Mutualistic Life with Ants

    DEFF Research Database (Denmark)

    Kooij, Pepijn Wilhelmus

    that forage on crude substrates such as insect frass and dry plant material, to large colonies of the leaf-cutting ants with several thousands to several million workers that provide live plant material to their fungus gardens. Leaf-cutting ants are the dominant herbivores of the Neo-tropics, and have a major...... on specific enzyme groups and Acromyrmex having an overall high enzyme activity. Finally, I show that the fungal symbiont of the leaf-cutting ant Acromyrmex echinatior produces large amounts of biodegrading enzymes in special structures called gongylidia. The ants eat these structures, but enzymes pass...

  17. Fungal infections of the urinary tract.

    Science.gov (United States)

    Sobel, J D; Vazquez, J A

    1999-12-01

    Funguria, fungal urinary tract infections, are most commonly caused by Candida species but may also be caused by Cryptococcus neoformans, Aspergillus species, and the endemic mycoses. Candiduria presents as an increasingly common nosocomial infection, which may involve all anatomic levels of the urinary tract, resulting in a spectrum of disease varying from asymptomatic candiduria to clinical sepsis. Although several successful systemic or local therapeutic options exist for the eradication of candiduria, knowledge of the pathogenesis and natural history of candiduria has lagged. This has resulted in confusion among practitioners as to when antifungal therapy is indicated. Treatment guidelines have recently been formulated and are described herein.

  18. Fungal symbionts alter plant responses to global change.

    Science.gov (United States)

    Kivlin, Stephanie N; Emery, Sarah M; Rudgers, Jennifer A

    2013-07-01

    While direct plant responses to global change have been well characterized, indirect plant responses to global change, via altered species interactions, have received less attention. Here, we examined how plants associated with four classes of fungal symbionts (class I leaf endophytes [EF], arbuscular mycorrhizal fungi [AMF], ectomycorrhizal fungi [ECM], and dark septate endophytes [DSE]) responded to four global change factors (enriched CO2, drought, N deposition, and warming). We performed a meta-analysis of 434 studies spanning 174 publications to search for generalizable trends in responses of plant-fungal symbioses to future environments. Specifically, we addressed the following questions: (1) Can fungal symbionts ameliorate responses of plants to global change? (2) Do fungal symbiont groups differ in the degree to which they modify plant response to global change? (3) Do particular global change factors affect plant-fungal symbioses more than others? In all global change scenarios, except elevated CO2, fungal symbionts significantly altered plant responses to global change. In most cases, fungal symbionts increased plant biomass in response to global change. However, increased N deposition reduced the benefits of symbiosis. Of the global change factors we considered, drought and N deposition resulted in the strongest fungal mediation of plant responses. Our analysis highlighted gaps in current knowledge for responses of particular fungal groups and revealed the importance of considering not only the nonadditive effects of multiple global change factors, but also the interactive effects of multiple fungal symbioses. Our results show that considering plant-fungal symbioses is critical to predicting ecosystem response to global change.

  19. Host habitat assessment by a parasitoid using fungal volatiles

    Directory of Open Access Journals (Sweden)

    Steidle Johannes LM

    2007-02-01

    patches. The female response to fungal volatiles is innate, suggesting that host-associated fungi played a crucial role in the evolution of host finding strategies of L. distinguendus. Research on the role of host-associated microorganisms in the chemically mediated orientation of parasitoids is still at the beginning. We expect an increasing recognition of this issue in the future.

  20. Algal and fungal diversity in Antarctic lichens.

    Science.gov (United States)

    Park, Chae Haeng; Kim, Kyung Mo; Elvebakk, Arve; Kim, Ok-Sun; Jeong, Gajin; Hong, Soon Gyu

    2015-01-01

    The composition of lichen ecosystems except mycobiont and photobiont has not been evaluated intensively. In addition, recent studies to identify algal genotypes have raised questions about the specific relationship between mycobiont and photobiont. In the current study, we analyzed algal and fungal community structures in lichen species from King George Island, Antarctica, by pyrosequencing of eukaryotic large subunit (LSU) and algal internal transcribed spacer (ITS) domains of the nuclear rRNA gene. The sequencing results of LSU and ITS regions indicated that each lichen thallus contained diverse algal species. The major algal operational taxonomic unit (OTU) defined at a 99% similarity cutoff of LSU sequences accounted for 78.7-100% of the total algal community in each sample. In several cases, the major OTUs defined by LSU sequences were represented by two closely related OTUs defined by 98% sequence similarity of ITS domain. The results of LSU sequences indicated that lichen-associated fungi belonged to the Arthoniomycetes, Eurotiomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes of the Ascomycota, and Tremellomycetes and Cystobasidiomycetes of the Basidiomycota. The composition of major photobiont species and lichen-associated fungal community were mostly related to the mycobiont species. The contribution of growth forms or substrates on composition of photobiont and lichen-associated fungi was not evident.

  1. Sexual reproduction of human fungal pathogens.

    Science.gov (United States)

    Heitman, Joseph; Carter, Dee A; Dyer, Paul S; Soll, David R

    2014-08-01

    We review here recent advances in our understanding of sexual reproduction in fungal pathogens that commonly infect humans, including Candida albicans, Cryptococcus neoformans/gattii, and Aspergillus fumigatus. Where appropriate or relevant, we introduce findings on other species associated with human infections. In particular, we focus on rapid advances involving genetic, genomic, and population genetic approaches that have reshaped our view of how fungal pathogens evolve. Rather than being asexual, mitotic, and largely clonal, as was thought to be prevalent as recently as a decade ago, we now appreciate that the vast majority of pathogenic fungi have retained extant sexual, or parasexual, cycles. In some examples, sexual and parasexual unions of pathogenic fungi involve closely related individuals, generating diversity in the population but with more restricted recombination than expected from fertile, sexual, outcrossing and recombining populations. In other cases, species and isolates participate in global outcrossing populations with the capacity for considerable levels of gene flow. These findings illustrate general principles of eukaryotic pathogen emergence with relevance for other fungi, parasitic eukaryotic pathogens, and both unicellular and multicellular eukaryotic organisms.

  2. Recombinant fungal entomopathogen RNAi target insect gene.

    Science.gov (United States)

    Hu, Qiongbo; Wu, Wei

    2016-11-01

    RNA interference (RNAi) technology is considered as an alternative for control of pests. However, RNAi has not been used in field conditions yet, since delivering exogenous ds/siRNA to target pests is very difficult. The laboratory methods of introducing the ds/siRNA into insects through feeding, micro feeding / dripping and injecting cannot be used in fields. Transgenic crop is perhaps the most effective application of RNAi for pest control, but it needs long-time basic researches in order to reduce the cost and evaluate the safety. Therefore, transgenic microbe is maybe a better choice. Entomopathogenic fungi generally invade the host insects through cuticle like chemical insecticides contact insect to control sucking sap pests. Isaria fumosorosea is a common fungal entomopathogen in whitefly, Bemisia tabaci. We constructed a recombinant strain of I. fumosorosea expressing specific dsRNA of whitefly's TLR7 gene. It could silence the TLR7 gene and improve the virulence against whitefly. Transgenic fungal entomopathogen has shown great potential to attain the application of RNAi technology for pests control in fields. In the future, the research interests should be focused on the selection of susceptible target pests and their vital genes, and optimizing the methods for screening genes and recombinants as well.

  3. Disulfide bonds and glycosylation in fungal peroxidases.

    Science.gov (United States)

    Limongi, P; Kjalke, M; Vind, J; Tams, J W; Johansson, T; Welinder, K G

    1995-01-15

    Four conserved disulfide bonds and N-linked and O-linked glycans of extracellular fungal peroxidases have been identified from studies of a lignin and a manganese peroxidase from Trametes versicolor, and from Coprinus cinereus peroxidase (CIP) and recombinant C. cinereus peroxidase (rCIP) expressed in Aspergillus oryzae. The eight cysteine residues are linked 1-3, 2-7, 4-5 and 6-8, and are located differently from the four conserved disulfide bridges present in the homologous plant peroxidases. CIP and rCIP were identical in their glycosylation pattern, although the extent of glycan chain heterogeneity depended on the fermentation batch. CIP and rCIP have one N-linked glycan composed only of GlcNAc and Man at residue Asn142, and two O-linked glycans near the C-terminus. The major glycoform consists of single Man residues at Thr331 and at Ser338. T. versicolor lignin isoperoxidase TvLP10 contains a single N-linked glycan composed of (GlcNAc)2Man5 bound to Asn103, whereas (GlcNAc)2Man3 was found in T. versicolor manganese isoperoxidase TvMP2 at the same position. In addition, mass spectrometry of the C-terminal peptide of TvMP2 indicated the presence of five Man residues in O-linked glycans. No phosphate was found in these fungal peroxidases.

  4. [Prevention of fungal infections in hospitalized patients].

    Science.gov (United States)

    Seeliger, H P; Schröter, G

    1984-06-01

    Hospital acquired infections due to fungi are primarily caused by yeast species of the genus Candida and mould species of the genus Aspergillus. Underlying disease with severely impaired defence mechanisms as well as certain forms of immunosuppressive and aggressive chemotherapy are the most important prerequisites for such secondary fungal infections. Aspergillus spec. usually infect man via exogenous routes, whereas Candida spec. mostly originate from the patient's own microbial flora. Under certain circumstances invasion of tissues follows (endomycosis). Exogenous Candida infections may likewise occur through contaminated hands of personnel and medical devices. The density of yeast cell distribution in hospital wards decreases with the distance from the primary source: the Candida infected human patient. Preventive measures protecting the patient at risk include: Permanent surveillance by routine cultural and serological examinations for the detection of an early infection of the skin, mouth, oesophagus, urinary tract, vagina and the bowel. Monitoring of patients is essential for early detection of dissemination and contributes to the control of fungal decontamination measures. Selective local decontamination is effected by the use of nonabsorbable compounds such as nystatin and amphotericin B in the gastrointestinal tract, and in oral and genital mucous membranes. Oral administration of ketoconazole has also been recommended. For the disinfection of skin appropriate chemicals are available. In the control of the environment of the endangered patient special attention must be paid to meticulous management of catheters. These measures are to be supported by careful disinfection policy concerning the hands of personnel and medical equipment.(ABSTRACT TRUNCATED AT 250 WORDS)

  5. Synthesis and assembly of fungal melanin.

    Science.gov (United States)

    Eisenman, Helene C; Casadevall, Arturo

    2012-02-01

    Melanin is a unique pigment with myriad functions that is found in all biological kingdoms. It is multifunctional, providing defense against environmental stresses such as ultraviolet (UV) light, oxidizing agents and ionizing radiation. Melanin contributes to the ability of fungi to survive in harsh environments. In addition, it plays a role in fungal pathogenesis. Melanin is an amorphous polymer that is produced by one of two synthetic pathways. Fungi may synthesize melanin from endogenous substrate via a 1,8-dihydroxynaphthalene (DHN) intermediate. Alternatively, some fungi produce melanin from L-3,4-dihydroxyphenylalanine (L-dopa). The detailed chemical structure of melanin is not known. However, microscopic studies show that it has an overall granular structure. In fungi, melanin granules are localized to the cell wall where they are likely cross-linked to polysaccharides. Recent studies suggest the fungal melanin may be synthesized in internal vesicles akin to mammalian melanosomes and transported to the cell wall. Potential applications of melanin take advantage of melanin's radioprotective properties and propensity to bind to a variety of substances.

  6. Fungal melanins differ in planar stacking distances.

    Science.gov (United States)

    Casadevall, Arturo; Nakouzi, Antonio; Crippa, Pier R; Eisner, Melvin

    2012-01-01

    Melanins are notoriously difficult to study because they are amorphous, insoluble and often associated with other biological materials. Consequently, there is a dearth of structural techniques to study this enigmatic pigment. Current models of melanin structure envision the stacking of planar structures. X ray diffraction has historically been used to deduce stacking parameters. In this study we used X ray diffraction to analyze melanins derived from Cryptococcus neoformans, Aspergillus niger, Wangiella dermatitides and Coprinus comatus. Analysis of melanin in melanized C. neoformans encapsulated cells was precluded by the fortuitous finding that the capsular polysaccharide had a diffraction spectrum that was similar to that of isolated melanin. The capsular polysaccharide spectrum was dominated by a broad non-Bragg feature consistent with origin from a repeating structural motif that may arise from inter-molecular interactions and/or possibly gel organization. Hence, we isolated melanin from each fungal species and compared diffraction parameters. The results show that the inferred stacking distances of fungal melanins differ from that reported for synthetic melanin and neuromelanin, occupying intermediate position between these other melanins. These results suggest that all melanins have a fundamental diffracting unit composed of planar graphitic assemblies that can differ in stacking distance. The stacking peak appears to be a distinguishing universal feature of melanins that may be of use in characterizing these enigmatic pigments.

  7. Acid protease production in fungal root endophytes.

    Science.gov (United States)

    Mayerhofer, Michael S; Fraser, Erica; Kernaghan, Gavin

    2015-01-01

    Fungal endophytes are ubiquitous in healthy root tissue, but little is known about their ecosystem functions, including their ability to utilize organic nutrient sources such as proteins. Root-associated fungi may secrete proteases to access the carbon and mineral nutrients within proteins in the soil or in the cells of their plant host. We compared the protein utilization patterns of multiple isolates of the root endophytes Phialocephala fortinii s.l., Meliniomyces variabilis and Umbelopsis isabellina with those of two ectomycorrhizal (ECM) fungi, Hebeloma incarnatulum and Laccaria bicolor, and the wood-decay fungus Irpex lacteus at pH values of 2-9 on liquid BSA media. We also assessed protease activity using a fluorescently labeled casein assay and gelatin zymography and characterized proteases using specific protease inhibitors. I. lacteus and U. isabellina utilized protein efficiently, while the ECM fungi exhibited poor protein utilization. ECM fungi secreted metallo-proteases and had pH optima above 4, while other fungi produced aspartic proteases with lower pH optima. The ascomycetous root endophytes M. variabilis and P. fortinii exhibited intermediate levels of protein utilization and M. variabilis exhibited a very low pH optimum. Comparing proteolytic profiles between fungal root endophytes and fungi with well defined ecological roles provides insight into the ecology of these cryptic root associates.

  8. The dawn of fungal pathogen genomics.

    Science.gov (United States)

    Xu, Jin-Rong; Peng, You-Liang; Dickman, Martin B; Sharon, Amir

    2006-01-01

    Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced fungal genomes. Several important plant pathogenic fungi are among those that have been sequenced or are being sequenced. Additional fungal pathogens are likely to be sequenced in the near future. Analysis of the available genomes has provided useful information about genes that may be important for plant infection and colonization. Genome features, such as repetitive sequences, telomeres, conserved syntenic blocks, and expansion of pathogenicity-related genes, are discussed in detail with Magnaporthe oryzae (M. grisea) and Fusarium graminearum as examples. Functional and comparative genomic studies in plant pathogenic fungi, although still in the early stages and limited to a few pathogens, have enormous potential to improve our understanding of the molecular mechanisms involved in host-pathogen interactions. Development of advanced genomics tools and infrastructure is critical for efficient utilization of the vast wealth of available genome sequence information and will form a solid foundation for systems biology studies of plant pathogenic fungi.

  9. Standard methods for fungal brood disease research.

    Science.gov (United States)

    Jensen, Annette Bruun; Aronstein, Kathrine; Flores, José Manuel; Vojvodic, Svjetlana; Palacio, María Alejandra; Spivak, Marla

    2013-01-01

    Chalkbrood and stonebrood are two fungal diseases associated with honey bee brood. Chalkbrood, caused by Ascosphaera apis, is a common and widespread disease that can result in severe reduction of emerging worker bees and thus overall colony productivity. Stonebrood is caused by Aspergillus spp. that are rarely observed, so the impact on colony health is not very well understood. A major concern with the presence of Aspergillus in honey bees is the production of airborne conidia, which can lead to allergic bronchopulmonary aspergillosis, pulmonary aspergilloma, or even invasive aspergillosis in lung tissues upon inhalation by humans. In the current chapter we describe the honey bee disease symptoms of these fungal pathogens. In addition, we provide research methodologies and protocols for isolating and culturing, in vivo and in vitro assays that are commonly used to study these host pathogen interactions. We give guidelines on the preferred methods used in current research and the application of molecular techniques. We have added photographs, drawings and illustrations to assist bee-extension personnel and bee scientists in the control of these two diseases.

  10. Fungal Aflatoxins Reduce Respiratory Mucosal Ciliary Function

    Science.gov (United States)

    Lee, Robert J.; Workman, Alan D.; Carey, Ryan M.; Chen, Bei; Rosen, Phillip L.; Doghramji, Laurel; Adappa, Nithin D.; Palmer, James N.; Kennedy, David W.; Cohen, Noam A.

    2016-01-01

    Aflatoxins are mycotoxins secreted by Aspergillus flavus, which can colonize the respiratory tract and cause fungal rhinosinusitis or bronchopulmonary aspergillosis. A. flavus is the second leading cause of invasive aspergillosis worldwide. Because many respiratory pathogens secrete toxins to impair mucociliary immunity, we examined the effects of acute exposure to aflatoxins on airway cell physiology. Using air-liquid interface cultures of primary human sinonasal and bronchial cells, we imaged ciliary beat frequency (CBF), intracellular calcium, and nitric oxide (NO). Exposure to aflatoxins (0.1 to 10 μM; 5 to 10 minutes) reduced baseline (~6–12%) and agonist-stimulated CBF. Conditioned media (CM) from A. fumigatus, A. niger, and A. flavus cultures also reduced CBF by ~10% after 60 min exposure, but effects were blocked by an anti-aflatoxin antibody only with A. flavus CM. CBF reduction required protein kinase C but was not associated with changes in calcium or NO. However, AFB2 reduced NO production by ~50% during stimulation of the ciliary-localized T2R38 receptor. Using a fluorescent reporter construct expressed in A549 cells, we directly observed activation of PKC activity by AFB2. Aflatoxins secreted by respiratory A. flavus may impair motile and chemosensory functions of airway cilia, contributing to pathogenesis of fungal airway diseases. PMID:27623953

  11. Management of recurrent postoperative fungal endophthalmitis

    Directory of Open Access Journals (Sweden)

    Anand Vinekar

    2014-01-01

    Full Text Available Aim: To report the management of recurrent postoperative fungal endophthalmitis (POFE after failed pars plana vitrectomy (PPV and antifungal therapy. Settings and Design: Tertiary Care Referral Centre in North India. Retrospective, single institution, interventional case-series. Materials and Methods: Six patients with microbiologically proven recurrent post-operative fungal endophthalmitis refractory to conventional management were included. The final recurrence was managed with intraocular lens (IOL explantation and re-PPV. Main outcome measures included preserved globe anatomy, visual acuity and retinal status. ′Anatomical success′ was defined as preserved anatomy of the globe, and absence of signs of inflammation. ′Functional success′ was defined as an attached retina and a best corrected visual acuity of better than 20/400. Results: Of the six cases of POFE, five were culture positive [Aspergillus flavus (1, Aspergillus fumigatus (2, Candida albicans (1 and Candida glabrata (1] and one was smear positive for yeast. All recurred (mean recurrences, 4 despite a mean of 2.17 PPVs and intravitreal amphotericin B. No recurrences were observed after IOL explantation with re - PPV (median follow-up, 37 months. Pre-study defined criteria for successful ′anatomical′ and ′functional′ outcomes were achieved in 83.3% and 50% respectively. Conclusion: This report highlights the effective role of combined IOL explantation with PPV in managing recurrent POFE.

  12. Regulation of Sterol Biosynthesis in the Human Fungal Pathogen Aspergillus fumigatus: Opportunities for Therapeutic Development

    Science.gov (United States)

    Dhingra, Sourabh; Cramer, Robert A.

    2017-01-01

    Sterols are a major component of eukaryotic cell membranes. For human fungal infections caused by the filamentous fungus Aspergillus fumigatus, antifungal drugs that target sterol biosynthesis and/or function remain the standard of care. Yet, an understanding of A. fumigatus sterol biosynthesis regulatory mechanisms remains an under developed therapeutic target. The critical role of sterol biosynthesis regulation and its interactions with clinically relevant azole drugs is highlighted by the basic helix loop helix (bHLH) class of transcription factors known as Sterol Regulatory Element Binding Proteins (SREBPs). SREBPs regulate transcription of key ergosterol biosynthesis genes in fungi including A. fumigatus. In addition, other emerging regulatory pathways and target genes involved in sterol biosynthesis and drug interactions provide additional opportunities including the unfolded protein response, iron responsive transcriptional networks, and chaperone proteins such as Hsp90. Thus, targeting molecular pathways critical for sterol biosynthesis regulation presents an opportunity to improve therapeutic options for the collection of diseases termed aspergillosis. This mini-review summarizes our current understanding of sterol biosynthesis regulation with a focus on mechanisms of transcriptional regulation by the SREBP family of transcription factors. PMID:28203225

  13. Development of Questionnaire for Self-Assessment of Regulatory Capture

    Energy Technology Data Exchange (ETDEWEB)

    Muhmood, Ul Hassan; Lee, Young Eal [Pakistan Nuclear Regulatory Authority, Islamabad (Pakistan); Choi, Kwang Sik [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

    2014-10-15

    Nuclear industry with its evolution in 60s came with a number of pros and cons. In order to avoid any accident or incident, highest safety standards and quality control mechanism were established. The relation of regulator with its licensee is critical in the sense of public safety and welfare. The situation when the regulator starts to work for the interests of the industry instead of the public interest and fails to cling with his mission is known as 'regulatory capture' which may cause a number of serious negative effects like radiological or radiation risk. According to George Stigler, as a rule regulation is acquired by the industry and is designed and operated primarily for its benefit. The phenomenon of regulatory capture may hamper the safety culture and can also be considered as regulatory failure. It is therefore necessary to clearly understand this type of government failure to avoid the happening of serious accidents like TMI and Fukushima in the future. This paper aims to explore whether the regulatory body works independently and effectively to achieve its assigned tasks and objectives. Hence we proposed a questionnaire for the self-assessment of regulatory capture within the regulatory body. It also includes the results of an experimental assessment which was carried out to check the relevance and reliability of the questions to this subject. This assessment survey was conducted with the officers and staff members of Pakistan Nuclear Regulatory Authority (PNRA). We checked the significance of the proposed questionnaire and found some of the questions like Q. 27, 30 and 33 (written in italic) are not directly related to the phenomenon of regulatory capture. However, the existence of the situation which has been asked in these questions may lead towards the hampering of regulatory culture.

  14. Impact of Climate Change on Five Major Crop Fungal Diseases: Building Climatic Indicators of Infection Risk

    Science.gov (United States)

    Launay, M.; Caubel, J.; Bourgeois, G.; Huard, F.; Garcia de Cortazar-Atauri, I.

    2013-12-01

    The climate change will modify the severity and occurrence of fungal crop diseases, as the bioclimatic niches of pathogens will shift according to temperature and rainfall patterns evolution. Therefore it becomes necessary to integrate fungal disease pressure assessment into evaluation tools of crop suitability at the regional level. The aim of this study was to build two climatic indicators, the Average Infection Efficiency (AIE) and the Number of Infection Days (NID), quantifying the potential effect of climate on infection intensity and occurrence. A simple and continuous function was developed to calculate them, which is easy to parameterize from experimental measurements, usable on large spatial scales and adaptable to various pathogens. The evolution of those climatic indicators was then studied for five major fungal crop diseases in Northern France, the phoma of oilseed rape, the potato late blight, the downy mildew of grape, the leaf rust of wheat and the net blotch of barley. These indicators were applied on a multisite analysis in Northern France. They were calculated during the crop cycle when the host plant is able to be infected, over the period between 1970 and 2100 for the balanced scenario of climate change A1B. In late spring and summer, higher temperatures combined with lower humidity reduced the risk of infection of potato late blight and downy mildew of grape. In autumn and spring the balance between warmer temperatures and lower humidity determined the risk of infection on oilseed rape and cereals: increased risk in late autumn and early spring, and decreased risk in early autumn and mid-spring when low humidity becomes limiting. This statement highlighted the need for using between year scale for a relevant analysis of climate change impact on infection risk. The indicators we developed are thus useful for land management at regional scale and medium term, in particular for stakeholders who need decision support tools through which they could

  15. [Fungal allergy in chronic rhinosinusitis with or without polyps].

    Science.gov (United States)

    Erbek, Selim S; Topal, Ozgül; Erbek, Seyra; Cakmak, Ozcan

    2008-01-01

    Fungi, by systemic or local allergic effect, may play a role in the pathogenesis of chronic rhinosinusitis (CRS). We investigated the incidence of fungal allergy in patients with CRS and its effect on the clinical characteristics of the disease. The study included 127 patients, aged 18 years or over, with CRS (42 females, 85 males; mean age 43+/-12 years; range 19 to 78 years). Fungal allergy was determined by skin prick test and its effect was analyzed on blood eosinophil and total immunoglobulin E levels, the presence of polyps, and paranasal sinus computed tomography scores. Eighty-five patients (66.9%) were found to have allergy. The incidence of allergy did not differ between patients with and without polyps (p>0.05). House dust mites (62.2%) were the most frequent allergens. The incidence of fungal allergy was 38.8% in allergic patients. Isolated fungal allergy was detected in two patients (1.6%). The most frequent fungal allergens were Aspergillus, followed by Alternaria, and Penicillium. No association was found between fungal allergy and blood eosinophil and total immunoglobulin E levels, presence of polyps, or paranasal sinus computed tomography scores (p>0.05). The incidence of fungal allergy in patients with CRS was found to be high in this study. Tissue culture studies are required to determine the definitive relationship between fungal allergy and clinical features of CRS.

  16. Structure and biosynthesis of fungal alpha-glucans

    NARCIS (Netherlands)

    Grün, Christian Hugo

    2003-01-01

    The fungal cell wall is unique among eukaryotes and therefore it forms an ideal target for the development of novel antifungal drugs. Fungal cell morphology and integrity depend on a cell-surrounding wall, which is composed of glycoproteins and polysaccharides. Disrupting enzymes that are involved i

  17. Fungal community assembly in the Amazonian Dark Earth

    NARCIS (Netherlands)

    Reis Lucheta, Adriano; Souza Cannavan, F.S.; Roesch, L.; Tsai, S.M.; Kuramae, E.E.

    2016-01-01

    Here, we compare the fungal community composition and diversity in Amazonian Dark Earth (ADE) and the respective non-anthropogenic origin adjacent (ADJ) soils from four different sites in Brazilian Central Amazon using pyrosequencing of 18S ribosomal RNA (rRNA) gene. Fungal community composition in

  18. New perspectives towards analising fungal communities in terrestrial environments

    NARCIS (Netherlands)

    Kowalchuk, G.A.

    1999-01-01

    Fungi play key roles in numerous ecosystem functions, and recent advances in the study of fungal diversity and ecology have led to a greater appreciation of this group of microeukaryotes. The application of a variety of nucleic acid techniques to fungal classification and phylogeny has led to a numb

  19. Root fungal associations in some non-orchidaceous vascular lithophytes

    Directory of Open Access Journals (Sweden)

    Thangavelu Muthukumar

    2016-01-01

    Full Text Available ABSTRACT Plant roots in natural ecosystems are colonized by a diverse group of fungi among which the most common and widespread are arbuscular mycorrhizal (AM and dark septate endophyte (DSE fungi. Though AM and DSE fungal associations are well reported for terricolous plant species, they are rather poorly known for lithophytic plant species. In this study, we examined AM and DSE fungal association in 72 non-orchidaceous vascular plant species growing as lithophytes in Siruvani Hills, Western Ghats of Tamilnadu, India. Sixty-nine plant species had AM and 58 species had DSE fungal associations. To our knowledge, we report AM fungal association in 42 and DSE fungal association in 53 plant species for the first time. There were significant differences in total root length colonization and root length colonized by different AM and DSE fungal structures among plant species. In contrast, the differences in AM and DSE fungal colonization among plants in various life-forms and lifecycles were not significant. AM morphology reported for the first time in 56 plant species was dominated by intermediate type AM morphology. A significant negative relationship existed between total root length colonized by AM and DSE fungi. These results clearly suggest that AM and DSE fungal associations are widespread in lithophytes.

  20. Neglected fungal zoonoses : hidden threats to man and animals

    NARCIS (Netherlands)

    Seyedmousavi, S; Guillot, J; Tolooe, A; Verweij, P E; de Hoog, G S

    2015-01-01

    Zoonotic fungi can be naturally transmitted between animals and humans, and in some cases cause significant public health problems. A number of mycoses associated with zoonotic transmission are among the group of the most common fungal diseases, worldwide. It is, however, notable that some fungal di

  1. Neglected fungal zoonoses: hidden threats to man and animals

    NARCIS (Netherlands)

    Seyedmousavi, S.; Guillot, J.; Tolooe, A.; Verweij, P.E.; Hoog, G.S. de

    2015-01-01

    Zoonotic fungi can be naturally transmitted between animals and humans, and in some cases cause significant public health problems. A number of mycoses associated with zoonotic transmission are among the group of the most common fungal diseases, worldwide. It is, however, notable that some fungal di

  2. UV-guided isolation of fungal metabolites by HSCCC

    DEFF Research Database (Denmark)

    Dalsgaard, P.W.; Nielsen, K.F.; Larsen, Thomas Ostenfeld

    2005-01-01

    Analytical standardised reversed phase liquid chromatography (RPLC) data can be helpful in finding a suitable solvent combination for isolation of fungal metabolites by high-speed counter current chromatography. Analysis of the distribution coefficient (K-D) of fungal metabolites in a series of b...

  3. Invasive fungal infections in patients with chronic granulomatous disease

    NARCIS (Netherlands)

    Henriet, S.S.V.; Verweij, P.E.; Holland, S.M.; Warris, A.

    2013-01-01

    Invasive fungal infections are a major threat for chronic granulomatous disease (CGD) patients. The present study provides a comprehensive overview of published invasive fungal infections in the CGD host through an extensive review of epidemiological, clinical, diagnostic and therapeutic data. In ad

  4. The Top 10 fungal pathogens in molecular plant pathology

    NARCIS (Netherlands)

    Dean, R.; Kan, van J.A.L.; Pretorius, Z.A.; Hammond-Kosack, K.E.; Pietro, Di A.; Spanu, P.D.; Rudd, J.J.; Dickman, M.; Kahmann, R.; Ellis, J.; Foster, G.D.

    2012-01-01

    The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a ‘Top 10’ based on scientific/economic importance. The survey generated 495 votes from the international co

  5. Fungal community assembly in the Amazonian Dark Earth

    NARCIS (Netherlands)

    Lucheta, A.R.; Souza Cannavan, F.S.; Roesch, L.; Tsai, S.M.; Kuramae, E.E.

    2016-01-01

    Here, we compare the fungal community composition and diversity in Amazonian Dark Earth (ADE) and the respective non-anthropogenic origin adjacent (ADJ) soils from four different sites in Brazilian Central Amazon using pyrosequencing of 18S ribosomal RNA (rRNA) gene. Fungal community composition in

  6. Fungal/bacterial ratios in grassland with contrasting nitrogen management

    NARCIS (Netherlands)

    Vries, de F.T.; Hoffland, E.; Eekeren, van N.J.M.; Brussaard, L.; Bloem, J.

    2006-01-01

    It is frequently hypothesised that high soil fungal/bacterial ratios are indicative for more sustainable agricultural systems. Increased F / B ratios have been reported in extensively managed grasslands. To determine the shifts in fungal/bacterial biomass ratio as influenced by grassland management

  7. The Top 10 fungal pathogens in molecular plant pathology

    NARCIS (Netherlands)

    Dean, R.; Kan, van J.A.L.; Pretorius, Z.A.; Hammond-Kosack, K.E.; Pietro, Di A.; Spanu, P.D.; Rudd, J.J.; Dickman, M.; Kahmann, R.; Ellis, J.; Foster, G.D.

    2012-01-01

    The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a ‘Top 10’ based on scientific/economic importance. The survey generated 495 votes from the international

  8. The Top 10 fungal pathogens in molecular plant pathology

    NARCIS (Netherlands)

    Dean, R.; Kan, van J.A.L.; Pretorius, Z.A.; Hammond-Kosack, K.E.; Pietro, Di A.; Spanu, P.D.; Rudd, J.J.; Dickman, M.; Kahmann, R.; Ellis, J.; Foster, G.D.

    2012-01-01

    The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a ‘Top 10’ based on scientific/economic importance. The survey generated 495 votes from the international co

  9. First genomic survey of human skin fungal diversity

    Science.gov (United States)

    Fungal infections of the skin affect 29 million people in the United States. In the first study of human fungal skin diversity, National Institutes of Health researchers sequenced the DNA of fungi that thrive at different skin sites of healthy adults to d

  10. Inositol Polyphosphate Kinases, Fungal Virulence and Drug Discovery

    Directory of Open Access Journals (Sweden)

    Cecilia Li

    2016-09-01

    Full Text Available Opportunistic fungi are a major cause of morbidity and mortality world-wide, particularly in immunocompromised individuals. Developing new treatments to combat invasive fungal disease is challenging given that fungal and mammalian host cells are eukaryotic, with similar organization and physiology. Even therapies targeting unique fungal cell features have limitations and drug resistance is emerging. New approaches to the development of antifungal drugs are therefore needed urgently. Cryptococcus neoformans, the commonest cause of fungal meningitis worldwide, is an accepted model for studying fungal pathogenicity and driving drug discovery. We recently characterized a phospholipase C (Plc1-dependent pathway in C. neoformans comprising of sequentially-acting inositol polyphosphate kinases (IPK, which are involved in synthesizing inositol polyphosphates (IP. We also showed that the pathway is essential for fungal cellular function and pathogenicity. The IP products of the pathway are structurally diverse, each consisting of an inositol ring, with phosphate (P and pyrophosphate (PP groups covalently attached at different positions. This review focuses on (1 the characterization of the Plc1/IPK pathway in C. neoformans; (2 the identification of PP-IP5 (IP7 as the most crucial IP species for fungal fitness and virulence in a mouse model of fungal infection; and (3 why IPK enzymes represent suitable candidates for drug development.

  11. Epigenetic regulation of development and pathogenesis in fungal plant pathogens.

    Science.gov (United States)

    Dubey, Akanksha; Jeon, Junhyun

    2017-08-01

    Evidently, epigenetics is at forefront in explaining the mechanisms underlying the success of human pathogens and in the identification of pathogen-induced modifications within host plants. However, there is a lack of studies highlighting the role of epigenetics in the modulation of the growth and pathogenicity of fungal plant pathogens. In this review, we attempt to highlight and discuss the role of epigenetics in the regulation of the growth and pathogenicity of fungal phytopathogens using Magnaporthe oryzae, a devastating fungal plant pathogen, as a model system. With the perspective of wide application in the understanding of the development, pathogenesis and control of other fungal pathogens, we attempt to provide a synthesized view of the epigenetic studies conducted on M. oryzae to date. First, we discuss the mechanisms of epigenetic modifications in M. oryzae and their impact on fungal development and pathogenicity. Second, we highlight the unexplored epigenetic mechanisms and areas of research that should be considered in the near future to construct a holistic view of epigenetic functioning in M. oryzae and other fungal plant pathogens. Importantly, the development of a complete understanding of the modulation of epigenetic regulation in fungal pathogens can help in the identification of target points to combat fungal pathogenesis. © 2016 BSPP AND JOHN WILEY & SONS LTD.

  12. Natural occurrence of fungi and fungal metabolites in moldy tomatoes

    DEFF Research Database (Denmark)

    Andersen, B.; Frisvad, Jens Christian

    2004-01-01

    . extracted, and analyzed for fungal metabolites. Extracts from pure cultures were compared with extracts from the moldy tomatoes and fungal metabolite standards in two HPLC systems with DAD and FLD detection. The results showed that Penicillium tularense, Stemphylium eturmiunum. and S. cf. lycopersici were...

  13. A novel method to scale up fungal endophyte isolations

    Science.gov (United States)

    Estimations of species diversity are influenced by sampling intensity which in turn is influenced by methodology. For fungal endophyte diversity studies, the methodology includes surface-sterilization prior to isolation of endophytes. Surface-sterilization is an essential component of fungal endophy...

  14. Fusion and fission of genes define a metric between fungal genomes.

    Directory of Open Access Journals (Sweden)

    Pascal Durrens

    2008-10-01

    Full Text Available Gene fusion and fission events are key mechanisms in the evolution of gene architecture, whose effects are visible in protein architecture when they occur in coding sequences. Until now, the detection of fusion and fission events has been performed at the level of protein sequences with a post facto removal of supernumerary links due to paralogy, and often did not include looking for events defined only in single genomes. We propose a method for the detection of these events, defined on groups of paralogs to compensate for the gene redundancy of eukaryotic genomes, and apply it to the proteomes of 12 fungal species. We collected an inventory of 1,680 elementary fusion and fission events. In half the cases, both composite and element genes are found in the same species. Per-species counts of events correlate with the species genome size, suggesting a random mechanism of occurrence. Some biological functions of the genes involved in fusion and fission events are slightly over- or under-represented. As already noted in previous studies, the genes involved in an event tend to belong to the same functional category. We inferred the position of each event in the evolution tree of the 12 fungal species. The event localization counts for all the segments of the tree provide a metric that depicts the "recombinational" phylogeny among fungi. A possible interpretation of this metric as distance in adaptation space is proposed.

  15. Politically Induced Regulatory Risk and Independent Regulatory Agencies

    OpenAIRE

    Strausz, Roland

    2015-01-01

    Uncertainty in election outcomes generates politically induced regulatory risk. Political parties' risk attitudes towards such risk depend on a fluctuation effect that hurts both parties and an output--expansion effect that benefits at least one party. Notwithstanding the parties' risk attitudes, political parties have incentives to negotiate away all regulatory risk by pre-electoral bargaining. Efficient pre-electoral bargaining outcomes fully eliminate politically induced regulatory risk. P...

  16. Population Dynamics of Genetic Regulatory Networks

    Science.gov (United States)

    Braun, Erez

    2005-03-01

    Unlike common objects in physics, a biological cell processes information. The cell interprets its genome and transforms the genomic information content, through the action of genetic regulatory networks, into proteins which in turn dictate its metabolism, functionality and morphology. Understanding the dynamics of a population of biological cells presents a unique challenge. It requires to link the intracellular dynamics of gene regulation, through the mechanism of cell division, to the level of the population. We present experiments studying adaptive dynamics of populations of genetically homogeneous microorganisms (yeast), grown for long durations under steady conditions. We focus on population dynamics that do not involve random genetic mutations. Our experiments follow the long-term dynamics of the population distributions and allow to quantify the correlations among generations. We focus on three interconnected issues: adaptation of genetically homogeneous populations following environmental changes, selection processes on the population and population variability and expression distributions. We show that while the population exhibits specific short-term responses to environmental inputs, it eventually adapts to a robust steady-state, largely independent of external conditions. Cycles of medium-switch show that the adapted state is imprinted in the population and that this memory is maintained for many generations. To further study population adaptation, we utilize the process of gene recruitment whereby a gene naturally regulated by a specific promoter is placed under a different regulatory system. This naturally occurring process has been recognized as a major driving force in evolution. We have recruited an essential gene to a foreign regulatory network and followed the population long-term dynamics. Rewiring of the regulatory network allows us to expose their complex dynamics and phase space structure.

  17. Clinical utility of caspofungin eye drops in fungal keratitis.

    Science.gov (United States)

    Neoh, Chin Fen; Daniell, Mark; Chen, Sharon C-A; Stewart, Kay; Kong, David C M

    2014-08-01

    Treatment of fungal keratitis remains challenging. To date, only the polyenes and azoles are commonly used topically in the management of fungal keratitis. Natamycin, a polyene, is the only antifungal eye drop that is commercially available; the remainder are prepared in-house and are used in an 'off-label' manner. Failure of medical treatment for fungal keratitis is common, hence there is a need for more effective topical antifungal therapy. To increase the antifungal eye drop armamentarium, it is important to investigate the utility of other classes of antifungal agents for topical use. Caspofungin, an echinocandin antifungal agent, could potentially be used to address the existing shortcomings. However, little is known about the usefulness of topically administered caspofungin. This review will briefly explore the incidence, epidemiology and antifungal treatment of fungal keratitis. It will focus primarily on evidence related to the efficacy, safety and practicality of using caspofungin eye drops in fungal keratitis.

  18. Fungal endophytes characterization from four species of Diplazium Swartz

    Science.gov (United States)

    Affina-Eliya, A. A.; Noraini, T.; Nazlina, I.; Ruzi, A. R.

    2014-09-01

    Four species on genus Diplazium namely Diplazium tomentosum, D. sorzogonense, D. asperum and D. accedens of Peninsular Malaysia were studied for presence of fungal endophyte. The objective of this study is to characterize fungal endophytes in the rhizome of four Diplazium species. The rhizome was surface sterilized and incubated to isolate fungal endophytes. Characterization of the colonies was performed by macroscopic morphological, microscopic identification, types of hyphae and mycelium, and spore structure. For isolation that produces spores, the structure of conidiophores and conidia were identified. From this study, four fungal have been isolated and determined as Aspergillus sp. (isolates AE 1), Aspergillus fumigatus (isolates AE 2), Aspergillus versicolor (isolates AE 3) and Verticillium sp. (isolates AE 4). The fungal isolates from this study were classified from the same family Moniliaceae.

  19. Interpretation of "fungal spikes" in Permian-Triassic boundary sections

    Science.gov (United States)

    Hochuli, Peter A.

    2016-09-01

    Abundant occurrences of the palynomorph Reduviasporonites have been described as ;fungal spike; from several Permian/Triassic boundary sections and related to the supposed destruction of woody vegetation by fungal pathogens during the Permian/Triassic extinction event. The biological affinity of this taxa considered by some authors of fungal origin is still controversially discussed since there is geochemical evidence that it is most probably related to algae. The abundance peak of this species is used by some authors as a stratigraphic marker, notably in terrestrial Permian/Triassic boundary sections from South China. Illustrations of the reported fungal remains however show potentially erroneous taxonomic identification of Reduviasporonites, and, based on differences in thermal maturation, they may represent recent contamination. Here Reduviasporonites chalastus of Early Triassic age is illustrated together with recent fungal remains originating from a strongly weathered and otherwise barren sample from a Middle Triassic section.

  20. Fungal polyketide azaphilone pigments as future natural food colorants?

    Science.gov (United States)

    Mapari, Sameer A S; Thrane, Ulf; Meyer, Anne S

    2010-06-01

    The recent approval of fungal carotenoids as food colorants by the European Union has strengthened the prospects for fungal cell factories for the production of polyketide pigments. Fungal production of colorants has the main advantage of making the manufacturer independent of the seasonal supply of raw materials, thus minimizing batch-to-batch variations. Here, we review the potential of polyketide pigments produced from chemotaxonomically selected non-toxigenic fungal strains (e.g. Penicillium and Epicoccum spp.) to serve as food colorants. We argue that the production of polyketide azaphilone pigments from such potentially safe hosts is advantageous over traditional processes that involve Monascus spp., which risks co-production of the mycotoxin citrinin. Thus, there is tremendous potential for the development of robust fungal production systems for polyketide pigments, both to tailor functionality and to expand the color palette of contemporary natural food colorants.

  1. Immunoglobulins in defense, pathogenesis, and therapy of fungal diseases.

    Science.gov (United States)

    Casadevall, Arturo; Pirofski, Liise-Anne

    2012-05-17

    Only two decades ago antibodies to fungi were thought to have little or no role in protection against fungal diseases. However, subsequent research has provided convincing evidence that certain antibodies can modify the course of fungal infection to the benefit or detriment of the host. Hybridoma technology was the breakthrough that enabled the characterization of antibodies to fungi, illuminating some of the requirements for antibody efficacy. As discussed in this review, fungal-specific antibodies mediate protection through direct actions on fungal cells and through classical mechanisms such as phagocytosis and complement activation. Although mechanisms of antibody-mediated protection are often species-specific, numerous fungal antigens can be targeted to generate vaccines and therapeutic immunoglobulins. Furthermore, the study of antibody function against medically important fungi has provided fresh immunological insights into the complexity of humoral immunity that are likely to apply to other pathogens.

  2. The role of the cell wall in fungal pathogenesis.

    Science.gov (United States)

    Arana, David M; Prieto, Daniel; Román, Elvira; Nombela, César; Alonso-Monge, Rebeca; Pla, Jesús

    2009-05-01

    Fungal infections are a serious health problem. In recent years, basic research is focusing on the identification of fungal virulence factors as promising targets for the development of novel antifungals. The wall, as the most external cellular component, plays a crucial role in the interaction with host cells mediating processes such as adhesion or phagocytosis that are essential during infection. Specific components of the cell wall (called PAMPs) interact with specific receptors in the immune cell (called PRRs), triggering responses whose molecular mechanisms are being elucidated. We review here the main structural carbohydrate components of the fungal wall (glucan, mannan and chitin), how their biogenesis takes place in fungi and the specific receptors that they interact with. Different model fungal pathogens are chosen to illustrate the functional consequences of this interaction. Finally, the identification of the key components will have important consequences in the future and will allow better approaches to treat fungal infections.

  3. Allergic fungal sinusitis and eosinophilic mucin rhinosinusitis: diagnostic criteria.

    Science.gov (United States)

    Uri, N; Ronen, O; Marshak, T; Parpara, O; Nashashibi, M; Gruber, M

    2013-09-01

    Chronic sinusitis is one of the most common otolaryngological diagnoses. Allergic fungal sinusitis and eosinophilic mucin rhinosinusitis can easily be misdiagnosed and treated as chronic sinusitis, causing continuing harm. To better identify and characterise these two subgroups of patients, who may suffer from a systemic disease requiring multidisciplinary treatment and prolonged follow up. A retrospective, longitudinal study of all patients diagnosed with allergic fungal sinusitis or eosinophilic mucin rhinosinusitis within one otolaryngology department over a 15-year period. Thirty-four patients were identified, 26 with eosinophilic mucin rhinosinusitis and 8 with allergic fungal sinusitis. Orbital involvement at diagnosis was commoner in allergic fungal sinusitis patients (50 per cent) than eosinophilic mucin rhinosinusitis patients (7.7 per cent; p sinusitis patients. Allergic fungal sinusitis and eosinophilic mucin rhinosinusitis have the same clinical presentation but different clinical courses. The role of fungus and the ability to confirm its presence are still problematic issues, and additional studies are required.

  4. Acute fungal sinusitis in neutropenic patients of Namazi hospital/ Shiraz

    Directory of Open Access Journals (Sweden)

    Parisa Badiee

    2008-09-01

    Full Text Available Introduction: Fungal sinusitis is a well known disease in immunocompromised patients, but recently many reports have indicated an increased prevalence of fungal sinusitis in otherwise healthy individuals. The aim of this study was to assess the frequency of invasive fungal sinusitis (IFS in neutropenic patients and to determine outcome factors that may affect their survival. Methods: A total of 142 patients who were undergoing chemotherapy were followed by clinical and radiological features suggestive of fungal sinusitis. Patients with fever, headache, facial swelling and radiological finding underwent endoscopic sinus surgery. The biopsy materials were studied by mycological and histopathological methods. Results: Eleven from 142 patients were identified to have IFS. The ethiologic agents were Aspergillus flavus (5 cases, Alternaria sp. (3 cases, Aspergillus fumigatus (2 cases and mucor (1 case. Eight of 11 cases died. Conclusions: Invasive fungal sinusitis causes a high rate of mortality among immunocompromised patients. Therefore, early diagnosis with aggressive medical and surgical intervention is critical for survival.

  5. Fungicide effects on fungal community composition in the wheat phyllosphere.

    Science.gov (United States)

    Karlsson, Ida; Friberg, Hanna; Steinberg, Christian; Persson, Paula

    2014-01-01

    The fungicides used to control diseases in cereal production can have adverse effects on non-target fungi, with possible consequences for plant health and productivity. This study examined fungicide effects on fungal communities on winter wheat leaves in two areas of Sweden. High-throughput 454 sequencing of the fungal ITS2 region yielded 235 operational taxonomic units (OTUs) at the species level from the 18 fields studied. It was found that commonly used fungicides had moderate but significant effect on fungal community composition in the wheat phyllosphere. The relative abundance of several saprotrophs was altered by fungicide use, while the effect on common wheat pathogens was mixed. The fungal community on wheat leaves consisted mainly of basidiomycete yeasts, saprotrophic ascomycetes and plant pathogens. A core set of six fungal OTUs representing saprotrophic species was identified. These were present across all fields, although overall the difference in OTU richness was large between the two areas studied.

  6. Clinical research: regulatory issues.

    Science.gov (United States)

    Wermeling, D P

    1999-02-01

    The regulatory issues faced by institutions performing clinical research are described. Many institutions do not have on staff an expert who understands the regulatory issues involved in managing investigational new drug research and who knows the institution's obligations under the federal rules. Because pharmacists understand the FDA regulations that apply to the management of drugs in clinical research, institutions are asking pharmacists to expand their role and manage clinical research offices. Many authorities govern various aspects of investigational drug research. FDA has published regulations for good clinical practice (GCP), and the International Conference on Harmonisation is developing an international standard for the proper management of clinical trials. The guidelines published by the Joint Commission on Accreditation of Healthcare Organizations aim to protect patients who are in the institution to receive health care and also participate in clinical trials. The Social Security Administration Acts specifically state that only items and services that are reasonable and necessary for the diagnosis and treatment of injury or disease can be billed to the government; research-related billings are excluded from coverage. Proper management of drug research is crucial to the success of a research program that is integrated with patient care.

  7. Toxicogenomics in regulatory ecotoxicology

    Science.gov (United States)

    Ankley, Gerald T.; Daston, George P.; Degitz, Sigmund J.; Denslow, Nancy D.; Hoke, Robert A.; Kennedy, Sean W.; Miracle, Ann L.; Perkins, Edward J.; Snape, Jason; Tillitt, Donald E.; Tyler, Charles R.; Versteeg, Donald

    2006-01-01

    Recently, we have witnessed an explosion of different genomic approaches that, through a combination of advanced biological, instrumental, and bioinformatic techniques, can yield a previously unparalleled amount of data concerning the molecular and biochemical status of organisms. Fueled partially by large, well-publicized efforts such as the Human Genome Project, genomic research has become a rapidly growing topical area in multiple biological disciplines. Since 1999, when the term “toxicogenomics” was coined to describe the application of genomics to toxicology (1), a rapid increase in publications on the topic has occurred (Figure 1). The potential utility of toxicogenomics in toxicological research and regulatory activities has been the subject of scientific discussions and, as with any new technology, has evoked a wide range of opinion (2–6). VIEWPOINT © 2006 american chemical Society july 1, 2006 / EnvironmEntal SciEncE & tEchnology n 4055 The purpose of this feature article is to consider the roles of toxicogenomics in the field of regulatory ecotoxicology, explore current limitations in the science and practice of genomics, and propose possible avenues to approach and resolve some of the major challenges. A significant amount of input to our analysis came from a workshop sponsored by the Society of Environmental Toxicology and Chemistry (SETAC) in Pellston, Mich., in September 2005. A complete list of names and affiliations of the experts participating in that workshop is provided online in Table 1 of the Supporting Information for this paper.

  8. Model simulations of fungal spore distribution over the Indian region

    Science.gov (United States)

    Ansari, Tabish U.; Valsan, Aswathy E.; Ojha, N.; Ravikrishna, R.; Narasimhan, Balaji; Gunthe, Sachin S.

    2015-12-01

    Fungal spores play important role in the health of humans, animals, and plants by constituting a class of the primary biological aerosol particles (PBAPs). Additionally, these could mediate the hydrological cycle by acting as nuclei for ice and cloud formation (IN and CCN respectively). Various processes in the biosphere and the variations in the meteorological conditions control the releasing mechanism of spores through active wet and dry discharge. In the present paper, we simulate the concentration of fungal spores over the Indian region during three distinct meteorological seasons by combining a numerical model (WRF-Chem) with the fungal spore emissions based on land-use type. Maiden high-resolution regional simulations revealed large spatial gradient and strong seasonal dependence in the concentration of fungal spores over the Indian region. The fungal spore concentrations are found to be the highest during winter (0-70 μg m-3 in December), moderately higher during summer (0-35 μg m-3 in May) and lowest during the monsoon (0-25 μg m-3 in July). The elevated concentrations during winter are attributed to the shallower boundary layer trapping the emitted fungal spores in smaller volume. In contrast, the deeper boundary layer mixing in May and stronger monsoonal-convection in July distribute the fungal spores throughout the lower troposphere (∼5 km). We suggest that the higher fungal spore concentrations during winter could have potential health impacts. While, stronger vertical mixing could enable fungal spores to influence the cloud formation during summer and monsoon. Our study provides the first information about the distribution and seasonal variation of fungal spores over the densely populated and observationally sparse Indian region.

  9. Selection of Infective Arbuscular Mycorrhizal Fungal Isolates for Field Inoculation

    Directory of Open Access Journals (Sweden)

    Elisa Pellegrino

    2010-09-01

    Full Text Available Arbuscular mycorrhizal (AM fungi play a key role in host plant growth and health, nutrient and water uptake, plant community diversity and dynamics. AM fungi differ in their symbiotic performance, which is the result of the interaction of two fungal characters, infectivity and efficiency. Infectivity is the ability of a fungal isolate to establish rapidly an extensive mycorrhizal symbiosis and is correlated with pre-symbiotic steps of fungal life cycle, such as spore germination and hyphal growth. Here, different AM fungal isolates were tested, with the aim of selecting infective endophytes for field inoculation. Greenhouse and microcosm experiments were performed in order to assess the ability of 12 AM fungal isolates to produce spores, colonize host roots and to perform initial steps of symbiosis establishment, such as spore germination and hyphal growth. AM fungal spore production and root colonization were significantly different among AM fungal isolates. Spore and sporocarp densities ranged from 0.8 to 7.4 and from 0.6 to 2.0 per gram of soil, respectively, whereas root colonization ranged from 2.9 to 72.2%. Percentage of spore or sporocarp germination ranged from 5.8 to 53.3% and hyphal length from 4.7 to 79.8 mm. The ordination analysis (Redundancy Analysis, RDA showed that environmental factors explained about 60% of the whole variance and their effect on fungal infectivity variables was significant (P = 0.002. The biplot clearly showed that variables which might be used to detect infective AM fungal isolates were hyphal length and root colonization. Such analysis may allow the detection of the best parameters to select efficient AM fungal isolates to be used in agriculture.

  10. Aspergillus nidulans Synthesize Insect Juvenile Hormones upon Expression of a Heterologous Regulatory Protein and in Response to Grazing by Drosophila melanogaster Larvae

    DEFF Research Database (Denmark)

    Nielsen, Morten Thrane; Klejnstrup, Marie Louise; Rohlfs, Marko;

    2013-01-01

    Secondary metabolites are known to serve a wide range of specialized functions including communication, developmental control and defense. Genome sequencing of several fungal model species revealed that the majority of predicted secondary metabolite related genes are silent in laboratory strains......, indicating that fungal secondary metabolites remain an underexplored resource of bioactive molecules. In this study, we combine heterologous expression of regulatory proteins in Aspergillus nidulans with systematic variation of growth conditions and observe induced synthesis of insect juvenile hormone...... induced synthesis of juvenile hormone in A. nidulans indicating a possible role of juvenile hormone biosynthesis in affecting fungal-insect antagonisms....

  11. Fungal stress biology: a preface to the Fungal Stress Responses special edition.

    Science.gov (United States)

    Rangel, Drauzio E N; Alder-Rangel, Alene; Dadachova, Ekaterina; Finlay, Roger D; Kupiec, Martin; Dijksterhuis, Jan; Braga, Gilberto U L; Corrochano, Luis M; Hallsworth, John E

    2015-08-01

    There is currently an urgent need to increase global food security, reverse the trends of increasing cancer rates, protect environmental health, and mitigate climate change. Toward these ends, it is imperative to improve soil health and crop productivity, reduce food spoilage, reduce pesticide usage by increasing the use of biological control, optimize bioremediation of polluted sites, and generate energy from sustainable sources such as biofuels. This review focuses on fungi that can help provide solutions to such problems. We discuss key aspects of fungal stress biology in the context of the papers published in this Special Issue of Current Genetics. This area of biology has relevance to pure and applied research on fungal (and indeed other) systems, including biological control of insect pests, roles of saprotrophic fungi in agriculture and forestry, mycotoxin contamination of the food-supply chain, optimization of microbial fermentations including those used for bioethanol production, plant pathology, the limits of life on Earth, and astrobiology.

  12. The role of enzymes in fungus-growing ant evolution

    DEFF Research Database (Denmark)

    de Fine Licht, Henrik Hjarvard

    not been done. Such studies are important as the single specific fungal adaptation that can (almost) be seen with the bare eye (gongylidia; inflated hyphal tips that are preferentially eaten by the ants and their larvae) evolved earlier and therefore does not characterize the transition to leafcutting......, showed that this enzyme is exclusively found in the gardens of leaf-cutting ants, where it is significantly upregulated in the gongylidia. I’ll discuss the possible role of this enzyme and other fungal modifications in the evolution of the leafcutter ants and their non-leafcutting attine relatives....

  13. Origin and evolution of carnivorism in the Ascomycota (fungi).

    Science.gov (United States)

    Yang, Ence; Xu, Lingling; Yang, Ying; Zhang, Xinyu; Xiang, Meichun; Wang, Chengshu; An, Zhiqiang; Liu, Xingzhong

    2012-07-03

    Carnivorism is one of the basic life strategies of fungi. Carnivorous fungi possess the ability to trap and digest their preys by sophisticated trapping devices. However, the origin and development of fungal carnivorism remains a gap in evolution biology. In this study, five protein-encoding genes were used to construct the phylogeny of the carnivorous fungi in the phylum Ascomycota; these fungi prey on nematodes by means of specialized trapping structures such as constricting rings and adhesive traps. Our analysis revealed a definitive pattern of evolutionary development for these trapping structures. Molecular clock calibration based on two fossil records revealed that fungal carnivorism diverged from saprophytism about 419 Mya, which was after the origin of nematodes about 550-600 Mya. Active carnivorism (fungi with constricting rings) and passive carnivorism (fungi with adhesive traps) diverged from each other around 246 Mya, shortly after the occurrence of the Permian-Triassic extinction event about 251.4 Mya. The major adhesive traps evolved around 198-208 Mya, which was within the time frame of the Triassic-Jurassic extinction event about 201.4 Mya. However, no major carnivorous ascomycetes divergence was correlated to the Cretaceous-Tertiary extinction event, which occurred more recently (about 65.5 Mya). Therefore, a causal relationship between mass extinction events and fungal carnivorism evolution is not validated in this study. More evidence including additional fossil records is needed to establish if fungal carnivorism evolution was a response to mass extinction events.

  14. The Fungal Biome of the Oral Cavity.

    Science.gov (United States)

    Chandra, Jyotsna; Retuerto, Mauricio; Mukherjee, Pranab K; Ghannoum, Mahmoud

    2016-01-01

    Organisms residing in the oral cavity (oral microbiota) contribute to health and disease, and influence diseases like gingivitis, periodontitis, and oral candidiasis (the most common oral complication of HIV-infection). These organisms are also associated with cancer and other systemic diseases including upper respiratory infections. There is limited knowledge regarding how oral microbes interact together and influence the host immune system. Characterizing the oral microbial community (oral microbiota) in health and disease represents a critical step in gaining insight into various members of this community. While most of the studies characterizing oral microbiota have focused on bacterial community, there are few encouraging studies characterizing the oral mycobiome (the fungal component of the oral microbiota). Our group recently characterized the oral mycobiome in health and disease focusing on HIV. In this chapter we will describe the methods used by our group for characterization of the oral mycobiome.

  15. Fungal morphogenetic changes inside the mammalian host.

    Science.gov (United States)

    Trevijano-Contador, Nuria; Rueda, Cristina; Zaragoza, Oscar

    2016-09-01

    One of the main features of the majority of pathogenic fungi is the ability to switch between different types of morphological forms. These changes include the transition between cells of different shapes (such as the formation of pseudohyphae and hyphae), or the massive growth of the blastoconidia and formation of titan cells. Morphological changes occur during infection, and there is extensive evidence that they play a key role in processes required for disease, such as adhesion, invasion and dissemination, immune recognition evasion, and phagocytosis avoidance. In the present review, we will provide an overview of how morphological transitions contribute to the development of fungal disease, with special emphasis in two cases: Candida albicans as an example of yeast that switches between blastoconidia and filaments, and Cryptococcus neoformans as an example of a fungus that changes the size without modifying the shape of the cell.

  16. Symbioses of grasses with seedborne fungal endophytes.

    Science.gov (United States)

    Schardl, Christopher L; Leuchtmann, Adrian; Spiering, Martin J

    2004-01-01

    Grasses (family Poaceae) and fungi of the family Clavicipitaceae have a long history of symbiosis ranging in a continuum from mutualisms to antagonisms. This continuum is particularly evident among symbioses involving the fungal genus Epichloe (asexual forms = Neotyphodium spp.). In the more mutualistic symbiota, the epichloe endophytes are vertically transmitted via host seeds, and in the more antagonistic symbiota they spread contagiously and suppress host seed set. The endophytes gain shelter, nutrition, and dissemination via host propagules, and can contribute an array of host fitness enhancements including protection against insect and vertebrate herbivores and root nematodes, enhancements of drought tolerance and nutrient status, and improved growth particularly of the root. In some systems, such as the tall fescue N. coenophialum symbioses, the plant may depend on the endophyte under many natural conditions. Recent advances in endophyte molecular biology promise to shed light on the mechanisms of the symbioses and host benefits.

  17. Fungal endophytes: diversity and functional roles

    Science.gov (United States)

    Rodriguez, R.J.; White, J.F.; Arnold, A.E.; Redman, R.S.

    2009-01-01

    All plants in natural ecosystems appear to be symbiotic with fungal endophytes. This highly diverse group of fungi can have profound impacts on plant communities through increasing fitness by conferring abiotic and biotic stress tolerance, increasing biomass and decreasing water consumption, or decreasing fitness by altering resource allocation. Despite more than 100 yr of research resulting in thousands of journal articles, the ecological significance of these fungi remains poorly characterized. Historically, two endophytic groups (clavicipitaceous (C) and nonclavicipitaceous (NC)) have been discriminated based on phylogeny and life history traits. Here, we show that NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts. Using this framework, we contrast the life histories, interactions with hosts and potential roles in plant ecophysiology of C- and NC-endophytes, and highlight several key questions for future work in endophyte biology.

  18. Fungicide resistance assays for fungal plant pathogens.

    Science.gov (United States)

    Secor, Gary A; Rivera, Viviana V

    2012-01-01

    Fungicide resistance assays are useful to determine if a fungal pathogen has developed resistance to a fungicide used to manage the disease it causes. Laboratory assays are used to determine loss of sensitivity, or resistance, to a fungicide and can explain fungicide failures and for developing successful fungicide recommendations in the field. Laboratory assays for fungicide resistance are conducted by measuring reductions in growth or spore germination of fungi in the presence of fungicide, or by molecular procedures. This chapter describes two techniques for measuring fungicide resistance, using the sugarbeet leaf spot fungus Cercospora beticola as a model for the protocol. Two procedures are described for fungicides from two different classes; growth reduction for triazole (sterol demethylation inhibitor; DMI) fungicides, and inhibition of spore germination for quinone outside inhibitor (QoI) fungicides.

  19. Recent progress in vaccines against fungal diseases.

    Science.gov (United States)

    Cassone, Antonio; Casadevall, Arturo

    2012-08-01

    Diseases caused by fungi are increasingly impacting the health of the human population and now account for a large fraction of infectious disease complications in individuals with impaired immunity or breached tissue defenses. Antifungal therapy is often of limited effectiveness in these patients, resulting into treatment failures, chronic infections and unacceptable rates of mortality, morbidity and their associated costs. Consequently there is a real medical need for new treatments and preventive measures to combat fungal diseases and, toward this goal, safe and efficacious vaccines would constitute major progress. After decades of complacency and neglect of this critically important field of research, remarkable progress has been made in recent years. A number of highly immunogenic and protective vaccine formulations in preclinical setting have been developed, and at least two have undergone Phase 1 clinical trials as preventive and/or therapeutic tools against candidiasis.

  20. [Fungal flora in houses (author's transl)].

    Science.gov (United States)

    Mallea, M; Renard, M; Charpin, J

    1982-01-01

    In certain cases, allergic respiratory phenomena appear to be connected with a particular dwelling place. This observations, if it is not explained by a specific allergen (eg. an animal), raises the possible contribution of domestic moulds. The author shows the results of a study on domestic moulds in 65 houses in the Bouches-du-Rhône by culture on Petri dishes. The species most often detected were Cladosporium, Penicillium, Aspergillus, Alternaria. In some houses identical fungi were found to those in the atmosphere, in others greater numbers were found inside than outside. The study of fungal spores is of great interest; it gives an idea of their numerical importance which can be considerable; in addition besides those fungi which are present in the routine battery of tests, it may show other species that should perhaps be considered in the diagnostic aetiology.

  1. Fungal Glucosylceramide-Specific Camelid Single Domain Antibodies Are Characterized by Broad Spectrum Antifungal Activity

    Directory of Open Access Journals (Sweden)

    Barbara De Coninck

    2017-06-01

    Full Text Available Chemical crop protection is widely used to control plant diseases. However, the adverse effects of pesticide use on human health and environment, resistance development and the impact of regulatory requirements on the crop protection market urges the agrochemical industry to explore innovative and alternative approaches. In that context, we demonstrate here the potential of camelid single domain antibodies (VHHs generated against fungal glucosylceramides (fGlcCer, important pathogenicity factors. To this end, llamas were immunized with purified fGlcCer and a mixture of mycelium and spores of the fungus Botrytis cinerea, one of the most important plant pathogenic fungi. The llama immune repertoire was subsequently cloned in a phage display vector to generate a library with a diversity of at least 108 different clones. This library was incubated with fGlcCer to identify phages that bind to fGlcCer, and VHHs that specifically bound fGlcCer but not mammalian or plant-derived GlcCer were selected. They were shown to inhibit the growth of B. cinerea in vitro, with VHH 41D01 having the highest antifungal activity. Moreover, VHH 41D01 could reduce disease symptoms induced by B. cinerea when sprayed on tomato leaves. Based on all these data, anti-fGlcCer VHHs show the potential to be used as an alternative approach to combat fungal plant diseases.

  2. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

    KAUST Repository

    Kuo, Dwight

    2010-07-23

    Background: Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we compared gene expression patterns across three evolutionarily distant species - Saccharomyces cerevisiae, Candida glabrata and Kluyveromyces lactis - over time following fluconazole exposure. Results: Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity. In support of this hypothesis we find that only Saccharomyces becomes more azole resistant in ergosterol-supplemented media; that this depends on sterol importers Aus1 and Pdr11; and that transgenic expression of sterol importers in Kluyveromyces alleviates its drug sensitivity. Conclusions: We have compared the dynamic transcriptional responses of three diverse yeast species to fluconazole treatment using a novel clustering algorithm. This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity. In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways.

  3. Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters

    Directory of Open Access Journals (Sweden)

    Tina eNetzker

    2015-04-01

    Full Text Available Microorganisms form diverse multispecies communities in various ecosystems. The high abundance of fungal and bacterial species in these consortia results in specific communication between the microorganisms. A key role in this communication is played by secondary metabolites (SMs, which are also called natural products. Recently, it was shown that interspecies ‘talk’ between microorganisms represents a physiological trigger to activate silent gene clusters leading to the formation of novel SMs by the involved species. This review focuses on mixed microbial cultivation, mainly between bacteria and fungi, with a special emphasis on the induced formation of fungal SMs in co-cultures. In addition, the role of chromatin remodeling in the induction is examined, and methodical perspectives for the analysis of natural products are presented. As an example for an intermicrobial interaction elucidated at the molecular level, we discuss the specific interaction between the filamentous fungi Aspergillus nidulans and Aspergillus fumigatus with the soil bacterium Streptomyces rapamycinicus, which provides an excellent model system to enlighten molecular concepts behind regulatory mechanisms and will pave the way to a novel avenue of drug discovery through targeted activation of silent SM gene clusters through co-cultivations of microorganisms.

  4. Integrating large-scale data and RNA technology to protect crops from fungal pathogens

    Directory of Open Access Journals (Sweden)

    Ian Joseph Girard

    2016-05-01

    Full Text Available With a rapidly growing human population it is expected that plant science researchers and the agricultural community will need to increase food productivity using less arable land. This challenge is complicated by fungal pathogens and diseases, many of which can severely impact crop yield. Current measures to control fungal pathogens are either ineffective or have adverse effects on the agricultural enterprise. Thus, developing new strategies through research innovation to protect plants from pathogenic fungi is necessary to overcome these hurdles. RNA sequencing technologies are increasing our understanding of the underlying genes and gene regulatory networks mediating disease outcomes. The application of invigorating next generation sequencing strategies to study plant-pathogen interactions has and will provide unprecedented insight into the complex patterns of gene activity responsible for crop protection. However, questions remain about how biological processes in both the pathogen and the host are specified in space directly at the site of infection and over the infection period. The integration of cutting edge molecular and computational tools will provide plant scientists with the arsenal required to identify genes and molecules that play a role in plant protection. Large scale RNA sequence data can then be used to protect plants by targeting genes essential for pathogen viability in the production of stably transformed lines expressing RNA interference molecules, or through foliar applications of double stranded RNA.

  5. Extremotolerance in fungi: evolution on the edge.

    Science.gov (United States)

    Gostincar, Cene; Grube, Martin; de Hoog, Sybren; Zalar, Polona; Gunde-Cimerman, Nina

    2010-01-01

    Our planet offers many opportunities for life on the edge: high and low temperatures, high salt concentrations, acidic and basic conditions and toxic environments, to name but a few extremes. Recent studies have revealed the diversity of fungi that can occur in stressful environments that are hostile to most eukaryotes. We review these studies here, with the additional purpose of proposing some mechanisms that would allow for the evolutionary adaptation of eukaryotic microbial life under extreme conditions. We focus, in particular, on life in ice and life at high salt concentrations, as there is a surprising similarity between the fungal populations in these two kinds of environments, both of which are characterized by low water activity. We propose steps of evolution of generalist species towards the development of specialists in extreme habitats. We argue that traits present in some fungal groups, such as asexuality, synthesis of melanin-like pigments and a flexible morphology, are preadaptations that facilitate persistence and eventual adaptation to conditions on the ecological edge, as well as biotope switches. These processes are important for understanding the evolution of extremophiles; moreover, they have implications for the emergence of novel fungal pathogens.

  6. Fungal ovicidal activity on Toxocara canis eggs.

    Science.gov (United States)

    De Souza Maia Filho, Fernando; Nunes Vieira, Juliana; Aires Berne, Maria Elisabeth; Stoll, Franciele Elisa; Da Silva Nascente, Patricia; Pötter, Luciana; Brayer Pereira, Daniela Isabel

    2013-01-01

    Visceral toxocariasis is a parasitic zoonosis caused by Toxocara canis. The prevalence of this parasite in dogs, soil contamination and the resistance of eggs increase human exposure to the disease. Moreover, the difficulties of the control measures justify the need for alternative ones. The objective of this study was to evaluate the in vitro ovicidal activity of fungi isolated from soils from public places in the city of Pelotas, Rio Grande do Sul, Brazil, on Toxocara canis. Samples of soil from ten localities were inoculated onto Petri dishes with 2% water-agar (WA) that contained antibiotics, and incubated at 25°C/21 days. Isolated fungi were tested in vitro for ovicidal activity, with five replicates. One mL of an embryonated Toxocara canis egg suspension (10(3) eggs) was poured over the fungal cultures after 10 days of growth. At intervals of 7, 14 and 21 days, 100 eggs were removed from each plaque and evaluated by optical microscopy. Acremonium, Aspergillus, Bipolaris, Fusarium, Gliocladium, Mucor and Trichoderma were isolated from the soil. A significant ovicidal type 3 effect was observed in Trichoderma, Fusarium solani complex and Acremonium. Those isolates from the genus Trichoderma showed their ovicidal effect on the 14th day of fungus-egg interaction. The other fungal genera tested showed a type 2 effect. These results suggest that the use of Trichoderma and Fusarium solani complex in biological control of T. canis is promising; however, further studies should be performed. Copyright © 2012 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  7. Fungal infection risk groups among school children

    Directory of Open Access Journals (Sweden)

    Elżbieta Ejdas

    2014-08-01

    Full Text Available The aim of the study was to evaluate the relationship between ocurrence of fungi in children and living environment (city - countryside, sex, age, diet, undergone diseases therapy with antibiotics and exposure to hospital environment, and to indicate children potentially vulnerable to fungal infections. The material was consisted of swabs collected from the oral cavily, the throat and the nose of healthy children, aged 6-9 and 10-15, from both urban and rural environmens. Candida albicans, the basic aetiological factor in thc majority of mycoses recorded in humans, unquestionably prevailed in the group of the 13 speciec of yeast-like fungi and yeasts isolated. Records of C. glabrata and C. krusei increasing numbers of whose strains show resistance to basic antimycoties, as well as relatively frequent records of Trichosporon beigelii, Saccharomycopsis capsularis and Saccharomyces sp., fungi whose expansiveness and enzymatic activity have been growing, may be considered disconcerting. Vulnerability to fungal infection increases following anti-bacterial antibiotic therapy in the majority of subjects regardless season or age. This is particularly true primarily of the most stable ontocoenosis of the throat. Younger children, on the other hand, are the most vulnerable foUowing infection of the respiratory system. Fungi are likely to colonise the nose in this case. Children living in the countryside who had been ll immediately prior to the collection of the material constitute the highest risk group of the occurrence of fungi in any of the ontocoenoses studied. A greater number of positive inoculations were recorded in these children in comparison to the children from the city. It may be indicative of a more extensive spectrum of natural reservoirs of fungi and the vectors of their transmission in rural areas than those in the city, lower health hygiene and lower immunity or of a more common carriage of fungi among rural children.

  8. Primer sets developed for fungal functional genes reveal shifts in functionality of fungal community in soils

    Directory of Open Access Journals (Sweden)

    Emilia Silja Hannula

    2016-11-01

    Full Text Available Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.

  9. The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research

    Indian Academy of Sciences (India)

    K McCluskey; A Wiest; M Plamann

    2010-03-01

    The Fungal Genetics Stock Center (FGSC) was established in 1960 to ensure that important strains used in early genetics research were available to subsequent generations of fungal geneticists. Originally, only mutant strains were held. At present, any organism that has had its genome sequenced is a genetic system and so the FGSC has added many new organisms. The FGSC is well integrated in its core community and, as research came to depend on cloned genes, vectors and gene libraries, the FGSC included these materials. When the community expanded to include plant and human pathogens, the FGSC adopted these systems as well. Wild isolates from around the world have also proven instrumental in answering important questions. The FGSC holds tremendous diversity of the Neurospora species, which form the core of the collection. The growth in the number of strains distributed illustrates the growth in research on fungi. Because of its position near the centre of the fungal genetics effort, the FGSC is also the first to see trends in research directions. One recent example is the 300% jump in requests for strains of Neurospora crassa carrying a mutation that makes them sensitive to high salt concentration. These strains were seldom requested over many years, but became among our most popular resources following the demonstration of their utility in studying fungicide resistance. This exemplifies why materials need to be preserved without regard to their immediate perceived value and reinforces the need for long-term support for preservation of a broad variety of genetic resources.

  10. Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification.

    Science.gov (United States)

    Baker, Christopher R; Booth, Lauren N; Sorrells, Trevor R; Johnson, Alexander D

    2012-09-28

    We examine how different transcriptional network structures can evolve from an ancestral network. By characterizing how the ancestral mode of gene regulation for genes specific to a-type cells in yeast species evolved from an activating paradigm to a repressing one, we show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel regulatory mode. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species.

  11. Regulatory mark; Marco regulatorio

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2009-10-15

    This chapter is based on a work performed in distinct phases. The first phase consisted in of the analysis regulatory legislation existent in Brazil for the sugar-alcohol sector since the beginning of the X X century. This analysis allowed the identification of non existent points and legal devices related to the studied aspects, and that were considered as problematic for the sector expansion. In the second phase, related treaties and international agreements was studied and possible obstacles for the brazilian bio ethanol exportation for the international market. Initiatives were examined at European Union, United States of America, Caribbean and countries of the sub-Saharan Africa. In this phase, policies were identified related to the incentives and adoption of use of bio fuels added to the gasoline in countries or group of countries considered as key for the consolidation of bio ethanol as a world commodity.

  12. Regulatory considerations for biosimilars

    Directory of Open Access Journals (Sweden)

    Ranjani Nellore

    2010-01-01

    Full Text Available Currently there is considerable interest in the legislative debate around generic biological drugs or "biosimilars" in the EU and US due to the large, lucrative market that it offers to the industry. While some countries have issued a few regulatory guidelines as well as product specific requirements, there is no general consensus as to a single, simple mechanism similar to the bioequivalence determination that leads to approval of generic small molecules all over the world. The inherent complex nature of the molecules, along with complicated manufacturing and analytical techniques to characterize them make it difficult to rely on a single human pharmacokinetic study for assurance of safety and efficacy. In general, the concept of comparability has been used for evaluation of the currently approved "similar" biological where a step by step assessment on the quality, preclinical and clinical aspects is made. In India, the focus is primarily on the availability and affordability of life-saving drugs. In this context every product needs to be evaluated on its own merit irrespective of the innovator brand. The formation of the National Biotechnology Regulatory Authority may provide a step in the right direction for regulation of these complex molecules. However, in order to have an efficient machinery for initial approval and ongoing oversight with a country-specific focus, cooperation with international authorities for granting approvals and continuous risk-benefit review is essential. Several steps are still needed for India to be perceived as a country that leads the world in providing quality biological products.

  13. 75 FR 54210 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of...

    Science.gov (United States)

    2010-09-03

    ...-2010-032] Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of... Transactions August 30, 2010. On June 17, 2010, the Financial Industry Regulatory Authority, Inc....

  14. Resource availability controls fungal diversity across a plant diversity gradient

    Science.gov (United States)

    Waldrop, M.P.; Zak, D.R.; Blackwood, C.B.; Curtis, C.D.; Tilman, D.

    2006-01-01

    Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales. ?? 2006 Blackwell Publishing Ltd/CNRS.

  15. Fungal contamination of poultry litter: a public health problem.

    Science.gov (United States)

    Viegas, C; Carolino, E; Malta-Vacas, J; Sabino, R; Viegas, S; Veríssimo, C

    2012-01-01

    Although numerous studies have been conducted on microbial contaminants associated with various stages related to poultry and meat products processing, only a few reported on fungal contamination of poultry litter. The goals of this study were to (1) characterize litter fungal contamination and (2) report the incidence of keratinophilic and toxigenic fungi presence. Seven fresh and 14 aged litter samples were collected from 7 poultry farms. In addition, 27 air samples of 25 litters were also collected through impaction method, and after laboratory processing and incubation of collected samples, quantitative colony-forming units (CFU/m³) and qualitative results were obtained. Twelve different fungal species were detected in fresh litter and Penicillium was the most frequent genus found (59.9%), followed by Alternaria (17.8%), Cladosporium (7.1%), and Aspergillus (5.7%). With respect to aged litter, 19 different fungal species were detected, with Penicillium sp. the most frequently isolated (42.3%), followed by Scopulariopsis sp. (38.3%), Trichosporon sp. (8.8%), and Aspergillus sp. (5.5%). A significant positive correlation was found between litter fungal contamination (CFU/g) and air fungal contamination (CFU/m³). Litter fungal quantification and species identification have important implications in the evaluation of potential adverse health risks to exposed workers and animals. Spreading of poultry litter in agricultural fields is a potential public health concern, since keratinophilic (Scopulariopsis and Fusarium genus) as well as toxigenic fungi (Aspergillus, Fusarium, and Penicillium genus) were isolated.

  16. The protective role of immunoglobulins in fungal infections and inflammation.

    Science.gov (United States)

    Elluru, Sri Ramulu; Kaveri, Srini V; Bayry, Jagadeesh

    2015-03-01

    Increased incidence of fungal infections in the immunocompromised individuals and fungi-mediated allergy and inflammatory conditions in immunocompetent individuals is a cause of concern. Consequently, there is a need for efficient therapeutic alternatives to treat fungal infections and inflammation. Several studies have demonstrated that antibodies or immunoglobulins have a role in restricting the fungal burden and their clearance. However, based on the data from monoclonal antibodies, it is now evident that the efficacy of antibodies in fungal infections is dependent on epitope specificity, abundance of protective antibodies, and their isotype. Antibodies confer protection against fungal infections by multiple mechanisms that include direct neutralization of fungi and their antigens, inhibition of growth of fungi, modification of gene expression, signaling and lipid metabolism, causing iron starvation, inhibition of polysaccharide release, and biofilm formation. Antibodies promote opsonization of fungi and their phagocytosis, complement activation, and antibody-dependent cell toxicity. Passive administration of specific protective monoclonal antibodies could also prove to be beneficial in drug resistance cases, to reduce the dosage and associated toxic symptoms of anti-fungal drugs. The longer half-life of the antibodies and flexibilities to modify their structure/forms are additional advantages. The clinical data obtained with two monoclonal antibodies should incite interests in translating pre-clinical success into the clinics. The anti-inflammatory and immunoregulatory role of antibodies in fungal inflammation could be exploited by intravenous immunoglobulin or IVIg.

  17. Fungal root endophytes of the carnivorous plant Drosera rotundifolia.

    Science.gov (United States)

    Quilliam, Richard S; Jones, David L

    2010-06-01

    As carnivorous plants acquire substantial amounts of nutrients from the digestion of their prey, mycorrhizal associations are considered to be redundant; however, fungal root endophytes have rarely been examined. As endophytic fungi can have profound impacts on plant communities, we aim to determine the extent of fungal root colonisation of the carnivorous plant Drosera rotundifolia at two points in the growing season (spring and summer). We have used a culture-dependent method to isolate fungal endophytes and diagnostic polymerase chain reaction methods to determine arbuscular mycorrhizal fungi colonisation. All of the roots sampled contained culturable fungal root endophytes; additionally, we have provided molecular evidence that they also host arbuscular mycorrhizal fungi. Colonisation showed seasonal differences: Roots in the spring were colonised by Articulospora tetracladia, two isolates of uncultured ectomycorrhizal fungi, an unidentified species of fungal endophyte and Trichoderma viride, which was present in every plant sampled. In contrast, roots in the summer were colonised by Alatospora acuminata, an uncultured ectomycorrhizal fungus, Penicillium pinophilum and an uncultured fungal clone. Although the functional roles of fungal endophytes of D. rotundifolia are unknown, colonisation may (a) confer abiotic stress tolerance, (b) facilitate the acquisition of scarce nutrients particularly at the beginning of the growing season or (c) play a role in nutrient signalling between root and shoot.

  18. INCIDENCE OF ALLERGIC FUNGAL SINUSITIS AMONG PATIENTS WITH CHRONIC RHINOSINUSITIS

    Directory of Open Access Journals (Sweden)

    Vivek Gupta

    2017-09-01

    Full Text Available BACKGROUND This study aims to evaluate the incidence of allergic fungal sinusitis among patients with chronic rhinosinusitis. Chronic rhinosinusitis (CRS is a widely prevalent condition globally as well as in India. Fungal rhinosinusitis is classified into two subgroups: three invasive forms (acute necrotizing, chronic invasive, granulomatous invasive, and two noninvasive forms (fungal ball and allergic fungal. MATERIALS AND METHODS Patients attending the Department of ENT at Adesh institute of medical science & research, Bathinda (Punjab between Jan 2016 and Dec 2016 one year duration 82 cases were included in this retrospective analysis with features suggestive of chronic rhinosinusitis. Based on clinical, endoscopic and radiological parameters, 82 cases were diagnosed to have rhinosinusitis. In these cases, postoperatively after HPE examination, 16 cases were confirmed to have mycotic infection. RESULTS Out of 16 cases, In Allergic fungal rhino sinusitis(AFRS, Aspergillus flavus (A. flavus was the most common fungus isolated ten cases (71.42%.. In fungal ball, A. flavus was isolated in two cases (14.25% and Aspergillus niger (A. niger was isolated in two cases (14.25%. In invasive fungal rhinosinusitis (IFRS mucormycosis was isolated in two cases (12.5%. CONCLUSION The incidence of ARFS is about 12.2% of chronic rhinosinusitis. The commonest age group is second & third decade.

  19. Neutrophil extracellular traps involvement in corneal fungal infection

    Science.gov (United States)

    Zhao, Yingying; Zhang, Fan; Wan, Ting; Fan, Fangli; Xie, Xin; Lin, Zhenyun

    2016-01-01

    Purpose Neutrophils release neutrophil extracellular traps (NETs) when defending against invading microorganisms. We investigated the existence of NETs in fungal keratitis. Methods Fourteen patients with unilateral fungal keratitis were included. Detailed information about each patient was recorded, including (1) patient history (onset of symptoms and previous therapy), (2) ocular examination findings by slit-lamp biomicroscopy, (3) laboratory findings from direct smear examination and culture of corneal scrapings, (4) NET formation, and (5) treatment strategy and prognosis. Immunofluorescence staining was used to evaluate the existence of NETs on corneal scrapings. The relationship between the quantification of NETs and the clinical character of the fungal keratitis was identified. Results NETs were identified in all 14 patients. Patients with a higher grade of NET formation and fewer fungal hyphae always showed a good treatment response and a short course of infection. NETs were consistently found mixed with fungal hyphae in the corneal scrapings from infected patients. No statistical significance was found between the grade of NETs formed and the course of infection before presentation, and no relationship between the quantification of NETs and the size of the ulcer was found. Conclusions The results suggest that NETs are involved in fungal keratitis. The number of NETs in infected corneas may provide a tool for evaluating the prognosis for fungal keratitis. PMID:27559290

  20. Modulation of host-cell MAPkinase signaling during fungal infection

    Directory of Open Access Journals (Sweden)

    Nir Osherov

    2015-10-01

    Full Text Available Fungal infections contribute substantially to human suffering and mortality. The interaction between fungal pathogens and their host involves the invasion and penetration of the surface epithelium, activation of cells of the innate immune system and the generation of an effective response to block infection. Numerous host-cell signaling pathways are activated during fungal infection. This review will focus on the main fungal pathogens Aspergillus fumigatus, Candida albicans and Cryptococcus neoformans and their ability to activate the host MAP-kinase signaling pathways leading to cytokine secretion, increased cell motility and killing of the pathogen. Both epithelial and innate immune cells specifically recognize fungal antigens and in particular cell surface polysaccharides such as β-glucans and react to them by activating multiple signaling pathways, including those containing MAP-kinase modules. Recent findings suggest that the host response to fungal infection utilizes the MAP-kinase pathway to differentiate between commensal and pathogenic fungi to selectively react only to the pathogenic forms. However, the paucity of relevant publications strongly emphasize that our understanding of host MAP-kinase signaling in response to fungal infection is still at a very early stage. It is clear, based on studies of host MAP-kinase signaling during viral and bacterial infections, that in fungi as well, a wealth of exciting findings await us.