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Sample records for diverse secretome generated

  1. Generational diversity.

    Science.gov (United States)

    Kramer, Linda W

    2010-01-01

    Generational diversity has proven challenges for nurse leaders, and generational values may influence ideas about work and career planning. This article discusses generational gaps, influencing factors and support, and the various generational groups present in today's workplace as well as the consequences of need addressing these issues. The article ends with a discussion of possible solutions.

  2. Managing Generational Diversity

    Science.gov (United States)

    O'Donovan, Eamonn

    2009-01-01

    Many school leaders have explored the issue of diversity when it comes to students, teachers and staff. Their focus typically has been on gender and ethnicity. However, generational diversity, an area of diversity that warrants serious consideration, has received less attention. Generational intelligence is important today for two reasons. First…

  3. Lytic Polysaccharide Monooxygenases - Studies of Fungal Secretomes and Enzyme Properties

    DEFF Research Database (Denmark)

    Nekiunaite, Laura

    degradation, were also identified upstream the LPMO genes, providing evidence for a co-regulatory mechanism of LPMOs and amylolytic hydrolases. The second part of the PhD thesis is focused on understanding the binding properties of LPMOs to starch and starch mimic substrate. It was shown that LPMOs possessing...... to different substrates at the protein level. It could help to design better enzyme cocktails that increase efficiency of biomass degradation. The secretomes of A. nidulans revealed differences in growth and secretion of enzymes, depending on the type and properties of starches. A common characteristic...... conversion as they produce a wide diversity of degrading enzymes. In the first part of this PhD thesis, the secretomes of the well-known fungus Aspergillus nidulans grown on cereal and legume starches were analyzed. Secretomics is a powerful tool to unravel secretion patterns of fungi and their response...

  4. Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display

    Directory of Open Access Journals (Sweden)

    Dragana eGagic

    2016-04-01

    Full Text Available Microbial surface and secreted proteins (the secretome contain a large number of proteins that interact with other microbes, host and/or environment. These proteins are exported by the coordinated activities of the protein secretion machinery present in the cell. A group of phage, called filamentous phage, have the ability to hijack the cellular protein secretion machinery in order to amplify and assemble via a secretion-like process. This ability has been harnessed in the use of filamentous phage of Escherichia coli in biotechnology applications, including screening large libraries of variants for binding to bait of interest, from tissues in vivo to pure proteins or even inorganic substrates. In this review we discuss the roles of secretome proteins in pathogenic and non-pathogenic bacteria and corresponding secretion pathways. We describe the basics of phage display technology and its variants applied to discovery of bacterial proteins that have functions of interest for bacterial colonization and pathogenesis, through filamentous phage display library screening. Published literature also shows that phage display is suitable for secretome protein display as a tool for identification immunogenic peptides and can be used for discovery of vaccine candidates. Secretome selection aided by next-generation sequence analysis can also be used for selective display of the secretome at a microbial community scale, the latter revealing the richness of secretome functions of interest and surprising versatility in filamentous phage display of secretome proteins from large number of Gram-negative as well as Gram-positive bacteria and archaea.

  5. Diversity Generation in Evolving Microbial Populations

    DEFF Research Database (Denmark)

    Markussen, Trine

    as each subpopulation colonized separate geographical niches. This highly complex population diversity was observed to be stably maintained during long-term evolution. Before diversification of the DK1 clone, a regulatory mutation was found to be fixed in the population causing alteration of multiple......Organisms have evolved and diversified since the beginning of life. Although, generation and maintenance of diversity within ecosystems has been a central concern in ecology and evolutionary biology, little is known of the evolutionary processes driving diversification. Especially, diversification...... in relation to chronic infection is a major concern as high population diversity has been predicted to result in survival and persistence of the infecting microbe. Therefore, understanding within-host dynamics and population diversification is necessary for optimal diagnosis and therapeutic treatment. Chronic...

  6. Quantitative iTRAQ-based secretome analysis reveals species-specific and temporal shifts in carbon utilization strategies among manganese(II)-oxidizing Ascomycete fungi

    Energy Technology Data Exchange (ETDEWEB)

    Zeiner, Carolyn A.; Purvine, Samuel O.; Zink, Erika M.; Paša-Tolić, Ljiljana; Chaput, Dominique L.; Wu, Si; Santelli, Cara M.; Hansel, Colleen M.

    2017-09-01

    Fungi generate a wide range of extracellular hydrolytic and oxidative enzymes and reactive metabolites, collectively known as the secretome, that synergistically drive plant litter decomposition in the environment. While secretome studies of model organisms have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or directly compared temporal patterns of enzyme utilization among diverse species. Thus, the mechanisms of carbon (C) degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of iTRAQ proteomics and custom bioinformatic analyses to compare the protein composition of the secretomes of four manganese(II)-oxidizing Ascomycete fungi over a three-week time course. We demonstrate that although the fungi produce a similar suite of extracellular enzymes, they exhibit striking differences in the regulation of these enzymes among species and over time, revealing species-specific and temporal shifts in C utilization strategies as they degrade the same substrate. Specifically, our findings suggest that Paraconiothyrium sporulosum AP3s5-JAC2a and Alternaria alternata SRC1lrK2f employ sequential enzyme secretion patterns concomitant with decreasing resource availability, Stagonospora sp. SRC1lsM3a preferentially degrades proteinaceous substrate before switching to carbohydrates, and Pyrenochaeta sp. DS3sAY3a utilizes primarily peptidases to aggressively attack carbon sources in a concentrated burst. This work highlights the diversity of operative metabolic strategies among cellulose-degrading Ascomycetes and enhances our understanding of their role in C turnover in the environment.

  7. HCSD: the human cancer secretome database

    DEFF Research Database (Denmark)

    Feizi, Amir; Banaei-Esfahani, Amir; Nielsen, Jens

    2015-01-01

    The human cancer secretome database (HCSD) is a comprehensive database for human cancer secretome data. The cancer secretome describes proteins secreted by cancer cells and structuring information about the cancer secretome will enable further analysis of how this is related with tumor biology...... database is limiting the ability to query the increasing community knowledge. We therefore developed the Human Cancer Secretome Database (HCSD) to fulfil this gap. HCSD contains >80 000 measurements for about 7000 nonredundant human proteins collected from up to 35 high-throughput studies on 17 cancer...... types. It has a simple and user friendly query system for basic and advanced search based on gene name, cancer type and data type as the three main query options. The results are visualized in an explicit and interactive manner. An example of a result page includes annotations, cross references, cancer...

  8. A periodic pattern generator for dental diversity

    Directory of Open Access Journals (Sweden)

    Streelman J Todd

    2008-07-01

    Full Text Available Abstract Background Periodic patterning of iterative structures is a fundamental process during embryonic organization and development. Studies have shown how gene networks are employed to pattern butterfly eyespots, fly bristles and vertebrate epithelial appendages such as teeth, feathers, hair and mammary glands. Despite knowledge of how these features are organized, little is known about how diversity in periodic patterning is generated in nature. We address this problem through the molecular analysis of oral jaw dental diversity in Lake Malawi cichlids, where closely related species exhibit from 1 to 20 rows of teeth, with total teeth counts ranging from around 10 to 700. Results We investigate the expression of conserved gene networks (involving bmp2, bmp4, eda, edar, fgf8, pax9, pitx2, runx2, shh and wnt7b known to pattern iterative structures and teeth in other vertebrates. We show that spatiotemporal variation in expression pattern reflects adult morphological diversity among three closely related Malawi cichlid species. Combinatorial epithelial expression of pitx2 and shh appears to govern the competence both of initial tooth sites and future tooth rows. Epithelial wnt7b and mesenchymal eda are expressed in the inter-germ and inter-row regions, and likely regulate the spacing of these shh-positive units. Finally, we used chemical knockdown to demonstrate the fundamental role of hedgehog signalling and initial placode formation in the organization of the periodically patterned cichlid dental programme. Conclusion Coordinated patterns of gene expression differ among Malawi species and prefigure the future-ordered distribution of functional teeth of specific size and spacing. This variation in gene expression among species occurs early in the developmental programme for dental patterning. These data show how a complex multi-rowed vertebrate dentition is organized and how developmental tinkering of conserved gene networks during iterative

  9. The secretome signature of reactive glial cells and its pathological implications.

    Science.gov (United States)

    Jha, Mithilesh Kumar; Seo, Minchul; Kim, Jong-Heon; Kim, Byung-Gyu; Cho, Je-Yoel; Suk, Kyoungho

    2013-11-01

    Glial cells are non-neuronal components of the central nervous system (CNS). They are endowed with diverse functions and are provided with tools to detect their own activities and those of neighboring neurons. Glia and neurons are in continuous reciprocal communication under both physiological and neuropathological conditions, and glia secrete various guidance factors or proteinaceous signals that service vital neuronal-glial interactions in health and disease. Analysis and profiling of glial secretome, especially of microglia and astrocytes, have raised new expectations for the diagnosis and treatment of CNS disorders, and the availability of a catalog of glia-secreted proteins might provide an origin for further research on the complex extracellular signaling mediated by glial cells. Components of the glial secretome play important roles as mediators and modulators of brain structure and function during neuroprotection and neurodegeneration. Therapeutic hypothermia has been acclaimed an effective modulator of brain injury via its substantial effect on the protein expression profiles of glia. Furthermore, emerging proteomic tools and methodologies make feasible the documentation of the reactive glial secretome signature. This review focuses on reactive glial cells and the uniqueness of their secretome during diverse neuropathological conditions. This article is part of a Special Issue entitled: An Updated Secretome. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. The current landscape of the mesenchymal stromal cell secretome: A new paradigm for cell-free regeneration.

    Science.gov (United States)

    Konala, Vijay Bhaskar Reddy; Mamidi, Murali Krishna; Bhonde, Ramesh; Das, Anjan Kumar; Pochampally, Radhika; Pal, Rajarshi

    2016-01-01

    The unique properties of mesenchymal stromal/stem cells (MSCs) to self-renew and their multipotentiality have rendered them attractive to researchers and clinicians. In addition to the differentiation potential, the broad repertoire of secreted trophic factors (cytokines) exhibiting diverse functions such as immunomodulation, anti-inflammatory activity, angiogenesis and anti-apoptotic, commonly referred to as the MSC secretome, has gained immense attention in the past few years. There is enough evidence to show that the one important pathway by which MSCs participate in tissue repair and regeneration is through its secretome. Concurrently, a large body of MSC research has focused on characterization of the MSC secretome; this includes both soluble factors and factors released in extracellular vesicles, for example, exosomes and microvesicles. This review provides an overview of our current understanding of the MSC secretome with respect to their potential clinical applications. Copyright © 2015 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

  11. Three Principles of Diversity-Generating Biosynthesis.

    Science.gov (United States)

    Gu, Wenjia; Schmidt, Eric W

    2017-10-17

    Natural products are significant therapeutic agents and valuable drug leads. This is likely owing to their three-dimensional structural complexity, which enables them to form complex interactions with biological targets. Enzymes from natural product biosynthetic pathways show great potential to generate natural product-like compounds and libraries. Many challenges still remain in biosynthesis, such as how to rationally synthesize small molecules with novel structures and how to generate maximum chemical diversity. In this Account, we describe recent advances from our laboratory in the synthesis of natural product-like libraries using natural biosynthetic machinery. Our work has focused on the pat and tru biosynthetic pathways to patellamides, trunkamide, and related compounds from cyanobacterial symbionts in marine tunicates. These belong to the cyanobactin class of natural products, which are part of the larger group of ribosomally synthesized and post-translationally modified peptides (RiPPs). These results have enabled the synthesis of rationally designed small molecules and libraries covering more than 1 million estimated derivatives. Because the RiPPs are translated on the ribosome and then enzymatically modified, they are highly compatible with recombinant technologies. This is important because it means that the resulting natural products, their derivatives, and wholly new compounds can be synthesized using the tools of genetic engineering. The RiPPs also represent possibly the most widespread group of bioactive natural products, although this is in part because of the broad definition of what constitutes a RiPP. In addition, the underlying ideas may form the basis for broad-substrate biosynthetic pathways beyond the RiPPs. For example, some of the ideas about kinetic ordering of broad substrate pathways may apply to polyketide or nonribosomal peptide biosynthesis as well. While making these products, we have sought to understand what makes biosynthetic

  12. Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts

    Directory of Open Access Journals (Sweden)

    Normand Philippe

    2008-01-01

    Full Text Available Abstract Background Frankia sp. strains, the nitrogen-fixing facultative endosymbionts of actinorhizal plants, have long been proposed to secrete hydrolytic enzymes such as cellulases, pectinases, and proteases that may contribute to plant root penetration and formation of symbiotic root nodules. These or other secreted proteins might logically be involved in the as yet unknown molecular interactions between Frankia and their host plants. We compared the genome-based secretomes of three Frankia strains representing diverse host specificities. Signal peptide detection algorithms were used to predict the individual secretomes of each strain, and the set of secreted proteins shared among the strains, termed the core Frankia secretome. Proteins in the core secretome may be involved in the actinorhizal symbiosis. Results The Frankia genomes have conserved Sec (general secretory and Tat (twin arginine translocase secretion systems. The potential secretome of each Frankia strain comprised 4–5% of the total proteome, a lower percentage than that found in the genomes of other actinobacteria, legume endosymbionts, and plant pathogens. Hydrolytic enzymes made up only a small fraction of the total number of predicted secreted proteins in each strain. Surprisingly, polysaccharide-degrading enzymes were few in number, especially in strain CcI3, with more esterolytic, lipolytic and proteolytic enzymes having signal peptides. A total of 161 orthologous proteins belong to the core Frankia secretome. Of these, 52 also lack homologs in closely related actinobacteria, and are termed "Frankia-specific." The genes encoding these conserved secreted proteins are often clustered near secretion machinery genes. Conclusion The predicted secretomes of Frankia sp. are relatively small and include few hydrolases, which could reflect adaptation to a symbiotic lifestyle. There are no well-conserved secreted polysaccharide-degrading enzymes present in all three Frankia

  13. Cortical development: the art of generating cell diversity

    OpenAIRE

    Götz, Magdalena; Sommer, Lukas

    2005-01-01

    The fascinating question of how the enormous diversity of neuronal and glial cells in the cerebral cortex is generated during development was recently discussed at a meeting on cortical development and stem cells in Greece. What emerged from this meeting is an equally fascinating answer, namely that precursor diversity at rather early stages of development anticipates later cell type diversity.

  14. Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi.

    Science.gov (United States)

    Zeiner, Carolyn A; Purvine, Samuel O; Zink, Erika M; Paša-Tolić, Ljiljana; Chaput, Dominique L; Haridas, Sajeet; Wu, Si; LaButti, Kurt; Grigoriev, Igor V; Henrissat, Bernard; Santelli, Cara M; Hansel, Colleen M

    2016-01-01

    Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.

  15. Comparative Analysis of Secretome Profiles of Manganese(II-Oxidizing Ascomycete Fungi.

    Directory of Open Access Journals (Sweden)

    Carolyn A Zeiner

    Full Text Available Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a. We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.

  16. Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Zeiner, Carolyn A.; Purvine, Samuel O.; Zink, Erika M.; Paša-Tolić, Ljiljana; Chaput, Dominique L.; Haridas, Sajeet; Wu, Si; LaButti, Kurt; Grigoriev, Igor V.; Henrissat, Bernard; Santelli, Cara M.; Hansel, Colleen M.; Pöggeler, Stefanie

    2016-07-19

    Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.

  17. Next-generation sequencing for investigating the diversity of ...

    African Journals Online (AJOL)

    pathogenic bacteria in water. Recent technological advances in next-generation sequencing (NGS) offer better prospects for detection of pathogenic microorganisms and investigating their diversity [11]. NGS can quickly generate huge amounts of DNA reads, and the technique is affordable [12]. In this study, the pathogens ...

  18. Generational diversity: what nurse managers need to know.

    Science.gov (United States)

    Hendricks, Joyce M; Cope, Vicki C

    2013-03-01

    This article presents a discussion of generational differences and their impact on the nursing workforce and how this impact affects the work environment. The global nursing workforce represents four generations of nurses. This generational diversity frames attitudes, beliefs, work habits and expectations associated with the role of the nurse in the provision of care and in the way the nurse manages their day-to-day activities. An electronic search of MEDLINE, PubMed and Cinahl databases was performed using the words generational diversity, nurse managers and workforce. The search was limited to 2000-2012. Generational differences present challenges to contemporary nurse managers working in a healthcare environment which is complex and dynamic, in terms of managing nurses who think and behave in a different way because of disparate core personal and generational values, namely, the three Cs of communication, commitment and compensation. An acceptance of generational diversity in the workplace allows a richer scope for practice as the experiences and knowledge of each generation in the nursing environment creates an environment of acceptance and harmony facilitating retention of nurses. Acknowledgement of generational characteristics provides the nurse manager with strategies which focus on mentoring and motivation; communication, the increased use of technology and the ethics of nursing, to bridge the gap between generations of nurses and to increase nursing workforce cohesion. © 2012 Blackwell Publishing Ltd.

  19. Three-Dimensional Bioprinting Nanotechnologies towards Clinical Application of Stem Cells and Their Secretome in Salivary Gland Regeneration

    Directory of Open Access Journals (Sweden)

    Joao N. Ferreira

    2016-01-01

    Full Text Available Salivary gland (SG functional damage and severe dry mouth (or xerostomia are commonly observed in a wide range of medical conditions from autoimmune to metabolic disorders as well as after radiotherapy to treat specific head and neck cancers. No effective therapy has been developed to completely restore the SG functional damage on the long-term and reverse the poor quality of life of xerostomia patients. Cell- and secretome-based strategies are currently being tested in vitro and in vivo for the repair and/or regeneration of the damaged SG using (1 epithelial SG stem/progenitor cells from salispheres or explant cultures as well as (2 nonepithelial stem cell types and/or their bioactive secretome. These strategies will be the focus of our review. Herein, innovative 3D bioprinting nanotechnologies for the generation of organotypic cultures and SG organoids/mini-glands will also be discussed. These bioprinting technologies will allow researchers to analyze the secretome components and extracellular matrix production, as well as their biofunctional effects in 3D mini-glands ex vivo. Improving our understanding of the SG secretome is critical to develop effective secretome-based therapies towards the regeneration and/or repair of all SG compartments for proper restoration of saliva secretion and flow into the oral cavity.

  20. Assessment of the genetic diversity in five generations of a ...

    African Journals Online (AJOL)

    SERVER

    time, and genetic similarity could reach closer to 100% at 18-19 generation of this line. Key words: Litopenaeus vannamei, genetic diversity, genetic drift, ... of exotic pathogens (Batalha et al., 2002). Apart from the remarkable development of shrimp culture in ..... distance among the stocks (Table 4). y = 0.2948Ln(x) + 0.1385.

  1. Harnessing the Helminth Secretome for Therapeutic Immunomodulators

    Science.gov (United States)

    Anandarajah, Emmanuela M.; Meissner, Kamila A.; Brattig, Norbert; Liebau, Eva

    2014-01-01

    Helminths are the largest and most complex pathogens to invade and live within the human body. Since they are not able to outpace the immune system by rapid antigen variation or faster cell division or retreat into protective niches not accessible to immune effector mechanisms, their long-term survival depends on influencing and regulating the immune responses away from the mode of action most damaging to them. Immunologists have focused on the excretory and secretory products that are released by the helminths, since they can change the host environment by modulating the immune system. Here we give a brief overview of the helminth-associated immune response and the currently available helminth secretome data. We introduce some major secretome-derived immunomodulatory molecules and describe their potential mode of action. Finally, the applicability of helminth-derived therapeutic proteins in the treatment of allergic and autoimmune inflammatory disease is discussed. PMID:25133189

  2. Harnessing the Helminth Secretome for Therapeutic Immunomodulators

    Directory of Open Access Journals (Sweden)

    Dana Ditgen

    2014-01-01

    Full Text Available Helminths are the largest and most complex pathogens to invade and live within the human body. Since they are not able to outpace the immune system by rapid antigen variation or faster cell division or retreat into protective niches not accessible to immune effector mechanisms, their long-term survival depends on influencing and regulating the immune responses away from the mode of action most damaging to them. Immunologists have focused on the excretory and secretory products that are released by the helminths, since they can change the host environment by modulating the immune system. Here we give a brief overview of the helminth-associated immune response and the currently available helminth secretome data. We introduce some major secretome-derived immunomodulatory molecules and describe their potential mode of action. Finally, the applicability of helminth-derived therapeutic proteins in the treatment of allergic and autoimmune inflammatory disease is discussed.

  3. Comparative analysis of the secretomes of Schizophyllum commune and other wood-decay basidiomycetes during solid-state fermentation reveals its unique lignocellulose-degrading enzyme system.

    Science.gov (United States)

    Zhu, Ning; Liu, Jiawen; Yang, Jinshui; Lin, Yujian; Yang, Yi; Ji, Lei; Li, Meng; Yuan, Hongli

    2016-01-01

    The genome of Schizophyllum commune encodes a diverse repertoire of degradative enzymes for plant cell wall breakdown. Recent comparative genomics study suggests that this wood decayer likely has a mode of biodegradation distinct from the well-established white-rot/brown-rot models. However, much about the extracellular enzyme system secreted by S. commune during lignocellulose deconstruction remains unknown and the underlying mechanism is poorly understood. In this study, extracellular proteins of S. commune colonizing Jerusalem artichoke stalk were analyzed and compared with those of two white-rot fungi Phanerochaete chrysosporium and Ceriporiopsis subvermispora and a brown-rot fungus Gloeophyllum trabeum. Under solid-state fermentation (SSF) conditions, S. commune displayed considerably higher levels of hydrolytic enzyme activities in comparison with those of P. chrysosporium, C. subvermispora and G. trabeum. During biodegradation process, this fungus modified the lignin polymer in a way which was consistent with a hydroxyl radical attack, similar to that of G. trabeum. The crude enzyme cocktail derived from S. commune demonstrated superior performance over a commercial enzyme preparation from Trichoderma longibrachiatum in the hydrolysis of pretreated lignocellulosic biomass at low enzyme loadings. Secretomic analysis revealed that compared with three other fungi, this species produced a higher diversity of carbohydrate-degrading enzymes, especially hemicellulases and pectinases acting on polysaccharide backbones and side chains, and a larger set of enzymes potentially supporting the generation of hydroxyl radicals. In addition, multiple non-hydrolytic proteins implicated in enhancing polysaccharide accessibility were identified in the S. commune secretome, including lytic polysaccharide monooxygenases (LPMOs) and expansin-like proteins. Plant lignocellulose degradation by S. commune involves a hydroxyl radical-mediated mechanism for lignocellulose modification

  4. Control of Secreted Protein Gene Expression and the Mammalian Secretome by the Metabolic Regulator PGC-1α.

    Science.gov (United States)

    Minsky, Neri; Roeder, Robert G

    2017-01-06

    Secreted proteins serve pivotal roles in the development of multicellular organisms, acting as structural matrix, extracellular enzymes, and signal molecules. However, how the secretome is regulated remains incompletely understood. Here we demonstrate, unexpectedly, that peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α), a critical transcriptional co-activator of metabolic gene expression, functions to down-regulate the expression of diverse genes encoding secreted molecules and extracellular matrix components to modulate the secretome. Using cell lines, primary cells, and mice, we show that both endogenous and exogenous PGC-1α down-regulate the expression of numerous genes encoding secreted molecules. Mechanistically, results obtained using mRNA stability measurements as well as intronic RNA expression analysis are consistent with a transcriptional effect of PGC-1α on the expression of genes encoding secreted proteins. Interestingly, PGC-1α requires the central heat shock response regulator heat shock factor protein 1 (HSF1) to affect some of its targets, and both factors co-reside on several target genes encoding secreted molecules in cells. Finally, using a mass spectrometric analysis of secreted proteins, we demonstrate that PGC-1α modulates the secretome of mouse embryonic fibroblasts. Our results define a link between a key pathway controlling metabolic regulation and the regulation of the mammalian secretome. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Secretome Signature of Invasive Glioblastoma Multiforme

    OpenAIRE

    Formolo, Catherine A.; Williams, Russell; Gordish-Dressman, Heather; MacDonald, Tobey J.; Lee, Norman H.; Hathout, Yetrib

    2011-01-01

    The incurability of malignant glioblastomas is mainly attributed to their highly invasive nature coupled with resistance to chemo- and radiation therapy. Because invasiveness is partially dictated by the proteins these tumors secrete we used SILAC to characterize the secretomes of four glioblastoma cell lines (LN18, T98, U118 and U87). Although U87 and U118 cells both secreted high levels of well-known invasion promoting proteins, a Matrigel invasion assay showed U87 cells to be eight times m...

  6. Next generation sequencing technologies: tool to study avian virus diversity.

    Science.gov (United States)

    Kapgate, S S; Barbuddhe, S B; Kumanan, K

    2015-03-01

    Increased globalisation, climatic changes and wildlife-livestock interface led to emergence of novel viral pathogens or zoonoses that have become serious concern to avian, animal and human health. High biodiversity and bird migration facilitate spread of the pathogen and provide reservoirs for emerging infectious diseases. Current classical diagnostic methods designed to be virus-specific or aim to be limited to group of viral agents, hinder identifying of novel viruses or viral variants. Recently developed approaches of next-generation sequencing (NGS) provide culture-independent methods that are useful for understanding viral diversity and discovery of novel virus, thereby enabling a better diagnosis and disease control. This review discusses the different possible steps of a NGS study utilizing sequence-independent amplification, high-throughput sequencing and bioinformatics approaches to identify novel avian viruses and their diversity. NGS lead to the identification of a wide range of new viruses such as picobirnavirus, picornavirus, orthoreovirus and avian gamma coronavirus associated with fulminating disease in guinea fowl and is also used in describing viral diversity among avian species. The review also briefly discusses areas of viral-host interaction and disease associated causalities with newly identified avian viruses.

  7. Next generation sequencing reveals the hidden diversity of zooplankton assemblages.

    Directory of Open Access Journals (Sweden)

    Penelope K Lindeque

    Full Text Available BACKGROUND: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. METHODOLOGY/PRINCIPLE FINDINGS: Plankton net hauls (200 µm were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. CONCLUSIONS: Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may

  8. Secretome signature of invasive glioblastoma multiforme.

    Science.gov (United States)

    Formolo, Catherine A; Williams, Russell; Gordish-Dressman, Heather; MacDonald, Tobey J; Lee, Norman H; Hathout, Yetrib

    2011-07-01

    The incurability of malignant glioblastomas is mainly attributed to their highly invasive nature coupled with resistance to chemo- and radiation therapy. Because invasiveness is partially dictated by the proteins these tumors secrete we used SILAC to characterize the secretomes of four glioblastoma cell lines (LN18, T98, U118 and U87). Although U87 and U118 cells both secreted high levels of well-known invasion promoting proteins, a Matrigel invasion assay showed U87 cells to be eight times more invasive than U118 cells, suggesting that additional proteins secreted by U87 cells may contribute to the highly invasive phenotype. Indeed, we identified a number of proteins highly or exclusively expressed by U87 cells as compared to the less invasive cell lines. The most striking of these include ADAM9, ADAM10, cathepsin B, cathepsin L1, osteopontin, neuropilin-1, semaphorin-7A, suprabasin, and chitinase-3-like protein 1. U87 cells also expressed significantly low levels of some cell adhesion proteins such as periostin and EMILIN-1. Correlation of secretome profiles with relative levels of invasiveness using Pavlidis template matching further indicated potential roles for these proteins in U87 glioblastoma invasion. Antibody inhibition of CH3L1 reduced U87 cell invasiveness by 30%.

  9. Plasmodium falciparum secretome in erythrocyte and beyond

    Directory of Open Access Journals (Sweden)

    Rani eSoni

    2016-02-01

    Full Text Available Plasmodium falciparum is the causative agent of deadly malaria disease. It is an intracellular eukaryote and completes its multi-stage life cycle spanning the two hosts viz, mosquito and human. In order to habituate within host environment, parasite conform several strategies to evade host immune responses such as surface antigen polymorphism or modulation of host immune system and it is mediated by secretion of proteins from parasite to the host erythrocyte and beyond, collectively known as, malaria secretome. In this review, we will discuss about the deployment of parasitic secretory protein in mechanism implicated for immune evasion, protein trafficking, providing virulence, changing permeability and cyto-adherence of infected erythrocyte. We will be covering the possibilities of developing malaria secretome as a drug/vaccine target. This gathered information will be worthwhile in depicting a well-organized picture for host-pathogen interplay during the malaria infection and may also provide some clues for development of novel anti-malarial therapies.

  10. Motor neurons and the generation of spinal motor neurons diversity

    Directory of Open Access Journals (Sweden)

    Nicolas eStifani

    2014-10-01

    Full Text Available Motor neurons (MNs are neuronal cells located in the central nervous system (CNS controlling a variety of downstream targets. This function infers the existence of MN subtypes matching the identity of the targets they innervate. To illustrate the mechanism involved in the generation of cellular diversity and the acquisition of specific identity, this review will focus on spinal motor neurons (SpMNs that have been the core of significant work and discoveries during the last decades. SpMNs are responsible for the contraction of effector muscles in the periphery. Humans possess more than 500 different skeletal muscles capable to work in a precise time and space coordination to generate complex movements such as walking or grasping. To ensure such refined coordination, SpMNs must retain the identity of the muscle they innervate.Within the last two decades, scientists around the world have produced considerable efforts to elucidate several critical steps of SpMNs differentiation. During development, SpMNs emerge from dividing progenitor cells located in the medial portion of the ventral neural tube. MN identities are established by patterning cues working in cooperation with intrinsic sets of transcription factors. As the embryo develop, MNs further differentiate in a stepwise manner to form compact anatomical groups termed pools connecting to a unique muscle target. MN pools are not homogeneous and comprise subtypes according to the muscle fibers they innervate.This article aims to provide a global view of MN classification as well as an up-to-date review of the molecular mechanisms involved in the generation of SpMN diversity. Remaining conundrums will be discussed since a complete understanding of those mechanisms constitutes the foundation required for the elaboration of prospective MN regeneration therapies.

  11. Generation of diversity in Streptococcus mutans genes demonstrated by MLST.

    Directory of Open Access Journals (Sweden)

    Thuy Do

    2010-02-01

    Full Text Available Streptococcus mutans, consisting of serotypes c, e, f and k, is an oral aciduric organism associated with the initiation and progression of dental caries. A total of 135 independent Streptococcus mutans strains from caries-free and caries-active subjects isolated from various geographical locations were examined in two versions of an MLST scheme consisting of either 6 housekeeping genes [accC (acetyl-CoA carboxylase biotin carboxylase subunit, gki (glucokinase, lepA (GTP-binding protein, recP (transketolase, sodA (superoxide dismutase, and tyrS (tyrosyl-tRNA synthetase] or the housekeeping genes supplemented with 2 extracellular putative virulence genes [gtfB (glucosyltransferase B and spaP (surface protein antigen I/II] to increase sequence type diversity. The number of alleles found varied between 20 (lepA and 37 (spaP. Overall, 121 sequence types (STs were defined using the housekeeping genes alone and 122 with all genes. However pi, nucleotide diversity per site, was low for all loci being in the range 0.019-0.007. The virulence genes exhibited the greatest nucleotide diversity and the recombination/mutation ratio was 0.67 [95% confidence interval 0.3-1.15] compared to 8.3 [95% confidence interval 5.0-14.5] for the 6 concatenated housekeeping genes alone. The ML trees generated for individual MLST loci were significantly incongruent and not significantly different from random trees. Analysis using ClonalFrame indicated that the majority of isolates were singletons and no evidence for a clonal structure or evidence to support serotype c strains as the ancestral S. mutans strain was apparent. There was also no evidence of a geographical distribution of individual isolates or that particular isolate clusters were associated with caries. The overall low sequence diversity suggests that S. mutans is a newly emerged species which has not accumulated large numbers of mutations but those that have occurred have been shuffled as a consequence of

  12. Fungal Secretome Analysis via PepSAVI-MS: Identification of the Bioactive Peptide KP4 from Ustilago maydis

    Science.gov (United States)

    Kirkpatrick, Christine L.; Parsley, Nicole C.; Bartges, Tessa E.; Cooke, Madeline E.; Evans, Wilaysha S.; Heil, Lilian R.; Smith, Thomas J.; Hicks, Leslie M.

    2018-02-01

    Fungal secondary metabolites represent a rich and largely untapped source for bioactive molecules, including peptides with substantial structural diversity and pharmacological potential. As methods proceed to take a deep dive into fungal genomes, complimentary methods to identify bioactive components are required to keep pace with the expanding fungal repertoire. We developed PepSAVI-MS to expedite the search for natural product bioactive peptides and herein demonstrate proof-of-principle applicability of the pipeline for the discovery of bioactive peptides from fungal secretomes via identification of the antifungal killer toxin KP4 from Ustilago maydis P4. This work opens the door to investigating microbial secretomes with a new lens, and could have broad applications across human health, agriculture, and food safety. [Figure not available: see fulltext.

  13. Secretome-based Manganese(II) Oxidation by Filamentous Ascomycete Fungi

    Science.gov (United States)

    Zeiner, C. A.; Purvine, S.; Zink, E.; Paša-Tolić, L.; Chaput, D.; Wu, S.; Santelli, C. M.; Hansel, C. M.

    2017-12-01

    Manganese (Mn) oxides are among the strongest oxidants in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and Mn peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Through a combination of chemical and in-gel assays, bulk mass spectrometry, and iTRAQ proteomics, we demonstrate enzymatic Mn(II) oxidation in the secretomes of three phylogenetically diverse Ascomycetes that were isolated from Mn-laden sediments. Candidate Mn(II)-oxidizing enzymes were species-specific and included bilirubin oxidase and tyrosinase in Stagonospora sp. SRC1lsM3a, GMC oxidoreductase in Paraconiothyrium sporulosum AP3s5-JAC2a, and FAD-binding oxidoreductases in Pyrenochaeta sp. DS3sAY3a. These findings were supported by full proteomic characterization of the secretomes, which revealed a lack of Mn, lignin, and versatile peroxidases in these Ascomycetes but a substantially higher proportion of LMCOs and GMC oxidoreductases compared to wood-rot Basidiomycetes. We also identified the potential for indirect enzymatic Mn(II) oxidation by hydroxyl radical, as the secretomes were rich in diverse lignocellulose-degrading enzymes that could participate in Fenton chemistry. A link between Mn(II) oxidation and carbon oxidation analogous to white-rot Basidiomycetes remains unknown in these Ascomycetes. Interestingly, growth rates on rich medium were unaffected by the presence of Mn(II), and the production of Mn(II)-oxidizing proteins in the secretome was constitutive and not inducible by Mn(II). Thus, no physiological benefit of Mn(II) oxidation in these Ascomycetes has yet been identified, and Mn(II) oxidation appears to be a side reaction. Future work will explore the lignin-degrading capacity of

  14. Construction and Screening of a Lentiviral Secretome Library.

    Science.gov (United States)

    Liu, Tao; Jia, Panpan; Ma, Huailei; Reed, Sean A; Luo, Xiaozhou; Larman, H Benjamin; Schultz, Peter G

    2017-06-22

    Over 2,000 human proteins are predicted to be secreted, but the biological function of the many of these proteins is still unknown. Moreover, a number of these proteins may act as new therapeutic agents or be targets for the development of therapeutic antibodies. To further explore the extracellular proteome, we have developed a secretome-enriched open reading frame (ORF) library that can be readily screened for autocrine activity in cell-based phenotypic or reporter assays. Next-generation sequencing (NGS) and database analysis predict that the library contains approximately 900 ORFs encoding known secreted proteins (accounting for 77.8% of the library), as well as genes encoding potentially unknown secreted proteins. In a proof-of-principle study, human TF-1 cells were screened for proliferative factors, and the known cytokine GMCSF was identified as a dominant hit. This library offers a relatively low-cost and straightforward approach for functional autocrine screens of secreted proteins. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Comparative secretome analysis of rat stomach under different nutritional status

    Directory of Open Access Journals (Sweden)

    Lucia L. Senin

    2015-06-01

    Full Text Available The fact that gastric surgery is at the moment the most effective treatment to fight against obesity highlights the relevance of gastric derived proteins as potential targets to treat this pathology. Taking advantage of a previously established gastric explant model for endocrine studies, the proteomic analysis of gastric secretome was performed. To validate this gastric explant system for proteomic analysis, the identification of ghrelin, a classical gastric derived peptide, was performed by MS. In addition, the differential analysis of gastric secretomes under differential nutritional status (control feeding vs fasting vs re-feeding was performed. The MS identified proteins are showed in the present manuscript. The data supplied in this article is related to the research article entitled “Comparative secretome analysis of rat stomach under different nutritional status” [1].

  16. Proteomic Studies of Cholangiocarcinoma and Hepatocellular Carcinoma Cell Secretomes

    OpenAIRE

    Srisomsap, Chantragan; Sawangareetrakul, Phannee; Subhasitanont, Pantipa; Chokchaichamnankit, Daranee; Chiablaem, Khajeelak; Bhudhisawasdi, Vaharabhongsa; Wongkham, Sopit; Svasti, Jisnuson

    2009-01-01

    Cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC) occur with relatively high incidence in Thailand. The secretome, proteins secreted from cancer cells, are potentially useful as biomarkers of the diseases. Proteomic analysis was performed on the secreted proteins of cholangiocarcinoma (HuCCA-1) and hepatocellular carcinoma (HCC-S102, HepG2, SK-Hep-1, and Alexander) cell lines. The secretomes of the five cancer cell lines were analyzed by SDS-PAGE combined with LC/MS/MS. Sixty-eight...

  17. Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses.

    Directory of Open Access Journals (Sweden)

    Sandra Renier

    Full Text Available Genome-scale prediction of subcellular localization (SCL is not only useful for inferring protein function but also for supporting proteomic data. In line with the secretome concept, a rational and original analytical strategy mimicking the secretion steps that determine ultimate SCL was developed for Gram-positive (monoderm bacteria. Based on the biology of protein secretion, a flowchart and decision trees were designed considering (i membrane targeting, (ii protein secretion systems, (iii membrane retention, and (iv cell-wall retention by domains or post-translocational modifications, as well as (v incorporation to cell-surface supramolecular structures. Using Listeria monocytogenes as a case study, results were compared with known data set from SCL predictors and experimental proteomics. While in good agreement with experimental extracytoplasmic fractions, the secretomics-based method outperforms other genomic analyses, which were simply not intended to be as inclusive. Compared to all other localization predictors, this method does not only supply a static snapshot of protein SCL but also offers the full picture of the secretion process dynamics: (i the protein routing is detailed, (ii the number of distinct SCL and protein categories is comprehensive, (iii the description of protein type and topology is provided, (iv the SCL is unambiguously differentiated from the protein category, and (v the multiple SCL and protein category are fully considered. In that sense, the secretomics-based method is much more than a SCL predictor. Besides a major step forward in genomics and proteomics of protein secretion, the secretomics-based method appears as a strategy of choice to generate in silico hypotheses for experimental testing.

  18. Mass spectrometric analysis of the secretome of Candida albicans

    NARCIS (Netherlands)

    Sorgo, A.G.; Heilmann, C.J.; Dekker, H.L.; Brul, S.; de Koster, C.G.; Klis, F.M.

    2010-01-01

    The pathogenic fungus Candida albicans secretes a considerable number of hydrolases and other proteins. In-depth studies of the C. albicans secretome could thus provide new candidates for diagnostic markers and vaccine development. We compared various growth conditions differing in pH, temperature

  19. Proteomic techniques for characterisation of mesenchymal stem cell secretome.

    Czech Academy of Sciences Publication Activity Database

    Kupcová Skalníková, Helena

    2013-01-01

    Roč. 95, č. 12 (2013), s. 2196-2211 ISSN 0300-9084 R&D Projects: GA MŠk ED2.1.00/03.0124; GA TA ČR TA01011466 Institutional support: RVO:67985904 Keywords : mesenchymal stem cells * secretome * exosome * conditioned medium * proteomics Subject RIV: CE - Biochemistry Impact factor: 3.123, year: 2013

  20. Lignin depolymerization by fungal secretomes and a microbial sink

    Energy Technology Data Exchange (ETDEWEB)

    Salvachúa, Davinia; Katahira, Rui; Cleveland, Nicholas S.; Khanna, Payal; Resch, Michael G.; Black, Brenna A.; Purvine, Samuel O.; Zink, Erika M.; Prieto, Alicia; Martínez, María J.; Martínez, Angel T.; Simmons, Blake A.; Gladden, John M.; Beckham, Gregg T.

    2016-08-25

    In Nature, powerful oxidative enzymes secreted by white rot fungi and some bacteria catalyze lignin depolymerization and some microbes are able to catabolize the resulting aromatic compounds as carbon and energy sources. Taken together, these two processes offer a potential route for microbial valorization of lignin. However, many challenges remain in realizing this concept, including that oxidative enzymes responsible for lignin depolymerization also catalyze polymerization of low molecular weight (LMW) lignin. Here, multiple basidiomycete secretomes were screened for ligninolytic enzyme activities in the presence of a residual lignin solid stream from a corn stover biorefinery, dubbed DMR-EH (Deacetylation, Mechanical Refining, and Enzymatic Hydrolysis) lignin. Two selected fungal secretomes, with high levels of laccases and peroxidases, were utilized for DMR-EH lignin depolymerization assays. The secretome from Pleurotus eryngii, which exhibited the highest laccase activity, reduced the lignin average molecular weight by 63% and 75% at pH 7 compared to the Mw of the control treated at the same conditions and the initial DMR-EH lignin, respectively, and was applied in further depolymerization assays as a function of time. As repolymerization was observed after 3 days of incubation, an aromatic-catabolic microbe (Pseudomonas putida KT2440) was incubated with the fungal secretome and DMR-EH lignin. These experiments demonstrated that the presence of the bacterium enhances lignin depolymerization, likely due to bacterial catabolism of LMW lignin, which may partially prevent repolymerization. In addition, proteomics was also applied to the P. eryngii secretome to identify the enzymes present in the fungal cocktail utilized for the depolymerization assays, which highlighted a significant number of glucose/ methanol/choline (GMC) oxidoreductases and laccases. Overall, this study demonstrates that ligninolytic enzymes can be used to partially depolymerize a solid, high

  1. Assessment of the genetic diversity in five generations of a ...

    African Journals Online (AJOL)

    Genetic variation among and within five generations of an inbred commercial captive line of Litopenaeus vannamei and genetic distance among them were evaluated by random amplified polymorphic DNA (RAPD), using descriptive and genetic similarity analyses for dominant markers at single- and multi-populational level ...

  2. Gene regulation networks generate diverse pigmentation patterns in plants.

    Science.gov (United States)

    Albert, Nick W; Davies, Kevin M; Schwinn, Kathy E

    2014-01-01

    The diversity of pigmentation patterns observed in plants occurs due to the spatial distribution and accumulation of colored compounds, which may also be associated with structural changes to the tissue. Anthocyanins are flavonoids that provide red/purple/blue coloration to plants, often forming complex patterns such as spots, stripes, and vein-associated pigmentation, particularly in flowers. These patterns are determined by the activity of MYB-bHLH-WDR (MBW) transcription factor complexes, which activate the anthocyanin biosynthesis genes, resulting in anthocyanin pigment accumulation. Recently, we established that the MBW complex controlling anthocyanin synthesis acts within a gene regulation network that is conserved within at least the Eudicots. This network involves hierarchy, reinforcement, and feedback mechanisms that allow for stringent and responsive regulation of the anthocyanin biosynthesis genes. The gene network and mobile nature of the WDR and R3-MYB proteins provide exciting new opportunities to explore the basis of pigmentation patterning, and to investigate the evolutionary history of the MBW components in land plants.

  3. Distributed generation and distribution market diversity in Europe

    International Nuclear Information System (INIS)

    Lopes Ferreira, H.; Costescu, A.; L'Abbate, A.; Minnebo, P.; Fulli, G.

    2011-01-01

    The unbundling of the electricity power system will play a key role on the deployment of distributed generation (DG) in European distribution systems evolving towards Smart Grids. The present paper firstly reviews the relevant European Union (EU) regulatory framework: specific attention is paid to the concept of unbundling of power distribution sector in Europe. Afterwards, the focus is on the current state of penetration of DG technologies in the EU Member States and the corresponding interrelations with distribution features. A comparison between the unbundling of the distribution and supply markets using econometric indicators such as the Herfindahl-Hirschmann (I HH ) and the Shannon-Wiener (I SW ) indices is then presented. Finally, a comparative analysis between these indices and the current level of penetration of distributed generation in most EU is shown; policy recommendations conclude the paper. - Highlights: →The EU regulatory framework and the concept of unbundling are addressed. →A comparison between the unbundling of the distribution and supply markets is shown. →The Herfindahl-Hirschmann and the Shannon-Wiener econometric indices are applied. →A comparison between the indices and the penetration level of DG in EU is presented. →A comparison between the indices and the penetration level of DG in EU is presented.

  4. Comparative Secretome Analysis of Trichoderma reesei and Aspergillus niger during Growth on Sugarcane Biomass.

    Directory of Open Access Journals (Sweden)

    Gustavo Pagotto Borin

    Full Text Available Our dependence on fossil fuel sources and concern about the environment has generated a worldwide interest in establishing new sources of fuel and energy. Thus, the use of ethanol as a fuel is advantageous because it is an inexhaustible energy source and has minimal environmental impact. Currently, Brazil is the world's second largest producer of ethanol, which is produced from sugarcane juice fermentation. However, several studies suggest that Brazil could double its production per hectare by using sugarcane bagasse and straw, known as second-generation (2G bioethanol. Nevertheless, the use of this biomass presents a challenge because the plant cell wall structure, which is composed of complex sugars (cellulose and hemicelluloses, must be broken down into fermentable sugar, such as glucose and xylose. To achieve this goal, several types of hydrolytic enzymes are necessary, and these enzymes represent the majority of the cost associated with 2G bioethanol processing. Reducing the cost of the saccharification process can be achieved via a comprehensive understanding of the hydrolytic mechanisms and enzyme secretion of polysaccharide-hydrolyzing microorganisms. In many natural habitats, several microorganisms degrade lignocellulosic biomass through a set of enzymes that act synergistically. In this study, two fungal species, Aspergillus niger and Trichoderma reesei, were grown on sugarcane biomass with two levels of cell wall complexity, culm in natura and pretreated bagasse. The production of enzymes related to biomass degradation was monitored using secretome analyses after 6, 12 and 24 hours. Concurrently, we analyzed the sugars in the supernatant.Analyzing the concentration of monosaccharides in the supernatant, we observed that both species are able to disassemble the polysaccharides of sugarcane cell walls since 6 hours post-inoculation. The sugars from the polysaccharides such as arabinoxylan and β-glucan (that compose the most external

  5. Uterine secretomics: a window on the maternal-embryo interface.

    Science.gov (United States)

    Cheong, Ying; Boomsma, Carolien; Heijnen, Cobi; Macklon, Nick

    2013-03-15

    The analysis of endometrial secretions offers a window on human peri-implantation events that have hitherto been difficult to study noninvasively. Uterine secretomic analysis provides a sensitive means of interrogating the contents of secretions, which have been shown to play a key role in determining endometrial receptivity and embryo-endometrial signaling, and in providing a nourishing environment to the preimplantation embryo. Compared with other means of assessing the endometrium with genomics or proteomics, secretomics offers a nondisruptive approach, allowing analysis during conception cycles. It also provides information on the downstream molecular profile directly encountered by the embryo, offering an integrated review of the complete endometrial surface rather than information representative of only a discrete biopsy site. In this article, recent data derived from uterine secretomics are reviewed. In addition to in vivo studies, recent data from in vitro studies that are changing our understanding of the role of the endometrium in embryo selection are reviewed. Finally, the role of uterine secretions in nutrition and early development programming of the embryo is considered. Copyright © 2013 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  6. Secretome profiling of primary human skeletal muscle cells.

    Science.gov (United States)

    Hartwig, Sonja; Raschke, Silja; Knebel, Birgit; Scheler, Mika; Irmler, Martin; Passlack, Waltraud; Muller, Stefan; Hanisch, Franz-Georg; Franz, Thomas; Li, Xinping; Dicken, Hans-Dieter; Eckardt, Kristin; Beckers, Johannes; de Angelis, Martin Hrabe; Weigert, Cora; Häring, Hans-Ulrich; Al-Hasani, Hadi; Ouwens, D Margriet; Eckel, Jürgen; Kotzka, Jorg; Lehr, Stefan

    2014-05-01

    The skeletal muscle is a metabolically active tissue that secretes various proteins. These so-called myokines have been proposed to affect muscle physiology and to exert systemic effects on other tissues and organs. Yet, changes in the secretory profile may participate in the pathophysiology of metabolic diseases. The present study aimed at characterizing the secretome of differentiated primary human skeletal muscle cells (hSkMC) derived from healthy, adult donors combining three different mass spectrometry based non-targeted approaches as well as one antibody based method. This led to the identification of 548 non-redundant proteins in conditioned media from hSkmc. For 501 proteins, significant mRNA expression could be demonstrated. Applying stringent consecutive filtering using SignalP, SecretomeP and ER_retention signal databases, 305 proteins were assigned as potential myokines of which 12 proteins containing a secretory signal peptide were not previously described. This comprehensive profiling study of the human skeletal muscle secretome expands our knowledge of the composition of the human myokinome and may contribute to our understanding of the role of myokines in multiple biological processes. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge. © 2013.

  7. Investigation of the indigenous fungal community populating barley grains: Secretomes and xylanolytic potential

    DEFF Research Database (Denmark)

    Sultan, Abida; Frisvad, Jens Christian; Andersen, Birgit

    2017-01-01

    on medium containing barley flour or wheat arabinoxylan as sole carbon source. Their secretomes and xylanase activities were analyzed using SDS-PAGE and enzyme assays and were found to vary according to species and carbon source. Secretomes were dominated by cell wall degrading enzymes with xylanases...

  8. Understanding Generational Diversity: Strategic Human Resource Management and Development across the Generational "Divide"

    Science.gov (United States)

    Amayah, Angela Titi; Gedro, Julie

    2014-01-01

    There are more generations in today's workforce than ever before, which has the possibility to create challenges for Human Resource professionals. The purpose of this article is to interrogate existing stereotypes and generalities about the characteristics of different generations with respect to the workplace, and to offer suggestions for…

  9. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

    Directory of Open Access Journals (Sweden)

    Niko eBeerenwinkel

    2012-09-01

    Full Text Available Many viruses, including the clinically relevant RNA viruses HIV and HCV, exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different next-generation sequencing platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of next-generation sequencing to estimate viral diversity.

  10. Diversity Generator Mechanisms Are Essential Components of Biological Systems: The Two Queen Hypothesis

    Directory of Open Access Journals (Sweden)

    Eric Muraille

    2018-02-01

    Full Text Available Diversity is widely known to fuel adaptation and evolutionary processes and increase robustness at the population, species and ecosystem levels. The Neo-Darwinian paradigm proposes that the diversity of biological entities is the consequence of genetic changes arising spontaneously and randomly, without regard for their usefulness. However, a growing body of evidence demonstrates that the evolutionary process has shaped mechanisms, such as horizontal gene transfer mechanisms, meiosis and the adaptive immune system, which has resulted in the regulated generation of diversity among populations. Though their origins are unrelated, these diversity generator (DG mechanisms share common functional properties. They (i contribute to the great unpredictability of the composition and/or behavior of biological systems, (ii favor robustness and collectivism among populations and (iii operate mainly by manipulating the systems that control the interaction of living beings with their environment. The definition proposed here for DGs is based on these properties and can be used to identify them according to function. Interestingly, prokaryotic DGs appear to be mainly reactive, as they generate diversity in response to environmental stress. They are involved in the widely described Red Queen/arms race/Cairnsian dynamic. The emergence of multicellular organisms harboring K selection traits (longer reproductive life cycle and smaller population size has led to the acquisition of a new class of DGs that act anticipatively to stress pressures and generate a distinct dynamic called the “White Queen” here. The existence of DGs leads to the view of evolution as a more “intelligent” and Lamarckian-like process. Their repeated selection during evolution could be a neglected example of convergent evolution and suggests that some parts of the evolutionary process are tightly constrained by ecological factors, such as the population size, the generation time and

  11. Diversity Generator Mechanisms Are Essential Components of Biological Systems: The Two Queen Hypothesis.

    Science.gov (United States)

    Muraille, Eric

    2018-01-01

    Diversity is widely known to fuel adaptation and evolutionary processes and increase robustness at the population, species and ecosystem levels. The Neo-Darwinian paradigm proposes that the diversity of biological entities is the consequence of genetic changes arising spontaneously and randomly, without regard for their usefulness. However, a growing body of evidence demonstrates that the evolutionary process has shaped mechanisms, such as horizontal gene transfer mechanisms, meiosis and the adaptive immune system, which has resulted in the regulated generation of diversity among populations. Though their origins are unrelated, these diversity generator (DG) mechanisms share common functional properties. They (i) contribute to the great unpredictability of the composition and/or behavior of biological systems, (ii) favor robustness and collectivism among populations and (iii) operate mainly by manipulating the systems that control the interaction of living beings with their environment. The definition proposed here for DGs is based on these properties and can be used to identify them according to function. Interestingly, prokaryotic DGs appear to be mainly reactive, as they generate diversity in response to environmental stress. They are involved in the widely described Red Queen/arms race/Cairnsian dynamic. The emergence of multicellular organisms harboring K selection traits (longer reproductive life cycle and smaller population size) has led to the acquisition of a new class of DGs that act anticipatively to stress pressures and generate a distinct dynamic called the "White Queen" here. The existence of DGs leads to the view of evolution as a more "intelligent" and Lamarckian-like process. Their repeated selection during evolution could be a neglected example of convergent evolution and suggests that some parts of the evolutionary process are tightly constrained by ecological factors, such as the population size, the generation time and the intensity of

  12. Comparative secretome analysis of Trichoderma asperellum S4F8 and Trichoderma reesei Rut C30 during solid-state fermentation on sugarcane bagasse.

    Science.gov (United States)

    Marx, Isa Jacoba; van Wyk, Niël; Smit, Salome; Jacobson, Daniel; Viljoen-Bloom, Marinda; Volschenk, Heinrich

    2013-11-29

    The lignocellulosic enzymes of Trichoderma species have received particular attention with regard to biomass conversion to biofuels, but the production cost of these enzymes remains a significant hurdle for their commercial application. In this study, we quantitatively compared the lignocellulolytic enzyme profile of a newly isolated Trichoderma asperellum S4F8 strain with that of Trichoderma reesei Rut C30, cultured on sugarcane bagasse (SCB) using solid-state fermentation (SSF). Comparison of the lignocellulolytic enzyme profiles of S4F8 and Rut C30 showed that S4F8 had significantly higher hemicellulase and β-glucosidase enzyme activities. Liquid chromatography tandem mass spectrometry analysis of the two fungal secretomes enabled the detection of 815 proteins in total, with 418 and 397 proteins being specific for S4F8 and Rut C30, respectively, and 174 proteins being common to both strains. In-depth analysis of the associated biological functions and the representation of glycoside hydrolase family members within the two secretomes indicated that the S4F8 secretome contained a higher diversity of main and side chain hemicellulases and β-glucosidases, and an increased abundance of some of these proteins compared with the Rut C30 secretome. In SCB SSF, T. asperellum S4F8 produced a more complex lignocellulolytic cocktail, with enhanced hemicellulose and cellobiose hydrolysis potential, compared with T. reesei Rut C30. This bodes well for the development of a more cost-effective and efficient lignocellulolytic enzyme cocktail from T. asperellum for lignocellulosic feedstock hydrolysis.

  13. Secretome analysis of Trypanosoma cruzi by proteomics studies.

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    Jean-Yves Brossas

    Full Text Available Chagas disease is a debilitating often fatal disease resulting from infection by the protozoan parasite Trypanosoma cruzi. Chagas disease is endemic in 21 countries of the Americas, and it is an emerging disease in other countries as a result of migration. Given the chronic nature of the infection where intracellular parasites persist for years, the diagnosis of T. cruzi by direct detection is difficult, whereas serologic tests though sensitive may yield false-positive results. The development of new rapid test based on the identification of soluble parasitic antigens in serum would be a real innovation in the diagnosis of Chagas disease.To identify new soluble biomarkers that may improve diagnostic tests, we investigated the proteins secreted by T. cruzi using mass spectrometric analyses of conditioned culture media devoid of serum collected during the emergence of trypomastigotes from infected Vero cells. In addition, we compared the secretomes of two T. cruzi strains from DTU Tc VI (VD and CL Brener.Analysis of the secretome collected during the emergence of trypomastigotes from Vero cells led to the identification of 591 T. cruzi proteins. Three hundred sixty three proteins are common to both strains and most belong to different multigenic super families (i.e. TcS, GP63, MASP, and DGF1. Ultimately we have established a list of 94 secreted proteins, common to both DTU Tc VI strains that do not belong to members of multigene families.This study provides the first comparative analysis of the secretomes from two distinct T. cruzi strains of DTU TcVI. This led us to identify a subset of common secreted proteins that could potentially serve as serum markers for T. cruzi infection. Their potential could now be evaluated, with specific antibodies using sera collected from patients and residents from endemic regions.

  14. Secretome analysis of Trypanosoma cruzi by proteomics studies.

    Science.gov (United States)

    Brossas, Jean-Yves; Gulin, Julián Ernesto Nicolás; Bisio, Margarita Maria Catalina; Chapelle, Manuel; Marinach-Patrice, Carine; Bordessoules, Mallaury; Palazon Ruiz, George; Vion, Jeremy; Paris, Luc; Altcheh, Jaime; Mazier, Dominique

    2017-01-01

    Chagas disease is a debilitating often fatal disease resulting from infection by the protozoan parasite Trypanosoma cruzi. Chagas disease is endemic in 21 countries of the Americas, and it is an emerging disease in other countries as a result of migration. Given the chronic nature of the infection where intracellular parasites persist for years, the diagnosis of T. cruzi by direct detection is difficult, whereas serologic tests though sensitive may yield false-positive results. The development of new rapid test based on the identification of soluble parasitic antigens in serum would be a real innovation in the diagnosis of Chagas disease. To identify new soluble biomarkers that may improve diagnostic tests, we investigated the proteins secreted by T. cruzi using mass spectrometric analyses of conditioned culture media devoid of serum collected during the emergence of trypomastigotes from infected Vero cells. In addition, we compared the secretomes of two T. cruzi strains from DTU Tc VI (VD and CL Brener). Analysis of the secretome collected during the emergence of trypomastigotes from Vero cells led to the identification of 591 T. cruzi proteins. Three hundred sixty three proteins are common to both strains and most belong to different multigenic super families (i.e. TcS, GP63, MASP, and DGF1). Ultimately we have established a list of 94 secreted proteins, common to both DTU Tc VI strains that do not belong to members of multigene families. This study provides the first comparative analysis of the secretomes from two distinct T. cruzi strains of DTU TcVI. This led us to identify a subset of common secreted proteins that could potentially serve as serum markers for T. cruzi infection. Their potential could now be evaluated, with specific antibodies using sera collected from patients and residents from endemic regions.

  15. In-depth proteomic profiling of the uveal melanoma secretome

    Science.gov (United States)

    Prendergast, Samuel; Simpson, Deborah; Hammond, Dean E.; Madigan, Michele C.; Beynon, Robert J.; Coupland, Sarah E.

    2016-01-01

    Uveal melanoma (UM), the most common primary intraocular tumour in adults, is characterised by a high frequency of metastases to the liver, typically with a fatal outcome. Proteins secreted from cancer cells (‘secretome’) are biologically important molecules thought to contribute to tumour progression. We examined the UM secretome by applying a label-free nanoLCMS/MS proteomic approach to profile proteins secreted into culture media by primary UM tumours with a high− (HR; n = 11) or low− (LR; n = 4) metastatic risk, compared to normal choroidal melanocytes (NCM) from unaffected post-mortem eyes. Across the three groups, 1843 proteins were identified at a 1% false discovery rate; 758 of these by at least 3 unique peptides, and quantified. The majority (539/758, 71%) of proteins were classified as secreted either by classical (144, 19%), non-classical (43, 6%) or exosomal (352, 46%) mechanisms. Bioinformatic analyzes showed that the secretome composition reflects biological differences and similarities of the samples. Ingenuity® pathway analysis of the secreted protein dataset identified abundant proteins involved in cell proliferation-, growth- and movement. Hepatic fibrosis/hepatic stellate cell activation and the mTORC1-S6K signalling axis were among the most differentially regulated biological processes in UM as compared with NCM. Further analysis of proteins upregulated ≥ 2 in HR-UM only, identified exosomal proteins involved in extracellular matrix remodelling and cancer cell migration/invasion; as well as classically secreted proteins, possibly representing novel biomarkers of metastatic disease. In conclusion, UM secretome analysis identifies novel proteins and pathways that may contribute to metastatic development at distant sites, particularly in the liver. PMID:27391064

  16. Cheating in Business Schools, the Millennial Generation, Gender and Racial Diversity: Has the Paradigm Shifted?

    Science.gov (United States)

    Mathison, David L.

    2010-01-01

    Cheating in college is not new. In 1960 over 50 percent of students admitted they cheated. In the second decade of the 21st century has anything changed? This research project looked at three possible new variables, the Millennial Generation, Gender, and Diversity. Results suggest the amount of reported cheating remains the same even with current…

  17. Challenges to the Learning Organization in the Context of Generational Diversity and Social Networks

    Science.gov (United States)

    Kaminska, Renata; Borzillo, Stefano

    2018-01-01

    Purpose: The purpose of this paper is to gain a better understanding of the challenges to the emergence of a learning organization (LO) posed by a context of generational diversity and an enterprise social networking system (ESNS). Design/methodology/approach: This study uses a qualitative methodology based on an analysis of 20 semi-structured…

  18. Behavioral Diversity Generation in Autonomous Exploration Through Reuse of Past Experience

    Directory of Open Access Journals (Sweden)

    Fabien eBenureau

    2016-03-01

    Full Text Available The production of behavioral diversity---producing a diversity of effects---is an essential strategy for robots exploring the world when facing situations where interaction possibilities are unknown or non-obvious. It allows to discover new aspects of the environment that cannot be inferred or deduced from available knowledge. However, creating behavioral diversity in situations where it is the most crucial---new and unknown ones---is far from trivial. In particular in large and redundant sensorimotor spaces, only small areas are interesting to explore for any practical purpose. When the environment does not provide clues or gradient toward those areas, trying to discover those areas relies on chance. To address this problem, we introduce a method to create behavioral diversity in a new sensorimotor task by re-enacting actions that allowed to produce behavioral diversity in a previous task, along with a measure that quantifies this diversity. We show that our method can learn how to interact with an object by reusing experience from another, that it adapts to instances of morphological changes and of dissimilarity between tasks, and how scaffolding behaviors can emerge by simply switching the attention of the robot to different parts of the environment. Finally, we show that the method can robustly use simulated experiences and crude cognitive models to generate behavioral diversity in real robots.

  19. Therapeutic Potential of Dental Pulp Stem Cell Secretome for Alzheimer's Disease Treatment: An In Vitro Study

    Science.gov (United States)

    Ahmed, Nermeen El-Moataz Bellah; Murakami, Masashi; Hirose, Yujiro; Nakashima, Misako

    2016-01-01

    The secretome obtained from stem cell cultures contains an array of neurotrophic factors and cytokines that might have the potential to treat neurodegenerative conditions. Alzheimer's disease (AD) is one of the most common human late onset and sporadic neurodegenerative disorders. Here, we investigated the therapeutic potential of secretome derived from dental pulp stem cells (DPSCs) to reduce cytotoxicity and apoptosis caused by amyloid beta (Aβ) peptide. We determined whether DPSCs can secrete the Aβ-degrading enzyme, neprilysin (NEP), and evaluated the effects of NEP expression in vitro by quantitating Aβ-degrading activity. The results showed that DPSC secretome contains higher concentrations of VEGF, Fractalkine, RANTES, MCP-1, and GM-CSF compared to those of bone marrow and adipose stem cells. Moreover, treatment with DPSC secretome significantly decreased the cytotoxicity of Aβ peptide by increasing cell viability compared to nontreated cells. In addition, DPSC secretome stimulated the endogenous survival factor Bcl-2 and decreased the apoptotic regulator Bax. Furthermore, neprilysin enzyme was detected in DPSC secretome and succeeded in degrading Aβ 1–42 in vitro in 12 hours. In conclusion, our study demonstrates that DPSCs may serve as a promising source for secretome-based treatment of Alzheimer's disease. PMID:27403169

  20. Cancer Secretome May Influence BSP and DSP Expression in Human Salivary Gland Cells.

    Science.gov (United States)

    Hamilton, Samantha Lynn; Ferando, Blake; Eapen, Asha Sarah; Yu, Jennifer Chian; Joy, Anita Rose

    2017-03-01

    One of the biggest challenges in managing head and neck cancers, especially salivary gland cancers, is the identification of secreted biomarkers of the disease that can be evaluated noninvasively. A relevant source of enriched tumor markers could potentially be found in the tumor secretome. Although numerous studies have evaluated secretomes from various cancers, the influence of the cancer secretome derived from salivary gland cancers on the behavior of normal cells has not yet been elucidated. Our data indicate that secretome derived from salivary gland cancer cells can influence the expression of two potential biomarkers of oral cancer-namely, bone sialoprotein (BSP) and dentin sialoprotein (DSP)-in normal salivary gland cells. Using routine immunohistochemistry, immunofluorescence, and immunoblotting techniques, we demonstrate an enrichment of BSP and DSP in human salivary gland (HSG) cancer tissue, unique localizations of BSP and DSP in HSG cancer cells, and enriched expression of BSP and DSP in normal salivary gland cells exposed to a cancer secretome. The secretome domain of the cancer microenvironment could alter signaling cascades responsible for normal cell proliferation, migration, and invasion, thus enhancing cancer cell survival and the potential for cancer progression. The cancer secretome may be critical in maintaining and stimulating "cancer-ness," thus potentially promoting specific hallmarks of metastasis.

  1. Proteomic Studies of Cholangiocarcinoma and Hepatocellular Carcinoma Cell Secretomes

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    Chantragan Srisomsap

    2010-01-01

    Full Text Available Cholangiocarcinoma (CCA and hepatocellular carcinoma (HCC occur with relatively high incidence in Thailand. The secretome, proteins secreted from cancer cells, are potentially useful as biomarkers of the diseases. Proteomic analysis was performed on the secreted proteins of cholangiocarcinoma (HuCCA-1 and hepatocellular carcinoma (HCC-S102, HepG2, SK-Hep-1, and Alexander cell lines. The secretomes of the five cancer cell lines were analyzed by SDS-PAGE combined with LC/MS/MS. Sixty-eight proteins were found to be expressed only in HuCCA-1. Examples include neutrophil gelatinase-associated lipocalin (lipocalin 2, laminin 5 beta 3, cathepsin D precursor, desmoplakin, annexin IV variant, and annexin A5. Immunoblotting was used to confirm the presence of lipocalin 2 in conditioned media and cell lysate of 5 cell lines. The results showed that lipocalin 2 was a secreted protein which is expressed only in the conditioned media of the cholangiocarcinoma cell line. Study of lipocalin 2 expression in different types of cancer and normal tissues from cholangiocarcinoma patients showed that lipocalin 2 was expressed only in the cancer tissues. We suggest that lipocalin 2 may be a potential biomarker for cholangiocarcinoma.

  2. Processing of Snake Venom Metalloproteinases: Generation of Toxin Diversity and Enzyme Inactivation

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    Ana M. Moura-da-Silva

    2016-06-01

    Full Text Available Snake venom metalloproteinases (SVMPs are abundant in the venoms of vipers and rattlesnakes, playing important roles for the snake adaptation to different environments, and are related to most of the pathological effects of these venoms in human victims. The effectiveness of SVMPs is greatly due to their functional diversity, targeting important physiological proteins or receptors in different tissues and in the coagulation system. Functional diversity is often related to the genetic diversification of the snake venom. In this review, we discuss some published evidence that posit that processing and post-translational modifications are great contributors for the generation of functional diversity and for maintaining latency or inactivation of enzymes belonging to this relevant family of venom toxins.

  3. Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF

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    Schillinger Thomas

    2012-08-01

    Full Text Available Abstract Background Diversity Generating Retroelements (DGRs are genetic cassettes that can introduce tremendous diversity into a short, defined region of the genome. They achieve hypermutation through replacement of the variable region with a strongly mutated cDNA copy generated by the element-encoded reverse transcriptase. In contrast to “selfish” retroelements such as group II introns and retrotransposons, DGRs impart an advantage to their host by increasing its adaptive potential. DGRs were discovered in a bacteriophage, but since then additional examples have been identified in some bacterial genomes. Results Here we present the program DiGReF that allowed us to comprehensively screen available databases for DGRs. We identified 155 DGRs which are found in all major classes of bacteria, though exhibiting sporadic distribution across species. Phylogenetic analysis and sequence comparison showed that DGRs move between genomes by associating with various mobile elements such as phages, transposons and plasmids. The DGR cassettes exhibit high flexibility in the arrangement of their components and easily acquire additional paralogous target genes. Surprisingly, the genomic data alone provide new insights into the molecular mechanism of DGRs. Most notably, our data suggest that the template RNA is transcribed separately from the rest of the element. Conclusions DiGReF is a valuable tool to detect DGRs in genome data. Its output allows comprehensive analysis of various aspects of DGR biology, thus deepening our understanding of the role DGRs play in prokaryotic genome plasticity, from the global down to the molecular level.

  4. Overcoming viral escape with vaccines that generate and display antigen diversity in vivo

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    García-Quintanilla Albert

    2007-11-01

    Full Text Available Abstract Background Viral diversity is a key problem for the design of effective and universal vaccines. Virtually, a vaccine candidate including most of the diversity for a given epitope would force the virus to create escape mutants above the viability threshold or with a high fitness cost. Presentation of the hypothesis Therefore, I hypothesize that priming the immune system with polyvalent vaccines where each single vehicle generates and displays multiple antigen variants in vivo, will elicit a broad and long-lasting immune response able to avoid viral escape. Testing the hypothesis To this purpose, I propose the use of yeasts that carry virus-like particles designed to pack the antigen-coding RNA inside and replicate it via RNA-dependent RNA polymerase. This would produce diversity in vivo limited to the target of interest and without killing the vaccine vehicle. Implications of the hypothesis This approach is in contrast with peptide cocktails synthesized in vitro and polyvalent strategies where every cell or vector displays a single or definite number of mutants; but similarly to all them, it should be able to overcome original antigenic sin, avoid major histocompatibility complex restriction, and elicit broad cross-reactive immune responses. Here I discuss additional advantages such as minimal global antagonism or those derived from using a yeast vehicle, and potential drawbacks like autoimmunity. Diversity generated by this method could be monitored both genotypically and phenotypically, and therefore selected or discarded before use if needed.

  5. Endothelial Progenitor Cell Secretome and Oligovascular Repair in a Mouse Model of Prolonged Cerebral Hypoperfusion.

    Science.gov (United States)

    Maki, Takakuni; Morancho, Anna; Martinez-San Segundo, Pablo; Hayakawa, Kazuhide; Takase, Hajime; Liang, Anna C; Gabriel-Salazar, Marina; Medina-Gutiérrez, Esperanza; Washida, Kazuo; Montaner, Joan; Lok, Josephine; Lo, Eng H; Arai, Ken; Rosell, Anna

    2018-04-01

    Endothelial progenitor cells (EPCs) have been extensively investigated as a therapeutic approach for repairing the vascular system in cerebrovascular diseases. Beyond vascular regeneration per se, EPCs may also release factors that affect the entire neurovascular unit. Here, we aim to study the effects of the EPC secretome on oligovascular remodeling in a mouse model of white matter injury after prolonged cerebral hypoperfusion. The secretome of mouse EPCs was analyzed with a proteome array. In vitro, the effects of the EPC secretome and its factor angiogenin were assessed on primary oligodendrocyte precursor cells and mature human cerebral microvascular endothelial cells (hCMED/D3). In vivo, mice were subjected to permanent bilateral common carotid artery stenosis, then treated with EPC secretome at 24 hours and at 1 week, and cognitive outcome was evaluated with the Y maze test together with oligodendrocyte precursor cell proliferation/differentiation and vascular density in white matter at 4 weeks. Multiple growth factors, cytokines, and proteases were identified in the EPC secretome, including angiogenin. In vitro, the EPC secretome significantly enhanced endothelial and oligodendrocyte precursor cell proliferation and potentiated oligodendrocyte precursor cell maturation. Angiogenin was proved to be a key factor since pharmacological blockade of angiogenin signaling negated the positive effects of the EPC secretome. In vivo, treatment with the EPC secretome increased vascular density, myelin, and mature oligodendrocytes in white matter and rescued cognitive function in the mouse hypoperfusion model. Factors secreted by EPCs may ameliorate white matter damage in the brain by boosting oligovascular remodeling. © 2018 American Heart Association, Inc.

  6. Dataset for the proteomic inventory and quantitative analysis of the breast cancer hypoxic secretome associated with osteotropism

    DEFF Research Database (Denmark)

    Cox, T.R.; Schoof, Erwin; Gartland, A.

    2015-01-01

    The cancer secretome includes all of the macromolecules secreted by cells into their microenvironment. Cancer cell secretomes are significantly different to that of normal cells reflecting the changes that normal cells have undergone during their transition to malignancy. More importantly, cancer...... secretomes are known to be active mediators of both local and distant host cells and play an important role in the progression and dissemination of cancer. Here we have quantitatively profiled both the composition of breast cancer secretomes associated with osteotropism, and their modulation under normoxic...

  7. Secretome analysis of Trichoderma reesei and Aspergillus niger cultivated by submerged and sequential fermentation processes: Enzyme production for sugarcane bagasse hydrolysis.

    Science.gov (United States)

    Florencio, Camila; Cunha, Fernanda M; Badino, Alberto C; Farinas, Cristiane S; Ximenes, Eduardo; Ladisch, Michael R

    2016-08-01

    Cellulases and hemicellulases from Trichoderma reesei and Aspergillus niger have been shown to be powerful enzymes for biomass conversion to sugars, but the production costs are still relatively high for commercial application. The choice of an effective microbial cultivation process employed for enzyme production is important, since it may affect titers and the profile of protein secretion. We used proteomic analysis to characterize the secretome of T. reesei and A. niger cultivated in submerged and sequential fermentation processes. The information gained was key to understand differences in hydrolysis of steam exploded sugarcane bagasse for enzyme cocktails obtained from two different cultivation processes. The sequential process for cultivating A. niger gave xylanase and β-glucosidase activities 3- and 8-fold higher, respectively, than corresponding activities from the submerged process. A greater protein diversity of critical cellulolytic and hemicellulolytic enzymes were also observed through secretome analyses. These results helped to explain the 3-fold higher yield for hydrolysis of non-washed pretreated bagasse when combined T. reesei and A. niger enzyme extracts from sequential fermentation were used in place of enzymes obtained from submerged fermentation. An enzyme loading of 0.7 FPU cellulase activity/g glucan was surprisingly effective when compared to the 5-15 times more enzyme loadings commonly reported for other cellulose hydrolysis studies. Analyses showed that more than 80% consisted of proteins other than cellulases whose role is important to the hydrolysis of a lignocellulose substrate. Our work combined proteomic analyses and enzymology studies to show that sequential and submerged cultivation methods differently influence both titers and secretion profile of key enzymes required for the hydrolysis of sugarcane bagasse. The higher diversity of feruloyl esterases, xylanases and other auxiliary hemicellulolytic enzymes observed in the enzyme

  8. Analytical and computational approaches to define the Aspergillus niger secretome

    Energy Technology Data Exchange (ETDEWEB)

    Tsang, Adrian; Butler, Gregory D.; Powlowski, Justin; Panisko, Ellen A.; Baker, Scott E.

    2009-03-01

    We used computational and mass spectrometric approaches to characterize the Aspergillus niger secretome. The 11,200 gene models predicted in the genome of A. niger strain ATCC 1015 were the data source for the analysis. Depending on the computational methods used, 691 to 881 proteins were predicted to be secreted proteins. We cultured A. niger in six different media and analyzed the extracellular proteins produced using mass spectrometry. A total of 222 proteins were identified, with 39 proteins expressed under all six conditions and 74 proteins expressed under only one condition. The secreted proteins identified by mass spectrometry were used to guide the correction of about 20 gene models. Additional analysis focused on extracellular enzymes of interest for biomass processing. Of the 63 glycoside hydrolases predicted to be capable of hydrolyzing cellulose, hemicellulose or pectin, 94% of the exo-acting enzymes and only 18% of the endo-acting enzymes were experimentally detected.

  9. Dynamics of the Skeletal Muscle Secretome during Myoblast Differentiation

    DEFF Research Database (Denmark)

    Henningsen, Jeanette; Rigbolt, Kristoffer T G; Blagoev, Blagoy

    2010-01-01

    During recent years, increased efforts have focused on elucidating the secretory function of skeletal muscle. Through secreted molecules, skeletal muscle affects local muscle biology in an auto/paracrine manner as well as having systemic effects on other tissues. Here we used a quantitative...... proteomics platform to investigate the factors secreted during the differentiation of murine C2C12 skeletal muscle cells. Using triple encoding stable isotope labeling by amino acids in cell culture, we compared the secretomes at three different time points of muscle differentiation and followed the dynamics...... of the skeletal muscle as a prominent secretory organ. In addition to previously reported molecules, we identified many secreted proteins that have not previously been shown to be released from skeletal muscle cells nor shown to be differentially released during the process of myogenesis. We found 188...

  10. Mesenchymal stem cell secretome and regenerative therapy after cancer.

    Science.gov (United States)

    Zimmerlin, Ludovic; Park, Tea Soon; Zambidis, Elias T; Donnenberg, Vera S; Donnenberg, Albert D

    2013-12-01

    Cancer treatment generally relies on tumor ablative techniques that can lead to major functional or disfiguring defects. These post-therapy impairments require the development of safe regenerative therapy strategies during cancer remission. Many current tissue repair approaches exploit paracrine (immunomodulatory, pro-angiogenic, anti-apoptotic and pro-survival effects) or restoring (functional or structural tissue repair) properties of mesenchymal stem/stromal cells (MSC). Yet, a major concern in the application of regenerative therapies during cancer remission remains the possible triggering of cancer recurrence. Tumor relapse implies the persistence of rare subsets of tumor-initiating cancer cells which can escape anti-cancer therapies and lie dormant in specific niches awaiting reactivation via unknown stimuli. Many of the components required for successful regenerative therapy (revascularization, immunosuppression, cellular homing, tissue growth promotion) are also critical for tumor progression and metastasis. While bi-directional crosstalk between tumorigenic cells (especially aggressive cancer cell lines) and MSC (including tumor stroma-resident populations) has been demonstrated in a variety of cancers, the effects of local or systemic MSC delivery for regenerative purposes on persisting cancer cells during remission remain controversial. Both pro- and anti-tumorigenic effects of MSC have been reported in the literature. Our own data using breast cancer clinical isolates have suggested that dormant-like tumor-initiating cells do not respond to MSC signals, unlike actively dividing cancer cells which benefited from the presence of supportive MSC. The secretome of MSC isolated from various tissues may partially diverge, but it includes a core of cytokines (i.e. CCL2, CCL5, IL-6, TGFβ, VEGF), which have been implicated in tumor growth and/or metastasis. This article reviews published models for studying interactions between MSC and cancer cells with a focus

  11. Genome-wide computational analysis of the secretome of brown algae (Phaeophyceae).

    Science.gov (United States)

    Terauchi, Makoto; Yamagishi, Takahiro; Hanyuda, Takeaki; Kawai, Hiroshi

    2017-04-01

    Brown algae have evolved complex multicellularity in the heterokont lineage. They are phylogenetically distant to land plants, fungi and animals. Especially, the members of Laminariales (so-called kelps) have developed highly differentiated tissues. Extracellular matrix (ECM) plays pivotal roles in a number of essential processes in multicellular organisms, such as cell adhesion, cell and tissue differentiations, cell-to-cell communication, and responses to environmental stimuli. In these processes, a set of extracellular secreted proteins called the secretome operates remodeling of the physicochemical nature of ECM and signal transduction by interacting with cell surface proteins and signaling molecules. Characterization of the secretome is a critical step to clarify the contributions of ECM to the multicellularity of brown algae. However, the identity of the brown algal secretome has been poorly understood. In order to reveal the repertory of the brown algal secretome and its involvement in the evolution of Laminariales, we conducted a genome-wide analysis of the brown algal secretome utilizing the published complete genome data of Ectocarpus siliculosus and Saccharina japonica as well as newly obtained RNA-seq data of seven laminarialean species (Agarum clathratum, Alaria crassifolia, Aureophycus aleuticus, Costaria costata, Pseudochorda nagaii, Saccharina angustata and Undaria pinnatifida) largely covering the laminarialean families. We established the in silico pipeline to systematically and accurately detect the secretome by combining multiple prediction algorithms for the N-terminal signal peptide and transmembrane domain within the protein sequence. From 16,189 proteins of E. siliculosus and 18,733 proteins of S. japonica, 552 and 964 proteins respectively were predicted to be classified as the secretome. Conserved domain analysis showed that the domain repertory were very similar to each other, and that of the brown algal secretome was partially common

  12. Generation of Immunoglobulin diversity in human gut-associated lymphoid tissue.

    Science.gov (United States)

    Spencer, Jo; Barone, Francesca; Dunn-Walters, Deborah

    2009-06-01

    The organised gut associated lymphoid tissue (GALT) exists adjacent to an extensive and diverse luminal flora. The follicle associated epithelium and associated dendritic cells and lymphocytes form a tightly fortified gateway between the flora and the host that permits connectivity between them and chronic activation of the lymphoid compartment. As a consequence, plasma cell precursors are generated continuously, and in abundance, in GALT by clonal proliferation. Clonal proliferation alone on this scale would reduce the spectrum of B cell specificity. To compensate, GALT also houses molecular machinery that diversifies the receptor repertoire by somatic hypermutation, class switch recombination and receptor revision. These three processes of enhancing the diversity of mature B cells ensure that although clonally related plasma cells may secrete immunoglobulin side by side in the mucosa they rarely have identical antigen binding sites.

  13. Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine

    Science.gov (United States)

    Bokulich, Nicholas A.; Joseph, C. M. Lucy; Allen, Greg; Benson, Andrew K.; Mills, David A.

    2012-01-01

    While wine fermentation has long been known to involve complex microbial communities, the composition and role of bacteria other than a select set of lactic acid bacteria (LAB) has often been assumed either negligible or detrimental. This study served as a pilot study for using barcoded amplicon next-generation sequencing to profile bacterial community structure in wines and grape musts, comparing the taxonomic depth achieved by sequencing two different domains of prokaryotic 16S rDNA (V4 and V5). This study was designed to serve two goals: 1) to empirically determine the most taxonomically informative 16S rDNA target region for barcoded amplicon sequencing of wine, comparing V4 and V5 domains of bacterial 16S rDNA to terminal restriction fragment length polymorphism (TRFLP) of LAB communities; and 2) to explore the bacterial communities of wine fermentation to better understand the biodiversity of wine at a depth previously unattainable using other techniques. Analysis of amplicons from the V4 and V5 provided similar views of the bacterial communities of botrytized wine fermentations, revealing a broad diversity of low-abundance taxa not traditionally associated with wine, as well as atypical LAB communities initially detected by TRFLP. The V4 domain was determined as the more suitable read for wine ecology studies, as it provided greater taxonomic depth for profiling LAB communities. In addition, targeted enrichment was used to isolate two species of Alphaproteobacteria from a finished fermentation. Significant differences in diversity between inoculated and uninoculated samples suggest that Saccharomyces inoculation exerts selective pressure on bacterial diversity in these fermentations, most notably suppressing abundance of acetic acid bacteria. These results determine the bacterial diversity of botrytized wines to be far higher than previously realized, providing further insight into the fermentation dynamics of these wines, and demonstrate the utility of next-generation

  14. In the time of significant generational diversity - surgical leadership must step up!

    Science.gov (United States)

    Money, Samuel R; O'Donnell, Mark E; Gray, Richard J

    2014-02-01

    The diverse attitudes and motivations of surgeons and surgical trainees within different age groups present an important challenge for surgical leaders and educators. These challenges to surgical leadership are not unique, and other industries have likewise needed to grapple with how best to manage these various age groups. The authors will herein explore management and leadership for surgeons in a time of age diversity, define generational variations within "Baby-Boomer", "Generation X" and "Generation Y" populations, and identify work ethos concepts amongst these three groups. The surgical community must understand and embrace these concepts in order to continue to attract a stellar pool of applicants from medical school. By not accepting the changing attitudes and motivations of young trainees and medical students, we may disenfranchise a high percentage of potential future surgeons. Surgical training programs will fill, but will they contain the highest quality trainees? Copyright © 2013 Royal College of Surgeons of Edinburgh (Scottish charity number SC005317) and Royal College of Surgeons in Ireland. Published by Elsevier Ltd. All rights reserved.

  15. The in vitro secretome of Mycosphaerella fijiensis induces cell death in banana leaves.

    Science.gov (United States)

    Chuc-Uc, José; Brito-Argáez, Ligia; Canto-Canché, Blondy; Tzec-Simá, Miguel; Rodríguez-García, Cecilia; Peraza-Echeverría, Leticia; Peraza-Echeverría, Santy; James-Kay, Andrew; Cruz-Cruz, Carlos Alberto; Peña-Rodríguez, Luis Manuel; Islas-Flores, Ignacio

    2011-06-01

    The hemibiotrophic filamentous fungus Mycosphaerella fijiensis causes the banana foliar disease known as black Sigatoka, responsible for major worldwide losses in the banana fruit industry. In this work the in vitro secretome of M. fijiensis was characterized. Native and denaturant polyacrylamide gel protease assays showed the M. fijiensis secretome contains protease activity capable of degrading gelatin. Necrotic lesions on leaves were produced by application of the in vitro secretome to the surface of one black Sigatoka-resistant banana wild species, one susceptible cultivar and the non-host plant Carica papaya. To distinguish if necrosis by the secretome is produced by phytotoxins or proteins, the latter ones were precipitated with ammonium sulfate and applied in native or denatured forms onto leaves of the same three plant species. Proteins applied in both preparations were able to produce necrotic lesions. Application of Pronase, a commercial bacterial protease suggested that the necrosis was, at least in part, caused by protease activity from the M. fijiensis secretome. The ability to cause necrotic lesions between M. fijiensis secreted- and ammonium sulfate-precipitated proteins, and purified lipophilic or hydrophilic phytotoxins, was compared. The results suggested that leaf necrosis arises from the combined action of non-host specific hydrolytic activities from the secreted proteins and the action of phytotoxins. This is the first characterization of the M. fijiensis protein secretome produced in vitro but, more importantly, it is also the first time the M. fijiensis secretome has been shown to contain virulence factors capable of causing necrosis to its natural host. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  16. Being trusted: How team generational age diversity promotes and undermines trust in cross‐boundary relationships

    Science.gov (United States)

    2015-01-01

    Summary We examine how demographic context influences the trust that boundary spanners experience in their dyadic relationships with clients. Because of the salience of age as a demographic characteristic as well as the increasing prevalence of age diversity and intergenerational conflict in the workplace, we focus on team age diversity as a demographic social context that affects trust between boundary spanners and their clients. Using social categorization theory and theories of social capital, we develop and test our contextual argument that a boundary spanner's experience of being trusted is influenced by the social categorization processes that occur in dyadic interactions with a specific client and, simultaneously, by similar social categorization processes that influence the degree to which the client team as a whole serves as a cooperative resource for demographically similar versus dissimilar boundary spanner–client dyads. Using a sample of 168 senior boundary spanners from the consulting industry, we find that generational diversity among client team members from a client organization undermines the perception of being trusted within homogeneous boundary spanner–client dyads while it enhances the perception of being trusted within heterogeneous dyads. The perception of being trusted is an important aspect of cross‐boundary relationships because it influences coordination and the costs associated with coordination. © 2015 The Author Journal of Organizational Behavior Published by John Wiley & Sons Ltd PMID:27721558

  17. Being trusted: How team generational age diversity promotes and undermines trust in cross-boundary relationships.

    Science.gov (United States)

    Williams, Michele

    2016-04-01

    We examine how demographic context influences the trust that boundary spanners experience in their dyadic relationships with clients. Because of the salience of age as a demographic characteristic as well as the increasing prevalence of age diversity and intergenerational conflict in the workplace, we focus on team age diversity as a demographic social context that affects trust between boundary spanners and their clients. Using social categorization theory and theories of social capital, we develop and test our contextual argument that a boundary spanner's experience of being trusted is influenced by the social categorization processes that occur in dyadic interactions with a specific client and, simultaneously, by similar social categorization processes that influence the degree to which the client team as a whole serves as a cooperative resource for demographically similar versus dissimilar boundary spanner-client dyads. Using a sample of 168 senior boundary spanners from the consulting industry, we find that generational diversity among client team members from a client organization undermines the perception of being trusted within homogeneous boundary spanner-client dyads while it enhances the perception of being trusted within heterogeneous dyads. The perception of being trusted is an important aspect of cross-boundary relationships because it influences coordination and the costs associated with coordination. © 2015 The Author Journal of Organizational Behavior Published by John Wiley & Sons Ltd.

  18. Diversity in theory and practice: A review with application to the evolution of renewable energy generation in the UK

    International Nuclear Information System (INIS)

    Cooke, Henrietta; Keppo, Ilkka; Wolf, Steven

    2013-01-01

    There is clear consensus on the value of diversity as applied to energy systems, with the concept being a central reference for governments, industry and civil society organizations. Given its importance in policy debates, we have sought to explore the specification and measurement of diversity. We show that although conceptualisation of diversity has developed over recent years, along with increasingly elegant mathematical representations, the concept is, at core, subjective and irreducibly context specific. Subjectivity derives from determination of boundaries and the placement of objects into categories, the acts that make assessment of diversity possible. We illustrate this point with an empirical analysis of the diversity of renewable energy generation in the UK over the past century. By applying a range of different indices and classifications to this dataset, we demonstrate that the ‘diversity story’ told is different in each case. As such we argue that the analysis of diversity must be produced and consumed critically. Attempts to expand, manage, measure or comment upon the diversity of a system, be it an ecosystem, an organization, an economy, or an energy portfolio, demand rigor, reflexivity and, most importantly, transparency. - Highlights: • We review concepts of diversity and approaches to diversity measurement. • We examine the inherent subjectivity associated with any such measurement. • We illustrate this by applying different diversity indices to the same dataset. • The dataset used is the UK renewable energy portfolio over the past 100 years. • Different measures yield different results telling different ‘diversity stories’

  19. Towards a broader understanding of generational diversity at work : methodological and empirical contributions from a multi-cultural study

    OpenAIRE

    Gonçalves, João André Ferreira

    2015-01-01

    Tese de mestrado, Psicologia (Secção de Psicologia dos Recursos Humanos, do Trabalho e das Organizações), Universidade de Lisboa, Faculdade de Psicologia, 2015 Despite a disarray of popular literature concerning generational diversity in the workplace, the scientific research in this domain is still scarce and seeks stronger theoretical grounding. Regarding this problematic, the present work aims to contribute to a broader understanding of generational diversity in the workplace, by ...

  20. Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis.

    Directory of Open Access Journals (Sweden)

    Antoine Claessens

    2014-12-01

    Full Text Available The most polymorphic gene family in P. falciparum is the ∼60 var genes distributed across parasite chromosomes, both in the subtelomeres and in internal regions. They encode hypervariable surface proteins known as P. falciparum erythrocyte membrane protein 1 (PfEMP1 that are critical for pathogenesis and immune evasion in Plasmodium falciparum. How var gene sequence diversity is generated is not currently completely understood. To address this, we constructed large clone trees and performed whole genome sequence analysis to study the generation of novel var gene sequences in asexually replicating parasites. While single nucleotide polymorphisms (SNPs were scattered across the genome, structural variants (deletions, duplications, translocations were focused in and around var genes, with considerable variation in frequency between strains. Analysis of more than 100 recombination events involving var exon 1 revealed that the average nucleotide sequence identity of two recombining exons was only 63% (range: 52.7-72.4% yet the crossovers were error-free and occurred in such a way that the resulting sequence was in frame and domain architecture was preserved. Var exon 1, which encodes the immunologically exposed part of the protein, recombined in up to 0.2% of infected erythrocytes in vitro per life cycle. The high rate of var exon 1 recombination indicates that millions of new antigenic structures could potentially be generated each day in a single infected individual. We propose a model whereby var gene sequence polymorphism is mainly generated during the asexual part of the life cycle.

  1. Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis.

    Science.gov (United States)

    Claessens, Antoine; Hamilton, William L; Kekre, Mihir; Otto, Thomas D; Faizullabhoy, Adnan; Rayner, Julian C; Kwiatkowski, Dominic

    2014-12-01

    The most polymorphic gene family in P. falciparum is the ∼60 var genes distributed across parasite chromosomes, both in the subtelomeres and in internal regions. They encode hypervariable surface proteins known as P. falciparum erythrocyte membrane protein 1 (PfEMP1) that are critical for pathogenesis and immune evasion in Plasmodium falciparum. How var gene sequence diversity is generated is not currently completely understood. To address this, we constructed large clone trees and performed whole genome sequence analysis to study the generation of novel var gene sequences in asexually replicating parasites. While single nucleotide polymorphisms (SNPs) were scattered across the genome, structural variants (deletions, duplications, translocations) were focused in and around var genes, with considerable variation in frequency between strains. Analysis of more than 100 recombination events involving var exon 1 revealed that the average nucleotide sequence identity of two recombining exons was only 63% (range: 52.7-72.4%) yet the crossovers were error-free and occurred in such a way that the resulting sequence was in frame and domain architecture was preserved. Var exon 1, which encodes the immunologically exposed part of the protein, recombined in up to 0.2% of infected erythrocytes in vitro per life cycle. The high rate of var exon 1 recombination indicates that millions of new antigenic structures could potentially be generated each day in a single infected individual. We propose a model whereby var gene sequence polymorphism is mainly generated during the asexual part of the life cycle.

  2. Dataset for the proteomic inventory and quantitative analysis of the breast cancer hypoxic secretome associated with osteotropism

    Directory of Open Access Journals (Sweden)

    Thomas R. Cox

    2015-12-01

    Full Text Available The cancer secretome includes all of the macromolecules secreted by cells into their microenvironment. Cancer cell secretomes are significantly different to that of normal cells reflecting the changes that normal cells have undergone during their transition to malignancy. More importantly, cancer secretomes are known to be active mediators of both local and distant host cells and play an important role in the progression and dissemination of cancer. Here we have quantitatively profiled both the composition of breast cancer secretomes associated with osteotropism, and their modulation under normoxic and hypoxic conditions. We detect and quantify 162 secretome proteins across all conditions which show differential hypoxic induction and association with osteotropism. Mass Spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000397 and the complete proteomic, bioinformatic and biological analyses are reported in Cox et al. (2015 [1].

  3. Temperature modulates the secretome of the phytopathogenic fungus Lasiodiplodia theobromae

    Directory of Open Access Journals (Sweden)

    Carina Félix

    2016-08-01

    Full Text Available Environmental alterations modulate host-microorganism interactions. Little is known about how climate changes can trigger pathogenic features on symbiont or mutualistic microorganisms. Current climate models predict increased environmental temperatures.The exposing of phytopathogens to these changing conditions can have particularly relevant consequences for economically important species and for humans. The impact on pathogen/host interaction and the shift on their biogeographical range can induce different levels of virulence in new hosts, allowing massive losses in agricultural and health fields.Lasiodiplodia theobromae is a phytopathogenic fungus responsible for a number of diseases in various plants. It has also been described as an opportunist pathogen in humans, causing infections with different levels of severity. Lasiodiplodia theobromae has a high capacity of adaptation to different environments, such as woody plants, moist argillaceous soils or even humans, being able to grow and infect hosts in a wide range of temperatures (9ºC-39ºC. Nonetheless, the effect of an increase of temperature, as predicted in climate change models, on L. theobromae is unknown.Here we explore the effect of temperature on two strains of L. theobromae – an environmental strain CAA019, and a clinical strain, CBS339.90.We show that both strains are cytotoxic to mammalian cells but while the environmental strain is cytotoxic mainly at 25ºC, the clinical strain is cytotoxic mainly at 30ºC and 37ºC.Extracellular gelatinolytic, xylanolytic, amylolytic and cellulolytic activities at 25ºC and 37ºC were characterized by zymography and the secretome of both strains grown at 25ºC, 30ºC and 37ºC were characterized by electrophoresis and by Orbitrap LC-MS/MS. More than 75% of the proteins were identified, mostly enzymes (glycosyl hydrolases and proteases. The strains showed different protein profiles, which were affected by growth temperature. Also, strain

  4. Partnerships Generating a Workforce Pipeline: Empowering Young People, from Diverse Backgrounds, to Become Tomorrow's Scientific Leaders

    Science.gov (United States)

    Nguyen, T.; Goodwin, L.; Talley, D. M.

    2011-12-01

    There is a critical need to build students' scientific understanding and prepare them to fill the roles of future decision-makers and the scientific workforce. In particular, efforts are needed to reach the underserved communities, which represent the greatest untapped talent pool in the sciences. In order to build future leadership in this arena, we must employ innovative approaches that generate young peoples' interest and develop their capabilities early in their education so that an increased number will enter college interested in and prepared to pursue careers in scientific fields. Partnerships between early and informal education providers and scientists from academia, industry, and government agencies are essential to generate a pipeline of students able to and interested in making this transition. Ocean Discovery Institute's partnership model uses authentic scientific discovery to generate the spark that makes young people, from the most urban and diverse backgrounds, eager to learn. As these young people work alongside science mentors to discover the world around them, they discover themselves and their future as scientific leaders. The success of this model includes increasing students' science performance, attendance in college, selection of science and conservation majors, and contributions directly to the field of geoscience. Content assessments, surveys, interviews, and tracking data demonstrate 73% of student graduates declaring majors in science and conservation fields, higher scores on standardized tests relative to their peers, and contributions to science research including 10 publications and more than 30 scientific presentations. In addition, robust and long-term partnerships have been established with institutions including the University of San Diego, Scripps Institution of Oceanography, Sempra Energy, and the National Oceanic & Atmospheric Administration. We will share lessons learned from over ten years of experience in partnering with

  5. Cellulomonas fimi secretomes: In vivo and in silico approaches for the lignocellulose bioconversion.

    Science.gov (United States)

    Spertino, Stefano; Boatti, Lara; Icardi, Sara; Manfredi, Marcello; Cattaneo, Chiara; Marengo, Emilio; Cavaletto, Maria

    2018-03-20

    Lignocellulose degradation is a challenging step for value added products and biofuels production. Cellulomonas fimi secretes complex mixtures of carbohydrate active enzymes (CAZymes) which synergistically degrade cellulose and hemicelluloses. Their characterization may provide new insights for enzymatic cocktails implementation. Bioinformatic analysis highlighted 1127 secreted proteins, constituting the in silico secretome, graphically represented in a 2DE map. According to Blast2GO functional annotation, many of these are involved in carbohydrates metabolism. In vivo secretomes were obtained, growing C. fimi on glucose, CMC or wheat straw for 24 h. Zymography revealed degradative activity on carbohydrates and proteomic analysis identified some CAZymes, only in secretomes obtained with CMC and wheat straw. An interaction between cellobiohydrolases is proposed as a strategy adopted by soluble multimodular cellulases. Such approach can be crucial for a better characterization and industrial exploitation of the synergism among C. fimi enzymes. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. Analysis of secretome of breast cancer cell line with an optimized semi-shotgun method

    International Nuclear Information System (INIS)

    Tang Xiaorong; Yao Ling; Chen Keying; Hu Xiaofang; Xu Lisa; Fan Chunhai

    2009-01-01

    Secretome, the totality of secreted proteins, is viewed as a promising pool of candidate cancer biomarkers. Simple and reliable methods for identifying secreted proteins are highly desired. We used an optimized semi-shotgun liquid chromatography followed by tandem mass spectrometry (LC-MS/MS) method to analyze the secretome of breast cancer cell line MDA-MB-231. A total of 464 proteins were identified. About 63% of the proteins were classified as secreted proteins, including many promising breast cancer biomarkers, which were thought to be correlated with tumorigenesis, tumor development and metastasis. These results suggest that the optimized method may be a powerful strategy for cell line secretome profiling, and can be used to find potential cancer biomarkers with great clinical significance. (authors)

  7. Evaluation of Different Feeds for Their Potential to Generate Methane and Change Methanogen Diversity

    Directory of Open Access Journals (Sweden)

    Seon-Ho Kim

    2013-12-01

    Full Text Available Optimization of the dietary formulation is the most effective way to reduce methane. Nineteen feed ingredients (brans, vegetable proteins, and grains were evaluated for their potential to generate methane and change methanogen diversity using an in vitro ruminal fermentation technique. Feed formulations categorized into high, medium and low production based on methane production of each ingredient were then subjected to in vitro fermentation to determine the real methane production and their effects on digestibility. Methanogen diversity among low, medium and high-methane producing groups was analyzed by PCR-DGGE. The highest methane production was observed in Korean wheat bran, soybean and perilla meals, and wheat and maize of brans, vegetable protein and cereal groups, respectively. On the other hand, corn bran, cotton seed meal and barley led to the lowest production in the same groups. Nine bacteria and 18 methanogen 16s rDNA PCR-DGGE dominant bands were identified with 83% to 99% and 92% to 100% similarity, respectively. Overall, the results of this study showed that methane emissions from ruminants can be mitigated through proper selection of feed ingredients to be used in the formulation of diets.

  8. A genomic perspective on the generation and maintenance of genetic diversity in herbivorous insects.

    Science.gov (United States)

    Gloss, Andrew D; Groen, Simon C; Whiteman, Noah K

    2016-11-01

    Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales-from variation within populations to divergence among populations-to form a comprehensive view of adaptation in herbivorous insects.

  9. Selective ligand recognition by a diversity-generating retroelement variable protein.

    Directory of Open Access Journals (Sweden)

    Jason L Miller

    2008-06-01

    Full Text Available Diversity-generating retroelements (DGRs recognize novel ligands through massive protein sequence variation, a property shared uniquely with the adaptive immune response. Little is known about how recognition is achieved by DGR variable proteins. Here, we present the structure of the Bordetella bacteriophage DGR variable protein major tropism determinant (Mtd bound to the receptor pertactin, revealing remarkable adaptability in the static binding sites of Mtd. Despite large dissimilarities in ligand binding mode, principles underlying selective recognition were strikingly conserved between Mtd and immunoreceptors. Central to this was the differential amplification of binding strengths by avidity (i.e., multivalency, which not only relaxed the demand for optimal complementarity between Mtd and pertactin but also enhanced distinctions among binding events to provide selectivity. A quantitatively similar balance between complementarity and avidity was observed for Bordetella bacteriophage DGR as occurs in the immune system, suggesting that variable repertoires operate under a narrow set of conditions to recognize novel ligands.

  10. Cardiosphere Derived Cells from Pediatric End-Stage Heart Failure Patients Have Enhanced Functional Activity due to the Heat Shock Response Regulating the Secretome

    Science.gov (United States)

    Sharma, Sudhish; Mishra, Rachana; Simpson, David; Wehman, Brody; Colletti, Evan J.; Deshmukh, Savitha; Datla, Srinivasa Raju; Balachandran, Keerti; Guo, Yin; Chen, Ling; Siddiqui, Osama T.; Kaushal, Shalesh; Kaushal, Sunjay

    2016-01-01

    We have demonstrated that human neonatal cardiosphere derived cells (CDCs) derived from the young are more regenerative due to their robust secretome. However, it is unclear how the decompensated pediatric heart impacts the functional activity of their CDCs. Our aim was to characterize the potency of pediatric CDCs derived from normal functioning myocardium of control heart disease (CHD) patients to those generated from age matched end stage heart failure (ESHF) patients and determine the mechanisms involved. ESHF derived CDCs contained a higher number of c-kit+, Islet-1+, and Sca-1+ cells. When transplanted into an infarcted rodent model, ESHF derived CDCs significantly demonstrated higher restoration of ventricular function, prevented adverse remodeling, and enhanced angiogenesis when compared to CHD patients. The superior functional recovery of the ESHF derived CDCs was mediated in part by increased SDF-1α and VEGF-A secretion resulting in augmented recruitment of endogenous stem cells and proliferation of cardiomyocytes. We determined the mechanism is due to the secretome directed by the heat shock response (HSR), which is supported by three lines of evidence. Firstly, gain of function studies demonstrated that increased HSR induced the lower functioning CHD derived CDCs to significantly restore myocardial function. Secondly, loss-of function studies targeting the HSR impaired the ability of the ESHF derived CDCs to functionally recover the injured myocardium. Finally, the native ESHF myocardium had an increased number of c-kit+ CSCs. These findings suggest that the HSR enhances the functional activity of ESHF derived CDCs by increasing their secretome activity, notably SDF-1α and VEGF-A. PMID:25752510

  11. MacroEvoLution: A New Method for the Rapid Generation of Novel Scaffold-Diverse Macrocyclic Libraries.

    Science.gov (United States)

    Saupe, Jörn; Kunz, Oliver; Haustedt, Lars Ole; Jakupovic, Sven; Mang, Christian

    2017-09-04

    Macrocycles are a structural class bearing great promise for future challenges in medicinal chemistry. Nevertheless, there are few flexible approaches for the rapid generation of structurally diverse macrocyclic compound collections. Here, an efficient method for the generation of novel macrocyclic peptide-based scaffolds is reported. The process, named here as "MacroEvoLution", is based on a cyclization screening approach that gives reliable access to novel macrocyclic architectures. Classification of building blocks into specific pools ensures that scaffolds with orthogonally addressable functionalities are generated, which can easily be used for the generation of structurally diverse compound libraries. The method grants rapid access to novel scaffolds with scalable synthesis (multi gram scale) and the introduction of further diversity at a late stage. Despite being developed for peptidic systems, the approach can easily be extended for the synthesis of systems with a decreased peptidic character. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  12. MacroEvoLution: A New Method for the Rapid Generation of Novel Scaffold‐Diverse Macrocyclic Libraries

    Science.gov (United States)

    Saupe, Jörn; Kunz, Oliver; Haustedt, Lars Ole; Jakupovic, Sven

    2017-01-01

    Abstract Macrocycles are a structural class bearing great promise for future challenges in medicinal chemistry. Nevertheless, there are few flexible approaches for the rapid generation of structurally diverse macrocyclic compound collections. Here, an efficient method for the generation of novel macrocyclic peptide‐based scaffolds is reported. The process, named here as “MacroEvoLution”, is based on a cyclization screening approach that gives reliable access to novel macrocyclic architectures. Classification of building blocks into specific pools ensures that scaffolds with orthogonally addressable functionalities are generated, which can easily be used for the generation of structurally diverse compound libraries. The method grants rapid access to novel scaffolds with scalable synthesis (multi gram scale) and the introduction of further diversity at a late stage. Despite being developed for peptidic systems, the approach can easily be extended for the synthesis of systems with a decreased peptidic character. PMID:28715083

  13. Mesenchymal Stem Cells Secretome as a Modulator of the Neurogenic Niche: Basic Insights and Therapeutic Opportunities

    Directory of Open Access Journals (Sweden)

    Antonio eSalgado

    2015-07-01

    Full Text Available Neural stem cells (NSCs and mesenchymal stem cells (MSCs share few characteristics apart from self-renewal and multipotency. In fact, the neurogenic and osteogenic stem cell niches derive from two distinct embryonary structures; while the later originates from the mesoderm, as all the connective tissues do, the first derives from the ectoderm. Therefore, it is highly unlikely that stem cells isolated from one niche could form terminally differentiated cells from the other. Additionally, these two niches are associated to tissues/systems (e.g bone and central nervous system that have markedly different needs and display diverse functions within the human body. Nevertheless they do share common features. For instance, the differentiation of both NSCs and MSCs is intimately associated with the bone morphogenetic protein family. Moreover, both NSCs and MSCs secrete a panel of common growth factors, such as nerve growth factor (NGF, glial derived neurotrophic factor (GDNF, and brain derived neurotrophic factor (BDNF, among others. But it is not the features they share but the interaction between them that seem most important, and worth exploring; namely, it has already been shown that there are mutually beneficially effects when these cell types are co-cultured in vitro. In fact the use of MSCs, and their secretome, become a strong candidate to be used as a therapeutic tool for CNS applications, namely by triggering the endogenous proliferation and differentiation of neural progenitors, among other mechanisms. Quite interestingly it was recently revealed that MSCs could be found in the human brain, in the vicinity of capillaries. In the present review we highlight how MSCs and NSCs in the neurogenic niches interact. Furthermore, we propose directions on this field and explore the future therapeutic possibilities that may arise from the combination/interaction of MSCs and NSCs.

  14. Haplotype diversity generated by ancient recombination-like events in the MHC of Indian rhesus macaques.

    Science.gov (United States)

    Doxiadis, Gaby G M; de Groot, Nanine; Otting, Nel; de Vos-Rouweler, Annemiek J M; Bolijn, Maria J; Heijmans, Corrine M C; de Groot, Natasja G; van der Wiel, Marit K H; Remarque, Edmond J; Vangenot, Christelle; Nunes, José M; Sanchez-Mazas, Alicia; Bontrop, Ronald E

    2013-08-01

    The Mamu-A, Mamu-B, and Mamu-DRB genes of the rhesus macaque show several levels of complexity such as allelic heterogeneity (polymorphism), copy number variation, differential segregation of genes/alleles present on a haplotype (diversity) and transcription level differences. A combination of techniques was implemented to screen a large panel of pedigreed Indian rhesus macaques (1,384 individuals representing the offspring of 137 founding animals) for haplotype diversity in an efficient and inexpensive manner. This approach allowed the definition of 140 haplotypes that display a relatively low degree of region variation as reflected by the presence of only 17 A, 18 B and 22 DRB types, respectively, exhibiting a global linkage disequilibrium comparable to that in humans. This finding contrasts with the situation observed in rhesus macaques from other geographic origins and in cynomolgus monkeys from Indonesia. In these latter populations, nearly every haplotype appears to be characterised by a unique A, B and DRB region. In the Indian population, however, a reshuffling of existing segments generated "new" haplotypes. Since the recombination frequency within the core MHC of the Indian rhesus macaques is relatively low, the various haplotypes were most probably produced by recombination events that accumulated over a long evolutionary time span. This idea is in accord with the notion that Indian rhesus macaques experienced a severe reduction in population during the Pleistocene due to a bottleneck caused by geographic changes. Thus, recombination-like processes appear to be a way to expand a diminished genetic repertoire in an isolated and relatively small founder population.

  15. Next generation sequencing characterizes the extent of HLA diversity in an Argentinian registry population.

    Science.gov (United States)

    Hurley, C K; Hou, L; Lazaro, A; Gerfen, J; Enriquez, E; Galarza, P; Rodriguez Cardozo, M B; Halagan, M; Maiers, M; Behm, D; Ng, J

    2018-03-01

    Next generation DNA sequencing is used to determine the HLA-A, -B, -C, -DRB1, and -DQB1 assignments of 1472 unrelated volunteers for the unrelated donor registry in Argentina. The analysis characterized all HLA exons and introns for class I alleles; at least exons 2, 3 for HLA-DRB1; and exons 2 to 6 for HLA-DQB1. Of the distinct alleles present, there are 330 class I and 98 class II. The majority (~98%) of the cumulative allele frequency at each locus is contributed by alleles that appear at a frequency of at least 1 in 1000. Fourteen (18.2%) of the 77 novel class I and II alleles carry nonsynonymous variation within their exons; 52 (75.4%) class I novel alleles carry only single, apparently random, nucleotide variation within their introns/untranslated regions. Alleles encoding protein variation not usually detected by typing focused only on the exons encoding the antigen recognition domain are 1.0% of the class I assignments and 7.3% of the class II assignments (predominantly DQB1*02:02:01, DQB1*03:19:01, and DRB1*14:54:01). Updates to the common and well documented list of alleles include 10 alleles previously thought to be uncommon but that are found at least 30 times. Five locus haplotypes estimated using the expectation-maximization algorithm as present 3 or more times total 187. While the known HLA diversity continues to increase, the conservation of known allele sequences is remarkable. Overall, the HLA diversity observed in the Argentinian population reflects its European and Native American ancestry. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Human astrocytes: secretome profiles of cytokines and chemokines.

    Directory of Open Access Journals (Sweden)

    Sung S Choi

    Full Text Available Astrocytes play a key role in maintenance of neuronal functions in the central nervous system by producing various cytokines, chemokines, and growth factors, which act as a molecular coordinator of neuron-glia communication. At the site of neuroinflammation, astrocyte-derived cytokines and chemokines play both neuroprotective and neurotoxic roles in brain lesions of human neurological diseases. At present, the comprehensive profile of human astrocyte-derived cytokines and chemokines during inflammation remains to be fully characterized. We investigated the cytokine secretome profile of highly purified human astrocytes by using a protein microarray. Non-stimulated human astrocytes in culture expressed eight cytokines, including G-CSF, GM-CSF, GROα (CXCL1, IL-6, IL-8 (CXCL8, MCP-1 (CCL2, MIF and Serpin E1. Following stimulation with IL-1β and TNF-α, activated astrocytes newly produced IL-1β, IL-1ra, TNF-α, IP-10 (CXCL10, MIP-1α (CCL3 and RANTES (CCL5, in addition to the induction of sICAM-1 and complement component 5. Database search indicated that most of cytokines and chemokines produced by non-stimulated and activated astrocytes are direct targets of the transcription factor NF-kB. These results indicated that cultured human astrocytes express a distinct set of NF-kB-target cytokines and chemokines in resting and activated conditions, suggesting that the NF-kB signaling pathway differentially regulates gene expression of cytokines and chemokines in human astrocytes under physiological and inflammatory conditions.

  17. Infection related stress adaptations in the secretome and wall proteome of Candida albicans

    NARCIS (Netherlands)

    Sorgo, A.G.

    2013-01-01

    Alice Sorgo's main research question concerns the adaptability of the wall proteome and secretome of the opportunistic pathogenic fungus Candida albicans. The question is how do these subproteomes adapt to environmental stess (high temperatures, iron restriction, antifungal drugs) and how do these

  18. Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing

    Energy Technology Data Exchange (ETDEWEB)

    Dumortier, Jerome; Streblow, Daniel N.; Moses, Ashlee V.; Jacobs, Jon M.; Kreklywich, Craig N.; Camp, David G.; Smith, Richard D.; Orloff, Susan L.; Nelson, Jay

    2008-07-01

    Human cytomegalovirus (HCMV) is implicated in the acceleration of a number of vascular diseases including transplant vascular sclerosis (TVS), the lesion associated with chronic rejection (CR) of solid organ transplants. Although the virus persists in the allograft throughout the course of disease, few cells are directly infected by CMV. This observation is in contrast to the global effects that CMV has on the acceleration of TVS/CR, suggesting that CMV infection indirectly promotes the vascular disease process. Recent transcriptome analysis of CMV-infected heart allografts indicates that the virus induces cytokines and growth factors associated with angiogenesis (AG) and wound healing (WH), suggesting that CMV may accelerate TVS/CR through the induction and secretion of AG/WH factors from infected cells. We analyzed virus-free supernatants from HCMV-infected cells (HCMV secretomes) for growth factors, by mass spectrometry and immunoassays, and found that the HCMV secretome contains over 1,000 cellular proteins, many of which are involved in AG/WH. Importantly, functional assays demonstrated that CMV but not herpes simplex virus secretomes not only induce AG/WH but also promote neovessel stabilization and endothelial cell survival for 2 weeks. These findings suggest that CMV acceleration of TVS occurs through virus-induced growth factors and cytokines in the CMV secretome.

  19. Fungal secretomics to probe the biological functions of lytic polysaccharide monooxygenases

    DEFF Research Database (Denmark)

    Berrin, Jean-Guy; Rosso, Marie-Noëlle; Abou Hachem, Maher

    2017-01-01

    to starch, the main carbon storage reservoir. In this review, we focus on the identification of lytic polysaccharide monooxygenases (LPMOs) and their redox partners in fungal secretomes to highlight the biological functions of these remarkable enzyme systems and we discuss future trends related to LPMO...

  20. Secretomes of Mycoplasma hyopneumoniae and Mycoplasma flocculare reveal differences associated to pathogenesis.

    Science.gov (United States)

    Paes, Jéssica A; Lorenzatto, Karina R; de Moraes, Sofia N; Moura, Hercules; Barr, John R; Ferreira, Henrique B

    2017-02-10

    Mycoplasma hyopneumoniae and Mycoplasma flocculare cohabit the porcine respiratory tract. However, M. hyopneumoniae causes the porcine enzootic pneumonia, while M. flocculare is a commensal bacterium. Comparative analyses demonstrated high similarity between these species, which includes the sharing of all predicted virulence factors. Nevertheless, studies related to soluble secretomes of mycoplasmas were little known, although they are important for bacterial-host interactions. The aim of this study was to perform a comparative analysis between the soluble secreted proteins repertoires of the pathogenic Mycoplasma hyopneumoniae and its closely related commensal Mycoplasma flocculare. For that, bacteria were cultured in medium with reduced serum concentration and secreted proteins were identified by a LC-MS/MS proteomics approach. Altogether, 62 and 26 proteins were identified as secreted by M. hyopneumoniae and M. flocculare, respectively, being just seven proteins shared between these bacteria. In M. hyopneumoniae secretome, 15 proteins described as virulence factors were found; while four putative virulence factors were identified in M. flocculare secretome. For the first time, clear differences related to virulence were found between these species, helping to elucidate the pathogenic nature of M. hyopneumoniae to swine hosts. For the first time, the secretomes of two porcine respiratory mycoplasmas, namely the pathogenic M. hyopneumoniae and the commensal M. flocculare were compared. The presented results revealed previously unknown differences between these two genetically related species, some of which are associated to the M. hyopneumoniae ability to cause porcine enzootic pneumonia. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium

    Science.gov (United States)

    Amber J. Vanden Wymelenberg; Jill Gaskell; Michael Mozuch; Grzegorz Sabat; John Ralph; Oleksandr Skyba; Shawn D Mansfield; Robert A. Blanchette; Diego Martinez; Igor Grigoriev; Philip J Kersten; Daniel Cullen

    2010-01-01

    Cellulose degradation by brown rot fungi, such as Postia placenta, is poorly understood relative to the phylogenetically related white rot basidiomycete, Phanerochaete chrysosporium. To elucidate the number, structure, and regulation of genes involved in lignocellulosic cell wall attack, secretome and transcriptome analyses were performed on both wood decay fungi...

  2. Investigating the secretome : Lessons about the cells that comprise the heart

    Czech Academy of Sciences Publication Activity Database

    Šťastná, Miroslava; Van Eyk, J.E.

    2012-01-01

    Roč. 5, č. 1 (2012), o8-o18 ISSN 1942-325X Institutional research plan: CEZ:AV0Z40310501 Keywords : secretomes * proteomics * cardiovascular diseases Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 6.728, year: 2012

  3. High Resolution Proteomic Analysis of the Cervical Cancer Cell Lines Secretome Documents Deregulation of Multiple Proteases.

    Science.gov (United States)

    Pappa, Kalliopi I; Kontostathi, Georgia; Makridakis, Manousos; Lygirou, Vasiliki; Zoidakis, Jerome; Daskalakis, George; Anagnou, Nicholas P

    2017-01-01

    Oncogenic infection by HPV, eventually leads to cervical carcinogenesis, associated by deregulation of specific pathways and protein expression at the intracellular and secretome level. Thus, secretome analysis can elucidate the biological mechanisms contributing to cervical cancer. In the present study we systematically analyzed its constitution in four cervical cell lines employing a highly sensitive proteomic technology coupled with bioinformatics analysis. LC/MS-MS proteomics and bioinformatics analysis were performed in the secretome of four informative cervical cell lines SiHa (HPV16 + ), HeLa (HPV18 + ), C33A (HPV - ) and HCK1T (normal). The proteomic pattern of each cancer cell line compared to HCK1T was identified and a detailed bioinformatics analysis disclosed inhibition of matrix metalloproteases in cancer cell lines. This prediction was further confirmed via zymography for MMP-2 and MMP-9, western blot analysis for ADAM10 and by MRM for TIMP1. The differential expression of important secreted proteins such as CATD, FUCA1 and SOD2 was also confirmed by western blot analysis. MRM-targeted proteomics analysis confirmed the differential expression of CATD, CATB, SOD2, QPCT and NEU1. High resolution proteomics analysis of cervical cancer secretome revealed significantly deregulated biological processes and proteins implicated in cervical carcinogenesis. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  4. Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing

    Science.gov (United States)

    Alana Alexander; Debbie Steel; Beth Slikas; Kendra Hoekzema; Colm Carraher; Matthew Parks; Richard Cronn; C. Scott Baker

    2012-01-01

    Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20...

  5. Multicomponent domino processes based on the organocatalytic generation of conjugated acetylides: efficient synthetic manifolds for diversity-oriented molecular construction.

    Science.gov (United States)

    Tejedor, David; González-Cruz, David; Santos-Expósito, Alicia; Marrero-Tellado, Jose Juan; de Armas, Pedro; García-Tellado, Fernando

    2005-06-06

    The organocatalytic generation of a strong base by the action of a good nucleophile is the base for the in situ catalytic generation of conjugated acetylides in the presence of aldehydes or activated ketones. The method is affordable in a multicomponent, domino format able to generate a chemically diverse set of multifunctionalized adducts that are very well suited for diversity-oriented molecular construction. The domino process involves a nucleophile as catalyst and a terminal conjugated alkyne (H-C[triple chemical bond]C-Z) and an aldehyde or activated ketone as building blocks. The chemical outcome of this process changes dramatically as a function of the nucleophile (tertiary amine or phosphine), temperature, stoichiometry, and solvent. These multicomponent domino processes achieve molecular construction with good atom economy and, very importantly, with an exquisite chemo-differentiating incorporation of identical starting units into the products (nondegenerated chemical output). These properties convert the H-C[triple chemical bond]C-Z unit into a specific building block for diversity-oriented molecular construction. Applications to the modular and diversity-oriented synthesis of relevant heterocycles are discussed. A protocol involving two coupled domino processes linked in a one-pot manner will be discussed as an efficient synthetic manifold for the modular and diversity-oriented construction of multisubstituted nitrogen-containing heterocycles.

  6. Proteomic Profile of Unstable Atheroma Plaque: Increased Neutrophil Defensin 1, Clusterin, and Apolipoprotein E Levels in Carotid Secretome.

    Science.gov (United States)

    Aragonès, Gemma; Auguet, Teresa; Guiu-Jurado, Esther; Berlanga, Alba; Curriu, Marta; Martinez, Salomé; Alibalic, Ajla; Aguilar, Carmen; Hernández, Esteban; Camara, María-Luisa; Canela, Núria; Herrero, Pol; Ruyra, Xavier; Martín-Paredero, Vicente; Richart, Cristóbal

    2016-03-04

    Because of the clinical significance of carotid atherosclerosis, the search for novel biomarkers has become a priority. The aim of the present study was to compare the protein secretion profile of the carotid atherosclerotic plaque (CAP, n = 12) and nonatherosclerotic mammary artery (MA, n = 10) secretomes. We used a nontargeted proteomic approach that incorporated tandem immunoaffinity depletion, iTRAQ labeling, and nanoflow liquid chromatography coupled to high-resolution mass spectrometry. In total, 162 proteins were quantified, of which 25 showed statistically significant differences in secretome levels between carotid atherosclerotic plaque and nondiseased mammary artery. We found increased levels of neutrophil defensin 1, apolipoprotein E, clusterin, and zinc-alpha-2-glycoprotein in CAP secretomes. Results were validated by ELISA assays. Also, differentially secreted proteins are involved in pathways such as focal adhesion and leukocyte transendothelial migration. In conclusion, this study provides a subset of identified proteins that are differently expressed in secretomes of clinical significance.

  7. Ecology and evolution in microbial systems: the generation and maintenance of diversity in phage-host interactions.

    Science.gov (United States)

    Jessup, Christine M; Forde, Samantha E

    2008-06-01

    Insights gained from studying the interactions between viruses and bacteria have important implications for the ecology and evolution of virus-host interactions in many environments and for pathogen-host and predator-prey interactions in general. Here, we focus on the generation and maintenance of diversity, highlighting recent laboratory and field experiments with microorganisms.

  8. Use of Long-Term E. Coli Cultures: To Study Generation of Genetic Diversity & Teach General Microbiology Laboratory Skills

    Science.gov (United States)

    Petrie, Angela; Finkel, Steven E.; Erbe, Jarrod

    2005-01-01

    A novel method of studying the generation of genetic diversity in an undergraduate microbiology laboratory is described. The basis of this approach is the accumulation of mutations that confer a competitive advantage, or growth advantage in stationary phase (GASP) phenotype, to E. coli grown in stationary phase for extended periods of time.

  9. Alpha-arylphorin is a mitogen in the Heliothis virescens midgut cell secretome upon Cry1Ac intoxication

    Directory of Open Access Journals (Sweden)

    Anais Castagnola

    2017-10-01

    Full Text Available Insecticidal crystal (Cry proteins produced by the bacterium Bacillus thuringiensis (Bt target cells in the midgut epithelium of susceptible larvae. While the mode of action of Cry toxins has been extensively investigated, the midgut response to Cry intoxication and its regulation are not well characterized. In this work, we describe the secreted proteome (secretome of primary mature midgut cell cultures from Heliothis virescens larvae after exposure to Cry1Ac toxin compared to control buffer treatment. The Cry1Ac-induced secretome caused higher proliferation and differentiation and an overall reduction in total cell mortality over time in primary H. virescens midgut stem cell cultures when compared to treatment with control buffer secretome. Differential proteomics identified four proteins with significant differences in abundance comparing Cry1Ac-treated and control secretomes. The most significant difference detected in the Cry1Ac secretome was an arylphorin subunit alpha protein not detected in the control secretome. Feeding of purified alpha-arylphorin to H. virescens larvae resulted in midgut hyperplasia and significantly reduced susceptibility to Cry1Ac toxin compared to controls. These data identify alpha-arylphorin as a protein with a new putative role in the midgut regeneration process in response to Cry1Ac intoxication and possibly pathogen/abiotic stress, identifying alpha-arylphorin as a potential gene to target with insecticidal gene silencing for pest control.

  10. Second generation sequencing for elucidating the diversity of bacteria and plasmids in soil

    DEFF Research Database (Denmark)

    Holmsgaard, Peter Nikolai

    . The relative abundance of IncP-1β1 plasmids also increased. In papers four and five, the mobile genetic elements and bacterial diversity, respectively, was studied over a pesticide spraying season in the same BPS used in paper three. The addition of pesticides decreased overall bacterial diversity...

  11. Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

    Science.gov (United States)

    Hori, Chiaki; Ishida, Takuya; Igarashi, Kiyohiko; Samejima, Masahiro; Suzuki, Hitoshi; Master, Emma; Ferreira, Patricia; Ruiz-Dueñas, Francisco J.; Held, Benjamin; Canessa, Paulo; Larrondo, Luis F.; Schmoll, Monika; Druzhinina, Irina S.; Kubicek, Christian P.; Gaskell, Jill A.; Kersten, Phil; St. John, Franz; Glasner, Jeremy; Sabat, Grzegorz; Splinter BonDurant, Sandra; Syed, Khajamohiddin; Yadav, Jagjit; Mgbeahuruike, Anthony C.; Kovalchuk, Andriy; Asiegbu, Fred O.; Lackner, Gerald; Hoffmeister, Dirk; Rencoret, Jorge; Gutiérrez, Ana; Sun, Hui; Lindquist, Erika; Barry, Kerrie; Riley, Robert; Grigoriev, Igor V.; Henrissat, Bernard; Kües, Ursula; Berka, Randy M.; Martínez, Angel T.; Covert, Sarah F.; Blanchette, Robert A.; Cullen, Daniel

    2014-01-01

    Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes. PMID:25474575

  12. The secretome of Trametes versicolor grown on tomato juice medium and purification of the secreted oxidoreductases including a versatile peroxidase.

    Science.gov (United States)

    Carabajal, Maira; Kellner, Harald; Levin, Laura; Jehmlich, Nico; Hofrichter, Martin; Ullrich, René

    2013-10-10

    The present work was carried out with the aim to analyze the secretome of Trametes versicolor BAFC 2234 grown on tomato juice medium supplemented with copper and manganese. T. versicolor BAFC 2234 was selected among diverse wood dwelling agaricomycetes from Argentina by its ability to cause a strong white rot on hardwood and in addition to show high tolerance toward phenolic compounds. A considerable number of the identified proteins were related to the degradation/modification of lignocelluloses. Hydrolases, peroxidases and phenoloxidases were the most abundant enzymes produced under the above-mentioned culture conditions. The lignin-modifying oxidoreductases laccase, manganese peroxidase (MnP) and versatile peroxidase (VP) were successfully purified - the latter for the first time from T. versicolor. The native VP protein has a molecular mass of 45kDa and an isoelectric point of pH 3.7. The study clearly shows that complex plant-based media being rich in phenolics, such as tomato juice, can stimulate the secretion of a broad set of extracellular lignocellulolytic enzymes. Using such natural products as fungal culture media may give the opportunity to investigate plant biomass decomposition as well as the biodegradation of organic pollutants in an environment close to nature. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Single-cell protein secretomic signatures as potential correlates to tumor cell lineage evolution and cell-cell interaction

    Directory of Open Access Journals (Sweden)

    Minsuk eKwak

    2013-02-01

    Full Text Available Secreted proteins including cytokines, chemokines and growth factors represent important functional regulators mediating a range of cellular behavior and cell-cell paracrine/autocrine signaling, e.g. in the immunological system, tumor microenvironment or stem cell niche. Detection of these proteins is of great value not only in basic cell biology but also for diagnosis and therapeutic monitoring of human diseases such as cancer. However, due to co-production of multiple effector proteins from a single cell, referred to as polyfunctionality, it is biologically informative to measure a panel of secreted proteins, or secretomic signature, at the level of single cells. Recent evidence further indicates that a genetically-identical cell population can give rise to diverse phenotypic differences. It is known that cytokines, for example, in the immune system define the effector functions and lineage differentiation of immune cells. In this Perspective Article, we hypothesize that protein secretion profile may represent a universal measure to identify the definitive correlate in the larger context of cellular functions to dissect cellular heterogeneity and evolutionary lineage relationship in human cancer.

  14. Secretome Prediction of Two M. tuberculosis Clinical Isolates Reveals Their High Antigenic Density and Potential Drug Targets

    Science.gov (United States)

    Cornejo-Granados, Fernanda; Zatarain-Barrón, Zyanya L.; Cantu-Robles, Vito A.; Mendoza-Vargas, Alfredo; Molina-Romero, Camilo; Sánchez, Filiberto; Del Pozo-Yauner, Luis; Hernández-Pando, Rogelio; Ochoa-Leyva, Adrián

    2017-01-01

    The Excreted/Secreted (ES) proteins play important roles during Mycobacterium tuberculosis invasion, virulence, and survival inside the host and they are a major source of immunogenic proteins. However, the molecular complexity of the bacillus cell wall has made difficult the experimental isolation of the total bacterial ES proteins. Here, we reported the genomes of two Beijing genotype M. tuberculosis clinical isolates obtained from patients from Vietnam (isolate 46) and South Africa (isolate 48). We developed a bioinformatics pipeline to predict their secretomes and observed that ~12% of the genome-encoded proteins are ES, being PE, PE-PGRS, and PPE the most abundant protein domains. Additionally, the Gene Ontology, KEGG pathways and Enzyme Classes annotations supported the expected functions for the secretomes. The ~70% of an experimental secretome compiled from literature was contained in our predicted secretomes, while only the 34–41% of the experimental secretome was contained in the two previously reported secretomes for H37Rv. These results suggest that our bioinformatics pipeline is better to predict a more complete set of ES proteins in M. tuberculosis genomes. The predicted ES proteins showed a significant higher antigenic density measured by Abundance of Antigenic Regions (AAR) value than the non-ES proteins and also compared to random constructed secretomes. Additionally, we predicted the secretomes for H37Rv, H37Ra, and two M. bovis BCG genomes. The antigenic density for BGG and for isolates 46 and 48 was higher than the observed for H37Rv and H37Ra secretomes. In addition, two sets of immunogenic proteins previously reported in patients with tuberculosis also showed a high antigenic density. Interestingly, mice infected with isolate 46 showed a significant lower survival rate than the ones infected with isolate 48 and both survival rates were lower than the one previously reported for the H37Rv in the same murine model. Finally, after a

  15. Stem cell secretome-rich nanoclay hydrogel: a dual action therapy for cardiovascular regeneration

    Science.gov (United States)

    Waters, Renae; Pacelli, Settimio; Maloney, Ryan; Medhi, Indrani; Ahmed, Rafeeq P. H.; Paul, Arghya

    2016-03-01

    A nanocomposite hydrogel with photocrosslinkable micro-porous networks and a nanoclay component was successfully prepared to control the release of growth factor-rich stem cell secretome. The proven pro-angiogenic and cardioprotective potential of this new bioactive system provides a valuable therapeutic platform for cardiac tissue repair and regeneration.A nanocomposite hydrogel with photocrosslinkable micro-porous networks and a nanoclay component was successfully prepared to control the release of growth factor-rich stem cell secretome. The proven pro-angiogenic and cardioprotective potential of this new bioactive system provides a valuable therapeutic platform for cardiac tissue repair and regeneration. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr07806g

  16. Secretome data from Trichoderma reesei and Aspergillus niger cultivated in submerged and sequential fermentation methods

    Directory of Open Access Journals (Sweden)

    Camila Florencio

    2016-09-01

    Full Text Available The cultivation procedure and the fungal strain applied for enzyme production may influence levels and profile of the proteins produced. The proteomic analysis data presented here provide critical information to compare proteins secreted by Trichoderma reesei and Aspergillus niger when cultivated through submerged and sequential fermentation processes, using steam-explosion sugarcane bagasse as inducer for enzyme production. The proteins were organized according to the families described in CAZy database as cellulases, hemicellulases, proteases/peptidases, cell-wall-protein, lipases, others (catalase, esterase, etc., glycoside hydrolases families, predicted and hypothetical proteins. Further detailed analysis of this data is provided in “Secretome analysis of Trichoderma reesei and Aspergillus niger cultivated by submerged and sequential fermentation process: enzyme production for sugarcane bagasse hydrolysis” C. Florencio, F.M. Cunha, A.C Badino, C.S. Farinas, E. Ximenes, M.R. Ladisch (2016 [1]. Keywords: Tricoderma reesei, Aspergillus Niger, Enzyme Production, Secretome

  17. Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans.

    OpenAIRE

    Min Ni; Marianna Feretzaki; Wenjun Li; Anna Floyd-Averette; Piotr Mieczkowski; Fred S Dietrich; Joseph Heitman

    2013-01-01

    Aneuploidy is known to be deleterious and underlies several common human diseases, including cancer and genetic disorders such as trisomy 21 in Down's syndrome. In contrast, aneuploidy can also be advantageous and in fungi confers antifungal drug resistance and enables rapid adaptive evolution. We report here that sexual reproduction generates phenotypic and genotypic diversity in the human pathogenic yeast Cryptococcus neoformans, which is globally distributed and commonly infects individual...

  18. An Inductive Discussion of the Interrelationships between Nursing Shortage, Horizontal Violence, Generational Diversity, and Healthy Work Environments

    Directory of Open Access Journals (Sweden)

    Francesca Armmer

    2017-09-01

    Full Text Available The complex features of the nursing shortage, horizontal violence, generational diversity and healthy work environments have frequently been addressed within the context of their singular characteristics, challenges and potential solutions. Yet it is the interrelationships of these phenomena that holds solutions to the overarching challenges facing nurses and the nursing profession. Through an inductive approach, a preliminary discussion and related strategies to address the highlighted challenges have been proposed.

  19. Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans.

    Directory of Open Access Journals (Sweden)

    Min Ni

    2013-09-01

    Full Text Available Aneuploidy is known to be deleterious and underlies several common human diseases, including cancer and genetic disorders such as trisomy 21 in Down's syndrome. In contrast, aneuploidy can also be advantageous and in fungi confers antifungal drug resistance and enables rapid adaptive evolution. We report here that sexual reproduction generates phenotypic and genotypic diversity in the human pathogenic yeast Cryptococcus neoformans, which is globally distributed and commonly infects individuals with compromised immunity, such as HIV/AIDS patients, causing life-threatening meningoencephalitis. C. neoformans has a defined a-α opposite sexual cycle; however, >99% of isolates are of the α mating type. Interestingly, α cells can undergo α-α unisexual reproduction, even involving genotypically identical cells. A central question is: Why would cells mate with themselves given that sex is costly and typically serves to admix preexisting genetic diversity from genetically divergent parents? In this study, we demonstrate that α-α unisexual reproduction frequently generates phenotypic diversity, and the majority of these variant progeny are aneuploid. Aneuploidy is responsible for the observed phenotypic changes, as chromosome loss restoring euploidy results in a wild-type phenotype. Other genetic changes, including diploidization, chromosome length polymorphisms, SNPs, and indels, were also generated. Phenotypic/genotypic changes were not observed following asexual mitotic reproduction. Aneuploidy was also detected in progeny from a-α opposite-sex congenic mating; thus, both homothallic and heterothallic sexual reproduction can generate phenotypic diversity de novo. Our study suggests that the ability to undergo unisexual reproduction may be an evolutionary strategy for eukaryotic microbial pathogens, enabling de novo genotypic and phenotypic plasticity and facilitating rapid adaptation to novel environments.

  20. European Socio-cultural Change and Generational Diversity in the Post-Soviet Workforce.

    Directory of Open Access Journals (Sweden)

    Madara APSALONE

    2016-12-01

    Full Text Available In times of increased retirement age and senior employees staying in workforce longer, successfully managing generational differences in the workforce forms an increasingly important challenge for modern day management. In many ways, generations may vary in attitudes and approaches, reflecting deeper differences in their core values. This might be particularly true for the Post-Soviet countries, where earlier generations were educated and started their careers within a completely different socio-economic system. In this study we explore differences in approaches towards values and attitudes amongst four generations of retail sector employees – starting from those, who were still to great extent exposed to pre-Soviet values, continuing with employees, who started their careers during the Soviet times, and ending with those, who were educated and entered the workforce after the collapse of the Soviet Union. 208 Latvian service employees were surveyed to assess their personal values and likelihood of dishonest and unethical behavior from four generations currently active in the workforce - Post-War generation, Early Gen X, Transition generation and Millennials. We confirmed that despite dual morality and ambiguous ethics in the Soviet Union, older generations reported higher likelihood of honest behavior than younger generations. And Post-War and Early Generation X also rated honesty and responsibility higher as their personal values. We also found significant differences between Early Generation X and the Transition generation in a post-Soviet context.

  1. Secretome analysis to elucidate metalloprotease-dependent ectodomain shedding of glycoproteins during neuronal differentiation.

    Science.gov (United States)

    Tsumagari, Kazuya; Shirakabe, Kyoko; Ogura, Mayu; Sato, Fuminori; Ishihama, Yasushi; Sehara-Fujisawa, Atsuko

    2017-02-01

    Many membrane proteins are subjected to limited proteolyses at their juxtamembrane regions, processes referred to as ectodomain shedding. Shedding ectodomains of membrane-bound ligands results in activation of downstream signaling pathways, whereas shedding those of cell adhesion molecules causes loss of cell-cell contacts. Secreted proteomics (secretomics) using high-resolution mass spectrometry would be strong tools for both comprehensive identification and quantitative measurement of membrane proteins that undergo ectodomain shedding. In this study, to elucidate the ectodomain shedding events that occur during neuronal differentiation, we establish a strategy for quantitative secretomics of glycoproteins released from differentiating neuroblastoma cells into culture medium with or without GM6001, a broad-spectrum metalloprotease inhibitor. Considering that most of transmembrane and secreted proteins are N-glycosylated, we include a process of N-glycosylated peptides enrichment as well as isotope tagging in our secretomics workflow. Our results show that differentiating N1E-115 neurons secrete numerous glycosylated polypeptides in metalloprotease-dependent manners. They are derived from cell adhesion molecules such as NCAM1, CADM1, L1CAM, various transporters and receptor proteins. These results show the landscape of ectodomain shedding and other secretory events in differentiating neurons and/or during axon elongation, which should help elucidate the mechanism of neurogenesis and the pathogenesis of neurological disorders. © 2017 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

  2. Comparative analysis of the in vitro and in planta secretomes from Mycosphaerella fijiensis isolates.

    Science.gov (United States)

    Escobar-Tovar, Lina; Guzmán-Quesada, Mauricio; Sandoval-Fernández, Jorge A; Gómez-Lim, Miguel A

    2015-06-01

    Black Sigatoka, a devastating disease of bananas and plantains worldwide, is caused by the fungus Mycosphaerella fijiensis. Several banana cultivars such as 'Yangambi Km 5' and Calcutta IV, have been known to be resistant to the fungus, but the resistance has been broken in 'Yangambi Km 5' in Costa Rica. Since the resistance of this variety still persists in Mexico, the aim of this study was to compare the in vitro and in planta secretomes from two avirulent and virulent M. fijiensis isolates using proteomics and bioinformatics approaches. We aimed to identify differentially expressed proteins in fungal isolates that differ in pathogenicity and that might be responsible for breaking the resistance in 'Yangambi Km 5'. We were able to identify 90 protein spots in the secretomes of fungal isolates encoding 42 unique proteins and 35 differential spots between them. Proteins involved in carbohydrate transport and metabolism were more prevalent. Several proteases, pathogenicity-related, ROS detoxification and unknown proteins were also highly or specifically expressed by the virulent isolate in vitro or during in planta infection. An unknown protein representing a virulence factor candidate was also identified. These results demonstrated that the secretome reflects major differences between both M. fijiensis isolates. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  3. Macrophage activation and polarization modify P2X7 receptor secretome influencing the inflammatory process.

    Science.gov (United States)

    de Torre-Minguela, Carlos; Barberà-Cremades, Maria; Gómez, Ana I; Martín-Sánchez, Fátima; Pelegrín, Pablo

    2016-03-03

    The activation of P2X7 receptor (P2X7R) on M1 polarized macrophages induces the assembly of the NLRP3 inflammasome leading to the release of pro-inflammatory cytokines and the establishment of the inflammatory response. However, P2X7R signaling to the NLRP3 inflammasome is uncoupled on M2 macrophages without changes on receptor activation. In this study, we analyzed P2X7R secretome in wild-type and P2X7R-deficient macrophages polarized either to M1 or M2 and proved that proteins released after P2X7R stimulation goes beyond caspase-1 secretome. The characterization of P2X7R-secretome reveals a new function of this receptor through a fine-tuning of protein release. We found that P2X7R stimulation in macrophages is able to release potent anti-inflammatory proteins, such as Annexin A1, independently of their polarization state suggesting for first time a potential role for P2X7R during resolution of the inflammation and not linked to the release of pro-inflammatory cytokines. These results are of prime importance for the development of therapeutics targeting P2X7R.

  4. The Diacetyl-Exposed Human Airway Epithelial Secretome: New Insights into Flavoring-Induced Airways Disease.

    Science.gov (United States)

    Brass, David M; Gwinn, William M; Valente, Ashlee M; Kelly, Francine L; Brinkley, Christie D; Nagler, Andrew E; Moseley, M Arthur; Morgan, Daniel L; Palmer, Scott M; Foster, Matthew W

    2017-06-01

    Bronchiolitis obliterans (BO) is an increasingly important lung disease characterized by fibroproliferative airway lesions and decrements in lung function. Occupational exposure to the artificial food flavoring ingredient diacetyl, commonly used to impart a buttery flavor to microwave popcorn, has been associated with BO development. In the occupational setting, diacetyl vapor is first encountered by the airway epithelium. To better understand the effects of diacetyl vapor on the airway epithelium, we used an unbiased proteomic approach to characterize both the apical and basolateral secretomes of air-liquid interface cultures of primary human airway epithelial cells from four unique donors after exposure to an occupationally relevant concentration (∼1,100 ppm) of diacetyl vapor or phosphate-buffered saline as a control on alternating days. Basolateral and apical supernatants collected 48 h after the third exposure were analyzed using one-dimensional liquid chromatography tandem mass spectrometry. Paired t tests adjusted for multiple comparisons were used to assess differential expression between diacetyl and phosphate-buffered saline exposure. Of the significantly differentially expressed proteins identified, 61 were unique to the apical secretome, 81 were unique to the basolateral secretome, and 11 were present in both. Pathway enrichment analysis using publicly available databases revealed that proteins associated with matrix remodeling, including degradation, assembly, and new matrix organization, were overrepresented in the data sets. Similarly, protein modifiers of epidermal growth factor receptor signaling were significantly altered. The ordered changes in protein expression suggest that the airway epithelial response to diacetyl may contribute to BO pathogenesis.

  5. Composition of the Schistosoma mansoni worm secretome: Identification of immune modulatory Cyclophilin A.

    Directory of Open Access Journals (Sweden)

    Achilleas Floudas

    2017-10-01

    Full Text Available The helminth Schistosoma mansoni modulates the infected host's immune system to facilitate its own survival, by producing excretory/secretory molecules that interact with a variety of the host's cell types including those of the immune system. Herein, we characterise the S. mansoni adult male worm secretome and identify 111 proteins, including 7 vaccine candidates and several molecules with potential immunomodulatory activity. Amongst the molecules present in the secretome, a 17-19kDa protein analogous to human cyclophilin A was identified. Given the ability of cyclophilin A to modulate the immune system by regulating antigen presenting cell activity, we sought to determine whether recombinant S. mansoni Cyclophilin A (rSmCypA is capable of modulating bone-marrow derived dendritic cell (BMDC and T cell responses under in vitro conditions. rSmCypA was enzymatically active and able to alter the pro-inflammatory cytokine profile of LPS-activated dendritic cells. rSmCypA also modulated DC function in the induction of CD4+ T cell proliferation with a preferential expansion of Treg cells. This work demonstrates the unique protein composition of the S. mansoni male worm secretome and immunomodulatory activity of S. mansoni Cyclophilin A.

  6. Mesenchymal Stem Cell Secretome: Toward Cell-Free Therapeutic Strategies in Regenerative Medicine.

    Science.gov (United States)

    Vizoso, Francisco J; Eiro, Noemi; Cid, Sandra; Schneider, Jose; Perez-Fernandez, Roman

    2017-08-25

    Earlier research primarily attributed the effects of mesenchymal stem cell (MSC) therapies to their capacity for local engrafting and differentiating into multiple tissue types. However, recent studies have revealed that implanted cells do not survive for long, and that the benefits of MSC therapy could be due to the vast array of bioactive factors they produce, which play an important role in the regulation of key biologic processes. Secretome derivatives, such as conditioned media or exosomes, may present considerable advantages over cells for manufacturing, storage, handling, product shelf life and their potential as a ready-to-go biologic product. Nevertheless, regulatory requirements for manufacturing and quality control will be necessary to establish the safety and efficacy profile of these products. Among MSCs, human uterine cervical stem cells (hUCESCs) may be a good candidate for obtaining secretome-derived products. hUCESCs are obtained by Pap cervical smear, which is a less invasive and painful method than those used for obtaining other MSCs (for example, from bone marrow or adipose tissue). Moreover, due to easy isolation and a high proliferative rate, it is possible to obtain large amounts of hUCESCs or secretome-derived products for research and clinical use.

  7. Controlled Inhibition of the Mesenchymal Stromal Cell Pro-inflammatory Secretome via Microparticle Engineering

    Directory of Open Access Journals (Sweden)

    Sudhir H. Ranganath

    2016-06-01

    Full Text Available Mesenchymal stromal cells (MSCs are promising therapeutic candidates given their potent immunomodulatory and anti-inflammatory secretome. However, controlling the MSC secretome post-transplantation is considered a major challenge that hinders their clinical efficacy. To address this, we used a microparticle-based engineering approach to non-genetically modulate pro-inflammatory pathways in human MSCs (hMSCs under simulated inflammatory conditions. Here we show that microparticles loaded with TPCA-1, a small-molecule NF-κB inhibitor, when delivered to hMSCs can attenuate secretion of pro-inflammatory factors for at least 6 days in vitro. Conditioned medium (CM derived from TPCA-1-loaded hMSCs also showed reduced ability to attract human monocytes and prevented differentiation of human cardiac fibroblasts to myofibroblasts, compared with CM from untreated or TPCA-1-preconditioned hMSCs. Thus, we provide a broadly applicable bioengineering solution to facilitate intracellular sustained release of agents that modulate signaling. We propose that this approach could be harnessed to improve control over MSC secretome post-transplantation, especially to prevent adverse remodeling post-myocardial infarction.

  8. Diversity of fuel sources for electricity generation in an evolving U.S. power sector

    Science.gov (United States)

    DiLuccia, Janelle G.

    Policymakers increasingly have shown interest in options to boost the relative share of renewable or clean electricity generating sources in order to reduce negative environmental externalities from fossil fuels, guard against possible resource constraints, and capture economic advantages from developing new technologies and industries. Electric utilities and non-utility generators make decisions regarding their generation mix based on a number of different factors that may or may not align with societal goals. This paper examines the makeup of the electric power sector to determine how the type of generator and the presence (or lack) of competition in electricity markets at the state level may relate to the types of fuel sources used for generation. Using state-level electricity generation data from the U.S. Energy Information Administration from 1990 through 2010, this paper employs state and time fixed-effects regression modeling to attempt to isolate the impacts of state-level restructuring policies and the emergence of non-utility generators on states' generation from coal, from fossil fuel and from renewable sources. While the analysis has significant limitations, I do find that state-level electricity restructuring has a small but significant association with lowering electricity generation from coal specifically and fossil fuels more generally. Further research into the relationship between competition and fuel sources would aid policymakers considering legislative options to influence the generation mix.

  9. User Generated Diversity - Some reflections on how to improve the quality of amateur productions

    NARCIS (Netherlands)

    Helberger, N.; Leurdijk, A.G.D.; Munck, S.G.E. de

    2010-01-01

    The potential of user created content to make a meaningful contribution to media diversity is subject to debates. Central to these debates is the argument of the quality of amateur productions. This article will take a close look at this argument, and make some suggestions on how to improve the

  10. User generated diversity: some reflections on how to improve the quality of amateur productions

    NARCIS (Netherlands)

    Helberger, N.; Leurdijk, A.; de Munck, S.

    2010-01-01

    The potential of user created content to make a meaningful contribution to media diversity is subject to debates. Central to these debates is the argument of the quality of amateur productions. This article will take a close look at this argument, and make some suggestions on how to improve the

  11. A Systematic Review: The Next Generation Science Standards and the Increased Cultural Diversity

    Science.gov (United States)

    Asowayan, Alaa A.; Ashreef, Samaar Y.; Omar, Sozan H.

    2017-01-01

    This systematic review aims to explore the effect of NGSS on students' academic excellence. Specifically, considering increased cultural diversity, it is appropriate to identify student's science-related values, respectful features of teachers' cultural competence, and underlying challenges and detect in what ways these objectives are addressed by…

  12. Generational diversity in associate degree nursing students: Teaching styles and preferences in Pennsylvania

    Science.gov (United States)

    Kitko, Jennifer V.

    2011-12-01

    Nursing educators face the challenge of meeting the needs of a multi-generational classroom. The reality of having members from the Veteran and Baby Boomer generations in a classroom with Generation X and Y students provides an immediate need for faculty to examine students' teaching method preferences as well as their own use of teaching methods. Most importantly, faculty must facilitate an effective multi-generational learning environment. Research has shown that the generation to which a person belongs is likely to affect the ways in which he/she learns (Hammill, 2005). Characterized by its own attitudes, behaviors, beliefs, and motivational needs, each generation also has distinct educational expectations. It is imperative, therefore, that nurse educators be aware of these differences and develop skills through which to communicate with the different generations, thereby reducing teaching/learning problems in the classroom. This is a quantitative, descriptive study that compared the teaching methods preferred by different generations of associate degree nursing students with the teaching methods that the instructors actually use. The research study included 289 participants; 244 nursing student participants and 45 nursing faculty participants from four nursing departments in colleges in Pennsylvania. Overall, the results of the study found many statistically significant findings. The results of the ANOVA test revealed eight statistically significant findings among Generation Y, Generation X and Baby boomers. The preferred teaching methods included: lecture, self-directed learning, web-based course with no class meetings, important for faculty to know my name, classroom structure, know why I am learning what I am learning, learning for the sake of learning and grade is all that matters. Lecture was found to be the most frequently used teaching method by faculty as well as the most preferred teaching methods by students. Overall, the support for a variety of

  13. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

    Directory of Open Access Journals (Sweden)

    Eriksson Nicholas

    2011-04-01

    Full Text Available Abstract Background With next-generation sequencing technologies, experiments that were considered prohibitive only a few years ago are now possible. However, while these technologies have the ability to produce enormous volumes of data, the sequence reads are prone to error. This poses fundamental hurdles when genetic diversity is investigated. Results We developed ShoRAH, a computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. The software was run on simulated data and on real data obtained in wet lab experiments to assess its reliability. Conclusions ShoRAH is implemented in C++, Python, and Perl and has been tested under Linux and Mac OS X. Source code is available under the GNU General Public License at http://www.cbg.ethz.ch/software/shorah.

  14. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.

    Science.gov (United States)

    Zagordi, Osvaldo; Bhattacharya, Arnab; Eriksson, Nicholas; Beerenwinkel, Niko

    2011-04-26

    With next-generation sequencing technologies, experiments that were considered prohibitive only a few years ago are now possible. However, while these technologies have the ability to produce enormous volumes of data, the sequence reads are prone to error. This poses fundamental hurdles when genetic diversity is investigated. We developed ShoRAH, a computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. The software was run on simulated data and on real data obtained in wet lab experiments to assess its reliability. ShoRAH is implemented in C++, Python, and Perl and has been tested under Linux and Mac OS X. Source code is available under the GNU General Public License at http://www.cbg.ethz.ch/software/shorah.

  15. Single-neuron diversity generated by Protocadherin-β cluster in mouse central and peripheral nervous systems

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    Keizo eHirano

    2012-08-01

    Full Text Available The generation of complex neural circuits depends on the correct wiring of neurons with diverse individual characteristics. To understand the complexity of the nervous system, the molecular mechanisms for specifying the identity and diversity of individual neurons must be elucidated. The clustered protocadherins (Pcdh in mammals consist of approximately 50 Pcdh genes (Pcdh-α, Pcdh-β, and Pcdh-γ that encode cadherin-family cell surface adhesion proteins. Individual neurons express a random combination of Pcdh-α and Pcdh-γ, whereas the expression patterns for the Pcdh-β genes, 22 one-exon genes in mouse, are not fully understood. Here we show that the Pcdh-β genes are expressed in a 3’-polyadenylated form in mouse brain. In situ hybridization using a pan-Pcdh-β probe against a conserved Pcdh-β sequence showed widespread labeling in the brain, with prominent signals in the olfactory bulb, hippocampus, and cerebellum. In situ hybridization with specific probes for individual Pcdh-β genes showed their expression to be scattered in Purkinje cells from P10 to P150. The scattered expression patterns were confirmed by performing a newly developed single-cell 3’-RACE analysis of Purkinje cells, which clearly demonstrated that the Pcdh-β genes are expressed monoallelically and combinatorially in individual Purkinje cells. Scattered expression patterns of individual Pcdh-β genes were also observed in pyramidal neurons in the hippocampus and cerebral cortex, neurons in the trigeminal and dorsal root ganglion, GABAergic interneurons, and cholinergic neurons. Our results extend previous observations of diversity at the single-neuron level generated by Pcdh expression and suggest that the Pcdh-β cluster genes contribute to specifying the identity and diversity of individual neurons.

  16. Exploring the potential of second-generation sequencing in diverse biological contexts

    DEFF Research Database (Denmark)

    Fordyce, Sarah Louise

    studies, and thus the principle aim of this thesis research was to explore and improve methods for SGS of non-conventional and/or challenging templates. These templates include forensic blood samples for short tandem repeat characterization, ancient RNA from maize kernels, and predominantly 2009 pandemic...... H1N1 influenza A virus genomes. The results of these studies demonstrate the power of SGS for gaining insight into the genetic variation of diverse biological samples and highlight the importance of using optimized protocols for sequencing non-conventional samples....

  17. Diversity and Inclusion in Information Technology from an Age Perspective: Motivating and Managing Information Technology Professionals across Multiple Generations in the Workforce

    Science.gov (United States)

    Kenan-Smalls, Yottie Marie

    2011-01-01

    The purpose of this quantitative study was to investigate diversity and inclusion from an age perspective among information technology (IT) professionals that were categorized as 4 different generations in the workforce today: Traditionalists, Baby Boomers, Generation X, and Generation Y. At the same time, this study sought to examine motivational…

  18. An Interspecies Comparative Analysis of the Predicted Secretomes of the Necrotrophic Plant Pathogens Sclerotinia sclerotiorum and Botrytis cinerea.

    Science.gov (United States)

    Heard, Steph; Brown, Neil A; Hammond-Kosack, Kim

    2015-01-01

    Phytopathogenic fungi form intimate associations with host plant species and cause disease. To be successful, fungal pathogens communicate with a susceptible host through the secretion of proteinaceous effectors, hydrolytic enzymes and metabolites. Sclerotinia sclerotiorum and Botrytis cinerea are economically important necrotrophic fungal pathogens that cause disease on numerous crop species. Here, a powerful bioinformatics pipeline was used to predict the refined S. sclerotiorum and B. cinerea secretomes, identifying 432 and 499 proteins respectively. Analyses focusing on S. sclerotiorum revealed that 16% of the secretome encoding genes resided in small, sequence heterogeneous, gene clusters that were distributed over 13 of the 16 predicted chromosomes. Functional analyses highlighted the importance of plant cell hydrolysis, oxidation-reduction processes and the redox state to the S. sclerotiorum and B. cinerea secretomes and potentially host infection. Only 8% of the predicted proteins were distinct between the two secretomes. In contrast to S. sclerotiorum, the B. cinerea secretome lacked CFEM- or LysM-containing proteins. The 115 fungal and oomycete genome comparison identified 30 proteins specific to S. sclerotiorum and B. cinerea, plus 11 proteins specific to S. sclerotiorum and 32 proteins specific to B. cinerea. Expressed sequence tag (EST) and proteomic analyses showed that 246 S. sclerotiorum secretome encoding genes had EST support, including 101 which were only expressed in vitro and 49 which were only expressed in planta, whilst 42 predicted proteins were experimentally proven to be secreted. These detailed in silico analyses of two important necrotrophic pathogens will permit informed choices to be made when candidate effector proteins are selected for function analyses in planta.

  19. Modeling and prediction of regional municipal solid waste generation and diversion in Canada using machine learning approaches.

    Science.gov (United States)

    Kannangara, Miyuru; Dua, Rahul; Ahmadi, Leila; Bensebaa, Farid

    2018-04-01

    The main objective of this study was to develop models for accurate prediction of municipal solid waste (MSW) generation and diversion based on demographic and socio-economic variables, with planned application of generating Canada-wide MSW inventories. Models were generated by mapping residential MSW quantities with socio-economic and demographic parameters of 220 municipalities in the province of Ontario, Canada. Two machine learning algorithms, namely decision trees and neural networks, were applied to build the models. Socio-economic variables were derived from Canadian Census data at regional and municipal levels. A data pre-processing and integration framework was developed in Matlab® computing software to generate datasets with sufficient data quantity and quality for modeling. Results showed that machine learning algorithms can be successfully used to generate waste models with good prediction performance. Neural network models had the best performance, describing 72% of variation in the data. The approach proposed in this study demonstrates the feasibility of creating tools that helps in regional waste planning by means of sourcing, pre-processing, integrating and modeling of publically available data from various sources. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

  20. A neural circuitry that emphasizes spinal feedback generates diverse behaviours of human locomotion.

    Science.gov (United States)

    Song, Seungmoon; Geyer, Hartmut

    2015-08-15

    It is often assumed that central pattern generators, which generate rhythmic patterns without rhythmic inputs, play a key role in the spinal control of human locomotion. We propose a neural control model in which the spinal control generates muscle stimulations mainly through integrated reflex pathways with no central pattern generator. Using a physics-based neuromuscular human model, we show that this control network is sufficient to compose steady and transitional 3-D locomotion behaviours, including walking and running, acceleration and deceleration, slope and stair negotiation, turning, and deliberate obstacle avoidance. The results suggest feedback integration to be functionally more important than central pattern generation in human locomotion across behaviours. In addition, the proposed control architecture may serve as a guide in the search for the neurophysiological origin and circuitry of spinal control in humans. Neural networks along the spinal cord contribute substantially to generating locomotion behaviours in humans and other legged animals. However, the neural circuitry involved in this spinal control remains unclear. We here propose a specific circuitry that emphasizes feedback integration over central pattern generation. The circuitry is based on neurophysiologically plausible muscle-reflex pathways that are organized in 10 spinal modules realizing limb functions essential to legged systems in stance and swing. These modules are combined with a supraspinal control layer that adjusts the desired foot placements and selects the leg that is to transition into swing control during double support. Using physics-based simulation, we test the proposed circuitry in a neuromuscular human model that includes neural transmission delays, musculotendon dynamics and compliant foot-ground contacts. We find that the control network is sufficient to compose steady and transitional 3-D locomotion behaviours including walking and running, acceleration and

  1. Aberrant clones: Birth order generates life history diversity in Greater Duckweed, Spirodela polyrhiza.

    Science.gov (United States)

    Mejbel, Hebah S; Simons, Andrew M

    2018-02-01

    Environmental unpredictability is known to result in the evolution of bet-hedging traits. Variable dormancy enhances survival through harsh conditions, and is widely cited as a diversification bet-hedging trait. The floating aquatic plant, Spirodela polyrhiza (Greater Duckweed), provides an opportunity to study diversification because although partially reliable seasonal cues exist, its growing season is subject to an unpredictable and literally "hard" termination when the surface water freezes, and overwinter survival depends on a switch from production of normal daughter fronds to production of dense, sinking "turions" prior to freeze-over. The problem for S. polyrhiza is that diversified dormancy behavior must be generated among clonally produced, genetically identical offspring. Variation in phenology has been observed in the field, but its sources are unknown. Here, we investigate sources of phenological variation in turion production , and test the hypothesis that diversification in turion phenology is generated within genetic lineages through effects of parental birth order. As expected, phenotypic plasticity to temperature is expressed along a thermal gradient; more interestingly, parental birth order was found to have a significant and strong effect on turion phenology: Turions are produced earlier by late birth-order parents. These results hold regardless of whether turion phenology is measured as first turion birth order, time to first turion, or turion frequency. This study addresses a question of current interest on potential mechanisms generating diversification, and suggests that consistent phenotypic differences across birth orders generate life history variation.

  2. Temporally Diverse Excitation Generates Direction-Selective Responses in ON- and OFF-Type Retinal Starburst Amacrine Cells

    Directory of Open Access Journals (Sweden)

    James W. Fransen

    2017-02-01

    Full Text Available The complexity of sensory receptive fields increases from one synaptic stage to the next. In many cases, increased complexity is achieved through spatiotemporal interactions between convergent excitatory and inhibitory inputs. Here, we present evidence that direction selectivity (DS, a complex emergent receptive field property of retinal starburst amacrine cells (SACs, is generated by spatiotemporal interactions between functionally diverse excitatory inputs. Electrophysiological whole-cell recordings from ON and OFF SACs show distinct temporal differences in excitation following proximal compared with distal stimulation of their receptive fields. Distal excitation is both faster and more transient, ruling out passive filtering by the dendrites and indicating a task-specific specialization. Model simulations demonstrate that this specific organization of excitation generates robust DS responses in SACs, consistent with elementary motion detector models. These results indicate that selective integration of spatiotemporally patterned excitation is a computational mechanism for motion detection in the mammalian retina.

  3. Propionibacterium acnes: disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

    DEFF Research Database (Denmark)

    Mollerup, Sarah; Friis-Nielsen, Jens; Vinner, Lasse

    2016-01-01

    Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions, but is also a proven contaminant of human samples and surgical wounds. Its...... significance as a pathogen is consequently a matter of debate.In the present study we investigated the presence of P. acnes DNA in 250 next generation sequencing datasets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were either subjected to microbial...... enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun-sequenced.We detected high proportions of P. acnes in enriched samples, particularly skin derived and other tissue samples, with levels being higher in enriched compared to shotgun-sequenced samples. P. acnes...

  4. Partial promoter substitutions generating transcriptional sentinels of diverse signaling pathways in embryonic stem cells and mice

    Science.gov (United States)

    Serup, Palle; Gustavsen, Carsten; Klein, Tino; Potter, Leah A.; Lin, Robert; Mullapudi, Nandita; Wandzioch, Ewa; Hines, Angela; Davis, Ashley; Bruun, Christine; Engberg, Nina; Petersen, Dorthe R.; Peterslund, Janny M. L.; MacDonald, Raymond J.; Grapin-Botton, Anne; Magnuson, Mark A.; Zaret, Kenneth S.

    2012-01-01

    SUMMARY Extracellular signals in development, physiology, homeostasis and disease often act by regulating transcription. Herein we describe a general method and specific resources for determining where and when such signaling occurs in live animals and for systematically comparing the timing and extent of different signals in different cellular contexts. We used recombinase-mediated cassette exchange (RMCE) to test the effect of successively deleting conserved genomic regions of the ubiquitously active Rosa26 promoter and substituting the deleted regions for regulatory sequences that respond to diverse extracellular signals. We thereby created an allelic series of embryonic stem cells and mice, each containing a signal-responsive sentinel with different fluorescent reporters that respond with sensitivity and specificity to retinoic acids, bone morphogenic proteins, activin A, Wnts or Notch, and that can be adapted to any pathway that acts via DNA elements. PMID:22888097

  5. The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.

    Science.gov (United States)

    Kim, Hyeun Bum; Isaacson, Richard E

    2015-06-12

    The importance of the gut microbiota of animals is widely acknowledged because of its pivotal roles in the health and well being of animals. The genetic diversity of the gut microbiota contributes to the overall development and metabolic needs of the animal, and provides the host with many beneficial functions including production of volatile fatty acids, re-cycling of bile salts, production of vitamin K, cellulose digestion, and development of immune system. Thus the intestinal microbiota of animals has been the subject of study for many decades. Although most of the older studies have used culture dependent methods, the recent advent of high throughput sequencing of 16S rRNA genes has facilitated in depth studies exploring microbial populations and their dynamics in the animal gut. These culture independent DNA based studies generate large amounts of data and as a result contribute to a more detailed understanding of the microbiota dynamics in the gut and the ecology of the microbial populations. Of equal importance, is being able to identify and quantify microbes that are difficult to grow or that have not been grown in the laboratory. Interpreting the data obtained from this type of study requires using basic principles of microbial diversity to understand importance of the composition of microbial populations. In this review, we summarize the literature on culture independent studies of the pig gut microbiota with an emphasis on its succession and alterations caused by diverse factors. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Next-generation sequencing reveals cryptic mtDNA diversity of Plasmodium relictum in the Hawaiian Islands

    Science.gov (United States)

    Jarvi, S.I.; Farias, M.E.; Lapointe, D.A.; Belcaid, M.; Atkinson, C.T.

    2013-01-01

    Next-generation 454 sequencing techniques were used to re-examine diversity of mitochondrial cytochrome b lineages of avian malaria (Plasmodium relictum) in Hawaii. We document a minimum of 23 variant lineages of the parasite based on single nucleotide transitional changes, in addition to the previously reported single lineage (GRW4). A new, publicly available portal (Integroomer) was developed for initial parsing of 454 datasets. Mean variant prevalence and frequency was higher in low elevation Hawaii Amakihi (Hemignathus virens) with Avipoxvirus-like lesions (P = 0·001), suggesting that the variants may be biologically distinct. By contrast, variant prevalence and frequency did not differ significantly among mid-elevation Apapane (Himatione sanguinea) with or without lesions (P = 0·691). The low frequency and the lack of detection of variants independent of GRW4 suggest that multiple independent introductions of P. relictum to Hawaii are unlikely. Multiple variants may have been introduced in heteroplasmy with GRW4 or exist within the tandem repeat structure of the mitochondrial genome. The discovery of multiple mitochondrial lineages of P. relictum in Hawaii provides a measure of genetic diversity within a geographically isolated population of this parasite and suggests the origins and evolution of parasite diversity may be more complicated than previously recognized.

  7. Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

    Directory of Open Access Journals (Sweden)

    Weihong Qi

    2009-09-01

    Full Text Available Mycobacterium ulcerans is the causative agent of Buruli ulcer, the third most common mycobacterial disease after tuberculosis and leprosy. It is an emerging infectious disease that afflicts mainly children and youths in West Africa. Little is known about the evolution and transmission mode of M. ulcerans, partially due to the lack of known genetic polymorphisms among isolates, limiting the application of genetic epidemiology. To systematically profile single nucleotide polymorphisms (SNPs, we sequenced the genomes of three M. ulcerans strains using 454 and Solexa technologies. Comparison with the reference genome of the Ghanaian classical lineage isolate Agy99 revealed 26,564 SNPs in a Japanese strain representing the ancestral lineage. Only 173 SNPs were found when comparing Agy99 with two other Ghanaian isolates, which belong to the two other types previously distinguished in Ghana by variable number tandem repeat typing. We further analyzed a collection of Ghanaian strains using the SNPs discovered. With 68 SNP loci, we were able to differentiate 54 strains into 13 distinct SNP haplotypes. The average SNP nucleotide diversity was low (average 0.06-0.09 across 68 SNP loci, and 96% of the SNP locus pairs were in complete linkage disequilibrium. We estimated that the divergence of the M. ulcerans Ghanaian clade from the Japanese strain occurred 394 to 529 thousand years ago. The Ghanaian subtypes diverged about 1000 to 3000 years ago, or even much more recently, because we found evidence that they evolved significantly faster than average. Our results offer significant insight into the evolution of M. ulcerans and provide a comprehensive report on genetic diversity within a highly clonal M. ulcerans population from a Buruli ulcer endemic region, which can facilitate further epidemiological studies of this pathogen through the development of high-resolution tools.

  8. Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale

    Science.gov (United States)

    Moore, Geromy G.; Elliott, Jacalyn L.; Singh, Rakhi; Horn, Bruce W.; Dorner, Joe W.; Stone, Eric A.; Chulze, Sofia N.; Barros, German G.; Naik, Manjunath K.; Wright, Graeme C.; Hell, Kerstin; Carbone, Ignazio

    2013-01-01

    Aflatoxins are produced by Aspergillus flavus and A. parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture, with aflatoxin B1 being the most carcinogenic natural compound known. Sexual reproduction in these species occurs between individuals belonging to different vegetative compatibility groups (VCGs). We examined natural genetic variation in 758 isolates of A. flavus, A. parasiticus and A. minisclerotigenes sampled from single peanut fields in the United States (Georgia), Africa (Benin), Argentina (Córdoba), Australia (Queensland) and India (Karnataka). Analysis of DNA sequence variation across multiple intergenic regions in the aflatoxin gene clusters of A. flavus, A. parasiticus and A. minisclerotigenes revealed significant linkage disequilibrium (LD) organized into distinct blocks that are conserved across different localities, suggesting that genetic recombination is nonrandom and a global occurrence. To assess the contributions of asexual and sexual reproduction to fixation and maintenance of toxin chemotype diversity in populations from each locality/species, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 mating-type individuals, which is indicative of a sexually recombining population. All samples were clone-corrected using multi-locus sequence typing which associates closely with VCG. For both A. flavus and A. parasiticus, when the proportions of MAT1-1 and MAT1-2 were significantly different, there was more extensive LD in the aflatoxin cluster and populations were fixed for specific toxin chemotype classes, either the non-aflatoxigenic class in A. flavus or the B1-dominant and G1-dominant classes in A. parasiticus. A mating type ratio close to 1∶1 in A. flavus, A. parasiticus and A. minisclerotigenes was associated with higher recombination rates in the aflatoxin cluster and less pronounced chemotype differences in populations. This work shows that the reproductive nature of the population (more

  9. Sexuality generates diversity in the aflatoxin gene cluster: evidence on a global scale.

    Directory of Open Access Journals (Sweden)

    Geromy G Moore

    Full Text Available Aflatoxins are produced by Aspergillus flavus and A. parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture, with aflatoxin B₁ being the most carcinogenic natural compound known. Sexual reproduction in these species occurs between individuals belonging to different vegetative compatibility groups (VCGs. We examined natural genetic variation in 758 isolates of A. flavus, A. parasiticus and A. minisclerotigenes sampled from single peanut fields in the United States (Georgia, Africa (Benin, Argentina (Córdoba, Australia (Queensland and India (Karnataka. Analysis of DNA sequence variation across multiple intergenic regions in the aflatoxin gene clusters of A. flavus, A. parasiticus and A. minisclerotigenes revealed significant linkage disequilibrium (LD organized into distinct blocks that are conserved across different localities, suggesting that genetic recombination is nonrandom and a global occurrence. To assess the contributions of asexual and sexual reproduction to fixation and maintenance of toxin chemotype diversity in populations from each locality/species, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 mating-type individuals, which is indicative of a sexually recombining population. All samples were clone-corrected using multi-locus sequence typing which associates closely with VCG. For both A. flavus and A. parasiticus, when the proportions of MAT1-1 and MAT1-2 were significantly different, there was more extensive LD in the aflatoxin cluster and populations were fixed for specific toxin chemotype classes, either the non-aflatoxigenic class in A. flavus or the B₁-dominant and G₁-dominant classes in A. parasiticus. A mating type ratio close to 1∶1 in A. flavus, A. parasiticus and A. minisclerotigenes was associated with higher recombination rates in the aflatoxin cluster and less pronounced chemotype differences in populations. This work shows that the reproductive nature of

  10. The Ewing sarcoma secretome and its response to activation of Wnt/beta-catenin signaling.

    Science.gov (United States)

    Hawkins, Allegra G; Basrur, Venkatesha; da Veiga Leprevost, Felipe; Pedersen, Elisabeth; Sperring, Colin; Nesvizhskii, Alexey I; Lawlor, Elizabeth R

    2018-01-31

    Tumor: tumor microenvironment (TME) interactions are critical for tumor progression and the composition and structure of the local extracellular matrix (ECM) are key determinants of tumor metastasis. We recently reported that activation of Wnt/beta-catenin signaling in Ewing sarcoma cells induces widespread transcriptional changes that are associated with acquisition of a metastatic tumor phenotype. Significantly, ECM protein-encoding genes were found to be enriched among Wnt/beta-catenin induced transcripts, leading us to hypothesize that activation of canonical Wnt signaling might induce changes in the Ewing sarcoma secretome. To address this hypothesis, conditioned media from Ewing sarcoma cell lines cultured in the presence or absence of Wnt3a was collected for proteomic analysis. Label-free mass spectrometry was used to identify and quantify differentially secreted proteins. We then used in silico databases to identify only proteins annotated as secreted. Comparison of the secretomes of two Ewing sarcoma cell lines revealed numerous shared proteins, as well as a degree of heterogeneity, in both basal and Wnt-stimulated conditions. Gene set enrichment analysis of secreted proteins revealed that Wnt stimulation reproducibly resulted in increased secretion of proteins involved in ECM organization, ECM receptor interactions, and collagen formation. In particular, Wnt-stimulated Ewing sarcoma cells upregulated secretion of structural collagens, as well as matricellular proteins, such as the metastasis-associated protein, tenascin C (TNC). Interrogation of published databases confirmed reproducible correlations between Wnt/beta-catenin activation and TNC and COL1A1 expression in patient tumors. In summary, this first study of the Ewing sarcoma secretome reveals that Wnt/beta-catenin activated tumor cells upregulate secretion of ECM proteins. Such Wnt/beta-catenin mediated changes are likely to impact on tumor: TME interactions that contribute to metastatic

  11. Direct identification of the Meloidogyne incognita secretome reveals proteins with host cell reprogramming potential.

    Directory of Open Access Journals (Sweden)

    Stéphane Bellafiore

    2008-10-01

    Full Text Available The root knot nematode, Meloidogyne incognita, is an obligate parasite that causes significant damage to a broad range of host plants. Infection is associated with secretion of proteins surrounded by proliferating cells. Many parasites are known to secrete effectors that interfere with plant innate immunity, enabling infection to occur; they can also release pathogen-associated molecular patterns (PAMPs, e.g., flagellin that trigger basal immunity through the nematode stylet into the plant cell. This leads to suppression of innate immunity and reprogramming of plant cells to form a feeding structure containing multinucleate giant cells. Effectors have generally been discovered using genetics or bioinformatics, but M. incognita is non-sexual and its genome sequence has not yet been reported. To partially overcome these limitations, we have used mass spectrometry to directly identify 486 proteins secreted by M. incognita. These proteins contain at least segmental sequence identity to those found in our 3 reference databases (published nematode proteins; unpublished M. incognita ESTs; published plant proteins. Several secreted proteins are homologous to plant proteins, which they may mimic, and they contain domains that suggest known effector functions (e.g., regulating the plant cell cycle or growth. Others have regulatory domains that could reprogram cells. Using in situ hybridization we observed that most secreted proteins were produced by the subventral glands, but we found that phasmids also secreted proteins. We annotated the functions of the secreted proteins and classified them according to roles they may play in the development of root knot disease. Our results show that parasite secretomes can be partially characterized without cognate genomic DNA sequence. We observed that the M. incognita secretome overlaps the reported secretome of mammalian parasitic nematodes (e.g., Brugia malayi, suggesting a common parasitic behavior and a possible

  12. Defining the predicted protein secretome of the fungal wheat leaf pathogen Mycosphaerella graminicola.

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    Alexandre Morais do Amaral

    Full Text Available The Dothideomycete fungus Mycosphaerella graminicola is the causal agent of Septoria tritici blotch, a devastating disease of wheat leaves that causes dramatic decreases in yield. Infection involves an initial extended period of symptomless intercellular colonisation prior to the development of visible necrotic disease lesions. Previous functional genomics and gene expression profiling studies have implicated the production of secreted virulence effector proteins as key facilitators of the initial symptomless growth phase. In order to identify additional candidate virulence effectors, we re-analysed and catalogued the predicted protein secretome of M. graminicola isolate IPO323, which is currently regarded as the reference strain for this species. We combined several bioinformatic approaches in order to increase the probability of identifying truly secreted proteins with either a predicted enzymatic function or an as yet unknown function. An initial secretome of 970 proteins was predicted, whilst further stringent selection criteria predicted 492 proteins. Of these, 321 possess some functional annotation, the composition of which may reflect the strictly intercellular growth habit of this pathogen, leaving 171 with no functional annotation. This analysis identified a protein family encoding secreted peroxidases/chloroperoxidases (PF01328 which is expanded within all members of the family Mycosphaerellaceae. Further analyses were done on the non-annotated proteins for size and cysteine content (effector protein hallmarks, and then by studying the distribution of homologues in 17 other sequenced Dothideomycete fungi within an overall total of 91 predicted proteomes from fungal, oomycete and nematode species. This detailed M. graminicola secretome analysis provides the basis for further functional and comparative genomics studies.

  13. An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

    Directory of Open Access Journals (Sweden)

    Martens-Uzunova Elena S

    2010-10-01

    Full Text Available Abstract Background The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence of a N-terminal signal peptide (SP and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted. However, prediction of a SP does not guarantee that the protein is actually secreted and current in silico prediction methods suffer from gene-model errors introduced during genome annotation. Results A majority rule based classifier that also evaluates signal peptide predictions from the best homologs of three neighbouring Aspergillus species was developed to create an improved list of potential signal peptide containing proteins encoded by the Aspergillus niger genome. As a complement to these in silico predictions, the secretome associated with growth and upon carbon source depletion was determined using a shotgun proteomics approach. Overall, some 200 proteins with a predicted signal peptide were identified to be secreted proteins. Concordant changes in the secretome state were observed as a response to changes in growth/culture conditions. Additionally, two proteins secreted via a non-classical route operating in A. niger were identified. Conclusions We were able to improve the in silico inventory of A. niger secretory proteins by combining different gene-model predictions from neighbouring Aspergilli and thereby avoiding prediction conflicts associated with inaccurate gene-models. The expected accuracy of signal peptide prediction for proteins that lack homologous sequences in the proteomes of related species is 85%. An experimental validation of the predicted proteome confirmed in silico predictions.

  14. Bacillus anthracis secretome time course under host-simulated conditions and identification of immunogenic proteins

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    Whittington Jessica

    2007-07-01

    Full Text Available Abstract Background The secretion time course of Bacillus anthracis strain RA3R (pXO1+/pXO2- during early, mid, and late log phase were investigated under conditions that simulate those encountered in the host. All of the identified proteins were analyzed by different software algorithms to characterize their predicted mode of secretion and cellular localization. In addition, immunogenic proteins were identified using sera from humans with cutaneous anthrax. Results A total of 275 extracellular proteins were identified by a combination of LC MS/MS and MALDI-TOF MS. All of the identified proteins were analyzed by SignalP, SecretomeP, PSORT, LipoP, TMHMM, and PROSITE to characterize their predicted mode of secretion, cellular localization, and protein domains. Fifty-three proteins were predicted by SignalP to harbor the cleavable N-terminal signal peptides and were therefore secreted via the classical Sec pathway. Twenty-three proteins were predicted by SecretomeP for secretion by the alternative Sec pathway characterized by the lack of typical export signal. In contrast to SignalP and SecretomeP predictions, PSORT predicted 171 extracellular proteins, 7 cell wall-associated proteins, and 6 cytoplasmic proteins. Moreover, 51 proteins were predicted by LipoP to contain putative Sec signal peptides (38 have SpI sites, lipoprotein signal peptides (13 have SpII sites, and N-terminal membrane helices (9 have transmembrane helices. The TMHMM algorithm predicted 25 membrane-associated proteins with one to ten transmembrane helices. Immunogenic proteins were also identified using sera from patients who have recovered from anthrax. The charge variants (83 and 63 kDa of protective antigen (PA were the most immunodominant secreted antigens, followed by charge variants of enolase and transketolase. Conclusion This is the first description of the time course of protein secretion for the pathogen Bacillus anthracis. Time course studies of protein secretion and

  15. Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques.

    Science.gov (United States)

    Gobet, Angélique; Boetius, Antje; Ramette, Alban

    2014-09-01

    Changes in richness and bacterial community structure obtained via 454 Massively Parallel Tag Sequencing (MPTS) and Automated Ribosomal Intergenic Analysis (ARISA) were systematically compared to determine whether and how the ecological knowledge obtained from both molecular techniques could be combined. We evaluated community changes over time and depth in marine coastal sands at different levels of taxonomic resolutions, sequence corrections and sequence abundances. Although richness over depth layers or sampling dates greatly varied [∼ 30% and 70-80% new operational taxonomic units (OTU) between two samples with ARISA and MPTS respectively], overall patterns of community variations were similar with both approaches. Alpha-diversity estimated by ARISA-derived OTU was most similar to that obtained from MPTS-derived OTU defined at the order level. Similar patterns of OTU replacement were also found with MPTS at the family level and with 20-25% rare types removed. Using ARISA or MPTS datasets with lower resolution, such as those containing only resident OTU, yielded a similar set of significant contextual variables explaining bacterial community changes. Hence, ARISA as a rapid and low-cost fingerprinting technique represents a valid starting point for more in-depth exploration of community composition when complemented by the detailed taxonomic description offered by MPTS. © 2013 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Automatic generation control of multi-area power systems with diverse energy sources using Teaching Learning Based Optimization algorithm

    Directory of Open Access Journals (Sweden)

    Rabindra Kumar Sahu

    2016-03-01

    Full Text Available This paper presents the design and analysis of Proportional-Integral-Double Derivative (PIDD controller for Automatic Generation Control (AGC of multi-area power systems with diverse energy sources using Teaching Learning Based Optimization (TLBO algorithm. At first, a two-area reheat thermal power system with appropriate Generation Rate Constraint (GRC is considered. The design problem is formulated as an optimization problem and TLBO is employed to optimize the parameters of the PIDD controller. The superiority of the proposed TLBO based PIDD controller has been demonstrated by comparing the results with recently published optimization technique such as hybrid Firefly Algorithm and Pattern Search (hFA-PS, Firefly Algorithm (FA, Bacteria Foraging Optimization Algorithm (BFOA, Genetic Algorithm (GA and conventional Ziegler Nichols (ZN for the same interconnected power system. Also, the proposed approach has been extended to two-area power system with diverse sources of generation like thermal, hydro, wind and diesel units. The system model includes boiler dynamics, GRC and Governor Dead Band (GDB non-linearity. It is observed from simulation results that the performance of the proposed approach provides better dynamic responses by comparing the results with recently published in the literature. Further, the study is extended to a three unequal-area thermal power system with different controllers in each area and the results are compared with published FA optimized PID controller for the same system under study. Finally, sensitivity analysis is performed by varying the system parameters and operating load conditions in the range of ±25% from their nominal values to test the robustness.

  17. Generation of individual diversity: a too neglected fundamental property of adaptive immune system

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    Eric eMuraille

    2014-05-01

    Full Text Available The fitness gains resulting from development of the adaptive immune system (AIS during evolution are still the subject of hot debate. A large random repertoire of antigenic receptors is costly to develop and could be the source of autoimmune reactions. And yet, despite their drawbacks, AIS-like systems seem to have been independently acquired in several phyla of metazoans with very different anatomies, longevities and lifestyles. This article is a speculative attempt to explore the selective pressures which favoured this striking convergent evolution. It is well known that the AIS enables an organism to produce a specific immune response against all natural or artificial antigenic structures. However, it is frequently neglected that this response is highly variable among individuals. In practice, each individual possesses a private adaptive immune repertoire. This individualisation of immune defences implies that invasion and escape immune mechanisms developed by pathogens will certainly not always be successful as the specific targets and organisation of the immune response are somewhat unpredictable. In a population where individuals display heterogeneous immune responses to infection, the probability that a pathogen is able to infect all individuals could be reduced compared to a homogeneous population. This suggests that the individual diversity of the immune repertoire is not a by-product of the AIS but of its fundamental properties and could be in part responsible for repeated selection and conservation of the AIS during metazoan evolution. The capacity of the AIS to improve the management of cooperative or parasitic symbiotic relationships at the individual level could be a secondary development due to its progressive integration into the innate immune system. This hypothesis constitutes a new scenario for AIS emergence and explains the selection of MHC restriction and MHC diversification.

  18. Analysing and Navigating Natural Products Space for Generating Small, Diverse, But Representative Chemical Libraries.

    Science.gov (United States)

    O'Hagan, Steve; Kell, Douglas B

    2018-01-01

    Armed with the digital availability of two natural products libraries, amounting to some 195 885 molecular entities, we ask the question of how we can best sample from them to maximize their "representativeness" in smaller and more usable libraries of 96, 384, 1152, and 1920 molecules. The term "representativeness" is intended to include diversity, but for numerical reasons (and the likelihood of being able to perform a QSAR) it is necessary to focus on areas of chemical space that are more highly populated. Encoding chemical structures as fingerprints using the RDKit "patterned" algorithm, we first assess the granularity of the natural products space using a simple clustering algorithm, showing that there are major regions of "denseness" but also a great many very sparsely populated areas. We then apply a "hybrid" hierarchical K-means clustering algorithm to the data to produce more statistically robust clusters from which representative and appropriate numbers of samples may be chosen. There is necessarily again a trade-off between cluster size and cluster number, but within these constraints, libraries containing 384 or 1152 molecules can be found that come from clusters that represent some 18 and 30% of the whole chemical space, with cluster sizes of, respectively, 50 and 27 or above, just about sufficient to perform a QSAR. By using the online availability of molecules via the Molport system (www.molport.com), we are also able to construct (and, for the first time, provide the contents of) a small virtual library of available molecules that provided effective coverage of the chemical space described. Consistent with this, the average molecular similarities of the contents of the libraries developed is considerably smaller than is that of the original libraries. The suggested libraries may have use in molecular or phenotypic screening, including for determining possible transporter substrates. © 2017 The Authors. Biotechnology Journal Published by Wiley

  19. Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster.

    Science.gov (United States)

    Miller, Danny E; Cook, Kevin R; Yeganeh Kazemi, Nazanin; Smith, Clarissa B; Cockrell, Alexandria J; Hawley, R Scott; Bergman, Casey M

    2016-03-08

    Multiply inverted balancer chromosomes that suppress exchange with their homologs are an essential part of the Drosophila melanogaster genetic toolkit. Despite their widespread use, the organization of balancer chromosomes has not been characterized at the molecular level, and the degree of sequence variation among copies of balancer chromosomes is unknown. To map inversion breakpoints and study potential diversity in descendants of a structurally identical balancer chromosome, we sequenced a panel of laboratory stocks containing the most widely used X chromosome balancer, First Multiple 7 (FM7). We mapped the locations of FM7 breakpoints to precise euchromatic coordinates and identified the flanking sequence of breakpoints in heterochromatic regions. Analysis of SNP variation revealed megabase-scale blocks of sequence divergence among currently used FM7 stocks. We present evidence that this divergence arose through rare double-crossover events that replaced a female-sterile allele of the singed gene (sn(X2)) on FM7c with a sequence from balanced chromosomes. We propose that although double-crossover events are rare in individual crosses, many FM7c chromosomes in the Bloomington Drosophila Stock Center have lost sn(X2) by this mechanism on a historical timescale. Finally, we characterize the original allele of the Bar gene (B(1)) that is carried on FM7, and validate the hypothesis that the origin and subsequent reversion of the B(1) duplication are mediated by unequal exchange. Our results reject a simple nonrecombining, clonal mode for the laboratory evolution of balancer chromosomes and have implications for how balancer chromosomes should be used in the design and interpretation of genetic experiments in Drosophila.

  20. The performance of a Solar Aided Power Generation plant with diverse “configuration-operation” combinations

    International Nuclear Information System (INIS)

    Qin, Jiyun; Hu, Eric; Nathan, Graham J.

    2016-01-01

    Highlights: • Four configurations of solar preheaters have been proposed. • Three typical operation strategies of solar preheaters have been identified. • 12 “configuration-operation” combinations has been proposed. • There are superior combinations to achieve the highest solar thermal performance. - Abstract: Solar Aided Power Generation is an efficient way to integrate solar thermal energy into a fossil fuel fired power plant for solar power generation purposes. In this particular power plant, the solar heat is used to displace the extraction steam to preheat the feedwater to the boiler. The heat exchanger, which facilitates the heat exchange between the solar heat carried by the heat transfer fluid and the feedwater, is termed a solar preheater. Four possible configurations of the solar preheater, namely Parallel 1, Parallel 2, Series 1 and Series 2, are proposed in this paper. In this type of plant, the extraction steam flow rates must be adjusted according to the solar input. The ways to control the extraction steam flow rates are termed solar preheater operation strategies. Three typical strategies: the Constant Temperature control, Variable Temperature control with high to low temperature feedwater heater displacement and Variable Temperature control with low to high temperature feedwater heater displacement have been identified. Each configuration can be operated with one of the three strategies, resulting in twelve “configuration-operation” combinations/scenarios (shown in Table 1). Previous assessments and modelling of such a plant have only been based on a single combination. In this paper, a Solar Aided Power Generation plant, modified from a typical 300 MW power plant, is used to understand the plant’s performance for all twelve of the available combinations. The results show that the instantaneous and annual technical performances of such a plant are dependent on the combinations used. The scenario 10 (Table 1) is superior to the

  1. Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement

    Energy Technology Data Exchange (ETDEWEB)

    Le Coq, Johanne; Ghosh, Partho (UCSD)

    2012-06-19

    Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd ({approx}16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 10{sup 20} potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation.

  2. The Phanerochaete chrysosporium secretome : database predictions and initial mass spectrometry peptide identifications in cellulose-grown medium

    Science.gov (United States)

    Amber J. Vanden Wymelenberg; Grzegorz Sabat; Diego Martinez; Alex S. Rajangam; Tuula T. Teeri; Jill A. Gaskell; Philip J. Kersten; Daniel Cullen

    2005-01-01

    The white rot basidiomycete, Phanerochaete chrysosporium, employs an array of extracellular enzymes to completely degrade the major polymers of wood : cellulose, hemicellulose and lignin. Towards the identification of participating enzymes, 268 likely secreted proteins were predicted using SignalP and TargetP algorithms. To assess the reliability of secretome...

  3. High and Low Doses of Ionizing Radiation Induce Different Secretome Profiles in a Human Skin Model

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qibin; Matzke, Melissa M.; Schepmoes, Athena A.; Moore, Ronald J.; Webb-Robertson, Bobbie-Jo M.; Hu, Zeping; Monroe, Matthew E.; Qian, Weijun; Smith, Richard D.; Morgan, William F.

    2014-03-18

    It is postulated that secreted soluble factors are important contributors of bystander effect and adaptive responses observed in low dose ionizing radiation. Using multidimensional liquid chromatography-mass spectrometry based proteomics, we quantified the changes of skin tissue secretome – the proteins secreted from a full thickness, reconstituted 3-dimensional skin tissue model 48 hr after exposure to 3, 10 and 200 cGy of X-rays. Overall, 135 proteins showed statistical significant difference between the sham (0 cGy) and any of the irradiated groups (3, 10 or 200 cGy) on the basis of Dunnett adjusted t-test; among these, 97 proteins showed a trend of downregulation and 9 proteins showed a trend of upregulation with increasing radiation dose. In addition, there were 21 and 8 proteins observed to have irregular trends with the 10 cGy irradiated group either having the highest or the lowest level among all three radiated doses. Moreover, two proteins, carboxypeptidase E and ubiquitin carboxyl-terminal hydrolase isozyme L1 were sensitive to ionizing radiation, but relatively independent of radiation dose. Conversely, proteasome activator complex subunit 2 protein appeared to be sensitive to the dose of radiation, as rapid upregulation of this protein was observed when radiation doses were increased from 3, to 10 or 200 cGy. These results suggest that different mechanisms of action exist at the secretome level for low and high doses of ionizing radiation.

  4. Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis.

    Science.gov (United States)

    Bianco, Linda; Perrotta, Gaetano

    2015-03-12

    Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation.

  5. Effector-mining in the poplar rust fungus Melampsora larici populina secretome

    Directory of Open Access Journals (Sweden)

    Cecile eLorrain

    2015-12-01

    Full Text Available The poplar leaf rust fungus, Melampsora larici-populina has been established as a tree-microbe interaction model. Understanding the molecular mechanisms controlling infection by pathogens appears essential for durable management of tree plantations. In biotrophic plant parasites, effectors are known to condition host cell colonization. Thus, investigation of candidate secreted effector proteins is a major goal in the poplar-poplar rust interaction. Unlike oomycetes, fungal effectors do not share conserved motifs and candidate prediction relies on a set of a priori criteria established from reported bona fide effectors. Secretome prediction, genome-wide analysis of gene families and transcriptomics of M. larici-populina have led to catalogues of more than a thousand secreted proteins. Automatized effector mining pipelines hold great promise for rapid and systematic identification and prioritization of candidate secreted effector proteins for functional characterization. In this review, we report on and discuss the current status of the poplar rust fungus secretome and prediction of candidate effectors in this species.

  6. Prediction of the in planta Phakopsora pachyrhizi secretome and potential effector families.

    Science.gov (United States)

    de Carvalho, Mayra C da C G; Costa Nascimento, Leandro; Darben, Luana M; Polizel-Podanosqui, Adriana M; Lopes-Caitar, Valéria S; Qi, Mingsheng; Rocha, Carolina S; Carazzolle, Marcelo Falsarella; Kuwahara, Márcia K; Pereira, Goncalo A G; Abdelnoor, Ricardo V; Whitham, Steven A; Marcelino-Guimarães, Francismar C

    2017-04-01

    Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, can cause losses greater than 80%. Despite its economic importance, there is no soybean cultivar with durable ASR resistance. In addition, the P. pachyrhizi genome is not yet available. However, the availability of other rust genomes, as well as the development of sample enrichment strategies and bioinformatics tools, has improved our knowledge of the ASR secretome and its potential effectors. In this context, we used a combination of laser capture microdissection (LCM), RNAseq and a bioinformatics pipeline to identify a total of 36 350 P. pachyrhizi contigs expressed in planta and a predicted secretome of 851 proteins. Some of the predicted secreted proteins had characteristics of candidate effectors: small size, cysteine rich, do not contain PFAM domains (except those associated with pathogenicity) and strongly expressed in planta. A comparative analysis of the predicted secreted proteins present in Pucciniales species identified new members of soybean rust and new Pucciniales- or P. pachyrhizi-specific families (tribes). Members of some families were strongly up-regulated during early infection, starting with initial infection through haustorium formation. Effector candidates selected from two of these families were able to suppress immunity in transient assays, and were localized in the plant cytoplasm and nuclei. These experiments support our bioinformatics predictions and show that these families contain members that have functions consistent with P. pachyrhizi effectors. © 2016 BSPP AND JOHN WILEY & SONS LTD.

  7. Type 2 diabetes alters mesenchymal stem cell secretome composition and angiogenic properties.

    Science.gov (United States)

    Ribot, Jonathan; Caliaperoumal, Guavri; Paquet, Joseph; Boisson-Vidal, Catherine; Petite, Herve; Anagnostou, Fani

    2017-02-01

    This study aimed at characterizing the impact of type 2 diabetes mellitus (T2DM) on the bone marrow mesenchymal stem cell (BMMSC) secretome and angiogenic properties. BMMSCs from Zucker diabetic fatty rats (ZDF) (a T2DM model) and Zucker LEAN littermates (control) were cultured. The supernatant conditioned media (CM) from BMMSCs of diabetic and control rats were collected and analysed. Compared to results obtained using CM from LEAN-BMMSCs, the bioactive content of ZDF-BMMSC CM (i) differently affects endothelial cell (HUVEC) functions in vitro by inducing increased (3.5-fold; P CATD, FMOD LTBP1 and LTBP2, which are involved in angiogenesis and/or extracellular matrix composition. Addition of neutralizing antibodies against IGF-1, LTBP1 or LTBP2 in the CM of BMMSCs from diabetic rats decreased its stimulatory effect on HUVEC migration by approximately 60%, 40% or 40%, respectively. These results demonstrate that BMMSCs from T2DM rats have a unique secretome with distinct angiogenic properties and provide new insights into the role of BMMSCs in aberrant angiogenesis in the diabetic milieu. © 2016 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  8. Secretome Identifies Tenascin-X as a Potent Marker of Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Marianne Kramer

    2015-01-01

    Full Text Available CA-125 has been a valuable marker for the follow-up of ovarian cancer patients but it is not sensitive enough to be used as diagnostic marker. We had already used secretomic methods to identify proteins differentially secreted by serous ovarian cancer cells compared to healthy ovarian cells. Here, we evaluated the secretion of these proteins by ovarian cancer cells during the follow-up of one patient. Proteins that correlated with CA-125 levels were screened using serum samples from ovarian cancer patients as well as benign and healthy controls. Tenascin-X secretion was shown to correlate with CA-125 value in the initial case study. The immunohistochemical detection of increased amount of tenascin-X in ovarian cancer tissues compared to healthy tissues confirms the potent interest in tenascin-X as marker. We then quantified the tenascin-X level in serum of patients and identified tenascin-X as potent marker for ovarian cancer, showing that secretomic analysis is suitable for the identification of protein biomarkers when combined with protein immunoassay. Using this method, we determined tenascin-X as a new potent marker for serous ovarian cancer.

  9. Genome, transcriptome, and secretome analysis of wood decay fungus postia placenta supports unique mechanisms of lignocellulose conversion

    Energy Technology Data Exchange (ETDEWEB)

    Martinez, Diego [Los Alamos National Laboratory; Challacombe, Jean F [Los Alamos National Laboratory; Misra, Monica [Los Alamos National Laboratory; Xie, Gary [Los Alamos National Laboratory; Brettin, Thomas [Los Alamos National Laboratory; Morgenstern, Ingo [CLARK UNIV; Hibbett, David [CLARK UNIV.; Schmoll, Monika [UNIV WIEN; Kubicek, Christian P [UNIV WIEN; Ferreira, Patricia [CIB, CSIC, MADRID; Ruiz - Duenase, Francisco J [CIB, CSIC, MADRID; Martinez, Angel T [CIB, CSIC, MADRID; Kersten, Phil [FOREST PRODUCTS LAB; Hammel, Kenneth E [FOREST PRODUCTS LAB; Vanden Wymelenberg, Amber [U. WISCONSIN; Gaskell, Jill [FOREST PRODUCTS LAB; Lindquist, Erika [DOE JGI; Sabati, Grzegorz [U. WISCONSIN; Bondurant, Sandra S [U. WISCONSIN; Larrondo, Luis F [U. CATHOLICA DE CHILE; Canessa, Paulo [U. CATHOLICA DE CHILE; Vicunna, Rafael [U. CATHOLICA DE CHILE; Yadavk, Jagiit [U. CINCINATTI; Doddapaneni, Harshavardhan [U. CINCINATTI; Subramaniank, Venkataramanan [U. CINCINATTI; Pisabarro, Antonio G [PUBLIC U. NAVARRE; Lavin, Jose L [PUBLIC U. NAVARRE; Oguiza, Jose A [PUBLIC U. NAVARRE; Master, Emma [U. TORONTO; Henrissat, Bernard [CNRS, MARSEILLE; Coutinho, Pedro M [CNRS, MARSEILLE; Harris, Paul [NOVOZYMES, INC.; Magnuson, Jon K [PNNL; Baker, Scott [PNNL; Bruno, Kenneth [PNNL; Kenealy, William [MASCOMA, INC.; Hoegger, Patrik J [GEORG-AUGUST-U.; Kues, Ursula [GEORG-AUGUST-U; Ramaiva, Preethi [NOVOZYMES, INC.; Lucas, Susan [DOE JGI; Salamov, Asaf [DOE JGI; Shapiro, Harris [DOE JGI; Tuh, Hank [DOE JGI; Chee, Christine L [UNM; Teter, Sarah [NOVOZYMES, INC.; Yaver, Debbie [NOVOZYMES, INC.; James, Tim [MCMASTER U.; Mokrejs, Martin [CHARLES U.; Pospisek, Martin [CHARLES U.; Grigoriev, Igor [DOE JGI; Rokhsar, Dan [DOE JGI; Berka, Randy [NOVOZYMES; Cullen, Dan [FOREST PRODUCTS LAB

    2008-01-01

    Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative {beta}-1-4 endoglucanase were expressed at high levels relative to glucose grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC{center_dot}MSIMS). Also upregulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H202. These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H202 react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons to the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost.

  10. Spatial regulation of a common precursor from two distinct genes generates metabolite diversity

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Chun-Jun; Sun, Wei-Wen; Bruno, Kenneth S.; Oakley, Berl R.; Keller, Nancy P.; Wang, Clay C.

    2015-07-13

    In secondary metabolite biosynthesis, core synthetic genes such as polyketide synthase genes or non-ribosomal peptide synthase genes usually encode proteins that generate various backbone precursors. These precursors are modified by other tailoring enzymes to yield a large variety of different secondary metabolites. The number of core synthesis genes in a given species correlates, therefore, with the number of types of secondary metabolites the organism can produce. In our study, heterologous expression of all the A. terreus NRPS-like genes showed that two NRPS-like proteins, encoded by atmelA and apvA, release the same natural product, aspulvinone E. More interestingly, further experiments revealed that the aspulvinone E produced by two different genes accumulates in different fungal compartments. And this spatial control of aspulvinone E production is likely to be regulated by their own specific promoters. Comparative genomics indicates that atmelA and apvA might share a same ancestral gene and the gene apvA is inserted in a highly conserved region in Aspergillus species that contains genes coding for life-essential proteins. The study also identified one trans-prenyltransferase AbpB which is capable of prenylating two different substrates aspulvinones and butyrolactones. In total, our study shows the first example in which the locally distribution of the same natural product could lead to its incorporation into different SM pathways.

  11. Expanded therapeutic potential in activity space of next-generation 5-nitroimidazole antimicrobials with broad structural diversity

    Science.gov (United States)

    Miyamoto, Yukiko; Kalisiak, Jarosław; Korthals, Keith; Lauwaet, Tineke; Cheung, Dae Young; Lozano, Ricardo; Cobo, Eduardo R.; Upcroft, Peter; Upcroft, Jacqueline A.; Berg, Douglas E.; Gillin, Frances D.; Fokin, Valery V.; Sharpless, K. Barry; Eckmann, Lars

    2013-01-01

    Metronidazole and other 5-nitroimidazoles (5-NI) are among the most effective antimicrobials available against many important anaerobic pathogens, but evolving resistance is threatening their long-term clinical utility. The common 5-NIs were developed decades ago, yet little 5-NI drug development has since taken place, leaving the true potential of this important drug class unexplored. Here we report on a unique approach to the modular synthesis of diversified 5-NIs for broad exploration of their antimicrobial potential. Many of the more than 650 synthesized compounds, carrying structurally diverse functional groups, have vastly improved activity against a range of microbes, including the pathogenic protozoa Giardia lamblia and Trichomonas vaginalis, and the bacterial pathogens Helicobacter pylori, Clostridium difficile, and Bacteroides fragilis. Furthermore, they can overcome different forms of drug resistance, and are active and nontoxic in animal infection models. These findings provide impetus to the development of structurally diverse, next-generation 5-NI drugs as agents in the antimicrobial armamentarium, thus ensuring their future viability as primary therapeutic agents against many clinically important infections. PMID:24101497

  12. Temporally Diverse Excitation Generates Direction-Selective Responses in ON- and OFF-Type Retinal Starburst Amacrine Cells.

    Science.gov (United States)

    Fransen, James W; Borghuis, Bart G

    2017-02-07

    The complexity of sensory receptive fields increases from one synaptic stage to the next. In many cases, increased complexity is achieved through spatiotemporal interactions between convergent excitatory and inhibitory inputs. Here, we present evidence that direction selectivity (DS), a complex emergent receptive field property of retinal starburst amacrine cells (SACs), is generated by spatiotemporal interactions between functionally diverse excitatory inputs. Electrophysiological whole-cell recordings from ON and OFF SACs show distinct temporal differences in excitation following proximal compared with distal stimulation of their receptive fields. Distal excitation is both faster and more transient, ruling out passive filtering by the dendrites and indicating a task-specific specialization. Model simulations demonstrate that this specific organization of excitation generates robust DS responses in SACs, consistent with elementary motion detector models. These results indicate that selective integration of spatiotemporally patterned excitation is a computational mechanism for motion detection in the mammalian retina. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  13. Secretome of Aggregated Embryonic Stem Cell-Derived Mesenchymal Stem Cell Modulates the Release of Inflammatory Factors in Lipopolysaccharide-Induced Peripheral Blood Mononuclear Cells

    Science.gov (United States)

    Mohammadi Ghahhari, Nastaran; Maghsood, Faezeh; Jahandideh, Saeed; Lotfinia, Majid; Lak, Shirin; Johari, Behrooz; Azarnezhad, Asaad; Kadivar, Mehdi

    2018-07-01

    Bone marrow mesenchymal stem cells (BM-MSCs) have emerged as a potential therapy for various inflammatory diseases. Because of some limitations, several recent studies have suggested the use of embryonic stem cell-derived MSCs (ESC-MSCs) as an alternative for BM-MSCs. Some of the therapeutic effects of the ESC-MSCs are related to the secretion of a broad array of cytokines and growth factors, known as secretome. Harnessing this secretome for therapeutic applications requires the optimization of production of secretary molecules. It has been shown that aggregation of MSCs into 3D spheroids, as a preconditioning strategy, can enhance immunomodulatory potential of such cells. In this study, we investigated the effect of secretome derived from human ESC-MSCs (hESC-MSCs) spheroids on secretion of IL-1β, IL-10, and tumor necrosis factor α (TNF-α) from lipopolysaccharide (LPS)-induced peripheral blood mononuclear cells (PBMCs). In the present study, after immunophenotyping and considering mesodermal differentiation of hESC-MSCs, the cells were non-adherently grown to prepare 3D aggregates, and then conditioned medium or secretome was extracted from the cultures. Afterwards, the anti-inflammatory effects of the secretome were assessed in an in vitro model of inflammation. Results from this study showed that aggregate-prepared secretome from hESC-MSCs was able to significantly decrease the secretion of TNF-α (301.7 ± 5.906, p strategy to increase immunomodulatory characteristics of hESC-MSCs.

  14. Proteomic analysis of mycelium and secretome of different Botrytis cinerea wild-type strains.

    Science.gov (United States)

    González-Fernández, Raquel; Aloria, Kerman; Valero-Galván, José; Redondo, Inmaculada; Arizmendi, Jesús M; Jorrín-Novo, Jesús V

    2014-01-31

    The necrotrophic fungus Botrytis cinerea is a very damaging phytopathogen of wide host range and environmental persistence. It is difficult to control because of its genetic versatility, expressed in the many phenotypical differences among isolates. The genomes of the B. cinerea B05.10 and T4 strains have been recently sequenced, becoming a model system for necrotrophic pathogens, and thus opening new alternatives for functional genomics analysis. In this work, the mycelium and secreted proteome of six wild-type strains with different host range, and grown in liquid minimal medium, have been analyzed by using complementary gel-based (1-DE and 2-DE) and gel-free/label-free (nUPLC-MS(E)) approaches. We found differences in the protein profiles among strains belonging to both the mycelium and the secretome. A total of 47 and 51 variable proteins were identified in the mycelium and the secretome, respectively. Some of them, such as malate dehydrogenase or peptidyl-prolyl cis-trans isomerase from the mycelium, and endopolygalacturonase, aspartic protease or cerato-platanin protein from the secretome have been reported as virulence factors, which are involved in host-tissue invasion, pathogenicity or fungal development. The necrotrophic fungus Botrytis cinerea is an important phytopathogen of wide host range and environmental persistence, causing substantial economic losses worldwide. In this work, the mycelium and secreted proteome of six B. cinerea wild-type strains with different host range have been analyzed by using complementary gel-based and gel-free/label-free approaches. Fungal genetic versatility was confirmed at the proteome level for both mycelium proteome and secreted proteins. A high number of hypothetical proteins with conserved domains related to toxin compounds or to unknown functions were identified, having qualitative differences among strains. The identification of hypothetical proteins suggests that the B. cinerea strains differ mostly in processes

  15. Diversification and coevolution in brood pollination mutualisms: Windows into the role of biotic interactions in generating biological diversity.

    Science.gov (United States)

    Hembry, David H; Althoff, David M

    2016-10-01

    Brood pollination mutualisms-interactions in which specialized insects are both the pollinators (as adults) and seed predators (as larvae) of their host plants-have been influential study systems for coevolutionary biology. These mutualisms include those between figs and fig wasps, yuccas and yucca moths, leafflowers and leafflower moths, globeflowers and globeflower flies, Silene plants and Hadena and Perizoma moths, saxifrages and Greya moths, and senita cacti and senita moths. The high reciprocal diversity and species-specificity of some of these mutualisms have been cited as evidence that coevolution between plants and pollinators drives their mutual diversification. However, the mechanisms by which these mutualisms diversify have received less attention. In this paper, we review key hypotheses about how these mutualisms diversify and what role coevolution between plants and pollinators may play in this process. We find that most species-rich brood pollination mutualisms show significant phylogenetic congruence at high taxonomic scales, but there is limited evidence for the processes of both cospeciation and duplication, and there are no unambiguous examples known of strict-sense contemporaneous cospeciation. Allopatric speciation appears important across multiple systems, particularly in the insects. Host-shifts appear to be common, and widespread host-shifts by pollinators may displace other pollinator lineages. There is relatively little evidence for a "coevolution through cospeciation" model or that coevolution promotes speciation in these systems. Although we have made great progress in understanding the mechanisms by which brood pollination mutualisms diversify, many opportunities remain to use these intriguing symbioses to understand the role of biotic interactions in generating biological diversity. © 2016 Botanical Society of America.

  16. Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV using amplicon next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Wycliff M Kinoti

    Full Text Available PCR amplicon next generation sequencing (NGS analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.

  17. Characterization of HSP27 phosphorylation sites in human atherosclerotic plaque secretome

    DEFF Research Database (Denmark)

    Durán, Mari-Carmen; Boeri-Erba, Elisabetta; Mohammed, Shabaz

    2007-01-01

    spectrometry (MS). Among the identified proteins, two isoforms of heat shock protein 27 (HSP27), a protein recently described as a potential biomarker of atherosclerosis, were detected. However, the putative mechanisms in which HSP27 isoforms could be involved in the atherosclerotic process are unknown. Thus......, the role that phosphorylated HSP27 could play in the atherosclerotic process is actually under study. The present work shows the strategies employed to characterize the phosphorylation in the HSP27 secreted by atheroma plaque samples. The application of liquid chromatography tandem mass spectrometry (MS......-lymphocytes). These interactions can be mediated by proteins secreted from these cells, which therefore exert an important role in the atherosclerotic process. We recently described a novel strategy for the characterization of the human atherosclerotic plaque secretome, combining two-dimensional gel electrophoresis and mass...

  18. Secretomics identifies Fusarium graminearum proteins involved in the interaction with barley and wheat

    DEFF Research Database (Denmark)

    Yang, Fen; Jensen, Jens D.; Svensson, Birte

    2012-01-01

    or wheat flour as the sole nutrient source to mimic the host–pathogen interaction. A gel‐based proteomics approach was employed to identify the proteins secreted into the culture medium. Sixty‐nine unique fungal proteins were identified in 154 protein spots, including enzymes involved in the degradation......Fusarium graminearum is a phytopathogenic fungus primarily infecting small grain cereals, including barley and wheat. Secreted enzymes play important roles in the pathogenicity of many fungi. In order to access the secretome of F. graminearum, the fungus was grown in liquid culture with barley...... of cell walls, starch and proteins. Of these proteins, 35% had not been identified in previous in planta or in vitro studies, 70% were predicted to contain signal peptides and a further 16% may be secreted in a nonclassical manner. Proteins identified in the 72 spots showing differential appearance...

  19. Analysis of membrane proteome and secretome in cells over-expressing ADAM17 using quantitative proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Kawahara, R.; Simabuco, F.M. [Laboratorio Nacional de Biociencias - LNBIO, Campinas, SP (Brazil); Yokoo, S.; Paes Leme, A.F. [Laboratorio Nacional de Luz Sincrotron (LNLS), Campinas, SP (Brazil); Sherman, N. [University of Virginia, Charlottesville, VA (United States)

    2012-07-01

    Full text: A disintegrin and metalloproteinase (ADAM) protease is involved in proteolytic ectodomain shedding of several membrane-associated proteins and modulation of key cell signaling pathways in the tumor microenvironment. In this study, we examined the effect of over-expressing the full length human ADAM17 in membrane and secreted proteins. To this end, we constructed a stable Flp-In T-RExHEK293 cells expressing ADAM17 by tetracycline induction. These cells were grown in Dulbeccos modified Eagles medium containing light lysine, arginine or heavy, L-Arg-13C615N4 and L-Lys -13C615N2 (SILAC: stable isotope labeling with amino acid in cell culture) media and they were treated with an ADAM17 activator, phorbolester (PMA). Controls such as Flp-In T-RExHEK293 cell without PMA treatment and without ADAM17 cloned were cultivated in light medium. The ADAM17 overexpression was induced with tetracycline 500 ng/ml for 24 hours. Cells in a heavy condition were treated with PMA 50 ng/ml for 1 hour and vehicle DMSO was used as control in a light cell condition. The extracellular media were collected, concentrated and used to evaluate the secretome and a cell surface biotinylation-based approach was used to capture cell surface-associated proteins. The biotinylated proteins were eluted with dithiothreitol, alkylated with iodoacetamide and then digested with trypsin. The resulting peptides were subjected to LC-MS/MS analysis on an ETD enabled Orbitrap Velos instrument. The results showed different proteins up or down regulated in membrane and secretome analysis which might represent potential molecules involved in signaling or ADAM17 regulation events. (author)

  20. Proteome and Secretome Characterization of Glioblastoma-Derived Neural Stem Cells.

    Science.gov (United States)

    Okawa, Satoshi; Gagrica, Sladjana; Blin, Carla; Ender, Christine; Pollard, Steven M; Krijgsveld, Jeroen

    2017-04-01

    Glioblastoma multiforme (GBM) (grade IV astrocytoma) is the most common and aggressive primary brain tumor. GBM consists of heterogeneous cell types including a subset of stem cell-like cells thought to sustain tumor growth. These tumor-initiating glioblastoma multiforme-derived neural stem (GNS) cells as well as their genetically normal neural stem (NS) counterparts can be propagated in culture as relatively pure populations. Here, we perform quantitative proteomics to globally characterize and compare total proteome plus the secreted proteome (secretome) between GNS cells and NS cells. Proteins and pathways that distinguish malignant cancer (GNS) stem cells from their genetically normal counterparts (NS cells) might have value as new biomarkers or therapeutic targets. Our analysis identified and quantified ∼7,500 proteins in the proteome and ∼2,000 in the secretome, 447 and 138 of which were differentially expressed, respectively. Notable tumor-associated processes identified using gene set enrichment analysis included: extracellular matrix interactions, focal adhesion, cell motility, and cell signaling. We focused on differentially expressed surface proteins, and identified 26 that participate in ligand-receptor pairs that play a prominent role in tumorigenesis. Immunocytochemistry and immunoblotting confirmed that CD9, a recently identified marker of adult subventricular zone NS cells, was consistently enriched across a larger set of primary GNS cell lines. CD9 may, therefore, have value as a GNS-specific surface marker and a candidate therapeutic target. Altogether, these findings support the notion that increased cell-matrix and cell-cell adhesion molecules play a crucial role in promoting the tumor initiating and infiltrative properties of GNS cells. Stem Cells 2017;35:967-980. © 2016 AlphaMed Press.

  1. Resolving breast cancer heterogeneity by searching reliable protein cancer biomarkers in the breast fluid secretome

    International Nuclear Information System (INIS)

    Mannello, Ferdinando; Ligi, Daniela

    2013-01-01

    One of the major goals in cancer research is to find and evaluate the early presence of biomarkers in human fluids and tissues. To resolve the complex cell heterogeneity of a tumor mass, it will be useful to characterize the intricate biomolecular composition of tumor microenvironment (the so called cancer secretome), validating secreted proteins as early biomarkers of cancer initiation and progression. This approach is not broadly applicable because of the paucity of well validated and FDA-approved biomarkers and because most of the candidate biomarkers are mainly organ-specific rather than tumor-specific. For these reasons, there is an urgent need to identify and validate a panel of biomarker combinations for early detection of human tumors. This is especially important for breast cancer, the cancer spread most worldwide among women. It is well known that patients with early diagnosed breast cancer live longer, require less extensive treatment and fare better than patients with more aggressive and/or advanced disease. In the frame of searching breast cancer biomarkers (especially using nipple aspirate fluid mirroring breast microenvironment), studies have highlighted an optimal combination of well-known biomarkers: uPA + PAI-1 + TF. When individually investigated they did not show perfect accuracy in predicting the presence of breast cancer, whereas the triple combination has been demonstrated to be highly predictive of pre-cancer and/or cancerous conditions, approaching 97-100% accuracy. Despite the heterogeneous composition of breast cancer and the difficulties to find specific breast cancer biomolecules, the noninvasive analysis of the nipple aspirate fluid secretome may significantly improve the discovery of promising biomarkers, helping also the differentiation among benign and invasive breast diseases, opening new frontiers in early oncoproteomics

  2. Angiogenin induces modifications in the astrocyte secretome: relevance to amyotrophic lateral sclerosis.

    Science.gov (United States)

    Skorupa, Alexandra; Urbach, Serge; Vigy, Oana; King, Matthew A; Chaumont-Dubel, Séverine; Prehn, Jochen H M; Marin, Philippe

    2013-10-08

    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease affecting lower and upper motoneurons. Recent studies have shown that both motor neurons and non-neuronal neighbouring cells such as astrocytes and microglia contribute to disease pathology. Loss-of-function mutations in the angiogenin (ANG) gene have been identified in ALS patients. Angiogenin is enriched in motor neurons and exerts neuroprotective effects in vitro and in vivo. We have recently shown that motoneurons secrete angiogenin, and that secreted angiogenin is exclusively taken up by astrocytes, suggesting a paracrine mechanism of neuroprotection. To gain insights into astrocyte effectors of angiogenin-induced neuroprotection, we examined alterations in the astrocyte secretome induced by angiogenin treatment using quantitative proteomics based on Stable Isotope Labelling by Amino Acids in Cell Culture (SILAC). We identified 2128 proteins in conditioned media from primary cultured mouse astrocytes, including 1247 putative secreted proteins. Of these, 60 proteins showed significant regulation of secretion in response to angiogenin stimulation. Regulated proteins include chemokines and cytokines, proteases and protease inhibitors as well as proteins involved in reorganising the extracellular matrix. In conclusion, this proteomic analysis increases our knowledge of the astrocyte secretome and reveals potential molecular substrates underlying the paracrine, neuroprotective effects of angiogenin. This study provides the most extensive list of astrocyte-secreted proteins available and reveals novel potential molecular substrates of astrocyte-neuron communication. It also identifies a set of astrocyte-derived proteins that might slow down ALS disease progression. It should be relevant to a large readership of neuroscientists and clinicians, in particular those with an interest in the physiological and pathological roles of astrocytes and in the molecular and cellular mechanisms underlying

  3. Generation and structural validation of a library of diverse xyloglucan-derived oligosaccharides, including an update on xyloglucan nomenclature.

    Science.gov (United States)

    Tuomivaara, Sami T; Yaoi, Katsuro; O'Neill, Malcolm A; York, William S

    2015-01-30

    Xyloglucans are structurally complex plant cell wall polysaccharides that are involved in cell growth and expansion, energy metabolism, and signaling. Determining the structure-function relationships of xyloglucans would benefit from the availability of a comprehensive and structurally diverse collection of rigorously characterized xyloglucan oligosaccharides. Here, we present a workflow for the semi-preparative scale generation and purification of neutral and acidic xyloglucan oligosaccharides using a combination of enzymatic and chemical treatments and size-exclusion chromatography. Twenty-six of these oligosaccharides were purified to near homogeneity and their structures validated using a combination of matrix-assisted laser desorption/ionization mass spectrometry, high-performance anion exchange chromatography, and 1H nuclear magnetic resonance spectroscopy. Mass spectrometry and analytical chromatography were compared as methods for xyloglucan oligosaccharide quantification. 1H chemical shifts were assigned using two-dimensional correlation spectroscopy. A comprehensive update of the nomenclature describing xyloglucan side-chain structures is provided for reference. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. High diversity of genes and plasmids encoding resistance to third-generation cephalosporins and quinolones in clinical Escherichia coli from commercial poultry flocks in Italy

    DEFF Research Database (Denmark)

    Niero, Giulia; Bortolaia, Valeria; Vanni, Michele

    2018-01-01

    The aim was to investigate occurrence and diversity of plasmid-mediated resistance to third-generation cephalosporins (3GC) and quinolones in clinical Escherichia coli from 200 industrial poultry farms across Italy. E. coli was isolated from colibacillosis lesions in turkeys (n = 109), broilers (...

  5. Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region

    KAUST Repository

    Arif, Chatchanit

    2014-09-01

    The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.

  6. Unravelling the Neospora caninum secretome through the secreted fraction (ESA) and quantification of the discharged tachyzoite using high-resolution mass spectrometry-based proteomics

    Science.gov (United States)

    2013-01-01

    Background The apicomplexan parasite Neospora caninum causes neosporosis, a disease that leads to abortion or stillbirth in cattle, generating an economic impact on the dairy and beef cattle trade. As an obligatory intracellular parasite, N. caninum needs to invade the host cell in an active manner to survive. The increase in parasite cytosolic Ca2+ upon contact with the host cell mediates critical events, including the exocytosis of phylum-specific secretory organelles and the activation of the parasite invasion motor. Because invasion is considered a requirement for pathogen survival and replication within the host, the identification of secreted proteins (secretome) involved in invasion may be useful to reveal interesting targets for therapeutic intervention. Methods To chart the currently missing N. caninum secretome, we employed mass spectrometry-based proteomics to identify proteins present in the N. caninum tachyzoite using two different approaches. The first approach was identifying the proteins present in the tachyzoite-secreted fraction (ESA). The second approach was determining the relative quantification through peptide stable isotope labelling of the tachyzoites submitted to an ethanol secretion stimulus (discharged tachyzoite), expecting to identify the secreted proteins among the down-regulated group. Results As a result, 615 proteins were identified at ESA and 2,011 proteins quantified at the discharged tachyzoite. We have analysed the connection between the secreted and the down-regulated proteins and searched for putative regulators of the secretion process among the up-regulated proteins. An interaction network was built by computational prediction involving the up- and down-regulated proteins. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD000424. Conclusions The comparison between the protein abundances in ESA and their measure in the discharged tachyzoite allowed for a more precise

  7. Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow

    DEFF Research Database (Denmark)

    Deshmukh, Atul S; Cox, Juergen; Jensen, Lars Juhl

    2015-01-01

    the secretome of lipid-induced insulin-resistant skeletal muscle cells. Our workflow identified 1073 putative secreted proteins including 32 growth factors, 25 cytokines, and 29 metalloproteinases. In addition to previously reported proteins, we report hundreds of novel ones. Intriguingly, ∼40% of the secreted......-resistant conditions. Our study demonstrates an efficient combined experimental and bioinformatics workflow to identify putative secreted proteins from insulin-resistant skeletal muscle cells, which could easily be adapted to other cellular models....

  8. Inferring alterations in cell-to-cell communication in HER2+ breast cancer using secretome profiling of three cell models

    Science.gov (United States)

    Klinke, David J.; Kulkarni, Yogesh M.; Wu, Yueting; Byrne-Hoffman, Christina

    2015-01-01

    Challenges in demonstrating durable clinical responses to molecular-targeted therapies has sparked a re-emergence in viewing cancer as an evolutionary process. In somatic evolution, cellular variants are introduced through a random process of somatic mutation and are selected for improved fitness through a competition for survival. In contrast to Darwinian evolution, cellular variants that are retained may directly alter the fitness competition. If cell-to-cell communication is important for selection, the biochemical cues secreted by malignant cells that emerge should be altered to bias this fitness competition. To test this hypothesis, we compared the proteins secreted in vitro by two human HER2+ breast cancer cell lines (BT474 and SKBR3) relative to a normal human mammary epithelial cell line (184A1) using a proteomics workflow that leveraged two-dimensional gel electrophoresis (2DE) and MALDI-TOF mass spectrometry. Supported by the 2DE secretome maps and identified proteins, the two breast cancer cell lines exhibited secretome profiles that were similar to each other and, yet, were distinct from the 184A1 secretome. Using protein-protein interaction and pathway inference tools for functional annotation, the results suggest that all three cell lines secrete exosomes, as confirmed by scanning electron microscopy. Interestingly, the HER2+ breast cancer cell line exosomes are enriched in proteins involved in antigen processing and presentation and glycolytic metabolism. These pathways are associated with two of the emerging hallmarks of cancer: evasion of tumor immunosurveillance and deregulating cellular energetics. PMID:24752654

  9. Secretome analyses of Aβ(1-42) stimulated hippocampal astrocytes reveal that CXCL10 is involved in astrocyte migration.

    Science.gov (United States)

    Lai, Wenjia; Wu, Jing; Zou, Xiao; Xie, Jian; Zhang, Liwei; Zhao, Xuyang; Zhao, Minzhi; Wang, Qingsong; Ji, Jianguo

    2013-02-01

    Amyloid-beta (Aβ) aggregation plays an important role in the development of Alzheimer's disease (AD). In the AD brain, amyloid plaques are surrounded by reactive astrocytes, and many essential functions of astrocytes have been reported to be mediated by protein secretion. However, the roles of activated astrocytes in AD progression are under intense debate. To provide an in-depth view of the secretomes of activated astrocytes, we present in this study a quantitative profile of rat hippocampal astrocyte secretomes at multiple time points after both brief and sustained Aβ(1-42) stimulation. Using SILAC labeling and LC-MS/MS analyses, we identified 19 up-regulated secreted proteins after Aβ(1-42) treatment. These differentially expressed proteins have been suggested to be involved in key aspects of biological processes, such as cell recruitment, Aβ clearance, and regulation of neurogenesis. Particularly, we validated the role played by CXCL10 in promoting astrocyte aggregation around amyloid plagues through in vitro cell migration analysis. This research provides global, quantitative profiling of astrocyte secretomes produced on Aβ stimulation and hence provides a detailed molecular basis for the relationship between amyloid plaques and astrocyte aggregation; the findings thus have important implications for further investigations into AD development and therapy.

  10. Detecting exact breakpoints of deletions with diversity in hepatitis B viral genomic DNA from next-generation sequencing data.

    Science.gov (United States)

    Cheng, Ji-Hong; Liu, Wen-Chun; Chang, Ting-Tsung; Hsieh, Sun-Yuan; Tseng, Vincent S

    2017-10-01

    Many studies have suggested that deletions of Hepatitis B Viral (HBV) are associated with the development of progressive liver diseases, even ultimately resulting in hepatocellular carcinoma (HCC). Among the methods for detecting deletions from next-generation sequencing (NGS) data, few methods considered the characteristics of virus, such as high evolution rates and high divergence among the different HBV genomes. Sequencing high divergence HBV genome sequences using the NGS technology outputs millions of reads. Thus, detecting exact breakpoints of deletions from these big and complex data incurs very high computational cost. We proposed a novel analytical method named VirDelect (Virus Deletion Detect), which uses split read alignment base to detect exact breakpoint and diversity variable to consider high divergence in single-end reads data, such that the computational cost can be reduced without losing accuracy. We use four simulated reads datasets and two real pair-end reads datasets of HBV genome sequence to verify VirDelect accuracy by score functions. The experimental results show that VirDelect outperforms the state-of-the-art method Pindel in terms of accuracy score for all simulated datasets and VirDelect had only two base errors even in real datasets. VirDelect is also shown to deliver high accuracy in analyzing the single-end read data as well as pair-end data. VirDelect can serve as an effective and efficient bioinformatics tool for physiologists with high accuracy and efficient performance and applicable to further analysis with characteristics similar to HBV on genome length and high divergence. The software program of VirDelect can be downloaded at https://sourceforge.net/projects/virdelect/. Copyright © 2017. Published by Elsevier Inc.

  11. Differences in Stem Cell Processing Lead to Distinct Secretomes Secretion-Implications for Differential Results of Previous Clinical Trials of Stem Cell Therapy for Myocardial Infarction.

    Science.gov (United States)

    Wernly, Bernhard; Gonçalves, Inês; Kiss, Attila; Paar, Vera; Mösenlechner, Tobias; Leisch, Michael; Santer, David; Motloch, Lukas Jaroslaw; Klein, Klaus U; Tretter, Eva V; Kretzschmar, Daniel; Podesser, Bruno; Jung, Christian; Hoppe, Uta C; Lichtenauer, Michael

    2017-09-01

    Stem cell therapy for acute myocardial infarction (AMI) seemed to be a promising therapy, however, large clinical trials brought differential outcome. It has been shown that paracrine effects of secretomes of stem cells rather than cell therapy might play a fundamental role. The present study seeks to compare cell processing protocols of clinical trials and investigate effects of differential cell culture conditions on chemokine secretion and functional effects. Different secretomes are compared regarding IL-8, VEGF, MCP-1, and TNF-alpha secretion. Secretome mediated effects are evaluated on endothelial cell (HUVEC) tube formation and migration. Cardioprotective signaling kinases in human cardiomyocytes are determined by Western immunoblotting. Cells processed according to the REPAIR-AMI protocol secrete significantly higher amounts of IL-8 (487.3 ± 1231.1 vs 9.1 ± 8.2 pg mL -1 ; p Cell processing conditions have a major impact on the composition of the secretome. The REPAIR-AMI secretome significantly enhances proangiogenic chemokine secretion, angiogenesis, cell migration, and cardioprotective signaling pathways. These results might explain differential outcomes between clinical trials. Optimizing cell processing protocols with special regards to paracrine factors, might open a new therapeutic concept for improving patient outcome. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Identification of colonic fibroblast secretomes reveals secretory factors regulating colon cancer cell proliferation.

    Science.gov (United States)

    Chen, Sun-Xia; Xu, Xiao-En; Wang, Xiao-Qing; Cui, Shu-Jian; Xu, Lei-Lei; Jiang, Ying-Hua; Zhang, Yang; Yan, Hai-Bo; Zhang, Qian; Qiao, Jie; Yang, Peng-Yuan; Liu, Feng

    2014-10-14

    Stromal microenvironment influences tumor cell proliferation and migration. Fibroblasts represent the most abundant stromal constituents. Here, we established two pairs of normal fibroblast (NF) and cancer-associated fibroblast (CAF) cultures from colorectal adenocarcinoma tissues and the normal counterparts. The NFs and CAFs were stained positive for typical fibroblast markers and inhibited colon cancer (CC) cell proliferation in in vitro cocultures and in xenograft mouse models. The fibroblast conditioned media were analyzed using LC-MS and 227 proteins were identified at a false discovery rate of 1.3%, including 131 putative secretory and 20 plasma membrane proteins. These proteins were enriched for functional categories of extracellular matrix, adhesion, cell motion, inflammatory response, redox homeostasis and peptidase inhibitor. Secreted protein acidic and rich in cysteine, transgelin, follistatin-related protein 1 (FSTL1) and decorin was abundant in the fibroblast secretome as confirmed by Western blot. Silencing of FSTL1 and transgelin in colonic fibroblast cell line CCD-18Co induced an accelerated proliferation of CC cells in cocultures. Exogenous FSTL1 attenuates CC cell proliferation in a negative fashion. FSTL1 was upregulated in CC patient plasma and cancerous tissues but had no implication in prognosis. Our results provided novel insights into the molecular signatures and modulatory role of CC associated fibroblasts. In this study, a label-free LC-MS was performed to analyze the secretomes of two paired primary fibroblasts, which were isolated from fresh surgical specimen of colorectal adenocarcinoma and adjacent normal colonic tissues and exhibited negative modulatory activity for colon cancer cell growth in in vitro cocultures and in vivo xenograph mouse models. Follistatin-related protein 1 was further revealed to be one of the stroma-derived factors of potential suppression role for colon cancer cell proliferation. Our results provide novel

  13. Proteomic Investigation of Rhizoctonia solani AG 4 Identifies Secretome and Mycelial Proteins with roles in Plant Cell Wall Degradation and Virulence

    KAUST Repository

    Lakshman, Dilip

    2016-03-28

    Rhizoctonia solani AG 4 is a soilborne necrotrophic fungal plant pathogen that causes economically important diseases on agronomic crops worldwide. Here we used a proteomics approach to characterize both intracellular proteins and the secretome of R. solani AG 4 isolate Rs23A under several growth conditions; the secretome being highly important in pathogenesis. From over 500 total secretome and soluble intracellular protein spots from 2-D gels, 457 protein spots were analyzed and 318 proteins positively matched with fungal proteins of known function by comparison with available R. solani genome databases specific for anastomosis groups 1-IA, 1-IB, and 3. These proteins were categorized to possible cellular locations and functional groups; and for some proteins their putative roles in plant cell wall degradation and virulence. The majority of the secreted proteins were grouped to extracellular regions and contain hydrolase activity.

  14. Secretome analysis defines the major role of SecDF in Staphylococcus aureus virulence.

    Directory of Open Access Journals (Sweden)

    Chantal Quiblier

    Full Text Available The Sec pathway plays a prominent role in protein export and membrane insertion, including the secretion of major bacterial virulence determinants. The accessory Sec constituent SecDF has been proposed to contribute to protein export. Deletion of Staphylococcus aureus secDF has previously been shown to reduce resistance, to alter cell separation, and to change the expression of certain virulence factors. To analyse the impact of the secDF deletion in S. aureus on protein secretion, a quantitative secretome analysis was performed. Numerous Sec signal containing proteins involved in virulence were found to be decreased in the supernatant of the secDF mutant. However, two Sec-dependent hydrolases were increased in comparison to the wild type, suggesting additional indirect, regulatory effects to occur upon deletion of secDF. Adhesion, invasion, and cytotoxicity of the secDF mutant were reduced in human umbilical vein endothelial cells. Virulence was significantly reduced using a Galleria mellonella insect model. Altogether, SecDF is a promising therapeutic target for controlling S. aureus infections.

  15. Proteomic Analysis of the Secretome of Cellulomonas fimi ATCC 484 and Cellulomonas flavigena ATCC 482.

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    Warren W Wakarchuk

    Full Text Available The bacteria in the genus Cellulomonas are known for their ability to degrade plant cell wall biomass. Cellulomonas fimi ATCC 484 and C. flavigena ATCC 482 have been the subject of much research into secreted cellulases and hemicellulases. Recently the genome sequences of both C. fimi ATCC 484 and C. flavigena ATCC 482 were published, and a genome comparison has revealed their full spectrum of possible carbohydrate-active enzymes (CAZymes. Using mass spectrometry, we have compared the proteins secreted by C. fimi and C. flavigena during growth on the soluble cellulose substrate, carboxymethylcellulose (CMC, as well as a soluble xylan fraction. Many known C. fimi CAZymes were detected, which validated our analysis, as were a number of new CAZymes and other proteins that, though identified in the genome, have not previously been observed in the secretome of either organism. Our data also shows that many of these are co-expressed on growth of either CMC or xylan. This analysis provides a new perspective on Cellulomonas enzymes and provides many new CAZyme targets for characterization.

  16. Proteomic Analysis of the Secretome of Cellulomonas fimi ATCC 484 and Cellulomonas flavigena ATCC 482.

    Science.gov (United States)

    Wakarchuk, Warren W; Brochu, Denis; Foote, Simon; Robotham, Anna; Saxena, Hirak; Erak, Tamara; Kelly, John

    2016-01-01

    The bacteria in the genus Cellulomonas are known for their ability to degrade plant cell wall biomass. Cellulomonas fimi ATCC 484 and C. flavigena ATCC 482 have been the subject of much research into secreted cellulases and hemicellulases. Recently the genome sequences of both C. fimi ATCC 484 and C. flavigena ATCC 482 were published, and a genome comparison has revealed their full spectrum of possible carbohydrate-active enzymes (CAZymes). Using mass spectrometry, we have compared the proteins secreted by C. fimi and C. flavigena during growth on the soluble cellulose substrate, carboxymethylcellulose (CMC), as well as a soluble xylan fraction. Many known C. fimi CAZymes were detected, which validated our analysis, as were a number of new CAZymes and other proteins that, though identified in the genome, have not previously been observed in the secretome of either organism. Our data also shows that many of these are co-expressed on growth of either CMC or xylan. This analysis provides a new perspective on Cellulomonas enzymes and provides many new CAZyme targets for characterization.

  17. An optimized approach to recover secreted proteins from fibroblast conditioned-media for secretomic analysis

    Directory of Open Access Journals (Sweden)

    Bastien ePare

    2016-03-01

    Full Text Available The proteins secreted by a particular type of cell, the secretome, play important roles in the regulation of many physiological processes via paracrine/autocrine mechanisms, and they are of increasing interest to help understanding rare diseases and to identify potential biomarkers and therapeutic targets. To facilitate ongoing research involving secreted proteins, we revisited cell culture protocols and whole secreted protein enrichment protocols. A reliable method for culturing and precipitating secreted protein from patient-derived fibroblast conditioned-medium was established. The method is based on the optimization of cell confluency and incubation time conditions. The well-established carrier-based TCA-DOC protein precipitation method was consistently found to give higher protein recovery yield. According to our results, we therefore propose that protein enrichment should be performed by TCA-DOC precipitation method 48 hours at 95% of confluence in a serum-deprived culture medium. Given the importance of secreted proteins as a source to elucidate the pathogenesis of rare diseases, especially neurological disorders, this approach may help to discover novel candidate biomarkers with potential clinical significance.

  18. Peptidomics and Secretomics of the Mammalian Peripheral Sensory-Motor System.

    Science.gov (United States)

    Tillmaand, Emily G; Yang, Ning; Kindt, Callie A C; Romanova, Elena V; Rubakhin, Stanislav S; Sweedler, Jonathan V

    2015-12-01

    The dorsal root ganglion (DRG) and its anatomically and functionally associated spinal nerve and ventral and dorsal roots are important components of the peripheral sensory-motor system in mammals. The cells within these structures use a number of peptides as intercellular signaling molecules. We performed a variety of mass spectrometry (MS)-based characterizations of peptides contained within and secreted from these structures, and from isolated and cultured DRG cells. Liquid chromatography-Fourier transform MS was utilized in DRG and nerve peptidome analysis. In total, 2724 peptides from 296 proteins were identified in tissue extracts. Neuropeptides are among those detected, including calcitonin gene-related peptide I, little SAAS, and known hemoglobin-derived peptides. Solid phase extraction combined with direct matrix-assisted laser desorption/ionization time-of-flight MS was employed to investigate the secretome of these structures. A number of peptides were detected in the releasate from semi-intact preparations of DRGs and associated nerves, including neurofilament- and myelin basic protein-related peptides. A smaller set of analytes was observed in releasates from cultured DRG neurons. The peptide signals observed in the releasates have been mass-matched to those characterized and identified in homogenates of entire DRGs and associated nerves. This data aids our understanding of the chemical composition of the mammalian peripheral sensory-motor system, which is involved in key physiological functions such as nociception, thermoreception, itch sensation, and proprioception.

  19. Revealing Glycoproteins in the Secretome of MCF-7 Human Breast Cancer Cells

    Directory of Open Access Journals (Sweden)

    Aik-Aun Tan

    2015-01-01

    Full Text Available Breast cancer is one of the major issues in the field of oncology, reported with a higher prevalence rate in women worldwide. In attempt to reveal the potential biomarkers for breast cancer, the findings of differentially glycosylated haptoglobin and osteonectin in previous study have drawn our attention towards glycoproteins of secretome from the MCF-7 cancer cell line. In the present study, further analyses were performed on the medium of MCF-7 cells by subjecting it to two-dimensional analyses followed by image analysis in contrast to the medium of human mammary epithelial cells (HMEpC as a negative control. Carboxypeptidase A4 (CPA4, alpha-1-antitrypsin (AAT, haptoglobin (HP, and HSC70 were detected in the medium of MCF-7, while only CPA4 and osteonectin (ON were detected in HMEpC medium. In addition, CPA4 was detected as upregulated in the MCF-7 medium. Further analysis by lectin showed that CPA4, AAT, HP, and HSC70 were secreted as N-glycan in the medium of MCF-7, with HP also showing differentially N-glycosylated isoforms. For the HMEpC, only CPA4 was detected as N-glycan. No O-glycan was detected in the medium of HMEpC but MCF-7 expressed O-glycosylated CPA4 and HSC70. All these revealed that glycoproteins could be used as glycan-based biomarkers for the prognosis of breast cancer.

  20. The Plant Ovule Secretome: A Different View toward Pollen-Pistil Interactions.

    Science.gov (United States)

    Liu, Yang; Joly, Valentin; Dorion, Sonia; Rivoal, Jean; Matton, Daniel P

    2015-11-06

    During plant sexual reproduction, continuous exchange of signals between the pollen and the pistil (stigma, style, and ovary) plays important roles in pollen recognition and selection, establishing breeding barriers and, ultimately, leading to optimal seed set. After navigating through the stigma and the style, pollen tubes (PTs) reach their final destination, the ovule. This ultimate step is also regulated by numerous signals emanating from the embryo sac (ES) of the ovule. These signals encompass a wide variety of molecules, but species-specificity of the pollen-ovule interaction relies mainly on secreted proteins and their receptors. Isolation of candidate genes involved in pollen-pistil interactions has mainly relied on transcriptomic approaches, overlooking potential post-transcriptional regulation. To address this issue, ovule exudates were collected from the wild potato species Solanum chacoense using a tissue-free gravity-extraction method (tf-GEM). Combined RNA-seq and mass spectrometry-based proteomics led to the identification of 305 secreted proteins, of which 58% were ovule-specific. Comparative analyses using mature ovules (attracting PTs) and immature ovules (not attracting PTs) revealed that the last maturation step of ES development affected almost half of the ovule secretome. Of 128 upregulated proteins in anthesis stage, 106 were not regulated at the mRNA level, emphasizing the importance of post-transcriptional regulation in reproductive development.

  1. Peptidomics and Secretomics of the Mammalian Peripheral Sensory-Motor System

    Science.gov (United States)

    Tillmaand, Emily G.; Yang, Ning; Kindt, Callie A. C.; Romanova, Elena V.; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

    2015-12-01

    The dorsal root ganglion (DRG) and its anatomically and functionally associated spinal nerve and ventral and dorsal roots are important components of the peripheral sensory-motor system in mammals. The cells within these structures use a number of peptides as intercellular signaling molecules. We performed a variety of mass spectrometry (MS)-based characterizations of peptides contained within and secreted from these structures, and from isolated and cultured DRG cells. Liquid chromatography-Fourier transform MS was utilized in DRG and nerve peptidome analysis. In total, 2724 peptides from 296 proteins were identified in tissue extracts. Neuropeptides are among those detected, including calcitonin gene-related peptide I, little SAAS, and known hemoglobin-derived peptides. Solid phase extraction combined with direct matrix-assisted laser desorption/ionization time-of-flight MS was employed to investigate the secretome of these structures. A number of peptides were detected in the releasate from semi-intact preparations of DRGs and associated nerves, including neurofilament- and myelin basic protein-related peptides. A smaller set of analytes was observed in releasates from cultured DRG neurons. The peptide signals observed in the releasates have been mass-matched to those characterized and identified in homogenates of entire DRGs and associated nerves. This data aids our understanding of the chemical composition of the mammalian peripheral sensory-motor system, which is involved in key physiological functions such as nociception, thermoreception, itch sensation, and proprioception.

  2. Analytical Methods for Energy Diversity and Security. Portfolio Optimization in the Energy Sector: A Tribute to the work of Dr. Shimon Awerbuch. Chapter 7. The role of wind generation in enhancing Scotland's energy diversity and security

    International Nuclear Information System (INIS)

    Jansen, J.C.; Beurskens, L.W.M.

    2008-11-01

    This volume aims at professionals in academia, industry and government interested in the rapidly evolving area at the nexus between energy and climate change policy. The cutting-edge international contributions allow for a wide coverage of the topic. Energy Diversity and Security focuses on the consideration of financial risk in the energy sector. It describes how tools borrowed from financial economic theory, in particular mean-variance portfolio theory, can provide insights on the costs and benefits of diversity, and thus inform investment decision making in conditions of uncertainty. It gives the reader an in-depth understanding of how to manage risk at a time when the world's focus is on this area. The book provides insights from leading authorities in the area of energy security. It gives readers abundant, rigorous analysis and guidance at a critical time in facing the twin challenges of energy security and climate change. The book also highlights the role of clean energy technology in moving towards future diverse and intelligent electricity systems. In this chapter attention is paid to the role of wind generation in enhancing Scotland's energy diversity and security

  3. Deepening Understanding of Prior Knowledge: What Diverse First-Generation College Students in the U.S. Can Teach Us

    Science.gov (United States)

    Castillo-Montoya, Milagros

    2017-01-01

    Educational research indicates that teachers revealing and utilizing students' prior knowledge supports students' academic learning. Yet, the variation in students' prior knowledge is not fully known. To better understand students' prior knowledge, I drew on sociocultural learning theories to examine racially and ethnically diverse college…

  4. Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells.

    Science.gov (United States)

    Ma'ayeh, Showgy Y; Liu, Jingyi; Peirasmaki, Dimitra; Hörnaeus, Katarina; Bergström Lind, Sara; Grabherr, Manfred; Bergquist, Jonas; Svärd, Staffan G

    2017-12-01

    Giardia intestinalis is a non-invasive protozoan parasite that causes giardiasis in humans, the most common form of parasite-induced diarrhea. Disease mechanisms are not completely defined and very few virulence factors are known. To identify putative virulence factors and elucidate mechanistic pathways leading to disease, we have used proteomics to identify the major excretory-secretory products (ESPs) when Giardia trophozoites of WB and GS isolates (assemblages A and B, respectively) interact with intestinal epithelial cells (IECs) in vitro. The main parts of the IEC and parasite secretomes are constitutively released proteins, the majority of which are associated with metabolism but several proteins are released in response to their interaction (87 and 41 WB and GS proteins, respectively, 76 and 45 human proteins in response to the respective isolates). In parasitized IECs, the secretome profile indicated effects on the cell actin cytoskeleton and the induction of immune responses whereas that of Giardia showed anti-oxidation, proteolysis (protease-associated) and induction of encystation responses. The Giardia secretome also contained immunodominant and glycosylated proteins as well as new candidate virulence factors and assemblage-specific differences were identified. A minor part of Giardia ESPs had signal peptides (29% for both isolates) and extracellular vesicles were detected in the ESPs fractions, suggesting alternative secretory pathways. Microscopic analyses showed ESPs binding to IECs and partial internalization. Parasite ESPs reduced ERK1/2 and P38 phosphorylation and NF-κB nuclear translocation. Giardia ESPs altered gene expression in IECs, with a transcriptional profile indicating recruitment of immune cells via chemokines, disturbances in glucose homeostasis, cholesterol and lipid metabolism, cell cycle and induction of apoptosis. This is the first study identifying Giardia ESPs and evaluating their effects on IECs. It highlights the importance of

  5. Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells.

    Directory of Open Access Journals (Sweden)

    Showgy Y Ma'ayeh

    2017-12-01

    Full Text Available Giardia intestinalis is a non-invasive protozoan parasite that causes giardiasis in humans, the most common form of parasite-induced diarrhea. Disease mechanisms are not completely defined and very few virulence factors are known.To identify putative virulence factors and elucidate mechanistic pathways leading to disease, we have used proteomics to identify the major excretory-secretory products (ESPs when Giardia trophozoites of WB and GS isolates (assemblages A and B, respectively interact with intestinal epithelial cells (IECs in vitro.The main parts of the IEC and parasite secretomes are constitutively released proteins, the majority of which are associated with metabolism but several proteins are released in response to their interaction (87 and 41 WB and GS proteins, respectively, 76 and 45 human proteins in response to the respective isolates. In parasitized IECs, the secretome profile indicated effects on the cell actin cytoskeleton and the induction of immune responses whereas that of Giardia showed anti-oxidation, proteolysis (protease-associated and induction of encystation responses. The Giardia secretome also contained immunodominant and glycosylated proteins as well as new candidate virulence factors and assemblage-specific differences were identified. A minor part of Giardia ESPs had signal peptides (29% for both isolates and extracellular vesicles were detected in the ESPs fractions, suggesting alternative secretory pathways. Microscopic analyses showed ESPs binding to IECs and partial internalization. Parasite ESPs reduced ERK1/2 and P38 phosphorylation and NF-κB nuclear translocation. Giardia ESPs altered gene expression in IECs, with a transcriptional profile indicating recruitment of immune cells via chemokines, disturbances in glucose homeostasis, cholesterol and lipid metabolism, cell cycle and induction of apoptosis.This is the first study identifying Giardia ESPs and evaluating their effects on IECs. It highlights the

  6. Differential secretome analysis of Pseudomonas syringae pv tomato using gel-free MS proteomics

    Directory of Open Access Journals (Sweden)

    Jörg eSchumacher

    2014-07-01

    Full Text Available The plant pathogen Pseudomonas syringae pv. tomato (DC3000 causes virulence by delivering effector proteins into host plant cells through its type three secretion system (T3SS. In response to the plant environment DC3000 expresses hypersensitive response and pathogenicity genes (hrp. Pathogenesis depends on the ability of the pathogen to manipulate the plant metabolism and to inhibit plant immunity, which depends to a large degree on the plant’s capacity to recognise both pathogen and microbial determinants (PAMP/MAMP-triggered immunity. We have developed and employed MS-based shotgun and targeted proteomics to (i elucidate the extracellular and secretome composition of DC3000 and (ii evaluate temporal features of the assembly of the T3SS and the secretion process together with its dependence of pH. The proteomic screen, under hrp inducing in vitro conditions, of extracellular and cytoplasmatic fractions indicated the segregated presence of not only T3SS implicated proteins such as HopK1, HrpK1, HrpA1 and Avrpto1, but also of proteins not usually associated with the T3SS or with pathogenicity. Using multiple reaction monitoring MS (MRM-MS to quantify HrpA1 and Avrpto1, we found that HrpA1 is rapidly expressed, at a strict pH-dependent rate and is post-translationally processed extracellularly. These features appear to not interfere with rapid Avrpto1 expression and secretion but may suggest some temporal post-translational regulatory mechanism of the T3SS assembly. The high specificity and sensitivity of the MRM-MS approach should provide a powerful tool to measure secretion and translocation in infected tissues.

  7. The carbon starvation response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome

    Directory of Open Access Journals (Sweden)

    Nitsche Benjamin M

    2012-08-01

    Full Text Available Abstract Background Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening starvation conditions, carbon from endogenous resources becomes mobilized to fuel maintenance and self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal starvation responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. Results This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger. Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon starvation. Compared to the exponential growth transcriptome, about 50% (7,292 of all genes displayed differential gene expression during at least one of the starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. Conclusions This study is the first system-wide analysis of the carbon starvation response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The

  8. Rapid mutation of Spirulina platensis by a new mutagenesis system of atmospheric and room temperature plasmas (ARTP and generation of a mutant library with diverse phenotypes.

    Directory of Open Access Journals (Sweden)

    Mingyue Fang

    Full Text Available In this paper, we aimed to improve the carbohydrate productivity of Spirulina platensis by generating mutants with increased carbohydrate content and growth rate. ARTP was used as a new mutagenesis tool to generate a mutant library of S. platensis with diverse phenotypes. Protocol for rapid mutation of S. platensis by 60 s treatment with helium driven ARTP and high throughput screening method of the mutants using the 96-well microplate and microplate reader was established. A mutant library of 62 mutants was then constructed and ideal mutants were selected out. The characteristics of the mutants after the mutagenesis inclined to be stable after around 9(th subculture, where the total mutation frequency and positive mutation frequency in terms of specific growth rate reached 45% and 25%, respectively. The mutants in mutant library showed diverse phenotypes in terms of cell growth rate, carbohydrate content and flocculation intensity. The positive mutation frequency in terms of cellular carbohydrate content with the increase by more than 20% percent than the wild strain was 32.3%. Compared with the wild strain, the representative mutants 3-A10 and 3-B2 showed 40.3% and 78.0% increase in carbohydrate content, respectively, while the mutant 4-B3 showed 10.5% increase in specific growth rate. The carbohydrate contents of the representative mutants were stable during different subcultures, indicating high genetic stability. ARTP was demonstrated to be an effective and non-GMO mutagenesis tool to generate the mutant library for multicellular microalgae.

  9. Rapid mutation of Spirulina platensis by a new mutagenesis system of atmospheric and room temperature plasmas (ARTP) and generation of a mutant library with diverse phenotypes.

    Science.gov (United States)

    Fang, Mingyue; Jin, Lihua; Zhang, Chong; Tan, Yinyee; Jiang, Peixia; Ge, Nan; Heping Li; Xing, Xinhui

    2013-01-01

    In this paper, we aimed to improve the carbohydrate productivity of Spirulina platensis by generating mutants with increased carbohydrate content and growth rate. ARTP was used as a new mutagenesis tool to generate a mutant library of S. platensis with diverse phenotypes. Protocol for rapid mutation of S. platensis by 60 s treatment with helium driven ARTP and high throughput screening method of the mutants using the 96-well microplate and microplate reader was established. A mutant library of 62 mutants was then constructed and ideal mutants were selected out. The characteristics of the mutants after the mutagenesis inclined to be stable after around 9(th) subculture, where the total mutation frequency and positive mutation frequency in terms of specific growth rate reached 45% and 25%, respectively. The mutants in mutant library showed diverse phenotypes in terms of cell growth rate, carbohydrate content and flocculation intensity. The positive mutation frequency in terms of cellular carbohydrate content with the increase by more than 20% percent than the wild strain was 32.3%. Compared with the wild strain, the representative mutants 3-A10 and 3-B2 showed 40.3% and 78.0% increase in carbohydrate content, respectively, while the mutant 4-B3 showed 10.5% increase in specific growth rate. The carbohydrate contents of the representative mutants were stable during different subcultures, indicating high genetic stability. ARTP was demonstrated to be an effective and non-GMO mutagenesis tool to generate the mutant library for multicellular microalgae.

  10. A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants.

    Science.gov (United States)

    Mbareche, Hamza; Veillette, Marc; Bonifait, Laetitia; Dubuis, Marie-Eve; Benard, Yves; Marchand, Geneviève; Bilodeau, Guillaume J; Duchaine, Caroline

    2017-12-01

    Composting is used all over the world to transform different types of organic matter through the actions of complex microbial communities. Moving and handling composting material may lead to the emission of high concentrations of bioaerosols. High exposure levels are associated with adverse health effects among compost industry workers. Fungal spores are suspected to play a role in many respiratory illnesses. There is a paucity of information related to the detailed fungal diversity in compost as well as in the aerosols emitted through composting activities. The aim of this study was to analyze the fungal diversity of both organic matter and aerosols present in facilities that process domestic compost and facilities that process pig carcasses. This was accomplished using a next generation sequencing approach that targets the ITS1 genomic region. Multivariate analyses revealed differences in the fungal community present in samples coming from compost treating both raw materials. Furthermore, results show that the compost type affects the fungal diversity of aerosols emitted. Although 8 classes were evenly distributed in all samples, Eurotiomycetes were more dominant in carcass compost while Sordariomycetes were dominant in domestic compost. A large diversity profile was observed in bioaerosols from both compost types showing the presence of a number of pathogenic fungi newly identified in bioaerosols emitted from composting plants. Members of the family Herpotrichiellaceae and Gymnoascaceae which have been shown to cause human diseases were detected in compost and air samples. Moreover, some fungi were identified in higher proportion in air compared to compost. This is the first study to identify a high level of fungal diversity in bioaerosols present in composting plants suggesting a potential exposure risk for workers. This study suggests the need for creating guidelines that address human exposure to bioaerosols. The implementation of technical and organizational

  11. Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies.

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    Sotirios Vasileiadis

    Full Text Available The novel multi-million read generating sequencing technologies are very promising for resolving the immense soil 16S rRNA gene bacterial diversity. Yet they have a limited maximum sequence length screening ability, restricting studies in screening DNA stretches of single 16S rRNA gene hypervariable (V regions. The aim of the present study was to assess the effects of properties of four consecutive V regions (V3-6 on commonly applied analytical methodologies in bacterial ecology studies. Using an in silico approach, the performance of each V region was compared with the complete 16S rRNA gene stretch. We assessed related properties of the soil derived bacterial sequence collection of the Ribosomal Database Project (RDP database and concomitantly performed simulations based on published datasets. Results indicate that overall the most prominent V region for soil bacterial diversity studies was V3, even though it was outperformed in some of the tests. Despite its high performance during most tests, V4 was less conserved along flanking sites, thus reducing its ability for bacterial diversity coverage. V5 performed well in the non-redundant RDP database based analysis. However V5 did not resemble the full-length 16S rRNA gene sequence results as well as V3 and V4 did when the natural sequence frequency and occurrence approximation was considered in the virtual experiment. Although, the highly conserved flanking sequence regions of V6 provide the ability to amplify partial 16S rRNA gene sequences from very diverse owners, it was demonstrated that V6 was the least informative compared to the rest examined V regions. Our results indicate that environment specific database exploration and theoretical assessment of the experimental approach are strongly suggested in 16S rRNA gene based bacterial diversity studies.

  12. Unraveling the in vitro secretome of the phytopathogen Botrytis cinerea to understand the interaction with its hosts

    Directory of Open Access Journals (Sweden)

    Raquel eGonzález-Fernández

    2015-10-01

    Full Text Available Botrytis cinerea is a necrotrophic fungus with high adaptability to different environments and hosts. It secretes a large number of extracellular proteins, which favor plant tissue penetration and colonization, thus contributing to virulence. Secretomics is a proteomics sub-discipline which study the secreted proteins and their secretion mechanisms, so-called secretome. By using proteomics as experimental approach, many secreted proteins by B. cinerea have been identified from in vitro experiments, and belonging to different functional categories: i cell wall-degrading enzymes such as pectinesterases, and endo-polygalacturonases; ii proteases involved in host protein degradation such as an aspartic protease; iii proteins related to the oxidative burst such as glyoxal oxidase; iv proteins which may induce the plant hypersensitive response such as a cerato-platanin domain-containing protein; and v proteins related to production and secretion of toxins such as malate dehydrogenase. In this mini-review, we made an overview of the proteomics contribution to the study and knowledge of the B. cinerea extracellular secreted proteins based on our current work carried out from in vitro experiments, and recent published papers both in vitro and in planta studies on this fungi. We hypothesize on the putative functions of these secreted proteins, and their connection to the biology of the B. cinerea interaction with its hosts.

  13. Methods for proteomics-based analysis of the human muscle secretome using an in vitro exercise model.

    Science.gov (United States)

    Scheler, Mika; de Angelis, Martin Hrabě; Al-Hasani, Hadi; Häring, Hans-Ulrich; Weigert, Cora; Lehr, Stefan

    2015-01-01

    Over the last decade, the skeletal muscle as a secretory organ gained in importance. A growing number of peptides are described which are produced and released by the muscle fibers and work in an autocrine, paracrine, and endocrine fashion. The contraction-induced secretion of these myokines is considered to contribute to the health-promoting effects of exercise. To gain further insights into the molecular processes that occur during contraction an in vitro exercise model, electric pulse stimulation (EPS), was established. Recent publications show that this model is suitable to electro-stimulate human skeletal muscle cells and thus mimic muscle contraction in vitro. Here, we provide a detailed protocol for the proteomics-based analysis of the human muscle secretome, starting with the cultivation of human myotubes and their electric pulse stimulation, ending with sample preparation for targeted and untargeted proteome analysis of the cell culture supernatant. This whole workflow should allow deeper insights into the complex nature of the muscle secretome and the identification of new myokines which might help to understand the crosstalk of the working muscle with different organs and the beneficial effects of exercise.

  14. Analysis of the outer membrane proteome and secretome of Bacteroides fragilis reveals a multiplicity of secretion mechanisms.

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    Marlena M Wilson

    Full Text Available Bacteroides fragilis is a widely distributed member of the human gut microbiome and an opportunistic pathogen. Cell surface molecules produced by this organism likely play important roles in colonization, communication with other microbes, and pathogenicity, but the protein composition of the outer membrane (OM and the mechanisms used to transport polypeptides into the extracellular space are poorly characterized. Here we used LC-MS/MS to analyze the OM proteome and secretome of B. fragilis NCTC 9343 grown under laboratory conditions. Of the 229 OM proteins that we identified, 108 are predicted to be lipoproteins, and 61 are predicted to be TonB-dependent transporters. Based on their proximity to genes encoding TonB-dependent transporters, many of the lipoprotein genes likely encode proteins involved in nutrient or small molecule uptake. Interestingly, protease accessibility and biotinylation experiments indicated that an unusually large fraction of the lipoproteins are cell-surface exposed. We also identified three proteins that are members of a novel family of autotransporters, multiple potential type I protein secretion systems, and proteins that appear to be components of a type VI secretion apparatus. The secretome consisted of lipoproteins and other proteins that might be substrates of the putative type I or type VI secretion systems. Our proteomic studies show that B. fragilis differs considerably from well-studied Gram-negative bacteria such as Escherichia coli in both the spectrum of OM proteins that it produces and the range of secretion strategies that it utilizes.

  15. Visually representing the generation of older consumers as a diverse audience: Towards a multidimensional market segmentation typology

    NARCIS (Netherlands)

    Loos, Eugène; Ekström, M.

    2014-01-01

    Television commercials and advertising often represent the generation of older consumers as eternally youthful, active and rich. Representations of senior citizens as fragile people needing services and products to help them to survive are also used, but less frequently. As individual differences

  16. Visually representing the generation of older consumers as a diverse audience: towards a multidimensional market segmentation typology

    NARCIS (Netherlands)

    Loos, E.; Ekström, M.

    2014-01-01

    Television commercials and advertising often represent the generation of older consumers as eternally youthful, active and rich. Representations of senior citizens as fragile people needing services and products to help them to survive are also used, but less frequently. As individual differences

  17. Identification of five novel tectiviruses in Bacillus strains: analysis of a highly variable region generating genetic diversity.

    Science.gov (United States)

    Jalasvuori, Matti; Palmu, Saara; Gillis, Annika; Kokko, Hanna; Mahillon, Jacques; Bamford, Jaana K H; Fornelos, Nadine

    2013-01-01

    Our biosphere is abundant with unique and small genes for which no homologs are known. These genes, often referred to as orphans or ORFans, are commonly found in bacteriophage genomes but their origins remain unclear. We discovered five novel tectivirus-like genetic elements by screening more than five-hundred Bacillus strains. A highly variable region (HVR) of these viruses was shown to harbor ORFans in most of these otherwise well-conserved bacteriophages. Previous studies demonstrated that mutations close to this region dramatically alter bacteriophage gene regulation, suggesting that the acquisition of those ORFans may provide a source of genetic diversity that is then subject to genetic selection during bacteriophage evolution. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  18. A mutant Brassica napus (canola) population for the identification of new genetic diversity via TILLING and next generation sequencing.

    Science.gov (United States)

    Gilchrist, Erin J; Sidebottom, Christine H D; Koh, Chu Shin; Macinnes, Tanya; Sharpe, Andrew G; Haughn, George W

    2013-01-01

    We have generated a Brassica napus (canola) population of 3,158 EMS-mutagenised lines and used TILLING to demonstrate that the population has a high enough mutation density that it will be useful for identification of mutations in genes of interest in this important crop species. TILLING is a reverse genetics technique that has been successfully used in many plant and animal species. Classical TILLING involves the generation of a mutagenised population, followed by screening of DNA samples using a mismatch-specific endonuclease that cleaves only those PCR products that carry a mutation. Polyacrylamide gel detection is then used to visualise the mutations in any gene of interest. We have used this TILLING technique to identify 432 unique mutations in 26 different genes in B. napus (canola cv. DH12075). This reflects a mutation density ranging from 1/56 kb to 1/308 kb (depending on the locus) with an average of 1/109 kb. We have also successfully verified the utility of next generation sequencing technology as a powerful approach for the identification of rare mutations in a population of plants, even in polyploid species such as B. napus. Most of the mutants we have identified are publically available.

  19. A mutant Brassica napus (canola population for the identification of new genetic diversity via TILLING and next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Erin J Gilchrist

    Full Text Available We have generated a Brassica napus (canola population of 3,158 EMS-mutagenised lines and used TILLING to demonstrate that the population has a high enough mutation density that it will be useful for identification of mutations in genes of interest in this important crop species. TILLING is a reverse genetics technique that has been successfully used in many plant and animal species. Classical TILLING involves the generation of a mutagenised population, followed by screening of DNA samples using a mismatch-specific endonuclease that cleaves only those PCR products that carry a mutation. Polyacrylamide gel detection is then used to visualise the mutations in any gene of interest. We have used this TILLING technique to identify 432 unique mutations in 26 different genes in B. napus (canola cv. DH12075. This reflects a mutation density ranging from 1/56 kb to 1/308 kb (depending on the locus with an average of 1/109 kb. We have also successfully verified the utility of next generation sequencing technology as a powerful approach for the identification of rare mutations in a population of plants, even in polyploid species such as B. napus. Most of the mutants we have identified are publically available.

  20. Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity.

    Science.gov (United States)

    Karan, M; Evans, D S; Reilly, D; Schulte, K; Wright, C; Innes, D; Holton, T A; Nikles, D G; Dickinson, G R

    2012-03-01

    Khaya senegalensis (African mahogany or dry-zone mahogany) is a high-value hardwood timber species with great potential for forest plantations in northern Australia. The species is distributed across the sub-Saharan belt from Senegal to Sudan and Uganda. Because of heavy exploitation and constraints on natural regeneration and sustainable planting, it is now classified as a vulnerable species. Here, we describe the development of microsatellite markers for K. senegalensis using next-generation sequencing to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. Next-generation sequencing yielded 93,943 sequences with an average read length of 234 bp. The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. Twenty-one microsatellite loci were tested with 11 showing reliable amplification and polymorphism in K. senegalensis. The 11 novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. STRUCTURE analysis shows two major clusters, one comprising mainly accessions from west Africa (Senegal to Benin) and the second based in the far eastern limits of the range in Sudan and Uganda. Higher levels of genetic diversity were found in material from western Africa. This suggests that new seed collections from this region may yield more diverse genotypes than those originating from Sudan and Uganda in eastern Africa. © 2011 Blackwell Publishing Ltd.

  1. Changing MADS-Box Transcription Factor Protein-Protein Interactions as a Mechanism for Generating Floral Morphological Diversity.

    Science.gov (United States)

    Bartlett, Madelaine E

    2017-12-01

    Flowers display fantastic morphological diversity. Despite extreme variability in form, floral organ identity is specified by a core set of deeply conserved proteins-the floral MADS-box transcription factors. This indicates that while core gene function has been maintained, MADS-box transcription factors have evolved to regulate different downstream genes. Thus, the evolution of gene regulation downstream of the MADS-box transcription factors is likely central to the evolution of floral form. Gene regulation is determined by the combination of transcriptional regulators present at a particular cis-regulatory element at a particular time. Therefore, the interactions between transcription factors can be of profound importance in determining patterns of gene regulation. Here, after a short primer on flowers and floral morphology, I discuss the centrality of protein-protein interactions to MADS-box transcription factor function, and review the evidence that the evolution of MADS-box protein-protein interactions is a key driver in the evolution of gene regulation downstream of the MADS-box genes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  2. A Method for Extracting High-Quality RNA from Diverse Plants for Next-Generation Sequencing and Gene Expression Analyses

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    Roxana Yockteng

    2013-12-01

    Full Text Available Premise of the study: To study gene expression in plants, high-quality RNA must be extracted in quantities sufficient for subsequent cDNA library construction. Field-based collections are often limited in quantity and quality of tissue and are typically preserved in RNAlater. Obtaining sufficient and high-quality yield from variously preserved samples is essential to studies of comparative biology. We present a protocol for the extraction of high-quality RNA from even the most recalcitrant plant tissues. Methods and Results: Tissues from mosses, cycads, and angiosperm floral organs and leaves were preserved in RNAlater or frozen fresh at −80°C. Extractions were performed and quality was measured for yield and purity. Conclusions: This protocol results in the extraction of high-quality RNA from a variety of plant tissues representing vascular and nonvascular plants. RNA was used for cDNA synthesis to generate libraries for next-generation sequencing and for expression studies using quantitative PCR (qPCR and semiquantitative reverse transcription PCR (RT-PCR.

  3. Increased natural reproduction and genetic diversity one generation after cessation of a steelhead trout (Oncorhynchus mykiss) conservation hatchery program.

    Science.gov (United States)

    Berejikian, Barry A; Van Doornik, Donald M

    2018-01-01

    Spatial and temporal fluctuations in productivity and abundance confound assessments of captive propagation programs aimed at recovery of Threatened and Endangered populations. We conducted a 17 year before-after-control-impact experiment to determine the effects of a captive rearing program for anadromous steelhead trout (Oncorhynchus mykiss) on a key indicator of natural spawner abundance (naturally produced nests or 'redds'). The supplemented population exhibited a significant (2.6-fold) increase in redd abundance in the generation following supplementation. Four non-supplemented (control) populations monitored over the same 17 year period exhibited stable or decreasing trends in redd abundance. Expected heterozygosity in the supplemented population increased significantly. Allelic richness increased, but to a lesser (non-significant) degree. Estimates of the effective number of breeders increased from a harmonic mean of 24.4 in the generation before supplementation to 38.9 after supplementation. Several non-conventional aspects of the captive rearing program may have contributed to the positive response in the natural population.

  4. Stressors and barriers to using mental health services among diverse groups of first-generation immigrants to the United States.

    Science.gov (United States)

    Saechao, Fay; Sharrock, Sally; Reicherter, Daryn; Livingston, James D; Aylward, Alexandra; Whisnant, Jill; Koopman, Cheryl; Kohli, Sarita

    2012-02-01

    This study examined stressors and barriers to using mental health services among first-generation immigrants in San Jose, California. Focus groups for 30 immigrants from Cambodia, Eastern Europe, Iran, Iraq, Africa, and Vietnam were audio-recorded, translated and transcribed. Two researchers coded the data and identified themes pertaining to mental health stressors and barriers. Six primary stressors were identified: economic, discrimination, acculturation due to language differences, enculturation, parenting differences, and finding suitable employment. Primary barriers included: stigma, lack of a perceived norm in country of origin for using mental health services, competing cultural practices, lack of information, language barriers, and cost. A conceptual model is presented that may be used to inform the design and implementation of mental health services for this population.

  5. Limited genetic diversity and purifying selection in Iranian Plasmodium falciparum Generative Cell Specific 1 (PfGCS1), a potential target for transmission-blocking vaccine.

    Science.gov (United States)

    Mehrizi, Akram Abouie; Zakeri, Sedigheh; Djadid, Navid Dinparast

    2014-03-01

    Among vaccines, those that have an impact on transmission are in priority for malaria elimination and eradication. One of the new identified transmission-blocking vaccine (TBV) candidate antigens is Generative Cell Specific 1 (GCS1) located on the male gametocytes of Plasmodium species. Since the antigenic diversity could hamper vaccine development, it is essential to determine the gene diversity of gcs1 in global malaria-endemic areas in order to develop efficient TBVs. Therefore, in this study, nucleotide diversity and selection in the Plasmodium falciparum GCS1 (PfGCS1) antigen were analyzed in 36 Iranian clinical isolates by using PCR sequencing in order to provide useful information on this TBV candidate antigen. For this purpose, successful sequence analysis was carried out in 36 isolates. The results showed three single-nucleotide polymorphisms including one synonymous (G1475A) and two non-synonymous (A697G and G1479A) mutations leading to 3 distinct haplotypes with different frequencies: GCS1-A (N184/D445, 16.7%), GCS1-B (S184/D445, 63.9%), and GCS1-C (N184/N445, 19.4%). The overall nucleotide diversity (π) for all 36 sequences of Iranian pfgcs1 was 0.00066±0.00012, and the dN-dS value (-0.00028) was negative, suggesting the possible action of purifying selection in this gene. Epitope mapping prediction of PfGCS1 antigen showed that most of the potential linear and conformational B-cell epitopes are located in conserved regions. However, N184S and D445N mutations were also involved in linear and conformational B-cell epitopes, respectively that should be considered in vaccine design. In conclusion, the present study showed a very low genetic diversity of pfgcs1 gene among Iranian isolates. Considering PfGCS1 as a conserved TBV candidate, our data provides valuable information to develop a PfGCS1-based TBV. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Development of Genomic Microsatellite Markers in Carthamus tinctorius L. (Safflower) Using Next Generation Sequencing and Assessment of Their Cross-Species Transferability and Utility for Diversity Analysis.

    Science.gov (United States)

    Ambreen, Heena; Kumar, Shivendra; Variath, Murali Tottekkad; Joshi, Gopal; Bali, Sapinder; Agarwal, Manu; Kumar, Amar; Jagannath, Arun; Goel, Shailendra

    2015-01-01

    Safflower (Carthamus tinctorius L.), an Asteraceae member, yields high quality edible oil rich in unsaturated fatty acids and is resilient to dry conditions. The crop holds tremendous potential for improvement through concerted molecular breeding programs due to the availability of significant genetic and phenotypic diversity. Genomic resources that could facilitate such breeding programs remain largely underdeveloped in the crop. The present study was initiated to develop a large set of novel microsatellite markers for safflower using next generation sequencing. Low throughput genome sequencing of safflower was performed using Illumina paired end technology providing ~3.5X coverage of the genome. Analysis of sequencing data allowed identification of 23,067 regions harboring perfect microsatellite loci. The safflower genome was found to be rich in dinucleotide repeats followed by tri-, tetra-, penta- and hexa-nucleotides. Primer pairs were designed for 5,716 novel microsatellite sequences with repeat length ≥ 20 bases and optimal flanking regions. A subset of 325 microsatellite loci was tested for amplification, of which 294 loci produced robust amplification. The validated primers were used for assessment of 23 safflower accessions belonging to diverse agro-climatic zones of the world leading to identification of 93 polymorphic primers (31.6%). The numbers of observed alleles at each locus ranged from two to four and mean polymorphism information content was found to be 0.3075. The polymorphic primers were tested for cross-species transferability on nine wild relatives of cultivated safflower. All primers except one showed amplification in at least two wild species while 25 primers amplified across all the nine species. The UPGMA dendrogram clustered C. tinctorius accessions and wild species separately into two major groups. The proposed progenitor species of safflower, C. oxyacantha and C. palaestinus were genetically closer to cultivated safflower and formed a

  7. Use of respondent driven sampling (RDS generates a very diverse sample of men who have sex with men (MSM in Buenos Aires, Argentina.

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    Alex Carballo-Diéguez

    Full Text Available Prior research focusing on men who have sex with men (MSM conducted in Buenos Aires, Argentina, used convenience samples that included mainly gay identified men. To increase MSM sample representativeness, we used Respondent Driven Sampling (RDS for the first time in Argentina. Using RDS, under certain specified conditions, the observed estimates for the percentage of the population with a specific trait are asymptotically unbiased. We describe, the diversity of the recruited sample, from the point of view of sexual orientation, and contrast the different subgroups in terms of their HIV sexual risk behavior.500 MSM were recruited using RDS. Behavioral data were collected through face-to-face interviews and Web-based CASI.In contrast with prior studies, RDS generated a very diverse sample of MSM from a sexual identity perspective. Only 24.5% of participants identified as gay; 36.2% identified as bisexual, 21.9% as heterosexual, and 17.4% were grouped as "other." Gay and non-gay identified MSM differed significantly in their sexual behavior, the former having higher numbers of partners, more frequent sexual contacts and less frequency of condom use. One third of the men (gay, 3%; bisexual, 34%, heterosexual, 51%; other, 49% reported having had sex with men, women and transvestites in the two months prior to the interview. This population requires further study and, potentially, HIV prevention strategies tailored to such diversity of partnerships. Our results highlight the potential effectiveness of using RDS to reach non-gay identified MSM. They also present lessons learned in the implementation of RDS to recruit MSM concerning both the importance and limitations of formative work, the need to tailor incentives to circumstances of the less affluent potential participants, the need to prevent masking, and the challenge of assessing network size.

  8. Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses

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    Wang Tzi-Yuan

    2011-08-01

    Full Text Available Abstract Background Neocallimastix patriciarum is one of the common anaerobic fungi in the digestive tracts of ruminants that can actively digest cellulosic materials, and its cellulases have great potential for hydrolyzing cellulosic feedstocks. Due to the difficulty in culture and lack of a genome database, it is not easy to gain a global understanding of the glycosyl hydrolases (GHs produced by this anaerobic fungus. Results We have developed an efficient platform that uses a combination of transcriptomic and proteomic approaches to N. patriciarum to accelerate gene identification, enzyme classification and application in rice straw degradation. By conducting complementary studies of transcriptome (Roche 454 GS and Illumina GA IIx and secretome (ESI-Trap LC-MS/MS, we identified 219 putative GH contigs and classified them into 25 GH families. The secretome analysis identified four major enzymes involved in rice straw degradation: β-glucosidase, endo-1,4-β-xylanase, xylanase B and Cel48A exoglucanase. From the sequences of assembled contigs, we cloned 19 putative cellulase genes, including the GH1, GH3, GH5, GH6, GH9, GH18, GH43 and GH48 gene families, which were highly expressed in N. patriciarum cultures grown on different feedstocks. Conclusions These GH genes were expressed in Pichia pastoris and/or Saccharomyces cerevisiae for functional characterization. At least five novel cellulases displayed cellulytic activity for glucose production. One β-glucosidase (W5-16143 and one exocellulase (W5-CAT26 showed strong activities and could potentially be developed into commercial enzymes.

  9. Facile synthesis of novel magnetic silica nanoparticles functionalized with layer-by-layer detonation nanodiamonds for secretome study.

    Science.gov (United States)

    Li, Hong; Wang, Yi; Zhang, Lei; Lu, Haojie; Zhou, Zhongjun; Wei, Liming; Yang, Pengyuan

    2015-12-07

    Novel magnetic silica nanoparticles functionalized with layer-by-layer detonation nanodiamonds (dNDs) were prepared by coating single submicron-size magnetite particles with silica and subsequently modified with dNDs. The resulting layer-by-layer dND functionalized magnetic silica microspheres (Fe3O4@SiO2@[dND]n) exhibit a well-defined magnetite-core-silica-shell structure and possess a high content of magnetite, which endow them with high dispersibility and excellent magnetic responsibility. Meanwhile, dNDs are known for their high affinity and biocompatibility towards peptides or proteins. Thus, a novel convenient, fast and efficient pretreatment approach of low-abundance peptides or proteins was successfully established with Fe3O4@SiO2@[dND]n microspheres. The signal intensity of low-abundance peptides was improved by at least two to three orders of magnitude in mass spectrometry analysis. The novel microsphere also showed good tolerance to salt. Even with a high concentration of salt, peptides or proteins could be isolated effectively from samples. Therefore, the convenient and efficient enrichment process of this novel layer-by-layer dND-functionalized microsphere makes it a promising candidate for isolation of protein in a large volume of culture supernatant for secretome analysis. In the application of Fe3O4@SiO2@[dND]n in the secretome of hepatoma cells, 1473 proteins were identified and covered a broad range of pI and molecular weight, including 377 low molecular weight proteins.

  10. Quantitative Secretomic Analysis Identifies Extracellular Protein Factors That Modulate the Metastatic Phenotype of Non-Small Cell Lung Cancer.

    Science.gov (United States)

    Hu, Rongkuan; Huffman, Kenneth E; Chu, Michael; Zhang, Yajie; Minna, John D; Yu, Yonghao

    2016-02-05

    Lung cancer is the leading cause of cancer-related deaths for men and women in the United States, with non-small cell lung cancer (NSCLC) representing 85% of all diagnoses. Late stage detection, metastatic disease and lack of actionable biomarkers contribute to the high mortality rate. Proteins in the extracellular space are known to be critically involved in regulating every stage of the pathogenesis of lung cancer. To investigate the mechanism by which secreted proteins contribute to the pathogenesis of NSCLC, we performed quantitative secretomic analysis of two isogenic NSCLC cell lines (NCI-H1993 and NCI-H2073) and an immortalized human bronchial epithelial cell line (HBEC3-KT) as control. H1993 was derived from a chemo-naïve metastatic tumor, while H2073 was derived from the primary tumor after etoposide/cisplatin therapy. From the conditioned media of these three cell lines, we identified and quantified 2713 proteins, including a series of proteins involved in regulating inflammatory response, programmed cell death and cell motion. Gene Ontology (GO) analysis indicates that a number of proteins overexpressed in H1993 media are involved in biological processes related to cancer metastasis, including cell motion, cell-cell adhesion and cell migration. RNA interference (RNAi)-mediated knock down of a number of these proteins, including SULT2B1, CEACAM5, SPRR3, AGR2, S100P, and S100A14, leads to dramatically reduced migration of these cells. In addition, meta-analysis of survival data indicates NSCLC patients whose tumors express higher levels of several of these secreted proteins, including SULT2B1, CEACAM5, SPRR3, S100P, and S100A14, have a worse prognosis. Collectively, our results provide a potential molecular link between deregulated secretome and NSCLC cell migration/metastasis. In addition, the identification of these aberrantly secreted proteins might facilitate the development of biomarkers for early detection of this devastating disease.

  11. Oxidation of Wine Polyphenols by Secretomes of Wild Botrytis cinerea Strains from White and Red Grape Varieties and Determination of Their Specific Laccase Activity.

    Science.gov (United States)

    Zimdars, Sabrina; Hitschler, Julia; Schieber, Andreas; Weber, Fabian

    2017-12-06

    Processing of Botrytis cinerea-infected grapes leads to enhanced enzymatic browning reactions mainly caused by the enzyme laccase which is able to oxidize a wide range of phenolic compounds. The extent of color deterioration depends on the activity of the enzymes secreted by the fungus. The present study revealed significant differences in the oxidative properties of secretomes of several B. cinerea strains isolated from five grape varieties. The presumed laccase-containing secretomes varied in their catalytic activity toward six phenolic compounds present in grapes. All strains led to identical product profiles for five of six substrates, but two strains showed deviating product profiles during gallic acid oxidation. Fast oxidation of caffeic acid, ferulic acid, and malvidin 3-O-glucoside was observed. Product formation rates and relative product concentrations were determined. The results reflect the wide range of enzyme activity and the corresponding different impact on color deterioration by B. cinerea.

  12. In situ Generated Ruthenium Catalyst Systems Bearing Diverse N-Heterocyclic Carbene Precursors for Atom-Economic Amide Synthesis from Alcohols and Amines.

    Science.gov (United States)

    Cheng, Hua; Xiong, Mao-Qian; Cheng, Chuan-Xiang; Wang, Hua-Jing; Lu, Qiang; Liu, Hong-Fu; Yao, Fu-Bin; Chen, Cheng; Verpoort, Francis

    2018-02-16

    The transition-metal-catalyzed direct synthesis of amides from alcohols and amines is herein demonstrated as a highly environmentally benign and atom-economic process. Among various catalyst systems, in situ generated N-heterocyclic carbene (NHC)-based ruthenium (Ru) halide catalyst systems have been proven to be active for this transformation. However, these existing catalyst systems usually require an additional ligand to achieve satisfactory results. In this work, through extensive screening of a diverse variety of NHC precursors, we discovered an active in situ catalyst system for efficient amide synthesis without any additional ligand. Notably, this catalyst system was found to be insensitive to the electronic effects of the substrates, and various electron-deficient substrates, which were not highly reactive with our previous catalyst systems, could be employed to afford the corresponding amides efficiently. Furthermore, mechanistic investigations were performed to provide a rationale for the high activity of the optimized catalyst system. NMR-scale reactions indicated that the rapid formation of a Ru hydride intermediate (signal at δ=-7.8 ppm in the 1 H NMR spectrum) after the addition of the alcohol substrate should be pivotal in establishing the high catalyst activity. Besides, HRMS analysis provided possible structures of the in situ generated catalyst system. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. A secretome analysis reveals that PPARα is upregulated by fractionated-dose γ-irradiation in three-dimensional keratinocyte cultures

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jee Yong; Kim, Hyun Ji; Yi, Jae Youn [Korea Institute of Radiation and Medical Sciences, Daejeon (Korea, Republic of)

    2016-05-15

    A three-dimensional (3D) environment composed of properly interconnected and differentiated cells that allows communication and cooperation among cells via secreted molecules would be expected to more accurately reflect cellular responses. Here, we investigated γ-irradiation-induced changes in the secretome of 3D-cultured keratinocytes. An analysis of keratinocyte secretome profiles following fractionated-dose γ-irradiation revealed changes in genes involved in cell adhesion, angiogenesis, and the immune system. Notably, peroxisome proliferator-activated receptor-(PPARα) was upregulated in response to fractionated-dose γ-irradiation. This upregulation was associated with an increase in the transcription of known PPARα target genes, including angiopoietin-like protein 4, dermokine and kallikrein-related peptide 12, which were differentially regulated by fractionated-dose γ-irradiation. Collectively, our data imply a mechanism linking γ-irradiation and secretome changes, and suggest that these changes could play a significant role in the coordinated cellular responses to harmful ionizing radiation, such as those associated with radiation therapy. This extension of our understanding of γ-irradiation-induced secretome changes has the potential to improve radiation therapy strategies. Control of inflammatory waves, improved wound healing, and stabilization of the skin barrier are imperative for minimizing such injuries. Therefore, PPARα agonists and antagonists have the potential to become important therapeutic agents for the treatment of γ-irradiation induced skin damage. Specifically, our analysis suggests that the undesirable consequences of long-term exposure to ionizing radiation could be alleviated by PPARα agonists.

  14. Characterization of the cellulolytic secretome of Trichoderma harzianum during growth on sugarcane bagasse and analysis of the activity boosting effects of swollenin.

    Science.gov (United States)

    A L Rocha, Vanessa; N Maeda, Roberto; Pereira, Nei; F Kern, Marcelo; Elias, Luisa; Simister, Rachael; Steele-King, Clare; Gómez, Leonardo D; McQueen-Mason, Simon J

    2016-03-01

    This study demonstrates the production of an active enzyme cocktail produced by growing Trichoderma harzianum on sugarcane bagasse. The component enzymes were identified by LCMS-MS. Glycosyl hydrolases were the most abundant class of proteins, representing 67% of total secreted protein. Other carbohydrate active enzymes involved in cell wall deconstruction included lytic polysaccharide mono-oxygenases (AA9), carbohydrate-binding modules, carbohydrate esterases and swollenin, all present at levels of 1%. In total, proteases and lipases represented 5 and 1% of the total secretome, respectively, with the rest of the secretome being made up of proteins of unknown or putative function. This enzyme cocktail was efficient in catalysing the hydrolysis of sugarcane bagasse cellulolignin to fermentable sugars for potential use in ethanol production. Apart from mapping the secretome of T. harzianum, which is a very important tool to understand the catalytic performance of enzyme cocktails, the gene coding for T. harzianum swollenin was expressed in Aspergillus niger. This novel aspect in this work, allowed increasing the swollenin concentration by 95 fold. This is the first report about the heterologous expression of swollenin from T. harzianum, and the findings are of interest in enriching enzyme cocktail with this important accessory protein which takes part in the cellulose amorphogenesis. Despite lacking detectable glycoside activity, the addition of swollenin of T. harzianum increased by two-fold the hydrolysis efficiency of a commercial cellulase cocktail. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:327-336, 2016. © 2016 American Institute of Chemical Engineers.

  15. Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation.

    Science.gov (United States)

    Han, Dohyun; Jin, Jonghwa; Woo, Jongmin; Min, Hophil; Kim, Youngsoo

    2014-07-01

    Astrocytes are the most abundant cells in the CNS, but their function remains largely unknown. Characterization of the whole-cell proteome and secretome in astrocytes would facilitate the study of their functions in various neurodegenerative diseases and astrocyte-neuron communication. To build a reference proteome, we established a C8-D1A astrocyte proteome to a depth of 7265 unique protein groups using a novel strategy that combined two-step digestion, filter-aided sample preparation, StageTip-based high pH fractionation, and high-resolution MS. Nearly, 6000 unique protein groups were identified from conditioned media of astrocyte cultures, constituting the largest astrocyte secretome that has been reported. High-confidence whole-cell proteomes and secretomes are valuable resources in studying astrocyte function by label-free quantitation and bioinformatics analysis. All MS data have been deposited in the ProteomeXchange with identifier PXD000501 (http://proteomecentral.proteomexchange.org/dataset/PXD000501). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Sol-Generating Chemical Vapor into Liquid (SG-CViL) deposition – a facile method for encapsulation of diverse cell types in silica matrices

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, Robert [New Mexico Inst. of Mining and Technology, Socorro, NM (United States). Materials Engineering Dept.; Rogelj, Snezna [New Mexico Inst. of Mining and Technology, Socorro, NM (United States). Biology Dept.; Harper, Jason C. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Bioenergy and Biodefense Technologies Dept.; Tartis, Michaelann [New Mexico Inst. of Mining and Technology, Socorro, NM (United States). Materials and Chemical Engineering Dept.

    2014-12-12

    In nature, cells perform a variety of complex functions such as sensing, catalysis, and energy conversion which hold great potential for biotechnological device construction. However, cellular sensitivity to ex vivo environments necessitates development of bio–nano interfaces which allow integration of cells into devices and maintain their desired functionality. In order to develop such an interface, the use of a novel Sol-Generating Chemical Vapor into Liquid (SG-CViL) deposition process for whole cell encapsulation in silica was explored. In SG-CViL, the high vapor pressure of tetramethyl orthosilicate (TMOS) is utilized to deliver silica into an aqueous medium, creating a silica sol. Cells are then mixed with the resulting silica sol, facilitating encapsulation of cells in silica while minimizing cell contact with the cytotoxic products of silica generating reactions (i.e. methanol), and reduce exposure of cells to compressive stresses induced from silica condensation reactions. Using SG-CVIL, Saccharomyces cerevisiae (S. cerevisiae) engineered with an inducible beta galactosidase system were encapsulated in silica solids and remained both viable and responsive 29 days post encapsulation. By tuning SG-CViL parameters, thin layer silica deposition on mammalian HeLa and U87 human cancer cells was also achieved. Thus, the ability to encapsulate various cell types in either a multi cell (S. cerevisiae) or a thin layer (HeLa and U87 cells) fashion shows the promise of SG-CViL as an encapsulation strategy for generating cell–silica constructs with diverse functions for incorporation into devices for sensing, bioelectronics, biocatalysis, and biofuel applications.

  17. Genetic richness and diversity in Cryptosporidium hominis and C. parvum reveals major knowledge gaps and a need for the application of "next generation" technologies--research review.

    Science.gov (United States)

    Jex, Aaron R; Gasser, Robin B

    2010-01-01

    Cryptosporidium species (apicomplexan protists) are a major cause of diarrhoeal disease (= cryptosporidiosis) in humans worldwide. The impact of cryptosporidiosis is also compounded by the spread of HIV/AIDS and a lack of cost-effective anti-cryptosporidial chemotherapeutics or vaccines. Mitigation of the impact of cryptosporidiosis in humans needs to focus on prevention and control strategies, built on a sound understanding of the epidemiology of Cryptosporidium species. Refined epidemiological studies rely on the use of molecular tools employing informative genetic markers. Currently, the 60-kDa glycoprotein gene (gp60) is the most suitable and widely used genetic marker for Cryptosporidium species infecting humans. Here, we undertake an analysis of all publicly-available gp60 sequence data and associated literature for C. hominis and C. parvum, and yield useful insights into the richness, diversity and distribution of genetic variants, and link these variants to human cryptosporidiosis. This global analysis reveals that, despite high genetic richness in Cryptosporidium isolates from humans, there is a surprisingly low diversity. It also highlights limited knowledge about the genetics of cryptosporidiosis in developing nations and in many animals that might act as infection sources. Clearly, there is a major need for more comprehensive studies of Cryptosporidium infecting humans and other animals in Africa and Asia. As molecular technologies improve and become affordable, future studies should utilize "next generation" sequencing and bioinformatic platforms to conduct comparative 'genome sequence surveys' to test the validity of current genetic classifications based on gp60 data. Complemented by in vitro and in vivo investigations, these biotechnological advances will also assist significantly in the search for new intervention strategies against human cryptosporidiosis.

  18. An atmospheric turbulence model for spatiotemporal variability of geographically-diverse, aggregated wind-generated electricity to accelerate wide-scale wind energy deployment (Invited)

    Science.gov (United States)

    Lundquist, J. K.; Handschy, M.

    2013-12-01

    During the year 2012, the cumulative wind power capacity installed in the United States could provide roughly 4.4% of electricity demand. Although the wind resource can provide many times over the entire US electrical needs, and costs for onshore wind deployment are continually dropping, the variability of the wind represents one of the greatest remaining barriers to wide-scale wind deployment. This study focuses on the nature of this variability. We quantify the axiom 'geographic diversity reduces variability' (of wind generation) by relating resource variability characteristics to the well-understood physical phenomena of turbulence in the Earth's atmosphere. Many existing studies focus on datasets of a few years' duration in a particular geographic area; such results are difficult to generalize. Our approach builds on the fundamental nonlinear characteristics of turbulence in the atmosphere to characterize wind speed and power generation correlations between wind plants from local to continental scales. The resulting general principles enable estimation of the benefits of geographic aggregation absent detailed site-specific historical data, thereby enabling more efficient transmission grid models, expediting transmission plans, and providing a framework for evaluating the requirements and benefits of electric storage at higher wind penetrations. To validate these general principles, we compare them to observed inter-station correlations in a number of wind-speed data sets, including a 40-year Canadian dataset that spans the continent of North America, as well as shorter-duration datasets in smaller regions within the United States. This presentation will present general rules for the dependence of correlation between wind turbines on separation and time scale. We suggest these general rules could help shift renewable integration planning from simulation towards optimization.

  19. A diverse repertoire of human immunoglobulin variable genes in a chicken B cell line is generated by both gene conversion and somatic hypermutation

    Directory of Open Access Journals (Sweden)

    Philip A. Leighton

    2015-03-01

    Full Text Available Chicken immune responses to human proteins are often more robust than rodent responses because of the phylogenetic relationship between the different species. For discovery of a diverse panel of unique therapeutic antibody candidates, chickens therefore represent an attractive host for human-derived targets. Recent advances in monoclonal antibody technology, specifically new methods for the molecular cloning of antibody genes directly from primary B cells, has ushered in a new era of generating monoclonal antibodies from non-traditional host animals that were previously inaccessible through hybridoma technology. However, such monoclonals still require post-discovery humanization in order to be developed as therapeutics. To obviate the need for humanization, a modified strain of chickens could be engineered to express a human sequence immunoglobulin variable region repertoire. Here, human variable genes introduced into the chicken immunoglobulin loci through gene targeting were evaluated for their ability to be recognized and diversified by the native chicken recombination machinery that is present in the B-lineage cell line DT40. After expansion in culture the DT40 population accumulated genetic mutants that were detected via deep sequencing. Bioinformatic analysis revealed that the human targeted constructs are performing as expected in the cell culture system, and provide a measure of confidence that they will be functional in transgenic animals.

  20. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS)

    Science.gov (United States)

    Gofton, Alexander W.; Paparini, Andrea; Codello, Annachiara; Greay, Telleasha; Gillett, Amber; Warren, Kristin; Irwin, Peter; Ryan, Una

    2017-01-01

    Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus), particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS)-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani) removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2–39.8%) were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2–39.8%), T. gilletti (25%, 95% CI: 18.7–32.3%), T. copemani (27.4%, 95% CI: 20.8–34.8%) and T. vegrandis (10.1%, 95% CI: 6.0–15.7%). Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0–3.3%), and a novel species (Trypanosoma sp. AB-2017) was identified at a prevalence of 4.8% (95% CI: 2.1–9.2%). Mixed infections with up to five species were present in 27.4% (95% CI: 21–35%) of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2–9%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS) within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides

  1. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus and their ticks identified using next-generation sequencing (NGS.

    Directory of Open Access Journals (Sweden)

    Amanda D Barbosa

    Full Text Available Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus, particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2-39.8% were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2-39.8%, T. gilletti (25%, 95% CI: 18.7-32.3%, T. copemani (27.4%, 95% CI: 20.8-34.8% and T. vegrandis (10.1%, 95% CI: 6.0-15.7%. Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0-3.3%, and a novel species (Trypanosoma sp. AB-2017 was identified at a prevalence of 4.8% (95% CI: 2.1-9.2%. Mixed infections with up to five species were present in 27.4% (95% CI: 21-35% of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2-9%. Overall, a considerably higher proportion (79.7% of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides new insights

  2. Integration of Breast Cancer Secretomes with Clinical Data Elucidates Potential Serum Markers for Disease Detection, Diagnosis, and Prognosis.

    Science.gov (United States)

    Ziegler, Yvonne S; Moresco, James J; Yates, John R; Nardulli, Ann M

    2016-01-01

    Cancer cells secrete factors that influence adjacent cell behavior and can lead to enhanced proliferation and metastasis. To better understand the role of these factors in oncogenesis and disease progression, estrogen and progesterone receptor positive MCF-7 cells, triple negative breast cancer MDA-MB-231, DT22, and DT28 cells, and MCF-10A non-transformed mammary epithelial cells were grown in 3D cultures. A special emphasis was placed on triple negative breast cancer since these tumors are highly aggressive and no targeted treatments are currently available. The breast cancer cells secreted factors of variable potency that stimulated proliferation of the relatively quiescent MCF-10A cells. The conditioned medium from each cell line was subjected to mass spectrometry analysis and a variety of secreted proteins were identified including glycolytic enzymes, proteases, protease inhibitors, extracellular matrix proteins, and insulin-like growth factor binding proteins. An investigation of the secretome from each cell line yielded clues about strategies used for breast cancer proliferation and metastasis. Some of the proteins we identified may be useful in the development of a serum-based test for breast cancer detection, diagnosis, prognosis, and monitoring.

  3. Molecular Therapy for Degenerative Disc Disease: Clues from Secretome Analysis of the Notochordal Cell-Rich Nucleus Pulposus

    Science.gov (United States)

    Matta, Ajay; Karim, M. Zia; Isenman, David E.; Erwin, W. Mark

    2017-01-01

    Degenerative disc disease (DDD) is associated with spinal pain often leading to long-term disability. However, the non-chondrodystrophic canine intervertebral disc is protected from the development of DDD, ostensibly due to its retention of notochordal cells (NC) in the nucleus pulposus (NP). In this study, we hypothesized that secretome analysis of the NC-rich NP will lead to the identification of key proteins that delay the onset of DDD. Using mass-spectrometry, we identified 303 proteins including components of TGFβ- and Wnt-signaling, anti-angiogeneic factors and proteins that inhibit axonal ingrowth in the bioactive fractions of serum free, notochordal cell derived conditioned medium (NCCM). Ingenuity Pathway Analysis revealed TGFβ1 and CTGF as major hubs in protein interaction networks. In vitro treatment with TGFβ1 and CTGF promoted the synthesis of healthy extra-cellular matrix proteins, increased cell proliferation and reduced cell death in human degenerative disc NP cells. A single intra-discal injection of recombinant TGFβ1 and CTGF proteins in a pre-clinical rat-tail disc injury model restored the NC and stem cell rich NP. In conclusion, we demonstrate the potential of TGFβ1 and CTGF to mitigate the progression of disc degeneration and the potential use of these molecules in a molecular therapy to treat the degenerative disc. PMID:28358123

  4. Evaluation of selected static methods used to estimate element mobility, acid-generating and acid-neutralizing potentials associated with geologically diverse mining wastes

    Science.gov (United States)

    Hageman, Philip L.; Seal, Robert R.; Diehl, Sharon F.; Piatak, Nadine M.; Lowers, Heather

    2015-01-01

    A comparison study of selected static leaching and acid–base accounting (ABA) methods using a mineralogically diverse set of 12 modern-style, metal mine waste samples was undertaken to understand the relative performance of the various tests. To complement this study, in-depth mineralogical studies were conducted in order to elucidate the relationships between sample mineralogy, weathering features, and leachate and ABA characteristics. In part one of the study, splits of the samples were leached using six commonly used leaching tests including paste pH, the U.S. Geological Survey (USGS) Field Leach Test (FLT) (both 5-min and 18-h agitation), the U.S. Environmental Protection Agency (USEPA) Method 1312 SPLP (both leachate pH 4.2 and leachate pH 5.0), and the USEPA Method 1311 TCLP (leachate pH 4.9). Leachate geochemical trends were compared in order to assess differences, if any, produced by the various leaching procedures. Results showed that the FLT (5-min agitation) was just as effective as the 18-h leaching tests in revealing the leachate geochemical characteristics of the samples. Leaching results also showed that the TCLP leaching test produces inconsistent results when compared to results produced from the other leaching tests. In part two of the study, the ABA was determined on splits of the samples using both well-established traditional static testing methods and a relatively quick, simplified net acid–base accounting (NABA) procedure. Results showed that the traditional methods, while time consuming, provide the most in-depth data on both the acid generating, and acid neutralizing tendencies of the samples. However, the simplified NABA method provided a relatively fast, effective estimation of the net acid–base account of the samples. Overall, this study showed that while most of the well-established methods are useful and effective, the use of a simplified leaching test and the NABA acid–base accounting method provide investigators fast

  5. Generational Phenomenology

    African Journals Online (AJOL)

    denise

    by Xers, and how Millennials not only accept but expect diversity (320 ff.). However, nothing is actually said to the effect that generational relations might be affected by the different styles of thinking, speaking, and values of women. Moreover, it seems likely that generations and their relations are different for people of color,.

  6. Computational prediction of secretion systems and secretomes of Brucella: identification of novel type IV effectors and their interaction with the host.

    Science.gov (United States)

    Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S; Dinakaran, Vasudevan; Sridhar, Jayavel; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

    2016-01-01

    Brucella spp. are facultative intracellular pathogens that cause brucellosis in various mammals including humans. Brucella survive inside the host cells by forming vacuoles and subverting host defence systems. This study was aimed to predict the secretion systems and the secretomes of Brucella spp. from 39 complete genome sequences available in the databases. Furthermore, an attempt was made to identify the type IV secretion effectors and their interactions with host proteins. We predicted the secretion systems of Brucella by the KEGG pathway and SecReT4. Brucella secretomes and type IV effectors (T4SEs) were predicted through genome-wide screening using JVirGel and S4TE, respectively. Protein-protein interactions of Brucella T4SEs with their hosts were analyzed by HPIDB 2.0. Genes coding for Sec and Tat pathways of secretion and type I (T1SS), type IV (T4SS) and type V (T5SS) secretion systems were identified and they are conserved in all the species of Brucella. In addition to the well-known VirB operon coding for the type IV secretion system (T4SS), we have identified the presence of additional genes showing homology with T4SS of other organisms. On the whole, 10.26 to 14.94% of total proteomes were found to be either secreted (secretome) or membrane associated (membrane proteome). Approximately, 1.7 to 3.0% of total proteomes were identified as type IV secretion effectors (T4SEs). Prediction of protein-protein interactions showed 29 and 36 host-pathogen specific interactions between Bos taurus (cattle)-B. abortus and Ovis aries (sheep)-B. melitensis, respectively. Functional characterization of the predicted T4SEs and their interactions with their respective hosts may reveal the secrets of host specificity of Brucella.

  7. Quantitative Proteomic Analysis of Type III Secretome of Enteropathogenic Escherichia coli Reveals an Expanded Effector Repertoire for Attaching/Effacing Bacterial Pathogens*

    Science.gov (United States)

    Deng, Wanyin; Yu, Hong B.; de Hoog, Carmen L.; Stoynov, Nikolay; Li, Yuling; Foster, Leonard J.; Finlay, B. Brett

    2012-01-01

    Type III secretion systems are central to the pathogenesis and virulence of many important Gram-negative bacterial pathogens, and elucidation of the secretion mechanism and identification of the secreted substrates are critical to our understanding of their pathogenic mechanisms and developing potential therapeutics. Stable isotope labeling with amino acids in cell culture-based mass spectrometry is a quantitative and highly sensitive proteomics tool that we have previously used to successfully analyze the type III secretomes of Citrobacter rodentium and Salmonella enterica serovar Typhimurium. In this report, stable isotope labeling with amino acids in cell culture was used to analyze the type III secretome of enteropathogenic Escherichia coli (EPEC), an important human pathogen, which, together with enterohemorrhagic E. coli and C. rodentium, represents the family of attaching and effacing bacterial pathogens. We not only confirmed all 25 known EPEC type III-secreted proteins and effectors previously identified by conventional molecular and bioinformatical techniques but also identified several new type III-secreted proteins, including two novel effectors, C_0814/NleJ and LifA, that were shown to be translocated into host cells. LifA is a known virulence factor believed to act as a toxin as well as an adhesin, but its mechanism of secretion and function is not understood. With a predicted molecular mass of 366 kDa, LifA is the largest type III effector identified thus far in any pathogen. We further demonstrated that Efa1, ToxB, and Z4332 (homologs of LifA in enterohemorrhagic E. coli) are also type III effectors. This study has comprehensively characterized the type III secretome of EPEC, expanded the repertoire of type III-secreted effectors for the attaching and effacing pathogens, and provided new insights into the mode of function for LifA/Efa1/ToxB/Z4332, an important family of virulence factors. PMID:22661456

  8. Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici.

    Science.gov (United States)

    Xia, Chongjing; Wang, Meinan; Cornejo, Omar E; Jiwan, Derick A; See, Deven R; Chen, Xianming

    2017-01-01

    Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is one of the most destructive diseases of wheat worldwide. Planting resistant cultivars is an effective way to control this disease, but race-specific resistance can be overcome quickly due to the rapid evolving Pst population. Studying the pathogenicity mechanisms is critical for understanding how Pst virulence changes and how to develop wheat cultivars with durable resistance to stripe rust. We re-sequenced 7 Pst isolates and included additional 7 previously sequenced isolates to represent balanced virulence/avirulence profiles for several avirulence loci in seretome analyses. We observed an uneven distribution of heterozygosity among the isolates. Secretome comparison of Pst with other rust fungi identified a large portion of species-specific secreted proteins, suggesting that they may have specific roles when interacting with the wheat host. Thirty-two effectors of Pst were identified from its secretome. We identified candidates for Avr genes corresponding to six Yr genes by correlating polymorphisms for effector genes to the virulence/avirulence profiles of the 14 Pst isolates. The putative AvYr76 was present in the avirulent isolates, but absent in the virulent isolates, suggesting that deleting the coding region of the candidate avirulence gene has produced races virulent to resistance gene Yr76 . We conclude that incorporating avirulence/virulence phenotypes into correlation analysis with variations in genomic structure and secretome, particularly presence/absence polymorphisms of effectors, is an efficient way to identify candidate Avr genes in Pst . The candidate effector genes provide a rich resource for further studies to determine the evolutionary history of Pst populations and the co-evolutionary arms race between Pst and wheat. The Avr candidates identified in this study will lead to cloning avirulence genes in Pst , which will enable us to understand molecular mechanisms

  9. Quantitative proteomic analysis of type III secretome of enteropathogenic Escherichia coli reveals an expanded effector repertoire for attaching/effacing bacterial pathogens.

    Science.gov (United States)

    Deng, Wanyin; Yu, Hong B; de Hoog, Carmen L; Stoynov, Nikolay; Li, Yuling; Foster, Leonard J; Finlay, B Brett

    2012-09-01

    Type III secretion systems are central to the pathogenesis and virulence of many important Gram-negative bacterial pathogens, and elucidation of the secretion mechanism and identification of the secreted substrates are critical to our understanding of their pathogenic mechanisms and developing potential therapeutics. Stable isotope labeling with amino acids in cell culture-based mass spectrometry is a quantitative and highly sensitive proteomics tool that we have previously used to successfully analyze the type III secretomes of Citrobacter rodentium and Salmonella enterica serovar Typhimurium. In this report, stable isotope labeling with amino acids in cell culture was used to analyze the type III secretome of enteropathogenic Escherichia coli (EPEC), an important human pathogen, which, together with enterohemorrhagic E. coli and C. rodentium, represents the family of attaching and effacing bacterial pathogens. We not only confirmed all 25 known EPEC type III-secreted proteins and effectors previously identified by conventional molecular and bioinformatical techniques but also identified several new type III-secreted proteins, including two novel effectors, C_0814/NleJ and LifA, that were shown to be translocated into host cells. LifA is a known virulence factor believed to act as a toxin as well as an adhesin, but its mechanism of secretion and function is not understood. With a predicted molecular mass of 366 kDa, LifA is the largest type III effector identified thus far in any pathogen. We further demonstrated that Efa1, ToxB, and Z4332 (homologs of LifA in enterohemorrhagic E. coli) are also type III effectors. This study has comprehensively characterized the type III secretome of EPEC, expanded the repertoire of type III-secreted effectors for the attaching and effacing pathogens, and provided new insights into the mode of function for LifA/Efa1/ToxB/Z4332, an important family of virulence factors.

  10. Pseudorabies virus infected porcine epithelial cell line generates a diverse set of host microRNAs and a special cluster of viral microRNAs.

    Directory of Open Access Journals (Sweden)

    Yi-Quan Wu

    Full Text Available Pseudorabies virus (PRV belongs to Alphaherpesvirinae subfamily that causes huge economic loss in pig industry worldwide. It has been recently demonstrated that many herpesviruses encode microRNAs (miRNAs, which play crucial roles in viral life cycle. However, the knowledge about PRV-encoded miRNAs is still limited. Here, we report a comprehensive analysis of both viral and host miRNA expression profiles in PRV-infected porcine epithelial cell line (PK-15. Deep sequencing data showed that the ∼4.6 kb intron of the large latency transcript (LLT functions as a primary microRNA precursor (pri-miRNA that encodes a cluster of 11 distinct miRNAs in the PRV genome, and 209 known and 39 novel porcine miRNAs were detected. Viral miRNAs were further confirmed by stem-loop RT-PCR and northern blot analysis. Intriguingly, all of these viral miRNAs exhibited terminal heterogeneity both at the 5' and 3' ends. Seven miRNA genes produced mature miRNAs from both arms and two of the viral miRNA genes showed partially overlapped in their precursor regions. Unexpectedly, a terminal loop-derived small RNA with high abundance and one special miRNA offset RNA (moRNA were processed from a same viral miRNA precursor. The polymorphisms of viral miRNAs shed light on the complexity of host miRNA-processing machinery and viral miRNA-regulatory mechanism. The swine genes and PRV genes were collected for target prediction of the viral miRNAs, revealing a complex network formed by both host and viral genes. GO enrichment analysis of host target genes suggests that PRV miRNAs are involved in complex cellular pathways including cell death, immune system process, metabolic pathway, indicating that these miRNAs play significant roles in virus-cells interaction of PRV and its hosts. Collectively, these data suggest that PRV infected epithelial cell line generates a diverse set of host miRNAs and a special cluster of viral miRNAs, which might facilitate PRV replication in cells.

  11. Exoproteome and secretome derived broad spectrum novel drug and vaccine candidates in Vibrio cholerae targeted by Piper betel derived compounds.

    Directory of Open Access Journals (Sweden)

    Debmalya Barh

    Full Text Available Vibrio cholerae is the causal organism of the cholera epidemic, which is mostly prevalent in developing and underdeveloped countries. However, incidences of cholera in developed countries are also alarming. Because of the emergence of new drug-resistant strains, even though several generic drugs and vaccines have been developed over time, Vibrio infections remain a global health problem that appeals for the development of novel drugs and vaccines against the pathogen. Here, applying comparative proteomic and reverse vaccinology approaches to the exoproteome and secretome of the pathogen, we have identified three candidate targets (ompU, uppP and yajC for most of the pathogenic Vibrio strains. Two targets (uppP and yajC are novel to Vibrio, and two targets (uppP and ompU can be used to develop both drugs and vaccines (dual targets against broad spectrum Vibrio serotypes. Using our novel computational approach, we have identified three peptide vaccine candidates that have high potential to induce both B- and T-cell-mediated immune responses from our identified two dual targets. These two targets were modeled and subjected to virtual screening against natural compounds derived from Piper betel. Seven compounds were identified first time from Piper betel to be highly effective to render the function of these targets to identify them as emerging potential drugs against Vibrio. Our preliminary validation suggests that these identified peptide vaccines and betel compounds are highly effective against Vibrio cholerae. Currently we are exhaustively validating these targets, candidate peptide vaccines, and betel derived lead compounds against a number of Vibrio species.

  12. Impact of the lectin chaperone calnexin on the stress response, virulence and proteolytic secretome of the fungal pathogen Aspergillus fumigatus.

    Directory of Open Access Journals (Sweden)

    Margaret V Powers-Fletcher

    Full Text Available Calnexin is a membrane-bound lectin chaperone in the endoplasmic reticulum (ER that is part of a quality control system that promotes the accurate folding of glycoproteins entering the secretory pathway. We have previously shown that ER homeostasis is important for virulence of the human fungal pathogen Aspergillus fumigatus, but the contribution of calnexin has not been explored. Here, we determined the extent to which A. fumigatus relies on calnexin for growth under conditions of environmental stress and for virulence. The calnexin gene, clxA, was deleted from A. fumigatus and complemented by reconstitution with the wild type gene. Loss of clxA altered the proteolytic secretome of the fungus, but had no impact on growth rates in either minimal or complex media at 37°C. However, the ΔclxA mutant was growth impaired at temperatures above 42°C and was hypersensitive to acute ER stress caused by the reducing agent dithiothreitol. In contrast to wild type A. fumigatus, ΔclxA hyphae were unable to grow when transferred to starvation medium. In addition, depleting the medium of cations by chelation prevented ΔclxA from sustaining polarized hyphal growth, resulting in blunted hyphae with irregular morphology. Despite these abnormal stress responses, the ΔclxA mutant remained virulent in two immunologically distinct models of invasive aspergillosis. These findings demonstrate that calnexin functions are needed for growth under conditions of thermal, ER and nutrient stress, but are dispensable for surviving the stresses encountered in the host environment.

  13. Extensive remodeling of the Pseudomonas syringae pv. avellanae type III secretome associated with two independent host shifts onto hazelnut

    Directory of Open Access Journals (Sweden)

    O’Brien Heath E

    2012-07-01

    Full Text Available Abstract Background Hazelnut (Corylus avellana decline disease in Greece and Italy is caused by the convergent evolution of two distantly related lineages of Pseudomonas syringae pv. avellanae (Pav. We sequenced the genomes of three Pav isolates to determine if their convergent virulence phenotype had a common genetic basis due to either genetic exchange between lineages or parallel evolution. Results We found little evidence for horizontal transfer (recombination of genes between Pav lineages, but two large genomic islands (GIs have been recently acquired by one of the lineages. Evolutionary analyses of the genes encoding type III secreted effectors (T3SEs that are translocated into host cells and are important for both suppressing and eliciting defense responses show that the two Pav lineages have dramatically different T3SE profiles, with only two shared putatively functional T3SEs. One Pav lineage has undergone unprecedented secretome remodeling, including the acquisition of eleven new T3SEs and the loss or pseudogenization of 15, including five of the six core T3SE families that are present in the other Pav lineage. Molecular dating indicates that divergence within both of the Pav lineages predates their observation in the field. This suggest that both Pav lineages have been cryptically infecting hazelnut trees or wild relatives for many years, and that the emergence of hazelnut decline in the 1970s may have been due to changes in agricultural practice. Conclusions These data show that divergent lineages of P. syringae can converge on identical disease etiology on the same host plant using different virulence mechanisms and that dramatic shifts in the arsenal of T3SEs can accompany disease emergence.

  14. Proteomic analysis of extracellular vesicles from a Plasmodium falciparum Kenyan clinical isolate defines a core parasite secretome

    Science.gov (United States)

    Abdi, Abdirahman; Yu, Lu; Goulding, David; Rono, Martin K.; Bejon, Philip; Choudhary, Jyoti; Rayner, Julian

    2017-01-01

    Background: Many pathogens secrete effector molecules to subvert host immune responses, to acquire nutrients, and/or to prepare host cells for invasion. One of the ways that effector molecules are secreted is through extracellular vesicles (EVs) such as exosomes. Recently, the malaria parasite P. falciparum has been shown to produce EVs that can mediate transfer of genetic material between parasites and induce sexual commitment. Characterizing the content of these vesicles may improve our understanding of P. falciparum pathogenesis and virulence. Methods: Previous studies of P. falciparum EVs have been limited to long-term adapted laboratory isolates. In this study, we isolated EVs from a Kenyan P. falciparum clinical isolate that had been adapted to in vitro culture for a relatively shorter period, and characterized their protein content by mass spectrometry (data are available via ProteomeXchange, with identifier PXD006925). Results: We show that P. falciparum extracellular vesicles ( PfEVs) are enriched in proteins found within the exomembrane compartments of infected erythrocytes such as Maurer’s clefts (MCs), as well as the secretory endomembrane compartments in the apical end of the merozoites, suggesting that PfEVs may play a role in parasite-host interactions. Comparison of this dataset with previously published datasets helps to define a core secretome present in PfEVs. Conclusions: P. falciparum extracellular vesicles contain virulence-associated parasite proteins. Analysis of PfEVs contents from a range of clinical isolates, and their functional validation may improve our understanding of the virulence mechanisms of the parasite, and potentially identify new targets for interventions or diagnostics. PMID:28944300

  15. Extensive remodeling of the Pseudomonas syringae pv. avellanae type III secretome associated with two independent host shifts onto hazelnut.

    Science.gov (United States)

    O'Brien, Heath E; Thakur, Shalabh; Gong, Yunchen; Fung, Pauline; Zhang, Jianfeng; Yuan, Lijie; Wang, Pauline W; Yong, Choseung; Scortichini, Marco; Guttman, David S

    2012-07-16

    Hazelnut (Corylus avellana) decline disease in Greece and Italy is caused by the convergent evolution of two distantly related lineages of Pseudomonas syringae pv. avellanae (Pav). We sequenced the genomes of three Pav isolates to determine if their convergent virulence phenotype had a common genetic basis due to either genetic exchange between lineages or parallel evolution. We found little evidence for horizontal transfer (recombination) of genes between Pav lineages, but two large genomic islands (GIs) have been recently acquired by one of the lineages. Evolutionary analyses of the genes encoding type III secreted effectors (T3SEs) that are translocated into host cells and are important for both suppressing and eliciting defense responses show that the two Pav lineages have dramatically different T3SE profiles, with only two shared putatively functional T3SEs. One Pav lineage has undergone unprecedented secretome remodeling, including the acquisition of eleven new T3SEs and the loss or pseudogenization of 15, including five of the six core T3SE families that are present in the other Pav lineage. Molecular dating indicates that divergence within both of the Pav lineages predates their observation in the field. This suggest that both Pav lineages have been cryptically infecting hazelnut trees or wild relatives for many years, and that the emergence of hazelnut decline in the 1970s may have been due to changes in agricultural practice. These data show that divergent lineages of P. syringae can converge on identical disease etiology on the same host plant using different virulence mechanisms and that dramatic shifts in the arsenal of T3SEs can accompany disease emergence.

  16. Characterization of the secretome of human tooth germ stem cells (hTGSCs) reveals neuro-protection by fine-tuning micro-environment.

    Science.gov (United States)

    Yalvaç, Mehmet Emir; Yarat, Aysen; Mercan, Dilek; Rizvanov, Albert A; Palotás, András; Şahin, Fikrettin

    2013-08-01

    Bone-marrow-derived mesenchymal stem cells (MSCs) demonstrate neuro-protective effects in several disease models. By producing growth-factors, cytokines and chemokines, they promote survival of neurons in damaged brain areas. Alternative MSC sources, such as human tooth germ stem cells (hTGSCs), have been investigated for their neuro-protective properties. They ameliorate effects of neuro-toxic agents by paracrine mechanisms, however these secreted bio-active molecules are not yet characterized. Therefore, the current study aimed to provide a detailed analysis of the secretome of hTGSCs. Brain cells were exposed to various toxic materials, including Alzheimer's β-amyloid peptide (β-AP) and 6-hydroxy-dopamine (6-OHDA). When co-cultured with hTGSCs, the activity of a number of anti-oxidant enzymes (catalase, glutathione-s-transferase, glutathione-peroxidase, superoxide-dismutase) was increased and neuronal death/apoptosis was subsequently reduced. The composition of the secreted bio-active materials is influenced by various pre-existing factors such as oxygen and glucose deprivation and the age of cells (passage number). This report reveals for the first time that the neuro-protective secretome of hTGSCs and the micro-environment of cells have a mutual and dynamic impact on one another. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Bone Marrow Stromal Antigen 2 Is a Novel Plasma Biomarker and Prognosticator for Colorectal Carcinoma: A Secretome-Based Verification Study

    Directory of Open Access Journals (Sweden)

    Sum-Fu Chiang

    2015-01-01

    Full Text Available Background. The cancer cell secretome has been recognized as a valuable reservoir for identifying novel serum/plasma biomarkers for different cancers, including colorectal cancer (CRC. This study aimed to verify four CRC cell-secreted proteins (tumor-associated calcium signal transducer 2/trophoblast cell surface antigen 2 (TACSTD2/TROP2, tetraspanin-6 (TSPAN6, bone marrow stromal antigen 2 (BST2, and tumor necrosis factor receptor superfamily member 16 (NGFR as potential plasma CRC biomarkers. Methods. The study population comprises 152 CRC patients and 152 controls. Target protein levels in plasma and tissue samples were assessed by ELISA and immunohistochemistry, respectively. Results. Among the four candidate proteins examined by ELISA in a small sample set, only BST2 showed significantly elevated plasma levels in CRC patients versus controls. Immunohistochemical analysis revealed the overexpression of BST2 in CRC tissues, and higher BST2 expression levels correlated with poorer 5-year survival (46.47% versus 65.57%; p=0.044. Further verification confirmed the elevated plasma BST2 levels in CRC patients (2.35 ± 0.13 ng/mL versus controls (1.04 ± 0.03 ng/mL (p<0.01, with an area under the ROC curve (AUC being 0.858 comparable to that of CEA (0.867. Conclusion. BST2, a membrane protein selectively detected in CRC cell secretome, may be a novel plasma biomarker and prognosticator for CRC.

  18. In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins.

    Science.gov (United States)

    Li, Xianyu; Jiang, Jing; Zhao, Xinyuan; Zhao, Yan; Cao, Qichen; Zhao, Qing; Han, Huanhuan; Wang, Jifeng; Yu, Zixiang; Peng, Bo; Ying, Wantao; Qian, Xiaohong

    2016-04-19

    Cancer cell metastasis is a major cause of cancer fatality. But the underlying molecular mechanisms remain incompletely understood, which results in the lack of efficient diagnosis, therapy and prevention approaches. Here, we report a systematic study on the secretory proteins (secretome) and secretory N-glycoproteins (N-glycosecretome) of four human hepatocellular carcinoma (HCC) cell lines with different metastatic potential, to explore the molecular mechanism of metastasis and supply the clues for effective measurement of diagnosis and therapy. Totally, 6242 unique gene products (GPs) and 1637 unique N-glycosites from 635 GPs were confidently identified. About 4000 GPs on average were quantified in each of the cell lines, 1156 of which show differential expression (pproteins were secretory proteins and proteins correlated to cell movement were significantly activated with the increasing of metastatic potential of the cell lines. Twenty-three GPs increased both in the secretome and the N-glycosecretome were chosen as candidates and verified by western blot analysis, and 10 of them were chosen for immunohistochemistry (IHC) analysis. The cumulative survival rates of the patients with candidate (FAT1, DKK3) suggested that these proteins might be used as biomarkers for HCC diagnosis. In addition, a comparative analysis with the published core human plasma database (1754 GPs) revealed that there were 182 proteins not presented in the human plasma database but identified by our studies, some of which were selected and verified successfully by western blotting in human plasma.

  19. Mapping N-linked Glycosylation Sites in the Secretome and Whole Cells of Aspergillus niger Using Hydrazide Chemistry and Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lu; Aryal, Uma K.; Dai, Ziyu; Mason, Alisa C.; Monroe, Matthew E.; Tian, Zhixin; Zhou, Jianying; Su, Dian; Weitz, Karl K.; Liu, Tao; Camp, David G.; Smith, Richard D.; Baker, Scott E.; Qian, Weijun

    2012-01-01

    Protein glycosylation is known to play an essential role in both cellular functions and the secretory pathways; however, little information is available on the dynamics of glycosylated N-linked glycosites of fungi. Herein we present the first extensive mapping of glycosylated N-linked glycosites in industrial strain Aspergillus niger by applying an optimized solid phase enrichment of glycopeptide protocol using hydrazide modified magnetic beads. The enrichment protocol was initially optimized using mouse plasma and A. niger secretome samples, which was then applied to profile N-linked glycosites from both the secretome and whole cell lysates of A. niger. A total of 847 unique N-linked glycosites and 330 N-linked glycoproteins were confidently identified by LC-MS/MS. Based on gene ontology analysis, the identified N-linked glycoproteins in the whole cell lysate were primarily localized in the plasma membrane, endoplasmic reticulum, golgi apparatus, lysosome, and storage vacuoles. The identified N-linked glycoproteins are involved in a wide range of biological processes including gene regulation and signal transduction, protein folding and assembly, protein modification and carbohydrate metabolism. The extensive coverage of glycosylated N-linked glycosites along with identification of partial N-linked glycosylation in those enzymes involving in different biochemical pathways provide useful information for functional studies of N-linked glycosylation and their biotechnological applications in A. niger.

  20. Issues in Diversity Management

    Science.gov (United States)

    2008-01-01

    Generation X born between1965 to 1980, and Generational Y or Millennial born after 1980). A review of the literature shows a number of differing...organizations on diversity outreach) (Knouse & Stewart, 2003). Leadership Commitment and buy in. To be effective, the leadership must buy -in to the...1964), Generation X (born 1965 to 1980), and Millennials or Generation Y (born after 1980). From the military perspective, there are significant

  1. Characterization of Clostridium thermocellum (B8) secretome and purified cellulosomes for lignocellulosic biomass degradation.

    Science.gov (United States)

    Osiro, Karen O; de Camargo, Brenda R; Satomi, Rachel; Hamann, Pedro Ricardo V; Silva, Jéssica Pinheiro; de Sousa, Marcelo Valle; Quirino, Betania F; Aquino, Elaine N; Felix, Carlos R; Murad, André Melro; Noronha, Eliane F

    2017-02-01

    The main goal of the present study was a complete proteomic characterization of total proteins eluted from residual substrate-bound proteins (RSBP), and cellulosomes secreted by Clostridium thermocellum B8 during growth in the presence of microcrystalline cellulose as a carbon source. The second goal was to evaluate their potential use as enzymatic blends for hydrolyzing agro-industrial residues to produce fermentable sugars. Protein identification through LC-MS/MS mass spectrometry showed that the RSBP sample, in addition to cellulosomal proteins, contains a wide variety of proteins, including those without a well-characterized role in plant cell wall degradation. The RSBP subsample defined as purified cellulosomes (PC) consists mainly of glycoside hydrolases grouped in families 5, 8, 9, 10 and 48. Dynamic light scattering, DLS, analysis of PC resulted in two protein peaks (pi1 and pi2) presenting molecular masses in agreement with those previously described for cellulosomes and polycellulosomes. These peaks weren't detected after PC treatment with 1.0% Tween. PC and RSBP presented maximal activities at temperatures ranging from 60° to 70°C and at pH 5.0. RSBP retained almost all of its activity after incubation at 50, 60 and 70°C and PC showed remarkable thermostability at 50 and 60°C. RSBP holocellullolytic activities were inhibited by phenolic compounds, while PC showed either increasing activity or a lesser degree of inhibition. RSBP and PC hydrolyze sugar cane straw, cotton waste and microcrystalline cellulose, liberating a diversity of saccharides; however, the highest concentration of released sugar was obtained for assays carried out using PC as an enzymatic blend and after ten days at 50°C. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome

    Directory of Open Access Journals (Sweden)

    Sandhya Verma

    2017-06-01

    Full Text Available Transcription factors (TFs are the key players in gene expression and their study is highly significant for shedding light on the molecular mechanisms and evolutionary history of organisms. During host–pathogen interaction, extensive reprogramming of gene expression facilitated by TFs is likely to occur in both host and pathogen. To date, the knowledge about TF repertoire in filamentous fungi is in infancy. The necrotrophic fungus Ascochyta rabiei, that causes destructive Ascochyta blight (AB disease of chickpea (Cicer arietinum, demands more comprehensive study for better understanding of Ascochyta-legume pathosystem. In the present study, we performed the genome-wide identification and analysis of TFs in A. rabiei. Taking advantage of A. rabiei genome sequence, we used a bioinformatic approach to predict the TF repertoire of A. rabiei. For identification and classification of A. rabiei TFs, we designed a comprehensive pipeline using a combination of BLAST and InterProScan software. A total of 381 A. rabiei TFs were predicted and divided into 32 fungal specific families of TFs. The gene structure, domain organization and phylogenetic analysis of abundant families of A. rabiei TFs were also carried out. Comparative study of A. rabiei TFs with that of other necrotrophic, biotrophic, hemibiotrophic, symbiotic, and saprotrophic fungi was performed. It suggested presence of both conserved as well as unique features among them. Moreover, cis-acting elements on promoter sequences of earlier predicted A. rabiei secretome were also identified. With the help of published A. rabiei transcriptome data, the differential expression of TF and secretory protein coding genes was analyzed. Furthermore, comprehensive expression analysis of few selected A. rabiei TFs using quantitative real-time polymerase chain reaction revealed variety of expression patterns during host colonization. These genes were expressed in at least one of the time points tested post

  3. Cathepsin B gene disruption induced Leishmania donovani proteome remodeling implies cathepsin B role in secretome regulation.

    Directory of Open Access Journals (Sweden)

    Teklu Kuru Gerbaba

    Full Text Available Leishmania cysteine proteases are potential vaccine candidates and drug targets. To study the role of cathepsin B cysteine protease, we have generated and characterized cathepsin B null mutant L. donovani parasites. L. donovani cathepsin B null mutants grow normally in culture, but they show significantly attenuated virulence inside macrophages. Quantitative proteome profiling of wild type and null mutant parasites indicates cathepsin B disruption induced remodeling of L. donovani proteome. We identified 83 modulated proteins, of which 65 are decreased and 18 are increased in the null mutant parasites, and 66% (55/83 of the modulated proteins are L. donovani secreted proteins. Proteins involved in oxidation-reduction (trypanothione reductase, peroxidoxins, tryparedoxin, cytochromes and translation (ribosomal proteins are among those decreased in the null mutant parasites, and most of these proteins belong to the same complex network of proteins. Our results imply virulence role of cathepsin B via regulation of Leishmania secreted proteins.

  4. Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases.

    Science.gov (United States)

    Meinhardt, Lyndel W; Costa, Gustavo Gilson Lacerda; Thomazella, Daniela P T; Teixeira, Paulo José P L; Carazzolle, Marcelo Falsarella; Schuster, Stephan C; Carlson, John E; Guiltinan, Mark J; Mieczkowski, Piotr; Farmer, Andrew; Ramaraj, Thiruvarangan; Crozier, Jayne; Davis, Robert E; Shao, Jonathan; Melnick, Rachel L; Pereira, Gonçalo A G; Bailey, Bryan A

    2014-02-27

    The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp. We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase. Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the

  5. Label-free proteomic analysis of environmental acidification-influenced Streptococcus pyogenes secretome reveals a novel acid-induced protein histidine triad protein A (HtpA) involved in necrotizing fasciitis.

    Science.gov (United States)

    Wen, Yao-Tseng; Wang, Jie-Siou; Tsai, Shu-Han; Chuan, Chiang-Ni; Wu, Jiunn-Jong; Liao, Pao-Chi

    2014-09-23

    Streptococcus pyogenes is responsible for various diseases. During infection, bacteria must adapt to adverse environments, such as the acidic environment. Acidic stimuli may stimulate S. pyogenes to invade into deeper tissue. However, how this acidic stimulus causes S. pyogenes to manipulate its secretome for facilitating invasion remains unclear. The dynamic label-free LC-MS/MS profiling identified 97 proteins, which are influenced by environmental acidification. Among these, 33 (34%) of the identified proteins were predicted to be extracellular proteins. Interestingly, classical secretory proteins comprise approximately 90% of protein abundance of the secretome in acidic condition at the stationary phase. One acid-induced secreted protein, HtpA, was selected to investigate its role in invasive infection. The mouse infected by the htpA deficient mutant showed lower virulence and smaller lesion area than the wild-type strain. The mutant strain was more efficiently cleared at infected skin than the wild-type strain. Besides, the relative phagocytosis resistance is lower in the mutant strain than in the wild-type strain. These data indicate that a novel acid-induced virulence factor, HtpA, which improves anti-phagocytosis ability for causing necrotizing fasciitis. Our investigation provides vital information for documenting the broad influences and mechanisms underlying the invasive behavior of S. pyogenes in an acidified environment. The acidified infected environment may facilitate S. pyogenes invasion from the mucosa to the deeper subepithelial tissue. The acid stimuli have been considered to affect the complex regulatory network of S. pyogenes for causing severe infections. Many of secreted virulence factors influenced by acidified environment may also play a crucial role in pathogenesis of invasive disease. To investigate temporal secretome changes under acidic environment, a comparative secretomics approach using label-free LC-MS/MS was undertaken to analyze

  6. The Role of Nuclear Power in Reducing Risk of the Fossil Fuel Prices and Diversity of Electricity Generation in Tunisia: A Portfolio Approach

    Science.gov (United States)

    Abdelhamid, Mohamed Ben; Aloui, Chaker; Chaton, Corinne; Souissi, Jomâa

    2010-04-01

    This paper applies real options and mean-variance portfolio theories to analyze the electricity generation planning into presence of nuclear power plant for the Tunisian case. First, we analyze the choice between fossil fuel and nuclear production. A dynamic model is presented to illustrate the impact of fossil fuel cost uncertainty on the optimal timing to switch from gas to nuclear. Next, we use the portfolio theory to manage risk of the electricity generation portfolio and to determine the optimal fuel mix with the nuclear alternative. Based on portfolio theory, the results show that there is other optimal mix than the mix fixed for the Tunisian mix for the horizon 2010-2020, with lower cost for the same risk degree. In the presence of nuclear technology, we found that the optimal generating portfolio must include 13% of nuclear power technology share.

  7. Specificity fingerprinting of retaining beta-1,4-glycanases in the Cellulomonas fimi secretome using two fluorescent mechanism-based probes.

    Science.gov (United States)

    Hekmat, Omid; Florizone, Christine; Kim, Young-Wan; Eltis, Lindsay D; Warren, R Antony J; Withers, Stephen G

    2007-11-23

    Functional proteomics methods are crucial for activity- and mechanism-based investigation of enzymes in biological systems at a post-translational stage. Glycosidases have central roles in cellular metabolism and its regulation, and their dysfunction can have detrimental effects. These enzymes also play key roles in biomass conversion. A functional profiling methodology was developed for direct, fluorescence-based, in-gel analysis of retaining beta-glycosidases. Two spectrally nonoverlapping fluorescent, mechanism-based probes containing different recognition elements for retaining cellulases and xylanases were prepared. The specificity-based covalent labelling of retaining glycanases by the two probes was demonstrated in model enzyme mixtures. Using the two probes and mass spectrometry, the secretomes of the biomass-converting bacterium Cellulomonas fimi, under induction by different polyglycan growth substrates, were analysed to obtain a specificity profile of the C. fimi retaining beta-glycanases. This is a facile strategy for the analysis of glycosidases produced by biomass-degrading organisms.

  8. Diversity Index

    Data.gov (United States)

    Town of Chapel Hill, North Carolina — This map service summarizes racial and ethnic diversity in the United States in 2012.The Diversity Index shows the likelihood that two persons chosen at random from...

  9. Molecular Profiling of the Phytophthora plurivora Secretome: A Step towards Understanding the Cross-Talk between Plant Pathogenic Oomycetes and Their Hosts

    Science.gov (United States)

    Fleischmann, Frank; Dalio, Ronaldo J. D.; Di Maro, Antimo; Scognamiglio, Monica; Fiorentino, Antonio; Parente, Augusto; Osswald, Wolfgang; Chambery, Angela

    2014-01-01

    The understanding of molecular mechanisms underlying host–pathogen interactions in plant diseases is of crucial importance to gain insights on different virulence strategies of pathogens and unravel their role in plant immunity. Among plant pathogens, Phytophthora species are eliciting a growing interest for their considerable economical and environmental impact. Plant infection by Phytophthora phytopathogens is a complex process coordinated by a plethora of extracellular signals secreted by both host plants and pathogens. The characterization of the repertoire of effectors secreted by oomycetes has become an active area of research for deciphering molecular mechanisms responsible for host plants colonization and infection. Putative secreted proteins by Phytophthora species have been catalogued by applying high-throughput genome-based strategies and bioinformatic approaches. However, a comprehensive analysis of the effective secretome profile of Phytophthora is still lacking. Here, we report the first large-scale profiling of P. plurivora secretome using a shotgun LC-MS/MS strategy. To gain insight on the molecular signals underlying the cross-talk between plant pathogenic oomycetes and their host plants, we also investigate the quantitative changes of secreted protein following interaction of P. plurivora with the root exudate of Fagus sylvatica which is highly susceptible to the root pathogen. We show that besides known effectors, the expression and/or secretion levels of cell-wall-degrading enzymes were altered following the interaction with the host plant root exudate. In addition, a characterization of the F. sylvatica root exudate was performed by NMR and amino acid analysis, allowing the identification of the main released low-molecular weight components, including organic acids and free amino acids. This study provides important insights for deciphering the extracellular network involved in the highly susceptible P. plurivora-F. sylvatica interaction

  10. Embracing Diversity

    NARCIS (Netherlands)

    S. Puntoni (Stefano)

    2015-01-01

    markdownabstract__Abstract__ Societies are vastly more diverse today than they used to be and, in many industries, developing theories and approaches that recognize and capitalize on this greater consumer diversity is crucial. In business schools, diversity tends to be discussed only in relation

  11. RecJ, ExoI and RecG are required for genome maintenance but not for generation of genetic diversity by repeat-mediated phase variation in Haemophilus influenzae

    International Nuclear Information System (INIS)

    Kumar, Gaurav A.; Woodhall, Mark R.; Hood, Derek W.; Moxon, E. Richard; Bayliss, Christopher D.

    2008-01-01

    High levels of genetic diversity are generated in Haemophilus influenzae populations through DNA repeat-mediated phase variation and recombination with DNA fragments acquired by uptake from the external milieu. Conversely, multiple pathways for maintenance of the genome sequence are encoded in H. influenzae genomes. In Escherichia coli, mutations in single-stranded-DNA exonucleases destabilise tandem DNA repeats whilst inactivation of recG can stabilise repeat tracts. These enzymes also have varying effects on recombination. Deletion mutations were constructed in H. influenzae genes encoding homologs of ExoI, RecJ and RecG whilst ExoVII was refractory to mutation. Inactivation of RecJ and RecG, but not ExoI, increased sensitivity to irradiation with ultraviolet light. An increase in spontaneous mutation rate was not observed in single mutants but only when both RecJ and ExoI were mutated. None of the single- or double-mutations increased or decreased the rates of slippage in tetranucleotide repeat tracts. Furthermore, the exonuclease mutants did not exhibit significant defects in horizontal gene transfer. We conclude that RecJ, ExoI and RecG are required for maintenance of the H. influenzae genome but none of these enzymes influence the generation of genetic diversity through mutations in the tetranucleotide repeat tracts of this species

  12. RecJ, ExoI and RecG are required for genome maintenance but not for generation of genetic diversity by repeat-mediated phase variation in Haemophilus influenzae

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Gaurav A.; Woodhall, Mark R.; Hood, Derek W.; Moxon, E. Richard [Molecular Infectious Diseases Group, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS (United Kingdom); Bayliss, Christopher D. [Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH (United Kingdom)], E-mail: cdb12@le.ac.uk

    2008-04-02

    High levels of genetic diversity are generated in Haemophilus influenzae populations through DNA repeat-mediated phase variation and recombination with DNA fragments acquired by uptake from the external milieu. Conversely, multiple pathways for maintenance of the genome sequence are encoded in H. influenzae genomes. In Escherichia coli, mutations in single-stranded-DNA exonucleases destabilise tandem DNA repeats whilst inactivation of recG can stabilise repeat tracts. These enzymes also have varying effects on recombination. Deletion mutations were constructed in H. influenzae genes encoding homologs of ExoI, RecJ and RecG whilst ExoVII was refractory to mutation. Inactivation of RecJ and RecG, but not ExoI, increased sensitivity to irradiation with ultraviolet light. An increase in spontaneous mutation rate was not observed in single mutants but only when both RecJ and ExoI were mutated. None of the single- or double-mutations increased or decreased the rates of slippage in tetranucleotide repeat tracts. Furthermore, the exonuclease mutants did not exhibit significant defects in horizontal gene transfer. We conclude that RecJ, ExoI and RecG are required for maintenance of the H. influenzae genome but none of these enzymes influence the generation of genetic diversity through mutations in the tetranucleotide repeat tracts of this species.

  13. Functional diversity of human basic helix-loop-helix transcription factor TCF4 isoforms generated by alternative 5' exon usage and splicing.

    Directory of Open Access Journals (Sweden)

    Mari Sepp

    Full Text Available BACKGROUND: Transcription factor 4 (TCF4 alias ITF2, E2-2, ME2 or SEF2 is a ubiquitous class A basic helix-loop-helix protein that binds to E-box DNA sequences (CANNTG. While involved in the development and functioning of many different cell types, recent studies point to important roles for TCF4 in the nervous system. Specifically, human TCF4 gene is implicated in susceptibility to schizophrenia and TCF4 haploinsufficiency is the cause of the Pitt-Hopkins mental retardation syndrome. However, the structure, expression and coding potential of the human TCF4 gene have not been described in detail. PRINCIPAL FINDINGS: In the present study we used human tissue samples to characterize human TCF4 gene structure and TCF4 expression at mRNA and protein level. We report that although widely expressed, human TCF4 mRNA expression is particularly high in the brain. We demonstrate that usage of numerous 5' exons of the human TCF4 gene potentially yields in TCF4 protein isoforms with 18 different N-termini. In addition, the diversity of isoforms is increased by alternative splicing of several internal exons. For functional characterization of TCF4 isoforms, we overexpressed individual isoforms in cultured human cells. Our analysis revealed that subcellular distribution of TCF4 isoforms is differentially regulated: Some isoforms contain a bipartite nuclear localization signal and are exclusively nuclear, whereas distribution of other isoforms relies on heterodimerization partners. Furthermore, the ability of different TCF4 isoforms to regulate E-box controlled reporter gene transcription is varied depending on whether one or both of the two TCF4 transcription activation domains are present in the protein. Both TCF4 activation domains are able to activate transcription independently, but act synergistically in combination. CONCLUSIONS: Altogether, in this study we have described the inter-tissue variability of TCF4 expression in human and provided evidence

  14. A High Diversity in Chitinolytic and Chitosanolytic Species and Enzymes and Their Oligomeric Products Exist in Soil with a History of Chitin and Chitosan Exposure

    Directory of Open Access Journals (Sweden)

    Malathi Nampally

    2015-01-01

    Full Text Available Chitin is one of the most abundant biomolecules on earth, and its partially de-N-acetylated counterpart, chitosan, is one of the most promising biotechnological resources due to its diversity in structure and function. Recently, chitin and chitosan modifying enzymes (CCMEs have gained increasing interest as tools to engineer chitosans with specific functions and reliable performance in biotechnological and biomedical applications. In a search for novel CCME, we isolated chitinolytic and chitosanolytic microorganisms from soils with more than ten-years history of chitin and chitosan exposure and screened them for chitinase and chitosanase isoenzymes as well as for their patterns of oligomeric products by incubating their secretomes with chitosan polymers. Of the 60 bacterial strains isolated, only eight were chitinolytic and/or chitosanolytic, while 20 out of 25 fungal isolates were chitinolytic and/or chitosanolytic. The bacterial isolates produced rather similar patterns of chitinolytic and chitosanolytic enzymes, while the fungal isolates produced a much broader range of different isoenzymes. Furthermore, diverse mixtures of oligosaccharides were formed when chitosan polymers were incubated with the secretomes of select fungal species. Our study indicates that soils with a history of chitin and chitosan exposure are a good source of novel CCME for chitosan bioengineering.

  15. A High Diversity in Chitinolytic and Chitosanolytic Species and Enzymes and Their Oligomeric Products Exist in Soil with a History of Chitin and Chitosan Exposure

    Science.gov (United States)

    Nampally, Malathi; Rajulu, M. B. Govinda; Gillet, Dominique; Suryanarayanan, T. S.; Moerschbacher, Bruno B.

    2015-01-01

    Chitin is one of the most abundant biomolecules on earth, and its partially de-N-acetylated counterpart, chitosan, is one of the most promising biotechnological resources due to its diversity in structure and function. Recently, chitin and chitosan modifying enzymes (CCMEs) have gained increasing interest as tools to engineer chitosans with specific functions and reliable performance in biotechnological and biomedical applications. In a search for novel CCME, we isolated chitinolytic and chitosanolytic microorganisms from soils with more than ten-years history of chitin and chitosan exposure and screened them for chitinase and chitosanase isoenzymes as well as for their patterns of oligomeric products by incubating their secretomes with chitosan polymers. Of the 60 bacterial strains isolated, only eight were chitinolytic and/or chitosanolytic, while 20 out of 25 fungal isolates were chitinolytic and/or chitosanolytic. The bacterial isolates produced rather similar patterns of chitinolytic and chitosanolytic enzymes, while the fungal isolates produced a much broader range of different isoenzymes. Furthermore, diverse mixtures of oligosaccharides were formed when chitosan polymers were incubated with the secretomes of select fungal species. Our study indicates that soils with a history of chitin and chitosan exposure are a good source of novel CCME for chitosan bioengineering. PMID:26273652

  16. Identity, Diversity and Diversity Management

    DEFF Research Database (Denmark)

    Holck, Lotte; Muhr, Sara Louise; Villeseche, Florence

    2016-01-01

    The purpose of this paper is to examine the relationship between the identity and diversity literatures and discuss how a better understanding of the theoretical connections between the two informs both diversity research and diversity management practices. Design/methodology/approach – Literature...... review followed by a discussion of the theoretical and practical consequences of connecting the identity and diversity literatures. Findings – The authors inform future research in three ways. First, by showing how definitions of identity influence diversity theorizing in specific ways. Second......, the authors explore how such definitions entail distinct foci regarding how diversity should be analyzed and interventions actioned. Third, the authors discuss how theoretical coherence between definitions of identity and diversity perspectives – as well as knowledge about a perspective’s advantages...

  17. Application of next-generation sequencing technology to study genetic diversity and identify unique SNP markers in bread wheat from Kazakhstan.

    Science.gov (United States)

    Shavrukov, Yuri; Suchecki, Radoslaw; Eliby, Serik; Abugalieva, Aigul; Kenebayev, Serik; Langridge, Peter

    2014-09-28

    New SNP marker platforms offer the opportunity to investigate the relationships between wheat cultivars from different regions and assess the mechanism and processes that have led to adaptation to particular production environments. Wheat breeding has a long history in Kazakhstan and the aim of this study was to explore the relationship between key varieties from Kazakhstan and germplasm from breeding programs for other regions. The study revealed 5,898 polymorphic markers amongst ten cultivars, of which 2,730 were mapped in the consensus genetic map. Mapped SNP markers were distributed almost equally across the A and B genomes, with between 279 and 484 markers assigned to each chromosome. Marker coverage was approximately 10-fold lower in the D genome. There were 863 SNP markers identified as unique to specific cultivars, and clusters of these markers (regions containing more than three closely mapped unique SNPs) showed specific patterns on the consensus genetic map for each cultivar. Significant intra-varietal genetic polymorphism was identified in three cultivars (Tzelinnaya 3C, Kazakhstanskaya rannespelaya and Kazakhstanskaya 15). Phylogenetic analysis based on inter-varietal polymorphism showed that the very old cultivar Erythrospermum 841 was the most genetically distinct from the other nine cultivars from Kazakhstan, falling in a clade together with the American cultivar Sonora and genotypes from Central and South Asia. The modern cultivar Kazakhstanskaya 19 also fell into a separate clade, together with the American cultivar Thatcher. The remaining eight cultivars shared a single sub-clade but were categorised into four clusters. The accumulated data for SNP marker polymorphisms amongst bread wheat genotypes from Kazakhstan may be used for studying genetic diversity in bread wheat, with potential application for marker-assisted selection and the preparation of a set of genotype-specific markers.

  18. Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II

    Directory of Open Access Journals (Sweden)

    Archer John

    2012-03-01

    Full Text Available Abstract Background Next generation sequencing provides detailed insight into the variation present within viral populations, introducing the possibility of treatment strategies that are both reactive and predictive. Current software tools, however, need to be scaled up to accommodate for high-depth viral data sets, which are often temporally or spatially linked. In addition, due to the development of novel sequencing platforms and chemistries, each with implicit strengths and weaknesses, it will be helpful for researchers to be able to routinely compare and combine data sets from different platforms/chemistries. In particular, error associated with a specific sequencing process must be quantified so that true biological variation may be identified. Results Segminator II was developed to allow for the efficient comparison of data sets derived from different sources. We demonstrate its usage by comparing large data sets from 12 influenza H1N1 samples sequenced on both the 454 Life Sciences and Illumina platforms, permitting quantification of platform error. For mismatches median error rates at 0.10 and 0.12%, respectively, suggested that both platforms performed similarly. For insertions and deletions median error rates within the 454 data (at 0.3 and 0.2%, respectively were significantly higher than those within the Illumina data (0.004 and 0.006%, respectively. In agreement with previous observations these higher rates were strongly associated with homopolymeric stretches on the 454 platform. Outside of such regions both platforms had similar indel error profiles. Additionally, we apply our software to the identification of low frequency variants. Conclusion We have demonstrated, using Segminator II, that it is possible to distinguish platform specific error from biological variation using data derived from two different platforms. We have used this approach to quantify the amount of error present within the 454 and Illumina platforms in

  19. Diversity Management

    DEFF Research Database (Denmark)

    Ravazzani, Silvia

    2018-01-01

    discourse and practice, and possible overarching approaches guiding organizations. It goes on to elucidate elements linked to the implementation of diversity management: positive and negative outcomes, most spread practices including communication, and contingency factors shaping the understanding......This entry provides an overview of diversity management which, in the context of organizations, consists in the strategic process of harnessing the potential of all employees to create an inclusive environment and, at the same time, contribute to meeting organizational goals. The entry first...... describes the complex construct of diversity that has been variously conceptualized in the literature, embracing multiple social and informational diversity dimensions such as gender, age, culture, values, and workstyle. This is followed by illustration of the historical development of diversity-management...

  20. Generative Contexts

    Science.gov (United States)

    Lyles, Dan Allen

    Educational research has identified how science, technology, engineering, and mathematics (STEM) practice and education have underperforming metrics in racial and gender diversity, despite decades of intervention. These disparities are part of the construction of a culture of science that is alienating to these populations. Recent studies in a social science framework described as "Generative Justice" have suggested that the context of social and scientific practice might be modified to bring about more just and equitable relations among the disenfranchised by circulating the value they and their non-human allies create back to them in unalienated forms. What is not known are the underlying principles of social and material space that makes a system more or less generative. I employ an autoethnographic method at four sites: a high school science class; a farm committed to "Black and Brown liberation"; a summer program geared towards youth environmental mapping; and a summer workshop for Harlem middle school students. My findings suggest that by identifying instances where material affinity, participatory voice, and creative solidarity are mutually reinforcing, it is possible to create educational contexts that generate unalienated value, and circulate it back to the producers themselves. This cycle of generation may help explain how to create systems of justice that strengthen and grow themselves through successive iterations. The problem of lack of diversity in STEM may be addressed not merely by recruiting the best and the brightest from underrepresented populations, but by changing the context of STEM education to provide tools for its own systematic restructuring.

  1. Troubling Diversity?

    DEFF Research Database (Denmark)

    Jæger, Kirsten; Jensen, Annie Aarup

    2009-01-01

    are related to recent contributions to diversity management theory and intercultural communication theory, calling for a strengthened focus on the historical, political, and social dimensions of intercultural contact. In continuation of these trends, an alternative, theoretical framework...

  2. Understanding Diversity

    NARCIS (Netherlands)

    D.L. van Knippenberg (Daan)

    2007-01-01

    textabstractDaan van Knippenberg is Professor of Organizational Behavior at RSM Erasmus University, Erasmus University Rotterdam, The Netherlands. His research interests include work group performance, especially work group diversity and group decision making, leadership, in particular the roles of

  3. Gender Diversities

    DEFF Research Database (Denmark)

    Agustin, Lise Rolandsen; Siim, Birte

    2014-01-01

    The article analyses the European Year for Combating Poverty and Social Exclusion (2010) (EY 2010) with the aim of identifying the nature of gender diversities in EU policies. We argue that the EU handles issues related to gender and diversity in particular ways; this approach is characterized...... by non-citizen/citizen and redistribution/recognition divisions. Employing intersectionality as the methodological approach to gender diversities, the article shows how gender and ethnicity are articulated in the policy-making process which led to the adoption of EY 201, the activities undertaken during...... the EY 2010, and the evaluation of EY 2010. The case study is suitable for developing a dynamic multi-level model for analysing gendered diversities at the transnationmal level: It illustrates how the EU policy frame interacts with particular national contexts in promoting or hundering the advancement...

  4. Doing Diversity

    DEFF Research Database (Denmark)

    Just, Sine Nørholm; Christiansen, Tanja Juul

    2012-01-01

    invite audiences to take up subject positions, understood as combinations of identity and agency. Danish diversity management rhetoric functions as an illustrative example; in analyzing this type of rhetoric we show how subjects are called into restrained positions of similarity/difference and thereby...... demonstrate the explanatory potential of the performative framework. Subsequently, we discuss how the concept of personae may provide a basis for alternatives to the restrictive positioning that currently dominates diversity management rhetoric....

  5. Capturing Nature's Diversity

    Science.gov (United States)

    Pascolutti, Mauro; Campitelli, Marc; Nguyen, Bao; Pham, Ngoc; Gorse, Alain-Dominique; Quinn, Ronald J.

    2015-01-01

    Natural products are universally recognized to contribute valuable chemical diversity to the design of molecular screening libraries. The analysis undertaken in this work, provides a foundation for the generation of fragment screening libraries that capture the diverse range of molecular recognition building blocks embedded within natural products. Physicochemical properties were used to select fragment-sized natural products from a database of known natural products (Dictionary of Natural Products). PCA analysis was used to illustrate the positioning of the fragment subset within the property space of the non-fragment sized natural products in the dataset. Structural diversity was analysed by three distinct methods: atom function analysis, using pharmacophore fingerprints, atom type analysis, using radial fingerprints, and scaffold analysis. Small pharmacophore triplets, representing the range of chemical features present in natural products that are capable of engaging in molecular interactions with small, contiguous areas of protein binding surfaces, were analysed. We demonstrate that fragment-sized natural products capture more than half of the small pharmacophore triplet diversity observed in non fragment-sized natural product datasets. Atom type analysis using radial fingerprints was represented by a self-organizing map. We examined the structural diversity of non-flat fragment-sized natural product scaffolds, rich in sp3 configured centres. From these results we demonstrate that 2-ring fragment-sized natural products effectively balance the opposing characteristics of minimal complexity and broad structural diversity when compared to the larger, more complex fragment-like natural products. These naturally-derived fragments could be used as the starting point for the generation of a highly diverse library with the scope for further medicinal chemistry elaboration due to their minimal structural complexity. This study highlights the possibility to capture a

  6. PROS-1/Prospero Is a Major Regulator of the Glia-Specific Secretome Controlling Sensory-Neuron Shape and Function in C. elegans.

    Science.gov (United States)

    Wallace, Sean W; Singhvi, Aakanksha; Liang, Yupu; Lu, Yun; Shaham, Shai

    2016-04-19

    Sensory neurons are an animal's gateway to the world, and their receptive endings, the sites of sensory signal transduction, are often associated with glia. Although glia are known to promote sensory-neuron functions, the molecular bases of these interactions are poorly explored. Here, we describe a post-developmental glial role for the PROS-1/Prospero/PROX1 homeodomain protein in sensory-neuron function in C. elegans. Using glia expression profiling, we demonstrate that, unlike previously characterized cell fate roles, PROS-1 functions post-embryonically to control sense-organ glia-specific secretome expression. PROS-1 functions cell autonomously to regulate glial secretion and membrane structure, and non-cell autonomously to control the shape and function of the receptive endings of sensory neurons. Known glial genes controlling sensory-neuron function are PROS-1 targets, and we identify additional PROS-1-dependent genes required for neuron attributes. Drosophila Prospero and vertebrate PROX1 are expressed in post-mitotic sense-organ glia and astrocytes, suggesting conserved roles for this class of transcription factors. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  7. The Apoplastic Secretome of Trichoderma virens During Interaction With Maize Roots Shows an Inhibition of Plant Defence and Scavenging Oxidative Stress Secreted Proteins

    Directory of Open Access Journals (Sweden)

    Guillermo Nogueira-Lopez

    2018-04-01

    Full Text Available In Nature, almost every plant is colonized by fungi. Trichoderma virens is a biocontrol fungus which has the capacity to behave as an opportunistic plant endophyte. Even though many plants are colonized by this symbiont, the exact mechanisms by which Trichoderma masks its entrance into its plant host remain unknown, but likely involve the secretion of different families of proteins into the apoplast that may play crucial roles in the suppression of plant immune responses. In this study, we investigated T. virens colonization of maize roots under hydroponic conditions, evidencing inter- and intracellular colonization by the fungus and modifications in root morphology and coloration. Moreover, we show that upon host penetration, T. virens secretes into the apoplast an arsenal of proteins to facilitate inter- and intracellular colonization of maize root tissues. Using a gel-free shotgun proteomics approach, 95 and 43 secretory proteins were identified from maize and T. virens, respectively. A reduction in the maize secretome (36% was induced by T. virens, including two major groups, glycosyl hydrolases and peroxidases. Furthermore, T. virens secreted proteins were mainly involved in cell wall hydrolysis, scavenging of reactive oxygen species and secondary metabolism, as well as putative effector-like proteins. Levels of peroxidase activity were reduced in the inoculated roots, suggesting a strategy used by T. virens to manipulate host immune responses. The results provide an insight into the crosstalk in the apoplast which is essential to maintain the T. virens-plant interaction.

  8. A secretome view of colonisation factors in Shiga toxin-encoding Escherichia coli (STEC): from enterohaemorrhagic E. coli (EHEC) to related enteropathotypes.

    Science.gov (United States)

    Monteiro, Ricardo; Ageorges, Valentin; Rojas-Lopez, Maricarmen; Schmidt, Herbert; Weiss, Agnes; Bertin, Yolande; Forano, Evelyne; Jubelin, Grégory; Henderson, Ian R; Livrelli, Valérie; Gobert, Alain P; Rosini, Roberto; Soriani, Marco; Desvaux, Mickaël

    2016-08-01

    Shiga toxin-encoding Escherichia coli (STEC) regroup strains that carry genes encoding Shiga toxin (Stx). Among intestinal pathogenic E. coli, enterohaemorrhagic E. coli (EHEC) constitute the major subgroup of virulent STEC. EHEC cause serious human disease such as haemorrhagic colitis and haemolytic-uremic syndrome. While EHEC have evolved from enteropathogenic E. coli, hybrids with enteroaggregative E. coli have recently emerged. Of note, some enteroinvasive E. coli also belong to the STEC group. While the LEE (locus of enterocyte effacement) is a key and prominent molecular determinant in the pathogenicity, neither all EHEC nor STEC contain the LEE, suggesting that they possess additional virulence and colonisation factors. Currently, nine protein secretion systems have been described in diderm-lipopolysaccharide bacteria (archetypal Gram-negative) and can be involved in the secretion of extracellular effectors, cell-surface proteins or assembly of cell-surface organelles, such as flagella or pili. In this review, we focus on the secretome of STEC and related enteropathotypes, which are relevant to the colonisation of biotic and abiotic surfaces. Considering the wealth of potential protein trafficking mechanisms, the different combinations of colonisation factors and modulation of their expression is further emphasised with regard to the ecophysiology of STEC. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Working Paper 78: Policy recommendations to the EU Commission, Changing families and sustainable societies: Policy contexts and diversity over the life course and across generations (2017) : Collaborative research project financed by the European Union’s Seventh Framework Programme 2013-2017 (Grant no. 320116, FP7-SSH-2012-1)

    OpenAIRE

    Carlson, Laura; Oláh, Livia; Hobson, Barbara

    2017-01-01

    These policy recommendations are based on main findings of the largescale EU Seventh Framework project, Changing families and sustainable societies: Policy contexts and diversity over the life course and across generations (FamiliesAndSocieties). This executive summary highlights a few of the key policy recommendations: • Policy makers ought to be aware of the remarkable diversity of family forms and relationships in contemporary Europe, and aim for a better understanding of the nature and me...

  10. Understanding the degradation of Congo red and bacterial diversity in an air-cathode microbial fuel cell being evaluated for simultaneous azo dye removal from wastewater and bioelectricity generation.

    Science.gov (United States)

    Sun, Jian; Li, Youming; Hu, Yongyou; Hou, Bin; Zhang, Yaping; Li, Sizhe

    2013-04-01

    We investigated the mechanism of Congo red degradation and bacterial diversity in a single-chambered microbial fuel cell (MFC) incorporating a microfiltration membrane and air-cathode. The MFC was operated continuously for more than 4 months using a mixture of Congo red and glucose as fuel. We demonstrated that the Congo red azo bonds were reduced at the anode to form aromatic amines. This is consistent with the known mechanism of anaerobic biodegradation of azo dyes. The MFC developed a less dense biofilm at the anode in the presence of Congo red compared to its absence indicating that Congo red degradation negatively affected biofilm formation. Denaturing gradient gel electrophoresis and direct 16S ribosomal DNA gene nucleotide sequencing revealed that the microbial communities differed depending on whether Congo red was present in the MFC. Geobacter-like species known to generate electricity were detected in the presence or absence of Congo red. In contrast, Azospirillum, Methylobacterium, Rhodobacter, Desulfovibrio, Trichococcus, and Bacteroides species were only detected in its presence. These species were most likely responsible for degrading Congo red.

  11. When Generations Collide

    Science.gov (United States)

    Fogg, Piper

    2008-01-01

    When four generations converge in the academic workplace, it can create serious culture clashes. It is happening across college campuses--in offices as diverse as admissions, student affairs, legal affairs, and technology. It is especially striking in the faculty ranks, where generational challenges have extra significance amid recruiting efforts,…

  12. Transcriptome and secretome analyses of the wood decay fungus Wolfiporia cocos support alternative mechanisms of lignocellulose conversion

    Science.gov (United States)

    Jill Gaskell; Robert A. Blanchette; Philip E. Stewart; Sandra Splinter BonDurant; Marie Adams; Grzegorz Sabat; Philip Kersten; Daniel Cullen

    2016-01-01

    Certain wood decay basidiomycetes, collectively referred to as brown rot fungi, rapidly depolymerize cellulose while leaving behind the bulk of cell wall lignin as a modified residue. The mechanism(s) employed is unclear, but considerable evidence implicates the involvement of diffusible oxidants generated via Fenton-like chemistry. Toward a better understanding of...

  13. Diversity: The Business Case?

    Science.gov (United States)

    Jones, B.

    2013-12-01

    Understanding perceptions and managing expectations are learnable skills that do not necessarily come with project funding. Finding life balance as one moves through a STEM career path poses unique challenges that require a certain skill set that is not always intuitive. Some of those challenges include: selecting grad or post doc positions; balancing work and family commitments; and dealing with employer/advisor perceptions and expectations. As in nature, the STEM enterprise requires multiple perspectives to flourish (necessity of peer review), and in a changing environment (e.g., budget, generations, technology, etc.), embracing diversity in thought and application may help drive the evolution of STEM in the U.S. Many Agencies and organizations have ';workforce development' programs that focus on preparing the next generation of scientists and engineers at the graduate and undergraduate level that focus on preparing students in the diverse disciplines that are unique to those Agency and organizational missions. While financial support certainly is critical to assist students in Science Technology Engineering and Mathematics (STEM) and other fields, professional development is just as important to equip students with a balanced arsenal of tactics to be successful professionals in the STEM workforce of today. Success in these efforts requires an honest look at the issue of inequality in the STEM ecosystem... meaning, what initiatives have been successful in addressing the imbalance in sources of thought and application, therefore promoting the importance of diversity.

  14. Strength in diversity

    CERN Multimedia

    2012-01-01

    Diversity has always been science’s big secret, yet it’s a secret we’ve always been keen to share. CERN was founded on the basis of bringing a diverse mix of people together to pursue common aims, and it’s one of the things that’s driven this Organization’s success over the decades.   Now, we are launching a new diversity programme aimed at strengthening our tradition of inclusiveness. This programme is being launched with a range of key goals in mind for the 2012-2014 timeframe. We’ll be striving to achieve a fair gender balance across all professional categories, and to provide strong gender role models across the Organization. We’ll be improving our career development processes to allow people to progress through both technical and managerial pathways, and we’ll be re-launching workshops that bring people from diverse professions and generations together to share their experience on key aspects of lif...

  15. Diverse Multilateralism

    DEFF Research Database (Denmark)

    Wuthnow, Joel; Li, Xin; Qi, Lingling

    2012-01-01

    This article addresses Chinas multilateral diplomacy by identifying four distinct strategies: watching, engaging, circumventing, and shaping. The typology builds on two literatures: power transition theory, and the more recent “assertiveness” discourse in the West. Drawing from a range of cases...... in both the economic and security domains, the article argues that China’s multilateralism is diverse, and that it cannot be un-problematically characterized as either status-quo or revisionist in nature. However, the general trend appears to be towards engagement, but with an assertive tact as China......’s interests become further entangled in the business of international institutions....

  16. Cardiac Stem Cell Secretome Protects Cardiomyocytes from Hypoxic Injury Partly via Monocyte Chemotactic Protein-1-Dependent Mechanism

    Directory of Open Access Journals (Sweden)

    Chi-Yeon Park

    2016-05-01

    Full Text Available Cardiac stem cells (CSCs were known to secrete diverse paracrine factors leading to functional improvement and beneficial left ventricular remodeling via activation of the endogenous pro-survival signaling pathway. However, little is known about the paracrine factors secreted by CSCs and their roles in cardiomyocyte survival during hypoxic condition mimicking the post-myocardial infarction environment. We established Sca-1+/CD31− human telomerase reverse transcriptase-immortalized CSCs (Sca-1+/CD31− CSCshTERT, evaluated their stem cell properties, and paracrine potential in cardiomyocyte survival during hypoxia-induced injury. Sca-1+/CD31− CSCshTERT sustained proliferation ability even after long-term culture exceeding 100 population doublings, and represented multi-differentiation potential into cardiomyogenic, endothelial, adipogenic, and osteogenic lineages. Dominant factors secreted from Sca-1+/CD31− CSCshTERT were EGF, TGF-β1, IGF-1, IGF-2, MCP-1, HGF R, and IL-6. Among these, MCP-1 was the most predominant factor in Sca-1+/CD31− CSCshTERT conditioned medium (CM. Sca-1+/CD31− CSCshTERT CM increased survival and reduced apoptosis of HL-1 cardiomyocytes during hypoxic injury. MCP-1 silencing in Sca-1+/CD31− CSCshTERT CM resulted in a significant reduction in cardiomyocyte apoptosis. We demonstrated that Sca-1+/CD31− CSCshTERT exhibited long-term proliferation capacity and multi-differentiation potential. Sca-1+/CD31− CSCshTERT CM protected cardiomyocytes from hypoxic injury partly via MCP-1-dependent mechanism. Thus, they are valuable sources for in vitro and in vivo studies in the cardiovascular field.

  17. Enzyme Activities of Two Recombinant Heme-Containing Peroxidases, TvDyP1 and TvVP2, Identified from the Secretome of Trametes versicolor.

    Science.gov (United States)

    Amara, Sawsan; Perrot, Thomas; Navarro, David; Deroy, Aurélie; Benkhelfallah, Amine; Chalak, Amani; Daou, Marianne; Chevret, Didier; Faulds, Craig B; Berrin, Jean-Guy; Morel-Rouhier, Mélanie; Gelhaye, Eric; Record, Eric

    2018-04-15

    Trametes versicolor is a wood-inhabiting agaricomycete known for its ability to cause strong white-rot decay on hardwood and for its high tolerance of phenolic compounds. The goal of the present work was to gain insights into the molecular biology and biochemistry of the heme-including class II and dye-decolorizing peroxidases secreted by this fungus. Proteomic analysis of the secretome of T. versicolor BRFM 1218 grown on oak wood revealed a set of 200 secreted proteins, among which were the dye-decolorizing peroxidase Tv DyP1 and the versatile peroxidase Tv VP2. Both peroxidases were heterologously produced in Escherichia coli , biochemically characterized, and tested for the ability to oxidize complex substrates. Both peroxidases were found to be active against several substrates under acidic conditions, and Tv DyP1 was very stable over a relatively large pH range of 2.0 to 6.0, while Tv VP2 was more stable at pH 5.0 to 6.0 only. The thermostability of both enzymes was also tested, and Tv DyP1 was globally found to be more stable than Tv VP2. After 180 min of incubation at temperatures ranging from 30 to 50°C, the activity of Tv VP2 drastically decreased, with 10 to 30% of the initial activity retained. Under the same conditions, Tv DyP1 retained 20 to 80% of its enzyme activity. The two proteins were catalytically characterized, and Tv VP2 was shown to accept a wider range of reducing substrates than Tv DyP1. Furthermore, both enzymes were found to be active against two flavonoids, quercetin and catechin, found in oak wood, with Tv VP2 displaying more rapid oxidation of the two compounds. They were tested for the ability to decolorize five industrial dyes, and Tv VP2 presented a greater ability to oxidize and decolorize the dye substrates than Tv DyP1. IMPORTANCE Trametes versicolor is a wood-inhabiting agaricomycete known for its ability to cause strong white-rot decay on hardwood and for its high tolerance of phenolic compounds. Among white-rot fungi, the

  18. An Algorithmic Diversity Diet?

    DEFF Research Database (Denmark)

    Sørensen, Jannick Kirk; Schmidt, Jan-Hinrik

    2016-01-01

    diet system however triggers not only the classic discussion of the reach – distinctiveness balance for PSM, but also shows that ‘diversity’ is understood very differently in algorithmic recommender system communities than it is editorially and politically in the context of PSM. The design...... of a diversity diet system generates questions not just about editorial power, personal freedom and techno-paternalism, but also about the embedded politics of recommender systems as well as the human skills affiliated with PSM editorial work and the nature of PSM content....

  19. Teaching Diversity

    Directory of Open Access Journals (Sweden)

    Kay Young McChesney

    2015-10-01

    Full Text Available This article is targeted to faculty teaching race and ethnicity, racism, diversity, and multicultural courses. Many students equate race with skin color. The premise of this article is that to teach students about the social construction of race, teachers must first know enough science to teach students that race is not biological. This article examines the biology of race by showing how advances in DNA sequencing led to genetics research that supports arguments that race is not biological. DNA comparisons show that all human populations living today are one species that came from Africa. The article explains the migration of humans out of Africa about 60,000 years ago and how they populated Australia, then Asia, Europe, and the Americas. The article shows how recent research maps the timing of the migration and admixture of specific population groups into Europe and India. The article shows how a mutation in one nucleotide can result in a trait like blue eyes, or Hemoglobin S (which confers resistance to malaria, which can be subject to evolution through natural selection. DNA comparisons show how natural selection shaped the genetics of human skin color to adapt to less UV light in the northern latitudes of Europe and Asia. The article shows that there is no relation between skin color or other “racial” characteristics and complex traits like intelligence. The science in this article will help teachers explain that as race is not biological, race is socially constructed and culturally enacted.

  20. Diversity Gain through Antenna Blocking

    Directory of Open Access Journals (Sweden)

    V. Dehghanian

    2012-01-01

    Full Text Available As part of the typical usage mode, interaction between a handheld receiver antenna and the operator's RF absorbing body and nearby objects is known to generate variability in antenna radiation characteristics through blocking and pattern changes. It is counterintuitive that random variations in blocking can result in diversity gain of practical applicability. This diversity gain is quantified from a theoretical and experimental perspective. Measurements carried out at 1947.5 MHz verify the theoretical predictions, and a diversity gain of 3.1 dB was measured through antenna blocking and based on the utilized measurement setup. The diversity gain can be exploited to enhance signal detectability of handheld receivers based on a single antenna in indoor multipath environments.

  1. Diverse Classrooms, Diverse Curriculum, Diverse Complications: Three Teacher Perspectives

    Science.gov (United States)

    Ungemah, Lori D.

    2015-01-01

    Racial, ethnic, linguistic, and religious diversity continues to increase in classrooms. Many call for a more diverse curriculum, but curricular diversity brings its own challenges to both teachers and students. These three vignettes are drawn from my ethnographic data at Atlantic High School in Brooklyn, New York, where I worked for ten years as…

  2. Civilizing Teacher Education? Learning with Diversity

    Science.gov (United States)

    Allan, Julie

    2011-01-01

    Social capital theorist Robert Putnam (2007) argued that diversity produces fear and leads people to disconnect from one another. For student teachers, diversity of whatever kind--ethnicity, religion, class, disability, gender, or sexuality--generates fear and an expectation that it has to be managed. Civic education within teacher education has a…

  3. Does staff diversity imply openness to diversity?

    DEFF Research Database (Denmark)

    Lauring, Jakob; Selmer, Jan

    2013-01-01

    Purpose – Post-secondary educational organizations are currently some of the most diverse settings to be found. However, few educational studies have dealt with staff diversity and hardly any has looked outside the USA. The purpose of this paper is to present a study of members of international...... university departments in Denmark. The authors set out to investigate the relationship between different types of staff diversity and openness to diversity in terms of linguistic, visible, value, and informational heterogeneity. Design/methodology/approach – This study uses responses from 489 staff members......, was unrelated or negatively associated with positive diversity attitudes. Originality/value – Few studies deal with the role of staff diversity and no prior studies the authors know of have examined the link between diversity types and openness to diversity....

  4. Managing Workplace Diversity

    OpenAIRE

    Harold Andrew Patrick; Vincent Raj Kumar

    2012-01-01

    Diversity management is a process intended to create and maintain a positive work environment where the similarities and differences of individuals are valued. The literature on diversity management has mostly emphasized on organization culture; its impact on diversity openness; human resource management practices; institutional environments and organizational contexts to diversity-related pressures, expectations, requ...

  5. Intersectionality, Diversity and Gender

    DEFF Research Database (Denmark)

    Agustin, Lise Rolandsen; Siim, Birte

    2016-01-01

    In the discourses of Danish politicians on ethno-national diversity and integration, the notion of diversity is gendered, especially the articulation of the ‘working woman’ and her labor market participation. Equality, diversity and gender are, thus, intertwined in political, discursive......’ debates about gender and diversity within the national and transnational European Polity....

  6. U.S. Army’s Diversity Strategic Plan: The Attitude and Knowledge of Today’s U.S. Army Majors

    Science.gov (United States)

    2013-06-14

    2000 Source: Jamie Notter, Generational Diversity in the Workplace , Notter Consulting http://www.notterconsulting.com/Articles...astute Army.23 Ethnic Diversity. This is also referred to as multiculturalism that relates to multiple cultures. It relates to diverse population...in the workplace . Generational Diversity. This is sometimes stated as generational gap or age diversity. This refers to a group of people defined

  7. What factors shape genetic diversity in cetaceans?

    Science.gov (United States)

    Vachon, Felicia; Whitehead, Hal; Frasier, Timothy R

    2018-02-01

    Understanding what factors drive patterns of genetic diversity is a central aspect of many biological questions, ranging from the inference of historical demography to assessing the evolutionary potential of a species. However, as a larger number of datasets have become available, it is becoming clear that the relationship between the characteristics of a species and its genetic diversity is more complex than previously assumed. This may be particularly true for cetaceans, due to their relatively long lifespans, long generation times, complex social structures, and extensive ranges. In this study, we used microsatellite and mitochondrial DNA data from a systematic literature review to produce estimates of diversity for both markers across 42 cetacean species. Factors relating to demography, distribution, classification, biology, and behavior were then tested using phylogenetic methods and linear models to assess their relative influence on the genetic diversity of both marker types. The results show that while relative nuclear diversity is correlated with population size, mitochondrial diversity is not. This is particularly relevant given the widespread use of mitochondrial DNA to infer historical demography. Instead, mitochondrial diversity was mostly influenced by the range and social structure of the species. In addition to population size, habitat type (neritic vs. oceanic) had a significant correlation with relative nuclear diversity. Combined, these results show that many often-unconsidered factors are likely influencing patterns of genetic diversity in cetaceans, with implications regarding how to interpret, and what can be inferred from, existing patterns of diversity.

  8. Generating Units

    Data.gov (United States)

    Department of Homeland Security — Generating Units are any combination of physically connected generators, reactors, boilers, combustion turbines, and other prime movers operated together to produce...

  9. Diversity Statements: How Faculty Applicants Address Diversity

    Science.gov (United States)

    Schmaling, Karen B.; Trevino, Amira Y.; Lind, Justin R.; Blume, Arthur W.; Baker, Dana L.

    2015-01-01

    The purpose of the present study was to examine application materials for assistant professor positions in 3 academic disciplines. Applicants were asked to write a diversity statement describing how they would advance diversity through their research, teaching, and service. The sample included application materials submitted by 191 candidates for…

  10. CERN Diversity Newsletter - September 2016

    CERN Document Server

    Guinot, Genevieve

    2016-01-01

    Quarterly CERN Diversity Newsletter, informing on recent and ongoing diversity activities, and interesting reads, videos and other links related to diversity. Subscribe here: https://diversity.web.cern.ch/2015/07/subscribe-diversity-newsletter

  11. CERN Diversity Newsletter - April 2017

    CERN Document Server

    AUTHOR|(CDS)2069427; Koutava, Ioanna; CERN. Geneva. HR Department

    2017-01-01

    The CERN Diversity Newsletter, informing on recent and ongoing diversity activities, and interesting reads, videos and other links related to diversity. Subscribe here: https://diversity.web.cern.ch/2015/07/subscribe-diversity-newsletter

  12. CERN Diversity Newsletter - March 2016

    CERN Document Server

    Kaltenhauser, Kristin; CERN. Geneva. HR Department

    2016-01-01

    Quarterly CERN Diversity Newsletter, informing on recent and ongoing diversity activities, and interesting reads, videos and other links related to diversity. Subscribe here: https://diversity.web.cern.ch/2015/07/subscribe-diversity-newsletter

  13. Diversity as Polyphony

    DEFF Research Database (Denmark)

    Trittin, Hannah; Schoeneborn, Dennis

    2017-01-01

    In this paper, we propose reconceptualizing diversity management from a communication-centered perspective. We base our proposal on the observation that the literature on diversity management, both in the instrumental and critical traditions, is primarily concerned with fostering the diversity...... as the range of individual opinions and societal discourses that get expressed and can find resonance in organizational settings. We contribute to the literature on diversity management by moving away from a focus on individual-bound and inalterable criteria of diversity and toward a reconceptualization...... of diversity management as dynamic processes of voice articulation and mediation...

  14. Hybrid diversity method utilizing adaptive diversity function for recovering unknown aberrations in an optical system

    Science.gov (United States)

    Dean, Bruce H. (Inventor)

    2009-01-01

    A method of recovering unknown aberrations in an optical system includes collecting intensity data produced by the optical system, generating an initial estimate of a phase of the optical system, iteratively performing a phase retrieval on the intensity data to generate a phase estimate using an initial diversity function corresponding to the intensity data, generating a phase map from the phase retrieval phase estimate, decomposing the phase map to generate a decomposition vector, generating an updated diversity function by combining the initial diversity function with the decomposition vector, generating an updated estimate of the phase of the optical system by removing the initial diversity function from the phase map. The method may further include repeating the process beginning with iteratively performing a phase retrieval on the intensity data using the updated estimate of the phase of the optical system in place of the initial estimate of the phase of the optical system, and using the updated diversity function in place of the initial diversity function, until a predetermined convergence is achieved.

  15. Managing Workplace Diversity

    Directory of Open Access Journals (Sweden)

    Harold Andrew Patrick

    2012-04-01

    Full Text Available Diversity management is a process intended to create and maintain a positive work environment where the similarities and differences of individuals are valued. The literature on diversity management has mostly emphasized on organization culture; its impact on diversity openness; human resource management practices; institutional environments and organizational contexts to diversity-related pressures, expectations, requirements, and incentives; perceived practices and organizational outcomes related to managing employee diversity; and several other issues. The current study examines the potential barriers to workplace diversity and suggests strategies to enhance workplace diversity and inclusiveness. It is based on a survey of 300 IT employees. The study concludes that successfully managing diversity can lead to more committed, better satisfied, better performing employees and potentially better financial performance for an organization.

  16. Diversity is our strength!

    Science.gov (United States)

    Rivers, Rose; Freeman, James

    2002-01-01

    Valuing and appreciating diversity are key requirements for health care organizations faced with increasingly diverse workforces and patient populations. Diversity issues are central to effectively functioning teams, patient outcomes, staff satisfaction, recruitment, and retention. Shands HealthCare, a health care system containing a large teaching medical center and several community hospitals and clinics centered around Gainesville, Florida, made a commitment to take the necessary steps to make diversity a priority and strategic initiative. A systemwide diversity initiative was launched in 1998. Diversity was defined, and organizational leaders were developed as "Ambassadors for Diversity." The Ambassadors developed an extensive training program that all staff and managers attend upon hiring. The primary goal of the program is to create a culture of respect and appreciation for diversity. Over 2,500 employees and managers have attended the training.

  17. International diversity management

    DEFF Research Database (Denmark)

    Lauring, Jakob

    2013-01-01

    While the concern with demographic diversity in organizations has increased during recent years, international diversity management still remains an understudied area. This is unfortunate since the transfer of diversity management practices within multinational corporations faces particular...... challenges in balancing between global integration and local responsiveness. The aim of this paper is to illustrate some of the central problems that multinational corporations need to deal with when transferring diversity management practices from headquarters to local subsidiaries. This is illustrated...

  18. Leadership and Diversity

    Science.gov (United States)

    Coleman, Marianne

    2012-01-01

    As part of the special edition recognizing the 40th anniversary of "Educational Management Administration & Leadership" this article reviews the coverage of leadership and diversity issues in the journal. The majority of articles concerning diversity have focused on gender, with attention turning to the wider concept of diversity since the year…

  19. Diversity cognition and climates

    NARCIS (Netherlands)

    van Knippenberg, D.; Homan, A.C.; van Ginkel, W.; Roberson, Q.M.

    2013-01-01

    Demographic diversity at work can yield performance benefits but also invite psychological disengagement and be a source of interpersonal tension. In managing this double-edged sword of demographic diversity, the role of diversity cognition (beliefs, attitudes) and climates seems particularly

  20. An investigation of the relationship between innovation and cultural diversity.

    Science.gov (United States)

    Kandler, Anne; Laland, Kevin N

    2009-08-01

    In this paper we apply reaction-diffusion models to explore the relationship between the rate of behavioural innovation and the level of cultural diversity. We investigate how both independent invention and the modification and refinement of established innovations impact on cultural dynamics and diversity. Further, we analyse these relationships in the presence of biases in cultural learning and find that the introduction of new variants typically increases cultural diversity substantially in the short term, but may decrease long-term diversity. Independent invention generally supports higher levels of cultural diversity than refinement. Repeated patterns of innovation through refinement generate characteristic oscillating trends in diversity, with increasing trends towards greater average diversity observed for medium but not low innovation rates. Conformity weakens the relationship between innovation and diversity. The level of cultural diversity, and pattern of temporal dynamics, potentially provide clues as to the underlying process, which can be used to interpret empirical data.

  1. Personalized medicine and human genetic diversity.

    Science.gov (United States)

    Lu, Yi-Fan; Goldstein, David B; Angrist, Misha; Cavalleri, Gianpiero

    2014-07-24

    Human genetic diversity has long been studied both to understand how genetic variation influences risk of disease and infer aspects of human evolutionary history. In this article, we review historical and contemporary views of human genetic diversity, the rare and common mutations implicated in human disease susceptibility, and the relevance of genetic diversity to personalized medicine. First, we describe the development of thought about diversity through the 20th century and through more modern studies including genome-wide association studies (GWAS) and next-generation sequencing. We introduce several examples, such as sickle cell anemia and Tay-Sachs disease that are caused by rare mutations and are more frequent in certain geographical populations, and common treatment responses that are caused by common variants, such as hepatitis C infection. We conclude with comments about the continued relevance of human genetic diversity in medical genetics and personalized medicine more generally. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  2. Instant Generation

    Science.gov (United States)

    Loveland, Elaina

    2017-01-01

    Generation Z students (born between 1995-2010) have replaced millennials on college campuses. Generation Z students are entrepreneurial, desire practical skills with their education, and are concerned about the cost of college. This article presents what need to be known about this new generation of students.

  3. Isotope generator

    International Nuclear Information System (INIS)

    1979-01-01

    The patent describes an isotope generator incorporating the possibility of stopping elution before the elution vessel is completely full. Sterile ventilation of the whole system can then occur, including of both generator reservoir and elution vessel. A sterile, and therefore pharmaceutically acceptable, elution fluid is thus obtained and the interior of the generator is not polluted with non-sterile air. (T.P.)

  4. The diversity challenge in directed protein evolution.

    Science.gov (United States)

    Wong, Tuck Seng; Zhurina, Daria; Schwaneberg, Ulrich

    2006-05-01

    Over the past decade, we have witnessed a bloom in the field of evolutive protein engineering which is fueled by advances in molecular biology techniques and high-throughput screening technology. Directed protein evolution is a powerful algorithm using iterative cycles of random mutagenesis and screening for tailoring protein properties to our needs in industrial applications and for elucidating proteins' structure function relationships. This review summarizes, categorizes and discusses advantages and disadvantages of random mutagenesis methods used for generating genetic diversity. These random mutagenesis methods have been classified into four main categories depending on the method employed for nucleotide substitutions: enzyme based methods (Category I), synthetic chemistry based methods (Category II), whole cell methods (Category III) and combined methods (Category I-II, I-III and II-III). The basic principle of each method is discussed and varied mutagenic conditions are summarized in Tables and compared (benchmarked) to each other in terms of: mutational bias, controllable mutation frequency, ability to generate consecutive nucleotide substitutions and subset diversity, dependency on gene length, technical simplicity/robustness and cost-effectiveness. The latter comparison shows how highly-biased and limited current diversity creating methods are. Based on these limitations, strategies for generating diverse mutant libraries are proposed and discussed (RaMuS-Flowchart; KISS principle). We hope that this review provides, especially for researchers just entering the field of directed evolution, a guide for developing successful directed evolution strategies by selecting complementary methods for generating diverse mutant libraries.

  5. Linking Diversity and Differentiation

    Directory of Open Access Journals (Sweden)

    Hans-Rolf Gregorius

    2010-03-01

    Full Text Available Generally speaking, the term differentiation refers to differences between collections for the distribution of specified traits of their members, while diversity deals with (effective numbers of trait states (types. Counting numbers of types implies discrete traits such as alleles and genotypes in population genetics or species and taxa in ecology. Comparisons between the concepts of differentiation and diversity therefore primarily refer to discrete traits. Diversity is related to differentiation through the idea that the total diversity of a subdivided collection should be composed of the diversity within the subcollections and a complement called “diversity between subcollections”. The idea goes back to the perception that the mixing of differentiated collections increases diversity. Several existing concepts of “diversity between subcollections” are based on this idea. Among them, β-diversity and fixation (inadvertently called differentiation are the most prominent in ecology and in population genetics, respectively. The pertaining measures are shown to quantify the effect of differentiation in terms of diversity components, though from a dual perspective: the classical perspective of differentiation between collections for their type compositions, and the reverse perspective of differentiation between types for their collection affiliations. A series of measures of diversity-oriented differentiation is presented that consider this dual perspective at two levels of diversity partitioning: the overall type or subcollection diversity and the joint type-subcollection diversity. It turns out that, in contrast with common notions, the measures of fixation (such as FST or GST refer to the perspective of type rather than subcollection differentiation. This unexpected observation strongly suggests that the popular interpretations of fixation measures must be reconsidered.

  6. Generational Differences in Work Attitudes : A comparative analysis of Generation Y and preceding generations from companies in Sweden

    OpenAIRE

    Sajjadi, Amir; Åkesson Castillo, Lars Christian Felipe; Sun, Bicen

    2012-01-01

    Introduction: A population that can live and work longer has resulted in a wider range of generations being active in the workplace simultaneously and the diverse multi-generational work environment is a new challenge for human resource management. The most recent generation that is entering the job market is Generation Y, which is also referred to as Millennials. Currently, organizations and Human Resource departments are facing the issue of Generation Y entering the workforce and the issue ...

  7. Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity.

    Science.gov (United States)

    Pardikes, Nicholas A; Lumpkin, Will; Hurtado, Paul J; Dyer, Lee A

    2018-01-01

    Most of earth's biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships

  8. Tagging like Humans: Diverse and Distinct Image Annotation

    KAUST Repository

    Wu, Baoyuan

    2018-03-31

    In this work we propose a new automatic image annotation model, dubbed {\\\\bf diverse and distinct image annotation} (D2IA). The generative model D2IA is inspired by the ensemble of human annotations, which create semantically relevant, yet distinct and diverse tags. In D2IA, we generate a relevant and distinct tag subset, in which the tags are relevant to the image contents and semantically distinct to each other, using sequential sampling from a determinantal point process (DPP) model. Multiple such tag subsets that cover diverse semantic aspects or diverse semantic levels of the image contents are generated by randomly perturbing the DPP sampling process. We leverage a generative adversarial network (GAN) model to train D2IA. Extensive experiments including quantitative and qualitative comparisons, as well as human subject studies, on two benchmark datasets demonstrate that the proposed model can produce more diverse and distinct tags than the state-of-the-arts.

  9. The Advising Workplace: Generational Differences and Challenges

    Science.gov (United States)

    Gordon, Virginia; Steele, Peg

    2005-01-01

    The American workplace today is unlike any other in history because for the first time it is made up of four distinct generations. The advising workplaces on today's college campuses mirror this generational diversity. Four generations and their different perceptions of work attitudes and values, management expectations, communication patterns,…

  10. Putting Diversity to Work

    DEFF Research Database (Denmark)

    Holck, Lotte

    2016-01-01

    Purpose: The purpose of this article is to critically explore why a diversity agenda in favor of equal opportunities failed despite apparent organizational support and commitment to diversity. Design/methodology/approach: Drawing on data from a municipal center, this study inquires into how....... Accordingly, change efforts must necessarily address diversity in a situated perspective and as intersecting with key organizational power dynamics gaining impetus from macro discourses on diversity and difference. Originality/value: Few critical diversity scholars engage with practitioners and reflect...... organizational dynamics of power and hierarchy influence change efforts to alter practices of inequality. The study is positioned within critical diversity research and structured around an analysis of the researcher’s fieldwork experiences. Findings: The analysis examines into why change efforts failed despite...

  11. Media Diversity in Deutschland

    OpenAIRE

    Bayer, Julia

    2013-01-01

    An der Schnittstelle von Ethnologie und Journalismus untersucht die Arbeit die Entwicklungen und Potenziale von "Media Diversity" für die deutschen Medien. Unter dem Begriff Media Diversity entwickelt sich seit einigen Jahren ein relativ neuer und vielversprechender Ansatz, die etablierten Konventionen medialer Berichterstattung herauszufordern und um andere Perspektiven zu erweitern. Fürs Erste lässt sich Media Diversity als Konzept skizzieren, das beansprucht, die in einer Gesellschaft best...

  12. Diversity in marketing practice

    OpenAIRE

    Torres, Ann Marie

    2009-01-01

    Theory development in marketing has received periodic debate. In the spirit of reappraisal, this thesis endeavours to explain the nature of diversity in marketing practice found among firms and the manner in which marketing practice is related to organisational performance. The specific research goals are to explore: the nature of diversity in marketing practice, as linked to strategic archetypes; whether there is evidence of order in the diversity of marketing practice that can be linked to ...

  13. Diversity does not travel!

    DEFF Research Database (Denmark)

    Lund, Rebecca; Meriläinen, Susan; Tienari, Janne

    2013-01-01

    In this chapter we offer insights into the social construction of diversity in Finnish organizations and society. In Finnish organizations, gender is highlighted while other markers of diversity are blotted out. 'Non-Finns' become subject to cultural assimilation. The US-based concept of Diversit...... Management becomes adopted and adapted in particular ways. Standardized concepts of diversity and its management do not travel, rather they become translated locally. In organizational practice, globalization is slow and laborious....

  14. The concept of detection of diversion through nuclear material accountancy

    International Nuclear Information System (INIS)

    Akiba, Mitsunori

    2004-01-01

    Nuclear material accountancy begins with the nuclear material accounting activities which are undertaken by facility operators. These activities and corresponding accounting information generated are verified through independent inspections. For bulk handling facilities, two diversion strategies, diversion into MUF and diversion into D, are assumed. These diversion have to be detected by inspectorate quantitatively. The procedures to meet detection goals, that is, significant quantity, detection time and detection probability is studied and clarified. Inspection activities are designed to detect diversion into D. It was found that the detection goal of diversion into D is set in advance and whether diversion is within ISQ or not is verified. Material balance based on operator declaration which may includes falsification is evaluated for diversion into MUF detection capability for it depends on a facility scale. (author)

  15. River Diversions and Shoaling

    National Research Council Canada - National Science Library

    Letter, Jr., Joseph V; Pinkard, Jr., C. F; Raphelt, Nolan K

    2008-01-01

    This Coastal and Hydraulics Engineering Technical Note describes the current knowledge of the potential impacts of river diversions on channel morphology, especially induced sedimentation in the river channel...

  16. The interplay of diversity training and diversity beliefs on team creativity in nationality diverse teams

    NARCIS (Netherlands)

    Homan, A.C.; Buengeler, C.; Eckhoff, R.A.; van Ginkel, W.P.; Voelpel, S.C.

    2015-01-01

    Attaining value from nationality diversity requires active diversity management, which organizations often employ in the form of diversity training programs. Interestingly, however, the previously reported effects of diversity training are often weak and, sometimes, even negative. This situation

  17. A novel complexity-to-diversity strategy for the diversity-oriented synthesis of structurally diverse and complex macrocycles from quinine.

    Science.gov (United States)

    Ciardiello, J J; Stewart, H L; Sore, H F; Galloway, W R J D; Spring, D R

    2017-06-01

    Recent years have witnessed a global decline in the productivity and advancement of the pharmaceutical industry. A major contributing factor to this is the downturn in drug discovery successes. This can be attributed to the lack of structural (particularly scaffold) diversity and structural complexity exhibited by current small molecule screening collections. Macrocycles have been shown to exhibit a diverse range of biological properties, with over 100 natural product-derived examples currently marketed as FDA-approved drugs. Despite this, synthetic macrocycles are widely considered to be a poorly explored structural class within drug discovery, which can be attributed to their synthetic intractability. Herein we describe a novel complexity-to-diversity strategy for the diversity-oriented synthesis of novel, structurally complex and diverse macrocyclic scaffolds from natural product starting materials. This approach exploits the inherent structural (including functional) and stereochemical complexity of natural products in order to rapidly generate diversity and complexity. Readily-accessible natural product-derived intermediates serve as structural templates which can be divergently functionalized with different building blocks to generate a diverse range of acyclic precursors. Subsequent macrocyclisation then furnishes compounds that are each based around a distinct molecular scaffold. Thus, high levels of library scaffold diversity can be rapidly achieved. In this proof-of-concept study, the natural product quinine was used as the foundation for library synthesis, and six novel structurally diverse, highly complex and functionalized macrocycles were generated. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Generative Semantics.

    Science.gov (United States)

    King, Margaret

    The first section of this paper deals with the attempts within the framework of transformational grammar to make semantics a systematic part of linguistic description, and outlines the characteristics of the generative semantics position. The second section takes a critical look at generative semantics in its later manifestations, and makes a case…

  19. Generative collectives

    NARCIS (Netherlands)

    van Osch, W.; Avital, M.; Sabherwal, R.; Sumner, M.

    2010-01-01

    Analyzing generative group activities against the backdrop of an increasingly connected world, this theory development paper introduces the concept of "generative collectives" as a new framework for classifying internet-based collectives and a novel theoretical lens for explaining why some

  20. Sound generator

    NARCIS (Netherlands)

    Berkhoff, Arthur P.

    2008-01-01

    A sound generator, particularly a loudspeaker, configured to emit sound, comprising a rigid element (2) enclosing a plurality of air compartments (3), wherein the rigid element (2) has a back side (B) comprising apertures (4), and a front side (F) that is closed, wherein the generator is provided

  1. Sound generator

    NARCIS (Netherlands)

    Berkhoff, Arthur P.

    2010-01-01

    A sound generator, particularly a loudspeaker, configured to emit sound, comprising a rigid element (2) enclosing a plurality of air compartments (3), wherein the rigid element (2) has a back side (B) comprising apertures (4), and a front side (F) that is closed, wherein the generator is provided

  2. Pulse Generator

    Science.gov (United States)

    Greer, Lawrence (Inventor)

    2017-01-01

    An apparatus and a computer-implemented method for generating pulses synchronized to a rising edge of a tachometer signal from rotating machinery are disclosed. For example, in one embodiment, a pulse state machine may be configured to generate a plurality of pulses, and a period state machine may be configured to determine a period for each of the plurality of pulses.

  3. Sound generator

    NARCIS (Netherlands)

    Berkhoff, Arthur P.

    2007-01-01

    A sound generator, particularly a loudspeaker, configured to emit sound, comprising a rigid element (2) enclosing a plurality of air compartments (3), wherein the rigid element (2) has a back side (B) comprising apertures (4), and a front side (F) that is closed, wherein the generator is provided

  4. Generative Semantics

    Science.gov (United States)

    Bagha, Karim Nazari

    2011-01-01

    Generative semantics is (or perhaps was) a research program within linguistics, initiated by the work of George Lakoff, John R. Ross, Paul Postal and later McCawley. The approach developed out of transformational generative grammar in the mid 1960s, but stood largely in opposition to work by Noam Chomsky and his students. The nature and genesis of…

  5. Linking Diversity and Disparity Measures

    Directory of Open Access Journals (Sweden)

    Sahadeb Sarkar

    2012-07-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman","serif";} The purpose of this paper is to examine links between the diversity measures (Patil and Taillie 1982 and the disparity measures (Lindsay 1994, quantities apparently developed for somewhat different purposes. We demonstrate that numerous diversity measures satisfying all the desirable criteria mentioned by Patil and Taillie can be defined by the generating functions of certain disparities and the associated residual adjustment functions. This provides the statistician and the ecologist a wide class of flexible indices for the statistical measurement of diversity.

  6. Global patterns of amphibian phylogenetic diversity

    DEFF Research Database (Denmark)

    Fritz, Susanne; Rahbek, Carsten

    2012-01-01

    phylogeny (2792 species). We combined each tree with global species distributions to map four indices of phylogenetic diversity. To investigate congruence between global spatial patterns of amphibian species richness and phylogenetic diversity, we selected Faith’s phylogenetic diversity (PD) index......Aim  Phylogenetic diversity can provide insight into how evolutionary processes may have shaped contemporary patterns of species richness. Here, we aim to test for the influence of phylogenetic history on global patterns of amphibian species richness, and to identify areas where macroevolutionary...... processes such as diversification and dispersal have left strong signatures on contemporary species richness. Location  Global; equal-area grid cells of approximately 10,000 km2. Methods  We generated an amphibian global supertree (6111 species) and repeated analyses with the largest available molecular...

  7. Life Complexity and Diversity

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 12. Life Complexity and Diversity Whither Diversity. Madhav Gadgil. Series Article Volume 1 Issue 12 December 1996 pp 17-25. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/001/12/0017-0025 ...

  8. Global Diversity and Leadership.

    Science.gov (United States)

    Ruiz, Art

    2003-01-01

    Argues that global diversity has become a business imperative in today's business climate. Global diversity is of core importance even for companies that are considered domestic. Suggests community colleges need help in understanding their customer base and their shifting values in order to meet their needs and win customer loyalty. (NB)

  9. Chapter 16: Species Diversity

    African Journals Online (AJOL)

    zargaran

    2012-05-03

    May 3, 2012 ... 2008; Zargaran et al., 2008), the oak cynipid gall wasps diversity is yet to be studied. Nazemi et al. (2008) reported species richness of oak gall wasps from. Kurdistan, Ilam and Kermanshah provinces of Iran. Reducing the oak gall wasps diversity will be as an alarm for environmental health of oak forests.

  10. Diversity in Leadership

    Science.gov (United States)

    Beer, Janet

    2015-01-01

    This paper presents a lecture given at the 17th Annual Lecture of the Association of University Administrators (AUA). The subject of the lecture is equality and diversity in higher education (HE) leadership, or possibly the absence of equality and diversity. The author focuses on what can be done to ensure that capable women enter HE leadership…

  11. Making diversity policies work

    NARCIS (Netherlands)

    M. Shemla (Meir)

    2017-01-01

    textabstractManaging diversity in organizations is one of the defining issues of our time. Most institutions try to promote the creation of a diverse, creative workforce, but unfortunately, even after several decades of work, how this is created is still very unclear. A more scientific approach

  12. Segmentation models diversity for object proposals

    NARCIS (Netherlands)

    Manfredi, M.; Grana, C.; Cucchiara, R.; Smeulders, A.W.M.

    In this paper we present a segmentation proposal method which employs a box-hypotheses generation step followed by a lightweight segmentation strategy. Inspired by interactive segmentation, for each automatically placed bounding-box we compute a precise segmentation mask. We introduce diversity in

  13. Phylogenetic diversity of Mesorhizobium in chickpea

    Indian Academy of Sciences (India)

    2014-04-29

    Apr 29, 2014 ... 3RAK College of Agriculture, Sehore 466 001, India. 4CGIAR Generation Challenge Program, C/o CIMMYT, Mexico, DF 06600, Mexico. *Corresponding author (Fax, 91-40-30713074; Email, r.k.varshney@cgiar.org). Crop domestication, in general, has reduced genetic diversity in cultivated gene pool of ...

  14. Microsatellite analysis of intracultivar diversity in 'Chinnarasam ...

    African Journals Online (AJOL)

    Their leaves were sampled to study intracultivar diversity following microsatellite analysis. The dendrogram generated based on unweighted pair group mean with arithmetic average, showed three major groups of accessions, which followed geographical separation. Twenty out of 109 mango-specific micro satellites ...

  15. Issues of Cultural Diversity in School Mathematics.

    Science.gov (United States)

    Ruthven, Kenneth

    2001-01-01

    Explores cultural diversity in school mathematics and the issues raised for mathematics education. Examines the curricular roots of school mathematics in relation to scholarly mathematics, and the mathematics of past generations and different social groups. Notes some of the complexities in seeking to 'culturalize' school mathematics by bringing…

  16. Managing Protean Diversity

    DEFF Research Database (Denmark)

    Marfelt, Mikkel Mouritz; Muhr, Sara Louise

    2016-01-01

    . In this article, we follow the call for critically investigating the contexts influencing diversity management by analyzing the development of a global human resource management project initiated to promote a culturally diverse workforce. We find that despite good intentions, as well as support from the top...... management, the project dissolves through micropolitics and power dynamics. We contribute to the critical literature on workforce diversity by identifying how organizational contextual dynamics influence the way the concept of workforce diversity is constructed and understood at work. Based on these findings......Recently, global workforce diversity and its management have received criticism for not paying attention to the contextual influence stemming from socially constructed dialectics of power and politics. These contextual dynamics, however, tend to be viewed as external to the organization...

  17. The marine diversity spectrum

    DEFF Research Database (Denmark)

    Reuman, Daniel C.; Gislason, Henrik; Barnes, Carolyn

    2014-01-01

    of taxonomy (all the species in a region regardless of clade) are much less studied but are equally important and will illuminate a different set of ecological and evolutionary processes. We develop and test a mechanistic model of how diversity varies with body mass in marine ecosystems. The model predicts...... the form of the diversity spectrum', which quantifies the distribution of species' asymptotic body masses, is a species analogue of the classic size spectrum of individuals, and which we have found to be a new and widely applicable description of diversity patterns. The marine diversity spectrum...... is predicted to be approximately linear across an asymptotic mass range spanning seven orders of magnitude. Slope -0 center dot 5 is predicted for the global marine diversity spectrum for all combined pelagic zones of continental shelf seas, and slopes for large regions are predicted to lie between -0 center...

  18. Steam generator tube failures

    Energy Technology Data Exchange (ETDEWEB)

    MacDonald, P.E.; Shah, V.N.; Ward, L.W.; Ellison, P.G.

    1996-04-01

    A review and summary of the available information on steam generator tubing failures and the impact of these failures on plant safety is presented. The following topics are covered: pressurized water reactor (PWR), Canadian deuterium uranium (CANDU) reactor, and Russian water moderated, water cooled energy reactor (VVER) steam generator degradation, PWR steam generator tube ruptures, the thermal-hydraulic response of a PWR plant with a faulted steam generator, the risk significance of steam generator tube rupture accidents, tubing inspection requirements and fitness-for-service criteria in various countries, and defect detection reliability and sizing accuracy. A significant number of steam generator tubes are defective and are removed from service or repaired each year. This wide spread damage has been caused by many diverse degradation mechanisms, some of which are difficult to detect and predict. In addition, spontaneous tube ruptures have occurred at the rate of about one every 2 years over the last 20 years, and incipient tube ruptures (tube failures usually identified with leak detection monitors just before rupture) have been occurring at the rate of about one per year. These ruptures have caused complex plant transients which have not always been easy for the reactor operators to control. Our analysis shows that if more than 15 tubes rupture during a main steam line break, the system response could lead to core melting. Although spontaneous and induced steam generator tube ruptures are small contributors to the total core damage frequency calculated in probabilistic risk assessments, they are risk significant because the radionuclides are likely to bypass the reactor containment building. The frequency of steam generator tube ruptures can be significantly reduced through appropriate and timely inspections and repairs or removal from service.

  19. Steam generator tube failures

    International Nuclear Information System (INIS)

    MacDonald, P.E.; Shah, V.N.; Ward, L.W.; Ellison, P.G.

    1996-04-01

    A review and summary of the available information on steam generator tubing failures and the impact of these failures on plant safety is presented. The following topics are covered: pressurized water reactor (PWR), Canadian deuterium uranium (CANDU) reactor, and Russian water moderated, water cooled energy reactor (VVER) steam generator degradation, PWR steam generator tube ruptures, the thermal-hydraulic response of a PWR plant with a faulted steam generator, the risk significance of steam generator tube rupture accidents, tubing inspection requirements and fitness-for-service criteria in various countries, and defect detection reliability and sizing accuracy. A significant number of steam generator tubes are defective and are removed from service or repaired each year. This wide spread damage has been caused by many diverse degradation mechanisms, some of which are difficult to detect and predict. In addition, spontaneous tube ruptures have occurred at the rate of about one every 2 years over the last 20 years, and incipient tube ruptures (tube failures usually identified with leak detection monitors just before rupture) have been occurring at the rate of about one per year. These ruptures have caused complex plant transients which have not always been easy for the reactor operators to control. Our analysis shows that if more than 15 tubes rupture during a main steam line break, the system response could lead to core melting. Although spontaneous and induced steam generator tube ruptures are small contributors to the total core damage frequency calculated in probabilistic risk assessments, they are risk significant because the radionuclides are likely to bypass the reactor containment building. The frequency of steam generator tube ruptures can be significantly reduced through appropriate and timely inspections and repairs or removal from service

  20. Chamaedorea: diverse species in diverse habitats

    Directory of Open Access Journals (Sweden)

    1992-01-01

    Full Text Available DIVERSES ESPÈCES DANS DIVERS HABITATS. Des espèces extraordinairement diverses se trouvant dans des habitats également divers caractérisent Chamaedorea, un genre qui compte environ 90 espèces dioïques limitées aux sous-bois des forêts néo-tropicales constamment dans la pluie et les nuages du Mexique à la Bolivie et à l’Équateur. Une vaste gamme de formes biologiques, de tiges, de feuilles, d’inflorescences, de fleurs, et de fruits reflète la diversité des espèces. Bien que le genre soit plus riche en espèces dans les forêts denses et humides situées entre 800-1,500 mètres d’altitude, quelques espèces exceptionnelles se trouvent dans des forêts moins denses et/ou occasionnellement sèches, sur des substances dures ou dans d’autres habitats inhabituels. DIVERSAS ESPECIES EN DIVERSOS HÁBITATS. Especies notablemente diversas presentes en habitats igualmente diversos caracterizan a Chamaedorea, un genero de aproximadamente 90 especies dioicas limitadas al sotobosque de los bosques lluviosos y nubosos neotropicales desde Mexico hasta Bolivia y Ecuador. Una amplia gama de formas biológicas, tallos, hojas, inflorescencias, flores, y frutos refleja la diversidad de las especies. Aunque el género es más rico en especies en los bosques densos y húmedos de 800-1,500 metros de altura, unas pocas especies excepcionales ocurren en bosques abiertos o ocasionalmente secos, en substrato severo o en otros habitats extraordinarios. Remarkably diverse species occurring in equally diverse habitats characterize Chamaedorea, a genus of about 90, dioecious species restricted to the understory of neotropical rain and cloud forests from Mexico to Bolivia and Ecuador. A vast array of habits, stems, leaves, inflorescences, flowers, and fruits reflect the diversity of species. Although the genus is most species-rich in dense, moist or wet, diverse forests from 800-1,500 meters elevation, a few exceptional species occur in open and/or seasonally

  1. Flywheel Generator

    OpenAIRE

    Yuniarsih, Pratitis; Bachtiyar, Fahmi; Rosyidin, Mufti; Prabawanto, Trisakti

    2014-01-01

    Lately, the needs of energy is increasing but its availability is very limited. Therefore,it is important to do more research on energy reform. Generator is one of the alternative energy which commonly used by the public, but it has a minus value such as the voltage instability and low efficiency of the generator . Based on those issues,so we made an application flywheel in electrical generator, which aims to produce a concept of power efficiency increase, stabilize the output voltage of the ...

  2. Diverse crowds using diverse methods improves the scientific dialectic.

    Science.gov (United States)

    Motyl, Matt; Iyer, Ravi

    2015-01-01

    In science, diversity is vital to the development of new knowledge. We agree with Duarte et al. that we need more political diversity in social psychology, but contend that we need more religious diversity and methodological diversity as well. If some diversity is good, more is better (especially in science).

  3. Unravelling the Neospora caninum secretome through the secreted fraction (ESA) and quantification of the discharged tachyzoite using high-resolution mass spectrometry-based proteomics

    NARCIS (Netherlands)

    Pollo-Oliveira, L.; Post, H.; Acencio, M.L.; Lemke, N.; van den Toorn, H.W.P.; Tragante Do O, V.; Heck, A.J.R.; Altelaar, A.F.M.; Yatsuda, A.P.

    2013-01-01

    Background The apicomplexan parasite Neospora caninum causes neosporosis, a disease that leads to abortion or stillbirth in cattle, generating an economic impact on the dairy and beef cattle trade. As an obligatory intracellular parasite, N. caninum needs to invade the host cell in an active manner

  4. How diversity gets lost

    DEFF Research Database (Denmark)

    Oudshoorn, Nelly; Neven, Louis; Stienstra, M.

    2016-01-01

    This article adopts an intersectional approach to investigate how age, gender, and diversity are represented, silenced, or prioritized in design. Based on a comparative study of design practices of information and communication technologies (ICTs) for young girls and older people, this article...... describes differences and similarities in the ways in which designers tried to cope with diversity. Ultimately diversity was neglected, and the developers relied on hegemonic views of gender and age, constructed older people and young girls as an “other,” and consequently their input was neglected...

  5. Trust in Diverse Teams

    DEFF Research Database (Denmark)

    Clausen, Lisbeth

    Multicultural membership and diversity in teams are important to maintain effectiveness in organizations in a global business environment. Multicultural teams offer great potential in international collaboration just as top management teams are becoming increasingly diversified. However...... with change in particular ways: Each team is analyzed in relation to its global (HQ) mandate, local (national) stakeholders and organizational context. It is found that communication energy, resources and team mandate underscore the sense of trust in high performing teams. Diversity is understood...... as nationalities, gender, functional expertise and international experience. The study contributes insights to diverse teams through a processual study of micro-processes in global organizational contexts crossing multicultural boundaries....

  6. Religious diversity and pluralism

    DEFF Research Database (Denmark)

    Ahlin, Lars; Borup, Jørn; Fibiger, Marianne Qvortrup

    2012-01-01

    . Religious diversity has grown in Denmark with the arrival of new immigrant groups and with new forms and interpretations of traditional religious and spiritual traditions. More importantly, the relations and interactions between religious groups -- the hallmarks of religious pluralism -- are still incipient....... Both religious diversity and religious pluralism build on assumptions of stable relationships between religion and religious adherents and clear-cut boundaries between religious groups, assumptions which may be difficult to sustain in late modern societies. This article gives an overview of the Project......'s findings and discusses theoretical challenges related to religious diversity and religious pluralism....

  7. CERN Diversity Newsletter - July 2015

    CERN Document Server

    Kaltenhauser, Kristin; CERN. Geneva. HR Department

    2015-01-01

    The first official edition of the CERN Diversity Newsletter, informing on recent and ongoing diversity activities, and interesting reads, videos and other links related to diversity. Subscribe here: https://diversity.web.cern.ch/2015/07/subscribe-diversity-newsletter

  8. Analysis of genetic diversity in bambara groundnut [ Vigna ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity among 100 selected bambara groundnut [Vigna subterranea (L.) Verdc] landraces from a diverse geographic area of Tanzania. Eleven informative AFLP primer combinations generated a total of 49 scorable polymorphic amplification ...

  9. Epistemological Diversity and Moral Ends of Research in Instructed SLA

    Science.gov (United States)

    Ortega, Lourdes

    2012-01-01

    In this article I explore epistemological diversity in the field of second language acquisition (SLA) from the perspective that obtains if we examine the moral ends of research, and we ask: In what ways does epistemological diversity relate to enhancing the social value and educational relevance of the research generated by the instructed SLA…

  10. Cultural Diversity and Teamwork. ERIC Digest No. 152.

    Science.gov (United States)

    Lankard, Bettina A.

    In today's society, when increasing numbers of employees are being expected to work in teams and when cultural diversity is becoming commonplace in schools and workplaces, it is imperative that vocational and career educators prepare students for future interactions in a culturally diverse workplace. Communication differences between generations,…

  11. Creating a Diversity of Mathematical Experiences for Tertiary Students.

    Science.gov (United States)

    Ball, Geoff; Stephenson, Brian; Smith, Geoff; Wood, Leigh; Coupland, Mary; Crawford, Kathryn

    1998-01-01

    Describes a process for creating a more diverse set of experiences for undergraduate students in mathematics by focusing on linear algebra. Emphasizes that the diversity of the activities is generated in part through the use of a taxonomy that addresses the nature of the activities rather than a hierarchy of levels of difficulty. Contains 13…

  12. Multicriteria diversity analysis

    Energy Technology Data Exchange (ETDEWEB)

    Stirling, Andy, E-mail: a.c.stirling@sussex.ac.u [SPRU-Science and Technology Policy Research, Freeman Centre, University of Sussex, Sussex BN1 9QE (United Kingdom)

    2010-04-15

    This paper outlines a novel general framework for analysing energy diversity. A critical review of different reasons for policy interest reveals that diversity is more than a supply security strategy. There are particular synergies with strategies for transitions to sustainability. Yet - despite much important work - policy analysis tends to address only a subset of the properties of diversity and remains subject to ambiguity, neglect and special pleading. Developing earlier work, the paper proposes a more comprehensive heuristic framework, accommodating a wide range of different disciplinary and socio-political perspectives. It is argued that the associated multicriteria diversity analysis method provides a more systematic, complete and transparent way to articulate disparate perspectives and approaches and so help to inform more robust and accountable policymaking.

  13. Diverse by Default

    DEFF Research Database (Denmark)

    Holck, Lotte

    arguments that arise from migrants’ paradoxical situation. To improve their situation, the article discusses whether alternative conceptualization of talents, ‘high potentials’, and making the ambitions of diverse employees more prominent in strategic human resource management can be a relavant strategy...... defined by precarization and high demand especially in the service industry. Drawing on the qualitative data from the case company, Service, I inquire how a diverse composition of employees happened by coincidence, has turned into an advantage of extending the conventional diversity business case......: Employing highlyskilled, career-minded migrants in low-skilled postions, migrants are simultaneously casted as a disposable, replicable and temporary resource, the ‘ideal worker’, AND as a ‘high potential’ for first line management. This extended business case of diversity draws on multifaceted business...

  14. Managing biological diversity

    Science.gov (United States)

    Samson, Fred B.; Knopf, Fritz L.

    1993-01-01

    Biological diversity is the variety of life and accompanying ecological processes (Off. Technol. Assess. 1987, Wilcove and Samson 1987, Keystone 1991). Conservation of biological diversity is a major environmental issue (Wilson 1988, Counc. Environ. Quality 1991). The health and future of the earth's ecological systems (Lubchenco et al. 1991), global climate change (Botkin 1990), and an ever-increasing rate in loss of species, communities, and ecological systems (Myers 1990) are among issues drawing biological diversity to the mainstream of conservation worldwide (Int. Union Conserv. Nat. and Nat. Resour. [IUCN] et al. 1991). The legal mandate for conserving biological diversity is now in place (Carlson 1988, Doremus 1991). More than 19 federal laws govern the use of biological resources in the United States (Rein 1991). The proposed National Biological Diversity Conservation and Environmental Research Act (H.R. 585 and S.58) notes the need for a national biological diversity policy, would create a national center for biological diversity research, and recommends a federal interagency strategy for ecosystem conservation. There are, however, hard choices ahead for the conservation of biological diversity, and biologists are grappling with how to set priorities in research and management (Roberts 1988). We sense disillusion among field biologists and managers relative to how to operationally approach the seemingly overwhelming charge of conserving biological diversity. Biologists also need to respond to critics like Hunt (1991) who suggest a tree farm has more biological diversity than an equal area of old-growth forest. At present, science has played only a minor role in the conservation of biological diversity (Weston 1992) with no unified approach available to evaluate strategies and programs that address the quality and quantity of biological diversity (Murphy 1990, Erwin 1992). Although actions to conserve biological diversity need to be clearly defined by

  15. Evaluating human genetic diversity

    National Research Council Canada - National Science Library

    This book assesses the scientific value and merit of research on human genetic differences--including a collection of DNA samples that represents the whole of human genetic diversity--and the ethical...

  16. PULSE GENERATOR

    Science.gov (United States)

    Roeschke, C.W.

    1957-09-24

    An improvement in pulse generators is described by which there are produced pulses of a duration from about 1 to 10 microseconds with a truly flat top and extremely rapid rise and fall. The pulses are produced by triggering from a separate input or by modifying the current to operate as a free-running pulse generator. In its broad aspect, the disclosed pulse generator comprises a first tube with an anode capacitor and grid circuit which controls the firing; a second tube series connected in the cathode circuit of the first tube such that discharge of the first tube places a voltage across it as the leading edge of the desired pulse; and an integrator circuit from the plate across the grid of the second tube to control the discharge time of the second tube, determining the pulse length.

  17. Does Labor Diversity Promote Entrepreneurship?

    DEFF Research Database (Denmark)

    Marino, Marianna; Parrotta, Pierpaolo; Pozzoli, Dario

    We find evidence that workforce educational diversity promotes entrepreneurial behavior of employees as well as the formation of new firms, whereas diversity in demographics hinders transitions to selfemployment. Ethnic diversity favors entrepreneurship in financial and business services....

  18. Generation of Campylobacter jejuni genetic diversity in vivo

    NARCIS (Netherlands)

    Boer, de P.; Wagenaar, J.A.; Achterberg, R.P.; Putten, van J.P.M.; Schouls, L.M.; Duim, B.

    2002-01-01

    Molecular epidemiology studies suggest that horizontal genetic exchange is a major cause of pathogen biodiversity. We tested this concept for the bacterial enteropathogen Campylobacter jejuni by seeking direct in vivo evidence for the exchange of genetic material among Campylobacter strains. For

  19. Steroid promiscuity: Diversity of enzyme action. Preface.

    Science.gov (United States)

    Lathe, Richard; Kotelevtsev, Yuri; Mason, J Ian

    2015-07-01

    This Special Issue on the topic of Steroid and Sterol Signaling: Promiscuity and Diversity, dwells on the growing realization that the 'one ligand, one binding site' and 'one enzyme, one reaction' concepts are out of date. Focusing on cytochromes P450 (CYP), hydroxysteroid dehydrogenases (HSDs), and related enzymes, the Special Issue highlights that a single enzyme can bind to diverse substrates, and in different conformations, and can catalyze multiple different conversions (and in different directions), thereby, generating an unexpectedly wide spectrum of ligands that can have subtly different biological actions. This article is part of a Special Issue entitled 'Steroid/Sterol Signaling' . Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Extraction of transcript diversity from scientific literature.

    Directory of Open Access Journals (Sweden)

    Parantu K Shah

    2005-06-01

    Full Text Available Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term "alternative splicing" to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts is publicly available at http://www.bork.embl.de/LSAT/.

  1. Generation Next

    Science.gov (United States)

    Hawkins, B. Denise

    2010-01-01

    There is a shortage of accounting professors with Ph.D.s who can prepare the next generation. To help reverse the faculty deficit, the American Institute of Certified Public Accountants (CPAs) has created the new Accounting Doctoral Scholars program by pooling more than $17 million and soliciting commitments from more than 70 of the nation's…

  2. Separation of cell survival, growth, migration, and mesenchymal transdifferentiation effects of fibroblast secretome on tumor cells of head and neck squamous cell carcinoma.

    Science.gov (United States)

    Metzler, Veronika Maria; Pritz, Christian; Riml, Anna; Romani, Angela; Tuertscher, Raphaela; Steinbichler, Teresa; Dejaco, Daniel; Riechelmann, Herbert; Dudás, József

    2017-11-01

    Fibroblasts play a central role in tumor invasion, recurrence, and metastasis in head and neck squamous cell carcinoma. The aim of this study was to investigate the influence of tumor cell self-produced factors and paracrine fibroblast-secreted factors in comparison to indirect co-culture on cancer cell survival, growth, migration, and epithelial-mesenchymal transition using the cell lines SCC-25 and human gingival fibroblasts. Thereby, we particularly focused on the participation of the fibroblast-secreted transforming growth factor beta-1.Tumor cell self-produced factors were sufficient to ensure tumor cell survival and basic cell growth, but fibroblast-secreted paracrine factors significantly increased cell proliferation, migration, and epithelial-mesenchymal transition-related phenotype changes in tumor cells. Transforming growth factor beta-1 generated individually migrating disseminating tumor cell groups or single cells separated from the tumor cell nest, which were characterized by reduced E-cadherin expression. At the same time, transforming growth factor beta-1 inhibited tumor cell proliferation under serum-starved conditions. Neutralizing transforming growth factor beta antibody reduced the cell migration support of fibroblast-conditioned medium. Transforming growth factor beta-1 as a single factor was sufficient for generation of disseminating tumor cells from epithelial tumor cell nests, while other fibroblast paracrine factors supported tumor nest outgrowth. Different fibroblast-released factors might support tumor cell proliferation and invasion, as two separate effects.

  3. NASFAA Diversity and Inclusion: Recommendations of the Professional Diversity Caucus

    Science.gov (United States)

    National Association of Student Financial Aid Administrators, 2015

    2015-01-01

    NASFAA's Diversity and Inclusion Report emphasizes the importance of diversity and inclusivity to NASFAA. Included in this report is a diversity statement developed by NASFAA's Professional Diversity Caucus, and approved by NASFAA's Board in March of 2015. The Caucus convened in the summer of 2014 to better understand issues related to diversity…

  4. Teaching for Diversity: Addressing Diversity Issues in Responsive ESL Instruction

    Science.gov (United States)

    Fu, Jing

    2013-01-01

    Student diversity has become a typical phenomenon in American public schools. The impact of increasing diversity on literacy instruction is unchallenged. Teachers reinforce this message by often citing ESL student diversity as a barrier for literacy teaching. In order to better understand the complexity of diversity issues, I explored two ESL…

  5. Cluster generator

    Science.gov (United States)

    Donchev, Todor I [Urbana, IL; Petrov, Ivan G [Champaign, IL

    2011-05-31

    Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.

  6. Promoting Linguistic Diversity

    DEFF Research Database (Denmark)

    Daryai-Hansen, Petra Gilliyard

    2005-01-01

    To face up to the omnipresence of ‘Anglo-American’, conferences on language policy today address the issue of promoting linguistic diversity. This especially applies to contemporary Europe. Nevertheless, these conferences, which can be regarded as a kind of laboratories or academic microcosm, do ...... not subscribe to clear language policies. Consequently, the predominant language is here, as elsewhere, the Anglo-American. This article outlines the deep division between the postulate of linguistic diversity and reality, and is a call for soul-searching.......To face up to the omnipresence of ‘Anglo-American’, conferences on language policy today address the issue of promoting linguistic diversity. This especially applies to contemporary Europe. Nevertheless, these conferences, which can be regarded as a kind of laboratories or academic microcosm, do...

  7. Automatic generation control of interconnected power system with ...

    African Journals Online (AJOL)

    In this paper, automatic generation control (AGC) of two area interconnected power system having diverse sources of power generation is studied. A two area power system comprises power generations from hydro, thermal and gas sources in area-1 and power generations from hydro and thermal sources in area-2. All the ...

  8. Prices and species diversity

    DEFF Research Database (Denmark)

    Sauer, Johannes

    . Based on a biologically defined species diver-sity index we incorporate biodiversity either as a desirable output or biodiversity loss as a detrimental input. Beside quantitative shadow price measures the main contribu-tion of the work is the evidence that parametric scores of environmental efficiency...... of biodiversity and the appropriate incorporation in stochastic fron-tier models to achieve more realistic measures of production efficiency. We use the empirical example of tobacco production drawing from as well as affecting species diversity in the surrounding forests. We apply a shadow profit distance...

  9. Authoritarian Disbeliefs in Diversity.

    Science.gov (United States)

    Asbrock, Frank; Kauff, Mathias

    2015-01-01

    Ethnic diversity poses a threat to authoritarians, as it indicates non-conformism to group norms and poses a threat to group conformity. According to authoritarian dynamic theory, threats elicit authoritarian reactions in people with authoritarian predispositions. In the present article we tested a mediation model derived from authoritarian dynamic theory in a sample of 171 students. As expected, authoritarian predisposition negatively predicted diversity beliefs. This effect was fully mediated by an authoritarian manifestation, that is, authoritarian aggression. The two other components of right-wing authoritarianism, authoritarian submission and conventionalism, did not mediate the effect. Results confirm contemporary research on authoritarianism and the differentiation of authoritarian predispositions and its manifestations.

  10. Diversity begets diversity: host expansions and the diversification of plant-feeding insects

    Directory of Open Access Journals (Sweden)

    Nylin Sören

    2006-01-01

    Full Text Available Abstract Background Plant-feeding insects make up a large part of earth's total biodiversity. While it has been shown that herbivory has repeatedly led to increased diversification rates in insects, there has been no compelling explanation for how plant-feeding has promoted speciation rates. There is a growing awareness that ecological factors can lead to rapid diversification and, as one of the most prominent features of most insect-plant interactions, specialization onto a diverse resource has often been assumed to be the main process behind this diversification. However, specialization is mainly a pruning process, and is not able to actually generate diversity by itself. Here we investigate the role of host colonizations in generating insect diversity, by testing if insect speciation rate is correlated with resource diversity. Results By applying a variant of independent contrast analysis, specially tailored for use on questions of species richness (MacroCAIC, we show that species richness is strongly correlated with diversity of host use in the butterfly family Nymphalidae. Furthermore, by comparing the results from reciprocal sister group selection, where sister groups were selected either on the basis of diversity of host use or species richness, we find that it is likely that diversity of host use is driving species richness, rather than vice versa. Conclusion We conclude that resource diversity is correlated with species richness in the Nymphalidae and suggest a scenario based on recurring oscillations between host expansions – the incorporation of new plants into the repertoire – and specialization, as an important driving force behind the diversification of plant-feeding insects.

  11. The interplay of diversity training and diversity beliefs on team creativity in nationality diverse teams.

    Science.gov (United States)

    Homan, Astrid C; Buengeler, Claudia; Eckhoff, Robert A; van Ginkel, Wendy P; Voelpel, Sven C

    2015-09-01

    Attaining value from nationality diversity requires active diversity management, which organizations often employ in the form of diversity training programs. Interestingly, however, the previously reported effects of diversity training are often weak and, sometimes, even negative. This situation calls for research on the conditions under which diversity training helps or harms teams. We propose that diversity training can increase team creativity, but only for teams with less positive pretraining diversity beliefs (i.e., teams with a greater need for such training) and that are sufficiently diverse in nationality. Comparing the creativity of teams that attended nationality diversity training versus control training, we found that for teams with less positive diversity beliefs, diversity training increased creative performance when the team's nationality diversity was high, but undermined creativity when the team's nationality diversity was low. Diversity training had less impact on teams with more positive diversity beliefs, and training effects were not contingent upon these teams' diversity. Speaking to the underlying process, we showed that these interactive effects were driven by the experienced team efficacy of the team members. We discuss theoretical and practical implications for nationality diversity management. (c) 2015 APA, all rights reserved).

  12. Magnet Free Generators - 3rd Generation Wind Turbine Generators

    DEFF Research Database (Denmark)

    Jensen, Bogi Bech; Mijatovic, Nenad; Henriksen, Matthew Lee

    2013-01-01

    This paper presents an introduction to superconducting wind turbine generators, which are often referred to as 3rd generation wind turbine generators. Advantages and challenges of superconducting generators are presented with particular focus on possible weight and efficiency improvements. A comp....... A comparison of the rare earth usage in different topologies of permanent magnet generators and superconducting generators is also presented....

  13. Generation Expansion Planning Considering Integrating Large-scale Wind Generation

    DEFF Research Database (Denmark)

    Zhang, Chunyu; Ding, Yi; Østergaard, Jacob

    2013-01-01

    necessitated the inclusion of more innovative and sophisticated approaches in power system investment planning. A bi-level generation expansion planning approach considering large-scale wind generation was proposed in this paper. The first phase is investment decision, while the second phase is production...... optimization decision. A multi-objective PSO (MOPSO) algorithm was introduced to solve this optimization problem, which can accelerate the convergence and guarantee the diversity of Pareto-optimal front set as well. The feasibility and effectiveness of the proposed bi-level planning approach and the MOPSO...

  14. Estimating the diversity of dinosaurs

    OpenAIRE

    Wang, Steve C.; Dodson, Peter

    2006-01-01

    Despite current interest in estimating the diversity of fossil and extant groups, little effort has been devoted to estimating the diversity of dinosaurs. Here we estimate the diversity of nonavian dinosaurs at ≈1,850 genera, including those that remain to be discovered. With 527 genera currently described, at least 71% of dinosaur genera thus remain unknown. Although known diversity declined in the last stage of the Cretaceous, estimated diversity was steady, suggesting that dinosaurs as a w...

  15. Managing Generation Y towards Organizational Excellence

    OpenAIRE

    Uduwawela, Shehani Romesha

    2015-01-01

    The workforce today comprises of several distinctive generations working along together, with Generation Y (Gen Y) being the latest entry to the workplace. This latest entrance of employees has raised concern from organizations owing to their diverse work ethics, characteristics, and traits, which are significantly different to the previous generational cohorts. It is reported that Gen Ys enter the workforce with high expectations and are subjected to influence from varied factors that impact...

  16. Separation, Separatism and Diversity.

    Science.gov (United States)

    Hasegawa, Maya

    1991-01-01

    In the United States, once legal integration was achieved and the White male culture was challenged for real power, minority groups began to question the wisdom of cultural and social integration and celebrate diversity. An acceptable line between healthy separation and unhealthy separatism must be found. (MSE)

  17. Diversity without representation

    CSIR Research Space (South Africa)

    Scholes, RJ

    2006-07-01

    Full Text Available Since the 1992 United Nations ‘Earth Summit’ conference in Rio de Janeiro, Brazil, biodiversity has received increasing attention from scientists, governments and the public worldwide. There is growing recognition that the diversity of life on Earth...

  18. Diversity & Community: Maintaining Allegiances.

    Science.gov (United States)

    Pena, Devon G.

    1990-01-01

    The quest for diversity must overcome the resistance of traditional White, male faculty to redefining the mission and curriculum of the liberal arts college. Change will be difficult, but it must occur if liberal arts colleges are to survive and maintain a central and relevant place in multicultural America. (MSE)

  19. Workplace Diversity Issues.

    Science.gov (United States)

    1999

    This document contains three symposium papers on workplace diversity issues. "Expanding Theories of Career Development: Adding the Voices of African American Women in the White Academy" (Mary V. Alfred) questions the validity of existing career development models for women and minority groups and examines the professional development of…

  20. Designing Diverse Learning Styles.

    Science.gov (United States)

    Williamson, Ronald D.

    1998-01-01

    Presents strategies for middle level principals to strengthen their instructional program. Includes suggestions for creating a climate receptive to change by raising staff awareness of their own learning style diversity; modeling values through using instructional tools such as Bloom's Taxonomy in interaction with staff; and using stories,…

  1. Meeting diversity in ergonomics

    NARCIS (Netherlands)

    Pikaar, R.N.; Koningsveld, E.A.P.; Settels, P.J.M.

    2007-01-01

    Key Features: Offers the conceptual tools for creating more adaptable ergonomic designs to meet the needs of diverse human populations, Unlock the strategic business value found in ergonomically safe and comfortable products, Learn from in-depth case studies how ergonomic intervention was

  2. What Is Diversity Pedagogy?

    Science.gov (United States)

    Sheets, Rosa Hernandez

    2009-01-01

    Diversity Pedagogy Theory (DPT) is a set of principles that point out the natural and inseparable connection between culture and cognition. In other words, to be effective as a teacher, he/she must understand and acknowledge the critical role culture plays in the teaching-learning process. DPT maintains that culturally inclusive teachers (a)…

  3. Thai marine fungal diversity

    OpenAIRE

    Rattaket Choeyklin; Souwalak Phongpaichit; Ittichai Chatmala; Jariya Sakayaroj; Apiradee Pilantanapak; E.B. Gareth Jones

    2006-01-01

    The marine fungal diversity of Thailand was investigated and 116 Ascomycota, 3 Basidiomycota, 28 anamorphic fungi, 7 Stramenopiles recorded, with 30 tentatively identified. These species have primarily been collected from driftwood and attached decayed wood of mangrove trees. The holotype number of 15 taxa is from Thailand and 33 are new records from the country.

  4. Thai marine fungal diversity

    Directory of Open Access Journals (Sweden)

    Rattaket Choeyklin

    2006-07-01

    Full Text Available The marine fungal diversity of Thailand was investigated and 116 Ascomycota, 3 Basidiomycota, 28 anamorphic fungi, 7 Stramenopiles recorded, with 30 tentatively identified. These species have primarily been collected from driftwood and attached decayed wood of mangrove trees. The holotype number of 15 taxa is from Thailand and 33 are new records from the country.

  5. Life Complexity and Diversity

    Indian Academy of Sciences (India)

    As a result, human beings have not only destroyed, but deliberately promoted the diversity onife. The wolf was among the first living species to be moulded by human design. It gave rise to the domestic dog with many new physical and behavioural traits fitting its role as a hunting companion and a. Figure 4 A schematic.

  6. Banking on Diversity

    Science.gov (United States)

    Roach, Ronald

    2010-01-01

    Few organizations have as racially and culturally diverse a work force as the organizations that make up the World Bank Group. Of its 13,000 employees, nearly 60 percent of whom are located in downtown Washington, D.C., and the rest scattered across 160 offices around the globe, nearly every nation in the world is represented in the World Bank…

  7. Managing Diverse Stakeholders

    OpenAIRE

    Pipkin, Erin; Porter, Sean; Clark, Rickie

    2017-01-01

    For every public project, there is a diverse group of stakeholders who need and want information. During this session we outline important stakeholders, how and when to involve them in the planning process, and how targeted messaging might be the key to your project’s success. We also discuss how to identify and manage stakeholders who oppose your project.

  8. Meeting diversity in ergonomics

    NARCIS (Netherlands)

    Looze, M.P. de; Pikaar, R.

    2006-01-01

    The plenary lectures from the 16th World Congress on Ergonomics, Maastricht, July 10-14, 2006, have been documented in this special issue. Its theme was ‘Meeting Diversity'. The contributions, ranging from scientific papers to technical notes or short statements, cover different aspects of the

  9. Life: Complexity and Diversity

    Indian Academy of Sciences (India)

    His fascination for the diversity of life has prompted him to study a whole range of life forms from paper wasps to anchovies, mynas to elephants, goldenrods to bamboos. Figure 1 ... nucleic acids,for assembling proteins and in tum a whole range of ... balloons; as flying lizards gliding from tree to tree and birds flying fr~m the ...

  10. Measuring Cultural Diversity

    DEFF Research Database (Denmark)

    Patsiurko, Natalka; Campbell, John L.; Hall, John A.

    2012-01-01

    Many claim that national economic success depends upon cultural homogeneity. We collect new time-series data and develop new measures of ethnic, linguistic and religious fractionalization for the OECD countries. We show that cultural diversity may vary by type across countries and over short...

  11. Life: Complexity and Diversity

    Indian Academy of Sciences (India)

    Research, Bangalore. His fascination for the .... largest being an egg of the ostrich, largely loaded with stored food. So, to achieve larger sizes .... viruses and fungi. Packing Species. The diversity of living organisms has exploded, hand in hand with the evolving complexity of their interactions in communi- ties. In the dance ...

  12. Diversity Networking Reception

    Science.gov (United States)

    2014-03-01

    Join us at the APS Diversity Reception to relax, network with colleagues, and learn about programs and initiatives for women, underrepresented minorities, and LGBT physicists. You'll have a great time meeting friends in a supportive environment and making connections.

  13. Human diversity in images

    CERN Document Server

    Laëtitia Pedroso

    2010-01-01

    A photo contest is being jointly organized by the CERN Equal Opportunities team and the CERN Photo Club. All you need to do is submit a photo or quotation. The contest is open to everyone.   Diversity at CERN You don’t need to be a photographer or to have sophisticated photographic equipment to capture CERN’s diversity of working styles, gender, age, ethnic, origin and physical ability. Its many facets are all around you! The emphasis of the initiative is on capturing this diversity in an image using creativity, intuition and cultural empathy. You can also contribute with a quotation (whether or not you specify who said it is optional) telling the organizers what strikes you about diversity at CERN. The photo entries and a collection of the quotations will be displayed in an exhibition to be held in May in the Main Building, as well as on the CERN Photo Club website. The best photos will be awarded prizes. So over to you: dig deep inside human nature, explore individual tal...

  14. Life Complexity and Diversity

    Indian Academy of Sciences (India)

    It is as if the stage is cleared from time to time to make for fresh beginnings, with major bouts of extinction. Humans are amongst the most complex products of evolution having in turn populated the world with ever growing numbers of complex artefacts. These artefacts are now threatening to overwhelm the diversity of life.

  15. Life: Complexity and Diversity

    Indian Academy of Sciences (India)

    This promotes a con- tinual increase in the diversity of life over evolutionary time. Ways of Life. Decomposing, photosynthesizing and feeding on other organ- isms are three ... As living organisms have adopted these newer ways of life and invaded an .... honeyguide flies in stages towards the hive with the badger following it ...

  16. Chapter 16: Species Diversity

    African Journals Online (AJOL)

    zargaran

    2012-05-03

    May 3, 2012 ... In this survey, the oak gall wasps (Hymenoptera: Cynipidae: Cynipini) were collected from oak forests of West-Azerbaijan Province in six sites, from April to October. Species richness, heterogeneity, evenness and true diversity were measured. Based on the result of this study, 37 of oak gall wasps species ...

  17. Life: Complexity and Diversity

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 4. Life : Complexity and Diversity Growing Larger. Madhav Gadgil. Series Article Volume 1 Issue 4 April 1996 pp 15-22. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/001/04/0015-0022 ...

  18. Narrating Peoplehood amidst Diversity

    DEFF Research Database (Denmark)

    Böss, Michael

    In Narrating Peoplehood amidst Diversity, 16 internationally renowned scholars reflect on the nature and history of peoplehood and discuss how narratives inform national identities, public culture and academic historiography. The book is a timely contribution to the ongoing debate on belonging...

  19. Composition: Unity - Diversity series

    DEFF Research Database (Denmark)

    Bergstrøm-Nielsen, Carl

    2015-01-01

    Unity-Diversity series are open compositions to be realised by improvising musicians. See more about my composition practise in the entry "Composition - General Introduction". This work is licensed under a Creative Commons "by-nc" License. You may for non-commercial purposes use and distribute it...

  20. Power generation

    International Nuclear Information System (INIS)

    Nunez, Anibal D.

    2001-01-01

    In the second half of twentieth century, nuclear power became an industrial reality. Now the operating 433 power plants, the 37 plants under construction, near 9000 years/reactor with only one serious accident with emission of radioactive material to the environment (Chernobyl) show the maturity of this technology. Today nuclear power contribute a 17% to the global generation and an increase of 75 % of the demand of electricity is estimated for 2020 while this demand is expected to triplicate by 2050. How this requirement can be satisfied? All the indicators seems to demonstrate that nuclear power will be the solution because of the shortage of other sources, the increase of the prices of the non renewable fuels and the scarce contribution of the renewable ones. In addition, the climatic changes produced by the greenhouse effect make even more attractive nuclear power. The situation of Argentina is analyzed and compared with other countries. The convenience of an increase of nuclear power contribution to the total national generation seems clear and the conclusion of the construction of the Atucha II nuclear power plant is recommended

  1. Molecular Technique to Understand Deep Microbial Diversity

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

  2. Unity through Diversity: Value-in-Diversity Beliefs, Work Group Diversity, and Group Identification

    NARCIS (Netherlands)

    D.L. van Knippenberg (Daan); S.A. Haslam (Alexander); M.J. Platow (Michael)

    2007-01-01

    textabstractResearch on work group diversity has more or less neglected the possibility that reactions to diversity may be informed by individuals' beliefs about the value of diversity (vs. homogeneity) for their work group. We studied the role of such diversity beliefs as a moderator of the

  3. Generation III+ Reactor Portfolio

    International Nuclear Information System (INIS)

    2010-03-01

    While the power generation needs of utilities are unique and diverse, they are all faced with the double challenge of meeting growing electricity needs while curbing CO 2 emissions. To answer these diverse needs and help tackle this challenge, AREVA has developed several reactor models which are briefly described in this document: The EPR TM Reactor: designed on the basis of the Konvoi (Germany) and N4 (France) reactors, the EPRTM reactor is an evolutionary model designed to achieve best-in-class safety and operational performance levels. The ATMEA1 TM reactor: jointly designed by Mitsubishi Heavy Industries and AREVA through ATMEA, their common company. This reactor design benefits from the competencies and expertise of the two mother companies, which have commissioned close to 130 reactor units. The KERENA TM reactor: Designed on the basis of the most recent German BWR reactors (Gundremmingen) the KERENA TM reactor relies on proven technology while also including innovative, yet thoroughly tested, features. The optimal combination of active and passive safety systems for a boiling water reactor achieves a very low probability of severe accident

  4. Next generation breeding.

    Science.gov (United States)

    Barabaschi, Delfina; Tondelli, Alessandro; Desiderio, Francesca; Volante, Andrea; Vaccino, Patrizia; Valè, Giampiero; Cattivelli, Luigi

    2016-01-01

    The genomic revolution of the past decade has greatly improved our understanding of the genetic make-up of living organisms. The sequencing of crop genomes has completely changed our vision and interpretation of genome organization and evolution. Re-sequencing allows the identification of an unlimited number of markers as well as the analysis of germplasm allelic diversity based on allele mining approaches. High throughput marker technologies coupled with advanced phenotyping platforms provide new opportunities for discovering marker-trait associations which can sustain genomic-assisted breeding. The availability of genome sequencing information is enabling genome editing (site-specific mutagenesis), to obtain gene sequences desired by breeders. This review illustrates how next generation sequencing-derived information can be used to tailor genomic tools for different breeders' needs to revolutionize crop improvement. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  5. Life Cycle Stage-resolved Proteomic Analysis of the Excretome/Secretome from Strongyloides ratti—Identification of Stage-specific Proteases*

    Science.gov (United States)

    Soblik, Hanns; Younis, Abuelhassan Elshazly; Mitreva, Makedonka; Renard, Bernhard Y.; Kirchner, Marc; Geisinger, Frank; Steen, Hanno; Brattig, Norbert W.

    2011-01-01

    A wide range of biomolecules, including proteins, are excreted and secreted from helminths and contribute to the parasite's successful establishment, survival, and reproduction in an adverse habitat. Excretory and secretory proteins (ESP) are active at the interface between parasite and host and comprise potential targets for intervention. The intestinal nematode Strongyloides spp. exhibits an exceptional developmental plasticity in its life cycle characterized by parasitic and free-living generations. We investigated ESP from infective larvae, parasitic females, and free-living stages of the rat parasite Strongyloides ratti, which is genetically very similar to the human pathogen, Strongyloides stercoralis. Proteomic analysis of ESP revealed 586 proteins, with the largest number of stage-specific ESP found in infective larvae (196), followed by parasitic females (79) and free-living stages (35). One hundred and forty proteins were identified in all studied stages, including anti-oxidative enzymes, heat shock proteins, and carbohydrate-binding proteins. The stage-selective ESP of (1) infective larvae included an astacin metalloproteinase, the L3 Nie antigen, and a fatty acid retinoid-binding protein; (2) parasitic females included a prolyl oligopeptidase (prolyl serine carboxypeptidase), small heat shock proteins, and a secreted acidic protein; (3) free-living stages included a lysozyme family member, a carbohydrate-hydrolyzing enzyme, and saponin-like protein. We verified the differential expression of selected genes encoding ESP by qRT-PCR. ELISA analysis revealed the recognition of ESP by antibodies of S. ratti-infected rats. A prolyl oligopeptidase was identified as abundant parasitic female-specific ESP, and the effect of pyrrolidine-based prolyl oligopeptidase inhibitors showed concentration- and time-dependent inhibitory effects on female motility. The characterization of stage-related ESP from Strongyloides will help to further understand the interaction of

  6. Identification of novel candidate biomarkers of epithelial ovarian cancer by profiling the secretomes of three-dimensional genetic models of ovarian carcinogenesis.

    Science.gov (United States)

    Lawrenson, Kate; Mhawech-Fauceglia, Paulette; Worthington, Jenny; Spindler, Tassja J; O'Brien, Darragh; Lee, Janet M; Spain, Georgia; Sharifian, Maryam; Wang, Guisong; Darcy, Kathleen M; Pejovic, Tanja; Sowter, Heidi; Timms, John F; Gayther, Simon A

    2015-10-15

    Epithelial ovarian cancer (EOC) is still considered the most lethal gynecological malignancy and improved early detection of ovarian cancer is crucial to improving patient prognoses. To address this need, we tested whether candidate EOC biomarkers can be identified using three-dimensional (3D) in vitro models. We quantified changes in the abundance of secreted proteins in a 3D genetic model of early-stage EOC, generated by expressing CMYC and KRAS(G) (12) (V) in TERT-immortalized normal ovarian epithelial cells. Cellular proteins were labeled in live cells using stable isotopic amino acid analogues, and secreted proteins identified and quantified using liquid chromatography-tandem mass spectrometry. Thirty-seven and 55 proteins were differentially expressed by CMYC and CMYC+KRAS(G) (12) (V) expressing cells respectively (p 2-fold). We evaluated expression of the top candidate biomarkers in ∼210 primary EOCs: CHI3L1 and FKBP4 are both expressed by >96% of primary EOCs, and FASN and API5 are expressed by 86 and 75% of cases. High expression of CHI3L1 and FKBP4 was associated with worse patient survival (p = 0.042 and p = 0.002, respectively). Expression of LGALS3BP was positively associated with recurrence (p = 0.0001) and suboptimal debulking (p = 0.018) suggesting that these proteins may be novel prognostic biomarkers. Furthermore, within early stage tumours (I/II), high expression of API5, CHI3L1 and FASN was associated with high tumour grade (p = 3 × 10(-4) , p = 0.016, p = 0.010, respectively). We show in vitro cell biology models of early-stage cancer development can be used to identify novel candidate biomarkers for disease, and report the identification of proteins that represent novel potential candidate diagnostic and prognostic biomarkers for this highly lethal disease. © 2014 UICC.

  7. A Clustering Graph Generator

    Energy Technology Data Exchange (ETDEWEB)

    Winlaw, Manda [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); De Sterck, Hans [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-10-26

    In very simple terms a network can be de ned as a collection of points joined together by lines. Thus, networks can be used to represent connections between entities in a wide variety of elds including engi- neering, science, medicine, and sociology. Many large real-world networks share a surprising number of properties, leading to a strong interest in model development research and techniques for building synthetic networks have been developed, that capture these similarities and replicate real-world graphs. Modeling these real-world networks serves two purposes. First, building models that mimic the patterns and prop- erties of real networks helps to understand the implications of these patterns and helps determine which patterns are important. If we develop a generative process to synthesize real networks we can also examine which growth processes are plausible and which are not. Secondly, high-quality, large-scale network data is often not available, because of economic, legal, technological, or other obstacles [7]. Thus, there are many instances where the systems of interest cannot be represented by a single exemplar network. As one example, consider the eld of cybersecurity, where systems require testing across diverse threat scenarios and validation across diverse network structures. In these cases, where there is no single exemplar network, the systems must instead be modeled as a collection of networks in which the variation among them may be just as important as their common features. By developing processes to build synthetic models, so-called graph generators, we can build synthetic networks that capture both the essential features of a system and realistic variability. Then we can use such synthetic graphs to perform tasks such as simulations, analysis, and decision making. We can also use synthetic graphs to performance test graph analysis algorithms, including clustering algorithms and anomaly detection algorithms.

  8. Idea generation

    DEFF Research Database (Denmark)

    Tollestrup, Christian H. T.; Laursen, Linda Nhu

    2015-01-01

    . Using a straight proposal creation process is expected to create proposals that operate within the present sociocultural meaning. Whereas an approach seeking ambiguity and discrepancy in the initial ideation sparks a deeper sense-making process, which in return creates proposals that can be interpreted...... as having new sociocultural meaning in line with Vergantis definition of radical innovation. This paper discusses the results of an experiment with 32 students on idea generation and product concept development. The experiment was setup as and A-B comparison between two set of students with the same...... objective: designing a new coffee machine for a specific brand, but one group was asked to seek ambiguity and dissonance before creating proposals. Results indicate a very clear difference in the outcome in terms of radical changes in relation to. Group A produced 12 out of 16 proposals in the Styling...

  9. Valuing Gender Diversity in Teams

    DEFF Research Database (Denmark)

    Lauring, Jakob; Villeseche, Florence

    2015-01-01

    Team gender diversity has been much debated in many different contexts – not least since the search for a main effect of diversity on performance was launched. However, results have so far been inconclusive, and a number of scholars suggest that more attention should be directed at contextual...... factors which could influence the effect of gender diversity on team performance. In this study, we explore the effect of positive diversity attitudes and assess the degree of gender diversity where such group attitudes have greater impact. This is done by using a sample of 1085 leaders of academic...... research teams. Findings show that positive diversity attitude in the form of group openness to diversity is strongly associated with team performance. We also find a moderating effect of gender diversity meaning that the effect of openness to diversity is stronger when gender groups are more balanced...

  10. Desired Diversity and Symptomatic Anxiety

    DEFF Research Database (Denmark)

    Friis Christensen, Jannick; Muhr, Sara Louise

    2018-01-01

    This paper conceptualises organisational diversity as constituted by psychoanalytic lack. Empirically, we show how diversity as Lacanian lack is understood as nothing in or of itself, but as an empty signifier with no signified. The lack of diversity becomes a catalyst for desiring particular ideas...... of diversity that, however, constantly change due to the empty form of diversity. Anxiety manifests itself in the obsession of unobtainable idealised forms of diversity as well as in the uncertainty associated with the traumatic experience of always falling short of what is desired in an object...... – the experience of failed diversity. Conclusively, we discuss the productive potential of the power of lack. The impossibility of diversity is what, at once, conditions the possibility of diversity. We therefore suggest that the symptomatic anxiety provoked by the lack should be enjoyed in order to engage...

  11. Valuing Gender Diversity in Teams

    DEFF Research Database (Denmark)

    Lauring, Jakob; Villeseche, Florence

    Team gender diversity has been much debated in many different contexts – not least since the search for a main effect of diversity on performance was launched. However, results have so far been inconclusive, and a number of scholars suggest that more attention should be directed at contextual...... factors which could influence the effect of gender diversity on team performance. In this study, we explore the effect of positive diversity attitudes and assess the degree of gender diversity where such group attitudes have greater impact. This is done by using a sample of 1085 leaders of academic...... research teams. Findings show that positive diversity attitude in the form of group openness to diversity is strongly associated with team performance. We also find a moderating effect of gender diversity meaning that the effect of openness to diversity is stronger when gender groups are more balanced...

  12. Imposing genetic diversity.

    Science.gov (United States)

    Sparrow, Robert

    2015-01-01

    The idea that a world in which everyone was born "perfect" would be a world in which something valuable was missing often comes up in debates about the ethics of technologies of prenatal testing and preimplantation genetic diagnosis (PGD). This thought plays an important role in the "disability critique" of prenatal testing. However, the idea that human genetic variation is an important good with significant benefits for society at large is also embraced by a wide range of figures writing in the bioethics literature, including some who are notoriously hostile to the idea that we should not select against disability. By developing a number of thought experiments wherein we are to contemplate increasing genetic diversity from a lower baseline in order to secure this value, I argue that this powerful intuition is more problematic than is generally recognized, especially where the price of diversity is the well-being of particular individuals.

  13. Managing molecular diversity.

    Science.gov (United States)

    Perez, Juan J

    2005-02-01

    The present work provides an overview of the different methods used in molecular diversity analysis. Issues like identifying voids in proprietary databases, reducing the number of redundancies present in databases, or designing focused libraries by grouping compounds similar to a template with the aim to fine tune its properties, are potent diversity analysis tools that may be used to optimize molecules based on their properties and specifically, to speed up the process of lead discovery and optimization. The present work describes first methods that are used to describe molecular systems. This is followed by a section devoted to describe different measures of similarity between molecules, to finish with a description of different methods used to select subsets molecules according to the constraints imposed. The final section deals with the validation of these methods, based on different studies available in the literature.

  14. Equal opportunities in diversity

    CERN Multimedia

    Laëtitia Pedroso

    2010-01-01

    Promoting equal opportunities at CERN and advising the Director-General on all related matters is the task of the Equal Opportunities Officer, Doris Chromek-Burckhart, and Tim Smith, chair of the Equal Opportunities Advisory Panel. Changes are being introduced: in future, the focus of their work will be broadened to cover all aspects of diversity promotion.   The term "equal opportunities" has always been broader in scope than the equal treatment of men and women but this is what it has traditionally been confined to in practice. "We wanted to change how people see our mission", explains Doris Chromek-Burckhart. The word "diversity" has much wider connotations than "equal opportunities" and makes it clearer that we are also dealing with differences in nationality, religion, age, culture and physical ability”. Getting away from the old clichés is vital to ensuring equal treatment for everyone. The diversit...

  15. Air Force Leadership Diversity

    Science.gov (United States)

    2017-04-06

    College, Air University, Maxwell AFB, AL. He grew up as part of an Air Force family, entered active duty in 1996, and is a career Aircraft Maintenance... artificially limit them to capping out at O-6 if we want to encourage diversity in our most senior leadership levels as we seek to create a stronger...but I am not sure it does. I find it interesting that as of 31 December 2016 the Deputy Chief of Staff for Intelligence , Surveillance and

  16. Diverse Image Annotation

    KAUST Repository

    Wu, Baoyuan

    2017-11-09

    In this work we study the task of image annotation, of which the goal is to describe an image using a few tags. Instead of predicting the full list of tags, here we target for providing a short list of tags under a limited number (e.g., 3), to cover as much information as possible of the image. The tags in such a short list should be representative and diverse. It means they are required to be not only corresponding to the contents of the image, but also be different to each other. To this end, we treat the image annotation as a subset selection problem based on the conditional determinantal point process (DPP) model, which formulates the representation and diversity jointly. We further explore the semantic hierarchy and synonyms among the candidate tags, and require that two tags in a semantic hierarchy or in a pair of synonyms should not be selected simultaneously. This requirement is then embedded into the sampling algorithm according to the learned conditional DPP model. Besides, we find that traditional metrics for image annotation (e.g., precision, recall and F1 score) only consider the representation, but ignore the diversity. Thus we propose new metrics to evaluate the quality of the selected subset (i.e., the tag list), based on the semantic hierarchy and synonyms. Human study through Amazon Mechanical Turk verifies that the proposed metrics are more close to the humans judgment than traditional metrics. Experiments on two benchmark datasets show that the proposed method can produce more representative and diverse tags, compared with existing image annotation methods.

  17. Knowing Generation Y: a new generation of nurses in practice.

    Science.gov (United States)

    Chung, Stephanie M

    Generation Y is commonly defined as those people born between 1980 and 2000, now aged in their 20s and 30s. Their grandparents experienced post-World War II reconstruction, their parents the economic boom of the 1980s. There are currently 81 million individuals in the Generation Y cohort in the USA, making it the second-largest, and possibly most influential, cohort since World War II (Manion, 2009). Members of Generation Y are diverse, technologically advanced and vocal about their opinions. They tend to resist traditional hierarchy, want recognition/reward for achievements and distrust institutions. Knowing these characteristics is useful for nurse managers, preceptors and team members working with members of Generation Y. Studies have proven that Generation Y is challenging the nursing workforce through rapid turnover (Cogin, 2012). This article explores a theoretical model that predicts retention and/or turnover of nurses in light of Generation Y behaviours and motivators-for example, moving from agency to agency rather than devoting many years to a single practice. Further research is needed to find out whether these behaviours and motivators are unique to Generation Y alone.

  18. Discriminatory Diversity Definitions: The Ironic Consequences of Managerial Diversity Conceptions

    OpenAIRE

    Ho, Geoffrey C.

    2013-01-01

    Recent research has documented the increasing managerialization of diversity definitions (i.e., the focus on non-legal dimensions of diversity; Edelman et al., 2001). In three studies, we examine how managerial diversity definitions may affect the perpetuation and enhancement of social inequality in organizations. In Study 1 we find in a survey that organizations with managerial diversity definitions are more likely to have employees who believe their organizations do not have racial diversit...

  19. Celebrating diversity at CERN

    CERN Document Server

    2014-01-01

    With international women’s day coming up on 8 March, along with the recent appointment of a new Diversity Programme Leader, it seems timely to take a look at how far we’ve come over recent years in promoting gender equality at CERN. In short, the news is good, but we still have some way to travel.   CERN does not have a policy of positive discrimination, but rather one of presenting a level playing field. We work to ensure, for example, that the diversity of candidates presented for interview reflects the diversity of applicants. It’s an approach that is having the desired effect. Overall, the percentage of female staff members has risen from 17% to 20% over the last decade, with parity being achieved among professional administrators and significant advances being made among research and applied physicists, engineers and technicians. At recruitment, our approach is working: we’re managing to attract growing numbers of women. This brings us to the phen...

  20. Plasma generator

    International Nuclear Information System (INIS)

    Omichi, Takeo; Yamanaka, Toshiyuki.

    1976-01-01

    Object: To recycle a coolant in a sealed hollow portion formed interiorly of a plasma limiter itself to thereby to cause direct contact between the coolant and the plasma limiter and increase of contact area therebetween to cool the plasma limiter. Structure: The heat resulting from plasma generated during operation and applied to the body of the plasma limiter is transmitted to the coolant, which recycles through an inlet and outlet pipe, an inlet and outlet nozzle and a hollow portion to hold the plasma limiter at a level less than a predetermined temperature. On the other hand, the heater wire is, at the time of emergency operation, energized to heat the plasma limiter, but this heat is transmitted to the limiter body to increase the temperature thereof. However, the coolant recycling the hollow portion comes into direct contact with the limiter body, and since the plasma limiter surround the hollow portion, the heat amount transmitted from the limiter body to the coolant increases to sufficiently cool the plasma limiter. (Yoshihara, H.)

  1. Diversity mindsets and the performance of diverse teams

    NARCIS (Netherlands)

    van Knippenberg, D.; van Ginkel, W.P.; Homan, A.C.

    2013-01-01

    Diversity can enhance as well as disrupt team performance. Diversity beliefs and climates may play an important moderating role in these effects, but it is unclear what form these should take to promote the positive effects of diversity. Addressing this question in an integration of research in team

  2. Managing a culturally diverse workforce : Diversity perspectives in organizations

    NARCIS (Netherlands)

    Podsiadlowski, Astrid; Gröschke, Daniela; Kogler, Marina; Springer, Cornelia; van der Zee, Karen

    The authors conducted two studies to analyze why and how organizations approach and manage cultural diversity in the Austrian workplace and to identify organizations' diversity perspectives. In Study 1, 29 interviews revealed insights into organizational approaches to diversity and how these

  3. Diversity Management in the Workplace

    OpenAIRE

    Hana Urbancová; Helena Čermáková; Hana Vostrovská

    2016-01-01

    Diversity is a phenomenon which is increasingly manifesting itself in the globalized society; therefore, it is observable in various areas of human activity, and thus also in the labour market and work teams. Age, sex, ethnicity and nationality, creed or disabilities are among the parameters of diversity. The aim of the article is to identify and evaluate the implementation of Diversity Management in workplaces, whilst bearing in mind researched factors of diversity. The results were gained b...

  4. Discovering Diversity in Marketing Practice

    OpenAIRE

    Murray, John; O'Driscoll, Aidan; Torres, Ann

    2002-01-01

    Marketing practice varies among firms. However, the prescriptive literature emphasises a universal view of practice, a “one-size-fits-all” view. This paper addresses the issue of explaining diversity in competitive space and over time. Diversity in competitive space reflects the existence of different routes to high performance. Diversity over time reflects some combination of change in the individual firm and change in a population of firms. In the former case, diversity is shaped by organis...

  5. Diversity in the Workplace. Symposium.

    Science.gov (United States)

    2002

    Three papers comprise this symposium on diversity in the workplace. "Factors That Assist and Barriers That Hinder the Success of Diversity Initiatives in Multinational Corporations" (Rose Mary Wentling) reports that factors that assisted in the success were classified under diversity department, human, and work environment; barriers were…

  6. Knowledge sharing in diverse organizations

    DEFF Research Database (Denmark)

    Lauring, Jakob; Selmer, Jan

    2012-01-01

    It has been argued that both strengths and weaknesses of diversity in organisations stem from the different demographic, national, linguistic, social and cultural backgrounds of their members. However, few attempts have been made to link different types of diversity to knowledge sharing despite t...... of these findings for the management of knowledge in intensive diverse organisations are discussed in detail....

  7. Managing Diversity within Cooperative Extension.

    Science.gov (United States)

    Ewert, D. Merrill; Rice, Jennifer A. King

    1994-01-01

    Six focus groups analyzed findings of a literature review on cultural diversity's effects on productivity and effectiveness. Action steps for Cooperative Extension were outlined: implementing affirmative action, valuing diversity, managing diversity, creating new management structures, and establishing a more supportive environment. (SK)

  8. Diversity-Guided Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    2002-01-01

    Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few algorit...

  9. Analyzing viewpoint diversity in twitter

    NARCIS (Netherlands)

    Bozdag, V.E.; Gao, Q.; Warnier, M.E.; Houben, G.J.P.M.

    2013-01-01

    Information diversity has a long tradition in human history. Recently there have been claims that diversity is diminishing in information available in social networks. On the other hand, some studies suggest that diversity is actually quite high in social networks such as Twitter. However these

  10. Phytochemical diversity drives plant-insect community diversity.

    Science.gov (United States)

    Richards, Lora A; Dyer, Lee A; Forister, Matthew L; Smilanich, Angela M; Dodson, Craig D; Leonard, Michael D; Jeffrey, Christopher S

    2015-09-01

    What are the ecological causes and consequences of variation in phytochemical diversity within and between plant taxa? Despite decades of natural products discovery by organic chemists and research by chemical ecologists, our understanding of phytochemically mediated ecological processes in natural communities has been restricted to studies of either broad classes of compounds or a small number of well-characterized molecules. Until now, no studies have assessed the ecological causes or consequences of rigorously quantified phytochemical diversity across taxa in natural systems. Consequently, hypotheses that attempt to explain variation in phytochemical diversity among plants remain largely untested. We use spectral data from crude plant extracts to characterize phytochemical diversity in a suite of co-occurring plants in the tropical genus Piper (Piperaceae). In combination with 20 years of data focused on Piper-associated insects, we find that phytochemical diversity has a direct and positive effect on the diversity of herbivores but also reduces overall herbivore damage. Elevated chemical diversity is associated with more specialized assemblages of herbivores, and the cascading positive effect of phytochemistry on herbivore enemies is stronger as herbivore diet breadth narrows. These results are consistent with traditional hypotheses that predict positive associations between plant chemical diversity, insect herbivore diversity, and trophic specialization. It is clear from these results that high phytochemical diversity not only enhances the diversity of plant-associated insects but also contributes to the ecological predominance of specialized insect herbivores.

  11. Phytochemical diversity drives plant–insect community diversity

    Science.gov (United States)

    Richards, Lora A.; Dyer, Lee A.; Forister, Matthew L.; Smilanich, Angela M.; Dodson, Craig D.; Leonard, Michael D.; Jeffrey, Christopher S.

    2015-01-01

    What are the ecological causes and consequences of variation in phytochemical diversity within and between plant taxa? Despite decades of natural products discovery by organic chemists and research by chemical ecologists, our understanding of phytochemically mediated ecological processes in natural communities has been restricted to studies of either broad classes of compounds or a small number of well-characterized molecules. Until now, no studies have assessed the ecological causes or consequences of rigorously quantified phytochemical diversity across taxa in natural systems. Consequently, hypotheses that attempt to explain variation in phytochemical diversity among plants remain largely untested. We use spectral data from crude plant extracts to characterize phytochemical diversity in a suite of co-occurring plants in the tropical genus Piper (Piperaceae). In combination with 20 years of data focused on Piper-associated insects, we find that phytochemical diversity has a direct and positive effect on the diversity of herbivores but also reduces overall herbivore damage. Elevated chemical diversity is associated with more specialized assemblages of herbivores, and the cascading positive effect of phytochemistry on herbivore enemies is stronger as herbivore diet breadth narrows. These results are consistent with traditional hypotheses that predict positive associations between plant chemical diversity, insect herbivore diversity, and trophic specialization. It is clear from these results that high phytochemical diversity not only enhances the diversity of plant-associated insects but also contributes to the ecological predominance of specialized insect herbivores. PMID:26283384

  12. Production diversity and dietary diversity in smallholder farm households

    Science.gov (United States)

    Sibhatu, Kibrom T.; Krishna, Vijesh V.; Qaim, Matin

    2015-01-01

    Undernutrition and micronutrient malnutrition remain problems of significant magnitude in large parts of the developing world. Improved nutrition requires not only better access to food for poor population segments, but also higher dietary quality and diversity. Because many of the poor and undernourished people are smallholder farmers, diversifying production on these smallholder farms is widely perceived as a useful approach to improve dietary diversity. However, empirical evidence on the link between production and consumption diversity is scarce. Here, this issue is addressed with household-level data from Indonesia, Kenya, Ethiopia, and Malawi. Regression models show that on-farm production diversity is positively associated with dietary diversity in some situations, but not in all. When production diversity is already high, the association is not significant or even turns negative, because of foregone income benefits from specialization. Analysis of other factors reveals that market access has positive effects on dietary diversity, which are larger than those of increased production diversity. Market transactions also tend to reduce the role of farm diversity for household nutrition. These results suggest that increasing on-farm diversity is not always the most effective way to improve dietary diversity in smallholder households and should not be considered a goal in itself. Additional research is needed to better understand how agriculture and food systems can be made more nutrition-sensitive in particular situations. PMID:26261342

  13. Cycles in fossil diversity

    Energy Technology Data Exchange (ETDEWEB)

    Rohde, Robert A.; Muller, Richard A.

    2004-10-20

    It is well-known that the diversity of life appears to fluctuate during the course the Phanerozoic, the eon during which hard shells and skeletons left abundant fossils (0-542 Ma). Using Sepkoski's compendium of the first and last stratigraphic appearances of 36380 marine genera, we report a strong 62 {+-} 3 Myr cycle, which is particularly strong in the shorter-lived genera. The five great extinctions enumerated by Raup and Sepkoski may be an aspect of this cycle. Because of the high statistical significance, we also consider contributing environmental factors and possible causes.

  14. Trust in Diverse Teams

    DEFF Research Database (Denmark)

    Clausen, Lisbeth

    Multicultural membership and diversity in teams are important to maintain effectiveness in organizations in a global business environment. Multicultural teams offer great potential in international collaboration just as top management teams are becoming increasingly diversified. However...... and interviews with managers from the US, Europe, China and Japan. The study presents a conceptual framework - a ‘trust buffer’ – which enables analysis and exemplification of the dynamics and challenges of teams as drivers of change. Each team has strategically important tasks, unique capacities and deal...

  15. Media Pluralism and Diversity

    DEFF Research Database (Denmark)

    In the western world, a diverse and pluralistic media landscape is deemed essential for democracy. But how universal is media pluralism as a concept underpinning media policies? To what extent do normative approaches, regulatory dimensions and monitoring systems differ throughout the world...... challenges for media pluralism policies in the light of a fast changing media environment. The book is unique in that it confronts insights from all parts of the world and from a broad range of disciplines including law, economics, media studies, and sociology....

  16. The duplicity of diversity

    DEFF Research Database (Denmark)

    Olwig, Karen Fog

    2015-01-01

    ‘Diversity’ has become a key term in recent years, yet it has been criticized for being a vague concept with different and contradictory meanings. This article demonstrates that there are at least three inherent meanings of the term: (1) discerned difference attributed with positive or negative v...... is recognized and actively employed. This is shown through an analysis of the ways in which immigrants from the English-speaking Caribbean to Denmark have been perceived and received as foreigners since the 1960s as representing different kinds of diversity....

  17. 43 CFR 418.16 - Using water for power generation.

    Science.gov (United States)

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Using water for power generation. 418.16... Operations and Management § 418.16 Using water for power generation. All use of Project water for power generation must be incidental to releases charged against Project diversions, precautionary drawdown...

  18. Trip generation characteristics of special generators

    Science.gov (United States)

    2010-03-01

    Special generators are introduced in the sequential four-step modeling procedure to represent certain types of facilities whose trip generation characteristics are not fully captured by the standard trip generation module. They are also used in the t...

  19. Tobacco Diversity in Indonesia

    Directory of Open Access Journals (Sweden)

    Djajadi Djajadi

    2015-09-01

    Full Text Available Tobacco variants in Indonesia are very diverse which can be identified from their morphology or their characteristics. This is related to tobacco long adaptation in different agro ecology of plantation areas which spread out at 15 provinces, from dry to irrigated land and from low land to high land areas. Tobacco has been introduced in Indonesia for more than four centuries and mostly used as cigarette. This commodity and its products are still economically important for government and farmer income. It contributes in government income which reached up to 114 trillion rupiahs and farmer income up to 70% in 2014. Tobacco diversity in Indonesia can be grouped according to their growing season and their usage in cigarette blending. Tobaccos which grown at the end of wet season and harvested in dry season are called Voor Oogst tobaccos, otherwise tobaccos which grown at dry season and harvested in wet season are called Na Oogst tobaccos. Based on their usage, tobaccos are categorized as main ingredients for kretek cigarette, Rolled Your Own (RYO cigarette, and cigar industries.

  20. Practical exercises in diversity

    CERN Multimedia

    Anaïs Schaeffer

    2013-01-01

    On 4 July, the Bulletin took part in an interactive workshop in the framework of the CERN Diversity programme. And it was time very well spent. Read on…   Discussion on the theme "unconscious bias". The participants begin to gather in the Pump Room (Building 2016) around 1.30 p.m. With name-tags stuck to our chests, we take our places at Table 7, which we now realise we selected for ourselves at random. Some people have already arrived, and after some tentative, courteous introductions, the atmosphere at the “sevens table” begins to warm up. A few minutes later, the workshop begins. Alan Richter, CEO of HR consultancy firm QED Consulting is the Master of Ceremonies. First exercise, “the circle”, or how to prove that diversity starts right under your nose. Skiers to the left, non-skiers to the right. The overwhelming majority are skiers. How do the non-skiers feel about finding themselves in the minority? Uncomfortable? Exc...

  1. Bilirubin present in diverse angiosperms.

    Science.gov (United States)

    Pirone, Cary; Johnson, Jodie V; Quirke, J Martin E; Priestap, Horacio A; Lee, David

    2010-01-01

    Bilirubin is an orange-yellow tetrapyrrole produced from the breakdown of heme by mammals and some other vertebrates. Plants, algae and cyanobacteria synthesize molecules similar to bilirubin, including the protein-bound bilins and phytochromobilin which harvest or sense light. Recently, we discovered bilirubin in the arils of Strelitzia nicolai, the White Bird of Paradise Tree, which was the first example of this molecule in a higher plant. Subsequently, we identified bilirubin in both the arils and the flowers of Strelitzia reginae, the Bird of Paradise Flower. In the arils of both species, bilirubin is present as the primary pigment, and thus functions to produce colour. Previously, no tetrapyrroles were known to generate display colour in plants. We were therefore interested in determining whether bilirubin is broadly distributed in the plant kingdom and whether it contributes to colour in other species. In this paper, we use HPLC/UV and HPLC/UV/electrospray ionization-tandem mass spectrometry (HPLC/UV/ESI-MS/MS) to search for bilirubin in 10 species across diverse angiosperm lineages. Bilirubin was present in eight species from the orders Zingiberales, Arecales and Myrtales, but only contributed to colour in species within the Strelitziaceae. The wide distribution of bilirubin in angiosperms indicates the need to re-assess some metabolic details of an important and universal biosynthetic pathway in plants, and further explore its evolutionary history and function. Although colour production was limited to the Strelitziaceae in this study, further sampling may indicate otherwise.

  2. Climate change and cultural diversity.

    Science.gov (United States)

    Wisner, Ben

    2010-01-01

    Cultures and climate are changing. These changes interact with local knowledge and practice. Research has focused on technical questions, such as how small farmers and livestock keepers understand seasonal forecasts, veterinary problems or market conditions. However, there is a more holistic way of engaging local knowledge. Rural people utilise external technical ideas and tools, even complex ones, that complement their own concepts and experience of change. However, there are obstacles to overcome in generating such hybrid local knowledge. Firstly, there is a long history of domination of rural people by urban elites, including the assumed superiority of urban or high culture versus rural, vernacular or low culture. A second obstacle comes from the frequent use of science as justification to force rural people to do what governments want. Experience of exclusion and displacement has left a residue of bitterness and suspicion among many rural people. A third obstacle involves misuse of one-size-fits-all methods. No single, homogeneous knowledge exists in a locality. Rather there are women's forms of knowledge and the knowledge of men and elders and the knowledge of young people and children, which are differentiated also by occupation and by ethnicity. In the face of such cultural diversity an incompetent use of standardised participatory methods yields poor results and may alienate residents.

  3. Healthcare leadership's diversity paradox.

    Science.gov (United States)

    Silver, Reginald

    2017-02-06

    Purpose The purpose of this research study was to obtain healthcare executives' perspectives on diversity in executive healthcare leadership. The study focused on identifying perspectives about diversity and its potential impact on the access of healthcare services by people of color. The study also identified perspectives about factors that influence the attainment of executive healthcare roles by people of color. Design/methodology/approach A convenience sample of healthcare executives was obtained. The executives identified themselves as belonging to one of two subgroups, White healthcare executives or executives of color. Participants were interviewed telephonically in a semi-structured format. The interviews were transcribed and entered into a qualitative software application. The data were codified and important themes were identified. Findings The majority of the study participants perceive that diversity of the executive healthcare leadership team is important. There were differences in perspective among the subgroups as it relates to solutions to improve access to healthcare by people of color. There were also differences in perspective among the subgroups, as it relates to explaining the underrepresentation of people of color in executive healthcare leadership roles. Research limitations/implications This research effort benefited from the subject matter expertise of 24 healthcare executives from two states. Expansion of the number of survey participants and broadening the geographical spread of where participants were located may have yielded more convergence and/or more divergence in perspectives about key topics. Practical implications The findings from this research study serve to add to the existing body of literature on diversity in executive healthcare leadership. The findings expand on the importance of key elements in contemporary literature such as diversity, cultural competency and perspectives about the need for representation of people of

  4. Growth-dependent secretome of Candida utilis

    NARCIS (Netherlands)

    Buerth, C.; Heilmann, C.J.; Klis, F.M.; de Koster, C.G.; Ernst, J.F.; Tielker, D.

    2011-01-01

    Recently, the food yeast Candida utilis has emerged as an excellent host for production of heterologous proteins. Since secretion of the recombinant product is advantageous for its purification, we characterized the secreted proteome of C. utilis. Cells were cultivated to the exponential or

  5. Robust signaling networks of the adipose secretome

    NARCIS (Netherlands)

    Breitling, Rainer

    Type 2 diabetes is a prototypical complex systems disease that has a strong hereditary component and etiologic links with a sedentary lifestyle, overeating and obesity. Adipose tissue has been shown to be a central driver of type 2 diabetes progression, establishing and maintaining a chronic state

  6. Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

    Science.gov (United States)

    Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard

    2017-12-28

    The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

  7. Evolution and genetic diversity of Theileria.

    Science.gov (United States)

    Sivakumar, Thillaiampalam; Hayashida, Kyoko; Sugimoto, Chihiro; Yokoyama, Naoaki

    2014-10-01

    Theileria parasites infect a wide range of domestic and wild ruminants worldwide, causing diseases with varying degrees of severity. A broad classification, based on the parasite's ability to transform the leukocytes of host animals, divides Theileria into two groups, consisting of transforming and non-transforming species. The evolution of transforming Theileria has been accompanied by drastic changes in its genetic makeup, such as acquisition or expansion of gene families, which are thought to play critical roles in the transformation of host cells. Genetic variation among Theileria parasites is sometimes linked with host specificity and virulence in the parasites. Immunity against Theileria parasites primarily involves cell-mediated immune responses in the host. Immunodominance and major histocompatibility complex class I phenotype-specificity result in a host immunity that is tightly focused and strain-specific. Immune escape in Theileria is facilitated by genetic diversity in its antigenic determinants, which potentially results in a loss of T cell receptor recognition in its host. In the recent past, several reviews have focused on genetic diversity in the transforming species, Theileriaparva and Theileriaannulata. In contrast, genetic diversity in Theileriaorientalis, a benign non-transforming parasite, which occasionally causes disease outbreaks in cattle, has not been extensively examined. In this review, therefore, we provide an outline of the evolution of Theileria, which includes T. orientalis, and discuss the possible mechanisms generating genetic diversity among parasite populations. Additionally, we discuss the potential implications of a genetically diverse parasite population in the context of Theileria vaccine development. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Evolution of peptidase diversity.

    Science.gov (United States)

    Page, Michael J; Di Cera, Enrico

    2008-10-31

    A wide variety of peptidases associate with vital biological pathways, but the origin and evolution of their tremendous diversity are poorly defined. Application of the MEROPS classification to a comprehensive set of genomes yields a simple pattern of peptidase distribution and provides insight into the organization of proteolysis in all forms of life. Unexpectedly, a near ubiquitous core set of peptidases is shown to contain more types than those unique to higher multicellular organisms. From this core group, an array of eukaryote-specific peptidases evolved to yield well known intracellular and extracellular processes. The paucity of peptidase families unique to higher metazoa suggests gains in proteolytic network complexity required a limited number of biochemical inventions. These findings provide a framework for deeper investigation into the evolutionary forces that shaped each peptidase family and a roadmap to develop a timeline for their expansion as an interconnected system.

  9. Absorptive Capacity and Diversity

    DEFF Research Database (Denmark)

    Kristinsson, Kári

    international business, organizational economics, strategic management, technology management and last but not least neo-Schumpeterian economics. The goal of this dissertation is to examine what many consider as neglected arguments from the work by Cohen and Levinthal and thereby illuminate an otherwise......One of the most influential contributions to neo-Schumpeterian economics is Cohen and Levinthal‘s papers on absorptive capacity. Since their publication in the late 1980s and early 1990s the concept absorptive capacity has had substantial impact on research in economics and management, including...... overlooked area of research. Although research based on Cohen and Levinthal‘s work has made considerable impact, there is scarcity of research on certain fundamental points argued by Cohen and Levinthal. Among these is the importance of employee diversity as well as the type and nature of interaction between...

  10. Analyses of the microbial diversity across the human microbiome.

    Directory of Open Access Journals (Sweden)

    Kelvin Li

    next-generation sequence data, further revealing that low abundant taxa serve as an important reservoir of genetic diversity in the human microbiome.

  11. Assessing nutritional diversity of cropping systems in African villages.

    Directory of Open Access Journals (Sweden)

    Roseline Remans

    Full Text Available BACKGROUND: In Sub-Saharan Africa, 40% of children under five years in age are chronically undernourished. As new investments and attention galvanize action on African agriculture to reduce hunger, there is an urgent need for metrics that monitor agricultural progress beyond calories produced per capita and address nutritional diversity essential for human health. In this study we demonstrate how an ecological tool, functional diversity (FD, has potential to address this need and provide new insights on nutritional diversity of cropping systems in rural Africa. METHODS AND FINDINGS: Data on edible plant species diversity, food security and diet diversity were collected for 170 farms in three rural settings in Sub-Saharan Africa. Nutritional FD metrics were calculated based on farm species composition and species nutritional composition. Iron and vitamin A deficiency were determined from blood samples of 90 adult women. Nutritional FD metrics summarized the diversity of nutrients provided by the farm and showed variability between farms and villages. Regression of nutritional FD against species richness and expected FD enabled identification of key species that add nutrient diversity to the system and assessed the degree of redundancy for nutrient traits. Nutritional FD analysis demonstrated that depending on the original composition of species on farm or village, adding or removing individual species can have radically different outcomes for nutritional diversity. While correlations between nutritional FD, food and nutrition indicators were not significant at household level, associations between these variables were observed at village level. CONCLUSION: This study provides novel metrics to address nutritional diversity in farming systems and examples of how these metrics can help guide agricultural interventions towards adequate nutrient diversity. New hypotheses on the link between agro-diversity, food security and human nutrition are

  12. Assessing nutritional diversity of cropping systems in African villages.

    Science.gov (United States)

    Remans, Roseline; Flynn, Dan F B; DeClerck, Fabrice; Diru, Willy; Fanzo, Jessica; Gaynor, Kaitlyn; Lambrecht, Isabel; Mudiope, Joseph; Mutuo, Patrick K; Nkhoma, Phelire; Siriri, David; Sullivan, Clare; Palm, Cheryl A

    2011-01-01

    In Sub-Saharan Africa, 40% of children under five years in age are chronically undernourished. As new investments and attention galvanize action on African agriculture to reduce hunger, there is an urgent need for metrics that monitor agricultural progress beyond calories produced per capita and address nutritional diversity essential for human health. In this study we demonstrate how an ecological tool, functional diversity (FD), has potential to address this need and provide new insights on nutritional diversity of cropping systems in rural Africa. Data on edible plant species diversity, food security and diet diversity were collected for 170 farms in three rural settings in Sub-Saharan Africa. Nutritional FD metrics were calculated based on farm species composition and species nutritional composition. Iron and vitamin A deficiency were determined from blood samples of 90 adult women. Nutritional FD metrics summarized the diversity of nutrients provided by the farm and showed variability between farms and villages. Regression of nutritional FD against species richness and expected FD enabled identification of key species that add nutrient diversity to the system and assessed the degree of redundancy for nutrient traits. Nutritional FD analysis demonstrated that depending on the original composition of species on farm or village, adding or removing individual species can have radically different outcomes for nutritional diversity. While correlations between nutritional FD, food and nutrition indicators were not significant at household level, associations between these variables were observed at village level. This study provides novel metrics to address nutritional diversity in farming systems and examples of how these metrics can help guide agricultural interventions towards adequate nutrient diversity. New hypotheses on the link between agro-diversity, food security and human nutrition are generated and strategies for future research are suggested calling for

  13. Tourism and diversity

    Directory of Open Access Journals (Sweden)

    Zsuzsanna Bacsi

    2017-10-01

    Full Text Available Cultural attractions are often linked to unique features of the host population, and are often related to a national minority or a segment of the population that preserved their traditions. Ethnically or religiously varied countries may often have such unique attractions, that seem exotic and appealing to tourists. Multiculturality is often an attraction for tourism, offering generally an authentic experience for visitors of different backgrounds. Besides, an ethnically or linguistically varied population can also provide a linguisticaly more skilful labour force, that is more sensitive to the needs of visitors coming from different cultures, and thus create a more comfortable environment for them. The issue of multicultural societies has recently become a sensitive issue, due to global mass migration. There is a belief that ethnic or cultural fractionalisation would necessarily bring about difficulties of understanding and cooperation, leading to lower economic performance, less stable economic and social processes and, ultimately a slowdown of economic output. The resulting conflicts, difficulties may frighten away tourists and lead to the vulnerability of the tourism sector in very heterogeneous countries. On the other hand, ethnic fractionalisation and the resulting cultural diversity can be welcome as valuable resources as the varied pool of knowledge, traditions, skills, customs, that can enhance innovative ideas and creativity. In the present paper evidence is looked for the relationship between ethnic, linguistic and religious diversity and tourism performance in a cross-country statistical analysis of 155 countries of the world. Statistical analysis of 155 countries show, that although there is a tendency of lower tourism performance with greated fractionalisation of the society, the most popular and successful tourism destinations are often multicultural and multiethnic societies.

  14. Whose Diversity Counts? The Politics and Paradoxes of Modern Diversity

    Directory of Open Access Journals (Sweden)

    Lauren Baker

    2013-06-01

    Full Text Available Is “diversity” a modern concept, like indigeneity or biodiversity, which is conceived precisely at the time that it seems to be threatened and on the verge of disappearing? In the face of perceived threats to diversity, projects and policies have been crafted to protect, promote, or conserve diversity, but in doing so they have often demonstrated a paradoxical propensity toward purity and authority in representations of diversity. Perceptions of “pure” natural diversity might represent native forests comprised solely of native species; “pure” cultural diversity might represent indigenous peoples who still speak indigenous languages and wear native dress. If purity is emblematic of diversity, what, then, is the place of hybrid landscapes and peoples? In our study, we draw on a range of examples—of agrobiodiversity conservation in Bolivia, satellite mapping initiatives in Madagascar and Ecuador, scientific authority about anthropogenic climate change, indigenous language and identity in Peru, and a comparison of the Amazon and Atlantic Forest in Brazil—to demonstrate gaps between representations of diversity, and the heterogeneous local realities they obscure. We suggest that hybridity is a form of diversity unto itself—albeit a form of diversity that is more complex, and thus harder to codify and categorize.

  15. Self generation, small generation, and embedded generation issues

    International Nuclear Information System (INIS)

    2001-01-01

    The New Brunswick Market Design Committee for electric power restructuring has been directed to examine issues regarding cogeneration and small-scale, on-site generation and how they will fit within the framework of the bilateral contract market. The Committee will also have to deal with issues of generation embedded in a distribution system. The Committee has defined cogeneration as the simultaneous production of electricity and useful thermal energy. Self-generation has been defined as small-scale power generation by an end-user, while embedded generation has been defined as a generation facility that is located within a distribution utility but is not directly connected to the transmission system. The Committee has postponed its decision on whether embedded generation will be eligible to participate under the bilateral contract market for electricity. This report discusses general issues such as the physical support of generation, market support of generation, transition issues and policy issues. It also discusses generation support issues such as operating reserves, transmission tariff issues, and distribution tariffs. Market support issues such as transmission access for generation sales were also considered, along with market access for generation sales, and net metering for behind the meter generation. 7 refs., 1 tab

  16. First-Generation Women and Identity Intersectionality

    Science.gov (United States)

    Kouzoukas, Georgia

    2017-01-01

    With a considerable focus to increase America's degree completion rates amongst our diverse population, higher education policymakers and researchers have examined the college access, persistence, and completion rates of first-generation students. However, minimal research has addressed the heterogeneous student population through a gendered or…

  17. Educating the next generation of nature entrepreneurs

    Science.gov (United States)

    Judith C. Jobse; Loes Witteveen; Judith Santegoets; Daan van der Linde

    2015-01-01

    With this paper, it is illustrated that a focus on entrepreneurship training in the nature and wilderness sector is relevant for diverse organisations and situations. The first curricula on nature entrepreneurship are currently being developed. In this paper the authors describe a project that focusses on educating the next generation of nature entrepreneurs, reflect...

  18. From Diversity Management to Diversimilation

    DEFF Research Database (Denmark)

    Holck, Lotte; Muhr, Sara Louise

    “Diversimilation” as a corporate response to diversity By PhD fellow Lotte Holck, Copenhagen Business School (IOA) Abstract Across the North Atlantic organizations struggle to harvest the perceived ’ fruits’ of diversity of enhanced organizational learning and requisite variety enriching task...... performance in response to globalized markets and customers – but by means of different approaches to organizing diversity (Klarsfeld 2012, Embrick 2011, Banting 2010, Holvino & Kamp 2009, Matten & Moon 2008, Risberg & Søderberg 2008, Campbell 2007, Boxenbaum 2007). The argument of this paper...... is that this is partly due to the history of diversity and maturity of the diversity agenda, where especially the US confrontation with and acknowledgement of a colonial past has made way for a more "advanced" approach valuing diversity, while in a Danish context - through distancing itself from having an explicit...

  19. Cultural Diversity and Team Performance

    DEFF Research Database (Denmark)

    Hoogendoorn, Sander; Van Praag, Mirjam

    One of the most salient and relevant dimensions of team heterogeneity is cultural background. We measure the impact of cultural diversity on the performance of business teams using a field experiment. Companies are set up by teams of undergraduate students in business studies in realistic though...... similar circumstances. We vary the cultural composition of otherwise randomly composed teams in a multi-cultural student population. Our data indicate that a moderate level of cultural diversity has no effect on team performance in terms of business outcomes (sales, profits and profits per share). However......, if at least the majority of team members is culturally diverse then more cultural diversity seems to affect the performance of teams positively. Our data suggest that this might be related to the more diverse pool of relevant knowledge facilitating (mutual) learning within culturally diverse teams....

  20. Leadership Competencies for Managing Diversity

    OpenAIRE

    Jan Visagie; Herman Linde; Werner Havenga

    2011-01-01

    The new understanding of diversity involves more than increasing the number of different identity groups on the payroll. An important proposal is that the experience of diversity in an organisation results from pervasive styles of management. This article dealt with the specific paradigms of diversitymanagement and leadership style theory used to address the research problem in the empirical study, namely ‘Is diversity management experience related to leadership styles or competencies?’ The m...

  1. Diversity in the dermatology workforce.

    Science.gov (United States)

    Hinojosa, Jorge A; Pandya, Amit G

    2016-12-01

    The United States is becoming increasingly diverse, and minorities are projected to represent the majority of our population in the near future. Unfortunately, health disparities still exist for these groups, and inequalities have also become evident in the field of dermatology. There is currently a lack of diversity within the dermatology workforce. Potential solutions to these health care disparities include increasing cultural competence for all physicians and improving diversity in the dermatology workforce. ©2016 Frontline Medical Communications.

  2. Diversity Strategies for Nuclear Power Plant Instrumentation and Control Systems

    International Nuclear Information System (INIS)

    Wood, Richard Thomas; Belles, Randy; Cetiner, Mustafa Sacit; Holcomb, David Eugene; Korsah, Kofi; Loebl, Andy; Mays, Gary T.; Muhlheim, Michael David; Mullens, James Allen; Poore, Willis P. III; Qualls, A.L.; Wilson, Thomas L.; Waterman, Michael E.

    2010-01-01

    technology, and (3) different architectures within the same technology. Using this convention, the first diversity usage family, designated Strategy A, is characterized by fundamentally diverse technologies. Strategy A at the system or platform level is illustrated by the example of analog and digital implementations. The second diversity usage family, designated Strategy B, is achieved through the use of distinctly different technologies. Strategy B can be described in terms of different digital technologies, such as the distinct approaches represented by general-purpose microprocessors and field-programmable gate arrays. The third diversity usage family, designated Strategy C, involves the use of variations within a technology. An example of Strategy C involves different digital architectures within the same technology, such as that provided by different microprocessors (e.g., Pentium and Power PC). The grouping of diversity criteria combinations according to Strategies A, B, and C establishes baseline diversity usage and facilitates a systematic organization of strategic approaches for coping with CCF vulnerabilities. Effectively, these baseline sets of diversity criteria constitute appropriate CCF mitigating strategies for digital safety systems. The strategies represent guidance on acceptable diversity usage and can be applied directly to ensure that CCF vulnerabilities identified through a D3 assessment have been adequately resolved. Additionally, a framework has been generated for capturing practices regarding diversity usage and a tool has been developed for the systematic assessment of the comparative effect of proposed diversity strategies (see Appendix A).

  3. Diversity Strategies for Nuclear Power Plant Instrumentation and Control Systems

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Richard Thomas [ORNL; Belles, Randy [ORNL; Cetiner, Mustafa Sacit [ORNL; Holcomb, David Eugene [ORNL; Korsah, Kofi [ORNL; Loebl, Andy [ORNL; Mays, Gary T [ORNL; Muhlheim, Michael David [ORNL; Mullens, James Allen [ORNL; Poore III, Willis P [ORNL; Qualls, A L [ORNL; Wilson, Thomas L [ORNL; Waterman, Michael E. [U.S. Nuclear Regulatory Commission

    2010-02-01

    the same technology, and (3) different architectures within the same technology. Using this convention, the first diversity usage family, designated Strategy A, is characterized by fundamentally diverse technologies. Strategy A at the system or platform level is illustrated by the example of analog and digital implementations. The second diversity usage family, designated Strategy B, is achieved through the use of distinctly different technologies. Strategy B can be described in terms of different digital technologies, such as the distinct approaches represented by general-purpose microprocessors and field-programmable gate arrays. The third diversity usage family, designated Strategy C, involves the use of variations within a technology. An example of Strategy C involves different digital architectures within the same technology, such as that provided by different microprocessors (e.g., Pentium and Power PC). The grouping of diversity criteria combinations according to Strategies A, B, and C establishes baseline diversity usage and facilitates a systematic organization of strategic approaches for coping with CCF vulnerabilities. Effectively, these baseline sets of diversity criteria constitute appropriate CCF mitigating strategies for digital safety systems. The strategies represent guidance on acceptable diversity usage and can be applied directly to ensure that CCF vulnerabilities identified through a D3 assessment have been adequately resolved. Additionally, a framework has been generated for capturing practices regarding diversity usage and a tool has been developed for the systematic assessment of the comparative effect of proposed diversity strategies (see Appendix A).

  4. Knowledge, Skills, and Dispositions for Diversity

    Science.gov (United States)

    Jones, Anne

    2011-01-01

    The purposes of this research are to explore how currently assessed diversity knowledge, diversity skills, and diversity dispositions of pre-service teachers (PST) relate to each other and further to surmise if the presence of diversity knowledge, diversity skills, and diversity dispositions manifests in cultural efficacy and a general cultural…

  5. Diversity Management in the Workplace

    Directory of Open Access Journals (Sweden)

    Hana Urbancová

    2016-01-01

    Full Text Available Diversity is a phenomenon which is increasingly manifesting itself in the globalized society; therefore, it is observable in various areas of human activity, and thus also in the labour market and work teams. Age, sex, ethnicity and nationality, creed or disabilities are among the parameters of diversity. The aim of the article is to identify and evaluate the implementation of Diversity Management in workplaces, whilst bearing in mind researched factors of diversity. The results were gained by conducting a primary survey by questionnaire in organizations (n = 315. The results showed that a total of 41.9% of selected organizations operating in the Czech Republic implement Diversity Management. The largest part of organizations operate in the tertiary sector (69.7%. The survey results show the situation concerning Diversity Management in the selected organizations and support the oppinion that Diversity Management is a current global matter and its concerns all organizations. The research parameters influenced the application of Diversity Management in organizations (Cramer’s V is from 0.176 to 0.430. One of the recommendations for organizations is that they devote more attention to this phenomenon, as qualified human resources is on the decline and adequate attention will once again need to be devoted to groups of potential workers who have hitherto been overlooked. Diversity Management represents a new opportunity for organizations to build the employer’s good brand and attract knowledge workers.

  6. Diversity-Guided Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    2002-01-01

    Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few...... algorithms have used a measure to guide the search. The diversity-guided evolutionary algorithm (DGEA) uses the wellknown distance-to-average-point measure to alternate between phases of exploration (mutation) and phases of exploitation (recombination and selection). The DGEA showed remarkable results...

  7. WATER DIVERSION MODEL

    Energy Technology Data Exchange (ETDEWEB)

    J.B. Case

    1999-12-21

    The distribution of seepage in the proposed repository will be highly variable due in part to variations in the spatial distribution of percolations. The performance of the drip shield and the backfill system may divert the water flux around the waste packages to the invert. Diversion will occur along the drift surface, within the backfill, at the drip shield, and at the Waste Package (WP) surface, even after the drip shield and WP have been breached by corrosion. The purpose and objective of this Analysis and Modeling Report (AMR) are to develop a conceptual model and constitutive properties for bounding the volume and rate of seepage water that flows around the drip shield (CRWMS M&O 1999c). This analysis model is to be compatible with the selected repository conceptual design (Wilkins and Heath, 1999) and will be used to evaluate the performance of the Engineered Barrier System (EBS), and to provide input to the EBS Water Distribution and Removal Model. This model supports the Engineered Barrier System (EBS) postclosure performance assessment for the Site Recommendation (SR). This document characterizes the hydrological constitutive properties of the backfill and invert materials (Section 6.2) and a third material that represents a mixture of the two. These include the Overton Sand which is selected as a backfill (Section 5.2), crushed tuff which is selected as the invert (Section 5.1), and a combined material (Sections 5.9 and 5.10) which has retention and hydraulic conductivity properties intermediate to the selected materials for the backfill and the invert. The properties include the grain size distribution, the dry bulk density and porosity, the moisture retention, the intrinsic permeability, the relative permeability, and the material thermal properties. The van Genuchten relationships with curve fit parameters are used to define the basic retention relationship of moisture potential to volumetric moisture content, and the basic relationship of unsaturated

  8. WATER DIVERSION MODEL

    International Nuclear Information System (INIS)

    J.B. Case

    1999-01-01

    The distribution of seepage in the proposed repository will be highly variable due in part to variations in the spatial distribution of percolations. The performance of the drip shield and the backfill system may divert the water flux around the waste packages to the invert. Diversion will occur along the drift surface, within the backfill, at the drip shield, and at the Waste Package (WP) surface, even after the drip shield and WP have been breached by corrosion. The purpose and objective of this Analysis and Modeling Report (AMR) are to develop a conceptual model and constitutive properties for bounding the volume and rate of seepage water that flows around the drip shield (CRWMS MandO 1999c). This analysis model is to be compatible with the selected repository conceptual design (Wilkins and Heath, 1999) and will be used to evaluate the performance of the Engineered Barrier System (EBS), and to provide input to the EBS Water Distribution and Removal Model. This model supports the Engineered Barrier System (EBS) postclosure performance assessment for the Site Recommendation (SR). This document characterizes the hydrological constitutive properties of the backfill and invert materials (Section 6.2) and a third material that represents a mixture of the two. These include the Overton Sand which is selected as a backfill (Section 5.2), crushed tuff which is selected as the invert (Section 5.1), and a combined material (Sections 5.9 and 5.10) which has retention and hydraulic conductivity properties intermediate to the selected materials for the backfill and the invert. The properties include the grain size distribution, the dry bulk density and porosity, the moisture retention, the intrinsic permeability, the relative permeability, and the material thermal properties. The van Genuchten relationships with curve fit parameters are used to define the basic retention relationship of moisture potential to volumetric moisture content, and the basic relationship of

  9. Leading Generation Y

    National Research Council Canada - National Science Library

    Newman, Jill M

    2008-01-01

    .... Whether referred to as the Millennial Generation, Generation Y or the Next Generation, the Army needs to consider the gap between Boomers, Generation X and the Soldiers that fill our junior ranks...

  10. Why Diversity for Diversity's Sake Won't Work

    Science.gov (United States)

    Delton, Jennifer

    2007-01-01

    Proponents of "diversity hiring" insist that faculty members of color have a different perspective on issues of race and ethnicity that will increase students' understanding of the multiracial, multicultural world they will inhabit in the 21st century. The mere presence of "diverse" faculty members will prepare students for workplace realities,…

  11. Diversity Management and Respect for Diversity at Schools

    Science.gov (United States)

    Saylik, Ahmet; Polatcan, Mahmut; Saylik, Numan

    2016-01-01

    The purpose of the study is to examine employees' individual attitudes towards diversity management and respect for diversity in secondary education in views of secondary school administrators and teachers, and to explore the relationship between these concepts. According to the results of the study, administrators and teachers in secondary…

  12. Diversity in High Schools and Diversity Management: A Qualitative Study

    Science.gov (United States)

    Ordu, Aydan

    2015-01-01

    The purpose of the present study is to present the diversities in high schools and opinions of teachers about management of these diversities. The sample of the study is from nine teachers working at the official high schools in the center of Denizli in Turkey. In this qualitative study, the data are collected with a semi-structured interview form…

  13. Effects of complex life cycles on genetic diversity: cyclical parthenogenesis.

    Science.gov (United States)

    Rouger, R; Reichel, K; Malrieu, F; Masson, J P; Stoeckel, S

    2016-11-01

    Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).

  14. Danshen diversity defeating dementia.

    Science.gov (United States)

    Hügel, Helmut M; Jackson, Neale

    2014-02-01

    Salvia miltiorrhiza (danshen) is widely used for the clinical treatment of cerebral ischemia and cardiovascular diseases. Its diverse molecular makeup of simple and poly hydroxycinnamic acids and diterpenoid quinones are also associated with its beneficial health effects such as improved cognitive deficits in mice, protection of neuronal cells, prevention of amyloid fibril formation and preformed amyloid fibril disaggregation related to Alzheimer's disease. Whilst the in vitro studies have therapeutic promise, the anti-dementia effect/impact of danshen however depends on its absorbed constituents and pharmacokinetic properties. Both the water and lipid danshen fractions have been shown to have low oral bioavailability and at physiological pH, the polyphenolic carboxylate anions are not brain permeable. To tap into the many neuroprotective and other biological benefits of danshen, the key challenge resides in developing danshen nanopharmaceuticals, semi-synthetic pro-drug forms of its constituents to improve its biocompatability, that is, absorption, circulation in bloodstream and optimization of BBB permeability. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. Diversity of Food Allergy.

    Science.gov (United States)

    Moriyama, Tatsuya

    2015-01-01

    Food allergy is defined as an immune system-mediated adverse reaction to food components. Food allergic reactions are mostly IgE mediated and also known as immediate type hypersensitivity (type I reaction). There are several characteristic clinical types of food allergy, such as Anaphylaxis, Food-dependent exercise-induced anaphylaxis (FDEIA), and Oral allergy syndrome (OAS). In addition, food allergy is also classified into two types (class 1 and class 2) based on the pathophysiological mechanism. In the class 2 food allergy, pollen allergy causes plant food allergy; therefore this type of allergy is sometimes called Pollen-food allergy syndrome (PFAS). The risk of food allergy (allergenicity) may vary with the treatment of the food allergens. The formation or status of the causative food affects its allergenicity. Class 1 food allergens are generally heat-, enzyme-, and low pH-resistant glycoproteins ranging in size from 10 to 70 kD. Class 1 food allergens induce allergic sensitization via the gastrointestinal tract and are responsible for systemic reactions. Class 2 food allergens are generally heat-labile, susceptible to digestion, and highly homologous with pollen allergens. Taken together, it may be important to consider the diversity of food allergy in order to fight against food allergy.

  16. Diversity among African pygmies.

    Directory of Open Access Journals (Sweden)

    Fernando V Ramírez Rozzi

    Full Text Available Although dissimilarities in cranial and post-cranial morphology among African pygmies groups have been recognized, comparative studies on skull morphology usually pull all pygmies together assuming that morphological characters are similar among them and different with respect to other populations. The main aim of this study is to compare cranial morphology between African pygmies and non-pygmies populations from Equatorial Africa derived from both the Eastern and the Western regions in order to test if the greatest morphological difference is obtained in the comparison between pygmies and non-pygmies. Thirty three-dimensional (3D landmarks registered with Microscribe in four cranial samples (Western and Eastern pygmies and non-pygmies were obtained. Multivariate analysis (generalized Procrustes analysis, Mahalanobis distances, multivariate regression and complementary dimensions of size were evaluated with ANOVA and post hoc LSD. Results suggest that important cranial shape differentiation does occur between pygmies and non-pygmies but also between Eastern and Western populations and that size changes and allometries do not affect similarly Eastern and Western pygmies. Therefore, our findings raise serious doubt about the fact to consider African pygmies as a homogenous group in studies on skull morphology. Differences in cranial morphology among pygmies would suggest differentiation after divergence. Although not directly related to skull differentiation, the diversity among pygmies would probably suggest that the process responsible for reduced stature occurred after the split of the ancestors of modern Eastern and Western pygmies.

  17. The diverse applications of plasma

    Science.gov (United States)

    Sharma, Mukul; Dubey, Shivani; Darwhekar, Gajanan; Jain, Sudhir Kumar

    2015-07-01

    Plasma being the fourth state of matter has always been an attraction for Physicists and Chemists. With the advent of time, plasma energy has been recognized in having widening horizons in the field of Biomedical Sciences. Plasma medicine can be subdivided into three main fields; Non-thermal atmospheric-pressure direct plasma for medical therapy; Plasma-assisted modification of bio-relevant surfaces and Plasma-based bio-decontamination and sterilization. The basis of the research is that as it has free carrier molecules, it has the ability to target specific cells and regulate functions like wound healing. Plasma does not harm healthy human cells but can kill bacteria and possibly even cancer cells to help treat various diseases. Nosocomial infection control, prevention and containment of contagious diseases, disinfection of medical devices, surface treatment (heat and UV sensitive surfaces) are research of interest. Recent success in generating plasma at very low temperature ie. Cold plasma makes the therapy painless. It has the ability to activate cellular responses and important mechanisms in the body. They target specific molecules such as prothrombin for blood coagulation, cytokines for killing bacteria, and angiogenesis for tissue regeneration. Plasma has bactericidal, fungicidal and virucidal properties. Plasma technology has flourishing future in diverse fields like Textiles, Nanofabrication, Automotives, Waste management, Microbiology, Food Hygiene, Medical Science like Skin treatments, sterilisation of wounds, Hand disinfection, Dental treatments etc. Food hygiene using plasma can be achieved in disinfection of food containers, food surface disinfection, hygiene in food handling, preparation and packaging. Therefore Plasma is most promising field for budding Scientist for fluorishing research in Biological Sciences.

  18. The diverse applications of plasma

    International Nuclear Information System (INIS)

    Sharma, Mukul; Darwhekar, Gajanan; Dubey, Shivani; Jain, Sudhir Kumar

    2015-01-01

    Plasma being the fourth state of matter has always been an attraction for Physicists and Chemists. With the advent of time, plasma energy has been recognized in having widening horizons in the field of Biomedical Sciences. Plasma medicine can be subdivided into three main fields; Non-thermal atmospheric-pressure direct plasma for medical therapy; Plasma-assisted modification of bio-relevant surfaces and Plasma-based bio-decontamination and sterilization. The basis of the research is that as it has free carrier molecules, it has the ability to target specific cells and regulate functions like wound healing. Plasma does not harm healthy human cells but can kill bacteria and possibly even cancer cells to help treat various diseases. Nosocomial infection control, prevention and containment of contagious diseases, disinfection of medical devices, surface treatment (heat and UV sensitive surfaces) are research of interest. Recent success in generating plasma at very low temperature ie. Cold plasma makes the therapy painless. It has the ability to activate cellular responses and important mechanisms in the body. They target specific molecules such as prothrombin for blood coagulation, cytokines for killing bacteria, and angiogenesis for tissue regeneration. Plasma has bactericidal, fungicidal and virucidal properties. Plasma technology has flourishing future in diverse fields like Textiles, Nanofabrication, Automotives, Waste management, Microbiology, Food Hygiene, Medical Science like Skin treatments, sterilisation of wounds, Hand disinfection, Dental treatments etc. Food hygiene using plasma can be achieved in disinfection of food containers, food surface disinfection, hygiene in food handling, preparation and packaging. Therefore Plasma is most promising field for budding Scientist for fluorishing research in Biological Sciences

  19. The diverse applications of plasma

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Mukul, E-mail: mukulsharma@acropolis.edu.in; Darwhekar, Gajanan, E-mail: gdarwhekar@acropolis.edu.in [Acropolis Institute of Pharmaceutical Education & Research, Indore MP India (India); Dubey, Shivani, E-mail: dubeyshivani08@rediffmail.com [Mata Gujri College of Professional Studies, Indore MP India (India); Jain, Sudhir Kumar, E-mail: sudhirkjain1@rediffmail.com [School of Studies in Microbiology, Vikram University, Ujjain MP India (India)

    2015-07-31

    Plasma being the fourth state of matter has always been an attraction for Physicists and Chemists. With the advent of time, plasma energy has been recognized in having widening horizons in the field of Biomedical Sciences. Plasma medicine can be subdivided into three main fields; Non-thermal atmospheric-pressure direct plasma for medical therapy; Plasma-assisted modification of bio-relevant surfaces and Plasma-based bio-decontamination and sterilization. The basis of the research is that as it has free carrier molecules, it has the ability to target specific cells and regulate functions like wound healing. Plasma does not harm healthy human cells but can kill bacteria and possibly even cancer cells to help treat various diseases. Nosocomial infection control, prevention and containment of contagious diseases, disinfection of medical devices, surface treatment (heat and UV sensitive surfaces) are research of interest. Recent success in generating plasma at very low temperature ie. Cold plasma makes the therapy painless. It has the ability to activate cellular responses and important mechanisms in the body. They target specific molecules such as prothrombin for blood coagulation, cytokines for killing bacteria, and angiogenesis for tissue regeneration. Plasma has bactericidal, fungicidal and virucidal properties. Plasma technology has flourishing future in diverse fields like Textiles, Nanofabrication, Automotives, Waste management, Microbiology, Food Hygiene, Medical Science like Skin treatments, sterilisation of wounds, Hand disinfection, Dental treatments etc. Food hygiene using plasma can be achieved in disinfection of food containers, food surface disinfection, hygiene in food handling, preparation and packaging. Therefore Plasma is most promising field for budding Scientist for fluorishing research in Biological Sciences.

  20. Strategies for Designing and Monitoring Malaria Vaccines Targeting Diverse Antigens

    Science.gov (United States)

    Barry, Alyssa E.; Arnott, Alicia

    2014-01-01

    After more than 50 years of intensive research and development, only one malaria vaccine candidate, “RTS,S,” has progressed to Phase 3 clinical trials. Despite only partial efficacy, this candidate is now forecast to become the first licensed malaria vaccine. Hence, more efficacious second-generation malaria vaccines that can significantly reduce transmission are urgently needed. This review will focus on a major obstacle hindering development of effective malaria vaccines: parasite antigenic diversity. Despite extensive genetic diversity in leading candidate antigens, vaccines have been and continue to be formulated using recombinant antigens representing only one or two strains. These vaccine strains represent only a small fraction of the diversity circulating in natural parasite populations, leading to escape of non-vaccine strains and challenging investigators’ abilities to measure strain-specific efficacy in vaccine trials. Novel strategies are needed to overcome antigenic diversity in order for vaccine development to succeed. Many studies have now cataloged the global diversity of leading Plasmodium falciparum and Plasmodium vivax vaccine antigens. In this review, we describe how population genetic approaches can be applied to this rich data source to predict the alleles that best represent antigenic diversity, polymorphisms that contribute to it, and to identify key polymorphisms associated with antigenic escape. We also suggest an approach to summarize the known global diversity of a given antigen to predict antigenic diversity, how to select variants that best represent the strains circulating in natural parasite populations and how to investigate the strain-specific efficacy of vaccine trials. Use of these strategies in the design and monitoring of vaccine trials will not only shed light on the contribution of genetic diversity to the antigenic diversity of malaria, but will also maximize the potential of future malaria vaccine candidates. PMID