WorldWideScience

Sample records for genome question microbes

  1. Microbes Online: an integrated portal for comparative functional genomics

    OpenAIRE

    Arkin, Adam P.

    2014-01-01

    Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi, as well as 1000s of viruses and plasmids. In addition to standard comparative genomic analysis, including gene prediction, sequence homology, domain identification, gene family assignments and functional annotations from E.C. and GO, MicrobesOnline integrates data from ...

  2. MicrobesOnline: an integrated portal for comparative functional genomics

    OpenAIRE

    Joachimiak, Marcin P.

    2014-01-01

    The Virtual Institute for Microbial Stress and Survival (VIMSS, http://vimss.lbl.gov/) funded by the Dept. of Energy's Genomics:GTL Program, is dedicated to using integrated environmental, functional genomic, and comparative sequence and phylogeny data to understand mechanisms by which microbes and microbial communities survive in uncertain environments while carrying out processes of interest for bioremediation and energy generation. To support this work, VIMSS has developed a Web portal, al...

  3. Plant microbe interactions in post genomic era: perspectives and applications

    Directory of Open Access Journals (Sweden)

    Jahangir Imam

    2016-09-01

    Full Text Available Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various ‘omics’ tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.

  4. Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications.

    Science.gov (United States)

    Imam, Jahangir; Singh, Puneet K; Shukla, Pratyoosh

    2016-01-01

    Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various 'omics' tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.

  5. Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications

    OpenAIRE

    Imam, Jahangir; Singh, Puneet K.; Shukla, Pratyoosh

    2016-01-01

    Deciphering plant–microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various ‘omics’ tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in ...

  6. MicrobesOnline: an integrated portal for comparative and functional genomics

    Energy Technology Data Exchange (ETDEWEB)

    Dehal, Paramvir; Joachimiak, Marcin; Price, Morgan; Bates, John; Baumohl, Jason; Chivian, Dylan; Friedland, Greg; Huang, Kathleen; Keller, Keith; Novichkov, Pavel; Dubchak, Inna; Alm, Eric; Arkin, Adam

    2011-07-14

    Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

  7. MicrobesOnline: an integrated portal for comparative and functional genomics

    Energy Technology Data Exchange (ETDEWEB)

    Dehal, Paramvir S.; Joachimiak, Marcin P.; Price, Morgan N.; Bates, John T.; Baumohl, Jason K.; Chivian, Dylan; Friedland, Greg D.; Huang, Katherine H.; Keller, Keith; Novichkov, Pavel S.; Dubchak, Inna L.; Alm, Eric J.; Arkin, Adam P.

    2009-09-17

    Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

  8. Science channel: addressing evolutionary questions using whole genome sequencing

    OpenAIRE

    Kentaro K. Shimizu; Akiyama, Reiko; Hatakeyama, Masaomi

    2015-01-01

    Recently, technical advance in gene analysis opened a new perspective in research on evolution. At the University of Zurich in Switzerland, we visited the Evolutionary Ecological Genomics group and Functional Genomics Center Zurich addressing evolutionary questions using latest technologies.

  9. The evolution of genome mining in microbes – a review

    DEFF Research Database (Denmark)

    Ziemert, Nadine; Alanjary, Mohammad; Weber, Tilmann

    2016-01-01

    clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews......Covering: 2006 to 2016. The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene...

  10. Genome-based bioprospecting of microbes for new therapeutics.

    Science.gov (United States)

    Zotchev, Sergey B; Sekurova, Olga N; Katz, Leonard

    2012-12-01

    Bioprospecting of natural sources for new medicines has a long and successful history, exemplified by the fact that over 50% of all drugs currently on the market are either derived from or inspired by natural products. However, development of new natural product-based therapeutics has been on the decline over the past 20 years, mainly owing to frequent re-discovery of already known compounds coupled with high costs for screening, characterization and development. With the onset of the genomic era allowing rapid sequencing and analysis of bacterial and fungal genomes, it became evident that these organisms possess 'hidden treasures' in the form of gene clusters potentially governing biosynthesis of novel biologically active compounds. This review highlights current progress in mining for and expression of these gene clusters, which may revolutionize the drug discovery pipelines in the near future.

  11. How do natural, uncultivated microbes interact with organic matter? Insights from single cell genomics and metagenomics

    Science.gov (United States)

    Lloyd, K. G.; Bird, J.; Schreiber, L.; Petersen, D.; Kjeldsen, K.; Schramm, A.; Stepanauskas, R.; Jørgensen, B. B.

    2013-12-01

    Since most of the microbes in marine sediments remain uncultured, little is known about the mechanisms by which these natural communities degrade organic matter (OM). Likewise, little is known about the make-up of labile OM in marine sediments beyond general functional classes such as proteins, carbohydrates, and lipids, measured as monomers. However, microbes have complex interactions with specific polymers within these functional classes, which can be indicated by a microbe's enzymatic toolkit. We found that four single cell genomes of archaea have very different peptidase compositions than four single cells of bacteria, suggesting that archaea and bacteria may play different roles in OM degradation. We also found that predicted extracellular cysteine peptidases, which require chemically reducing conditions, were common in IMG database metagenomes from marine sediments, and absent in those from seawater. This suggests that the pathways, and not just the rates, of OM degradation may differ between seawater and sediments. By comparing enzyme classes in different organisms, or in different types of marine environments, we present an emerging view of the microbial potential for specific carbon remineralization pathways in marine sediments. In addition, the methods we present hold promise for characterizing OM degradation in any environment where genomic information is available.

  12. Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

    Directory of Open Access Journals (Sweden)

    Stefania eMagnusdottir

    2015-04-01

    Full Text Available The human gut microbiota supplies its host with essential nutrients, including B-vitamins. Using the PubSEED platform, we systematically assessed the genomes of 256 common human gut bacteria for the presence of biosynthesis pathways for eight B-vitamins: biotin, cobalamin, folate, niacin, pantothenate, pyridoxine, riboflavin, and thiamin. On the basis of the presence and absence of genome annotations, we predicted that each of the eight vitamins was produced by 40-65% of the 256 human gut microbes. The distribution of synthesis pathways was diverse; some genomes had all eight biosynthesis pathways, whereas others contained no de novo synthesis pathways. We compared our predictions to experimental data from 16 organisms and found 88% of our predictions to be in agreement with published data. In addition, we identified several pairs of organisms whose vitamin synthesis pathway pattern complemented those of other organisms. This analysis suggests that human gut bacteria actively exchange B-vitamins among each other, thereby enabling the survival of organisms that do not synthesize any of these essential cofactors. This result indicates the co-evolution of the gut microbes in the human gut environment. Our work presents the first comprehensive assessment of the B-vitamin synthesis capabilities of the human gut microbiota. We propose that in addition to diet, the gut microbiota is an important source of B-vitamins, and that changes in the gut microbiota composition can severely affect our dietary B-vitamin requirements.

  13. The MICROBE Project, A Report from the Interagency Working Group on Microbial Genomics

    Science.gov (United States)

    2001-01-01

    and microalgae ) comprise most of the earth’s biomass, maintain its environments, and hold the key to understanding the history of life on Earth...human pathogens and microbes of relevance to energy production and energy-related bioremediation , reflecting the larger and longer- term investments...algae, difficult-to- culture microbes, and unique protozoa. • microbes involved with bioremediation for improving the environment and bioindicator species

  14. How do natural, uncultivated microbes interact with organic matter? Insights from single cell genomics and metagenomics

    DEFF Research Database (Denmark)

    Lloyd, Karen; Bird, Jordan; Schreiber, Lars

    Abstract Since most of the microbes in marine sediments remain uncultured, little is known about the mechanisms by which these natural communities degrade organic matter (OM). Likewise, little is known about the make-up of labile OM in marine sediments beyond general functional classes such as pr...... such as proteins, carbohydrates, and lipids, measured as monomers. However, microbes have complex interactions with specific polymers within these functional classes, which can be indicated by a microbe's enzymatic toolkit. We ...

  15. The extended nutrigenomics - understanding the interplay between the genomes of food, gut microbes, and human host

    NARCIS (Netherlands)

    Kussmann, M.; Bladeren, van P.J.

    2011-01-01

    Comprehensive investigation of nutritional health effects at the molecular level requires the understanding of the interplay between three genomes, the food, the gut microbial, and the human host genome. Food genomes are researched for discovery and exploitation of macro- and micronutrients as well

  16. The extended nutrigenomics - understanding the interplay between the genomes of food, gut microbes, and human host

    NARCIS (Netherlands)

    Kussmann, M.; Bladeren, van P.J.

    2011-01-01

    Comprehensive investigation of nutritional health effects at the molecular level requires the understanding of the interplay between three genomes, the food, the gut microbial, and the human host genome. Food genomes are researched for discovery and exploitation of macro- and micronutrients as well

  17. Acquiring Reference Genomes from Uncultured Microbes by Micromanipulation and Low-complexity Metagenomics

    DEFF Research Database (Denmark)

    Karst, Søren Michael; Albertsen, Mads; Nielsen, Jeppe Lund

    on isolation and amplification of genomic DNA from a single or few clonal cells has proven efficient for this purpose although very tedious. The aim of this study was to apply the methodology of single cell genomics to filamentous organisms and microcolonies of specific species from microbial communities....... Draft genomes were assembled from contig bins and validated by screening for essential single copy genes. Draft genomes were annotated using RAST and IMG/ER. Forty five single filaments/microcolonies have been isolated of which 13 samples passed validation and proceeded to sequencing. In the initial...

  18. Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis.

    Directory of Open Access Journals (Sweden)

    Samuel A Shelburne

    Full Text Available Disease can be conceptualized as the result of interactions between infecting microbe and holobiont, the combination of a host and its microbial communities. It is likely that genomic variation in the host, infecting microbe, and commensal microbiota are key determinants of infectious disease clinical outcomes. However, until recently, simultaneous, multiomic investigation of infecting microbe and holobiont components has rarely been explored. Herein, we characterized the infecting microbe, host, micro- and mycobiomes leading up to infection onset in a leukemia patient that developed invasive mucormycosis. We discovered that the patient was infected with a strain of the recently described Mucor velutinosus species which we determined was hypervirulent in a Drosophila challenge model and has a predisposition for skin dissemination. After completing the infecting M. velutinosus genome and genomes from four other Mucor species, comparative pathogenomics was performed and assisted in identifying 66 M. velutinosus-specific putatively secreted proteins, including multiple novel secreted aspartyl proteinases which may contribute to the unique clinical presentation of skin dissemination. Whole exome sequencing of the patient revealed multiple non-synonymous polymorphisms in genes critical to control of fungal proliferation, such as TLR6 and PTX3. Moreover, the patient had a non-synonymous polymorphism in the NOD2 gene and a missense mutation in FUT2, which have been linked to microbial dysbiosis and microbiome diversity maintenance during physiologic stress, respectively. In concert with host genetic polymorphism data, the micro- and mycobiome analyses revealed that the infection developed amid a dysbiotic microbiome with low α-diversity, dominated by staphylococci. Additionally, longitudinal mycobiome data showed that M. velutinosus DNA was detectable in oral samples preceding disease onset. Our genome-level study of the host-infecting microbe

  19. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes.

    Science.gov (United States)

    Jelokhani-Niaraki, Saber; Tahmoorespur, Mojtaba; Minuchehr, Zarrin; Nassiri, Mohammad Reza

    2015-03-01

    During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.

  20. The Extended Nutrigenomics - Understanding the Interplay between the Genomes of Food, Gut Microbes, and Human Host.

    Science.gov (United States)

    Kussmann, Martin; Van Bladeren, Peter J

    2011-01-01

    Comprehensive investigation of nutritional health effects at the molecular level requires the understanding of the interplay between three genomes, the food, the gut microbial, and the human host genome. Food genomes are researched for discovery and exploitation of macro- and micronutrients as well as specific bioactives, with those genes coding for bioactive proteins and peptides being of central interest. The human gut microbiota encompasses a complex ecosystem in the intestine with profound impact on host metabolism. It is being studied at genomic and, more recently, also at proteomic and metabonomic level. Humans are being characterized at the level of genetic pre-disposition and inter-individual variability in terms of (i) response to nutritional interventions and direction of health trajectories; (ii) epigenetic, metabolic programming at certain life stages with health consequences later in life and even for subsequent generations; and (iii) acute genomic expression as a holistic response to diet, monitored at gene transcript, protein and metabolite level. Modern nutrition science explores health-related aspects of bioactive food components, thereby promoting health, preventing, or delaying the onset of disease, optimizing performance and assessing benefits and risks in individuals and subpopulations. Personalized nutrition means adapting food to individual needs, depending on the human host's life stage, -style, and -situation. Traditionally, nutrigenomics and nutri(epi)genetics are seen as the key sciences to understand human variability in preferences and requirements for diet as well as responses to nutrition. This article puts the three nutrition and health-relevant genomes into perspective, namely the food, the gut microbial and the human host's genome, and calls for an "extended nutrigenomics" approach in order to build the future tools for personalized nutrition, health maintenance, and disease prevention. We discuss examples of these genomes

  1. Exploring Genomic Diversity Using Metagenomics of Deep-Sea Subsurface Microbes from the Louisville Seamount and the South Pacific Gyre

    Science.gov (United States)

    Tully, B. J.; Sylvan, J. B.; Heidelberg, J. F.; Huber, J. A.

    2014-12-01

    There are many limitations involved with sampling microbial diversity from deep-sea subsurface environments, ranging from physical sample collection, low microbial biomass, culturing at in situ conditions, and inefficient nucleic acid extractions. As such, we are continually modifying our methods to obtain better results and expanding what we know about microbes in these environments. Here we present analysis of metagenomes sequences from samples collected from 120 m within the Louisville Seamount and from the top 5-10cm of the sediment in the center of the south Pacific gyre (SPG). Both systems are low biomass with ~102 and ~104 cells per cm3 for Louisville Seamount samples analyzed and the SPG sediment, respectively. The Louisville Seamount represents the first in situ subseafloor basalt and the SPG sediments represent the first in situ low biomass sediment microbial metagenomes. Both of these environments, subseafloor basalt and sediments underlying oligotrophic ocean gyres, represent large provinces of the seafloor environment that remain understudied. Despite the low biomass and DNA generated from these samples, we have generated 16 near complete genomes (5 from Louisville and 11 from the SPG) from the two metagenomic datasets. These genomes are estimated to be between 51-100% complete and span a range of phylogenetic groups, including the Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi, and unclassified bacterial groups. With these genomes, we have assessed potential functional capabilities of these organisms and performed a comparative analysis between the environmental genomes and previously sequenced relatives to determine possible adaptations that may elucidate survival mechanisms for these low energy environments. These methods illustrate a baseline analysis that can be applied to future metagenomic deep-sea subsurface datasets and will help to further our understanding of microbiology within these environments.

  2. Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans

    Science.gov (United States)

    Liu, Liwei; Hao, Tingting; Xie, Zhoujie; Horsman, Geoff P.; Chen, Yihua

    2016-01-01

    Streptococcus mutans is a major pathogen causing human dental caries. As a Gram-positive bacterium with a small genome (about 2 Mb) it is considered a poor source of natural products. Due to a recent explosion in genomic data available for S. mutans strains, we were motivated to explore the natural product production potential of this organism. Bioinformatic characterization of 169 publically available genomes of S. mutans from human dental caries revealed a surprisingly rich source of natural product biosynthetic gene clusters. Anti-SMASH analysis identified one nonribosomal peptide synthetase (NRPS) gene cluster, seven polyketide synthase (PKS) gene clusters and 136 hybrid PKS/NRPS gene clusters. In addition, 211 ribosomally synthesized and post-translationally modified peptides (RiPPs) clusters and 615 bacteriocin precursors were identified by a combined analysis using BAGEL and anti-SMASH. S. mutans harbors a rich and diverse natural product genetic capacity, which underscores the importance of probing the human microbiome and revisiting species that have traditionally been overlooked as “poor” sources of natural products. PMID:27869143

  3. Genomics in a changing arctic: critical questions await the molecular ecologist.

    Science.gov (United States)

    Wullschleger, Stan D; Breen, Amy L; Iversen, Colleen M; Olson, Matthew S; Näsholm, Torgny; Ganeteg, Ulrika; Wallenstein, Matthew D; Weston, David J

    2015-05-01

    Molecular ecology is poised to tackle a host of interesting questions in the coming years. The Arctic provides a unique and rapidly changing environment with a suite of emerging research needs that can be addressed through genetics and genomics. Here we highlight recent research on boreal and tundra ecosystems and put forth a series of questions related to plant and microbial responses to climate change that can benefit from technologies and analytical approaches contained within the molecular ecologist's toolbox. These questions include understanding (i) the mechanisms of plant acquisition and uptake of N in cold soils, (ii) how these processes are mediated by root traits, (iii) the role played by the plant microbiome in cycling C and nutrients within high-latitude ecosystems and (iv) plant adaptation to extreme Arctic climates. We highlight how contributions can be made in these areas through studies that target model and nonmodel organisms and emphasize that the sequencing of the Populus and Salix genomes provides a valuable resource for scientific discoveries related to the plant microbiome and plant adaptation in the Arctic. Moreover, there exists an exciting role to play in model development, including incorporating genetic and evolutionary knowledge into ecosystem and Earth System Models. In this regard, the molecular ecologist provides a valuable perspective on plant genetics as a driver for community biodiversity, and how ecological and evolutionary forces govern community dynamics in a rapidly changing climate. © 2015 John Wiley & Sons Ltd.

  4. Resolving the question of trypanosome monophyly: a comparative genomics approach using whole genome data sets with low taxon sampling.

    Science.gov (United States)

    Leonard, Guy; Soanes, Darren M; Stevens, Jamie R

    2011-07-01

    Since the first attempts to classify the evolutionary history of trypanosomes, there have been conflicting reports regarding their true phylogenetic relationships and, in particular, their relationships with other vertebrate trypanosomatids, e.g. Leishmania sp., as well as with the many insect parasitising trypanosomatids. Perhaps the issue that has provided most debate is that concerning the monophyly (or otherwise) of genus Trypanosoma and, even with the advent of molecular methods, the findings of numerous studies have varied significantly depending on the gene sequences analysed, number of taxa included, choice of outgroup and phylogenetic methodology. While of arguably limited applied importance, resolution of the question as to whether or not trypanosomes are monophyletic is critical to accurate evaluation of competing, mutually exclusive evolutionary scenarios for these parasites, namely the 'vertebrate-first' or 'insect-first' hypotheses. Therefore, a new approach, which could overcome previous limitations was needed. At its most simple, the problem can be defined within the framework of a trifurcated tree with three hypothetical positions at which the root can be placed. Using BLASTp and whole-genome gene-by-gene phylogenetic analyses of Trypanosoma brucei, Trypanosoma cruzi, Leishmania major and Naegleria gruberi, we have identified 599 gene markers--putative homologues--that were shared between the genomes of these four taxa. Of these, 75 homologous gene families that demonstrate monophyly of the kinetoplastids were identified. We then used these data sets in combination with an additional outgroup, Euglena gracilis, coupled with large-scale gene concatenation and diverse phylogenetic techniques to investigate the relative branching order of T. brucei, T. cruzi and L. major. Our findings confirm the monophyly of genus Trypanosoma and demonstrate that <1% of the analysed gene markers shared between the genomes of T. brucei, T. cruzi and L. major reject

  5. The Extended Nutrigenomics – Understanding the Interplay between the Genomes of Food, Gut Microbes and Human Host

    Directory of Open Access Journals (Sweden)

    Martin eKussmann

    2011-05-01

    Full Text Available Comprehensive investigation of nutritional health effects at molecular level requires understanding the interplay between three genomes, the food, the gut microbial and the human host genome. Food genomes are researched for exploitation of macro- and micronutrients as well as bioactives, with the genes coding for bioactive proteins and peptides being of central interest. The human gut microbiota encompasses a complex intestinal ecosystem with profound impact on host metabolism. It is studied at genomic, proteomic and metabolomic level. Humans are characterized at the level of: genetic predisposition and variability in terms of dietary response and direction of health trajectories; epigenetic, metabolic programming at certain life stages with health consequences later in life and for subsequent generations; and acute genomic expression as a holistic response to diet, monitored at gene transcript, protein and metabolite level.Modern nutrition science explores health aspects of bioactive food components, thereby promoting health, preventing or delaying the onset of disease, optimizing performance and assessing benefits and risks. Personalized nutrition means adapting food to individual needs, depending on the human host’s life stage, -style and -situation. Traditionally, nutrigenomics and nutri(epigenetics have been seen as the key sciences to understand human variability in preferences and requirements for diet as well as responses to nutrition. This article puts the three nutrition and health-relevant genomes into perspective, i.e. the food, the gut microbial and the human host’s genome, and calls for an extended nutrigenomics approach to build the future tools for personalized nutrition, health maintenance and disease prevention. We discuss examples of these genomes, proteomes, transcriptomes and metabolomes under the overarching term genomics that covers all Omics rather than the sole study of DNA and RNA.

  6. Genomics research of the single cell microbes%单细胞微生物基因组学研究

    Institute of Scientific and Technical Information of China (English)

    陆光涛; 何勇强; 唐纪良

    2001-01-01

    It is a review paper which introdues the single cell microbes’ complete genome sequencing,the sequence annotation and the main contents of th e further research on genomics.%本文介绍了单细胞微生物基因组测序,全基因组序列的注释,以及基因组进一步研究的主要内容。

  7. Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge.

    Science.gov (United States)

    Tian, Ren-Mao; Zhang, Weipeng; Cai, Lin; Wong, Yue-Him; Ding, Wei; Qian, Pei-Yuan

    2017-01-01

    functional features are determined by both the symbiotic relationship and host type. Moreover, analyses of the genome of an AOA suggest that microbes play different roles in biochemical cycles in the sponge body. Our findings provide new insights into invertebrate-associated bacteria in cold seep environments.

  8. Microbes of deep marine sediments as viewed by metagenomics

    Science.gov (United States)

    Biddle, J.

    2015-12-01

    Ten years after the first deep marine sediment metagenome was produced, questions still exist about the nucleic acid sequences we have retrieved. Current data sets, including the Peru Margin, Costa Rica Margin and Iberian Margin show that consistently, data forms larger assemblies at depth due to the reduced complexity of the microbial community. But are these organisms active or preserved? At SMTZs, a change in the assembly statistics is noted, as well as an increase in cell counts, suggesting that cells are truly active. As depth increases, genome sizes are consistently large, suggesting that much like soil microbes, sedimentary microbes may maintain a larger reportorie of genomic potential. Functional changes are seen with depth, but at many sites are not correlated to specific geochemistries. Individual genomes show changes with depth, which raises interesting questions on how the subsurface is settled and maintained. The subsurface does have a distinct genomic signature, including unusual microbial groups, which we are now able to analyze for total genomic content.

  9. A 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre

    2014-01-01

    of the fossil record, this study confirms that genomic information can be recovered from extremely damaged DNA molecules, even in the presence of significant levels of human contamination. Together with the recent characterization of a 700,000-year-old horse genome, this study opens the Middle Pleistocene...

  10. A global census of marine microbes

    Digital Repository Service at National Institute of Oceanography (India)

    Amaral-Zettler, L.; Artigas, L.F.; Baross, J.; LokaBharathi, P.A; Boetius, A; Chandramohan, D.; Herndl, G.; Kogure, K.; Neal, P.; Pedros-Alio, C.; Ramette, A; Schouten, S.; Stal, L.; Thessen, A; De Leeuw, J.; Sogin, M.

    In this chapter we provide a brief history of what is known about marine microbial diversity, summarize our achievements in performing a global census of marine microbes, and reflect on the questions and priorities for the future of the marine...

  11. Key questions in the genetics and genomics of eco-evolutionary dynamics.

    Science.gov (United States)

    Hendry, A P

    2013-12-01

    Increasing acceptance that evolution can be 'rapid' (or 'contemporary') has generated growing interest in the consequences for ecology. The genetics and genomics of these 'eco-evolutionary dynamics' will be--to a large extent--the genetics and genomics of organismal phenotypes. In the hope of stimulating research in this area, I review empirical data from natural populations and draw the following conclusions. (1) Considerable additive genetic variance is present for most traits in most populations. (2) Trait correlations do not consistently oppose selection. (3) Adaptive differences between populations often involve dominance and epistasis. (4) Most adaptation is the result of genes of small-to-modest effect, although (5) some genes certainly have larger effects than the others. (6) Adaptation by independent lineages to similar environments is mostly driven by different alleles/genes. (7) Adaptation to new environments is mostly driven by standing genetic variation, although new mutations can be important in some instances. (8) Adaptation is driven by both structural and regulatory genetic variation, with recent studies emphasizing the latter. (9) The ecological effects of organisms, considered as extended phenotypes, are often heritable. Overall, the study of eco-evolutionary dynamics will benefit from perspectives and approaches that emphasize standing genetic variation in many genes of small-to-modest effect acting across multiple traits and that analyze overall adaptation or 'fitness'. In addition, increasing attention should be paid to dominance, epistasis and regulatory variation.

  12. Microbial issues pertaining to the canadian concept for the disposal of nuclear fuel waste. Questions a examiner quant aux microbes lors du developpement du concept canadien de stockage permanent des dechets de combustible nucleaire

    Energy Technology Data Exchange (ETDEWEB)

    Stroes-Gascoyne, S.; West, J.M.

    1994-01-01

    This report formulates a number of views and positions on microbiological factors that could influence the performance of a disposal vault in plutonic rock. Microbiological factors discussed include the presence and survival of microbes, biofilms, corrosion, biodegradation (of emplaced materials), gas production, geochemical changes, radionuclide migration, colloid formation, mutation, pathogens and methylation. Not all issues can be fully resolved with the current state of knowledge. Studies being performed to underscore and strengthen current knowledge are briefly discussed.

  13. Soil microbes and plant fertilization.

    Science.gov (United States)

    Miransari, Mohammad

    2011-12-01

    With respect to the adverse effects of chemical fertilization on the environment and their related expenses, especially when overused, alternative methods of fertilization have been suggested and tested. For example, the combined use of chemical fertilization with organic fertilization and/or biological fertilization is among such methods. It has been indicated that the use of organic fertilization with chemical fertilization is a suitable method of providing crop plants with adequate amount of nutrients, while environmentally and economically appropriate. In this article, the importance of soil microbes to the ecosystem is reviewed, with particular emphasis on the role of plant growth-promoting rhizobacteria, arbuscular mycorrhizal fungi, and endophytic bacteria in providing necessary nutrients for plant growth and yield production. Such microbes are beneficial to plant growth through colonizing plant roots and inducing mechanisms by which plant growth increases. Although there has been extensive research work regarding the use of microbes as a method of fertilizing plants, it is yet a question how the efficiency of such microbial fertilization to the plant can be determined and increased. In other words, how the right combination of chemical and biological fertilization can be determined. In this article, the most recent advances regarding the effects of microbial fertilization on plant growth and yield production in their combined use with chemical fertilization are reviewed. There are also some details related to the molecular mechanisms affecting the microbial performance and how the use of biological techniques may affect the efficiency of biological fertilization.

  14. Microbes as forensic indicators.

    Science.gov (United States)

    Alan, G; Sarah, J P

    2012-09-01

    The forensic potential of microorganisms is becoming increasingly apparent as a consequence of advances in molecular sciences and genomics. This review discusses instances in which microbes, and in particular bacteria, can impact upon forensic investigations. There is increasing evidence that humans have an extremely diverse 'microbiome' that may prove useful in determining ethnicity, country of origin, and even personal identity. The human microbiome differs between regions of the body and may prove useful for determining the nature of stains such as those caused by saliva and vaginal fluid: it may even be possible to link the stains to the person responsible for them. Similarly, the composition of the microbiome present in a soil sample may prove a useful indicator of geographic origin or as a means of linking people, animals, or objects together or to a specific location. Microorganisms are important in the decay process and also influence the presence and concentration of alcohol, drugs, and other chemicals of forensic relevance. There is also a possibility that the entry of microorganisms into the body during the agonal period may prove useful for the diagnosis of drowning. The transmission of infectious diseases, and in particular sexually-transmitted diseases, can provide evidence linking a victim and a suspect. Microorganisms that cause fatal infections are not always identified at the time of death and may lead to the death being considered 'suspicious'. If a fatal infection can be linked to a hospital or medical procedure it can lead to prosecutions and therefore it is important to determine when and where an infection was acquired. Similarly, naturally acquired infections need to be distinguished from those that result from malicious transmission. Microorganisms can therefore provide evidence in many different forensic scenarios but most of the work is still at the experimental stage and there are therefore many opportunities for further research.

  15. Microbes: mini iron factories.

    Science.gov (United States)

    Joshi, Kumar Batuk

    2014-12-01

    Microbes have flourished in extreme habitats since beginning of the Earth and have played an important role in geological processes like weathering, mineralization, diagenesis, mineral formation and destruction. Biotic mineralization is one of the most fascinating examples of how microbes have been influencing geological processes. Iron oxidizing and reducing bacteria are capable of precipitating wide varieties of iron oxides (magnetite), carbonates (siderite) and sulphides (greigite) via controlled or induced mineralization processes. Microbes have also been considered to play an important role in the history of evolution of sedimentary rocks on Earth from the formation of banded iron formations during the Archean to modern biotic bog iron and ochre deposits. Here, we discuss the role that microbes have been playing in precipitation of iron and the role and importance of interdisciplinary studies in the field of geology and biology in solving some of the major geological mysteries.

  16. Microbes: Mini Iron Factories

    OpenAIRE

    Joshi, Kumar Batuk

    2014-01-01

    Microbes have flourished in extreme habitats since beginning of the Earth and have played an important role in geological processes like weathering, mineralization, diagenesis, mineral formation and destruction. Biotic mineralization is one of the most fascinating examples of how microbes have been influencing geological processes. Iron oxidizing and reducing bacteria are capable of precipitating wide varieties of iron oxides (magnetite), carbonates (siderite) and sulphides (greigite) via con...

  17. MicrobeWorld Radio and Communications Initiative

    Energy Technology Data Exchange (ETDEWEB)

    Barbara Hyde

    2006-11-22

    MicrobeWorld is a 90-second feature broadcast daily on more than 90 public radio stations and available from several sources as a podcast, including www.microbeworld.org. The feature has a strong focus on the use and adapatbility of microbes as alternative sources of energy, in bioremediation, their role in climate, and especially the many benefits and scientific advances that have resulting from decoding microbial genomes. These audio features are permanantly archived on an educational outreach site, microbeworld.org, where they are linked to the National Science Education Standards. They are also being used by instructors at all levels to introduce students to the multiple roles and potential of microbes, including a pilot curriculum program for middle-school students in New York.

  18. Hidden Worlds of Marine Microbes

    Science.gov (United States)

    Armbrust, E. V.

    2016-12-01

    Every drop of seawater contains fantastically diverse groups of microbes that control key biogeochemical processes in the ocean and determine the habitability of our planet. The challenge is to scale from this world of individual cells to ecosystem function and ultimately to ocean basin processes. Our work begins with microscopic marine diatoms because they are responsible for about twenty percent of the photosynthesis that occurs on Earth each year, they form the base of highly productive marine food webs, and they help regulate past and current fluxes of CO2 into the ocean. Diatoms evolved in a dilute environment where they are never free from the influences of other microbes. We explore the specifics of these interactions via model diatom/bacteria systems that can be manipulated in the laboratory - one includes an antagonistic bacterium that inhibits the growth of diatoms and a second includes a synergistic bacterium that enhances the growth of diatoms. We scale up from the cellular level to population-level interactions through use of our continuous flow cytometer, SeaFlow, which taps into a ship's seawater intake system to provide a continuous read-out of abundance, size and type of the smallest phytoplankton. We use this data to estimate division rates and mortality rates of these phytoplankton across thousands of kilometers of ocean basins. We tie these scales together with genomic approaches in both laboratory experiments and in open ocean field studies to document how interactions with the environment and between microbes drive specific adaptations. Our ultimate goal is to understand how microbial communities will respond to and will help shape future ocean conditions.

  19. Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge

    OpenAIRE

    Ren-Mao Tian; Weipeng Zhang; Lin Cai; Yue-Him Wong; Wei Ding; Pei-Yuan Qian; Gilbert, Jack A.

    2017-01-01

    ABSTRACT As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored ?differential coverage binning? method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses sugges...

  20. Microorganisms (Microbes), Role of

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2013-01-01

    Microorganisms (microbes) are those life forms too small to be seen by the naked eye; that is, those that require a microscope or other form of magnification in order to be observed. The term microorganism is thus a functional description rather than a taxonomic one, and the grouping includes...

  1. Microorganisms (Microbes), Role of

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2013-01-01

    Microorganisms (microbes) are those life forms too small to be seen by the naked eye; that is, those that require a microscope or other form of magnification in order to be observed. The term microorganism is thus a functional description rather than a taxonomic one, and the grouping includes a w...

  2. Extremophilic microbes: Diversity and perspectives

    Digital Repository Service at National Institute of Oceanography (India)

    Satyanarayana, T.; Raghukumar, C.; Shivaji, S.

    and grow in extreme en-vironments. The enzymes of these microbes, which function in extreme environments (extremozymes), have several biotechnological applications. Antibiotics, compatible solutes and other compounds obtainable from these microbes are also...

  3. Molecular ecology of aquatic microbes

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    Abstracts of reports are presented from a meeting on Molecular Ecology of Aquatic Microbes. Topics included: opportunities offered to aquatic ecology by molecular biology; the role of aquatic microbes in biogeochemical cycles; characterization of the microbial community; the effect of the environment on aquatic microbes; and the targeting of specific biological processes.

  4. A systems biology approach to studying the role of microbes in human health.

    Science.gov (United States)

    Thiele, Ines; Heinken, Almut; Fleming, Ronan M T

    2013-02-01

    Host-microbe interactions play a crucial role in human health and disease. Of the various systems biology approaches, reconstruction of genome-scale metabolic networks combined with constraint-based modeling has been particularly successful at in silico predicting the phenotypic characteristics of single organisms. Here, we summarize recent studies, which have applied this approach to investigate microbe-microbe and host-microbe metabolic interactions. This approach can be also expanded to investigate the properties of an entire microbial community, as well as single organisms within the community. We illustrate that the constraint-based modeling approach is suitable to model host-microbe interactions at molecular resolution and will enable systematic investigation of metabolic links between the human host and its microbes. Such host-microbe models, combined with experimental data, will ultimately further our understanding of how microbes influence human health.

  5. Biofuels: from microbes to molecules

    National Research Council Canada - National Science Library

    Lu, Xuefeng

    2014-01-01

    .... The production of different biofuel molecules including hydrogen, methane, ethanol, butanol, higher chain alcohols, isoprenoids and fatty acid derivatives, from genetically engineered microbes...

  6. Microbe-microbe interactions in mixed culture food fermentations

    NARCIS (Netherlands)

    Smid, E.J.; Lacroix, C.

    2013-01-01

    Most known natural and industrial food fermentation processes are driven by either simple or complex communities of microorganisms. Obviously, these fermenting microbes will not only interact with the fermentable substrate but also with each other. These microbe–microbe interactions are complex but

  7. Radiation induced pesticidal microbes

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ki Yup; Lee, Y. K.; Kim, J. S.; Kim, J. K.; Lee, S. J.; Lim, D. S

    2001-01-01

    To isolate pesticidal microbes against plant pathogenic fungi, 4 strains of bacteria(K1. K3, K4, YS1) were isolated from mushroom compost and hot spring. K4, K1, K3, YS1 strain showed wide antifungal spectrum and high antifungal activities against 12 kinds of fungi. Specific proteins and the specific transcribed genes were found from the YS1 and its radiation-induced mutants. And knock-out mutants of antifungal activity were derived by transposon mutagenesis. From these knock-out mutants, the antifungal activity related genes and its modification by gamma-ray radiation are going to be studied. These results suggested that radiation could be an useful tool for the induction of functional mutants.

  8. Amphibian skin may select for rare environmental microbes.

    Science.gov (United States)

    Walke, Jenifer B; Becker, Matthew H; Loftus, Stephen C; House, Leanna L; Cormier, Guy; Jensen, Roderick V; Belden, Lisa K

    2014-11-01

    Host-microbe symbioses rely on the successful transmission or acquisition of symbionts in each new generation. Amphibians host a diverse cutaneous microbiota, and many of these symbionts appear to be mutualistic and may limit infection by the chytrid fungus, Batrachochytrium dendrobatidis, which has caused global amphibian population declines and extinctions in recent decades. Using bar-coded 454 pyrosequencing of the 16S rRNA gene, we addressed the question of symbiont transmission by examining variation in amphibian skin microbiota across species and sites and in direct relation to environmental microbes. Although acquisition of environmental microbes occurs in some host-symbiont systems, this has not been extensively examined in free-living vertebrate-microbe symbioses. Juvenile bullfrogs (Rana catesbeiana), adult red-spotted newts (Notophthalmus viridescens), pond water and pond substrate were sampled at a single pond to examine host-specificity and potential environmental transmission of microbiota. To assess population level variation in skin microbiota, adult newts from two additional sites were also sampled. Cohabiting bullfrogs and newts had distinct microbial communities, as did newts across the three sites. The microbial communities of amphibians and the environment were distinct; there was very little overlap in the amphibians' core microbes and the most abundant environmental microbes, and the relative abundances of OTUs that were shared by amphibians and the environment were inversely related. These results suggest that, in a host species-specific manner, amphibian skin may select for microbes that are generally in low abundance in the environment.

  9. SOLiD™ sequencing of genomes of clinical isolates of Leishmania donovani from India confirm leptomonas co-infection and raise some key questions.

    Directory of Open Access Journals (Sweden)

    Neeloo Singh

    Full Text Available BACKGROUND: Known as 'neglected disease' because relatively little effort has been applied to finding cures, leishmaniasis kills more than 150,000 people every year and debilitates millions more. Visceral leishmaniasis (VL, also called Kala Azar (KA or black fever in India, claims around 20,000 lives every year. Whole genome analysis presents an excellent means to identify new targets for drugs, vaccine and diagnostics development, and also provide an avenue into the biological basis of parasite virulence in the L. donovani complex prevalent in India. METHODOLOGY/PRINCIPAL FINDINGS: In our presently described study, the next generation SOLiD™ platform was successfully utilized for the first time to carry out whole genome sequencing of L. donovani clinical isolates from India. We report the exceptional occurrence of insect trypanosomatids in clinical cases of visceral leishmaniasis (Kala Azar patients in India. We confirm with whole genome sequencing analysis data that isolates which were sequenced from Kala Azar (visceral leishmaniasis cases were genetically related to Leptomonas. The co-infection in splenic aspirate of these patients with a species of Leptomonas and how likely is it that the infection might be pathogenic, are key questions which need to be investigated. We discuss our results in the context of some important probable hypothesis in this article. CONCLUSIONS/SIGNIFICANCE: Our intriguing results of unusual cases of Kala Azar found to be most similar to Leptomonas species put forth important clinical implications for the treatment of Kala Azar in India. Leptomonas have been shown to be highly susceptible to several standard leishmaniacides in vitro. There is very little divergence among these two species viz. Leishmania sp. and L. seymouri, in terms of genomic sequence and organization. A more extensive perception of the phenomenon of co-infection needs to be addressed from molecular pathogenesis and eco

  10. Microbe Phobia and Kitchen Microbiology.

    Science.gov (United States)

    Williams, Robert P.; Gillen, Alan L.

    1991-01-01

    The authors present an exercise designed to help students overcome the misconception that most microbes make people sick. The activity helps students of all ages understand the important benefits of microbes such as in making bread, soy sauce, cheese, and wine. The role of microorganisms in processing cocoa and coffee and growing plants is also…

  11. Study of Host–Microbe Interactions in Zebrafish

    Science.gov (United States)

    Milligan-Myhre, Kathryn; Charette, Jeremy R.; Phennicie, Ryan T.; Stephens, W. Zac; Rawls, John F.; Guillemin, Karen; Kim, Carol H.

    2015-01-01

    All animals are ecosystems, home to diverse microbial populations. Animal-associated microbes play important roles in the normal development and physiology of their hosts, but can also be agents of infectious disease. Traditionally, mice have been used to study pathogenic and beneficial associations between microbes and vertebrate animals. The zebrafish is emerging as a valuable new model system for host-microbe interaction studies, affording researchers with the opportunity to survey large populations of hosts and to visualize microbe-host associations at a cellular level in living animals. This chapter provides detailed protocols for the analysis of zebrafish-associated microbial communities, the derivation and husbandry of germ-free zebrafish, and the modeling of infectious disease in different stages of zebrafish development via different routes of inoculation. These protocols offer a starting point for researchers to address a multitude of questions about animals’ coexistence with microorganisms. PMID:21951527

  12. Microbes central to human reproduction.

    Science.gov (United States)

    Reid, Gregor; Brigidi, Patrizia; Burton, Jeremy P; Contractor, Nikhat; Duncan, Sylvia; Fargier, Emilie; Hill, Colin; Lebeer, Sarah; Martín, Rocio; McBain, Andrew J; Mor, Gil; O'Neill, Catherine; Rodríguez, Juan Miguel; Swann, Jonathan; van Hemert, Saskia; Ansell, Juliett

    2015-01-01

    As studies uncover the breadth of microbes associated with human life, opportunities will emerge to manipulate and augment their functions in ways that improve health and longevity. From involvement in the complexities of reproduction and fetal/infant development, to delaying the onset of disease, and indeed countering many maladies, microbes offer hope for human well-being. Evidence is emerging to suggest that microbes may play a beneficial role in body sites traditionally viewed as being sterile. Although further evidence is required, we propose that much of medical dogma is about to change significantly through recognition and understanding of these hitherto unrecognized microbe-host interactions. A meeting of the International Scientific Association for Probiotics and Prebiotics held in Aberdeen, Scotland (June 2014), presented new views and challenged established concepts on the role of microbes in reproduction and health of the mother and infant. This article summarizes some of the main aspects of these discussions.

  13. Microbes in the coral holobiont: partners through evolution, development, and ecological interactions.

    Science.gov (United States)

    Thompson, Janelle R; Rivera, Hanny E; Closek, Collin J; Medina, Mónica

    2014-01-01

    In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health-not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions.

  14. Microbes in the coral holobiont: partners through evolution, development, and ecological interactions

    Directory of Open Access Journals (Sweden)

    Janelle Renee Thompson

    2015-01-01

    Full Text Available In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health – not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al., 2013 in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: 1 How do corals and their microbiome affect each other’s genomes? 2 How does coral development depend on microbial partners? 3 How is homeostasis maintained between corals and their microbial symbionts? 4 How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions.

  15. Microbes in the coral holobiont: partners through evolution, development, and ecological interactions

    Science.gov (United States)

    Thompson, Janelle R.; Rivera, Hanny E.; Closek, Collin J.; Medina, Mónica

    2015-01-01

    In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health—not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions. PMID:25621279

  16. Biofuels from microbes.

    Science.gov (United States)

    Antoni, Dominik; Zverlov, Vladimir V; Schwarz, Wolfgang H

    2007-11-01

    Today, biomass covers about 10% of the world's primary energy demand. Against a backdrop of rising crude oil prices, depletion of resources, political instability in producing countries and environmental challenges, besides efficiency and intelligent use, only biomass has the potential to replace the supply of an energy hungry civilisation. Plant biomass is an abundant and renewable source of energy-rich carbohydrates which can be efficiently converted by microbes into biofuels, of which, only bioethanol is produced on an industrial scale today. Biomethane is produced on a large scale, but is not yet utilised for transportation. Biobutanol is on the agenda of several companies and may be used in the near future as a supplement for gasoline, diesel and kerosene, as well as contributing to the partially biological production of butyl-t-butylether, BTBE as does bioethanol today with ETBE. Biohydrogen, biomethanol and microbially made biodiesel still require further development. This paper reviews microbially made biofuels which have potential to replace our present day fuels, either alone, by blending, or by chemical conversion. It also summarises the history of biofuels and provides insight into the actual production in various countries, reviewing their policies and adaptivity to the energy challenges of foreseeable future.

  17. Enterococci: yin - yang microbes

    Directory of Open Access Journals (Sweden)

    Andreja Čanžek Majhenič

    2006-03-01

    Full Text Available This review deals with the duality of enterococci, which can be illustrated by their yin - yang behaviour. The rough nature of this specific group of lactic acid bacteria promotes their dissemination in various environments where they significantly influence the outcome of a certain process. In the technological meaning, enterococci are leading microbes in fermentation processes of traditional foods, where their detrimental spoilage activities are equally significant. As therapeutics, enterococci manifest the probiotic properties through their positive effects on maintaining of the normal intestinal microflora, on stimulation of the immune system, on improved nutritional value of food and with the production of antimicrobial compounds (bacteriocins. At the same time, enterococci present an emerging pool of opportunistic pathogens for humans as they cause disease, possess agents for antibiotic resistance and their transfer mechanisms, and are frequently armed with potential virulence factors. Despite the yin - yang characteristics of enterococci, the long history of safe use of certain strains of enterococci in food/feed, and reliable identification and classification of enterococci with phenotypic methods supported with modern genetic tools, enables selection of promising enterococci, which could be safely used as starter cultures or food/feed additives.

  18. Explosives, Genomics, and the Environment

    Directory of Open Access Journals (Sweden)

    Kieran C. O’Doherty

    2013-03-01

    Full Text Available RDX is an explosive that is also a neurotoxin and implicated in adverse health outcomes. Because of its widespread use in military and civilian operations, there is growing concern about potential environmental and health implications. One promising method of bioremediation involves genomic studies of soil microbes. These health concerns and technological issues intersect with social and political dimensions raising questions about public responses to genomic technologies and the degree of environmental accounting expected from the military. In cases of novel technologies entering into contested social spaces, public engagement can be useful to inform broader policy debates. Building on previous work, in this article, we outline the rationale, methods, and results of a public deliberation on these issues. To our knowledge, this is the first study of its kind on the issues of RDX pollution and microbial genomics, and thus provides an important baseline on public sentiment on these issues.

  19. Chemiluminescence and bioluminescence microbe detection

    Science.gov (United States)

    Taylor, R. E.; Chappelle, E.; Picciolo, G. L.; Jeffers, E. L.; Thomas, R. R.

    1978-01-01

    Automated biosensors for online use with NASA Water Monitoring System employs bioluminescence and chemiluminescence techniques to rapidly measure microbe contamination of water samples. System eliminates standard laboratory procedures requiring time duration of 24 hours or longer.

  20. The ``Adopt A Microbe'' project: Web-based interactive education connected with scientific ocean drilling

    Science.gov (United States)

    Orcutt, B. N.; Bowman, D.; Turner, A.; Inderbitzen, K. E.; Fisher, A. T.; Peart, L. W.; Iodp Expedition 327 Shipboard Party

    2010-12-01

    We launched the "Adopt a Microbe" project as part of Integrated Ocean Drilling Program (IODP) Expedition 327 in Summer 2010. This eight-week-long education and outreach effort was run by shipboard scientists and educators from the research vessel JOIDES Resolution, using a web site (https://sites.google.com/site/adoptamicrobe) to engage students of all ages in an exploration of the deep biosphere inhabiting the upper ocean crust. Participants were initially introduced to a cast of microbes (residing within an ‘Adoption Center’ on the project website) that live in the dark ocean and asked to select and virtually ‘adopt’ a microbe. A new educational activity was offered each week to encourage learning about microbiology, using the adopted microbe as a focal point. Activities included reading information and asking questions about the adopted microbes (with subsequent responses from shipboard scientists), writing haiku about the adopted microbes, making balloon and fabric models of the adopted microbes, answering math questions related to the study of microbes in the ocean, growing cultures of microbes, and examining the gases produced by microbes. In addition, the website featured regular text, photo and video updates about the science of the expedition using a toy microbe as narrator, as well as stories written by shipboard scientists from the perspective of deep ocean microbes accompanied by watercolor illustrations prepared by a shipboard artist. Assessment methods for evaluating the effectiveness of the Adopt a Microbe project included participant feedback via email and online surveys, website traffic monitoring, and online video viewing rates. Quantitative metrics suggest that the “Adope A Microbe” project was successful in reaching target audiences and helping to encourage and maintain interest in topics related to IODP Expedition 327. The “Adopt A Microbe” project mdel can be adapted for future oceanographic expeditions to help connect the

  1. Emerging Sponge Models of Animal-Microbe Symbioses

    Science.gov (United States)

    Pita, Lucia; Fraune, Sebastian; Hentschel, Ute

    2016-01-01

    Sponges have a significant impact on marine benthic communities, they are of biotechnological interest owing to their production of bioactive natural compounds, and they promise to provide insights into conserved mechanisms of host–microbe interactions in basal metazoans. The natural variability of sponge-microbe associations across species and environments provides a meaningful ecological and evolutionary framework to investigate animal-microbial symbiosis through experimentation in the field and also in aquaria. In addition, next-generation sequencing technologies have shed light on the genomic repertoire of the sponge host and revealed metabolic capacities and symbiotic lifestyle features of their microbiota. However, our understanding of symbiotic mechanisms is still in its infancy. Here, we discuss the potential and limitations of the sponge-microbe symbiosis as emerging models for animal-associated microbiota. PMID:28066403

  2. Microbes can help explain the evolution of host altruism

    Science.gov (United States)

    Lewin-Epstein, Ohad; Aharonov, Ranit; Hadany, Lilach

    2017-01-01

    The evolution of altruistic behaviour, which is costly to the donor but beneficial for the recipient, is among the most intriguing questions in evolutionary biology. Several theories have been proposed to explain it, including kin selection, group selection and reciprocity. Here we propose that microbes that manipulate their hosts to act altruistically could be favoured by selection, and may play a role in the widespread occurrence of altruism. Using computational models, we find that microbe-induced altruism can explain the evolution of host altruistic behaviour under wider conditions than host-centred theories, including in a fully mixed host population, without repeating interactions or individual recognition. Our results suggest that factors such as antibiotics that kill microbes might negatively affect cooperation in a wide range of organisms. PMID:28079112

  3. Principles of Plant-Microbe Interactions - Microbes for Sustainable Agriculture

    Science.gov (United States)

    Crops lack resistance to many soilborne pathogens and rely on antagonistic microbes recruited from the soil microbiome to protect their roots. Disease-suppressive soils, the best examples of microbial-based defense, are soils in which a pathogen does not establish or persist, establishes but causes ...

  4. Coral reef microbes : the influences of benthic primary producers, nutrient availability, and anthropogenic stressors on community structure and metabolism

    OpenAIRE

    Kelly, Linda Ellen Wegley

    2013-01-01

    Genomic studies of marine microbes have advanced our understanding of community ecology and the vast array of metabolisms microbes utilize for acquiring energy and nutrients in the ocean. The structure of microbial communities overlying coral reefs have been shown to reflect ecosystem health. For example, algal-dominated reefs are inhabited by more pathogen-like microbes. The objective of my PhD thesis was to use metagenomics to investigate the microbial communities associated with the coral ...

  5. Questioning Techniques.

    Science.gov (United States)

    Patterson, Michelle

    1999-01-01

    Questions are so much a part of the classroom routine and they should stimulate learning and thinking. Introduces the Questioning and Understanding to Improve Learning and Thinking (QUILT) method which incorporates Bloom's Taxonomy and wait time. (ASK)

  6. The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types.

    Science.gov (United States)

    Lang, Jenna M; Eisen, Jonathan A; Zivkovic, Angela M

    2014-01-01

    Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some "probiotic" health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 10(9) CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 10(6) and 1.4 × 10(6) CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories

  7. Integrated studies of uncultured microbes in the global ocean (Invited)

    Science.gov (United States)

    Dupont, C.; Rusch, D.; Martiny, A.; Lasken, R.

    2010-12-01

    The Global Ocean Sampling (GOS) initiative at the J. Craig Venter Institute represents the most extensive metagenomic study of a single environment. Early findings highlighted the potential of shotgun metagenomics to expand our knowledge of marine microbial biodiversity and physiology. However, it also became clear that many of the abundant marine microbes remain uncultured, hindering a direct connection between phylogeny and ecophysiology. In two recent studies, a combination of single cell genomics and aggressive assembly of binned metagenomic data have resulted in the acquisition of multiple genomes for two uncultured but globally relevant organisms. Metabolic reconstructions of the whole genomes revealed unique physiological adaptations in marine Prochlorococcus to high nutrient, low Fe regions of the global ocean and illuminated the potential ecological role of the gamma-proteobacterial 16S clade SAR86. The internal reference genomes also facilitate fragment recruitment based biogeographical studies, both at the whole genome level and the protein level.

  8. Microbes encapsulated within crosslinkable polymers

    Energy Technology Data Exchange (ETDEWEB)

    Chidambaram, Devicharan; Liu, Ying; Rafailovich, Miriam H

    2013-02-05

    The invention relates to porous films comprising crosslinked electrospun hydrogel fibers. Viable microbes are encapsulated within the crosslinked electrospun hydrogel fibers. The crosslinked electrospun hydrogel fibers are water insoluble and permeable. The invention also relates to methods of making and using such porous films.

  9. Experimental evolution as an underutilized tool for studying beneficial animal-microbe interactions

    Directory of Open Access Journals (Sweden)

    Kim Loan Hoang

    2016-09-01

    Full Text Available Microorganisms play a significant role in the evolution and functioning of the eukaryotes with which they interact. Much of our understanding of beneficial host-microbe interactions stems from studying already established associations; we often infer the genotypic and environmental conditions that led to the existing host-microbe relationships. However, several outstanding questions remain, including understanding how host and microbial (internal traits, and ecological and evolutionary (external processes, influence the origin of beneficial host-microbe associations. Experimental evolution has helped address a range of evolutionary and ecological questions across different model systems; however, it has been greatly underutilized as a tool to study beneficial host-microbe associations. In this review, we suggest ways in which experimental evolution can further our understanding of the proximate and ultimate mechanisms shaping mutualistic interactions between eukaryotic hosts and microbes. By tracking beneficial interactions under defined conditions or evolving novel associations among hosts and microbes with little prior evolutionary interaction, we can link specific genotypes to phenotypes that can be directly measured. Moreover, this approach will help address existing puzzles in beneficial symbiosis research: how symbioses evolve, how symbioses are maintained, and how both host and microbe influence their partner’s evolutionary trajectories. By bridging theoretical predictions and empirical tests, experimental evolution provides us with another approach to test hypotheses regarding the evolution of beneficial host-microbe associations.

  10. Safety of novel microbes for human consumption

    NARCIS (Netherlands)

    Brodmann, Theodor; Endo, Akihito; Gueimonde, Miguel; Vinderola, Gabriel; Kneifel, Wolfgang; Vos, de Willem M.; Salminen, Seppo; Gómez-Gallego, Carlos

    2017-01-01

    Novel microbes are either newly isolated genera and species from natural sources or bacterial strains derived from existing bacteria. Novel microbes are gaining increasing attention for the general aims to preserve and modify foods and to modulate gut microbiota. The use of novel microbes to

  11. Can chatter between microbes prevent cholera?

    Science.gov (United States)

    Thompson, Jessica A; Oliveira, Rita Almeida; Xavier, Karina B

    2014-12-01

    Tackling the global rise in antibiotic resistance requires new therapies against infectious microbes. A recent microbiome study identified commensal gut bacteria that reduce colonisation by the cholera pathogen, Vibrio cholerae. This antagonistic interaction might be mediated by quorum sensing, suggesting that these natural microbe-microbe interactions can help prevent infectious disease. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Current development and application of soybean genomics

    Institute of Scientific and Technical Information of China (English)

    Lingli HE; Jing ZHAO; Man ZHAO; Chaoying HE

    2011-01-01

    Soybean (Glycine max),an important domesticated species originated in China,constitutes a major source of edible oils and high-quality plant proteins worldwide.In spite of its complex genome as a consequence of an ancient tetraploidilization,platforms for map-based genomics,sequence-based genomics,comparative genomics and functional genomics have been well developed in the last decade,thus rich repertoires of genomic tools and resources are available,which have been influencing the soybean genetic improvement.Here we mainly review the progresses of soybean (including its wild relative Glycine soja) genomics and its impetus for soybean breeding,and raise the major biological questions needing to be addressed.Genetic maps,physical maps,QTL and EST mapping have been so well achieved that the marker assisted selection and positional cloning in soybean is feasible and even routine.Whole genome sequencing and transcriptomic analyses provide a large collection of molecular markers and predicted genes,which are instrumental to comparative genomics and functional genomics.Comparative genomics has started to reveal the evolution of soybean genome and the molecular basis of soybean domestication process.Microarrays resources,mutagenesis and efficient transformation systems become essential components of soybean functional genomics.Furthermore,phenotypic functional genomics via both forward and reverse genetic approaches has inferred functions of many genes involved in plant and seed development,in response to abiotic stresses,functioning in plant-pathogenic microbe interactions,and controlling the oil and protein content of seed.These achievements have paved the way for generation of transgenic or genetically modified (GM) soybean crops.

  13. Curiosity Questions

    Science.gov (United States)

    Nelsen, Jane; DeLorenzo, Chip

    2010-01-01

    Have you ever found yourself lecturing a child, with the best of intentions, in an attempt to help him or her learn a lesson or process a situation in a manner that you feel will be productive? Curiosity questions, which the authors also call What and How questions, help children process an experience, event, or natural consequence so that they…

  14. Neutrophils, from marrow to microbes

    DEFF Research Database (Denmark)

    Borregaard, Niels

    2010-01-01

    . Neutrophils circulate in the blood as dormant cells. At sites of infection, endothelial cells capture bypassing neutrophils and guide them through the endothelial cell lining whereby the neutrophils are activated and tuned for the subsequent interaction with microbes. Once in tissues, neutrophils kill...... microorganisms by microbicidal agents liberated from granules or generated by metabolic activation. As a final act, neutrophils can extrude stands of DNA with bactericidal proteins attached that act as extracellular traps for microorganisms....

  15. Microbes and animal olfactory communication: Where do we go from here?

    Science.gov (United States)

    Ezenwa, Vanessa O; Williams, Allison E

    2014-09-01

    We know that microbes contribute to the production of odors that some animals use to communicate, but how common is this phenomenon? Recent studies capitalizing on new molecular technologies are uncovering fascinating associations between microbes and odors of wild animals, but causality is difficult to ascertain. Fundamental questions about the nature of these unique host-microbe interactions also remain unanswered. For instance, do microbes benefit from signaling associations with hosts? How does microbial community structure influence signal production? How do hosts regulate microbes in order to generate appropriate signals? Here, we review the current state of knowledge on microbially produced signals in animals and discuss key research foci that can advance our understanding of microbial-based signaling in the animal world. © 2014 WILEY Periodicals, Inc.

  16. Cooperation and conflict in host-microbe relations.

    Science.gov (United States)

    Ulvestad, Elling

    2009-05-01

    Hosts and microbes associate in a variety of relations along a continuum ranging from symbiotic to pathogenic. Defence mechanisms have been evolutionarily selected in both hosts and microbes to protect the organism's integrity. Such defences have to be utilized with caution. They must be adapted to the tasks at hand; otherwise any symbiotic relation would be impossible. To explain this cautionary use of defences we need to understand how life on Earth evolved into cooperative and competing entities at various levels of organization. The purpose of this article is to review theory and selected mechanisms relating to the evolution and development of host-microbe interactions, with special emphasis on host responses. The rationale is that without theory, extrapolations from misleading observations can dominate and distort, for a significant time, the course of a scientific field. The argument is set forth that social evolution theory provides a conceptual framework for addressing questions relating to interaction between hosts and microbes. The article is a partial summary of arguments presented in my book Defending life - the nature of host-parasite relations.

  17. Genetic mechanisms of prebiotic oligosaccharide metabolism in probiotic microbes.

    Science.gov (United States)

    Goh, Yong Jun; Klaenhammer, Todd R

    2015-01-01

    Recent insights into the relationship between the human gut and its resident microbiota have revolutionized our appreciation of this symbiosis and its impact on health and disease development. Accumulating evidence on probiotic and prebiotic interventions has demonstrated promising effects on promoting gastrointestinal health by modulating the microbiota toward the enrichment of beneficial microorganisms. However, the precise mechanisms of how prebiotic nondigestible oligosaccharides are metabolized by these beneficial microbes in vivo remain largely unknown. Genome sequencing of probiotic lactobacilli and bifidobacteria has revealed versatile carbohydrate metabolic gene repertoires dedicated to the catabolism of various oligosaccharides. In this review, we highlight recent findings on the genetic mechanisms involved in the utilization of prebiotic fructooligosaccharides, β-galactooligosaccharides, human milk oligosaccharides, and other prebiotic candidates by these probiotic microbes.

  18. Microbes Drive Evolution of Animals and Plants: the Hologenome Concept

    Directory of Open Access Journals (Sweden)

    Eugene Rosenberg

    2016-03-01

    Full Text Available The hologenome concept of evolution postulates that the holobiont (host plus symbionts with its hologenome (host genome plus microbiome is a level of selection in evolution. Multicellular organisms can no longer be considered individuals by the classical definitions of the term. Every natural animal and plant is a holobiont consisting of the host and diverse symbiotic microbes and viruses. Microbial symbionts can be transmitted from parent to offspring by a variety of methods, including via cytoplasmic inheritance, coprophagy, direct contact during and after birth, and the environment. A large number of studies have demonstrated that these symbionts contribute to the anatomy, physiology, development, innate and adaptive immunity, and behavior and finally also to genetic variation and to the origin and evolution of species. Acquisition of microbes and microbial genes is a powerful mechanism for driving the evolution of complexity. Evolution proceeds both via cooperation and competition, working in parallel.

  19. Predominately Uncultured Microbes as Sources of Bioactive Agents

    Science.gov (United States)

    Newman, David J.

    2016-01-01

    In this short review, I am discussing the relatively recent awareness of the role of symbionts in plant, marine-invertebrates and fungal areas. It is now quite obvious that in marine-invertebrates, a majority of compounds found are from either as yet unculturable or poorly culturable microbes, and techniques involving “state of the art” genomic analyses and subsequent computerized analyses are required to investigate these interactions. In the plant kingdom evidence is amassing that endophytes (mainly fungal in nature) are heavily involved in secondary metabolite production and that mimicking the microbial interactions of fermentable microbes leads to involvement of previously unrecognized gene clusters (cryptic clusters is one name used), that when activated, produce previously unknown bioactive molecules. PMID:27917159

  20. Microbes Drive Evolution of Animals and Plants: the Hologenome Concept.

    Science.gov (United States)

    Rosenberg, Eugene; Zilber-Rosenberg, Ilana

    2016-03-31

    The hologenome concept of evolution postulates that the holobiont (host plus symbionts) with its hologenome (host genome plus microbiome) is a level of selection in evolution. Multicellular organisms can no longer be considered individuals by the classical definitions of the term. Every natural animal and plant is a holobiont consisting of the host and diverse symbiotic microbes and viruses. Microbial symbionts can be transmitted from parent to offspring by a variety of methods, including via cytoplasmic inheritance, coprophagy, direct contact during and after birth, and the environment. A large number of studies have demonstrated that these symbionts contribute to the anatomy, physiology, development, innate and adaptive immunity, and behavior and finally also to genetic variation and to the origin and evolution of species. Acquisition of microbes and microbial genes is a powerful mechanism for driving the evolution of complexity. Evolution proceeds both via cooperation and competition, working in parallel. Copyright © 2016 Rosenberg and Zilber-Rosenberg.

  1. Thousand Questions

    DEFF Research Database (Denmark)

    Soon, Winnie; Pritchard, Helen

    2016-01-01

    In this work the network asks “If I wrote you a love letter would you write back?” Like the love letters which appeared mysteriously on the noticeboards of Manchester University’s Computer Department in the 1950s, thousands of texts circulate as computational processes perform the questions...... (perhaps as an expanded Turing test) on its listeners. These questions are extracted in real-time from Twitter with the keyword search of the ‘?’ symbol to create a spatio-temporal experience. The computerized voice the audience hears is a collective one, an entanglement of humans and non...

  2. Mind the gap; seven reasons to close fragmented genome assemblies.

    Science.gov (United States)

    Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi

    2016-05-01

    Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions.

  3. Critical Questions.

    Science.gov (United States)

    Worthy, Jo; Hoffman, James V.

    1998-01-01

    Offers responses from four readers of this journal, all reading and/or classroom teachers, to a question posed by another teacher: whether children who have had limited literacy experiences should start reading in whole-language readers and/or trade books or whether they should start in controlled-vocabulary preprimers. (SR)

  4. Thousand Questions

    DEFF Research Database (Denmark)

    2012-01-01

    (perhaps as an expanded Turing test) on its listeners. These questions are extracted in real-time from Twitter with the keyword search of the ‘?’ symbol to create a spatio-temporal experience. The computerized voice the audience hears is a collective one, an entanglement of humans and non...

  5. Microorganisms in environmental management: microbes and environment

    National Research Council Canada - National Science Library

    Satyanarayana, T; Johri, B. N; Prakash, Anil

    2012-01-01

    "This survey of recent scientific progress in usefully applying microbes to both environmental management and biotechnology is informed by acknowledgement of the polluting effects on the world around...

  6. Nitrate storage and dissimilatory nitrate reduction by eukaryotic microbes

    DEFF Research Database (Denmark)

    Kamp, Anja; Høgslund, Signe; Risgaard-Petersen, Nils;

    2015-01-01

    The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly...... and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate...... storage and dissimilatory nitrate reduction by diverse marine eukaryotes placed into an eco-physiological context. The advantage of intracellular nitrate storage for anaerobic energy conservation in oxygen-depleted habitats is explained and the life style enabled by this metabolic trait is described...

  7. 2010 MARINE MICROBES GORDON RESEARCH CONFERENCE (JULY 4-9, 2010 - TILTON SCHOOL, TILTON NH)

    Energy Technology Data Exchange (ETDEWEB)

    David Kirchman

    2010-04-09

    Marine microbes include representatives from all three kingdoms of life and collectively carry out virtually all forms of metabolisms found on the planet. Because of this metabolic and genetic diversity, these microbes mediate many of the reactions making up global biogeochemical cycles which govern the flow of energy and material in the biosphere. The goal of this conference is to bring together approaches and concepts from studies of microbial evolution, genomics, ecology, and oceanography in order to gain new insights into marine microbes and their biogeochemical functions. The integration of scales, from genes to global cycles, will result in a better understanding of marine microbes and of their contribution to the carbon cycle and other biogeochemical processes.

  8. My Questions

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    I have many questions.I think hard and cannot find the answers.I wonder what the world is in reality.Is there any answer to the mystery of the world?I ask what it is like to be outside the earth.Are there any people on other planets1?How many planets are there in the universe?I wonder a lot about this and that.

  9. Neutrophils, from marrow to microbes

    DEFF Research Database (Denmark)

    Borregaard, Niels

    2010-01-01

    . Neutrophils circulate in the blood as dormant cells. At sites of infection, endothelial cells capture bypassing neutrophils and guide them through the endothelial cell lining whereby the neutrophils are activated and tuned for the subsequent interaction with microbes. Once in tissues, neutrophils kill......Neutrophils are produced in the bone marrow from stem cells that proliferate and differentiate to mature neutrophils fully equipped with an armory of granules. These contain proteins that enable the neutrophil to deliver lethal hits against microorganisms, but also to cause great tissue damage...... microorganisms by microbicidal agents liberated from granules or generated by metabolic activation. As a final act, neutrophils can extrude stands of DNA with bactericidal proteins attached that act as extracellular traps for microorganisms....

  10. Commonalities in Symbiotic Plant-Microbe Signalling

    NARCIS (Netherlands)

    Holmer, R.; Rutten, L.J.J.; Kohlen, W.; Velzen, van R.; Geurts, R.

    2017-01-01

    Plants face the problem that they have to discriminate symbionts from a diverse pool of soil microbes, including pathogens. Studies on different symbiotic systems revealed commonalities in plant-microbe signalling. In this chapter we focus on four intimate symbiotic interactions: two mycorrhizal

  11. Modulation of host immunity by beneficial microbes

    NARCIS (Netherlands)

    Zamioudis, C; Pieterse, C.M.J.

    2012-01-01

    In nature, plants abundantly form beneficial associations with soilborne microbes that are important for plant survival and, as such, affect plant biodiversity and ecosystem functioning. Classical examples of symbiotic microbes are mycorrhizal fungi that aid in the uptake of water and minerals, and

  12. Modulation of host immunity by beneficial microbes

    NARCIS (Netherlands)

    Zamioudis, C; Pieterse, C.M.J.

    2012-01-01

    In nature, plants abundantly form beneficial associations with soilborne microbes that are important for plant survival and, as such, affect plant biodiversity and ecosystem functioning. Classical examples of symbiotic microbes are mycorrhizal fungi that aid in the uptake of water and minerals, and

  13. The Antarctic cryptoendolithic microbial ecosystem as a model for studying microbes in shale and coal

    Energy Technology Data Exchange (ETDEWEB)

    Vestal, J.R. (University of Cincinnati, Cincinnati, OH (USA). Dept. of Biological Sciences)

    1991-04-01

    In Antarctica, there exists a complete microbial ecosystem that lives hidden within the pore spaces of sandstone (cryptoendolithic). Studying microbes within this solid matrix has presented certain technical problems which have been overcome. This has allowed studies to be conducted that have shown the effects of the physical and chemical environment on growth and metabolism of the microbes in these rocks. Similar microbial communities have recently been discovered that can exist within the solid matrix of shale and coal. Even though the community and environment are different from the Antarctic microbes, many of the methods and hypotheses regarding their existence are the same. Answers to questions relating how and why these microbes exist in shale and coal may have important implications for coal desulfurization, or degradation of the shale matrix to release hydrocarbons. 40 refs., 1 fig., 1 tab.

  14. Perchlorate reduction by microbes inhabiting oil reservoirs

    Science.gov (United States)

    Liebensteiner, Martin; Stams, Alfons; Lomans, Bart

    2014-05-01

    Microbial perchlorate and chlorate reduction is a unique type of anaerobic respiration as during reduction of (per)chlorate chlorite is formed, which is then split into chloride and molecular oxygen. In recent years it was demonstrated that (per)chlorate-reducing bacteria may employ oxygenase-dependent pathways for the degradation of aromatic and aliphatic hydrocarbons. These findings suggested that (per)chlorate may be used as oxygen-releasing compound in anoxic environments that contain hydrocarbons, such as polluted soil sites and oil reservoirs. We started to study perchlorate reduction by microbes possibly inhabiting oil reservoirs. One of the organisms studied was Archaeoglobus fulgidus. This extremely thermophilic archaeon is known as a major contributor to souring in hot oil reservoirs. A. fulgidus turned out to be able to use perchlorate as terminal electron acceptor for growth with lactate (Liebensteiner et al 2013). Genome based physiological experiments indicated that A. fulgidus possesses a novel perchlorate reduction pathway. Perchlorate is first reduced to chlorite, but chlorite is not split into chloride and molecular oxygen as occurs in bacteria. Rather, chlorite reacts chemically with sulfide, forming oxidized sulfur compounds, which are reduced to sulfide in the electron transport chain by the archaeon. The dependence of perchlorate reduction on sulfur compounds could be shown. The implications of our findings as novel strategy for microbiological enhanced oil recovery and for souring mitigation are discussed. Liebensteiner MG, Pinkse MWH, Schaap PJ, Stams AJM and Lomans BP (2013) Archaeal (per)chlorate reduction at high temperature, a matter of abiotic-biotic reactions. Science 340: 85-87

  15. Inference of Environmental Factor-Microbe and Microbe-Microbe Associations from Metagenomic Data Using a Hierarchical Bayesian Statistical Model.

    Science.gov (United States)

    Yang, Yuqing; Chen, Ning; Chen, Ting

    2017-01-25

    The inference of associations between environmental factors and microbes and among microbes is critical to interpreting metagenomic data, but compositional bias, indirect associations resulting from common factors, and variance within metagenomic sequencing data limit the discovery of associations. To account for these problems, we propose metagenomic Lognormal-Dirichlet-Multinomial (mLDM), a hierarchical Bayesian model with sparsity constraints, to estimate absolute microbial abundance and simultaneously infer both conditionally dependent associations among microbes and direct associations between microbes and environmental factors. We empirically show the effectiveness of the mLDM model using synthetic data, data from the TARA Oceans project, and a colorectal cancer dataset. Finally, we apply mLDM to 16S sequencing data from the western English Channel and report several associations. Our model can be used on both natural environmental and human metagenomic datasets, promoting the understanding of associations in the microbial community.

  16. Uncharted Microbial World: Microbes and Their Activities in the Environment

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, Caroline; Buckley, Merry.

    2007-12-31

    systems with features like clear physical boundaries, limited microbial diversity, and manipulability with the goal of understanding fundamental principles that may apply to more complex systems. A great deal of microbial genetic and phenotypic diversity remains to be explored, and the commercial and medical potential locked up in these unknowns should compel the field to move forward. Future microbiology research will build on the successes of the past using new techniques and approaches. Uncultivated microbes hold great promise for industry, medicine, and the recycling of precious resources, and research and technology must make inroads in overcoming the barriers that prevent their study. In many cases, we will no longer be able to rely on isolated, pure cultures of microorganisms, but must use communities of microorganisms, which presently are poorly understood. Indeed, community-level studies can benefit from deconstructing microbial communities and analyzing the component members separately, but this is not feasible in every system. The effects of perturbation on microbial communities also require study. Humans rely on the services of microbes in innumerable ways, but we have little or no predictive understanding of how microbial communities respond to disturbance. Research must address current limitations in detecting microscale interactions among microbes by enhancing current technologies and fostering new microscopic tools, biosensors, and gas sensors for appropriate small scales. Genomics, which has enabled great progress in microbiology research of individual species, must be applied to communities of microorganisms. This will require improved methods of DNA extraction and amplification from environmental samples and improved strategies for DNA sequence assembly. In the future, genome sequencing efforts should continue the exploration of evolutionarily diverse microbes, as well as help reveal the mechanisms by which closely related microbes evolve. Technological

  17. The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

    Directory of Open Access Journals (Sweden)

    Jenna M. Lang

    2014-12-01

    Full Text Available Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some “probiotic” health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered.We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1 the Average American (AMERICAN: focused on convenience foods, (2 USDA recommended (USDA: emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3 Vegan (VEGAN: excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis.Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 109 CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 106 and 1.4 × 106 CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG

  18. Zhongyuan Offers Drilling Service for Microbes

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhiyu

    2001-01-01

    @@ No. 1 Drilling Company of Zhongyuan Petroleum Exploration Bureau and US-based Microbes Inc.signed a drilling engineering contract for six wells in Jilin Oil Field worth more than 11 million yuan in mid-October 2001.

  19. Plant interactions with microbes and insects: from molecular mechanisms to ecology

    NARCIS (Netherlands)

    Pieterse, C.M.J.; Dicke, M.

    2007-01-01

    Plants are members of complex communities and interact both with antagonists and beneficial organisms. An important question in plant defense-signaling research is how plants integrate signals induced by pathogens, beneficial microbes and insects into the most appropriate adaptive response. Molecula

  20. Experimental Activities in Primary School to Learn about Microbes in an Oral Health Education Context

    Science.gov (United States)

    Mafra, Paulo; Lima, Nelson; Carvalho, Graça S.

    2015-01-01

    Experimental science activities in primary school enable important cross-curricular learning. In this study, experimental activities on microbiology were carried out by 16 pupils in a Portuguese grade-4 classroom (9-10?years old) and were focused on two problem-questions related to microbiology and health: (1) do your teeth carry microbes? (2) why…

  1. Ordinary Stoichiometry of Extraordinary Microbes

    Science.gov (United States)

    Neveu, M.; Poret-Peterson, A. T.; Anbar, A. D.; Elser, J. J.

    2013-12-01

    Life on Earth seems to be composed of the same chemical elements in relatively conserved stoichiometric proportions. However, this observation is largely based on observations of biota from habitats spanning a moderate range of temperature and chemical composition (e.g., temperate lakes, forests, grasslands, oceanic phytoplankton). Whether this stoichiometry is conserved in settings that differ radically from such "normal" planetary settings may provide insight into the habitability of environments with radically different stoichiometries, and into possible stoichiometries for putative life beyond Earth. Here we report the first measurements of elemental stoichiometries of microbial extremophiles from hot springs of Yellowstone National Park (YNP). These phototrophic and chemotrophic microbes were collected in locations spanning large ranges of temperature (ambient to boiling) and pH (1 to 9). Microbial biomass was carefully extracted from hot spring sediment substrata following a procedure adapted from [1], which conserves cellular elemental abundances [2]. Their C and N contents were determined by Elemental Analysis Isotope Ratio Mass Spectrometry, and their P and trace element (Mg, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, and non-biogenic Al and Ti) contents were measured by Inductively Coupled Plasma Mass Spectrometry. Residual mineral contamination was an issue in some samples with low measured C and N; we eliminated these from our results. Even in the remaining samples, contamination sometimes prevented accurate determinations of cellular Mg, Ca, Mn, and Fe abundances; however, the cellular Ni, Cu, Zn, and Mo contents were several-fold above contamination level. Although hot spring water and sediment elemental abundances varied by orders of magnitude, the data showed that the extremophiles have a major and trace element stoichiometry similar to those previously measured in "normal" microbial biomass [3-6]. For example, biomass C:N:P ratios resembled those

  2. Gut microbes may facilitate insect herbivory of chemically defended plants.

    Science.gov (United States)

    Hammer, Tobin J; Bowers, M Deane

    2015-09-01

    The majority of insect species consume plants, many of which produce chemical toxins that defend their tissues from attack. How then are herbivorous insects able to develop on a potentially poisonous diet? While numerous studies have focused on the biochemical counter-adaptations to plant toxins rooted in the insect genome, a separate body of research has recently emphasized the role of microbial symbionts, particularly those inhabiting the gut, in plant-insect interactions. Here we outline the "gut microbial facilitation hypothesis," which proposes that variation among herbivores in their ability to consume chemically defended plants can be due, in part, to variation in their associated microbial communities. More specifically, different microbes may be differentially able to detoxify compounds toxic to the insect, or be differentially resistant to the potential antimicrobial effects of some compounds. Studies directly addressing this hypothesis are relatively few, but microbe-plant allelochemical interactions have been frequently documented from non-insect systems-such as soil and the human gut-and thus illustrate their potential importance for insect herbivory. We discuss the implications of this hypothesis for insect diversification and coevolution with plants; for example, evolutionary transitions to host plant groups with novel allelochemicals could be initiated by heritable changes to the insect microbiome. Furthermore, the ecological implications extend beyond the plant and insect herbivore to higher trophic levels. Although the hidden nature of microbes and plant allelochemicals make their interactions difficult to detect, recent molecular and experimental techniques should enable research on this neglected, but likely important, aspect of insect-plant biology.

  3. Can Terrestrial Microbes Grow on Mars?

    Science.gov (United States)

    Rothschild, Lynn

    2012-01-01

    The theme for AbSciCon 2012 is "Exploring Life: Past and Present, Near and Far." The conference will address our current understanding of life - from processes at the molecular level to those which operate at planetary scales. Studying these aspects of life on Earth provides an essential platform from which to examine the potential for life on other worlds, both within our solar system and beyond. Mars exhibits a variety of extreme environments characterized by high UV and ionizing radiation flux, low pressure anoxic atmosphere, scarce or absent liquid water, extreme low temperatures, etc. The ability of terrestrial microorganisms to survive and adapt to the Mars environment has profound implications for astrobiology, planetary protection, and Mars life detection missions. At the NASA Ames Synthetic Biology Initiative, we believe that synthetic biology has the potential to revolutionize human space exploration. As such, the initiative is dedicated to applying the tools and techniques of synthetic biology to space exploration and astrobiology. Biological solutions will be invaluable for space exploration because they are not resource intensive, and they are versatile and self-renewing. An understanding of how to work with DNA in an unfavorable environment is paramount to utilizing biological tools on space missions. Furthermore, the ability to adjust life to the parameters of Mars is vital both to discovering what life on Mars might look like, and to using biological tools under such conditions. As a first step, we need an energy-efficient, low cost means of transporting, storing, and protecting genomic DNA, DNA parts, and whole microbial strains. Our goal is to develop and demonstrate viable and superior alternatives to standard DNA storage methods, which can be optimized to the conditions of space exploration, using synthetic biology as a tool. This includes protocols and kit designs for easy and repeatable DNA and strain recovery from protective storage

  4. Modulation of host immunity by beneficial microbes.

    Science.gov (United States)

    Zamioudis, Christos; Pieterse, Corné M J

    2012-02-01

    In nature, plants abundantly form beneficial associations with soilborne microbes that are important for plant survival and, as such, affect plant biodiversity and ecosystem functioning. Classical examples of symbiotic microbes are mycorrhizal fungi that aid in the uptake of water and minerals, and Rhizobium bacteria that fix atmospheric nitrogen for the plant. Several other types of beneficial soilborne microbes, such as plant-growth-promoting rhizobacteria and fungi with biological control activity, can stimulate plant growth by directly suppressing deleterious soilborne pathogens or by priming aboveground plant parts for enhanced defense against foliar pathogens or insect herbivores. The establishment of beneficial associations requires mutual recognition and substantial coordination of plant and microbial responses. A growing body of evidence suggests that beneficial microbes are initially recognized as potential invaders, after which an immune response is triggered, whereas, at later stages of the interaction, mutualists are able to short-circuit plant defense responses to enable successful colonization of host roots. Here, we review our current understanding of how symbiotic and nonsymbiotic beneficial soil microbes modulate the plant immune system and discuss the role of local and systemic defense responses in establishing the delicate balance between the two partners.

  5. Genitalia-associated microbes in insects.

    Science.gov (United States)

    Otti, Oliver

    2015-03-01

    In sexual reproduction different types of symbiotic relationships between insects and microbes have become established. For example, some bacteria have evolved almost exclusive vertical transmission and even define the compatibility of insect mating partners. Many strictly sexually transmitted diseases have also been described in insects. Apart from such rather specific relationships the role of opportunistic infections in the reproductive process has been widely neglected. Opportunistic microbes transmitted passively during mating might impose an energetic cost, as the immune system will need to be alert and will use resources to fight potential intruders. Through mating wounds and contaminated reproductive organs opportunistic microbes might be transferred to mating partners and even enter the body cavity. Females as the "receiving" sex are particularly likely to have evolved adaptations to avoid or reduce opportunistic infections. Males of several species show highly complex seminal fluids, which as well as containing components that influence a males' fertilization success, also possess antimicrobial substances. The role of antimicrobials in the reproductive process is not well understood. Some evidence hints at the protection of sperm against microbes, indicating a role for natural selection in shaping the evolution of reproductive traits. By highlighting the potential importance of microbes in sexual selection and their role in reproduction in general I will make a case for studies in sexual selection, especially the ones investigating postcopulatory processes, that should incorporate environmental, as well as genotypic variation, in reproductive traits.

  6. Impact of genomics on microbial food safety

    NARCIS (Netherlands)

    Abee, T.; Schaik, van W.; Siezen, R.J.

    2004-01-01

    Genome sequences are now available for many of the microbes that cause food-borne diseases. The information contained in pathogen genome sequences, together with the development of themed and whole-genome DNA microarrays and improved proteomics techniques, might provide tools for the rapid detection

  7. Natural transfer of viable microbes in space.

    Science.gov (United States)

    Mileikowsky, C; Cucinotta, F A; Wilson, J W; Gladman, B; Horneck, G; Lindegren, L; Melosh, J; Rickman, H; Valtonen, M; Zheng, J Q

    2000-06-01

    The possibility and probability of natural transfer of viable microbes from Mars to Earth and Earth to Mars traveling in meteoroids during the first 0.5 Ga and the following 4 Ga are investigated, including: --radiation protection against the galactic cosmic ray nuclei and the solar rays, dose rates as a function of the meteorite's radial column mass (radius x density), combined with dose rates generated by natural radioactivity within the meteorite; and survival curves for some bacterial species using NASA's HZETRN transport code --other factors affecting microbe survival: vacuum; central meteorite temperatures at launch, orbiting, and arrival; pressure and acceleration at launch; spontaneous DNA decay; metal ion migration --mean sizes and numbers of unshocked meteorites ejected and percentage falling on Earth, using current semiempirical results --viable flight times for the microbe species Bacillus subtilis and Deinococcus radiodurans R1 --the approximate fraction of microbes (with properties like the two species studied) viably arriving on Earth out of those ejected from Mars during the period 4 Ga BP to the present time, and during the 700 Ma from 4.5 to 3.8 Ga. Similarly, from Earth to Mars. The conclusion is that if microbes existed or exist on Mars, viable transfer to Earth is not only possible but also highly probable, due to microbes' impressive resistance to the dangers of space transfer and to the dense traffic of billions of martian meteorites which have fallen on Earth since the dawn of our planetary system. Earth-to-Mars transfer is also possible but at a much lower frequency.

  8. Metals, minerals and microbes: geomicrobiology and bioremediation.

    Science.gov (United States)

    Gadd, Geoffrey Michael

    2010-03-01

    Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social

  9. Electrifying microbes for the production of chemicals

    DEFF Research Database (Denmark)

    Tremblay, Pier-Luc; Zhang, Tian

    2015-01-01

    Powering microbes with electrical energy to produce valuable chemicals such as biofuels has recently gained traction as a biosustainable strategy to reduce our dependence on oil. Microbial electrosynthesis (MES) is one of the bioelectrochemical approaches developed in the last decade that could...... have critical impact on the current methods of chemical synthesis. MES is a process in which electroautotrophic microbes use electrical current as electron source to reduce CO2 to multicarbon organics. Electricity necessary for MES can be harvested from renewable resources such as solar energy, wind...

  10. Functional metagenomics to decipher food-microbe-host crosstalk.

    Science.gov (United States)

    Larraufie, Pierre; de Wouters, Tomas; Potocki-Veronese, Gabrielle; Blottière, Hervé M; Doré, Joël

    2015-02-01

    The recent developments of metagenomics permit an extremely high-resolution molecular scan of the intestinal microbiota giving new insights and opening perspectives for clinical applications. Beyond the unprecedented vision of the intestinal microbiota given by large-scale quantitative metagenomics studies, such as the EU MetaHIT project, functional metagenomics tools allow the exploration of fine interactions between food constituents, microbiota and host, leading to the identification of signals and intimate mechanisms of crosstalk, especially between bacteria and human cells. Cloning of large genome fragments, either from complex intestinal communities or from selected bacteria, allows the screening of these biological resources for bioactivity towards complex plant polymers or functional food such as prebiotics. This permitted identification of novel carbohydrate-active enzyme families involved in dietary fibre and host glycan breakdown, and highlighted unsuspected bacterial players at the top of the intestinal microbial food chain. Similarly, exposure of fractions from genomic and metagenomic clones onto human cells engineered with reporter systems to track modulation of immune response, cell proliferation or cell metabolism has allowed the identification of bioactive clones modulating key cell signalling pathways or the induction of specific genes. This opens the possibility to decipher mechanisms by which commensal bacteria or candidate probiotics can modulate the activity of cells in the intestinal epithelium or even in distal organs such as the liver, adipose tissue or the brain. Hence, in spite of our inability to culture many of the dominant microbes of the human intestine, functional metagenomics open a new window for the exploration of food-microbe-host crosstalk.

  11. New CRISPR–Cas systems from uncultivated microbes

    Science.gov (United States)

    Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; Probst, Alexander J.; Anantharaman, Karthik; Thomas, Brian C.; Doudna, Jennifer A.; Banfield, Jillian F.

    2016-12-01

    CRISPR–Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR–Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR–Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR–Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR–Cas system. In bacteria, we discovered two previously unknown systems, CRISPR–CasX and CRISPR–CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

  12. New CRISPR-Cas systems from uncultivated microbes

    Science.gov (United States)

    Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; Probst, Alexander J.; Anantharaman, Karthik; Thomas, Brian C.; Doudna, Jennifer A.; Banfield, Jillian F.

    2017-02-01

    CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

  13. Plant - microbe interactions under Global Change: the microbial perspective

    Science.gov (United States)

    Richter, Andreas

    2017-04-01

    There is ample evidence that both microorganisms and plants will respond to Global Changes, such as enhanced temperatures, increased nitrogen deposition and atmospheric CO2 concentrations, or biodiversity loss. Plant and microbial activities are linked, amongst other factors, by belowground carbon allocation and aboveground nutrient allocation, which may be altered under Global Changes to different extents. The effect of Global Changes on the interaction of plants and microbes is therefore often difficult to predict. In my talk, I will look at plant-microbe interactions from a microbial perspective. I will ask the question what the direct and indirect (plant-mediated) effects of Global Changes are on microbial activities in soil and what this in turn means for plants and for ecosystem-scale fluxes. I will present results from an in-situ drought experiment, from a long-term soil warming experiment and from a plant diversity experiment, where we investigated microbial growth and turnover, carbon and nutrient use efficiency and gross nutrient transformation rates.

  14. Gut Microbes Linked to Rheumatoid Arthritis

    Science.gov (United States)

    ... of microorganisms that live in and on the human body. These microbes outnumber the body’s cells by 10 ... this is indeed the case.” — by Carol Torgan, Ph.D. Related Links Feeling Out of ... Autoimmune Diseases Rheumatoid Arthritis References: Expansion ...

  15. Plant immune responses triggered by beneficial microbes

    NARCIS (Netherlands)

    Wees, A.C.M. van; Ent, S. van der; Pieterse, C.M.J.

    2008-01-01

    Beneficial soil-borne microorganisms, such as plant growth promoting rhizobacteria and mycorrhizal fungi,can improve plant performance by inducing systemic defense responses that confer broad-spectrum resistance to plant pathogens and even insect herbivores. Different beneficial microbe-associated m

  16. Natural products from microbes associated with insects

    DEFF Research Database (Denmark)

    Beemelmanns, Christine; Guo, Huijuan; Rischer, Maja;

    2016-01-01

    Here we review discoveries of secondary metabolites from microbes associated with insects. We mainly focus on natural products, where the ecological role has been at least partially elucidated, and/or the pharmaceutical properties evaluated, and on compounds with unique structural features. We...

  17. Induced systemic resistance by beneficial microbes

    NARCIS (Netherlands)

    Pieterse, Corné M J|info:eu-repo/dai/nl/113115113; Zamioudis, Christos|info:eu-repo/dai/nl/313964742; Berendsen, Roeland L.|info:eu-repo/dai/nl/304824151; Weller, David M.; van Wees, Saskia C M|info:eu-repo/dai/nl/185445373; Bakker, Peter A H M|info:eu-repo/dai/nl/074744623

    2014-01-01

    Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth-promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of patho

  18. Induced systemic resistance by beneficial microbes

    NARCIS (Netherlands)

    Pieterse, C.M.J.; Zamioudis, C.; Berendsen, R.L.; Weller, D.M.; Van Wees, S.C.M.; Bakker, P.A.H.M.

    2014-01-01

    Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of patho

  19. Induced systemic resistance by beneficial microbes

    NARCIS (Netherlands)

    Pieterse, C.M.J.; Zamioudis, C.; Berendsen, R.L.; Weller, D.M.; Van Wees, S.C.M.; Bakker, P.A.H.M.

    2014-01-01

    Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of patho

  20. Human gut microbes use multiple transporters to distinguish vitamin B12 analogs and compete in the gut

    Science.gov (United States)

    Degnan, Patrick H.; Barry, Natasha A.; Mok, Kenny C.; Taga, Michiko E.; Goodman, Andrew L.

    2014-01-01

    Summary Genomic and metagenomic sequencing efforts, including human microbiome projects, reveal that microbes often encode multiple systems that appear to accomplish the same task. Whether these predictions reflect actual functional redundancies is unclear. We report that the prominent human gut symbiont Bacteroides thetaiotaomicron employs three functional, homologous vitamin B12 transporters that in at least two cases confer a competitive advantage in the presence of distinct B12 analogs (corrinoids). In the mammalian gut, microbial fitness can be determined by the presence or absence of a single transporter. The total number of distinct corrinoid transporter families in the human gut microbiome likely exceeds those observed in B. thetaiotaomicron by an order of magnitude. These results demonstrate that human gut microbes use elaborate mechanisms to capture and differentiate corrinoids in vivo and that apparent redundancies observed in these genomes can instead reflect hidden specificities that determine whether a microbe will colonize its host. PMID:24439897

  1. The impact of genomics on population genetics of parasitic diseases.

    Science.gov (United States)

    Hupalo, Daniel N; Bradic, Martina; Carlton, Jane M

    2015-02-01

    Parasites, defined as eukaryotic microbes and parasitic worms that cause global diseases of human and veterinary importance, span many lineages in the eukaryotic Tree of Life. Historically challenging to study due to their complicated life-cycles and association with impoverished settings, their inherent complexities are now being elucidated by genome sequencing. Over the course of the last decade, projects in large sequencing centers, and increasingly frequently in individual research labs, have sequenced dozens of parasite reference genomes and field isolates from patient populations. This 'tsunami' of genomic data is answering questions about parasite genetic diversity, signatures of evolution orchestrated through anti-parasitic drug and host immune pressure, and the characteristics of populations. This brief review focuses on the state of the art of parasitic protist genomics, how the peculiar genomes of parasites are driving creative methods for their sequencing, and the impact that next-generation sequencing is having on our understanding of parasite population genomics and control of the diseases they cause.

  2. Multiscale simulation of microbe structure and dynamics.

    Science.gov (United States)

    Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V; Cheluvaraja, Srinath C; Ortoleva, Peter J

    2011-10-01

    A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin.

  3. Microbe inhibition by Tribolium flour beetles varies with beetle species, strain, sex, and microbe group.

    Science.gov (United States)

    Prendeville, Holly R; Stevens, Lori

    2002-06-01

    Tribolium flour beetles produce defensive compounds, including quinones, putatively aimed at deterring predators and inhibiting microbes. Here we examine how effective the defensive secretions of Tribolium confusum and T. castaneum are at inhibiting growth of various microbes and how this varies with species, geographic strain, and sex of the beetles. We explore differences at both the kingdom and species level of common flour microbes in their susceptibility to defensive compounds. Beetle species and strains vary in their ability to inhibit microbial growth. In addition, microbes vary in their sensitivity to the beetles' defense compounds. The capability to suppress microbial growth is likely under stabilizing selection with optimum quinone production varying among populations and may be dependent on several environmental factors including temperature, humidity, and predators.

  4. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast.

    Science.gov (United States)

    Libkind, Diego; Hittinger, Chris Todd; Valério, Elisabete; Gonçalves, Carla; Dover, Jim; Johnston, Mark; Gonçalves, Paula; Sampaio, José Paulo

    2011-08-30

    Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement.

  5. Uncharted Microbial World: Microbes and Their Activities in the Environment

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, Caroline; Buckley, Merry

    2007-12-31

    systems with features like clear physical boundaries, limited microbial diversity, and manipulability with the goal of understanding fundamental principles that may apply to more complex systems. A great deal of microbial genetic and phenotypic diversity remains to be explored, and the commercial and medical potential locked up in these unknowns should compel the field to move forward. Future microbiology research will build on the successes of the past using new techniques and approaches. Uncultivated microbes hold great promise for industry, medicine, and the recycling of precious resources, and research and technology must make inroads in overcoming the barriers that prevent their study. In many cases, we will no longer be able to rely on isolated, pure cultures of microorganisms, but must use communities of microorganisms, which presently are poorly understood. Indeed, community-level studies can benefit from deconstructing microbial communities and analyzing the component members separately, but this is not feasible in every system. The effects of perturbation on microbial communities also require study. Humans rely on the services of microbes in innumerable ways, but we have little or no predictive understanding of how microbial communities respond to disturbance. Research must address current limitations in detecting microscale interactions among microbes by enhancing current technologies and fostering new microscopic tools, biosensors, and gas sensors for appropriate small scales. Genomics, which has enabled great progress in microbiology research of individual species, must be applied to communities of microorganisms. This will require improved methods of DNA extraction and amplification from environmental samples and improved strategies for DNA sequence assembly. In the future, genome sequencing efforts should continue the exploration of evolutionarily diverse microbes, as well as help reveal the mechanisms by which closely related microbes evolve. Technological

  6. MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

    Directory of Open Access Journals (Sweden)

    Feng Xueyang

    2012-08-01

    Full Text Available Abstract Background Concurrent with the efforts currently underway in mapping microbial genomes using high-throughput sequencing methods, systems biologists are building metabolic models to characterize and predict cell metabolisms. One of the key steps in building a metabolic model is using multiple databases to collect and assemble essential information about genome-annotations and the architecture of the metabolic network for a specific organism. To speed up metabolic model development for a large number of microorganisms, we need a user-friendly platform to construct metabolic networks and to perform constraint-based flux balance analysis based on genome databases and experimental results. Results We have developed a semi-automatic, web-based platform (MicrobesFlux for generating and reconstructing metabolic models for annotated microorganisms. MicrobesFlux is able to automatically download the metabolic network (including enzymatic reactions and metabolites of ~1,200 species from the KEGG database (Kyoto Encyclopedia of Genes and Genomes and then convert it to a metabolic model draft. The platform also provides diverse customized tools, such as gene knockouts and the introduction of heterologous pathways, for users to reconstruct the model network. The reconstructed metabolic network can be formulated to a constraint-based flux model to predict and analyze the carbon fluxes in microbial metabolisms. The simulation results can be exported in the SBML format (The Systems Biology Markup Language. Furthermore, we also demonstrated the platform functionalities by developing an FBA model (including 229 reactions for a recent annotated bioethanol producer, Thermoanaerobacter sp. strain X514, to predict its biomass growth and ethanol production. Conclusion MicrobesFlux is an installation-free and open-source platform that enables biologists without prior programming knowledge to develop metabolic models for annotated microorganisms in the KEGG

  7. Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome.

    Science.gov (United States)

    Bakker, Matthew G; Schlatter, Daniel C; Otto-Hanson, Lindsey; Kinkel, Linda L

    2014-03-01

    A conceptual model emphasizing direct host-microbe interactions has dominated work on host-associated microbiomes. To understand plant-microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant-plant and microbe-microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and Streptomyces populations via 454 pyrosequencing. Host plant species and plant richness treatments altered networks of coassociation among bacterial taxa, suggesting the potential for host plant effects on the soil microbiome to include changes in microbial interaction dynamics and, consequently, co-evolution. Taxa that were coassociated in the rhizosphere of a given host plant species often showed consistent correlations between operational taxonomic unit (OTU) relative abundance and Streptomyces antagonistic activity, in the rhizosphere of that host. However, in the rhizosphere of a different host plant species, the same OTUs showed no consistency, or a different pattern of responsiveness to such biotic habitat characteristics. The diversity and richness of bacterial and Streptomyces communities exhibited distinct relationships with biotic and abiotic soil characteristics. The rhizosphere soil microbiome is influenced by a complex and nested array of factors at varying spatial scales, including plant community, plant host, soil edaphics and microbial taxon and community characteristics. © 2013 John Wiley & Sons Ltd.

  8. Induced systemic resistance by beneficial microbes.

    Science.gov (United States)

    Pieterse, Corné M J; Zamioudis, Christos; Berendsen, Roeland L; Weller, David M; Van Wees, Saskia C M; Bakker, Peter A H M

    2014-01-01

    Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth-promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of pathogens and insect herbivores. A wide variety of root-associated mutualists, including Pseudomonas, Bacillus, Trichoderma, and mycorrhiza species sensitize the plant immune system for enhanced defense without directly activating costly defenses. This review focuses on molecular processes at the interface between plant roots and ISR-eliciting mutualists, and on the progress in our understanding of ISR signaling and systemic defense priming. The central role of the root-specific transcription factor MYB72 in the onset of ISR and the role of phytohormones and defense regulatory proteins in the expression of ISR in aboveground plant parts are highlighted. Finally, the ecological function of ISR-inducing microbes in the root microbiome is discussed.

  9. Electrifying microbes for the production of chemicals

    Directory of Open Access Journals (Sweden)

    Pier-Luc eTremblay

    2015-03-01

    Full Text Available Powering microbes with electrical energy to produce valuable chemicals such as biofuels has recently gained traction as a biosustainable strategy to reduce our dependence on oil. Microbial electrosynthesis (MES is one of the bioelectrochemical approaches developed in the last decade that could have critical impact on the current methods of chemical synthesis. MES is a process in which electroautotrophic microbes use electrical current as electron source to reduce CO2 to multicarbon organics. Electricity necessary for MES can be harvested from renewable resources such as solar energy, wind turbine or wastewater treatment processes. The net outcome is that renewable energy is stored in the covalent bonds of organic compounds synthesized from greenhouse gas. This review will discuss the future of MES and the challenges that lie ahead for its development into a mature technology.

  10. Darwin, microbes and evolution by natural selection.

    Science.gov (United States)

    Moxon, E Richard

    2011-01-01

    Born 200 years ago, Darwin's revolutionary ideas were derived largely from his observations on life forms that evolved relatively recently, including various flowering plants, worms, birds and domesticated animals. Yet, life appeared on planet earth close to 4 billion years ago in the form of unicellular organisms collectively called bacteria. It was only shortly after "On the Origin of Species" was published (1859) that the "germ theory" of infectious diseases was formulated. Microbes (viruses, bacteria, fungi and microparasites) received scant mention in Darwin's writings, although pioneers of the Golden Age of Bacteriology, such as Louis Pasteur (1822-1895), were contemporaries. Today, microbes offer extraordinary testimony and powerful model systems of direct relevance to the essentials of Darwinian selection, such as understanding microbial-host interactions, the evolution of pathogens and the emergence of drug- or vaccine-related resistance.

  11. Ecological Interactions Between Metals and Microbes

    Energy Technology Data Exchange (ETDEWEB)

    Konopka, Allan E.

    2004-06-01

    Analyses of chromium resistant microbes. Culturable xylene-degrading and chromate-resistant microbes were obtained from chronically cocontaminated soil using a microcosm enrichment technique, and shown to correlate to dominant soil populations using culture independent techniques. The soil microbial community proved able to mount a respiratory response to addition of xylene in the presence of chromate. The majority of isolates belonged to the ubiquitous but poorly studied high %G+C Gram positive genus Arthrobacter, and exhibited considerable genotypic and phenotypic variability. Phenotypic assays uncovered a wide variation in the levels of chromate resistance, even between very closely related strains. Primers designed against conserved motifs in the known chrA chromate efflux gene failed to detect similar sequences among the chromate resistant Arthrobacter isolates obtained through enrichment.

  12. Dietary microbes modulate transgenerational cancer risk.

    Science.gov (United States)

    Poutahidis, Theofilos; Varian, Bernard J; Levkovich, Tatiana; Lakritz, Jessica R; Mirabal, Sheyla; Kwok, Caitlin; Ibrahim, Yassin M; Kearney, Sean M; Chatzigiagkos, Antonis; Alm, Eric J; Erdman, Susan E

    2015-04-01

    Environmental factors are suspected in the increase of obesity and cancer in industrialized countries but are poorly understood. Here, we used animal models to test how future generations may be affected by Westernized diets. We discover long-term consequences of grandmothers' in utero dietary exposures, leading to high rates of obesity and frequent cancers of lung and liver in two subsequent generations of mice. Transgenerational effects were transplantable using diet-associated bacteria communities alone. Consequently, feeding of beneficial microbes was sufficient to lower transgenerational risk for cancer and obesity regardless of diet history. Targeting microbes may be a highly effective population-based approach to lower risk for cancer. ©2015 American Association for Cancer Research.

  13. The Study of the Microbes Degraded Polystyrene

    Directory of Open Access Journals (Sweden)

    Zhi-Long Tang

    2017-01-01

    Full Text Available Under the observation that Tenebrio molitor and Zophobas morio could eat polystyrene (PS, we setup the platform to screen the gut microbes of these two worms. To take advantage of that Tenebrio molitor and Zophobas morio can eat and digest polystyrene as its diet, we analyzed these special microbes with PS plate and PS turbidity system with time courses. There were two strains TM1 and ZM1 which isolated from Tenebrio molitor and Zophobas morio, and were identified by 16S rDNA sequencing. The results showed that TM1 and ZM1 were cocci-like and short rod shape Gram-negative bacteria under microscope. The PS plate and turbidity assay showed that TM1 and ZM1 could utilize polystyrene as their carbon sources. The further study of PS degraded enzyme and cloning warrants our attention that this platform will be an excellent tools to explore and solve this problem.

  14. Working with miraculous microbes against corrosion

    Institute of Scientific and Technical Information of China (English)

    XIN Ling

    2009-01-01

    @@ Microorganisms, despite of their simple structure and tiny size, are often vital to humans and the environment. You might know about their contributions to the Earth's carbon cycle and amazing ability to decompose waste products. But have you ever heard of microbes that eat away undersea metal, or those who protect iron from corrosion? Some may even wow you with the feat to generate electricity and clean up polluted water!

  15. An Astrobiology Microbes Exhibit and Education Module

    Science.gov (United States)

    Lindstrom, Marilyn M.; Allen, Jaclyn S.; Stocco, Karen; Tobola, Kay; Olendzenski, Lorraine

    2001-01-01

    Telling the story of NASA-sponsored scientific research to the public in exhibits is best done by partnerships of scientists and museum professionals. Likewise, preparing classroom activities and training teachers to use them should be done by teams of teachers and scientists. Here we describe how we used such partnerships to develop a new astrobiology augmentation to the Microbes! traveling exhibit and a companion education module. "Additional information is contained in the original extended abstract."

  16. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  17. The MicrOBS study around Taiwan

    Science.gov (United States)

    Liang, C.; Lee, C.

    2007-12-01

    Since 2005, we have managed 16 MicrOBS, designed by the French IFREMER, to study the earthquake and crustal structute around Taiwan. The instrument itself is very light (20 kgs) and easy to operate. This OBS has a measuring period up to 2 weeks in the seafloor. We have conducted the works, aiming to get a better understanding of the ¡§marine¡¨ earthquakes, from the in situ small event to the big earthquake. For example, a study of the seismic gaps in the offshore region becomes workable as compare with the time when we only have the land seismological instruments. We have also used this instrument to obtain a detail study of the gas hydrate and free gas zone. Whenever a large seismic source is available, we then conduct the local and regional crustal studies, such as in the Philippine Sea and South China Sea. In the last 3 years, we have directed 285 deployments of MicrOBS around Taiwan. More than 80 per cent of the natural earthquakes in Taiwan (in an average of about 15,000 events of Mm greater than 2 events per year) were occurred in offshore area. Big earthquakes (i.e. Mm greater than 6) are more often happen in the offshore area than that in the onshore region. Therefore, the tools (MicrOBS and OBS) to measure these ¡§marine¡¨ earthquakes become essential to understand the character and origin of crustal dynamics, particularly in the seismogenic zone.

  18. Microfluidic Experiments Studying Pore Scale Interactions of Microbes and Geochemistry

    Science.gov (United States)

    Chen, M.; Kocar, B. D.

    2016-12-01

    Understanding how physical phenomena, chemical reactions, and microbial behavior interact at the pore-scale is crucial to understanding larger scale trends in groundwater chemistry. Recent studies illustrate the utility of microfluidic devices for illuminating pore-scale physical-biogeochemical processes and their control(s) on the cycling of iron, uranium, and other important elements 1-3. These experimental systems are ideal for examining geochemical reactions mediated by microbes, which include processes governed by complex biological phenomenon (e.g. biofilm formation, etc.)4. We present results of microfluidic experiments using a model metal reducing bacteria and varying pore geometries, exploring the limitations of the microorganisms' ability to access tight pore spaces, and examining coupled biogeochemical-physical controls on the cycling of redox sensitive metals. Experimental results will provide an enhanced understanding of coupled physical-biogeochemical processes transpiring at the pore-scale, and will constrain and compliment continuum models used to predict and describe the subsurface cycling of redox-sensitive elements5. 1. Vrionis, H. A. et al. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71, 6308-6318 (2005). 2. Pearce, C. I. et al. Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions. Environ. Sci. Technol. 46, 7992-8000 (2012). 3. Zhang, C., Liu, C. & Shi, Z. Micromodel investigation of transport effect on the kinetics of reductive dissolution of hematite. Environ. Sci. Technol. 47, 4131-4139 (2013). 4. Ginn, T. R. et al. Processes in microbial transport in the natural subsurface. Adv. Water Resour. 25, 1017-1042 (2002). 5. Scheibe, T. D. et al. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb. Biotechnol. 2, 274-286 (2009).

  19. Microbes, Immunity, and Behavior: Psychoneuroimmunology Meets the Microbiome.

    Science.gov (United States)

    Dinan, Timothy G; Cryan, John F

    2017-01-01

    There is now a large volume of evidence to support the view that the immune system is a key communication pathway between the gut and brain, which plays an important role in stress-related psychopathologies and thus provides a potentially fruitful target for psychotropic intervention. The gut microbiota is a complex ecosystem with a diverse range of organisms and a sophisticated genomic structure. Bacteria within the gut are estimated to weigh in excess of 1 kg in the adult human and the microbes within not only produce antimicrobial peptides, short chain fatty acids, and vitamins, but also most of the common neurotransmitters found in the human brain. That the microbial content of the gut plays a key role in immune development is now beyond doubt. Early disruption of the host-microbe interplay can have lifelong consequences, not just in terms of intestinal function but in distal organs including the brain. It is clear that the immune system and nervous system are in continuous communication in order to maintain a state of homeostasis. Significant gaps in knowledge remain about the effect of the gut microbiota in coordinating the immune-nervous systems dialogue. However, studies using germ-free animals, infective models, prebiotics, probiotics, and antibiotics have increased our understanding of the interplay. Early life stress can have a lifelong impact on the microbial content of the intestine and permanently alter immune functioning. That early life stress can also impact adult psychopathology has long been appreciated in psychiatry. The challenge now is to fully decipher the molecular mechanisms that link the gut microbiota, immune, and central nervous systems in a network of communication that impacts behavior patterns and psychopathology, to eventually translate these findings to the human situation both in health and disease. Even at this juncture, there is evidence to pinpoint key sites of communication where gut microbial interventions either with drugs

  20. Veillonella, Firmicutes: Microbes disguised as Gram negatives

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla; Ozen, Asli; Andersen, Sandra Christine

    2013-01-01

    to 20 other Firmicutes genomes; a further 101 prokaryotic genomes were included, covering 26 phyla. Thus a total of 145 prokaryotic genomes were analyzed by various methods to investigate the apparent conflict of the Veillonella Gram stain and their taxonomic position within the Firmicutes. Comparison......,350 shared proteins, although less than half of these are found in any given Clostridium genome. Only 27 proteins are found conserved in all analyzed prokaryote genomes. Veillonella has distinct metabolic properties, and significant similarities to genomes of Proteobacteria are not detected...... related to Gram-negative species. Though the Negativicutes stain Gram-negative and possess two membranes, the genome and proteome analysis presented here confirm their place within the (mainly) Gram positive phylum of the Firmicutes. Further studies are required to unveil the evolutionary history...

  1. Microbial genomic taxonomy.

    Science.gov (United States)

    Thompson, Cristiane C; Chimetto, Luciane; Edwards, Robert A; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L

    2013-12-23

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups.

  2. Plant-driven selection of microbes in the rhizosphere and plant-microbe feedbacks

    Directory of Open Access Journals (Sweden)

    Adil ESSARIOUI

    2017-09-01

    Full Text Available Plant impacts on soil microbial communities and plant-microbe feedbacks have become the focus of much research. Recent advances in plant-microbe interactions investigations show that plants are able to shape their rhizosphere microbiome through diverse mechanisms. In this review, we gather findings from across multiple studies on the role of plants in altering the structure and functions of microbes in the rhizosphere. In addition, we discuss the roles of diverse phytochemicals in mediating these effects. Finally, we highlight that selective enrichment of specific microorganisms in the rhizosphere has either negative feedbacks, with pathogen accumulation in the rhizosphere; or, perhaps most importantly, positive feedbacks as a result of the recruitment of a beneficial microflora. Insights into the mechanisms that underpin plant selection of microbial communities with positive feedbacks will provide new opportunities to increase crop production.

  3. Modeling physiological responses of soil microbes to drought (Invited)

    Science.gov (United States)

    Manzoni, S.; Katul, G. G.; Porporato, A. M.; Schaeffer, S. M.; Schimel, J.

    2013-12-01

    Biogeochemical models predict soil carbon (C) under varying environmental conditions, aiming to disentangle the effects of predicted changes in temperature and moisture regimes on C storage. While much work focuses on temperature sensitivity of decomposition, relatively less is known about decomposer responses to changes in soil moisture. Heterotrophic respiration is known to decline as soils become drier, but the underlying physiological mechanisms are not clear and rarely accounted for in models. In particular, we ask: what are the effects of different drought response strategies on C storage potential and the shape of the respiration-moisture relation? We have developed a process-based model to address these questions, including the main physiological responses thought to play a role under varying moisture conditions: i) dormancy, ii) patterns of extra-cellular enzyme production, and iii) osmoregulation. We show that these different drought response strategies play a major role in the long-term partitioning of soil C among stable and labile pools. In very dry conditions, microbes shifting to dormant state tend to favor long-term (steady state) accumulation of stable C at the expenses of microbial biomass, while increasing investment in enzymes leads to accumulation of dissolved organic C, which in turn may partly overcome the diffusion limitations imposed by dry soils. In contrast, entering a dormant state early during a dry down allows microbes to save C by respiring less (due to lowered active biomass), avoid C starvation when substrate diffusion breaks down, and use available C for growth and maintenance rather than osmoregulation. Hence, this strategy explains why little osmolytes are found in microbial biomass subjected to experimental drought. We conclude by highlighting how our results can be implemented in Earth System Models without excessively increasing their complexity.

  4. Natural products from microbes associated with insects

    Directory of Open Access Journals (Sweden)

    Christine Beemelmanns

    2016-02-01

    Full Text Available Here we review discoveries of secondary metabolites from microbes associated with insects. We mainly focus on natural products, where the ecological role has been at least partially elucidated, and/or the pharmaceutical properties evaluated, and on compounds with unique structural features. We demonstrate that the exploration of specific microbial–host interactions, in combination with multidisciplinary dereplication processes, has emerged as a successful strategy to identify novel chemical entities and to shed light on the ecology and evolution of defensive associations.

  5. Revisiting Routine Questions

    Science.gov (United States)

    Hughes, Rebecca; Monaghan, John; Shingadia, Eisha; Vaughan, Stephen

    2006-01-01

    What is a routine question? The focus of this paper is routine questions and time (in years) since a hitherto routine question was last attempted by the solver. The data comes from undergraduate students' work on solving two calculus questions. The data was selected for reporting purposes because it is well documented and because it threw up…

  6. Question analysis for Indonesian comparative question

    Science.gov (United States)

    Saelan, A.; Purwarianti, A.; Widyantoro, D. H.

    2017-01-01

    Information seeking is one of human needs today. Comparing things using search engine surely take more times than search only one thing. In this paper, we analyzed comparative questions for comparative question answering system. Comparative question is a question that comparing two or more entities. We grouped comparative questions into 5 types: selection between mentioned entities, selection between unmentioned entities, selection between any entity, comparison, and yes or no question. Then we extracted 4 types of information from comparative questions: entity, aspect, comparison, and constraint. We built classifiers for classification task and information extraction task. Features used for classification task are bag of words, whether for information extraction, we used lexical, 2 previous and following words lexical, and previous label as features. We tried 2 scenarios: classification first and extraction first. For classification first, we used classification result as a feature for extraction. Otherwise, for extraction first, we used extraction result as features for classification. We found that the result would be better if we do extraction first before classification. For the extraction task, classification using SMO gave the best result (88.78%), while for classification, it is better to use naïve bayes (82.35%).

  7. PCR-activated cell sorting for cultivation-free enrichment and sequencing of rare microbes.

    Directory of Open Access Journals (Sweden)

    Shaun W Lim

    Full Text Available Microbial systems often exhibit staggering diversity, making the study of rare, interesting species challenging. For example, metagenomic analyses of mixed-cell populations are often dominated by the sequences of the most abundant organisms, while those of rare microbes are detected only at low levels, if at all. To overcome this, selective cultivation or fluorescence-activated cell sorting (FACS can be used to enrich for the target species prior to sequence analysis; however, since most microbes cannot be grown in the lab, cultivation strategies often fail, while cell sorting requires techniques to uniquely label the cell type of interest, which is often not possible with uncultivable microbes. Here, we introduce a culture-independent strategy for sorting microbial cells based on genomic content, which we term PCR-activated cell sorting (PACS. This technology, which utilizes the power of droplet-based microfluidics, is similar to FACS in that it uses a fluorescent signal to uniquely identify and sort target species. However, PACS differs importantly from FACS in that the signal is generated by performing PCR assays on the cells in microfluidic droplets, allowing target cells to be identified with high specificity with suitable design of PCR primers and TaqMan probes. The PACS assay is general, requires minimal optimization and, unlike antibody methods, can be developed without access to microbial antigens. Compared to non-specific methods in which cells are sorted based on size, granularity, or the ability to take up dye, PACS enables genetic sequence-specific sorting and recovery of the cell genomes. In addition to sorting microbes, PACS can be applied to eukaryotic cells, viruses, and naked nucleic acids.

  8. The question of questions in Malaysian English

    OpenAIRE

    Asniah Alias; Radina Mohamad Deli

    2013-01-01

    This paper examined the forms that interrogatives and tag questions can take when used by young Malaysian speakers of English language in oral communication. It offers a description of the features for both question forms as produced by the respondents compared to those of Singapore English (SE) and Standard British English (SBE). The influence of domains and the issue of mother tongue interference in relation to the subjects’ usage of such features will also be investigated. Data were obtain...

  9. Will ocean acidification affect marine microbes?

    Science.gov (United States)

    Joint, Ian; Doney, Scott C; Karl, David M

    2011-01-01

    The pH of the surface ocean is changing as a result of increases in atmospheric carbon dioxide (CO(2)), and there are concerns about potential impacts of lower pH and associated alterations in seawater carbonate chemistry on the biogeochemical processes in the ocean. However, it is important to place these changes within the context of pH in the present-day ocean, which is not constant; it varies systematically with season, depth and along productivity gradients. Yet this natural variability in pH has rarely been considered in assessments of the effect of ocean acidification on marine microbes. Surface pH can change as a consequence of microbial utilization and production of carbon dioxide, and to a lesser extent other microbially mediated processes such as nitrification. Useful comparisons can be made with microbes in other aquatic environments that readily accommodate very large and rapid pH change. For example, in many freshwater lakes, pH changes that are orders of magnitude greater than those projected for the twenty second century oceans can occur over periods of hours. Marine and freshwater assemblages have always experienced variable pH conditions. Therefore, an appropriate null hypothesis may be, until evidence is obtained to the contrary, that major biogeochemical processes in the oceans other than calcification will not be fundamentally different under future higher CO(2)/lower pH conditions.

  10. Collective decision-making in microbes

    Science.gov (United States)

    Ross-Gillespie, Adin; Kümmerli, Rolf

    2014-01-01

    Microbes are intensely social organisms that routinely cooperate and coordinate their activities to express elaborate population level phenotypes. Such coordination requires a process of collective decision-making, in which individuals detect and collate information not only from their physical environment, but also from their social environment, in order to arrive at an appropriately calibrated response. Here, we present a conceptual overview of collective decision-making as it applies to all group-living organisms; we introduce key concepts and principles developed in the context of animal and human group decisions; and we discuss, with appropriate examples, the applicability of each of these concepts in microbial contexts. In particular, we discuss the roles of information pooling, control skew, speed vs. accuracy trade-offs, local feedbacks, quorum thresholds, conflicts of interest, and the reliability of social information. We conclude that collective decision-making in microbes shares many features with collective decision-making in higher taxa, and we call for greater integration between this fledgling field and other allied areas of research, including in the humanities and the physical sciences. PMID:24624121

  11. Diversity of microbes in amniotic fluid.

    Science.gov (United States)

    DiGiulio, Daniel B

    2012-02-01

    Recent polymerase chain reaction (PCR)-based studies estimate the prevalence of microbial invasion of the amniotic cavity (MIAC) to be ≥30-50% higher than that detected by cultivation-based methods. Some species that have been long implicated in causing MIAC remain among the common invaders (e.g. Ureaplasma spp., Mycoplasma spp., Fusobacterium spp. Streptococcus spp., Bacteroides spp. and Prevotella spp.). Yet we now know from studies based on PCR of the 16S ribosomal DNA that cultivation-resistant anaerobes belonging to the family Fusobacteriaceae (particularly Sneathia sanguinegens, and Leptotrichia spp.) are also commonly found in amniotic fluid. Other diverse microbes detected by PCR of amniotic fluid include as-yet uncultivated and uncharacterized species. The presence of some microbial taxa is associated with specific host factors (e.g. Candida spp. and an indwelling intrauterine device). It appears that MIAC is polymicrobial in 24-67% of cases, but the potential role of pathogen synergy is poorly understood. A causal relationship between diverse microbes, as detected by PCR, and preterm birth is supported by types of association (e.g. space, time and dose) proposed as alternatives to Koch's postulates for inferring causality from molecular findings. The microbial census of the amniotic cavity remains unfinished. A more complete understanding may inform future research directions leading to improved strategies for preventing, diagnosing and treating MIAC.

  12. Collective decision-making in microbes.

    Science.gov (United States)

    Ross-Gillespie, Adin; Kümmerli, Rolf

    2014-01-01

    Microbes are intensely social organisms that routinely cooperate and coordinate their activities to express elaborate population level phenotypes. Such coordination requires a process of collective decision-making, in which individuals detect and collate information not only from their physical environment, but also from their social environment, in order to arrive at an appropriately calibrated response. Here, we present a conceptual overview of collective decision-making as it applies to all group-living organisms; we introduce key concepts and principles developed in the context of animal and human group decisions; and we discuss, with appropriate examples, the applicability of each of these concepts in microbial contexts. In particular, we discuss the roles of information pooling, control skew, speed vs. accuracy trade-offs, local feedbacks, quorum thresholds, conflicts of interest, and the reliability of social information. We conclude that collective decision-making in microbes shares many features with collective decision-making in higher taxa, and we call for greater integration between this fledgling field and other allied areas of research, including in the humanities and the physical sciences.

  13. Biological Function of REE in Plants & Microbes

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Rare earth elements (REE) and their compounds are widely applied in agronomic and medical fields for many years. The bioinorganic chemical research of REE during the past few years indicates that REE play important roles in the promotion of photosynthetic rate as well as root absorption, regulation of hormone and nitrogen metabolism, and suppression of microbes, etc. The metallic or non-metallic targets of key biomolecule in various physiological processes can be chosen by REE for the chelation or replacement, which enables REE to regulate the biological functions or behaviors of those biomolecule and consequently leads to significant embodiment of biological function of REE in plants and microbes.Overdose of REE, however, shows an inhibitory effect on living organisms. Therefore, this paper proposes two suggestions that will be available in the extension of full use of REE's biological function. One is to obey the dose law of REE and control REE concentrations within a safe range. The other is to further test the bioaccumulation and long-period influence of REE on organisms.

  14. Soil plant microbe interactions in phytoremediation.

    Science.gov (United States)

    Karthikeyan, R; Kulakow, P A

    2003-01-01

    Use of vegetation in remediation of soil and groundwater contaminated with organic materials is a promising, cost-effective alternative to the more established treatment methods used at hazardous waste sites. Plants can transpire groundwater and lower the concentrations of organic contaminants in soils and groundwater. The evapotranspirational activity of vegetation acts as a natural pump-and-treatment system. Plants have shown the capacity to absorb, uptake, and convert organic contaminants to less toxic metabolites in laboratory and field studies. Vegetation also plays a significant role in bioremediation. This is because plants stimulate the degradation of organic compounds in the rhizosphere by the release of root exudates and enzymes. Success of any plant-based remediation system depends on the interaction of plants with the surrounding soil medium and the contaminant. Knowing the fate of an organic contaminant in the soil can help determine the persistence of the contaminant in the terrestrial environment and ultimately the success of any remediation method. Also, an understanding is needed of soil-plant-microbe interactions that determine the fate of organic contaminants in the soil-plant ecosystem. This paper presents an overview of the subsurface environment and fate and transport processes of organic contaminants as affected by soil-plant-microbe interactions.

  15. Degradation of Microbes for the Crude Oil Contaminants

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    Production and storage-transportation of crude oil can not only give rise to soil pollution but also destroy ecological environment. Degradation of microbes for oily soil was studied with the instnunent, Geofina Hydrocarbon Meter (GHM), by experimental analysis qualitatively and quantitatively in the paper. Analytical result showed that the crude oil could be considerably degraded by eating-oil microbes in oily soil and the number of eating-oil microbes increased while the working hours of oil-well risi...

  16. Rhizosphere interactions: root exudates, microbes and microbial communities

    National Research Council Canada - National Science Library

    Huang, Xing-Feng; Chaparro, Jacqueline M; Reardon, Kenneth F; Zhang, Ruifu; Shen, Qirong; Vivanco, Jorge M

    2014-01-01

    .... In this review, we summarize recent progress made in unraveling the interactions between plants and rhizosphere microbes through plant root exudates, focusing on how root exudate compounds mediate...

  17. Investigating the context-dependency of plant-soil-AMF-microbe interactions along a pollution gradient

    Science.gov (United States)

    Glassman, S. I.; Casper, B. B.

    2010-12-01

    Background/Question/Methods Investigating how arbuscular mycorrhizal fungi (AMF)-plant interactions vary with edaphic conditions provides an opportunity to test the context-dependency of interspecific interactions, which is currently recognized as a major avenue of future research. We study plant-mycorrhiza symbiotic relationships along a gradient of heavy metal contamination at a recently revegetated “Superfund” site on Blue Mountain, in Palmerton, Pennsylvania. We investigated the interactions involving the native mycorrhizal fungi, non-mycorrhizal soil microbes, soil, and two plant species (a C3 and C4 grass) along the contamination gradient. The native C3 study species Deschampsia flexuosa, is dominant along the gradient and established naturally; the C4 Sorghastrum nutans, is native to Pennsylvania but not to the site and was introduced during restoration. Because C4 grasses are obligate mycotrophs, we expected S. nutans to have a different effect on and response to the soil symbiont community than the C3 grass. We carried out a full factorial greenhouse experiment using field-collected seeds of D. flexuosa and S. nutans, soil, AMF spores, and non-mycorrhizal microbes from both high and low contaminated ends of the gradient. After 11 weeks of growth in the greenhouses, we harvested above and belowground plant biomass, and quantified AMF root colonization and AMF sporulation. Results/Conclusions Our results indicate that context-dependent function is an important factor driving specific ecological interactions between plants and soil microbes. We found that soil origin significantly affected plant growth. Plants from both species grew much larger in soil from low contaminated (LC) origin than high contaminated (HC) origin. Furthermore, we found that the efficacy of AMF in promoting plant growth depended on AMF origin. Specifically, AMF from LC improved growth of D. flexuosa best in either soil background and improved survivorship of S. nutans in HC soil

  18. A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

    Directory of Open Access Journals (Sweden)

    Glass John I

    2010-07-01

    Full Text Available Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT. Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the

  19. Classroom Questioning Strategies

    Institute of Scientific and Technical Information of China (English)

    陈小林

    2013-01-01

      Interaction has been playing a more and more important role in language research since the early 1970s,when the communicative teaching method was widely applied in language teaching. Questioning is the most common classroom interaction. This thesis analyzed the influence on students' immediate oral production by applying different teacher questioning strategies including teacher's question types,teacher question modification and teacher feedback.

  20. Asking Questions in Academia

    DEFF Research Database (Denmark)

    Hansen, Annette Skovsted

    2014-01-01

    Motivation for the activity In academia the most important skill is to ask academically relevant and sound questions. This is not easy and students need to practice asking questions orally and in writing before they write research papers.......Motivation for the activity In academia the most important skill is to ask academically relevant and sound questions. This is not easy and students need to practice asking questions orally and in writing before they write research papers....

  1. Exam Question Exchange.

    Science.gov (United States)

    Alexander, John J., Ed.

    1983-01-01

    Acceptable answers are provided for two chemistry questions. The first question is related to the prediction of the appearance of non-first-order proton nuclear magnetic resonance (NMR) spectra. The second question is related to extraterrestrial kinetic theory of gases. (JN)

  2. Interfacing with questions

    DEFF Research Database (Denmark)

    Soon, Winnie

    2016-01-01

    This article discusses an artistic project entitled If I wrote you a love letter would you write back (and thousands of other questions): a piece of software that utilizes Twitter web API to query questions, drawing unpredictable questions in real-time from the distributed database of Twitter...

  3. Improving Student Question Classification

    Science.gov (United States)

    Heiner, Cecily; Zachary, Joseph L.

    2009-01-01

    Students in introductory programming classes often articulate their questions and information needs incompletely. Consequently, the automatic classification of student questions to provide automated tutorial responses is a challenging problem. This paper analyzes 411 questions from an introductory Java programming course by reducing the natural…

  4. Arsenic transport in prokaryotes and eukaryotic microbes.

    Science.gov (United States)

    Rosen, Barry P; Tamás, Markus J

    2010-01-01

    Aquaporins (AQPs) and aquaglyceroporins facilitate transport of a broad spectrum of substrates such as water, glycerol and other small uncharged solutes. More recently, AQPs ave also been shown to facilitate diffusion of metalloids such as arsenic (As) and antimony (Sb). At neutral pH, the trivalent forms of these metalloids are structurally similar to glycerol and hence they can enter cells through AQPs. As- and Sb-containing compounds are toxic to cells, yet both metalloids are used as chemotherapeutic agents for treating acute promyelocytic leukemia and diseases caused by protozoan parasites. In this chapter, we will review the role of AQPs and other proteins in metalloid transport in prokaryotes and eukaryotic microbes.

  5. Gut ecosystem: how microbes help us.

    Science.gov (United States)

    Martín, R; Miquel, S; Ulmer, J; Langella, P; Bermúdez-Humarán, L G

    2014-09-01

    The human gut houses one of the most complex and abundant ecosystems composed of up to 1013-1014 microorganisms. Although the anthropocentric concept of life has concealed the function of microorganisms inside us, the important role of gut bacterial community in human health is well recognised today. Moreover, different microorganims, which are commonly present in a large diversity of food products, transit through our gut every day adding in some cases a beneficial effect to our health (probiotics). This crosstalk is concentrated mainly in the intestinal epithelium, where microbes provide the host with essential nutrients and modulation of the immune system. Furthermore, microorganisms also display antimicrobial activities maintaining a gut ecosystem stable. This review summarises some of the recent findings on the interaction of both commensal and probiotic bacteria with each other and with the host. The aim is to highlight the cooperative status found in healthy individuals as well as the importance of this crosstalk in the maintenance of human homeostasis.

  6. Engineering microbes with synthetic biology frameworks.

    Science.gov (United States)

    Leonard, Effendi; Nielsen, David; Solomon, Kevin; Prather, Kristala Jones

    2008-12-01

    Typically, the outcome of biologically engineered unit operations cannot be controlled a priori due to the incorporation of ad hoc design into complex natural systems. To mitigate this problem, synthetic biology presents a systematic approach to standardizing biological components for the purpose of increasing their programmability and robustness when assembled with the aim to achieve novel biological functions. A complex engineered biological system using only standardized biological components is yet to exist. Nevertheless, current attempts to create and to implement modular, standardized biological components pave the way for the future creation of highly predictable artificial biological systems. Although synthetic biology frameworks can be applied to any biological engineering endeavor, this article will focus on providing a brief overview of advances in the field and its recent utilization for the engineering of microbes.

  7. Inactivation of microbes using ultrasound: a review.

    Science.gov (United States)

    Piyasena, P; Mohareb, E; McKellar, R C

    2003-11-01

    Alternative methods for pasteurization and sterilization are gaining importance, due to increased consumer demand for new methods of food processing that have a reduced impact on nutritional content and overall food quality. Ultrasound processing or sonication is one of the alternative technologies that has shown promise in the food industry. Sonication alone is not very effective in killing bacteria in food; however, the use of ultrasound coupled with pressure and/or heat is promising. Thermosonic (heat plus sonication), manosonic (pressure plus sonication), and manothermosonic (heat and pressure plus sonication) treatments are likely the best methods to inactivate microbes, as they are more energy-efficient and effective in killing microorganisms. Ultrasonic processing is still in its infancy and requires a great deal of future research in order to develop the technology on an industrial scale, and to more fully elucidate the effect of ultrasound on the properties of foods.

  8. Question-Asking and Question-Exploring

    Science.gov (United States)

    Sands, Lorraine; Carr, Margaret; Lee, Wendy

    2012-01-01

    The Centre of Innovation Research at Greerton Early Childhood Centre was characterised as a dispositional milieu where working theories were explored through a narrative research methodology. As the research progressed, the teachers at Greerton strengthened the way we were listening to, and watching out for young children's questions to enable…

  9. The Plot Thickens: Diet Microbe Interactions May Modulate Thrombosis Risk.

    Science.gov (United States)

    Martínez-Del Campo, Ana; Romano, Kymberleigh A; Rey, Federico E; Balskus, Emily P

    2016-04-12

    Thrombosis plays an important role in cardiovascular disease (CVD). Platelet activation is an essential step in the genesis and propagation of atherothrombotic complications. In a recent publication, Zhu and colleagues report that gut microbe-derived TMAO enhances platelet responsiveness and thrombosis, providing a novel mechanistic connection between microbes and CVD (Zhu et al., 2016).

  10. Irradiation of Microbes from Spent Nuclear Fuel Storage Pool Environments

    Energy Technology Data Exchange (ETDEWEB)

    Breckenridge, C.R.; Watkins, C.S.; Bruhn, D.F.; Roberto, F.F.; Tsang, M.N.; Pinhero, P.J. [INEEL (US); Brey, R.F. [ISU (US); Wright, R.N.; Windes, W.F.

    1999-09-03

    Microbes have been isolated and identified from spent nuclear fuel storage pools at the Idaho National Engineering and Environmental Laboratory (INEEL). Included among these are Corynebacterium aquaticum, Pseudomonas putida, Comamonas acidovorans, Gluconobacter cerinus, Micrococcus diversus, Rhodococcus rhodochrous, and two strains of sulfate-reducing bacteria (SRB). We examined the sensitivity of these microbes to a variety of total exposures of radiation generated by a 6-MeV linear accelerator (LINAC). The advantage of using a LINAC is that it provides a relatively quick screen of radiation tolerance. In the first set of experiments, we exposed each of the aforementioned microbes along with four additional microbes, pseudomonas aeruginosa, Micrococcus luteus, Escherchia coli, and Deinococcus radiodurans to exposures of 5 x 10{sup 3} and 6 x 10{sup 4} rad. All microbial specimens withstood the lower exposure with little or no reduction in cell population. Upon exposing the microbes to the larger dose of 6 x 10{sup 4} rad, we observed two distinct groupings: microbes that demonstrate resistance to radiation, and microbes that display intolerance through a dramatic reduction from their initial population. Microbes in the radiation tolerant grouping were exposed to 1.1 x 10{sup 5} rad to examine the extent of their resistance. We observe a correlation between radiation resistance and gram stain. The gram-positive species we examined seem to demonstrate a greater radiation resistance.

  11. Safety of Novel Microbes for Human Consumption: Practical Examples of Assessment in the European Union.

    Science.gov (United States)

    Brodmann, Theodor; Endo, Akihito; Gueimonde, Miguel; Vinderola, Gabriel; Kneifel, Wolfgang; de Vos, Willem M; Salminen, Seppo; Gómez-Gallego, Carlos

    2017-01-01

    Novel microbes are either newly isolated genera and species from natural sources or bacterial strains derived from existing bacteria. Novel microbes are gaining increasing attention for the general aims to preserve and modify foods and to modulate gut microbiota. The use of novel microbes to improve health outcomes is of particular interest because growing evidence points to the importance of gut microbiota in human health. As well, some recently isolated microorganisms have promise for use as probiotics, although in-depth assessment of their safety is necessary. Recent examples of microorganisms calling for more detailed evaluation include Bacteroides xylanisolvens, Akkermansia muciniphila, fructophilic lactic acid bacteria (FLAB), and Faecalibacterium prausnitzii. This paper discusses each candidate's safety evaluation for novel food or novel food ingredient approval according to European Union (EU) regulations. The factors evaluated include their beneficial properties, antibiotic resistance profiling, history of safe use (if available), publication of the genomic sequence, toxicological studies in agreement with novel food regulations, and the qualified presumptions of safety. Sufficient evidences have made possible to support and authorize the use of heat-inactivated B. xylanisolvens in the European Union. In the case of A. muciniphila, the discussion focuses on earlier safety studies and the strain's suitability. FLAB are also subjected to standard safety assessments, which, along with their proximity to lactic acid bacteria generally considered to be safe, may lead to novel food authorization in the future. Further research with F. prausnitzii will increase knowledge about its safety and probiotic properties and may lead to its future use as novel food. Upcoming changes in EUU Regulation 2015/2283 on novel food will facilitate the authorization of future novel products and might increase the presence of novel microbes in the food market.

  12. Safety of Novel Microbes for Human Consumption: Practical Examples of Assessment in the European Union

    Directory of Open Access Journals (Sweden)

    Theodor Brodmann

    2017-09-01

    Full Text Available Novel microbes are either newly isolated genera and species from natural sources or bacterial strains derived from existing bacteria. Novel microbes are gaining increasing attention for the general aims to preserve and modify foods and to modulate gut microbiota. The use of novel microbes to improve health outcomes is of particular interest because growing evidence points to the importance of gut microbiota in human health. As well, some recently isolated microorganisms have promise for use as probiotics, although in-depth assessment of their safety is necessary. Recent examples of microorganisms calling for more detailed evaluation include Bacteroides xylanisolvens, Akkermansia muciniphila, fructophilic lactic acid bacteria (FLAB, and Faecalibacterium prausnitzii. This paper discusses each candidate's safety evaluation for novel food or novel food ingredient approval according to European Union (EU regulations. The factors evaluated include their beneficial properties, antibiotic resistance profiling, history of safe use (if available, publication of the genomic sequence, toxicological studies in agreement with novel food regulations, and the qualified presumptions of safety. Sufficient evidences have made possible to support and authorize the use of heat-inactivated B. xylanisolvens in the European Union. In the case of A. muciniphila, the discussion focuses on earlier safety studies and the strain's suitability. FLAB are also subjected to standard safety assessments, which, along with their proximity to lactic acid bacteria generally considered to be safe, may lead to novel food authorization in the future. Further research with F. prausnitzii will increase knowledge about its safety and probiotic properties and may lead to its future use as novel food. Upcoming changes in EUU Regulation 2015/2283 on novel food will facilitate the authorization of future novel products and might increase the presence of novel microbes in the food market.

  13. The Establishment of the Biosafety Microbe Laboratory

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ With the increasingly serious issue of "Food Quality and Safety", the question of "whether people can get hygienic and healthy food" has been a social concern attracting much attention from the Chinese government.

  14. Terrestrial microbes in martian and chondritic meteorites

    Science.gov (United States)

    Airieau, S.; Picenco, Y.; Andersen, G.

    2007-08-01

    Introduction: The best extraterrestrial analogs for microbiology are meteorites. The chemistry and mineralogy of Asteroid Belt and martian (SNC) meteorites are used as tracers of processes that took place in the early solar system. Meteoritic falls, in particular those of carbonaceous chondrites, are regarded as pristine samples of planetesimal evolution as these rocks are primitive and mostly unprocessed since the formation of the solar system 4.56 billion years ago. Yet, questions about terrestrial contamination and its effects on the meteoritic isotopic, chemical and mineral characteristics often arise. Meteorites are hosts to biological activity as soon as they are in contact with the terrestrial biosphere, like all rocks. A wide biodiversity was found in 21 chondrites and 8 martian stones, and was investigated with cell culture, microscopy techniques, PCR, and LAL photoluminetry. Some preliminary results are presented here. The sample suite included carbonaceous chondrites of types CR, CV, CK, CO, CI, and CM, from ANSMET and Falls. Past studies documented the alteration of meteorites by weathering and biological activity [1]-[4]. Unpublished observations during aqueous extraction for oxygen isotopic analysis [5], noted the formation of biofilms in water in a matter of days. In order to address the potential modification of meteoritic isotopic and chemical signatures, the culture of microbial contaminating species was initiated in 2005, and after a prolonged incubation, some of the species obtained from cell culture were analyzed in 2006. The results are preliminary, and a systematic catalog of microbial contaminants is developing very slowly due to lack of funding. Methods: The primary method was cell culture and PCR. Chondrites. Chondritic meteorite fragments were obtained by breaking stones of approximately one gram in sterile mortars. The core of the rocks, presumably less contaminated than the surface, was used for the present microbial study, and the

  15. Questions and information systems

    CERN Document Server

    Lauer, Thomas W; Graesser, Arthur C

    2013-01-01

    The design and functioning of an information system improve to the extent that the system can handle the questions people ask. Surprisingly, however, researchers in the cognitive, computer, and information sciences have not thoroughly examined the multitude of relationships between information systems and questions -- both question asking and answering. The purpose of this book is to explicitly examine these relationships. Chapter contributors believe that questions play a central role in the analysis, design, and use of different kinds of natural or artificial information systems such as huma

  16. Belowground microbes mitigate plant-plant competition.

    Science.gov (United States)

    Fonseca, Márcia Bacelar; Dias, Teresa; Carolino, Maria Manuela; França, Marcel Giovanni Costa; Cruz, Cristina

    2017-09-01

    Dimorphandra wilsonii, a Cerrado endemic Fabaceae tree, is threatened by land-use changes. The few remaining individuals occur in areas dominated by alien grasses like Urochloa decumbens. We tested the impact of nitrogen (N) availability and symbionts' presence on mitigating the effects of competition from U. decumbens. Dimorphandra wilsonii seedlings were 50-week pot-cultivated under limiting (3mM) or non-limiting (10mM) N, with or without U. decumbens, and inoculated or not with a N-fixer (Bradyrhizobium sp.) and an arbuscular mycorrhizal fungus (AMF - Glomus etunicatum), both forming symbioses in the field. Since D. wilsonii seedlings grew more and 'lost' fewer nutrients under the symbionts' presence, symbionts mitigated plant-plant competition. Under limiting N, inoculated D. wilsonii seedlings grew more (despite no nodulation), but N fixation was only suggested when inoculated D. wilsonii seedlings competed with U. decumbens. D. wilsonii(13)C, and substrate's carbon and respiration suggest that only the microbes performing key functions received plant carbon. Under non-limiting N, inoculated D. wilsonii seedlings became enriched in (13)C, substrate accumulated carbon and microbial respiration increased, suggesting a more generalist microbial community. Data suggest inoculating D. wilsonii seeds/seedlings with AMF and N-fixers as a conservation measure. However, long-term field-studies need to confirm these conclusions. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Microbes are trophic analogs of animals.

    Science.gov (United States)

    Steffan, Shawn A; Chikaraishi, Yoshito; Currie, Cameron R; Horn, Heidi; Gaines-Day, Hannah R; Pauli, Jonathan N; Zalapa, Juan E; Ohkouchi, Naohiko

    2015-12-01

    In most ecosystems, microbes are the dominant consumers, commandeering much of the heterotrophic biomass circulating through food webs. Characterizing functional diversity within the microbiome, therefore, is critical to understanding ecosystem functioning, particularly in an era of global biodiversity loss. Using isotopic fingerprinting, we investigated the trophic positions of a broad diversity of heterotrophic organisms. Specifically, we examined the naturally occurring stable isotopes of nitrogen ((15)N:(14)N) within amino acids extracted from proteobacteria, actinomycetes, ascomycetes, and basidiomycetes, as well as from vertebrate and invertebrate macrofauna (crustaceans, fish, insects, and mammals). Here, we report that patterns of intertrophic (15)N-discrimination were remarkably similar among bacteria, fungi, and animals, which permitted unambiguous measurement of consumer trophic position, independent of phylogeny or ecosystem type. The observed similarities among bacterial, fungal, and animal consumers suggest that within a trophic hierarchy, microbiota are equivalent to, and can be interdigitated with, macrobiota. To further test the universality of this finding, we examined Neotropical fungus gardens, communities in which bacteria, fungi, and animals are entwined in an ancient, quadripartite symbiosis. We reveal that this symbiosis is a discrete four-level food chain, wherein bacteria function as the apex carnivores, animals and fungi are meso-consumers, and the sole herbivores are fungi. Together, our findings demonstrate that bacteria, fungi, and animals can be integrated within a food chain, effectively uniting the macro- and microbiome in food web ecology and facilitating greater inclusion of the microbiome in studies of functional diversity.

  18. The SAPHO syndrome--are microbes involved?

    Science.gov (United States)

    Assmann, G; Simon, P

    2011-06-01

    The syndrome of synovitis, acne, pustulosis, hyperostosis and osteitis (SAPHO) includes a rare group of chronic, relapsing, inflammatory osteoarticular disorders that is conventionally associated with manifestations in the skin. Diagnostic dilemmas can arise due to incomplete manifestations or confusion generated through mimicking of other conditions, such as osteomyelitis. The aetiology of this syndrome remains unclear, but probably involves genetic, immunological and infectious mechanisms. The possible pathogenetic role of infectious agents in genetically predisposed individuals, resulting in a 'reactive osteitis', has been suggested because microbes such as Propionibacterium acnes have been recovered from bone biopsy samples. However, this hypothesis has not been demonstrated as yet. Current knowledge with regard to treatment of this syndrome is based on results reported from small case studies and, thus, is still empiric. The use of antibiotics, instituted based on the isolation of Propionibacterium acnes, has been reported to show conflicting results. Promising results for potential future application have recently been reported for treatment of SAPHO with bisphosphonates and antagonists of tumour necrosis factor-α. This review aims to evaluate the existing knowledge on the SAPHO syndrome and to provide information on symptoms, diagnosis and treatment options for this disease.

  19. Asking the Right Questions.

    Science.gov (United States)

    Galvin, Ruth Mehrtens

    1990-01-01

    Like good researchers, writers about research need to be able to tell whether scientific findings are valid. Six questions, to be asked of the researcher, can help the writer explain to others. A healthy skepticism is also important; there may be signals that more questions should be asked. (MSE)

  20. Epistemology: 5 Questions

    DEFF Research Database (Denmark)

    Epistemology: 5 Questions is a collection of short interviews based on 5 questions presented to some of the most influential and prominent scholars in epistemology. We hear their views on epistemology with particular emphasis on the intersection between mainstream and formal approaches to the field......; the aim, scope, the future direction of epistemology and how their work fits in these respects...

  1. Legal Philosophy - Five Questions

    DEFF Research Database (Denmark)

    This collection gathers together a host of the most eminent contemporary legal philosophers, who writes about their take on legal philosophy, its fundamental questions and potential.......This collection gathers together a host of the most eminent contemporary legal philosophers, who writes about their take on legal philosophy, its fundamental questions and potential....

  2. Let's Switch Questioning Around

    Science.gov (United States)

    Tovani, Cris

    2015-01-01

    English teacher Cris Tovani knows from her experiences teaching elementary school that students are naturally curious. But, too often, students are so trained to be question answerers that by the time they reach high school, they no longer form questions of their own and instead focus on trying to figure out what answer the teacher wants. Tovani…

  3. Centrality of host cell death in plant-microbe interactions.

    Science.gov (United States)

    Dickman, Martin B; Fluhr, Robert

    2013-01-01

    Programmed cell death (PCD) is essential for proper growth, development, and cellular homeostasis in all eukaryotes. The regulation of PCD is of central importance in plant-microbe interactions; notably, PCD and features associated with PCD are observed in many host resistance responses. Conversely, pathogen induction of inappropriate cell death in the host results in a susceptible phenotype and disease. Thus, the party in control of PCD has a distinct advantage in these battles. PCD processes appear to be of ancient origin, as indicated by the fact that many features of cell death strategy are conserved between animals and plants; however, some of the details of death execution differ. Mammalian core PCD genes, such as caspases, are not present in plant genomes. Similarly, pro- and antiapoptotic mammalian regulatory elements are absent in plants, but, remarkably, when expressed in plants, successfully impact plant PCD. Thus, subtle structural similarities independent of sequence homology appear to sustain operational equivalence. The vacuole is emerging as a key organelle in the modulation of plant PCD. Under different signals for cell death, the vacuole either fuses with the plasmalemma membrane or disintegrates. Moreover, the vacuole appears to play a key role in autophagy; evidence suggests a prosurvival function for autophagy, but other studies propose a prodeath phenotype. Here, we describe and discuss what we know and what we do not know about various PCD pathways and how the host integrates signals to activate salicylic acid and reactive oxygen pathways that orchestrate cell death. We suggest that it is not cell death as such but rather the processes leading to cell death that contribute to the outcome of a given plant-pathogen interaction.

  4. Biodiversity of genes encoding anti-microbial traits within plant associated microbes

    Directory of Open Access Journals (Sweden)

    Walaa Kamel Mousa

    2015-04-01

    Full Text Available The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produce a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous genes. We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.

  5. Investigation of the Interplanetary Transfer of Microbes in the Tanpopo Mission at the Exposed Facility of the International Space Station

    Science.gov (United States)

    Kawaguchi, Yuko; Yokobori, Shin-ichi; Hashimoto, Hirofumi; Yano, Hajime; Tabata, Makoto; Kawai, Hideyuki; Yamagishi, Akihiko

    2016-05-01

    The Tanpopo mission will address fundamental questions on the origin of terrestrial life. The main goal is to test the panspermia hypothesis. Panspermia is a long-standing hypothesis suggesting the interplanetary transport of microbes. Another goal is to test the possible origin of organic compounds carried from space by micrometeorites before the terrestrial origin of life. To investigate the panspermia hypothesis and the possible space origin of organic compounds, we performed space experiments at the Exposed Facility (EF) of the Japanese Experiment Module (JEM) of the International Space Station (ISS). The mission was named Tanpopo, which in Japanese means dandelion. We capture any orbiting microparticles, such as micrometeorites, space debris, and terrestrial particles carrying microbes as bioaerosols, by using blocks of silica aerogel. We also test the survival of microbial species and organic compounds in the space environment for up to 3 years. The goal of this review is to introduce an overview of the Tanpopo mission with particular emphasis on the investigation of the interplanetary transfer of microbes. The Exposed Experiment Handrail Attachment Mechanism with aluminum Capture Panels (CPs) and Exposure Panels (EPs) was exposed on the EF-JEM on May 26, 2015. The first CPs and EPs will be returned to the ground in mid-2016. Possible escape of terrestrial microbes from Earth to space will be evaluated by investigating the upper limit of terrestrial microbes by the capture experiment. Possible mechanisms for transfer of microbes over the stratosphere and an investigation of the effect of the microbial cell-aggregate size on survivability in space will also be discussed.

  6. Investigation of the Interplanetary Transfer of Microbes in the Tanpopo Mission at the Exposed Facility of the International Space Station.

    Science.gov (United States)

    Kawaguchi, Yuko; Yokobori, Shin-Ichi; Hashimoto, Hirofumi; Yano, Hajime; Tabata, Makoto; Kawai, Hideyuki; Yamagishi, Akihiko

    2016-05-01

    The Tanpopo mission will address fundamental questions on the origin of terrestrial life. The main goal is to test the panspermia hypothesis. Panspermia is a long-standing hypothesis suggesting the interplanetary transport of microbes. Another goal is to test the possible origin of organic compounds carried from space by micrometeorites before the terrestrial origin of life. To investigate the panspermia hypothesis and the possible space origin of organic compounds, we performed space experiments at the Exposed Facility (EF) of the Japanese Experiment Module (JEM) of the International Space Station (ISS). The mission was named Tanpopo, which in Japanese means dandelion. We capture any orbiting microparticles, such as micrometeorites, space debris, and terrestrial particles carrying microbes as bioaerosols, by using blocks of silica aerogel. We also test the survival of microbial species and organic compounds in the space environment for up to 3 years. The goal of this review is to introduce an overview of the Tanpopo mission with particular emphasis on the investigation of the interplanetary transfer of microbes. The Exposed Experiment Handrail Attachment Mechanism with aluminum Capture Panels (CPs) and Exposure Panels (EPs) was exposed on the EF-JEM on May 26, 2015. The first CPs and EPs will be returned to the ground in mid-2016. Possible escape of terrestrial microbes from Earth to space will be evaluated by investigating the upper limit of terrestrial microbes by the capture experiment. Possible mechanisms for transfer of microbes over the stratosphere and an investigation of the effect of the microbial cell-aggregate size on survivability in space will also be discussed. Panspermia-Astrobiology-Low-Earth orbit. Astrobiology 16, 363-376.

  7. What is a Question?

    Science.gov (United States)

    Knuth, Kevin H.; Clancy, Daniel (Technical Monitor)

    2002-01-01

    A given question can be defined in terms of the set of statements or assertions that answer it. Application of the logic of inference to this set of assertions allows one to derive the logic of inquiry among questions. There are interesting symmetries between the logics of inference and inquiry; where probability describes the degree to which a premise implies an assertion, there exists an analogous quantity that describes the bearing or relevance that a question has on an outstanding issue. These have been extended to suggest that the logic of inquiry results in functional relationships analogous to, although more general than, those found in information theory. Employing lattice theory, I examine in greater detail the structure of the space of assertions and questions demonstrating that the symmetries between the logical relations in each of the spaces derive directly from the lattice structure. Furthermore, I show that while symmetries between the spaces exist, the two lattices are not isomorphic. The lattice of assertions is described by a Boolean lattice 2(sup N) whereas the lattice of real questions is shown to be a sublattice of the free distributive lattice FD(N) = 2(sup 2(sup N)). Thus there does not exist a one-to-one mapping of assertions to questions, there is no reflection symmetry between the two spaces, and questions in general do not possess unique complements. Last, with these lattice structures in mind, I discuss the relationship between probability, relevance and entropy.

  8. Integrating Environmental Genomics and Biogeochemical Models: a Gene-centric Approach

    Science.gov (United States)

    Reed, D. C.; Algar, C. K.; Huber, J. A.; Dick, G.

    2013-12-01

    Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models that uses genomics data and provides predictions that are readily testable using cutting-edge molecular tools. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modelled to examine key questions about cryptic sulphur cycling and dinitrogen production pathways in OMZs. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

  9. Dielectrophoretic analysis of microbes in water.

    Science.gov (United States)

    Betts, W B; Brown, A P

    1998-12-01

    Traditional microbiological methods are still used extensively for analysis of micro-organisms in water. However, they are inefficient due to a high labour input requirement, a low sample capacity, and often a long time lag before results are available. Analytical stages involving incubation and growth (enrichments and colony isolation) contribute the greatest delay in reporting, although subsequent identification can also be protracted. The use of electrometric growth analysers (measuring impedance, conductance or capacitance changes) is now more common in water microbiology. Although these instruments can provide more rapid results and provide increased handling capacity, the bacterial generation times required to provide detectable changes cause delays and suitable selective media are not fully developed for all microbes of interest. Most other recent methods have equally disappointing drawbacks and thus extensive research continues in order to realise the ambition of 'real-time' analytical microbiology. Several research groups have demonstrated the potential of dielectrophoresis in providing microbial concentration, separation and identification systems which are not limited by bacterial growth and are therefore extremely rapid. Dielectrophoresis occurs when cells are placed in non-uniform electric fields. The cells move towards the electrodes (regardless of the direction of the applied field) as determined by their dielectric properties (conductivity and permittivity) rather than by their charge as occurs in electrophoresis. Also, the polarisability of the cells, and therefore the polarity and magnitude of the dielectrophoretic force, varies as a function of the electric field frequency. Because the dielectric properties of a particular cell type have characteristic frequency-dependent components, if cell collection at electrodes is observed across a frequency range, the collection spectrum produced is distinctive for the cell type under investigation. This

  10. Environmental restoration using plant-microbe bioaugmentation

    Energy Technology Data Exchange (ETDEWEB)

    Kingsley, M.T.; Metting, F.B.; Fredrickson, J.K.; Seidler, R.J.

    1993-04-01

    Land farming, for the purpose of bioremediation, refers traditionally to the spreading of contaminated soil, sediments, or other material over land; mechanically mixing it; incorporating various amendments, such as fertilizer or mulch; and sometimes inoculating with degradative microorganisms. Populations of bacteria added to soils often decline rapidly and become metabolically inactive. To efficiently degrade contaminants, microorganisms must be metabolically active. Thus, a significant obstacle to the successful use of microorganisms for environmental applications is their long-term survival and the expression of their degradative genes in situ. Rhizosphere microorganisms are known to be more metabolically active than those in bulk soil, because they obtain carbon and energy from root exudates and decaying root matter. Rhizosphere populations are also more abundant, often containing 10[sup 8] or more culturable bacteria per gram of soil, and bacterial populations on the rhizoplane can exceed 10[sup 9]/g root. Many of the critical parameters that influence the competitive ability of rhizosphere bacteria have not been identified, but microorganisms have frequently been introduced into soil (bioaugmentation) as part of routine or novel agronomic practices. However, the use of rhizosphere bacteria and their in situ stimulation by plant roots for degrading organic contaminants has received little attention. Published studies have demonstrated the feasibility of using rhizobacteria (Pseudomonas putida) for the rapid removal of chlorinated pesticides from contaminated soil, and to promote germination of radish seeds in the presence of otherwise phytotoxic levels of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), and phenoxyacetic acid (PAA). The present investigation was undertaken to determine if these strains (Pseudomonas putida PP0301/pRO101 and PP0301/pRO103) could be used to bioremediate 2,4-D-amended soil via plant-microbe bioaugmentation.

  11. Environmental restoration using plant-microbe bioaugmentation

    Energy Technology Data Exchange (ETDEWEB)

    Kingsley, M.T.; Fredrickson, J.K.; Metting, F.B.; Seidler, R.J.

    1993-04-01

    Land farming, for the purpose of bioremediation, refers traditionally to the spreading of contaminated soil, sediments, or other material over land; mechanically mixing it; incorporating various amendments, such as fertilizer or mulch; and sometimes inoculating with degradative microorganisms. Populations of bacteria added to soils often decline rapidly and become metabolically inactive. To efficiently degrade contaminants, microorganisms must be metabolically active. Thus, a significant obstacle to the successful use of microorganisms for environmental applications is their long-term survival and the expression of their degradative genes in situ. Rhizosphere microorganisms are known to be more metabolically active than those in bulk soil, because they obtain carbon and energy from root exudates and decaying root matter. Rhizosphere populations are also more abundant, often containing 10{sup 8} or more culturable bacteria per gram of soil, and bacterial populations on the rhizoplane can exceed 10{sup 9}/g root. Many of the critical parameters that influence the competitive ability of rhizosphere bacteria have not been identified, but microorganisms have frequently been introduced into soil (bioaugmentation) as part of routine or novel agronomic practices. However, the use of rhizosphere bacteria and their in situ stimulation by plant roots for degrading organic contaminants has received little attention. Published studies have demonstrated the feasibility of using rhizobacteria (Pseudomonas putida) for the rapid removal of chlorinated pesticides from contaminated soil, and to promote germination of radish seeds in the presence of otherwise phytotoxic levels of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), and phenoxyacetic acid (PAA). The present investigation was undertaken to determine if these strains (Pseudomonas putida PPO301/pRO101 and PPO301/pRO103) could be used to bioremediate 2,4-D-amended soil via plant-microbe bioaugmentation.

  12. Collective unconscious: how gut microbes shape human behavior.

    Science.gov (United States)

    Dinan, Timothy G; Stilling, Roman M; Stanton, Catherine; Cryan, John F

    2015-04-01

    The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.

  13. The importance of engineering physiological functionality into microbes

    NARCIS (Netherlands)

    Zhang, Y.; Zhu, Y.; Zhu, Y.; Li, Y.

    2009-01-01

    Good physiological performance of industrial microbes is crucial for successful bioprocesses. Conventional metabolism-oriented engineering strategies often fail to obtain expected phenotypes owing to focusing narrowly on targeted metabolic capabilities while neglecting microbial physiological respon

  14. Host-microbe interactions in the developing zebrafish

    Science.gov (United States)

    Kanther, Michelle; Rawls, John F.

    2010-01-01

    Summary of recent advances The amenability of the zebrafish to in vivo imaging and genetic analysis has fueled expanded use of this vertebrate model to investigate the molecular and cellular foundations of host-microbe relationships. Study of microbial encounters in zebrafish hosts has concentrated on developing embryonic and larval stages, when the advantages of the zebrafish model are maximized. A comprehensive understanding of these host-microbe interactions requires appreciation of the developmental context into which a microbe is introduced, as well as the effects of that microbial challenge on host ontogeny. In this review, we discuss how in vivo imaging and genetic analysis in zebrafish has advanced our knowledge of host-microbe interactions in the context of a developing vertebrate host. We focus on recent insights into immune cell ontogeny and function, commensal microbial relationships in the intestine, and microbial pathogenesis in zebrafish hosts. PMID:20153622

  15. Feasibilities of consolidated bioprocessing microbes: from pretreatment to biofuel production.

    Science.gov (United States)

    Parisutham, Vinuselvi; Kim, Tae Hyun; Lee, Sung Kuk

    2014-06-01

    Lignocelluloses are rich sugar treasures, which can be converted to useful commodities such as biofuel with the help of efficient combination of enzymes and microbes. Although several bioprocessing approaches have been proposed, biofuel production from lignocelluloses is limited because of economically infeasible technologies for pretreatment, saccharification and fermentation. Use of consolidated bioprocessing (CBP) microbes is the most promising method for the cost-effective production of biofuels. However, lignocelluloses are obtained from highly diverse environment and hence are heterogeneous in nature. Therefore, it is necessary to develop and integrate tailor-designed pretreatment processes and efficient microbes that can thrive on many different kinds of biomass. In this review, the progress towards the construction of consolidated bioprocessing microbes, which can efficiently convert heterogeneous lignocellulosic biomass to bioenergy, has been discussed; in addition, the potential and constraints of current bioprocessing technologies for cellulosic biofuel production have been discussed.

  16. ON REICH'S OPEN QUESTION

    Institute of Scientific and Technical Information of China (English)

    张石生

    2003-01-01

    Under more general form and more general conditions an affirmative answer to Reich's open question is given. The results presented also extend and improve some recent results of Reich, Shioji, Takahashi and Wittmann.

  17. Mind the gap; seven reasons to close fragmented genome assemblies

    Science.gov (United States)

    Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including tho...

  18. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies

    Science.gov (United States)

    Meena, Kamlesh K.; Sorty, Ajay M.; Bitla, Utkarsh M.; Choudhary, Khushboo; Gupta, Priyanka; Pareek, Ashwani; Singh, Dhananjaya P.; Prabha, Ratna; Sahu, Pramod K.; Gupta, Vijai K.; Singh, Harikesh B.; Krishanani, Kishor K.; Minhas, Paramjit S.

    2017-01-01

    Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding

  19. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies.

    Science.gov (United States)

    Meena, Kamlesh K; Sorty, Ajay M; Bitla, Utkarsh M; Choudhary, Khushboo; Gupta, Priyanka; Pareek, Ashwani; Singh, Dhananjaya P; Prabha, Ratna; Sahu, Pramod K; Gupta, Vijai K; Singh, Harikesh B; Krishanani, Kishor K; Minhas, Paramjit S

    2017-01-01

    Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding

  20. Microbes in the upper atmosphere and unique opportunities for astrobiology research.

    Science.gov (United States)

    Smith, David J

    2013-10-01

    Microbial taxa from every major biological lineage have been detected in Earth's upper atmosphere. The goal of this review is to communicate (1) relevant astrobiology questions that can be addressed with upper atmosphere microbiology studies and (2) available sampling methods for collecting microbes at extreme altitudes. Precipitation, mountain stations, airplanes, balloons, rockets, and satellites are all feasible routes for conducting aerobiology research. However, more efficient air samplers are needed, and contamination is also a pervasive problem in the field. Measuring microbial signatures without false positives in the upper atmosphere might contribute to sterilization and bioburden reduction methods for proposed astrobiology missions. Intriguingly, environmental conditions in the upper atmosphere resemble the surface conditions of Mars (extreme cold, hypobaria, desiccation, and irradiation). Whether terrestrial microbes are active in the upper atmosphere is an area of intense research interest. If, in fact, microbial metabolism, growth, or replication is achievable independent of Earth's surface, then the search for habitable zones on other worlds should be broadened to include atmospheres (e.g., the high-altitude clouds of Venus). Furthermore, viable cells in the heavily irradiated upper atmosphere of Earth could help identify microbial genes or enzymes that bestow radiation resistance. Compelling astrobiology questions on the origin of life (if the atmosphere synthesized organic aerosols), evolution (if airborne transport influenced microbial mutation rates and speciation), and panspermia (outbound or inbound) are also testable in Earth's upper atmosphere.

  1. Complete Genome of Bacillus thuringiensis Myophage Spock

    OpenAIRE

    Maroun, Justin W.; Whitcher, Kelvin J.; Chamakura, Karthik R.; Kuty Everett, Gabriel F.

    2013-01-01

    Bacillus thuringiensis is a Gram-positive, sporulating soil microbe with valuable pesticide-producing properties. The study of bacteriophages of B. thuringiensis could provide new biotechnological tools for the use of this bacterium. Here, we present the complete annotated genome of Spock, a myophage of B. thuringiensis, and describe its features.

  2. Collateral sensitivity of antibiotic-resistant microbes.

    Science.gov (United States)

    Pál, Csaba; Papp, Balázs; Lázár, Viktória

    2015-07-01

    Understanding how evolution of microbial resistance towards a given antibiotic influences susceptibility to other drugs is a challenge of profound importance. By combining laboratory evolution, genome sequencing, and functional analyses, recent works have charted the map of evolutionary trade-offs between antibiotics and have explored the underlying molecular mechanisms. Strikingly, mutations that caused multidrug resistance in bacteria simultaneously enhanced sensitivity to many other unrelated drugs (collateral sensitivity). Here, we explore how this emerging research sheds new light on resistance mechanisms and the way it could be exploited for the development of alternative antimicrobial strategies.

  3. Lifestyles of the effector-rich: genome-enabled characterization of bacterial plant pathogens

    Science.gov (United States)

    Genome sequencing of bacterial plant pathogens is providing transformative insights into the complex network of molecular plant-microbe interactions mediated by extracellular effectors during pathogenesis. Bacterial pathogens sequenced to completion are phylogenetically diverse and vary significant...

  4. Convergent evolution of filamentous microbes towards evasion of glycan-triggered immunity

    NARCIS (Netherlands)

    Rovenich, Hanna; Zuccaro, Alga; Thomma, Bart P.H.J.

    2016-01-01

    I. II. III. IV. V. VI. References Summary: All filamentous microbes produce and release a wide range of glycans, which are essential determinants of microbe-microbe and microbe-host interactions. Major cell wall constituents, such as chitin and β-glucans, are elicitors of host immune responses.

  5. Asking the Right Questions

    DEFF Research Database (Denmark)

    Richter, Line

    are part of everyday life, children are often the most vulnerable. The project was carried out to shed light on mainly two types of diseases - malaria and diarrheal diseases - that strike children. In practice the academic backgrounds of the researchers played a role in the methodological approach...... to the field. By emphasizing the logos in methodology this paper wishes to underscore that where anthropology sets itself apart from public health is, among other, in the way anthropologists think about method and how this affects fieldwork practices as well as analyses. By tracing two concepts, hygiene......, is the ability to move beyond even the best hidden assumptions and question our own questions, thereby enabling us to ask the right questions....

  6. The Question Concerning Thinking

    DEFF Research Database (Denmark)

    Riis, Søren

    2008-01-01

    Martin Heidegger's thought-provoking essay "The Question Concerning Technology" (1977a) placed technology at the heart of philosophy. Heidegger tried to show that the essence of technology provokes humans to think about the world in a very dangerous way. Yet if we follow Heidegger's analysis......, by doing so, we will in the end realize two important things. First, that Heidegger's declaration of the end of philosophy in fact also means the end of anything we can meaningfully call thinking. Second, that Heidegger's own thinking is completely different from his own ideal of thinking. Our question...

  7. The social question revisited

    DEFF Research Database (Denmark)

    Kenneth, Petersson; Olsson, Ulf; Krejsler, John B.

    2015-01-01

    The focus of this chapter is the re-installation of the social question as a historical practice. The purpose is to investigate how historic figures return and are applied in contemporary political discourses, more precisely in the context of education, education policy and teacher education...... the diversity of relevant populations “without obstacles related to their social and economic background”. In the 19th century the social question was raised in a context of industrialization of societies. It dealt with suggestions about disintegration of predominant social structures and the management...

  8. Perspectives of plant-associated microbes in heavy metal phytoremediation.

    Science.gov (United States)

    Rajkumar, M; Sandhya, S; Prasad, M N V; Freitas, H

    2012-01-01

    "Phytoremediation" know-how to do-how is rapidly expanding and is being commercialized by harnessing the phyto-microbial diversity. This technology employs biodiversity to remove/contain pollutants from the air, soil and water. In recent years, there has been a considerable knowledge explosion in understanding plant-microbes-heavy metals interactions. Novel applications of plant-associated microbes have opened up promising areas of research in the field of phytoremediation technology. Various metabolites (e.g., 1-aminocyclopropane-1-carboxylic acid deaminase, indole-3-acetic acid, siderophores, organic acids, etc.) produced by plant-associated microbes (e.g., plant growth promoting bacteria, mycorrhizae) have been proposed to be involved in many biogeochemical processes operating in the rhizosphere. The salient functions include nutrient acquisition, cell elongation, metal detoxification and alleviation of biotic/abiotic stress in plants. Rhizosphere microbes accelerate metal mobility, or immobilization. Plants and associated microbes release inorganic and organic compounds possessing acidifying, chelating and/or reductive power. These functions are implicated to play an essential role in plant metal uptake. Overall the plant-associated beneficial microbes enhance the efficiency of phytoremediation process directly by altering the metal accumulation in plant tissues and indirectly by promoting the shoot and root biomass production. The present work aims to provide a comprehensive review of some of the promising processes mediated by plant-associated microbes and to illustrate how such processes influence heavy metal uptake through various biogeochemical processes including translocation, transformation, chelation, immobilization, solubilization, precipitation, volatilization and complexation of heavy metals ultimately facilitating phytoremediation. Copyright © 2012 Elsevier Inc. All rights reserved.

  9. Questioning Danish Cartoon Images

    DEFF Research Database (Denmark)

    Bojsen, Heidi

    2007-01-01

    Danes today when it is considered demeaning and racist in most other countries. The conclusion does emphatically not plead in favour of law enforced limitations of the freedom of expression, but does question the prevalent "freedom of ignorance" concerning black identities which means...

  10. Questions English Teachers Ask.

    Science.gov (United States)

    Shuman, R. Baird

    This volume is based on the responses of 374 English teachers at the secondary and college levels to a letter asking them to describe the questions that most perplex them professionally. Answers are provided by 88 leaders in English education, including James R. Squire, Walter H. MacGinitie, R. Baird Shuman, Sheila Schwartz, and Ken Macrorie. The…

  11. Game Theory: 5 Questions

    DEFF Research Database (Denmark)

    Hendricks, Vincent F.

    Game Theory is a collection of short interviews based on 5 questions presented to some of the most influential and prominent scholars in game theory. We hear their views on game theory, its aim, scope, use, the future direction of game theory and how their work fits in these respects....

  12. Question: Who Can Vote?

    Science.gov (United States)

    Rodeheaver, Misty D.; Haas, Mary E.

    2008-01-01

    This year's rollercoaster primary elections and the pending national election, with an anticipated record voter turnout, provide the perfect backdrop for an examination of the questions: (1) Who can vote?; and (2) Who will vote? Historically, the American government refused voting rights to various groups based on race, gender, age, and even…

  13. Future Research Questions

    NARCIS (Netherlands)

    Walpoth, B.; Daanen, H.A.M.

    2014-01-01

    Immersion hypothermia in humans is described in about 500 scientific papers during a Pubmed search in medical literature with keywords ‘Immersion’, ‘Hypothermia’ and ‘Human’ as of 2014. Many questions still remain, the most important of which are described in this chapter.

  14. Game Theory: 5 Questions

    DEFF Research Database (Denmark)

    Hendricks, Vincent F.

    Game Theory is a collection of short interviews based on 5 questions presented to some of the most influential and prominent scholars in game theory. We hear their views on game theory, its aim, scope, use, the future direction of game theory and how their work fits in these respects....

  15. Explorative analysis of microbes, colloids and gases

    Energy Technology Data Exchange (ETDEWEB)

    Hallbeck, Lotta; Pedersen, Karsten (Microbial Analytics Sweden AB, Goeteborg (Sweden))

    2008-08-15

    The overall objectives of the hydrogeochemical description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. In this report, part of the final hydrogeochemical evaluation work of the site investigation at the Forsmark site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry, hydrochemistry, hydrogeochemistry, microbiology, geomicrobiology, analytical chemistry etc. The resulting site descriptive model version, mainly based on 2.2 data and complementary 2.3 data, was carried out during September 2006 to December 2007. This report focuses on microbiology, colloids and gases: - Microbes (Chapter 1): Several methods must be used to characterize active microbial communities in groundwater. Microbial parameters of interest are the total number of cells (TNC) and the presence of various metabolic groups of microorganisms. Different microbial groups influence the environment in different ways, depending on what metabolic group is dominant. Typically, the following redox couples are utilized by bacteria in granitic groundwater: H{sub 2}O/O{sub 2}, NO{sub 3}-/N{sub 2}, Mn2+/Mn(IV), Fe2+/Fe(III), S2-/SO{sub 4}2-, CH{sub 4}/CO{sub 2}, CH{sub 3}COOH/CO{sub 2}, and H{sub 2}/H+. The data will indicate the activity of specific microbial populations at particular sites and how they may affect the geochemistry. - Colloids (Chapter 2): Particles in the size range from 1 to 1x10-3 mum are regarded as colloids. Their small size prohibits them from settling, which gives them the

  16. Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?

    Science.gov (United States)

    Trujillo, Martha E; Bacigalupe, Rodrigo; Pujic, Petar; Igarashi, Yasuhiro; Benito, Patricia; Riesco, Raúl; Médigue, Claudine; Normand, Philippe

    2014-01-01

    Endophytic microorganisms live inside plants for at least part of their life cycle. According to their life strategies, bacterial endophytes can be classified as "obligate" or "facultative". Reports that members of the genus Micromonospora, Gram-positive Actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestrial to a facultative endophytic life. The aim of this work was to analyse the genome sequence of Micromonospora lupini Lupac 08 isolated from a nitrogen fixing nodule of the legume Lupinus angustifolius and to identify genomic traits that provide information on this new plant-microbe interaction. The genome of M. lupini contains a diverse array of genes that may help its survival in soil or in plant tissues, while the high number of putative plant degrading enzyme genes identified is quite surprising since this bacterium is not considered a plant-pathogen. Functionality of several of these genes was demonstrated in vitro, showing that Lupac 08 degraded carboxymethylcellulose, starch and xylan. In addition, the production of chitinases detected in vitro, indicates that strain Lupac 08 may also confer protection to the plant. Micromonospora species appears as new candidates in plant-microbe interactions with an important potential in agriculture and biotechnology. The current data strongly suggests that a beneficial effect is produced on the host-plant.

  17. Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?

    Directory of Open Access Journals (Sweden)

    Martha E Trujillo

    Full Text Available Endophytic microorganisms live inside plants for at least part of their life cycle. According to their life strategies, bacterial endophytes can be classified as "obligate" or "facultative". Reports that members of the genus Micromonospora, Gram-positive Actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestrial to a facultative endophytic life. The aim of this work was to analyse the genome sequence of Micromonospora lupini Lupac 08 isolated from a nitrogen fixing nodule of the legume Lupinus angustifolius and to identify genomic traits that provide information on this new plant-microbe interaction. The genome of M. lupini contains a diverse array of genes that may help its survival in soil or in plant tissues, while the high number of putative plant degrading enzyme genes identified is quite surprising since this bacterium is not considered a plant-pathogen. Functionality of several of these genes was demonstrated in vitro, showing that Lupac 08 degraded carboxymethylcellulose, starch and xylan. In addition, the production of chitinases detected in vitro, indicates that strain Lupac 08 may also confer protection to the plant. Micromonospora species appears as new candidates in plant-microbe interactions with an important potential in agriculture and biotechnology. The current data strongly suggests that a beneficial effect is produced on the host-plant.

  18. Evolutionary engineering by genome shuffling.

    Science.gov (United States)

    Biot-Pelletier, Damien; Martin, Vincent J J

    2014-05-01

    An upsurge in the bioeconomy drives the need for engineering microorganisms with increasingly complex phenotypes. Gains in productivity of industrial microbes depend on the development of improved strains. Classical strain improvement programmes for the generation, screening and isolation of such mutant strains have existed for several decades. An alternative to traditional strain improvement methods, genome shuffling, allows the directed evolution of whole organisms via recursive recombination at the genome level. This review deals chiefly with the technical aspects of genome shuffling. It first presents the diversity of organisms and phenotypes typically evolved using this technology and then reviews available sources of genetic diversity and recombination methodologies. Analysis of the literature reveals that genome shuffling has so far been restricted to microorganisms, both prokaryotes and eukaryotes, with an overepresentation of antibiotics- and biofuel-producing microbes. Mutagenesis is the main source of genetic diversity, with few studies adopting alternative strategies. Recombination is usually done by protoplast fusion or sexual recombination, again with few exceptions. For both diversity and recombination, prospective methods that have not yet been used are also presented. Finally, the potential of genome shuffling for gaining insight into the genetic basis of complex phenotypes is also discussed.

  19. A molecular study of microbe transfer between distant environments.

    Directory of Open Access Journals (Sweden)

    Sean D Hooper

    Full Text Available BACKGROUND: Environments and their organic content are generally not static and isolated, but in a constant state of exchange and interaction with each other. Through physical or biological processes, organisms, especially microbes, may be transferred between environments whose characteristics may be quite different. The transferred microbes may not survive in their new environment, but their DNA will be deposited. In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances. METHODOLOGY: By studying synonymous nucleotide composition, oligomer frequency and orthology between predicted genes in metagenomics data from two environments, terrestrial and aquatic, and by correlating with phylogenetic mappings, we find that both environments are likely to contain trace amounts of microbes which have been far removed from their original habitat. We also suggest a bias in direction from soil to sea, which is consistent with the cycles of planetary wind and water. CONCLUSIONS: Our findings support the Baas-Becking hypothesis formulated in 1934, which states that due to dispersion and population sizes, microbes are likely to be found in widely disparate environments. Furthermore, the availability of genetic material from distant environments is a possible font of novel gene functions for lateral gene transfer.

  20. MAMP (Microbe-Associated Molecular Pattern triggered immunity in Plants

    Directory of Open Access Journals (Sweden)

    Mari-Anne eNewman

    2013-05-01

    Full Text Available Plants are sessile organisms that are under constant attack from microbes. They rely on both preformed defenses, and their innate immune system to ward of the microbial pathogens. Preformed defences include for example the cell wall and cuticle, which act as physical barriers to microbial colonization. The plant immune system is composed of surveillance systems that perceive several general microbe elicitors, which allow plants to switch from growth and development into a defense mode, rejecting most potentially harmful microbes. The elicitors are essential structures for pathogen survival and are conserved among pathogens. The conserved microbe-specific molecules, referred to as microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs, are recognized by the plant innate immune systems pattern recognition receptors (PRRs. General elicitors like flagellin (Flg, elongation factor Tu (EF-Tu, peptidoglycan (PGN, lipopolysaccharides (LPS, Ax21 (Activator of XA21-mediated immunity in rice, fungal chitin and β-glucans from oomycetes are recognized by plant surface localized PRRs. Several of the MAMPs and their corresponding PRRs have, in recent years, been identified. This review focuses on the current knowledge regarding important MAMPs from bacteria, fungi and oomycetes, their structure, the plant PRRs that recognizes them, and how they induce MAMP-triggered immunity (MTI in plants.

  1. Microfabricated microbial fuel cell arrays reveal electrochemically active microbes.

    Directory of Open Access Journals (Sweden)

    Huijie Hou

    Full Text Available Microbial fuel cells (MFCs are remarkable "green energy" devices that exploit microbes to generate electricity from organic compounds. MFC devices currently being used and studied do not generate sufficient power to support widespread and cost-effective applications. Hence, research has focused on strategies to enhance the power output of the MFC devices, including exploring more electrochemically active microbes to expand the few already known electricigen families. However, most of the MFC devices are not compatible with high throughput screening for finding microbes with higher electricity generation capabilities. Here, we describe the development of a microfabricated MFC array, a compact and user-friendly platform for the identification and characterization of electrochemically active microbes. The MFC array consists of 24 integrated anode and cathode chambers, which function as 24 independent miniature MFCs and support direct and parallel comparisons of microbial electrochemical activities. The electricity generation profiles of spatially distinct MFC chambers on the array loaded with Shewanella oneidensis MR-1 differed by less than 8%. A screen of environmental microbes using the array identified an isolate that was related to Shewanella putrefaciens IR-1 and Shewanella sp. MR-7, and displayed 2.3-fold higher power output than the S. oneidensis MR-1 reference strain. Therefore, the utility of the MFC array was demonstrated.

  2. Dissecting Biological Dark Matter: Single Cell Genetic Analysis of TM7, a Rare and Uncultivated Microbe from the Human Mouth

    Energy Technology Data Exchange (ETDEWEB)

    Fenner, Marsha W; Marcy, Yann; Ouverney, Cleber; Bik, Elisabeth M.; Losekann, Tina; Ivanova, Natalia; Martin, H. Garcia; Szeto, E.; Platt, Darren; Hugenholtz, Philip; Relman, David A.; Quake, Stephen R.

    2007-07-01

    We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community.

  3. Statistical Methods in Integrative Genomics

    OpenAIRE

    Richardson, Sylvia; Tseng, George C.; Sun, Wei

    2016-01-01

    Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and f...

  4. Friends with social benefits: host-microbe interactions as a driver of brain evolution and development?

    Science.gov (United States)

    Stilling, Roman M; Bordenstein, Seth R; Dinan, Timothy G; Cryan, John F

    2014-01-01

    The tight association of the human body with trillions of colonizing microbes that we observe today is the result of a long evolutionary history. Only very recently have we started to understand how this symbiosis also affects brain function and behavior. In this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. In particular, we explore the integration of human brain development with evolution, symbiosis, and RNA biology, which together represent a "social triangle" that drives human social behavior and cognition. We argue that, in order to understand how inter-kingdom communication can affect brain adaptation and plasticity, it is inevitable to consider epigenetic mechanisms as important mediators of genome-microbiome interactions on an individual as well as a transgenerational time scale. Finally, we unite these interpretations with the hologenome theory of evolution. Taken together, we propose a tighter integration of neuroscience fields with host-associated microbiology by taking an evolutionary perspective.

  5. A Vavilovian approach to discovering crop-associated microbes with potential to enhance plant immunity

    Directory of Open Access Journals (Sweden)

    Iago Lowe Hale

    2014-09-01

    Full Text Available Through active associations with a diverse community of largely non-pathogenic microbes, a plant may be thought of as possessing an extended genotype, an interactive cross-organismal genome with potential, exploitable implications for plant immunity. The successful enrichment of plant microbiomes with beneficial species has led to numerous commercial applications, and the hunt for new biocontrol organisms continues. Increasingly flexible and affordable sequencing technologies, supported by increasingly comprehensive taxonomic databases, make the characterization of non-model crop-associated microbiomes a widely accessible research method toward this end; and such studies are becoming more frequent. A summary of this emerging literature reveals, however, the need for a more systematic research lens in the face of what is already a metagenomics data deluge. Considering the processes and consequences of crop evolution and domestication, we assert that the judicious integration of in situ crop wild relatives into phytobiome research efforts presents a singularly powerful tool for separating signal from noise, thereby facilitating a more efficient means of identifying candidate plant-associated microbes with the potential for enhanci

  6. Friends with Social Benefits: Host-Microbe Interactions as a Driver of Brain Evolution and Development?

    Directory of Open Access Journals (Sweden)

    Roman M Stilling

    2014-10-01

    Full Text Available The tight association of the human body with trillions of colonizing microbes that we observe today is the result of a long evolutionary history. Only very recently have we started to understand how this symbiosis also affects brain function and behaviour. Here in this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. In particular, we explore the integration of human brain development with evolution, symbiosis, and RNA biology, which together represent a ‘social triangle’ that drives human social behaviour and cognition. We argue that, in order to understand how inter-kingdom communication can affect brain adaptation and plasticity, it is inevitable to consider epigenetic mechanisms as important mediators of genome-microbiome interactions on an individual as well as a transgenerational time scale. Finally, we unite these interpretations with the hologenome theory of evolution. Taken together, we propose a tighter integration of neuroscience fields with host-associated microbiology by taking an evolutionary perspective.

  7. Beneficial interactions between plants and soil microbes

    DEFF Research Database (Denmark)

    Ravnskov, S.

    2012-01-01

    The microbial community in the rhizosphere plays a key role in plant growth and -health, either directly by influencing plant nutrient uptake and by causing disease, or indirectly via microbial interactions in the rhizosphere. The majority of field grown crops (70-80 %) naturally form symbiosis...... competition by AM fungi, changes of plant root structure, root-exudations, nutrient uptake and growth as well as AMF induction of plant defence have been investigated. Moreover, a bacterial community structure associated to AM structures has been demonstrated and some of these bacteria have shown antagonistic...... potential against pathogens. This raises the question whether it is the AMF or the associated bacteria, which control the pathogens. So far, a general mechanism for AMF control with soil-borne pathogens has not been identified, but investigations of more mechanisms and interplays between them might...

  8. Questions about elastic waves

    CERN Document Server

    Engelbrecht, Jüri

    2015-01-01

    This book addresses the modelling of mechanical waves by asking the right questions about them and trying to find suitable answers. The questions follow the analytical sequence from elementary understandings to complicated cases, following a step-by-step path towards increased knowledge. The focus is on waves in elastic solids, although some examples also concern non-conservative cases for the sake of completeness. Special attention is paid to the understanding of the influence of microstructure, nonlinearity and internal variables in continua. With the help of many mathematical models for describing waves, physical phenomena concerning wave dispersion, nonlinear effects, emergence of solitary waves, scales and hierarchies of waves as well as the governing physical parameters are analysed. Also, the energy balance in waves and non-conservative models with energy influx are discussed. Finally, all answers are interwoven into the canvas of complexity.

  9. Regenerative Endodontics: Burning Questions.

    Science.gov (United States)

    Smith, Anthony J; Cooper, Paul R

    2017-09-01

    Pulp regeneration and its clinical translation into regenerative endodontic procedures are receiving increasing research attention, leading to significant growth of the published scientific and clinical literature within these areas. Development of research strategies, which consider patient-, clinician-, and scientist-based outcomes, will allow greater focus on key research questions driving more rapid clinical translation. Three key areas of focus for these research questions should include cells, signaling, and infection/inflammation. A translational pathway is envisaged in which clinical approaches are increasingly refined to provide regenerative endodontic protocols that are based on a robust understanding of the physiological processes and events responsible for the normal secretion, structure, and biological behavior of pulpal tissue. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  10. Quantum theory from questions

    CERN Document Server

    Hoehn, Philipp A

    2016-01-01

    We reconstruct the explicit formalism of qubit quantum theory from elementary rules on an observer's information acquisition. Our approach is purely operational: we consider an observer O interrogating a system S with binary questions and define S's state as O's `catalogue of knowledge' about S; no ontic assumptions are necessary. From the rules we derive the state spaces for N qubits and show that (a) they coincide with the set of density matrices over N qubit Hilbert spaces; (b) states evolve unitarily under the group $\\rm{PSU}(2^N)$ according to the von Neumann evolution equation; and (c) the binary questions by means of which O interrogates the systems corresponds to projective measurements on Pauli operators with outcome probabilities given by the Born rule. Besides offering a novel conceptual perspective on qubit quantum theory, the reconstruction also unravels new structural insights. Namely, we show that, in a quadratic information measure, (d) qubits satisfy informational complementarity inequalities...

  11. GLAMM: Genome-Linked Application for Metabolic Maps

    Energy Technology Data Exchange (ETDEWEB)

    Bates, John; Chivian, Dylan; Arkin, Adam

    2011-05-29

    The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks, and investigating the construction of novel, transgenic pathways. This simple, user-friendly interface is tightly integrated with the comparative genomics tools of MicrobesOnline. GLAMM is available for free to the scientific community at glamm.lbl.gov.

  12. GLAMM: Genome-Linked Application for Metabolic Maps

    Energy Technology Data Exchange (ETDEWEB)

    Bates, John; Chivian, Dylan; Arkin, Adam

    2011-05-29

    The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks, and investigating the construction of novel, transgenic pathways. This simple, user-friendly interface is tightly integrated with the comparative genomics tools of MicrobesOnline. GLAMM is available for free to the scientific community at glamm.lbl.gov.

  13. Microbes Should Be Central to Ecological Education and Outreach

    Directory of Open Access Journals (Sweden)

    Albert Barberán

    2015-09-01

    Full Text Available Our planet is changing rapidly, and responding to the ensuing environmental challenges will require an informed citizenry that can understand the inherent complexity of ecological systems. However, microorganisms are usually neglected in the narratives that we use to understand nature. Here, we advocate for the inclusion of microbial ecology across education levels and delineate the often neglected benefits of incorporating microbes into ecology curricula. We provide examples across education levels, from secondary school (by considering one’s self as a microbial ecosystem, to higher education (by incorporating our knowledge of the global ecological role and medical application of microbes, to the general public (by engagement through citizen-science projects. The greater inclusion of microbes in ecological education and outreach will not only help us appreciate the natural world we are part of, but will ultimately aid in building a citizenry better prepared to make informed decisions on health and environmental policies.

  14. Gut microbes of mammalian herbivores facilitate intake of plant toxins.

    Science.gov (United States)

    Kohl, Kevin D; Weiss, Robert B; Cox, James; Dale, Colin; Dearing, M Denise

    2014-10-01

    The foraging ecology of mammalian herbivores is strongly shaped by plant secondary compounds (PSCs) that defend plants against herbivory. Conventional wisdom holds that gut microbes facilitate the ingestion of toxic plants; however, this notion lacks empirical evidence. We investigated the gut microbiota of desert woodrats (Neotoma lepida), some populations of which specialise on highly toxic creosote bush (Larrea tridentata). Here, we demonstrate that gut microbes are crucial in allowing herbivores to consume toxic plants. Creosote toxins altered the population structure of the gut microbiome to facilitate an increase in abundance of genes that metabolise toxic compounds. In addition, woodrats were unable to consume creosote toxins after the microbiota was disrupted with antibiotics. Last, ingestion of toxins by naïve hosts was increased through microbial transplants from experienced donors. These results demonstrate that microbes can enhance the ability of hosts to consume PSCs and therefore expand the dietary niche breadth of mammalian herbivores.

  15. Theory of microbe motion in a poisoned environment.

    Science.gov (United States)

    Hoell, Christian; Löwen, Hartmut

    2011-10-01

    The motility of a microorganism which tries to avoid a poisoned environment by chemotaxis is studied within a simple model which couples its velocity to the concentration field of the poison. The latter is time independent but inhomogeneous in space. The presence of the poison is assumed to irreversibly reduce the propulsion speed. The model is solved analytically for different couplings of the total poison dose experienced by the microbe to the propulsion mechanism. In a stationary poison field resulting from a constant emission of a fixed point source, we find a power law for the distance traveled by the microbe as a function of time with a nonuniversal exponent which depends on the coupling in the model. With an inverted sign in the couplings, the acceleration of microbe motion induced by a food field can also be described.

  16. Questions to Luce Irigaray

    OpenAIRE

    Ince, Kate

    1996-01-01

    This article traces the "dialogue" between the work of the philosophers Luce Irigaray and Emmanuel Levinas. It attempts to construct a more nuanced discussion than has been given to date of Irigaray's critique of Levinas, particularly as formulated in 'Questions to Emmanuel Levinas' (Irigaray 1991). It suggests that the concepts of the feminine and of voluptuosity articulated by Levinas have more to contribute to Irigaray's project of an ethics of sexual difference than she herself sometimes ...

  17. 501 reading comprehension questions

    CERN Document Server

    2014-01-01

    This updated edition offers the most extensive and varied practice for all types of questions students might face on standardized and in-class tests. With this guide, students will learn to develop expert reading strategies, understand how to read faster and with greater comprehension, overcome reading anxiety, and increase appreciation of reading for pleasure. This book's step-by-step approach provides graduated coverage that moves from the basics to more advanced reading.

  18. Eight Questions about Corruption

    OpenAIRE

    Jakob Svensson

    2005-01-01

    This paper will discuss eight frequently asked questions about public corruption: (1) What is corruption? (2) Which countries are the most corrupt? (3) What are the common characteristics of countries with high corruption? (4) What is the magnitude of corruption? (5) Do higher wages for bureaucrats reduce corruption? (6) Can competition reduce corruption? (7) Why have there been so few (recent) successful attempts to fight corruption? (8) Does corruption adversely affect growth?

  19. Questioning Many Mysteries

    Science.gov (United States)

    Martin, Sara F.

    2015-04-01

    The first section of this memoir queries my formative years. Indirectly I address the question, did my childhood and early years make a difference in my choice of career? Why and how did I begin my journey to becoming a scientist? Did I choose the field of solar astronomy or did circumstances dictate it for me? In the second section, I travel through my work environments and experiences, talking about interactions and aspects of being a scientist that do not appear in our research papers. What parts of my research were happenstances and what parts did I plan? What does it feel like to be on scientific quests? Using examples in my journey, I also turn to questions that have intrigued me throughout my sojourn as a solar astronomer. How do scientific discoveries come about? What factors lead to little discoveries? And what factors lead to major exciting discoveries? Are there timely questions we do not think to ask? How can small, seemingly scattered pieces of knowledge suddenly coalesce into a deeper understanding - what is called the "Aha!" experience - the times when our mental light switches on, and with child-like wonder we behold a "big picture"?

  20. The Emerging Microbe Project: Developing Clinical Care Plans Based on Pathogen Identification and Clinical Case Studies.

    Science.gov (United States)

    O'Donnell, Lauren A; Perry, Michael W; Doup, Dane't R

    2015-12-01

    For many students in the health sciences, including doctor of pharmacy (PharmD) students, basic and clinical sciences often appear detached from each other. In the infectious disease field, PharmD students additionally struggle with mastering the diversity of microorganisms and the corresponding therapies. The objective of this study was to design an interdisciplinary project that integrates fundamental microbiology with clinical research and decision-making skills. The Emerging Microbe Project guided students through the identification of a microorganism via genetic sequence analysis. The unknown microbe provided the basis for a patient case that asked the student to design a therapeutic treatment strategy for an infected patient. Outside of lecture, students had two weeks to identify the pathogen using nucleotide sequences, compose a microbiology report on the pathogen, and recommend an appropriate therapeutic treatment plan for the corresponding clinical case. We hypothesized that the students would develop a better understanding of the interplay between basic microbiology and infectious disease clinical practice, and that they would gain confidence and skill in independently selecting appropriate antimicrobial therapies for a new disease state. The exercise was conducted with PharmD students in their second professional year of pharmacy school in a required infectious disease course. Here, we demonstrate that the Emerging Microbe Project significantly improved student learning through two assessment strategies (assignment grades and exam questions), and increased student confidence in clinical infectious disease practice. This exercise could be modified for other health sciences students or undergraduates depending upon the level of clinical focus required of the course.

  1. The Emerging Microbe Project: Developing Clinical Care Plans Based on Pathogen Identification and Clinical Case Studies

    Directory of Open Access Journals (Sweden)

    Lauren A. O'Donnell

    2015-08-01

    Full Text Available For many students in the health sciences, including doctor of pharmacy (PharmD students, basic and clinical sciences often appear detached from each other. In the infectious disease field, PharmD students additionally struggle with mastering the diversity of microorganisms and the corresponding therapies. The objective of this study was to design an interdisciplinary project that integrates fundamental microbiology with clinical research and decision-making skills. The Emerging Microbe Project guided students through the identification of a microorganism via genetic sequence analysis. The unknown microbe provided the basis for a patient case that asked the student to design a therapeutic treatment strategy for an infected patient. Outside of lecture, students had two weeks to identify the pathogen using nucleotide sequences, compose a microbiology report on the pathogen, and recommend an appropriate therapeutic treatment plan for the corresponding clinical case. We hypothesized that the students would develop a better understanding of the interplay between basic microbiology and infectious disease clinical practice, and that they would gain confidence and skill in independently selecting appropriate antimicrobial therapies for a new disease state. The exercise was conducted with PharmD students in their second professional year of pharmacy school in a required infectious disease course. Here, we demonstrate that the Emerging Microbe Project significantly improved student learning through two assessment strategies (assignment grades and exam questions, and increased student confidence in clinical infectious disease practice. This exercise could be modified for other health sciences students or undergraduates depending upon the level of clinical focus required of the course.

  2. Microbes bind complement inhibitor factor H via a common site.

    Directory of Open Access Journals (Sweden)

    T Meri

    Full Text Available To cause infections microbes need to evade host defense systems, one of these being the evolutionarily old and important arm of innate immunity, the alternative pathway of complement. It can attack all kinds of targets and is tightly controlled in plasma and on host cells by plasma complement regulator factor H (FH. FH binds simultaneously to host cell surface structures such as heparin or glycosaminoglycans via domain 20 and to the main complement opsonin C3b via domain 19. Many pathogenic microbes protect themselves from complement by recruiting host FH. We analyzed how and why different microbes bind FH via domains 19-20 (FH19-20. We used a selection of FH19-20 point mutants to reveal the binding sites of several microbial proteins and whole microbes (Haemophilus influenzae, Bordetella pertussis, Pseudomonas aeruginosa, Streptococcus pneumonia, Candida albicans, Borrelia burgdorferi, and Borrelia hermsii. We show that all studied microbes use the same binding region located on one side of domain 20. Binding of FH to the microbial proteins was inhibited with heparin showing that the common microbial binding site overlaps with the heparin site needed for efficient binding of FH to host cells. Surprisingly, the microbial proteins enhanced binding of FH19-20 to C3b and down-regulation of complement activation. We show that this is caused by formation of a tripartite complex between the microbial protein, FH, and C3b. In this study we reveal that seven microbes representing different phyla utilize a common binding site on the domain 20 of FH for complement evasion. Binding via this site not only mimics the glycosaminoglycans of the host cells, but also enhances function of FH on the microbial surfaces via the novel mechanism of tripartite complex formation. This is a unique example of convergent evolution resulting in enhanced immune evasion of important pathogens via utilization of a "superevasion site."

  3. The microbe-free plant: fact or artifact?

    Science.gov (United States)

    Partida-Martínez, Laila P; Heil, Martin

    2011-01-01

    Plant-microbe interactions are ubiquitous. Plants are threatened by pathogens, but they are even more commonly engaged in neutral or mutualistic interactions with microbes: belowground microbial plant associates are mycorrhizal fungi, Rhizobia, and plant-growth promoting rhizosphere bacteria, aboveground plant parts are colonized by internally living bacteria and fungi (endophytes) and by microbes in the phyllosphere (epiphytes). We emphasize here that a completely microbe-free plant is an exotic exception rather than the biologically relevant rule. The complex interplay of such microbial communities with the host-plant affects multiple vital parameters such as plant nutrition, growth rate, resistance to biotic and abiotic stressors, and plant survival and distribution. The mechanisms involved reach from direct ones such as nutrient acquisition, the production of plant hormones, or direct antibiosis, to indirect ones that are mediated by effects on host resistance genes or via interactions at higher trophic levels. Plant-associated microbes are heterotrophic and cause costs to their host plant, whereas the benefits depend on the current environment. Thus, the outcome of the interaction for the plant host is highly context dependent. We argue that considering the microbe-free plant as the "normal" or control stage significantly impairs research into important phenomena such as (1) phenotypic and epigenetic plasticity, (2) the "normal" ecological outcome of a given interaction, and (3) the evolution of plants. For the future, we suggest cultivation-independent screening methods using direct PCR from plant tissue of more than one fungal and bacterial gene to collect data on the true microbial diversity in wild plants. The patterns found could be correlated to host species and environmental conditions, in order to formulate testable hypotheses on the biological roles of plant endophytes in nature. Experimental approaches should compare different host

  4. The microbe-free plant: fact or artefact?

    Directory of Open Access Journals (Sweden)

    Laila P. Pamela Partida-Martinez

    2011-12-01

    Full Text Available Plant-microbe interactions are ubiquitous. Plants are often colonized by pathogens but even more commonly engaged in neutral or mutualistic interactions with microbes: below-ground microbial plant associates are mycorrhizal fungi, Rhizobia and rhizosphere bacteria, above-ground plant parts are colonized by bacterial and fungal endophytes and by microbes in the phyllosphere. We emphasize here that a completely microbe-free plant is an exotic exception rather than the biologically relevant rule. The complex interplay of such microbial communities with the host plant affects plant nutrition, growth rate, resistance to biotic and abiotic stress, and plant survival and distribution. The mechanisms involved reach from nutrient acquisition, the production of plant hormones or direct antibiosis to effects on host resistance genes or interactions at higher trophic levels. Plant-associated microbes are heterotrophic and cause costs to their host plant, whereas the benefits depend on the environment. Thus, the outcome of the interaction is highly context-dependent. Considering the microbe-free plant as the ‘normal’ or control stage significantly impairs research into important phenomena such as (1 phenotypic and epigenetic plasticity, (2 the ‘normal’ ecological outcome of a given interaction and (3 the evolution of plants. For the future, we suggest cultivation-independent screening methods using direct PCR from plant tissue of more than one fungal and bacterial gene to collect data on the true microbial diversity in wild plants. The patterns found could be correlated to host species and environmental conditions, in order to formulate testable hypotheses on the biological roles of plant endophytes in nature. Experimental approaches should compare different host-endophyte combinations under various environmental conditions and study at the genetic, transcriptional and physiological level the parameters that shift the interaction along the mutualism

  5. Ecological interactions between metals and microbes that impact bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Allan Konopka; Cindy Nakatsu

    2004-03-17

    Distinct microbial communities had been found in contaminated soils that varied in their concentrations of Pb, Cr and aromatic compounds. It is difficult to distinguish between their effects as their presence is highly correlated. Microcosms were constructed in which either Pb{sup +2} or CrO{sub 4}{sup -2} was added at levels that produced acute modest or severe acute effects (50 or 90% reduction). We previously reported on changes in microbial activity and broad patterns of Bacterial community composition. These results showed that addition of an organic energy source selected for a relatively small number of phylotypes and the addition of Pb or Cr(VI) modulated the community response. We sequenced dominant phylotypes from microcosms amended with xylene and Cr(VI) and from those with the simple addition of glucose only. In both cases, the dominant selected phylotypes were diverse. We found a number of distinct Arthrobacter strains, as well as several Pseudomonas spp. In addition, the high GC-content bands belonged to members of the genera Nocardioides and Rhodococcus. The focus of amended microcosm work has now shifted to anaerobic processes. The reduction of Cr(VI) to Cr(III) as a detoxification mechanism is of greater interest, as is the specific role of particular physiological groups of anaerobes in mediating Cr(VI) detoxification. The correlation between microbial activity, community structure, and metal level has been analyzed on 150 mg of soil collected at spatial scales <1, 5, 15 and 50 cm. There was no correlation between metal content and activity level. Soils <1 cm apart could differ in activity 10-fold and extractable Pb and Cr 7-fold. Therefore, we turned to geostatistical analysis. There was spatial periodicity which is likely to reflect the heterogeneous distribution of active microbes and metal contaminants. Variograms indicated that the range of spatial dependence was up to 20 cm. To visualize the spatial relationships between the primary variate

  6. UNDERSTANDING SOCIAL INTERACTIONS OF MICROBES USING TRANSCRIPTOMICS : A CODICIL

    Directory of Open Access Journals (Sweden)

    Prem Saran Tirumalai

    2015-06-01

    Full Text Available Sociobiology of microbes is an emerging branch of science that has delivered interesting and intriguing research findings over the last few years. The revelations are such that the research perspective of microbes is gradually drifting from pure culture analysis to community analysis. We review to substantiate the need for microbial socio-bio studies and codicil the decade long research pursuit and their findings using advanced technologies of Microarrays and Next Generation Sequencing, prompting for more lunge in transcriptomic and metatranscriptomic studies.

  7. Metagenomic search strategies for interactions among plants and multiple microbes

    Directory of Open Access Journals (Sweden)

    Ulrich Karl Melcher

    2014-06-01

    Full Text Available Plants harbor multiple microbes. Metagenomics can facilitate understanding of the significance, for the plant, of the microbes and of the interactions among them. However, current approaches to metagenomic analysis of plants are computationally time-consuming. Efforts to speed the discovery process include improvement of computational speed, condensing the sequencing reads into smaller datasets before BLAST searches, simplifying the target database of BLAST searches, and flipping the roles of metagenomic and reference datasets. The latter is exemplified by the E-probe diagnostic nucleic acid analysis (EDNA approach originally devised for improving analysis during plant quarantine.

  8. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, David [DOE JGI Public Affairs Manager

    2013-01-01

    The mission of the U.S. Department of Energy Joint Genome Institute (DOE JGI) is to serve the diverse scientific community as a user facility, enabling the application of large-scale genomics and analysis of plants, microbes, and communities of microbes to address the DOE mission goals in bioenergy and the environment. The DOE JGI's sequencing efforts fall under the Eukaryote Super Program, which includes the Plant and Fungal Genomics Programs; and the Prokaryote Super Program, which includes the Microbial Genomics and Metagenomics Programs. In 2012, several projects made news for their contributions to energy and environment research.

  9. Using Nematostella vectensis to study the interactions between genome, epigenome and bacteria in a changing environment

    Directory of Open Access Journals (Sweden)

    Sebastian Fraune

    2016-08-01

    Full Text Available The phenotype of an animal cannot be explained entirely by its genes. It is now clear that factors other than the genome contribute to the ecology and evolution of animals. Two fundamentally important factors are the associated microbiota and epigenetic regulations. Unlike the genes and regulatory regions of the genome, epigenetics and microbial composition can be rapidly modified, and may thus represent mechanisms for rapid acclimation to a changing environment. At present, the individual functions of epigenetics, microbiomes, and genomic mutations are largely studied in isolation, particularly for species in marine ecosystems. This single variable approach leaves significant questions open for how these mechanisms intersect in the acclimation and adaptation of organisms in different environments. Here, we propose that the starlet sea anemone, Nematostella vectensis, is a model of choice to investigate the complex interplay between adaptation as well as physiological and molecular plasticity in coastal ecosystems. N. vectensis’ geographic range spans four distinct coastlines, including a wide thermocline along the Atlantic coast of North America. N. vectensis is a particularly powerful invertebrate model for studying genome-environment interactions due to (1 the availability of a well-annotated genome, including preexisting data on genome methylation, histone modifications and miRNAs, (2 an extensive molecular toolkit including well-developed protocols for gene suppression and transgenesis, and (3 the simplicity of culture and experimentation in the laboratory. Taken together, N. vectensis has the tractability to connect the functional relationships between a host animal, microbes, and genome modifications to determine mechanisms underlying phenotypic plasticity and local adaptation.

  10. Staying Alive: Measuring Intact Viable Microbes with Electrospray Ionization Mass Spectrometry

    Science.gov (United States)

    Forsberg, Erica; Fang, Mingliang; Siuzdak, Gary

    2017-01-01

    Mass spectrometry has traditionally been the technology of choice for small molecule analysis, making significant inroads into metabolism, clinical diagnostics, and pharmacodynamics since the 1960s. In the mid-1980s, with the discovery of electrospray ionization (ESI) for biomolecule analysis, a new door opened for applications beyond small molecules. Initially, proteins were widely examined, followed by oligonucleotides and other nonvolatile molecules. Then in 1991, three intriguing studies reported using mass spectrometry to examine noncovalent protein complexes, results that have been expanded on for the last 25 years. Those experiments also raised the questions: How soft is ESI, and can it be used to examine even more complex interactions? Our lab addressed these questions with the analyses of viruses, which were initially tested for viability following electrospray ionization and their passage through a quadrupole mass analyzer by placing them on an active medium that would allow them to propagate. This observation has been replicated on multiple different systems, including experiments on an even bigger microbe, a spore. The question of analysis was also addressed in the early 2000s with charge detection mass spectrometry. This unique technology could simultaneously measure mass-to-charge and charge, allowing for the direct determination of the mass of a virus. More recent experiments on spores and enveloped viruses have given us insight into the range of mass spectrometry's capabilities (reaching 100 trillion Da), beginning to answer fundamental questions regarding the complexity of these organisms beyond proteins and genes, and how small molecules are integral to these supramolecular living structures.

  11. The Art of Asking Questions.

    Science.gov (United States)

    Sykes, Rosetta A.

    1979-01-01

    A rationale is given for the use of questioning techniques and strategies in classroom instruction. B. Bloom's Taxonomy of Educational Objectives is presented as one framework for questions. Five pitfalls, including avoiding vague questions and personal pronouns, are discussed. (CL)

  12. Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface.

    Directory of Open Access Journals (Sweden)

    J Jeffrey Morris

    Full Text Available The phytoplankton community in the oligotrophic open ocean is numerically dominated by the cyanobacterium Prochlorococcus, accounting for approximately half of all photosynthesis. In the illuminated euphotic zone where Prochlorococcus grows, reactive oxygen species are continuously generated via photochemical reactions with dissolved organic matter. However, Prochlorococcus genomes lack catalase and additional protective mechanisms common in other aerobes, and this genus is highly susceptible to oxidative damage from hydrogen peroxide (HOOH. In this study we showed that the extant microbial community plays a vital, previously unrecognized role in cross-protecting Prochlorococcus from oxidative damage in the surface mixed layer of the oligotrophic ocean. Microbes are the primary HOOH sink in marine systems, and in the absence of the microbial community, surface waters in the Atlantic and Pacific Ocean accumulated HOOH to concentrations that were lethal for Prochlorococcus cultures. In laboratory experiments with the marine heterotroph Alteromonas sp., serving as a proxy for the natural community of HOOH-degrading microbes, bacterial depletion of HOOH from the extracellular milieu prevented oxidative damage to the cell envelope and photosystems of co-cultured Prochlorococcus, and facilitated the growth of Prochlorococcus at ecologically-relevant cell concentrations. Curiously, the more recently evolved lineages of Prochlorococcus that exploit the surface mixed layer niche were also the most sensitive to HOOH. The genomic streamlining of these evolved lineages during adaptation to the high-light exposed upper euphotic zone thus appears to be coincident with an acquired dependency on the extant HOOH-consuming community. These results underscore the importance of (indirect biotic interactions in establishing niche boundaries, and highlight the impacts that community-level responses to stress may have in the ecological and evolutionary outcomes for co

  13. Social Epistemology: 5 Questions

    DEFF Research Database (Denmark)

    Social Epistemology: 5 Questions is a collection of interviews with some of the world’s most influential scholars working on social epistemology from a range of disciplinary perspectives. We hear their views on social epistemology; its aim, scope, use, broader intellectual environment, future...... direction, and how the work of the interviewees fits in these respects. Interviews with David Bloor, Cristina Bicchieri, Richard Bradley, Lorraine Code, Hans van Ditmarsch, Miranda Fricker, Steve Fuller, Sanford Goldberg, Alvin Goldman, Philip Kitcher, Martin Kusch, Jennifer Lackey, Helen E. Longino, Philip...

  14. Microbe-independent entry of oomycete RxLR effectors and fungal RxLR-like effectors into plant and animal cells is specific and reproducible.

    Science.gov (United States)

    Tyler, Brett M; Kale, Shiv D; Wang, Qunqing; Tao, Kai; Clark, Helen R; Drews, Kelly; Antignani, Vincenzo; Rumore, Amanda; Hayes, Tristan; Plett, Jonathan M; Fudal, Isabelle; Gu, Biao; Chen, Qinghe; Affeldt, Katharyn J; Berthier, Erwin; Fischer, Gregory J; Dou, Daolong; Shan, Weixing; Keller, Nancy P; Martin, Francis; Rouxel, Thierry; Lawrence, Christopher B

    2013-06-01

    A wide diversity of pathogens and mutualists of plant and animal hosts, including oomycetes and fungi, produce effector proteins that enter the cytoplasm of host cells. A major question has been whether or not entry by these effectors can occur independently of the microbe or requires machinery provided by the microbe. Numerous publications have documented that oomycete RxLR effectors and fungal RxLR-like effectors can enter plant and animal cells independent of the microbe. A recent reexamination of whether the RxLR domain of oomycete RxLR effectors is sufficient for microbe-independent entry into host cells concluded that the RxLR domains of Phytophthora infestans Avr3a and of P. sojae Avr1b alone are NOT sufficient to enable microbe-independent entry of proteins into host and nonhost plant and animal cells. Here, we present new, more detailed data that unambiguously demonstrate that the RxLR domain of Avr1b does show efficient and specific entry into soybean root cells and also into wheat leaf cells, at levels well above background nonspecific entry. We also summarize host cell entry experiments with a wide diversity of oomycete and fungal effectors with RxLR or RxLR-like motifs that have been independently carried out by the seven different labs that coauthored this letter. Finally we discuss possible technical reasons why specific cell entry may have been not detected by Wawra et al. (2013).

  15. Mathematics make microbes beautiful, beneficial, and bountiful.

    Science.gov (United States)

    Jungck, John R

    2012-01-01

    Microbiology is a rich area for visualizing the importance of mathematics in terms of designing experiments, data mining, testing hypotheses, and visualizing relationships. Historically, Nobel Prizes have acknowledged the close interplay between mathematics and microbiology in such examples as the fluctuation test and mutation rates using Poisson statistics by Luria and Delbrück and the use of graph theory of polyhedra by Caspar and Klug. More and more contemporary microbiology journals feature mathematical models, computational algorithms and heuristics, and multidimensional visualizations. While revolutions in research have driven these initiatives, a commensurate effort needs to be made to incorporate much more mathematics into the professional preparation of microbiologists. In order not to be daunting to many educators, a Bloom-like "Taxonomy of Quantitative Reasoning" is shared with explicit examples of microbiological activities for engaging students in (a) counting, measuring, calculating using image analysis of bacterial colonies and viral infections on variegated leaves, measurement of fractal dimensions of beautiful colony morphologies, and counting vertices, edges, and faces on viral capsids and using graph theory to understand self assembly; (b) graphing, mapping, ordering by applying linear, exponential, and logistic growth models of public health and sanitation problems, revisiting Snow's epidemiological map of cholera with computational geometry, and using interval graphs to do complementation mapping, deletion mapping, food webs, and microarray heatmaps; (c) problem solving by doing gene mapping and experimental design, and applying Boolean algebra to gene regulation of operons; (d) analysis of the "Bacterial Bonanza" of microbial sequence and genomic data using bioinformatics and phylogenetics; (e) hypothesis testing-again with phylogenetic trees and use of Poisson statistics and the Luria-Delbrück fluctuation test; and (f) modeling of

  16. Trick questions: cosmopolitan hospitality

    Directory of Open Access Journals (Sweden)

    Eleanor Byrne

    2013-08-01

    Full Text Available Byrne’s paper consists of two parallel texts. The first explores the limits of cosmopolitanism in practice, taking as its subject the Life in the UK Citizenship Test, inaugurated under the Labour Government in 2005. It argues that the test exemplifies the predicament of all attempts at cosmopolitan hospitality as unconditional welcoming, through a discussion of the relation between questioning and welcoming the stranger. Establishing the relationship between cosmopolitanism and hospitality as envisaged in Derrida’s reading of Kant it asks what kind of cosmopolitan hospitality is either possible or desirable by exploring what Derrida calls the ‘perversions’ inherent in the structures of hospitality. It focuses on the concept of the ‘trick questions’ that the state asks the foreigner observed by Derrida in his reading of The Apology of Socrates; questions that seem to invite answers but foreclose the possibilities of a free response. The second text asks how this logic that Derrida identifies can be pushed or coaxed into new ways of addressing the perceived threats of ‘unconditional’ hospitality through a reading of ‘unconditional hospitality’ as queer in the work of Tove Jansson.

  17. The Gentle Art of Questioning: Writing Great Clicker Questions

    Science.gov (United States)

    Chasteen, Stephanie

    2012-02-01

    How does a teacher use questioning effectively? This workshop will focus on writing those questions that engage students, spark their curiosity, help recap material, give you insight into their thinking, or help them learn critical ideas in physics. We will focus on ``peer instruction'' -- a research-tested method of requiring students to discuss challenging questions with one another. We will investigate the surprising power of multiple-choice questions to achieve critical thinking skills. Finally, we will look at writing questions that align with our goals for students, discuss the elements of effective questions, and practice writing questions and work on improving them.

  18. Questions and Questioning Techniques: A View of Indonesian Students’ Preferences

    Directory of Open Access Journals (Sweden)

    Debora Tri Ragawanti

    2009-01-01

    Full Text Available This study investigated students’ preference on teacher’s questions and questionings techniques and more importantly on how they could facilitate or impede their learning. The results on teacher’s questioning techniques showed that random nomination was more preferred than pre-arranged format nomination. In addition, techniques of nominating volunteering students and of giving wait-time were disliked by most student-respondents. As for types of question, the yes/no question was favored by most of the respondents. Different from the yes/no question, the number of respondents leaning forward to the analysis question, questions about fact of life, and questions to state opinion did not show a significant difference from the number of those leaning against the same questions.

  19. Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture.

    Science.gov (United States)

    Berg, Gabriele

    2009-08-01

    Plant-associated microorganisms fulfill important functions for plant growth and health. Direct plant growth promotion by microbes is based on improved nutrient acquisition and hormonal stimulation. Diverse mechanisms are involved in the suppression of plant pathogens, which is often indirectly connected with plant growth. Whereas members of the bacterial genera Azospirillum and Rhizobium are well-studied examples for plant growth promotion, Bacillus, Pseudomonas, Serratia, Stenotrophomonas, and Streptomyces and the fungal genera Ampelomyces, Coniothyrium, and Trichoderma are model organisms to demonstrate influence on plant health. Based on these beneficial plant-microbe interactions, it is possible to develop microbial inoculants for use in agricultural biotechnology. Dependent on their mode of action and effects, these products can be used as biofertilizers, plant strengtheners, phytostimulators, and biopesticides. There is a strong growing market for microbial inoculants worldwide with an annual growth rate of approximately 10%. The use of genomic technologies leads to products with more predictable and consistent effects. The future success of the biological control industry will benefit from interdisciplinary research, e.g., on mass production, formulation, interactions, and signaling with the environment, as well as on innovative business management, product marketing, and education. Altogether, the use of microorganisms and the exploitation of beneficial plant-microbe interactions offer promising and environmentally friendly strategies for conventional and organic agriculture worldwide.

  20. The high life: Transport of microbes in the atmosphere

    Science.gov (United States)

    Smith, David J.; Griffin, Dale W.; Jaffe, Daniel A.

    2011-07-01

    Microbes (bacteria, fungi, algae, and viruses) are the most successful types of life on Earth because of their ability to adapt to new environments, reproduce quickly, and disperse globally. Dispersal occurs through a number of vectors, such as migrating animals or the hydrological cycle, but transport by wind may be the most common way microbes spread. General awareness of airborne microbes predates the science of microbiology. People took advantage of wild airborne yeasts to cultivate lighter, more desirable bread as far back as ancient Egypt by simply leaving a mixture of grain and liquids near an open window. In 1862, Louis Pasteur's quest to disprove spontaneous generation resulted in the discovery that microbes were actually single-celled, living creatures, prevalent in the environment and easily killed with heat (pasteurization). His rudimentary experiments determined that any nutrient medium left open to the air would eventually teem with microbial life because of free-floating, colonizing cells. The same can happen in a kitchen: Opportunistic fungal and bacterial cells cause food items exposed to the air to eventually spoil.

  1. Phenolic Acids in Plant-Soil-Microbe System: A Review

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Phenolic acids are very common compounds in pedosphere. The objective of this review was to summarize the current knowledge of the behaviors of phenolic acids in plant-soil-microbe system. When phenolic acids originated from leaching, decomposition and exudation of living and dead plant tissues enter soils, they can react physicochemically with soil particle surfaces and/or incorporate into humic matter. Phenolic acids desorbed from soil particle surfaces and remained in solution phase can be utilized by microbe as carbon sources and absorbed by plants. The degradation products of phenolic acids by microbe include some organic and/or inorganic compounds such as new phenolic acids. In addition, phenolic acids in soils can stimulate population and activity of microbe. Phenolic acids can inhibit plants growth by affecting ion leakage, phytohormone activity, membrane permeability, hydraulic conductivity, net nutrient uptake, and enzyme activity. Behaviors of phenolic acids in soils are influenced by other organic compounds (phenolic acids, methionine, glucose, etc.) and/or inorganic ions. The role of phenolic acids as allelopathic agents should not be neglected only based on their low specific concentrations in natural soils, because numbers and interactions of phenolic acids will increase their allelopathic activities.

  2. Microbes from raw milk for fermented dairy products

    NARCIS (Netherlands)

    Wouters, J.T.M.; Ayad, E.H.E.; Hugenholtz, J.; Smit, G.

    2002-01-01

    Milk has a high nutritive value, not only For the new-born mammal and for the human consumer, but also for microbes. Raw milk kept at roam temperature will be liable to microbial spoilage. After some days, the milk will spontaneously become sour. This is generally due to the activity of lactic acid

  3. Seeing is believing: what experiments with microbes reveal about evolution.

    Science.gov (United States)

    van Ditmarsch, Dave; Xavier, Joao B

    2014-01-01

    Darwin's theory of natural selection is among the most powerful ideas in science, yet evolutionary ideas remain challenged to this day. This is in part because evolution often cannot be directly observed. Simple experiments with microbes can change that by enabling direct observation of evolutionary processes.

  4. Photoheterotrophic microbes in the Arctic Ocean in summer and winter.

    Science.gov (United States)

    Cottrell, Matthew T; Kirchman, David L

    2009-08-01

    Photoheterotrophic microbes, which are capable of utilizing dissolved organic materials and harvesting light energy, include coccoid cyanobacteria (Synechococcus and Prochlorococcus), aerobic anoxygenic phototrophic (AAP) bacteria, and proteorhodopsin (PR)-containing bacteria. Our knowledge of photoheterotrophic microbes is largely incomplete, especially for high-latitude waters such as the Arctic Ocean, where photoheterotrophs may have special ecological relationships and distinct biogeochemical impacts due to extremes in day length and seasonal ice cover. These microbes were examined by epifluorescence microscopy, flow cytometry, and quantitative PCR (QPCR) assays for PR and a gene diagnostic of AAP bacteria (pufM). The abundance of AAP bacteria and PR-containing bacteria decreased from summer to winter, in parallel with a threefold decrease in the total prokaryotic community. In contrast, the abundance of Synechococcus organisms did not decrease in winter, suggesting that their growth was supported by organic substrates. Results from QPCR assays revealed no substantial shifts in the community structure of AAP bacteria and PR-containing bacteria. However, Arctic PR genes were different from those found at lower latitudes, and surprisingly, they were not similar to those in Antarctic coastal waters. Photoheterotrophic microbes appear to compete successfully with strict heterotrophs during winter darkness below the ice, but AAP bacteria and PR-containing bacteria do not behave as superior competitors during the summer.

  5. The high life: Transport of microbes in the atmosphere

    Science.gov (United States)

    Smith, D.J.; Griffin, Dale W.; Jaffe, D.A.

    2011-01-01

    Microbes (bacteria, fungi, algae, and viruses) are the most successful types of life on Earth because of their ability to adapt to new environments, reproduce quickly, and disperse globally. Dispersal occurs through a number of vectors, such as migrating animals or the hydrological cycle, but transport by wind may be the most common way microbes spread. General awareness of airborne microbes predates the science of microbiology. People took advantage of wild airborne yeasts to cultivate lighter, more desirable bread as far back as ancient Egypt by simply leaving a mixture of grain and liquids near an open window. In 1862, Louis Pasteur's quest to disprove spontaneous generation resulted in the discovery that microbes were actually single-celled, living creatures, prevalent in the environment and easily killed with heat (pasteurization). His rudimentary experiments determined that any nutrient medium left open to the air would eventually teem with microbial life because of free-floating, colonizing cells. The same can happen in a kitchen: Opportunistic fungal and bacterial cells cause food items exposed to the air to eventually spoil.

  6. Microbes in Beach Sands: Integrating Environment, Ecology and Public Health.

    Science.gov (United States)

    Whitman, Richard; Harwood, Valerie J; Edge, Thomas A; Nevers, Meredith; Byappanahalli, Muruleedhara; Vijayavel, Kannappan; Brandão, João; Sadowsky, Michael J; Alm, Elizabeth Wheeler; Crowe, Allan; Ferguson, Donna; Ge, Zhongfu; Halliday, Elizabeth; Kinzelman, Julie; Kleinheinz, Greg; Przybyla-Kelly, Kasia; Staley, Christopher; Staley, Zachery; Solo-Gabriele, Helena M

    2014-09-01

    Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in

  7. Unproven (questionable) cancer therapies.

    Science.gov (United States)

    Brigden, M L

    1995-11-01

    More than half of all cancer patients use some form of alternative treatment during the course of their illness. Alternative therapies are often started early in patients' illness, and their use is frequently not acknowledged to health care professionals. Some alternative therapies are harmful, and their promoters may be fraudulent. Persons who try alternative cancer therapies may not be poorly educated but may ultimately abandon conventional treatment. Recent attention has focused on aspects of questionable therapies that make these treatments attractive to patients and that may be perceived as being deficient in the practice of conventional health care professionals. Physicians with patients with cancer should always make sure that unproven therapies are discussed early in the therapeutic relationship. They should also attempt to be aware of alternative therapies that are in vogue in their particular geographic area.

  8. From Questions to Queries

    Directory of Open Access Journals (Sweden)

    M. Drlík

    2007-12-01

    Full Text Available The extension of (Internet databases forceseveryone to become more familiar with techniques of datastorage and retrieval because users’ success often dependson their ability to pose right questions and to be able tointerpret their answers. University programs pay moreattention to developing database programming skills than todata exploitation skills. To educate our students to become“database users”, the authors intensively exploit supportivetools simplifying the production of database elements astables, queries, forms, reports, web pages, and macros.Videosequences demonstrating “standard operations” forcompleting them have been prepared to enhance out-ofclassroomlearning. The use of SQL and other professionaltools is reduced to the cases when the wizards are unable togenerate the intended construct.

  9. The social question revisited

    DEFF Research Database (Denmark)

    Kenneth, Petersson; Olsson, Ulf; Krejsler, John B.

    2015-01-01

    of social and political unrest, poverty and lack of morality. In the name of European Union social integration is thus organized differently as compared to former times. There are, nevertheless similarities. In both cases educational systems become key arenas for integrating social groups......The focus of this chapter is the re-installation of the social question as a historical practice. The purpose is to investigate how historic figures return and are applied in contemporary political discourses, more precisely in the context of education, education policy and teacher education...... and raising the level of knowledge and competences in society. Higher education, in this case teacher education, is supposed to develop potentials of individuals and maximize “their contribution to a sustainable and democratic knowledge-based society.” Consequently; student cohorts should reflect...

  10. The questions for Machiavelli

    Directory of Open Access Journals (Sweden)

    Lakićević Dragan D.

    2010-01-01

    Full Text Available The main intention of the work that deals with the Nicolo Machiavelli thought is to point out the obvious paradox between the high political goal and the legitimating of all possible means for its realization. Are evil deeds inevitable in the sphere of politics and under what circumstances the immorality contained in political acts could be transformed into common good? The text asks additional questions such as about the accomplishments of ambitious political projects, the relationship among the ideologist and the representative of political power, the transformations of the means into the ends, the use of violence and indoctrination in political acts, revolutionary and evolutionary political methods, etc. The author claims that political technologies recommended by Machiavelli basically haven't diminished, but have taken on more modern and more adequate forms.

  11. The Deflection Question

    Science.gov (United States)

    Greenberg, A. H.; Nesvold, E.; van Heerden, E.; Erasmus, N.; Marchis, F.

    2016-12-01

    On 15 February, 2013, a 15 m diameter asteroid entered the Earth's atmosphere over Russia. The resulting shockwave injured nearly 1500 people, and incurred 33 million (USD) in infrastructure damages. The Chelyabinsk meteor served as a forceful demonstration of the threat posed to Earth by the hundreds of potentially hazardous objects (PHOs) that pass near the Earth every year. Although no objects have yet been discovered on an impact course for Earth, an impact is virtually statistically guaranteed at some point in the future. While many impactor deflection technologies have been proposed, humanity has yet to demonstrate the ability to divert an impactor when one is found. Developing and testing any single proposed technology will require significant research time and funding. This leaves open an obvious question - towards which technologies should funding and research be directed, in order to maximize our preparedness for when an impactor is eventually found? To help answer this question, we have created a detailed framework for analyzing various deflection technologies and their effectiveness. Using an n-body integrator (REBOUND), we have simulated the attempted deflections of a population of Earth-impacting objects with a variety of velocity perturbations (∂Vs), and measured the effects that these perturbations had on impact probability. We then mapped the ∂Vs applied in the orbital simulations to the technologies capable of achieving those perturbations, and analyzed which set of technologies would be most effective at preventing a PHO from impacting the earth. As a final step, we used the results of these simulations to train a machine learning algorithm. This algorithm, combined with a simulated PHO population, can predict which technologies are most likely to be needed. The algorithm can also reveal which impactor observables (mass, spin, orbit, etc.) have the greatest effect on the choice of deflection technology. These results can be used as a tool to

  12. Automatic Chinese Factual Question Generation

    Science.gov (United States)

    Liu, Ming; Rus, Vasile; Liu, Li

    2017-01-01

    Question generation is an emerging research area of artificial intelligence in education. Question authoring tools are important in educational technologies, e.g., intelligent tutoring systems, as well as in dialogue systems. Approaches to generate factual questions, i.e., questions that have concrete answers, mainly make use of the syntactical…

  13. MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes

    Science.gov (United States)

    Ma, Wei; Huang, Chuanbo; Zhou, Yuan; Li, Jianwei; Cui, Qinghua

    2017-01-01

    The microbiota colonized on human body is renowned as “a forgotten organ” due to its big impacts on human health and disease. Recently, microbiome studies have identified a large number of microbes differentially regulated in a variety of conditions, such as disease and diet. However, methods for discovering biological patterns in the differentially regulated microbes are still limited. For this purpose, here, we developed a web-based tool named MicroPattern to discover biological patterns for a list of microbes. In addition, MicroPattern implemented and integrated an algorithm we previously presented for the calculation of disease similarity based on disease-microbe association data. MicroPattern first grouped microbes into different sets based on the associated diseases and the colonized positions. Then, for a given list of microbes, MicroPattern performed enrichment analysis of the given microbes on all of the microbe sets. Moreover, using MicroPattern, we can also calculate disease similarity based on the shared microbe associations. Finally, we confirmed the accuracy and usefulness of MicroPattern by applying it to the changed microbes under the animal-based diet condition. MicroPattern is freely available at http://www.cuilab.cn/micropattern. PMID:28071710

  14. New evidence of microbe origin for ferromanganese nodules from the East Pacific deep sea floor

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Using a fluorescence microscope and EPMA,abundant microbe "bodies" and clear microbic fluorescent microstructure are determined in the ferromanganese nodules recently collected from the East Pacific deep sea floor.The microbic fluorescent structure shows a close relation to the formation of the ferromanganese nodules.According to their morphological features,the microbes are classified into two types:one is named clumpy microbe,which takes a bar-shaped manganese mineral as a pillar and grows like fasciculate coral,resulting in irregular cauliflorate nodules with rough surfaces; the other is called filamentous microbe,which grows in very thin arcuate and/or concentric circular laminae composed of a microbe layer and a metal (manganese and iron)-rich layer,leading to potato-shaped nodules with relatively smooth surfaces.It also can be seen that the two types of microbes are intergrown together,resulting in nodules complicated in compositions and shapes.

  15. New evidence of microbe origin for ferromanganese nodules from the East Pacific deep sea floor

    Institute of Scientific and Technical Information of China (English)

    胡文宣; 周怀阳; 顾连兴; 张文兰; 陆现彩; 符琦; 潘建明; 张海生

    2000-01-01

    Using a fluorescence microscope and EPMA, abundant microbe "bodies" and clear mi-crobic fluorescent microstructure are determined in the ferromanganese nodules recently collected from the East Pacific deep sea floor. The microbic fluorescent structure shows a close relation to the formation of the ferromanganese nodules. According to their morphological features, the microbes are classified into two types: one is named clumpy microbe, which takes a bar-shaped manganese mineral as a pillar and grows like fasciculate coral, resulting in irregular cauliflorate nodules with rough surfaces; the other is called filamentous microbe, which grows in very thin arcuate and/or concentric circular laminae composed of a microbe layer and a metal (manganese and iron)-rich layer, leading to potato-shaped nodules with relatively smooth surfaces. It also can be seen that the two types of microbes are intergrown together, resulting in nodules complicated in compositions and shapes.

  16. Metagenomic analysis of Atriplex microbiomes: Investigating Plant-microbe interactions that enhance adaptation to extreme habitats

    Science.gov (United States)

    Cryptic symbiotic microbes influence host adaptation by improving nutrient uptake or stress tolerance. Current technologies for increasing plant productivity, whether for food and fuel production or for restoration and remediation, often utilize approaches that bypass, rather than leverage, microb...

  17. Networking in microbes: conjugative elements and plasmids in the genus Alteromonas.

    Science.gov (United States)

    López-Pérez, Mario; Ramon-Marco, Nieves; Rodriguez-Valera, Francisco

    2017-01-05

    To develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time. We have found nine different plasmids of sizes ranging from 85 to 600 Kb, most of them were found in a single strain. Networks of gene similarity could be established among six of the plasmids that were also connected with another cluster of plasmids found in Shewanella strains. The cargo genes found in these plasmids included cassettes found before in chromosome flexible genomic islands of Alteromonas strains. We describe also the plasmids pAMCP48-600 and pAMCP49-600, the largest found in Alteromonas thus far (ca. 600 Kb) and containing all the hallmarks to be classified as chromids. We found in them some housekeeping genes and a cluster that code for an exocellular polysaccharide. They could represent the transport vectors for the previously described replacement flexible genomic islands. Integrative and conjugative elements (ICEs) were more common than plasmids and showed similar patterns of variation with cargo genes coding for components of additive flexible genomic islands. A nearly identical ICE was found in A. mediterranea MED64 and Vibrio cholera AHV1003 isolated from a human pathogen, indicating the potential exchange of these genes across phylogenetic distances exceeding the family threshold. We have seen evidence of how CEs can be vectors to transfer gene cassettes acquired in the chromosomal flexible genomic islands, both of the additive and replacement kind. These CEs showed evidence of how genetic material is exchanged among members of the same species but also

  18. Nanodesign: some basic questions

    CERN Document Server

    Schommers, Wolfram

    2013-01-01

    There is no doubt that nanoscience will be the dominant direction for technology in this century, and that this science will influence our lives to a large extent as well as open completely new perspectives on all scientific and technological disciplines. To be able to produce optimal nanosystems with tailor-made properties, it is necessary to analyze and construct such systems in advance by adequate theoretical and computational methods. Since we work in nanoscience and nanotechnology at the ultimate level, we have to apply the basic laws of physics. What methods and tools are relevant here? The book gives an answer to this question. The background of the theoretical methods and tools is critically discussed, and also the world view on which these physical laws are based. Such a debate is not only of academic interest but is of highly general concern, and this is because we constantly move in nanoscience and nanotechnology between two extreme poles, between infinite life and total destruction . On the one ...

  19. [Genomics and functional genomics in microbiology].

    Science.gov (United States)

    Encarnación-Guevara, Sergio

    2006-01-01

    Functional genomics is changing our understanding of biology and changing our approach to biological research. It brings about concerted, high-throughput genetics with analyses of gene transcripts, proteins, and metabolites to answer the ultimate question posed by all genome-sequencing projects: what is the biological function of each and every gene? Functional genomics is stimulating a change in the research paradigm away from the analysis of single genes, proteins, or metabolites towards the analysis of each of these parameters on a global scale. By identifying and measuring several, if not the entire, molecular group of actors that take part in a given biological process, functional genomics offers the panorama of obtaining a truly holistic representation of life. Functional genomics methods are defined by high-throughput methods which are, not necessarily hypothesis-dependent. They offer insights into mRNA expression, protein expression, protein localization, and protein interactions and may cast light on the flow of information within signaling pathways. At its beginning, biology involved observing nature and experimenting on its isolated parts. Genomic research now generates new types of complex observational data derived from nature. This review describes the tools that are currently being used for functional genomics work and considers the impact that this new discipline on microbiology research.

  20. Evolutionary adaptation in three-way interactions between plants, microbes and arthropods

    NARCIS (Netherlands)

    Biere, A.; Tack, A.J.M.

    2013-01-01

    Evolutionary adaptations in interactions between plants, microbes and arthropods are generally studied in interactions that involve only two of these groups, that is, plants and microbes, plants and arthropods or arthropods and microbes. We review the accumulating evidence from a wide variety of

  1. Intracellular plant microbe associations: secretory pathways and the formation of perimicrobial compartments

    NARCIS (Netherlands)

    Ivanov, S.E.; Fedorova, E.; Bisseling, T.

    2010-01-01

    Plants can establish intracellular interactions with symbiotic as well as pathogenic microbes. Such intracellular accommodation of microbes always involves the formation of a host membrane compartment - the interface between the cytoplasm of the host and the microbe. These are the so-called perimicr

  2. Between two fern genomes.

    Science.gov (United States)

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.

  3. Safety assessment of sFat-1 transgenic pigs by detecting their co-habitant microbe in intestinal tract.

    Science.gov (United States)

    Tang, Maoxue; Zheng, Xinmin; Cheng, Wenke; Jin, Erhui; Chen, Hongxing; Yang, Shulin; Cui, Wentao; Li, Kui

    2011-08-01

    Transgenic pigs containing sFat-1 (synthesized fatty acid desaturase-1) gene were produced by DNA microinjection. The meat of these pigs contain ω-3 unsaturated fatty acid which is beneficial to the health of human being. The aim of this study is to assess the effects of expression of sFat-1 in pig on the health of animal themselves and on the safety of environment from the angle of the changes in microbe population of pig intestinal tract. Four F1 male semi-sibling of sFat-1 transgenic pigs and four F1 female semi-sibling of sFat-1 transgenic pigs were used as experimental animals, together with their none transgenic siblings as control animals. For inspection of any change in populations of microbial flora in various parts of intestinal tract and feces of sFat-1 transgenic pigs total aerobe, total anaerobe, main beneficial bacteria and main harmful bacteria were cultured and analyzed. At the same time foreign gene drift was assessed by PCR amplifying foreign fragment in samples of total aerobe and total anaerobe. Results indicated that in comparison with control pig microbe population of various species in different parts of intestinal tract and feces of sFat-1 transgenic pig remained unchanged and foreign gene sequence could not be detected in DNA of total aerobe and total anaerobe. In conclusion, the data of this study suggest that microbe population in intestinal tract and feces of transgenic pig was not influenced by the expression of transferred foreign gene sFat-1 and also foreign gene drifting from animal genome to microbial genome must be a rare incident.

  4. On genomics, kin, and privacy.

    Science.gov (United States)

    Telenti, Amalio; Ayday, Erman; Hubaux, Jean Pierre

    2014-01-01

    The storage of greater numbers of exomes or genomes raises the question of loss of privacy for the individual and for families if genomic data are not properly protected. Access to genome data may result from a personal decision to disclose, or from gaps in protection. In either case, revealing genome data has consequences beyond the individual, as it compromises the privacy of family members. Increasing availability of genome data linked or linkable to metadata through online social networks and services adds one additional layer of complexity to the protection of genome privacy.  The field of computer science and information technology offers solutions to secure genomic data so that individuals, medical personnel or researchers can access only the subset of genomic information required for healthcare or dedicated studies.

  5. Questioning Strategies of English Teachers

    Institute of Scientific and Technical Information of China (English)

    李梅

    2014-01-01

    AMY.B.M.TSUI thinks that most of the interactive learning starts with the teachers ’questioning. Richard and Lock-art (1994) think that the proper questioning can help the students to acquire the second language. Jin Chuanbao ( 1997) even thinks that the questioning process of the teachers should become the core of the class. Though almost all of the teachers are ques-tioning, they know little about the questioning strategies. In this case, it is urgent to study this subject. The present study reveals some problems of four teachers’questioning strategies in Junior Middle School. I hope some helpful ideas can be found in the thesis.

  6. A question of authority

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, Earl W.(BATTELLE (PACIFIC NW LAB))

    2003-10-15

    A Question of Authority. This article deals with a certain scenario and several reviewers are to give their opinion. This one is in regards to - Suspending an IACUC approved animal use activity is about the last thing a research institution wants to do. Consider the predicament that the Great Eastern University IACUC faced when Dr. Janet Jenkins, the Attending Veterinarian, suspended all animal use activity on an approved protocol of Dr. Roy Maslo. Jenkins had the IACUCs authority to temporarily suspend a protocol, subject to review by a quorum of the full committee. She alleged that Maslo used mice from his breeding colony, not purchased rats, to begin a new study. Jenkins saw Maslos technicians bringing mouse cages to a procedure room and setting up for a minor survival surgery. She asked them to wait until she clarified things as she felt confident that the protocol called for rats. She called Maslo and asked him if the study had been approved for mice, to which he responded affirmatively. Still not feeling quite assured, she went to her office, reviewed the protocol, and found only rat studies described. She also called the IACUC office to see if there were any approved amendments which she may not have received, and was told that there were none. By the time she returned, one procedure was completed. Understandably upset, she informed the technicians and Maslo that any further activity on the protocol was suspended until the issue was resolved. Jenkins informed the IACUC chairman who in turned called an emergency meeting of the committee.

  7. Endophytic and Epiphytic Microbes as Sources of Bioactive Agents

    Directory of Open Access Journals (Sweden)

    David J. Newman

    2015-05-01

    Full Text Available Beginning with the report by Stierle and Strobel in 1993 on taxol(R production by an endophytic fungus 1, it is possible that a number of the agents now used as leads to treatments of diseases in man, are not produced by the plant or invertebrate host from which they were first isolated and identified.They are probably the product of a microbe in, on or around the macroorganism. At times there is an intricate dance between a precursor produced by a microbe, and interactions within the macroorganism, or in certain cases, a fungus, that ends up with the production of a novel agent that has potential as a treatment for a human disease. This report will give examples from insects, plants and marine invertebrates.

  8. Endophytic and Epiphytic Microbes as ``Sources'' of Bioactive Agents

    Science.gov (United States)

    Newman, David; Cragg, Gordon

    2015-05-01

    Beginning with the report by Stierle and Strobel in 1993 on taxol(R) production by an endophytic fungus 1, it is possible that a number of the agents now used as leads to treatments of diseases in man, are not produced by the plant or invertebrate host from which they were first isolated and identified.They are probably the product of a microbe in, on or around the macroorganism. At times there is an intricate “dance” between a precursor produced by a microbe, and interactions within the macroorganism, or in certain cases, a fungus, that ends up with the production of a novel agent that has potential as a treatment for a human disease. This report will give examples from insects, plants and marine invertebrates.

  9. Accumulator-Based Deep-Sea Microbe Gastight Sampling Technique

    Institute of Scientific and Technical Information of China (English)

    HUANG Zhong-hua; LIU Shao-jun; JIN Bo

    2006-01-01

    The accumulator is used as a pressure compensation device to realize deep-sea microbe gastight sampling. Four key states of the accumulator are proposed to describe the pressure compensation process and a corresponding mathematical model is established to investigate the relationship between the results of pressure compensation and the parameters of the accumulator. Simulation results show that during the falling process of the sampler, the accumulator's real opening pressure is greater than its precharge pressure; when the sampling depth is 6000 m and the accumulator's precharge pressure is less than 30 MPa, to increase the accumulator's precharge pressure can improve pressure compensation results obviously. Laboratory experiments at 60 MPa show that the accumulator is an effective and reliable pressure compensation device for deep-sea microbe samplers. The success in sea trial at a depth of 2000 m in the South China Sea shows that the mathematical model and laboratory experiment results are reliable.

  10. Exploring laser-guided metal deposition through a microbe metabolite

    OpenAIRE

    2009-01-01

    Purpose: The purpose of the paper is to describe exploring laser-guided metal deposition through a microbe metabolite.Design/methodology/approach: A maskless micro-fabrication of laser-guided deposition process through the metabolite of Acidophilic bacteria Thiobacillus ferrooxidans (T.f.) is explored.Findings: The authors have conducted an analysis of the metal deposition process using the point thermal-source of the Nd:YAG laser through the metabolite of Acidophilic bacteria Thiobacillus. A...

  11. Drone Transport of Microbes in Blood and Sputum Laboratory Specimens.

    Science.gov (United States)

    Amukele, Timothy K; Street, Jeff; Carroll, Karen; Miller, Heather; Zhang, Sean X

    2016-10-01

    Unmanned aerial vehicles (UAVs) could potentially be used to transport microbiological specimens. To examine the impact of UAVs on microbiological specimens, blood and sputum culture specimens were seeded with usual pathogens and flown in a UAV for 30 ± 2 min. Times to recovery, colony counts, morphologies, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identifications of the flown and stationary specimens were similar for all microbes studied.

  12. Microbial electrosynthesis: understanding and strengthening microbe-electrode interactions

    DEFF Research Database (Denmark)

    Tremblay, Pier-Luc; Höglund, Daniel; Ammam, Fariza;

    2014-01-01

    Powering microbes with electrical energy to produce valuable chemicals such as biofuels has recently gained traction as a biosustainable production strategy for the reduction of our dependence to oil. Microbial electrosynthesis (MES) is one of the few bioelectrochemical approaches developed......, and a general lack of knowledge about electron transfer mechanisms have been the main obstacles to MES commercialization todate. Developing genetic systems for known electroautotrophs, screening for better MES chassis organisms and superior electrochemical hardware, establishing alternative MES processes...

  13. Antibiotic Resistance Questions and Answers

    Science.gov (United States)

    ... on the Farm Get Smart About Antibiotics Week Antibiotic Resistance Questions and Answers Language: English (US) Español ( ... Many ear infections Top of Page Questions about Antibiotic Resistance Examples of How Antibiotic Resistance Spreads Click for ...

  14. Stimulated Growth of Aerobic Microbes Using Calcium Peroxide

    Institute of Scientific and Technical Information of China (English)

    LIU Shejiang; LI Mujin; JIANG Bin; LI Xingang

    2006-01-01

    With continuous and slow oxygen-release characteristic,calcium peroxide (CaO2) has been a new source of supplying oxygen for aerobic microbes in bioremediation of contaminated groundwater.Batch experiments were conducted to evaluate the oxygen-release rate of CaO2 reacting with water,the regulation of high pH,as well as the growth of mixed aerobic microbes in the medium containing CaO2.The results show that the oxygen-release process of CaO2 comprises three phases.In the first phase,dissolved oxygen levels of water increased sharply,and average oxygen-release rates increased as the adding weight of CaO2 increased.However,the rates almost ly.As the necessary components of medium,potassium dihydrogen phosphate (KH2PO4) and ammonium sulphate ((NH4)2SO4) at a certain ratio could regulate pH caused by CaO2 from 12.1 to the range of 6.5-8.5,which is helpful for microbial growth.In addition,diauxic growth curve observed in the medium containing CaO2 suggested that the growth of mixed aerobic microbes could be stimulated by the addition of CaO2.

  15. Single microbe trap and release in sub-microfluidics

    Energy Technology Data Exchange (ETDEWEB)

    Vasdekis, Andreas E. [Swiss Federal Inst. of Technology, Lausanne (Switzerland); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2013-02-08

    Lab-on-a-chip systems have substantially impacted the way life-sciences are explored; life on earth, however, comprises mostly of microbes, which due to their sub-micron dimensions and high mobility are more challenging to dynamically manipulate on-a-chip. To address this challenge, we developed a high resolution microfluidic system (submicrofluidics) fabricated by direct electron beam lithography that is capable of trapping single microbes and releasing them upon demand. The fabrication method enabled the integration of sub-micron indentations (400 nm) with millimetre-scale fluidic channels rapidly in a single processing step. The larger channels deliver the cell suspension and reagents, while the sub-micron indentations immobilize the cells by locally increasing the hydrodynamic resistance. By volume exclusion, single cell trapping was possible in this system without any surface treatment. By increasing the flow rate, the microbes overcome the trap barrier and pass through the narrow indentation without undergoing lysis with kinetics that depend on their size. The fabrication method and its performance are described, along with microbial characterisations using E. coli.

  16. Fossil genes and microbes in the oldest ice on earth.

    Science.gov (United States)

    Bidle, Kay D; Lee, Sanghoon; Marchant, David R; Falkowski, Paul G

    2007-08-14

    Although the vast majority of ice that formed on the Antarctic continent over the past 34 million years has been lost to the oceans, pockets of ancient ice persist in the Dry Valleys of the Transantarctic Mountains. Here we report on the potential metabolic activity of microbes and the state of community DNA in ice derived from Mullins and upper Beacon Valleys. The minimum age of the former is 100 ka, whereas that of the latter is approximately 8 Ma, making it the oldest known ice on Earth. In both samples, radiolabeled substrates were incorporated into macromolecules, and microbes grew in nutrient-enriched meltwaters, but metabolic activity and cell viability were critically compromised with age. Although a 16S rDNA-based community reconstruction suggested relatively low bacterial sequence diversity in both ice samples, metagenomic analyses of community DNA revealed many diverse orthologs to extant metabolic genes. Analyses of five ice samples, spanning the last 8 million years in this region, demonstrated an exponential decline in the average community DNA size with a half-life of approximately 1.1 million years, thereby constraining the geological preservation of microbes in icy environments and the possible exchange of genetic material to the oceans.

  17. Insights into the Roles of Gut Microbes in Obesity

    Directory of Open Access Journals (Sweden)

    Yolanda Sanz

    2008-01-01

    Full Text Available Obesity is a major public health issue as it enhances the risk of suffering several chronic diseases of increasing prevalence. Obesity results from an imbalance between energy intake and expenditure, associated with a chronic low-grade inflammation. Gut microbes are considered to contribute to body weight regulation and related disorders by influencing metabolic and immune host functions. The gut microbiota as a whole improves the host's ability to extract and store energy from the diet leading to body weight gain, while specific commensal microbes seem to exert beneficial effects on bile salt, lipoprotein, and cholesterol metabolism. The gut microbiota and some probiotics also regulate immune functions, protecting the host form infections and chronic inflammation. In contrast, dysbiosis and endotoxaemia may be inflammatory factors responsible for developing insulin resistance and body weight gain. In the light of the link between the gut microbiota, metabolism, and immunity, the use of dietary strategies to modulate microbiota composition is likely to be effective in controlling metabolic disorders. Although so far only a few preclinical and clinical trials have demonstrated the effects of specific gut microbes and prebiotics on biological markers of these disorders, the findings indicate that advances in this field could be of value in the struggle against obesity and its associated-metabolic disorders.

  18. Amino acids in the rhizosphere: from plants to microbes.

    Science.gov (United States)

    Moe, Luke A

    2013-09-01

    Often referred to as the "building blocks of proteins", the 20 canonical proteinogenic amino acids are ubiquitous in biological systems as the functional units in proteins. Sometimes overlooked are their varying additional roles that include serving as metabolic intermediaries, playing structural roles in bioactive natural products, acting as cosubstrates in enzymatic transformations, and as key regulators of cellular physiology. Amino acids can also serve as biological sources of both carbon and nitrogen and are found in the rhizosphere as a result of lysis or cellular efflux from plants and microbes and proteolysis of existing peptides. While both plants and microbes apparently prefer to take up nitrogen in its inorganic form, their ability to take up and use amino acids may confer a selective advantage in certain environments where organic nitrogen is abundant. Further, certain amino acids (e.g., glutamate and proline) and their betaines (e.g., glycine betaine) serve as compatible solutes necessary for osmoregulation in plants and microbes and can undergo rapid cellular flux. This ability is of particular importance in an ecological niche such as the rhizosphere, which is prone to significant variations in solute concentrations. Amino acids are also shown to alter key phenotypes related to plant root growth and microbial colonization, symbiotic interactions, and pathogenesis in the rhizosphere. This review will focus on the sources, transport mechanisms, and potential roles of the 20 canonical proteinogenic amino acids in the rhizosphere.

  19. Plant root-microbe communication in shaping root microbiomes.

    Science.gov (United States)

    Lareen, Andrew; Burton, Frances; Schäfer, Patrick

    2016-04-01

    A growing body of research is highlighting the impacts root-associated microbial communities can have on plant health and development. These impacts can include changes in yield quantity and quality, timing of key developmental stages and tolerance of biotic and abiotic stresses. With such a range of effects it is clear that understanding the factors that contribute to a plant-beneficial root microbiome may prove advantageous. Increasing demands for food by a growing human population increases the importance and urgency of understanding how microbiomes may be exploited to increase crop yields and reduce losses caused by disease. In addition, climate change effects may require novel approaches to overcoming abiotic stresses such as drought and salinity as well as new emerging diseases. This review discusses current knowledge on the formation and maintenance of root-associated microbial communities and plant-microbe interactions with a particular emphasis on the effect of microbe-microbe interactions on the shape of microbial communities at the root surface. Further, we discuss the potential for root microbiome modification to benefit agriculture and food production.

  20. Microbes as targets and mediators of allelopathy in plants.

    Science.gov (United States)

    Cipollini, Don; Rigsby, Chad M; Barto, E Kathryn

    2012-06-01

    Studies of allelopathy in terrestrial systems have experienced tremendous growth as interest has risen in describing biochemical mechanisms responsible for structuring plant communities, determining agricultural and forest productivity, and explaining invasive behaviors in introduced organisms. While early criticisms of allelopathy involved issues with allelochemical production, stability, and degradation in soils, an understanding of the chemical ecology of soils and its microbial inhabitants has been increasingly incorporated in studies of allelopathy, and recognized as an essential predictor of the outcome of allelopathic interactions between plants. Microbes can mediate interactions in a number of ways with both positive and negative outcomes for surrounding plants and plant communities. In this review, we examine cases where soil microbes are the target of allelopathic plants leading to indirect effects on competing plants, provide examples where microbes play either a protective effect on plants against allelopathic competitors or enhance allelopathic effects, and we provide examples where soil microbial communities have changed through time in response to allelopathic plants with known or potential effects on plant communities. We focus primarily on interactions involving wild plants in natural systems, using case studies of some of the world's most notorious invasive plants, but we also provide selected examples from agriculturally managed systems. Allelopathic interactions between plants cannot be fully understood without considering microbial participants, and we conclude with suggestions for future research.

  1. The Questions of Liberal Education

    Science.gov (United States)

    Arcilla, Rene V.

    2007-01-01

    There is a certain kind of liberal educator who bases his or her practice on a particular attitude toward the "Big Questions." The questions of fundamental literacy in K-12 education, or of expertise in vocational and professional education, may be just as important, but they are seen as quite different in kind. Indeed, the questions of liberal…

  2. The Hermeneutics of Educational Questioning

    Science.gov (United States)

    Bingham, Charles

    2005-01-01

    This article looks at the practice of educational questioning using the philosophical hermeneutics of Hans-Georg Gadamer. It first looks at questions and statements from a hermeneutic perspective, demonstrating some of the differences and similarities between the two. It then details Gadamer's notion of the "true question", asking whether it is…

  3. Disjunctive questions, intonation, and highlighting

    NARCIS (Netherlands)

    F. Roelofsen; S. van Gool

    2009-01-01

    This paper examines how intonation affects the interpretation of disjunctive questions. The semantic effect of a question is taken to be three-fold. First, it raises an issue. In the tradition of inquisitive semantics, we model this by assuming that a question proposes several possible updates of th

  4. Does Anyone Have Any Questions?

    Science.gov (United States)

    Finkelstein, Judith M.; Ritter, Virginia F.

    The purpose of this study was to determine if answering a child's question with a question produces further analytical questioning by the child. A sample of 80 children in nursery-kindergarten, first, second and third grades (ages ranging from 4-9 years) were divided into two groups. An abstract painting by Kandinsky was shown individually to each…

  5. The Hermeneutics of Educational Questioning

    Science.gov (United States)

    Bingham, Charles

    2005-01-01

    This article looks at the practice of educational questioning using the philosophical hermeneutics of Hans-Georg Gadamer. It first looks at questions and statements from a hermeneutic perspective, demonstrating some of the differences and similarities between the two. It then details Gadamer's notion of the "true question", asking whether it is…

  6. Children Who Question Their Heterosexuality

    Science.gov (United States)

    Carver, Priscilla R.; Egan, Susan K.; Perry, David G.

    2004-01-01

    Many gay, lesbian, and bisexual adults report a period of childhood sexual questioning--an uneasy questioning of their heterosexuality brought on by same-sex attractions and motivating same-sex sexual exploration. This article evaluates hypotheses about the correlates, causes, and consequences of childhood sexual questioning. Participants were 182…

  7. Draft Genome Sequence of Enterobacter ludwigii NCR3, a Heavy Metal–Resistant Rhizobacterium

    Science.gov (United States)

    Egidi, Eleonora; Wood, Jennifer L.; Aracic, Sanja; Kannan, Ruban; McDonald, Lachlan; Bell, Carolyn A.; Fox, Edward M.; Liu, Wuxing

    2016-01-01

    We report here the draft genome of Enterobacter ludwigii NCR3, a Gram-negative bacterium isolated from the Carpobrotus rossii (Haw.) Schwantes rhizosphere. The analysis of the ~4.8-Mb draft genome shows that this strain harbors several genes associated with heavy metal resistance and plant growth–promoting activity, suggesting its potential application in microbe-assisted phytoremediation.

  8. A metasystem of framework model organisms to study emergence of new host-microbe adaptations.

    Directory of Open Access Journals (Sweden)

    Suresh Gopalan

    Full Text Available An unintended consequence of global industrialization and associated societal rearrangements is new interactions of microbes and potential hosts (especially mammals and plants, providing an opportunity for the rapid emergence of host-microbe adaptation and eventual establishment of new microbe-related diseases. We describe a new model system comprising the model plant Arabidopsis thaliana and several microbes, each representing different modes of interaction, to study such "maladaptations". The model microbes include human and agricultural pathogens and microbes that are commonly considered innocuous. The system has a large knowledge base corresponding to each component organism and is amenable to high-throughput automation assisted perturbation screens for identifying components that modulate host-pathogen interactions. This would aid in the study of emergence and progression of host-microbe maladaptations in a controlled environment.

  9. Arts and Techniques of Questioning

    Institute of Scientific and Technical Information of China (English)

    管楠

    2012-01-01

      Most learners learn English from teachers in classrooms, therefore, classroom instruction is very important. However, teachers’questioning plays a very significant part in classroom teaching. It is not only an important part of classroom interaction but also an effective way of learning second language as wel. On the one hand, it is through question and answer exchange that teachers interactwithstudents.Onthe other hand, it isalsothroughinteractionwiththeirteachersand peers that ESLlearners learn the target language. Teachers’ aims of questioning, question types, teachers’modification of questions, the wait-time, the feedback and the assessment providedby teacherswil affectclassroom interaction.

  10. Frequently Asked Questions about Genetic and Genomic Science

    Science.gov (United States)

    ... acute lymphoblastic leukemia [cancer.gov] is stem cell transplantation therapy. There has been much debate nationally about the use of embryonic stem cells, especially about the creation of human embryos for use in experiments. In 1995, Congress enacted ...

  11. Exploring Arabidopsis thaliana Root Endophytes via Single-Cell Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Lundberg, Derek; Woyke, Tanja; Tringe, Susannah; Dangl, Jeff

    2014-03-19

    Land plants grow in association with microbial communities both on their surfaces and inside the plant (endophytes). The relationships between microbes and their host can vary from pathogenic to mutualistic. Colonization of the endophyte compartment occurs in the presence of a sophisticated plant immune system, implying finely tuned discrimination of pathogens from mutualists and commensals. Despite the importance of the microbiome to the plant, relatively little is known about the specific interactions between plants and microbes, especially in the case of endophytes. The vast majority of microbes have not been grown in the lab, and thus one of the few ways of studying them is by examining their DNA. Although metagenomics is a powerful tool for examining microbial communities, its application to endophyte samples is technically difficult due to the presence of large amounts of host plant DNA in the sample. One method to address these difficulties is single-cell genomics where a single microbial cell is isolated from a sample, lysed, and its genome amplified by multiple displacement amplification (MDA) to produce enough DNA for genome sequencing. This produces a single-cell amplified genome (SAG). We have applied this technology to study the endophytic microbes in Arabidopsis thaliana roots. Extensive 16S gene profiling of the microbial communities in the roots of multiple inbred A. thaliana strains has identified 164 OTUs as being significantly enriched in all the root endophyte samples compared to their presence in bulk soil.

  12. Genomics and marine microbial ecology.

    Science.gov (United States)

    Pedrós-Alió, Carlos

    2006-09-01

    Genomics has brought about a revolution in all fields of biology. Before the development of microbial ecology in the 1970s, microbes were not even considered in marine ecological studies. Today we know that half of the total primary production of the planet must be credited to microorganisms. This and other discoveries have changed dramatically the perspective and the focus of marine microbial ecology. The application of genomics-based approaches has provided new challenges and has allowed the discovery of novel functions, an appreciation of the great diversity of microorganisms, and the introduction of controversial ideas regarding the concepts of species, genome, and niche. Nevertheless, thorough knowledge of the traditional disciplines of biology is necessary to explore the possibilities arising from these new insights. This work reviews the different genomic techniques that can be applied to marine microbial ecology, including both sequencing of the complete genomes of microorganisms and metagenomics, which, in turn, can be complemented with the study of mRNAs (transcriptomics) and proteins (proteomics). The example of proteorhodopsin illustrates the type of information that can be gained from these approaches. A genomics perspective constitutes a map that will allow microbiologists to focus their research on potentially more productive aspects.

  13. Can multiple-choice questions simulate free-response questions?

    CERN Document Server

    Lin, Shih-Yin

    2016-01-01

    We discuss a study to evaluate the extent to which free-response questions could be approximated by multiple-choice equivalents. Two carefully designed research-based multiple-choice questions were transformed into a free-response format and administered on the final exam in a calculus-based introductory physics course. The original multiple-choice questions were administered in another similar introductory physics course on final exam. Findings suggest that carefully designed multiple-choice questions can reflect the relative performance of the free-response questions while maintaining the benefits of ease of grading and quantitative analysis, especially if the different choices in the multiple-choice questions are weighted to reflect the different levels of understanding that students display.

  14. DNA Repair and Genome Maintenance in Bacillus subtilis

    OpenAIRE

    2012-01-01

    Summary: From microbes to multicellular eukaryotic organisms, all cells contain pathways responsible for genome maintenance. DNA replication allows for the faithful duplication of the genome, whereas DNA repair pathways preserve DNA integrity in response to damage originating from endogenous and exogenous sources. The basic pathways important for DNA replication and repair are often conserved throughout biology. In bacteria, high-fidelity repair is balanced with low-fidelity repair and mutage...

  15. Microbes in thawing permafrost: the unknown variable in the climate change equation

    Energy Technology Data Exchange (ETDEWEB)

    Graham, David E [ORNL; Wallenstein, Matthew D [Colorado State University, Fort Collins; Vishnivetskaya, T. [University of Tennessee, Knoxville (UTK); Waldrop, Mark P. [U.S. Geological Survey, Menlo Park, CA; Phelps, Tommy Joe [ORNL; Pfiffner, Susan M. [University of Tennessee, Knoxville (UTK); Onstott, T. C. [Princeton University; Whyte, Lyle [McGill University, Montreal, Quebec; Rivkina, Elizaveta [Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences; Gilichinsky, David A [Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences; Elias, Dwayne A [ORNL; Mackelprang, Rachel [U.S. Department of Energy, Joint Genome Institute; Verberkmoes, Nathan C [ORNL; Hettich, Robert {Bob} L [ORNL; Wagner, Dirk [Alfred Wegener Institute for Polar and Marine Research, Potsdam, Germany; Wullschleger, Stan D [ORNL; Jansson, Janet [Lawrence Berkeley National Laboratory (LBNL)

    2012-01-01

    Considering that 25% of Earth s terrestrial surface is underlain by permafrost (ground that has been continuously frozen for at least 2 years), our understanding of the diversity of microbial life in this extreme habitat is surprisingly limited. Taking into account the total mass of perennially frozen sediment (up to several hundred meters deep), permafrost contains a huge amount of buried, ancient organic carbon (Tarnocai et al., 2009). In addition, permafrost is warming rapidly in response to global climate change (Romanovsky et al., 2010), potentially leading to widespread thaw and a larger, seasonally thawed soil active layer. This concern has prompted the question: will permafrost thawing lead to the release of massive amounts of carbon dioxide (CO2) and methane (CH4) into the atmosphere? This question can only be answered by understanding how the microbes residing in permafrost will respond to thaw, through processes such as respiration, fermentation, methanogenesis and CH4 oxidation (Schuur et al., 2009). Predicting future carbon fluxes is complicated by the diversity of permafrost environments, ranging from high mountains, southern boreal forests, frozen peatlands and Pleistocene ice complexes (yedoma) up to several hundred meters deep, which vary widely in soil composition, soil organic matter (SOM) quality, hydrology and thermal regimes (Figure 1). Permafrost degradation can occur in many forms: thaw can progress downward from seasonally-thawed active layer soils in warming climates or laterally because of changes in surface or groundwater flow paths (Grosse et al., 2011). Permafrost degradation can sometimes lead to dramatic changes in ecosystem structure and function

  16. Genomic Data Commons and Genomic Cloud Pilots - Google Hangout

    Science.gov (United States)

    Join us for a live, moderated discussion about two NCI efforts to expand access to cancer genomics data: the Genomic Data Commons and Genomic Cloud Pilots. NCI subject matters experts will include Louis M. Staudt, M.D., Ph.D., Director Center for Cancer Genomics, Warren Kibbe, Ph.D., Director, NCI Center for Biomedical Informatics and Information Technology, and moderated by Anthony Kerlavage, Ph.D., Chief, Cancer Informatics Branch, Center for Biomedical Informatics and Information Technology. We welcome your questions before and during the Hangout on Twitter using the hashtag #AskNCI.

  17. Genomic Data Commons and Genomic Cloud Pilots - Google Hangout

    Science.gov (United States)

    Join us for a live, moderated discussion about two NCI efforts to expand access to cancer genomics data: the Genomic Data Commons and Genomic Cloud Pilots. NCI subject matters experts will include Louis M. Staudt, M.D., Ph.D., Director Center for Cancer Genomics, Warren Kibbe, Ph.D., Director, NCI Center for Biomedical Informatics and Information Technology, and moderated by Anthony Kerlavage, Ph.D., Chief, Cancer Informatics Branch, Center for Biomedical Informatics and Information Technology. We welcome your questions before and during the Hangout on Twitter using the hashtag #AskNCI.

  18. The genomics of adaptation.

    Science.gov (United States)

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

  19. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  20. Instance-Based Question Answering

    Science.gov (United States)

    2006-12-01

    included factoid questions grouped around a set of target entities. For example, for the target entity “ Franz Kafka ”, associated questions included: “Where...from Franz Schubert. A year later he did on Dec 5th.”). Depending on the task, an answer extractor may identify very small, factoid candidates which...IWP): Paraphrase Ac- quisition and Applications, 2003. [55] A. Ittycheriah, M. Franz , and S. Roukos. Ibm’s statistical question answering system - trec

  1. [Plant-microbe symbioses as an evolutionary continuum].

    Science.gov (United States)

    Provorov, N A

    2009-01-01

    In spite of enormous taxonomic, structural and functional diversity of plant-microbe interactions, they are characterized by a historical succession which allows us to consider different forms of symbioses as the components of an evolutionary continuum. Their ancestral form is represented by arbuscular mycorrhiza (AM) which originated at the outset of terrestrial flora evolution and constituted a key factor for the land colonization by plants. In the course of AM evolution the plant acquired a basal set of genes for regulating the performance of microbes which colonize the root tissues. Later, these genes were repeatedly reorganized to meet the involvement of novel mutualistic symbionts (N2-fixing bacteria, ectomycorrhizal fungi, endophytes and epiphytes) and pathogens into the symbiotic interactions. Form the microbial side, the evolutionary succession of mutualism and antagonism is restricted to the defensive symbioses formed by plants with the ergot fungi, Clavibacter, Bacillus and Pseudomonas bacteria. Involvement of the similar systems for symbiotic interactions may be related to convergent evolution in the distant microorganisms (adaptation to the conservative host defense/regulatory factors), to molecular mimicry (imitation of the mechanisms of interaction used by the more ancient symbionts) or to the horizontal gene transfer. The hypotheses of the successive substitution of symbionts is suggested to address the relationships between AM and N2-fixing nodular symbioses in dicotyledons plants. AM formation is considered as a source of preadaptations responsible for the substitution of glomalean fungi which occupied the plant symbiotic compartments by the actinomycetes Frankia (in Rosid I plants) which were exchanged for the more competitive root nodule bacteria (in legumes). The development of nutritional symbioses with microbes is considered as an ancestral function of plant roots which were later supplemented or substituted with the function of assimilating

  2. And the next question is powerful questions for sticky moments

    CERN Document Server

    Alexander, Rachel

    2012-01-01

    A very practical and easy to use book of 3,000+ powerful questions, forming part of every coach''s / manager''s toolkit; it enables you to easily find key questions in some of the most distinctive areas of coaching, such as confidence, communications & leadership.

  3. Commonly Asked Questions in Thermodynamics

    CERN Document Server

    Assael, Marc J

    2011-01-01

    Have you ever had a question that keeps persisting and for which you cannot find a clear answer? Is the question seemingly so "simple" that the problem is glossed over in most resources, or skipped entirely? CRC Press/Taylor and Francis is pleased to introduce Commonly Asked Questions in Thermodynamics, the first in a new series of books that address the questions that frequently arise in today's major scientific and technical disciplines. Designed for a wide audience, from students and researchers to practicing professionals in related areas, the books are organized in a user friend

  4. Beneficial microbes affect endogenous mechanisms controlling root development

    Science.gov (United States)

    Verbon, Eline H.; Liberman, Louisa M.

    2016-01-01

    Plants have incredible developmental plasticity, enabling them to respond to a wide range of environmental conditions. Among these conditions is the presence of plant growth-promoting rhizobacteria (PGPR) in the soil. Recent studies show that PGPR affect root growth and development within Arabidopsis thaliana root. These effects lead to dramatic changes in root system architecture, that significantly impact aboveground plant growth. Thus, PGPR may promote shoot growth via their effect on root developmental programs. This review focuses on contextualizing root developmental changes elicited by PGPR in light of our understanding of plant-microbe interactions and root developmental biology. PMID:26875056

  5. Role of microbes in the ecology of marine environment

    Digital Repository Service at National Institute of Oceanography (India)

    Das, A.; DeSouza, M.J.B.D.; LokaBharathi, P.A.

    area of the seabed of the Indian Ocean are most promising for the extraction of strategic metals from them. The next article gives a realistic account of researches on coral reefs in the country. It is really unfortunate that coral research which... in the country who has developed interest on corals and coral reefs is the author of the present article Dr. M.V.M. Wafar. His article is followed by an account on microbes which play a very important ecological role in the marine environment, including...

  6. Metabolic engineering of microbes for oligosaccharide and polysaccharide synthesis

    Directory of Open Access Journals (Sweden)

    Chen Rachel

    2006-07-01

    Full Text Available Abstract Metabolic engineering has recently been embraced as an effective tool for developing whole-cell biocatalysts for oligosaccharide and polysaccharide synthesis. Microbial catalysts now provide a practical means to derive many valuable oligosaccharides, previously inaccessible through other methods, in sufficient quantities to support research and clinical applications. The synthesis process based upon these microbes is scalable as it avoids expensive starting materials. Most impressive is the high product concentrations (up to 188 g/L achieved through microbe-catalyzed synthesis. The overall cost for selected molecules has been brought to a reasonable range (estimated $ 30–50/g. Microbial synthesis of oligosaccharides and polysaccharides is a carbon-intensive and energy-intensive process, presenting some unique challenges in metabolic engineering. Unlike nicotinamide cofactors, the required sugar nucleotides are products of multiple interacting pathways, adding significant complexity to the metabolic engineering effort. Besides the challenge of providing the necessary mammalian-originated glycosyltransferases in active form, an adequate uptake of sugar acceptors can be an issue when another sugar is necessary as a carbon and energy source. These challenges are analyzed, and various strategies used to overcome these difficulties are reviewed in this article. Despite the impressive success of the microbial coupling strategy, there is a need to develop a single strain that can achieve at least the same efficiency. Host selection and the manner with which the synthesis interacts with the central metabolism are two important factors in the design of microbial catalysts. Additionally, unlike in vitro enzymatic synthesis, product degradation and byproduct formation are challenges of whole-cell systems that require additional engineering. A systematic approach that accounts for various and often conflicting requirements of the synthesis holds

  7. Fossil genes and microbes in the oldest ice on Earth

    OpenAIRE

    Bidle, Kay D.; Lee, Sanghoon; Marchant, David R.; Falkowski, Paul G

    2007-01-01

    Although the vast majority of ice that formed on the Antarctic continent over the past 34 million years has been lost to the oceans, pockets of ancient ice persist in the Dry Valleys of the Transantarctic Mountains. Here we report on the potential metabolic activity of microbes and the state of community DNA in ice derived from Mullins and upper Beacon Valleys. The minimum age of the former is 100 ka, whereas that of the latter is ≈8 Ma, making it the oldest known ice on Earth. In both sample...

  8. Applications of Carboxylic Acid Reductases in Oleaginous Microbes

    Energy Technology Data Exchange (ETDEWEB)

    Resch, Michael G.; Linger, Jeffrey; McGeehan, John; Tyo, Keith; Beckham, Gregg

    2016-04-24

    Carboxylic acid reductases (CARs) are recently emerging reductive enzymes for the direct production of aldehydes from biologically-produced carboxylic acids. Recent work has demonstrated that these powerful enzymes are able to reduce a very broad range of volatile- to long-chain fatty acids as well as aromatic acids. Here, we express four CAR enzymes from different fungal origins to test their activity against fatty acids commonly produced in oleaginous microbes. These in vitro results will inform metabolic engineering strategies to conduct mild biological reduction of carboxylic acids in situ, which is conventionally done via hydrotreating catalysis at high temperatures and hydrogen pressures.

  9. Biodegradation of DTP and PET Fiber by Microbe

    Institute of Scientific and Technical Information of China (English)

    张健飞; 王晓春; 巩继贤; 顾振亚

    2003-01-01

    The degradation of diethylene glycol terephthalate (DTP) and polyethylene terephthalate (PET) fiber by microbe was studied.The degree of DTP degradation was determined by High Performance Liquid Chromatography (HPLC) to be more than 90%.The products after degradation of DTP and PET fiber were various.The degradation of DTP can be described by the first-order reaction model.The degradation of PET fiber was found to be little,but surface erosion of PET fiber could be clearly seen from the SEM photographs indicating there occurred some traces of biodegradation on the PET fiber surface.

  10. Questioning Questions: Elementary Teachers' Adaptations of Investigation Questions Across the Inquiry Continuum

    Science.gov (United States)

    Biggers, Mandy

    2017-01-01

    Questioning is a central practice in science classrooms. However, not every question translates into a "good" science investigation. Questions that drive science investigations can be provided by many sources including the teacher, the curriculum, or the student. The variations in the source of investigation questions were explored in this study. A dataset of 120 elementary science classroom videos and associated lesson plans from 40 elementary teachers (K-5) across 21 elementary school campuses were scored on an instrument measuring the amount of teacher-direction or student-direction of the lessons' investigation questions. Results indicated that the investigation questions were overwhelmingly teacher directed in nature, with no opportunities for students to develop their own questions for investigation. This study has implications for researchers and practitioners alike, calling attention to the teacher-directed nature of investigation questions in existing science curriculum materials, and the need for teacher training in instructional strategies to adapt their existing curriculum materials across the continuum of teacher-directed and student-directed investigation questions. Teachers need strategies for adapting the teacher-directed questions provided in their existing curriculum materials in order to allow students the opportunity to engage in this essential scientific practice.

  11. Burkholderia xernovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

    Energy Technology Data Exchange (ETDEWEB)

    Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Denef, Vincent [University of California, Berkeley; Konstantinidis, Konstantinos T [Michigan State University, East Lansing; Vergez, Lisa [Lawrence Livermore National Laboratory (LLNL); Agullo, Loreine [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Reyes, Valeria Latorre [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Hauser, Loren John [ORNL; Cordova, Macarena [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Gomez, Luis [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Gonzalez, Myriam [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Land, Miriam L [ORNL; Lao, Victoria [Lawrence Livermore National Laboratory (LLNL); Larimer, Frank W [ORNL; LiPuma, John J [University of Michigan; Mahenthiralingam, Eshwar [Cardiff University, Wales; Malfatti, Stephanie [Lawrence Livermore National Laboratory (LLNL); Marx, Christopher J [Harvard University; Parnell, J Jacob [Michigan State University, East Lansing; Ramette, Alban [Michigan State University, East Lansing; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Seeger, Michael [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Smith, Daryl [University of British Columbia, Vancouver; Spilker, Theodore [University of Michigan; Sul, Woo Jun [Michigan State University, East Lansing; Tsoi, Tamara V [Michigan State University, East Lansing; Zhulin, Igor B [University of Tennessee, Knoxville (UTK) & Oak Ridge National Laboratory (ORNL); Tiedje, James M. [Michigan State University, East Lansing

    2006-01-01

    Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven 'central aromatic' and twenty 'peripheral aromatic' pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.

  12. The relaxing ori-ter balance of Mycoplasma genomes

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Mycoplasma are wall-less bacteria with small genomes, which are thought to have resulted from massive genome reductive processes, during which the ori-ter balance may be disrupted. For technical difficulties, ori and ter have been located only in a few Mycoplasma strains. Using the Z curve method, we were able to locate turning points on the Mycoplasma genomes, with the minimum and maximum points co-locating with ori or ter in the reference genomes. Assuming Z curve correctly located ori and ter, we calculated the distances from ori to ter in both directions on the circular genome and calculated the ori-ter balance status. The Mycoplasma genomes were not balanced, possibly as a result of close association of Mycoplasma with hosts, where there would be no other microbes for Mycoplasma to compete with for nutrients, so fastest possible growth related to balanced genomes might not be needed by Mycoplasma, leading to a relaxing ori-ter balance.

  13. Effect Of Spaceflight On Microbial Gene Expression And Virulence: Preliminary Results From Microbe Payload Flown On-Board STS-115

    Science.gov (United States)

    Wilson, J. W.; HonerzuBentrup, K,; Schurr, M. J.; Buchanan, K.; Morici, L.; Hammond, T.; Allen, P.; Baker, C.; Ott, C. M.; Nelman-Gonzalez M.; Schurr, J. R.; Pierson, D. L.; Stodieck, L.; Hing, S.; Hammond, T.; Allen, P.; Baker, C.; Parra, M.; Dumars, P.; Stefanyshyn-Piper, H. M.; Nickerson, C. A.

    2007-01-01

    Human presence in space, whether permanent or temporary, is accompanied by the presence of microbes. However, the extent of microbial changes in response to spaceflight conditions and the corresponding changes to infectious disease risk is unclear. Previous studies have indicated that spaceflight weakens the immune system in humans and animals. In addition, preflight and in-flight monitoring of the International Space Station (ISS) and other spacecraft indicates the presence of opportunistic pathogens and the potential of obligate pathogens. Altered antibiotic resistance of microbes in flight has also been shown. As astronauts and cosmonauts live for longer periods in a closed environment, especially one using recycled water and air, there is an increased risk to crewmembers of infectious disease events occurring in-flight. Therefore, understanding how the space environment affects microorganisms and their disease potential is critically important for spaceflight missions and requires further study. The goal of this flight experiment, operationally called MICROBE, is to utilize three model microbial pathogens, Salmonella typhimurium, Pseudomonas aeruginosa, and Candida albicans to examine the global effects of spaceflight on microbial gene expression and virulence attributes. Specifically, the aims are (1) to perform microarray-mediated gene expression profiling of S. typhimurium, P. aeruginosa, and C. albicans, in response to spaceflight in comparison to ground controls and (2) to determine the effect of spaceflight on the virulence potential of these microorganisms immediately following their return from spaceflight using murine models. The model microorganisms were selected as they have been isolated from preflight or in-flight monitoring, represent different degrees of pathogenic behavior, are well characterized, and have sequenced genomes with available microarrays. In particular, extensive studies of S. typhimurium by the Principal Investigator, Dr. Nickerson

  14. Possibilities and obstacles in recovery of genomes from elusive microbes in complex metagenomes

    DEFF Research Database (Denmark)

    Karst, Søren Michael; Albertsen, Mads; Nielsen, Jeppe Lund;

    different growth conditions (O2 /-O2 x Glucose/Butyrate/Casein) for 7 days at 20 °C. Interesting samples were identified using Illumina V4 16S amplicon time series of each growth condition. Twelve enrichment samples were subsequently selected for metagenomics and sequenced on the Illumina platform (300 Gbp...

  15. Medicines from microbes : exploiting the power of computational genomics for natural products discovery and engineering

    NARCIS (Netherlands)

    Medema, Marinus Hendrik

    2013-01-01

    Bacteriën, schimmels en planten produceren allerlei chemische stofjes, waarvan velen medicinaal worden toegepast als bijvoorbeeld antibiotica, chemotherapeutica, cholesterolverlagende middelen of immunosuppressiva. Er is een groeiende vraag naar meer van zulke stofjes, met name omdat bacteriën op

  16. The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

    Energy Technology Data Exchange (ETDEWEB)

    Boundy-Mills, K.; Hess, Matthias; Bennett, A. R.; Ryan, Matthew; Kang, Seogchan; Nobles, David; Eisen, Jonathan A.; Inderbitzin, Patrik; Sitepu, Irnayuli R.; Torok, Tamas; Brown, Daniel R; Cho, Juliana; Wertz, John E.; Mukherjee, Supratim; Cady, Sherry L.; McCluskey, Kevin

    2015-09-01

    The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is "to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind." Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

  17. Probability and Statistics: 5 Questions

    DEFF Research Database (Denmark)

    Probability and Statistics: 5 Questions is a collection of short interviews based on 5 questions presented to some of the most influential and prominent scholars in probability and statistics. We hear their views on the fields, aims, scopes, the future direction of research and how their work fits...

  18. The give and take of host-microbe symbioses.

    Science.gov (United States)

    Gerardo, Nicole M

    2013-07-17

    Studying the association between mealybugs and two bacterial symbionts, Husnik et al. (2013) demonstrated that both integration of metabolic pathways across the partners' genomes and horizontal gene transfer from diverse bacteria into the insect host genome are integral to symbiosis.

  19. The Value Question in Metaphysics.

    Science.gov (United States)

    Kahane, Guy

    2012-07-01

    Much seems to be at stake in metaphysical questions about, for example, God, free will or morality. One thing that could be at stake is the value of the universe we inhabit-how good or bad it is. We can think of competing philosophical positions as describing possibilities, ways the world might turn out to be, and to which value can be assigned. When, for example, people hope that God exists, or fear that we do not possess free will, they express attitudes towards these possibilities, attitudes that presuppose answers to questions about their comparative value. My aim in this paper is to distinguish these evaluative questions from related questions with which they can be confused, to identify structural constraints on their proper pursuit, and to address objections to their very coherence. Answers to such evaluative questions offer one measure of the importance of philosophical disputes.

  20. Environmental bacteriophages : viruses of microbes in aquatic ecosystems

    Directory of Open Access Journals (Sweden)

    Télesphore eSIME - NGANDO

    2014-07-01

    Full Text Available Since the discovery 2-3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms (http://www.isvm.org/, was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea, as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e. phages in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.

  1. Study of microbes having potentiality for biodegradation of plastics.

    Science.gov (United States)

    Ghosh, Swapan Kumar; Pal, Sujoy; Ray, Sumanta

    2013-07-01

    Plastic is a broad name given to the different types of organic polymers having high molecular weight and is commonly derived from different petrochemicals. Plastics are generally not biodegradable or few are degradable but in a very slow rate. Day by day, the global demand of these polymers is sharply increasing; however, considering their abundance and potentiality in causing different environmental hazards, there is a great concern in the possible methods of degradation of plastics. Recently, there have been some debates at the world stage about the potential degradation procedures of these synthetic polymers and microbial degradation has emerged as one of the potential alternative ways of degradation of plastics. Alternatively, some scientists have also reported many adverse effects of these polymers in human health, and thus, there is an immediate need of a potential screening of some potential microbes to degrade these synthetic polymers. In this review, we have taken an attempt to accumulate all information regarding the chemical nature along with some potential microbes and their enzymatic nature of biodegradation of plastics along with some key factors that affect their biodegradability.

  2. Mg isotope fractionation during microbe-mineral interactions

    Science.gov (United States)

    Kim, Insu; Ryu, Jong-sik; Lee, Kwang-sik; Lee, Dongho

    2014-05-01

    Magnesium is involved in various biogeochemical processes important to the global climate change over geological time-scale. Mg isotopes allow us to directly trace the Mg cycle in the Earth's surface but the factors controlling Mg isotopic compositions have not fully understood yet. Here, we conducted a batch experiment using two bacterial species (Shewanella putrefaciens and Burkholderia fungorum) and three major Mg-bearing minerals (biotite, dolomite and hornblende). All elemental concentrations increased by 336 h and then reached to steady-state values, of which Mg concentrations varied depending on minerals and bacterial species. This result indicates that the mineral dissolution is affect by the presence of microbes, which either provide organic acids or attach onto mineral surface. The Mg isotopic compositions of initial minerals biotite, dolomite and hornblende are -0.35o of biotite, -0.99o of dolomite, and -0.24o of hornblende, in δ26Mg. Similarly, δ26Mg values increased by 336 h and reached to steady-state values, which also varied with minerals and microbes. During dissolution of three minerals, the light isotope of Mg is preferentially incorporated into the dissolved phases and then the dissolved δ26Mg values become consistent with those of minerals with the time.

  3. Bioprospecting Sponge-Associated Microbes for Antimicrobial Compounds.

    Science.gov (United States)

    Indraningrat, Anak Agung Gede; Smidt, Hauke; Sipkema, Detmer

    2016-05-02

    Sponges are the most prolific marine organisms with respect to their arsenal of bioactive compounds including antimicrobials. However, the majority of these substances are probably not produced by the sponge itself, but rather by bacteria or fungi that are associated with their host. This review for the first time provides a comprehensive overview of antimicrobial compounds that are known to be produced by sponge-associated microbes. We discuss the current state-of-the-art by grouping the bioactive compounds produced by sponge-associated microorganisms in four categories: antiviral, antibacterial, antifungal and antiprotozoal compounds. Based on in vitro activity tests, identified targets of potent antimicrobial substances derived from sponge-associated microbes include: human immunodeficiency virus 1 (HIV-1) (2-undecyl-4-quinolone, sorbicillactone A and chartarutine B); influenza A (H1N1) virus (truncateol M); nosocomial Gram positive bacteria (thiopeptide YM-266183, YM-266184, mayamycin and kocurin); Escherichia coli (sydonic acid), Chlamydia trachomatis (naphthacene glycoside SF2446A2); Plasmodium spp. (manzamine A and quinolone 1); Leishmania donovani (manzamine A and valinomycin); Trypanosoma brucei (valinomycin and staurosporine); Candida albicans and dermatophytic fungi (saadamycin, 5,7-dimethoxy-4-p-methoxylphenylcoumarin and YM-202204). Thirty-five bacterial and 12 fungal genera associated with sponges that produce antimicrobials were identified, with Streptomyces, Pseudovibrio, Bacillus, Aspergillus and Penicillium as the prominent producers of antimicrobial compounds. Furthemore culture-independent approaches to more comprehensively exploit the genetic richness of antimicrobial compound-producing pathways from sponge-associated bacteria are addressed.

  4. Fluorogenic Cell-Based Biosensors for Monitoring Microbes

    Science.gov (United States)

    Curtis, Theresa; Salazar, Noe; Tabb, Joel; Chase, Chris

    2010-01-01

    Fluorogenic cell-based sensor systems for detecting microbes (especially pathogenic ones) and some toxins and allergens are undergoing development. These systems harness the natural signaltransduction and amplification cascades that occur in mast cells upon activation with antigens. These systems include (1) fluidic biochips for automated containment of samples, reagents, and wastes and (2) sensitive, compact fluorometers for monitoring the fluorescent responses of mast cells engineered to contain fluorescent dyes. It should be possible to observe responses within minutes of adding immune complexes. The systems have been shown to work when utilizing either immunoglobulin E (IgE) antibodies or traditionally generated rat antibodies - a promising result in that it indicates that the systems could be developed to detect many target microbes. Chimeric IgE antibodies and rat immunoglobulin G (IgG) antibodies could be genetically engineered for recognizing biological and chemical warfare agents and airborne and food-borne allergens. Genetic engineering efforts thus far have yielded (1) CD14 chimeric antibodies that recognize both Grampositive and Gram-negative bacteria and bind to the surfaces of mast cells, eliciting a degranulation response and (2) rat IgG2a antibodies that act similarly in response to low levels of canine parvovirus.

  5. Phytophagous insect-microbe mutualisms and adaptive evolutionary diversification.

    Science.gov (United States)

    Janson, Eric M; Stireman, John O; Singer, Michael S; Abbot, Patrick

    2008-05-01

    Adaptive diversification is a process intrinsically tied to species interactions. Yet, the influence of most types of interspecific interactions on adaptive evolutionary diversification remains poorly understood. In particular, the role of mutualistic interactions in shaping adaptive radiations has been largely unexplored, despite the ubiquity of mutualisms and increasing evidence of their ecological and evolutionary importance. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification, using herbivorous insects and their microbial mutualists as exemplars. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. In this perspective, we examine microbial mutualist mediation of ecological opportunity and ecologically based divergent natural selection for their insect hosts. We also explore the conditions and mechanisms by which microbial mutualists may either facilitate or impede adaptive evolutionary diversification. These include effects on the availability of novel host plants or adaptive zones, modifying host-associated fitness trade-offs during host shifts, creating or reducing enemy-free space, and, overall, shaping the evolution of ecological (host plant) specialization. Although the conceptual framework presented here is built on phytophagous insect-microbe mutualisms, many of the processes and predictions are broadly applicable to other mutualisms in which host ecology is altered by mutualistic interactions.

  6. Environmental bacteriophages: viruses of microbes in aquatic ecosystems.

    Science.gov (United States)

    Sime-Ngando, Télesphore

    2014-01-01

    Since the discovery 2-3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms, (http://www.isvm.org/) was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea), as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.

  7. Microbes produce nanobacteria-like structures, avoiding cell entombment

    Science.gov (United States)

    Bontognali, Tomaso R. R.; Vasconcelos, Crisógono; Warthmann, Rolf J.; Dupraz, Christophe; Bernasconi, Stefano M.; McKenzie, Judith A.

    2008-08-01

    Microsedimentary structures referred to as nanobacteria-likeparticles were described from modern carbonate environments,where they form in close spatial association with sulfate-reducingbacteria (SRB). However, the exact mechanism of their formation,as well as their paleontological significance, remains controversial.Here we report on an investigation of microbe-mineral interactionsin experimentally produced carbonate globules. The experimentswere carried out under anoxic conditions at 30 °C with Desulfovibriobrasiliensis, a SRB known to mediate dolomite formation. Weobserved that extracellular polymeric substances (EPS) secretedby the microbial community play a key role in the mineralizationprocess. Nanobacteria-like particles represent the early stageof carbonate nucleation within the EPS, which progressivelyevolve to larger globules displaying a grainy texture. We excludedthe possibilities that these structures are fossils of nanobacteria,dissolution surfaces, or artifacts created during sample preparation.D. brasiliensis cells are predominantly located outside of theEPS aggregates where mineral growth takes place. As a result,they remain mobile and are rarely entombed within the mineral.This self-preservation behavior may not be limited to D. brasiliensis.Other microbes may produce, or may have produced during thegeological past, biogenic minerals through a similar process.Mineralization within EPS explains why microbial relics arenot necessarily present in biogenic carbonates.

  8. Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila

    Directory of Open Access Journals (Sweden)

    Patrice D. Cani

    2017-09-01

    Full Text Available Metabolic disorders associated with obesity and cardiometabolic disorders are worldwide epidemic. Among the different environmental factors, the gut microbiota is now considered as a key player interfering with energy metabolism and host susceptibility to several non-communicable diseases. Among the next-generation beneficial microbes that have been identified, Akkermansia muciniphila is a promising candidate. Indeed, A. muciniphila is inversely associated with obesity, diabetes, cardiometabolic diseases and low-grade inflammation. Besides the numerous correlations observed, a large body of evidence has demonstrated the causal beneficial impact of this bacterium in a variety of preclinical models. Translating these exciting observations to human would be the next logic step and it now appears that several obstacles that would prevent the use of A. muciniphila administration in humans have been overcome. Moreover, several lines of evidence indicate that pasteurization of A. muciniphila not only increases its stability but more importantly increases its efficacy. This strongly positions A. muciniphila in the forefront of next-generation candidates for developing novel food or pharma supplements with beneficial effects. Finally, a specific protein present on the outer membrane of A. muciniphila, termed Amuc_1100, could be strong candidate for future drug development. In conclusion, as plants and its related knowledge, known as pharmacognosy, have been the source for designing drugs over the last century, we propose that microbes and microbiomegnosy, or knowledge of our gut microbiome, can become a novel source of future therapies.

  9. Utilizing thermophilic microbe in lignocelluloses based bioethanol production: Review

    Science.gov (United States)

    Sriharti, Agustina, Wawan; Ratnawati, Lia; Rahman, Taufik; Salim, Takiyah

    2017-01-01

    The utilization of thermophilic microbe has attracted many parties, particularly in producing an alternative fuel like ethanol. Bioethanol is one of the alternative energy sources substituting for earth oil in the future. The advantage of using bioethanol is that it can reduce pollution levels and global warming because the result of bioethanol burning doesn't bring in a net addition of CO2 into environment. Moreover, decrease in the reserves of earth oil globally has also contributed to the notion on searching renewable energy resources such as bioethanol. Indonesia has a high biomass potential and can be used as raw material for bioethanol. The utilization of these raw materials will reduce fears of competition foodstuffs for energy production. The enzymes that play a role in degrading lignocelluloses are cellulolytic, hemicellulolytic, and lignolytic in nature. The main enzyme with an important role in bioethanol production is a complex enzyme capable of degrading lignocelluloses. The enzyme can be produced by the thermophilik microbes of the groups of bacteria and fungi such as Trichoderma viride, Clostridium thermocellum, Bacillus sp. Bioethanol production is heavily affected by raw material composition, microorganism type, and the condition of fermentation used.

  10. Questions

    DEFF Research Database (Denmark)

    Larsen, Steen Nepper

    2012-01-01

    Bidrag til festskrift til Jesper Hoffmeyer i anledning af hans 70 års dag i Don Favineau, Paul Cobley & Kalevi Kull (eds.): "A More Developed Sign. Interpreting the Work of Jesper Hoffmeyer". Antologien udg. som særnummer af Tartu Semiotics Library Nr. 10 og mit bidrag forefindes på p. 217-220....

  11. Comparative Microbial Genomics and Forensics.

    Science.gov (United States)

    Massey, Steven E

    2016-08-01

    Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

  12. The structure and dynamics of complex microbe-host interaction networks

    OpenAIRE

    Björk, Johannes

    2016-01-01

    Microbes form intricate and intimate relationships with most animals and plants, many of which are crucial for host development, health and functioning. Microbe--host symbiotic associations are poorly explored in comparison with other species interaction networks. The current paradigm on symbiosis research stems from species-poor systems where pairwise and reciprocally specialised interactions between a single microbe and host that coevolve are the norm. These symbioses involving just a few s...

  13. Plant traits related to nitrogen uptake influence plant-microbe competition

    OpenAIRE

    Moreau, Delphine; Pivato, Barbara; Bru, David; Busset, Hugues; Deau, Florence; Faivre, Céline; Matejicek, Annick; Strbik, Florence; Mougel, Christophe

    2015-01-01

    Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits ...

  14. Host-microbe interactions in distal airways: relevance to chronic airway diseases.

    Science.gov (United States)

    Martin, Clémence; Burgel, Pierre-Régis; Lepage, Patricia; Andréjak, Claire; de Blic, Jacques; Bourdin, Arnaud; Brouard, Jacques; Chanez, Pascal; Dalphin, Jean-Charles; Deslée, Gaetan; Deschildre, Antoine; Gosset, Philippe; Touqui, Lhousseine; Dusser, Daniel

    2015-03-01

    This article is the summary of a workshop, which took place in November 2013, on the roles of microorganisms in chronic respiratory diseases. Until recently, it was assumed that lower airways were sterile in healthy individuals. However, it has long been acknowledged that microorganisms could be identified in distal airway secretions from patients with various respiratory diseases, including cystic fibrosis (CF) and non-CF bronchiectasis, chronic obstructive pulmonary disease, asthma and other chronic airway diseases (e.g. post-transplantation bronchiolitis obliterans). These microorganisms were sometimes considered as infectious agents that triggered host immune responses and contributed to disease onset and/or progression; alternatively, microorganisms were often considered as colonisers, which were considered unlikely to play roles in disease pathophysiology. These concepts were developed at a time when the identification of microorganisms relied on culture-based methods. Importantly, the majority of microorganisms cannot be cultured using conventional methods, and the use of novel culture-independent methods that rely on the identification of microorganism genomes has revealed that healthy distal airways display a complex flora called the airway microbiota. The present article reviews some aspects of current literature on host-microbe (mostly bacteria and viruses) interactions in healthy and diseased airways, with a special focus on distal airways.

  15. Host–microbe interactions in distal airways: relevance to chronic airway diseases

    Directory of Open Access Journals (Sweden)

    Clémence Martin

    2015-03-01

    Full Text Available This article is the summary of a workshop, which took place in November 2013, on the roles of microorganisms in chronic respiratory diseases. Until recently, it was assumed that lower airways were sterile in healthy individuals. However, it has long been acknowledged that microorganisms could be identified in distal airway secretions from patients with various respiratory diseases, including cystic fibrosis (CF and non-CF bronchiectasis, chronic obstructive pulmonary disease, asthma and other chronic airway diseases (e.g. post-transplantation bronchiolitis obliterans. These microorganisms were sometimes considered as infectious agents that triggered host immune responses and contributed to disease onset and/or progression; alternatively, microorganisms were often considered as colonisers, which were considered unlikely to play roles in disease pathophysiology. These concepts were developed at a time when the identification of microorganisms relied on culture-based methods. Importantly, the majority of microorganisms cannot be cultured using conventional methods, and the use of novel culture-independent methods that rely on the identification of microorganism genomes has revealed that healthy distal airways display a complex flora called the airway microbiota. The present article reviews some aspects of current literature on host–microbe (mostly bacteria and viruses interactions in healthy and diseased airways, with a special focus on distal airways.

  16. Simulation of Neurocomputing Based on Photophobic Reactions of Euglena: Toward Microbe-Based Neural Network Computing

    Science.gov (United States)

    Ozasa, Kazunari; Aono, Masashi; Maeda, Mizuo; Hara, Masahiko

    In order to develop an adaptive computing system, we investigate microscopic optical feedback to a group of microbes (Euglena gracilis in this study) with a neural network algorithm, expecting that the unique characteristics of microbes, especially their strategies to survive/adapt against unfavorable environmental stimuli, will explicitly determine the temporal evolution of the microbe-based feedback system. The photophobic reactions of Euglena are extracted from experiments, and built in the Monte-Carlo simulation of a microbe-based neurocomputing. The simulation revealed a good performance of Euglena-based neurocomputing. Dynamic transition among the solutions is discussed from the viewpoint of feedback instability.

  17. The rhizosphere priming effect explained by microscale interactions among enzyme producing microbes

    Science.gov (United States)

    Kaiser, Christina; Dieckmann, Ulf; Franklin, Oskar

    2017-04-01

    Addition of small amounts of labile carbon (C), for example by root exudations, have been found to accelerate soil organic matter decomposition ('Priming Effect'). Possible explanations that have been suggested so far are that this C increases microbial turnover or - by increasing nitrogen (N) limitation of microbes - triggers increased mining of microbes for nutrients. Individual-based modeling of microbes at the microscale offer a new and alternative explanation for the emergence of the priming effect: Enzyme producing microbes benefit from proximity to other enzyme producing microbes since this increases their return of investment for each enzyme produced. The benefit grows the more microbes are close to each other, such that growth of a patch of microbes becomes a self-enhancing process. Our results show that there is a 'tipping point' - a critical size of such a patch, or number of spatially related microbes, which is necessary to start this process. In a model setting where soil microbes are C limited and thus only grow slowly, the addition of a small amount of labile C in a certain area is sufficient to trigger the emergence of such a growing microbial patch which consequently increases long-term decomposition rates of soil organic matter far beyond the initial labile C input in the model.

  18. Phrasal Paraphrase Based Question Reformulation for Archived Question Retrieval.

    Science.gov (United States)

    Zhang, Yu; Zhang, Wei-Nan; Lu, Ke; Ji, Rongrong; Wang, Fanglin; Liu, Ting

    2013-01-01

    Lexical gap in cQA search, resulted by the variability of languages, has been recognized as an important and widespread phenomenon. To address the problem, this paper presents a question reformulation scheme to enhance the question retrieval model by fully exploring the intelligence of paraphrase in phrase-level. It compensates for the existing paraphrasing research in a suitable granularity, which either falls into fine-grained lexical-level or coarse-grained sentence-level. Given a question in natural language, our scheme first detects the involved key-phrases by jointly integrating the corpus-dependent knowledge and question-aware cues. Next, it automatically extracts the paraphrases for each identified key-phrase utilizing multiple online translation engines, and then selects the most relevant reformulations from a large group of question rewrites, which is formed by full permutation and combination of the generated paraphrases. Extensive evaluations on a real world data set demonstrate that our model is able to characterize the complex questions and achieves promising performance as compared to the state-of-the-art methods.

  19. Phrasal Paraphrase Based Question Reformulation for Archived Question Retrieval.

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    Full Text Available Lexical gap in cQA search, resulted by the variability of languages, has been recognized as an important and widespread phenomenon. To address the problem, this paper presents a question reformulation scheme to enhance the question retrieval model by fully exploring the intelligence of paraphrase in phrase-level. It compensates for the existing paraphrasing research in a suitable granularity, which either falls into fine-grained lexical-level or coarse-grained sentence-level. Given a question in natural language, our scheme first detects the involved key-phrases by jointly integrating the corpus-dependent knowledge and question-aware cues. Next, it automatically extracts the paraphrases for each identified key-phrase utilizing multiple online translation engines, and then selects the most relevant reformulations from a large group of question rewrites, which is formed by full permutation and combination of the generated paraphrases. Extensive evaluations on a real world data set demonstrate that our model is able to characterize the complex questions and achieves promising performance as compared to the state-of-the-art methods.

  20. Evolution of microbes and viruses: A paradigm shift in evolutionary biology?

    Directory of Open Access Journals (Sweden)

    Eugene V. Koonin

    2012-09-01

    Full Text Available When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain ‘ribosomal Tree of Life’ that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: i pervasive horizontal gene transfer (HGT, in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment of the Tree of Life concept, ii Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and iii evolution of evolvability, i.e. dedicated mechanisms for evolution such as vehicles for HGT and stress-induced mutagenesis systems. In the non-cellular part of the microbial world, phylogenomics and metagenomics of viruses and related selfish genetic elements revealed enormous genetic and molecular diversity and extremely high abundance of viruses that come across as the dominant biological entities on earth. Furthermore, the perennial arms race between viruses and their hosts is one of the defining factors of evolution. Thus, microbial phylogenomics adds new dimensions to the fundamental picture of evolution even as the principle of descent with modification discovered by Darwin and the laws of population genetics remain at the core of evolutionary

  1. Explaining errors in children's questions.

    Science.gov (United States)

    Rowland, Caroline F

    2007-07-01

    The ability to explain the occurrence of errors in children's speech is an essential component of successful theories of language acquisition. The present study tested some generativist and constructivist predictions about error on the questions produced by ten English-learning children between 2 and 5 years of age. The analyses demonstrated that, as predicted by some generativist theories [e.g. Santelmann, L., Berk, S., Austin, J., Somashekar, S. & Lust. B. (2002). Continuity and development in the acquisition of inversion in yes/no questions: dissociating movement and inflection, Journal of Child Language, 29, 813-842], questions with auxiliary DO attracted higher error rates than those with modal auxiliaries. However, in wh-questions, questions with modals and DO attracted equally high error rates, and these findings could not be explained in terms of problems forming questions with why or negated auxiliaries. It was concluded that the data might be better explained in terms of a constructivist account that suggests that entrenched item-based constructions may be protected from error in children's speech, and that errors occur when children resort to other operations to produce questions [e.g. Dabrowska, E. (2000). From formula to schema: the acquisition of English questions. Cognitive Liguistics, 11, 83-102; Rowland, C. F. & Pine, J. M. (2000). Subject-auxiliary inversion errors and wh-question acquisition: What children do know? Journal of Child Language, 27, 157-181; Tomasello, M. (2003). Constructing a language: A usage-based theory of language acquisition. Cambridge, MA: Harvard University Press]. However, further work on constructivist theory development is required to allow researchers to make predictions about the nature of these operations.

  2. Comparative genomics of plant-asssociated Pseudomonas spp.: Insights into diversity and inheritance of traits involved in multitrophic interactions

    NARCIS (Netherlands)

    Loper, J.E.; Hassan, K.A.; Mavrodi, D.V.; Davis II, E.W.; Lim, C.K.; Shaffer, B.T.; Elbourne, L.D.H.; Stockwell, V.O.; Hartney, S.L.; Breakwell, K.; Henkels, M.D.; Tetu, S.G.; Rangel, L.I.; Kidarsa, T.A.; Wilson, N.L.; Mortel, van de J.E.; Song, C.; Blumhagen, R.; Radune, D.; Hostetler, J.B.; Brinkac, L.M.; Durkin, A.C.; Kluepfel, D.A.; Wechter, W.P.; Anderson, A.J.; Kim, Y.C.; Pierson III, L.S.; Pierson, E.A.; Lindow, S.E.; Kobayashi, D.Y.; Raaijmakers, J.; Weller, D.M.; Thomashow, L.S.; Allen, A.E.; Paulsen, I.T.

    2012-01-01

    We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multi

  3. The biology of habitat dominance; can microbes behave as weeds?

    Science.gov (United States)

    Cray, Jonathan A; Bell, Andrew N W; Bhaganna, Prashanth; Mswaka, Allen Y; Timson, David J; Hallsworth, John E

    2013-09-01

    Competition between microbial species is a product of, yet can lead to a reduction in, the microbial diversity of specific habitats. Microbial habitats can resemble ecological battlefields where microbial cells struggle to dominate and/or annihilate each other and we explore the hypothesis that (like plant weeds) some microbes are genetically hard-wired to behave in a vigorous and ecologically aggressive manner. These 'microbial weeds' are able to dominate the communities that develop in fertile but uncolonized--or at least partially vacant--habitats via traits enabling them to out-grow competitors; robust tolerances to habitat-relevant stress parameters and highly efficient energy-generation systems; avoidance of or resistance to viral infection, predation and grazers; potent antimicrobial systems; and exceptional abilities to sequester and store resources. In addition, those associated with nutritionally complex habitats are extraordinarily versatile in their utilization of diverse substrates. Weed species typically deploy multiple types of antimicrobial including toxins; volatile organic compounds that act as either hydrophobic or highly chaotropic stressors; biosurfactants; organic acids; and moderately chaotropic solutes that are produced in bulk quantities (e.g. acetone, ethanol). Whereas ability to dominate communities is habitat-specific we suggest that some microbial species are archetypal weeds including generalists such as: Pichia anomala, Acinetobacter spp. and Pseudomonas putida; specialists such as Dunaliella salina, Saccharomyces cerevisiae, Lactobacillus spp. and other lactic acid bacteria; freshwater autotrophs Gonyostomum semen and Microcystis aeruginosa; obligate anaerobes such as Clostridium acetobutylicum; facultative pathogens such as Rhodotorula mucilaginosa, Pantoea ananatis and Pseudomonas aeruginosa; and other extremotolerant and extremophilic microbes such as Aspergillus spp., Salinibacter ruber and Haloquadratum walsbyi. Some microbes

  4. Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution.

    Directory of Open Access Journals (Sweden)

    Pierre-Marc Delaux

    2014-07-01

    Full Text Available Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant-microbe symbiosis, arbuscular mycorrhization (AM, as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales. Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.

  5. Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution.

    Directory of Open Access Journals (Sweden)

    Pierre-Marc Delaux

    2014-07-01

    Full Text Available Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant-microbe symbiosis, arbuscular mycorrhization (AM, as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales. Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.

  6. Solar physics: Dynamo theory questioned

    Science.gov (United States)

    Charbonneau, Paul

    2016-07-01

    Observations of X-ray emission -- a diagnostic tool for the mechanisms driving stellar magnetic fields -- from four cool stars call into question accepted models of magnetic-field generation in the Sun and stars. See Letter p.526

  7. LGBT Caregiving: Frequently Asked Questions

    Science.gov (United States)

    ... FCA - A A + A You are here Home LGBT Caregiving: Frequently Asked Questions Order this publication Printer- ... service or organization is open to working with LGBT families? Kudos to you for managing to “go ...

  8. Frequent Questions About Universal Waste

    Science.gov (United States)

    Frequent questions such as Who is affected by the universal waste regulations? What is “mercury-containing equipment”? How are waste batteries managed under universal waste? How are waste pesticides managed under universal waste?

  9. HPV Vaccine - Questions and Answers

    Science.gov (United States)

    ... and Media Resources News Newsletters Events Redirect for HPV Vaccine FAQ Recommend on Facebook Tweet Share Compartir ... to the address below. http://www.cdc.gov/hpv/parents/questions-answers.html File Formats Help: How ...

  10. Question Inventory on Tobacco (QIT)

    Data.gov (United States)

    U.S. Department of Health & Human Services — 1965, 1966, 1970, 1974-2017. Centers for Disease Control and Prevention (CDC). Office on Smoking and Health (OSH). Tobacco-Related Survey Questions. The QIT is a...

  11. Questions to Ask Your Doctor

    Science.gov (United States)

    ... to MBCN Contact Us Questions to ask your doctor Medical appointments can be stressful. To better deal ... for you. If diagnosed by your primary care physician Where do you send your metastatic patients for ...

  12. Questions Students Ask: Beta Decay.

    Science.gov (United States)

    Koss, Jordan; Hartt, Kenneth

    1988-01-01

    Answers a student's question about the emission of a positron from a nucleus. Discusses the problem from the aspects of the uncertainty principle, beta decay, the Fermi Theory, and modern physics. (YP)

  13. Climate Leadership Awards Frequent Questions

    Science.gov (United States)

    Provides answers to frequently asked questions regarding the Climate Leadership Awards, sponsored by EPA's Center for Corporate Climate Leadership with co-sponsorship from the Center for Climate and Energy Solutions and The Climate Registry.

  14. Frequently Asked Questions about Pharmacogenomics

    Science.gov (United States)

    ... Care Specific Genetic Disorders Frequently Asked Questions About Pharmacogenomics Enlarge What is pharmacogenomics? What might pharmacogenomics mean ... page, you will need Adobe Reader. What is pharmacogenomics? Pharmacogenomics uses information about a person's genetic makeup, ...

  15. Question Inventory on Tobacco (QIT)

    Data.gov (United States)

    U.S. Department of Health & Human Services — 1965, 1966, 1970, 1974-2015, 2017. Centers for Disease Control and Prevention (CDC). Office on Smoking and Health (OSH). Survey Questions (Tobacco Use). The QIT is...

  16. Key Questions in Thoracic Surgery

    OpenAIRE

    Subotic, Dragan R.

    2016-01-01

    This 1000-page textbook encompasses much more than the title suggests. In fact, the title “Key questions in thoracic surgery and pulmonology” would be more fitting. The specific format of the book, with precise questions and evidence-based, but equally clear answers covering all relevant fields of pulmonology and thoracic surgery, makes this 40-chapter book a “must read” not only for residents, but also for senior pulmonologists and thoracic surgeons.

  17. Protein Electrochemistry: Questions and Answers.

    Science.gov (United States)

    Fourmond, V; Léger, C

    This chapter presents the fundamentals of electrochemistry in the context of protein electrochemistry. We discuss redox proteins and enzymes that are not photoactive. Of course, the principles described herein also apply to photobioelectrochemistry, as discussed in later chapters of this book. Depending on which experiment is considered, electron transfer between proteins and electrodes can be either direct or mediated, and achieved in a variety of configurations: with the protein and/or the mediator free to diffuse in solution, immobilized in a thick, hydrated film, or adsorbed as a sub-monolayer on the electrode. The experiments can be performed with the goal to study the protein or to use it. Here emphasis is on mechanistic studies, which are easier in the configuration where the protein is adsorbed and electron transfer is direct, but we also explain the interpretation of signals obtained when diffusion processes affect the response.This chapter is organized as a series of responses to questions. Questions 1-5 are related to the basics of electrochemistry: what does "potential" or "current" mean, what does an electrochemical set-up look like? Questions 6-9 are related to the distinction between adsorbed and diffusive redox species. The answers to questions 10-13 explain the interpretation of slow and fast scan voltammetry with redox proteins. Questions 14-19 deal with catalytic electrochemistry, when the protein studied is actually an enzyme. Questions 20, 21 and 22 are general.

  18. Detection of circular polarization in light scattered from photosynthetic microbes

    CERN Document Server

    Sparks, William B; Germer, Thomas A; Chen, Feng; DasSarma, Shiladitya; DasSarma, Priya; Robb, Frank T; Manset, Nadine; Kolokolova, Ludmilla; Reid, Neill; Macchetto, F Duccio; Martin, William; 10.1073/pnas.0810215106

    2009-01-01

    The identification of a universal biosignature that could be sensed remotely is critical to the prospects for success in the search for life elsewhere in the universe. A candidate universal biosignature is homochirality, which is likely to be a generic property of all biochemical life. Due to the optical activity of chiral molecules, it has been hypothesized that this unique characteristic may provide a suitable remote sensing probe using circular polarization spectroscopy. Here, we report the detection of circular polarization in light scattered by photosynthetic microbes. We show that the circular polarization appears to arise from circular dichroism of the strong electronic transitions of photosynthetic absorption bands. We conclude that circular polarization spectroscopy could provide a powerful remote sensing technique for generic life searches.

  19. How auxin and cytokinin phytohormones modulate root microbe interactions

    Directory of Open Access Journals (Sweden)

    Stéphane Boivin

    2016-08-01

    Full Text Available A large range of microorganisms can associate with plants, resulting in neutral, friendly or hostile interactions. The ability of plants to recognize compatible and incompatible microorganisms and to limit or promote their colonization is therefore crucial for their survival. Elaborated communication networks determine the degree of association between the host plant and the invading microorganism. Central to these regulations of plant microbe interactions, phytohormones modulate microorganism plant associations and coordinate cellular and metabolic responses associated to the progression of microorganisms across different plant tissues. We review here hormonal regulations, focusing on auxin and cytokinin phytohormones, involved in the interactions between plant roots and soil microorganisms, including bacteria and fungi associations, either beneficial (symbiotic or detrimental (pathogenic. The aim is to highlight similarities and differences in cytokinin/auxin functions amongst various compatible versus incompatible associations.

  20. Microarray tools to unveil viral-microbe interactions in nature

    Directory of Open Access Journals (Sweden)

    Fernando eSantos

    2014-07-01

    Full Text Available The interactions between viruses and their microbial hosts play a central role in the control of microbial communities in nature. However, the study of such interactions within the uncultured majority is technically very challenging. Here, we review how microarray tools can be used to analyze the interactions between viruses and their microbial hosts in nature, away from laboratory pure culture-based models. We show examples of how DNA arrays have been used to study the expression of viral assemblages in natural samples, and to assign viruses to hosts within uncultured communities. Finally, we briefly discuss the possibilities of protein and glycan arrays to gain insight into the ways microbes interact with their viruses.

  1. Receptor kinase signaling pathways in plant-microbe interactions.

    Science.gov (United States)

    Antolín-Llovera, Meritxell; Ried, Martina K; Binder, Andreas; Parniske, Martin

    2012-01-01

    Plant receptor-like kinases (RLKs) function in diverse signaling pathways, including the responses to microbial signals in symbiosis and defense. This versatility is achieved with a common overall structure: an extracytoplasmic domain (ectodomain) and an intracellular protein kinase domain involved in downstream signal transduction. Various surfaces of the leucine-rich repeat (LRR) ectodomain superstructure are utilized for interaction with the cognate ligand in both plant and animal receptors. RLKs with lysin-motif (LysM) ectodomains confer recognitional specificity toward N-acetylglucosamine-containing signaling molecules, such as chitin, peptidoglycan (PGN), and rhizobial nodulation factor (NF), that induce immune or symbiotic responses. Signaling downstream of RLKs does not follow a single pattern; instead, the detailed analysis of brassinosteroid (BR) signaling, innate immunity, and symbiosis revealed at least three largely nonoverlapping pathways. In this review, we focus on RLKs involved in plant-microbe interactions and contrast the signaling pathways leading to symbiosis and defense.

  2. Harnessing plant-microbe interactions for enhancing farm productivity.

    Science.gov (United States)

    Macdonald, Catriona; Singh, Brajesh

    2014-01-01

    Declining soil fertility and farm productivity is a major global concern in order to achieve food security for a burgeoning world population. It is reported that improving soil health alone can increase productivity by 10-15% and in combination with efficient plant traits, farm productivity can be increased up to 50-60%. In this article we explore the emerging microbial and bioengineering technologies, which can be employed to achieve the transformational increase in farm productivity and can simultaneously enhance environmental outcomes i.e., low green house gas (GHG) emissions. We argue that metagenomics, meta-transcriptomics and metabolomics have potential to provide fundamental knowledge on plant-microbes interactions necessary for new innovations to increase farm productivity. Further, these approaches provide tools to identify and select novel microbial/gene resources which can be harnessed in transgenic and designer plant technologies for enhanced resource use efficiencies.

  3. Arsenic-Microbe-Mineral Interactions in Mining-Affected Environments

    Directory of Open Access Journals (Sweden)

    Karen A. Hudson-Edwards

    2013-10-01

    Full Text Available The toxic element arsenic (As occurs widely in solid and liquid mine wastes. Aqueous forms of arsenic are taken up in As-bearing sulfides, arsenides, sulfosalts, oxides, oxyhydroxides, Fe-oxides, -hydroxides, -oxyhydroxides and -sulfates, and Fe-, Ca-Fe- and other arsenates. Although a considerable body of research has demonstrated that microbes play a significant role in the precipitation and dissolution of these As-bearing minerals, and in the alteration of the redox state of As, in natural and simulated mining environments, the molecular-scale mechanisms of these interactions are still not well understood. Further research is required using traditional and novel mineralogical, spectroscopic and microbiological techniques to further advance this field, and to help design remediation schemes.

  4. Beyond the genome: The ethics of DNA testing

    Energy Technology Data Exchange (ETDEWEB)

    Fackelmann, K.A.

    1994-11-05

    This article looks at the implications of identification of specific genes in the human genome. Ethical questions concerning inherited conditions include privacy, paternity, judgement, society versus individual.

  5. Effect of Mineral and Microbe Interactions on Biomass Yield

    Science.gov (United States)

    Pena, S. A.; Block, K. A.; Katz, A.; Gottlieb, P.

    2016-12-01

    The ecological feedback of microbes (bacteria and viruses) in association with minerals is virtually unexplored in the context of characterizing how carbon cycles in the terrestrial ecosystem. These interactions include the ability for bacteriophage to control bacteria populations, the ability of minerals to provide a substrate for bacteria growth, and the effect of minerals on bacteriophage viability. We investigate bacteriophage aggregation with minerals in the clay size fraction (virus experiments, bacteriophage Φ6 was suspended with the minerals smectite, illite, kaolinite, and goethite at low divalent cation concentrations so aggregation was in the reaction limited colloidal aggregation (RLCA) regime, at neutral pH and room temperature conditions. Virus remained viable at a 1:1 virus-clay ratio for clays, and at an approximate 100:1 ratio for goethite. However, the number of plaque forming units was reduced by 99%. Electron micrographs show viable as well as partially disassembled virus, similar to the results found by Block et al. 2014. We found that inactivation of a 4 x 1011 cm-3 concentration of bacteriophage Φ6 by smectite, illite, kaolinite, and goethite, required a minimum sediment concentration of 1.5 x 1011 cm-3, 1.4 x 1011 cm-3, 2.5 x 1011 cm-3, and 1.1 x 109 cm-3, respectively. Mineral biofilms were generated by suspension of tropical soil clays with gram-positive and gram-negative microbes and characterized by x-ray diffraction and imaged by electron microscopy (SEM and TEM). Mineral biomass produced by gram negative organisms were subjected to virus infection to determine influence of minerals on community resilience. Lastly, we report biomass yield in each instance to quantify the influence of mineral composition on total biomass production.

  6. Climate change driven plant-metal-microbe interactions.

    Science.gov (United States)

    Rajkumar, Mani; Prasad, Majeti Narasimha Vara; Swaminathan, Sandhya; Freitas, Helena

    2013-03-01

    Various biotic and abiotic stress factors affect the growth and productivity of crop plants. Particularly, the climatic and/or heavy metal stress influence various processes including growth, physiology, biochemistry, and yield of crops. Climatic changes particularly the elevated atmospheric CO₂ enhance the biomass production and metal accumulation in plants and help plants to support greater microbial populations and/or protect the microorganisms against the impacts of heavy metals. Besides, the indirect effects of climatic change (e.g., changes in the function and structure of plant roots and diversity and activity of rhizosphere microbes) would lead to altered metal bioavailability in soils and concomitantly affect plant growth. However, the effects of warming, drought or combined climatic stress on plant growth and metal accumulation vary substantially across physico-chemico-biological properties of the environment (e.g., soil pH, heavy metal type and its bio-available concentrations, microbial diversity, and interactive effects of climatic factors) and plant used. Overall, direct and/or indirect effects of climate change on heavy metal mobility in soils may further hinder the ability of plants to adapt and make them more susceptible to stress. Here, we review and discuss how the climatic parameters including atmospheric CO₂, temperature and drought influence the plant-metal interaction in polluted soils. Other aspects including the effects of climate change and heavy metals on plant-microbe interaction, heavy metal phytoremediation and safety of food and feed are also discussed. This review shows that predicting how plant-metal interaction responds to altering climatic change is critical to select suitable crop plants that would be able to produce more yields and tolerate multi-stress conditions without accumulating toxic heavy metals for future food security.

  7. Potential for mercury reduction by microbes in the high arctic.

    Science.gov (United States)

    Poulain, Alexandre J; Ní Chadhain, Sinéad M; Ariya, Parisa A; Amyot, Marc; Garcia, Edenise; Campbell, Peter G C; Zylstra, Gerben J; Barkay, Tamar

    2007-04-01

    The contamination of polar regions due to the global distribution of anthropogenic pollutants is of great concern because it leads to the bioaccumulation of toxic substances, methylmercury among them, in Arctic food chains. Here we present the first evidence that microbes in the high Arctic possess and express diverse merA genes, which specify the reduction of ionic mercury [Hg(II)] to the volatile elemental form [Hg(0)]. The sampled microbial biomass, collected from microbial mats in a coastal lagoon and from the surface of marine macroalgae, was comprised of bacteria that were most closely related to psychrophiles that had previously been described in polar environments. We used a kinetic redox model, taking into consideration photoredox reactions as well as mer-mediated reduction, to assess if the potential for Hg(II) reduction by Arctic microbes can affect the toxicity and environmental mobility of mercury in the high Arctic. Results suggested that mer-mediated Hg(II) reduction could account for most of the Hg(0) that is produced in high Arctic waters. At the surface, with only 5% metabolically active cells, up to 68% of the mercury pool was resolved by the model as biogenic Hg(0). At a greater depth, because of incident light attenuation, the significance of photoredox transformations declined and merA-mediated activity could account for up to 90% of Hg(0) production. These findings highlight the importance of microbial redox transformations in the biogeochemical cycling, and thus the toxicity and mobility, of mercury in polar regions.

  8. On the total number of genes and their length distribution in complete microbial genomes

    DEFF Research Database (Denmark)

    Skovgaard, Marie; Jensen, L.J.; Brunak, Søren;

    2001-01-01

    In sequenced microbial genomes, some of the annotated genes are actually not protein-coding genes, but rather open reading frames that occur by chance. Therefore, the number of annotated genes is higher than the actual number of genes for most of these microbes. Comparison of the length distribut......In sequenced microbial genomes, some of the annotated genes are actually not protein-coding genes, but rather open reading frames that occur by chance. Therefore, the number of annotated genes is higher than the actual number of genes for most of these microbes. Comparison of the length...

  9. Analysis of plant microbe interactions in the era of next generation sequencing technologies

    Directory of Open Access Journals (Sweden)

    Claudia eKnief

    2014-05-01

    Full Text Available Next generation sequencing (NGS technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the pant associated microbiota to demonstrate the worth of the new methods.

  10. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  11. The Use of Evolutionary Approaches to Understand Single Cell Genomes

    Directory of Open Access Journals (Sweden)

    Haiwei eLuo

    2015-03-01

    Full Text Available The vast majority of environmental bacteria and archaea remain uncultivated, yet their genome sequences are rapidly becoming available through single cell sequencing technologies. Reconstructing metabolism is one common way to make use of genome sequences of ecologically important bacteria, but molecular evolutionary analysis is another approach that, while currently underused, can reveal important insights into the function of these uncultivated microbes in nature. Because genome sequences from single cells are often incomplete, metabolic reconstruction based on genome content can be compromised. However, this problem does not necessarily impede the use of phylogenomic and population genomic approaches that are based on patterns of polymorphisms and substitutions at nucleotide and amino acid sites. These approaches explore how various evolutionary forces act to assemble genetic diversity within and between lineages. In this mini-review, I present examples illustrating the benefits of analyzing single cell genomes using evolutionary approaches.

  12. Analysis of intra-genomic GC content homogeneity within prokaryotes

    DEFF Research Database (Denmark)

    Bohlin, J; Snipen, L; Hardy, S.P.

    2010-01-01

    both aerobic and facultative microbes. Although an association has previously been found between mean genomic GC content and oxygen requirement, our analysis suggests that no such association exits when phylogenetic bias is accounted for. A significant association between GCVAR and mean GC content......Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how...... the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content...

  13. Phytochemicals that modulate amino acid and peptide catabolism by caprine rumen microbes

    Science.gov (United States)

    Background: Microbe-derived ionophores and macrolide antibiotics are often added to ruminant diets, and growth promotion and feed efficiency are among the benefits. One mechanism is inhibition of microbes that catabolize amino acids or peptides and produce ammonia. Plants also produce antimicrobial ...

  14. Expression of defensin paralogs across house fly life history: insights into fly-microbe interactions

    Science.gov (United States)

    House flies have a life-long association with microbe-rich environments. Larvae directly ingest bacteria in decaying substrates utilizing them for nutritional purposes. Adult house flies ephemerally associate with microbes, ingesting them either by direct feeding or indirectly during grooming. The h...

  15. Biogeographical diversity of plant associated microbes in arcto-alpine plants

    NARCIS (Netherlands)

    Kumar, Manoj Gopala Krishnan

    2016-01-01

    Terrestrial plants and microbes have co-evolved since the emergence of the former on Earth. Associations with microorganisms can be either beneficial or detrimental for plants. Microbes can be found in the soil surrounding the plant roots, but also in all plant tissues, including seeds. In arcto-alp

  16. Update History of This Database - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us MicrobeDB.jp Update History of This Database Date Update contents 2017/06/29 Archive V2 is r...ion Download License Update History of This Database Site Policy | Contact Us Update History of This Database - MicrobeDB.jp | LSDB Archive ...

  17. Microbe-associated molecular pattern (MAMP) signatures, synergy, size and charge

    DEFF Research Database (Denmark)

    Aslam, Shazia N.; Erbs, Gitte; Morrissey, Kate L.

    2009-01-01

    Triggering of defences by microbes has mainly been investigated using single elicitors or microbe-associated molecular patterns (MAMPs), but MAMPs are released in planta as complex mixtures together with endogenous oligogalacturonan (OGA) elicitor. We investigated the early responses in Arabidopsis...

  18. Plant-microbe and plant-insect interactions meet common grounds

    NARCIS (Netherlands)

    Schenk, P.; McGrath, K.C.; Lorito, M.; Pieterse, C.M.J.

    2008-01-01

    Plant–microbe and plant–insect interactions are of global importance for agriculture and of high interest to many plant scientists, microbiologists and entomologists. Traditionally, plant–microbe and plant–insect interactions have been looked at as two separate issues, but in recent years it has bec

  19. Plant-microbe and plant-insect interactions meet common grounds

    NARCIS (Netherlands)

    Schenk, P.; McGrath, K.C.; Lorito, M.; Pieterse, C.M.J.

    2008-01-01

    Plant–microbe and plant–insect interactions are of global importance for agriculture and of high interest to many plant scientists, microbiologists and entomologists. Traditionally, plant–microbe and plant–insect interactions have been looked at as two separate issues, but in recent years it has

  20. Biofilms for Babies: Introducing Microbes and Biofilms to Preschool-Aged Children

    Directory of Open Access Journals (Sweden)

    Jillian M. Couto

    2017-05-01

    Full Text Available Microbes are beneficial to life on our planet as they facilitate natural processes such as global nutrient cycling in our environment. This article details a 30-minute activity to introduce pre-school children ranging from 3 to 5 years of age to microbes and biofilms in the natural environment.

  1. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  2. Foreign language didactics: Identity questions

    Directory of Open Access Journals (Sweden)

    Michaela Píšová

    2011-06-01

    Full Text Available The efforts to emancipate foreign language didactics have been an ongoingand non-linear process launched in our country in the 50s of the previous century.Its key aspects may be presented as foreign language didactics identity questions.These include explicit delineation of the object and methodology of foreign languagedidactics on the basis of developmental analysis, current state of knowledge andtrends/approaches to the discipline. The issues related to the full-fledged scientificstatus of foreign language didactics are discussed both on a domain-general level(questions relevant for the whole field of subject didactics and on a domain-specificlevel (foreign language didactics specific questions.

  3. Bringing quantum mechanics to life: from Schr\\"{o}dinger's cat to Schr\\"{o}dinger's microbe

    CERN Document Server

    Yin, Zhang-qi

    2016-01-01

    The question whether quantum mechanics is complete and the nature of the transition between quantum mechanics and classical mechanics have intrigued physicists for decades. There have been many experimental breakthroughs in creating larger and larger quantum superposition and entangled states since Erwin Schr\\"{o}dinger proposed his famous thought experiment of putting a cat in a superposition of both alive and dead states in 1935. Remarkably, recent developments in quantum optomechanics and electromechanics may lead to the realization of quantum superposition of living microbes soon. Recent evidences also suggest that quantum coherence may play an important role in several biological processes. In this review, we first give a brief introduction to basic concepts in quantum mechanics and the Schr\\"{o}dinger's cat thought experiment. We then review developments in creating quantum superposition and entangled states and the realization of quantum teleportation. Non-trivial quantum effects in photosynthetic ligh...

  4. Development of bioleaching: proteomics and genomics approach in metals extraction process

    Directory of Open Access Journals (Sweden)

    M. Azizur Rahman

    2016-08-01

    Full Text Available Microbes are key components of the structure and function of bioleaching process. Increasing consciousness of the role of microbes has led to a quick growth of descriptive and investigational studies of their abundance and activities. However, the detail information of complex functional molecules contain in promising microbes which are very important for understanding microbial processes in bioleaching, are lacking. Therefore, molecular functions of microbes in the bioleaching process are very essential to understand about the microbial activities, especially in the process of the extraction of metals in mineral industries. In this review, the current state of proteomics and genomics of bioleaching in metals extraction processes and the major developments of these analytical methods at industrial scales are highlighted.

  5. Research progress in genomics of environmental and industrial microorganisms

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Microbes contribute to geochemical cycles in the ecosystem.They also play important roles in biodegradation and bioremediation of contaminated environments,and have great potential in energy conversion and regeneration.Up to date,at least 150 genomes of non-pathogenic microbes have been sequenced,of which,the majority are bacteria from various environments or of industrial uses.The emerging field ’metagenomics’ in combination with the high-throughput sequencing technology offers opportunities to discover new functions of microbes in the environment on a large scale,and has become the ’hot spot’ in the field of environmental microbiology.Seven genomes of bacteria from various extreme environments,including high temperature,high and low pressure,and extreme acidic regions,have been sequenced by researchers in China,leading to the discovery of metabolic pathways,genetic functions and new enzymes,which are related to the niches those bacteria occupy.These results were published in Nature,PNAS,Genome Research and other top international journals.In the meantime,several groups in China have started ’metagenomics’ programs.The outcomes of these researches are expected to generate a considerable number of novel findings,taking Chinese researchers to the frontier of genomics for environmental and industrial microorganisms.

  6. Research progress in genomics of environmental and industrial microorganisms

    Institute of Scientific and Technical Information of China (English)

    WANG Lei; LIU Bin; ZHOU ZheMin

    2009-01-01

    Microbes contribute to geochemical cycles in the ecosystem. They also play important roles in bio-degradation and bioremediation of contaminated environments, and have great potential in energy conversion and regeneration. Up to date, at least 150 genomes of non-pathogenic microbes have been sequenced, of which, the majority are bacteria from various environments or of industrial uses. The emerging field 'metagenomics' in combination with the high-throughput sequencing technology offers opportunities to discover new functions of microbes in the environment on a large scale, and has be-come the 'hot spot' in the field of environmental microbiology. Seven genomes of bacteria from various extreme environments, including high temperature, high and low pressure, and extreme acidic regions, have been sequenced by researchers in China, leading to the discovery of metabolic pathways, genetic functions and new enzymes, which are related to the niches those bacteria occupy. These results were published in Nature, PNAS, Genome Research and other top international journals. In the meantime, several groups in China have started 'metagenomics' programs. The outcomes of these researches are expected to generate a considerable number of novel findings, taking Chinese researchers to the fron-tier of genomics for environmental and industrial microorganisms.

  7. Urban microbiomes and urban ecology: how do microbes in the built environment affect human sustainability in cities?

    Science.gov (United States)

    King, Gary M

    2014-09-01

    Humans increasingly occupy cities. Globally, about 50% of the total human population lives in urban environments, and in spite of some trends for deurbanization, the transition from rural to urban life is expected to accelerate in the future, especially in developing nations and regions. The Republic of Korea, for example, has witnessed a dramatic rise in its urban population, which now accounts for nearly 90% of all residents; the increase from about 29% in 1955 has been attributed to multiple factors, but has clearly been driven by extraordinary growth in the gross domestic product accompanying industrialization. While industrialization and urbanization have unarguably led to major improvements in quality of life indices in Korea and elsewhere, numerous serious problems have also been acknowledged, including concerns about resource availability, water quality, amplification of global warming and new threats to health. Questions about sustainability have therefore led Koreans and others to consider deurbanization as a management policy. Whether this offers any realistic prospects for a sustainable future remains to be seen. In the interim, it has become increasingly clear that built environments are no less complex than natural environments, and that they depend on a variety of internal and external connections involving microbes and the processes for which microbes are responsible. I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems. I also identify important knowledge gaps and unanswered questions about urban microbiomes that must be addressed to develop a robust, predictive and general understanding of urban biology and ecology that can be used to inform policy-making for sustainable systems.

  8. Microbes versus microbes

    DEFF Research Database (Denmark)

    Jordan, Kieran; Dalmasso, Marion; Zentek, Juergen

    2014-01-01

    Foodborne illness continues as a considerable threat to public health. Despite improved hygiene management systems and increased regulation, pathogenic bacteria still contaminate food, causing sporadic cases of illness and disease outbreaks worldwide. For many centuries, microbial antagonism has...... been used in food processing to improve food safety. An understanding of the mode of action of this microbial antagonism has been gained in recent years and potential applications in food and feed safety are now being explored. This review focuses on the potential opportunities presented...

  9. Functional genomics in reproductive medicine.

    Science.gov (United States)

    Barratt, Christopher L R; Hughes, David C; Afnan, Masoud; Brewis, Ian A

    2002-02-01

    The British Fertility Society organised a workshop on Functional Genomics in Reproductive Medicine at the University of Birmingham on 13-14 September 2001. The primary aim was to inform delegates about the power of the technology that has been made available after completion of the sequencing of the human genome, and to stimulate debate about using functional genomics to address both clinical and scientific questions in reproductive medicine. Three specific areas were addressed: proteomics, gene expression and bioinformatics. Although the sophistication and plethora of techniques available were obvious, major limitations in the technology were also discussed. The future promises to be very challenging indeed.

  10. Arts and Techniques of Questioning

    Institute of Scientific and Technical Information of China (English)

    Sun Yu

    2011-01-01

    Most learners learn English from teachers in classroom. Therefore, classroom instruction plays a very important role. Teachers' questioning constitutes a very significant aspect of classroom teaching. It is not only an important part of classroom interaction but an effective way of learning second language as well.

  11. Understanding Bitcoins: Facts and Questions

    OpenAIRE

    Bruno Saboia de Albuquerque; Marcelo de Castro Callado

    2015-01-01

    The objective of this work is to do a research challenge about the digital currency named Bitcoins, as well as exploit the general concept behind digital currencies and cryptocurrencies, and enumerate some of its current criticism and problems. Such currencies usage and public knowledge is increasing hastily on the last few months, and many questions arise with its popularity.

  12. Questioning Mechanisms During Complex Learning

    Science.gov (United States)

    1992-03-11

    is probably a general phenomenon in this culture that tutors are reluctant to give negative feedback on students’ errors and poor answers. Instead of...1991). Questioning in classrooms: A sociolinguistic perspective. Review of £’fiu!r’aiona1 R.ear.h, L, 157-178. Carroll, J. M., Mack, R. L., Lewis, C

  13. Understanding Bitcoins: Facts and Questions

    Directory of Open Access Journals (Sweden)

    Bruno Saboia de Albuquerque

    2015-03-01

    Full Text Available The objective of this work is to do a research challenge about the digital currency named Bitcoins, as well as exploit the general concept behind digital currencies and cryptocurrencies, and enumerate some of its current criticism and problems. Such currencies usage and public knowledge is increasing hastily on the last few months, and many questions arise with its popularity.

  14. Recent advances in fruit crop genomics

    Directory of Open Access Journals (Sweden)

    Qiang XU,Chaoyang LIU,Manosh Kumar BISWAS,Zhiyong PAN,Xiuxin DENG

    2014-02-01

    Full Text Available In recent years, dramatic progress has been made in the genomics of fruit crops. The publication of a dozen fruit crop genomes represents a milestone for both functional genomics and breeding programs in fruit crops. Rapid advances in high-throughput sequencing technology have revolutionized the manner and scale of genomics in fruit crops. Research on fruit crops is encompassing a wide range of biological questions which are unique and cannot be addressed in a model plant such as Arabidopsis. This review summarizes recent achievements of research on the genome, transcriptome, proteome, miRNAs and epigenome of fruit crops.

  15. Dynamics of genome rearrangement in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Aaron E Darling

    Full Text Available Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of "symmetric inversions"-inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings

  16. BISRU: Synthetic Microbes for Moon, Mars and Beyond

    Science.gov (United States)

    Cumbers, J.; Rothchild, L.

    2010-04-01

    Synthetic biology and genomics will bring a new range of designer organisms into being and give us new tools for the manipulation and control of these organisms. BISRU or biological in situ resource utilization is the use of such genetically modified organisms in space.

  17. Identification of Soil Microbes Capable of Utilizing Cellobiosan.

    Directory of Open Access Journals (Sweden)

    Jieni Lian

    Full Text Available Approximately 100 million tons of anhydrosugars, such as levoglucosan and cellobiosan, are produced through biomass burning every year. These sugars are also produced through fast pyrolysis, the controlled thermal depolymerization of biomass. While the microbial pathways associated with levoglucosan utilization have been characterized, there is little known about cellobiosan utilization. Here we describe the isolation and characterization of six cellobiosan-utilizing microbes from soil samples. Each of these organisms is capable of using both cellobiosan and levoglucosan as sole carbon source, though both minimal and rich media cellobiosan supported significantly higher biomass production than levoglucosan. Ribosomal sequencing was used to identify the closest reported match for these organisms: Sphingobacterium multivorum, Acinetobacter oleivorans JC3-1, Enterobacter sp SJZ-6, and Microbacterium sps FXJ8.207 and 203 and a fungal species Cryptococcus sp. The commercially-acquired Enterobacter cloacae DSM 16657 showed growth on levoglucosan and cellobiosan, supporting our isolate identification. Analysis of an existing database of 16S rRNA amplicons from Iowa soil samples confirmed the representation of our five bacterial isolates and four previously-reported levoglucosan-utilizing bacterial isolates in other soil samples and provided insight into their population distributions. Phylogenetic analysis of the 16S rRNA and 18S rRNA of strains previously reported to utilize levoglucosan and our newfound isolates showed that the organisms isolated in this study are distinct from previously described anhydrosugar-utilizing microbial species.

  18. Economical evolution: microbes reduce the synthetic cost of extracellular proteins.

    Science.gov (United States)

    Smith, Daniel R; Chapman, Matthew R

    2010-08-24

    Protein evolution is not simply a race toward improved function. Because organisms compete for limited resources, fitness is also affected by the relative economy of an organism's proteome. Indeed, many abundant proteins contain relatively high percentages of amino acids that are metabolically less taxing for the cell to make, thus reducing cellular cost. However, not all abundant proteins are economical, and many economical proteins are not particularly abundant. Here we examined protein composition and found that the relative synthetic cost of amino acids constrains the composition of microbial extracellular proteins. In Escherichia coli, extracellular proteins contain, on average, fewer energetically expensive amino acids independent of their abundance, length, function, or structure. Economic pressures have strategically shaped the amino acid composition of multicomponent surface appendages, such as flagella, curli, and type I pili, and extracellular enzymes, including type III effector proteins and secreted serine proteases. Furthermore, in silico analysis of Pseudomonas syringae, Mycobacterium tuberculosis, Saccharomyces cerevisiae, and over 25 other microbes spanning a wide range of GC content revealed a broad bias toward more economical amino acids in extracellular proteins. The synthesis of any protein, especially those rich in expensive aromatic amino acids, represents a significant investment. Because extracellular proteins are lost to the environment and not recycled like other cellular proteins, they present a greater burden on the cell, as their amino acids cannot be reutilized during translation. We hypothesize that evolution has optimized extracellular proteins to reduce their synthetic burden on the cell.

  19. The Indirect Effect of UV: Some Good News for Microbes?

    Science.gov (United States)

    Rothschild, Lynn J.; Purcell, Diane; Rogoff, Dana; Wilson, Cindy; Brass, James A. (Technical Monitor)

    2002-01-01

    Ultraviolet (UV) radiation is of great concern because its biological effects are predominantly harmful. UV damage may be direct or indirect, the latter mediated through the photochemical production of reactive oxygen species such as hydrogen peroxide. We measured the effect of H2O2 on various microbes both in the lab and in nature. At our study site in Yellowstone National Park, there is a UV-induced diurnal fluctuation of H2O2 extending up to one micron. Levels of DNA synthesis resulting from exposure to H2O2 were measured in several algal mats. Within naturally-occurring concentrations of H2O2, DNA synthesis increased. Laboratory studies showed that similar concentrations of H2O2 induce mitosis. We hypothesize that the low levels of H2O2 encountered in nature are inducing mitotic division. At higher levels of H2O2 a second peak in DNA synthesis was found which we interpret to represent DNA damage repair. These experiments suggest that in nature, the low levels of H2O2 produced may have a mitogenic rather than damaging effect. Assuming early levels of UV radiation were substantially higher at the time protists evolved, differential mitogenic effects could have influenced protistan evolution. With H2O2 likely to be present on such bodies as Mars and Europa, the response of organisms will be concentration-dependent and not linear.

  20. Marine Drugs from Sponge-Microbe Association—A Review

    Directory of Open Access Journals (Sweden)

    Tresa Remya A. Thomas

    2010-04-01

    Full Text Available The subject of this review is the biodiversity of marine sponges and associated microbes which have been reported to produce therapeutically important compounds, along with the contextual information on their geographic distribution. Class Demospongiae and the orders Halichondrida, Poecilosclerida and Dictyoceratida are the richest sources of these compounds. Among the microbial associates, members of the bacterial phylum Actinobacteria and fungal division Ascomycota have been identified to be the dominant producers of therapeutics. Though the number of bacterial associates outnumber the fungal associates, the documented potential of fungi to produce clinically active compounds is currently more important than that of bacteria. Interestingly, production of a few identical compounds by entirely different host-microbial associations has been detected in both terrestrial and marine environments. In the Demospongiae, microbial association is highly specific and so to the production of compounds. Besides, persistent production of bioactive compounds has also been encountered in highly specific host-symbiont associations. Though spatial and temporal variations are known to have a marked effect on the quality and quantity of bioactive compounds, only a few studies have covered these dimensions. The need to augment production of these compounds through tissue culture and mariculture has also been stressed. The reviewed database of these compounds is available at www.niobioinformatics.in/drug.php.

  1. The battle for chitin recognition in plant-microbe interactions.

    Science.gov (United States)

    Sánchez-Vallet, Andrea; Mesters, Jeroen R; Thomma, Bart P H J

    2015-03-01

    Fungal cell walls play dynamic functions in interaction of fungi with their surroundings. In pathogenic fungi, the cell wall is the first structure to make physical contact with host cells. An important structural component of fungal cell walls is chitin, a well-known elicitor of immune responses in plants. Research into chitin perception has sparked since the chitin receptor from rice was cloned nearly a decade ago. Considering the widespread nature of chitin perception in plants, pathogens evidently evolved strategies to overcome detection, including alterations in the composition of cell walls, modification of their carbohydrate chains and secretion of effectors to provide cell wall protection or target host immune responses. Also non-pathogenic fungi contain chitin in their cell walls and are recipients of immune responses. Intriguingly, various mutualists employ chitin-derived signaling molecules to prepare their hosts for the mutualistic relationship. Research on the various types of interactions has revealed different molecular components that play crucial roles and, moreover, that various chitin-binding proteins contain dissimilar chitin-binding domains across species that differ in affinity and specificity. Considering the various strategies from microbes and hosts focused on chitin recognition, it is evident that this carbohydrate plays a central role in plant-fungus interactions.

  2. Engineering plant-microbe symbiosis for rhizoremediation of heavy metals.

    Science.gov (United States)

    Wu, Cindy H; Wood, Thomas K; Mulchandani, Ashok; Chen, Wilfred

    2006-02-01

    The use of plants for rehabilitation of heavy-metal-contaminated environments is an emerging area of interest because it provides an ecologically sound and safe method for restoration and remediation. Although a number of plant species are capable of hyperaccumulation of heavy metals, the technology is not applicable for remediating sites with multiple contaminants. A clever solution is to combine the advantages of microbe-plant symbiosis within the plant rhizosphere into an effective cleanup technology. We demonstrated that expression of a metal-binding peptide (EC20) in a rhizobacterium, Pseudomonas putida 06909, not only improved cadmium binding but also alleviated the cellular toxicity of cadmium. More importantly, inoculation of sunflower roots with the engineered rhizobacterium resulted in a marked decrease in cadmium phytotoxicity and a 40% increase in cadmium accumulation in the plant root. Owing to the significantly improved growth characteristics of both the rhizobacterium and plant, the use of EC20-expressing P. putida endowed with organic-degrading capabilities may be a promising strategy to remediate mixed organic-metal-contaminated sites.

  3. Exploring laser-guided metal deposition through a microbe metabolite

    Directory of Open Access Journals (Sweden)

    H. Hocheng

    2009-12-01

    Full Text Available Purpose: The purpose of the paper is to describe exploring laser-guided metal deposition through a microbe metabolite.Design/methodology/approach: A maskless micro-fabrication of laser-guided deposition process through the metabolite of Acidophilic bacteria Thiobacillus ferrooxidans (T.f. is explored.Findings: The authors have conducted an analysis of the metal deposition process using the point thermal-source of the Nd:YAG laser through the metabolite of Acidophilic bacteria Thiobacillus. An analytical model adopting the moving point heat source on the substrate and heat transfer conditions is presented. The thermal field generated by the laser input energy is investigated.Practical implications: Though the mechanism of the laser-assisted deposition process is not fully revealed by biologist yet, the current model provides a means of control of the line deposition of metals.Originality/value: Based on the fundamental knowledge of how the line width varies with laser power and scanning speed, more investigation of the mini-scale heat convection and the threshold temperature of chemical reaction is expected in the future for further understanding of this novel metal deposition method triggered and written by laser.

  4. Linking plant nutritional status to plant-microbe interactions.

    Directory of Open Access Journals (Sweden)

    Lilia C Carvalhais

    Full Text Available Plants have developed a wide-range of adaptations to overcome nutrient limitation, including changes to the quantity and composition of carbon-containing compounds released by roots. Root-associated bacteria are largely influenced by these compounds which can be perceived as signals or substrates. Here, we evaluate the effect of root exudates collected from maize plants grown under nitrogen (N, phosphate (P, iron (Fe and potassium (K deficiencies on the transcriptome of the plant growth promoting rhizobacterium (PGPR Bacillus amyloliquefaciens FZB42. The largest shifts in gene expression patterns were observed in cells exposed to exudates from N-, followed by P-deficient plants. Exudates from N-deprived maize triggered a general stress response in FZB42 in the exponential growth phase, which was evidenced by the suppression of numerous genes involved in protein synthesis. Exudates from P-deficient plants induced bacterial genes involved in chemotaxis and motility whilst exudates released by Fe and K deficient plants did not cause dramatic changes in the bacterial transcriptome during exponential growth phase. Global transcriptional changes in bacteria elicited by nutrient deficient maize exudates were significantly correlated with concentrations of the amino acids aspartate, valine and glutamate in root exudates suggesting that transcriptional profiling of FZB42 associated with metabolomics of N, P, Fe and K-deficient maize root exudates is a powerful approach to better understand plant-microbe interactions under conditions of nutritional stress.

  5. The role of lipids in host microbe interactions.

    Science.gov (United States)

    Lang, Roland; Mattner, Jochen

    2017-06-01

    Lipids are one of the major subcellular constituents and serve as signal molecules, energy sources, metabolic precursors and structural membrane components in various organisms. The function of lipids can be modified by multiple biochemical processes such as (de-)phosphorylation or (de-)glycosylation, and the organization of fatty acids into distinct cellular pools and subcellular compartments plays a pivotal role for the morphology and function of various cell populations. Thus, lipids regulate, for example, phagosome formation and maturation within host cells and thus, are critical for the elimination of microbial pathogens. Vice versa, microbial pathogens can manipulate the lipid composition of phagosomal membranes in host cells, and thus avoid their delivery to phagolysosomes. Lipids of microbial origin belong also to the strongest and most versatile inducers of mammalian immune responses upon engagement of distinct receptors on myeloid and lymphoid cells. Furthermore, microbial lipid toxins can induce membrane injuries and cell death. Thus, we will review here selected examples for mutual host-microbe interactions within the broad and divergent universe of lipids in microbial defense, tissue injury and immune evasion.

  6. The symbiont side of symbiosis: do microbes really benefit?

    Directory of Open Access Journals (Sweden)

    Justine Rebecca Garcia

    2014-09-01

    Full Text Available Microbial associations are integral to all eukaryotes. Mutualism, the interaction of two species for the benefit of both, is an important aspect of microbial associations, with evidence that multicellular organisms in particular benefit from microbes. However, the microbe’s perspective has largely been ignored, and it is unknown whether most microbial symbionts benefit from their associations with hosts. It has been presumed that microbial symbionts receive host-derived nutrients or a competition-free environment with reduced predation, but there have been few empirical tests, or even critical assessments, of these assumptions. We evaluate these hypotheses based on available evidence, which indicate reduced competition and predation are not universal benefits for symbionts. Some symbionts do receive nutrients from their host, but this has not always been linked to a corresponding increase in symbiont fitness. We recommend experiments to test symbiont fitness using current experimental systems of symbiosis and detail considerations for other systems. Incorporating symbiont fitness into symbiosis research will provide insight into the evolution of mutualistic interactions and cooperation in general.

  7. Diet, genes, and microbes: complexities of colon cancer prevention.

    Science.gov (United States)

    Birt, Diane F; Phillips, Gregory J

    2014-01-01

    Colorectal cancer is one of the leading causes of cancer-related deaths in the United States, and generally, as countries climb the economic ladder, their rates of colon cancer increase. Colon cancer was an early disease where key genetic mutations were identified as important in disease progression, and there is considerable interest in determining whether specific mutations sensitize the colon to cancer prevention strategies. Epidemiological studies have revealed that fiber- and vegetable-rich diets and physical activity are associated with reduced rates of colon cancer, while consumption of red and processed meat, or alcoholic beverages, and overconsumption as reflected in obesity are associated with increased rates. Animal studies have probed these effects and suggested directions for further refinement of diet in colon cancer prevention. Recently a central role for the microorganisms in the gastrointestinal tract in colon cancer development is being probed, and it is hypothesized that the microbes may integrate diet and host genetics in the etiology of the disease. This review provides background on dietary, genetic, and microbial impacts on colon cancer and describes an ongoing project using rodent models to assess the ability of digestion-resistant starch in the integration of these factors with the goal of furthering colon cancer prevention.

  8. Microbe-surface interactions in biofouling and biocorrosion processes.

    Science.gov (United States)

    Beech, Iwona B; Sunner, Jan A; Hiraoka, Kenzo

    2005-09-01

    The presence of microorganisms on material surfaces can have a profound effect on materials performance. Surface-associated microbial growth, i.e. a biofilm, is known to instigate biofouling. The presence of biofilms may promote interfacial physico-chemical reactions that are not favored under abiotic conditions. In the case of metallic materials, undesirable changes in material properties due to a biofilm (or a biofouling layer) are referred to as biocorrosion or microbially influenced corrosion (MIC). Biofouling and biocorrosion occur in aquatic and terrestrial habitats varying in nutrient content, temperature, pressure and pH. Interfacial chemistry in such systems reflects a wide variety of physiological activities carried out by diverse microbial populations thriving within biofilms. Biocorrosion can be viewed as a consequence of coupled biological and abiotic electron-transfer reactions, i.e. redox reactions of metals, enabled by microbial ecology. Microbially produced extracellular polymeric substances (EPS), which comprise different macromolecules, mediate initial cell adhesion to the material surface and constitute a biofilm matrix. Despite their unquestionable importance in biofilm development, the extent to which EPS contribute to biocorrosion is not well-understood. This review offers a current perspective on material/microbe interactions pertinent to biocorrosion and biofouling, with EPS as a focal point, while emphasizing the role atomic force spectroscopy and mass spectrometry techniques can play in elucidating such interactions.

  9. MECHANISMS OF MICROBE-HOST-INTERACTION IN CROHN'S DISEASE: DYSBIOSIS VS. PATHOBIONT SELECTION

    Directory of Open Access Journals (Sweden)

    Ludovica F. Buttó

    2015-11-01

    Full Text Available Crohn’s disease (CD is a systemic chronic inflammatory condition mainly characterized by discontinuous transmural pathology of the gastrointestinal tract and frequent extra-intestinal manifestations with intermittent episodes of remission and relapse. Genome-wide association studies identified a number of risk loci that, catalyzed by environmental triggers, result in the loss of tolerance towards commensal bacteria based on dysregulated innate effector functions and anti-microbial defense, leading to exacerbated adaptive immune responses responsible for chronic immune-mediated tissue damage. In this review, we discuss the interrelated role of changes in the intestinal microbiota, epithelial barrier integrity and immune cell functions on the pathogenesis of CD, describing the current approaches available to investigate the molecular mechanisms underlying the disease. Substantial effort has been dedicated to define disease-associated changes in the intestinal microbiota (dysbiosis and to link pathobionts to the aetiology of IBD. A cogent definition of dysbiosis is lacking, as well as an agreement of whether pathobionts or complex shifts in the microbiota trigger inflammation in the host. Among the rarely available animal models, SAMP/Yit and TNFdeltaARE mice are the best known displaying a transmural CD-like phenotype. New hypothesis-driven mouse models e.g. epithelial-specific Caspase8-/-, ATG16L1-/- and XBP-1-/- mice validate pathway-focused function of specific CD-associated risk genes highlighting the role of Paneth cells in antimicrobial defense. To study the causal role of bacteria in initiating inflammation in the host, the use of germfree mouse models is indispensable. Unraveling the interactions of genes, immune cells and microbes constitute a criterion for the development of safe, reliable and effective treatment options for CD.

  10. Functional biogeography of ocean microbes revealed through non-negative matrix factorization.

    Directory of Open Access Journals (Sweden)

    Xingpeng Jiang

    Full Text Available The direct "metagenomic" sequencing of genomic material from complex assemblages of bacteria, archaea, viruses and microeukaryotes has yielded new insights into the structure of microbial communities. For example, analysis of metagenomic data has revealed the existence of previously unknown microbial taxa whose spatial distributions are limited by environmental conditions, ecological competition, and dispersal mechanisms. However, differences in genotypes that might lead biologists to designate two microbes as taxonomically distinct need not necessarily imply differences in ecological function. Hence, there is a growing need for large-scale analysis of the distribution of microbial function across habitats. Here, we present a framework for investigating the biogeography of microbial function by analyzing the distribution of protein families inferred from environmental sequence data across a global collection of sites. We map over 6,000,000 protein sequences from unassembled reads from the Global Ocean Survey dataset to [Formula: see text] protein families, generating a protein family relative abundance matrix that describes the distribution of each protein family across sites. We then use non-negative matrix factorization (NMF to approximate these protein family profiles as linear combinations of a small number of ecological components. Each component has a characteristic functional profile and site profile. Our approach identifies common functional signatures within several of the components. We use our method as a filter to estimate functional distance between sites, and find that an NMF-filtered measure of functional distance is more strongly correlated with environmental distance than a comparable PCA-filtered measure. We also find that functional distance is more strongly correlated with environmental distance than with geographic distance, in agreement with prior studies. We identify similar protein functions in several components and

  11. On a question of Gross

    Science.gov (United States)

    Banerjee, Abhijit

    2007-03-01

    Using the notion of weighted sharing of sets we prove two uniqueness theorems which improve the results proved by Fang and Qiu [H. Qiu, M. Fang, A unicity theorem for meromorphic functions, Bull. Malaysian Math. Sci. Soc. 25 (2002) 31-38], Lahiri and Banerjee [I. Lahiri, A. Banerjee, Uniqueness of meromorphic functions with deficient poles, Kyungpook Math. J. 44 (2004) 575-584] and Yi and Lin [H.X. Yi, W.C. Lin, Uniqueness theorems concerning a question of Gross, Proc. Japan Acad. Ser. A 80 (2004) 136-140] and thus provide an answer to the question of Gross [F. Gross, Factorization of meromorphic functions and some open problems, in: Proc. Conf. Univ. Kentucky, Lexington, KY, 1976, in: Lecture Notes in Math., vol. 599, Springer, Berlin, 1977, pp. 51-69], under a weaker hypothesis.

  12. Cancer Genome Anatomy Project (CGAP) | Office of Cancer Genomics

    Science.gov (United States)

    CGAP generated a wide range of genomics data on cancerous cells that are accessible through easy-to-use online tools. Researchers, educators, and students can find "in silico" answers to biological questions through the CGAP website. Request a free copy of the CGAP Website Virtual Tour CD from ocg@mail.nih.gov to learn how to navigate the website.

  13. Foreign language didactics: Identity questions

    OpenAIRE

    Michaela Píšová

    2011-01-01

    The efforts to emancipate foreign language didactics have been an ongoingand non-linear process launched in our country in the 50s of the previous century.Its key aspects may be presented as foreign language didactics identity questions.These include explicit delineation of the object and methodology of foreign languagedidactics on the basis of developmental analysis, current state of knowledge andtrends/approaches to the discipline. The issues related to the full-fledged scientificstatus of ...

  14. Mitochondrial genomes as living ‘fossils’

    OpenAIRE

    2013-01-01

    The huge variation between mitochondrial genomes makes untangling their evolutionary histories difficult. Richardson et al. report on the remarkably unaltered ‘fossil’ genome of the tulip tree, giving us many clues as to how the mitochondrial genomes of flowering plants have evolved over the last 150 million years, and raising questions about how such extraordinary sequence conservation can be maintained. See research article http://www.biomedcentral.com/1741-7007/11/29.

  15. Enhancement Effect of Gold Nanoparticles on the Bioactivity of Hydrogen-producing Microbe

    Institute of Scientific and Technical Information of China (English)

    LIU Guangzhen; MA Zhanfang; SHEN Jianquan

    2006-01-01

    In order to increase the yield of hydrogen production for hydrogen-producing microbe, the enhancement effect of nanometer- sized gold particles on the activity of hydrogen-producing microbe was studied. The yields of hydrogen production in the system added by gold nanoparticles of 6 nm and 12 nm in diameter were obviously increased by about 17% and 9% in contrast to that in blank system. The experimental results indicate that gold nanoparticles could significantly enhance the bioactivity of hydrogen-producing microbe.

  16. Helping plants to deal with insects: the role of beneficial soil-borne microbes.

    Science.gov (United States)

    Pineda, Ana; Zheng, Si-Jun; van Loon, Joop J A; Pieterse, Corné M J; Dicke, Marcel

    2010-09-01

    Several soil-borne microbes such as mycorrhizal fungi and plant growth-promoting rhizobacteria can help plants to deal with biotic and abiotic stresses via plant growth promotion and induced resistance. Such beneficial belowground microbes interact in a bidirectional way via the plant with aboveground insects such as herbivores, their natural enemies and pollinators. The role of these interactions in natural and agricultural ecosystems is receiving increased attention, and the molecular and physiological mechanisms involved in these interactions should be the focus of more attention. Here, we review the recent discoveries on plant-mediated interactions between beneficial belowground microbes and aboveground insects.

  17. Some open questions in hydrodynamics

    CERN Document Server

    Dyndal, Mateusz

    2014-01-01

    When speaking of unsolved problems in physics, this is surprising at first glance to discuss the case of fluid mechanics. However, there are many deep open questions that come with the theory of fluid mechanics. In this paper, we discuss some of them that we classify in two categories, the long term behavior of solutions of equations of hydrodynamics and the definition of initial (boundary) conditions. The first set of questions come with the non-relativistic theory based on the Navier-Stokes equations. Starting from smooth initial conditions, the purpose is to understand if solutions of Navier-Stokes equations remain smooth with the time evolution. Existence for just a finite time would imply the evolution of finite time singularities, which would have a major influence on the development of turbulent phenomena. The second set of questions come with the relativistic theory of hydrodynamics. There is an accumulating evidence that this theory may be relevant for the description of the medium created in high en...

  18. Questions as a tool to design

    DEFF Research Database (Denmark)

    Aurisicchio, Marco; Ahmed, Saeema; Wallace, Ken

    2007-01-01

    This paper describes an interpretation of design activity through investigating design questions. From a number of previous studies two types of question have been identified: 1) reasoning questions; and 2) strategic questions. Strategic questions are part of an experienced designers approach to ...

  19. Soft Physics and Intermittency Open Question(s) in Krakow

    CERN Document Server

    Peschanski, R

    1993-01-01

    This contribution contains a summary of the Krakow meeting on Soft Physics and Fluctuations. It emphasizes both the experimental and the theoretical investigations on correlations/fluctuations and intermittency in multi-particle processes and discusses of the present status of this concept. A clarification of the main open questions in this field of research is now within reach, thanks to the studies presented at the meeting. Summary Talk of the Krakow Workshop on Multiparticle Physics, May, 4-7, 1993. E-mail contact: pesch@amoco.saclay.cea.fr

  20. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

    KAUST Repository

    Wang, Yong

    2011-12-21

    The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

  1. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments.

    Directory of Open Access Journals (Sweden)

    Yong Wang

    Full Text Available The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed.

  2. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.

    Science.gov (United States)

    Smokvina, Tamara; Wels, Michiel; Polka, Justyna; Chervaux, Christian; Brisse, Sylvain; Boekhorst, Jos; van Hylckama Vlieg, Johan E T; Siezen, Roland J

    2013-01-01

    Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon) are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis, in order to link

  3. The increasing role of genetics and genomics in women's health.

    Science.gov (United States)

    Klein, Elisabeth Lisa Z

    2014-01-01

    Genetic and genomic testing are a clinical reality in health care today. Persons at risk for disease or who are simply curious about their genomes can have them analyzed. An individual's genome is a function of ancestry, family history and personal health and environmental exposures. Clinical and pharmacologic information can be obtained through genomic analysis. Genomic testing can be done by health care providers but some results can now be obtained through direct-to-consumer tests. Many ethical questions are being raised regarding genomic testing. Nurses can provide more optimal care by understanding the process of genomic testing as well as the implications of the results.

  4. Genomic Medicine

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-04-01

    disease; thus, conducts may be undertaken like selection of embryos or opting for adoption. Although genetic studies of molecular profiles are promissory, there are questions on how these are requested and how the results are communicated to the patients, their clinical use, application of the pre-symptomatic diagnosis – especially in children, the bad intended use of this information by medical insurance companies considering pre-existing conditions, and finally, the great amount of information and its application in populations where prior studies of association have not been conducted may be cause for concern. In developed nations, these types of exams are requested without medical prescription in pharmacies that mail the results directly to the interested party.  It is worrisome what can happen to patients upon receiving this information; for example, if the report indicates susceptibility to Alzheimer’s or cancer, without medical support to identify the presentation risks and the possibility of transmitting the disease to their offspring.  This suggests the validity, more than ever, of genetic counseling when delivering analysis results. On the other hand, insurance companies must consider molecular genetic profiles as a preventive tool that permits improving service quality while lowering costs; for instance, in cancer cases where prophylaxis measures are notably less costly than treatment. Another aspect to bear in mind is that association studies of genetic polymorphism and disease need thousands of cases and controls, making them very costly for implementation in Colombia. For this reason, the exams include the ancestral report for the purpose of interpreting the results according to ethnic origin.  For now, this is the most adequate conduct considering that it will take a long time before validation studies can be conducted. As with all great progress in medicine, genomics opens a path that will bring enormous benefit inasmuch as the criteria for good

  5. GENOMIC MEDICINE

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-03-01

    ; thus, conducts may be undertaken like selection of embryos or opting for adoption.Although genetic studies of molecular profiles are promissory, there are questions on how these are requested and how the results are communicated to the patients, their clinical use, application of the pre-symptomatic diagnosis – especially in children, the bad intended use of this information by medical insurance companies considering pre-existing conditions, and finally, the great amount of information and its application in populations where prior studies of association have not been conducted may be cause for concern.In developed nations, these types of exams are requested without medical prescription in pharmacies that mail the results directly to the interested party. It is worrisome what can happen to patients upon receiving this information; for example, if the report indicates susceptibility to Alzheimer’s or cancer, without medical support to identify the presentation risks and the possibility of transmitting the disease to their offspring. This suggests the validity, more than ever, of genetic counseling when delivering analysis results.On the other hand, insurance companies must consider molecular genetic profiles as a preventive tool that permits improving service quality while lowering costs; for instance, in cancer cases where prophylaxis measures are notably less costly than treatment.Another aspect to bear in mind is that association studies of genetic polymorphism and disease need thousands of cases and controls, making them very costly for implementation in Colombia. For this reason, the exams include the ancestral report for the purpose of interpreting the results according to ethnic origin. For now, this is the most adequate conduct considering that it will take a long time before validation studies can be conducted.As with all great progress in medicine, genomics opens a path that will bring enormous benefit inasmuch as the criteria for good medical practices

  6. God in Question: Questioning as a Prerequisite for Theology

    Directory of Open Access Journals (Sweden)

    Martin Kočí

    2014-10-01

    Full Text Available There are questions that are so important that it is a pity to spoil them with answers. No doubt, the question of God is one of them. Contrary to many presuppositions, theology is not capable of providing us with the final answers in this respect. On the contrary, theology professed as fides quaerens intellectum is an ongoing struggle with questions. Modernity interrupted this paradigm of theological questioning. Theology was withdrawn from the realm of understanding and shifted to the realm of explanation. Modernity brought the univocalization of God. Nonetheless, the attempts to tackle the question of God lead to hegemonic narratives about God. Such narratives are rightly criticized in a postmodern context for their totalizing pretensions. The problem of postmodern criticism is its one-sided emphasis on the apophatic dimension of theological discourse. I propose that theology can go a step further beyond postmodernity. In order to do so, I deal with the Czech philosopher Jan Patočka, who provides an opportunity to rethink God from the perspective of questioning in a new way. Patočka’s insistence on problematicity is the main reading key of his work. In this line of though, I interpret Patočka’s student Tomáš Halík and his thesis about the necessity to take the metaphor of an unknown God into account. I argue that theology must avoid the temptation to remove God from the question and make a well-known God of him. The time has come for theologians to turn their answers back into questions and dwell with them. Bůh jako otázka: Tázání jako předpoklad teologie Některé otázky jsou tak důležité, že je škoda kazit je odpověďmi. Není pochyb, že otázka po Bohu je jednou z nich. Navzdory mnoha předpokladům, ani teologie není schopna poskytnout v tomto ohledu konečné odpovědi. Teologie pojatá jako fides quaerens intellectum je nepřetržitý nekončící zápas s otázkami. Moderna narušila toto paradigma teologick

  7. Questions concerning the nuclear wastes; Les dechets nucleaires en questions

    Energy Technology Data Exchange (ETDEWEB)

    Daures, Pierre [ed.] [Electricite de France (EDF), 75 - Paris (France)

    1998-07-01

    At present, 75% of the electricity in France is of nuclear origin. Most of French people approve this mode of energy production and agree upon the continuation of the electronuclear sector exploitation. However, as any industry, the nuclear industry produces wastes which constitute a keen preoccupation of the public opinion. The nuclear program, even at its very inception, has provided the appropriate mastering of radioactive wastes by reducing their volume, by conditioning, reprocessing and storing, expressing continually its carefulness for population protection as well as for environment defence against the radiological effects. Pursuing its policy of transparency the EDF demonstrated openness and understanding towards questions raised by anyone. This brochure gives answers to the following 17 questions: -what the nuclear wastes are, which is their origin? - what is their amount? - are the nuclear waste dangerous? - how to treat the nuclear wastes? - are the radioactive waste storage sure? - is the nuclear waste transportation sure? - are these solutions sure? - why searches for long-lived radioactive wastes? - what is transmutation? - shall we bequeath to the next generations our nuclear wastes? - are there particular problems in nuclear power plant decommissioning? - what the wastes issued from decommissioning become? - are the costs of reprocessing and decommissioning taken into account in the price of the kWh? - were the nuclear wastes taken into account since the nuclear program inception? - who manages the nuclear wastes? - why France accepted the reprocessing of nuclear wastes produced in foreign countries? - is there an international policy for nuclear wastes?.

  8. A Reflection on Teacher Questioning Types

    Directory of Open Access Journals (Sweden)

    Kasih Elisabeth Roostini

    2011-07-01

    Full Text Available Abstract This small-scale research is expected to serve as a reflective means for teachers so that they can explore their questioning types in their own classroom. It analyzed questioning types used by three teachers of general English classes. The questioning types were classified based on three dimensions—purpose, form, and function. The purpose-based questioning types, based on Long and Sato’s findings (1983, were classified into two: referential and display. The form-based questioning types, based on the classification of question types by Celce-Murcia and Larsen-Freeman (1999 and Biber et al. (1999, were classified into four major types: yes/no-questions, wh-questions, tag questions, and alternative questions. The function-based questioning types, based on Long and Sato’s findings (1983, were classified into three sub-types: comprehension checks, confirmation checks, and clarification requests.           The data, obtained from three recorded class meetings, were transcribed and analyzed to see what questioning types each teacher employed and to obtain the number and percentage distribution of questioning types each teacher used. The results showed that referential questions were more frequently used than display questions at higher levels. There were a substantial number of incomplete questions, a form-based questioning type that did not belong to the classification of form-based questioning types employed in this study. The predominant use of incomplete questions in a communicative classroom should be reviewed as this questioning type required accuracy, rather than promoting language practice. The third type, the function-based questioning types, did not occur frequently at all the three stages. This study suggests that teachers use incomplete questions less frequently and try to use other form-based questioning types. It also encourages teachers to reflect on their own teaching and pursue their professional development.

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

    Directory of Open Access Journals (Sweden)

    Romantschuk Martin

    2008-12-01

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

  10. Insight and analysis problem solving in microbes to machines.

    Science.gov (United States)

    Clark, Kevin B

    2015-11-01

    A key feature for obtaining solutions to difficult problems, insight is oftentimes vaguely regarded as a special discontinuous intellectual process and/or a cognitive restructuring of problem representation or goal approach. However, this nearly century-old state of art devised by the Gestalt tradition to explain the non-analytical or non-trial-and-error, goal-seeking aptitude of primate mentality tends to neglect problem-solving capabilities of lower animal phyla, Kingdoms other than Animalia, and advancing smart computational technologies built from biological, artificial, and composite media. Attempting to provide an inclusive, precise definition of insight, two major criteria of insight, discontinuous processing and problem restructuring, are here reframed using terminology and statistical mechanical properties of computational complexity classes. Discontinuous processing becomes abrupt state transitions in algorithmic/heuristic outcomes or in types of algorithms/heuristics executed by agents using classical and/or quantum computational models. And problem restructuring becomes combinatorial reorganization of resources, problem-type substitution, and/or exchange of computational models. With insight bounded by computational complexity, humans, ciliated protozoa, and complex technological networks, for example, show insight when restructuring time requirements, combinatorial complexity, and problem type to solve polynomial and nondeterministic polynomial decision problems. Similar effects are expected from other problem types, supporting the idea that insight might be an epiphenomenon of analytical problem solving and consequently a larger information processing framework. Thus, this computational complexity definition of insight improves the power, external and internal validity, and reliability of operational parameters with which to classify, investigate, and produce the phenomenon for computational agents ranging from microbes to man-made devices.

  11. Adaptation Mechanisms in the Evolution of Moss Defenses to Microbes.

    Science.gov (United States)

    Ponce de León, Inés; Montesano, Marcos

    2017-01-01

    Bryophytes, including mosses, liverworts and hornworts are early land plants that have evolved key adaptation mechanisms to cope with abiotic stresses and microorganisms. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. In addition, early land plants acquired novel defense mechanisms to protect plant tissues from pre-existing microbial pathogens. Due to its evolutionary stage linking unicellular green algae to vascular plants, the non-vascular moss Physcomitrella patens is an interesting organism to explore the adaptation mechanisms developed in the evolution of plant defenses to microbes. Cellular and biochemical approaches, gene expression profiles, and functional analysis of genes by targeted gene disruption have revealed that several defense mechanisms against microbial pathogens are conserved between mosses and flowering plants. P. patens perceives pathogen associated molecular patterns by plasma membrane receptor(s) and transduces the signal through a MAP kinase (MAPK) cascade leading to the activation of cell wall associated defenses and expression of genes that encode proteins with different roles in plant resistance. After pathogen assault, P. patens also activates the production of ROS, induces a HR-like reaction and increases levels of some hormones. Furthermore, alternative metabolic pathways are present in P. patens leading to the production of a distinct metabolic scenario than flowering plants that could contribute to defense. P. patens has acquired genes by horizontal transfer from prokaryotes and fungi, and some of them could represent adaptive benefits for resistance to biotic stress. In this review, the current knowledge related to the evolution of plant defense responses against pathogens will be discussed, focusing on the latest advances made in the model plant P. patens.

  12. Scaling Soil Microbe-Water Interactions from Pores to Ecosystems

    Science.gov (United States)

    Manzoni, S.; Katul, G. G.

    2014-12-01

    The spatial scales relevant to soil microbial activity are much finer than scales relevant to whole-ecosystem function and biogeochemical cycling. On the one hand, how to link such different scales and develop scale-aware biogeochemical and ecohydrological models remains a major challenge. On the other hand, resolving these linkages is becoming necessary for testing ecological hypotheses and resolving data-theory inconsistencies. Here, the relation between microbial respiration and soil moisture expressed in water potential is explored. Such relation mediates the water availability effects on ecosystem-level heterotrophic respiration and is of paramount importance for understanding CO2 emissions under increasingly variable rainfall regimes. Respiration has been shown to decline as the soil dries in a remarkably consistent way across climates and soil types (open triangles in Figure). Empirical models based on these respiration-moisture relations are routinely used in Earth System Models to predict moisture effects on ecosystem respiration. It has been hypothesized that this consistency in microbial respiration decline is due to breakage of water film continuity causing in turn solute diffusion limitations in dry conditions. However, this hypothesis appears to be at odds with what is known about soil hydraulic properties. Water film continuity estimated from soil water retention (SWR) measurements at the 'Darcy' scale breaks at far less negative water potential (tools from percolation theory, it is demonstrated that hydrological measurements can be spatially downscaled at a micro-level relevant to microbial activity. Such downscaling resolves the inconsistency between respiration thresholds and hydrological thresholds. This result, together with observations of residual microbial activity well below -15 MPa (dashed back curve in Figure), lends support to the hypothesis that soil microbes are substrate-limited in dry conditions.

  13. Adaptation Mechanisms in the Evolution of Moss Defenses to Microbes

    Science.gov (United States)

    Ponce de León, Inés; Montesano, Marcos

    2017-01-01

    Bryophytes, including mosses, liverworts and hornworts are early land plants that have evolved key adaptation mechanisms to cope with abiotic stresses and microorganisms. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. In addition, early land plants acquired novel defense mechanisms to protect plant tissues from pre-existing microbial pathogens. Due to its evolutionary stage linking unicellular green algae to vascular plants, the non-vascular moss Physcomitrella patens is an interesting organism to explore the adaptation mechanisms developed in the evolution of plant defenses to microbes. Cellular and biochemical approaches, gene expression profiles, and functional analysis of genes by targeted gene disruption have revealed that several defense mechanisms against microbial pathogens are conserved between mosses and flowering plants. P. patens perceives pathogen associated molecular patterns by plasma membrane receptor(s) and transduces the signal through a MAP kinase (MAPK) cascade leading to the activation of cell wall associated defenses and expression of genes that encode proteins with different roles in plant resistance. After pathogen assault, P. patens also activates the production of ROS, induces a HR-like reaction and increases levels of some hormones. Furthermore, alternative metabolic pathways are present in P. patens leading to the production of a distinct metabolic scenario than flowering plants that could contribute to defense. P. patens has acquired genes by horizontal transfer from prokaryotes and fungi, and some of them could represent adaptive benefits for resistance to biotic stress. In this review, the current knowledge related to the evolution of plant defense responses against pathogens will be discussed, focusing on the latest advances made in the model plant P. patens. PMID:28360923

  14. Cr isotope fractionation in metal-mineral-microbe interactions

    Science.gov (United States)

    Zhang, Qiong; Porcelli, Don; Thompson, Ian; Amor, Ken; Galer, Stephen

    2016-04-01

    Microbes interact with metals and minerals in the environments, altering their physical and chemical state whilst in turn the metals and minerals affect microbial growth, activity and survival. The interactions between Cr, Fe minerals and bacteria were investigated in this study. Cr(VI) reduction experiments by two iron-reducing bacteria, Pseudomonas fluorescens LB 300 and Shewanella oneidensis MR 1, in the presence of two iron oxide minerals, goethite and hematite, were conducted. Both minerals were found to inhibit the Cr(VI) reduction rate by Pseudomonas fluorescens LB 300 but accelerated Shewanella oneidensis MR 1. The Cr isotopic fractionation factor generated by both bacteria was mostly independent of the presence of the minerals, except for hematite with Pseudomonas fluorescens LB 300, where the ɛ was much higher. Aqueous Fe(III) in the solution did not have any detectable impact on either bacterial Cr reduction rates or the isotopic fractionation factors, indicating that the reduction of Cr(VI) occurred prior to that of Fe(III). The presence of aqueous Fe(II) induced a very fast abiotic reduction of Cr, but had little impact on the bacterial Cr reduction rates or its isotope fractionations. The evidence suggests that the different impact that Fe minerals had on the bacteria were related to the way they attached to the minerals and the difference in the reduction mechanism. SEM images confirmed that the attachment of Pseudomonas fluorescens LB 300 on the mineral surfaces were much more tightly packed than that of Shewanella oneidensis MR 1, so reducing mineral-metal interactions.

  15. Nutrient subsidies to belowground microbes impact aboveground food web interactions.

    Science.gov (United States)

    Hines, Jes; Megonigal, J Patrick; Denno, Robert F

    2006-06-01

    Historically, terrestrial food web theory has been compartmentalized into interactions among aboveground or belowground communities. In this study we took a more synthetic approach to understanding food web interactions by simultaneously examining four trophic levels and investigating how nutrient (nitrogen and carbon) and detrital subsidies impact the ability of the belowground microbial community to alter the abundance of aboveground arthropods (herbivores and predators) associated with the intertidal cord grass Spartina alterniflora. We manipulated carbon, nitrogen, and detrital resources in a field experiment and measured decomposition rate, soil nitrogen pools, plant biomass and quality, herbivore density, and arthropod predator abundance. Because carbon subsidies impact plant growth only indirectly (microbial pathways), whereas nitrogen additions both directly (plant uptake) and indirectly (microbial pathways) impact plant primary productivity, we were able to assess the effect of both belowground soil microbes and nutrient availability on aboveground herbivores and their predators. Herbivore density in the field was suppressed by carbon supplements. Carbon addition altered soil microbial dynamics (net potential ammonification, litter decomposition rate, DON [dissolved organic N] concentration), which limited inorganic soil nitrogen availability and reduced plant size as well as predator abundance. Nitrogen addition enhanced herbivore density by increasing plant size and quality directly by increasing inorganic soil nitrogen pools, and indirectly by enhancing microbial nitrification. Detritus adversely affected aboveground herbivores mainly by promoting predator aggregation. To date, the effects of carbon and nitrogen subsidies on salt marshes have been examined as isolated effects on either the aboveground or the belowground community. Our results emphasize the importance of directly addressing the soil microbial community as a factor that influences

  16. Cloud computing for comparative genomics.

    Science.gov (United States)

    Wall, Dennis P; Kudtarkar, Parul; Fusaro, Vincent A; Pivovarov, Rimma; Patil, Prasad; Tonellato, Peter J

    2010-05-18

    Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems.

  17. Memory in microbes: quantifying history-dependent behavior in a bacterium.

    Directory of Open Access Journals (Sweden)

    Denise M Wolf

    Full Text Available Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These "memory" effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE synthesis and estimate the capacity of these systems and growth dynamics to 'remember' 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy.

  18. Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium

    Energy Technology Data Exchange (ETDEWEB)

    Wolf, Denise M.; Fontaine-Bodin, Lisa; Bischofs, Ilka; Price, Gavin; Keasling, Jay; Arkin, Adam P.

    2007-11-15

    Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These"memory" effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenologicalmeasure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesisand estimate the capacity of these systems and growth dynamics to"remember" 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cellhistory, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy.

  19. Memory in microbes: quantifying history-Dependent behavior in a bacterium.

    Energy Technology Data Exchange (ETDEWEB)

    Wolf, Denise M.; Fontaine-Bodin, Lisa; Bischofs, Ilka; Price, Gavin; Keaslin, Jay; Arkin, Adam P.

    2007-11-15

    Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These"memory" effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesis and estimate the capacity of these systems and growth dynamics to 'remember' 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy.

  20. Gross nitrogen fluxes in intact beech-soil-microbe systems under experimentally simulated climate change

    Science.gov (United States)

    Tejedor, Javier; Bilela, Silvija; Gasche Gasche, Rainer; Gschwendtner, Silvia; Leberecht, Martin; Bimüller, Carolin; Kögel-Knabner, Ingrid; Polle, Andrea; Schloter, Michael; Rennenberg, Heinz; Dannenmann, Michael

    2013-04-01

    The vulnerability of beech forests of Central Europe to projected climate change conditions is a current matter of debate and concern. In order to investigate the response of N cycling in a typical beech forest to projected climate change conditions, we transplanted small lysimeters with intact beech-soil systems from a slope with N-exposure (representing present day climate conditions) to a slope with S exposure (serving as a warmer and drier model climate for future conditions). Lysimeters transfers within the N exposure served as control. After an equilibration period of 1 year, three isotope labeling/harvest cycles were performed: (1) comparison between N and S slopes under ambient conditions; (2) comparison between N and S slopes after intensified drought at S exposure; (3) rewetting after the drought period. Homogenous triple isotope labeling (15N/13C glutamine, 15NH4+, 15NO3-) in combination with 15N tracing and -pool dilution approaches as well as molecular analyses of nitrogen cycling genes and mycorrhiza morphotyping allowed to simultaneously quantify all N turnover processes in the intact beech-soil-microbe system. Nitrate was the major N source of beech seedlings with little importance of ammonium and no importance of glutamine. Experimental simulation of climate change resulted in significantly reduced gene copies of ammonia oxidizing bacteria in soil (AOB), a dramatic attenuation of microbial gross nitrate production from 252±83 mg N m-2 day-1 for the control treatment to 49±29 mg N m-2 day-1 for the climate change treatment and associated strong declines in soil nitrate concentrations as well as nitrate uptake by microorganisms and beech, which could not be compensated by uptake of ammonium or glutamine. Therefore, N content of beech seedlings was strongly reduced in the climate change treatment. Hence our data provide a microbial mechanism to explain nutritional limitations of beech under higher temperatures and drought and raise questions about

  1. Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

    NARCIS (Netherlands)

    Bohlin, J.; Passel, van M.W.J.

    2012-01-01

    Background: We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and

  2. Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

    NARCIS (Netherlands)

    Bohlin, J.; Passel, van M.W.J.

    2012-01-01

    Background: We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and p

  3. Draft Genome Sequence of the Shellfish Larval Probiotic Bacillus pumilus RI06-95.

    Science.gov (United States)

    Hamblin, Meagan; Spinard, Edward; Gomez-Chiarri, Marta; Nelson, David R; Rowley, David C

    2015-09-03

    Bacillus pumilus RI06-95 is a marine bacterium isolated in Narragansett, Rhode Island, which has shown probiotic activity against marine pathogens in larval shellfish. We report the genome of B. pumilus RI06-95, which provides insight into the microbe's probiotic ability and may be used in future studies of the probiotic mechanism.

  4. Comparative evaluation of the genomes of three common Drosophila-associated bacteria.

    Science.gov (United States)

    Petkau, Kristina; Fast, David; Duggal, Aashna; Foley, Edan

    2016-09-15

    Drosophila melanogaster is an excellent model to explore the molecular exchanges that occur between an animal intestine and associated microbes. Previous studies in Drosophila uncovered a sophisticated web of host responses to intestinal bacteria. The outcomes of these responses define critical events in the host, such as the establishment of immune responses, access to nutrients, and the rate of larval development. Despite our steady march towards illuminating the host machinery that responds to bacterial presence in the gut, there are significant gaps in our understanding of the microbial products that influence bacterial association with a fly host. We sequenced and characterized the genomes of three common Drosophila-associated microbes: Lactobacillus plantarum, Lactobacillus brevis and Acetobacter pasteurianus For each species, we compared the genomes of Drosophila-associated strains to the genomes of strains isolated from alternative sources. We found that environmental Lactobacillus strains readily associated with adult Drosophila and were similar to fly isolates in terms of genome organization. In contrast, we identified a strain of A. pasteurianus that apparently fails to associate with adult Drosophila due to an inability to grow on fly nutrient food. Comparisons between association competent and incompetent A. pasteurianus strains identified a short list of candidate genes that may contribute to survival on fly medium. Many of the gene products unique to fly-associated strains have established roles in the stabilization of host-microbe interactions. These data add to a growing body of literature that examines the microbial perspective of host-microbe relationships.

  5. No vacancy: how beneficial microbes cooperate with immunity to provide colonization resistance to pathogens.

    Science.gov (United States)

    Sassone-Corsi, Martina; Raffatellu, Manuela

    2015-05-01

    The mammalian intestine harbors a community of trillions of microbes, collectively known as the gut microbiota, which coevolved with the host in a mutually beneficial relationship. Among the numerous gut microbial species, certain commensal bacteria are known to provide health benefits to the host when administered in adequate amounts and, as such, are labeled "probiotics." We review some of the mechanisms by which probiotics and other beneficial commensals provide colonization resistance to pathogens. The battle for similar nutrients and the bacterial secretion of antimicrobials provide a direct means of competition between beneficial and harmful microbes. Beneficial microbes can also indirectly diminish pathogen colonization by stimulating the development of innate and adaptive immunity, as well as the function of the mucosal barrier. Altogether, we gather and present evidence that beneficial microbes cooperate with host immunity in an effort to shut out pathogens.

  6. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many...

  7. SIX QUESTIONS IN TEACHING LISTENING

    Institute of Scientific and Technical Information of China (English)

    WangHui

    2004-01-01

    This paper addresses problems common in the listening classes, namely, lack of motivation, orientation and sense of achievement and the presence of pressure, fear and frustration. The author examines different factors in the teaching of listening and poses 6 questions that might help teachers to reflect on their teaching. The conclusion is that the aim of listening class is to develop rather than test listening strategies and skills; that students need to be provided with communicative tasks before and while listening; that materials should be realistic, varied and graded ; that listening should be integrated with other skills development; and finally, that learner autonomy provides the ultimate solution to listening problems.

  8. [The place of functional genomics in oncological research].

    Science.gov (United States)

    Bálint, Bálint L; Nagy, László

    2013-03-01

    The 1000 genomes project changed the way how we see the human genome. The rapid development of the deep sequencing technologies is raising several practical questions, and the way how we answer these questions will affect deeply the future of the oncological reseach in Hungary. In our manuscript we give a short overview of the results of the 1000 genomes project and we present the place of the functional genomic investigations between other genomic tools. Based on the recent development in the field we summarize the challenges that have to be addressed in the next couple of years.

  9. Study on Microbes and Their Effects on Rare Earth Extraction in Weathering Crust of Granite

    Institute of Scientific and Technical Information of China (English)

    陈炳辉; 毋福海; 刘琥琥

    2001-01-01

    Microbes were cultured from the samples at various depths in a weathering profile of RE-bearing granite in Gonghe RE mine, Guangdong Province. The cultured microbes, existing at a depth of 0.2~12 m and being more plentiful within 3 m in the profile,include bacteria (Bacillus,Enterobacter, Escherichia, Alkaligenes, Neisseria, Staphylococcus and anaerobic bacteria such as Clostridium), fungi (Aspergillus niger, Aspergillus flavus, Penicillium, Mucor and Saccharomycete) and actinomyces. Experiments were made under room temperature by using solutions of the cultured microbes and their metabolites, compared with distilled water and the culture solution without microbes, to leach RE from the sample of the weathering crust. The results are shown by the experiments: (1) The mixed microbes cultured from the profile and their metabolites increase the quantity of RE leached from the sample and reduce the pH of the solutions. (2) The ability to leach RE from the sample varies with various microbes, decreasing in a sequence of fungi (Mucor, saccharomycete, Aspegillus and Penicillium), zymotic bacilli (Enterobacter, Escherichia etc.), Staphylococcus, zymotic Bacillus, actinomyces and Alkaligenes. (3) The RE leached with bacteria is mainly related to the pH value of the solutions influenced by the metabolites of the bacteria; whereas that leached with fungi is mainly related to the adsorption and imbibition of RE by the fungi and the complexing of RE with their metabolites. (4) Compared with that leached with ammonium sulfate, the fractionation of the RE leached with microbes is characterized by higher δCe, lower δEu and lower ratios of NLa/Sm and NGd/Yb. The result of the fractionation of RE accords with the distribution of RE in the various layers of a profile of weathering crust of granite in South China. The experimental results indicate that microbes and their metabolites should play a positive role in the mobilization, migration and fractionation of RE in the

  10. Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions

    OpenAIRE

    Vishal Kumar; Mehak Baweja; Puneet Kumar Singh; Pratyoosh Shukla

    2016-01-01

    Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant–microbe interaction plays an important role to balance the ecosystem. The present review explores plant–microbe interactions using gene editing and system biolo...

  11. Engineering of bio-hybrid materials by electrospinning polymer-microbe fibers

    OpenAIRE

    LIU, Ying; Rafailovich, Miriam H.; Malal, Ram; Cohn, Daniel; Chidambaram, Dev

    2009-01-01

    Although microbes have been used in industrial and niche applications for several decades, successful immobilization of microbes while maintaining their usefulness for any desired application has been elusive. Such a functionally bioactive system has distinct advantages over conventional batch and continuous-flow microbial reactor systems that are used in various biotechnological processes. This article describes the use of polyethylene oxide99-polypropylene oxide67-polyethylene oxide99 tribl...

  12. The impact of beneficial plant-associated microbes on plant phenotypic plasticity.

    Science.gov (United States)

    Goh, Chooi-Hua; Veliz Vallejos, Debora F; Nicotra, Adrienne B; Mathesius, Ulrike

    2013-07-01

    Plants show phenotypic plasticity in response to changing or extreme abiotic environments; but over millions of years they also have co-evolved to respond to the presence of soil microbes. Studies on phenotypic plasticity in plants have focused mainly on the effects of the changing environments on plants' growth and survival. Evidence is now accumulating that the presence of microbes can alter plant phenotypic plasticity in a broad range of traits in response to a changing environment. In this review, we discuss the effects of microbes on plant phenotypic plasticity in response to changing environmental conditions, and how this may affect plant fitness. By using a range of specific plant-microbe interactions as examples, we demonstrate that one way that microbes can alleviate the effect of environmental stress on plants and thus increase plant fitness is to remove the stress, e.g., nutrient limitation, directly. Furthermore, microbes indirectly affect plant phenotypic plasticity and fitness through modulation of plant development and defense responses. In doing so, microbes affect fitness by both increasing or decreasing the degree of phenotypic plasticity, depending on the phenotype and the environmental stress studied, with no clear difference between the effect of prokaryotic and eukaryotic microbes in general. Additionally, plants have the ability to modulate microbial behaviors, suggesting that they manipulate bacteria, enhancing interactions that help them cope with stressful environments. Future challenges remain in the identification of the many microbial signals that modulate phenotypic plasticity, the characterization of plant genes, e.g. receptors, that mediate the microbial effects on plasticity, and the elucidation of the molecular mechanisms that link phenotypic plasticity with fitness. The characterization of plant and microbial mutants defective in signal synthesis or perception, together with carefully designed glasshouse or field experiments that

  13. Effects of Earthworm and Microbe on Soil Nutrients and Heavy Metals

    Institute of Scientific and Technical Information of China (English)

    SHEN Wei-bao; YANG Hong-qiang

    2008-01-01

    Earthworm and microbe are very important soil organisms. They play an important role in the stability of ecosystem and the bioavailability of nutrients and heavy metals in soils. This article reviewed the function of earthworm and microbes in improving soil structure and controlling soil nutrients as well as their effects on the bioavailability of heavy metals in soil through bioabsorption, enrichment, precipitation, dissolution, and oxidation-reduction. The aim is to provide a certain theoretical basis for modern agricultural production.

  14. No question about exciting questions in cell biology.

    Directory of Open Access Journals (Sweden)

    Thomas D Pollard

    2013-12-01

    Full Text Available Although we have a good grasp of many important processes in cell biology, including knowledge of many molecules involved and how they interact with each other, we still do not understand most of the dynamical features that are the essence of living systems. Fortunately, we now have the ability to dissect biological systems in enough detail to understand their dynamics, including the use of mathematical models to account for past observations and predict future experiments. This deep level of mechanistic understanding should be our goal—not simply to satisfy our scientific curiosity, but also to understand the causes of disease well enough to predict risks, make early diagnoses, and treat effectively. Many big questions remain to be answered before we reach this goal of understanding cellular dynamics.

  15. No question about exciting questions in cell biology.

    Science.gov (United States)

    Pollard, Thomas D

    2013-12-01

    Although we have a good grasp of many important processes in cell biology, including knowledge of many molecules involved and how they interact with each other, we still do not understand most of the dynamical features that are the essence of living systems. Fortunately, we now have the ability to dissect biological systems in enough detail to understand their dynamics, including the use of mathematical models to account for past observations and predict future experiments. This deep level of mechanistic understanding should be our goal—not simply to satisfy our scientific curiosity, but also to understand the causes of disease well enough to predict risks, make early diagnoses, and treat effectively. Many big questions remain to be answered before we reach this goal of understanding cellular dynamics.

  16. Les questions de migrations internationales

    Science.gov (United States)

    Samman, Mouna Liliane

    1993-03-01

    International migrations have growing implications for both countries of origin and countries of destination. In the latter, the presence of foreigners and of members of their families today creates problems of integration, causes argument and brings mounting xenophobia. Paralleling political, economic and social measures taken by public authorities to respond to these difficulties, education needs to assist in defusing the resulting social tensions by preparing the minds of learners and helping to develop new attitudes. In particular, when educational programmes address questions of international migration, these should be treated in the framework of historical evolution so that their real significance and their true temporal and spatial dimensions become apparent. It is also important that the growing interdependence between countries should be made plain, that national history should be placed in its international context, and that the true consequences of these developments should be made clear. In this context, learners need to be acquainted with Human Rights, thereby stressing universal moral values and the role of the individual. Lastly, questions relating to international migration are usually presented in the media in a selective and partial manner, and the young people who take in this information often accept the hasty judgments which are made of situations as proven facts. This is why all teaching about international migration needs to be considered or reconsidered in the light of the complementary or competing actions of the media.

  17. Pisa Question and Reasoning Skill

    Directory of Open Access Journals (Sweden)

    Ersoy Esen

    2017-01-01

    Full Text Available The objective of the study is to determine the level of the reasoning skills of the secondary school students. This research has been conducted during the academic year of 2015-2016 with the participation of 51 students in total, from a province in the Black Sea region of Turkey by using random sampling method. Case study method has been used in this study, since it explains an existing situation. In this study, content analysis from the qualitative research methods was carried out. In order to ensure the validity of the scope, agreement percentage formula was used and expert opinions were sought.The problem named Holiday from the Chapter 1 of the normal units in Problem Solving Questions from PISA (Program for International Student Assessments [35] are used as the data collection tool for the study. The problem named Holiday consists of two questions. Applied problems were evaluated according to the mathematical reasoning stages of TIMSS (2003. The findings suggest that the students use proportional reasoning while solving the problems and use the geometric shapes to facilitate the solution of the problem. When they come across problems related to each other, it is observed that they create connections between the problems based on the results of the previous problem. In conclusion, the students perform crosscheck to ensure that their solutions to the problems are accurate.

  18. Are Quantum Theory Questions Epistemic?

    Directory of Open Access Journals (Sweden)

    Viviana Yaccuzzi Polisena

    2013-12-01

    Full Text Available How to displace-move quantum theory [Ǭ] questions-problems to philosophy? Seeing the collapse of our society’s cultural-intellectual-morals, the philosophy of the 21st century has to contribute to the formation of new principles-formalisms: the big task of the contemporary philosophy ©] is to innovate, to transform the building of the knowledge! Which is the role of the contemporary philosopher? (Noam Chomsky. Building science so that it is more human, out of the scientific mercantilism so that it does not continue transgressing that which is most precious: the thought-life. The ideas that I propose demand a deep cultural-epistemiologicscientific-philosophical-ethical rethinking that goes from quantum entities up to life in society. The starting idea is «the quantum [Ǭ], the paradigm of the contemporary science ©]» (Bernard D’Espagnat. I propose to displace-move questions of the quantum theory [Ǭ]: spin, measure, layering to the field of philosophy (φ to build generic symbols. Can the contemporary episteme model the collapse of the ? For a philosopher, can understanding the importance and the behaviour of the spin bring something new to philosophy ? Can information of the states of the spin be used to observe in a holographic way the pattern energy-information contained in the quantum entities? Is quantum [Ǭ] physics mechanical?

  19. Evaluative Conditioning: The "How" Question.

    Science.gov (United States)

    Jones, Christopher R; Olson, Michael A; Fazio, Russell H

    2010-01-01

    Evaluative conditioning (EC) refers to attitude formation or change toward an object due to that object's mere co-occurrence with another valenced object or objects. This chapter focuses on the "how" question, that is, the question of what cognitive processes intervene between mere co-occurrence and attitude formation or change. Though EC has typically been thought of as occurring through a single, albeit contentious, mechanism, we begin by pointing out that both the heterogeneity of EC methodologies and the abundance of inconsistent results suggest that multiple processes with different characteristics can produce EC. We describe how the earliest posited process of EC, Pavlovian conditioning or signal learning, is a valid mechanism of EC that appears to have operated in some experiments but is unlikely to have operated in others and also cannot account for various EC findings. We describe other mechanisms of EC, when they can be expected to occur, and what characteristics they have. We particularly focus our attention on a process model of EC we have recently introduced, the implicit misattribution model. Finally, we describe the implications of a multi-process view of EC, which we argue can help resolve theoretical controversies and further the application of EC as a practical intervention for influencing attitudes in various domains.

  20. Microstructured block copolymer surfaces for control of microbe capture and aggregation

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, Ryan R [ORNL; Shubert, Katherine R [ORNL; Morrell, Jennifer L. [University of Tennessee, Knoxville (UTK); Lokitz, Bradley S [ORNL; Doktycz, Mitchel John [ORNL; Retterer, Scott T [ORNL

    2014-01-01

    The capture and arrangement of surface-associated microbes is influenced by biochemical and physical properties of the substrate. In this report, we develop lectin-functionalized substrates containing patterned, three-dimensional polymeric structures of varied shapes and densities and use these to investigate the effects of topology and spatial confinement on lectin-mediated microbe capture. Films of poly(glycidyl methacrylate)-block-4,4-dimethyl-2-vinylazlactone (PGMA-b-PVDMA) were patterned on silicon surfaces into line or square grid patterns with 5 m wide features and varied edge spacing. The patterned films had three-dimensional geometries with 900 nm film thickness. After surface functionalization with wheat germ agglutinin, the size of Pseudomonas fluorescens aggregates captured was dependent on the pattern dimensions. Line patterns with edge spacing of 5 m or less led to the capture of individual microbes with minimal formation of aggregates, while grid patterns with the same spacing also captured individual microbes with further reduction in aggregation. Both geometries allowed for increases in aggregate size distribution with increased in edge spacing. These engineered surfaces combine spatial confinement with affinity-based microbe capture based on exopolysaccharide content to control the degree of microbe aggregation, and can also be used as a platform to investigate intercellular interactions and biofilm formation in microbial populations of controlled sizes.

  1. Role of viruses and other microbes in the pathogenesis of type 1 diabetes.

    Science.gov (United States)

    Kondrashova, Anita; Hyöty, Heikki

    2014-01-01

    Type 1 diabetes is caused by an immune-mediated destruction of insulin producing beta-cells in the pancreas. The risk of the disease is determined by interactions between more than 40 different susceptibility genes and yet unidentified environmental factors. The rapidly increasing incidence indicates that these environmental agents have a significant role in the pathogenesis. Microbes have associated with both increased and decreased risk reflecting their possible role as risk or protective factors. Two main hypotheses have been proposed to explain these effects: the hygiene hypothesis suggests that microbial exposures in early childhood stimulate immunoregulatory mechanisms which control autoimmune reactions (analogy with allergy), while the triggering hypothesis suggests that specific microbes damage insulin producing cells. Certain viruses, particularly enteroviruses, are currently the main candidates for such risk microbes. Enteroviruses cause diabetes in animals and have associated with increased risk of type 1 diabetes in epidemiological studies. They have also been detected in the pancreas of diabetic patients. Possible protective effect of microbes has been studied in animal models and in epidemiological studies, where certain enteral microbes (e.g. hepatitis A virus and Helicobacter pylori) and patterns of gut microbiome have associated with low risk of type 1 diabetes. In conclusion, these microbial effects offer attractive possibilities for the development of preventive interventions for type 1 diabetes based on the elimination of triggering agents (e.g. enterovirus vaccines) or use of protective microbes as probiotics.

  2. Combined ESTs from plant-microbe interactions: using GC counting to determine the species of origin.

    Science.gov (United States)

    Huitema, Edgar; Torto, Trudy A; Styer, Allison; Kamoun, Sophien

    2003-01-01

    A diversity of microorganisms establishes intimate associations with plants. Whether pathogenic or symbiotic, such interactions are the result of complex recognition events between plants and microbes, leading to signaling cascades and regulation of countless genes involved in the interaction. A key step in unraveling the mysteries of plant-microbe interactions lies in defining the transcriptional changes that occur in both the host and the microbe during their association. The sum of the transcripts, from both host and microbe, which are produced during their association, has been defined as the interaction transcriptome. One approach to analyze interaction transcriptomes is to perform large-scale sequencing of cDNAs (expressed sequence tags or ESTs) obtained from infected plant tissue and representing a mixture of host and microbe sequences. In some cases, the two organisms have markedly different GC content, allowing most ESTs to be easily distinguished on this basis. In this chapter, we describe a GC counting method to determine the species of origin of ESTs obtained from interactions between plants and oomycetes or other high GC content microbes.

  3. Engineering of bio-hybrid materials by electrospinning polymer-microbe fibers

    Science.gov (United States)

    Liu, Ying; Rafailovich, Miriam H.; Malal, Ram; Cohn, Daniel; Chidambaram, Dev

    2009-01-01

    Although microbes have been used in industrial and niche applications for several decades, successful immobilization of microbes while maintaining their usefulness for any desired application has been elusive. Such a functionally bioactive system has distinct advantages over conventional batch and continuous-flow microbial reactor systems that are used in various biotechnological processes. This article describes the use of polyethylene oxide99-polypropylene oxide67-polyethylene oxide99 triblock polymer fibers, created via electrospinning, to encapsulate microbes of 3 industrially relevant genera, namely, Pseudomonas, Zymomonas, and Escherichia. The presence of bacteria inside the fibers was confirmed by fluorescence microscopy and SEM. Although the electrospinning process typically uses harsh organic solvents and extreme conditions that generally are harmful to bacteria, we describe techniques that overcome these limitations. The encapsulated microbes were viable for several months, and their metabolic activity was not affected by immobilization; thus they could be used in various applications. Furthermore, we have engineered a microbe-encapsulated cross-linked fibrous polymeric material that is insoluble. Also, the microbe-encapsulated active matrix permits efficient exchange of nutrients and metabolic products between the microorganism and the environment. The present results demonstrate the potential of the electrospinning technique for the encapsulation and immobilization of bacteria in the form of a synthetic biofilm, while retaining their metabolic activity. This study has wide-ranging implications in the engineering and use of novel bio-hybrid materials or biological thin-film catalysts. PMID:19667172

  4. Altered Carbohydrates Allocation by Associated Bacteria-fungi Interactions in a Bark Beetle-microbe Symbiosis.

    Science.gov (United States)

    Zhou, Fangyuan; Lou, Qiaozhe; Wang, Bo; Xu, Letian; Cheng, Chihang; Lu, Min; Sun, Jianghua

    2016-02-03

    Insect-microbe interaction is a key area of research in multiplayer symbiosis, yet little is known about the role of microbe-microbe interactions in insect-microbe symbioses. The red turpentine beetle (RTB) has destroyed millions of healthy pines in China and forms context-dependent relationships with associated fungi. The adult-associated fungus Leptographium procerum have played key roles in RTB colonization. However, common fungal associates (L. procerum and Ophiostoma minus) with RTB larvae compete for carbohydrates. Here, we report that dominant bacteria associated with RTB larvae buffer the competition by inhibiting the growth and D-glucose consumption of O. minus. However, they didn't inhibit the growth of L. procerum and forced this fungus to consume D-pinitol before consuming D-glucose, even though D-glucose was available and a better carbon source not only for L. procerum but also for RTB larvae and associated bacteria. This suggests the most frequently isolated bacteria associated with RTB larvae could affect fungal growth and the sequence of carbohydrate consumption. Thus, this regulates carbohydrate allocation in the RTB larva-microbe community, which may in turn benefit RTB larvae development. We also discuss the mechanism of carbohydrate allocation in the RTB larva-microbe community, and its potential contribution to the maintenance of a symbiotic community.

  5. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris.

    Science.gov (United States)

    Oberbeckmann, Sonja; Osborn, A Mark; Duhaime, Melissa B

    2016-01-01

    Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET

  6. The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects.

    Science.gov (United States)

    Papanicolaou, Alexie

    2016-01-01

    Many research programs on non-model species biology have been empowered by genomics. In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called "genome projects". The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication. In this opinion paper I outline four key insights that have facilitated maintaining genomic communities: the key role of computational capability, the iterative process of building genomic resources, the value of community participation and the importance of manual curation. Taken together, these ideas can and do ensure the longevity of genome projects and the growing non-model species community can use them to focus a discussion with regards to its future genomic infrastructure.

  7. Nitrate storage and dissimilatory nitrate reduction by eukaryotic microbes

    DEFF Research Database (Denmark)

    Kamp, Anja; Høgslund, Signe; Risgaard-Petersen, Nils

    2015-01-01

    and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate....... A first compilation of intracellular nitrate inventories in various marine sediments is presented, indicating that intracellular nitrate pools vastly exceed porewater nitrate pools. The relative contribution by foraminifers to total sedimentary denitrification is estimated for different marine settings...

  8. Beneficial Plant Microbe Interaction in Adverse Climatic Condition

    OpenAIRE

    Mohammad Oves

    2015-01-01

    There are two well-known old American and Japanese quotes "snug as a bug in a rug” and ‘Tade kuu mushi mo suki-zuki’ which means very comfortable and everyone has their own tastes respectively, both quotes are best fit for beneficial plantmicrobes (PM) interactions. Most of the plants interact largely with diverse microorganisms in their surrounding environment but the question arises why PM interaction exist everywhere in agroecosystem with sustainability? PM interactions were occurred from ...

  9. The genomics of microbial domestication in the fermented food environment.

    Science.gov (United States)

    Gibbons, John G; Rinker, David C

    2015-12-01

    Shortly after the agricultural revolution, the domestication of bacteria, yeasts, and molds, played an essential role in enhancing the stability, quality, flavor, and texture of food products. These domestication events were probably the result of human food production practices that entailed the continual recycling of isolated microbial communities in the presence of abundant agricultural food sources. We suggest that within these novel agrarian food niches the metabolic requirements of those microbes became regular and predictable resulting in rapid genomic specialization through such mechanisms as pseudogenization, genome decay, interspecific hybridization, gene duplication, and horizontal gene transfer. The ultimate result was domesticated strains of microorganisms with enhanced fermentative capacities.

  10. Appearance questions can be misleading

    DEFF Research Database (Denmark)

    Hansen, Mikkel; Markman, Ellen M.

    2005-01-01

    Preschoolers' success on the appearance-reality task is a milestone in theory-of-mind development. On the standard task children see a deceptive object, such as a sponge that looks like a rock, and are asked, "What is this really?" and "What does this look like?" Children below 4 1/2 years of age...... fail saying that the object not only is a sponge but also looks like a sponge. We propose that young children's difficulty stems from ambiguity in the meaning of "looks like." This locution can refer to outward appearance ("Peter looks like Paul") but in fact often refers to likely reality ("That looks...... like Jim"). We propose that "looks like" is taken to refer to likely reality unless the reality is already part of the common ground of the conversation. Because this joint knowledge is unclear to young children on the appearance-reality task, they mistakenly think the appearance question is about...

  11. Questions and Answers about BSP

    Directory of Open Access Journals (Sweden)

    D.B. Skillicorn

    1997-01-01

    Full Text Available Bulk Synchronous Parallelism (BSP is a parallel programming model that abstracts from low-level program structures in favour of supersteps. A superstep consists of a set of independent local computations, followed by a global communication phase and a barrier synchronisation. Structuring programs in this way enables their costs to be accurately determined from a few simple architectural parameters, namely the permeability of the communication network to uniformly-random traffic and the time to synchronise. Although permutation routing and barrier synch ronisations are widely regarded as inherently expensive, this is not the case. As a result, the structure imposed by BSP does not reduce performance, while bringing considerable benefits for application building. This paper answers the most common questions we are asked about BSP and justifies its claim to be a major step forward in parallel programming.

  12. Questioning Strategy in English Teaching

    Institute of Scientific and Technical Information of China (English)

    李顺梅

    2015-01-01

    Learner autonomy has been a hot issue discussed by educators in recent years.Because it is believed that the ulti-mate goal of educating is to help students learn autonomously and actively not only in school but also,after graduation,for their whole life.Many people misunderstand the meaning of learner autonomy as learners learn something totally independent from teacher or learn after class.This is not the truth;teacher is indispensible to promote learner autonomy.Therefore,English teacher bears a great respon-sibility of fostering and promoting learner autonomy in the classroom.Questioning is the most frequently used and easiest method in the various teaching methods.

  13. Questions That Engage Students in Mathematical Thinking.

    Science.gov (United States)

    Ilaria, Daniel R.

    Teacher questions are an important part of a student-inquiry classroom. This research examines two different student-centered settings to determine the teacher questions that engaged students in mathematical thinking. It reports on questions asked in both a research setting and a high school classroom. Discursive and retracing questions are…

  14. How fisheries management can benefit from genomics?

    Science.gov (United States)

    Valenzuela-Quiñonez, Fausto

    2016-09-01

    Fisheries genomics is an emerging field that advocates the application of genomic tools to address questions in fisheries management. Genomic approaches bring a new paradigm for fisheries management by making it possible to integrate adaptive diversity to understand fundamental aspects of fisheries resources. Hence, this review is focused on the relevance of genomic approaches to solve fisheries-specific questions. Particularly the detection of adaptive diversity (outlier loci) provides unprecedented opportunity to understand bio-complexity, increased power to trace processed sample origin to allow enforcement and the potential to understand the genetic basis of micro-evolutionary effects of fisheries-induced evolution and climate change. The understanding of adaptive diversity patterns will be the cornerstone of the future links between fisheries and genomics. These studies will help stakeholders anticipate the potential effects of fishing or climate change on the resilience of fisheries stocks; consequently, in the near future, fisheries sciences might integrate evolutionary principles with fisheries management.

  15. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  16. On Effective Questioning in English Classes

    Institute of Scientific and Technical Information of China (English)

    夏慧芳

    2010-01-01

    Teachers' questioning has traditionally been viewed as an important constituent of teacher talk and the core of effective teaching in classroom context.Questioning is the basic means used by teachers to challenge students to think,appraise teaching results and help students to realize their desired goals,thus,playing a key role in the second language acquisition.This paper will first introduce the definition and types of teachers'questioning and the criteria for effective questioning.It will also give some practical suggestions for practice effective questioning,focusing on good questions,wait-time,feedback and allocation of questions.

  17. Socrates' questions: a focus for nursing.

    Science.gov (United States)

    Bunkers, Sandra S

    2004-07-01

    This column focuses on the philosophical dialogue originated by Socrates. Six questions that Socrates would ask the ancient Greeks are explored in discussing a book written by Phillips entitled Six Questions of Socrates. These questions were: What is virtue? What is moderation? What is justice? What is good? What is courage? What is piety? A human becoming perspective is used as a lens to view the discussion on these questions and the question is posed, "What would it be like to frame discussions on health and quality of life around Socrates' questions?" Parse's teaching-learning processes are presented as a means of creating an environment where dialogue on these questions can occur.

  18. Two-way plant mediated interactions between root-associated microbes and insects: from ecology to mechanisms

    Directory of Open Access Journals (Sweden)

    Nurmi ePangesti

    2013-10-01

    Full Text Available Plants are members of complex communities and function as a link between above- and below-ground organisms. Associations between plants and soil-borne microbes commonly occur and have often been found beneficial for plant fitness. Root-associated microbes may trigger physiological changes in the host plant that influence interactions between plants and aboveground insects at several trophic levels. Aboveground, plants are under continuous attack by insect herbivores and mount multiple responses that also have systemic effects on belowground microbes. Until recently, both ecological and mechanistic studies have mostly focused on exploring these below- and above-ground interactions using simplified systems involving both single microbe and herbivore species, which is far from the naturally occurring interactions. Increasing the complexity of the systems studied is required to increase our understanding of microbe - plant - insect interactions and to gain more benefit from the use of non-pathogenic microbes in agriculture. In this review, we explore how colonization by either single non-pathogenic microbe species or a community of such microbes belowground affects plant growth and defense and how this affects the interactions of plants with aboveground insects at different trophic levels. Moreover, we review how plant responses to foliar herbivory by insects belonging to different feeding guilds affect interactions of plants with non-pathogenic soil-borne microbes. The role of phytohormones in coordinating plant growth, plant defenses against foliar herbivores while simultaneously establishing associations with non-pathogenic soil microbes is discussed.

  19. Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012.

    Science.gov (United States)

    Gilbert, Jack A; Bao, Yiming; Wang, Hui; Sansone, Susanna-Assunta; Edmunds, Scott C; Morrison, Norman; Meyer, Folker; Schriml, Lynn M; Davies, Neil; Sterk, Peter; Wilkening, Jared; Garrity, George M; Field, Dawn; Robbins, Robert; Smith, Daniel P; Mizrachi, Ilene; Moreau, Corrie

    2012-05-25

    This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation.

  20. Functional genomics for food fermentation processes.

    Science.gov (United States)

    Smid, E J; Hugenholtz, J

    2010-01-01

    This review describes recent scientific and technological drivers of food fermentation research. In addition, a number of practical implications of the results of this development will be highlighted. The first part of the manuscript elaborates on the message that genome sequence information gives us an unprecedented view on the biodiversity of microbes in food fermentation. This information can be made applicable for tailoring relevant characteristics of food products through fermentation. The second part deals with the integration of genome sequence data into metabolic models and the use of these models for a number of topics that are relevant for food fermentation processes. The final part will be about metagenomics approaches to reveal the complexity and understand the functionality of undefined complex microbial consortia used in a diverse range of food fermentation processes.