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Sample records for microbe probe studying

  1. Principles of Chemical Biology: From Sexy Fatty Acids and EBV probes to Anti-Acid Antibiotic via Post-Biotics and Host-Microbe Metabolic Complementarity.

    Science.gov (United States)

    2017-06-22

    This month: The role of fatty acids in sex determination; a probe to monitor and inhibit EBNA1 at the same time; a biological role for post-biotics; what happens when you mix microbes, hosts, and drugs; and an antibiotic that cross-protects with acid. Copyright © 2017. Published by Elsevier Ltd.

  2. NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.

    Science.gov (United States)

    Levy, Roie; Carr, Rogan; Kreimer, Anat; Freilich, Shiri; Borenstein, Elhanan

    2015-05-17

    Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm. NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms' niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds. The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.

  3. NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

    OpenAIRE

    Levy, Roie; Carr, Rogan; Kreimer, Anat; Freilich, Shiri; Borenstein, Elhanan

    2015-01-01

    Background Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host...

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

    Science.gov (United States)

    Hooper, Sean D; Raes, Jeroen; Foerstner, Konrad U; Harrington, Eoghan D; Dalevi, Daniel; Bork, Peer

    2008-07-09

    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. 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. 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.

  5. 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.

  6. Application of RNA-seq and Bioimaging Methods to Study Microbe-Microbe Interactions and Their Effects on Biofilm Formation and Gene Expression

    DEFF Research Database (Denmark)

    Amador Hierro, Cristina Isabel; Sternberg, Claus; Jelsbak, Lars

    2017-01-01

    Complex interactions between pathogenic bacteria, the microbiota, and the host can modify pathogen physiology and behavior. We describe two different experimental approaches to study microbe-microbe interactions in in vitro systems containing surface-associated microbial populations. One method i...

  7. A Molecular Study of Microbe Transfer between Distant Environments

    OpenAIRE

    Hooper, Sean D.; Raes, Jeroen; Foerstner, Konrad U.; Harrington, Eoghan D.; Dalevi, Daniel; Bork, Peer

    2008-01-01

    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 molecu...

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

    Science.gov (United States)

    Gopalan, Suresh; Ausubel, Frederick M

    2008-01-01

    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. The Microbe Directory: An annotated, searchable inventory of microbes' characteristics.

    Science.gov (United States)

    Shaaban, Heba; Westfall, David A; Mohammad, Rawhi; Danko, David; Bezdan, Daniela; Afshinnekoo, Ebrahim; Segata, Nicola; Mason, Christopher E

    2018-01-05

    The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes' characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY-Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism's taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart ( https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.

  10. Investigating Microbe-Mineral Interactions: Recent Advances in X-Ray and Electron Microscopy and Redox-Sensitive Methods

    Science.gov (United States)

    Miot, Jennyfer; Benzerara, Karim; Kappler, Andreas

    2014-05-01

    Microbe-mineral interactions occur in diverse modern environments, from the deep sea and subsurface rocks to soils and surface aquatic environments. They may have played a central role in the geochemical cycling of major (e.g., C, Fe, Ca, Mn, S, P) and trace (e.g., Ni, Mo, As, Cr) elements over Earth's history. Such interactions include electron transfer at the microbe-mineral interface that left traces in the rock record. Geomicrobiology consists in studying interactions at these organic-mineral interfaces in modern samples and looking for traces of past microbe-mineral interactions recorded in ancient rocks. Specific tools are required to probe these interfaces and to understand the mechanisms of interaction between microbes and minerals from the scale of the biofilm to the nanometer scale. In this review, we focus on recent advances in electron microscopy, in particular in cryoelectron microscopy, and on a panel of electrochemical and synchrotron-based methods that have recently provided new understanding and imaging of the microbe-mineral interface, ultimately opening new fields to be explored.

  11. 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.

  12. 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

  13. 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.

  14. Cooperation and cheating in microbes

    Science.gov (United States)

    Gore, Jeff

    2011-03-01

    Understanding the cooperative and competitive dynamics within and between species is a central challenge in evolutionary biology. Microbial model systems represent a unique opportunity to experimentally test fundamental theories regarding the evolution of cooperative behaviors. In this talk I will describe our experiments probing cooperation in microbes. In particular, I will compare the cooperative growth of yeast in sucrose and the cooperative inactivation of antibiotics by bacteria. In both cases we find that cheater strains---which don't contribute to the public welfare---are able to take advantage of the cooperator strains. However, this ability of cheaters to out-compete cooperators occurs only when cheaters are present at low frequency, thus leading to steady-state coexistence. These microbial experiments provide fresh insight into the evolutionary origin of cooperation.

  15. Microbes safely, effectively bioremediate oil field pits

    International Nuclear Information System (INIS)

    Shaw, B.; Block, C.S.; Mills, C.H.

    1995-01-01

    Natural and augmented bioremediation provides a safe, environmental, fast, and effective solution for removing hydrocarbon stains from soil. In 1992, Amoco sponsored a study with six bioremediation companies, which evaluated 14 different techniques. From this study, Amoco continued using Environmental Protection Co.'s (EPC) microbes for bioremediating more than 145 sites near Farmington, NM. EPC's microbes proved effective on various types of hydrocarbon molecules found in petroleum stained soils from heavy crude and paraffin to volatiles such as BTEX (benzene, toluene, ethylbenzene, xylene) compounds. Controlled laboratory tests have shown that these microbes can digest the hydrocarbon molecules with or without free oxygen present. It is believed that this adaptation gives these microbes their resilience. The paper describes the bioremediation process, environmental advantages, in situ and ex situ bioremediation, goals of bioremediation, temperature effects, time, cost, and example sites that were treated

  16. 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.

  17. The microbe capture experiment in space: Fluorescence microscopic detection of microbes captured by aerogel

    Science.gov (United States)

    Sugino, Tomohiro; Yokobori, Shin-Ichi; Yang, Yinjie; Kawaguchi, Yuko; Okudaira, Kyoko; Tabata, Makoto; Kawai, Hideyuki; Hasegawa, Sunao; Yamagishi, Akihiko

    Microbes have been collected at the altitude up to about 70 km in the sampling experiment done by several groups[1]. We have also collected high altitude microbes, by using an airplane and balloons[2][3][4][5]. We collected new deinococcal strain (Deinococcus aetherius and Deinococ-cus aerius) and several strains of spore-forming bacilli from stratosphere[2][4][5]. However, microbe sampling in space has never been reported. On the other hand, "Panspermia" hy-pothesis, where terrestrial life is originated from outside of Earth, has been proposed[6][7][8][9]. Recent report suggesting existence of the possible microbe fossils in the meteorite of Mars origin opened the serious debate on the possibility of migration of life embedded in meteorites (and cosmic dusts)[10][11]. If we were able to find terrestrial microbes in space, it would suggest that the terrestrial life can travel between astronomical bodies. We proposed a mission "Tanpopo: Astrobiology Exposure and Micrometeoroid Capture Experiments" to examine possible inter-planetary migration of microbes, organic compounds and meteoroids on Japan Experimental Module of the International Space Station (ISS)[12]. Two of six sub themes in this mission are directly related to interplanetary migration of microbes. One is the direct capturing experi-ment of microbes (probably within the particles such as clay) in space by the exposed ultra-low density aerogel. Another is the exposure experiment to examine survivability of the microbes in harsh space environment. They will tell us the possibility of interplanetary migration of microbes (life) from Earth to outside of Earth (or vise versa). In this report, we will report whether aerogel that have been used for the collection of space debris and cosmic dusts can be used for microbe sampling in space. We will discuss how captured particles by aerogel can be detected with DNA-specific fluorescent dye, and how to distinguish microbes from other mate-rials (i.e. aerogel and

  18. 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.

  19. Roles and Importance of Microbes in the Radioactive Waste Disposal

    International Nuclear Information System (INIS)

    Baik, Min Hoon; Lee, Seung Yeop; Roh, Yeol

    2009-01-01

    Recently the importance and interest for the microbes has been increased because several important results for the effects of microbes on the radioactive waste disposal have been published continuously. In this study, research status and major results on the various roles and effects of microbes in the radioactive waste disposal have been investigated. We investigated and summarized the roles and major results of microbes in a multi-barrier system consisting of an engineered barrier and a natural barrier which is considered in radioactive waste disposal systems. For the engineered barrier, we discussed about the effects of microbes on the corrosion of a waste container and investigated the survival possibility and roles of microbes in a compacted bentonite buffer. For the natural barrier, the roles of microbes present in groundwaters and rocks were discussed and summarized with major results from natural analogue studies. Furthermore, we investigated and summarized the roles and various interactions processes of microbes and their effects on the radionuclide migration and retardation including recent research status. Therefore, it is expected that the effects and roles of microbes on the radioactive waste disposal can be rigorously evaluated if further researches are carried out for a long-term behavior of the disposal system in the deep geological environments and for the effects of microbes on the radionuclide migration through geological media.

  20. Meet the Microbes through the Microbe World Activities with Microbe the Magnificent and Mighty Microbe.

    Science.gov (United States)

    Frame, Kathy, Ed.; Ryan, Karen, Ed.

    The activities presented in this book are the product of the Community Outreach Initiative of the Microbial Literacy Collaborative (MLC). This activity book presents a balanced view of microbes, their benefits, and the diseases they cause. Each activity starts with an interesting introductory statement and includes goals, activity time, time to…

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

    OpenAIRE

    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 systems, including plant- and arthropod-associated microbes, and symbionts as well as antagonists, that selection and adaptation in seemingly two-way interactions between plants and microbes, plants a...

  2. 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

  3. Host-microbe and microbe-microbe interactions in the evolution of obligate plant parasitism.

    Science.gov (United States)

    Kemen, Ariane C; Agler, Matthew T; Kemen, Eric

    2015-06-01

    Research on obligate biotrophic plant parasites, which reproduce only on living hosts, has revealed a broad diversity of filamentous microbes that have independently acquired complex morphological structures, such as haustoria. Genome studies have also demonstrated a concerted loss of genes for metabolism and lytic enzymes, and gain of diversity of genes coding for effectors involved in host defense suppression. So far, these traits converge in all known obligate biotrophic parasites, but unexpected genome plasticity remains. This plasticity is manifested as transposable element (TE)-driven increases in genome size, observed to be associated with the diversification of virulence genes under selection pressure. Genome expansion could result from the governing of the pathogen response to ecological selection pressures, such as host or nutrient availability, or to microbial interactions, such as competition, hyperparasitism and beneficial cooperations. Expansion is balanced by alternating sexual and asexual cycles, as well as selfing and outcrossing, which operate to control transposon activity in populations. In turn, the prevalence of these balancing mechanisms seems to be correlated with external biotic factors, suggesting a complex, interconnected evolutionary network in host-pathogen-microbe interactions. Therefore, the next phase of obligate biotrophic pathogen research will need to uncover how this network, including multitrophic interactions, shapes the evolution and diversity of pathogens. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  4. Recent Research Status on the Microbes in the Radioactive Waste Disposal and Identification of Aerobic Microbes in a Groundwater Sampled from the KAERI Underground Research Tunnel(KURT)

    International Nuclear Information System (INIS)

    Baik, Min Hoon; Lee, Seung Yeop; Cho, Won Jin

    2006-11-01

    In this report, a comprehensive review on the research results and status for the various effects of microbes in the radioactive waste disposal including definition and classification of microbes, and researches related with the waste containers, engineered barriers, natural barriers, natural analogue studies, and radionuclide migration and retardation. Cultivation, isolation, and classification of aerobic microbes found in a groundwater sampled from the KAERI Underground Research Tunnel (KURT) located in the KAERI site have carried out and over 20 microbes were found to be present in the groundwater. Microbial identification by a 16S rDNA genetic analysis of the selected major 10 aerobic microbes was performed and the identified microbes were characterized

  5. Mechanisms of Heavy Metal Sequestration in Soils: Plant-Microbe Interactions and Organic Matter Aging

    Energy Technology Data Exchange (ETDEWEB)

    Teresa W.-M. Fan; Richard M. Higashi; David Crowley; Andrew N. Lane: Teresa A. Cassel; Peter G. Green

    2004-12-31

    For stabilization of heavy metals at contaminated sites, the three way interaction among soil organic matter (OM)-microbes-plants, and their effect on heavy metal binding is critically important for long-term sustainability, a factor that is poorly understood at the molecular level. Using a soil aging system, the humification of plant matter such as wheat straw was probed along with the effect on microbial community on soil from the former McClellan Air Force Base.

  6. Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City.

    Directory of Open Access Journals (Sweden)

    Julia M Maritz

    Full Text Available Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with-and potential exchange of-microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter and June (Summer 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills.Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency.We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes.

  7. Where the Wild Microbes Are: Education and Outreach on Sub-Seafloor Microbes

    Science.gov (United States)

    Cooper, S. K.; Kurtz, K.; Orcutt, B.; Strong, L.; Collins, J.; Feagan, A.

    2014-12-01

    Sub-seafloor microbiology has the power to spark the imaginations of children, students and the general public with its mysterious nature, cutting-edge research, and connections to the search for extraterrestrial life. These factors have been utilized to create a number of educational and outreach products to bring subsurface microbes to non-scientist audiences in creative and innovative ways. The Adopt a Microbe curriculum for middle school students provides hands-on activities and investigations for students to learn about microbes and the on-going research about them, and provides opportunities to connect with active expeditions. A new series of videos engages non-scientists with stories about research expeditions and the scientists themselves. A poster and associated activities explore the nature of science using a microbiologist and her research as examples. A new e-book for young children will engage them with age-appropriate text and illustrations. These projects are multidisciplinary, involve science and engineering practices, are available to all audiences and provide examples of high level and meaningful partnerships between scientists and educators and the kinds of products that can result. Subseafloor microbiology projects such as these, aimed at K-12 students and the general public, have the potential to entice the interest of the next generation of microbe scientists and increase general awareness of this important science.

  8. Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions.

    Science.gov (United States)

    Gao, Jian; Sasse, Joelle; Lewald, Kyle M; Zhalnina, Kateryna; Cornmesser, Lloyd T; Duncombe, Todd A; Yoshikuni, Yasuo; Vogel, John P; Firestone, Mary K; Northen, Trent R

    2018-04-10

    Beneficial plant-microbe interactions offer a sustainable biological solution with the potential to boost low-input food and bioenergy production. A better mechanistic understanding of these complex plant-microbe interactions will be crucial to improving plant production as well as performing basic ecological studies investigating plant-soil-microbe interactions. Here, a detailed description for ecosystem fabrication is presented, using widely available 3D printing technologies, to create controlled laboratory habitats (EcoFABs) for mechanistic studies of plant-microbe interactions within specific environmental conditions. Two sizes of EcoFABs are described that are suited for the investigation of microbial interactions with various plant species, including Arabidopsis thaliana, Brachypodium distachyon, and Panicum virgatum. These flow-through devices allow for controlled manipulation and sampling of root microbiomes, root chemistry as well as imaging of root morphology and microbial localization. This protocol includes the details for maintaining sterile conditions inside EcoFABs and mounting independent LED light systems onto EcoFABs. Detailed methods for addition of different forms of media, including soils, sand, and liquid growth media coupled to the characterization of these systems using imaging and metabolomics are described. Together, these systems enable dynamic and detailed investigation of plant and plant-microbial consortia including the manipulation of microbiome composition (including mutants), the monitoring of plant growth, root morphology, exudate composition, and microbial localization under controlled environmental conditions. We anticipate that these detailed protocols will serve as an important starting point for other researchers, ideally helping create standardized experimental systems for investigating plant-microbe interactions.

  9. Food microbe tracker: a web-based tool for storage and comparison of food-associated microbes.

    Science.gov (United States)

    Vangay, Pajau; Fugett, Eric B; Sun, Qi; Wiedmann, Martin

    2013-02-01

    Large amounts of molecular subtyping information are generated by the private sector, academia, and government agencies. However, use of subtype data is limited by a lack of effective data storage and sharing mechanisms that allow comparison of subtype data from multiple sources. Currently available subtype databases are generally limited in scope to a few data types (e.g., MLST. net) or are not publicly available (e.g., PulseNet). We describe the development and initial implementation of Food Microbe Tracker, a public Web-based database that allows archiving and exchange of a variety of molecular subtype data that can be cross-referenced with isolate source data, genetic data, and phenotypic characteristics. Data can be queried with a variety of search criteria, including DNA sequences and banding pattern data (e.g., ribotype or pulsed-field gel electrophoresis type). Food Microbe Tracker allows the deposition of data on any bacterial genus and species, bacteriophages, and other viruses. The bacterial genera and species that currently have the most entries in this database are Listeria monocytogenes, Salmonella, Streptococcus spp., Pseudomonas spp., Bacillus spp., and Paenibacillus spp., with over 40,000 isolates. The combination of pathogen and spoilage microorganism data in the database will facilitate source tracking and outbreak detection, improve discovery of emerging subtypes, and increase our understanding of transmission and ecology of these microbes. Continued addition of subtyping, genetic or phenotypic data for a variety of microbial species will broaden the database and facilitate large-scale studies on the diversity of food-associated microbes.

  10. 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

  11. 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…

  12. Engineered microbes and methods for microbial oil production

    Energy Technology Data Exchange (ETDEWEB)

    Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

    2018-01-09

    Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.

  13. Engineered microbes and methods for microbial oil production

    Science.gov (United States)

    Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

    2015-02-10

    Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.

  14. Honey Bee Health: The Potential Role of Microbes

    Science.gov (United States)

    Microbes, are a diverse group of unicellular organisms that include bacteria, fungi, archaea, protists, and sometimes viruses. Bees carry a diverse assemblage of microbes (mostly bacteria and fungi). Very few are pathogenic; most microbes are likely commensal or even beneficial to the colony. Mic...

  15. 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

    across the three dietary patterns and for meals clustered based on whether they were raw or cooked. Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbes, beyond probiotics taken as supplements-i.e., ingested with food-are important contributors to the composition, inter-individual variation, and function of our gut microbiota.

  16. Turning the table: plants consume microbes as a source of nutrients.

    Directory of Open Access Journals (Sweden)

    Chanyarat Paungfoo-Lonhienne

    Full Text Available Interactions between plants and microbes in soil, the final frontier of ecology, determine the availability of nutrients to plants and thereby primary production of terrestrial ecosystems. Nutrient cycling in soils is considered a battle between autotrophs and heterotrophs in which the latter usually outcompete the former, although recent studies have questioned the unconditional reign of microbes on nutrient cycles and the plants' dependence on microbes for breakdown of organic matter. Here we present evidence indicative of a more active role of plants in nutrient cycling than currently considered. Using fluorescent-labeled non-pathogenic and non-symbiotic strains of a bacterium and a fungus (Escherichia coli and Saccharomyces cerevisiae, respectively, we demonstrate that microbes enter root cells and are subsequently digested to release nitrogen that is used in shoots. Extensive modifications of root cell walls, as substantiated by cell wall outgrowth and induction of genes encoding cell wall synthesizing, loosening and degrading enzymes, may facilitate the uptake of microbes into root cells. Our study provides further evidence that the autotrophy of plants has a heterotrophic constituent which could explain the presence of root-inhabiting microbes of unknown ecological function. Our discovery has implications for soil ecology and applications including future sustainable agriculture with efficient nutrient cycles.

  17. 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 ...

  18. Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development.

    Science.gov (United States)

    Bing, XiaoLi; Gerlach, Joseph; Loeb, Gregory; Buchon, Nicolas

    2018-03-20

    Drosophila suzukii Matsumura is an invasive species of vinegar fly that has become a prominent pest of berries and other soft-skinned fruits. Unlike most other Drosophila species, female D. suzukii flies lay their eggs in ripening and ripe fruits and larvae develop within the fruit. To understand how D. suzukii larvae utilize ripe and ripening fruits, which usually have low levels of protein, we investigated the microbiota of field-captured and laboratory-reared D. suzukii flies and further examined the combined influence of diet and microbes on host fitness. Field-captured flies were associated with diverse microbiota, which varied significantly with sampling location and season. In contrast, laboratory-reared flies possessed strikingly lower bacterial abundance and diversity. A comparison of conventionally reared (CR) and germ-free (GF) flies revealed that the microbiota of D. suzukii does not alter its development significantly but decreases its life span under conditions of a nutrient-sufficient diet. However, the microbiota is essential for D. suzukii development on strawberry-based or blueberry-based fruit diets. This developmental failure could be rescued by reassociation with single bacterial or fungal species or by the addition of a high quantity of heat-killed microbes. In addition, we found that proteins are limiting with respect to fly development on fruit-based diets and that GF flies show signs of protein starvation. Taken together, our study results demonstrate that the microbiota provides key proteins required for the development of D. suzukii reared on fresh fruit. Our work shows that the impact of microbes on fly fitness depends strongly on nutritional conditions. IMPORTANCE Animals are commonly associated with specific microbes, which play important roles in host development and fitness. However, little information about the function of microbes has been available for the important invasive pest Drosophila suzukii , also known as Spotted

  19. 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.

  20. An ultrasonic method for separation of epiphytic microbes from freshwater submerged macrophytes.

    Science.gov (United States)

    Cai, Xianlei; Gao, Guang; Yang, Jing; Tang, Xiangming; Dai, Jiangyu; Chen, Dan; Song, Yuzhi

    2014-07-01

    Epiphytic microbes are common inhabitants of freshwater submerged macrophytes, which play an important role in aquatic ecosystems. An important precondition for studying the epiphytic microbes is having an effective method of separating the attached microbes from the host macrophytes. We developed an ultrasound-based method for separating epiphytic microbes from freshwater submerged macrophytes, optimized the conditions of ultrasonic separation with an orthogonal experimental design, and compared the optimized ultrasonic method with manual separation. This method can be particularly useful for freshwater submerged macrophytes having a complex morphology. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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

    categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked.Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbes, beyond probiotics taken as supplements—i.e., ingested with food—are important contributors to the composition, inter-individual variation, and function of our gut microbiota.

  2. Do forest soil microbes have the potential to resist plant invasion? A case study in Dinghushan Biosphere Reserve (South China)

    Science.gov (United States)

    Chen, Bao-Ming; Li, Song; Liao, Hui-Xuan; Peng, Shao-Lin

    2017-05-01

    Successful invaders must overcome biotic resistance, which is defined as the reduction in invasion success caused by the resident community. Soil microbes are an important source of community resistance to plant invasions, and understanding their role in this process requires urgent investigation. Therefore, three forest communities along successional stages and four exotic invasive plant species were selected to test the role of soil microbes of three forest communities in resisting the exotic invasive plant. Our results showed that soil microbes from a monsoon evergreen broadleaf forest (MEBF) (late-successional stage) had the greatest resistance to the invasive plants. Only the invasive species Ipomoea triloba was not sensitive to the three successional forest soils. Mycorrhizal fungi in early successional forest Pinus massonina forest (PMF) or mid-successional forest pine-broadleaf mixed forest (PBMF) soil promoted the growth of Mikania micrantha and Eupatorium catarium, but mycorrhizal fungi in MEBF soil had no significant effects on their growth. Pathogens plus other non-mycorrhizal microbes in MEBF soil inhibited the growth of M. micrantha and E. catarium significantly, and only inhibited root growth of E. catarium when compared with those with mycorrhizal fungi addition. The study suggest that soil mycorrhizal fungi of early-mid-successional forests benefit invasive species M. micrantha and E. catarium, while soil pathogens of late-successional forest may play an important role in resisting M. micrantha and E. catarium. The benefit and resistance of the soil microbes are dependent on invasive species and related to forest succession. The study gives a possible clue to control invasive plants by regulating soil microbes of forest community to resist plant invasion.

  3. Chemical signaling involved in plant-microbe interactions.

    Science.gov (United States)

    Chagas, Fernanda Oliveira; Pessotti, Rita de Cassia; Caraballo-Rodríguez, Andrés Mauricio; Pupo, Mônica Tallarico

    2018-03-05

    Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.

  4. Coercion in the Evolution of Plant-Microbe Communication: A Perspective.

    Science.gov (United States)

    Rowe, S L; Norman, J S; Friesen, M L

    2018-06-06

    Plants and microbes are dependent on chemical signals as a means of interkingdom communication. There are two predicted paths for the evolution of these signals. Ritualization is the oft-assumed pathway for the evolution of plant-microbe communication systems. In this process, chemical signals, which benefit both receiver and sender, evolve from chemical cues, which benefit only the receiver. However, plant-microbe signaling may evolve from coercive interactions as well, a process known as sensory manipulation. Here, we aim to highlight the prevalence of coercive interactions and discuss sensory manipulation in the context of plant-microbe interactions. We present two examples of stabilized coercion: microbial coercion of plants via the release of phytohormones and plant coercion of microbes via manipulation of quorum-sensing compounds. Furthermore, we provide an evolutionary framework for the emergence of signaling from coercive plant-microbe interactions through the process of sensory manipulation. We hope that researchers will recognize the relevance of coercive interactions in plant-microbe systems and consider sensory manipulation as a plausible evolutionary trajectory for the emergence of plant-microbe signaling.

  5. Musing over Microbes in Microgravity: Microbial Physiology Flight Experiment

    Science.gov (United States)

    Schweickart, Randolph; McGinnis, Michael; Bloomberg, Jacob; Lee, Angie (Technical Monitor)

    2002-01-01

    New York City, the most populated city in the United States, is home to over 8 million humans. This means over 26,000 people per square mile! Imagine, though, what the view would be if you peeked into the world of microscopic organisms. Scientists estimate that a gram of soil may contain up to 1 billion of these microbes, which is as much as the entire human population of China! Scientists also know that the world of microbes is incredibly diverse-possibly 10,000 different species in one gram of soil - more than all the different types of mammals in the world. Microbes fill every niche in the world - from 20 miles below the Earth's surface to 20 miles above, and at temperatures from less than -20 C to hotter than water's boiling point. These organisms are ubiquitous because they can adapt quickly to changing environments, an effective strategy for survival. Although we may not realize it, microbes impact every aspect of our lives. Bacteria and fungi help us break down the food in our bodies, and they help clean the air and water around us. They can also cause the dark, filmy buildup on the shower curtain as well as, more seriously, illness and disease. Since humans and microbes share space on Earth, we can benefit tremendously from a better understanding of the workings and physiology of the microbes. This insight can help prevent any harmful effects on humans, on Earth and in space, as well as reap the benefits they provide. Space flight is a unique environment to study how microbes adapt to changing environmental conditions. To advance ground-based research in the field of microbiology, this STS-107 experiment will investigate how microgravity affects bacteria and fungi. Of particular interest are the growth rates and how they respond to certain antimicrobial substances that will be tested; the same tests will be conducted on Earth at the same times. Comparing the results obtained in flight to those on Earth, we will be able to examine how microgravity induces

  6. 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.

  7. 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.

  8. The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics

    Science.gov (United States)

    Mohammad, Rawhi; Danko, David; Bezdan, Daniela; Afshinnekoo, Ebrahim; Segata, Nicola; Mason, Christopher E.

    2018-01-01

    The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes’ characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY—Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism’s taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart ( https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe. PMID:29630066

  9. Textiles and Microbes

    Science.gov (United States)

    Freney, Jean; Renaud, François N. R.

    Microbes can be carried by and even multiply on textiles. The first real, premeditated, microbiological warfare happened in 1763, during the Anglo-French wars in North America, when Native American emissaries were given blankets or handkerchiefs contaminated with smallpox. Thus, a small epidemic started and spread rapidly, causing considerable damage to the rank and file of the Native Americans. Nowadays, it could be said that textiles could be vectors of infections in hospitals or communities. The making of antimicrobial textiles could prevent them from becoming a reservoir of microbes in the transmission of infections and in cases of voluntary contamination in a terrorist threat for example. However, methods have to show that textiles are really active and do not attack the cutaneous flora they are in contact with. In this chapter, the role of textiles in the transmission of infections is summarized and the main characteristics of antimicrobial textiles are described.

  10. Research progress and application prospect of radiation-resistant prokaryotic microbe

    International Nuclear Information System (INIS)

    Wang Wei; Zhu Jing; Zhang Zhidong; Tang Qiyong; Chen Ming

    2013-01-01

    Radiation-resistant microbe is becoming the research hotspot because of its special life phenomenon and physiological mechanism. Radiation-resistant bacteria are one kind of the most studied radiation-resistant microbe. This article summarized some aspects of the research on radiation-resistant bacteria, including the radiation resistant bacteria resources, and discussed its potential application prospects in the environmental engineering, biotechnology, human health, military and space et al. (authors)

  11. Macrophage–Microbe Interactions: Lessons from the Zebrafish Model

    Directory of Open Access Journals (Sweden)

    Nagisa Yoshida

    2017-12-01

    Full Text Available Macrophages provide front line defense against infections. The study of macrophage–microbe interplay is thus crucial for understanding pathogenesis and infection control. Zebrafish (Danio rerio larvae provide a unique platform to study macrophage–microbe interactions in vivo, from the level of the single cell to the whole organism. Studies using zebrafish allow non-invasive, real-time visualization of macrophage recruitment and phagocytosis. Furthermore, the chemical and genetic tractability of zebrafish has been central to decipher the complex role of macrophages during infection. Here, we discuss the latest developments using zebrafish models of bacterial and fungal infection. We also review novel aspects of macrophage biology revealed by zebrafish, which can potentiate development of new therapeutic strategies for humans.

  12. Clinical laboratory evaluation of the Auto-Microbic system for rapid identification of Enterobacteriaceae.

    OpenAIRE

    Hasyn, J J; Cundy, K R; Dietz, C C; Wong, W

    1981-01-01

    The capability of the Auto-Microbic system (Vitek Systems, Inc., Hazelwood, Mo.) has been expanded to identify members of the family Enterobacteriaceae with the use of a sealed, disposable accessory card (the Enterobacteriaceae Biochemical Card) containing 26 biochemical tests. To judge the accuracy of the AutoMicrobic system's identification in a hospital laboratory, 933 Enterobacteriaceae isolates were studied. The AutoMicrobic system provided the correct identification for 905 of the isola...

  13. A place for host-microbe symbiosis in the comparative physiologist's toolbox.

    Science.gov (United States)

    Kohl, Kevin D; Carey, Hannah V

    2016-11-15

    Although scientists have long appreciated that metazoans evolved in a microbial world, we are just beginning to appreciate the profound impact that host-associated microbes have on diverse aspects of animal biology. The enormous growth in our understanding of host-microbe symbioses is rapidly expanding the study of animal physiology, both technically and conceptually. Microbes associate functionally with various body surfaces of their hosts, although most reside in the gastrointestinal tract. Gut microbes convert dietary and host-derived substrates to metabolites such as short-chain fatty acids, thereby providing energy and nutrients to the host. Bacterial metabolites incorporated into the host metabolome can activate receptors on a variety of cell types and, in doing so, alter host physiology (including metabolism, organ function, biological rhythms, neural activity and behavior). Given that host-microbe interactions affect diverse aspects of host physiology, it is likely that they influence animal ecology and, if they confer fitness benefits, the evolutionary trajectory of a species. Multiple variables - including sampling regime, environmental parameters, host metadata and analytical methods - can influence experimental outcomes in host-microbiome studies, making careful experimental design and execution crucial to ensure reproducible and informative studies in the laboratory and field. Integration of microbiomes into comparative physiology and ecophysiological investigations can reveal the potential impacts of the microbiota on physiological responses to changing environments, and is likely to bring valuable insights to the study of host-microbiome interactions among a broad range of metazoans, including humans. © 2016. Published by The Company of Biologists Ltd.

  14. Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution.

    Science.gov (United States)

    Gatheru Waigi, Michael; Sun, Kai; Gao, Yanzheng

    2017-09-01

    Soil pollution has become a major concern in various terrestrial ecosystems worldwide. One in situ soil bioremediation strategy that has gained popularity recently is microbe-assisted phytoremediation, which is promising for remediating pollutants. Sphingomonads, a versatile bacteria group comprising four well-known genera, are ubiquitous in vegetation grown in contaminated soils. These Gram-negative microbes have been investigated for their ability to induce innate plant growth-promoting (PGP) traits, including the formation of phytohormones, siderophores, and chelators, in addition to their evolutionary adaptations enabling biodegradation and microbe-assisted removal of contaminants. However, their capacity for bacterial-assisted phytoremediation has to date been undervalued. Here, we highlight the specific features, roles, advantages, and challenges associated with using sphingomonads in plant-microbe interactions, from the perspective of future phytotechnologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. MVP: a microbe-phage interaction database.

    Science.gov (United States)

    Gao, Na L; Zhang, Chengwei; Zhang, Zhanbing; Hu, Songnian; Lercher, Martin J; Zhao, Xing-Ming; Bork, Peer; Liu, Zhi; Chen, Wei-Hua

    2018-01-04

    Phages invade microbes, accomplish host lysis and are of vital importance in shaping the community structure of environmental microbiota. More importantly, most phages have very specific hosts; they are thus ideal tools to manipulate environmental microbiota at species-resolution. The main purpose of MVP (Microbe Versus Phage) is to provide a comprehensive catalog of phage-microbe interactions and assist users to select phage(s) that can target (and potentially to manipulate) specific microbes of interest. We first collected 50 782 viral sequences from various sources and clustered them into 33 097 unique viral clusters based on sequence similarity. We then identified 26 572 interactions between 18 608 viral clusters and 9245 prokaryotes (i.e. bacteria and archaea); we established these interactions based on 30 321 evidence entries that we collected from published datasets, public databases and re-analysis of genomic and metagenomic sequences. Based on these interactions, we calculated the host range for each of the phage clusters and accordingly grouped them into subgroups such as 'species-', 'genus-' and 'family-' specific phage clusters. MVP is equipped with a modern, responsive and intuitive interface, and is freely available at: http://mvp.medgenius.info. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Development of conductivity probe and temperature probe for in-situ measurements in hydrological studies

    International Nuclear Information System (INIS)

    Chandra, U.; Galindo, B.J.; Castagnet, A.C.G.

    1981-05-01

    A conductivity probe and a temperature probe have been developed for in-situ measurements in various hydrological field studies. The conductivity probe has platinum electrodes and is powered with two 12 volt batteries. The sensing element of the temperature probe consists of a resistor of high coefficient of temperature. Response of the conductivity probe is measured in a milliampere mater while the resistance of the thermistor is read by a digital meter. The values of conductivity and temperature are derived from respective calibration. The probes are prototype and their range of measurement can be improved depending upon the requirement of the field problem. (Author) [pt

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

    International Nuclear Information System (INIS)

    Breckenridge, C.R.; Watkins, C.S.; Bruhn, D.F.; Roberto, F.F.; Tsang, M.N.; Pinhero, P.J.; Brey, R.F.; Wright, R.N.; Windes, W.F.

    1999-01-01

    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 3 and 6 x 10 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 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 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

  18. 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.

  19. 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

  20. Study, design and manufacture eddy current probes for industry applications

    International Nuclear Information System (INIS)

    Nguyen Phuc; Nguyen Van Thuy; Vuong Binh Duong; Do Minh Duc; Trinh Dinh Truong; Tran Trong Duc; Do Tung Khanh; Dang Quang Trung

    2016-01-01

    This study is based on the studying, designing and manufacturing of eddy current probes for industry applications. The main tasks of this study include: i) Describes the overview and classification of eddy current probes (which can be classified into three categories based on the mode of operation: absolute eddy current probe, differential eddy current probe and reflect eddy current probe); ii) Describes the three methods of probe designing and manufacturing (including experimental, analytical and numerical designs); iii) Describes the designing and manufacturing of eddy current probes for industry applications, which based on experimental and analytical methods. Based on this study, we have successfully manufactured some current probes (including absolute eddy current probe, differential eddy current probe and reflect eddy current probe) for surface and tube inspections. (author)

  1. Three-dimensional optofluidic device for isolating microbes

    Science.gov (United States)

    Keloth, A.; Paterson, L.; Markx, G. H.; Kar, A. K.

    2015-03-01

    Development of efficient methods for isolation and manipulation of microorganisms is essential to study unidentified and yet-to-be cultured microbes originating from a variety of environments. The discovery of novel microbes and their products have the potential to contribute to the development of new medicines and other industrially important bioactive compounds. In this paper we describe the design, fabrication and validation of an optofluidic device capable of redirecting microbes within a flow using optical forces. The device holds promise to enable the high throughput isolation of single microbes for downstream culture and analysis. Optofluidic devices are widely used in clinical research, cell biology and biomedical engineering as they are capable of performing analytical functions such as controlled transportation, compact and rapid processing of nanolitres to millilitres of clinical or biological samples. We have designed and fabricated a three dimensional optofluidic device to control and manipulate microorganisms within a microfluidic channel. The device was fabricated in fused silica by ultrafast laser inscription (ULI) followed by selective chemical etching. The unique three-dimensional capability of ULI is utilized to integrate microfluidic channels and waveguides within the same substrate. The main microfluidic channel in the device constitutes the path of the sample. Optical waveguides are fabricated at right angles to the main microfluidic channel. The potential of the optical scattering force to control and manipulate microorganisms is discussed in this paper. A 980 nm continuous wave (CW) laser source, coupled to the waveguide, is used to exert radiation pressure on the particle and particle migrations at different flow velocities are recorded. As a first demonstration, device functionality is validated using fluorescent microbeads and initial trials with microalgae are presented.

  2. Accuracy of micro four-point probe measurements on inhomogeneous samples: A probe spacing dependence study

    DEFF Research Database (Denmark)

    Wang, Fei; Petersen, Dirch Hjorth; Østerberg, Frederik Westergaard

    2009-01-01

    In this paper, we discuss a probe spacing dependence study in order to estimate the accuracy of micro four-point probe measurements on inhomogeneous samples. Based on sensitivity calculations, both sheet resistance and Hall effect measurements are studied for samples (e.g. laser annealed samples...... the probe spacing is smaller than 1/40 of the variation wavelength, micro four-point probes can provide an accurate record of local properties with less than 1% measurement error. All the calculations agree well with previous experimental results.......) with periodic variations of sheet resistance, sheet carrier density, and carrier mobility. With a variation wavelength of ¿, probe spacings from 0.0012 to 1002 have been applied to characterize the local variations. The calculations show that the measurement error is highly dependent on the probe spacing. When...

  3. Spatial heterogeneity in soil microbes alters outcomes of plant competition.

    Directory of Open Access Journals (Sweden)

    Karen C Abbott

    Full Text Available Plant species vary greatly in their responsiveness to nutritional soil mutualists, such as mycorrhizal fungi and rhizobia, and this responsiveness is associated with a trade-off in allocation to root structures for resource uptake. As a result, the outcome of plant competition can change with the density of mutualists, with microbe-responsive plant species having high competitive ability when mutualists are abundant and non-responsive plants having high competitive ability with low densities of mutualists. When responsive plant species also allow mutualists to grow to greater densities, changes in mutualist density can generate a positive feedback, reinforcing an initial advantage to either plant type. We study a model of mutualist-mediated competition to understand outcomes of plant-plant interactions within a patchy environment. We find that a microbe-responsive plant can exclude a non-responsive plant from some initial conditions, but it must do so across the landscape including in the microbe-free areas where it is a poorer competitor. Otherwise, the non-responsive plant will persist in both mutualist-free and mutualist-rich regions. We apply our general findings to two different biological scenarios: invasion of a non-responsive plant into an established microbe-responsive native population, and successional replacement of non-responders by microbe-responsive species. We find that resistance to invasion is greatest when seed dispersal by the native plant is modest and dispersal by the invader is greater. Nonetheless, a native plant that relies on microbial mutualists for competitive dominance may be particularly vulnerable to invasion because any disturbance that temporarily reduces its density or that of the mutualist creates a window for a non-responsive invader to establish dominance. We further find that the positive feedbacks from associations with beneficial soil microbes create resistance to successional turnover. Our theoretical

  4. Spatial heterogeneity in soil microbes alters outcomes of plant competition.

    Science.gov (United States)

    Abbott, Karen C; Karst, Justine; Biederman, Lori A; Borrett, Stuart R; Hastings, Alan; Walsh, Vonda; Bever, James D

    2015-01-01

    Plant species vary greatly in their responsiveness to nutritional soil mutualists, such as mycorrhizal fungi and rhizobia, and this responsiveness is associated with a trade-off in allocation to root structures for resource uptake. As a result, the outcome of plant competition can change with the density of mutualists, with microbe-responsive plant species having high competitive ability when mutualists are abundant and non-responsive plants having high competitive ability with low densities of mutualists. When responsive plant species also allow mutualists to grow to greater densities, changes in mutualist density can generate a positive feedback, reinforcing an initial advantage to either plant type. We study a model of mutualist-mediated competition to understand outcomes of plant-plant interactions within a patchy environment. We find that a microbe-responsive plant can exclude a non-responsive plant from some initial conditions, but it must do so across the landscape including in the microbe-free areas where it is a poorer competitor. Otherwise, the non-responsive plant will persist in both mutualist-free and mutualist-rich regions. We apply our general findings to two different biological scenarios: invasion of a non-responsive plant into an established microbe-responsive native population, and successional replacement of non-responders by microbe-responsive species. We find that resistance to invasion is greatest when seed dispersal by the native plant is modest and dispersal by the invader is greater. Nonetheless, a native plant that relies on microbial mutualists for competitive dominance may be particularly vulnerable to invasion because any disturbance that temporarily reduces its density or that of the mutualist creates a window for a non-responsive invader to establish dominance. We further find that the positive feedbacks from associations with beneficial soil microbes create resistance to successional turnover. Our theoretical results constitute an

  5. Some Case Studies on Metal-Microbe Interactions to Remediate Heavy Metals- Contaminated Soils in Korea

    Science.gov (United States)

    Chon, Hyo-Taek

    2015-04-01

    Conventional physicochemical technologies to remediate heavy metals-contaminated soil have many problems such as low efficiency, high cost and occurrence of byproducts. Recently bioremediation technology is getting more and more attention. Bioremediation is defined as the use of biological methods to remediate and/or restore the contaminated land. The objectives of bioremediation are to degrade hazardous organic contaminants and to convert hazardous inorganic contaminants to less toxic compounds of safe levels. The use of bioremediation in the treatment of heavy metals in soils is a relatively new concept. Bioremediation using microbes has been developed to remove toxic heavy metals from contaminated soils in laboratory scale to the contaminated field sites. Recently the application of cost-effective and environment-friendly bioremediation technology to the heavy metals-contaminated sites has been gradually realized in Korea. The merits of bioremediation include low cost, natural process, minimal exposure to the contaminants, and minimum amount of equipment. The limitations of bioremediation are length of remediation, long monitoring time, and, sometimes, toxicity of byproducts for especially organic contaminants. From now on, it is necessary to prove applicability of the technologies to contaminated sites and to establish highly effective, low-cost and easy bioremediation technology. Four categories of metal-microbe interactions are generally biosorption, bioreduction, biomineralization and bioleaching. In this paper, some case studies of the above metal-microbe interactions in author's lab which were published recently in domestic and international journals will be introduced and summarized.

  6. Companion animals symposium: role of microbes in canine and feline health.

    Science.gov (United States)

    Kil, D Y; Swanson, K S

    2011-05-01

    Whether in an ocean reef, a landfill, or a gastrointestinal tract (GIT), invisible communities of highly active and adaptable microbes prosper. Over time, mammals have developed a symbiosis with microbes that are important inhabitants not only in the GIT, but also in the mouth, skin, and urogenital tract. In the GIT, the number of commensal microbes exceeds the total number of host cells by at least 10 times. The GIT microbes play a critical role in nutritional, developmental, defensive, and physiologic processes in the host. Recent evidence also suggests a role of GIT microbes in metabolic phenotype and disease risk (e.g., obesity, metabolic syndrome) of the host. Proper balance is a key to maintaining GIT health. Balanced microbial colonization is also important for other body regions such as the oral cavity, the region with the greatest prevalence of disease in dogs and cats. A significant obstruction to studying microbial populations has been the lack of tools to identify and quantify microbial communities accurately and efficiently. Most of the current knowledge of microbial populations has been established by traditional cultivation methods that are not only laborious, time-consuming, and often inaccurate, but also greatly limited in scope. However, recent advances in molecular-based techniques have resulted in a dramatic improvement in studying microbial communities. These DNA-based high-throughput technologies have enabled us to more clearly characterize the identity and metabolic activity of microbes living in the host and their association with health and diseases. Despite this recent progress, however, published data pertaining to microbial communities of dogs and cats are still lacking in comparison with data in humans and other animals. More research is required to provide a more detailed description of the canine and feline microbiome and its role in health and disease.

  7. 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...

  8. Wired to the roots: impact of root-beneficial microbe interactions on aboveground plant physiology and protection.

    Science.gov (United States)

    Kumar, Amutha Sampath; Bais, Harsh P

    2012-12-01

    Often, plant-pathogenic microbe interactions are discussed in a host-microbe two-component system, however very little is known about how the diversity of rhizospheric microbes that associate with plants affect host performance against pathogens. There are various studies, which specially direct the importance of induced systemic defense (ISR) response in plants interacting with beneficial rhizobacteria, yet we don't know how rhizobacterial associations modulate plant physiology. In here, we highlight the many dimensions within which plant roots associate with beneficial microbes by regulating aboveground physiology. We review approaches to study the causes and consequences of plant root association with beneficial microbes on aboveground plant-pathogen interactions. The review provides the foundations for future investigations into the impact of the root beneficial microbial associations on plant performance and innate defense responses.

  9. Visualizing conserved gene location across microbe genomes

    Science.gov (United States)

    Shaw, Chris D.

    2009-01-01

    This paper introduces an analysis-based zoomable visualization technique for displaying the location of genes across many related species of microbes. The purpose of this visualizatiuon is to enable a biologist to examine the layout of genes in the organism of interest with respect to the gene organization of related organisms. During the genomic annotation process, the ability to observe gene organization in common with previously annotated genomes can help a biologist better confirm the structure and function of newly analyzed microbe DNA sequences. We have developed a visualization and analysis tool that enables the biologist to observe and examine gene organization among genomes, in the context of the primary sequence of interest. This paper describes the visualization and analysis steps, and presents a case study using a number of Rickettsia genomes.

  10. 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).

  11. Expanding Single Particle Mass Spectrometer Analyses for the Identification of Microbe Signatures in Sea Spray Aerosol.

    Science.gov (United States)

    Sultana, Camille M; Al-Mashat, Hashim; Prather, Kimberly A

    2017-10-03

    Ocean-derived microbes in sea spray aersosol (SSA) have the potential to influence climate and weather by acting as ice nucleating particles in clouds. Single particle mass spectrometers (SPMSs), which generate in situ single particle composition data, are excellent tools for characterizing aerosols under changing environmental conditions as they can provide high temporal resolution and require no sample preparation. While SPMSs have proven capable of detecting microbes, these instruments have never been utilized to definitively identify aerosolized microbes in ambient sea spray aersosol. In this study, an aerosol time-of-flight mass spectrometer was used to analyze laboratory generated SSA produced from natural seawater in a marine aerosol reference tank. We present the first description of a population of biological SSA mass spectra (BioSS), which closely match the ion signatures observed in previous terrestrial microbe studies. The fraction of BioSS dramatically increased in the largest supermicron particles, consistent with field and laboratory measurements of microbes ejected by bubble bursting, further supporting the assignment of BioSS mass spectra as microbes. Finally, as supported by analysis of inorganic ion signals, we propose that dry BioSS particles have heterogeneous structures, with microbes adhered to sodium chloride nodules surrounded by magnesium-enriched coatings. Consistent with this structure, chlorine-containing ion markers were ubiquitous in BioSS spectra and identified as possible tracers for distinguishing recently aerosolized marine from terrestrial microbes.

  12. Synchrotron X-ray Investigations of Mineral-Microbe-Metal Interactions

    International Nuclear Information System (INIS)

    Kemner, Kenneth M.; O'Loughlin, Edward J.; Kelly, Shelly D.; Boyanov, Maxim I.

    2005-01-01

    Interactions between microbes and minerals can play an important role in metal transformations (i.e. changes to an element's valence state, coordination chemistry, or both), which can ultimately affect that element's mobility. Mineralogy affects microbial metabolism and ecology in a system; microbes, in turn, can affect the system's mineralogy. Increasingly, synchrotron-based X-ray experiments are in routine use for determining an element's valence state and coordination chemistry, as well as for examining the role of microbes in metal transformations.

  13. 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.

  14. 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.

  15. [Development of a microenvironment test chamber for airborne microbe research].

    Science.gov (United States)

    Zhan, Ningbo; Chen, Feng; Du, Yaohua; Cheng, Zhi; Li, Chenyu; Wu, Jinlong; Wu, Taihu

    2017-10-01

    One of the most important environmental cleanliness indicators is airborne microbe. However, the particularity of clean operating environment and controlled experimental environment often leads to the limitation of the airborne microbe research. This paper designed and implemented a microenvironment test chamber for airborne microbe research in normal test conditions. Numerical simulation by Fluent showed that airborne microbes were evenly dispersed in the upper part of test chamber, and had a bottom-up concentration growth distribution. According to the simulation results, the verification experiment was carried out by selecting 5 sampling points in different space positions in the test chamber. Experimental results showed that average particle concentrations of all sampling points reached 10 7 counts/m 3 after 5 minutes' distributing of Staphylococcus aureus , and all sampling points showed the accordant mapping of concentration distribution. The concentration of airborne microbe in the upper chamber was slightly higher than that in the middle chamber, and that was also slightly higher than that in the bottom chamber. It is consistent with the results of numerical simulation, and it proves that the system can be well used for airborne microbe research.

  16. Quantitative Analysis of Microbes in Water Tank of G.A. Siwabessy Reactor

    International Nuclear Information System (INIS)

    Itjeu Karliana; Diah Dwiana Lestiani

    2003-01-01

    The quality of water in reactor system has an important role because it could effect the function as a coolant and the operation of reactor indirectly. The study of microbe analyzes has been carried out to detect the existence of microbes in water tank and quantitative analyzes of microbes also has been applied as a continuation of the previous study. The samples is taken out from the end side of reactor GA Siwabessy's tank, inoculated in TSA (Tripcase Soy Agar) medium, put in incubator at 30 - 35 o C for 4 days. The results of experiment show the reconfirmation for the existence of bacteria and the un-existence of yield. The quantitative analysis with TPC method show the growth rate of bacteria is twice in 24 hours. (author)

  17. Probes for edge plasma studies of TFTR (invited)

    International Nuclear Information System (INIS)

    Manos, D.M.; Budny, R.V.; Kilpatrick, S.; Stangeby, P.; Zweben, S.

    1986-01-01

    Tokamak fusion test reactor (TFTR) probes are designed to study the interaction of the plasma with material surfaces such as the wall and limiters, and to study the transport of particles and energy between the core and edge. Present probe heads have evolved from prototypes in Princeton large torus (PLT), poloidal divertor experiment (PDX) [Princeton BETA experiment (PBX)], and the initial phase of TFTR operation. The newest heads are capable of making several simultaneous measurements and include Langmuir probes, heat flux probes, magnetic coils, rotating calorimeter fast ion probes, and sample exposure specimens. This paper describes these probe heads and presents some of the data they and their prototypes have acquired. The paper emphasizes measurement of transient plasma effects such as fast ion loss during auxiliary heating, the evolution of the edge plasma during heating, compression, and free expansion, and fluctuations in the edge plasma

  18. MEMS and the microbe

    NARCIS (Netherlands)

    Ingham, C.J.; Vlieg, J.E.T.V.H.

    2008-01-01

    In recent years, relatively simple MEMS fabrications have helped accelerate our knowledge of the microbial cell. Current progress and challenges in the application of lab-on-a-chip devices to the viable microbe are reviewed. Furthermore, the degree to which microbiologists are becoming the engineers

  19. Host-Microbe Interactions in Microgravity: Assessment and Implications

    Directory of Open Access Journals (Sweden)

    Jamie S. Foster

    2014-05-01

    Full Text Available Spaceflight imposes several unique stresses on biological life that together can have a profound impact on the homeostasis between eukaryotes and their associated microbes. One such stressor, microgravity, has been shown to alter host-microbe interactions at the genetic and physiological levels. Recent sequencing of the microbiomes associated with plants and animals have shown that these interactions are essential for maintaining host health through the regulation of several metabolic and immune responses. Disruptions to various environmental parameters or community characteristics may impact the resiliency of the microbiome, thus potentially driving host-microbe associations towards disease. In this review, we discuss our current understanding of host-microbe interactions in microgravity and assess the impact of this unique environmental stress on the normal physiological and genetic responses of both pathogenic and mutualistic associations. As humans move beyond our biosphere and undergo longer duration space flights, it will be essential to more fully understand microbial fitness in microgravity conditions in order to maintain a healthy homeostasis between humans, plants and their respective microbiomes.

  20. Host-microbe interactions in microgravity: assessment and implications.

    Science.gov (United States)

    Foster, Jamie S; Wheeler, Raymond M; Pamphile, Regine

    2014-05-26

    Spaceflight imposes several unique stresses on biological life that together can have a profound impact on the homeostasis between eukaryotes and their associated microbes. One such stressor, microgravity, has been shown to alter host-microbe interactions at the genetic and physiological levels. Recent sequencing of the microbiomes associated with plants and animals have shown that these interactions are essential for maintaining host health through the regulation of several metabolic and immune responses. Disruptions to various environmental parameters or community characteristics may impact the resiliency of the microbiome, thus potentially driving host-microbe associations towards disease. In this review, we discuss our current understanding of host-microbe interactions in microgravity and assess the impact of this unique environmental stress on the normal physiological and genetic responses of both pathogenic and mutualistic associations. As humans move beyond our biosphere and undergo longer duration space flights, it will be essential to more fully understand microbial fitness in microgravity conditions in order to maintain a healthy homeostasis between humans, plants and their respective microbiomes.

  1. Thermo-tolerant phosphate-solubilizing microbes for multi-functional biofertilizer preparation.

    Science.gov (United States)

    Chang, Cheng-Hsiung; Yang, Shang-Shyng

    2009-02-01

    In order to prepare the multi-functional biofertilizer, thermo-tolerant phosphate-solubilizing microbes including bacteria, actinomycetes, and fungi were isolated from different compost plants and biofertilizers. Except Streptomycesthermophilus J57 which lacked pectinase, all isolates possessed amylase, CMCase, chitinase, pectinase, protease, lipase, and nitrogenase activities. All isolates could solubilize calcium phosphate and Israel rock phosphate; various isolates could solubilize aluminum phosphate, iron phosphate, and hydroxyapatite. During composting, biofertilizers inoculated with the tested microbes had a significantly higher temperature, ash content, pH, total nitrogen, soluble phosphorus content, and germination rate than non-inoculated biofertilizer; total organic carbon and carbon-to-nitrogen ratio showed the opposite pattern. Adding these microbes can shorten the period of maturity, improve the quality, increase the soluble phosphorus content, and enhance the populations of phosphate-solubilizing and proteolytic microbes in biofertilizers. Therefore, inoculating thermo-tolerant phosphate-solubilizing microbes into agricultural and animal wastes represents a practical strategy for preparing multi-functional biofertilizer.

  2. Simulated microbe removal around finger rings using different hand sanitation methods.

    Science.gov (United States)

    Alur, Archana A; Rane, Madhavi J; Scheetz, James P; Lorenz, Douglas J; Gettleman, Lawrence

    2009-09-01

    It is our opinion that the CDC and the WHO have underestimated cross-contamination under examination gloves in dental clinics while wearing jewelry, such as finger rings. These agencies only "recommend" removing jewelry, and only washing hands for 15 seconds with soap and warm water before donning gloves. This study examined several washing procedures and finger rings using simulated microbes. A gloved rubber hand manikin was made and fitted with a fresh disposable vinyl glove. Four fingers were fitted with rings or no ring, dusted with simulated microbes, and washed with a scrub brush for 5, 15, and 25 seconds under 20 degrees C and 40 degrees C water alone, or with liquid hand soap. Light levels (in lux) of fluorescent powder before and after washing were measured and delta scores calculated for changes in light levels, equivalent to effectiveness of hand washing procedures. A full-factorial, 3-factor analysis of variance (ANOVA) was used to test for differences among levels of the three study factors-time, temperature, and soap use. Tukey's post hoc honestly significant difference (HSD) test was applied to significant factors to examine pair-wise differences between factor levels. It was found that the longer the hands with rings were washed with a scrub brush under flowing water, the more simulated microbes were removed. By 25 seconds, all methods were essentially the same. Simulated microbes were more difficult to remove from the palm compared to the back of the hand. The liquid hand soap used in this study was more effective with warm water than cold. When given a choice of washing with cold water up to 15 seconds, it would be preferable not to use soap to remove simulated microbes. Qualitatively, the outer surface of finger rings were more effectively cleaned than the crevice below the ring, and the ring with a stone setting appeared to accumulate and retain simulated microbes more than other rings. The most effective treatment was washing with warm water

  3. Soil-Plant-Microbe Interactions in Stressed Agriculture Management: A Review

    Institute of Scientific and Technical Information of China (English)

    Shobhit Raj VIMAL; Jay Shankar SINGH; Naveen Kumar ARORA; Surendra SINGH

    2017-01-01

    The expected rise in temperature and decreased precipitation owing to climate change and unabated anthropogenic activities add complexity and uncertainty to agro-industry.The impact of soil nutrient imbalance,mismanaged use of chemicals,high temperature,flood or drought,soil salinity,and heavy metal pollutions,with regard to food security,is increasingly being explored worldwide.This review describes the role of soil-plant-microbe interactions along with organic manure in solving stressed agriculture problems.Beneficial microbes associated with plants are known to stimulate plant growth and enhance plant resistance to biotic (diseases) and abiotic (salinity,drought,pollutions,etc.) stresses.The plant growth-promoting rhizobacteria (PGPR) and mycorrhizae,a key component of soil microbiota,could play vital roles in the maintenance of plant fitness and soil health under stressed environments.The application of organic manure as a soil conditioner to stressed soils along with suitable microbial strains could further enhance the plant-microbe associations and increase the crop yield.A combination of plant,stress-tolerant microbe,and organic amendment represents the tripartite association to offer a favourable environment to the proliferation of beneficial rhizosphere microbes that in turn enhance the plant growth performance in disturbed agro-ecosystem.Agriculture land use patterns with the proper exploitation of plant-microbe associations,with compatible beneficial microbial agents,could be one of the most effective strategies in the management of the concerned agriculture lands owing to climate change resilience.However,the association of such microbes with plants for stressed agriculture management still needs to be explored in greater depth.

  4. Molecular detection of drug resistance in microbes by isotopic techniques: The IAEA experience

    International Nuclear Information System (INIS)

    Dar, L.; Boussaha, A.; Padhy, A.K.; Khan, B.

    2003-01-01

    The International Atomic Energy Agency (IAEA) supports various programmes on the uses of radionuclide techniques in the management of human communicable diseases. An important issue, being addressed through several technology transfer projects, is the detection of drug resistance in microbes by radioisotope based molecular-biology diagnostic procedures. The techniques employed include dot blot hybridisation with P-32 labelled oligonucleotide probes to detect point mutations, associated with drug resistance, in microbial genes amplified by the polymerase chain reaction (PCR). Molecular methods have been used for the detection of drug resistance in the malarial parasite, Plasmodium falciparum, and in Mycobacterium tuberculosis. Radioisotope based molecular-biology methods have been demonstrated to have comparative advantages in being sensitive, specific, cost-effective, and suitable for application to large-scale molecular surveillance for drug resistance. (author)

  5. 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

  6. Microbes as interesting source of novel insecticides: A review ...

    African Journals Online (AJOL)

    ... strains with good insecticidal properties can be identified, evaluated and utilized for pest control. This paper reviews the insecticidal properties of microbes and their potential utility in pest management. Keywords: Microbes, insecticides, metabolites, pest management. African Journal of Biotechnology, Vol 13(26) 2582- ...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    in the last decade that could significantly change the current ways of synthesizing chemicals. MES is a process in which electroautotrophic microbes reduce CO2 to multicarbon organics using electrical current as a source of electron. Electricity necessary for MES can be harvested from renewable resources...... relying on co-cultures and investigating extracellular electron transfer from the cathode to the microbes are some of the strategies that we are implementing to transform MES into a commercially viable technology....... such as solar energy, wind turbine or wastewater treatment processes. The net outcome is that renewable energy get store in the covalent bonds of valuable chemicals synthesized from greenhouse gas. However, low electron transferrates from the electrode to microbes, poor adherence of cells on the electrode...

  8. Big Data Approaches To Coral-Microbe Symbiosis

    Science.gov (United States)

    Zaneveld, J.; Pollock, F. J.; McMinds, R.; Smith, S.; Payet, J.; Hanna, B.; Welsh, R.; Foster, A.; Ohdera, A.; Shantz, A. A.; Burkepile, D. E.; Maynard, J. A.; Medina, M.; Vega Thurber, R.

    2016-02-01

    Coral reefs face increasing challenges worldwide, threatened by overfishing and nutrient pollution, which drive growth of algal competitors of corals, and periods of extreme temperature, which drive mass coral bleaching. I will discuss two projects that examine how coral's complex relationships with microorganisms affect the response of coral colonies and coral species to environmental challenge. Microbiological studies have documented key roles for coral's microbial symbionts in energy harvest and defense against pathogens. However, the evolutionary history of corals and their microbes is little studied. As part of the Global Coral Microbiome Project, we are characterizing bacterial, archaeal, fungal, and Symbiodinium diversity across >1400 DNA samples from all major groups of corals, collected from 15 locations worldwide. This collection will allow us to ask how coral- microbe associations evolved over evolutionary time, and to determine whether microbial symbiosis helps predict the relative vulnerability of certain coral species to environmental stress. In the second project, we experimentally characterized how the long-term effects of human impacts such as overfishing and nutrient pollution influence coral-microbe symbiosis. We conducted a three-year field experiment in the Florida Keys applying nutrient pollution or simulated overfishing to reef plots, and traced the effects on reef communities, coral microbiomes, and coral health. The results show that extremes of temperature and algal competition destabilize coral microbiomes, increasing pathogen blooms, coral disease, and coral death. Surprisingly, these local stressors interacted strongly with thermal stress: the greatest microbiome disruption, and >80% of coral mortality happened in the hottest periods. Thus, overfishing and nutrient pollution may interact with increased climate-driven episodes of sub-bleaching thermal stress to increase coral mortality by disrupt reef communities down to microbial scales.

  9. The study on microb and organic metallogenetic process of the interlayer oxidized zone uranium deposit. A case study of the Shihongtan uranium deposit in Turpan-Hami basin

    International Nuclear Information System (INIS)

    Qiao Haiming; Shang Gaofeng

    2010-01-01

    Microbial and organic process internationally leads the field in the study of metallogenetic process presently. Focusing on Shi Hongtan uranium deposit, a typical interlayer oxidized zone sandstone-type deposit, this paper analyzes the geochemical characteristics of microb and organic matter in the deposit, and explores the interaction of microb and organic matter. It considers that the anaerobic bacterium actively takes part in the formation of the interlayer oxidized zone, as well as the mobilization and migration of uranium. In the redox (oxidation-reduction) transition zone, sulphate-reducing bacteria reduced sulphate to stink damp, lowing Eh and acidifying pH in the groundwater, which leads to reducing and absorbing of uranium, by using light hydrocarbon which is the product of the biochemical process of organism and the soluble organic matter as the source of carbon. The interaction of microb and organic matter controls the metallogenetic process of uranium in the deposit. (authors)

  10. A Hydroponic Co-cultivation System for Simultaneous and Systematic Analysis of Plant/Microbe Molecular Interactions and Signaling.

    Science.gov (United States)

    Nathoo, Naeem; Bernards, Mark A; MacDonald, Jacqueline; Yuan, Ze-Chun

    2017-07-22

    An experimental design mimicking natural plant-microbe interactions is very important to delineate the complex plant-microbe signaling processes. Arabidopsis thaliana-Agrobacterium tumefaciens provides an excellent model system to study bacterial pathogenesis and plant interactions. Previous studies of plant-Agrobacterium interactions have largely relied on plant cell suspension cultures, the artificial wounding of plants, or the artificial induction of microbial virulence factors or plant defenses by synthetic chemicals. However, these methods are distinct from the natural signaling in planta, where plants and microbes recognize and respond in spatial and temporal manners. This work presents a hydroponic cocultivation system where intact plants are supported by metal mesh screens and cocultivated with Agrobacterium. In this cocultivation system, no synthetic phytohormone or chemical that induces microbial virulence or plant defense is supplemented. The hydroponic cocultivation system closely resembles natural plant-microbe interactions and signaling homeostasis in planta. Plant roots can be separated from the medium containing Agrobacterium, and the signaling and responses of both the plant hosts and the interacting microbes can be investigated simultaneously and systematically. At any given timepoint/interval, plant tissues or bacteria can be harvested separately for various "omics" analyses, demonstrating the power and efficacy of this system. The hydroponic cocultivation system can be easily adapted to study: 1) the reciprocal signaling of diverse plant-microbe systems, 2) signaling between a plant host and multiple microbial species (i.e. microbial consortia or microbiomes), 3) how nutrients and chemicals are implicated in plant-microbe signaling, and 4) how microbes interact with plant hosts and contribute to plant tolerance to biotic or abiotic stresses.

  11. Utilization of oil palm empty bunches waste as biochar-microbes for improving availibity of soil nutrients

    Directory of Open Access Journals (Sweden)

    G . I . Ichriani

    2016-01-01

    Full Text Available There are about 23% waste oil palm empty fruit bunches (OPEFB of total waste generated from the production of crude palm oil in oil palm plantations. Pyrolysis technology can be used to convert waste into biochar and further can be utilized for the improvement of soil. Biochar-microbes of OPEFB are biochar from OPEFB biomass that enriched with soil microbes. Biochar-microbes is expected to be used for the improvement of the soil and plants. Therefore the purpose of this research was to study the ability of biochar-microbes OPEFB to increase availability of the nutrients in sandy soils. The process of making biochar done by using slow pyrolysis technology by heating 300oC and 400oC for 2 and 3 hours, and with sizes 40 and 80 mesh, as well as indigenous microbial Bulkhorderia nodosa G.52.Rif1 and Trichoderma sp. added. The biochar production and research were conducted in the Department of Forestry Laboratory and in the Department of Agronomy Laboratory, Faculty of Agriculture, Palangka Raya University. In general, the study showed that biochar-microbes could maintain the soil pH value and tends to increase the soil pH, increasing the holding capacity of sandy soil to the elements of P and K as well as increasing the availability of nutrients N, P and K. Furthermore, this study showed that the biochar process by 400oC heating for 3 hours and 40 mesh with microbes or without microbes were the best effect on the improvement of the quality of holding capacity and the nutrients supply in sandy soils.

  12. 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.

  13. 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 Arabidops...

  14. Transcriptomic profiling of microbe-microbe interactions reveals the specific response of the biocontrol strain P. fluorescens In5 to the phytopathogen Rhizoctonia solani

    DEFF Research Database (Denmark)

    Hennessy, Rosanna Catherine; Glaring, Mikkel Andreas; Olsson, Stefan

    2017-01-01

    reads per sample. RESULTS: No significant changes in global gene expression were recorded during dual-culture of P. fluorescens In5 with any of the two pathogens but rather each pathogen appeared to induce expression of a specific set of genes. A particularly strong transcriptional response to R. solani...... and in particular the fungus R. solani. This highlights the importance of studying microbe-microbe interactions to gain a better understanding of how different systems function in vitro and ultimately in natural systems where biocontrol agents can be used for the sustainable management of plant diseases....

  15. The interactions between nanoscale zero-valent iron and microbes in the subsurface environment: A review

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Yankai [College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082 (China); Dong, Haoran, E-mail: dongh@hnu.edu.cn [College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082 (China); Zeng, Guangming; Tang, Lin; Jiang, Zhao; Zhang, Cong; Deng, Junmin; Zhang, Lihua; Zhang, Yi [College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082 (China)

    2017-01-05

    Highlights: • The interactions between various microbes and NZVI were summarized. • The adverse and positive effects of NZVI on the growth of microbes were reviewed. • The synergistic effects of NZVI and bacteria on pollutant removal were reviewed. • The effects of iron-reducing bacteria on the aged NZVI were reviewed. • Future challenges to study the interactions between NZVI and microbes are suggested. - Abstract: Nanoscale zero-valent iron (NZVI) particles, applied for in-situ subsurface remediation, are inevitable to interact with various microbes in the remediation sites directly or indirectly. This review summarizes their interactions, including the effects of NZVI on microbial activity and growth, the synergistic effect of NZVI and microbes on the contaminant removal, and the effects of microbes on the aging of NZVI. NZVI could exert either inhibitive or stimulative effects on the growth of microbes. The mechanisms of NZVI cytotoxicity (i.e., the inhibitive effect) include physical damage and biochemical destruction. The stimulative effects of NZVI on certain bacteria are associated with the creation of appropriate living environment, either through providing electron donor (e.g., H{sub 2}) or carbon sources (e.g., the engineered organic surface modifiers), or through eliminating the noxious substances that can cause bactericidal consequence. As a result of the positive interaction, the combination of NZVI and some microbes shows synergistic effect on contaminant removal. Additionally, the aged NZVI can be utilized by some iron-reducing bacteria, resulting in the transformation of Fe(III) to Fe(II), which can further contribute to the contaminant reduction. However, the Fe(III)-reduction process can probably induce environmental risks, such as environmental methylation and remobilization of the previously entrapped heavy metals.

  16. The interactions between nanoscale zero-valent iron and microbes in the subsurface environment: A review

    International Nuclear Information System (INIS)

    Xie, Yankai; Dong, Haoran; Zeng, Guangming; Tang, Lin; Jiang, Zhao; Zhang, Cong; Deng, Junmin; Zhang, Lihua; Zhang, Yi

    2017-01-01

    Highlights: • The interactions between various microbes and NZVI were summarized. • The adverse and positive effects of NZVI on the growth of microbes were reviewed. • The synergistic effects of NZVI and bacteria on pollutant removal were reviewed. • The effects of iron-reducing bacteria on the aged NZVI were reviewed. • Future challenges to study the interactions between NZVI and microbes are suggested. - Abstract: Nanoscale zero-valent iron (NZVI) particles, applied for in-situ subsurface remediation, are inevitable to interact with various microbes in the remediation sites directly or indirectly. This review summarizes their interactions, including the effects of NZVI on microbial activity and growth, the synergistic effect of NZVI and microbes on the contaminant removal, and the effects of microbes on the aging of NZVI. NZVI could exert either inhibitive or stimulative effects on the growth of microbes. The mechanisms of NZVI cytotoxicity (i.e., the inhibitive effect) include physical damage and biochemical destruction. The stimulative effects of NZVI on certain bacteria are associated with the creation of appropriate living environment, either through providing electron donor (e.g., H_2) or carbon sources (e.g., the engineered organic surface modifiers), or through eliminating the noxious substances that can cause bactericidal consequence. As a result of the positive interaction, the combination of NZVI and some microbes shows synergistic effect on contaminant removal. Additionally, the aged NZVI can be utilized by some iron-reducing bacteria, resulting in the transformation of Fe(III) to Fe(II), which can further contribute to the contaminant reduction. However, the Fe(III)-reduction process can probably induce environmental risks, such as environmental methylation and remobilization of the previously entrapped heavy metals.

  17. Anti-radiation microbe separated from traditional Chinese medicine

    International Nuclear Information System (INIS)

    Zou Zhaohui; Zhao Junqi; Deng Gangqiao; Wang Qian; Li Wenge; Peng Ling; Luo Zhiping

    2007-01-01

    One batch of Jinsuo pills, a kind of Chinese herbal medicine, treated by standardized irradiation process but failed to meet the sanitation requirement. Radiation resistant microbe was separated from the pills sample and the Gram stain showed positive, the colony of the microbe is milky white and concentric circle shape. It is observed as one of bacillus by microscope, its D 10 values in physiological saline and filter paper are 6.75 and 7.18 kGy, respectively. (authors)

  18. TANPOPO: Microbe and micrometeoroid capture experiments on International Space Station.

    Science.gov (United States)

    Yamagishi, Akihiko; Kobayashi, Kensei; Yano, Hajime; Yokobori, Shinichi; Hashimoto, Hirofumi; Kawai, Hideyuki; Yamashita, Masamichi

    There is a long history of the microbe-collection experiments at high altitude. Microbes have been collected using balloons, aircraft and meteorological rockets from 1936 to 1976. Spore forming fungi and Bacilli, and Micrococci have been isolated in these experiments. It is not clear how high do microbes go up. If the microbes might have been present even at higher altitudes, the fact would endorse the possibility of interplanetary migration of life. TANPOPO, dandelion, is the name of a grass whose seeds with floss are spread by the wind. We propose the analyses of interplanetary migration of microbes, organic compounds and meteoroids on Japan Experimental Module (JEM) of the International Space Station (ISS). Ultra low-density aerogel will be used to capture micrometeoroid and debris. Particles captured by aerogel will be used for several analyses after the initial inspection of the gel and tracks. Careful analysis of the tracks in the aerogel will provide the size and velocity dependence of debris flux. The particles will be analyzed for mineralogical, organic and microbiological characteristics. Aerogels are ready for production in Japan. Aerogels and trays are space proven. All the analytical techniques are ready. The Tanpopo mission was accepted as a candidate experiments on Exposed Facility of ISS-JEM.

  19. 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.

  20. Radiation induced pesticidal microbes

    International Nuclear Information System (INIS)

    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

  1. Rarity in aquatic microbes: placing protists on the map.

    Science.gov (United States)

    Logares, Ramiro; Mangot, Jean-François; Massana, Ramon

    2015-12-01

    Most microbial richness at any given time tends to be represented by low-abundance (rare) taxa, which are collectively referred to as the "rare biosphere". Here we review works on the rare biosphere using high-throughput sequencing (HTS), with a particular focus on unicellular eukaryotes or protists. Evidence thus far indicates that the rare biosphere encompasses dormant as well as metabolically active microbes that could potentially play key roles in ecosystem functioning. Rare microbes appear to have biogeography, and sometimes the observed patterns can be similar to what is observed among abundant taxa, suggesting similar community-structuring mechanisms. There is limited evidence indicating that the rare biosphere contains taxa that are phylogenetically distantly related to abundant counterparts; therefore, the rare biosphere may act as a reservoir of deep-branching phylogenetic diversity. The potential role of the rare biosphere as a bank of redundant functions that can help to maintain continuous ecosystem function following oscillations in taxonomic abundances is hypothesized as its main ecological role. Future studies focusing on rare microbes are crucial for advancing our knowledge of microbial ecology and evolution and unveiling their links with ecosystem function. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  2. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, Caroline; Buckley, Merry

    2007-12-31

    Microbes are the foundation for all of life. From the air we breathe to the soil we rely on for farming to the water we drink, everything humans need to survive is intimately coupled with the activities of microbes. Major advances have been made in the understanding of disease and the use of microorganisms in the industrial production of drugs, food products and wastewater treatment. However, our understanding of many complicated microbial environments (the gut and teeth), soil fertility, and biogeochemical cycles of the elements is lagging behind due to their enormous complexity. Inadequate technology and limited resources have stymied many lines of investigation. Today, most environmental microorganisms have yet to be isolated and identified, let alone rigorously studied. The American Academy of Microbiology convened a colloquium in Seattle, Washington, in February 2007, to deliberate the way forward in the study of microorganisms and microbial activities in the environment. Researchers in microbiology, marine science, pathobiology, evolutionary biology, medicine, engineering, and other fields discussed ways to build on and extend recent successes in microbiology. The participants made specific recommendations for targeting future research, improving methodologies and techniques, and enhancing training and collaboration in the field. Microbiology has made a great deal of progress in the past 100 years, and the useful applications for these new discoveries are numerous. Microorganisms and microbial products are now used in industrial capacities ranging from bioremediation of toxic chemicals to probiotic therapies for humans and livestock. On the medical front, studies of microbial communities have revealed, among other things, new ways for controlling human pathogens. The immediate future for research in this field is extremely promising. In order to optimize the effectiveness of community research efforts in the future, scientists should include manageable

  4. Preliminary biological screening of microbes isolated from cow dung ...

    African Journals Online (AJOL)

    Preliminary biological screening of microbes isolated from cow dung in Kampar. KC Teo, SM Teoh. Abstract. Five distinct morphologically and physiologically isolates were isolated from cow dung at Kampar, Perak, Malaysia and cultured on nutrient agar (NA) plates. Morphological studies including microscopic examination ...

  5. How Do Small Things Make a Big Difference? Activities to Teach about Human-Microbe Interactions.

    Science.gov (United States)

    Jasti, Chandana; Hug, Barbara; Waters, Jillian L; Whitaker, Rachel J

    2014-11-01

    Recent scientific studies are providing increasing evidence for how microbes living in and on us are essential to our good health. However, many students still think of microbes only as germs that harm us. The classroom activities presented here are designed to shift student thinking on this topic. In these guided inquiry activities, students investigate human-microbe interactions as they work together to interpret and analyze authentic data from published articles and develop scientific models. Through the activities, students learn and apply ecological concepts as they come to see the human body as a fascinatingly complex ecosystem.

  6. How Do Small Things Make a Big Difference? Activities to Teach about Human–Microbe Interactions

    Science.gov (United States)

    JASTI, CHANDANA; HUG, BARBARA; WATERS, JILLIAN L.; WHITAKER, RACHEL J.

    2014-01-01

    Recent scientific studies are providing increasing evidence for how microbes living in and on us are essential to our good health. However, many students still think of microbes only as germs that harm us. The classroom activities presented here are designed to shift student thinking on this topic. In these guided inquiry activities, students investigate human–microbe interactions as they work together to interpret and analyze authentic data from published articles and develop scientific models. Through the activities, students learn and apply ecological concepts as they come to see the human body as a fascinatingly complex ecosystem. PMID:25520526

  7. Harnessing Insect-Microbe Chemical Communications To Control Insect Pests of Agricultural Systems.

    Science.gov (United States)

    Beck, John J; Vannette, Rachel L

    2017-01-11

    Insect pests cause serious economic, yield, and food safety problems to managed crops worldwide. Compounding these problems, insect pests often vector pathogenic or toxigenic microbes to plants. Previous work has considered plant-insect and plant-microbe interactions separately. Although insects are well-understood to use plant volatiles to locate hosts, microorganisms can produce distinct and abundant volatile compounds that in some cases strongly attract insects. In this paper, we focus on the microbial contribution to plant volatile blends, highlighting the compounds emitted and the potential for variation in microbial emission. We suggest that these aspects of microbial volatile emission may make these compounds ideal for use in agricultural applications, as they may be more specific or enhance methods currently used in insect control or monitoring. Our survey of microbial volatiles in insect-plant interactions suggests that these emissions not only signal host suitability but may indicate a distinctive time frame for optimal conditions for both insect and microbe. Exploitation of these host-specific microbe semiochemicals may provide important microbe- and host-based attractants and a basis for future plant-insect-microbe chemical ecology investigations.

  8. Towards a systems understanding of plant-microbe interactions

    Directory of Open Access Journals (Sweden)

    Akira eMine

    2014-08-01

    Full Text Available Plants are closely associated with microorganisms including pathogens and mutualists that influence plant fitness. Molecular genetic approaches have uncovered a number of signaling components from both plants and microbes and their mode of actions. However, signaling pathways are highly interconnected and influenced by diverse sets of environmental factors. Therefore, it is important to have systems views in order to understand the true nature of plant-microbe interactions. Indeed, systems biology approaches have revealed previously overlooked or misinterpreted properties of the plant immune signaling network. Experimental reconstruction of biological networks using exhaustive combinatorial mutants is particularly powerful to elucidate network structure and properties and relationships among network components. Recent advances in metagenomics of microbial communities associated with plants further point to the importance of systems approaches and open a research area of microbial community reconstruction. In this review, we highlight the importance of a systems understanding of plant-microbe interactions, with a special emphasis on reconstruction strategies.

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

    Science.gov (United States)

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

    2015-08-01

    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 related to 'nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic-nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere. microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere differed significantly between plant species and these differences depended on nitrogen availability. The results suggest that the rate of nitrogen uptake per unit of root biomass and per day is a key plant trait, explaining why the effect of nitrogen availability on the structure of the bacterial community depends on the plant species. We also showed that the abundance of nitrate reducing bacteria always decreased with increasing nitrogen uptake per unit of root biomass per day, indicating that there was competition for nitrate between plants and nitrate reducing bacteria. This study demonstrates that nitrate-reducing microorganisms may be adversely affected by plants with a high nitrogen uptake rate. Our work puts forward the role of traits related to nitrogen in plant-microbe interactions, whereas carbon is commonly considered as the main driver. It also suggests that plant traits related to ecophysiological processes, such as nitrogen uptake rates, are more

  10. Biosurfactant Producing Microbes from Oil Contaminated Soil - Isolation, Screening and Characterization

    OpenAIRE

    , A Pandey; , D Nandi; , N Prasad; , S Arora

    2016-01-01

    Th1s paper bas1cally deals W1th 1solat10n, productıon and characterızatıon of biosurfactant producing microbes from oil contaminated soil sample. In this paper, we are comparing and discussing different methods to screen & characterize microbes from soil which can degrade oil due to their biosurfactant producing activity which helps in reduction of surface tension of oil. Oils used to check the biosurfactant activity of microbes, were engine oil and vegetable oil. Further isolation of...

  11. Dipteran larvae and microbes facilitate nutrient sequestration in the Nepenthes gracilis pitcher plant host.

    Science.gov (United States)

    Lam, Weng Ngai; Chong, Kwek Yan; Anand, Ganesh S; Tan, Hugh Tiang Wah

    2017-03-01

    The fluid-containing traps of Nepenthes carnivorous pitcher plants (Nepenthaceae) are often inhabited by organisms known as inquilines. Dipteran larvae are key components of such communities and are thought to facilitate pitcher nitrogen sequestration by converting prey protein into inorganic nitrogen, although this has never been demonstrated in Nepenthes Pitcher fluids are also inhabited by microbes, although the relationship(s) between these and the plant is still unclear. In this study, we examined the hypothesis of digestive mutualism between N. gracilis pitchers and both dipteran larvae and fluid microbes. Using dipteran larvae, prey and fluid volumes mimicking in situ pitcher conditions, we conducted in vitro experiments and measured changes in available fluid nitrogen in response to dipteran larvae and microbe presence. We showed that the presence of dipteran larvae resulted in significantly higher and faster releases of ammonium and soluble protein into fluids in artificial pitchers, and that the presence of fluid microbes did likewise for ammonium. We showed also that niche segregation occurs between phorid and culicid larvae, with the former fragmenting prey carcasses and the latter suppressing fluid microbe levels. These results clarify the relationships between several key pitcher-dwelling organisms, and show that pitcher communities facilitate nutrient sequestration in their host. © 2017 The Author(s).

  12. Interactions between exotic invasive plants and soil microbes in the rhizosphere suggest that 'everything is not everywhere'.

    Science.gov (United States)

    Rout, Marnie E; Callaway, Ragan M

    2012-07-01

    The study of soil biota in the context of exotic plant invasions has led to an explosion in our understanding of the ecological roles of many different groups of microbes that function in roots or at the root-soil interface. Part of this progress has been the emergence of two biogeographic patterns involving invasive plants and soil microbes. First, in their non-native ranges invasive plants commonly interact differently with the same soil microbes than native plants. Second, in their native ranges, plants that are invasive elsewhere commonly interact functionally with soil microbes differently in their home ranges than they do in their non-native ranges. These studies pose a challenge to a long-held paradigm about microbial biogeography - the idea that microbes are not limited by dispersal and are thus free from the basic taxonomic, biogeographical and evolutionary framework that characterizes all other life on Earth. As an analogy, the global distribution of animals that function as carnivores does not negate the fascinating evolutionary biogeographic patterns of carnivores. Other challenges to this notion come from new measurements of genetic differences among microbes across geographic boundaries, which also suggest that meaningful biogeographic patterns exist for microorganisms. We expand this discussion of whether or not 'everything is everywhere' by using the inherently biogeographic context of plant invasions by reviewing the literature on interactions among invasive plants and the microorganisms in the rhizosphere. We find that these interactions can be delineated at multiple scales: from individual plants to continents. Thus the microbes that regulate major aspects of plant biology do not appear to be exempt from the fundamental evolutionary processes of geographical isolation and natural selection. At the important scales of taxonomy, ecotype and ecosystem functions, the fundamental ecology of invaders and soil microbes indicates that everything might

  13. Endogenous System Microbes as Treatment Process ...

    Science.gov (United States)

    Monitoring the efficacy of treatment strategies to remove pathogens in decentralized systems remains a challenge. Evaluating log reduction targets by measuring pathogen levels is hampered by their sporadic and low occurrence rates. Fecal indicator bacteria are used in centralized systems to indicate the presence of fecal pathogens, but are ineffective decentralized treatment process indicators as they generally occur at levels too low to assess log reduction targets. System challenge testing by spiking with high loads of fecal indicator organisms, like MS2 coliphage, has limitations, especially for large systems. Microbes that are endogenous to the decentralized system, occur in high abundances and mimic removal rates of bacterial, viral and/or parasitic protozoan pathogens during treatment could serve as alternative treatment process indicators to verify log reduction targets. To identify abundant microbes in wastewater, the bacterial and viral communities were examined using deep sequencing. Building infrastructure-associated bacteria, like Zoogloea, were observed as dominant members of the bacterial community in graywater. In blackwater, bacteriophage of the order Caudovirales constituted the majority of contiguous sequences from the viral community. This study identifies candidate treatment process indicators in decentralized systems that could be used to verify log removal during treatment. The association of the presence of treatment process indic

  14. Desferrioxamine and desferrioxamine-caffeine as carriers of aluminum and gallium to microbes via the Trojan Horse Effect.

    Science.gov (United States)

    Huayhuaz, Jesus Antonio Alvarado; Vitorino, Hector Aguilar; Campos, Othon Souto; Serrano, Silvia Helena Pires; Kaneko, Telma Mary; Espósito, Breno Pannia

    2017-05-01

    Iron acquisition by bacteria and fungi involves in several cases the promiscuous usage of siderophores. Thus, antibiotic resistance from these microorganisms can be circumvented through a strategy of loading toxic metals into siderophores (Trojan Horse Effect). Desferrioxamine (dfo) and its cell-permeant derivative desferrioxamine-caffeine (dfcaf) were complexed with aluminum or gallium for this purpose. The complexes Me(dfo) and Me(dfcaf) (Me=Al 3+ and Ga 3+ ) were synthesized and characterized by mass spectroscopy and cyclic voltammetry. Their relative stabilities were studied through competitive equilibria with fluorescent probes calcein, fluorescein-desferrioxamine and 8-hydroxyquinoline. Me(dfo) and Me(dfcaf) were consistently more toxic than free Me 3+ against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Candida albicans, demonstrating the Trojan Horse Effect. Wide spectrum antimicrobial action can be obtained by loading non-essential or toxic metal ions to microbes via a convenient siderophore carrier. Copyright © 2017 Elsevier GmbH. All rights reserved.

  15. Life under the Microscope: Children's Ideas about Microbes

    Science.gov (United States)

    Allen, Michael; Bridle, Georgina; Briten, Elizabeth

    2015-01-01

    Microbes (by definition) are tiny living things that are only visible through a microscope and include bacteria, viruses, fungi, and protoctists (mainly single-celled life forms such as amoebae and algae). Although people are familiar with the effects of microbes, such as infectious disease and food spoilage, because of their lack of visibility,…

  16. Burstiness in Viral Bursts: How Stochasticity Affects Spatial Patterns in Virus-Microbe Dynamics

    Science.gov (United States)

    Lin, Yu-Hui; Taylor, Bradford P.; Weitz, Joshua S.

    Spatial patterns emerge in living systems at the scale of microbes to metazoans. These patterns can be driven, in part, by the stochasticity inherent to the birth and death of individuals. For microbe-virus systems, infection and lysis of hosts by viruses results in both mortality of hosts and production of viral progeny. Here, we study how variation in the number of viral progeny per lysis event affects the spatial clustering of both viruses and microbes. Each viral ''burst'' is initially localized at a near-cellular scale. The number of progeny in a single lysis event can vary in magnitude between tens and thousands. These perturbations are not accounted for in mean-field models. Here we developed individual-based models to investigate how stochasticity affects spatial patterns in virus-microbe systems. We measured the spatial clustering of individuals using pair correlation functions. We found that increasing the burst size of viruses while maintaining the same production rate led to enhanced clustering. In this poster we also report on preliminary analysis on the evolution of the burstiness of viral bursts given a spatially distributed host community.

  17. Microbe participation in aroma production during soy sauce fermentation.

    Science.gov (United States)

    Harada, Risa; Yuzuki, Masanobu; Ito, Kotaro; Shiga, Kazuki; Bamba, Takeshi; Fukusaki, Eiichiro

    2018-06-01

    Soy sauce is a traditional Japanese fermented seasoning that contains various constituents such as amino acids, organic acids, and volatiles that are produced during the long fermentation process. Although studies regarding the correlation between microbes and aroma constituents have been performed, there are no reports about the influences of the microbial products, such as lactic acid, acetic acid, and ethanol, during fermentation. Because it is known that these compounds contribute to microbial growth and to changes in the constituent profile by altering the moromi environment, understanding the influence of these compounds is important. Metabolomics, the comprehensive study of low molecular weight metabolites, is a promising strategy for the deep understanding of constituent contributions to food characteristics. Therefore, the influences of microbes and their products such as lactic acid, acetic acid, and ethanol on aroma profiles were investigated using gas chromatography/mass spectrometry (GC/MS)-based metabolic profiling. The presence of aroma constituents influenced by microbes and chemically influenced by lactic acid, acetic acid, and ethanol were proposed. Most of the aroma constituents were not produced by adding ethanol alone, confirming the participation of yeast in aroma production. It was suggested that lactic acid bacterium relates to a key aromatic compound, 2,5-dimethyl-4-hydroxy-3(2H)-furanone. However, most of the measured aroma constituents changed similarly in both samples with lactic acid bacterium and acids. Thus, it was clear that the effect of lactic acid and acetic acid on the aroma profile was significant. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  18. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences

    Directory of Open Access Journals (Sweden)

    Jiang Tao

    2011-10-01

    Full Text Available Abstract Background Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Results Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Conclusions Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

  19. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences.

    Science.gov (United States)

    Ruegger, Paul M; Della Vedova, Gianluca; Jiang, Tao; Borneman, James

    2011-10-10

    Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint) to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

  20. Ecological suicide in microbes.

    Science.gov (United States)

    Ratzke, Christoph; Denk, Jonas; Gore, Jeff

    2018-05-01

    The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment. Examples are the cooperative breakdown of complex nutrients in microbes or the construction of elaborate architectures in social insects, in which the individual profits from the collective actions of her peers. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them, for example by resource depletion or the production of toxic byproducts. Here we find an extreme type of negative interactions, in which Paenibacillus sp. bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon that we call ecological suicide. Modification of the pH is more pronounced at higher population densities, and thus ecological suicide is more likely to occur with increasing bacterial density. Correspondingly, promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances-such as antibiotics-can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We found ecological suicide in a wide variety of microbes, suggesting that it could have an important role in microbial ecology and evolution.

  1. 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...

  2. Why microbes will rule the world – and our industries

    DEFF Research Database (Denmark)

    Lykke, Anne Wärme; Palsson, Bernhard; Nielsen, Jens

    2017-01-01

    Microbes have ruled the world for approximately 4 billion years. But the future actually depends on their dominance, some would argue. Why? Because microbes, as well as mammalian cells, can be engineered into producing high-value chemicals and medicine. Therefore, scientists at The Novo Nordisk...... Foundation Center for Biosustainability are hard at work developing cell factories to benefit us all....

  3. Ortholog - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us MicrobeDB.jp Ortholog Data detail Data name Ortholog DOI 10.18908/lsdba.nbdc01181-010.V002 V...814 triples - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Ortholog - MicrobeDB.jp | LSDB Archive ...

  4. Effects of microbes on the immune system

    National Research Council Canada - National Science Library

    Fujinami, Robert S; Cunningham, Madeleine W

    2000-01-01

    .... The book synthesizes recent discoveries on the various mechanisms by which microbes subvert the immune response and on the role of these immunologic mechanisms in the pathogenesis of infectious diseases...

  5. 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.

  6. Soil microbes and successful invasions of an exotic weed Eupatorium adenophorum

    International Nuclear Information System (INIS)

    Zhou, P.; Tang, T.; Zhao, P.; Chen, J.

    2016-01-01

    The effects of soil microbes collected from the two invasive species Eupatorium adenophorum and E. odoratum and the two native species E. japonicum and E. chinense on the growth and biomass of E. adenophorum was examined to explore a possible link between soil microbes and successful invasions of the weed species E. adenophorum. In most cases, plant height, stem diameter, root number and root length were significantly enhanced when E. adenophorum was grown in sterilized soils compared with those when one was grown in non-sterilized soils collected from the rhizosphere of E. adenophorum, E. japonicum and E. chinense. In contrast, the growth and biomass of E. adenophorum were apparently inhibited when grown in soils collected from the rhizosphere of E. odoratum. Plant height, stem diameter, leaf area per plant and root length of E. adenophorum was greater when it was grown in soils collected from the rhizosphere of E. adenophorum compared with those when it was grown in soils collected from the rhizosphere of E. odoratum, but the enhancement considerably greater when it was grown in soils collected from the rhizosphere of E. japonicum and E. chinense compared with those when it was grown in soils collected from the rhizosphere of E. adenophorum. In addition, the biomass allocation of E. adenophorum was not significantly affected by soil microbes and soil sources. These Results suggest that although the competitive advantage of the invasive weed E. adenophorum is not achieved solely by soil microbes, successful invasions of E. adenophorum may result partly from its release from the harmful soil microbes in its native range and the positive feedbacks of soil microbes from itself and the native species in its invading range. (author)

  7. Electrifying microbes for the production of chemicals

    DEFF Research Database (Denmark)

    Tremblay, Pier-Luc; Zhang, Tian

    2015-01-01

    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......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...... 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....

  8. 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.

  9. Diversity, Localization, and Physiological Properties of Filamentous Microbes Belonging to Chloroflexi Subphylum I in Mesophilic and Thermophilic Methanogenic Sludge Granules

    Science.gov (United States)

    Yamada, Takeshi; Sekiguchi, Yuji; Imachi, Hiroyuki; Kamagata, Yoichi; Ohashi, Akiyoshi; Harada, Hideki

    2005-01-01

    We previously reported that the thermophilic filamentous anaerobe Anaerolinea thermophila, which is the first cultured representative of subphylum I of the bacterial phylum Chloroflexi, not only was one of the predominant constituents of thermophilic sludge granules but also was a causative agent of filamentous sludge bulking in a thermophilic (55°C) upflow anaerobic sludge blanket (UASB) reactor in which high-strength organic wastewater was treated (Y. Sekiguchi, H. Takahashi, Y. Kamagata, A. Ohashi, and H. Harada, Appl. Environ. Microbiol. 67:5740-5749, 2001). To further elucidate the ecology and function of Anaerolinea-type filamentous microbes in UASB sludge granules, we surveyed the diversity, distribution, and physiological properties of Chloroflexi subphylum I microbes residing in UASB granules. Five different types of mesophilic and thermophilic UASB sludge were used to analyze the Chloroflexi subphylum I populations. 16S rRNA gene cloning-based analyses using a 16S rRNA gene-targeted Chloroflexi-specific PCR primer set revealed that all clonal sequences were affiliated with the Chloroflexi subphylum I group and that a number of different phylotypes were present in each clone library, suggesting the ubiquity and vast genetic diversity of these populations in UASB sludge granules. Subsequent fluorescence in situ hybridization (FISH) of the three different types of mesophilic sludge granules using a Chloroflexi-specific probe suggested that all probe-reactive cells had a filamentous morphology and were widely distributed within the sludge granules. The FISH observations also indicated that the Chloroflexi subphylum I bacteria were not always the predominant populations within mesophilic sludge granules, in contrast to thermophilic sludge granules. We isolated two mesophilic strains and one thermophilic strain belonging to the Chloroflexi subphylum I group. The physiological properties of these isolates suggested that these populations may contribute to the

  10. Sub-micron opto-chemical probes for studying living neurons

    Science.gov (United States)

    Hossein-Zadeh, M.; Delgado, J.; Schweizer, F.; Lieberman, R.

    2017-02-01

    We have fabricated sub-micron opto-chemical probes for pH, oxygen and calcium monitoring and demonstrated their application in intracellular and extracellular monitoring of neurons (cortical neuronal cultures and acute hippocampal slices). Using these probes, we have measured extracellular pH in the stratum radiatum of the CA1 region of mouse hippocampus upon stimulation of presynaptic Schaffer collateral axons. Synaptic transmission was monitored using standard electrophysiological techniques. We find that the local pH transiently changes in response to synaptic stimulation. In addition, the geometry of the functionalized region on the probe combined with high sensitivity imaging enables simultaneous monitoring of spatially adjacent but distinct compartments. As proof of concept we impaled cultured neurons with the probe measured calcium and pH inside as well as directly outside of neurons as we changed the pH and calcium concentration in the physiological solution in the perfusion chamber. As such these probes can be used to study the impact of the environment on both cellular and extra-cellular space. Additionally as the chemical properties of the surrounding medium can be controlled and monitored with high precision, these probes enable differential measurement of the target parameter referenced to a stable bath. This approach eliminates the uncertainties associated with non-chemical fluctuations in the fluorescent emission and result in a self-calibrated opto-chemical probe. We have also demonstrated multifunctional probes that are capable of measuring up to three parameters in the extracellular space in brain slices.

  11. Preferences for different nitrogen forms by coexisting plant species and soil microbes.

    Science.gov (United States)

    Harrison, Kathryn A; Bol, Roland; Bardgett, Richard D

    2007-04-01

    The growing awareness that plants might use a variety of nitrogen (N) forms, both organic and inorganic, has raised questions about the role of resource partitioning in plant communities. It has been proposed that coexisting plant species might be able to partition a limited N pool, thereby avoiding competition for resources, through the uptake of different chemical forms of N. In this study, we used in situ stable isotope labeling techniques to assess whether coexisting plant species of a temperate grassland (England, UK) display preferences for different chemical forms of N, including inorganic N and a range of amino acids of varying complexity. We also tested whether plants and soil microbes differ in their preference for different N forms, thereby relaxing competition for this limiting resource. We examined preferential uptake of a range of 13C15N-labeled amino acids (glycine, serine, and phenylalanine) and 15N-labeled inorganic N by coexisting grass species and soil microbes in the field. Our data show that while coexisting plant species simultaneously take up a variety of N forms, including inorganic N and amino acids, they all showed a preference for inorganic N over organic N and for simple over the more complex amino acids. Soil microbes outcompeted plants for added N after 50 hours, but in the long-term (33 days) the proportion of added 15N contained in the plant pool increased for all N forms except for phenylalanine, while the proportion in the microbial biomass declined relative to the first harvest. These findings suggest that in the longer-term plants become more effective competitors for added 15N. This might be due to microbial turnover releasing 15N back into the plant-soil system or to the mineralization and subsequent plant uptake of 15N transferred initially to the organic matter pool. We found no evidence that soil microbes preferentially utilize any of the N forms added, despite previous studies showing that microbial preferences for N forms

  12. Theoretical study of the effect of probe shape on adhesion force between probe and substrate in atomic force microscope experiment

    OpenAIRE

    Yang, Li; Hu, Junhui; Kong, Lingjiang

    2017-01-01

    The quantitative description of adhesion force dependence on the probe shapes are of importance in many scientific and industrial fields. In order to elucidate how the adhesion force varied with the probe shape in atomic force microscope manipulation experiment, we performed a theoretical study of the influences of the probe shape (the sphere and parabolic probe) on the adhesion force at different humidity. We found that the combined action of the triple point and the Kelvin radius guiding th...

  13. Protein-based stable isotope probing.

    Science.gov (United States)

    Jehmlich, Nico; Schmidt, Frank; Taubert, Martin; Seifert, Jana; Bastida, Felipe; von Bergen, Martin; Richnow, Hans-Hermann; Vogt, Carsten

    2010-12-01

    We describe a stable isotope probing (SIP) technique that was developed to link microbe-specific metabolic function to phylogenetic information. Carbon ((13)C)- or nitrogen ((15)N)-labeled substrates (typically with >98% heavy label) were used in cultivation experiments and the heavy isotope incorporation into proteins (protein-SIP) on growth was determined. The amount of incorporation provides a measure for assimilation of a substrate, and the sequence information from peptide analysis obtained by mass spectrometry delivers phylogenetic information about the microorganisms responsible for the metabolism of the particular substrate. In this article, we provide guidelines for incubating microbial cultures with labeled substrates and a protocol for protein-SIP. The protocol guides readers through the proteomics pipeline, including protein extraction, gel-free and gel-based protein separation, the subsequent mass spectrometric analysis of peptides and the calculation of the incorporation of stable isotopes into peptides. Extraction of proteins and the mass fingerprint measurements of unlabeled and labeled fractions can be performed in 2-3 d.

  14. INTERACTIONS AMONG PHOSPHATE AMENDMENTS, MICROBES AND URANIUM MOBILITY IN CONTAMINATED SEDIMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Knox, A

    2007-08-30

    The use of sequestering agents for the transformation of radionuclides in low concentrations in contaminated soils/sediments offers considerable potential for long-term environmental cleanup. This study evaluated the influence of four phosphate amendments and two microbial amendments on U availability. The synchrotron X-ray fluorescence mapping of the untreated U-contaminated sediment showed that U was closely associated with Mn. All tested phosphate amendments reduced aqueous U concentration more than 90%, likely due to formation of insoluble phosphate precipitates. The addition of A. piechaudii and P. putida alone were found to reduce U concentrations 63% and 31% respectively. Uranium sorption in phosphate treatments was significantly reduced in the presence of microbes. However, increased microbial activity in the treated sediment led to reduction of phosphate effectiveness. The average U concentration in 1 M MgCl{sub 2} extract from U amended sediment was 437 {micro}g/kg, but in the same sediment without microbes (autoclaved sediment), the extractable U concentration was only 103 {micro}g/kg. When the autoclaved amended sediment was treated with autoclaved biological apatite, U concentration in the 1 M MgCl{sub 2} extract was {approx}0 {micro}g/kg. Together these tests suggest that microbes may enhance U leaching and reduce phosphate amendment remedial effectiveness.

  15. Interactive effects of global climate change and pollution on marine microbes: the way ahead.

    Science.gov (United States)

    Coelho, Francisco J R C; Santos, Ana L; Coimbra, Joana; Almeida, Adelaide; Cunha, Angela; Cleary, Daniel F R; Calado, Ricardo; Gomes, Newton C M

    2013-06-01

    Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future.

  16. Performance of duckweed and effective microbes in reducing arsenic in paddy and paddy soil

    Science.gov (United States)

    Ng, C. A.; Wong, L. Y.; Lo, P. K.; Bashir, M. J. K.; Chin, S. J.; Tan, S. P.; Chong, C. Y.; Yong, L. K.

    2017-04-01

    In this study phytoremediation plant (duckweed) and effective microbes were used to investigate their effectiveness in reducing arsenic concentration in paddy soil and paddy grain. The results show that using duckweed alone is a better choice as it could decrease the arsenic concentration in paddy by 27.697 % and 8.268 % in paddy grain and paddy husk respectively. The study also found out that the concentration of arsenic in soil would affect the performance of duckweed and also delayed the reproduction rate of duckweed. Using the mixture of effective microbes and duckweed together to decrease arsenic in paddy was noticed having the least potential in reducing the arsenic concentration in paddy.

  17. 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.

  18. Sterilization of microbes by using various plasma jets

    Energy Technology Data Exchange (ETDEWEB)

    Uhm, Han S.; Choi, Eun H.; Cho, Guang S. [Kwangwoon University, Seoul (Korea, Republic of); Hong, Yong C. [National Fusion Research Institute, Daejeon (Korea, Republic of)

    2012-03-15

    Sterilization of various microbes was carried out by using several plasma jets. Argon plasma jets penetrate deep into ambient air and create a path for oxygen radicals to sterilize microbes including spores. A sterilization experiment with bacterial endospores indicates that an argon-oxygen plasma jet very effectively kills endospores of Bacillus atrophaeus (ATCC 9372), thereby demonstrating its capability to clean surfaces and its usefulness for reinstating contaminated equipment as free from toxic biological agents. The key element of the sterilization is oxygen radicals. The penciltype configuration produces a long, cold plasma jet capable of reaching 3.5 cm and having various excited plasma species shown through the optical emission spectrum. Operation of an air plasma jet at 2 W in a pencil-type electrode provides an excellent opportunity for sterilization of microbes. An electron microscope was used to observe the effects of the plasma on bacterial cell morphology. Transmission electron micrographs showed morphological changes in E. coli cells treated with an atmospheric plasma at 75 W for 2 min. The treated cells had severe cytoplasmic deformations and leakage of bacterial chromosome. The chromosomal DNA was either attached to the bacterial cells or released freely into the surrounding medium. The results clearly explain the loss of viability of bacterial cells after plasma treatment.

  19. Metabolomic Fingerprints of Individual Algal Cells Using the Single-Probe Mass Spectrometry Technique

    Directory of Open Access Journals (Sweden)

    Mei Sun

    2018-04-01

    Full Text Available Traditional approaches for the assessment of physiological responses of microbes in the environment rely on bulk filtration techniques that obscure differences among populations as well as among individual cells. Here, were report on the development on a novel micro-scale sampling device, referred to as the “Single-probe,” which allows direct extraction of metabolites from living, individual phytoplankton cells for mass spectrometry (MS analysis. The Single-probe is composed of dual-bore quartz tubing which is pulled using a laser pipette puller and fused to a silica capillary and a nano-ESI. For this study, we applied Single-probe MS technology to the marine dinoflagellate Scrippsiella trochoidea, assaying cells grown under different illumination levels and under nitrogen (N limiting conditions as a proof of concept for the technology. In both experiments, significant differences in the cellular metabolome of individual cells could readily be identified, though the vast majority of detected metabolites could not be assigned to KEGG pathways. Using the same approach, significant changes in cellular lipid complements were observed, with individual lipids being both up- and down-regulated under light vs. dark conditions. Conversely, lipid content increased across the board under N limitation, consistent with an adjustment of Redfield stoichiometry to reflect higher C:N and C:P ratios. Overall, these data suggest that the Single-probe MS technique has the potential to allow for near in situ metabolomic analysis of individual phytoplankton cells, opening the door to targeted analyses that minimize cell manipulation and sampling artifacts, while preserving metabolic variability at the cellular level.

  20. A new theory of plant-microbe nutrient competition resolves inconsistencies between observations and model predictions.

    Science.gov (United States)

    Zhu, Qing; Riley, William J; Tang, Jinyun

    2017-04-01

    Terrestrial plants assimilate anthropogenic CO 2 through photosynthesis and synthesizing new tissues. However, sustaining these processes requires plants to compete with microbes for soil nutrients, which therefore calls for an appropriate understanding and modeling of nutrient competition mechanisms in Earth System Models (ESMs). Here, we survey existing plant-microbe competition theories and their implementations in ESMs. We found no consensus regarding the representation of nutrient competition and that observational and theoretical support for current implementations are weak. To reconcile this situation, we applied the Equilibrium Chemistry Approximation (ECA) theory to plant-microbe nitrogen competition in a detailed grassland 15 N tracer study and found that competition theories in current ESMs fail to capture observed patterns and the ECA prediction simplifies the complex nature of nutrient competition and quantitatively matches the 15 N observations. Since plant carbon dynamics are strongly modulated by soil nutrient acquisition, we conclude that (1) predicted nutrient limitation effects on terrestrial carbon accumulation by existing ESMs may be biased and (2) our ECA-based approach may improve predictions by mechanistically representing plant-microbe nutrient competition. © 2016 by the Ecological Society of America.

  1. Host-microbe interactions in the gut of Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Takayuki eKuraishi

    2013-12-01

    Full Text Available Many insect species subsist on decaying and contaminated matter and are thus exposed to large quantities of microorganisms. To control beneficial commensals and combat infectious pathogens, insects must be armed with efficient systems for microbial recognition, signaling pathways, and effector molecules. The molecular mechanisms regulating these host-microbe interactions in insects have been largely clarified in Drosophila melanogaster with its powerful genetic and genomic tools. Here we review recent advances in this field, focusing mainly on the relationships between microbes and epithelial cells in the intestinal tract where the host exposure to the external environment is most frequent.

  2. Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level

    Directory of Open Access Journals (Sweden)

    Zixi Chen

    2017-09-01

    Full Text Available Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS, and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented.

  3. Study of Strongly Coupled Systems via Probe Brane Constructions

    Science.gov (United States)

    Chang, Han-Chih

    In this thesis, we present our study towards better understanding of the strongly coupled systems with extra matter content in the fundamental representation of some prescribed global symmetry group in the quenched approximation, with the toolkit of holography via a probe brane construction. Specically, for the defect conformal systems, we unearth and quantify the phase trasition diagram, and novel supersymmetric vacua in the top-down model of the D3/D5 probe brane system. For further quantify various non-Fermi quantum liquid phases realized through the holographical probe brane construction, we then propose and verify the method to include the backreaction of entanglement entropy due to the probe branes at the leading order, which can potentially be used to detect topological phase transitions. We will recapitulate the main results of our works, in collaboration with Prof. Andreas Karch, published in the following journals: "Minimal Submanifolds asymptotic to AdS4 xS2 in AdS5xS5', JHEP, vol.1404, p.037, 2014; "The Novel Solutions of Finite-Density D3/D5 Probe Brane System and Their Implications for Stability'', JHEP, vol.1210, p.060, 2014; "Entanglement Entropy for Probe Branes'', JHEP, vol.1401, p.180, 2014.

  4. Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila-microbe interactions.

    Science.gov (United States)

    Broderick, Nichole A

    2016-05-26

    Drosophila melanogaster lives, breeds and feeds on fermenting fruit, an environment that supports a high density, and often a diversity, of microorganisms. This association with such dense microbe-rich environments has been proposed as a reason that D. melanogaster evolved a diverse and potent antimicrobial peptide (AMP) response to microorganisms, especially to combat potential pathogens that might occupy this niche. Yet, like most animals, D. melanogaster also lives in close association with the beneficial microbes that comprise its microbiota, or microbiome, and recent studies have shown that antimicrobial peptides (AMPs) of the epithelial immune response play an important role in dictating these interactions and controlling the host response to gut microbiota. Moreover, D. melanogaster also eats microbes for food, consuming fermentative microbes of decaying plant material and their by-products as both larvae and adults. The processes of nutrient acquisition and host defence are remarkably similar and use shared functions for microbe detection and response, an observation that has led to the proposal that the digestive and immune systems have a common evolutionary origin. In this manner, D. melanogaster provides a powerful model to understand how, and whether, hosts differentiate between the microbes they encounter across this spectrum of associations.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'. © 2016 The Author(s).

  5. Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila–microbe interactions

    Science.gov (United States)

    2016-01-01

    Drosophila melanogaster lives, breeds and feeds on fermenting fruit, an environment that supports a high density, and often a diversity, of microorganisms. This association with such dense microbe-rich environments has been proposed as a reason that D. melanogaster evolved a diverse and potent antimicrobial peptide (AMP) response to microorganisms, especially to combat potential pathogens that might occupy this niche. Yet, like most animals, D. melanogaster also lives in close association with the beneficial microbes that comprise its microbiota, or microbiome, and recent studies have shown that antimicrobial peptides (AMPs) of the epithelial immune response play an important role in dictating these interactions and controlling the host response to gut microbiota. Moreover, D. melanogaster also eats microbes for food, consuming fermentative microbes of decaying plant material and their by-products as both larvae and adults. The processes of nutrient acquisition and host defence are remarkably similar and use shared functions for microbe detection and response, an observation that has led to the proposal that the digestive and immune systems have a common evolutionary origin. In this manner, D. melanogaster provides a powerful model to understand how, and whether, hosts differentiate between the microbes they encounter across this spectrum of associations. This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’. PMID:27160597

  6. 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...

  7. Use of gamma probe in 131I thyroid uptake studies

    International Nuclear Information System (INIS)

    Sarmento, Andrea Gondim Leitao

    2002-11-01

    Evaluation of thyroid uptake by administration of radioactive iodine is a well-defined procedure to assess patient thyroid function. In general, nuclear medicine institutions use gamma cameras coupled to pinhole collimators to perform uptake studies. With the growing use of intraoperative gamma probes in the radioguided surgical techniques, several institutions are purchasing this new and portable equipment, which can technically be also employed to assess patient's thyroid function, permitting further other applications of gamma cameras. The aim of the study was to compare thyroid uptake trails carried out with both gamma camera and intraoperative gamma probe, in order to evaluate the possible use of gamma probe for this purpose. At first a preliminary study of feasibility was carried out using a neck phantom to verify equipment efficiency with known activities of 131 I. Henceforth, work data from 12 patients undergone studies of thyroid uptakes were evaluated, 24 hours after oral administration of 370 kBq of 131 I. The maximum difference observed between the values obtained with both equipment was 60%, which demonstrated the feasibility of the proposed protocol and made clear that gamma probe can be useful for thyroid uptake studies. (author)

  8. Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development

    Directory of Open Access Journals (Sweden)

    XiaoLi Bing

    2018-03-01

    Full Text Available Drosophila suzukii Matsumura is an invasive species of vinegar fly that has become a prominent pest of berries and other soft-skinned fruits. Unlike most other Drosophila species, female D. suzukii flies lay their eggs in ripening and ripe fruits and larvae develop within the fruit. To understand how D. suzukii larvae utilize ripe and ripening fruits, which usually have low levels of protein, we investigated the microbiota of field-captured and laboratory-reared D. suzukii flies and further examined the combined influence of diet and microbes on host fitness. Field-captured flies were associated with diverse microbiota, which varied significantly with sampling location and season. In contrast, laboratory-reared flies possessed strikingly lower bacterial abundance and diversity. A comparison of conventionally reared (CR and germ-free (GF flies revealed that the microbiota of D. suzukii does not alter its development significantly but decreases its life span under conditions of a nutrient-sufficient diet. However, the microbiota is essential for D. suzukii development on strawberry-based or blueberry-based fruit diets. This developmental failure could be rescued by reassociation with single bacterial or fungal species or by the addition of a high quantity of heat-killed microbes. In addition, we found that proteins are limiting with respect to fly development on fruit-based diets and that GF flies show signs of protein starvation. Taken together, our study results demonstrate that the microbiota provides key proteins required for the development of D. suzukii reared on fresh fruit. Our work shows that the impact of microbes on fly fitness depends strongly on nutritional conditions.

  9. Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development

    Science.gov (United States)

    Bing, XiaoLi; Gerlach, Joseph; Loeb, Gregory

    2018-01-01

    ABSTRACT Drosophila suzukii Matsumura is an invasive species of vinegar fly that has become a prominent pest of berries and other soft-skinned fruits. Unlike most other Drosophila species, female D. suzukii flies lay their eggs in ripening and ripe fruits and larvae develop within the fruit. To understand how D. suzukii larvae utilize ripe and ripening fruits, which usually have low levels of protein, we investigated the microbiota of field-captured and laboratory-reared D. suzukii flies and further examined the combined influence of diet and microbes on host fitness. Field-captured flies were associated with diverse microbiota, which varied significantly with sampling location and season. In contrast, laboratory-reared flies possessed strikingly lower bacterial abundance and diversity. A comparison of conventionally reared (CR) and germ-free (GF) flies revealed that the microbiota of D. suzukii does not alter its development significantly but decreases its life span under conditions of a nutrient-sufficient diet. However, the microbiota is essential for D. suzukii development on strawberry-based or blueberry-based fruit diets. This developmental failure could be rescued by reassociation with single bacterial or fungal species or by the addition of a high quantity of heat-killed microbes. In addition, we found that proteins are limiting with respect to fly development on fruit-based diets and that GF flies show signs of protein starvation. Taken together, our study results demonstrate that the microbiota provides key proteins required for the development of D. suzukii reared on fresh fruit. Our work shows that the impact of microbes on fly fitness depends strongly on nutritional conditions. PMID:29559576

  10. Antimicrobial blue light: a drug-free approach for inactivating pathogenic microbes

    Science.gov (United States)

    Wang, Ying; Dai, Tianhong

    2018-02-01

    Due to the growing global threat of antibiotic resistance, there is a critical need for the development of alternative therapeutics for infectious diseases. Antimicrobial blue light (aBL), as an innovative non-antibiotic approach, has attracted increasing attention. This paper discussed the basic concepts of aBL and recent findings in the studies of aBL. It is commonly hypothesized that the antimicrobial property of aBL is attributed to the presence of endogenous photosensitizing chromophores in microbial cells, which produce cytotoxic reactive oxygen species upon light irradiation. A wide range of important microbes are found to be susceptible to aBL inactivation. Studies have also shown there exist therapeutic windows where microbes are selectively inactivated by aBL while host cells are preserved. The combination of aBL with some other agents result in synergistically improved antimicrobial efficacy. Future efforts should be exerted on the standardization of study design for evaluating aBL efficacy, further elucidation of the mechanism of action, optimization of the technical parameters, and translation of this technique to clinic.

  11. Microstructured Block Copolymer Surfaces for Control of Microbe Adhesion and Aggregation

    Directory of Open Access Journals (Sweden)

    Ryan R. Hansen

    2014-03-01

    Full Text Available The attachment and arrangement of microbes onto a substrate is influenced by both the biochemical and physical surface properties. 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 immobilization. Films of poly(glycidyl methacrylate-block-4,4-dimethyl-2-vinylazlactone (PGMA-b-PVDMA were patterned on silicon surfaces into line arrays or square grid patterns with 5 μm wide features and varied pitch. 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 immobilized was dependent on the pattern dimensions. Films patterned as parallel lines or square grids with a pitch of 10 μm or less led to the immobilization of individual microbes with minimal formation of aggregates. Both geometries allowed for incremental increases in aggregate size distribution with each increase in pitch. These engineered surfaces combine spatial confinement with affinity-based capture to control the extent of microbe adhesion and aggregation, and can also be used as a platform to investigate intercellular interactions and biofilm formation in microbial populations of controlled sizes.

  12. The effects of packaging materials on microbe population in irradiated traditional herbal medicines

    International Nuclear Information System (INIS)

    Bagiawati, Sri; Hilmy, Nazly

    1983-01-01

    Microbial population and moisture content of traditional herbal medicines contaminated with 3 kinds of aerobic microbes, packed in 5 kinds of plastic packaging materials, followed by irradiation at minimum dose of 5 kGy and stored for 6 months were investigated. The highest reduction of microbial counts during storage was observed on samples packed in polyethylene bags. All of packaging materials used were found to be impermeable to microbes and water vapour. Radiation and packaging materials used acted synergistically to inactivate microbes durind storage. The microbial counts decreased as much as 2 to 4 log cycles during storage. (author)

  13. The role of microbes in snowmelt and radiative forcing on an Alaskan icefield

    Science.gov (United States)

    Ganey, Gerard Q.; Loso, Michael G.; Burgess, Annie Bryant; Dial, Roman J.

    2017-10-01

    A lack of liquid water limits life on glaciers worldwide but specialized microbes still colonize these environments. These microbes reduce surface albedo, which, in turn, could lead to warming and enhanced glacier melt. Here we present results from a replicated, controlled field experiment to quantify the impact of microbes on snowmelt in red-snow communities. Addition of nitrogen-phosphorous-potassium fertilizer increased alga cell counts nearly fourfold, to levels similar to nitrogen-phosphorus-enriched lakes; water alone increased counts by half. The manipulated alga abundance explained a third of the observed variability in snowmelt. Using a normalized-difference spectral index we estimated alga abundance from satellite imagery and calculated microbial contribution to snowmelt on an icefield of 1,900 km2. The red-snow area extended over about 700 km2, and in this area we determined that microbial communities were responsible for 17% of the total snowmelt there. Our results support hypotheses that snow-dwelling microbes increase glacier melt directly in a bio-geophysical feedback by lowering albedo and indirectly by exposing low-albedo glacier ice. Radiative forcing due to perennial populations of microbes may match that of non-living particulates at high latitudes. Their contribution to climate warming is likely to grow with increased melt and nutrient input.

  14. Nonribosomal Peptides from Marine Microbes and Their Antimicrobial and Anticancer Potential

    Directory of Open Access Journals (Sweden)

    Shivankar Agrawal

    2017-11-01

    Full Text Available Marine environments are largely unexplored and can be a source of new molecules for the treatment of many diseases such as malaria, cancer, tuberculosis, HIV etc. The Marine environment is one of the untapped bioresource of getting pharmacologically active nonribosomal peptides (NRPs. Bioprospecting of marine microbes have achieved many remarkable milestones in pharmaceutics. Till date, more than 50% of drugs which are in clinical use belong to the nonribosomal peptide or mixed polyketide-nonribosomal peptide families of natural products isolated from marine bacteria, cyanobacteria and fungi. In recent years large numbers of nonribosomal have been discovered from marine microbes using multi-disciplinary approaches. The present review covers the NRPs discovered from marine microbes and their pharmacological potential along with role of genomics, proteomics and bioinformatics in discovery and development of nonribosomal peptides drugs.

  15. Study of probe-sample distance for biomedical spectra measurement

    Directory of Open Access Journals (Sweden)

    Li Lei

    2011-11-01

    Full Text Available Abstract Background Fiber-based optical spectroscopy has been widely used for biomedical applications. However, the effect of probe-sample distance on the collection efficiency has not been well investigated. Method In this paper, we presented a theoretical model to maximize the illumination and collection efficiency in designing fiber optic probes for biomedical spectra measurement. This model was in general applicable to probes with single or multiple fibers at an arbitrary incident angle. In order to demonstrate the theory, a fluorescence spectrometer was used to measure the fluorescence of human finger skin at various probe-sample distances. The fluorescence spectrum and the total fluorescence intensity were recorded. Results The theoretical results show that for single fiber probes, contact measurement always provides the best results. While for multi-fiber probes, there is an optimal probe distance. When a 400- μm excitation fiber is used to deliver the light to the skin and another six 400- μm fibers surrounding the excitation fiber are used to collect the fluorescence signal, the experimental results show that human finger skin has very strong fluorescence between 475 nm and 700 nm under 450 nm excitation. The fluorescence intensity is heavily dependent on the probe-sample distance and there is an optimal probe distance. Conclusions We investigated a number of probe-sample configurations and found that contact measurement could be the primary choice for single-fiber probes, but was very inefficient for multi-fiber probes. There was an optimal probe-sample distance for multi-fiber probes. By carefully choosing the probe-sample distance, the collection efficiency could be enhanced by 5-10 times. Our experiments demonstrated that the experimental results of the probe-sample distance dependence of collection efficiency in multi-fiber probes were in general agreement with our theory.

  16. Earthworms, Microbes and the Release of C and N in Biochar Amended Soil

    Science.gov (United States)

    Land application of biochar has the potential to increase soil fertility and sequester carbon. It is unclear how soil microbes and earthworms interact with biochar and affect release or retention of nutrients. In order to determine the effects and interactions among soil microbes, earthworms, and bi...

  17. Study on indoor pollution by microbes grown in a solar house in Tokyo; Tokyo no solar house ni okeru kabi no jittai chosa

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, T; Aihara, M; Nakanishi, R; Ito, H [Ochanomizu University, Tokyo (Japan)

    1997-11-25

    Indoor pollution by microbes grown in a solar house is studied. It is a reinforced concrete building, having a total floor area of 260m{sup 2}, equipped with a flat type solar collector on the roof and a lighting window on the north, the former having an area of 16m{sup 2} and slanted at 60deg and the latter slanted at 60deg. It is also provided with a semi-underground room, to utilize heat capacity of soil for coolness in summer and warmness in winter. It provides a residential space throughout the year, with no artificial heating or air-conditioning system, naturally ventilated with air taken into the underground room and released out of a triangular shape on the roof. The building is also passively conditioned, being totally insulated with expanded polystyrene. Energy saving is the most important consideration for the solar house, slightly forcing the residents to exercise patience. For this reason, the solar house often smells musty, and pollution with microbes is quantitatively investigated. Microbes evolve more in the underground room than in the space above groun, because of higher humidity in the former. Accelerated ventilation or slight artificial air-conditioning will solve the trouble. 1 refs., 7 figs.

  18. Engineering tailored nanoparticles with microbes: quo vadis?

    Science.gov (United States)

    Prasad, Ram; Pandey, Rishikesh; Barman, Ishan

    2016-01-01

    In the quest for less toxic and cleaner methods of nanomaterials production, recent developments in the biosynthesis of nanoparticles have underscored the important role of microorganisms. Their intrinsic ability to withstand variable extremes of temperature, pressure, and pH coupled with the minimal downstream processing requirements provide an attractive route for diverse applications. Yet, controlling the dispersity and facile tuning of the morphology of the nanoparticles of desired chemical compositions remains an ongoing challenge. In this Focus Review, we critically review the advances in nanoparticle synthesis using microbes, ranging from bacteria and fungi to viruses, and discuss new insights into the cellular mechanisms of such formation that may, in the near future, allow complete control over particle morphology and functionalization. In addition to serving as paradigms for cost-effective, biocompatible, and eco-friendly synthesis, microbes hold the promise for a unique template for synthesis of tailored nanoparticles targeted at therapeutic and diagnostic platform technologies. © 2015 Wiley Periodicals, Inc.

  19. Wars between microbes on roots and fruits [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Ben Lugtenberg

    2017-03-01

    Full Text Available Microbes in nature often live in unfavorable conditions. To survive, they have to occupy niches close to food sources and efficiently utilize nutrients that are often present in very low concentrations. Moreover, they have to possess an arsenal of attack and defense mechanisms against competing bacteria. In this review, we will discuss strategies used by microbes to compete with each other in the rhizosphere and on fruits, with a focus on mechanisms of inter- and intra-species antagonism. Special attention will be paid to the recently discovered roles of volatile organic compounds. Several microbes with proven capabilities in the art of warfare are being applied in products used for the biological control of plant diseases, including post-harvest control of fruits and vegetables.

  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. Dual oxidase in mucosal immunity and host-microbe homeostasis.

    Science.gov (United States)

    Bae, Yun Soo; Choi, Myoung Kwon; Lee, Won-Jae

    2010-07-01

    Mucosal epithelia are in direct contact with microbes, which range from beneficial symbionts to pathogens. Accordingly, hosts must have a conflicting strategy to combat pathogens efficiently while tolerating symbionts. Recent progress has revealed that dual oxidase (DUOX) plays a key role in mucosal immunity in organisms that range from flies to humans. Information from the genetic model of Drosophila has advanced our understanding of the regulatory mechanism of DUOX and its role in mucosal immunity. Further investigations of DUOX regulation in response to symbiotic or non-symbiotic bacteria and the in vivo consequences in host physiology will give a novel insight into the microbe-controlling system of the mucosa. Copyright 2010 Elsevier Ltd. All rights reserved.

  2. Study on the interaction mechanism between the special geological environment and their extreme geo-microbes in Dagang Oilfield by combined methods

    Science.gov (United States)

    Yao, Jun

    2010-05-01

    Geo-microbes and their function were widespread ever since life appeared on the earth. Geo-microbiological process has left a rich and colorful material record in the geological body of earth, the most critical record of which is all sorts of organic hieroglyph and various forms of organic matter derived from bio-organisms, and oil field is the most ideal geological location to preserve these organic matters. It have already produced or might produce petroleum and natural gas sedimentary rocks under natural conditions, also known as olefiant (gas) rock or the parent rock, which is the product of the interaction between the life-system and earth environmental system in the specific geological conditions and integrate the whole microbial ecosystem in the geological time. The microbial community under extreme geological environment of Dagang Oilfield is relatively simple, therefore it is quite easy to investigate the special relationship between geo-microbes and biogeochemistry. We have mastered a large number of information related with the geological condition and biological species of Dagang Oilfield; what's more we also have isolated a number of archimycetes strains with different extremophiles capacity from the core samples collected in the Dagang oil field. At present, we are to proceed with the cooperative research at Environment School of Yale University and Institute of the Earth's biosphere using these strains. In the future, we will work together to carry out geological surveys in the field using international first-class equipment and methods and study the geological environment of Dagang Oilfield utilizing isotope techniques and mineral phase analysis method. Meanwhile we are going to undertake the on-line monitoring of the overall microbial activity of these collected geological samples, the specific metabolic activity of these extreme strains of microorganisms and the biomarkers produced during their metabolic processes under laboratory conditions

  3. A microbent fiber optic pH sensor

    NARCIS (Netherlands)

    Thomas Lee, S.; Aneeshkumar, B.N.; Radhakrishnan, P.; Vallabhan, C.P.G.; Nampoori, V.P.N.

    2002-01-01

    Optical fiber sensors developed for measuring pH values usually employ an unclad and unstrained section of the fiber. In this paper, we describe the design and fabrication of a microbent fiber optic sensor that can be used for pH sensing. In order to obtain the desired performance, a permanently

  4. Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe.

    Science.gov (United States)

    Lamichhane, Santosh; Sen, Partho; Dickens, Alex M; Orešič, Matej; Bertram, Hanne Christine

    2018-04-30

    It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. Study of submelt laser induced junction nonuniformities using Therma-Probe

    DEFF Research Database (Denmark)

    Rosseel, E.; Bogdanowicz, J; Clarysse, T.

    2010-01-01

    to standard and micro-four-point probe sheet resistance data, secondary ion mass spectrometry, and Hall measurements obtained during earlier studies. Besides the impact of the nonuniformities on the “conventional” thermal wave signal, they found a strong correlation to the dc reflectance of the probe laser...... both at macroscopic and microscopic levels. In this work, the authors present high resolution Therma-Probe® measurements to assess the junction nonuniformity on 0.5 keV boron junctions and zoom in on the effect of temperature variations and multiple subsequent laser scans. The results are compared...... (lambda = 675 nm). The dc probe reflectance is dominated by free carriers and is highly correlated to the sheet resistance both on blanket wafers and on real device wafers. ©2010 American Vacuum Society...

  6. 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.

  7. Enzymes from solvent-tolerant microbes: useful biocatalysts for non-aqueous enzymology.

    Science.gov (United States)

    Gupta, Anshu; Khare, S K

    2009-01-01

    Solvent-tolerant microbes are a newly emerging class that possesses the unique ability to thrive in the presence of organic solvents. Their enzymes adapted to mediate cellular and metabolic processes in a solvent-rich environment and are logically stable in the presence of organic solvents. Enzyme catalysis in non-aqueous/low-water media is finding increasing applications for the synthesis of industrially important products, namely peptides, esters, and other trans-esterification products. Solvent stability, however, remains a prerequisite for employing enzymes in non-aqueous systems. Enzymes, in general, get inactivated or give very low rates of reaction in non-aqueous media. Thus, early efforts, and even some recent ones, have aimed at stabilization of enzymes in organic media by immobilization, surface modifications, mutagenesis, and protein engineering. Enzymes from solvent-tolerant microbes appear to be the choicest source for studying solvent-stable enzymes because of their unique ability to survive in the presence of a range of organic solvents. These bacteria circumvent the solvent's toxic effects by virtue of various adaptations, e.g. at the level of the cytoplasmic membrane, by degradation and transformation of solvents, and by active excretion of solvents. The recent screening of these exotic microbes has generated some naturally solvent-stable proteases, lipases, cholesterol oxidase, cholesterol esterase, cyclodextrin glucanotransferase, and other important enzymes. The unique properties of these novel biocatalysts have great potential for applications in non-aqueous enzymology for a range of industrial processes.

  8. Prediction of microbe-disease association from the integration of neighbor and graph with collaborative recommendation model.

    Science.gov (United States)

    Huang, Yu-An; You, Zhu-Hong; Chen, Xing; Huang, Zhi-An; Zhang, Shanwen; Yan, Gui-Ying

    2017-10-16

    Accumulating clinical researches have shown that specific microbes with abnormal levels are closely associated with the development of various human diseases. Knowledge of microbe-disease associations can provide valuable insights for complex disease mechanism understanding as well as the prevention, diagnosis and treatment of various diseases. However, little effort has been made to predict microbial candidates for human complex diseases on a large scale. In this work, we developed a new computational model for predicting microbe-disease associations by combining two single recommendation methods. Based on the assumption that functionally similar microbes tend to get involved in the mechanism of similar disease, we adopted neighbor-based collaborative filtering and a graph-based scoring method to compute association possibility of microbe-disease pairs. The promising prediction performance could be attributed to the use of hybrid approach based on two single recommendation methods as well as the introduction of Gaussian kernel-based similarity and symptom-based disease similarity. To evaluate the performance of the proposed model, we implemented leave-one-out and fivefold cross validations on the HMDAD database, which is recently built as the first database collecting experimentally-confirmed microbe-disease associations. As a result, NGRHMDA achieved reliable results with AUCs of 0.9023 ± 0.0031 and 0.9111 in the validation frameworks of fivefold CV and LOOCV. In addition, 78.2% microbe samples and 66.7% disease samples are found to be consistent with the basic assumption of our work that microbes tend to get involved in the similar disease clusters, and vice versa. Compared with other methods, the prediction results yielded by NGRHMDA demonstrate its effective prediction performance for microbe-disease associations. It is anticipated that NGRHMDA can be used as a useful tool to search the most potential microbial candidates for various diseases, and therefore

  9. Experimental studies of the large Debye length probe theory in a continuum plasma

    International Nuclear Information System (INIS)

    Kamitsuma, M.; Chen, S.

    1977-01-01

    The Laplace limit probe theory for continuum plasmas, i.e., probe theory under the condition r/sub p//lambda/sub D/→0, where r/sub p/ is probe radius and lambda/sub D/ is Debye length, has been experimentally studied. The results show that the application limit of this theory is r/sub p//lambda/sub D/=0.44 for a spherical probe and r/sub p//lambda/sub D/=0.23 for a cylindrical probe

  10. 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......, suggesting that eukaryotes may rival prokaryotes in terms of dissimilatory nitrate reduction. Finally, this review article sketches some evolutionary perspectives of eukaryotic nitrate metabolism and identifies open questions that need to be addressed in future investigations....... 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...

  11. The mucosal firewalls against commensal intestinal microbes.

    Science.gov (United States)

    Macpherson, Andrew J; Slack, Emma; Geuking, Markus B; McCoy, Kathy D

    2009-07-01

    Mammals coexist with an extremely dense microbiota in the lower intestine. Despite the constant challenge of small numbers of microbes penetrating the intestinal surface epithelium, it is very unusual for these organisms to cause disease. In this review article, we present the different mucosal firewalls that contain and allow mutualism with the intestinal microbiota.

  12. Enriching Metal-Oxidizing Microbes from Marine Sediment on Cathodic Currents

    Science.gov (United States)

    Rowe, A. R.; Nealson, K. H.

    2013-12-01

    The ability of organisms to transfer electrons to and from substrates outside the cell is reshaping the way we look at microbial respiration. While this process, termed extracellular electron transport (EET), has been described in a number of metal reducing organisms, current evidence suggests that this process is widespread in nature and across physiologies. Additionally, it has been speculated that these previously overlooked electrochemical interactions may play an important role in global biogeochemical cycles. Requirements for EET could play a role in why the ';uncultured majority' have so far been resistant to culturing. As such, we are currently developing culturing techniques to target microbes capable of utilizing insoluble electron acceptors utilizing electrochemical techniques. Microbe-electrode interactions are analogous to the reactions that occur between microbes and minerals and may provide an apt way to mimic the environmental conditions (i.e., insoluble electron donor/acceptor at specific redox potentials) required for culturing specialized or EET dependent metabolisms. It has been previously demonstrated that aquatic sediments are capable of utilizing anodes as electron acceptors, thereby generating a current. While, it is known that microbes utilize electrons from a cathode for the reduction of different metals and oxygen in microbial fuel cells, currently there are no reports of environmental enrichments of microbes using cathodes. Replicate microcosms from marine sediments (sampled from Catalina Harbor, California) were incubated with ITO plated glass electrodes. Negative current production at -400mV (vs. Ag/AgCl reference electrodes) potentials was sustained for four weeks. Secondary enrichments were then constructed using the cathode as the primary electron source and a variety of anaerobic terminal electron acceptors--Nitrate, Fe3+, and SO42-. Positive current was maintained in enrichment cultures (compared to abiotic control containing

  13. Scientists discover how deadly fungal microbes enter host cells

    OpenAIRE

    Whyte, Barry James

    2010-01-01

    A research team led by scientists at the Virginia Bioinformatics Institute at Virginia Tech has discovered a fundamental entry mechanism that allows dangerous fungal microbes to infect plants and cause disease.

  14. Do airborne microbes matter for atmospheric chemistry and cloud formation?

    Science.gov (United States)

    Konstantinidis, Konstantinos T

    2014-06-01

    The role of airborne microbial cells in the chemistry of the atmosphere and cloud formation remains essentially speculative. Recent studies have indicated that microbes might be more important than previously anticipated for atmospheric processes. However, more work and direct communication between microbiologists and atmospheric scientists and modellers are necessary to better understand and model bioaerosol-cloud-precipitation-climate interactions. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  15. Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes.

    Science.gov (United States)

    Gerardo, Nicole; Hurst, Gregory

    2017-12-27

    Over the past decade, there has been a pronounced shift in the study of host-microbe associations, with recognition that many of these associations are beneficial, and often critical, for a diverse array of hosts. There may also be pronounced benefits for the microbes, though this is less well empirically understood. Significant progress has been made in understanding how ecology and evolution shape simple associations between hosts and one or a few microbial species, and this work can serve as a foundation to study the ecology and evolution of host associations with their often complex microbial communities (microbiomes).

  16. Influence of probe geometry on the response of an electrostatic probe

    DEFF Research Database (Denmark)

    Johansson, Torben; Crichton, George C; McAllister, Iain Wilson

    1999-01-01

    The response of an electrostatic probe is examined with reference to the probe geometry. The study involves the evaluation of the probe lambda function, from which response-related characteristic parameters can be derived. These parameters enable the probe detection sensitivity Se and spatial...

  17. Induction of Systemic Resistance against Insect Herbivores in Plants by Beneficial Soil Microbes

    Directory of Open Access Journals (Sweden)

    Md. Harun-Or Rashid

    2017-10-01

    Full Text Available Soil microorganisms with growth-promoting activities in plants, including rhizobacteria and rhizofungi, can improve plant health in a variety of different ways. These beneficial microbes may confer broad-spectrum resistance to insect herbivores. Here, we provide evidence that beneficial microbes modulate plant defenses against insect herbivores. Beneficial soil microorganisms can regulate hormone signaling including the jasmonic acid, ethylene and salicylic acid pathways, thereby leading to gene expression, biosynthesis of secondary metabolites, plant defensive proteins and different enzymes and volatile compounds, that may induce defenses against leaf-chewing as well as phloem-feeding insects. In this review, we discuss how beneficial microbes trigger induced systemic resistance against insects by promoting plant growth and highlight changes in plant molecular mechanisms and biochemical profiles.

  18. Impact of anti-acidification microbial consortium on carbohydrate metabolism of key microbes during food waste composting.

    Science.gov (United States)

    Song, Caihong; Li, Mingxiao; Qi, Hui; Zhang, Yali; Liu, Dongming; Xia, Xunfeng; Pan, Hongwei; Xi, Beidou

    2018-07-01

    This study investigated the effect of anti-acidification microbial consortium (AAMC), which act synergistically for rapid bioconversion of organic acids on carbohydrate metabolism of key microbes in the course of food waste (FW) composting by metaproteomics. AAMC was inoculated to the composting mass and compared with treatment with alkaline compounds and the control without any amendment. Inoculating AAMC could effectively accelerate carbohydrate degradation process and improve composting efficiency. Carbohydrate metabolic network profiles showed the inoculation with AAMC could increase significantly the types of enzymes catalysing the degradation of lignin, cellulose and hemicellulose. Furthermore, AAMC inoculum could increase not only diversities of microbes producing key enzymes in metabolism pathways of acetic and propionic acids, but also the amounts of these key enzymes. The increase of diversities of microbes could disperse the pressure from acidic adversity on microorganisms which were capable to degrade acetic and propionic acids. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. Diet, gut microbes, and the pathogenesis of inflammatory bowel diseases.

    Science.gov (United States)

    Dolan, Kyle T; Chang, Eugene B

    2017-01-01

    The rising incidence of inflammatory bowel diseases in recent decades has notably paralleled changing lifestyle habits in Western nations, which are now making their way into more traditional societies. Diet plays a key role in IBD pathogenesis, and there is a growing appreciation that the interaction between diet and microbes in a susceptible person contributes significantly to the onset of disease. In this review, we examine what is known about dietary and microbial factors that promote IBD. We summarize recent findings regarding the effects of diet in IBD epidemiology from prospective population cohort studies, as well as new insights into IBD-associated dysbiosis. Microbial metabolism of dietary components can influence the epithelial barrier and the mucosal immune system, and understanding how these interactions generate or suppress inflammation will be a significant focus of IBD research. Our knowledge of dietary and microbial risk factors for IBD provides important considerations for developing therapeutic approaches through dietary modification or re-shaping the microbiota. We conclude by calling for increased sophistication in designing studies on the role of diet and microbes in IBD pathogenesis and disease resolution in order to accelerate progress in response to the growing challenge posed by these complex disorders. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Volume 10 No. 11 November 2010 4340 SOIL MICROBE ...

    African Journals Online (AJOL)

    user

    2010-11-11

    Nov 11, 2010 ... SOIL MICROBE MEDIATED ZINC UPTAKE IN SOY BEAN: A REVIEW. Jefwa JM. 1* .... Porg, lipid Plp, high-energetic~P, sugar. Psuc and .... encouragement to prepare this presentation. ... Enviroquest Ltd Ontario, Canada.

  1. Formation of a symbiotic host-microbe interface: the role of SNARE-mediated regulation of exocytosis

    NARCIS (Netherlands)

    Huisman, Rik

    2018-01-01

    At the heart of endosymbiosis microbes are hosted inside living cells in specialized membrane compartments that from a host-microbe interface, where nutrients and signal are efficiently exchanged. Such symbiotic interfaces include arbuscules produced by arbuscular mycorrhiza (AM) and

  2. 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......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 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 ...

  3. Correlation of soil microbes and soil micro-environment under long-term safflower (Carthamus tinctorius L.) plantation in China.

    Science.gov (United States)

    Lu, Shuang; Quan, Wang; Wang, Shao-Ming; Liu, Hong-Ling; Tan, Yong; Zeng, Guang-Ping; Zhang, Xia

    2013-04-01

    Microbial community structure and ecological functions are influenced by interactions between above and belowground biota. There is an urgent need for intensive monitoring of microbes feedback of soil micro-ecosystem for setting up a good agricultural practice. Recent researches have revealed that many soils characteristic can effect microbial community structure. In the present study factors affecting microbial community structure and soil in Carthamus tinctorius plantations in arid agricultural ecosystem of northern Xinjiang, China were identified. The result of the study revealed that soil type was the key factor in safflower yield; Unscientific field management resulted high fertility level (bacteria dominant) of soil to turn to low fertility level (fungi dominant), and Detruded Canonical Correspondence Analysis (DCCA) showed that soil water content, organic matter, available N, P and K were the dominant factors affecting distribution of microbial community. Soil water content showed a significant positive correlation with soil microbes quantity (P soil microbe quantity (P < 0.05).

  4. Microbes and associated soluble and volatile chemicals on periodically wet household surfaces.

    Science.gov (United States)

    Adams, Rachel I; Lymperopoulou, Despoina S; Misztal, Pawel K; De Cassia Pessotti, Rita; Behie, Scott W; Tian, Yilin; Goldstein, Allen H; Lindow, Steven E; Nazaroff, William W; Taylor, John W; Traxler, Matt F; Bruns, Thomas D

    2017-09-26

    Microorganisms influence the chemical milieu of their environment, and chemical metabolites can affect ecological processes. In built environments, where people spend the majority of their time, very little is known about how surface-borne microorganisms influence the chemistry of the indoor spaces. Here, we applied multidisciplinary approaches to investigate aspects of chemical microbiology in a house. We characterized the microbial and chemical composition of two common and frequently wet surfaces in a residential setting: kitchen sink and bathroom shower. Microbial communities were studied using culture-dependent and independent techniques, including targeting RNA for amplicon sequencing. Volatile and soluble chemicals from paired samples were analyzed using state-of-the-art techniques to explore the links between the observed microbiota and chemical exudates. Microbial analysis revealed a rich biological presence on the surfaces exposed in kitchen sinks and bathroom shower stalls. Microbial composition, matched for DNA and RNA targets, varied by surface type and sampling period. Bacteria were found to have an average of 25× more gene copies than fungi. Biomass estimates based on qPCR were well correlated with measured total volatile organic compound (VOC) emissions. Abundant VOCs included products associated with fatty acid production. Molecular networking revealed a diversity of surface-borne compounds that likely originate from microbes and from household products. Microbes played a role in structuring the chemical profiles on and emitted from kitchen sinks and shower stalls. Microbial VOCs (mVOCs) were predominately associated with the processing of fatty acids. The mVOC composition may be more stable than that of microbial communities, which can show temporal and spatial variation in their responses to changing environmental conditions. The mVOC output from microbial metabolism on kitchen sinks and bathroom showers should be apparent through careful

  5. Microbes on a bottle: substrate, season and geography influence community composition of microbes colonizing marine plastic debris

    OpenAIRE

    Carter, Dee A.; 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 com...

  6. Mining with microbes

    International Nuclear Information System (INIS)

    Rawlings., D.E.; Silver, S.

    1995-01-01

    Microbes are playing increasingly important roles in commercial mining operations, where they are being used in the open-quotes bioleachingclose quotes of copper, uranium, and gold ores. Direct leaching is when microbial metabolism changes the redox state of the metal being harvested, rendering it more soluble. Indirect leaching includes redox chemistry of other metal cations that are then coupled in chemical oxidation or reduction of the harvested metal ion and microbial attack upon and solubilization of the mineral matrix in which the metal is physically embedded. In addition, bacterial cells are used to detoxify the waste cyanide solution from gold-mining operations and as open-quotes absorbantsclose quotes of the mineral cations. Bacterial cells may replace activated carbon or alternative biomass. With an increasing understanding of microbial physiology, biochemistry and molecular genetics, rational approaches to improving these microbial activities become possible. 40 refs., 3 figs

  7. Two-way plant mediated interactions between root-associated microbes and insects: from ecology to mechanisms

    NARCIS (Netherlands)

    Pangesti, N.P.D.; Pineda Gomez, A.M.; Pieterse, C.M.J.; Dicke, M.; Loon, van J.J.A.

    2013-01-01

    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

  8. Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells.

    Science.gov (United States)

    Atarashi, Koji; Tanoue, Takeshi; Ando, Minoru; Kamada, Nobuhiko; Nagano, Yuji; Narushima, Seiko; Suda, Wataru; Imaoka, Akemi; Setoyama, Hiromi; Nagamori, Takashi; Ishikawa, Eiji; Shima, Tatsuichiro; Hara, Taeko; Kado, Shoichi; Jinnohara, Toshi; Ohno, Hiroshi; Kondo, Takashi; Toyooka, Kiminori; Watanabe, Eiichiro; Yokoyama, Shin-Ichiro; Tokoro, Shunji; Mori, Hiroshi; Noguchi, Yurika; Morita, Hidetoshi; Ivanov, Ivaylo I; Sugiyama, Tsuyoshi; Nuñez, Gabriel; Camp, J Gray; Hattori, Masahira; Umesaki, Yoshinori; Honda, Kenya

    2015-10-08

    Intestinal Th17 cells are induced and accumulate in response to colonization with a subgroup of intestinal microbes such as segmented filamentous bacteria (SFB) and certain extracellular pathogens. Here, we show that adhesion of microbes to intestinal epithelial cells (ECs) is a critical cue for Th17 induction. Upon monocolonization of germ-free mice or rats with SFB indigenous to mice (M-SFB) or rats (R-SFB), M-SFB and R-SFB showed host-specific adhesion to small intestinal ECs, accompanied by host-specific induction of Th17 cells. Citrobacter rodentium and Escherichia coli O157 triggered similar Th17 responses, whereas adhesion-defective mutants of these microbes failed to do so. Moreover, a mixture of 20 bacterial strains, which were selected and isolated from fecal samples of a patient with ulcerative colitis on the basis of their ability to cause a robust induction of Th17 cells in the mouse colon, also exhibited EC-adhesive characteristics. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Laser-Assisted Atom Probe Tomography of Deformed Minerals: A Zircon Case Study.

    Science.gov (United States)

    La Fontaine, Alexandre; Piazolo, Sandra; Trimby, Patrick; Yang, Limei; Cairney, Julie M

    2017-04-01

    The application of atom probe tomography to the study of minerals is a rapidly growing area. Picosecond-pulsed, ultraviolet laser (UV-355 nm) assisted atom probe tomography has been used to analyze trace element mobility within dislocations and low-angle boundaries in plastically deformed specimens of the nonconductive mineral zircon (ZrSiO4), a key material to date the earth's geological events. Here we discuss important experimental aspects inherent in the atom probe tomography investigation of this important mineral, providing insights into the challenges in atom probe tomography characterization of minerals as a whole. We studied the influence of atom probe tomography analysis parameters on features of the mass spectra, such as the thermal tail, as well as the overall data quality. Three zircon samples with different uranium and lead content were analyzed, and particular attention was paid to ion identification in the mass spectra and detection limits of the key trace elements, lead and uranium. We also discuss the correlative use of electron backscattered diffraction in a scanning electron microscope to map the deformation in the zircon grains, and the combined use of transmission Kikuchi diffraction and focused ion beam sample preparation to assist preparation of the final atom probe tip.

  10. 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.

  11. Mobile Game Probes

    DEFF Research Database (Denmark)

    Borup Lynggaard, Aviaja

    2006-01-01

    This paper will examine how probes can be useful for game designers in the preliminary phases of a design process. The work is based upon a case study concerning pervasive mobile phone games where Mobile Game Probes have emerged from the project. The new probes are aimed towards a specific target...... group and the goal is to specify the probes so they will cover the most relevant areas for our project. The Mobile Game Probes generated many interesting results and new issues occurred, since the probes came to be dynamic and favorable for the process in new ways....

  12. Microbes, molecules, maladies and man | Duse | South African ...

    African Journals Online (AJOL)

    South African Medical Journal. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 92, No 3 (2002) >. Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register. Microbes, molecules, maladies and man. AG Duse. Abstract.

  13. Long-range transport of airborne microbes over the global tropical and subtropical ocean

    KAUST Repository

    Mayol, Eva; Arrieta, J M; Jimé nez, Maria A.; Martí nez-Asensio, Adriá n; Garcias Bonet, Neus; Dachs, Jordi; Gonzá lez-Gaya, Belé n; Royer, Sarah-J.; Bení tez-Barrios, Veró nica M.; Fraile-Nuez, Eugenio; Duarte, Carlos M.

    2017-01-01

    The atmosphere plays a fundamental role in the transport of microbes across the planet but it is often neglected as a microbial habitat. Although the ocean represents two thirds of the Earth's surface, there is little information on the atmospheric microbial load over the open ocean. Here we provide a global estimate of microbial loads and air-sea exchanges over the tropical and subtropical oceans based on the data collected along the Malaspina 2010 Circumnavigation Expedition. Total loads of airborne prokaryotes and eukaryotes were estimated at 2.2 × 1021 and 2.1 × 1021 cells, respectively. Overall 33-68% of these microorganisms could be traced to a marine origin, being transported thousands of kilometres before re-entering the ocean. Moreover, our results show a substantial load of terrestrial microbes transported over the oceans, with abundances declining exponentially with distance from land and indicate that islands may act as stepping stones facilitating the transoceanic transport of terrestrial microbes.The extent to which the ocean acts as a sink and source of airborne particles to the atmosphere is unresolved. Here, the authors report high microbial loads over the tropical Atlantic, Pacific and Indian oceans and propose islands as stepping stones for the transoceanic transport of terrestrial microbes..

  14. Long-range transport of airborne microbes over the global tropical and subtropical ocean

    KAUST Repository

    Mayol, Eva

    2017-07-28

    The atmosphere plays a fundamental role in the transport of microbes across the planet but it is often neglected as a microbial habitat. Although the ocean represents two thirds of the Earth\\'s surface, there is little information on the atmospheric microbial load over the open ocean. Here we provide a global estimate of microbial loads and air-sea exchanges over the tropical and subtropical oceans based on the data collected along the Malaspina 2010 Circumnavigation Expedition. Total loads of airborne prokaryotes and eukaryotes were estimated at 2.2 × 1021 and 2.1 × 1021 cells, respectively. Overall 33-68% of these microorganisms could be traced to a marine origin, being transported thousands of kilometres before re-entering the ocean. Moreover, our results show a substantial load of terrestrial microbes transported over the oceans, with abundances declining exponentially with distance from land and indicate that islands may act as stepping stones facilitating the transoceanic transport of terrestrial microbes.The extent to which the ocean acts as a sink and source of airborne particles to the atmosphere is unresolved. Here, the authors report high microbial loads over the tropical Atlantic, Pacific and Indian oceans and propose islands as stepping stones for the transoceanic transport of terrestrial microbes..

  15. 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.

  16. Fluorescence spectral studies on interaction of fluorescent probes with Bovine Serum Albumin (BSA)

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Kaushik, E-mail: ghoshfcy@iitr.ac.in; Rathi, Sweety; Arora, Deepshikha

    2016-07-15

    Interaction of 2-(1-(naphthale-1-ylimino)ethyl)phenol (1), 2-methoxy-4-(((4-methoxyphenyl)imino)methyl)phenol (2) and 2-methoxy-4-((naphthalene-1-ylimino)methyl)phenol (3) with Bovine Serum Albumin (BSA) was examined. Fluorescence spectral data were obtained from the probes by varying the concentration of BSA as well as from BSA by varying the concentration of probes. Synchronous fluorescence measurements were performed and binding constants of the probes were calculated. To understand mode of quenching, Stern–Volmer plot, absorption spectral studies and life time measurements were performed. Förster resonance energy transfer (FRET) was also scrutinized. - Highlights: • Schiff bases with pendant phenolato function and interaction with BSA. • Synchronous fluorescence studies and a preferred interaction with tryptophan. • Probable interaction of probes with Trp-213 residue in the hydrophobic cavity. • 1:1 binding stoichiometry of probes and BSA in Benesi–Hildebrand graph.

  17. 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

  18. Prominent Human Health Impacts from Several Marine Microbes: History, Ecology, and Public Health Implications

    Directory of Open Access Journals (Sweden)

    P. K. Bienfang

    2011-01-01

    Full Text Available This paper overviews several examples of important public health impacts by marine microbes and directs readers to the extensive literature germane to these maladies. These examples include three types of dinoflagellates (Gambierdiscus spp., Karenia brevis, and Alexandrium fundyense, BMAA-producing cyanobacteria, and infectious microbes. The dinoflagellates are responsible for ciguatera fish poisoning, neurotoxic shellfish poisoning, and paralytic shellfish poisoning, respectively, that have plagued coastal populations over time. Research interest on the potential for marine cyanobacteria to contribute BMAA into human food supplies has been derived by BMAA's discovery in cycad seeds and subsequent implication as the putative cause of amyotrophic lateral sclerosis/parkinsonism dementia complex among the Chamorro people of Guam. Recent UPLC/MS analyses indicate that recent reports that BMAA is prolifically distributed among marine cyanobacteria at high concentrations may be due to analyte misidentification in the analytical protocols being applied for BMAA. Common infectious microbes (including enterovirus, norovirus, Salmonella, Campylobacter, Shigella, Staphylococcus aureus, Cryptosporidium, and Giardia cause gastrointestinal and skin-related illness. These microbes can be introduced from external human and animal sources, or they can be indigenous to the marine environment.

  19. 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

  20. United States Department of Agriculture-Agricultural Research Service research programs on microbes for management of plant-parasitic nematodes.

    Science.gov (United States)

    Meyer, Susan L F

    2003-01-01

    Restrictions on the use of conventional nematicides have increased the need for new methods of managing plant-parasitic nematodes. Consequently, nematode-antagonistic microbes, and active compounds produced by such organisms, are being explored as potential additions to management practices. Programs in this area at the USDA Agricultural Research Service investigate applied biocontrol agents, naturally occurring beneficial soil microbes and natural compounds. Specific research topics include use of plant growth-promoting rhizobacteria and cultural practices for management of root-knot and ring nematodes, determination of management strategies that enhance activity of naturally occurring Pasteuria species (bacterial obligate parasites of nematodes), studies on interactions between biocontrol bacteria and bacterial-feeding nematodes, and screening of microbes for compounds active against plant-parasitic nematodes. Some studies involve biocontrol agents that are active against nematodes and soil-borne plant-pathogenic fungi, or combinations of beneficial bacteria and fungi, to manage a spectrum of plant diseases or to increase efficacy over a broader range of environmental conditions. Effective methods or agents identified in the research programs are investigated as additions to existing management systems for plant-parasitic nematodes.

  1. [Origin of the plague microbe Yersinia pestis: structure of the process of speciation].

    Science.gov (United States)

    Suntsov, V V

    2012-01-01

    The origin and evolution of the plague microbe Yersinia pestis are considered in the context of propositions of modern Darwinism. It was shown that the plague pathogen diverged from the pseudotuberculous microbe Yersinia pseudotuberculosis O:1b in the mountain steppe landscapes of Central Asia in the Sartan: 22000-15000 years ago. Speciation occurred in the tarbagan (Marmota sibirica)--flea (Oropsylla silantiewi) parasitic system. The structure of the speciation process included six stages: isolation, genetic drift, enhancement of intrapopulational polymorphism, the beginning of pesticin synthesis (genetic conflict and emergence of hiatus), specialization (stabilization of characteristics), and adaptive irradiation (transformation of the monotypic species Y. pestis tarbagani into a polytypic species). The scenario opens up wide prospects for construction of the molecular phylogeny of the plague microbe Y. pestis and for investigation of the biochemical and molecular-genetic aspects of "Darwinian" evolution of pathogens from many other nature-focal infections.

  2. Extracellular vesicles modulate host-microbe responses by altering TLR2 activity and phagocytosis.

    Directory of Open Access Journals (Sweden)

    Jeroen van Bergenhenegouwen

    Full Text Available Oral delivery of Gram positive bacteria, often derived from the genera Lactobacillus or Bifidobacterium, can modulate immune function. Although the exact mechanisms remain unclear, immunomodulatory effects may be elicited through the direct interaction of these bacteria with the intestinal epithelium or resident dendritic cell (DC populations. We analyzed the immune activation properties of Lactobacilli and Bifidobacterium species and made the surprising observation that cellular responses in vitro were differentially influenced by the presence of serum, specifically the extracellular vesicle (EV fraction. In contrast to the tested Lactobacilli species, tested Bifidobacterium species induce TLR2/6 activity which is inhibited by the presence of EVs. Using specific TLR ligands, EVs were found to enhance cellular TLR2/1 and TLR4 responses while TLR2/6 responses were suppressed. No effect could be observed on cellular TLR5 responses. We determined that EVs play a role in bacterial aggregation, suggesting that EVs interact with bacterial surfaces. EVs were found to slightly enhance DC phagocytosis of Bifidobacterium breve whereas phagocytosis of Lactobacillus rhamnosus was virtually absent upon serum EV depletion. DC uptake of a non-microbial substance (dextran was not affected by the different serum fractions suggesting that EVs do not interfere with DC phagocytic capacity but rather modify the DC-microbe interaction. Depending on the microbe, combined effects of EVs on TLR activity and phagocytosis result in a differential proinflammatory DC cytokine release. Overall, these data suggest that EVs play a yet unrecognized role in host-microbe responses, not by interfering in recipient cellular responses but via attachment to, or scavenging of, microbe-associated molecular patterns. EVs can be found in any tissue or bodily fluid, therefore insights into EV-microbe interactions are important in understanding the mechanism of action of potential

  3. Influence of probe motion on laser probe temperature in circulating blood.

    Science.gov (United States)

    Hehrlein, C; Splinter, R; Littmann, L; Tuntelder, J R; Tatsis, G P; Svenson, R H

    1991-01-01

    The purpose of this study was to evaluate the effect of probe motion on laser probe temperature in various blood flow conditions. Laser probe temperatures were measured in an in vitro blood circulation model consisting of 3.2 nm-diameter plastic tubes. A 2.0 mm-diameter metal probe attached to a 300 microns optical quartz fiber was coupled to an argon laser. Continuous wave 4 watts and 8 watts of laser power were delivered to the fiber tip corresponding to a 6.7 +/- 0.5 and 13.2 +/- 0.7 watts power setting at the laser generator. The laser probe was either moved with constant velocity or kept stationary. A thermocouple inserted in the lateral portion of the probe was used to record probe temperatures. Probe temperature changes were found with the variation of laser power, probe velocity, blood flow, and duration of laser exposure. Probe motion significantly reduced probe temperatures. After 10 seconds of 4 watts laser power the probe temperature in stagnant blood decreased from 303 +/- 18 degrees C to 113 +/- 17 degrees C (63%) by moving the probe with a velocity of 5 cm/sec. Blood flow rates of 170 ml/min further decreased the probe temperature from 113 +/- 17 degrees C to 50 +/- 8 degrees C (56%). At 8 watts of laser power a probe temperature reduction from 591 +/- 25 degrees C to 534 +/- 36 degrees C (10%) due to 5 cm/sec probe velocity was noted. Probe temperatures were reduced to 130 +/- 30 degrees C (78%) under the combined influence of 5 cm/sec probe velocity and 170 ml/min blood flow.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. Metagenomic Profiling of Soil Microbes to Mine Salt Stress Tolerance Genes

    Directory of Open Access Journals (Sweden)

    Vasim Ahmed

    2018-02-01

    Full Text Available Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation. 16S rRNA gene sequence analysis has indicated the dominance of halophilic/halotolerant phylotypes affiliated to Proteobacteria, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Acidobacteria. A functional metagenomics approach led to the identification of osmotolerant clones SSR1, SSR4, SSR6, SSR2 harboring BCAA_ABCtp, GSDH, STK_Pknb, and duf3445 genes. Furthermore, transposon mutagenesis, genetic, physiological and functional studies in close association has confirmed the role of these genes in osmotolerance. Enhancement in host osmotolerance possibly though the cytosolic accumulation of amino acids, reducing equivalents and osmolytes involving BCAA-ABCtp, GSDH, and STKc_PknB. Decoding of the genetic elements prevalent within these microbes can be exploited either as such for ameliorating soils or their genetically modified forms can assist crops to resist and survive in saline environment.

  5. Intra-operative probe for brain cancer: feasibility study

    Science.gov (United States)

    Vu Thi, M. H.; Charon, Y.; Duval, M. A.; Lefebvre, F.; Menard, L.; Pitre, S.; Pinot, L.; Siebert, R.

    2007-07-01

    The present work aims a new medical probe for surgeons devoted to brain cancers, in particular glioblastoma multiforme. Within the last years, our group has started the development of a new intra-operative beta imaging probe. More recently, we took an alternative approach for the same application: a fluorescence probe. In both cases the purpose is to differentiate normal from tumor brain tissue. In a first step, we developed set-ups capable to measure autofluorescence. They are based on a dedicated epi-fluorescence design and on specific fiber optic probes. Relative signal amplitude, spectral shape and fluorescence lifetime measurements are foreseen to distinguish normal and cancer tissue by analyzing fluorophores like NADH, lipopigments and porphyrines. The autofluorescence spectra are recorded in the 460-640 nm range with a low resolution spectrometer. For lifetime measurements a fast detector (APD) is used together with a TCSPC-carte. Intrinsic wavelength- and time-resolutions are a few nm and 200 ps, respectively. Different samples have been analyzed to validate our new detection system and to allow a first configuration of our medical fluorescence probe. First results from the tissue measurements are shown.

  6. Effects of different microbes on fermenting feed for sea cucumber ( Apostichopus japonicus)

    Science.gov (United States)

    Jiang, Yan; Wang, Yingeng; Mai, Kangsen; Zhang, Zheng; Liao, Meijie; Rong, Xiaojun

    2015-10-01

    The effects of different microbes on fermenting feed for sea cucumber ( Apostichopus japonicus) were compared to select the optimal fermentation strain in this study. Saccharomgces cerevisae, Candida utilis, Bacillus subtilis and Geotrichum candidum were independently added into the experimental compound feed, while only saline was mixed with the control feed. The fermentation treatments were inoculated with 10% seed solution under the condition of 25°C and 70% water content, which lasted for 5 days to elucidate the optimal microbe strain for fermenting effect. Physicochemical indexes and sensorial characteristics were measured per day during the fermentation. The indexes included dry matter recovery (DMR), crude protein (CP), the percentage of amino acid nitrogen to total nitrogen (AA-N/tN), the percentage of ammonia nitrogen to total nitrogen (NH3-N/tN), and the ratio of fermentation strains and vibrios to the total microbes, color, smell and viscosity. The results showed that DMR, CP and AA-N/tN of the S. cerevisae group reached the highest level on day 3, but the ratio of fermentation strain was second to C. utilis group. In addition, its NH3-N/tN and the ratio of vibrios were maintained at low levels, and the sensory evaluation score including smell, color and viscosity was the highest in S. cerevisae group on day 3. Therefore, S. cerevisae could be the optimal strain for the feed fermentation for sea cucumber. This research developed a new production method of fermentation feed for sea cucumber.

  7. Microbial conversion of food wastes for biofertilizer production with thermophilic lipolytic microbes

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, Shu-Hsien; Yang, Shang-Shyng [Institute of Microbiology and Biochemistry, National Taiwan University, Taipei 10617, (Taiwan); Liu, Ching-Piao [Department of Biological Science and Technology, Meiho Institute of Technology, Pingtung 91201, (Taiwan)

    2007-05-15

    Food waste is approximately one quarter of the total garbage in Taiwan. To investigate the feasibility of microbial conversion of food waste to multiple functional biofertilizer, food waste was mixed with bulking materials, inoculated with thermophilic and lipolytic microbes and incubated at 50{sup o}C in a mechanical composter. Microbial inoculation enhanced the degradation of food wastes, increased the total nitrogen and the germination rate of alfalfa seed, shortened the maturity period and improved the quality of biofertilizer. In food waste inoculated with thermophilic and lipolytic Brevibacillus borstelensis SH168 for 28 days, total nitrogen increased from 2.01% to 2.10%, ash increased from 24.94% to 29.21%, crude fat decreased from 4.88% to 1.34% and the C/N ratio decreased from 18.02 to 17.65. Each gram of final product had a higher population of thermophilic microbes than mesophilic microbes. Microbial conversion of food waste to biofertilizer is a feasible and potential technology in the future to maintain the natural resources and to reduce the impact on environmental quality. (author)

  8. Towards a General Equation for the Survival of Microbes Transferred between Solar System Bodies

    Science.gov (United States)

    Fries, M.; Steele, A.

    2014-01-01

    It should be possible to construct a general equation describing the survival of microbes transferred between Solar System bodies. Such an equation will be useful for constraining the likelihood of transfer of viable organisms between bodies throughout the lifetime of the Solar System, and for refining Planetary Protection constraints placed on future missions. We will discuss the construction of such an equation, present a plan for definition of pertinent factors, and will describe what research will be necessary to quantify those factors. Description: We will examine the case of microbes transferred between Solar System bodies as residents in meteorite material ejected from one body (the "intial body") and deposited on another (the "target body"). Any microbes transferred in this fashion will experience four distinct phases between their initial state on the initial body, up to the point where they colonize the target body. Each of these phases features phenomena capable of reducing or exterminating the initial microbial population. They are: 1) Ejection: Material is ejected from the initial body, imparting shock followed by rapid desiccation and cooling. 2) Transport: Material travels through interplanetary space to the target body, exposing a hypothetical microbial population to extended desiccation, irradiation, and temperature extremes. 3) Infall: Material is deposited on the target body, diminishing the microbial population through shock, mass loss, and heating. 4) Adaptation: Any microbes which survive the previous three phases must then adapt to new chemophysical conditions of the target body. Differences in habitability between the initial and target bodies dominate this phase. A suitable general-form equation can be assembled from the above factors by defining the initial number of microbes in an ejected mass and applying multiplicitive factors based on the physical phenomena inherent to each phase. It should be possible to present the resulting equation

  9. Studies of impurity recycling by the collector probe technique

    International Nuclear Information System (INIS)

    Hildebrandt, D.; Grote, H.; Herrmann, A.; Laux, M.; Pech, P.; Reiner, H.D.; Wolff, H.

    1987-01-01

    In order to study recycling effects of the nonintrinsic impurity Li discharges with and without LiD-pellet injection were investigated. The observed maximum impurity level of Li in the SOL plasma of discharges without injection reaches less than 10% of that observed in discharges with injection. The measurements offer the possibility to distinguish between influxes from the wall and those which reach the collector probe via the core plasma. The time evolution, orientation and radial dependence of the impurity fluxes are characteristic features of their origin. The consideration of all these features facilitates a better understanding of collector probe measurements in the SOL-plasma. (orig.)

  10. 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."

  11. 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.

  12. 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. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  13. Deep-Sea Microbes: Linking Biogeochemical Rates to -Omics Approaches

    Science.gov (United States)

    Herndl, G. J.; Sintes, E.; Bayer, B.; Bergauer, K.; Amano, C.; Hansman, R.; Garcia, J.; Reinthaler, T.

    2016-02-01

    Over the past decade substantial progress has been made in determining deep ocean microbial activity and resolving some of the enigmas in understanding the deep ocean carbon flux. Also, metagenomics approaches have shed light onto the dark ocean's microbes but linking -omics approaches to biogeochemical rate measurements are generally rare in microbial oceanography and even more so for the deep ocean. In this presentation, we will show by combining metagenomics, -proteomics and biogeochemical rate measurements on the bulk and single-cell level that deep-sea microbes exhibit characteristics of generalists with a large genome repertoire, versatile in utilizing substrate as revealed by metaproteomics. This is in striking contrast with the apparently rather uniform dissolved organic matter pool in the deep ocean. Combining the different -omics approaches with metabolic rate measurements, we will highlight some major inconsistencies and enigmas in our understanding of the carbon cycling and microbial food web structure in the dark ocean.

  14. Cultural probes

    DEFF Research Database (Denmark)

    Madsen, Jacob Østergaard

    The aim of this study was thus to explore cultural probes (Gaver, Boucher et al. 2004), as a possible methodical approach, supporting knowledge production on situated and contextual aspects of occupation.......The aim of this study was thus to explore cultural probes (Gaver, Boucher et al. 2004), as a possible methodical approach, supporting knowledge production on situated and contextual aspects of occupation....

  15. Eavesdropping on plant-insect-microbe chemical communications in agricultural ecology: a virtual issue on semiochemicals

    Science.gov (United States)

    Studies of plant-insect interactions, and more recently the interactions among plants, insects, and microbes, have revealed that volatiles often facilitate insect movement, aggregation, and host location by herbivores, predators and parasitoids, all of which could be used to help protect agriculture...

  16. Microbes in biological processes for municipal landfill leachate treatment: Community, function and interaction

    DEFF Research Database (Denmark)

    Zhang, Duoying; Vahala, Riku; Wang, Yu

    2016-01-01

    Landfill leachate (LFL) contains high strength of ammonium and complex organic substances including biodegradable volatile fatty acids (VFAs), refractory aquatic humic substances (AHS) and micro-scale xenobiotic organic chemicals (XOCs), which promotes the diverse microbial community in LFL...... treatment bioreactors. These microbes cooperate to remove nitrogen, biodegrade organic matters, eliminate the toxicity of XOCs and produce energy. In these diverse microbes, some show dominant in the bioreactor and are prevalent in many kinds of LFL treatment bio-processes, such as Brocadia from the phylum...

  17. Digestion of crude protein and organic matter of leaves by rumen microbes in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Ciszuk, A.; Murphy, M.

    1982-01-01

    22 leaf specimens, of which 6 were from an energy-woods project, were studied by incubation in vitro with rumen microbes or pepsin-hydrochloric acid. Several were also examined in situ using the nylon-bag technique. Many leaves, despite their low fiber and high crude protein content, gave low values for organic matter digestibility. The crude protein degradation by rumen microbes or pepsin-hydrochloric acid was low, on average, compared with hay. There was a wide variation among leaf specimens. Variation was also found as regards ammonia production in short-term (4 hours) incubation. No close correlation was found between crude protein content and crude protein degradation, or between the estimates of ruminal degradation and of pepsin-hydrochloric acid digestibility. This suggest that there are leaves that gives ruminants substantial amounts of digestible protein yet escape ruminal fermentation. (Refs. 12).

  18. Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea.

    Science.gov (United States)

    Yu, Tiantian; Li, Meng; Niu, Mingyang; Fan, Xibei; Liang, Wenyue; Wang, Fengping

    2018-01-01

    In marine sediments, microorganisms are known to play important roles in nitrogen cycling; however, the composition and quantity of microbes taking part in each process of nitrogen cycling are currently unclear. In this study, two different types of marine sediment samples (shallow bay and deep-sea sediments) in the South China Sea (SCS) were selected to investigate the microbial community involved in nitrogen cycling. The abundance and composition of prokaryotes and seven key functional genes involved in five processes of the nitrogen cycle [nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonia oxidation (anammox)] were presented. The results showed that a higher abundance of denitrifiers was detected in shallow bay sediments, while a higher abundance of microbes involved in ammonia oxidation, anammox, and DNRA was found in the deep-sea sediments. Moreover, phylogenetic differentiation of bacterial amoA, nirS, nosZ, and nrfA sequences between the two types of sediments was also presented, suggesting environmental selection of microbes with the same geochemical functions but varying physiological properties.

  19. Degradation of 2,4-D in soils by Fe₃O₄ nanoparticles combined with stimulating indigenous microbes.

    Science.gov (United States)

    Fang, Guodong; Si, Youbin; Tian, Chao; Zhang, Gangya; Zhou, Dongmei

    2012-03-01

    Degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) in soils by Fe₃O₄ nanoparticles combined with soil indigenous microbes was investigated, and the effects of Fe₃O₄ nanoparticles on soil microbial populations and enzyme activities were also studied. The soils contaminated with 2,4-D were treated with Fe₃O₄ nanoparticles. The microbial populations and enzyme activities were analyzed by dilution plate method and chemical assay, respectively, and the concentration of 2,4-D in soil was determined by high-performance liquid chromatography (HPLC). The results indicated that Fe₃O₄ nanoparticles combined with soil indigenous microbes led to a higher degradation efficiency of 2,4-D than the treatments with Fe₃O₄ nanoparticles or indigenous microbes alone. The degradation of 2,4-D in soils followed the pseudo first-order kinetic. The half-lives of 2,4-D degradation (DT₅₀) of the combined treatments were 0.9, 1.9 and 3.1 days in a Red soil, Vertisol and Alfisol, respectively, which implied that the DT₅₀ of the combination treatments were significantly shorter than that of the treatments Fe₃O₄ nanoparticles or indigenous microbes alone. The effects of Fe₃O₄ nanoparticles on soil microbial populations and enzyme activities were also investigated and compared with the α-Fe₂O₃ nanoparticles. The results suggested that the α-Fe₂O₃ nanoparticles had only comparatively small effects on degradation of 2,4-D in soils, while the Fe₃O₄ nanoparticles not only degraded 2,4-D in soils but also increased the soil microbial populations and enzyme activities; the maximum increase in enzyme activities were 67.8% (amylase), 53.8% (acid phosphatase), 26.5% (catalase) and 38.0% (urease), compared with the untreated soil. Moreover, the introduction of Fe₃O₄ nanoparticles at the different dosage resulted in a variable degradation efficiency of 2,4-D in soil. The method of combining Fe₃O₄ nanoparticles with indigenous soil microbes may

  20. Cell-autonomous defense, re-organization and trafficking of membranes in plant-microbe interactions.

    Science.gov (United States)

    Dörmann, Peter; Kim, Hyeran; Ott, Thomas; Schulze-Lefert, Paul; Trujillo, Marco; Wewer, Vera; Hückelhoven, Ralph

    2014-12-01

    Plant cells dynamically change their architecture and molecular composition following encounters with beneficial or parasitic microbes, a process referred to as host cell reprogramming. Cell-autonomous defense reactions are typically polarized to the plant cell periphery underneath microbial contact sites, including de novo cell wall biosynthesis. Alternatively, host cell reprogramming converges in the biogenesis of membrane-enveloped compartments for accommodation of beneficial bacteria or invasive infection structures of filamentous microbes. Recent advances have revealed that, in response to microbial encounters, plasma membrane symmetry is broken, membrane tethering and SNARE complexes are recruited, lipid composition changes and plasma membrane-to-cytoskeleton signaling is activated, either for pre-invasive defense or for microbial entry. We provide a critical appraisal on recent studies with a focus on how plant cells re-structure membranes and the associated cytoskeleton in interactions with microbial pathogens, nitrogen-fixing rhizobia and mycorrhiza fungi. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  1. Population dynamics of soil microbes and diversity of Bacillus ...

    African Journals Online (AJOL)

    ONOS

    2010-01-25

    Jan 25, 2010 ... Population dynamics of soil microbes and diversity of ... 25.78, 25.78, 86.26, 24.73, 68.0, 26.8 and 26.8 kDa proteins and equivalent to Cyt, Cry5 and Cry2 toxins ..... Molecular weight (kDa) of protein fractions of the BT isolates.

  2. Diffusion studies on permeable nitroxyl spin probes through bilayer lipid membranes: A low frequency ESR study

    International Nuclear Information System (INIS)

    Meenakumari, V.; Benial, A. Milton Franklin; Utsumi, Hideo; Ichikawa, Kazuhiro; Yamada, Ken-ichi; Hyodo, Fuminori; Jawahar, A.

    2015-01-01

    Electron spin resonance (ESR) studies were carried out for permeable 2mM 14 N-labeled deutrated 3 Methoxy carbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl (MC-PROXYL) in pure water and 1mM, 2mM, 3mM, 4mM concentration of 14N-labeled deutrated MC-PROXYL in 400mM concentration of liposomal solution by using a 300 MHz ESR spectrometer. The ESR parameters such as linewidth, hyperfine coupling constant, g-factor, partition parameter and permeability were reported for these samples. The line broadening was observed for the nitroxyl spin probe in the liposomal solution. The line broadening indicates that the high viscous nature of the liposomal solution. The partition parameter and permeability values indicate the maximum diffusion of nitroxyl spin probes in the bilayer lipid membranes at 2 mM concentration of nitroxyl radical. This study illustrates that ESR can be used to differentiate between the intra and extra- membrane water by loading the liposome vesicles with a lipid-permeable nitroxyl spin probe. From the ESR results, the spin probe concentration was optimized as 2mM in liposomal solution for ESR phantom studies/imaging, invivo and invitro experiments

  3. Planetary protection protecting earth and planets against alien microbes

    International Nuclear Information System (INIS)

    Leys, N.

    2006-01-01

    Protecting Earth and planets against the invasion of 'alien life forms' is not military science fiction, but it is the peaceful daily job of engineers and scientists of space agencies. 'Planetary Protection' is preventing microbial contamination of both the target planet and the Earth when sending robots on interplanetary space mission. It is important to preserve the 'natural' conditions of other planets and to not bring with robots 'earthly microbes' (forward contamination) when looking for 'spores of extra terrestrial life'. The Earth and its biosphere must be protected from potential extraterrestrial biological contamination when returning samples of other planets to the Earth (backward contamination). The NASA-Caltech Laboratory for Planetary Protection of Dr. Kasthuri Venkateswaran at the Jet Propulsion Laboratory (JPL) (California, USA) routinely monitors and characterizes the microbes of NASA spacecraft assembly rooms and space robots prior to flight. They have repeatedly isolated Cupriavidus and Ralstonia strains pre-flight from spacecraft assembly rooms (floor and air) and surfaces of space robots such as the Mars Odyssey Orbiter (La Duc et al., 2003). Cupriavidus and Ralstonia strains have also been found in-flight, in ISS cooling water and Shuttle drinking water (Venkateswaran et al., Pyle et al., Ott et al., all unpublished). The main objective of this study is to characterise the Cupriavidus and Ralstonia strains isolated at JPL and compare them to the Cupriavidus metallidurans CH34T model strain, isolated from a Belgian contaminated soil and studied since 25 years at SCK-CEN and to enhance our knowledge by performing additional tests at JPL and gathering information regarding the environmental conditions and the cleaning and isolation methods used in such spacecraft assembling facilities

  4. Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism - case study of Faecalibacterium prausnitzii

    Science.gov (United States)

    Prévoteau, Antonin; Geirnaert, Annelies; Arends, Jan B. A.; Lannebère, Sylvain; van de Wiele, Tom; Rabaey, Korneel

    2015-07-01

    Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 104 to 5 × 107 cells.mL-1). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM kcat = 5.3×105 s-1, at 37 °C) and glucose (KM = 6 μM kcat = 2.4 × 105 s-1). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.

  5. Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism--case study of Faecalibacterium prausnitzii.

    Science.gov (United States)

    Prévoteau, Antonin; Geirnaert, Annelies; Arends, Jan B A; Lannebère, Sylvain; Van de Wiele, Tom; Rabaey, Korneel

    2015-07-01

    Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 10(4) to 5 × 10(7) cells.mL(-1)). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM; kcat = 5.3 × 10(5) s(-1), at 37 °C) and glucose (KM = 6 μM; kcat = 2.4 × 10(5) s(-1)). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.

  6. Comparative gut physiology symposium: The microbe-gut-brain axis

    Science.gov (United States)

    The Comparative Gut Physiology Symposium titled “The Microbe-Gut-Brain Axis” was held at the Joint Annual Meeting of the American Society of Animal Science and the American Dairy Science Association on Thursday, July 21, 2016, in Salt Lake City Utah. The goal of the symposium was to present basic r...

  7. Tropical forest soil microbes and climate warming: An Andean-Amazon gradient and `SWELTR'

    Science.gov (United States)

    Nottingham, A.; Turner, B. L.; Fierer, N.; Whitaker, J.; Ostle, N. J.; McNamara, N. P.; Bardgett, R.; Silman, M.; Bååth, E.; Salinas, N.; Meir, P.

    2017-12-01

    Climate warming predicted for the tropics in the coming century will result in average temperatures under which no closed canopy forest exists today. There is, therefore, great uncertainty associated with the direction and magnitude of feedbacks between tropical forests and our future climate - especially relating to the response of soil microbes and the third of global soil carbon contained in tropical forests. While warming experiments are yet to be performed in tropical forests, natural temperature gradients are powerful tools to investigate temperature effects on soil microbes. Here we draw on studies from a 3.5 km elevation gradient - and 20oC mean annual temperature gradient - in Peruvian tropical forest, to investigate how temperature affects the structure of microbial communities, microbial metabolism, enzymatic activity and soil organic matter cycling. With decreased elevation, soil microbial diversity increased and community composition shifted, from taxa associated with oligotrophic towards copiotrophic traits. A key role for temperature in shaping these patterns was demonstrated by a soil translocation experiment, where temperature-manipulation altered the relative abundance of specific taxa. Functional implications of these community composition shifts were indicated by changes in enzyme activities, the temperature sensitivity of bacterial and fungal growth rates, and the presence of temperature-adapted iso-enzymes at different elevations. Studies from a Peruvian elevation transect indicated that soil microbial communities are adapted to long-term (differences with elevation) and short-term (translocation responses) temperature changes. These findings indicate the potential for adaptation of soil microbes in tropical soils to future climate warming. However, in order to evaluate the sensitivity of these processes to climate warming in lowland forests, in situ experimentation is required. Finally, we describe SWELTR (Soil Warming Experiment in Lowland

  8. Study on low frequency probe characterization for concrete application

    International Nuclear Information System (INIS)

    Amry Amin Abas; Mohd Pauzi Ismail

    2002-01-01

    Ultrasonic testing has been widely used in metal and non-metal material. For non-metal material such as concrete, a probe emitting low frequency ultrasonic wave is applied. This paper describes the comparison between three custom made probes using same design and piezoelectric crystal. The only difference is the backing material, which comprise of three different materials. Characterization of each transducer is compared in order to understand the effects of backing material in the probe. (Author)

  9. 73Se, an unusual PAC probe applied to the study of semiconductors

    International Nuclear Information System (INIS)

    Vianden, R.

    1990-01-01

    The isotope 73 Se was produced by an (α,3n) reaction from 72 Ge in order to study the applicability of this probe to PAC defect studies in semiconductors. Measurements before and after annealing recoil implanted samples showed that the quadrupole interaction of the 66 keV state in the daughter isotope 73 As with the lattice damage created by the implantation is comparable to that found for 111 In in Ge. This indicates that 73 Se can be a suitable probe for defect studies in semiconductors with nuclear methods. (orig.)

  10. Progress of CRISPR-Cas based genome editing in Photosynthetic microbes

    NARCIS (Netherlands)

    Naduthodi, M.I.S.; Barbosa, M.J.; Oost, van der J.

    2018-01-01

    The carbon footprint caused by unsustainable development and its environmental and economic impact has become a major concern in the past few decades. Photosynthetic microbes such as microalgae and cyanobacteria are capable of accumulating value-added compounds from carbon dioxide, and have been

  11. Minimizing mixing intensity to improve the performance of rice straw anaerobic digestion via enhanced development of microbe-substrate aggregates.

    Science.gov (United States)

    Kim, Moonkyung; Kim, Byung-Chul; Choi, Yongju; Nam, Kyoungphile

    2017-12-01

    The aim of this work was to study the effect of the differential development of microbe-substrate aggregates at different mixing intensities on the performance of anaerobic digestion of rice straw. Batch and semi-continuous reactors were operated for up to 50 and 300days, respectively, under different mixing intensities. In both batch and semi-continuous reactors, minimal mixing conditions exhibited maximum methane production and lignocellulose biodegradability, which both had strong correlations with the development of microbe-substrate aggregates. The results implied that the aggregated microorganisms on the particulate substrate played a key role in rice straw hydrolysis, determining the performance of anaerobic digestion. Increasing the mixing speed from 50 to 150rpm significantly reduced the methane production rate by disintegrating the microbe-substrate aggregates in the semi-continuous reactor. A temporary stress of high-speed mixing fundamentally affected the microbial communities, increasing the possibility of chronic reactor failure. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Heavy Metal Stress, Signaling, and Tolerance Due to Plant-Associated Microbes: An Overview

    Science.gov (United States)

    Tiwari, Shalini; Lata, Charu

    2018-01-01

    Several anthropogenic activities including mining, modern agricultural practices, and industrialization have long-term detrimental effect on our environment. All these factors lead to increase in heavy metal concentration in soil, water, and air. Soil contamination with heavy metals cause several environmental problems and imparts toxic effect on plant as well as animals. In response to these adverse conditions, plants evolve complex molecular and physiological mechanisms for better adaptability, tolerance, and survival. Nowadays conventional breeding and transgenic technology are being used for development of metal stress resistant varieties which, however, are time consuming and labor intensive. Interestingly the use of microbes as an alternate technology for improving metal tolerance of plants is gaining momentum recently. The use of these beneficial microorganisms is considered as one of the most promising methods for safe crop-management practices. Interaction of plants with soil microorganisms can play a vital role in acclimatizing plants to metalliferous environments, and can thus be explored to improve microbe-assisted metal tolerance. Plant-associated microbes decrease metal accumulation in plant tissues and also help to reduce metal bioavailability in soil through various mechanisms. Nowadays, a novel phytobacterial strategy, i.e., genetically transformed bacteria has been used to increase remediation of heavy metals and stress tolerance in plants. This review takes into account our current state of knowledge of the harmful effects of heavy metal stress, the signaling responses to metal stress, and the role of plant-associated microbes in metal stress tolerance. The review also highlights the challenges and opportunities in this continued area of research on plant–microbe–metal interaction. PMID:29681916

  13. Nitrilase enzymes and their role in plant–microbe interactions

    Science.gov (United States)

    Howden, Andrew J. M.; Preston, Gail M.

    2009-01-01

    Summary Nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. Nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms is relatively underexplored. Current research suggests that nitrilases play important roles in a range of biological processes. In the context of plant–microbe interactions they may have roles in hormone synthesis, nutrient assimilation and detoxification of exogenous and endogenous nitriles. Nitrilases are produced by both plant pathogenic and plant growth‐promoting microorganisms, and their activities may have a significant impact on the outcome of plant–microbe interactions. In this paper we review current knowledge of the role of nitriles and nitrilases in plants and plant‐associated microorganisms, and discuss how greater understanding of the natural functions of nitrilases could be applied to benefit both industry and agriculture. PMID:21255276

  14. Microbes, Minerals and Electrodes at the Sanford Underground Research Facility (SURF): Electrochemistry 4100 ft below the surface.

    Science.gov (United States)

    Rowe, A. R.; Abuyen, K.; Casar, C. P.; Osburn, M. R.; Kruger, B.; El-Naggar, M.; Amend, J.

    2017-12-01

    Little is known about the importance of mineral oxidation processes in subsurface environments. This stems, in part from our limited insight into the biochemistry of many of these metabolisms, especially where redox interactions with solid surfaces is concerned. To this aim, we have been developing electrochemical cultivation techniques, to target enrichment and isolation of microbes capable of oxidative extracellular electron transfer (oxEET)—transfer of electrons from the exterior of the cell to the interior. Our previous worked focused on marine sediments; using an electrode poised at a given redox potential to isolate mineral-oxidizing microbes. Electrode oxidizing microbes isolated from these enrichments belong to the genera Thioclava, Marinobacter, Halomonas, Idiomarina, Thalassospira, and Pseudamonas; organisms commonly detected in marine and deep sea sediments but not generally associated with mineral, sulfur and/or iron oxidation. At the Sanford Underground Research Facility (SURF) in Leed, South Dakota, we have been utilizing similar electrocultivation techniques to understand: 1) the potential for mineral oxidation by subsurface microbes, 2) their selective colonization on mineral vs. electrode surfaces, as well as 3) the community composition of microbes capable of these metabolic interactions. An electrochemical and mineral enrichment scheme was designed and installed into a sulfidic groundwater flow, located at the 4100 ft level of the former gold mine. The communities enriched on electrodes (graphite and indium tin oxide coated glass) and minerals (sulfur, pyrite, and schists from the location) were compared to the long-term ground water microbial community observed. Ultimately, these observations will help inform the potential activity of a lithotrophic microbes in situ and will in turn guide our culturing efforts.

  15. 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

    2011-01-01

    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. PMID:21873232

  16. The Physical Microbe; An introduction to noise, control, and communication in the prokaryotic cell

    Science.gov (United States)

    Hagen, Stephen J.

    2017-10-01

    Physical biology is a fusion of biology and physics. This book narrows down the scope of physical biology by focusing on the microbial cell; exploring the physical phenomena of noise, feedback, and variability that arise in the cellular information-processing circuits used by bacteria. It looks at the microbe from a physics perspective, asking how the cell optimizes its function to live within the constraints of physics. It introduces a physical and information-based (as opposed to microbiological) perspective on communication and signalling between microbes.

  17. Mechanistic studies of the genetically encoded fluorescent protein voltage probe ArcLight.

    Directory of Open Access Journals (Sweden)

    Zhou Han

    Full Text Available ArcLight, a genetically encoded fluorescent protein voltage probe with a large ΔF/ΔV, is a fusion between the voltage sensing domain of the Ciona instestinalis voltage sensitive phosphatase and super ecliptic pHluorin carrying a single mutation (A227D in the fluorescent protein. Without this mutation the probe produces only a very small change in fluorescence in response to voltage deflections (∼ 1%. The large signal afforded by this mutation allows optical detection of action potentials and sub-threshold electrical events in single-trials in vitro and in vivo. However, it is unclear how this single mutation produces a probe with such a large modulation of its fluorescence output with changes in membrane potential. In this study, we identified which residues in super ecliptic pHluorin (vs eGFP are critical for the ArcLight response, as a similarly constructed probe based on eGFP also exhibits large response amplitude if it carries these critical residues. We found that D147 is responsible for determining the pH sensitivity of the fluorescent protein used in these probes but by itself does not result in a voltage probe with a large signal. We also provide evidence that the voltage dependent signal of ArcLight is not simply sensing environmental pH changes. A two-photon polarization microscopy study showed that ArcLight's response to changes in membrane potential includes a reorientation of the super ecliptic pHluorin. We also explored different changes including modification of linker length, deletion of non-essential amino acids in the super ecliptic pHluorin, adding a farnesylation site, using tandem fluorescent proteins and other pH sensitive fluorescent proteins.

  18. Multifrequency scanning probe microscopy study of nanodiamond agglomerates

    Science.gov (United States)

    Aravind, Vasudeva; Lippold, Stephen; Li, Qian; Strelcov, Evgheny; Okatan, Baris; Legum, Benjamin; Kalinin, Sergei; Clarion University Team; Oak Ridge National Laboratory Team

    Due to their rich surface chemistry and excellent mechanical properties and non-toxic nature, nanodiamond particles have found applications such as biomedicine, tribology and lubrication, targeted drug delivery systems, tissue scaffolds and surgical implants. Although single nanodiamond particles have diameters about 4-5nm, they tend to form agglomerates. While these agglomerates can be useful for some purposes, many applications of nanodiamonds require single particle, disaggregated nanodiamonds. This work is oriented towards studying forces and interactions that contribute to agglomeration in nanodiamonds. In this work, using multifrequency scanning probe microscopy techniques, we show that agglomerate sizes can vary between 50-100nm in raw nanodiamonds. Extremeties of particles and Interfaces between agglomerates show dissipative forces with scanning probe microscope tip, indicating agglomerates could act as points of increased adhesion, thus reducing lubricating efficiency when nanodiamonds are used as lubricant additives. This research was conducted at the Center for Nanophase Materials Sciences, which is a DOE Office of Science User Facility.

  19. Potential impact of global climate change on benthic deep-sea microbes.

    Science.gov (United States)

    Danovaro, Roberto; Corinaldesi, Cinzia; Dell'Anno, Antonio; Rastelli, Eugenio

    2017-12-15

    Benthic deep-sea environments are the largest ecosystem on Earth, covering ∼65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH) and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor). However, the responses of the benthic deep-sea biota to such shifts remain largely unknown. This applies particularly to deep-sea microbes, which include bacteria, archaea, microeukaryotes and their viruses. Understanding the potential impacts of global change on the benthic deep-sea microbial assemblages and the consequences on the functioning of the ocean interior is a priority to better forecast the potential consequences at global scale. Here we explore the potential changes in the benthic deep-sea microbiology expected in the coming decades using case studies on specific systems used as test models. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. Dual-probe decoherence microscopy: probing pockets of coherence in a decohering environment

    International Nuclear Information System (INIS)

    Jeske, Jan; Cole, Jared H; Müller, Clemens; Marthaler, Michael; Schön, Gerd

    2012-01-01

    We study the use of a pair of qubits as a decoherence probe of a nontrivial environment. This dual-probe configuration is modelled by three two-level systems (TLSs), which are coupled in a chain in which the middle system represents an environmental TLS. This TLS resides within the environment of the qubits and therefore its coupling to perturbing fluctuations (i.e. its decoherence) is assumed much stronger than the decoherence acting on the probe qubits. We study the evolution of such a tripartite system including the appearance of a decoherence-free state (dark state) and non-Markovian behaviour. We find that all parameters of this TLS can be obtained from measurements of one of the probe qubits. Furthermore, we show the advantages of two qubits in probing environments and the new dynamics imposed by a TLS that couples to two qubits at once. (paper)

  1. Microbes at Surface-Air Interfaces: The Metabolic Harnessing of Relative Humidity, Surface Hygroscopicity, and Oligotrophy for Resilience

    Science.gov (United States)

    Stone, Wendy; Kroukamp, Otini; Korber, Darren R.; McKelvie, Jennifer; Wolfaardt, Gideon M.

    2016-01-01

    The human environment is predominantly not aqueous, and microbes are ubiquitous at the surface-air interfaces with which we interact. Yet microbial studies at surface-air interfaces are largely survival-oriented, whilst microbial metabolism has overwhelmingly been investigated from the perspective of liquid saturation. This study explored microbial survival and metabolism under desiccation, particularly the influence of relative humidity (RH), surface hygroscopicity, and nutrient availability on the interchange between these two phenomena. The combination of a hygroscopic matrix (i.e., clay or 4,000 MW polyethylene glycol) and high RH resulted in persistent measurable microbial metabolism during desiccation. In contrast, no microbial metabolism was detected at (a) hygroscopic interfaces at low RH, and (b) less hygroscopic interfaces (i.e., sand and plastic/glass) at high or low RH. Cell survival was conversely inhibited at high RH and promoted at low RH, irrespective of surface hygroscopicity. Based on this demonstration of metabolic persistence and survival inhibition at high RH, it was proposed that biofilm metabolic rates might inversely influence whole-biofilm resilience, with ‘resilience’ defined in this study as a biofilm’s capacity to recover from desiccation. The concept of whole-biofilm resilience being promoted by oligotrophy was supported in desiccation-tolerant Arthrobacter spp. biofilms, but not in desiccation-sensitive Pseudomonas aeruginosa biofilms. The ability of microbes to interact with surfaces to harness water vapor during desiccation was demonstrated, and potentially to harness oligotrophy (the most ubiquitous natural condition facing microbes) for adaptation to desiccation. PMID:27746774

  2. Evolution, human-microbe interactions, and life history plasticity.

    Science.gov (United States)

    Rook, Graham; Bäckhed, Fredrik; Levin, Bruce R; McFall-Ngai, Margaret J; McLean, Angela R

    2017-07-29

    A bacterium was once a component of the ancestor of all eukaryotic cells, and much of the human genome originated in microorganisms. Today, all vertebrates harbour large communities of microorganisms (microbiota), particularly in the gut, and at least 20% of the small molecules in human blood are products of the microbiota. Changing human lifestyles and medical practices are disturbing the content and diversity of the microbiota, while simultaneously reducing our exposures to the so-called old infections and to organisms from the natural environment with which human beings co-evolved. Meanwhile, population growth is increasing the exposure of human beings to novel pathogens, particularly the crowd infections that were not part of our evolutionary history. Thus some microbes have co-evolved with human beings and play crucial roles in our physiology and metabolism, whereas others are entirely intrusive. Human metabolism is therefore a tug-of-war between managing beneficial microbes, excluding detrimental ones, and channelling as much energy as is available into other essential functions (eg, growth, maintenance, reproduction). This tug-of-war shapes the passage of each individual through life history decision nodes (eg, how fast to grow, when to mature, and how long to live). Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. NASA and international studies of the Solar Probe Mission

    Science.gov (United States)

    Randolph, James E.

    1992-01-01

    A review is presented summarizing the history and current status of the studies of the Solar Probe Mission by NASA and other space agencies. The technology and scientific challenges of the mission are addressed in these studies and can be met with current instrument and technology capabilities. The specific set of experiments recommended by a scientific advisory group to the NASA study for integration into the design concept is discussed.

  4. 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.

  5. 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.

  6. Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes.

    Directory of Open Access Journals (Sweden)

    Martin Laurence

    Full Text Available Unbiased high-throughput sequencing of whole metagenome shotgun DNA libraries is a promising new approach to identifying microbes in clinical specimens, which, unlike other techniques, is not limited to known sequences. Unlike most sequencing applications, it is highly sensitive to laboratory contaminants as these will appear to originate from the clinical specimens. To assess the extent and diversity of sequence contaminants, we aligned 57 "1000 Genomes Project" sequencing runs from six centers against the four largest NCBI BLAST databases, detecting reads of diverse contaminant species in all runs and identifying the most common of these contaminant genera (Bradyrhizobium in assembled genomes from the NCBI Genome database. Many of these microorganisms have been reported as contaminants of ultrapure water systems. Studies aiming to identify novel microbes in clinical specimens will greatly benefit from not only preventive measures such as extensive UV irradiation of water and cross-validation using independent techniques, but also a concerted effort to sequence the complete genomes of common contaminants so that they may be subtracted computationally.

  7. Comparative study of size dependent four-point probe sheet resistance measurement on laser annealed ultra-shallow junctions

    DEFF Research Database (Denmark)

    Petersen, Dirch Hjorth; Lin, Rong; Hansen, Torben Mikael

    2008-01-01

    have been used to characterize the sheet resistance uniformity of millisecond laser annealed USJs. They verify, both experimentally and theoretically, that the probe pitch of a four-point probe can strongly affect the measured sheet resistance. Such effect arises from the sensitivity (or "spot size......In this comparative study, the authors demonstrate the relationship/correlation between macroscopic and microscopic four-point sheet resistance measurements on laser annealed ultra-shallow junctions (USJs). Microfabricated cantilever four-point probes with probe pitch ranging from 1.5 to 500 mu m......") of an in-line four-point probe. Their study shows the benefit of the spatial resolution of the micro four-point probe technique to characterize stitching effects resulting from the laser annealing process....

  8. Does plant-Microbe interaction confer stress tolerance in plants: A review?

    Science.gov (United States)

    Kumar, Akhilesh; Verma, Jay Prakash

    2018-03-01

    The biotic and abiotic stresses are major constraints for crop yield, food quality and global food security. A number of parameters such as physiological, biochemical, molecular of plants are affected under stress condition. Since the use of inorganic fertilizers and pesticides in agriculture practices cause degradation of soil fertility and environmental pollutions. Hence it is necessary to develop safer and sustainable means for agriculture production. The application of plant growth promoting microbes (PGPM) and mycorrhizal fungi enhance plant growth, under such conditions. It offers an economically fascinating and ecologically sound ways for protecting plants against stress condition. PGPM may promote plant growth by regulating plant hormones, improve nutrition acquisition, siderophore production and enhance the antioxidant system. While acquired systemic resistance (ASR) and induced systemic resistance (ISR) effectively deal with biotic stress. Arbuscular mycorrhiza (AM) enhance the supply of nutrients and water during stress condition and increase tolerance to stress. This plant-microbe interaction is vital for sustainable agriculture and industrial purpose, because it depends on biological processes and replaces conventional agriculture practices. Therefore, microbes may play a key role as an ecological engineer to solve environmental stress problems. So, it is a feasible and potential technology in future to feed global population at available resources with reduced impact on environmental quality. In this review, we have attempted to explore about abiotic and biotic stress tolerant beneficial microorganisms and their modes of action to enhance the sustainable agricultural production. Copyright © 2017 Elsevier GmbH. All rights reserved.

  9. Heavy Metal Stress, Signaling, and Tolerance Due to Plant-Associated Microbes: An Overview

    Directory of Open Access Journals (Sweden)

    Shalini Tiwari

    2018-04-01

    Full Text Available Several anthropogenic activities including mining, modern agricultural practices, and industrialization have long-term detrimental effect on our environment. All these factors lead to increase in heavy metal concentration in soil, water, and air. Soil contamination with heavy metals cause several environmental problems and imparts toxic effect on plant as well as animals. In response to these adverse conditions, plants evolve complex molecular and physiological mechanisms for better adaptability, tolerance, and survival. Nowadays conventional breeding and transgenic technology are being used for development of metal stress resistant varieties which, however, are time consuming and labor intensive. Interestingly the use of microbes as an alternate technology for improving metal tolerance of plants is gaining momentum recently. The use of these beneficial microorganisms is considered as one of the most promising methods for safe crop-management practices. Interaction of plants with soil microorganisms can play a vital role in acclimatizing plants to metalliferous environments, and can thus be explored to improve microbe-assisted metal tolerance. Plant-associated microbes decrease metal accumulation in plant tissues and also help to reduce metal bioavailability in soil through various mechanisms. Nowadays, a novel phytobacterial strategy, i.e., genetically transformed bacteria has been used to increase remediation of heavy metals and stress tolerance in plants. This review takes into account our current state of knowledge of the harmful effects of heavy metal stress, the signaling responses to metal stress, and the role of plant-associated microbes in metal stress tolerance. The review also highlights the challenges and opportunities in this continued area of research on plant–microbe–metal interaction.

  10. Plant-microbe interaction in aquatic system and their role in the management of water quality: a review

    Science.gov (United States)

    Srivastava, Jatin K.; Chandra, Harish; Kalra, Swinder J. S.; Mishra, Pratibha; Khan, Hena; Yadav, Poonam

    2017-06-01

    Microbial assemblage as biofilm around the aquatic plant forms a firm association that largely depends upon the mutual supplies of nutrients, e.g., microbes interact with plants in an aquatic system most likely for organic carbon and oxygen, whereas plants receive defensive immunity and mineral exchange. Apart from the mutual benefits, plant-microbe interactions also influence the water quality especially at rhizosphere providing inherent ability to the aquatic system for the mitigation of pollution from the water column. The review presents and in-depth information along with certain research advancements made in the field of ecological and bio/chemical aspects of plant-microbe interactions and the underlying potential to improve water quality.

  11. Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans

    DEFF Research Database (Denmark)

    Zhang, Li; Bahl, Martin Iain; Roager, Henrik Munch

    2017-01-01

    Microbiota transplantation to germ-free animals is a powerful method to study involvement of gut microbes in the aetiology of metabolic syndrome. Owing to large interpersonal variability in gut microbiota, studies with broad coverage of donors are needed to elucidate the establishment of human......, thereby allowing us to explore the extent of microbial spread between cages in a well-controlled environment. Despite high group-wise similarity between obese and control human microbiotas, transplanted mice in the four isolators developed distinct gut bacterial composition and activity, body mass gain......, and insulin resistance. Spread of microbes between cages within isolators interacted with establishment of the transplanted microbiotas in mice, and contributed to the transmission of metabolic phenotypes. Our findings highlight the impact of donor variability and reveal that inter-individual spread...

  12. Aminoacid composition of wheat grain gluten under microbe impact

    Directory of Open Access Journals (Sweden)

    Sokolova М. G.

    2012-11-01

    Full Text Available The study was focused on characteristics of gluten, protein and aminoacids content in wheat grain under the impact of microbe preparations including bacteria of Azotobacter and Bacillus geni, which inhabit plant rhizosphere. The increase of aminoacids leveland particularly the level of essential aminoacids in wheat grain under bacterization was demonstrated, this fact accounting for the quality of grain as an important protein source. Increase of aminoacids content with the use of biopreparations on low-fertile soil ensures acquisition of biologically valuable grain with the decrease of mineral fertilizers dosage and emphasizes the role of biopreparations in the production of ecologically pure high quality products. The latter is due to introdcution of environmentally safe agricultural methods.

  13. Metagenomics, metaMicrobesOnline and Kbase Data Integration (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Dehal, Paramvir

    2011-10-12

    Berkeley Lab's Paramvir Dehal on "Managing and Storing large Datasets in MicrobesOnline, metaMicrobesOnline and the DOE Knowledgebase" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  14. Microbe assisted phyto remediation of oil sludge and role of amendments: a mesocosm study

    International Nuclear Information System (INIS)

    Nanekar, S; Dhote, M.; Kashyap, S.; Singh, S. K.; Juwarkar, A. A.

    2015-01-01

    A mescosom study was evaluated to the influence of amendments such as microbial consortium, plant (Vetiveria zizanioides), bulking agent (wheat husk) and nutrients on remediation of oil sludge over a period of 90 days. The experiment was conducted in a 15 m2 plot which was divided into eight units comprising of soil sludge mixture (1:1) at CSIR-NEERI premises. During the experiment, oil degradation was estimated gravimetrically and poly aromatic hydrocarbons were quantified on GC-MS. Additionally, dehydrogenase activity was also monitored. The treatment integrated with bulking agent, nutrients, consortium and plant resulted in 28-fold increased dehydrogenase activity and complete mineralization of higher poly aromatic hydrocarbons. Furthermore, 72.8 % total petroleum hydrocarbons degradation was observed in bulked treatment with plant, nutrients and consortium followed by 69.6 and 65.4 % in bioaugmented treatments with and without nutrients, respectively, as compared to control (33.4 %). A lysimeter study was also conducted simultaneously using Vetiver and consortium to monitor groundwater contamination by heavy metals in oil sludge which showed a marked decrease in the concentrations of metals such as lead and cadmium in leachates. This study validates a holistic approach for remediation of oil sludge contaminated soils/sites which is a burning issue since decades by the use of microbe assisted phyto remediation technology which not only solves the problem of oil contamination but also takes care of heavy metal contamination.

  15. Do volatiles produced by nectar-dwelling microbes affect honey bee preferences?

    Science.gov (United States)

    The microbiome of plants mediates many interactions in natural and managed systems. Among these, plant-pollinator interactions are important for ensuring high crop yields, pollinator health and successful plant reproduction. Despite initial work demonstrating effects of floral microbes on pollinatio...

  16. 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.

  17. Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes

    OpenAIRE

    Saad Rama; Rizkallah Mariam R; Aziz Ramy K

    2012-01-01

    Abstract The influence of resident gut microbes on xenobiotic metabolism has been investigated at different levels throughout the past five decades. However, with the advance in sequencing and pyrotagging technologies, addressing the influence of microbes on xenobiotics had to evolve from assessing direct metabolic effects on toxins and botanicals by conventional culture-based techniques to elucidating the role of community composition on drugs metabolic profiles through DNA sequence-based ph...

  18. Microfour-point probe for studying electronic transport through surface states

    DEFF Research Database (Denmark)

    Petersen, Christian Leth; Grey, Francois; Shiraki, I.

    2000-01-01

    Microfour-point probes integrated on silicon chips have been fabricated with probe spacings in the range 4-60 mum. They provide a simple robust device for electrical transport measurements at surfaces, bridging the gap between conventional macroscopic four-point probes and scanning tunneling...... transport through surface states, which is not observed on the macroscopic scale, presumably due to scattering at atomic steps. (C) 2000 American Institute of Physics....

  19. 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…

  20. Mobile Probing and Probes

    DEFF Research Database (Denmark)

    Duvaa, Uffe; Ørngreen, Rikke; Weinkouff Mathiasen, Anne-Gitte

    2013-01-01

    Mobile probing is a method, developed for learning about digital work situations, as an approach to discover new grounds. The method can be used when there is a need to know more about users and their work with certain tasks, but where users at the same time are distributed (in time and space......). Mobile probing was inspired by the cultural probe method, and was influenced by qualitative interview and inquiry approaches. The method has been used in two subsequent projects, involving school children (young adults at 15-17 years old) and employees (adults) in a consultancy company. Findings point...... to mobile probing being a flexible method for uncovering the unknowns, as a way of getting rich data to the analysis and design phases. On the other hand it is difficult to engage users to give in depth explanations, which seem easier in synchronous dialogs (whether online or face2face). The development...

  1. Mobile Probing and Probes

    DEFF Research Database (Denmark)

    Duvaa, Uffe; Ørngreen, Rikke; Weinkouff, Anne-Gitte

    2012-01-01

    Mobile probing is a method, which has been developed for learning about digital work situations, as an approach to discover new grounds. The method can be used when there is a need to know more about users and their work with certain tasks, but where users at the same time are distributed (in time...... and space). Mobile probing was inspired by the cultural probe method, and was influenced by qualitative interview and inquiry approaches. The method has been used in two subsequent projects, involving school children (young adults at 15-17 years old) and employees (adults) in a consultancy company. Findings...... point to mobile probing being a flexible method for uncovering the unknowns, as a way of getting rich data to the analysis and design phases. On the other hand it is difficult to engage users to give in depth explanations, which seem easier in synchronous dialogs (whether online or face2face...

  2. Characterization of coating probe with Ti-DLC for electrical scanning probe microscope

    International Nuclear Information System (INIS)

    Shia Xiaolei; Guo Liqiu; Bai Yang; Qiao Lijie

    2011-01-01

    In electrical scanning probe microscope (ESPM) applications, the wear and conductivity of the probe are undoubtedly serious concerns since they affect the integrity of the measurements. This study investigates the characterization of Ti doped diamond-like-carbon (DLC) as coating material on a silicon cantilever for ESPM. We deposited a layer of Ti-DLC thin film on the surface of Si cantilever by magnetron sputtering. The morphology and composition of the Ti-DLC films were characterized by scanning electron microscopy and Raman spectroscopy, respectively. We also compared the wear resistance, electric conductivity and scanning image quality of the Ti-DLC-coated probes with those of commercially available conductive probes. The results showed that the electric conductivity and the scanning image quality of the Ti-DLC-coated probes were the same as the commercial conductive probes, while the wear resistance and service life was significantly better.

  3. 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.

  4. Nitrilase enzymes and their role in plant-microbe interactions.

    Science.gov (United States)

    Howden, Andrew J M; Preston, Gail M

    2009-07-01

    Nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. Nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms is relatively underexplored. Current research suggests that nitrilases play important roles in a range of biological processes. In the context of plant-microbe interactions they may have roles in hormone synthesis, nutrient assimilation and detoxification of exogenous and endogenous nitriles. Nitrilases are produced by both plant pathogenic and plant growth-promoting microorganisms, and their activities may have a significant impact on the outcome of plant-microbe interactions. In this paper we review current knowledge of the role of nitriles and nitrilases in plants and plant-associated microorganisms, and discuss how greater understanding of the natural functions of nitrilases could be applied to benefit both industry and agriculture. © 2009 The Authors. Journal compilation © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

  5. Accuracy of probing attachment levels using a new computerized cemento-enamel junction probe.

    Science.gov (United States)

    Deepa, R; Prakash, Shobha

    2012-01-01

    The assessment of clinical attachment level (CAL) represents the gold standard for diagnosing and monitoring periodontal disease. The aim of the present study was to evaluate the performance of the newly introduced cemento-enamel junction (CEJ) probe in detecting CAL, using CEJ as a fixed reference point, and to compare the CEJ probe with the Florida stent probe (FSP) as well as with a standard manual probe, University of North Carolina-15 (UNC-15). Three examiners recorded the probing attachment level in 384 sites in case group (chronic periodontitis), and in 176 sites, in control group (healthy periodontal status), using the three probes. Subjects included both the sexes and ranged from 35 to 45 years. The experimental design was structured to balance the intra- and inter-examiner consistency at the same site during the two visits. CEJ probe showed higher intra-and inter-examiner consistency over both FSP and UNC-15 in both the case and control groups. Frequency distribution of differences of various magnitudes of repeated measurements ≤1 mm was in the higher range of 86.8% to 87.5% for CEJ probe. The FSP was more reproducible than UNC-15 in detecting relative attachment level (RAL). CEJ automated probe was found to have greatest potential for accuracy and consistency in detecting CAL than FSP and UNC-15. The automated probes appeared to be more reproducible than manual probes.

  6. Effect of cryopreservation and lyophilization on viability and growth of strict anaerobic human gut microbes.

    Science.gov (United States)

    Bircher, Lea; Geirnaert, Annelies; Hammes, Frederik; Lacroix, Christophe; Schwab, Clarissa

    2018-04-17

    Strict anaerobic gut microbes have been suggested as 'next-generation probiotics' for treating several intestinal disorders. The development of preservation techniques is of major importance for therapeutic application. This study investigated cryopreservation (-80°C) and lyophilization survival and storage stability (4°C for 3 months) of the strict anaerobic gut microbes Bacteroides thetaiotaomicron, Faecalibacterium prausnitzii, Roseburia intestinalis, Anaerostipes caccae, Eubacterium hallii and Blautia obeum. To improve preservation survival, protectants sucrose and inulin (both 5% w/v) were added for lyophilization and were also combined with glycerol (15% v/v) for cryopreservation. Bacterial fitness, evaluated by maximum growth rate and lag phase, viability and membrane integrity were determined using a standardized growth assay and by flow cytometry as markers for preservation resistance. Lyophilization was more detrimental to viability and fitness than cryopreservation, but led to better storage stability. Adding sucrose and inulin enhanced viability and the proportion of intact cells during lyophilization of all strains. Viability of protectant-free B. thetaiotaomicron, A. caccae and F. prausnitzii was above 50% after cryopreservation and storage and increased to above 80% if protectants were present. The addition of glycerol, sucrose and inulin strongly enhanced the viability of B. obeum, E. hallii and R. intestinalis from 0.03-2% in protectant-free cultures to 11-37%. This is the first study that quantitatively compared the effect of cryopreservation and lyophilization and the addition of selected protectants on viability and fitness of six strict anaerobic gut microbes. Our results suggest that efficiency of protectants is process- and species-specific. © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  7. Preparation and quality test of superparamagnetic iron oxide labeled antisense oligodeoxynucleotide probe: a preliminary study.

    Science.gov (United States)

    Wen, Ming; Li, Bibo; Ouyang, Yu; Luo, Yi; Li, Shaolin

    2009-06-01

    Molecular imaging of tumor antisense gene techniques have been applied to the study of magnetic resonance (MR) gene imaging associated with malignant tumors. In this study, we designed, synthesized, and tested a novel molecular probe, in which the antisense oligodeoxynucleotide (ASODN) was labeled with superparamagnetic iron oxide (SPIO), and its efficiency was examined by in vitro MR imaging after SK-Br-3 mammary carcinoma cell lines (oncocytes) transfection. The SPIO-labeled ASODN probe was prepared through SPIO conjugated to ASODN using a chemical cross linking method. Its morphology and size were detected by atomic force microscope, size distribution were detected by laser granulometer, the conjugating rate and biological activity were determined by high performance liquid chromatography, and the stability was determined by polyacrylamide gel electrophoresis. After that, the probes were transfected into the SK-Br-3 oncocytes, cellular iron uptake was analyzed qualitatively at light and electron microscopy and was quantified at atomic absorption spectrometry, and the signal change of the transfected cells was observed and measured using MR imaging. The morphology of the SPIO-labeled ASODN probe was mostly spherical with well-distributed scattering, and the diameters were between 25 and 40 nm (95%) by atomic force microscope and laser granulometer, the conjugating rate of the probe was 99%. Moreover, this probe kept its activity under physiological conditions and could conjugate with antisense oligodeoxynucleotide. In addition, light microscopy revealed an intracellular uptake of iron oxides in the cytosol and electron microscopic studies revealed a lysosomal deposition of iron oxides in the transfected SK-Br-3 oncocytes by antisense probes, some of them gathered stacks, and the iron content of the group of transfected SK-Br-3 oncocytes by antisense probe is significantly higher (18.37 +/- 0.42 pg) than other contrast groups, the MR imaging showed that

  8. [Effects of different organic fertilizers on the microbes in rhizospheric soil of flue-cured tobacco].

    Science.gov (United States)

    Zhang, Yun-Wei; Xu, Zhi; Tang, Li; Li, Yan-Hong; Song, Jian-Qun; Xu, Jian-Qin

    2013-09-01

    A field experiment was conducted to study the effects of applying different organic fertilizers (refined organic fertilizer and bio-organic fertilizer) and their combination with 20% reduced chemical fertilizers on the microbes in rhizospheric soil of flue-cured tobacco, the resistance of the tobacco against bacterial wilt, and the tobacco yield and quality. As compared with conventional chemical fertilization (CK), applying refined organic fertilizer (ROF) or bio-organic fertilizer (BIO) in combining with 20% reduced chemical fertilization increased the bacterial number and the total microbial number in the rhizospheric soil significantly. Applying BIO in combining with 20% reduced chemical fertilization also increased the actinomyces number in the rhizospheric soil significantly, with an increment of 44.3% as compared with that under the application of ROF in combining with 20% reduced chemical fertilization, but decreased the fungal number. As compared with CK, the ROF and BIO increased the carbon use capacity of rhizospheric microbes significantly, and the BIO also increased the capacity of rhizospheric microbes in using phenols significantly. Under the application of ROF and BIO, the disease incidence and the disease index of bacterial wilt were decreased by 4% and 8%, and 23% and 15.9%, and the proportions of high grade tobacco leaves increased significantly by 10.5% and 9.7%, respectively, as compared with those in CK. BIO increased the tobacco yield and its output value by 17.1% and 18.9% , respectively, as compared with ROF.

  9. Applications of DNA-Stable Isotope Probing in Bioremediation Studies

    Science.gov (United States)

    Chen, Yin; Vohra, Jyotsna; Murrell, J. Colin

    DNA-stable isotope probing, a method to identify active microorganisms without the prerequisite of cultivation, has been widely applied in the study of microorganisms involved in the degradation of environmental pollutants. Recent advances and technique considerations in applying DNA-SIP in bioremediation are highlighted. A detailed protocol of a DNA-SIP experiment is provided.

  10. Study of Perylenetetracarboxylic Acid Dimethylimide Films by Cyclic Thermal Desorption and Scanning Probe Microscopy

    Science.gov (United States)

    Pochtennyi, A. E.; Lappo, A. N.; Il'yushonok, I. P.

    2018-02-01

    Some results of studying the direct-current (DC) conductivity of perylenetetracarboxylic acid dimethylimide films by cyclic oxygen thermal desorption are presented. The microscopic parameters of hopping electron transport over localized impurity and intrinsic states were determined. The bandgap width and the sign of major current carriers were determined by scanning probe microscopy methods (atomic force microscopy, scanning probe spectroscopy, and photoassisted Kelvin probe force microscopy). The possibility of the application of photoassisted scanning tunneling microscopy for the nanoscale phase analysis of photoconductive films is discussed.

  11. Grow Plants the Organic Way: Give Them the Soil Microbes They Crave

    Directory of Open Access Journals (Sweden)

    Phil Mixter

    2013-03-01

    Full Text Available Review of: Teaming with Microbes: The Organic Gardener’s Guide to the Soil Food Web, revised ed.; Jeff Lowenfels and Wayne Lewis; (2010. Timber Press Inc., Portland, OR. 220 pages.

  12. Life Redefined: Microbes Built with Arsenic

    Energy Technology Data Exchange (ETDEWEB)

    Webb, Sam (SLAC and Felisa Wolfe-Simon, NASA and U.S. Geological Survey)

    2011-03-22

    Life can survive in many harsh environments, from extreme heat to the presence of deadly chemicals. However, life as we know it has always been based on the same six elements -- carbon, oxygen, nitrogen, hydrogen, sulfur and phosphorus. Now it appears that even this rule has an exception. In the saline and poisonous environment of Mono Lake, researchers have found a bacterium that can grow by incorporating arsenic into its structure in place of phosphorus. X-ray images taken at SLAC's synchrotron light source reveal that this microbe may even use arsenic as a building block for DNA. Please join us as we describe this discovery, which rewrites the textbook description of how living cells work.

  13. Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators.

    Science.gov (United States)

    Vannette, Rachel L; Fukami, Tadashi

    2016-06-01

    Secondary metabolites that are present in floral nectar have been hypothesized to enhance specificity in plant-pollinator mutualism by reducing larceny by non-pollinators, including microorganisms that colonize nectar. However, few studies have tested this hypothesis. Using synthetic nectar, we conducted laboratory and field experiments to examine the effects of five chemical compounds found in nectar on the growth and metabolism of nectar-colonizing yeasts and bacteria, and the interactive effects of these compounds and nectar microbes on the consumption of nectar by pollinators. In most cases, focal compounds inhibited microbial growth, but the extent of these effects depended on compound identity, concentration, and microbial species. Moreover, most compounds did not substantially decrease sugar metabolism by microbes, and microbes reduced the concentration of some compounds in nectar. Using artificial flowers in the field, we also found that the common nectar yeast Metschnikowia reukaufii altered nectar consumption by small floral visitors, but only in nectar containing catalpol. This effect was likely mediated by a mechanism independent of catalpol metabolism. Despite strong compound-specific effects on microbial growth, our results suggest that the secondary metabolites tested here are unlikely to be an effective general defense mechanism for preserving nectar sugars for pollinators. Instead, our results indicate that microbial colonization of nectar could reduce the concentration of secondary compounds in nectar and, in some cases, reduce deterrence to pollinators.

  14. Soil microbes shift C-degrading activity along an ambient and experimental nitrogen gradient

    Science.gov (United States)

    Moore, J.; Frey, S. D.

    2017-12-01

    The balance between soil carbon (C) accumulation and decomposition is determined in large part by the activity and biomass of soil microbes, and yet their sensitivity to global changes remains unresolved. Atmospheric nitrogen (N) deposition has increased 22% (for NH4+) in the last two decades despite initiation of the Clean Air Act. Nitrogen deposition alters ecosystem processes by changing nutrient availability and soil pH, creating physiologically stressful environments that select for stress tolerant microbes. The functional fungal community may switch from domination by species with traits associated with decomposition via oxidative enzymes to traits associated with stress tolerance if global changes push fungal physiological limits. We examined changes in soil microbial activity across seven sites representing a gradient of ambient atmospheric N deposition, and five of these sites also had long-term N addition experiments. We measured changes in abundance of decomposition genes and C mineralization rates as indicators of microbial activity. We expected microbes to be less active with high N deposition, thus decreasing C mineralization rates. We found that C mineralization rates declined with total N deposition (ambient plus experimental additions), and this decline was more sensitive to N deposition where it occurred naturally compared to experimental treatments. Carbon mineralization declined by 3% in experimentally fertilized soils compared to 10% in control soils for every 1 kg/ha/y increase in ambient N deposition. Thus, microbes exposed to ambient levels of N deposition (2 - 12 kg/ha/y) had a stronger response than those exposed to fertilized soils (20 - 50 kg/ha/y). Long-term experimental N-addition seems to have selected for a microbial community that is tolerant of high N deposition. In sum, we provide evidence that soil microbial activity responded to N deposition, and may shift over time to a community capable of tolerating environmental change.

  15. Genetic engineering microbes for bioremediation/ biorecovery of uranium

    International Nuclear Information System (INIS)

    Apte, S.K.; Rao, A.S.; Appukuttan, D.; Nilgiriwala, K.S.; Acharya, C.

    2005-01-01

    Bioremediation (both bioremoval and biorecovery) of metals is considered a feasible, economic and eco-friendly alternative to chemical methods of metal extraction, particularly when the metal concentration is very low. Scanty distribution along with poor ore quality makes biomining of uranium an attractive preposition. Biosorption, bioprecipitation or bioaccumulation of uranium, aided by recombinant DNA technology, offer a promising technology for recovery of uranium from acidic or alkaline nuclear waste, tailings or from sea-water. Genetic engineering of bacteria, with a gene encoding an acid phosphatase, has yielded strains that can bioprecipitate uranium from very low concentrations at acidic-neutral pH, in a relatively short time. Organisms overproducing alkaline phosphatase have been selected for uranium precipitation from alkaline waste. Such abilities have now been transferred to the radioresistant microbe Deinococcus radiodurans to facilitate in situ bioremediation of nuclear waste, with some success. Sulfate-reducing bacteria are being characterized for bioremediation of uranium in tailings with the dual objective of uranium precipitation and reduction of sulfate to sulphide. Certain marine cyanobacteria have shown promise for uranium biosorption to extracellular polysaccharides, and intracellular accumulation involving metal sequestering metallothionin proteins. Future work is aimed at understanding the genetic basis of these abilities and to engineer them into suitable organisms subsequently. As photosynthetic, nitrogen-fixing microbes, which are considerably resistant to ionizing radiations, cyanobacteria hold considerable potential for bioremediation of nuclear waste. (author)

  16. Biofuels from microbes

    Energy Technology Data Exchange (ETDEWEB)

    Antoni, D. [Technische Univ. Muenchen, Freising-Weihenstephan (Germany). Inst. of Resource and Energy Technology; Zverlov, V.V.; Schwarz, W.H. [Technische Univ. Muenchen, Freising-Weihenstephan (Germany). Dept. of Microbiology

    2007-11-15

    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. (orig.)

  17. 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.

  18. Conformation of bovine submaxillary mucin layers on hydrophobic surface as studied by biomolecular probes

    DEFF Research Database (Denmark)

    Pakkanen, Kirsi I.; Madsen, Jan Busk; Lee, Seunghwan

    2015-01-01

    In the present study, the conformational changes of bovine submaxillary mucin (BSM) adsorbed on a hydrophobic surface (polystyrene (PS)) as a function of concentration in bulk solution (up to 2mg/mL) have been investigated with biomolecular probe-based approaches, including bicinchoninic acid (BCA),enzyme-linkedimmunosorbentassay(EIA...... solution. Adsorbed masses of BSM onto hydrophobic surface, as probe by BCA, showed a continuously increasing trend up to 2mg/mL. But, the signals from EIA and ELLA, which probe the concentration of available unglycosylatedC-terminals and the central glycosylated regions, respectively, showed complicated...

  19. Fungal innate immunity induced by bacterial microbe-associated molecular patterns (MAMPs)

    DEFF Research Database (Denmark)

    Ip Cho, Simon; Sundelin, Thomas; Erbs, Gitte

    2016-01-01

    Plants and animals detect bacterial presence through Microbe-Associated Molecular Patterns (MAMPs) which induce an innate immune response. The field of fungal-bacterial interaction at the molecular level is still in its infancy and little is known about MAMPs and their detection by fungi. Exposin...

  20. Bioprospecting of South African Plants as a Unique Resource for Bioactive Endophytic Microbes

    Directory of Open Access Journals (Sweden)

    Muna Ali Abdalla

    2018-05-01

    Full Text Available South Africa has a long history and strong belief in traditional herbal medicines. Using ethnobotanical knowledge as a lead, a large number of South African medicinal plants have been discovered to possess a wide spectrum of pharmacological properties. In this review, bioprospecting of endophytes is highlighted by following the advantages of the ethnomedicinal approach together with identifying unique medicinal plants where biological activity may be due to endophytes. This review focuses on the current status of South African medicinal plants to motivate the research community to harness the benefits of ethnobotanical knowledge to investigate the presence of endophytic microbes from the most potent South African medicinal plants. The potential chemical diversity and subsequent putative medicinal value of endophytes is deserving of further research. A timely and comprehensive review of literature on recently isolated endophytes and their metabolites was conducted. Worldwide literature from the last 2 years demonstrating the importance of ethnobotanical knowledge as a useful approach to discover endophytic microbes was documented. Information was obtained from scientific databases such as Pubmed, Scopus, Scirus, Google Scholar, Dictionary of Natural Products, Chemical Abstracts Services, official websites, and scientific databases on ethnomedicines. Primary sources such as books, reports, dissertations, and thesises were accessed where available. Recently published information on isolated endophytes with promising bioactivity and their bioactive natural products worldwide (2015-2017 was summarized. The potential value of South African medicinal plants as sources of endophytes is discussed. The insights provided through this study indicate that medicinal plants in South Africa are highly under-investigated sources of potentially useful endophytic microbes. New approaches may be used by medicinal plant scientists for further exploration of natural

  1. Production of Fatty Acid-Derived Valuable Chemicals in Synthetic Microbes

    International Nuclear Information System (INIS)

    Yu, Ai-Qun; Pratomo Juwono, Nina Kurniasih; Leong, Susanna Su Jan; Chang, Matthew Wook

    2014-01-01

    Fatty acid derivatives, such as hydroxy fatty acids, fatty alcohols, fatty acid methyl/ethyl esters, and fatty alka(e)nes, have a wide range of industrial applications including plastics, lubricants, and fuels. Currently, these chemicals are obtained mainly through chemical synthesis, which is complex and costly, and their availability from natural biological sources is extremely limited. Metabolic engineering of microorganisms has provided a platform for effective production of these valuable biochemicals. Notably, synthetic biology-based metabolic engineering strategies have been extensively applied to refactor microorganisms for improved biochemical production. Here, we reviewed: (i) the current status of metabolic engineering of microbes that produce fatty acid-derived valuable chemicals, and (ii) the recent progress of synthetic biology approaches that assist metabolic engineering, such as mRNA secondary structure engineering, sensor-regulator system, regulatable expression system, ultrasensitive input/output control system, and computer science-based design of complex gene circuits. Furthermore, key challenges and strategies were discussed. Finally, we concluded that synthetic biology provides useful metabolic engineering strategies for economically viable production of fatty acid-derived valuable chemicals in engineered microbes.

  2. Production of Fatty Acid-Derived Valuable Chemicals in Synthetic Microbes

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Ai-Qun; Pratomo Juwono, Nina Kurniasih [Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore (Singapore); Synthetic Biology Research Program, National University of Singapore, Singapore (Singapore); Leong, Susanna Su Jan [Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore (Singapore); Synthetic Biology Research Program, National University of Singapore, Singapore (Singapore); Singapore Institute of Technology, Singapore (Singapore); Chang, Matthew Wook, E-mail: bchcmw@nus.edu.sg [Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore (Singapore); Synthetic Biology Research Program, National University of Singapore, Singapore (Singapore)

    2014-12-23

    Fatty acid derivatives, such as hydroxy fatty acids, fatty alcohols, fatty acid methyl/ethyl esters, and fatty alka(e)nes, have a wide range of industrial applications including plastics, lubricants, and fuels. Currently, these chemicals are obtained mainly through chemical synthesis, which is complex and costly, and their availability from natural biological sources is extremely limited. Metabolic engineering of microorganisms has provided a platform for effective production of these valuable biochemicals. Notably, synthetic biology-based metabolic engineering strategies have been extensively applied to refactor microorganisms for improved biochemical production. Here, we reviewed: (i) the current status of metabolic engineering of microbes that produce fatty acid-derived valuable chemicals, and (ii) the recent progress of synthetic biology approaches that assist metabolic engineering, such as mRNA secondary structure engineering, sensor-regulator system, regulatable expression system, ultrasensitive input/output control system, and computer science-based design of complex gene circuits. Furthermore, key challenges and strategies were discussed. Finally, we concluded that synthetic biology provides useful metabolic engineering strategies for economically viable production of fatty acid-derived valuable chemicals in engineered microbes.

  3. Transfer of Nickel from Polluted Soil to Pisum sativum L. and Raphanus sativus L. under Composted Green Amendment and Native Soil Microbes

    Directory of Open Access Journals (Sweden)

    Nafady Nivien Allam

    2017-08-01

    Full Text Available The effect of compost, inoculation with native soil microbes and their residual effects on bioavailability of nickel by peas (Pisum sativum L. and radish (Raphanus sativus L. grown on polluted soil were investigated in pot experiments. Plants were amendment with different compost levels (0, 0.2, 0.4, 0.6% of soil dry weight and inoculated with different native soil microbes (4 fungal species, one bacterial species, 4 species of arbuscular mycorrhizal fungi isolated from the polluted soil under study. Significant increases in the biomass of pea and radish plants were observed as a result of amendment application and their residual effects. The mycorrhizal dependency (MD of pea plants was lower than of radish plants. The highest reductions of Ni levels in both plants were observed by the simultaneous applications of compost with microbes or mycorrhizal fungi to polluted soils. Soil pH increased significantly (p < 0.05 as a result of applying native microbes especially with arbuscular mycorrhizal fungi (AMF alone or combined with compost. The DTPA extractability of soil Ni was significantly decreased with increasing soil pH (p < 0.05. The minimum transfer factor of Ni from polluted soil were 0.067 and 0.089 for pea and radish plants, respectively which were attained as a result of applying compost (0.6% of soil weight inoculated with mycorrhizal fungi. From the results, we can conclude that the use of compost and native soil microbes as a soil remediate could be an effective strategy for soil remediation.

  4. The Use of Stuffed Microbes in an Undergraduate Microbiology Course Increases Engagement and Student Learning

    Directory of Open Access Journals (Sweden)

    Ginny Webb

    2015-08-01

    Full Text Available Student engagement, attention, and attendance during a microbiology lecture are crucial for student learning.  In addition, it is challenging to cover a large number of infectious diseases during a one-semester introductory microbiology course.  The use of visual aids helps students retain the information presented during a lecture.  Here, I discuss the use of stuffed, plush microbes as visual aids during an introductory microbiology course.  The incorporation of these stuffed microbes during a microbiology lecture results in an increase in engagement, interest, attendance, and retention of material.

  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. Study of defects and radiation damage in solids by field-ion and atom-probe microscopy

    International Nuclear Information System (INIS)

    Seidman, D.N.

    1979-06-01

    A brief review is presented of: the basic physical principles of the field-ion and atom-probe microscopes; the many applications of these instruments to the study of defects and radiation damage in solids; and the application of the atom-probe field-ion microscope to the study of the behavior of implanted 3 He and 4 He in tungsten

  7. Disease - 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 ...File name: disease.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/...iption Download License Update History of This Database Site Policy | Contact Us Disease - MicrobeDB.jp | LSDB Archive ...

  8. Spatial distribution of residence time, microbe and storage volume of groundwater in headwater catchments

    Science.gov (United States)

    Tsujimura, Maki; Ogawa, Mahiro; Yamamoto, Chisato; Sakakibara, Koichi; Sugiyama, Ayumi; Kato, Kenji; Nagaosa, Kazuyo; Yano, Shinjiro

    2017-04-01

    Headwater catchments in mountainous region are the most important recharge area for surface and subsurface waters, and time and stock information of the water is principal to understand hydrological processes in the catchments. Also, a variety of microbes are included in the groundwater and spring water, and those varies in time and space, suggesting that information of microbe could be used as tracer for groundwater flow system. However, there have been few researches to evaluate the relationship among the residence time, microbe and storage volume of the groundwater in headwater catchments. We performed an investigation on age dating using SF6 and CFCs, microbe counting in the spring water, and evaluation of groundwater storage volume based on water budget analysis in 8 regions underlain by different lithology, those are granite, dacite, sedimentary rocks, serpentinite, basalt and volcanic lava all over Japan. We conducted hydrometric measurements and sampling of spring water in base flow conditions during the rainless periods 2015 and 2016 in those regions, and SF6, CFCs, stable isotopic ratios of oxygen-18 and deuterium, inorganic solute concentrations and total number of prokaryotes were determined on all water samples. Residence time of spring water ranged from 0 to 16 years in all regions, and storage volume of the groundwater within topographical watershed was estimated to be 0.1 m to 222 m in water height. The spring with the longer residence time tends to have larger storage volume in the watershed, and the spring underlain by dacite tends to have larger storage volume as compared with that underlain by sand stone and chert. Also, total number of prokaryotes in the spring water ranged from 103 to 105 cells/mL, and the spring tends to show clear increasing of total number of prokaryotes with decreasing of residence time. Thus, we observed a certain relationship among residence time, storage volume and total number of prokaryotes in the spring water, and

  9. Monitoring Acidophilic Microbes with Real-Time Polymerase Chain Reaction (PCR) Assays

    Energy Technology Data Exchange (ETDEWEB)

    Frank F. Roberto

    2008-08-01

    Many techniques that are used to characterize and monitor microbial populations associated with sulfide mineral bioleaching require the cultivation of the organisms on solid or liquid media. Chemolithotrophic species, such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, or thermophilic chemolithotrophs, such as Acidianus brierleyi and Sulfolobus solfataricus can grow quite slowly, requiring weeks to complete efforts to identify and quantify these microbes associated with bioleach samples. Real-time PCR (polymerase chain reaction) assays in which DNA targets are amplified in the presence of fluorescent oligonucleotide primers, allowing the monitoring and quantification of the amplification reactions as they progress, provide a means of rapidly detecting the presence of microbial species of interest, and their relative abundance in a sample. This presentation will describe the design and use of such assays to monitor acidophilic microbes in the environment and in bioleaching operations. These assays provide results within 2-3 hours, and can detect less than 100 individual microbial cells.

  10. Flavor Profile of Chinese Liquor Is Altered by Interactions of Intrinsic and Extrinsic Microbes.

    Science.gov (United States)

    Wu, Qun; Kong, Yu; Xu, Yan

    2016-01-15

    The flavor profile of Chinese liquor is the result of the metabolic activity of its microbial community. Given the importance of the microbial interaction, a novel way to control the liquor's flavor is by regulating the composition of the community. In this study, we efficiently improved the liquor's flavor by perturbing the intrinsic microbial metabolism with extrinsic microbes. We first constructed a basic microbial group (intrinsic) containing Saccharomyces cerevisiae, Wickerhamomyces anomalus, and Issatchenkia orientalis and added special flavor producers (extrinsic), Saccharomyces uvarum and Saccharomyces servazzii, to this intrinsic group. Upon the addition of the extrinsic microbes, the maximum specific growth rates of S. cerevisiae and I. orientalis increased from 6.19 to 43.28/day and from 1.15 to 14.32/day, respectively, but that of W. anomalus changed from 1.00 to 0.96/day. In addition, most volatile compounds known to be produced by the extrinsic strains were not produced. However, more esters, alcohols, and acids were produced by S. cerevisiae and I. orientalis. Six compounds were significantly different by random forest analysis after perturbation. Among them, increases in ethyl hexanoate, isobutanol, and 3-methylbutyric acid were correlated with S. cerevisiae and I. orientalis, and a decrease in geranyl acetone was correlated with W. anomalus. Variations in ethyl acetate and 2-phenylethanol might be due to the varied activity of W. anomalus and S. cerevisiae. This work showed the effect of the interaction between the intrinsic and extrinsic microbes on liquor flavor, which would be beneficial for improving the quality of Chinese liquor. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  11. The Effect of Antibacterial Formula Hand Cleaners on the Elimination of Microbes on Hands

    Science.gov (United States)

    Coleman, J. R.

    2002-05-01

    : The purpose of this project is to find out which one of the antibacterial hand cleanser (antibacterial bar soap, antibacterial liquid hand soap, and liquid hand sanitizer) is more effective in eliminating microbes. If antibacterial- formula liquid hand soap is used on soiled hands, then it will be more effective in eliminating microbes. Germs are microorganisms that cause disease and can spread from person-to-person. Bacteria are a kind of microbe, an example of which is Transient Flora that is often found on hands. Hand washing prevents germs from spreading to others. During the procedure, swabs were used to take samples before and after the soiled hands had been washed with one of the antibacterial hand cleansers. Nutrient Easygel was poured into petri dishes to harden for 1 day, and then samples were swabbed on the gel. The Petri dishes were placed in an incubator for 24 hours, and then data was recorded accordingly. The antibacterial liquid hand soap was sufficient in eliminating the majority of bacteria. The hands had 65% of the bacteria on them, and after the liquid hand soap was used only 37% of the bacteria remained.

  12. Utilization of mixed cellulolytic microbes from termite extract, elephant faecal solution and buffalo ruminal fluid to increase in vitro digestibility of King Grass

    Directory of Open Access Journals (Sweden)

    Agung Prabowo

    2007-06-01

    Full Text Available Cellulose is a compound of plant cell walls which is difficult to be degraded because it composed of glucose monomers linked by β-(1.4-bound. It will be hydrolysed by cellulase enzyme secreted by cellulolytic microbes. The effective digestion of cellulose needs high activity of cellulase enzyme. This research aims to increase in vitro king grass digestibility utilizing mixed cellulolytic microbes of termite extract, elephant faecal solution, and buffalo ruminal fluid. Twelve syringes contained gas test media were randomly divided into four treatments based on sources of microbe (SM, namely: S (SM: cattle ruminal fluid [S], RGK (SM: mixed cellulolytic microbes of termite extract, elephant faecal solution, and buffalo ruminal fluid [RGK], with composition 1 : 1 : 1, S-RGK (SM: S + RGK, with composition 1:1, and TM (without given treatment microbe. Digestibility was measured using gas test method. Average of gas production treatment of S-RGK (70.2 + 0.6 ml was higher and significantly different (P<0.01 compared to treatment of S (60.3 + 0.8 ml, RGK (40.8 + 2.3 ml, and TM (13.3 + 2.0 ml. Utilization of mixed cellulolytic microbes of termite extract, elephant faecal solution, and buffalo ruminal fluid (RGK that combined with microbes of cattle ruminal fluid (S could increase in vitro digestibility of king grass.

  13. Exploring the Optimal Strategy to Predict Essential Genes in Microbes

    Directory of Open Access Journals (Sweden)

    Yao Lu

    2011-12-01

    Full Text Available Accurately predicting essential genes is important in many aspects of biology, medicine and bioengineering. In previous research, we have developed a machine learning based integrative algorithm to predict essential genes in bacterial species. This algorithm lends itself to two approaches for predicting essential genes: learning the traits from known essential genes in the target organism, or transferring essential gene annotations from a closely related model organism. However, for an understudied microbe, each approach has its potential limitations. The first is constricted by the often small number of known essential genes. The second is limited by the availability of model organisms and by evolutionary distance. In this study, we aim to determine the optimal strategy for predicting essential genes by examining four microbes with well-characterized essential genes. Our results suggest that, unless the known essential genes are few, learning from the known essential genes in the target organism usually outperforms transferring essential gene annotations from a related model organism. In fact, the required number of known essential genes is surprisingly small to make accurate predictions. In prokaryotes, when the number of known essential genes is greater than 2% of total genes, this approach already comes close to its optimal performance. In eukaryotes, achieving the same best performance requires over 4% of total genes, reflecting the increased complexity of eukaryotic organisms. Combining the two approaches resulted in an increased performance when the known essential genes are few. Our investigation thus provides key information on accurately predicting essential genes and will greatly facilitate annotations of microbial genomes.

  14. Understanding Plant-Microbe Interactions for Phytoremediation of Petroleum-Polluted Soil

    Science.gov (United States)

    Nie, Ming; Wang, Yijing; Yu, Jiayi; Xiao, Ming; Jiang, Lifen; Yang, Ji; Fang, Changming; Chen, Jiakuan; Li, Bo

    2011-01-01

    Plant-microbe interactions are considered to be important processes determining the efficiency of phytoremediation of petroleum pollution, however relatively little is known about how these interactions are influenced by petroleum pollution. In this experimental study using a microcosm approach, we examined how plant ecophysiological traits, soil nutrients and microbial activities were influenced by petroleum pollution in Phragmites australis, a phytoremediating species. Generally, petroleum pollution reduced plant performance, especially at early stages of plant growth. Petroleum had negative effects on the net accumulation of inorganic nitrogen from its organic forms (net nitrogen mineralization (NNM)) most likely by decreasing the inorganic nitrogen available to the plants in petroleum-polluted soils. However, abundant dissolved organic nitrogen (DON) was found in petroleum-polluted soil. In order to overcome initial deficiency of inorganic nitrogen, plants by dint of high colonization of arbuscular mycorrhizal fungi might absorb some DON for their growth in petroleum-polluted soils. In addition, through using a real-time polymerase chain reaction method, we quantified hydrocarbon-degrading bacterial traits based on their catabolic genes (i.e. alkB (alkane monooxygenase), nah (naphthalene dioxygenase) and tol (xylene monooxygenase) genes). This enumeration of target genes suggests that different hydrocarbon-degrading bacteria experienced different dynamic changes during phytoremediation and a greater abundance of alkB was detected during vegetative growth stages. Because phytoremediation of different components of petroleum is performed by different hydrocarbon-degrading bacteria, plants’ ability of phytoremediating different components might therefore vary during the plant life cycle. Phytoremediation might be most effective during the vegetative growth stages as greater abundances of hydrocarbon-degrading bacteria containing alkB and tol genes were observed

  15. Biological invasions: economic and environmental costs of alien plant, animal, and microbe species

    National Research Council Canada - National Science Library

    Pimentel, David

    2011-01-01

    ...: Economic and Environmental Costs of Alien Plant, Animal, and Microbe Species, this reference discusses how non-native species invade new ecosystems and the subsequent economic and environmental effects of these species...

  16. Errors of first-order probe correction for higher-order probes in spherical near-field antenna measurements

    DEFF Research Database (Denmark)

    Laitinen, Tommi; Nielsen, Jeppe Majlund; Pivnenko, Sergiy

    2004-01-01

    An investigation is performed to study the error of the far-field pattern determined from a spherical near-field antenna measurement in the case where a first-order (mu=+-1) probe correction scheme is applied to the near-field signal measured by a higher-order probe.......An investigation is performed to study the error of the far-field pattern determined from a spherical near-field antenna measurement in the case where a first-order (mu=+-1) probe correction scheme is applied to the near-field signal measured by a higher-order probe....

  17. Recovery of diverse microbes in high turbidity surface water samples using dead-end ultrafiltration.

    Science.gov (United States)

    Mull, Bonnie; Hill, Vincent R

    2012-12-01

    Dead-end ultrafiltration (DEUF) has been reported to be a simple, field-deployable technique for recovering bacteria, viruses, and parasites from large-volume water samples for water quality testing and waterborne disease investigations. While DEUF has been reported for application to water samples having relatively low turbidity, little information is available regarding recovery efficiencies for this technique when applied to sampling turbid water samples such as those commonly found in lakes and rivers. This study evaluated the effectiveness of a DEUF technique for recovering MS2 bacteriophage, enterococci, Escherichia coli, Clostridium perfringens, and Cryptosporidium parvum oocysts in surface water samples having elevated turbidity. Average recovery efficiencies for each study microbe across all turbidity ranges were: MS2 (66%), C. parvum (49%), enterococci (85%), E. coli (81%), and C. perfringens (63%). The recovery efficiencies for MS2 and C. perfringens exhibited an inversely proportional relationship with turbidity, however no significant differences in recovery were observed for C. parvum, enterococci, or E. coli. Although ultrafilter clogging was observed, the DEUF method was able to process 100-L surface water samples at each turbidity level within 60 min. This study supports the use of the DEUF method for recovering a wide array of microbes in large-volume surface water samples having medium to high turbidity. Published by Elsevier B.V.

  18. In-situ Monitoring of Plant-microbe Communication to Understand the Influence of Soil Properties on Symbiotic Biological Nitrogen Fixation

    Science.gov (United States)

    Webster, T.; Del Valle, I.; Cheng, H. Y.; Silberg, J. J.; Masiello, C. A.; Lehmann, J.

    2016-12-01

    Plant-microbe signaling is important for many symbiotic and pathogenic interactions. While this signaling often occurs in soils, very little research has evaluated the role that the soil mineral and organic matter matrix plays in plant-microbe communication. One hurdle to these studies is the lack of simple tools for evaluating how soil mineral phases and organic matter influence the availability of plant-produced flavonoids that initiate the symbiosis between nitrogen-fixing bacteria and legumes. Because of their range of hydrophobic and electrostatic properties, flavonoids represent an informative class of signaling molecules. In this presentation, we will describe studies examining the bioavailable concentrations of flavonoids in soils using traditional techniques, such as high-pressure liquid chromatography and fluorescent microbial biosensors. Additionally, we will describe our progress developing a Rhizobium leguminosarum reporter that can be deployed into soils to report on flavonoid levels. This new microbial reporter is designed so that Rhizobium only generates a volatile gas signal when it encounters a defined concentration of flavonoids. By monitoring the output of this biosensor using gas chromatography-mass spectrometry during real time during soil incubations, we are working to establish the impact of soil organic matter, pH, and mineral phases on the reception of these signaling molecules. We expect that the findings from these studies will be useful for recommending soil management strategies that can enhance the communication between legumes and nitrogen fixing bacteria. This research highlights the importance of studying the role of soil as a mediator of plant-microbe communication.

  19. Positron probe to study the freezing of nanodroplets

    International Nuclear Information System (INIS)

    Pujari, P.K.

    2010-01-01

    Positron is an excellent in situ probe to study the phase behavior of fluid confined in nanodomains. The study of phase behavior (freezing/melting) of nano confined fluid or nanodroplet has great relevance in fundamental research as well as applications in nano-tribology, nanofabrication, membrane separation, interfacial adhesion and lubrication. It is seen that the properties of freezing/melting of nanodroplets are different from their bulk behavior due to the combined effects of finite size, surface force, surface anisotropy, pore disorder and reduced dimensionality. We have used positron annihilation spectroscopy (PAS) to study the freezing/melting behavior of different organic liquids like benzene, ethylene glycol and isopropanol confined in nanopores of ZSM5 zeolite and silica gel

  20. Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?

    KAUST Repository

    Bang, Corinna

    2018-02-15

    From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host–microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents.

  1. Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?

    KAUST Repository

    Bang, Corinna; Dagan, Tal; Deines, Peter; Dubilier, Nicole; Duschl, Wolfgang J.; Fraune, Sebastian; Hentschel, Ute; Hirt, Heribert; Hü lter, Nils; Lachnit, Tim; Picazo, Devani; Pita, Lucia; Pogoreutz, Claudia; Radecker, Nils; Saad, Maged; Schmitz, Ruth A.; Schulenburg, Hinrich; Voolstra, Christian R.; Weiland-Brä uer, Nancy; Ziegler, Maren; Bosch, Thomas C.G.

    2018-01-01

    From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host–microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents.

  2. Aspheric surface measurement using capacitive probes

    Science.gov (United States)

    Tao, Xin; Yuan, Daocheng; Li, Shaobo

    2017-02-01

    With the application of aspheres in optical fields, high precision and high efficiency aspheric surface metrology becomes a hot research topic. We describe a novel method of non-contact measurement of aspheric surface with capacitive probe. Taking an eccentric spherical surface as the object of study, the averaging effect of capacitive probe measurement and the influence of tilting the capacitive probe on the measurement results are investigated. By comparing measurement results from simultaneous measurement of the capacitive probe and contact probe of roundness instrument, this paper indicates the feasibility of using capacitive probes to test aspheric surface and proposes the compensation method of measurement error caused by averaging effect and the tilting of the capacitive probe.

  3. Uptake, Accumulation and Toxicity of Silver Nanoparticle in Autotrophic Plants, and Heterotrophic Microbes: A Concentric Review

    Science.gov (United States)

    Tripathi, Durgesh K.; Tripathi, Ashutosh; Shweta; Singh, Swati; Singh, Yashwant; Vishwakarma, Kanchan; Yadav, Gaurav; Sharma, Shivesh; Singh, Vivek K.; Mishra, Rohit K.; Upadhyay, R. G.; Dubey, Nawal K.; Lee, Yonghoon; Chauhan, Devendra K.

    2017-01-01

    Nanotechnology is a cutting-edge field of science with the potential to revolutionize today’s technological advances including industrial applications. It is being utilized for the welfare of mankind; but at the same time, the unprecedented use and uncontrolled release of nanomaterials into the environment poses enormous threat to living organisms. Silver nanoparticles (AgNPs) are used in several industries and its continuous release may hamper many physiological and biochemical processes in the living organisms including autotrophs and heterotrophs. The present review gives a concentric know-how of the effects of AgNPs on the lower and higher autotrophic plants as well as on heterotrophic microbes so as to have better understanding of the differences in effects among these two groups. It also focuses on the mechanism of uptake, translocation, accumulation in the plants and microbes, and resulting toxicity as well as tolerance mechanisms by which these microorganisms are able to survive and reduce the effects of AgNPs. This review differentiates the impact of silver nanoparticles at various levels between autotrophs and heterotrophs and signifies the prevailing tolerance mechanisms. With this background, a comprehensive idea can be made with respect to the influence of AgNPs on lower and higher autotrophic plants together with heterotrophic microbes and new insights can be generated for the researchers to understand the toxicity and tolerance mechanisms of AgNPs in plants and microbes. PMID:28184215

  4. EPR spin probe and spin label studies of some low molecular and polymer micelles

    Science.gov (United States)

    Wasserman, A. M.; Kasaikin, V. A.; Timofeev, V. P.

    1998-12-01

    The rotational mobility of spin probes of different shape and size in low molecular and polymer micelles has been studied. Several probes having nitroxide fragment localized either in the vicinity of micelle interface or in the hydrocarbon core have been used. Upon increasing the number of carbon atoms in hydrocarbon chain of detergent from 7 to 13 (sodium alkyl sulfate micelles) or from 12 to 16 (alkyltrimethylammonium bromide micelles) the rotational mobility of spin probes is decreased by the factor 1.5-2.0. The spin probe rotational mobility in polymer micelles (the complexes of alkyltrimethylammonium bromides and polymethacrylic or polyacrylic acids) is less than mobility in free micelles of the same surfactants. The study of EPR-spectra of spin labeled polymethacrylic acid (PMA) indicated that formation of water soluble complexes of polymer and alkyltrimethylammonium bromides in alkaline solutions (pH 9) does not affect the polymer segmental mobility. On the other hand, the polymer complexes formation in slightly acidic water solution (pH 6) breaks down the compact PMA conformation, thus increasing the polymer segmental mobility. Possible structures of polymer micelles are discussed.

  5. Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

    Science.gov (United States)

    Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

    2011-01-01

    Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in

  6. Diversity of Cellulolytic Microbes and the Biodegradation of Municipal Solid Waste by a Potential Strain

    Science.gov (United States)

    Gautam, S. P.; Bundela, P. S.; Pandey, A. K.; Jamaluddin; Awasthi, M. K.; Sarsaiya, S.

    2012-01-01

    Municipal solid waste contains high amounts of cellulose, which is an ideal organic waste for the growth of most of microorganism as well as composting by potential microbes. In the present study, Congo red test was performed for screening of microorganism, and, after selecting a potential strains, it was further used for biodegradation of organic municipal solid waste. Forty nine out of the 250 different microbes tested (165 belong to fungi and 85 to bacteria) produced cellulase enzyme and among these Trichoderma viride was found to be a potential strain in the secondary screening. During the biodegradation of organic waste, after 60 days, the average weight losses were 20.10% in the plates and 33.35% in the piles. There was an increase in pH until 20 days. pH however, stabilized after 30 days in the piles. Temperature also stabilized as the composting process progressed in the piles. The high temperature continued until 30 days of decomposition, after which the temperature dropped to 40°C and below during the maturation. Good quality compost was obtained in 60 days. PMID:22518141

  7. Dietary inclusion of direct fed microbe on the growth performance of ...

    African Journals Online (AJOL)

    The birds were obtained from a reputable hatchery and randomly assigned to four dietary treatments, each with three replicate of ten birds. ... The results show that the growth performance of the broiler chicken fed diet containing different level of direct fed microbes did not differ significantly (P>0.05) in initial weight, final ...

  8. Study of modification methods of probes for critical-dimension atomic-force microscopy by the deposition of carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Ageev, O. A., E-mail: ageev@sfedu.ru [Southern Federal University, Institute for Nanotechnologies, Electronics, and Electronic Equipment Engineering (Russian Federation); Bykov, Al. V. [NT-MDT (Russian Federation); Kolomiitsev, A. S.; Konoplev, B. G.; Rubashkina, M. V.; Smirnov, V. A.; Tsukanova, O. G. [Southern Federal University, Institute for Nanotechnologies, Electronics, and Electronic Equipment Engineering (Russian Federation)

    2015-12-15

    The results of an experimental study of the modification of probes for critical-dimension atomicforce microscopy (CD-AFM) by the deposition of carbon nanotubes (CNTs) to improve the accuracy with which the surface roughness of vertical walls is determined in submicrometer structures are presented. Methods of the deposition of an individual CNT onto the tip of an AFM probe via mechanical and electrostatic interaction between the probe and an array of vertically aligned carbon nanotubes (VACNTs) are studied. It is shown that, when the distance between the AFM tip and a VACNT array is 1 nm and the applied voltage is within the range 20–30 V, an individual carbon nanotube is deposited onto the tip. On the basis of the results obtained in the study, a probe with a carbon nanotube on its tip (CNT probe) with a radius of 7 nm and an aspect ratio of 1:15 is formed. Analysis of the CNT probe demonstrates that its use improves the resolution and accuracy of AFM measurements, compared with the commercial probe, and also makes it possible to determine the roughness of the vertical walls of high-aspect structures by CD-AFM. The results obtained can be used to develop technological processes for the fabrication and reconditioning of special AFM probes, including those for CD-AFM, and procedures for the interoperational express monitoring of technological process parameters in the manufacturing of elements for micro- and nanoelectronics and micro- and nanosystem engineering.

  9. Use of a combined penetrometer-TDR moisture probe for soil compaction studies

    International Nuclear Information System (INIS)

    Pedro Vaz, C.M.

    2004-01-01

    measurement technique, we have developed a combined cone penetrometer-TDR moisture probe by wrapping two TDR wires around the penetrometer rod (combined rod TDR) as a double helix, so that both soil water content and penetration resistance can be measured simultaneously and at approximately the same location within the soil profile. The main advantage of the coiled design is that relative long travel times can be obtained, allowing accurate water content measurements for small-sized TDR probes. The objective of this lecture is to present the combined penetrometer-TDR probe as a new tool to study soil compaction. The presentation will cover the following topics: Theory of the dynamic cone penetrometer; Laboratory calibration of a coiled TDR moisture probe and application of the mixing model; Field calibration and use of the combined penetrometer-coiled TDR moisture probe; Penetration resistance, bulk density, water content and potential relationships; Practical applications of the combined penetrometer-coiled TDR moisture probe

  10. MiDAS Field Guide – a Comprehensive Online Source of Information About the Microbes of Activated Sludge

    DEFF Research Database (Denmark)

    Nierychlo, Marta; McIlroy, Simon Jon; Saunders, Aaron Marc

    this information in MiDAS field guide (www.midasfieldguide.org). MiDAS taxonomy gives a solid foundation for the study of microbial ecology of the wastewater treatment processes. The online MiDAS field guide links the identity of genera that are important for the wastewater treatment process to details about...... guide to the microbes of activated sludge by comparing microbial community composition in 32 WWTPs located worldwide. This will facilitate a better understanding of the ecology of the ecosystem of activated sludge. Reference: McIlroy et al. MiDAS: the field guide to the microbes of activated sludge...... on a survey of 25 full-scale Danish wastewater treatment plants over 6 years and using MiDAS taxonomy, we have collected more than 150 key organisms in activated sludge wastewater treatment systems, linked their identity with available information on their function and distribution and included...

  11. 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. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Titanium pigmentation. An electron probe microanalysis study

    International Nuclear Information System (INIS)

    Dupre, A.; Touron, P.; Daste, J.; Lassere, J.; Bonafe, J.L.; Viraben, R.

    1985-01-01

    A patient had an unusual pigmentary disease induced by titanium dioxide. The use of a topical cream containing titanium dioxide caused a xanthomalike appearance on the patient's penis. Electron probe microanalysis was valuable in establishing the cause of this balanitis

  13. Chimpanzees create and modify probe tools functionally: A study with zoo-housed chimpanzees.

    Science.gov (United States)

    Hopper, Lydia M; Tennie, Claudio; Ross, Stephen R; Lonsdorf, Elizabeth V

    2015-02-01

    Chimpanzees (Pan troglodytes) use tools to probe for out-of-reach food, both in the wild and in captivity. Beyond gathering appropriately-sized materials to create tools, chimpanzees also perform secondary modifications in order to create an optimized tool. In this study, we recorded the behavior of a group of zoo-housed chimpanzees when presented with opportunities to use tools to probe for liquid foods in an artificial termite mound within their enclosure. Previous research with this group of chimpanzees has shown that they are proficient at gathering materials from within their environment in order to create tools to probe for the liquid food within the artificial mound. Extending beyond this basic question, we first asked whether they only made and modified probe tools when it was appropriate to do so (i.e. when the mound was baited with food). Second, by collecting continuous data on their behavior, we also asked whether the chimpanzees first (intentionally) modified their tools prior to probing for food or whether such modifications occurred after tool use, possibly as a by-product of chewing and eating the food from the tools. Following our predictions, we found that tool modification predicted tool use; the chimpanzees began using their tools within a short delay of creating and modifying them, and the chimpanzees performed more tool modifying behaviors when food was available than when they could not gain food through the use of probe tools. We also discuss our results in terms of the chimpanzees' acquisition of the skills, and their flexibility of tool use and learning. © 2014 Wiley Periodicals, Inc.

  14. Studies of radiation induced membrane damage in lymphocytes using fluorescent probes

    International Nuclear Information System (INIS)

    Nikesch, W.

    1974-01-01

    The fluorescent probes perylene (PER), 1-anilino-8-naphthalene sulfonic acid (ANS), and fluorescein diacetate (FDA) were used to investigate membrane changes caused by ionizing radiation. Probe response to various other perturbations (variation of pH, temperature, and salt concentration, and treatment with phythohemagglutinin (PHA) and saponins) was also investigated to better understand membrane-probe interactions. ANS was used to probe the membrane surface, PER to probe the membrane interior, and FDA to investigate membrane integrity. Polarization of fluorescent light from ANS and PER was used to investigate the microviscosity and order of the membrane surface and interior respectively. Irradiated cells (600 R) were shown to have a decreased rate of hydrolysis of FDA probably due to cytoplasmic changes effecting the enzymatic reaction. Also evident was an increase in loss of intracellular fluorescein and a decrease in PER polarization indicating that the cells have a decreased membrane integrity, possibly the result of an increased disorganization of the phospholipid hydrocarbon chains in the membrane interior. Experiments with PHA link the decreased membrane integrity with the eventual interphase death of the cells. In general it is shown that the fluorescent probes ANS, PER, and FDA provide useful ways to investigate order and microviscosity in the cell membrane surface and interior, membrane surface charges, internal membrane polarity changes, and membrane integrity. (U.S.)

  15. Probe Microscopic Studies of DNA Molecules on Carbon Nanotubes

    Directory of Open Access Journals (Sweden)

    Kazuo Umemura

    2016-10-01

    Full Text Available Hybrids of DNA and carbon nanotubes (CNTs are promising nanobioconjugates for nanobiosensors, carriers for drug delivery, and other biological applications. In this review, nanoscopic characterization of DNA-CNT hybrids, in particular, characterization by scanning probe microscopy (SPM, is summarized. In many studies, topographical imaging by atomic force microscopy has been performed. However, some researchers have demonstrated advanced SPM operations in order to maximize its unique and valuable functions. Such sophisticated approaches are attractive and will have a significant impact on future studies of DNA-CNT hybrids.

  16. Eddy-current probe design

    International Nuclear Information System (INIS)

    Kincaid, T.G.; McCary, R.O.

    1983-01-01

    This paper describes theoretical and experimental work directed toward finding the optimum probe dimensions and operating frequency for eddy current detection of half-penny surface cracks in nonmagnetic conducting materials. The study applies to probes which excite an approximately uniform spatial field over the length of the crack at the surface of the material. In practical terms, this means that the probe is not smaller than the crack length in any of its critical dimensions. The optimization of a simple coil probe is first analyzed in detail. It is shown that signal-to-noise ratio and lift-off discrimination are maximized by a pancake coil with mean radius not greater than the crack length, operated at a frequency which gives a skin depth equal to the crack depth. The results obtained for the simple coil are then used as a basis for discussion of the design of coils with ferrite cores and shields, and for the design of recording head type probes

  17. BRC - 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 ...table). Data file File name: brc.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/LATEST/brc.ta...rains in JCM. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us BRC - MicrobeDB.jp | LSDB Archive ...

  18. SRA - 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 ...e following table). Data file File name: sra.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/L...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us SRA - MicrobeDB.jp | LSDB Archive ...

  19. LINKING MICROBES TO CLIMATE: INCORPORATING MICROBIAL ACTIVITY INTO CLIMATE MODELS COLLOQUIUM

    Energy Technology Data Exchange (ETDEWEB)

    DeLong, Edward; Harwood, Caroline; Reid, Ann

    2011-01-01

    This report explains the connection between microbes and climate, discusses in general terms what modeling is and how it applied to climate, and discusses the need for knowledge in microbial physiology, evolution, and ecology to contribute to the determination of fluxes and rates in climate models. It recommends with a multi-pronged approach to address the gaps.

  20. Microbe and Mineral Mediated Transformation of Heavy Metals, Radionuclides, and Organic Contaminants

    Science.gov (United States)

    Gerlach, R.

    2011-12-01

    Microorganisms influence their surroundings in many ways and humans have utilized microbially catalyzed reactions for benefit for centuries. Over the past few decades, microorganisms have been used for the control of contaminant transport in subsurface environments where many microbe mineral interactions occur. This presentation will discuss microbially influenced mineral formation and transformation as well as their influence on the fate of organic contaminants such as chlorinated aliphatics & 2,4,6-trinitrotoluene (TNT), heavy metals such as chromium, and radionuclides such as uranium & strontium. Both, batch and flow experiments have been performed, which monitor the net effect of microbe mineral interactions on the fate of these contaminants. This invited presentation will place an emphasis on the relative importance of direct microbial (i.e. biotic) transformations, mineral-mediated transformations as well as other abiotic reactions influencing the fate of environmental contaminants. Experiments will be summarized and placed in context of past and future engineered applications for the control of subsurface contaminants.

  1. Biotin in microbes, the genes involved in its biosynthesis, its biochemical role and perspectives for biotechnological production.

    Science.gov (United States)

    Streit, W R; Entcheva, P

    2003-03-01

    Biotin (vitamin H) is one of the most fascinating cofactors involved in central pathways in pro- and eukaryotic cell metabolism. Since its original discovery in 1901, research has led to the discovery of the complete biotin biosynthesis pathways in many different microbes and much work has been done on the highly intriguing and complex biochemistry of biotin biosynthesis. While humans and animals require several hundred micrograms of biotin per day, most microbes, plants and fungi appear to be able to synthesize the cofactor themselves. Biotin is added to many food, feed and cosmetic products, creating a world market of 10-30 t/year. However, the majority of the biotin sold is synthesized in a chemical process. Since the chemical synthesis is linked with a high environmental burden, much effort has been put into the development of biotin-overproducing microbes. A summary of biotin biosynthesis and its biological role is presented; and current strategies for the improvement of microbial biotin production using modern biotechnological techniques are discussed.

  2. Study of polarization properties of fiber-optics probes with use of a binary phase plate.

    Science.gov (United States)

    Alferov, S V; Khonina, S N; Karpeev, S V

    2014-04-01

    We conduct a theoretical and experimental study of the distribution of the electric field components in the sharp focal domain when rotating a zone plate with a π-phase jump placed in the focused beam. Comparing the theoretical and experimental results for several kinds of near-field probes, an analysis of the polarization sensitivity of different types of metal-coated aperture probes is conducted. It is demonstrated that with increasing diameter of the non-metal-coated tip part there occurs an essential redistribution of sensitivity in favor of the transverse electric field components and an increase of the probe's energy throughput.

  3. Heap bioleaching of uranium from low-grade granite-type ore by mixed acidophilic microbes

    International Nuclear Information System (INIS)

    Xuegang Wang; Zhongkui Zhou

    2017-01-01

    We evaluated uranium bioleaching from low-grade, granite-type uranium ore using mixed acidophilic microbes from uranium mine leachate. A 4854-ton plant-scale heap bioleaching process achieved sustained leaching with a uranium leaching efficiency of 88.3% using a pH of 1.0-2.0 and an Fe"3"+ dosage of 3.0-5.5 g/L. Acid consumption amounted to 25.8 g H_2SO_4 kg"-"1 ore. Uranium bioleaching follows a diffusion-controlled kinetic model with a correlation coefficient of 0.9136. Almost all uranium was dissolved in aqueous solution, except those encapsulated in quartz particles. Therefore, heap bioleaching by mixed acidophilic microbes enables efficient, economical, large-scale recovery of uranium from low-grade ores. (author)

  4. Characteristics of the repair - deficient mutants 1435 plague microbe strain

    International Nuclear Information System (INIS)

    Temiralieva, G.A.

    1977-01-01

    Repair-deficient mutants 1435 A uvr - hcr - , 1435-17 uvr - hcr + and 1435-35 lon have been obtained from 1435 plague microbe strain, isolated from a large gerbil living in the Central Asian desert region. The mutants have the same cultural-morphological and enzymatic characteristics, the same need in growth factors and similar virulence determinants as the original strain, but they do not cause death of the experimental animals

  5. Gut microbes in correlation with mood: case study in a closed experimental human life support system.

    Science.gov (United States)

    Li, L; Su, Q; Xie, B; Duan, L; Zhao, W; Hu, D; Wu, R; Liu, H

    2016-08-01

    Gut microbial community, which may influence our mood, can be shaped by modulating the gut ecosystem through dietary strategies. Understanding the gut-brain correlationship in healthy people is important for maintenance of mental health and prevention of mental illnesses. A case study on the correlation between gut microbial alternation and mood swing of healthy adults was conducted in a closed human life support system during a 105-day experiment. Gut microbial community structures were analyzed using high-throughput sequencing every 2 weeks. A profile of mood states questionnaire was used to record the mood swings. Correlation between gut microbes and mood were identified with partial least squares discrimination analysis. Microbial community structures in the three healthy adults were strongly correlated with mood states. Bacterial genera Roseburia, Phascolarctobacterium, Lachnospira, and Prevotella had potential positive correlation with positive mood, while genera Faecalibacterium, Bifidobacterium, Bacteroides, Parabacteroides, and Anaerostipes were correlated with negative mood. Among which, Faecalibacterium spp. had the highest abundance, and showed a significant negative correlation with mood. Our results indicated that the composition of microbial community could play a role in emotional change in mentally physically healthy adults. © 2016 John Wiley & Sons Ltd.

  6. Sensitivity studies on the multi-sensor conductivity probe measurement technique for two-phase flows

    Energy Technology Data Exchange (ETDEWEB)

    Worosz, Ted [Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, 230 Reber Building, University Park, PA 16802 (United States); Bernard, Matt [The United States Nuclear Regulatory Commission, 11545 Rockville Pike, Rockville, MD 20852 (United States); Kong, Ran; Toptan, Aysenur [Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, 230 Reber Building, University Park, PA 16802 (United States); Kim, Seungjin, E-mail: skim@psu.edu [Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, 230 Reber Building, University Park, PA 16802 (United States); Hoxie, Chris [The United States Nuclear Regulatory Commission, 11545 Rockville Pike, Rockville, MD 20852 (United States)

    2016-12-15

    Highlights: • Revised conductivity probe circuit to eliminate signal “ghosting” among sensors. • Higher sampling frequencies suggested for bubble number frequency and a{sub i} measurements. • Two-phase parameter sensitivity to measurement duration and bubble number investigated. • Sensors parallel to pipe wall recommended for symmetric bubble velocity measurements. • Sensor separation distance ratio (s/d) greater than four minimizes bubble velocity error. - Abstract: The objective of this study is to advance the local multi-sensor conductivity probe measurement technique through systematic investigation into several practical aspects of a conductivity probe measurement system. Firstly, signal “ghosting” among probe sensors is found to cause artificially high bubble velocity measurements and low interfacial area concentration (a{sub i}) measurements that depend on sampling frequency and sensor impedance. A revised electrical circuit is suggested to eliminate this artificial variability. Secondly, the sensitivity of the probe measurements to sampling frequency is investigated in 13 two-phase flow conditions with superficial liquid and gas velocities ranging from 1.00–5.00 m/s and 0.17–2.0 m/s, respectively. With increasing gas flow rate, higher sampling frequencies, greater than 100 kHz in some cases, are required to adequately capture the bubble number frequency and a{sub i} measurements. This trend is due to the increase in gas velocity and the transition to the slug flow regime. Thirdly, the sensitivity of the probe measurements to the measurement duration as well as the sample number is investigated for the same flow conditions. Measurements of both group-I (spherical/distorted) and group-II (cap/slug/churn-turbulent) bubbles are found to be relatively insensitive to both the measurement duration and the number of bubbles, as long as the measurements are made for a duration long enough to capture a collection of samples characteristic to a

  7. Hydrothermal Fluid Permeability, Temperature, and Nutrient Fluxes: Three Controls on the Structure and the Dynamics of Subsurface Extremophilic Microbe Communities

    Science.gov (United States)

    Ryan, M. P.; Yang, J.

    2002-05-01

    We continue to develop a set of models whose aim is to provide broad constraints on the range of possible community structures for subsurface thermally-tolerant microbes. We combine studies of the three-dimensional internal structure of the dike and sill complexes of active volcanoes, studies of the scale- and direction-dependent 3-D in-situ permeability of intrusive and extrusive rocks from in-situ and laboratory data, numerical modelling of hydrothermal convection in volcanic interiors, data on the optimal metabolic and life-limiting thermal requirements of extremophilic microbes, with the set of nutrients and nutrient pathways required for the survival of given species of thermophiles and hyperthermophiles. With this mix of data bases and analysis tools, we can begin to divine a set of broad theoretical guidelines for constraining the structure and dynamics of extremophilic communities in the subsurface environments of volcanoes. We are searching for the first-order controls on transport. The effects of mineral attachment, detachment, and microbial reproduction may be incorporated in refinements of this basic model. Critical thermal intervals and/or isotherms that correlate with (1) optimal metabolic and (2) life-limiting temperatures for thermophilic microbes are, e.g., in degrees Celcius: Thermus thermophilius [70, 85]; Thermomicrobium roseum [70-75, 85]; Thermus aquaticus [70, 79]; and Sulfolobus acidocaldarius [70-75, 90]. Numerical models of the convective migration of thermophilic (50-80 C), and hyperthermophilic (80-113 C) microbes and their macromolecular amino acid building blocks (113- ~200 C) have been developed that explicitly incorporate the roles of fractures and fluid properties. Fluid transport properties are evaluated through the optimal metabolic and life-limiting temperate ranges and beyond. These models quantify our intuition with respect to controls on community structure and dynamics. Important relationships appear to be: (1) Great

  8. Indoor Air '93. Particles, microbes, radon

    International Nuclear Information System (INIS)

    Kalliokoski, P.; Jantunen, M.; Seppaenen, O.

    1993-01-01

    The conference was held in Helsinki, Finland, July 4-8, 1993. The proceedings of the conference were published in 6 volumes. The main topics of the volume 5 are: (1) particles, fibers and dust - their concentrations and sources in buildings, (2) Health effects of particles, (3) Need of asbestos replacement and encapsulation, (4) Seasonal and temporal variation of fungal and bacterial concentration, (5) The evaluation of microbial contamination of buildings, (6) New methods and comparison of different methods for microbial sampling and evaluation, (7) Microbes in building materials and HVAC-systems, (8) Prevention of microbial contamination in buildings, (9) Dealing with house dust mites, (10) Radon measurements and surveys in different countries, (11) The identification of homes with high radon levels, (12) The measurement methods and prediction of radon levels in buildings, and (13) Prevention of radon penetration from the soil

  9. The Hsp90 Complex in Microbes and Man | Center for Cancer Research

    Science.gov (United States)

    Why would cancer researchers be interested in how a bacteria named Escherichia coli (E. coli) rebuilds its cellular proteins after they have been inactivated by environmental stress such as heat?  The answer lies in a protein remodeling mechanism that is shared by microbes and man.

  10. Four-probe measurements with a three-probe scanning tunneling microscope

    International Nuclear Information System (INIS)

    Salomons, Mark; Martins, Bruno V. C.; Zikovsky, Janik; Wolkow, Robert A.

    2014-01-01

    We present an ultrahigh vacuum (UHV) three-probe scanning tunneling microscope in which each probe is capable of atomic resolution. A UHV JEOL scanning electron microscope aids in the placement of the probes on the sample. The machine also has a field ion microscope to clean, atomically image, and shape the probe tips. The machine uses bare conductive samples and tips with a homebuilt set of pliers for heating and loading. Automated feedback controlled tip-surface contacts allow for electrical stability and reproducibility while also greatly reducing tip and surface damage due to contact formation. The ability to register inter-tip position by imaging of a single surface feature by multiple tips is demonstrated. Four-probe material characterization is achieved by deploying two tips as fixed current probes and the third tip as a movable voltage probe

  11. Four-probe measurements with a three-probe scanning tunneling microscope

    Energy Technology Data Exchange (ETDEWEB)

    Salomons, Mark [National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta T6G 2M9 (Canada); Martins, Bruno V. C.; Zikovsky, Janik; Wolkow, Robert A., E-mail: rwolkow@ualberta.ca [National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta T6G 2M9 (Canada); Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1 (Canada)

    2014-04-15

    We present an ultrahigh vacuum (UHV) three-probe scanning tunneling microscope in which each probe is capable of atomic resolution. A UHV JEOL scanning electron microscope aids in the placement of the probes on the sample. The machine also has a field ion microscope to clean, atomically image, and shape the probe tips. The machine uses bare conductive samples and tips with a homebuilt set of pliers for heating and loading. Automated feedback controlled tip-surface contacts allow for electrical stability and reproducibility while also greatly reducing tip and surface damage due to contact formation. The ability to register inter-tip position by imaging of a single surface feature by multiple tips is demonstrated. Four-probe material characterization is achieved by deploying two tips as fixed current probes and the third tip as a movable voltage probe.

  12. Four-probe measurements with a three-probe scanning tunneling microscope.

    Science.gov (United States)

    Salomons, Mark; Martins, Bruno V C; Zikovsky, Janik; Wolkow, Robert A

    2014-04-01

    We present an ultrahigh vacuum (UHV) three-probe scanning tunneling microscope in which each probe is capable of atomic resolution. A UHV JEOL scanning electron microscope aids in the placement of the probes on the sample. The machine also has a field ion microscope to clean, atomically image, and shape the probe tips. The machine uses bare conductive samples and tips with a homebuilt set of pliers for heating and loading. Automated feedback controlled tip-surface contacts allow for electrical stability and reproducibility while also greatly reducing tip and surface damage due to contact formation. The ability to register inter-tip position by imaging of a single surface feature by multiple tips is demonstrated. Four-probe material characterization is achieved by deploying two tips as fixed current probes and the third tip as a movable voltage probe.

  13. Arsenic mineral dissolution and possible mobilization in mineral-microbe-groundwater environment.

    Science.gov (United States)

    Islam, A B M R; Maity, Jyoti Prakash; Bundschuh, Jochen; Chen, Chien-Yen; Bhowmik, Bejon Kumar; Tazaki, Kazue

    2013-11-15

    Arsenic (As) is widely distributed in the nature as ores or minerals. It has been attracted much attention for the global public health issue, especially for groundwater As contamination. The aim of this study was to elucidate the characteristics of microbes in groundwater where As-minerals were dissolved. An ex situ experiment was conducted with 7 standard As-minerals in bacteria-free groundwater and stored in experimental vessels for 1 year without supplementary nutrients. The pH (6.7-8.4) and EhS.H.E. (24-548 mV) changed between initial (0 day) and final stages (365 days) of experiment. The dissolution of As was detected higher from arsenolite (4240 ± 8.69 mg/L) and native arsenic (4538 ± 9.02 mg/L), whereas moderately dissolved from orpiment (653 ± 3.56 mg/L) and realgar (319 ± 2.56 mg/L) in compare to arsenopyrite (85 ± 1.25mg/L) and tennantite (3 ± 0.06 mg/L). Optical microscopic, scanning electron microscopic observations and flurometric enumeration revealed the abundance of As-resistant bacillus, coccus and filamentous types of microorganisms on the surface of most of As-mineral. 4'-6-Diamidino-2-phenylindole (DAPI)-stained epifluorescence micrograph confirmed the presence of DNA and carboxyfluorescein diacetate (CFDA) staining method revealed the enzymatically active bacteria on the surface of As-minerals such as in realgar (As4S4). Therefore, the microbes enable to survive and mobilize the As in groundwater by dissolution/bioweathering of As-minerals. Copyright © 2012. Published by Elsevier B.V.

  14. NeuroMEMS: Neural Probe Microtechnologies

    Directory of Open Access Journals (Sweden)

    Sam Musallam

    2008-10-01

    Full Text Available Neural probe technologies have already had a significant positive effect on our understanding of the brain by revealing the functioning of networks of biological neurons. Probes are implanted in different areas of the brain to record and/or stimulate specific sites in the brain. Neural probes are currently used in many clinical settings for diagnosis of brain diseases such as seizers, epilepsy, migraine, Alzheimer’s, and dementia. We find these devices assisting paralyzed patients by allowing them to operate computers or robots using their neural activity. In recent years, probe technologies were assisted by rapid advancements in microfabrication and microelectronic technologies and thus are enabling highly functional and robust neural probes which are opening new and exciting avenues in neural sciences and brain machine interfaces. With a wide variety of probes that have been designed, fabricated, and tested to date, this review aims to provide an overview of the advances and recent progress in the microfabrication techniques of neural probes. In addition, we aim to highlight the challenges faced in developing and implementing ultralong multi-site recording probes that are needed to monitor neural activity from deeper regions in the brain. Finally, we review techniques that can improve the biocompatibility of the neural probes to minimize the immune response and encourage neural growth around the electrodes for long term implantation studies.

  15. Induction of abiotic stress tolerance in plants by endophytic microbes.

    Science.gov (United States)

    Lata, R; Chowdhury, S; Gond, S K; White, J F

    2018-04-01

    Endophytes are micro-organisms including bacteria and fungi that survive within healthy plant tissues and promote plant growth under stress. This review focuses on the potential of endophytic microbes that induce abiotic stress tolerance in plants. How endophytes promote plant growth under stressful conditions, like drought and heat, high salinity and poor nutrient availability will be discussed. The molecular mechanisms for increasing stress tolerance in plants by endophytes include induction of plant stress genes as well as biomolecules like reactive oxygen species scavengers. This review may help in the development of biotechnological applications of endophytic microbes in plant growth promotion and crop improvement under abiotic stress conditions. Increasing human populations demand more crop yield for food security while crop production is adversely affected by abiotic stresses like drought, salinity and high temperature. Development of stress tolerance in plants is a strategy to cope with the negative effects of adverse environmental conditions. Endophytes are well recognized for plant growth promotion and production of natural compounds. The property of endophytes to induce stress tolerance in plants can be applied to increase crop yields. With this review, we intend to promote application of endophytes in biotechnology and genetic engineering for the development of stress-tolerant plants. © 2018 The Society for Applied Microbiology.

  16. Progress of CRISPR-Cas Based Genome Editing in Photosynthetic Microbes.

    Science.gov (United States)

    Naduthodi, Mihris Ibnu Saleem; Barbosa, Maria J; van der Oost, John

    2018-02-03

    The carbon footprint caused by unsustainable development and its environmental and economic impact has become a major concern in the past few decades. Photosynthetic microbes such as microalgae and cyanobacteria are capable of accumulating value-added compounds from carbon dioxide, and have been regarded as environmentally friendly alternatives to reduce the usage of fossil fuels, thereby contributing to reducing the carbon footprint. This light-driven generation of green chemicals and biofuels has triggered the research for metabolic engineering of these photosynthetic microbes. CRISPR-Cas systems are successfully implemented across a wide range of prokaryotic and eukaryotic species for efficient genome editing. However, the inception of this genome editing tool in microalgal and cyanobacterial species took off rather slowly due to various complications. In this review, we elaborate on the established CRISPR-Cas based genome editing in various microalgal and cyanobacterial species. The complications associated with CRISPR-Cas based genome editing in these species are addressed along with possible strategies to overcome these issues. It is anticipated that in the near future this will result in improving and expanding the microalgal and cyanobacterial genome engineering toolbox. © 2018 The Authors. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  17. Study of protein-probe complexation equilibria and protein-surfactant interaction using charge transfer fluorescence probe methyl ester of N,N-dimethylamino naphthyl acrylic acid

    Energy Technology Data Exchange (ETDEWEB)

    Mahanta, Subrata; Balia Singh, Rupashree; Bagchi, Arnab [Department of Chemistry University of Calcutta 92, A.P.C. Road, Kolkata 700009 (India); Nath, Debnarayan [Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032 (India); Guchhait, Nikhil, E-mail: nguchhait@yahoo.co [Department of Chemistry University of Calcutta 92, A.P.C. Road, Kolkata 700009 (India)

    2010-06-15

    In this paper, we demonstrate the interaction between intramolecular charge transfer (ICT) probe-Methyl ester of N,N-dimethylamino naphthyl acrylic acid (MDMANA) with bovine serum albumin (BSA) using absorption and fluorescence emission spectroscopy. The nature of probe protein binding interaction, fluorescence resonance energy transfer from protein to probe and time resolved fluorescence decay measurement predict that the probe molecule binds strongly to the hydrophobic cavity of the protein. Furthermore, the interaction of the anionic surfactant sodium dodecyl sulphate (SDS) with water soluble protein BSA has been investigated using MDMANA as fluorescenece probe. The changes in the spectral characteristics of charge transfer fluorescence probe MDMANA in BSA-SDS environment reflects well the nature of the protein-surfactant binding interaction such as specific binding, non-cooperative binding, cooperative binding and saturation binding.

  18. Hyperpolarized NMR Probes for Biological Assays

    Directory of Open Access Journals (Sweden)

    Sebastian Meier

    2014-01-01

    Full Text Available During the last decade, the development of nuclear spin polarization enhanced (hyperpolarized molecular probes has opened up new opportunities for studying the inner workings of living cells in real time. The hyperpolarized probes are produced ex situ, introduced into biological systems and detected with high sensitivity and contrast against background signals using high resolution NMR spectroscopy. A variety of natural, derivatized and designed hyperpolarized probes has emerged for diverse biological studies including assays of intracellular reaction progression, pathway kinetics, probe uptake and export, pH, redox state, reactive oxygen species, ion concentrations, drug efficacy or oncogenic signaling. These probes are readily used directly under natural conditions in biofluids and are often directly developed and optimized for cellular assays, thus leaving little doubt about their specificity and utility under biologically relevant conditions. Hyperpolarized molecular probes for biological NMR spectroscopy enable the unbiased detection of complex processes by virtue of the high spectral resolution, structural specificity and quantifiability of NMR signals. Here, we provide a survey of strategies used for the selection, design and use of hyperpolarized NMR probes in biological assays, and describe current limitations and developments.

  19. Probing the recreational home –The cultural probe as a communicative tool for researcher and user

    OpenAIRE

    Kristav, Per

    2005-01-01

    How can qualitative, ethnographic and emotional aspects from probe users be mapped at the same time as they get something meaningful in return? The emphasis is here on intellectual rewards during probe work rather than future good designs that in a long term perspective can be beneficial for the probe user. This case study has elaborated the traditional use of cultural probes [1] with a selection of ten families with small children in the Öresund region. The idea was to evoke thoughts abou...

  20. Using microbes as a key tool to unravel the mechanism of autophagy and the functions of the ATG proteins

    Directory of Open Access Journals (Sweden)

    Mario Mauthe

    2016-12-01

    Full Text Available The study of microbe infections has always been a very effective approach to unveil and dissect cellular pathways. Autophagy is not an exception. Although some of the breakthrough discoveries in the field were obtained using yeast, pathogens have been and still are a great tool to discover and characterize new molecular and functional aspects of autophagy. Research on pathogens has helped to acquire knowledge about selective types of autophagy and the assembly of the autophagy machinery, i.e the autophagy-related (ATG proteins, but also about alternative cellular roles of this pathway, such as secretion. Finally, microbes have also served to discover and characterize unconventional functions of the ATG proteins, which are uncoupled from their role in autophagy. In our recent study, we have taken advantage of viruses as a screening tool to determine the extent of the unconventional functions of the ATG proteome and characterize one of them.

  1. Oligonucleotides as probes for studying polymerization reactions in dilute aqueous solution

    Science.gov (United States)

    Kolb, V.; Orgel, L. E.; Miller, S. L. (Principal Investigator)

    1994-01-01

    We have prepared a [32P]-labled oligonucleotide probe carrying a free primary amine at its 3'-terminus. This probe is used to initiate polymerization of aziridine (ethyleneimine) in aqueous solution. The nature of the oligomeric products and the kinetics of their formation are then monitored by gel electrophoresis. Our results are generally consistent with those obtained using conventional techniques. We have also investigated the effect of polyanionic templates on the rate of oligomerization of aziridine. We find that water-soluble polyanions generally accelerate the polymerization. The sodium salt of polymethacrylic acid is the most effective of the templates that we studied. The methods introduced in this paper should be applicable to a variety of polymerization reactions in aqueous solution. They should greatly simplify the screening of potentially prebiotic polymerization reactions.

  2. Effects of Gut Microbes on Nutrient Absorption and Energy Regulation

    OpenAIRE

    Krajmalnik-Brown, Rosa; Ilhan, Zehra-Esra; Kang, Dae-Wook; DiBaise, John K.

    2012-01-01

    Malnutrition may manifest as either obesity or undernutrition. Accumulating evidence suggests that the gut microbiota plays an important role in the harvest, storage, and expenditure of energy obtained from the diet. The composition of the gut microbiota has been shown to differ between lean and obese humans and mice; however, the specific roles that individual gut microbes play in energy harvest remain uncertain. The gut microbiota may also influence the development of conditions characteriz...

  3. The Chemistry of Plant–Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance

    Science.gov (United States)

    Mhlongo, Msizi I.; Piater, Lizelle A.; Madala, Ntakadzeni E.; Labuschagne, Nico; Dubery, Ian A.

    2018-01-01

    Plant roots communicate with microbes in a sophisticated manner through chemical communication within the rhizosphere, thereby leading to biofilm formation of beneficial microbes and, in the case of plant growth-promoting rhizomicrobes/-bacteria (PGPR), resulting in priming of defense, or induced resistance in the plant host. The knowledge of plant–plant and plant–microbe interactions have been greatly extended over recent years; however, the chemical communication leading to priming is far from being well understood. Furthermore, linkage between below- and above-ground plant physiological processes adds to the complexity. In metabolomics studies, the main aim is to profile and annotate all exo- and endo-metabolites in a biological system that drive and participate in physiological processes. Recent advances in this field has enabled researchers to analyze 100s of compounds in one sample over a short time period. Here, from a metabolomics viewpoint, we review the interactions within the rhizosphere and subsequent above-ground ‘signalomics’, and emphasize the contributions that mass spectrometric-based metabolomic approaches can bring to the study of plant-beneficial – and priming events. PMID:29479360

  4. Formulation of microbes inoculum: AMF, PSB and Rhizobium isolated of ex-coal mining site for Acacia crassicarpa Cunn. Ex-benth seedlings

    Directory of Open Access Journals (Sweden)

    ENNY WIDYATI

    2007-07-01

    Full Text Available The shoddier succeed land revegetation particularly caused by least adaptability of the seedlings planted on this site. To encourage their growth and survival rate it can be achieved by means do inoculation with the compatible functional microbes such as rhizobium, Psolubilizing bacteria (PSB and/or arbuscular-mycorrhiza fungy (AMF. This reserach is aimed to formulate the most compatible inoculant to support the growth of A. crassicarpa seedlings. Compatibility study is carried out in RCB design with 3 replications, each contain 5 seedlings. Height and biomass are accessed to measure the growth responses of the seedlings. The result showed that the best reponse is given by consortia that consist of the three kinds of these microbes. This increase the shoot biomass (137% compare to the control. The consortia also improved N 164%, P 335% and K 167% in the plant tissues. While pure AMF improved absorption of N plants 80%, P 383% and K 51% compare to the control. It is suggested that to prepare the A. crassicarpa seedlings is better inoculated by consortium of microbes or AMF as a sole inoculant.

  5. Study of sapphire probe tip wear when scanning on different materials

    International Nuclear Information System (INIS)

    Nicolet, Anaïs; Küng, Alain; Meli, Felix

    2012-01-01

    The accuracy of today's coordinate measuring machines (CMM) has reached a level at which exact knowledge of each component is required. The role of the probe tip is particularly crucial as it is in contact with the sample surface. Understanding how the probe tip wears off will help to narrow the measurement errors. In this work, wear of a sapphire sphere was studied for different scanning conditions and with different sample materials. Wear depth on the probe was investigated using an automated process in situ on the METAS micro-CMM and completed by measurements with an atomic force microscope. We often found a linear dependence between the wear depth and the scan length ranging from 0.5 to 9 nm m −1 , due to variations in scan speed, contact force or sample material. In the case of steel, the wear rate is proportional to the scan speed, while for aluminum several processes seem to interact. A large amount of debris was visible after the tests. Except for aluminum, wear was visible only on the sphere and not on the sample. Sapphire/steel is the worst combination in terms of wear, whereas the combination sapphire/ceramic exhibits almost no wear. (paper)

  6. Where do pulse oximeter probes break?

    Science.gov (United States)

    Crede, S; Van der Merwe, G; Hutchinson, J; Woods, D; Karlen, W; Lawn, J

    2014-06-01

    Pulse oximetry, a non-invasive method for accurate assessment of blood oxygen saturation (SPO2), is an important monitoring tool in health care facilities. However, it is often not available in many low-resource settings, due to expense, overly sophisticated design, a lack of organised procurement systems and inadequate medical device management and maintenance structures. Furthermore medical devices are often fragile and not designed to withstand the conditions of low-resource settings. In order to design a probe, better suited to the needs of health care facilities in low-resource settings this study aimed to document the site and nature of pulse oximeter probe breakages in a range of different probe designs in a low to middle income country. A retrospective review of job cards relating to the assessment and repair of damaged or faulty pulse oximeter probes was conducted at a medical device repair company based in Cape Town, South Africa, specializing in pulse oximeter probe repairs. 1,840 job cards relating to the assessment and repair of pulse oximeter probes were reviewed. 60.2 % of probes sent for assessment were finger-clip probes. For all probes, excluding the neonatal wrap probes, the most common point of failure was the probe wiring (>50 %). The neonatal wrap most commonly failed at the strap (51.5 %). The total cost for quoting on the broken pulse oximeter probes and for the subsequent repair of devices, excluding replacement components, amounted to an estimated ZAR 738,810 (USD $98,508). Improving the probe wiring would increase the life span of pulse oximeter probes. Increasing the life span of probes will make pulse oximetry more affordable and accessible. This is of high priority in low-resource settings where frequent repair or replacement of probes is unaffordable or impossible.

  7. Toward design-based engineering of industrial microbes.

    Science.gov (United States)

    Tyo, Keith E J; Kocharin, Kanokarn; Nielsen, Jens

    2010-06-01

    Engineering industrial microbes has been hampered by incomplete knowledge of cell biology. Thus an iterative engineering cycle of modeling, implementation, and analysis has been used to increase knowledge of the underlying biology while achieving engineering goals. Recent advances in Systems Biology technologies have drastically improved the amount of information that can be collected in each iteration. As well, Synthetic Biology tools are melding modeling and molecular implementation. These advances promise to move microbial engineering from the iterative approach to a design-oriented paradigm, similar to electrical circuits and architectural design. Genome-scale metabolic models, new tools for controlling expression, and integrated -omics analysis are described as key contributors in moving the field toward Design-based Engineering. Copyright 2010 Elsevier Ltd. All rights reserved.

  8. Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp.

    Science.gov (United States)

    Gomez, Andres; Rothman, Jessica M; Petrzelkova, Klara; Yeoman, Carl J; Vlckova, Klara; Umaña, Juan D; Carr, Monica; Modry, David; Todd, Angelique; Torralba, Manolito; Nelson, Karen E; Stumpf, Rebecca M; Wilson, Brenda A; Blekhman, Ran; White, Bryan A; Leigh, Steven R

    2016-02-01

    Although the critical role that our gastrointestinal microbes play in host physiology is now well established, we know little about the factors that influenced the evolution of primate gut microbiomes. To further understand current gut microbiome configurations and diet-microbe co-metabolic fingerprints in primates, from an evolutionary perspective, we characterized fecal bacterial communities and metabolomic profiles in 228 fecal samples of lowland and mountain gorillas (G. g. gorilla and G. b. beringei, respectively), our closest evolutionary relatives after chimpanzees. Our results demonstrate that the gut microbiomes and metabolomes of these two species exhibit significantly different patterns. This is supported by increased abundance of metabolites and bacterial taxa associated with fiber metabolism in mountain gorillas, and enrichment of markers associated with simple sugar, lipid and sterol turnover in the lowland species. However, longitudinal sampling shows that both species' microbiomes and metabolomes converge when hosts face similar dietary constraints, associated with low fruit availability in their habitats. By showing differences and convergence of diet-microbe co-metabolic fingerprints in two geographically isolated primate species, under specific dietary stimuli, we suggest that dietary constraints triggered during their adaptive radiation were potential factors behind the species-specific microbiome patterns observed in primates today.

  9. Temporal variation selects for diet–microbe co-metabolic traits in the gut of Gorilla spp

    Science.gov (United States)

    Gomez, Andres; Rothman, Jessica M; Petrzelkova, Klara; Yeoman, Carl J; Vlckova, Klara; Umaña, Juan D; Carr, Monica; Modry, David; Todd, Angelique; Torralba, Manolito; Nelson, Karen E; Stumpf, Rebecca M; Wilson, Brenda A; Blekhman, Ran; White, Bryan A; Leigh, Steven R

    2016-01-01

    Although the critical role that our gastrointestinal microbes play in host physiology is now well established, we know little about the factors that influenced the evolution of primate gut microbiomes. To further understand current gut microbiome configurations and diet–microbe co-metabolic fingerprints in primates, from an evolutionary perspective, we characterized fecal bacterial communities and metabolomic profiles in 228 fecal samples of lowland and mountain gorillas (G. g. gorilla and G. b. beringei, respectively), our closest evolutionary relatives after chimpanzees. Our results demonstrate that the gut microbiomes and metabolomes of these two species exhibit significantly different patterns. This is supported by increased abundance of metabolites and bacterial taxa associated with fiber metabolism in mountain gorillas, and enrichment of markers associated with simple sugar, lipid and sterol turnover in the lowland species. However, longitudinal sampling shows that both species' microbiomes and metabolomes converge when hosts face similar dietary constraints, associated with low fruit availability in their habitats. By showing differences and convergence of diet–microbe co-metabolic fingerprints in two geographically isolated primate species, under specific dietary stimuli, we suggest that dietary constraints triggered during their adaptive radiation were potential factors behind the species-specific microbiome patterns observed in primates today. PMID:26315972

  10. 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.

  11. Traversing probe system

    Science.gov (United States)

    Mashburn, Douglas N.; Stevens, Richard H.; Woodall, Harold C.

    1977-01-01

    This invention comprises a rotatable annular probe-positioner which carries at least one radially disposed sensing probe, such as a Pitot tube having a right-angled tip. The positioner can be coaxially and rotatably mounted within a compressor casing or the like and then actuated to orient the sensing probe as required to make measurements at selected stations in the annulus between the positioner and compressor casing. The positioner can be actuated to (a) selectively move the probe along its own axis, (b) adjust the yaw angle of the right-angled probe tip, and (c) revolve the probe about the axis common to the positioner and casing. A cam plate engages a cam-follower portion of the probe and normally rotates with the positioner. The positioner includes a first-motor-driven ring gear which effects slidable movement of the probe by rotating the positioner at a time when an external pneumatic cylinder is actuated to engage the cam plate and hold it stationary. When the pneumatic cylinder is not actuated, this ring gear can be driven to revolve the positioner and thus the probe to a desired circumferential location about the above-mentioned common axis. A second motor-driven ring gear included in the positioner can be driven to rotate the probe about its axis, thus adjusting the yaw angle of the probe tip. The positioner can be used in highly corrosive atmosphere, such as gaseous uranium hexafluoride.

  12. Traversing probe system

    International Nuclear Information System (INIS)

    Mashburn, D.N.; Stevens, R.H.; Woodall, H.C.

    1977-01-01

    This invention comprises a rotatable annular probe-positioner which carries at least one radially disposed sensing probe, such as a Pitot tube having a right-angled tip. The positioner can be coaxially and rotatably mounted within a compressor casing or the like and then actuated to orient the sensing probe as required to make measurements at selected stations in the annulus between the positioner and compressor casing. The positioner can be actuated to (a) selectively move the probe along its own axis, (b) adjust the yaw angle of the right-angled probe tip, and (c) revolve the probe about the axis common to the positioner and casing. A cam plate engages a cam-follower portion of the probe and normally rotates with the positioner. The positioner includes a first-motor-driven ring gear which effects slidable movement of the probe by rotating the positioner at a time when an external pneumatic cylinder is actuated to engage the cam plate and hold it stationary. When the pneumatic cylinder is not actuated, this ring gear can be driven to revolve the positioner and thus the probe to a desired circumferential location about the above-mentioned common axis. A second motor-driven ring gear included in the positioner can be driven to rotate the probe about its axis, thus adjusting the yaw angle of the probe tip. The positioner can be used in highly corrosive atmosphere, such as gaseous uranium hexafluoride. 10 claims, 6 figures

  13. Interaction of a ballistic probe with gaseous media

    International Nuclear Information System (INIS)

    Kucerovsky, Zden; Greason, William D

    2008-01-01

    Free-flying metal probes are used to determine charge densities in gaseous media containing free charge or low density plasma. The trajectory of the probe is ensured either by gravity or by propelling the probe to a certain velocity at the launch site. While travelling, the probe charge changes from its launch-site magnitude to that related to the space charge density existing along the trajectory. The degree to which the probe's arrival-site charge magnitude matches the space charge density in the area of interest depends on the probe shape and on the charge exchange processes between the probe body and the medium. The paper studies a probe acting as a free-flying charge carrier in air, and discusses the problems that may lead to an imbalance between the charge collected by the probe in the area of interest and the charge measured at the arrival site. The analysis and the described experiments are of the ballistic type: a small, triboelectrically pre-charged metal probe was propelled on a horizontal path, and the charge carried by the probe was measured at several points along the trajectory by means of contact-free induction rings; the initial and final charges were determined by static Faraday cups. A charge disparity was found under certain conditions, and its degree explained by the effects of the charge carrier potential. The studied probe charges ranged from 10 to 50 nF, and the fly-times needed to cross a one-meter path ranged from 20 to 40 ms. The probe to gas charge exchange experiments and their analysis yielded conditions under which the probe lost approximately 10 % of its charge. The results of our study may be of interest to those who intend to use the free-flying probe technique for the determination of space charge density.

  14. An experimental study of simultaneous ablation with dual probes in radiofrequency thermal ablation

    International Nuclear Information System (INIS)

    Jang, Il Soo; Rhim, Hyun Chul; Koh, Byung Hee; Cho, On Koo; Seo, Heung Suk; Kim, Yong Soo; Kim, Young Sun; Heo, Jeong Nam

    2003-01-01

    To determine the differences between sequential ablation with a single probe and simultaneous ablation with dual probes. Using two 14-gauge expandable probes (nine internal prongs with 4-cm deployment), radiofrequency was applied sequentially (n=8) or simultaneously (n=8) to ten ex-vivo cow livers. Before starting ablation, two RF probes with an inter-probe space of 2 cm (n=8) or 3 cm (n=8) were inserted. In the sequential group, switching the connecting cable to an RF generator permitted ablation with the second probe just after ablation with the first probe had finished. In the simultaneous group, single ablation was performed only after connecting the shafts of both RF probes using a connection device. Each ablation lasted 7 minutes at a target temperature of 105-110 .deg. C. The size and shape of the ablated area, and total ablation time were then compared between the two groups. With 2-cm spacing, the group, mean length and overlapping width of ablated lesions were, respectively, 5.20 and 5.05 cm in the sequential group (n=4), and 5.81 and 5.65 cm in the simultaneous group (n=4). With 3-cm spacing, the corresponding figures were 4.99 and 5.60 cm in the sequential group (n=4), and 6.04 and 6.78 cm in the simultaneous group (n=4). With 2-cm spacing, the mean depth of the proximal waist was 0.58 cm in the sequential (group and 0.28 cm in the simultaneous group, while with 3-cm spacing, the corresponding figures were 1.65 and 1.48 cm. In neither group was there a distal waist. Mean total ablation time was 23.4 minutes in the sequential group and 14 minutes in the simultaneous group. In terms of ablation size and ablation time, simultaneous radiofrequency ablation with dual probes is superior to sequential ablation with a single probe. A simultaneous approach will enable an operator to overcome difficulty in probe repositioning during overlapping ablation, resulting in complete ablation with a successful safety margin

  15. Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes

    DEFF Research Database (Denmark)

    Shepelin, Denis; Hansen, Anne Sofie Lærke; Lennen, Rebecca

    2018-01-01

    , we focus primarily on a more challenging problem-the use of evolutionary engineering for improving the production of chemicals in microbes directly. We describe recent developments in evolutionary engineering strategies, in general, and discuss, in detail, case studies where production of a chemical......Microbial cell factories have proven to be an economical means of production for many bulk, specialty, and fine chemical products. However, we still lack both a holistic understanding of organism physiology and the ability to predictively tune enzyme activities in vivo, thus slowing down rational...... engineering of industrially relevant strains. An alternative concept to rational engineering is to use evolution as the driving force to select for desired changes, an approach often described as evolutionary engineering. In evolutionary engineering, in vivo selections for a desired phenotype are combined...

  16. Signals and cues in the evolution of plant-microbe communication.

    Science.gov (United States)

    Padje, Anouk Van't; Whiteside, Matthew D; Kiers, E Toby

    2016-08-01

    Communication has played a key role in organismal evolution. If sender and receiver have a shared interest in propagating reliable information, such as when they are kin relatives, then effective communication can bring large fitness benefits. However, interspecific communication (among different species) is more prone to dishonesty. Over the last decade, plants and their microbial root symbionts have become a model system for studying interspecific molecular crosstalk. However, less is known about the evolutionary stability of plant-microbe communication. What prevents partners from hijacking or manipulating information to their own benefit? Here, we focus on communication between arbuscular mycorrhizal fungi and their host plants. We ask how partners use directed signals to convey specific information, and highlight research on the problem of dishonest signaling. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Prediction of highly expressed genes in microbes based on chromatin accessibility

    Directory of Open Access Journals (Sweden)

    Ussery David W

    2007-02-01

    Full Text Available Abstract Background It is well known that gene expression is dependent on chromatin structure in eukaryotes and it is likely that chromatin can play a role in bacterial gene expression as well. Here, we use a nucleosomal position preference measure of anisotropic DNA flexibility to predict highly expressed genes in microbial genomes. We compare these predictions with those based on codon adaptation index (CAI values, and also with experimental data for 6 different microbial genomes, with a particular interest in experimental data from Escherichia coli. Moreover, position preference is examined further in 328 sequenced microbial genomes. Results We find that absolute gene expression levels are correlated with the position preference in many microbial genomes. It is postulated that in these regions, the DNA may be more accessible to the transcriptional machinery. Moreover, ribosomal proteins and ribosomal RNA are encoded by DNA having significantly lower position preference values than other genes in fast-replicating microbes. Conclusion This insight into DNA structure-dependent gene expression in microbes may be exploited for predicting the expression of non-translated genes such as non-coding RNAs that may not be predicted by any of the conventional codon usage bias approaches.

  18. The Oxford Probe: an open access five-hole probe for aerodynamic measurements

    Science.gov (United States)

    Hall, B. F.; Povey, T.

    2017-03-01

    The Oxford Probe is an open access five-hole probe designed for experimental aerodynamic measurements. The open access probe can be manufactured by the end user via additive manufacturing (metal or plastic). The probe geometry, drawings, calibration maps, and software are available under a creative commons license. The purpose is to widen access to aerodynamic measurement techniques in education and research environments. There are many situations in which the open access probe will allow results of comparable accuracy to a well-calibrated commercial probe. We discuss the applications and limitations of the probe, and compare the calibration maps for 16 probes manufactured in different materials and at different scales, but with the same geometrical design.

  19. The Oxford Probe: an open access five-hole probe for aerodynamic measurements

    International Nuclear Information System (INIS)

    Hall, B F; Povey, T

    2017-01-01

    The Oxford Probe is an open access five-hole probe designed for experimental aerodynamic measurements. The open access probe can be manufactured by the end user via additive manufacturing (metal or plastic). The probe geometry, drawings, calibration maps, and software are available under a creative commons license. The purpose is to widen access to aerodynamic measurement techniques in education and research environments. There are many situations in which the open access probe will allow results of comparable accuracy to a well-calibrated commercial probe. We discuss the applications and limitations of the probe, and compare the calibration maps for 16 probes manufactured in different materials and at different scales, but with the same geometrical design. (paper)

  20. On the truncation of the azimuthal mode spectrum of high-order probes in probe-corrected spherical near-field antenna measurements

    DEFF Research Database (Denmark)

    Pivnenko, Sergey; Laitinen, Tommi

    2011-01-01

    Azimuthal mode (m mode) truncation of a high-order probe pattern in probe-corrected spherical near-field antenna measurements is studied in this paper. The results of this paper provide rules for appropriate and sufficient m-mode truncation for non-ideal first-order probes and odd-order probes wi...

  1. Microbes Characteristics in Groundwater Flow System in Mountainous Area

    Science.gov (United States)

    Yamamoto, Chisato; Tsujimura, Maki; Kato, Kenji; Sakakibara, Koichi; Ogawa, Mahiro; Sugiyama, Ayumi; Nagaosa, Kazuyo

    2017-04-01

    We focus on a possibility of microbes as a tracer for groundwater flow investigation. Some previous papers showed that the total number of prokaryotes in groundwater has correlation with depth and geology (Parkes et al., 1994; Griebler et al., 2009; Kato et al., 2012). However, there are few studies investigating both microbe characteristics and groundwater flow system. Therefore, we investigated a relationship between the total number of prokaryotes and age of spring water and groundwater. Intensive field survey was conducted at four mountainous areas, namely Mt. Fuji (volcano), a headwater at Mt. Setohachi, a headwater at River Oi and a headwater at River Nagano underlain by volcanic lava at Mt. Fuji, granite at Mt. Setohachi and sedimentary rock at River Oi and River Nagano. We collected totally 40 spring water/ groundwater samples in these mountainous areas in October 2015, August, October and November 2016 and analyzed concentration of inorganic ions, the stable isotopes of oxygen - 18, deuterium, CFCs and SF6. Also, we counted prokaryotic cells under the epifluorescence microscopy after fixation and filteration. The total number of prokaryotes in the spring water/ groundwater ranged from 1.0×102 to 7.0×103cells mL-1 at the Mt. Fuji, 1.3×104 to 2.7×105cells mL-1 at Mt. Setohachi, 3.1×104cells mL-1 at River Oi and 1.8×105 to 3.2×106cells mL-1 at River Nagano. The SF6 age of the spring water/ groundwater ranged from 8 to 64 years at Mt. Fuji, 2 to 32.5 years at Mt. Setohachi, 2.5 years at River Oi and 15 to 16 years at River Nagano. The total number of prokaryotes showed a clear negative correlation with residence time of spring water/ groundwater in all regions. Especially the prokaryotes number increased in the order of 102 cells mL-1 with decreasing of residence time in approximately 10 years in the groundwater and spring water with the age less than 15 years.

  2. Microbes and Viruses Are Bugging the Gut in Celiac Disease. Are They Friends or Foes?

    Science.gov (United States)

    Lerner, Aaron; Arleevskaya, Marina; Schmiedl, Andreas; Matthias, Torsten

    2017-01-01

    The links between microorganisms/viruses and autoimmunity are complex and multidirectional. A huge number of studies demonstrated the triggering impact of microbes and viruses as the major environmental factors on the autoimmune and inflammatory diseases. However, growing evidences suggest that infectious agents can also play a protective role or even abrogate these processes. This protective crosstalk between microbes/viruses and us might represent a mutual beneficial equilibrium relationship between two cohabiting ecosystems. The protective pathways might involve post-translational modification of proteins, decreased intestinal permeability, Th1 to Th2 immune shift, induction of apoptosis, auto-aggressive cells relocation from the target organ, immunosuppressive extracellular vesicles and down regulation of auto-reactive cells by the microbial derived proteins. Our analysis demonstrates that the interaction of the microorganisms/viruses and celiac disease (CD) is always a set of multidirectional processes. A deeper inquiry into the CD interplay with Herpes viruses and Helicobacter pylori demonstrates that the role of these infections, suggested to be potential CD protectors, is not as controversial as for the other infectious agents. The outcome of these interactions might be due to a balance between these multidirectional processes.

  3. Diversity of Cellulolytic Microbes and the Biodegradation of Municipal Solid Waste by a Potential Strain

    Directory of Open Access Journals (Sweden)

    S. P. Gautam

    2012-01-01

    Full Text Available Municipal solid waste contains high amounts of cellulose, which is an ideal organic waste for the growth of most of microorganism as well as composting by potential microbes. In the present study, Congo red test was performed for screening of microorganism, and, after selecting a potential strains, it was further used for biodegradation of organic municipal solid waste. Forty nine out of the 250 different microbes tested (165 belong to fungi and 85 to bacteria produced cellulase enzyme and among these Trichoderma viride was found to be a potential strain in the secondary screening. During the biodegradation of organic waste, after 60 days, the average weight losses were 20.10% in the plates and 33.35% in the piles. There was an increase in pH until 20 days. pH however, stabilized after 30 days in the piles. Temperature also stabilized as the composting process progressed in the piles. The high temperature continued until 30 days of decomposition, after which the temperature dropped to 40°C and below during the maturation. Good quality compost was obtained in 60 days.

  4. Microbes and Viruses Are Bugging the Gut in Celiac Disease. Are They Friends or Foes?

    Directory of Open Access Journals (Sweden)

    Aaron Lerner

    2017-08-01

    Full Text Available The links between microorganisms/viruses and autoimmunity are complex and multidirectional. A huge number of studies demonstrated the triggering impact of microbes and viruses as the major environmental factors on the autoimmune and inflammatory diseases. However, growing evidences suggest that infectious agents can also play a protective role or even abrogate these processes. This protective crosstalk between microbes/viruses and us might represent a mutual beneficial equilibrium relationship between two cohabiting ecosystems. The protective pathways might involve post-translational modification of proteins, decreased intestinal permeability, Th1 to Th2 immune shift, induction of apoptosis, auto-aggressive cells relocation from the target organ, immunosuppressive extracellular vesicles and down regulation of auto-reactive cells by the microbial derived proteins. Our analysis demonstrates that the interaction of the microorganisms/viruses and celiac disease (CD is always a set of multidirectional processes. A deeper inquiry into the CD interplay with Herpes viruses and Helicobacter pylori demonstrates that the role of these infections, suggested to be potential CD protectors, is not as controversial as for the other infectious agents. The outcome of these interactions might be due to a balance between these multidirectional processes.

  5. Probe Techniques. Introductory Remarks

    Energy Technology Data Exchange (ETDEWEB)

    Emeleus, K. G. [School of Physics and Applied Mathematics, Queen' s University, Belfast (United Kingdom)

    1968-04-15

    In this brief introduction to the session on probes, the history of theii development is first touched on briefly. Reference is then made to the significance of the work to be described by Medicus, for conductivity and recombination calculations, and by Lam and Su, for a wide range of medium and higher pressure plasmas. Finally, a number of other probe topics are mentioned, including multiple probes; probes in electronegative plasmas; resonance probes; probes in noisy discharges; probes as oscillation detectors; use of probes where space-charge is not negligible. (author)

  6. Probe-diverse ptychography

    Energy Technology Data Exchange (ETDEWEB)

    Peterson, I., E-mail: isaac.russellpeterson@rmit.edu.au [ARC Centre of Excellence for Coherent X-ray Science, the University of Melbourne, School of Physics, Victoria 3010 (Australia); Harder, R. [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States); Robinson, I.K. [Research Complex at Harwell, Didcot, Oxfordshire OX11 0DE (United Kingdom); London Centre for Nanotechnology, University College London, London WC1H 0AH (United Kingdom)

    2016-12-15

    We propose an extension of ptychography where the target sample is scanned separately through several probes with distinct amplitude and phase profiles and a diffraction image is recorded for each probe and each sample translation. The resulting probe-diverse dataset is used to iteratively retrieve high-resolution images of the sample and all probes simultaneously. The method is shown to yield significant improvement in the reconstructed sample image compared to the image obtained using the standard single-probe ptychographic phase-retrieval scheme.

  7. The bee microbiome: Impact on bee health and model for evolution and ecology of host-microbe interactions

    Science.gov (United States)

    Engel, Philipp; Kwong, Waldan K.; McFrederick, Quinn; Anderson, Kirk E.; Barribeau, Seth Michael; Chandler, James Angus; Cornman, Robert S.; Dainat, Jacques; de Miranda, Joachim R.; Doublet, Vincent; Emery, Olivier; Evans, Jay D.; Farinelli, Laurent; Flenniken, Michelle L.; Granberg, Fredrik; Grasis, Juris A.; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G.; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J.; Powell, Eli; Sadd, Ben M.; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Song, Se Jin; Schwarz, Ryan S.; vanEngelsdorp, Dennis; Dainat, Benjamin

    2016-01-01

    As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

  8. The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions

    Directory of Open Access Journals (Sweden)

    Philipp Engel

    2016-05-01

    Full Text Available As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

  9. The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.

    Science.gov (United States)

    Engel, Philipp; Kwong, Waldan K; McFrederick, Quinn; Anderson, Kirk E; Barribeau, Seth Michael; Chandler, James Angus; Cornman, R Scott; Dainat, Jacques; de Miranda, Joachim R; Doublet, Vincent; Emery, Olivier; Evans, Jay D; Farinelli, Laurent; Flenniken, Michelle L; Granberg, Fredrik; Grasis, Juris A; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J; Powell, Eli; Sadd, Ben M; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Song, Se Jin; Schwarz, Ryan S; vanEngelsdorp, Dennis; Dainat, Benjamin

    2016-04-26

    As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health. Copyright © 2016 Engel et al.

  10. A Hair & a Fungus: Showing Kids the Size of a Microbe

    Science.gov (United States)

    Richter, Dana L.

    2013-01-01

    A simple method is presented to show kids the size of a microbe--a fungus hypha--compared to a human hair. Common household items are used to make sterile medium on a stove or hotplate, which is dispensed in the cells of a weekly plastic pill box. Mold fungi can be easily and safely grown on the medium from the classroom environment. A microscope…

  11. Study of a Laser-Produced Plasma by Langmuir Probes

    DEFF Research Database (Denmark)

    Chang, C. T.; Hasimi, M.; Pant, H. C.

    1977-01-01

    -emission peak and the main plasma from the target. The flow velocity, density and electron temperature of the plasma were determined. The expansion of the plasma was found to be adiabatic, yielding gamma =5/3. The spatial distribution of the plasma was observed to be strongly anisotropic.......The structure, the parameters and the expansion of the plasma produced by focusing a 7 J, 20 ns Nd-glass laser on stainless-steel and glass targets suspended in a high-vacuum chamber were investigated by Langmuir probes. It was observed that the probe signals consisted of a photoelectric...

  12. Soil Microbes and soil microbial proteins: interactions with clay minerals

    International Nuclear Information System (INIS)

    Spence, A.; Kelleher, B. P.

    2009-01-01

    Bacterial enumeration in soil environments estimates that the population may reach approximately 10 1 0 g - 1 of soil and comprise up to 90% of the total soil microbial biomass. Bacteria are present in soils as single cells or multicell colonies and often strongly adsorb onto mineral surfaces such as sand and clay. The interactions of microbes and microbial biomolecules with these minerals have profound impacts on the physical, chemical and biological properties of soils. (Author)

  13. Enrichment of degrading microbes and bioremediation of petrochemical contaminants in polluted soil

    International Nuclear Information System (INIS)

    Li, G.; Huang, W.; Zhang, X.; Lerner, D.N.

    2000-01-01

    Soil at a site near Zibo City, China, is polluted with hydrocarbons at concentrations up to 200 g kg -1 dry soil. Samples contained 10 7 microbial cells g -1 dry soil, and the concentration of aerobic degradation bacteria is 10 7 cells g -1 dry soil. The most active species were Xanthomonas, Bacillus and Hyphomicrobium. The nitrogen and phosphorus contents of the polluted soil are typically 0.1 %, and are sufficient to sustain natural or enhanced biodegradation. The BAC (Biological Activated Carbon) system was used to enrich indigenous microbes to enhance bioremediation rates in the laboratory. The BAC used the large surface area and sorption characteristics to fix bacteria and media, and effectively culture and enrich the microbes. Effluent from the BAC system contained up to 4 x 10 11 cells ml -1 , and was introduced to the contaminated soil to enhance biodegradation. The results indicated that the natural biodegradation rate of the petroleum hydrocarbons is lower than the BAC enhanced bioremediation rate, 1.7% as opposed to 42% in 32 days. (Author)

  14. Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria.

    Science.gov (United States)

    Gulledge, J; Ahmad, A; Steudler, P A; Pomerantz, W J; Cavanaugh, C M

    2001-10-01

    Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family Methylocystaceae (type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family, Methylocystis and Methylosinus, were identified. Two other probes target, as a single group, a majority of the known methanotrophs belonging to the family Methylococcaceae (type I/X methanotrophs). The remaining probes target members of individual genera of the Methylococcaceae, including Methylobacter, Methylomonas, Methylomicrobium, Methylococcus, and Methylocaldum. One of the family-level probes also covers all methanotrophic endosymbionts of marine mollusks for which 16S rRNA sequences have been published. The two known species of the newly described genus Methylosarcina gen. nov. are covered by a probe that otherwise targets only members of the closely related genus Methylomicrobium. None of the probes covers strains of the newly proposed genera Methylocella and "Methylothermus," which are polyphyletic with respect to the recognized methanotrophic families. Empirically determined midpoint dissociation temperatures were 49 to 57 degrees C for all probes. In dot blot screening against RNA from positive- and negative-control strains, the probes were specific to their intended targets. The broad coverage and high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available.

  15. Developing microbe-plant interactions for applications in plant-growth promotion and disease control, production of useful compounds, remediation, and carbon sequestration

    Energy Technology Data Exchange (ETDEWEB)

    Wu, C.H.; Bernard, S.; Andersen, G.L.; Chen, W.

    2009-03-01

    Interactions between plants and microbes are an integral part of our terrestrial ecosystem. Microbe-plant interactions are being applied in many areas. In this review, we present recent reports of applications in the areas of plant-growth promotion, biocontrol, bioactive compound and biomaterial production, remediation and carbon sequestration. Challenges, limitations and future outlook for each field are discussed.

  16. Theoretical study of a flat eddy current probe

    International Nuclear Information System (INIS)

    Bouchard, A.; Dumont-Fillon, J.; Labbe, G.

    1976-01-01

    A mathematical model for the computation of the impedance of an eddy current probe has been determined in the case of flat product testing. Various applications are discussed with particular emphasis on ferromagnetic materials [fr

  17. Electrical resistivity probes

    Science.gov (United States)

    Lee, Ki Ha; Becker, Alex; Faybishenko, Boris A.; Solbau, Ray D.

    2003-10-21

    A miniaturized electrical resistivity (ER) probe based on a known current-voltage (I-V) electrode structure, the Wenner array, is designed for local (point) measurement. A pair of voltage measuring electrodes are positioned between a pair of current carrying electrodes. The electrodes are typically about 1 cm long, separated by 1 cm, so the probe is only about 1 inch long. The electrodes are mounted to a rigid tube with electrical wires in the tube and a sand bag may be placed around the electrodes to protect the electrodes. The probes can be positioned in a borehole or on the surface. The electrodes make contact with the surrounding medium. In a dual mode system, individual probes of a plurality of spaced probes can be used to measure local resistance, i.e. point measurements, but the system can select different probes to make interval measurements between probes and between boreholes.

  18. Study of defects and radiation damage in solids by field-ion and atom-probe microscopy

    International Nuclear Information System (INIS)

    Seidman, D.N.

    1982-01-01

    An attempt is made to introduce the reader to the basic physical ideas involved in the field-ion and atom-probe field-ion microscope techniques, and to the applications of these techniques to the study of defects and radiation damage in solids. The final section discusses, in precise form, the application of the atom-probe field-ion microscope to the study of the behavior of implanted 3 He and 4 He atoms in tungsten. The paper is heavily referenced so that the reader can pursue his specific research interest in detail

  19. Mathematical study of probe arrangement and nanoparticle injection effects on heat transfer during cryosurgery.

    Science.gov (United States)

    Mirkhalili, Seyyed Mostafa; Ramazani S A, Ahmad; Nazemidashtarjandi, Saeed

    2015-11-01

    Blood vessels, especially large vessels have a greater thermal effect on freezing tissue during cryosurgery. Vascular networks act as heat sources in tissue, and cause failure in cryosurgery and reappearance of cancer. The aim of this study is to numerically simulate the effect of probe location and multiprobe on heat transfer distribution. Furthermore, the effect of nanoparticles injection is studied. It is shown that the small probes location near large blood vessels could help to reduce the necessary time for tissue freezing. Nanoparticles injection shows that the thermal effect of blood vessel in tissue is improved. Using Au, Ag and diamond nanoparticles have the most growth of ice ball during cryosurgery. However, polytetrafluoroethylene (PTFE) nanoparticle can be used to protect normal tissue around tumor cell due to its influence on reducing heat transfer in tissue. Introduction of Au, Ag and diamond nanoparticles combined with multicryoprobe in this model causes reduction of tissue average temperature about 50% compared to the one probe. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Studies on the Electrical Characteristics of a DC Glow Discharge by Using Langmuir Probe

    International Nuclear Information System (INIS)

    Safaai, S. S.; Yap, S. L.; Wong, C. S.; Muniandy, S. V.; Smith, P. W.

    2010-01-01

    Electrical characteristics of a DC glow discharge are studied with the aim of determining the suitable parameters for stable operation of the dusty plasma system. The presence of dust particles in plasma significantly alters the charged particle equilibrium in the plasma and leads to various phenomena. Argon plasma produced by DC glow discharge is investigated with a further goal of studying dusty plasma phenomena. The discharge system has two disc-shaped parallel plate electrodes. The electrodes are enclosed in a large cylindrical stainless steel chamber filled with argon gas. Two important physical parameters affecting the condition of the discharge are the gas pressure and the inter-electrode distance. A single Langmuir probe based on the Keithley source meter is used to determine the electron temperature of the positive column. A custom designed probe is employed to determine the potential distribution between the electrodes during the discharge. The I-V characteristic curve and the Langmuir probe measurement are then used to determine the electron energy distribution of the glow discharge plasma.

  1. Characterisation of target plasma required for REB-plasma interaction studies using cylindrical Langmuir probes

    International Nuclear Information System (INIS)

    Roychowdhury, P.; Paithankar, A.S.; Iyyengar, S.K.; Rohatgi, V.K.

    1987-01-01

    The target plasma required for relativistic electron beam (REB)-plasma interaction studies has been generated by coaxial plasma gun. The measurement of electron density and temperature has been carried out using cylindrical Langmuir probes. Probes both oriented parallel and transverse to the flow have been used. The spatial as well as temporal variation of electron density and temperature have been studied. The typical electron density and temperature measured by probe were in the range of 9.0-3.5 x 10 13 cm -3 and 5-7 eV respectively. The typical e-folding decay time of density was 6.2 μs, while no appreciable change in electron temperature was observed until 10 μs after the peak density. The density decays by about 50% at distance of 30 cm from the gun. The plasma flow velocity has been measured by the time of flight technique and was found to be 2.5 x 10 6 cm s -1 . The plasma radius measured by dosimeter film, at distance of 30 cm from the gun was 3 cm. (author)

  2. Study of plasma-material surface interaction using langmuir probe technique during plasma treatment

    International Nuclear Information System (INIS)

    Saloum, S.; Akel, M.

    2012-01-01

    In this study, we tried to understand the plasma-surface interactions by using Langmuir probes. Two different types of plasmas were studied, the first is the electropositive plasma in Argon and the second is the electronegative plasma in Sulfur Hexafluoride. In the first type, the effects of Argon gas pressure, the injection of Helium in the remote zone and the substrate bias on the measurements of the Electron Energy Probability Function (EEPF) and on the plasma parameters (electron density (n e ), effective electron temperature (T e ff), plasma potential (V p ) and floating potential (V f )) have been investigated. The obtained EEPFs and plasma parameters have been used to control two remote plasma processes. The first is the remote Plasma Enhanced Chemical Vapor Deposition (PE-CVD) of thin films, on silicon wafers, from Hexamethyldisiloxane (HMDSO) precursor diluted in the remote Ar-He plasma. The second is the pure Argon remote plasma treatment of polymethylmethacrylate (PMMA) polymer surface. In the second type, the plasma diagnostics were performed in the remote zone as a function of SF 6 flow rate, where relative concentrations of fluorine atoms were measured using actinometry optical emission spectroscopy; electron density, electron temperature and plasma potential were determined using single cylindrical Langmuir probe, positive ion flux and negative ion fraction were determined using an planar probe. The silicon etching process in SF 6 plasma was studied. (author)

  3. Study of plasma-material surface interaction using Langmuir probe technique during plasma treatment

    International Nuclear Information System (INIS)

    Saloum, S.; Akel, M.

    2009-06-01

    In this study, we tried to understand the plasma-surface interactions by using Langmuir probes. Two different types of plasmas were studied, the first is the electropositive plasma in Argon and the second is the electronegative plasma in Sulfur Hexafluoride. In the first type, the effects of Argon gas pressure, the injection of Helium in the remote zone and the substrate bias on the measurements of the Electron Energy Probability Function (EEPF) and on the plasma parameters (electron density (n e ), effective electron temperature (T e ff), plasma potential (V p ) and floating potential (V f )) have been investigated. The obtained EEPFs and plasma parameters have been used to control two remote plasma processes. The first is the remote Plasma Enhanced Chemical Vapor Deposition (PE-CVD) of thin films, on silicon wafers, from Hexamethyldisoloxane (HMDSO) precursor diluted in the remote Ar-He plasma. The second is the pure Argon remote plasma treatment of polymethylmethacrylate (PMMA) polymer surface. In the second type, the plasma diagnostics were performed in the remote zone as a function of SF 6 flow rate, where relative concentrations of fluorine atoms were measured using actinometry optical emission spectroscopy; electron density, electron temperature and plasma potential were determined using single cylindrical Langmuir probe, positive ion flux and negative ion fraction were determined using an planar probe. The silicon etching process in SF 6 plasma was studied. (author)

  4. Study on electrostatic and electromagnetic probes operated in ceramic and metallic depositing plasmas

    International Nuclear Information System (INIS)

    Styrnoll, T; Bienholz, S; Awakowicz, P; Lapke, M

    2014-01-01

    This paper discusses plasma probe diagnostics, namely the multipole resonance probe (MRP) and Langmuir probe (LP), operated in depositing plasmas. The aim of this work is to show that the combination of both probes provides stable and robust measurements and clear determination of plasma parameters for metallic and ceramic coating processes. The probes use different approaches to determine plasma parameters, e.g. electron density n e and electron temperature T e . The LP is a well-established plasma diagnostic, and its applicability in technological plasmas is well documented. The LP is a dc probe that performs a voltage sweep and analyses the measured current, which makes it insensitive against conductive metallic coating. However, once the LP is dielectrically coated with a ceramic film, its functionality is constricted. In contrast, the MRP was recently presented as a monitoring tool, which is insensitive to coating with dielectric ceramics. It is a new plasma diagnostic based on the concept of active plasma resonance spectroscopy, which uses the universal characteristic of all plasmas to resonate on or near the electron plasma frequency. The MRP emits a frequency sweep and the absorption of the signal, the |S 11 | parameter, is analysed. Since the MRP concept is based on electromagnetic waves, which are able to transmit dielectrics, it is insensitive to dielectric coatings. But once the MRP is metallized with a thin conductive film, no undisturbed RF-signal can be emitted into the plasma, which leads to falsified plasma parameter. In order to compare both systems, during metallic or dielectric coating, the probes are operated in a magnetron CCP, which is equipped with a titanium target. We present measurements in metallic and dielectric coating processes with both probes and elaborate advantages and problems of each probe operated in each coating environment. (paper)

  5. Femtosecond Pump-Push-Probe and Pump-Dump-Probe Spectroscopy of Conjugated Polymers: New Insight and Opportunities.

    Science.gov (United States)

    Kee, Tak W

    2014-09-18

    Conjugated polymers are an important class of soft materials that exhibit a wide range of applications. The excited states of conjugated polymers, often referred to as excitons, can either deactivate to yield the ground state or dissociate in the presence of an electron acceptor to form charge carriers. These interesting properties give rise to their luminescence and the photovoltaic effect. Femtosecond spectroscopy is a crucial tool for studying conjugated polymers. Recently, more elaborate experimental configurations utilizing three optical pulses, namely, pump-push-probe and pump-dump-probe, have been employed to investigate the properties of excitons and charge-transfer states of conjugated polymers. These studies have revealed new insight into femtosecond torsional relaxation and detrapping of bound charge pairs of conjugated polymers. This Perspective highlights (1) the recent achievements by several research groups in using pump-push-probe and pump-dump-probe spectroscopy to study conjugated polymers and (2) future opportunities and potential challenges of these techniques.

  6. Studies of spin excitations with electromagnetic and hadronic probes

    International Nuclear Information System (INIS)

    Lindgren, R.A.; Petrovich, F.

    1982-01-01

    Excitation of unnatural parity states, predominantly of high spin, using electromagnetic and hadronic probes, is discussed. Spectroscopic strengths are deduced from studies of (e,e'), (p,p'), (π.π'), and (p,n) for states whose doorway is the stretched particle-hole configuration. These levels are excited primarily through the isovector electromagnetic-nucleon magnetization coupling, nucleon-nucleon tensor coupling, and pion-nucleon spin-orbit coupling. The extracted isovector spectroscopic strength is typically 38% of the extreme single particle-hole model and about 66% of that predicted by more realistic nuclear structure calculations. The observed isoscalar strength is only about one half of the isovector strength. The results obtained with the three different probes are quite consistent. The primary conclusion is that the missing strength for these high spin excitations is at least as large as for the low spin M1 and GT excitations. This implies the existence of other important quenching mechanisms since the Δ-N -1 mechanism involved in the discussion of the low spin excitation affects only the isovector transitions and contributes little to high spin excitations. A method for using (e,e') and π + /π - cross section ratios to separate and determine the absolute isoscalar and isovector spin densities for T 0 to T 0 transitions in N is not equal to Z nuclei is also discussed and some comments on extracting information from (e,e') and (p,p') studies at high q on low spin 1 + and 2 - levels are presented. 78 references

  7. Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions.

    Science.gov (United States)

    Badur, Ahmet H; Plutz, Matthew J; Yalamanchili, Geethika; Jagtap, Sujit Sadashiv; Schweder, Thomas; Unfried, Frank; Markert, Stephanie; Polz, Martin F; Hehemann, Jan-Hendrik; Rao, Christopher V

    2017-08-04

    Polysaccharide degradation by marine microbes represents one of the largest and most rapid heterotrophic transformations of organic matter in the environment. Microbes employ systems of complementary carbohydrate-specific enzymes to deconstruct algal or plant polysaccharides (glycans) into monosaccharides. Because of the high diversity of glycan substrates, the functions of these enzymes are often difficult to establish. One solution to this problem may lie within naturally occurring microdiversity; varying numbers of enzymes, due to gene loss, duplication, or transfer, among closely related environmental microbes create metabolic differences akin to those generated by knock-out strains engineered in the laboratory used to establish the functions of unknown genes. Inspired by this natural fine-scale microbial diversity, we show here that it can be used to develop hypotheses guiding biochemical experiments for establishing the role of these enzymes in nature. In this work, we investigated alginate degradation among closely related strains of the marine bacterium Vibrio splendidus One strain, V. splendidus 13B01, exhibited high extracellular alginate lyase activity compared with other V. splendidus strains. To identify the enzymes responsible for this high extracellular activity, we compared V. splendidus 13B01 with the previously characterized V. splendidus 12B01, which has low extracellular activity and lacks two alginate lyase genes present in V. splendidus 13B01. Using a combination of genomics, proteomics, biochemical, and functional screening, we identified a polysaccharide lyase family 7 enzyme that is unique to V. splendidus 13B01, secreted, and responsible for the rapid digestion of extracellular alginate. These results demonstrate the value of querying the enzymatic repertoires of closely related microbes to rapidly pinpoint key proteins with beneficial functions. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Antimicrobial photodynamic inactivation: a bright new technique to kill resistant microbes

    OpenAIRE

    Hamblin, Michael R

    2016-01-01

    Photodynamic therapy (PDT) uses photosensitizers (non-toxic dyes) that are activated by absorption of visible light to form reactive oxygen species (including singlet oxygen) that can oxidize biomolecules and destroy cells. Antimicrobial photodynamic inactivation (aPDI) can treat localized infections. aPDI neither causes any resistance to develop in microbes, nor is affected by existing drug resistance status. We discuss some recent developments in aPDI. New photosensitizers including polycat...

  9. Langmuir probe studies on a RF ion source for NBI

    International Nuclear Information System (INIS)

    McNeely, P.; Heineman, B.; Kraus, W.; Riedl, R.; Speth, E.; Vollmer, O.

    2001-01-01

    IPP Garching has been developing a RF ion source for H - production. In order to improve the data quality a new scanning probe system with passive RF compensation has been installed on the Type VI ion source on the BATMAN test stand. Using this probe, measurements have been carried out to study changes to the plasma parameters (electron density, electron temperature, and plasma potential) due to variation in the source operating conditions. The data were collected at a source pressure of 0.5 Pa and with 60±5 kW applied RF power. Presented are some of the results of these measurements, focusing on the effect of: argon seeding, addition of Cs to the source, and the newly added Faraday screen. The electron density behaves in a fashion that agrees with the theory of ambipolar diffusion. Typically there is little change to the average electron energy observed regardless of which effect is considered. The plasma potential shows the most significant changes with external source conditions, both in value for all cases and shape when the Faraday screen was added

  10. New atom probe approaches to studying segregation in nanocrystalline materials.

    Science.gov (United States)

    Samudrala, S K; Felfer, P J; Araullo-Peters, V J; Cao, Y; Liao, X Z; Cairney, J M

    2013-09-01

    Atom probe is a technique that is highly suited to the study of nanocrystalline materials. It can provide accurate atomic-scale information about the composition of grain boundaries in three dimensions. In this paper we have analysed the microstructure of a nanocrystalline super-duplex stainless steel prepared by high pressure torsion (HPT). Not all of the grain boundaries in this alloy display obvious segregation, making visualisation of the microstructure challenging. In addition, the grain boundaries present in the atom probe data acquired from this alloy have complex shapes that are curved at the scale of the dataset and the interfacial excess varies considerably over the boundaries, making the accurate characterisation of the distribution of solute challenging using existing analysis techniques. In this paper we present two new data treatment methods that allow the visualisation of boundaries with little or no segregation, the delineation of boundaries for further analysis and the quantitative analysis of Gibbsian interfacial excess at boundaries, including the capability of excess mapping. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. High spatial resolution Kelvin probe force microscopy with coaxial probes

    International Nuclear Information System (INIS)

    Brown, Keith A; Westervelt, Robert M; Satzinger, Kevin J

    2012-01-01

    Kelvin probe force microscopy (KPFM) is a widely used technique to measure the local contact potential difference (CPD) between an AFM probe and the sample surface via the electrostatic force. The spatial resolution of KPFM is intrinsically limited by the long range of the electrostatic interaction, which includes contributions from the macroscopic cantilever and the conical tip. Here, we present coaxial AFM probes in which the cantilever and cone are shielded by a conducting shell, confining the tip–sample electrostatic interaction to a small region near the end of the tip. We have developed a technique to measure the true CPD despite the presence of the shell electrode. We find that the behavior of these probes agrees with an electrostatic model of the force, and we observe a factor of five improvement in spatial resolution relative to unshielded probes. Our discussion centers on KPFM, but the field confinement offered by these probes may improve any variant of electrostatic force microscopy. (paper)

  12. Overview of wall probes for erosion and deposition studies in the TEXTOR tokamak

    Directory of Open Access Journals (Sweden)

    M. Rubel

    2017-05-01

    Full Text Available An overview of diagnostic tools – test limiters and collector probes – used over the years for material migration studies in the TEXTOR tokamak is presented. Probe transfer systems are shown and their technical capabilities are described. This is accompanied by a brief presentation of selected results and conclusions from the research on material erosion – deposition processes including tests of candidate materials (e.g. W, Mo, carbon-based composites for plasma-facing components in controlled fusion devices. The use of tracer techniques and methods for analysis of materials retrieved from the tokamak are summarized. The impact of research on the reactor wall technology is addressed.

  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.; hide

    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. Plasma density measurement with ring-type cutoff probe

    International Nuclear Information System (INIS)

    Kim, D.W.; You, S.J.; Na, B.K.; Kim, J.H.; Shin, Y.H.; Chang, H.Y.; Oh, W.Y.

    2013-01-01

    We proposed a cutoff probe with a ring-type detection tip enclosing a bar-type radiation tip. A comparative study between a proposed ring-type cutoff (RTC) probe and a conventional bar-type cutoff (BTC) probe showed that the RTC probe solved the problem of the BTC probe, the large measurement uncertainty of the electron density in a capacitively coupled plasma source. This improved characteristics of the RTC probe might have originated from the geometrical structure of the RTC probe concerning the monopole antennae radiation. This proposed cutoff probe can be expected to expand the applicable diagnostic range and to enhance the sensitivity of the cutoff probe. - Highlights: ► A cutoff probe with a ring type detection tip is proposed. ► Comparative experiment and simulation were conducted. ► The proposed probe showed a small uncertainty of measured plasma density. ► Improved characteristics might be originated from the geometrical structure

  15. In-vitro accuracy and reproducibility evaluation of probing depth measurements of selected periodontal probes

    Directory of Open Access Journals (Sweden)

    K.N. Al Shayeb

    2014-01-01

    Conclusion: Depth measurements with the Chapple UB-CF-15 probe were more accurate and reproducible compared to measurements with the Vivacare TPS and Williams 14 W probes. This in vitro model may be useful for intra-examiner calibration or clinician training prior to the clinical evaluation of patients or in longitudinal studies involving periodontal evaluation.

  16. New Record of Rhinopoma microphyllum with the Invested Parasites and Microbes in the Developed Ecotourism Area of South Lombok Island NTB

    Science.gov (United States)

    Fajri, S. R.; NPrimawati, S.; Hadi, I.; Tresnani, G.

    2018-01-01

    Rhinopoma microphyllum is a bat species that lives in a habitat covered by grove of trees and shrubs in the primary forest vegetation. These species is included in the IUCN Red List list with Least Concern (LC) status or at the least information. This study was to describe of R. microphyllum as a new record in the southern of Lombok, and to examine the parasites and microbes that infest it. The study was carried out in the developed ecotourism area of southern Lombok Island of NTB during February-April 2017. A modified net and quadrant for cave ceiling was used to collect bat sample. Ectoparasite collection was done by combing the bat’s hair and the falling specimens were collected. The endoparasite examination was done by the flotation methods of intestinal contents, while microbial examination was done by collecting the microbes from oral cavity and feces. The results showed the discovery of R. microphyllum in two ecotourism development sites, The Buwun Cave and The Gale Gale Bangkang Cave Prabu Village, Central Lombok. The endoparasit examination found 4 species of endoparasit, 1 species of Coccidia sp, 2 species of Trematodes from Lecithodendridae Family (Prosthodendrium sp and Acanthatrium sp) and 1 unidentified Nematode specimen. The ectoparasite examination found only 1 species, Ischnopsyllus hexactenus (The long Eared Bat Flea), and the microbes found from oral cavity analysis are the Gram positive Coccus (Stphylococcus aureus) and faecal analysis are the Coccobacil Gram negative (Providensia penneri).

  17. Study on a New Ultraviolet Sterilizer to the Surface Disinfection of the Ultrasound Probe.

    Science.gov (United States)

    Chen, Gui Qiu; Chen, Yu Hao; Yi, Liang; Yin, Jin; Gao, Qiong; Song, Jiang Nan; Li, Shi Kang; Chen, Pei Hou; Guo, Gui Ping

    2018-02-01

    We studied the disinfection effect of a new ultraviolet (UV) sterilizer and its utilization on ultrasound probe surfaces. Carrier quantitative germicidal tests, simulated on-the-spot trials, and organic substance influence tests were used to carry out experimental observation. Artificially infected probes were disinfected using the sterilizer or a germicidal lamp for comparison. The total number and types of bacteria were determined and identified. Our results demonstrated the sterilizer had the best disinfection effect among three different disinfection methods in hospital. The sterilizer has been used in a hospital setting for 2 years with no notable damage to the ultrasound probe instrument. It has the advantages of fast disinfection, high disinfection effect, and good compatibility with the ultrasound instrument, worthy of being a promoted application in medical institutions. Copyright © 2018 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  18. Novel Acoustic Feedback Cancellation Approaches In Hearing Aid Applications Using Probe Noise and Probe Noise Enhancement

    DEFF Research Database (Denmark)

    Guo, Meng; Jensen, Søren Holdt; Jensen, Jesper

    2012-01-01

    . In many cases, this bias problem causes the cancellation system to fail. The traditional probe noise approach, where a noise signal is added to the loudspeaker signal can, in theory, prevent the bias. However, in practice, the probe noise level must often be so high that the noise is clearly audible...... and annoying; this makes the traditional probe noise approach less useful in practical applications. In this work, we explain theoretically the decreased convergence rate when using low-level probe noise in the traditional approach, before we propose and study analytically two new probe noise approaches...... the proposed approaches much more attractive in practical applications. We demonstrate this through a simulation experiment with audio signals in a hearing aid acoustic feedback cancellation system, where the convergence rate is improved by as much as a factor of 10....

  19. Divergent utilization patterns of grass fructan, inulin, and other nonfiber carbohydrates by ruminal microbes

    Science.gov (United States)

    Fructans are an important nonfiber carbohydrate in cool-season grasses. Their fermentation by ruminal microbes is not well described, though such information is needed to understand their nutritional value to ruminants. Our objective was to compare kinetics and product formation of orchardgrass fruc...

  20. Use of ultrafast dispersed pump-dump-probe and pump-repump-probe spectroscopies to explore the light-induced dynamics of peridinin in solution

    NARCIS (Netherlands)

    Papagiannakis, E.; Vengris, M.; Larsen, D.S.; van Stokkum, I.H.M.; Hiller, R.G.; van Grondelle, R.

    2006-01-01

    Optical pump-induced dynamics of the highly asymmetric carotenoid peridinin in methanol was studied by dispersed pump-probe, pump-dump-probe, and pump-repump-probe transient absorption spectroscopy in the visible region. Dispersed pump-probe measurements show that the decay of the initially excited

  1. Characterization of Fiber Optic CMM Probe System

    Energy Technology Data Exchange (ETDEWEB)

    K.W.Swallow

    2007-05-15

    This report documents a study completed on the fiber optic probe system that is a part of the Werth optical CMM. This study was necessary due to a lack of documentation from the vendor for the proper use and calibration of the fiber probe, and was performed in support of the Lithographie Galvanoformung Abformung (LIGA) development program at the FM&T. As a result of this study, a better understanding of the fiber optic probe has been developed, including guidelines for its proper use and calibration.

  2. Metagenome Analysis of Protein Domain Collocation within Cellulase Genes of Goat Rumen Microbes

    Directory of Open Access Journals (Sweden)

    SooYeon Lim

    2013-08-01

    Full Text Available In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below E−10 using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4 were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below 10−5. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

  3. Pump-probe study of the formation of rubidium molecules by ultrafast photoassociation of ultracold atoms

    Science.gov (United States)

    McCabe, David J.; England, Duncan G.; Martay, Hugo E. L.; Friedman, Melissa E.; Petrovic, Jovana; Dimova, Emiliya; Chatel, Béatrice; Walmsley, Ian A.

    2009-09-01

    An experimental pump-probe study of the photoassociative creation of translationally ultracold rubidium molecules is presented together with numerical simulations of the process. The formation of loosely bound excited-state dimers is observed as a first step toward a fully coherent pump-dump approach to the stabilization of Rb2 into its lowest ground vibrational states. The population that contributes to the pump-probe process is characterized and found to be distinct from a background population of preassociated molecules.

  4. Scanning Probe Optical Tweezers: a new tool to study DNA-protein interactions

    NARCIS (Netherlands)

    Huisstede, J.H.G.

    2006-01-01

    The main goal of the work described in this thesis is to construct a microscope in which OT and scanning probe microscopy (SPM) are combined, to be able to localize proteins while simultaneously controlling the tension within the DNA molecule. This apparatus enables the study of the effect of

  5. Automated analysis of calcium spiking profiles with CaSA software: two case studies from root-microbe symbioses.

    Science.gov (United States)

    Russo, Giulia; Spinella, Salvatore; Sciacca, Eva; Bonfante, Paola; Genre, Andrea

    2013-12-26

    Repeated oscillations in intracellular calcium (Ca2+) concentration, known as Ca2+ spiking signals, have been described in plants for a limited number of cellular responses to biotic or abiotic stimuli and most notably the common symbiotic signaling pathway (CSSP) which mediates the recognition by their plant hosts of two endosymbiotic microbes, arbuscular mycorrhizal (AM) fungi and nitrogen fixing rhizobia. The detailed analysis of the complexity and variability of the Ca2+ spiking patterns which have been revealed in recent studies requires both extensive datasets and sophisticated statistical tools. As a contribution, we have developed automated Ca2+ spiking analysis (CaSA) software that performs i) automated peak detection, ii) statistical analyses based on the detected peaks, iii) autocorrelation analysis of peak-to-peak intervals to highlight major traits in the spiking pattern.We have evaluated CaSA in two experimental studies. In the first, CaSA highlighted unpredicted differences in the spiking patterns induced in Medicago truncatula root epidermal cells by exudates of the AM fungus Gigaspora margarita as a function of the phosphate concentration in the growth medium of both host and fungus. In the second study we compared the spiking patterns triggered by either AM fungal or rhizobial symbiotic signals. CaSA revealed the existence of different patterns in signal periodicity, which are thought to contribute to the so-called Ca2+ signature. We therefore propose CaSA as a useful tool for characterizing oscillatory biological phenomena such as Ca2+ spiking.

  6. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  7. Immobilization and mineralization of N and P by heterotrophic microbes during leaf decomposition

    Science.gov (United States)

    Beth Cheever; Erika Kratzer; Jackson Webster

    2012-01-01

    According to theory, the rate and stoichiometry of microbial mineralization depend, in part, on nutrient availability. For microbes associated with leaves in streams, nutrients are available from both the water column and the leaf. Therefore, microbial nutrient cycling may change with nutrient availability and during leaf decomposition. We explored spatial and temporal...

  8. Effects of the fungicide metiram in outdoor freshwater microcosms: responses of invertebrates, primany producers and microbes

    OpenAIRE

    Ronghua, Lin; Buijse-Bogdan, L.L.; Rocha Dimitrov, M.; Dohmen, P.; Kosol, Sujitra; Maltby, L.; Roessink, I.; Sinkeldam, J.A.; Smidt, H.; Wijngaarden, van, R.P.A.; Brock, T.C.M.

    2012-01-01

    The ecological impact of the dithiocarbamate fungicide metiram was studied in outdoor freshwater microcosms, consisting of 14 enclosures placed in an experimental ditch. The microcosms were treated three times (interval 7 days) with the formulated product BAS 222 28F (Polyram®). Intended metiram concentrations in the overlying water were 0, 4, 12, 36, 108 and 324 μg a.i./L. Responses of zooplankton, macroinvertebrates, phytoplankton, macrophytes, microbes and community metabolism endpoints we...

  9. Counting probe

    International Nuclear Information System (INIS)

    Matsumoto, Haruya; Kaya, Nobuyuki; Yuasa, Kazuhiro; Hayashi, Tomoaki

    1976-01-01

    Electron counting method has been devised and experimented for the purpose of measuring electron temperature and density, the most fundamental quantities to represent plasma conditions. Electron counting is a method to count the electrons in plasma directly by equipping a probe with the secondary electron multiplier. It has three advantages of adjustable sensitivity, high sensitivity of the secondary electron multiplier, and directional property. Sensitivity adjustment is performed by changing the size of collecting hole (pin hole) on the incident front of the multiplier. The probe is usable as a direct reading thermometer of electron temperature because it requires to collect very small amount of electrons, thus it doesn't disturb the surrounding plasma, and the narrow sweep width of the probe voltage is enough. Therefore it can measure anisotropy more sensitively than a Langmuir probe, and it can be used for very low density plasma. Though many problems remain on anisotropy, computer simulation has been carried out. Also it is planned to provide a Helmholtz coil in the vacuum chamber to eliminate the effect of earth magnetic field. In practical experiments, the measurement with a Langmuir probe and an emission probe mounted to the movable structure, the comparison with the results obtained in reverse magnetic field by using a Helmholtz coil, and the measurement of ionic sound wave are scheduled. (Wakatsuki, Y.)

  10. Recent developments in systems biology and metabolic engineering of plant microbe interactions

    Directory of Open Access Journals (Sweden)

    Vishal Kumar

    2016-09-01

    Full Text Available 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 biology tools towards the comprehension in improvement of plant traits. Further, system biology tools like FBA, OptKnock and constrain based modeling helps in understanding such interactions as a whole. In addition, various gene editing tools have been summarized and a strategy has been hypothesized for the development of disease free plants. Furthermore, we have tried to summarize the predictions through data retrieved from various types of sources such as high throughput sequencing data (e.g. single nucleotide polymorphism (SNP detection, RNA-seq, proteomics and metabolic models have been reconstructed from such sequences for species communities. It is well known fact that systems biology approaches and modeling of biological networks will enable us to learn the insight of such network and will also help further in understanding these interactions.

  11. Magnetic Probe to Study Plasma Jets for Magneto-Inertial Fusion

    Energy Technology Data Exchange (ETDEWEB)

    Martens, Daniel [Los Alamos National Laboratory; Hsu, Scott C. [Los Alamos National Laboratory

    2012-08-16

    A probe has been constructed to measure the magnetic field of a plasma jet generated by a pulsed plasma rail-gun. The probe consists of two sets of three orthogonally-oriented commercial chip inductors to measure the three-dimensional magnetic field vector at two separate positions in order to give information about the magnetic field evolution within the jet. The strength and evolution of the magnetic field is one of many factors important in evaluating the use of supersonic plasma jets for forming imploding spherical plasma liners as a standoff driver for magneto-inertial fusion.

  12. Mobile probes

    DEFF Research Database (Denmark)

    Ørngreen, Rikke; Jørgensen, Anna Neustrup; Noesgaard, Signe Schack

    2016-01-01

    A project investigating the effectiveness of a collection of online resources for teachers' professional development used mobile probes as a data collection method. Teachers received questions and tasks on their mobile in a dialogic manner while in their everyday context as opposed...... to in an interview. This method provided valuable insight into the contextual use, i.e. how did the online resource transfer to the work practice. However, the research team also found that mobile probes may provide the scaffolding necessary for individual and peer learning at a very local (intra-school) community...... level. This paper is an initial investigation of how the mobile probes process proved to engage teachers in their efforts to improve teaching. It also highlights some of the barriers emerging when applying mobile probes as a scaffold for learning....

  13. Atom probe, AFM and STM study on vacuum fired stainless steel

    International Nuclear Information System (INIS)

    Stupnik, A.; Frank, P.; Leisch, M.

    2008-01-01

    Full text: Stainless steel is one of the most commonly used structural materials for vacuum equipment. An efficient method to reduce the outgassing rate from stainless steel is a high temperature bakeout in vacuum (vacuum firing). This procedure reduces significantly the amount of dissolved hydrogen in the bulk. For the outgassing process the recombination rate of hydrogen atoms to the molecules plays the determining role and recombination is strongly related to the surface structure and composition. To get more detailed information about the surface morphology and composition AFM, STM and atom probe studies were carried out. Experiments on AISI 304L stainless steel samples show that the surface reconstructs completely during vacuum firing and large atomically flat terraces bounded by bunched steps and facets are formed. The large flat terraces can be assigned to (111) planes. The bunched steps and facets are corresponding in orientation almost to (110) planes and (100) planes. Surface inspection after vacuum firing by Auger electron spectroscopy (AES) gives reason for a composition change indicated by a reduction of the chromium signal in relation to the iron and nickel signal. Since the information depth of AES covers several atomic layers not only the top atomic layer of the sample surface is probed. For this reason 3D atom probe was used as well suited tool to investigate the segregation behavior of this alloy with the goal to examine the change in local chemical composition due to the high temperature treatment. As a result of vacuum firing the atom probe experiments show a significant enrichment of nickel at the top surface layer. In the second atomic layer chromium enrichment is detected. After vacuum firing the average composition below the second atomic layer shows certain chromium depletion up to 2 nm in depth. The observed changes in surface chemistry influence recombination and desorption probability from the surface and may contribute to the present

  14. Electrochemical studies of redox probes in self-organized lyotropic ...

    Indian Academy of Sciences (India)

    Administrator

    quinone|hydroquinone, methyl viologen and ferrocenemethanol probes in a lyotropic hexagonal columnar phase (H1 phase) using cyclic voltammetry and electrochemical impedance ..... hydrogen bond of hydroquinone during oxidation is.

  15. Chromosome-specific DNA Repeat Probes

    Energy Technology Data Exchange (ETDEWEB)

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

    2006-03-16

    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

  16. Nanobits: customizable scanning probe tips

    DEFF Research Database (Denmark)

    Kumar, Rajendra; Shaik, Hassan Uddin; Sardan Sukas, Özlem

    2009-01-01

    We present here a proof-of-principle study of scanning probe tips defined by planar nanolithography and integrated with AFM probes using nanomanipulation. The so-called 'nanobits' are 2-4 mu m long and 120-150 nm thin flakes of Si3N4 or SiO2, fabricated by electron beam lithography and standard s...

  17. Highly anisotropic mobility in solution processed TIPS-pentacene film studied by independently driven four GaIn probes

    Science.gov (United States)

    Yoshimoto, Shinya; Takahashi, Kohtaro; Suzuki, Mitsuharu; Yamada, Hiroko; Miyahara, Ryosuke; Mukai, Kozo; Yoshinobu, Jun

    2017-08-01

    We have studied in-plane anisotropy in the field-effect mobility of solution-processed organic semiconductor 6,13-bis(triisopropylsilylethynyl)pentacene by using independently driven four gallium indium (Ga-In) probes. Liquid-metal Ga-In probes are highly effective for reproducible conductivity measurements of organic thin films. We demonstrated that a high mobility anisotropy of 44 was obtained by using a square four-probe method and a feedback circuit to keep the channel potential constant. The present method minimized the influences of the contact resistance and the insensitivity of anisotropy in a linear arrangement in two-dimensional field-effect transistors.

  18. Dispersal, density dependence, and population dynamics of a fungal microbe on leaf surfaces.

    Science.gov (United States)

    Woody, Scott T; Ives, Anthony R; Nordheim, Erik V; Andrews, John H

    2007-06-01

    Despite the ubiquity and importance of microbes in nature, little is known about their natural population dynamics, especially for those that occupy terrestrial habitats. Here we investigate the dynamics of the yeast-like fungus Aureobasidium pullulans (Ap) on apple leaves in an orchard. We asked three questions. (1) Is variation in fungal population density among leaves caused by variation in leaf carrying capacities and strong density-dependent population growth that maintains densities near carrying capacity? (2) Do resident populations have competitive advantages over immigrant cells? (3) Do Ap dynamics differ at different times during the growing season? To address these questions, we performed two experiments at different times in the growing season. Both experiments used a 2 x 2 factorial design: treatment 1 removed fungal cells from leaves to reveal density-dependent population growth, and treatment 2 inoculated leaves with an Ap strain engineered to express green fluorescent protein (GFP), which made it possible to track the fate of immigrant cells. The experiments showed that natural populations of Ap vary greatly in density due to sustained differences in carrying capacities among leaves. The maintenance of populations close to carrying capacities indicates strong density-dependent processes. Furthermore, resident populations are strongly competitive against immigrants, while immigrants have little impact on residents. Finally, statistical models showed high population growth rates of resident cells in one experiment but not in the other, suggesting that Ap experiences relatively "good" and "bad" periods for population growth. This picture of Ap dynamics conforms to commonly held, but rarely demonstrated, expectations of microbe dynamics in nature. It also highlights the importance of local processes, as opposed to immigration, in determining the abundance and dynamics of microbes on surfaces in terrestrial systems.

  19. Gut-associated microbes of Drosophila melanogaster

    Science.gov (United States)

    Broderick, Nichole; Lemaitre, Bruno

    2012-01-01

    There is growing interest in using Drosophila melanogaster to elucidate mechanisms that underlie the complex relationships between a host and its microbiota. In addition to the many genetic resources and tools Drosophila provides, its associated microbiota is relatively simple (1–30 taxa), in contrast to the complex diversity associated with vertebrates (> 500 taxa). These attributes highlight the potential of this system to dissect the complex cellular and molecular interactions that occur between a host and its microbiota. In this review, we summarize what is known regarding the composition of gut-associated microbes of Drosophila and their impact on host physiology. We also discuss these interactions in the context of their natural history and ecology and describe some recent insights into mechanisms by which Drosophila and its gut microbiota interact. “Workers with Drosophila have been considered fortunate in that they deal with the first multicellular invertebrate to be cultured monoxenically (Delcourt and Guyenot, 1910); the first to be handled axenically on a semisynthetic diet (Guyenot, 1917); and the first to be grown on a defined diet (Schultz et al., 1946). This list of advantages is somewhat embarrassing, since it implies an interest in nutrition that, in reality, was only secondary. The very first studies were concerned with the reduction of variability in genetic experiments (Delcourt and Guyenot, 1910) and standardization of the nutritional environment.” -James Sang, 1959 Ann NY Acad 1 PMID:22572876

  20. A telemetry study on the chronic effects of microdialyis probe implantation on the activity pattern and temperature rhythm of the rat

    NARCIS (Netherlands)

    Drijfhout, W.J.; Kemper, R.H.A.; Meerlo, P.; Koolhaas, J.M.; Grol, C.J.; Westerink, B.H.C.

    1995-01-01

    The present study describes the effects of implantation of microdialysis probes on temperature and activity rhythms of the rat, measured with a telemetry system. For comparison two widely used types of microdialysis probes were investigated, a transcerebral probe, inserted into the pineal gland and

  1. Diverse effects of arsenic on selected enzyme activities in soil-plant-microbe interactions.

    Science.gov (United States)

    Lyubun, Yelena V; Pleshakova, Ekaterina V; Mkandawire, Martin; Turkovskaya, Olga V

    2013-11-15

    Under the influence of pollutants, enzyme activities in plant-microbe-soil systems undergo changes of great importance in predicting soil-plant-microbe interactions, regulation of metal and nutrient uptake, and, ultimately, improvement of soil health and fertility. We evaluated the influence of As on soil enzyme activities and the effectiveness of five field crops for As phytoextraction. The initial As concentration in soil was 50mg As kg(-1) soil; planted clean soil, unplanted polluted soil, and unplanted clean soil served as controls. After 10 weeks, the growth of the plants elevated soil dehydrogenase activity relative to polluted but unplanted control soils by 2.4- and 2.5-fold for sorghum and sunflower (respectively), by 3-fold for ryegrass and sudangrass, and by 5.2-fold for spring rape. Soil peroxidase activity increased by 33% with ryegrass and rape, while soil phosphatase activity was directly correlated with residual As (correlation coefficient R(2)=0.7045). We conclude that soil enzyme activities should be taken into account when selecting plants for phytoremediation. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Turbidity and microbes removal from water using an electrochemical filter

    International Nuclear Information System (INIS)

    Venkateswaran, G.; Gokhale, B.K.; Belapurkar, A.D.; Kumbhar, A.G.; Balaji, V.

    2004-01-01

    An in-house designed and fabricated Electrochemical fibrous graphite filter (ECF) was used to remove turbidity and microbes. The filter was found to be effective in removing sub micron size indium turbidity from RAPS-1 moderator water, iron turbidity from Active Process Cooling Water (APCW) of Kaiga Generating Station and microbial reduction from process cooling water RAPS-2. Unlike conventional turbidity removal by addition of coagulants and biocide chemical additions for purification, ECF is a clean way to remove the turbidity without contaminating the system and is best suited for close loop systems

  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. Primitive chain network simulations of probe rheology.

    Science.gov (United States)

    Masubuchi, Yuichi; Amamoto, Yoshifumi; Pandey, Ankita; Liu, Cheng-Yang

    2017-09-27

    Probe rheology experiments, in which the dynamics of a small amount of probe chains dissolved in immobile matrix chains is discussed, have been performed for the development of molecular theories for entangled polymer dynamics. Although probe chain dynamics in probe rheology is considered hypothetically as single chain dynamics in fixed tube-shaped confinement, it has not been fully elucidated. For instance, the end-to-end relaxation of probe chains is slower than that for monodisperse melts, unlike the conventional molecular theories. In this study, the viscoelastic and dielectric relaxations of probe chains were calculated by primitive chain network simulations. The simulations semi-quantitatively reproduced the dielectric relaxation, which reflects the effect of constraint release on the end-to-end relaxation. Fair agreement was also obtained for the viscoelastic relaxation time. However, the viscoelastic relaxation intensity was underestimated, possibly due to some flaws in the model for the inter-chain cross-correlations between probe and matrix chains.

  5. Effects of Ionizing Radiation on Surface Infesting Microbes of Stored Grain

    International Nuclear Information System (INIS)

    Maity, J.P.; Chanda, S.; Chakraborty, A.; Santra, S.C.

    2005-09-01

    Spoilage of nutritional value of stored grains and seeds by the surface-infesting microbes, especially those producing mycotoxins, has been a worldwide economic problem. In this perspective our present work aims at probing into the potential of gamma rays to reduce the microbial infestation on stored grain surface and additionally to focus differential radiation sensitivity, if any, of the different fungi in response to gradient of gamma exposure. Co-60 source at 250 C emitting gamma rays at 1173 and 1332 keV energy (0.12 kGy/h) was used in the range of 0.5-6 kGy (absorbed dose) for irradiating some common stored seeds in India namely rice (Oryza sativa. Cv-2233 and Oryza sativa. Cv-Shankar), Bengal gram (Cicer arietinum. Cv-local), wheat (Triticum aestivum) and Mung (Phaseolus mungo). Gamma irradiation results in dose-dependent delay in colony formation and growth inhibition of the fungi on the seed surface. Differential rate of depletion was noted for different fungi. Effective absorbed dose for depletion of Alternaria sp., Aspergillus sp was 1 to 2 kGy while that for Tricoderma sp., Curvularia sp was 0.5-1 kGy. Complete inhibition of all the selected fungi was found above 2.5 kGy. Germinating potential of the irradiated grains remained unaffected upto an absorbed dose of 2kGy while their respective nutritional value in terms of protein and carbohydrate content was not significantly altered. Higher doses of exposure however, documented delayed seed germination. Colony forming ability (CFA) of the exposed fungi documented significant variation between fungi attached to the seed surface and that when isolated from the host. Alternaria sp, Aspergillus sp or Curvularia sp exhibited total inhibition of CFA at a much lower dose (1-3 kGy) in isolated conditions than that when seed attached (>4kGy). On the other hand Trichoderma sp expressed a different trend revealing more sensitivity in seed attached condition. Such differential response possibly reflects species

  6. Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry.

    Science.gov (United States)

    Stasulli, Nikolas M; Shank, Elizabeth A

    2016-11-01

    The ability of microbes to secrete bioactive chemical signals into their environment has been known for over a century. However, it is only in the last decade that imaging mass spectrometry has provided us with the ability to directly visualize the spatial distributions of these microbial metabolites. This technology involves collecting mass spectra from multiple discrete locations across a biological sample, yielding chemical ‘maps’ that simultaneously reveal the distributions of hundreds of metabolites in two dimensions. Advances in microbial imaging mass spectrometry summarized here have included the identification of novel strain- or coculture-specific compounds, the visualization of biotransformation events (where one metabolite is converted into another by a neighboring microbe), and the implementation of a method to reconstruct the 3D subsurface distributions of metabolites, among others. Here we review the recent literature and discuss how imaging mass spectrometry has spurred novel insights regarding the chemical consequences of microbial interactions.

  7. Ontology - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available gzip) consists of some directories (see the following table). Data file File name: ontology....tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/LATEST/ontology.tar.gz File size: 9...he NCBI Taxonomy and INSDC ontology files were obtained from the DDBJ web site. O...ples Data item Description ontology/meo/meo.ttl An ontology for describing organismal habitats (especially focused on microbes). onto...logy/meo/meo_fma_mapping.ttl An ontology mapping files t

  8. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  9. Plasma probe characteristics in low density hydrogen pulsed plasmas

    International Nuclear Information System (INIS)

    Astakhov, D I; Lee, C J; Bijkerk, F; Goedheer, W J; Ivanov, V V; Krivtsun, V M; Zotovich, A I; Zyryanov, S M; Lopaev, D V

    2015-01-01

    Probe theories are only applicable in the regime where the probe’s perturbation of the plasma can be neglected. However, it is not always possible to know, a priori, that a particular probe theory can be successfully applied, especially in low density plasmas. This is especially difficult in the case of transient, low density plasmas. Here, we applied probe diagnostics in combination with a 2D particle-in-cell model, to an experiment with a pulsed low density hydrogen plasma. The calculations took into account the full chamber geometry, including the plasma probe as an electrode in the chamber. It was found that the simulations reproduce the time evolution of the probe IV characteristics with good accuracy. The disagreement between the simulated and probe measured plasma density is attributed to the limited applicability of probe theory to measurements of low density pulsed plasmas on a similarly short time scale as investigated here. Indeed, in the case studied here, probe measurements would lead to, either a large overestimate, or underestimate of the plasma density, depending on the chosen probe theory. In contrast, the simulations of the plasma evolution and the probe characteristics do not suffer from such strict applicability limits. These studies show that probe theory cannot be justified through probe measurements. However, limiting cases of probe theories can be used to estimate upper and lower bounds on plasma densities. These theories include and neglect orbital motion, respectively, with different collisional terms leading to intermediate estimates. (paper)

  10. Study of defects, radiation damage and implanted gases in solids by field-ion and atom-probe microscopy

    International Nuclear Information System (INIS)

    Seidman, D.N.; Amano, J.; Wagner, A.

    1980-10-01

    The ability of the field-ion microscope to image individual atoms has been applied, at Cornell University, to the study of fundamental properties of point defects in irradiated or quenched metals. The capability of the atom probe field-ion microscope to determine the chemistry - that is, the mass-to-charge ratio - of a single ion has been used to investigate the behavior of different implanted species in metals. A brief review is presented of: (1) the basic physical principles of the field-ion and atom-probe microscopes; (2) the many applications of these instruments to the study of defects and radiation damage in solids; and (3) the application of the atom-probe field-ion microscope to the study of the behavior of implanted 3 He and 4 He atoms in tungsten. The paper is heavily referenced so that the reader can pursue his specific research interests in detail

  11. β-Isocyanoalanine as an IR probe: comparison of vibrational dynamics between isonitrile and nitrile-derivatized IR probes.

    Science.gov (United States)

    Maj, Michał; Ahn, Changwoo; Kossowska, Dorota; Park, Kwanghee; Kwak, Kyungwon; Han, Hogyu; Cho, Minhaeng

    2015-05-07

    An infrared (IR) probe based on isonitrile (NC)-derivatized alanine 1 was synthesized and the vibrational properties of its NC stretching mode were investigated using FTIR and femtosecond IR pump-probe spectroscopy. It is found that the NC stretching mode is very sensitive to the hydrogen-bonding ability of solvent molecules. Moreover, its transition dipole strength is larger than that of nitrile (CN) in nitrile-derivatized IR probe 2. The vibrational lifetime of the NC stretching mode is found to be 5.5 ± 0.2 ps in both D2O and DMF solvents, which is several times longer than that of the azido (N3) stretching mode in azido-derivatized IR probe 3. Altogether these properties suggest that the NC group can be a very promising sensing moiety of IR probes for studying the solvation structure and dynamics of biomolecules.

  12. Agronomic effect of empty fruit bunches compost, anorganic fertilizer and endophytic microbes in oil palm main nursery used Ganoderma endemic soil

    Science.gov (United States)

    Hanum, H.; Lisnawita; Tantawi, A. R.

    2018-02-01

    Using of Ganoderma endemic soil in oil palm main nursery is not recomended because produce bad quality seedling. The application of organic and anorganic fertilizer and endophytic microbes are the alternative for solving the problem. The objective of this research is to evaluate the effect of empty fruit bunches compost, anorganic fertilizer and endophytic microbes on growth of oil palm seedling in main nursery. This research used factorial randomized block design. The first factor was combination of empty fruit bunches compost and anorganic fertilizer, The second factor was endophytic microbes consisting of Trichoderma and Aspergillus. The results showed that interaction effect of the both treatment factor used increased growth of seedling in third and fourth month after application. The best growth of seedling was on the treatment of empty fruit bunches compost combined with anorganic fertilizer 150% recommended dosage and Trichoderma viride.

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

    Science.gov (United States)

    2001-01-01

    functional genomics tools (gene chips, technologies, etc.), comparative genomics, proteomics tools, novel culture techniques, in situ analyses, and...interested in supporting microarray/chip development for gene expression analysis for agricultural microbes, bioinformatics, and proteomics , and the...including one fungus ) in various stages of progress. The closely integrated Natural and Accelerated Bioremediation Research Program in the Office of

  14. Response of electrostatic probes to eccentric charge distributions

    DEFF Research Database (Denmark)

    Johansson, Torben; McAllister, Iain Wilson

    2001-01-01

    The response of an electrostatic probe mounted in an electrode is examined with reference to eccentric charge distributions. The study involves using the probe λ function to derive a characteristic parameter. This parameter enables the response of the probe to different degrees of eccentricity...

  15. ProbeZT: Simulation of transport coefficients of molecular electronic junctions under environmental effects using Büttiker's probes

    Science.gov (United States)

    Korol, Roman; Kilgour, Michael; Segal, Dvira

    2018-03-01

    We present our in-house quantum transport package, ProbeZT. This program provides linear response coefficients: electrical and electronic thermal conductances, as well as the thermopower of molecular junctions in which electrons interact with the surrounding thermal environment. Calculations are performed based on the Büttiker probe method, which introduces decoherence, energy exchange and dissipation effects phenomenologically using virtual electrode terminals called probes. The program can realize different types of probes, each introducing various environmental effects, including elastic and inelastic scattering of electrons. The molecular system is described by an arbitrary tight-binding Hamiltonian, allowing the study of different geometries beyond simple one-dimensional wires. Applications of the program to study the thermoelectric performance of molecular junctions are illustrated. The program also has a built-in functionality to simulate electron transport in double-stranded DNA molecules based on a tight-binding (ladder) description of the junction.

  16. A Common Probe Design for Multiple Planetary Destinations

    Science.gov (United States)

    Hwang, H. H.; Allen, G. A., Jr.; Alunni, A. I.; Amato, M. J.; Atkinson, D. H.; Bienstock, B. J.; Cruz, J. R.; Dillman, R. A.; Cianciolo, A. D.; Elliott, J. O.; hide

    2018-01-01

    Atmospheric probes have been successfully flown to planets and moons in the solar system to conduct in situ measurements. They include the Pioneer Venus multi-probes, the Galileo Jupiter probe, and Huygens probe. Probe mission concepts to five destinations, including Venus, Jupiter, Saturn, Uranus, and Neptune, have all utilized similar-shaped aeroshells and concept of operations, namely a 45-degree sphere cone shape with high density heatshield material and parachute system for extracting the descent vehicle from the aeroshell. Each concept designed its probe to meet specific mission requirements and to optimize mass, volume, and cost. At the 2017 International Planetary Probe Workshop (IPPW), NASA Headquarters postulated that a common aeroshell design could be used successfully for multiple destinations and missions. This "common probe"� design could even be assembled with multiple copies, properly stored, and made available for future NASA missions, potentially realizing savings in cost and schedule and reducing the risk of losing technologies and skills difficult to sustain over decades. Thus the NASA Planetary Science Division funded a study to investigate whether a common probe design could meet most, if not all, mission needs to the five planetary destinations with extreme entry environments. The Common Probe study involved four NASA Centers and addressed these issues, including constraints and inefficiencies that occur in specifying a common design. Study methodology: First, a notional payload of instruments for each destination was defined based on priority measurements from the Planetary Science Decadal Survey. Steep and shallow entry flight path angles (EFPA) were defined for each planet based on qualification and operational g-load limits for current, state-of-the-art instruments. Interplanetary trajectories were then identified for a bounding range of EFPA. Next, 3-degrees-of-freedom simulations for entry trajectories were run using the entry state

  17. Internalisation of microbes in vegetables: microbial load of Ghanaian vegetables and the relationship with different water sources of irrigation.

    Science.gov (United States)

    Donkor, Eric S; Lanyo, R; Kayang, Boniface B; Quaye, Jonathan; Edoh, Dominic A

    2010-09-01

    The occurrence of pathogens in the internal parts of vegetables is usually associated with irrigation water or contaminated soil and could pose risk to consumers as the internalised pathogens are unaffected by external washing. This study was carried out to assess the rate of internalisation of microbes in common Ghanaian vegetables. Standard microbiological methods were employed in microbial enumeration of vegetables collected at the market and farm levels, as well as irrigation water and soil samples. The overall mean counts of vegetables were 4.0 x 10(3) cfu g(-1); 8.1 x 10(2) cfu g(-1); 2.0 x 10(2) cfu g(-1); 3.5 x 10(2) cfu g(-1) for total bacteria, coliform counts, faecal coliform counts and yeast counts, respectively. The rate of internalisation of coliforms in vegetables irrigated with stream/well water was 2.7 times higher than those irrigated with pipe water. The mean coliform counts (4.7 x 10(7) cfu g(-1)) and faecal coliform counts (1.8 x 10(6) cfu g(-1)) of soil samples were similar to those of stream water suggesting both sources exerted similar contamination rates on the vegetables. Generally, there were no significant variations between the rates of internalisation of microbes at the market and farm levels at p vegetables mainly occurred at the farm level. The study has shown that microbial contamination of vegetables in Ghana is not limited to the external surface, but internal vegetable parts could harbour high microbial loads and pose risk to consumers. Safety practices associated with the commodity should therefore not be limited to external washing only. There is the additional need of heating vegetables to eliminate microbes both externally and internally before consumption.

  18. Nuclear borehole probes - theory and experiments

    International Nuclear Information System (INIS)

    Joergensen, J.L.; Korsbech, U.; Gynther Nielsen, K.; Oelgaard, P.L.

    1985-06-01

    The report gives a summary of the theoretical and expeimental work on borehole probes that has been performed since 1971 at The Department of Electrophysics, The Technical University of Denmark. The first part of the report concerns the use of a spectral natural gamma-ray probe (SNG-probe), which is used for measurements of the spectral distribution of the gamma-rays of the geological strata around a borehole. In general the spectrum is divided into three parts - the gamma-rays from potassium-40, from thorium-232 and daughters, and from uranium-238 and daughters. A set of curves showing the intensities of the gamm-radiation from K, Th, and U versus depth is called a SNG-log. If proper calibrated, the SNG-log gives the concentration of Th, U, and K in the formation surrounding the borehole. Initially the basis for an interpretation of SNG-logs is discussed. Then follows a description og some SNG-problems designed and built by The Department of Electrophysics, and a discussion of the calibration of SNG-probes. Some examples of SNG-logs are presented, and some general comments on the use of SNG-logs are given. The second part of the report concerns mainly the development of theoretical models for neutron-neutron probes, gamma-gamma probes, and pulsed-neutron probes. The purpose of this work has been to examine how well the models correlate with measured results and - where reasonable agreement is found - to use the models in studies of the factors that affect the probe responses in interpretation of experimental results and in probe design. (author)

  19. Growth Rates of Microbes in the Oceans.

    Science.gov (United States)

    Kirchman, David L

    2016-01-01

    A microbe's growth rate helps to set its ecological success and its contribution to food web dynamics and biogeochemical processes. Growth rates at the community level are constrained by biomass and trophic interactions among bacteria, phytoplankton, and their grazers. Phytoplankton growth rates are approximately 1 d(-1), whereas most heterotrophic bacteria grow slowly, close to 0.1 d(-1); only a few taxa can grow ten times as fast. Data from 16S rRNA and other approaches are used to speculate about the growth rate and the life history strategy of SAR11, the most abundant clade of heterotrophic bacteria in the oceans. These strategies are also explored using genomic data. Although the methods and data are imperfect, the available data can be used to set limits on growth rates and thus on the timescale for changes in the composition and structure of microbial communities.

  20. Microbes vs. chemistry in the origin of the anaerobic gut lumen.

    Science.gov (United States)

    Friedman, Elliot S; Bittinger, Kyle; Esipova, Tatiana V; Hou, Likai; Chau, Lillian; Jiang, Jack; Mesaros, Clementina; Lund, Peder J; Liang, Xue; FitzGerald, Garret A; Goulian, Mark; Lee, Daeyeon; Garcia, Benjamin A; Blair, Ian A; Vinogradov, Sergei A; Wu, Gary D

    2018-04-17

    The succession from aerobic and facultative anaerobic bacteria to obligate anaerobes in the infant gut along with the differences between the compositions of the mucosally adherent vs. luminal microbiota suggests that the gut microbes consume oxygen, which diffuses into the lumen from the intestinal tissue, maintaining the lumen in a deeply anaerobic state. Remarkably, measurements of luminal oxygen levels show nearly identical pO 2 (partial pressure of oxygen) profiles in conventional and germ-free mice, pointing to the existence of oxygen consumption mechanisms other than microbial respiration. In vitro experiments confirmed that the luminal contents of germ-free mice are able to chemically consume oxygen (e.g., via lipid oxidation reactions), although at rates significantly lower than those observed in the case of conventionally housed mice. For conventional mice, we also show that the taxonomic composition of the gut microbiota adherent to the gut mucosa and in the lumen throughout the length of the gut correlates with oxygen levels. At the same time, an increase in the biomass of the gut microbiota provides an explanation for the reduction of luminal oxygen in the distal vs. proximal gut. These results demonstrate how oxygen from the mammalian host is used by the gut microbiota, while both the microbes and the oxidative chemical reactions regulate luminal oxygen levels, shaping the composition of the microbial community throughout different regions of the gut.

  1. Survey of Hawksbill Turtle (Eretmochelys imbricate Health Condition in Terms of Parasites and Microbes in Alas Purwo National Park, Indonesia

    Directory of Open Access Journals (Sweden)

    Qurrota A'yunin

    2017-07-01

    Full Text Available Indonesian waters have six types of turtles that can live, spawn and breed. Sea turtle conservation becomes an important and urgent program to be done in order to protect and save sea turtle population in Indonesia. One of the factors that most affect the turtle population is the cause of degradation of pathogenic factors. Alas Purwo National Park, East Java, there is some communities that have activities turtle conservation. Conservation is done by securing and protecting turtle eggs. Turtle eggs that have hatched are released into the sea once it is ready. This study aims was to determine the type of bacteria and fungi that infect hatchlings and environmental factors that influence. This research is descriptive method to Hawksbill turtle (Eretmochelys imbricate is by way of random sampling. Sampling of microbes in sea turtle was conducted using cotton swab method and then microbes was cultured and indentified in laboratory. The results showed The kind of parasites and microbes which were indentified in hatching and adult Hawksbill sea turtles were fungus with genus Aspergillus sp., Geotrichum sp., Fusarium sp., and Gliocladium sp. ; bacteria are Pseudomonas aeruginosa and Enterobacter cloaceae; and parasite is Chelonibia testudinaria barnacles.  The parameter average value of water in pond indicated 28.1 – 29.2°C for temperature, 32 - 34 ‰ for salinity, 7.78 – 8.2 for pH, and 3.86 – 4.21 mg/L for DO.

  2. A symbiosis-dedicated SYNTAXIN OF PLANTS 13II isoform controls the formation of a stable host-microbe interface in symbiosis.

    Science.gov (United States)

    Huisman, Rik; Hontelez, Jan; Mysore, Kirankumar S; Wen, Jiangqi; Bisseling, Ton; Limpens, Erik

    2016-09-01

    Arbuscular mycorrhizal (AM) fungi and rhizobium bacteria are accommodated in specialized membrane compartments that form a host-microbe interface. To better understand how these interfaces are made, we studied the regulation of exocytosis during interface formation. We used a phylogenetic approach to identify target soluble N-ethylmaleimide-sensitive factor-attachment protein receptors (t-SNAREs) that are dedicated to symbiosis and used cell-specific expression analysis together with protein localization to identify t-SNAREs that are present on the host-microbe interface in Medicago truncatula. We investigated the role of these t-SNAREs during the formation of a host-microbe interface. We showed that multiple syntaxins are present on the peri-arbuscular membrane. From these, we identified SYNTAXIN OF PLANTS 13II (SYP13II) as a t-SNARE that is essential for the formation of a stable symbiotic interface in both AM and rhizobium symbiosis. In most dicot plants, the SYP13II transcript is alternatively spliced, resulting in two isoforms, SYP13IIα and SYP13IIβ. These splice-forms differentially mark functional and degrading arbuscule branches. Our results show that vesicle traffic to the symbiotic interface is specialized and required for its maintenance. Alternative splicing of SYP13II allows plants to replace a t-SNARE involved in traffic to the plasma membrane with a t-SNARE that is more stringent in its localization to functional arbuscules. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  3. Probe Storage

    NARCIS (Netherlands)

    Gemelli, Marcellino; Abelmann, Leon; Engelen, Johannes Bernardus Charles; Khatib, M.G.; Koelmans, W.W.; Zaboronski, Olog; Campardo, Giovanni; Tiziani, Federico; Laculo, Massimo

    2011-01-01

    This chapter gives an overview of probe-based data storage research over the last three decades, encompassing all aspects of a probe recording system. Following the division found in all mechanically addressed storage systems, the different subsystems (media, read/write heads, positioning, data

  4. Probing of flowing electron plasmas

    International Nuclear Information System (INIS)

    Himura, H.; Nakashima, C.; Saito, H.; Yoshida, Z.

    2001-01-01

    Probing of streaming electron plasmas with finite temperature is studied. For the first time, a current-voltage characteristic of an electric probe is measured in electron plasmas. Due to the fast flow of the electron plasmas, the characteristic curve spreads out significantly and exhibits a long tail. This feature can be explained calculating the currents collected to the probe. In flowing electron plasmas, the distribution function observed in the laboratory frame is non-Maxwellian even if the plasmas come to a state of thermal equilibrium. Another significant feature of the characteristic is that it determines a floating potential where the current equals zero, despite there being very few ions in the electron plasma. A high impedance probe, which is popularly used to determine the space potential of electron plasmas, outputs the potential. The method is available only for plasmas with density much smaller than the Brillouin limit

  5. Modeling the Insertion Mechanics of Flexible Neural Probes Coated with Sacrificial Polymers for Optimizing Probe Design

    Directory of Open Access Journals (Sweden)

    Sagar Singh

    2016-03-01

    Full Text Available Single-unit recording neural probes have significant advantages towards improving signal-to-noise ratio and specificity for signal acquisition in brain-to-computer interface devices. Long-term effectiveness is unfortunately limited by the chronic injury response, which has been linked to the mechanical mismatch between rigid probes and compliant brain tissue. Small, flexible microelectrodes may overcome this limitation, but insertion of these probes without buckling requires supporting elements such as a stiff coating with a biodegradable polymer. For these coated probes, there is a design trade-off between the potential for successful insertion into brain tissue and the degree of trauma generated by the insertion. The objective of this study was to develop and validate a finite element model (FEM to simulate insertion of coated neural probes of varying dimensions and material properties into brain tissue. Simulations were performed to predict the buckling and insertion forces during insertion of coated probes into a tissue phantom with material properties of brain. The simulations were validated with parallel experimental studies where probes were inserted into agarose tissue phantom, ex vivo chick embryonic brain tissue, and ex vivo rat brain tissue. Experiments were performed with uncoated copper wire and both uncoated and coated SU-8 photoresist and Parylene C probes. Model predictions were found to strongly agree with experimental results (<10% error. The ratio of the predicted buckling force-to-predicted insertion force, where a value greater than one would ideally be expected to result in successful insertion, was plotted against the actual success rate from experiments. A sigmoidal relationship was observed, with a ratio of 1.35 corresponding to equal probability of insertion and failure, and a ratio of 3.5 corresponding to a 100% success rate. This ratio was dubbed the “safety factor”, as it indicated the degree to which the coating

  6. A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

    Directory of Open Access Journals (Sweden)

    Jasper J. van Thor

    2015-01-01

    Full Text Available In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe” which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.

  7. Dynamical study of the radial structure of the fluctuations measured by a reciprocating Langmuir probe in Tore Supra

    International Nuclear Information System (INIS)

    Devynck, P.; Antar, G.; Wang, G.; Garbet, X.; Gunn, J.; Pascal, J.Y.

    1999-01-01

    The fluctuations in the Scrape Off Layer (S.O.L.) of Tore Supra are studied with a movable Langmuir probe biased to ion saturation current. The probe system consists of three probes separated poloidally (0.68 cm between two nearby probes). The probe has no magnetic connection to the mid plane limiter on which the plasma is leaning, but the radial profile of the ion saturation current fluctuations displays a dip at the limiter position. At the same location the ion saturation current displays a dip at the limiter position. At the same location the ion saturation current displays an inflexion point. A correlation analysis technique is developed to study the radial behaviour of the fluctuations. It reveals that this dip is associated with a reduction of the poloidal velocity of the fluctuations with no sign reversal. In the dip the mean poloidal correlation length of the fluctuations is also reduced. These observations are consistent with a reduction of the fluctuations by a shear of the radial electric field created at the limiter surface. The autocorrelation time is also calculated. It increases slightly in the dip and is found to be sensitive to both the convection time and lifetime of the turbulent structures, because these quantities are of the same order. (authors)

  8. Einstein Inflationary Probe (EIP)

    Science.gov (United States)

    Hinshaw, Gary

    2004-01-01

    I will discuss plans to develop a concept for the Einstein Inflation Probe: a mission to detect gravity waves from inflation via the unique signature they impart to the cosmic microwave background (CMB) polarization. A sensitive CMB polarization satellite may be the only way to probe physics at the grand-unified theory (GUT) scale, exceeding by 12 orders of magnitude the energies studied at the Large Hadron Collider. A detection of gravity waves would represent a remarkable confirmation of the inflationary paradigm and set the energy scale at which inflation occurred when the universe was a fraction of a second old. Even a strong upper limit to the gravity wave amplitude would be significant, ruling out many common models of inflation, and pointing to inflation occurring at much lower energy, if at all. Measuring gravity waves via the CMB polarization will be challenging. We will undertake a comprehensive study to identify the critical scientific requirements for the mission and their derived instrumental performance requirements. At the core of the study will be an assessment of what is scientifically and experimentally optimal within the scope and purpose of the Einstein Inflation Probe.

  9. Directional rf probe for measurement of conductivity of flowing plasmas

    International Nuclear Information System (INIS)

    Jayakumar, R.; Chakravarthy, D.P.; Rohatgi, V.K.

    1977-01-01

    An electrodeless immersible rf probe for measurement of plasma conductivity in the range 0.01 to 100 mho/m has been designed and fabricated. The probe, with an overall diameter of 11 mm, employs unidirectional electromagnetic field lines which reduce the inaccuracies caused by insertion of the probe in a flowing plasma. In the range studied the probe output shows a linear relationship with the conductivity of the medium. Such probes are of interest in the study of MHD and reentry plasmas

  10. Rapid Reactivation of Deep Subsurface Microbes in the Presence of C-1 Compounds

    Directory of Open Access Journals (Sweden)

    Pauliina Rajala

    2015-02-01

    Full Text Available Microorganisms in the deep biosphere are believed to conduct little metabolic activity due to low nutrient availability in these environments. However, destructive penetration to long-isolated bedrock environments during construction of underground waste repositories can lead to increased nutrient availability and potentially affect the long-term stability of the repository systems, Here, we studied how microorganisms present in fracture fluid from a depth of 500 m in Outokumpu, Finland, respond to simple carbon compounds (C-1 compounds in the presence or absence of sulphate as an electron acceptor. C-1 compounds such as methane and methanol are important intermediates in the deep subsurface carbon cycle, and electron acceptors such as sulphate are critical components of oxidation processes. Fracture fluid samples were incubated in vitro with either methane or methanol in the presence or absence of sulphate as an electron acceptor. Metabolic response was measured by staining the microbial cells with fluorescent dyes that indicate metabolic activity and transcriptional response with RT-qPCR. Our results show that deep subsurface microbes exist in dormant states but rapidly reactivate their transcription and respiration systems in the presence of C-1 substrates, particularly methane. Microbial activity was further enhanced by the addition of sulphate as an electron acceptor. Sulphate- and nitrate-reducing microbes were particularly responsive to the addition of C-1 compounds and sulphate. These taxa are common in deep biosphere environments and may be affected by conditions disturbed by bedrock intrusion, as from drilling and excavation for long-term storage of hazardous waste.

  11. Probiotic microbes sustain youthful serum testosterone levels and testicular size in aging mice.

    Directory of Open Access Journals (Sweden)

    Theofilos Poutahidis

    Full Text Available The decline of circulating testosterone levels in aging men is associated with adverse health effects. During studies of probiotic bacteria and obesity, we discovered that male mice routinely consuming purified lactic acid bacteria originally isolated from human milk had larger testicles and increased serum testosterone levels compared to their age-matched controls. Further investigation using microscopy-assisted histomorphometry of testicular tissue showed that mice consuming Lactobacillus reuteri in their drinking water had significantly increased seminiferous tubule cross-sectional profiles and increased spermatogenesis and Leydig cell numbers per testis when compared with matched diet counterparts This showed that criteria of gonadal aging were reduced after routinely consuming a purified microbe such as L. reuteri. We tested whether these features typical of sustained reproductive fitness may be due to anti-inflammatory properties of L. reuteri, and found that testicular mass and other indicators typical of old age were similarly restored to youthful levels using systemic administration of antibodies blocking pro-inflammatory cytokine interleukin-17A. This indicated that uncontrolled host inflammatory responses contributed to the testicular atrophy phenotype in aged mice. Reduced circulating testosterone levels have been implicated in many adverse effects; dietary L. reuteri or other probiotic supplementation may provide a viable natural approach to prevention of male hypogonadism, absent the controversy and side-effects of traditional therapies, and yield practical options for management of disorders typically associated with normal aging. These novel findings suggest a potential high impact for microbe therapy in public health by imparting hormonal and gonad features of reproductive fitness typical of much younger healthy individuals.

  12. Is Drosophila-microbe association species-specific or region specific? A study undertaken involving six Indian Drosophila species.

    Science.gov (United States)

    Singhal, Kopal; Khanna, Radhika; Mohanty, Sujata

    2017-06-01

    The present work aims to identify the microbial diversity associated with six Indian Drosophila species using next generation sequencing (NGS) technology and to discover the nature of their distribution across species and eco-geographic regions. Whole fly gDNA of six Drosophila species were used to generate sequences in an Illumina platform using NGS technology. De novo based assembled raw reads were blasted against the NR database of NCBI using BLASTn for identification of their bacterial loads. We have tried to include Drosophila species from different taxonomical groups and subgroups and from three different eco-climatic regions India; four species belong to Central India, while the rest two, D. melanogaster and D. ananassae, belong to West and South India to determine both their species-wise and region-wide distribution. We detected the presence of 33 bacterial genera across all six study species, predominated by the class Proteobacteria. Amongst all, D. melanogaster was found to be the most diverse by carrying around 85% of the bacterial diversity. Our findings infer both species-specific and environment-specific nature of the bacterial species inhabiting the Drosophila host. Though the present results are consistent with most of the earlier studies, they also remain incoherent with some. The present study outcome on the host-bacteria association and their species specific adaptation may provide some insight to understand the host-microbial interactions and the phenotypic implications of microbes on the host physiology. The knowledge gained may be importantly applied into the recent insect and pest population control strategy going to implement through gut microflora in India and abroad.

  13. Study of ablation and implosion stages in wire arrays using coupled ultraviolet and X-ray probing diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, A. A.; Ivanov, V. V.; Astanovitskiy, A. L.; Wiewior, P. P.; Chalyy, O. [University of Nevada Reno, Reno, Nevada 89557 (United States); Papp, D. [University of Nevada Reno, Reno, Nevada 89557 (United States); ELI-ALPS, ELI-Hu Nkft., H-6720 Szeged (Hungary)

    2015-11-15

    Star and cylindrical wire arrays were studied using laser probing and X-ray radiography at the 1-MA Zebra pulse power generator at the University of Nevada, Reno. The Leopard laser provided backlighting, producing a laser plasma from a Si target which emitted an X-ray probing pulse at the wavelength of 6.65 Å. A spherically bent quartz crystal imaged the backlit wires onto X-ray film. Laser probing diagnostics at the wavelength of 266 nm included a 3-channel polarimeter for Faraday rotation diagnostic and two-frame laser interferometry with two shearing interferometers to study the evolution of the plasma electron density at the ablation and implosion stages. Dynamics of the plasma density profile in Al wire arrays at the ablation stage were directly studied with interferometry, and expansion of wire cores was measured with X-ray radiography. The magnetic field in the imploding plasma was measured with the Faraday rotation diagnostic, and current was reconstructed.

  14. Blinded Comparison between an In-Air Reverberation Method and an Electronic Probe Tester in the Detection of Ultrasound Probe Faults.

    Science.gov (United States)

    Dudley, Nicholas J; Woolley, Darren J

    2017-12-01

    The aim of this study was to perform a blinded trial, comparing the results of a visual inspection of the in-air reverberation pattern with the results of an electronic probe tester in detecting ultrasound probe faults. Sixty-two probes were tested. A total of 28 faults were found, 3 only by in-air reverberation assessment and 2 only by the electronic probe tester. The electronic probe tester provided additional information regarding the location of the fault in 74% of the cases in which both methods detected a fault. It is possible to detect the majority of probe faults by visual inspection and in-air reverberation assessment. The latter provides an excellent first-line test, easily performed on a daily basis by equipment users. An electronic probe tester is required if detailed evaluation of faults is necessary. Copyright © 2017 World Federation for Ultrasound in Medicine and Biology. All rights reserved.

  15. Active probing of plasma edge turbulence and feedback studies on the Texas Experimental Tokamak (TEXT)

    International Nuclear Information System (INIS)

    Uckan, T.; Richards, B.; Bengtson, R.D.

    1993-08-01

    A novel experiment is under way on the Texas Experimental Tokamak (TEXT) to actively modify the turbulence at the plasma edge by launching waves using electrostatic probes in the shadow of the limiter. The experiments are carried out with a wave launching system consisting of two Langmuir probes, which are about 1.8 cm apart in the poloidal direction, with respect to the magnetic field. These probes are operated in the electron side of the (I,V) characteristic. The probe tips are fed separately by independent ac power supplies. Measurements indicate that the wave, launched with a typical frequency image of 15--50 kHz from the edge of the machine top, is received by sensing probes located halfway around the torus. The detected signal strength depends on the frequency of the wave, the plasma current, and the phasing of the applied ac signal between the launching probes. Modifications to the spectra of the density and potential fluctuations are observed. These experiments have been extended to control of the edge plasma fluctuation level using feedback to explore its effects on confinement. When the launcher is driven by the floating potential of the fluctuating plasma at the location of the launching probes, then the fluctuations are suppressed or excited, depending on the phasing between the probe tips, both locally and at the downstream sensing probes. The fluctuation-induced particle flux also varies with the feedback phasing

  16. Paramagnetic probes to study PrNi5?

    International Nuclear Information System (INIS)

    Hutchinson, W.D.; Harker, S.J.; Stewart, G.A.; Chaplin, D.H.; Kaplan, N.

    1996-01-01

    The Van-Vleck paramagnet PrNi 5 has been the focus of many studies in the past as a result of its usefulness as a nuclear cooling agent. Extensive continuous wave praseodymium NMR measurements have been carried out on this compound. However pulsed NMR and therefore precise relaxation measurements particularly at mK temperatures have proved elusive. In this work we have proposed to use radiative gamma-ray detection to indirectly measure Pr NMR in PrNi 5 via cross relaxation to suitable paramagnetic impurity probes placed at Ni lattice sites. 57 Co was chosen as the most compatible nuclear orientation isotope with an appropriate nuclear g-factor. The choice of 57 Co also allows the use of Moessbauer spectroscopy to check the site occupancy. This poster details the production of a 57 Co doped PrNi 5 single crystal specimen including the specimen preparation problems encountered, 57 Fe Moessbauer and preliminary nuclear orientation measurements

  17. Efflux pump-deficient mutants as a platform to search for microbes that produce antibiotics.

    Science.gov (United States)

    Molina-Santiago, Carlos; Udaondo, Zulema; Daddaoua, Abdelali; Roca, Amalia; Martín, Jesús; Pérez-Victoria, Ignacio; Reyes, Fernando; Ramos, Juan-Luis

    2015-07-01

    Pseudomonas putida DOT-T1E-18 is a strain deficient in the major antibiotic efflux pump (TtgABC) that exhibits an overall increased susceptibility to a wide range of drugs when compared with the wild-type strain. We used this strain as a platform to search for microbes able to produce antibiotics that inhibit growth. A collection of 2400 isolates from soil, sediments and water was generated and a drop assay developed to identify, via growth inhibition halos, strains that prevent the growth of DOT-T1E-18 on solid Luria-Bertani plates. In this study, 35 different isolates that produced known and unknown antibiotics were identified. The most potent inhibitor of DOT-T1E-18 growth was an isolate named 250J that, through multi-locus sequence analysis, was identified as a Pseudomonas sp. strain. Culture supernatants of 250J contain four different xantholysins that prevent growth of Gram-positive bacteria, Gram-negative and fungi. Two of the xantholysins were produced in higher concentrations and purified. Xantholysin A was effective against Bacillus, Lysinibacillus and Rhodococcus strains, and the effect against these microbes was enhanced when used in combination with other antibiotics such as ampicillin, gentamicin and kanamycin. Xantholysin C was also efficient against Gram-positive bacteria and showed an interesting antimicrobial effect against Pseudomonas strains, and a synergistic inhibitory effect with ampicillin, chloramphenicol and gentamicin. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  18. Modular Rake of Pitot Probes

    Science.gov (United States)

    Dunlap, Timothy A.; Henry, Michael W.; Homyk, Raymond P.

    2004-01-01

    The figure presents selected views of a modular rake of 17 pitot probes for measuring both transient and steady-state pressures in a supersonic wind tunnel. In addition to pitot tubes visible in the figure, the probe modules contain (1) high-frequency dynamic-pressure transducers connected through wires to remote monitoring circuitry and (2) flow passages that lead to tubes that, in turn, lead to remote steady-state pressure transducers. Prior pitot-probe rakes were fabricated as unitary structures, into which the individual pitot probes were brazed. Repair or replacement of individual probes was difficult, costly, and time-consuming because (1) it was necessary to remove entire rakes in order to unbraze individual malfunctioning probes and (2) the heat of unbrazing a failed probe and of brazing a new probe in place could damage adjacent probes. In contrast, the modules in the present probe are designed to be relatively quickly and easily replaceable with no heating and, in many cases, without need for removal of the entire rake from the wind tunnel. To remove a malfunctioning probe, one first removes a screw-mounted V-cross-section cover that holds the probe and adjacent probes in place. Then one removes a screw-mounted cover plate to gain access to the steady-state pressure tubes and dynamicpressure wires. Next, one disconnects the tube and wires of the affected probe. Finally, one installs a new probe in the reverse of the aforementioned sequence. The wire connections can be made by soldering, but to facilitate removal and installation, they can be made via miniature plugs and sockets. The connections between the probe flow passages and the tubes leading to the remote pressure sensors can be made by use of any of a variety of readily available flexible tubes that can be easily pulled off and slid back on for removal and installation, respectively.

  19. Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes.

    Science.gov (United States)

    Saad, Rama; Rizkallah, Mariam R; Aziz, Ramy K

    2012-11-30

    The influence of resident gut microbes on xenobiotic metabolism has been investigated at different levels throughout the past five decades. However, with the advance in sequencing and pyrotagging technologies, addressing the influence of microbes on xenobiotics had to evolve from assessing direct metabolic effects on toxins and botanicals by conventional culture-based techniques to elucidating the role of community composition on drugs metabolic profiles through DNA sequence-based phylogeny and metagenomics. Following the completion of the Human Genome Project, the rapid, substantial growth of the Human Microbiome Project (HMP) opens new horizons for studying how microbiome compositional and functional variations affect drug action, fate, and toxicity (pharmacomicrobiomics), notably in the human gut. The HMP continues to characterize the microbial communities associated with the human gut, determine whether there is a common gut microbiome profile shared among healthy humans, and investigate the effect of its alterations on health. Here, we offer a glimpse into the known effects of the gut microbiota on xenobiotic metabolism, with emphasis on cases where microbiome variations lead to different therapeutic outcomes. We discuss a few examples representing how the microbiome interacts with human metabolic enzymes in the liver and intestine. In addition, we attempt to envisage a roadmap for the future implications of the HMP on therapeutics and personalized medicine.

  20. Design study of an entry probe spectro-reflectometer

    Science.gov (United States)

    Sill, G. T.; Fink, U.

    1986-01-01

    A wind tunnel was built to simulate the rapid movement of an entry probe through the Jupiter atmosphere. Wind speeds range from 1 to 50 meters per second in a closed system. Wind velocity and temperature probes as well as a cryogenically cooled cold finger can be placed in the 6 inch diameter viewing section. The initial testing of the wind tunnel involved running sectional profiles through the observation port of air currents of 0.1 to 3.0 atmosphere. The velocity profile was very uniform throughout the cross section of the experimental port, with the exception of the wall effects. The deposition of cooled volatiles using the wind tunnel was not performed. However, measurements of the deposition of H2O ice on a cryogenically cooled thickness modulator were made under ambient conditions, namely room temperature and pressure. In the Frost Depositon Test Facility, ice deposition was measured at thicknesses of about a half millimeter and frost was produced whose thickness reflectivity could easily be measured by reflectance spectroscopy.

  1. STM-SQUID probe microscope

    International Nuclear Information System (INIS)

    Hayashi, Tadayuki; Tachiki, Minoru; Itozaki, Hideo

    2007-01-01

    We have developed a STM-SQUID probe microscope. A high T C SQUID probe microscope was combined with a scanning tunneling microscope for investigation of samples at room temperature in air. A high permeability probe needle was used as a magnetic flux guide to improve the spatial resolution. The probe with tip radius of less than 100 nm was prepared by microelectropolishing. The probe was also used as a scanning tunneling microscope tip. Topography of the sample surface could be measured by the scanning tunneling microscope with high spatial resolution prior to observation by SQUID microscopy. The SQUID probe microscope image could be observed while keeping the distance from the sample surface to the probe tip constant. We observed a topographic image and a magnetic image of Ni fine pattern and also a magnetically recorded hard disk. Furthermore we have investigated a sample vibration method of the static magnetic field emanating from a sample with the aim of achieving a higher signal-to-noise (S/N) ratio

  2. Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines.

    Science.gov (United States)

    Gajigan, Andrian P; Yñiguez, Aletta T; Villanoy, Cesar L; San Diego-McGlone, Maria Lourdes; Jacinto, Gil S; Conaco, Cecilia

    2018-01-01

    Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region.

  3. Study of borehole probing methods to improve the ground characterization

    Science.gov (United States)

    Naeimipour, Ali

    partially condition of discontinuities. Two of the more promising tools have been tested during this project, which are QL40OBI Optical TV and Slim Borehole Scanner (SBS) manufacture by ALT-Mount Sopris and DMT, respectively. The field experiment with QL40OBI showed that the images generated for downward and sub-horizontal boreholes are of good quality and can be used to evaluate the joint conditions. However, this device is not suitable for use inside the upward drillholes. The Slim Borehole Scanner (SBS) manufactured by DMT in Germany has the required features for borescoping the roofbolt holes. This includes the ease of operation and suitable geometry along with an unwrapped 360-degree picture of the borehole wall. This instrument was concluded to be the best option yet for obtaining images from boreholes with any arbitrary orientation. In addition, a new tool, called Rock Strength Borehole Probe (RSBP), was developed for estimation of the rock strength through scratching the rock surface in the borehole. This device is designed to be a light, flexible, quick, non-disruptive, and cost effective alternative to estimate the rock strength inside the boreholes in underground mines and tunnels. An extensive number of laboratory tests under variable conditions were conducted to develop equations to estimate the Uniaxial Compressive Strength (UCS) and Brazilian Tensile Strength (BTS) of the rock from measured cutting forces. In these experiments, 27 different rock types were tested by full scale scratch tests, including the cutting tests by a miniature disc. The results show a good correlation between the normal force and the compressive strength of sedimentary/metamorphic rock if the depth of scratch is known. No significant correlation was observed for igneous rocks, due to the impacts of grain size. Current studies show promising results for using RSBP. The laboratory and field tests proved the functionality of this tool. This probe is capable of entering boreholes of 45 mm

  4. New atom probe approaches to studying segregation in nanocrystalline materials

    International Nuclear Information System (INIS)

    Samudrala, S.K.; Felfer, P.J.; Araullo-Peters, V.J.; Cao, Y.; Liao, X.Z.; Cairney, J.M.

    2013-01-01

    Atom probe is a technique that is highly suited to the study of nanocrystalline materials. It can provide accurate atomic-scale information about the composition of grain boundaries in three dimensions. In this paper we have analysed the microstructure of a nanocrystalline super-duplex stainless steel prepared by high pressure torsion (HPT). Not all of the grain boundaries in this alloy display obvious segregation, making visualisation of the microstructure challenging. In addition, the grain boundaries present in the atom probe data acquired from this alloy have complex shapes that are curved at the scale of the dataset and the interfacial excess varies considerably over the boundaries, making the accurate characterisation of the distribution of solute challenging using existing analysis techniques. In this paper we present two new data treatment methods that allow the visualisation of boundaries with little or no segregation, the delineation of boundaries for further analysis and the quantitative analysis of Gibbsian interfacial excess at boundaries, including the capability of excess mapping. - Highlights: ► New data treatment methods allow delineation of grain boundaries, even without segregation. ► Proxigrams calculated from the surfaces accurately show the extent of segregation. ► Tessellation of the data volume can be used to map the Gibbsian interfacial excess

  5. New atom probe approaches to studying segregation in nanocrystalline materials

    Energy Technology Data Exchange (ETDEWEB)

    Samudrala, S.K.; Felfer, P.J.; Araullo-Peters, V.J. [School of Aerospace, Mechanical and Mechatronic Engineering, University of Sydney, NSW 2006 (Australia); The Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006 (Australia); Cao, Y.; Liao, X.Z. [School of Aerospace, Mechanical and Mechatronic Engineering, University of Sydney, NSW 2006 (Australia); Cairney, J.M., E-mail: julie.cairney@sydney.edu.au [School of Aerospace, Mechanical and Mechatronic Engineering, University of Sydney, NSW 2006 (Australia); The Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006 (Australia)

    2013-09-15

    Atom probe is a technique that is highly suited to the study of nanocrystalline materials. It can provide accurate atomic-scale information about the composition of grain boundaries in three dimensions. In this paper we have analysed the microstructure of a nanocrystalline super-duplex stainless steel prepared by high pressure torsion (HPT). Not all of the grain boundaries in this alloy display obvious segregation, making visualisation of the microstructure challenging. In addition, the grain boundaries present in the atom probe data acquired from this alloy have complex shapes that are curved at the scale of the dataset and the interfacial excess varies considerably over the boundaries, making the accurate characterisation of the distribution of solute challenging using existing analysis techniques. In this paper we present two new data treatment methods that allow the visualisation of boundaries with little or no segregation, the delineation of boundaries for further analysis and the quantitative analysis of Gibbsian interfacial excess at boundaries, including the capability of excess mapping. - Highlights: ► New data treatment methods allow delineation of grain boundaries, even without segregation. ► Proxigrams calculated from the surfaces accurately show the extent of segregation. ► Tessellation of the data volume can be used to map the Gibbsian interfacial excess.

  6. Studying the sensitivity of monotop probes to compressed supersymmetric scenarios at the LHC

    CERN Document Server

    Fuks, Benjamin; Wilcock, Alexandra

    2015-01-01

    We investigate the sensitivity of the Large Hadron Collider to supersymmetric setups using monotop probes in which the signal is a single top quark produced in association with missing transverse energy. Our prospective study relies on Monte Carlo simulations of 300 invfb of proton- proton collisions at a centre-of-mass energy of 14 TeV and considers both leptonic and hadronic monotop decays. We present analysis strategies sensitive to regions of the supersymmetric parameter space which feature small superparticle mass splittings and illustrate their strengths in the context of a particular set of benchmark scenarios. Finally, we compare the regions of parameter space expected to be accessible with monotops probes during the next run of the LHC to the reach of more traditional search strategies employed by the ATLAS and CMS collaborations, where available.

  7. Proximal Probes Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Proximal Probes Facility consists of laboratories for microscopy, spectroscopy, and probing of nanostructured materials and their functional properties. At the...

  8. Sandwich hybridization probes for the detection of Pseudo-nitzschia (Bacillariophyceae) species: An update to existing probes and a description of new probes.

    Science.gov (United States)

    Bowers, Holly A; Marin, Roman; Birch, James M; Scholin, Christopher A

    2017-12-01

    New sandwich hybridization assay (SHA) probes for detecting Pseudo-nitzschia species (P. arenysensis, P. fraudulenta, P. hasleana, P. pungens) are presented, along with updated cross-reactivity information on historical probes (SHA and FISH; fluorescence in situ hybridization) targeting P. australis and P. multiseries. Pseudo-nitzschia species are a cosmopolitan group of diatoms that produce varying levels of domoic acid (DA), a neurotoxin that can accumulate in finfish and shellfish and transfer throughout the food web. Consumption of infected food sources can lead to illness in humans (amnesic shellfish poisoning; ASP) and marine wildlife (domoic acid poisoning; DAP). The threat of human illness, along with economic loss from fishery closures has resulted in the implementation of monitoring protocols and intensive ecological studies. SHA probes have been instrumental in some of these efforts, as the technique performs well in complex heterogeneous sample matrices and has been adapted to benchtop and deployable (Environmental Sample Processor) platforms. The expanded probe set will enhance future efforts towards understanding spatial, temporal and successional patterns in species during bloom and non-bloom periods. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Atom probe microanalysis: Principles and applications to materials problems

    International Nuclear Information System (INIS)

    Miller, M.K.; Smith, G.D.W.

    1987-01-01

    A historical background and general introduction to field emission and field-ionization, field-ion microscopy, and the atom probe is given. Physical principles of field ion microscopy are explained, followed by interpretation of images. Types of atom probes are discussed, as well as the instrumentation used in atomic probe microanalysis. Methods of atom probe analysis and data representation are covered, along with factors affecting performance and statistical analysis of atom probe data. Finally, some case studies and special types of analyses are presented

  10. Influence of probe geometry on pitot-probe displacement in supersonic turbulent flow

    Science.gov (United States)

    Allen, J. M.

    1975-01-01

    An experiment was conducted to determine the varying effects of six different probe-tip and support-shaft configurations on pitot tube displacement. The study was stimulated by discrepancies between supersonic wind-tunnel tests conducted by Wilson and Young (1949) and Allen (1972). Wilson (1973) had concluded that these discrepancies were caused by differences in probe geometry. It is shown that in fact, no major differences in profiles of streamwise velocity over streamwise velocity at boundary-layer edge vs normal coordinate over boundary-layer total thickness result from geometry. The true cause of the discrepancies, however, remains to be discovered.

  11. A complex probe for tokamak plasma edge conditions

    International Nuclear Information System (INIS)

    Castro, R.M. de; Silva, R.P. da; Heller, M.V.A.P.; Caldas, I.L.; Nascimento, I.C.; Degasperi, F.T.

    1995-01-01

    The study of the physical processes that occur in the plasma edge of tokamak machines has recently grown due to the evidence that these processes influence those that occur in the center of the plasma column. Experimental studies show the existence of a strong level of fluctuations in the plasma edge. The results of these studies indicate that these fluctuations enhance particle and energy transport and degrade the confinement. In order to investigate these processes in the plasma edge of the TBR-1 Tokamak, a Langmuir probe array, a triple and a set of magnetic probes have been designed and constructed. With this set probes the mean and fluctuation values of the magnetic field were detected and correlated with the fluctuating parameters obtained with the electrostatic probes. (author). 7 refs., 5 figs

  12. Imaging optical probe for pressurized steam-water environment

    International Nuclear Information System (INIS)

    Donaldson, M.R.; Pulfrey, R.E.

    1979-01-01

    An air-cooled imaging optical probe, with an outside diameter of 25.4 mm, has been developed to provide high resolution viewing of flow regimes in a steam-water environment at 343 0 C and 15.2 MPa. The design study considered a 3-m length probe. A 0.3-m length probe prototype was fabricated and tested. The optical probe consists of a 3.5-mm diameter optics train surrounded by two coaxial coolant flow channels and two coaxial insulating dead air spaces. With air flowing through the probe at 5.7 g/s, thermal analysis shows that no part of the optics train will exceed 93 0 C when a 3-m length probe is immersed in a 343 0 C environment. Computer stress analysis plus actual tests show that the probe can operate successfully with conservative safety factors. The imaging optical probe was tested five times in the design environment at the semiscale facility at the INEL. Two-phase flow regimes in the high temperature, high pressure, steam-water blowdown and reflood experiments were recorded on video tape for the first time with the imaging optical probe

  13. Reproducibility of the cutoff probe for the measurement of electron density

    Energy Technology Data Exchange (ETDEWEB)

    Kim, D. W.; Oh, W. Y. [Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701 (Korea, Republic of); You, S. J., E-mail: sjyou@cnu.ac.kr [Department of Physics, Chungnam National University, Daejeon 305-701 (Korea, Republic of); Kwon, J. H.; You, K. H.; Seo, B. H.; Kim, J. H., E-mail: jhkim86@kriss.re.kr [Center for Vacuum Technology, Korea Research Institute of Standards and Science, Daejeon 305-306 (Korea, Republic of); Yoon, J.-S. [Plasma Technology Research Center, National Fusion Research Institute, Gunsan 573-540 (Korea, Republic of)

    2016-06-15

    Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great reproducibility for the electron density measurement, i.e., there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.

  14. Reproducibility of the cutoff probe for the measurement of electron density

    International Nuclear Information System (INIS)

    Kim, D. W.; Oh, W. Y.; You, S. J.; Kwon, J. H.; You, K. H.; Seo, B. H.; Kim, J. H.; Yoon, J.-S.

    2016-01-01

    Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great reproducibility for the electron density measurement, i.e., there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.

  15. 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.

  16. Nuclear probes in physical and geochemical studies of natural diamonds

    International Nuclear Information System (INIS)

    Sellschop, J.P.F.

    In this review the emphasis is directed to the use of nuclear particles for the analysis of impurities in diamond from an interest in both the observed physical properties and genesis of diamond and the inter-relation between these two aspects. However (nuclear) radiation can be used more specifically: from the inter-relation of elemental impurities chemical and geochemical information can be deduced, from energy variation depth distributions of selected impurities can be determined, the prospect of lattice location of impurities exists from the use of extremely finely collimated beams of nuclear particles, which are used also for probing the inter-atomic fields, and finally all nuclear probes excite luminescence in diamonds

  17. The response of electrostatic probes via the λ-function

    DEFF Research Database (Denmark)

    Rerup, T.O.; Crichton, George C; McAllister, Iain Wilson

    1994-01-01

    The response of an electrostatic probe is examined with reference to a planar spacer. The study involves the numerical calculation of the probe λ-function, from which response-related characteristic parameters can be derived. These parameters enable the probe detection sensitivity and spatial...

  18. Contamination effects on fixed-bias Langmuir probes

    Energy Technology Data Exchange (ETDEWEB)

    Steigies, C. T. [Institut fuer Experimentelle und Angewandte Physik, Christian-Albrechts-Universitaet zu Kiel, 24098 Kiel (Germany); Barjatya, A. [Department of Physical Sciences, Embry-Riddle Aeronautical University, Daytona Beach, Florida 32114 (United States)

    2012-11-15

    Langmuir probes are standard instruments for plasma density measurements on many sounding rockets. These probes can be operated in swept-bias as well as in fixed-bias modes. In swept-bias Langmuir probes, contamination effects are frequently visible as a hysteresis between consecutive up and down voltage ramps. This hysteresis, if not corrected, leads to poorly determined plasma densities and temperatures. With a properly chosen sweep function, the contamination parameters can be determined from the measurements and correct plasma parameters can then be determined. In this paper, we study the contamination effects on fixed-bias Langmuir probes, where no hysteresis type effect is seen in the data. Even though the contamination is not evident from the measurements, it does affect the plasma density fluctuation spectrum as measured by the fixed-bias Langmuir probe. We model the contamination as a simple resistor-capacitor circuit between the probe surface and the plasma. We find that measurements of small scale plasma fluctuations (meter to sub-meter scale) along a rocket trajectory are not affected, but the measured amplitude of large scale plasma density variation (tens of meters or larger) is attenuated. From the model calculations, we determine amplitude and cross-over frequency of the contamination effect on fixed-bias probes for different contamination parameters. The model results also show that a fixed bias probe operating in the ion-saturation region is affected less by contamination as compared to a fixed bias probe operating in the electron saturation region.

  19. Laser-heated emissive plasma probe.

    Science.gov (United States)

    Schrittwieser, Roman; Ionita, Codrina; Balan, Petru; Gstrein, Ramona; Grulke, Olaf; Windisch, Thomas; Brandt, Christian; Klinger, Thomas; Madani, Ramin; Amarandei, George; Sarma, Arun K

    2008-08-01

    Emissive probes are standard tools in laboratory plasmas for the direct determination of the plasma potential. Usually they consist of a loop of refractory wire heated by an electric current until sufficient electron emission. Recently emissive probes were used also for measuring the radial fluctuation-induced particle flux and other essential parameters of edge turbulence in magnetized toroidal hot plasmas [R. Schrittwieser et al., Plasma Phys. Controlled Fusion 50, 055004 (2008)]. We have developed and investigated various types of emissive probes, which were heated by a focused infrared laser beam. Such a probe has several advantages: higher probe temperature without evaporation or melting and thus higher emissivity and longer lifetime, no deformation of the probe in a magnetic field, no potential drop along the probe wire, and faster time response. The probes are heated by an infrared diode laser with 808 nm wavelength and an output power up to 50 W. One probe was mounted together with the lens system on a radially movable probe shaft, and radial profiles of the plasma potential and of its oscillations were measured in a linear helicon discharge.

  20. Laser-heated emissive plasma probe

    International Nuclear Information System (INIS)

    Schrittwieser, Roman; Ionita, Codrina; Balan, Petru; Gstrein, Ramona; Grulke, Olaf; Windisch, Thomas; Brandt, Christian; Klinger, Thomas; Madani, Ramin; Amarandei, George; Sarma, Arun K.

    2008-01-01

    Emissive probes are standard tools in laboratory plasmas for the direct determination of the plasma potential. Usually they consist of a loop of refractory wire heated by an electric current until sufficient electron emission. Recently emissive probes were used also for measuring the radial fluctuation-induced particle flux and other essential parameters of edge turbulence in magnetized toroidal hot plasmas [R. Schrittwieser et al., Plasma Phys. Controlled Fusion 50, 055004 (2008)]. We have developed and investigated various types of emissive probes, which were heated by a focused infrared laser beam. Such a probe has several advantages: higher probe temperature without evaporation or melting and thus higher emissivity and longer lifetime, no deformation of the probe in a magnetic field, no potential drop along the probe wire, and faster time response. The probes are heated by an infrared diode laser with 808 nm wavelength and an output power up to 50 W. One probe was mounted together with the lens system on a radially movable probe shaft, and radial profiles of the plasma potential and of its oscillations were measured in a linear helicon discharge

  1. Laser-heated emissive plasma probe

    Science.gov (United States)

    Schrittwieser, Roman; Ionita, Codrina; Balan, Petru; Gstrein, Ramona; Grulke, Olaf; Windisch, Thomas; Brandt, Christian; Klinger, Thomas; Madani, Ramin; Amarandei, George; Sarma, Arun K.

    2008-08-01

    Emissive probes are standard tools in laboratory plasmas for the direct determination of the plasma potential. Usually they consist of a loop of refractory wire heated by an electric current until sufficient electron emission. Recently emissive probes were used also for measuring the radial fluctuation-induced particle flux and other essential parameters of edge turbulence in magnetized toroidal hot plasmas [R. Schrittwieser et al., Plasma Phys. Controlled Fusion 50, 055004 (2008)]. We have developed and investigated various types of emissive probes, which were heated by a focused infrared laser beam. Such a probe has several advantages: higher probe temperature without evaporation or melting and thus higher emissivity and longer lifetime, no deformation of the probe in a magnetic field, no potential drop along the probe wire, and faster time response. The probes are heated by an infrared diode laser with 808nm wavelength and an output power up to 50W. One probe was mounted together with the lens system on a radially movable probe shaft, and radial profiles of the plasma potential and of its oscillations were measured in a linear helicon discharge.

  2. Acetaldehyde production by major oral microbes.

    Science.gov (United States)

    Moritani, K; Takeshita, T; Shibata, Y; Ninomiya, T; Kiyohara, Y; Yamashita, Y

    2015-09-01

    To assess acetaldehyde (ACH) production by bacteria constituting the oral microbiota and the inhibitory effects of sugar alcohols on ACH production. The predominant bacterial components of the salivary microbiota of 166 orally healthy subjects were determined by barcoded pyrosequencing analysis of the 16S rRNA gene. Bacterial ACH production from ethanol or glucose was measured using gas chromatography. In addition, inhibition by four sugars and five sugar alcohols of ACH production was assayed. Forty-one species from 16 genera were selected as predominant and prevalent bacteria based on the following criteria: identification in ≥95% of the subjects, ≥1% of mean relative abundance or ≥5% of maximum relative abundance. All Neisseria species tested produced conspicuous amounts of ACH from ethanol, as did Rothia mucilaginosa, Streptococcus mitis and Prevotella histicola exhibited the ability to produce ACH. In addition, xylitol and sorbitol inhibited ACH production by Neisseria mucosa by more than 90%. The oral microbiota of orally healthy subjects comprises considerable amounts of bacteria possessing the ability to produce ACH, an oral carcinogen. Consumption of sugar alcohols may regulate ACH production by oral microbes. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Comparative study of the active sites in zeolites by different probe molecules

    Directory of Open Access Journals (Sweden)

    ALINE AUROUX

    2005-03-01

    Full Text Available This review summarizes some of the recently published results concerning the acid sites in the zeolites ZSM-5 and Y studied by temperature-programmed desorption (TPD and adsorption calorimetry using different probe molecules NH3, CO, N2O and n-hexane. For the first time it has been shown that the acid sites in hydrated zeolites are accessible for n-hexane adsorption

  4. Innovative SPM Probes for Energy-Storage Science: MWCNT-Nanopipettes to Nanobattery Probes

    Science.gov (United States)

    Larson, Jonathan; Talin, Alec; Pearse, Alexander; Kozen, Alexander; Reutt-Robey, Janice

    As energy-storage materials and designs continue to advance, new tools are needed to direct and explore ion insertion/de-insertion at well-defined battery materials interfaces. Scanned probe tips, assembled from actual energy-storage materials, permit SPM measures of local cathode-anode (tip-sample) interactions, including ion transfer. We present examples of ``cathode'' MWCNT-terminated STM probe tips interacting with Li(s)/Si(111) anode substrates. The MWCNT tip functions as both SPM probe and Li-nanopipette,[1] for controlled transport and manipulation of Li. Local field conditions for lithium ionization and transfer are determined and compared to electrostatic models. Additional lithium metallic and oxide tips have been prepared by thin film deposition on conventional W tips, the latter of which effectively functions as a nanobattery. We demonstrate use of these novel probe materials in the local lithiation of low-index Si anode interfaces, probing local barriers for lithium insertion. Prospects and limitations of these novel SPM probes will be discussed. U.S. Department of Energy Award Number DESC0001160.

  5. License - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us MicrobeDB.jp License License to Use This Database Last updated : 2017/06/29 You may use this database...the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attribut...ion-Share Alike 4.0 International . If you use data from this database, please be sure attribute this database... Creative Commons Attribution-Share Alike 4.0 International is found here . With regard to this database, yo

  6. Pilot tests of microbe-soil combined treatment of waste drilling sludge

    OpenAIRE

    Lirong Chen; Min Huang; Xuebin Jiang; Hui Li; Qiang Chen; Min Zhang; Shenglin Li

    2015-01-01

    Microbe-soil combined treatment is a newly developed technology in view of the defects of the curing process and waste drilling mud slag properties. In particular, 0.3%–0.5% bioremediation reagents were fully mixed with the waste drilling sludge according to its wet and dry degree, and 1.5 folds to twice weight of more finely ground soil was added in the mix, which was covered by soil of 5–15 cm thick and thereby grasses or greeneries were planted on the soil. The process was successfully app...

  7. Investigations of Probe Induced Perturbations in a Hall Thruster

    International Nuclear Information System (INIS)

    D. Staack; Y. Raitses; N.J. Fisch

    2002-01-01

    An electrostatic probe used to measure spatial plasma parameters in a Hall thruster generates perturbations of the plasma. These perturbations are examined by varying the probe material, penetration distance, residence time, and the nominal thruster conditions. The study leads us to recommendations for probe design and thruster operating conditions to reduce discharge perturbations, including metal shielding of the probe insulator and operation of the thruster at lower densities

  8. Theory of NMR probe design

    International Nuclear Information System (INIS)

    Schnall, M.D.

    1988-01-01

    The NMR probe is the intrinsic part of the NMR system which allows transmission of a stimulus to a sample and the reception of a resulting signal from a sample. NMR probes are used in both imaging and spectroscopy. Optimal probe design is important to the production of adequate signal/moise. It is important for anyone using NMR techniques to understand how NMR probes work and how to optimize probe design

  9. Studying the sensitivity of monotop probes to compressed supersymmetric scenarios at the LHC

    International Nuclear Information System (INIS)

    Fuks, Benjamin; Richardson, Peter; Wilcock, Alexandra

    2015-01-01

    We investigate the sensitivity of the Large Hadron Collider to supersymmetric setups using monotop probes in which the signal is a single top quark produced in association with missing transverse energy. Our prospective study relies on Monte Carlo simulations of 300 fb -1 of proton-proton collisions at a centre-of-mass energy of 14 TeV and considers both leptonic and hadronic monotop decays. We present analysis strategies sensitive to regions of the supersymmetric parameter space which feature small superparticle mass splittings and illustrate their strengths in the context of a particular set of benchmark scenarios. Finally, we compare the regions of parameter space expected to be accessible with monotops probes during the next run of the LHC to the reach of more traditional search strategies employed by the ATLAS and CMS collaborations, where available. (orig.)

  10. Human Skin Is the Largest Epithelial Surface for Interaction with Microbes.

    Science.gov (United States)

    Gallo, Richard L

    2017-06-01

    Human skin contains an abundant and diverse population of microbial organisms. Many of these microbes inhabit follicular structures of the skin. Furthermore, numerous studies have shown that the interaction of some members of the skin microbiome with host cells will result in changes in cell function. However, estimates of the potential for the microbiome to influence human health through skin have ignored the inner follicular surface, and therefore vastly underestimated the potential of the skin microbiome to have a systemic effect on the human body. By calculating the surface area of follicular and the interfollicular epithelial surface it is shown that skin provides a vast interface for interactions with the microbiome. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

  11. Large Observatory for x-ray Timing (LOFT-P): a Probe-class mission concept study

    Science.gov (United States)

    Wilson-Hodge, Colleen A.; Ray, Paul S.; Chakrabarty, Deepto; Feroci, Marco; Alvarez, Laura; Baysinger, Michael; Becker, Chris; Bozzo, Enrico; Brandt, Soren; Carson, Billy; Chapman, Jack; Dominguez, Alexandra; Fabisinski, Leo; Gangl, Bert; Garcia, Jay; Griffith, Christopher; Hernanz, Margarita; Hickman, Robert; Hopkins, Randall; Hui, Michelle; Ingram, Luster; Jenke, Peter; Korpela, Seppo; Maccarone, Tom; Michalska, Malgorzata; Pohl, Martin; Santangelo, Andrea; Schanne, Stephane; Schnell, Andrew; Stella, Luigi; van der Klis, Michiel; Watts, Anna; Winter, Berend; Zane, Silvia

    2016-07-01

    LOFT-P is a mission concept for a NASA Astrophysics Probe-Class (matter? What are the effects of strong gravity on matter spiraling into black holes? It would be optimized for sub-millisecond timing of bright Galactic X-ray sources including X-ray bursters, black hole binaries, and magnetars to study phenomena at the natural timescales of neutron star surfaces and black hole event horizons and to measure mass and spin of black holes. These measurements are synergistic to imaging and high-resolution spectroscopy instruments, addressing much smaller distance scales than are possible without very long baseline X-ray interferometry, and using complementary techniques to address the geometry and dynamics of emission regions. LOFT-P would have an effective area of >6 m2, > 10x that of the highly successful Rossi X-ray Timing Explorer (RXTE). A sky monitor (2-50 keV) acts as a trigger for pointed observations, providing high duty cycle, high time resolution monitoring of the X-ray sky with 20 times the sensitivity of the RXTE All-Sky Monitor, enabling multi-wavelength and multimessenger studies. A probe-class mission concept would employ lightweight collimator technology and large-area solid-state detectors, segmented into pixels or strips, technologies which have been recently greatly advanced during the ESA M3 Phase A study of LOFT. Given the large community interested in LOFT (>800 supporters*, the scientific productivity of this mission is expected to be very high, similar to or greater than RXTE ( 2000 refereed publications). We describe the results of a study, recently completed by the MSFC Advanced Concepts Office, that demonstrates that such a mission is feasible within a NASA probe-class mission budget.

  12. Glycine uptake in heath plants and soil microbes responds to elevated temperature, CO2 and drought

    DEFF Research Database (Denmark)

    Andresen, Luise C.; Michelsen, Anders; Jonasson, Sven

    2009-01-01

    the responses to single factors treatments. The soil microbes were superior to plants in the short-term competition for the added glycine, as indicated by an 18 times larger 15N recovery in the microbial biomass compared to the plant biomass. The soil microbes acquired glycine largely as an intact compound (87...... here present results from a field experiment in which the effects of these three climate change factors are investigated solely and in all combinations at a temperate heath dominated by heather (Calluna vulgaris) and wavy hair-grass (Deschampsia flexuosa). Climate induced increases in plant production...... may increase plant root exudation of dissolved organic compounds such as amino acids, and the release of amino acids during decomposition of organic matter. Such free amino acids in soil serve as substrates for soil microorganisms and are also acquired as nutrients directly by plants. We investigated...

  13. In vitro effects of copper nanoparticles on plant pathogens, beneficial microbes and crop plants

    Energy Technology Data Exchange (ETDEWEB)

    Banik, S.; Pérez-de-Luque, A.

    2017-07-01

    Copper-based chemicals are effectively used as antimicrobials in agriculture. However, with respect to its nanoparticulate form there has been limited number of studies. In this investigation, in vitro tests on effect of copper nanoparticles (CuNPs) against plant pathogenic fungi, oomycete, bacteria, beneficial microbes Trichoderma harzianum and Rhizobium spp., and wheat seeds were conducted. Integration of CuNPs with non-nano copper like copper oxychloride (CoC) at 50 mg/L concentration each recorded 76% growth inhibition of the oomycete Phytophthora cinnamomi in vitro compared to the control. CuNPs also showed synergistic inhibitory effect with CoC on mycelial growth and sporulation of A. alternata. Pseudomonas syringae was inhibited at 200 mg/L of CuNPs. CuNPs were not significantly biocidal against Rhizobium spp. and Trichoderma harzianum compared to CoC. Evaluation of the effect of CuNP on wheat revealed that rate of germination of wheat seeds was higher in presence of CuNPs and CoC compared to control. Germination vigor index, root length, shoot dry weight and seed metabolic efficiency of wheat were negatively affected. At low concentration, CuNPs promoted the growth of the plant pathogenic fungi Botrytis fabae, Fusarium oxysporum f.sp. ciceris, F.oxysporum f.sp. melonis, Alternaria alternate and P. syringae, and sporulation of T. harzianum. Synergistic effect of CuNPs and CoC in inhibiting P. cinnamomi offers a possibility of developing new fungicide formulation for better control of the oomycetes. Non-biocidal effect of CuNPs against beneficial microbes indicates its potential use in the agri-ecosystem.

  14. In vitro effects of copper nanoparticles on plant pathogens, beneficial microbes and crop plants

    International Nuclear Information System (INIS)

    Banik, S.; Pérez-de-Luque, A.

    2017-01-01

    Copper-based chemicals are effectively used as antimicrobials in agriculture. However, with respect to its nanoparticulate form there has been limited number of studies. In this investigation, in vitro tests on effect of copper nanoparticles (CuNPs) against plant pathogenic fungi, oomycete, bacteria, beneficial microbes Trichoderma harzianum and Rhizobium spp., and wheat seeds were conducted. Integration of CuNPs with non-nano copper like copper oxychloride (CoC) at 50 mg/L concentration each recorded 76% growth inhibition of the oomycete Phytophthora cinnamomi in vitro compared to the control. CuNPs also showed synergistic inhibitory effect with CoC on mycelial growth and sporulation of A. alternata. Pseudomonas syringae was inhibited at 200 mg/L of CuNPs. CuNPs were not significantly biocidal against Rhizobium spp. and Trichoderma harzianum compared to CoC. Evaluation of the effect of CuNP on wheat revealed that rate of germination of wheat seeds was higher in presence of CuNPs and CoC compared to control. Germination vigor index, root length, shoot dry weight and seed metabolic efficiency of wheat were negatively affected. At low concentration, CuNPs promoted the growth of the plant pathogenic fungi Botrytis fabae, Fusarium oxysporum f.sp. ciceris, F.oxysporum f.sp. melonis, Alternaria alternate and P. syringae, and sporulation of T. harzianum. Synergistic effect of CuNPs and CoC in inhibiting P. cinnamomi offers a possibility of developing new fungicide formulation for better control of the oomycetes. Non-biocidal effect of CuNPs against beneficial microbes indicates its potential use in the agri-ecosystem.

  15. Pump-probe studies of travelling coherent longitudinal acoustic phonon oscillations in GaAs

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Y.; Qi, J.; Tolk, Norman [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, 37235 (United States); Miller, J. [Naval air Warfare Center Weapons Division, China Lake, CA 93555 (United States); Cho, Y.J.; Liu, X.; Furdyna, J.K. [Department of Physics, University of Notre Dame, Notre Dame, IN 46556 (United States); Shahbazyan, T.V. [Department of Physics, Jackson State University, MS 39217 (United States)

    2008-07-01

    We report comprehensive studies of long-lived oscillations in femtosecond optical pump-probe measurements on GaAs based systems. The oscillations arise from a photo-generated coherent longitudinal acoustic phonon wave at the sample surface, which subsequently travels from the surface into the GaAs substrate, thus providing information on the optical properties of the material as a function of time/depth. Wavelength-dependent studies of the oscillations near the bandgap of GaAs indicate strong correlations to the optical properties of GaAs. We also use the coherent longitudinal acoustic phonon waves to probe a thin buried Ga{sub 0.1}In{sub 0.9}As layers non-invasively. The observed phonon oscillations experience a reduction in amplitude and a phase change at wavelengths near the bandgap of the GaAs, when it passes through the thin Ga{sub x}In{sub 1-x}As layer. The layer depth and thicknesses can be extracted from the oscillation responses. A model has been developed that satisfactorily characterizes the experimental results. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  16. Chromenoquinoline-based thiol probes: a study on the quencher position for controlling fluorescent Off-On characteristics.

    Science.gov (United States)

    Kand, Dnyaneshwar; Kalle, Arunasree Marasanapalli; Talukdar, Pinaki

    2013-02-13

    The design, synthesis and thiol sensing ability of chromenoquinoline-based fluorescent probes 4, 5 and 6 and are reported here. The relative position of the maleimide moiety was varied along the chromenoquinoline fluorophore to decrease the background fluorescence. Lower background fluorescence in probes 4 and 6 was rationalized by the smaller k(r)/k(nr) values compared to that of probe 5. An intramolecular charge transfer (ICT) mechanism was proposed for quenching and the extent was dependent on the position of the maleimide quencher. Fluorescent Off-On characteristics were evaluated by theoretical calculations. All probes were selective only towards thiol containing amino acids. Thiol sensing by probes 4 and 6 were much better compared to 5. Probe 4 displayed a better fluorescence response for less hindered thiol (185-, 223- and 156-fold for Hcy, Cys and GSH, respectively), while for probe 6, a higher enhancement in fluorescence was observed with more hindered thiols (180-, 205- and 245-fold for Hcy, Cys and GSH, respectively). The better response to bulkier thiol, GSH by probe 6 was attributed to the steric crowding at the C-4 position and bulkiness of the GSH group which force the succinimide unit to be in a nearly orthogonal conformation. This spatial arrangement was important in reducing the fluorescence quenching ability of the succinimide moiety. The application of probes 4, 5 and 6 was demonstrated by naked eye detection thiols using a 96-well plate system as well as by live-cell imaging.

  17. “The Farmer’s Dilemma”—an Interrupted Case Study for Learning Bacterial Genetics in the Context of the Impact of Microbes on the Organic Food Industry and Biotechnology

    Directory of Open Access Journals (Sweden)

    Richard Stewart

    2013-09-01

    Full Text Available Case studies are well established pedagogical tools for engaging students in learning and offer the opportunity to use real world examples to give context to student learning. Finding a case study story that meets learning outcomes and resonates with students is a challenge. Our solution was an end-of-semester, capstone project for the honors students in our general microbiology course. “The Farmer’s Dilemma,” an interrupted case study with associated questions, was developed from a story line proposed by the students. The case and associated teaching notes indicate how we actively engage students in learning bacterial genetics via a story about the impact of microbes on the organic food industry and biotechnology.

  18. Microbes, Mineral Evolution, and the Rise of Microcontinents-Origin and Coevolution of Life with Early Earth.

    Science.gov (United States)

    Grosch, Eugene G; Hazen, Robert M

    2015-10-01

    Earth is the most mineralogically diverse planet in our solar system, the direct consequence of a coevolving geosphere and biosphere. We consider the possibility that a microbial biosphere originated and thrived in the early Hadean-Archean Earth subseafloor environment, with fundamental consequences for the complex evolution and habitability of our planet. In this hypothesis paper, we explore possible venues for the origin of life and the direct consequences of microbially mediated, low-temperature hydrothermal alteration of the early oceanic lithosphere. We hypothesize that subsurface fluid-rock-microbe interactions resulted in more efficient hydration of the early oceanic crust, which in turn promoted bulk melting to produce the first evolved fragments of felsic crust. These evolved magmas most likely included sialic or tonalitic sheets, felsic volcaniclastics, and minor rhyolitic intrusions emplaced in an Iceland-type extensional setting as the earliest microcontinents. With the further development of proto-tectonic processes, these buoyant felsic crustal fragments formed the nucleus of intra-oceanic tonalite-trondhjemite-granitoid (TTG) island arcs. Thus microbes, by facilitating extensive hydrothermal alteration of the earliest oceanic crust through bioalteration, promoted mineral diversification and may have been early architects of surface environments and microcontinents on young Earth. We explore how the possible onset of subseafloor fluid-rock-microbe interactions on early Earth accelerated metavolcanic clay mineral formation, crustal melting, and subsequent metamorphic mineral evolution. We also consider environmental factors supporting this earliest step in geosphere-biosphere coevolution and the implications for habitability and mineral evolution on other rocky planets, such as Mars.

  19. Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes

    Directory of Open Access Journals (Sweden)

    Saad Rama

    2012-11-01

    Full Text Available Abstract The influence of resident gut microbes on xenobiotic metabolism has been investigated at different levels throughout the past five decades. However, with the advance in sequencing and pyrotagging technologies, addressing the influence of microbes on xenobiotics had to evolve from assessing direct metabolic effects on toxins and botanicals by conventional culture-based techniques to elucidating the role of community composition on drugs metabolic profiles through DNA sequence-based phylogeny and metagenomics. Following the completion of the Human Genome Project, the rapid, substantial growth of the Human Microbiome Project (HMP opens new horizons for studying how microbiome compositional and functional variations affect drug action, fate, and toxicity (pharmacomicrobiomics, notably in the human gut. The HMP continues to characterize the microbial communities associated with the human gut, determine whether there is a common gut microbiome profile shared among healthy humans, and investigate the effect of its alterations on health. Here, we offer a glimpse into the known effects of the gut microbiota on xenobiotic metabolism, with emphasis on cases where microbiome variations lead to different therapeutic outcomes. We discuss a few examples representing how the microbiome interacts with human metabolic enzymes in the liver and intestine. In addition, we attempt to envisage a roadmap for the future implications of the HMP on therapeutics and personalized medicine.

  20. Microbiology and Biodegradation: Deep Ultraviolet Microscopy for the Detection, Quantification, and Characterization of Microbes

    Science.gov (United States)

    2015-11-16

    Approved for Public Release; Distribution Unlimited Final Report: 14.3 Microbiology and Biodegradation: Deep Ultraviolet Microscopy for the Detection...Fluroesence; Raman Spectroscopy; Microbiology REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 10. SPONSOR/MONITOR’S ACRONYM(S) ARO...14.3 Microbiology and Biodegradation: Deep Ultraviolet Microscopy for the Detection, Quantification, and Characterization of Microbes Report Title