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Sample records for microbes produce proteins

  1. Engineering microbes to produce biofuels.

    Science.gov (United States)

    Wackett, Lawrence P

    2011-06-01

    The current biofuels landscape is chaotic. It is controlled by the rules imposed by economic forces and driven by the necessity of finding new sources of energy, particularly motor fuels. The need is bringing forth great creativity in uncovering new candidate fuel molecules that can be made via metabolic engineering. These next generation fuels include long-chain alcohols, terpenoid hydrocarbons, and diesel-length alkanes. Renewable fuels contain carbon derived from carbon dioxide. The carbon dioxide is derived directly by a photosynthetic fuel-producing organism(s) or via intermediary biomass polymers that were previously derived from carbon dioxide. To use the latter economically, biomass depolymerization processes must improve and this is a very active area of research. There are competitive approaches with some groups using enzyme based methods and others using chemical catalysts. With the former, feedstock and end-product toxicity loom as major problems. Advances chiefly rest on the ability to manipulate biological systems. Computational and modular construction approaches are key. For example, novel metabolic networks have been constructed to make long-chain alcohols and hydrocarbons that have superior fuel properties over ethanol. A particularly exciting approach is to implement a direct utilization of solar energy to make a usable fuel. A number of approaches use the components of current biological systems, but re-engineer them for more direct, efficient production of fuels. Copyright © 2010 Elsevier Ltd. All rights reserved.

  2. Screening for novel laccase-producing microbes.

    Science.gov (United States)

    Kiiskinen, L-L; Rättö, M; Kruus, K

    2004-01-01

    To discover novel laccases potential for industrial applications. Fungi were cultivated on solid media containing indicator compounds that enabled the detection of laccases as specific colour reactions. The indicators used were Remazol Brilliant Blue R (RBBR), Poly R-478, guaiacol and tannic acid. The screening work resulted in isolation of 26 positive fungal strains. Liquid cultivations of positive strains confirmed that four efficient laccase producers were found in the screening. Biochemical characteristics of the four novel laccases were typical for fungal laccases in terms of molecular weight, pH optima and pI. The laccases showed good thermal stability at 60 degrees C. Plate-test screening based on polymeric dye compounds, guaiacol and tannic acid is an efficient way to discover novel laccase producers. The results indicated that screening for laccase activity can be performed with guaiacol and RBBR or Poly R-478. Laccases have many potential industrial applications including textile dye decolourization, delignification of pulp and effluent detoxification. It is essential to find novel, efficient enzymes to further develop these applications. This study showed that relatively simple plate test screening method can be used for discovery of novel laccases. Copyright 2004 The Society for Applied Microbiology

  3. 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...

  4. Plasma membrane protein trafficking in plant-microbe interactions: a plant cell point of view

    Directory of Open Access Journals (Sweden)

    Nathalie eLeborgne-Castel

    2014-12-01

    Full Text Available In order to ensure their physiological and cellular functions, plasma membrane (PM proteins must be properly conveyed from their site of synthesis, i.e. the endoplasmic reticulum, to their final destination, the PM, through the secretory pathway. PM protein homeostasis also relies on recycling and/or degradation, two processes that are initiated by endocytosis. Vesicular membrane trafficking events to and from the PM have been shown to be altered when plant cells are exposed to mutualistic or pathogenic microbes. In this review, we will describe the fine-tune regulation of such alterations, and their consequence in PM protein activity. We will consider the formation of intracellular perimicrobial compartments, the PM protein trafficking machinery of the host, and the delivery or retrieval of signaling and transport proteins such as pattern-recognition receptors, producers of reactive oxygen species, and sugar transporters.

  5. 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)

  6. 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.

  7. 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).

  8. Bactericidal Permeability-Increasing Proteins Shape Host-Microbe Interactions

    Directory of Open Access Journals (Sweden)

    Fangmin Chen

    2017-04-01

    Full Text Available We characterized bactericidal permeability-increasing proteins (BPIs of the squid Euprymna scolopes, EsBPI2 and EsBPI4. They have molecular characteristics typical of other animal BPIs, are closely related to one another, and nest phylogenetically among invertebrate BPIs. Purified EsBPIs had antimicrobial activity against the squid’s symbiont, Vibrio fischeri, which colonizes light organ crypt epithelia. Activity of both proteins was abrogated by heat treatment and coincubation with specific antibodies. Pretreatment under acidic conditions similar to those during symbiosis initiation rendered V. fischeri more resistant to the antimicrobial activity of the proteins. Immunocytochemistry localized EsBPIs to the symbiotic organ and other epithelial surfaces interacting with ambient seawater. The proteins differed in intracellular distribution. Further, whereas EsBPI4 was restricted to epithelia, EsBPI2 also occurred in blood and in a transient juvenile organ that mediates hatching. The data provide evidence that these BPIs play different defensive roles early in the life of E. scolopes, modulating interactions with the symbiont.

  9. 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.

  10. Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein

    DEFF Research Database (Denmark)

    Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

    2016-01-01

    An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal...... derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff...... between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used...

  11. 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...

  12. Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein.

    Science.gov (United States)

    Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

    2016-11-08

    An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources.

  13. Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein

    Science.gov (United States)

    Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

    2016-11-01

    An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources.

  14. 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...

  15. MAMP (microbe-associated molecular pattern)-induced changes in plasma membrane-associated proteins.

    Science.gov (United States)

    Uhlíková, Hana; Solanský, Martin; Hrdinová, Vendula; Šedo, Ondrej; Kašparovský, Tomáš; Hejátko, Jan; Lochman, Jan

    2017-03-01

    Plant plasma membrane associated proteins play significant roles in Microbe-Associated Molecular Pattern (MAMP) mediated defence responses including signal transduction, membrane transport or energetic metabolism. To elucidate the dynamics of proteins associated with plasma membrane in response to cryptogein, a well-known MAMP of defence reaction secreted by the oomycete Phytophthora cryptogea, 2D-Blue Native/SDS gel electrophoresis of plasma membrane fractions was employed. This approach revealed 21 up- or down-regulated protein spots of which 15 were successfully identified as proteins related to transport through plasma membrane, vesicle trafficking, and metabolic enzymes including cytosolic NADP-malic enzyme and glutamine synthetase. Observed changes in proteins were also confirmed on transcriptional level by qRT-PCR analysis. In addition, a significantly decreased accumulation of transcripts observed after employment of a mutant variant of cryptogein Leu41Phe, exhibiting a conspicuous defect in induction of resistance, sustains the contribution of identified proteins in cryptogein-triggered cellular responses. Our data provide further evidence for dynamic MAMP-induced changes in plasma membrane associated proteins. Copyright © 2016 Elsevier GmbH. All rights reserved.

  16. A study on the long term effect of biofilm produced by biosurfactant producing microbe on medical implant

    International Nuclear Information System (INIS)

    Prabhawathi, Veluchamy; Thirunavukarasu, Kathirvel; Doble, Mukesh

    2014-01-01

    Low density polyethylene (LDPE) is used as a long term medical implant. Biofilm forming ability of two pathogenic microorganisms, namely, Bacillus subtilis (B. subtilis) and Pseudomonas aeruginosa (P. aeruginosa) on this polymer and the differences in the properties of these matrices are studied for a year. There are very few long term studies on biofilms formed on medical implants. After three months, colonies of B. subtilis were two times higher when compared to those of P. aeruginosa. And at the end of one year, they were two orders of magnitude higher than the later. The exopolysaccharide (EPS) and biosurfactant recovered from the polymer surface after three months were 21 and 10.4 μg/cm 2 for B. subtilis and 13 and 8.6 μg/cm 2 for P. aeruginosa. After one year, these were higher in B. subtilis (50 and 37.1 μg/cm 2 , respectively) than in P. aeruginosa (34.1 and 31.8 μg/cm 2 , respectively). B. subtilis consisted of protein controlling the community and sporulation development, while P. aeruginosa had either housekeeping or metabolic proteins. The EPS in the respective biofilm consisted of biosurfactants produced by B. subtilis (surfactins, m/z = 1029 to 1134) and P. aeruginosa (rhamnolipids, m/z = 568 to 705). Thermogravimetric analysis indicated that LDPE incubated with these organisms underwent a weight loss of 4 and 3% after three months and 11.1 and 9.2% after one year, respectively at 435 °C. Laccase and manganese peroxidase were detected in the biofilm which could be involved in the degradation. The biosurfactant of these microorganisms altered the hydrophobicity of the surface, favoring their attachment and proliferation. - Highlights: • Early P.aeru biofilm had genes needed for motility but later for housekeeping. • Early B. sub biofilm had genes needed for its formation but later for maturity. • Cells and matrix components in B. sub biofilm are higher than in P.aeru. • Compositions of these two biofilms are different. • So they need

  17. A study on the long term effect of biofilm produced by biosurfactant producing microbe on medical implant

    Energy Technology Data Exchange (ETDEWEB)

    Prabhawathi, Veluchamy; Thirunavukarasu, Kathirvel; Doble, Mukesh, E-mail: mukeshd@iitm.ac.in

    2014-07-01

    Low density polyethylene (LDPE) is used as a long term medical implant. Biofilm forming ability of two pathogenic microorganisms, namely, Bacillus subtilis (B. subtilis) and Pseudomonas aeruginosa (P. aeruginosa) on this polymer and the differences in the properties of these matrices are studied for a year. There are very few long term studies on biofilms formed on medical implants. After three months, colonies of B. subtilis were two times higher when compared to those of P. aeruginosa. And at the end of one year, they were two orders of magnitude higher than the later. The exopolysaccharide (EPS) and biosurfactant recovered from the polymer surface after three months were 21 and 10.4 μg/cm{sup 2} for B. subtilis and 13 and 8.6 μg/cm{sup 2} for P. aeruginosa. After one year, these were higher in B. subtilis (50 and 37.1 μg/cm{sup 2}, respectively) than in P. aeruginosa (34.1 and 31.8 μg/cm{sup 2}, respectively). B. subtilis consisted of protein controlling the community and sporulation development, while P. aeruginosa had either housekeeping or metabolic proteins. The EPS in the respective biofilm consisted of biosurfactants produced by B. subtilis (surfactins, m/z = 1029 to 1134) and P. aeruginosa (rhamnolipids, m/z = 568 to 705). Thermogravimetric analysis indicated that LDPE incubated with these organisms underwent a weight loss of 4 and 3% after three months and 11.1 and 9.2% after one year, respectively at 435 °C. Laccase and manganese peroxidase were detected in the biofilm which could be involved in the degradation. The biosurfactant of these microorganisms altered the hydrophobicity of the surface, favoring their attachment and proliferation. - Highlights: • Early P.aeru biofilm had genes needed for motility but later for housekeeping. • Early B. sub biofilm had genes needed for its formation but later for maturity. • Cells and matrix components in B. sub biofilm are higher than in P.aeru. • Compositions of these two biofilms are different.

  18. Effects of the fungicide metiram in outdoor freshwater microcosms: responses of invertebrates, primary producers and microbes.

    Science.gov (United States)

    Lin, Ronghua; Buijse, Laura; Dimitrov, Mauricio R; Dohmen, Peter; Kosol, Sujitra; Maltby, Lorraine; Roessink, Ivo; Sinkeldam, Jos A; Smidt, Hauke; Van Wijngaarden, René P A; Brock, Theo C M

    2012-07-01

    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 were investigated. Dissipation half-life (DT₅₀) of metiram was approximately 1-6 h in the water column of the microcosm test system and the metabolites formed were not persistent. Multivariate analysis indicated treatment-related effects on the zooplankton (NOEC(community) = 36 μg a.i./L). Consistent treatment-related effects on the phytoplankton and macroinvertebrate communities and on the sediment microbial community could not be demonstrated or were minor. There was no evidence that metiram affected the biomass, abundance or functioning of aquatic hyphomycetes on decomposing alder leaves. The most sensitive populations in the microcosms comprised representatives of Rotifera with a NOEC of 12 μg a.i./L on isolated sampling days and a NOEC of 36 μg a.i./L on consecutive samplings. At the highest treatment-level populations of Copepoda (zooplankton) and the blue-green alga Anabaena (phytoplankton) also showed a short-term decline on consecutive sampling days (NOEC = 108 μg a.i./L). Indirect effects in the form of short-term increases in the abundance of a few macroinvertebrate and several phytoplankton taxa were also observed. The overall community and population level no-observed-effect concentration (NOEC(microcosm)) was 12-36 μg a.i./L. At higher treatment levels, including the test systems that received the highest dose, ecological recovery of affected measurement endpoints was fast (effect period < 8 weeks).

  19. Medium-Throughput Screen of Microbially Produced Serotonin via a G-Protein-Coupled Receptor-Based Sensor.

    Science.gov (United States)

    Ehrenworth, Amy M; Claiborne, Tauris; Peralta-Yahya, Pamela

    2017-10-17

    Chemical biosensors, for which chemical detection triggers a fluorescent signal, have the potential to accelerate the screening of noncolorimetric chemicals produced by microbes, enabling the high-throughput engineering of enzymes and metabolic pathways. Here, we engineer a G-protein-coupled receptor (GPCR)-based sensor to detect serotonin produced by a producer microbe in the producer microbe's supernatant. Detecting a chemical in the producer microbe's supernatant is nontrivial because of the number of other metabolites and proteins present that could interfere with sensor performance. We validate the two-cell screening system for medium-throughput applications, opening the door to the rapid engineering of microbes for the increased production of serotonin. We focus on serotonin detection as serotonin levels limit the microbial production of hydroxystrictosidine, a modified alkaloid that could accelerate the semisynthesis of camptothecin-derived anticancer pharmaceuticals. This work shows the ease of generating GPCR-based chemical sensors and their ability to detect specific chemicals in complex aqueous solutions, such as microbial spent medium. In addition, this work sets the stage for the rapid engineering of serotonin-producing microbes.

  20. Corruption of host seven-transmembrane proteins by pathogenic microbes: a common theme in animals and plants?

    Science.gov (United States)

    Panstruga, Ralph; Schulze-Lefert, Paul

    2003-04-01

    Human diseases like AIDS, malaria, and pneumonia are caused by pathogens that corrupt host chemokine G-protein coupled receptors for molecular docking. Comparatively, little is known about plant host factors that are required for pathogenesis and that may serve as receptors for the entry of pathogenic microbes. Here, we review potential analogies between human chemokine receptors and the plant seven-transmembrane MLO protein, a candidate serving a dual role as docking molecule and defence modulator for the phytopathogenic powdery mildew fungus.

  1. Producing methane, methanol and electricity from organic waste of fermentation reaction using novel microbes.

    Science.gov (United States)

    Dhiman, Saurabh Sudha; Shrestha, Namita; David, Aditi; Basotra, Neha; Johnson, Glenn R; Chadha, Bhupinder S; Gadhamshetty, Venkataramana; Sani, Rajesh K

    2018-06-01

    Residual solid and liquid streams from the one-pot CRUDE (Conversion of Raw and Untreated Disposal into Ethanol) process were treated with two separate biochemical routes for renewable energy transformation. The solid residual stream was subjected to thermophilic anaerobic digestion (TAD), which produced 95 ± 7 L methane kg -1 volatile solid with an overall energy efficiency of 12.9 ± 1.7%. A methanotroph, Methyloferula sp., was deployed for oxidation of mixed TAD biogas into methanol. The residual liquid stream from CRUDE process was used in a Microbial Fuel Cell (MFC) to produce electricity. Material balance calculations confirmed the integration of biochemical routes (i.e. CRUDE, TAD, and MFC) for developing a sustainable approach of energy regeneration. The current work demonstrates the utilization of different residual streams originated after food waste processing to release minimal organic load to the environment. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Metabolites produced by antagonistic microbes inhibit the principal avocado pathogens in vitro

    Directory of Open Access Journals (Sweden)

    Sara Ramírez R.

    2015-04-01

    Full Text Available The demand for Hass avocado in the global market exceeds the supply by over 50%. Colombia has a remarkable advantage as a producer in the region due to its high yields. However, the productivity of this crop can be seriously affected by diseases such as root rot, caused by Phytophthora cinnamomi, postharvest body rot and stem end rot, caused by Colletotrichum sp. and Phomopsis sp., respectively. The potential of 76 bacterial isolates obtained from avocado rhizosphere to produce inhibitory metabolites against avocado's pathogens was evaluated. The antagonistic effect of the rhizobacteria against P. cinnamomi, Colletotrichum sp. and Phomopsis sp. was tested through dual cultures. Thirty-six percent of the tested isolates presented inhibition halos against P. cinnamomi, 36% against Colletotrichum sp. and 67% against Phomopsis sp. Additionally, three isolates were selected for fermentation tests using different broth cultures. The extracts obtained from fermentations in the minimal medium of isolates ARP5.1 and AED06 showed inhibitory activity against the evaluated pathogens, but this effect was not observed with the AED26 extract. The media supplemented with copper chloride did not enhance activity of the extracts. These results suggest that using microbial metabolic extracts is a viable alternative for controlling avocado pathogens in vitro.

  3. 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.

  4. Cultivating Insect Cells To Produce Recombinant Proteins

    Science.gov (United States)

    Spaulding, Glenn; Goodwin, Thomas; Prewett, Tacey; Andrews, Angela; Francis, Karen; O'Connor, Kim

    1996-01-01

    Method of producing recombinant proteins involves growth of insect cells in nutrient solution in cylindrical bioreactor rotating about cylindrical axis, oriented horizontally and infecting cells with viruses into which genes of selected type cloned. Genes in question those encoding production of desired proteins. Horizontal rotating bioreactor preferred for use in method, denoted by acronym "HARV", described in "High-Aspect-Ratio Rotating Cell-Culture Vessel" (MSC-21662).

  5. Protein interaction networks at the host-microbe interface in Diaphorina citri, the insect vector of the citrus greening pathogen.

    Science.gov (United States)

    Ramsey, J S; Chavez, J D; Johnson, R; Hosseinzadeh, S; Mahoney, J E; Mohr, J P; Robison, F; Zhong, X; Hall, D G; MacCoss, M; Bruce, J; Cilia, M

    2017-02-01

    The Asian citrus psyllid ( Diaphorina citri) is the insect vector responsible for the worldwide spread of ' Candidatus Liberibacter asiaticus' (CLas), the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that D. citri transmission of CLas is more efficient when bacteria are acquired by nymphs when compared with adults. We hypothesize that expression changes in the D. citri immune system and commensal microbiota occur during development and regulate vector competency. In support of this hypothesis, more proteins, with greater fold changes, were differentially expressed in response to CLas in adults when compared with nymphs, including insect proteins involved in bacterial adhesion and immunity. Compared with nymphs, adult insects had a higher titre of CLas and the bacterial endosymbionts Wolbachia, Profftella and Carsonella. All Wolbachia and Profftella proteins differentially expressed between nymphs and adults are upregulated in adults, while most differentially expressed Carsonella proteins are upregulated in nymphs. Discovery of protein interaction networks has broad applicability to the study of host-microbe relationships. Using protein interaction reporter technology, a D. citri haemocyanin protein highly upregulated in response to CLas was found to physically interact with the CLas coenzyme A (CoA) biosynthesis enzyme phosphopantothenoylcysteine synthetase/decarboxylase. CLas pantothenate kinase, which catalyses the rate-limiting step of CoA biosynthesis, was found to interact with a D. citri myosin protein. Two Carsonella enzymes involved in histidine and tryptophan biosynthesis were found to physically interact with D. citri proteins. These co-evolved protein interaction networks at the host-microbe interface are highly specific targets for controlling the insect vector responsible for the spread of citrus greening.

  6. Plasma membrane protein trafficking in plant–microbe interactions: a plant cell point of view

    OpenAIRE

    Nathalie Leborgne-Castel,; Bouhidel, Karim

    2014-01-01

    In order to ensure their physiological and cellular functions, plasma membrane (PM) proteins must be properly conveyed from their site of synthesis, i.e., the endoplasmic reticulum, to their final destination, the PM, through the secretory pathway. PM protein homeostasis also relies on recycling and/or degradation, two processes that are initiated by endocytosis. Vesicular membrane trafficking events to and from the PM have been shown to be altered when plant cells are exposed to mutualistic ...

  7. Saccharification of Agricultural Lignocellulose Feedstocks and Protein-Level Responses by a Termite Gut-Microbe Bioreactor

    International Nuclear Information System (INIS)

    Rajarapu, Swapna Priya; Scharf, Michael E.

    2017-01-01

    This study investigated saccharification and protein-level responses to the candidate biofuel feedstocks corn stover (CS) and soybean residue (SR) by the gut of a lower termite. The focus termite was Reticulitermes flavipes, which is a highly efficient digester of wood lignocellulose that houses a mixture of prokaryotic and eukaryotic microbes in its gut. Our specific objectives were to (i) measure saccharification potential of the CS and SR feedstocks by termite gut protein extracts, (ii) identify specific proteins in the termite gut responding to feeding on CS and SR diets, and (iii) evaluate gut lignocellulase and accessory enzyme activity responses to CS and SR feeding. Cellulose paper was the control diet. Although CS was saccharified at higher levels, termite gut protein extracts saccharified both CS and SR irrespective of feedstock loading. Consumption of the CS and SR feedstocks by termites resulted in surprisingly few differences in gut protein profiles, with the main exception being elevated myosin abundance with SR feeding. Activity of potential lignocellulases and accessory enzymes was generally similar between CS and SR fed guts as well; however, cellobiohydrolase/exoglucanase activity was higher with CS feeding and glutathione peroxidase activity with SR feeding. These findings have significance from two perspectives. First, SR feeding/digestion appears to cause physiological stress in the termite gut that likely would extend to other types of microbial environments including those within industrial bioreactors. Second, because termites can survive on exclusive CS and SR diets and their guts exhibit clear CS and SR saccharification activity, this validates the R. flavipes system as a potential source for CS and SR degrading enzymes; in particular, cellobiohydrolases/exoglucanases and glutathione peroxidases from this system may play roles in CS and SR breakdown.

  8. Saccharification of Agricultural Lignocellulose Feedstocks and Protein-Level Responses by a Termite Gut-Microbe Bioreactor

    Energy Technology Data Exchange (ETDEWEB)

    Rajarapu, Swapna Priya; Scharf, Michael E., E-mail: mscharf@purdue.edu [Department of Entomology, Purdue University, West Lafayette, IN (United States)

    2017-04-07

    This study investigated saccharification and protein-level responses to the candidate biofuel feedstocks corn stover (CS) and soybean residue (SR) by the gut of a lower termite. The focus termite was Reticulitermes flavipes, which is a highly efficient digester of wood lignocellulose that houses a mixture of prokaryotic and eukaryotic microbes in its gut. Our specific objectives were to (i) measure saccharification potential of the CS and SR feedstocks by termite gut protein extracts, (ii) identify specific proteins in the termite gut responding to feeding on CS and SR diets, and (iii) evaluate gut lignocellulase and accessory enzyme activity responses to CS and SR feeding. Cellulose paper was the control diet. Although CS was saccharified at higher levels, termite gut protein extracts saccharified both CS and SR irrespective of feedstock loading. Consumption of the CS and SR feedstocks by termites resulted in surprisingly few differences in gut protein profiles, with the main exception being elevated myosin abundance with SR feeding. Activity of potential lignocellulases and accessory enzymes was generally similar between CS and SR fed guts as well; however, cellobiohydrolase/exoglucanase activity was higher with CS feeding and glutathione peroxidase activity with SR feeding. These findings have significance from two perspectives. First, SR feeding/digestion appears to cause physiological stress in the termite gut that likely would extend to other types of microbial environments including those within industrial bioreactors. Second, because termites can survive on exclusive CS and SR diets and their guts exhibit clear CS and SR saccharification activity, this validates the R. flavipes system as a potential source for CS and SR degrading enzymes; in particular, cellobiohydrolases/exoglucanases and glutathione peroxidases from this system may play roles in CS and SR breakdown.

  9. Effects of alternative protein sources on rumen microbes and productivity of dairy cows

    Directory of Open Access Journals (Sweden)

    Metha Wanapat

    2011-01-01

    Full Text Available This experiment was conducted to investigate the effect of various protein sources on digestibility, rumen fermentation, milk yield and milk composition in dairy cows. Four Holstein Friesian native crossbred cows in early lactating were randomly assigned according to a 4x4 Latin square design. The dietary treatments containing different protein sources in concentrate diets were soybean meal (SBM, cassava hay (CH, Leucaena leucocephala (LL and yeast-fermented cassava chips (YEFECAP, with ad libitum intake of urea-treated rice straw. Digestibility of DM, OM, NDF and ADF was not different among treatments (P>0.05 while CP digestibility was highest (P<0.05 in CH and YEFECAP supplemented groups. Ruminal NH3-N and BUN concentrations varied among protein sources and were highest in SBM and LL fed groups (P<0.05. Ruminal total volatile fatty acid (VFA and propionic acid were found highest in cows receiving CH and YEFECAP (P<0.05. Ruminal fungi, proteolytic and cellulolytic bacteria were highest when YEFECAP was supplemented. Milk fat and milk protein were significantly increased (P<0.05 in cows fed with CH and YEFECAP. Based on this study, it was concluded that providing CH or YEFECAP as protein source in concentrate diets could improve rumen fermentation and milk production in lactating dairy cows fed on rice straw.

  10. Exploring the Plant–Microbe Interface by Profiling the Surface-Associated Proteins of Barley Grains

    DEFF Research Database (Denmark)

    Sultan, Abida; Andersen, Birgit; Svensson, Birte

    2016-01-01

    Cereal grains are colonized by a microbial community that actively interacts with the plant via secretion of various enzymes, hormones, and metabolites. Microorganisms decompose plant tissues by a collection of depolymerizing enzymes, including β-1,4-xylanases, that are in turn inhibited by plant...... xylanase inhibitors. To gain insight into the importance of the microbial consortia and their interaction with barley grains, we used a combined gel-based (2-DE coupled to MALDI-TOF-TOF MS) and gel-free (LC–MS/MS) proteomics approach complemented with enzyme activity assays to profile the surface......-associated proteins and xylanolytic activities of two barley cultivars. The surface-associated proteome was dominated by plant proteins with roles in defense and stress-responses, while the relatively less abundant microbial (bacterial and fungal) proteins were involved in cell-wall and polysaccharide degradation...

  11. Determination of possible effects of mineral concentration on protein synthesis by rumen microbes in vitro

    International Nuclear Information System (INIS)

    Nikolic, J.A.; Jovanovic, M.; Andric, R.

    1976-01-01

    The aim of the present investigation was to determine the effect of different concentrations of sulphide, magnesium and zinc on protein synthesis by rumen micro-organisms in vitro. Rumen content was taken from a young bull fed a diet based on maize and dried sugar beet pulp (2/1) supplemented with urea. The rate of incorporation of 35 S from Na 2 35 SO 4 in relation to the mean specific radioactivity of the sulphide pool was used to estimate the overall rate of microbial protein synthesis. It was found that the rate of protein synthesis and the net rate of utilization of ammonia-N were not affected by differences in mean sulphide concentration from 3.6-8.0 mg/litre. The rate of reduction of sulphate appeared not to be affected by the addition of sodium sulphide to the medium. The rate and efficiency of protein synthesis by rumen micro-organisms were not significantly affected by increasing the concentration of total magnesium from 8.4-15.3 mg/100 ml. The values for soluble magnesium varied widely (1.2-7.8 mg/100 ml), and appeared to be partly dependent on the pH of the medium. Zinc concentrations varying from 5.2-12.4 mg/litre did not influence the overall rate of protein synthesis, although the efficiency tended to be higher when the concentration of zinc was greater. Concentrations of soluble zinc were low (0.3-1.15 mg/litre), and not influenced by changes in the concentration of total zinc. It was concluded that increasing the concentrations of the examined elements above the basic values did not lead consistently to an improved production of microbial protein but, on the other hand, had no obvious detrimental effect on microbial metabolic activity within the limits studied. (author)

  12. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

    Science.gov (United States)

    Hatzenpichler, Roland; Scheller, Silvan; Tavormina, Patricia L; Babin, Brett M; Tirrell, David A; Orphan, Victoria J

    2014-01-01

    Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non-canonical amino acid tagging (BONCAT), is based on the in vivo incorporation of the non-canonical amino acid L-azidohomoalanine (AHA), a surrogate for l-methionine, followed by fluorescent labelling of AHA-containing cellular proteins by azide-alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)-targeted fluorescence in situ hybridization (FISH), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT-FISH to study microbial physiology in situ. A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano-scale secondary ion mass spectrometry (15NH3 assimilation) for individual cells within a sediment-sourced enrichment culture showed concordance between AHA-positive cells and 15N enrichment. BONCAT-FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single-cell level. PMID:24571640

  13. Getting to the Edge: Protein dynamical networks as a new frontier in plant-microbe interactions

    Directory of Open Access Journals (Sweden)

    Cassandra C Garbutt

    2014-06-01

    Full Text Available A systems perspective on diverse phenotypes, mechanisms of infection, and responses to environmental stresses can lead to considerable advances in agriculture and medicine. A significant promise of systems biology within plants is the development of disease-resistant crop varieties, which would maximize yield output for food, clothing, building materials and biofuel production. A systems or -omics perspective frames the next frontier in the search for enhanced knowledge of plant network biology. The functional understanding of network structure and dynamics s is vital to expanding our knowledge of how the intercellular communication processes are executed. . This review article will systematically discuss various levels of organization of systems biology beginning with the building blocks termed –omes and ending with complex transcriptional and protein-protein interaction networks. We will also highlight the prevailing computational modeling approaches of biological regulatory network dynamics. The latest developments in the -omics approach will be reviewed and discussed to underline and highlight novel technologies and research directions in plant network biology.

  14. Fusion proteins useful for producing pinene

    Energy Technology Data Exchange (ETDEWEB)

    Peralta-Yahya, Pamela P.; Keasling, Jay D

    2016-06-28

    The present invention provides for a modified host cell comprising a heterologous pinene synthase (PS), or enzymatically active fragment or variant thereof, and optionally a geranyl pyrophosphate synthase (GPPS), or enzymatically active fragment or variant thereof, or a fusion protein comprising: (a) a PS and (b) a GPPS linked by a linker.

  15. Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots.

    Science.gov (United States)

    Bressan, Mélanie; Roncato, Marie-Anne; Bellvert, Floriant; Comte, Gilles; Haichar, Feth Zahar; Achouak, Wafa; Berge, Odile

    2009-11-01

    A specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolysed into glucose and biocidal products. Among them, isothiocyanates are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated with living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere. A transgenic Arabidopsis thaliana line producing an exogenous glucosinolate and the associated wild-type plant associated were grown under an enriched (13)CO(2) atmosphere in natural soil. DNA from the rhizospheric soil was separated by density gradient centrifugation. Bacterial (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Acidobacteria), Archaea and fungal community structures were analysed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. Roots of the transgenic plant line presented an altered profile of glucosinolates and other minor additional modifications. These modifications significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Our results showed that even a minor modification in plant root could have important repercussions for soil microbial communities.

  16. Human Cells as Platform to Produce Gamma-Carboxylated Proteins.

    Science.gov (United States)

    de Sousa Bomfim, Aline; de Freitas, Marcela Cristina Corrêa; Covas, Dimas Tadeu; de Sousa Russo, Elisa Maria

    2018-01-01

    The gamma-carboxylated proteins belong to a family of proteins that depend on vitamin K for normal biosynthesis. The major representative gamma-carboxylated proteins are the coagulation system proteins, for example, factor VII, factor IX, factor X, prothrombin, and proteins C, S, and Z. These molecules have harbored posttranslational modifications, such as glycosylation and gamma-carboxylation, and for this reason they need to be produced in mammalian cell lines. Human cells lines have emerged as the most promising alternative to the production of gamma-carboxylated proteins. In this chapter, the methods to generate human cells as a platform to produce gamma-carboxylated proteins, for example the coagulation factors VII and IX, are presented. From the cell line modification up to the vitamin K adaptation of the produced cells is described in the protocols presented in this chapter.

  17. Insect Larvae: A New Platform to Produce Commercial Recombinant Proteins.

    Science.gov (United States)

    Targovnik, Alexandra M; Arregui, Mariana B; Bracco, Lautaro F; Urtasun, Nicolas; Baieli, Maria F; Segura, Maria M; Simonella, Maria A; Fogar, Mariela; Wolman, Federico J; Cascone, Osvaldo; Miranda, Maria V

    2016-01-01

    In Biotechnology, the expression of recombinant proteins is a constantly growing field and different hosts are used for this purpose. Some valuable proteins cannot be produced using traditional systems. Insects from the order Lepidoptera infected with recombinant baculovirus have appeared as a good choice to express high levels of proteins, especially those with post-translational modifications. Lepidopteran insects, which are extensively distributed in the world, can be used as small protein factories, the new biofactories. Species like Bombyx mori (silkworm) have been analyzed in Asian countries to produce a great number of recombinant proteins for use in basic and applied science and industry. Many proteins expressed in this larva have been commercialized. Several recombinant proteins produced in silkworms have already been commercialized. On the other hand, species like Spodoptera frugiperda, Heliothis virescens, Rachiplusia nu, Helicoverpa zea and Trichoplusia ni are widely distributed in both the occidental world and Europe. The expression of recombinant proteins in larvae has the advantage of its low cost in comparison with insect cell cultures. A wide variety of recombinant proteins, including enzymes, hormones and vaccines, have been efficiently expressed with intact biological activity. The expression of pharmaceutically proteins, using insect larvae or cocoons, has become very attractive. This review describes the use of insect larvae as an alternative to produce commercial recombinant proteins.

  18. Comparative proteomic analysis in pea treated with microbial consortia of beneficial microbes reveals changes in the protein network to enhance resistance against Sclerotinia sclerotiorum.

    Science.gov (United States)

    Jain, Akansha; Singh, Akanksha; Singh, Surendra; Singh, Vinay; Singh, Harikesh Bahadur

    2015-06-15

    Microbial consortia may provide protection against pathogenic ingress via enhancing plant defense responses. Pseudomonas aeruginosa PJHU15, Trichoderma harzianum TNHU27 and Bacillus subtilis BHHU100 were used either singly or in consortia in the pea rhizosphere to observe proteome level changes upon Sclerotinia sclerotiorum challenge. Thirty proteins were found to increase or decrease differentially in 2-DE gels of pea leaves, out of which 25 were identified by MALDI-TOF MS or MS/MS. These proteins were classified into several functional categories including photosynthesis, respiration, phenylpropanoid metabolism, protein synthesis, stress regulation, carbohydrate and nitrogen metabolism and disease/defense-related processes. The respective homologue of each protein identified was trapped in Pisum sativum and a phylogenetic tree was constructed to check the ancestry. The proteomic view of the defense response to S. sclerotiorum in pea, in the presence of beneficial microbes, highlights the enhanced protection that can be provided by these microbes in challenged plants. Copyright © 2015 Elsevier GmbH. All rights reserved.

  19. Romanian plant produces protein concentrate from paraffin-nourished yeasts

    Energy Technology Data Exchange (ETDEWEB)

    1985-01-01

    One of the world's few factories in which proteins are produced by continuous biotechnology is located in Romania. Here, at the bioproteins plant, microorganisms are converted into a flour which contains a protein concentrate that is so essential to the fattening of swine, cattle, sheep, fowl, and fish. These microorganisms are Candida type yeasts. The culture medium in which they are grown contains sulfates and phosphates. Paraffin, a petroleum product, supplies the carbon that is essential to the microorganisms viability.

  20. Pharmaceutical proteins produced in plant bioreactor in recent years ...

    African Journals Online (AJOL)

    Plant bioreactor, also called molecular farming, has enormous potential to produce recombinant proteins infinitely. Products expressed in plants have natural physico-chemical properties and bioactivities. Plant bioreactor could be a safe, economic and convenient production system, and can been widely applied in ...

  1. The Solubility of Cr-Organic Produced by Hydrolysis, Bioprocess and Bioremediation and its Effect on Fermented Rate, Digestibility and Rumen Microbe Population (in vitro

    Directory of Open Access Journals (Sweden)

    UH Tanuwiria

    2010-09-01

    Full Text Available The research was conducted to study the production of organic chromium from the leather tanning waste and its effect on in vitro rumen fermentation activities. The research was divided into two phases. The first phase was production of organic chromium by alkali hydrolysis, S cereviceae bioprocess, and duckweed bioremediation that perceived solubility in neutral and acid solution. The second phase was the supplementation of organic-Cr in ration seen from in-vitro fermented rate, digestibility and microbe rumen population. Research was conducted experimentally using 4x4 factorial patterns, on the basis of Completely Randomized Design (CRD with three replications in each experimental unit. The first factor was the type of organic-Cr and the second factor was the supplement in ration at four levels, 1, 2, 3 and 4 ppm. The results of this research indicated that organic chromium can be synthesized by alkali hydrolysis, S cereviseae bioprocess and the activity of duckweed bioremediation. Among the three of processes referred, the highest level of Cr was obtained from S cereviseae bioprocess that was originated from leather-tanning waste. The levels of organic-Cr that was resulted from alkali hydrolysis, bioprocess from Cl3Cr.6H2O, bioprocess from Cr leather-tanning waste, and from duckweed bioremediation were 354, 1011, 3833 and 310 mg/kg, respectively. Organic-Cr characteristic of each product has relatively similar in ferment ability, dry matter and organic matter digestibility and rumen ecosystem. There is an indication that dry matter and organic matter digestibility and rumen microbe population in ration that was added with organic Cr from alkali hydrolysis was higher than other supplements. (Animal Production 12(3: 175-183 (2010Key Words: organic-Cr, rumen fermentation activities, rumen microbe population

  2. 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.

  3. 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

  4. Functional properties of proteins isolated from industrially produced sunflower meal

    Directory of Open Access Journals (Sweden)

    Petia Ivanova

    2014-10-01

    Full Text Available Protein isolate 1 (PI1 and protein isolate 2 (PI2 were prepared from industrially produced sunflower meal by using isoelectric and ethanol precipitation respectively. The water absorption capacity of PI1 was 6 times higher than that of PI2 and was significantly reduced by the presence of 0.03 M and 0.25 M NaCl. Oil absorption capacity of both protein isolates was not influenced by NaCl supplementation. Foam capacity of PI1 and PI2 was pH-dependent. While the foam capacity of both isolates was improved by either 0.03 M or 0.25 M NaCl, the foam stability was negatively influenced by the addition of NaCl at all pH values with except for pH 4. Emulsifying activity of PI1 and PI2 was lowest at pH 4. The emulsions exhibited relatively high stability (> 90% under all studied conditions. Knowledge of the influence of pH and boundary concentrations of NaCl on the functionality of sunflower meal protein isolates could be beneficial for their future potential application in food industry.

  5. 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.)

  6. Genetic transformation of an obligate anaerobe, P. gingivalis for FMN-green fluorescent protein expression in studying host-microbe interaction.

    Directory of Open Access Journals (Sweden)

    Chul Hee Choi

    Full Text Available The recent introduction of "oxygen-independent" flavin mononucleotide (FMN-based fluorescent proteins (FbFPs is of major interest to both eukaryotic and prokaryotic microbial biologists. Accordingly, we demonstrate for the first time that an obligate anaerobe, the successful opportunistic pathogen of the oral cavity, Porphyromonas gingivalis, can be genetically engineered for expression of the non-toxic green FbFP. The resulting transformants are functional for studying dynamic bacterial processes in living host cells. The visualization of the transformed P. gingivalis (PgFbFP revealed strong fluorescence that reached a maximum emission at 495 nm as determined by fluorescence microscopy and spectrofluorometry. Human primary gingival epithelial cells (GECs were infected with PgFbFP and the bacterial invasion of host cells was analyzed by a quantitative fluorescence microscopy and antibiotic protection assays. The results showed similar levels of intracellular bacteria for both wild type and PgFbFP strains. In conjunction with organelle specific fluorescent dyes, utilization of the transformed strain provided direct and accurate determination of the live/metabolically active P. gingivalis' trafficking in the GECs over time. Furthermore, the GECs were co-infected with PgFbFP and the ATP-dependent Clp serine protease-deficient mutant (ClpP- to study the differential fates of the two strains within the same host cells. Quantitative co-localization analyses displayed the intracellular PgFbFP significantly associated with the endoplasmic reticulum network, whereas the majority of ClpP- organisms trafficked into the lysosomes. Hence, we have developed a novel and reliable method to characterize live host cell-microbe interactions and demonstrated the adaptability of FMN-green fluorescent protein for studying persistent host infections induced by obligate anaerobic organisms.

  7. Genetic transformation of an obligate anaerobe, P. gingivalis for FMN-green fluorescent protein expression in studying host-microbe interaction.

    Science.gov (United States)

    Choi, Chul Hee; DeGuzman, Jefferson V; Lamont, Richard J; Yilmaz, Özlem

    2011-04-15

    The recent introduction of "oxygen-independent" flavin mononucleotide (FMN)-based fluorescent proteins (FbFPs) is of major interest to both eukaryotic and prokaryotic microbial biologists. Accordingly, we demonstrate for the first time that an obligate anaerobe, the successful opportunistic pathogen of the oral cavity, Porphyromonas gingivalis, can be genetically engineered for expression of the non-toxic green FbFP. The resulting transformants are functional for studying dynamic bacterial processes in living host cells. The visualization of the transformed P. gingivalis (PgFbFP) revealed strong fluorescence that reached a maximum emission at 495 nm as determined by fluorescence microscopy and spectrofluorometry. Human primary gingival epithelial cells (GECs) were infected with PgFbFP and the bacterial invasion of host cells was analyzed by a quantitative fluorescence microscopy and antibiotic protection assays. The results showed similar levels of intracellular bacteria for both wild type and PgFbFP strains. In conjunction with organelle specific fluorescent dyes, utilization of the transformed strain provided direct and accurate determination of the live/metabolically active P. gingivalis' trafficking in the GECs over time. Furthermore, the GECs were co-infected with PgFbFP and the ATP-dependent Clp serine protease-deficient mutant (ClpP-) to study the differential fates of the two strains within the same host cells. Quantitative co-localization analyses displayed the intracellular PgFbFP significantly associated with the endoplasmic reticulum network, whereas the majority of ClpP- organisms trafficked into the lysosomes. Hence, we have developed a novel and reliable method to characterize live host cell-microbe interactions and demonstrated the adaptability of FMN-green fluorescent protein for studying persistent host infections induced by obligate anaerobic organisms.

  8. Chemical Changes in Proteins Produced by Thermal Processing.

    Science.gov (United States)

    Dutson, T. R.; Orcutt, M. W.

    1984-01-01

    Discusses effects of thermal processing on proteins, focusing on (1) the Maillard reaction; (2) heat denaturation of proteins; (3) aggregation, precipitation, gelation, and degradation; and (4) other thermally induced protein reactions. Also discusses effects of thermal processing on muscle foods, egg proteins, fruits and vegetables, and cereal…

  9. Protein substitution to produce a processed cheese with high ...

    African Journals Online (AJOL)

    Multiple studies report the beneficial effects of BCAAs supplementation to improve plasma amino acids imbalance, several neurologic diseases, protein energy malnutrition, and subsequently the survival rate of cirrhotic patients. Methods: In the present study we used a protein substitution technique to synthesize a new ...

  10. N-Glycosylation of Plant-produced Recombinant Proteins

    NARCIS (Netherlands)

    Bosch, H.J.; Castilho, A.; Loos, A.; Schots, A.; Steinkeller, H.

    2013-01-01

    Plants are gaining increasingly acceptance as a production platform for recombinant proteins. One reason for this is their ability to carry out posttranslational protein modifications in a similar if not identical way as mammalian cells. The capability of plants to carry out human-like complex

  11. Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis.

    Science.gov (United States)

    Mahajan, Gaurang; Mande, Shekhar C

    2017-04-04

    A comprehensive map of the human-M. tuberculosis (MTB) protein interactome would help fill the gaps in our understanding of the disease, and computational prediction can aid and complement experimental studies towards this end. Several sequence-based in silico approaches tap the existing data on experimentally validated protein-protein interactions (PPIs); these PPIs serve as templates from which novel interactions between pathogen and host are inferred. Such comparative approaches typically make use of local sequence alignment, which, in the absence of structural details about the interfaces mediating the template interactions, could lead to incorrect inferences, particularly when multi-domain proteins are involved. We propose leveraging the domain-domain interaction (DDI) information in PDB complexes to score and prioritize candidate PPIs between host and pathogen proteomes based on targeted sequence-level comparisons. Our method picks out a small set of human-MTB protein pairs as candidates for physical interactions, and the use of functional meta-data suggests that some of them could contribute to the in vivo molecular cross-talk between pathogen and host that regulates the course of the infection. Further, we present numerical data for Pfam domain families that highlights interaction specificity on the domain level. Not every instance of a pair of domains, for which interaction evidence has been found in a few instances (i.e. structures), is likely to functionally interact. Our sorting approach scores candidates according to how "distant" they are in sequence space from known examples of DDIs (templates). Thus, it provides a natural way to deal with the heterogeneity in domain-level interactions. Our method represents a more informed application of local alignment to the sequence-based search for potential human-microbial interactions that uses available PPI data as a prior. Our approach is somewhat limited in its sensitivity by the restricted size and

  12. Pharmaceutical proteins produced in plant bioreactor in recent years

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-29

    Dec 29, 2008 ... increasing demand of protein diagnostics and therapeutics, the ... market prospect and commercial value. This is known as ... vaccine for oral deliver needs no exceptional storage conditions .... immune response in intestine.

  13. Protein substitution to produce a processed cheese with high ...

    African Journals Online (AJOL)

    Hoida A.M. El-Shazly

    for liver enzymes; serum total and differential cholesterol profile, serum albumin, globulin and total protein along with .... Colorimetric method was used to determine AST and ALT ..... Studies on inter-organ ammonia exchange in liver cirrhosis ...

  14. The Search for Violacein-Producing Microbes to Combat Batrachochytrium dendrobatidis: A Collaborative Research Project between Secondary School and College Research Students

    Directory of Open Access Journals (Sweden)

    Larra Agate

    2015-10-01

    Full Text Available In this citizen science–aided, college laboratory–based microbiology research project, secondary school students collaborate with college research students on an investigation centered around bacterial species in the local watershed. This study specifically investigated the prevalence of violacein-producing bacterial isolates, as violacein has been demonstrated as a potential bioremediation treatment for outbreaks of the worldwide invasive chytrid, Batrachochytrium dendrobatidis (Bd. The impact of this invasion has been linked to widespread amphibian decline, and tracking of the spread of Bd is currently ongoing. Secondary school students participated in this research project by sterilely collecting water samples from a local watershed, documenting the samples, and completing the initial sample plating in a BSL1 environment. In the second phase of this project, trained college students working in courses and as research assistants in the academic year and summer term in a BSL2 laboratory facility were able to use physiological, biochemical, and molecular techniques to further identify individual isolates as well as characterize their properties. Collaboration between these learning spaces provides an increased interest in the community for environmentally relevant research projects and allows for an expansion of the research team to increase study robustness.

  15. degradable protein sources on performance of high-producing dairy ...

    African Journals Online (AJOL)

    with high-quality, low·degradable protein sources prOViding47% UDP is advocated for ... saliva and through the rumen wall (Waldo, 1968). Based on this type of ... of the feed industry, but is based on very little solid evidence. (Huber, 1984). Chalupa ...... of rumen fermentation in relation to ammonia concentration. Br. J. Nutr.

  16. 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

  17. 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…

  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. 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....

  20. 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.

  1. A robust and rapid method of producing soluble, stable, and functional G-protein coupled receptors.

    Directory of Open Access Journals (Sweden)

    Karolina Corin

    Full Text Available Membrane proteins, particularly G-protein coupled receptors (GPCRs, are notoriously difficult to express. Using commercial E. coli cell-free systems with the detergent Brij-35, we could rapidly produce milligram quantities of 13 unique GPCRs. Immunoaffinity purification yielded receptors at >90% purity. Secondary structure analysis using circular dichroism indicated that the purified receptors were properly folded. Microscale thermophoresis, a novel label-free and surface-free detection technique that uses thermal gradients, showed that these receptors bound their ligands. The secondary structure and ligand-binding results from cell-free produced proteins were comparable to those expressed and purified from HEK293 cells. Our study demonstrates that cell-free protein production using commercially available kits and optimal detergents is a robust technology that can be used to produce sufficient GPCRs for biochemical, structural, and functional analyses. This robust and simple method may further stimulate others to study the structure and function of membrane proteins.

  2. 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.

  3. Conformational and functional variants of CD44-targeted protein nanoparticles bio-produced in bacteria

    International Nuclear Information System (INIS)

    Pesarrodona, Mireia; Conchillo-Solé, Oscar; Unzueta, Ugutz; Xu, Zhikun; Ferrer-Miralles, Neus; Daura, Xavier; Vázquez, Esther; Villaverde, Antonio; Fernández, Yolanda; Foradada, Laia; Schwartz, Simó Jr; Abasolo, Ibane; Sánchez-Chardi, Alejandro; Roldán, Mónica; Villegas, Sandra; Rinas, Ursula

    2016-01-01

    Biofabrication is attracting interest as a means to produce nanostructured functional materials because of its operational versatility and full scalability. Materials based on proteins are especially appealing, as the structure and functionality of proteins can be adapted by genetic engineering. Furthermore, strategies and tools for protein production have been developed and refined steadily for more than 30 years. However, protein conformation and therefore activity might be sensitive to production conditions. Here, we have explored whether the downstream strategy influences the structure and biological activities, in vitro and in vivo, of a self-assembling, CD44-targeted protein-only nanoparticle produced in Escherichia coli. This has been performed through the comparative analysis of particles built from soluble protein species or protein versions obtained by in vitro protein extraction from inclusion bodies, through mild, non-denaturing procedures. These methods have been developed recently as a convenient alternative to the use of toxic chaotropic agents for protein resolubilization from protein aggregates. The results indicate that the resulting material shows substantial differences in its physicochemical properties and its biological performance at the systems level, and that its building blocks are sensitive to the particular protein source. (paper)

  4. Caught in the act: discovering secreted proteins from fungi and oomycetes in action

    DEFF Research Database (Denmark)

    Roth, Doris; Grell, Morten Nedergaard; Jensen, Annette Bruun

    Host-microbe relationships largely rely on secreted proteins like enzymes, virulence factors and antimicrobial peptides. To discover proteins secreted by microbe and host during the interaction with each other, we produced dual-organism cDNA libraries from three different fungus- or oomycete-infe......, by applying a similar strategy with a fungus-only library. As a result, we will show that our approach is widely applicable and allows us to deepen the understanding a variety of different host-microbe systems.......Host-microbe relationships largely rely on secreted proteins like enzymes, virulence factors and antimicrobial peptides. To discover proteins secreted by microbe and host during the interaction with each other, we produced dual-organism cDNA libraries from three different fungus- or oomycete...

  5. Biofuels: from microbes to molecules

    National Research Council Canada - National Science Library

    Lu, Xuefeng

    2014-01-01

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

  6. Microbe-microbe interactions in mixed culture food fermentations

    NARCIS (Netherlands)

    Smid, E.J.; Lacroix, C.

    2013-01-01

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

  7. Leaching and heating process as alternative to produce fish protein powder from Kilka (Clupeonella cultiventris caspia

    Directory of Open Access Journals (Sweden)

    KAVEH RAHMANIFARAH

    2014-05-01

    Full Text Available Rahmanifarah K, Shabanpour B, Shaviklo AR, Aalami M. 2014. Leaching and heating process as alternative to produce fish protein powder from Kilka (Clupeonella cultiventris caspia. Nusantara Bioscience 6: 1-6. The effect of protein extraction procedures (leached mince and heated suspension on selected properties of fish protein powder (proximate composition, pH, color, density, viscosity, fat adsorption, emulsifying capacity, emulsifying stability, foaming capacity, foaming stability, WBC, protein solubility in water, hygroscopicity, Trichloroacetic acid (TCA-soluble peptides and free sulfhydryl groups was investigated. Results showed that Fish protein powder (FPP produced by leaching mince (LM have higher protein, moisture, ash, pH, L*, viscosity, emulsion capacity, emulsion stability, foam capacity, foam stability, water binding capacity (WBC, protein solubility, hygroscopicity, TCA soluble peptides and free sulfhydryl group content than heated suspension (HS (P0.05. Overall, it was observed that high temperature during heating of suspension in HS method makes possible protein denaturation and aggregation. Consequently, based on functional, chemical and physical properties, extraction of fish protein by leaching process was found to be suitable for the production of fish protein powder.

  8. Liquid Whey Protein Concentrates Produced by Ultrafiltration as Primary Raw Materials for Thermal Dairy Gels

    Directory of Open Access Journals (Sweden)

    Marta Henriques

    2017-01-01

    Full Text Available The aim of this work is to study the gelation properties of liquid whey protein concentrates (LWPC produced by ultrafiltration (UF as raw material for thermally induced gels intended for food applications. LWPC thermal gelation was performed using different types of LWPC (non-defatted, defatted and diafiltered of different protein mass fractions and pH. Most of the produced gels showed viscoelastic behaviour. Non-defatted LWPC gave stronger heat-induced gels with a more cohesive microstructure, a higher water holding capacity and also higher elastic modulus (G’ and viscous modulus (G’’. Gel properties were not improved in products with lower content of non-protein compounds. As expected, the increase in protein mass fraction positively influences protein interactions. However, the pH is responsible for the equilibrium between attraction and repulsion forces in the gel components that influence gel hardness and water holding capacity.

  9. 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

  10. Microbe Phobia and Kitchen Microbiology.

    Science.gov (United States)

    Williams, Robert P.; Gillen, Alan L.

    1991-01-01

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

  11. The composition and functional properties of whey protein concentrates produced from buttermilk are comparable with those of whey protein concentrates produced from skimmed milk.

    Science.gov (United States)

    Svanborg, Sigrid; Johansen, Anne-Grethe; Abrahamsen, Roger K; Skeie, Siv B

    2015-09-01

    The demand for whey protein is increasing in the food industry. Traditionally, whey protein concentrates (WPC) and isolates are produced from cheese whey. At present, microfiltration (MF) enables the utilization of whey from skim milk (SM) through milk protein fractionation. This study demonstrates that buttermilk (BM) can be a potential source for the production of a WPC with a comparable composition and functional properties to a WPC obtained by MF of SM. Through the production of WPC powder and a casein- and phospholipid (PL)-rich fraction by the MF of BM, sweet BM may be used in a more optimal and economical way. Sweet cream BM from industrial churning was skimmed before MF with 0.2-µm ceramic membranes at 55 to 58°C. The fractionations of BM and SM were performed under the same conditions using the same process, and the whey protein fractions from BM and SM were concentrated by ultrafiltration and diafiltration. The ultrafiltration and diafiltration was performed at 50°C using pasteurized tap water and a membrane with a 20-kDa cut-off to retain as little lactose as possible in the final WPC powders. The ultrafiltrates were subsequently spray dried, and their functional properties and chemical compositions were compared. The amounts of whey protein and PL in the WPC powder from BM (BMWPC) were comparable to the amounts found in the WPC from SM (SMWPC); however, the composition of the PL classes differed. The BMWPC contained less total protein, casein, and lactose compared with SMWPC, as well as higher contents of fat and citric acid. No difference in protein solubility was observed at pH values of 4.6 and 7.0, and the overrun was the same for BMWPC and SMWPC; however, the BMWPC made less stable foam than SMWPC. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  12. 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.

  13. Dengue-2 Structural Proteins Associate with Human Proteins to Produce a Coagulation and Innate Immune Response Biased Interactome

    Directory of Open Access Journals (Sweden)

    Soares Luis RB

    2011-01-01

    -viral response processes, and predicts that the interaction of dengue proteins with a proposed human protein interaction network produces a modified biological outcome that may be behind the hallmark pathologies of dengue infection.

  14. Composition, structure and functional properties of protein concentrates and isolates produced from walnut (Juglans regia L.).

    Science.gov (United States)

    Mao, Xiaoying; Hua, Yufei

    2012-01-01

    In this study, composition, structure and the functional properties of protein concentrate (WPC) and protein isolate (WPI) produced from defatted walnut flour (DFWF) were investigated. The results showed that the composition and structure of walnut protein concentrate (WPC) and walnut protein isolate (WPI) were significantly different. The molecular weight distribution of WPI was uniform and the protein composition of DFWF and WPC was complex with the protein aggregation. H(0) of WPC was significantly higher (p structure of WPI was similar to WPC. WPI showed big flaky plate like structures; whereas WPC appeared as a small flaky and more compact structure. The most functional properties of WPI were better than WPC. In comparing most functional properties of WPI and WPC with soybean protein concentrate and isolate, WPI and WPC showed higher fat absorption capacity (FAC). Emulsifying properties and foam properties of WPC and WPI in alkaline pH were comparable with that of soybean protein concentrate and isolate. Walnut protein concentrates and isolates can be considered as potential functional food ingredients.

  15. 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.

  16. 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....

  17. Structural and evolutionary aspects of two families of non-catalytic domains present in starch and glycogen binding proteins from microbes, plants and animals

    DEFF Research Database (Denmark)

    Janeček, Štefan; Svensson, Birte; MacGregor, E. Ann

    2011-01-01

    kinase SNF1 complex, and an adaptor–regulator related to the SNF1/AMPK family, AKINβγ. CBM20s and CBM48s of amylolytic enzymes occur predominantly in the microbial world, whereas the non-amylolytic proteins containing these modules are mostly of plant and animal origin. Comparison of amino acid sequences...... that they exhibit independent behaviour, i.e. each family forms its own part in an evolutionary tree, with enzyme specificity (protein function) being well represented within each family. The distinction between CBM20 and CBM48 families is not sharp since there are representatives in both CBM families that possess...

  18. A dual-specificity isoform of the protein kinase inhibitor PKI produced by alternate gene splicing.

    Science.gov (United States)

    Kumar, Priyadarsini; Walsh, Donal A

    2002-03-15

    We have previously shown that the protein kinase inhibitor beta (PKIbeta) form of the cAMP-dependent protein kinase inhibitor exists in multiple isoforms, some of which are specific inhibitors of the cAMP-dependent protein kinase, whereas others also inhibit the cGMP-dependent enzyme [Kumar, Van Patten and Walsh (1997), J. Biol. Chem. 272, 20011-20020]. We have now demonstrated that the switch from a cAMP-dependent protein kinase (PKA)-specific inhibitor to one with dual specificity arises as a consequence of alternate gene splicing. We have confirmed using bacterially produced pure protein that a single inhibitor species has dual specificity for both PKA and cGMP-dependent protein kinase (PKG), inhibiting each with very high and closely similar inhibitory potencies. The gene splicing converted a protein with 70 amino acids into one of 109 amino acids, and did not change the inhibitory potency to PKA, but changed it from a protein that had no detectable PKG inhibitory activity to one that now inhibited PKG in the nanomolar range.

  19. 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.

  20. 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

  1. Genetic Transformation of an Obligate Anaerobe, P. gingivalis for FMN-Green Fluorescent Protein Expression in Studying Host-Microbe Interaction

    OpenAIRE

    Choi, Chul Hee; DeGuzman, Jefferson V.; Lamont, Richard J.; Yilmaz, Özlem

    2011-01-01

    The recent introduction of "oxygen-independent" flavin mononucleotide (FMN)-based fluorescent proteins (FbFPs) is of major interest to both eukaryotic and prokaryotic microbial biologists. Accordingly, we demonstrate for the first time that an obligate anaerobe, the successful opportunistic pathogen of the oral cavity, Porphyromonas gingivalis, can be genetically engineered for expression of the non-toxic green FbFP. The resulting transformants are functional for studying dynamic bacterial pr...

  2. Effect of salseed-meal tannins on protein synthesis, /sup 35/S incorporation and cellulose digestibility by rumen microbes in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Singh, K; Arora, S P [Haryana Agricultural Univ., Hissar (India)

    1980-10-01

    Tannins from seed-meal of sal (Shorea robusta Gaertn. F.) were fractionated after treatments into ethyl acetate (EA) and lead acetate (LA) fractions. In trial 1, incorporation of /sup 35/S from (NH/sub 4/)/sub 2//sup 35/SO/sub 4/ into microbial protein declined due to the effect of both 2% EA and LA fractions as compared to control. Microbial protein synthesis was depressed significantly (P < 0.01) in treatments containing 1.0 and 2.0% of EA fractions, and 0.5, 1.0 and 2.0% of LA fractions. The microbial cellulolytic activity also exhibited a similar trend in experiment 2. In experiment 3, in which all parameters were studied simultaneously, a significant depression was found in the values of microbial protein synthesis, /sup 35/S incorporation and cellulolysis at all levels of both the tannin fractions. It may be inferred that both the tannin fractions from salseed-meal showed antimicrobial activity and LA fraction seems to be more deleterious than EA fraction for rumen metabolism. The experiments were conducted in vitro using rumen liquor of a non-pregnant dry cow having permanent rumen fistula.

  3. [A study of recombinant human sestrin 1 and sestrin 2 proteins produced in a prokaryotic system].

    Science.gov (United States)

    Rai, N; Kumar, R; Haque, Md A; Hassan, Md I; Dey, S

    2017-01-01

    Sestrins are highly conserved stress-inducible proteins capable of suppressing the production of ROS and signalling through mTORC1. Here we report a study of human sestrin1 (sesn1) and sestrin2 (sesn2) proteins produced in a pET28^(+) vector based prokaryotic system. Mass spectrometry analysis, western blot and surface plasmon resonance (SPR) of affinity purified sesn1 and sesn2 proteins confirmed their identity; biophysical characteristics were observed using circular dichroism (CD) showing that sesn1 and sesn2 have a predominant α-helical structure. Here we describe a simple, one step purification process to purify a large amount of sestrin proteins with significant yield. Further study of recombinant human sestrins may further facilitate the understanding of their roles in eukaryotic cells.

  4. Virus-producing cells determine the host protein profiles of HIV-1 virion cores

    Science.gov (United States)

    2012-01-01

    Background Upon HIV entry into target cells, viral cores are released and rearranged into reverse transcription complexes (RTCs), which support reverse transcription and also protect and transport viral cDNA to the site of integration. RTCs are composed of viral and cellular proteins that originate from both target and producer cells, the latter entering the target cell within the viral core. However, the proteome of HIV-1 viral cores in the context of the type of producer cells has not yet been characterized. Results We examined the proteomic profiles of the cores purified from HIV-1 NL4-3 virions assembled in Sup-T1 cells (T lymphocytes), PMA and vitamin D3 activated THP1 (model of macrophages, mMΦ), and non-activated THP1 cells (model of monocytes, mMN) and assessed potential involvement of identified proteins in the early stages of infection using gene ontology information and data from genome-wide screens on proteins important for HIV-1 replication. We identified 202 cellular proteins incorporated in the viral cores (T cells: 125, mMΦ: 110, mMN: 90) with the overlap between these sets limited to 42 proteins. The groups of RNA binding (29), DNA binding (17), cytoskeleton (15), cytoskeleton regulation (21), chaperone (18), vesicular trafficking-associated (12) and ubiquitin-proteasome pathway-associated proteins (9) were most numerous. Cores of the virions from SupT1 cells contained twice as many RNA binding proteins as cores of THP1-derived virus, whereas cores of virions from mMΦ and mMN were enriched in components of cytoskeleton and vesicular transport machinery, most probably due to differences in virion assembly pathways between these cells. Spectra of chaperones, cytoskeletal proteins and ubiquitin-proteasome pathway components were similar between viral cores from different cell types, whereas DNA-binding and especially RNA-binding proteins were highly diverse. Western blot analysis showed that within the group of overlapping proteins, the level of

  5. A New Bacillus licheniformis Mutant Strain Producing Serine Protease Efficient for Hvdrolvqis of Sov Meal Proteins.

    Science.gov (United States)

    Kostyleva, E V; Sereda, A S; Velikoretskaya, I A; Nefedova, L I; Sharikov, A Yu; Tsurikova, N V; Lobanov, N S; Semenova, M V; Sinitsyn, A P

    2016-07-01

    Induced mutagenesis with y-irradiation of the industrial strain Bacillus licheniformis-60 VKM B-2366,D was used to obtain a new highly active producer of an extracellular serine protease, Bacillus licheni- formis7 145. Samples of dry.concentrated preparations of serine protease produced by the original and mutant strains were obtained, and identity of their protein composition was'established. Alkaline serine protease sub- tilisin DY was the main component of the preparations. The biochemical and physicochemical properties of the Protolkheterm-145 enzyme preparation obtained from the mutant strain were studied. It exhibited pro- teolytic activity (1.5 times higher than the preparation from the initial strain) within broad ranges of pH (5- 11) and temperature (30-70'C).-Efficient hydrolysis of extruded soy meal protein at high concentrations (2 to 50%) in-the reaction mixture was.the main advantage of the Protolikheterm 145 preparation. Compared to,. the preparation obtained using the initial strain, the new preparation with increased proteolytic-activity pro- vided for more complete hydrolysis of the main non-nutritious soy,proteins.(glycinin and 0-conglycinin) with the yield of soluble protein increased by 19-28%, which decreased the cost of bioconversion of the protein- aceous material and indicated promise of the new preparation in resource-saving technologies for processing soy meals and cakes.

  6. Selection of antifungal protein-producing molds from dry-cured meat products.

    Science.gov (United States)

    Acosta, Raquel; Rodríguez-Martín, Andrea; Martín, Alberto; Núñez, Félix; Asensio, Miguel A

    2009-09-30

    To control unwanted molds in dry-cured meats it is necessary to allow the fungal development essential for the desired characteristics of the final product. Molds producing antifungal proteins could be useful to prevent hazards due to the growth of mycotoxigenic molds. The objective has been to select Penicillium spp. that produce antifungal proteins against toxigenic molds. To obtain strains adapted to these products, molds were isolated from dry-cured ham. A first screening with 281 isolates by the radial inhibition assay revealed that 166 were active against some of the toxigenic P. echinulatum, P. commune, and Aspergillusniger used as reference molds. The activity of different extracts from cultured medium was evaluated by a microspectroscopic assay. Molds producing active chloroform extracts were eliminated from further consideration. A total of 16 Penicillium isolates were screened for antifungal activity from both cell-free media and the aqueous residues obtained after chloroform extraction. The cell-free media of 10 isolates that produced a strong inhibition of the three reference molds were fractionated by FPLC on a cationic column. For protein purification, the fractions of the three molds that showed high inhibitory activity were further chromatographed on a gel filtration column, and the subfractions containing the highest absorbance peaks were assayed against the most sensitive reference molds. One subfraction each from strains AS51D and RP42C from Penicilliumchrysogenum confirmed the inhibitory activity against the reference molds. SDS-PAGE revealed a single band from each subfraction, with estimated molecular masses of 37kDa for AS51D and 9kDa for RP42C. Although further characterisation is required, both these proteins and the producing strains can be of interest to control unwanted molds on foods.

  7. The Absent in Melanoma 2-Like Receptor IFN-Inducible Protein 16 as an Inflammasome Regulator in Systemic Lupus Erythematosus: The Dark Side of Sensing Microbes

    Directory of Open Access Journals (Sweden)

    Valeria Caneparo

    2018-05-01

    Full Text Available Absent in melanoma 2 (AIM2-like receptors (ALRs are a newly characterized class of pathogen recognition receptors (PRRs involved in cytosolic and nuclear pathogen DNA recognition. In recent years, two ALR family members, the interferon (IFN-inducible protein 16 (IFI16 and AIM2, have been linked to the pathogenesis of various autoimmune diseases, among which systemic lupus erythematosus (SLE has recently gained increasing attention. SLE patients are indeed often characterized by constitutively high serum IFN levels and increased expression of IFN-stimulated genes due to an abnormal response to pathogens and/or incorrect self-DNA recognition process. Consistently, we and others have shown that IFI16 is overexpressed in a wide range of autoimmune diseases where it triggers production of specific autoantibodies. In addition, evidence from mouse models supports a model whereby ALRs are required for IFN-mediated host response to both exogenous and endogenous DNA. Following interaction with cytoplasmic or nuclear nucleic acids, ALRs can form a functional inflammasome through association with the adaptor ASC [apoptosis-associated speck-like protein containing a caspase recruitment domain (CARD] and with procaspase-1. Importantly, inflammasome-mediated upregulation of IL-1β and IL-18 production positively correlates with SLE disease severity. Therefore, targeting ALR sensors and their downstream pathways represents a promising alternative therapeutic approach for SLE and other systemic autoimmune diseases.

  8. Utilization of {sup 15}N-Diammonium Phosphate by Ruminants to Produce Milk and Meat Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Piva, G.; Silva, S. [Istituto di Zootecnicae di Chimica Agraria, Facolta di Agraria Univ. Cattolicas. Cuore, Piacenza (Italy)

    1968-07-01

    The authors investigated the alimentary role of diammonium phosphate (DAP) in ruminants. For this study DAP labelled with {sup 15}N was used; analysis of the {sup 15}N atomic per cent excess was made with an Italelettronica mass spectrophotometer (model SP 21 F) and the amino acid determination by a Beckman-Spinco amino acid analyser (model 120B) fitted with a preparative column. For the experiment 7 g of DAP at 15 and 20 at. % excess {sup 15}N were administered once to mature lactating and non-lactating sheep, respectively. The measurement of {sup 15}N in the protein and isolated amino acids of milk and meat showed: (1) The milk protein produced in the first 24 h contained the highest atomic per cent excess of {sup 15}SN, 0.093; (2) That the supplemental {sup 15}N was found in all the amino acids of milk proteins except tryptophane. The atomic per cent excess of {sup 15}N was observed to vary between the various amino acids. These results confirmed previous observations on bacterial protein synthesized from DAP. (3) Muscle protein {sup 15}N maximized on the third day after administration of the {sup 15}N-DAP, with an atomic per cent excess of 0.040; (4) The atomic per cent excess of {sup 15}N in the individual amino acids of muscle protein is significant in only two amino' acids, serine and cystine; and (5) That after 8 d of adaptation there are no traces of DAP in milk or meat proteins, urine or faeces. The authors conclude that the ruminant, after a period of adaptation and through the mediation of ruminant microorganisms, is able to use the nitrogen of diammonium phosphate for the synthesis of milk and meat proteins. (author)

  9. Antioxidant activity of pea protein hydrolysates produced by batch fermentation with lactic acid bacteria

    Directory of Open Access Journals (Sweden)

    Stanisavljević Nemanja S.

    2015-01-01

    Full Text Available Nine Lactobacillus strains known for surface proteinase activity were chosen from our collection and tested for their ability to grow in pea seed protein-based medium, and to hydrolyze purified pea proteins in order to produce peptides with antioxidant (AO activity. Two strains, Lactobacillus rhamnosus BGT10 and Lactobacillus zeae LMG17315, exhibited strong proteolytic activity against pea proteins. The AO activity of the pea hydrolysate fraction, MW <10 kDa, obtained by the fermentation of purified pea proteins with Lactobacillus rhamnosus BGT10, was tested by standard spectrophotometric assays (DPPH, ABTS, Fe3+-reducing capacity and the recently developed direct current (DC polarographic assay. The low molecular weight fraction of the obtained hydrolysate was separated using ion exchange chromatography, while the AO activity of eluted fractions was determined by means of a sensitive DC polarographic assay without previous concentration of samples. Results revealed that the fraction present in low abundance that contained basic peptides possessed the highest antioxidant activity. Based on the obtained results, it can be concluded that Lactobacillus rhamnosus BGT10 should be further investigated as a candidate strain for large-scale production of bioactive peptides from legume proteins. [Projekat Ministartsva nauke Republike Srbije, br. 173005 i br. 173026

  10. 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 ...

  11. Alga-Produced Cholera Toxin-Pfs25 Fusion Proteins as Oral Vaccines

    Science.gov (United States)

    Gregory, James A.; Topol, Aaron B.; Doerner, David Z.

    2013-01-01

    Infectious diseases disproportionately affect indigent regions and are the greatest cause of childhood mortality in developing countries. Practical, low-cost vaccines for use in these countries are paramount to reducing disease burdens and concomitant poverty. Algae are a promising low-cost system for producing vaccines that can be orally delivered, thereby avoiding expensive purification and injectable delivery. We engineered the chloroplast of the eukaryotic alga Chlamydomonas reinhardtii to produce a chimeric protein consisting of the 25-kDa Plasmodium falciparum surface protein (Pfs25) fused to the β subunit of the cholera toxin (CtxB) to investigate an alga-based whole-cell oral vaccine. Pfs25 is a promising malaria transmission-blocking vaccine candidate that has been difficult to produce in traditional recombinant systems due to its structurally complex tandem repeats of epidermal growth factor-like domains. The noncatalytic CtxB domain of the cholera holotoxin assembles into a pentameric structure and acts as a mucosal adjuvant by binding GM1 ganglioside receptors on gut epithelial cells. We demonstrate that CtxB-Pfs25 accumulates as a soluble, properly folded and functional protein within algal chloroplasts, and it is stable in freeze-dried alga cells at ambient temperatures. In mice, oral vaccination using freeze-dried algae that produce CtxB-Pfs25 elicited CtxB-specific serum IgG antibodies and both CtxB- and Pfs25-specific secretory IgA antibodies. These data suggest that algae are a promising system for production and oral delivery of vaccine antigens, but as an orally delivered adjuvant, CtxB is best suited for eliciting secretory IgA antibodies for vaccine antigens against pathogens that invade mucosal surfaces using this strategy. PMID:23603678

  12. Development of ELISA for the detection of transgenic vegetative insecticidal protein in GM crops/produce.

    Science.gov (United States)

    Kumar, R

    2012-01-11

    In the process of the development of insect-resistant genetically modified (GM) crops and also to evaluate the consistency in the expression of toxin under field conditions, immunological assays are commonly being used. An immunoassay was developed to support the labelling of vegetative insecticidal protein (Vip3A)-based GM produce. The developed ELISA for the measurement of Vip3A is a triple antibody sandwich procedure utilising a polyclonal capture antibody (mouse anti-Vip3A) and a polyclonal detection antibody (rabbit anti-Vip3A) followed by use of a third HRP-conjugated anti-species antibody (goat anti-rabbit IgG). The limit of detection limit of the ELISA assay was 16 ng ml(-1) with a linear quantification range from approximately 31 to 500 ng ml(-1) of Vip3A protein. Furthermore, the assay was in-house validated with GM brinjal samples. The assay was specific, sensitive and reproducible, which can be helpful to detect and track down the spread of unapproved and intentionally/unintentionally released GM produce harbouring Vip protein.

  13. Expression of nucleolar-related proteins in porcine preimplantation embryos produced in vivo and in vitro

    DEFF Research Database (Denmark)

    Bjerregaard, Bolette; Wrenzycki, Christine; Strejcek, Frantisek

    2004-01-01

    The expression of nucleolar-related proteins was studied as an indirect marker of the ribosomal RNA (rRNA) gene activation in porcine embryos up to the blastocyst stage produced in vivo and in vitro. A group of the in vivo-developed embryos were cultured with alpha-amanitin to block the de novo...... proteins pRb and p130, which are involved in cell-cycle regulation, was assessed by semiquantitative RT-PCR up to the blastocyst stage. Toward the end of third cell cycle, the nuclei in non-alpha-amanitin-treated, in vivo-produced embryos displayed different stages of transformation of the nuclear...... was delayed in porcine embryos produced in vitro compared to the in vivo-derived counterparts with respect to mRNAs encoding PAF53 and UBF. Moreover, differences existed in the mRNA expression patterns of pRb between in vivo- and in vitro-developed embryos. These findings show, to our knowledge for the first...

  14. Scalable organic solvent free supercritical fluid spray drying process for producing dry protein formulations.

    Science.gov (United States)

    Nuchuchua, O; Every, H A; Hofland, G W; Jiskoot, W

    2014-11-01

    In this study, we evaluated the influence of supercritical carbon dioxide (scCO2) spray drying conditions, in the absence of organic solvent, on the ability to produce dry protein/trehalose formulations at 1:10 and 1:4 (w/w) ratios. When using a 4L drying vessel, we found that decreasing the solution flow rate and solution volume, or increasing the scCO2 flow rate resulted in a significant reduction in the residual water content in dried products (Karl Fischer titration). The best conditions were then used to evaluate the ability to scale the scCO2 spray drying process from 4L to 10L chamber. The ratio of scCO2 and solution flow rate was kept constant. The products on both scales exhibited similar residual moisture contents, particle morphologies (SEM), and glass transition temperatures (DSC). After reconstitution, the lysozyme activity (enzymatic assay) and structure (circular dichroism, HP-SEC) were fully preserved, but the sub-visible particle content was slightly increased (flow imaging microscopy, nanoparticle tracking analysis). Furthermore, the drying condition was applicable to other proteins resulting in products of similar quality as the lysozyme formulations. In conclusion, we established scCO2 spray drying processing conditions for protein formulations without an organic solvent that holds promise for the industrial production of dry protein formulations. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Multiple growth hormone-binding proteins are expressed on insulin-producing cells

    DEFF Research Database (Denmark)

    Møldrup, A; Billestrup, N; Thorn, N A

    1989-01-01

    The insulin-producing rat islet tumor cell line, RIN-5AH, expresses somatogen binding sites and responds to GH by increased proliferation and insulin production. Affinity cross-linking shows that RIN-5AH cells contain two major GH-binding subunits of Mr 100-130K (110K), which appear to exist as d....... It is concluded that the RIN-5AH cells have multiple GH-binding proteins which may mediate signals for either proliferation and/or insulin production....

  16. Coupling of anaerobic waste treatment to produce protein- and lipid-rich bacterial biomass

    Science.gov (United States)

    Steinberg, Lisa M.; Kronyak, Rachel E.; House, Christopher H.

    2017-11-01

    Future long-term manned space missions will require effective recycling of water and nutrients as part of a life support system. Biological waste treatment is less energy intensive than physicochemical treatment methods, yet anaerobic methanogenic waste treatment has been largely avoided due to slow treatment rates and safety issues concerning methane production. However, methane is generated during atmosphere regeneration on the ISS. Here we propose waste treatment via anaerobic digestion followed by methanotrophic growth of Methylococcus capsulatus to produce a protein- and lipid-rich biomass that can be directly consumed, or used to produce other high-protein food sources such as fish. To achieve more rapid methanogenic waste treatment, we built and tested a fixed-film, flow-through, anaerobic reactor to treat an ersatz wastewater. During steady-state operation, the reactor achieved a 97% chemical oxygen demand (COD) removal rate with an organic loading rate of 1740 g d-1 m-3 and a hydraulic retention time of 12.25 d. The reactor was also tested on three occasions by feeding ca. 500 g COD in less than 12 h, representing 50x the daily feeding rate, with COD removal rates ranging from 56-70%, demonstrating the ability of the reactor to respond to overfeeding events. While investigating the storage of treated reactor effluent at a pH of 12, we isolated a strain of Halomonas desiderata capable of acetate degradation under high pH conditions. We then tested the nutritional content of the alkaliphilic Halomonas desiderata strain, as well as the thermophile Thermus aquaticus, as supplemental protein and lipid sources that grow in conditions that should preclude pathogens. The M. capsulatus biomass consisted of 52% protein and 36% lipids, the H. desiderata biomass consisted of 15% protein and 7% lipids, and the Thermus aquaticus biomass consisted of 61% protein and 16% lipids. This work demonstrates the feasibility of rapid waste treatment in a compact reactor design

  17. RNA-protein interactions in plant disease: hackers at the dinner table.

    Science.gov (United States)

    Spanu, Pietro D

    2015-09-01

    Plants are the source of most of our food, whether directly or as feed for the animals we eat. Our dinner table is a trophic level we share with the microbes that also feed on the primary photosynthetic producers. Microbes that enter into close interactions with plants need to evade or suppress detection and host immunity to access nutrients. They do this by deploying molecular tools - effectors - which target host processes. The mode of action of effector proteins in these events is varied and complex. Recent data from diverse systems indicate that RNA-interacting proteins and RNA itself are delivered by eukaryotic microbes, such as fungi and oomycetes, to host plants and contribute to the establishment of successful interactions. This is evidence that pathogenic microbes can interfere with the host software. We are beginning to see that pathogenic microbes are capable of hacking into the plants' immunity programs. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

  18. Heat Shock Protein 47: A Novel Biomarker of Phenotypically Altered Collagen-Producing Cells

    International Nuclear Information System (INIS)

    Taguchi, Takashi; Nazneen, Arifa; Al-Shihri, Abdulmonem A.; Turkistani, Khadijah A.; Razzaque, Mohammed S.

    2011-01-01

    Heat shock protein 47 (HSP47) is a collagen-specific molecular chaperone that helps the molecular maturation of various types of collagens. A close association between increased expression of HSP47 and the excessive accumulation of collagens is found in various human and experimental fibrotic diseases. Increased levels of HSP47 in fibrotic diseases are thought to assist in the increased assembly of procollagen, and thereby contribute to the excessive deposition of collagens in fibrotic areas. Currently, there is not a good universal histological marker to identify collagen-producing cells. Identifying phenotypically altered collagen-producing cells is essential for the development of cell-based therapies to reduce the progression of fibrotic diseases. Since HSP47 has a single substrate, which is collagen, the HSP47 cellular expression provides a novel universal biomarker to identify phenotypically altered collagen-producing cells during wound healing and fibrosis. In this brief article, we explained why HSP47 could be used as a universal marker for identifying phenotypically altered collagen-producing cells

  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. EXTRACELLULAR PROTEINS PRODUCED BY DIFFERENT SPECIES OF THE FUNGUS TRICHODERMA ON SECONDARY PAPER MILL SLUDGE SUBSTRATE

    Directory of Open Access Journals (Sweden)

    Ida Vaskova,

    2012-01-01

    Full Text Available Kraft pulping is the most commonly used pulping process in the pulp and paper industry. In this process wood chips are chemically delignified using sodium sulfide and sodium hydroxide. Delignification is usually followed by mechanical fiberization and a bleaching process of the resulting wood pulp. In addition to lignin-free wood pulp, this process also produces waste that contains residues of used chemicals, lignin, cellulose, hemicelluloses, and small amounts of other wood components. Because of the worldwide large-scale production of paper, the sludge from paper mills contributes significantly to environmental pollution. Although there have been great efforts being made to utilize this lignin-rich material, sludge is mostly disposed in landfills or incinerated in a boiler. This research project used secondary sludge as a substrate for 7 wood-decay fungi taxonomically belonging to the genus Trichoderma. The examined fungi expressed the capability of consuming sludge components as a carbon source to produce extracellular proteins. The proteins were separated by gel electrophoresis. Before and after fungi cultivation, the sludge was analyzed by Fourier transform infrared spectroscopy (FTIR.

  1. Human Protein C produces anticoagulation and increased fibrinolytic activity in the cat

    International Nuclear Information System (INIS)

    Burdick, M.D.; Schaub, R.G.

    1986-01-01

    The effect of activated human Protein C (PCa) infusion on the coagulation and fibrinolytic systems of the Nembutal anesthetized cat was assessed. Human Protein C was activated by incubation with thrombin or by passage over a column of thrombin immobilized on CNBr Sepharose 4B. Cats were given bolus i.v. injections of either vehicle or PCa in a dose range of 3-16 μg/mL of calculated whole body volume. Citrated blood samples (9:1) were taken from a femoral vein prior to and at 5, 10, 20, 30, 60, 120, and 180 min. after PCa. Activated partial thromboplastin time (APTT), thrombin time (TT) euglobulin clot lysis (ECLT) and I-125 fibrin release (FR) was measured. Vehicle treated cats had no change in any parameter. PCa produced a dose and time dependent prolongation of APTT while TT was unchanged. Anticoagulation was evident immediately after PCa infusion and began to normalize within 20 min. Fibrinolytic activity measured by ECLT and FR was also stimulated by PCa but was not evident until 40-60 minutes after PCa injection. The results show that human PCa induces anticoagulation effects in the cat similar to other species. However, stimulation of fibrinolysis requires a longer period of time before expression. This delay of fibrinolytic stimulation should be considered when assessing the effects of human Protein C in other species

  2. Effects of Dietary Supplementation with Hainanmycin on Protein Degradation and Populations of Ammonia-producing Bacteria

    Directory of Open Access Journals (Sweden)

    Z. B. Wang

    2013-05-01

    Full Text Available An in vitro fermentation was conducted to determine the effects of hainanmycin on protein degradation and populations of ammonia-producing bacteria. The substrates (DM basis for in vitro fermentation consisted of alfalfa hay (31.7%, Chinese wild rye grass hay (28.3%, ground corn grain (24.5%, soybean meal (15.5% with a forage: concentrate of 60:40. Treatments were the control (no additive and hainanmycin supplemented at 0.1 (H0.1, 1 (H1, 10 (H10, and 100 mg/kg (H100 of the substrates. After 24 h of fermentation, the highest addition level of hainanmycin decreased total VFA concentration and increased the final pH. The high addition level of hainanmycin (H1, H10, and H100 reduced (p0.05. After 24 h of fermentation, H10 and H100 increased (p<0.05 concentrations of peptide nitrogen and AA nitrogen and proteinase activity, and decreased (p<0.05 NH3-N concentration and deaminase activity compared with control. Peptidase activitives were not affected by hainanmycin. Hainanmycin supplementation only inhibited the growth of Butyrivibrio fibrisolvens, which is one of the species of low deaminative activity. Hainanmycin supplementation also decreased (p<0.05 relative population sizes of hyper-ammonia-producing species, except for H0.1 on Clostridium aminophilum. It was concluded that dietary supplementation with hainanmycin could improve ruminal fermentation and modify protein degradation by changing population size of ammonia-producing bacteria in vitro; and the addition level of 10 mg/kg appeared to achieve the best results.

  3. Structure-volume relationships: singular volume effects produced by cupric ion-globular protein interaction.

    Science.gov (United States)

    Katz, S; Shinaberry, G; Heck, E L; Squire, W

    1980-08-05

    The nature of the volume isotherms produced by the coordination of Cu(II) with ovalbumin and bovine serum albumin differs substantially from the adsorption isotherms produced by these systems. Whereas there was increased binding of Cu(II) associated with a pH increase from pH 5.3 to pH 7.4, the volume isotherms for these systems did not exhibit this type of pH dependence. The volume changes were determined at 30.0 +/- 0.001 degrees C with microdilatometers which could be read to 0.01 muL. The binding isotherms for ovalbumin at pH 5.3 and 7.4 and for bovine serum albumin at pH 5.3 was resolved by a Scatchard plot to yield the appropriate thermodynamic parameters. An algorithm was derived to calculate the distribution of the individual PMi complexes, i.e., PMi-1 + M in equilibrium (Ki) PMi where i equals 1, 2, 3, ..., n moles of cation, M, bound per mole of protein, P, for the above systems. The volume isotherms were then resolved in terms of the constituent delta Vi terms, i.e., the volume change produced by the formation of the individual PMi complexes. These values were verified by an independent graphical differentiation procedure. The coordination of Cu(II) to BSA at pH 7.4 produced a cooperative adsorption isotherm which was not amenable to a Scatchard analysis. The resultant anomalous volume isotherm was resolved into a component related to Cu(II)-site interaction and a negative volume effect attributable to a conformational change induced by complex formation. This structural transition which occurs at physiological pH may constitute a control mechanism for regulating the serum level of Cu(II) and possibly other divalent ions.

  4. Effective non-denaturing purification method for improving the solubility of recombinant actin-binding proteins produced by bacterial expression.

    Science.gov (United States)

    Chung, Jeong Min; Lee, Sangmin; Jung, Hyun Suk

    2017-05-01

    Bacterial expression is commonly used to produce recombinant and truncated mutant eukaryotic proteins. However, heterologous protein expression may render synthesized proteins insoluble. The conventional method used to express a poorly soluble protein, which involves denaturation and refolding, is time-consuming and inefficient. There are several non-denaturing approaches that can increase the solubility of recombinant proteins that include using different bacterial cell strains, altering the time of induction, lowering the incubation temperature, and employing different detergents for purification. In this study, we compared several non-denaturing protocols to express and purify two insoluble 34 kDa actin-bundling protein mutants. The solubility of the mutant proteins was not affected by any of the approaches except for treatment with the detergent sarkosyl. These results indicate that sarkosyl can effectively improve the solubility of insoluble proteins during bacterial expression. Copyright © 2016. Published by Elsevier Inc.

  5. Mass-spectrometry data for Rhizoctonia solani proteins produced during infection of wheat and vegetative growth

    Directory of Open Access Journals (Sweden)

    Jonathan P. Anderson

    2016-09-01

    Full Text Available Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato, legumes and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about how R. solani causes disease. The data described in this article is derived from applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Comparisons of the data for sample types in this set will be useful to identify metabolic pathway changes as the fungus switches from saprophytic to a pathogenic lifestyle or pathogenicity related proteins contributing to the ability to cause disease on wheat. The data set is deposited in the PRIDE archive under identifier PRIDE: PXD002806. Keywords: Fungal pathogenesis, Wheat, Rhizoctonia solani, Basidiomycete

  6. Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin.

    Science.gov (United States)

    Svitil, A L; Chadhain, S; Moore, J A; Kirchman, D L

    1997-02-01

    Relatively little is known about the number, diversity, and function of chitinases produced by bacteria, even though chitin is one of the most abundant polymers in nature. Because of the importance of chitin, especially in marine environments, we examined chitin-degrading proteins in the marine bacterium Vibrio harveyi. This bacterium had a higher growth rate and more chitinase activity when grown on (beta)-chitin (isolated from squid pen) than on (alpha)-chitin (isolated from snow crab), probably because of the more open structure of (beta)-chitin. When exposed to different types of chitin, V. harveyi excreted several chitin-degrading proteins into the culture media. Some chitinases were present with all of the tested chitins, while others were unique to a particular chitin. We cloned and identified six separate chitinase genes from V. harveyi. These chitinases appear to be unique based on DNA restriction patterns, immunological data, and enzyme activity. This marine bacterium and probably others appear to synthesize separate chitinases for efficient utilization of different forms of chitin and chitin by-products.

  7. Small bugs, big business: the economic power of the microbe.

    Science.gov (United States)

    Demain, A L

    2000-10-01

    The versatility of microbial biosynthesis is enormous. The most industrially important primary metabolites are the amino acids, nucleotides, vitamins, solvents, and organic acids. Millions of tons of amino acids are produced each year with a total multibillion dollar market. Many synthetic vitamin production processes are being replaced by microbial fermentations. In addition to the multiple reaction sequences of fermentations, microorganisms are extremely useful in carrying out biotransformation processes. These are becoming essential to the fine chemical industry in the production of single-isomer intermediates. Microbially produced secondary metabolites are extremely important to our health and nutrition. As a group, they have tremendous economic importance. The antibiotic market amounts to almost 30 billion dollars and includes about 160 antibiotics and derivatives such as the beta-lactam peptide antibiotics, the macrolide polyketide erythromycin, tetracyclines, aminoglycosides and others. Other important pharmaceutical products produced by microrganisms are hypocholesterolemic agents, enzyme inhibitors, immunosuppressants and antitumor compounds, some having markets of over 1 billion dollars per year. Agriculturally important secondary metabolites include coccidiostats, animal growth promotants, antihelmintics and biopesticides. The modern biotechnology industry has made a major impact in the business world, biopharmaceuticals (recombinant protein drugs, vaccines and monoclonal antibodies) having a market of 15 billion dollars. Recombinant DNA technology has also produced a revolution in agriculture and has markedly increased markets for microbial enzymes. Molecular manipulations have been added to mutational techniques as means of increasing titers and yields of microbial procresses and in discovery of new drugs. Today, microbiology is a major participant in global industry. The best is yet to come as microbes move into the environmental and energy sectors.

  8. Manufacturing process used to produce long-acting recombinant factor VIII Fc fusion protein.

    Science.gov (United States)

    McCue, Justin; Kshirsagar, Rashmi; Selvitelli, Keith; Lu, Qi; Zhang, Mingxuan; Mei, Baisong; Peters, Robert; Pierce, Glenn F; Dumont, Jennifer; Raso, Stephen; Reichert, Heidi

    2015-07-01

    Recombinant factor VIII Fc fusion protein (rFVIIIFc) is a long-acting coagulation factor approved for the treatment of hemophilia A. Here, the rFVIIIFc manufacturing process and results of studies evaluating product quality and the capacity of the process to remove potential impurities and viruses are described. This manufacturing process utilized readily transferable and scalable unit operations and employed multi-step purification and viral clearance processing, including a novel affinity chromatography adsorbent and a 15 nm pore size virus removal nanofilter. A cell line derived from human embryonic kidney (HEK) 293H cells was used to produce rFVIIIFc. Validation studies evaluated identity, purity, activity, and safety. Process-related impurity clearance and viral clearance spiking studies demonstrate robust and reproducible removal of impurities and viruses, with total viral clearance >8-15 log10 for four model viruses (xenotropic murine leukemia virus, mice minute virus, reovirus type 3, and suid herpes virus 1). Terminal galactose-α-1,3-galactose and N-glycolylneuraminic acid, two non-human glycans, were undetectable in rFVIIIFc. Biochemical and in vitro biological analyses confirmed the purity, activity, and consistency of rFVIIIFc. In conclusion, this manufacturing process produces a highly pure product free of viruses, impurities, and non-human glycan structures, with scale capabilities to ensure a consistent and adequate supply of rFVIIIFc. Copyright © 2015 Biogen. Published by Elsevier Ltd.. All rights reserved.

  9. 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...

  10. 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.

  11. Cortical spreading depression produces a neuroprotective effect activating mitochondrial uncoupling protein-5

    Directory of Open Access Journals (Sweden)

    Viggiano E

    2016-07-01

    Full Text Available Emanuela Viggiano,1,2 Vincenzo Monda,1 Antonietta Messina,1 Fiorenzo Moscatelli,3 Anna Valenzano,3 Domenico Tafuri,4 Giuseppe Cibelli,3 Bruno De Luca,1 Giovanni Messina,1,3 Marcellino Monda1 1Department of Experimental Medicine, Section of Human Physiology and Unit of Dietetics and Sports Medicine, Second University of Naples, Naples, 2Department of Medicine, University of Padua, Padua, 3Department of Clinical and Experimental Medicine, University of Foggia, Foggia, 4Department of Motor Sciences and Wellness, University of Naples “Parthenope”, Naples, Italy Abstract: Depression of electrocorticogram propagating over the cortex surface results in cortical spreading depression (CSD, which is probably related to the pathophysiology of stroke, epilepsy, and migraine. However, preconditioning with CSD produces neuroprotection to subsequent ischemic episodes. Such effects require the expression or activation of several genes, including neuroprotective ones. Recently, it has been demonstrated that the expression of the uncoupling proteins (UCPs 2 and 5 is amplified during brain ischemia and their expression exerts a long-term effect upon neuron protection. To evaluate the neuroprotective consequence of CSD, the expression of UCP-5 in the brain cortex was measured following CSD induction. CSD was evoked in four samples of rats, which were sacrificed after 2 hours, 4 hours, 6 hours, and 24 hours. Western blot analyses were carried out to measure UCP-5 concentrations in the prefrontal cortices of both hemispheres, and immunohistochemistry was performed to determine the localization of UCP-5 in the brain cortex. The results showed a significant elevation in UCP-5 expression at 24 hours in all cortical strata. Moreover, UCP-5 was triggered by CSD, indicating that UCP-5 production can have a neuroprotective effect. Keywords: cortical spreading depression, neuroprotective effect, uncoupling protein-5

  12. Effects of insecticidal crystal proteins (Cry proteins) produced by genetically modified maize (Bt maize) on the nematode Caenorhabditis elegans

    International Nuclear Information System (INIS)

    Höss, Sebastian; Menzel, Ralph; Gessler, Frank; Nguyen, Hang T.; Jehle, Johannes A.; Traunspurger, Walter

    2013-01-01

    The genetically modified maize MON89034 × MON88017 expresses different crystal (Cry) proteins with pesticidal activity against the European corn borer (Cry1.105; Cry2Ab2) and the Western corn root worm (Cry3Bb1). Non-target organisms, such as soil nematodes, might be exposed to the Cry proteins that enter the soil in course of crop growing. Therefore, the risk of those proteins for nematodes was assessed by testing their toxic effects on Caenorhabditis elegans. All three insecticidal Cry proteins showed dose-dependent inhibitory effects on C. elegans reproduction (EC50: 0.12–0.38 μmol L −1 ), however, at concentrations that were far above the expected soil concentrations. Moreover, a reduced toxicity was observed when Cry proteins were added jointly. A C. elegans mutant strain deficient for receptors for the nematicidal Cry5B was also resistant against Cry1.105 and Cry2Ab2, suggesting that these Cry proteins bound to the same or similar receptors as nematicidal Cry proteins and thereby affect the reproduction of C. elegans. -- Highlights: •Insecticidal Cry proteins dose-dependently inhibited the reproduction of C. elegans. •Mixture toxicity was lower than expected from concentration-additive single effects. •Genes for MAPK-defense-pathway were up-regulated in presence of Cry protein mixture. •Knock-out strains deficient for Cry5B-receptors showed lower susceptibility to insecticidal Cry proteins. •Toxicity of insecticidal Cry-proteins on C. elegans occurred at concentrations far above expected field concentrations. -- Insecticidal Cry proteins expressed by genetically modified maize act on nematodes via a similar mode of action as nematicidal Cry proteins, however, at concentrations far above expected soil levels

  13. 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.

  14. 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.

  15. Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence

    Directory of Open Access Journals (Sweden)

    Kim Dong Seon

    2012-11-01

    Full Text Available Abstract Background Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to protein products. Here, we analyzed annotated human protein-coding exons and identified human-specific splice sites that arose after the human-chimpanzee divergence. Results We analyzed multiple alignments of the annotated human protein-coding exons and their respective orthologous mammalian genome sequences to identify 85 novel splice sites (50 splice acceptors and 35 donors in the human genome. The novel protein-coding exons, which are expressed either constitutively or alternatively, produce novel protein isoforms by insertion, deletion, or frameshift. We found three cases in which the human-specific isoform conferred novel molecular function in the human cells: the human-specific IMUP protein isoform induces apoptosis of the trophoblast and is implicated in pre-eclampsia; the intronization of a part of SMOX gene exon produces inactive spermine oxidase; the human-specific NUB1 isoform shows reduced interaction with ubiquitin-like proteins, possibly affecting ubiquitin pathways. Conclusions Although the generation of novel protein isoforms does not equate to adaptive evolution, we propose that these cases are useful candidates for a molecular functional study to identify proteomic changes that might bring about novel phenotypes during human evolution.

  16. 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.

  17. 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.

  18. Characterization of pro-inflammatory flagellin proteins produced by Lactobacillus ruminis and related motile Lactobacilli.

    Directory of Open Access Journals (Sweden)

    B Anne Neville

    Full Text Available Lactobacillus ruminis is one of at least twelve motile but poorly characterized species found in the genus Lactobacillus. Of these, only L. ruminis has been isolated from mammals, and this species may be considered as an autochthonous member of the gastrointestinal microbiota of humans, pigs and cows. Nine L. ruminis strains were investigated here to elucidate the biochemistry and genetics of Lactobacillus motility. Six strains isolated from humans were non-motile while three bovine isolates were motile. A complete set of flagellum biogenesis genes was annotated in the sequenced genomes of two strains, ATCC25644 (human isolate and ATCC27782 (bovine isolate, but only the latter strain produced flagella. Comparison of the L. ruminis and L. mali DSM20444(T motility loci showed that their genetic content and gene-order were broadly similar, although the L. mali motility locus was interrupted by an 11.8 Kb region encoding rhamnose utilization genes that is absent from the L. ruminis motility locus. Phylogenetic analysis of 39 motile bacteria indicated that Lactobacillus motility genes were most closely related to those of motile carnobacteria and enterococci. Transcriptome analysis revealed that motility genes were transcribed at a significantly higher level in motile L. ruminis ATCC27782 than in non-motile ATCC25644. Flagellin proteins were isolated from L. ruminis ATCC27782 and from three other Lactobacillus species, while recombinant flagellin of aflagellate L. ruminis ATCC25644 was expressed and purified from E. coli. These native and recombinant Lactobacillus flagellins, and also flagellate L. ruminis cells, triggered interleukin-8 production in cultured human intestinal epithelial cells in a manner suppressed by short interfering RNA directed against Toll-Like Receptor 5. This study provides genetic, transcriptomic, phylogenetic and immunological insights into the trait of flagellum-mediated motility in the lactobacilli.

  19. Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment.

    Directory of Open Access Journals (Sweden)

    David F Gruber

    Full Text Available We report the identification and characterization of two new members of a family of bilirubin-inducible fluorescent proteins (FPs from marine chlopsid eels and demonstrate a key region of the sequence that serves as an evolutionary switch from non-fluorescent to fluorescent fatty acid-binding proteins (FABPs. Using transcriptomic analysis of two species of brightly fluorescent Kaupichthys eels (Kaupichthys hyoproroides and Kaupichthys n. sp., two new FPs were identified, cloned and characterized (Chlopsid FP I and Chlopsid FP II. We then performed phylogenetic analysis on 210 FABPs, spanning 16 vertebrate orders, and including 163 vertebrate taxa. We show that the fluorescent FPs diverged as a protein family and are the sister group to brain FABPs. Our results indicate that the evolution of this family involved at least three gene duplication events. We show that fluorescent FABPs possess a unique, conserved tripeptide Gly-Pro-Pro sequence motif, which is not found in non-fluorescent fatty acid binding proteins. This motif arose from a duplication event of the FABP brain isoforms and was under strong purifying selection, leading to the classification of this new FP family. Residues adjacent to the motif are under strong positive selection, suggesting a further refinement of the eel protein's fluorescent properties. We present a phylogenetic reconstruction of this emerging FP family and describe additional fluorescent FABP members from groups of distantly related eels. The elucidation of this class of fish FPs with diverse properties provides new templates for the development of protein-based fluorescent tools. The evolutionary adaptation from fatty acid-binding proteins to fluorescent fatty acid-binding proteins raises intrigue as to the functional role of bright green fluorescence in this cryptic genus of reclusive eels that inhabit a blue, nearly monochromatic, marine environment.

  20. Erabulenols, inhibitors of cholesteryl ester transfer protein produced by Penicillium sp. FO-5637. I.Production, isolation and biological properties.

    Science.gov (United States)

    Tomoda, H; Tabata, N; Masuma, R; Si, S Y; Omura, S

    1998-07-01

    Penicillium sp. FO-5637, a soil isolate, was found to produce a series of inhibitors of cholesteryl ester transfer protein (CETP). Novel active compounds, designated erabulenols A and B, were isolated from the fermentation broth of the producing strain by solvent extraction, ODS column chromatography and HPLC. Erabulenols A and B inhibit human CETP activity with IC50 values of 47.7 and 58.2 microM in an in vitro assay system containing 200 microM BSA, respectively.

  1. Physicochemical composition and glycemic index of whole grain bread produced from composite flours of quality protein maize and wheat

    Directory of Open Access Journals (Sweden)

    C. T. Akanbi

    2016-01-01

    Full Text Available This study entails quality assessment of whole grain bread produced from composite flours of quality protein maize and wheat. Quality protein maize and wheat were processed into flours and mixed at various ratios for bread production. The proximate compositions, physical properties, glycemic response, functional and sensory properties of the samples were evaluated using standard methods. The result showed no significant difference (p<0.05 in the proximate composition parameters of the bread samples. The loaf height (2.50 - 3.95 cm, volume (291.00 - 415.00 cm3 and specific volume(1.72 - 2.42 cm3/g decreased significantly with increasing level of quality protein maize, however, loaf length was not affected by the substitution of quality protein maize. The result of the functional properties showed that final viscosity, water absorption and swelling capacity increased with increasing level of quality protein maize. The result of the glycemic response showed that the inclusion of quality protein maize resulted in decline in the blood glucose content (glycemic index of the products. The bread samples were generally acceptable however; bread with 100% wheat was the most preferred. The result of the sensory properties showed that there was significant difference (p<0.05 in the texture and taste of 100% wheat bread and the other samples. The study concluded that substitution of quality protein maize with wheat produced acceptable whole grain loaves that have positive effect on the reduction of blood glucose level.

  2. Microbial proteins produced from cannery wastes. II. Different cellulosic wastes used as substrate

    Energy Technology Data Exchange (ETDEWEB)

    Lee, H.C.; Chen, S.H.; Chang, J.S.; Lee, S.C.

    1980-01-01

    The production of protein by the cultivation of Cellulomonas species 34 on cellulosic wastes was studied. Maximum protein production on bamboo shoot husks was 4.77 g/L in 48 h when aeration was 1 vol./min, stirring rate was 1000 rpm, and substrate concentration was 3%. The chemical compounds of asparagus peel and pineapple peel and the conditions for their treatment with NaOH for protein fermentation are given.

  3. Lactobacillus casei BL23 Produces Microvesicles Carrying Proteins That Have Been Associated with Its Probiotic Effect

    Directory of Open Access Journals (Sweden)

    A. Paula Domínguez Rubio

    2017-09-01

    Full Text Available Archaea, bacteria, and eukarya secrete membrane microvesicles (MVs as a mechanism for intercellular communication. We report the isolation and characterization of MVs from the probiotic strain Lactobacillus casei BL23. MVs were characterized using analytical high performance techniques, DLS, AFM and TEM. Similar to what has been described for other Gram-positive bacteria, MVs were on the nanometric size range (30–50 nm. MVs carried cytoplasmic components such as DNA, RNA and proteins. Using a proteomic approach (LC-MS, we identified a total of 103 proteins; 13 exclusively present in the MVs. The MVs content included cell envelope associated and secretory proteins, heat and cold shock proteins, several metabolic enzymes, proteases, structural components of the ribosome, membrane transporters, cell wall-associated hydrolases and phage related proteins. In particular, we identified proteins described as mediators of Lactobacillus’ probiotic effects such as p40, p75 and the product of LCABL_31160, annotated as an adhesion protein. The presence of these proteins suggests a role for the MVs in the bacteria-gastrointestinal cells interface. The expression and further encapsulation of proteins into MVs of GRAS (Generally Recognized as Safe bacteria could represent a scientific novelty, with applications in food, nutraceuticals and clinical therapies.

  4. Statins inhibit protein lipidation and induce the unfolded protein response in the non-sterol producing nematode Caenorhabditis elegans

    DEFF Research Database (Denmark)

    Mörck, Catarina; Elmelund-Præstekær, Louise Cathrine Braun; Kurth, Caroline

    2009-01-01

    of lipid moieties for protein prenylation. The nematode Caenorhabditis elegans possesses a mevalonate pathway that lacks the branch leading to cholesterol synthesis, and thus represents an ideal organism to specifically study the noncholesterol roles of the pathway. Inhibiting HMG-CoA reductase in C....... elegans using statins or RNAi leads to developmental arrest and loss of membrane association of a GFP-based prenylation reporter. The unfolded protein response (UPR) is also strongly activated, suggesting that impaired prenylation of small GTPases leads to the accumulation of unfolded proteins and ER...... and fatty acid composition were unaffected in statin-treated worms, even though they showed reduced staining with Nile red. We conclude that inhibitors of HMG-CoA reductase or of farnesyl transferases induce the UPR by inhibiting the prenylation of M57.2 substrates, resulting in developmental arrest in C...

  5. Exploiting translational coupling for the selection of cells producing toxic recombinant proteins from expression vectors.

    Science.gov (United States)

    Tagliavia, Marcello; Cuttitta, Angela

    2016-01-01

    High rates of plasmid instability are associated with the use of some expression vectors in Escherichia coli, resulting in the loss of recombinant protein expression. This is due to sequence alterations in vector promoter elements caused by the background expression of the cloned gene, which leads to the selection of fast-growing, plasmid-containing cells that do not express the target protein. This phenomenon, which is worsened when expressing toxic proteins, results in preparations containing very little or no recombinant protein, or even in clone loss; however, no methods to prevent loss of recombinant protein expression are currently available. We have exploited the phenomenon of translational coupling, a mechanism of prokaryotic gene expression regulation, in order to select cells containing plasmids still able to express recombinant proteins. Here we designed an expression vector in which the cloned gene and selection marker are co-expressed. Our approach allowed for the selection of the recombinant protein-expressing cells and proved effective even for clones encoding toxic proteins.

  6. Main Strategies of Plant Expression System Glycoengineering for Producing Humanized Recombinant Pharmaceutical Proteins.

    Science.gov (United States)

    Rozov, S M; Permyakova, N V; Deineko, E V

    2018-03-01

    Most the pharmaceutical proteins are derived not from their natural sources, rather their recombinant analogs are synthesized in various expression systems. Plant expression systems, unlike mammalian cell cultures, combine simplicity and low cost of procaryotic systems and the ability for posttranslational modifications inherent in eucaryotes. More than 50% of all human proteins and more than 40% of the currently used pharmaceutical proteins are glycosylated, that is, they are glycoproteins, and their biological activity, pharmacodynamics, and immunogenicity depend on the correct glycosylation pattern. This review examines in detail the similarities and differences between N- and O-glycosylation in plant and mammalian cells, as well as the effect of plant glycans on the activity, pharmacokinetics, immunity, and intensity of biosynthesis of pharmaceutical proteins. The main current strategies of glycoengineering of plant expression systems aimed at obtaining fully humanized proteins for pharmaceutical application are summarized.

  7. Ascorbic acid glycation of lens proteins produces UVA sensitizers similar to those in human lens

    International Nuclear Information System (INIS)

    Ortwerth, B.J.; Linetsky, Mikhail; Olesen, P.R.

    1995-01-01

    Soluble calf lens proteins were extensively glycated during a 4 week incubation with ascorbic acid in the presence of oxygen. Amino acids analysis of the dialyzed proteins removed at weekly intervals showed an increasing loss of lysine, arginine and histidine, consistent with the extensive protein cross-linking observed. Irradiation of the dialyzed samples with UVA light (1.0 kJ/cm 2 total illumination through a 338 nm cutoff filter) caused an increasing loss of tryptophan, an additional loss of histidine and the production of micromolar concentrations of hydrogen peroxide. No alteration in amino acid content and no photolytic effects were seen in proteins incubated without ascorbic acid in proteins incubated with glucose for 4 weeks. The rate of hydrogen peroxide formation was linear with each glycated sample with a maximum production of 25 nmol/mg protein illuminated. The possibility that the sensitizer activity was due to an ascorbate-induced oxidation of tryptophan was eliminated by the presence of a heavy metal ion chelator during the incubation and by showing equivalent effects with ascorbate-incubated ribonuclease A, which is devoid of tryptophan. The ascorbate-incubated samples displayed increasing absorbance at wavelengths above 300 nm and increasing fluorescence (340/430) as glycation proceeded. The spectra of the 4 week glycated proteins were identical to those obtained with a solubilized water-insoluble fraction from human lens, which is known to have UVA sensitizer activity. (Author)

  8. Intracellular proteins produced by mammalian cells in response to environmental stress

    Science.gov (United States)

    Goochee, Charles F.; Passini, Cheryl A.

    1988-01-01

    The nature of the response of mammalian cells to environmental stress is examined by reviewing results of studies where cultured mouse L cells and baby hamster kidney cells were exposed to heat shock and the synthesis of heat-shock proteins and stress-response proteins (including HSP70, HSC70, HSP90, ubiquitin, and GRP70) in stressed and unstressed cells was evaluated using 2D-PAGE. The intracellular roles of the individual stress response proteins are discussed together with the regulation of the stress response system.

  9. 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

  10. Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays.

    Science.gov (United States)

    Hager, Roland; Burns, Jonathan R; Grydlik, Martyna J; Halilovic, Alma; Haselgrübler, Thomas; Schäffler, Friedrich; Howorka, Stefan

    2016-06-01

    The biofunctionalization of nanopatterned surfaces with DNA origami nanostructures is an important topic in nanobiotechnology. An unexplored challenge is, however, to co-immobilize proteins with DNA origami at pre-determined substrate sites in high contrast relative to the nontarget areas. The immobilization should, in addition, preferably be achieved on a transparent substrate to allow ultrasensitive optical detection. If successful, specific co-binding would be a step towards stoichiometrically defined arrays with few to individual protein molecules per site. Here, we successfully immobilize with high specificity positively charged avidin proteins and negatively charged DNA origami nanoplates on 100 nm-wide carbon nanoislands while suppressing undesired adsorption to surrounding nontarget areas. The arrays on glass slides achieve unprecedented selectivity factors of up to 4000 and allow ultrasensitive fluorescence read-out. The co-immobilization onto the nanoislands leads to layered biomolecular architectures, which are functional because bound DNA origami influences the number of capturing sites on the nanopatches for other proteins. The novel hybrid DNA origami-protein nanoarrays allow the fabrication of versatile research platforms for applications in biosensing, biophysics, and cell biology, and, in addition, represent an important step towards single-molecule protein arrays. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Serum from Nipah Virus Patients Recognises Recombinant Viral Proteins Produced in Escherichia coli.

    Science.gov (United States)

    Tiong, Vunjia; Lam, Chui-Wan; Phoon, Wai-Hong; AbuBakar, Sazaly; Chang, Li-Yen

    2017-01-24

    The genes for Nipah virus (NiV) proteins were amplified from viral RNA, cloned into the plasmid pTriEx-3 Hygro, expressed, and purified using immobilized metal affinity chromatography. The recombinant N, F, and G NiV proteins (rNiV-N, rNiV-F, and rNiV-G), were successfully expressed in Escherichia coli and purified with a yield of 4, 16, and 4 mg/L, respectively. All 3 recombinant viral proteins reacted with all 19 samples of NiV-positive human sera. The rNiV-N and rNiV-G proteins were the most immunogenic. The recombinant viral proteins did not react with any of the 12 NiV-negative sera. However, serum from a patient with a late-onset relapsing NiV infection complication was found to be primarily reactive to rNiV-G only. Additionally, there is a distinctive variation in the profile of antigen-reactive bands between the sample from a case of relapsing NiV encephalitis and that of acute NiV infection. The overall findings of this study suggest that the recombinant viral proteins have the potential to be developed further for use in the detection of NiV infection, and continuous biosurveillance of NiV infection in resource-limited settings.

  12. Use of γ-irradiation to produce films from whey, casein and soya proteins: structure and functionals characteristics

    International Nuclear Information System (INIS)

    Lacroix, M.; Le, T.C.; Ouattara, B.; Yu, H.; Letendre, M.; Sabato, S.F.; Mateescu, M.A.; Patterson, G.

    2002-01-01

    γ-irradiation and thermal treatments have been used to produce sterilized cross-linked films. Formulations containing variable concentrations of calcium caseinate and whey proteins (whey protein isolate (WPI) and commercial whey protein concentrate) or mixture of soya protein isolate (SPI) with WPI was investigated on the physico-chemical properties of these films. Results showed that the mechanical properties of cross-linked films improved significantly the puncture strength for all types of films. Size-exclusion chromatography showed for no cross-linked proteins, a molecular mass of around 40 kDa. The soluble fractions of the cross-linked proteins molecular distributions were between 600 and 3800 kDa. γ-irradiation seems to modify to a certain extent the conformation of proteins which will adopt structures more ordered and more stable, as suggested by X-ray diffraction analysis. Microstructure observations showed that the mechanical characteristics of these films are closely related to their microscopic structure. Water vapor permeability of films based on SPI was also significantly decreased when irradiated. Microbial resistance was also evaluated for cross-linked films. Results showed that the level of biodegradation of cross-linked films was 36% after 60 d of fermentation in the presence of Pseudomonas aeruginosa

  13. Use of {gamma}-irradiation to produce films from whey, casein and soya proteins: structure and functionals characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Lacroix, M. E-mail: monique.lacroix@inrs-iaf.uquebec.ca; Le, T.C.; Ouattara, B.; Yu, H.; Letendre, M.; Sabato, S.F.; Mateescu, M.A.; Patterson, G

    2002-03-01

    {gamma}-irradiation and thermal treatments have been used to produce sterilized cross-linked films. Formulations containing variable concentrations of calcium caseinate and whey proteins (whey protein isolate (WPI) and commercial whey protein concentrate) or mixture of soya protein isolate (SPI) with WPI was investigated on the physico-chemical properties of these films. Results showed that the mechanical properties of cross-linked films improved significantly the puncture strength for all types of films. Size-exclusion chromatography showed for no cross-linked proteins, a molecular mass of around 40 kDa. The soluble fractions of the cross-linked proteins molecular distributions were between 600 and 3800 kDa. {gamma}-irradiation seems to modify to a certain extent the conformation of proteins which will adopt structures more ordered and more stable, as suggested by X-ray diffraction analysis. Microstructure observations showed that the mechanical characteristics of these films are closely related to their microscopic structure. Water vapor permeability of films based on SPI was also significantly decreased when irradiated. Microbial resistance was also evaluated for cross-linked films. Results showed that the level of biodegradation of cross-linked films was 36% after 60 d of fermentation in the presence of Pseudomonas aeruginosa.

  14. Acidogenic fermentation characteristics of different types of protein-rich substrates in food waste to produce volatile fatty acids.

    Science.gov (United States)

    Shen, Dongsheng; Yin, Jun; Yu, Xiaoqin; Wang, Meizhen; Long, Yuyang; Shentu, Jiali; Chen, Ting

    2017-03-01

    In this study, tofu and egg white, representing typical protein-rich substrates in food waste based on vegetable and animal protein, respectively, were investigated for producing volatile fatty acids (VFAs) by acidogenic fermentation. VFA production, composition, conversion pathways and microbial communities in acidogenesis from tofu and egg white with and without hydrothermal (HT) pretreatment were compared. The results showed HT pretreatment could improve the VFA production of tofu but not for egg white. The optimum VFA yields were 0.46g/gVS (tofu with HT) and 0.26g/gVS (egg white without HT), respectively. Tofu could directly produce VFAs through the Stickland reaction, while egg white was converted to lactate and VFAs simultaneously. About 30-40% of total protein remained in all groups after fermentation. Up to 50% of the unconverted soluble protein in the HT groups was protease. More lactate-producing bacteria, mainly Leuconostoc and Lactobacillus, were present during egg white fermentation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Biostimulant action of a plant-derived protein hydrolysate produced through enzymatic hydrolysis

    Directory of Open Access Journals (Sweden)

    Giuseppe eColla

    2014-09-01

    Full Text Available The aim of this study was to evaluate the biostimulant action (hormone like activity, nitrogen uptake, and growth stimulation of a plant-derived protein hydrolysate by means of two laboratory bioassays: a corn (Zea mays L. coleoptile elongation rate test (experiment 1, a rooting test on tomato cuttings (experiment 2; and two greenhouse experiments: a dwarf pea (Pisum sativum L. growth test (experiment 3, and a tomato (Solanum lycopersicum L. nitrogen uptake trial (experiment 4. Protein hydrolysate treatments of corn caused an increase in coleoptile elongation rate when compared to the control, in a dose-dependent fashion, with no significant differences between the four concentrations tested (0.375, 0.75, 1.5, and 3.0 ml/L, and inodole-3-acetic acid (IAA treatment. The auxin-like effect of the protein hydrolysate on corn has been also observed in the rooting experiment of tomato cuttings. The shoot, root dry weight, root length, and root area were significantly higher by 21%, 35%, 24%, and 26%, respectively in tomato treated plants with the protein hydrolysate at 6 ml/L than untreated plants. In experiment 3, the application of the protein hydrolysate at all doses (0.375, 0.75, 1.5, and 3.0 ml/L significantly increased the shoot length of the giberellin (GA-deficient dwarf pea plants by an average value of 33% in comparison with the control treatment. Increasing the concentration of the protein hydrolysate from 0 to 10 ml/L increased the total dry biomass, SPAD index, and leaf nitrogen content by 20.5%, 15% and 21.5%, respectively. Thus the application of plant-derived protein hydrolysate containing amino acids and small peptides elicited a hormone-like activity, enhanced nitrogen uptake and consequently crop performances.

  16. Structural and functional features of self-assembling protein nanoparticles produced in endotoxin-free Escherichia coli.

    Science.gov (United States)

    Rueda, Fabián; Céspedes, María Virtudes; Sánchez-Chardi, Alejandro; Seras-Franzoso, Joaquin; Pesarrodona, Mireia; Ferrer-Miralles, Neus; Vázquez, Esther; Rinas, Ursula; Unzueta, Ugutz; Mamat, Uwe; Mangues, Ramón; García-Fruitós, Elena; Villaverde, Antonio

    2016-04-08

    Production of recombinant drugs in process-friendly endotoxin-free bacterial factories targets to a lessened complexity of the purification process combined with minimized biological hazards during product application. The development of nanostructured recombinant materials in innovative nanomedical activities expands such a need beyond plain functional polypeptides to complex protein assemblies. While Escherichia coli has been recently modified for the production of endotoxin-free proteins, no data has been so far recorded regarding how the system performs in the fabrication of smart nanostructured materials. We have here explored the nanoarchitecture and in vitro and in vivo functionalities of CXCR4-targeted, self-assembling protein nanoparticles intended for intracellular delivery of drugs and imaging agents in colorectal cancer. Interestingly, endotoxin-free materials exhibit a distinguishable architecture and altered size and target cell penetrability than counterparts produced in conventional E. coli strains. These variant nanoparticles show an eventual proper biodistribution and highly specific and exclusive accumulation in tumor upon administration in colorectal cancer mice models, indicating a convenient display and function of the tumor homing peptides and high particle stability under physiological conditions. The observations made here support the emerging endotoxin-free E. coli system as a robust protein material producer but are also indicative of a particular conformational status and organization of either building blocks or oligomers. This appears to be promoted by multifactorial stress-inducing conditions upon engineering of the E. coli cell envelope, which impacts on the protein quality control of the cell factory.

  17. Efficacy of locally produced papain enzyme for the production of protein bait for bactrocera invadens (diptera: tephritidae) control in Ghana

    International Nuclear Information System (INIS)

    Aggrey-Korsah, R.

    2014-07-01

    Autolysed brewery yeast waste is currently being used as cost effective protein bait for Bactrocera invadens control the world over to replace commercial protein hydrolysate bait formulations. However, significant reduction in production cost can be achieved when all the production materials are from local sources. This experiment was aimed at assessing the efficacy of locally produced papain extracted from 'Red lady' pawpaw fruit latex and skin peel to be used for protein bait production. Aqueous two-phase extraction of papain from pawpaw fruit latex with 15 % (NH 4 ) 2 SO 4 - 8 % PEG recovered 64.72 ± 2.08 % papain into the supernatant with 7.33 % proteolytic activity yield and a fold purification of 58.11 ± 1.67. Proteolytic activity and protein concentration measured for the aqueous two-phase extracts of pawpaw skin peel were significantly higher (p= 0.00) than crude extracts of skin peel. However, the aqueous two phase extraction of papain from skin peel needs to be optimised further since SDS-PAGE showed no visible bands in the different phase extracts. Gamma irradiation at 10 KGy increased the proteolytic activity of crude papain by 21.69 % of the non-irradiated papain and subsequently increased the specific activity by 18.51 % but the protein concentration was not affected. Protein baits prepared with crude papain extracted from the pawpaw fruit latex and skin peels were evaluated in laboratory bioassays with wild flies reared from field collected infested mangoes. The source of papain did not affect the protein bait recovery, the pH and protein concentration though colour of bait differed for crude fruit latex papain bait (dark brown) and skin peel papain bait (light brown). The bait preparations had equal attractance to male and female B. invadens. Mean attractance to protein baits produced with fruit latex and skin peel papain baits were between 25.00 ± 7.56 % and 47.50 ± 11.09 % respectively for males, 25.00 ± 13.13 % and 32.86 ± 8

  18. Role of foam drainage in producing protein aggregates in foam fractionation.

    Science.gov (United States)

    Li, Rui; Zhang, Yuran; Chang, Yunkang; Wu, Zhaoliang; Wang, Yanji; Chen, Xiang'e; Wang, Tao

    2017-10-01

    It is essential to obtain a clear understanding of the foam-induced protein aggregation to reduce the loss of protein functionality in foam fractionation. The major effort of this work is to explore the roles of foam drainage in protein aggregation in the entire process of foam fractionation with bovine serum albumin (BSA) as a model protein. The results show that enhancing foam drainage increased the desorption of BSA molecules from the gas-liquid interface and the local concentration of desorbed molecules in foam. Therefore, it intensified the aggregation of BSA in foam fractionation. Simultaneously, it also accelerated the flow of BSA aggregates from rising foam into the residual solution along with the drained liquid. Because enhancing foam drainage increased the relative content of BSA molecules adsorbed at the gas-liquid interface, it also intensified the aggregation of BSA during both the defoaming process and the storage of the foamate. Furthermore, enhancing foam drainage more readily resulted in the formation of insoluble BSA aggregates. The results are highly important for a better understanding of foam-induced protein aggregation in foam fractionation. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. 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.

  20. Growh performance, nitrogen balance and urinary purine derivatives in growing-furring mink (Mustela vison) fed bacterial protein produced from natural gas

    DEFF Research Database (Denmark)

    Ahlstrøm, Ø.; Tauson, Anne-Helene; Hellwing, Anne Louise Frydendahl

    2006-01-01

    A bacterial protein meal (BPM), containing 70% crude protein and produced on natural gas, was evaluated versus fish meal as protein source for mink in the growing-furring period (June 29-November 26). BPM, rich in nucleic acids, accounted for 0 (control), 20 and 40% of dietary crude protein...

  1. Combining protein extraction and anaerobic digestion to produce feed, fuel and fertilizer from green biomass – An organic biorefinery concept

    DEFF Research Database (Denmark)

    Fernandez, Maria Santamaria; Salces, Beatriz Molinuevo; Lübeck, Mette

    Organically grown green biomass (red clover, clover grass) was investigated as a resource for organic feed and organic fertilizer by combination of proteins extraction and anaerobic digestion of the residues. Extraction of proteins from both crops revealed very favourable amino acid composition...... for the use as animal feed. The residual 90% of organic matter, leaving the separation as solid press cake and brown juice was subjected to anaerobic digestion to produce biogas and fertilizer. Methane yields of 220-310 and 430-540 ml CH4/g VS were obtained for press cake and brown juice, respectively...

  2. 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...

  3. 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...

  4. 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

  5. Ultra-Thin Optically Transparent Carbon Electrodes Produced from Layers of Adsorbed Proteins

    Science.gov (United States)

    Alharthi, Sarah A.; Benavidez, Tomas E.; Garcia, Carlos D.

    2013-01-01

    This work describes a simple, versatile, and inexpensive procedure to prepare optically transparent carbon electrodes, using proteins as precursors. Upon adsorption, the protein-coated substrates were pyrolyzed under reductive conditions (5% H2) to form ultra-thin, conductive electrodes. Because proteins spontaneously adsorb to interfaces forming uniform layers, the proposed method does not require a precise control of the preparation conditions, specialized instrumentation, or expensive precursors. The resulting electrodes were characterized by a combination of electrochemical, optical, and spectroscopic means. As a proof-of-concept, the optically-transparent electrodes were also used as substrate for the development of an electrochemical glucose biosensor. The proposed films represent a convenient alternative to more sophisticated, and less available, carbon-based nanomaterials. Furthermore, these films could be formed on a variety of substrates, without classical limitations of size or shape. PMID:23421732

  6. 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.

  7. 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 ...

  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. Protein-free transfection of CHO host cells with an IgG-fusion protein: selection and characterization of stable high producers and comparison to conventionally transfected clones.

    Science.gov (United States)

    Lattenmayer, Christine; Loeschel, Martina; Schriebl, Kornelia; Steinfellner, Willibald; Sterovsky, Thomas; Trummer, Evelyn; Vorauer-Uhl, Karola; Müller, Dethardt; Katinger, Hermann; Kunert, Renate

    2007-04-15

    In order to improve the current techniques of cell cultivation in the absence of serum, we have developed a protein-free transfection protocol for CHO cells, based on the Nucleofector technology. After starting with a heterogeneous pool of primary transfectants which express the fusion protein EpoFc, we isolated single clones and compared them with parallel clones generated by lipofection in serum-dependent cultivation. Our intensive characterization program was based on determination of specific productivity (q(p)) and analysis of genetic parameters. In two nucleofection experiments, transfection with 5 microg of DNA resulted in best productivities of the primary cell pools. After subcloning, the q(p) could be raised up to 27 pg x cells(-1) x day(-1). While the serum-dependent transfectants exhibited specific productivities up to 57 pg x cells(-1) x day(-1) in serum-dependent cultivation, a significant decrease that resulted in the range of q(p) of the protein-free transfectants was observed after switching to protein-free conditions. Investigation of genetic parameters revealed higher mRNA levels and gene copy numbers (GCN) for the protein-free adapted serum-dependent transfectants. Therefore, we assume that problems during protein-free adaptation (PFA) lead to a less efficient translation machinery after serum deprivation. We describe the generation of stable-producing recombinant CHO clones by protein-free transfection of a protein-free adapted host cell line, which reduces the risk of adverse clonal changes after PFA. The main advantage of this approach is the earlier predictability of clone behavior, which makes the generation of production clones by protein-free transfection, a viable and highly efficient strategy for recombinant cell line development. (c) 2006 Wiley Periodicals, Inc.

  11. Lipoxygenase activity of soybean and protein evaluation of soy milk produced from irradiated grains

    International Nuclear Information System (INIS)

    Barros, Erica A.; Broetto, Fernando; Costa, Vladimir E.

    2011-01-01

    Soybean and its derivative are considered as a functional food because it has high quality protein and are used for the prevention of chronic degenerative diseases. The irradiation technique is used in soybeans to increase shelf life and avoid problems in plant products consumed raw or processed. However, the controversy in the literature that the irradiation dose up 10 kGy food can alter the functional properties and structures of macronutrients. With the prospect of more information on the use of radiation on soybeans, the objective of this study was to determine the activity of lipoxygenase in soybeans and to evaluate possible changes in the protein content of soymilk processed from grain-BRS 213, BRS 258 and Embrapa 48 subjected to dosages of 2.5 , 5.0 and 10.0 kGy of gamma radiation. The soybean cultivars were wrapped in plastic bags and subjected to gamma radiation source 60 Co, Gammacell 220 (Atomic Energy of Canada Ltd.), except the control. The grains irradiated induced reduction of enzyme activity. The results for the protein content of soymilk were similar, appropriate to that required by ANVISA and showed little protein solubility for cultivars BRS-258 and Embrapa48. It was concluded that the technique of irradiation beyond to keep the nutritional value of soy can contribute to the organoleptic quality of soymilk. (author)

  12. Bone morphogenic protein 4 produced in endothelial cells by oscillatory shear stress stimulates an inflammatory response

    Science.gov (United States)

    Sorescu, George P.; Sykes, Michelle; Weiss, Daiana; Platt, Manu O.; Saha, Aniket; Hwang, Jinah; Boyd, Nolan; Boo, Yong C.; Vega, J. David; Taylor, W. Robert; hide

    2003-01-01

    Atherosclerosis is now viewed as an inflammatory disease occurring preferentially in arterial regions exposed to disturbed flow conditions, including oscillatory shear stress (OS), in branched arteries. In contrast, the arterial regions exposed to laminar shear (LS) are relatively lesion-free. The mechanisms underlying the opposite effects of OS and LS on the inflammatory and atherogenic processes are not clearly understood. Here, through DNA microarrays, protein expression, and functional studies, we identify bone morphogenic protein 4 (BMP4) as a mechanosensitive and pro-inflammatory gene product. Exposing endothelial cells to OS increased BMP4 protein expression, whereas LS decreased it. In addition, we found BMP4 expression only in the selective patches of endothelial cells overlying foam cell lesions in human coronary arteries. The same endothelial patches also expressed higher levels of intercellular cell adhesion molecule-1 (ICAM-1) protein compared with those of non-diseased areas. Functionally, we show that OS and BMP4 induced ICAM-1 expression and monocyte adhesion by a NFkappaB-dependent mechanism. We suggest that BMP4 is a mechanosensitive, inflammatory factor playing a critical role in early steps of atherogenesis in the lesion-prone areas.

  13. Lipoxygenase activity of soybean and protein evaluation of soy milk produced from irradiated grains

    Energy Technology Data Exchange (ETDEWEB)

    Barros, Erica A., E-mail: ericabarros@fca.unesp.br [UNESP - Fazenda Experimental Lageado, Botucatu, SP (Brazil). Fac. de Ciencias Agronomicas; Broetto, Fernando, E-mail: broetto@ibb.unesp.br [UNESP - Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, SP (Brazil). Inst. de Biociencias. Dept. de Quimica e Bioquimica; Costa, Vladimir E., E-mail: vladimir@ibb.unesp.br [UNESP - Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, SP (Brazil). Inst. de Biociencias. Dept. de Fisica e Biofisica

    2011-07-01

    Soybean and its derivative are considered as a functional food because it has high quality protein and are used for the prevention of chronic degenerative diseases. The irradiation technique is used in soybeans to increase shelf life and avoid problems in plant products consumed raw or processed. However, the controversy in the literature that the irradiation dose up 10 kGy food can alter the functional properties and structures of macronutrients. With the prospect of more information on the use of radiation on soybeans, the objective of this study was to determine the activity of lipoxygenase in soybeans and to evaluate possible changes in the protein content of soymilk processed from grain-BRS 213, BRS 258 and Embrapa 48 subjected to dosages of 2.5 , 5.0 and 10.0 kGy of gamma radiation. The soybean cultivars were wrapped in plastic bags and subjected to gamma radiation source {sup 60}Co, Gammacell 220 (Atomic Energy of Canada Ltd.), except the control. The grains irradiated induced reduction of enzyme activity. The results for the protein content of soymilk were similar, appropriate to that required by ANVISA and showed little protein solubility for cultivars BRS-258 and Embrapa48. It was concluded that the technique of irradiation beyond to keep the nutritional value of soy can contribute to the organoleptic quality of soymilk. (author)

  14. Deletion of PTEN Produces Deficits in Conditioned Fear and Increases Fragile X Mental Retardation Protein

    Science.gov (United States)

    Lugo, Joaquin N.; Smith, Gregory D.; Morrison, Jessica B.; White, Jessika

    2013-01-01

    The phosphatase and tensin homolog detected on chromosome 10 (PTEN) gene product modulates activation of the phosphatidylinositol 3-kinase (PI3K)/AKT pathway. The PI3K pathway has been found to be involved in the regulation of the fragile X mental retardation protein, which is important for long-term depression and in the formation of new…

  15. Complete genome sequence of Klebsiella pneumoniae J1, a protein-based microbial flocculant-producing bacterium.

    Science.gov (United States)

    Pang, Changlong; Li, Ang; Cui, Di; Yang, Jixian; Ma, Fang; Guo, Haijuan

    2016-02-20

    Klebsiella pneumoniae J1 is a Gram-negative strain, which belongs to a protein-based microbial flocculant-producing bacterium. However, little genetic information is known about this species. Here we carried out a whole-genome sequence analysis of this strain and report the complete genome sequence of this organism and its genetic basis for carbohydrate metabolism, capsule biosynthesis and transport system. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Exploitation of starch industry liquid by-product to produce bioactive peptides from rice hydrolyzed proteins.

    Science.gov (United States)

    Dei Piu', Lucilla; Tassoni, Annalisa; Serrazanetti, Diana Isabella; Ferri, Maura; Babini, Elena; Tagliazucchi, Davide; Gianotti, Andrea

    2014-07-15

    Small peptides show higher antioxidant capacity than native proteins and may be absorbed in the intestine without further digestion. In our study, a protein by-product from rice starch industry was hydrolyzed with commercial proteolytic enzymes (Alcalase, Neutrase, Flavourzyme) and microbial whole cells of Bacillus spp. and the released peptides were tested for antioxidant activity. Among enzymes, Alcalase was the most performing, while microbial proteolytic activity was less efficient. Conversely, the antioxidant activity was higher in the samples obtained by microbial hydrolysis and particularly with Bacillus pumilus AG1. The sequences of low molecular weight antioxidant peptides were determined and analyzed for aminoacidic composition. The results obtained so far suggest that the hydrolytic treatment of this industrial by-product, with selected enzymes and microbial systems, can allow its exploitation for the production of functional additives and supplements rich in antioxidant peptides, to be used in new food formulas for human consumption. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Influence of peptides and proteins produced by cyanobacterium Microcystis aeruginosa on the coagulation of turbid waters

    Czech Academy of Sciences Publication Activity Database

    Šafaříková, Jana; Barešová, Magdalena; Pivokonský, Martin; Kopecká, Ivana

    2013-01-01

    Roč. 18, October (2013), s. 49-57 ISSN 1383-5866 R&D Projects: GA ČR GAP105/11/0247 Institutional research plan: CEZ:AV0Z20600510 Institutional support: RVO:67985874 Keywords : Cellular organic matter (COM) * Coagulation * Microcystis aeruginosa * Peptides/proteins * Turbidity removal Subject RIV: BK - Fluid Dynamics Impact factor: 3.065, year: 2013 http://www.sciencedirect.com/science/article/pii/S1383586613004152

  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. Application of Ionizing Radiations to Produce New Polysaccharides and Proteins with Enhanced Functionality

    International Nuclear Information System (INIS)

    Al Assaf, S.

    2006-01-01

    Treatment of polysaccharides with ionizing radiation either in the solid state or in aqueous solution leads to degradation, whereas application of radiation to process synthetic polymers to introduce structural changes and special performance characteristics is now a thriving industry. Using a mediating gas associated during the radiation treatment prevents the degradation of natural polymers and enables the introduction of different molecular and functional characteristics, as previously achieved with synthetic polymers. For example, the molecular weight can be increased and standardised, protein distribution reorganised and modified to ensure better emulsification, viscosity and viscoelasticity enhanced, leading when required to hydrogel formation. More than one hydrocolloid can also be integrated into a single matrix using this process. Protein, within demineralised bone, too can be modified to give enhanced osteoinductive capacity. This experience has led to additional patented and proprietary processes, using standard food processing techniques, to promote changes in a wide range of hydrocolloids which emulates and extend those which occur naturally. The lecture will describe these structural changes and their functional role by reference to several hydrocolloids, including acacia gums, pectin, ispaghula and hyaluronan, bone morphogenic protein. Applications in food products, dietary fibre and medical products will be illustrated

  20. Agitation down-regulates immunoglobulin binding protein EibG expression in Shiga toxin-producing Escherichia coli (STEC.

    Directory of Open Access Journals (Sweden)

    Thorsten Kuczius

    Full Text Available Shiga toxin (Stx-producing Escherichia coli (STEC carrying eibG synthesize Escherichia coli immunoglobulin binding protein (EibG. EibG nonspecifically binds to immunoglobulins and tends to aggregate in multimers but is poorly expressed in wild-type strains. To study synthesis of the proteins and their regulation in the pathogens, we identified natural growth conditions that increased EibG synthesis. EibG proteins as well as corresponding mRNA were highly expressed under static growth conditions while shearing stress created by agitation during growth repressed protein synthesis. Further regulation effects were driven by reduced oxygen tension, and pH up-regulated EibG expression, but to a lesser extent than growth conditions while decreased temperature down-regulated EibG. Bacteria with increased EibG expression during static growth conditions showed a distinct phenotype with chain formation and biofilm generation, which disappeared with motion. High and low EibG expression was reversible indicating a process with up- and down-regulation of the protein expression. Our findings indicate that shear stress represses EibG expression and might reduce bacterial attachments to cells and surfaces.

  1. Human Immunodeficiency Virus-Type 1 LTR DNA contains an intrinsic gene producing antisense RNA and protein products

    Directory of Open Access Journals (Sweden)

    Hsiao Chiu-Bin

    2006-11-01

    Full Text Available Abstract Background While viruses have long been shown to capitalize on their limited genomic size by utilizing both strands of DNA or complementary DNA/RNA intermediates to code for viral proteins, it has been assumed that human retroviruses have all their major proteins translated only from the plus or sense strand of RNA, despite their requirement for a dsDNA proviral intermediate. Several studies, however, have suggested the presence of antisense transcription for both HIV-1 and HTLV-1. More recently an antisense transcript responsible for the HTLV-1 bZIP factor (HBZ protein has been described. In this study we investigated the possibility of an antisense gene contained within the human immunodeficiency virus type 1 (HIV-1 long terminal repeat (LTR. Results Inspection of published sequences revealed a potential transcription initiator element (INR situated downstream of, and in reverse orientation to, the usual HIV-1 promoter and transcription start site. This antisense initiator (HIVaINR suggested the possibility of an antisense gene responsible for RNA and protein production. We show that antisense transcripts are generated, in vitro and in vivo, originating from the TAR DNA of the HIV-1 LTR. To test the possibility that protein(s could be translated from this novel HIV-1 antisense RNA, recombinant HIV antisense gene-FLAG vectors were designed. Recombinant protein(s were produced and isolated utilizing carboxy-terminal FLAG epitope (DYKDDDDK sequences. In addition, affinity-purified antisera to an internal peptide derived from the HIV antisense protein (HAP sequences identified HAPs from HIV+ human peripheral blood lymphocytes. Conclusion HIV-1 contains an antisense gene in the U3-R regions of the LTR responsible for both an antisense RNA transcript and proteins. This antisense transcript has tremendous potential for intrinsic RNA regulation because of its overlap with the beginning of all HIV-1 sense RNA transcripts by 25 nucleotides. The

  2. Decreased Bacterial Attachment and Protein Adsorption to Coatings Produced by Low Enegy Plasma Polymerization

    DEFF Research Database (Denmark)

    Andersen, T.E.; Kingshott, Peter; Benter, M.

    .figure) .and E. coli grown on uncoated silicone compared to PP-PVP coated silicone (right figure). Results from the flow chamber analysis shows PP-PVP to be very good at preventing E. coli colonization during prolonged growth in flow chamber. At this point other surfaces and bacteria remains to be tested...... adsorption and bacteria attachment/colonization. This is emphasized by the fact that long dwelling urinary catheters, which is a typical silicone medical device, causes 5% per day incidence of urinary tract infection [1,2]. A demand therefore exists for surface modifications providing the silicone material......-coated crystals were then treated with one of the plasma polymerized coatings. Adsorption of fibrinogen, human serum albumin or immunoglobulin G was measured using a QCM-D instrument [5] (model E4, Q-Sense AB, Vastra Frolunda, Sweden) using a solution of 50llg/1 protein in PBS buffer. Results and Discussion: Our...

  3. Safety evaluation of a milk-based protein powder produced by a novel manufacturing technique.

    Science.gov (United States)

    LeBeau, A; Matulka, R; Comstock, B

    2017-05-01

    TruActive™ NF is a novel, fat-free, milk-based protein powder to be added to food to increase protein content and is manufactured using non-thermal treatment to reduce potential pathogens most relevant to protecting public health. TruActive™ NF was evaluated for potential pathogens of concern to public health regulators; none were detected. The estimated daily intake (EDI) of TruActive™ NF at a 90 th percentile consumption for the powder in nutritional beverages and bars is 14,700 mg/day. In vitro genotoxicity testing revealed that concentrations of TruActive™ NF up to 5000 μg/plate did not induce point mutations in selected strains. Oral administration of TruActive™ NF to male Sprague-Dawley rats in an in vivo mammalian chromosomal aberration assay did not induce chromosomal aberrations or significantly affect mitosis in bone marrow cells at 2000 mg/kg. Male and female Sprague-Dawley rats were administered TruActive™ NF at concentrations of 7.5%, 15%, and 30% of the diet during a 28-day subacute dietary study followed by a 14-day recovery period. Some parameters were altered at the 30% diet concentration. The No Observed Adverse Effect Level (NOAEL) in the 28-day dietary study was at 15% of the diet (11,812 mg/kg bw/day for male rats and 11,521 mg/kg bw/day for female rats). Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. 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.

  5. Polycyclic aromatic hydrocarbon-emulsifier protein produced by Aspergillus brasiliensis (niger) in an airlift bioreactor following an electrochemical pretreatment.

    Science.gov (United States)

    Sánchez-Vázquez, Victor; Shirai, Keiko; González, Ignacio; Gutiérrez-Rojas, Mariano

    2018-05-01

    An emulsifier protein (EP) was produced and easily separated from oil-contaminated water as an economical substrate when Aspergillus brasiliensis, pretreated in a solid state culture with a controlled electric field, was used in an airlift bioreactor. The hydrocarbon-EP comprised 19.5% of the total protein, its purification enhanced the specific emulsifying activity (EA) seven times. The influence of operational conditions (pH and salt concentration) on the EA were assessed to characterise the emulsion stability. The EA was increased by 19% in alkaline environments (pH 7-11), but it was not affected by the presence of salt (0-35 g L -1 ). On the other hand, preheating the EP samples (60 °C) enhanced the EA by 2.5 times. Based on analysis of its EA, this EP can be applied as a bioremediation enhancer in contaminated soils. Copyright © 2018 Elsevier Ltd. All rights reserved.

  6. 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.

  7. Selenite reduction by anaerobic microbial aggregates: Microbial community structure, and proteins associated to the produced selenium spheres.

    Directory of Open Access Journals (Sweden)

    Graciela eGonzalez-Gil

    2016-04-01

    Full Text Available Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0, insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20 % and Pseudomonadaceae (c.a.10 % were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (~200 m of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

  8. An endogenously produced fragment of cardiac myosin-binding protein C is pathogenic and can lead to heart failure.

    Science.gov (United States)

    Razzaque, Md Abdur; Gupta, Manish; Osinska, Hanna; Gulick, James; Blaxall, Burns C; Robbins, Jeffrey

    2013-08-16

    A stable 40-kDa fragment is produced from cardiac myosin-binding protein C when the heart is stressed using a stimulus, such as ischemia-reperfusion injury. Elevated levels of the fragment can be detected in the diseased mouse and human heart, but its ability to interfere with normal cardiac function in the intact animal is unexplored. To understand the potential pathogenicity of the 40-kDa fragment in vivo and to investigate the molecular pathways that could be targeted for potential therapeutic intervention. We generated cardiac myocyte-specific transgenic mice using a Tet-Off inducible system to permit controlled expression of the 40-kDa fragment in cardiomyocytes. When expression of the 40-kDa protein is induced by crossing the responder animals with tetracycline transactivator mice under conditions in which substantial quantities approximating those observed in diseased hearts are reached, the double-transgenic mice subsequently experience development of sarcomere dysgenesis and altered cardiac geometry, and the heart fails between 12 and 17 weeks of age. The induced double-transgenic mice had development of cardiac hypertrophy with myofibrillar disarray and fibrosis, in addition to activation of pathogenic MEK-ERK pathways. Inhibition of MEK-ERK signaling was achieved by injection of the mitogen-activated protein kinase (MAPK)/ERK inhibitor U0126. The drug effectively improved cardiac function, normalized heart size, and increased probability of survival. These results suggest that the 40-kDa cardiac myosin-binding protein C fragment, which is produced at elevated levels during human cardiac disease, is a pathogenic fragment that is sufficient to cause hypertrophic cardiomyopathy and heart failure.

  9. Selenite Reduction by Anaerobic Microbial Aggregates: Microbial Community Structure, and Proteins Associated to the Produced Selenium Spheres

    KAUST Repository

    Gonzalez-Gil, Graciela

    2016-04-26

    Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0), insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20%) and Pseudomonadaceae (c.a.10%) were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (∼200 μm) of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano)spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS) analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

  10. Stability of lime essential oil microparticles produced with protein-carbohydrate blends.

    Science.gov (United States)

    Campelo, Pedro Henrique; Sanches, Edgar Aparecido; Fernandes, Regiane Victória de Barros; Botrel, Diego Alvarenga; Borges, Soraia Vilela

    2018-03-01

    The objective of this work was to analyze the influence of maltodextrin equivalent dextrose on the lime essential oil reconstitution, storage, release and protection properties. Four treatments were evaluated: whey protein concentrate (WPC), and blends of maltodextrin with dextrose equivalents of 5 (WM5), 10 (WM10) and 20 (WM20). The reconstitution and storage properties of the microparticles (solubility, wettability and density), water kinetics adsorption, sorption isotherms, thermogravimetric properties, controlled release and degradation kinetics of encapsulated lime essential oil were studied to measure the quality of the encapsulated materials. The results of the study indicated that the DE degree influences the characteristics of reconstitution, storage, controlled release and degradation characteristics of encapsulated bioactive compounds. The increase in dextrose equivalent improves microparticle solubility, wettability and density, mainly due to the size of the maltodextrin molecules. The adsorption kinetics and sorption isotherm curves confirmed the increase in the hygroscopicity of maltodextrins with higher degrees of polymerization. The size of the maltodextrin chains influenced the release and protection of the encapsulated lime essential oil. Finally, the maltodextrin polymerization degree can be considered a parameter that will influence the physicochemical properties of microencapsulated food. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Inhibition of fatty acid binding proteins elevates brain anandamide levels and produces analgesia.

    Directory of Open Access Journals (Sweden)

    Martin Kaczocha

    Full Text Available The endocannabinoid anandamide (AEA is an antinociceptive lipid that is inactivated through cellular uptake and subsequent catabolism by fatty acid amide hydrolase (FAAH. Fatty acid binding proteins (FABPs are intracellular carriers that deliver AEA and related N-acylethanolamines (NAEs to FAAH for hydrolysis. The mammalian brain expresses three FABP subtypes: FABP3, FABP5, and FABP7. Recent work from our group has revealed that pharmacological inhibition of FABPs reduces inflammatory pain in mice. The goal of the current work was to explore the effects of FABP inhibition upon nociception in diverse models of pain. We developed inhibitors with differential affinities for FABPs to elucidate the subtype(s that contributes to the antinociceptive effects of FABP inhibitors. Inhibition of FABPs reduced nociception associated with inflammatory, visceral, and neuropathic pain. The antinociceptive effects of FABP inhibitors mirrored their affinities for FABP5, while binding to FABP3 and FABP7 was not a predictor of in vivo efficacy. The antinociceptive effects of FABP inhibitors were mediated by cannabinoid receptor 1 (CB1 and peroxisome proliferator-activated receptor alpha (PPARα and FABP inhibition elevated brain levels of AEA, providing the first direct evidence that FABPs regulate brain endocannabinoid tone. These results highlight FABPs as novel targets for the development of analgesic and anti-inflammatory therapeutics.

  12. Specific chemical and structural damage to proteins produced by synchrotron radiation.

    Science.gov (United States)

    Weik, M; Ravelli, R B; Kryger, G; McSweeney, S; Raves, M L; Harel, M; Gros, P; Silman, I; Kroon, J; Sussman, J L

    2000-01-18

    Radiation damage is an inherent problem in x-ray crystallography. It usually is presumed to be nonspecific and manifested as a gradual decay in the overall quality of data obtained for a given crystal as data collection proceeds. Based on third-generation synchrotron x-ray data, collected at cryogenic temperatures, we show for the enzymes Torpedo californica acetylcholinesterase and hen egg white lysozyme that synchrotron radiation also can cause highly specific damage. Disulfide bridges break, and carboxyl groups of acidic residues lose their definition. Highly exposed carboxyls, and those in the active site of both enzymes, appear particularly susceptible. The catalytic triad residue, His-440, in acetylcholinesterase, also appears to be much more sensitive to radiation damage than other histidine residues. Our findings have direct practical implications for routine x-ray data collection at high-energy synchrotron sources. Furthermore, they provide a direct approach for studying the radiation chemistry of proteins and nucleic acids at a detailed, structural level and also may yield information concerning putative "weak links" in a given biological macromolecule, which may be of structural and functional significance.

  13. Clonality, outer-membrane proteins profile and efflux pump in KPC- producing Enterobacter sp. in Brazil.

    Science.gov (United States)

    Rosa, Juliana Ferraz; Rizek, Camila; Marchi, Ana Paula; Guimaraes, Thais; Miranda, Lourdes; Carrilho, Claudia; Levin, Anna S; Costa, Silvia F

    2017-03-17

    Carbapenems resistance in Enterobacter spp. has increased in the last decade, few studies, however, described the mechanisms of resistance in this bacterium. This study evaluated clonality and mechanisms of carbapenems resistance in clinical isolates of Enterobacter spp. identified in three hospitals in Brazil (Hospital A, B and C) over 7-year. Antibiotics sensitivity, pulsed-field gel electrophoresis (PFGE), PCR for carbapenemase and efflux pump genes were performed for all carbapenems-resistant isolates. Outer-membrane protein (OMP) was evaluated based on PFGE profile. A total of 130 isolates of Enterobacter spp were analyzed, 44/105 (41, 9%) E. aerogenes and 8/25 (32,0%) E. cloacae were resistant to carbapenems. All isolates were susceptible to fosfomycin, polymyxin B and tigecycline. KPC was present in 88.6% of E. aerogenes and in all E. cloacae resistant to carbapenems. The carbapenems-resistant E. aerogenes identified in hospital A belonged to six clones, however, a predominant clone was identified in this hospital over the study period. There is a predominant clone in Hospital B and Hospital C as well. The mechanisms of resistance to carbapenems differ among subtypes. Most of the isolates co-harbored blaKPC, blaTEM and /or blaCTX associated with decreased or lost of 35-36KDa and or 39 KDa OMP. The efflux pump AcrAB-TolC gene was only identified in carbapenems-resistant E. cloacae. There was a predominant clone in each hospital suggesting that cross-transmission of carbapenems-resistant Enterobacter spp. was frequent. The isolates presented multiple mechanisms of resistance to carbapenems including OMP alteration.

  14. Validation of the manufacturing process used to produce long-acting recombinant factor IX Fc fusion protein.

    Science.gov (United States)

    McCue, J; Osborne, D; Dumont, J; Peters, R; Mei, B; Pierce, G F; Kobayashi, K; Euwart, D

    2014-07-01

    Recombinant factor IX Fc (rFIXFc) fusion protein is the first of a new class of bioengineered long-acting factors approved for the treatment and prevention of bleeding episodes in haemophilia B. The aim of this work was to describe the manufacturing process for rFIXFc, to assess product quality and to evaluate the capacity of the process to remove impurities and viruses. This manufacturing process utilized a transferable and scalable platform approach established for therapeutic antibody manufacturing and adapted for production of the rFIXFc molecule. rFIXFc was produced using a process free of human- and animal-derived raw materials and a host cell line derived from human embryonic kidney (HEK) 293H cells. The process employed multi-step purification and viral clearance processing, including use of a protein A affinity capture chromatography step, which binds to the Fc portion of the rFIXFc molecule with high affinity and specificity, and a 15 nm pore size virus removal nanofilter. Process validation studies were performed to evaluate identity, purity, activity and safety. The manufacturing process produced rFIXFc with consistent product quality and high purity. Impurity clearance validation studies demonstrated robust and reproducible removal of process-related impurities and adventitious viruses. The rFIXFc manufacturing process produces a highly pure product, free of non-human glycan structures. Validation studies demonstrate that this product is produced with consistent quality and purity. In addition, the scalability and transferability of this process are key attributes to ensure consistent and continuous supply of rFIXFc. © 2014 The Authors. Haemophilia Published by John Wiley & Sons Ltd.

  15. The role of glomalin, a protein produced by arbuscular mycorrhizal fungi, in sequestering potentially toxic elements

    International Nuclear Information System (INIS)

    Gonzalez-Chavez, M.C.; Carrillo-Gonzalez, R.; Wright, S.F.; Nichols, K.A.

    2004-01-01

    Naturally occurring soil organic compounds stabilize potentially toxic elements (PTEs) such as Cu, Cd, Pb, and Mn. The hypothesis of this work was that an insoluble glycoprotein, glomalin, produced in copious amounts on hyphae of arbuscular mycorrhizal fungi (AMF) sequesters PTEs. Glomalin can be extracted from laboratory cultures of AMF and from soils. Three different experiments were conducted. Experiment 1 showed that glomalin extracted from two polluted soils contained 1.6-4.3 mg Cu, 0.02-0.08 mg Cd, and 0.62-1.12 mg Pb/g glomalin. Experiment 2 showed that glomalin from hyphae of an isolate of Gigaspora rosea sequestered up to 28 mg Cu/g in vitro. Experiment 3 tested in vivo differences in Cu sequestration by Cu-tolerant and non-tolerant isolates of Glomus mosseae colonizing sorghum. Plants were fed with nutrient solution containing 0.5, 10 or 20 μM of Cu. Although no differences between isolates were detected, mean values for the 20 μM Cu level were 1.6, 0.4, and 0.3 mg Cu/g for glomalin extracted from hyphae, from sand after removal of hyphae and from hyphae attached to roots, respectively. Glomalin should be considered for biostabilization leading to remediation of polluted soils. - Glomalin may be useful in remediation of toxic elements in soils

  16. The role of glomalin, a protein produced by arbuscular mycorrhizal fungi, in sequestering potentially toxic elements

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez-Chavez, M.C.; Carrillo-Gonzalez, R.; Wright, S.F.; Nichols, K.A

    2004-08-01

    Naturally occurring soil organic compounds stabilize potentially toxic elements (PTEs) such as Cu, Cd, Pb, and Mn. The hypothesis of this work was that an insoluble glycoprotein, glomalin, produced in copious amounts on hyphae of arbuscular mycorrhizal fungi (AMF) sequesters PTEs. Glomalin can be extracted from laboratory cultures of AMF and from soils. Three different experiments were conducted. Experiment 1 showed that glomalin extracted from two polluted soils contained 1.6-4.3 mg Cu, 0.02-0.08 mg Cd, and 0.62-1.12 mg Pb/g glomalin. Experiment 2 showed that glomalin from hyphae of an isolate of Gigaspora rosea sequestered up to 28 mg Cu/g in vitro. Experiment 3 tested in vivo differences in Cu sequestration by Cu-tolerant and non-tolerant isolates of Glomus mosseae colonizing sorghum. Plants were fed with nutrient solution containing 0.5, 10 or 20 {mu}M of Cu. Although no differences between isolates were detected, mean values for the 20 {mu}M Cu level were 1.6, 0.4, and 0.3 mg Cu/g for glomalin extracted from hyphae, from sand after removal of hyphae and from hyphae attached to roots, respectively. Glomalin should be considered for biostabilization leading to remediation of polluted soils. - Glomalin may be useful in remediation of toxic elements in soils.

  17. 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).

  18. 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.

  19. New cell line development for antibody-producing Chinese hamster ovary cells using split green fluorescent protein

    Directory of Open Access Journals (Sweden)

    Kim Yeon-Gu

    2012-05-01

    Full Text Available Abstract Background The establishment of high producer is an important issue in Chinese hamster ovary (CHO cell culture considering increased heterogeneity by the random integration of a transfected foreign gene and the altered position of the integrated gene. Fluorescence-activated cell sorting (FACS-based cell line development is an efficient strategy for the selection of CHO cells in high therapeutic protein production. Results An internal ribosome entry site (IRES was introduced for using two green fluorescence protein (GFP fragments as a reporter to both antibody chains, the heavy chain and the light chain. The cells co-transfected with two GFP fragments showed the emission of green fluorescence by the reconstitution of split GFP. The FACS-sorted pool with GFP expression had a higher specific antibody productivity (qAb than that of the unsorted pool. The qAb was highly correlated with the fluorescence intensity with a high correlation coefficient, evidenced from the analysis of median GFP and qAb in individual selected clones. Conclusions This study proved that the fragment complementation for split GFP could be an efficient indication for antibody production on the basis of high correlation of qAb with reconstitution of GFP. Taken together, we developed an efficient FACS-based screening method for high antibody-producing CHO cells with the benefits of the split GFP system.

  20. Maltose binding protein-fusion enhances the bioactivity of truncated forms of pig myostatin propeptide produced in E. coli.

    Directory of Open Access Journals (Sweden)

    Sang Beum Lee

    Full Text Available Myostatin (MSTN is a potent negative regulator of skeletal muscle growth. MSTN propeptide (MSTNpro inhibits MSTN binding to its receptor through complex formation with MSTN, implying that MSTNpro can be a useful agent to improve skeletal muscle growth in meat-producing animals. Four different truncated forms of pig MSTNpro containing N-terminal maltose binding protein (MBP as a fusion partner were expressed in E. coli, and purified by the combination of affinity chromatography and gel filtration. The MSTN-inhibitory capacities of these proteins were examined in an in vitro gene reporter assay. A MBP-fused, truncated MSTNpro containing residues 42-175 (MBP-Pro42-175 exhibited the same MSTN-inhibitory potency as the full sequence MSTNpro. Truncated MSTNpro proteins containing either residues 42-115 (MBP-Pro42-115 or 42-98 (MBP-Pro42-98 also exhibited MSTN-inhibitory capacity even though the potencies were significantly lower than that of full sequence MSTNpro. In pull-down assays, MBP-Pro42-175, MBP-Pro42-115, and MBP-Pro42-98 demonstrated their binding to MSTN. MBP was removed from the truncated MSTNpro proteins by incubation with factor Xa to examine the potential role of MBP on MSTN-inhibitory capacity of those proteins. Removal of MBP from MBP-Pro42-175 and MBP-Pro42-98 resulted in 20-fold decrease in MSTN-inhibitory capacity of Pro42-175 and abolition of MSTN-inhibitory capacity of Pro42-98, indicating that MBP as fusion partner enhanced the MSTN-inhibitory capacity of those truncated MSTNpro proteins. In summary, this study shows that MBP is a very useful fusion partner in enhancing MSTN-inhibitory potency of truncated forms of MSTNpro proteins, and MBP-fused pig MSTNpro consisting of amino acid residues 42-175 is sufficient to maintain the full MSTN-inhibitory capacity.

  1. 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...

  2. 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.

  3. 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.

  4. High protein- and high lipid-producing microalgae from Outback Australia as potential feedstock for animal feed and biodiesel

    Directory of Open Access Journals (Sweden)

    Van Thang eDuong

    2015-05-01

    Full Text Available Microalgal biomass can be used for biodiesel, feed and food production. Collection and identification of local microalgal strains in the Northern Territory – Australia was conducted to identify strains with high protein and lipid contents as potential feedstock for animal feed and biodiesel production, respectively. A total of 36 strains were isolated from 13 samples collected from a variety of freshwater locations, such as dams, ponds and streams and subsequently classified by 18S rDNA sequencing. All of the strains were green microalgae and predominantly belong to Chlorella sp., Scenedesmus sp., Desmodesmus sp., Chlamydomonas sp., Pseudomuriella sp., Tetraedron caudatum, Graesiella emersonii and Mychonastes timauensis. Among the fastest growing strains, Scenedesmus sp. NT1d possessed the highest content of protein; reaching up to 33% of its dry weight. In terms of lipid production, Chlorella sp. NT8a and Scenedesmus dimorphus NT8e produced the highest triglyceride contents of 116.9 µg mL-1 culture and 99.13 µg mL-1, respectively, as measured by gas chromatography-mass spectroscopy (GC-MS of fatty acid methyl esters (FAMEs. These strains may present suitable candidates for biodiesel production after further optimization of culturing conditions, while their protein-rich biomass could be used for animal feed.

  5. 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.

  6. Andrastins A-C, new protein farnesyltransferase inhibitors produced by Penicillium sp. FO-3929. I. Producing strain, fermentation, isolation, and biological activities.

    Science.gov (United States)

    Omura, S; Inokoshi, J; Uchida, R; Shiomi, K; Masuma, R; Kawakubo, T; Tanaka, H; Iwai, Y; Kosemura, S; Yamamura, S

    1996-05-01

    New protein farnesyltransferase inhibitors, andrastins A-C, have been discovered in the cultured broth of Penicillium sp. FO-3929. Andrastins extracted from broth supernatant were purified by silica gel chromatography, ODS chromatography and HPLC. The IC50 of andrastins A, B, and C against protein farnesyltransferase were 24.9, 47.1, and 13.3 microM, respectively.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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...

  13. 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)

  14. 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.

  15. Identification of Potential Plants Producing Tannin-protein Complex for a-amylase as Botanical Pesticide

    Directory of Open Access Journals (Sweden)

    Asriyah Firdausi

    2013-05-01

    Full Text Available Research  on  the  development  of  botanical  pesticides  should  be developed  through  new  methods,  such  as  by  inhibiting the  activity  of  digestive enzymes  by  secondary  metabolites.  The  aim  of  this  study  was  to  identify some  of  potential  plants  as  a  source  of  tannin-protein  complexes  to  inhibitthe  activity  of  - amylase.  The  study  of  identification  of  potential  plants producing  the  active  ingredient  tannin-protein  complex  was  divided  into  three stages,  1  identification  of  potential  plants  producing  tannin,  2  isolation  of tannin-protein  complexes,  and  3  in  vitro  test  of  tannin-protein  complexes effect  of  the  -amylase activity.  Some  of  the observed  plants  were  sidaguri  leaf (Sida rhombifolia, melinjo leaf (Gnetum gnemon, gamal leaf (Gliricidia sepium,lamtoro  leaf  (Leucaena  leucocephala ,  betel  nut  (Areca  catechu ,  and  crude gambier  (Uncaria  gambir a s  a  source of  tannins  and  melinjo  seed was  used  asprotein  source.  Betel  nut  and  melinjo  seed  were  the  best  source  of  tannin-protein  complex,  tannin  content  1.77  mg  TAE/mL  with  antioxidant  activity  of  90%,the  ability  to  inhibit  the  activity  of  -amylase by  95%  with  IC 50  values  of 10 mg/mL.Key words: Tannin, protein, -amylase, botanical pesticides,Areca catechu, Gnetum gnemon.

  16. 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.

  17. Fractionation of whey protein isolate with supercritical carbon dioxide to produce enriched alpha-lactalbumin and beta-lactoglobulin food ingredients

    Science.gov (United States)

    A potentially economical and environmentally friendly whey protein fractionation process was developed using supercritical carbon dioxide (SCO2) as an acid to produce enriched fractions of alpha-lactalbumin (a-LA) and beta-lactoglobulin (b-LG) from whey protein isolate. To prepare the fractions, so...

  18. 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.

  19. 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.

  20. 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.

  1. 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...

  2. 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."

  3. 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.

  4. 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.

  5. Multiple length peptide-pheromone variants produced by Streptococcus pyogenes directly bind Rgg proteins to confer transcriptional regulation.

    Science.gov (United States)

    Aggarwal, Chaitanya; Jimenez, Juan Cristobal; Nanavati, Dhaval; Federle, Michael J

    2014-08-08

    Streptococcus pyogenes, a human-restricted pathogen, accounts for substantial mortality related to infections worldwide. Recent studies indicate that streptococci produce and respond to several secreted peptide signaling molecules (pheromones), including those known as short hydrophobic peptides (SHPs), to regulate gene expression by a quorum-sensing mechanism. Upon transport into the bacterial cell, pheromones bind to and modulate activity of receptor proteins belonging to the Rgg family of transcription factors. Previously, we reported biofilm regulation by the Rgg2/3 quorum-sensing circuit in S. pyogenes. The aim of this study was to identify the composition of mature pheromones from cell-free culture supernatants that facilitate biofilm formation. Bioluminescent reporters were employed to detect active pheromones in culture supernatants fractionated by reverse-phase chromatography, and mass spectrometry was used to characterize their properties. Surprisingly, multiple SHPs that varied by length were detected. Synthetic peptides of each variant were tested individually using bioluminescence reporters and biofilm growth assays, and although activities differed widely among the group, peptides comprising the C-terminal eight amino acids of the full-length native peptide were most active. Direct Rgg/SHP interactions were determined using a fluorescence polarization assay that utilized FITC-labeled peptide ligands. Peptide receptor affinities were seen to be as low as 500 nm and their binding affinities directly correlated with observed bioactivity. Revelation of naturally produced pheromones along with determination of their affinity for cognate receptors are important steps forward in designing compounds whose purpose is positioned for future therapeutics aimed at treating infections through the interference of bacterial communication. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Preparation and physicochemical properties of protein concentrate and isolate produced from Acacia tortilis (Forssk.) Hayne ssp. raddiana.

    Science.gov (United States)

    Embaby, Hassan E; Swailam, Hesham M; Rayan, Ahmed M

    2018-02-01

    The composition and physicochemical properties of defatted acacia flour (DFAF), acacia protein concentrate (APC) and acacia protein isolate (API) were evaluated. The results indicated that API had lower, ash and fat content, than DFAF and APC. Also, significant difference in protein content was noticed among DFAF, APC and API (37.5, 63.7 and 91.8%, respectively). Acacia protein concentrate and isolates were good sources of essential amino acids except cystine and methionine. The physicochemical and functional properties of acacia protein improved with the processing of acacia into protein concentrate and protein isolate. The results of scanning electron micrographs showed that DFAF had a compact structure; protein concentrate were, flaky, and porous type, and protein isolate had intact flakes morphology.

  7. Selection and protein sds-page identification of a new high-producing polysaccharide strain of Spirulina platensis

    International Nuclear Information System (INIS)

    Wang Zhiping; Liu Yanhui

    2004-01-01

    The relationship between anti-radiation capacity and polysaccharide contents of ten Spirulina platensis strains were studied. The results showed that the correlation coefficient between 60 Co γ-ray half-lethal dose (LD 50 ) and polysaccharide contents of the 10 strains was 0.9873. After the single cells or spheroplasts of Sp-08 were treated by 0.6%EMS and 2.4 kGy 60 Co γ-ray irradiation, four morphological mutant named Sp-08A, Sp-08B, Sp-08C and Sp-08D, which could endure about 7.0 kGy γ-ray irradiation, were obtained. The polysaccharide contents of Sp-08A, Sp-08B, Sp-08C and Sp-08D, were 32.8%, 17.3%, 3.4% and 42.3% higher than that of their parent Sp-08, respectively. The results of protein SDS-PAGE analysis showed that the heredity of Sp-08A, Sp-08C and Sp-08D were mutated. Therefore, Sp-08A was a perfect high-producing polysaccharide strain with excellent characteristics of morphology and growth. Now, Sp-08A is applied in mass cultivation and industrialization. (authors)

  8. Conditional Function of Autoaggregative Protein Cah and Common cah Mutations in Shiga Toxin-Producing Escherichia coli.

    Science.gov (United States)

    Carter, Michelle Qiu; Brandl, Maria T; Kudva, Indira T; Katani, Robab; Moreau, Matthew R; Kapur, Vivek

    2018-01-01

    Cah is a calcium-binding autotransporter protein involved in autoaggregation and biofilm formation. Although cah is widespread in Shiga toxin-producing Escherichia coli (STEC), we detected mutations in cah at a frequency of 31.3% in this pathogen. In STEC O157:H7 supershedder strain SS17, a large deletion results in a smaller coding sequence, encoding a protein lacking the C-terminal 71 amino acids compared with Cah in STEC O157:H7 strain EDL933. We examined the function of Cah in biofilm formation and host colonization to better understand the selective pressures for cah mutations. EDL933-Cah played a conditional role in biofilm formation in vitro : it enhanced E. coli DH5α biofilm formation on glass surfaces under agitated culture conditions that prevented autoaggregation but inhibited biofilm formation under hydrostatic conditions that facilitated autoaggregation. This function appeared to be strain dependent since Cah-mediated biofilm formation was diminished when an EDL933 cah gene was expressed in SS17. Deletion of cah in EDL933 enhanced bacterial attachment to spinach leaves and altered the adherence pattern of EDL933 to bovine recto-anal junction squamous epithelial (RSE) cells. In contrast, in trans expression of EDL933 cah in SS17 increased its attachment to leaf surfaces, and in DH5α, it enhanced its adherence to RSE cells. Hence, the ecological function of Cah appears to be modulated by environmental conditions and other bacterial strain-specific properties. Considering the prevalence of cah in STEC and its role in attachment and biofilm formation, cah mutations might be selected in ecological niches in which inactivation of Cah would result in an increased fitness in STEC during colonization of plants or animal hosts. IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) harbors genes encoding diverse adhesins, and many of these are known to play an important role in bacterial attachment and host colonization. We demonstrated here that the

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Further enhanced production of heterologous proteins by double-gene disruption (ΔAosedD ΔAovps10) in a hyper-producing mutant of Aspergillus oryzae.

    Science.gov (United States)

    Zhu, Lin; Maruyama, Jun-ichi; Kitamoto, Katsuhiko

    2013-07-01

    The filamentous fungus Aspergillus oryzae is used as one of the most favored hosts for heterologous protein production due to its ability to secrete large amounts of proteins into the culture medium. We previously generated a hyper-producing mutant strain of A. oryzae, AUT1, which produced 3.2- and 2.6-fold higher levels of bovine chymosin (CHY) and human lysozyme (HLY), respectively, compared with the wild-type strain. However, further enhancement of heterologous protein production by multiple gene disruption is difficult because of the low gene-targeting efficiency in strain AUT1. Here, we disrupted the ligD gene, which is involved in nonhomologous recombination, and the pyrG gene to create uridine/uracil auxotrophy in strain AUT1, to generate a hyper-producing mutant applicable to pyrG marker recycling with highly efficient gene targeting. We generated single and double disruptants of the tripeptidyl peptidase gene AosedD and vacuolar sorting receptor gene Aovps10 in the hyper-producing mutant background, and found that all disruptants showed significant increases in heterologous protein production. Particularly, double disruption of the Aovps10 and AosedD genes increased the production levels of CHY and HLY by 1.6- and 2.1-fold, respectively, compared with the parental strain. Thus, we successfully generated a fungal host for further enhancing the heterologous protein production ability by combining mutational and molecular breeding techniques.

  14. Insect cells are superior to Escherichia coli in producing malaria proteins inducing IgG targeting PfEMP1 on infected erythrocytes

    Directory of Open Access Journals (Sweden)

    Joergensen Louise

    2010-11-01

    Full Text Available Abstract Background The PFD1235w Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1 antigen is associated with severe malaria in children and can be expressed on the surface of infected erythrocytes (IE adhering to ICAM1. However, the exact three-dimensional structure of this PfEMP1 and its surface-exposed epitopes are unknown. An insect cell and Escherichia coli based system was used to express single and double domains encoded by the pfd1235w var gene. The resulting recombinant proteins have been evaluated for yield and purity and their ability to induce rat antibodies, which react with the native PFD1235w PfEMP1 antigen expressed on 3D7PFD1235w-IE. Their recognition by human anti-malaria antibodies from previously infected Tanzanian donors was also analysed. Methods The recombinant proteins were run on SDS-PAGE and Western blots for quantification and size estimation. Insect cell and E. coli-produced recombinant proteins were coupled to a bead-based Luminex assay to measure the plasma antibody reactivity of 180 samples collected from Tanzanian individuals. The recombinant proteins used for immunization of rats and antisera were also tested by flow cytometry for their ability to surface label 3D7PFD1235w-IE. Results All seven pAcGP67A constructs were successfully expressed as recombinant protein in baculovirus-infected insect cells and subsequently produced to a purity of 60-97% and a yield of 2-15 mg/L. By comparison, only three of seven pET101/D-TOPO constructs expressed in the E. coli system could be produced at all with purity and yield ranging from 3-95% and 6-11 mg/L. All seven insect cell, but only two of the E. coli produced proteins induced antibodies reactive with native PFD1235w expressed on 3D7PFD1235w-IE. The recombinant proteins were recognized in an age- and transmission intensity-dependent manner by antibodies from 180 Tanzanian individuals in a bead-based Luminex assay. Conclusions The baculovirus based insect cell

  15. 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.

  16. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.

    Science.gov (United States)

    Sharpton, Thomas J; Jospin, Guillaume; Wu, Dongying; Langille, Morgan G I; Pollard, Katherine S; Eisen, Jonathan A

    2012-10-13

    New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as "Sifting Families," or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology-based analyses. We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/).

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Scale-down of continuous protein producing Saccharomyces cerevisiae cultivations using a two compartment system

    DEFF Research Database (Denmark)

    Wright, Naia Risager; Rønnest, Nanna Petersen; Thykær, Jette

    2016-01-01

    ml standard continuous cultivations. It was found that substrate gradients within a limited range result in increased productivity of the heterologous protein under regulation of the glycolytic TPI promoter and delay the decrease of protein and trehalose production during continuous cultivation...

  2. Multi-omic profiling of EPO-producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael

    2015-01-01

    Chinese hamster ovary (CHO) cells are the preferred production host for many therapeutic proteins. The production of heterologous proteins in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi-omics approach was applied...

  3. Nitrogen and energy balance in growing mink (Mustela vison) fed different levels of bacterial protein meal produced with natural gas

    DEFF Research Database (Denmark)

    Hellwing, Anne Louise Frydendahl; Tauson, Anne-Helene; Ahlstrøm, Øystein

    2005-01-01

    The objective of this study was to estimate the effect of increasing the dietary content of bacterial protein meal (BPM) on energy and protein metabolism in growing mink kits. Sixteen male mink kits of the standard brown genotype were randomly fed one of four diets: A control (Diet III) and 60% (...

  4. The cAMP-dependent protein kinase inhibitor H-89 attenuates the bioluminescence signal produced by Renilla Luciferase.

    Directory of Open Access Journals (Sweden)

    Katie J Herbst

    2009-05-01

    Full Text Available Investigations into the regulation and functional roles of kinases such as cAMP-dependent protein kinase (PKA increasingly rely on cellular assays. Currently, there are a number of bioluminescence-based assays, for example reporter gene assays, that allow the study of the regulation, activity, and functional effects of PKA in the cellular context. Additionally there are continuing efforts to engineer improved biosensors that are capable of detecting real-time PKA signaling dynamics in cells. These cell-based assays are often utilized to test the involvement of PKA-dependent processes by using H-89, a reversible competitive inhibitor of PKA.We present here data to show that H-89, in addition to being a competitive PKA inhibitor, attenuates the bioluminescence signal produced by Renilla luciferase (RLuc variants in a population of cells and also in single cells. Using 10 microM of luciferase substrate and 10 microM H-89, we observed that the signal from RLuc and RLuc8, an eight-point mutation variant of RLuc, in cells was reduced to 50% (+/-15% and 54% (+/-14% of controls exposed to the vehicle alone, respectively. In vitro, we showed that H-89 decreased the RLuc8 bioluminescence signal but did not compete with coelenterazine-h for the RLuc8 active site, and also did not affect the activity of Firefly luciferase. By contrast, another competitive inhibitor of PKA, KT5720, did not affect the activity of RLuc8.The identification and characterization of the adverse effect of H-89 on RLuc signal will help deconvolute data previously generated from RLuc-based assays looking at the functional effects of PKA signaling. In addition, for the current application and future development of bioluminscence assays, KT5720 is identified as a more suitable PKA inhibitor to be used in conjunction with RLuc-based assays. These principal findings also provide an important lesson to fully consider all of the potential effects of experimental conditions on a cell

  5. A fungal biofilm reactor based on metal structured packing improves the quality of a Gla::GFP fusion protein produced by Aspergillus oryzae.

    Science.gov (United States)

    Zune, Q; Delepierre, A; Gofflot, S; Bauwens, J; Twizere, J C; Punt, P J; Francis, F; Toye, D; Bawin, T; Delvigne, F

    2015-08-01

    Fungal biofilm is known to promote the excretion of secondary metabolites in accordance with solid-state-related physiological mechanisms. This work is based on the comparative analysis of classical submerged fermentation with a fungal biofilm reactor for the production of a Gla::green fluorescent protein (GFP) fusion protein by Aspergillus oryzae. The biofilm reactor comprises a metal structured packing allowing the attachment of the fungal biomass. Since the production of the target protein is under the control of the promoter glaB, specifically induced in solid-state fermentation, the biofilm mode of culture is expected to enhance the global productivity. Although production of the target protein was enhanced by using the biofilm mode of culture, we also found that fusion protein production is also significant when the submerged mode of culture is used. This result is related to high shear stress leading to biomass autolysis and leakage of intracellular fusion protein into the extracellular medium. Moreover, 2-D gel electrophoresis highlights the preservation of fusion protein integrity produced in biofilm conditions. Two fungal biofilm reactor designs were then investigated further, i.e. with full immersion of the packing or with medium recirculation on the packing, and the scale-up potentialities were evaluated. In this context, it has been shown that full immersion of the metal packing in the liquid medium during cultivation allows for a uniform colonization of the packing by the fungal biomass and leads to a better quality of the fusion protein.

  6. Wild blueberry polyphenol-protein food ingredients produced by three drying methods: Comparative physico-chemical properties, phytochemical content, and stability during storage.

    Science.gov (United States)

    Correia, Roberta; Grace, Mary H; Esposito, Debora; Lila, Mary Ann

    2017-11-15

    Particulate colloidal aggregate food ingredients were prepared by complexing wheat flour, chickpea flour, coconut flour and soy protein isolate with aqueous wild blueberry pomace extracts, then spray drying, freeze drying, or vacuum oven drying to prepare dry, flour-like matrices. Physico-chemical attributes, phytochemical content and stability during storage were compared. Eighteen anthocyanins peaks were identified for samples. Spray dried matrices produced with soy protein isolate had the highest concentration of polyphenols (156.2mg GAE/g) and anthocyanins (13.4mg/g) and the most potent DPPH scavenging activity (714.1μmolesTE/g). Spray dried blueberry polyphenols complexed with protein were protected from degradation during 16weeks at 4°C and 20°C. Soy protein isolate more efficiently captured and stabilized wild blueberry pomace phytochemicals than other protein sources. Overall, spray drying the blueberry extracts complexed with protein proved to be an environment-friendly strategy to produce stable functional ingredients with multiple applications for the food industry. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Long-lived radicals produced by γ-irradiation or vital activity in plants, animals, cells, and protein solution: their observation and inhomogeneous decay dynamics

    International Nuclear Information System (INIS)

    Miyazaki, Tetsuo; Morikawa, Akiyuki; Kumagai, Jun; Ikehata, Masateru; Koana, Takao; Kikuchi, Shoshi

    2002-01-01

    Long-lived radicals produced by γ-irradiation or vital activity in plants, animals, cells, and protein (albumin) solution were studied by electron spin resonance spectroscopy. Long-lived radicals produced by vital activity exist in biological systems, such as plants, animals, and cells, in the range of 0.1-20 nmol g -1 . Since vital organs keep the radicals at a constant concentration, the radicals are probably related to life conservation. Long-lived radicals are also produced by γ-irradiation of cells or protein solution. The radicals decay after death of living things or after γ-irradiation. We found that the decay dynamics in all biological systems can be expressed by the same kinetic equation of an inhomogeneous reaction

  8. Cloning and Characterization of a Unique Cytotoxic Protein Parasporin-5 Produced by Bacillus thuringiensis A1100 Strain

    Directory of Open Access Journals (Sweden)

    Keisuke Ekino

    2014-06-01

    Full Text Available Parasporin is the cytocidal protein present in the parasporal inclusion of the non-insecticidal Bacillus thuringiensis strains, which has no hemolytic activity but has cytocidal activities, preferentially killing cancer cells. In this study, we characterized a cytocidal protein that belongs to this category, which was designated parasporin-5 (PS5. PS5 was purified from B. thuringiensis serovar tohokuensis strain A1100 based on its cytocidal activity against human leukemic T cells (MOLT-4. The 50% effective concentration (EC50 of PS5 to MOLT-4 cells was approximately 0.075 μg/mL. PS5 was expressed as a 33.8-kDa inactive precursor protein and exhibited cytocidal activity only when degraded by protease at the C-terminal into smaller molecules of 29.8 kDa. Although PS5 showed no significant homology with other known parasporins, a Position Specific Iterative-Basic Local Alignment Search Tool (PSI-BLAST search revealed that the protein showed slight homology to, not only some B. thuringiensis Cry toxins, but also to aerolysin-type β-pore-forming toxins (β-PFTs. The recombinant PS5 protein could be obtained as an active protein only when it was expressed in a precursor followed by processing with proteinase K. The cytotoxic activities of the protein against various mammalian cell lines were evaluated. PS5 showed strong cytocidal activity to seven of 18 mammalian cell lines tested, and low to no cytotoxicity to the others.

  9. The dual role of microbes in corrosion.

    Science.gov (United States)

    Kip, Nardy; van Veen, Johannes A

    2015-03-01

    Corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. It is a world-wide problem with great societal and economic consequences. Current corrosion control strategies based on chemically produced products are under increasing pressure of stringent environmental regulations. Furthermore, they are rather inefficient. Therefore, there is an urgent need for environmentally friendly and sustainable corrosion control strategies. The mechanisms of microbially influenced corrosion and microbially influenced corrosion inhibition are not completely understood, because they cannot be linked to a single biochemical reaction or specific microbial species or groups. Corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. Information on the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments is scarce. As some microorganisms are able to both cause and inhibit corrosion, we pay particular interest to their potential role as corrosion-controlling agents. We show interesting interfaces in which scientists from different disciplines such as microbiology, engineering and art conservation can collaborate to find solutions to the problems caused by corrosion.

  10. The dual role of microbes in corrosion

    Science.gov (United States)

    Kip, Nardy; van Veen, Johannes A

    2015-01-01

    Corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. It is a world-wide problem with great societal and economic consequences. Current corrosion control strategies based on chemically produced products are under increasing pressure of stringent environmental regulations. Furthermore, they are rather inefficient. Therefore, there is an urgent need for environmentally friendly and sustainable corrosion control strategies. The mechanisms of microbially influenced corrosion and microbially influenced corrosion inhibition are not completely understood, because they cannot be linked to a single biochemical reaction or specific microbial species or groups. Corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. Information on the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments is scarce. As some microorganisms are able to both cause and inhibit corrosion, we pay particular interest to their potential role as corrosion-controlling agents. We show interesting interfaces in which scientists from different disciplines such as microbiology, engineering and art conservation can collaborate to find solutions to the problems caused by corrosion. PMID:25259571

  11. Sphingolipid biosynthesis in man and microbes.

    Science.gov (United States)

    Harrison, Peter J; Dunn, Teresa M; Campopiano, Dominic J

    2018-06-04

    A new review covering up to 2018Sphingolipids are essential molecules that, despite their long history, are still stimulating interest today. The reasons for this are that, as well as playing structural roles within cell membranes, they have also been shown to perform a myriad of cell signalling functions vital to the correct function of eukaryotic and prokaryotic organisms. Indeed, sphingolipid disregulation that alters the tightly-controlled balance of these key lipids has been closely linked to a number of diseases such as diabetes, asthma and various neuropathologies. Sphingolipid biogenesis, metabolism and regulation is mediated by a large number of enzymes, proteins and second messengers. There appears to be a core pathway common to all sphingolipid-producing organisms but recent studies have begun to dissect out important, species-specific differences. Many of these have only recently been discovered and in most cases the molecular and biochemical details are only beginning to emerge. Where there is a direct link from classic biochemistry to clinical symptoms, a number a drug companies have undertaken a medicinal chemistry campaign to try to deliver a therapeutic intervention to alleviate a number of diseases. Where appropriate, we highlight targets where natural products have been exploited as useful tools. Taking all these aspects into account this review covers the structural, mechanistic and regulatory features of sphingolipid biosynthetic and metabolic enzymes.

  12. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource

    Directory of Open Access Journals (Sweden)

    Sharpton Thomas J

    2012-10-01

    Full Text Available Abstract Background New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. Results We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as “Sifting Families,” or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology–based analyses. Conclusions We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/.

  13. 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

  14. 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- ...

  15. 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.

  16. Comparison of techniques of detecting immunoglobulin-binding protein reactivity to immunoglobulin produced by different avian and mammalian species.

    Science.gov (United States)

    Justiz-Vaillant, A A; Akpaka, P E; McFarlane-Anderson, N; Smikle, M F

    2013-01-01

    The rationale of this study was to use several immunological assays to investigate the reactivity of immunoglobulin binding protein (IBP) to immunoglobulins from various avian and mammalian species. The IBP studied were Staphylococcal protein A (SpA), Streptococcal protein G (SpG), Peptostreptococcal protein L (SpL) and recombinant protein LA (SpLA). The various immunological techniques used were double immunodiffusion (Ouchterlony technique) that tested positive high protein reactivities, direct and competitive enzyme-linked immunosorbent assays (ELISAs) that tested moderate and low positive protein binding capacities, respectively. In addition to sandwich ELISAs, immunoblot analyses and Ig-purification by SpA-affinity chromatography, which were sensitive tests and helpful in the screening and confirmatory tests were also used. The Ouchterlony technique showed that compared to the other proteins, SpLA had the highest range of reactivity with animal sera and purified immunoglobulins while SpL was least reactive. With the direct ELISA, SpL reacted with the raccoon sera, rabbit IgG and with IgY from bantam hens and pigeons. While with the direct ELISA, SpA reacted with sera from skunk, coyote, raccoon, mule, donkey and human. The sandwich ELISA revealed high reactivity of both SpG and SpLA with mammalian sera titres ranging from 1:32 (raccoon serum) to 1:1024 (mule and donkey sera). These results suggest that IBP can be used for the detection of immunoglobulin using various immunological assays and this is important for the diagnosis of infectious diseases in animal and bird populations studied and in the purification of immunoglobulins.

  17. The expression of a xylanase targeted to ER-protein bodies provides a simple strategy to produce active insoluble enzyme polymers in tobacco plants.

    Directory of Open Access Journals (Sweden)

    Immaculada Llop-Tous

    Full Text Available BACKGROUND: Xylanases deserve particular attention due to their potential application in the feed, pulp bleaching and paper industries. We have developed here an efficient system for the production of an active xylanase in tobacco plants fused to a proline-rich domain (Zera of the maize storage protein γ-zein. Zera is a self-assembling domain able to form protein aggregates in vivo packed in newly formed endoplasmic reticulum-derived organelles known as protein bodies (PBs. METHODOLOGY/PRINCIPAL FINDINGS: Tobacco leaves were transiently transformed with a binary vector containing the Zera-xylanase coding region, which was optimized for plant expression, under the control of the 35S CaMV promoter. The fusion protein was efficiently expressed and stored in dense PBs, resulting in yields of up to 9% of total protein. Zera-xylanase was post-translationally modified with high-mannose-type glycans. Xylanase fused to Zera was biologically active not only when solubilized from PBs but also in its insoluble form. The resistance of insoluble Zera-xylanase to trypsin digestion demonstrated that the correct folding of xylanase in PBs was not impaired by Zera oligomerization. The activity of insoluble Zera-xylanase was enhanced when substrate accessibility was facilitated by physical treatments such as ultrasound. Moreover, we found that the thermostability of the enzyme was improved when Zera was fused to the C-terminus of xylanase. CONCLUSION/SIGNIFICANCE: In the present work we have successfully produced an active insoluble aggregate of xylanase fused to Zera in plants. Zera-xylanase chimeric protein accumulates within ER-derived protein bodies as active aggregates that can easily be recovered by a simple density-based downstream process. The production of insoluble active Zera-xylanase protein in tobacco outlines the potential of Zera as a fusion partner for producing enzymes of biotechnological relevance. Zera-PBs could thus become efficient and low

  18. Purification of inclusion bodies using PEG precipitation under denaturing conditions to produce recombinant therapeutic proteins from Escherichia coli.

    Science.gov (United States)

    Chen, Huanhuan; Li, Ninghuan; Xie, Yueqing; Jiang, Hua; Yang, Xiaoyi; Cagliero, Cedric; Shi, Siwei; Zhu, Chencen; Luo, Han; Chen, Junsheng; Zhang, Lei; Zhao, Menglin; Feng, Lei; Lu, Huili; Zhu, Jianwei

    2017-07-01

    It has been documented that the purification of inclusion bodies from Escherichia coli by size exclusion chromatography (SEC) may benefit subsequent refolding and recovery of recombinant proteins. However, loading volume and the high cost of the column limits its application in large-scale manufacturing of biopharmaceutical proteins. We report a novel process using polyethylene glycol (PEG) precipitation under denaturing conditions to replace SEC for rapid purification of inclusion bodies containing recombinant therapeutic proteins. Using recombinant human interleukin 15 (rhIL-15) as an example, inclusion bodies of rhIL-15 were solubilized in 7 M guanidine hydrochloride, and rhIL-15 was precipitated by the addition of PEG 6000. A final concentration of 5% (w/v) PEG 6000 was found to be optimal to precipitate target proteins and enhance recovery and purity. Compared to the previously reported S-200 size exclusion purification method, PEG precipitation was easier to scale up and achieved the same protein yields and quality of the product. PEG precipitation also reduced manufacturing time by about 50 and 95% of material costs. After refolding and further purification, the rhIL-15 product was highly pure and demonstrated a comparable bioactivity with a rhIL-15 reference standard. Our studies demonstrated that PEG precipitation of inclusion bodies under denaturing conditions holds significant potential as a manufacturing process for biopharmaceuticals from E. coli protein expression systems.

  19. Purification and characterization of ribosomal proteins L27 and L30 having antimicrobial activity produced by the Lactobacillus salivarius SGL 03.

    Science.gov (United States)

    Pidutti, P; Federici, F; Brandi, J; Manna, L; Rizzi, E; Marini, U; Cecconi, D

    2018-02-01

    The aim of this study was to investigate the antimicrobial potential of proteins secreted by a new strain of Lactobacillus salivarius. The secretome of L. salivarius SGL 03 strain was analysed by gel-assisted fractionation and MS/MS to identify low-molecular-mass proteins. This strategy allowed us to identify 10 secreted proteins. Then, a combination of heterologous expression and agar well diffusion was used to characterize them as to their antimicrobial activity, mechanisms of action and stability. Our findings indicate that L27 and L30 proteins of the 50S ribosomal subunit have antimicrobial activity against Streptococcus pyogenes, Streptococcus uberis and Enterococcus faecium. In addition, both proteins are bactericidal against S. pyogenes and maintain their antimicrobial activity after different protease treatments, at acidic pH, after heat treatment, and if stored in a refrigerated ambient at least at 4°C. The overall results demonstrated that the L27 and L30 ribosomal proteins are of interest as new antimicrobial molecules to prevent the growth of S. pyogenes, S. uberis and E. faecium. Our results provide the first insight into the extra-ribosomal activity of L27 and L30 secreted proteins of L. salivarius. This study demonstrated the capacity of L. salivarius SGL 03 to produce antimicrobial molecules and suggested this strain as a promising probiotic candidate. © 2017 The Society for Applied Microbiology.

  20. Cloning and Expression of Plantaricin W Produced by Lactobacillus plantarum U10 Isolate from "Tempoyak" Indonesian Fermented Food as Immunity Protein in Lactococcus lactis.

    Science.gov (United States)

    Lages, Aksar Chair; Mustopa, Apon Zaenal; Sukmarini, Linda; Suharsono

    2015-10-01

    Plantaricins, one of bacteriocin produced by Lactobacillus plantarum, are already known to have activities against several pathogenic bacterium. L. plantarum U10 isolated from "tempoyak," an Indonesian fermented food, produced one kind of plantaricin designated as plantaricin W (plnW). The plnW is suggested as a putative membrane location of protein and has similar conserved motif which is important as immunity to bacteriocin itself. Thus, due to study about this plantaricin, several constructs have been cloned and protein was analyzed in Lactococcus lactis. In this study, plnW gene was successfully cloned into vector NICE system pNZ8148 and created the transformant named L. lactis NZ3900 pNZ8148-WU10. PlnW protein was 25.3 kDa in size. The concentration of expressed protein was significantly increased by 10 ng/mL nisin induction. Furthermore, PlnW exhibited protease activity with value of 2.22 ± 0.05 U/mL and specific activity about 1.65 ± 0.03 U/mg protein with 50 ng/mL nisin induction. Immunity study showed that the PlnW had immunity activity especially against plantaricin and rendered L. lactis recombinant an immunity broadly to other bacteriocins such as pediocin, fermentcin, and acidocin.

  1. Triosephosphate isomerase is a common crystallization contaminant of soluble His-tagged proteins produced in Escherichia coli

    International Nuclear Information System (INIS)

    Kozlov, Guennadi; Vinaik, Roohi; Gehring, Kalle

    2013-01-01

    Crystals of E. coli triosephosphate isomerase were obtained as a contaminant and its structure was determined to 1.85 Å resolution. Attempts to crystallize several mammalian proteins overexpressed in Escherichia coli revealed a common contaminant, triosephosphate isomerase, a protein involved in glucose metabolism. Even with triosephosphate isomerase present in very small amounts, similarly shaped crystals appeared in the crystallization drops in a number of polyethylene glycol-containing conditions. All of the target proteins were His-tagged and their purification involved immobilized metal-affinity chromatography (IMAC), a step that was likely to lead to triosephosphate isomerase contamination. Analysis of the triosephosphate isomerase crystals led to the structure of E. coli triosephosphate isomerase at 1.85 Å resolution, which is a significant improvement over the previous structure

  2. Selenite Reduction by Anaerobic Microbial Aggregates: Microbial Community Structure, and Proteins Associated to the Produced Selenium Spheres

    KAUST Repository

    Gonzalez-Gil, Graciela; Lens, Piet N. L.; Saikaly, Pascal

    2016-01-01

    that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS) analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from

  3. Construct design, production, and characterization of Plasmodium falciparum 48/45 R0.6C subunit protein produced in Lactococcus lactis as candidate vaccine.

    Science.gov (United States)

    Singh, Susheel K; Roeffen, Will; Mistarz, Ulrik H; Chourasia, Bishwanath Kumar; Yang, Fen; Rand, Kasper D; Sauerwein, Robert W; Theisen, Michael

    2017-05-31

    The sexual stages of Plasmodium falciparum are responsible for the spread of the parasite in malaria endemic areas. The cysteine-rich Pfs48/45 protein, exposed on the surface of sexual stages, is one of the most advanced antigens for inclusion into a vaccine that will block transmission. However, clinical Pfs48/45 sub-unit vaccine development has been hampered by the inability to produce high yields of recombinant protein as the native structure is required for the induction of functional transmission-blocking (TB) antibodies. We have investigated a downstream purification process of a sub-unit (R0.6C) fragment representing the C-terminal 6-Cys domain of Pfs48/45 (6C) genetically fused to the R0 region (R0) of asexual stage Glutamate Rich Protein expressed in Lactococcus lactis. A series of R0.6C fusion proteins containing features, which aim to increase expression levels or to facilitate protein purification, were evaluated at small scale. None of these modifications affected the overall yield of recombinant protein. Consequently, R0.6C with a C-terminal his tag was used for upstream and downstream process development. A simple work-flow was developed consisting of batch fermentation followed by two purification steps. As such, the recombinant protein was purified to homogeneity. The composition of the final product was verified by HPLC, mass spectrometry, SDS-PAGE and Western blotting with conformation dependent antibodies against Pfs48/45. The recombinant protein induced high levels of functional TB antibodies in rats. The established production and purification process of the R0.6C fusion protein provide a strong basis for further clinical development of this candidate transmission blocking malaria vaccine.

  4. Coating Nanoparticles with Plant-Produced Transferrin-Hydrophobin Fusion Protein Enhances Their Uptake in Cancer Cells

    DEFF Research Database (Denmark)

    Reuter, Lauri J.; Shahbazi, Mohammad-Ali; Makila, Ermei M.

    2017-01-01

    can be expressed in Nicotiana benthamiana plants as a fusion with Trichoderma reesei hydrophobins HFBI, HFBII, or HFBIV. Transferrin-HFBIV was further expressed in tobacco BY-2 suspension cells. Both partners of the fusion protein retained their functionality; the hydrophobin moiety enabled migration...... to a surfactant phase in an aqueous two-phase system, and the transferrin moiety was able to reversibly bind iron. Coating porous silicon nanoparticles with the fusion protein resulted in uptake of the nanoparticles in human cancer cells. This study provides a proof-of concept for the functionalization...

  5. Biofilm production by clinical isolates of Pseudomonas aeruginosa and structural changes in LasR protein of isolates non biofilm-producing

    Directory of Open Access Journals (Sweden)

    Jailton Lobo da Costa Lima

    2018-03-01

    Full Text Available Introduction: Biofilm production is an important mechanism for the survival of Pseudomonas aeruginosa and its relationship with antimicrobial resistance represents a challenge for patient therapeutics. P. aeruginosa is an opportunistic pathogen frequently associated to nosocomial infections, especially in imunocompromised hosts. Objectives: Analyze the phenotypic biofilm production in P. aeruginosa isolates, describe clonal profiles, and analyze quorum sensing (QS genes and the occurrence of mutations in the LasR protein of non-biofilm producing isolates. Methods: Isolates were tested for biofilm production by measuring cells adherence to the microtiter plates. Clonal profile analysis was carried out through ERIC-PCR, QS genes were by specific PCR. Results: The results showed that 77.5% of the isolates were considered biofilm producers. The results of genotyping showed 38 distinct genetic profiles. As for the occurrence of the genes, 100% of the isolates presented the lasR, rhlI and rhlR genes, and 97.5%, presented the lasI gene. In this study nine isolates were not biofilm producers. However, all presented the QS genes. Amplicons related to genes were sequenced in three of the nine non-biofilm-producing isolates (all presenting different genetic similarity profile and aligned to the sequences of those genes in P. aeruginosa strain PAO1 (standard biofilm-producing strain. Alignment analysis showed an insertion of three nucleotides (T, C and G causing the addition of an amino acid valine in the sequence of the LasR protein, in position 53. Conclusion: The modeling of the resulting LasR protein showed a conformational change in its structure, suggesting that this might be the reason why these isolates are unable to produce biofilm. Keywords: Pseudomonas aeruginosa, Biofilm, Multiresistance, Quorum sensing (QS

  6. 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

  7. Flowers and Wild Megachilid Bees Share Microbes.

    Science.gov (United States)

    McFrederick, Quinn S; Thomas, Jason M; Neff, John L; Vuong, Hoang Q; Russell, Kaleigh A; Hale, Amanda R; Mueller, Ulrich G

    2017-01-01

    Transmission pathways have fundamental influence on microbial symbiont persistence and evolution. For example, the core gut microbiome of honey bees is transmitted socially and via hive surfaces, but some non-core bacteria associated with honey bees are also found on flowers, and these bacteria may therefore be transmitted indirectly between bees via flowers. Here, we test whether multiple flower and wild megachilid bee species share microbes, which would suggest that flowers may act as hubs of microbial transmission. We sampled the microbiomes of flowers (either bagged to exclude bees or open to allow bee visitation), adults, and larvae of seven megachilid bee species and their pollen provisions. We found a Lactobacillus operational taxonomic unit (OTU) in all samples but in the highest relative and absolute abundances in adult and larval bee guts and pollen provisions. The presence of the same bacterial types in open and bagged flowers, pollen provisions, and bees supports the hypothesis that flowers act as hubs of transmission of these bacteria between bees. The presence of bee-associated bacteria in flowers that have not been visited by bees suggests that these bacteria may also be transmitted to flowers via plant surfaces, the air, or minute insect vectors such as thrips. Phylogenetic analyses of nearly full-length 16S rRNA gene sequences indicated that the Lactobacillus OTU dominating in flower- and megachilid-associated microbiomes is monophyletic, and we propose the name Lactobacillus micheneri sp. nov. for this bacterium.

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

    Science.gov (United States)

    Carvalhais, Lilia C; Dennis, Paul G; Fan, Ben; Fedoseyenko, Dmitri; Kierul, Kinga; Becker, Anke; von Wiren, Nicolaus; Borriss, Rainer

    2013-01-01

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

  9. Structure based modification of Bluetongue virus helicase protein VP6 to produce a viable VP6-truncated BTV

    Energy Technology Data Exchange (ETDEWEB)

    Matsuo, Eiko [Microbiology and Immunology, Division of Animal Science, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe-City 657-8501 (Japan); Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT (United Kingdom); Leon, Esther; Matthews, Steve J. [Division of Molecular Biosciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ (United Kingdom); Roy, Polly, E-mail: polly.roy@lshtm.ac.uk [Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT (United Kingdom)

    2014-09-05

    Highlights: • NMR analysis on BTV VP6 reveals two large loop regions. • The loss of a loop (aa 34–130) does not affect the overall fold of the protein. • A region of VP6 (aa 34–92) is not required for BTV replication. • A region of VP6 (aa 93–130) plays an essential role in the virus replication. - Abstract: Bluetongue virus core protein VP6 is an ATP hydrolysis dependent RNA helicase. However, despite much study, the precise role of VP6 within the viral capsid and its structure remain unclear. To investigate the requirement of VP6 in BTV replication, we initiated a structural and biological study. Multinuclear nuclear magnetic resonance spectra were assigned on his-tagged full-length VP6 (329 amino acid residues) as well as several truncated VP6 variants. The analysis revealed a large structured domain with two large loop regions that exhibit significant conformational exchange. One of the loops (amino acid position 34–130) could be removed without affecting the overall fold of the protein. Moreover, using a BTV reverse genetics system, it was possible to demonstrate that the VP6-truncated BTV was viable in BHK cells in the absence of any helper VP6 protein, suggesting that a large portion of this loop region is not absolutely required for BTV replication.

  10. Multi-omic profiling of EPO producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael

    Heterologous protein production in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi-omics approach was applied to characterize the physiological impact of erythropoietin production, and discover production bottlenecks, ...

  11. Online analysis of protein inclusion bodies produced in E. coli by monitoring alterations in scattered and reflected light.

    Science.gov (United States)

    Ude, Christian; Ben-Dov, Nadav; Jochums, André; Li, Zhaopeng; Segal, Ester; Scheper, Thomas; Beutel, Sascha

    2016-05-01

    The online monitoring of recombinant protein aggregate inclusion bodies during microbial cultivation is an immense challenge. Measurement of scattered and reflected light offers a versatile and non-invasive measurement technique. Therefore, we investigated two methods to detect the formation of inclusion bodies and monitor their production: (1) online 180° scattered light measurement (λ = 625 nm) using a sensor platform during cultivation in shake flask and (2) online measurement of the light reflective interference using a porous Si-based optical biosensor (SiPA). It could be shown that 180° scattered light measurement allows monitoring of alterations in the optical properties of Escherichia coli BL21 cells, associated with the formation of inclusion bodies during cultivation. A reproducible linear correlation between the inclusion body concentration of the non-fluorescent protein human leukemia inhibitory factor (hLIF) carrying a thioredoxin tag and the shift ("Δamp") in scattered light signal intensity was observed. This was also observed for the glutathione-S-transferase-tagged green fluorescent protein (GFP-GST). Continuous online monitoring of reflective interference spectra reveals a significant increase in the bacterium refractive index during hLIF production in comparison to a non-induced reference that coincide with the formation of inclusion bodies. These online monitoring techniques could be applied for fast and cost-effective screening of different protein expression systems.

  12. Terrestrial microbes in martian and chondritic meteorites

    Science.gov (United States)

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

    2007-08-01

    remaining fragments of the samples were used for amino acid and isotopic analyses [6]. Some samples were fragments of dried and wet meteorites isolated in centrifuge tubes after a 10-day water extraction. Sabouraud Dextrose (dilutions 1:10 and 1:1000), Bacto Agar, LB Broth Miller (dilutions 1:10 and 1:1000), and R2A agar (1:1 and 1:1000), were autoclaved and cooled in culture plates inside a clean hood for cell culture. Some controls retained sterile moist agar still adhering to the perimeter of the plates for up to 18 months, and validated the sterile technique. Cell culture, PCR and microscopy documented a diversity of archea, prokaryotes and eukaryotes in these samples [7]. The plates displaying microbial growth at room temperature after 6 weeks or less were used to produce streak plates and isolate colonies of individual species for long term freezing in Eppendorf tubes. Any plate with biological growth along the perimeter of the plate was discarded. The plates without microbial activity after 6 weeks were stored in a fridge for 18 months. Control plates, exposed to the clean hood, laboratory room, used gloves, and weighing paper used in the analyses, sustained the prolonged storage with no sign of microbial activity that could be related to the analysis method. Dust grains and water extracts from the meteorites were spread on agar surfaces in cell culture Petri dishes in a clean hood. SNC samples.In early 2005, the surface of SNC stones in the USNM curation facility were brushed with sterile swabs. Fallen dust grains were collected on weighing paper and isolated in sterile tubes. The sample suite included Zagami USNM 6545, Lafayette USNM 1505, Los Angeles USNM 7052, Shergotty USNM 321, Nakhla USNM 5892, Nakhla USNM 426 (117.4 g) and Nakhla USNM 426 (18.2 g), and Chassigny USNMMNHN 2524. The controls, worker's gloves, blank swabs, and weighing paper exhibited no microbial activity in subsequent months. The cell culture was conducted with Sabouraud Dextrose and R2A only

  13. 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.

  14. Modification of the BAX System PCR assay for detecting Salmonella in beef, produce, and soy protein isolate. Performance Tested Method 100201.

    Science.gov (United States)

    Peng, Linda X; Wallace, Morgan; Andaloro, Bridget; Fallon, Dawn; Fleck, Lois; Delduco, Dan; Tice, George

    2011-01-01

    The BAX System PCR assay for Salmonella detection in foods was previously validated as AOAC Research Institute (RI) Performance Tested Method (PTM) 100201. New studies were conducted on beef and produce using the same media and protocol currently approved for the BAX System PCR assay for E. coli O157:H7 multiplex (MP). Additionally, soy protein isolate was tested for matrix extension using the U.S. Food and Drug Administration-Bacteriological Analytical Manual (FDA-BAM) enrichment protocols. The studies compared the BAX System method to the U.S. Department of Agriculture culture method for detecting Salmonella in beef and the FDA-BAM culture method for detecting Salmonella in produce and soy protein isolate. Method comparison studies on low-level inoculates showed that the BAX System assay for Salmonella performed as well as or better than the reference method for detecting Salmonella in beef and produce in 8-24 h enrichment when the BAX System E. coli O157:H7 MP media was used, and soy protein isolate in 20 h enrichment with lactose broth followed by 3 h regrowth in brain heart infusion broth. An inclusivity panel of 104 Salmonella strains with diverse serotypes was tested by the BAX System using the proprietary BAX System media and returned all positive results. Ruggedness factors involved in the enrichment phase were also evaluated by testing outside the specified parameters, and none of the factors examined affected the performance of the assay.

  15. Enzymatic protein hydrolysates from high pressure-pretreated isolated pea proteins have better antioxidant properties than similar hydrolysates produced from heat pretreatment.

    Science.gov (United States)

    Girgih, Abraham T; Chao, Dongfang; Lin, Lin; He, Rong; Jung, Stephanie; Aluko, Rotimi E

    2015-12-01

    Isolated pea protein (IPP) dispersions (1%, w/v) were pretreated with high pressure (HP) of 200, 400, or 600 MPa for 5 min at 24 °C or high temperature (HT) for 30 min at 100 °C prior to hydrolysis with 1% (w/w) Alcalase. HP pretreatment of IPP at 400 and 600 MPa levels led to significantly (P40%) oxygen radical absorption capacity (ORAC) of hydrolysates. 2,2-Diphenyl-1-picrylhydrazyl, superoxide radical and hydroxyl radical scavenging activities of pea protein hydrolysates were also significantly (PProtein hydrolysates from HT IPP showed no ORAC, superoxide or hydroxyl scavenging activity but had significantly (Pprotein hydrolysates had weaker antioxidant properties than glutathione but overall, the HP pretreatment was superior to HT pretreatment in facilitating enzymatic release of antioxidant peptides from IPP. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. High Protein- and High Lipid-Producing Microalgae from Northern Australia as Potential Feedstock for Animal Feed and Biodiesel

    OpenAIRE

    Duong, Van Thang; Ahmed, Faruq; Thomas-Hall, Skye R.; Quigley, Simon; Nowak, Ekaterina; Schenk, Peer M.

    2015-01-01

    Microalgal biomass can be used for biodiesel, feed, and food production. Collection and identification of local microalgal strains in the Northern Territory, Australia was conducted to identify strains with high protein and lipid contents as potential feedstock for animal feed and biodiesel production, respectively. A total of 36 strains were isolated from 13 samples collected from a variety of freshwater locations, such as dams, ponds, and streams and subsequently classified by 18S rDNA sequ...

  17. High protein- and high lipid-producing microalgae from Outback Australia as potential feedstock for animal feed and biodiesel

    OpenAIRE

    Van Thang eDuong; Faruq eAhmed; Skye R Thomas-Hall; Katia eNowak; Peer M Schenk

    2015-01-01

    Microalgal biomass can be used for biodiesel, feed and food production. Collection and identification of local microalgal strains in the Northern Territory – Australia was conducted to identify strains with high protein and lipid contents as potential feedstock for animal feed and biodiesel production, respectively. A total of 36 strains were isolated from 13 samples collected from a variety of freshwater locations, such as dams, ponds and streams and subsequently classified by 18S rDNA seque...

  18. Utilization of waste as biogas substrateby dominan microbes identified

    Science.gov (United States)

    Nurlina, E.; Sambasri, S.; Hartati, E.; Safitri, R.; Hodijat, A.

    2018-05-01

    Indonesia as the tropics have a source of biomass feedstock which is very large, so the waste biomass can be used optimally as an energy source in the form of biogas. This study was conducted to obtain alternative energy from domestic waste materials, given the limited availability of petroleum and natural gas sourced from fossil fuels. This methodology is an experimental method, the process conditions at room temperature 25-27 °C, pH adjusted to the growth of microbes to produce biogas, retention time 20-60 days, the bioreactor is operated with a batch system, the volume of waste in the bioreactor is made permanent, so that the production of biogas in large scale will increase the pressure inside the bioreactor. Biogas is formed accommodated then distributed to the stove. Factors that determine the formation of biogas is a microbial species capable methanogens convert acetate into biogas. From the results of microbial identification of the isolates in the bioreactor, has identified three types of bacteria methanogens namely Methanospirillum hungatei, Methanobacterium polustre and Methanolacinapoynteri. The results of this study, domestic waste can be utilized as a substrate in biogas production, with the highest methane composition reaches 50.79%. This result is expected to increase public knowledge to utilize the waste into biogas as a renewable energy to sufficient the energy needs of household, so it does not depend on the energy derived from fossil fuels.

  19. Detoxification of Fusaric Acid by the Soil Microbe Mucor rouxii.

    Science.gov (United States)

    Crutcher, Frankie K; Puckhaber, Lorraine S; Bell, Alois A; Liu, Jinggao; Duke, Sara E; Stipanovic, Robert D; Nichols, Robert L

    2017-06-21

    Fusarium oxysporum f. sp. vasinfectum race 4 (VCG0114), which causes root rot and wilt of cotton (Gossypium hirsutum and G. barbadense), has been identified recently for the first time in the western hemisphere in certain fields in the San Joaquin Valley of California. This pathotype produces copious quantities of the plant toxin fusaric acid (5-butyl-2-pyridinecarboxylic acid) compared to other isolates of F. oxysporum f. sp. vasinfectum (Fov) that are indigenous to the United States. Fusaric acid is toxic to cotton plants and may help the pathogen compete with other microbes in the soil. We found that a laboratory strain of the fungus Mucor rouxii converts fusaric acid into a newly identified compound, 8-hydroxyfusaric acid. The latter compound is significantly less phytotoxic to cotton than the parent compound. On the basis of bioassays of hydroxylated analogues of fusaric acid, hydroxylation of the butyl side chain of fusaric acid may affect a general detoxification of fusaric acid. Genes that control this hydroxylation may be useful in developing biocontrol agents to manage Fov.

  20. Microbe-surface interactions in biofouling and biocorrosion processes.

    Science.gov (United States)

    Beech, Iwona B; Sunner, Jan A; Hiraoka, Kenzo

    2005-09-01

    The presence of microorganisms on material surfaces can have a profound effect on materials performance. Surface-associated microbial growth, i.e. a biofilm, is known to instigate biofouling. The presence of biofilms may promote interfacial physico-chemical reactions that are not favored under abiotic conditions. In the case of metallic materials, undesirable changes in material properties due to a biofilm (or a biofouling layer) are referred to as biocorrosion or microbially influenced corrosion (MIC). Biofouling and biocorrosion occur in aquatic and terrestrial habitats varying in nutrient content, temperature, pressure and pH. Interfacial chemistry in such systems reflects a wide variety of physiological activities carried out by diverse microbial populations thriving within biofilms. Biocorrosion can be viewed as a consequence of coupled biological and abiotic electron-transfer reactions, i.e. redox reactions of metals, enabled by microbial ecology. Microbially produced extracellular polymeric substances (EPS), which comprise different macromolecules, mediate initial cell adhesion to the material surface and constitute a biofilm matrix. Despite their unquestionable importance in biofilm development, the extent to which EPS contribute to biocorrosion is not well-understood. This review offers a current perspective on material/microbe interactions pertinent to biocorrosion and biofouling, with EPS as a focal point, while emphasizing the role atomic force spectroscopy and mass spectrometry techniques can play in elucidating such interactions.

  1. Genomic analysis of the aconidial and high-performance protein producer, industrially relevant Aspergillus niger SH2 strain.

    Science.gov (United States)

    Yin, Chao; Wang, Bin; He, Pan; Lin, Ying; Pan, Li

    2014-05-15

    Aspergillus niger is usually regarded as a beneficial species widely used in biotechnological industry. Obtaining the genome sequence of the widely used aconidial A. niger SH2 strain is of great importance to understand its unusual production capability. In this study we assembled a high-quality genome sequence of A. niger SH2 with approximately 11,517 ORFs. Relatively high proportion of genes enriched for protein expression related FunCat items verify its efficient capacity in protein production. Furthermore, genome-wide comparative analysis between A. niger SH2 and CBS513.88 reveals insights into unique properties of A. niger SH2. A. niger SH2 lacks the gene related with the initiation of asexual sporulation (PrpA), leading to its distinct aconidial phenotype. Frame shift mutations and non-synonymous SNPs in genes of cell wall integrity signaling, β-1,3-glucan synthesis and chitin synthesis influence its cell wall development which is important for its hyphal fragmentation during industrial high-efficiency protein production. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Identification and Characterization of an Antifungal Protein, AfAFPR9, Produced by Marine-Derived Aspergillus fumigatus R9.

    Science.gov (United States)

    Rao, Qi; Guo, Wenbin; Chen, Xinhua

    2015-05-01

    A fungal strain, R9, was isolated from the South Atlantic sediment sample and identified as Aspergillus fumigatus. An antifungal protein, AfAFPR9, was purified from the culture supernatant of Aspergillus fumigatus R9. AfAFPR9 was identified to be restrictocin, which is a member of the ribosome-inactivating proteins (RIPs), by MALDI-TOF-TOF-MS. AfAFPR9 displayed antifungal activity against plant pathogenic Fusarium oxysporum, Alternaria longipes, Colletotrichum gloeosporioides, Paecilomyces variotii, and Trichoderma viride at minimum inhibitory concentrations of 0.6, 0.6, 1.2, 1.2, and 2.4 μg/disc, respectively. Moreover, AfAFPR9 exhibited a certain extent of thermostability, and metal ion and denaturant tolerance. The iodoacetamide assay showed that the disulfide bridge in AfAFPR9 was indispensable for its antifungal action. The cDNA encoding for AfAFPR9 was cloned from A. fumigatus R9 by RTPCR and heterologously expressed in E. coli. The recombinant AfAFPR9 protein exhibited obvious antifungal activity against C. gloeosporioides, T. viride, and A. longipes. These results reveal the antifungal properties of a RIP member (AfAFPR9) from marine-derived Aspergillus fumigatus and indicated its potential application in controlling plant pathogenic fungi.

  3. Nanocomposited coatings produced by laser-assisted process to prevent silicone hydogels from protein fouling and bacterial contamination

    International Nuclear Information System (INIS)

    Huang, Guobang; Chen, Yi; Zhang, Jin

    2016-01-01

    Graphical abstract: Nanocomposited-coating was deposited on silicone hydrogel by using the matrix-assisted pulsed laser evaporation (MAPLE) process. The ZnO–PEG nanocomposited coating reduces over 50% protein absorption on silicone hydrogel, and can inhibit the bacterial growth efficiently. - Highlights: • We developed a nanocomposited coating to prevent silicone hydrogel from biofouling. • Matrix-assisted pulsed laser evaporation can deposit inorganic–organic nanomaterials. • The designed nanocomposited coating reduces protein absorption by over 50%. • The designed nanocomposited coating shows significant antimicrobial efficiency. - Abstract: Zinc oxide (ZnO) nanoparticles incorporating with polyethylene glycol (PEG) were deposited together on the surface of silicone hydrogel through matrix-assisted pulsed laser evaporation (MAPLE). In this process, frozen nanocomposites (ZnO–PEG) in isopropanol were irradiated under a pulsed Nd:YAG laser at 532 nm for 1 h. Our results indicate that the MAPLE process is able to maintain the chemical backbone of polymer and prevent the nanocomposite coating from contamination. The ZnO–PEG nanocomposited coating reduces over 50% protein absorption on silicone hydrogel. The cytotoxicity study shows that the ZnO–PEG nanocomposites deposited on silicone hydrogels do not impose the toxic effect on mouse NIH/3T3 cells. In addition, MAPLE-deposited ZnO–PEG nanocomposites can inhibit the bacterial growth significantly.

  4. 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.

  5. Environmental restoration using plant-microbe bioaugmentation

    International Nuclear Information System (INIS)

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

    1993-04-01

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

  6. Research Advances and Detection Methodologies for Microbe-Derived Acetylcholinesterase Inhibitors: A Systemic Review

    Directory of Open Access Journals (Sweden)

    Jingqian Su

    2017-01-01

    Full Text Available Acetylcholinesterase inhibitors (AChEIs are an attractive research subject owing to their potential applications in the treatment of neurodegenerative diseases. Fungi and bacteria are major producers of AChEIs. Their active ingredients of fermentation products include alkaloids, terpenoids, phenylpropanoids, and steroids. A variety of in vitro acetylcholinesterase inhibitor assays have been developed and used to measure the activity of acetylcholinesterases, including modified Ellman’s method, thin layer chromatography bioautography, and the combined liquid chromatography-mass spectrometry/modified Ellman’s method. In this review, we provide an overview of the different detection methodologies, the microbe-derived AChEIs, and their producing strains.

  7. Forkhead box protein A2, a pioneer factor for hepatogenesis, is involved in the expression of hepatic phenotype of alpha-fetoprotein-producing adenocarcinoma.

    Science.gov (United States)

    Yamamura, Nobuhisa; Fugo, Kazunori; Kishimoto, Takashi

    2017-09-01

    Alpha-fetoprotein (AFP)-producing adenocarcinoma is a high-malignant variant of adenocarcinoma with a hepatic or fetal-intestinal phenotype. The number of cases of AFP-producing adenocarcinomas is increasing, but the molecular mechanism underlying the aberrant production of AFP is unclear. Here we sought to assess the role of Forkhead box A (FoxA)2, which is a pioneer transcription factor in the differentiation of hepatoblasts. FoxA2 expression was investigated in five cases of AFP-producing gastric adenocarcinomas by immunohistochemistry, and all cases showed FoxA2 expression. Chromatin immunoprecipitation revealed the DNA binding of FoxA2 on the regulatory element of AFP gene in AFP-producing adenocarcinoma cells. The inhibition of FoxA2 expression with siRNA reduced the mRNA expression of liver-specific proteins, including AFP, albumin, and transferrin. The inhibition of FoxA2 also reduced the expressions of liver-enriched nuclear factors, i.e., hepatocyte nuclear factor (HNF) 4α and HNF6, although the expressions of HNF1α and HNF1β were not affected. The same effect as FoxA2 knockdown in AFP producing adenocarcinoma cells was also observed in hepatocellular carcinoma cells. Our results suggest that FoxA2 plays a key role in the expression of hepatic phenotype of AFP-producing adenocarcinomas. Copyright © 2017 Elsevier GmbH. All rights reserved.

  8. 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.

  9. 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.

  10. 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.

  11. 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)

  12. 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...

  13. Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners

    Directory of Open Access Journals (Sweden)

    Haft Daniel H

    2011-01-01

    Full Text Available Abstract Background Enzymes in the radical SAM (rSAM domain family serve in a wide variety of biological processes, including RNA modification, enzyme activation, bacteriocin core peptide maturation, and cofactor biosynthesis. Evolutionary pressures and relationships to other cellular constituents impose recognizable grammars on each class of rSAM-containing system, shaping patterns in results obtained through various comparative genomics analyses. Results An uncharacterized gene cluster found in many Actinobacteria and sporadically in Firmicutes, Chloroflexi, Deltaproteobacteria, and one Archaeal plasmid contains a PqqE-like rSAM protein family that includes Rv0693 from Mycobacterium tuberculosis. Members occur clustered with a strikingly well-conserved small polypeptide we designate "mycofactocin," similar in size to bacteriocins and PqqA, precursor of pyrroloquinoline quinone (PQQ. Partial Phylogenetic Profiling (PPP based on the distribution of these markers identifies the mycofactocin cluster, but also a second tier of high-scoring proteins. This tier, strikingly, is filled with up to thirty-one members per genome from three variant subfamilies that occur, one each, in three unrelated classes of nicotinoproteins. The pattern suggests these variant enzymes require not only NAD(P, but also the novel gene cluster. Further study was conducted using SIMBAL, a PPP-like tool, to search these nicotinoproteins for subsequences best correlated across multiple genomes to the presence of mycofactocin. For both the short chain dehydrogenase/reductase (SDR and iron-containing dehydrogenase families, aligning SIMBAL's top-scoring sequences to homologous solved crystal structures shows signals centered over NAD(P-binding sites rather than over substrate-binding or active site residues. Previous studies on some of these proteins have revealed a non-exchangeable NAD cofactor, such that enzymatic activity in vitro requires an artificial electron acceptor such

  14. 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.

  15. 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.

  16. 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

  17. [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.

  18. Use of a molecular genetic platform technology to produce human Wnt proteins reveals distinct local and distal signaling abilities.

    Directory of Open Access Journals (Sweden)

    Jennifer L Green

    Full Text Available Functional and mechanistic studies of Wnt signaling have been severely hindered by the inaccessibility of bioactive proteins. To overcome this long-standing barrier, we engineered and characterized a panel of Chinese hamster ovary (CHO cell lines with inducible transgenes encoding tagged and un-tagged human WNT1, WNT3A, WNT5A, WNT7A, WNT11, WNT16 or the soluble Wnt antagonist Fzd8CRD, all integrated into an identical genomic locus. Using a quantitative real-time bioluminescence assay, we show that cells expressing WNT1, 3A and 7A stimulate Wnt/beta-catenin reporter activity, while the other WNT expressing cell lines interfere with this activation. Additionally, in contrast to WNT3A, WNT1 only exhibits activity when cell-associated, and thus only signals to neighboring cells. The reporter assay also revealed a rapid decline of Wnt activity at 37°C, indicating that Wnt activity is highly labile. These engineered cell lines will reduce the cost of making and purifying Wnt proteins and serve as a continuous, reliable and regulatable source of Wnts to research laboratories around the world.

  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. 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

  1. Multi-omic profiling of EPO-producing CHO cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael

    The Chinese hamster ovary (CHO) cell line is the predominant mammalian cell factory for production of therapeutic glycoproteins. In this work, we aimed to study bottlenecks in the secretory pathway associated with the production of human erythropoietin (EPO) in CHO cells. In connection to this, we...... discovered indications of metabolic adaptation of the amino acid catabolism in favor of heterologous protein production. We established a panel of stably EPO expressing CHO-K1 clones spanning a 25-fold productivity range and characterized the clones in batch and chemostat cultures. For this, we employed...... a multi-omic physiological characterization including metabolic foot printing of amino acids, metabolite fingerprinting of glycolytic intermediates, NAD(P)H-/NAD(P)+ and adenosine nucleotide phosphates. We used qPCR, qRT-PCR, western blots and Affymetrix CHO microarrays to assess EPO gene copy numbers...

  2. Cyclodextrin-Complexed Ocimum basilicum Leaves Essential Oil Increases Fos Protein Expression in the Central Nervous System and Produce an Antihyperalgesic Effect in Animal Models for Fibromyalgia

    Directory of Open Access Journals (Sweden)

    Simone S. Nascimento

    2014-12-01

    Full Text Available O. basilicum leaves produce essential oils (LEO rich in monoterpenes. The short half-life and water insolubility are limitations for LEO medical uses. β-Cyclodextrin (β-CD has been employed to improve the pharmacological properties of LEO. We assessed the antihyperalgesic profile of LEO, isolated or complexed in β-CD (LEO/β-CD, on an animal model for fibromyalgia. Behavioral tests: mice were treated every day with either LEO/β-CD (25, 50 or 100 mg/kg, p.o., LEO (25 mg/kg, p.o., tramadol (TRM 4 mg/kg, i.p. or vehicle (saline, and 60 min after treatment behavioral parameters were assessed. Therefore, mice were evaluated for mechanical hyperalgesia (von Frey, motor coordination (Rota-rod and muscle strength (Grip Strength Metter in a mice fibromyalgia model. After 27 days, we evaluated the central nervous system (CNS pathways involved in the effect induced by experimental drugs through immunofluorescence protocol to Fos protein. The differential scanning analysis (DSC, thermogravimetry/derivate thermogravimetry (TG/DTG and infrared absorption spectroscopy (FTIR curves indicated that the products prepared were able to incorporate the LEO efficiently. Oral treatment with LEO or LEO-βCD, at all doses tested, produced a significant reduction of mechanical hyperalgesia and we were able to significantly increase Fos protein expression. Together, our results provide evidence that LEO, isolated or complexed with β-CD, produces analgesic effects on chronic non-inflammatory pain as fibromyalgia.

  3. Synthetic biology of microbes synthesizing polyhydroxyalkanoates (PHA

    Directory of Open Access Journals (Sweden)

    Guo-Qiang Chen

    2016-12-01

    Full Text Available Microbial polyhydroxyalkanoates (PHA have been produced as bioplastics for various purposes. Under the support of China National Basic Research 973 Project, we developed synthetic biology methods to diversify the PHA structures into homo-, random, block polymers with improved properties to better meet various application requirements. At the same time, various pathways were assembled to produce various PHA from glucose as a simple carbon source. At the end, Halomonas bacteria were reconstructed to produce PHA in changing morphology for low cost production under unsterile and continuous conditions. The synthetic biology will advance the PHA into a bio- and material industry.

  4. A novel water-based process produces eco-friendly bio-adhesive made from green cross-linked soybean soluble polysaccharide and soy protein.

    Science.gov (United States)

    Yuan, Cheng; Chen, Mingsong; Luo, Jing; Li, Xiaona; Gao, Qiang; Li, Jianzhang

    2017-08-01

    In this study, an eco-friendly soy protein adhesive was developed that utilized two components from soybean meal without addition of any toxic material. A plant-based, water-soluble and inexpensive soybean soluble polysaccharide was used as the novel renewable material to combine with soy protein to produce a soy protein adhesive. Three-plywood was fabricated with the resulting adhesive, and its wet shear strength was measured. The results showed the wet shear strength of plywood bonded by the adhesive reached 0.99MPa, meeting the water resistance requirement for interior use panels. This improvement was attributed to the following reasons: (1) Combination of cross-linked soybean soluble polysaccharide and soy protein formed an interpenetrating network structure, improving the thermal stability and water resistance of the cured adhesive. (2) Adding CL-SSPS decreased the adhesive viscosity to 15.14Pas, which increased the amount of the adhesive that penetrate the wood's surface and formed more interlocks. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. 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.

  6. Adenine-N-oxide produced from adenine with gamma-rays and its binding to SH protein

    Energy Technology Data Exchange (ETDEWEB)

    Yamamoto, O [Hiroshima Univ. (Japan). Research Inst. for Nuclear Medicine and Biology

    1980-12-01

    /sup 14/C-labeled adenine aqueous solution was irradiated with /sup 60/Co gamma-rays. The yield of adenine-7-N-oxide, a radiolytic product, was determined by Sephadex G-10 column chromatography and TLC autoradiography. The apparent productive yield was very low, but the true yield should be much higher because of the reversible reaction to adenine and the easy decomposition of the N-oxide itself. Using synthesized /sup 14/C-adenine-7-N-oxide, noncovalent binding of this N-oxide to urease, an SH protein, was confirmed in comparison between the presence and absence of SDS by Ultrogel AcA 22 column chromatography. The noncovalent binding of the gamma-irradiated /sup 35/S-cysteine was also observed. The yield reached a limit in O/sub 2/ easier than in N/sub 2/ as the atmosphere for DNA irradiation. These results support an interaction structure, chemical bonds N-O---H-S-, for noncovalent binding which may be applied to the biological system as a radiation-induced damage.

  7. Explorative analysis of microbes, colloids and gases

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-08-15

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

  8. Explorative analysis of microbes, colloids and gases

    International Nuclear Information System (INIS)

    Hallbeck, Lotta; Pedersen, Karsten

    2008-08-01

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

  9. 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...

  10. Differential expression of SOS genes in an E. coli mutant producing unstable lexA protein enhances excision repair but inhibits mutagenesis

    International Nuclear Information System (INIS)

    Peterson, K.R.; Ganesan, A.K.; Mount, D.W.; Stanford Univ., CA)

    1986-01-01

    The SOS response is displayed following treatments which damage DNA or inhibit DNA replication. Two associated activities include enhanced capacity for DNA repair resulting from derepression of the recA, uvrA, uvrB and uvrD genes and increased mutagenesis due to derepression of recA, umuC and umuD. These changes are the consequence of the derepression of at least seventeen unlinked operons negatively regulated by LexA repressor. Following treatments that induce the SOS response, a signal molecule interacts with RecA protein, converting it to an activated form. Activated RecA protein facilitates the proteolytic cleavage of LexA repressor, which results in derepression of the regulon. The cell then enters a new physiological state during which time DNA repair processes are augmented. The lexA41 mutant of E. coli is a uv-resistant derivative of another mutant, lexA3, which produces a repressor that is not cleaved following inducing treatments. The resultant protein is unstable. Lac operon fusions to most of the genes in the SOS regulon were used to show that the various damage-inducible genes were derepressed to different extents. uvrA, B, and D were almost fully derepressed. Consistent with this finding, the rate of removal of T4 endonuclease V-sensitive sites was more rapid in the uv-irradiated lexA41 mutant than in normal cells, suggesting a more active excision repair system. We propose that the instability of the LexA41 protein reduces the intracellular concentration of repressor to a level that allows a high level of excision repair. The additional observation that SOS mutagenesis was only weakly induced in a lexA41 uvrA - mutant implies that the mutant protein partially represses one or more genes whose products promote SOS mutagenesis. 17 refs., 4 figs., 1 tab

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Insight and analysis problem solving in microbes to machines.

    Science.gov (United States)

    Clark, Kevin B

    2015-11-01

    A key feature for obtaining solutions to difficult problems, insight is oftentimes vaguely regarded as a special discontinuous intellectual process and/or a cognitive restructuring of problem representation or goal approach. However, this nearly century-old state of art devised by the Gestalt tradition to explain the non-analytical or non-trial-and-error, goal-seeking aptitude of primate mentality tends to neglect problem-solving capabilities of lower animal phyla, Kingdoms other than Animalia, and advancing smart computational technologies built from biological, artificial, and composite media. Attempting to provide an inclusive, precise definition of insight, two major criteria of insight, discontinuous processing and problem restructuring, are here reframed using terminology and statistical mechanical properties of computational complexity classes. Discontinuous processing becomes abrupt state transitions in algorithmic/heuristic outcomes or in types of algorithms/heuristics executed by agents using classical and/or quantum computational models. And problem restructuring becomes combinatorial reorganization of resources, problem-type substitution, and/or exchange of computational models. With insight bounded by computational complexity, humans, ciliated protozoa, and complex technological networks, for example, show insight when restructuring time requirements, combinatorial complexity, and problem type to solve polynomial and nondeterministic polynomial decision problems. Similar effects are expected from other problem types, supporting the idea that insight might be an epiphenomenon of analytical problem solving and consequently a larger information processing framework. Thus, this computational complexity definition of insight improves the power, external and internal validity, and reliability of operational parameters with which to classify, investigate, and produce the phenomenon for computational agents ranging from microbes to man-made devices. Copyright

  16. The dual role of microbes in corrosion

    NARCIS (Netherlands)

    Kip, D.J.; Van Veen, J.A.

    2015-01-01

    Corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. It is a world-wide problem with great societal and economic consequences. Current corrosion control strategies based on chemically produced

  17. Taurine: A Potential Ergogenic Aid for Preventing Muscle Damage and Protein Catabolism and Decreasing Oxidative Stress Produced by Endurance Exercise

    Directory of Open Access Journals (Sweden)

    Flávia G. De Carvalho

    2017-09-01

    Full Text Available The aim of this study was to evaluate the effects of taurine and chocolate milk supplementation on oxidative stress and protein metabolism markers, and aerobic parameters in triathletes.Methods: A double-blind, crossover study was conducted with 10 male triathletes, aged 30.9 ± 1.3 year, height 1.79 ± 0.01 m and body weight 77.45 ± 2.4 kg. Three grams of taurine and 400 ml of chocolate milk (TAUchoc, or a placebo (chocolate milk (CHOC was ingested post exercise for 8 weeks. Oxidative stress marker levels, and 24 h urinary nitrogen, creatinine, and urea excretion were measured before and after 8 weeks of training and supplementation with TAUchoc or CHOC. A maximal incremental running test on a treadmill was performed in order to evaluate aerobic parameters: Vmax, heart rate (HR and rate of perceived exertion (RPE.Results: TAUchoc treatment during the 8 weeks resulted in increased taurine plasma levels (PRE 201.32 ± 29.03 μmol/L and POST 234.36 ± 35.51 μmol/L, p = 0.01, decreased malondialdehyde levels (19.4%, p = 0.03 and urinary nitrogen excretion (−33%, p = 0.03, and promoted positive nitrogen balance (p = 0.01. There were no changes in reduced glutathione (TAUchoc PRE 0.72 ± 0.08 mmol/L and POST 0.83 ± 0.08 mmol/L; CHOC PRE 0.69 ± 0.08 mmol/L and POST 0.81 ± 0.06 mmol/L, vitamin E plasma levels (TAUchoc PRE 33.99 ± 2.52 μmol/L and 35.95 ± 2.80 μmol/L and CHOC PRE 31.48 ± 2.12 μmol/L and POST 33.77 ± 3.64 μmol/L, or aerobic parameters, which were obtained in the last phase of the maximal incremental running test (Vmax TAUchoc PRE 13 ± 1.4 km/h and POST 13.22 ± 1.34 km/h; CHOC PRE 13.11 ± 2.34 km/h and POST 13.11 ± 2.72 km/h, the heart rate values were TAUchoc PRE 181.89 ± 24.18 bpm and POST 168.89 ± 46.56 bpm; CHOC PRE 181.56 ± 2.14 bpm and POST 179.78 ± 3.4 bpm, and the RPE were TAUchoc PRE 8.33 ± 2.4 AU and POST 9.1 ± 2.1 AU; CHOC PRE 8.11 ± 4.94 AU and POST 8.78 ± 2.78 AU.Conclusion: Taurine supplementation

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

    Science.gov (United States)

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

    2014-01-01

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

  19. 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...

  20. 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.

  1. 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

  2. Veillonella, Firmicutes: Microbes disguised as Gram negatives.

    Science.gov (United States)

    Vesth, Tammi; Ozen, Aslı; Andersen, Sandra C; Kaas, Rolf Sommer; Lukjancenko, Oksana; Bohlin, Jon; Nookaew, Intawat; Wassenaar, Trudy M; Ussery, David W

    2013-12-20

    The Firmicutes represent a major component of the intestinal microflora. The intestinal Firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. Although most Firmicutes are Gram positive, members of the class Negativicutes, including the genus Veillonella, stain Gram negative. Veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerobes. In this work, the genomes of 24 Negativicutes, including eight Veillonella spp., are compared to 20 other Firmicutes genomes; a further 101 prokaryotic genomes were included, covering 26 phyla. Thus a total of 145 prokaryotic genomes were analyzed by various methods to investigate the apparent conflict of the Veillonella Gram stain and their taxonomic position within the Firmicutes. Comparison of the genome sequences confirms that the Negativicutes are distantly related to Clostridium spp., based on 16S rRNA, complete genomic DNA sequences, and a consensus tree based on conserved proteins. The genus Veillonella is relatively homogeneous: inter-genus pair-wise comparison identifies at least 1,350 shared proteins, although less than half of these are found in any given Clostridium genome. Only 27 proteins are found conserved in all analyzed prokaryote genomes. Veillonella has distinct metabolic properties, and significant similarities to genomes of Proteobacteria are not detected, with the exception of a shared LPS biosynthesis pathway. The clade within the class Negativicutes to which the genus Veillonella belongs exhibits unique properties, most of which are in common with Gram-positives and some with Gram negatives. They are only distantly related to Clostridia, but are even less closely related to Gram-negative species. Though the Negativicutes stain Gram-negative and possess two membranes, the genome and proteome analysis presented here confirm their place within the

  3. 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

  4. 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.

  5. Use of a Chimeric Hsp70 to Enhance the Quality of Recombinant Plasmodium falciparum S-Adenosylmethionine Decarboxylase Protein Produced in Escherichia coli

    Science.gov (United States)

    Makhoba, Xolani Henry; Burger, Adélle; Coertzen, Dina; Zininga, Tawanda; Birkholtz, Lyn-Marie; Shonhai, Addmore

    2016-01-01

    S-adenosylmethionine decarboxylase (PfAdoMetDC) from Plasmodium falciparum is a prospective antimalarial drug target. The production of recombinant PfAdoMetDC for biochemical validation as a drug target is important. The production of PfAdoMetDC in Escherichia coli has been reported to result in unsatisfactory yields and poor quality product. The co-expression of recombinant proteins with molecular chaperones has been proposed as one way to improve the production of the former in E. coli. E. coli heat shock proteins DnaK, GroEL-GroES and DnaJ have previously been used to enhance production of some recombinant proteins. However, the outcomes were inconsistent. An Hsp70 chimeric protein, KPf, which is made up of the ATPase domain of E. coli DnaK and the substrate binding domain of P. falciparum Hsp70 (PfHsp70) has been previously shown to exhibit chaperone function when it was expressed in E. coli cells whose resident Hsp70 (DnaK) function was impaired. We proposed that because of its domain constitution, KPf would most likely be recognised by E. coli Hsp70 co-chaperones. Furthermore, because it possesses a substrate binding domain of plasmodial origin, KPf would be primed to recognise recombinant PfAdoMetDC expressed in E. coli. First, using site-directed mutagenesis, followed by complementation assays, we established that KPf with a mutation in the hydrophobic residue located in its substrate binding cavity was functionally compromised. We further co-expressed PfAdoMetDC with KPf, PfHsp70 and DnaK in E. coli cells either in the absence or presence of over-expressed GroEL-GroES chaperonin. The folded and functional status of the produced PfAdoMetDC was assessed using limited proteolysis and enzyme assays. PfAdoMetDC co-expressed with KPf and PfHsp70 exhibited improved activity compared to protein co-expressed with over-expressed DnaK. Our findings suggest that chimeric KPf may be an ideal Hsp70 co-expression partner for the production of recombinant plasmodial

  6. 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.

  7. 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.

  8. Structure and function of complex carbohydrates active in regulating plant-microbe interactions

    Energy Technology Data Exchange (ETDEWEB)

    Albersheim, P; Darvill, A G; McNeil, M

    1981-01-01

    A key regulatory role of complex carbohydrates in the interactions between plants and microbes has been established. The complex carbohydrates act as regulatory molecules or hormones in that the carbohydrates induce de novo protein synthesis in receptive cells. The first complex carbohydrate recognized to possess such regulatory properties is a polysaccharide (PS) present in the walls of fungi. Hormonal concentrations of this PS elicit plant cells to accumulate phytoalexins (antibiotics). More recently we have recognized that a PS in the walls of growing plant cells also elicits phytoalexin accumulation; microbes and viruses may cause the release of active fragments of this endogenous elicitor. Another PS in plant cell walls is the Proteinase Inhibitor Inducing Factor (PIIF). This hormone appears to protect plants by inducing synthesis in plants of proteins which specifically inhibit digestive enzymes of insects and bacteria. Glycoproteins secreted by incompatible races (races that do not infect the plant) of a fungal pathogen of soybeans protect seedlings from attack by compatible races. Glycoproteins from compatible races do not protect the seedlings. The acidic PS secreted by the nitrogen-fixing rhizobia appear to function in the infection of legumes by the rhizobia. W.D. Bauer and his co-workers have evidence that these PS are required for the development of root hairs capable of being infected by symbiont rhizobia. Current knowledge of the structures of these biologically active complex carbohydrates will be presented.

  9. Characterization of anti-P monoclonal antibodies directed against the ribosomal protein-RNA complex antigen and produced using Murphy Roths large autoimmune-prone mice.

    Science.gov (United States)

    Sato, H; Onozuka, M; Hagiya, A; Hoshino, S; Narita, I; Uchiumi, T

    2015-02-01

    Autoantibodies, including anti-ribosomal P proteins (anti-P), are thought to be produced by an antigen-driven immune response in systemic lupus erythematosus (SLE). To test this hypothesis, we reconstituted the ribosomal antigenic complex in vitro using human P0, phosphorylated P1 and P2 and a 28S rRNA fragment covering the P0 binding site, and immunized Murphy Roths large (MRL)/lrp lupus mice with this complex without any added adjuvant to generate anti-P antibodies. Using hybridoma technology, we subsequently obtained 34 clones, each producing an anti-P monoclonal antibody (mAb) that recognized the conserved C-terminal tail sequence common to all three P proteins. We also obtained two P0-specific monoclonal antibodies, but no antibody specific to P1, P2 or rRNA fragment. Two types of mAbs were found among these anti-P antibodies: one type (e.g. 9D5) reacted more strongly with the phosphorylated P1 and P2 than that with their non-phosphorylated forms, whereas the other type (e.g. 4H11) reacted equally with both phosphorylated and non-phosphorylated forms of P1/P2. Both 9D5 and 4H11 inhibited the ribosome/eukaryotic elongation factor-2 (eEF-2)-coupled guanosine triphosphate (GTP)ase activity. However, preincubation with a synthetic peptide corresponding to the C-terminal sequence common to all three P proteins, but not the peptide that lacked the last three C-terminal amino acids, mostly prevented the mAb-induced inhibition of GTPase activity. Thus, at least two types of anti-P were produced preferentially following the immunization of MRL mice with the reconstituted antigenic complex. Presence of multiple copies of the C-termini, particularly that of the last three C-terminal amino acid residues, in the antigenic complex appears to contribute to the immunogenic stimulus. © 2014 British Society for Immunology.

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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 ...

  16. 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

  17. 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

  18. Engineering microbes for efficient production of chemicals

    Science.gov (United States)

    Gong, Wei; Dole, Sudhanshu; Grabar, Tammy; Collard, Andrew Christopher; Pero, Janice G; Yocum, R Rogers

    2015-04-28

    This present invention relates to production of chemicals from microorganisms that have been genetically engineered and metabolically evolved. Improvements in chemical production have been established, and particular mutations that lead to those improvements have been identified. Specific examples are given in the identification of mutations that occurred during the metabolic evolution of a bacterial strain genetically engineered to produce succinic acid. This present invention also provides a method for evaluating the industrial applicability of mutations that were selected during the metabolic evolution for increased succinic acid production. This present invention further provides microorganisms engineered to have mutations that are selected during metabolic evolution and contribute to improved production of succinic acid, other organic acids and other chemicals of commercial interest.

  19. The utilization of microbes as a fermentation agent to reduce saponin in Trembesi leaves (Sammanea saman)

    Science.gov (United States)

    Sariri, A. K.; Mulyono, A. M. W.; Tari, A. I. N.

    2018-03-01

    This objective of this research was to observe the utilization of microbes as a fermentation agent of trembesi leaves that can increase the quality of trembesi leaves as ruminants feed. Before fermentation, trembesi leaves were divided into three treatments. They were control = non-agentic in fermentation, D-An = the addition of Aspergillus niger as fermentation agent, and D-Lp = the addition of Lactobacillus plantarum as fermentation agent. Each treatment experienced five repetitions. The experimental design used a randomized direct pattern group design. The analysis included proximate analysis consisting of water content, crude protein content, crude fiber content, lipid content, mineral content (ash) and saponin content after fermentation. It could be concluded that the utilization of Aspergillus niger and Lactobacillus plantarum in fermentation could decrease saponin content and could increase the nutrient content of trembesi leaves by increasing crude protein content otherwise by decreasing crude fiber content of trembesi leaves.

  20. Membrane trafficking pathways and their roles in plant-microbe interactions.

    Science.gov (United States)

    Inada, Noriko; Ueda, Takashi

    2014-04-01

    Membrane trafficking functions in the delivery of proteins that are newly synthesized in the endoplasmic reticulum (ER) to their final destinations, such as the plasma membrane (PM) and the vacuole, and in the internalization of extracellular components or PM-associated proteins for recycling or degradative regulation. These trafficking pathways play pivotal roles in the rapid responses to environmental stimuli such as challenges by microorganisms. In this review, we provide an overview of the current knowledge of plant membrane trafficking and its roles in plant-microbe interactions. Although there is little information regarding the mechanism of pathogenic modulation of plant membrane trafficking thus far, recent research has identified many membrane trafficking factors as possible targets of microbial modulation.

  1. 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.

  2. Knock-in of Enhanced Green Fluorescent Protein or/and Human Fibroblast Growth Factor 2 Gene into β-Casein Gene Locus in the Porcine Fibroblasts to Produce Therapeutic Protein.

    Science.gov (United States)

    Lee, Sang Mi; Kim, Ji Woo; Jeong, Young-Hee; Kim, Se Eun; Kim, Yeong Ji; Moon, Seung Ju; Lee, Ji-Hye; Kim, Keun-Jung; Kim, Min-Kyu; Kang, Man-Jong

    2014-11-01

    Transgenic animals have become important tools for the production of therapeutic proteins in the domestic animal. Production efficiencies of transgenic animals by conventional methods as microinjection and retrovirus vector methods are low, and the foreign gene expression levels are also low because of their random integration in the host genome. In this study, we investigated the homologous recombination on the porcine β-casein gene locus using a knock-in vector for the β-casein gene locus. We developed the knock-in vector on the porcine β-casein gene locus and isolated knock-in fibroblast for nuclear transfer. The knock-in vector consisted of the neomycin resistance gene (neo) as a positive selectable marker gene, diphtheria toxin-A gene as negative selection marker, and 5' arm and 3' arm from the porcine β-casein gene. The secretion of enhanced green fluorescent protein (EGFP) was more easily detected in the cell culture media than it was by western blot analysis of cell extract of the HC11 mouse mammary epithelial cells transfected with EGFP knock-in vector. These results indicated that a knock-in system using β-casein gene induced high expression of transgene by the gene regulatory sequence of endogenous β-casein gene. These fibroblasts may be used to produce transgenic pigs for the production of therapeutic proteins via the mammary glands.

  3. 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

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

    Directory of Open Access Journals (Sweden)

    Glass John I

    2010-07-01

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

  5. Effects of the fungicide metiram in outdoor freshwater microcosms: responses of invertebrates, primany producers and microbes

    NARCIS (Netherlands)

    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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. Development, evaluation, and laboratory validation of immunoassays for the diagnosis of equine infectious anemia (EIA) using recombinant protein produced from a synthetic p26 gene of EIA virus.

    Science.gov (United States)

    Singha, Harisankar; Goyal, Sachin K; Malik, Praveen; Khurana, Sandip K; Singh, Raj K

    2013-12-01

    Equine infectious anemia (EIA)-a retroviral disease caused by equine infectious anemia virus (EIAV)-is a chronic, debilitating disease of horses, mules, and donkeys. EIAV infection has been reported worldwide and is recognized as pathogen of significant economic importance to the horse industry. This disease falls under regulatory control program in many countries including India. Control of EIA is based on identification of inapparent carriers by detection of antibodies to EIAV in serologic tests and "Stamping Out" policy. The current internationally accepted test for diagnosis of EIA is the agar gel immune-diffusion test (AGID), which detects antibodies to the major gag gene (p26) product. The objective of this study was to develop recombinant p26 based in-house immunoassays [enzyme linked immunosorbent assays (ELISA), and AGID] for EIA diagnosis. The synthetic p26 gene of EIAV was expressed in Escherichia coli and diagnostic potential of recombinant p26 protein were evaluated in ELISA and AGID on 7,150 and 1,200 equine serum samples, respectively, and compared with commercial standard AGID kit. The relative sensitivity and specificity of the newly developed ELISA were 100 and 98.6 %, respectively. Whereas, relative sensitivity and specificity of the newly developed AGID were in complete agreement in respect to commercial AGID kit. Here, we have reported the validation of an ELISA and AGID on large number of equine serum samples using recombinant p26 protein produced from synthetic gene which does not require handling of pathogenic EIAV. Since the indigenously developed reagents would be economical than commercial diagnostic kit, the rp26 based-immunoassays could be adopted for the sero-diagnosis and control of EIA in India.

  11. Use of chitin and chitosan to produce new chitooligosaccharides by chitinase Chit42: enzymatic activity and structural basis of protein specificity.

    Science.gov (United States)

    Kidibule, Peter Elias; Santos-Moriano, Paloma; Jiménez-Ortega, Elena; Ramírez-Escudero, Mercedes; Limón, M Carmen; Remacha, Miguel; Plou, Francisco José; Sanz-Aparicio, Julia; Fernández-Lobato, María

    2018-03-22

    Chitinases are ubiquitous enzymes that have gained a recent biotechnological attention due to their ability to transform biological waste from chitin into valued chito-oligomers with wide agricultural, industrial or medical applications. The biological activity of these molecules is related to their size and acetylation degree. Chitinase Chit42 from Trichoderma harzianum hydrolyses chitin oligomers with a minimal of three N-acetyl-D-glucosamine (GlcNAc) units. Gene chit42 was previously characterized, and according to its sequence, the encoded protein included in the structural Glycoside Hydrolase family GH18. Chit42 was expressed in Pichia pastoris using fed-batch fermentation to about 3 g/L. Protein heterologously expressed showed similar biochemical properties to those expressed by the natural producer (42 kDa, optima pH 5.5-6.5 and 30-40 °C). In addition to hydrolyse colloidal chitin, this enzyme released reducing sugars from commercial chitosan of different sizes and acetylation degrees. Chit42 hydrolysed colloidal chitin at least 10-times more efficiently (defined by the k cat /K m ratio) than any of the assayed chitosan. Production of partially acetylated chitooligosaccharides was confirmed in reaction mixtures using HPAEC-PAD chromatography and mass spectrometry. Masses corresponding to (D-glucosamine) 1-8 -GlcNAc were identified from the hydrolysis of different substrates. Crystals from Chit42 were grown and the 3D structure determined at 1.8 Å resolution, showing the expected folding described for other GH18 chitinases, and a characteristic groove shaped substrate-binding site, able to accommodate at least six sugar units. Detailed structural analysis allows depicting the features of the Chit42 specificity, and explains the chemical nature of the partially acetylated molecules obtained from analysed substrates. Chitinase Chit42 was expressed in a heterologous system to levels never before achieved. The enzyme produced small partially acetylated

  12. 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.

  13. 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.

  14. 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.

  15. 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...

  16. 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

  17. 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.

  18. 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...

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Reactive Transport Modeling of Microbe-mediated Fe (II) Oxidation for Enhanced Oil Recovery

    Science.gov (United States)

    Surasani, V.; Li, L.

    2011-12-01

    Microbially Enhanced Oil Recovery (MEOR) aims to improve the recovery of entrapped heavy oil in depleted reservoirs using microbe-based technology. Reservoir ecosystems often contain diverse microbial communities those can interact with subsurface fluids and minerals through a network of nutrients and energy fluxes. Microbe-mediated reactions products include gases, biosurfactants, biopolymers those can alter the properties of oil and interfacial interactions between oil, brine, and rocks. In addition, the produced biomass and mineral precipitates can change the reservoir permeability profile and increase sweeping efficiency. Under subsurface conditions, the injection of nitrate and Fe (II) as the electron acceptor and donor allows bacteria to grow. The reaction products include minerals such as Fe(OH)3 and nitrogen containing gases. These reaction products can have large impact on oil and reservoir properties and can enhance the recovery of trapped oil. This work aims to understand the Fe(II) oxidation by nitrate under conditions relevant to MEOR. Reactive transport modeling is used to simulate the fluid flow, transport, and reactions involved in this process. Here we developed a complex reactive network for microbial mediated nitrate-dependent Fe (II) oxidation that involves both thermodynamic controlled aqueous reactions and kinetic controlled Fe (II) mineral reaction. Reactive transport modeling is used to understand and quantify the coupling between flow, transport, and reaction processes. Our results identify key parameter controls those are important for the alteration of permeability profile under field conditions.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Immunoradiometric assay for the determination of E. coli proteins in recombinant dna derived human growth hormone produced at IPEN-CNEN/SP

    International Nuclear Information System (INIS)

    Soares, Carlos R.J.

    1995-01-01

    An immunoradiometric assay (IRMA) for the determination of multiple antigens was set up in order to quantify E. coli (ECP) in lots of purified recombinant human growth hormone (rec-hGH). SDS-PAGE and Western Blotting techniques were carried out, in parallel, to confirm the results obtained by IRMA and to provide more information about the contaminants. Anti-ECP antibodies were obtained by rabbit immunization with ECP, which were submitted to the same purification process utilized for rec-hGH with the exception of the last step. A strain-process-specific assay was thus set up. The antiserum obtained was purified through an affinity column prepared with the same ECP used for immunization, this provided an highly sensitive assay (0,03 ng ECP/mL). This IRMA was shown to be specific, not presenting any cross reaction with hGH and studies carried out on precision, accuracy and linearity of response with dilution confirmed its validity as one of the fundamental purity tests for rec-hGH produced at IPEN-CNEN/SP, whose principles can be easily extended to the analysis of other similar products. These studies have also shown that the utilization of an affinity column, prepared with the described anti-ECP antiserum was very effective, providing rec-hGH lots with less then 10 parts per million (0,001%) of contaminating proteins. (author). 45 refs., 15 figs., 11 tabs

  9. Accumulation of dry matter and nitrogen in the developing seeds of high protein mutant lines of Triticum Aestivum (L.) produced by the IAEA

    International Nuclear Information System (INIS)

    Mir Ali, N.; Nabulsi, I.

    1993-03-01

    Accumulation patterns of dry matter and nitrogen in the developing seeds of nine mutant lines produced by the IAEA and their mother Triticum Aestivum (L.) line were studied. The experiments lasted 2 years under rain fed conditions. Significant differences were found among the lines in dry matter and nitrogen rates, and periods of accumulation, whereas no significant differences were found in the final seed weight of the lines. The highest rates of accumulation for dry matter and nitrogen were accompanied with the shortest period of accumulation in two late flowering mutant lines. However, these two lines were the lowest in their yield per plot. The other mutant lines achieved the high nitrogen percentage in their seeds through the relative reduction in dry matter accumulation rate compared to their mother line rather than through higher rate of nitrogen accumulation. This study revealed some of the potential reasons behind the higher percentage of protein in the seeds of the mutant lines under investigation. (author). 17 refs., 3 figs., 2 tabs

  10. 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.

  11. 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...

  12. 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.

  13. Environmental science. Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes.

    Science.gov (United States)

    Worden, Alexandra Z; Follows, Michael J; Giovannoni, Stephen J; Wilken, Susanne; Zimmerman, Amy E; Keeling, Patrick J

    2015-02-13

    The profound influence of marine plankton on the global carbon cycle has been recognized for decades, particularly for photosynthetic microbes that form the base of ocean food chains. However, a comprehensive model of the carbon cycle is challenged by unicellular eukaryotes (protists) having evolved complex behavioral strategies and organismal interactions that extend far beyond photosynthetic lifestyles. As is also true for multicellular eukaryotes, these strategies and their associated physiological changes are difficult to deduce from genome sequences or gene repertoires—a problem compounded by numerous unknown function proteins. Here, we explore protistan trophic modes in marine food webs and broader biogeochemical influences. We also evaluate approaches that could resolve their activities, link them to biotic and abiotic factors, and integrate them into an ecosystems biology framework. Copyright © 2015, American Association for the Advancement of Science.

  14. 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.

  15. 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...

  16. Inherited prion disease A117V is not simply a proteinopathy but produces prions transmissible to transgenic mice expressing homologous prion protein.

    Directory of Open Access Journals (Sweden)

    Emmanuel A Asante

    Full Text Available Prions are infectious agents causing fatal neurodegenerative diseases of humans and animals. In humans, these have sporadic, acquired and inherited aetiologies. The inherited prion diseases are caused by one of over 30 coding mutations in the human prion protein (PrP gene (PRNP and many of these generate infectious prions as evidenced by their experimental transmissibility by inoculation to laboratory animals. However, some, and in particular an extensively studied type of Gerstmann-Sträussler-Scheinker syndrome (GSS caused by a PRNP A117V mutation, are thought not to generate infectious prions and instead constitute prion proteinopathies with a quite distinct pathogenetic mechanism. Multiple attempts to transmit A117V GSS have been unsuccessful and typical protease-resistant PrP (PrP(Sc, pathognomonic of prion disease, is not detected in brain. Pathogenesis is instead attributed to production of an aberrant topological form of PrP, C-terminal transmembrane PrP ((CtmPrP. Barriers to transmission of prion strains from one species to another appear to relate to structural compatibility of PrP in host and inoculum and we have therefore produced transgenic mice expressing human 117V PrP. We found that brain tissue from GSS A117V patients did transmit disease to these mice and both the neuropathological features of prion disease and presence of PrP(Sc was demonstrated in the brains of recipient transgenic mice. This PrP(Sc rapidly degraded during laboratory analysis, suggesting that the difficulty in its detection in patients with GSS A117V could relate to post-mortem proteolysis. We conclude that GSS A117V is indeed a prion disease although the relative contributions of (CtmPrP and prion propagation in neurodegeneration and their pathogenetic interaction remains to be established.

  17. Inherited prion disease A117V is not simply a proteinopathy but produces prions transmissible to transgenic mice expressing homologous prion protein.

    Science.gov (United States)

    Asante, Emmanuel A; Linehan, Jacqueline M; Smidak, Michelle; Tomlinson, Andrew; Grimshaw, Andrew; Jeelani, Asif; Jakubcova, Tatiana; Hamdan, Shyma; Powell, Caroline; Brandner, Sebastian; Wadsworth, Jonathan D F; Collinge, John

    2013-01-01

    Prions are infectious agents causing fatal neurodegenerative diseases of humans and animals. In humans, these have sporadic, acquired and inherited aetiologies. The inherited prion diseases are caused by one of over 30 coding mutations in the human prion protein (PrP) gene (PRNP) and many of these generate infectious prions as evidenced by their experimental transmissibility by inoculation to laboratory animals. However, some, and in particular an extensively studied type of Gerstmann-Sträussler-Scheinker syndrome (GSS) caused by a PRNP A117V mutation, are thought not to generate infectious prions and instead constitute prion proteinopathies with a quite distinct pathogenetic mechanism. Multiple attempts to transmit A117V GSS have been unsuccessful and typical protease-resistant PrP (PrP(Sc)), pathognomonic of prion disease, is not detected in brain. Pathogenesis is instead attributed to production of an aberrant topological form of PrP, C-terminal transmembrane PrP ((Ctm)PrP). Barriers to transmission of prion strains from one species to another appear to relate to structural compatibility of PrP in host and inoculum and we have therefore produced transgenic mice expressing human 117V PrP. We found that brain tissue from GSS A117V patients did transmit disease to these mice and both the neuropathological features of prion disease and presence of PrP(Sc) was demonstrated in the brains of recipient transgenic mice. This PrP(Sc) rapidly degraded during laboratory analysis, suggesting that the difficulty in its detection in patients with GSS A117V could relate to post-mortem proteolysis. We conclude that GSS A117V is indeed a prion disease although the relative contributions of (Ctm)PrP and prion propagation in neurodegeneration and their pathogenetic interaction remains to be established.

  18. Endogenous proteolytic cleavage of disease-associated prion protein to produce C2 fragments is strongly cell- and tissue-dependent.

    Science.gov (United States)

    Dron, Michel; Moudjou, Mohammed; Chapuis, Jérôme; Salamat, Muhammad Khalid Farooq; Bernard, Julie; Cronier, Sabrina; Langevin, Christelle; Laude, Hubert

    2010-04-02

    The abnormally folded form of the prion protein (PrP(Sc)) accumulating in nervous and lymphoid tissues of prion-infected individuals can be naturally cleaved to generate a N-terminal-truncated fragment called C2. Information about the identity of the cellular proteases involved in this process and its possible role in prion biology has remained limited and controversial. We investigated PrP(Sc) N-terminal trimming in different cell lines and primary cultured nerve cells, and in the brain and spleen tissue from transgenic mice infected by ovine and mouse prions. We found the following: (i) the full-length to C2 ratio varies considerably depending on the infected cell or tissue. Thus, in primary neurons and brain tissue, PrP(Sc) accumulated predominantly as untrimmed species, whereas efficient trimming occurred in Rov and MovS cells, and in spleen tissue. (ii) Although C2 is generally considered to be the counterpart of the PrP(Sc) proteinase K-resistant core, the N termini of the fragments cleaved in vivo and in vitro can actually differ, as evidenced by a different reactivity toward the Pc248 anti-octarepeat antibody. (iii) In lysosome-impaired cells, the ratio of full-length versus C2 species dramatically increased, yet efficient prion propagation could occur. Moreover, cathepsin but not calpain inhibitors markedly inhibited C2 formation, and in vitro cleavage by cathepsins B and L produced PrP(Sc) fragments lacking the Pc248 epitope, strongly arguing for the primary involvement of acidic hydrolases of the endolysosomal compartment. These findings have implications on the molecular analysis of PrP(Sc) and cell pathogenesis of prion infection.

  19. Endogenous Proteolytic Cleavage of Disease-associated Prion Protein to Produce C2 Fragments Is Strongly Cell- and Tissue-dependent*

    Science.gov (United States)

    Dron, Michel; Moudjou, Mohammed; Chapuis, Jérôme; Salamat, Muhammad Khalid Farooq; Bernard, Julie; Cronier, Sabrina; Langevin, Christelle; Laude, Hubert

    2010-01-01

    The abnormally folded form of the prion protein (PrPSc) accumulating in nervous and lymphoid tissues of prion-infected individuals can be naturally cleaved to generate a N-terminal-truncated fragment called C2. Information about the identity of the cellular proteases involved in this process and its possible role in prion biology has remained limited and controversial. We investigated PrPSc N-terminal trimming in different cell lines and primary cultured nerve cells, and in the brain and spleen tissue from transgenic mice infected by ovine and mouse prions. We found the following: (i) the full-length to C2 ratio varies considerably depending on the infected cell or tissue. Thus, in primary neurons and brain tissue, PrPSc accumulated predominantly as untrimmed species, whereas efficient trimming occurred in Rov and MovS cells, and in spleen tissue. (ii) Although C2 is generally considered to be the counterpart of the PrPSc proteinase K-resistant core, the N termini of the fragments cleaved in vivo and in vitro can actually differ, as evidenced by a different reactivity toward the Pc248 anti-octarepeat antibody. (iii) In lysosome-impaired cells, the ratio of full-length versus C2 species dramatically increased, yet efficient prion propagation could occur. Moreover, cathepsin but not calpain inhibitors markedly inhibited C2 formation, and in vitro cleavage by cathepsins B and L produced PrPSc fragments lacking the Pc248 epitope, strongly arguing for the primary involvement of acidic hydrolases of the endolysosomal compartment. These findings have implications on the molecular analysis of PrPSc and cell pathogenesis of prion infection. PMID:20154089

  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. 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.

  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. 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.

  4. Engineering microbes for tolerance to next-generation biofuels

    Directory of Open Access Journals (Sweden)

    Dunlop Mary J

    2011-09-01

    Full Text Available Abstract A major challenge when using microorganisms to produce bulk chemicals such as biofuels is that the production targets are often toxic to cells. Many biofuels are known to reduce cell viability through damage to the cell membrane and interference with essential physiological processes. Therefore, cells must trade off biofuel production and survival, reducing potential yields. Recently, there have been several efforts towards engineering strains for biofuel tolerance. Promising methods include engineering biofuel export systems, heat shock proteins, membrane modifications, more general stress responses, and approaches that integrate multiple tolerance strategies. In addition, in situ recovery methods and media supplements can help to ease the burden of end-product toxicity and may be used in combination with genetic approaches. Recent advances in systems and synthetic biology provide a framework for tolerance engineering. This review highlights recent targeted approaches towards improving microbial tolerance to next-generation biofuels with a particular emphasis on strategies that will improve production.

  5. Overproduction, purification and characterization of human interferon alpha2a-human serum albumin fusion protein produced in methilotropic yeast Pichia pastoris

    Science.gov (United States)

    Ningrum, R. A.; Santoso, A.; Herawati, N.

    2017-05-01

    Human interferon alpha2a (hIFNα2a) is a therapeutic protein that used in cancer and hepatitis B/C therapy. The main problem of using hIFNα-2a is its short elimination half life due to its low molecular weight. Development of higher molecular weight protein by albumin fusion technology is a rational strategy to solve the problem. In our previous research we constructed an open reading frame (ORF) encoding hIFNα2a-human serum albumin (HSA) fusion protein that expressed in Pichia pastoris (P. pastoris) protease deficient strain SMD1168. This research was performed to overproduce, purify and characterize the fusion protein. To overproduce the protein, cultivation was performed in buffered complex medium containing glyserol (BMGY) for 24 h and protein overproduction was applied in buffered complex medium containing methanol (BMMY) for 48 hours at 30°C. The fusion protein was purified by blue sepharose affinity chromatography. Molecular weight characterization by SDS PAGE corresponds with its theoretical size, 85 kDa. Western blot analysis demonstrated that the fusion protein was recognized by anti hIFNα2 and anti HSA monoclonal antibody as well. Amino acid sequence of the fusion protein was determined by LC MS/MS2 mass spectrometry with trypsin as proteolitic enzyme. There were three fragments that identified as hIFNα2a and seven fragments that identified as HSA. Total identified amino acids were 150 residues with 20% coverage from total residues. To conclude, hIFNα2a-HSA fusion protein was overproduced, purified and characterized. Characterization based on molecular weight, antibody recognition and amino acid sequence confirmed that the fusion protein has correct identity as theoretically thought.

  6. Overproduction, purification and characterization of human interferon alpha2a-human serum albumin fusion protein produced in methilotropic yeast Pichia pastoris

    International Nuclear Information System (INIS)

    Ningrum, R A; Santoso, A; Herawati, N

    2017-01-01

    Human interferon alpha2a (hIFNα2a) is a therapeutic protein that used in cancer and hepatitis B/C therapy. The main problem of using hIFNα-2a is its short elimination half life due to its low molecular weight. Development of higher molecular weight protein by albumin fusion technology is a rational strategy to solve the problem. In our previous research we constructed an open reading frame (ORF) encoding hIFNα2a-human serum albumin (HSA) fusion protein that expressed in Pichia pastoris (P. pastoris) protease deficient strain SMD1168. This research was performed to overproduce, purify and characterize the fusion protein. To overproduce the protein, cultivation was performed in buffered complex medium containing glyserol (BMGY) for 24 h and protein overproduction was applied in buffered complex medium containing methanol (BMMY) for 48 hours at 30°C. The fusion protein was purified by blue sepharose affinity chromatography. Molecular weight characterization by SDS PAGE corresponds with its theoretical size, 85 kDa. Western blot analysis demonstrated that the fusion protein was recognized by anti hIFNα2 and anti HSA monoclonal antibody as well. Amino acid sequence of the fusion protein was determined by LC MS/MS2 mass spectrometry with trypsin as proteolitic enzyme. There were three fragments that identified as hIFNα2a and seven fragments that identified as HSA. Total identified amino acids were 150 residues with 20% coverage from total residues. To conclude, hIFNα2a-HSA fusion protein was overproduced, purified and characterized. Characterization based on molecular weight, antibody recognition and amino acid sequence confirmed that the fusion protein has correct identity as theoretically thought. (paper)

  7. Does a Common Pathway Transduce Symbiotic Signals in Plant-Microbe Interactions?

    Science.gov (United States)

    Genre, Andrea; Russo, Giulia

    2016-01-01

    Recent years have witnessed major advances in our knowledge of plant mutualistic symbioses such as the rhizobium-legume symbiosis (RLS) and arbuscular mycorrhizas (AM). Some of these findings caused the revision of longstanding hypotheses, but one of the most solid theories is that a conserved set of plant proteins rules the transduction of symbiotic signals from beneficial glomeromycetes and rhizobia in a so-called common symbiotic pathway (CSP). Nevertheless, the picture still misses several elements, and a few crucial points remain unclear. How does one common pathway discriminate between - at least - two symbionts? Can we exclude that microbes other than AM fungi and rhizobia also use this pathway to communicate with their host plants? We here discuss the possibility that our current view is biased by a long-lasting focus on legumes, whose ability to develop both AM and RLS is an exception among plants and a recent innovation in their evolution; investigations in non-legumes are starting to place legume symbiotic signaling in a broader perspective. Furthermore, recent studies suggest that CSP proteins act in a wider scenario of symbiotic and non-symbiotic signaling. Overall, evidence is accumulating in favor of distinct activities for CSP proteins in AM and RLS, depending on the molecular and cellular context where they act.

  8. Bovine NK cells can produce gamma interferon in response to the secreted mycobacterial proteins ESAT-6 and MPP14 but not in response to MPB70

    DEFF Research Database (Denmark)

    Olsen, Ingrid; Boysen, P.; Kulberg, S.

    2005-01-01

    to the Mycobacterium tuberculosis complex-specific protein ESAT-6, MPP14 from Mycobacterium avium subsp. paratuberculosis, and purified protein derivative (PPD) from M. tuberculosis. In contrast, no response was induced by MPB70, which is another M. tuberculosis complex-specific secreted antigen. The production of IFN...

  9. From where and how do plants and microbes get nitrogen? Revisiting paradigms of soil nitrogen availability

    Science.gov (United States)

    Grandy, S.

    2017-12-01

    Despite decades of research progress, soil biogeochemists are still debating in different ecosystems what pools and fluxes provide N to plants and microbes. Current concepts argue that N mineralization regulates the supply of N for plants and microorganisms, and is a `gatekeeper' for environmental N losses. The prevailing paradigm also argues that the chemistry of plant litter inputs (e.g. initial C:N ratio) primarily drives N mineralization rates, existing as a universal regulator of a switch between net N immobilization versus net N mineralization. However, decomposer community enzyme upregulation drives proteolysis, the exocellular first step in N mineralization; then, cellular carbon use efficiency and stoichiometry are internal microbial physiological processes driving ammonification rates. Further, N mineralization is only one of multiple, microbial-driven sequences in soils that regulate bioavailable N. Emerging evidence and new conceptual models from both the ecological and biogeoscience communities argue that while depolymerization is a critical first step, clay minerals may be an important and overlooked mediator of bioavailable N, and especially in the soil rhizosphere they are both a large source and sink for N. Mineral-associated organic matter (MAOM) can hold up to 20x more N than particulate fractions, is a rich reservoir of proteins, amino acids, and nucleic acids, and is mobilized by microbes and their interactions with plants. We use this and other emerging information to develop a new model of N availability in soils, highlighting: mineralization is strongly influenced by microbial physiological traits; the various steps in N mineralization have different drivers and can become decoupled; minerals are a strong sink and source for bioavailable N that is regulated by interactions between plants and microbial communities; and plants are a driving force in the soil N cycle for their ability to prime mineral N, and influence the structure and function

  10. 64 kDa protein is a candidate for a thyrotropin-releasing hormone receptor in prolactin-producing rat pituitary tumor cells (GH4C1 cells)

    International Nuclear Information System (INIS)

    Wright, M.; Hogset, A.; Alestrom, P.; Gautvik, K.M.

    1988-01-01

    A thyrotropin-releasing hormone (TRH) binding protein of 64 kDa has been identified by covalently crosslinking [ 3 H]TRH to GH4C1 cells by ultraviolet illumination. The crosslinkage of [ 3 H]TRH is UV-dose dependent and is inhibited by an excess of unlabeled TRH. A 64 kDa protein is also detected on immunoblots using an antiserum raised against GH4C1 cell surface epitopes. In a closely related cell line (GH12C1) which does not bind [ 3 H]TRH, the 64 kDa protein cannot be demonstrated by [ 3 H]TRH crosslinking nor by immunoblotting. These findings indicate that the 64 kDa protein is a candidate for a TRH-receptor protein in GH4C1 cells

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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...

  18. 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.

  19. Brain-derived neurotrophic factor is produced by skeletal muscle cells in response to contraction and enhances fat oxidation via activation of AMP-activated protein kinase

    DEFF Research Database (Denmark)

    Matthews, V B; Åström, Maj-Brit; Chan, M H S

    2009-01-01

    C12 skeletal muscle cells were electrically stimulated to mimic contraction. L6 myotubes and isolated rat extensor digitorum longus muscles were treated with BDNF and phosphorylation of the proteins AMP-activated protein kinase (AMPK) (Thr(172)) and acetyl coenzyme A carboxylase beta (ACCbeta) (Ser...... kinase (p44/42 Thr(202)/Tyr(204)) phosphorylation in these muscles. In addition, phosphorylation of ACCbeta was markedly elevated in the Bdnf electroporated muscles. CONCLUSIONS/INTERPRETATION: These data identify BDNF as a contraction-inducible protein in skeletal muscle that is capable of enhancing...

  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. Direct Ethanol Production from Breadfruit Starch (Artocarpus communis Forst. by Engineered Simultaneous Saccharification and Fermentation (ESSF using Microbes Consortium

    Directory of Open Access Journals (Sweden)

    Iftachul Farida

    2015-02-01

    Full Text Available Breadfruit (Artocarpus communis Forst. is one of sources for ethanol production, which has high starch content (89%. Ethanol production from breadfruit starch was conducted by Simultaneous Saccharification and Fermentation (SSF technology using microbes consortium. The aim of the research was to examine a method to produce ethanol by SSF technology using microbes consortium at high yield and efficiency. The main research consisted of two treatments, namely normal SSF and enginereed SSF. The results showed that normal SSF using aeration and agitation during cultivation could produce ethanol at 11.15 ± 0.18 g/L, with the yield of product (Yp/s 0.34 g ethanol/g substrate; and yield of biomass (Yx/s 0.29 g cell/g substrate, respectively. A better result was obtained using engineered SSF in which aeration was stopped after biomass condition has reached the end of the exponential phase. The ethanol produced was 12.75 ± 0.04 g/L, with the yields of product (Yp/s 0.41 g ethanol/g substrate, and the yield of cell (Yx/s 0.09 g cell/g substrate.

  2. 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.

  3. Lung Homeostasis: Influence of Age, Microbes, and the Immune System.

    Science.gov (United States)

    Lloyd, Clare M; Marsland, Benjamin J

    2017-04-18

    Pulmonary immune homeostasis is maintained by a network of tissue-resident cells that continually monitor the external environment, and in health, instruct tolerance to innocuous inhaled particles while ensuring that efficient and rapid immune responses can be mounted against invading pathogens. Here we review the multiple pathways that underlie effective lung immunity in health, and discuss how these may be affected by external environmental factors and contribute to chronic inflammation during disease. In this context, we examine the current understanding of the impact of the microbiota in immune development and function and in the setting of the threshold for immune responses that maintains the balance between tolerance and chronic inflammation in the lung. We propose that host interactions with microbes are critical for establishing the immune landscape of the lungs. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. 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...

  5. 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.

  6. Busting dust: from cosmic grains to terrestrial microbes

    International Nuclear Information System (INIS)

    Mendis, D.A.

    2001-01-01

    Electrostatic charging can have important consequences for both the growth and disruption of microparticulates immersed in a plasma. In this topical review, my emphasis is on the latter process, while I extend the term microparticulates not only to include ordinary inanimate cosmic or terrestrial dust but also to include terrestrial microbes whose sizes range from tens of nanometers (viruses) to tens of micrometers (bacteria). Following a description of the basic mechanism of electrostatic disruption of a solid body, I will discuss the role of size, shape and surface irregularity on the process. I will also consider the mitigating role of electric field emission of electrons on the disruption process of a negatively charged grain as its size falls below a critical size. I will conclude by reviewing some early evidence for the electrostatic disruption of cosmic grains, and the very recent evidence for the electrostatic disruption of the bacterial cell membranes in terrestrial sterilization experiments. (orig.)

  7. 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.

  8. 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.

  9. 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

  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. 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 ...

  12. 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...

  13. 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

  14. 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,…

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

    NARCIS (Netherlands)

    Kumar, Manoj Gopala Krishnan

    2016-01-01

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

  16. 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.

  17. 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.

  18. 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...

  19. Identifying the functional part of heparin-binding protein (HBP) as a monocyte stimulator and the novel role of monocytes as HBP producers

    DEFF Research Database (Denmark)

    Schou, Morten; Djurup, René; Norris, Kjeld

    2011-01-01

    Heparin-binding protein (HBP), an evolutionary ancient and biologically highly important molecule in inflammation, is an inactive serine protease due to mutations in the catalytic triad. The histidine (position 41) in the conserved sequence TAAHC is mutated to serine and this sequence (TAASC) pla...

  20. Solid state fermentation of carinata (Brassica carinata) meal using various fungal strains to produce a protein-rich product for feed application

    Science.gov (United States)

    In this study, the efficacy of several fungal strains to reduce GLS (GLS) content and enhance protein content during solid state fermentation (SSF) of carinata meal was evaluated. Solid state fermentation of hexane extracted (HE) and cold pressed (CP) carinata meals were performed at 50% moisture co...

  1. An anti-tumor protein produced by Trichinella spiralis and identified by screening a T7 phage display library, induces apoptosis in human hepatoma H7402 cells

    Science.gov (United States)

    Trichinella spiralis infection confers effective resistance to tumor cell expansion. In this study, a T7 phage cDNA display library was constructed to express genes encoded by T. spiralis. Organic phase multi-cell screening was used to sort through candidate proteins in a transfected human chronic m...

  2. Incidence of Lettuce mosaic virus in lettuce and its detection by polyclonal antibodies produced against recombinant coat protein expressed in Escherichia coli.

    Science.gov (United States)

    Sharma, Prachi; Sharma, Susheel; Singh, Jasvir; Saha, Swati; Baranwal, V K

    2016-04-01

    Lettuce mosaic virus (LMV), a member of the genus Potyvirus of family Potyviridae, causes mosaic disease in lettuce has recently been identified in India. The virus is seed borne and secondary infection occurs through aphids. To ensure virus freedom in seeds it is important to develop diagnostic tools, for serological methods the production of polyclonal antibodies is a prerequisite. The coat protein (CP) gene of LMV was amplified, cloned and expressed using pET-28a vector in Escherichia coli BL21DE3 competent cells. The LMV CP was expressed as a fusion protein containing a fragment of the E. coli His tag. The LMV CP/His protein reacted positively with a commercial antiserum against LMV in an immunoblot assay. Polyclonal antibodies purified from serum of rabbits immunized with the fusion protein gave positive results when LMV infected lettuce (Lactuca sativa) was tested at 1:1000 dilution in PTA-ELISA. These were used for specific detection of LMV in screening lettuce accessions. The efficacy of the raised polyclonal antiserum was high and it can be utilized in quarantine and clean seed production. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Growing Azolla to produce sustainable protein feed: the effect of differing species and CO2 concentrations on biomass productivity and chemical composition.

    Science.gov (United States)

    Brouwer, Paul; Schluepmann, Henriette; Nierop, Klaas Gj; Elderson, Janneke; Bijl, Peter K; van der Meer, Ingrid; de Visser, Willem; Reichart, Gert-Jan; Smeekens, Sjef; van der Werf, Adrie

    2018-03-24

    Since available arable land is limited and nitrogen fertilizers pollute the environment, cropping systems ought to be developed that do not rely on them. Here we investigate the rapidly growing, N 2 -fixing Azolla/Nostoc symbiosis for its potential productivity and chemical composition to determine its potential as protein feed. In a small production system, cultures of Azolla pinnata and Azolla filiculoides were continuously harvested for over 100 days, yielding an average productivity of 90.0-97.2 kg dry weight (DW) ha -1  d -1 . Under ambient CO 2 levels, N 2 fixation by the fern's cyanobacterial symbionts accounted for all nitrogen in the biomass. Proteins made up 176-208 g kg -1 DW (4.9 × total nitrogen), depending on species and CO 2 treatment, and contained more essential amino acids than protein from soybean. Elevated atmospheric CO 2 concentrations (800 ppm) significantly boosted biomass production by 36-47%, without decreasing protein content. Choice of species and CO 2 concentrations further affected the biomass content of lipids (79-100 g kg -1 DW) and (poly)phenols (21-69 g kg -1 DW). By continuous harvesting, high protein yields can be obtained from Azolla cultures, without the need for nitrogen fertilization. High levels of (poly)phenols likely contribute to limitations in the inclusion rate of Azolla in animal diets and need further investigation. © 2018 The Authors. Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2018 The Authors. Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

  4. SUN family proteins Sun4p, Uth1p and Sim1p are secreted from Saccharomyces cerevisiae and produced dependently on oxygen level.

    Directory of Open Access Journals (Sweden)

    Evgeny Kuznetsov

    Full Text Available The SUN family is comprised of proteins that are conserved among various yeasts and fungi, but that are absent in mammals and plants. Although the function(s of these proteins are mostly unknown, they have been linked to various, often unrelated cellular processes such as those connected to mitochondrial and cell wall functions. Here we show that three of the four Saccharomyces cerevisiae SUN family proteins, Uth1p, Sim1p and Sun4p, are efficiently secreted out of the cells in different growth phases and their production is affected by the level of oxygen. The Uth1p, Sim1p, Sun4p and Nca3p are mostly synthesized during the growth phase of both yeast liquid cultures and colonies. Culture transition to slow-growing or stationary phases is linked with a decreased cellular concentration of Sim1p and Sun4p and with their efficient release from the cells. In contrast, Uth1p is released mainly from growing cells. The synthesis of Uth1p and Sim1p, but not of Sun4p, is repressed by anoxia. All four proteins confer cell sensitivity to zymolyase. In addition, Uth1p affects cell sensitivity to compounds influencing cell wall composition and integrity (such as Calcofluor white and Congo red differently when growing on fermentative versus respiratory carbon sources. In contrast, Uth1p is essential for cell resistance to boric acids irrespective of carbon source. In summary, our novel findings support the hypothesis that SUN family proteins are involved in the remodeling of the yeast cell wall during the various phases of yeast culture development and under various environmental conditions. The finding that Uth1p is involved in cell sensitivity to boric acid, i.e. to a compound that is commonly used as an important antifungal in mycoses, opens up new possibilities of investigating the mechanisms of boric acid's action.

  5. Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines.

    Science.gov (United States)

    LaBute, Montiago X; Zhang, Xiaohua; Lenderman, Jason; Bennion, Brian J; Wong, Sergio E; Lightstone, Felice C

    2014-01-01

    Late-stage or post-market identification of adverse drug reactions (ADRs) is a significant public health issue and a source of major economic liability for drug development. Thus, reliable in silico screening of drug candidates for possible ADRs would be advantageous. In this work, we introduce a computational approach that predicts ADRs by combining the results of molecular docking and leverages known ADR information from DrugBank and SIDER. We employed a recently parallelized version of AutoDock Vina (VinaLC) to dock 906 small molecule drugs to a virtual panel of 409 DrugBank protein targets. L1-regularized logistic regression models were trained on the resulting docking scores of a 560 compound subset from the initial 906 compounds to predict 85 side effects, grouped into 10 ADR phenotype groups. Only 21% (87 out of 409) of the drug-protein binding features involve known targets of the drug subset, providing a significant probe of off-target effects. As a control, associations of this drug subset with the 555 annotated targets of these compounds, as reported in DrugBank, were used as features to train a separate group of models. The Vina off-target models and the DrugBank on-target models yielded comparable median area-under-the-receiver-operating-characteristic-curves (AUCs) during 10-fold cross-validation (0.60-0.69 and 0.61-0.74, respectively). Evidence was found in the PubMed literature to support several putative ADR-protein associations identified by our analysis. Among them, several associations between neoplasm-related ADRs and known tumor suppressor and tumor invasiveness marker proteins were found. A dual role for interstitial collagenase in both neoplasms and aneurysm formation was also identified. These associations all involve off-target proteins and could not have been found using available drug/on-target interaction data. This study illustrates a path forward to comprehensive ADR virtual screening that can potentially scale with increasing number

  6. Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines.

    Directory of Open Access Journals (Sweden)

    Montiago X LaBute

    Full Text Available Late-stage or post-market identification of adverse drug reactions (ADRs is a significant public health issue and a source of major economic liability for drug development. Thus, reliable in silico screening of drug candidates for possible ADRs would be advantageous. In this work, we introduce a computational approach that predicts ADRs by combining the results of molecular docking and leverages known ADR information from DrugBank and SIDER. We employed a recently parallelized version of AutoDock Vina (VinaLC to dock 906 small molecule drugs to a virtual panel of 409 DrugBank protein targets. L1-regularized logistic regression models were trained on the resulting docking scores of a 560 compound subset from the initial 906 compounds to predict 85 side effects, grouped into 10 ADR phenotype groups. Only 21% (87 out of 409 of the drug-protein binding features involve known targets of the drug subset, providing a significant probe of off-target effects. As a control, associations of this drug subset with the 555 annotated targets of these compounds, as reported in DrugBank, were used as features to train a separate group of models. The Vina off-target models and the DrugBank on-target models yielded comparable median area-under-the-receiver-operating-characteristic-curves (AUCs during 10-fold cross-validation (0.60-0.69 and 0.61-0.74, respectively. Evidence was found in the PubMed literature to support several putative ADR-protein associations identified by our analysis. Among them, several associations between neoplasm-related ADRs and known tumor suppressor and tumor invasiveness marker proteins were found. A dual role for interstitial collagenase in both neoplasms and aneurysm formation was also identified. These associations all involve off-target proteins and could not have been found using available drug/on-target interaction data. This study illustrates a path forward to comprehensive ADR virtual screening that can potentially scale with

  7. Polysome profiling of mAb producing CHO cell lines links translational control of cell proliferation and recombinant mRNA loading onto ribosomes with global and recombinant protein synthesis.

    Science.gov (United States)

    Godfrey, Charlotte L; Mead, Emma J; Daramola, Olalekan; Dunn, Sarah; Hatton, Diane; Field, Ray; Pettman, Gary; Smales, C Mark

    2017-08-01

    mRNA translation is a key process determining growth, proliferation and duration of a Chinese hamster ovary (CHO) cell culture and influences recombinant protein synthesis rate. During bioprocessing, CHO cells can experience stresses leading to reprogramming of translation and decreased global protein synthesis. Here we apply polysome profiling to determine reprogramming and translational capabilities in host and recombinant monoclonal antibody-producing (mAb) CHO cell lines during batch culture. Recombinant cell lines with the fastest cell specific growth rates were those with the highest global translational efficiency. However, total ribosomal capacity, determined from polysome profiles, did not relate to the fastest growing or highest producing mAb cell line, suggesting it is the ability to utilise available machinery that determines protein synthetic capacity. Cell lines with higher cell specific productivities tended to have elevated recombinant heavy chain transcript copy numbers, localised to the translationally active heavy polysomes. The highest titre cell line was that which sustained recombinant protein synthesis and maintained high recombinant transcript copy numbers in polysomes. Investigation of specific endogenous transcripts revealed a number that maintained or reprogrammed into heavy polysomes, identifying targets for potential cell engineering or those with 5' untranslated regions that might be utilised to enhance recombinant transcript translation. © 2017 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. A Macrocyclic Agouti-Related Protein/[Nle4, DPhe7]α-Melanocyte Stimulating Hormone Chimeric Scaffold Produces Sub-nanomolar Melanocortin Receptor Ligands

    OpenAIRE

    Ericson, Mark D.; Freeman, Katie T.; Schnell, Sathya M.; Haskell-Luevano, Carrie

    2017-01-01

    The melanocortin system consists of five receptor subtypes, endogenous agonists, and naturally occurring antagonists. These receptors and ligands have been implicated in numerous biological pathways including processes linked to obesity and food intake. Herein, a truncation structure-activity relationship study of chimeric agouti-related protein (AGRP)/[Nle4, DPhe7]α-Melanocyte Stimulating Hormone (NDP-MSH) ligands is reported. The tetrapeptide His-DPhe-Arg-Trp or tripeptide DPhe-Arg-Trp repl...

  9. A mammalian model for Laron syndrome produced by targeted disruption of the mouse growth hormone receptor/binding protein gene (the Laron mouse)

    OpenAIRE

    Zhou, Yihua; Xu, Bixiong C.; Maheshwari, Hiralal G.; He, Li; Reed, Michael; Lozykowski, Maria; Okada, Shigeru; Cataldo, Lori; Coschigamo, Karen; Wagner, Thomas E.; Baumann, Gerhard; Kopchick, John J.

    1997-01-01

    Laron syndrome [growth hormone (GH) insensitivity syndrome] is a hereditary dwarfism resulting from defects in the GH receptor (GHR) gene. GHR deficiency has not been reported in mammals other than humans. Many aspects of GHR dysfunction remain unknown because of ethical and practical limitations in studying humans. To create a mammalian model for this disease, we generated mice bearing a disrupted GHR/binding protein (GHR/BP) gene through a homologous gene targeting approach. Homozygous GHR/...

  10. Microbes versus microbes

    DEFF Research Database (Denmark)

    Jordan, Kieran; Dalmasso, Marion; Zentek, Juergen

    2014-01-01

    been used in food processing to improve food safety. An understanding of the mode of action of this microbial antagonism has been gained in recent years and potential applications in food and feed safety are now being explored. This review focuses on the potential opportunities presented......Foodborne illness continues as a considerable threat to public health. Despite improved hygiene management systems and increased regulation, pathogenic bacteria still contaminate food, causing sporadic cases of illness and disease outbreaks worldwide. For many centuries, microbial antagonism has......, and the limitations, of using microbial antagonism as a biocontrol mechanism to reduce contamination along the food chain; including animal feed as its first link. © 2014 Society of Chemical Industry....

  11. A mammalian model for Laron syndrome produced by targeted disruption of the mouse growth hormone receptor/binding protein gene (the Laron mouse)

    Science.gov (United States)

    Zhou, Yihua; Xu, Bixiong C.; Maheshwari, Hiralal G.; He, Li; Reed, Michael; Lozykowski, Maria; Okada, Shigeru; Cataldo, Lori; Coschigamo, Karen; Wagner, Thomas E.; Baumann, Gerhard; Kopchick, John J.

    1997-01-01

    Laron syndrome [growth hormone (GH) insensitivity syndrome] is a hereditary dwarfism resulting from defects in the GH receptor (GHR) gene. GHR deficiency has not been reported in mammals other than humans. Many aspects of GHR dysfunction remain unknown because of ethical and practical limitations in studying humans. To create a mammalian model for this disease, we generated mice bearing a disrupted GHR/binding protein (GHR/BP) gene through a homologous gene targeting approach. Homozygous GHR/BP knockout mice showed severe postnatal growth retardation, proportionate dwarfism, absence of the GHR and GH binding protein, greatly decreased serum insulin-like growth factor I and elevated serum GH concentrations. These characteristics represent the phenotype typical of individuals with Laron syndrome. Animals heterozygous for the GHR/BP defect show only minimal growth impairment but have an intermediate biochemical phenotype, with decreased GHR and GH binding protein expression and slightly diminished insulin-like growth factor I levels. These findings indicate that the GHR/BP-deficient mouse (Laron mouse) is a suitable model for human Laron syndrome that will prove useful for the elucidation of many aspects of GHR/BP function that cannot be obtained in humans. PMID:9371826

  12. A mammalian model for Laron syndrome produced by targeted disruption of the mouse growth hormone receptor/binding protein gene (the Laron mouse).

    Science.gov (United States)

    Zhou, Y; Xu, B C; Maheshwari, H G; He, L; Reed, M; Lozykowski, M; Okada, S; Cataldo, L; Coschigamo, K; Wagner, T E; Baumann, G; Kopchick, J J

    1997-11-25

    Laron syndrome [growth hormone (GH) insensitivity syndrome] is a hereditary dwarfism resulting from defects in the GH receptor (GHR) gene. GHR deficiency has not been reported in mammals other than humans. Many aspects of GHR dysfunction remain unknown because of ethical and practical limitations in studying humans. To create a mammalian model for this disease, we generated mice bearing a disrupted GHR/binding protein (GHR/BP) gene through a homologous gene targeting approach. Homozygous GHR/BP knockout mice showed severe postnatal growth retardation, proportionate dwarfism, absence of the GHR and GH binding protein, greatly decreased serum insulin-like growth factor I and elevated serum GH concentrations. These characteristics represent the phenotype typical of individuals with Laron syndrome. Animals heterozygous for the GHR/BP defect show only minimal growth impairment but have an intermediate biochemical phenotype, with decreased GHR and GH binding protein expression and slightly diminished insulin-like growth factor I levels. These findings indicate that the GHR/BP-deficient mouse (Laron mouse) is a suitable model for human Laron syndrome that will prove useful for the elucidation of many aspects of GHR/BP function that cannot be obtained in humans.

  13. 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.

  14. Role of intestinal microbes on body nitrogen accumulation in germfree, gnotobiotic and conventional mice

    Energy Technology Data Exchange (ETDEWEB)

    Yamanaka, M; Nomura, T [Central Inst. for Experimental Animals, Tokyo (Japan); Kametka, M

    1974-10-01

    In order to observe the influence of intestinal microbes, nitrogen (N) of the carcasses and of the gut contents of 80-day-old germfree (GF), Escherichia coli (E. coli) or Staphylococcus epidermidis (Staph.) monocontaminated (at 56 days of age) gnotobiotic (GB) and conventional (CV) mice was estimated. The body weight of CV mice was greater than that of GF and both GB mice. The same tendencies were also shown in the weights of liver and kidney. However, there were no remarkable differences between GF and GB mice. Total N of the whole carcass per 100 g of body weight (except for intestinal contents) of CV mice was higher than that of other mice. The rank was CV, Staph., E. coli and GF mice. There was no major difference in /sup 15/N accumulation in the whole carcass, liver and leg muscles of three mice in each group two days after they were given a 0.2% /sup 15/N-labelled secondary ammonium phosphate-supplemented diet in any group, but accumulation in CV mice tended to be higher than in GF and GB mice. Total N of the whole intestinal contents per 100 g of body weight was high in GF, E. coli, Staph. and CV mice in that order. N in cecal contents in GF and both GB mice was remarkably higher than that in CV mice. The ratio of protein N to total N of gut contents showed almost the same tendencies in all groups until the lower part of the small intestine, however from the cecum the tendencies were different. CV mice showed an especially high protein N ratio and high total N per unit chromic oxide of intestinal contents until the cecum, but they decreased in the colon and rectum, which might suggest more reabsorption of non-protein N in the cecum, colon and rectum than in GF and both GB mice.

  15. Role of intestinal microbes on body nitrogen accumulation in germfree, gnotobiotic and conventional mice

    International Nuclear Information System (INIS)

    Yamanaka, Masanori; Nomura, Tatsuji; Kametka, Masao.

    1974-01-01

    In order to observe the influence of intestinal microbes, nitrogen (N) of the carcasses and of the gut contents of 80-day-old germfree (GF), Escherichia coli (E. coli) or Staphylococcus epidermidis (Staph.) monocontaminated (at 56 days of age) gnotobiotic (GB) and conventional (CV) mice was estimated. The body weight of CV mice was greater than that of GF and both GB mice. The same tendencies were also shown in the weights of liver and kidney. However, there were no remarkable differences between GF and GB mice. Total N of the whole carcass per 100 g of body weight (except for intestinal contents) of CV mice was higher than that of other mice. The rank was CV, Staph., E. coli and GF mice. There was no major difference in 15 N accumulation in the whole carcass, liver and leg muscles of three mice in each group two days after they were given a 0.2% 15 N-labelled secondary ammonium phosphate-supplemented diet in any group, but accumulation in CV mice tended to be higher than in GF and GB mice. Total N of the whole intestinal contents per 100 g of body weight was high in GF, E. coli, Staph. and CV mice in that order. N in cecal contents in GF and both GB mice was remarkably higher than that in CV mice. The ratio of protein N to total N of gut contents showed almost the same tendencies in all groups until the lower part of the small intestine, however from the cecum the tendencies were different. CV mice showed an especially high protein N ratio and high total N per unit chromic oxide of intestinal contents until the cecum, but they decreased in the colon and rectum, which might suggest more reabsorption of non-protein N in the cecum, colon and rectum than in GF and both GB mice. (auth.)

  16. 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.

  17. Effects of Different Dietary Protein Sources on Amino Acid Profiles of Ruminal Microbes in Goats%日粮不同蛋白质来源对山羊瘤胃微生物氨基酸组成的影响

    Institute of Scientific and Technical Information of China (English)

    王洪荣; 王梦芝; 曹恒春; 李国祥; 徐爱秋

    2009-01-01

    The main objective was to study the variation in the amino acid (AA) profile of microbial fractions obtained after feeding 4 kinds of dietary protein feedstuffs to Xuhuai Goat. Four goats fitted with rumen cannula were used in a 4×4 Latin square design. And artificial diets were divided into 4 groups according to the nitrogen source: group A (feather meal group), group B (corn gluten meal group), group C (soybean meal group), and group D (fish meal group). Results showed that, yields of microbial crude protein (MCP) varied with dietary protein, and the lowest was in group A (10. 765 0 mg/mL),while the highest was in group C (13. 975 0 mg/mL) (P<0.01). The microbial AA-N ratio was also alerted by dietary pro-tein. Group C recorded the lowest value, and the opposite was found in group D that recording the highest peak. Further multiple regression analysis showed that AA-N ratio (Y) had a negative/positive correlation with bacteria (X1)/protozoa (X2) group, and the regression equation was: Y= 15. 469-10. 098X1 + 1. 498X2(R2= 0. 944). It was also observed that,across all rations, significant differences were found between protozoa and bacteria in AA content for some but not all amino acids. Such as protozoal Val was significantly higher than that of bacterial; while bacterial Lys was significantly higher than that of protozoal. Additionally, within each microbial fraction, significant differences in the content of AA were found a-mong rations. For bacteria, significant difference was detected in Arg only (P,(0.05); for protozoa, Met, Leu and His showed significant differences (P<0.05). And the variations of AA were related to the changes of microbial population in some degree. It was concluded that yields, AA-N ratio, and AA profile of ruminal MCP were all affected by dietary protein.%本文主要研究不同蛋白质饲料对瘤胃微生物蛋白产量及其氨基酸(AA)组成模式影响的规律.以4只瘘管山羊作为试验动物,分为A组(羽毛粉组)

  18. The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation.

    Science.gov (United States)

    Engels, Christina; Ruscheweyh, Hans-Joachim; Beerenwinkel, Niko; Lacroix, Christophe; Schwab, Clarissa

    2016-01-01

    Eubacterium hallii is considered an important microbe in regard to intestinal metabolic balance due to its ability to utilize glucose and the fermentation intermediates acetate and lactate, to form butyrate and hydrogen. Recently, we observed that E. hallii is capable of metabolizing glycerol to 3-hydroxypropionaldehyde (3-HPA, reuterin) with reported antimicrobial properties. The key enzyme for glycerol to 3-HPA conversion is the cobalamin-dependent glycerol/diol dehydratase PduCDE which also utilizes 1,2-propanediol (1,2-PD) to form propionate. Therefore our primary goal was to investigate glycerol to 3-HPA metabolism and 1,2-PD utilization by E. hallii along with its ability to produce cobalamin. We also investigated the relative abundance of E. hallii in stool of adults using 16S rRNA and pduCDE based gene screening to determine the contribution of E. hallii to intestinal propionate formation. We found that E. hallii utilizes glycerol to produce up to 9 mM 3-HPA but did not further metabolize 3-HPA to 1,3-propanediol. Utilization of 1,2-PD in the presence and absence of glucose led to the formation of propanal, propanol and propionate. E. hallii formed cobalamin and was detected in stool of 74% of adults using 16S rRNA gene as marker gene (n = 325). Relative abundance of the E. hallii 16S rRNA gene ranged from 0 to 0.59% with a mean relative abundance of 0.044%. E. hallii PduCDE was detected in 63 to 81% of the metagenomes depending on which subunit was investigated beside other taxons such as Ruminococcus obeum, R. gnavus, Flavonifractor plautii, Intestinimonas butyriciproducens, and Veillonella spp. In conclusion, we identified E. hallii as a common gut microbe with the ability to convert glycerol to 3-HPA, a step that requires the production of cobalamin, and to utilize 1,2-PD to form propionate. Our results along with its ability to use a broad range of substrates point at E. hallii as a key species within the intestinal trophic chain with the potential to

  19. The common gut microbe Eubacterium hallii also contributes to intestinal propionate formation

    Directory of Open Access Journals (Sweden)

    Christina eEngels

    2016-05-01

    Full Text Available Eubacterium hallii is considered an important microbe in regard to intestinal metabolic balance due to its ability to utilize glucose and the fermentation intermediates acetate and lactate, to form butyrate and hydrogen. Recently, we observed that E. hallii is capable of metabolizing glycerol to 3-hydroxypropionaldehyde (3-HPA, reuterin with reported antimicrobial properties. The key enzyme for glycerol to 3-HPA conversion is the cobalamin-dependent glycerol/diol dehydratase PduCDE which also utilizes 1,2-propanediol (1,2-PD to form propionate. Therefore our primary goal was to investigate glycerol to 3-HPA metabolism and 1,2-PD utilization by E. hallii along with its ability to produce cobalamin. We also investigated the relative abundance of E. hallii in stool of adults using 16S rRNA and pduCDE based gene screening to determine the contribution of E. hallii to intestinal propionate formation. We found that E. hallii utilizes glycerol to produce up to 9 mM 3-HPA but did not further metabolize 3-HPA to 1,3-propanediol (1,3-PD. Utilization of 1,2-PD in the presence and absence of glucose led to the formation of propanal, propanol and propionate. E. hallii formed cobalamin and was detected in stool of 74% of adults using 16S rRNA gene as marker gene (n = 325. Relative abundance of the E. hallii 16S rRNA gene ranged from 0 to 0.59% with a mean relative abundance of 0.044%. E. hallii PduCDE was detected in 63 to 81% of the metagenomes depending on which subunit was investigated beside other taxons such as Ruminococcus obeum, Ruminococcus gnavus, Flavonifractor prautii, Intestinimonas butyriciproducens, and Veillonella spp. In conclusion, we identified E. hallii as a common gut microbe with the ability to convert glycerol to 3-HPA, a step that requires the production of cobalamin, and to utilize 1,2-PD to form propionate. Our results along with its ability to use a broad range of substrates point at E. hallii as a key species within the intestinal

  20. 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.

  1. Relationship Between Hepatic Albumin and Sulphate Synthesis and its Use in Measurement of the Absolute Rate of Synthesis of Liver-Produced Plasma Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Awwad, H. K.; Sheraki, A. S. [Department of Radiology and Radiological Sciences, Cancer Institute, University of Cairo, Cairo (Egypt); Radioisotope Unit, Medical Research Institute, Alexandria (Egypt)

    1971-02-15

    A model is proposed whereby serum albumin synthesis is expressed in terms of production of inorganic sulphate in the liver and the entire organism, following the administration of {sup 35}S-L-cystine. The basis assumption involved is that the precursor amino acid pool for albumin synthesis in the liver is either identical with that of inorganic sulphate synthesis or that the two pools concerned are in rapid equilibrium with each other so that they can be treated as a single pool. The feasibility of the proposed model was tested by comparing the synthesis rate of rat serum albumin with the catabolic rate of the radioiodinated protein measured in the same animal. A good agreement between the two rates was noted in a group of adult rats, whereas an excess of anabolism was noted in young growing animals. In rats fed low-protein diet, the synthesis rate exceeded the catabolic rate; both being subnormal. The equilibrium between hepatic and plasma radiosulphate concentration was complete within four hours following the injection of {sup 35}S-cystine. The total radiosulphate production could then be evaluated after such an interval from the urinary excretion and serum concentration multiplied by the volume of the sulphate space. Lack of significant re-utilization was demonstrated following the injection of radiosulphate. This is a decided advantage of the proposed method. However, extensive re-utilization of selenate selenium in the synthesis of the seleno-analogues of sulphur-amino acids was shown. This could explain the poor yield of radioselenate following the injection of {sup 75}Se-selenocystine and precludes the use of the latter agent as a tracer for measurement of synthesis of plasma proteins. (author)

  2. Insect cells are superior to Escherichia coli in producing malaria proteins inducing IgG targeting PfEMP1 on infected erythrocytes

    DEFF Research Database (Denmark)

    Victor, Michala E; Bengtsson, Anja; Andersen, Gorm

    2010-01-01

    -exposed epitopes are unknown. An insect cell and Escherichia coli based system was used to express single and double domains encoded by the pfd1235w var gene. The resulting recombinant proteins have been evaluated for yield and purity and their ability to induce rat antibodies, which react with the native PFD1235w...... PfEMP1 antigen expressed on 3D7PFD1235w-IE. Their recognition by human anti-malaria antibodies from previously infected Tanzanian donors was also analysed....

  3. “Inclonals”: IgGs and IgG-enzyme fusion proteins produced in an E. coli expression-refolding system

    OpenAIRE

    Hakim, Rahely; Benhar, Itai

    2009-01-01

    Full-length antibodies and antibodies that ferry a cargo to target cells are desired biopharmaceuticals. We describe the production of full-length IgGs and IgG-toxin fusion proteins in E. coli. In the presented examples of anti CD30 and anti EGF-receptor antibodies, the antibody heavy and light chains or toxin fusions thereof were expressed in separate bacterial cultures, where they accumulated as insoluble inclusion bodies. Following refolding and purification, high yields (up to 50 mg/L of ...

  4. Ratio of dietary rumen degradable protein to rumen undegradable protein affects nitrogen partitioning but does not affect the bovine milk proteome produced by mid-lactation Holstein dairy cows.

    Science.gov (United States)

    Tacoma, R; Fields, J; Ebenstein, D B; Lam, Y-W; Greenwood, S L

    2017-09-01

    Little is known about the bovine milk proteome or whether it can be affected by diet. The objective of this study was to determine if the dietary rumen degradable protein (RDP):rumen undegradable protein (RUP) ratio could alter the bovine milk proteome. Six Holstein cows (parity: 2.5 ± 0.8) in mid lactation were blocked by days in milk (80 ± 43 d in milk) and milk yield (57.5 ± 6.0 kg) and randomly assigned to treatment groups. The experiment was conducted as a double-crossover design consisting of three 21-d periods. Within each period, treatment groups received diets with either (1) a high RDP:RUP ratio (RDP treatment: 62.4:37.6% of crude protein) or (2) a low RDP:RUP ratio (RUP treatment: 51.3:48.7% of crude protein). Both diets were isonitrogenous and isoenergetic (crude protein: 18.5%, net energy for lactation: 1.8 Mcal/kg of dry matter). To confirm N and energy status of cows, dry matter intake was determined daily, rumen fluid samples were collected for volatile fatty acid analysis, blood samples were collected for plasma glucose, β-hydroxybutyrate, urea nitrogen, and fatty acid analysis, and total 24-h urine and fecal samples were collected for N analysis. Milk samples were collected to determine the general milk composition and the protein profile. Milk samples collected for high-abundance protein analysis were subjected to HPLC analysis to determine the content of α-casein, β-casein, and κ-casein, as well as α-lactalbumin and β-lactoglobulin. Samples collected for low-abundance protein analysis were fractionated, enriched using ProteoMiner treatment, and separated using sodium dodecyl sulfate-PAGE. After excision and digestion, the peptides were analyzed using liquid chromatography (LC) tandem mass spectrometry (MS/MS). The LC-MS/MS data were analyzed using PROC GLIMMIX of SAS (version 9.4, SAS Institute Inc., Cary, NC) and adjusted using the MULTTEST procedure. All other parameters were analyzed using PROC MIXED of SAS. No treatment differences

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

    Directory of Open Access Journals (Sweden)

    Jenna M. Lang

    2014-12-01

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

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

    Science.gov (United States)

    Shepelin, Denis; Hansen, Anne Sofie Lærke; Lennen, Rebecca; Luo, Hao; Herrgård, Markus J

    2018-05-11

    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 with either generation of spontaneous mutations or some form of targeted or random mutagenesis. Evolutionary engineering has been used to successfully engineer easily selectable phenotypes, such as utilization of a suboptimal nutrient source or tolerance to inhibitory substrates or products. In this review, 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 has been successfully achieved through evolutionary engineering by coupling production to cellular growth.

  7. Metabolic engineering of volatile isoprenoids in plants and microbes.

    Science.gov (United States)

    Vickers, Claudia E; Bongers, Mareike; Liu, Qing; Delatte, Thierry; Bouwmeester, Harro

    2014-08-01

    The chemical properties and diversity of volatile isoprenoids lends them to a broad variety of biological roles. It also lends them to a host of biotechnological applications, both by taking advantage of their natural functions and by using them as industrial chemicals/chemical feedstocks. Natural functions include roles as insect attractants and repellents, abiotic stress protectants in pathogen defense, etc. Industrial applications include use as pharmaceuticals, flavours, fragrances, fuels, fuel additives, etc. Here we will examine the ways in which researchers have so far found to exploit volatile isoprenoids using biotechnology. Production and/or modification of volatiles using metabolic engineering in both plants and microorganisms are reviewed, including engineering through both mevalonate and methylerythritol diphosphate pathways. Recent advances are illustrated using several case studies (herbivores and bodyguards, isoprene, and monoterpene production in microbes). Systems and synthetic biology tools with particular utility for metabolic engineering are also reviewed. Finally, we discuss the practical realities of various applications in modern biotechnology, explore possible future applications, and examine the challenges of moving these technologies forward so that they can deliver tangible benefits. While this review focuses on volatile isoprenoids, many of the engineering approaches described here are also applicable to non-isoprenoid volatiles and to non-volatile isoprenoids. © 2014 John Wiley & Sons Ltd.

  8. Anaerobic Probiotics: The Key Microbes for Human Health.

    Science.gov (United States)

    El Enshasy, Hesham; Malik, Khairuddin; Malek, Roslinda Abd; Othman, Nor Zalina; Elsayed, Elsayed Ahmed; Wadaan, Mohammad

    Human gastrointestinal microbiota (HGIM) incorporate a large number of microbes from different species. Anaerobic bacteria are the dominant organisms in this microbial consortium and play a crucial role in human health. In addition to their functional role as the main source of many essential metabolites for human health, they are considered as biotherapeutic agents in the regulation of different human metabolites. They are also important in the prevention and in the treatment of different physical and mental diseases. Bifidobacteria are the dominant anaerobic bacteria in HGIM and are widely used in the development of probiotic products for infants, children and adults. To develop bifidobacteria-based bioproducts, therefore, it is necessary to develop a large-scale biomass production platform based on a good understanding of the ideal medium and bioprocessing parameters for their growth and viability. In addition, high cell viability should be maintained during downstream processing and storage of probiotic cell powder or the final formulated product. In this work we review the latest information about the biology, therapeutic activities, cultivation and industrial production of bifidobacteria.

  9. 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.

  10. The role of lipids in host microbe interactions.

    Science.gov (United States)

    Lang, Roland; Mattner, Jochen

    2017-06-01

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

  11. Of genes and microbes: solving the intricacies in host genomes.

    Science.gov (United States)

    Wang, Jun; Chen, Liang; Zhao, Na; Xu, Xizhan; Xu, Yakun; Zhu, Baoli

    2018-05-01

    Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.

  12. Designer cells programming quorum-sensing interference with microbes.

    Science.gov (United States)

    Sedlmayer, Ferdinand; Hell, Dennis; Müller, Marius; Ausländer, David; Fussenegger, Martin

    2018-05-08

    Quorum sensing is a promising target for next-generation anti-infectives designed to address evolving bacterial drug resistance. The autoinducer-2 (AI-2) is a key quorum-sensing signal molecule which regulates bacterial group behaviors and is recognized by many Gram-negative and Gram-positive bacteria. Here we report a synthetic mammalian cell-based microbial-control device that detects microbial chemotactic formyl peptides through a formyl peptide sensor (FPS) and responds by releasing AI-2. The microbial-control device was designed by rewiring an artificial receptor-based signaling cascade to a modular biosynthetic AI-2 production platform. Mammalian cells equipped with the microbial-control gene circuit detect formyl peptides secreted from various microbes with high sensitivity and respond with robust AI-2 production, resulting in control of quorum sensing-related behavior of pathogenic Vibrio harveyi and attenuation of biofilm formation by the human pathogen Candida albicans. The ability to manipulate mixed microbial populations through fine-tuning of AI-2 levels may provide opportunities for future anti-infective strategies.

  13. Molecular mechanisms of nematode-nematophagous microbe interactions: basis for biological control of plant-parasitic nematodes.

    Science.gov (United States)

    Li, Juan; Zou, Chenggang; Xu, Jianping; Ji, Xinglai; Niu, Xuemei; Yang, Jinkui; Huang, Xiaowei; Zhang, Ke-Qin

    2015-01-01

    Plant-parasitic nematodes cause significant damage to a broad range of vegetables and agricultural crops throughout the world. As the natural enemies of nematodes, nematophagous microorganisms offer a promising approach to control the nematode pests. Some of these microorganisms produce traps to capture and kill the worms from the outside. Others act as internal parasites to produce toxins and virulence factors to kill the nematodes from within. Understanding the molecular basis of microbe-nematode interactions provides crucial insights for developing effective biological control agents against plant-parasitic nematodes. Here, we review recent advances in our understanding of the interactions between nematodes and nematophagous microorganisms, with a focus on the molecular mechanisms by which nematophagous microorganisms infect nematodes and on the nematode defense against pathogenic attacks. We conclude by discussing several key areas for future research and development, including potential approaches to apply our recent understandings to develop effective biocontrol strategies.

  14. Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes.

    Science.gov (United States)

    Hehemann, Jan-Hendrik; Kelly, Amelia G; Pudlo, Nicholas A; Martens, Eric C; Boraston, Alisdair B

    2012-11-27

    Humans host an intestinal population of microbes--collectively referred to as the gut microbiome--which encode the carbohydrate active enzymes, or CAZymes, that are absent from the human genome. These CAZymes help to extract energy from recalcitrant polysaccharides. The question then arises as to if and how the microbiome adapts to new carbohydrate sources when modern humans change eating habits. Recent metagenome analysis of microbiomes from healthy American, Japanese, and Spanish populations identified putative CAZymes obtained by horizontal gene transfer from marine bacteria, which suggested that human gut bacteria evolved to degrade algal carbohydrates-for example, consumed in form of sushi. We approached this hypothesis by studying such a polysaccharide utilization locus (PUL) obtained by horizontal gene transfer by the gut bacterium Bacteroides plebeius. Transcriptomic and growth experiments revealed that the PUL responds to the polysaccharide porphyran from red algae, enabling growth on this carbohydrate but not related substrates like agarose and carrageenan. The X-ray crystallographic and biochemical analysis of two proteins encoded by this PUL, BACPLE_01689 and BACPLE_01693, showed that they are β-porphyranases belonging to glycoside hydrolase families 16 and 86, respectively. The product complex of the GH86 at 1.3 Å resolution highlights the molecular details of porphyran hydrolysis by this new porphyranase. Combined, these data establish experimental support for the argument that CAZymes and associated genes obtained from extrinsic microbes add new catabolic functions to the human gut microbiome.

  15. Effect of rice straw silage treated with rumen microbes of buffalo on digestibility and ecosystem of cattle rumen

    Directory of Open Access Journals (Sweden)

    Thalib A

    2000-03-01

    Full Text Available Treatment of rice straw silage with addition of buffalo rumen microbes was conducted to improve the ruminal digestion of rice straw in ongole cattle. Three fistulated cattles were each introduced to dietary treatment: I. Untreated rice straw (JPTP, II. Rice straw ensilaged with buffalo rumen microbes (SJPMR-Kr, and ID. Elephant grass (RG. All diets were formulated isonitrogeneous (14% crude protein and fed to animals over a period of 4 weeks. After 4 weeks of feeding trial, rwnen fluid of the animals were evaluated to digest its own basal diet (as substrate. The results show that cumulative gas production resulting from the substrate fermented (96 hours by rumen fluid from cattle fed diet II is 205% of the diet I and 151 % of the diet ID. Measurements of DMD of the substrates after the gas production procedure show the similar trend (ie. DM digestibilities for JPTP= 33%; SJPMR-Kr= 54% dan RG= 45%. Means of in sacco DMD (72 hours incubation confirm the results of gas production (ie. in sacco DM Digestibilities for JPTP= 35%; SJPMR-Kr= 44% and RG= 39%. All results described between treatments are highly significant different (P0.05, except for total VFA (ie. JPTP= 0.52 mg Inri; SJPMR-Kr= 3,37 mg Inri and RG= 3.15 mg Inri.

  16. 瘤胃微生物多样性与定量%Rumial Microbes: Diversity and Quantification

    Institute of Scientific and Technical Information of China (English)

    马涛; 刁其玉

    2015-01-01

    Ruminants are able to utilize fibrous feed as a source of energy and nutrients due to the ruminal mi-crobes, composed mainly of bacteria, fungi, and ciliate protozoa. Ruminal microbes play different roles in feed digestion and act synergistically to ferment dietary carbohydrates and proteins. This review reported the latest methods for assessment of ruminal microbial diversity, particularly molecular techniques, which allows people to gain new insights into rumen functions.%反刍动物由于瘤胃微生物的存在能够分解并利用饲料中的纤维素来提供能量和蛋白质. 瘤胃微生物主要包括细菌、真菌和原虫,三者在消化饲料过程中分工明确,共同实现碳水化合物和蛋白质的分解. 本文综述了定量瘤胃微生物群落多样性的新方法,尤其是分子生物学的应用,进一步提高人们对于瘤胃功能的认识水平.

  17. Tiny and Hidden but Changing Your World: The Importance of Soil Microbes to Climate Change

    Science.gov (United States)

    Waldo, N.; Neumann, R. B.

    2017-12-01

    When most people think about global climate change they think about massive power plants billowing smoke and expansive glaciers melting to nothingness. What the public often overlooks is how natural processes invisible to the naked eye can be changed by the climate, and the fact that the natural response to those changes can further alter the climate. Scientists call these reactions "feedback cycles", and understanding them is crucial to predicting the true impact of human activities. In our research, we study one particular feedback cycle: the effect of increased plant productivity on methane emissions from wetlands. Globally, wetlands account for about a third of annual emissions of methane, the second most important greenhouse gas after carbon dioxide. This heat-trapping gas is generated in the soil of wetlands by microscopic organisms that consume, among other things, proteins and sugars released by the roots of plants. As the atmosphere becomes warmer and richer in carbon dioxide, these plants will grow larger and faster, releasing more of this microbe food into the soil. Our current research seeks to understand how that will affect the microbial ecosystem, and through it the emissions of methane gas.

  18. Combined Creutzfeldt-Jakob/ Alzheimer's Disease Cases are Important in Search for Microbes in Alzheimer's Disease.

    Science.gov (United States)

    Bastian, Frank O

    2017-01-01

    The question whether Alzheimer's disease is infectious as brought up in the recent editorial published in the Journal of Alzheimer's Disease is complicated by the controversy whether the causal agent is a microbe or a misfolded host protein (amyloid). The replicating amyloid (prion) theory, based upon data from studies of Creutzfeldt-Jakob disease (CJD) and other transmissible spongiform encephalopathies (TSEs), has been challenged since the prion can be separated from TSE infectivity, and spiroplasma, a wall-less bacterium, has been shown to be involved in the pathogenesis of CJD. Further support for a microbial cause for AD comes from occurrence of mixed CJD/AD cases involving up to 15% of AD brains submitted to brain banks. The association of CJD with AD suggests a common etiology rather than simply being a medical curiosity. A co-infection with the transmissible agent of CJD, which we propose to be a Spiroplasma sp., would explain the diversity of bacteria shown to be associated with cases of AD.

  19. 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.

  20. 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

  1. 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)

  2. The composition of readily available carbon sources produced by fermentation of fish faeces is affected by dietary protein:energy ratios

    DEFF Research Database (Denmark)

    Letelier-Gordo, Carlos Octavio; Larsen, Bodil Katrine; Dalsgaard, Johanne

    2017-01-01

    , 17, 19, 21 and 23 g/MJ) to rainbow trout (Oncorhynchus mykiss) on the production of volatile fatty acids (VFAs) and ethanol during 7 days fermentation of the produced fish faeces. The total yields of VFAs and ethanol obtained (expressed as chemical oxygen demand (COD)) ranged between 0.21–0.24 g...... of acetic and valeric acid. Changing the diet composition thus affects the composition of readily available carbon that can be derived from the faeces. This can be applied to enhance on-farm single sludge denitrification and reduce the need for adding external carbon sources such as e.g. methanol....

  3. Natural variation in floral nectar proteins of two Nicotiana attenuata accessions.

    Science.gov (United States)

    Seo, Pil Joon; Wielsch, Natalie; Kessler, Danny; Svatos, Ales; Park, Chung-Mo; Baldwin, Ian T; Kim, Sang-Gyu

    2013-07-13

    Floral nectar (FN) contains not only energy-rich compounds to attract pollinators, but also defense chemicals and several proteins. However, proteomic analysis of FN has been hampered by the lack of publically available sequence information from nectar-producing plants. Here we used next-generation sequencing and advanced proteomics to profile FN proteins in the opportunistic outcrossing wild tobacco, Nicotiana attenuata. We constructed a transcriptome database of N. attenuata and characterized its nectar proteome using LC-MS/MS. The FN proteins of N. attenuata included nectarins, sugar-cleaving enzymes (glucosidase, galactosidase, and xylosidase), RNases, pathogen-related proteins, and lipid transfer proteins. Natural variation in FN proteins of eleven N. attenuata accessions revealed a negative relationship between the accumulation of two abundant proteins, nectarin1b and nectarin5. In addition, microarray analysis of nectary tissues revealed that protein accumulation in FN is not simply correlated with the accumulation of transcripts encoding FN proteins and identified a group of genes that were specifically expressed in the nectary. Natural variation of identified FN proteins in the ecological model plant N. attenuata suggests that nectar chemistry may have a complex function in plant-pollinator-microbe interactions.

  4. Fungus-Mediated Preferential Bioleaching of Waste Material Such as Fly - Ash as a Means of Producing Extracellular, Protein Capped, Fluorescent and Water Soluble Silica Nanoparticles

    Science.gov (United States)

    Khan, Shadab Ali; Uddin, Imran; Moeez, Sana; Ahmad, Absar

    2014-01-01

    In this paper, we for the first time show the ability of the mesophilic fungus Fusarium oxysporum in the bioleaching of waste material such as Fly-ash for the extracellular production of highly crystalline and highly stable, protein capped, fluorescent and water soluble silica nanoparticles at ambient conditions. When the fungus Fusarium oxysporum is exposed to Fly-ash, it is capable of selectively leaching out silica nanoparticles of quasi-spherical morphology within 24 h of reaction. These silica nanoparticles have been completely characterized by UV-vis spectroscopy, Photoluminescence (PL), Transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and Energy dispersive analysis of X-rays (EDAX). PMID:25244567

  5. Fungus-mediated preferential bioleaching of waste material such as fly - ash as a means of producing extracellular, protein capped, fluorescent and water soluble silica nanoparticles.

    Directory of Open Access Journals (Sweden)

    Shadab Ali Khan

    Full Text Available In this paper, we for the first time show the ability of the mesophilic fungus Fusarium oxysporum in the bioleaching of waste material such as Fly-ash for the extracellular production of highly crystalline and highly stable, protein capped, fluorescent and water soluble silica nanoparticles at ambient conditions. When the fungus Fusarium oxysporum is exposed to Fly-ash, it is capable of selectively leaching out silica nanoparticles of quasi-spherical morphology within 24 h of reaction. These silica nanoparticles have been completely characterized by UV-vis spectroscopy, Photoluminescence (PL, Transmission electron microscopy (TEM, X-ray diffraction (XRD, Fourier transform infrared spectroscopy (FTIR and Energy dispersive analysis of X-rays (EDAX.

  6. Expression of ankyrin repeat and suppressor of cytokine signaling box protein 4 (Asb-4) in proopiomelanocortin neurons of the arcuate nucleus of mice produces a hyperphagic, lean phenotype.

    Science.gov (United States)

    Li, Ji-Yao; Chai, Biao-Xin; Zhang, Weizhen; Wang, Hui; Mulholland, Michael W

    2010-01-01

    Ankyrin repeat and suppressor of cytokine signaling box-containing protein 4 (Asb-4) is specifically expressed in the energy homeostasis-related brain areas and colocalizes with proopiomelanocortin (POMC) neurons of the arcuate nucleus (ARC). Injection of insulin into the third ventricle of the rat brain increased Asb-4 mRNA expression in the paraventricular nucleus but not in the ARC of the hypothalamus, whereas injection of leptin (ip) increased Asb-4 expression in both mouse paraventricular nucleus and ARC. A transgenic mouse in which Myc-tagged Asb-4 is specifically expressed in POMC neurons of the ARC was made and used to study the effects of Asb-4 on ingestive behavior and metabolic rate. Animals with overexpression of Asb-4 in POMC neurons demonstrated an increase in food intake. However, POMC-Asb-4 transgenic animals gained significantly less weight from 6-30 wk of age. The POMC-Asb-4 mice had reduced fat mass and increased lean mass and lower levels of blood leptin. The transgenic animals were resistant to high-fat diet-induced obesity. Transgenic mice had significantly higher rates of oxygen consumption and carbon dioxide production than wild-type mice during both light and dark periods. The locomotive activity of transgenic mice was increased. The overexpression of Asb-4 in POMC neurons increased POMC mRNA expression in the ARC. The transgenic animals had no observed effect on peripheral glucose metabolism and the activity of the autonomic nervous system. These results indicate that Asb-4 is a key regulatory protein in the central nervous system, involved in the control of feeding behavior and metabolic rate.

  7. Immobilization of anode-attached microbes in a microbial fuel cell.

    KAUST Repository

    Wagner, Rachel C

    2012-01-03

    Current-generating (exoelectrogenic) bacteria in bioelectrochemical systems (BESs) may not be culturable using standard in vitro agar-plating techniques, making isolation of new microbes a challenge. More in vivo like conditions are needed where bacteria can be grown and directly isolated on an electrode. While colonies can be developed from single cells on an electrode, the cells must be immobilized after being placed on the surface. Here we present a proof-of-concept immobilization approach that allows exoelectrogenic activity of cells on an electrode based on applying a layer of latex to hold bacteria on surfaces. The effectiveness of this procedure to immobilize particles was first demonstrated using fluorescent microspheres as bacterial analogs. The latex coating was then shown to not substantially affect the exoelectrogenic activity of well-developed anode biofilms in two different systems. A single layer of airbrushed coating did not reduce the voltage produced by a biofilm in a microbial fuel cell (MFC), and more easily applied dip-and-blot coating reduced voltage by only 11% in a microbial electrolysis cell (MEC). This latex immobilization procedure will enable future testing of single cells for exoelectrogenic activity on electrodes in BESs.

  8. Ecotoxicological effects of decabromodiphenyl ether and cadmium contamination on soil microbes and enzymes.

    Science.gov (United States)

    Zhang, Wei; Zhang, Meng; An, Shuai; Xiong, Bang; Li, Hui; Cui, Changzheng; Lin, Kuangfei

    2012-08-01

    The ecotoxicological effects of decabromodiphenyl ether (BDE209) and cadmium (Cd) contamination on soil culturable microbial population, enzyme activity and bacterial community structure were investigated. Results of the indoor incubation test runs performed on many series of control and contaminated soil samples have demonstrated some notable toxic effects due to long term exposure to either or both contaminants. The two contaminants produced notable yet different toxic effects on the test microbes; the population of the exposed species generally declined according to certain dose-response relationships. The soil culturable microbial population and enzyme activity data show that the sensitivity to one or both contaminants followed the order of: bacteria>fungi>actinomycete and urease>saccharase, respectively. The interaction between BDE209 and Cd was dependent on both the exposure dose and time and that the joint toxic effects were synergistic, antagonistic or additive. The PCR-DGGE analysis data of species composition and richness suggest the synergistic combined effects on bacterial community structure during the 30d exposure. Pseudomonas tuomuerensis strain CCM 7280 and Pseudomonas alcaliphila strain AL15-21 were enriched, indicating these species might be major functional populations and highly tolerant. Such observations have provided the useful information of potential ecotoxicological effects of BDE209 and Cd contamination in the environment. Copyright © 2012 Elsevier Inc. All rights reserved.

  9. Natural Pathogen Control Chemistry to Replace Toxic Treatment of Microbes and Biofilm in Cooling Towers

    Science.gov (United States)

    Brouse, Lon; Brouse, Richard; Brouse, Daniel

    2017-01-01

    Application of toxic antibacterial agents is considered necessary to control prevalent fresh water microorganisms that grow in evaporative cooling water systems, but can adversely affect the environment and human health. However, natural antibacterial water chemistry has been applied in industrial cooling water systems for over 10 years to inhibit microorganisms with excellent results. The water chemistry method concentrates natural minerals in highly-softened water to produce elevated pH and dissolved solids, while maintaining low calcium and magnesium content. The method provides further benefits in water conservation, and generates a small volume of non-toxic natural salt concentrate for cost efficient separation and disposal if required. This report describes the antimicrobial effects of these chemistry modifications in the cooling water environment and the resultant collective inhibition of microbes, biofilm, and pathogen growth. This article also presents a novel perspective of parasitic microbiome functional relationships, including “Trojan Protozoans” and biofilms, and the function of polyvalent metal ions in the formation and inhibition of biofilms. Reducing global dependence on toxic antibacterial agents discharged to the environment is an emerging concern due to their impact on the natural microbiome, plants, animals and humans. Concurrently, scientists have concluded that discharge of antibacterial agents plays a key role in development of pathogen resistance to antimicrobials as well as antibiotics. Use of natural antibacterial chemistry can play a key role in managing the cooling water environment in a more ecologically sustainable manner. PMID:28420074

  10. Immobilization of anode-attached microbes in a microbial fuel cell.

    KAUST Repository

    Wagner, Rachel C; Porter-Gill, Sikandar; Logan, Bruce E

    2012-01-01

    Current-generating (exoelectrogenic) bacteria in bioelectrochemical systems (BESs) may not be culturable using standard in vitro agar-plating techniques, making isolation of new microbes a challenge. More in vivo like conditions are needed where bacteria can be grown and directly isolated on an electrode. While colonies can be developed from single cells on an electrode, the cells must be immobilized after being placed on the surface. Here we present a proof-of-concept immobilization approach that allows exoelectrogenic activity of cells on an electrode based on applying a layer of latex to hold bacteria on surfaces. The effectiveness of this procedure to immobilize particles was first demonstrated using fluorescent microspheres as bacterial analogs. The latex coating was then shown to not substantially affect the exoelectrogenic activity of well-developed anode biofilms in two different systems. A single layer of airbrushed coating did not reduce the voltage produced by a biofilm in a microbial fuel cell (MFC), and more easily applied dip-and-blot coating reduced voltage by only 11% in a microbial electrolysis cell (MEC). This latex immobilization procedure will enable future testing of single cells for exoelectrogenic activity on electrodes in BESs.

  11. Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture

    Science.gov (United States)

    Wu, Linkun; Wang, Juanying; Huang, Weimin; Wu, Hongmiao; Chen, Jun; Yang, Yanqiu; Zhang, Zhongyi; Lin, Wenxiong

    2015-10-01

    Under consecutive monoculture, the biomass and quality of Rehmannia glutinosa declines significantly. Consecutive monoculture of R. glutinosa in a four-year field trial led to significant growth inhibition. Most phenolic acids in root exudates had cumulative effects over time under sterile conditions, but these effects were not observed in the rhizosphere under monoculture conditions. It suggested soil microbes might be involved in the degradation and conversion of phenolic acids from the monocultured plants. T-RFLP and qPCR analysis demonstrated differences in both soil bacterial and fungal communities during monoculture. Prolonged monoculture significantly increased levels of Fusarium oxysporum, but decreased levels of Pseudomonas spp. Abundance of beneficial Pseudomonas spp. with antagonistic activity against F. oxysporum was lower in extended monoculture soils. Phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth, sporulation, and toxin (3-Acetyldeoxynivalenol, 15-O-Acetyl-4-deoxynivalenol) production of pathogenic F. oxysporum while inhibiting growth of the beneficial Pseudomonas sp. W12. This study demonstrates that extended monoculture can alter the microbial community of the rhizosphere, leading to relatively fewer beneficial microorganisms and relatively more pathogenic and toxin-producing microorganisms, which is mediated by the root exudates.

  12. Biogeographic patterns in ocean microbes emerge in a neutral agent-based model.

    Science.gov (United States)

    Hellweger, Ferdi L; van Sebille, Erik; Fredrick, Neil D

    2014-09-12

    A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection. Copyright © 2014, American Association for the Advancement of Science.

  13. Glionitrin A, an antibiotic-antitumor metabolite derived from competitive interaction between abandoned mine microbes

    Energy Technology Data Exchange (ETDEWEB)

    Park, H.B.; Kown, H.C.; Lee, C.H.; Yang, H.O. [Korean Institute of Science & Technology KIST, Kangnung (Republic of Korea)

    2009-02-15

    The nutrient conditions present in abandoned coal mine drainages create an extreme environment where defensive and offensive microbial interactions could be critical for survival and fitness. Coculture of a mine drainage-derived Sphingomonas bacterial strain, KMK-001, and a mine drainage-derived Aspergillus fumigatus fungal strain, KMC-901, resulted in isolation of a new diketopiperazine disulfide, glionitrin A (1). Compound 1 was not detected in monoculture broths of KMK-001 or KMC-901. The structure of 1, a (3S,10aS) diketopiperazine disulfide containing a nitro aromatic ring, was based on analysis of MS, NMR, and circular dichroism spectra and confirmed by X-ray crystal data. Glionitrin A displayed significant antibiotic activity against a series of microbes including methicillin-resistant Staphylococcus aureus. An in vitro MTT cytotoxicity assay revealed that 1 had potent submicromolar cytotoxic activity against four human cancer cell lines: HCT-116, A549, AGS, and DU145. The results provide further evidence that microbial coculture can produce novel biologically relevant molecules.

  14. Innate Immune Responses Activated in Arabidopsis Roots by Microbe-Associated Molecular Patterns[W][OA

    Science.gov (United States)

    Millet, Yves A.; Danna, Cristian H.; Clay, Nicole K.; Songnuan, Wisuwat; Simon, Matthew D.; Werck-Reichhart, Danièle; Ausubel, Frederick M.

    2010-01-01

    Despite the fact that roots are the organs most subject to microbial interactions, very little is known about the response of roots to microbe-associated molecular patterns (MAMPs). By monitoring transcriptional activation of β-glucuronidase reporters and MAMP-elicited callose deposition, we show that three MAMPs, the flagellar peptide Flg22, peptidoglycan, and chitin, trigger a strong tissue-specific response in Arabidopsis thaliana roots, either at the elongation zone for Flg22 and peptidoglycan or in the mature parts of the roots for chitin. Ethylene signaling, the 4-methoxy-indole-3-ylmethylglucosinolate biosynthetic pathway, and the PEN2 myrosinase, but not salicylic acid or jasmonic acid signaling, play major roles in this MAMP response. We also show that Flg22 induces the cytochrome P450 CYP71A12-dependent exudation of the phytoalexin camalexin by Arabidopsis roots. The phytotoxin coronatine, an Ile-jasmonic acid mimic produced by Pseudomonas syringae pathovars, suppresses MAMP-activated responses in the roots. This suppression requires the E3 ubiquitin ligase COI1 as well as the transcription factor JIN1/MYC2 but does not rely on salicylic acid–jasmonic acid antagonism. These experiments demonstrate the presence of highly orchestrated and tissue-specific MAMP responses in roots and potential pathogen-encoded mechanisms to block these MAMP-elicited signaling pathways. PMID:20348432

  15. Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns.

    Science.gov (United States)

    Millet, Yves A; Danna, Cristian H; Clay, Nicole K; Songnuan, Wisuwat; Simon, Matthew D; Werck-Reichhart, Danièle; Ausubel, Frederick M

    2010-03-01

    Despite the fact that roots are the organs most subject to microbial interactions, very little is known about the response of roots to microbe-associated molecular patterns (MAMPs). By monitoring transcriptional activation of beta-glucuronidase reporters and MAMP-elicited callose deposition, we show that three MAMPs, the flagellar peptide Flg22, peptidoglycan, and chitin, trigger a strong tissue-specific response in Arabidopsis thaliana roots, either at the elongation zone for Flg22 and peptidoglycan or in the mature parts of the roots for chitin. Ethylene signaling, the 4-methoxy-indole-3-ylmethylglucosinolate biosynthetic pathway, and the PEN2 myrosinase, but not salicylic acid or jasmonic acid signaling, play major roles in this MAMP response. We also show that Flg22 induces the cytochrome P450 CYP71A12-dependent exudation of the phytoalexin camalexin by Arabidopsis roots. The phytotoxin coronatine, an Ile-jasmonic acid mimic produced by Pseudomonas syringae pathovars, suppresses MAMP-activated responses in the roots. This suppression requires the E3 ubiquitin ligase COI1 as well as the transcription factor JIN1/MYC2 but does not rely on salicylic acid-jasmonic acid antagonism. These experiments demonstrate the presence of highly orchestrated and tissue-specific MAMP responses in roots and potential pathogen-encoded mechanisms to block these MAMP-elicited signaling pathways.

  16. Foot-and-mouth disease virus-like particles produced by a SUMO fusion protein system in Escherichia coli induce potent protective immune responses in guinea pigs, swine and cattle

    Science.gov (United States)

    2013-01-01

    Foot-and-mouth disease virus (FMDV) causes a highly contagious infection in cloven-hoofed animals. The format of FMD virus-like particles (VLP) as a non-replicating particulate vaccine candidate is a promising alternative to conventional inactivated FMDV vaccines. In this study, we explored a prokaryotic system to express and assemble the FMD VLP and validated the potential of VLP as an FMDV vaccine candidate. VLP composed entirely of FMDV (Asia1/Jiangsu/China/2005) capsid proteins (VP0, VP1 and VP3) were simultaneously produced as SUMO fusion proteins by an improved SUMO fusion protein system in E. coli. Proteolytic removal of the SUMO moiety from the fusion proteins resulted in the assembly of VLP with size and shape resembling the authentic FMDV. Immunization of guinea pigs, swine and cattle with FMD VLP by intramuscular inoculation stimulated the FMDV-specific antibody response, neutralizing antibody response, T-cell proliferation response and secretion of cytokine IFN-γ. In addition, immunization with one dose of the VLP resulted in complete protection of these animals from homologous FMDV challenge. The 50% protection dose (PD50) of FMD VLP in cattle is up to 6.34. These results suggest that FMD VLP expressed in E. coli are an effective vaccine in guinea pigs, swine and cattle and support further development of these VLP as a vaccine candidate for protection against FMDV. PMID:23826638

  17. Influence of humic substances on plant-microbes interactions in the rhizosphere

    Science.gov (United States)

    Puglisi, Edoardo; Pascazio, Silvia; Spaccini, Riccardo; Crecchio, Carmine; Trevisan, Marco; Piccolo, Alessandro

    2013-04-01

    Humic substances are known to play a wide range of effects on the physiology of plant and microbes. This is of particular relevance in the rhizosphere of terrestrial environments, where the reciprocal interactions between plants roots, soil constituents and microorganisms strongly influence the plants acquisition of nutrients. Chemical advances are constantly improving our knowledge on humic substances: their supra-molecular architecture, as well as the moltitude of their chemical constituents, many of which are biologically active. An approach for linking the structure of humic substances with their biological activity in the rhizosphere is the use of rhizoboxes, which allow applying a treatment (e.g., an amendment with humic substances) in an upper soil-plant compartment and take measurements in a lower isolated rhizosphere compartment that can be sampled at desired distances from the rhizoplane. This approach can be adopted to assess the effects of several humic substances, as well as composted materials, on maize plants rhizodeposition of carbon, and in turn on the structure and activity of rhizosphere microbial communities. In order to gain a complete understanding of processes occurring in the complex soil-plant-microorganisms tripartite system, rhizobox experiments can be coupled with bacterial biosensors for the detection and quantification of bioavailable nutrients, chemical analyses of main rhizodeposits constituents, advanced chemical characterizations of humic substances, DNA-fingerprinting of microbial communities, and multivariate statistical approaches to manage the dataset produced and to infer general conclusions. By such an approach it was found that humic substances are significantly affecting the amount of carbon deposited by plant roots. This induction effect is more evident for substances with more hydrophobic and complex structure, thus supporting the scientific hypothesis of the "microbial loop model", which assumes that plants feed

  18. Scaling Soil Microbe-Water Interactions from Pores to Ecosystems

    Science.gov (United States)

    Manzoni, S.; Katul, G. G.

    2014-12-01

    The spatial scales relevant to soil microbial activity are much finer than scales relevant to whole-ecosystem function and biogeochemical cycling. On the one hand, how to link such different scales and develop scale-aware biogeochemical and ecohydrological models remains a major challenge. On the other hand, resolving these linkages is becoming necessary for testing ecological hypotheses and resolving data-theory inconsistencies. Here, the relation between microbial respiration and soil moisture expressed in water potential is explored. Such relation mediates the water availability effects on ecosystem-level heterotrophic respiration and is of paramount importance for understanding CO2 emissions under increasingly variable rainfall regimes. Respiration has been shown to decline as the soil dries in a remarkably consistent way across climates and soil types (open triangles in Figure). Empirical models based on these respiration-moisture relations are routinely used in Earth System Models to predict moisture effects on ecosystem respiration. It has been hypothesized that this consistency in microbial respiration decline is due to breakage of water film continuity causing in turn solute diffusion limitations in dry conditions. However, this hypothesis appears to be at odds with what is known about soil hydraulic properties. Water film continuity estimated from soil water retention (SWR) measurements at the 'Darcy' scale breaks at far less negative water potential (micro-level relevant to microbial activity. Such downscaling resolves the inconsistency between respiration thresholds and hydrological thresholds. This result, together with observations of residual microbial activity well below -15 MPa (dashed back curve in Figure), lends support to the hypothesis that soil microbes are substrate-limited in dry conditions.

  19. 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.

  20. 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

  1. Development of transgenic rats producing human β-amyloid precursor protein as a model for Alzheimer's disease: Transgene and endogenous APP genes are regulated tissue-specifically

    Directory of Open Access Journals (Sweden)

    Chan Anthony WS

    2008-02-01

    Full Text Available Abstract Background Alzheimer's disease (AD is a devastating neurodegenerative disorder that affects a large and growing number of elderly individuals. In addition to idiopathic disease, AD is also associated with autosomal dominant inheritance, which causes a familial form of AD (FAD. Some instances of FAD have been linked to mutations in the β-amyloid protein precursor (APP. Although there are numerous mouse AD models available, few rat AD models, which have several advantages over mice, have been generated. Results Fischer 344 rats expressing human APP driven by the ubiquitin-C promoter were generated via lentiviral vector infection of Fischer 344 zygotes. We generated two separate APP-transgenic rat lines, APP21 and APP31. Serum levels of human amyloid-beta (Aβ40 were 298 pg/ml for hemizygous and 486 pg/ml for homozygous APP21 animals. Serum Aβ42 levels in APP21 homozygous rats were 135 pg/ml. Immunohistochemistry in brain showed that the human APP transgene was expressed in neurons, but not in glial cells. These findings were consistent with independent examination of enhanced green fluorescent protein (eGFP in the brains of eGFP-transgenic rats. APP21 and APP31 rats expressed 7.5- and 3-times more APP mRNA, respectively, than did wild-type rats. Northern blots showed that the human APP transgene, driven by the ubiquitin-C promoter, is expressed significantly more in brain, kidney and lung compared to heart and liver. A similar expression pattern was also seen for the endogenous rat APP. The unexpected similarity in the tissue-specific expression patterns of endogenous rat APP and transgenic human APP mRNAs suggests regulatory elements within the cDNA sequence of APP. Conclusion This manuscript describes the generation of APP-transgenic inbred Fischer 344 rats. These are the first human AD model rat lines generated by lentiviral infection. The APP21 rat line expresses high levels of human APP and could be a useful model for AD. Tissue

  2. 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...

  3. 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.

  4. Nanoparticle-Based Delivery of Anaplasma marginale Membrane Proteins; VirB9-1 and VirB10 Produced in the Pichia pastoris Expression System.

    Science.gov (United States)

    Zhang, Bing; Cavallaro, Antonio S; Mody, Karishma T; Zhang, Jun; Deringer, James R; Brown, Wendy C; Mahony, Timothy J; Yu, Chengzhong; Mitter, Neena

    2016-11-05

    Bovine anaplasmosis or cattle-tick fever is a tick-borne haemolytic disease caused by the rickettsial haemoparasite Anaplasma marginale in tropical and subtropical areas of the world. While difficult to express, the proteins VirB9-1 and VirB10 are immunogenic components of the outer membrane type IV secretion system that have been identified as candidate antigens for vaccines targeting of A. marginale . Soluble VirB9-1 and VirB10 were successfully expressed using Pichia pastoris . When formulated with the self-adjuvanting silica vesicles, SV-100 (diameter: 50 nm, and pore entrance size: 6 nm), 200 µg of VirB9-1 and VirB10 were adsorbed per milligram of nanoparticle. The VirB9-1 and VirB10, SV-100 formulations were shown to induce higher antibody responses in mice compared to the QuilA formulations. Moreover, intracellular staining of selected cytokines demonstrated that both VirB9-1 and VirB10 formulations induced cell-mediated immune responses in mice. Importantly, the SV-100 VirB9-1 and VirB10 complexes were shown to specifically stimulate bovine T-cell linages derived from calves immunised with A. marginale outer membrane fractions, suggesting formulations will be useful for bovine immunisation and protection studies. Overall this study demonstrates the potential of self-adjuvanting silica vesicle formulations to address current deficiencies in vaccine delivery applications.

  5. A Macrocyclic Agouti-Related Protein/[Nle4,DPhe7]α-Melanocyte Stimulating Hormone Chimeric Scaffold Produces Subnanomolar Melanocortin Receptor Ligands.

    Science.gov (United States)

    Ericson, Mark D; Freeman, Katie T; Schnell, Sathya M; Haskell-Luevano, Carrie

    2017-01-26

    The melanocortin system consists of five receptor subtypes, endogenous agonists, and naturally occurring antagonists. These receptors and ligands have been implicated in numerous biological pathways including processes linked to obesity and food intake. Herein, a truncation structure-activity relationship study of chimeric agouti-related protein (AGRP)/[Nle4,DPhe7]α-melanocyte stimulating hormone (NDP-MSH) ligands is reported. The tetrapeptide His-DPhe-Arg-Trp or tripeptide DPhe-Arg-Trp replaced the Arg-Phe-Phe sequence in the AGRP active loop derivative c[Pro-Arg-Phe-Phe-Xxx-Ala-Phe-DPro], where Xxx was the native Asn of AGRP or a diaminopropionic (Dap) acid residue previously shown to increase antagonist potency at the mMC4R. The Phe, Ala, and Dap/Asn residues were successively removed to generate a 14-member library that was assayed for agonist activity at the mouse MC1R, MC3R, MC4R, and MC5R. Two compounds possessed nanomolar agonist potency at the mMC4R, c[Pro-His-DPhe-Arg-Trp-Asn-Ala-Phe-DPro] and c[Pro-His-DPhe-Arg-Trp-Dap-Ala-DPro], and may be further developed to generate novel melanocortin probes and ligands for understanding and treating obesity.

  6. Ethylene emission and PR protein synthesis in ACC deaminase producing Methylobacterium spp. inoculated tomato plants (Lycopersicon esculentum Mill.) challenged with Ralstonia solanacearum under greenhouse conditions.

    Science.gov (United States)

    Yim, Woojong; Seshadri, Sundaram; Kim, Kiyoon; Lee, Gillseung; Sa, Tongmin

    2013-06-01

    Bacteria of genus Methylobacterium have been found to promote plant growth and regulate the level of ethylene in crop plants. This work is aimed to test the induction of defense responses in tomato against bacterial wilt by stress ethylene level reduction mediated by the ACC deaminase activity of Methylobacterium strains. Under greenhouse conditions, the disease index value in Methylobacterium sp. inoculated tomato plants was lower than control plants. Plants treated with Methylobacterium sp. challenge inoculated with Ralstonia solanacearum (RS) showed significantly reduced disease symptoms and lowered ethylene emission under greenhouse condition. The ACC and ACO (1-aminocyclopropane-1-carboxylate oxidase) accumulation in tomato leaves were significantly reduced with Methylobacterium strains inoculation. While ACC oxidase gene expression was found higher in plants treated with R. solanacearum than Methylobacterium sp. treatment, PR proteins related to induced systemic resistance like β-1,3-glucanase, PAL, PO and PPO were increased in Methylobacterium sp. inoculated plants. A significant increase in β-1,3-glucanase and PAL gene expression was found in all the Methylobacterium spp. treatments compared to the R. solanacearum treatment. This study confirms the activity of Methylobacterium sp. in increasing the defense enzymes by modulating the ethylene biosynthesis pathway and suggests the use of methylotrophic bacteria as potential biocontrol agents in tomato cultivation. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  7. Antioxidant and ACE-inhibitory activities of hemp (Cannabis sativa L.) protein hydrolysates produced by the proteases AFP, HT, Pro-G, actinidin and zingibain.

    Science.gov (United States)

    Teh, Sue-Siang; Bekhit, Alaa El-Din A; Carne, Alan; Birch, John

    2016-07-15

    Hemp protein isolates (HPIs) were hydrolysed by proteases (AFP, HT, ProG, actinidin and zingibain). The enzymatic hydrolysis of HPIs was evaluated through the degree of hydrolysis and SDS-PAGE profiles. The bioactive properties of the resultant hydrolysates (HPHs) were accessed through ORAC, DPPḢ scavenging and ACE-inhibitory activities. The physical properties of the resultant HPHs were evaluated for their particle sizes, zeta potential and surface hydrophobicity. HT had the highest rate of caseinolytic activity at the lowest concentration (0.1 mg mL(-1)) compared to other proteases that required concentration of 100 mg mL(-1) to achieve their maximum rate of caseinolytic activity. This led to the highest degree of hydrolysis of HPIs by HT in the SDS-PAGE profiles. Among all proteases and substrates, HT resulted in the highest bioactivities (ORAC, DPPḢ scavenging and ACE-inhibitory activities) generated from alkali extracted HPI in the shortest time (2 h) compared to the other protease preparations. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Electrical stimulation with periodic alternating intervals stimulates neuronal cells to produce neurotrophins and cytokines through activation of mitogen-activated protein kinase pathways.

    Science.gov (United States)

    Yamamoto, Kenta; Yamamoto, Toshiro; Honjo, Kenichi; Ichioka, Hiroaki; Oseko, Fumishige; Kishida, Tsunao; Mazda, Osam; Kanamura, Narisato

    2015-12-01

    Peripheral neuropathy is a representative complication of dental surgery. Electrical therapy, based on electrical stimulation with periodic alternating intervals (ES-PAI), may promote nerve regeneration after peripheral nerve injury in a non-invasive manner, potentially providing an effective therapy for neuropathy. This study aimed to analyze the molecular mechanisms underlying the nerve recovery stimulated by ES-PAI. In brief, ES-PAI was applied to a neuronal cell line, Neuro2A, at various intensities using the pulse generator apparatus, FREUDE. Cell viability, neurotrophin mRNA expression, and cytokine production were examined using a tetrazolium-based assay, real-time RT-PCR, and ELISA, respectively. Mitogen-activated protein kinase (MAPK) signaling was assessed using flow cytometry. It was found that ES-PAI increased the viability of cells and elevated expression of nerve growth factor (NGF) and neurotrophin-3 (NT-3); ESPAI also augmented vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) expression, which was restored by addition of p38 inhibitors. Phosphorylation of p38 and extracellular signal-regulated kinase 1/2 (ERK-1/2) was augmented by ES-PAI. Hence, ES-PAI may ameliorate peripheral neuropathy by promoting neuronal cell proliferation and production of neurogenic factors by activating p38 and ERK-1/2 pathways. © 2015 Eur J Oral Sci.

  9. Effects of diet energy concentration and an exogenous carbohydrase on growth performance of weanling pigs fed diets containing canola meal produced from high protein or conventional canola seeds

    DEFF Research Database (Denmark)

    Pedersen, Trine Friis; Liu, Yanhong; Stein, Hans H.

    2016-01-01

    The objectives were to determine effects of diet NE and an exogenous carbohydrase on growth performance and physiological parameters of weanling pigs fed a corn-soybean meal (SBM) diet or diets containing high protein canola meal (CM-HP) or conventional canola meal (CM-CV). A total of 492 pigs...... (initial BW: 9.15 ± 0.06 kg) were used in a randomized complete block design with 12 dietary treatments and 9 pens per treatment. A control diet based on corn and SBM and 4 diets containing 20% or 30% CM-HP or 20% or 30% CM-CV were formulated to a similar NE by adjusting inclusion of choice white grease....... Four additional diets also contained 20% or 30% CM-HP or 20% or 30% CM-CV, but no additional choice white grease, and NE in these diets, therefore, was less than in the control diet. The control diet and the diets containing 30% CM-HP or CM-CV without increased choice white grease were also formulated...

  10. 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.

  11. 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)

  12. 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.

  13. Modulating bacterial and gut mucosal interactions with engineered biofilm matrix proteins.

    Science.gov (United States)

    Duraj-Thatte, Anna M; Praveschotinunt, Pichet; Nash, Trevor R; Ward, Frederick R; Joshi, Neel S

    2018-02-22

    Extracellular appendages play a significant role in mediating communication between bacteria and their host. Curli fibers are a class of bacterial fimbria that is highly amenable to engineering. We demonstrate the use of engineered curli fibers to rationally program interactions between bacteria and components of the mucosal epithelium. Commensal E. coli strains were engineered to produce recombinant curli fibers fused to the trefoil family of human cytokines. Biofilms formed from these strains bound more mucins than those producing wild-type curli fibers, and modulated mucin rheology as well. When treated with bacteria producing the curli-trefoil fusions mammalian cells behaved identically in terms of their migration behavior as when they were treated with the corresponding soluble trefoil factors. Overall, this demonstrates the potential utility of curli fibers as a scaffold for the display of bioactive domains and an untapped approach to rationally modulating host-microbe interactions using bacterial matrix proteins.

  14. Nanoparticle-Based Delivery of Anaplasma marginale Membrane Proteins; VirB9-1 and VirB10 Produced in the Pichia pastoris Expression System

    Directory of Open Access Journals (Sweden)

    Bing Zhang

    2016-11-01

    Full Text Available Bovine anaplasmosis or cattle-tick fever is a tick-borne haemolytic disease caused by the rickettsial haemoparasite Anaplasma marginale in tropical and subtropical areas of the world. While difficult to express, the proteins VirB9-1 and VirB10 are immunogenic components of the outer membrane type IV secretion system that have been identified as candidate antigens for vaccines targeting of A. marginale. Soluble VirB9-1 and VirB10 were successfully expressed using Pichia pastoris. When formulated with the self-adjuvanting silica vesicles, SV-100 (diameter: 50 nm, and pore entrance size: 6 nm, 200 µg of VirB9-1 and VirB10 were adsorbed per milligram of nanoparticle. The VirB9-1 and VirB10, SV-100 formulations were shown to induce higher antibody responses in mice compared to the QuilA formulations. Moreover, intracellular staining of selected cytokines demonstrated that both VirB9-1 and VirB10 formulations induced cell-mediated immune responses in mice. Importantly, the SV-100 VirB9-1 and VirB10 complexes were shown to specifically stimulate bovine T-cell linages derived from calves immunised with A. marginale outer membrane fractions, suggesting formulations will be useful for bovine immunisation and protection studies. Overall this study demonstrates the potential of self-adjuvanting silica vesicle formulations to address current deficiencies in vaccine delivery applications.

  15. Haploinsufficiency of the E3 ubiquitin ligase C-terminus of heat shock cognate 70 interacting protein (CHIP produces specific behavioral impairments.

    Directory of Open Access Journals (Sweden)

    Bethann McLaughlin

    Full Text Available The multifunctional E3 ubiquitin ligase CHIP is an essential interacting partner of HSP70, which together promote the proteasomal degradation of client proteins. Acute CHIP overexpression provides neuroprotection against neurotoxic mitochondrial stress, glucocorticoids, and accumulation of toxic amyloid fragments, as well as genetic mutations in other E3 ligases, which have been shown to result in familial Parkinson's disease. These studies have created a great deal of interest in understanding CHIP activity, expression and modulation. While CHIP knockout mice have the potential to provide essential insights into the molecular control of cell fate and survival, the animals have been difficult to characterize in vivo due to severe phenotypic and behavioral dysfunction, which have thus far been poorly characterized. Therefore, in the present study we conducted a battery of neurobehavioral and physiological assays of adult CHIP heterozygotic (HET mutant mice to provide a better understanding of the functional consequence of CHIP deficiency. We found that CHIP HET mice had normal body and brain weight, body temperature, muscle tone and breathing patterns, but do have a significant elevation in baseline heart rate. Meanwhile basic behavioral screens of sensory, motor, emotional and cognitive functions were normative. We observed no alterations in performance in the elevated plus maze, light-dark preference and tail suspension assays, or two simple cognitive tasks: novel object recognition and spontaneous alternation in a Y maze. Significant deficits were found, however, when CHIP HET mice performed wire hang, inverted screen, wire maneuver, and open field tasks. Taken together, our data indicate a clear subset of behaviors that are altered at baseline in CHIP deficient animals, which will further guide whole animal studies of the effects of CHIP dysregulation on cardiac function, brain circuitry and function, and responsiveness to environmental and

  16. Conserved Patterns of Microbial Immune Escape: Pathogenic Microbes of Diverse Origin Target the Human Terminal Complement Inhibitor Vitronectin via a Single Common Motif.

    Directory of Open Access Journals (Sweden)

    Teresia Hallström

    Full Text Available Pathogenicity of many microbes relies on their capacity to resist innate immunity, and to survive and persist in an immunocompetent human host microbes have developed highly efficient and sophisticated complement evasion strategies. Here we show that different human pathogens including Gram-negative and Gram-positive bacteria, as well as the fungal pathogen Candida albicans, acquire the human terminal complement regulator vitronectin to their surface. By using truncated vitronectin fragments we found that all analyzed microbial pathogens (n = 13 bound human vitronectin via the same C-terminal heparin-binding domain (amino acids 352-374. This specific interaction leaves the terminal complement complex (TCC regulatory region of vitronectin accessible, allowing inhibition of C5b-7 membrane insertion and C9 polymerization. Vitronectin complexed with the various microbes and corresponding proteins was thus functionally active and inhibited complement-mediated C5b-9 deposition. Taken together, diverse microbial pathogens expressing different structurally unrelated vitronectin-binding molecules interact with host vitronectin via the same conserved region to allow versatile control of the host innate immune response.

  17. 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.

  18. 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.

  19. 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.

  20. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris.

    Science.gov (United States)

    Oberbeckmann, Sonja; Osborn, A Mark; Duhaime, Melissa B

    2016-01-01

    Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET

  1. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris

    Science.gov (United States)

    Osborn, A. Mark

    2016-01-01

    Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5–6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae—all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the

  2. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris.

    Directory of Open Access Journals (Sweden)

    Sonja Oberbeckmann

    Full Text Available Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate (PET drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates and diatoms (e.g. Coscinodiscophytina, Bacillariophytina. The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact

  3. Producing cement

    Energy Technology Data Exchange (ETDEWEB)

    Stone, E G

    1923-09-12

    A process and apparatus are described for producing Portland cement in which pulverized shale is successively heated in a series of inclined rotary retorts having internal stirrers and oil gas outlets, which are connected to condensers. The partially treated shale is removed from the lowermost retort by a conveyor, then fed separately or conjointly into pipes and thence into a number of vertically disposed retorts. Each of these retorts may be fitted interiorly with vertical arranged conveyors which elevate the shale and discharge it over a lip, from whence it falls to the bottom of the retorts. The lower end of each casing is furnished with an adjustable discharge door through which the spent shale is fed to a hopper, thence into separate trucks. The oil gases generated in the retorts are exhausted through pipes to condensers. The spent shale is conveyed to a bin and mixed while hot with ground limestone. The admixed materials are then ground and fed to a rotary kiln which is fired by the incondensible gases derived from the oil gases obtained in the previous retorting of the shale. The calcined materials are then delivered from the rotary kiln to rotary coolers. The waste gases from the kiln are utilized for heating the retorts in which the ground shale is heated for the purpose of extracting therefrom the contained hydrocarbon oils and gases.

  4. Inhibition of human MCF-7 breast cancer cells and HT-29 colon cancer cells by rice-produced recombinant human insulin-like growth binding protein-3 (rhIGFBP-3.

    Directory of Open Access Journals (Sweden)

    Stanley C K Cheung

    Full Text Available BACKGROUND: Insulin-like growth factor binding protein-3 (IGFBP-3 is a multifunctional molecule which is closely related to cell growth, apoptosis, angiogenesis, metabolism and senescence. It combines with insulin-like growth factor-I (IGF-I to form a complex (IGF-I/IGFBP-3 that can treat growth hormone insensitivity syndrome (GHIS and reduce insulin requirement in patients with diabetes. IGFBP-3 alone has been shown to have anti-proliferation effect on numerous cancer cells. METHODOLOGY/PRINCIPAL FINDINGS: We reported here an expression method to produce functional recombinant human IGFBP-3 (rhIGFBP-3 in transgenic rice grains. Protein sorting sequences, signal peptide and endoplasmic reticulum retention tetrapeptide (KDEL were included in constructs for enhancing rhIGFBP-3 expression. Western blot analysis showed that only the constructs with signal peptide were successfully expressed in transgenic rice grains. Both rhIGFBP-3 proteins, with or without KDEL sorting sequence inhibited the growth of MCF-7 human breast cancer cells (65.76 ± 1.72% vs 45.00 ± 0.86%, p < 0.05; 50.84 ± 1.97% vs 45.00 ± 0.86%, p < 0.01 respectively and HT-29 colon cancer cells (65.14 ± 3.84% vs 18.01 ± 13.81%, p < 0.05 and 54.7 ± 9.44% vs 18.01 ± 13.81%, p < 0.05 respectively when compared with wild type rice. CONCLUSION/SIGNIFICANCE: These findings demonstrated the feasibility of producing biological active rhIGFBP-3 in rice using a transgenic approach, which will definitely encourage more research on the therapeutic use of hIGFBP-3 in future.

  5. 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.

  6. Screening concepts for the isolation of biosurfactant producing microorganisms.

    Science.gov (United States)

    Walter, Vanessa; Syldatk, Christoph; Hausmann, Rudolf

    2010-01-01

    This chapter gives an overview of current methods for the isolation of biosurfactant producing microbes. The common screening methods for biosurfactants are presented. Sampling and isolation of bacteria are the basis for screening of biosurfactant producing microbes. Hydrocarbon-contaminated sites are the most promising for the isolation of biosurfactant producing microbes, but many strains have also been isolated from undisturbed sites. In subsequent steps the isolates have to be characterized in order to identify the strains which are interesting for a further investigation. Several techniques have been developed for identifying biosurfactant producing strains. Most of them are directly based on the surface or interfacial activity of the culture supernatant. Apart from that, some screening methods explore the hydrophobicity of the cell surface. This trait also gives an indication on biosurfactant production. In recent years automation and miniaturization have led to the development of high throughput methods for screening. High throughput screening (HTS) for analyzing large amounts of potential candidates or whole culture collections is reflected in the end. However, no new principals have been introduced by HTS methods.

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

    African Journals Online (AJOL)

    SAM

    2014-06-25

    Jun 25, 2014 ... Viruses, bacteria, fungi and protozoa that are known to produce an ... Trichoderma viride, ..... instance, beewalf wasps has been found with antibiotic- ..... thuringiensis-induced mortality vary across a range of Lepidoptera.

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

    African Journals Online (AJOL)

    user

    2011-02-28

    Feb 28, 2011 ... Susceptibilities of five isolates to 17 different types of antibiotics were evaluated using the ... All isolates produced protease, lipase and esterase lipase. Further ... Cow dung is excreted by bovine animal species which.

  9. Ecological and Clinical Consequences of Antibiotic Subsistence by Environmental Microbes

    DEFF Research Database (Denmark)

    Dantas, Gautam; Sommer, Morten Otto Alexander

    2011-01-01

    This chapter contains sections titled: Introduction Environmental Origins of Resistance: The Producer Hypothesis Resistome of other Soil Bacteria: Response to the Producers? Early Reports of Antibiotic Catabolism by Soil Bacteria The Antibiotic Subsistome: Who and how much? Antibiotic Subsistence...... as a Scavenger Phenotype Ecological Consequences of the Antibiotic Subsistome Investigating Connections Between Subsistomes and Resistomes Metagenomic Functional Selections for Discovering Genes Enabling Antibiotic Subsistence and Resistance Antibiotic Subsistence by Pathogenic Bacteria Concluding Remarks...

  10. Molecular cross-talk between sponge host and associated microbes

    Digital Repository Service at National Institute of Oceanography (India)

    Wang, X.; Brandt, D.; Thakur, N.L.; Wiens, M.; Batel, R.; Schroder, H.C.; Muller, W.E.G.

    cited in modern textbooks, e.g. in Pechenik (2000), in which sponges are assumed to be composed of functionally independent cells. The introduction of molecular cloning of genes, coding for “informative” proteins increased in a rapid, self...). The first report in line with this new strategy was on the cloning of a galectin from the demosponge Geodia cydonium (Pfeifer et al., 1993; Hirabayashi and Kasai, 1993). This protein is known to be crucially important for cell-cell interactions (Müller et...

  11. 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.

  12. Diversification of Type VI Secretion System Toxins Reveals Ancient Antagonism among Bee Gut Microbes

    Directory of Open Access Journals (Sweden)

    Margaret I. Steele

    2017-12-01

    Full Text Available Microbial communities are shaped by interactions among their constituent members. Some Gram-negative bacteria employ type VI secretion systems (T6SSs to inject protein toxins into neighboring cells. These interactions have been theorized to affect the composition of host-associated microbiomes, but the role of T6SSs in the evolution of gut communities is not well understood. We report the discovery of two T6SSs and numerous T6SS-associated Rhs toxins within the gut bacteria of honey bees and bumble bees. We sequenced the genomes of 28 strains of Snodgrassella alvi, a characteristic bee gut microbe, and found tremendous variability in their Rhs toxin complements: altogether, these strains appear to encode hundreds of unique toxins. Some toxins are shared with Gilliamella apicola, a coresident gut symbiont, implicating horizontal gene transfer as a source of toxin diversity in the bee gut. We use data from a transposon mutagenesis screen to identify toxins with antibacterial function in the bee gut and validate the function and specificity of a subset of these toxin and immunity genes in Escherichia coli. Using transcriptome sequencing, we demonstrate that S. alvi T6SSs and associated toxins are upregulated in the gut environment. We find that S. alvi Rhs loci have a conserved architecture, consistent with the C-terminal displacement model of toxin diversification, with Rhs toxins, toxin fragments, and cognate immunity genes that are expressed and confer strong fitness effects in vivo. Our findings of T6SS activity and Rhs toxin diversity suggest that T6SS-mediated competition may be an important driver of coevolution within the bee gut microbiota.

  13. Insights into the Structure and Metabolic Function of Microbes That Shape Pelagic Iron-Rich Aggregates ( Iron Snow )

    Energy Technology Data Exchange (ETDEWEB)

    Lu, S [Friedrich Schiller University Jena, Jena Germany; Chourey, Karuna [ORNL; REICHE, M [Friedrich Schiller University Jena, Jena Germany; Nietzsche, S [Friedrich Schiller University Jena, Jena Germany; Shah, Manesh B [ORNL; Hettich, Robert {Bob} L [ORNL; Kusel, K [Friedrich Schiller University Jena, Jena Germany

    2013-01-01

    Metaproteomics combined with total nucleic acid-based methods aided in deciphering the roles of microorganisms in the formation and transformation of iron-rich macroscopic aggregates (iron snow) formed in the redoxcline of an acidic lignite mine lake. Iron snow had high total bacterial 16S rRNA gene copies, with 2 x 109 copies g (dry wt)-1 in the acidic (pH 3.5) central lake basin and 4 x 1010 copies g (dry wt)-1 in the less acidic (pH 5.5) northern lake basin. Active microbial communities in the central basin were dominated by Alphaproteobacteria (36.6%) and Actinobacteria (21.4%), and by Betaproteobacteria (36.2%) in the northern basin. Microbial Fe-cycling appeared to be the dominant metabolism in the schwertmannite-rich iron snow, because cloning and qPCR assigned up to 61% of active bacteria as Fe-cycling bacteria (FeB). Metaproteomics revealed 70 unique proteins from central basin iron snow and 283 unique proteins from 43 genera from northern basin. Protein identification provided a glimpse into in situ processes, such as primary production, motility, metabolism of acidophilic FeB, and survival strategies of neutrophilic FeB. Expression of carboxysome shell proteins and RubisCO indicated active CO2 fixation by Fe(II) oxidizers. Flagellar proteins from heterotrophs indicated their activity to reach and attach surfaces. Gas vesicle proteins related to CO2-fixing Chlorobium suggested that microbes could influence iron snow sinking. We suggest that iron snow formed by autotrophs in the redoxcline acts as a microbial parachute, since it is colonized by motile heterotrophs during sinking which start to dissolve schwertmannite.

  14. Polythene and Plastics-degrading microbes from the mangrove soil

    Directory of Open Access Journals (Sweden)

    K Kathiresan

    2003-09-01

    Full Text Available Biodegradation of polythene bags and plastic cups was analyzed after 2, 4, 6, and 9 months of incubation in the mangrove soil. The biodegradation of polythene bags was significantly higher (up to 4.21% in 9 months than that of plastic cups (up to 0.25% in 9 months. Microbial counts in the degrading materials were recorded up to 79.67 x 10 4 per gram for total heterotrophic bacteria, and up to 55.33 x 10 2 per gram for fungi. The microbial species found associated with the degrading materials were identified as five Gram positive and two Gram negative bacteria, and eight fungal species of Aspergillus. The species that were predominant were Streptococcus, Staphylococcus, Micrococcus (Gram +ve, Moraxella, and Pseudomonas (Gram -ve and two species of fungi (Aspergillus glaucus and A. niger. Efficacy of the microbial species in degradation of plastics and polythene was analyzed in shaker cultures. Among the bacteria, Pseudomonas species degraded 20.54% of polythene and 8.16% of plastics in one-month period. Among the fungal species, Aspergillus glaucus degraded 28.80% of polythene and 7.26% of plastics in one-month period. This work reveals that the mangrove soil is a good source of microbes capable of degrading polythene and plasticsLa biodegradación de las bolsas de polietileno y vasos de plástico fue analizada después de 2, 4, 6 y 9 meses de incubación en suelo de manglar. La biodegradación de las bolsas fue significativamente más alta (hasta 4.21% en 9 meses que los vasos plásticos (hasta 0.25% en 9 meses. Los conteos microbianos en los materiales degradados mostraron hasta 79.67 x 10(4 por gramo para las bacterias heterotroficas totales, y hasta 55.33 x 10² por gramo para los hongos. Se identificó 5 especies microbianas Gram positivas, 2 Gram negativas, y 8 especies de hongos del género Aspergillus en asociación con materiales degradados. Las especies predominantes fueron Streptococcus, Staphylococcus, Micrococcus (Gram +, Moraxella

  15. 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.

  16. 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 matur