bluuebunny/crossref_metadata_2025 huggingface dataset:
Technical Justification and Choice for Remediation Methods
Authors: Morton Mark , Jayamaha Janaka
Published: August 2012

When out of normal material or very high activity is encountered in a Deactivation & Decommissioning (D&D) project, special considerations are needed. As the source term increases, the level of attention to planning, project cost and risk management must increase as well. WorleyParsons (WP) is engaged in identifying, screening and documenting (with follow on project design expected) the various remediation methods available to remove highly contaminated soils discovered under a hot cell. Soil dose rates have been measured in the 70 to 100 Sieverts/hour range, with radionuclide mix to be defined in mid to late summer 2011 from samples collected in June 2011. The scope of this project is to identify remedial techniques and removal methods (means and methods) and develop a set of technically implementable remedial alternatives (alternatives). These remedial alternatives will be screened by a Technical Panel consisting of WP and client experts using a WP defined screening process to narrow the list of alternatives. Transparency and un-biased choice of actions is key to owner and public confidence in the process and the choice of the ultimate path forward. The poster will show Phase 1 — how potential remedial techniques and removal methods (means and methods) were first identified, catalogued and initial screened. Following the initial screening, the remaining means and methods are combined to form an alternative — a stabilization means with a removal method are matched with a waste container to from an alternative. A rough order of magnitude (ROM) cost estimate and high level schedule are also developed for each alternative. In parallel with the above, screening criteria with associated design attributes were identified and given a weight factor and attribute value, which are then multiplied together and used to develop a decision matrix for the developed alternatives. Two parallel processes — screening criteria development and alternative development — are being pursued to allow better focus on each while not prejudicing the final alternative selection. Phase 2 actions — the expert panel - grade each alternative against the pre-approved screening criteria using the decision matrix that compiles results — real time but blind to the panel. The top two to four scores from this last effort will proceed to a pre-conceptual, conceptual design phase and the expert panel reconvened to make the final decision on the remediation methods to be used for removing the soil / contamination.
Progress in International Cooperation on Regulation of Legacy Management: Experience and New Developments in Norwegian Cooperation Programmes
Authors: Sneve Malgorzata Karpov
Published: August 2012

This paper describes the Norwegian Radiation Protection Authority’s experience in regulatory cooperation projects in Russia and elsewhere, with special focus on legacy issues. These legacies include many different kinds of objects and activities, including: obsolete large waste sources, such as those used in radioisotope thermoelectric generators; remediation of former military sites used for storage of spent nuclear fuel and radioactive waste; and wastes from uranium mining and ore processing. The objectives of these bi-lateral cooperation programmes are to promote effective and efficient regulatory supervision, taking into account international recommendations and good practice in other countries. Individual projects organised within the programme address specific challenges which require practical local interpretation of ICRP recommendations, the International Atomic Energy Agency (IAEA) Basic Safety Standards and other IAEA requirements and guidance documents. In some cases, new regulatory documentation has been required, as well as new regulatory procedures. In the long term, the program is intended to lead to an enhanced and enduring safety culture. Positive experience in Russia encouraged the Norwegian government to extend the regulatory collaboration programme to countries in central Asia, using experience gained with Russian regulatory authorities as well as support from Russian Technical Support Organisations. The programmes are effectively evolving into a regional regulatory support group. Noting this experience, the paper includes suggestions for how international cooperation could be effective in addressing common radiation safety objectives while addressing local differences in technical, geographical, economic and cultural matters in each country. The continuing results from the cooperation will be used to provide input to the International Forum for Regulatory Supervision of Legacy Sites (RSLS) which was recently set up by the IAEA. The RSLS objectives mirror those of the bilateral activities described above and an outline is provided of the preliminary RSLS Work Plan.
NUMO’s Approach for Long-Term Safety Assessment
Authors: Ebashi Takeshi , Kaku Kenichi , Ishiguro Katsuhiko
Published: August 2012

One of NUMO’s policies for ensuring safety is staged and flexible project implementation and decision-making based on iterative confirmation of safety. The safety assessment takes the central role in multiple lines of reasoning and argumentation by providing a quantitative evaluation of long-term safety; a key aspect is uncertainty management. This paper presents NUMO’s basic strategies for long-term safety assessment based on the above policy. NUMO’s approach considering Japanese boundary conditions is demonstrated as a starting-point for evaluating the long-term safety of an actual site.
Chronicling a successful secondary implementation of Studio Physics
Authors: Kohl Patrick B. , Vincent Kuo H.
Published: August 2012

The Colorado School of Mines (CSM) has taught its first-semester calculus-based introductory physics course (Physics I) using a hybrid lecture/Studio Physics format since the spring of 1997. Starting in the fall of 2007, we have been converting the second semester of our calculus-based introductory physics course (Physics II) to a hybrid lecture/Studio Physics format, beginning from a traditional lecture/lab/recitation course. In this paper, we document the stages of this transformation, highlighting what has worked and what has not, and the challenges and benefits associated with the switch to Studio Physics. A major goal in this study is to develop a method for secondary implementations of Studio physics that keeps the time and resource investments manageable. We describe the history of Studio at CSM and characterize our progress via several metrics, including pre/post Conceptual Survey of Electricity and Magnetism (CSEM) scores, Colorado Learning About Science Survey scores (CLASS), exam scores, failure rates, and a variety of qualitative observations. Results suggest that Studio has increased student performance and satisfaction despite an aggressive expansion of class sizes in the past few years. Gains have been concentrated mostly in problem-solving skills and exam performance (as opposed to conceptual survey gains), in contrast to what has sometimes been seen in other studies.
Quantitative analysis of the damping of magnet oscillations by eddy currents in aluminum foil
Authors: Muiznieks Andris , Dudareva Inese
Published: August 2012

This paper considers damped rotational oscillations about the vertical axis of a cylindrical permanent magnet that is horizontally suspended by a vertical inelastic thread. The damping of the oscillations is caused by eddy currents induced in aluminum foil that is placed horizontally below the magnet. A simplified mathematical model of the damped oscillations is proposed and verified by experiment qualitatively and quantitatively. It is shown that the relative energy loss during one oscillation depends linearly on the number of layers of aluminum foil and on the oscillation period. To measure the relative changes of the oscillation amplitude, a magnetic field sensor and data collection interface are used.
Pointy ice-drops: How water freezes into a singular shape
Authors: Snoeijer Jacco H. , Brunet Philippe
Published: August 2012

A water drop that is gently deposited on a very cold surface freezes into a pointy ice-drop with a very sharp tip. The formation of this singular shape originates from the reduction of mass density during the freezing process and can be explained using a simplified model for which the universal structure of the singularity is revealed in full detail. The combination of a relatively simple, static experiment, and the accessible asymptotic analysis makes this system an ideal introduction to the topic of singularities.
Resource Letter GL-1: Gravitational Lensing
Authors: Treu Tommaso , Marshall Philip J. , Clowe Douglas
Published: August 2012

This Resource Letter provides a guide to a selection of the literature on gravitational lensing and its applications. Journal articles, books, popular articles, and websites are cited for the following topics: foundations of gravitational lensing, foundations of cosmology, history of gravitational lensing, strong lensing, weak lensing, and microlensing.
The RLC system: An invaluable test bench for students
Authors: Cafarelli Pierre , Champeaux Jean-Philippe , Sence Martine , Roy Nicolas
Published: August 2012

Future scientists and engineers must master fundamental notions of instrumentation. A lab session milestone based on the classical RLC circuit is proposed to check students’ theoretical and practical knowledge. Topics include impedance, signal and linear system analysis in the time and frequency domains, as well as the fundamental relations connecting them. The numerical implementation of the Fourier transform and its related pathologies (aliasing and leakage) are also discussed. Practical skills are evaluated through the intensive use of instruments and by presenting and solving potential problems that could alter the accuracy of measurement.
Rolling magnets down a conductive hill: Revisiting a classic demonstration of the effects of eddy currents
Authors: Tomasel Fernando G. , Marconi Mario C.
Published: August 2012

We re-examine the case of rare-earth magnets rolling down an inclined plane, presenting an approach to conducting quantitative investigations that results in high-quality experimental data connecting simple experiments to a handful of important applications of eddy currents. These include not only magnetic braking but also the characterization of conductive materials, measurement of the thickness of dielectric coatings, and nondestructive evaluation of conductive objects. The simplicity of the proposed experimental setups, which include the use of widely available smart phones to record video that can be post-processed with free software, makes these experiments appealing to high school and college physics students.
A semiquantitative treatment of surface charges in DC circuits
Authors: Müller Rainer
Published: August 2012

Surface charges play a major role in DC circuits because they help generate the electric field and potential distributions necessary to move the charges around the circuit. Unfortunately, it is generally regarded as a difficult task to determine the surface charge distribution for all but the simplest geometries. In this paper, we develop a graphical method for the approximate construction of surface charge distributions in DC circuits. This method allows us to determine (approximately) the location and the amount of surface charge for almost any circuit geometry. The accuracy of this semi-quantitative method is limited only by one’s ability to draw equipotential lines. We illustrate the method with several examples.
Understanding the damping of a quantum harmonic oscillator coupled to a two-level system using analogies to classical friction
Authors: Bhattacharya M. , Stoutimore M. J. A. , Osborn K. D. , Mizel Ari
Published: August 2012

A quantum harmonic oscillator coupled to a two-level system provides a tractable model of many physical systems from atoms in an optical cavity, to superconducting qubits coupled to an oscillator, to quantum dots in a photonic crystal. When the system experiences damping, the problem becomes considerably more complicated. We demonstrate how to gain insight by drawing analogies to classical damping. Specifically, we show how a quantum harmonic oscillator coupled to a damped two-level system can display two types of frictional behavior, corresponding to classical motion in a fluid and motion on a rough surface. We further show that this system can be tuned continuously between these two regimes.
The reciprocal relation of mutual inductance in a coupled circuit system
Authors: Wang Dake
Published: August 2012

The reciprocal relation of mutual inductance in a coupled circuit system is demonstrated theoretically. An alternating-current (AC) analysis is employed to investigate energy conservation in the system, with the only assumption being the steady-state operation of the circuit. This method can be adopted for teaching electromagnetism at the introductory level, provided the students have an adequate background in calculus.
Citizen Involvement in the U.S. Endangered Species Act
Authors: Brosi Berry J. , Biber Eric G. N.
Published: August 2012

Data on listed species refute critiques of citizen involvement in the U.S. Endangered Species Act.
Ending Microbial Myopia
Processes of Life
Essays in the Philosophy of Biology

by John Dupré

Oxford University Press, Oxford, 2012. 360 pp. $55, £30. ISBN 9780199691982.
Authors: Villabona-Arenas Christian Julian
Published: August 2012

Through considerations of developmental systems perspectives, epigenetics, and microbial life, Dupré challenges widely held assumptions about biology and evolution.
#FramingTheArtofScience
Epigenetics in the Age of Twitter
Pop Culture and Modern Science

by Gerald Weissmann

Bellevue Literary Press, New York, 2012. 256 pp. Paper, $18.95. ISBN 9781934137390.
Authors: Ingram Melissa A. C.
Published: August 2012

In this collection of essays, Weissmann explores the web of connections linking science and culture.
Effect of Rainfall-Induced Soil Geochemistry Dynamics on Grassland Soil Microbial Communities
Authors: Cruz-Martínez Karelyn , Rosling Anna , Zhang Yang , Song Mingzhou , Andersen Gary L. , Banfield Jillian F.
Published: August 2012

In Mediterranean-type grassland ecosystems, the timing of rainfall events controls biogeochemical cycles, as well as the phenology and productivity of plants and animals. Here, we investigate the effect of short-term (days) soil environmental conditions on microbial community structure and composition during a natural wetting and drying cycle. Soil samples were collected from a meadow in Northern California at four time points after the first two rainfall events of the rainy season. We used 16S rRNA microarrays (PhyloChip) to track changes in bacterial and archaeal community composition. Microbial communities at time points 1 and 3 were significantly different than communities at time points 2 and 4. Based on ordination analysis, the available carbon, soil moisture, and temperature explained most of the variation in community structure. For the first time, a complementary and more comprehensive approach using linear regression and generalized logical networks were used to identify linear and nonlinear associations among environmental variables and with the relative abundance of subfamilies. Changes in soil moisture and available carbon were correlated with the relative abundance of many phyla. Only the phylumActinobacteriashowed a lineage-specific relationship to soil moisture but not to carbon or nitrogen. The results indicate that the use of a high taxonomic rank in correlations with nutritional indicators might obscure divergent subfamily-level responses to environmental parameters. An important implication of this research is that there is short-term variation in microbial community composition driven in part by rainfall fluctuation that may not be evident in long-term studies with coarser time resolution.
Selection for Cu-Tolerant Bacterial Communities with Altered Composition, but Unaltered Richness, via Long-Term Cu Exposure
Authors: Berg Jeanette , Brandt Kristian K. , Al-Soud Waleed A. , Holm Peter E. , Hansen Lars H. , Sørensen Søren J. , Nybroe Ole
Published: August 2012

Toxic metal pollution affects the composition and metal tolerance of soil bacterial communities. However, there is virtually no knowledge concerning the responses of members of specific bacterial taxa (e.g., phyla or classes) to metal toxicity, and contradictory results have been obtained regarding the impact of metals on operational taxonomic unit (OTU) richness. We used tag-coded pyrosequencing of the 16S rRNA gene to elucidate the impacts of copper (Cu) on bacterial community composition and diversity within a well-described Cu gradient (20 to 3,537 μg g
−1
) stemming from industrial contamination with CuSO
4
more than 85 years ago. DNA sequence information was linked to analysis of pollution-induced community tolerance (PICT) to Cu, as determined by the [
3
H]leucine incorporation technique, and to chemical characterization of the soil. PICT was significantly correlated to bioavailable Cu, as determined by the results seen with a Cu-specific bioluminescent biosensor strain, demonstrating a specific community response to Cu. The relative abundances of members of several phyla or candidate phyla, including the
Proteobacteria
,
Bacteroidetes
,
Verrumicrobia
,
Chloroflexi
,
WS3
, and
Planctomycetes
, decreased with increasing bioavailable Cu, while members of the dominant phylum, the
Actinobacteria
, showed no response and members of the
Acidobacteria
showed a marked increase in abundance. Interestingly, changes in the relative abundances of classes frequently deviated from the responses of the phyla to which they belong. Despite the apparent Cu impacts on Cu resistance and community structure, bioavailable Cu levels did not show any correlation to bacterial OTU richness (97% similarity level). Our report highlights several bacterial taxa responding to Cu and thereby provides new guidelines for future studies aiming to explore the bacterial domain for members of metal-responding taxa.
Deletion of the Aspergillus flavus Orthologue of
A. nidulans fluG
Reduces Conidiation and Promotes Production of Sclerotia but Does Not Abolish Aflatoxin Biosynthesis
Authors: Chang Perng-Kuang , Scharfenstein Leslie L. , Mack Brian , Ehrlich Kenneth C.
Published: August 2012

The
fluG
gene is a member of a family of genes required for conidiation and sterigmatocystin production in
Aspergillus nidulans
. We examined the role of the
Aspergillus flavus fluG
orthologue in asexual development and aflatoxin biosynthesis. Deletion of
fluG
in
A. flavus
yielded strains with an approximately 3-fold reduction in conidiation but a 30-fold increase in sclerotial formation when grown on potato dextrose agar in the dark. The concurrent developmental changes suggest that
A. flavus
FluG exerts opposite effects on a mutual signaling pathway for both processes. The altered conidial development was in part attributable to delayed expression of
brlA
, a gene controlling conidiophore formation. Unlike the loss of sterigmatocystin production by
A. nidulans fluG
deletion strains, aflatoxin biosynthesis was not affected by the
fluG
deletion in
A. flavus
. In
A. nidulans
, FluG was recently found to be involved in the formation of dehydroaustinol, a component of a diffusible signal of conidiation. Coculturing experiments did not show a similar diffusible meroterpenoid secondary metabolite produced by
A. flavus
. These results suggest that the function of
fluG
and the signaling pathways related to conidiation are different in the two related aspergilli.
Specific Fusion of β-1,4-Endoglucanase and β-1,4-Glucosidase Enhances Cellulolytic Activity and Helps in Channeling of Intermediates
Authors: Adlakha Nidhi , Sawant Sneha , Anil Annamma , Lali Arvind , Yazdani Syed Shams
Published: August 2012

Identification and design of new cellulolytic enzymes with higher catalytic efficiency are a key factor in reducing the production cost of lignocellulosic bioalcohol. We report here identification of a novel β-glucosidase (Gluc1C) from
Paenibacillus
sp. strain MTCC 5639 and construction of bifunctional chimeric proteins based on Gluc1C and Endo5A, a β-1,4-endoglucanase isolated from MTCC 5639 earlier. The 448-amino-acid-long Gluc1C contained a GH superfamily 1 domain and hydrolyzed cellodextrin up to a five-sugar chain length, with highest efficiency toward cellobiose. Addition of Gluc1C improved the ability of Endo5A to release the reducing sugars from carboxymethyl cellulose. We therefore constructed six bifunctional chimeric proteins based on Endo5A and Gluc1C varying in the positions and sizes of linkers. One of the constructs, EG5, consisting of Endo5A-(G
4
S)
3
-Gluc1C, demonstrated 3.2- and 2-fold higher molar specific activities for β-glucosidase and endoglucanase, respectively, than Gluc1C and Endo5A alone. EG5 also showed 2-fold higher catalytic efficiency than individual recombinant enzymes. The thermal denaturation monitored by circular dichroism (CD) spectroscopy demonstrated that the fusion of Gluc1C with Endo5A resulted in increased thermostability of both domains by 5°C and 9°C, respectively. Comparative hydrolysis experiments done on alkali-treated rice straw and CMC indicated 2-fold higher release of product by EG5 than that by the physical mixture of Endo5A and Gluc1C, providing a rationale for channeling of intermediates. Addition of EG5 to a commercial enzyme preparation significantly enhanced release of reducing sugars from pretreated biomass, indicating its commercial applicability.
Recovery of Phenotypes Obtained by Adaptive Evolution through Inverse Metabolic Engineering
Authors: Hong Kuk-Ki , Nielsen Jens
Published: August 2012

In a previous study, system level analysis of adaptively evolved yeast mutants showing improved galactose utilization revealed relevant mutations. The governing mutations were suggested to be in the Ras/PKA signaling pathway and ergosterol metabolism. Here, site-directed mutants having one of the mutations
RAS2

Lys77

,
RAS2

Tyr112

, and
ERG5

Pro370

were constructed and evaluated. The mutants were also combined with overexpression of
PGM2
, earlier proved as a beneficial target for galactose utilization. The constructed strains were analyzed for their gross phenotype, transcriptome and targeted metabolites, and the results were compared to those obtained from reference strains and the evolved strains. The
RAS2

Lys77

mutation resulted in the highest specific galactose uptake rate among all of the strains with an increased maximum specific growth rate on galactose. The
RAS2

Tyr112

mutation also improved the specific galactose uptake rate and also resulted in many transcriptional changes, including ergosterol metabolism. The
ERG5

Pro370

mutation only showed a small improvement, but when it was combined with
PGM2
overexpression, the phenotype was almost the same as that of the evolved mutants. Combination of the
RAS2
mutations with
PGM2
overexpression also led to a complete recovery of the adaptive phenotype in galactose utilization. Recovery of the gross phenotype by the reconstructed mutants was achieved with much fewer changes in the genome and transcriptome than for the evolved mutants. Our study demonstrates how the identification of specific mutations by systems biology can direct new metabolic engineering strategies for improving galactose utilization by yeast.
Depletion of Cryptosporidium parvum Oocysts from Contaminated Sewage by Using Freshwater Benthic Pearl Clams (Hyriopsis schlegeli)
Authors: Izumi Toshihiko , Yagita Kenji , Izumiyama Shinji , Endo Takuro , Itoh Yasoo
Published: August 2012

The freshwater benthic pearl clam,
Hyriopsis schlegeli
, was experimentally exposed to
Cryptosporidium parvum
oocysts, and it was verified that the oocysts were eliminated predominantly via the fecal route, retaining their ability to infect cultured cells (HCT-8). The total fecal oocyst elimination rate was more than 90% within 5 days after exposure to the oocysts.
H. schlegeli
was able to survive in the final settling pond of a sewage plant for long periods, as confirmed by its pearl production. In the light of these findings, the clam was placed in the final settling pond in a trial to test its long-term efficacy in depleting oocysts contaminating the pond water. The number of clams placed was set to ensure a theoretical oocyst removal rate of around 50%, and the turbidity and the density of feed microbes in the overflow trough water of the pond were about 35% and 40 to 60% lower, respectively, than in the control water throughout the year. It was found that the clam feces containing oocysts were sufficiently heavy for them to settle to the bottom of the pond, despite the upward water flow. From these results, we concluded that efficient depletion of oocysts in the sewage water of small or midscale sewage treatment plants can be achieved by appropriate placement of
H. schlegeli
clams.
Terrestrial Runoff Controls the Bacterial Community Composition of Biofilms along a Water Quality Gradient in the Great Barrier Reef
Authors: Witt Verena , Wild Christian , Uthicke Sven
Published: August 2012

16S rRNA gene molecular analysis elucidated the spatiotemporal distribution of bacterial biofilm communities along a water quality gradient. Multivariate statistics indicated that terrestrial runoff, in particular dissolved organic carbon and chlorophyll
a
concentrations, induced shifts of specific bacterial communities between locations and seasons, suggesting microbial biofilms could be suitable bioindicators for water quality.
Substrate Specificity of Thiamine Pyrophosphate-Dependent 2-Oxo-Acid Decarboxylases in Saccharomyces cerevisiae
Authors: Romagnoli Gabriele , Luttik Marijke A. H. , Kötter Peter , Pronk Jack T. , Daran Jean-Marc
Published: August 2012

Fusel alcohols are precursors and contributors to flavor and aroma compounds in fermented beverages, and some are under investigation as biofuels. The decarboxylation of 2-oxo acids is a key step in the Ehrlich pathway for fusel alcohol production. InSaccharomyces cerevisiae, five genes share sequence similarity with genes encoding thiamine pyrophosphate-dependent 2-oxo-acid decarboxylases (2ODCs).PDC1,PDC5, andPDC6encode differentially regulated pyruvate decarboxylase isoenzymes;ARO10encodes a 2-oxo-acid decarboxylase with broad substrate specificity, andTHI3has not yet been shown to encode an active decarboxylase. Despite the importance of fusel alcohol production inS. cerevisiae, the substrate specificities of these five 2ODCs have not been systematically compared. When the five 2ODCs were individually overexpressed in apdc1Δpdc5Δpdc6Δaro10Δthi3Δ strain, only Pdc1, Pdc5, and Pdc6 catalyzed the decarboxylation of the linear-chain 2-oxo acids pyruvate, 2-oxo-butanoate, and 2-oxo-pentanoate in cell extracts. The presence of a Pdc isoenzyme was also required for the production ofn-propanol andn-butanol in cultures grown on threonine and norvaline, respectively, as nitrogen sources. These results demonstrate the importance of pyruvate decarboxylases in the natural production ofn-propanol andn-butanol byS. cerevisiae. No decarboxylation activity was found for Thi3 with any of the substrates tested. Only Aro10 and Pdc5 catalyzed the decarboxylation of the aromatic substrate phenylpyruvate, with Aro10 showing superior kinetic properties. Aro10, Pdc1, Pdc5, and Pdc6 exhibited activity with all branched-chain and sulfur-containing 2-oxo acids tested but with markedly different decarboxylation kinetics. The high affinity of Aro10 identified it as a key contributor to the production of branched-chain and sulfur-containing fusel alcohols.
Genetic Identification of a High-Affinity Ni Transporter and the Transcriptional Response to Ni Deprivation in Synechococcus sp. Strain WH8102
Authors: Dupont C. L. , Johnson D. A. , Phillippy K. , Paulsen I. T. , Brahamsha B. , Palenik B.
Published: August 2012

One biological need for Ni in marine cyanobacteria stems from the utilization of the Ni metalloenzyme urease for the assimilation of urea as a nitrogen source. In many of the same cyanobacteria, includingSynechococcussp. strain WH8102, an additional and obligate nutrient requirement for Ni results from usage of a Ni superoxide dismutase (Ni-SOD), which is encoded bysodN. To better understand the effects of Ni deprivation on WH8102, parallel microarray-based analysis of gene expression and gene knockout experiments were conducted. The global transcriptional response to Ni deprivation depends upon the nitrogen source provided for growth; fewer than 1% of differentially expressed genes for Ni deprivation on ammonium or urea were concordantly expressed. Surprisingly, genes for putative Ni transporters, including one colocalized on the genome withsodN,sodT, were not induced despite an increase in Ni transport. Knockouts of the putative Ni transporter genesodTappeared to be lethal in WH8102, so the genes forsodTandsodNin WH8102 were interrupted with the gene for Fe-SOD,sodB, and its promoter fromSynechococcussp. strain WH7803. ThesodT::sodBexconjugants were unable to grow at low Ni concentrations, confirming that SodT is a Ni transporter. ThesodN::sodBexconjugants displayed higher growth rates at low Ni concentrations than did the wild type, presumably due to a relaxed competition between urease and Ni-SOD for Ni. BothsodT::sodBandsodN::sodBlines exhibited an impaired ability to grow at low Fe concentrations. We propose a posttranslational allosteric SodT regulation involving the binding of Ni to a histidine-rich intracellular protein loop.
Stable Carbon Isotope Fractionation by Methylotrophic Methanogenic Archaea
Authors: Penger Jörn , Conrad Ralf , Blaser Martin
Published: August 2012

In natural environments methane is usually produced by aceticlastic and hydrogenotrophic methanogenic archaea. However, some methanogens can use C
1
compounds such as methanol as the substrate. To determine the contributions of individual substrates to methane production, the stable-isotope values of the substrates and the released methane are often used. Additional information can be obtained by using selective inhibitors (e.g., methyl fluoride, a selective inhibitor of acetoclastic methanogenesis). We studied stable carbon isotope fractionation during the conversion of methanol to methane in
Methanosarcina acetivorans
,
Methanosarcina barkeri
, and
Methanolobus zinderi
and generally found large fractionation factors (−83‰ to −72‰). We further tested whether methyl fluoride impairs methylotrophic methanogenesis. Our experiments showed that even though a slight inhibition occurred, the carbon isotope fractionation was not affected. Therefore, the production of isotopically light methane observed in the presence of methyl fluoride may be due to the strong fractionation by methylotrophic methanogens and not only by hydrogenotrophic methanogens as previously assumed.
Differences in the Fecal Concentrations and Genetic Diversities of Campylobacter jejuni Populations among Individual Cows in Two Dairy Herds
Authors: Rapp Delphine , Ross Colleen M. , Pleydell Eve J. , Muirhead Richard W.
Published: August 2012

Dairy cows have been identified as common carriers of
Campylobacter jejuni
, which causes many of the human gastroenteritis cases reported worldwide. To design on-farm management practices that control the human infection sourced from dairy cows, the first step is to acquire an understanding of the excretion patterns of the cow reservoir. We monitored the same 35 cows from two dairy farms for
C. jejuni
excretion fortnightly for up to 12 months. The objective was to examine the concentration of
C. jejuni
and assess the genetic relationship of the
C. jejuni
populations excreted by individual cows. Significant differences (
P
< 0.01) in
C. jejuni
fecal concentration were observed among the 35 cows, with median concentrations that varied by up to 3.6 log
10
· g
−1
feces. A total of 36 different genotypes were identified from the 514 positive samples by using enterobacterial repetitive intergenic consensus (ERIC)-PCR. Although 22 of these genotypes were excreted by more than one cow, the analysis of frequencies and distribution of the genotypes by model-based statistics revealed a high degree of individuality in the
C. jejuni
population in each cow. The observed variation in the frequency of excretion of a genotype among cows and the analysis by multilocus sequence typing (MLST) of these genotypes suggest that excretion of
C. jejuni
in high numbers is due to a successful adaptation of a particular genotype to a particular cow's gut environment, but that animal-related factors render some individual cows resistant to colonization by particular genotypes. The reasons for differences in
C. jejuni
colonization of animals warrant further investigation.
Virioplankton Community Structure in Tunisian Solar Salterns
Authors: Boujelben Ines , Yarza Pablo , Almansa Cristina , Villamor Judith , Maalej Sami , Antón Josefa , Santos Fernando
Published: August 2012

The microbial community inhabiting Sfax solar salterns on the east coast of Tunisia has been studied by means of different molecular and culture-dependent tools that have unveiled the presence of novel microbial groups as well as a community structure different from that of other coastal hypersaline environments. We have focused on the study of the viral assemblages of these salterns and their changes along the salinity gradient and over time. Viruses from three ponds (C4, M1, and TS) encompassing salinities from moderately hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in May and October 2009 and analyzed by transmission electron microscopy (TEM) and pulsed-field gel electrophoresis (PFGE). Additionally, for all three October samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios, increased along the salinity gradient, with around 10
10
virus-like particles (VLPs)/ml in close-to-saturation ponds, which represents the highest viral concentration reported so far for aquatic systems. Four distinct morphologies could be observed with TEM (spherical, tailed, spindled, and filamentous) but with various proportions in the different samples. Metagenomic analyses indicated that every pond harbored a distinct viral assemblage whose G+C content could be roughly correlated with that of the active part of the microbial community that may have constituted the putative hosts. As previously reported for hypersaline metaviromes, most sequences did not have matches in the databases, although some were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide frequency analyses indicated that (i) factors additional to salinity could be structuring viral communities and (ii) every metavirome had unique gene contents and dinucleotide frequencies. Comparison with hypersaline metaviromes available in the databases indicated that the viral assemblages present in close-to-saturation environments located thousands of kilometers apart presented some common traits among them in spite of their differences regarding the putative hosts. A small core metavirome for close-to-saturation systems was found that contained 7 sequences of around 100 nucleotides (nt) whose function was not hinted at by
in silico
search results, although it most likely represents properties essential for hyperhalophilic viruses.
Effect of Grape Seed Extract on Human Norovirus GII.4 and Murine Norovirus 1 in Viral Suspensions, on Stainless Steel Discs, and in Lettuce Wash Water
Authors: Li Dan , Baert Leen , Zhang Dongsheng , Xia Ming , Zhong Weiming , Van Coillie Els , Jiang Xi , Uyttendaele Mieke
Published: August 2012

The anti-norovirus (anti-NoV) effect of grape seed extract (GSE) was examined by plaque assay for murine norovirus 1 (MNV-1), cell-binding reverse transcription-PCR for human NoV GII.4, and saliva-binding enzyme-linked immunosorbent assay for human NoV GII.4 P particles, with or without the presence of interfering substances (dried milk and lettuce extract). GSE at 0.2 and 2 mg/ml was shown to reduce the infectivity of MNV-1 (>3-log PFU/ml) and the specific binding ability of NoV GII.4 to Caco-2 cells (>1-log genomic copies/ml), as well as of its P particles to salivary human histo-blood group antigen receptors (optical density at 450 nm of >0.8). These effects were decreased as increasing concentrations of dried milk (0.02 and 0.2%) or lettuce extract were added. Under an electron microscope, human NoV GII.4 virus-like particles showed inflation and deformation after treatment with GSE. Under conditions that simulated applications in the food industry, the anti-NoV effect of GSE using MNV-1 as a target organism was shown to be limited in surface disinfection (<1-log PFU/ml, analyzed in accordance with EN 13697:2001). However, a 1.5- to 2-log PFU/ml reduction in MNV-1 infectivity was noted when 2 mg of GSE/ml was used to sanitize water in the washing bath of fresh-cut lettuce, and this occurred regardless of the chemical oxygen demand (0 to 1,500 mg/ml) of the processing water.
The Tsetse Fly Obligate Mutualist Wigglesworthia morsitans Alters Gene Expression and Population Density via Exogenous Nutrient Provisioning
Authors: Snyder Anna K. , McLain Colin , Rio Rita V. M.
Published: August 2012

The obligate mutualist
Wigglesworthia morsitans
provisions nutrients to tsetse flies. The symbiont's response to thiamine (B
1
) supplementation of blood meals, specifically towards the regulation of thiamine biosynthesis and population density, is described. Despite an ancient symbiosis and associated genome tailoring,
Wigglesworthia
responds to nutrient availability, potentially accommodating a decreased need.
Coselection of Cadmium and Benzalkonium Chloride Resistance in Conjugative Transfers from Nonpathogenic Listeria spp. to Other Listeriae
Authors: Katharios-Lanwermeyer S. , Rakic-Martinez M. , Elhanafi D. , Ratani S. , Tiedje J. M. , Kathariou S.
Published: August 2012

Resistance to the quaternary ammonium disinfectant benzalkonium chloride (BC) may be an important contributor to the ability of
Listeria
spp. to persist in the processing plant environment. Although a plasmid-borne disinfectant resistance cassette (
bcrABC
) has been identified in
Listeria monocytogenes
, horizontal transfer of these genes has not been characterized. Nonpathogenic
Listeria
spp. such as
L. innocua
and
L. welshimeri
are more common than
L. monocytogenes
in food processing environments and may contribute to the dissemination of disinfectant resistance genes in listeriae, including
L. monocytogenes
. In this study, we investigated conjugative transfer of resistance to BC and to cadmium from nonpathogenic
Listeria
spp. to other nonpathogenic listeriae, as well as to
L. monocytogenes
. BC-resistant
L. welshimeri
and
L. innocua
harboring
bcrABC
, along with the cadmium resistance determinant
cadA2
, were able to transfer resistance to other nonpathogenic listeriae as well as to
L. monocytogenes
of diverse serotypes, including strains from the 2011 cantaloupe outbreak. Transfer among nonpathogenic
Listeria
spp. was noticeably higher at 25°C than at 37°C, whereas acquisition of resistance by
L. monocytogenes
was equally efficient at 25 and 37°C. When the nonpathogenic donors were resistant to both BC and cadmium, acquisition of cadmium resistance was an effective surrogate for transfer of resistance to BC, suggesting coselection between these resistance attributes. The results suggest that nonpathogenic
Listeria
spp. may behave as reservoirs for disinfectant and heavy metal resistance genes for other listeriae, including the pathogenic species
L. monocytogenes
.
Results of Continuous Monitoring of the Performance of Rubella Virus IgG and Hepatitis B Virus Surface Antibody Assays Using Trueness Controls in a Multicenter Trial
Authors: Kruk Tamara , Ratnam Sam , Preiksaitis Jutta , Lau Allan , Hatchette Todd , Horsman Greg , Van Caeseele Paul , Timmons Brian , Tipples Graham
Published: August 2012

We conducted a multicenter trial in Canada to assess the value of using trueness controls (TC) for rubella virus IgG and hepatitis B virus surface antibody (anti-HBs) serology to determine test performance across laboratories over time. TC were obtained from a single source with known international units. Seven laboratories using different test systems and kit lots included the TC in routine assay runs of the analytes. TC measurements of 1,095 rubella virus IgG and 1,195 anti-HBs runs were plotted on Levey-Jennings control charts for individual laboratories and analyzed using a multirule quality control (MQC) scheme as well as a single three-standard-deviation (3-SD) rule. All rubella virus IgG TC results were “in control” in only one of the seven laboratories. Among the rest, “out-of-control” results ranged from 5.6% to 10% with an outlier at 20.3% by MQC and from 1.1% to 5.6% with an outlier at 13.4% by the 3-SD rule. All anti-HBs TC results were “in control” in only two laboratories. Among the rest, “out-of-control” results ranged from 3.3% to 7.9% with an outlier at 19.8% by MQC and from 0% to 3.3% with an outlier at 10.5% by the 3-SD rule. In conclusion, through the continuous monitoring of assay performance using TC and quality control rules, our trial detected significant intra- and interlaboratory, test system, and kit lot variations for both analytes. In most cases the assay rejections could be attributable to the laboratories rather than to kit lots. This has implications for routine diagnostic screening and clinical practice guidelines and underscores the value of using an approach as described above for continuous quality improvement in result reporting and harmonization for these analytes.
The Aspergillus fumigatus Protein GliK Protects against Oxidative Stress and Is Essential for Gliotoxin Biosynthesis
Authors: Gallagher Lorna , Owens Rebecca A. , Dolan Stephen K. , O'Keeffe Grainne , Schrettl Markus , Kavanagh Kevin , Jones Gary W. , Doyle Sean
Published: August 2012

The function of a number of genes in the gliotoxin biosynthetic cluster (
gli
) in
Aspergillus fumigatus
remains unknown. Here, we demonstrate that
gliK
deletion from two strains of
A. fumigatus
completely abolished gliotoxin biosynthesis. Furthermore, exogenous H
2
O
2
(1 mM), but not gliotoxin, significantly induced
A. fumigatus gliK
expression (
P
= 0.0101). While both mutants exhibited significant sensitivity to both exogenous gliotoxin (
P
< 0.001) and H
2
O
2
(
P
< 0.01), unexpectedly, exogenous gliotoxin relieved H
2
O
2
-induced growth inhibition in a dose-dependent manner (0 to 10 μg/ml). Gliotoxin-containing organic extracts derived from
A. fumigatus
ATCC 26933 significantly inhibited (
P
< 0.05) the growth of the Δ
gliK
26933
deletion mutant. The
A. fumigatus
Δ
gliK
26933
mutant secreted metabolites, devoid of disulfide linkages or free thiols, that were detectable by reverse-phase high-performance liquid chromatography and liquid chromatography-mass spectrometry with
m/z
394 to 396. These metabolites (
m/z
394 to 396) were present at significantly higher levels in the culture supernatants of the
A. fumigatus
Δ
gliK
26933
mutant than in those of the wild type (
P
= 0.0024 [fold difference, 24] and
P
= 0.0003 [fold difference, 9.6], respectively) and were absent from
A. fumigatus
Δ
gliG
. Significantly elevated levels of ergothioneine were present in aqueous mycelial extracts of the
A. fumigatus
Δ
gliK
26933
mutant compared to the wild type (
P
< 0.001). Determination of the gliotoxin uptake rate revealed a significant difference (
P
= 0.0045) between that of
A. fumigatus
ATCC 46645 (9.3 pg/mg mycelium/min) and the Δ
gliK
46645
mutant (31.4 pg/mg mycelium/min), strongly suggesting that
gliK
absence and the presence of elevated ergothioneine levels impede exogenously added gliotoxin efflux. Our results confirm a role for
gliK
in gliotoxin biosynthesis and reveal new insights into gliotoxin functionality in
A. fumigatus
.
Genetic and Physical Interactions between Gα Subunits and Components of the Gβγ Dimer of Heterotrimeric G Proteins in Neurospora crassa
Authors: Won Susan , Michkov Alexander V. , Krystofova Svetlana , Garud Amruta V. , Borkovich Katherine A.
Published: August 2012

Heterotrimeric G proteins are critical regulators of growth and asexual and sexual development in the filamentous fungus
Neurospora crassa
. Three Gα subunits (GNA-1, GNA-2, and GNA-3), one Gβ subunit (GNB-1), and one Gγ subunit (GNG-1) have been functionally characterized, but genetic epistasis relationships between Gβ and Gα subunit genes have not been determined. Physical association between GNB-1 and FLAG-tagged GNG-1 has been previously demonstrated by coimmunoprecipitation, but knowledge of the Gα binding partners for the Gβγ dimer is currently lacking. In this study, the three
N. crassa
Gα subunits are analyzed for genetic epistasis with
gnb-1
and for physical interaction with the Gβγ dimer. We created double mutants lacking one Gα gene and
gnb-1
and introduced constitutively active, GTPase-deficient alleles for each Gα gene into the Δ
gnb-1
background. Genetic analysis revealed that
gna-3
is epistatic to
gnb-1
with regard to negative control of submerged conidiation.
gnb-1
is epistatic to
gna-2
and
gna-3
for aerial hyphal height, while
gnb-1
appears to act upstream of
gna-1
and
gna-2
during aerial conidiation. None of the activated Gα alleles restored female fertility to Δ
gnb-1
mutants, and the
gna-3
Q208L
allele inhibited formation of female reproductive structures, consistent with a need for Gα proteins to cycle through the inactive GDP-bound form for these processes. Coimmunoprecipitation experiments using extracts from the
gng-1
-FLAG strain demonstrated that the three Gα proteins interact with the Gβγ dimer. The finding that the Gβγ dimer interacts with all three Gα proteins is supported by epistasis between
gnb-1
and
gna-1
,
gna-2
, and
gna-3
for at least one function.
Structural Requirements for the Activity of the MirB Ferrisiderophore Transporter of Aspergillus fumigatus
Authors: Raymond-Bouchard Isabelle , Carroll Cassandra S. , Nesbitt Jason R. , Henry Kevin A. , Pinto Linda J. , Moinzadeh Mina , Scott Jamie K. , Moore Margo M.
Published: August 2012

Siderophores have been identified as virulence factors in the opportunistic fungal pathogen
Aspergillus fumigatus
. The 14-pass transmembrane protein MirB is postulated to function as a siderophore transporter, responsible for uptake of the hydroxamate siderophore
N,N
′,
N
″-triacetylfusarinine C (TAFC). Our aim was to identify amino acids of
A. fumigatus
MirB that are crucial for uptake of TAFC. Site-directed mutagenesis was used to create MirB mutants. Expression of wild-type and mutant proteins in the
Saccharomyces cerevisiae
strain PHY14, which lacks endogenous siderophore transporters, was confirmed by Western blotting. TAFC transport assays using
55
Fe-labeled TAFC and growth assays with Fe-TAFC as the sole iron source identified alanine 125, tyrosine 577, loop 3, and the second half of loop 7 (Loop7Del2) as crucial for function, since their substitution or deletion abrogated uptake completely. Wild-type MirB transported ferricrocin and coprogen as well as TAFC but not ferrichrysin. MirB was localized by fluorescence microscopy using antisera raised against a MirB extracellular loop peptide. Immunofluorescence microscopy showed that in yeast, wild-type MirB had a punctate distribution under the plasma membrane, as did the A125D and Y577A strains, indicating that the defect in transport of these mutants was unlikely to be due to mislocalization or degradation. MirB immunolocalization in
A. fumigatus
showed that the transporter was found in vesicles which cycled between the cytoplasm and the plasma membrane and was concentrated at the hyphal tips. The location of MirB was not influenced by the presence of the siderophore TAFC but was sensitive to internal iron stores.