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  • Environmental Microbiology  (51)
  • Pathogens & Pathogenicity  (51)
  • Food Policy  (45)
  • Mineral Physics, Rheology, Heat Flow and Volcanology  (29)
  • Oxford University Press  (176)
  • Elsevier
  • 2015-2019  (176)
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  • Oxford University Press  (176)
  • Elsevier
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  • 1
    Publication Date: 2017-01-05
    Description: New National School Lunch Program (NSLP) guidelines aim to reduce sodium and saturated fats, limit calories, and eliminate trans-fat and whole milk. This paper provides a novel approach to understanding how the healthfulness of NSLP participants’ entrée selections varies across socioeconomic and demographic groups. Unlike previous studies that rely on dietary recalls, we use a mixed logit model to examine students’ entrée choices in a school cafeteria. We estimate the likelihood that an entrée is selected from the available lunch choices as a function of the entrée’s nutrients (fat, carbohydrate, protein, and sodium) and entrée’s taste profile characteristics (e.g., Mexican, Pizza-like), as well as the student’s socio-economic and demographic characteristics. Using these estimates, we examine how changing the nutritional content of an offering impacts the probability of selecting each of the offerings. Free lunch recipients are more likely to choose entrées higher in fat but lower in sodium than other students. Full-price lunch recipients are the most responsive to changes in nutritional content of the offerings and are most likely to respond to changes in the nutritional content of the offered entrées by substituting a lunch brought from home for the school-purchased lunch. Replacing less healthy menu items with popular but healthier items reduces the selection of total calories, calories from fat, and sodium by approximately 4%, 18%, and 8%, respectively, over the study period. The new guidelines should be effective at improving the nutrition of school-age children, and potentially reducing childhood obesity, provided NSLP participation does not decline appreciably.
    Keywords: D12 - Consumer Economics: Empirical Analysis, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 2
    Publication Date: 2017-01-13
    Description: As a leading pathogen, Edwardsiella piscicida can cause hemorrhagic septicemia in fish and gastro-intestinal infections in humans. The two-component regulatory system EsrA-EsrB plays essential roles in pathogenesis through the type III and type VI secretion systems, and hemolysin production in E. piscicida . It is unclear whether other virulence- or stress response-associated genes are regulated by EsrA-EsrB. In this study, the proteomes of wild-type E. piscicida EIB202 and esrB mutant strains were compared to reveal EsrB regulon components after growth in Luria–Bertani broth (LB). Overall, the expression levels of nine genes exhibited significant changes, and five of them required the presence of EsrB, while others exhibited higher levels in the esrB mutant. The diverse functions of these proteins were identified, including amino acid metabolism, oxidative stress defense and energy production. Interestingly, superoxidase dismutase and thiol peroxidase were the most significantly down-regulated by EsrB. Furthermore, other reported reactive oxygen species (ROS) resistance-related genes were also down-regulated by EsrB as revealed by quantitative real-time. Compared with the wild-type and the complement strain esrB + , esrB displayed a significantly enhanced ROS resistance. These results demonstrated that EsrB plays important roles in the ROS resistance pathway in E. piscicida grown in LB conditions.
    Keywords: Pathogens & Pathogenicity
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  • 3
    Publication Date: 2017-01-13
    Description: The sepsis caused by Vibrio vulnificus is characterized by an average incubation period of 26 h and a high mortality rate exceeding 50%. The fast growth and dissemination of V. vulnificus in vivo lead to poor clinical outcomes in patients. Therefore, elucidation of the proliferation mechanisms of this organism in vivo may lead to the development of an effective therapeutic strategy. In this study, we focused on the low oxygen concentration in the intestinal milieu because of its drastic difference from that in air. Fumarate and nitrate reduction regulatory protein (FNR) is known to be a global transcriptional regulator for adaptation to anaerobic conditions in various bacteria. We generated a strain of V. vulnificus in which the fnr gene was replaced with an erythromycin resistance gene ( fnr :: erm mutant). When the fnr :: erm mutant was tested in a growth competition assay against the wild-type (WT) in vivo , the competitive index of fnr :: erm mutant to WT in the intestinal loop and liver was 0.378 ± 0.192 (mean ± SD) and 0.243 ± 0.123, respectively. These data suggested that FNR is important for the proliferation of V. vulnificus in the intestine to achieve a critical mass to be able to invade the systemic circulation.
    Keywords: Pathogens & Pathogenicity
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  • 4
    Publication Date: 2017-01-13
    Description: Animal-associated microbiotas form complex communities, which play crucial functions for their host, including susceptibility to infections. Despite increasing attention to bats as reservoirs of zoonotic pathogens, their microbiota is poorly documented, especially for samples potentially implicated in pathogen transmission such as urine and saliva. Here, using low-biomass individual samples, we examined the composition and structure of bacterial communities excreted by insectivorous bats, focusing on three body habitats (saliva, urine and faeces). We show that niche specialisation occurs as bacterial community composition was distinct across body habitats with the majority of phylotypes being body habitat specific. Our results suggest that urine harbours more diverse bacterial communities than saliva and faeces and reveal potentially zoonotic bacteria such as Leptospira , Rickettsia , Bartonella and Coxiella in all body habitats. Our study emphasised that, in addition to the traditional use of gut-associated samples such as faeces, both urine and saliva are also of interest because of their diverse microbiota and the potential transmission of pathogenic bacteria. Our results represent a critical baseline for future studies investigating the interactions between microbiota and infection dynamics in bats.
    Keywords: Environmental Microbiology
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  • 5
    Publication Date: 2017-01-05
    Description: We estimate the effects of changes in cotton adoption on children’s schooling and child labor in rural Burkina Faso. Using time and spatial variations, we find evidence that expansion of cotton farming has led to an increase in enrollment and to a reduction of participation in child labor for girls. There are, however, no detectable effects on boys. In theory, cotton adoption could increase household income, leading to increased demand for schooling and reduced child labor. On the other hand, because children are productive on cotton farms, adoption of cotton could increase the opportunity cost of child time and the demand for child labor. We provide suggestive evidence showing that boys are more productive than girls on cotton farms. Taken together, the results suggest that the income effect from cotton adoption might have been larger than the wage effect for girls, hence the overall positive impacts on school enrollment for girls.
    Keywords: O12 - Microeconomic Analyses of Economic Development, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, O15 - Human Resources ; Human Development ; Income Distribution ; Migration, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 6
    Publication Date: 2017-01-19
    Description: R-type bacteriocins are contractile phage tail-like structures that are bactericidal towards related bacterial species. The C-terminal region of the phage tail fiber protein determines target-binding specificity. The mutualistic bacteria Xenorhabdus nematophila and X. bovienii produce R-type bacteriocins (xenorhabdicins) that are selectively active against different Xenorhabdus species. We analyzed the P2-type remnant prophage clusters in draft sequences of nine strains of X. bovienii . The C-terminal tail fiber region in each of the respective strains was unique and consisted of mosaics of modular units. The region between the main tail fiber gene ( xbpH1 ) and the sheath gene ( xbpS1 ) contained a variable number of modules encoding tail fiber fragments. DNA inversion and module exchange between strains was involved in generating tail fiber diversity. Xenorhabdicin-enriched fractions from three different X. bovienii strains isolated from the same nematode species displayed distinct activities against each other. In one set of strains, the strain that produced highly active xenorhabdicin was able to eliminate a sensitive strain. In contrast, xenorhabdicin activity was not a determining factor in the competitive fitness of a second set of strains. These findings suggest that related strains of X. bovienii use xenorhabdicin and additional antagonistic molecules to compete against each other.
    Keywords: Environmental Microbiology
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  • 7
    Publication Date: 2017-01-19
    Description: Anabaena PCC7120 has two annotated toxin–antitoxin systems: MazEF and HicAB. Overexpression of either of the toxins severely inhibited the growth of Escherichia coli BL21(p lysS )(DE3). Of the two Anabaena toxins, MazF exhibited higher toxicity than HicA as evidenced by (i) 100-fold lower viability upon overexpression of MazF compared to HicA; (ii) complete loss of cell viability within 1 h of induction of MazF expression, as against 〉10 3 colony forming units mL –1 in case of HicA; (iii) inability to maintain the MazF overexpressing plasmid in E. coli cells; and (iv) neutralisation of the toxin was effective at the molar ratio of 1:1.9 for MazF:MazE and 13:1 for HicA:HicB, indicating higher antitoxin requirement for neutralisation of MazF. The growth inhibitory effect of MazF was found to be higher in lag phase cultures compared to mid-logarithmic phase cultures of E. coli , while the reverse was true for HicA. The results suggest possible distinct roles for MazEF and HicAB systems of Anabaena .
    Keywords: Environmental Microbiology
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  • 8
    Publication Date: 2017-01-08
    Description: Helicobacter pylori is an important cause of gastric pathologies and persistent infection can lead to stomach cancer. Virulent H. pylori strains encode a type IV secretion system responsible for translocation of the oncogenic CagA protein into cells of the gastric mucosa. Gene HP0522 encodes the essential component Cag (Cag3), and we show by gel filtration and cross-linking that purified Cag forms high molecular mass complexes. In contrast, its interaction partner CagT is mostly monomeric, but co-fractionates after gel filtration. Analysis by transmission electron microscopy revealed that purified Cag complexes can self-assemble ring-like structures. Cag-overexpressing Escherichia coli exhibits membrane-associated circular profiles in regions of the cell envelope with intense immunogold labelling with a Cag-specific antiserum. Our results suggest that Cag has the capacity to form macromolecular structures contributing to the assembly of the type IV secretion system.
    Keywords: Pathogens & Pathogenicity
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  • 9
    Publication Date: 2016-07-15
    Description: Invertebrate animal species that can withstand temperatures as high as 37°C, the human body temperature, are limited. In the present study, we utilized the two-spotted cricket, Gryllus bimaculatus , which lives in tropical and subtropical regions, as an animal model of human pathogenic bacterial infection. Injection of Pseudomonas aeruginosa or Staphylococcus aureus into the hemolymph killed crickets. Injected P. aeruginosa or S. aureus proliferated in the hemolymph until the cricket died. The ability of these pathogenic bacteria to kill the crickets was blocked by the administration of antibiotics. S. aureus gene-knockout mutants of virulence factors, including cvfA, agr and srtA , exhibited decreased killing ability compared with the parent strain. The dose at which 50% of crickets were killed by P. aeruginosa or S. aureus was not decreased at 37°C compared with that at 27°C. Injection of Listeria monocytogenes , which upregulates toxin expression at 37°C, killed crickets, and the dose at which 50% of crickets were killed was decreased at 37°C compared with that at 27°C. These findings suggest that the two-spotted cricket is a useful model animal for evaluating the virulence properties of various human pathogenic bacteria at variable temperature including 37°C.
    Keywords: Pathogens & Pathogenicity
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  • 10
    Publication Date: 2016-07-20
    Description: Four antibiotics (pamamycin, oligomycin A, oligomycin B and echinosporin) were isolated and characterized from the fermentation broth of the marine Streptomyces strains B8496 and B8739. Bioassays revealed that each of these compounds impaired motility and caused subsequent lysis of P. viticola zoospores in a dose- and time-dependent manner. Pamamycin displayed the strongest motility inhibitory and lytic activities (IC 50 0.1 μg mL –1 ) followed by oligomycin B (IC 50 0.15 and 0.2 μg mL –1 ) and oligomycin F (IC 50 0.3 and 0.5 μg mL –1 ). Oligomycin A and echinosporin also showed motility inhibitory activities against the zoospores with IC 50 values of 3.0 and 10.0 μg mL –1 , respectively. This is the first report of motility inhibitory and lytic activities of these antibiotics against zoospores of a phytopathogenic peronosporomycete. Structures of all the isolated compounds were determined based on detailed spectroscopic analysis.
    Keywords: Environmental Microbiology
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  • 11
    Publication Date: 2016-07-31
    Description: In sulfidic environments, microbes oxidize reduced sulfur compounds via several pathways. We used metagenomics to investigate sulfur metabolic pathways from microbial mat communities in two subterranean sulfidic streams in Lower Kane Cave, WY, USA and from Glenwood Hot Springs, CO, USA. Both unassembled and targeted recA gene assembly analyses revealed that these streams were dominated by Epsilonproteobacteria and Gammaproteobacteria , including groups related to Sulfurovum , Sulfurospirillum , Thiothrix and an epsilonproteobacterial group with no close cultured relatives. Genes encoding sulfide:quinone oxidoreductase (SQR) were abundant at all sites, but the specific SQR type and the taxonomic affiliation of each type differed between sites. The abundance of thiosulfate oxidation pathway genes (Sox) was not consistent between sites, although overall they were less abundant than SQR genes. Furthermore, the Sox pathway appeared to be incomplete in all samples. This work reveals both variations in sulfur metabolism within and between taxonomic groups found in these systems, and the presence of novel epsilonproteobacterial groups.
    Keywords: Environmental Microbiology
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  • 12
    Publication Date: 2016-07-31
    Description: Pseudomonas aeruginosa is an opportunistic pathogen with high resistance to a wide variety of antimicrobials. The multidrug resistance pump MexAB-OprM promotes the efflux of various antibiotics, mostly when mutations accumulate in the transcriptional regulators MexR, NalC and NalD, thereby causing MexAB-OprM overexpression. In this work, a characterization of 50 P. aeruginosa isolates obtained from Brazilian agricultural soils to determine the reasons of their resistance to aztreonam was done. The majority of the isolates showed higher aztreonam resistance than wild-type strain by MIC method. DNA sequence analysis of mexR , nalC and nalD genes from 13 of these isolates showed the amino acid substitution in NalC for all tested isolates, just one mutation was detected in MexR and none in NalD. Furthermore, an increase in the level of mexA expression by real-time RT-PCR analysis in eight isolates harboring mutations in NalC was found. Although there was not a relationship between MIC of aztreonam and the level of mexA expression, on the other hand, the results presented here suggest that novel mutations in NalC, including Arg 97 -Gly and Ala 186 -Thr, are related to MexAB-OprM overexpression causing aztreonam resistance in P. aeruginosa environmental isolates.
    Keywords: Environmental Microbiology
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  • 13
    Publication Date: 2016-07-31
    Description: The OmpA-like protein domain has been associated with peptidoglycan-binding proteins, and is often found in virulence factors of bacterial pathogens. The intracellular pathogen Legionella pneumophila encodes for six proteins that contain the OmpA-like domain, among them the highly conserved uncharacterized protein we named CmpA. Here we set out to characterize the CmpA protein and determine its contribution to intracellular survival of L. pneumophila . Secondary structure analysis suggests that CmpA is an inner membrane protein with a peptidoglycan-binding domain at the C-teminus. A cmpA mutant was able to replicate normally in broth, but failed to compete with an isogenic wild-type strain in an intracellular growth competition assay. The cmpA mutant also displayed significant intracellular growth defects in both the protozoan host Acanthamoeba castellanii and in primary bone marrow-derived macrophages, where uptake into the cells was also impaired. The cmpA phenotypes were completely restored upon expression of CmpA in trans . The data presented here establish CmpA as a novel virulence factor of L. pneumophila that is required for efficient intracellular replication in both mammalian and protozoan hosts.
    Keywords: Pathogens & Pathogenicity
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  • 14
    Publication Date: 2016-07-31
    Description: Sedge-dominated wetlands on the Qinghai–Tibetan Plateau are methane emission centers. Methanotrophs at these sites play a role in reducing methane emissions, but relatively little is known about the composition of active methanotrophs in these wetlands. Here, we used DNA stable isotope probing to identify the key active aerobic methanotrophs in three sedge-dominated wetlands on the plateau. We found that Methylocystis species were active in two peatlands, Hongyuan and Dangxiong. Methylobacter species were found to be active only in Dangxiong peat. Hongyuan peat had the highest methane oxidation rate, and cross-feeding of carbon from methanotrophs to methylotrophic Hyphomicrobium species was observed. Owing to a low methane oxidation rate during the incubation, the labeling of methanotrophs in Maduo wetland samples was not detected. Our results indicate that there are large differences in the activity of methanotrophs in the wetlands of this region.
    Keywords: Environmental Microbiology
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  • 15
    Publication Date: 2016-08-05
    Description: Here we present the generation and function of two sets of bacterial plasmids that harbor fluorescent genes encoding either blue, cyan, yellow or red fluorescent proteins. In the first set, protein expression is controlled by the strong and constitutive nptII promoter whereas in the second set, the strong tac promoter was chosen that underlies LacI q regulation. Furthermore, the plasmids are mobilizable, contain Tn 7 transposons and a temperature-sensitive origin of replication. Using Escherichia coli S17-1 as donor strain, the plasmids allow fast and convenient Tn 7 -transposon delivery into many enterobacterial hosts, such as the here-used E. coli O157:H7. This procedure omits the need of preparing competent recipient cells and antibiotic resistances are only transiently conferred to the recipients. As the fluorescence proteins show little to no overlap in fluorescence emission, the constructs are well suited for the study of multicolored synthetic bacterial communities during biofilm production or in host colonization studies, e.g. of plant surfaces. Furthermore, tac promoter-reporter constructs allow the generation of so-called reproductive success reporters, which allow to estimate past doublings of bacterial individuals after introduction into environments, emphasizing the role of individual cells during colonization.
    Keywords: Environmental Microbiology
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  • 16
    Publication Date: 2016-08-05
    Description: Shiga toxin-encoding Escherichia coli (STEC) regroup strains that carry genes encoding Shiga toxin (Stx). Among intestinal pathogenic E. coli , enterohaemorrhagic E. coli (EHEC) constitute the major subgroup of virulent STEC. EHEC cause serious human disease such as haemorrhagic colitis and haemolytic-uremic syndrome. While EHEC have evolved from enteropathogenic E. coli , hybrids with enteroaggregative E. coli have recently emerged. Of note, some enteroinvasive E. coli also belong to the STEC group. While the LEE (locus of enterocyte effacement) is a key and prominent molecular determinant in the pathogenicity, neither all EHEC nor STEC contain the LEE, suggesting that they possess additional virulence and colonisation factors. Currently, nine protein secretion systems have been described in diderm-lipopolysaccharide bacteria (archetypal Gram-negative) and can be involved in the secretion of extracellular effectors, cell-surface proteins or assembly of cell-surface organelles, such as flagella or pili. In this review, we focus on the secretome of STEC and related enteropathotypes, which are relevant to the colonisation of biotic and abiotic surfaces. Considering the wealth of potential protein trafficking mechanisms, the different combinations of colonisation factors and modulation of their expression is further emphasised with regard to the ecophysiology of STEC.
    Keywords: Pathogens & Pathogenicity
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  • 17
    Publication Date: 2016-06-23
    Description: Spa -typing and microarray techniques were used to study epidemiological changes in methicillin-resistant Staphylococcus aureus (MRSA) in South-East Austria. The population structure of 327 MRSA isolated between 2002 and 2012 was investigated. MRSA was assigned to 58 different spa types and 14 different MLST CC (multilocus sequence type clonal complexes); in particular, between 2007 and 2012, an increasing diversity in MRSA clones could be observed. The most abundant clonal complex was CC5. On the respective SCC mec cassettes, the CC5 isolates differed clearly within this decade and CC5/SCC mec I, the South German MRSA, predominant in 2002, was replaced by CC5/SCC mec II, the Rhine-Hesse MRSA in 2012. Whereas in many European countries MLST CC22-MRSA (EMRSA 15, the Barnim epidemic MRSA) is predominant, this clone occurred in Austria nearly 10 years later than in neighbouring countries. CC45, the Berlin EMRSA, epidemic in Germany, was only sporadically found in South-East Austria. The Irish ST8-MRSA-II represented by spa -type t190 was frequently found in 2002 and 2007, but disappeared in 2012. Our results demonstrate clonal replacement of MRSA clones within the last years in Austria. Ongoing surveillance is warranted for detection of changes within the MRSA population.
    Keywords: Environmental Microbiology
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  • 18
    Publication Date: 2016-06-23
    Description: This study aimed to investigate the effects of dietary fibre sources on the gut microbiota in suckling piglets, and to test the hypothesis that a moderate increase of dietary fibre may affect the gut microbiota during the suckling period. Suckling piglets were fed different fibre-containing diets or a control diet from postnatal day 7 to 22. Digesta samples from cecum, proximal colon and distal colon were used for Pig Intestinal Tract Chip analysis. The data showed that the effects of fibre-containing diet on the gut microbiota differed in the fibre source and gut location. The alfalfa diet increased Clostridium cluster XIVb and Sporobacter termitidis in the cecum compared to the pure cellulose diet. Compared to the control diet, the alfalfa diet also increased Coprococcus eutactus in the distal colon, while the pure cellulose diet decreased Eubacterium pyruvativorans in the cecum. The pure cellulose diet increased Prevotella ruminicola compared to the wheat bran diet. Interestingly, the alfalfa group had the lowest abundance of the potential pathogen Streptococcus suis in the cecum and distal colon. These results indicated that a moderate increase in dietary fibres affected the microbial composition in suckling piglets, and that the alfalfa inclusion produced some beneficial effects on the microbial communities.
    Keywords: Environmental Microbiology
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  • 19
    Publication Date: 2016-06-23
    Description: One function of the gut microbiota gaining recent attention, especially in herbivorous mammals and insects, is the metabolism of plant secondary metabolites (PSMs). We investigated whether this function exists within the gut communities of a specialist avian herbivore. We sequenced the cecal metagenome of the Greater Sage-Grouse ( Centrocercus urophasianus ), which specializes on chemically defended sagebrush ( Artemisia spp.). We predicted that the cecal metagenome of the sage-grouse would be enriched in genes associated with the metabolism of PSMs when compared to the metagenome of the domestic chicken. We found that representation of microbial genes associated with ‘xenobiotic degradation and metabolism’ was 3-fold higher in the sage-grouse cecal metagenomes when compared to that of the domestic chicken. Further, we identified a complete metabolic pathway for the degradation of phenol to pyruvate, which was not detected in the metagenomes of the domestic chicken, bovine rumen or 14 species of mammalian herbivores. Evidence of monoterpene degradation (a major class of PSMs in sagebrush) was less definitive, although we did detect genes for several enzymes associated with this process. Overall, our results suggest that the gut microbiota of specialist avian herbivores plays a similar role to the microbiota of mammalian and insect herbivores in degrading PSMs.
    Keywords: Environmental Microbiology
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  • 20
    Publication Date: 2016-06-23
    Description: The activity of levofloxacin against planktonic and biofilm Stenotrophomonas maltophilia cells and the role played by the multidrug efflux pump SmeDEF were evaluated under conditions relevant to the cystic fibrosis (CF) lung. MIC, MBC and MBEC of levofloxacin were assessed, against five CF strains, under ‘standard’ (CLSI-recommended) and ‘CF-like’ (pH 6.8, 5% CO 2 , in a synthetic CF sputum) conditions. Levofloxacin was tested against biofilms at concentrations (10, 50 and 100 μg mL –1 ) corresponding to achievable serum levels and sputum levels by aerosolisation. smeD expression was evaluated, under both conditions, in planktonic and biofilm cells by RT-PCR. The bactericidal effect of levofloxacin was decreased, in three out of five strains tested, under ‘CF-like’ conditions (MBC: 2–4 vs 8–16 μg mL –1 , under ‘standard’ and ‘CF-like’ conditions, respectively). Biofilm was intrinsically resistant to levofloxacin, regardless of conditions tested (MBECs ≥ 100 μg mL –1 for all strains). Only under ‘CF-like’ conditions, smeD expression increased during planktonic-to-biofilm transition, and in biofilm cells compared to stationary planktonic cells. Our findings confirmed that S. maltophilia biofilm is intrinsically resistant to therapeutic concentrations of levofloxacin. Under conditions relevant to CF, smeD overexpression could contribute to levofloxacin resistance. Further studies are warranted to define the clinical relevance of our findings .
    Keywords: Pathogens & Pathogenicity
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  • 21
    Publication Date: 2016-06-23
    Description: Auranofin is an FDA-approved gold-containing compound used for the treatment of rheumatoid arthritis. Recent reports of antimicrobial activity against protozoa and bacteria indicate that auranofin targets the reductive enzyme thioredoxin reductase (TrxR). We evaluated auranofin as well as five auranofin analogs containing N- heterocyclic carbenes (instead of the triethylphosphane present in auranofin) and five gold-carbene controls for their ability to inhibit or kill Helicobacter pylori in vitro . Auranofin completely inhibited bacterial growth at 1.2 μM. Purified H. pylori TrxR was inhibited by auranofin in a cell-free assay (IC 50 ~88 nM). The most active gold(I)- N- heterocyclic carbene compounds exhibited MICs comparable to auranofin against H. pylori (2 μM), while also exhibiting lower toxicities for human embryonic kidney cells (HEK-293T cells). Median toxic concentrations (TC 50 ) were 13–20-fold higher compared to auranofin indicating that they were less cytotoxic. The N- heterocyclic carbene analogs maybe well tolerated, but further evaluation is needed in vivo . Finally, auranofin was synergistic with the antibiotic amoxicillin, suggesting that targeting both the reductive enzyme TrxR and cell wall synthesis may be effective against H. pylori infections.
    Keywords: Pathogens & Pathogenicity
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  • 22
    Publication Date: 2016-06-23
    Description: Intracellular endosymbiotic bacteria are common and can play a crucial role for insect pathology. Therefore, such bacteria could be a potential key to our understanding of major losses of Western honey bees ( Apis mellifera ) colonies. However, the transmission and potential effects of endosymbiotic bacteria in A. mellifera and other Apis spp. are poorly understood. Here, we explore the prevalence and transmission of the genera Arsenophonus , Wolbachia , Spiroplasma and Rickettsia in Apis spp. Colonies of A. mellifera ( N = 33, with 20 eggs from worker brood cells and 100 adult workers each) as well as mated honey bee queens of A. cerana , A. dorsata and A. florea ( N = 12 each) were screened using PCR. While Wolbachia , Spiroplasma and Rickettsia were not detected, Arsenophonus spp. were found in 24.2% of A. mellifera colonies and respective queens as well as in queens of A. dorsata (8.3%) and A. florea (8.3%), but not in A. cerana . The absence of Arsenophonus spp. from reproductive organs of A. mellifera queens and surface-sterilized eggs does not support transovarial vertical transmission. Instead, horizontal transmission is most likely.
    Keywords: Environmental Microbiology
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  • 23
    Publication Date: 2016-05-05
    Description: We study a model of lava flow to determine its thermal and dynamic characteristics from thermal measurements of the lava at its surface. Mathematically this problem is reduced to solving an inverse boundary problem. Namely, using known conditions at one part of the model boundary we determine the missing condition at the remaining part of the boundary. We develop a numerical approach to the mathematical problem in the case of steady-state flow. Assuming that the temperature and the heat flow are prescribed at the upper surface of the model domain, we determine the flow characteristics in the entire model domain using a variational (adjoint) method. We have performed computations of model examples and showed that in the case of smooth input data the lava temperature and the flow velocity can be reconstructed with a high accuracy. As expected, a noise imposed on the smooth input data results in a less accurate solution, but still acceptable below some noise level. Also we analyse the influence of optimization methods on the solution convergence rate. The proposed method for reconstruction of physical parameters of lava flows can also be applied to other problems in geophysical fluid flows.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 24
    Publication Date: 2016-05-06
    Description: Studies of discrete volcanic explosions, that usually last less than 2 or 3 min, have suggested that the partitioning of seismic-acoustic energy is likely related to a range of physical mechanisms that depend on magma properties and other physical constraints such as the location of the fragmentation surface. In this paper, we explore the energy partition of a paroxysmal eruptive phase of Tungurahua volcano that lasted for over 4 hr, on 2006 July 14–15, using seismic-acoustic information recorded by stations on its flanks (near field). We find evidence of a linear scaling between seismic and acoustic energies, with time-dependent intensities, during the sustained explosive phase of the eruption. Furthermore, we argue that this scaling can be explained by two different processes: (1) the fragmentation region ultimately acts as the common source of energy producing both direct seismic waves, that travel through the volcanic edifice, and direct acoustic waves coming from a disturbed atmosphere above the summit; (2) the coupling of acoustic waves with the ground to cause seismic waves. Both processes are concurrent, however we have found that the first one is dominant for seismic records below 4 Hz. Here we use the linear scaling of intensities to construct seismic and acoustic indices, which, we argue, could be used to track an ongoing eruption. Thus, especially in strong paroxysms that can produce pyroclastic flows, the index correlation and their levels can be used as quantitative monitoring parameters to assess the volcanic hazard in real time. Additionally, we suggest from the linear scaling that the source type for both cases, seismic and acoustic, is dipolar and dominant in the near field.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 25
    Publication Date: 2016-05-08
    Description: Legionella feeleii is a Gram-negative pathogenic bacterium that causes Pontiac fever and pneumonia in humans. When L. feeleii serogroup 1 (ATCC 35072) was cultured on BCYE agar plates, two types of colonies were observed and exhibited differences in color, opacity and morphology. Since the two colony types are white rugose and brown translucent, they were termed as white rugose L. feeleii (WRLf) and brown translucent L. feeleii (BTLf), respectively. They exhibited different growth capacities in BYE broth in vitro , and it was found that WRLf could transform to BTLf. Under the electron microscope, it was observed that WRLf secreted materials which could be stained with ruthenium red, which was absent in BTLf. When U937 macrophages and HeLa cells were infected with the bacteria, WRLf manifested stronger internalization ability than BTLf. Intracellular growth in murine macrophages and Acanthamoeba cells was affected by the level of initial phagocytosis. WRLf was more resistant to human serum bactericidal action than BTLf. After being inoculated to guinea pigs, both organisms caused fever in the animals. These results suggest that ruthenium red-stained materials secreted in the surroundings may play a crucial role in determining L. feeleii colony morphology and virulence traits.
    Keywords: Pathogens & Pathogenicity
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  • 26
    Publication Date: 2016-05-12
    Description: Wood-rotting fungi possess remarkably diverse extracellular oxidation mechanisms, including enzymes, such as laccase and peroxidases, and Fenton chemistry. The ability to biologically drive Fenton chemistry by the redox cycling of quinones has previously been reported to be present in both ecologically diverging main groups of wood-rotting basidiomycetes. Therefore, we investigated whether it is even more widespread among fungal organisms. Screening of a diverse selection of a total of 18 ascomycetes and basidiomycetes for reduction of the model compound 2,6-dimethoxy benzoquinone revealed that all investigated strains were capable of reducing it to its corresponding hydroquinone. In a second step, depolymerization of the synthetic polymer polystyrene sulfonate was used as a proxy for quinone-dependent Fenton-based biodegradation capabilities. A diverse subset of the strains, including environmentally ubiquitous molds, white-rot fungi, as well as peatland and aquatic isolates, caused substantial depolymerization indicative for the effective employment of quinone redox cycling as biodegradation tool. Our results may also open up new paths to utilize diverse fungi for the bioremediation of recalcitrant organic pollutants.
    Keywords: Environmental Microbiology
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  • 27
    Publication Date: 2016-05-12
    Description: Piscirickettsia salmonis is a fastidious intracellular pathogen responsible for high mortality rates in farmed salmonids, with serious economic consequences for the Chilean aquaculture industry. Oxytetracycline and florfenicol are the most frequently used antibiotics against P. salmonis , but routine use could contribute to drug resistance. This study identified differentiated florfenicol susceptibilities in two P. salmonis strains, LF-89 and AUSTRAL-005. The less susceptible isolate, AUSTRAL-005, also showed a high ethidium bromide efflux rate, indicating a higher activity of general efflux pump genes than LF-89. The P. salmonis genome presented resistance nodulation division (RND) family members, a family containing typical multidrug resistance-related efflux pumps in Gram-negative bacteria. Additionally, efflux pump acrAB genes were overexpressed in AUSTRAL-005 following exposure to the tolerated maximal concentration of florfenicol, in contrast to LF-89. These results indicate that tolerated maximum concentrations of florfenicol can modulate RND gene expression and increase efflux pump activity. We propose that the acrAB efflux pump is essential for P. salmonis survival at critical florfenicol concentrations and for the generation of antibiotic-resistant bacterial strains.
    Keywords: Pathogens & Pathogenicity
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  • 28
    Publication Date: 2016-05-12
    Description: Ice-binding proteins (IBPs), such as antifreeze proteins (AFPs) and ice-nucleating proteins (INPs), have been described in diverse cold-adapted organisms, and their potential applications in biotechnology have been recognized in various fields. Currently, both IBPs are being applied to biotechnological processes, primarily in medicine and the food industry. However, our knowledge regarding the diversity of bacterial IBPs is limited; few studies have purified and characterized AFPs and INPs from bacteria. Phenotypically verified IBPs have been described in members belonging to Gammaproteobacteria, Actinobacteria and Flavobacteriia classes, whereas putative IBPs have been found in Gammaproteobacteria, Alphaproteobacteria and Bacilli classes. Thus, the main goal of this minireview is to summarize the current information on bacterial IBPs and their application in biotechnology, emphasizing the potential application in less explored fields such as agriculture. Investigations have suggested the use of INP-producing bacteria antagonists and AFPs-producing bacteria (or their AFPs) as a very attractive strategy to prevent frost damages in crops. UniProt database analyses of reported IBPs (phenotypically verified) and putative IBPs also show the limited information available on bacterial IBPs and indicate that major studies are required.
    Keywords: Environmental Microbiology
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  • 29
    Publication Date: 2016-05-12
    Description: Triazophos is a broad-spectrum and highly effective insecticide, and the residues of triazophos have been frequently detected in the environment. A triazophos-degrading bacterium, Burkholderia sp. SZL-1, was isolated from a long-term triazophos-polluted soil. Strain SZL-1 could hydrolyze triazophos to 1-phenyl-3-hydroxy-1,2,4-triazole, which was further utilized as the carbon sources for growth. The triazophos hydrolase gene trhA , cloned from strain SZL-1, was expressed and homogenously purified using Ni-nitrilotriacetic acid affinity chromatography. TrhA is 55 kDa and displays maximum activity at 25°C, pH 8.0. This enzyme still has nearly 60% activity at the range of 15°C–50°C for 30 min. TrhA was mutated by sequential error prone PCR and screened for improved activity for triazophos degradation. One purified variant protein (Val89-Gly89) named TrhA-M1 showed up to 3-fold improvement in specific activity against triazophos, and the specificity constants of K cat and K cat / K m for TrhA-M1 were improved up to 2.3- and 8.28-fold, respectively, compared to the wild-type enzyme. The results in this paper provided potential material for the contaminated soil remediation and hydrolase genetic structure research.
    Keywords: Environmental Microbiology
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  • 30
    Publication Date: 2016-05-12
    Description: Pseudomonas aeruginosa is an opportunistic pathogen, known to develop robust biofilms. Its biofilm development increases when antibiotics are presented at subminimal inhibitory concentrations (MICs) for reasons that remain unclear. In order to identify genes that affect biofilm development under such a sublethal antibiotic stress condition, we screened a transposon (Tn) mutant library of PAO1, a prototype P. aeruginosa strain. Among ~5000 mutants, a fiuA gene mutant was verified to form very defective biofilms in the presence of sub-MIC carbenicillin. The fiuA gene encodes ferrichrome receptor A, involved in the iron acquisition process. Of note, biofilm formation was not decreased in the pchpvd mutant defective in the production of pyochelin and pyoverdine, two well-characterized P. aeruginosa siderophore molecules. Moreover, fiuA , a non-polar fiuA deletion mutant, produced a significantly decreased level of elastase, a major virulence determinant. Mouse airway infection experiments revealed that the mutant expressed significantly less pathogenicity. Our results suggest that the fiuA gene has pleiotropic functions that affect P. aeruginosa biofilm development and virulence. The targeting of FiuA could enable the attenuation of P. aeruginosa virulence and may be suitable for the development of a drug that specifically controls the virulence of this important pathogen.
    Keywords: Pathogens & Pathogenicity
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  • 31
    Publication Date: 2016-05-12
    Description: The metal mining industry faces many large challenges in future years, among which is the increasing need to process low-grade ores as accessible higher grade ores become depleted. This is against a backdrop of increasing global demands for base and precious metals, and rare earth elements. Typically about 99% of solid material hauled to, and ground at, the land surface currently ends up as waste (rock dumps and mineral tailings). Exposure of these to air and water frequently leads to the formation of acidic, metal-contaminated run-off waters, referred to as acid mine drainage, which constitutes a severe threat to the environment. Formation of acid drainage is a natural phenomenon involving various species of lithotrophic (literally ‘rock-eating’) bacteria and archaea, which oxidize reduced forms of iron and/or sulfur. However, other microorganisms that reduce inorganic sulfur compounds can essentially reverse this process. These microorganisms can be applied on industrial scale to precipitate metals from industrial mineral leachates and acid mine drainage streams, resulting in a net improvement in metal recovery, while minimizing the amounts of leachable metals to the tailings storage dams. Here, we advocate that more extensive exploitation of microorganisms in metal mining operations could be an important way to green up the industry, reducing environmental risks and improving the efficiency and the economy of metal recovery.
    Keywords: Environmental Microbiology
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  • 32
    Publication Date: 2016-04-01
    Description: Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested on Nitrosopumilus maritimus , two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representative Nitrosomonas europaea . All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway.
    Keywords: Environmental Microbiology
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  • 33
    Publication Date: 2016-04-08
    Description: Activating transcription factor 3 (ATF3) is a stress-induced transcriptional regulator in eukaryote. The role of ATF3 in cancer has been well defined, but how ATF3 functions in bacterial infection is not well understood. Pneumococcal infection has been shown to induce ATF3 expression, which subsequently enhances cytokine production and provides protection from lethal Streptococcus pneumoniae infection, but the role of ATF3 in other Gram-positive (G + ) infections remains unclear. Here, we report that infection with other G + bacteria ( Staphylococcus aureus and Listeria monocytogenes ) and with G – bacteria (uropathogenic Escherichia coli ) also significantly induced ATF3 expression. Moreover, the production of cytokines (tumor necrosis factor alpha [TNF]-α, interleukin [IL]-1β, IL-6 and interferon [IFN]-) was enhanced by ATF3 in S. aureus and L. monocytogenes infection, but decreased in uropathogenic E. coli (UPEC) infection. In addition, in S. aureus and L. monocytogenes infections, ATF3 WT mice cleared bacteria more efficiently and had higher survival rates than ATF3 knockout mice. However, in UPEC infection, no significant difference was found in survival rate. Taken together, these data suggest that ATF3 provides protection from S. aureus and L. monocytogenes infections; however, the role of ATF3 in UPEC infection is more complicated and should be further elucidated.
    Keywords: Pathogens & Pathogenicity
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  • 34
    Publication Date: 2016-07-02
    Description: Peatlands of all latitudes play an integral role in global climate change by serving as a carbon sink and a primary source of atmospheric methane; however, the microbial ecology of mid-latitude peatlands is vastly understudied. Herein, next generation Illumina amplicon sequencing of small subunit rRNA genes was utilized to elucidate the microbial communities in three southern Appalachian peatlands. In contrast to northern peatlands, Proteobacteria dominated over Acidobacteria in all three sites. An average of 11 bacterial phyla was detected at relative abundance values 〉1%, with three candidate divisions (OP3, WS3 and NC10) represented, indicating high phylogenetic diversity. Physiological traits of isolates within the candidate alphaproteobacterial order, Ellin 329, obtained here and in previous studies indicate that bacteria of this order may be involved in hydrolysis of poly-, di- and monosaccharides. Community analyses indicate that Ellin 329 is the third most abundant order and is most abundant near the surface layers where plant litter decomposition should be primarily occurring. In sum, members of Ellin 329 likely play important roles in organic matter decomposition, in southern Appalachian peatlands and should be investigated further in other peatlands and ecosystem types.
    Keywords: Environmental Microbiology
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  • 35
    Publication Date: 2016-07-02
    Description: Marine viruses are the most abundant biological entity in the oceans, the majority of which infect bacteria and are known as bacteriophages. Yet, the bulk of bacteriophages form part of the vast uncultured dark matter of the microbial biosphere. In spite of the paucity of cultured marine bacteriophages, it is known that marine bacteriophages have major impacts on microbial population structure and the biogeochemical cycling of key elements. Despite the ecological relevance of marine bacteriophages, there are relatively few isolates with complete genome sequences. This minireview focuses on knowledge gathered from these genomes put in the context of viral metagenomic data and highlights key advances in the field, particularly focusing on genome structure and auxiliary metabolic genes.
    Keywords: Environmental Microbiology
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  • 36
    Publication Date: 2016-07-02
    Description: The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants ( Erepsia anceps , Phaenocoma prolifera and Leucadendron laureolum ). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera , whereas Deinococcus-Thermus dominated in L. laureolum , revealing species-specific host–bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth.
    Keywords: Environmental Microbiology
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  • 37
    Publication Date: 2016-07-02
    Description: The presence of carbapenemase gene bla KPC-2 in a wide variety of plasmids, especially conjugative plasmids, is key to the rapid, worldwide spread of carbapenemase enzymes. Thirty-eight, non-duplicated, carbapenem-resistant, clinical Klebsiella pneumoniae isolates were collected, all carrying bla KPC-2 -bearing plasmids. Relaxase analysis was used to classify these plasmids; 8 and 30 plasmids belonged to the MOB P3 and MOB F12 subfamilies, respectively. Phylogenetic analysis revealed two genetic subclades in the MOB F12 subfamily and suggested that these subclades might not have originated from the same ancestor. Crossing PCR, used to sequence fully the type IV secretion system (T4SS, essential structures for conjugative plasmids) of the MOB F12 plasmids, found that T4SSs were distinctively different in certain functional genes, e.g. traS and traG. In conclusion, this study delineated the evolution of bla KPC-2 -bearing plasmids at Huashan Hospital, Shanghai, China. The plasmids bearing bla KPC-2 were diverse and the MOB F12 plasmids were dominant in clinical K. pneumoniae isolates.
    Keywords: Pathogens & Pathogenicity
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  • 38
    Publication Date: 2016-07-03
    Description: The functioning of many natural and engineered environments is dependent on long distance electron transfer mediated through electrical currents. These currents have been observed in exoelectrogenic biofilms and it has been proposed that microbial biofilms can mediate electron transfer via electrical currents on the centimeter scale. However, direct evidence to confirm this hypothesis has not been demonstrated and the longest known electrical transfer distance for single species exoelectrogenic biofilms is limited to 100 μm. In the present study, biofilms were developed on electrodes with electrically non-conductive gaps from 50 μm to 1 mm and the in situ conductance of biofilms was evaluated over time. Results demonstrated that the exoelectrogenic mixed species biofilms in the present study possess the ability to transfer electrons through electrical currents over a distance of up to 1 mm, 10 times further than previously observed. Results indicate the possibility of interspecies interactions playing an important role in the spatial development of exoelectrogenic biofilms, suggesting that these biological networks might remain conductive even at longer distance. These findings have significant implications in regards to future optimization of microbial electrochemical systems.
    Keywords: Environmental Microbiology
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  • 39
    Publication Date: 2016-08-20
    Description: Concerns about the growing prevalence of obesity worldwide have led researchers and policy makers to investigate the potential health impact of fiscal policies such as taxes on unhealthy foods. A common instrument used to measure the relationship between food prices and food consumption is the price elasticity of demand. Using meta-regression analysis we assessed how differences in methodological approaches to estimating demand affected food price elasticities. Most methodological differences had a statistically significant impact on elasticity estimates, which stresses the importance of using meta-estimates or testing the sensitivity of simulation outcomes to a range of elasticity parameters before drawing policy conclusions.
    Keywords: D11 - Consumer Economics: Theory, H31 - Household, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 40
    Publication Date: 2016-08-28
    Description: Enteroaggregative Escherichia coli (EAEC) is an important diarrhoeal pathogen causing diseases in multiple epidemiological and clinical settings. In developing countries like India, diarrhoeal diseases are one of the major killers among paediatric population and oddly, few studies are available from Indian paediatric population on the variability of EAEC virulence genes. In this study, we examined the distribution of plasmid and chromosomal-encoded virulence determinants in EAEC isolates, and analysed cytokines response generated against EAEC with specific aggregative adherence fimbriae (AAF) type in duodenal biopsies using in vitro organ culture (IVOC) mimicking in vivo conditions. Different virulence marker combinations among strains were reflected as a function of specific adhesins signifying EAEC heterogeneity. fis gene emerged as an important genetic marker apart from aggA and aap . Further, EAEC infection in IVOC showed upregulation of IL-8, IL-1β, IL-6, TNF-α and TLR-5 expression. EAEC with AAFII induced significant TLR-5 and IL-8 response, conceivably owing to more pathogenicity markers. This study sheds light on the pattern of EAEC pathotypes prevalent in North Indian paediatric population and highlights the presence of unique virulence combinations in pathogenic strains. Thus, evident diversity in EAEC virulence and multifaceted bacteria-host crosstalk can provide useful insights for the strategic management of diarrhoeal diseases in India, where diarrhoeal outbreaks are more frequent.
    Keywords: Pathogens & Pathogenicity
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  • 41
    Publication Date: 2016-08-28
    Description: Bacteriophages are increasingly being used as water quality indicators. Two groups of phages infecting Escherichia coli , somatic and F-specific coliphages, are being considered as indicators of fecal and viral contamination for several types of water around the world. However, some uncertainties remain regarding which coliphages to assess. Recently, E. coli strain CB390 has been reported to be suitable for simultaneous detection of both groups, which seems to be more informative than determining only one of the groups. Here, a significant number of samples from different settings, mostly those where F-specific phages have been reported to outnumber somatic coliphages, are analyzed for somatic coliphages, F-specific RNA phages by standardized methods and coliphages detected by host strain CB390. The results presented here confirm that the numbers of phages counted using CB390 are equivalent to the sum of the somatic and F-specific coliphages counted independently in all settings. Hence the usefulness of this strain for simultaneous detection of somatic and F-specific coliphages is confirmed. Also, sets of data on the presence of coliphages in reclaimed and groundwater are reported.
    Keywords: Environmental Microbiology
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  • 42
    Publication Date: 2016-06-19
    Description: The expansion of offshore renewable energy infrastructure and the need for trans-continental shelf power transmission require the use of submarine high-voltage (HV) cables. These cables have maximum operating surface temperatures of up to 70 °C and are typically buried 1–2 m beneath the seabed, within the wide range of substrates found on the continental shelf. However, the heat flow pattern and potential effects on the sedimentary environments around such anomalously high heat sources in the near-surface sediments are poorly understood. We present temperature measurements from a 2-D laboratory experiment representing a buried submarine HV cable, and identify the thermal regimes generated within typical unconsolidated shelf sediments—coarse silt, fine sand and very coarse sand. We used a large (2 x 2.5 m 2 ) tank filled with water-saturated spherical glass beads (ballotini) and instrumented with a buried heat source and 120 thermocouples to measure the time-dependent 2-D temperature distributions. The observed and corresponding Finite Element Method simulations of the steady state heat flow regimes and normalized radial temperature distributions were assessed. Our results show that the heat transfer and thus temperature fields generated from submarine HV cables buried within a range of sediments are highly variable. Coarse silts are shown to be purely conductive, producing temperature increases of 〉10 °C up to 40 cm from the source of 60 °C above ambient; fine sands demonstrate a transition from conductive to convective heat transfer between cf. 20 and 36 °C above ambient, with 〉10 °C heat increases occurring over a metre from the source of 55 °C above ambient; and very coarse sands exhibit dominantly convective heat transfer even at very low ( cf. 7 °C) operating temperatures and reaching temperatures of up to 18 °C above ambient at a metre from the source at surface temperatures of only 18 °C. These findings are important for the surrounding near-surface environments experiencing such high temperatures and may have significant implications for chemical and physical processes operating at the grain and subgrain scale; biological activity at both microfaunal and macrofaunal levels; and indeed the operational performance of the cables themselves, as convective heat transport would increase cable current ratings, something neglected in existing standards.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 43
    Publication Date: 2016-06-04
    Description: It is well known that Methylosinus trichosporium OB3b has two forms of methane monooxygenase (MMO) responsible for the initial conversion of methane to methanol, a cytoplasmic (soluble) methane monooxygenase and a membrane-associated (particulate) methane monooxygenase, and that copper strongly regulates expression of these alternative forms of MMO. More recently, it has been discovered that M. trichosporium OB3b has multiple types of the methanol dehydrogenase (MeDH), i.e. the Mxa-type MeDH (Mxa-MeDH) and Xox-type MeDH (Xox-MeDH), and the expression of these two forms is regulated by the availability of the rare earth element (REE), cerium. Here, we extend these studies and show that lanthanum, praseodymium, neodymium and samarium also regulate expression of alternative forms of MeDH. The effect of these REEs on MeDH expression, however, was only observed in the absence of copper. Further, a mutant of M. trichosporium OB3b, where the Mxa-MeDH was knocked out, was able to grow in the presence of lanthanum, praseodymium and neodymium, but was not able to grow in the presence of samarium. Collectively, these data suggest that multiple levels of gene regulation by metals exist in M. trichosporium OB3b, but that copper overrides the effect of other metals by an as yet unknown mechanism.
    Keywords: Environmental Microbiology
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  • 44
    Publication Date: 2016-06-17
    Description: Coagulase-negative staphylococci are thought to act as reservoirs of antibiotic resistance genes that can be transferred to Staphylococcus aureus , thus hindering the combat of this bacterium. In this work, we analyzed the presence of plasmids conferring resistance to the antibiotic mupirocin—widely used to treat and prevent S. aureus infections in hospital environments—in nosocomial S. haemolyticus strains. About 12% of the 75 strains tested were resistant to mupirocin, and this phenotype was correlated with the presence of plasmids. These plasmids were shown to be diverse, being either conjugative or mobilizable, and capable of transferring mupirocin resistance to S. aureus . Our findings reinforce that S. haemolyticus , historically and mistakenly considered as a less important pathogen, is a reservoir of resistance genes which can be transferred to other bacteria, such as S. aureus , emphasizing the necessity of more effective strategies to detect and combat this emergent opportunistic pathogen.
    Keywords: Pathogens & Pathogenicity
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  • 45
    Publication Date: 2016-06-17
    Description: Emergence of races in Fusarium oxysporum f. sp. lycopersici ( Fol ) is caused by loss or mutation of at least one avirulence ( AVR ) gene. The product of AVR1 is a small protein (Avr1) secreted by Fol in tomato xylem sap during infection. This protein triggers Fol race 1 specific resistance (I) in tomato, indicating that AVR1 is an AVR gene. Deletion of AVR1 in race 1 resulted in the emergence of race 2, and an additional mutation in AVR2 generated race 3. Previously, we reported a new biotype of race 3, KoChi-1, in which AVR1 was truncated by a transposon Hormin , which suggested a new route to evolution of races in Fol . However, to date no race 2 isolate carrying Hormin -truncated AVR1 has been reported. In this report, we describe such isolates, represented by Chiba-5, in which Hormin insertion occurred in AVR1 at a position different from that in KoChi-1. AVR1 truncation in both isolates resulted in production of defective Avr1 proteins. Chiba-5 and KoChi-1 belong to different phylogenetic clades, A1 and A2, respectively, suggesting that insertion of Hormin in AVR1 in Chiba-5 and KoChi-1 occurred as independent evolutionary events.
    Keywords: Pathogens & Pathogenicity
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  • 46
    Publication Date: 2016-09-02
    Description: The LBIT-1200 strain of Bacillus thuringiensis was recently isolated from soil, and showed a 6.4 and 9.5 increase in toxicity, against Manduca sexta and Trichoplusia ni , respectively, compared to HD-73. However, LBIT-1200 was still highly similar to HD-73, including the production of bipyramidal crystals containing only one protein of ~130 000 kDa, its flagellin gene sequence related to the kurstaki serotype, plasmid and RepPCR patterns similar to HD-73, no production of β-exotoxin and no presence of VIP genes. Sequencing of its cry gene showed the presence of a cry1Ac -type gene with four amino acid differences, including two amino acid replacements in domain III, compared to Cry1Ac1, which may explain its higher toxicity. In conclusion, the LBIT-1200 strain is a variant of the HD-73 strain but shows a much higher toxicity, which makes this new strain an important candidate to be developed as a bioinsecticide, once it passes other tests, throughout its biotechnological development.
    Keywords: Pathogens & Pathogenicity
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  • 47
    Publication Date: 2016-09-14
    Description: Gastrointestinal (GI) leakage in Clostridium difficile -associated diarrhea (CDAD) is well known but is not routinely assessed in clinical practice. Serum (1-〉3)-β-D-glucan (BG), a fungal cell wall component used as a biomarker for invasive fungal disease, was tested in a CDAD mouse model with and without probiotics. Higher serum fluorescein isothiocyanate-dextran (FITC-dextran) and spontaneous gram-negative bacteremia, GI leakage indicators, were frequently found in CDAD mice, which died compared with those which survived. BG, serum macrophage inflammatory protein-2 and FITC-dextran but not quantitative blood bacterial count differentiated the clinical severity. Interestingly, a specific dose of Lactobacillus rhamnosus L34 attenuated CDAD and decreased serum BG and FITC-dextran, but not other parameters. BG also showed a higher area under the receiver operating characteristic curve for 7-day mortality than FITC-dextran. Fifty-five percent of CDAD mice with BG ≥ 60 pg/ml (the human negative cut-off value for invasive fungal disease) at 1 day after C. difficile gavage died within 7 days. In conclusion, s erum BG was elevated in mice with severe CDAD, an established model of GI leakage with a strong association with mortality rate. BG monitoring in patients with CDAD is of interest as both a potential prognostic tool and a therapeutic efficacy indicator.
    Keywords: Pathogens & Pathogenicity
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  • 48
    Publication Date: 2016-08-20
    Description: This paper reviews the situation in the agricultural sector and food security in Cuba, and particularly the transformations that have (not) taken place since 1990. We compare the Cuban transition with transitions in other "transition countries" and show that Cuba does not easily fit into one of the transition patterns, and, in a way, has characteristics of "a bit of everything". To conclude, we discuss the (potential) effects of the recent policy changes and the new economic reforms that were announced.
    Keywords: O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, P21 - Planning, Coordination, and Reform, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 49
    Publication Date: 2016-08-28
    Description: Chlamydial species are common intracellular parasites that cause various diseases, mainly characterized by persistent infection, which lead to inflammatory responses modulated by pattern recognition receptors (PRRs). The best understood PRRs are the extracellular Toll-like receptors, but recent significant advances have focused on two important proteins, NOD1 and NOD2, which are members of the intracellular nucleotide-binding oligomerization domain receptor family and are capable of triggering the host innate immune signaling pathways. This results in the production of pro-inflammatory cytokines, which is vital for an adequate host defense against intracellular chlamydial infection. NOD1/2 ligands are known to derive from peptidoglycan, and the latest research has resolved the paradox of whether chlamydial species possess this bacterial cell wall component; this finding is likely to promote in-depth investigations into the interaction between the NOD proteins and chlamydial pathogens. In this review, we summarize the basic characteristics and signal transduction functions of NOD1 and NOD2 and highlight the new research on the roles of NOD1 and NOD2 in the host defense against chlamydial infection.
    Keywords: Pathogens & Pathogenicity
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  • 50
    Publication Date: 2016-08-28
    Description: Two strains of Aeromonas salmonicida , YK and BG, were isolated from largemouth bronze gudgeon and northern whitefish in China, and identified as A. salmonicida subsp. salmonicida based on phylogenetic analysis of vapA and 16S rRNA gene sequences. YK and BG originated from freshwater fish, one of which belonged to the cyprinid family, and the strains showed a difference in virulence. Subsequently, we performed whole genome sequencing of the strains, and comparison of their genomic sequences to the genome of the A449 reference strain revealed various genomic rearrangements, including a new variant of the genomic island AsaGEI in BG, designated as AsaGEI2c . This is the first report on a GEI of A. salmonicida strain from China. Furthermore, both YK and BG strains contained a Tn7 transposon inserted at the same position in the chromosome. Finally, IS-dependent rearrangements on pAsa5 are deemed likely to have occurred, with omission of the resD gene in both strains as well as omission of genes related to the IncF conjugal transfer system in the YK isolate. This study demonstrates that A. salmonicida subsp. salmonicida can infect non-salmonids (cyprinids) in addition to salmonids, and that AsaGEI2c might be useful as a geographical indicator of Chinese A. salmonicida subsp. salmonicida isolates.
    Keywords: Pathogens & Pathogenicity
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  • 51
    Publication Date: 2016-07-09
    Description: If agricultural subsidies are largely capitalized into farmland values through their effect on rental rates, then expanding support for agriculture may not benefit farmers who rent the land they farm. Existing evidence on the incidence of subsidies on cash rental rates is mixed. Identification is obscured by unobserved or imprecisely measured factors that tend to be correlated with subsidies, especially land quality and time-varying factors like commodity prices and adverse weather events. A problem that has received less attention is the fact that subsidies and land quality on rented land may differ from owned land. Since most farms possess both rented and owned acreage, farm-level measures of subsidies, land values, and rental rates may bias estimated incidence. Using a new, field-level data set that, for the first time, precisely links subsidies to land parcels, we show that this bias is considerable: where farm-level estimates suggest an incidence of 42–49 cents of the marginal subsidy dollar, field-level estimates from the same farms indicate that landlords capture just 20–28 cents. The size of the farm and the duration of the rental arrangement have substantial effects. Incidence falls by 5–15 cents when doubling total operated acres, and the incidence falls by 0.1–0.8 cents with each additional year of the rental arrangement. Low incidence of subsidies on rents combined with the farm-size and duration effects suggest that farmers renting land have monopsony power.
    Keywords: H22 - Incidence, Q14 - Agricultural Finance, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 52
    Publication Date: 2016-07-09
    Description: Many countries adjust their trade policies counter-cyclically with food prices, to the extent that the use of restrictions by food-exporting countries has occasionally threatened the food security of food-importing countries. These trade policies are inconsistent with the terms-of-trade motivation often retained to characterize the payoff frontier of self-enforcing trade agreements, as they can worsen the terms of trade of the countries that apply them. This article analyzes trade policy coordination when trade policies are driven by terms-of-trade effects and a desire to reduce domestic food price volatility. This framework implies that importing and exporting countries have incentives to deviate from cooperation at different periods: the latter when prices are high and the former when prices are low. Since staple food prices tend to have asymmetric distributions, with more prices below than above the mean but with occasional spikes, a self-enforcing agreement generates asymmetric outcomes. Without cooperation, an importing country uses its trade policy more frequently because of the concentration of prices below the mean, but an exporting country has a greater incentive to deviate from a cooperative trade policy because positive deviations from the mean price are larger than negative ones. Thus, the asymmetry of the distribution of commodity prices can make it more difficult to discipline export taxes than tariffs in trade agreements.
    Keywords: F13 - Trade Policy ; International Trade Organizations, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 53
    Publication Date: 2016-07-09
    Description: Burkholderia pseudomallei is an intracellular Gram-negative bacterial pathogen and the causative agent of melioidosis, a widespread disease in Southeast Asia. Reactive nitrogen, in an intermediate form of nitric oxide (NO), is one of the first lines of defense used by host cells to eliminate intracellular pathogens, through the stimulation of inducible nitric oxide synthase (iNOS). Studies in phagocytotic cells have shown that the iNOS response is muted in B. pseudomallei infection, and implicated the rpoS sigma factor as a key regulatory factor mediating suppression. The liver is a main visceral organ affected by B. pseudomallei , and there is little knowledge about the interaction of liver cells and B. pseudomallei . This study investigated the induction of iNOS, as well as autophagic flux and light-chain 3 (LC3) localization in human liver (HC04) cells in response to infection with B. pseudomallei and its rpoS deficient mutant. Results showed that the rpoS mutant was unable to suppress iNOS induction and that the mutant showed less induction of autophagy and lower co-localization with LC3, and this was coupled with a lower intracellular growth rate. Combining these results suggest that B. pseudomallei rpoS is an important factor in establishing infection in liver cells.
    Keywords: Pathogens & Pathogenicity
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  • 54
    Publication Date: 2016-05-12
    Description: Polysulfides (S x 2– ) are sulfide oxidation intermediates that are important for a variety of environmentally relevant processes including pyrite formation, organic matter sulfidization, isotope exchange among reduced sulfur species, and metal chelation. In addition to their chemical reactivity, laboratory experiments with microbial cultures and enzymes indicate both indirect and direct roles for microorganisms in affecting polysulfide chemistry in natural environments through production and consumption. As polysulfides have been detected in a wide array of natural systems ranging from microbial mats to hydrothermal vents, constraining their biogeochemical cycling has broad impacts. However, many questions remain regarding the processes responsible for polysulfide dynamics in these environments and the precise role that microorganisms play in these processes. This review provides a summary of laboratory experiments investigating the role of polysulfides in microbial metabolism, and observations of polysulfides in the environment in order to provide further insight into and highlight open questions about this significant component of the sulfur cycle.
    Keywords: Environmental Microbiology
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  • 55
    Publication Date: 2016-07-09
    Description: We analyze the effects of the interactions that the two pillars of the European Union Common Agricultural Policy—market support and rural development—have on farmers’ uptake of organic farming practices. Special attention is given to the 2003 reform, which substantially altered the relative importance of the two types of support by decoupling direct agricultural payments from the production of a specific crop. In our empirical analysis we study the case of Sweden, making use of the variation in the timing of farmers’ decisions regarding participation in support programs. We estimate a dynamic non-linear unobserved effects probit model to account for unobserved individual heterogeneity and state dependence. Our results indicate the existence of a negative effect of the market support system in place when organic farming techniques were adopted before the 2003 reform. However, this effect is reversed by the introduction of decoupling. Furthermore, the effects of support differ between certified and non-certified organic production: both pillars have significant effects on non-certified organic farming, whereas certified organic farming is exclusively driven by agro-environmental subsidies.
    Keywords: C23 - Models with Panel Data, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 56
    Publication Date: 2016-02-20
    Description: A total of 65 spore-forming mercury-resistant bacteria were isolated from natural environments worldwide in order to understand the acquisition of additional genes by and dissemination of mercury resistance transposons across related Bacilli genera by horizontal gene movement. PCR amplification using a single primer complementary to the inverted repeat sequence of Tn MERI1 -like transposons showed that 12 of 65 isolates had a transposon-like structure. There were four types of amplified fragments: Tn 5084 , Tn 5085 , Tn d MER3 (a newly identified deleted transposon-like fragment) and Tn 6294 (a newly identified transposon). Tn d MER3 is a 3.5-kb sequence that carries a merRETPA operon with no merB or transposase genes. It is related to the mer operon of Bacillus licheniformis strain FA6-12 from Russia. DNA homology analysis shows that Tn 6294 is an 8.5-kb sequence that is possibly derived from Tn d MER3 by integration of a Tn MERI1 -type transposase and resolvase genes and in addition the merR2 and merB1 genes. Bacteria harboring Tn 6294 exhibited broad-spectrum mercury resistance to organomercurial compounds, although Tn 6294 had only merB1 and did not have the merB2 and merB3 sequences for organomercurial lyases found in Tn 5084 of B. cereus strain RC607. Strains with Tn 6294 encode mercuric reductase (MerA) of less than 600 amino acids in length with a single N-terminal mercury-binding domain, whereas MerA encoded by strains MB1 and RC607 has two tandem domains. Thus, Tn d MER3 and Tn 6294 are shorter prototypes for Tn MERI1 -like transposons. Identification of Tn 6294 in Bacillus sp. from Taiwan and in Paenibacillus sp. from Antarctica indicates the wide horizontal dissemination of Tn MERI1 -like transposons across bacterial species and geographical barriers.
    Keywords: Environmental Microbiology
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  • 57
    Publication Date: 2016-02-07
    Description: Fungi may play an important role in the production of the greenhouse gas nitrous oxide (N 2 O). Bipolaris sorokiniana is a ubiquitous saprobe found in soils worldwide, yet denitrification by this fungal strain has not previously been reported. We aimed to test if B. sorokiniana would produce N 2 O and CO 2 in the presence of organic and inorganic forms of nitrogen (N) under microaerobic and anaerobic conditions. Nitrogen source (organic-N, inorganic-N, no-N control) significantly affected N 2 O and CO 2 production both in the presence and absence of oxygen, which contrasts with bacterial denitrification. Inorganic N addition increased denitrification of N 2 O (from 0 to 0.3 μg N 2 0-N h –1  g –1 biomass) and reduced respiration of CO 2 (from 0.1 to 0.02 mg CO 2 h –1  g –1 biomass). Isotope analyses indicated that nitrite, rather than ammonium or glutamine, was transformed to N 2 O. Results suggest the source of N may play a larger role in fungal N 2 O production than oxygen status.
    Keywords: Environmental Microbiology
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  • 58
    Publication Date: 2016-02-20
    Description: Bacteriophages are viruses that infect bacteria. There are an estimated 10 31 phage on the planet, making them the most abundant form of life. We are rapidly approaching the centenary of their identification, and yet still have only a limited understanding of their role in the ecology and evolution of bacterial populations. Temperate prophage carriage is often associated with increased bacterial virulence. The rise in use of technologies, such as genome sequencing and transcriptomics, has highlighted more subtle ways in which prophages contribute to pathogenicity. This review discusses the current knowledge of the multifaceted effects that phage can exert on their hosts and how this may contribute to bacterial adaptation during infection.
    Keywords: Pathogens & Pathogenicity
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  • 59
    Publication Date: 2016-02-20
    Description: Legionella pneumophila is a pathogenic bacterium commonly found in water and responsible for severe pneumonia. Free-living amoebae are protozoa also found in water, which feed on bacteria by phagocytosis. Under favorable conditions, some L. pneumophila are able to resist phagocytic digestion and even multiply within amoebae. However, it is not clear whether L. pneumophila could infect at a same rate a large range of amoebae or if there is some selectivity towards specific amoebal genera or strains. Also, most studies have been performed using collection strains and not with freshly isolated strains. In our study, we assess the permissiveness of freshly isolated environmental strains of amoebae, belonging to three common genera (i.e. Acanthamoeba, Naegleria and Vermamoeba ), for growth of L. pneumophila at three different temperatures. Our results indicated that all the tested strains of amoebae were permissive to L. pneumophila Lens and that there was no significant difference between the strains. Intracellular proliferation was more efficient at a temperature of 40°C. In conclusion, our work suggests that, under favorable conditions, virulent strains of L. pneumophila could equally infect a large number of isolates of common freshwater amoeba genera.
    Keywords: Environmental Microbiology
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  • 60
    Publication Date: 2016-02-20
    Description: Phthiocerol dimycocerosates (PDIMs) and phenolic glycolipids (PGLs) contribute to the pathogenicity of several mycobacteria. Biosynthesis of these virulence factors requires polyketide synthases and other enzymes that represent potential targets for the development of adjuvant antivirulence drugs. We used six isogenic Mycobacterium marinum mutants, each with a different gene knockout in the PDIM/PGL biosynthetic pathway, to probe the pleiotropy of mutations leading to PDIM – PGL – , PDIM + PGL – or PDIM – PGL + phenotypes. We evaluated the M. marinum mutants for changes in antibiotic susceptibility, cell envelope permeability, biofilm formation, surface properties, sliding motility and virulence in an amoeba model. The analysis also permitted us to begin exploring the hypothesis that different gene knockouts rendering the same PDIM and/or PGL deficiency phenotypes lead to M. marinum mutants with equivalent pleiotropic profiles. Overall, the results of our study revealed a complex picture of pleiotropic patterns emerging from different gene knockouts, uncovered unexpected phenotypic inequalities between mutants, and provided new insight into the phenotypic consequences of gene knockouts in the PDIM/PGL biosynthetic pathway.
    Keywords: Pathogens & Pathogenicity
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  • 61
    Publication Date: 2016-02-20
    Description: Culture medium from an isolate of the fungus Aspergillus candidus was extracted, fractionated and examined to discover compounds antagonistic to plant-parasitic nematodes that are important pathogens of agricultural crops. Column, thin layer and preparative chromatographies and spectral and elemental analyses, were used to isolate and identify two major constituents of an active fraction (Fraction F) obtained from the medium. Compound 1 was identified as 2-hydroxypropane-1, 2, 3-tricarboxylic acid (citric acid). Compound 2 was identified as 3-hydroxy-5-methoxy-3-(methoxycarbonyl)-5-oxopentanoic acid, an isomer of 1, 2-dimethyl citrate. Compound 1 and a citric acid standard, each tested at 50 mg mL –1 in water, decreased hatch from eggs of the plant-parasitic nematode Meloidogyne incognita by more than 94%, and completely immobilized second-stage juveniles after 4–6 days exposure. Fraction F and Compounds 1 and 2 decreased the mobility of adults of the plant-parasitic nematode Ditylenchus destructor in vitro . Fraction F (25 mg mL –1 ) inhibited mobility 〉99% at 72 hrs. Compounds 1 and 2 (50 mg mL –1 ) each inhibited mobility more than 25% at 24 hr and more than 50% at 72 hr. This is the first assignment of nematode-antagonistic properties to specifically identified A. candidus metabolites.
    Keywords: Pathogens & Pathogenicity
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  • 62
    Publication Date: 2016-03-03
    Description: The presence of calcite in and near faults, as the dominant material, cement, or vein fill, indicates that the mechanical behaviour of carbonate-dominated material likely plays an important role in shallow- and mid-crustal faulting. To better understand the behaviour of calcite, under loading conditions relevant to earthquake nucleation, we sheared powdered gouge of Carrara Marble, 〉98 per cent CaCO 3 , at constant normal stresses between 1 and 100 MPa under water-saturated conditions at room temperature. We performed slide-hold-slide tests, 1–3000 s, to measure the amount of static frictional strengthening and creep relaxation, and velocity-stepping tests, 0.1–1000 μm s –1 , to evaluate frictional stability. We observe that the rates of frictional strengthening and creep relaxation decrease with increasing normal stress and diverge as shear velocity is increased from 1 to 3000 μm s –1 during slide-hold-slide experiments. We also observe complex frictional stability behaviour that depends on both normal stress and shearing velocity. At normal stresses less than 20 MPa, we observe predominantly velocity-neutral friction behaviour. Above 20 MPa, we observe strong velocity-strengthening frictional behaviour at low velocities, which then evolves towards velocity-weakening friction behaviour at high velocities. Microstructural analyses of recovered samples highlight a variety of deformation mechanisms including grain size reduction and localization, folding of calcite grains and fluid-assisted diffusion mass transfer processes promoting the development of calcite nanograins in the highly deformed portions of the experimental fault. Our combined analyses indicate that calcite fault gouge transitions from brittle to semi-brittle behaviour at high normal stress and slow sliding velocities. This transition has important implications for earthquake nucleation and propagation on faults in carbonate-dominated lithologies.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 63
    Publication Date: 2016-02-27
    Keywords: Pathogens & Pathogenicity
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  • 64
    Publication Date: 2016-02-25
    Description: An RNAi system based on T7 RNA polymerase (TRNAP) was designed and examined in Aspergillus fumigatus . This system consists of two elements; an inducible T7RNAP expressing cassette and an AMA1-based episomal RNAi plasmid. These constructs were transformed into the A. fumigatus protoplasts and the efficiency of this system was tested in downregulation of alb1 gene. Upon the induction of T7RNAP expression, the recombinant T7RNAP was able to recognize T7 promoters, which were located on the episomal plasmid and in opposite direction. As a result, the bidirectional transcription of alb1 fragment led to the silencing of the target gene. However, our results demonstrated that this silencing system is unstable and may not be applicable in preparation of RNAi libraries.
    Keywords: Pathogens & Pathogenicity
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  • 65
    Publication Date: 2016-02-03
    Description: The elastic properties of homogeneous, isotropic materials are well constrained. However, in heterogeneous and evolving materials, these essential properties are less well-explored. During sintering of volcanic ash particles by viscous processes as well as during compaction and cementation of sediments, microstructure and porosity undergo changes that affect bulk dynamic elastic properties. Here using a model system of glass particles as an analogue for initially granular rock-forming materials, we have determined porosity and P -wave velocity during densification. Using these results, we test models for the kinetics of densification and the resultant evolution of the elastic properties to derive a quantitative description of the coupling between the kinetics of isotropic densification and the evolving dynamic elastic moduli. We demonstrate the power of the resultant model on a wide range of data for non-coherent sediments as well as sedimentary and volcanic rocks. We propose that such constraints be viewed as an essential ingredient of time-dependent models for the deformation of evolving materials in volcanoes and sedimentary basins.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 66
    Publication Date: 2016-05-14
    Description: We present a study of the seismic velocity variations that occurred in the structure before the large 2010 eruption of Merapi volcano. For the first time to our knowledge, the technique of coda wave interferometry is applied to both families of similar events (multiplets) and to correlation functions of seismic noise. About half of the seismic events recorded at the summit stations belong to one of the ten multiplets identified, including 120 similar events that occurred in the last 20 hr preceding the eruption onset. Daily noise cross-correlation functions (NCF) were calculated for the six pairs of short-period stations available. Using the stretching method, we estimate time-series of apparent velocity variation (AVV) for each multiplet and each pair of stations. No significant velocity change is detected until September 2010. From 10 October to the beginning of the eruption on 26 October, a complex pattern of AVV is observed with amplitude of up to ±1.5 per cent. Velocity decrease is first observed from families of deep events and then from shallow earthquakes. In the same period, AVV with different signs and chronologies are estimated from NCF calculated for various station pairs. The location in the horizontal plane of the velocity perturbations related with the AVV obtained from NCF is estimated by using an approach based on the radiative transfer approximation. Although their spatial resolution is limited, the resulting maps display velocity decrease in the upper part of the edifice in the period 12–25 October. After the eruption onset, the pattern of velocity perturbations is significantly modified with respect to the previous one. We interpret these velocity variations in the framework of a scenario of magmatic intrusion that integrates most observations. The perturbation of the stress field associated with the magma migration can induce both decrease and increase of the seismic velocity of rocks. Thus the detected AVVs can be considered as precursors of volcanic eruptions in andesitic volcanoes, without taking their sign into account.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 67
    Publication Date: 2016-05-20
    Description: A simple diagnosis of the presence or absence of an infection is an uninformative metric when individuals differ considerably in their tolerance to different infection loads or resistance to rates of disease progression. Models that incorporate the relationship between the progression of the infection with the potential alternate outcomes provide a far more powerful predictive tool than diagnosis alone. The global decline of amphibians has been amplified by Batrachochytrium dendrobatidis , a pathogen that can cause the fatal disease chytridiomycosis. We measured the infection load and observed signs of disease in Litoria aurea . Receiver operating characteristic curves were used to quantify the dissimilarity between the infection loads of L. aurea that showed signs associated with chytridiomycosis and those that did not. Litoria aurea had a 78% probability of developing chytridiomycosis past a threshold of 68 zoospore equivalents (ZE) per swab and chytridiomycosis occurred within a variable range of 0.5–490 ZE. Studies should incorporate a species-specific threshold as a predictor of chytridiomycosis, rather than a binary diagnosis. Measures of susceptibility to chytridiomycosis must account not only for the ability of B. dendrobatidis to increase its abundance on the skin of amphibians but also to determine how each species tolerates these infection loads.
    Keywords: Pathogens & Pathogenicity
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  • 68
    Publication Date: 2016-03-24
    Description: The control and prevention of biofilm-related infections is an important public healthcare issue. Given the increasing antibiotic resistance among bacteria and fungi that cause serious infections in humans, promotion of new strategies combating microorganisms has been essential. One attractive approach to inactivate microorganisms is the use of semiconductor photo-catalysis, which has become the subject of extensive research. In this study, the bactericidal properties of four photo-catalysts, TiO 2 , TiO 2 -S, TiO 2 -Eu and TiO 2 -Eu-S, were investigated against established 24, 48, 72 and 96 h biofilms of Enterococcus . The exposure of biofilms to the catalysts induced the production of superoxide radical anions. The best photo-catalytic inactivation was achieved with the TiO 2 -Eu-S and TiO 2 -S nanopowders and 24 h biofilms. Transmission electron microscopy images showed significant changes in the structure of the biofilm cells following photo-inactivation. The results suggest that doping with europium and modifying the surface with sulphate groups enhanced the bactericidal activity of the TiO 2 nanoparticles against enterococcal biofilms.
    Keywords: Pathogens & Pathogenicity
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  • 69
    Publication Date: 2016-04-24
    Description: Growth media have been developed to facilitate the enrichment and isolation of acidophilic and acid-tolerant sulfate-reducing bacteria (aSRB) from environmental and industrial samples, and to allow their cultivation in vitro . The main features of the ‘standard’ solid and liquid devised media are as follows: (i) use of glycerol rather than an aliphatic acid as electron donor; (ii) inclusion of stoichiometric concentrations of zinc ions to both buffer pH and to convert potentially harmful hydrogen sulphide produced by the aSRB to insoluble zinc sulphide; (iii) inclusion of Acidocella aromatica (an heterotrophic acidophile that does not metabolize glycerol or yeast extract) in the gel underlayer of double layered (overlay) solid media, to remove acetic acid produced by aSRB that incompletely oxidize glycerol and also aliphatic acids (mostly pyruvic) released by acid hydrolysis of the gelling agent used (agarose). Colonies of aSRB are readily distinguished from those of other anaerobes due to their deposition and accumulation of metal sulphide precipitates. Data presented illustrate the effectiveness of the overlay solid media described for isolating aSRB from acidic anaerobic sediments and low pH sulfidogenic bioreactors.
    Keywords: Environmental Microbiology
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  • 70
    Publication Date: 2016-05-19
    Description: Whether direct farmer-to-consumer outlets compete with supermarkets on produce prices remains an empirical question; marketing costs are not consistently higher in one retail channel or the other. This study compared prices of 29 fruits and vegetables across North Carolina farmers’ markets, roadside stands, and supermarkets. Larger farmers’ markets had higher prices: three fruits and one vegetable were cheaper at a direct outlet, while four vegetables were cheaper at supermarkets. Weighting item prices by consumption share attenuated differences in mean price across outlets. Direct-retail outlets are price competitive and should be considered among other tools to boost fresh fruit and vegetable intake.
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 71
    Publication Date: 2016-05-25
    Description: The Pseudomonas aeruginosa Chp chemosensory system regulates twitching motility, intracellular adenosine 3 '' 5 ' -cyclic monophosphate (cAMP) levels and is postulated to be involved in directional twitching towards phosphatidylethanolamine (PE). Because PilJ is the only methyl-accepting chemotaxis protein (MCP) identified in the Chp system, we determined the role of PilJ in mediating signal transduction for the distinct outputs of this system. Mutants that lack the periplasmic domain of PilJ ( pilJ 74-273 ) showed lower levels of cAMP but retained directional twitching towards PE. While initial studies revealed reduced twitching motility by PilJ 74-273 , this was due to decreased cAMP levels. Our data illustrate the importance of the periplasmic domain of PilJ in regulating cAMP. This is the first time a defined domain within PilJ has been identified as having a distinct role in signal transduction.
    Keywords: Pathogens & Pathogenicity
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  • 72
    Publication Date: 2016-04-24
    Description: Histone-like nucleoid-structuring (H-NS) proteins, which are conserved in Gram-negative bacteria, bind DNA and act as the global transcriptional repressors. In this study, we identified and characterized the xrvC gene encoding a H-NS protein in Xathomonas oryzae pv. oryzae ( Xoo ) Philippines strain PXO99 A . Compared with the wild type, the xrvC -deficient mutant of PXO99 A (named PXO99 xrvC ) showed a reduced growth rate in both nutrient-rich and nutrient-limited media. Interestingly, PXO99 xrvC exhibited significantly reduced virulence on rice cultivar IRBB214, but its virulence on 31 other rice cultivars was not affected. Transcriptional analysis revealed that the expression of hrpG , hrpX and hpa1 and of 15 out of 18 tested non-TAL (transcription activator-like) effector genes was decreased significantly in the xrvC mutant compared with that in the wild type. In addition, loss of xrvC also impaired the induction of the rice susceptibility gene Os8N3 in IRBB214 by PXO99 A . Our results suggest that the xrvC gene is involved in bacterial growth, and it plays a vital role in virulence by positively regulating the expression of hrp genes and non-TAL effector genes in PXO99 A and the susceptibility gene Os8N3 in rice.
    Keywords: Pathogens & Pathogenicity
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  • 73
    Publication Date: 2016-04-24
    Description: In Xanthomonas oryzae pv. oryzae , the pathogen of bacterial leaf blight of rice, hrp gene expression is regulated by the key hrp regulators HrpG and HrpX. HrpG regulates hrpX and hrpA , and HrpX regulates the other hrp genes on hrpB–hrpF operons. We previously examined the expression of the HrpX-regulated hrp gene hrcU and demonstrated that hrp gene expression is highly induced in a certain nutrient-poor medium containing xylose. In the present study, we found that the induction level of HrpX-regulated hrp genes was higher in medium with xylose than in media with any other sugar sources (glucose, sucrose and fructose), but that expression of hrpG , hrpX and hrpA was independent of the sugar sources. In western blot analysis, the accumulation of HrpX was reduced in media with a sugar other than xylose, probably as a result of proteolysis, but the addition of xylose canceled this reduced accumulation of the protein. The results suggest that proteolysis of HrpX is an important hrp regulatory mechanism and that xylose specifically suppresses this proteolysis, resulting in active hrp gene expression in X. oryzae pv. oryzae .
    Keywords: Pathogens & Pathogenicity
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  • 74
    Publication Date: 2016-04-24
    Description: Antibiotic therapy has long term consequences in the intestinal microbiome. Clostridium difficile has a well-known role in antibiotic-associated diarrhea, but in addition, persistent infection with this organism may increase the risk for developing inflammatory bowel disease. Here, recent literature on how the intestinal microbiome is altered by antibiotic therapy is presented.
    Keywords: Pathogens & Pathogenicity
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  • 75
    Publication Date: 2016-03-13
    Description: A common dye of prussian blue (PB) as an indicator was used to develop a colorimetric method for detecting the efficacy of the antibiotics in vitro. Considering the electronic production capacity of microbial respiration, ferricyanide was employed in transferring electrons from target microorganism of Escherichia coli ( E. coli ) to produce ferrocyanide. Subsequently, ferrocyanide reacted with ferric ions to form PB. In view of relationship between the PB yield and the bacterial activity, the efficacy of the antibiotics on E. coli was directly detected at 700 nm of PB absorption. When the 5% activity of antibiotics on 20 isolates of E. coli was quantified as 5% efficacy, the applied concentrations of eight antibiotics, such as cefepime, ceftriaxone sodium, cefoperazone sodium, piperacillin sodium, amoxicillin, gentamicin, amikacin and levofloxacin were 2, 2, 4, 4, 10, 4, 8 and 8 μg mL –1 , respectively. To compare with minimum inhibitory concentration results obtained by Clinical and Laboratory Standards Institute broth macrodilution method, the results of PB methods showed good agreements except with gentamicin. Paired t- test result ( P ) also showed that difference between two methods was statistically significant ( P = 0.006).
    Keywords: Environmental Microbiology
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  • 76
    Publication Date: 2016-03-04
    Description: Metarhizium acridum is an entomopathogenic fungus commonly used as a bioinsecticide. The conidium is the fungal stage normally employed as field inoculum in biological control programs and must survive under field conditions such as high ultraviolet-B (UV-B) exposure. Light, which is an important stimulus for many fungi, has been shown to induce the production of M. robertsii conidia with increased stress tolerance. Here we show that a two-hour exposure to white or blue/UV-A light of fast-growing mycelium induces tolerance to subsequent UV-B irradiation. Red light, however, does not have the same effect. In addition, we established that this induction can take place with as little as 1 min of white-light exposure. This brief illumination scheme could be relevant in future studies of M. acridum photobiology and for the production of UV-B resistant mycelium used in mycelium-based formulations for biological control.
    Keywords: Environmental Microbiology
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  • 77
    Publication Date: 2016-03-04
    Description: Photorhabdus (Enterobacteriaceae) bacteria are pathogenic to insects and mutualistic with entomopathogenic Heterorhabditis nematodes . Photorhabdus luminescens subsp. akhurstii LN2, associated with Heterorhabditis indica LN2, shows nematicidal activity against H. bacteriophora H06 infective juveniles (IJs). In the present study, an rpoS mutant of P. luminescens LN2 was generated through allelic exchange to examine the effects of rpoS deletion on the nematicidal activity and nematode development. The results showed that P. luminescens LN2 required rpoS for nematicidal activity against H06 nematodes, normal IJ recovery and development of H. indica LN2, however, not for the bacterial colonization in LN2 and H06 IJs. This provides cues for further understanding the role of rpoS in the mutualistic association between entomopathogenic nematodes and their symbionts.
    Keywords: Environmental Microbiology
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  • 78
    Publication Date: 2016-03-13
    Description: The aim of the present study was to verify whether penicillin-resistant, ampicillin-susceptible Enterococcus faecalis (PRASEF) occurred in Brazil prior to the beginning of the 21st century, and to verify whether ampicillin susceptibility can predict susceptibility to other β-lactams in E. faecalis with this inconsistent phenotype. The presence of polymorphisms in the pbp4 gene and genetic diversity among the isolates were investigated. Of 21 PRASEF analyzed, 5 (23.8%) and 4 (19.0%) were imipenem and piperacillin resistant simultaneously by disk diffusion and broth dilution respectively, contradicting the current internationally accepted standards of susceptibility testing. Sequencing of pbp4 gene revealed an amino acid substitution (Asp-573-〉Glu) in all PRASEF isolates but not in the penicillin-susceptible, ampicillin-susceptible E. faecalis . Most PRASEF (90.5%) had related pulsed-field gel electrophoresis profiles, but were different from other PRASEF described to date. Results demonstrate that penicillin-resistant, ampicillin-susceptible phenotype was already a reality in the 1990s in E. faecalis isolates in different Brazilian states, and some of these isolates were also imipenem- and piperacillin-resistant; therefore, internationally accepted susceptibility criteria cannot be applied to these isolates. According to pbp4 gene sequencing, this study suggests that a specific amino acid substitution in pbp4 gene found in all PRASEF analyzed is associated with penicillin resistance.
    Keywords: Pathogens & Pathogenicity
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  • 79
    Publication Date: 2016-05-05
    Keywords: Pathogens & Pathogenicity
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  • 80
    Publication Date: 2016-05-05
    Description: Catechol 2, 3-dioxygenase (C23O) is the key enzyme for aerobic aromatic degradation. Based on clone libraries and quantitative real-time polymerase chain reaction, we characterized diversity and distribution patterns of C23O genes in surface sediments of the Bohai Sea. The results showed that sediments of the Bohai Sea were dominated by genes related to C23O subfamily I.2.A. The samples from wastewater discharge area (DG) and aquaculture farm (KL) showed distinct composition of C23O genes when compared to the samples from Bohai Bay (BH), and total organic carbon was a crucial determinant accounted for the composition variation. C6BH12-38 and C2BH2-35 displayed the highest gene copies and highest ratios to the 16S rRNA genes in KL, and they might prefer biologically labile aromatic hydrocarbons via aquaculture inputs. Meanwhile, C7BH3-48 showed the highest gene copies and highest ratios to the 16S rRNA genes in DG, and this could be selective effect of organic loadings from wastewater discharge. An evident increase in C6BH12-38 and C7BH3-48 gene copies and reduction in diversity of C23O genes in DG and KL indicated composition perturbations of C23O genes and potential loss in functional redundancy. We suggest that ecological habitat and trophic specificity could shape the distribution of C23O genes in the Bohai Sea sediments.
    Keywords: Environmental Microbiology
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  • 81
    Publication Date: 2016-05-06
    Description: The influx of groundwater into hot kimberlite deposits results in the reaction of water with olivine-rich rocks. The products of the reaction are serpentine and release of latent heat. The rise of temperature due to the heat release increases the rate of the reaction. Under certain conditions, this self-speeding up of the reaction can result in instabilities associated with a significantly higher final serpentinization in slightly warmer regions of the kimberlite deposit. We conduct linear stability analysis of serpentinization in an isolated volume of porous kimberlitic rocks saturated with water and an inert gas. There is a counteracting interplay between the heat release tending to destabilize the uniform distribution of parameters and the heat conduction tending to stabilize it by smoothing out temperature perturbations. We determine the critical spatial scale separating the parameters where one phenomenon dominates over another. The perturbations of longer-than-critical length grow, whereas the perturbations of shorter-than-critical length fade. The analytical results of the linear stability analysis are supported by direct numerical simulations using a full nonlinear model.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 82
    Publication Date: 2016-05-19
    Description: This paper investigates how the Fresh Fruit and Vegetable Program (FFVP), a nutrition assistance program that provides funding for the distribution of free fresh fruits and vegetables to students in participating schools, affects childhood obesity using a panel data set of Arkansas public schoolchildren with two different approaches. First, we combine matching methodology and difference-in-differences (DID) analysis. Second, we use the synthetic control method to compare each FFVP participating school to a similar, albeit synthetic, control school. Both analyses show that FFVP program causes an economically meaningful reduction in the obesity outcome of participating children.
    Keywords: I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 83
    Publication Date: 2016-05-20
    Description: LysR-type transcriptional regulators (LTTRs) regulate various cellular processes in bacteria. pnpR is an LTTR-encoding gene involved in the regulation of hydroquinone (HQ) degradation, and its effects on the cellular processes of Pseudomonas putida DLL-E4 were investigated at the physiological, biochemical and molecular levels. Reverse transcription polymerase chain reaction revealed that pnpR positively regulated its own expression and that of the pnpC1C2DECX1X2 operon; additionally, pnpR partially regulated the expression of pnpA when P. putida was grown on para -nitrophenol (PNP) or HQ. Strains DLL-E4 and DLL- pnpR exhibited similar cellular morphologies and growth rates. Transcriptome analysis revealed that pnpR regulated the expression of genes in addition to those involved in PNP degradation. A total of 20 genes were upregulated and 19 genes were downregulated by at least 2-fold in strain DLL- pnpR relative to strain DLL-E4. Bioinformatic analysis revealed putative PnpR-binding sites located in the upstream regions of genes involved in PNP degradation, carbon catabolite repression and other cellular processes. The utilization of L-aspartic acid, L-histidine, L-pyroglutamic acid, L-serine, -aminobutyric acid, D,L-lactic acid, D-saccharic acid, succinic acid and L-alaninamide was increased at least 1.3-fold in strain DLL- pnpR as shown by BIOLOG assays, indicating that pnpR plays a potential negative regulation role in the utilization of carbon sources.
    Keywords: Environmental Microbiology
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  • 84
    Publication Date: 2016-05-22
    Description: Inelastic deformation can either occur with dilatancy or compaction, implying differences in porosity changes, failure and petrophysical properties. In this study, the roles of water as a pore fluid, and of temperature, on the deformation and failure of a micritic limestone (white Tavel limestone, porosity 14.7 per cent) were investigated under triaxial stresses. For each sample, a hydrostatic load was applied up to the desired confining pressure (from 0 up to 85 MPa) at either room temperature or at 70 °C. Two pore fluid conditions were investigated at room temperature: dry and water saturated. The samples were deformed up to failure at a constant strain rate of ~10 –5 s –1 . The experiments were coupled with ultrasonic wave velocity surveys to monitor crack densities. The linear trend between the axial crack density and the relative volumetric strain beyond the onset of dilatancy suggests that cracks propagate at constant aspect ratio. The decrease of ultrasonic wave velocities beyond the onset of inelastic compaction in the semi-brittle regime indicates the ongoing interplay of shear-enhanced compaction and crack development. Water has a weakening effect on the onset of dilatancy in the brittle regime, but no measurable influence on the peak strength. Temperature lowers the confining pressure at which the brittle–semi-brittle transition is observed but does not change the stress states at the onset of inelastic compaction and at the post-yield onset of dilatancy.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 85
    Publication Date: 2016-05-19
    Description: This study considers the transition into farming and growth of new farmers in U.S. agriculture by examining land ownership and leasing trends. Our approach is to characterize the entire distribution by farmer age and farmer experience rather than using young versus old and beginning versus established farmer categories. We also use a linked-farms longitudinal approach to show trends over time in farmland expansion and contraction. We find that farms operated by older beginning farmers tend to be smaller and do not tend to grow over time. Our results show that it is mostly young farmers as opposed to all beginning farmers who rapidly expand their farm operations after entering agriculture. Our findings inform policy makers about the strategies that young and beginning farmers use to start their businesses and expand over time, and suggest more effective approaches for targeting loan programs to both young and beginning farmers.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 86
    Publication Date: 2016-04-24
    Description: We estimate the impact of Malawi's Farm Input Subsidy Program using an economy-wide approach. This approach yields benefit-cost ratios about 60% higher than existing partial equilibrium studies, a result of our accounting for indirect benefits. Fertilizer response rates remain the determining parameter for benefit-cost ratio levels. Even with lower-end response rates, the program is pro-poor and generates double-dividends through higher and more drought-resilient yields. Overall, for macro-economically significant programs, our approach strongly complements survey-based evaluations. For Malawi, our results buttress arguments for a focus on program improvements.
    Keywords: C68 - Computable General Equilibrium Models, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, O22 - Project Analysis, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 87
    Publication Date: 2016-04-24
    Description: "Agriculture by contract" ( $\hbox {A}\times \hbox {C}$ ) is the main Mexican government program aimed at mitigating price risks for agricultural producers in Mexico. $\hbox {A} \times \hbox {C}$ has unique features involving forward contracts and the provision of basis subsidies and subsidized exchange-traded futures options for both producers and intermediaries. A simulation model is developed to analyze the market and welfare effects of $\hbox {A}\times \hbox {C}$ . When applied to corn, results show that $\hbox {A}\times \hbox {C}$ exerts substantial impacts and causes large transfers across sectors. Even if $\hbox {A}\times \hbox {C}$ reduced intermediaries' market power to the largest extent feasible, results indicate that it would still cause important losses in aggregate welfare.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 88
    Publication Date: 2016-04-24
    Description: The Mycobacterium tuberculosis Rv0679c protein is a surface protein that contributes to host cell invasion. We previously showed that a single nucleotide transition of the Rv0679c gene leads to a single amino acid substitution from asparagine to lysine at codon 142 in the Beijing genotype family. In this study, we examined the immunological effect of this substitution. Several recombinant proteins were expressed in Escherichia coli and Mycobacterium smegmatis and characterized with antisera and two monoclonal antibodies named 5D4-C2 and 8G10-H2. A significant reduction of antibody binding was detected by enzyme-linked immunosorbent assay (ELISA) and western blot analysis in the Lys142-type protein. This reduction of 8G10-H2 binding was more significant, with the disappearance of a signal in the proteins expressed by recombinant mycobacteria in western blot analysis. In addition, epitope mapping analysis of the recombinant proteins showed a linear epitope by 5D4-C2 and a discontinuous epitope by 8G10-H2. The antibody recognizing the conformational epitope detected only mycobacterial Asn142-type recombinant protein. Our results suggest that a single amino acid substitution of Rv0679c has potency for antigenic change in Beijing genotype strains.
    Keywords: Pathogens & Pathogenicity
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  • 89
    Publication Date: 2016-03-31
    Description: The Agricultural Act of 2014 solidified insurance as the cornerstone of U.S. agricultural policy. The Congressional Budget Office (2014) estimates that this act will increase spending on agricultural insurance programs by $5.7 billion to a total of $89.8 billion over the next decade. In light of the sizable resources directed toward these programs, accurate rating of insurance contracts is of the utmost importance to producers, private insurance companies, and the federal government. Unlike most forms of insurance, agricultural insurance is plagued by a paucity of spatially correlated data. A novel interpretation of Bayesian Model Averaging is used to estimate a set of possibly similar densities that offers greater efficiency if the set of densities are similar while seemingly not losing any if the set of densities are dissimilar. Simulations indicate that finite sample performance—in particular small sample performance—is quite promising. The proposed approach does not require knowledge of the form or extent of any possible similarities, is relatively easy to implement, admits correlated data, and can be used with either parametric or nonparametric estimators. We use the proposed approach to estimate U.S. crop insurance premium rates for area-type programs and develop a test to evaluate its efficacy. An out-of-sample game between private insurance companies and the federal government highlights the policy implications for a variety of crop-state combinations. Consistent with the simulation results, the performance of the proposed approach with respect to rating area-type insurance—in particular small sample performance—remains quite promising.
    Keywords: Q16 - R&D ; Agricultural Technology ; Agricultural Extension Services, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 90
    Publication Date: 2016-03-31
    Description: Distributing healthy food is an important goal for hunger relief agencies, but they face many challenges in meeting it. Budgets for purchasing food are limited, and hunger relief agencies often have little influence over the nutritional quality of food they receive through donations. In a recent study, Healthy Eating Index (HEI) scores were calculated monthly using electronic invoice data for food shelves served by two major food banks in Minnesota. While the HEI is directly related to nutrition guidelines and provides great detail in its scoring, implementation requires careful measurement and classification of foods and a rather complex set of calculations. In addition, a significant portion of food distributed by food banks is mixed pallets of free "miscellaneous" that cannot readily be included in HEI calculations. We propose and test a less data- and labor-intensive measure for characterizing the healthfulness of food distributed by hunger relief agencies. This new measure, the Hunger Relief Nutrition Index (HRNI), facilitates nutritional assessment of miscellaneous foods, allows for easy aggregation of healthfulness scores across food sources and time periods, and correlates well with the HEI.
    Keywords: C81 - Methodology for Collecting, Estimating, and Organizing Microeconomic Data, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 91
    Publication Date: 2016-03-31
    Description: Gleaning is increasingly attracting the attention of food safety networks, including food banks, as a valuable tool that simultaneously reduces food loss and alleviates food insecurity. However, managing gleaning operations can be challenging because the arrival of gleaning opportunities and the attendance of gleaner volunteers are both stochastic. We develop a stochastic optimization model to characterize and optimize a gleaning operation. The food bank chooses the gleaning schedule, which affects the gleaner capacity and the number of gleaning opportunities scheduled. In a specific field study of the Food Bank of the Southern Tier in New York, we analyze the tradeoff between call and volume service levels to find the optimum schedule that maximizes the expected total volume gleaned. Moreover, we find that increasing the gleaning window and increasing slot availability can be used as substitute mechanisms for increasing the total volume gleaned. Additionally, we use our model to assess the impact of recruiting more volunteer gleaners.
    Keywords: C61 - Optimization Techniques ; Programming Models ; Dynamic Analysis, C63 - Computational Techniques, D24 - Production ; Cost ; Capital and Total Factor Productivity ; Capacity, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 92
    Publication Date: 2016-04-20
    Description: Listeria monocytogenes possesses the highest number of leucine-rich repeat (LRR)-containing proteins among all Gram-positive bacteria; these LRR-containing molecules are known as the ‘internalin’ family. To understand the functions of largely uncharacterized LRR-containing molecules, we constructed seven deletion mutants in the L. monocytogenes H7858 strain targeting genes in this family and tested their virulence. Among the seven mutants, the LMOh7858_0369 strain and the LMOh7858_2546 strain showed significantly impaired invasiveness of HepG2 cells. We further tested the virulence of these two strains in the intravascular sepsis model using BALB/c mice. Interestingly, the LMOh7858_0369 strain showed significant reduction in organ colonization, bacteremia and invasion of the brain compared with the parental wild-type strain. Host immune responses to listerial intravascular infection were measured at 24 and 72 h post-infection. Transcript levels of several proinflammatory cytokines and chemokines were significantly lower when induced by the lmOh7858_0369 strain than when induced by the wild type. These results suggest that the putative LRR-containing protein encoded by LMOh7858_0369 might be a novel virulence factor of the L. monocytogenes H7858 strain.
    Keywords: Pathogens & Pathogenicity
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  • 93
    Publication Date: 2016-04-20
    Description: Several Gram-positive pathogens scavenge host-derived heme to satisfy their nutritional iron requirement. However, heme is a toxic molecule capable of damaging the bacterial cell. Gram-positive pathogens within the phylum Firmicutes overcome heme toxicity by sensing heme through HssRS, a two-component system that regulates the heme detoxification transporter HrtAB. Here we show that heme sensing by HssRS and heme detoxification by HrtAB occur in the insect pathogen Bacillus thuringiensis . We find that in B. thuringiensis , HssRS directly regulates an operon, hrmXY , encoding hypothetical membrane proteins that are not found in other Firmicutes with characterized HssRS and HrtAB systems. This novel HssRS-regulated operon or its orthologs BMB171_c3178 and BMB171_c3330 are required for maximal heme resistance. Furthermore, the activity of HrmXY is not dependent on expression of HrtAB. These results suggest that B. thuringiensis senses heme through HssRS and induces expression of separate membrane-localized systems capable of overcoming different aspects of heme toxicity.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 94
    Publication Date: 2016-04-20
    Description: Landfills are significant global sources of atmospheric methane, but little is known about the ecology and community structure of methanogens in these sites. Here, we investigated the methanogen community based on methyl coenzyme M reductase A gene amplicons in the vertical profiles of three different sites at a municipal landfill complex in China. Links between methanogen communities and refuse properties were explored using multivariate analysis. Clone library results showed that most clones (92%) were related to the hydrogenotrophic methanogens, Methanomicrobiales. Almost all of the Methanomicrobiales clones retrieved in this study are members of the genus Methanoculleus . Eight clones were affiliated with the genus Methanofollis . The remaining clones were clustered within the genus Methanosarcina . Terminal restriction fragment length polymorphism profiles showed that the landfill was predominated by 22 taxa, making up 69%–96% of the community. Of these, a single taxon comprised 36%–65% of the communities across all sites and depths. Principal components analysis separated the methanogen community into three groups, irrespective of site or depth. Redundancy analysis suggested that total phosphorus and pH play roles in structuring methanogen communities in landfills.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 95
    Publication Date: 2016-04-20
    Description: The aim of this study was to understand the pathogenesis of motile aeromonas septicemia caused by an emergent, high virulent Aeromonas hydrophila (vAh) in channel catfish, Ictalurus punctatus . Adipose fin clipped catfish were challenged with vAh using a waterborne challenge method, and the distribution of vAh over a time course was detected and quantified using real-time polymerase chain reaction. The results showed that 77.8% of fish died within 48 h post challenge with mean day to death of 1.5 days. At 2 h post challenge, vAh (inferred from genomic DNA copies or genome equivalents) was detected in all external and internal tissues sampled. Gill had the highest vAh cells at 1 h post challenge. Spleen harbored the most vAh cells among internal organs at 4 h post challenge. The tissues/organs with most vAh cells detected at 8 h post challenge were adipose fin, blood, intestine, kidney and skin, while liver showed the highest vAh cells at 24 h post challenge. These results suggest that vAh was able to rapidly proliferate and spread, following wound infection, through the fish blood circulation system and cause mortality within 8–24 h.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 96
    Publication Date: 2016-04-20
    Description: The major Staphylococcus aureus autolysin, Atl, has been implicated in attachment to surfaces and release of extracellular DNA during biofilm formation under laboratory conditions. Consistent with this, polyclonal antibodies to the amidase and glucosaminidase domains of Atl inhibited in vitro biofilm formation. However, in a murine model of device-related infection the community-associated S. aureus strain USA300 LAC JE2 established a successful infection in the absence of atl . These data indicate that Atl activity is not required for biofilm production in this infection model and reveal the importance of characterizing the contribution of biofilm phenotypes to virulence under in vivo conditions.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 97
    Publication Date: 2016-02-10
    Description: The longstanding "cash versus food" debate has received renewed attention in both research and practice. This paper reviews key issues shaping the debate and presents new evidence from randomized and quasi-experimental evaluations that deliberately compare cash and in-kind food transfers in ten developing counties. Findings show that relative effectiveness cannot be generalized: although some differences emerge in terms of food consumption and dietary diversity, average impacts tend to depend on context, specific objectives, their measurement, and program design. Costs for cash transfers and vouchers tend to be significantly lower relative to in-kind food. Yet the consistency and robustness of methods for efficiency analyses varies greatly.
    Keywords: D61 - Allocative Efficiency ; Cost-Benefit Analysis, H53 - Government Expenditures and Welfare Programs, O12 - Microeconomic Analyses of Economic Development, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0257-3032
    Electronic ISSN: 1564-6971
    Topics: Economics
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  • 98
    Publication Date: 2016-02-12
    Description: Here we report a newly identified ‘Chalky back’ phenomenon in banana prawns ( Fenneropenaeus merguiensis ) farmed in North Queensland, Australia. This was characterized by localized white discoloured segmentation of the cervical groove, moreover, after cooking the prawns exploded, making them unfit for commercial sale. Histological examination revealed breakdown of gut and abdominal muscle tissue in some moribund specimens. We selectively isolated Vibrio spp., which are known prawn pathogens, from healthy and Chalky back specimens. Isolated bacteria were identified, typed and tested for the presence of eight virulence genes (VGs), biofilm formation, adherence and cytotoxicity to fish cells. In all, 32 isolates were recovered and identified as Vibrio harveyi , V. owensii , V. sinaloensis -like, V. campbellii , V. shilonii , Vibrio sp. and Photobacterium damselae using 16S rRNA gene sequencing. All V. harveyi carried VGs coding for haemolysin, tox R and flagella; formed biofilm; and adhered to both cell lines. This was similar to the V. sinaloensis -like strains that were only isolated from Chalky back specimens. Our data suggest that Vibrio spp. may play a role in the pathogenesis of Chalky back. This study is the first report of Chalky back phenomenon in farmed banana prawns that needs to be closely monitored by the industry.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 99
    Publication Date: 2016-02-12
    Description: Remote sensing thermal data of active lava flows allow the evaluation of effusion rates. This is made possible by a simple formula relating the lava effusion rate to the heat flux radiated per unit time from the surface of the flow. Due to the assumptions of the model, this formula implies that heat flux, surface temperature and lava temperature vary as a function of the flow thickness. These relationships, never verified or validated before, have been used by several authors as a proof of the weakness of the model. Here, multispectral infrared and visible imaging spectrometer (MIVIS) high spatial resolution (5–10 m) thermal data acquired during Etna's 2001 eruption were used to investigate downflow heat flux variations in the lava flow emitted from a vent located at 2100 m a.s.l. A high correlation between the downflow heat flux and the lava flow thickness (measured from a pre-existing digital elevation model) was found. Topography beneath the flow appears to play an important role both in lava emplacement mechanisms and flow dynamics. MIVIS-derived downflow effusion rates are consistent with the law of conservation of mass assessing the reliability of remote sensing techniques.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 100
    Publication Date: 2016-10-28
    Description: Many smallholder families are exceptionally prone to potentially catastrophic decreases in their incomes and access to food. Over the past decade, therefore, policy makers and economists have increasingly focused on potential mechanisms for expanding risk management strategies available to those families. Commercially provided weather-based index insurance products, perhaps partially funded by subsidies, have been of particular interest because of their apparent potential to provide payments to smallholder families when they are most in need of help. However, the empirical evidence from a wide range of studies indicates that, absent relatively substantial subsidies, small holder farmers will not purchase commercially priced index products or even "all risk" products where payments are tied to the farm's crop losses. There are three important reasons why this is the case. First, smallholder farmers already have many ways of managing their risks, including informal community-based initiatives, on-farm production decisions and off-farm work. Second, index insurance schemes are subject to considerable basis risk; families often do not receive an index insurance indemnity when they experience a substantial crop loss on their farms. Third, the fixed costs of delivering crop insurance to smallholders make such coverage expensive. The potential market for weather index insurance therefore may be limited to insuring relatively large groups of farmers, either directly or indirectly though providing micro finance and other lending institution with coverage against widespread loan defaults associated with catastrophic events like major droughts. Alternatively, weather indexes could simply be used to more accurately target emergency aid.
    Keywords: D61 - Allocative Efficiency ; Cost-Benefit Analysis, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0257-3032
    Electronic ISSN: 1564-6971
    Topics: Economics
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