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  • Pathogens & Pathogenicity  (51)
  • Food Policy  (45)
  • Mineral Physics, Rheology, Heat Flow and Volcanology  (29)
  • Genomics  (28)
  • Oxford University Press  (153)
  • Elsevier
  • 2015-2019  (153)
  • 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
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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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: 2017-01-05
    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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  • 5
    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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  • 6
    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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  • 7
    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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  • 8
    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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  • 9
    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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  • 10
    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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  • 11
    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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  • 12
    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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  • 13
    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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  • 14
    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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  • 15
    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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  • 16
    Publication Date: 2016-07-09
    Description: Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
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  • 17
    Publication Date: 2016-07-28
    Description: Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilization in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here, we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organization and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilization; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these ‘repressed transcripts’ have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies.
    Keywords: Genomics
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  • 18
    Publication Date: 2016-01-09
    Description: Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.
    Keywords: Genomics
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  • 19
    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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  • 20
    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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  • 21
    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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  • 22
    Publication Date: 2016-08-20
    Description: Advanced sequencing technologies have generated a plethora of data for many chromatin marks in multiple tissues and cell types, yet there is lack of a generalized tool for optimal utility of those data. A major challenge is to quantitatively model the epigenetic dynamics across both the genome and many cell types for understanding their impacts on differential gene regulation and disease. We introduce IDEAS, an i ntegrative and d iscriminative e pigenome a nnotation s ystem, for jointly characterizing epigenetic landscapes in many cell types and detecting differential regulatory regions. A key distinction between our method and existing state-of-the-art algorithms is that IDEAS integrates epigenomes of many cell types simultaneously in a way that preserves the position-dependent and cell type-specific information at fine scales, thereby greatly improving segmentation accuracy and producing comparable annotations across cell types.
    Keywords: Genomics
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  • 23
    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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  • 24
    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
    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: 2016-06-17
    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
    Print ISSN: 0378-1097
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  • 26
    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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  • 27
    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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  • 28
    Publication Date: 2016-09-03
    Description: A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 x 10 –4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 x 10 –5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS 1 , IS 2 , IS 5 and IS 186 . Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS 186 target-sites, 5'-GGGG(N6/N7)CCCC-3'. We also detected 48 long deletions not involving IS elements.
    Keywords: Genomics
    Print ISSN: 0305-1048
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  • 29
    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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  • 30
    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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  • 31
    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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  • 32
    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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  • 33
    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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  • 34
    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
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 35
    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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  • 36
    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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  • 37
    Publication Date: 2016-02-20
    Description: Genetic variants in or near miRNA genes can have profound effects on miRNA expression and targeting. As user-friendly software for the impact prediction of miRNA variants on a large scale is still lacking, we created a tool called miRVaS. miRVaS automates this prediction by annotating the location of the variant relative to functional regions within the miRNA hairpin (seed, mature, loop, hairpin arm, flanks) and by annotating all predicted structural changes within the miRNA due to the variant. In addition, the tool defines the most important region that is predicted to have structural changes and calculates a conservation score that is indicative of the reliability of the structure prediction. The output is presented in a tab-separated file, which enables fast screening, and in an html file, which allows visual comparison between wild-type and variant structures. All separate images are provided for downstream use. Finally, we tested two different approaches on a small test set of published functionally validated genetic variants for their capacity to predict the impact of variants on miRNA expression.
    Keywords: Genomics
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  • 38
    Publication Date: 2016-02-20
    Description: Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts ( trans -spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (‘NCLscan’), which utilized a stepwise alignment strategy to almost completely eliminate false calls (〉98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans -spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans -spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
    Keywords: Genomics
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  • 39
    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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  • 40
    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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  • 41
    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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  • 42
    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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  • 43
    Publication Date: 2016-02-27
    Keywords: Pathogens & Pathogenicity
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  • 44
    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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  • 45
    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
    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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  • 46
    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
    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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  • 47
    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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    Topics: Biology
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  • 48
    Publication Date: 2016-05-20
    Description: Visualization of chromosomal dynamics is important for understanding many fundamental intra-nuclear processes. Efficient and reliable live-cell multicolor labeling of chromosomal loci can realize this goal. However, the current methods are constrained mainly by insufficient labeling throughput, efficiency, flexibility as well as photostability. Here we have developed a new approach to realize dual-color chromosomal loci imaging based on a modified single-guide RNA (sgRNA) of the CRISPR/Cas9 system. The modification of sgRNA was optimized by structure-guided engineering of the original sgRNA, consisting of RNA aptamer insertions that bind fluorescent protein-tagged effectors. By labeling and tracking telomeres, centromeres and genomic loci, we demonstrate that the new approach is easy to implement and enables robust dual-color imaging of genomic elements. Importantly, our data also indicate that the fast exchange rate of RNA aptamer binding effectors makes our sgRNA-based labeling method much more tolerant to photobleaching than the Cas9-based labeling method. This is crucial for continuous, long-term tracking of chromosomal dynamics. Lastly, as our method is complementary to other live-cell genomic labeling systems, it is therefore possible to combine them into a plentiful palette for the study of native chromatin organization and genome ultrastructure dynamics in living cells.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 49
    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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  • 50
    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
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 51
    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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  • 52
    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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  • 53
    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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  • 54
    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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  • 55
    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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  • 56
    Publication Date: 2016-05-05
    Keywords: Pathogens & Pathogenicity
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  • 57
    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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  • 58
    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
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 59
    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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  • 60
    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
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 61
    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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  • 62
    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
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 63
    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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  • 64
    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
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 65
    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
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 66
    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
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 67
    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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  • 68
    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
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  • 69
    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
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  • 70
    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
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    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 71
    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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  • 72
    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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  • 73
    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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  • 74
    Publication Date: 2016-11-01
    Description: Presence of excess unaltered, wild-type (WT) DNA providing no information of biological or clinical value often masks rare alterations containing diagnostic or therapeutic clues in cancer, prenatal diagnosis, infectious diseases or organ transplantation. With the surge of high-throughput technologies there is a growing demand for removing unaltered DNA over large pools-of-sequences. Here we present nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO), a single-step approach with broad genome coverage that can remove WT-DNA from numerous sequences simultaneously, prior to genomic analysis. NaME-PrO employs a double-strand-DNA-specific nuclease and overlapping oligonucleotide-probes interrogating WT-DNA targets and guiding nuclease digestion to these sites. Mutation-containing DNA creates probe-DNA mismatches that inhibit digestion, thus subsequent DNA-amplification magnifies DNA-alterations at all selected targets. We demonstrate several-hundred-fold mutation enrichment in diverse human samples on multiple clinically relevant targets including tumor samples and circulating DNA in 50-plex reactions. Enrichment enables routine mutation detection at 0.01% abundance while by adjusting conditions it is possible to sequence mutations down to 0.00003% abundance, or to scan tumor-suppressor genes for rare mutations. NaME-PrO introduces a simple and highly parallel process to remove un-informative DNA sequences and unmask clinically and biologically useful alterations.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 75
    Publication Date: 2016-10-26
    Description: Edwardsiella tarda is distributed widely in a variety of hosts. Eha has recently been found to be its virulence regulator. In order to explore the mechanism of its regulation, we investigated the survival rates of wild type strain ET13, and its eha mutant and complemented strains in RAW264.7 macrophages under light microscopic observation as well as by counting bacterial CFUs on the plates. All of the different strains could live within the macrophages; however, the intracellular numbers of the wild type were significantly higher than the mutant when the incubation time extended 4 h or 6 h ( P 〈 0.05). Furthermore, more ROS were produced by the mutant-infected cells, indicating that Eha may enhance ET13's capacity to detoxify ROS. In agreement with this, we found that the mutant exhibited more sensitivity by H 2 O 2 disk inhibitory assay and less survival ability with H 2 O 2 treatment. We further demonstrated that the bacterial antioxidant enzymes SodC and KatG were regulated by Eha with qRT-PCR and β -galactosidase assay. Collectively, our data show Eha is required for E. tarda to resist the oxidative stress from the macrophages.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 76
    Publication Date: 2016-08-07
    Description: Direct interaction between pathogens and host cells often is a prerequisite for colonization, infection and dissemination. Regulated production of capsular polysaccharide (CPS), which is made of hyaluronic acid, is essential for the pathogenicity of Streptococcus equi subsp. Zooepidemicus (SEZ). Here, we constructed a CPS-deleted mutant and analyzed it along with the parental wild-type strain in attachment and invasion of mammalian epithelial and endothelial cell lines. The CPS-deleted mutant exhibited significant increase in adherence and invasion by several orders of magnitude compared with the wild-type strain through quantitative analysis and electron microscopy observation. After the wild-type strain was recovered from invaded cells, its morphology was analyzed by visual methods and scanning electron microscopy, which revealed that its capsule was almost completely absent. Capsule measurements showed a similar result in which CPS production was nearly attenuated to the same extent as in the CPS-deleted mutant. qPCR assays revealed a marked reduction in the transcriptional levels of the CPS biosynthesis genes, has operon. Moreover, the repression in capsular production was stable inheritance. Our findings indicate that SEZ is a facultative intracellular bacterium, capsule attenuation in SEZ contributes to attachment and invasion in interactions with host cells, and the active regulation of capsule breakdown is controlled by SEZ during internalization.
    Keywords: Pathogens & Pathogenicity
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  • 77
    Publication Date: 2016-08-20
    Description: How much has food abundance, attributable to U.S. public agricultural R&D, contributed to high and rising U.S. obesity rates? In this paper we investigate the effects of public investment in agricultural R&D on food prices, per capita calorie consumption, adult body weight, obesity, public healthcare expenditures related to obesity, and consumer welfare. We find that a 10% increase in the stream of annual U.S. public investment in agricultural R&D in the latter half of the twentieth century would have caused a modest increase in the average daily calorie consumption of American adults, resulting in small increases in public healthcare expenditures related to obesity. On the other hand, such an increase in spending would have generated very substantial consumer benefits, and net national benefits, given the very large benefit-cost ratios for agricultural R&D. This implies that current policy objectives of revising agricultural R&D priorities to pursue obesity objectives are likely to be comparatively unproductive and socially wasteful. Moreover, R&D lags of decades mean that such an approach would be totally ineffective in the immediate horizon.
    Keywords: I18 - Government Policy ; Regulation ; Public Health, Q16 - R&D ; Agricultural Technology ; Agricultural Extension Services, 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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  • 78
    Publication Date: 2016-12-07
    Description: This article reports spending results for the USDA's Healthy Incentives Pilot (HIP), which tested a 30% incentive on fruit and vegetable purchases with Supplemental Nutrition Assistance Program (SNAP) benefits. Self-reported mean usual monthly spending for all fruits and vegetables was $6.15 higher for randomly assigned HIP participant households than for a control group. Much of the additional spending appears to have taken place in ways that did not earn the incentive—spending with non-SNAP resources or in retailers that did not participate in HIP. This article investigates mechanisms that might explain the HIP impact on fruit and vegetable purchases that did not earn the incentive.
    Keywords: 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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  • 79
    Publication Date: 2016-12-22
    Description: We performed complex conductivity measurements on 28 core samples from the hole drilled for the Humu'ula Groundwater Research Project (Hawai'i Island, HI, USA). The complex conductivity measurements were performed at 4 different pore water conductivities (0.07, 0.5, 1.0 or 2.0, and 10 S m –1 prepared with NaCl) over the frequency range 1 mHz to 45 kHz at 22 ± 1 °C. The in-phase conductivity data are plotted against the pore water conductivity to determine, sample by sample, the intrinsic formation factor and the surface conductivity. The intrinsic formation factor is related to porosity by Archie's law with an average value of the cementation exponent m of 2.45, indicating that only a small fraction of the connected pore space controls the transport properties. Both the surface and quadrature conductivities are found to be linearly related to the cation exchange capacity of the material, which was measured with the cobalt hexamine chloride method. Surface and quadrature conductivities are found to be proportional to each other like for sedimentary siliclastic rocks. A Stern layer polarization model is used to explain these experimental results. Despite the fact that the samples contain some magnetite (up to 5 per cent wt.), we were not able to identify the effect of this mineral on the complex conductivity spectra. These results are very encouraging in showing that galvanometric induced polarization measurements can be used in volcanic areas to separate the bulk from the surface conductivity and therefore to define some alteration attributes. Such a goal cannot be achieved with resistivity alone.
    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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  • 80
    Publication Date: 2016-12-22
    Description: We investigate the relationship between complex conductivity spectra and both permeability and pore mean size and distribution of 22 core samples (21 volcanic rocks and 1 clayey sandstone). The volcanic core samples were extracted from a wellbore drilled for the Humu‘ula Groundwater Research Project in the Humu‘ula saddle region between Mauna Kea and Mauna Loa volcanoes (Hawaii). The quadrature conductivity spectra of volcanic rocks exhibit a subtle, but generally detectable, relaxation frequency in the range 0.3 Hz to 45 kHz similar to the relaxation frequency observed for clayey sandstones. We find a fair relationship between this relaxation frequency and the pore size determined by mercury porosimetry. Combined with the intrinsic formation factor of the core samples, the relaxation frequency can be used as an indicator of the permeability of the material. The predicted values of the permeability are grossly consistent with the permeability values to air (in the range 0.001–100 mD) within two orders of magnitude. The measured permeability values are highly correlated to the peak of the pore size distribution determined from mercury porosimetry divided by the intrinsic formation factor. By fitting the complex conductivity spectra with the pore size distribution, we obtain the normalized chargeability of the core samples, which is, in turn, highly correlated to the measured cation exchange capacity.
    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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  • 81
    Publication Date: 2016-12-23
    Description: Burkholderia pseudomallei causes melioidosis, a potentially fatal infectious disease in tropical and subtropical countries worldwide. The intracellular behaviour of this pathogen in host cells has been reported to impact the severity of melioidosis, including the development of septicaemia, a consequence of pneumonia melioidosis. We previously identified a predicted cation transporter protein, BPSS1228, that participates in the transitional stage of this intracellular pathogen. For further analysis, in this study B. pseudomallei bpss1228 mutant and complemented strains were constructed and bacterial infectivity on human lung epithelial cells, A549, investigated in vitro . Burkholderia pseudomallei bpss1228 mutant showed impaired bacterial adhesion and invasion into A549 cells compared with wild-type strain, while the deficient phenotypes were restored to wild-type levels by the complemented strain. Additionally, the inactivation of bpss1228 in the mutant strain affected flagella-based swimming on a semi-solid surface and resistance to acid stresses simulating intracellular environments. These observations of BPSS1228 relating to B. pseudomallei infection strategies shed a new light on its association with intracellular B. pseudomallei during the interaction with host cells.
    Keywords: Pathogens & Pathogenicity
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  • 82
    Publication Date: 2016-12-23
    Description: Formation of a transient sub-population of bacteria, referred to as persisters, is one of the most important and least understood mechanisms that bacteria employ to evade elimination. Persister cells appear to be slow-growing bacteria that are broadly protected from a wide range of antibiotics. Using both theoretical and experimental methods, we show that alternating the application and withdrawal of antibiotics can be an effective treatment—as long as the timing of the protocol is estimated with precision. More specifically, we demonstrate that timing the alternating treatment based on theoretical predictions is confirmed using experimental observations. These results support a large class of theoretical studies that show that, even without complete understanding of the biological mechanisms, these models can provide insight into properties of the system.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
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  • 83
    Publication Date: 2016-12-23
    Description: The phytopathogen Pseudomonas syringae pv. tabaci 11528 ( P. syringae 11528), causing wild-fire disease in soybean and tobacco plants, processes PsyI-PsyR quorum-sensing (QS) system, in which PsyI is the N -(3-oxo-hexanoyl)-homoserine lactone (3OC6-HSL) synthase. In comparison to P. syringae 11528 AHL-deficient mutant, 845 3OC6-HSL-dependent genes were identified using RNA sequencing (RNA-seq) in the AHL-deficient mutant grown with exogenous 3OC6-HSL in the transition from the exponential to the stationary phase, and many of them were associated with virulence, which were negatively regulated. The gene ontology and KEGG pathway enrichment analysis of those genes presented that the most pronounced regulation was involved in bacterial motility. Moreover, similar expression profiles of genes during growth phases were observed in both the wild type and the AHL-deficient mutant with exogenous 3OC6-HSL compared with the AHL-deficient mutant. These findings imply that 3OC6-HSL has a critical contribution to the QS-dependent regulation on gene expression, and 3OC6-HSL-dependent regulation may play a significant role in plant infection.
    Keywords: Pathogens & Pathogenicity
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  • 84
    Publication Date: 2016-12-29
    Description: Helicobacter pylori commonly infects the epithelial layer of the human stomach and in some individuals causes peptic ulcers, gastric adenocarcinoma or gastric lymphoma. Helicobacter pylori is a genetically diverse species, and the most important bacterial virulence factor that increases the risk of developing disease, versus asymptomatic colonization, is the cytotoxin associated gene pathogenicity island ( cag PAI). Socially housed rhesus macaques are often naturally infected with H. pylori similar to that which colonizes humans, but little is known about the cag PAI. Here we show that H. pylori strains isolated from naturally infected rhesus macaques have a cag PAI very similar to that found in human clinical isolates, and like human isolates, it encodes a functional type IV secretion system. These results provide further support for the relevance of rhesus macaques as a valid experimental model for H. pylori infection in humans.
    Keywords: Pathogens & Pathogenicity
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  • 85
    Publication Date: 2016-12-29
    Description: Sporisorium scitamineum is the fungus that causes sugarcane smut disease. Despite of the importance of sugarcane for Brazilian agribusiness and the persistence of the pathogen in most cropping areas, genetic variation studies are still missing for Brazilian isolates. In this study, sets of isolates were analyzed using two molecular markers (AFLP and telRFLP) and ITS sequencing. Twenty-two whips were collected from symptomatic plants in cultivated sugarcane fields of Brazil. A total of 41 haploid strains of compatible mating types were selected from individual teliospores and used for molecular genetic analyses. telRFLP and ITS analyses were expanded to six Argentine isolates, where the sugarcane smut was first recorded in America. Genetic relationship among strains suggests the human-mediated dispersal of S. scitamineum within the Brazilian territory and between the two neighboring countries. Two genetically distinct groups were defined by the combined analysis of AFLP and telRFLP. The opposite mating-type strains derived from single teliospores were clustered together into these main groups, but had not always identical haplotypes. telRFLP markers analyzed over two generations of selfing and controlled outcrossing confirmed the potential for emergence of new variants and occurrence of recombination, which are relevant events for evolution of virulence and environmental adaptation.
    Keywords: Pathogens & Pathogenicity
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  • 86
    Publication Date: 2016-10-16
    Description: DExD/H box RNA helicases play essential roles in various biological processes in prokaryotes and eukaryotes. By screening Pseudomonas aeruginosa strains with mutations in various DExD/H box helicase genes, we identified that deaD was required for bacterial cytotoxicity and virulence in a mouse acute pneumonia model. Compared to a wild-type strain and its complementation strain, the deaD mutant induced less production of proinflammatory cytokines, neutrophil infiltration and lung damage during infection. We further found that the RNA helicase activity of DeaD was required for the expression of type III secretion system (T3SS) genes. Overexpression of ExsA, a master activator of the T3SS, restored the expression of T3SS genes as well as the virulence of the deaD mutant, suggesting that the attenuated virulence of the deaD mutant was mainly due to the defective T3SS. Overall, our results reveal a role of DeaD in the virulence of P. aeruginosa .
    Keywords: Pathogens & Pathogenicity
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  • 87
    Publication Date: 2016-10-20
    Description: Klebsiella pneumoniae is an opportunistic pathogen that commonly causes nosocomial infections in the urinary tract, respiratory tract, lung, wound sites and blood in individuals with debilitating diseases. Klebsiella pneumoniae is still a cause of severe pneumonia in alcoholics in Africa and Asia, and the predominant primary pathogen of primary liver abscess in Taiwan and Southeast Asia, particularly in Asian and Hispanic patients, and individuals with diabetes mellitus. In the United States and Europe, K. pneumoniae infections are most frequently associated with nosocomial infections. The emergence of antibiotic-resistant strains of K. pneumoniae worldwide has become a cause of concern where extended-spectrum β-lactamases (ESBLs) and carbapenemase-producing strains have been isolated with increasing frequency. The pathogen's ability to form biofilms on inserted devices such as urinary catheter has been proposed as one of the important mechanisms in nosocomially acquired and persistent infections, adding to the increased resistance to currently used antibiotics. In this review, infections caused by K. pneumoniae , antibiotic resistance and formation of biofilm will be discussed.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
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  • 88
    Publication Date: 2016-11-10
    Description: The Puyehue-Cordón Caulle Volcanic Complex (PCCVC) is one of the best examples of tectonic control on volcanism at the Southern Volcanic Zone of the Andes (southern Chile). The PCCVC comprises several volcanic centres that erupted dominantly SiO 2 -rich magmas at the intersection of the trench-parallel Liquiñe-Ofqui Fault Zone (LOFZ) and an inherited NW–SE basement structure. The PCCVC began an explosive and later effusive eruption on 2011 June 4 causing decimetre- to metre-scale surface deformation that was observed by a series of Envisat ASAR satellite scenes. We modelled this data and complemented it with time-series of two continuous GPS stations and seismicity recorded by a local network. Deformation during the first 3 days of the eruption can be modelled either by two point sources aligned with the NW–SE Cordón Caulle graben or by a closing dyke with a significant component of left-lateral motion along the graben. These models are discussed with respect to their implications on the estimated rheology and the eruption mechanism. GPS observations near the volcanic complex reveal an additional, more localised effect related to the LOFZ in the south of the complex. Coeruptive deformation at the main geological structures of the PCCVC is further supported by relocated seismicity, which is concentrated along the Cordón Caulle graben and to the western side of the LOFZ.
    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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  • 89
    Publication Date: 2016-01-02
    Description: Coal fires are severe hazards to environment, health and safety throughout the world. Efficient and economical extinguishing of these fires requires that the extent of the subsurface coal fires should be delineated. Electrical and electromagnetic methods have been used to detect coal fires in recent years. However, the resistivity change of coal-bearing rocks at high temperature is rarely investigated. The resistivity characteristics of coal fires at different temperatures and depths are seldomly researched as well. In this paper, we present the results of measurements of several coal-bearing rocks’ resistivity and permeability under high temperature. Two major causes for the change in resistivity with increasing temperature are recognized, there are the increase of charge carriers and thermal fracturing, of which the first one is probably the dominant cause. A set of 2-D simulations is carried out to compare the relation of resolution and efficiency of coal fires detection to temperature and depth when adopting the electrical resistance tomography. The simulation results show that the resolution and efficiency decrease with the decrease of temperature and the increase of depth. Finally, the electrical resistance tomography is used to delineate coal fires in the Anjialing Open Pit Mine. Most low-resistivity regions are verified as coal-fire areas according to the long-term monitoring of borehole temperature. The results indicate that the electrical resistance tomography can be used as a tool for the detection of coal fires.
    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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  • 90
    Publication Date: 2016-11-17
    Description: In recent years, extraintestinal pathogenic Escherichia coli (ExPEC) has been found to pose a great threat to human and animal health, but its pathogenic mechanism is not fully understood yet. Capsular polysaccharide, an essential virulence factor in these bacteria, can damage the host immune system, and kpsM is a member of the gene cluster responsible for capsular polysaccharide synthesis. In this study, whole sequence alignment of the virulent strain PCN033 and the attenuated strain PCN061 revealed that kpsM exists in PCN033 but not in PCN061. To determine its function and biological characteristics, we deleted kpsM from PCN033 by homologous recombination. The results of adhesion assays, phagocytosis assays and serum bactericidal assays together with the results of colonization assays in mice indicate that the deletion of kpsM decreases the virulence of porcine ExPEC. Our findings about the biological characteristics of kpsM help to elucidate the complex pathogenic mechanism of ExPEC.
    Keywords: Pathogens & Pathogenicity
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    Topics: Biology
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  • 91
    Publication Date: 2016-12-01
    Description: The RAG1/RAG2 endonuclease initiates V(D)J recombination at antigen receptor loci but also binds to thousands of places outside of these loci. RAG2 localizes directly to lysine 4 trimethylated histone 3 (H3K4me3) through a plant homeodomain (PHD) finger. The relative contribution of RAG2-dependent and RAG1-intrinsic mechanisms in determining RAG1 binding patterns is not known. Through analysis of deep RAG1 ChIP-seq data, we provide a quantitative description of the forces underlying genome-wide targeting of RAG1. Surprisingly, sequence-specific DNA binding contributes minimally to RAG1 targeting outside of antigen receptor loci. Instead, RAG1 binding is driven by two distinct modes of interaction with chromatin: the first is driven by H3K4me3, promoter-focused and dependent on the RAG2 PHD, and the second is defined by H3K27Ac, enhancer-focused and dependent on ‘non-core’ portions of RAG1. Based on this and additional chromatin and genomic features, we formulated a predictive model of RAG1 targeting to the genome. RAG1 binding sites predicted by our model correlate well with observed patterns of RAG1-mediated breaks in human pro-B acute lymphoblastic leukemia. Overall, this study provides an integrative model for RAG1 genome-wide binding and off-target activity and reveals a novel role for the RAG1 non-core region in RAG1 targeting.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 92
    Publication Date: 2016-12-07
    Description: The food packages provided by the Supplemental Nutrition Program for Women, Infants, and Children (WIC) program changed in 2009. This article examines purchases of whole grain products before and after the change. Nielsen Homescan panel data from 2008 to 2010 provide information on households’ food purchases, demographics, and self-reported WIC participation status. We estimate the effect of WIC participation and the 2009 package change on whole grains purchases using a difference-in-difference method, and find that participation in the WIC program was associated with more whole grain purchases during the observed period; the package change in 2009 roughly doubled the associated effect of WIC participation on the purchases of whole grain products. These results are consistent with recommendations in the Dietary Guidelines for Americans and suggest that moderate innovations in the design of food assistance programs can lead to beneficial dietary choices.
    Keywords: D10 - General, I18 - Government Policy ; Regulation ; Public Health, 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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  • 93
    Publication Date: 2016-12-07
    Description: As US beef and pork prices approached record high levels in 2014, industry analysts expressed surprised at consumer response. Because the relative price swings have occurred only recently, traditional approaches to demand analysis that rely on historical data series may be less useful than is typically the case. Employing one of the largest and longest-running choice experiments, we analyze data on 110,295 choices made by 12,255 consumers observed over a year-long time period coinciding with historically high meat prices. Our findings reveal nonlinear demands for meat products, with demand being more inelastic at higher prices. Ground beef, steak, and pork chop demands are more sensitive to changes in chicken breast price than the reverse. Moreover, cross-price elasticities between disaggregate meat products shrink as prices rise. Consumers' incomes significantly affect demand inter-relationships. Higher income consumers are more likely to choose steak and chicken breasts and are less likely to choose ground beef, chicken wings, and deli ham than are lower income consumers. High-income consumers tend to be less responsive to own-price changes and more responsive to cross-price changes than lower income consumers. This analysis provides estimates of structural demand parameters that help explain current meat expenditure patterns, and the results have implications for the assumption of linearity often invoked in policy analyses. 
    Keywords: C83 - Survey Methods ; Sampling Methods, D12 - Consumer Economics: Empirical Analysis, Q11 - Aggregate Supply and Demand Analysis ; Prices, 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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  • 94
    Publication Date: 2016-12-16
    Description: Asexual development of phytopathogenic fungi such as Magnaporthe oryzae involves morphological changes that require spatiotemporal regulation of polarized growth. ADP-ribosylation factor 6 (Arf6) is a small GTPase known to regulate membrane trafficking and organization of the actin cytoskeleton at the cell surface, and consequently has an impact on cell morphology and polarity. In this study, we have functionally characterized the Arf6 homolog in M. oryzae , showing that arf6 exhibits hyperbranching at hyphal tips and morphologically abnormal conidia as a result of defective polarized growth. arf6 hyphae are also defective in endocytosis as evidenced by a significant delay of FM4-64 uptake. Most arf6 conidia display reduced conidial length, and have defects in conidial septum formation and nuclear distribution. Furthermore, arf6 conidia show a disorganized actin cytoskeleton with random distribution of actin patches at the cell cortex and reduced accumulation of tropomyosin. Arf6-GFP is found to concentrate at the septum area and possibly in endocytic vesicles. Taken together, our data indicate that Arf6 plays an essential role in endocytosis and polarity establishment during asexual development of M. oryzae.
    Keywords: Pathogens & Pathogenicity
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  • 95
    Publication Date: 2016-10-21
    Description: Accurate information on thermal conductivity and thermal diffusivity of materials is of central importance in relation to geoscience and engineering problems involving the transfer of heat. Several methods, including the classical divided bar technique, are available for laboratory measurements of thermal conductivity, but much fewer for thermal diffusivity. We have generalized the divided bar technique to the transient case in which thermal conductivity, volumetric heat capacity and thereby also thermal diffusivity are measured simultaneously. As the density of samples is easily determined independently, specific heat capacity can also be determined. The finite element formulation provides a flexible forward solution for heat transfer across the bar, and thermal properties are estimated by inverse Monte Carlo modelling. This methodology enables a proper quantification of experimental uncertainties on measured thermal properties and information on their origin. The developed methodology was applied to various materials, including a standard ceramic material and different rock samples, and measuring results were compared with results applying traditional steady-state divided bar and an independent line-source method. All measurements show highly consistent results and with excellent reproducibility and high accuracy. For conductivity the obtained uncertainty is typically 1–3 per cent, and for diffusivity uncertainty may be reduced to about 3–5 per cent. The main uncertainty originates from the presence of thermal contact resistance associated with the internal interfaces in the bar. These are not resolved during inversion and it is imperative that they are minimized. The proposed procedure is simple and may quite easily be implemented to the many steady-state divided bar systems in operation. A thermally controlled bath, as applied here, may not be needed. Simpler systems, such as applying temperature-controlled water directly from a tap, may also be applied.
    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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  • 96
    Publication Date: 2016-10-08
    Description: The transduction mediated by bacteriophages is considered to be one of the primary driving forces in horizontal gene transfer in staphylococci, which is crucial to their adaptation and successful evolution. For a transduction to be effective, it is generally accepted that the recipient strain should be susceptible to the transducing phage. In this study, we demonstrate that the plasmid DNAs are effectively transduced into the recipient Staphylococcus aureus strains in spite of their insensitivity to the lytic action of the transducing phage, provided that these phages adsorb effectively to the bacterial cells. The tetracycline and penicillinase plasmids were transduced to insensitive laboratory and clinical strains by bacteriophages 29, 52A and 80α as well as by prophage 53 and naturally occurring prophages induced from donor lysogenic strains. Comparable frequencies of transduction were achieved in both phage-sensitive and phage-insensitive recipient strains. We have demonstrated that such mechanisms as the restriction of DNA and lysogenic immunity which are responsible for insensitivity of cells to phages may not be a barrier to the transfer, maintenance and effective spread of plasmids to a wider range of potential recipients in the staphylococcal population.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 97
    Publication Date: 2015-08-11
    Description: The Special Supplemental Nutrition Program for Women, Infants and Children (WIC) Program is a key part of America's safety net, but its structure fails to incentivize participants to be cost-conscious in their purchases and may cause retailers to attach excessive markups to WIC products. We investigate cost containment in the WIC Program, with a focus on California. Results show that smaller vendors often charge considerably higher prices for WIC foods than their larger counterparts. However, larger vendors do not mark up WIC foods more or promote them less than comparable control products. Cost containment can be improved by targeting WIC Program sales to larger vendors when it is possible to do so without compromising participant access, and using large-vendor prices as a benchmark to limit prices set by smaller vendors.
    Keywords: D12 - Consumer Economics: Empirical Analysis, I38 - Government Policy ; Provision and Effects of Welfare Programs, 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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  • 98
    Publication Date: 2015-09-19
    Description: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 99
    Publication Date: 2015-08-29
    Description: Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage of this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled design (same individual at different time points) would overcome this problem but is often limited by the relatively small numbers of available paired samples and the statistics being used. To overcome these limitations, we have developed a new vector-based approach, termed three-component analysis, which incorporates temporal distance, signal intensity and variance into one single score for gene ranking and is combined with gene set enrichment analysis. We tested our method on a unique age-based sample set of human skin fibroblasts and combined genome-wide transcription, DNA methylation and histone methylation (H3K4me3 and H3K27me3) data. Importantly, our method can now for the first time demonstrate a clear age-dependent decrease in expression of genes coding for proteins involved in translation and ribosome function. Using analogies with data from lower organisms, we propose a model where age-dependent down-regulation of protein translation-related components contributes to extend human lifespan.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 100
    Publication Date: 2015-05-29
    Description: A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines G enomic O rigins T hrough T axonomic CHA llenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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