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Sample records for acid plfa analyses

  1. Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses.

    PubMed

    Chen, Yin; Dumont, Marc G; McNamara, Niall P; Chamberlain, Paul M; Bodrossy, Levente; Stralis-Pavese, Nancy; Murrell, J Colin

    2008-02-01

    The active methanotroph community was investigated for the first time in heather (Calluna)-covered moorlands and Sphagnum/Eriophorum-covered UK peatlands. Direct extraction of mRNA from these soils facilitated detection of expression of methane monooxygenase genes, which revealed that particulate methane monooxygenase and not soluble methane monooxygenase was probably responsible for CH(4) oxidation in situ, because only pmoA transcripts (encoding a subunit of particulate methane monooxygenase) were readily detectable. Differences in methanotroph community structures were observed between the Calluna-covered moorland and Sphagnum/Eriophorum-covered gully habitats. As with many other Sphagnum-covered peatlands, the Sphagnum/Eriophorum-covered gullies were dominated by Methylocystis. Methylocella and Methylocapsa-related species were also present. Methylobacter-related species were found as demonstrated by the use of a pmoA-based diagnostic microarray. In Calluna-covered moorlands, in addition to Methylocella and Methylocystis, a unique group of peat-associated type I methanotrophs (Gammaproteobacteria) and a group of uncultivated type II methanotrophs (Alphaproteobacteria) were also found. The pmoA sequences of the latter were only distantly related to Methylocapsa and also to the RA-14 group of methanotrophs, which are believed to be involved in oxidation of atmospheric concentrations of CH(4). Soil samples were also labelled with (13)CH(4), and subsequent analysis of the (13)C-labelled phospholipid fatty acids (PLFAs) showed that 16:1 omega 7, 18:1 omega 7 and 18:1 omega 9 were the major labelled PLFAs. The presence of (13)C-labelled 18:1 omega 9, which was not a major PLFA of any extant methanotrophs, indicated the presence of novel methanotrophs in this peatland.

  2. PLFA analyses of microbial communities associated with PAH-contaminated riverbank sediment.

    PubMed

    Pratt, Brenda; Riesen, Roland; Johnston, Carl G

    2012-10-01

    Sediment contaminated with polycyclic aromatic hydrocarbons (PAHs) is widely distributed in aquatic ecosystems. The microbial community structure of riverbank PAH-contaminated sediments was investigated using phospholipid-derived fatty acid (PLFA) analysis. Surface and subsurface riverbank sediment was collected from a highly contaminated site and from an uncontaminated site along the Mahoning River, OH. PAH concentrations, physical sediment characteristics, and other microbial community parameters (biomass as phospholipid phosphate (PLP) and activity) were also measured. PAHs were detected in all samples but were only quantifiable in the contaminated (250 μg/g g(-1)) subsurface sediment. Subsurface samples from both locations showed very similar PLP values and distribution of PLFAs, with 27-37 % of the microbial community structure being composed of sulfate reducing and other anaerobic bacteria. Principal components analysis indicated no correlation between PAH contamination and PLFA diversity. Although PLP and phospholipid fatty acid measurements of bacterial communities did not reflect the environmental differences among sites, the highly PAH-contaminated sediment showed the highest measured microbial activity (reduction of 1,200 nmol INT g(-1) h(-1)), likely from a population adapted to environmental pollutants, rates that are much higher than measured in many uncontaminated soil and sediment systems. These data warrant further investigation into community structure at the genetic level and indicate potential for bioremediation by indigenous microbes.

  3. Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses

    PubMed Central

    Stagnari, Fabio; Perpetuini, Giorgia; Tofalo, Rosanna; Campanelli, Gabriele; Leteo, Fabrizio; Della Vella, Umberto; Schirone, Maria; Suzzi, Giovanna; Pisante, Michele

    2014-01-01

    In the present study, long-term organic and conventional managements were compared at the experimental field of Monsampolo del Tronto (Marche region, Italy) with the aim of investigating soil chemical fertility and microbial community structure. A polyphasic approach, combining soil fertility indicators with microbiological analyses (plate counts, PCR-denaturing gradient gel electrophoresis [DGGE] and phospholipid fatty acid analysis [PLFA]) was applied. Organic matter, N as well as some important macro and micronutrients (K, P, Mg, Mn, Cu, and Zn) for crop growth, were more available under organic management. Bacterial counts were higher in organic management. A significant influence of management system and management x crop interaction was observed for total mesophilic bacteria, nitrogen fixing bacteria and actinobacteria. Interestingly, cultivable fungi were not detected in all analyzed samples. PLFA biomass was higher in the organic and Gram positive bacteria dominated the microbial community in both systems. Even if fungal biomass was higher in organic management, fungal PCR-DGGE fingerprinting revealed that the two systems were very similar in terms of fungal species suggesting that 10 years were not enough to establish a new dynamic equilibrium among ecosystem components. A better knowledge of soil biota and in particular of fungal community structure will be useful for the development of sustainable management strategies. PMID:25540640

  4. Analysis of phospholipid fatty acids (PLFA) to characterize microbial communities in aquifers

    NASA Astrophysics Data System (ADS)

    Green, Christopher T.; Scow, Kate M.

    This paper reviews published applications of lipid-based biochemical techniques for characterizing microbial communities in aquifers and other deep subsurface habitats. These techniques, such as phospholipid fatty acid (PLFA) analysis, can provide information on a variety of microbial characteristics, such as biomass, physiology, taxonomic and functional identity, and overall community composition. In addition, multivariate statistical analysis of lipid data can relate spatial or temporal changes in microbial communities to environmental factors. The use of lipid-based techniques in the study of groundwater microbiology is advantageous because they do not require culturing and can provide quantitative data on entire communities. However, combined effects of physiological and phylogenetic changes on the lipid composition of a community can confound interpretation of the data, and many questions remain about the validity of various lipid techniques. Despite these caveats, lipid-based research has begun to show trends in community composition in contaminated and pristine aquifers that contribute to our understanding of groundwater microbial ecology and have potential for use in optimization of bioremediation of groundwater pollutants. Résumé Ce papier passe en revue les applications des techniques biochimiques basées sur les lipides pour caractériser les communautés microbiennes présentes dans les aquifères et dans les autres habitats souterrains profonds. Ces techniques, telles que l'analyse des acides gras phospholipidiques (PLFA), peuvent fournir des informations sur un ensemble de caractères microbiens, tels que la biomasse, la physiologie, l'identité taxonomique et fonctionnelle, et surtout la composition de la communauté. En outre, l'analyse statistique multivariée des données sur les lipides peut établir les liens entre des changements spatiaux ou temporels dans la communauté microbienne et des facteurs environnementaux. L'utilisation des

  5. Characterization of lignocellulosic compositions' degradation during chicken manure composting with added biochar by phospholipid fatty acid (PLFA) and correlation analysis.

    PubMed

    Liu, Ning; Zhou, Jialiang; Han, Lujia; Huang, Guangqun

    2017-05-15

    Biorefractory high polymer lignocellulosic compositions may limit rapid composting and stable decomposition. Because their degradation during composting is not well understood, the correlation with microbial community profiles was assessed to reveal degradation mechanism of lignocellulosic compositions. Testing of chicken manure aerobic composting with added biochar was performed using phospholipid fatty acid (PLFA) and correlation analysis. Results demonstrated a good composting effect with good dynamic correlation between microbial characteristic (PLFA) and lignocellulosic compositions' degradation ratio. The prediction model for hemicellulose degradation ratio (R(2)=0.97, SEP=3.24) and the prediction model for cellulose degradation ratio (R(3)=0.94, SEP=3.09), built using PLFA 16:0-18:2ω6c and PLFA 18:2ω6c-18:3ω3 as the arguments had good predictive ability. Based on microbial analysis and quantitative characterization of the degradation ratio, the prediction models provided methodological support for delineating the mechanism of lignocellulosic compositions' degradation during chicken manure aerobic composting with added biochar.

  6. The effect of biochar amendment on the soil microbial community - PLFA analyses and 13C labeling results

    NASA Astrophysics Data System (ADS)

    Watzinger, A.; Feichtmair, S.; Rempt, F.; Anders, E.; Wimmer, B.; Kitzler, B.; Zechmeister-Boltenstern, S.; Horacek, M.; Zehetner, F.; Kloss, S.; Richoz, S.; Soja, G.

    2012-04-01

    The effects of biochar amendment on plant growth and on the chemical / physical soil characteristics are well explored but only few studies have investigated the impact on soil microorganisms. The response of the soil microbial community to biochar amendment was investigated by phospholipid fatty acid (PLFA) analysis in (i) a large scale pot experiment, (ii) a small scale pot experiment using 13C labeled biochar and (iii) an incubation study using 13C labeled biochar. In the large scale pot experiment, three different agricultural soils from Austria (Planosol, Cambisol, Chernozem) and four different types of biochar were investigated. In total, 25 treatments with 5 replicates each were set up and monitored over a year. The results from the pot experiments showed no significant influence of biochar amendment on the total microbial biomass in the first 100 days after biochar addition. However, discriminant analysis showed a distinction of biochar and control soils as well as a strong effect of the pyrolysis temperature on the microbial composition. The effect of biochar was dependent on the type of soil. In the Planosol, some PLFAs were affected positively, especially when adding biochar with a low pyrolysis temperature, in the first month. In the long term, microbial community composition altered. Growth of fungi and gram negative bacteria was enhanced. In the Chernozem, PLFAs from various microbial groups decreased in the long term. Variability in the incubation study was low. Consequently, many PLFAs were significantly affected by biochar amendment. Again, in the Planosol, gram negative bacteria, actinomycetes and, after 2 weeks, gram positive bacteria increased under biochar amendment whereas in the chernozem total microbial biomass and gram positive bacteria were negatively affected in the long term. The 13C labeling studies confirmed the low degradability of the biochar, i.e. no alteration of the content and the δ13C in the soil organic matter within 100 days

  7. Amino acid analyses of Apollo 14 samples.

    NASA Technical Reports Server (NTRS)

    Gehrke, C. W.; Zumwalt, R. W.; Kuo, K.; Aue, W. A.; Stalling, D. L.; Kvenvolden, K. A.; Ponnamperuma, C.

    1972-01-01

    Detection limits were between 300 pg and 1 ng for different amino acids, in an analysis by gas-liquid chromatography of water extracts from Apollo 14 lunar fines in which amino acids were converted to their N-trifluoro-acetyl-n-butyl esters. Initial analyses of water and HCl extracts of sample 14240 and 14298 samples showed no amino acids above background levels.

  8. Contributions of Understory and/or Overstory Vegetations to Soil Microbial PLFA and Nematode Diversities in Eucalyptus Monocultures

    PubMed Central

    Liu, Zhanfeng; Zhou, Lixia; Fu, Shenglei

    2014-01-01

    Ecological interactions between aboveground and belowground biodiversity have received many attentions in the recent decades. Although soil biodiversity declined with the decrease of plant diversity, many previous studies found plant species identities were more important than plant diversity in controlling soil biodiversity. This study focused on the responses of soil biodiversity to the altering of plant functional groups, namely overstory and understory vegetations, rather than plant diversity gradient. We conducted an experiment by removing overstory and/or understory vegetation to compare their effects on soil microbial phospholipid fatty acid (PLFA) and nematode diversities in eucalyptus monocultures. Our results indicated that both overstory and understory vegetations could affect soil microbial PLFA and nematode diversities, which manifested as the decrease in Shannon–Wiener diversity index (H′) and Pielou evenness index (J) and the increase in Simpson dominance index (λ) after vegetation removal. Soil microclimate change explained part of variance of soil biodiversity indices. Both overstory and understory vegetations positively correlated with soil microbial PLFA and nematode diversities. In addition, the alteration of soil biodiversity might be due to a mixing effect of bottom-up control and soil microclimate change after vegetation removal in the studied plantations. Given the studied ecosystem is common in humid subtropical and tropical region of the world, our findings might have great potential to extrapolate to large scales and could be conducive to ecosystem management and service. PMID:24427315

  9. Molecular differentiation of subsoil biopores of different origin by PLFA analysis

    NASA Astrophysics Data System (ADS)

    Banfield, Callum; Pausch, Johanna; Kuzyakov, Yakov

    2015-04-01

    Biologically generated macropores (biopores) are a key factor for propagation of root growth, nutrient mobilisation and acquisition from the subsoil. However, biopores of different origin, i.e. root-derived, earthworm-derived or of mixed origin, are difficult to distinguish visually in the field. Therefore, the objective of this study was to test molecular differentiation by means of phospholipds fatty acids (PLFA). 24 samples of biopore content of the three aforementioned origins and 8 bulk soil samples were taken from two soil depths (45 - 75 cm; 75 - 105 cm) and extracted twice by a solution of methanol, chloroform and citrate/KOH buffer (pH 4, v:v:v = 1:2:0.8). Following separation of phospholipids, derivatisation was by hydrolysation using NaOH in MeOH and methylation by adding BF3 and heating at 80°C. After further purification and preparation, samples were measured by gas chromatography - mass spectrometry (GC-MS). Generally, the abundance of PLFA differed only slightly between the upper and lower soil depth. Gram negative bacteria (16:1w7c, 18:1w7c and Cy17:0) were the most abundant microbial group in both depths and show clear enrichment in biopores, especially in the mixed-pore type. A similiar pattern was observed for fungi (18:2w6,9), but it was less pronounced in the deeper section. Actinomycetes (10Me16:0 and 10Me18:0) in contrast, show the highest enrichment in root-derived pores. Interestingly, highest abundance of AM fungi (16:1w5c) was found not in root-derived pores, but in the mixed-pore type. Protozoa (20:4w6) occured significantly higher in the earthworm-derived biopores. The majority of the gram positive bacteria (a15:0, i15:0, i17:0 and a17:0) showed no significant preference of habitat, i.e. in this case pore type or bulk soil. This is indicative for general decomposers of old soil organic matter. Thus we showed, that PLFA analysis not only a valuable molecular proxy for the differentiation of biopore types, but also provides deep insight

  10. Amino Acid Analyses of Acid Hydrolysates in Desert Varnish

    NASA Technical Reports Server (NTRS)

    Perry, Randall S.; Staley, James T.; Dworkin, Jason P.; Engel, Mike

    2001-01-01

    There has long been a debate as to whether rock varnish deposits are microbially mediated or are deposited by inorganic processes. Varnished rocks are found throughout the world primarily in arid and semi-arid regions. The varnish coats are typically up to 200 microns thick and are composed of clays and alternating layers enriched in manganese and iron oxides. The individual layers range in thickness from 1 micron to greater than 10 microns and may continue laterally for more than a 100 microns. Overlapping botryoidal structures are visible in thin section and scanning electron micrographs. The coatings also include small amounts of organic mater and detrital grains. Amino-acid hydrolysates offer a means of assessing the organic composition of rock varnish collected from the Sonoran Desert, near Phoenix, AZ. Chromatographic analyses of hydrolysates from powdered samples of rock varnish suggest that the interior of rock varnish is relatively enriched in amino acids and specifically in d-alanine and glutamic acid. Peptidoglycan (murein) is the main structural component of gram-positive bacterial cell walls. The d-enantiomer of alanine and glutamic acid are specific to peptidoglycan and are consequently an indicator for the presence of bacteria. D-alanine is also found in teichoic acid which is only found in gram-positive bacteria. Several researchers have cultured bacteria from the surface of rock varnish and most have been gram-positive, suggesting that gram-positive bacteria are intimately associated with varnish coatings and may play a role in the formation of varnish coatings.

  11. Investigation of petroleum residues and microbial PLFA in Barataria Bay sediments one year after the Deepwater Horizon oil spill

    NASA Astrophysics Data System (ADS)

    Clay, S.; Zimmerman, A. R.; Mahmoudi, N.; Silliman, B. R.; Slater, G. F.

    2012-12-01

    The Deepwater Horizon spill released crude oil into the Gulf of Mexico over a period of 3 months in 2010. Barataria Bay, Louisiana was among the most heavily impacted and extensively oil-contaminated coastlines. Studies conducted in the marshes show significant ecological and geologic effects from oil residues that reached the bay. Observation of the presence of an oil sheen associated with sediment disturbance raised the question as to whether petroleum residues were also present in the sediments of Barataria Bay. In order to address this question, six sediment cores were collected from non-oiled (#1 & 2) and oiled (#3-6) portions of Barataria Bay approximately one year after the Deepwater Horizon oil spill. Concentrations of n-alkanes, unresolved complex material (UCM) and polycyclic aromatic hydrocarbon (PAH) were determined in these upper sediments. In addition, concentrations of phospholipid fatty acids (PLFA) were determined to assess variations in microbial community abundance. Alkane concentrations ranged from 134 to 747 ng/g with chain lengths from C12 to C35. Most cores showed an odd over even preference (carbon preference index of 1.2 to 4.3) with highest concentrations of long chain compounds between C24 and C35 (average chain length 29 to 39), consistent with a terrestrial carbon source such as plant waxes. Core #6 however, in the southwest portion of the bay, had the lowest concentrations of alkanes, and shorter n-alkane chain lengths overall. Despite this difference, the core maintains a relatively high carbon preference index and average chain length compared to that which would be expected from oil contaminated sediments. Measured PAH concentrations were highly variable ranging from undetectable to 436 ng/g. These values are several orders of magnitude lower than what is generally seen in highly contaminated sediments. Further, UCM concentrations were negligible in the cores from the oiled regions. These findings suggest only a minimal presence of

  12. Stabilization of glucose-C in microbial cell membranes (PLFA) and cell walls (amino sugars) evaluated by 13C-labelling in a field experiment

    NASA Astrophysics Data System (ADS)

    Gunina, Anna; Kuzyakov, Yakov; Glaser, Bruno

    2015-04-01

    Microorganisms control carbon (C) cycle and strongly contribute to formation of soil organic matter. Strong differences in the turnover of microbial groups and cellular compounds complicate the assessment of their contribution to microbial food webs and C sequestration in soil in situ. The uptake and incorporation of 13C labeled glucose by microbial groups were traced during 50 days after the labeling under field conditions. 13C was analysed: i) in the cytosolic pool by chloroform fumigation extraction, ii) in cell membranes by phospholipid fatty acids (PLFA), iii) in cell walls by amino sugars, and iv) remaining in bulk soil. This allowed tracing C in microbial groups as well as cellular compounds. Mean residence times (MRT) of C in PLFA and the cytosol were 47 and 150 days, respectively. Such long cytosol MRT depends on its heterogeneous composition, which includes high and low molecular weight organics. Amino sugars were mainly originated from microbial residues and thus, observation periods higher than 1 year are required for estimation of their MRT. Relative 13C incorporation (13C portion in total pool C) was the highest for PLFAs (~1.5% at day 3), whereas 13C content of the cytosol and amino sugars was one and two orders of magnitude less, respectively. Relative 13C incorporation into amino sugars of living microorganisms showed only 0.57% on day 3. Therefore, the turnover of cell membrane components is two times faster than that of cell walls, even in living microorganisms. Both PLFAs and amino sugars showed that glucose C was preferentially used by bacteria. 13C incorporation into bacterial cell walls and membranes decreased with time, but increased or remained constant for fungi, reflecting faster turnover of bacteria than fungi. Consequently, bacteria contribute more to the decomposition of low molecular weight organics, whereas fungi consume bacterial products or necromass and contribute more to long-term C stabilisation. Thus, tracing of 13C in cellular

  13. Note on the chromatographic analyses of marine polyunsaturated fatty acids

    USGS Publications Warehouse

    Schultz, D.M.; Quinn, J.G.

    1977-01-01

    Gas-liquid chromatography was used to study the effects of saponification/methylation and thin-layer chromatographic isolation on the analyses of polyunsaturated fatty acids. Using selected procedures, the qualitative and quantitative distribution of these acids in marine organisms can be determined with a high degree of accuracy. ?? 1977 Springer-Verlag.

  14. Determination of microbial carbon sources and cycling during remediation of petroleum hydrocarbon impacted soil using natural abundance (14)C analysis of PLFA.

    PubMed

    Cowie, Benjamin R; Greenberg, Bruce M; Slater, Gregory F

    2010-04-01

    In a petroleum impacted land-farm soil in Sarnia, Ontario, compound-specific natural abundance radiocarbon analysis identified biodegradation by the soil microbial community as a major pathway for hydrocarbon removal in a novel remediation system. During remediation of contaminated soils by a plant growth promoting rhizobacteria enhanced phytoremediation system (PEPS), the measured Delta(14)C of phospholipid fatty acid (PLFA) biomarkers ranged from -793 per thousand to -897 per thousand, directly demonstrating microbial uptake and utilization of petroleum hydrocarbons (Delta(14)C(PHC) = -1000 per thousand). Isotopic mass balance indicated that more than 80% of microbial PLFA carbon was derived from petroleum hydrocarbons (PHC) and a maximum of 20% was obtained from metabolism of more modern carbon sources. These PLFA from the contaminated soils were the most (14)C-depleted biomarkers ever measured for an in situ environmental system, and this study demonstrated that the microbial community in this soil was subsisting primarily on petroleum hydrocarbons. In contrast, the microbial community in a nearby uncontaminated control soil maintained a more modern Delta(14)C signature than total organic carbon (Delta(14)C(PLFA) = +36 per thousand to -147 per thousand, Delta(14)C(TOC) = -148 per thousand), indicating preferential consumption of the most modern plant-derived fraction of soil organic carbon. Measurements of delta(13)C and Delta(14)C of soil CO(2) additionally demonstrated that mineralization of PHC contributed to soil CO(2) at the contaminated site. The CO(2) in the uncontaminated control soil exhibited substantially more modern Delta(14)C values, and lower soil CO(2) concentrations than the contaminated soils, suggesting increased rates of soil respiration in the contaminated soils. In combination, these results demonstrated that biodegradation in the soil microbial community was a primary pathway of petroleum hydrocarbon removal in the PEPS system. This study

  15. Standardizing methylation method during phospholipid fatty acid analysis to profile soil microbial communities.

    PubMed

    Chowdhury, Taniya Roy; Dick, Richard P

    2012-02-01

    Phospholipid fatty acid (PLFA) as biomarkers, is widely used to profile microbial communities in environmental samples. However, PLFA extraction and derivatization protocols are not standardized and have widely varied among published studies. Specifically investigators have used either HCl/MeOH or KOH/MeOH or both for the methylation step of PLFA analysis, without justification or research to support either one. It seems likely that each method could have very different outcomes and conclusions for PLFA based studies. Therefore, the objective of this study was to determine the effect of catalyst type for methylation on detecting PLFAs and implications for interpreting microbial profiling in soil. Fatty acid samples extracted from soils obtained from a wetland, an intermittently flooded site, and an adjacent upland site were subjected to HCl/MeOH or KOH/MeOH catalyzed methylation procedures during PLFA analyses. The methylation method using HCl/MeOH resulted in significantly higher concentrations of most PLFAs than the KOH/MeOH method. Another important outcome was that fatty acids with a methyl group (18:1ω,7c 11Me, TBSA 10Me 18:0, 10Me 18:0, 17:0 10Me and 16:0 10Me being an actinomycetes biomarker) could not be detected by HCl/MeOH catalyzed methylation but were found in appreciable concentrations with KOH/MeOH method. From our results, because the HCl/MeOH method did not detect the fatty acids containing methyl groups that could strongly influence the microbial community profile, we recommend that the KOH/MeOH catalyzed transesterification method should become the standard procedure for PLFA profiling of soil microbial communities.

  16. Unique Honey Bee (Apis mellifera) Hive Component-Based Communities as Detected by a Hybrid of Phospholipid Fatty-Acid and Fatty-Acid Methyl Ester Analyses

    PubMed Central

    2015-01-01

    Microbial communities (microbiomes) are associated with almost all metazoans, including the honey bee Apis mellifera. Honey bees are social insects, maintaining complex hive systems composed of a variety of integral components including bees, comb, propolis, honey, and stored pollen. Given that the different components within hives can be physically separated and are nutritionally variable, we hypothesize that unique microbial communities may occur within the different microenvironments of honey bee colonies. To explore this hypothesis and to provide further insights into the microbiome of honey bees, we use a hybrid of fatty acid methyl ester (FAME) and phospholipid-derived fatty acid (PLFA) analysis to produce broad, lipid-based microbial community profiles of stored pollen, adults, pupae, honey, empty comb, and propolis for 11 honey bee hives. Averaging component lipid profiles by hive, we show that, in decreasing order, lipid markers representing fungi, Gram-negative bacteria, and Gram-positive bacteria have the highest relative abundances within honey bee colonies. Our lipid profiles reveal the presence of viable microbial communities in each of the six hive components sampled, with overall microbial community richness varying from lowest to highest in honey, comb, pupae, pollen, adults and propolis, respectively. Finally, microbial community lipid profiles were more similar when compared by component than by hive, location, or sampling year. Specifically, we found that individual hive components typically exhibited several dominant lipids and that these dominant lipids differ between components. Principal component and two-way clustering analyses both support significant grouping of lipids by hive component. Our findings indicate that in addition to the microbial communities present in individual workers, honey bee hives have resident microbial communities associated with different colony components. PMID:25849080

  17. Identification of Biodegradation Pathways in a Multi-Process Phytoremediation System (MPPS) Using Natural Abundance 14C Analysis of PLFA

    NASA Astrophysics Data System (ADS)

    Cowie, B. R.; Greenberg, B. M.; Slater, G. F.

    2008-12-01

    Optimizing remediation of petroleum-contaminated soils requires thorough understanding of the mechanisms and pathways involved in a proposed remediation system. In many engineered and natural attenuation systems, multiple degradation pathways may contribute to observed contaminant mass losses. In this study, biodegradation in the soil microbial community was identified as a major pathway for petroleum hydrocarbon removal in a Multi-Process Phytoremediation System (MPPS) using natural abundance 14C analysis of Phospholipid Fatty Acids (PLFA). In contaminated soils, PLFA were depleted in Δ14C to less than -800‰, directly demonstrating microbial uptake and utilization of petroleum derived carbon (Δ14C = -992‰) during bioremediation. Mass balance indicated that more than 80% of microbial carbon was derived from petroleum hydrocarbons and a maximum of 20% was produced from metabolism of modern carbon sources. In contrast, in a nearby uncontaminated control soil, the microbial community maintained a nearly modern 14C signature, suggesting preferential degradation of more labile, recent carbon. Mass balance using δ13C and Δ14C of soil CO2 demonstrated that mineralization of petroleum carbon contributed 60-65% of soil CO2 at the contaminated site. The remainder was derived from atmospheric (27-30%) and decomposition of non- petroleum natural organic carbon (5-10%). The clean control exhibited substantially lower CO2 concentrations that were derived from atmospheric (55%) and natural organic carbon (45%) sources. This study highlights the value of using multiple carbon isotopes to identify degradation pathways in petroleum- contaminated soils undergoing phytoremediation and the power of natural abundance 14C to detect petroleum metabolism in natural microbial communities.

  18. Utilization of low molecular weight organics by soil microorganisms: combination of 13C-labelling with PLFA analysis

    NASA Astrophysics Data System (ADS)

    Gunina, Anna; Dippold, Michaela; Kuzyakov, Yakov

    2014-05-01

    Microbial metabolisation is the main transformation pathway of low molecular weight organic substances (LMWOS), but detailed knowledge concerning the fate of LMWOS in soils is strongly limited. Considering that various LMWOS classes enter biochemical cycles at different steps, we hypothesise that the percentage of their LMWOS-Carbon (C) used for microbial biomass (MB) production and consequently medium-term stabilisation in soil is different. We traced the three main groups of LMWOS: amino acids, sugars and carboxylic acids, by uniformly labelled 13C-alanine, -glutamate, -glucose, -ribose, -acetate and -palmitate. Incorporation of 13C from these LMWOS into MB (fumigation-extraction method) and into phospholipid fatty acids (PLFAs) (Bligh-Dyer extraction, purification and GC-C-IRMS measurement) was investigated under field conditions 3 d and 10 d after LMWOS application. The activity of microbial utilization of LMWOS for cell membrane construction was estimated by replacement of PLFA-C with 13C. Decomposition of LMWOS-C comprised 20-65% of the total label, whereas incorporation of 13C into MB amounted to 20-50% of initially applied 13C on day three and was reduced to 5-30% on day 10. Incorporation of 13C-labelled LMWOS into MB followed the trend sugars > carboxylic acids > amino acids. Differences in microbial utilisation between LMWOS were observed mainly at day 10. Thus, instead of initial rapid uptake, further metabolism within microbial cells accounts for the individual fate of C from different LMWOS in soils. Incorporation of 13C from each LMWOS into each PLFA occurred, which reflects the ubiquitous ability of all functional microbial groups for LMWOS utilization. The preferential incorporation of palmitate can be attributed to its role as a direct precursor for many fatty acids (FAs) and PLFA formation. Higher incorporation of alanine and glucose compared to glutamate, ribose and acetate reflect the preferential use of glycolysis-derived substances in the FAs

  19. Isotopic analyses of amino acids from the Murchison meteorite

    NASA Technical Reports Server (NTRS)

    Pizzarello, S.; Cronin, J. R.; Krishnamurthy, R. V.; Epstein, S.

    1991-01-01

    An account is given of the results of H-2, C-13 isotopic analyses of the Murchison meteorite incorporating an ultrafiltration step to exclude the possibility of fine particulate contaminants. The meteorite's amino acids were chromatographically separated in order to preclude isotopic enrichment by basic compounds other than the amino acids. The results indicate that the Murchison amino acids are isotopically highly unusual; delta-C-13 is elevated by about 40 percent, and delta-D by fully 2500 percent. This high D content of the meteorite's alpha-amino acids may be due to the synthesis of their molecular precursors by low-temperature ion-molecule reactions in an interstellar cloud.

  20. Investigating Freshwater Periphyton Community Response to Uranium with Phospholipid Fatty Acid and Denaturing Gradient Gel Electrophoresis Analyses

    SciTech Connect

    Small, Jack A.; Bunn, Amoret L.; McKinstry, Craig A.; Peacock, A. D.; Miracle, Ann L.

    2008-04-01

    Periphyton communities can be used as monitors of ecosystem health and as indicators of contamination in lotic systems. Measures of biomass, community structure and genetic diversity were used to investigate impacts of uranium exposure on periphyton. Laboratory exposures of periphyton in river water amended with uranium were performed for 5 days, followed by 2 days of uranium depuration in unamended river water. Productivity as measured by biomass was not affected by concentrations up to 100 µg L-1 uranium. Phospholipid fatty acid (PLFA) profiles and denaturing gradient gel electrophoresis (DGGE) banding patterns found no changes in community or genetic structure related to uranium exposure. We suggest that the periphyton community as a whole is not impacted by exposures of uranium up to a dose of 100 µg L-1. These findings have significance for the assessment and prediction of uranium impacts on aquatic ecosystems.

  1. Accumulated analyses of amino acid precursors in returned lunar samples

    NASA Technical Reports Server (NTRS)

    Fox, S. W.; Harada, K.; Hare, P. E.

    1973-01-01

    Six amino acids (glycine, alanine, aspartic acid, glutamic acid, serine, and threonine) obtained by hydrolysis of extracts have been quantitatively determined in ten collections of fines from five Apollo missions. Although the amounts found, 7-45 ng/g, are small, the lunar amino acid/carbon ratios are comparable to those of the carbonaceous chondrites, Murchison and Murray, as analyzed by the same procedures. Since both the ratios of amino acid to carbon, and the four or five most common types of proteinous amino acid found, are comparable for the two extraterrestrial sources despite different cosmophysical histories of the moon and meteorites, common cosmochemical processes are suggested.

  2. Amino acid analyses of R and CK chondrites

    NASA Astrophysics Data System (ADS)

    Burton, Aaron S.; McLain, Hannah; Glavin, Daniel P.; Elsila, Jamie E.; Davidson, Jemma; Miller, Kelly E.; Andronikov, Alexander V.; Lauretta, Dante; Dworkin, Jason P.

    2015-03-01

    Exogenous delivery of amino acids and other organic molecules to planetary surfaces may have played an important role in the origins of life on Earth and other solar system bodies. Previous studies have revealed the presence of indigenous amino acids in a wide range of carbon-rich meteorites, with the abundances and structural distributions differing significantly depending on parent body mineralogy and alteration conditions. Here we report on the amino acid abundances of seven type 3-6 CK chondrites and two Rumuruti (R) chondrites. Amino acid measurements were made on hot water extracts from these meteorites by ultrahigh-performance liquid chromatography with fluorescence detection and time-of-flight mass spectrometry. Of the nine meteorites analyzed, four were depleted in amino acids, and one had experienced significant amino acid contamination by terrestrial biology. The remaining four, comprised of two R and two CK chondrites, contained low levels of amino acids that were predominantly the straight chain, amino-terminal (n-ω-amino) acids β-alanine, and γ-amino-n-butyric acid. This amino acid distribution is similar to what we reported previously for thermally altered ureilites and CV and CO chondrites, and these n-ω-amino acids appear to be indigenous to the meteorites and not the result of terrestrial contamination. The amino acids may have been formed by Fischer-Tropsch-type reactions, although this hypothesis needs further testing.

  3. Assessing microbial utilization of free versus sorbed Alanine by using position-specific 13C labeling and 13C-PLFA analysis

    NASA Astrophysics Data System (ADS)

    Herschbach, Jennifer; Apostel, Carolin; Spielvogel, Sandra; Kuzyakov, Yakov; Dippold, Michaela

    2016-04-01

    Microbial utilization is a key transformation process of soil organic matter (SOM). Sorption of low molecular weight organic substances (LMWOS) to soil mineral surfaces blocks or delays microbial uptake and therefore mineralization of LMWOS to CO2, as well as all other biochemical transformations. We used position-specific labeling, a tool of isotope applications novel to soil science, combined with 13C-phospholipid fatty acid (PLFA) analysis, to assess microbial utilization of sorbed and non-sorbed Alanine in soil. Alanine has various functional groups enabling different sorption mechanisms via its positive charge (e.g. to clay minerals by cation exchange), as well as via its negative charge (e.g. to iron oxides by ligand exchange). To assess changes in the transformation pathways caused by sorption, we added uniformly and position-specifically 13C and 14C labeled Alanine to the Ap of a loamy Luvisol in a short-term (10 days) incubation experiment. To allow for sorption of the tracer solution to an aliquot of this soil, microbial activity was minimized in this subsample by sterilizing the soil by γ-radiation. After shaking, the remaining solutions were filtered and the non-sorbed Alanine was removed with Millipore water and then added to non-sterilized soil. For the free Alanine treatment, solutions with Alanine of similar amount and isotopic composition were prepared, added to the soil and incubated as well. The respired CO2 was trapped in NaOH and its 14C-activity was determined at increasing times intervals. Microbial utilization of Alanine's individual C positions was evaluated in distinct microbial groups classified by 13C-PLFA analysis. Sorption to soil minerals delayed respiration to CO2 and reduced initial respiration rate by 80%. Irrespective of sorption, the highest amount was respired from the carboxylic position (C-1), whereas the amino-bound (C-2) and the methylic position (C-3) were preferentially incorporated into PLFA of microorganisms due to the

  4. Using Position-Specific 13C and 14C Labeling and 13C-PLFA Analysis to Assess Microbial Transformations of Free Versus Sorbed Alanine

    NASA Astrophysics Data System (ADS)

    Apostel, C.; Herschbach, J.; Bore, E. K.; Kuzyakov, Y.; Dippold, M. A.

    2015-12-01

    Sorption of charged or partially charged low molecular weight organic substances (LMWOS) to soil mineral surfaces delays microbial uptake and therefore mineralization of LMWOS to CO2, as well as all other biochemical transformations. We used position-specific labeling, a tool of isotope applications novel to soil sciences, to compare the transformation mechanisms of sorbed and non-sorbed alanine in soil. Alanine as an amino acid links C- and N-cycles in soil and therefore is a model substance for the pool of LMWOS. To assess transformations of sorbed alanine, we added position-specific and uniformly 13C and 14C labeled alanine tracer to soil that had previously been sterilized by γ-radiation. The labeled soil was added to non-sterilized soil from the same site and incubated. Soil labeled with the same tracers without previous sorption was prepared and incubated as well. We captured the respired CO2 and determined its 14C-activity at increasing time intervals. The incorporation of 14C into microbial biomass was determined by chloroform fumigation extraction (CFE), and utilization of individual C positions by distinct microbial groups was evaluated by 13C-phospholipid fatty acid analysis (PLFA). A dual peak in the respired CO2 revealed two sorption mechanisms. To compare the fate of individual C atoms independent of their concentration and pool size in soil, we applied the divergence index (DI). The DI reveals the convergent or divergent behavior of C from individual molecule positions during microbial utilization. Alanine C-1 position was mainly oxidized to CO2, while its C-2 and C-3 were preferentially incorporated in microbial biomass and PLFA. This indicates that sorption by the COOH group does not protect this group from preferential oxidation. Microbial metabolism was determinative for the preferential oxidation of individual molecule positions. The use of position-specific labeling revealed mechanisms and kinetics of microbial utilization of sorbed and non

  5. Phospholipid fatty acid analysis as part of the Yucca Mountain Project. Final report

    SciTech Connect

    Ringelberg, D.B.; White, D.C.

    1996-09-01

    In support of the Yucca Mountain subsurface microbial characterization project phospholipid fatty acid (PLFA) analyses for viable microbial biomass, community composition and nutritional status were performed. Results showed a positive correlation between a decrease in viable biomass and increase in depth with the lowest biomass values being obtained from the Topopah Spring geologic horizon. A plot of the ratio of non-viable (diglyceride fatty acids) to viable (PLFA) cells also showed the lowest values to derive from the Topopah Spring horizon. Estimations of microbial community composition, made from the patterns of PLFA recovered from the sediment samples, revealed similarities between samples collected within the same geologic horizons: Tiva Canyon, Pre-Pah Canyon and Topopah Spring. Results indicated the presence of mixed communities composed of gram positive, gram negative, actinomycete and obligate anaerobic bacteria. Culturable organisms, recovered from similar sediments, were representative of the same bacterial classifications although gram positive bacterial isolates typically outnumbered gram negative isolates. Within the gram negative bacterial community, corroborative indicators of physiological stress were apparent in the Topopah Spring horizon.

  6. Searching for Extraterrestrial Amino Acids in a Contaminated Meteorite: Amino Acid Analyses of the Canakkale L6 Chondrite

    NASA Technical Reports Server (NTRS)

    Burton, A. S.; Elsila, J. E.; Glavin, D. P.; Dworkin, J. P.; Ornek, C. Y.; Esenoglu, H. H.; Unsalan, O.; Ozturk, B.

    2016-01-01

    Amino acids can serve as important markers of cosmochemistry, as their abundances and isomeric and isotopic compositions have been found to vary predictably with changes in parent body chemistry and alteration processes. Amino acids are also of astrobiological interest because they are essential for life on Earth. Analyses of a range of meteorites, including all groups of carbonaceous chondrites, along with H, R, and LL chondrites, ureilites, and a martian shergottite, have revealed that amino acids of plausible extraterrestrial origin can be formed in and persist after a wide range of parent body conditions. However, amino acid analyses of L6 chondrites to date have not provided evidence for indigenous amino acids. In the present study, we performed amino acid analysis on larger samples of a different L6 chondite, Canakkale, to determine whether or not trace levels of indigenous amino acids could be found. The Canakkale meteor was an observed fall in late July, 1964, near Canakkale, Turkey. The meteorite samples (1.36 and 1.09 g) analyzed in this study were allocated by C. Y. Ornek, along with a soil sample (1.5 g) collected near the Canakkale recovery site.

  7. Fatty acid profiles in Leishmania spp. isolates with natural resistance to nitric oxide and trivalent antimony.

    PubMed

    de Azevedo, Alana Freire; Dutra, Jorge Luís de Lisboa; Santos, Micheli Luize Barbosa; Santos, Darlisson de Alexandria; Alves, Péricles Barreto; de Moura, Tatiana Rodrigues; de Almeida, Roque Pacheco; Fernandes, Marcelo Ferreira; Scher, Ricardo; Fernandes, Roberta Pereira Miranda

    2014-01-01

    Fatty acids, especially those from phospholipids (PLFA), are essential membrane components that are present in relatively constant proportions in biological membranes under natural conditions. However, under harmful growth conditions, such as diseases, environmental changes, and chemical exposure, the fatty acid proportions might vary. If such changes could be identified and revealed to be specific for adverse situations, they could be used as biomarkers. Such biomarkers could facilitate the identification of virulence and resistance mechanisms to particular chemotherapeutic agents. Therefore, specific biomarkers could lead to better therapeutic decisions that would, in turn, enhance treatment effectiveness. The objective of this study was to compare the fatty acid profiles of trivalent antimony and nitric oxide (NO)-resistant and -sensitive Leishmania chagasi and Leishmania amazonensis isolates. Fatty acid methyl esters (FAMEs) were obtained from total lipids (MIDI), ester-linked lipids (ELFA), and ester-linked phospholipids (PLFA). FAMEs were analyzed by chromatography and mass spectrometry. Species- or resistance-associated differences in FAME profiles were assessed by nonmetric multidimensional scaling, multiresponse permutation procedures, and indicator species analyses. The isolate groups had different MIDI-FAME profiles. However, neither the ELFA nor PLFA profiles differed between the sensitive and resistant isolates. Levels of the fatty acid 18:1 Δ9c were increased in sensitive isolates (p < 0,001), whereas the fatty acid 20:4 Δ5,8,11,14 showed the opposite trend (p < 0.01). We conclude that these two fatty acids are potential biomarkers for NO and antimony resistance in L. chagasi and L. amazonensis and that they could be helpful in therapeutic diagnoses.

  8. Improved analyses for soil carbohydrates, amino acids, and phenols: Tools for understanding soil processes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A process-level understanding of soil carbon(C) and nitrogen (N) cycling will be facilitated by precise measurement of biochemical compounds in soil organic matter. This review summarizes some recent developments in analyses for soil carbohydrates, amino compounds (amino acids and amino sugars), and...

  9. An on-line potentiometric sequential injection titration process analyser for the determination of acetic acid.

    PubMed

    van Staden, J F; Mashamba, Mulalo G; Stefan, Raluca I

    2002-09-01

    An on-line potentiometric sequential injection titration process analyser for the determination of acetic acid is proposed. A solution of 0.1 mol L(-1) sodium chloride is used as carrier. Titration is achieved by aspirating acetic acid samples between two strong base-zone volumes into a holding coil and by channelling the stack of well-defined zones with flow reversal through a reaction coil to a potentiometric sensor where the peak widths were measured. A linear relationship between peak width and logarithm of the acid concentration was obtained in the range 1-9 g/100 mL. Vinegar samples were analysed without any sample pre-treatment. The method has a relative standard deviation of 0.4% with a sample frequency of 28 samples per hour. The results revealed good agreement between the proposed sequential injection and an automated batch titration method.

  10. Technical note: improved methodology for analyses of acid detergent fiber and acid detergent lignin.

    PubMed

    Raffrenato, E; Van Amburgh, M E

    2011-07-01

    The objective of this study was to evaluate the methodology of the acid detergent lignin (ADL) assay in an effort to evaluate particle loss, improve repeatability, and decrease variation within and among samples. The original ADL method relied on asbestos as a filtering aid, but that was removed in 1989 with the mandate from the Environmental Protection Agency to eliminate asbestos in the environment. Furthermore, recent work on fiber methodology indicated that pore size in the Gooch sintered glass crucible (40-60 μm) was too large to trap all of the small particles associated with neutral detergent fiber (NDF) and acid detergent fiber (ADF). Thus, any loss of ADF could potentially result in a loss of ADL. Sixty forages including conventional and brown midrib corn silages, alfalfa silages and hays, mature grasses, early vegetative grasses, and 9 feces samples, were analyzed sequentially for ADF and ADL as outlined in the 1973 procedure of Van Soest except for the use of the asbestos fiber. A glass microfiber filter with a 1.5-μm pore size was chosen as a filtering aid because it met the criteria required by the assay: glass, heat resistant, acid resistant, chemically inert, and hydrophobic. To compare with the current ADF and ADL assays, the assays were conducted with either no filter or the glass filter inserted into crucibles, rinsed with acetone, and then according to the 1973 procedure of Van Soest. The samples analyzed covered a range from 18.11 to 55.79% ADF and from 0.96 to 9.94% ADL on a dry matter (DM) basis. With the use of the filter, the mean ADF values increased 4.2% and mean ADL values increased 18.9%. Overall, both ADF and ADL values were greater with the use of the glass microfiber filter than without, indicating that as the type of sample analyzed changed, use of the Gooch crucible without the filtering aid results in particle loss. The adoption of the use of a small pore size (1.5 μm) glass microfiber filter to improve filtration and recovery

  11. Microbial transformations of free versus sorbed alanine analyzed by position-specific 13C and 14C labeling and 13C-PLFA analysis

    NASA Astrophysics Data System (ADS)

    Apostel, Carolin; Dippold, Michaela; Bore, Ezekiel; Kuzyakov, Yakov

    2015-04-01

    Sorption of charged or partially charged low molecular weight organic substances (LMWOS) to soil mineral surfaces delays microbial uptake and therefore mineralization of LMWOS to CO2, as well as all other biochemical transformations. We used position-specific labeling, a tool of isotope applications novel to soil sciences, to compare the transformation mechanisms of sorbed and non-sorbed alanine in soil. Alanine as an amino acid links C- and N-cycles in soil and therefore is a model representative for the pool of LMWOS. To assess transformations of sorbed alanine, we combined position-specifically and uniformly 13C and 14C labeled alanine tracer solution with a loamy haplic luvisol that had previously been sterilized by γ-radiation. After shaking the mixtures, the supernatant was removed, as was all non-sorbed alanine by repeated shaking with millipore water. The labeled soil was added to non-sterilized soil from the same site. To compare the effect of sorption, soil labeled with the same position-specifically labeled tracers without previous sorption was prepared and incubated as well. We captured the respired CO2 and determined its 14C-activity at increasing time steps. The incorporation of 14C into microbial biomass was determined by CFE, and utilization of individual C positions by distinct microbial groups was evaluated by 13C-PLFA analysis. A dual peak in the respired CO2 revealed the influence of two sorption mechanisms. Microbial uptake and transformation of the sorbed alanine was 3 times slower compared to non-sorbed alanine. To compare the fate of individual C atoms independent of their concentration and pool size in soil, we introduced the divergence index (DI). The DI reveals the convergent or divergent behaviour of C from individual molecule positions during microbial utilization. The DI revealed, that alanines C-1 position was mainly oxidized to CO2, while its C-2 and C-3 were preferentially incorporated in microbial biomass and PLFAs. This indicates

  12. Isotopic and molecular analyses of hydrocarbons and monocarboxylic acids of the Murchison meteorite

    NASA Technical Reports Server (NTRS)

    Krishnamurthy, R. V.; Epstein, S.; Cronin, John R.; Pizzarello, Sandra; Yuen, George U.

    1992-01-01

    The monocarboxylic acids and hydrocarbons of the Murchison meteorite (CM2) were isolated for isotropic analysis. The nonvolatile hydrocarbons were analyzed as crude methanol and benzene-methanol extracts and also after separation by silica gel chromatography into predominantly aliphatic, aromatic, and polar hydrocarbon fractions. The volatile hydrocarbons were obtained after progressive decomposition of the meteorite matrix by freeze-thaw, hot water, and acid treatment. Molecular analyses of the aromatic hydrocarbons showed them to comprise a complex suite of compounds in which pyrene, fluoranthene, phenanthrene, and acenaphthene were the most abundant components, a result similar to earlier analyses. The polar hydrocarbons also comprise a very complex mixture in which aromatic ketones, nitrogen, and sulfur heterocycles were identified. The monocarboxylic acids, aliphatic, aromatic, and polar hydrocarbons, and the indigenous volatile hydrocarbons were found to be D-rich. The deuterium enrichment observed in these compounds is suggestive. In two separate analyses, the delta-D values of the nonvolatile hydrocarbons were observed to increase in the following order: aliphatic-aromatic-polar. This finding is consistent with an early solar system or parent body conversion of aromatic to aliphatic compounds as well as the suggestion of pyrolytic formation of aromatic from aliphatic compounds.

  13. Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses.

    PubMed

    Masta, Susan E; Longhorn, Stuart J; Boore, Jeffrey L

    2009-01-01

    Phylogenetic analyses based on mitochondrial DNA have yielded widely differing relationships among members of the arthropod lineage Arachnida, depending on the nucleotide coding schemes and models of evolution used. We enhanced taxonomic coverage within the Arachnida greatly by sequencing seven new arachnid mitochondrial genomes from five orders. We then used all 13 mitochondrial protein-coding genes from these genomes to evaluate patterns of nucleotide and amino acid biases. Our data show that two of the six orders of arachnids (spiders and scorpions) have experienced shifts in both nucleotide and amino acid usage in all their protein-coding genes, and that these biases mislead phylogeny reconstruction. These biases are most striking for the hydrophobic amino acids isoleucine and valine, which appear to have evolved asymmetrical exchanges in response to shifts in nucleotide composition. To improve phylogenetic accuracy based on amino acid differences, we tested two recoding methods: (1) removing all isoleucine and valine sites and (2) recoding amino acids based on their physiochemical properties. We find that these methods yield phylogenetic trees that are consistent in their support of ancient intraordinal divergences within the major arachnid lineages. Further refinement of amino acid recoding methods may help us better delineate interordinal relationships among these diverse organisms.

  14. Isotopic analyses of nitrogenous compounds from the Murchison meteorite: ammonia, amines, amino acids, and polar hydrocarbons

    NASA Technical Reports Server (NTRS)

    Pizzarello, S.; Feng, X.; Epstein, S.; Cronin, J. R.

    1994-01-01

    The combined volatile bases (ammonia, aliphatic amines, and possibly other bases), ammonia, amino acids, and polar hydrocarbons were prepared from the Murchison meteorite for isotopic analyses. The volatile bases were obtained by cryogenic transfer after acid-hydrolysis of a hot-water extract and analyzed by combined gas chromatography-mass spectrometry of pentafluoropropionyl derivatives. The aliphatic amines present in this preparation comprise a mixture that includes both primary and secondary isomers through C5 at a total concentration of > or = 100 nmoles g-1. As commonly observed for meteoritic organic compounds, almost all isomers through C5 are present, and the concentrations within homologous series decrease with increasing chain length. Ammonia was chromatographically separated from the other volatile bases and found at a concentration of 1.1-1.3 micromoles g-1 meteorite. The ammonia analyzed includes contributions from ammonium salts and the hydrolysis of extractable organic compounds, e.g., carboxamides. Stable isotope analyses showed the volatile bases to be substantially enriched in the heavier isotopes, relative to comparable terrestrial compounds delta D < or = +1221%; delta 13C = +22%; delta 15N = +93%). Ammonia, per se, was found to have a somewhat lower delta 15N value (+69%) than the total volatile bases; consequently, a higher delta 15N (>93%) can be inferred for the other bases, which include the amines. Solvent-extractable polar hydrocarbons obtained separately were found to be enriched in 15N (delta 15N = +104%). Total amino acids, prepared from a hydrolyzed hot-water extract by cation exchange chromatography, gave a delta 15N of +94%, a value in good agreement with that obtained previously. Nitrogen isotopic data are also given for amino acid fractions separated chromatographically. The delta 15N values of the Murchison soluble organic compounds analyzed to date fall within a rather narrow range (delta 15N = +94 +/- 8%), an observation

  15. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism

    PubMed Central

    Wang, Lijie; Zhang, Tong; Watson, David G.; Silva, Ana Marta; Coombs, Graham H.

    2015-01-01

    Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts. PMID:26368322

  16. Discrimination of prey species of juvenile swordfish Xiphias gladius (Linnaeus, 1758) using signature fatty acid analyses

    NASA Astrophysics Data System (ADS)

    Young, Jock W.; Guest, Michaela A.; Lansdell, Matt; Phleger, Charles F.; Nichols, Peter D.

    2010-07-01

    Signature lipid and fatty acid analysis were used to discriminate the diet of swordfish ( Xiphias gladius, orbital fork length: 60-203 cm) from waters off eastern Australia. The fatty acid (FA) composition of a range of known prey (squid, myctophids, and other fishes) of swordfish, taken from stomach samples and from net tows, was compared with that of the white muscle tissue (WMT) of swordfish from the same region. Swordfish muscle was lipid rich (average 24-42% dry weight), as was the skeleton (28-41%). The robustness of the approach was also tested by comparison against a key squid prey species that was collected and stored using different protocols: (i) fresh frozen, (ii) fresh frozen, then thawed, and (iii) stomach content collection. The FA profiles were generally similar, with the ratio of docosahexaenoic acid (DHA) and palmitic acid (16:0) in particular showing no significant difference. Major fatty acids in swordfish WMT were 18:1ω9c, 16:0, 22:6ω3, and 18:0. Multidimensional scaling showed that the swordfish WMT grouped closely with small fish prey including myctophids, and not with squid. Squid contained markedly higher 22:6ω3 than swordfish. Individual prey species of the myctophidae could also be separated by the same technique. These results were supported by traditional stomach content analyses (SCA) that showed fish were the dominant prey for small swordfish sampled from southern waters whereas squid were the main prey in more northern waters, matching the FA patterns we found for the two regions. We propose that where general diet patterns are established, signature FA analysis has good potential to compliment or in some cases, replace temporal and spatial monitoring of trophic pathways for swordfish and other marine species.

  17. Microbial utilization of sugars in soil assessed by position-specific labeling and compound-specific 13C-PLFA-analysis

    NASA Astrophysics Data System (ADS)

    Apostel, Carolin; Dippold, Michaela; Glaser, Bruno; Kuzyakov, Yakov

    2014-05-01

    For the transformation of low molecular weight organic substances (LMWOS) in soil, which is an important process in the turnover of organic matter, microbial utilization is one of the most important processes. Position-specific labeling combined with compound-specific 13C-PLFA-analysis allows a closer look on the mechanisms of LMWOS transformation in soil. We assessed short- (3 and 10 days) and long-term (half year) transformations of monosaccharides by adding position-specifically 13C labeled glucose and ribose to soil in a field experiment conducted on an agriculturally used luvisol located in north-western Bavaria. We quantified the microbial utilization of the different functional groups by 13C-analysis of microbial biomass with the chloroform-fumigation-extraction method (CFE). 13C-PLFA analysis enabled us to distinguish individual microbial groups and compare their C-utilization. Preferential degradation of glucoses C-3 and C-4 respectively C-1 position enabled differentiation between the two main hexose metabolic pathways - glycolysis and the pentose phosphate pathway. Microbial groups revealed different incorporation of specific C positions into their PLFA. The highest incorporation was reached by the prokaryotic gram- negative groups. The application of position-specifically labeled substances, coupled with compound-specific 13C-PLFA analysis opens a new way to investigate the microbial transformations of LMWOS in soil. Observing single C atoms and their utilization by specific microbial groups allow conclusions about the mechanisms and kinetics of microbial utilization and interaction between these groups and therefore will improve our understanding of soil carbon fluxes.

  18. THE EFFECTS OF DIFFERENT SAMPLE CONCENTRATIONS ON THE STRUCTURE OF MICROBIAL COMMUNITIES USING PHOSPHOLIPID FATTY ACID ANALYSIS

    EPA Science Inventory

    Phospholipid fatty acid (PLFA) analysis is a powerful tool for determination of microbial community structures in soils and sediments. However, accurate determination of total microbial biomass and structure of the microbial community may be dependent on the concentration of the...

  19. Application of carbon and hydrogen stable isotope analyses to detect exogenous citric acid in Japanese apricot liqueur.

    PubMed

    Akamatsu, Fumikazu; Oe, Takaaki; Hashiguchi, Tomokazu; Hisatsune, Yuri; Kawao, Takafumi; Fujii, Tsutomu

    2017-08-01

    Japanese apricot liqueur manufacturers are required to control the quality and authenticity of their liqueur products. Citric acid made from corn is the main acidulant used in commercial liqueurs. In this study, we conducted spiking experiments and carbon and hydrogen stable isotope analyses to detect exogenous citric acid used as an acidulant in Japanese apricot liqueurs. Our results showed that the δ(13)C values detected exogenous citric acid originating from C4 plants but not from C3 plants. The δ(2)H values of citric acid decreased as the amount of citric acid added increased, whether the citric acid originated from C3 or C4 plants. Commercial liqueurs with declared added acidulant provided higher δ(13)C values and lower δ(2)H values than did authentic liqueurs and commercial liqueurs with no declared added acidulant. Carbon and hydrogen stable isotope analyses are suitable as routine methods for detecting exogenous citric acid in Japanese apricot liqueur.

  20. Amino acid and DNA analyses in a family with ornithine transcarbamylase deficiency.

    PubMed

    Hou, J W; Wang, T R

    1996-02-01

    Ornithine transcarbamylase (OTC) is a hepatic mitochondrial enzyme involved in the detoxification of ammonia by the urea cycle. OTC deficiency is an X-linked genetic disorder, usually causing neonatal or infantile hyperammonemia, coma and death. We attended a male newborn who had poor feeding since 30 hours of age, at which time, he then rapidly progressed to a comatose state. Hyperammonemia and liver dysfunction were noted. Analysis of plasma amino acids showed elevated levels of glutamine and alanine, but a decreased level of arginine and no citrulline. OTC deficiency was diagnosed by family history of early death of newborn males on the maternal side and characteristic biochemical findings. In addition, it was proved by Southern blot analysis of genomic DNA. Although OTC deficiency has been described as the most common inborn error of ureagenesis in humans, to our knowledge, this is the first report in a Chinese family confirmed by biochemical and DNA analyses.

  1. Organic Analysis in the Miller Range 090657 CR2 Chondrite: Part 2 Amino Acid Analyses

    NASA Technical Reports Server (NTRS)

    Burton, A. S.; Cao, T.; Nakamura-Messenger, K.; Berger, E. L.; Messenger, S.; Clemett, S. J.; Aponte, J. C.; Elsila, J. E.

    2016-01-01

    Primitive carbonaceous chondrites contain a wide variety of organic material, ranging from soluble discrete molecules to insoluble, unstructured kerogen-like components, as well as structured nano-globules of macromolecular carbon. The relationship between the soluble organic molecules, macromolecular organic material, and host minerals are poorly understood. Due to the differences in extractability of soluble and insoluble organic materials, the analysis methods for each differ and are often performed independently. The combination of soluble and insoluble analyses, when performed concurrently, can provide a wider understanding of spatial distribution, and elemental, structural and isotopic composition of organic material in primitive meteorites. Using macroscale extraction and analysis techniques in combination with in situ microscale observation, we have been studying both insoluble and soluble organic material in the primitive CR2 chondrite Miller Range (MIL) 090657. In accompanying abstracts (Cao et al. and Messenger et al.) we discuss insoluble organic material in the samples. By performing the consortium studies, we aim to improve our understanding of the relationship between the meteorite minerals and the soluble and insoluble organic phases and to delineate which species formed within the meteorite and those that formed in nebular or presolar environments. In this abstract, we present the results of amino acid analyses of MIL 090657 by ultra performance liquid chromatography with fluorescence detection and quadrupole-time of flight mass spectrometry. Amino acids are of interest because they are essential to life on Earth, and because they are present in sufficient structural, enantiomeric and isotopic diversity to allow insights into early solar system chemical processes. Furthermore, these are among the most isotopically anomalous species, yet at least some fraction are thought to have formed by aqueously-mediated processes during parent body alteration.

  2. HPLC and ELISA analyses of larval bile acids from Pacific and western brook lampreys

    USGS Publications Warehouse

    Yun, S.-S.; Scott, A.P.; Bayer, J.M.; Seelye, J.G.; Close, D.A.; Li, W.

    2003-01-01

    Comparative studies were performed on two native lamprey species, Pacific lamprey (Lampetra tridentata) and western brook lamprey (Lampetra richardsoni) from the Pacific coast along with sea lamprey (Petromyzon marinus) from the Great Lakes, to investigate their bile acid production and release. HPLC and ELISA analyses of the gall bladders and liver extract revealed that the major bile acid compound from Pacific and western brook larval lampreys was petromyzonol sulfate (PZS), previously identified as a migratory pheromone in larval sea lamprey. An ELISA for PZS has been developed in a working range of 20pg-10ng per well. The tissue concentrations of PZS in gall bladder were 127.40, 145.86, and 276.96??g/g body mass in sea lamprey, Pacific lamprey, and western brook lamprey, respectively. Releasing rates for PZS in the three species were measured using ELISA to find that western brook and sea lamprey released PZS 20 times higher than Pacific lamprey did. Further studies are required to determine whether PZS is a chemical cue in Pacific and western brook lampreys. ?? 2003 Elsevier Inc. All rights reserved.

  3. Stable isotope and signature fatty acid analyses suggest reef manta rays feed on demersal zooplankton.

    PubMed

    Couturier, Lydie I E; Rohner, Christoph A; Richardson, Anthony J; Marshall, Andrea D; Jaine, Fabrice R A; Bennett, Michael B; Townsend, Kathy A; Weeks, Scarla J; Nichols, Peter D

    2013-01-01

    Assessing the trophic role and interaction of an animal is key to understanding its general ecology and dynamics. Conventional techniques used to elucidate diet, such as stomach content analysis, are not suitable for large threatened marine species. Non-lethal sampling combined with biochemical methods provides a practical alternative for investigating the feeding ecology of these species. Stable isotope and signature fatty acid analyses of muscle tissue were used for the first time to examine assimilated diet of the reef manta ray Manta alfredi, and were compared with different zooplankton functional groups (i.e. near-surface zooplankton collected during manta ray feeding events and non-feeding periods, epipelagic zooplankton, demersal zooplankton and several different zooplankton taxa). Stable isotope δ(15)N values confirmed that the reef manta ray is a secondary consumer. This species had relatively high levels of docosahexaenoic acid (DHA) indicating a flagellate-based food source in the diet, which likely reflects feeding on DHA-rich near-surface and epipelagic zooplankton. However, high levels of ω6 polyunsaturated fatty acids and slightly enriched δ(13)C values in reef manta ray tissue suggest that they do not feed solely on pelagic zooplankton, but rather obtain part of their diet from another origin. The closest match was with demersal zooplankton, suggesting it is an important component of the reef manta ray diet. The ability to feed on demersal zooplankton is likely linked to the horizontal and vertical movement patterns of this giant planktivore. These new insights into the habitat use and feeding ecology of the reef manta ray will assist in the effective evaluation of its conservation needs.

  4. Stable Isotope and Signature Fatty Acid Analyses Suggest Reef Manta Rays Feed on Demersal Zooplankton

    PubMed Central

    Couturier, Lydie I. E.; Rohner, Christoph A.; Richardson, Anthony J.; Marshall, Andrea D.; Jaine, Fabrice R. A.; Bennett, Michael B.; Townsend, Kathy A.; Weeks, Scarla J.; Nichols, Peter D.

    2013-01-01

    Assessing the trophic role and interaction of an animal is key to understanding its general ecology and dynamics. Conventional techniques used to elucidate diet, such as stomach content analysis, are not suitable for large threatened marine species. Non-lethal sampling combined with biochemical methods provides a practical alternative for investigating the feeding ecology of these species. Stable isotope and signature fatty acid analyses of muscle tissue were used for the first time to examine assimilated diet of the reef manta ray Manta alfredi, and were compared with different zooplankton functional groups (i.e. near-surface zooplankton collected during manta ray feeding events and non-feeding periods, epipelagic zooplankton, demersal zooplankton and several different zooplankton taxa). Stable isotope δ15N values confirmed that the reef manta ray is a secondary consumer. This species had relatively high levels of docosahexaenoic acid (DHA) indicating a flagellate-based food source in the diet, which likely reflects feeding on DHA-rich near-surface and epipelagic zooplankton. However, high levels of ω6 polyunsaturated fatty acids and slightly enriched δ13C values in reef manta ray tissue suggest that they do not feed solely on pelagic zooplankton, but rather obtain part of their diet from another origin. The closest match was with demersal zooplankton, suggesting it is an important component of the reef manta ray diet. The ability to feed on demersal zooplankton is likely linked to the horizontal and vertical movement patterns of this giant planktivore. These new insights into the habitat use and feeding ecology of the reef manta ray will assist in the effective evaluation of its conservation needs. PMID:24167562

  5. Comparative Analyses of the Lipooligosaccharides from Nontypeable Haemophilus influenzae and Haemophilus haemolyticus Show Differences in Sialic Acid and Phosphorylcholine Modifications

    PubMed Central

    Post, Deborah M. B.; Ketterer, Margaret R.; Coffin, Jeremy E.; Reinders, Lorri M.; Munson, Robert S.; Bair, Thomas; Murphy, Timothy F.; Foster, Eric D.; Gibson, Bradford W.

    2016-01-01

    Haemophilus haemolyticus and nontypeable Haemophilus influenzae (NTHi) are closely related upper airway commensal bacteria that are difficult to distinguish phenotypically. NTHi causes upper and lower airway tract infections in individuals with compromised airways, while H. haemolyticus rarely causes such infections. The lipooligosaccharide (LOS) is an outer membrane component of both species and plays a role in NTHi pathogenesis. In this study, comparative analyses of the LOS structures and corresponding biosynthesis genes were performed. Mass spectrometric and immunochemical analyses showed that NTHi LOS contained terminal sialic acid more frequently and to a higher extent than H. haemolyticus LOS did. Genomic analyses of 10 strains demonstrated that H. haemolyticus lacked the sialyltransferase genes lic3A and lic3B (9/10) and siaA (10/10), but all strains contained the sialic acid uptake genes siaP and siaT (10/10). However, isothermal titration calorimetry analyses of SiaP from two H. haemolyticus strains showed a 3.4- to 7.3-fold lower affinity for sialic acid compared to that of NTHi SiaP. Additionally, mass spectrometric and immunochemical analyses showed that the LOS from H. haemolyticus contained phosphorylcholine (ChoP) less frequently than the LOS from NTHi strains. These differences observed in the levels of sialic acid and ChoP incorporation in the LOS structures from H. haemolyticus and NTHi may explain some of the differences in their propensities to cause disease. PMID:26729761

  6. Comparative Analyses of the Lipooligosaccharides from Nontypeable Haemophilus influenzae and Haemophilus haemolyticus Show Differences in Sialic Acid and Phosphorylcholine Modifications.

    PubMed

    Post, Deborah M B; Ketterer, Margaret R; Coffin, Jeremy E; Reinders, Lorri M; Munson, Robert S; Bair, Thomas; Murphy, Timothy F; Foster, Eric D; Gibson, Bradford W; Apicella, Michael A

    2016-01-04

    Haemophilus haemolyticus and nontypeable Haemophilus influenzae (NTHi) are closely related upper airway commensal bacteria that are difficult to distinguish phenotypically. NTHi causes upper and lower airway tract infections in individuals with compromised airways, while H. haemolyticus rarely causes such infections. The lipooligosaccharide (LOS) is an outer membrane component of both species and plays a role in NTHi pathogenesis. In this study, comparative analyses of the LOS structures and corresponding biosynthesis genes were performed. Mass spectrometric and immunochemical analyses showed that NTHi LOS contained terminal sialic acid more frequently and to a higher extent than H. haemolyticus LOS did. Genomic analyses of 10 strains demonstrated that H. haemolyticus lacked the sialyltransferase genes lic3A and lic3B (9/10) and siaA (10/10), but all strains contained the sialic acid uptake genes siaP and siaT (10/10). However, isothermal titration calorimetry analyses of SiaP from two H. haemolyticus strains showed a 3.4- to 7.3-fold lower affinity for sialic acid compared to that of NTHi SiaP. Additionally, mass spectrometric and immunochemical analyses showed that the LOS from H. haemolyticus contained phosphorylcholine (ChoP) less frequently than the LOS from NTHi strains. These differences observed in the levels of sialic acid and ChoP incorporation in the LOS structures from H. haemolyticus and NTHi may explain some of the differences in their propensities to cause disease.

  7. Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses

    PubMed Central

    Sheth, Bhavisha P.; Thaker, Vrinda S.

    2015-01-01

    Background: Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. Objective: To identify a herbal powder obtained from a herbalist in the local vicinity of Rajkot, Gujarat, using deoxyribonucleic acid (DNA) barcoding and molecular tools. Materials and Methods: The DNA was extracted from a herbal powder and selected Cassia species, followed by the polymerase chain reaction (PCR) and sequencing of the rbcL barcode locus. Thereafter the sequences were subjected to National Center for Biotechnology Information (NCBI) basic local alignment search tool (BLAST) analysis, followed by the protein three-dimension structure determination of the rbcL protein from the herbal powder and Cassia species namely Cassia fistula, Cassia tora and Cassia javanica (sequences obtained in the present study), Cassia Roxburghii, and Cassia abbreviata (sequences retrieved from Genbank). Further, the multiple and pairwise structural alignment were carried out in order to identify the herbal powder. Results: The nucleotide sequences obtained from the selected species of Cassia were submitted to Genbank (Accession No. JX141397, JX141405, JX141420). The NCBI BLAST analysis of the rbcL protein from the herbal powder showed an equal sequence similarity (with reference to different parameters like E value, maximum identity, total score, query coverage) to C. javanica and C. roxburghii. In order to solve the ambiguities of the BLAST result, a protein structural approach was implemented. The protein homology models obtained in the present study were submitted to the protein model database (PM0079748-PM0079753). The pairwise structural alignment of the herbal powder (as template) and C. javanica and C. roxburghii (as targets individually) revealed a close similarity of the herbal powder with C. javanica. Conclusion: A strategy as used here, incorporating the integrated use of DNA

  8. Amino acid analyses of type 3 chondrites Colony, Ornans, Chainpur, and Bishunpur

    NASA Astrophysics Data System (ADS)

    Chan, H.-S.; Martins, Zita; Sephton, Mark A.

    2012-09-01

    The CO3s Colony and Ornans and LL3s Chainpur and Bishunpur were analyzed for the first time for amino acids using gas chromatography-mass spectrometry (GC-MS). Type 3 chondrites have relatively unaltered metamorphic and petrological histories. Chainpur was the most amino acid rich of the four type 3 chondrites with a total amino acid abundance of 3330 parts per billion (ppb). The other type 3 chondrites had total amino acid abundances that ranged from 660 to 1110 ppb. A D/L ratio of <0.7 for all proteic amino acids suggests at least some amino acid terrestrial contamination. However, a small fraction of indigenous extraterrestrial amino acids cannot be excluded because of the presence of the nonprotein amino acid α-aminoisobutyric acid (α-AIB), and unusually high relative abundances (to glycine) of β-alanine and γ-ABA. The comparisons between the free and total amino acid contents of the samples also indicate a low free/total amino acid ratio (ranging from about 1:4 in CO chondrites to about 1:50 in Chainpur), which indicate that amino acids are present mainly in the bound form and were made detectable after acid hydrolysis.

  9. Effect of alpha-lipoic acid on relieving ammonia stress and hepatic proteomic analyses of broilers.

    PubMed

    Lu, M; Bai, J; Xu, B; Sun, Q Y; Wei, F X; Tang, X F; Zhang, H F; Li, J; Wang, G L; Yin, Q Q; Li, S Y

    2017-01-01

    Ammonia in poultry houses not only affects worker health but also induces a variety of poultry diseases. Alpha-lipoic acid (LA) is an effective antioxidant that protects cells against oxidative injury during various toxic and pathological processes. This study was designed to evaluate the mitigating effects of LA supplementation on ammonia stress and hepatic proteome changes in broilers. Male broilers (22 d old) were allocated to 3 groups: (1) a control group without ammonia stress (CTRL); (2) exposure to 70 ppm ammonia (AM); and (3) exposure to 70 ppm ammonia and dietary administration of 300 mg/kg LA (AM+LA). Ammonia exposure significantly decreased broiler growth performance and plasma glutathione peroxidase activity (P < 0.05), and increased plasma malondialdehyde content and glutamic-pyruvic transaminase activity (P < 0.05). These negative effects were eliminated by LA supplementation. Comparative proteomic analyses revealed 291 differentially expressed proteins in the AM group compared to the CTRL and AM+LA groups. A total of 30 proteins were differentially expressed between the AM/CTRL and (AM+LA)/AM groups. The addition of LA restored 24 of these proteins to control levels; these proteins were mainly related to transcription regulation, detoxification, protein translation and degradation, and immune and stress responses. The differentially expressed proteins included the high mobility group box (HMGB) and glutathione S-transferase (GST), which is closely related to immune response and oxidative stress, and collagens, which are implicated in liver injury. The addition of LA to broiler diet may reduce ammonia toxicity by maintaining the antioxidant system, xenobiotic metabolism, and metabolic pathways.

  10. Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast

    PubMed Central

    Misra, Ashish; Conway, Matthew F.; Johnnie, Joseph; Qureshi, Tabish M.; Lige, Bao; Derrick, Anne M.; Agbo, Eddy C.; Sriram, Ganesh

    2013-01-01

    Synthetic biology enables metabolic engineering of industrial microbes to synthesize value-added molecules. In this, a major challenge is the efficient redirection of carbon to the desired metabolic pathways. Pinpointing strategies toward this goal requires an in-depth investigation of the metabolic landscape of the organism, particularly primary metabolism, to identify precursor and cofactor availability for the target compound. The potent antimalarial therapeutic artemisinin and its precursors are promising candidate molecules for production in microbial hosts. Recent advances have demonstrated the production of artemisinin precursors in engineered yeast strains as an alternative to extraction from plants. We report the application of in silico and in vivo metabolic pathway analyses to identify metabolic engineering targets to improve the yield of the direct artemisinin precursor dihydroartemisinic acid (DHA) in yeast. First, in silico extreme pathway (ExPa) analysis identified NADPH-malic enzyme and the oxidative pentose phosphate pathway (PPP) as mechanisms to meet NADPH demand for DHA synthesis. Next, we compared key DHA-synthesizing ExPas to the metabolic flux distributions obtained from in vivo 13C metabolic flux analysis of a DHA-synthesizing strain. This comparison revealed that knocking out ethanol synthesis and overexpressing glucose-6-phosphate dehydrogenase in the oxidative PPP (gene YNL241C) or the NADPH-malic enzyme ME2 (YKL029C) are vital steps toward overproducing DHA. Finally, we employed in silico flux balance analysis and minimization of metabolic adjustment on a yeast genome-scale model to identify gene knockouts for improving DHA yields. The best strategy involved knockout of an oxaloacetate transporter (YKL120W) and an aspartate aminotransferase (YKL106W), and was predicted to improve DHA yields by 70-fold. Collectively, our work elucidates multiple non-trivial metabolic engineering strategies for improving DHA yield in yeast. PMID:23898325

  11. A microcalorimetric sensor for food and cosmetic analyses: l-Malic acid determination.

    PubMed

    Antonelli, Marta Letizia; Spadaro, Claudio; Tornelli, Rosalia Fortunata

    2008-02-15

    Enzymatic microcalorimetry has been successfully employed in the reliable determination of the l-malic acid concentration in some foods and cosmetic products. The l-malic acid concentration during the wine-making process is particularly useful in order to control the progress of the malo-lactic fermentation. Total acidity, taste and flavour characteristics of wine depend on the l-malic acid quantity still present. To point out the analytical methodology the dehydration process of l-malic acid, in the presence of Fumarase enzyme, has been used. The new method has been compared with a common spectrophotometric one. By the proposed calorimetric method the l-malic acid concentration in different types of food (white and red wines, fruits and soft beverages) has been determined. In some cosmetic products too the l-malic acid was quantified. The method outlined resulted simple, direct and reliable (good accuracy and precision), in particular it does not require any pre-treatment or clean up of the samples, save the dilution in buffer.

  12. Phospholipid Analyses for Microbial Community Composition in Alpine Acid Rock Drainage

    NASA Astrophysics Data System (ADS)

    Webster, C. E.; Tapp, J. B.; Pfiffner, S. M.

    2008-12-01

    This project is examining factors of non-anthropogenic acid rock drainage that influence microbial community composition in the Peekaboo Gulch drainage basin (Sawatch Range, Colorado). At this site, natural acid rock drainage outflows from acidic springs (pH=2.6) on Red Mountain. The acid drainage converges with South Fork Lake Creek (pH ~ 7.0, prior to convergence) two miles down gradient. Sediment samples were collected across confluences with gradient of pH, temperature, conductivity and metal concentration. In-situ parameter measurements ranged from 2.3 to 7.9 of pH, 3.8 to 16.6 degree Celsius for temperature, and 34.9 to 1820 for conductivity. Biomass as measured by phospholipids ranged from 280 to 95,900 pmol/g sediment. The only relationship between the in situ parameters and the phospholipid profiles is a weak positive correlation between pH and branched monounsaturated fatty acid methyl esters in that at a pH greater than 5.0 these fatty acid methyl esters were detected. The phospholipid profiles were diverse across the samples. These profiles changed with respect to the spatial relationship within the drainage pattern. The highest alpine samples contained greater relative abundances of monounsaturated fatty acid methyl esters compared to the lower alpine samples. Microbial community profiles shifted at each confluence depending on water source chemistry. Continuing research is needed to determine other biogeochemical factors that may influence these community shifts.

  13. Beyond H&E: integration of nucleic acid-based analyses into diagnostic pathology.

    PubMed

    Maes, R K; Langohr, I M; Wise, A G; Smedley, R C; Thaiwong, T; Kiupel, M

    2014-01-01

    Veterinary pathology of infectious, particularly viral, and neoplastic diseases has advanced significantly with the advent of newer molecular methodologies that can detect nucleic acid of infectious agents within microscopic lesions, differentiate neoplastic from nonneoplastic cells, or determine the suitability of a targeted therapy by detecting specific mutations in certain cancers. Polymerase chain reaction-based amplification of DNA or RNA and in situ hybridization are currently the most commonly used methods for nucleic acid detection. In contrast, the main methodology used for protein detection within microscopic lesions is immunohistochemistry. Other methods that allow for analysis of nucleic acids within a particular cell type or individual cells, such as laser capture microdissection, are also available in some laboratories. This review gives an overview of the factors that influence the accurate analysis of nucleic acids in formalin-fixed tissues, as well as of different approaches to detect such targets.

  14. THERMAL AND SPECTROSCOPIC ANALYSES OF CAUSTIC LIDE SOLVENT EXTRACTION SOLVENT CONTACTED WITH 16 MOLAR AND 8 MOLAR NITRIC ACID

    SciTech Connect

    Fondeur, F; David Hobbs, D; Samuel Fink, S

    2007-07-12

    Thermal and spectroscopic analyses were performed on multiple layers formed from contacting Caustic Side Solvent Extraction (CSSX) solvent with 1 M or 3 M nitric acid. A slow chemical reaction occurs (i.e., over several weeks) between the solvent and 1 M or 3 M nitric acid as evidenced by color changes and the detection of nitro groups in the infrared spectrum of the aged samples. Thermal analysis revealed that decomposition of the resulting mixture does not meet the definition of explosive or deflagrating material.

  15. THERMAL AND SPECTROSCOPIC ANALYSES OF CAUSTIC SIDE SOLVENT EXTRACTION SOLVENT CONTACTED WITH 1 MOLARAND 3 MOLAR NITRIC ACID

    SciTech Connect

    Fondeur, F; David Hobbs, D; Samuel Fink, S

    2007-07-23

    Thermal and spectroscopic analyses were performed on multiple layers formed from contacting Caustic Side Solvent Extraction (CSSX) solvent with 1 M or 3 M nitric acid. A slow chemical reaction occurs (i.e., over several weeks) between the solvent and 1 M or 3 M nitric acid as evidenced by color changes and the detection of nitro groups in the infrared spectrum of the aged samples. Thermal analysis revealed that decomposition of the resulting mixture does not meet the definition of explosive or deflagrating material.

  16. Spectroscopic analyses and studies on respective interaction of cyanuric acid and uric acid with bovine serum albumin and melamine

    NASA Astrophysics Data System (ADS)

    Chen, Dandan; Wu, Qiong; Wang, Jun; Wang, Qi; Qiao, Heng

    2015-01-01

    In this work, the fluorescence quenching was used to study the interaction of cyanuric acid (CYA) and uric acid (UA) with bovine serum albumin (BSA) at two different temperatures (283 K and 310 K). The bimolecular quenching constant (Kq), apparent quenching constant (Ksv), effective binding constant (KA) and corresponding dissociation constant (KD), binding site number (n) and binding distance (r) were calculated by adopting Stern-Volmer, Lineweaver-Burk, Double logarithm and overlap integral equations. The results show that CYA and UA are both able to obviously bind to BSA, but the binding strength order is BSA + CYA < BSA + UA. And then, the interactions of CYA and UA with melamine (MEL) under the same conditions were also studied by using similar methods. The results indicates that both CYA and UA can bind together closely with melamine (MEL). It is wished that these research results would facilitate the understanding the formation of kidney stones and gout in the body after ingesting excess MEL.

  17. Spent lead-acid battery recycling in China - A review and sustainable analyses on mass flow of lead.

    PubMed

    Sun, Zhi; Cao, Hongbin; Zhang, Xihua; Lin, Xiao; Zheng, Wenwen; Cao, Guoqing; Sun, Yong; Zhang, Yi

    2017-03-15

    Lead is classified to be one of the top heavy metal pollutants in China. The corresponding environmental issues especially during the management of spent lead-acid battery have already caused significant public awareness and concern. This research gives a brief overview on the recycling situation based on an investigation of the lead industry in China and also the development of technologies for spent lead-acid batteries. The main principles and research focuses of different technologies including pyrometallurgy, hydrometallurgy and greener technologies are summarized and compared. Subsequently, the circulability of lead based on the entire life cycle analyses of lead-acid battery is calculated. By considering different recycling schemes, the recycling situation of spent lead-acid battery in China can be understood semi-quantitatively. According to this research, 30% of the primary lead production can be shut down that the lead production can still ensure consecutive life cycle operation of lead-acid battery, if proper management of the spent lead-acid battery is implemented according to current lead industry situation in China. This research provides a methodology on the view of lead circulability in the whole life cycle of a specific product and is aiming to contribute more quantitative guidelines for efficient organization of lead industry in China.

  18. Effect of low temperature on highly unsaturated fatty acid biosynthesis in activated sludge.

    PubMed

    He, Su; Ding, Li-Li; Xu, Ke; Geng, Jin-Ju; Ren, Hong-Qiang

    2016-07-01

    Low temperature is a limiting factor for the microbial activity of activated sludge for sewage treatment plant in winter. Highly unsaturated fatty acid (UFA) biosynthesis, phospholipid fatty acid (PLFA) constituents and microbial structure in activated sludge at low temperature were investigated. Over 12 gigabases of metagenomic sequence data were generated with the Illumina HiSeq 2000 platform. The result showed 43.11% of phospholipid fatty acid (PLFA) in the activated sludge participated in UFA biosynthesis, and γ-Linolenic could be converted to Arachidonic acid at low temperature. The highly UFA biosynthesis in activated sludge was n-6 highly UFA biosynthesis, rather than n-3 highly UFA biosynthesis. The microbial community structures of activated sludge were analyzed by PLFA and high-throughput sequencing (HiSeq) simultaneously. Acidovorax, Pseudomonas, Flavobacterium and Polaromonas occupied higher percentage at 5°C, and genetic changes of highly UFA biosynthesis derived from microbial community structures change.

  19. Functional analyses of carnivorous plant-specific amino acid residues in S-like ribonucleases.

    PubMed

    Arai, Naoki; Nishimura, Emi; Kikuchi, Yo; Ohyama, Takashi

    2015-09-11

    Unlike plants with no carnivory, carnivorous plants seem to use S-like ribonucleases (RNases) as an enzyme for carnivory. Carnivorous plant-specific conserved amino acid residues are present at four positions around the conserved active site (CAS). The roles of these conserved amino acid residues in the enzymatic function were explored in the current study by preparing five recombinant variants of DA-I, the S-like RNase of Drosera adelae. The kcat and kcat/Km values of the enzymes revealed that among the four variants with a single mutation, the serine to glycine mutation at position 111 most negatively influenced the enzymatic activity. The change in the bulkiness of the amino acid residue side-chain seemed to be the major cause of the above effect. Modeling of the three dimensional (3D) structures strongly suggested that the S to G mutation at 111 greatly altered the overall enzyme conformation. The conserved four amino acid residues are likely to function in keeping the two histidine residues, which are essential for the cleavage of RNA strands, and the CAS in the most functional enzymatic conformation.

  20. Quantitative analyses of tartaric acid based on terahertz time domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Cao, Binghua; Fan, Mengbao

    2010-10-01

    Terahertz wave is the electromagnetic spectrum situated between microwave and infrared wave. Quantitative analysis based on terahertz spectroscopy is very important for the application of terahertz techniques. But how to realize it is still under study. L-tartaric acid is widely used as acidulant in beverage, and other food, such as soft drinks, wine, candy, bread and some colloidal sweetmeats. In this paper, terahertz time-domain spectroscopy is applied to quantify the tartaric acid. Two methods are employed to process the terahertz spectra of different samples with different content of tartaric acid. The first one is linear regression combining correlation analysis. The second is partial least square (PLS), in which the absorption spectra in the 0.8-1.4THz region are used to quantify the tartaric acid. To compare the performance of these two principles, the relative error of the two methods is analyzed. For this experiment, the first method does better than the second one. But the first method is suitable for the quantitative analysis of materials which has obvious terahertz absorption peaks, while for material which has no obvious terahertz absorption peaks, the second one is more appropriate.

  1. Spectroscopic analyses of the noncovalent self-assembly of cyanines upon various nucleic acid scaffolds.

    PubMed

    Achyuthan, Komandoor E; McClain, Jaime L; Zhou, Zhijun; Whitten, David G; Branch, Darren W

    2009-04-01

    We utilized self-assembly of cyanine chromophores to study the conformational changes in various types of nucleic acid scaffolds: single and double stranded DNA, linear or circular DNA and RNA. We identified a chromophore that became highly fluorescent after aggregating upon nucleic acids. Fluorescence from the aggregate was instantaneous after self-assembly. Temporal emission profiles displayed a biphasic trend demonstrating kinetic dependence for assembly and disassembly. Absorption spectra of the aggregate showed a red-shifted "shoulder" peak indicative of J-aggregate. Fluorescence from J-aggregates was also red-shifted. We utilized cyanine self-assembly to quantize various nucleic acids. The limits of detection and quantization for psiX174 DNA were 3 and 9 fmol, respectively. We similarly determined the sensitivity for various nucleic acids and established the optimum conditions for self-assembly. Collectively, the effects of methanol, salt, and full width at half maximum for cyanine fluorescence on DNA or carboxymethylamylose scaffolds, all suggested noncovalent, electrostatic, and hydrophobic forces were involved in supramolecular self-assembly. Our results facilitate a better understanding of supramolecular self-assembly.

  2. Specific catalysis of asparaginyl deamidation by carboxylic acids: kinetic, thermodynamic, and quantitative structure-property relationship analyses.

    PubMed

    Connolly, Brian D; Tran, Benjamin; Moore, Jamie M R; Sharma, Vikas K; Kosky, Andrew

    2014-04-07

    Asparaginyl (Asn) deamidation could lead to altered potency, safety, and/or pharmacokinetics of therapeutic protein drugs. In this study, we investigated the effects of several different carboxylic acids on Asn deamidation rates using an IgG1 monoclonal antibody (mAb1*) and a model hexapeptide (peptide1) with the sequence YGKNGG. Thermodynamic analyses of the kinetics data revealed that higher deamidation rates are associated with predominantly more negative ΔS and, to a lesser extent, more positive ΔH. The observed differences in deamidation rates were attributed to the unique ability of each type of carboxylic acid to stabilize the energetically unfavorable transition-state conformations required for imide formation. Quantitative structure property relationship (QSPR) analysis using kinetic data demonstrated that molecular descriptors encoding for the geometric spatial distribution of atomic properties on various carboxylic acids are effective determinants for the deamidation reaction. Specifically, the number of O-O and O-H atom pairs on carboxyl and hydroxyl groups with interatomic distances of 4-5 Å on a carboxylic acid buffer appears to determine the rate of deamidation. Collectively, the results from structural and thermodynamic analyses indicate that carboxylic acids presumably form multiple hydrogen bonds and charge-charge interactions with the relevant deamidation site and provide alignment between the reactive atoms on the side chain and backbone. We propose that carboxylic acids catalyze deamidation by stabilizing a specific, energetically unfavorable transition-state conformation of l-asparaginyl intermediate II that readily facilitates bond formation between the γ-carbonyl carbon and the deprotonated backbone nitrogen for cyclic imide formation.

  3. Spectroscopic analyses and studies on respective interaction of cyanuric acid and uric acid with bovine serum albumin and melamine.

    PubMed

    Chen, Dandan; Wu, Qiong; Wang, Jun; Wang, Qi; Qiao, Heng

    2015-01-25

    In this work, the fluorescence quenching was used to study the interaction of cyanuric acid (CYA) and uric acid (UA) with bovine serum albumin (BSA) at two different temperatures (283 K and 310 K). The bimolecular quenching constant (Kq), apparent quenching constant (Ksv), effective binding constant (KA) and corresponding dissociation constant (KD), binding site number (n) and binding distance (r) were calculated by adopting Stern-Volmer, Lineweaver-Burk, Double logarithm and overlap integral equations. The results show that CYA and UA are both able to obviously bind to BSA, but the binding strength order is BSA+CYA

  4. Supply Chain Modeling for Fluorspar and Hydrofluoric Acid and Implications for Further Analyses

    DTIC Science & Technology

    2015-04-01

    for other materials in the FY 2015 NDS Requirements Report, potential market responses to the fluorspar and HF shortfalls have been evaluated to...Information Services Limited, Fluorspar: Global Industry Markets and Outlook, 11th ed (London: Roskill, 2013), 19, 143. 7 Thomason, Analyses for the 2015...Industry Markets and Outlook, 142–144. 9 Department of Defense, Strategic and Critical Materials 2013 Report on Stockpile Requirements (Washington, DC

  5. Lignin, cutin, amino acid and carbohydrate analyses of marine particulate organic matter

    NASA Astrophysics Data System (ADS)

    Hedges, John I.

    Our group at the University of Washington has specifically designed methods for the analysis of lignin compounds [Hedges and Ertel, 1982], cutin acids [Goñi and Hedges, 1990a], amino acids [Cowie and Hedges, in press, 1991a, b] and various carbohydrates, including aldoses [Cowie and Hedges, 1984], cyclitols [Hedges and Weliky, 1989] and uronic acids [Walters and Hedges, 1988; Bergamaschi and Hedges, in preparation], in particulate samples from aquatic environments. All of these procedures are derivatives of previous methods that we have adapted for application to complex natural mixtures and tested on a variety of sample types, such as plankton, woods, soils and sediments, for precision, accuracy and yield efficiencies. All the methods are written up in detail and only will be summarized in the following sections. The remaining discussion, covering the various compound types in the order given above, will focus on unpublished procedural developments for each technique, special problems that are unique to each method and related tricks of the trade. Lignin analysis will be treated in most detail because it is the method with which we have had the longest and most detailed experience.

  6. An integrated portable hand-held analyser for real-time isothermal nucleic acid amplification.

    PubMed

    Smith, Matthew C; Steimle, George; Ivanov, Stan; Holly, Mark; Fries, David P

    2007-08-29

    A compact hand-held heated fluorometric instrument for performing real-time isothermal nucleic acid amplification and detection is described. The optoelectronic instrument combines a Printed Circuit Board/Micro Electro Mechanical Systems (PCB/MEMS) reaction detection/chamber containing an integrated resistive heater with attached miniature LED light source and photo-detector and a disposable glass waveguide capillary to enable a mini-fluorometer. The fluorometer is fabricated and assembled in planar geometry, rolled into a tubular format and packaged with custom control electronics to form the hand-held reactor. Positive or negative results for each reaction are displayed to the user using an LED interface. Reaction data is stored in FLASH memory for retrieval via an in-built USB connection. Operating on one disposable 3 V lithium battery >12, 60 min reactions can be performed. Maximum dimensions of the system are 150 mm (h) x 48 mm (d) x 40 mm (w), the total instrument weight (with battery) is 140 g. The system produces comparable results to laboratory instrumentation when performing a real-time nucleic acid sequence-based amplification (NASBA) reaction, and also displayed comparable precision, accuracy and resolution to laboratory-based real-time nucleic acid amplification instrumentation. A good linear response (R2 = 0.948) to fluorescein gradients ranging from 0.5 to 10 microM was also obtained from the instrument indicating that it may be utilized for other fluorometric assays. This instrument enables an inexpensive, compact approach to in-field genetic screening, providing results comparable to laboratory equipment with rapid user feedback as to the status of the reaction.

  7. Enhanced Sampling and Overfitting Analyses in Structural Refinement of Nucleic Acids into Electron Microscopy Maps

    PubMed Central

    Vashisth, Harish; Skiniotis, Georgios; Brooks, Charles L.

    2013-01-01

    Flexible-fitting computational algorithms are often useful to interpret low resolution maps of many macromolecular complexes generated by electron microscopy (EM) imaging. One such atomistic simulation technique is molecular dynamics flexible fitting (MDFF), which has been widely applied to generate structural models of large ribonucleoprotein assemblies such as the ribosome. We have previously shown that MDFF simulations of globular proteins are sensitive to the resolution of the target EM map, and the strength of restraints used to preserve the secondary structure elements during fitting (Vashisth et al. Structure 2012, 20, 1453–1462). In this work, we aim to systematically examine the quality of structural models of various nucleic acids obtained via MDFF by varying the map resolution and the strength of structural restraints. We also demonstrate how an enhanced conformational sampling technique for proteins, temperatureaccelerated molecular dynamics (TAMD), can be combined with MDFF for the structural refinement of nucleic acids in EMmaps. Finally, we also demonstrate application of TAMD-assisted MDFF (TAMDFF) on a RNA/protein complex and suggest that TAMDFF is a viable strategy for enhanced conformational fitting in target maps of ribonucleoprotein complexes. PMID:23506287

  8. Nucleic acid hybridization analyses confirm the presence of a hitherto unknown morbillivirus in Mediterranean dolphins.

    PubMed

    Bolt, G; Blixenkrone-Møller, M

    1994-08-15

    In 1990 an epidemic caused by a morbillivirus was noticed among Mediterranean dolphins. RNA was extracted from the tissues of dolphins and from cell cultures infected with a corresponding dolphin morbillivirus isolate. By nucleic acid hybridization this RNA was compared to RNA extracted from animal tissue or cell cultures infected with canine distemper virus (CDV), phocine distemper virus (PDV) or measles virus (MV). The presence of morbillivirus RNA in the dolphin tissue was demonstrated. Morbillivirus N, P, M and F gene mRNAs were detected in the RNA from dolphin morbillivirus infected cells. These mRNA species seemed to be of approximately the same size as the corresponding mRNA species of CDV, PDV and MV. The results of the comparison demonstrated that the dolphin morbillivirus is genetically different from CDV, PDV and MV. No indication of a close relationship between the dolphin isolate and either CDV, PDV or MV was found.

  9. Global trophic position comparison of two dominant mesopelagic fish families (Myctophidae, Stomiidae) using amino acid nitrogen isotopic analyses.

    PubMed

    Choy, C Anela; Davison, Peter C; Drazen, Jeffrey C; Flynn, Adrian; Gier, Elizabeth J; Hoffman, Joel C; McClain-Counts, Jennifer P; Miller, Todd W; Popp, Brian N; Ross, Steve W; Sutton, Tracey T

    2012-01-01

    The δ(15)N values of organisms are commonly used across diverse ecosystems to estimate trophic position and infer trophic connectivity. We undertook a novel cross-basin comparison of trophic position in two ecologically well-characterized and different groups of dominant mid-water fish consumers using amino acid nitrogen isotope compositions. We found that trophic positions estimated from the δ(15)N values of individual amino acids are nearly uniform within both families of these fishes across five global regions despite great variability in bulk tissue δ(15)N values. Regional differences in the δ(15)N values of phenylalanine confirmed that bulk tissue δ(15)N values reflect region-specific water mass biogeochemistry controlling δ(15)N values at the base of the food web. Trophic positions calculated from amino acid isotopic analyses (AA-TP) for lanternfishes (family Myctophidae) (AA-TP ∼2.9) largely align with expectations from stomach content studies (TP ∼3.2), while AA-TPs for dragonfishes (family Stomiidae) (AA-TP ∼3.2) were lower than TPs derived from stomach content studies (TP∼4.1). We demonstrate that amino acid nitrogen isotope analysis can overcome shortcomings of bulk tissue isotope analysis across biogeochemically distinct systems to provide globally comparative information regarding marine food web structure.

  10. Molar ratio iron: zinc and folic acid in Brazilian biscuits and snacks and test for classification using principal component analyses.

    PubMed

    Godoy, Adriana Teixeira; Rebelatto, Ana Paula; Borin-Nogueira, Alessandra; Lima-Pallone, Juliana Azevedo

    2014-06-01

    The aim of the present work was to evaluate molar ratio iron: zinc and the levels of folic acid in biscuit and snacks commercialized in Brazil, prepared with folic acid and iron fortified flours. These nutrients are important for human nutrition; however, iron can have a negative effect on zinc absorption. Molar ratio iron:zinc can indicate if there will be any problems for absorption of these nutrients. The folic acid content varied from 58 to 433 μg/100 g and iron and zinc levels varied from 2.9 to 9.4 mg/100 g and from 0.2 to 1.3 mg/100 g, respectively, for 75 analyzed samples. The average iron contents observed in the products and molar ratio iron:zinc (in average 8:1 for biscuits and 12.8:1 for snacks) could result in problems with the zinc absorption. Moreover, principal compo- nent analyses (PCA) indicated low uniformity in the distribution of minerals and vitamin in the majority of the samples, mainly among brands. The results indicated that for the majority of the samples tested folic acid and iron content was higher than expected for flours and could be useful to governmental authorities in their evaluation program of flour fortification.

  11. Global trophic position comparison of two dominant mesopelagic fish families (Myctophidae, Stomiidae) using amino acid nitrogen isotopic analyses

    USGS Publications Warehouse

    Choy, C. Anela; Davison, Peter C.; Drazen, Jeffrey C.; Flynn, Adrian; Gier, Elizabeth J.; Hoffman, Joel C.; McClain-Counts, Jennifer P.; Miller, Todd W.; Popp, Brian N.; Ross, Steve W.; Sutton, Tracey T.

    2012-01-01

    The δ15N values of organisms are commonly used across diverse ecosystems to estimate trophic position and infer trophic connectivity. We undertook a novel cross-basin comparison of trophic position in two ecologically well-characterized and different groups of dominant mid-water fish consumers using amino acid nitrogen isotope compositions. We found that trophic positions estimated from the δ15N values of individual amino acids are nearly uniform within both families of these fishes across five global regions despite great variability in bulk tissue δ15N values. Regional differences in the δ15N values of phenylalanine confirmed that bulk tissue δ15N values reflect region-specific water mass biogeochemistry controlling δ15N values at the base of the food web. Trophic positions calculated from amino acid isotopic analyses (AA-TP) for lanternfishes (family Myctophidae) (AA-TP ~2.9) largely align with expectations from stomach content studies (TP ~3.2), while AA-TPs for dragonfishes (family Stomiidae) (AA-TP ~3.2) were lower than TPs derived from stomach content studies (TP~4.1). We demonstrate that amino acid nitrogen isotope analysis can overcome shortcomings of bulk tissue isotope analysis across biogeochemically distinct systems to provide globally comparative information regarding marine food web structure.

  12. Time-resolved detection probe for homogeneous nucleic acid analyses in one-step format.

    PubMed

    Laitala, Ville; Ylikoski, Alice; Raussi, Hanna-Mari; Ollikka, Pia; Hemmilä, Ilkka

    2007-02-01

    We report here an extension of homogeneous assays based on fluorescence intensity and lifetime measuring on DNA hybridization. A novel decay probe that allows simple one-step nucleic acid detection with subnanomolar sensitivity, and is suitable for closed-tube applications, is introduced. The decay probe uses fluorescence resonance energy transfer (FRET) between a europium chelate donor and an organic fluorophore acceptor. The substantial change in the acceptor emission decay time on hybridization with the target sequence allows the direct separation of the hybridized and unhybridized probe populations in a time-resolved measurement. No additional sample manipulation or self-hybridization of the probes is required. The wavelength and decay time of a decay probe can be adjusted according to the selection of probe length and acceptor fluorophore, thereby making the probes applicable to multiplexed assays. Here we demonstrate the decay probe principle and decay probe-based, one-step, dual DNA assay using celiac disease-related target oligonucleotides (single-nucleotide polymorphisms [SNPs]) as model analytes. Decay probes showed specific response for their complementary DNA target and allowed good signal deconvolution based on simultaneous optical and temporal filtering. This technique potentially could be used to further increase the number of simultaneously detected DNA targets in a simple one-step homogeneous assay.

  13. Microbial Response to Soil Liming of Damaged Ecosystems Revealed by Pyrosequencing and Phospholipid Fatty Acid Analyses

    PubMed Central

    Narendrula-Kotha, Ramya; Nkongolo, Kabwe K.

    2017-01-01

    Aims To assess the effects of dolomitic limestone applications on soil microbial communities’ dynamics and bacterial and fungal biomass, relative abundance, and diversity in metal reclaimed regions. Methods and Results The study was conducted in reclaimed mining sites and metal uncontaminated areas. The limestone applications were performed over 35 years ago. Total microbial biomass was determined by Phospholipid fatty acids. Bacterial and fungal relative abundance and diversity were assessed using 454 pyrosequencing. There was a significant increase of total microbial biomass in limed sites (342 ng/g) compared to unlimed areas (149 ng/g). Chao1 estimates followed the same trend. But the total number of OTUs (Operational Taxonomic Units) in limed (463 OTUs) and unlimed (473 OTUs) soil samples for bacteria were similar. For fungi, OTUs were 96 and 81 for limed and unlimed soil samples, respectively. Likewise, Simpson and Shannon diversity indices revealed no significant differences between limed and unlimed sites. Bacterial and fungal groups specific to either limed or unlimed sites were identified. Five major bacterial phyla including Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, and Proteobacteria were found. The latter was the most prevalent phylum in all the samples with a relative abundance of 50%. Bradyrhizobiaceae family with 12 genera including the nitrogen fixing Bradirhizobium genus was more abundant in limed sites compared to unlimed areas. For fungi, Ascomycota was the most predominant phylum in unlimed soils (46%) while Basidiomycota phylum represented 86% of all fungi in the limed areas. Conclusion Detailed analysis of the data revealed that although soil liming increases significantly the amount of microbial biomass, the level of species diversity remain statistically unchanged even though the microbial compositions of the damaged and restored sites are different. Significance and Impact of the study Soil liming still have a significant

  14. A low fat diet enhances polyunsaturated fatty acid desaturation and elongation independent of n3 enrichment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Low fat diets are associated with risk reduction for chronic metabolic diseases compared to high fat diets. To evaluate effects of varied fat and fatty acid intake on lipid metabolism, phospholipid fatty acids (PLFA) were measured and delta 5 and 6 desaturase activities (D5D, D6D) were calculated in...

  15. Fatty acid and DNA analyses of Permian bacteria isolated from ancient salt crystals reveal differences with their modern relatives.

    PubMed

    Vreeland, Russell H; Rosenzweig, William D; Lowenstein, Tim; Satterfield, Cindy; Ventosa, Antonio

    2006-02-01

    The isolation of living microorganisms from primary 250-million-year-old (MYA) salt crystals has been questioned by several researchers. The most intense discussion has arisen from questions about the texture and age of the crystals used, the ability of organisms to survive 250 million years when exposed to environmental factors such as radiation and the close similarity between 16S rRNA sequences in the Permian and modern microbes. The data in this manuscript are not meant to provide support for the antiquity of the isolated bacterial strains. Rather, the data presents several comparisons between the Permian microbes and other isolates to which they appear related. The analyses include whole cell fatty acid profiling, DNA-DNA hybridizations, ribotyping, and random amplified polymorphic DNA amplification (RAPD). These data show that the Permian strains, studied here, differ significantly from their more modern relatives. These differences are accumulating in both phenotypic and molecular areas of the cells. At the fatty acid level the differences are approaching but have not reached separate species status. At the molecular level the variation appears to be distributed across the genome and within the gene regions flanking the highly conserved 16S rRNA itself. The data show that these bacteria are not identical and help to rule out questions of contamination by putatively modern strains.

  16. Effects of simple acid leaching of crushed and powdered geological materials on high-precision Pb isotope analyses

    NASA Astrophysics Data System (ADS)

    Todd, Erin; Stracke, Andreas; Scherer, Erik E.

    2015-07-01

    We present new results of simple acid leaching experiments on the Pb isotope composition of USGS standard reference material powders and on ocean island basalt whole rock splits and powders. Rock samples were leached with cold 6 N HCl in an ultrasonic bath, then on a hot plate, and washed with ultrapure H2O before sample digestion in HF-HNO3 and chromatographic purification of Pb. Lead isotope analyses were measured by Tl-doped MC-ICPMS. Intrasession and intersession analytical reproducibilities of repeated analyses of both synthetic Pb solutions and Pb from single digests of chemically processed natural samples were generally better than 100 ppm (2 SD). The comparison of leached and unleached samples shows that leaching consistently removes variable amounts of contaminants that differ in Pb isotopic composition for different starting materials. For repeated digests of a single sample, analyses of leached samples reproduce better than those of unleached ones, confirming that leaching effectively removes most of the heterogeneously distributed extraneous Pb. Nevertheless, the external reproducibility of leached samples is still up to an order of magnitude worse than that of Pb solution standards (˜100 ppm). More complex leaching methods employed by earlier studies yield Pb isotope ratios within error of those produced by our method and at similar levels of reproducibility, demonstrating that our simple leaching method is as effective as more complex leaching techniques. Therefore, any Pb isotope heterogeneity among multiple leached digests of samples in excess of the external reproducibility is attributed to inherent isotopic heterogeneity of the sample. The external precision of ˜100 ppm (2 SD) achieved for Pb isotope ratio determination by Tl-doped MC-ICPMS is thus sufficient for most rocks. The full advantage of the most precise Pb isotope analytical methods is only realized in cases where the natural isotopic heterogeneity among samples in a studied suite is

  17. Indications of human activity from amino acid and amino sugar analyses on Holocene sediments from lake Lonar, central India

    NASA Astrophysics Data System (ADS)

    Menzel, P.; Gaye, B.; Wiesner, M.; Prasad, S.; Basavaiah, N.; Stebich, M.; Anoop, A.; Riedel, N.; Brauer, A.

    2012-04-01

    The DFG funded HIMPAC (Himalaya: Modern and Past Climates) programme aims to reconstruct Holocene Indian Monsoon climate using a multi-proxy and multi-archive approach. First investigations made on sediments from a ca. 10 m long core covering the whole Holocene taken from the lake Lonar in central India's state Maharashtra, Buldhana District, serve to identify changes in sedimentation, lake chemistry, local vegetation and regional to supra-regional climate patterns. Lake Lonar occupies the floor of an impact crater that formed on the ~ 65 Ma old basalt flows of the Deccan Traps. It covers an area of ca. 1 km2 and is situated in India's core monsoon area. The modern lake has a maximum depth of about 5 m, is highly alkaline, and hyposaline, grouped in the Na-Cl-CO3 subtype of saline lakes. No out-flowing stream is present and only three small streams feed the lake, resulting in a lake level highly sensitive to precipitation and evaporation. The lake is eutrophic and stratified throughout most of the year with sub- to anoxic waters below 2 m depth. In this study the core sediments were analysed for their total amino acid (AA) and amino sugar (AS) content, the amino acid bound C and N percentage of organic C and total N in the sediment and the distribution of individual amino acids. The results roughly show three zones within the core separated by distinct changes in their AA content and distribution. (i) The bottom part of the core from ca. 12000 cal a BP to 11400 cal a BP with very low AA and AS percentage indicating high lithogenic contribution, most probably related to dry conditions. (ii) From 11400 cal a BP to 1200 cal a BP the sediments show moderate AA and AS percentages and low values for the ratios of proteinogenic AAs to their non-proteinogenic degradation products (e.g. ASP/β-ALA; GLU/γ-ABA). (iii) The top part of the core (< 1200 cal a BP) is characterised by an intense increase in total AA and AS, AA-C/Corg and AA-N/Ntotas well as in the ratio of

  18. Four Moloney murine leukemia virus-infected rat cell clones producing replication-defective particles: protein and nucleic acid analyses.

    PubMed Central

    Yoshimura, F K; Yamamura, J M

    1981-01-01

    Four cloned rat cell lines (NX-1 to -4) infected with Moloney murine leukemia virus and defective in virus replication were found to be all different by viral protein and nucleic acid analyses. All four clones produced noninfectious particles and, except for NX-2, at about the same level as wild type. Compared with wild-type virions these defective particles contained larger amounts of gag precursor proteins and very little or no p30 or p15. Analysis of intracellular precursor proteins revealed that NX-2 to -4 synthesized normal Pr65gag, whereas NX-1 produced a slightly smaller precursor. Both NX-1 and NX-4 synthesized an intracellular polyprotein with a size similar to that of wild-type Pr180 gag-pol. Restriction endonuclease analysis of NX-1 to -4 cellular DNA showed that each clone contained a single integrated provirus which possessed large terminal repeat sequences at both the 5' and 3' ends. The proviruses of NX-1 to -3 appeared normal by restriction endonuclease analysis, but NX-4 provirus had a deletion of 1,700 base pairs comprising part of the polymerase region. The noninfectious particles produced by all four clones packaged Moloney viral RNAs and rat RNAs of two different sizes. Images PMID:6165841

  19. A combined study based on experimental analyses and theoretical calculations on properties of poly (lactic acid) under annealing treatment

    NASA Astrophysics Data System (ADS)

    Loued, W.; Wéry, J.; Dorlando, A.; Alimi, K.

    2015-02-01

    In this paper, the significance of annealing, in two different atmospheres (air and vacuum), on the surface characteristics of poly (lactic acid) (PLA) films was investigated. X-ray diffraction (XRD) measurements correlated to atomic force microscopy (AFM) observations of the cast PLA films show that thermal treatment under air atmosphere is responsible for a significant increase of crystallinity with the increase of temperature. However, band gap energy of the title compound is slightly affected by annealing at different temperatures. As for the untreated PLA, the molecular geometry was optimized using density functional theory (DFT/B3LYP) method with 6-31g (d) basis set in ground state. From the optimized geometry, HOMO and LUMO energies and quantum chemical parameters were performed at B3LYP/6-31g (d). The theoretical results, applied to simulated optical spectra of the compound, were compared to the observed ones. On the basis of theoretical vibrational analyses, the thermodynamic properties were calculated at different temperatures, revealing the correlation between internal energy (U), enthalpy (H), entropy (S), Free energy (G) and temperatures.

  20. Phospholipid-Derived Fatty Acids and Quinones as Markers for Bacterial Biomass and Community Structure in Marine Sediments

    PubMed Central

    Kunihiro, Tadao; Veuger, Bart; Vasquez-Cardenas, Diana; Pozzato, Lara; Le Guitton, Marie; Moriya, Kazuyoshi; Kuwae, Michinobu; Omori, Koji; Boschker, Henricus T. S.; van Oevelen, Dick

    2014-01-01

    Phospholipid-derived fatty acids (PLFA) and respiratory quinones (RQ) are microbial compounds that have been utilized as biomarkers to quantify bacterial biomass and to characterize microbial community structure in sediments, waters, and soils. While PLFAs have been widely used as quantitative bacterial biomarkers in marine sediments, applications of quinone analysis in marine sediments are very limited. In this study, we investigated the relation between both groups of bacterial biomarkers in a broad range of marine sediments from the intertidal zone to the deep sea. We found a good log-log correlation between concentrations of bacterial PLFA and RQ over several orders of magnitude. This relationship is probably due to metabolic variation in quinone concentrations in bacterial cells in different environments, whereas PLFA concentrations are relatively stable under different conditions. We also found a good agreement in the community structure classifications based on the bacterial PLFAs and RQs. These results strengthen the application of both compounds as quantitative bacterial biomarkers. Moreover, the bacterial PLFA- and RQ profiles revealed a comparable dissimilarity pattern of the sampled sediments, but with a higher level of dissimilarity for the RQs. This means that the quinone method has a higher resolution for resolving differences in bacterial community composition. Combining PLFA and quinone analysis as a complementary method is a good strategy to yield higher resolving power in bacterial community structure. PMID:24769853

  1. Uptake of nitric acid, ammonia, and organics in orographic clouds: mass spectrometric analyses of droplet residual and interstitial aerosol particles

    NASA Astrophysics Data System (ADS)

    Schneider, Johannes; Mertes, Stephan; van Pinxteren, Dominik; Herrmann, Hartmut; Borrmann, Stephan

    2017-01-01

    Concurrent in situ analyses of interstitial aerosol and cloud droplet residues have been conducted at the Schmücke mountain site during the Hill Cap Cloud Thuringia campaign in central Germany in September and October 2010. Cloud droplets were sampled from warm clouds (temperatures between -3 and +16 °C) by a counterflow virtual impactor and the submicron-sized residues were analyzed by a compact time-of-flight aerosol mass spectrometer (C-ToF-AMS), while the interstitial aerosol composition was measured by an high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). During cloud-free periods, the submicron out-of-cloud aerosol was analyzed using both instruments, allowing for intercomparison between the two instruments. Further instrumentation included black carbon measurements and optical particle counters for the aerosol particles as well as optical sizing instrumentation for the cloud droplets. The results show that, under cloud conditions, on average 85 % of the submicron aerosol mass partitioned into the cloud liquid phase. Scavenging efficiencies of nitrate, ammonium, sulfate, and organics ranged between 60 and 100 %, with nitrate having, in general, the highest values. For black carbon, the scavenging efficiency was markedly lower (about 24 %). The nitrate and ammonium mass fractions were found to be markedly enhanced in cloud residues, indicating uptake of gaseous nitric acid and ammonia into the aqueous phase. This effect was found to be temperature dependent: at lower temperatures, the nitrate and ammonium mass fractions in the residues were higher. Also, the oxidation state of the organic matter in cloud residues was found to be temperature dependent: the O : C ratio was lower at higher temperatures. A possible explanation for this observation is a more effective uptake and/or higher concentrations of low-oxidized water-soluble volatile organic compounds, possibly of biogenic origin, at higher temperatures. Organic nitrates were observed

  2. Effects of n3 Intake on Plasma Phospholipid Fatty Acids and Sex Hormone Profiles in Postmenopausal Women: Potential for Breast Cancer Risk Reduction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Breast cancer risk is associated with dietary fat intake. Omega-6 fatty acids (n6) promote while omega-3 fatty acids (n3) inhibit tumorigenesis. Increased sex hormone (SH) concentrations are associated with risk of breast cancer. The effects of total fat and n3 on SH and PLFA were assessed in a f...

  3. AMINO ACID ANALYSES OF THE ANTARCTIC CM2 METEORITES ALH 83100 AND LEW 90500 USING LIQUID CHROMATOGRAPHY-TIME OF FLIGHT-MASS SPECTROMETRY

    NASA Technical Reports Server (NTRS)

    Glavin, D. P.; Dworkin, J. P.; Aubrey, A.; Botta, O.; Doty, J. H., III; Bada, J. L.

    2001-01-01

    The investigation of organic compounds in primitive carbonaceous meteorites provides a record of the chemical processes that occurred in the early solar system. In particular, amino acids have been shown to be potential indicators in tracing the nature of carbonaceous chondrite parent bodies [ 13. The delivery of amino acids by carbonaceous chondrites to the early Earth could have been any important source of the Earth's prebiotic organic inventory [2]. Over 80 different amino acids have been detected in the Murchison CM2 meteorite, most of them completely non-existent in the terrestrial biosphere [3]. We have optimized a new liquid chromatography-time-of-flight-mass spectrometry (LC-ToF-MS) technique coupled with OPAMAC derivatization in order to detect amino acids in meteorite extracts by UV fluorescence and exact mass simultaneously. The detection limit of the LC-ToF-MS instrument for amino acids is at least 3 orders of magnitude lower than traditional GC-MS techniques. Here we report on the first analyses of amino acids and their enantiomeric abundances in the CM2 carbonaceous meteorites ALH 83100, LEW 90500, and Murchison using this new LC-ToF-MS instrument configuration. Amino acid analyses of any kind for the CM meteorite ALH 83100 have not previously been reported.

  4. Lipid fatty acid profile analyses in liver and serum in rats with nonalcoholic steatohepatitis using improved gas chromatography-mass spectrometry methodology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fatty acids (FA) are essential components of lipids and exhibit important biological functions. The analyses of FAs are routinely carried out by gas chromatography-mass spectrometry, after multi-step sample preparation. In this study, several key experimental factors were carefully examined, validat...

  5. A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data.

    PubMed

    Stanimirova, I; Woznica, A; Plociniczak, T; Kwasniewski, M; Karczewski, J

    2016-11-01

    The aim of this work was to check whether a methodology based on the analysis of data that contain the entire phospholipid fatty acid, PLFA, compositions of water samples can be successfully used to interpret spatial and temporal changes in the microbial communities in water reservoirs. The proposed methodology consists of the construction of a modified weighted multivariate mixture model for the PLFA profiles of the water samples collected in a given monitoring campaign and the identification of latent PLFA components through a comparison with the known PLFA profiles of some cultivated or non-cultivated microbial communities. A 16S rDNA analysis of some of the selected water samples in the monitoring campaign was performed in order to verify the results of the PLFA analysis. The results showed that the proposed methodology can be useful for a dynamic and sensitive evaluation of changes in the microbial quality of water before and after flash flooding and can help in taking a decision regarding further risk assessment.

  6. Determination of microbial biomass and its community structure from the distribution of phospholipid ester-linked fatty acids in sediments of Hiroshima Bay and its adjacent bays

    NASA Astrophysics Data System (ADS)

    Rajendran, N.; Matsuda, O.; Imamura, N.; Urushigawa, Y.

    1992-05-01

    Phospholipid ester-linked fatty acid (PLFA) composition in sediment samples collected from 20 sampling stations of Hiroshima Bay and its adjacent bays are reported. Thirty-one individual fatty acids were identified in the sediments which comprised of saturated, monounsaturated, polyunsaturated and branched fatty acids. A majority of these fatty acids are characteristic of aerobic and anaerobic bacteria especially sulphate-reducing bacteria. PLFA profiles in the sediments varied among the stations indicating the differences in the contributing microbial communities. The calculated biomass also varied from 0·3 × 10 7 to 2·6 × 10 7 cells g -1 dry weight sediment. The shift in microbial community structure within the study area is understood from the seven clusters obtained by the similarity analysis of PLFA composition. The results of environmental parameters revealed the existence of both oxic and anoxic conditions in the study area and the PLFA composition in sediments is discussed in relation to these environmental parameters. Low concentrations of polyunsaturated fatty acids (PUFA) determined in sediments, characteristic of microeukaryotes, could be attributed to the existing environmental conditions and pollution in the study area. Small quantities of long chain fatty acids in sediments indicated that the terrestrial input is low.

  7. Characterization of D-glucaric acid using NMR, x-ray crystal structure, and MM3 molecular modeling analyses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    D-glucaric acid was characterized in solution by comparing NMR spectra from the isotopically unlabeled molecule with those from D-glucaric acid labeled with deuterium or carbon-13 atoms. The NMR studies provided unequivocal assignments for all carbon atoms and non-hydroxyl protons of the molecule. ...

  8. Demersal fishes from the Antarctic shelf and deep sea: A diet study based on fatty acid patterns and gut content analyses

    NASA Astrophysics Data System (ADS)

    Würzberg, Laura; Peters, Janna; Flores, Hauke; Brandt, Angelika

    2011-10-01

    The gut contents and fatty acid composition of 49 fish belonging to five Antarctic demersal families (Nototheniidae, Macrouridae, Channichtyidae, Bathydraconidae and Artedidraconidae) sampled at two stations at the Southern Ocean shelf and deep sea (600 and 2150 m) were analysed in order to identify their main food resource by linking trophic biomarkers with the dietary items found in the fish guts. Main food items of most fish analysed were amphipod crustaceans (e.g. in 63% of Trematomus bernachii guts) and polychaetes (e.g. in 80% of Bathydraco sp. guts), but other food items including fish, other crustaceans and gastropods were also ingested. The most prominent fatty acids found were 20:5( n-3), 16:0, 22:6( n-3) and 18:1( n-9). The results of gut content and fatty acid analyses indicate that all fish except the Channichthyidae share similar food resources irrespective of their depth distribution, i.e. benthic amphipods and polychaetes. A difference of the dietary spectrum can be observed with ontogenetic phases rather than between species, as high values of typical calanoid copepod marker fatty acids as 22:1( n-11) indicate that younger (smaller) specimens include more zooplankton in their diet.

  9. Profiling of soil fatty acids using comprehensive two-dimensional gas chromatography with mass spectrometry detection.

    PubMed

    Zeng, Annie Xu; Chin, Sung-Tong; Patti, Antonio; Marriott, Philip J

    2013-11-22

    Profiling of phospholipid fatty acids (PLFA) represents a challenging goal for distinguishing the diversity of microbial communities and biomass in the complex and heterogeneous soil ecosystem. Comprehensive two-dimensional gas chromatography (GC×GC) coupled with simultaneous flame ionisation and mass spectrometry detection was applied as a culture-independent method for PLFA profiling of microbial classification in forest soil. A number of column sets were evaluated for the GC×GC separation of fatty acid methyl esters (FAME). Due to better isomeric separation and compound patterns on the 2D contour plot, an apolar-polar column combination was selected for soil microbial PLFA characterisation. A comprehensive view of PLFA composition with carbon chain length varying from 12 to 20 was observed in forest soil samples, with the commonly reported bacterial FAME of iso-/anteiso-, methyl-branched-, cyclopropyl-, and hydroxyl-substituted FA identified by their mass spectral and retention time according to authentic standards. Notably, some uncommon oxygenated FAME were found in high abundance and were further characterised by GC×GC coupled with high resolution mass spectrometry. This tentatively revealed geometric pairs of methyl 9,10-epoxyoctadecanoate isomers.

  10. Oxalic Acid from Lentinula edodes Culture Filtrate: Antimicrobial Activity on Phytopathogenic Bacteria and Qualitative and Quantitative Analyses

    PubMed Central

    Kwak, A-Min; Lee, In-Kyoung; Lee, Sang-Yeop

    2016-01-01

    The culture filtrate of Lentinula edodes shows potent antimicrobial activity against the plant pathogenic bacteria Ralstonia solanacearum. Bioassay-guided fractionation was conducted using Diaion HP-20 column chromatography, and the insoluble active compound was not adsorbed on the resin. Further fractionation by high-performance liquid chromatography (HPLC) suggested that the active compounds were organic acids. Nine organic acids were detected in the culture filtrate of L. edodes; oxalic acid was the major component and exhibited antibacterial activity against nine different phytopathogenic bacteria. Quantitative analysis by HPLC revealed that the content of oxalic acid was higher in the water extract from spent mushroom substrate than in liquid culture. This suggests that the water extract of spent L. edodes substrate is an eco-friendly control agent for plant diseases. PMID:28154495

  11. Integrated Transcriptome and Metabolic Analyses Reveals Novel Insights into Free Amino Acid Metabolism in Huangjinya Tea Cultivar

    PubMed Central

    Zhang, Qunfeng; Liu, Meiya; Ruan, Jianyun

    2017-01-01

    The chlorotic tea variety Huangjinya, a natural mutant, contains enhanced levels of free amino acids in its leaves, which improves the drinking quality of its brewed tea. Consequently, this chlorotic mutant has a higher economic value than the non-chlorotic varieties. However, the molecular mechanisms behind the increased levels of free amino acids in this mutant are mostly unknown, as are the possible effects of this mutation on the overall metabolome and biosynthetic pathways in tea leaves. To gain further insight into the effects of chlorosis on the global metabolome and biosynthetic pathways in this mutant, Huangjinya plants were grown under normal and reduced sunlight, resulting in chlorotic and non-chlorotic leaves, respectively; their leaves were analyzed using transcriptomics as well as targeted and untargeted metabolomics. Approximately 5,000 genes (8.5% of the total analyzed) and ca. 300 metabolites (14.5% of the total detected) were significantly differentially regulated, thus indicating the occurrence of marked effects of light on the biosynthetic pathways in this mutant plant. Considering primary metabolism, including that of sugars, amino acids, and organic acids, significant changes were observed in the expression of genes involved in both nitrogen (N) and carbon metabolism. The suite of changes not only generated an increase in amino acids, including glutamic acid, glutamine, and theanine, but it also elevated the levels of free ammonium, citrate, and α-ketoglutarate, and lowered the levels of mono- and di-saccharides and of caffeine as compared with the non-chlorotic leaves. Taken together, our results suggest that the increased levels of amino acids in the chlorotic vs. non-chlorotic leaves are likely due to increased protein catabolism and/or decreased glycolysis and diminished biosynthesis of nitrogen-containing compounds other than amino acids, including chlorophyll, purines, nucleotides, and alkaloids. PMID:28321230

  12. Transcriptome and metabolome analyses of sugar and organic acid metabolism in Ponkan (Citrus reticulata) fruit during fruit maturation.

    PubMed

    Lin, Qiong; Wang, Chengyang; Dong, Wencheng; Jiang, Qing; Wang, Dengliang; Li, Shaojia; Chen, Ming; Liu, Chunrong; Sun, Chongde; Chen, Kunsong

    2015-01-01

    Ponkan (Citrus reticulata Blanco cv. Ponkan) is an important mandarin citrus in China. However, the low ratio of sugars to organic acids makes it less acceptable for consumers. In this work, three stages (S120, early development stage; S195, commercial harvest stage; S205, delayed harvest stage) of Ponkan fruit were selected for study. Among 28 primary metabolites analyzed in fruit, sugars increased while organic acids in general decreased. RNA-Seq analysis was carried out and 19,504 genes were matched to the Citrus clementina genome, with 85 up-regulated and 59 down-regulated genes identified during fruit maturation. A sucrose phosphate synthase (SPS) gene was included in the up-regulated group, and this was supported by the transcript ratio distribution. Expression of two asparagine transferases (AST), and a specific ATP-citrate lyase (ACL) and glutamate decarboxylase (GAD) members increased during fruit maturation. It is suggested that SPS, AST, ACL and GAD coordinately contribute to sugar accumulation and organic acid degradation during Ponkan fruit maturation. Both the glycolysis pathway and TCA cycle were accelerated during later maturation, indicating the flux change from sucrose metabolism to organic acid metabolism was enhanced, with citrate degradation occurring mainly through the gamma-aminobutyric acid (GABA) and acetyl-CoA pathways.

  13. AquaLite, a bioluminescent label for immunoassay and nucleic acid detection: quantitative analyses at the attomol level

    NASA Astrophysics Data System (ADS)

    Smith, David F.; Stults, Nancy L.

    1996-04-01

    AquaLiteR is a direct, bioluminescent label capable of detecting attomol levels of analyte in clinical immunoassays and assays for the quantitative measurement of nucleic acids. Bioluminescent immunoassays (BIAs) require no radioisotopes and avoid complex fluorescent measurements and many of the variables of indirect enzyme immunoassays (EIAs). AquaLite, a recombinant form of the photoprotein aequorin from a bioluminescent jellyfish, is coupled directly to antibodies to prepare bioluminescent conjugates for assay development. When the AquaLite-antibody complex is exposed to a solution containing calcium ions, a flash of blue light ((lambda) max equals 469 nm) is generated. The light signal is measured in commercially available luminometers that simultaneously inject a calcium solution and detect subattomol photoprotein levies in either test tubes or microtiter plates. Immunometric or 'sandwich' type assays are available for the quantitative measurement of human endocrine hormones and nucleic acids. The AquaLite TSH assay can detect 1 attomol of thyroid stimulating hormone (TSH) in 0.2 mL of human serum and is a useful clinical tool for diagnosing hyperthyroid patients. AquaLite-based nucleic acid detection permits quantifying attomol levels of specific nucleic acid markers and represents possible solution to the difficult problem of quantifying the targets of nucleic acid amplification methods.

  14. Eicosapentaenoic acid prevents high fat diet-induced metabolic disorders: Genomic and metabolomic analyses of underlying mechanism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previously our lab demonstrated eicosapenaenoic acid (EPA)'s ability to prevent high-fat (HF) diet-induced obesity by decreasing insulin resistance, glucose intolerance and inflammation. In the current study, we used genomic and metabolomic approaches to further investigate the molecular basis for t...

  15. Genome-wide meta-analyses identify novel loci associated with n-3 and n-6 polyunsaturated fatty acid levels in Chinese and European-ancestry populations.

    PubMed

    Hu, Yao; Li, Huaixing; Lu, Ling; Manichaikul, Ani; Zhu, Jingwen; Chen, Yii-Der I; Sun, Liang; Liang, Shuang; Siscovick, David S; Steffen, Lyn M; Tsai, Michael Y; Rich, Stephen S; Lemaitre, Rozenn N; Lin, Xu

    2016-03-15

    Epidemiological studies suggest that levels of n-3 and n-6 long-chain polyunsaturated fatty acids are associated with risk of cardio-metabolic outcomes across different ethnic groups. Recent genome-wide association studies in populations of European ancestry have identified several loci associated with plasma and/or erythrocyte polyunsaturated fatty acids. To identify additional novel loci, we carried out a genome-wide association study in two population-based cohorts consisting of 3521 Chinese participants, followed by a trans-ethnic meta-analysis with meta-analysis results from 8962 participants of European ancestry. Four novel loci (MYB, AGPAT4, DGAT2 and PPT2) reached genome-wide significance in the trans-ethnic meta-analysis (log10(Bayes Factor) ≥ 6). Of them, associations of MYB and AGPAT4 with docosatetraenoic acid (log10(Bayes Factor) = 11.5 and 8.69, respectively) also reached genome-wide significance in the Chinese-specific genome-wide association analyses (P = 4.15 × 10(-14) and 4.30 × 10(-12), respectively), while associations of DGAT2 with gamma-linolenic acid (log10(Bayes Factor) = 6.16) and of PPT2 with docosapentaenoic acid (log10(Bayes Factor) = 6.24) were nominally significant in both Chinese- and European-specific genome-wide association analyses (P ≤ 0.003). We also confirmed previously reported loci including FADS1, NTAN1, NRBF2, ELOVL2 and GCKR. Different effect sizes in FADS1 and independent association signals in ELOVL2 were observed. These results provide novel insight into the genetic background of polyunsaturated fatty acids and their differences between Chinese and European populations.

  16. Authentication of farmed and wild turbot (Psetta maxima) by fatty acid and isotopic analyses combined with chemometrics.

    PubMed

    Busetto, Maria L; Moretti, Vittorio M; Moreno-Rojas, Jose M; Caprino, Fabio; Giani, Ivan; Malandra, Renato; Bellagamba, Federica; Guillou, Claude

    2008-04-23

    Fatty acid composition and stable isotope ratios of carbon (delta(13)C) and nitrogen (delta(15)N) were determined in muscle tissue of turbot (Psetta maxima). The multivariate analysis of the data was performed to evaluate their utility in discriminating wild and farmed fish. Wild (n=30) and farmed (n=30) turbot of different geographical origins (Denmark, The Netherlands, and Spain) were sampled from March 2006 to February 2007. The application of linear discriminant analysis (LDA) and soft independent modeling of class analogy (SIMCA) to analytical data demonstrated the combination of fatty acids and isotopic measurements to be a promising method to discriminate between wild and farmed fish and between wild fish of different geographical origin. In particular, IRMS (Isotope Ratio Mass Spectrometry) alone did not permit us to separate completely farmed from wild samples, resulting in some overlaps between Danish wild and Spanish farmed turbot. On the other hand, fatty acids alone differentiated between farmed and wild samples by 18:2n-6 but were not able to distinguish between the two groups of wild turbot. When applying LDA isotope ratios, 18:2n-6, 18:3n-3, and 20:4n-6 fatty acids were decisive to distinguish farmed from wild turbot of different geographical origin, while delta(15)N, 18:2n-6, and 20:1n-11 were chosen to classify wild samples from different fishing zones. In both cases, 18:2n-6 and delta(15)N were determinant for classification purposes. We would like to emphasize that IRMS produces rapid results and could be the most promising technique to distinguish wild fish of different origin. Similarly, fatty acid composition could be used to easily distinguish farmed from wild samples.

  17. Development of SI-traceable C-peptide certified reference material NMIJ CRM 6901-a using isotope-dilution mass spectrometry-based amino acid analyses.

    PubMed

    Kinumi, Tomoya; Goto, Mari; Eyama, Sakae; Kato, Megumi; Kasama, Takeshi; Takatsu, Akiko

    2012-07-01

    A certified reference material (CRM) is a higher-order calibration material used to enable a traceable analysis. This paper describes the development of a C-peptide CRM (NMIJ CRM 6901-a) by the National Metrology Institute of Japan using two independent methods for amino acid analysis based on isotope-dilution mass spectrometry. C-peptide is a 31-mer peptide that is utilized for the evaluation of β-cell function in the pancreas in clinical testing. This CRM is a lyophilized synthetic peptide having the human C-peptide sequence, and contains deamidated and pyroglutamylated forms of C-peptide. By adding water (1.00 ± 0.01) g into the vial containing the CRM, the C-peptide solution in 10 mM phosphate buffer saline (pH 6.6) is reconstituted. We assigned two certified values that represent the concentrations of total C-peptide (mixture of C-peptide, deamidated C-peptide, and pyroglutamylated C-peptide) and C-peptide. The certified concentration of total C-peptide was determined by two amino acid analyses using pre-column derivatization liquid chromatography-mass spectrometry and hydrophilic chromatography-mass spectrometry following acid hydrolysis. The certified concentration of C-peptide was determined by multiplying the concentration of total C-peptide by the ratio of the relative area of C-peptide to that of the total C-peptide measured by liquid chromatography. The certified value of C-peptide (80.7 ± 5.0) mg/L represents the concentration of the specific entity of C-peptide; on the other hand, the certified value of total C-peptide, (81.7 ± 5.1) mg/L can be used for analyses that does not differentiate deamidated and pyroglutamylated C-peptide from C-peptide itself, such as amino acid analyses and immunochemical assays.

  18. Microbial contributions to C and N dynamics in decaying litter elucidated by amino acid and amino sugar analyses

    NASA Astrophysics Data System (ADS)

    Hobara, S.; Osono, T.; Noro, K.; Hirota, M.; Benner, R. H.

    2011-12-01

    There is still much to be revealed about carbon (C) and nitrogen (N) dynamics in terrestrial soil systems. The objectives of this study were to identify molecular changes in composition during plant litter decomposition and gain insights about microbial contributions to C and N dynamics in decaying litter. Litter bag experiments with three plant species, Miscanthus sinensis, Pinus densiflora and Quercus crispula, were conducted for three years, and the concentrations of C, N, amino acids and amino sugars were determined at various times during the experiments. Mass loss (AFDW) ranged from 66-90% for the plant tissues. The weight %C remained fairly constant, whereas the weight %N increased throughout the study indicating N immobilization was occurring. The percentages of C as amino acids and amino sugars also increased throughout the study suggesting these biomolecules were largely of microbial origin. The increasing yields of amino acids and amino sugars were inversely related to overall C loss from the litter material. As microorganisms degraded the plant litter they left behind molecular signatures that were useful predictors of the extent of overall degradation. The C/N ratio of litter decreased throughout the study and was inversely related to galactosamine yields. The glucosamine/galactosamine (GlcN/GalN) ratio gradually declined to values near 2 by the end of the study. Galactoasamine is more abundant in bacteria than fungi, and the declining GlcN/GalN ratio suggest the relative contributions of bacterial to litter C and N increased relative to contributions from fungi. A cluster analysis of 0- and 36-month litters based on amino acid and amino sugar composition showed that 0-month litters of three plant species were separated from 36-month litters, suggesting common diagenetic pathways during decomposition irrespective of plant species. The microbial decomposers contribute to N immobilization and their contributions to the C and N content of litter increases

  19. Lipidomic analyses of the mouse brain after antidepressant treatment: evidence for endogenous release of long-chain fatty acids?

    PubMed

    Lee, Lynette Hui-Wen; Shui, Guanghou; Farooqui, Akhlaq A; Wenk, Markus R; Tan, Chay-Hoon; Ong, Wei-Yi

    2009-08-01

    Recently, there has been considerable interest in a possible link between changes in brain polyunsaturated fatty acids, neural membrane phospholipid degradation, serotonergic neurotransmission, and depression. The present study aims to examine effects of antidepressants on lipids in different regions of the brain at individual molecular species level, using the novel technique of lipidomics. Balb/C mice received daily intraperitoneal (i.p.) injections of 10 mg/kg of the antidepressants maprotiline, fluoxetine and paroxetine for 4 wk. The prefrontal cortex, hippocampus, striatum and cerebellum were harvested, and lipid profiles compared to those of saline-injected mice. Treatment with maprotiline and paroxetine, but not fluoxetine, resulted in significant decreases in phosphatidylcholine (PC) species, PC36:1, PC38:3, PC40:2p, PC40:6, PC40:5, PC42:7p, PC42:6p and PC42:5p in the prefrontal neocortex. The decreases in phospholipids were accompanied by increases in lysophospholipid species, lysoPC16:0, lysoPC18:2 and lysoPC18:0 in the prefrontal cortex, indicating increase in phospholipase A2 activity and possible release of long-chain fatty acids. Maprotiline and paroxetine treatment also resulted in decreases in sphingomyelin and increases in several ceramide species in the prefrontal cortex. It is postulated that endogenous release of long-chain fatty acids may be related to the mechanism of action of maprotiline and paroxetine.

  20. Effects of folic acid on overall and site-specific cancer incidence during the randomised trials: meta-analyses of data on 50 000 individuals

    PubMed Central

    Vollset, Stein Emil; Clarke, Robert; Lewington, Sarah; Ebbing, Marta; Halsey, Jim; Lonn, Eva; Armitage, Jane; Manson, JoAnn E; Hankey, Graeme J; Spence, J David; Galan, Pilar; Bønaa, Kaare H; Jamison, Rex; Gaziano, J Michael; Guarino, Peter; Baron, John A; Logan, Richard FA; Giovannucci, Edward L; den Heijer, Martin; Ueland, Per M; Bennett, Derrick; Collins, Rory; Peto, Richard

    2013-01-01

    Summary Background Some countries fortify flour with folic acid to prevent neural tube defects but others do not, partly because of concerns about cancer risks. We aimed to assess the effects of folic acid supplementation on site-specific cancer rates in the randomised trials. Methods Meta-analyses of data on each individual in all placebo-controlled trials of folic acid for prevention of cardiovascular disease (10 trials, n=46,969) or colorectal adenoma (3 trials, n=2652) that recorded cancer incidence and recruited >500 participants. All trials were evenly randomised. Risk ratios (RRs) compare those allocated folic acid vs those allocated placebo, giving cancer incidence rate ratios (among those still free of cancer) during, but not after the scheduled treatment period. Findings During a weighted mean follow-up duration of 5.5 years, allocation to folic acid quadrupled plasma folate, but had no statistically significant effect on overall cancer incidence (1904 vs 1809 cancers, RR=1.06 [95%CI 0.99–1.13], p=0.10; trend with duration of treatment p=0.46). There was no significant heterogeneity between the results of individual trials (p=0.23), or between the cadiovascular prevention trials and the adenoma prevention trials (p=0.13). Moreover, there was no significant effect of folic acid supplementation on the incidence of cancer of the large intestine, prostate, lung, breast or any other specific site. Interpretation Folic acid supplementation does not substantially increase or decrease site-specific cancer incidence during the first 5 years of treatment. Funding British Heart Foundation, Medical Research Council, Cancer Research UK, Food Standards Agency. PMID:23352552

  1. Association analyses between brain-expressed fatty-acid binding protein (FABP) genes and schizophrenia and bipolar disorder.

    PubMed

    Iwayama, Yoshimi; Hattori, Eiji; Maekawa, Motoko; Yamada, Kazuo; Toyota, Tomoko; Ohnishi, Tetsuo; Iwata, Yasuhide; Tsuchiya, Kenji J; Sugihara, Genichi; Kikuchi, Mitsuru; Hashimoto, Kenji; Iyo, Masaomi; Inada, Toshiya; Kunugi, Hiroshi; Ozaki, Norio; Iwata, Nakao; Nanko, Shinichiro; Iwamoto, Kazuya; Okazaki, Yuji; Kato, Tadafumi; Yoshikawa, Takeo

    2010-03-05

    Deficits in prepulse inhibition (PPI) are a biological marker for psychiatric illnesses such as schizophrenia and bipolar disorder. To unravel PPI-controlling mechanisms, we previously performed quantitative trait loci (QTL) analysis in mice, and identified Fabp7, that encodes a brain-type fatty acid binding protein (Fabp), as a causative gene. In that study, human FABP7 showed genetic association with schizophrenia. FABPs constitute a gene family, of which members FABP5 and FABP3 are also expressed in the brain. These FABP proteins are molecular chaperons for polyunsaturated fatty acids (PUFAs) such as arachidonic and docosahexaenoic acids. Additionally, the involvement of PUFAs has been documented in the pathophysiology of schizophrenia and mood disorders. Therefore in this study, we examined the genetic roles of FABP5 and 3 in schizophrenia (N = 1,900 in combination with controls) and FABP7, 5, and 3 in bipolar disorder (N = 1,762 in the case-control set). Three single nucleotide polymorphisms (SNPs) from FABP7 showed nominal association with bipolar disorder, and haplotypes of the same gene showed empirical associations with bipolar disorder even after correction of multiple testing. We could not perform association studies on FABP5, due to the lack of informative SNPs. FABP3 displayed no association with either disease. Each FABP is relatively small and it is assumed that there are multiple regulatory elements that control gene expression. Therefore, future identification of unknown regulatory elements will be necessary to make a more detailed analysis of their genetic contribution to mental illnesses.

  2. Understanding field variation, quantum chemical modeling and molecular orbital analyses of trans-3-(trans-4-imidazolyl) acrylic acid

    NASA Astrophysics Data System (ADS)

    Gayathri, R.; Arivazhagan, M.

    2017-02-01

    In this work, a joint experimental (FTIR and FT-Raman) and theoretical (DFT and ab-initio) study on the structure and the vibrations of Trans-3-(trans-4-imidazolyl) acrylic acid (TTIAA) are compared and analyzed. The assignment of each normal mode has been made using the observed and calculated frequencies. The optimized geometries, harmonic vibrational wavenumbers and intensities of vibrational bands of trans-3-(trans-4-imidazolyl) acrylic acid (TTIAA) have been carried out using the HF/B3LYP method using the standard 6311++G(d,p) basis set calculations in this investigation. The result describes the variation in electrostatic and transport properties for zero and various external applied field. The variation in MPA charges are small due to the application of EFs: however, in most cases it is found to be systematic and almost uniform. When the field increases from 0.00 to 0.02 VÅ-1, the hybridization of molecular levels broadens the DOS and decreases the HLG from 3.6609 to 1.2325 eV; the decrease of band gap at the high field indicates that this molecule exhibit considerable electrical conductivity. Fukui indices to determine the local reactive site for the molecular systems during electrophilic, nucleophilic, radical and dual descriptor attacks. The results clearly show the superiority of MPA scheme. This study may be useful to design new molecules with more electrical conductivity.

  3. Trophic interactions of the pelagic ecosystem over the Reykjanes Ridge as evaluated by fatty acid and stable isotope analyses

    NASA Astrophysics Data System (ADS)

    Petursdottir, H.; Gislason, A.; Falk-Petersen, S.; Hop, H.; Svavarsson, J.

    2008-01-01

    Trophic relationships of the important oceanic crustacean species Calanus finmarchicus, Meganyctiphanes norvegica and Sergestes arcticus, as well as the mesopelagic fishes Maurolicus muelleri, Benthosema glaciale and Sebastes mentella, were investigated over the Reykjanes Ridge in June 2003 and in June 2004. Measurements were performed of length, wet weight, dry weight, total lipid, lipid class, fatty acid and fatty alcohol profiles and stable isotopes (δ 13C and δ 15N). High amounts of the Calanus lipid markers, 20:1(n-9) and 22:1(n-11) in these species confirm the importance of Calanus spp. in this ecosystem. Comparisons of fatty acid/alcohol profiles by multivariate analysis revealed two main trophic pathways over the Reykjanes Ridge. In one pathway, Calanus spp. was an important part of the diet for the small mesopelagic fish species M. muelleri and B. glaciale and the shrimp S. arcticus, whereas in the other pathway, the euphausiid M. norvegica was the dominant food for the redfish S. mentella, and Calanus spp. were of less importance. M. muelleri and the smaller B. glaciale feed on C. finmarchicus, whereas the larger B. glaciale and S. arcticus select the larger, deeper-living C. hyperboreus. All investigated species are true pelagic species except for the shrimp S. arcticus, which seems to have a benthic feeding habit as well. The δ 15N levels show that of the species investigated, C. finmarchicus occupies the lowest trophic level (2.0) and the redfish, S. mentella, the highest (4.2). All the species were lipid rich, typical for subarctic pelagic ecosystem. Calanus finmarchicus, S. arcticus and B. glaciale store wax esters as their lipid stores, while M. norvegica, M. muelleri and S. mentella store triacylglycerols.

  4. Phospholipid Fatty Acid Composition and Heavy Metal Tolerance of Soil Microbial Communities along Two Heavy Metal-Polluted Gradients in Coniferous Forests

    PubMed Central

    Pennanen, T.; Frostegard, A.; Fritze, H.; Baath, E.

    1996-01-01

    The effects of long-term heavy metal deposition on microbial community structure and the level of bacterial community tolerance were studied along two different gradients in Scandinavian coniferous forest soils. One was near the Harjavalta smelter in Finland, and one was at Ronnskar in Sweden. Phospholipid fatty acid (PLFA) analysis revealed a gradual change in soil microbial communities along both pollution gradients, and most of the individual PLFAs changed similarly to metal pollution at both sites. The relative quantities of the PLFAs br18:0, br17:0, i16:0, and i16:1 increased with increasing heavy metal concentration, while those of 20:4 and 18:2(omega)6, which is a predominant PLFA in many fungi, decreased. The fungal part of the microbial biomass was found to be more sensitive to heavy metals. This resulted in a decreased fungal/bacterial biomass ratio along the pollution gradient towards the smelters. The thymidine incorporation technique was used to study the heavy metal tolerance of the bacteria. The bacterial community at the Harjavalta smelter, exposed mainly to Cu deposition, exhibited an increased tolerance to Cu but not to Cd, Ni, and Zn. At the Ronnskar smelter the deposition consisting of a mixture of metals increased the bacterial community tolerance to all tested metals. Both the PLFA pattern and the bacterial community tolerance were affected at lower soil metal concentrations than were bacterial counts and bacterial activities. At Harjavalta the increased Cu tolerance of the bacteria and the change in the PLFA pattern of the microbial community were found at the same soil Cu concentrations. This indicated that the altered PLFA pattern was at least partly due to an altered, more metal-tolerant bacterial community. At Ronnskar, where the PLFA data varied more, a correlation between bacterial community tolerance and an altered PLFA pattern was found up to 10 to 15 km from the smelter. Farther away changes in the PLFA pattern could not be explained

  5. Pharmacopeial compliance of fish oil-containing parenteral lipid emulsion mixtures: Globule size distribution (GSD) and fatty acid analyses.

    PubMed

    Driscoll, David F; Ling, Pei-Ra; Bistrian, Bruce R

    2009-09-08

    Recently, the United States Pharmacopeia (USP) has established Chapter 729 with GSD limits for all lipid emulsions where the mean droplet size (MDS) must be <500 nm and the percent of fat larger than 5 microm (PFAT(5)) must be <0.05%, irrespective of the final lipid concentration. As well, the European Pharmacopeia (EP) Monograph no. 1352 specifies n3-fatty acid (FA) limits (EPA+DHA> or =45%; total n3 or T-n3> or =60%) for fish oil. We assessed compliance with USP physical and EP chemical limits of two fish oil-containing lipid emulsion mixtures. All lipid emulsions passed USP 729 limits. No samples tested had an MDS >302 nm or a PFAT(5) value >0.011%. Only one product met EP limits while the other failed. All emulsions tested were extremely fine dispersions and easily met USP 729 GSD limits. The n3-FAs profiles were lower in one, despite being labeled to contain 50% more fish oil than the other product. This latter finding suggests the n3-FA content of the fish oil source and/or the applied manufacturing processes in these products is different.

  6. Transcriptomic Analyses of Ascorbic Acid and Carotenoid Metabolites Influenced by Root Restriction during Grape Berry Development and Ripening.

    PubMed

    Leng, Feng; Tang, Dandan; Lin, Qiong; Cao, Jinping; Wu, Di; Wang, Shiping; Sun, Chongde

    2017-03-08

    Ascorbic acid (AsA) and carotenoids are recognized as crucial metabolites for various biological processes in plants. The contents of AsA and carotenoids in fruits are influenced by external environmental stimuli, such as water, temperature, light, and hormones. However, it is still not clear whether it can be affected by root restriction (RR) treatment. In this study, "Summer Black" grape berries (Vitis vinifera × V. labrusca) under RR and control treatments during development and ripening were used as materials. The results showed that RR significantly increased the contents of AsA, and the transcript VIT_08s0040g03150 related to AsA recycling pathways may be the main regulator for AsA. Similarly, the contents of most of the carotenoids at the earlier stages significantly increased by RR; the enzyme crtB encoded by VIT_12s0028g00960 and the enzyme crtZ encoded by VIT_02s0025g00240 and VIT_16s0050g01090 were inferred to play major roles in the carotenoid metabolic pathways.

  7. Electrochemical, HPLC and electrospray ionization mass spectroscopic analyses of peroxycitric acid coexisting with citric acid and hydrogen peroxide in aqueous solution.

    PubMed

    Ferdousi, Begum Nadira; Islam, Md Mominul; Okajima, Takeyoshi; Ohsaka, Takeo

    2008-02-15

    We successfully determined the molecular structure of peroxycitric acid (PCA) coexisting in the aqueous equilibrium mixture with citric acid (CA; 1,2,3-tricarboxylic-2-hydroxy propane) and hydrogen peroxide (H(2)O(2)) by a combined use of reversed-phase HPLC (RP-HPLC), potentiometric, hydrodynamic chronocoulometric (HCC) and electrospray ionization mass spectroscopic (ESI-MS) methods. Firstly, the RP-HPLC was employed to separate CA, PCA and H(2)O(2) coexisting in the equilibrium mixture and the concentration of CA consumed (DeltaC(CA)) in the formation of PCA that was evidenced to be fairly stable during the RP-HPLC measurement was quantitatively measured based on the standard calibration curve of CA. Secondly, the total oxidant concentration (C(Ox)) corresponding to peroxycarboxylic (-COOOH) group in PCA in the equilibrium mixture was determined using potentiometric measurement. The ratio of C(Ox)/DeltaC(CA) was found to be 1.07, which indicates that only one -COOH group in CA molecule is oxidized to the corresponding -COOOH group in PCA molecule. Thirdly, using the HCC technique the diffusion coefficient of PCA, which could be electroreduced at a more positive potential by 1.0 V than the coexisting H(2)O(2), was independently measured as 0.3 x 10(-5)cm(2)s(-1) and at the same time, by considering DeltaC(CA) as the concentration of PCA, the number of electrons (n) required for the reduction of PCA was determined to be 2. The result obtained from RP-HPLC and HCC, i.e., n=2 which is equivalent to one -COOOH group in PCA, is in agreement with that obtained from the combination of RP-HPLC and potentiometric measurements. Finally, the structure of PCA was proposed to contain one -COOOH group with a molecular mass of 208 confirmed by negative ion ESI-MS method. A probable molecular structure of PCA was discussed.

  8. Trophic Dynamics of Filter Feeding Bivalves in the Yangtze Estuarine Intertidal Marsh: Stable Isotope and Fatty Acid Analyses.

    PubMed

    Wang, Sikai; Jin, Binsong; Qin, Haiming; Sheng, Qiang; Wu, Jihua

    2015-01-01

    Benthic bivalves are important links between primary production and consumers, and are essential intermediates in the flow of energy through estuarine systems. However, information on the diet of filter feeding bivalves in estuarine ecosystems is uncertain, as estuarine waters contain particulate matter from a range of sources and as bivalves are opportunistic feeders. We surveyed bivalves at different distances from the creek mouth at the Yangtze estuarine marsh in winter and summer, and analyzed trophic dynamics using stable isotope (SI) and fatty acid (FA) techniques. Different bivalve species had different spatial distributions in the estuary. Glauconome chinensis mainly occurred in marshes near the creek mouth, while Sinonovacula constricta preferred the creek. Differences were found in the diets of different species. S. constricta consumed more diatoms and bacteria than G. chinensis, while G. chinensis assimilated more macrophyte material. FA markers showed that plants contributed the most (38.86 ± 4.25%) to particular organic matter (POM) in summer, while diatoms contributed the most (12.68 ± 1.17%) during winter. Diatoms made the largest contribution to the diet of S. constricta in both summer (24.73 ± 0.44%) and winter (25.51 ± 0.59%), and plants contributed no more than 4%. This inconsistency indicates seasonal changes in food availability and the active feeding habits of the bivalve. Similar FA profiles for S. constricta indicated that the bivalve had a similar diet composition at different sites, while different δ13C results suggested the diet was derived from different carbon sources (C4 plant Spartina alterniflora and C3 plant Phragmites australis and Scirpus mariqueter) at different sites. Species-specific and temporal and/or spatial variability in bivalve feeding may affect their ecological functions in intertidal marshes, which should be considered in the study of food webs and material flows in estuarine ecosystems.

  9. Physiological and molecular analyses of black and yellow seeded Brassica napus regulated by 5-aminolivulinic acid under chromium stress.

    PubMed

    Gill, Rafaqat A; Ali, Basharat; Islam, Faisal; Farooq, Muhammad A; Gill, Muhammad B; Mwamba, Theodore M; Zhou, Weijun

    2015-09-01

    Brassica napus L. is a promising oilseed crop among the oil producing species. So, it is prime concern to screen the metal tolerant genotypes in order to increase the oilseed rape production through the utilization of pollutant soil regimes. Nowadays, use of plant growth regulators against abiotic stress is one of the major objectives of researchers. In this study, an attempt was carried out to analyze the pivotal role of exogenously applied 5-amenolevulinic acid (ALA) on alleviating chromium (Cr)-toxicity in black and yellow seeded B. napus. Plants of two cultivars (ZS 758 - a black seed type, and Zheda 622 - a yellow seed type) were treated with 400 μM Cr with or without 15 and 30 mg/L ALA. Results showed that exogenously applied ALA improved the plant growth and increased ALA contents; however, it decreased the Cr concentration in B. napus leaves under Cr-toxicity. Moreover, exogenous ALA reduced oxidative stress by up-regulating antioxidant enzyme activities and their related gene expression. Further, results suggested that stress responsive protein's transcript level such as HSP90-1 and MT-1 were increased under Cr stress alone in both cultivars. Exogenously applied ALA further enhanced the expression rate in both genotypes and obviously results were found in favor of cultivar ZS 758. The ultrastructural changes were observed more obvious in yellow seeded than black seeded cultivar; however, exogenously applied ALA helped the plants to recover their cell turgidity under Cr stress. The present study describes a detailed molecular mechanism how ALA regulates the plant growth by improving antioxidant machinery and related transcript levels, cellular modification as well as stress related genes expression under Cr-toxicity.

  10. Trophic Dynamics of Filter Feeding Bivalves in the Yangtze Estuarine Intertidal Marsh: Stable Isotope and Fatty Acid Analyses

    PubMed Central

    Wang, Sikai; Jin, Binsong; Qin, Haiming; Sheng, Qiang; Wu, Jihua

    2015-01-01

    Benthic bivalves are important links between primary production and consumers, and are essential intermediates in the flow of energy through estuarine systems. However, information on the diet of filter feeding bivalves in estuarine ecosystems is uncertain, as estuarine waters contain particulate matter from a range of sources and as bivalves are opportunistic feeders. We surveyed bivalves at different distances from the creek mouth at the Yangtze estuarine marsh in winter and summer, and analyzed trophic dynamics using stable isotope (SI) and fatty acid (FA) techniques. Different bivalve species had different spatial distributions in the estuary. Glauconome chinensis mainly occurred in marshes near the creek mouth, while Sinonovacula constricta preferred the creek. Differences were found in the diets of different species. S. constricta consumed more diatoms and bacteria than G. chinensis, while G. chinensis assimilated more macrophyte material. FA markers showed that plants contributed the most (38.86 ± 4.25%) to particular organic matter (POM) in summer, while diatoms contributed the most (12.68 ± 1.17%) during winter. Diatoms made the largest contribution to the diet of S. constricta in both summer (24.73 ± 0.44%) and winter (25.51 ± 0.59%), and plants contributed no more than 4%. This inconsistency indicates seasonal changes in food availability and the active feeding habits of the bivalve. Similar FA profiles for S. constricta indicated that the bivalve had a similar diet composition at different sites, while different δ13C results suggested the diet was derived from different carbon sources (C4 plant Spartina alterniflora and C3 plant Phragmites australis and Scirpus mariqueter) at different sites. Species-specific and temporal and/or spatial variability in bivalve feeding may affect their ecological functions in intertidal marshes, which should be considered in the study of food webs and material flows in estuarine ecosystems. PMID:26261984

  11. Assignment of fatty acid-beta-oxidizing syntrophic bacteria to Syntrophomonadaceae fam. nov. on the basis of 16S rRNA sequence analyses

    NASA Technical Reports Server (NTRS)

    Zhao, H.; Yang, D.; Woese, C. R.; Bryant, M. P.

    1993-01-01

    After enrichment from Chinese rural anaerobic digestor sludge, anaerobic, sporing and nonsporing, saturated fatty acid-beta-oxidizing syntrophic bacteria were isolated as cocultures with H2- and formate-utilizing Methanospirillum hungatei or Desulfovibrio sp. strain G-11. The syntrophs degraded C4 to C8 saturated fatty acids, including isobutyrate and 2-methylbutyrate. They were adapted to grow on crotonate and were isolated as pure cultures. The crotonate-grown pure cultures alone did not grow on butyrate in either the presence or the absence of some common electron acceptors. However, when they were reconstituted with M. hungatei, growth on butyrate again occurred. In contrast, crotonate-grown Clostridium kluyveri and Clostridium sticklandii, as well as Clostridium sporogenes, failed to grow on butyrate when these organisms were cocultured with M. hungatei. The crotonate-grown pure subcultures of the syntrophs described above were subjected to 16S rRNA sequence analysis. Several previously documented fatty acid-beta-oxidizing syntrophs grown in pure cultures with crotonate were also subjected to comparative sequence analyses. The sequence analyses revealed that the new sporing and nonsporing isolates and other syntrophs that we sequenced, which had either gram-negative or gram-positive cell wall ultrastructure, all belonged to the phylogenetically gram-positive phylum. They were not closely related to any of the previously known subdivisions in the gram-positive phylum with which they were compared, but were closely related to each other, forming a new subdivision in the phylum. We recommend that this group be designated Syntrophomonadaceae fam. nov.; a description is given.

  12. Sensitivity analyses of MAGIC modelled predictions of future impacts of whole-tree harvest on soil calcium supply and stream acid neutralizing capacity.

    PubMed

    Zetterberg, Therese; Köhler, Stephan J; Löfgren, Stefan

    2014-10-01

    Forest biofuel is a main provider of energy in Sweden and the market is expected to grow even further in the future. Removal of logging residues via harvest can lead to short-term acidification but the long-term effects are largely unknown. The objectives of this study were to 1) model the long-term effect of whole-tree harvest (WTH) on soil and stream water acidity and 2) perform sensitivity analyses by varying the amounts of logging residues, calcium (Ca(2+)) concentrations in tree biomass and site productivity in nine alternate scenarios. Data from three Swedish forested catchments and the Model of Acidification of Groundwater in Catchments (MAGIC) were used to simulate changes in forest soil exchangeable Ca(2+) pools and stream water acid neutralizing capacity (ANC) at Gammtratten, Kindla and Aneboda. Large depletions in soil Ca(2+) supply and a reversal of the positive trend in stream ANC were predicted for all three sites after WTH. However, the magnitude of impact on stream ANC varied depending on site and the concentration of mobile strong acid anions. Contrary to common beliefs, the largest decrease in modelled ANC was observed at the well-buffered site Gammtratten. The effects at Kindla and Aneboda were much more limited and not large enough to offset the general recovery from acidification. Varying the tree biomass Ca(2+) concentrations exerted the largest impact on modelled outcome. Site productivity was the second most important variable whereas changing biomass amounts left on site only marginally affected the results. The outcome from the sensitivity analyses pointed in the same direction of change as in the base scenario, except for Kindla where soil Ca(2+) pools were predicted to be replenished under a given set of input data. The reliability of modelled outcome would increase by using site-specific Ca(2+) concentrations in tree biomass and field determined identification of site productivity.

  13. Analyses of mitochondrial amino acid sequence datasets support the proposal that specimens of Hypodontus macropi from three species of macropodid hosts represent distinct species

    PubMed Central

    2013-01-01

    Background Hypodontus macropi is a common intestinal nematode of a range of kangaroos and wallabies (macropodid marsupials). Based on previous multilocus enzyme electrophoresis (MEE) and nuclear ribosomal DNA sequence data sets, H. macropi has been proposed to be complex of species. To test this proposal using independent molecular data, we sequenced the whole mitochondrial (mt) genomes of individuals of H. macropi from three different species of hosts (Macropus robustus robustus, Thylogale billardierii and Macropus [Wallabia] bicolor) as well as that of Macropicola ocydromi (a related nematode), and undertook a comparative analysis of the amino acid sequence datasets derived from these genomes. Results The mt genomes sequenced by next-generation (454) technology from H. macropi from the three host species varied from 13,634 bp to 13,699 bp in size. Pairwise comparisons of the amino acid sequences predicted from these three mt genomes revealed differences of 5.8% to 18%. Phylogenetic analysis of the amino acid sequence data sets using Bayesian Inference (BI) showed that H. macropi from the three different host species formed distinct, well-supported clades. In addition, sliding window analysis of the mt genomes defined variable regions for future population genetic studies of H. macropi in different macropodid hosts and geographical regions around Australia. Conclusions The present analyses of inferred mt protein sequence datasets clearly supported the hypothesis that H. macropi from M. robustus robustus, M. bicolor and T. billardierii represent distinct species. PMID:24261823

  14. Microbial Substrate Usage Indicated by C-14 Contents of Phospholipid Fatty Acids From Soil Organic Matter

    NASA Astrophysics Data System (ADS)

    Rethemeyer, J.; Nadeau, M. J.; Grootes, P. M.; Kramer, C.; Gleixner, G.

    2004-05-01

    Phospholipid fatty acids (PLFA's) are generally associated with viable (bacterial) cell membranes. They are thought to be short-lived under normal soil conditions. We compare the C-14 levels in PLFA's obtained from soil samples from the,clean" experimental site at Rotthalmünster (Germany) with those from the agricultural research station at Halle (Germany), where the soil is contaminated with,old" carbon from lignite mining and industry. The most abundant PLFA's were isolated via preparative capillary gas chromatography of their methyl-esters at the Max-Planck Institute, Jena, and their C-14 concentration was determined via accelerator mass spectrometry at the Leibniz-Labor, Kiel. The C-14 levels of three mono-unsaturated fatty acids (n-C17:1, n-C18:1 (and n-C16:1)) are not statistically significant different from those of the contemporaneous atmosphere, indicating these fatty acids were derived from fresh plant material. C-14 levels significantly above those of the atmosphere in three saturated fatty acids (i/a-C15:0, n-C16:0 and cy-C18:0) from the surface soil of Rotthalmünster must derive from carbon fixed from the atmosphere several years earlier, when levels of bomb-C-14, remaining from the atmospheric nuclear weapons tests, especially of the early 1960's, were still higher. Lower C-14 levels in the same compounds from the Halle surface soil indicate the incorporation of "old" contaminant carbon. A below- atmospheric C-14 concentration in n-C18:0 in Rotthalmünster surface soil may reflect the partial incorporation of carbon from older, pre-bomb times. The C-14 concentrations show these PLFA's were synthesized predominantly from recent to sub-recent photosynthetic compounds, while the significant differences in C-14 concentration, observed between the PLFA's, indicate their production from soil organic matter fractions of different (recent) age and C-14 content. The Halle results show "old" carbon may be incorporated into PLFA's and thus reenter the soil

  15. Rhizosphere bacterial carbon turnover is higher in nucleic acids than membrane lipids: implications for understanding soil carbon cycling

    PubMed Central

    Malik, Ashish A.; Dannert, Helena; Griffiths, Robert I.; Thomson, Bruce C.; Gleixner, Gerd

    2015-01-01

    Using a pulse chase 13CO2 plant labeling experiment we compared the flow of plant carbon into macromolecular fractions of rhizosphere soil microorganisms. Time dependent 13C dilution patterns in microbial cellular fractions were used to calculate their turnover time. The turnover times of microbial biomolecules were found to vary: microbial RNA (19 h) and DNA (30 h) turned over fastest followed by chloroform fumigation extraction-derived soluble cell lysis products (14 days), while phospholipid fatty acids (PLFAs) had the slowest turnover (42 days). PLFA/NLFA 13C analyses suggest that both mutualistic arbuscular mycorrhizal and saprophytic fungi are dominant in initial plant carbon uptake. In contrast, high initial 13C enrichment in RNA hints at bacterial importance in initial C uptake due to the dominance of bacterial derived RNA in total extracts of soil RNA. To explain this discrepancy, we observed low renewal rate of bacterial lipids, which may therefore bias lipid fatty acid based interpretations of the role of bacteria in soil microbial food webs. Based on our findings, we question current assumptions regarding plant-microbe carbon flux and suggest that the rhizosphere bacterial contribution to plant assimilate uptake could be higher. This highlights the need for more detailed quantitative investigations with nucleic acid biomarkers to further validate these findings. PMID:25914679

  16. Promoter analyses and transcriptional profiling of eggplant polyphenol oxidase 1 gene (SmePPO1) reveal differential response to exogenous methyl jasmonate and salicylic acid.

    PubMed

    Shetty, Santoshkumar M; Chandrashekar, Arun; Venkatesh, Yeldur P

    2012-05-01

    The transcriptional regulation of multigenic eggplant (Solanum melongena) polyphenol oxidase genes (SmePPO) is orchestrated by their corresponding promoters which mediate developmentally regulated expression in response to myriad biotic and abiotic factors. However, information on structural features of SmePPO promoters and modulation of their expression by plant defense signals are lacking. In the present study, SmePPOPROMOTERs were cloned by genome walking, and their transcription start sites (TSS) were determined by RLM-RACE. Extensive sequence analyses revealed the presence of evolutionarily conserved and over-represented putative cis-acting elements involved in light-regulated transcription, biosynthetic pathways (phenylpropanoid/flavonoid), hormone signaling (abscisic acid, gibberellic acid, jasmonate and salicylate), elicitor and stress responses (cold/dehydration responses), sugar metabolism and plant defense signaling (W-BOX/WRKY) that are common to SmePPOPROMOTER1 and 2. The TSS for SmePPO genes are located 9-15bp upstream of ATG with variable lengths of 5' untranslated regions. Transcriptional profiling of SmePPOs in eggplant seedlings has indicated differential response to methyl jasmonate (MeJA) or salicylic acid (SA) treatment. In planta, while MeJA elicited expression of all the six SmePPOs, SA was only able to induce the expression of SmePPO4-6. Interestingly, in dual treatment, SA considerably repressed the MeJA-induced expression of SmePPOs. Functional dissection of SmePPOPROMOTER1 by deletion analyses using Agrobacterium-mediated transient expression in tobacco leaves has shown that MeJA enhances the SmePPOPROMOTER1-β-glucuronidase (GUS) expression in vivo, while SA does not. Histochemical and quantitative GUS assays have also indicated the negative effect of SA on MeJA-induced expression of SmePPOPROMOTER1. By combining in silico analyses, transcriptional profiling and expression of SmePPOPROMOTER1-GUS fusions, the role of SA on the modulation

  17. Inferring Phytoplankton, Terrestrial Plant and Bacteria Bulk δ¹³C Values from Compound Specific Analyses of Lipids and Fatty Acids.

    PubMed

    Taipale, Sami J; Peltomaa, Elina; Hiltunen, Minna; Jones, Roger I; Hahn, Martin W; Biasi, Christina; Brett, Michael T

    2015-01-01

    Stable isotope mixing models in aquatic ecology require δ13C values for food web end members such as phytoplankton and bacteria, however it is rarely possible to measure these directly. Hence there is a critical need for improved methods for estimating the δ13C ratios of phytoplankton, bacteria and terrestrial detritus from within mixed seston. We determined the δ13C values of lipids, phospholipids and biomarker fatty acids and used these to calculate isotopic differences compared to the whole-cell δ13C values for eight phytoplankton classes, five bacterial taxa, and three types of terrestrial organic matter (two trees and one grass). The lipid content was higher amongst the phytoplankton (9.5±4.0%) than bacteria (7.3±0.8%) or terrestrial matter (3.9±1.7%). Our measurements revealed that the δ13C values of lipids followed phylogenetic classification among phytoplankton (78.2% of variance was explained by class), bacteria and terrestrial matter, and there was a strong correlation between the δ13C values of total lipids, phospholipids and individual fatty acids. Amongst the phytoplankton, the isotopic difference between biomarker fatty acids and bulk biomass averaged -10.7±1.1‰ for Chlorophyceae and Cyanophyceae, and -6.1±1.7‰ for Cryptophyceae, Chrysophyceae and Diatomophyceae. For heterotrophic bacteria and for type I and type II methane-oxidizing bacteria our results showed a -1.3±1.3‰, -8.0±4.4‰, and -3.4±1.4‰ δ13C difference, respectively, between biomarker fatty acids and bulk biomass. For terrestrial matter the isotopic difference averaged -6.6±1.2‰. Based on these results, the δ13C values of total lipids and biomarker fatty acids can be used to determine the δ13C values of bulk phytoplankton, bacteria or terrestrial matter with ± 1.4‰ uncertainty (i.e., the pooled SD of the isotopic difference for all samples). We conclude that when compound-specific stable isotope analyses become more widely available, the determination of

  18. Inferring Phytoplankton, Terrestrial Plant and Bacteria Bulk δ¹³C Values from Compound Specific Analyses of Lipids and Fatty Acids

    PubMed Central

    Taipale, Sami J.; Peltomaa, Elina; Hiltunen, Minna; Jones, Roger I.; Hahn, Martin W.; Biasi, Christina; Brett, Michael T.

    2015-01-01

    Stable isotope mixing models in aquatic ecology require δ13C values for food web end members such as phytoplankton and bacteria, however it is rarely possible to measure these directly. Hence there is a critical need for improved methods for estimating the δ13C ratios of phytoplankton, bacteria and terrestrial detritus from within mixed seston. We determined the δ13C values of lipids, phospholipids and biomarker fatty acids and used these to calculate isotopic differences compared to the whole-cell δ13C values for eight phytoplankton classes, five bacterial taxa, and three types of terrestrial organic matter (two trees and one grass). The lipid content was higher amongst the phytoplankton (9.5±4.0%) than bacteria (7.3±0.8%) or terrestrial matter (3.9±1.7%). Our measurements revealed that the δ13C values of lipids followed phylogenetic classification among phytoplankton (78.2% of variance was explained by class), bacteria and terrestrial matter, and there was a strong correlation between the δ13C values of total lipids, phospholipids and individual fatty acids. Amongst the phytoplankton, the isotopic difference between biomarker fatty acids and bulk biomass averaged -10.7±1.1‰ for Chlorophyceae and Cyanophyceae, and -6.1±1.7‰ for Cryptophyceae, Chrysophyceae and Diatomophyceae. For heterotrophic bacteria and for type I and type II methane-oxidizing bacteria our results showed a -1.3±1.3‰, -8.0±4.4‰, and -3.4±1.4‰ δ13C difference, respectively, between biomarker fatty acids and bulk biomass. For terrestrial matter the isotopic difference averaged -6.6±1.2‰. Based on these results, the δ13C values of total lipids and biomarker fatty acids can be used to determine the δ13C values of bulk phytoplankton, bacteria or terrestrial matter with ± 1.4‰ uncertainty (i.e., the pooled SD of the isotopic difference for all samples). We conclude that when compound-specific stable isotope analyses become more widely available, the determination of

  19. Direct incorporation of fatty acids into microbial phospholipids in soils: Position-specific labeling tells the story

    NASA Astrophysics Data System (ADS)

    Dippold, Michaela A.; Kuzyakov, Yakov

    2016-02-01

    Fatty acids have been used as plant and microbial biomarkers, and knowledge about their transformation pathways in soils and sediments is crucial for interpreting fatty acid signatures, especially because the formation, recycling and decomposition processes are concurrent. We analyzed the incorporation of free fatty acids into microbial fatty acids in soil by coupling position-specific 13C labeling with compound-specific 13C analysis. Position-specifically and uniformly 13C labeled palmitate were applied in an agricultural Luvisol. Pathways of fatty acids were traced by analyzing microbial utilization of 13C from individual molecule positions of palmitate and their incorporation into phospholipid fatty acids (PLFA). The fate of palmitate 13C in the soil was characterized by the main pathways of microbial fatty acid metabolism: Odd positions (C-1) were preferentially oxidized to CO2 in the citric acid cycle, whereas even positions (C-2) were preferentially incorporated into microbial biomass. This pattern is a result of palmitate cleavage to acetyl-CoA and its further use in the main pathways of C metabolism. We observed a direct, intact incorporation of more than 4% of the added palmitate into the PLFA of microbial cell membranes, indicating the important role of palmitate as direct precursor for microbial fatty acids. Palmitate 13C was incorporated into PLFA as intact alkyl chain, i.e. the C backbone of palmitate was not cleaved, but palmitate was incorporated either intact or modified (e.g. desaturated, elongated or branched) according to the fatty acid demand of the microbial community. These modifications of the incorporated palmitate increased with time. Future PLFA studies must therefore consider the recycling of existing plant and microbial-derived fatty acids. This study demonstrates the intact uptake and recycling of free fatty acids such as palmitate in soils, as well as the high turnover and transformation of cellular PLFA. Knowledge about the intact

  20. Microarray and Functional Gene Analyses of Sulfate-Reducing Prokaryotes in Low-Sulfate, Acidic Fens Reveal Cooccurrence of Recognized Genera and Novel Lineages

    PubMed Central

    Loy, Alexander; Küsel, Kirsten; Lehner, Angelika; Drake, Harold L.; Wagner, Michael

    2004-01-01

    Low-sulfate, acidic (approximately pH 4) fens in the Lehstenbach catchment in the Fichtelgebirge mountains in Germany are unusual habitats for sulfate-reducing prokaryotes (SRPs) that have been postulated to facilitate the retention of sulfur and protons in these ecosystems. Despite the low in situ availability of sulfate (concentration in the soil solution, 20 to 200 μM) and the acidic conditions (soil and soil solution pHs, approximately 4 and 5, respectively), the upper peat layers of the soils from two fens (Schlöppnerbrunnen I and II) of this catchment displayed significant sulfate-reducing capacities. 16S rRNA gene-based oligonucleotide microarray analyses revealed stable diversity patterns for recognized SRPs in the upper 30 cm of both fens. Members of the family “Syntrophobacteraceae” were detected in both fens, while signals specific for the genus Desulfomonile were observed only in soils from Schlöppnerbrunnen I. These results were confirmed and extended by comparative analyses of environmentally retrieved 16S rRNA and dissimilatory (bi)sulfite reductase (dsrAB) gene sequences; dsrAB sequences from Desulfobacca-like SRPs, which were not identified by microarray analysis, were obtained from both fens. Hypotheses concerning the ecophysiological role of these three SRP groups in the fens were formulated based on the known physiological properties of their cultured relatives. In addition to these recognized SRP lineages, six novel dsrAB types that were phylogenetically unrelated to all known SRPs were detected in the fens. These dsrAB sequences had no features indicative of pseudogenes and likely represent novel, deeply branching, sulfate- or sulfite-reducing prokaryotes that are specialized colonists of low-sulfate habitats. PMID:15574893

  1. The use of amino acid analyses in (palaeo-) limnological investigations: A comparative study of four Indian lakes in different climate regimes

    NASA Astrophysics Data System (ADS)

    Menzel, Philip; Anupama, Krishnamurthy; Basavaiah, Nathani; Das, Brijraj Krishna; Gaye, Birgit; Herrmann, Nicole; Prasad, Sushma

    2015-07-01

    In the present study, we report the results of comprehensive amino acid (AA) analyses of four Indian lakes from different climate regimes. We focus on the investigation of sediment cores retrieved from the lakes but data of modern sediment as well as vascular plant, soil, and suspended particulate matter samples from individual lakes are also presented. Commonly used degradation and organic matter source indices are tested for their applicability to the lake sediments, and we discuss potential reasons for possible limitations. A principal component analysis including the monomeric AA composition of organic matter of all analysed samples indicates that differences in organic matter sources and the environmental properties of the individual lakes are responsible for the major variability in monomeric AA distribution of the different samples. However, the PCA also gives a factor that most probably separates the samples according to their state of organic matter degradation. Using the factor loadings of the individual AA monomers, we calculate a lake sediment degradation index (LI) that might be applicable to other palaeo-lake investigations.

  2. Effects of humic acid on arsenic(V) removal by zero-valent iron from groundwater with special references to corrosion products analyses.

    PubMed

    Rao, Pinhua; Mak, Mark S H; Liu, Tongzhou; Lai, Keith C K; Lo, Irene M C

    2009-04-01

    The effects of humic acid (HA) on As(V) removal by zero-valent iron (Fe(0)) from groundwater, associated with corrosion products analyses, were investigated using batch experiments. It was found that arsenic was rapidly removed from groundwater possibly due to its adsorption and co-precipitation with the corrosion products of Fe(0). The removal rate of arsenic by Fe(0) was inhibited in the presence of HA probably because of the formation of soluble Fe-humate in groundwater which hindered the production of iron precipitates. A longer reaction time was then required for arsenic removal. Such an influence of HA on arsenic removal increased with increasing HA concentration from 5 to 25mgL(-1). The binding capacity of HA for dissolved Fe was estimated to be about 0.75mg Femg(-1) HA. When the complexation of HA with dissolved Fe was saturated, further corrosion of Fe(0) would produce precipitates, which significantly accelerated the removal of arsenic from groundwater via adsorption and co-precipitation with the corrosion products. Iron (hydr)oxides such as maghemite, lepidocrocite, and magnetite were characterized by XRD analyses as the corrosion products, while As(V) was found on the surface of these corrosion products as detected by fourier transform infrared spectrometry and X-ray photoelectron spectroscopy.

  3. Regeneration of somatic embryos in Theobroma cacao L. in temporary immersion bioreactor and analyses of free amino acids in different tissues.

    PubMed

    Niemenak, Nicolas; Saare-Surminski, Katja; Rohsius, Christina; Ndoumou, Denis Omokolo; Lieberei, Reinhard

    2008-04-01

    The present study aimed at developing temporary immersion bioreactor techniques for multiplication of cacao somatic embryos. Temporary Immersion System (TIS), i.e. flooding of plant tissue at regular time intervals provides an efficient way to propagate plants. Somatic embryos were regenerated in twin flask bioreactors. The TIS proved to be suitable for mass regeneration of somatic embryos and for their subsequent direct sowing. The number of embryos after 3 months of culture was significantly higher in TIS cultures than in the solid medium variant. TIS also improved embryo development regarding the conversion to torpedo shaped forms. Matured embryos derived from TIS and pre-treated with 6% sucrose were converted into plants after direct sowing. Additionally to the influence of culture conditions on the development of somatic embryogenesis the content and composition of free amino acids were analysed. The content of free amino acids in somatic embryos rose as immersion frequency increased. The endogenous free GABA content in embryogenic callus was significantly higher than in non-embryogenic callus.

  4. SALDI-TOF-MS analyses of small molecules (citric acid, dexasone, vitamins E and A) using TiO2 nanocrystals as substrates.

    PubMed

    Popović, Iva A; Nešić, Maja; Vranješ, Mila; Šaponjić, Zoran; Petković, Marijana

    2016-10-01

    Surface-assisted laser desorption/ionisation time-of-flight mass spectrometry (SALDI-TOF-MS) might be the method of choice for the analysis of low mass molecules (less than m/z 500). Titanium dioxide (TiO2) nanocrystals as a substrate for SALDI-TOF-MS improve the reproducibility of the signal intensities and prevent the fragmentation of some molecules upon laser irradiation, as we have previously shown. In addition, variously shaped and sized TiO2 nanocrystals/substrates for SALDI-MS could be used for quantification of small molecules, which are otherwise difficult to detect with the assistance of organic matrices. TiO2-assisted LDI-MS spectra could be acquired with excellent reproducibility and repeatability and with low detection limit. In the current study, we analysed the spectra of dexasone, citric acid, vitamin E and vitamin A acquired with TiO2 nanocrystals of various shapes and dimensions, i.e. the colloidal TiO2 nanoparticles (TiO2 NPs), TiO2 prolate nanospheroids (TiO2 PNSs) and TiO2 nanotubes (TiO2 NTs). Various shapes and dimensions of substrates were used since these factors determine desorption and ionisation processes. The homogeneity on the target plate was compared based on signal-to-noise values of peaks of interest of analysed molecules as well as the within-day and day-to-day repeatability. In summary, the obtained results show that the applicability of individual TiO2 nanocrystals depends on the analyte. Signals which are acquired with the assistance of TiO2 PNSs have the highest sensitivity and reproducibility (the smallest standard deviation), even compared with those in the LDI mode. This implies that TiO2 PNSs could also be suitable for quantitative analyses of small molecules.

  5. A comparison of sole carbon source utilization patterns and phospholipid fatty acid profiles to detect changes in the root microflora of hydroponically grown crops.

    PubMed

    Khalil, S; Bååth, E; Alsanius, B; Englund, J E; Sundin, P; Gertsson, U E; Jensén, P

    2001-04-01

    Sole carbon source utilization (SCSU) patterns and phospholipid fatty acid (PLFA) profiles were compared with respect to their potential to characterize root-inhabiting microbial communities of hydroponically grown crops. Sweet pepper (Capsicum annum cv. Evident), lettuce (Lactuca sativa cv. Grand Rapids), and four different cultivars of tomato (Lycopersicon esculentum cvs. Gitana, Armada, Aromata, and Elin) were grown in 1-L black plastic beakers placed in a cultivation chamber with artificial light. In addition to the harvest of the plants after 6 weeks, plants of one tomato cultivar, cv. Gitana, were also harvested after 4 and 8 weeks. The cultivation in this study was performed twice. Principal component analysis was used to analyze the data. Both characterization methods had the ability to discriminate between the root microflora of different plant species, cultivars, and one tomato cultivar at different ages. Differences in both SCSU patterns and PLFA profiles were larger between plant species than between cultivars, but for both methods the largest differences were between the two cultivations. Still, the differences between treatments were always due to differences in the same PLFAs in both cultivations. This was not the case for the SCSU patterns when different plant ages were studied. Furthermore, PLFA profiles showed less variation between replicates than did SCSU patterns. This larger variation observed among the SCSU data indicates that PLFA may be more useful to detect changes in the root microflora of hydroponically grown crops than the SCSU technique.

  6. Enhancing Phospholipid Fatty Acid Profiling of Soil Bacterial Communities via Substrate- Specific 13C-labelling

    NASA Astrophysics Data System (ADS)

    Evershed, R. P.; Maxfield, P. J.; Bingham, E. M.; Dildar, N.; Brennand, E. L.; Hornibrook, E.

    2008-12-01

    A range of culture-independent methods, has recently emerged to study environmental microorganisms in situ[1]. One such method is phospholipid fatty acid (PLFA) analysis, wherein these ubiquitous membrane lipids provide a powerful tool for the study of unculturable soil microorganisms. PLFA analyses have been used to investigate the impacts of a wide range of environmental factors on the soil microbial community. An acknowledged shortcoming of the PLFAs approach is the lack the chemotaxonoic specificity, which restricts the ability of the method to probe the activities of specific functional groups of the microbial community selectively. However, the selectivity of PLFAs analyses can be enhanced by incubating soils with 13C- labelled substrates followed by gas chromatography-combustion-isotope ratio mass spectrometry to reveal the specific PLFAs incorporating the 13C-label. The application of this approach will be demonstrated through our recent work on methanotrophic bacteria in soils. We applied this approach initially to mineral soils[2] and then extended chemotaxonomic assessments by using a combination of 13C-labelled PLFAs and hopanoids [3]. We have used this approach to explore the properties of high affinity methanotrophs in a range of environments, investigating the relationship between methane oxidation rates and the nature and magnitude of the methanotrophic community for the first time[4,5] More recently we extended the technique using a novel time series 13C-labelling of PLFAs[6] to estimate the rate and progression of 13C- label incorporation and turnover of methanotrophic populations. This modified approach has been used to investigate the impacts of various environmental variables, e.g. soil type, vegetation cover and land use, on the methanotrophic biomass[7.8]. The unique nature of the 13CH4 as a gaseous substate/carbon source means that can be readily introduced into soils via a specific subset of the soil microbial biomass, thereby offering many

  7. Microbial sulfate reduction and metal attenuation in pH 4 acid mine water

    USGS Publications Warehouse

    Church, C.D.; Wilkin, R.T.; Alpers, C.N.; Rye, R.O.; Blaine, R.B.

    2007-01-01

    Sediments recovered from the flooded mine workings of the Penn Mine, a Cu-Zn mine abandoned since the early 1960s, were cultured for anaerobic bacteria over a range of pH (4.0 to 7.5). The molecular biology of sediments and cultures was studied to determine whether sulfate-reducing bacteria (SRB) were active in moderately acidic conditions present in the underground mine workings. Here we document multiple, independent analyses and show evidence that sulfate reduction and associated metal attenuation are occurring in the pH-4 mine environment. Water-chemistry analyses of the mine water reveal: (1) preferential complexation and precipitation by H2S of Cu and Cd, relative to Zn; (2) stable isotope ratios of 34S/32S and 18O/16O in dissolved SO4 that are 2-3 ??? heavier in the mine water, relative to those in surface waters; (3) reduction/oxidation conditions and dissolved gas concentrations consistent with conditions to support anaerobic processes such as sulfate reduction. Scanning electron microscope (SEM) analyses of sediment show 1.5-micrometer, spherical ZnS precipitates. Phospholipid fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analyses of Penn Mine sediment show a high biomass level with a moderately diverse community structure composed primarily of iron- and sulfate-reducing bacteria. Cultures of sediment from the mine produced dissolved sulfide at pH values near 7 and near 4, forming precipitates of either iron sulfide or elemental sulfur. DGGE coupled with sequence and phylogenetic analysis of 16S rDNA gene segments showed populations of Desulfosporosinus and Desulfitobacterium in Penn Mine sediment and laboratory cultures. ?? 2007 Church et al; licensee BioMed Central Ltd.

  8. Phospholipid Fatty Acids as Physiological Indicators of Paracoccus denitrificans Encapsulated in Silica Sol-Gel Hydrogels

    PubMed Central

    Trögl, Josef; Jirková, Ivana; Kuráň, Pavel; Akhmetshina, Elmira; Brovdyová, Tat′jána; Sirotkin, Alexander; Kirilina, Tatiana

    2015-01-01

    The phospholipid fatty acid (PLFA) content was determined in samples of Paracoccus denitrificans encapsulated in silica hydrogel films prepared from prepolymerized tetramethoxysilane (TMOS). Immediately after encapsulation the total PLFA concentration was linearly proportional to the optical density (600 nm) of the input microbial suspension (R2 = 0.99). After 7 days this relationship remained linear, but with significantly decreased slope, indicating a higher extinction of bacteria in suspensions of input concentration 108 cells/mL and higher. trans-Fatty acids, indicators of cytoplasmatic membrane disturbances, were below the detection limit. The cy/pre ratio (i.e., ratio of cyclopropylated fatty acids (cy17:0 + cy19:0) to their metabolic precursors (16:1ω7 + 18:1ω7)), an indicator of the transition of the culture to a stationary growth-phase, decreased depending on co-immobilization of nutrients in the order phosphate buffer > mineral medium > Luria Broth rich medium. The ratio, too, was logarithmically proportional to cell concentration. These results confirm the applicability of total PLFA as an indicator for the determination of living biomass and cy/pre ratio for determination of nutrient limitation of microorganisms encapsulated in sol-gel matrices. This may be of interest for monitoring of sol-gel encapsulated bacteria proposed as optical recognition elements in biosensor construction, as well as other biotechnological applications. PMID:25690547

  9. Major and trace-element analyses of acid mine waters in the Leviathan Mine drainage basin, California/Nevada; October, 1981 to October, 1982

    USGS Publications Warehouse

    Ball, J.W.; Nordstrom, D.K.

    1985-01-01

    Water issuing from the inactive Leviathan open-pit sulfur mine has caused serious degradation of the water quality in the Leviathan/Bryant Creek drainage basin which drains into the East Fork of the Carson River. As part of a pollution abatement project of the California Regional Water Quality Control Board, the U.S. Geological Survey collected hydrologic and water quality data for the basin during 1981-82. During this period a comprehensive sampling survey was completed to provide information on trace metal attenuation during downstream transport and to provide data for interpreting geochemical processes. This report presents the analytical results from this sampling survey. Sixty-seven water samples were filtered and preserved on-site at 45 locations and at 3 different times. Temperature, discharge, pH, and Eh and specific conductance were measured on-site. Concentrations of 37 major and trace constituents were determined later in the laboratory on preserved samples. The quality of the analyses was checked by using two or more techniques to determine the concentrations including d.c.-argon plasma emission spectrometry (DCP), flame and flameless atomic absorption spectrophotometry, UV-visible spectrophotometry, hydride-generation atomic absorption spectrophotometry and ion chromatography. Additional quality control was obtained by comparing measured to calculated conductance, comparing measured to calculated Eh (from Fe-2 +/Fe-3+ determinations), charge balance calculations and mass balance calculations for conservative constituents at confluence points. Leviathan acid mine waters contain mg/L concentrations of As, Cr, Co, Cu, Mn, Ni, T1, V and Zn, and hundreds to thousands of mg/L concentrations of Al, Fe, and sulfate at pH values as low as 1.8. Other elements including Ba, B, Be, Bi, Cd , Mo, Sb, Se and Te are elevated above normal background concentrations and fall in the microgram/L range. The chemical and 34 S/32 S isotopic analyses demonstrate that these

  10. Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms

    SciTech Connect

    Goltsman, Daniela; Denef, Vincent; Singer, Steven; Verberkmoes, Nathan C; Lefsrud, Mark G; Mueller, Ryan; Dick, Gregory J.; Sun, Christine; Wheeler, Korin; Zelma, Adam; Baker, Brett J.; Hauser, Loren John; Land, Miriam L; Shah, Manesh B; Thelen, Michael P.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2009-01-01

    We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyl-dependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.

  11. Relatively rapid emplacement of dome-forming magma inferred from strain analyses: The case of the acid Latian dome complexes (Central Italy)

    NASA Astrophysics Data System (ADS)

    Cimarelli, C.; de Rita, D.

    2006-11-01

    We have analysed the relationship between the volcanic substratum and magma body emplacement for the acid dome complexes of Latium, Central Italy. Our study shows that the volcanic edifices, which are mainly Pleistocene cryptodomes and related explosive products, were derived from mantle magmas contaminated by crustal materials. The Cimini, Tolfa and Cerite-Manziate dome complexes of Latium show the following characteristics: a shallow laccolith origin; emplacement in basins that have identical tectonic evolution and geological structure; the same magmatic composition and density contrast between magma and host rock; and geochronological data that are inconsistent with field evidence. In the Cimini and Tolfa dome complexes, the deformation induced by shallow intrusions was accompanied by ˜ 200 m uplift of the sedimentary cover. The estimated pluton infilling time for the Cimini and Tolfa domes is 10 2 years while the strain rate required to uplift their Pliocene overburden by 200 m is ɛm' ˜ 10 - 9 s - 1 . The rapid evolution of the dome complexes is consistent with field data that show no relevant interruptions in the volcanic activity and no significant compositional changes in the volcanic products related to the extrusion of the domes. For the Cerite-Manziate dome complex, the minimal input rate of magma favoured a monogenetic style of volcanism, independent of the regional stress conditions.

  12. Application of Phospholipid Fatty Acids in the Evaluation of Post-Katrina Wetland Soils

    NASA Astrophysics Data System (ADS)

    Holloway, J. M.; Swarzenski, C. M.; Krauss, K. W.; Doyle, T. W.

    2008-12-01

    The combined effects of Hurricanes Katrina (landfall Aug. 29, 2005) and Rita (landfall Sept. 24, 2005) resulted in a catastrophic loss of wetlands, with an estimated decrease of 562 km2 of land area (Barras, 2006) along the Gulf Coast of Louisiana. A study was initiated following the 2005 hurricane season to characterize storm impacts on coastal marsh soils, measuring soil organic carbon, biogeochemistry of soil pore waters, and soil microbial communities using phospholipids fatty acids (PLFA). Areas selected for study include Caernarvon, which had the greatest land loss through Katrina, and the Barataria Preserve, a unit within the Jean Lafitte National Historic Park. Marshes ranged from fresh water to saline. PLFA concentrations were generally greater in surface soils (28-144 nmol PLFA/g dry soil at 0-5 cm) than deeper soil (27-77 nmol/g at 10-15 cm; 18-20 nmol/g at 35-45 cm) for soils collected in March 2006. There was a notable exception to this trend. The concentration of PLFAs was greater at 15cm (51 nmol/g) than 5cm (28 nmol/g) in a remnant salt marsh soil from Caernarvon. The ratio of 17:0cy/17:0, a stress indicator, was greater in the 5 and 15 cm depths for this soil (6.4 and 7.3, respectively) than in other soils collected at this date (1.9-6.4 at 5 cm; 1.2-5.4 at 15 cm). The inverted PLFA biomass and elevated 17:0cy/17:0 at this location may reflect disturbance from Katrina 6 months after the storm. Differences in microbial community structure were noted between fresh-water and salt marshes, with a general decrease in PLFA concentrations with increasing salinity. A resampling of surface soil in September, 2007 showed an increase in PLFA concentration (64-148 nmol/g) and decreased 17:0cy/17:0 ratio (1.5-3.8). In addition, there were shifts in surface microbial communities, including an increase in a16:0 in fresh water marsh soils and in overall increase in 18:1ωc, a biomarker for eukaryotic microorganisms, including algae and fungi. These shifts may

  13. The microbial communities and potential greenhouse gas production in boreal acid sulphate, non-acid sulphate, and reedy sulphidic soils.

    PubMed

    Šimek, Miloslav; Virtanen, Seija; Simojoki, Asko; Chroňáková, Alica; Elhottová, Dana; Krištůfek, Václav; Yli-Halla, Markku

    2014-01-01

    Acid sulphate (AS) soils along the Baltic coasts contain significant amounts of organic carbon and nitrogen in their subsoils. The abundance, composition, and activity of microbial communities throughout the AS soil profile were analysed. The data from a drained AS soil were compared with those from a drained non-AS soil and a pristine wetland soil from the same region. Moreover, the potential production of methane, carbon dioxide, and nitrous oxide from the soils was determined under laboratory conditions. Direct microscopic counting, glucose-induced respiration (GIR), whole cell hybridisation, and extended phospholipid fatty acid (PLFA) analysis confirmed the presence of abundant microbial communities in the topsoil and also in the deepest Cg2 horizon of the AS soil. The patterns of microbial counts, biomass and activity in the profile of the AS soil and partly also in the non-AS soil therefore differed from the general tendency of gradual decreases in soil profiles. High respiration in the deepest Cg2 horizon of the AS soil (5.66 μg Cg(-1)h(-1), as compared to 2.71 μg Cg(-1)h(-1) in a top Ap horizon) is unusual but reasonable given the large amount of organic carbon in this horizon. Nitrous oxide production peaked in the BCgc horizon of the AS and in the BC horizon of the non-AS soil, but the peak value was ten-fold higher in the AS soil than in the non-AS soil (82.3 vs. 8.6 ng Ng(-1)d(-1)). The data suggest that boreal AS soils on the Baltic coast contain high microbial abundance and activity. This, together with the abundant carbon and total and mineral nitrogen in the deep layers of AS soils, may result in substantial gas production. Consequently, high GHG emissions could occur, for example, when the generally high water table is lowered because of arable farming.

  14. Genomic and Functional Analyses of the 2-Aminophenol Catabolic Pathway and Partial Conversion of Its Substrate into Picolinic Acid in Burkholderia xenovorans LB400

    PubMed Central

    Agulló, Loreine; González, Myriam; Seeger, Michael

    2013-01-01

    2-aminophenol (2-AP) is a toxic nitrogen-containing aromatic pollutant. Burkholderia xenovorans LB400 possess an amn gene cluster that encodes the 2-AP catabolic pathway. In this report, the functionality of the 2-aminophenol pathway of B. xenovorans strain LB400 was analyzed. The amnRJBACDFEHG cluster located at chromosome 1 encodes the enzymes for the degradation of 2-aminophenol. The absence of habA and habB genes in LB400 genome correlates with its no growth on nitrobenzene. RT-PCR analyses in strain LB400 showed the co-expression of amnJB, amnBAC, amnACD, amnDFE and amnEHG genes, suggesting that the amn cluster is an operon. RT-qPCR showed that the amnB gene expression was highly induced by 2-AP, whereas a basal constitutive expression was observed in glucose, indicating that these amn genes are regulated. We propose that the predicted MarR-type transcriptional regulator encoded by the amnR gene acts as repressor of the amn gene cluster using a MarR-type regulatory binding sequence. This report showed that LB400 resting cells degrade completely 2-AP. The amn gene cluster from strain LB400 is highly identical to the amn gene cluster from P. knackmussi strain B13, which could not grow on 2-AP. However, we demonstrate that B. xenovorans LB400 is able to grow using 2-AP as sole nitrogen source and glucose as sole carbon source. An amnBA− mutant of strain LB400 was unable to grow with 2-AP as nitrogen source and glucose as carbon source and to degrade 2-AP. This study showed that during LB400 growth on 2-AP this substrate was partially converted into picolinic acid (PA), a well-known antibiotic. The addition of PA at lag or mid-exponential phase inhibited LB400 growth. The MIC of PA for strain LB400 is 2 mM. Overall, these results demonstrate that B. xenovorans strain LB400 posses a functional 2-AP catabolic central pathway, which could lead to the production of picolinic acid. PMID:24124510

  15. Characterization of Non-Starter Lactic Acid Bacteria from Italian Ewe Cheeses Based on Phenotypic, Genotypic, and Cell Wall Protein Analyses

    PubMed Central

    De Angelis, M.; Corsetti, A.; Tosti, N.; Rossi, J.; Corbo, M. R.; Gobbetti, M.

    2001-01-01

    Non-starter lactic acid bacteria (NSLAB) were isolated from 12 Italian ewe cheeses representing six different types of cheese, which in several cases were produced by different manufacturers. A total of 400 presumptive Lactobacillus isolates were obtained, and 123 isolates and 10 type strains were subjected to phenotypic, genetic, and cell wall protein characterization analyses. Phenotypically, the cheese isolates included 32% Lactobacillus plantarum isolates, 15% L. brevis isolates, 12% L. paracasei subsp. paracasei isolates, 9% L. curvatus isolates, 6% L. fermentum isolates, 6% L. casei subsp. casei isolates, 5% L. pentosus isolates, 3% L. casei subsp. pseudoplantarum isolates, and 1% L. rhamnosus isolates. Eleven percent of the isolates were not phenotypically identified. Although a randomly amplified polymorphic DNA (RAPD) analysis based on three primers and clustering by the unweighted pair group method with arithmetic average (UPGMA) was useful for partially differentiating the 10 type strains, it did not provide a species-specific DNA band or a combination of bands which permitted complete separation of all the species considered. In contrast, sodium dodecyl sulfate-polyacrylamide gel electrophoresis cell wall protein profiles clustered by UPGMA were species specific and resolved the NSLAB. The only exceptions were isolates phenotypically identified as L. plantarum and L. pentosus or as L. casei subsp. casei and L. paracasei subsp. paracasei, which were grouped together. Based on protein profiles, Italian ewe cheeses frequently contained four different species and 3 to 16 strains. In general, the cheeses produced from raw ewe milk contained a larger number of more diverse strains than the cheeses produced from pasteurized milk. The same cheese produced in different factories contained different species, as well as strains that belonged to the same species but grouped in different RAPD clusters. PMID:11319075

  16. Functional analyses of human and zebrafish 18-amino acid in-frame deletion pave the way for domain mapping of the cerebral cavernous malformation 3 protein.

    PubMed

    Voss, Katrin; Stahl, Sonja; Hogan, Benjamin M; Reinders, Joerg; Schleider, Elisa; Schulte-Merker, Stefan; Felbor, Ute

    2009-06-01

    Cerebral cavernous malformations (CCMs) may cause recurrent headaches, seizures, and hemorrhagic stroke and have been associated with loss-of-function mutations in CCM1/KRIT1, CCM2, and CCM3/programmed cell death 10 (PDCD10). The CCM3/PDCD10 amino acid sequence does not reveal significant homologies to protein domains with known structure. With the help of the only published human in-frame deletion of the CCM3 gene (c.97-?_150+?del), CCM3:p.L33_K50del, we have identified the interaction domain of CCM3 with the oxidant stress response serine/threonine kinase 25 (STK25, YSK1, SOK1) and with the mammalian Ste20-like kinase 4 (MST4, MASK). Consistently, nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) analyses revealed two STK25 phosphorylation sites at serine 39 and threonine 43. The corresponding in-frame deletion of zebrafish ccm3a, dccm3:p.L31_K48del, also resulted in impaired interaction with STK25 and MST4. In agreement with the observed redundant biochemical functionality of zebrafish ccm3a and its duplicate ccm3b, simultaneous inactivation of both genes resulted in a progressive cardiovascular phenotype in zebrafish indistinguishable from ccm1 and ccm2 mutants. The pronounced cardiovascular dilatations could be recapitulated by morpholino-induced in-frame skipping of the exon encoding the STK25 and MST4 binding site of zebrafish Ccm3a if Ccm3b was repressed in parallel. Using a novel zebrafish model of CCM, we could thus demonstrate that the newly mapped STK25 and MST4 interaction domain within the CCM3 protein plays a crucial role for vascular development in zebrafish.

  17. Characterization of fulvic acid fractions of dissolved organic matter during ice-out in a hyper-eutrophic, coastal pond in Antarctica

    NASA Astrophysics Data System (ADS)

    Cawley, Kaelin M.; McKnight, Diane M.; Miller, Penney; Cory, Rose; Fimmen, Ryan L.; Guerard, Jennifer; Dieser, Markus; Jaros, Christopher; Chin, Yu-Ping; Foreman, Christine

    2013-12-01

    Dissolved humic material (HDOM) is ubiquitous to all natural waters and its source material influences its chemical structure, reactivity, and bioavailability. While terrestrially derived HDOM reference materials distributed by the International Humic Substances Society (IHSS) have been readily available to engineering and scientific communities, a microbially derived reference HDOM was not, despite the well-characterized differences in the chemistry and reactivity of HDOM derived from terrestrial versus microbial sources. To address this gap, we collected a microbial reference fulvic acid from Pony Lake (PLFA) for distribution through the IHSS. Pony Lake is a saline coastal pond on Ross Island, Antarctica, where the landscape is devoid of terrestrial plants. Sample collection occurred over a 17-day period in the summer season at Pony Lake. During this time, the dissolved organic carbon (DOC) concentrations increased nearly two-fold, and the fulvic acid fraction (collected using the XAD-8 method) accounted for 14.6% of the DOC. During the re-concentration and desalting procedures we isolated two other chemically distinct fulvic acid fractions: (1) PLFA-2, which was high in carbohydrates and (2) PLFA-CER, which was high in nitrogen. The chemical characteristics (elemental analysis, optical characterization with UV-vis and fluorescence spectroscopy, and 13C NMR spectroscopy) of the three fulvic acid fractions helped to explain their behavior during isolation.

  18. delta 13C analyses of vegetable oil fatty acid components, determined by gas chromatography--combustion--isotope ratio mass spectrometry, after saponification or regiospecific hydrolysis.

    PubMed

    Woodbury, S E; Evershed, R P; Rossell, J B

    1998-05-01

    The delta 13C values of the major fatty acids of several different commercially important vegetable oils were measured by gas chromatography--combustion--isotope ratio mass spectrometry. The delta 13C values obtained were found to fall into two distinct groups, representing the C3 and C4 plants classes from which the oils were derived. The delta 13C values of the oils were measured by continuous flow elemental isotope ratio mass spectrometry and were found to be similar to their fatty acids, with slight differences between individual fatty acids. Investigations were then made into the influence on the delta 13C values of fatty acids of the position occupied on the glycerol backbone. Pancreatic lipase was employed to selectively hydrolyse fatty acids from the 1- and 3-positions with the progress of the reaction being followed by high-temperature gas chromatography in order to determine the optimum incubation time. The 2-monoacylglycerols were then isolated by thin-layer chromatography and fatty acid methyl esters prepared. The delta 13C values obtained indicate that fatty acids from any position on the glycerol backbone are isotopically identical. Thus, whilst quantification of fatty acid composition at the 2-position and measurement of delta 13C values of oils and their major fatty acids are useful criteria in edible oil purity assessment, measurement of delta 13C values of fatty acids from the 2-position does not assist with oil purity assignments.

  19. Does acute lead (Pb) contamination influence membrane fatty acid composition and freeze tolerance in intertidal blue mussels in arctic Greenland?

    PubMed

    Thyrring, Jakob; Juhl, Bodil Klein; Holmstrup, Martin; Blicher, Martin E; Sejr, Mikael K

    2015-11-01

    In their natural habitats, organisms are exposed to multiple stressors. Heavy metal contamination stresses the cell membrane due to increased peroxidation of lipids. Likewise, sub-zero air temperatures potentially reduce membrane functionality in ectothermal animals. We tested if acute lead (Pb) exposure for 7 days would influence survival in intertidal blue mussels (Mytilus edulis) after exposure to realistic sub-zero air temperatures. A full factorial experiment with five tissue Pb concentrations between 0 and 3500 μg Pb/g and six sub-zero temperatures from 0 to -17 °C were used to test the hypothesis that sub-lethal effects of Pb may increase the lethality caused by freezing in blue mussels exposed to temperatures simulating Greenland winter conditions. We found a significant effect of temperature on mortality. However, the short-term exposure to Pb did not result in any effects of Pb, nor did we find interactions between Pb and temperature. We analysed the relative abundance of major phospholipid fatty acids (PLFAs) in the gill tissue, but we found no significant effect of Pb tissue concentration on PLFA composition. Results suggest that Pb accumulation has limited effects on freeze tolerance and does not induce membrane damage in terms of persistent lipid peroxidation.

  20. Sociopolitical Analyses.

    ERIC Educational Resources Information Center

    Van Galen, Jane, Ed.; And Others

    1992-01-01

    This theme issue of the serial "Educational Foundations" contains four articles devoted to the topic of "Sociopolitical Analyses." In "An Interview with Peter L. McLaren," Mary Leach presented the views of Peter L. McLaren on topics of local and national discourses, values, and the politics of difference. Landon E.…

  1. In silico analyses of structural and allergenicity features of sapodilla (Manilkara zapota) acidic thaumatin-like protein in comparison with allergenic plant TLPs.

    PubMed

    Ashok Kumar, Hassan G; Venkatesh, Yeldur P

    2014-02-01

    Thaumatin-like proteins (TLPs) belong to the pathogenesis-related family (PR-5) of plant defense proteins. TLPs from only 32 plant genera have been identified as pollen or food allergens. IgE epitopes on allergens play a central role in food allergy by initiating cross-linking of specific IgE on basophils/mast cells. A comparative analysis of pollen- and food-allergenic TLPs is lacking. The main objective of this investigation was to study the structural and allergenicity features of sapodilla (Manilkara zapota) acidic TLP (TLP 1) by in silico methods. The allergenicity prediction of composite sequence of sapodilla TLP 1 (NCBI B3EWX8.1, G5DC91.1) was performed using FARRP, Allermatch and Evaller web tools. A homology model of the protein was generated using banana TLP template (1Z3Q) by HHPRED-MODELLER. B-cell linear epitope prediction was performed using BCpreds and BepiPred. Sapodilla TLP 1 matched significantly with allergenic TLPs from olive, kiwi, bell pepper and banana. IgE epitope prediction as performed using AlgPred indicated the presence of 2 epitopes (epitope 1: residues 36-48; epitope 2: residues 51-63), and a comprehensive analysis of all allergenic TLPs displayed up to 3 additional epitopes on other TLPs. It can be inferred from these analyses that plant allergenic TLPs generally carry 2-3 IgE epitopes. ClustalX alignments of allergenic TLPs indicate that IgE epitopes 1 and 2 are common in food allergenic TLPs, and IgE epitopes 2 and 3 are common in pollen allergenic TLPs; IgE epitope 2 overlaps with a portion of the thaumatin family signature. The secondary structural elements of TLPs vary markedly in regions 1 and 2 which harbor all the predicted IgE epitopes in all food and pollen TLPs in either of the region. Further, based on the number of IgE epitopes, food TLPs are grouped into rosid and non-rosid clades. The number and distribution of the predicted IgE epitopes among the allergenic TLPs may explain the specificity of food or pollen allergy as

  2. Phospholipid fatty acid biomarkers in a freshwater periphyton community exposed to uranium: discovery by non-linear statistical learning

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Bunn, Amoret L.; Bailey, Vanessa L.

    2011-01-01

    Phospholipid fatty acids (PLFA) have been widely used to characterize environmental microbial communities, generating community profiles that can distinguish phylogenetic or functional groups within the community. The poor specificity of organism groups with fatty acid biomarkers in the classic PLFA-microorganism associations is a confounding factor in many of the statistical classification/clustering approaches traditionally used to interpret PLFA profiles. In this paper we demonstrate that non-linear statistical learning methods, such as a support vector machine (SVM), can more accurately find patterns related to uranyl nitrate exposure in a freshwater periphyton community than linear methods, such as partial least squares discriminant analysis. In addition, probabilistic models of exposure can be derived from the identified lipid biomarkers to demonstrate the potential model-based approach that could be used in remediation. The SVM probability model separates dose groups at accuracies of ~87.0%, ~71.4%, ~87.5%, and 100% for the four groups; Control (non-amended system), low-dose (amended at 10 µg U L-1), medium dose (amended at 100 µg U L-1), and high dose (500 µg U L-1). The SVM model achieved an overall cross-validated classification accuracy of ~87% in contrast to ~59% for the best linear classifier.

  3. [A comprehensive signature biomarker analysis of the in-situ viable biomass, community composition, and nutritional status attributes of deep subsurface microbiota]. Final report

    SciTech Connect

    1998-09-01

    The TAN sites contains subsurface sediment contaminated with trichloroethylene (TC). A suite of microbiological analyses, including ester-linked phospholipid fatty acid (PLFA) analysis, were performed to ascertain the microbial ecology associated with TCE degradation processes. The objective of the PLFA analyses were: (1) to determine the distribution of viable microbes throughout a vertical depth profile through the TCE plume, (2) determine the community composition of the viable extant microbiota and (3) relate the data derived from the PLFA analyses to other measures of the in situ microbiota as well as to the presence of TCE degradative products.

  4. Component analyses of urinary nanocrystallites of uric acid stone formers by combination of high-resolution transmission electron microscopy, fast Fourier transformation, energy dispersive X-ray spectroscopy, X-ray diffraction and Fourier transform infrared spectroscopy.

    PubMed

    Sun, Xin-Yuan; Xue, Jun-Fa; Xia, Zhi-Yue; Ouyang, Jian-Ming

    2015-06-01

    This study aimed to analyse the components of nanocrystallites in urines of patients with uric acid (UA) stones. X-ray diffraction (XRD), Fourier transform infrared spectroscopy, high-resolution transmission electron microscopy (HRTEM), fast Fourier transformation (FFT) of HRTEM, and energy dispersive X-ray spectroscopy (EDS) were performed to analyse the components of these nanocrystallites. XRD and FFT showed that the main component of urinary nanocrystallites was UA, which contains a small amount of calcium oxalate monohydrate and phosphates. EDS showed the characteristic absorption peaks of C, O, Ca and P. The formation of UA stones was closely related to a large number of UA nanocrystallites in urine. A combination of HRTEM, FFT, EDS and XRD analyses could be performed accurately to analyse the components of urinary nanocrystallites.

  5. Postnatal changes in fatty acids composition of brown adipose tissue

    NASA Astrophysics Data System (ADS)

    Ohno, T.; Ogawa, K.; Kuroshima, A.

    1992-03-01

    It has been demonstrated that thermogenic activity of brown adipose tissue (BAT) is higher during the early postnatal period, decreasing towards a low adult level. The present study examined postnatal changes in the lipid composition of BAT. BAT from pre-weaning rats at 4 and 14 days old showed the following differences in lipid composition compared to that from adults of 12 weeks old. (i) Relative weight of interscapular BAT to body weight was markedly greater. (ii) BAT-triglyceride (TG) level was lower, while BAT-phospholipid (PL)level was higher. (iii) In TG fatty acids (FA) polyunsaturated fatty acids (PU; mol %), arachidonate index (AI), unsaturation index (UI) and PU/saturated FA (SA) were higher; rare FA such as eicosadienoate, bishomo- γ-linolenic acid and lignoceric acid in mol % were also higher. (iv) In PL-FA monounsaturated FA (MU) in mol % was lower; PU mol %, AI and UI were higher. These features in BAT of pre-weaning rats resembled those in the cold-acclimated adults, suggesting a close relationship of the PL-FA profile to high activity of BAT.

  6. Thermal And Spectroscopic Analyses Of Next Generation Caustic Side Solvent Extraction Solvent Contacted With 3, 8, And 16 Molar Nitric Acid

    SciTech Connect

    Fondeur, F. F.; Fink, S. D.

    2011-12-07

    A new solvent system referred to as Next Generation Solvent or NGS, has been developed at Oak Ridge National Laboratory for the removal of cesium from alkaline solutions in the Caustic Side Solvent Extraction process. The NGS is proposed for deployment at MCU{sup a} and at the Salt Waste Processing Facility. This work investigated the chemical compatibility between NGS and 16 M, 8 M, and 3 M nitric acid from contact that may occur in handling of analytical samples from MCU or, for 3 M acid, which may occur during contactor cleaning operations at MCU. This work shows that reactions occurred between NGS components and the high molarity nitric acid. Reaction rates are much faster in 8 M and 16 M nitric acid than in 3 M nitric acid. In the case of 16 M and 8 M nitric acid, the nitric acid reacts with the extractant to produce initially organo-nitrate species. The reaction also releases soluble fluorinated alcohols such as tetrafluoropropanol. With longer contact time, the modifier reacts to produce a tarry substance with evolved gases (NO{sub x} and possibly CO). Calorimetric analysis of the reaction product mixtures revealed that the organo-nitrates reaction products are not explosive and will not deflagrate.

  7. THERMAL AND SPECTROSCOPIC ANALYSES OF NEXT GENERATION CAUSTIC SIDE SOLVENT EXTRACTION SOLVENT CONTACTED WITH 3, 8, AND 16 MOLAR NITRIC ACID

    SciTech Connect

    Fondeur, F.; Fink, S.

    2011-09-30

    A new solvent system referred to as Next Generation Solvent or NGS, has been developed at Oak Ridge National Laboratory for the removal of cesium from alkaline solutions in the Caustic Side Solvent Extraction process. NGS is proposed for deployment at MCU and at the Salt Waste Processing Facility. This work investigated the chemical compatibility between NGS and 16 M, 8 M, and 3 M nitric acid from contact that may occur in handling of analytical samples from MCU or, for 3 M acid, which may occur during contactor cleaning operations at MCU. This work shows that reactions occurred between NGS components and the high molarity nitric acid. In the case of 16 M and 8 M nitric acid, initially organo-nitrate groups are generated and attach to the modifier and that with time oxidation reactions convert the modifier into a tarry substance with gases (NO{sub x} and possibly CO) evolving. Calorimetric analysis of the organonitrate revealed the reaction products are not explosive nor will they deflagrate. NGS exposure to 3 M nitric acid resulted in much slower reaction kinetics and that the generated products were not energetic. We recommended conducting Accelerated Rate calorimetry on the materials generated in the 16 M and 8 M nitric acid test. Also, we recommend continue monitoring of the samples contacting NGS with 3 M nitric acid.

  8. Clues on Acid-Sulfate Alteration and Hematite Formation on Earth and Mars From Iron Isotopic Analyses of Terrestrial Analogues From Hawaii

    NASA Technical Reports Server (NTRS)

    Nie, N. X.; Dauphas, N.; Morris, R. V

    2017-01-01

    The Mars Exploration Rover mission revealed the presence of rocks and minerals indicative of water-rock interactions on Mars. A range of mineralogies have been identified, including hematite spherules (i.e., blueberries), jarosite, Mg-, Ca-sulfates, silica-rich materials and silicate relics from basaltic rocks. The mineral assemblages have been interpreted to be derived from acid-sulfate alteration of basaltic materials. Indeed, the chemical compositions of rocks and soils at Home Plate in Gusev Crater follow the trends expected for acid-sulfate alteration.

  9. The effects of an oral preparation containing hyaluronic acid (Oralvisc®) on obese knee osteoarthritis patients determined by pain, function, bradykinin, leptin, inflammatory cytokines, and heavy water analyses.

    PubMed

    Nelson, F R; Zvirbulis, R A; Zonca, B; Li, K W; Turner, S M; Pasierb, M; Wilton, P; Martinez-Puig, D; Wu, W

    2015-01-01

    The purpose of this study was to determine the effects of an oral preparation containing hyaluronic acid on osteoarthritic knee joint pain and function as well as changes in inflammatory cytokines, bradykinin, and leptin. We also used heavy water to determine the turnover rates of glycosaminoglycans in synovial fluid. This was a double-blind, randomized, placebo-controlled study of 40 subjects over a period of 3 months. Visual analog scale, Western Ontario McMaster pain, and WOMAC function scores were recorded. Serum and synovial fluid were measured by enzyme-linked immunosorbent assays for inflammatory cytokines, bradykinin, and leptin. In 20 subjects, terminal heavy water ingestion was used for spectral analyses of serum and joint fluid samples. There were statistically significant improvements in pain and function. Both serum and synovial fluid samples showed significant decreases for a majority of inflammatory cytokines, leptin, and bradykinin in the oral hyaluronic acid preparation group. Heavy water analyses revealed a significant decrease in hyaluronic acid turnover in the synovial fluid of the treatment group. A preparation containing hyaluronic acid and other glycosaminoglycans holds promise for a safe and effective agent for the treatment for patients with knee osteoarthritis and who are overweight. Further studies will be required to see whether this is a disease-modifying agent.

  10. Investigating population structure of Sea Lamprey (Petromyzon marinus, L.) in Western Iberian Peninsula using morphological characters and heart fatty acid signature analyses.

    PubMed

    Lança, Maria João; Machado, Maria; Mateus, Catarina S; Lourenço, Marta; Ferreira, Ana F; Quintella, Bernardo R; Almeida, Pedro R

    2014-01-01

    This study hypothesizes the existence of three groups of sea lamprey Petromyzon marinus L. in Portugal (North/Central group, Tagus group, and Guadiana group), possibly promoted by seabed topography isolation during the oceanic phase of the life cycle. Within this context, our purpose was to analyze the existence of a stock structure on sea lamprey populations sampled in the major Portuguese river basins using both morphological characters and heart tissue fatty acid signature. In both cases, the multiple discriminant analysis revealed statistically significant differences among groups, and the overall corrected classification rate estimated from cross-validation procedure was particularly high for the cardiac muscle fatty acid profiles (i.e. 83.8%). Morphometric characters were much more useful than meristic ones to discriminate stocks, and the most important variables for group differentiation were eye length, second dorsal fin length and branchial length. Fatty acid analysis showed that all lampreys from the southern Guadiana group were correctly classified and not mixing with individuals from any other group, reflecting a typical heart fatty acid signature. Our results revealed that 89.5% and 72.2% of the individuals from the Tagus and North/Central groups, respectively, were also correctly classified, despite some degree of overlap between individuals from these groups. The fatty acids that contributed to the observed segregation were C16:0; C17:0; C18:1ω9; C20:3ω6 and C22:2ω6. Detected differences are probably related with environmental variables to which lampreys may have been exposed, which leaded to different patterns of gene expression. These results suggest the existence of three different sea lamprey stocks in Portugal, with implication in terms of management and conservation.

  11. Evaluation of Drosophila metabolic labeling strategies for in vivo quantitative proteomic analyses with applications to early pupa formation and amino acid starvation.

    PubMed

    Chang, Ying-Che; Tang, Hong-Wen; Liang, Suh-Yuen; Pu, Tsung-Hsien; Meng, Tzu-Ching; Khoo, Kay-Hooi; Chen, Guang-Chao

    2013-05-03

    Although stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics was first developed as a cell culture-based technique, stable isotope-labeled amino acids have since been successfully introduced in vivo into select multicellular model organisms by manipulating the feeding diets. An earlier study by others has demonstrated that heavy lysine labeled Drosophila melanogaster can be derived by feeding with an exclusive heavy lysine labeled yeast diet. In this work, we have further evaluated the use of heavy lysine and/or arginine for metabolic labeling of fruit flies, with an aim to determine its respective quantification accuracy and versatility. In vivo conversion of heavy lysine and/or heavy arginine to several nonessential amino acids was observed in labeled flies, leading to distorted isotope pattern and underestimated heavy to light ratio. These quantification defects can nonetheless be rectified at protein level using the normalization function. The only caveat is that such a normalization strategy may not be suitable for every biological application, particularly when modified peptides need to be individually quantified at peptide level. In such cases, we showed that peptide ratios calculated from the summed intensities of all isotope peaks are less affected by the heavy amino acid conversion and therefore less sequence-dependent and more reliable. Applying either the single Lys8 or double Lys6/Arg10 metabolic labeling strategy to flies, we quantitatively mapped the proteomic changes during the onset of metamorphosis and upon amino acid deprivation. The expression of a number of steroid hormone 20-hydroxyecdysone regulated proteins was found to be changed significantly during larval-pupa transition, while several subunits of the V-ATPase complex and components regulating actomyosin were up-regulated under starvation-induced autophagy conditions.

  12. Investigating Population Structure of Sea Lamprey (Petromyzon marinus, L.) in Western Iberian Peninsula Using Morphological Characters and Heart Fatty Acid Signature Analyses

    PubMed Central

    Lança, Maria João; Machado, Maria; Mateus, Catarina S.; Lourenço, Marta; Ferreira, Ana F.; Quintella, Bernardo R.; Almeida, Pedro R.

    2014-01-01

    This study hypothesizes the existence of three groups of sea lamprey Petromyzon marinus L. in Portugal (North/Central group, Tagus group, and Guadiana group), possibly promoted by seabed topography isolation during the oceanic phase of the life cycle. Within this context, our purpose was to analyze the existence of a stock structure on sea lamprey populations sampled in the major Portuguese river basins using both morphological characters and heart tissue fatty acid signature. In both cases, the multiple discriminant analysis revealed statistically significant differences among groups, and the overall corrected classification rate estimated from cross-validation procedure was particularly high for the cardiac muscle fatty acid profiles (i.e. 83.8%). Morphometric characters were much more useful than meristic ones to discriminate stocks, and the most important variables for group differentiation were eye length, second dorsal fin length and branchial length. Fatty acid analysis showed that all lampreys from the southern Guadiana group were correctly classified and not mixing with individuals from any other group, reflecting a typical heart fatty acid signature. Our results revealed that 89.5% and 72.2% of the individuals from the Tagus and North/Central groups, respectively, were also correctly classified, despite some degree of overlap between individuals from these groups. The fatty acids that contributed to the observed segregation were C16:0; C17:0; C18:1ω9; C20:3ω6 and C22:2ω6. Detected differences are probably related with environmental variables to which lampreys may have been exposed, which leaded to different patterns of gene expression. These results suggest the existence of three different sea lamprey stocks in Portugal, with implication in terms of management and conservation. PMID:25259723

  13. A certified urea reference material (NMIJ CRM 6006-a) as a reliable calibrant for the elemental analyses of amino acids and food samples.

    PubMed

    Itoh, Nobuyasu; Yamazaki, Taichi; Sato, Ayako; Numata, Masahiko; Takatsu, Akiko

    2014-01-01

    We examined the reliability of a certified reference material (CRM) for urea (NMIJ CRM 6006-a) as a calibrant for N, C, and H in elemental analyzers. Only the N content for this CRM is provided as an indicative value. To estimate the C and H contents of the urea CRM, we took into account the purity of the urea and the presence of other identified impurities. When we examined the use of various masses of the calibrant (0.2 to 2 mg), we unexpectedly observed low signal intensities for small masses of H and N, but these plateaued at about 2 mg. We therefore analyzed four amino acid CRMs and four food CRMs on a 2-mg scale with the urea CRM as the calibrant. For the amino acid CRMs, the differences in the analytical and theoretical contents (≤0.0026 kg/kg) were acceptable with good repeatability (≤0.0013 kg/kg in standard deviation; n = 4). For food CRMs, comparable repeatabilities to those obtained with amino acid CRMs (≤0.0025 kg/kg in standard deviation; n = 4) were obtained. The urea CRM can therefore be used as a reliable calibrant for C, H, and N in an elemental analyzer.

  14. Quantitative ‘Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids

    PubMed Central

    Fu, Jilagamazhi; Sharma, Parveen; Spicer, Vic; Krokhin, Oleg V.; Zhang, Xiangli; Fristensky, Brian; Cicek, Nazim; Sparling, Richard; Levin, David. B.

    2015-01-01

    Transcriptomes and proteomes of Pseudomonas putida LS46 cultured with biodiesel-derived waste glycerol or waste free fatty acids, as sole carbon sources, were compared under conditions that were either permissive or non-permissive for synthesis of medium chain length polyhydroxyalkanoates (mcl-PHA). The objectives of this study were to elucidate mechanisms that influence activation of biopolymer synthesis, intra-cellular accumulation, and monomer composition, and determine if these were physiologically specific to the carbon sources used for growth of P. putida LS46. Active mcl-PHA synthesis by P. putida LS46 was associated with high expression levels of key mcl-PHA biosynthesis genes and/or gene products including monomer-supplying proteins, PHA synthases, and granule-associated proteins. ‘Omics data suggested that expression of these genes were regulated by different genetic mechanisms in P. putida LS46 cells in different physiological states, when cultured on the two waste carbon sources. Optimal polymer production by P. putida LS46 was primarily limited by less efficient glycerol metabolism during mcl-PHA synthesis on waste glycerol. Mapping the ‘Omics data to the mcl-PHA biosynthetic pathway revealed significant variations in gene expression, primarily involved in: 1) glycerol transportation; 2) enzymatic reactions that recycle reducing equivalents and produce key mcl-PHA biosynthesis pathway intermediates (e.g. NADH/NADPH, acetyl-CoA). Active synthesis of mcl-PHAs was observed during exponential phase in cultures with waste free fatty acids, and was associated with the fatty acid beta-oxidation pathway. A putative Thioesterase in the beta-oxidation pathway that may regulate the level of fatty acid beta-oxidation intermediates, and thus carbon flux to mcl-PHA biosynthesis, was highly up-regulated. Finally, the data suggested that differences in expression of selected fatty acid metabolism and mcl-PHA monomer-supplying enzymes may play a role in determining

  15. Quantitative 'Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids.

    PubMed

    Fu, Jilagamazhi; Sharma, Parveen; Spicer, Vic; Krokhin, Oleg V; Zhang, Xiangli; Fristensky, Brian; Cicek, Nazim; Sparling, Richard; Levin, David B

    2015-01-01

    Transcriptomes and proteomes of Pseudomonas putida LS46 cultured with biodiesel-derived waste glycerol or waste free fatty acids, as sole carbon sources, were compared under conditions that were either permissive or non-permissive for synthesis of medium chain length polyhydroxyalkanoates (mcl-PHA). The objectives of this study were to elucidate mechanisms that influence activation of biopolymer synthesis, intra-cellular accumulation, and monomer composition, and determine if these were physiologically specific to the carbon sources used for growth of P. putida LS46. Active mcl-PHA synthesis by P. putida LS46 was associated with high expression levels of key mcl-PHA biosynthesis genes and/or gene products including monomer-supplying proteins, PHA synthases, and granule-associated proteins. 'Omics data suggested that expression of these genes were regulated by different genetic mechanisms in P. putida LS46 cells in different physiological states, when cultured on the two waste carbon sources. Optimal polymer production by P. putida LS46 was primarily limited by less efficient glycerol metabolism during mcl-PHA synthesis on waste glycerol. Mapping the 'Omics data to the mcl-PHA biosynthetic pathway revealed significant variations in gene expression, primarily involved in: 1) glycerol transportation; 2) enzymatic reactions that recycle reducing equivalents and produce key mcl-PHA biosynthesis pathway intermediates (e.g. NADH/NADPH, acetyl-CoA). Active synthesis of mcl-PHAs was observed during exponential phase in cultures with waste free fatty acids, and was associated with the fatty acid beta-oxidation pathway. A putative Thioesterase in the beta-oxidation pathway that may regulate the level of fatty acid beta-oxidation intermediates, and thus carbon flux to mcl-PHA biosynthesis, was highly up-regulated. Finally, the data suggested that differences in expression of selected fatty acid metabolism and mcl-PHA monomer-supplying enzymes may play a role in determining the

  16. 2H NMR and 13C-IRMS analyses of acetic acid from vinegar, 18O-IRMS analysis of water in vinegar: international collaborative study report.

    PubMed

    Thomas, Freddy; Jamin, Eric

    2009-09-01

    An international collaborative study of isotopic methods applied to control the authenticity of vinegar was organized in order to support the recognition of these procedures as official methods. The determination of the 2H/1H ratio of the methyl site of acetic acid by SNIF-NMR (site-specific natural isotopic fractionation-nuclear magnetic resonance) and the determination of the 13C/12C ratio, by IRMS (isotope ratio mass spectrometry) provide complementary information to characterize the botanical origin of acetic acid and to detect adulterations of vinegar using synthetic acetic acid. Both methods use the same initial steps to recover pure acetic acid from vinegar. In the case of wine vinegar, the determination of the 18O/16O ratio of water by IRMS allows to differentiate wine vinegar from vinegars made from dried grapes. The same set of vinegar samples was used to validate these three determinations. The precision parameters of the method for measuring delta13C (carbon isotopic deviation) were found to be similar to the values previously obtained for similar methods applied to wine ethanol or sugars extracted from fruit juices: the average repeatability (r) was 0.45 per thousand, and the average reproducibility (R) was 0.91 per thousand. As expected from previous in-house study of the uncertainties, the precision parameters of the method for measuring the 2H/1H ratio of the methyl site were found to be slightly higher than the values previously obtained for similar methods applied to wine ethanol or fermentation ethanol in fruit juices: the average repeatability was 1.34 ppm, and the average reproducibility was 1.62 ppm. This precision is still significantly smaller than the differences between various acetic acid sources (delta13C and delta18O) and allows a satisfactory discrimination of vinegar types. The precision parameters of the method for measuring delta18O were found to be similar to the values previously obtained for other methods applied to wine and

  17. Higher PUFA and n-3 PUFA, conjugated linoleic acid, α-tocopherol and iron, but lower iodine and selenium concentrations in organic milk: a systematic literature review and meta- and redundancy analyses.

    PubMed

    Średnicka-Tober, Dominika; Barański, Marcin; Seal, Chris J; Sanderson, Roy; Benbrook, Charles; Steinshamn, Håvard; Gromadzka-Ostrowska, Joanna; Rembiałkowska, Ewa; Skwarło-Sońta, Krystyna; Eyre, Mick; Cozzi, Giulio; Larsen, Mette Krogh; Jordon, Teresa; Niggli, Urs; Sakowski, Tomasz; Calder, Philip C; Burdge, Graham C; Sotiraki, Smaragda; Stefanakis, Alexandros; Stergiadis, Sokratis; Yolcu, Halil; Chatzidimitriou, Eleni; Butler, Gillian; Stewart, Gavin; Leifert, Carlo

    2016-03-28

    Demand for organic milk is partially driven by consumer perceptions that it is more nutritious. However, there is still considerable uncertainty over whether the use of organic production standards affects milk quality. Here we report results of meta-analyses based on 170 published studies comparing the nutrient content of organic and conventional bovine milk. There were no significant differences in total SFA and MUFA concentrations between organic and conventional milk. However, concentrations of total PUFA and n-3 PUFA were significantly higher in organic milk, by an estimated 7 (95 % CI -1, 15) % and 56 (95 % CI 38, 74) %, respectively. Concentrations of α-linolenic acid (ALA), very long-chain n-3 fatty acids (EPA+DPA+DHA) and conjugated linoleic acid were also significantly higher in organic milk, by an 69 (95 % CI 53, 84) %, 57 (95 % CI 27, 87) % and 41 (95 % CI 14, 68) %, respectively. As there were no significant differences in total n-6 PUFA and linoleic acid (LA) concentrations, the n-6:n-3 and LA:ALA ratios were lower in organic milk, by an estimated 71 (95 % CI -122, -20) % and 93 (95 % CI -116, -70) %. It is concluded that organic bovine milk has a more desirable fatty acid composition than conventional milk. Meta-analyses also showed that organic milk has significantly higher α-tocopherol and Fe, but lower I and Se concentrations. Redundancy analysis of data from a large cross-European milk quality survey indicates that the higher grazing/conserved forage intakes in organic systems were the main reason for milk composition differences.

  18. Assessing the Accuracy and Precision of Inorganic Geochemical Data Produced through Flux Fusion and Acid Digestions: Multiple (60+) Comprehensive Analyses of BHVO-2 and the Development of Improved "Accepted" Values

    NASA Astrophysics Data System (ADS)

    Ireland, T. J.; Scudder, R.; Dunlea, A. G.; Anderson, C. H.; Murray, R. W.

    2014-12-01

    The use of geological standard reference materials (SRMs) to assess both the accuracy and the reproducibility of geochemical data is a vital consideration in determining the major and trace element abundances of geologic, oceanographic, and environmental samples. Calibration curves commonly are generated that are predicated on accurate analyses of these SRMs. As a means to verify the robustness of these calibration curves, a SRM can also be run as an unknown item (i.e., not included as a data point in the calibration). The experimentally derived composition of the SRM can thus be compared to the certified (or otherwise accepted) value. This comparison gives a direct measure of the accuracy of the method used. Similarly, if the same SRM is analyzed as an unknown over multiple analytical sessions, the external reproducibility of the method can be evaluated. Two common bulk digestion methods used in geochemical analysis are flux fusion and acid digestion. The flux fusion technique is excellent at ensuring complete digestion of a variety of sample types, is quick, and does not involve much use of hazardous acids. However, this technique is hampered by a high amount of total dissolved solids and may be accompanied by an increased analytical blank for certain trace elements. On the other hand, acid digestion (using a cocktail of concentrated nitric, hydrochloric and hydrofluoric acids) provides an exceptionally clean digestion with very low analytical blanks. However, this technique results in a loss of Si from the system and may compromise results for a few other elements (e.g., Ge). Our lab uses flux fusion for the determination of major elements and a few key trace elements by ICP-ES, while acid digestion is used for Ti and trace element analyses by ICP-MS. Here we present major and trace element data for BHVO-2, a frequently used SRM derived from a Hawaiian basalt, gathered over a period of over two years (30+ analyses by each technique). We show that both digestion

  19. Two step derivatization for the analyses of organic, amino acids and glycines on filter paper plasma by GC-MS/SIM.

    PubMed

    Yoon, Hye-Ran

    2007-03-01

    A rapid dried-filter paper plasma-spot analytical method was developed to quantify organic acids, amino acids, and glycines simultaneously in a two-step derivatization procedure with good sensitivity and specificity. The new method involves a two-step trimethylsilyl (TMS) - trifluoroacyl (TFA) derivatization procedure using GC-MS/ selective ion monitoring (GC-MS/SIM). The dried-filter paper plasma was fortified with an internal standard (tropate) as well as a standard mixture of distilled water and methanol. Methyl orange was added to the residue as an indicator. N-methyl-N-(trimethylsilyl-trifluoroacetamide) and N-methyl-bis-trifluoroacetamide were then added and heated to 60 degrees C for 10 and 15 min to produce the TMS and TFA derivatives, respectively. Using this method, the silylation of carboxylic functional groups was carried out, which was followed by the trifluoroacyl derivatization of the amino functional group. The derivatives were analyzed by GC-MS/SIM. A calibration cure showed a linear relationship for the target compounds between concentrations of 10-500 ng/mL. The limit of detection and quantification on a plasma spot were 10-90 ng/mL (S/N=9) and 80-500 ng/ mL, respectively. The correlation coefficient ranged from 0.938 and 0.999. When applied to the samples from positive patients, the method clearly differentiated normal subjects from the patients with various metabolic disorders such as PKU, MSUD, OTC and a Propionic Aciduria. The new developed method might be useful for making a rapid, sensitive and simultaneous diagnosis of inherited organic and amino acid disorders. In addition, this method is expected to be an alternative method for screening newborns for metabolic disorders in laboratories where expensive MS/MS is unavailable.

  20. Reproductive and feeding spatial dynamics of the black scabbardfish, Aphanopus carbo Lowe, 1839, in NE Atlantic inferred from fatty acid and stable isotope analyses

    NASA Astrophysics Data System (ADS)

    Farias, Inês; Figueiredo, Ivone; Janeiro, Ana Isabel; Bandarra, Narcisa Maria; Batista, Irineu; Morales-Nin, Beatriz

    2014-07-01

    The black scabbardfish (Aphanopus carbo) is a benthopelagic species widely distributed across the NE Atlantic, where it is admitted to perform a clockwise migration throughout its life cycle stimulated by feeding and reproduction. To overcome the limitations of direct observation of this species, fatty acids profile (FA) and δ15N and δ13C stable isotopes (SI) were analyzed in the muscle tissue of the black scabbardfish and related with diet and maturity. Specimens were collected in four geographic areas in the NE Atlantic: Iceland, the west of the British Isles, mainland Portugal, and Madeira. For all areas, the FA profile was related with the different phases of the reproductive cycle and with diet, whereas the SI were related with diet, environmental characteristics, such as latitude and depth, and particulate organic matter (POM). Stomach content of black scabbardfish caught off mainland Portugal was analyzed and the most frequent prey item identified was the lophogastrid crustacean Gnathophausia zoea, followed by the cephalopod Mastigotheutis spp. and the teleost Rouleina maderensis. For specimens from Iceland and the west of the British Isles, monounsaturated fatty acids (MUFA) were the most important FA, followed by polyunsaturated (PUFA) and saturated FA (SFA), whereas for specimens from mainland Portugal and from Madeira the sequences were PUFA>MUFA>SFA and PUFA>SFA>MUFA, respectively. Immature specimens from the first three areas were found to be accumulating oleic acid which is an intermediate product of the metabolic pathway that transforms SFA to MUFA and these into PUFA. Specimens caught off Madeira were mature and showed a significant prevalence of ARA and DHA which are PUFA with an important role in reproduction. δ15N was significantly higher in the muscle of black scabbardfish from Madeira, whereas δ13C was significantly lower in specimens from Iceland. The low isotopic ratios as well as the prevalence of certain fatty acid trophic markers (FATM

  1. Spatial variability of mercury and polyunsaturated fatty acids in the European perch (Perca fluviatilis) - Implications for risk-benefit analyses of fish consumption.

    PubMed

    Strandberg, Ursula; Palviainen, Marjo; Eronen, Aslak; Piirainen, Sirpa; Laurén, Ari; Akkanen, Jarkko; Kankaala, Paula

    2016-12-01

    This study evaluated the spatial variability of risks and benefits of consuming fish from humic and clear lakes. Mercury in fish is a potential risk for human health, but risk assessment may be confounded by selenium, which has been suggested to counterbalance mercury toxicity. In addition to the risks, fish are also rich in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), which are known to be beneficial for cardiovascular health and brain cognitive function in humans. We found that the concentrations of EPA + DHA and mercury in European perch (Perca fluviatilis) vary spatially and are connected with lake water chemistry and catchment characteristics. The highest mercury concentrations and the lowest EPA + DHA concentrations were found in perch from humic lakes with high proportion of peatland (30-50%) in the catchment. In addition, the ratio of selenium to mercury in perch muscle was ≥1 suggesting that selenium may counterbalance mercury toxicity. The observed variation in mercury and EPA + DHA content in perch from different lakes indicate that the risks and benefits of fish consumption vary spatially, and are connected with lake water chemistry and catchment characteristics. In general, consumption of perch from humic lakes exposed humans to greater risks (higher concentrations of mercury), but provided less benefits (lower concentrations of EPA + DHA) than consumption of perch from clear lakes.

  2. Structure-Function Analyses of a Caffeic Acid O-Methyltransferase from Perennial Ryegrass Reveal the Molecular Basis for Substrate Preference[W][OA

    PubMed Central

    Louie, Gordon V.; Bowman, Marianne E.; Tu, Yi; Mouradov, Aidyn; Spangenberg, German; Noel, Joseph P.

    2010-01-01

    Lignin forms from the polymerization of phenylpropanoid-derived building blocks (the monolignols), whose modification through hydroxylation and O-methylation modulates the chemical and physical properties of the lignin polymer. The enzyme caffeic acid O-methyltransferase (COMT) is central to lignin biosynthesis. It is often targeted in attempts to engineer the lignin composition of transgenic plants for improved forage digestibility, pulping efficiency, or utility in biofuel production. Despite intensive investigation, the structural determinants of the regiospecificity and substrate selectivity of COMT remain poorly defined. Reported here are x-ray crystallographic structures of perennial ryegrass (Lolium perenne) COMT (Lp OMT1) in open conformational state, apo- and holoenzyme forms and, most significantly, in a closed conformational state complexed with the products S-adenosyl-l-homocysteine and sinapaldehyde. The product-bound complex reveals the post-methyl-transfer organization of COMT’s catalytic groups with reactant molecules and the fully formed phenolic-ligand binding site. The core scaffold of the phenolic ligand forges a hydrogen-bonding network involving the 4-hydroxy group that anchors the aromatic ring and thereby permits only metahydroxyl groups to be positioned for transmethylation. While distal from the site of transmethylation, the propanoid tail substituent governs the kinetic preference of ryegrass COMT for aldehydes over alcohols and acids due to a single hydrogen bond donor for the C9 oxygenated moiety dictating the preference for an aldehyde. PMID:21177481

  3. Functional Analyses of Caffeic Acid O-Methyltransferase and Cinnamoyl-CoA-Reductase Genes from Perennial Ryegrass (Lolium perenne)[W

    PubMed Central

    Tu, Yi; Rochfort, Simone; Liu, Zhiqian; Ran, Yidong; Griffith, Megan; Badenhorst, Pieter; Louie, Gordon V.; Bowman, Marianne E.; Smith, Kevin F.; Noel, Joseph P.; Mouradov, Aidyn; Spangenberg, German

    2010-01-01

    Cinnamoyl CoA-reductase (CCR) and caffeic acid O-methyltransferase (COMT) catalyze key steps in the biosynthesis of monolignols, which serve as building blocks in the formation of plant lignin. We identified candidate genes encoding these two enzymes in perennial ryegrass (Lolium perenne) and show that the spatio-temporal expression patterns of these genes in planta correlate well with the developmental profile of lignin deposition. Downregulation of CCR1 and caffeic acid O-methyltransferase 1 (OMT1) using an RNA interference–mediated silencing strategy caused dramatic changes in lignin level and composition in transgenic perennial ryegrass plants grown under both glasshouse and field conditions. In CCR1-deficient perennial ryegrass plants, metabolic profiling indicates the redirection of intermediates both within and beyond the core phenylpropanoid pathway. The combined results strongly support a key role for the OMT1 gene product in the biosynthesis of both syringyl- and guaiacyl-lignin subunits in perennial ryegrass. Both field-grown OMT1-deficient and CCR1-deficient perennial ryegrass plants showed enhanced digestibility without obvious detrimental effects on either plant fitness or biomass production. This highlights the potential of metabolic engineering not only to enhance the forage quality of grasses but also to produce optimal feedstock plants for biofuel production. PMID:20952635

  4. A close relationship between Cercozoa and Foraminifera supported by phylogenetic analyses based on combined amino acid sequences of three cytoskeletal proteins (actin, alpha-tubulin, and beta-tubulin).

    PubMed

    Takishita, Kiyotaka; Inagaki, Yuji; Tsuchiya, Masashi; Sakaguchi, Miako; Maruyama, Tadashi

    2005-12-05

    Recently, there has been increasing molecular evidence of phylogenetic affinity between Cercozoa and Foraminifera in the eukaryotic lineage. We performed phylogenetic analyses based on the combined (concatenated) amino acid sequence data of actin, alpha-tubulin, and beta-tubulin from a wide variety of eukaryotes, including the foraminifers Planoglabratella opercularis and Reticulomyxa filosa, as well as cercomonad and chlorarachniophyte members of Cercozoa. A monophyletic lineage composed of two foraminiferan species branched with the centroheliozoan species Raphidiophrys contractilis was reconstructed in both Bayesian and maximum-likelihood (ML) analyses under 'linked' models, enforcing a single set of the parameters (the parameter for among-site rate variation and branch lengths) on the entire combined alignment. Considering the extremely divergent nature of Foraminifera and Raphidiophyrs tubulins, the union of these lineages recovered is most probably a long-branch attraction artifact due to ignoring gene-specific evolutionary processes. On the other hand, the foraminiferan lineage was within the radiation of Cercozoa in Bayesian analyses under 'unlinked' model conditions, accommodating differences in evolutionary processes across the three genes in the combined alignment. The Foraminifera+Cercozoa affinity recovered in the latter multi-gene analyses is most likely genuine, and thus our data presented here provide further support for the close relationship between these two protist lineages.

  5. 7 CFR 94.102 - Analyses available.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ..., Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) COMMODITY LABORATORY TESTING PROGRAMS... analyses for total ash, fat by acid hydrolysis, moisture, salt, protein, beta-carotene,...

  6. 7 CFR 94.102 - Analyses available.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ..., Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) COMMODITY LABORATORY TESTING PROGRAMS... analyses for total ash, fat by acid hydrolysis, moisture, salt, protein, beta-carotene,...

  7. Assimilation of toluene carbon along a bacteria-protist food chain determined by 13C-enrichment of biomarker fatty acids.

    PubMed

    Mauclaire, Laurie; Pelz, Oliver; Thullner, Martin; Abraham, Wolf-Rainer; Zeyer, Josef

    2003-12-01

    A food chain consisting of toluene, toluene-degrading Pseudomonas sp. PS+ and a bacterivorous flagellated amoebae Vahlkampfia sp. was established in a batch culture. This culture was amended with [U-13C]toluene and served as a model system to elucidate the flux of carbon in the food chain by quantifying bacterial biovolumes and 13C enrichment of phospholipid fatty acid (PLFA) biomarkers of the bacteria and the heterotrophic protists. Major PLFA detected in the batch co-culture included those derived from Pseudomonas sp. PS+ (16:1omega7c and 18:1omega7c) and Vahlkampfia sp. (20:4omega6c and 20:3omega6c). A numerical model including consumption of toluene by the bacteria and predation of the bacteria by the heterotrophic protists was adjusted to the measured toluene carbon, bacterial carbon and delta13C values of bacterial and protist biomass. Using this model, we estimated that 28+/-7% of the consumed toluene carbon was transformed into bacterial biomass, and 12+/-4% of the predated bacterial carbon was incorporated into heterotrophic protist biomass. Our study showed that the 13C enrichment of PLFA biomarkers coupled to biomass determination via biovolume calculations is a suitable method to trace carbon fluxes in protist-inclusive microbial food chains because it does not require the separation of protist cells from bacterial cells and soil particles.

  8. Lyophilized brain tumor specimens can be used for histologic, nucleic acid, and protein analyses after 1 year of room temperature storage

    PubMed Central

    Mareninov, Sergey; De Jesus, Jason; Sanchez, Desiree E.; Kay, Andrew B.; Wilson, Ryan W.; Babic, Ivan; Chen, Weidong; Telesca, Donatello; Lou, Jerry J.; Mirsadraei, Leili; Gardner, Tracie P.; Khanlou, Negar; Vinters, Harry V.; Shafa, Bob B.; Lai, Albert; Liau, Linda M.; Mischel, Paul S.; Cloughesy, Timothy F.

    2013-01-01

    Frozen tissue, a gold standard biospecimen, can yield well preserved nucleic acids and proteins after over a decade but is vulnerable to thawing and has substantial fiscal, spatial, and environmental costs. A long-term room temperature biospecimen storage alternative that preserves broad analytical utility can potentially empower tissue-based research. As there is scant data on the analytical utility of lyophilized brain tumor biospecimens, we evaluated lyophilized (freeze-dried) samples stored for 1 year at room temperature. Lyophilized tumor tissue processed into paraffin sections produced good histology. Yields of extracted DNA, RNA, and protein approximated those of frozen tissue. After 1 year, lyophilized samples yielded high molecular weight DNA that permitted copy number variation analysis, IDH 1 mutation detection, and MGMT promoter methylation PCR. A 27 % decrease in RIN scores over the 1 year suggests that RNA degradation was inhibited though incompletely. Nevertheless, RT-PCR studies on lyophilized tissue performed similarly to frozen tissue. In contrast to FFPE tissues where protein bands were absent or shifted to a lower molecular weight, lyophilized samples showed similar protein bands as frozen tissue on SDS-PAGE analysis. Lyophilized tissue performed similarly to frozen tissue for Western blots and enzyme activity assays. Immunohistochemistry of lyophilized tissue that were processed into FFPE blocks often required longer incubation times for staining than standard FFPE samples but generally provided robust antigen detection. This preliminary study suggests that lyophilization has promise for long-term room temperature storage while permitting varied tests; however, further work is required to better stabilize nucleic acids particularly RNA. PMID:23640138

  9. Evaluation of metal and radionuclide data from neutron activation and acid-digestion-based spectrometry analyses of background soils: Significance in environmental restoration

    SciTech Connect

    Lee, S.Y.; Watkins, D.R.; Jackson, B.L.; Schmoyer, R.L.; Lietzke, D.A.; Burgoa, B.B.; Branson, J.T.; Ammons, J.T.

    1995-12-31

    A faster, more cost-effective, and higher-quality data acquisition procedure for natural background-level metals and radionuclides in soils is needed for remedial investigations of contaminated sites. In this project, a total of 120 soil samples were collected from uncontaminated areas on and near the Oak Ridge Reservation. The samples were taken at three different depths and from three different geologic groups to establish background concentrations of metals and radionuclides. The objective of this presentation is to discuss the advantages and disadvantages of neutron activation analysis (NAA) compared with those of acid-digestion-based spectrometry (ADS) methods; the advantages and disadvantages were evaluated from Al, Sb, As, Cr, Co, Fe, Mg, Mn, Hg, K, Ag, {sup 232}Th, {sup 235}U, {sup 238}U, V, and Zn data. The ADS methods used for this project were inductively coupled plasma (ICP), ICP-mass spectrometry (ICP-MS), and alpha spectrometry. The scatter plots showed that the NAA results for As, Co, Fe, Mn, {sup 232}Th, and {sup 238}U are reasonably correlated with the results from the other analytical methods. Compared to NAA, however, the ADS methods underestimated Al, Cr, Mg, K, V, and Zn. The skew distributions were caused by incomplete dissolution of the analytes during acid digestion of the soil samples. Because of the high detection limits of the spectrometric methods, the NAA results and the ADS results for some elements, including Sb, Hg, and Ag, did not show a definite relationship. The NAA results were highly correlated with the alpha spectrometry results for {sup 232}Th and {sup 238}U but poorly correlated for {sup 235}U, probably because of a larger counting error associated with the lower activity of the isotope. The NAA methods, including the delayed neutron counting method, were far superior techniques for quantifying background levels of radionuclides ({sup 232}Th, {sup 235}U, and {sup 238}U) and metals (Al, Cr, Mg, K, V, and Zn) in soils.

  10. The family of ferrocene-stabilized silylium ions: synthesis, 29Si NMR characterization, Lewis acidity, substituent scrambling, and quantum-chemical analyses.

    PubMed

    Müther, Kristine; Hrobárik, Peter; Hrobáriková, Veronika; Kaupp, Martin; Oestreich, Martin

    2013-12-02

    The purpose of this systematic experimental and theoretical study is to deeply understand the unique bonding situation in ferrocene-stabilized silylium ions as a function of the substituents at the silicon atom and to learn about the structure parameters that determine the (29)Si NMR chemical shift and electrophilicity of these strong Lewis acids. For this, ten new members of the family of ferrocene-stabilized silicon cations were prepared by a hydride abstraction reaction from silanes with the trityl cation and characterized by multinuclear (1)H and (29)Si NMR spectroscopy. A closer look at the NMR spectra revealed that additional minor sets of signals were not impurities but silylium ions with substitution patterns different from that of the initially formed cation. Careful assignment of these signals furnished experimental proof that sterically less hindered silylium ions are capable of exchanging substituents with unreacted silane precursors. Density functional theory calculations provided mechanistic insight into that substituent transfer in which the migrating group is exchanged between two silicon fragments in a concerted process involving a ferrocene-bridged intermediate. Moreover, the quantum-chemical analysis of the (29)Si NMR chemical shifts revealed a linear relationship between δ((29)Si) values and the Fe···Si distance for subsets of silicon cations. An electron localization function and electron localizability indicator analysis shows a three-center two-electron bonding attractor between the iron, silicon, and C'(ipso) atoms, clearly distinguishing the silicon cations from the corresponding carbenium ions and boranes. Correlations between (29)Si NMR chemical shifts and Lewis acidity, evaluated in terms of fluoride ion affinities, are seen only for subsets of silylium ions, sometimes with non-intuitive trends, indicating a complicated interplay of steric and electronic effects on the degree of the Fe···Si interaction.

  11. Structural, Biochemical, and Phylogenetic Analyses Suggest That Indole-3-Acetic Acid Methyltransferase Is an Evolutionarily Ancient Member of the SABATH Family

    SciTech Connect

    Zhao,N.; Ferrer, J.; Ross, J.; Guan, J.; Yang, Y.; Pichersky, E.; Noel, J.; Chen, F.

    2008-01-01

    The plant SABATH protein family encompasses a group of related small-molecule methyltransferases (MTs) that catalyze the S-adenosyl-L-methionine-dependent methylation of natural chemicals encompassing widely divergent structures. Indole-3-acetic acid (IAA) methyltransferase (IAMT) is a member of the SABATH family that modulates IAA homeostasis in plant tissues through methylation of IAA's free carboxyl group. The crystal structure of Arabidopsis (Arabidopsis thaliana) IAMT (AtIAMT1) was determined and refined to 2.75 Angstroms resolution. The overall tertiary and quaternary structures closely resemble the two-domain bilobed monomer and the dimeric arrangement, respectively, previously observed for the related salicylic acid carboxyl methyltransferase from Clarkia breweri (CbSAMT). To further our understanding of the biological function and evolution of SABATHs, especially of IAMT, we analyzed the SABATH gene family in the rice (Oryza sativa) genome. Forty-one OsSABATH genes were identified. Expression analysis showed that more than one-half of the OsSABATH genes were transcribed in one or multiple organs. The OsSABATH gene most similar to AtIAMT1 is OsSABATH4. Escherichia coli-expressed OsSABATH4 protein displayed the highest level of catalytic activity toward IAA and was therefore named OsIAMT1. OsIAMT1 exhibited kinetic properties similar to AtIAMT1 and poplar IAMT (PtIAMT1). Structural modeling of OsIAMT1 and PtIAMT1 using the experimentally determined structure of AtIAMT1 reported here as a template revealed conserved structural features of IAMTs within the active-site cavity that are divergent from functionally distinct members of the SABATH family, such as CbSAMT. Phylogenetic analysis revealed that IAMTs from Arabidopsis, rice, and poplar (Populus spp.) form a monophyletic group. Thus, structural, biochemical, and phylogenetic evidence supports the hypothesis that IAMT is an evolutionarily ancient member of the SABATH family likely to play a critical role in

  12. Morphological and morphometric analyses of crushed sciatic nerves after application of a purified protein from natural latex and hyaluronic acid hydrogel.

    PubMed

    Barreiros, Vanessa Cristina Pereira; Dias, Fernando José; Iyomasa, Mamie Mizusaki; Coutinho-Netto, Joaquim; de Sousa, Luiz Gustavo; Fazan, Valéria Paula Sassoli; Antunes, Ricardo de Souza; Watanabe, Ii-Sei; Issa, João Paulo Mardegan

    2014-10-01

    Hyaluronic acid hydrogels (HAHs) have been used as a carrier of substances and factors in the repair of nervous tissue. Natural latex protein (Hevea brasiliensis, F1) has shown positive effects in treating various types of tissues, including peripheral nerves. This study evaluated the F1 associated with a HAH in a controlled crush injury (axonotmesis) of the sciatic nerve in Wistar rats. The samples were photomicrographed for morphometric and quantitative analyzes using ImageJ 1.47k software (NIH, Bethesda, MD). Morphological, quantitative (myelin area/nerve area ratio and capillary density) and morphometric (minimum nerve fiber diameter, G-Ratio) data revealed an improvement in the recovery of the sciatic nerve with the application of HAH and the combination of HAH and F1 after 4 and 8 weeks of nerve injury. The most efficacious results were observed with the combination of both substances, F1 and HAH, revealing the regenerative capacity of this new biomaterial, which was hardly tested on nerve tissue.

  13. Computational and Statistical Analyses of Amino Acid Usage and Physico-Chemical Properties of the Twelve Late Embryogenesis Abundant Protein Classes

    PubMed Central

    Jaspard, Emmanuel; Macherel, David; Hunault, Gilles

    2012-01-01

    Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs. PMID:22615859

  14. Drug-eluting coating of ginsenoside Rg1 and Re incorporated poly(lactic-co-glycolic acid) on stainless steel 316L: Physicochemical and drug release analyses.

    PubMed

    Miswan, Zulaika; Lukman, Siti Khadijah; Abd Majid, Fadzilah Adibah; Loke, Mun Fai; Saidin, Syafiqah; Hermawan, Hendra

    2016-12-30

    Active ingredients of ginsenoside, Rg1 and Re, are able to inhibit the proliferation of vascular smooth muscle cells and promote the growth of vascular endothelial cells. These capabilities are of interest for developing a novel drug-eluting stent to potentially solve the current problem of late-stent thrombosis and poor endotheliazation. Therefore, this study was aimed to incorporate ginsenoside into degradable coating of poly(lactic-co-glycolic acid) (PLGA). Drug mixture composed of ginseng extract and 10% to 50% of PLGA (xPLGA/g) was coated on electropolished stainless steel 316L substrate by using a dip coating technique. The coating was characterized principally by using attenuated total reflectance-Fourier transform infrared spectroscopy, scanning electron microscopy and contact angle analysis, while the drug release profile of ginsenosides Rg1 and Re was determined by using mass spectrometry at a one month immersion period. Full and homogenous coating coverage with acceptable wettability was found on the 30PLGA/g specimen. All specimens underwent initial burst release dependent on their composition. The 30PLGA/g and 50PLGA/g specimens demonstrated a controlled drug release profile having a combination of diffusion- and swelling-controlled mechanisms of PLGA. The study suggests that the 30PLGA/g coated specimen expresses an optimum composition which is seen as practicable for developing a controlled release drug-eluting stent.

  15. Strong linkage of polar cod (Boreogadus saida) to sea ice algae-produced carbon: Evidence from stomach content, fatty acid and stable isotope analyses

    NASA Astrophysics Data System (ADS)

    Kohlbach, Doreen; Schaafsma, Fokje L.; Graeve, Martin; Lebreton, Benoit; Lange, Benjamin Allen; David, Carmen; Vortkamp, Martina; Flores, Hauke

    2017-03-01

    The polar cod (Boreogadus saida) is considered an ecological key species, because it reaches high stock biomasses and constitutes an important carbon source for seabirds and marine mammals in high-Arctic ecosystems. Young polar cod (1-2 years) are often associated with the underside of sea ice. To evaluate the impact of changing Arctic sea ice habitats on polar cod, we examined the diet composition and quantified the contribution of ice algae-produced carbon (αIce) to the carbon budget of polar cod. Young polar cod were sampled in the ice-water interface layer in the central Arctic Ocean during late summer 2012. Diets and carbon sources of these fish were examined using 4 approaches: (1) stomach content analysis, (2) fatty acid (FA) analysis, (3) bulk nitrogen and carbon stable isotope analysis (BSIA) and (4) compound-specific stable isotope analysis (CSIA) of FAs. The ice-associated (sympagic) amphipod Apherusa glacialis dominated the stomach contents by mass, indicating a high importance of sympagic fauna in young polar cod diets. The biomass of food measured in stomachs implied constant feeding at daily rates of ∼1.2% body mass per fish, indicating the potential for positive growth. FA profiles of polar cod indicated that diatoms were the primary carbon source, indirectly obtained via amphipods and copepods. The αIce using bulk isotope data from muscle was estimated to be >90%. In comparison, αIce based on CSIA ranged from 34 to 65%, with the highest estimates from muscle and the lowest from liver tissue. Overall, our results indicate a strong dependency of polar cod on ice-algae produced carbon. This suggests that young polar cod may be particularly vulnerable to changes in the distribution and structure of sea ice habitats. Due to the ecological key role of polar cod, changes at the base of the sea ice-associated food web are likely to affect the higher trophic levels of high-Arctic ecosystems.

  16. Gene expression analyses in tomato near isogenic lines provide evidence for ethylene and abscisic acid biosynthesis fine-tuning during arbuscular mycorrhiza development.

    PubMed

    Fracetto, Giselle Gomes Monteiro; Peres, Lázaro Eustáquio Pereira; Lambais, Marcio Rodrigues

    2017-03-11

    Plant responses to the environment and microorganisms, including arbuscular mycorrhizal fungi, involve complex hormonal interactions. It is known that abscisic acid (ABA) and ethylene may be involved in the regulation of arbuscular mycorrhiza (AM) and that part of the detrimental effects of ABA deficiency in plants is due to ethylene overproduction. In this study, we aimed to determine whether the low susceptibility to mycorrhizal colonization in ABA-deficient mutants is due to high levels of ethylene and whether AM development is associated with changes in the steady-state levels of transcripts of genes involved in the biosynthesis of ethylene and ABA. For that, tomato (Solanum lycopersicum) ethylene overproducer epinastic (epi) mutant and the ABA-deficient notabilis (not) and sitiens (sit) mutants, in the same Micro-Tom (MT) genetic background, were inoculated with Rhizophagus clarus, and treated with the ethylene biosynthesis inhibitor aminoethoxyvinylglycine (AVG). The development of AM, as well as the steady-state levels of transcripts involved in ethylene (LeACS2, LeACO1 and LeACO4) and ABA (LeNCED) biosynthesis, was determined. The intraradical colonization in epi, not and sit mutants was significantly reduced compared to MT. The epi mutant completely restored the mycorrhizal colonization to the levels of MT with the application of 10 µM of AVG, probably due to the inhibition of the ACC synthase gene expression. The steady-state levels of LeACS2 and LeACO4 transcripts were induced in mycorrhizal roots of MT, whereas the steady-state levels of LeACO1 and LeACO4 transcripts were significantly induced in sit, and the steady-state levels of LeNCED transcripts were significantly induced in all genotypes and in mycorrhizal roots of epi mutants treated with AVG. The reduced mycorrhizal colonization in sit mutants seems not to be limited by ethylene production via ACC oxidase regulation. Both ethylene overproduction and ABA deficiency impaired AM fungal

  17. Short-term monitoring of aridland lichen cover and biomass using photography and fatty acids

    USGS Publications Warehouse

    Bowker, M.A.; Johnson, N.C.; Belnap, J.; Koch, G.W.

    2008-01-01

    Biological soil crust (BSC) communities (composed of lichens, bryophytes, and cyanobacteria) may be more dynamic on short-time scales than previously thought, requiring new and informative short-term monitoring techniques. We used repeat digital photography and image analysis, which revealed a change in area of a dominant BSC lichen, Collema tenax. The data generated correlated well with gross photosynthesis (r=0.57) and carotenoid content (r=0.53), two variables that would be expected to be positively related to lichen area. We also extracted fatty acids from lichen samples and identified useful phospholipid fatty acid (PLFA) indicators for the Collema mycobiont (20:1, 15:0, 23:0), and the Collema photobiont (18:3??3). The 18:3??3 correlated well with chlorophyll a (r=0.66), a more traditional proxy for cyanobacterial biomass. We also compared total PLFA as a proxy for total Collema biomass with our photographically generated areal change data, and found them to be moderately correlated (r=0.44). Areal change proved to be responsive on short-time scales, while fatty acid techniques were information-rich, providing data on biomass of lichens, and both photo- and mycobionts separately, in addition to the physiological status of the mycobiont. Both techniques should be refined and tested in field situations. ?? 2007 Elsevier Ltd. All rights reserved.

  18. Australian Acid Playa Lake as a Mars Analog: Results from Sediment Lipid Analysis

    NASA Astrophysics Data System (ADS)

    Graham, H.; Baldridge, A. M.; Stern, J. C.

    2015-12-01

    The ephemeral saline acidic lakes on the Yilgarn Craton of Western Australia have been suggested as geochemical analogues to martian terrains. Both are characterized by interbedded phyllosilicates and hydrated sulfates. On Mars, these areas indicate shifting environmental conditions, from the neutral/alkaline and wet conditions that dominated during the Noachian era to the more familiar dry, acidic conditions that began in the Hesperian. The habitability of such a dynamic environment can be informed by investigation of the Yilgarn Lake system. Previous work has found phospholipid fatty acids (PLFA) evidence of microbial communities in sections of sediment cores taken from Lake Gilmore. These communities include both Gram-positive and -negative bacteria, Actinomycetes, and even methanotrophs. Given recurring detection of methane on the martian surface, evidence of a methane cycling community in an analogous environment is of particular interest. In this study we analyze the carbon isotope composition of bulk organic material as well as extracted lipids from the Lake Gilmore sediment cores at both a near-shore and mid-lake location. These analyses reveal very low accumulations of organic carbon, concentrated primarily in the gypsum-rich near-shore core. The near-shore sediments show a down-core decrease in abundance of organic carbon as well as depletion in the carbon isotope composition (δ13C) with depth. Bulk carbon did not exhibit the unique, highly depleted, diagnostic signature associated with methanotrophic biomass. Compound-specific isotope analysis (CSIA) of carbon in extracted methanotroph PFLAs can confirm the presence of a methane cycling metabolism at depth. Also, additional extractions have isolated lipids associated with lake-edge grasses. These analyses consider both the chain-length distribution and carbon CSIA of these lipids in order to understand the effect of terrestrial detritus on any preserved methanotroph carbon signal, given the very low

  19. Combined experimental and theoretical studies on the molecular structures, spectroscopy, and inhibitor activity of 3-(2-thienyl)acrylic acid through AIM, NBO,FT-IR, FT-Raman, UV and HOMO-LUMO analyses, and molecular docking

    NASA Astrophysics Data System (ADS)

    Issaoui, N.; Ghalla, H.; Bardak, F.; Karabacak, M.; Aouled Dlala, N.; Flakus, H. T.; Oujia, B.

    2017-02-01

    In this work, the molecular structures and vibrational spectral analyses of 3-(2-Theinyl)acrylic acid (3-2TAA) monomer and dimer structures have been reported by using density functional theory calculations at B3LYP/6-311++G(d,p) level of theory. The complete assignments of the fundamental vibrational modes were obtained using potential energy distribution. Intermolecular interactions were analyzed by orbital NBO and topological AIM approaches. The electronic properties have been carried out using TD-DFT approach. Great agreements between experimental and theoretical values were achieved throughout the analysis of structural parameters and spectroscopic features. Inhibitor characteristics on human monoamine oxidase B (MAOB) enzyme of two determined stable conformers of 3-2TAA (β and γ) along with four selective inhibitors, namely safinamide, a coumarin analogue, farnesol, and phenyethylhydrazine were investigated via molecular docking. Moreover, molecular electrostatic potential (MEP) and temperature dependency of thermodynamic functions have been reported.

  20. Sulfur K-edge XANES and acid volatile sulfide analyses of changes in chemical speciation of S and Fe during sequential extraction of trace metals in anoxic sludge from biogas reactors.

    PubMed

    Shakeri Yekta, Sepehr; Gustavsson, Jenny; Svensson, Bo H; Skyllberg, Ulf

    2012-01-30

    The effect of sequential extraction of trace metals on sulfur (S) speciation in anoxic sludge samples from two lab-scale biogas reactors augmented with Fe was investigated. Analyses of sulfur K-edge X-ray absorption near edge structure (S XANES) spectroscopy and acid volatile sulfide (AVS) were conducted on the residues from each step of the sequential extraction. The S speciation in sludge samples after AVS analysis was also determined by S XANES. Sulfur was mainly present as FeS (≈ 60% of total S) and reduced organic S (≈ 30% of total S), such as organic sulfide and thiol groups, in the anoxic solid phase. Sulfur XANES and AVS analyses showed that during first step of the extraction procedure (the removal of exchangeable cations), a part of the FeS fraction corresponding to 20% of total S was transformed to zero-valent S, whereas Fe was not released into the solution during this transformation. After the last extraction step (organic/sulfide fraction) a secondary Fe phase was formed. The change in chemical speciation of S and Fe occurring during sequential extraction procedure suggests indirect effects on trace metals associated to the FeS fraction that may lead to incorrect results. Furthermore, by S XANES it was verified that the AVS analysis effectively removed the FeS fraction. The present results identified critical limitations for the application of sequential extraction for trace metal speciation analysis outside the framework for which the methods were developed.

  1. Department of Energy's team's analyses of Soviet designed VVERs

    SciTech Connect

    Not Available

    1989-09-01

    This document provides Appendices A thru K of this report. The topics discussed respectively are: radiation induced embrittlement and annealing of reactor pressure vessel steels; loss of coolant accident blowdown analyses; LOCA blowdown response analyses; non-seismic structural response analyses; seismic analyses; S'' seal integrity; reactor transient analyses; fire protection; aircraft impacts; and boric acid induced corrosion. (FI).

  2. Microbial carbon cycling in oligotrophic regional aquifers near the Tono Uranium Mine, Japan as inferred from δ 13C and Δ 14C values of in situ phospholipid fatty acids and carbon sources

    NASA Astrophysics Data System (ADS)

    Mills, Christopher T.; Amano, Yuki; Slater, Gregory F.; Dias, Robert F.; Iwatsuki, Teruki; Mandernack, Kevin W.

    2010-07-01

    Microorganisms are ubiquitous in deep subsurface environments, but their role in the global carbon cycle is not well-understood. The natural abundance δ 13C and Δ 14C values of microbial membrane phospholipid fatty acids (PLFAs) were measured and used to assess the carbon sources of bacteria in sedimentary and granitic groundwaters sampled from three boreholes in the vicinity of the Tono Uranium Mine, Gifu, Japan. Sample storage experiments were performed and drill waters analyzed to characterize potential sources of microbial contamination. The most abundant PLFA structures in all waters sampled were 16:0, 16:1ω7 c, cy17:0, and 18:1ω7 c. A PLFA biomarker for type II methanotrophs, 18:1ω8 c, comprised 3% and 18% of total PLFAs in anoxic sedimentary and granitic waters, respectively, sampled from the KNA-6 borehole. The presence of this biomarker was unexpected given that type II methanotrophs are considered obligate aerobes. However, a bacterium that grows aerobically with CH 4 as the sole energy source and which also produces 56% of its total PLFAs as 18:1ω8 c was isolated from both waters, providing additional evidence for the presence of type II methanotrophs. The Δ 14C values determined for type II methanotroph PLFAs in the sedimentary (-861‰) and granite (-867‰) waters were very similar to the Δ 14C values of dissolved inorganic carbon (DIC) in each water (˜-850‰). This suggests that type II methanotrophs ultimately derive all their carbon from inorganic sources, whether directly from DIC and/or from CH 4 produced by the reduction of DIC. In contrast, δ 13C values of type II PLFAs in the sedimentary (-93‰) and granite (-60‰) waters indicate that these organisms use different carbon assimilation schemes in each environment despite very similar δ13C values (˜-95‰) for each water. The δ 13C PLFA values (-28‰ to -45‰) of non-methanotrophic bacteria in the KNA-6 LTL water do not clearly distinguish between heterotrophic and autotrophic

  3. Co-extraction of DNA and PLFA from soil samples.

    PubMed

    Brewer, Sheridan; Techtmann, Stephen M; Mahmoudi, Nagissa; Niang, Dijibril; Pfiffner, Susan; Hazen, Terry C

    2015-08-01

    Lipid/DNA co-extraction from one sample is attractive in limiting biases associated with microbial community analysis from separate extractions. We sought to enhance established co-extraction methods and use high-throughput 16S rRNA sequencing to identify preferentially extracted taxa from co-extracted DNA. Co-extraction results in low DNA yields and distinct community structure changes.

  4. p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses*

    PubMed Central

    Hünten, Sabine; Kaller, Markus; Drepper, Friedel; Oeljeklaus, Silke; Bonfert, Thomas; Erhard, Florian; Dueck, Anne; Eichner, Norbert; Friedel, Caroline C.; Meister, Gunter; Zimmer, Ralf; Warscheid, Bettina; Hermeking, Heiko

    2015-01-01

    We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics (pulsed stable isotope labeling with amino acids in cell culture/pSILAC) in the colorectal cancer cell line SW480. This was combined with mRNA and noncoding RNA expression analyses by next generation sequencing (RNA-, miR-Seq). Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated proteins (542 up, 569 down), mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down) and lncRNAs (270 up, 123 down). Changes in protein and mRNA expression levels showed a positive correlation (r = 0.50, p < 0.0001). In total, we detected 133 direct p53 target genes that were differentially expressed and displayed p53 occupancy in the vicinity of their promoter. More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the down-regulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3′-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed up-regulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibits proliferation in SW480 cells. Furthermore, KLF12, HMGB1 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486–5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of KLF12, HMGB1 and CIT was detected in advanced stages of cancer. In conclusion, the integration of multiple omics methods allowed the comprehensive identification of direct and indirect effectors of p53 that provide new insights and leads into the

  5. Potential of a newly developed high-speed near-infrared (NIR) camera (Compovision) in polymer industrial analyses: monitoring crystallinity and crystal evolution of polylactic acid (PLA) and concentration of PLA in PLA/Poly-(R)-3-hydroxybutyrate (PHB) blends.

    PubMed

    Ishikawa, Daitaro; Nishii, Takashi; Mizuno, Fumiaki; Sato, Harumi; Kazarian, Sergei G; Ozaki, Yukihiro

    2013-12-01

    This study was carried out to evaluate a new high-speed hyperspectral near-infrared (NIR) camera named Compovision. Quantitative analyses of the crystallinity and crystal evolution of biodegradable polymer, polylactic acid (PLA), and its concentration in PLA/poly-(R)-3-hydroxybutyrate (PHB) blends were investigated using near-infrared (NIR) imaging. This NIR camera can measure two-dimensional NIR spectral data in the 1000-2350 nm region obtaining images with wide field of view of 150 × 250 mm(2) (approximately 100  000 pixels) at high speeds (in less than 5 s). PLA with differing crystallinities between 0 and 50% blended samples with PHB in ratios of 80/20, 60/40, 40/60, 20/80, and pure films of 100% PLA and PHB were prepared. Compovision was used to collect respective NIR spectra in the 1000-2350 nm region and investigate the crystallinity of PLA and its concentration in the blends. The partial least squares (PLS) regression models for the crystallinity of PLA were developed using absorbance, second derivative, and standard normal variate (SNV) spectra from the most informative region of the spectra, between 1600 and 2000 nm. The predicted results of PLS models achieved using the absorbance and second derivative spectra were fairly good with a root mean square error (RMSE) of less than 6.1% and a determination of coefficient (R(2)) of more than 0.88 for PLS factor 1. The results obtained using the SNV spectra yielded the best prediction with the smallest RMSE of 2.93% and the highest R(2) of 0.976. Moreover, PLS models developed for estimating the concentration of PLA in the blend polymers using SNV spectra gave good predicted results where the RMSE was 4.94% and R(2) was 0.98. The SNV-based models provided the best-predicted results, since it can reduce the effects of the spectral changes induced by the inhomogeneity and the thickness of the samples. Wide area crystal evolution of PLA on a plate where a temperature slope of 70-105 °C had occurred was also

  6. UHPLC-ESI-MS/MS and GC-MS Analyses on Phenolic, Fatty Acid and Essential Oil of Verbascum pinetorum with Antioxidant, Anticholinesterase, Antimicrobial and DNA Damage Protection Effects

    PubMed Central

    Boğa, Mehmet; Ertaş, Abdulselam; Yılmaz, Mustafa Abdullah; Kızıl, Murat; Çeken, Bircan; Haşimi, Nesrin; Özden, Tuğba Yılmaz; Demirci, Serpil; Yener, İsmail; Deveci, Özcan

    2016-01-01

    This paper is the first phytochemical and ABTS cation radical decolorisation activity, cupric reducing antioxidant capacity, anticholinesterase and DNA damage protection effect of endemic Verbascum pinetorum (Boiss.) O. Kuntze. Phenolic profile of V. pinetorum were qualified and quantified by UHPLC-ESI-MS/MS analysis. Malic acid (47250.61±2504.28 µg/g) and luteolin (7651.96±527.98 µg/g) were found as most abundant compounds for metanol and acetone extracts, respectively. Fatty acid and essential oil compositions were determined by GC-MS analysis. The main components of fatty acid were found to be palmitic (27.1%) and stearic (22.1%) acids. The main compounds of the essential oil were cineole (16.9%) and α-selinene (16.4%). The acetone extract was found to be more active than BHT used as a standard in β-carotene-linoleic acid test system. In DPPH free radical scavenging activity, the acetone and methanol extracts showed higher activity than BHT at all tested concentrations. The acetone, methanol and water extracts showed strong inhibition while the acetone extract showed better activity than BHT and α-tocopherol which were used as standards in ABTS cation radical scavenging and cupric reducing antioxidant capacity assays, respectively. All extracts were found to be inactive in antialzheimer activity. The acetone extract exhibited moderate antimicrobial activity against C. albicans. The methanol extract of V. pinetorum were found no significant effect on DNA cleavage protection. PMID:27980574

  7. Correlation analyses on binding affinity of sialic acid analogues and anti-influenza drugs with human neuraminidase using ab initio MO calculations on their complex structures--LERE-QSAR analysis (IV).

    PubMed

    Hitaoka, Seiji; Matoba, Hiroshi; Harada, Masataka; Yoshida, Tatsusada; Tsuji, Daisuke; Hirokawa, Takatsugu; Itoh, Kohji; Chuman, Hiroshi

    2011-10-24

    We carried out full ab initio fragment molecular orbital (FMO) calculations for complexes comprising human neuraminidase-2 (hNEU2) and sialic acid analogues including anti-influenza drugs zanamivir (Relenza) and oseltamivir (Tamiflu) in order to examine the variation in the observed inhibitory activity toward hNEU2 at the atomic and electronic levels. We recently proposed the LERE (linear expression by representative energy terms)-QSAR (quantitative structure-activity relationship) procedure. LERE-QSAR analysis quantitatively revealed that the complex formation is driven by hydrogen-bonding and electrostatic interaction of hNEU2 with sialic acid analogues. The most potent inhibitory activity, that of zanamivir, is attributable to the strong electrostatic interaction of a positively charged guanidino group in zanamivir with negatively charged amino acid residues in hNEU2. After we confirmed that the variation in the observed inhibitory activity among sialic acid analogues is excellently reproducible with the LERE-QSAR equation, we examined the reason for the remarkable difference between the inhibitory potencies of oseltamivir as to hNEU2 and influenza A virus neuraminidase-1 (N1-NA). Several amino acid residues in close contact with a positively charged amino group in oseltamivir are different between hNEU2 and N1-NA. FMO-IFIE (interfragment interaction energy) analysis showed that the difference in amino acid residues causes a remarkably large difference between the overall interaction energies of oseltamivir with hNEU2 and N1-NA. The current results will be useful for the development of new anti-influenza drugs with high selectivity and without the risk of adverse side effects.

  8. Spacelab Charcoal Analyses

    NASA Technical Reports Server (NTRS)

    Slivon, L. E.; Hernon-Kenny, L. A.; Katona, V. R.; Dejarme, L. E.

    1995-01-01

    This report describes analytical methods and results obtained from chemical analysis of 31 charcoal samples in five sets. Each set was obtained from a single scrubber used to filter ambient air on board a Spacelab mission. Analysis of the charcoal samples was conducted by thermal desorption followed by gas chromatography/mass spectrometry (GC/MS). All samples were analyzed using identical methods. The method used for these analyses was able to detect compounds independent of their polarity or volatility. In addition to the charcoal samples, analyses of three Environmental Control and Life Support System (ECLSS) water samples were conducted specifically for trimethylamine.

  9. Wavelet Analyses and Applications

    ERIC Educational Resources Information Center

    Bordeianu, Cristian C.; Landau, Rubin H.; Paez, Manuel J.

    2009-01-01

    It is shown how a modern extension of Fourier analysis known as wavelet analysis is applied to signals containing multiscale information. First, a continuous wavelet transform is used to analyse the spectrum of a nonstationary signal (one whose form changes in time). The spectral analysis of such a signal gives the strength of the signal in each…

  10. Apollo 14 microbial analyses

    NASA Technical Reports Server (NTRS)

    Taylor, G. R.

    1972-01-01

    Extensive microbiological analyses that were performed on the Apollo 14 prime and backup crewmembers and ancillary personnel are discussed. The crewmembers were subjected to four separate and quite different environments during the 137-day monitoring period. The relation between each of these environments and observed changes in the microflora of each astronaut are presented.

  11. Atmospheric tether mission analyses

    NASA Technical Reports Server (NTRS)

    1996-01-01

    NASA is considering the use of tethered satellites to explore regions of the atmosphere inaccessible to spacecraft or high altitude research balloons. This report summarizes the Lockheed Martin Astronautics (LMA) effort for the engineering study team assessment of an Orbiter-based atmospheric tether mission. Lockheed Martin responsibilities included design recommendations for the deployer and tether, as well as tether dynamic analyses for the mission. Three tether configurations were studied including single line, multistrand (Hoytether) and tape designs.

  12. Effect of environmental conditions on the fatty acid fingerprint of microbial communities

    NASA Astrophysics Data System (ADS)

    Biryukov, Mikhail; Dippold, Michaela; Kuzyakov, Yakov

    2014-05-01

    Lipid biomarkers, especially phospholipids, are routinely used to characterize microbial community structure in environmental samples. Interpretations of these fingerprints mainly depend on rare results of pure cultures which were cultivated under standardized batch conditions. However, membrane lipids (e.g. phopholipid biomarker) build up the interface between microorganisms and their environment and consequently are prone to be adapted according to the environmental conditions. We cultivated several bacteria, isolated from soil (gram-positive and gram-negative) under various conditions e.g. C supply and temperature regimes. Effect of growth conditions on phospholipids fatty acid (PLFA) as well as neutral lipid fatty acids (NLFA) and glycolipid fatty acids (GLFA) was investigated by conventional method of extraction and derivatization, followed by assessments with gas chromatography mass spectrometry (GC-MS). In addition, phospholipids were measured as intact molecules by ultra high performance liquid chromatography - quadrupole - time of flight mass spectrometer (UHPLC-Q-ToF) to further assess the composition of headgroups with fatty acids residues and their response on changing environmental conditions. PLFA fingerprints revealed a strong effect of growth stage, C supply and temperature e.g. decrease of temperature increased the amount of branched and/or unsaturated fatty acids to maintain the membrane fluidity. This strongly changes the ratio of specific to unspecific fatty acids depending on environmental conditions. Therefore, amounts of specific fatty acids cannot be used to assess biomass of a functional microbial group in soil. Intracellular neutral lipids depended less on environmental conditions reflecting a more stable biomarker group but also showed less specific fatty acids then PLFA. Therefore, combination of several lipid classes is suggested as more powerful tool to assess amounts and functionality of environmental microbial communities. Further

  13. Calibration of amino acid racemization (AAR) kinetics in United States mid-Atlantic Coastal Plain Quaternary mollusks using 87Sr/ 86Sr analyses: Evaluation of kinetic models and estimation of regional Late Pleistocene temperature history

    USGS Publications Warehouse

    Wehmiller, J. F.; Harris, W.B.; Boutin, B.S.; Farrell, K.M.

    2012-01-01

    The use of amino acid racemization (AAR) for estimating ages of Quaternary fossils usually requires a combination of kinetic and effective temperature modeling or independent age calibration of analyzed samples. Because of limited availability of calibration samples, age estimates are often based on model extrapolations from single calibration points over wide ranges of D/L values. Here we present paired AAR and 87Sr/ 86Sr results for Pleistocene mollusks from the North Carolina Coastal Plain, USA. 87Sr/ 86Sr age estimates, derived from the lookup table of McArthur et al. [McArthur, J.M., Howarth, R.J., Bailey, T.R., 2001. Strontium isotopic stratigraphy: LOWESS version 3: best fit to the marine Sr-isotopic curve for 0-509 Ma and accompanying Look-up table for deriving numerical age. Journal of Geology 109, 155-169], provide independent age calibration over the full range of amino acid D/L values, thereby allowing comparisons of alternative kinetic models for seven amino acids. The often-used parabolic kinetic model is found to be insufficient to explain the pattern of racemization, although the kinetic pathways for valine racemization and isoleucine epimerization can be closely approximated with this function. Logarithmic and power law regressions more accurately represent the racemization pathways for all amino acids. The reliability of a non-linear model for leucine racemization, developed and refined over the past 20 years, is confirmed by the 87Sr/ 86Sr age results. This age model indicates that the subsurface record (up to 80m thick) of the North Carolina Coastal Plain spans the entire Quaternary, back to ???2.5Ma. The calibrated kinetics derived from this age model yield an estimate of the effective temperature for the study region of 11??2??C., from which we estimate full glacial (Last Glacial Maximum - LGM) temperatures for the region on the order of 7-10??C cooler than present. These temperatures compare favorably with independent paleoclimate information

  14. LDEF Satellite Radiation Analyses

    NASA Technical Reports Server (NTRS)

    Armstrong, T. W.; Colborn, B. L.

    1996-01-01

    Model calculations and analyses have been carried out to compare with several sets of data (dose, induced radioactivity in various experiment samples and spacecraft components, fission foil measurements, and LET spectra) from passive radiation dosimetry on the Long Duration Exposure Facility (LDEF) satellite, which was recovered after almost six years in space. The calculations and data comparisons are used to estimate the accuracy of current models and methods for predicting the ionizing radiation environment in low earth orbit. The emphasis is on checking the accuracy of trapped proton flux and anisotropy models.

  15. Quantitative analyses of the bacterial microbiota of rearing environment, tilapia and common carp cultured in earthen ponds and inhibitory activity of its lactic acid bacteria on fish spoilage and pathogenic bacteria.

    PubMed

    Kaktcham, Pierre Marie; Temgoua, Jules-Bocamdé; Ngoufack Zambou, François; Diaz-Ruiz, Gloria; Wacher, Carmen; Pérez-Chabela, María de Lourdes

    2017-02-01

    The present study aimed to evaluate the bacterial load of water, Nile Tilapia and common Carp intestines from earthen ponds, isolate lactic acid bacteria (LAB) and assess their antimicrobial activity against fish spoilage and pathogenic bacteria. Following enumeration and isolation of microorganisms the antimicrobial activity of the LAB isolates was evaluated. Taxonomic identification of selected antagonistic LAB strains was assessed, followed by partial characterisation of their antimicrobial metabolites. Results showed that high counts (>4 log c.f.u ml(-1) or 8 log c.f.u g(-1)) of total aerobic bacteria were recorded in pond waters and fish intestines. The microbiota were also found to be dominated by Salmonella spp., Vibrio spp., Staphylococcus spp. and Escherichia coli. LAB isolates (5.60%) exhibited potent direct and extracellular antimicrobial activity against the host-derived and non host-derived spoilage and pathogenic bacteria. These antagonistic isolates were identified and Lactococcus lactis subsp. lactis was found as the predominant (42.85%) specie. The strains displayed the ability to produce lactic, acetic, butyric, propionic and valeric acids. Bacteriocin-like inhibitory substances with activity against Gram-positive and Gram-negative (Vibrio spp. and Pseudomonas aeruginosa) bacteria were produced by three L. lactis subsp. lactis strains. In this study, the LAB from the microbiota of fish and pond water showed potent antimicrobial activity against fish spoilage or pathogenic bacteria from the same host or ecological niche. The studied Cameroonian aquatic niche is an ideal source of antagonistic LAB that could be appropriate as new fish biopreservatives or disease control agents in aquaculture under tropical conditions in particular or worldwide in general.

  16. EEG analyses with SOBI.

    SciTech Connect

    Glickman, Matthew R.; Tang, Akaysha

    2009-02-01

    The motivating vision behind Sandia's MENTOR/PAL LDRD project has been that of systems which use real-time psychophysiological data to support and enhance human performance, both individually and of groups. Relevant and significant psychophysiological data being a necessary prerequisite to such systems, this LDRD has focused on identifying and refining such signals. The project has focused in particular on EEG (electroencephalogram) data as a promising candidate signal because it (potentially) provides a broad window on brain activity with relatively low cost and logistical constraints. We report here on two analyses performed on EEG data collected in this project using the SOBI (Second Order Blind Identification) algorithm to identify two independent sources of brain activity: one in the frontal lobe and one in the occipital. The first study looks at directional influences between the two components, while the second study looks at inferring gender based upon the frontal component.

  17. Network Class Superposition Analyses

    PubMed Central

    Pearson, Carl A. B.; Zeng, Chen; Simha, Rahul

    2013-01-01

    Networks are often used to understand a whole system by modeling the interactions among its pieces. Examples include biomolecules in a cell interacting to provide some primary function, or species in an environment forming a stable community. However, these interactions are often unknown; instead, the pieces' dynamic states are known, and network structure must be inferred. Because observed function may be explained by many different networks (e.g., for the yeast cell cycle process [1]), considering dynamics beyond this primary function means picking a single network or suitable sample: measuring over all networks exhibiting the primary function is computationally infeasible. We circumvent that obstacle by calculating the network class ensemble. We represent the ensemble by a stochastic matrix , which is a transition-by-transition superposition of the system dynamics for each member of the class. We present concrete results for derived from Boolean time series dynamics on networks obeying the Strong Inhibition rule, by applying to several traditional questions about network dynamics. We show that the distribution of the number of point attractors can be accurately estimated with . We show how to generate Derrida plots based on . We show that -based Shannon entropy outperforms other methods at selecting experiments to further narrow the network structure. We also outline an experimental test of predictions based on . We motivate all of these results in terms of a popular molecular biology Boolean network model for the yeast cell cycle, but the methods and analyses we introduce are general. We conclude with open questions for , for example, application to other models, computational considerations when scaling up to larger systems, and other potential analyses. PMID:23565141

  18. Network class superposition analyses.

    PubMed

    Pearson, Carl A B; Zeng, Chen; Simha, Rahul

    2013-01-01

    Networks are often used to understand a whole system by modeling the interactions among its pieces. Examples include biomolecules in a cell interacting to provide some primary function, or species in an environment forming a stable community. However, these interactions are often unknown; instead, the pieces' dynamic states are known, and network structure must be inferred. Because observed function may be explained by many different networks (e.g., ≈ 10(30) for the yeast cell cycle process), considering dynamics beyond this primary function means picking a single network or suitable sample: measuring over all networks exhibiting the primary function is computationally infeasible. We circumvent that obstacle by calculating the network class ensemble. We represent the ensemble by a stochastic matrix T, which is a transition-by-transition superposition of the system dynamics for each member of the class. We present concrete results for T derived from boolean time series dynamics on networks obeying the Strong Inhibition rule, by applying T to several traditional questions about network dynamics. We show that the distribution of the number of point attractors can be accurately estimated with T. We show how to generate Derrida plots based on T. We show that T-based Shannon entropy outperforms other methods at selecting experiments to further narrow the network structure. We also outline an experimental test of predictions based on T. We motivate all of these results in terms of a popular molecular biology boolean network model for the yeast cell cycle, but the methods and analyses we introduce are general. We conclude with open questions for T, for example, application to other models, computational considerations when scaling up to larger systems, and other potential analyses.

  19. Plasma phospholipid fatty acids and CHD in older men: Whitehall study of London civil servants.

    PubMed

    Clarke, Robert; Shipley, Martin; Armitage, Jane; Collins, Rory; Harris, William

    2009-07-01

    Dietary fatty acids (FA) are the major determinants of blood lipids, and measurements of plasma phospholipid FA (PL-FA) composition that reflect the dietary intake of FA may provide insights into the relationships between diet and CHD. We assessed CHD mortality associations with PL-FA (SFA, PUFA and MUFA) levels measured in a nested case-control study of 116 cases of CHD death and 239 controls that were frequency-matched for age and employment grade. The participants had plasma levels of total cholesterol, LDL-cholesterol (LDL-C), HDL-cholesterol, apo B and apo A1, C-reactive protein (CRP) and fibrinogen recorded. SFA levels were significantly positively correlated with total cholesterol, LDL-C, apo B, CRP protein and fibrinogen. By contrast, phospholipid-PUFA were inversely associated with CRP, but not with any of the lipids. A higher SFA content (top v. bottom quarter) was associated with a 2-fold higher risk of CHD (OR and 95 % CI: OR 2.12; 95 % CI: 1.13, 3.99), and an equivalent difference in PUFA was associated with a halving in CHD risk (OR 0.49; 95 % CI: 0.26, 0.94), but MUFA was unrelated to CHD risk. These associations were substantially attenuated, after additional adjustment for lipids and inflammatory markers. Higher levels of saturated fat and lower levels of polyunsaturated fats were each associated with a higher risk of CHD in elderly men, and these associations were partly explained by their effects on blood lipids and biomarkers of inflammation.

  20. Synthesis, structural investigation and thermal analyses of a novel coordination compound [Cd(DAT) 6](HTNR) 2·3.5H 2O (DAT = 1,5-diaminotetrazole, H 2TNR = styphnic acid)

    NASA Astrophysics Data System (ADS)

    Cui, Yan; Zhang, Tong-Lai; Zhang, Jian-Guo; Yang, Li; Hu, Xiao-Chun; Zhang, Jin

    2008-10-01

    A novel coordination compound [Cd(DAT) 6](HTNR) 2·3.5H 2O has been synthesized by using 1,5-diaminotetrazole (DAT) as ligand and characterized by applying X-ray single crystal diffraction, elemental analysis and FT-IR spectroscopy. The central cadmium (II) cation is coordinated by six N atoms of six DAT ligand molecules to form a six-coordinated and slightly distorted octahedral structure. With the extensive intermolecular hydrogen bonds, molecular units of [Cd(DAT) 6](HTNR) 2·3.5H 2O are linked together to form a 3D net structure with pore canals. Mulliken charge distribution of DAT in bulk state has been obtained from the density functional theory (DFT) with the B3LYP method employing the 6-31G ∗∗ basis sets to interpret the reason why the coordination site of DAT is N(4) atom of the tetrazole ring. Thermal decomposition mechanism of the title compound was predicted based on DSC, TG-DTG and FT-IR analyses results. The kinetic parameters of the first exothermic process of the title compound were studied by applying the Kissinger's and Ozawa-Doyle's methods.

  1. Performance analyses of a pH-shift and DOT-shift integrated fed-batch fermentation process for the production of ganoderic acid and Ganoderma polysaccharides by medicinal mushroom Ganoderma lucidum.

    PubMed

    Tang, Ya-Jie; Zhang, Wei; Zhong, Jian-Jiang

    2009-03-01

    Investigations on Ganoderma lucidum fermentation suggested that the responses of the cell growth and metabolites biosynthesis to pH and dissolved oxygen tension (DOT) were different. The ganoderic acid (GA) production of 321.6 mg/L was obtained in the pH-shift culture by combining a 4-day culture at pH 3.0 with the following 6-day culture at pH 4.5, which was higher by 45% and 300% compared with the culture at pH 3.0 and 4.5, respectively. The GA production of 487.1mg/L was achieved in the DOT-shift culture by combining a 6-day culture at 25% of DOT with a following 6-day culture at 10% of DOT, which was higher by 43% and 230% compared with the culture at 25% and 10% of DOT, respectively. A fed-batch fermentation process by combining the above-mentioned pH-shift and DOT-shift strategies resulted in a significant synergistic enhancement of GA accumulation up to 754.6 mg/L, which is the highest reported in the submerged fermentation of G. lucidum in stirred-tank bioreactor.

  2. An application of target profiling analyses in the hepatotoxicity assessment of herbal medicines: comparative characteristic fingerprint and bile acid profiling of Senecio vulgaris L. and Senecio scandens Buch.-Ham.

    PubMed

    Xiong, Aizhen; Fang, Lianxiang; Yang, Xiao; Yang, Fan; Qi, Meng; Kang, Hong; Yang, Li; Tsim, Karl Wah-Keung; Wang, Zhengtao

    2014-11-01

    The toxicity assessment of herbal medicines is important for human health and appropriate utilization of these medicines. However, challenges have to be overcome because of the complexity of coexisting multiple components in herbal medicines and the highly interconnected organismal system. In this study, a target profiling approach was established by combining the characteristic fingerprint analysis of herbal chemicals with potential toxicity through a precursor ion scan-based mass spectroscopy and the target profiling analysis of biomarkers responsible for the toxicity. Through this newly developed approach, the comparative hepatotoxicity assessment of two herbal medicines from the same genus, Senecio vulgaris L. and Senecio scandens Buch.-Ham, was performed. Significant differences were found between the two species in their chemical markers (i.e., pyrrolizidine alkaloids) and biomarkers (i.e., bile acids) responsible for their toxicities. This result was consistent with the conventional toxicity assessment conducted by histopathological examination and clinical serum index assay on experimental animal models. In conclusion, this study provided a new approach for the hepatotoxicity assessment of herbal medicines containing pyrrolizidine alkaloids, which are widely distributed in various herbal medicines. The target profiling approach may shed light on the toxicity assessment of other herbal medicines with potential toxicity.

  3. Genome-wide analyses of the transcriptomes of salicylic acid-deficient versus wild-type plants uncover Pathogen and Circadian Controlled 1 (PCC1) as a regulator of flowering time in Arabidopsis.

    PubMed

    Segarra, Silvia; Mir, Ricardo; Martínez, Cristina; León, José

    2010-01-01

    Salicylic acid (SA) has been characterized as an activator of pathogen-triggered resistance of plants. SA also regulates developmental processes such as thermogenesis in floral organs and stress-induced flowering. To deepen our knowledge of the mechanism underlying SA regulation of flowering time in Arabidopsis, we compared the transcriptomes of SA-deficient late flowering genotypes with wild-type plants. Down- or up-regulated genes in SA-deficient plants were screened for responsiveness to ultraviolet (UV)-C light, which accelerates flowering in Arabidopsis. Among them, only Pathogen and Circadian Controlled 1 (PCC1) was up-regulated by UV-C light through a SA-dependent process. Moreover, UV-C light-activated expression of PCC1 was also dependent on the flowering activator CONSTANS (CO). PCC1 gene has a circadian-regulated developmental pattern of expression with low transcript levels after germination that increased abruptly by day 10. RNAi plants with very low expression of PCC1 gene were late flowering, defective in UV-C light acceleration of flowering and contained FLOWERING LOCUS T (FT) transcript levels below 5% of that detected in wild-type plants. Although PCC1 seems to function between CO and FT in the photoperiod-dependent flowering pathway, transgenic plants overexpressing a Glucocorticoid Receptor (GR)-fused version of CO strongly activated FT but not PCC1 after dexamethasone treatment.

  4. Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils

    PubMed Central

    Quideau, Sylvie A.; McIntosh, Anne C.S.; Norris, Charlotte E.; Lloret, Emily; Swallow, Mathew J.B.; Hannam, Kirsten

    2016-01-01

    Phospholipid fatty acids (PLFAs) are key components of microbial cell membranes. The analysis of PLFAs extracted from soils can provide information about the overall structure of terrestrial microbial communities. PLFA profiling has been extensively used in a range of ecosystems as a biological index of overall soil quality, and as a quantitative indicator of soil response to land management and other environmental stressors. The standard method presented here outlines four key steps: 1. lipid extraction from soil samples with a single-phase chloroform mixture, 2. fractionation using solid phase extraction columns to isolate phospholipids from other extracted lipids, 3. methanolysis of phospholipids to produce fatty acid methyl esters (FAMEs), and 4. FAME analysis by capillary gas chromatography using a flame ionization detector (GC-FID). Two standards are used, including 1,2-dinonadecanoyl-sn-glycero-3-phosphocholine (PC(19:0/19:0)) to assess the overall recovery of the extraction method, and methyl decanoate (MeC10:0) as an internal standard (ISTD) for the GC analysis. PMID:27685177

  5. The linoleic acid and trans fatty acids of margarines.

    PubMed

    Beare-Rogers, J L; Gray, L M; Hollywood, R

    1979-09-01

    Fifty brands of margarine were analysed for cis-polyunsaturated acids by lipoxidase, for trans fatty acid by infared spectroscopy, and for fatty acid composition by gas-liquid chromatography. High concentrations of trans fatty acids tended to be associated with low concentrations of linoleic acid. Later analyses on eight of the brands, respresenting various proportions of linoleic to trans fatty acids, indicated that two of them contained still higher levels of trans fatty acids (greater than 60%) and negligible amounts of linoleic acid. It is proposed that margarine could be a vehicle for the distribution of some dietary linoleic acid and that the level of linoleic acid and the summation of the saturated plus trans fatty acids be known to ascertain nutritional characteristics.

  6. NOAA's National Snow Analyses

    NASA Astrophysics Data System (ADS)

    Carroll, T. R.; Cline, D. W.; Olheiser, C. M.; Rost, A. A.; Nilsson, A. O.; Fall, G. M.; Li, L.; Bovitz, C. T.

    2005-12-01

    NOAA's National Operational Hydrologic Remote Sensing Center (NOHRSC) routinely ingests all of the electronically available, real-time, ground-based, snow data; airborne snow water equivalent data; satellite areal extent of snow cover information; and numerical weather prediction (NWP) model forcings for the coterminous U.S. The NWP model forcings are physically downscaled from their native 13 km2 spatial resolution to a 1 km2 resolution for the CONUS. The downscaled NWP forcings drive an energy-and-mass-balance snow accumulation and ablation model at a 1 km2 spatial resolution and at a 1 hour temporal resolution for the country. The ground-based, airborne, and satellite snow observations are assimilated into the snow model's simulated state variables using a Newtonian nudging technique. The principle advantages of the assimilation technique are: (1) approximate balance is maintained in the snow model, (2) physical processes are easily accommodated in the model, and (3) asynoptic data are incorporated at the appropriate times. The snow model is reinitialized with the assimilated snow observations to generate a variety of snow products that combine to form NOAA's NOHRSC National Snow Analyses (NSA). The NOHRSC NSA incorporate all of the available information necessary and available to produce a "best estimate" of real-time snow cover conditions at 1 km2 spatial resolution and 1 hour temporal resolution for the country. The NOHRSC NSA consist of a variety of daily, operational, products that characterize real-time snowpack conditions including: snow water equivalent, snow depth, surface and internal snowpack temperatures, surface and blowing snow sublimation, and snowmelt for the CONUS. The products are generated and distributed in a variety of formats including: interactive maps, time-series, alphanumeric products (e.g., mean areal snow water equivalent on a hydrologic basin-by-basin basis), text and map discussions, map animations, and quantitative gridded products

  7. Fate of microbial nitrogen, carbon, hydrolysable amino acids, monosaccharides, and fatty acids in sediment

    NASA Astrophysics Data System (ADS)

    Veuger, Bart; van Oevelen, Dick; Middelburg, Jack J.

    2012-04-01

    The fate of microbial carbon, nitrogen, hydrolysable amino acids (HAAs), monosaccharides, and fatty acids in sediment was investigated experimentally. The microbial community of a tidal flat sediment was labeled with 13C-enriched glucose and 15N-enriched ammonium, and sediment was incubated for up to 371 days. Analysis of total concentrations and 13C- and 15N content of bulk sediment, hydrolysable amino acids (including D-alanine), monosaccharides, total fatty acids (TFAs), and phospholipid-derived fatty acids (PLFAs) allowed us to trace the fate of microbial biomass and -detritus and the major biochemical groups therein (proteins, carbohydrates, and lipids) over intermediate time scales (weeks-months). Moreover, the unidentified fraction of the labeled material (i.e. not analyzed as HAA, FA, or carbohydrate) provided information on the formation and fate of molecularly uncharacterizable organic matter. Loss of 13C and 15N from the sediment was slow (half live of 433 days) which may have been due to the permanently anoxic conditions in the experiment. Loss rates for the different biochemical groups were also low with the following order of loss rate constants: PLFA > TFA > HAA > monosaccharides. The unidentified 13C-pool was rapidly formed (within days) and then decreased relatively slowly, resulting in a gradual relative accumulation of this pool over time. Degradation and microbial reworking of the labeled material resulted in subtle, yet consistent, diagenetic changes within the different biochemical groups. In the HAA pool, glycine, lysine, and proline were lost relatively slowly (i.e. best preserved) while there was no accumulation of D-alanine relative to L-alanine, indicating no relative accumulation of bacterial macromolecules rich in D-alanine. In the fatty acid pool, there was very little difference between PLFAs and TFAs, indicating a very similar lability of these pools. Differences between individual fatty acids included a relatively slow loss of i15

  8. Analyse des hydrocarbures et des acides gras dans les sédiments superficiels prélevés à proximité du rejet des eaux usées de la zone industrielle de la ville d'El Jadida (Côte Atlantique Marocaine)

    NASA Astrophysics Data System (ADS)

    Lançar, I. T.; Bouchry, N.; Tabyaoui, B.; Mille, G.; Doumenq, P.

    1999-03-01

    Marine sediments collected near the El Jadida industrial sewage (Moroccan Atlantic Coastal) have been analysed in order to determine and to compare the amounts of : extractable organic matter, saturated and aromatic hydrocarbons and fatty acids. The quantitative and qualitative analysis of hydrocarbons (saturated and aromatics) is useful to know the origine of these compounds. Generally, petroleum hydrocarbons are predominant, but biogenic hydrocarbons are also present. The analysis are conducted by capillary gas chromatography, capillary gas chromatography/mass spectrometry and U.V. fluorescence (synchronous excitation) methods. Des sédiments marins prélevés sur le littoral d'El Jadida, à proximité d'une zone de rejet industriel, ont été analysés afin de déterminer et de comparer le taux de matière organique extractible, d'hydrocarbures saturés et aromatiques et d'acides gras. Les résultats des études qualitatives et quantitatives des hydrocarbures (saturés et aromatiques) permettent de déterminer l'origine des hydrocarbures présents dans les sédiments. Les hydrocarbures d'origine pétrolière sont généralement prédominants. Les analyses sont réalisées par chromatographie en phase gazeuse, par couplage chromatographie en phase gazeuse-spectrométrie de masse et par fluorescence U.V. (technique d'excitation -émission synchrones).

  9. EEO Implications of Job Analyses.

    ERIC Educational Resources Information Center

    Lacy, D. Patrick, Jr.

    1979-01-01

    Discusses job analyses as they relate to the requirements of Title VII of the Civil Rights Act of 1964, the Equal Pay Act of 1963, and the Rehabilitation Act of 1973. Argues that job analyses can establish the job-relatedness of entrance requirements and aid in defenses against charges of discrimination. Journal availability: see EA 511 615.

  10. Analysing the ventricular fibrillation waveform.

    PubMed

    Reed, Matthew J; Clegg, Gareth R; Robertson, Colin E

    2003-04-01

    The surface electrocardiogram associated with ventricular fibrillation has been of interest to researchers for some time. Over the last few decades, techniques have been developed to analyse this signal in an attempt to obtain more information about the state of the myocardium and the chances of successful defibrillation. This review looks at the implications of analysing the VF waveform and discusses the various techniques that have been used, including fast Fourier transform analysis, wavelet transform analysis and mathematical techniques such as chaos theory.

  11. EPOXI Trajectory and Maneuver Analyses

    NASA Technical Reports Server (NTRS)

    Chung, Min-Kun J.; Bhaskaran, Shyamkumar; Chesley, Steven R.; Halsell, C. Allen; Helfrich, Clifford E.; Jefferson, David C.; McElrath, Timothy P.; Rush, Brian P.; Wang, Tseng-Chan M.; Yen, Chen-wan L.

    2011-01-01

    The EPOXI mission is a NASA Discovery Mission of Opportunity combining two separate investigations: Extrasolar Planet Observation and Characterization (EPOCh) and Deep Impact eXtended Investigation (DIXI). Both investigations reused the DI instruments and spacecraft that successfully flew by the comet Tempel-1 (4 July 2005). For EPOCh, the goal was to find exoplanets with the high resolution imager, while for DIXI it was to fly by the comet Hartley 2 (4 Nov 2010). This paper documents the navigation experience of the earlier ma-neuver analyses critical for the EPOXI mission including statistical ?V analyses and other useful analyses in designing maneuvers. It also recounts the trajectory design leading up to the final reference trajectory to Hartley 2.

  12. Feed analyses and their interpretation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Compositional analysis is central to determining the nutritional value of feedstuffs. The utility of the values and how they should be used depends on how representative the feed subsample is, the nutritional relevance of the assays, analytical variability of the analyses, and whether a feed is suit...

  13. Analysing Children's Drawings: Applied Imagination

    ERIC Educational Resources Information Center

    Bland, Derek

    2012-01-01

    This article centres on a research project in which freehand drawings provided a richly creative and colourful data source of children's imagined, ideal learning environments. Issues concerning the analysis of the visual data are discussed, in particular, how imaginative content was analysed and how the analytical process was dependent on an…

  14. Cyanide analyses for risk and treatability assessments

    SciTech Connect

    MacFarlane, I.D.; Elseroad, H.J.; Pergrin, D.E.; Logan, C.M.

    1994-12-31

    Cyanide, an EPA priority pollutant and target analyte, is typically measured as total. However, cyanide complexation, information which is not acquired through total cyanide analysis, is often a driver of cyanide toxicity and treatability. A case study of a former manufacture gas plant (MGP) is used to demonstrate the usability of various cyanide analytical methods for risk and treatability assessments. Several analytical methods, including cyanide amenable to chlorination and weak acid dissociable cyanide help test the degree of cyanide complexation. Generally, free or uncomplexed cyanide is more biologically available, toxic, and reactive than complexed cyanide. Extensive site testing has shown that free and weakly dissociable cyanide composes only a small fraction of total cyanide as would be expected from the literature, and that risk assessment will be more realistic considering cyanide form. Likewise, aqueous treatment for cyanide can be properly tested if cyanide form is accounted for. Weak acid dissociable cyanide analyses proved to be the most reliable (and potentially acceptable) cyanide method, as well as represent the most toxic and reactive cyanide forms.

  15. Workload analyse of assembling process

    NASA Astrophysics Data System (ADS)

    Ghenghea, L. D.

    2015-11-01

    The workload is the most important indicator for managers responsible of industrial technological processes no matter if these are automated, mechanized or simply manual in each case, machines or workers will be in the focus of workload measurements. The paper deals with workload analyses made to a most part manual assembling technology for roller bearings assembling process, executed in a big company, with integrated bearings manufacturing processes. In this analyses the delay sample technique have been used to identify and divide all bearing assemblers activities, to get information about time parts from 480 minutes day work time that workers allow to each activity. The developed study shows some ways to increase the process productivity without supplementary investments and also indicated the process automation could be the solution to gain maximum productivity.

  16. Nonlinear structural crash dynamics analyses

    NASA Technical Reports Server (NTRS)

    Hayduk, R. J.; Thomson, R. G.; Wittlin, G.; Kamat, M. P.

    1979-01-01

    Presented in this paper are the results of three nonlinear computer programs, KRASH, ACTION and DYCAST used to analyze the dynamic response of a twin-engine, low-wing airplane section subjected to a 8.38 m/s (27.5 ft/s) vertical impact velocity crash condition. This impact condition simulates the vertical sink rate in a shallow aircraft landing or takeoff accident. The three distinct analysis techniques for nonlinear dynamic response of aircraft structures are briefly examined and compared versus each other and the experimental data. The report contains brief descriptions of the three computer programs, the respective aircraft section mathematical models, pertinent data from the experimental test performed at NASA Langley, and a comparison of the analyses versus test results. Cost and accuracy comparisons between the three analyses are made to illustrate the possible uses of the different nonlinear programs and their future potential.

  17. Supplementary report on antilock analyses

    NASA Technical Reports Server (NTRS)

    Zellner, J. W.

    1985-01-01

    Generic modulator analysis was performed to quantify the effects of dump and reapply pressure rates on antilock stability and performance. Analysis will include dump and reapply rates, and lumped modulator delay. Based on the results of the generic modulator analysis and earlier toggle optimization analysis (with Mitsubishi modulator), a recommended preliminary antilock design was synthesized and its response and performance simulated. The results of these analyses are documented.

  18. Analysing photonic structures in plants

    PubMed Central

    Vignolini, Silvia; Moyroud, Edwige; Glover, Beverley J.; Steiner, Ullrich

    2013-01-01

    The outer layers of a range of plant tissues, including flower petals, leaves and fruits, exhibit an intriguing variation of microscopic structures. Some of these structures include ordered periodic multilayers and diffraction gratings that give rise to interesting optical appearances. The colour arising from such structures is generally brighter than pigment-based colour. Here, we describe the main types of photonic structures found in plants and discuss the experimental approaches that can be used to analyse them. These experimental approaches allow identification of the physical mechanisms producing structural colours with a high degree of confidence. PMID:23883949

  19. Laser power beaming system analyses

    NASA Technical Reports Server (NTRS)

    Zeiders, Glenn W., Jr.

    1993-01-01

    The successful demonstration of the PAMELA adaptive optics hardware and the fabrication of the BTOS truss structure were identified by the program office as the two most critical elements of the NASA power beaming program, so it was these that received attention during this program. Much of the effort was expended in direct program support at MSFC, but detailed technical analyses of the AMP deterministic control scheme and the BTOS truss structure (both the JPL design and a spherical one) were prepared and are attached, and recommendations are given.

  20. Summary of LDEF battery analyses

    NASA Technical Reports Server (NTRS)

    Johnson, Chris; Thaller, Larry; Bittner, Harlin; Deligiannis, Frank; Tiller, Smith; Sullivan, David; Bene, James

    1992-01-01

    Tests and analyses of NiCd, LiSO2, and LiCf batteries flown on the Long Duration Exposure Facility (LDEF) includes results from NASA, Aerospace, and commercial labs. The LiSO2 cells illustrate six-year degradation of internal components acceptable for space applications, with up to 85 percent battery capacity remaining on discharge of some returned cells. LiCf batteries completed their mission, but lost any remaining capacity due to internal degradation. Returned NiCd batteries tested an GSFC showed slight case distortion due to pressure build up, but were functioning as designed.

  1. Analysing photonic structures in plants.

    PubMed

    Vignolini, Silvia; Moyroud, Edwige; Glover, Beverley J; Steiner, Ullrich

    2013-10-06

    The outer layers of a range of plant tissues, including flower petals, leaves and fruits, exhibit an intriguing variation of microscopic structures. Some of these structures include ordered periodic multilayers and diffraction gratings that give rise to interesting optical appearances. The colour arising from such structures is generally brighter than pigment-based colour. Here, we describe the main types of photonic structures found in plants and discuss the experimental approaches that can be used to analyse them. These experimental approaches allow identification of the physical mechanisms producing structural colours with a high degree of confidence.

  2. Aspartic acid

    MedlinePlus

    ... also called asparaginic acid. Aspartic acid helps every cell in the body work. It plays a role in: Hormone production and release Normal nervous system function Plant sources of aspartic acid include: Legumes such as ...

  3. Folic Acid

    MedlinePlus

    Folic acid is a B vitamin. It helps the body make healthy new cells. Everyone needs folic acid. For women who may get pregnant, it is really important. Getting enough folic acid before and during pregnancy can prevent major birth ...

  4. Folic Acid

    MedlinePlus

    Folic acid is used to treat or prevent folic acid deficiency. It is a B-complex vitamin needed by ... Folic acid comes in tablets. It usually is taken once a day. Follow the directions on your prescription label ...

  5. THOR Turbulence Electron Analyser: TEA

    NASA Astrophysics Data System (ADS)

    Fazakerley, Andrew; Moore, Tom; Owen, Chris; Pollock, Craig; Wicks, Rob; Samara, Marilia; Rae, Jonny; Hancock, Barry; Kataria, Dhiren; Rust, Duncan

    2016-04-01

    Turbulence Heating ObserveR (THOR) is the first mission ever flown in space dedicated to plasma turbulence. The Turbulence Electron Analyser (TEA) will measure the plasma electron populations in the mission's Regions of Interest. It will collect a 3D electron velocity distribution with cadences as short as 5 ms. The instrument will be capable of measuring energies up to 30 keV. TEA consists of multiple electrostatic analyser heads arranged so as to measure electrons arriving from look directions covering the full sky, i.e. 4 pi solid angle. The baseline concept is similar to the successful FPI-DES instrument currently operating on the MMS mission. TEA is intended to have a similar angular resolution, but a larger geometric factor. In comparison to earlier missions, TEA improves on the measurement cadence. For example, MMS FPI-DES routinely operates at 30 ms cadence. The objective of measuring distributions at rates as fast as 5 ms is driven by the mission's scientific requirements to resolve electron gyroscale size structures, where plasma heating and fluctuation dissipation is predicted to occur. TEA will therefore be capable of making measurements of the evolution of distribution functions across thin (a few km) current sheets travelling past the spacecraft at up to 600 km/s, of the Power Spectral Density of fluctuations of electron moments and of distributions fast enough to match frequencies with waves expected to be dissipating turbulence (e.g. with 100 Hz whistler waves).

  6. Isotope analyses of fossil small mammals in karstic sites

    NASA Astrophysics Data System (ADS)

    Garcia Alix, Antonio; Delgado Huertas, Antonio

    2016-04-01

    Fossil skeletal accumulations in kartstic complexes, such as caves, are quite common, especially during the Pliocene and Quaternary. These fossil assemblages are sometimes difficult to study, as specimens from different ages can be found together (time averaging). The traditional approach to study this kind of paleontological sites was taphonomic (understanding the origin and other factors affecting the bone accumulation) and/or taxonomic (systematic description of the remains). However, other kinds of analyses, such as biogeochemical techniques to reconstruct past diets and environments, are being more frequently used. Small-mammals have a wide geographical distribution, and their remains (bones and teeth) are extensively represented in the fossil record; therefore, isotopic analyses in fossil small-mammals are a powerful tool to reconstruct paleoenvironments. Field samples for small-mammal studies yield large amounts of sediment-residues that need to be reduced in the laboratory (usually by means of diluted hydrochloric or acetic acid). Therefore, samples of fossil small-mammal for isotopic analyses usually receive two different acid treatments: one to reduce the carbonate residue of the sediment, and afterwards another one to remove digenetic carbonates from the ground sample. Those treatments, along with the small size of the remains, may increase the probability of chemical fractionation during those pre-treatment stages. Those acid treatments are even more aggressive in kasrtic fossil localities, as limestone has to be dissolved to extract the small mammal remains. In this abstract, we present the results of two different treatments carried out in limestone from the Pliocene karstic locality of Moreda (Guadix Basin, Spain) and a control sample. One batch of samples were treated with a solution of 1M acetic acid-acetate calcium buffer (ph 4,5), and the rest with diluted acetic acid (at 15% concentration, Ph 2,2), which is the most used to reduce the sediments

  7. [Effects of different tillage methods on phospholipid fatty acids and enzyme activities in calcareous cinnamon soil].

    PubMed

    Pei, Xue-Xia; Dang, Jian-You; Zhang, Ding-Yi; Wang, Jiao-Ai; Zhang, Jing

    2014-08-01

    In order to study changes of physical and chemical characteristics and microbial activities in soil under different tillage methods, effects of four tillage methods, rotary tillage (RT), subsoil tillage (ST), conventional tillage (CT) with corn straw returned to soil, and rotary tillage with no corn straw returned to soil (CK), on phospholipid fatty acids (PLFA) characteristics and hydrolase enzymes activities in calcareous cinnamon soil were investigated. The results showed that soil hydrolase enzymes activities, nutrient contents, microbial diversity varied greatly with the different tillage methods. Returning corn straw to soil increased the kinds, amount of soil total PLFAs, bacteria PLFAs and actonomycetes PLFAs, while decreased the fungi PLFAs, indicating that fungi was more adaptable than bacteria to an infertile environment. ST and CT resulted in higher amounts of total PLFAs, which were 74.7% and 53.3% higher than that of CK, indicating they were more beneficial to the growth of plants. They could also improve soil physical and chemical properties, increase alk-phosphatase, protease and urease activities, which would provide a favorable soil condition for high and stable crop yields.

  8. Perturbation analyses of intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Koyama, Yohei M.; Kobayashi, Tetsuya J.; Ueda, Hiroki R.

    2011-08-01

    Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the

  9. Analyses to improve operational flexibility

    SciTech Connect

    Trikouros, N.G.

    1986-01-01

    Operational flexibility is greatly enhanced if the technical bases for plant limits and design margins are fully understood, and the analyses necessary to evaluate the effect of plant modifications or changes in operating modes on these parameters can be performed as required. If a condition should arise that might jeopardize a plant limit or reduce operational flexibility, it would be necessary to understand the basis for the limit or the specific condition limiting operational flexibility and be capable of performing a reanalysis to either demonstrate that the limit will not be violated or to change the limit. This paper provides examples of GPU Nuclear efforts in this regard. Examples of Oyster Creek and Three Mile Island operating experiences are discussed.

  10. Uncertainty and Sensitivity Analyses Plan

    SciTech Connect

    Simpson, J.C.; Ramsdell, J.V. Jr.

    1993-04-01

    Hanford Environmental Dose Reconstruction (HEDR) Project staff are developing mathematical models to be used to estimate the radiation dose that individuals may have received as a result of emissions since 1944 from the US Department of Energy's (DOE) Hanford Site near Richland, Washington. An uncertainty and sensitivity analyses plan is essential to understand and interpret the predictions from these mathematical models. This is especially true in the case of the HEDR models where the values of many parameters are unknown. This plan gives a thorough documentation of the uncertainty and hierarchical sensitivity analysis methods recommended for use on all HEDR mathematical models. The documentation includes both technical definitions and examples. In addition, an extensive demonstration of the uncertainty and sensitivity analysis process is provided using actual results from the Hanford Environmental Dose Reconstruction Integrated Codes (HEDRIC). This demonstration shows how the approaches used in the recommended plan can be adapted for all dose predictions in the HEDR Project.

  11. Chemical analyses of provided samples

    NASA Technical Reports Server (NTRS)

    Becker, Christopher H.

    1993-01-01

    Two batches of samples were received and chemical analysis was performed of the surface and near surface regions of the samples by the surface analysis by laser ionization (SALI) method. The samples included four one-inch optics and several paint samples. The analyses emphasized surface contamination or modification. In these studies, pulsed sputtering by 7 keV Ar+ and primarily single-photon ionization (SPI) by coherent 118 nm radiation (at approximately 5 x 10(exp 5) W/cm(sup 2) were used. For two of the samples, also multiphoton ionization (MPI) at 266 nm (approximately 5 x 10(exp 11) W/cm(sup 2) was used. Most notable among the results was the silicone contamination on Mg2 mirror 28-92, and that the Long Duration Exposure Facility (LDEF) paint sample had been enriched in K and Na and depleted in Zn, Si, B, and organic compounds relative to the control paint.

  12. Geomorphic analyses from space imagery

    NASA Technical Reports Server (NTRS)

    Morisawa, M.

    1985-01-01

    One of the most obvious applications of space imagery to geomorphological analyses is in the study of drainage patterns and channel networks. LANDSAT, high altitude photography and other types of remote sensing imagery are excellent for depicting stream networks on a regional scale because of their broad coverage in a single image. They offer a valuable tool for comparing and analyzing drainage patterns and channel networks all over the world. Three aspects considered in this geomorphological study are: (1) the origin, evolution and rates of development of drainage systems; (2) the topological studies of network and channel arrangements; and (3) the adjustment of streams to tectonic events and geologic structure (i.e., the mode and rate of adjustment).

  13. Genetic Analyses of Integrin Signaling

    PubMed Central

    Wickström, Sara A.; Radovanac, Korana; Fässler, Reinhard

    2011-01-01

    The development of multicellular organisms, as well as maintenance of organ architecture and function, requires robust regulation of cell fates. This is in part achieved by conserved signaling pathways through which cells process extracellular information and translate this information into changes in proliferation, differentiation, migration, and cell shape. Gene deletion studies in higher eukaryotes have assigned critical roles for components of the extracellular matrix (ECM) and their cellular receptors in a vast number of developmental processes, indicating that a large proportion of this signaling is regulated by cell-ECM interactions. In addition, genetic alterations in components of this signaling axis play causative roles in several human diseases. This review will discuss what genetic analyses in mice and lower organisms have taught us about adhesion signaling in development and disease. PMID:21421914

  14. Isotopic signatures by bulk analyses

    SciTech Connect

    Efurd, D.W.; Rokop, D.J.

    1997-12-01

    Los Alamos National Laboratory has developed a series of measurement techniques for identification of nuclear signatures by analyzing bulk samples. Two specific applications for isotopic fingerprinting to identify the origin of anthropogenic radioactivity in bulk samples are presented. The first example is the analyses of environmental samples collected in the US Arctic to determine the impact of dumping of radionuclides in this polar region. Analyses of sediment and biota samples indicate that for the areas sampled the anthropogenic radionuclide content of sediments was predominantly the result of the deposition of global fallout. The anthropogenic radionuclide concentrations in fish, birds and mammals were very low. It can be surmised that marine food chains are presently not significantly affected. The second example is isotopic fingerprinting of water and sediment samples from the Rocky Flats Facility (RFP). The largest source of anthropogenic radioactivity presently affecting surface-waters at RFP is the sediments that are currently residing in the holding ponds. One gram of sediment from a holding pond contains approximately 50 times more plutonium than 1 liter of water from the pond. Essentially 100% of the uranium in Ponds A-1 and A-2 originated as depleted uranium. The largest source of radioactivity in the terminal Ponds A-4, B-5 and C-2 was naturally occurring uranium and its decay product radium. The uranium concentrations in the waters collected from the terminal ponds contained 0.05% or less of the interim standard calculated derived concentration guide for uranium in waters available to the public. All of the radioactivity observed in soil, sediment and water samples collected at RFP was naturally occurring, the result of processes at RFP or the result of global fallout. No extraneous anthropogenic alpha, beta or gamma activities were detected. The plutonium concentrations in Pond C-2 appear to vary seasonally.

  15. Acid Rain

    USGS Publications Warehouse

    Bricker, Owen P.; Rice, Karen C.

    1995-01-01

    Although acid rain is fading as a political issue in the United States and funds for research in this area have largely disappeared, the acidity of rain in the Eastern United States has not changed significantly over the last decade, and it continues to be a serious environmental problem. Acid deposition (commonly called acid rain) is a term applied to all forms of atmospheric deposition of acidic substances - rain, snow, fog, acidic dry particulates, aerosols, and acid-forming gases. Water in the atmosphere reacts with certain atmospheric gases to become acidic. For example, water reacts with carbon dioxide in the atmosphere to produce a solution with a pH of about 5.6. Gases that produce acids in the presence of water in the atmosphere include carbon dioxide (which converts to carbonic acid), oxides of sulfur and nitrogen (which convert to sulfuric and nitric acids}, and hydrogen chloride (which converts to hydrochloric acid). These acid-producing gases are released to the atmosphere through natural processes, such as volcanic emissions, lightning, forest fires, and decay of organic matter. Accordingly, precipitation is slightly acidic, with a pH of 5.0 to 5.7 even in undeveloped areas. In industrialized areas, most of the acid-producing gases are released to the atmosphere from burning fossil fuels. Major emitters of acid-producing gases include power plants, industrial operations, and motor vehicles. Acid-producing gases can be transported through the atmosphere for hundreds of miles before being converted to acids and deposited as acid rain. Because acids tend to build up in the atmosphere between storms, the most acidic rain falls at the beginning of a storm, and as the rain continues, the acids "wash out" of the atmosphere.

  16. Acid Rain.

    ERIC Educational Resources Information Center

    Openshaw, Peter

    1987-01-01

    Provides some background information on acid deposition. Includes a historical perspective, describes some effects of acid precipitation, and discusses acid rain in the United Kingdom. Contains several experiments that deal with the effects of acid rain on water quality and soil. (TW)

  17. Genetic analyses of captive Alala (Corvus hawaiiensis) using AFLP analyses

    USGS Publications Warehouse

    Jarvi, Susan I.; Bianchi, Kiara R.

    2006-01-01

    affected by the mutation rate at microsatellite loci, thus introducing a bias. Also, the number of loci that can be studied is frequently limited to fewer than 10. This theoretically represents a maximum of one marker for each of 10 chromosomes. Dominant markers like AFLP allow a larger fraction of the genome to be screened. Large numbers of loci can be screened by AFLP to resolve very small individual differences that can be used for identification of individuals, estimates of pairwise relatedness and, in some cases, for parentage analyses. Since AFLP is a dominant marker (can not distinguish between +/+ homozygote versus +/- heterozygote), it has limitations for parentage analyses. Only when both parents are homozygous for the absence of alleles (-/-) and offspring show a presence (+/+ or +/-) can the parents be excluded. In this case, microsatellites become preferable as they have the potential to exclude individual parents when the other parent is unknown. Another limitation of AFLP is that the loci are generally less polymorphic (only two alleles/locus) than microsatellite loci (often >10 alleles/locus). While generally fewer than 10 highly polymorphic microsatellite loci are enough to exclude and assign parentage, it might require up to 100 or more AFLP loci. While there are pros and cons to different methodologies, the total number of loci evaluated by AFLP generally offsets the limitations imposed due to the dominant nature of this approach and end results between methods are generally comparable. Overall objectives of this study were to evaluate the level of genetic diversity in the captive population of Alala, to compare genetic data with currently available pedigree information, and to determine the extent of relatedness of mating pairs and among founding individuals.

  18. 10 CFR 436.24 - Uncertainty analyses.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 3 2012-01-01 2012-01-01 false Uncertainty analyses. 436.24 Section 436.24 Energy... Procedures for Life Cycle Cost Analyses § 436.24 Uncertainty analyses. If particular items of cost data or... by conducting additional analyses using any standard engineering economics method such as...

  19. 10 CFR 436.24 - Uncertainty analyses.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 3 2014-01-01 2014-01-01 false Uncertainty analyses. 436.24 Section 436.24 Energy... Procedures for Life Cycle Cost Analyses § 436.24 Uncertainty analyses. If particular items of cost data or... by conducting additional analyses using any standard engineering economics method such as...

  20. Genomic analyses of the CAM plant pineapple.

    PubMed

    Zhang, Jisen; Liu, Juan; Ming, Ray

    2014-07-01

    The innovation of crassulacean acid metabolism (CAM) photosynthesis in arid and/or low CO2 conditions is a remarkable case of adaptation in flowering plants. As the most important crop that utilizes CAM photosynthesis, the genetic and genomic resources of pineapple have been developed over many years. Genetic diversity studies using various types of DNA markers led to the reclassification of the two genera Ananas and Pseudananas and nine species into one genus Ananas and two species, A. comosus and A. macrodontes with five botanical varieties in A. comosus. Five genetic maps have been constructed using F1 or F2 populations, and high-density genetic maps generated by genotype sequencing are essential resources for sequencing and assembling the pineapple genome and for marker-assisted selection. There are abundant expression sequence tag resources but limited genomic sequences in pineapple. Genes involved in the CAM pathway has been analysed in several CAM plants but only a few of them are from pineapple. A reference genome of pineapple is being generated and will accelerate genetic and genomic research in this major CAM crop. This reference genome of pineapple provides the foundation for studying the origin and regulatory mechanism of CAM photosynthesis, and the opportunity to evaluate the classification of Ananas species and botanical cultivars.

  1. Photovoltaics: Life-cycle Analyses

    SciTech Connect

    Fthenakis V. M.; Kim, H.C.

    2009-10-02

    Life-cycle analysis is an invaluable tool for investigating the environmental profile of a product or technology from cradle to grave. Such life-cycle analyses of energy technologies are essential, especially as material and energy flows are often interwoven, and divergent emissions into the environment may occur at different life-cycle-stages. This approach is well exemplified by our description of material and energy flows in four commercial PV technologies, i.e., mono-crystalline silicon, multi-crystalline silicon, ribbon-silicon, and cadmium telluride. The same life-cycle approach is applied to the balance of system that supports flat, fixed PV modules during operation. We also discuss the life-cycle environmental metrics for a concentration PV system with a tracker and lenses to capture more sunlight per cell area than the flat, fixed system but requires large auxiliary components. Select life-cycle risk indicators for PV, i.e., fatalities, injures, and maximum consequences are evaluated in a comparative context with other electricity-generation pathways.

  2. Comparison between Inbreeding Analyses Methodologies.

    PubMed

    Esparza, Mireia; Martínez-Abadías, Neus; Sjøvold, Torstein; González-José, Rolando; Hernández, Miquel

    2015-12-01

    Surnames are widely used in inbreeding analysis, but the validity of results has often been questioned due to the failure to comply with the prerequisites of the method. Here we analyze inbreeding in Hallstatt (Austria) between the 17th and the 19th centuries both using genealogies and surnames. The high and significant correlation of the results obtained by both methods demonstrates the validity of the use of surnames in this kind of studies. On the other hand, the inbreeding values obtained (0.24 x 10⁻³ in the genealogies analysis and 2.66 x 10⁻³ in the surnames analysis) are lower than those observed in Europe for this period and for this kind of population, demonstrating the falseness of the apparent isolation of Hallstatt's population. The temporal trend of inbreeding in both analyses does not follow the European general pattern, but shows a maximum in 1850 with a later decrease along the second half of the 19th century. This is probably due to the high migration rate that is implied by the construction of transport infrastructures around the 1870's.

  3. Helicopter tail rotor noise analyses

    NASA Technical Reports Server (NTRS)

    George, A. R.; Chou, S. T.

    1986-01-01

    A study was made of helicopter tail rotor noise, particularly that due to interactions with the main rotor tip vortices, and with the fuselage separation mean wake. The tail rotor blade-main rotor tip vortex interaction is modelled as an airfoil of infinite span cutting through a moving vortex. The vortex and the geometry information required by the analyses are obtained through a free wake geometry analysis of the main rotor. The acoustic pressure-time histories for the tail rotor blade-vortex interactions are then calculated. These acoustic results are compared to tail rotor loading and thickness noise, and are found to be significant to the overall tail rotor noise generation. Under most helicopter operating conditions, large acoustic pressure fluctuations can be generated due to a series of skewed main rotor tip vortices passing through the tail rotor disk. The noise generation depends strongly upon the helicopter operating conditions and the location of the tail rotor relative to the main rotor.

  4. Proteins analysed as virtual knots

    NASA Astrophysics Data System (ADS)

    Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.

    2017-02-01

    Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.

  5. Network analyses in systems pharmacology

    PubMed Central

    Berger, Seth I.; Iyengar, Ravi

    2009-01-01

    Systems pharmacology is an emerging area of pharmacology which utilizes network analysis of drug action as one of its approaches. By considering drug actions and side effects in the context of the regulatory networks within which the drug targets and disease gene products function, network analysis promises to greatly increase our knowledge of the mechanisms underlying the multiple actions of drugs. Systems pharmacology can provide new approaches for drug discovery for complex diseases. The integrated approach used in systems pharmacology can allow for drug action to be considered in the context of the whole genome. Network-based studies are becoming an increasingly important tool in understanding the relationships between drug action and disease susceptibility genes. This review discusses how analysis of biological networks has contributed to the genesis of systems pharmacology and how these studies have improved global understanding of drug targets, suggested new targets and approaches for therapeutics, and provided a deeper understanding of the effects of drugs. Taken together, these types of analyses can lead to new therapeutic options while improving the safety and efficacy of existing medications. Contact: ravi.iyengar@mssm.edu PMID:19648136

  6. Proteins analysed as virtual knots

    PubMed Central

    Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.

    2017-01-01

    Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important. PMID:28205562

  7. MSL SAM-like Analyses of Hawaiian Altered Basaltic Materials: Implications for Analyses by the Mars Science Laboratory

    NASA Astrophysics Data System (ADS)

    McAdam, A.; Eigenbrode, J. L.; Young, K. E.; Bleacher, J. E.; Knudson, C. A.; Rogers, D.; Glotch, T. D.; Sutter, B.; Mahaffy, P. R.; Navarro-Gonzalez, R.; Downs, R. T.

    2015-12-01

    Samples of basaltic materials were collected during several traverses of the Kau Desert on the leeward side of the Kilauea Volcano, Hawaii, conducted by the Remote, In Situ, and Synchrotron Studies for Science and Exploration (RIS4E) team, a node of the Solar System Exploration and Research Virtual Institute (SSERVI) program. Some of these samples had been exposed to circumneutral to slightly acidic alteration conditions from exposure to fog/rain, and acidic fog/rain, while others had been exposed to more acidic conditions due to proximity to fumaroles. The samples consisted of basalts with coatings, sands and soils, and ash, and were collected using organically clean protocols to enable investigation of organic chemistry and organic-mineral associations, in addition to mineralogy. The Mars Science Laboratory (MSL) rover has analyzed basaltic materials inferred to have been altered under conditions ranging from circumneutral to acidic, but several aspects of the Sample Analysis at Mars (SAM) instrument suite results are still being investigated and analyses of relevant terrestrial analogs can play an important role in interpretation of the data. For example, all materials analyzed to date have a significant amorphous component. Comparisons of the mineralogy obtained with the MSL CheMin instrument and volatiles evolved during SAM analyses indicate that, by mass balance, some portion of the volatiles, such as SO2 and H2O, are likely associated with this component. Many of the RIS4E samples also have a significant amorphous component, and field x-ray diffraction (XRD) and x-ray fluorescence (XRF) data indicate differences in the chemistry of this material in samples exposed to different alteration conditions. Preliminary SAM-like analyses indicate that the amorphous materials in some of these samples evolve volatiles such as H2O and SO2 during heating. Here we will discuss these results, and others, obtained through SAM-like analyses of selected samples.

  8. Effects of different agricultural managements in soil microbial community structure in a semi-arid Mediterranean region.

    NASA Astrophysics Data System (ADS)

    García-Orenes, Fuensanta; Morugan, Alicia; Mataix-Solera, Jorge; Scow, Kate

    2013-04-01

    Agriculture has been practiced in semi-arid Mediterranean regions for 10.000 years and in many cases these practices have been unsuitable causing land degradation for millennium and an important loss of soil quality. The land management can provide solutions to find the best agricultural practices in order to maintain the soil quality and get a sustainable agriculture model. Microbiological properties are the most sensitive and rapid indicators of soil perturbations and land use managements. The study of microbial community and diversity has an important interest as indicators of changes in soil quality. The main objective of this work was to asses the effect of different agricultural management practices in soil microbial community (evaluated as abundance of phospholipid fatty acids, PLFA). Four different treatments were selected, based on the most commonly practices applied by farmers in the study area, "El Teularet Experimental Station", located at the Enguera Range in the southern part of the Valencia province (eastern Spain). These treatments were: a) ploughing, b) herbicides c) mulch, using the types applied by organic farmers to develop a sustainable agriculture, such as oat straw and d) control that was established as plot where the treatment was abandonment after farming. An adjacent area with the same type of soil, but with natural vegetation was used as a standard or reference high quality soil. Soil samples were taken to evaluate the changes in microbial soil structure, analysing the abundance of PLFA. The results showed a major content of total PLFA in soils treated with oats straw, being these results similar to the content of PLFA in the soil with natural vegetation, also these soils were similar in the distribution of abundance of different PLFA studied. However, the herbicide and tillage treatments showed great differences regarding the soil used as reference (soil under natural vegetation).

  9. Analyses of Transistor Punchthrough Failures

    NASA Technical Reports Server (NTRS)

    Nicolas, David P.

    1999-01-01

    The failure of two transistors in the Altitude Switch Assembly for the Solid Rocket Booster followed by two additional failures a year later presented a challenge to failure analysts. These devices had successfully worked for many years on numerous missions. There was no history of failures with this type of device. Extensive checks of the test procedures gave no indication for a source of the cause. The devices were manufactured more than twenty years ago and failure information on this lot date code was not readily available. External visual exam, radiography, PEID, and leak testing were performed with nominal results Electrical testing indicated nearly identical base-emitter and base-collector characteristics (both forward and reverse) with a low resistance short emitter to collector. These characteristics are indicative of a classic failure mechanism called punchthrough. In failure analysis punchthrough refers to an condition where a relatively low voltage pulse causes the device to conduct very hard producing localized areas of thermal runaway or "hot spots". At one or more of these hot spots, the excessive currents melt the silicon. Heavily doped emitter material diffuses through the base region to the collector forming a diffusion pipe shorting the emitter to base to collector. Upon cooling, an alloy junction forms between the pipe and the base region. Generally, the hot spot (punch-through site) is under the bond and no surface artifact is visible. The devices were delidded and the internal structures were examined microscopically. The gold emitter lead was melted on one device, but others had anomalies in the metallization around the in-tact emitter bonds. The SEM examination confirmed some anomalies to be cosmetic defects while other anomalies were artifacts of the punchthrough site. Subsequent to these analyses, the contractor determined that some irregular testing procedures occurred at the time of the failures heretofore unreported. These testing

  10. Obeticholic Acid

    MedlinePlus

    Obeticholic acid is used alone or in combination with ursodiol (Actigall, Urso) to treat primary biliary cholangitis (PBC; a ... were not treated successfully with ursodiol alone. Obeticholic acid is in a class of medications called farnesoid ...

  11. Aminocaproic Acid

    MedlinePlus

    Aminocaproic acid is used to control bleeding that occurs when blood clots are broken down too quickly. This type ... the baby is ready to be born). Aminocaproic acid is also used to control bleeding in the ...

  12. Acid mucopolysaccharides

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/003368.htm Acid mucopolysaccharides To use the sharing features on this page, please enable JavaScript. Acid mucopolysaccharides is a test that measures the amount ...

  13. Aristolochic Acids

    MedlinePlus

    ... Sciences NIH-HHS www.niehs.nih.gov Aristolochic Acids Key Points Report on Carcinogens Status Known to be human carcinogens Aristolochia Clematitis Aristolochic Acids n Known human carcinogens n Found in certain ...

  14. Ascorbic Acid

    MedlinePlus

    Ascorbic acid is used to prevent and treat scurvy, a disease caused by a lack of vitamin C in ... Ascorbic acid comes in extended-release (long-acting) capsules and tablets, lozenges, syrup, chewable tablets, and liquid drops to ...

  15. Ethacrynic Acid

    MedlinePlus

    Ethacrynic acid, a 'water pill,' is used to treat swelling and fluid retention caused by various medical problems. It ... Ethacrynic acid comes as a tablet to take by mouth. It is usually taken once or twice a day ...

  16. Amino acids

    MedlinePlus

    ... page: //medlineplus.gov/ency/article/002222.htm Amino acids To use the sharing features on this page, please enable JavaScript. Amino acids are organic compounds that combine to form proteins . ...

  17. Pawnee Nation Energy Option Analyses

    SciTech Connect

    Matlock, M.; Kersey, K.; Riding In, C.

    2009-07-21

    Pawnee Nation of Oklahoma Energy Option Analyses In 2003, the Pawnee Nation leadership identified the need for the tribe to comprehensively address its energy issues. During a strategic energy planning workshop a general framework was laid out and the Pawnee Nation Energy Task Force was created to work toward further development of the tribe’s energy vision. The overarching goals of the “first steps” project were to identify the most appropriate focus for its strategic energy initiatives going forward, and to provide information necessary to take the next steps in pursuit of the “best fit” energy options. Description of Activities Performed The research team reviewed existing data pertaining to the availability of biomass (focusing on woody biomass, agricultural biomass/bio-energy crops, and methane capture), solar, wind and hydropower resources on the Pawnee-owned lands. Using these data, combined with assumptions about costs and revenue streams, the research team performed preliminary feasibility assessments for each resource category. The research team also reviewed available funding resources and made recommendations to Pawnee Nation highlighting those resources with the greatest potential for financially-viable development, both in the near-term and over a longer time horizon. Findings and Recommendations Due to a lack of financial incentives for renewable energy, particularly at the state level, combined mediocre renewable energy resources, renewable energy development opportunities are limited for Pawnee Nation. However, near-term potential exists for development of solar hot water at the gym, and an exterior wood-fired boiler system at the tribe’s main administrative building. Pawnee Nation should also explore options for developing LFGTE resources in collaboration with the City of Pawnee. Significant potential may also exist for development of bio-energy resources within the next decade. Pawnee Nation representatives should closely monitor

  18. Valproic Acid

    MedlinePlus

    Valproic acid is used alone or with other medications to treat certain types of seizures. Valproic acid is also used to treat mania (episodes of ... to relieve headaches that have already begun. Valproic acid is in a class of medications called anticonvulsants. ...

  19. Integrated Waste Treatment Unit (IWTU) Input Coal Analyses and Off-Gass Filter (OGF) Content Analyses

    SciTech Connect

    Jantzen, Carol M.; Missimer, David M.; Guenther, Chris P.; Shekhawat, Dushyant; VanEssendelft, Dirk T.; Means, Nicholas C.

    2015-04-23

    A full engineering scale Fluidized Bed Steam Reformer (FBSR) system is being used at the Idaho Nuclear Technology and Engineering Center (INTEC) to stabilize acidic Low Activity Waste (LAW) known as Sodium Bearing Waste (SBW). The INTEC facility, known as the Integrated Waste Treatment Unit (IWTU), underwent an Operational Readiness Review (ORR) and a Technology Readiness Assessment (TRA) in March 2014. The IWTU began non-radioactive simulant processing in late 2014 and by January, 2015 ; the IWTU had processed 62,000 gallons of simulant. The facility is currently in a planned outage for inspection of the equipment and will resume processing simulated waste feed before commencing to process 900,000 gallons of radioactive SBW. The SBW acidic waste will be made into a granular FBSR product (carbonate based) for disposal in the Waste Isolation Pilot Plant (WIPP). In the FBSR process calcined coal is used to create a CO2 fugacity to force the waste species to convert to carbonate species. The quality of the coal, which is a feed input, is important because the reactivity, moisture, and volatiles (C,H,N,O, and S) in the coal impact the reactions and control of the mineralizing process in the primary steam reforming vessel, the Denitration and Mineralizing Reformer (DMR). Too much moisture in the coal can require that additional coal be used. However since moisture in the coal is only a small fraction of the moisture from the fluidizing steam this can be self-correcting. If the coal reactivity or heating value is too low then the coal feedrate needs to be adjusted to achieve the desired heat generation. Too little coal and autothermal heat generation in the DMR cannot be sustained and/or the carbon dioxide fugacity will be too low to create the desired carbonate mineral species. Too much coal and excess S and hydroxide species can form. Excess sulfur from coal that (1) is too rich in sulfur or (2) from overfeeding coal can promote wall scale and contribute to corrosion

  20. Amino and fatty acids in carbonaceous meteorites

    NASA Technical Reports Server (NTRS)

    Kvenvolden, K. A.

    1974-01-01

    Analyses of two carbonaceous meteorites have provided much of the latest evidence which seems to support Oparin's theory on the origin of life. The meteorites involved are the Murray meteorite, which fell in 1950, and the Murchison meteorite, which fell in 1969. The amino acids in the two meteorites are similar in composition. Eight of the twenty amino acids found belong to amino acids present in proteins. A number of monocarboxylic and dicarboxylic fatty acids were also found in the meteorites.

  1. High perfomance liquid chromatography in pharmaceutical analyses.

    PubMed

    Nikolin, Branko; Imamović, Belma; Medanhodzić-Vuk, Saira; Sober, Miroslav

    2004-05-01

    electrochemical detection is nearly always associated with a major frontal peak than tails considerably. To date, the most sensitive method has been the reductive electrochemical detection and giving the excellent results in the investigation on some classes of drugs. Several high performance liquid chromatography oxidative electrochemical methods have been developed for the analyses of drugs and metabolites in body fluids. Mass spectrometer as specific detector with all variation of ionisation and interface (thermo spray, moving belt etc. ) or liquid chromatography-tandem mass spectrometry2,3,4,5). NMR as selective and specific detector in high performance liquid chromatography today is also in used. The development of a non-aqueous eluent for ion-exchange separation on silica has provided an excellent system which, when used in conjugation with an electrochemical detector, permits the analyses of an extensive range of especially basic drugs and metabolites. New packing materials such as polymeric, base deactivated silica's, pyrolysed carbon and the internal surface packing should offer the improved stability and higher efficiencies for certain classes of the compounds such as basic drugs. Microbore columns should become more accepted since they offer not only improved sensitivity but also a lower solvent consumption and consequently the reduced needs to dispose of noxious solvents. Many analyses of basic drugs are still performed by the same method of the ion-exchange chromatography on unmodified silica columns with an eluent buffered to about pH 9. Neutral or weakly acidic drugs for instance barbiturates can be chromatographed on a reversed phase system whilst acidic drugs for example paracetamol, cannabis are separated either by ion suppression or ion-pair chromatography on a reversed-phase packing material. In micelar liquid chromatography micelar mobile phases in reversed-phase instead of conventional hydro organic mobile phase is used. In micelar liquid chromatography

  2. Fatty acids - trans fatty acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The data supporting a negative effect of dietary trans fatty acids on cardiovascular disease risk is consistent. The primary dietary sources of trans fatty acids include partially hydrogenated fat and rudiment fat. The adverse effect of trans fatty acids on plasma lipoprotein profiles is consisten...

  3. Chiral Analyses of Organic Compounds in Carbonaceous Meteorites

    NASA Technical Reports Server (NTRS)

    Pizzarello, Sandra

    2004-01-01

    Contents include the following: 1. Characterization of Tagish Lake organic content. The first two grant years were largely devoted to the molecular and isotopic analyses of Tagish Lake organic composition. This carbonaceous meteorite fell in Canada in the winter of the year 2000, and its exceptional atmospheric entry and subsequent recovery (e. g., the sample was recovered and stored by avoiding hand contact and above freezing temperatures) contributed in providing a rare and pristine extraterrestrial material. 2. Chiral analyses of Murchison and Murray soluble organics. One of the most intriguing finding in regard to soluble meteorite organics is the presence within the amino acid suite of some compounds displaying L-enantiomeric excesses. This configuration is exclusive in the amino acids of terrestrial proteins and the finding has raised speculations of a possible role of amino acids from meteorites in the origin of homochirality on the early Earth. The main objective for this NASA funding was the characterization of enantiomeric excesses in meteorites and we have conducted several studies toward establishing their distribution and indignity.

  4. A potential plant-derived antifungal acetylenic acid mediates its activity by interfering with fatty acid homeostasis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    6-Nonadecynoic acid (6-NDA), a plant-derived acetylenic acid, exhibits strong inhibitory activity against the human fungal pathogens Candida albicans, Aspergillus fumigatus, and Trichophyton mentagrophytes. In the present study, transcriptional profiling coupled with mutant and biochemical analyses...

  5. MELCOR analyses for accident progression issues

    SciTech Connect

    Dingman, S.E.; Shaffer, C.J.; Payne, A.C.; Carmel, M.K. )

    1991-01-01

    Results of calculations performed with MELCOR and HECTR in support of the NUREG-1150 study are presented in this report. The analyses examined a wide range of issues. The analyses included integral calculations covering an entire accident sequence, as well as calculations that addressed specific issues that could affect several accident sequences. The results of the analyses for Grand Gulf, Peach Bottom, LaSalle, and Sequoyah are described, and the major conclusions are summarized. 23 refs., 69 figs., 8 tabs.

  6. Electron/proton spectrometer certification documentation analyses

    NASA Technical Reports Server (NTRS)

    Gleeson, P.

    1972-01-01

    A compilation of analyses generated during the development of the electron-proton spectrometer for the Skylab program is presented. The data documents the analyses required by the electron-proton spectrometer verification plan. The verification plan was generated to satisfy the ancillary hardware requirements of the Apollo Applications program. The certification of the spectrometer requires that various tests, inspections, and analyses be documented, approved, and accepted by reliability and quality control personnel of the spectrometer development program.

  7. /sup 14/CO/sub 2/ pulse-/sup 12/CO/sub 2/ chase analyses of C/sub 4/-acid metabolism in C/sub 3/-C/sub 4/ intermediate species of Flaveria at the CO/sub 2/ compensation concentration (r). [Flaveria floridana; Flaveria anomala

    SciTech Connect

    Chastain, C.J.; Chollet, R.

    1987-04-01

    Photosynthetic C/sub 4/-acid metabolism in leaves of C/sub 3/-C/sub 4/ intermediate Flaveria species was examined by /sup 14/CO/sub 2/ pulse-/sup 12/CO/sub 2/ chase experiments conducted at external CO/sub 2/-levels approximating air and ..gamma... Analysis of the percent distribution of /sup 14/C after a 10-s pulse showed an enhanced labeling of malate and aspartate at ..gamma.. in the C/sub 3/-C/sub 4/ species. This stimulation of /sup 14/CO/sub 2/ fixation by PEP carboxylase ranged from 1.7-(F. floridana) to 3.6-fold (F. anomala). A /sup 12/CO/sub 2/-chase at ..gamma.. revealed a significant turnover of C/sub 4/ acids for only F. floridana. C/sub 4/-acid labeling in C/sub 3/ and C/sub 4/ Flaveria species was relatively unresponsive to changes in pCO/sub 2/. These data imply that the C/sub 3/-C/sub 4/ intermediate Flaveria species with less advanced C/sub 4/ attributes have a greater capacity for increased CO/sub 2/ fixation via PEP carboxylase at ..gamma.. versus air. Thus, labeling of C/sub 3/-C/sub 4/ leaves at ..sigma.. may be an effective tool for assessing the degree of true C/sub 4/-photosynthesis as well as the potential mechanism involved in reducing photorespiration.

  8. Acid rain

    SciTech Connect

    Elsworth, S.

    1985-01-01

    This book was written in a concise and readable style for the lay public. It's purpose was to make the public aware of the damage caused by acid rain and to mobilize public opinion to favor the elimination of the causes of acid rain.

  9. Asparagusic acid.

    PubMed

    Mitchell, Stephen C; Waring, Rosemary H

    2014-01-01

    Asparagusic acid (1,2-dithiolane-4-carboxylic acid) is a simple sulphur-containing 5-membered heterocyclic compound that appears unique to asparagus, though other dithiolane derivatives have been identified in non-food species. This molecule, apparently innocuous toxicologically to man, is the most probable culprit responsible for the curious excretion of odorous urine following asparagus ingestion. The presence of the two adjacent sulphur atoms leads to an enhanced chemical reactivity, endowing it with biological properties including the ability to substitute potentially for α-lipoic acid in α-keto-acid oxidation systems. This brief review collects the scattered data available in the literature concerning asparagusic acid and highlights its properties, intermediary metabolism and exploratory applications.

  10. Acid rain

    SciTech Connect

    Sweet, W.

    1980-06-20

    Acid precipitation includes not only rain but also acidified snow, hail and frost, as well as sulfur and nitrogen dust. The principal source of acid precipitation is pollution emitted by power plants and smelters. Sulfur and nitrogen compounds contained in the emissions combine with moisture to form droplets with a high acid content - sometimes as acidic as vinegar. When sufficiently concentrated, these acids can kill fish and damage material structures. Under certain circumstances they may reduce crop and forest yields and cause or aggravate respiratory diseases in humans. During the summer, especially, pollutants tend to collect over the Great Lakes in high pressure systems. Since winds typically are westerly and rotate clockwise around high pressure systems, the pollutants gradually are dispersed throughout the eastern part of the continent.

  11. 49 CFR 1180.7 - Market analyses.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 8 2011-10-01 2011-10-01 false Market analyses. 1180.7 Section 1180.7..., TRACKAGE RIGHTS, AND LEASE PROCEDURES General Acquisition Procedures § 1180.7 Market analyses. (a) For... identify and address relevant markets and issues, and provide additional information as requested by...

  12. 49 CFR 1180.7 - Market analyses.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 8 2010-10-01 2010-10-01 false Market analyses. 1180.7 Section 1180.7..., TRACKAGE RIGHTS, AND LEASE PROCEDURES General Acquisition Procedures § 1180.7 Market analyses. (a) For... identify and address relevant markets and issues, and provide additional information as requested by...

  13. Aviation System Analysis Capability Executive Assistant Analyses

    NASA Technical Reports Server (NTRS)

    Roberts, Eileen; Kostiuk, Peter

    1999-01-01

    This document describes the analyses that may be incorporated into the Aviation System Analysis Capability Executive Assistant. The document will be used as a discussion tool to enable NASA and other integrated aviation system entities to evaluate, discuss, and prioritize analyses.

  14. 49 CFR 1180.7 - Market analyses.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 8 2014-10-01 2014-10-01 false Market analyses. 1180.7 Section 1180.7 Transportation Other Regulations Relating to Transportation (Continued) SURFACE TRANSPORTATION BOARD, DEPARTMENT..., TRACKAGE RIGHTS, AND LEASE PROCEDURES General Acquisition Procedures § 1180.7 Market analyses. (a)...

  15. 49 CFR 1180.7 - Market analyses.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 8 2012-10-01 2012-10-01 false Market analyses. 1180.7 Section 1180.7 Transportation Other Regulations Relating to Transportation (Continued) SURFACE TRANSPORTATION BOARD, DEPARTMENT..., TRACKAGE RIGHTS, AND LEASE PROCEDURES General Acquisition Procedures § 1180.7 Market analyses. (a)...

  16. 49 CFR 1180.7 - Market analyses.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 8 2013-10-01 2013-10-01 false Market analyses. 1180.7 Section 1180.7 Transportation Other Regulations Relating to Transportation (Continued) SURFACE TRANSPORTATION BOARD, DEPARTMENT..., TRACKAGE RIGHTS, AND LEASE PROCEDURES General Acquisition Procedures § 1180.7 Market analyses. (a)...

  17. 10 CFR 436.24 - Uncertainty analyses.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Procedures for Life Cycle Cost Analyses § 436.24 Uncertainty analyses. If particular items of cost data or... impact of uncertainty on the calculation of life cycle cost effectiveness or the assignment of rank order... and probabilistic analysis. If additional analysis casts substantial doubt on the life cycle...

  18. 10 CFR 436.24 - Uncertainty analyses.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Procedures for Life Cycle Cost Analyses § 436.24 Uncertainty analyses. If particular items of cost data or... impact of uncertainty on the calculation of life cycle cost effectiveness or the assignment of rank order... and probabilistic analysis. If additional analysis casts substantial doubt on the life cycle...

  19. 10 CFR 436.24 - Uncertainty analyses.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Procedures for Life Cycle Cost Analyses § 436.24 Uncertainty analyses. If particular items of cost data or... impact of uncertainty on the calculation of life cycle cost effectiveness or the assignment of rank order... and probabilistic analysis. If additional analysis casts substantial doubt on the life cycle...

  20. The combined effects of urea application and simulated acid rain on soil acidification and microbial community structure.

    PubMed

    Liu, Xingmei; Zhou, Jian; Li, Wanlu; Xu, Jianming; Brookes, Philip C

    2014-05-01

    Our aim was to test the effects of simulated acid rain (SAR) at different pHs, when applied to fertilized and unfertilized soils, on the leaching of soil cations (K, Ca, Mg, Na) and Al. Their effects on soil pH, exchangeable H(+) and Al(3+) and microbial community structure were also determined. A Paleudalfs soil was incubated for 30 days, with and without an initial application of urea (200 mg N kg(-1)soil) as nitrogen (N) fertilizer. The soil was held in columns and leached with SAR at three pH levels. Six treatments were tested: SAR of pH 2.5, 4.0 and 5.6 leaching on unfertilized soil (T1, T2 and T3), and on soils fertilized with urea (T4, T5 and T6). Increasing acid inputs proportionally increased cation leaching in both unfertilized and fertilized soils. Urea application increased the initial Ca and Mg leaching, but had no effect on the total concentrations of Ca, Mg and K leached. There was no significant difference for the amount of Na leached between the different treatments. The SAR pH and urea application had significant effects on soil pH, exchangeable H(+) and Al(3+). Urea application, SAR treated with various pH, and the interactions between them all had significant impacts on total phospholipid fatty acids (PLFAs). The highest concentration of total PLFAs occurred in fertilized soils with SAR pH5.6 and the lowest in soils leached with the lowest SAR pH. Soils pretreated with urea then leached with SARs of pH 4.0 and 5.6 had larger total PLFA concentrations than soil without urea. Bacterial, fungal, actinomycete, Gram-negative and Gram-positive bacterial PLFAs had generally similar trends to total PLFAs.

  1. Operator-free flow injection analyser

    PubMed Central

    de Faria, Lourival C.

    1991-01-01

    A flow injection analyser has been constructed to allow an operator-free determination of up to 40 samples. Besides the usual FIA apparatus, the analyser includes a home-made sample introduction device made with three electromechanical three-way valves and an auto-sampler from Technicon which has been adapted to be commanded by an external digital signal. The analyser is controlled by a single board SDK-8085 microcomputer. The necessary interface to couple the analyser components to the microcomputer is also described. The analyser was evaluated for a Cr(VI)-FIA determination showing a very good performance with a relative standard deviation for 15 signals from the injection of 100 μl of a 1.0 mg.ml-1 standard Cr(VI) solution being equal to 0.5%. PMID:18924899

  2. Preparation and characterization Al3+-bentonite Turen Malang for esterification fatty acid (palmitic acid, oleic acid and linoleic acid)

    NASA Astrophysics Data System (ADS)

    Abdulloh, Abdulloh; Aminah, Nanik Siti; Triyono, Mudasir, Trisunaryanti, Wega

    2016-03-01

    Catalyst preparation and characterization of Al3+-bentonite for esterification of palmitic acid, oleic acid and linoleic acid has been done. Al3+-bentonite catalyst was prepared from natural bentonite of Turen Malang through cation exchange reaction using AlCl3 solution. The catalysts obtained were characterized by XRD, XRF, pyridine-FTIR and surface area analyser using the BET method. Catalyst activity test of Al3+-bentonite for esterification reaction was done at 65°C using molar ratio of metanol-fatty acid of 30:1 and 0.25 g of Al3+-bentonite catalyst for the period of ½, 1, 2, 3, 4 and 5 hours. Based on the characterization results, the Al3+-bentonite Turen Malang catalyst has a d-spacing of 15.63 Ǻ, acid sites of Brönsted and Lewis respectively of 230.79 µmol/g and 99.39 µmol/g, surface area of 507.3 m2/g and the average of radius pore of 20.09 Å. GC-MS analysis results of the oil phase after esterification reaction showed the formation of biodiesel (FAME: Fatty acid methyl ester), namely methyl palmitate, methyl oleate and methyl linoleate. The number of conversions resulted in esterification reaction using Al3+-bentonite Turen Malang catalyst was 74.61%, 37.75%, and 20, 93% for the esterification of palmitic acid, oleic acid and linoleic acid respectively.

  3. Acid fog

    SciTech Connect

    Hileman, B.

    1983-03-01

    Fog in areas of southern California previously thought to be pollution-free has been shown to have a pH as low as 1.69. It has been found to be most acidic after smoggy days, suggesting that it forms on the aerosol associated with the previously exiting smog. Studies on Whiteface Mountain in the Adirondacks show that fog water is often 10 times as acidic as rainwater. As a result of their studies, California plans to spend $4 million on acid deposition research in the coming year. (JMT)

  4. Biogeography of sulfate-reducing prokaryotes in river floodplains.

    PubMed

    Miletto, Marzia; Loy, Alexander; Antheunisse, A Martijn; Loeb, Roos; Bodelier, Paul L E; Laanbroek, Hendrikus J

    2008-06-01

    In this study, a large-scale field survey was conducted to describe the biogeography of sulfate-reducing prokaryotes (SRPs) in river floodplains. Fingerprints obtained with three methods, i.e. 16S rRNA gene-based oligonucleotide microarray, dsrB-based denaturing gradient gel electrophoresis (DGGE) and polar lipid-derived fatty acid (PLFA) analyses, were used as a proxy to describe the SRPs community diversity. Each set of profiles was subjected to a combined multivariate/correlation analysis in order to compare SRP community profiles and to highlight the environmental variables influencing the SRPs distribution along environmental gradients. Floodplain soils harbored distinct SRP communities displaying biogeographic patterns. Nearly all profiles from the tidal sites consistently separated from the nontidal sites, independently from the screening method and the multivariate statistics used. The distribution of the microarray/DGGE/PLFA-based fingerprints in the principal component plots could be correlated to eight soil variables, i.e. soil organic matter, total nitrogen, total phosphorous and total potassium, and extractable ammonium, nitrate, phosphate and sulfate, as well as seven pore water variables, i.e. phosphate, sulfate, sulfide, chloride, sodium, potassium and magnesium ions. Indication of a salinity- and plant nutrient-dependent distribution of SRPs related to Desulfosarcina, Desulfomonile and Desulfobacter was suggested by microarray, DGGE and PLFA analyses.

  5. Phytic acid increases mucin and endogenous amino acid losses from the gastrointestinal tract of chickens.

    PubMed

    Onyango, Edward M; Asem, Elikplimi K; Adeola, Olayiwola

    2009-03-01

    The influence of the form of phytic acid on the regulation of mucin and endogenous losses of amino acids, nitrogen and energy in chickens was investigated. Forty-eight 10-week-old male broilers were grouped by weight into eight blocks of six cages with one bird per cage. Birds received by intubation six dextrose-based combinations of phytic acid and phytase arranged in a 3 x 2 factorial consisting of phytic acid form (no phytic acid, 1.0 g free phytic acid or 1.3 g magnesium-potassium phytate) and phytase (0 or 1000 units). Each bird received the assigned combination added to 25 g dextrose at each of the two feedings on the first day of experimentation. All excreta were collected continuously for 54 h following feeding and frozen until analysed. Frozen excreta were thawed, pooled for each bird, lyophilised, ground, and analysed for DM, energy, nitrogen, amino acids, mucin, and sialic and uric acids. Chickens fed either magnesium-potassium phytate or free phytic acid showed increased (P < 0.05) loss of crude mucin and sialic acid. The amount of crude mucin lost was significantly greater (P < 0.05) with magnesium-potassium phytate than with free phytic acid treatment. Both phytic acid treatments also increased (P < 0.05) endogenous loss of threonine, proline and serine. In conclusion, the form of phytic acid fed to chickens affects the extent of mucin and endogenous amino acid losses from the gastrointestinal tract.

  6. Level II Ergonomic Analyses, Dover AFB, DE

    DTIC Science & Technology

    1999-02-01

    IERA-RS-BR-TR-1999-0002 UNITED STATES AIR FORCE IERA Level II Ergonomie Analyses, Dover AFB, DE Andrew Marcotte Marilyn Joyce The Joyce...Project (070401881, Washington, DC 20503. 1. AGENCY USE ONLY (Leave blank) 2. REPORT DATE 4. TITLE AND SUBTITLE Level II Ergonomie Analyses, Dover...1.0 INTRODUCTION 1-1 1.1 Purpose Of The Level II Ergonomie Analyses : 1-1 1.2 Approach 1-1 1.2.1 Initial Shop Selection and Administration of the

  7. Mefenamic Acid

    MedlinePlus

    ... as mefenamic acid may cause ulcers, bleeding, or holes in the stomach or intestine. These problems may ... like coffee grounds, blood in the stool, or black and tarry stools.Keep all appointments with your ...

  8. Acid Rain

    MedlinePlus

    ... EPA Is Doing Acid Rain Program Cross-State Air Pollution Rule Progress Reports Educational Resources Kid's Site for ... Monitoring National Atmospheric Deposition Program (NADP) Exit Interstate Air Pollution Transport Contact Us to ask a question, provide ...

  9. Folic Acid

    MedlinePlus

    ... folic acid can hide signs that you lack vitamin B12, which can cause nerve damage. 10 Do I ... Rosenberg, I.H., et al. (2007). Folate and vitamin B12 status in relation to anemia, macrocytosis and cognitive ...

  10. Acid Precipitation

    ERIC Educational Resources Information Center

    Likens, Gene E.

    1976-01-01

    Discusses the fact that the acidity of rain and snow falling on parts of the U.S. and Europe has been rising. The reasons are still not entirely clear and the consequences have yet to be well evaluated. (MLH)

  11. Acidic precipitation

    SciTech Connect

    Martin, H.C.

    1987-01-01

    At the International Symposium on Acidic Precipitation, over 400 papers were presented, and nearly 200 of them are included here. They provide an overview of the present state of the art of acid rain research. The Conference focused on atmospheric science (monitoring, source-receptor relationships), aquatic effects (marine eutrophication, lake acidification, impacts on plant and fish populations), and terrestrial effects (forest decline, soil acidification, etc.).

  12. Interactive graphics for functional data analyses.

    PubMed

    Wrobel, Julia; Park, So Young; Staicu, Ana Maria; Goldsmith, Jeff

    Although there are established graphics that accompany the most common functional data analyses, generating these graphics for each dataset and analysis can be cumbersome and time consuming. Often, the barriers to visualization inhibit useful exploratory data analyses and prevent the development of intuition for a method and its application to a particular dataset. The refund.shiny package was developed to address these issues for several of the most common functional data analyses. After conducting an analysis, the plot shiny() function is used to generate an interactive visualization environment that contains several distinct graphics, many of which are updated in response to user input. These visualizations reduce the burden of exploratory analyses and can serve as a useful tool for the communication of results to non-statisticians.

  13. Quality control considerations in performing washability analyses

    SciTech Connect

    Graham, R.D.

    1984-10-01

    The author describes, in considerable detail, the procedures for carrying out washability analyses as laid down in ASTM Standard Test Method D4371. These include sampling, sample preparation, hydrometer standardisation, washability testing, and analysis of specific gravity fractions.

  14. SCM Forcing Data Derived from NWP Analyses

    DOE Data Explorer

    Jakob, Christian

    2008-01-15

    Forcing data, suitable for use with single column models (SCMs) and cloud resolving models (CRMs), have been derived from NWP analyses for the ARM (Atmospheric Radiation Measurement) Tropical Western Pacific (TWP) sites of Manus Island and Nauru.

  15. Anthocyanin analyses of Vaccinium fruit dietary supplements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vaccinium fruit ingredients within dietary supplements were identified by comparisons with anthocyanin analyses of known Vaccinium profiles (demonstration of anthocyanin fingerprinting). Available Vaccinium supplements were purchased and analyzed; their anthocyanin profiles (based on HPLC separation...

  16. Comparison with Russian analyses of meteor impact

    SciTech Connect

    Canavan, G.H.

    1997-06-01

    The inversion model for meteor impacts is used to discuss Russian analyses and compare principal results. For common input parameters, the models produce consistent estimates of impactor parameters. Directions for future research are discussed and prioritized.

  17. 49 CFR 1572.107 - Other analyses.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... ASSESSMENTS Standards for Security Threat Assessments § 1572.107 Other analyses. (a) TSA may determine that an... the search conducted under this part reveals extensive foreign or domestic criminal convictions,...

  18. A History of Rotorcraft Comprehensive Analyses

    NASA Technical Reports Server (NTRS)

    Johnson, Wayne

    2013-01-01

    A history of the development of rotorcraft comprehensive analyses is presented. Comprehensive analyses are digital computer programs that calculate the aeromechanical behavior of the rotor and aircraft, bringing together the most advanced models of the geometry, structure, dynamics, and aerodynamics available in rotary wing technology. The development of the major codes of the last five decades from industry, government, and universities is described. A number of common themes observed in this history are discussed.

  19. Analyses and forecasts with LAWS winds

    NASA Technical Reports Server (NTRS)

    Wang, Muyin; Paegle, Jan

    1994-01-01

    Horizontal fluxes of atmospheric water vapor are studied for summer months during 1989 and 1992 over North and South America based on analyses from European Center for Medium Range Weather Forecasts, US National Meteorological Center, and United Kingdom Meteorological Office. The calculations are performed over 20 deg by 20 deg box-shaped midlatitude domains located to the east of the Rocky Mountains in North America, and to the east of the Andes Mountains in South America. The fluxes are determined from operational center gridded analyses of wind and moisture. Differences in the monthly mean moisture flux divergence determined from these analyses are as large as 7 cm/month precipitable water equivalent over South America, and 3 cm/month over North America. Gridded analyses at higher spatial and temporal resolution exhibit better agreement in the moisture budget study. However, significant discrepancies of the moisture flux divergence computed from different gridded analyses still exist. The conclusion is more pessimistic than Rasmusson's estimate based on station data. Further analysis reveals that the most significant sources of error result from model surface elevation fields, gaps in the data archive, and uncertainties in the wind and specific humidity analyses. Uncertainties in the wind analyses are the most important problem. The low-level jets, in particular, are substantially different in the different data archives. Part of the reason for this may be due to the way the different analysis models parameterized physical processes affecting low-level jets. The results support the inference that the noise/signal ratio of the moisture budget may be improved more rapidly by providing better wind observations and analyses than by providing better moisture data.

  20. Prismatic analyser concept for neutron spectrometers

    SciTech Connect

    Birk, Jonas O.; Jacobsen, Johan; Hansen, Rasmus L.; Lefmann, Kim; Markó, Márton; Niedermayer, Christof; Freeman, Paul G.; Christensen, Niels B.; Månsson, Martin; Rønnow, Henrik M.

    2014-11-15

    Developments in modern neutron spectroscopy have led to typical sample sizes decreasing from few cm to several mm in diameter samples. We demonstrate how small samples together with the right choice of analyser and detector components makes distance collimation an important concept in crystal analyser spectrometers. We further show that this opens new possibilities where neutrons with different energies are reflected by the same analyser but counted in different detectors, thus improving both energy resolution and total count rate compared to conventional spectrometers. The technique can readily be combined with advanced focussing geometries and with multiplexing instrument designs. We present a combination of simulations and data showing three different energies simultaneously reflected from one analyser. Experiments were performed on a cold triple axis instrument and on a prototype inverse geometry Time-of-flight spectrometer installed at PSI, Switzerland, and shows excellent agreement with the predictions. Typical improvements will be 2.0 times finer resolution and a factor of 1.9 in flux gain compared to a focussing Rowland geometry, or of 3.3 times finer resolution and a factor of 2.4 in flux gain compared to a single flat analyser slab.

  1. Acid Rain

    USGS Publications Warehouse

    Bricker, Owen P.; Rice, Karen C.

    1993-01-01

    Acid deposition, or acid rain as it is more commonly referred to, has become a widely publicized environmental issue in the U.S. over the past decade. The term usually conjures up images of fish kills, dying forests, "dead" lakes, and damage to monuments and other historic artifacts. The primary cause of acid deposition is emission of S02 and NOx to the atmosphere during the combustion of fossil fuels. Oxidation of these compounds in the atmosphere forms strong acids - H2SO4 and HNO3 - which are returned to the Earth in rain, snow, fog, cloud water, and as dry deposition.Although acid deposition has only recently been recognized as an environmental problem in the U.S., it is not a new phenomenon (Cogbill & Likens 1974). As early as the middle of the 17th century in England, the deleterious effects of industrial emissions on plants, animals, and humans, and the atmospheric transport of pollutants between England and France had become issues of concern (Evelyn 1661, Graunt 1662). It is interesting that well over three hundred years ago in England, recommendations were made to move industry outside of towns and build higher chimneys to spread the pollution into "distant parts." Increasing the height of smokestacks has helped alleviate local problems, but has exacerbated others. In the U.S. the height of the tallest smokestack has more than doubled, and the average height of smokestacks has tripled since the 1950s (Patrick et al 1981). This trend occurred in most industrialized nations during the 20th century and has had the effect of transforming acid rain from a local urban problem into a problem of global scale.

  2. Acid Rain

    USGS Publications Warehouse

    Bricker, Owen P.; Rice, Karen C.; Dietrich, W.E.; Sposito, Garrison

    1997-01-01

    Acid deposition, or acid rain as it is more commonly referred to, has become a widely publicized environmental issue in the U.S. over the past decade. The term usually conjures up images of fish kills, dying forests, "dead" lakes, and damage to monuments and other historic artifacts. The primary cause of acid deposition is emission of S02 and NOx to the atmosphere during the combustion of fossil fuels. Oxidation of these compounds in the atmosphere forms strong acids - H2SO4 and HNO3 - which are returned to the Earth in rain, snow, fog, cloud water, and as dry deposition.Although acid deposition has only recently been recognized as an environmental problem in the U.S., it is not a new phenomenon (Cogbill & Likens 1974). As early as the middle of the 17th century in England, the deleterious effects of industrial emissions on plants, animals, and humans, and the atmospheric transport of pollutants between England and France had become issues of concern (Evelyn 1661, Graunt 1662). It is interesting that well over three hundred years ago in England, recommendations were made to move industry outside of towns and build higher chimneys to spread the pollution into "distant parts." Increasing the height of smokestacks has helped alleviate local problems, but has exacerbated others. In the U.S. the height of the tallest smokestack has more than doubled, and the average height of smokestacks has tripled since the 1950s (Patrick et al 1981). This trend occurred in most industrialized nations during the 20th century and has had the effect of transforming acid rain from a local urban problem into a problem of global scale.

  3. Salicylic acids

    PubMed Central

    Hayat, Shamsul; Irfan, Mohd; Wani, Arif; Nasser, Alyemeni; Ahmad, Aqil

    2012-01-01

    Salicylic acid is well known phytohormone, emerging recently as a new paradigm of an array of manifestations of growth regulators. The area unleashed yet encompassed the applied agriculture sector to find the roles to strengthen the crops against plethora of abiotic and biotic stresses. The skipped part of integrated picture, however, was the evolutionary insight of salicylic acid to either allow or discard the microbial invasion depending upon various internal factors of two interactants under the prevailing external conditions. The metabolic status that allows the host invasion either as pathogenesis or symbiosis with possible intermediary stages in close systems has been tried to underpin here. PMID:22301975

  4. Geomagnetic local and regional harmonic analyses.

    USGS Publications Warehouse

    Alldredge, L.R.

    1982-01-01

    Procedures are developed for using rectangular and cylindrical harmonic analyses in local and regional areas. Both the linear least squares analysis, applicable when component data are available, and the nonlinear least squares analysis, applicable when only total field data are available, are treated. When component data are available, it is advantageous to work with residual fields obtained by subtracting components derived from a harmonic potential from the observed components. When only total field intensity data are available, they must be used directly. Residual values cannot be used. Cylindrical harmonic analyses are indicated when fields tend toward cylindrical symmetry; otherwise, rectangular harmonic analyses will be more advantageous. Examples illustrating each type of analysis are given.-Author

  5. NEUTRONICS ANALYSES FOR SNS TARGETS DEPOSITIONS

    SciTech Connect

    Popova, Irina I; Remec, Igor; Gallmeier, Franz X

    2016-01-01

    In order to deposit Spallation Neutron Source (SNS) spent facility components replaced due to end-of-life radiation-induced material damage or burn-up, or because of mechanical failure or design improvements, waste classification analyses are being performed. These analyses include an accurate estimate of the radionuclide inventory, on which base components are classified and an appropriate container for transport and storage is determined. After the choice for the container is made, transport calculations are performed for the facility component to be placed inside the container, ensuring compliance with waste management regulations. When necessary, additional shielding is added. Most of the effort is concentrated on the target deposition, which normally takes place once or twice per year. Additionally, the second target station (STS) is in a process of design and waste management analyses for the STS target are being developed to support a deposition plan

  6. Proteomic Analyses of the Vitreous Humour

    PubMed Central

    Angi, Martina; Kalirai, Helen; Coupland, Sarah E.; Damato, Bertil E.; Semeraro, Francesco; Romano, Mario R.

    2012-01-01

    The human vitreous humour (VH) is a transparent, highly hydrated gel, which occupies the posterior segment of the eye between the lens and the retina. Physiological and pathological conditions of the retina are reflected in the protein composition of the VH, which can be sampled as part of routine surgical procedures. Historically, many studies have investigated levels of individual proteins in VH from healthy and diseased eyes. In the last decade, proteomics analyses have been performed to characterise the proteome of the human VH and explore networks of functionally related proteins, providing insight into the aetiology of diabetic retinopathy and proliferative vitreoretinopathy. Recent proteomic studies on the VH from animal models of autoimmune uveitis have identified new signalling pathways associated to autoimmune triggers and intravitreal inflammation. This paper aims to guide biological scientists through the different proteomic techniques that have been used to analyse the VH and present future perspectives for the study of intravitreal inflammation using proteomic analyses. PMID:22973072

  7. A qualitative method for analysing multivoicedness

    PubMed Central

    Aveling, Emma-Louise; Gillespie, Alex; Cornish, Flora

    2015-01-01

    ‘Multivoicedness’ and the ‘multivoiced Self’ have become important theoretical concepts guiding research. Drawing on the tradition of dialogism, the Self is conceptualised as being constituted by a multiplicity of dynamic, interacting voices. Despite the growth in literature and empirical research, there remains a paucity of established methodological tools for analysing the multivoiced Self using qualitative data. In this article, we set out a systematic, practical ‘how-to’ guide for analysing multivoicedness. Using theoretically derived tools, our three-step method comprises: identifying the voices of I-positions within the Self’s talk (or text), identifying the voices of ‘inner-Others’, and examining the dialogue and relationships between the different voices. We elaborate each step and illustrate our method using examples from a published paper in which data were analysed using this method. We conclude by offering more general principles for the use of the method and discussing potential applications. PMID:26664292

  8. [Hydrocyanic acid content in cerals and cereal products].

    PubMed

    Lehmann, G; Zinsmeister, H D; Erb, N; Neunhoeffer, O

    1979-03-01

    In the above paper for the first time a systematic study of the amount of hydrocyanic acid in grains and cereal products is reported. Among 24 analysed wheat, rye, maize and oats types, the presence of hydrocyanic acid could be identified in 19 cases in their Karyopses. Similar is the result with 28 among 31 analysed cereal products. The content of hydrocyanic acid lies between 0.1 and 45 microgram/100 gr dried mass.

  9. Advanced laser stratospheric monitoring systems analyses

    NASA Technical Reports Server (NTRS)

    Larsen, J. C.

    1984-01-01

    This report describes the software support supplied by Systems and Applied Sciences Corporation for the study of Advanced Laser Stratospheric Monitoring Systems Analyses under contract No. NAS1-15806. This report discusses improvements to the Langley spectroscopic data base, development of LHS instrument control software and data analyses and validation software. The effect of diurnal variations on the retrieved concentrations of NO, NO2 and C L O from a space and balloon borne measurement platform are discussed along with the selection of optimum IF channels for sensing stratospheric species from space.

  10. Analysing particulate deposition to plant canopies

    NASA Astrophysics Data System (ADS)

    Bache, D. H.

    Experimental measurements of the deposition of Lycopodium spores to a plant canopy were analysed to generate specific estimates of the relative significance of sedimentation, impaction and the effective foliage density fp. For the particular case analysed impaction appeared to be the dominating trapping mechanism and it was demonstrated that considerable aerodynamic shading was present. Using an estimate of fp. a consistant picture emerged in the behaviour of the canopy when both wet and dry and when tested against independent data on the trapping characteristics of individual elements. These conclusions differed significantly from those derived using a model in which impaction was neglected and lead to an apparent overestimate of fp.

  11. Diet-induced changes in iron and n-3 fatty acid status and associations with cognitive performance in 8-11-year-old Danish children: secondary analyses of the Optimal Well-Being, Development and Health for Danish Children through a Healthy New Nordic Diet School Meal Study.

    PubMed

    Sørensen, Louise Bergmann; Damsgaard, Camilla Trab; Dalskov, Stine-Mathilde; Petersen, Rikke Agnete; Egelund, Niels; Dyssegaard, Camilla Brørup; Stark, Ken D; Andersen, Rikke; Tetens, Inge; Astrup, Arne; Michaelsen, Kim Fleisher; Lauritzen, Lotte

    2015-11-28

    Fe and n-3 long-chain PUFA (n-3 LCPUFA) have both been associated with cognition, but evidence remains inconclusive in well-nourished school-aged children. In the Optimal Well-Being, Development and Health for Danish Children through a Healthy New Nordic Diet (OPUS) School Meal Study, the 3-month intervention increased reading performance, inattention, impulsivity and dietary intake of fish and Fe. This study investigated whether the intervention influenced n-3 LCPUFA and Fe status and, if so, explored how these changes correlated with the changes in cognitive performance. The study was a cluster-randomised cross-over trial comparing school meals with packed lunch (control). At baseline and after each treatment, we measured serum ferritin, whole-blood n-3 LCPUFA and Hb, and performance in reading, mathematics and d2-test of attention. Data were analysed using mixed models (n 726) and principal component analysis of test performances (n 644), which showed two main patterns: 'school performance' and 'reading comprehension'. The latter indicated that children with good reading comprehension were also more inattentive and impulsive (i.e. higher d2-test error%). The intervention improved 'school performance' (P=0·015), 'reading comprehension' (P=0·043) and EPA+DHA status 0·21 (95% CI 0·15, 0·27) w/w % (P<0·001), but it did not affect serum ferritin or Hb. At baseline, having small Fe stores was associated with poorer 'school performance' in girls, but with better 'reading comprehension' in both boys and girls. Both baseline EPA+DHA status and the intervention-induced increase in EPA+DHA status was positively associated with 'school performance', suggesting that n-3 LCPUFA could potentially explain approximately 20 % of the intervention effect. These exploratory associations indicate that increased fish intake might explain some of the increase in reading performance and inattention in the study.

  12. Selenious acid

    Integrated Risk Information System (IRIS)

    Selenious acid ; CASRN 7783 - 00 - 8 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic E

  13. Dichloroacetic acid

    Integrated Risk Information System (IRIS)

    EPA 635 / R - 03 / 007 www.epa.gov / iris TOXICOLOGICAL REVIEW OF DICHLOROACETIC ACID ( CAS No . 79 - 43 - 6 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS ) August 2003 U.S . Environmental Protection Agency Washington , DC DISCLAIMER This document has been revi

  14. Trichloroacetic acid

    Integrated Risk Information System (IRIS)

    EPA / 635 / R - 09 / 003F www.epa.gov / iris TOXICOLOGICAL REVIEW OF TRICHLOROACETIC ACID ( CAS No . 76 - 03 - 9 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS ) September 2011 U.S . Environmental Protection Agency Washington , DC ii DISCLAIMER This document has

  15. Acid rain

    SciTech Connect

    Not Available

    1984-06-01

    An overview is presented of acid rain and the problems it causes to the environment worldwide. The acidification of lakes and streams is having a dramatic effect on aquatic life. Aluminum, present in virtually all forest soils, leaches out readily under acid conditions and interferes with the gills of all fish, some more seriously than others. There is evidence of major damage to forests in European countries. In the US, the most severe forest damage appears to be in New England, New York's Adirondacks, and the central Appalachians. This small region is part of a larger area of the Northeast and Canada that appears to have more acid rainfall than the rest of the country. It is downwind from major coal burning states, which produce about one quarter of US SO/sub 2/ emissions and one sixth of nitrogen oxide emissions. Uncertainties exist over the causes of forest damage and more research is needed before advocating expensive programs to reduce rain acidity. The President's current budget seeks an expansion of research funds from the current $30 million per year to $120 million.

  16. Benzoic acid

    Integrated Risk Information System (IRIS)

    Benzoic acid ; CASRN 65 - 85 - 0 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Effec

  17. Formic acid

    Integrated Risk Information System (IRIS)

    Formic acid ; CASRN 64 - 18 - 6 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Effect

  18. Acrylic acid

    Integrated Risk Information System (IRIS)

    Acrylic acid ( CASRN 79 - 10 - 7 ) Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Eff

  19. Phosphoric acid

    Integrated Risk Information System (IRIS)

    Phosphoric acid ; CASRN 7664 - 38 - 2 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic

  20. Cacodylic acid

    Integrated Risk Information System (IRIS)

    Cacodylic acid ; CASRN 75 - 60 - 5 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Eff

  1. OH-radical induced degradation of hydroxybenzoic- and hydroxycinnamic acids and formation of aromatic products—A gamma radiolysis study

    NASA Astrophysics Data System (ADS)

    Krimmel, Birgit; Swoboda, Friederike; Solar, Sonja; Reznicek, Gottfried

    2010-12-01

    The OH-radical induced degradation of hydroxybenzoic acids (HBA), hydroxycinnamic acids (HCiA) and methoxylated derivatives, as well as of chlorogenic acid and rosmarinic acid was studied by gamma radiolysis in aerated aqueous solutions. Primary aromatic products resulting from an OH-radical attachment to the ring (hydroxylation), to the position occupied by the methoxyl group (replacement -OCH 3 by -OH) as well as to the propenoic acid side chain of the cinnamic acids (benzaldehyde formations) were analysed by HPLC-UV and LC-ESI-MS. A comparison of the extent of these processes is given for 3,4-dihydroxybenzoic acid, vanillic acid, isovanillic acid, syringic acid, cinnamic acid, 4-hydroxycinnamic acid, caffeic acid, ferulic acid, isoferulic acid, chlorogenic acid, and rosmarinic acid. For all cinnamic acids and derivatives benzaldehydes were significant oxidation products. With the release of caffeic acid from chlorogenic acid the cleavage of a phenolic glycoside could be demonstrated. Reaction mechanisms are discussed.

  2. 7 CFR 94.302 - Analyses available and locations of laboratories.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... processed poultry products for moisture, fat, salt, protein, nitrites, and added citric acid. (b) Deboned... portions will be analyzed separately for moisture, protein, salt, and fat. Moisture to protein ratios will..., and protein analyses. Additional poultry commodities and related products for specific USDA...

  3. Integrated Metagenomics and Metatranscriptomics Analyses of Root-Associated Soil from Transgenic Switchgrass

    PubMed Central

    Smartt, Abby; Wang, Jun; Utturkar, Sagar; Frank, Ashley; Bi, Meng; Liu, Jiang; Williams, Daniel; Xu, Tingting; Eldridge, Melanie; Arreaza, Andres; Rogers, Alexandra; Gonzalez, Hector Castro; Layton, Alice C.; Baxter, Holly L.; Mazarei, Mitra; DeBruyn, Jennifer M.; Stewart, C. Neal; Brown, Steven D.; Hauser, Loren J.

    2014-01-01

    The benefits of using transgenic switchgrass with decreased levels of caffeic acid 3-O-methyltransferase (COMT) as biomass feedstock have been clearly demonstrated. However, its effect on the soil microbial community has not been assessed. Here we report metagenomic and metatranscriptomic analyses of root-associated soil from COMT switchgrass compared with nontransgenic counterparts. PMID:25125642

  4. Microbially induced organic acid underdeposit attack in a gas pipeline

    SciTech Connect

    Dias, O.C.; Bromel, M.C. )

    1990-04-01

    A leaking undersea carbon-steel gas pipeline was investigated, and attack was confined to low areas where water had accumulated.Analyses showed that pitting, which occurred under deposits, was caused by organic acids generated by bacteria. The metabolic activities of anaerobic sporeformers produce these acids. Alkyl amine carboxylic acid and metronidizole were effective deterrents at low concentrations.

  5. Azelaic acid.

    PubMed

    Nazzaro-Porro, M

    1987-12-01

    This review is an update on the literature accumulated over the past 10 years following the original observation that azelaic acid, a naturally occurring and nontoxic C9 dicarboxylic acid, possesses significant biologic properties and a potential as a therapeutic agent. These studies have shown that azelaic acid is a reversible inhibitor of tyrosinase and other oxidoreductases in vitro and that it inhibits mitochondrial respiration. It can also inhibit anaerobic glycolysis. Both in vitro and in vivo it has an antimicrobial effect on both aerobic and anaerobic (Propionibacterium acnes) microorganisms. In tissue culture it exerts a dose- and time-dependent cytotoxic effect on malignant melanocytes, associated with mitochondrial damage and inhibition of deoxyribonucleic acid (DNA) synthesis. Tumoral cell lines not containing tyrosinase are equally affected. Normal cells in culture exposed to the same concentrations of the diacid that are toxic for tumoral cells are in general not damaged. Radioactive azelaic acid has been shown to penetrate tumoral cells at a higher level than normal cells of the corresponding line. Topically applied (a 20% cream), it has been shown to be of therapeutic value in skin disorders of different etiologies. Its beneficial effect on various forms of acne (comedogenic, papulopustular, nodulocystic) has been clearly demonstrated. Particularly important is its action on abnormal melanocytes, which has led to the possibility of obtaining good results on melasma and highly durable therapeutic responses on lentigo maligna. It is also capable of causing regression of cutaneous malignant melanoma, but its role in melanoma therapy remains to be investigated.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. The past, present and future of microbiome analyses

    SciTech Connect

    White, Richard Allen; Callister, Stephen J.; Moore, Ronald J.; Baker, Erin S.; Jansson, Janet K.

    2016-09-29

    Microbes evolved on Earth approximately 3.5 billion years ago and eventually occupied every habitable environment in its biosphere. While microorganisms are responsible for key functions on Earth including carbon and nutrient cycling and determining the health and disease of its inhabitants (i.e. plants and animals), >99% of the estimated trillions of microbes have yet to be discovered.1 In addition, high microbial diversity has made it difficult to study specific functions carried out by complex microbial communities within "microbiomes", such as those inhabiting the soil and human gut.2,3 Fortunately, technological advances over the last few decades have greatly facilitated studies of complex microbiomes and their functions. Here we will specifically discuss advances related to nucleic acid sequencing and mass spectrometry analyses that have enabled exploration and understanding of complex microbiomes in a range of environments and our own bodies.4,5,6,7

  7. Reproducible analyses of microbial food for advanced life support systems

    NASA Technical Reports Server (NTRS)

    Petersen, Gene R.

    1988-01-01

    The use of yeasts in controlled ecological life support systems (CELSS) for microbial food regeneration in space required the accurate and reproducible analysis of intracellular carbohydrate and protein levels. The reproducible analysis of glycogen was a key element in estimating overall content of edibles in candidate yeast strains. Typical analytical methods for estimating glycogen in Saccharomyces were not found to be entirely aplicable to other candidate strains. Rigorous cell lysis coupled with acid/base fractionation followed by specific enzymatic glycogen analyses were required to obtain accurate results in two strains of Candida. A profile of edible fractions of these strains was then determined. The suitability of yeasts as food sources in CELSS food production processes is discussed.

  8. Mangrove succession enriches the sediment microbial community in South China

    NASA Astrophysics Data System (ADS)

    Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

    2016-06-01

    Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.

  9. Mangrove succession enriches the sediment microbial community in South China

    PubMed Central

    Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

    2016-01-01

    Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession. PMID:27265262

  10. Mangrove succession enriches the sediment microbial community in South China.

    PubMed

    Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

    2016-06-06

    Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.

  11. Automated Quality Assurance of Online NIR Analysers

    PubMed Central

    Aaljoki, Kari

    2005-01-01

    Modern NIR analysers produce valuable data for closed-loop process control and optimisation practically in real time. Thus it is highly important to keep them in the best possible shape. Quality assurance (QA) of NIR analysers is an interesting and complex issue because it is not only the instrument and sample handling that has to be monitored. At the same time, validity of prediction models has to be assured. A system for fully automated QA of NIR analysers is described. The system takes care of collecting and organising spectra from various instruments, relevant laboratory, and process management system (PMS) data. Validation of spectra is based on simple diagnostics values derived from the spectra. Predictions are validated against laboratory (LIMS) or other online analyser results (collected from PMS). The system features automated alarming, reporting, trending, and charting functions for major key variables for easy visual inspection. Various textual and graphical reports are sent to maintenance people through email. The software was written with Borland Delphi 7 Enterprise. Oracle and PMS ODBC interfaces were used for accessing LIMS and PMS data using appropriate SQL queries. It will be shown that it is possible to take actions even before the quality of predictions is seriously affected, thus maximising the overall uptime of the instrument. PMID:18924628

  12. Uncertainty quantification approaches for advanced reactor analyses.

    SciTech Connect

    Briggs, L. L.; Nuclear Engineering Division

    2009-03-24

    The original approach to nuclear reactor design or safety analyses was to make very conservative modeling assumptions so as to ensure meeting the required safety margins. Traditional regulation, as established by the U. S. Nuclear Regulatory Commission required conservatisms which have subsequently been shown to be excessive. The commission has therefore moved away from excessively conservative evaluations and has determined best-estimate calculations to be an acceptable alternative to conservative models, provided the best-estimate results are accompanied by an uncertainty evaluation which can demonstrate that, when a set of analysis cases which statistically account for uncertainties of all types are generated, there is a 95% probability that at least 95% of the cases meet the safety margins. To date, nearly all published work addressing uncertainty evaluations of nuclear power plant calculations has focused on light water reactors and on large-break loss-of-coolant accident (LBLOCA) analyses. However, there is nothing in the uncertainty evaluation methodologies that is limited to a specific type of reactor or to specific types of plant scenarios. These same methodologies can be equally well applied to analyses for high-temperature gas-cooled reactors and to liquid metal reactors, and they can be applied to steady-state calculations, operational transients, or severe accident scenarios. This report reviews and compares both statistical and deterministic uncertainty evaluation approaches. Recommendations are given for selection of an uncertainty methodology and for considerations to be factored into the process of evaluating uncertainties for advanced reactor best-estimate analyses.

  13. Cosmetology: Task Analyses. Competency-Based Education.

    ERIC Educational Resources Information Center

    Henrico County Public Schools, Glen Allen, VA. Virginia Vocational Curriculum Center.

    These task analyses are designed to be used in combination with the "Trade and Industrial Education Service Area Resource" in order to implement competency-based education in the cosmetology program in Virginia. The task analysis document contains the task inventory, suggested task sequence lists, and content outlines for the secondary…

  14. The Economic Cost of Homosexuality: Multilevel Analyses

    ERIC Educational Resources Information Center

    Baumle, Amanda K.; Poston, Dudley, Jr.

    2011-01-01

    This article builds on earlier studies that have examined "the economic cost of homosexuality," by using data from the 2000 U.S. Census and by employing multilevel analyses. Our findings indicate that partnered gay men experience a 12.5 percent earnings penalty compared to married heterosexual men, and a statistically insignificant earnings…

  15. Written Case Analyses and Critical Reflection.

    ERIC Educational Resources Information Center

    Harrington, Helen L.; And Others

    1996-01-01

    The study investigated the use of case-based pedagogy to develop critical reflection in prospective teachers. Analysis of students written analyses of dilemma-based cases found patterns showing evidence of students open-mindedness, sense of professional responsibility, and wholeheartedness in approach to teaching. (DB)

  16. Chemical Analyses of Silicon Aerogel Samples

    SciTech Connect

    van der Werf, I.; Palmisano, F.; De Leo, Raffaele; Marrone, Stefano

    2008-04-01

    After five years of operating, two Aerogel counters: A1 and A2, taking data in Hall A at Jefferson Lab, suffered a loss of performance. In this note possible causes of degradation have been studied. In particular, various chemical and physical analyses have been carried out on several Aerogel tiles and on adhesive tape in order to reveal the presence of contaminants.

  17. Automated Quality Assurance of Online NIR Analysers.

    PubMed

    Aaljoki, Kari

    2005-01-01

    Modern NIR analysers produce valuable data for closed-loop process control and optimisation practically in real time. Thus it is highly important to keep them in the best possible shape. Quality assurance (QA) of NIR analysers is an interesting and complex issue because it is not only the instrument and sample handling that has to be monitored. At the same time, validity of prediction models has to be assured. A system for fully automated QA of NIR analysers is described. The system takes care of collecting and organising spectra from various instruments, relevant laboratory, and process management system (PMS) data. Validation of spectra is based on simple diagnostics values derived from the spectra. Predictions are validated against laboratory (LIMS) or other online analyser results (collected from PMS). The system features automated alarming, reporting, trending, and charting functions for major key variables for easy visual inspection. Various textual and graphical reports are sent to maintenance people through email. The software was written with Borland Delphi 7 Enterprise. Oracle and PMS ODBC interfaces were used for accessing LIMS and PMS data using appropriate SQL queries. It will be shown that it is possible to take actions even before the quality of predictions is seriously affected, thus maximising the overall uptime of the instrument.

  18. Analysing Simple Electric Motors in the Classroom

    ERIC Educational Resources Information Center

    Yap, Jeff; MacIsaac, Dan

    2006-01-01

    Electromagnetic phenomena and devices such as motors are typically unfamiliar to both teachers and students. To better visualize and illustrate the abstract concepts (such as magnetic fields) underlying electricity and magnetism, we suggest that students construct and analyse the operation of a simply constructed Johnson electric motor. In this…

  19. Correlation Functions Aid Analyses Of Spectra

    NASA Technical Reports Server (NTRS)

    Beer, Reinhard; Norton, Robert H., Jr.

    1989-01-01

    New uses found for correlation functions in analyses of spectra. In approach combining elements of both pattern-recognition and traditional spectral-analysis techniques, spectral lines identified in data appear useless at first glance because they are dominated by noise. New approach particularly useful in measurement of concentrations of rare species of molecules in atmosphere.

  20. Functional Analyses and Treatment of Precursor Behavior

    ERIC Educational Resources Information Center

    Najdowski, Adel C.; Wallace, Michele D.; Ellsworth, Carrie L.; MacAleese, Alicia N.; Cleveland, Jackie

    2008-01-01

    Functional analysis has been demonstrated to be an effective method to identify environmental variables that maintain problem behavior. However, there are cases when conducting functional analyses of severe problem behavior may be contraindicated. The current study applied functional analysis procedures to a class of behavior that preceded severe…

  1. A Call for Conducting Multivariate Mixed Analyses

    ERIC Educational Resources Information Center

    Onwuegbuzie, Anthony J.

    2016-01-01

    Several authors have written methodological works that provide an introductory- and/or intermediate-level guide to conducting mixed analyses. Although these works have been useful for beginning and emergent mixed researchers, with very few exceptions, works are lacking that describe and illustrate advanced-level mixed analysis approaches. Thus,…

  2. Microstructure Analyses of NA-Nanodiamond Particles

    DTIC Science & Technology

    2016-08-01

    NOTES 14. ABSTRACT The purification process of detonation diamond nanoparticles was perfectly accomplished using nitric acid at high...temperature and pressure. The transmission electron microscopy and electron diffraction technique revealed detonation diamond nanoparticles...microscope (SEM) Diamond nanoparticles 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT SAR 18. NUMBER OF PAGES 13 19a

  3. Morphological Analyses of Spring Wheat (CIMMYT cv. PCYT-10) Somaclones

    NASA Technical Reports Server (NTRS)

    Campbell, W. F.; Carman, J. G.; Hashim, Z. N.

    1990-01-01

    The objectives of this study were to induce callus from single immature wheat embryos, produce multiple seedlings from the induced callus, and analyse the somaclonal regenerants for potential grain production in a space garden. Immature wheat, Triticum aestivum L. (cv. PCYT-10), embryos were excised 10 to 12 days post-anthesis and cultured on modified Murashige and Skoog's inorganic salts. Embryos cultured on medium containing kinetin (6-furfurylaminopurine) at 0.5mg/l plus 2 or 3mg/l dicamba (1-methoxy-3,6- dichlorobenzoic acid) or 0.2mg/l 2,4-dichlorophenoxyacetic acid produced calli from which 24, 35 and 39% of the explant tissue exhibited regenerants, respectively. The size of flag leaves, plant heights, tillers per plant, spike lengths, awn lengths, and seeds per spike were significantly different in regenerants of two-selfed recurrent generations (SC(sub 1), SC(sub 2)) than in parental controls. However, there were no significant differences in spikelets per spike between the SC(sub 2) and parental controls. Desirable characteristics that were obtained included longer spikes, more seeds per spike, supernumerary spikelets, and larger flag leaves, variants that should be useful in wheat improvement programs.

  4. Hydroxycarboxylic acids and salts

    DOEpatents

    Kiely, Donald E; Hash, Kirk R; Kramer-Presta, Kylie; Smith, Tyler N

    2015-02-24

    Compositions which inhibit corrosion and alter the physical properties of concrete (admixtures) are prepared from salt mixtures of hydroxycarboxylic acids, carboxylic acids, and nitric acid. The salt mixtures are prepared by neutralizing acid product mixtures from the oxidation of polyols using nitric acid and oxygen as the oxidizing agents. Nitric acid is removed from the hydroxycarboxylic acids by evaporation and diffusion dialysis.

  5. Quantitative Analyse und Visualisierung der Herzfunktionen

    NASA Astrophysics Data System (ADS)

    Sauer, Anne; Schwarz, Tobias; Engel, Nicole; Seitel, Mathias; Kenngott, Hannes; Mohrhardt, Carsten; Loßnitzer, Dirk; Giannitsis, Evangelos; Katus, Hugo A.; Meinzer, Hans-Peter

    Die computergestützte bildbasierte Analyse der Herzfunktionen ist mittlerweile Standard in der Kardiologie. Die verfügbaren Produkte erfordern meist ein hohes Maß an Benutzerinteraktion und somit einen erhöhten Zeitaufwand. In dieser Arbeit wird ein Ansatz vorgestellt, der dem Kardiologen eine größtenteils automatische Analyse der Herzfunktionen mittels MRT-Bilddaten ermöglicht und damit Zeitersparnis schafft. Hierbei werden alle relevanten herzphysiologsichen Parameter berechnet und mithilfe von Diagrammen und Graphen visualisiert. Diese Berechnungen werden evaluiert, indem die ermittelten Werte mit manuell vermessenen verglichen werden. Der hierbei berechnete mittlere Fehler liegt mit 2,85 mm für die Wanddicke und 1,61 mm für die Wanddickenzunahme immer noch im Bereich einer Pixelgrösse der verwendeten Bilder.

  6. Reliability of chemical analyses of water samples

    SciTech Connect

    Beardon, R.

    1989-11-01

    Ground-water quality investigations require reliable chemical analyses of water samples. Unfortunately, laboratory analytical results are often unreliable. The Uranium Mill Tailings Remedial Action (UMTRA) Project`s solution to this problem was to establish a two phase quality assurance program for the analysis of water samples. In the first phase, eight laboratories analyzed three solutions of known composition. The analytical accuracy of each laboratory was ranked and three laboratories were awarded contracts. The second phase consists of on-going monitoring of the reliability of the selected laboratories. The following conclusions are based on two years experience with the UMTRA Project`s Quality Assurance Program. The reliability of laboratory analyses should not be taken for granted. Analytical reliability may be independent of the prices charged by laboratories. Quality assurance programs benefit both the customer and the laboratory.

  7. Sensitivity in risk analyses with uncertain numbers.

    SciTech Connect

    Tucker, W. Troy; Ferson, Scott

    2006-06-01

    Sensitivity analysis is a study of how changes in the inputs to a model influence the results of the model. Many techniques have recently been proposed for use when the model is probabilistic. This report considers the related problem of sensitivity analysis when the model includes uncertain numbers that can involve both aleatory and epistemic uncertainty and the method of calculation is Dempster-Shafer evidence theory or probability bounds analysis. Some traditional methods for sensitivity analysis generalize directly for use with uncertain numbers, but, in some respects, sensitivity analysis for these analyses differs from traditional deterministic or probabilistic sensitivity analyses. A case study of a dike reliability assessment illustrates several methods of sensitivity analysis, including traditional probabilistic assessment, local derivatives, and a ''pinching'' strategy that hypothetically reduces the epistemic uncertainty or aleatory uncertainty, or both, in an input variable to estimate the reduction of uncertainty in the outputs. The prospects for applying the methods to black box models are also considered.

  8. Center for Naval Analyses Annual Report 1982.

    DTIC Science & Technology

    1982-01-01

    recipients, alike, was due mainly to temporary rather than permanent layoffs ; they were unemployed for about the same length of time, and their post- layoff ...equal to 70 percent of average weekly wages for 52 weeks in the two years following layoff ) apparently encouraged workers to remain unemployed longer...Institute for Defense Analyses. William A. Nierenberg, Director of the Scripps Institution of Oceanog- raphy. Member, NASA Advisory Council. Member

  9. [Resistance analyses for recirculated membrane bioreactor].

    PubMed

    Yang, Qi; Huang, Xia; Shang, Hai-Tao; Wen, Xiang-Hua; Qian, Yi

    2006-11-01

    The resistance analyses for recirculated membrane bioreactor by the resistance-in-series model and the modified gel-polarization model respectively were extended to the turbulent ultrafiltration system. The experiments are carried out by dye wastewater in a tubular membrane module, it is found that the permeate fluxes are predicted very well by these models for turbinate systems. And the resistance caused by the concentration polarization is studied; the gel layer resistance is the most important of all the resistances.

  10. [Clinical research=design*measurements*statistical analyses].

    PubMed

    Furukawa, Toshiaki

    2012-06-01

    A clinical study must address true endpoints that matter for the patients and the doctors. A good clinical study starts with a good clinical question. Formulating a clinical question in the form of PECO can sharpen one's original question. In order to perform a good clinical study one must have a knowledge of study design, measurements and statistical analyses: The first is taught by epidemiology, the second by psychometrics and the third by biostatistics.

  11. Optimizing header strength utilizing finite element analyses

    NASA Astrophysics Data System (ADS)

    Burchett, S. N.

    Finite element techniques have been successfully applied as a design tool in the optimization of high strength headers for pyrotechnic-driven actuators. These techniques have been applied to three aspects of the design process of a high strength header. The design process was a joint effort of experts from several disciplines including design engineers, material scientists, test engineers, manufacturing engineers, and structural analysts. Following material selection, finite element techniques were applied to evaluate the residual stresses due to manufacturing which were developed in the high strength glass ceramic-to-metal seal headers. Results from these finite element analyses were used to identify header designs which were manufacturable and had a minimum residual stress state. Finite element techniques were than applied to obtain the response of the header due to pyrotechnic burn. The results provided realistic upper bounds on the pressure containment ability of various preliminary header designs and provided a quick and inexpensive method of strengthening and refining the designs. Since testing of the headers was difficult and sometimes destructive, results of the analyses were also used to interpret test results and identify failure modes. In this paper, details of the finite element element techniques including the models used, material properties, material failure models, and loading will be presented. Results from the analyses showing the header failure process will also be presented. This paper will show that significant gains in capability and understanding can result when finite element techniques are included as an integral part of the design process of complicated high strength headers.

  12. Evaluation of the Technicon Axon analyser.

    PubMed

    Martínez, C; Márquez, M; Cortés, M; Mercé, J; Rodriguez, J; González, F

    1990-01-01

    An evaluation of the Technicon Axon analyser was carried out following the guidelines of the 'Sociedad Española de Química Clínica' and the European Committee for Clinical Laboratory Standards.A photometric study revealed acceptable results at both 340 nm and 404 nm. Inaccuracy and imprecision were lower at 404 nm than at 340 nm, although poor dispersion was found at both wavelengths, even at low absorbances. Drift was negligible, the imprecision of the sample pipette delivery system was greater for small sample volumes, the reagent pipette delivery system imprecision was acceptable and the sample diluting system study showed good precision and accuracy.Twelve analytes were studied for evaluation of the analyser under routine working conditions. Satisfactory results were obtained for within-run imprecision, while coefficients of variation for betweenrun imprecision were much greater than expected. Neither specimenrelated nor specimen-independent contamination was found in the carry-over study. For all analytes assayed, when comparing patient sample results with those obtained in a Hitachi 737 analyser, acceptable relative inaccuracy was observed.

  13. Advances in nucleic acid-based detection methods.

    PubMed Central

    Wolcott, M J

    1992-01-01

    Laboratory techniques based on nucleic acid methods have increased in popularity over the last decade with clinical microbiologists and other laboratory scientists who are concerned with the diagnosis of infectious agents. This increase in popularity is a result primarily of advances made in nucleic acid amplification and detection techniques. Polymerase chain reaction, the original nucleic acid amplification technique, changed the way many people viewed and used nucleic acid techniques in clinical settings. After the potential of polymerase chain reaction became apparent, other methods of nucleic acid amplification and detection were developed. These alternative nucleic acid amplification methods may become serious contenders for application to routine laboratory analyses. This review presents some background information on nucleic acid analyses that might be used in clinical and anatomical laboratories and describes some recent advances in the amplification and detection of nucleic acids. PMID:1423216

  14. Distribution of Amino Acids in Lunar Regolith

    NASA Technical Reports Server (NTRS)

    Elsila, J. E.; Callahan, M. P.; Glavin, D. P.; Dworkin, J. P.; Noble, S. K.; Gibson, E. K., Jr.

    2014-01-01

    One of the most eagerly studied questions upon initial return of lunar samples was whether significant amounts of organic compounds, including amino acids, were present. Analyses during the 1970s produced only tentative and inconclusive identifications of indigenous amino acids. Those analyses were hampered by analytical difficulties including relative insensitivity to certain compounds, the inability to separate chiral enantiomers, and the lack of compound-specific isotopic measurements, which made it impossible to determine whether the detected amino acids were indigenous to the lunar samples or the results of contamination. Numerous advances have been made in instrumentation and methodology for amino acid characterization in extraterrestrial samples in the intervening years, yet the origin of amino acids in lunar regolith samples has been revisited only once for a single lunar sample, (3) and remains unclear. Here, we present initial data from the analyses of amino acid abundances in 12 lunar regolith samples. We discuss these abundances in the context of four potential amino acid sources: (1) terrestrial biological contamination; (2) contamination from lunar module (LM) exhaust; (3) derivation from solar windimplanted precursors; and (4) exogenous delivery from meteorites.

  15. Acidic domains around nucleic acids.

    PubMed Central

    Lamm, G; Pack, G R

    1990-01-01

    The hydrogen ion concentration in the vicinity of DNA was mapped out within the Poisson-Boltzmann approximation. Experimental conditions were modeled by assuming Na-DNA to be solvated in a buffer solution containing 45 mM Tris and 3 mM Mg cations at pH 7.5. Three regions of high H+ concentration (greater than 10 microM) are predicted: one throughout the minor groove of DNA and two localized in the major groove near N7 of guanine and C5 of cytosine for a G.C base pair. These acidic domains correlate well with the observed covalent binding sites of benzo[a]pyrene epoxide (N2 of guanine) and of aflatoxin B1 epoxide (N7 of guanine), chemical carcinogens that presumably undergo acid catalysis to form highly reactive carbocations that ultimately bind to DNA. It is suggested that these regions of high H+ concentration may also be of concern in understanding interactions involving proteins and noncarcinogenic molecules with or near nucleic acids. PMID:2123348

  16. Iminodicarboxylic acids in the Murchison meteorite: Evidence of Strecker reactions

    NASA Astrophysics Data System (ADS)

    Lerner, Narcinda R.; Cooper, George W.

    2005-06-01

    α-Amino acids and α-hydroxy acids are well known constituents of several carbonaceous meteorites. One proposed mechanism of their formation is the reactions of CN -, NH 3, aldehydes and ketones in aqueous solution, a Strecker-like synthesis. Iminodicarboxylic acids, relatively unusual in molecular structure, are significant by-products of laboratory Strecker syntheses of α-amino acids. It is therefore notable that an analogous suite of imino acids has not been reported in CM2 chondrites where amino and hydroxy acids are abundant. In this work, aqueous extracts of the Murchison meteorite were examined for the presence of imino acids; GC-MS and HPLC molecular analyses revealed a complex suite of such acids. With the exception of one of the seven-carbon members, all of the C4 through C7 imino acids were observed in Murchison. These observations suggest that the Strecker synthesis made, at least, some contribution to the formation of extraterrestrial amino acids.

  17. Identification of fatty acids in canine seminal plasma.

    PubMed

    Díaz, R; Inostroza, K; Risopatrón, J; Sanchez, R; Sepúlveda, N

    2014-03-01

    Seminal plasma contains various biochemical components associated with sperm function. However, there is limited information regarding the fatty acid composition of seminal plasma and their effect on sperm. The aim of this study was to identify the fatty acid content in canine seminal plasma using gas chromatography. Twelve ejaculates were studied, the seminal plasma was obtained by centrifugation and then the lipids were extracted, methylated and analysed by chromatography. The total lipids in the seminal plasma were 2.5 ± 0.3%, corresponding to 85% saturated fatty acids (SFA) and 15% unsaturated fatty acids (UFA). The greatest proportions of SFA were palmitic acid (30.4%), stearic acid (23.4%) and myristic acid (5.3%) and of UFA oleic acid (9.0%). Therefore, the protocols and techniques used enabled the identification of 18 different fatty acids in canine seminal plasma, which constitutes a good method to evaluate and quantify the fatty acid profile in this species.

  18. Stable isotopic analyses in paleoclimatic reconstruction

    SciTech Connect

    Wigand, P.E.

    1995-09-01

    Most traditional paleoclimatic proxy data have inherent time lags between climatic input and system response that constrain their use in accurate reconstruction of paleoclimate chronology, scaling of its variability, and the elucidation of the processes that determine its impact on the biotic and abiotic environment. With the exception of dendroclimatology, and studies of short-lived organisms and pollen recovered from annually varved lacustrine sediments, significant periods of time ranging from years, to centuries, to millennia may intervene between climate change and its first manifestation in paleoclimatic proxy data records. Reconstruction of past climate through changes in plant community composition derived from pollen sequences and plant remains from ancient woodrat middens, wet environments and dry caves all suffer from these lags. However, stable isotopic analyses can provide more immediate indication of biotic response to climate change. Evidence of past physiological response of organisms to changes in effective precipitation as climate varies can be provided by analyses of the stable isotopic content of plant macrofossils from various contexts. These analyses consider variation in the stable isotopic (hydrogen, oxygen and carbon) content of plant tissues as it reflects (1) past global or local temperature through changes in meteoric (rainfall) water chemistry in the case of the first two isotopes, and (2) plant stress through changes in plant respiration/transpiration processes under differing water availability, and varying atmospheric CO, composition (which itself may actually be a net result of biotic response to climate change). Studies currently being conducted in the Intermountain West indicate both long- and short-term responses that when calibrated with modem analogue studies have the potential of revealing not only the timing of climate events, but their direction, magnitude and rapidity.

  19. Quality of reporting of dental survival analyses.

    PubMed

    Layton, D M; Clarke, M

    2014-12-01

    To explore the quality of reporting (writing and graphics) of articles that used time-to-event analyses to report dental treatment outcomes. A systematic search of the top 50 dental journals in 2008 produced the sample of articles for this analysis. Articles reporting treatment outcomes with (n = 95) and without (n = 91) time-to-event statistics were reviewed. Survival descriptive words used in the two groups were analysed (Pearson's chi-square). The quality of life tables, survival curves and time-to-event statistics were assessed (Kappa analysed agreement) and explored. Words describing dental outcomes 'over time' were more common in time-to-event compared with control articles (77%, 3%, P < 0.001). Non-specific use of 'rate' was common across both groups. Life tables and survival curves were used by 39% and 48% of the time-to-event articles, with at least one used by 82%. Construction quality was poor: 21% of life tables and 28% of survival curves achieved an acceptable standard. Time-to-event statistical reporting was poor: 3% achieved a high and 59% achieved an acceptable standard. The survival statistic, summary figure and standard error were reported in 76%, 95% and 20% of time-to-event articles. Individual statistical terms and graphic aids were common within and unique to time-to-event articles. Unfortunately, important details were regularly omitted from statistical descriptions and survival figures making the overall quality poor. It is likely this will mean such articles will be incorrectly indexed in databases, missed by searchers and unable to be understood completely if identified.

  20. Combustion Devices CFD Team Analyses Review

    NASA Technical Reports Server (NTRS)

    Rocker, Marvin

    2008-01-01

    A variety of CFD simulations performed by the Combustion Devices CFD Team at Marshall Space Flight Center will be presented. These analyses were performed to support Space Shuttle operations and Ares-1 Crew Launch Vehicle design. Results from the analyses will be shown along with pertinent information on the CFD codes and computational resources used to obtain the results. Six analyses will be presented - two related to the Space Shuttle and four related to the Ares I-1 launch vehicle now under development at NASA. First, a CFD analysis of the flow fields around the Space Shuttle during the first six seconds of flight and potential debris trajectories within those flow fields will be discussed. Second, the combusting flows within the Space Shuttle Main Engine's main combustion chamber will be shown. For the Ares I-1, an analysis of the performance of the roll control thrusters during flight will be described. Several studies are discussed related to the J2-X engine to be used on the upper stage of the Ares I-1 vehicle. A parametric study of the propellant flow sequences and mixture ratios within the GOX/GH2 spark igniters on the J2-X is discussed. Transient simulations will be described that predict the asymmetric pressure loads that occur on the rocket nozzle during the engine start as the nozzle fills with combusting gases. Simulations of issues that affect temperature uniformity within the gas generator used to drive the J-2X turbines will described as well, both upstream of the chamber in the injector manifolds and within the combustion chamber itself.

  1. Time-Series Analyses of Transcriptomes and Proteomes Reveal Molecular Networks Underlying Oil Accumulation in Canola

    PubMed Central

    Wan, Huafang; Cui, Yixin; Ding, Yijuan; Mei, Jiaqin; Dong, Hongli; Zhang, Wenxin; Wu, Shiqi; Liang, Ying; Zhang, Chunyu; Li, Jiana; Xiong, Qing; Qian, Wei

    2017-01-01

    Understanding the regulation of lipid metabolism is vital for genetic engineering of canola (Brassica napus L.) to increase oil yield or modify oil composition. We conducted time-series analyses of transcriptomes and proteomes to uncover the molecular networks associated with oil accumulation and dynamic changes in these networks in canola. The expression levels of genes and proteins were measured at 2, 4, 6, and 8 weeks after pollination (WAP). Our results show that the biosynthesis of fatty acids is a dominant cellular process from 2 to 6 WAP, while the degradation mainly happens after 6 WAP. We found that genes in almost every node of fatty acid synthesis pathway were significantly up-regulated during oil accumulation. Moreover, significant expression changes of two genes, acetyl-CoA carboxylase and acyl-ACP desaturase, were detected on both transcriptomic and proteomic levels. We confirmed the temporal expression patterns revealed by the transcriptomic analyses using quantitative real-time PCR experiments. The gene set association analysis show that the biosynthesis of fatty acids and unsaturated fatty acids are the most significant biological processes from 2-4 WAP and 4-6 WAP, respectively, which is consistent with the results of time-series analyses. These results not only provide insight into the mechanisms underlying lipid metabolism, but also reveal novel candidate genes that are worth further investigation for their values in the genetic engineering of canola. PMID:28119706

  2. Method of performing computational aeroelastic analyses

    NASA Technical Reports Server (NTRS)

    Silva, Walter A. (Inventor)

    2011-01-01

    Computational aeroelastic analyses typically use a mathematical model for the structural modes of a flexible structure and a nonlinear aerodynamic model that can generate a plurality of unsteady aerodynamic responses based on the structural modes for conditions defining an aerodynamic condition of the flexible structure. In the present invention, a linear state-space model is generated using a single execution of the nonlinear aerodynamic model for all of the structural modes where a family of orthogonal functions is used as the inputs. Then, static and dynamic aeroelastic solutions are generated using computational interaction between the mathematical model and the linear state-space model for a plurality of periodic points in time.

  3. Thermal structure analyses for CSM testbed (COMET)

    NASA Technical Reports Server (NTRS)

    Xue, David Y.; Mei, Chuh

    1994-01-01

    This document is the final report for the project entitled 'Thermal Structure Analyses for CSM Testbed (COMET),' for the period of May 16, 1992 - August 15, 1994. The project was focused on the investigation and development of finite element analysis capability of the computational structural mechanics (CSM) testbed (COMET) software system in the field of thermal structural responses. The stages of this project consisted of investigating present capabilities, developing new functions, analysis demonstrations, and research topics. The appendices of this report list the detailed documents of major accomplishments and demonstration runstreams for future references.

  4. Further analyses of Rio Cuarto impact glass

    NASA Technical Reports Server (NTRS)

    Schultz, Peter H.; Bunch, T. E.; Koeberl, C.; Collins, W.

    1993-01-01

    Initial analyses of the geologic setting, petrology, and geochemistry of glasses recovered from within and around the elongate Rio Cuarto (RC) craters in Argentina focused on selected samples in order to document the general similarity with impactites around other terrestrial impact craters and to establish their origin. Continued analysis has surveyed the diversity in compositions for a range of samples, examined further evidence for temperature and pressure history, and compared the results with experimentally fused loess from oblique hypervelocity impacts. These new results not only firmly establish their impact origin but provide new insight on the impact process.

  5. Laser power beaming system analyses. Final report

    SciTech Connect

    Zeiders, G.W. Jr.

    1993-08-01

    The successful demonstration of the PAMELA adaptive optics hardware and the fabrication of the BTOS truss structure were identified by the program office as the two most critical elements of the NASA power beaming program, so it was these that received attention during this program. Much of the effort was expended in direct program support at MSFC, but detailed technical analyses of the AMP deterministic control scheme and the BTOS truss structure (both the JPL design and a spherical one) were prepared and are attached, and recommendations are given.

  6. Environmental monitoring final report: groundwater chemical analyses

    SciTech Connect

    Not Available

    1984-02-01

    This report presents the results of analyses of groundwater qualtiy at the SRC-I Demonstration Plant site in Newman, Kentucky. Samples were obtained from a network of 23 groundwater observation wells installed during previous studies. The groundwater was well within US EPA Interim Primary Drinking Water Standards for trace metals, radioactivity, and pesticides, but exceeded the standard for coliform bacteria. Several US EPA Secondary Drinking Water Standards were exceeded, namely, manganese, color, iron, and total dissolved solids. Based on the results, Dames and Moore recommend that all wells should be sterilized and those wells built in 1980 should be redeveloped. 1 figure, 6 tables.

  7. Fundamentals of fungal molecular population genetic analyses.

    PubMed

    Xu, Jianping

    2006-07-01

    The last two decades have seen tremendous growth in the development and application of molecular methods in the analyses of fungal species and populations. In this paper, I provide an overview of the molecular techniques and the basic analytical tools used to address various fundamental population and evolutionary genetic questions in fungi. With increasing availability and decreasing cost, DNA sequencing is becoming a mainstream data acquisition method in fungal evolutionary genetic studies. However, other methods, especially those based on the polymerase chain reaction, remain powerful in addressing specific questions for certain groups of taxa. These developments are bringing fungal population and evolutionary genetics into mainstream ecology and evolutionary biology.

  8. Analyses of containment structures with corrosion damage

    SciTech Connect

    Cherry, J.L.

    1996-12-31

    Corrosion damage to a nuclear power plant containment structure can degrade the pressure capacity of the vessel. For the low-carbon, low- strength steels used in containments, the effect of corrosion on material properties is discussed. Strain-to-failure tests, in uniaxial tension, have been performed on corroded material samples. Results were used to select strain-based failure criteria for corroded steel. Using the ABAQUS finite element analysis code, the capacity of a typical PWR Ice Condenser containment with corrosion damage has been studied. Multiple analyses were performed with the locations of the corrosion the containment, and the amount of corrosion varied in each analysis.

  9. Effect of rice straw application on microbial community and activity in paddy soil under different water status.

    PubMed

    Pan, Fuxia; Li, Yaying; Chapman, Stephen James; Yao, Huaiying

    2016-03-01

    Rice straw application and flooding are common practices in rice production, both of which can induce changes in the microbial community. This study used soil microcosms to investigate the impact of water status (saturated and nonsaturated) and straw application (10 g kg(-1) soil) on soil microbial composition (phospholipid fatty acid analysis) and activity (MicroResp(™) method). Straw application significantly increased total PLFA amount and individual PLFA components independent of soil moisture level. The amount of soil fungal PLFA was less than Gram-negative, Gram-positive, and actinomycete PLFA, except the drained treatment with rice straw application, which had higher fungal PLFA than actinomycete PLFA at the initial incubation stage. Straw amendment and waterlogging had different effects on microbial community structure and substrate-induced pattern. PLFA profiles were primarily influenced by straw application, whereas soil water status had the greater influence on microbial respiration. Of the variation in PLFA and respiration data, straw accounted for 30.1 and 16.7 %, while soil water status explained 7.5 and 29.1 %, respectively. Our results suggest that (1) the size of microbial communities in paddy soil is more limited by carbon substrate availability rather than by the anaerobic conditions due to waterlogging and (2) that soil water status is more important as a control of fungal growth and microbial community activity.

  10. Folic Acid and Pregnancy

    MedlinePlus

    ... Feeding Your 1- to 2-Year-Old Folic Acid and Pregnancy KidsHealth > For Parents > Folic Acid and ... before conception and during early pregnancy . About Folic Acid Folic acid, sometimes called folate, is a B ...

  11. Molecular cloning of chicken aggrecan. Structural analyses.

    PubMed Central

    Chandrasekaran, L; Tanzer, M L

    1992-01-01

    The large, aggregating chondroitin sulphate proteoglycan of cartilage, aggrecan, has served as a generic model of proteoglycan structure. Molecular cloning of aggrecans has further defined their amino acid sequences and domain structures. In this study, we have obtained the complete coding sequence of chicken sternal cartilage aggrecan by a combination of cDNA and genomic DNA sequencing. The composite sequence is 6117 bp in length, encoding 1951 amino acids. Comparison of chicken aggrecan protein primary structure with rat, human and bovine aggrecans has disclosed both similarities and differences. The domains which are most highly conserved at 70-80% identity are the N-terminal domains G1 and G2 and the C-terminal domain G3. The chondroitin sulphate domain of chicken aggrecan is smaller than that of rat and human aggrecans and has very distinctive repeat sequences. It has two separate sections, one comprising 12 consecutive Ser-Gly-Glu repeats of 20 amino acids each, adjacent to the other which has 23 discontinuous Ser-Gly-Glu repeats of 10 amino acids each; this latter region, N-terminal to the former one, appears to be unique to chicken aggrecan. The two regions contain a total of 94 potential chondroitin sulphate attachment sites. Genomic comparison shows that, although chicken exons 11-14 are identical in size to the rat and human exons, chicken exon 10 is the smallest of the three species. This is also reflected in the size of its chondroitin sulphate coding region and in the total number of Ser-Gly pairs. The putative keratan sulphate domain shows 31-45% identity with the other species and lacks the repetitive sequences seen in the others. In summary, while the linear arrangement of specific domains of chicken aggrecan is identical to that in the aggrecans of other species, and while there is considerable identity of three separate domains, chicken aggrecan demonstrates unique features, notably in its chondroitin sulphate domain and its keratan sulphate

  12. Nonindependence and sensitivity analyses in ecological and evolutionary meta-analyses.

    PubMed

    Noble, Daniel W A; Lagisz, Malgorzata; O'dea, Rose E; Nakagawa, Shinichi

    2017-01-30

    Meta-analysis is an important tool for synthesizing research on a variety of topics in ecology and evolution, including molecular ecology, but can be susceptible to nonindependence. Nonindependence can affect two major interrelated components of a meta-analysis: (i) the calculation of effect size statistics and (ii) the estimation of overall meta-analytic estimates and their uncertainty. While some solutions to nonindependence exist at the statistical analysis stages, there is little advice on what to do when complex analyses are not possible, or when studies with nonindependent experimental designs exist in the data. Here we argue that exploring the effects of procedural decisions in a meta-analysis (e.g. inclusion of different quality data, choice of effect size) and statistical assumptions (e.g. assuming no phylogenetic covariance) using sensitivity analyses are extremely important in assessing the impact of nonindependence. Sensitivity analyses can provide greater confidence in results and highlight important limitations of empirical work (e.g. impact of study design on overall effects). Despite their importance, sensitivity analyses are seldom applied to problems of nonindependence. To encourage better practice for dealing with nonindependence in meta-analytic studies, we present accessible examples demonstrating the impact that ignoring nonindependence can have on meta-analytic estimates. We also provide pragmatic solutions for dealing with nonindependent study designs, and for analysing dependent effect sizes. Additionally, we offer reporting guidelines that will facilitate disclosure of the sources of nonindependence in meta-analyses, leading to greater transparency and more robust conclusions.

  13. Yeast genes involved in response to lactic acid and acetic acid: acidic conditions caused by the organic acids in Saccharomyces cerevisiae cultures induce expression of intracellular metal metabolism genes regulated by Aft1p.

    PubMed

    Kawahata, Miho; Masaki, Kazuo; Fujii, Tsutomu; Iefuji, Haruyuki

    2006-09-01

    Using two types of genome-wide analysis to investigate yeast genes involved in response to lactic acid and acetic acid, we found that the acidic condition affects metal metabolism. The first type is an expression analysis using DNA microarrays to investigate 'acid shock response' as the first step to adapt to an acidic condition, and 'acid adaptation' by maintaining integrity in the acidic condition. The other is a functional screening using the nonessential genes deletion collection of Saccharomyces cerevisiae. The expression analysis showed that genes involved in stress response, such as YGP1, TPS1 and HSP150, were induced under the acid shock response. Genes such as FIT2, ARN1 and ARN2, involved in metal metabolism regulated by Aft1p, were induced under the acid adaptation. AFT1 was induced under acid shock response and under acid adaptation with lactic acid. Moreover, green fluorescent protein-fused Aft1p was localized to the nucleus in cells grown in media containing lactic acid, acetic acid, or hydrochloric acid. Both analyses suggested that the acidic condition affects cell wall architecture. The depletion of cell-wall components encoded by SED1, DSE2, CTS1, EGT2, SCW11, SUN4 and YNL300W and histone acetyltransferase complex proteins encoded by YID21, EAF3, EAF5, EAF6 and YAF9 increased resistance to lactic acid. Depletion of the cell-wall mannoprotein Sed1p provided resistance to lactic acid, although the expression of SED1 was induced by exposure to lactic acid. Depletion of vacuolar membrane H+-ATPase and high-osmolarity glycerol mitogen-activated protein kinase proteins caused acid sensitivity. Moreover, our quantitative PCR showed that expression of PDR12 increased under acid shock response with lactic acid and decreased under acid adaptation with hydrochloric acid.

  14. Fractal and multifractal analyses of bipartite networks.

    PubMed

    Liu, Jin-Long; Wang, Jian; Yu, Zu-Guo; Xie, Xian-Hua

    2017-03-31

    Bipartite networks have attracted considerable interest in various fields. Fractality and multifractality of unipartite (classical) networks have been studied in recent years, but there is no work to study these properties of bipartite networks. In this paper, we try to unfold the self-similarity structure of bipartite networks by performing the fractal and multifractal analyses for a variety of real-world bipartite network data sets and models. First, we find the fractality in some bipartite networks, including the CiteULike, Netflix, MovieLens (ml-20m), Delicious data sets and (u, v)-flower model. Meanwhile, we observe the shifted power-law or exponential behavior in other several networks. We then focus on the multifractal properties of bipartite networks. Our results indicate that the multifractality exists in those bipartite networks possessing fractality. To capture the inherent attribute of bipartite network with two types different nodes, we give the different weights for the nodes of different classes, and show the existence of multifractality in these node-weighted bipartite networks. In addition, for the data sets with ratings, we modify the two existing algorithms for fractal and multifractal analyses of edge-weighted unipartite networks to study the self-similarity of the corresponding edge-weighted bipartite networks. The results show that our modified algorithms are feasible and can effectively uncover the self-similarity structure of these edge-weighted bipartite networks and their corresponding node-weighted versions.

  15. Waste Stream Analyses for Nuclear Fuel Cycles

    SciTech Connect

    N. R. Soelberg

    2010-08-01

    A high-level study was performed in Fiscal Year 2009 for the U.S. Department of Energy (DOE) Office of Nuclear Energy (NE) Advanced Fuel Cycle Initiative (AFCI) to provide information for a range of nuclear fuel cycle options (Wigeland 2009). At that time, some fuel cycle options could not be adequately evaluated since they were not well defined and lacked sufficient information. As a result, five families of these fuel cycle options are being studied during Fiscal Year 2010 by the Systems Analysis Campaign for the DOE NE Fuel Cycle Research and Development (FCRD) program. The quality and completeness of data available to date for the fuel cycle options is insufficient to perform quantitative radioactive waste analyses using recommended metrics. This study has been limited thus far to qualitative analyses of waste streams from the candidate fuel cycle options, because quantitative data for wastes from the front end, fuel fabrication, reactor core structure, and used fuel for these options is generally not yet available.

  16. Used Fuel Management System Interface Analyses - 13578

    SciTech Connect

    Howard, Robert; Busch, Ingrid; Nutt, Mark; Morris, Edgar; Puig, Francesc; Carter, Joe; Delley, Alexcia; Rodwell, Phillip; Hardin, Ernest; Kalinina, Elena; Clark, Robert; Cotton, Thomas

    2013-07-01

    Preliminary system-level analyses of the interfaces between at-reactor used fuel management, consolidated storage facilities, and disposal facilities, along with the development of supporting logistics simulation tools, have been initiated to provide the U.S. Department of Energy (DOE) and other stakeholders with information regarding the various alternatives for managing used nuclear fuel (UNF) generated by the current fleet of light water reactors operating in the United States. An important UNF management system interface consideration is the need for ultimate disposal of UNF assemblies contained in waste packages that are sized to be compatible with different geologic media. Thermal analyses indicate that waste package sizes for the geologic media under consideration by the Used Fuel Disposition Campaign may be significantly smaller than the canisters being used for on-site dry storage by the nuclear utilities. Therefore, at some point along the UNF disposition pathway, there could be a need to repackage fuel assemblies already loaded and being loaded into the dry storage canisters currently in use. The implications of where and when the packaging or repackaging of commercial UNF will occur are key questions being addressed in this evaluation. The analysis demonstrated that thermal considerations will have a major impact on the operation of the system and that acceptance priority, rates, and facility start dates have significant system implications. (authors)

  17. Computational analyses of multilevel discourse comprehension.

    PubMed

    Graesser, Arthur C; McNamara, Danielle S

    2011-04-01

    The proposed multilevel framework of discourse comprehension includes the surface code, the textbase, the situation model, the genre and rhetorical structure, and the pragmatic communication level. We describe these five levels when comprehension succeeds and also when there are communication misalignments and comprehension breakdowns. A computer tool has been developed, called Coh-Metrix, that scales discourse (oral or print) on dozens of measures associated with the first four discourse levels. The measurement of these levels with an automated tool helps researchers track and better understand multilevel discourse comprehension. Two sets of analyses illustrate the utility of Coh-Metrix in discourse theory and educational practice. First, Coh-Metrix was used to measure the cohesion of the text base and situation model, as well as potential extraneous variables, in a sample of published studies that manipulated text cohesion. This analysis helped us better understand what was precisely manipulated in these studies and the implications for discourse comprehension mechanisms. Second, Coh-Metrix analyses are reported for samples of narrative and science texts in order to advance the argument that traditional text difficulty measures are limited because they fail to accommodate most of the levels of the multilevel discourse comprehension framework.

  18. Fractal and multifractal analyses of bipartite networks

    PubMed Central

    Liu, Jin-Long; Wang, Jian; Yu, Zu-Guo; Xie, Xian-Hua

    2017-01-01

    Bipartite networks have attracted considerable interest in various fields. Fractality and multifractality of unipartite (classical) networks have been studied in recent years, but there is no work to study these properties of bipartite networks. In this paper, we try to unfold the self-similarity structure of bipartite networks by performing the fractal and multifractal analyses for a variety of real-world bipartite network data sets and models. First, we find the fractality in some bipartite networks, including the CiteULike, Netflix, MovieLens (ml-20m), Delicious data sets and (u, v)-flower model. Meanwhile, we observe the shifted power-law or exponential behavior in other several networks. We then focus on the multifractal properties of bipartite networks. Our results indicate that the multifractality exists in those bipartite networks possessing fractality. To capture the inherent attribute of bipartite network with two types different nodes, we give the different weights for the nodes of different classes, and show the existence of multifractality in these node-weighted bipartite networks. In addition, for the data sets with ratings, we modify the two existing algorithms for fractal and multifractal analyses of edge-weighted unipartite networks to study the self-similarity of the corresponding edge-weighted bipartite networks. The results show that our modified algorithms are feasible and can effectively uncover the self-similarity structure of these edge-weighted bipartite networks and their corresponding node-weighted versions. PMID:28361962

  19. Analyses of containment structures with corrosion damage

    SciTech Connect

    Cherry, J.L.

    1997-01-01

    Corrosion damage that has been found in a number of nuclear power plant containment structures can degrade the pressure capacity of the vessel. This has prompted concerns regarding the capacity of corroded containments to withstand accident loadings. To address these concerns, finite element analyses have been performed for a typical PWR Ice Condenser containment structure. Using ABAQUS, the pressure capacity was calculated for a typical vessel with no corrosion damage. Multiple analyses were then performed with the location of the corrosion and the amount of corrosion varied in each analysis. Using a strain-based failure criterion, a {open_quotes}lower bound{close_quotes}, {open_quotes}best estimate{close_quotes}, and {open_quotes}upper bound{close_quotes} failure level was predicted for each case. These limits were established by: determining the amount of variability that exists in material properties of typical containments, estimating the amount of uncertainty associated with the level of modeling detail and modeling assumptions, and estimating the effect of corrosion on the material properties.

  20. Integrated Genomic Analyses of Ovarian Carcinoma

    PubMed Central

    2011-01-01

    Summary The Cancer Genome Atlas (TCGA) project has analyzed mRNA expression, miRNA expression, promoter methylation, and DNA copy number in 489 high-grade serous ovarian adenocarcinomas (HGS-OvCa) and the DNA sequences of exons from coding genes in 316 of these tumors. These results show that HGS-OvCa is characterized by TP53 mutations in almost all tumors (96%); low prevalence but statistically recurrent somatic mutations in 9 additional genes including NF1, BRCA1, BRCA2, RB1, and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three miRNA subtypes, four promoter methylation subtypes, a transcriptional signature associated with survival duration and shed new light on the impact on survival of tumors with BRCA1/2 and CCNE1 aberrations. Pathway analyses suggested that homologous recombination is defective in about half of tumors, and that Notch and FOXM1 signaling are involved in serous ovarian cancer pathophysiology. PMID:21720365

  1. Autisme et douleur – analyse bibliographique

    PubMed Central

    Dubois, Amandine; Rattaz, Cécile; Pry, René; Baghdadli, Amaria

    2010-01-01

    La présente analyse bibliographique a pour objectif de réaliser un bilan des travaux publiés dans le champ de la douleur et de l’autisme. L’article aborde, dans un premier temps, les études publiées concernant les modes d’expression de la douleur observés dans cette population. Différentes hypothèses permettant d’expliquer les particularités expressives des personnes avec autisme sont ensuite passées en revue : excès d’endorphines, particularités dans le traitement sensoriel, déficit sociocommunicatif. Cette analyse bibliographique aborde, pour terminer, la question de l’évaluation et de la prise en compte de la douleur chez les personnes avec autisme. Les auteurs concluent à l’absence d’homogénéité des résultats des études publiées et au besoin de poursuivre les recherches afin de parvenir à des données consensuelles sur un domaine d’étude encore peu exploité au plan scientifique. Sur un plan clinique, l’approfondissement des connaissances dans ce domaine devrait permettre de mettre au point des outils d’évaluation de la douleur et d’ainsi en assurer une meilleure prise en charge au quotidien. PMID:20808970

  2. NEXT Ion Thruster Performance Dispersion Analyses

    NASA Technical Reports Server (NTRS)

    Soulas, George C.; Patterson, Michael J.

    2008-01-01

    The NEXT ion thruster is a low specific mass, high performance thruster with a nominal throttling range of 0.5 to 7 kW. Numerous engineering model and one prototype model thrusters have been manufactured and tested. Of significant importance to propulsion system performance is thruster-to-thruster performance dispersions. This type of information can provide a bandwidth of expected performance variations both on a thruster and a component level. Knowledge of these dispersions can be used to more conservatively predict thruster service life capability and thruster performance for mission planning, facilitate future thruster performance comparisons, and verify power processor capabilities are compatible with the thruster design. This study compiles the test results of five engineering model thrusters and one flight-like thruster to determine unit-to-unit dispersions in thruster performance. Component level performance dispersion analyses will include discharge chamber voltages, currents, and losses; accelerator currents, electron backstreaming limits, and perveance limits; and neutralizer keeper and coupling voltages and the spot-to-plume mode transition flow rates. Thruster level performance dispersion analyses will include thrust efficiency.

  3. Bioinformatics tools for analysing viral genomic data.

    PubMed

    Orton, R J; Gu, Q; Hughes, J; Maabar, M; Modha, S; Vattipally, S B; Wilkie, G S; Davison, A J

    2016-04-01

    The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing.

  4. [On the nonexistence of propionic acid in various kinds of breeds (author's transl)].

    PubMed

    Lück, E; Oeser, H; Remmert, K H; Sabel, J

    1975-05-30

    Analyses of 45 samples of sour dough and various kinds of bread have shown that no appreciable amounts of propionic acid are formed during sour dough fermentation. Bread has no natural propionic acid content.

  5. Understanding Acid Rain

    ERIC Educational Resources Information Center

    Damonte, Kathleen

    2004-01-01

    The term acid rain describes rain, snow, or fog that is more acidic than normal precipitation. To understand what acid rain is, it is first necessary to know what an acid is. Acids can be defined as substances that produce hydrogen ions (H+), when dissolved in water. Scientists indicate how acidic a substance is by a set of numbers called the pH…

  6. New Bioactive Fatty Acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many oxygenated fatty acids are bioactive compounds. Nocardia cholesterolicum and Flavobacterium DS5 convert oleic acid to 10 hydroxy stearic acid and linoleic acid to 10-hydroxy-12(Z)-octadecanoic acid. Pseudomonas aeruginosa PR3 converts oleic acid to new compounds, 7,10-dihydroxy-8(E)-octadecen...

  7. New bioactive fatty acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many oxygenated fatty acids are bioactive compounds. Nocardia cholesterolicum and Flavobacterium DS5 convert oleic acid to 10 hydroxy stearic acid and linoleic acid to 10-hydroxy-12(Z)-octadecanoic acid. Pseudomonas aeruginosa PR3 converts oleic acid to the new compounds, 7,10-dihydroxy-8(E)-octad...

  8. Physicochemical and Phytochemical Analyses of Copra and Oil of Cocos nucifera L. (West Coast Tall Variety)

    PubMed Central

    Ghosh, Probir Kumar; Bhattacharjee, Paramita; Mitra, Souvik; Poddar-Sarkar, Mousumi

    2014-01-01

    Coconut copra from West coast tall variety, cultivated in Kerala, India, was subjected to aqueous and solvent extractions (using n-hexane). Additionally, oil was extracted from the copra in Soxhlet assembly using petroleum ether (b.p. 60–80°C). Physicochemical and phytochemical analyses were conducted for the extracts and the oil, with commercial coconut oil as the experimental control. The physicochemical analyses showed that the aqueous extract of copra was milky-white in color with a sweet odor, while the solvent extract was pale yellow and odorless. The commercial oil had 0.08 ± 0.02% oleic acid and a TOTOX value of 7.73 ± 0.78, lower than the Soxhlet extracted oil. Among all the extracts and oils, best phytochemical properties, antioxidant activity (DPPH activity, IC50 value 0.04 ± 0.01 mg/mL), total phenol (0.96 ± 0.04 mg gallic acid eq./g dry copra), reducing power (40.49 ± 1.84 mg BHT eq./g dry copra), and anti-inflammatory activity (NO activity, IC50  value 0.77 ± 0.06 mg/mL) were obtained in the commercial coconut oil, followed by the Soxhlet extracted oil, aqueous extract, and solvent extract. Fatty acid composition analyses showed mainly medium chain fatty acids in the copra oil with lauric acid as the predominant fatty acid (51.88% and 44.84% in Soxhlet extracted and commercial oils, resp.). PMID:26904626

  9. Physicochemical and Phytochemical Analyses of Copra and Oil of Cocos nucifera L. (West Coast Tall Variety).

    PubMed

    Ghosh, Probir Kumar; Bhattacharjee, Paramita; Mitra, Souvik; Poddar-Sarkar, Mousumi

    2014-01-01

    Coconut copra from West coast tall variety, cultivated in Kerala, India, was subjected to aqueous and solvent extractions (using n-hexane). Additionally, oil was extracted from the copra in Soxhlet assembly using petroleum ether (b.p. 60-80°C). Physicochemical and phytochemical analyses were conducted for the extracts and the oil, with commercial coconut oil as the experimental control. The physicochemical analyses showed that the aqueous extract of copra was milky-white in color with a sweet odor, while the solvent extract was pale yellow and odorless. The commercial oil had 0.08 ± 0.02% oleic acid and a TOTOX value of 7.73 ± 0.78, lower than the Soxhlet extracted oil. Among all the extracts and oils, best phytochemical properties, antioxidant activity (DPPH activity, IC50 value 0.04 ± 0.01 mg/mL), total phenol (0.96 ± 0.04 mg gallic acid eq./g dry copra), reducing power (40.49 ± 1.84 mg BHT eq./g dry copra), and anti-inflammatory activity (NO activity, IC50  value 0.77 ± 0.06 mg/mL) were obtained in the commercial coconut oil, followed by the Soxhlet extracted oil, aqueous extract, and solvent extract. Fatty acid composition analyses showed mainly medium chain fatty acids in the copra oil with lauric acid as the predominant fatty acid (51.88% and 44.84% in Soxhlet extracted and commercial oils, resp.).

  10. Acid rain

    SciTech Connect

    Boyle, R.H.; Boyle, R.A.

    1983-01-01

    Acid rain, says Boyle is a chemical leprosy eating into the face of North America and Europe, perhaps the major ecological problem of our time. Boyle describes the causes and scope of the phenomenon; the effects on man, wildlife, water, and our cultural heritage. He probes the delays of politicians and the frequent self-serving arguments advanced by industry in the face of what scientists have proved. The solutions he offers are to strengthen the Clean Air Act and require emission reductions that can be accomplished by establishing emission standards on a regional or bubble basis, burn low-sulfur coal, install scrubbers at critical plants, and invest in alternative energy sources. 73 references, 1 figure.

  11. Time series analyses of global change data.

    PubMed

    Lane, L J; Nichols, M H; Osborn, H B

    1994-01-01

    The hypothesis that statistical analyses of historical time series data can be used to separate the influences of natural variations from anthropogenic sources on global climate change is tested. Point, regional, national, and global temperature data are analyzed. Trend analyses for the period 1901-1987 suggest mean annual temperatures increased (in degrees C per century) globally at the rate of about 0.5, in the USA at about 0.3, in the south-western USA desert region at about 1.2, and at the Walnut Gulch Experimental Watershed in south-eastern Arizona at about 0.8. However, the rates of temperature change are not constant but vary within the 87-year period. Serial correlation and spectral density analysis of the temperature time series showed weak periodicities at various frequencies. The only common periodicity among the temperature series is an apparent cycle of about 43 years. The temperature time series were correlated with the Wolf sunspot index, atmospheric CO(2) concentrations interpolated from the Siple ice core data, and atmospheric CO(2) concentration data from Mauna Loa measurements. Correlation analysis of temperature data with concurrent data on atmospheric CO(2) concentrations and the Wolf sunspot index support previously reported significant correlation over the 1901-1987 period. Correlation analysis between temperature, atmospheric CO(2) concentration, and the Wolf sunspot index for the shorter period, 1958-1987, when continuous Mauna Loa CO(2) data are available, suggest significant correlation between global warming and atmospheric CO(2) concentrations but no significant correlation between global warming and the Wolf sunspot index. This may be because the Wolf sunspot index apparently increased from 1901 until about 1960 and then decreased thereafter, while global warming apparently continued to increase through 1987. Correlation of sunspot activity with global warming may be spurious but additional analyses are required to test this hypothesis

  12. Comparative Transcriptional Analyses of Francisella tularensis and Francisella novicida

    PubMed Central

    Waldo, Robert H.; Belland, Robert J.; Klose, Karl E.

    2016-01-01

    Francisella tularensis is composed of a number of subspecies with varied geographic distribution, host ranges, and virulence. In view of these marked differences, comparative functional genomics may elucidate some of the molecular mechanism(s) behind these differences. In this study a shared probe microarray was designed that could be used to compare the transcriptomes of Francisella tularensis subsp. tularensis Schu S4 (Ftt), Francisella tularensis subsp. holarctica OR960246 (Fth), Francisella tularensis subsp. holarctica LVS (LVS), and Francisella novicida U112 (Fn). To gain insight into expression differences that may be related to the differences in virulence of these subspecies, transcriptomes were measured from each strain grown in vitro under identical conditions, utilizing a shared probe microarray. The human avirulent Fn strain exhibited high levels of transcription of genes involved in general metabolism, which are pseudogenes in the human virulent Ftt and Fth strains, consistent with the process of genome decay in the virulent strains. Genes encoding an efflux system (emrA2 cluster of genes), siderophore (fsl operon), acid phosphatase, LPS synthesis, polyamine synthesis, and citrulline ureidase were all highly expressed in Ftt when compared to Fn, suggesting that some of these may contribute to the relative high virulence of Ftt. Genes expressed at a higher level in Ftt when compared to the relatively less virulent Fth included genes encoding isochorismatases, cholylglycine hydrolase, polyamine synthesis, citrulline ureidase, Type IV pilus subunit, and the Francisella Pathogenicity Island protein PdpD. Fth and LVS had very few expression differences, consistent with the derivation of LVS from Fth. This study demonstrated that a shared probe microarray designed to detect transcripts in multiple species/subspecies of Francisella enabled comparative transcriptional analyses that may highlight critical differences that underlie the relative pathogenesis of

  13. Precise Chemical Analyses of Planetary Surfaces

    NASA Technical Reports Server (NTRS)

    Kring, David; Schweitzer, Jeffrey; Meyer, Charles; Trombka, Jacob; Freund, Friedemann; Economou, Thanasis; Yen, Albert; Kim, Soon Sam; Treiman, Allan H.; Blake, David; Lisse, Carey

    1996-01-01

    We identify the chemical elements and element ratios that should be analyzed to address many of the issues identified by the Committee on Planetary and Lunar Exploration (COMPLEX). We determined that most of these issues require two sensitive instruments to analyze the necessary complement of elements. In addition, it is useful in many cases to use one instrument to analyze the outermost planetary surface (e.g. to determine weathering effects), while a second is used to analyze a subsurface volume of material (e.g., to determine the composition of unaltered planetary surface material). This dual approach to chemical analyses will also facilitate the calibration of orbital and/or Earth-based spectral observations of the planetary body. We determined that in many cases the scientific issues defined by COMPLEX can only be fully addressed with combined packages of instruments that would supplement the chemical data with mineralogic or visual information.

  14. FACS binding assay for analysing GDNF interactions.

    PubMed

    Quintino, Luís; Baudet, Aurélie; Larsson, Jonas; Lundberg, Cecilia

    2013-08-15

    Glial cell-line derived neurotrophic factor (GDNF) is a secreted protein with great therapeutic potential. However, in order to analyse the interactions between GDNF and its receptors, researchers have been mostly dependent of radioactive binding assays. We developed a FACS-based binding assay for GDNF as an alternative to current methods. We demonstrated that the FACS-based assay using TGW cells allowed readily detection of GDNF binding and displacement to endogenous receptors. The dissociation constant and half maximal inhibitory concentration obtained were comparable to other studies using standard binding assays. Overall, this FACS-based, simple to perform and adaptable to high throughput setup, provides a safer and reliable alternative to radioactive methods.

  15. Phylogenomic Analyses Support Traditional Relationships within Cnidaria.

    PubMed

    Zapata, Felipe; Goetz, Freya E; Smith, Stephen A; Howison, Mark; Siebert, Stefan; Church, Samuel H; Sanders, Steven M; Ames, Cheryl Lewis; McFadden, Catherine S; France, Scott C; Daly, Marymegan; Collins, Allen G; Haddock, Steven H D; Dunn, Casey W; Cartwright, Paulyn

    2015-01-01

    Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses using different partition schemes and models of molecular evolution, as well as topology tests for alternative phylogenetic relationships, support the monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly of Hexacorallia is weak due to the equivocal position of Ceriantharia. Taken together, these results further resolve deep cnidarian relationships, largely support traditional phylogenetic views on relationships, and provide a historical framework for studying the evolutionary processes involved in one of the most ancient animal radiations.

  16. Determining Significant Endpoints for Ecological risk Analyses

    SciTech Connect

    Hinton, Thimas G.; Bedford, Joel

    1999-06-01

    Our interest is in obtaining a scientifically defensible endpoint for measuring ecological risks to populations exposed to chronic, low-level radiation, and radiation with concomitant exposure to chemicals. To do so, we believe that we must understand the extent to which molecular damage is detrimental at the individual and population levels of biological organization. Ecological risk analyses based on molecular damage, without an understanding of the impacts to higher levels of biological organization, could cause cleanup strategies on DOE sites to be overly conservative and unnecessarily expensive. Our goal is to determine the relevancy of sublethal cellular damage to the performance of individuals and populations. We think that we can achieve this by using novel biological dosimeters in controlled, manipulative dose/effects experiments, and by coupling changes in metabolic rates and energy allocation patterns to meaningful population response variables such as age-specific survivorship, reproductive output, age at maturity and longevity.

  17. [Use of pharmacoeconomics analyses to health protection].

    PubMed

    Drozd, Mariola

    2002-01-01

    The pharmacoeconomics makes possible a most favourable utilization of capital resources appropriated for the health protection. For the use of economic analysis health and effects of disease and its treatment are represented in absolute values having a common base--money. The economic analysis is usually carried out from a certain perspective. Something, what is an expense for someone can be a profit for someone else. This work is a review of available Polish literature describing main assumptions of the pharmoeconomics and its instruments--the pharmacoeconomic analyses. As a result of the review it has been ascertained that a modern medicine can not do without economics. At present the capital resources are constantly too small, profitability of an employed method of the therapy or drug must be assessed all the time.

  18. An introduction to modern missing data analyses.

    PubMed

    Baraldi, Amanda N; Enders, Craig K

    2010-02-01

    A great deal of recent methodological research has focused on two modern missing data analysis methods: maximum likelihood and multiple imputation. These approaches are advantageous to traditional techniques (e.g. deletion and mean imputation techniques) because they require less stringent assumptions and mitigate the pitfalls of traditional techniques. This article explains the theoretical underpinnings of missing data analyses, gives an overview of traditional missing data techniques, and provides accessible descriptions of maximum likelihood and multiple imputation. In particular, this article focuses on maximum likelihood estimation and presents two analysis examples from the Longitudinal Study of American Youth data. One of these examples includes a description of the use of auxiliary variables. Finally, the paper illustrates ways that researchers can use intentional, or planned, missing data to enhance their research designs.

  19. Neutronic Analyses of the Trade Demonstration Facility

    SciTech Connect

    Rubbia, C.

    2004-09-15

    The TRiga Accelerator-Driven Experiment (TRADE), to be performed in the TRIGA reactor of the ENEA-Casaccia Centre in Italy, consists of the coupling of an external proton accelerator to a target to be installed in the central channel of the reactor scrammed to subcriticality. This pilot experiment, aimed at a global demonstration of the accelerator-driven system concept, is based on an original idea of C. Rubbia. The present paper reports the results of some neutronic analyses focused on the feasibility of TRADE. Results show that all relevant experiments (at different power levels in a wide range of subcriticalities) can be carried out with relatively limited modifications to the present TRIGA reactor.

  20. Error analyses for a gravity gradiometer mission

    NASA Technical Reports Server (NTRS)

    Kahn, W. D.; Von Bun, F. O.

    1985-01-01

    This paper addresses the usefulness of an orbiting gravity gradiometer as a sensor for mapping the fine structure of the earth gravity field. The exact knowledge of this field is essential for studies of the solid earth and the dynamics of the oceans. Although the earth gravity tensor, measured by a gradiometer assembly, has nine components, only five components are independent. This latter fact is as a consequence of the symmetry and conservative nature of the earth's gravity field. The most dominant component is the radial one. The error analyses considered here are therefore based only upon a single axis gradiometer sensing this radial component. The expected global gravity and geoid errors for a 50 x 50-km (1/2 x 1/2 deg) area utilizing a spaceborne gradiometer with a precision of 0.001 EU in a 160-km circular polar orbit are about 3 mGAL and 5 cm, respectively.

  1. TRACE ELEMENT ANALYSES OF URANIUM MATERIALS

    SciTech Connect

    Beals, D; Charles Shick, C

    2008-06-09

    The Savannah River National Laboratory (SRNL) has developed an analytical method to measure many trace elements in a variety of uranium materials at the high part-per-billion (ppb) to low part-per-million (ppm) levels using matrix removal and analysis by quadrapole ICP-MS. Over 35 elements were measured in uranium oxides, acetate, ore and metal. Replicate analyses of samples did provide precise results however none of the materials was certified for trace element content thus no measure of the accuracy could be made. The DOE New Brunswick Laboratory (NBL) does provide a Certified Reference Material (CRM) that has provisional values for a series of trace elements. The NBL CRM were purchased and analyzed to determine the accuracy of the method for the analysis of trace elements in uranium oxide. These results are presented and discussed in the following paper.

  2. Project analysis and integration economic analyses summary

    NASA Technical Reports Server (NTRS)

    Macomber, H. L.

    1986-01-01

    An economic-analysis summary was presented for the manufacture of crystalline-silicon modules involving silicon ingot/sheet, growth, slicing, cell manufacture, and module assembly. Economic analyses provided: useful quantitative aspects for complex decision-making to the Flat-plate Solar Array (FSA) Project; yardsticks for design and performance to industry; and demonstration of how to evaluate and understand the worth of research and development both to JPL and other government agencies and programs. It was concluded that future research and development funds for photovoltaics must be provided by the Federal Government because the solar industry today does not reap enough profits from its present-day sales of photovoltaic equipment.

  3. Spatially explicit analyses unveil density dependence.

    PubMed Central

    Veldtman, Ruan; McGeoch, Melodie A.

    2004-01-01

    Density-dependent processes are fundamental in the understanding of species population dynamics. Whereas the benefits of considering the spatial dimension in population biology are widely acknowledged, the implications of doing so for the statistical detection of spatial density dependence have not been examined. The outcome of traditional tests may therefore differ from those that include ecologically relevant locational information on both the prey species and natural enemy. Here, we explicitly incorporate spatial information on individual counts when testing for density dependence between an insect herbivore and its parasitoids. The spatially explicit approach used identified significant density dependence more frequently and in different instances than traditional methods. The form of density dependence detected also differed between methods. These results demonstrate that the explicit consideration of patch location in density-dependence analyses is likely to significantly alter current understanding of the prevalence and form of spatial density dependence in natural populations. PMID:15590593

  4. Ensemble decadal predictions from analysed initial conditions.

    PubMed

    Troccoli, Alberto; Palmer, T N

    2007-08-15

    Sensitivity experiments using a coupled model initialized from analysed atmospheric and oceanic observations are used to investigate the potential for interannual-to-decadal predictability. The potential for extending seasonal predictions to longer time scales is explored using the same coupled model configuration and initialization procedure as used for seasonal prediction. It is found that, despite model drift, climatic signals on interannual-to-decadal time scales appear to be detectable. Two climatic states have been chosen: one starting in 1965, i.e. ahead of a period of global cooling, and the other in 1994, ahead of a period of global warming. The impact of initial conditions and of the different levels of greenhouse gases are isolated in order to gain insights into the source of predictability.

  5. Life cycle analyses and resource assessments.

    PubMed

    Fredga, Karl; Mäler, Karl-Göran

    2010-01-01

    Prof. Ulgiati stresses that we should always use an ecosystem view when transforming energy from one form to another. Sustainable growth and development of both environmental and human-dominated systems require optimum use of available resources for maximum power output. We have to adapt to the laws of nature because nature has to take care of all the waste products we produce. The presentation addresses a much needed shift away from linear production and consumption pattern, toward reorganization of economies and lifestyle that takes complexity--of resources, of the environment and of the economy--into proper account. The best way to reach maximum yield from the different kinds of biomass is to use biorefineries. Biorefinery is defined as the sustainable processing of biomass into a spectrum of marketable products like heat, power, fuels, chemicals, food, feed, and materials. However, biomass from agricultural land must be used for the production of food and not fuel. Prof. Voss focuses on the sustainability of energy supply chains and energy systems. Life cycle analyses (LCA) provides the conceptual framework for a comprehensive comparative evaluation of energy supply options with regard to their resource requirements as well as the health and environmental impact. Full scope LCA considers not only the emissions from plant operation, construction, and decommissioning but also the environmental burdens and resource requirements associated with the entire lifetime of all relevant upstream and downstream processes within the energy chain. This article describes the results of LCA analyses for state-of-the-art heating and electricity systems as well as of advanced future systems. Total costs are used as a measure for the overall resource consumption.

  6. Topological Analyses of Symmetric Eruptive Prominences

    NASA Astrophysics Data System (ADS)

    Panasenco, O.; Martin, S. F.

    Erupting prominences (filaments) that we have analyzed from Hα Doppler data at Helio Research and from SOHO/EIT 304 Å, show strong coherency between their chirality, the direction of the vertical and lateral motions of the top of the prominences, and the directions of twisting of their legs. These coherent properties in erupting prominences occur in two patterns of opposite helicity; they constitute a form of dynamic chirality called the ``roll effect." Viewed from the positive network side as they erupt, many symmetrically-erupting dextral prominences develop rolling motion toward the observer along with right-hand helicity in the left leg and left-hand helicity in the right leg. Many symmetricaly-erupting sinistral prominences, also viewed from the positive network field side, have the opposite pattern: rolling motion at the top away from the observer, left-hand helical twist in the left leg, and right-hand twist in the right leg. We have analysed the motions seen in the famous movie of the ``Grand Daddy" erupting prominence and found that it has all the motions that define the roll effect. From our analyses of this and other symmetric erupting prominences, we show that the roll effect is an alternative to the popular hypothetical configuration of an eruptive prominence as a twisted flux rope or flux tube. Instead we find that a simple flat ribbon can be bent such that it reproduces nearly all of the observed forms. The flat ribbon is the most logical beginning topology because observed prominence spines already have this topology prior to eruption and an initial long magnetic ribbon with parallel, non-twisted threads, as a basic form, can be bent into many more and different geometrical forms than a flux rope.

  7. Reporting guidelines for population pharmacokinetic analyses.

    PubMed

    Dykstra, Kevin; Mehrotra, Nitin; Tornøe, Christoffer Wenzel; Kastrissios, Helen; Patel, Bela; Al-Huniti, Nidal; Jadhav, Pravin; Wang, Yaning; Byon, Wonkyung

    2015-06-01

    The purpose of this work was to develop a consolidated set of guiding principles for reporting of population pharmacokinetic (PK) analyses based on input from a survey of practitioners as well as discussions between industry, consulting and regulatory scientists. The survey found that identification of population covariate effects on drug exposure and support for dose selection (where population PK frequently serves as preparatory analysis to exposure-response modeling) are the main areas of influence for population PK analysis. The proposed guidelines consider two main purposes of population PK reports (1) to present key analysis findings and their impact on drug development decisions, and (2) as documentation of the analysis methods for the dual purpose of enabling review of the analysis and facilitating future use of the models. This work also identified two main audiences for the reports: (1) a technically competent group responsible for in-depth review of the data, methodology, and results, and (2) a scientifically literate, but not technically adept group, whose main interest is in the implications of the analysis for the broader drug development program. We recommend a generalized question-based approach with six questions that need to be addressed throughout the report. We recommend eight sections (Synopsis, Introduction, Data, Methods, Results, Discussion, Conclusions, Appendix) with suggestions for the target audience and level of detail for each section. A section providing general expectations regarding population PK reporting from a regulatory perspective is also included. We consider this an important step towards industrialization of the field of pharmacometrics such that non-technical audience also understands the role of pharmacometrics analyses in decision making. Population PK reports were chosen as representative reports to derive these recommendations; however, the guiding principles presented here are applicable for all pharmacometric reports

  8. Analyse de formes par moiré

    NASA Astrophysics Data System (ADS)

    Harthong, J.; Sahli, H.; Poinsignon, R.; Meyrueis, P.

    1991-01-01

    We present a mathematical analysis of moiré phenomena for shape recognition. The basic theoretical concept - and tool - will be the contour function. We show that the mathematical analysis is greatly simplified by the systematic recourse to this tool. The analysis presented permits a simultaneous treatment of two different modes of implementing the moiré technique : the direct mode (widely used and well-known), and the converse mode (scarcely used). The converse mode consists in computing and designing a grating especially for one model of object, in such a manner that if (and only if) the object is in conformity with the prescribed model, the resulting moiré fringes are parallel straight lines. We give explicit formulas and algorithms for such computations. Nous présentons une analyse mathématique du moiré permettant une reconnaissance des formes. Le concept théorique de base est celui de “ fonction de contour ”. Nous montrons que l'analyse mathématique est simplifiée en faisant appel à ces fonctions. De plus, la méthode proposée permet de traiter d'une manière unifiée les deux différents modes d'utilisation des techniques de moiré : le mode direct (le plus utilisé et le mieux connu), et le moiré inverse, qui consiste, pour un modèle d'objet donné, à calculer et réaliser un réseau spécifique, tel que si (et seulement si) un objet est conforme au modèle, les franges de moiré obtenues seront des lignes droites parallèles. Nous proposons des formules explicites et des algorithmes pour ces traitements.

  9. ANALYSES OF WOUND EXUDATES FOR CLOSTRIDIAL TOXINS

    PubMed Central

    Noyes, Howard E.; Pritchard, William L.; Brinkley, Floyd B.; Mendelson, Janice A.

    1964-01-01

    Noyes, Howard E. (Walter Reed Army Institute of Research, Washington, D.C.), William L. Pritchard, Floyd B. Brinkley, and Janice A. Mendelson. Analyses of wound exudates for clostridial toxins. J. Bacteriol. 87:623–629. 1964.—Earlier studies indicated that death of goats with traumatic wounds of the hindquarter could be related to the number of clostridia in the wounds, and that toxicity of wound exudates for mice and guinea pigs could be partially neutralized by commercial trivalent gas gangrene antitoxin. This report describes in vitro and in vivo analyses of wound exudates for known clostridial toxins. Wounds were produced by detonation of high-explosive pellets. Wound exudates were obtained by cold saline extraction of both necrotic tissues and gauze sponges used to cover the wounds. Exudates were sterilized by Seitz filtration in the cold. In vitro tests were used to measure alpha-, theta-, and mu-toxins of Clostridium perfringens and the epsilon-toxin of C. novyi. Mouse protection tests, employing commercial typing antisera, were used to analyze exudates for other clostridial toxins. Lethality of wound exudates for mice could be related to (i) the numbers of clostridia present in the wound, (ii) survival time of the goats, and (iii) positive lecithovitellin (LV) tests of the exudates. However, the LV tests could not be neutralized by antitoxin specific for C. perfringens alpha-toxin. Mice were not protected by typing antisera specific for types A, C, or D C. perfringens or C. septicum but were protected by antisera specific for type B C. perfringens and types A and B C. novyi. PMID:14127581

  10. Energy adjustment methods applied to alcohol analyses.

    PubMed

    Johansen, Ditte; Andersen, Per K; Overvad, Kim; Jensen, Gorm; Schnohr, Peter; Sørensen, Thorkild I A; Grønbaek, Morten

    2003-01-01

    When alcohol consumption is related to outcome, associations between alcohol type and health outcomes may occur simply because of the ethanol in the beverage type. When one analyzes the consequences of consumption of beer, wine, and spirits, the total alcohol intake must therefore be taken into account. However, owing to the linear dependency between total alcohol intake and the alcohol content of each beverage type, the effects cannot be separated from each other or from the effect of ethanol. In nutritional epidemiology, similar problems regarding intake of macronutrients and total energy intake have been addressed, and four methods have been proposed to solve the problem: energy partition, standard, density, and residual. The aim of this study was to evaluate the usefulness of the energy adjustment methods in alcohol analyses by using coronary heart disease as an example. Data obtained from the Copenhagen City Heart Study were used. The standard and energy partition methods yielded similar results for continuous, and almost similar results for categorical, alcohol variables. The results from the density method differed, but nevertheless were concordant with these. Beer and wine drinkers, in comparison with findings for nondrinkers, had lower risk of coronary heart disease. Except for the case of men drinking beer, the effect seemed to be associated with drinking one drink per week. The standard method derives influence of substituting alcohol types at constant total alcohol intake and complements the estimates of adding consumption of a particular alcohol type to the total intake. For most diseases, the effect of ethanol predominates over that of substances in the beverage type, which makes the density method less relevant in alcohol analyses.

  11. Molecular and functional analyses of amino acid decarboxylases involved in cuticle tanning in Tribolium castaneum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aspartate 1-decarboxylase (ADC) and dopa decarboxylase (DDC) provide b–alanine and dopamine used in insect cuticle tanning. Beta-alanine is conjugated with dopamine to yield N-b-alanyldopamine (NBAD), a substrate for the phenoloxidase laccase that catalyzes the synthesis of cuticle protein cross-li...

  12. Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids.

    PubMed Central

    Southern, E M; Case-Green, S C; Elder, J K; Johnson, M; Mir, K U; Wang, L; Williams, J C

    1994-01-01

    Arrays of oligonucleotides corresponding to a full set of complements of a known sequence can be made in a single series of base couplings in which each base in the complement is added in turn. Coupling is carried out on the surface of a solid support such as a glass plate, using a device which applies reagents in a defined area. The device is displaced by a fixed movement after each coupling reaction so that consecutive couplings overlap only a portion of previous ones. The shape and size of the device and the amount by which it is displaced at each step determines the length of the oligonucleotides. Certain shapes create arrays of oligonucleotides from mononucleotides up to a given length in a single series of couplings. The array is used in a hybridisation reaction to a labelled target sequence, and shows the hybridisation behaviour of every oligonucleotide in the target sequence with its complement in the array. Applications include sequence comparison to test for mutation, analysis of secondary structure, and optimisation of PCR primer and antisense oligonucleotide design. Images PMID:7514785

  13. [Structural Analyses of Toll-like Receptor Sensing Single-stranded Nucleic Acids and Its Application].

    PubMed

    Shimizu, Toshiyuki

    2016-01-01

    Toll-like receptors (TLRs) are a family of pattern-recognition receptors that recognize microbial components and initiate subsequent immune responses. TLR7 and TLR8 recognize single-stranded (ss)RNA and initiate innate immune responses. Moreover, several small-molecule compounds have been identified as TLR7 and TLR8 activators. We determined the crystal structures of unliganded and ligand-induced activated human TLR8 dimers. Upon ligand stimulation, the TLR8 dimer was reorganized such that the two C-termini were brought into proximity. Ligand binding induces reorganization of the TLR8 dimer, which enables downstream signaling processes. To elucidate how TLR8 recognizes its natural ligand, ssRNA, as well as how the receptor can be activated by ssRNA that is structurally and chemically very different from the chemical ligands, we performed crystallographic studies of TLR8 in complex with ssRNA. TLR8 recognizes, at distinct sites, uridine and small oligonucleotides derived from the degradation of ssRNA. Uridine bound the site on the dimerization interface where small chemical ligands are recognized, whereas short oligonucleotides bound a newly identified site. Based on structural information, new compounds have been developed. We describe the crystal structure of a newly developed agonist, C2-butyl furo[2,3-c]quinolone.

  14. Characterization of different Californian strains of Xylella fastidiosa by fatty acid methyl ester (FAME) analyses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Detection and characterization of different subspecies of Xylella fastidiosa are often dependent upon genotyping. However, complementary methods to detect and characterize different X. fastidiosa strains based on phenotype are needed to confirm conclusions. Characterization of the composition of fat...

  15. Isothermal Amplification of Nucleic Acids.

    PubMed

    Zhao, Yongxi; Chen, Feng; Li, Qian; Wang, Lihua; Fan, Chunhai

    2015-11-25

    Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.

  16. Editorial Commentary: Knee Hyaluronic Acid Viscosupplementation Reduces Osteoarthritis Pain.

    PubMed

    Lubowitz, James H

    2015-10-01

    In contrast to the AAOS knee osteoarthritis guidelines, systematic review of overlapping meta-analyses shows that viscosupplementation with intra-articular hyaluronic acid injection reduces knee osteoarthritis pain and improves function according to the highest level of evidence.

  17. Database-Driven Analyses of Astronomical Spectra

    NASA Astrophysics Data System (ADS)

    Cami, Jan

    2012-03-01

    Spectroscopy is one of the most powerful tools to study the physical properties and chemical composition of very diverse astrophysical environments. In principle, each nuclide has a unique set of spectral features; thus, establishing the presence of a specific material at astronomical distances requires no more than finding a laboratory spectrum of the right material that perfectly matches the astronomical observations. Once the presence of a substance is established, a careful analysis of the observational characteristics (wavelengths or frequencies, intensities, and line profiles) allows one to determine many physical parameters of the environment in which the substance resides, such as temperature, density, velocity, and so on. Because of this great diagnostic potential, ground-based and space-borne astronomical observatories often include instruments to carry out spectroscopic analyses of various celestial objects and events. Of particular interest is molecular spectroscopy at infrared wavelengths. From the spectroscopic point of view, molecules differ from atoms in their ability to vibrate and rotate, and quantum physics inevitably causes those motions to be quantized. The energies required to excite vibrations or rotations are such that vibrational transitions generally occur at infrared wavelengths, whereas pure rotational transitions typically occur at sub-mm wavelengths. Molecular vibration and rotation are coupled though, and thus at infrared wavelengths, one commonly observes a multitude of ro-vibrational transitions (see Figure 13.1). At lower spectral resolution, all transitions blend into one broad ro-vibrational molecular band. The isotope. Molecular spectroscopy thus allows us to see a difference of one neutron in an atomic nucleus that is located at astronomical distances! Since the detection of the first interstellar molecules (the CH [21] and CN [14] radicals), more than 150 species have been detected in space, ranging in size from diatomic

  18. Efficient ALL vs. ALL collision risk analyses

    NASA Astrophysics Data System (ADS)

    Escobar, D.; Paskowitz, M.; Agueda, A.; Garcia, G.; Molina, M.

    2011-09-01

    In recent years, the space debris has gained a lot of attention due to the increasing amount of uncontrolled man-made objects orbiting the Earth. This population poses a significant and constantly growing thread to operational satellites. In order to face this thread in an independent manner, ESA has launched an initiative for the development of a European SSA System where GMV is participating via several activities. Apart from those activities financed by ESA, GMV has developed closeap, a tool for efficient conjunction assessment and collision probability prediction. ESÁs NAPEOS has been selected as computational engine and numerical propagator to be used in the tool, which can be considered as an add-on to the standard NAPEOS package. closeap makes use of the same orbit computation, conjunction assessment and collision risk algorithms implemented in CRASS, but at the same time both systems are completely independent. Moreover, the implementation in closeap has been validated against CRASS with excellent results. This paper describes the performance improvements implemented in closeap at algorithm level to ensure that the most time demanding scenarios (e.g., all catalogued objects are analysed against each other - all vs. all scenarios -) can be analysed in a reasonable amount of time with commercial-off-the-shelf hardware. However, the amount of space debris increases steadily due to the human activities. Thus, the number of objects involved in a full collision assessment is expected to increase notably and, consequently, the computational cost, which scales as the square of the number of objects, will increase as well. Additionally, orbit propagation algorithms that are computationally expensive might be needed to predict more accurately the trajectories of the space debris. In order to cope with such computational needs, the next natural step in the development of collision assessment tools is the use of parallelization techniques. In this paper we investigate

  19. Microbial community structure and metabolic property of biofilms in vermifiltration for liquid-state sludge stabilization using PLFA profiles.

    PubMed

    Zhao, Chunhui; Xing, Meiyan; Yang, Jian; Lu, Yongsen; Lv, Baoyi

    2014-01-01

    To investigate effects of earthworms on microbial community structure and metabolic properties of biofilms in vermifiltration for liquid-state sludge stabilization, a vermifilter (VF) with earthworms and a conventional biofilter (BF) without earthworms were compared. The Shannon index of fungi in VF was 16% higher than that in BF, which indicated earthworm activities significantly enhanced fungi diversity. The ratio of monounsaturated to saturated (mono:sat) PLFAs of VF biofilms was higher than that of BF biofilms, which indicated the physiological and nutritional stress for microbial community in VF was relieved due to the increasing of soluble substances caused by the earthworm ingestion. Further investigation showed that the burrowing action of earthworms promoted the aeration condition and led to aerobic microorganisms were predominant in VF. Those results indicated earthworms improved microbial community structure and metabolic properties of biofilms and thus resulted in the overall optimization of the vermifiltration system for liquid-state sludge stabilization.

  20. Evolution and Structural Analyses of Glossina morsitans (Diptera; Glossinidae) Tetraspanins.

    PubMed

    Murungi, Edwin K; Kariithi, Henry M; Adunga, Vincent; Obonyo, Meshack; Christoffels, Alan

    2014-11-12

    Tetraspanins are important conserved integral membrane proteins expressed in many organisms. Although there is limited knowledge about the full repertoire, evolution and structural characteristics of individual members in various organisms, data obtained so far show that tetraspanins play major roles in membrane biology, visual processing, memory, olfactory signal processing, and mechanosensory antennal inputs. Thus, these proteins are potential targets for control of insect pests. Here, we report that the genome of the tsetse fly, Glossina morsitans (Diptera: Glossinidae) encodes at least seventeen tetraspanins (GmTsps), all containing the signature features found in the tetraspanin superfamily members. Whereas six of the GmTsps have been previously reported, eleven could be classified as novel because their amino acid sequences do not map to characterized tetraspanins in the available protein data bases. We present a model of the GmTsps by using GmTsp42Ed, whose presence and expression has been recently detected by transcriptomics and proteomics analyses of G. morsitans. Phylogenetically, the identified GmTsps segregate into three major clusters. Structurally, the GmTsps are largely similar to vertebrate tetraspanins. In view of the exploitation of tetraspanins by organisms for survival, these proteins could be targeted using specific antibodies, recombinant large extracellular loop (LEL) domains, small-molecule mimetics and siRNAs as potential novel and efficacious putative targets to combat African trypanosomiasis by killing the tsetse fly vector.

  1. PRECLOSURE CONSEQUENCE ANALYSES FOR LICENSE APPLICATION

    SciTech Connect

    S. Tsai

    2005-01-12

    Radiological consequence analyses are performed for potential releases from normal operations in surface and subsurface facilities and from Category 1 and Category 2 event sequences during the preclosure period. Surface releases from normal repository operations are primarily from radionuclides released from opening a transportation cask during dry transfer operations of spent nuclear fuel (SNF) in Dry Transfer Facility 1 (DTF 1), Dry Transfer Facility 2 (DTF 2), the Canister Handling facility (CHF), or the Fuel Handling Facility (FHF). Subsurface releases from normal repository operations are from resuspension of waste package surface contamination and neutron activation of ventilated air and silica dust from host rock in the emplacement drifts. The purpose of this calculation is to demonstrate that the preclosure performance objectives, specified in 10 CFR 63.111(a) and 10 CFR 63.111(b), have been met for the proposed design and operations in the geologic repository operations area. Preclosure performance objectives are discussed in Section 6.2.3 and are summarized in Tables 1 and 2.

  2. Social Media Analyses for Social Measurement

    PubMed Central

    Schober, Michael F.; Pasek, Josh; Guggenheim, Lauren; Lampe, Cliff; Conrad, Frederick G.

    2016-01-01

    Demonstrations that analyses of social media content can align with measurement from sample surveys have raised the question of whether survey research can be supplemented or even replaced with less costly and burdensome data mining of already-existing or “found” social media content. But just how trustworthy such measurement can be—say, to replace official statistics—is unknown. Survey researchers and data scientists approach key questions from starting assumptions and analytic traditions that differ on, for example, the need for representative samples drawn from frames that fully cover the population. New conversations between these scholarly communities are needed to understand the potential points of alignment and non-alignment. Across these approaches, there are major differences in (a) how participants (survey respondents and social media posters) understand the activity they are engaged in; (b) the nature of the data produced by survey responses and social media posts, and the inferences that are legitimate given the data; and (c) practical and ethical considerations surrounding the use of the data. Estimates are likely to align to differing degrees depending on the research topic and the populations under consideration, the particular features of the surveys and social media sites involved, and the analytic techniques for extracting opinions and experiences from social media. Traditional population coverage may not be required for social media content to effectively predict social phenomena to the extent that social media content distills or summarizes broader conversations that are also measured by surveys. PMID:27257310

  3. Characterization of branch complexity by fractal analyses

    USGS Publications Warehouse

    Alados, C.L.; Escos, J.; Emlen, J.M.; Freeman, D.C.

    1999-01-01

    The comparison between complexity in the sense of space occupancy (box-counting fractal dimension D(c) and information dimension D1) and heterogeneity in the sense of space distribution (average evenness index f and evenness variation coefficient J(cv)) were investigated in mathematical fractal objects and natural branch structures. In general, increased fractal dimension was paired with low heterogeneity. Comparisons between branch architecture in Anthyllis cytisoides under different slope exposure and grazing impact revealed that branches were more complex and more homogeneously distributed for plants on northern exposures than southern, while grazing had no impact during a wet year. Developmental instability was also investigated by the statistical noise of the allometric relation between internode length and node order. In conclusion, our study demonstrated that fractal dimension of branch structure can be used to analyze the structural organization of plants, especially if we consider not only fractal dimension but also shoot distribution within the canopy (lacunarity). These indexes together with developmental instability analyses are good indicators of growth responses to the environment.

  4. Consumption patterns and perception analyses of hangwa.

    PubMed

    Kwock, Chang Geun; Lee, Min A; Park, So Hyun

    2012-03-01

    Hangwa is a traditional food, corresponding to the current consumption trend, in need of marketing strategies to extend its consumption. Therefore, the purpose of this study was to analyze consumers' consumption patterns and perception of Hangwa to increase consumption in the market. A questionnaire was sent to 250 consumers by e-mail from Oct 8∼23, 2009 and the data from 231 persons were analyzed in this study. Statistical, descriptive, paired samples t-test, and importance-performance analyses were conducted using SPSS WIN 17.0. According to the results, Hangwa was purchased mainly 'for present' (39.8%) and the main reasons for buying it were 'traditional image' (33.3%) and 'taste' (22.5%). When importance and performance of attributes considered in purchasing Hangwa were evaluated, performance was assessed to be lower than importance for all attributes. The attributes in the first quadrant with a high importance and a high performance were 'a sanitary process', 'a rigorous quality mark' and 'taste', which were related with quality of the products. In addition, those with a high importance but a low performance were 'popularization through advertisement', 'promotion through mass media', 'conversion of thought on traditional foods', 'a reasonable price' and 'a wide range of price'. In conclusion, Hangwa manufacturers need to diversify products and extend the expiration date based on technologies to promote its consumption. In terms of price, Hangwa should become more available by lowering the price barrier for consumers who are sensitive to price.

  5. Reproducibility of neuroimaging analyses across operating systems.

    PubMed

    Glatard, Tristan; Lewis, Lindsay B; Ferreira da Silva, Rafael; Adalat, Reza; Beck, Natacha; Lepage, Claude; Rioux, Pierre; Rousseau, Marc-Etienne; Sherif, Tarek; Deelman, Ewa; Khalili-Mahani, Najmeh; Evans, Alan C

    2015-01-01

    Neuroimaging pipelines are known to generate different results depending on the computing platform where they are compiled and executed. We quantify these differences for brain tissue classification, fMRI analysis, and cortical thickness (CT) extraction, using three of the main neuroimaging packages (FSL, Freesurfer and CIVET) and different versions of GNU/Linux. We also identify some causes of these differences using library and system call interception. We find that these packages use mathematical functions based on single-precision floating-point arithmetic whose implementations in operating systems continue to evolve. While these differences have little or no impact on simple analysis pipelines such as brain extraction and cortical tissue classification, their accumulation creates important differences in longer pipelines such as subcortical tissue classification, fMRI analysis, and cortical thickness extraction. With FSL, most Dice coefficients between subcortical classifications obtained on different operating systems remain above 0.9, but values as low as 0.59 are observed. Independent component analyses (ICA) of fMRI data differ between operating systems in one third of the tested subjects, due to differences in motion correction. With Freesurfer and CIVET, in some brain regions we find an effect of build or operating system on cortical thickness. A first step to correct these reproducibility issues would be to use more precise representations of floating-point numbers in the critical sections of the pipelines. The numerical stability of pipelines should also be reviewed.

  6. Statistical analyses of a screen cylinder wake

    NASA Astrophysics Data System (ADS)

    Mohd Azmi, Azlin; Zhou, Tongming; Zhou, Yu; Cheng, Liang

    2017-02-01

    The evolution of a screen cylinder wake was studied by analysing its statistical properties over a streamwise range of x/d={10-60}. The screen cylinder was made of a stainless steel screen mesh of 67% porosity. The experiments were conducted in a wind tunnel at a Reynolds number of 7000 using an X-probe. The results were compared with those obtained in the wake generated by a solid cylinder. It was observed that the evolution of the statistics in the wake of the screen cylinder was different from that of a solid cylinder, reflecting the differences in the formation of the organized large-scale vortices in both wakes. The streamwise evolution of the Reynolds stresses, energy spectra and cross-correlation coefficients indicated that there exists a critical location that differentiates the screen cylinder wake into two regions over the measured streamwise range. The formation of the fully formed large-scale vortices was delayed until this critical location. Comparison with existing results for screen strips showed that although the near-wake characteristics and the vortex formation mechanism were similar between the two wake generators, variation in the Strouhal frequencies was observed and the self-preservation states were non-universal, reconfirming the dependence of a wake on its initial condition.

  7. Stereological analyses of the whole human pancreas

    PubMed Central

    Poudel, Ananta; Fowler, Jonas L.; Zielinski, Mark C.; Kilimnik, German; Hara, Manami

    2016-01-01

    The large size of human tissues requires a practical stereological approach to perform a comprehensive analysis of the whole organ. We have developed a method to quantitatively analyze the whole human pancreas, as one of the challenging organs to study, in which endocrine cells form various sizes of islets that are scattered unevenly throughout the exocrine pancreas. Furthermore, the human pancreas possesses intrinsic characteristics of intra-individual variability, i.e. regional differences in endocrine cell/islet distribution, and marked inter-individual heterogeneity regardless of age, sex and disease conditions including obesity and diabetes. The method is built based on large-scale image capture, computer-assisted unbiased image analysis and quantification, and further mathematical analyses, using widely-used software such as Fiji/ImageJ and MATLAB. The present study includes detailed protocols of every procedure as well as all the custom-written computer scripts, which can be modified according to specific experimental plans and specimens of interest. PMID:27658965

  8. Trend Analyses of Nitrate in Danish Groundwater

    NASA Astrophysics Data System (ADS)

    Hansen, B.; Thorling, L.; Dalgaard, T.; Erlandsen, M.

    2012-04-01

    This presentation assesses the long-term development in the oxic groundwater nitrate concentration and nitrogen (N) loss due to intensive farming in Denmark. Firstly, up to 20-year time-series from the national groundwater monitoring network enable a statistically systematic analysis of distribution, trends and trend reversals in the groundwater nitrate concentration. Secondly, knowledge about the N surplus in Danish agriculture since 1950 is used as an indicator of the potential loss of N. Thirdly, groundwater recharge CFC (Chlorofluorocarbon) age determination allows linking of the first two dataset. The development in the nitrate concentration of oxic groundwater clearly mirrors the development in the national agricultural N surplus, and a corresponding trend reversal is found in groundwater. Regulation and technical improvements in the intensive farming in Denmark have succeeded in decreasing the N surplus by 40% since the mid 1980s while at the same time maintaining crop yields and increasing the animal production of especially pigs. Trend analyses prove that the youngest (0-15 years old) oxic groundwater shows more pronounced significant downward nitrate trends (44%) than the oldest (25-50 years old) oxic groundwater (9%). This amounts to clear evidence of the effect of reduced nitrate leaching on groundwater nitrate concentrations in Denmark. Are the Danish groundwater monitoring strategy obtimal for detection of nitrate trends? Will the nitrate concentrations in Danish groundwater continue to decrease or are the Danish nitrate concentration levels now appropriate according to the Water Framework Directive?

  9. Social Media Analyses for Social Measurement.

    PubMed

    Schober, Michael F; Pasek, Josh; Guggenheim, Lauren; Lampe, Cliff; Conrad, Frederick G

    2016-01-01

    Demonstrations that analyses of social media content can align with measurement from sample surveys have raised the question of whether survey research can be supplemented or even replaced with less costly and burdensome data mining of already-existing or "found" social media content. But just how trustworthy such measurement can be-say, to replace official statistics-is unknown. Survey researchers and data scientists approach key questions from starting assumptions and analytic traditions that differ on, for example, the need for representative samples drawn from frames that fully cover the population. New conversations between these scholarly communities are needed to understand the potential points of alignment and non-alignment. Across these approaches, there are major differences in (a) how participants (survey respondents and social media posters) understand the activity they are engaged in; (b) the nature of the data produced by survey responses and social media posts, and the inferences that are legitimate given the data; and (c) practical and ethical considerations surrounding the use of the data. Estimates are likely to align to differing degrees depending on the research topic and the populations under consideration, the particular features of the surveys and social media sites involved, and the analytic techniques for extracting opinions and experiences from social media. Traditional population coverage may not be required for social media content to effectively predict social phenomena to the extent that social media content distills or summarizes broader conversations that are also measured by surveys.

  10. Phylogenomic Analyses Support Traditional Relationships within Cnidaria

    PubMed Central

    Zapata, Felipe; Goetz, Freya E.; Smith, Stephen A.; Howison, Mark; Siebert, Stefan; Church, Samuel H.; Sanders, Steven M.; Ames, Cheryl Lewis; McFadden, Catherine S.; France, Scott C.; Daly, Marymegan; Collins, Allen G.; Haddock, Steven H. D.; Dunn, Casey W.; Cartwright, Paulyn

    2015-01-01

    Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses using different partition schemes and models of molecular evolution, as well as topology tests for alternative phylogenetic relationships, support the monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly of Hexacorallia is weak due to the equivocal position of Ceriantharia. Taken together, these results further resolve deep cnidarian relationships, largely support traditional phylogenetic views on relationships, and provide a historical framework for studying the evolutionary processes involved in one of the most ancient animal radiations. PMID:26465609

  11. Comparative sequence analyses of sixteen reptilian paramyxoviruses

    USGS Publications Warehouse

    Ahne, W.; Batts, W.N.; Kurath, G.; Winton, J.R.

    1999-01-01

    Viral genomic RNA of Fer-de-Lance virus (FDLV), a paramyxovirus highly pathogenic for reptiles, was reverse transcribed and cloned. Plasmids with significant sequence similarities to the hemagglutinin-neuraminidase (HN) and polymerase (L) genes of mammalian paramyxoviruses were identified by BLAST search. Partial sequences of the FDLV genes were used to design primers for amplification by nested polymerase chain reaction (PCR) and sequencing of 518-bp L gene and 352-bp HN gene fragments from a collection of 15 previously uncharacterized reptilian paramyxoviruses. Phylogenetic analyses of the partial L and HN sequences produced similar trees in which there were two distinct subgroups of isolates that were supported with maximum bootstrap values, and several intermediate isolates. Within each subgroup the nucleotide divergence values were less than 2.5%, while the divergence between the two subgroups was 20-22%. This indicated that the two subgroups represent distinct virus species containing multiple virus strains. The five intermediate isolates had nucleotide divergence values of 11-20% and may represent additional distinct species. In addition to establishing diversity among reptilian paramyxoviruses, the phylogenetic groupings showed some correlation with geographic location, and clearly demonstrated a low level of host species-specificity within these viruses. Copyright (C) 1999 Elsevier Science B.V.

  12. Recent Advances in Cellular Glycomic Analyses

    PubMed Central

    Furukawa, Jun-ichi; Fujitani, Naoki; Shinohara, Yasuro

    2013-01-01

    A large variety of glycans is intricately located on the cell surface, and the overall profile (the glycome, given the entire repertoire of glycoconjugate-associated sugars in cells and tissues) is believed to be crucial for the diverse roles of glycans, which are mediated by specific interactions that control cell-cell adhesion, immune response, microbial pathogenesis and other cellular events. The glycomic profile also reflects cellular alterations, such as development, differentiation and cancerous change. A glycoconjugate-based approach would therefore be expected to streamline discovery of novel cellular biomarkers. Development of such an approach has proven challenging, due to the technical difficulties associated with the analysis of various types of cellular glycomes; however, recent progress in the development of analytical methodologies and strategies has begun to clarify the cellular glycomics of various classes of glycoconjugates. This review focuses on recent advances in the technical aspects of cellular glycomic analyses of major classes of glycoconjugates, including N- and O-linked glycans, derived from glycoproteins, proteoglycans and glycosphingolipids. Articles that unveil the glycomics of various biologically important cells, including embryonic and somatic stem cells, induced pluripotent stem (iPS) cells and cancer cells, are discussed. PMID:24970165

  13. Informative prior distributions for ELISA analyses.

    PubMed

    Klauenberg, Katy; Walzel, Monika; Ebert, Bernd; Elster, Clemens

    2015-07-01

    Immunoassays are capable of measuring very small concentrations of substances in solutions and have an immense range of application. Enzyme-linked immunosorbent assay (ELISA) tests in particular can detect the presence of an infection, of drugs, or hormones (as in the home pregnancy test). Inference of an unknown concentration via ELISA usually involves a non-linear heteroscedastic regression and subsequent prediction, which can be carried out in a Bayesian framework. For such a Bayesian inference, we are developing informative prior distributions based on extensive historical ELISA tests as well as theoretical considerations. One consideration regards the quality of the immunoassay leading to two practical requirements for the applicability of the priors. Simulations show that the additional prior information can lead to inferences which are robust to reasonable perturbations of the model and changes in the design of the data. On real data, the applicability is demonstrated across different laboratories, for different analytes and laboratory equipment as well as for previous and current ELISAs with sigmoid regression function. Consistency checks on real data (similar to cross-validation) underpin the adequacy of the suggested priors. Altogether, the new priors may improve concentration estimation for ELISAs that fulfill certain design conditions, by extending the range of the analyses, decreasing the uncertainty, or giving more robust estimates. Future use of these priors is straightforward because explicit, closed-form expressions are provided. This work encourages development and application of informative, yet general, prior distributions for other types of immunoassays.

  14. Evaluation of the Hitachi 717 analyser.

    PubMed

    Biosca, C; Antoja, F; Sierra, C; Douezi, H; Macià, M; Alsina, M J; Galimany, R

    1989-01-01

    The selective multitest Boehringer Mannheim Hitachi 717 analyser was evaluated according to the guidelines of the Comisión de Instrumentación de la Sociedad Española de Química Clinica and the European Committee for Clinical Laboratory Standards. The evaluation was performed in two steps: examination of the analytical units and evaluation in routine operation.THE EVALUATION OF THE ANALYTICAL UNITS INCLUDED A PHOTOMETRIC STUDY: the inaccuracy is acceptable for 340 and 405 nm; the imprecision ranges from 0.12 to 0.95% at 340 nm and from 0.30 to 0.73 at 405 nm, the linearity shows some dispersion at low absorbance for NADH at 340 nm, the drift is negligible, the imprecision of the pipette delivery system increases when the sample pipette operates with 3 mul, the reagent pipette imprecision is acceptable and the temperature control system is good.UNDER ROUTINE WORKING CONDITIONS, SEVEN DETERMINATIONS WERE STUDIED: glucose, creatinine, iron, total protein, AST, ALP and calcium. The within-run imprecision (CV) ranged from 0.6% for total protein and AST to 6.9% for iron. The between run imprecision ranged from 2.4% for glucose to 9.7% for iron. Some contamination was found in the carry-over study. The relative inaccuracy is good for all the constituents assayed.

  15. Evaluation of the Olympus AU-510 analyser.

    PubMed

    Farré, C; Velasco, J; Ramón, F

    1991-01-01

    The selective multitest Olympus AU-510 analyser was evaluated according to the recommendations of the Comision de Instrumentacion de la Sociedad Española de Quimica Clinica and the European Committee for Clinical Laboratory Standards. The evaluation was carried out in two stages: an examination of the analytical units and then an evaluation in routine work conditions. The operational characteristics of the system were also studied.THE FIRST STAGE INCLUDED A PHOTOMETRIC STUDY: dependent on the absorbance, the inaccuracy varies between +0.5% to -0.6% at 405 nm and from -5.6% to 10.6% at 340 nm; the imprecision ranges between -0.22% and 0.56% at 405 nm and between 0.09% and 2.74% at 340 nm. Linearity was acceptable, apart from a very low absorbance for NADH at 340 nm; and the imprecision of the serum sample pipetter was satisfactory.TWELVE SERUM ANALYTES WERE STUDIED UNDER ROUTINE CONDITIONS: glucose, urea urate, cholesterol, triglycerides, total bilirubin, creatinine, phosphate, iron, aspartate aminotransferase, alanine aminotransferase and gamma-glutamyl transferase.The within-run imprecision (CV%) ranged from 0.67% for phosphate to 2.89% for iron and the between-run imprecision from 0.97% for total bilirubin to 7.06% for iron. There was no carryover in a study of the serum sample pipetter. Carry-over studies with the reagent and sample pipetters shows some cross contamination in the iron assay.

  16. CFD analyses of coolant channel flowfields

    NASA Technical Reports Server (NTRS)

    Yagley, Jennifer A.; Feng, Jinzhang; Merkle, Charles L.

    1993-01-01

    The flowfield characteristics in rocket engine coolant channels are analyzed by means of a numerical model. The channels are characterized by large length to diameter ratios, high Reynolds numbers, and asymmetrical heating. At representative flow conditions, the channel length is approximately twice the hydraulic entrance length so that fully developed conditions would be reached for a constant property fluid. For the supercritical hydrogen that is used as the coolant, the strong property variations create significant secondary flows in the cross-plane which have a major influence on the flow and the resulting heat transfer. Comparison of constant and variable property solutions show substantial differences. In addition, the property variations prevent fully developed flow. The density variation accelerates the fluid in the channels increasing the pressure drop without an accompanying increase in heat flux. Analyses of the inlet configuration suggest that side entry from a manifold can affect the development of the velocity profile because of vortices generated as the flow enters the channel. Current work is focused on studying the effects of channel bifurcation on the flow field and the heat transfer characteristics.

  17. Seismic Soil-Structure Interaction Analyses of a Deeply Embedded Model Reactor – SASSI Analyses

    SciTech Connect

    Nie J.; Braverman J.; Costantino, M.

    2013-10-31

    This report summarizes the SASSI analyses of a deeply embedded reactor model performed by BNL and CJC and Associates, as part of the seismic soil-structure interaction (SSI) simulation capability project for the NEAMS (Nuclear Energy Advanced Modeling and Simulation) Program of the Department of Energy. The SASSI analyses included three cases: 0.2 g, 0.5 g, and 0.9g, all of which refer to nominal peak accelerations at the top of the bedrock. The analyses utilized the modified subtraction method (MSM) for performing the seismic SSI evaluations. Each case consisted of two analyses: input motion in one horizontal direction (X) and input motion in the vertical direction (Z), both of which utilized the same in-column input motion. Besides providing SASSI results for use in comparison with the time domain SSI results obtained using the DIABLO computer code, this study also leads to the recognition that the frequency-domain method should be modernized so that it can better serve its mission-critical role for analysis and design of nuclear power plants.

  18. Community shifts and carbon translocation within metabolically-active rhizosphere microorganisms in grasslands under elevated CO2

    NASA Astrophysics Data System (ADS)

    Denef, K.; Bubenheim, H.; Lenhart, K.; Vermeulen, J.; van Cleemput, O.; Boeckx, P.; Müller, C.

    2007-05-01

    The aim of this study was to identify the microbial communities that are actively involved in the assimilation of rhizosphere-C and are most sensitive in their activity to elevated atmospheric CO2 in grassland ecosystems. For this, we analyzed 13C signatures in microbial biomarker phospholipid fatty acids (PLFA) from an in situ 13CO2 pulse-labeling experiment in the Gießen Free-Air Carbon dioxide Enrichment grasslands (GiFACE, Germany) exposed to ambient and elevated (i.e. 50% above ambient) CO2 concentrations. Carbon-13 PLFA measurements at 3 h, 10 h and 11 months after the pulse-labeling indicated a much faster transfer of newly produced rhizosphere-C to fungal compared to bacterial PLFA. After 11 months, the proportion of 13C had decreased in fungal PLFA but had increased in bacterial PLFA compared to a few hours after the pulse-labeling. Nevertheless, a significant proportion of the rapidly assimilated rhizosphere-C was still present in fungal PLFA after 11 months. These results demonstrate the dominant role of fungi in the immediate assimilation of rhizodeposits in grassland ecosystems, while also suggesting a long-term retention of rhizosphere-C in the fungal mycelium as well as a possible translocation of the rhizosphere-C from the fungal to bacterial biomass. Elevated CO2 caused an increase in the relative abundance of root-derived PLFA-C in the saprotrophic fungal PLFA 18:2ω6,9 as well as arbuscular mycorrhizal fungal PLFA 16:1ω5, but a decrease in the saprotrophic fungal biomarker PLFA 18:1ω9. This suggests enhanced rhizodeposit-C assimilation only by selected fungal communities under elevated CO2.

  19. Irbic acid, a dicaffeoylquinic acid derivative from Centella asiatica cell cultures.

    PubMed

    Antognoni, Fabiana; Perellino, Nicoletta Crespi; Crippa, Sergio; Dal Toso, Roberto; Danieli, Bruno; Minghetti, Anacleto; Poli, Ferruccio; Pressi, Giovanna

    2011-10-01

    3,5-O-dicaffeoyl-4-O-malonilquinic acid (1) (irbic acid) has been isolated for the first time from cell cultures of Centella asiatica and till now it has never been reported to be present in the intact plant. Evidence of its structure was obtained by spectroscopic analyses (MS/NMR). Besides 1, cell cultures produce also the known 3,5-O-dicaffeoylquinic acid, chlorogenic acid, and the triferulic acid 2 (4-O-8'/4'-O-8″-didehydrotriferulic acid). Biological activities were evaluated for compound 1, which showed to have a strong radical scavenging capacity, together with a high inhibitory activity on collagenase. This suggests a possible utilization of this substance as a topical agent to reduce the skin ageing process.

  20. Characteristics and formation of amino acids and hydroxy acids of the Murchison meteorite

    NASA Technical Reports Server (NTRS)

    Cronin, J. R.; Cooper, G. W.; Pizzarello, S.

    1995-01-01

    Eight characteristics of the unique suite of amino acids and hydroxy acids found in the Murchison meteorite can be recognized on the basis of detailed molecular and isotopic analyses. The marked structural correspondence between the alpha-amino acids and alpha-hydroxy acids and the high deuterium/hydrogen ratio argue persuasively for their formation by aqueous phase Strecker reactions in the meteorite parent body from presolar, i.e., interstellar, aldehydes, ketones, ammonia, and hydrogen cyanide. The characteristics of the meteoritic suite of amino acids and hydroxy acids are briefly enumerated and discussed with regard to their consonance with this interstellar-parent body formation hypothesis. The hypothesis has interesting implications for the organic composition of both the primitive parent body and the presolar nebula.

  1. The Core Mouse Response to Infection by Neospora Caninum Defined by Gene Set Enrichment Analyses

    PubMed Central

    Ellis, John; Goodswen, Stephen; Kennedy, Paul J; Bush, Stephen

    2012-01-01

    In this study, the BALB/c and Qs mouse responses to infection by the parasite Neospora caninum were investigated in order to identify host response mechanisms. Investigation was done using gene set (enrichment) analyses of microarray data. GSEA, MANOVA, Romer, subGSE and SAM-GS were used to study the contrasts Neospora strain type, Mouse type (BALB/c and Qs) and time post infection (6 hours post infection and 10 days post infection). The analyses show that the major signal in the core mouse response to infection is from time post infection and can be defined by gene ontology terms Protein Kinase Activity, Cell Proliferation and Transcription Initiation. Several terms linked to signaling, morphogenesis, response and fat metabolism were also identified. At 10 days post infection, genes associated with fatty acid metabolism were identified as up regulated in expression. The value of gene set (enrichment) analyses in the analysis of microarray data is discussed. PMID:23012496

  2. Fracturing and brittleness index analyses of shales

    NASA Astrophysics Data System (ADS)

    Barnhoorn, Auke; Primarini, Mutia; Houben, Maartje

    2016-04-01

    The formation of a fracture network in rocks has a crucial control on the flow behaviour of fluids. In addition, an existing network of fractures , influences the propagation of new fractures during e.g. hydraulic fracturing or during a seismic event. Understanding of the type and characteristics of the fracture network that will be formed during e.g. hydraulic fracturing is thus crucial to better predict the outcome of a hydraulic fracturing job. For this, knowledge of the rock properties is crucial. The brittleness index is often used as a rock property that can be used to predict the fracturing behaviour of a rock for e.g. hydraulic fracturing of shales. Various terminologies of the brittleness index (BI1, BI2 and BI3) exist based on mineralogy, elastic constants and stress-strain behaviour (Jin et al., 2014, Jarvie et al., 2007 and Holt et al., 2011). A maximum brittleness index of 1 predicts very good and efficient fracturing behaviour while a minimum brittleness index of 0 predicts a much more ductile shale behaviour. Here, we have performed systematic petrophysical, acoustic and geomechanical analyses on a set of shale samples from Whitby (UK) and we have determined the three different brittleness indices on each sample by performing all the analyses on each of the samples. We show that each of the three brittleness indices are very different for the same sample and as such it can be concluded that the brittleness index is not a good predictor of the fracturing behaviour of shales. The brittleness index based on the acoustic data (BI1) all lie around values of 0.5, while the brittleness index based on the stress strain data (BI2) give an average brittleness index around 0.75, whereas the mineralogy brittleness index (BI3) predict values below 0.2. This shows that by using different estimates of the brittleness index different decisions can be made for hydraulic fracturing. If we would rely on the mineralogy (BI3), the Whitby mudstone is not a suitable

  3. Integrated Field Analyses of Thermal Springs

    NASA Astrophysics Data System (ADS)

    Shervais, K.; Young, B.; Ponce-Zepeda, M. M.; Rosove, S.

    2011-12-01

    A group of undergraduate researchers through the SURE internship offered by the Southern California Earthquake Center (SCEC) have examined thermal springs in southern Idaho, northern Utah as well as mud volcanoes in the Salton Sea, California. We used an integrated approach to estimate the setting and maximum temperature, including water chemistry, Ipad-based image and data-base management, microbiology, and gas analyses with a modified Giggenbach sampler.All springs were characterized using GISRoam (tmCogent3D). We are performing geothermometry calculations as well as comparisons with temperature gradient data on the results while also analyzing biological samples. Analyses include water temperature, pH, electrical conductivity, and TDS measured in the field. Each sample is sealed and chilled and delivered to a water lab within 12 hours.Temperatures are continuously monitored with the use of Solinst Levelogger Juniors. Through partnership with a local community college geology club, we receive results on a monthly basis and are able to process initial data earlier in order to evaluate data over a longer time span. The springs and mudpots contained microbial organisms which were analyzed using methods of single colony isolation, polymerase chain reaction, and DNA sequencing showing the impact of the organisms on the springs or vice versa. Soon we we will collect gas samples at sites that show signs of gas. This will be taken using a hybrid of the Giggenbach method and our own methods. Drawing gas samples has proven a challenge, however we devised a method to draw out gas samples utilizing the Giggenbach flask, transferring samples to glass blood sample tubes, replacing NaOH in the Giggenbach flask, and evacuating it in the field for multiple samples using a vacuum pump. We also use a floating platform devised to carry and lower a levelogger, to using an in-line fuel filter from a tractor in order to keep mud from contaminating the equipment.The use of raster

  4. Assessing the reproducibility of discriminant function analyses

    PubMed Central

    Andrew, Rose L.; Albert, Arianne Y.K.; Renaut, Sebastien; Rennison, Diana J.; Bock, Dan G.

    2015-01-01

    Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. Even if data files are securely stored and accessible, they must also be accompanied by accurate labels and identifiers. To assess how often problems with metadata or data curation affect the reproducibility of published results, we attempted to reproduce Discriminant Function Analyses (DFAs) from the field of organismal biology. DFA is a commonly used statistical analysis that has changed little since its inception almost eight decades ago, and therefore provides an opportunity to test reproducibility among datasets of varying ages. Out of 100 papers we initially surveyed, fourteen were excluded because they did not present the common types of quantitative result from their DFA or gave insufficient details of their DFA. Of the remaining 86 datasets, there were 15 cases for which we were unable to confidently relate the dataset we received to the one used in the published analysis. The reasons ranged from incomprehensible or absent variable labels, the DFA being performed on an unspecified subset of the data, or the dataset we received being incomplete. We focused on reproducing three common summary statistics from DFAs: the percent variance explained, the percentage correctly assigned and the largest discriminant function coefficient. The reproducibility of the first two was fairly high (20 of 26, and 44 of 60 datasets, respectively), whereas our success rate with the discriminant function coefficients was lower (15 of 26 datasets). When considering all three summary statistics, we were able to completely reproduce 46 (65%) of 71 datasets. While our results show that a majority of studies are reproducible, they highlight the fact that many studies still are not the

  5. Analysing policy transfer: perspectives for operational research.

    PubMed

    Bissell, K; Lee, K; Freeman, R

    2011-09-01

    Policy transfer occurs regularly. In essence, a strategy developed elsewhere is taken up and applied in another policy context. Yet what precisely is policy transfer and, more importantly, under what conditions does it occur? This paper describes policy transfer and addresses three main questions, exploring what perspectives of policy transfer might contribute to operational research (OR) efforts. First, what facilitates the transfer of OR results into policy and practice? Second, what facilitates effective lesson-drawing about OR results and processes between and within countries? And third, what would increase the amount of OR being carried out by low- and middle-income countries and used to inform policy and practice at local and global levels? Mexico's adoption and adaptation of the DOTS strategy is used here as an example of policy transfer. Policy transfer is relevant to all countries, levels and arenas of people, institutions and organisations involved in health. With a more systematic analysis of learning and policy processes, OR policy and practice outcomes could be improved at all levels, from local to global. Policy transfer offers theory and concepts for analysing OR from a new perspective. The present paper proposes a model of the policy transfer process for qualitative research use. Comprehensive policy transfer research, given its length, complexity and need for qualitative researchers, should not be envisaged for all OR projects. All OR projects could, however, incorporate some concepts and practical tools inspired from this model. This should help to plan, evaluate and improve OR processes and the resulting changes in policy and practice.

  6. SEDS Tether M/OD Damage Analyses

    NASA Technical Reports Server (NTRS)

    Hayashida, K. B.; Robinson, J. H.; Hill, S. A.

    1997-01-01

    The Small Expendable Deployer System (SEDS) was designed to deploy an endmass at the end of a 20-km-long tether which acts as an upper stage rocket, and the threats from the meteoroid and orbital debris (M/OD) particle environments on SEDS components are important issues for the safety and success of any SEDS mission. However, the possibility of severing the tether due to M/OD particle impacts is an even more serious concern, since the SEDS tether has a relatively large exposed area to the M/OD environments although its diameter is quite small. The threats from the M/OD environments became a very important issue for the third SEDS mission, since the project office proposed using the shuttle orbiter as a launch platform instead of the second stage of a Delta II expendable rocket, which was used for the first two SEDS missions. A series of hyper-velocity impact tests were performed at the Johnson Space Center and Arnold Engineering Development Center to help determine the critical particle sizes required to sever the tether. The computer hydrodynamic code or hydrocode called CTH, developed by the Sandia National Laboratories, was also used to simulate the damage on the SEDS tether caused by both the orbital debris and test particle impacts. The CTH hydrocode simulation results provided the much needed information to help determine the critical particle sizes required to sever the tether. The M/OD particle sizes required to sever the tether were estimated to be less than 0.1 cm in diameter from these studies, and these size particles are more abundant in low-Earth orbit than larger size particles. Finally, the authors performed the M/OD damage analyses for the three SEDS missions; i.e., SEDS-1, -2, and -3 missions, by using the information obtained from the hypervelocity impact test and hydrocode simulations results.

  7. Differentiating tremor patients using spiral analyses.

    PubMed

    Koirala, N; Muthuraman, M; Anjum, T; Chaitanya, C V; Helmolt, V F; Mideksa, K G; Lange, K; Schmidt, G; Schneider, S; Deuschl, G

    2015-01-01

    Essential tremor follows an autosomal dominant type of inheritance in the majority of patients, yet its genetic basis has not been identified. The age of onset in this tremor is bimodal, one in young age and another when they are old. The old onset is referred to as senile tremor in this study. The precise pathology is still not completely understood for both these tremors. We wanted to develop an easy diagnostic tool to differentiate these two tremors clinically. In this study, the spirals were asked to be drawn by 30 patients, 15 from each group. The spirals were recorded digitally from each hand, with and without the spiral template, using a Wacom intuos version 4 tablets. The aim of the study was to look at the easy diagnostic measures from these spirals to distinguish the two cohorts of patients. The first measure was to use the well-known clinical scores like the number of complete circles without the template, width, height, axis, and degree of severity. The second measure was to estimate the peak frequency and the peak amplitude for the position, velocity, and acceleration data, in the frequency domain. The well-known clinical scores, most of them, did not show any significant difference between the two patient cohorts except the degree of severity which showed significant difference. The peak frequency and the peak amplitude in most of the data were not significantly different between the two cohorts of patients, only the peak amplitude from the acceleration data showed significant difference. Thus, we could use these two parameters to differentiate between the two tremors patient groups, which would be an easy clinical diagnostic tool without the need for any complicated analyses.

  8. Comparative mutational analyses of influenza A viruses

    PubMed Central

    Cheung, Peter Pak-Hang; Rogozin, Igor B.; Choy, Ka-Tim; Ng, Hoi Yee

    2015-01-01

    The error-prone RNA-dependent RNA polymerase (RdRP) and external selective pressures are the driving forces for RNA viral diversity. When confounded by selective pressures, it is difficult to assess if influenza A viruses (IAV) that have a wide host range possess comparable or distinct spontaneous mutational frequency in their RdRPs. We used in-depth bioinformatics analyses to assess the spontaneous mutational frequencies of two RdRPs derived from human seasonal (A/Wuhan/359/95; Wuhan) and H5N1 (A/Vietnam/1203/04; VN1203) viruses using the mini-genome system with a common firefly luciferase reporter serving as the template. High-fidelity reverse transcriptase was applied to generate high-quality mutational spectra which allowed us to assess and compare the mutational frequencies and mutable motifs along a target sequence of the two RdRPs of two different subtypes. We observed correlated mutational spectra (τ correlation P < 0.0001), comparable mutational frequencies (H3N2:5.8 ± 0.9; H5N1:6.0 ± 0.5), and discovered a highly mutable motif “(A)AAG” for both Wuhan and VN1203 RdRPs. Results were then confirmed with two recombinant A/Puerto Rico/8/34 (PR8) viruses that possess RdRP derived from Wuhan or VN1203 (RG-PR8×WuhanPB2, PB1, PA, NP and RG-PR8×VN1203PB2, PB1, PA, NP). Applying novel bioinformatics analysis on influenza mutational spectra, we provide a platform for a comprehensive analysis of the spontaneous mutation spectra for an RNA virus. PMID:25404565

  9. Soil grain analyses at Meridiani Planum, Mars

    USGS Publications Warehouse

    Weitz, C.M.; Anderson, R.C.; Bell, J.F.; Farrand, W. H.; Herkenhoff, K. E.; Johnson, J. R.; Jolliff, B.L.; Morris, R.V.; Squyres, S. W.; Sullivan, R.J.

    2006-01-01

    Grain-size analyses of the soils at Meridiani Planum have been used to identify rock souces for the grains and provide information about depositional processes under past and current conditions. Basaltic sand, dust, millimeter-size hematite-rich spherules interpreted as concretions, spherule fragments, coated partially buried spherules, basalt fragments, sedimentary outcrop fragments, and centimeter-size cobbles are concentrated on the upper surfaces of the soils as a lag deposit, while finer basaltic sands and dust dominate the underlying soils. There is a bimodal distribution of soil grain sizes with one population representing grains <125 ??m and the other falling between 1-4.5 mm. Soils within craters like Eagle and Endurance show a much greater diversity of grain morphologies compared to the plains. The spherules found in the plains soils are approximately 1-2 mm smaller in size than those seen embedded in the outcrop rocks of Eagle and Endurance craters. The average major axis for all unfractured spherules measured in the soils and outcrop rocks is 2.87 ?? 1.18 mm, with a trend toward decreasing spherule sizes in both the soils and outcrop rocks as the rover drove southward. Wind ripples seen across the plains of Meridiani are dominated by similar size (1.3-1.7 mm) hematite-rich grains, and they match in size the larger grains on plains ripples at Gusev Crater. Larger clasts and centimeter-size cobbles that are scattered on the soils have several spectral and compositional types, reflecting multiple origins. The cobbles tend to concentrate within ripple troughs along the plains and in association with outcrop exposures. Copyright 2006 by the American Geophysical Union.

  10. Finite Element analyses of soil bioengineered slopes

    NASA Astrophysics Data System (ADS)

    Tamagnini, Roberto; Switala, Barbara Maria; Sudan Acharya, Madhu; Wu, Wei; Graf, Frank; Auer, Michael; te Kamp, Lothar

    2014-05-01

    Soil Bioengineering methods are not only effective from an economical point of view, but they are also interesting as fully ecological solutions. The presented project is aimed to define a numerical model which includes the impact of vegetation on slope stability, considering both mechanical and hydrological effects. In this project, a constitutive model has been developed that accounts for the multi-phase nature of the soil, namely the partly saturated condition and it also includes the effects of a biological component. The constitutive equation is implemented in the Finite Element (FE) software Comes-Geo with an implicit integration scheme that accounts for the collapse of the soils structure due to wetting. The mathematical formulation of the constitutive equations is introduced by means of thermodynamics and it simulates the growth of the biological system during the time. The numerical code is then applied in the analysis of an ideal rainfall induced landslide. The slope is analyzed for vegetated and non-vegetated conditions. The final results allow to quantitatively assessing the impact of vegetation on slope stability. This allows drawing conclusions and choosing whenever it is worthful to use soil bioengineering methods in slope stabilization instead of traditional approaches. The application of the FE methods show some advantages with respect to the commonly used limit equilibrium analyses, because it can account for the real coupled strain-diffusion nature of the problem. The mechanical strength of roots is in fact influenced by the stress evolution into the slope. Moreover, FE method does not need a pre-definition of any failure surface. FE method can also be used in monitoring the progressive failure of the soil bio-engineered system as it calculates the amount of displacements and strains of the model slope. The preliminary study results show that the formulated equations can be useful for analysis and evaluation of different soil bio

  11. Trend analyses with river sediment rating curves

    USGS Publications Warehouse

    Warrick, Jonathan A.

    2015-01-01

    Sediment rating curves, which are fitted relationships between river discharge (Q) and suspended-sediment concentration (C), are commonly used to assess patterns and trends in river water quality. In many of these studies it is assumed that rating curves have a power-law form (i.e., C = aQb, where a and b are fitted parameters). Two fundamental questions about the utility of these techniques are assessed in this paper: (i) How well to the parameters, a and b, characterize trends in the data? (ii) Are trends in rating curves diagnostic of changes to river water or sediment discharge? As noted in previous research, the offset parameter, a, is not an independent variable for most rivers, but rather strongly dependent on b and Q. Here it is shown that a is a poor metric for trends in the vertical offset of a rating curve, and a new parameter, â, as determined by the discharge-normalized power function [C = â (Q/QGM)b], where QGM is the geometric mean of the Q values sampled, provides a better characterization of trends. However, these techniques must be applied carefully, because curvature in the relationship between log(Q) and log(C), which exists for many rivers, can produce false trends in â and b. Also, it is shown that trends in â and b are not uniquely diagnostic of river water or sediment supply conditions. For example, an increase in â can be caused by an increase in sediment supply, a decrease in water supply, or a combination of these conditions. Large changes in water and sediment supplies can occur without any change in the parameters, â and b. Thus, trend analyses using sediment rating curves must include additional assessments of the time-dependent rates and trends of river water, sediment concentrations, and sediment discharge.

  12. Computational Analyses of Pressurization in Cryogenic Tanks

    NASA Technical Reports Server (NTRS)

    Ahuja, Vineet; Hosangadi, Ashvin; Lee, Chun P.; Field, Robert E.; Ryan, Harry

    2010-01-01

    A comprehensive numerical framework utilizing multi-element unstructured CFD and rigorous real fluid property routines has been developed to carry out analyses of propellant tank and delivery systems at NASA SSC. Traditionally CFD modeling of pressurization and mixing in cryogenic tanks has been difficult primarily because the fluids in the tank co-exist in different sub-critical and supercritical states with largely varying properties that have to be accurately accounted for in order to predict the correct mixing and phase change between the ullage and the propellant. For example, during tank pressurization under some circumstances, rapid mixing of relatively warm pressurant gas with cryogenic propellant can lead to rapid densification of the gas and loss of pressure in the tank. This phenomenon can cause serious problems during testing because of the resulting decrease in propellant flow rate. With proper physical models implemented, CFD can model the coupling between the propellant and pressurant including heat transfer and phase change effects and accurately capture the complex physics in the evolving flowfields. This holds the promise of allowing the specification of operational conditions and procedures that could minimize the undesirable mixing and heat transfer inherent in propellant tank operation. In our modeling framework, we incorporated two different approaches to real fluids modeling: (a) the first approach is based on the HBMS model developed by Hirschfelder, Beuler, McGee and Sutton and (b) the second approach is based on a cubic equation of state developed by Soave, Redlich and Kwong (SRK). Both approaches cover fluid properties and property variation spanning sub-critical gas and liquid states as well as the supercritical states. Both models were rigorously tested and properties for common fluids such as oxygen, nitrogen, hydrogen etc were compared against NIST data in both the sub-critical as well as supercritical regimes.

  13. On study design in neuroimaging heritability analyses

    NASA Astrophysics Data System (ADS)

    Koran, Mary Ellen; Li, Bo; Jahanshad, Neda; Thornton-Wells, Tricia A.; Glahn, David C.; Thompson, Paul M.; Blangero, John; Nichols, Thomas E.; Kochunov, Peter; Landman, Bennett A.

    2014-03-01

    Imaging genetics is an emerging methodology that combines genetic information with imaging-derived metrics to understand how genetic factors impact observable structural, functional, and quantitative phenotypes. Many of the most well-known genetic studies are based on Genome-Wide Association Studies (GWAS), which use large populations of related or unrelated individuals to associate traits and disorders with individual genetic factors. Merging imaging and genetics may potentially lead to improved power of association in GWAS because imaging traits may be more sensitive phenotypes, being closer to underlying genetic mechanisms, and their quantitative nature inherently increases power. We are developing SOLAR-ECLIPSE (SE) imaging genetics software which is capable of performing genetic analyses with both large-scale quantitative trait data and family structures of variable complexity. This program can estimate the contribution of genetic commonality among related subjects to a given phenotype, and essentially answer the question of whether or not the phenotype is heritable. This central factor of interest, heritability, offers bounds on the direct genetic influence over observed phenotypes. In order for a trait to be a good phenotype for GWAS, it must be heritable: at least some proportion of its variance must be due to genetic influences. A variety of family structures are commonly used for estimating heritability, yet the variability and biases for each as a function of the sample size are unknown. Herein, we investigate the ability of SOLAR to accurately estimate heritability models based on imaging data simulated using Monte Carlo methods implemented in R. We characterize the bias and the variability of heritability estimates from SOLAR as a function of sample size and pedigree structure (including twins, nuclear families, and nuclear families with grandparents).

  14. [Teichoic acids from lactic acid bacteria].

    PubMed

    Livins'ka, O P; Harmasheva, I L; Kovalenko, N K

    2012-01-01

    The current view of the structural diversity of teichoic acids and their involvement in the biological activity of lactobacilli has been reviewed. The mechanisms of effects of probiotic lactic acid bacteria, in particular adhesive and immunostimulating functions have been described. The prospects of the use of structure data of teichoic acid in the assessment of intraspecific diversity of lactic acid bacteria have been also reflected.

  15. Chlorate analyses in matrices of animal origin.

    PubMed

    Smith, David J; Taylor, Joshua B

    2011-03-09

    Sodium chlorate is being developed as a potential food-safety tool for use in the livestock industry because of its effectiveness in decreasing concentrations of certain Gram-negative pathogens in the gastrointestinal tracts of food animals. A number of studies with sodium chlorate in animals have demonstrated that concentrations of chlorate in meat, milk, wastes, and gastrointestinal contents range from parts per billion to parts per thousand, depending upon chlorate dose, matrix, and time lapse after dosing. Although a number of analytical methods exist for chlorate salts, very few were developed for use in animal-derived matrices, and none have anticipated the range of chlorate concentrations that have been observed in animal wastes and products. To meet the analytical needs of this development work, LC-MS, ion chromatographic, and colorimetric methods were developed to measure chlorate residues in a variety of matrices. The LC-MS method utilizes a Cl(18)O(3)(-) internal standard, is applicable to a variety of matrices, and provides quantitative assessment of samples from 0.050 to 2.5 ppm. Due to ion suppression, matrix-matched standard curves are appropriate when using LC-MS to measure chlorate in animal-derived matrices. A colorimetric assay based on the acid-catalyzed oxidation of o-tolidine proved valuable for measuring ≥20 ppm quantities of chlorate in blood serum and milk, but not urine, samples. Ion chromatography was useful for measuring chlorate residues in urine and in feces when chlorate concentrations exceeded 100 ppm, but no effort was made to maximize ion chromatographic sensitivity. Collectively, these methods offer the utility of measuring chlorate in a variety of animal-derived matrices over a wide range of chlorate concentrations.

  16. Organic acids tunably catalyze carbonic acid decomposition.

    PubMed

    Kumar, Manoj; Busch, Daryle H; Subramaniam, Bala; Thompson, Ward H

    2014-07-10

    Density functional theory calculations predict that the gas-phase decomposition of carbonic acid, a high-energy, 1,3-hydrogen atom transfer reaction, can be catalyzed by a monocarboxylic acid or a dicarboxylic acid, including carbonic acid itself. Carboxylic acids are found to be more effective catalysts than water. Among the carboxylic acids, the monocarboxylic acids outperform the dicarboxylic ones wherein the presence of an intramolecular hydrogen bond hampers the hydrogen transfer. Further, the calculations reveal a direct correlation between the catalytic activity of a monocarboxylic acid and its pKa, in contrast to prior assumptions about carboxylic-acid-catalyzed hydrogen-transfer reactions. The catalytic efficacy of a dicarboxylic acid, on the other hand, is significantly affected by the strength of an intramolecular hydrogen bond. Transition-state theory estimates indicate that effective rate constants for the acid-catalyzed decomposition are four orders-of-magnitude larger than those for the water-catalyzed reaction. These results offer new insights into the determinants of general acid catalysis with potentially broad implications.

  17. Free Amino-acid Concentrations in Fetal Fluids

    PubMed Central

    Cockburn, F.; Robins, S. P.; Forfar, J. O.

    1970-01-01

    The pattern of free amino-acid concentrations in maternal venous plasma, fetal umbilical arterial plasma, fetal urine, and amniotic fluid at 15 to 20 weeks' gestation has been determined. Free amino-acid concentrations were greater in fetal plasma than in maternal plasma, amniotic fluid, or fetal urine. The ratios of amino-acid concentrations in fetal umbilical arterial plasma and urine indicate that the fetal kidney can effectively conserve amino-acids, possibly reaching an adult level of competence in this respect. There was little correlation between amino-acid concentrations in the fluids analysed with the exception of that between amniotic fluid and fetal urine. PMID:5472758

  18. Plasma amino acids

    MedlinePlus

    Amino acids blood test ... types of methods used to determine the individual amino acid levels in the blood. ... test is done to measure the level of amino acids in the blood. An increased level of a ...

  19. Uric acid - urine

    MedlinePlus

    ... page: //medlineplus.gov/ency/article/003616.htm Uric acid urine test To use the sharing features on this page, please enable JavaScript. The uric acid urine test measures the level of uric acid ...

  20. Facts about Folic Acid

    MedlinePlus

    ... Information For... Media Policy Makers Facts About Folic Acid Language: English Español (Spanish) Recommend on Facebook Tweet ... of the baby's brain and spine. About folic acid Folic acid is a B vitamin. Our bodies ...

  1. Stomach acid test

    MedlinePlus

    Gastric acid secretion test ... of the cells in the stomach to release acid. The stomach contents are then removed and analyzed. ... 3.5). These numbers are converted to actual acid production in units of milliequivalents per hour in ...

  2. Methylmalonic acid blood test

    MedlinePlus

    ... page: //medlineplus.gov/ency/article/003565.htm Methylmalonic acid blood test To use the sharing features on this page, please enable JavaScript. The methylmalonic acid blood test measures the amount of methylmalonic acid ...

  3. Uric acid test (image)

    MedlinePlus

    Uric acid urine test is performed to check for the amount of uric acid in urine. Urine is collected over a 24 ... testing. The most common reason for measuring uric acid levels is in the diagnosis or treatment of ...

  4. Fatty Acid Oxidation Disorders

    MedlinePlus

    ... other health conditions > Fatty acid oxidation disorders Fatty acid oxidation disorders E-mail to a friend Please ... these disorders, go to genetests.org . What fatty acid oxidation disorders are tested for in newborn screening? ...

  5. Chlorogenic Acids Biosynthesis in Centella asiatica Cells Is not Stimulated by Salicylic Acid Manipulation.

    PubMed

    Ncube, E N; Steenkamp, P A; Madala, N E; Dubery, I A

    2016-07-01

    Exogenous application of synthetic and natural elicitors of plant defence has been shown to result in mass production of secondary metabolites with nutraceuticals properties in cultured cells. In particular, salicylic acid (SA) treatment has been reported to induce the production of phenylpropanoids, including cinnamic acid derivatives bound to quinic acid (chlorogenic acids). Centella asiatica is an important medicinal plant with several therapeutic properties owing to its wide spectrum of secondary metabolites. We investigated the effect of SA on C. asiatica cells by monitoring perturbation of chlorogenic acids in particular. Different concentrations of SA were used to treat C. asiatica cells, and extracts from both treated and untreated cells were analysed using an optimised UHPLC-QTOF-MS/MS method. Semi-targeted multivariate data analyses with the aid of principal component analysis (PCA) and orthogonal projection to latent structures-discriminant analysis (OPLS-DA) revealed a concentration-dependent metabolic response. Surprisingly, a range of chlorogenic acid derivatives were found to be downregulated as a consequence of SA treatment. Moreover, irbic acid (3,5-O-dicaffeoyl-4-O-malonilquinic acid) was found to be a dominant CGA in C. asiatica cells, although the SA treatment also had a negative effect on its concentration. Overall SA treatment was found to be an ineffective elicitor of CGA production in cultured C. asiatica cells.

  6. Amino acid determination in some edible Mexican insects.

    PubMed

    Ladrón de Guevara, O; Padilla, P; García, L; Pino, J M; Ramos-Elorduy, J

    1995-06-01

    The amino acid contents of edible insects from different provinces of Mexico and reference proteins were analysed by reversed-phase high-performance liquid chromatography and ion exchange chromatography. The insect amino acid contents were higher than the adult requirements indicated by the WHO/FAO pattern.

  7. A new flavellagic acid derivative and phloroglucinol from Rhodomyrtus tomentosa.

    PubMed

    Hiranrat, A; Chitbankluoi, W; Mahabusarakam, W; Limsuwan, S; Voravuthikunchai, S P

    2012-01-01

    A new flavellagic acid derivative, 3,3',4,4'-tetra-O-methylflavellagic acid and six known compounds were isolated from the stems of Rhodomyrtus tomentosa while a new phloroglucinol, named rhodomyrtosone I, and six known compounds were isolated from the fruit. Their structures were elucidated by spectroscopic analyses as well as by comparisons with related compounds.

  8. Palmitic Acid and Health: Introduction.

    PubMed

    Agostoni, Carlo; Moreno, Luis; Shamir, Raanan

    2016-09-09

    Interest in the dietary role and metabolic effect of saturated fatty acids has been recently renewed on the basis of epidemiologic observations and economical approach to health and well-being. Saturated fats may favorably increase blood HDL-Cholesterol levels without significant changes of the total cholesterol/HDL-Cholesterol ratio. Also, the negative effect of saturated fat on cardiovascular diseases risk has recently been challenged. Palmitic acid, among all, may have special structural and functional roles in utero and in infancy, and indeed is it is being delivered in a unique form in human milk. Future research should include objective cost-benefit analyses when disentangling the role of saturated fats in dietary recommendations.

  9. Dermatoglyphic analyses in children with cerebral palsy.

    PubMed

    Simsek, S; Taskiran, H; Karakaya, N; Fistik, T; Solak, M; Cakmak, E A

    1998-01-01

    This study was intended to elucidate the diagnostic values of dermatoglyphic features on the 45 cerebral palsy (CP) patients (28 boys and 17 girls). There were 50 healthy children in the control group. Dermatoglyphic samples were obtained from the both groups by using the paper and ink method and than analysed. The types of dermal patterns of fingertips, the counts of total ridges, the counts of a-b ridges, the values of atd angles, presence or absence of dermal patterns in the hypothenar, thenar/I, II, III, IV interdigital areas, presence of absence of the palmar flexion lines, were compared between the children with CP and control group. It was found that arch, radial loop, whorl prints have increased and ulnar print has decreased in boys investigated which was significant statistically (p < 0.001). No difference was found between investigation and control groups of girls (p > 0.05). The total ridge counts in boys and girls of the investigation group were found significantly decreasing according to the control group (p < 0.001). There was an important decrease in the counts of a-b ridges of investigation group as compared to controls. It was significant in boys (p < 0.01) but not in girls (p > 0.05). The values of atd angles of the investigation group have increased in the control group (p < 0.001 in girls and p < 0.01 in boys). The dermal prints in the hypothenar, thenar/I, II, III and IV interdigital areas showed important differences in the investigation group when compared with the control group (p < 0.01). No clear distinction occurred between the two groups from the viewpoint of palmar flexion lines (p > 0.05). In conclusion, remarkable differences in comparison to controls were found in the dermatoglyphic features of CP cases. In our opinion, by undertaking more studies on the subject and examining a higher number of cases it will be possible to obtain useful data in CP cases indicative of etiologically.

  10. Genome-Facilitated Analyses of Geomicrobial Processes

    SciTech Connect

    Kenneth H. Nealson

    2012-05-02

    that makes up chitin, virtually all of the strains were in fact capable. This led to the discovery of a great many new genes involved with chitin and NAG metabolism (7). In a similar vein, a detailed study of the sugar utilization pathway revealed a major new insight into the regulation of sugar metabolism in this genus (19). Systems Biology and Comparative Genomics of the shewanellae: Several publications were put together describing the use of comparative genomics for analyses of the group Shewanella, and these were a logical culmination of our genomic-driven research (10,15,18). Eight graduate students received their Ph.D. degrees doing part of the work described here, and four postdoctoral fellows were supported. In addition, approximately 20 undergraduates took part in projects during the grant period.

  11. Molecular Biomarker Analyses Using Circulating Tumor Cells

    PubMed Central

    Punnoose, Elizabeth A.; Atwal, Siminder K.; Spoerke, Jill M.; Savage, Heidi; Pandita, Ajay; Yeh, Ru-Fang; Pirzkall, Andrea; Fine, Bernard M.; Amler, Lukas C.; Chen, Daniel S.; Lackner, Mark R.

    2010-01-01

    Background Evaluation of cancer biomarkers from blood could significantly enable biomarker assessment by providing a relatively non-invasive source of representative tumor material. Circulating Tumor Cells (CTCs) isolated from blood of metastatic cancer patients hold significant promise in this regard. Methodology/Principal Findings Using spiked tumor-cells we evaluated CTC capture on different CTC technology platforms, including CellSearch® and two biochip platforms, and used the isolated CTCs to develop and optimize assays for molecular characterization of CTCs. We report similar performance for the various platforms tested in capturing CTCs, and find that capture efficiency is dependent on the level of EpCAM expression. We demonstrate that captured CTCs are amenable to biomarker analyses such as HER2 status, qRT-PCR for breast cancer subtype markers, KRAS mutation detection, and EGFR staining by immunofluorescence (IF). We quantify cell surface expression of EGFR in metastatic lung cancer patient samples. In addition, we determined HER2 status by IF and FISH in CTCs from metastatic breast cancer patients. In the majority of patients (89%) we found concordance with HER2 status from patient tumor tissue, though in a subset of patients (11%), HER2 status in CTCs differed from that observed in the primary tumor. Surprisingly, we found CTC counts to be higher in ER+ patients in comparison to HER2+ and triple negative patients, which could be explained by low EpCAM expression and a more mesenchymal phenotype of tumors belonging to the basal-like molecular subtype of breast cancer. Conclusions/Significance Our data suggests that molecular characterization from captured CTCs is possible and can potentially provide real-time information on biomarker status. In this regard, CTCs hold significant promise as a source of tumor material to facilitate clinical biomarker evaluation. However, limitations exist from a purely EpCAM based capture system and addition of antibodies

  12. Static and dynamic analyses of tensegrity structures

    NASA Astrophysics Data System (ADS)

    Nishimura, Yoshitaka

    Tensegrity structures are a class of truss structures consisting of a continuous set of tension members (cables) and a discrete set of compression members (bars). Since tensegrity structures are light weight and can be compactly stowed and deployed, cylindrical tensegrity modules have been proposed for space structures. From a view point of structural dynamics, tensegrity structures pose a new set of problems, i.e., initial shape finding. Initial configurations of tensegrity structures must be computed by imposing a pre-stressability condition to initial equilibrium equations. There are ample qualitative statements regarding the initial geometry of cylindrical and spherical tensegrity modules. Quantitative initial shape anlyses have only been performed on one-stage and two-stage cylindrical modules. However, analytical expressions for important geometrical parameters such as twist angles and overlap ratios lack the definition of the initial shape of both cylindrical and spherical tensegrity modules. In response to the above needs, a set of static and dynamic characterization procedures for tensegrity modules was first developed. The procedures were subsequently applied to Buckminster Fuller's spherical tensegrity modules. Both the initial shape and the corresponding pre-stress mode were analytically obtained by using the graphs of the tetrahedral, octahedral (cubic), and icosahedral (dodecahedral) groups. For pre-stressed configurations, modal analyses were conducted to classify a large number of infinitesimal mechanism modes. The procedures also applied tocyclic cylindrical tensegrity modules with an arbitrary number of stages. It was found that both the Maxwell number and the number of infinitesimal mechanism modes are independent of the number of stages in the axial direction. A reduced set of equilibrium equations was derived by incorporating cyclic symmetry and the flip, or quasi-flip, symmetry of the cylindrical modules. For multi-stage modules with more than

  13. Dietary conjugated linoleic acid and long-chain n-3 fatty acids in mammary and prostate cancer protection: a review.

    PubMed

    Heinze, Verónica M; Actis, Adriana B

    2012-02-01

    The role of dietary fatty acids on cancer is still controversial. To examine the current literature on the protective role of conjugated linoleic acid (CLA) and marine long-chain fatty acids [eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)] and the risk of breast and prostate cancer, data from 41 case-control and cohort studies and relevant in vitro and animal experiments were included in this 2000-2010 revision. Epidemiological studies on CLA intake or its tissue concentration related to breast and prostate tumorigenesis are not conclusive; EPA and DHA intake have shown important inverse associations just in some studies. Additional research on the analysed association is required.

  14. Acid distribution in phosphoric acid fuel cells

    SciTech Connect

    Okae, I.; Seya, A.; Umemoto, M.

    1996-12-31

    Electrolyte acid distribution among each component of a cell is determined by capillary force when the cell is not in operation, but the distribution under the current load conditions had not been clear so far. Since the loss of electrolyte acid during operation is inevitable, it is necessary to store enough amount of acid in every cell. But it must be under the level of which the acid disturbs the diffusion of reactive gases. Accordingly to know the actual acid distribution during operation in a cell is very important. In this report, we carried out experiments to clarify the distribution using small single cells.

  15. Hexanitrostilbene Recrystallized from Nitric Acid

    DTIC Science & Technology

    1979-09-19

    process. The author wishes to acknowledge Mr. Daniel Polansky for the X-Ray/N-Ray, Ms. Eleonore Kayser for the chemical analyses and nitric acid...recrystallized HNS-II using a pH meter and a solvent mixture consisting of 90% H2 0 and 10% DMSO by volume. The method was developed by Eleonore Kayser...65-142, 26 Aug 1965. 4. Syrop, Leroy J., "Process for Recrystallizing Hexanitrostilbene," U. S. Patent 3,699,176, 17 Oct 1972. 5. Kayser, Eleonore G

  16. Hyaluronic acid and tendon lesions

    PubMed Central

    Kaux, Jean-François; Samson, Antoine; Crielaard, Jean-Michel

    2015-01-01

    Summary Introduction recently, the viscoelastic properties of hyaluronic acid (HA) on liquid connective tissue have been proposed for the treatment of tendinopathies. Some fundamental studies show encouraging results on hyaluronic acid’s ability to promote tendon gliding and reduce adhesion as well as to improve tendon architectural organisation. Some observations also support its use in a clinical setting to improve pain and function. This literature review analyses studies relating to the use of hyaluronic acid in the treatment of tendinopathies. Methods this review was constructed using the Medline database via Pubmed, Scopus and Google Scholar. The key words hyaluronic acid, tendon and tendinopathy were used for the research. Results in total, 28 articles (in English and French) on the application of hyaluronic acid to tendons were selected for their relevance and scientific quality, including 13 for the in vitro part, 7 for the in vivo animal part and 8 for the human section. Conclusions preclinical studies demonstrate encouraging results: HA permits tendon gliding, reduces adhesions, creates better tendon architectural organisation and limits inflammation. These laboratory observations appear to be supported by limited but encouraging short-term clinical results on pain and function. However, controlled randomised studies are still needed. PMID:26958533

  17. Individual variation and intraclass correlation in arachidonic acid and eicosapentaenoic acid in chicken muscle

    PubMed Central

    2010-01-01

    Chicken meat with reduced concentration of arachidonic acid (AA) and reduced ratio between omega-6 and omega-3 fatty acids has potential health benefits because a reduction in AA intake dampens prostanoid signaling, and the proportion between omega-6 and omega-3 fatty acids is too high in our diet. Analyses for fatty acid determination are expensive, and finding the optimal number of analyses to give reliable results is a challenge. The objective of the present study was i) to analyse the intraclass correlation of different fatty acids in five meat samples, of one gram each, within the same chicken thigh, and ii) to study individual variations in the concentrations of a range of fatty acids and the ratio between omega-6 and omega-3 fatty acid concentrations among fifteen chickens. Fifteen newly hatched broilers were fed a wheat-based diet containing 4% rapeseed oil and 1% linseed oil for three weeks. Five muscle samples from the mid location of the thigh of each chicken were analysed for fatty acid composition. The intraclass correlation (sample correlation within the same animal) was 0.85-0.98 for the ratios of total omega-6 to total omega-3 fatty acids and of AA to eicosapentaenoic acid (EPA). This indicates that when studying these fatty acid ratios, one sample of one gram per animal is sufficient. However, due to the high individual variation between chicken for these ratios, a relatively high number of animals (minimum 15) are required to obtain a sufficiently high power to reveal significant effects of experimental factors (e.g. feeding regimes). The present experiment resulted in meat with a favorable concentration ratio between omega-6 and omega-3 fatty acids. The AA concentration varied from 1.5 to 2.8 g/100 g total fatty acids in thigh muscle in the fifteen broilers, and the ratio between AA and EPA concentrations ranged from 2.3 to 3.9. These differences among the birds may be due to genetic variance that can be exploited by breeding for lower AA

  18. First Super-Earth Atmosphere Analysed

    NASA Astrophysics Data System (ADS)

    2010-12-01

    The atmosphere around a super-Earth exoplanet has been analysed for the first time by an international team of astronomers using ESO's Very Large Telescope. The planet, which is known as GJ 1214b, was studied as it passed in front of its parent star and some of the starlight passed through the planet's atmosphere. We now know that the atmosphere is either mostly water in the form of steam or is dominated by thick clouds or hazes. The results will appear in the 2 December 2010 issue of the journal Nature. The planet GJ 1214b was confirmed in 2009 using the HARPS instrument on ESO's 3.6-metre telescope in Chile (eso0950) [1]. Initial findings suggested that this planet had an atmosphere, which has now been confirmed and studied in detail by an international team of astronomers, led by Jacob Bean (Harvard-Smithsonian Center for Astrophysics), using the FORS instrument on ESO's Very Large Telescope. "This is the first super-Earth to have its atmosphere analysed. We've reached a real milestone on the road toward characterising these worlds," said Bean. GJ 1214b has a radius of about 2.6 times that of the Earth and is about 6.5 times as massive, putting it squarely into the class of exoplanets known as super-Earths. Its host star lies about 40 light-years from Earth in the constellation of Ophiuchus (the Serpent Bearer). It is a faint star [2], but it is also small, which means that the size of the planet is large compared to the stellar disc, making it relatively easy to study [3]. The planet travels across the disc of its parent star once every 38 hours as it orbits at a distance of only two million kilometres: about seventy times closer than the Earth orbits the Sun. To study the atmosphere, the team observed the light coming from the star as the planet passed in front of it [4]. During these transits, some of the starlight passes through the planet's atmosphere and, depending on the chemical composition and weather on the planet, specific wavelengths of light are

  19. Molecular Genetic Characterization of Terreic Acid Pathway in Aspergillus terreus

    DOE PAGES

    Guo, Chun-Jun; Sun, Wei-wen; Bruno, Kenneth S.; ...

    2014-09-29

    Terreic acid is a natural product derived from 6-methylsalicylic acid (6-MSA). A compact gene cluster for its biosynthesis was characterized. Isolation of the intermediates and shunt products from the mutant strains, in combined with bioinformatic analyses, allowed us to propose a biosynthetic pathway for terreic acid. Lastly, defining the pathway and the genes involved will facilitate the engineering of this molecule with interesting antimicrobial and antitumor bioactivities.

  20. FY01 Supplemental Science and Performance Analyses, Volume 1: Scientific Bases and Analyses, Rev 00

    SciTech Connect

    David Dobson

    2001-06-30

    The U.S. Department of Energy (DOE) is considering the possible recommendation of a site at Yucca Mountain, Nevada, for development as a geologic repository for the disposal of high-level radioactive waste and spent nuclear fuel. To facilitate public review and comment, in May 2001 the DOE released the Yucca Mountain Science and Engineering Report (S&ER) (DOE 2001 [DIRS 153849]), which presents technical information supporting the consideration of the possible site recommendation. The report summarizes the results of more than 20 years of scientific and engineering studies. A decision to recommend the site has not been made: the DOE has provided the S&ER and its supporting documents as an aid to the public in formulating comments on the possible recommendation. When the S&ER (DOE 2001 [DIRS 153849]) was released, the DOE acknowledged that technical and scientific analyses of the site were ongoing. Therefore, the DOE noted in the Federal Register Notice accompanying the report (66 FR 23 013 [DIRS 155009], p. 2) that additional technical information would be released before the dates, locations, and times for public hearings on the possible recommendation were announced. This information includes: (1) the results of additional technical studies of a potential repository at Yucca Mountain, contained in this FY01 Supplemental Science and Performance Analyses: Vol. 1, Scientific Bases and Analyses; and FY01 Supplemental Science and Performance Analyses: Vol. 2, Performance Analyses (McNeish 2001 [DIRS 155023]) (collectively referred to as the SSPA) and (2) a preliminary evaluation of the Yucca Mountain site's preclosure and postclosure performance against the DOE's proposed site suitability guidelines (10 CFR Part 963 [64 FR 67054] [DIRS 124754]). By making the large amount of information developed on Yucca Mountain available in stages, the DOE intends to provide the public and interested parties with time to review the available materials and to formulate and submit

  1. Residual Strength Analyses of Monolithic Structures

    NASA Technical Reports Server (NTRS)

    Forth, Scott (Technical Monitor); Ambur, Damodar R. (Technical Monitor); Seshadri, B. R.; Tiwari, S. N.

    2003-01-01

    Finite-element fracture simulation methodology predicts the residual strength of damaged aircraft structures. The methodology uses the critical crack-tip-opening-angle (CTOA) fracture criterion to characterize the fracture behavior of the material. The CTOA fracture criterion assumes that stable crack growth occurs when the crack-tip angle reaches a constant critical value. The use of the CTOA criterion requires an elastic- plastic, finite-element analysis. The critical CTOA value is determined by simulating fracture behavior in laboratory specimens, such as a compact specimen, to obtain the angle that best fits the observed test behavior. The critical CTOA value appears to be independent of loading, crack length, and in-plane dimensions. However, it is a function of material thickness and local crack-front constraint. Modeling the local constraint requires either a three-dimensional analysis or a two-dimensional analysis with an approximation to account for the constraint effects. In recent times as the aircraft industry is leaning towards monolithic structures with the intention of reducing part count and manufacturing cost, there has been a consistent effort at NASA Langley to extend critical CTOA based numerical methodology in the analysis of integrally-stiffened panels.In this regard, a series of fracture tests were conducted on both flat and curved aluminum alloy integrally-stiffened panels. These flat panels were subjected to uniaxial tension and during the test, applied load-crack extension, out-of-plane displacements and local deformations around the crack tip region were measured. Compact and middle-crack tension specimens were tested to determine the critical angle (wc) using three-dimensional code (ZIP3D) and the plane-strain core height (hJ using two-dimensional code (STAGS). These values were then used in the STAGS analysis to predict the fracture behavior of the integrally-stiffened panels. The analyses modeled stable tearing, buckling, and crack

  2. Runtime and Pressurization Analyses of Propellant Tanks

    NASA Technical Reports Server (NTRS)

    Field, Robert E.; Ryan, Harry M.; Ahuja, Vineet; Hosangadi, Ashvin; Lee, Chung P.

    2007-01-01

    Multi-element unstructured CFD has been utilized at NASA SSC to carry out analyses of propellant tank systems in different modes of operation. The three regimes of interest at SSC include (a) tank chill down (b) tank pressurization and (c) runtime propellant draw-down and purge. While tank chill down is an important event that is best addressed with long time-scale heat transfer calculations, CFD can play a critical role in the tank pressurization and runtime modes of operation. In these situations, problems with contamination of the propellant by inclusion of the pressurant gas from the ullage causes a deterioration of the quality of the propellant delivered to the test article. CFD can be used to help quantify the mixing and propellant degradation. During tank pressurization under some circumstances, rapid mixing of relatively warm pressurant gas with cryogenic propellant can lead to rapid densification of the gas and loss of pressure in the tank. This phenomenon can cause serious problems during testing because of the resulting decrease in propellant flow rate. With proper physical models implemented, CFD can model the coupling between the propellant and pressurant including heat transfer and phase change effects and accurately capture the complex physics in the evolving flowfields. This holds the promise of allowing the specification of operational conditions and procedures that could minimize the undesirable mixing and heat transfer inherent in propellant tank operation. It should be noted that traditional CFD modeling is inadequate for such simulations because the fluids in the tank are in a range of different sub-critical and supercritical states and elaborate phase change and mixing rules have to be developed to accurately model the interaction between the ullage gas and the propellant. We show a typical run-time simulation of a spherical propellant tank, containing RP-1 in this case, being pressurized with room-temperature nitrogen at 540 R. Nitrogen

  3. The complete mitochondrial genomes of four cockroaches (Insecta: Blattodea) and phylogenetic analyses within cockroaches.

    PubMed

    Cheng, Xue-Fang; Zhang, Le-Ping; Yu, Dan-Na; Storey, Kenneth B; Zhang, Jia-Yong

    2016-07-15

    Three complete mitochondrial genomes of Blaberidae (Insecta: Blattodea) (Gromphadorhina portentosa, Panchlora nivea, Blaptica dubia) and one complete mt genome of Blattidae (Insecta: Blattodea) (Shelfordella lateralis) were sequenced to further understand the characteristics of cockroach mitogenomes and reconstruct the phylogenetic relationship of Blattodea. The gene order and orientation of these four cockroach genomes were similar to known cockroach mt genomes, and contained 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The mt genomes of Blattodea exhibited a characteristics of a high A+T composition (70.7%-74.3%) and dominant usage of the TAA stop codon. The AT content of the whole mt genome, PCGs and total tRNAs in G. portentosa was the lowest in known cockroaches. The presence of a 71-bp intergenic spacer region between trnQ and trnM was a unique feature in B. dubia, but absent in other cockroaches, which can be explained by the duplication/random loss model. Based on the nucleotide and amino acid datasets of the 13 PCGs genes, neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and bayesian inference (BI) analyses were used to rebuild the phylogenetic relationship of cockroaches. All phylogenetic analyses consistently placed Isoptera as the sister cluster to Cryptocercidae of Blattodea. Ectobiidae and Blaberidae (Blaberoidea) formed a sister clade to Blattidae. Corydiidae is a sister clade of all the remaining cockroach species with a high value in NJ and MP analyses of nucleotide and amino acid datasets, and ML and BI analyses of the amino acid dataset.

  4. Organic geochemistry of amino acids: Precambrian to recent

    SciTech Connect

    Engel, M.H.; Macko, S.A.

    1985-01-01

    Since the discovery of amino acids in fossils (Abelson, 1954), considerable effort has been made to elucidate the origin and distribution of amino acids in geologic materials. Racemization and decomposition reactions of amino acids and peptides derived via the natural hydrolysis of protein constituents of organisms have been extensively studied. While the ubiquity of amino acids presents a challenge for discerning their indigeneity in geologic samples, careful analyses have resulted in successful applications of amino acid racemization and decomposition reactions for investigations of geochronologic, paleoclimatic, stratigraphic, diagenetic and chemotaxonomic problems for Quaternary age samples. An investigation of amino acids in sediments from Baffin Island fjords indicates that their distribution may also provide data with respect to the relative contributions of marine and terrigenous organic matter to recent sediments. While the absence of unstable amino acids and the presence of racemic amino acids in a sample may preclude very recent contamination, the possibility of retardation of amino acid racemization rates subsequent to geopolymer formation must also be considered. Studies of amino acids in Paleozoic, Mesozoic and early Cenozoic age samples are limited. Precambrian samples, however, have received much attention, given the potential (however slight) for isolating compounds representative of the earliest living systems. A future approach for elucidating the origin(s) of amino acids in ancient samples may be analyses of their individual stable isotopic compositions.

  5. Analyses of 1999 PM Data for the PM NAAQS Review

    EPA Pesticide Factsheets

    These files document all analyses conducted in association with the EPA memorandum from Terence Fitz-Simons, Scott Mathias, and Mike Rizzo titled Analyses of 1999 PM Data for the PM NAAQS Review, November 17, 2000.

  6. The contents of the neuro-excitatory amino acid β-ODAP (β-N-oxalyl-l-α,β-diaminopropionic acid), and other free and protein amino acids in the seeds of different genotypes of grass pea (Lathyrus sativus L.).

    PubMed

    Fikre, Asnake; Korbu, Lijalem; Kuo, Yu-Haey; Lambein, Fernand

    2008-09-15

    The free and protein amino acids of nine different genotypes of grass pea (Lathyrus sativus L.) seeds were analysed by HPLC with pre-column PITC (phenyl isothiocyanate) derivatisation. Among the free amino acids, homoarginine was quantitatively the most important (up to 0.8% seed weight) and stable while the neuro-excitatory amino acid β-ODAP (β-N-oxalyl-l-α,β-diaminopropionic acid) showed highest variation (0.02-0.54%) in the nine genotypes examined. Among protein amino acids, glutamic acid was quantitatively most significant, followed by aspartic acid, arginine, leucine, lysine and proline. The sulphur amino acid, methionine, showed the lowest concentration in all the L. sativus genotypes, and also in lentil (Lens culinaris) and in soybean (Glycine max) seeds analysed at the same time.

  7. Pan-cancer analyses of the nuclear receptor superfamily

    PubMed Central

    Long, Mark D.; Campbell, Moray J.

    2016-01-01

    Nuclear receptors (NR) act as an integrated conduit for environmental and hormonal signals to govern genomic responses, which relate to cell fate decisions. We review how their integrated actions with each other, shared co-factors and other transcription factors are disrupted in cancer. Steroid hormone nuclear receptors are oncogenic drivers in breast and prostate cancer and blockade of signaling is a major therapeutic goal. By contrast to blockade of receptors, in other cancers enhanced receptor function is attractive, as illustrated initially with targeting of retinoic acid receptors in leukemia. In the post-genomic era large consortia, such as The Cancer Genome Atlas, have developed a remarkable volume of genomic data with which to examine multiple aspects of nuclear receptor status in a pan-cancer manner. Therefore to extend the review of NR function we have also undertaken bioinformatics analyses of NR expression in over 3000 tumors, spread across six different tumor types (bladder, breast, colon, head and neck, liver and prostate). Specifically, to ask how the NR expression was distorted (altered expression, mutation and CNV) we have applied bootstrapping approaches to simulate data for comparison, and also compared these NR findings to 12 other transcription factor families. Nuclear receptors were uniquely and uniformly downregulated across all six tumor types, more than predicted by chance. These approaches also revealed that each tumor type had a specific NR expression profile but these were most similar between breast and prostate cancer. Some NRs were down-regulated in at least five tumor types (e.g. NR3C2/MR and NR5A2/LRH-1)) whereas others were uniquely down-regulated in one tumor (e.g. NR1B3/RARG). The downregulation was not driven by copy number variation or mutation and epigenetic mechanisms maybe responsible for the altered nuclear receptor expression. PMID:27200367

  8. Statistical power analyses using G*Power 3.1: tests for correlation and regression analyses.

    PubMed

    Faul, Franz; Erdfelder, Edgar; Buchner, Axel; Lang, Albert-Georg

    2009-11-01

    G*Power is a free power analysis program for a variety of statistical tests. We present extensions and improvements of the version introduced by Faul, Erdfelder, Lang, and Buchner (2007) in the domain of correlation and regression analyses. In the new version, we have added procedures to analyze the power of tests based on (1) single-sample tetrachoric correlations, (2) comparisons of dependent correlations, (3) bivariate linear regression, (4) multiple linear regression based on the random predictor model, (5) logistic regression, and (6) Poisson regression. We describe these new features and provide a brief introduction to their scope and handling.

  9. Non-destructive infrared analyses: a method for provenance analyses of sandstones

    NASA Astrophysics Data System (ADS)

    Bowitz, Jörg; Ehling, Angela

    2008-12-01

    Infrared spectroscopy (IR spectroscopy) is commonly applied in the laboratory for mineral analyses in addition to XRD. Because such technical efforts are time and cost consuming, we present an infrared-based mobile method for non-destructive mineral and provenance analyses of sandstones. IR spectroscopy is based on activating chemical bonds. By irradiating a mineral mixture, special bonds are activated to vibrate depending on the bond energy (resonance vibration). Accordingly, the energy of the IR spectrum will be reduced thereby generating an absorption spectrum. The positions of the absorption maxima within the spectral region indicate the type of the bonds and in many cases identify minerals containing these bonds. The non-destructive reflection spectroscopy operates in the near infrared region (NIR) and can detect all common clay minerals as well as sulfates, hydroxides and carbonates. The spectra produced have been interpreted by computer using digital mineral libraries that have been especially collected for sandstones. The comparison of all results with XRD, RFA and interpretations of thin sections demonstrates impressively the accuracy and reliability of this method. Not only are different minerals detectable, but also differently ordered kaolinites and varieties of illites can be identified by the shape and size of the absorption bands. Especially clay minerals and their varieties in combination with their relative contents form the characteristic spectra of sandstones. Other components such as limonite, hematite and amorphous silica also influence the spectra. Sandstones, similar in colour and texture, often can be identified by their characteristic reflectance spectra. Reference libraries with more than 60 spectra of important German sandstones have been created to enable entirely computerized interpretations and identifications of these dimension stones. The analysis of infrared spectroscopy results is demonstrated with examples of different sandstones

  10. Rapid Radiochemical Analyses in Support of Fukushima Nuclear Accident - 13196

    SciTech Connect

    Maxwell, Sherrod L.; Culligan, Brian K.; Hutchison, Jay B.

    2013-07-01

    precipitations, followed by Sr-Resin separation and gas flow proportional counting. To achieve a lower detection limit for analysis of some of the Japanese soil samples, a 10 gram aliquot of soil was taken, acid-leached and processed with similar preconcentration chemistry. The MDA using this approach was ∼0.03 pCi/g (1.1 mBq/g)/, which is less than the 0.05-0.10 pCi/g {sup 90}Sr levels found in soil as a result of global fallout. The chemical yields observed for the Japanese soil samples was typically 75-80% and the laboratory control sample (LCS) and matrix spike (MS) results looked very good for this work Individual QC results were well within the ± 25% acceptable range and the average of these results does not show significant bias. Additional data for a radiostrontium in soil method for 50 gram samples will also be presented, which appears to be a significant step forward based on looking at the current literature, with higher chemical yields for even larger sample aliquots and lower MDA [5, 6, 7] Hou et al surveyed a wide range of separation methods for Pu in waters and environmental solid samples [8]. While there are many actinide methods in the scientific literature, few would be considered rapid due to the tedious and time-consuming steps involved. For actinide analyses in soil, a new rapid method for the determination of actinide isotopes in soil samples using both alpha spectrometry and inductively-coupled plasma mass spectrometry was employed. The new rapid soil method utilizes an acid leaching method, iron/titanium hydroxide precipitation, a lanthanum fluoride soil matrix removal step, and a rapid column separation process with TEVA Resin. The large soil matrix is removed easily and rapidly using these two simple precipitations with high chemical recoveries and effective removal of interferences. [9, 10] Vacuum box technology and rapid flow rates were used to reduce analytical time. Challenges associated with the mineral content in the volcanic soil will be

  11. RAPID RADIOCHEMICAL ANALYSES IN SUPPORT OF FUKUSHIMA NUCLEAR ACCIDENT

    SciTech Connect

    Maxwell, S.

    2012-11-07

    by Sr-Resin separation and gas flow proportional counting. To achieve a lower detection limit for analysis of some of the Japanese soil samples, a 10 gram aliquot of soil was taken, acid-leached and processed with similar preconcentration chemistry. The MDA using this approach was ~0.03 pCi/g (1.1 mBq/g)/, which is less than the 0.05-0.10 pCi/g {sup 90}Sr levels found in soil as a result of global fallout. The chemical yields observed for the Japanese soil samples was typically 75-80% and the laboratory control sample (LCS) and matrix spike (MS) results looked very good for this work Individual QC results were well within the ± 25% acceptable range and the average of these results does not show significant bias. Additional data for a radiostrontium in soil method for 50 gram samples will also be presented, which appears to be a significant step forward based on looking at the current literature, with higher chemical yields for even larger sample aliquots and lower MDA. Hou et al surveyed a wide range of separation methods for Pu in waters and environmental solid samples. While there are many actinide methods in the scientific literature, few would be considered rapid due to the tedious and time-consuming steps involved. For actinide analyses in soil, a new rapid method for the determination of actinide isotopes in soil samples using both alpha spectrometry and inductively-coupled plasma mass spectrometry was employed. The new rapid soil method utilizes an acid leaching method, iron/titanium hydroxide precipitation, a lanthanum fluoride soil matrix removal step, and a rapid column separation process with TEVA Resin. The large soil matrix is removed easily and rapidly using these two simple precipitations with high chemical recoveries and effective removal of interferences. Vacuum box technology and rapid flow rates were used to reduce analytical time. Challenges associated with the mineral content in the volcanic soil will be discussed. Air filter samples were

  12. Fatty acid composition of California grown almonds.

    PubMed

    Sathe, S K; Seeram, N P; Kshirsagar, H H; Heber, D; Lapsley, K A

    2008-11-01

    Eight almond (Prunus dulcis L.) cultivars from 12 different California counties, collected during crop years 2004 to 2005 and 2005 to 2006, were extracted with petroleum ether. The extracts were subjected to GC-MS analyses to determine fatty acid composition of soluble lipids. Results indicated palmitic (C16:0), oleic (C18:1), linoleic (C18:2), and alpha-linolenic (C18:3) acid, respectively, accounted for 5.07% to 6.78%, 57.54% to 73.94%, 19.32% to 35.18%, and 0.04% to 0.10%; of the total lipids. Oleic and linoleic acid were inversely correlated (r=-0.99, P= 0.05) and together accounted for 91.16% to 94.29% of the total soluble lipids. Statistically, fatty acid composition was significantly affected by cultivar and county.

  13. [Recovery of Staphylococcus aureus after acid damage].

    PubMed

    Assis, E M; de Carvalho, E P; Asquieri, E R; da Silva, F V; Robbs, P G

    1995-01-01

    The growth behavior of S. aureus in fresh cheese (Minas and Mozzarella) during their shelf life was studied in this research. The possibility of injury to this microorganism caused by increasing acidity was also investigated. Raw milk was inoculated with S. aureus FRIA-100 with approximately 10(6) cells/ml and cheese production was carried out according to normal procedures. They were stored at 7 degrees C during 40 days for Minas cheese and during 60 days for Mozzarella cheese. At 2 to 3 days intervals the following analyses were performed: acidity, pH, S. aureus count on Baird-Parker agar by traditional methods and by the method recommended by the American Public Health Association, to count repair of injured cells. We were certain of the presence of injured S. aureus when acidity was in the range of 0.7 to 0.8% expressed as lactic acid and when the count was 1.3 log higher.

  14. Acid tolerance in amphibians

    SciTech Connect

    Pierce, B.A.

    1985-04-01

    Studies of amphibian acid tolerance provide information about the potential effects of acid deposition on amphibian communities. Amphibians as a group appear to be relatively acid tolerant, with many species suffering increased mortality only below pH 4. However, amphibians exhibit much intraspecific variation in acid tolerance, and some species are sensitive to even low levels of acidity. Furthermore, nonlethal effects, including depression of growth rates and increases in developmental abnormalities, can occur at higher pH.

  15. Analysis of Chiral Carboxylic Acids in Meteorites

    NASA Technical Reports Server (NTRS)

    Burton, A. S.; Elsila, J. E.; Hein, J. E.; Aponte, J. C.; Parker, E. T.; Glavin, D. P.; Dworkin, J. P.

    2015-01-01

    Homochirality of amino acids in proteins and sugars in DNA and RNA is a critical feature of life on Earth. In the absence of a chiral driving force, however, reactions leading to the synthesis of amino acids and sugars result in racemic mixtures. It is currently unknown whether homochirality was necessary for the origins of life or if it was a product of early life. The observation of enantiomeric excesses of certain amino acids of extraterrestrial origins in meteorites provides evidence to support the hypothesis that there was a mechanism for the preferential synthesis or destruction of a particular amino acid enantiomer [e.g., 1-3]. The cause of the observed chiral excesses is un-clear, although at least in the case of the amino acid isovaline, the degree of aqueous alteration that occurred on the meteorite parent body is correlated to the isovaline L-enantiomeric excess [3, 4]. This suggests that chiral symmetry is broken and/or amplified within the meteorite parent bodies. Besides amino acids, there have been only a few reports of other meteoritic compounds found in enantiomeric excess: sugars and sugar acids [5, 6] and the hydroxy acid lactic acid [7]. Determining whether or not additional types of molecules in meteorites are also present in enantiomeric excesses of extraterrestrial information will provide insights into mechanisms for breaking chiral symmetry. Though the previous measurements (e.g., enantiomeric composition of lactic acid [7], and chiral carboxylic acids [8]) were made by gas chromatography-mass spectrometry, the potential for increased sensitivity of liquid chromatography-mass spectrometry (LC-MS) analyses is important because for many meteorite samples, only small sample masses are available for study. Furthermore, at least in the case of amino acids, many of the largest amino acid enantiomeric excesses were observed in samples that contained lower abundances (tens of ppb) of a given amino acid enantiomer. In the present work, we describe

  16. Xanthan from sulphuric acid treated tapioca pulp: influence of acid concentration on xanthan fermentation.

    PubMed

    Gunasekar, V; Reshma, K R; Treesa, Greeshma; Gowdhaman, D; Ponnusami, V

    2014-02-15

    Xanthan gum was produced by fermentation of sulphuric acid pre-treated tapioca pulp. Effect of sulphuric acid concentration (0.5%, 2.5% and 5.0%) on xanthan fermentation was investigated. Maximum xanthan yield (7.1g/l) was obtained with 0.5% sulphuric acid pre-treatment. Further, increase in sulphuric acid concentration caused formation of inhibitory substance and lowered xanthan yield. The product was confirmed as xanthan using FTIR, (1)H NMR analyses. Viscosity was measured by Brookfield viscometer and the molecular weight was determined from the intrinsic viscosity. The results confirmed that the yield and quality of xanthan produced were strongly influenced by the acid concentration.

  17. Identification of diamino acids in the Murchison meteorite

    NASA Astrophysics Data System (ADS)

    Meierhenrich, Uwe J.; Muñoz Caro, Guillermo M.; Hendrik Bredehöft, Jan; Jessberger, Elmar K.; Thiemann, Wolfram H.-P.

    Amino acids identified in the Murchison chondritic meteorite by molecular and isotopic analysis are thought to have been delivered to the early Earth by asteroids, comets, and interplanetary dust particles where they may have triggered the appearance of life by assisting in the synthesis of proteins via prebiotic polycondensation reactions [Oró, J. (1961) Nature 190, 389-390; Chyba, C. F. & Sagan, C. (1992) Nature 355, 125-132]. We report the identification of diamino acids in the Murchison meteorite by new enantioselective GC-MS analyses. DL-2,3-diaminopropanoic acid, DL-2,4-diaminobutanoic acid, 4,4'-diaminoisopentanoic acid, 3,3'-diaminoisobutanoic acid, and 2,3-diaminobutanoic acid were detected in the parts per billion range after chemical transformation into N,N-diethoxycarbonyl ethyl ester derivatives. The chiral diamino acids show a racemic ratio. Laboratory data indicate that diamino acids support the formation of polypeptide structures under primitive Earth conditions [Brack, A. & Orgel, L. E. (1975) Nature 256, 383-387] and suggest polycondensation reactions of diamino acids into early peptide nucleic acid material as one feasible pathway for the prebiotic evolution of DNA and RNA genomes [Joyce, G. F. (2002) Nature 418, 214-221]. The results obtained in this study favor the assumption that not only amino acids (as the required monomers of proteins) form in interstellar/circumstellar environments, but also the family of diamino monocarboxylic acids, which might have been relevant in prebiotic chemistry.

  18. Identification of diamino acids in the Murchison meteorite.

    PubMed

    Meierhenrich, Uwe J; Muñoz Caro, Guillermo M; Bredehöft, Jan Hendrik; Jessberger, Elmar K; Thiemann, Wolfram H-P

    2004-06-22

    Amino acids identified in the Murchison chondritic meteorite by molecular and isotopic analysis are thought to have been delivered to the early Earth by asteroids, comets, and interplanetary dust particles where they may have triggered the appearance of life by assisting in the synthesis of proteins via prebiotic polycondensation reactions [Oró, J. (1961) Nature 190, 389-390; Chyba, C. F. & Sagan, C. (1992) Nature 355, 125-132]. We report the identification of diamino acids in the Murchison meteorite by new enantioselective GC-MS analyses. dl-2,3-diaminopropanoic acid, dl-2,4-diaminobutanoic acid, 4,4'-diaminoisopentanoic acid, 3,3'-diaminoisobutanoic acid, and 2,3-diaminobutanoic acid were detected in the parts per billion range after chemical transformation into N,N-diethoxycarbonyl ethyl ester derivatives. The chiral diamino acids show a racemic ratio. Laboratory data indicate that diamino acids support the formation of polypeptide structures under primitive Earth conditions [Brack, A. & Orgel, L. E. (1975) Nature 256, 383-387] and suggest polycondensation reactions of diamino acids into early peptide nucleic acid material as one feasible pathway for the prebiotic evolution of DNA and RNA genomes [Joyce, G. F. (2002) Nature 418, 214-221]. The results obtained in this study favor the assumption that not only amino acids (as the required monomers of proteins) form in interstellar/circumstellar environments, but also the family of diamino monocarboxylic acids, which might have been relevant in prebiotic chemistry.

  19. Gas-phase acidities of aspartic acid, glutamic acid, and their amino acid amides

    NASA Astrophysics Data System (ADS)

    Li, Zhong; Matus, Myrna H.; Velazquez, Hector Adam; Dixon, David A.; Cassady, Carolyn J.

    2007-09-01

    Gas-phase acidities (GA or [Delta]Gacid) for the two most acidic common amino acids, aspartic acid and glutamic acid, have been determined for the first time. Because of the amide linkage's importance in peptides and as an aid in studying side chain versus main chain deprotonation, aspartic acid amide and glutamic acid amide were also studied. Experimental GA values were measured by proton transfer reactions in an electrospray ionization/Fourier transform ion cyclotron resonance mass spectrometer. Calculated GAs were obtained by density functional and molecular orbital theory approaches. The best agreement with experiment was found at the G3MP2 level; the MP2/CBS and B3LYP/aug-cc-pVDZ results are 3-4 kcal/mol more acidic than the G3MP2 results. Experiment shows that aspartic acid is more acidic than glutamic acid by ca. 3 kcal/mol whereas the G3MP2 results show a smaller acidity difference of 0.2 kcal/mol. Similarly, aspartic acid amide is experimentally observed to be ca. 2 kcal/mol more acidic than glutamic acid amide whereas the G3MP2 results show a correspondingly smaller energy difference of 0.7 kcal/mol. The computational results clearly show that the anions are all ring-like structures with strong hydrogen bonds between the OH or NH2 groups and the CO2- group from which the proton is removed. The two amino acids are main-chain deprotonated. In addition, use of the COSMO model for the prediction of the free energy differences in aqueous solution gave values in excellent agreement with the most recent experimental values for pKa. Glutamic acid is predicted to be more acidic than aspartic acid in aqueous solution due to differential solvation effects.

  20. Toxicity of adipic acid.

    PubMed

    Kennedy, Gerald L

    2002-05-01

    Adipic acid has very low acute toxicity in rats with an LD50 > 5000 mg/kg. Adipic acid produced mild to no skin irritation on intact guinea pig skin as a 50% concentration in propylene glycol; it was not a skin sensitizer. Adipic acid caused mild conjunctival irritation in washed rabbit eyes; in unwashed rabbit eyes, there was mild conjunctival irritation, minimal iritis, but no corneal effects. Adipic acid dust may irritate the mucous membranes of the lungs and nose. In a 2-year feeding study, rats fed adipic acid at concentrations up to 5% in the diet exhibited only weight loss. Adipic acid is not genetically active in a wide variety of assay systems. Adipic acid caused no developmental toxicity in mice, rats, rabbits, or hamsters when administered orally. Adipic acid is partially metabolized in humans; the balance is eliminated unchanged in the urine. Adipic acid is slightly to moderately toxic to fish, daphnia, and algae in acute tests.