Science.gov

Sample records for acid plfa analyses

  1. 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

  2. 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

  3. 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

  4. PLFA profiles of drinking water biofilters with different acetate and glucose loadings.

    PubMed

    Yu, Xin; Shi, Xu; Wei, Bo; Ye, Lin; Zhang, Shuting

    2009-08-01

    The biofilters fed with acetate or glucose and their phospholipid fatty acid (PLFA) profiles were investigated to observe the impact of organic matter concentrations on the microbial community structure in the drinking water production system. PLFA markers for bacteria were predominant in all of the biofilters and made up over half of the total PLFA content. PLFA diversity was compared and the biofilters fed with glucose had higher diversity. The Shannon-Wiener (or sometimes known as just Shannon diversity index) indices in the biofilters fed with acetate were from 0.68 to 0.97, while the indices in the biofilters fed with glucose were from 0.95 to 1.25. Principle components analysis showed that carbon sources and media depth were responsible for 68 and 17% of the total PLFA variance, respectively. The results indicated that PLFA analysis could be useful in illustrating microbial community structure in drinking water bioreactors, and microbial community structure was impacted by carbon substrates.

  5. Using PLFA Biomarkers and Natural Abundance Stable and Radiocarbon Isotopes to Characterize the Microbial Ecology and Metabolism of Methane Cycling

    NASA Astrophysics Data System (ADS)

    Mills, C. T.; Mandernack, K. W.; Slater, G. F.; Dias, R. F.

    2008-12-01

    Methane generated in the subsurface is a major source of atmospheric CH4, but its release is mitigated by CH4-oxidizing bacteria (methanotrophs). Therefore, it is important to understand the ecology of methanotroph communities in various environments. Phospholipid fatty acid (PLFA) analyses are a particularly useful method for characterizing these communities for two reasons: (1) Many type I and II methanotrophs produce specific PLFA biomarkers that can be used to estimate their populations, and (2) because CH4 is often very depleted in 13C and sometimes 14C, natural abundance δ13CPLFA and Δ14CPLFA values can be used to trace the flow of CH4- derived carbon through microbial ecosystems. We used these tools to evaluate the role of methanotrophs in carbon flow in three different environments: (1) a soil column overlying a coal bed methane (CBM) seep in southwest CO, and pristine, oligotrophic groundwaters within (2) sedimentary and (3) granitic host rocks in Japan. In the soil column impacted by CBM seepage, concentrations of the biomarker PLFAs for type I (16:1ω8cis) and type II (18:1ω8cis) methanotrophs were as high as 13 and 18 nmoles (g dry soil)-1, respectively. Depth profiles of methanotroph PLFA concentrations varied over different sampling dates indicating dynamic populations. δ13CPLFA values of the CBM soils (-25.1 to - 66.9‰) were substantially more negative than those for the control soil (-14.5 to -32.5‰) indicating that CBM is an important carbon source for the CBM-impacted soil microbial community. Δ14CPLFA values (-351 to -936‰) indicate the importance of 14C-dead CBM as a carbon source to the microbial communities, contributing 32 to 66% of total carbon in PLFA structures isolated from shallow soils and 67 to 97% for those isolated from deeper soils. The biomarker for type II methanotrophs, comprised 3 and 18% of total PLFAs in sedimentary and granitic groundwaters, respectively. The Δ14C values determined for type II methanotroph PLFAs

  6. 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.

  7. Contributions of understory and/or overstory vegetations to soil microbial PLFA and nematode diversities in Eucalyptus monocultures.

    PubMed

    Zhao, Jie; Wan, Songze; Zhang, Chenlu; 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.

  8. 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

  9. [Effects of Different Altitudes on Soil Microbial PLFA and Enzyme Activity in Two Kinds of Forests].

    PubMed

    Zeng, Qing-ping; He, Bing-hui; Mao, Qiao-zhi; Wu, Yao-peng; Huang, Qi; Li, Yuan

    2015-12-01

    The soil microbial community is an important part in soil ecosystem, and it is sensitive to the ecological environment. Phospholipid-derived fatty acids ( PLFA ) analysis was used to examine variations in soil microbial community diversity and its influencing factors. The results showed that: there existed 48 PLFAs that were significant in the soil samples from six altitudes. The PLFAs of six altitudes with the highest contents were i16:0, 10Me17:0, 10Me18:0 TBSA. The citrus forest exhibited richer soil PLFAs distribution both in type and amount than those in masson pine. The microbial activity and functional diversity of masson pine were increased with increasing altitudes, and citrus forest gradually decreased, the PLFA content of different microbial groups in each altitude were significantly different. The richness index, Shannon-Wiener index and Pielou evenness index of masson pine in low elevation were holistically higher than those in high elevation. However, the highest richness index of citrus forest was in low altitude, the highest Shannon-Wiener index and Pielou evenness index were in high altitude. The PLFAs content of different microbial groups were closely correlated to the soil enzyme activities and environmental factors. The PLFAs of bacteria, actinomycetes, G⁻ (Gram- positive), G⁺ (Gram-negative) were positively correlated with Ure(urease) , Ive(invertase) , CAT( catalase activity) and forest type, the PLFAs of fungi was significantly correlated with Ure, Ive, CAT, the PLFAs of bacteria, fungi, actinomycetes, G⁻ , G⁺ were significantly negatively or less correlated with elevation. Ure, Ive, CAT, forest type and elevation are the pivotal factors controlling the soil microbial biomass and activities.

  10. [Effects of Different Altitudes on Soil Microbial PLFA and Enzyme Activity in Two Kinds of Forests].

    PubMed

    Zeng, Qing-ping; He, Bing-hui; Mao, Qiao-zhi; Wu, Yao-peng; Huang, Qi; Li, Yuan

    2015-12-01

    The soil microbial community is an important part in soil ecosystem, and it is sensitive to the ecological environment. Phospholipid-derived fatty acids ( PLFA ) analysis was used to examine variations in soil microbial community diversity and its influencing factors. The results showed that: there existed 48 PLFAs that were significant in the soil samples from six altitudes. The PLFAs of six altitudes with the highest contents were i16:0, 10Me17:0, 10Me18:0 TBSA. The citrus forest exhibited richer soil PLFAs distribution both in type and amount than those in masson pine. The microbial activity and functional diversity of masson pine were increased with increasing altitudes, and citrus forest gradually decreased, the PLFA content of different microbial groups in each altitude were significantly different. The richness index, Shannon-Wiener index and Pielou evenness index of masson pine in low elevation were holistically higher than those in high elevation. However, the highest richness index of citrus forest was in low altitude, the highest Shannon-Wiener index and Pielou evenness index were in high altitude. The PLFAs content of different microbial groups were closely correlated to the soil enzyme activities and environmental factors. The PLFAs of bacteria, actinomycetes, G⁻ (Gram- positive), G⁺ (Gram-negative) were positively correlated with Ure(urease) , Ive(invertase) , CAT( catalase activity) and forest type, the PLFAs of fungi was significantly correlated with Ure, Ive, CAT, the PLFAs of bacteria, fungi, actinomycetes, G⁻ , G⁺ were significantly negatively or less correlated with elevation. Ure, Ive, CAT, forest type and elevation are the pivotal factors controlling the soil microbial biomass and activities. PMID:27012007

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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

  17. Comparative analyses of lysophosphatidic acid receptor-mediated signaling.

    PubMed

    Fukushima, Nobuyuki; Ishii, Shoichi; Tsujiuchi, Toshifumi; Kagawa, Nao; Katoh, Kazutaka

    2015-06-01

    Lysophosphatidic acid (LPA) is a bioactive lipid mediator that activates G protein-coupled LPA receptors to exert fundamental cellular functions. Six LPA receptor genes have been identified in vertebrates and are classified into two subfamilies, the endothelial differentiation genes (edg) and the non-edg family. Studies using genetically engineered mice, frogs, and zebrafish have demonstrated that LPA receptor-mediated signaling has biological, developmental, and pathophysiological functions. Computational analyses have also identified several amino acids (aa) critical for LPA recognition by human LPA receptors. This review focuses on the evolutionary aspects of LPA receptor-mediated signaling by comparing the aa sequences of vertebrate LPA receptors and LPA-producing enzymes; it also summarizes the LPA receptor-dependent effects commonly observed in mouse, frog, and fish. PMID:25732591

  18. Molecular analyses of an acidic transthyretin Asn 90 variant.

    PubMed Central

    Saraiva, M J; Almeida, M R; Alves, I L; Moreira, P; Gawinowicz, M; Costa, P P; Rauh, S; Banhzoff, A; Altland, K

    1991-01-01

    A mutation in transthyretin (TTR Asn 90) has been identified in the Portuguese and German populations. This variant has a lower pI and was found by screening analyses in 2/4,000 German subjects and in 4/1,200 Portuguese by using either double one-dimensional (D1-D) electrophoresis with isoelectric focusing (IEF) or hybrid isoelectric focusing in immobilized pH gradient (HIEF) as the final separation step. The Portuguese population sample was from the area where TTR Met 30-associated familial amyloidotic polyneuropathy (FAP) prevails, and it was divided into (a) a group of 500 individuals belonging to FAP kindreds and (b) a group of 700 collected at random. HIEF showed two particular situations: (1) one case, from an FAP kindred, was simultaneously carrier of the Met 30 substitution and the acidic variant, and (2) one individual, from the randomly selected Portuguese sample, had only the acidic monomer. Comparative peptide mapping, by HPLC, of the acidic variant carriers and of normal TTR showed the presence of an abnormal tryptic peptide, not present in the normal TTR digests, with an asparagine-for-histidine substitution at position 90 explained by a single base change of adenine for cytosine in the histidine codon. This was confirmed at the DNA level by RFLP analyses of PCR-amplified material after digestion with SphI and BsmI. In all carriers of the Asn 90 substitution, no indicators were found for an association with traits characteristic for FAP. Images Figure 1 Figure 3 PMID:1850190

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Sequential multiple analyses of atmospheric nitrous acid and nitrogen oxides.

    PubMed

    Toda, Kei; Hato, Yuki; Mori, Kotaro; Ohira, Shin-Ichi; Namihira, Takao

    2007-03-15

    Sequential injection analysis (SIA) was applied to multi-gas monitoring for atmospheric analysis. HONO, NO(2) or NO was collected in an individual diffusion scrubber in which the channel array was filled with either HCl or triethanolamine solution. All analytes were collected in the form of nitrite ions in the scrubber, and were transferred via a 12-port selection valve into a 2.5-ml syringe. The reagent, 3-amino-1,5-naphthalenedisulfonic acid (C-acid) solution was subsequently introduced into the syringe, and inter-mixed with the nitrite sample, whereafter the mixed solution was transferred to a heated reactor and held for 3min at 100 degrees C. After that, the sample/reagent solution was returned to the syringe and alkalinized. Then, the final solution was analyzed using a homemade fluorescence detector. Atmospheric HONO, NO(2) and NO were successfully monitored 3 or 4times/h. The limits of detection were 0.22, 0.28 and 0.35ppbv for HONO, NO(2) and NO, respectively. It was demonstrated for the first time that SIA is a good tool for multi-gas atmospheric analysis. These nitrogen-oxygen compounds are interconvertible, and the simultaneous measurement of these gases is important. Especially, HONO is a source of OH radicals which contribute greatly to atmospheric pollution, and indeed atmospheric chemistry. This method allows the three gases to be measured using one system. The NO(2) and NO data obtained by SIA was compared with those obtained using chemiluminescence instrument. SIA has been successfully applied to atmospheric measurements. Interestingly, it was observed that HONO levels rose toward the end of periods of rain.

  4. 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.

  5. Fatty acid analyses may provide insight into the progression of starvation among squamate reptiles.

    PubMed

    McCue, Marshall D

    2008-10-01

    Fasting-induced changes in fatty acid composition have been reported to occur within the body lipids of several types of animals; however, little is known about the changes in fatty acid profiles exhibited by reptiles subjected to prolonged fasting. This study characterizes the fatty acid profiles of six reptile species subjected to sublethal periods of fasting lasting 0, 56, 112, and 168 days. Analyses of fatty acid methyl esters (FAMEs) conducted on the total body lipids of rattlesnakes (Crotalus atrox), ratsnakes (Elaphe obsoleta), pythons (Python regius), boas (Boa constrictor), true vipers (Bitis gabonica), and monitor lizards (Varanus exanthematicus) revealed that all of the species exhibited similar characteristic changes in their fatty acid profiles during starvation stress. According to ANOVAs, the four most effective indicators of the onset of starvation were significant increases in the [1] fatty acid unsaturation index as well as ratios of [2] linoleic to palmitoleic acid, [3] oleic to palmitic, and [4] arachidonic to total fatty acid concentrations. The results of this study suggest that FAME analyses might be useful for identifying nutritional stress and/or starvation among squamate reptiles; however, forthcoming studies will be required to validate the generality of these responses. I also review the potential limitations of this approach, and suggest experiments that will be important for future applications of FAME analyses. Ultimately, it is hoped that FAME analyses can be used in conjunction with current practices as an additional tool to characterize the prevalence of starvation experienced by free-living reptiles.

  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. Associations between Homocysteine, Folic Acid, Vitamin B12 and Alzheimer's Disease: Insights from Meta-Analyses.

    PubMed

    Shen, Liang; Ji, Hong-Fang

    2015-01-01

    The associations between homocysteine (Hcy), folic acid, and vitamin B12 and Alzheimer's disease (AD) have gained much interest, while remaining controversial. We aim to perform meta-analyses to evaluate comprehensively: i) Hcy, folic acid, and vitamin B12 levels in AD patients in comparison with controls; and ii) the association between Hcy, folic acid, and vitamin B12 levels and risk of AD. A literature search was performed using Medline and Scopus databases. A total of 68 studies were identified and included in the meta-analyses. Stata 12.0 statistical software was used to perform the meta-analyses. First, AD patients may have higher level of Hcy, and lower levels of folate and vitamin B12 in plasma than controls. Further age-subgroup analysis showed no age effect for Hcy levels in plasma between AD patients and matched controls, while the differences in folate and vitamin B12 levels further enlarged with increased age. Second, data suggests that high Hcy and low folate levels may correlate with increased risk of AD occurrence. The comprehensive meta-analyses not only confirmed higher Hcy, lower folic acid, and vitamin B12 levels in AD patients than controls, but also implicated that high Hcy and low folic acid levels may be risk factors of AD. Further studies are encouraged to elucidate mechanisms linking these conditions.

  8. 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.

  9. Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage

    PubMed Central

    Chen, Lin-xing; Hu, Min; Huang, Li-nan; Hua, Zheng-shuang; Kuang, Jia-liang; Li, Sheng-jin; Shu, Wen-sheng

    2015-01-01

    The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments. PMID:25535937

  10. Analyses of Arabidopsis ecotypes reveal metabolic diversity to convert D-amino acids.

    PubMed

    Gördes, Dirk; Koch, Grit; Thurow, Kerstin; Kolukisaoglu, Uner

    2013-01-01

    For a long time D-enantiomers of proteinogenic L-amino acids were assumed to be physiologically irrelevant for plants. But there is growing evidence that D-amino acids (D-AAs) also fulfil important physiological functions in these organisms. However, the knowledge about the metabolic fate of D-AAs in plants is still scarce and more information about it is needed. To close this gap we established an optimized protocol for the processing and analysis of D- and L-AAs from large numbers of Arabidopsis lines. This included the application of 18 different D-AAs to seedlings, the extraction of free amino acids from the samples and the determination of 16 L-AAs and their corresponding D-enantiomers. To validate our approach we searched for genetic accessions with aberrant amino acid metabolism. Therefore we applied D-AAs on 17 ecotypes of Arabidopsis thaliana and analysed their free amino acid contents. These analyses confirmed the suitability of the system for the analysis of large sets of plant samples with enhanced velocity and improved accuracy. Furthermore, the resulting data led to the definition of standard amino acid profiles in response to D-AAs of Arabidopsis seedlings. Within these analyses the ecotype Landsberg erecta was found with aberrant metabolic patterns like drastically reduced capabilities to convert different D-AAs to D-alanine and D-glutamate. The presented experimental setup and results of this study offer starting points to dissect the metabolic pathway of D-AAs in plants.

  11. 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.

  12. Development and application of new nucleic acid-based technologies for microbial community analyses in foods.

    PubMed

    Rudi, Knut; Nogva, Hege K; Moen, Birgitte; Nissen, Hilde; Bredholt, Sylvia; Møretrø, Trond; Naterstad, Kristine; Holck, Askild

    2002-09-15

    Several challenges still persist in the analysis of microorganisms in foods, particularly in studies of complex communities. Nucleic acid-based methods are promising tools in addressing new questions concerning microbial communities. We have developed several new methods in the field of nucleic acid-based microbial community analyses. These methods cover both sample preparation and detection approaches. The sample preparation method involves simplified DNA purification using paramagnetic beads. As an extension of this method, the same paramagnetic beads are used for both cell separation and DNA purification. This enables full automation. The separate detection of viable and dead bacteria is a major issue in nucleic acid-based diagnostics. We have applied a living/dead dye that binds covalently to DNA and inhibits the PCR from dead cells. In addition, a DNA array-based detection assay has been developed. The assay combines the specificity obtained by enzymatic labeling of DNA probes with the possibility of detecting several targets simultaneously by DNA array hybridization. In combination with 16S rDNA amplification, this is a promising tool for community analyses. Also, we have developed a novel approach for multiplex quantitative PCR. The multiplex PCR has been combined with our DNA array-based detection method. Finally, we are now in the process of adapting a system for monitoring microbial growth and death in real-time through the tagging of bacteria with green fluorescent protein (GFP) combined with fluorescence detection using a high-resolution confocal laser scanner.

  13. 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.

  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. The stability of textile azo dyes in soil and their impact on microbial phospholipid fatty acid profiles.

    PubMed

    Imran, Muhammad; Shaharoona, Baby; Crowley, David E; Khalid, Azeem; Hussain, Sabir; Arshad, Muhammad

    2015-10-01

    The aim of this study was to examine the stability of structurally different azo dyes in soil and their impact on the microbial community composition by analyzing phospholipid fatty acid (PLFA) profiles. Sterile and non-sterile soils were amended with three azo dyes, including: Direct Red 81, Reactive Black 5 and Acid Yellow 19 at 160mgkg(-1) soil. The results showed that the azo dyes were quite stable and that large amounts of these dyes ranging from 17.3% to 87.5% were recoverable from the sterile and non-sterile soils after 14 days. The maximum amount of dye was recovered in the case of Direct Red 81. PLFA analysis showed that the azo dyes had a significant effect on microbial community structure. PLFA concentrations representing Gram-negative bacteria in dye-amended soil were substantially less as compared to the PLFA concentration of Gram-positive bacteria. Acid Yellow 19 dye had almost similar effects on the PLFA concentrations representing bacteria and fungi. In contrast, Reactive Black 5 had a greater negative effect on fungal PLFA than that on bacterial PLFA, while the opposite was observed in the case of Direct Red 81. To our knowledge, this is the first study reporting the stability of textile azo dyes in soil and their effects on soil microbial community composition.

  16. The stability of textile azo dyes in soil and their impact on microbial phospholipid fatty acid profiles.

    PubMed

    Imran, Muhammad; Shaharoona, Baby; Crowley, David E; Khalid, Azeem; Hussain, Sabir; Arshad, Muhammad

    2015-10-01

    The aim of this study was to examine the stability of structurally different azo dyes in soil and their impact on the microbial community composition by analyzing phospholipid fatty acid (PLFA) profiles. Sterile and non-sterile soils were amended with three azo dyes, including: Direct Red 81, Reactive Black 5 and Acid Yellow 19 at 160mgkg(-1) soil. The results showed that the azo dyes were quite stable and that large amounts of these dyes ranging from 17.3% to 87.5% were recoverable from the sterile and non-sterile soils after 14 days. The maximum amount of dye was recovered in the case of Direct Red 81. PLFA analysis showed that the azo dyes had a significant effect on microbial community structure. PLFA concentrations representing Gram-negative bacteria in dye-amended soil were substantially less as compared to the PLFA concentration of Gram-positive bacteria. Acid Yellow 19 dye had almost similar effects on the PLFA concentrations representing bacteria and fungi. In contrast, Reactive Black 5 had a greater negative effect on fungal PLFA than that on bacterial PLFA, while the opposite was observed in the case of Direct Red 81. To our knowledge, this is the first study reporting the stability of textile azo dyes in soil and their effects on soil microbial community composition. PMID:26074308

  17. 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.

  18. 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

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

    PubMed

    Westrop, Gareth D; Williams, Roderick A M; 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.

  20. Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses.

    PubMed

    Ludyga, Natalie; Grünwald, Barbara; Azimzadeh, Omid; Englert, Sonja; Höfler, Heinz; Tapio, Soile; Aubele, Michaela

    2012-02-01

    Tissues used for clinical diagnostics are mostly formalin-fixed and paraffin-embedded (FFPE) which provides many advantages. However, the quality of the obtained nucleic acids (NA) is reduced and this turns out to be a challenge for further molecular analyses. Although the spectrum of analyses of NA extracted from FFPE tissue has increased, the standard operating procedures for NA isolation from old tissue blocks still need to be improved. Here, we compared the efficiency of different NA extraction methods, using FFPE tissues of variable age and origin, with respect to downstream analyses. Our study showed that the phenol-chloroform isoamyl alcohol (PCI) and the commercial Qiagen protocol yielded samples with highest purity. The PCI protocol delivered the longest amplicons even from samples from the 1970s. We developed a short (1 h) tissue lysis procedure that turned out to be highly time- and cost-effective when DNA quality was tested using single and multiplex PCR. Compared to a 1-day lysis-protocol, the amplicons were only 100 bp shorter. In addition, single-copy genes used in daily routine were successfully amplified from long-term stored FFPE samples following 1-h tissue-lysis. The RNA integrity numbers (RIN) determined on RNA isolated from FFPE tissues indicated degraded RNA; however, all RINs were above the generally agreed threshold of 1.4. We showed that, depending on the purpose of the analysis, NA retrieved from FFPE tissues older than 40 years may be successfully used for molecular analysis.

  1. 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...

  2. 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.

  3. 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.

  4. Trophic position of deep-sea fish—Assessment through fatty acid and stable isotope analyses

    NASA Astrophysics Data System (ADS)

    Stowasser, G.; McAllen, R.; Pierce, G. J.; Collins, M. A.; Moffat, C. F.; Priede, I. G.; Pond, D. W.

    2009-05-01

    To investigate the trophic ecology of two of the dominant families of deep-sea fish (Macrouridae and Moridae) fatty acid and stable isotope analyses were applied to liver and muscle samples of five abundant species from the NE Atlantic. In conjunction with stomach content data these methods made it possible to identify differences in feeding strategies between the five study species as well as variation in feeding in relation to increasing depth and body size. Biomarkers identified strong similarities between Coryphaenoides armatus and Antimora rostrata though differences were found associating C. armatus more with the benthic food web whereas A. rostrata showed stronger links to the pelagic food web. While Lepidion eques was classified as a species linking benthic and benthopelagic food webs, both fatty acid and stable isotope data suggested that Coryphaenoides guentheri fed on an exclusively benthic diet . Coryphaenoides rupestris on the other hand were largely dependent on a copepod-based food web. Ontogenetic changes in feeding were found for both A. rostrata and C. armatus with the indication of a switch from active predation to scavenging occurring with increasing body size. Biomarkers also reflected the seasonal influx from the photic zone though changes were species-specific and probably reflected the variation in prey availability and abundance in response to these inputs. Our findings have thus demonstrated that the combined use of these biomarkers can elucidate trophic specialisations in situations where conventional methods alone previously provided insufficient data.

  5. 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.

  6. Characterization of sources for southern African aerosols through fatty acid and trajectory analyses

    NASA Astrophysics Data System (ADS)

    Billmark, Kaycie A.; Swap, Robert J.; Macko, Stephen A.

    2003-07-01

    Biogeochemical cycles in southern Africa are affected by emissions from extensive biomass burning. Emitted trace gases and aerosols frequently accumulate and recirculate in the well-defined synoptic pattern that persists for long time periods over southern Africa. The role of organic aerosols during atmospheric transport and the influence of neighboring air masses on biogeochemical dynamics in this nutrient-limited region are insufficiently studied. The Southern African Regional Science Initiative (SAFARI 2000) was conducted in part to investigate the impacts of this large-scale transport and deposition of increasingly anthropogenic emissions on southern African biogeochemical cycling. This study explores the understanding of regional atmospheric transport through the identification of chemical biomarkers to describe aerosols collected during the SAFARI 2000 dry season research campaign. Total suspended particulate aerosol samples were collected diurnally for a period of two weeks in Mongu, Zambia. Mongu is bordered by the Zambezi River on the west and the Miombo woodland savanna in all other directions. It also lies on the northern extent of the Kalahari Desert. This region is characterized by high biomass burning emissions of river floodplain grasses and woodland savanna during the dry season. Fatty acids were extracted from the collected aerosols and analyzed using gas chromatography. The resultant fatty acid compositions were examined for temporal patterns and trends. Furthermore, these results were compared to both synoptic meteorological patterns over the region, as well as to modeled air parcel trajectories, to gain insight into changes in aerosol composition resulting from changes in atmospheric transports from regions of different vegetation. The results of these analyses confirm that abundances of fatty acids are dependent on local and synoptic meteorology and can thus be used as an additional geochemical tracer to better describe aerosol sources and

  7. 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

  8. Folic acid alone or multivitamin containing folic acid intake during pregnancy and the risk of gestational hypertension and preeclampsia through meta-analyses

    PubMed Central

    Shim, Sang-Min; Yun, Yeo-Ul

    2016-01-01

    Objective The objective of this study was to assess the effect of folic acid and multivitamin use during pregnancy on the risk of developing of hypertensive disorder of pregnancy. Methods Two reviewers independently determined all prospective cohort study, retrospective cohort study, large population based cohort study, retrospective secondary analysis, and double blinded, placebo-controlled, randomized clinical trial published using PubMed Medline database, KERIS (Korea Education and Research Information Service), Scopus, and the Cochrane Central Register of controlled trials comparing before conception throughout pregnancy intake oral multivitamin containing folic acid or folic acid alone. Meta-analyses were estimated with odds ratios and 95% confidence intervals (CIs) using random effect analysis according to heterogeneity of studies. Results Data from six effect sizes from six studies involving 201,661 patients were enrolled. These meta-analyses showed multivitamin containing folic acid or folic acid alone was not significantly effective in reducing gestational hypertension or preeclampsia incidence (odds ratio, 0.91; 95% CI, 0.81 to 1.03) than the placebo. And the difference of effective sizes of preeclampsia and gestational hypertension according to two dependent variables, multivitamin and folic acid were not significant, respectively (point estimate, 0.66; 95% CI, 0.46 to 0.96). Conclusion These meta-analyses demonstrate multivitamin containing folic acid or folic acid alone was not significantly effective in reducing gestational hypertension or preeclampsia incidence. PMID:27004201

  9. 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

  10. 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

  11. 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.

  12. Stability Test and Quantitative and Qualitative Analyses of the Amino Acids in Pharmacopuncture Extracted from Scolopendra subspinipes mutilans

    PubMed Central

    Cho, GyeYoon; Han, KyuChul; Yoon, JinYoung

    2015-01-01

    Objectives: Scolopendra subspinipes mutilans (S. subspinipes mutilans) is known as a traditional medicine and includes various amino acids, peptides and proteins. The amino acids in the pharmacopuncture extracted from S. subspinipes mutilans by using derivatization methods were analyzed quantitatively and qualitatively by using high performance liquid chromatography (HPLC) over a 12 month period to confirm its stability. Methods: Amino acids of pharmacopuncture extracted from S. subspinipes mutilans were derived by using O-phthaldialdehyde (OPA) & 9-fluorenyl methoxy carbonyl chloride (FMOC) reagent and were analyzed using HPLC. The amino acids were detected by using a diode array detector (DAD) and a fluorescence detector (FLD) to compare a mixed amino acid standard (STD) to the pharmacopuncture from centipedes. The stability tests on the pharmacopuncture from centipedes were done using HPLC for three conditions: a room temperature test chamber, an acceleration test chamber, and a cold test chamber. Results: The pharmacopuncture from centipedes was prepared by using the method of the Korean Pharmacopuncture Institute (KPI) and through quantitative analyses was shown to contain 9 amino acids of the 16 amino acids in the mixed amino acid STD. The amounts of the amino acids in the pharmacopuncture from centipedes were 34.37 ppm of aspartate, 123.72 ppm of arginine, 170.63 ppm of alanine, 59.55 ppm of leucine and 57 ppm of lysine. The relative standard deviation (RSD %) results for the pharmacopuncture from centipedes had a maximum value of 14.95% and minimum value of 1.795% on the room temperature test chamber, the acceleration test chamber and the cold test chamber stability tests. Conclusion: Stability tests on and quantitative and qualitative analyses of the amino acids in the pharmacopuncture extracted from centipedes by using derivatization methods were performed by using HPLC. Through research, we hope to determine the relationship between time and the

  13. 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

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

    PubMed

    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 (13)C 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.

  15. Characterization of rapeseed (Brassica napus) oils by bulk C, O, H, and fatty acid C stable isotope analyses.

    PubMed

    Richter, Eva Katharina; Spangenberg, Jorge E; Kreuzer, Michael; Leiber, Florian

    2010-07-14

    Rapeseed ( Brassica napus ) oils differing in cultivar, sites of growth, and harvest year were characterized by fatty acid concentrations and carbon, hydrogen, and oxygen stable isotope analyses of bulk oils (delta(13)C(bulk), delta(2)H(bulk), delta(18)O(bulk) values) and individual fatty acids (delta(13)C(FA)). The delta(13)C(bulk), delta(2)H(bulk), and delta(18)O(bulk) values were determined by continuous flow combustion and high-temperature conversion elemental analyzer-isotope ratio mass spectrometry (EA/IRMS, TC-EA/IRMS). The delta(13)C(FA) values were determined using gas chromatography--combustion-isotope ratio mass spectrometry (GC/C/IRMS). For comparison, other C(3) vegetable oils rich in linolenic acid (flax and false flax oils) and rich in linoleic acid (poppy, sunflower, and safflower oils) were submitted to the same chemical and isotopic analyses. The bulk and molecular delta(13)C values were typical for C(3) plants. The delta(13)C value of palmitic acid (delta(13)C(16:0)) and n-3 alpha-linolenic acid (delta(13)C(18:3n-3)) differed (p < 0.001) between rape, flax, and poppy oils. Also within species, significant differences of delta(13)C(FA) were observed (p < 0.01). The hydrogen and oxygen isotope compositions of rape oil differed between cultivars (p < 0.05). Major differences in the individual delta(13)C(FA) values were found. A plant-specific carbon isotope fractionation occurs during the biosynthesis of the fatty acids and particularly during desaturation of C(18) acids in rape and flax. Bulk oil and specific fatty acid stable isotope analysis might be useful in tracing dietary lipids differing in their origin.

  16. Fatty acid composition analyses of the DCMU resistant mutants of Nannochloropsis oculata (eustigmatophyceae)

    NASA Astrophysics Data System (ADS)

    Jimin, Zhang; Shuang, Liu; Xue, Sun; Guanpin, Yang; Xuecheng, Zhang; Zhenhui, Gao

    2003-04-01

    Ultraviolet mutagenesis was applied to Nannochloropsis oculata and three mutants resistant to 3-(3, 4-dichlorophenyl)-1,1-dimethylurea (DCMU) were isolated. The cellular chlorophyll a and total lipid content of the wild are higher in the medium supplemented with DCMU than in the control without DCMU. Without DCMU, the growth rates and chlorophyll a contents of the mutants are similar to those of the wild. Significant changes of fatty acid content and composition have occurred in DCMU-resistant mutants growing in the medium supplemented with DCMU. The total lipid, palmitic acid (16:0), palmitoleic acid (16:1ω9) and oleic (18:1ω9) contents decrease significantly, while the vaccenic acid (18:1ω11) increases significantly and the EPA content of dried powder increases slightly in the mutants. The study may provide a basis to improve EPA content in Nannochloropsis oculata in the future.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. • Relationships between Soil Microbial Biomass Determined by Chloroform Fumigation-Extraction, Substrate-Induced Respiration, and Phospholipid Fatty Acid Analysis

    SciTech Connect

    Bailey, Vanessa L.; Peacock, A. D.; Smith, Jeff L.; Bolton, Harvey

    2002-09-01

    ABSTRACT-The soil microbial biomass (SMB) is responsible for many of the cycles and transformations of nutrients in soils. Three methods of measuring and describing this pool in soil are: (1) chloroform fumigation-extraction (CFE), (2) substrate-induced respiration (SIR), and (3) total extractable phospholipid fatty acids (PLFA). This study was conducted to seek a relationship between microbial PLFA and measures of SMB. Microbial PLFA was best predicted by CFE (R2 = 0.77); 1 nmol of PLFA corresponded to a flush of 2.4 mg C released by fumigation. This conversion factor will be useful in discussions of microbial populations and diversity and allow comparisons to literature in which only CFE is used to describe the size of the microbial biomass.

  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

    2014-04-01

    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. 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.

  4. Lysosomal acid lipase deficiency in rats: Lipid analyses and lipase activities in liver and spleen

    SciTech Connect

    Kuriyama, M.; Yoshida, H.; Suzuki, M.; Fujiyama, J.; Igata, A. )

    1990-09-01

    We report the biological characterization of an animal model of a genetic lipid storage disease analogous to human Wolman's disease. Affected rats accumulated cholesteryl esters (13.3-fold), free cholesterol (2.8-fold), and triglycerides (5.4-fold) in the liver, as well as cholesteryl esters (2.5-fold) and free cholesterol (1.33-fold) in the spleen. Triglycerides did not accumulate, and the levels actually decreased in the spleen. Analysis of the fatty acid composition of the cholesteryl esters and triglycerides showed high percentages of linoleic acid (18:2) and arachidonic acid (20:4) in both organs, especially in the liver. No accumulation of phospholipids, neutral glycosphingolipids, or gangliosides was found in the affected rats. Acid lipase activity for (14C)triolein, (14C)cholesteryl oleate, and 4-methyl-umbelliferyl oleate was deficient in both the liver and spleen of affected rats. Lipase activity at neutral pH was normal in both liver and spleen. Heterozygous rats showed intermediate utilization of these substrates in both organs at levels between those for affected rats and those for normal controls, although they did not accumulate any lipids. These data suggest that these rats represent an animal counterpart of Wolman's disease in humans.

  5. 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.

  6. 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. PMID:26235877

  7. Homology analyses of the protein sequences of fatty acid synthases from chicken liver, rat mammary gland, and yeast

    SciTech Connect

    Chang, Soo-Ik ); Hammes, G.G. )

    1989-11-01

    Homology analyses of the protein sequences of chicken liver and rat mammary gland fatty acid synthases were carried out. The amino acid sequences of the chicken and rat enzymes are 67% identical. If conservative substitutions are allowed, 78% of the amino acids are matched. A region of low homologies exists between the functional domains, in particular around amino acid residues 1059-1264 of the chicken enzyme. Homologies between the active sites of chicken and rat and of chicken and yeast enzymes have been analyzed by an alignment method. A high degree of homology exists between the active sites of the chicken and rat enzymes. However, the chicken and yeast enzymes show a lower degree of homology. The DADPH-binding dinucleotide folds of the {beta}-ketoacyl reductase and the enoyl reductase sites were identified by comparison with a known consensus sequence for the DADP- and FAD-binding dinucleotide folds. The active sites of all of the enzymes are primarily in hydrophobic regions of the protein. This study suggests that the genes for the functional domains of fatty acid synthase were originally separated, and these genes were connected to each other by using different connecting nucleotide sequences in different species. An alternative explanation for the differences in rat and chicken is a common ancestry and mutations in the joining regions during evolution.

  8. 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. PMID:17719904

  9. Metazoan remaining genes for essential amino acid biosynthesis: sequence conservation and evolutionary analyses.

    PubMed

    Costa, Igor R; Thompson, Julie D; Ortega, José Miguel; Prosdocimi, Francisco

    2014-12-24

    Essential amino acids (EAA) consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found that most metazoans lack the same set of enzymes responsible for the de novo EAA biosynthesis. Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, the set of all 49 enzymes responsible for the EAA de novo biosynthesis in yeast was retrieved. These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. Eight enzymes typically attributed to EAA pathways were found to be ubiquitous in metazoan genomes, suggesting a conserved functional role. In this study, we address the question of how these genes evolved after losing their pathway partners. To do this, we compared metazoan genes with their fungal and plant orthologs. Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS) and betaine-homocysteine S-methyltransferase (BHMT) diverged from the expected Tree of Life (ToL) relationships. High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed Python algorithm. Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons between metazoans/fungi and metazoans/plants, supporting the hypothesis that these two genes have undergone non-ToL evolution in animals.

  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. Global Trophic Position Comparison of Two Dominant Mesopelagic Fish Families (Myctophidae, Stomiidae) Using Amino Acid Nitrogen Isotopic Analyses

    PubMed Central

    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. PMID:23209656

  13. Functional analyses of three acyl-CoA synthetases involved in bile acid degradation in Pseudomonas putida DOC21.

    PubMed

    Barrientos, Álvaro; Merino, Estefanía; Casabon, Israël; Rodríguez, Joaquín; Crowe, Adam M; Holert, Johannes; Philipp, Bodo; Eltis, Lindsay D; Olivera, Elías R; Luengo, José M

    2015-01-01

    Pseudomonas putida DOC21, a soil-dwelling proteobacterium, catabolizes a variety of steroids and bile acids. Transposon mutagenesis and bioinformatics analyses identified four clusters of steroid degradation (std) genes encoding a single catabolic pathway. The latter includes three predicted acyl-CoA synthetases encoded by stdA1, stdA2 and stdA3 respectively. The ΔstdA1 and ΔstdA2 deletion mutants were unable to assimilate cholate or other bile acids but grew well on testosterone or 4-androstene-3,17-dione (AD). In contrast, a ΔstdA3 mutant grew poorly in media containing either testosterone or AD. When cells were grown with succinate in the presence of cholate, ΔstdA1 accumulated Δ(1/4) -3-ketocholate and Δ(1,4) -3-ketocholate, whereas ΔstdA2 only accumulated 7α,12α-dihydroxy-3-oxopregna-1,4-diene-20-carboxylate (DHOPDC). When incubated with testosterone or bile acids, ΔstdA3 accumulated 3aα-H-4α(3'propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP) or the corresponding hydroxylated derivative. Biochemical analyses revealed that StdA1 converted cholate, 3-ketocholate, Δ(1/4) -3-ketocholate, and Δ(1,4) -3-ketocholate to their CoA thioesters, while StdA2 transformed DHOPDC to DHOPDC-CoA. In contrast, purified StdA3 catalysed the CoA thioesterification of HIP and its hydroxylated derivatives. Overall, StdA1, StdA2 and StdA3 are acyl-CoA synthetases required for the complete degradation of bile acids: StdA1 and StdA2 are involved in degrading the C-17 acyl chain, whereas StdA3 initiates degradation of the last two steroid rings. The study highlights differences in steroid catabolism between Proteobacteria and Actinobacteria.

  14. 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

  15. Monounsaturated Fatty Acids and Risk of Cardiovascular Disease: Synopsis of the Evidence Available from Systematic Reviews and Meta-Analyses

    PubMed Central

    Schwingshackl, Lukas; Hoffmann, Georg

    2012-01-01

    No dietary recommendations for monounsaturated fatty acids (MUFA) are given by the National Institute of Medicine, the United States Department of Agriculture, European Food and Safety Authority and the American Diabetes Association. In contrast, the Academy of Nutrition and Dietetics, and the Canadian Dietetic Association both promote <25% MUFA of daily total energy consumption, while the American Heart Association sets a limit of 20% MUFA in their respective guidelines. The present review summarizes systematic reviews and meta-analyses of randomized controlled trials and cohort studies investigating the effects of MUFA on cardiovascular and diabetic risk factors, cardiovascular events and cardiovascular death. Electronic database Medline was searched for systematic reviews and meta-analyses using “monounsaturated fatty acids”, “monounsaturated fat”, and “dietary fat” as search terms with no restriction to calendar date or language. Reference lists and clinical guidelines were searched as well. Sixteen relevant papers were identified. Several studies indicated an increase of HDL-cholesterol and a corresponding decrease in triacylglycerols following a MUFA-rich diet. The effects on total and LDL-cholesterol appeared not consistent, but no detrimental effects on blood lipids were observed. Values for systolic and diastolic blood pressure were found to be reduced both during short- and long-term protocols using high amounts of MUFA as compared to low-MUFA diets. In type 2 diabetic subjects, MUFA exerted a hypoglycemic effect and reduced glycosylated hemoglobin in the long term. Data from meta-analyses exploring evidence from long-term prospective cohort studies provide ambiguous results with respect to the effects of MUFA on risk of coronary heart disease (CHD). One meta-analysis reported an increase in CHD events, however, most meta-analyses observed a lesser number of cases in participants subjected to a high-MUFA protocol. Although no detrimental side

  16. Daytime intragastric acid control: post hoc analyses of esomeprazole 20 mg and over-the-counter proton-pump inhibitors

    PubMed Central

    Katz, Philip; Kahrilas, Peter J.; Johnson, David A.; Lind, Tore; Röhss, Kerstin; Traxler, Barry; Hugo, Vincent; Dent, John

    2015-01-01

    Objectives: In mild gastroesophageal reflux disease, which accounts for the great majority of cases, the major burden of reflux occurs during daytime hours, after food intake. The aim of these analyses was to evaluate intragastric pH control during the typical 14-hour daytime awake period by proton-pump inhibitors (PPIs) given at over-the-counter (OTC) dosages. Methods: In one double-blind and three open-label, randomized, crossover studies, intragastric pH was monitored for 24 hours on day 5 of treatment. The 24-hour data have been reported previously. Post hoc analyses reassessed these studies for the 14-hour daytime period, comparing esomeprazole 20 mg with currently available OTC PPIs omeprazole, pantoprazole (not available in the US) and lansoprazole. Results: Subjects maintained intragastric pH >4 for a significantly greater mean percentage of the 14-hour daytime period with esomeprazole 20 mg compared with any of the PPI comparators at OTC dosages. Geometric mean ratios (95% confidence intervals) for esomeprazole 20 mg versus the comparators were: 1.45 (1.14–1.85; p = 0.003) versus omeprazole 20 mg; 2.50 (2.01–3.11; p < 0.0001) versus pantoprazole 20 mg; and 1.69 (1.46–1.97; p < 0.0001) and 1.89 (1.05–3.37; p = 0.03) versus lansoprazole 15 mg. A greater proportion of subjects had better pH control with esomeprazole than with the other PPIs (range: 69–97%). Conclusions: Across the 14-hour daytime period, esomeprazole 20 mg once daily given 30 minutes before breakfast for 5 days provided acid control for a significantly greater average proportion of time versus the PPI comparators omeprazole, pantoprazole and lansoprazole at currently available OTC dosages. PMID:26557888

  17. Total dietary fat and fatty acid content modifies plasma phospholipid fatty acids, desaturase activity indices, and urinary prostaglandin E in women

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Compared to diets high in fat, low fat diets are associated with reduced risk of cardiovascular disease. We hypothesized that a low fat (LF; 20% fat) and a low fat high omega-3 (n-3) fatty acid diet (LFn3; 23% fat with 3% as ALA, EPA and DHA) would enhance n-3 composition of PLFA and reduce urinary ...

  18. Signatures of Autotrophic and Heterotrophic Metabolic Activity in Enrichment Cultures from a Sulphur Oxidizing Acid Mine Site

    NASA Astrophysics Data System (ADS)

    Slater, G. F.; Bernier, L.; Cowie, B. R.; Warren, L. A.

    2006-12-01

    Delineating the role of microorganisms in geochemical processes of interest in natural environments requires the development of tools that provide the ability to distinguish amongst microbial activity associated with different metabolic guilds. The gap between phylogenetic characterization and phenotypic understanding remains, underscoring the need to consider alternative methods. Compound specific analysis of cellular components has the potential to differentiate between active metabolic processes supporting microbial communities and may be especially useful in extreme environments. The goal of this study was to determine whether the phospholipids fatty acid (PLFA) distribution and isotopic signatures associated with autotrophs and heterotrophs enriched from an acid mine drainage (AMD) system differed, and further whether natural consortial autotrophic isolates showed similar signatures to autotrophic pure strains of Acidithiobacillus ferrooxidans and A. thiooxidans. Two distinct initial enrichments with tetrathionate and CO2 yielded primarily autotrophic (95%) Acidithiobaccillus spp. sulphur oxidizing communities. The remaining microbial members of theses enrichments (<5%) were morphologically distinct and heterotrophic, as subculture of the consortial isolates in a medium amended with glucose but without tetrathionate selectively resulted in their visible growth. PLFA profiles and δ13C signatures from autotrophic (1) natural enrichments, pure cultures of (2) A. ferrooxidans and (3) A. thiooxidans were similar, but collectively differed from those of the natural heterotrophic enrichment cultures. The PLFA profiles for the heterotrophic communities were made up of primarily (88-99%) C16:0 and two isomers of C18:1. In contrast, the autotrophic communities had high proportions of C16:1 (up to 18%) as well as cyclo C17 and cyclo C19 PLFA that combined comprised 18 to 58% of the observed PLFA. The δ13C signatures of the PLFA also differed strongly between the two

  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. Application of a surface plasmon resonance sensor to analyses of amine compounds with the use of a polymer film and an acid-base reaction.

    PubMed

    Nishimura, Satoshi; Yoshidome, Toshifumi; Tokuda, Tomoyuki; Mitsushio, Masaru; Higo, Morihide

    2002-03-01

    A surface plasmon resonance (SPR) sensor was applied to analyses of some amine compounds (n-butylamine, isobutylamine, aniline, and N,N-dimethylaniline) by using a polymer film and an acid-base reaction in it. Poly(acrylamide) (PAA) was adopted as the polymer film and was immobilized on an Au film to prepare a sensor chip. Pivalic acid was entered into the PAA film as an acid. The PAA film with a thickness of 50 nm gave the highest sensitivity to the SPR sensor. Although water was better concerning the sensitivity for the SPR sensor as the solvent, ethanol was adopted because it dissolves well all of the amine compounds used. The Au film coated with the PAA film gave higher sensitivity for analyses of n-butylamine and isobutylamine, and lower sensitivity for analyses of aniline and N,N-dimethylaniline than an Au film without the PAA film. The PAA film containing pivalic acid gave 4-5 orders of magnitude higher sensitivity to the SPR sensor for analyses of all the amine compounds due to the reaction between pivalic acid and these amine compounds.

  1. Trophic importance of diatoms in an intertidal Zostera noltii seagrass bed: Evidence from stable isotope and fatty acid analyses

    NASA Astrophysics Data System (ADS)

    Lebreton, Benoit; Richard, Pierre; Galois, Robert; Radenac, Gilles; Pfléger, Camille; Guillou, Gaël; Mornet, Françoise; Blanchard, Gérard F.

    2011-03-01

    A current predominant paradigm emphasizes the role of epiphytic algae for invertebrates in most seagrass food webs. However, in some intertidal Zostera noltii beds, epiphyte biomass is very low compared to microphytobenthos and seagrass biomasses. We assessed the role of microphytobenthos in a temperate intertidal Z. noltii bed by combining stable isotope and fatty acid (FA) analyses on primary producers, composite sources — suspended particulate organic matter (SPOM) and sediment surface organic matter (SSOM) — and the main macrofaunal consumers. Z. noltii showed high δ 13C (-9.9‰) and high 18:2( n-6) and 18:3( n-3) contents. Microphytobenthos was slightly more 13C-depleted (-15.4‰) and had high levels of diatom markers: 14:0, 16:1( n-7)c, 20:5( n-3). Low mean δ 13C (-22.0‰) and large amounts of diatom and bacteria (18:1( n-7)c) markers indicated that SPOM was mainly composed of a mixture of fresh and decayed pelagic diatoms. Higher mean δ 13C (-17.9‰) and high amounts of diatom FAs were found in SSOM, showing that microphytobenthic diatoms dominate. Very low percentages of 18:2( n-6) and 18:3( n-3) in consumers indicated a low contribution of Z. noltii material to their diets. Grazers, deposit and suspension-deposit feeders had δ 13C close to microphytobenthos and high levels of diatom FAs, confirming that microphytobenthos represented the main part of their diet. Lower δ 13C and higher amounts of flagellate FAs - 22:6( n-3) and 16:4( n-3) - in suspension feeders indicated that their diet resulted from a mixture of SPOM and microphytobenthos. These results demonstrate that invertebrates do not consume high amounts of seagrass and highlight the main role of benthic diatoms in this intertidal seagrass bed.

  2. 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.

  3. Genetic analyses and quantitative trait loci detection, using a partial genome scan, for intramuscular fatty acid composition in Scottish Blackface sheep.

    PubMed

    Karamichou, E; Richardson, R I; Nute, G R; Gibson, K P; Bishop, S C

    2006-12-01

    Genetic parameters for LM fatty acid composition were estimated in Scottish Blackface sheep, previously divergently selected for carcass lean content (LEAN and FAT lines). Furthermore, QTL were identified for the same fatty acids. Fatty acid phenotypic measurements were made on 350 male lambs, at approximately 8 mo of age, and 300 of these lambs were genotyped across candidate regions on chromosomes 1, 2, 3, 5, 14, 18, 20, and 21. Fatty acid composition measurements included in total 17 fatty acids of 3 categories: saturated, monounsaturated, and polyunsaturated. Total i.m. fat content was estimated as the sum of the fatty acids. The FAT line had a greater i.m. fat content and more oleic acid, but less linoleic acid (18:2 n-6) and docosapentaenoic acid (22:5 n-3) than did the LEAN line. Saturated fatty acids were moderately heritable, ranging from 0.19 to 0.29, and total SFA were highly heritable (0.90). Monounsaturated fatty acids were moderately to highly heritable, with cis-vaccenic acid (18:1 n-7) being the most heritable (0.67), and total MUFA were highly heritable (0.73). Polyunsaturated fatty acids were also moderately to highly heritable; arachidonic acid (20:4 n-6) and CLA were the most heritable, with values of 0.60 and 0.48, respectively. The total PUFA were moderately heritable (0.40). The QTL analyses were performed using regression interval mapping techniques. In total, 21 chromosome-wide QTL were detected in 6 out of 8 chromosomal regions. The chromosome-wide, significant QTL affected 3 SFA, 5 MUFA, and 13 PUFA. The most significant result was a QTL affecting linolenic acid (18:3 n-3) on chromosome 2. This QTL segregated in 2 of the 9 families and explained 37.6% of the phenotypic variance. Also, 10 significant QTL were identified on chromosome 21, where 8 out of 10 QTL were segregating in the same families and detected at the same position. The results of this study demonstrate that altering carcass fatness will simultaneously change i.m. fat

  4. Effects of poultry manure on soil biochemical properties in phthalic acid esters contaminated soil.

    PubMed

    Gao, Jun; Qin, Xiaojian; Ren, Xuqin; Zhou, Haifeng

    2015-12-01

    This study aimed to evaluate the effects of poultry manure (PM) on soil biological properties in DBP- and DEHP-contaminated soils. An indoor incubation experiment was conducted. Soil microbial biomass C (Cmic), soil enzymatic activities, and microbial phospholipid fatty acid (PLFA) concentrations were measured during incubation period. The results indicated that except alkaline phosphatase activity, DBP and DEHP had negative effects on Cmic, dehydrogenase, urease, protease activities, and contents of total PLFA. However, 5 % PM treatment alleviated the negative effects of PAEs on the above biochemical parameters. In DBP-contaminated soil, 5 % PM amendment even resulted in dehydroenase activity and Cmic content increasing by 17.8 and 11.8 % on the day 15 of incubation, respectively. During the incubation periods, the total PLFA contents decreased maximumly by 17.2 and 11.6 % in DBP- and DEHP-contaminated soils without PM amendments, respectively. Compared with those in uncontaminated soil, the total PLFA contents increased slightly and the value of bacPLFA/fugalPLFA increased significantly in PAE-contaminated soils with 5 % PM amendment. Nevertheless, in both contaminated soils, the effects of 5 % PM amendment on the biochemical parameters were not observed with 10 % PM amendment. In 10 % PM-amended soils, DBP and DEHP had little effect on Cmic, soil enzymatic activities, and microbial community composition. At the end of incubation, the effects of PAEs on these parameters disappeared, irrespective of PM amendment. The application of PM ameliorated the negative effect of PAEs on soil biological environment. However, further work is needed to study the effect of PM on soil microbial gene expression in order to explain the change mechanisms of soil biological properties.

  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. PMID:27591599

  6. 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. ...

  7. 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.

  8. Identification and localization of amino acid substitutions between two phenobarbital-inducible rat hepatic microsomal cytochromes P-450 by micro sequence analyses.

    PubMed Central

    Yuan, P M; Ryan, D E; Levin, W; Shively, J E

    1983-01-01

    Two isozymes of rat liver microsomal cytochrome P-450--P-450b and P-450e--were compared by micro sequence analyses of their NH2 termini and tryptic fragments. These two phenobarbital-inducible hemoproteins, which are immunochemically indistinguishable with antibody against cytochrome P-450b, have extensive sequence homology. Automated Edman degradation of the native proteins revealed identical amino acids for the first 35 residues. Sequence determinations of the tryptic peptides, which constitute approximately 75% of each protein molecule, have thus far shown 10 amino acid differences between the two isozymes. Results of our amino acid sequence analyses established that two of the cDNAs, pcP-450pb1 and pcP-450pb4, reported by Fujii-Kuriyama et al. [Fujii-Kuriyama, Y., Mizukami, Y., Kamajiri, K., Sogawa, K. & Muramatsu, M. (1982) Proc. Natl. Acad. Sci. USA 79, 2793-2797] encode cytochrome P-450b whereas pcP-450pb2, a third cDNA whose nucleotide sequence differed slightly from that of the other two (six amino acid substitutions), encodes cytochrome P-450e. In addition to establishing the identity of these cloned cDNAs we provide direct evidence for seven additional amino acid differences between cytochromes P-450b and P-450e that occur beyond the region (Arg358) encoded by the cloned cDNA for cytochrome P-450e. Together, the amino acid sequences determined by micro sequence analysis and recombinant DNA techniques reveal 13 amino acid differences between these two isozymes. This report highlights the complementary nature of two different molecular approaches to elucidation of the amino acid sequences of isozymes with extensive structural homology. PMID:6572377

  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. Data on gender and subgroup specific analyses of omega-3 fatty acids in the Ludwigshafen Risk and Cardiovascular Health Study.

    PubMed

    Kleber, Marcus E; Delgado, Graciela E; Lorkowski, Stefan; März, Winfried; von Schacky, Clemens

    2016-09-01

    This paper contains additional data related to the research article "Omega-3 fatty acids and mortality in patients referred for coronary angiography - The Ludwigshafen Risk and Cardiovascular Health Study" (Kleber et al., in press) [1]. The data shows characteristics of the Ludwigshafen Risk and Cardiovascular Health (LURIC) study according to tertiles of omega-3 fatty acids as well as stratified by gender. The association of proportions of omega-3 fatty acids measured in erythrocyte membranes with different causes of death is investigated with a special focus on modeling the association of EPA with mortality in a nonlinear way. Further, the association of omega-3 fatty acids with all-cause mortality adjusted for high-sensitive C-reactive protein as a marker of systemic inflammation is examined as well as the association of EPA with cause-specific death.

  11. FTIR and {sup 31}P-NMR spectroscopic analyses of surface species in phosphate-catalyzed lactic acid conversion

    SciTech Connect

    Gunter, G.C.; Tam, M.S.; Miller, D.J.

    1996-11-01

    The surface species present on silica/alumina-supported sodium phosphates, active catalysts for the conversion of lactic acid to acrylic acid and 2,3-pentanedione, are examined by pre- and postreaction MAS {sup 31}P-NMR and FTIR spectroscopies. Species present following lactic acid conversion are identified by transmission FTIR of phosphates supported on silicon disks (as a model catalyst system) and verified by {sup 31}P-NMR and diffuse reflectance IR spectroscopy of actual catalysts used in reaction. Monosodium phosphate (NaH{sub 2}PO{sub 4}) condenses to a mixture of sodium polyphosphate (NaPO{sub 3}){sub n} and sodium trimetaphosphate (Na{sub 3}P{sub 3}O{sub 9}), which exhibit little catalytic activity for converting lactic acid to desired products. Disodium phosphate (Na{sub 2}HPO{sub 4}) condenses to tetrasodium pyrophosphate (Na{sub 4}P{sub 2}O{sub 7}), and proton transfer from lactic acid to pyrophosphate results in the formation of sodium lactate. Trisodium phosphate (Na{sub 3}PO{sub 4}) accepts a proton from lactic acid to form sodium lactate and disodium phosphate, which condenses to pyrophosphate. The presence of pyrophosphate and sodium lactate on supported disodium and trisodium phosphates explains their similar catalytic properties; the larger quantity of sodium lactate present on trisodium phosphate leads to higher conversions at lower temperatures. 40 refs., 14 figs., 2 tabs.

  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. PMID:25455100

  13. 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.

  14. 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.

  15. Evaluation of the retention pattern on ionic liquid columns for gas chromatographic analyses of fatty acid methyl esters.

    PubMed

    Lin, Chen-Chen; Wasta, Ziar; Mjøs, Svein A

    2014-07-11

    Fatty acid methyl esters from marine sources were analyzed by gas chromatography-mass spectrometry on three ionic liquid columns, SLB-IL61, SLB-IL82 and SLB-IL100 (Supelco). Retention indices (equivalent chain lengths) are reported for more than 100 compounds and the overlap patterns are evaluated from these data. The influence of chromatographic conditions on the retention indices of unsaturated fatty acid methyl esters is also evaluated. Compared to typical alternative phases the retention patterns on all three columns are highly dependent on the conditions. The SLB-IL61 phase had overlaps between nutritionally important fatty acids that could not be resolved by changing the chromatographic conditions. This column is therefore regarded as unsuitable for clinical and nutritional studies of the fatty acid composition, but similar overlaps may be avoided on IL82 and IL100. On all three columns double bonds close to the carboxyl group in the analytes contribute with limited retention, which makes it challenging to predict the retention of polyunsaturated fatty acid methyl esters. PMID:24873965

  16. Compound-specific carbon isotope analyses of individual long-chain alkanes and alkanoic acids in Harmattan aerosols

    NASA Astrophysics Data System (ADS)

    Simoneit, Bernd R. T.

    The higher molecular weight n-alkane, n-alkanol and n-alkanoic acid series from higher plant wax are ubiquitous components of aerosol particles in remote areas. The carbon isotopic compositions of individual n-alkanes and n-alkanoic acids have been determined in samples of Harmattan aerosol and composited vegetation wax from Nigeria. The data confirm the terrestrial origin of these compounds and support the distinction among the vegetation sources of C 4 plants (savannah) from C 3 and CAM plants (wet climate, mixed vegetation). The superimposed petroleum components from vehicular emissions in urban areas could not be differentiated from C 3 vegetation by compound-specific isotope analysis.

  17. Application of modified attapulgite in phthalate acid ester-contaminated soil: Effects on phthalate acid ester dissipation and the composition of soil microbial community.

    PubMed

    Gao, Jun; Shi, Yi-Ying; Zhou, Hai-Feng; Ren, Xu-Qin; Ji, Huai

    2016-08-01

    The effects of modified attapulgite (MA) on the dissipations of the plasticizers di-n-butyl phthalate (DBP) and di-(2-ethylhexyl) phthalate (DEHP) in soil, as well as on the composition of soil microbial community, were studied. DBP, DEHP (50 mg kg(-1) in soil, respectively), and MA (1, 5, and 10 % in soil) were mixed thoroughly with soil and incubated for 60 days. DBP- and DEHP-contaminated soils without MA were used as the controls. Both of DBP and DEHP residues in bulk soils and four soil fractions were measured at five incubation times 1, 7, 15, 30, and 60 days, and their dissipation kinetic equations were analyzed. The microbial phospholipid fatty acid (PLFA) concentrations were also measured at the end of experiment. Our results showed that the effect of modified attapulgite on DBP dissipation was related to its dosage in soil. The DEHP dissipation was both inhibited by MA at the 5 and 10 % rates in soils. The application of MA changed the content percentages but did not change the concentration order of phthalate acid esters (PAEs) in soil particle-size fractions. The total microbial PLFA content was significantly increased by 5 and 10 % MA in the contaminated soils. Meanwhile, the gram-negative (GN)/gram-positive (GP) ratios increased when MA was applied at the dosages of 5 and 10 % in DBP and 10 % in DEHP-contaminated soils. Principal component analysis (PCA) indicated that the change of bacteria PLFA, especially the GN bacterial PLFA, depended on the dosages of MA added into soil. The application of MA into soil has a positive effect on reducing the eco-toxicity of PAEs in soil based on the analysis of the soil microbial PLFA. PMID:27094276

  18. 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.

  19. Fatty acid patterns early after premature birth, simultaneously analysed in mothers' food, breast milk and serum phospholipids of mothers and infants

    PubMed Central

    Sabel, Karl-Göran; Lundqvist-Persson, Cristina; Bona, Elsa; Petzold, Max; Strandvik, Birgitta

    2009-01-01

    Background The supply of long-chain polyunsaturated fatty acids via the placenta is interrupted in premature infants, making them exclusively dependent on breast milk, which varies in fatty acid (FA) concentrations depending on the mother's diet. Objective To in a longitudinal study explore the relation between FA status in mothers and infants from an unselected cohort of prematures, not requiring intensive care. Design Breast milk and mothers' and infants' plasma phospholipid FA concentrations from birth to 44 weeks of gestational age were analysed and compared with mothers' food intake, assessed using a 3-day diary. Fatty acids were analysed by capillary gas-liquid chromatography. Results The energy intake was low in 75% of mothers, and 90% had low intake of essential FAs (EFAs). Dietary linoleic acid (LA, 18:2w6), but not w3 FAs, correlated to concentrations in breast milk. Infants' plasma and breast milk correlated for arachidonic (AA, 20:4w6), eicosapentaenoic (EPA, 20:5w3) and docosahexaenoic (DHA, 22:6w3) acids. A high concentration of mead acid (20:3w9) in the infants at birth correlated negatively to the concentrations of LA, AA and w3 FAs. Infants of mothers who stopped breastfeeding during the study period showed decreased DHA concentrations and increased w6/w3 ratios, with the opposite FA pattern seen in the mothers' plasma. Conclusion Although dietary w3 FAs were insufficient in an unselected cohort of mothers of premature infants, breastfeeding resulted in increased levels of DHA in the premature infants at the expense of the mothers, suggesting a general need to increase dietary w3 FAs during pregnancy and lactation. PMID:19515230

  20. 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...

  1. Proteome and Membrane Fatty Acid Analyses on Oligotropha carboxidovorans OM5 Grown under Chemolithoautotrophic and Heterotrophic Conditions

    PubMed Central

    Paul, Debarati; Kumar, Ranjit; Nanduri, Bindu; French, Todd; Pendarvis, Ken; Brown, Ashli; Lawrence, Mark L.; Burgess, Shane C.

    2011-01-01

    Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium able to utilize CO and H2 to derive energy for fixation of CO2. Thus, it is capable of growth using syngas, which is a mixture of varying amounts of CO and H2 generated by organic waste gasification. O. carboxidovorans is capable also of heterotrophic growth in standard bacteriologic media. Here we characterize how the O. carboxidovorans proteome adapts to different lifestyles of chemolithoautotrophy and heterotrophy. Fatty acid methyl ester (FAME) analysis of O. carboxidovorans grown with acetate or with syngas showed that the bacterium changes membrane fatty acid composition. Quantitative shotgun proteomic analysis of O. carboxidovorans grown in the presence of acetate and syngas showed production of proteins encoded on the megaplasmid for assimilating CO and H2 as well as proteins encoded on the chromosome that might have contributed to fatty acid and acetate metabolism. We found that adaptation to chemolithoautotrophic growth involved adaptations in cell envelope, oxidative homeostasis, and metabolic pathways such as glyoxylate shunt and amino acid/cofactor biosynthetic enzymes. PMID:21386900

  2. A Rapid and Accurate Extraction Procedure for Analysing Free Amino Acids in Meat Samples by GC-MS

    PubMed Central

    Barroso, Miguel A.; Ruiz, Jorge; Antequera, Teresa

    2015-01-01

    This study evaluated the use of a mixer mill as the homogenization tool for the extraction of free amino acids in meat samples, with the main goal of analyzing a large number of samples in the shortest time and minimizing sample amount and solvent volume. Ground samples (0.2 g) were mixed with 1.5 mL HCl 0.1 M and homogenized in the mixer mill. The final biphasic system was separated by centrifugation. The supernatant was deproteinized, derivatized and analyzed by gas chromatography. This procedure showed a high extracting ability, especially in samples with high free amino acid content (recovery = 88.73–104.94%). It also showed a low limit of detection and quantification (3.8 · 10−4–6.6 · 10−4 μg μL−1 and 1.3 · 10−3–2.2 · 10−2 μg μL−1, resp.) for most amino acids, an adequate precision (2.15–20.15% for run-to-run), and a linear response for all amino acids (R2 = 0.741–0.998) in the range of 1–100 µg mL−1. Moreover, it takes less time and requires lower amount of sample and solvent than conventional techniques. Thus, this is a cost and time efficient tool for homogenizing in the extraction procedure of free amino acids from meat samples, being an adequate option for routine analysis. PMID:25873963

  3. 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.

  4. 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

  5. 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

  6. Foodstuff analyses show that seafood and water are major perfluoroalkyl acids (PFAAs) sources to humans in Korea.

    PubMed

    Heo, Jin-Ju; Lee, Ji-Woo; Kim, Seung-Kyu; Oh, Jeong-Eun

    2014-08-30

    We measured concentrations of PFAAs in 397 foods, of 66 types, in Korea, and determined the daily human dietary PFAAs intake and the contribution of each foodstuff to that intake. The PFAAs concentration in the 66 different food types ranged from below the detection limit to 48.3ng/g. Perfluorooctane sulfonate (PFOS) and long-chain perfluorocarboxylic acids (PFCAs) were the dominant PFAAs in fish, shellfish, and processed foods, while perfluorooctanoic acid (PFOA) and short-chain PFCAs dominated dairy foodstuffs and beverages. The Korean adult dietary intake ranges, estimated for a range of scenarios, were 0.60-3.03 and 0.17-1.68ngkg(-1)bwd(-1) for PFOS and PFOA, respectively, which were lower than the total daily intake limits suggested by European Food Safety Authority (PFOS: 150ngkg(-1)bwd(-1); PFOA: 1500ngkg(-1)bwd(-1)). The major contributors to PFAAs dietary exposure varied with subject age and PFAAs. For example, fish was a major contributor of PFOS but dairy foods were major contributors of PFOA. However, tap water was a major contributor to PFOA intake when it was the main source of drinking water (rather than bottled water).

  7. Diet of Littoraria scabra, while vertically migrating on mangrove trees: Gut content, fatty acid, and stable isotope analyses

    NASA Astrophysics Data System (ADS)

    Alfaro, Andrea C.

    2008-09-01

    The snail, Littoraria scabra, is a dominant grazer on tropical mangrove trees, and may play an important role in the food web dynamics of these ecosystems. Its daily vertical migration to avoid tidal submersion results in exposure to varying food types and abundances. A comprehensive diet analysis - gut contents, fatty acid profiles, and stable isotopes ( δ15N and δ13C) - was conducted on snails migrating along mangrove trees and snails maintained in non-tidal mesocosms at Nananu-i-ra, Fiji Islands. In addition, fatty acid profiles and stable isotope signatures were obtained from surface scrapings of mangrove roots, trunks, branches, and leaves. Results from this multi-technique study indicate that L. scabra is mainly a generalist herbivore, which easily shifts diets depending on food availability, and which also has the ability to ingest and assimilate zooplankton. Ingestion of greater quantities of diverse foods (i.e., microalgae, foliose/corticated macrophytes, filamentous algae, mangrove tissues, zooplankton) takes place in the bottom areas of mangrove trees (roots and trunks) during low tides, while top areas (branches and leaves) provide limited food resources for snails feeding during high tides. However, snails preferentially assimilate microalgae and bacteria, regardless of their feeding habitat (different areas within mangrove trees and non-tidal mesocosms). The daily vertical movements of this snail result in variable feeding times, ingestion of different food types and amounts, and different assimilations. These findings also suggest that organic matter derived from mangrove tissues may not be readily transferred to higher trophic levels through this grazing pathway.

  8. Biochemical and phylogenetic analyses of a cold-active {beta}-galactosidase from the lactic acid bacterium Carnobacterium piscicola BA

    SciTech Connect

    Coombs, J.M.; Brenchley, J.E.

    1999-12-01

    The authors are investigating glycosyl hydrolases from new psychrophilic isolates to examine the adaptations of enzymes to low temperatures. A {beta}-galactosidase from isolate BA, which they have classified as a strain of the lactic acid bacterium Carnobacterium piscicola, was capable of hydrolyzing the chromogen 5-bromo-4-chloro-3-indolyl {beta}-D-galactopyranoside (X-Gal) at 4 C and possessed higher activity in crude cell lysates at 25 than at 37 C. Sequence analysis of a cloned DNA fragment encoding this activity revealed a gene cluster containing three glycosyl hydrolases with homology to an {alpha}-galactosidase and two {beta}-galactosidases. The larger of the two {beta}-galactosidase genes, bgaB, encoded the 76.9-kDa cold-active enzyme. This gene was homologous to family 42 glycosyl hydrolases, a group which contains several thermophilic enzymes but none from lactic acid bacteria. The bgaB gene from isolate BA was subcloned in Escherichia coli, and its enzyme, BgaB, was purified. The purified enzyme was highly unstable and required 10% glycerol to maintain activity. Its optimal temperature for activity was 30 C, and it was inactivated at 40 C in 10 min. The K{sub m} of freshly purified enzyme at 30 C was 1.7 mM, and the V{sub max} was 450 {micro}mol {sm{underscore}bullet} min{sup {minus}1}{sm{underscore}bullet}mg{sup {minus}1} with o-nitrophenyl {beta}-D-galactopyranoside. This cold-active enzyme is interesting because it is homologous to a thermophilic enzyme from Bacillus stearothermophilus, and comparisons could provide information about structural features important for activity at low temperatures.

  9. 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.

  10. Structure of a microbial community in soil after prolonged addition of low levels of simulated acid rain

    PubMed

    Pennanen; Fritze; Vanhala; Kiikkila; Neuvonen; Baath

    1998-06-01

    Humus samples were collected 12 growing seasons after the start of a simulated acid rain experiment situated in the subarctic environment. The acid rain was simulated with H2SO4, a combination of H2SO4 and HNO3, and HNO3 at two levels of moderate acidic loads close to the natural anthropogenic pollution levels of southern Scandinavia. The higher levels of acid applications resulted in acidification, as defined by humus chemistry. The concentrations of base cations decreased, while the concentrations of exchangeable H+, Al, and Fe increased. Humus pH decreased from 3.83 to 3.65. Basal respiration decreased with decreasing humus pH, and total microbial biomass, measured by substrate-induced respiration and total amount of phospholipid fatty acids (PLFA), decreased slightly. An altered PLFA pattern indicated a change in the microbial community structure at the higher levels of acid applications. In general, branched fatty acids, typical of gram-positive bacteria, increased in the acid plots. PLFA analysis performed on the bacterial community growing on agar plates also showed that the relative amount of PLFA specific for gram-positive bacteria increased due to the acidification. The changed bacterial community was adapted to the more acidic environment in the acid-treated plots, even though bacterial growth rates, estimated by thymidine and leucine incorporation, decreased with pH. Fungal activity (measured as acetate incorporation into ergosterol) was not affected. This result indicates that bacteria were more affected than fungi by the acidification. The capacity of the bacterial community to utilize 95 different carbon sources was variable and only showed weak correlations to pH. Differences in the toxicities of H2SO4 and HNO3 for the microbial community were not found.

  11. 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.

  12. 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.

  13. 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

  14. 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. PMID:26079286

  15. 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.

  16. 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. PMID:25046610

  17. 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

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

    PubMed

    Wu, Xianli; Tong, Yudong; Shankar, Kartik; Baumgardner, January N; Kang, Jie; Badeaux, Jamie; Badger, Thomas M; Ronis, Martin J J

    2011-01-26

    Fatty acids (FAs) are essential components of lipids and exhibit important biological functions. The analyses of FAs are routinely carried out by gas chromatography-mass spectrometry after multistep sample preparation. In this study, several key experimental factors were carefully examined, validated, and optimized to analyze free fatty acid (FFA) and FA profiles of triglycerides and phospholipids in serum or tissue samples. These factors included (1) methylation/transesterification reagents, (2) validation of internal standards, and (3) final step concentration of FA methyl esters. This new method was utilized to analyze FFAs and the FA profiles of triglycerides and phospholipids in the serum and liver from a recently established rat model of nonalcoholic steatohepatitis (NASH). In this model, rats were fed a 220 kcal kg (-3/4) day (-1) diet containing either 5 or 70% corn oil for 21 days using total enteral nutrition. FA compositions of the serum and liver were found to shift from a pattern dominated by saturated and monounsaturated FAs (C16:0/18:1) to one dominated by polyunsaturated C18:2 derived from dietary linoleic acid. Alteration of FA composition in liver after overfeeding of high polyunsaturated fat diets may contribute to the progression of pathological changes from steatosis to inflammation, necrosis, and fibrosis observed in NASH. PMID:21162572

  19. 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

  20. Changes in ester-linked phospholipid fatty acid profiles of subsurface bacteria during starvation and desiccation in a porous medium

    SciTech Connect

    Kieft, T.L.; Ringelberg, D.B.; White, D.C.

    1994-09-01

    Ester-linked phospholipid fatty acid (PLFA) profiles of a Pseudomonas aureofaciens strain and an Arthrobacter protophormiae strain, each isolated from a subsurface sediment, were quantified in a starvation experiment in a silica sand porous medium under moist and dry conditions. Washed cells were added to sand microcosms and maintained under saturated conditions or subjected to desiccation by slow drying over a period of 16 days. In a third treatment, cells were added to saturated microcosms along with organic nutrients and maintained under saturated conditions. The numbers of culturable cells of both bacterial strains declined to below detection level within 16 days in both the moist and dried nutrient-deprived conditions, while direct counts and total PLFAs remained relatively constant. Both strains of bacteria maintained culturability in the nutrient-amended microcosms. The dried P. aureofaciens cells showed increased ratios of saturated to unsaturated fatty acids, increased ratios of trans- to cis-monoenoic fatty acids, and increased ratios of cyclopropyl fatty acids to their monoenoic precursors. P. aureofaciens starved under moist conditions showed few changes in PLFA profiles during the 16-day incubation, whereas cells incubated in the presence of nutrients showed decreases in the ratios of both saturated fatty acids to unsaturated fatty acids and cyclopropyl fatty acids to their monoenoic precursors. The PLFA profiles of A. protophormiae changed very little in response to either nutrient deprivation or desiccation. Diglyceride fatty acids, proposedindicators of dead or lysed cells, remained relatively constant throughout the experiment. The results of this laboratory experiment can be useful for interpreting PLFA profiles of subsurface communities of microorganisms for the purpose of determining their physiological status. 43 refs., 8 figs.

  1. 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

  2. High intraspecific variability in the diet of a deep-sea nematode: Stable isotope and fatty acid analyses of Deontostoma tridentum on Chatham Rise, Southwest Pacific

    NASA Astrophysics Data System (ADS)

    Leduc, Daniel; Brown, Julie C. S.; Bury, Sarah J.; Lörz, Anne-Nina

    2015-03-01

    Small deep-sea organisms may exhibit a high degree of intraspecific variability in diet due to their ability to exploit a wide range of food sources and patchiness in food availability. Trophic interactions of small deep-sea benthic organisms, however, remain poorly understood. Here we describe spatial variation in diet/trophic level of the common deep-sea nematode Deontostoma tridentum on Chatham Rise, Southwest Pacific, using carbon and nitrogen stable isotope and fatty acid analyses. We also analysed sediment organic matter (SOM) and compared the isotopic composition of D. tridentum to other benthic and suprabenthic macrofaunal taxa with a variety of feeding modes. Variability in D. tridentum δ13C and δ15N signatures was high both among sites and within a single site on the southern flank of Chatham Rise. Among-site variation in SOM δ13C signatures was not sufficient to explain variation in nematode isotopic signatures. The presence of a positive correlation between δ13C and δ15N signatures of D. tridentum (both among and within sites) could suggest that differences in trophic level is the cause behind this variation. Nitrogen isotope data suggest the presence of 1-3 trophic levels in this species, which may reflect differences in prey availability, nematode body size, or habitat (benthic versus epizoic). Nematode δ15N values exceeded those of all other taxa we investigated, including other predators, but reasons for this enrichment remain unclear. The fatty acid composition of D. tridentum did not vary substantially between sites and was characterised by relatively high levels of 18:1n9 (15-20%) and polyunsaturated fatty acids (PUFAs; ~22%). Although limited inferences can be made based on fatty acid composition due to the potential impacts of non-dietary factors, high levels of PUFAs indicate that D. tridentum represents a good source of these essential nutrients to higher trophic levels. In conclusion, our results show that (1) some deep-sea organisms

  3. 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

  4. 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.

  5. Evolutionary analyses of the 12-kDa acidic ribosomal P-proteins reveal a distinct protein of higher plant ribosomes

    PubMed Central

    Szick, Kathleen; Springer, Mark; Bailey-Serres, Julia

    1998-01-01

    The P-protein complex of eukaryotic ribosomes forms a lateral stalk structure in the active site of the large ribosomal subunit and is thought to assist in the elongation phase of translation by stimulating GTPase activity of elongation factor-2 and removal of deacylated tRNA. The complex in animals, fungi, and protozoans is composed of the acidic phosphoproteins P0 (35 kDa), P1 (11–12 kDa), and P2 (11–12 kDa). Previously we demonstrated by protein purification and microsequencing that ribosomes of maize (Zea mays L.) contain P0, one type of P1, two types of P2, and a distinct P1/P2 type protein designated P3. Here we implemented distance matrices, maximum parsimony, and neighbor-joining analyses to assess the evolutionary relationships between the 12 kDa P-proteins of maize and representative eukaryotic species. The analyses identify P3, found to date only in mono- and dicotyledonous plants, as an evolutionarily distinct P-protein. Plants possess three distinct groups of 12 kDa P-proteins (P1, P2, and P3), whereas animals, fungi, and protozoans possess only two distinct groups (P1 and P2). These findings demonstrate that the P-protein complex has evolved into a highly divergent complex with respect to protein composition despite its critical position within the active site of the ribosome. PMID:9482893

  6. 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. PMID:27510281

  7. Survival and phospholipid fatty acid profiles of surface and subsurface bacteria in natural sediment microcosms

    SciTech Connect

    Kieft, T.L.; Wilch, E.; O`Connor, K.

    1997-04-01

    Although starvation survival has been characterized for many bacteria, few subsurface bacteria have been tested, and few if any have been tested in natural subsurface porous media. We hypothesized that subsurface bacteria may be uniquely adapted for long-term survival in situ. We further hypothesized that subsurface conditions (sediment type and moisture content) would influence microbial survival. We compared starvation survival capabilities of surface and subsurface strains of Pseudomonas fluorescens and a novel Arthrobacter sp. in microcosms composed of natural sediments. Bacteria were incubated for up to 64 weeks under saturated and unsaturated conditions in sterilized microcosms containing either a silty sand paleosol (buried soil) or a sandy silt nonpaleosol sediment. Direct counts, plate counts, and cell sizes were measured. Membrane phospholipid fatty acid (PLFA) profiles were quantified to determine temporal patterns of PLFA stress signatures and differences in PLFAs among strains and treatments. The Arthrobacter strains survived better than the P. fluorescens strains; however, differences in survival between surface and subsurface strains of each genus were not significant. Bacteria survived better in the paleosol than in the nonpaleosol and survived better under saturated conditions than under unsaturated conditions. Cell volumes of all strains decreased; however, sediment type and moisture did not influence rates of miniaturization. Both P.fluorescens strains showed PLFA stress signatures typical for gram-negative bacteria: increased ratios of saturated to unsaturated fatty acids, increased ratios of trans- to cis-monoenoic fatty acids, and increased ratios of cyclopropyl to monoenoic precursor fatty acids. The Arthrobacter strains showed few changes in PLFAs. Environmental conditions strongly influenced PLFA profiles. 40 refs., 7 figs.

  8. 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.

  9. 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

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

    PubMed Central

    Church, Clinton D; Wilkin, Richard T; Alpers, Charles N; Rye, Robert O; McCleskey, R Blaine

    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. PMID:17956615

  11. 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.

  12. Phospholipid fatty acids as physiological indicators of Paracoccus denitrificans encapsulated in silica sol-gel hydrogels.

    PubMed

    Trögl, Josef; Jirková, Ivana; Kuráň, Pavel; Akhmetshina, Elmira; Brovdyová, Taťjána; 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

  13. 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

  14. 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

  15. 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.

  16. Rat lung phospholipid fatty acid composition in prepregnant, pregnant, and lactating rats: relationship to ozone-induced pulmonary toxicity.

    PubMed

    Gunnison, A F; Finkelstein, I

    1997-01-01

    Our laboratory has demonstrated recently that pulmonary inflammation induced by acute ozone exposure is much more severe in late stage pregnant and lactating rats than in postlactating rats or age-matched virgin females. It is currently widely believed that such pulmonary damage results, at least in part, from the reaction of ozone at sites of unsaturation in phospholipid fatty acid (PLFA) molecules located in the epithelial fluid layer lining the lung surfaces and/or the plasma membranes of epithelial cells underlying this fluid layer. The objective of this study was to compare the PLFA composition of lung tissue and surfactant from ozone-sensitive late stage pregnant and lactating rats with comparable tissue from relatively ozone-insensitive age-matched prepregnant (virgin female) rats to explore the possibility that changes in lung PLFA composition during pregnancy and/or lactation contribute to the enhanced sensitivity of these physiologic states to ozone. In addition, the correlation of changes in plasma PLFA composition with those in lung was investigated. There were minor differences in the composition of lung tissue and surfactant PLFAs between prepregnant rats and pregnant rats at day 17 of gestation and only slightly greater differences between prepregnant and lactating rats. Changes from the prepregnant state in the PLFA composition of lung tissue, but not surfactant, correlated with changes in the plasma only in lactating rats and not in pregnant rats. Overall, the double bond index of PLFAs in surfactant and lung tissue was decreased in pregnant and lactating rats compared with prepregnant rats. Thus, the increased sensitivity of pregnant and lactating rats to ozone-induced lung injury cannot be attributed to an increased availability of unsaturated fatty acids. In addition, the arachidonic acid composition of phospholipids did not appear to explain differences between prepregnant rats and pregnant or lactating rats in their inflammatory response to

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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. Beyer's "Educational Studies and…

  6. Compound-Specific δ¹⁵N and δ¹³C Analyses of Amino Acids for Potential Discrimination between Organically and Conventionally Grown Wheat.

    PubMed

    Paolini, Mauro; Ziller, Luca; Laursen, Kristian Holst; Husted, Søren; Camin, Federica

    2015-07-01

    We present a study deploying compound-specific nitrogen and carbon isotope analysis of amino acids to discriminate between organically and conventionally grown plants. We focused on grain samples of common wheat and durum wheat grown using synthetic nitrogen fertilizers, animal manures, or green manures from nitrogen-fixing legumes. The measurement of amino acid δ(15)N and δ(13)C values, after protein hydrolysis and derivatization, was carried out using gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). Our results demonstrated that δ(13)C of glutamic acid and glutamine in particular, but also the combination of δ(15)N and δ(13)C of 10 amino acids, can improve the discrimination between conventional and organic wheat compared to stable isotope bulk tissue analysis. We concluded that compound-specific stable isotope analysis of amino acids represents a novel analytical tool with the potential to support and improve the certification and control procedures in the organic sector.

  7. 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.

  8. [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.

  9. Use of the Signature Fatty Acid 16:1ω5 as a Tool to Determine the Distribution of Arbuscular Mycorrhizal Fungi in Soil

    PubMed Central

    Ngosong, Christopher; Gabriel, Elke; Ruess, Liliane

    2012-01-01

    Biomass estimation of arbuscular mycorrhiza (AM) fungi, widespread plant root symbionts, commonly employs lipid biomarkers, predominantly the fatty acid 16:1ω5. We briefly reviewed the application of this signature fatty acid, followed by a case study comparing biochemical markers with microscopic techniques in an arable soil following a change to AM non-host plants after 27 years of continuous host crops, that is, two successive cropping seasons with wheat followed by amaranth. After switching to the non-host amaranth, spore biomass estimated by the neutral lipid fatty acid (NLFA) 16:1ω5 decreased to almost nil, whereas microscopic spore counts decreased by about 50% only. In contrast, AM hyphal biomass assessed by the phospholipid (PLFA) 16:1ω5 was greater under amaranth than wheat. The application of PLFA 16:1ω5 as biomarker was hampered by background level derived from bacteria, and further enhanced by its incorporation from degrading spores used as microbial resource. Meanwhile, biochemical and morphological assessments showed negative correlation for spores and none for hyphal biomass. In conclusion, the NLFA 16:1ω5 appears to be a feasible indicator for AM fungi of the Glomales group in the complex field soils, whereas the use of PLFA 16:1ω5 for hyphae is unsuitable and should be restricted to controlled laboratory studies. PMID:22830034

  10. 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.

  11. 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.

  12. Compound-Specific δ¹⁵N and δ¹³C Analyses of Amino Acids for Potential Discrimination between Organically and Conventionally Grown Wheat.

    PubMed

    Paolini, Mauro; Ziller, Luca; Laursen, Kristian Holst; Husted, Søren; Camin, Federica

    2015-07-01

    We present a study deploying compound-specific nitrogen and carbon isotope analysis of amino acids to discriminate between organically and conventionally grown plants. We focused on grain samples of common wheat and durum wheat grown using synthetic nitrogen fertilizers, animal manures, or green manures from nitrogen-fixing legumes. The measurement of amino acid δ(15)N and δ(13)C values, after protein hydrolysis and derivatization, was carried out using gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). Our results demonstrated that δ(13)C of glutamic acid and glutamine in particular, but also the combination of δ(15)N and δ(13)C of 10 amino acids, can improve the discrimination between conventional and organic wheat compared to stable isotope bulk tissue analysis. We concluded that compound-specific stable isotope analysis of amino acids represents a novel analytical tool with the potential to support and improve the certification and control procedures in the organic sector. PMID:25959490

  13. 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

    2013-05-01

    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.

  14. 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. PMID:25259723

  15. Proteomic and virus-induced gene silencing (VIGS) Analyses reveal that gossypol, brassinosteroids, and jasmonic acid contribute to the resistance of cotton to Verticillium dahliae.

    PubMed

    Gao, Wei; Long, Lu; Zhu, Long-Fu; Xu, Li; Gao, Wen-Hui; Sun, Long-Qing; Liu, Lin-Lin; Zhang, Xian-Long

    2013-12-01

    Verticillium wilt causes massive annual losses of cotton yield, but the mechanism of cotton resistance to Verticillium dahliae is complex and poorly understood. In this study, a comparative proteomic analysis was performed in resistant cotton (Gossypium barbadense cv7124) on infection with V. dahliae. A total of 188 differentially expressed proteins were identified by mass spectrometry (MALDI-TOF/TOF) analysis and could be classified into 17 biological processes based on Gene Ontology annotation. Most of these proteins were implicated in stimulus response, cellular processes and metabolic processes. Based on the proteomic analysis, several genes involved in secondary metabolism, reactive oxygen burst and phytohormone signaling pathways were identified for further physiological and molecular analysis. The roles of the corresponding genes were further characterized by employing virus-induced gene silencing (VIGS). Based on the results, we suggest that the production of gossypol is sufficient to affect the cotton resistance to V. dahliae. Silencing of GbCAD1, a key enzyme involving in gossypol biosynthesis, compromised cotton resistance to V. dahliae. Reactive oxygen species and salicylic acid signaling may be also implicated as regulators in cotton responsive to V. dahliae according to the analysis of GbSSI2, an important regulator in the crosstalk between salicylic acid and jasmonic acid signal pathways. Moreover, brassinosteroids and jasmonic acid signaling may play essential roles in the cotton disease resistance to V. dahliae. The brassinosteroids signaling was activated in cotton on inoculation with V. dahliae and the disease resistance of cotton was enhanced after exogenous application of brassinolide. Meanwhile, jasmonic acid signaling was also activated in cotton after inoculation with V. dahliae and brassinolide application. These data provide highlights in the molecular basis of cotton resistance to V. dahliae.

  16. 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

  17. 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.

  18. Analyses of a Polyhydroxyalkanoic Acid Granule-Associated 16-Kilodalton Protein and Its Putative Regulator in the pha Locus of Paracoccus denitrificans

    PubMed Central

    Maehara, Akira; Ueda, Shunsaku; Nakano, Hideo; Yamane, Tsuneo

    1999-01-01

    The polyhydroxyalkanoic acid (PHA) granule-associated 16-kDa protein (GA16 protein) of Paracoccus denitrificans was identified, and its corresponding gene was cloned and analyzed at the molecular level. The N-terminal amino acid sequence of GA16 protein revealed that its structural gene is located downstream from the PHA synthase gene (phaCPd) cloned recently (S. Ueda, T. Yabutani, A. Maehara, and T. Yamane, J. Bacteriol. 178:774–779, 1996). Gene walking around phaCPd revealed two new open reading frames (ORFs) possibly related to PHA synthesis, one of which was the phaPPd gene, encoding GA16 protein, and the other was the phaRPd gene, encoding a protein that is putatively involved in the regulation of the expression of phaPPd. Overproduction of PhaPPd was observed in Escherichia coli carrying phaPPd, but the overproduction was not observed in the presence of phaRPd. Coexpression of phaPPd and PHA biosynthesis genes in E. coli caused increases in both the number of poly-(3-hydroxybutyric acid) (PHB) granules and PHB content and caused decreases in both the size of the granules and the molecular weight of PHB. GA16 protein was considered a phasin protein. The phaRPd gene had significant similarities to stdC, a possible transcriptional factor of Comamonas testosteroni, as well as to other ORFs of unknown function previously found in other PHA-synthetic bacteria. PMID:10217786

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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. PMID:26878105

  4. 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

  5. Tracing carbon assimilation in endosymbiotic deep-sea hydrothermal vent Mytilid fatty acids by 13C-fingerprinting

    NASA Astrophysics Data System (ADS)

    Riou, V.; Bouillon, S.; Serrão Santos, R.; Dehairs, F.; Colaço, A.

    2010-09-01

    Bathymodiolus azoricus mussels thrive at Mid-Atlantic Ridge hydrothermal vents, where part of their energy requirements are met via an endosymbiotic association with chemolithotrophic and methanotrophic bacteria. In an effort to describe phenotypic characteristics of the two bacterial endosymbionts and to assess their ability to assimilate CO2, CH4 and multi-carbon compounds, we performed experiments in aquaria using 13C-labeled NaHCO3 (in the presence of H2S), CH4 or amino-acids and traced the incorporation of 13C into total and phospholipid fatty acids (tFA and PLFA, respectively). 14:0; 15:0; 16:0; 16:1(n - 7)c+t; 18:1(n - 13)c+t and (n - 7)c+t; 20:1(n - 7); 20:2(n - 9,15); 18:3(n - 7) and (n - 5,10,13) PLFA were labeled in the presence of H13CO3- (+H2S) and 13CH4, while the 12:0 compound became labeled only in the presence of H13CO3- (+H2S). In contrast, the 17:0; 18:0; 16:1(n - 9); 16:1(n - 8) and (n - 6); 18:1(n - 8); and 18:2(n - 7) PLFA were only labeled in the presence of 13CH4. Some of these symbiont-specific fatty acids also appeared to be labeled in mussel gill tFA when incubated with 13C-enriched amino acids, and so were mussel-specific fatty acids such as 22:2(n - 7,15). Our results provide experimental evidence for the potential of specific fatty acid markers to distinguish between the two endosymbiotic bacteria, shedding new light on C1 and multi-carbon compound metabolic pathways in B. azoricus and its symbionts.

  6. Tracing carbon assimilation in endosymbiotic deep-sea hydrothermal vent Mytilid fatty acids by 13C-fingerprinting

    NASA Astrophysics Data System (ADS)

    Riou, V.; Bouillon, S.; Serrão Santos, R.; Dehairs, F.; Colaço, A.

    2010-05-01

    Bathymodiolus azoricus mussels thrive at Mid-Atlantic Ridge hydrothermal vents, where part of their energy requirements are met via an endosymbiotic association with chemolithotrophic and methanotrophic bacteria. In an effort to describe phenotypic characteristics of the two bacterial endosymbionts and to assess their ability to assimilate CO2, CH4 and multi-carbon compounds, we performed experiments in aquaria using 13C-labeled NaHCO3 (in the presence of H2S), CH4 or amino-acids and traced the incorporation of 13C into total and phospholipid fatty acids (tFA and PLFA, respectively). 14:0, 15:0, 16:1(n-7)c+t and 18:1(n-7)c+t PLFA were labeled in the presence of H13CO3- (+H2S) and 13CH4, while the 12:0 compound became labeled only in the presence of H13CO3- (+H2S). In contrast, the 16:1(n-9), 16:1(n-8) and (n-6), 18:1(n-8)c and (n-7), 20:1(n-7) and 18:2(n-7) PLFA were only labeled in the presence of 13CH4. Some of these symbiont-specific fatty acids also appeared to be labeled in mussel gill tFA when incubated with 13C-enriched amino acids, and so were mussel-specific fatty acids such as 22:2(n-7,15). Our results provide experimental evidence for the potential of specific fatty acid markers to distinguish between the two endosymbiotic bacteria, shedding new light on C1 and multi-carbon compound metabolic pathways in B. azoricus and its symbionts.

  7. High-sensitivity matrix-assisted laser desorption/ionization Fourier transform mass spectrometry analyses of small carbohydrates and amino acids using oxidized carbon nanotubes prepared by chemical vapor deposition as matrix.

    PubMed

    Wang, Cui-hong; Li, Jian; Yao, Sheng-jun; Guo, Yin-long; Xia, Xing-hua

    2007-12-01

    In matrix-assisted laser desorption/ionization (MALDI) Fourier transform mass spectrometry (FTMS) analyses of small oligosaccharides and amino acids, high sensitivities for oligosaccharides (10 fmol) were obtained by introducing oxidized carbon nanotubes (CNTs) with short and open-end structure as valuable matrix. The CNTs were deposited in porous anodic alumina (PAA) templates by chemical vapor deposition. Transmission electron microscopy (TEM) images show that those CNTs include low levels of amorphous carbon. Thus, the background interference signals generally caused by amorphous carbon powder in CNTs can be reduced effectively. Experiments also confirmed that the FTMS signal intensity of CNTs prepared in PAA template is much lower than that of commercial multi-wall carbon nanotubes (MCNTs). Moreover, the purified process for CNTs with mixed acid (H2SO4 and HNO3) also contributed to the minimization of background. Intense signals corresponding to alkali cation adduct of neutral carbohydrates and amino acids have been acquired. In addition, reliable quantitative analyses for urine and corn root were also achieved successfully. The present work will open a new way to the application of oxidized CNTs as an effective matrix in MALDI MS research.

  8. 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

  9. 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

  10. 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

  11. Proteomics and functional analyses of pepper abscisic acid-responsive 1 (ABR1), which is involved in cell death and defense signaling.

    PubMed

    Choi, Du Seok; Hwang, Byung Kook

    2011-02-01

    Abscisic acid (ABA) is a key regulator of plant growth and development, as well as plant defense responses. A high-throughput in planta proteome screen identified the pepper (Capsicum annuum) GRAM (for glucosyltransferases, Rab-like GTPase activators, and myotubularins) domain-containing ABA-RESPONSIVE1 (ABR1), which is highly induced by infection with avirulent Xanthomonas campestris pv vesicatoria and also by treatment with ABA. The GRAM domain is essential for the cell death response and for the nuclear localization of ABR1. ABR1 is required for priming cell death and reactive oxygen species production, as well as ABA-salicylic acid (SA) antagonism. Silencing of ABR1 significantly compromised the hypersensitive response but enhanced bacterial pathogen growth and ABA levels in pepper. High levels of ABA in ABR1-silenced plants antagonized the SA levels induced by pathogen infection. Heterologous transgenic expression of ABR1 in Arabidopsis thaliana conferred enhanced resistance to Pseudomonas syringae pv tomato and Hyaloperonospora arabidopsidis infection. The susceptibility of the Arabidopsis ABR1 putative ortholog mutant, abr1, to these pathogens also supports the involvement of ABR1 in disease resistance. Together, these results reveal ABR1 as a novel negative regulator of ABA signaling and suggest that the nuclear ABR1 pool is essential for the cell death induction associated with ABA-SA antagonism.

  12. Omega-3 Fatty Acids, Depressive Symptoms, and Cognitive Performance in Patients With Coronary Artery Disease: Analyses From a Randomized, Double-Blind, Placebo-Controlled Trial.

    PubMed

    Mazereeuw, Graham; Herrmann, Nathan; Oh, Paul I; Ma, David W L; Wang, Cheng Tao; Kiss, Alexander; Lanctôt, Krista L

    2016-10-01

    This trial investigated the efficacy of omega-3 polyunsaturated fatty acid (n-3 PUFA) treatment for improving depressive symptoms and cognitive performance in patients with coronary artery disease (CAD) participating in cardiac rehabilitation. Patients with CAD aged 45 to 80 years were randomized to receive either 1.9-g/d n-3 PUFA treatment or placebo for 12 weeks. Depressive symptoms were measured using the Hamilton Depression Rating Scale (HAM-D, primary outcome) and the Beck Depression Inventory II (BDI-II). Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, criteria were used to identify a depressive episode at baseline. Cognitive performance was measured using a standardized battery for vascular cognitive impairment. In 92 patients (age, 61.7 ± 8.7 y; 76% male, 40% depressed; HAM-D, 6.9 ± 5.9; BDI-II, 12.3 ± 10.9; n = 45 n-3 PUFA, n = 47 placebo), depression decreased (HAM-D, F3,91 = 2.71 and P = 0.049; BDI-II, F3,91 = 6.24 and P < 0.01), and cognitive performance improved (attention/processing speed, F1,91 = 5.57, P = 0.02; executive function, F1,91 = 14.64, P < 0.01; visuospatial memory, F1,91 = 4.01, P = 0.04) over cardiac rehabilitation. Omega-3 PUFA treatment increased plasma eicosapentaenoic acid (F1,29 = 33.29, P < 0.01) and docosahexaenoic acid (F1,29 = 15.29, P < 0.01) concentrations but did not reduce HAM-D (F3,91 = 1.59, P = 0.20) or BDI-II (F3,91 = 0.46, P = 0.50) scores compared with placebo. Treatment did not improve cognitive performance; however, n-3 PUFAs significantly increased verbal memory compared with placebo in a subgroup of nondepressed patients (F1,54 = 4.16, P = 0.04). This trial suggests that n-3 PUFAs do not improve depressive and associated cognitive symptoms in those with CAD. The possible benefits of n-3 PUFAs for verbal memory may warrant investigation in well-powered studies. PMID:27529771

  13. Omega-3 Fatty Acids, Depressive Symptoms, and Cognitive Performance in Patients With Coronary Artery Disease: Analyses From a Randomized, Double-Blind, Placebo-Controlled Trial.

    PubMed

    Mazereeuw, Graham; Herrmann, Nathan; Oh, Paul I; Ma, David W L; Wang, Cheng Tao; Kiss, Alexander; Lanctôt, Krista L

    2016-10-01

    This trial investigated the efficacy of omega-3 polyunsaturated fatty acid (n-3 PUFA) treatment for improving depressive symptoms and cognitive performance in patients with coronary artery disease (CAD) participating in cardiac rehabilitation. Patients with CAD aged 45 to 80 years were randomized to receive either 1.9-g/d n-3 PUFA treatment or placebo for 12 weeks. Depressive symptoms were measured using the Hamilton Depression Rating Scale (HAM-D, primary outcome) and the Beck Depression Inventory II (BDI-II). Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, criteria were used to identify a depressive episode at baseline. Cognitive performance was measured using a standardized battery for vascular cognitive impairment. In 92 patients (age, 61.7 ± 8.7 y; 76% male, 40% depressed; HAM-D, 6.9 ± 5.9; BDI-II, 12.3 ± 10.9; n = 45 n-3 PUFA, n = 47 placebo), depression decreased (HAM-D, F3,91 = 2.71 and P = 0.049; BDI-II, F3,91 = 6.24 and P < 0.01), and cognitive performance improved (attention/processing speed, F1,91 = 5.57, P = 0.02; executive function, F1,91 = 14.64, P < 0.01; visuospatial memory, F1,91 = 4.01, P = 0.04) over cardiac rehabilitation. Omega-3 PUFA treatment increased plasma eicosapentaenoic acid (F1,29 = 33.29, P < 0.01) and docosahexaenoic acid (F1,29 = 15.29, P < 0.01) concentrations but did not reduce HAM-D (F3,91 = 1.59, P = 0.20) or BDI-II (F3,91 = 0.46, P = 0.50) scores compared with placebo. Treatment did not improve cognitive performance; however, n-3 PUFAs significantly increased verbal memory compared with placebo in a subgroup of nondepressed patients (F1,54 = 4.16, P = 0.04). This trial suggests that n-3 PUFAs do not improve depressive and associated cognitive symptoms in those with CAD. The possible benefits of n-3 PUFAs for verbal memory may warrant investigation in well-powered studies.

  14. 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

    2005-12-01

    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.

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

    PubMed

    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; Yong, William H

    2013-07-01

    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

  16. 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

    2013-12-01

    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.

  17. 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

  18. 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.

  19. Study of the microbial dynamics in the root environment of closed, hydroponic cultivation systems for tomato using phospholipid fatty acid profiles.

    PubMed

    Waechter-Kristensen, B; Khalil, S; Sundin, P; Englund, J E; Gertsson, U E; Jensen, P

    1996-12-01

    A more basic understanding of the microbial dynamics of closed, hydroponic cultivation systems is needed. We therefore initiated a study of the microbial community inhabiting the root environment, using phospholipid fatty acid (PLFA) profiles, and started to examine whether changes in the microbial population structure would result from the introduction of selected isolates of plant growth-promoting rhizobacteria (PGPR). Tomato were cultured in deep-flow systems with circulating nutrient solution. Bacteria were sampled from tomato roots at three locations, longitudinally, in the gutters of a control system and in two systems inoculated with PGPR. In the beginning of the gutters the PLFA profiles were similar in all systems, whereas the profiles differed in the gutter ends (following the direction of flow). In the control system, and in a treatment inoculated with two Gram-negative and one Gram-positive PGPR strain, the relative proportion of PLFAs characteristic to Gram-positive bacteria was highest at the end of the gutter. In a treatment inoculated only with a Gram-negative PGPR strain, the relative proportion of PLFAs characteristic of Gram-negative bacteria was highest at the end of the gutter. The results indicate a complex situation with different micro-environments distributed along the root mat. It can also be concluded that PLFA profiles may be useful tools in the study of the microbiology of closed hydroponic plant cultivation systems. PMID:11541571

  20. Structural, Biochemical, and Phylogenetic Analyses Suggest That Indole-3-Acetic Acid Methyltransferase Is an Evolutionarily Ancient Member of the SABATH Family1[W][OA

    PubMed Central

    Zhao, Nan; Ferrer, Jean-Luc; Ross, Jeannine; Guan, Ju; Yang, Yue; Pichersky, Eran; Noel, Joseph P.; Chen, Feng

    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 Å 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 IAA

  1. 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

  2. Enhancement of volatile fatty acid production by co-fermentation of food waste and excess sludge without pH control: The mechanism and microbial community analyses.

    PubMed

    Wu, Qing-Lian; Guo, Wan-Qian; Zheng, He-Shan; Luo, Hai-Chao; Feng, Xiao-Chi; Yin, Ren-Li; Ren, Nan-Qi

    2016-09-01

    The study provided a cost-effective and high-efficiency volatile fatty acid (VFA) production strategy by co-fermentation of food waste (FW) and excess sludge (ES) without artificial pH control. VFA production of 867.42mg COD/g-VS was obtained under the optimized condition: FW/ES 5, solid retention time 7d, organic loading rate 9g VS/L-d and temperature 40°C. Mechanism exploration revealed that the holistic biodegradability of substrate was greatly enhanced, and proper pH range (5.2-6.4) was formed by the high buffering capacity of the co-fermentation system itself, which effectively enhanced hydrolysis yield (63.04%) and acidification yield (83.46%) and inhibited methanogenesis. Moreover, microbial community analysis manifested that co-fermentation raised the relative abundances of hydrolytic and acidogenic bacteria including Clostridium, Sporanaerobacter, Tissierella and Bacillus, but suppressed the methanogen Anaerolineae, which also facilitated high VFA production. These results were of great guiding significance aiming for VFA recovery from FW and ES in large-scale. PMID:27289056

  3. Molecular and proteome analyses highlight the importance of the Cpx envelope stress system for acid stress and cell wall stability in Escherichia coli.

    PubMed

    Surmann, Kristin; Ćudić, Emina; Hammer, Elke; Hunke, Sabine

    2016-08-01

    Two-component systems (TCS) play a pivotal role for bacteria in stress regulation and adaptation. However, it is not well understood how these systems are modulated to meet bacterial demands. Especially, for those TCS using an accessory protein to integrate additional signals, no data concerning the role of the accessory proteins within the coordination of the response is available. The Cpx envelope stress two-component system, composed of the sensor kinase CpxA and the response regulator CpxR, is orchestrated by the periplasmic protein CpxP which detects misfolded envelope proteins and inhibits the Cpx system in unstressed cells. Using selected reaction monitoring, we observed that the amount of CpxA and CpxR, as well as their stoichiometry, are only marginally affected, but that a 10-fold excess of CpxP over CpxA is needed to switch off the Cpx system. Moreover, the relative quantification of the proteome identified not only acid stress response as a new indirect target of the Cpx system, but also suggests a general function of the Cpx system for cell wall stability.

  4. LC-MS/MS method development and validation for quantitative analyses of 2-aminothiazoline-4-carboxylic acid--a new cyanide exposure marker in post mortem blood.

    PubMed

    Giebułtowicz, Joanna; Rużycka, Monika; Fudalej, Marcin; Krajewski, Paweł; Wroczyński, Piotr

    2016-04-01

    2-aminothiazoline-4-carboxylic acid (ATCA) is a hydrogen cyanide metabolite that has been found to be a reliable biomarker of cyanide poisoning, because of its long-term stability in biological material. There are several methods of ATCA determination; however, they are restricted to extraction on mixed mode cation exchange sorbents. To date, there has been no reliable method of ATCA determination in whole blood, the most frequently used material in forensic analysis. This novel method for ATCA determination in post mortem specimen includes protein precipitation, and derivatization of interfering compounds and their later extraction with ethyl acetate. ATCA was quantitatively analyzed via high performance liquid chromatography-tandem mass spectrometry with positive electrospray ionization detection using a hydrophilic interaction liquid chromatography column. The method satisfied all validation criteria and was tested on the real samples with satisfactory results. Therefore, this analytical approach has been proven to be a tool for measuring endogenous levels of ATCA in post mortem specimens. To conclude, a novel, accurate and sensitive method of ATCA determination in post mortem blood was developed. The establishment of the method provides new possibilities in the field of forensic science.

  5. Requirement for Asn298 on D1 protein for oxygen evolution: analyses by exhaustive amino acid substitution in the green alga Chlamydomonas reinhardtii.

    PubMed

    Kuroda, Hiroshi; Kodama, Natsumi; Sun, Xiao-Yu; Ozawa, Shin-ichiro; Takahashi, Yuichiro

    2014-07-01

    PSII generates strong oxidants used for water oxidation. The secondary electron donor, Y(Z), is Tyr161 on PSII reaction center D1 protein and mediates electron transfer from the oxygen-evolving Mn(4)CaO(5) cluster to the primary electron donor, P680. The latest PSII crystal structure revealed the presence of a hydrogen bond network around Y(Z), which is anticipated to play important roles in the electron and proton transfer reactions. Y(Z) forms a hydrogen bond with His190 which in turn forms a hydrogen bond with Asn298 on D1 protein. Although functional roles of Y(Z) and His190 have already been characterized, little is known about the functional role of Asn298. Here we have generated 19 mutants from a green alga Chlamydomonas reinhardtii, in which the Asn298 has been substituted by each of the other 19 amino acid residues. All mutants showed significantly impaired or no photosynthetic growth. Seven mutants capable of photosynthetic growth showed oxygen-evolving activity although at a significantly reduced rate. Interestingly the oxygen-evolving activity of these mutants was markedly photosensitive. The 19 mutants accumulated PSII at variable levels and showed a light-induced electron transfer reaction from 1,5-diphenylcarbazide (DPC) to 2,6-dichlorophenolindophenol (DCIP), suggesting that Asn298 is important for the function and photoprotection of the Mn(4)CaO(5) cluster. PMID:24853102

  6. Molecular and proteome analyses highlight the importance of the Cpx envelope stress system for acid stress and cell wall stability in Escherichia coli.

    PubMed

    Surmann, Kristin; Ćudić, Emina; Hammer, Elke; Hunke, Sabine

    2016-08-01

    Two-component systems (TCS) play a pivotal role for bacteria in stress regulation and adaptation. However, it is not well understood how these systems are modulated to meet bacterial demands. Especially, for those TCS using an accessory protein to integrate additional signals, no data concerning the role of the accessory proteins within the coordination of the response is available. The Cpx envelope stress two-component system, composed of the sensor kinase CpxA and the response regulator CpxR, is orchestrated by the periplasmic protein CpxP which detects misfolded envelope proteins and inhibits the Cpx system in unstressed cells. Using selected reaction monitoring, we observed that the amount of CpxA and CpxR, as well as their stoichiometry, are only marginally affected, but that a 10-fold excess of CpxP over CpxA is needed to switch off the Cpx system. Moreover, the relative quantification of the proteome identified not only acid stress response as a new indirect target of the Cpx system, but also suggests a general function of the Cpx system for cell wall stability. PMID:27039284

  7. Microchemical studies of the pathogenesis of soman toxication and atropine-oxime treatment using nucleic acid cytophotometry (cytophotometric analyses of non-cholinergic mediated effects of soman toxication in rats). Annual summary report, 15 August 1981-14 September 1983

    SciTech Connect

    Anthony, A.; Bocan, T.M.A.; Doebler, J.A.; Nollenberger, E.L.

    1983-10-01

    Quantitative cytochemical analyses, using microscopic histochemical staining and scanning-integrating microdensitometry, were made of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), protein, and acetylcholinesterase (AChE) changes in central and peripheral tissue compartments of rats exposed to soman with and without various regimens of atropine-pralidoxime treatment. Hypoxia-acclimated rats were also used to evaluate the relationship between increased vascularization of tissues and susceptibility of rats to soman toxication. It was found that a critical aspect of soman toxicity is an impairment in RNA-protein synthetic capacity of neurons in various brain regions; this is not directly correlated with the extent of blood or brain AChE suppression, indicating the involvement of non-cholinergic mechanisms. Additional aspects of soman intoxication include cytochemical-cytomorphologic manifestations of hepatoxicity and mesenteric mast cell degranulation. Various antidotal regimens and also prior acclimation of rats to hypoxia tend to ameliorate the severity of brain RNA depletion. Among the putative noncholinergic mechanisms which could precipitate the observed nucleic acid response patterns are included the disruption of excitatory-inhibitory neurotransmitter functioning coupled with a stress-mediated impairment in CNS-endocrine homeostatic mechanisms.

  8. Investigation of Eu(III) immobilization on γ-Al2O3 surfaces by combining batch technique and EXAFS analyses: Role of contact time and humic acid

    NASA Astrophysics Data System (ADS)

    Yang, Shitong; Sheng, Guodong; Montavon, Gilles; Guo, Zhiqiang; Tan, Xiaoli; Grambow, Bernd; Wang, Xiangke

    2013-11-01

    Aluminum (hydr)oxides play an important role in the regulation of the composition of soil/water, sediment/water and other natural water systems. In this study, the interactions among Eu(III), humic acid (HA) and γ-Al2O3 were investigated using a combination of batch and extended X-ray absorption fine structure (EXAFS) techniques. Experiments were performed with varying contact times (2, 15, 60 and 180 d) at a pH of 6.5 for both the binary γ-Al2O3/Eu(III) and the ternary γ-Al2O3/HA/Eu(III) systems. In addition, two representative pH values (pH 6.5 for a near-neutral condition and pH 8.5 for an alkalescence condition) were selected to determine the sequestration mechanisms of Eu(III) in the ternary γ-Al2O3/HA/Eu(III) systems. To verify the specific binding modes and corresponding chemical species, a coordination geometry calculation and a quantitative comparison between the HA binding site concentration and the initial Eu(III) concentration were conducted along with EXAFS data analysis. The microstructure and thermodynamic stability of the formed Eu(III) species were dependent on various environmental parameters. For the binary γ-Al2O3/Eu(III) systems, quantitative analysis results of EXAFS spectra suggested the presence of two Eu(III) species within a contact time of 15 d. Using a coordination geometry calculation, the REu-Al values at ∼3.28 Å and ∼3.99 Å corresponded to the formation of edge-shared and corner-shared surface complexes, respectively. For samples reacted longer than 15 d, the appearance of an additional Eu-Eu shell at ∼3.50 Å was indicative of a structural rearrangement process, leading to the formation of thermodynamically stable surface polynuclear complexes. For the ternary γ-Al2O3/HA/Eu(III) systems, the EXAFS-derived structural parameters indicated the formation of 1:1 type B ternary complexes and binary corner-shared complexes at pH 6.5 after 2 d. In contrast, the Eu(III) sequestration mechanisms at pH 8.5 were mainly attributed

  9. 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.

  10. 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

  11. Illumina sequencing-based analyses of bacterial communities during short-chain fatty-acid production from food waste and sewage sludge fermentation at different pH values.

    PubMed

    Cheng, Weixiao; Chen, Hong; Yan, ShuHai; Su, Jianqiang

    2014-09-01

    Short-chain fatty acids (SCFAs) can be produced by primary and waste activated sludge anaerobic fermentation. The yield and product spectrum distribution of SCFAs can be significantly affected by different initial pH values. However, most studies have focused on the physical and chemical aspects of SCFA production by waste activated sludge fermentation at different pH values. Information on the bacterial community structures during acidogenic fermentation is limited. In this study, comparisons of the bacterial communities during the co-substrate fermentation of food wastes and sewage sludge at different pH values were performed using the barcoded Illumina paired-end sequencing method. The results showed that different pH environments harbored a characteristic bacterial community, including sequences related to Lactobacillus, Prevotella, Mitsuokella, Treponema, Clostridium, and Ureibacillus. The most abundant bacterial operational taxonomic units in the different pH environments were those related to carbohydrate-degrading bacteria, which are associated with constituents of co-substrate fermentation. Further analyses showed that during organic matter fermentation, a core microbiota composed of Firmicutes, Proteobacteria, and Bacteroidetes existed. Comparison analyses revealed that the bacterial community during fermentation was significantly affected by the pH, and that the diverse product distribution was related to the shift in bacterial communities.

  12. Fatty acids as a tool to understand microbial diversity and their role in food webs of Mediterranean temporary ponds.

    PubMed

    de Carvalho, Carla C C R; Caramujo, Maria-José

    2014-01-01

    Temporary Mediterranean ponds are complex ecosystems which support a high diversity of organisms that include heterotrophic microorganisms, algae, crustaceans, amphibians and higher plants, and have the potential to supply food and a resting place to migratory birds. The role of heterotrophs at the base of the food web in providing energy to the higher trophic levels was studied in temporary ponds in Central and Southern Portugal. The relative quantification of the hetero and autotrophic biomass at the base of the food web in each pond was derived from the polar fatty acid (PLFA) composition of seston through the application of the matrix factorization program CHEMTAX that used specific PLFA and their relative proportion as markers for e.g., classes of bacteria, algae and fungi. The species composition of the culturable microbial communities was identified through their fatty acid profiles. The biomass in the lower trophic level of some ponds presented an even proportion of auto to heterotrophic organisms whilst either bacteria or algae dominated in others. In a selected subset of ponds, the incorporation of bacterial fatty acids was observed to occur in potentially herbivorous zooplankton crustacean. Zooplankton consumed and incorporated bacterial fatty acids into their body tissues, including into their phospholipids, which indicates that energy of heterotrophic origin contributes to the aquatic food webs of temporary ponds. PMID:24786844

  13. Abscisic acid and CO2 signalling via calcium sensitivity priming in guard cells, new CDPK mutant phenotypes and a method for improved resolution of stomatal stimulus–response analyses

    PubMed Central

    Hubbard, Katharine E.; Siegel, Robert S.; Valerio, Gabriel; Brandt, Benjamin; Schroeder, Julian I.

    2012-01-01

    Background Stomatal guard cells are the regulators of gas exchange between plants and the atmosphere. Ca2+-dependent and Ca2+-independent mechanisms function in these responses. Key stomatal regulation mechanisms, including plasma membrane and vacuolar ion channels have been identified and are regulated by the free cytosolic Ca2+ concentration ([Ca2+]cyt). Scope Here we show that CO2-induced stomatal closing is strongly impaired under conditions that prevent intracellular Ca2+ elevations. Moreover, Ca2+ oscillation-induced stomatal closing is partially impaired in knock-out mutations in several guard cell-expressed Ca2+-dependent protein kinases (CDPKs) here, including the cpk4cpk11 double and cpk10 mutants; however, abscisic acid-regulated stomatal movements remain relatively intact in the cpk4cpk11 and cpk10 mutants. We further discuss diverse studies of Ca2+ signalling in guard cells, discuss apparent peculiarities, and pose novel open questions. The recently proposed Ca2+ sensitivity priming model could account for many of the findings in the field. Recent research shows that the stomatal closing stimuli abscisic acid and CO2 enhance the sensitivity of stomatal closing mechanisms to intracellular Ca2+, which has been termed ‘calcium sensitivity priming’. The genome of the reference plant Arabidopsis thaliana encodes for over 250 Ca2+-sensing proteins, giving rise to the question, how can specificity in Ca2+ responses be achieved? Calcium sensitivity priming could provide a key mechanism contributing to specificity in eukaryotic Ca2+ signal transduction, a topic of central interest in cell signalling research. In this article we further propose an individual stomatal tracking method for improved analyses of stimulus-regulated stomatal movements in Arabidopsis guard cells that reduces noise and increases fidelity in stimulus-regulated stomatal aperture responses ( Box 1). This method is recommended for stomatal response research, in parallel to previously

  14. 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).

  15. Strength and limits using 13C phospholipid fatty acid analysis in soil ecology

    NASA Astrophysics Data System (ADS)

    Watzinger, Andrea

    2016-04-01

    This presentation on microbial phospholipid biomarkers, their isotope analysis and their ability to reveal soil functions summarizes experiences gained by the author for more than 10 years. The amount and composition of phospholipid fatty acids (PLFAs) measured in environmental samples strongly depend on the methodology. To achieve comparable results the extraction, separation and methylation method must be kept constant. PLFAs patterns are sensitive to microbial community shifts even though the taxonomic resolution of PLFAs is low. The possibility to easily link lipid biomarkers with stable isotope techniques is identified as a major advantage when addressing soil functions. Measurement of PLFA isotopic ratios is sensitive and enables detecting isotopic fractionation. The difference between the carbon isotopic ratio of single PLFAs and their substrate (δ13C) can vary between -6 and +11‰. This difference derives from the fractionation during biosynthesis and from substrate inhomogeneity. Consequently, natural abundance studies are restricted to quantifying substrate uptake of the total microbial biomass. In contrast, artificial labelling enables quantifying carbon uptake into single PLFAs, but labelling success depends on homogeneous and undisturbed label application. Current developments in microbial ecology (e.g. 13C and 15N proteomics) and isotope techniques (online monitoring of CO2 isotope ratios) will likely improve soil functional interpretations in the future. 13C PLFA analysis will continue to contribute because it is affordable, sensitive and allows frequent sampling combined with the use of small amounts of 13C label.

  16. 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

  17. 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

  18. 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

    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

    2015-10-01

    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

  19. 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

  20. Environmental changes and the rise and fall of civilizations in the northern Horn of Africa: An approach combining δD analyses of land-plant derived fatty acids with multiple proxies in soil

    NASA Astrophysics Data System (ADS)

    Terwilliger, Valery J.; Eshetu, Zewdu; Disnar, Jean-Robert; Jacob, Jérémy; Paul Adderley, W.; Huang, Yongsong; Alexandre, Marcelo; Fogel, Marilyn L.

    2013-06-01

    The domains of the ancient polities D'MT and Aksum in the Horn of Africa's highlands are a superior natural system for evaluating roles of environmental change on the rise and fall of civilizations. To compare environmental changes of the times of the two polities, we analyzed stable hydrogen isotopic ratios (δD) of land-plant derived fatty acids (n-C26-30) and other proxies from soil sequences spanning the Holocene from the region. Three results suggest that trends in δD values unambiguously reflect changes in rainfall. First, increases in δD coincide with dry periods inferred from studies of eastern African lakes. Second, changes in δD values were parallel among sections during overlapping time intervals. Third, consideration of vegetation history did not alter directions of trends in δD values over time. By unambiguously recording precipitation, the δD values also enhanced interpretations of proxies that are affected by both climate and land clearing. Both D'MT (ca 2750-2350 cal y BP) and the Aksumite (ca 2100-1250 cal y BP) rose during wetter intervals of the drier part of the Holocene (after ca 6000 cal y BP). Analyses of charred matter indicated that fire had been a common agent of land clearing in all sites. The influence of climate on fire varied, however. Prior to the emergence of D'MT, δD values were correlated with C4:C3 plant ratios estimated from δ13C values. There are no C4 trees and precipitation may have been the main influence on canopy openness. After ca 4300 cal y BP, there was no significant relationship between δD and C4:C3 plant ratios suggesting that factors such as fire influenced canopy openness regardless of climate. Furthermore, the impact of land clearance differed between sites and between D'MT and the Aksumite's times. In one site, the interval from 3550 cal y BP to the decline of D'MT had several anomalies that suggested dramatic increases in thermal severity of fire and human impact. Among these were a large contribution of

  1. Detection of infections with hepatitis B virus, hepatitis C virus, and human immunodeficiency virus by analyses of dried blood spots - performance characteristics of the ARCHITECT system and two commercial assays for nucleic acid amplification

    PubMed Central

    2013-01-01

    Background Nowadays, dried blood spots (DBS) are primarily used to obtain diagnostic access to risk collectives such as intravenous drug users, who are prone to infections with hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV). Before DBS analyses can be used in this diagnostic context, however, a comprehensive evaluation of its performance characteristics must be conducted. To the best of our knowledge, the current study presents for the first time such essential data for the Abbott ARCHITECT system, which is currently the worldwide leading platform in this field of infection diagnostics. Methods The investigation comprised 1,762 paired serum/DBS samples and a total of 3,524 determinations with the Abbott ARCHITECT HBsAg, anti-HBc, anti-HBs, anti-HCV and HIV-1-p24-antigen/anti-HIV 1/2 assays as well as with the artus HBV LC PCR and VERSANT HCV RNA qualitative (TMA) tests. Results In the context of DBS testing, a specificity of 100% was recorded for the seven serological and molecular biological assays. The analytical sensitivity of HBsAg, anti-HBc, anti-HBs, anti-HCV, HIV-1-p24-antigen/anti-HIV 1/2, HBV DNA, and HCV RNA detections in DBS eluates was 98.6%, 97.1%, 97.5%, 97.8%, 100%, 93%, and 100%, respectively. Discussion/conclusions The results obtained indicate that it is today possible to reliably detect HBsAg, anti-HBc, anti-HBs, anti-HCV and HIV-1-p24 antigen/anti-HIV 1/2 with state-of-the-art analytical systems such as the Abbott ARCHITECT in DBS eluates even when a comparatively high elution volume of 1,000 μl is used. They also provide evidence for the inherent analytical limits of DBS testing, which primarily concern the anti-HBc/anti-HBs system for individuals with HIV infections and nucleic acid tests with relatively low analytical sensitivity. PMID:23497102

  2. A Column Experiment To Determine Black Shale Degradation And Colonization By Means of δ13C and 14C Analysis Of Phospholipid Fatty Acids And DNA Extraction

    NASA Astrophysics Data System (ADS)

    Seifert, A.; Gleixner, G.

    2008-12-01

    We investigated the degradation of black shale organic matter by microbial communities. We inoculated two columns respectively, with the fungi Schizophyllum commune, the gram-positive bacterium Pseudomonas putida and the gram-negative bacteria Streptomyces griseus and Streptomyces chartreusis. These microorganisms are known to degrade a wide variety of organic macromolecules. Additionally, we had two sets of control columns. To one set the same nutrient solution was added as to the inoculated columns and to the other set only sterile deionised water was supplied. All columns contained 1.5 kg of freshly crushed not autoclaved black shale material with a particle size of 0.63-2 mm. The columns were incubated at 28° C and 60% humidity in the dark. The aim was to investigate, which microorganisms live on black shales and if these microorganisms are able to degrade ancient organic matter. We used compound specific stable isotope measurement techniques and compound specific 14C-dating methods. After 183 days PLFAs were extracted from the columns to investigate the microbial community, furthermore we extracted on one hand total-DNA of column material and on the other hand DNA from pure cultures isolates which grew on Kinks-agar B, Starch-casein-nitrate-agar (SCN) and on complete-yeast-medium-agar (CYM). According to the PLFA analysis bacteria dominated in the columns, whereas in pure cultures more fungi were isolated. A principal component analysis revealed differences between the columns in accordance with the inoculation, but it seems that the inoculated microorganisms were replaced by the natural population. For AMS measurements palmitic acid (C 16:0) was re-isolated from total-PLFA-extract with a preparative fraction collector (PFC). Preliminary results of the study revealed that microorganisms are able to degrade black shale material and that PLFA analysis are useful methods to be combined with analysis of stable isotope and 14C measurements to study microbial

  3. Dose-dependent consumption of farmed Atlantic salmon (Salmo salar) increases plasma phospholipid n-3 fatty acids differentially

    PubMed Central

    Raatz, Susan K.; Rosenberger, Thad A.; Johnson, LuAnn K.; Wolters, William W.; Burr, Gary S; Picklo, Matthew J.

    2013-01-01

    Enhanced omega-3 fatty acid (n-3) intake benefits cardiovascular disease (CVD) risk reduction. Increasing consumption at a population level may be better addressed by diet than through supplementation. However, limited data are available on the effect of the dose response to fish intake on plasma levels of n-3 fatty acids. To compare the effects of different doses of farmed Atlantic salmon on plasma phospholipid fatty acid (PLFA) proportions and CVD risk biomarkers (glucose, insulin, HOMAIR, hsCRP, and IL-6) in healthy subjects we performed a randomized 3-period cross-over designed trial (4 wk treatment, 4-8 wk washout) to compare the effects of twice/wk consumption of farmed Atlantic salmon at doses of 90, 180, and 270 g in 19 apparently healthy men and women with a mean age of aged 40-65 years and a BMI between 25-34.9 kg/m2. All study visits were conducted at the USDA, ARS Grand Forks Human Nutrition Research Center. EPA and total n-3 were increased (p<0.05) by all treatments in a dose response manner, with total n-3 of 8.03 ± 0.26 and 9.21 ± 0.26 % for 180 and 270 g doses, respectively. Linoleic acid did not change in response to treatment while arachidonic acid (P<0.05) and total omega-6 fatty acids (n-6) decreased dose dependently (<0.0001). The addition of farmed Atlantic salmon to the diet twice/wk for 4 wk at portions of 180g and 270g modifies PLFA proportions of n-3 and n-6 in a level associated with decreased risk for CVD. PMID:23351633

  4. Mitogenomic analyses of eutherian relationships.

    PubMed

    Arnason, U; Janke, A

    2002-01-01

    Reasonably correct phylogenies are fundamental to the testing of evolutionary hypotheses. Here, we present phylogenetic findings based on analyses of 67 complete mammalian mitochondrial (mt) genomes. The analyses, irrespective of whether they were performed at the amino acid (aa) level or on nucleotides (nt) of first and second codon positions, placed Erinaceomorpha (hedgehogs and their kin) as the sister group of remaining eutherians. Thus, the analyses separated Erinaceomorpha from other traditional lipotyphlans (e.g., tenrecs, moles, and shrews), making traditional Lipotyphla polyphyletic. Both the aa and nt data sets identified the two order-rich eutherian clades, the Cetferungulata (comprising Pholidota, Carnivora, Perissodactyla, Artiodactyla, and Cetacea) and the African clade (Tenrecomorpha, Macroscelidea, Tubulidentata, Hyracoidea, Proboscidea, and Sirenia). The study corroborated recent findings that have identified a sister-group relationship between Anthropoidea and Dermoptera (flying lemurs), thereby making our own order, Primates, a paraphyletic assembly. Molecular estimates using paleontologically well-established calibration points, placed the origin of most eutherian orders in Cretaceous times, 70-100 million years before present (MYBP). The same estimates place all primate divergences much earlier than traditionally believed. For example, the divergence between Homo and Pan is estimated to have taken place approximately 10 MYBP, a dating consistent with recent findings in primate paleontology.

  5. SNS shielding analyses overview

    SciTech Connect

    Popova, Irina; Gallmeier, Franz; Iverson, Erik B; Lu, Wei; Remec, Igor

    2015-01-01

    This paper gives an overview on on-going shielding analyses for Spallation Neutron Source. Presently, the most of the shielding work is concentrated on the beam lines and instrument enclosures to prepare for commissioning, save operation and adequate radiation background in the future. There is on-going work for the accelerator facility. This includes radiation-protection analyses for radiation monitors placement, designing shielding for additional facilities to test accelerator structures, redesigning some parts of the facility, and designing test facilities to the main accelerator structure for component testing. Neutronics analyses are required as well to support spent structure management, including waste characterisation analyses, choice of proper transport/storage package and shielding enhancement for the package if required.

  6. Unique odd-chain polyenoic phospholipid fatty acids present in chytrid fungi.

    PubMed

    Akinwole, Philips O; Lefevre, Emilie; Powell, Martha J; Findlay, Robert H

    2014-09-01

    Chytrid fungi are ubiquitous components of aquatic and terrestrial ecosystems yet they remain understudied. To investigate the use of phospholipid fatty acids as phenotypic characteristics in taxonomic studies and biomarkers for ecological studies, 18 chytrid fungi isolated from soil to freshwater samples were grown in defined media and their phospholipid fatty acid profile determined. Gas chromatographic/mass spectral analysis indicated the presence of fatty acids typically associated with fungi, such as 16:1(n-7), 16:0, 18:2(n-6), 18:3(n-3) 18:1(n-9), and 18:0, as well as, a number of odd-chain length fatty acids, including two polyunsaturated C-17 fatty acids. Conversion to their 3-pyridylcarbinol ester facilitated GC-MS determination of double-bond positions and these fatty acid were identified as 6,9-17:2 [17:2(n-8)] and 6,9,12-17:3 [17:3(n-5)]. To the best of our knowledge, this is the first report of polyunsaturated C-17 fatty acids isolated from the phospholipids of chytrid fungi. Cluster analysis of PLFA profiles showed sufficient correlation with chytrid phylogeny to warrant inclusion of lipid analysis in species descriptions and the presence of several phospholipid fatty acids of restricted phylogenetic distributions suggests their usefulness as biomarkers for ecological studies. PMID:25119485

  7. 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.

  8. Adaptive response of Rhodococcus opacus PWD4 to salt and phenolic stress on the level of mycolic acids.

    PubMed

    de Carvalho, Carla C C R; Fischer, Martin A; Kirsten, Sandra; Würz, Birgit; Wick, Lukas Y; Heipieper, Hermann J

    2016-12-01

    Mycolata form a group of Gram-positive bacteria with unique cell envelope structures that are known for their high tolerance against antibiotics and both aromatic and aliphatic hydrocarbons. An important part of the unique surface structure of the mycolata is the presence of long chain α-alkyl-β-hydroxy fatty acids, the mycolic acids. In order to investigate the adaptive changes in the mycolic acid composition, we investigated the composition of mycolic acids during the response both to osmotic stress caused by NaCl and to 4-chlorophenol in Rhodococcus opacus PWD4. This bacterium was chosen as it is known to adapt to different kinds of stresses. In addition, it is a potential biocatalyst in bioremediation as well as for biotechnological applications. In the present study, cells of R. opacus PWD4, grown in liquid cultures, responded to toxic concentrations of NaCl by increasing the ratio between mycolic acids and membrane phospholipid fatty acids (MA/PLFA-ratio). Cells reacted to both NaCl and 4-chlorophenol by decreasing both the average chain length and the unsaturation index of their mycolic acids. These changes in mycolic acid composition correlated with increases in cell surface hydrophobicity and saturation of membrane fatty acids, demonstrating the relation between mycolic acid and phospholipid synthesis and their contribution to cell surface properties of R. opacus PWD4. PMID:27620730

  9. Adaptive response of Rhodococcus opacus PWD4 to salt and phenolic stress on the level of mycolic acids.

    PubMed

    de Carvalho, Carla C C R; Fischer, Martin A; Kirsten, Sandra; Würz, Birgit; Wick, Lukas Y; Heipieper, Hermann J

    2016-12-01

    Mycolata form a group of Gram-positive bacteria with unique cell envelope structures that are known for their high tolerance against antibiotics and both aromatic and aliphatic hydrocarbons. An important part of the unique surface structure of the mycolata is the presence of long chain α-alkyl-β-hydroxy fatty acids, the mycolic acids. In order to investigate the adaptive changes in the mycolic acid composition, we investigated the composition of mycolic acids during the response both to osmotic stress caused by NaCl and to 4-chlorophenol in Rhodococcus opacus PWD4. This bacterium was chosen as it is known to adapt to different kinds of stresses. In addition, it is a potential biocatalyst in bioremediation as well as for biotechnological applications. In the present study, cells of R. opacus PWD4, grown in liquid cultures, responded to toxic concentrations of NaCl by increasing the ratio between mycolic acids and membrane phospholipid fatty acids (MA/PLFA-ratio). Cells reacted to both NaCl and 4-chlorophenol by decreasing both the average chain length and the unsaturation index of their mycolic acids. These changes in mycolic acid composition correlated with increases in cell surface hydrophobicity and saturation of membrane fatty acids, demonstrating the relation between mycolic acid and phospholipid synthesis and their contribution to cell surface properties of R. opacus PWD4.

  10. 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…

  11. 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.

  12. Paramagnetic 13C and 15N NMR analyses of the push and pull effects in cytochrome c peroxidase and Coprinus cinereus peroxidase variants: functional roles of highly conserved amino acids around heme.

    PubMed

    Nonaka, Daisuke; Wariishi, Hiroyuki; Welinder, Karen G; Fujii, Hiroshi

    2010-01-12

    Paramagnetic (13)C and (15)N nuclear magnetic resonance (NMR) spectroscopy of heme-bound cyanide ((13)C(15)N) was applied to 11 cytochrome c peroxidase (CcP) and Coprinus cinereus peroxidase (CIP) mutants to investigate contributions to the push and pull effects of conserved amino acids around heme. The (13)C and (15)N NMR data for the distal His and Arg mutants indicated that distal His is the key amino acid residue creating the strong pull effect and that distal Arg assists. The mutation of distal Trp of CcP to Phe, the amino acid at this position in CIP, changed the push and pull effects so they resembled those of CIP, whereas the mutation of distal Phe of CIP to Trp changed this mutant to become CcP-like. The (13)C NMR shifts for the proximal Asp mutants clearly showed that the proximal Asp-His hydrogen bonding strengthens the push effect. However, even in the absence of a hydrogen bond, the push effect of proximal His in peroxidase is significantly stronger than in globins. Comparison of these NMR data with the compound I formation rate constants and crystal structures of these mutants showed that (1) the base catalysis of the distal His is more critical for rapid compound I formation than its acid catalysis, (2) the primary function of the distal Arg is to maintain the distal heme pocket in favor of rapid compound I formation via hydrogen bonding, and (3) the push effect is the major contributor to the differential rates of compound I formation in wild-type peroxidases.

  13. Information Omitted From Analyses.

    PubMed

    2015-08-01

    In the Original Article titled “Higher- Order Genetic and Environmental Structure of Prevalent Forms of Child and Adolescent Psychopathology” published in the February 2011 issue of JAMA Psychiatry (then Archives of General Psychiatry) (2011;68[2]:181-189), there were 2 errors. Although the article stated that the dimensions of psychopathology were measured using parent informants for inattention, hyperactivity-impulsivity, and oppositional defiant disorder, and a combination of parent and youth informants for conduct disorder, major depression, generalized anxiety disorder, separation anxiety disorder, social phobia, specific phobia, agoraphobia, and obsessive-compulsive disorder, all dimensional scores used in the reported analyses were actually based on parent reports of symptoms; youth reports were not used. In addition, whereas the article stated that each symptom dimension was residualized on age, sex, age-squared, and age by sex, the dimensions actually were only residualized on age, sex, and age-squared. All analyses were repeated using parent informants for inattention, hyperactivity-impulsivity, and oppositional defiant disorder, and a combination of parent and youth informants for conduct disorder,major depression, generalized anxiety disorder, separation anxiety disorder, social phobia, specific phobia, agoraphobia, and obsessive-compulsive disorder; these dimensional scores were residualized on age, age-squared, sex, sex by age, and sex by age-squared. The results of the new analyses were qualitatively the same as those reported in the article, with no substantial changes in conclusions. The only notable small difference was that major depression and generalized anxiety disorder dimensions had small but significant loadings on the internalizing factor in addition to their substantial loadings on the general factor in the analyses of both genetic and non-shared covariances in the selected models in the new analyses. Corrections were made to the

  14. 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

  15. Genetic analyses of GII.17 norovirus strains in diarrheal disease outbreaks from December 2014 to March 2015 in Japan reveal a novel polymerase sequence and amino acid substitutions in the capsid region.

    PubMed

    Matsushima, Y; Ishikawa, M; Shimizu, T; Komane, A; Kasuo, S; Shinohara, M; Nagasawa, K; Kimura, H; Ryo, A; Okabe, N; Haga, K; Doan, Y H; Katayama, K; Shimizu, H

    2015-01-01

    A novel GII.P17-GII.17 variant norovirus emerged as a major cause of norovirus outbreaks from December 2014 to March 2015 in Japan. Named Hu/GII/JP/2014/GII.P17-GII.17, this variant has a newly identified GII.P17 type RNA-dependent RNA polymerase, while the capsid sequence displays amino acid substitutions around histo-blood group antigen (HBGA) binding sites. Several variants caused by mutations in the capsid region have previously been observed in the GII.4 genotype. Monitoring the GII.17 variant's geographical spread and evolution is important.

  16. 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

  17. 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.

  18. Does bottle type and acid-washing influence trace element analyses by ICP-MS on water samples? A test covering 62 elements and four bottle types: high density polyethene (HDPE), polypropene (PP), fluorinated ethene propene copolymer (FEP) and perfluoroalkoxy polymer (PFA).

    PubMed

    Reimann, C; Siewers, U; Skarphagen, H; Banks, D

    1999-10-01

    Groundwater samples from 15 boreholes in crystalline bedrock aquifers in South Norway (Oslo area) have been collected in parallel in five different clear plastic bottle types (high density polyethene [HDPE], polypropene [PP, two manufacturers], fluorinated ethene propene copolymer [FEP] and perfluoroalkoxy polymer [PFA]. In the cases of polyethene and polypropene, parallel samples have been collected in factory-new (unwashed) bottles and acid-washed factory-new bottles. Samples have been analysed by ICP-MS techniques for a wide range of inorganic elements down to the ppt (ng/l) range. It was found that acid-washing of factory-new flasks had no clear systematic beneficial effect on analytical result. On the contrary, for the PP-bottles concentrations of Pb and Sn were clearly elevated in the acid-washed bottles. Likewise, for the vast majority of elements, bottle type was of no importance for analytical result. For six elements (Al, Cr, Hf, Hg, Pb and Sn) some systematic differences for one or more bottle types could be tentatively discerned, but in no case was the discrepancy of major cause for concern. The most pronounced effect was for Cr, with clearly elevated concentrations returned from the samples collected in HDPE bottles, regardless of acid-washing or not. For the above six elements, FEP or PFA bottles seemed to be marginally preferable to PP and HDPE. In general, cheap HDPE, factory new, unwashed flasks are suitable for sampling waters for ICP-MS ultra-trace analysis of the elements tested.

  19. LDEF Satellite Radiation Analyses

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

    This report covers work performed by Science Applications International Corporation (SAIC) under contract NAS8-39386 from the NASA Marshall Space Flight Center entitled LDEF Satellite Radiation Analyses. The basic objective of the study was to evaluate the accuracy of present models and computational methods for defining the ionizing radiation environment for spacecraft in Low Earth Orbit (LEO) by making comparisons with radiation measurements made on the Long Duration Exposure Facility (LDEF) satellite, which was recovered after almost six years in space. The emphasis of the work here is on predictions and comparisons with LDEF measurements of induced radioactivity and Linear Energy Transfer (LET) measurements. These model/data comparisons have been used to evaluate the accuracy of current models for predicting the flux and directionality of trapped protons for LEO missions.

  20. 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.

  1. Coiled-Coils at the Edge of Configurational Heterogeneity. Structural Analyses of Parallel and Antiparallel Homotetrameric Coiled-Coils Reveal Configurational Sensitivity to a Single Solvent-Exposed Amino Acid Substitution.†§

    PubMed Central

    Yadav, Maneesh K.; Leman, Luke J.; Price, Daniel J.; Brooks, Charles L.; Stout, C. David; Ghadiri, M. Reza

    2007-01-01

    A detailed understanding of the mechanisms by which particular amino acid sequences can give rise to more than one folded structure, such as for proteins that undergo large conformational changes or misfolding, is a long-standing objective of protein chemistry. Here we describe the crystal structures of a single coiled-coil peptide in distinct parallel and antiparallel tetrameric configurations and further describe the parallel or antiparallel crystal structures of several related peptide sequences; the antiparallel tetrameric assemblies represents the first crystal structures of GCN4-derived peptides exhibiting such a configuration. Intriguingly, substitution of a single solvent-exposed residue enabled the parallel coiled-coil tetramer GCN4-pLI to populate the antiparallel configuration, suggesting that the two configurations are close enough in energy for subtle sequence changes to have important structural consequences. We present a structural analysis of the small changes to helix register and side chain conformations that accommodate the two configurations, and have supplemented these results using solution studies and a molecular dynamics energetic analysis using a replica exchange methodology. Considering the previous examples of structural nonspecificity in coiled-coil peptides, the findings reported here not only emphasize the predisposition of the coiled-coil motif to adopt multiple configurations, but also call attention to the associated risk that observed crytstal structures may not represent the only (or even the major) species present in solution. PMID:16584182

  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. PMID:25234307

  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. 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.

  5. 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

  6. 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. PMID:23565141

  7. Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses.

    PubMed

    Rabbani, M Ashiq; Maruyama, Kyonoshin; Abe, Hiroshi; Khan, M Ayub; Katsura, Koji; Ito, Yusuke; Yoshiwara, Kyoko; Seki, Motoaki; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko

    2003-12-01

    To identify cold-, drought-, high-salinity-, and/or abscisic acid (ABA)-inducible genes in rice (Oryza sativa), we prepared a rice cDNA microarray including about 1700 independent cDNAs derived from cDNA libraries prepared from drought-, cold-, and high-salinity-treated rice plants. We confirmed stress-inducible expression of the candidate genes selected by microarray analysis using RNA gel-blot analysis and finally identified a total of 73 genes as stress inducible including 58 novel unreported genes in rice. Among them, 36, 62, 57, and 43 genes were induced by cold, drought, high salinity, and ABA, respectively. We observed a strong association in the expression of stress-responsive genes and found 15 genes that responded to all four treatments. Venn diagram analysis revealed greater cross talk between signaling pathways for drought, ABA, and high-salinity stresses than between signaling pathways for cold and ABA stresses or cold and high-salinity stresses in rice. The rice genome database search enabled us not only to identify possible known cis-acting elements in the promoter regions of several stress-inducible genes but also to expect the existence of novel cis-acting elements involved in stress-responsive gene expression in rice stress-inducible promoters. Comparative analysis of Arabidopsis and rice showed that among the 73 stress-inducible rice genes, 51 already have been reported in Arabidopsis with similar function or gene name. Transcriptome analysis revealed novel stress-inducible genes, suggesting some differences between Arabidopsis and rice in their response to stress.

  8. 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

  9. 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

  10. 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).

  11. 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.

  12. Feed analyses and their interpretation.

    PubMed

    Hall, Mary Beth

    2014-11-01

    Compositional analysis is central to determining the nutritional value of feedstuffs for use in ration formulation. The utility of the values and how they should be used depends on how representative the feed subsample is, the nutritional relevance and analytical variability of the assays, and whether an analysis is suitable to be applied to a particular feedstuff. Commercial analyses presently available for carbohydrates, protein, and fats have improved nutritionally pertinent description of feed fractions. Factors affecting interpretation of feed analyses and the nutritional relevance and application of currently available analyses are discussed.

  13. [Influences of fertilization and seasonal variation on microbial community in a Chinese mollisol].

    PubMed

    Bai, Zhen; He, Hong-Bo; Xie, Hong-Tu; Zhang, Ming; Zhang, Xu-Dong

    2008-11-01

    Fertilization and seasonal variation play very important roles in affecting microbial structure and activity, as a result, leading to the significant evolution of soil fertility. The effect of manure (MCK) and combined application of chemical fertilizers (NPK) on soil microbial biomass and structure were studied by measuring soil microbial biomass carbon (nitrogen) and phospholipid fatty acid (PLFA) in different microbial communities, with the nil-fertilization (CK) and fallow as controls. Results show the manure application significantly improves the soil nutrient contents and the amounts of Cmic and PLFA of different microbial communities. The amounts of fungal PLFA (8.40 nmol x g(-1)) and Cmic (322.5 mg x kg(-1)) and Nmic (57.9 mg x kg(-1)) are significantly higher than those of CK (5.4 nmo x g(-1), 152.6 mg x kg(-1), 32.1 mg x kg(-1), respectively) or NPK (3.5 nmol x g(-1), 144.3 mg x kg(-1), 30.7 mg x kg(-1), respectively). And the contents of Cmic, Nmic and PLFA of different microbial groups in NPK are lower than those in CK. Correlation analyses show the soil nutrient contents are significantly positively correlated with Cmic, different microbial PLFA contents and G(-)/total bacteria ratios, while negatively correlated with C+/G(-) bacteria ratio (p < 0.05). The principle component analysis of PLFA shows the microbial structures in different treatments and sampling dates are significantly different. Seasonal changes are also found to cause great fluctuations in soil basic properties, and microbial community structure in arable soils and fallow respectively cluster strictly together by sampling dates. The amount of Cmic is highest on April 11 (295.6 mg x kg(-1)), while Nmic (49.3 mg x kg(-1)) and PLFA contents are highest in summer (July-August); the lowest amounts of Cmic (184.2 mg x kg(-1)), Nmic (30.63 mg x kg(-1)) and PLFA exist on May 31. Fertilization and seasonal variations significantly affect soil fertility, microbial structure and activity. PMID

  14. 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...

  15. Mitogenomic analyses of caniform relationships.

    PubMed

    Arnason, Ulfur; Gullberg, Anette; Janke, Axel; Kullberg, Morgan

    2007-12-01

    Extant members of the order Carnivora split into two basal groups, Caniformia (dog-like carnivorans) and Feliformia (cat-like carnivorans). In this study we address phylogenetic relationships within Caniformia applying various methodological approaches to analyses of complete mitochondrial genomes. Pinnipeds are currently well represented with respect to mitogenomic data and here we add seven mt genomes to the non-pinniped caniform collection. The analyses identified a basal caniform divergence between Cynoidea and Arctoidea. Arctoidea split into three primary groups, Ursidae (including the giant panda), Pinnipedia, and a branch, Musteloidea, which encompassed Ailuridae (red panda), Mephitidae (skunks), Procyonidae (raccoons) and Mustelidae (mustelids). The analyses favored a basal arctoid split between Ursidae and a branch containing Pinnipedia and Musteloidea. Within the Musteloidea there was a preference for a basal divergence between Ailuridae and remaining families. Among the latter, the analyses identified a sister group relationship between Mephitidae and a branch that contained Procyonidae and Mustelidae. The mitogenomic distance between the wolf and the dog was shown to be at the same level as that of basal human divergences. The wolf and the dog are commonly considered as separate species in the popular literature. The mitogenomic result is inconsistent with that understanding at the same time as it provides insight into the time of the domestication of the dog relative to basal human mitogenomic divergences.

  16. Introduction to Project Materials Analyses

    ERIC Educational Resources Information Center

    Haley, Frances

    1972-01-01

    The author introduces twenty-six analyses, describes the method of analysis, includes a selection policy for this issue, and lists ten analysts. Each project, analyzed by the combined criteria of the CMAS and the NCSS Guidelines, is examined for background information, product characteristics, rationale and objectives, content, methodology,…

  17. 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…

  18. 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.

  19. 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 ...

  20. 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 ...

  1. Microbial transformations of isocupressic acid.

    PubMed

    Lin, S J; Rosazza, J P

    1998-07-01

    Microbial transformations of the labdane-diterpene isocupressic acid (1) with different microorganisms yielded several oxygenated metabolites that were isolated and characterized by MS and NMR spectroscopic analyses. Nocardia aurantia (ATCC 12674) catalyzed the cleavage of the 13,14-double bond to yield a new nor-labdane metabolite, 2. Cunninghamella elegans (-) (NRRL 1393) gave 7beta-hydroxyisocupressic acid (3) and labda-7,13(E)-diene-6beta,15, 17-triol-19-oic acid (4), and Mucor mucedo (ATCC 20094) gave 2alpha-hydroxyisocupressic acid (5) and labda-8(17),14-diene-2alpha, 13-diol-19-oic acid (6).

  2. Amino acids

    MedlinePlus

    ... amino acids are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan , and valine. Nonessential amino acids "Nonessential" means that our bodies produce an amino ...

  3. 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.

  4. Biological aerosol warner and analyser

    NASA Astrophysics Data System (ADS)

    Schlemmer, Harry; Kürbitz, Gunther; Miethe, Peter; Spieweck, Michael

    2006-05-01

    The development of an integrated sensor device BiSAM (Biological Sampling and Analysing Module) is presented which is designed for rapid detection of aerosol or dust particles potentially loaded with biological warfare agents. All functional steps from aerosol collection via immuno analysis to display of results are fully automated. The core component of the sensor device is an ultra sensitive rapid analyser PBA (Portable Benchtop Analyser) based on a 3 dimensional immuno filtration column of large internal area, Poly HRP marker technology and kinetic optical detection. High sensitivity despite of the short measuring time, high chemical stability of the micro column and robustness against interferents make the PBA an ideal tool for fielded sensor devices. It is especially favourable to combine the PBA with a bio collector because virtually no sample preparation is necessary. Overall, the BiSAM device is capable to detect and identify living micro organisms (bacteria, spores, viruses) as well as toxins in a measuring cycle of typically half an hour duration. In each batch up to 12 different tests can be run in parallel together with positive and negative controls to keep the false alarm rate low.

  5. 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)

  6. [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.

  7. Acid rain

    SciTech Connect

    Not Available

    1985-01-01

    This report has four parts: they discuss acid rain in relation to acid soils, agriculture, forests, and aquatic ecosystems. Among findings: modern sources of acid deposition from the atmosphere for all the acid soils in the world, nor even chiefly responsible for those of northern U.S. Agriculture has its problems, but acid precipitation is probably not one of them. More research is needed to determine to what extent acid precipitation is responsible for forest declines and for smaller detrimental effects on forest growth where no damage to the foliage is evident. Many lakes and streams are extremely sensitive to added acids.

  8. 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

  9. 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

  10. 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).

  11. [Network analyses in neuroimaging studies].

    PubMed

    Hirano, Shigeki; Yamada, Makiko

    2013-06-01

    Neurons are anatomically and physiologically connected to each other, and these connections are involved in various neuronal functions. Multiple important neural networks involved in neurodegenerative diseases can be detected using network analyses in functional neuroimaging. First, the basic methods and theories of voxel-based network analyses, such as principal component analysis, independent component analysis, and seed-based analysis, are described. Disease- and symptom-specific brain networks have been identified using glucose metabolism images in patients with Parkinson's disease. These networks enable us to objectively evaluate individual patients and serve as diagnostic tools as well as biomarkers for therapeutic interventions. Many functional MRI studies have shown that "hub" brain regions, such as the posterior cingulate cortex and medial prefrontal cortex, are deactivated by externally driven cognitive tasks; such brain regions form the "default mode network." Recent studies have shown that this default mode network is disrupted from the preclinical phase of Alzheimer's disease and is associated with amyloid deposition in the brain. Some recent studies have shown that the default mode network is also impaired in Parkinson's disease, whereas other studies have shown inconsistent results. These incongruent results could be due to the heterogeneous pharmacological status, differences in mesocortical dopaminergic impairment status, and concomitant amyloid deposition. Future neuroimaging network analysis studies will reveal novel and interesting findings that will uncover the pathomechanisms of neurological and psychiatric disorders. PMID:23735528

  12. Perturbation analyses of intermolecular interactions.

    PubMed

    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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. Serum bile acids in patients with hyperlipidaemia.

    PubMed Central

    Pennington, C R; Ross, P E; Bateson, M C; Bouchier, I A

    1978-01-01

    Individual serum bile acids were analysed by an improved gas liquid chromatography method in 12 patients with primary hyperlipidaemia. Total serum bile acid concentrations were raised in 10 subjects. Ursodeoxycholic acid was found in all 12 patients. It was present in significantly greater concentrations, accounted for a greater proportion of the total serum bile acids, and occurred more frequently than in patients with various forms of hepatobiliary disease. Patients with hyperlipidaemia had proportionately less deoxycholic acid than controls but more than patients with liver disease. There was proportionately less chenodeoxycholic acid in patients with hypercholesterolaemia, in whom the primary bile acid ratio was raised. PMID:627619

  18. 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.

  19. 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.

  20. 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 ...

  1. 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 ...

  2. 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 ...

  3. 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 ...

  4. 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 ...

  5. 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.

  6. Imprecise probabilities in engineering analyses

    NASA Astrophysics Data System (ADS)

    Beer, Michael; Ferson, Scott; Kreinovich, Vladik

    2013-05-01

    Probabilistic uncertainty and imprecision in structural parameters and in environmental conditions and loads are challenging phenomena in engineering analyses. They require appropriate mathematical modeling and quantification to obtain realistic results when predicting the behavior and reliability of engineering structures and systems. But the modeling and quantification is complicated by the characteristics of the available information, which involves, for example, sparse data, poor measurements and subjective information. This raises the question whether the available information is sufficient for probabilistic modeling or rather suggests a set-theoretical approach. The framework of imprecise probabilities provides a mathematical basis to deal with these problems which involve both probabilistic and non-probabilistic information. A common feature of the various concepts of imprecise probabilities is the consideration of an entire set of probabilistic models in one analysis. The theoretical differences between the concepts mainly concern the mathematical description of the set of probabilistic models and the connection to the probabilistic models involved. This paper provides an overview on developments which involve imprecise probabilities for the solution of engineering problems. Evidence theory, probability bounds analysis with p-boxes, and fuzzy probabilities are discussed with emphasis on their key features and on their relationships to one another. This paper was especially prepared for this special issue and reflects, in various ways, the thinking and presentation preferences of the authors, who are also the guest editors for this special issue.

  7. Wide area microprobe analyser (WAMPA)

    NASA Astrophysics Data System (ADS)

    Rogoyski, A.; Skidmore, B.; Maheswaran, V.; Wright, I.; Zarnecki, J.; Pillinger, C.

    2006-10-01

    Wide area microprobe analyser (WAMPA) represents a new scientific instrument concept for planetary exploration. WAMPA builds on recently published research such as sensor webs and distributed microsensors [The sensor web: a new instrument concept, SPIE Symposium on Integrated Optics, 20 26 January 2001, San Jose, CA; Design considerations for distributed microsensor systems, Proceedings of the IEEE 1999 Custom Integrated Circuits Conference (CICC ’99), May 1999, pp. 279 286] but adds new sensor and localisation concepts. WAMPA is driven by the recurrent theme in spacecraft and sensor design to achieve smaller, lighter and lower cost systems. The essential characteristics of the WAMPA design that differentiates it from other space science instruments are that WAMPA is both a wide area instrument, consisting of a distributed set of sensors, and that each probe is designed to use little, if any, power. It achieves the former by being utilised in large numbers (>10), requiring that the individual probes be low mass (<100g) and low volume (<10cm). It is envisaged that the probes would be dispersed by landers or rovers as mission support instruments rather than primary science instruments and would be used in hostile environments and rugged terrains where the lander/rover could not be risked (see Fig. 1).

  8. 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

  9. 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. PMID:26987150

  10. 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.

  11. Phospholipid and Respiratory Quinone Analyses From Extreme Environments

    NASA Astrophysics Data System (ADS)

    Pfiffner, S. M.

    2008-12-01

    Extreme environments on Earth have been chosen as surrogate sites to test methods and strategies for the deployment of space craft in the search for extraterrestrial life. Surrogate sites for many of the NASA astrobiology institutes include the South African gold mines, Canadian subpermafrost, Atacama Desert, and acid rock drainage. Soils, sediments, rock cores, fracture waters, biofilms, and service and drill waters represent the types of samples collected from these sites. These samples were analyzed by gas chromatography mass spectrometry for phospholipid fatty acid methyl esters and by high performance liquid chromatography atmospheric pressure chemical ionization tandem mass spectrometry for respiratory quinones. Phospholipid analyses provided estimates of biomass, community composition, and compositional changes related to nutritional limitations or exposure to toxic conditions. Similar to phospholipid analyses, respiratory quinone analyses afforded identification of certain types of microorganisms in the community based on respiration and offered clues to in situ redox conditions. Depending on the number of samples analyzed, selected multivariate statistical methods were applied to relate membrane lipid results with site biogeochemical parameters. Successful detection of life signatures and refinement of methodologies at surrogate sites on Earth will be critical for the recognition of extraterrestrial life. At this time, membrane lipid analyses provide useful information not easily obtained by other molecular techniques.

  12. 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).

  13. The effect of triclosan on microbial community structure in three soils.

    PubMed

    Butler, E; Whelan, M J; Ritz, K; Sakrabani, R; van Egmond, R

    2012-09-01

    The application of sewage sludge to land can expose soils to a range of associated chemical toxicants. In this paper we explore the effects of the broad spectrum anti-microbial compound triclosan on the phenotypic composition of the microbial communities of three soils of contrasting texture (loamy sand, sandy loam and clay) using phospholipid fatty-acid (PLFA) analysis. Each soil type was dosed and subsequently re-dosed 6 weeks later with triclosan at five nominal concentrations in microcosms (10, 100, 500, 1000 mg kg(-1) and a zero-dose control). PLFA profiles were analysed using multivariate statistics focussing on changes in the soil phenotypic community structure. Additionally, ratios of fungal:bacterial PLFA indicators and cyclo:mono-unsaturated PLFAs (a common stress indicator) were calculated. It was hypothesised that triclosan addition would alter the community structure in each soil with a particular effect on the fungal:bacterial ratio, since bacteria are likely to be more susceptible to triclosan than fungi. It was also hypothesised that the PLFA response to re-dosing would be suppressed due to acclimation. Although the microbial community structure changed over the course of the experiment, the response was complex. Soil type and time emerged as the most important explanatory factors. Principal component analysis was used to detect phenotypic responses to different doses of triclosan in each soil. As expected, there was a significant increase in the fungal:bacterial ratio with triclosan dose especially in treatments with the highest nominal concentrations. Furthermore, the PLFA response to re-dosing was negligible in all soils confirming the acclimation hypothesis.

  14. NOx analyser interefence from alkenes

    NASA Astrophysics Data System (ADS)

    Bloss, W. J.; Alam, M. S.; Lee, J. D.; Vazquez, M.; Munoz, A.; Rodenas, M.

    2012-04-01

    Nitrogen oxides (NO and NO2, collectively NOx) are critical intermediates in atmospheric chemistry. NOx abundance controls the levels of the primary atmospheric oxidants OH, NO3 and O3, and regulates the ozone production which results from the degradation of volatile organic compounds. NOx are also atmospheric pollutants in their own right, and NO2 is commonly included in air quality objectives and regulations. In addition to their role in controlling ozone formation, NOx levels affect the production of other pollutants such as the lachrymator PAN, and the nitrate component of secondary aerosol particles. Consequently, accurate measurement of nitrogen oxides in the atmosphere is of major importance for understanding our atmosphere. The most widely employed approach for the measurement of NOx is chemiluminescent detection of NO2* from the NO + O3 reaction, combined with NO2 reduction by either a heated catalyst or photoconvertor. The reaction between alkenes and ozone is also chemiluminescent; therefore alkenes may contribute to the measured NOx signal, depending upon the instrumental background subtraction cycle employed. This interference has been noted previously, and indeed the effect has been used to measure both alkenes and ozone in the atmosphere. Here we report the results of a systematic investigation of the response of a selection of NOx analysers, ranging from systems used for routine air quality monitoring to atmospheric research instrumentation, to a series of alkenes ranging from ethene to the biogenic monoterpenes, as a function of conditions (co-reactants, humidity). Experiments were performed in the European Photoreactor (EUPHORE) to ensure common calibration, a common sample for the monitors, and to unequivocally confirm the alkene (via FTIR) and NO2 (via DOAS) levels present. The instrument responses ranged from negligible levels up to 10 % depending upon the alkene present and conditions used. Such interferences may be of substantial importance

  15. Ergonomic analyses of downhill skiing.

    PubMed

    Clarys, J P; Publie, J; Zinzen, E

    1994-06-01

    The purpose of this study was to provide electromyographic feedback for (1) pedagogical advice in motor learning, (2) the ergonomics of materials choice and (3) competition. For these purposes: (1) EMG data were collected for the Stem Christie, the Stem Turn and the Parallel Christie (three basic ski initiation drills) and verified for the complexity of patterns; (2) integrated EMG (iEMG) and linear envelopes (LEs) were analysed from standardized positions, motions and slopes using compact, soft and competition skis; (3) in a simulated 'parallel special slalom', the muscular activity pattern and intensity of excavated and flat snow conditions were compared. The EMG data from the three studies were collected on location in the French Alps (Tignes). The analog raw EMG was recorded on the slopes with a portable seven-channel FM recorder (TEAC MR30) and with pre-amplified bipolar surface electrodes supplied with a precision instrumentation amplifier (AD 524, Analog Devices, Norwood, USA). The raw signal was full-wave rectified and enveloped using a moving average principle. This linear envelope was normalized according to the highest peak amplitude procedure per subject and was integrated in order to obtain a reference of muscular intensity. In the three studies and for all subjects (elite skiers: n = 25 in studies 1 and 2, n = 6 in study 3), we found a high level of co-contractions in the lower limb extensors and flexors, especially during the extension phase of the ski movement. The Stem Christie and the Parallel Christie showed higher levels of rhythmic movement (92 and 84%, respectively).(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8064970

  16. ITER Safety Analyses with ISAS

    NASA Astrophysics Data System (ADS)

    Gulden, W.; Nisan, S.; Porfiri, M.-T.; Toumi, I.; de Gramont, T. Boubée

    1997-06-01

    Detailed analyses of accident sequences for the International Thermonuclear Experimental Reactor (ITER), from an initiating event to the environmental release of activity, have involved in the past the use of different types of computer codes in a sequential manner. Since these codes were developed at different time scales in different countries, there is no common computing structure to enable automatic data transfer from one code to the other, and no possibility exists to model or to quantify the effect of coupled physical phenomena. To solve this problem, the Integrated Safety Analysis System of codes (ISAS) is being developed, which allows users to integrate existing computer codes in a coherent manner. This approach is based on the utilization of a command language (GIBIANE) acting as a “glue” to integrate the various codes as modules of a common environment. The present version of ISAS allows comprehensive (coupled) calculations of a chain of codes such as ATHENA (thermal-hydraulic analysis of transients and accidents), INTRA (analysis of in-vessel chemical reactions, pressure built-up, and distribution of reaction products inside the vacuum vessel and adjacent rooms), and NAUA (transport of radiological species within buildings and to the environment). In the near future, the integration of S AFALY (simultaneous analysis of plasma dynamics and thermal behavior of in-vessel components) is also foreseen. The paper briefly describes the essential features of ISAS development and the associated software architecture. It gives first results of a typical ITER accident sequence, a loss of coolant accident (LOCA) in the divertor cooling loop inside the vacuum vessel, amply demonstrating ISAS capabilities.

  17. 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...

  18. 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.

  19. 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

  20. 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

  1. 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

  2. Aspartic acid

    MedlinePlus

    ... Hormone production and release Normal nervous system function Plant sources of aspartic acid include: Legumes such as soybeans, garbanzo beans, and lentils Peanuts, almonds, walnuts, and flaxseeds Animal ...

  3. 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..., TRACKAGE RIGHTS, AND LEASE PROCEDURES General Acquisition Procedures § 1180.7 Market analyses. (a) For major and significant transactions, applicants shall submit impact analyses (exhibit 12) describing...

  4. 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..., TRACKAGE RIGHTS, AND LEASE PROCEDURES General Acquisition Procedures § 1180.7 Market analyses. (a) For major and significant transactions, applicants shall submit impact analyses (exhibit 12) describing...

  5. 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...

  6. 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

  7. 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.

  8. Usnic acid.

    PubMed

    Ingólfsdóttir, K

    2002-12-01

    Since its first isolation in 1844, usnic acid [2,6-diacetyl-7,9-dihydroxy-8,9b-dimethyl-1,3(2H,9bH)-dibenzo-furandione] has become the most extensively studied lichen metabolite and one of the few that is commercially available. Usnic acid is uniquely found in lichens, and is especially abundant in genera such as Alectoria, Cladonia, Usnea, Lecanora, Ramalina and Evernia. Many lichens and extracts containing usnic acid have been utilized for medicinal, perfumery, cosmetic as well as ecological applications. Usnic acid as a pure substance has been formulated in creams, toothpaste, mouthwash, deodorants and sunscreen products, in some cases as an active principle, in others as a preservative. In addition to antimicrobial activity against human and plant pathogens, usnic acid has been shown to exhibit antiviral, antiprotozoal, antiproliferative, anti-inflammatory and analgesic activity. Ecological effects, such as antigrowth, antiherbivore and anti-insect properties, have also been demonstrated. A difference in biological activity has in some cases been observed between the two enantiomeric forms of usnic acid. Recently health food supplements containing usnic acid have been promoted for use in weight reduction, with little scientific support. The emphasis of the current review is on the chemistry and biological activity of usnic acid and its derivatives in addition to rational and ecologically acceptable methods for provision of this natural compound on a large scale.

  9. 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.

  10. Acid rain

    SciTech Connect

    White, J.C. )

    1988-01-01

    This book presents the proceedings of the third annual conference sponsored by the Acid Rain Information Clearinghouse (ARIC). Topics covered include: Legal aspects of the source-receptor relationship: an energy perspective; Scientific uncertainty, agency inaction, and the courts; and Acid rain: the emerging legal framework.

  11. How Acidic Is Carbonic Acid?

    PubMed

    Pines, Dina; Ditkovich, Julia; Mukra, Tzach; Miller, Yifat; Kiefer, Philip M; Daschakraborty, Snehasis; Hynes, James T; Pines, Ehud

    2016-03-10

    Carbonic, lactic, and pyruvic acids have been generated in aqueous solution by the transient protonation of their corresponding conjugate bases by a tailor-made photoacid, the 6-hydroxy-1-sulfonate pyrene sodium salt molecule. A particular goal is to establish the pK(a) of carbonic acid H2CO3. The on-contact proton transfer (PT) reaction rate from the optically excited photoacid to the carboxylic bases was derived, with unprecedented precision, from time-correlated single-photon-counting measurements of the fluorescence lifetime of the photoacid in the presence of the proton acceptors. The time-dependent diffusion-assisted PT rate was analyzed using the Szabo-Collins-Kimball equation with a radiation boundary condition. The on-contact PT rates were found to follow the acidity order of the carboxylic acids: the stronger was the acid, the slower was the PT reaction to its conjugate base. The pK(a) of carbonic acid was found to be 3.49 ± 0.05 using both the Marcus and Kiefer-Hynes free energy correlations. This establishes H2CO3 as being 0.37 pK(a) units stronger and about 1 pK(a) unit weaker, respectively, than the physiologically important lactic and pyruvic acids. The considerable acid strength of intact carbonic acid indicates that it is an important protonation agent under physiological conditions. PMID:26862781

  12. 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.

  13. 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.

  14. Acid rain

    SciTech Connect

    Bess, F.D.

    1980-01-01

    The acid rain problem in the northeastern U.S. has been growing in severity and geographical areas affected. Acid rain has damaged, or will result in damage to visibility, physical structures and materials, aquatic life, timber, crops, and soils. The principal causes of acid rain in the northeastern U.S. are sulfur oxide and nitrogen oxide emissions from large power plants and smelters in the Ohio River Valley. Immediate corrective action and appropriate research are needed to reduce acid precipitation. Short-term programs that will define the rate of environmental deterioration, remaining environmental capacity to resist sudden deterioration, mechanisms of acid rain formation, and costs of various control options must be developed. (3 maps, 13 references, 1 table)

  15. 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. PMID:24099657

  16. 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)

  17. miRNA Expression Analyses in Prostate Cancer Clinical Tissues

    PubMed Central

    Bucay, Nathan; Shahryari, Varahram; Majid, Shahana; Yamamura, Soichiro; Mitsui, Yozo; Tabatabai, Z. Laura; Greene, Kirsten; Deng, Guoren; Dahiya, Rajvir; Tanaka, Yuichiro; Saini, Sharanjot

    2015-01-01

    A critical challenge in prostate cancer (PCa) clinical management is posed by the inadequacy of currently used biomarkers for disease screening, diagnosis, prognosis and treatment. In recent years, microRNAs (miRNAs) have emerged as promising alternate biomarkers for prostate cancer diagnosis and prognosis. However, the development of miRNAs as effective biomarkers for prostate cancer heavily relies on their accurate detection in clinical tissues. miRNA analyses in prostate cancer clinical specimens is often challenging owing to tumor heterogeneity, sampling errors, stromal contamination etc. The goal of this article is to describe a simplified workflow for miRNA analyses in archived FFPE or fresh frozen prostate cancer clinical specimens using a combination of quantitative real-time PCR (RT-PCR) and in situ hybridization (ISH). Within this workflow, we optimize the existing methodologies for miRNA extraction from FFPE and frozen prostate tissues and expression analyses by Taqman-probe based miRNA RT-PCR. In addition, we describe an optimized method for ISH analyses formiRNA detection in prostate tissues using locked nucleic acid (LNA)- based probes. Our optimized miRNA ISH protocol can be applied to prostate cancer tissue slides or prostate cancer tissue microarrays (TMA). PMID:26382040

  18. miRNA Expression Analyses in Prostate Cancer Clinical Tissues.

    PubMed

    Bucay, Nathan; Shahryari, Varahram; Majid, Shahana; Yamamura, Soichiro; Mitsui, Yozo; Tabatabai, Z Laura; Greene, Kirsten; Deng, Guoren; Dahiya, Rajvir; Tanaka, Yuichiro; Saini, Sharanjot

    2015-01-01

    A critical challenge in prostate cancer (PCa) clinical management is posed by the inadequacy of currently used biomarkers for disease screening, diagnosis, prognosis and treatment. In recent years, microRNAs (miRNAs) have emerged as promising alternate biomarkers for prostate cancer diagnosis and prognosis. However, the development of miRNAs as effective biomarkers for prostate cancer heavily relies on their accurate detection in clinical tissues. miRNA analyses in prostate cancer clinical specimens is often challenging owing to tumor heterogeneity, sampling errors, stromal contamination etc. The goal of this article is to describe a simplified workflow for miRNA analyses in archived FFPE or fresh frozen prostate cancer clinical specimens using a combination of quantitative real-time PCR (RT-PCR) and in situ hybridization (ISH). Within this workflow, we optimize the existing methodologies for miRNA extraction from FFPE and frozen prostate tissues and expression analyses by Taqman-probe based miRNA RT-PCR. In addition, we describe an optimized method for ISH analyses formiRNA detection in prostate tissues using locked nucleic acid (LNA)- based probes. Our optimized miRNA ISH protocol can be applied to prostate cancer tissue slides or prostate cancer tissue microarrays (TMA). PMID:26382040

  19. miRNA Expression Analyses in Prostate Cancer Clinical Tissues.

    PubMed

    Bucay, Nathan; Shahryari, Varahram; Majid, Shahana; Yamamura, Soichiro; Mitsui, Yozo; Tabatabai, Z Laura; Greene, Kirsten; Deng, Guoren; Dahiya, Rajvir; Tanaka, Yuichiro; Saini, Sharanjot

    2015-09-08

    A critical challenge in prostate cancer (PCa) clinical management is posed by the inadequacy of currently used biomarkers for disease screening, diagnosis, prognosis and treatment. In recent years, microRNAs (miRNAs) have emerged as promising alternate biomarkers for prostate cancer diagnosis and prognosis. However, the development of miRNAs as effective biomarkers for prostate cancer heavily relies on their accurate detection in clinical tissues. miRNA analyses in prostate cancer clinical specimens is often challenging owing to tumor heterogeneity, sampling errors, stromal contamination etc. The goal of this article is to describe a simplified workflow for miRNA analyses in archived FFPE or fresh frozen prostate cancer clinical specimens using a combination of quantitative real-time PCR (RT-PCR) and in situ hybridization (ISH). Within this workflow, we optimize the existing methodologies for miRNA extraction from FFPE and frozen prostate tissues and expression analyses by Taqman-probe based miRNA RT-PCR. In addition, we describe an optimized method for ISH analyses formiRNA detection in prostate tissues using locked nucleic acid (LNA)- based probes. Our optimized miRNA ISH protocol can be applied to prostate cancer tissue slides or prostate cancer tissue microarrays (TMA).

  20. 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.

  1. 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.

  2. 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.

  3. Organic analyses of the Murchison meteorite

    NASA Astrophysics Data System (ADS)

    Cooper, George

    Many compounds yielding clues to the organic chemistry and molecular composition of the early solar system have been identified in the Murchison meteorite. Among these are amino acid precursors: carboxy lactams, lactams, N-acetyl amino acids, and amino acid hydantoins (5-substituted hydantoins). Also found were precursors of acids: dicarboxylic acid mono amides, carboxylic acid amides, and cyclic imides. Precursors of hydroxy acids, hydroxy amides, are also numerous. Organic phosphorus compounds are reported. The corresponding organic sulfur compounds, sulfite, and water soluble and insoluble phosphate are also present. Laboratory experiments have indicated that unusual cyanate chemistry was possibly responsible for the formation of at least some of the amino and carboxylic acid precursors. A plausible mode of formation of the organic phosphorus and sulfur compounds, alkyl phosphonic and alkyl sulfonic acids, respectively, suggests a direct link between identified interstellar molecules and aqueous chemistry on the meteorite parent body. The compounds were extracted under gentle conditions to avoid, as much as possible, decomposition during extraction. The procedure included extraction of a powdered sample with room temperature water, cation and anion exchange chromatography, derivatization with the reagent N-methyl- N-(tert-butyl dimethyl silyl) trifluoro acetamide (MTBSTFA), and analysis by gas chromatography-mass spectrometry (GCMS) and high performance liquid chromatography (HPLC).

  4. 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.

  5. 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. PMID:24488523

  6. Tranexamic Acid

    MedlinePlus

    ... is used to treat heavy bleeding during the menstrual cycle (monthly periods) in women. Tranexamic acid is in ... tablets for more than 5 days in a menstrual cycle or take more than 6 tablets in a ...

  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 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)

  9. 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.).

  10. Vibrational Spectra of γ-Aminobutyric Acid

    NASA Astrophysics Data System (ADS)

    Suresh, D. M.; Sajan, D.; Laladas, K. P.; Joe, I. Hubert; Jayakumar, V. S.

    2008-11-01

    The NIR-FT Raman, FT-IR spectral analysis of γ-Aminobutyric acid (GABA) a simple amino acid is carried out by density functional computations. The vibrational spectra confirm the existence of NH3+ in GABA. Hydroxyl groups H-bonded to the different extents are analysed, supported by computed results.

  11. 49 CFR 1180.7 - Market analyses.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., an analysis of traffic flows indicating patterns of geographic competition or product competition... 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)...

  12. 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.

  13. 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...

  14. 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...

  15. 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...

  16. 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

  17. Transcriptional Analyses of Mandarins Seriously Infected by 'Candidatus Liberibacter asiaticus'.

    PubMed

    Xu, Meirong; Li, Ya; Zheng, Zheng; Dai, Zehan; Tao, Yang; Deng, Xiaoling

    2015-01-01

    A range of leaf symptoms, including blotchy mottle, yellowing, and small, upright leaves with a variety of chlorotic patterns resembling those induced by zinc deficiencies, are associated with huanglongbing (HLB, yellow shoot disease), a worldwide destructive citrus disease. HLB is presumably caused by the phloem-limited fastidious prokaryotic α-proteobacterium 'Candidatus Liberibacter spp.' Previous studies focused on the proteome and transcriptome analyses of citrus 5 to 35 weeks after 'Ca. L. spp.' inoculation. In this study, gene expression profiles were analyzed from mandarin Citrus reticulate Blanco cv. jiaogan leaves after a 2 year infection with 'Ca. L. asiaticus'. The Affymetrix microarray analysis explored 2,017 differentially expressed genes. Of the 1,364 genes had known functions, 938 (46.5%) were up-regulated. Genes related to photosynthesis, carbohydrate metabolic, and structure were mostly down-regulated, with rates of 92.7%, 61.0%, and 80.2%, respectively. Genes associated with oxidation-reduction and transport were mostly up-regulated with the rates of 75.0% and 64.6%, respectively. Our data analyses implied that the infection of 'Ca. L. asiaticus' could alter hormone crosstalk, inducing the jasmine acid pathway and depressing the ethylene and salicylic acid pathways in the citrus host. This study provides an enhanced insight into the host response of citrus to 'Ca. L. asiaticus' infection at a two-years infection stage. PMID:26196297

  18. 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.

  19. The identification of chlorinated acetones in analyses of aged triacetone triperoxide (TATP).

    PubMed

    Fitzgerald, Mark; Bilusich, Daniel

    2012-09-01

    The organic peroxide explosive triacetone triperoxide (TATP) is regularly encountered by law enforcement agents in various stages of its production, storage, or usage. In a previous study, it has been demonstrated that isolated, rigorously purified, TATP may degrade to form a series of chlorinated acetones when directly treated with excess concentrated hydrochloric acid. The current study extends this work to examine whether this phenomenon may be measured during the more feasible scenario of aging of rudimentarily purified TATP contaminated with trace reaction mixture. It was demonstrated that solid-phase microextraction gas chromatography/mass spectrometry analyses of aged TATP that was synthesized utilizing hydrochloric acid catalyst may identify the presence of the degradation products chloroacetone and 1,1-dichloroacetone. Upon aging of TATP synthesized utilizing either sulfuric or nitric acid catalyst, no acid specific degradation products could be identified. These findings may be exploited by forensic chemists in the analyses of TATP samples. PMID:22881036

  20. 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

  1. Functional analyses and treatment of precursor behavior.

    PubMed

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

    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 problem behavior (precursor behavior) and evaluated treatments based on the outcomes of the functional analyses of precursor behavior. Responding for all participants was differentiated during the functional analyses, and individualized treatments eliminated precursor behavior. These results suggest that functional analysis of precursor behavior may offer an alternative, indirect method to assess the operant function of severe problem behavior. PMID:18468282

  2. Functional Analyses and Treatment of Precursor Behavior

    PubMed Central

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

    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 problem behavior (precursor behavior) and evaluated treatments based on the outcomes of the functional analyses of precursor behavior. Responding for all participants was differentiated during the functional analyses, and individualized treatments eliminated precursor behavior. These results suggest that functional analysis of precursor behavior may offer an alternative, indirect method to assess the operant function of severe problem behavior. PMID:18468282

  3. 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.

  4. 49 CFR 1180.7 - Market analyses.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... OF TRANSPORTATION RULES OF PRACTICE RAILROAD ACQUISITION, CONTROL, MERGER, CONSOLIDATION PROJECT, TRACKAGE RIGHTS, AND LEASE PROCEDURES General Acquisition Procedures § 1180.7 Market analyses. (a) For... company's marketing plan and existing and potential competitive alternatives (inter- as well as...

  5. 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.

  6. 10 CFR 436.24 - Uncertainty analyses.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... DEPARTMENT OF ENERGY ENERGY CONSERVATION FEDERAL ENERGY MANAGEMENT AND PLANNING PROGRAMS Methodology and... by conducting additional analyses using any standard engineering economics method such as sensitivity... energy or water system alternative....

  7. 10 CFR 436.24 - Uncertainty analyses.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... DEPARTMENT OF ENERGY ENERGY CONSERVATION FEDERAL ENERGY MANAGEMENT AND PLANNING PROGRAMS Methodology and... by conducting additional analyses using any standard engineering economics method such as sensitivity... energy or water system alternative....

  8. 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...

  9. 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.

  10. Stearic Acid

    ERIC Educational Resources Information Center

    Young, Jay A.

    2004-01-01

    A chemical laboratory information profile (CLIP) is presented for the chemical, stearic acid. The profile lists the chemical's physical and harmful characteristics, exposure limits, and symptoms of major exposure, for the benefit of teachers and students, who use the chemical in the laboratory.

  11. Trichloroacetic acid

    Integrated Risk Information System (IRIS)

    Trichloroacetic acid ( TCA ) ; CASRN 76 - 03 - 9 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 Nonca

  12. 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

  13. 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

  14. Dichloroacetic acid

    Integrated Risk Information System (IRIS)

    Dichloroacetic acid ; CASRN 79 - 43 - 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 Noncarcinogeni

  15. 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

  16. 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

  17. 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

  18. 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

  19. [Hyaluronic acid].

    PubMed

    Pomarede, N

    2008-01-01

    Hyaluronic Acid (HA) is now a leader product in esthetic procedures for the treatment of wrinkles and volumes. The structure of HA, its metabolism, its physiological function are foremost breaking down then its use in aesthetic dermatology: steps of injection, possible side effects, benefits and downsides of the use of HA in aesthetic dermatology.

  20. 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.

  1. 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.

  2. [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.

  3. Fatty acids in recent sediments in the St. Lawrence estuary

    NASA Astrophysics Data System (ADS)

    Rodier, L.; Khalil, M. F.

    1982-11-01

    Surface sediments along the Rimouski section in the St. Lawrence estuary were sampled at the surface and at 10 cm depth. Fatty acids were extracted and analysed. Saturated and unsaturated fatty acid contents at the two depths vary with the nature of the sediments. The clay sediments rich in organic matter contain more fatty acids than the corresponding sand or gravel. Unsaturated fatty acids were more abundant in the surface sediments. Some iso- and anteiso-odd carbon fatty acids were detected in the sediments; these acids could indicate a microbial activity. Correlation is made with the fatty acid contents of the water column together with the surface microlayer of the estuarine water.

  4. Finite element analyses of CCAT preliminary design

    NASA Astrophysics Data System (ADS)

    Sarawit, Andrew T.; Kan, Frank W.

    2014-07-01

    This paper describes the development of the CCAT telescope finite element model (FEM) and the analyses performed to support the preliminary design work. CCAT will be a 25 m diameter telescope operating in the 0.2 to 2 mm wavelength range. It will be located at an elevation of 5600 m on Cerro Chajnantor in Northern Chile, near ALMA. The telescope will be equipped with wide-field cameras and spectrometers mounted at the two Nasmyth foci. The telescope will be inside an enclosure to protect it from wind buffeting, direct solar heating, and bad weather. The main structures of the telescope include a steel Mount and a carbon-fiber-reinforced-plastic (CFRP) primary truss. The finite element model developed in this study was used to perform modal, frequency response, seismic response spectrum, stress, and deflection analyses of telescope. Modal analyses of telescope were performed to compute the structure natural frequencies and mode shapes and to obtain reduced order modal output at selected locations in the telescope structure to support the design of the Mount control system. Modal frequency response analyses were also performed to compute transfer functions at these selected locations. Seismic response spectrum analyses of the telescope subject to the Maximum Likely Earthquake were performed to compute peak accelerations and seismic demand stresses. Stress analyses were performed for gravity load to obtain gravity demand stresses. Deflection analyses for gravity load, thermal load, and differential elevation drive torque were performed so that the CCAT Observatory can verify that the structures meet the stringent telescope surface and pointing error requirements.

  5. Montiporic acid D, a new polyacetylene carboxylic acid from scleractinian coral Montipora digitata.

    PubMed

    Kodani, Shinya; Sato, Kanna; Higuchi, Tomihiko; Casareto, Beatriz E; Suzuki, Yoshimi

    2013-10-01

    A new polyacetylene carboxylic acid named montiporic acid D (1) was isolated along with a known polyacetylene alcohol, (Z)-13,15-hexadecadien-2,4-diyn-1-ol (2) from scleractinian coral Montipora digitata. The structures of compounds were determined by analyses of NMR and MS spectra. PMID:23432335

  6. Fatty acids on continental sulfate aerosol particles

    NASA Astrophysics Data System (ADS)

    Tervahattu, H.; Juhanoja, J.; Vaida, V.; Tuck, A. F.; Niemi, J. V.; Kupiainen, K.; Kulmala, M.; VehkamäKi, H.

    2005-03-01

    Surface analyses of atmospheric aerosols from different continental sources, such as forest fires and coal and straw burning, show that organic surfactants are found on such aerosols. The predominant organic species detected by time-of-flight secondary ion mass spectrometry on the sulfate aerosols are fatty acids of different carbon chain length up to the C32 acid. These observations are consistent with literature accounts of functional group analysis of bulk samples, but this is the first direct evidence of fatty acid films on the surface of sulfate aerosols. Surface analysis leads to the conclusion that fatty acid films on continental aerosols may be more common than has been previously suggested.

  7. 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.

  8. 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. PMID:26359192

  9. 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.

  10. Meta-analyses of randomized controlled trials.

    PubMed

    Sacks, H S; Berrier, J; Reitman, D; Ancona-Berk, V A; Chalmers, T C

    1987-02-19

    A new type of research, termed meta-analysis, attempts to analyze and combine the results of previous reports. We found 86 meta-analyses of reports of randomized controlled trials in the English-language literature. We evaluated the quality of these meta-analyses, using a scoring method that considered 23 items in six major areas--study design, combinability, control of bias, statistical analysis, sensitivity analysis, and application of results. Only 24 meta-analyses (28 percent) addressed all six areas, 31 (36 percent) addressed five, 25 (29 percent) addressed four, 5 (6 percent) addressed three, and 1 (1 percent) addressed two. Of the 23 individual items, between 1 and 14 were addressed satisfactorily (mean +/- SD, 7.7 +/- 2.7). We conclude that an urgent need exists for improved methods in literature searching, quality evaluation of trials, and synthesizing of the results.

  11. 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

  12. 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

  13. Advanced toroidal facility vaccuum vessel stress analyses

    SciTech Connect

    Hammonds, C.J.; Mayhall, J.A.

    1987-01-01

    The complex geometry of the Advance Toroidal Facility (ATF) vacuum vessel required special analysis techniques in investigating the structural behavior of the design. The response of a large-scale finite element model was found for transportation and operational loading. Several computer codes and systems, including the National Magnetic Fusion Energy Computer Center Cray machines, were implemented in accomplishing these analyses. The work combined complex methods that taxed the limits of both the codes and the computer systems involved. Using MSC/NASTRAN cyclic-symmetry solutions permitted using only 1/12 of the vessel geometry to mathematically analyze the entire vessel. This allowed the greater detail and accuracy demanded by the complex geometry of the vessel. Critical buckling-pressure analyses were performed with the same model. The development, results, and problems encountered in performing these analyses are described. 5 refs., 3 figs.

  14. 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.

  15. 7 CFR 94.302 - Analyses available and locations of laboratories.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 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...

  16. 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...

  17. 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.

  18. Identifying, analysing and solving problems in practice.

    PubMed

    Hewitt-Taylor, Jaqui

    When a problem is identified in practice, it is important to clarify exactly what it is and establish the cause before seeking a solution. This solution-seeking process should include input from those directly involved in the problematic situation, to enable individuals to contribute their perspective, appreciate why any change in practice is necessary and what will be achieved by the change. This article describes some approaches to identifying and analysing problems in practice so that effective solutions can be devised. It includes a case study and examples of how the Five Whys analysis, fishbone diagram, problem tree analysis, and Seven-S Model can be used to analyse a problem.

  19. 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.

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

    PubMed

    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

  1. Leaf Litter Mixtures Alter Microbial Community Development: Mechanisms for Non-Additive Effects in Litter Decomposition

    PubMed Central

    Chapman, Samantha K.; Newman, Gregory S.; Hart, Stephen C.; Schweitzer, Jennifer A.; Koch, George W.

    2013-01-01

    To what extent microbial community composition can explain variability in ecosystem processes remains an open question in ecology. Microbial decomposer communities can change during litter decomposition due to biotic interactions and shifting substrate availability. Though relative abundance of decomposers may change due to mixing leaf litter, linking these shifts to the non-additive patterns often recorded in mixed species litter decomposition rates has been elusive, and links community composition to ecosystem function. We extracted phospholipid fatty acids (PLFAs) from single species and mixed species leaf litterbags after 10 and 27 months of decomposition in a mixed conifer forest. Total PLFA concentrations were 70% higher on litter mixtures than single litter types after 10 months, but were only 20% higher after 27 months. Similarly, fungal-to-bacterial ratios differed between mixed and single litter types after 10 months of decomposition, but equalized over time. Microbial community composition, as indicated by principal components analyses, differed due to both litter mixing and stage of litter decomposition. PLFA biomarkers a15∶0 and cy17∶0, which indicate gram-positive and gram-negative bacteria respectively, in particular drove these shifts. Total PLFA correlated significantly with single litter mass loss early in decomposition but not at later stages. We conclude that litter mixing alters microbial community development, which can contribute to synergisms in litter decomposition. These findings advance our understanding of how changing forest biodiversity can alter microbial communities and the ecosystem processes they mediate. PMID:23658639

  2. 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

  3. 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.

  4. 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

  5. Assessment of fatty acid intakes in vegans and omnivores.

    PubMed

    Roshanai, F; Sanders, T A

    1984-10-01

    Fatty acid intakes were estimated from 7-day weighed-food-intake date and from the analysis of 3-day duplicate food portions in a series of vegans and omnivore controls. Calculated and analysed values for monounsaturated fatty acids, linoleic and linolenic acids were generally in good agreement. Analysed saturated fatty acid intakes tended to be lower in the omnivores than the calculated values. The vegan subjects had very much lower intakes of saturated fatty acids and much higher intakes of linoleic acid compared with the omnivores; these differences were most marked between the men. The vegan diets were devoid of arachidonic acid, eicosapentaenoic and docosahexaenoic acids. Plasma total cholesterol and LDL cholesterol concentrations were significantly lower in the male vegans.

  6. 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.

  7. FAME: Software for analysing rock microstructures

    NASA Astrophysics Data System (ADS)

    Hammes, Daniel M.; Peternell, Mark

    2016-05-01

    Determination of rock microstructures leads to a better understanding of the formation and deformation of polycrystalline solids. Here, we present FAME (Fabric Analyser based Microstructure Evaluation), an easy-to-use MATLAB®-based software for processing datasets recorded by an automated fabric analyser microscope. FAME is provided as a MATLAB®-independent Windows® executable with an intuitive graphical user interface. Raw data from the fabric analyser microscope can be automatically loaded, filtered and cropped before analysis. Accurate and efficient rock microstructure analysis is based on an advanced user-controlled grain labelling algorithm. The preview and testing environments simplify the determination of appropriate analysis parameters. Various statistic and plotting tools allow a graphical visualisation of the results such as grain size, shape, c-axis orientation and misorientation. The FAME2elle algorithm exports fabric analyser data to an elle (modelling software)-supported format. FAME supports batch processing for multiple thin section analysis or large datasets that are generated for example during 2D in-situ deformation experiments. The use and versatility of FAME is demonstrated on quartz and deuterium ice samples.

  8. 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.

  9. Multiphase Method for Analysing Online Discussions

    ERIC Educational Resources Information Center

    Häkkinen, P.

    2013-01-01

    Several studies have analysed and assessed online performance and discourse using quantitative and qualitative methods. Quantitative measures have typically included the analysis of participation rates and learning outcomes in terms of grades. Qualitative measures of postings, discussions and context features aim to give insights into the nature…

  10. 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.

  11. 49 CFR 1180.7 - Market analyses.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... identify and address relevant markets and issues, and provide additional information as requested by the...). (b) For major transactions, applicants shall submit “full system” impact analyses (incorporating any... (including inter- and intramodal competition, product competition, and geographic competition) and...

  12. 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 courses…

  13. What's missing from avian global diversification analyses?

    PubMed

    Reddy, Sushma

    2014-08-01

    The accumulation of vast numbers of molecular phylogenetic studies has contributed to huge knowledge gains in the evolutionary history of birds. This permits subsequent analyses of avian diversity, such as how and why diversification varies across the globe and among taxonomic groups. However, available genetic data for these meta-analyses are unevenly distributed across different geographic regions and taxonomic groups. To comprehend the impact of this variation on the interpretation of global diversity patterns, I examined the availability of genetic data for possible biases in geographic and taxonomic sampling of birds. I identified three main disparities of sampling that are geographically associated with latitude (temperate, tropical), hemispheres (East, West), and range size. Tropical regions, which host the vast majority of species, are substantially less studied. Moreover, Eastern regions, such as the Old World Tropics and Australasia, stand out as being disproportionately undersampled, with up to half of communities not being represented in recent studies. In terms of taxonomic discrepancies, a majority of genetically undersampled clades are exclusively found in tropical regions. My analysis identifies several disparities in the key regions of interest of global diversity analyses. Differential sampling can have considerable impacts on these global comparisons and call into question recent interpretations of latitudinal or hemispheric differences of diversification rates. Moreover, this review pinpoints understudied regions whose biota are in critical need of modern systematic analyses.

  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. 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…

  16. Using Solo to Analyse Group Responses

    ERIC Educational Resources Information Center

    Reading, Chris; Lawrie, Christine

    2004-01-01

    The increased use of group work in teaching and learning has seen an increased need for knowledge about assessment of group work. This report considers exploratory research where the SOLO Taxonomy, previously used to analyse the quality of individual responses, is applied to group responses. The responses were created as part of an activity…

  17. 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…

  18. Impact analyses after pipe rupture. [PWR; BWR

    SciTech Connect

    Chun, R.C.; Chuang, T.Y.

    1983-12-13

    Two of the French pipe whip experiments are reproduced with the computer code WIPS. The WIPS results are in good agreement with the experimental data and the French computer code TEDEL. This justifies the use of its pipe element in conjunction with its U-bar element in a simplified method of impact analyses.

  19. 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.

  20. 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.

  1. Evaluation of the clinical chemistry analyser Olympus AU400.

    PubMed

    Lasnier, E; Mario, N; Boque, M C; You, S N; Vaubourdolle, M

    2000-10-01

    The Olympus AU400 analyser (Olympus, Tokyo, Japan) is an automated chemistry instrument for turbidimetric, spectrophotometric and ion selective electrode measurements. Overall analytical performances of the AU400 and the reagents provided by Olympus were evaluated according to the French Society of Clinical Biology guidelines. Twenty parameters including specific proteins, substrates, enzyme activities and electrolytes were tested. The linearity exceeded the specifications given by the manufacturer. Within- and between-run imprecision (CV%), evaluated at two levels, was below 1.5% for ion selective electrode parameters and 3% for other analytes, except for CO2, alkaline phosphatase at low levels and magnesium. Results compared well with those obtained with the analysers routinely used in our laboratory (Behring BNII, Olympus AU800 and Beckman CX3 Delta). The usual positive interferences from lipaemia and haemoglobin on total protein measurement were observed. Creatine kinase and alkaline phosphatase assays were the subject of positive and negative interference by haemoglobin, respectively. There was a negative interference by bilirubin in the uric acid, aspartate-amino transferase, creatine kinase and lactate dehydrogenase assays and a positive interference in the calcium assay. The system was found to be very easy to use and the workstation is user-friendly. PMID:11140621

  2. Devolatilisation kinetics and pyrolytic analyses of Tectona grandis (teak).

    PubMed

    Balogun, A O; Lasode, O A; McDonald, A G

    2014-03-01

    Devolatilisation kinetics and pyrolytic analyses were carried out on Tectona grandis (teak) using iso-conversional methods (Flynn-Wall-Ozawa and Starink) and analytical Py-GC/MS technique respectively. Proximate and elemental analyses were also performed and they showed that the ash and C contents and the HHV were 0.7%, 49.6% and 19.8MJ/kg respectively. Biomass sample was subjected to multiple heating rates (5-35K/min) in thermogravimetric experiments and kinetic parameters were evaluated from the non-isothermal TGA curves. The activation energy (E) varied between 222 and 300kJ/mol as a function of degree of conversion. Similarly, the pre-exponential frequency factor (A) varied between 9.6×10(17) and 9.55×10(24)min(-1). Analytical Py-GC/MS showed the presence of CO2, acetic acid, furan+2-butanone, levoglucosan, trans-coniferyl alcohol and lignin derivatives. The proportion of phenolic compounds identified was more than one-third with isoeugenol, acetoguaiacone, and 4-vinylguaiacol showing dominance. PMID:24486938

  3. Enantiomeric excesses in meteoritic amino acids

    NASA Technical Reports Server (NTRS)

    Cronin, J. R.; Pizzarello, S.

    1997-01-01

    Gas chromatographic-mass spectral analyses of the four stereoisomers of 2-amino-2,3-dimethylpentanoic acid (dl-alpha-methylisoleucine and dl-alpha-methylalloisoleucine) obtained from the Murchison meteorite show that the L enantiomer occurs in excess (7.0 and 9.1%, respectively) in both of the enantiomeric pairs. Similar results were obtained for two other alpha-methyl amino acids, isovaline and alpha-methylnorvaline, although the alpha hydrogen analogs of these amino acids, alpha-amino-n-butyric acid and norvaline, were found to be racemates. With the exception of alpha-amino-n-butyric acid, these amino acids are either unknown or of limited occurrence in the biosphere. Because carbonaceous chondrites formed 4.5 billion years ago, the results are indicative of an asymmetric influence on organic chemical evolution before the origin of life.

  4. Methylmalonic acid blood test

    MedlinePlus

    ... acid is a substance produced when proteins, called amino acids, in the body break down. The health care ... Cederbaum S, Berry GT. Inborn errors of carbohydrate, ammonia, amino acid, and organic acid metabolism. In: Gleason CA, Devaskar ...

  5. Folic Acid and Pregnancy

    MedlinePlus

    ... 5 Things to Know About Zika & Pregnancy 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 ...

  6. Glycomic analyses of ovarian follicles during development and atresia

    PubMed Central

    Hatzirodos, Nicholas; Nigro, Julie; Irving-Rodgers, Helen F.; Vashi, Aditya V.; Hummitzsch, Katja; Caterson, Bruce; Sullivan, Thomas R.; Rodgers, Raymond J.

    2012-01-01

    To examine the detailed composition of glycosaminoglycans during bovine ovarian follicular development and atresia, the specialized stromal theca layers were separated from the stratified epithelial granulosa cells of healthy (n = 6) and atretic (n = 6) follicles in each of three size ranges: small (3–5 mm), medium (6-9 mm) and large (10 mm or more) (n = 29 animals). Fluorophore-assisted carbohydrate electrophoresis analyses (on a per cell basis) and immunohistochemistry (n = 14) were undertaken. We identified the major disaccharides in thecal layers and the membrana granulosa as chondroitin sulfate-derived ∆uronic acid with 4-sulfated N-acetylgalactosamine and ∆uronic acid with 6-sulfated N-acetylgalactosamine and the heparan sulfate-derived Δuronic acid with N-acetlyglucosamine, with elevated levels in the thecal layers. Increasing follicle size and atresia was associated with increased levels of some disaccharides. We concluded that versican contains 4-sulfated N-acetylgalactosamine and it is the predominant 4-sulfated N-acetylgalactosamine proteoglycan in antral follicles. At least one other non- or 6-sulfated N-acetylgalactosamine proteoglycan(s), which is not decorin or an inter-α-trypsin inhibitor family member, is present in bovine antral follicles and associated with hitherto unknown groups of cells around some larger blood vessels. These areas stained positively for chondroitin/dermatan sulfate epitopes [antibodies 7D4, 3C5, and 4C3], similar to stem cell niches observed in other tissues. The sulfation pattern of heparan sulfate glycosaminoglycans appears uniform across follicles of different sizes and in healthy and atretic follicles. The heparan sulfate products detected in the follicles are likely to be associated with perlecan, collagen XVIII or betaglycan. PMID:22057033

  7. 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.

  8. Analysing organic transistors based on interface approximation

    SciTech Connect

    Akiyama, Yuto; Mori, Takehiko

    2014-01-15

    Temperature-dependent characteristics of organic transistors are analysed thoroughly using interface approximation. In contrast to amorphous silicon transistors, it is characteristic of organic transistors that the accumulation layer is concentrated on the first monolayer, and it is appropriate to consider interface charge rather than band bending. On the basis of this model, observed characteristics of hexamethylenetetrathiafulvalene (HMTTF) and dibenzotetrathiafulvalene (DBTTF) transistors with various surface treatments are analysed, and the trap distribution is extracted. In turn, starting from a simple exponential distribution, we can reproduce the temperature-dependent transistor characteristics as well as the gate voltage dependence of the activation energy, so we can investigate various aspects of organic transistors self-consistently under the interface approximation. Small deviation from such an ideal transistor operation is discussed assuming the presence of an energetically discrete trap level, which leads to a hump in the transfer characteristics. The contact resistance is estimated by measuring the transfer characteristics up to the linear region.

  9. Neuronal network analyses: premises, promises and uncertainties

    PubMed Central

    Parker, David

    2010-01-01

    Neuronal networks assemble the cellular components needed for sensory, motor and cognitive functions. Any rational intervention in the nervous system will thus require an understanding of network function. Obtaining this understanding is widely considered to be one of the major tasks facing neuroscience today. Network analyses have been performed for some years in relatively simple systems. In addition to the direct insights these systems have provided, they also illustrate some of the difficulties of understanding network function. Nevertheless, in more complex systems (including human), claims are made that the cellular bases of behaviour are, or will shortly be, understood. While the discussion is necessarily limited, this issue will examine these claims and highlight some traditional and novel aspects of network analyses and their difficulties. This introduction discusses the criteria that need to be satisfied for network understanding, and how they relate to traditional and novel approaches being applied to addressing network function. PMID:20603354

  10. 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.

  11. Identifying, analysing and solving problems in practice.

    PubMed

    Hewitt-Taylor, Jaqui

    When a problem is identified in practice, it is important to clarify exactly what it is and establish the cause before seeking a solution. This solution-seeking process should include input from those directly involved in the problematic situation, to enable individuals to contribute their perspective, appreciate why any change in practice is necessary and what will be achieved by the change. This article describes some approaches to identifying and analysing problems in practice so that effective solutions can be devised. It includes a case study and examples of how the Five Whys analysis, fishbone diagram, problem tree analysis, and Seven-S Model can be used to analyse a problem. PMID:22848969

  12. 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.

  13. Analyses and characterization of double shell tank

    SciTech Connect

    Not Available

    1994-10-04

    Evaporator candidate feed from tank 241-AP-108 (108-AP) was sampled under prescribed protocol. Physical, inorganic, and radiochemical analyses were performed on tank 108-AP. Characterization of evaporator feed tank waste is needed primarily for an evaluation of its suitability to be safely processed through the evaporator. Such analyses should provide sufficient information regarding the waste composition to confidently determine whether constituent concentrations are within not only safe operating limits, but should also be relevant to functional limits for operation of the evaporator. Characterization of tank constituent concentrations should provide data which enable a prediction of where the types and amounts of environmentally hazardous waste are likely to occur in the evaporator product streams.

  14. 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…

  15. [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.

  16. Inelastic and Dynamic Fracture and Stress Analyses

    NASA Technical Reports Server (NTRS)

    Atluri, S. N.

    1984-01-01

    Large deformation inelastic stress analysis and inelastic and dynamic crack propagation research work is summarized. The salient topics of interest in engine structure analysis that are discussed herein include: (1) a path-independent integral (T) in inelastic fracture mechanics, (2) analysis of dynamic crack propagation, (3) generalization of constitutive relations of inelasticity for finite deformations , (4) complementary energy approaches in inelastic analyses, and (5) objectivity of time integration schemes in inelastic stress analysis.

  17. 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.

  18. Bicyclic glutamic acid derivatives.

    PubMed

    Meyer, Udo; Bisel, Philippe; Weckert, Edgar; Frahm, August Wilhelm

    2006-05-15

    For the second-generation asymmetric synthesis of the trans-tris(homoglutamic) acids via Strecker reaction of chiral ketimines, the cyanide addition as the key stereodifferentiating step produces mixtures of diastereomeric alpha-amino nitrile esters the composition of which is independent of the reaction temperature and the type of the solvent, respectively. The subsequent hydrolysis is exclusively achieved with concentrated H(2)SO(4) yielding diastereomeric mixtures of three secondary alpha-amino alpha-carbamoyl-gamma-esters and two diastereomeric cis-fused angular alpha-carbamoyl gamma-lactams as bicyclic glutamic acid derivatives, gained from in situ stereomer differentiating cyclisation of the secondary cis-alpha-amino alpha-carbamoyl-gamma-esters. Separation was achieved by CC. The pure secondary trans-alpha-amino alpha-carbamoyl-gamma-esters cyclise on heating and treatment with concentrated H(2)SO(4), respectively, to diastereomeric cis-fused angular secondary alpha-amino imides. Their hydrogenolysis led to the enantiomeric cis-fused angular primary alpha-amino imides. The configuration of all compounds was completely established by NMR methods, CD-spectra, and by X-ray analyses of the (alphaR,1R,5R)-1-carbamoyl-2-(1-phenylethyl)-2-azabicyclo[3.3.0]octan-3-one and of the trans-alphaS,1S,2R-2-ethoxycarbonylmethyl-1-(1-phenylethylamino)cyclopentanecarboxamide. PMID:16596563

  19. Chromatographic determination of amino acids in foods.

    PubMed

    Peace, Robert W; Gilani, G Sarwar

    2005-01-01

    Amino acids in foods exist in a free form or bound in peptides, proteins, or nonpeptide bonded polymers. Naturally occurring L-amino acids are required for protein synthesis and are precursors for essential molecules, such as co-enzymes and nucleic acids. Nonprotein amino acids may also occur in animal tissues as metabolic intermediates or have other important functions. The development of bacterially derived food proteins, genetically modified foods, and new methods of food processing; the production of amino acids for food fortification; and the introduction of new plant food sources have meant that protein amino acids and amino acid enantiomers in foods can have both nutritional and safety implications for humans. There is, therefore, a need for the rapid and accurate determination of amino acids in foods. Determination of the total amino acid content of foods requires protein hydrolysis by various means that must take into account variations in stability of individual amino acids and resistance of different peptide bonds to the hydrolysis procedures. Modern methods for separation and quantitation of free amino acids either before or after protein hydrolysis include ion exchange chromatography, high performance liquid chromatography (LC), gas chromatography, and capillary electrophoresis. Chemical derivatization of amino acids may be required to change them into forms amenable to separation by the various chromatographic methods or to create derivatives with properties, such as fluorescence, that improve their detection. Official methods for hydrolysis and analysis of amino acids in foods for nutritional purposes have been established. LC is currently the most widely used analytical technique, although there is a need for collaborative testing of methods available. Newer developments in chromatographic methodology and detector technology have reduced sample and reagent requirements and improved identification, resolution, and sensitivity of amino acid analyses

  20. 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. PMID:26596827

  1. 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. PMID:26551336

  2. 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.

  3. Evaluation of Model Operational Analyses during DYNAMO

    NASA Astrophysics Data System (ADS)

    Ciesielski, Paul; Johnson, Richard

    2013-04-01

    A primary component of the observing system in the DYNAMO-CINDY2011-AMIE field campaign was an atmospheric sounding network comprised of two sounding quadrilaterals, one north and one south of the equator over the central Indian Ocean. During the experiment a major effort was undertaken to ensure the real-time transmission of these data onto the GTS (Global Telecommunication System) for dissemination to the operational centers (ECMWF, NCEP, JMA, etc.). Preliminary estimates indicate that ~95% of the soundings from the enhanced sounding network were successfully transmitted and potentially used in their data assimilation systems. Because of the wide use of operational and reanalysis products (e.g., in process studies, initializing numerical simulations, construction of large-scale forcing datasets for CRMs, etc.), their validity will be examined by comparing a variety of basic and diagnosed fields from two operational analyses (ECMWF and NCEP) to similar analyses based solely on sounding observations. Particular attention will be given to the vertical structures of apparent heating (Q1) and drying (Q2) from the operational analyses (OA), which are strongly influenced by cumulus parameterizations, a source of model infidelity. Preliminary results indicate that the OA products did a reasonable job at capturing the mean and temporal characteristics of convection during the DYNAMO enhanced observing period, which included the passage of two significant MJO events during the October-November 2011 period. For example, temporal correlations between Q2-budget derived rainfall from the OA products and that estimated from the TRMM satellite (i.e., the 3B42V7 product) were greater than 0.9 over the Northern Sounding Array of DYNAMO. However closer inspection of the budget profiles show notable differences between the OA products and the sounding-derived results in low-level (surface to 700 hPa) heating and drying structures. This presentation will examine these differences and

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. Analyses of Shuttle Orbiter approach and landing

    NASA Technical Reports Server (NTRS)

    Ashkenas, I. L.; Hoh, R. H.; Teper, G. L.

    1982-01-01

    A study of the Shuttle Orbiter approach and landing conditions is summarized. The causes of observed PIO-like flight deficiencies are listed, and possible corrective measures are examined. Closed-loop pilot/vehicle analyses are described, and a description is given of path-attitude stability boundaries. The latter novel approach is found to be of great value in delineating and illustrating the basic causes of this multiloop pilot control problem. It is shown that the analytical results are consistent with flight test and fixed-base simulation. Conclusions are drawn concerning possible improvements in the Shuttle Orbiter/Digital Flight Control System.

  9. 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.

  10. 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.

  11. 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.

  12. 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.).

  13. Special analyses reveal coke-deposit structure

    SciTech Connect

    Albright, L.F.

    1988-08-01

    A scanning electron microscope (SEM) and an energy dispersive X-ray analyzer (EDAX) have been used to obtain information that clarifies the three mechanisms of coke formation in ethylene furnaces, and to analyze the metal condition at the exit of furnace. The results can be used to examine furnace operations and develop improved ethylene plant practices. In this first of four articles on the analyses of coke and metal samples, the coking mechanisms and coke deposits in a section of tube from an actual ethylene furnace (Furnace A) from a plant on the Texas Gulf Coast are discussed. The second articles in the series will analyze the condition of the tube metal in the same furnace. To show how coke deposition and metal condition dependent on the operating parameters of an ethylene furnace, the third article in the series will show the coke deposition in a Texas Gulf Coast furnace tube (Furnace B) that operated at shorter residence time. The fourth article discusses the metal condition in that furnace. Some recommendations, based on the analyses and findings, are offered in the fourth article that could help extend the life of ethylene furnace tubes, and also improve overall ethylene plant operations.

  14. 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

  15. Repeatability of published microarray gene expression analyses.

    PubMed

    Ioannidis, John P A; Allison, David B; Ball, Catherine A; Coulibaly, Issa; Cui, Xiangqin; Culhane, Aedín C; Falchi, Mario; Furlanello, Cesare; Game, Laurence; Jurman, Giuseppe; Mangion, Jon; Mehta, Tapan; Nitzberg, Michael; Page, Grier P; Petretto, Enrico; van Noort, Vera

    2009-02-01

    Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005-2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.

  16. 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.

  17. 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)

  18. 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.

  19. Transportation systems analyses: Volume 1: Executive Summary

    NASA Astrophysics Data System (ADS)

    1993-05-01

    The principal objective of this study is to accomplish a systems engineering assessment of the nation's space transportation infrastructure. This analysis addresses the necessary elements to perform man delivery and return, cargo transfer, cargo delivery, payload servicing, and the exploration of the Moon and Mars. Specific elements analyzed, but not limited to, include the Space Exploration Initiative (SEI), the National Launch System (NLS), the current expendable launch vehicle (ELV) fleet, ground facilities, the Space Station Freedom (SSF), and other civil, military and commercial payloads. The performance of this study entails maintaining a broad perspective on the large number of transportation elements that could potentially comprise the U.S. space infrastructure over the next several decades. To perform this systems evaluation, top-level trade studies are conducted to enhance our understanding of the relationships between elements of the infrastructure. This broad 'infrastructure-level perspective' permits the identification of preferred infrastructures. Sensitivity analyses are performed to assure the credibility and usefulness of study results. This executive summary of the transportation systems analyses (TSM) semi-annual report addresses the SSF logistics resupply. Our analysis parallels the ongoing NASA SSF redesign effort. Therefore, there could be no SSF design to drive our logistics analysis. Consequently, the analysis attempted to bound the reasonable SSF design possibilities (and the subsequent transportation implications). No other strategy really exists until after a final decision is rendered on the SSF configuration.

  20. Hierarchical regression for analyses of multiple outcomes.

    PubMed

    Richardson, David B; Hamra, Ghassan B; MacLehose, Richard F; Cole, Stephen R; Chu, Haitao

    2015-09-01

    In cohort mortality studies, there often is interest in associations between an exposure of primary interest and mortality due to a range of different causes. A standard approach to such analyses involves fitting a separate regression model for each type of outcome. However, the statistical precision of some estimated associations may be poor because of sparse data. In this paper, we describe a hierarchical regression model for estimation of parameters describing outcome-specific relative rate functions and associated credible intervals. The proposed model uses background stratification to provide flexible control for the outcome-specific associations of potential confounders, and it employs a hierarchical "shrinkage" approach to stabilize estimates of an exposure's associations with mortality due to different causes of death. The approach is illustrated in analyses of cancer mortality in 2 cohorts: a cohort of dioxin-exposed US chemical workers and a cohort of radiation-exposed Japanese atomic bomb survivors. Compared with standard regression estimates of associations, hierarchical regression yielded estimates with improved precision that tended to have less extreme values. The hierarchical regression approach also allowed the fitting of models with effect-measure modification. The proposed hierarchical approach can yield estimates of association that are more precise than conventional estimates when one wishes to estimate associations with multiple outcomes. PMID:26232395

  1. 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.

  2. 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.

  3. ISFSI site boundary radiation dose rate analyses.

    PubMed

    Hagler, R J; Fero, A H

    2005-01-01

    Across the globe nuclear utilities are in the process of designing and analysing Independent Spent Fuel Storage Installations (ISFSI) for the purpose of above ground spent-fuel storage primarily to mitigate the filling of spent-fuel pools. Using a conjoining of discrete ordinates transport theory (DORT) and Monte Carlo (MCNP) techniques, an ISFSI was analysed to determine neutron and photon dose rates for a generic overpack, and ISFSI pad configuration and design at distances ranging from 1 to -1700 m from the ISFSI array. The calculated dose rates are used to address the requirements of 10CFR72.104, which provides limits to be enforced for the protection of the public by the NRC in regard to ISFSI facilities. For this overpack, dose rates decrease by three orders of magnitude through the first 200 m moving away from the ISFSI. In addition, the contributions from different source terms changes over distance. It can be observed that although side photons provide the majority of dose rate in this calculation, scattered photons and side neutrons take on more importance as the distance from the ISFSI is increased. PMID:16604670

  4. The influence of the branched-chain fatty acids pristanic acid and Refsum disease-associated phytanic acid on mitochondrial functions and calcium regulation of hippocampal neurons, astrocytes, and oligodendrocytes.

    PubMed

    Rönicke, Sabine; Kruska, Nicol; Kahlert, Stefan; Reiser, Georg

    2009-11-01

    Pristanic acid and phytanic acid are branched-chain fatty acids, which play an important role in diseases with peroxisomal impairment, like Refsum disease (MIM 266500), Zellwegers syndrome and alpha-methylacyl-CoA racemase deficiency (MIM 604489). Several studies revealed that the toxic activity of phytanic acid is mediated by multiple mitochondrial dysfunctions. However, the action of pristanic acid on brain cells is still completely unknown. Here, we exposed astrocytes, oligodendrocytes and neurons in mixed culture to pristanic acid and phytanic acid to analyse cellular consequences. Pristanic acid exerts a strong cytotoxic activity on brain cells, displayed by dramatic Ca2+ deregulation, in situ mitochondrial depolarization and cell death. Interestingly, pristanic acid strongly induced generation of reactive oxygen species (ROS), whereas phytanic acid exerts weaker effects on ROS production. In conclusion, pristanic acid as well as phytanic acid induced a complex array of toxic activities with mitochondrial dysfunction and Ca2+ deregulation.

  5. Dysembryoplastic neuroepithelial tumor: morphological, immunocytochemical, and deoxyribonucleic acid analyses in a pediatric series.

    PubMed

    Taratuto, A L; Pomata, H; Sevlever, G; Gallo, G; Monges, J

    1995-03-01

    Overtreatment by radiotherapy and/or chemotherapy for central nervous system tumors in infancy and childhood may be deleterious, so the recognition of surgically curable clinicopathological entities is mandatory. The dysembryoplastic neuroepithelial tumor is a complex multinodular lesion consisting of glial nodules, associated with a specific glioneuronal element and/or with focal cortical dysplasia, and occurring in young patients presenting with intractable, mostly complex partial, seizures without neurological deterioration. We report on 14 patients; 9 were from a series of 600 pediatric patients with intracranial central nervous system tumors studied at a single institution from 1988 to 1993, and 5 were referred from other pediatric hospitals. Six tumors were frontal, six were temporal, one was parietal, and one was occipitoparietal. Computed tomographic scans disclosed hypodense lesions with cystic appearances in 4 patients and slight focal postcontrast enhancements in only 2 patients, whereas magnetic resonance imaging, available for 7 of 14 patients, showed hypointense lesions in T1-weighted images and hyperintense lesions in T2-weighted images. Deformities of the overlying cranium were also observed in five patients. The age range at the time of surgery (excluding a 20-year-old male patient who underwent surgery at the main pediatric hospital) was 2.6 to 13 years, with a mean of 6.68 years. The male to female patient ratio was 10:4, and the duration of symptoms was 0.2 to 6 years.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. 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...

  7. Conservation Weighting Functions Enable Covariance Analyses to Detect Functionally Important Amino Acids

    PubMed Central

    Colwell, Lucy J.; Brenner, Michael P.; Murray, Andrew W.

    2014-01-01

    The explosive growth in the number of protein sequences gives rise to the possibility of using the natural variation in sequences of homologous proteins to find residues that control different protein phenotypes. Because in many cases different phenotypes are each controlled by a group of residues, the mutations that separate one version of a phenotype from another will be correlated. Here we incorporate biological knowledge about protein phenotypes and their variability in the sequence alignment of interest into algorithms that detect correlated mutations, improving their ability to detect the residues that control those phenotypes. We demonstrate the power of this approach using simulations and recent experimental data. Applying these principles to the protein families encoded by Dscam and Protocadherin allows us to make testable predictions about the residues that dictate the specificity of molecular interactions. PMID:25379728

  8. Molecular and Functional Analyses of Amino Acid Decarboxylases Involved in Cuticle Tanning in Tribolium castaneum*

    PubMed Central

    Arakane, Yasuyuki; Lomakin, Joseph; Beeman, Richard W.; Muthukrishnan, Subbaratnam; Gehrke, Stevin H.; Kanost, Michael R.; Kramer, Karl J.

    2009-01-01

    Aspartate 1-decarboxylase (ADC) and 3,4-dihydroxyphenylalanine decarboxylase (DDC) provide β-alanine and dopamine used in insect cuticle tanning. β-Alanine is conjugated with dopamine to yield N-β-alanyldopamine (NBAD), a substrate for the phenol oxidase laccase that catalyzes the synthesis of cuticle protein cross-linking agents and pigment precursors. We identified ADC and DDC genes in the red flour beetle, Tribolium castaneum (Tc), and investigated their functions. TcADC mRNA was most abundant prior to the pupal-adult molt. Injection of TcADC double-stranded (ds) RNA (dsTcADC) into mature larvae resulted in depletion of NBAD in pharate adults, accumulation of dopamine, and abnormally dark pigmentation of the adult cuticle. Injection of β-alanine, the expected product of ADC, into dsTcADC-treated pupae rescued the pigmentation phenotype, resulting in normal rust-red color. A similar pattern of catechol content consisting of elevated dopamine and depressed NBAD was observed in the genetic black mutants of Tribolium, in which levels of TcADC mRNA were drastically reduced. Furthermore, from the Tribolium black mutant and dsTcADC-injected insects both exhibited similar changes in material properties. Dynamic mechanical analysis of elytral cuticle from beetles with depleted TcADC transcripts revealed diminished cross-linking of cuticular components, further confirming the important role of oxidation products of NBAD as cross-linking agents during cuticle tanning. Injection of dsTcDDC into larvae produced a lethal pupal phenotype, and the resulting grayish pupal cuticle exhibited many small patches of black pigmentation. When dsTcDDC was injected into young pupae, the resulting adults had abnormally dark brown body color, but there was little mortality. Injection of dsTcDDC resulted in more than a 5-fold increase in levels of DOPA, indicating that lack of TcDDC led to accumulation of its substrate, DOPA. PMID:19366687

  9. 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...

  10. Trans fatty acids in a range of UK processed foods.

    PubMed

    Roe, Mark; Pinchen, Hannah; Church, Susan; Elahi, Selvarani; Walker, Margaret; Farron-Wilson, Melanie; Buttriss, Judith; Finglas, Paul

    2013-10-01

    A survey to determine the trans fatty acid content of a range of processed foods was carried out in response to recent reformulation work by the food industry to lower the artificial trans fatty acid content of processed products. Sixty two composite samples, made up of between 5 and 12 sub-samples, were collected in 2010 and were analysed for fatty acids, and a range of nutrients. The foods analysed included pizza, garlic bread, breakfast cereals, quiche, fat spreads, a range of fish and meat products, chips, savoury snacks, confectionery and ice cream. Levels of trans fatty acids were reduced considerably compared with previous UK analyses of similar foods where comparisons are possible. Concentrations of trans elaidic acid (t9-C18:1) from hydrogenated oils in all samples were <0.2g/100g food. These results confirm information provided by the food industry in 2007 on the levels of trans fats in key processed food sectors.

  11. Precipitation: its acidic nature.

    PubMed

    Frohliger, J O; Kane, R

    1975-08-01

    A comparison of the free hydrogen ion concentration and the total hydrogen ion concentration of rain samples shows that rain is a weak acid. The weak acid nature of rain casts doubt on the concepts that the acidity of rain is increasing and that these increases are due to strong acids such as sulfuric acid.

  12. Chapter 9: Analyses Using Disease Ontologies

    PubMed Central

    Shah, Nigam H.; Cole, Tyler; Musen, Mark A.

    2012-01-01

    Advanced statistical methods used to analyze high-throughput data such as gene-expression assays result in long lists of “significant genes.” One way to gain insight into the significance of altered expression levels is to determine whether Gene Ontology (GO) terms associated with a particular biological process, molecular function, or cellular component are over- or under-represented in the set of genes deemed significant. This process, referred to as enrichment analysis, profiles a gene-set, and is widely used to makes sense of the results of high-throughput experiments. The canonical example of enrichment analysis is when the output dataset is a list of genes differentially expressed in some condition. To determine the biological relevance of a lengthy gene list, the usual solution is to perform enrichment analysis with the GO. We can aggregate the annotating GO concepts for each gene in this list, and arrive at a profile of the biological processes or mechanisms affected by the condition under study. While GO has been the principal target for enrichment analysis, the methods of enrichment analysis are generalizable. We can conduct the same sort of profiling along other ontologies of interest. Just as scientists can ask “Which biological process is over-represented in my set of interesting genes or proteins?” we can also ask “Which disease (or class of diseases) is over-represented in my set of interesting genes or proteins?“. For example, by annotating known protein mutations with disease terms from the ontologies in BioPortal, Mort et al. recently identified a class of diseases—blood coagulation disorders—that were associated with a 14-fold depletion in substitutions at O-linked glycosylation sites. With the availability of tools for automatic annotation of datasets with terms from disease ontologies, there is no reason to restrict enrichment analyses to the GO. In this chapter, we will discuss methods to perform enrichment analysis using any

  13. 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

  14. Comparative Transcriptional Analyses of Francisella tularensis and Francisella novicida.

    PubMed

    Sarva, Siva T; 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

  15. Analyses of Intestinal Microbiota: Culture versus Sequencing.

    PubMed

    Hiergeist, Andreas; Gläsner, Joachim; Reischl, Udo; Gessner, André

    2015-01-01

    Analyzing human as well as animal microbiota composition has gained growing interest because structural components and metabolites of microorganisms fundamentally influence all aspects of host physiology. Originally dominated by culture-dependent methods for exploring these ecosystems, the development of molecular techniques such as high throughput sequencing has dramatically increased our knowledge. Because many studies of the microbiota are based on the bacterial 16S ribosomal RNA (rRNA) gene targets, they can, at least in principle, be compared to determine the role of the microbiome composition for developmental processes, host metabolism, and physiology as well as different diseases. In our review, we will summarize differences and pitfalls in current experimental protocols, including all steps from nucleic acid extraction to bioinformatical analysis which may produce variation that outweighs subtle biological differences. Future developments, such as integration of metabolomic, transcriptomic, and metagenomic data sets and standardization of the procedures, will be discussed. PMID:26323632

  16. 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.

  17. 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.

  18. 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.

  19. Comparative Analyses of Plant Transcription Factor Databases

    PubMed Central

    Ramirez, Silvia R; Basu, Chhandak

    2009-01-01

    Transcription factors (TFs) are proteinaceous complex, which bind to the promoter regions in the DNA and affect transcription initiation. Plant TFs control gene expressions and genes control many physiological processes, which in turn trigger cascades of biochemical reactions in plant cells. The databases available for plant TFs are somewhat abundant but all convey different information and in different formats. Some of the publicly available plant TF databases may be narrow, while others are broad in scopes. For example, some of the best TF databases are ones that are very specific with just one plant species, but there are also other databases that contain a total of up to 20 different plant species. In this review plant TF databases ranging from a single species to many will be assessed and described. The comparative analyses of all the databases and their advantages and disadvantages are also discussed. PMID:19721806

  20. Anthocyanin analyses of Vaccinium fruit dietary supplements.

    PubMed

    Lee, Jungmin

    2016-09-01

    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 high-performance liquid chromatography [HPLC] separation) indicated if products' fruit origin listings were authentic. Over 30% of the Vaccinium fruit (cranberry, lingonberry, bilberry, and blueberry; 14 of 45) products available as dietary supplements did not contain the fruit listed as ingredients. Six supplements contained no anthocyanins. Five others had contents differing from labeled fruit (e.g., bilberry capsules containing Andean blueberry fruit). Of the samples that did contain the specified fruit (n = 27), anthocyanin content ranged from 0.04 to 14.37 mg per capsule, tablet, or teaspoon (5 g). Approaches to utilizing anthocyanins in assessment of sample authenticity, and a discussion of the challenges with anthocyanin profiles in quality control are both presented. PMID:27625778

  1. 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.

  2. 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.

  3. Statistical analyses of the relative risk.

    PubMed Central

    Gart, J J

    1979-01-01

    Let P1 be the probability of a disease in one population and P2 be the probability of a disease in a second population. The ratio of these quantities, R = P1/P2, is termed the relative risk. We consider first the analyses of the relative risk from retrospective studies. The relation between the relative risk and the odds ratio (or cross-product ratio) is developed. The odds ratio can be considered a parameter of an exponential model possessing sufficient statistics. This permits the development of exact significance tests and confidence intervals in the conditional space. Unconditional tests and intervals are also considered briefly. The consequences of misclassification errors and ignoring matching or stratifying are also considered. The various methods are extended to combination of results over the strata. Examples of case-control studies testing the association between HL-A frequencies and cancer illustrate the techniques. The parallel analyses of prospective studies are given. If P1 and P2 are small with large samples sizes the appropriate model is a Poisson distribution. This yields a exponential model with sufficient statistics. Exact conditional tests and confidence intervals can then be developed. Here we consider the case where two populations are compared adjusting for sex differences as well as for the strata (or covariate) differences such as age. The methods are applied to two examples: (1) testing in the two sexes the ratio of relative risks of skin cancer in people living in different latitudes, and (2) testing over time the ratio of the relative risks of cancer in two cities, one of which fluoridated its drinking water and one which did not. PMID:540589

  4. 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

  5. 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

    2015-08-01

    The purpose of this work was to develop a consolidated set of guiding principles for the 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 (in which population PK frequently serves as preparatory analysis for exposure-response modeling) are the main areas of influence for population PK analysis. The proposed guidelines consider 2 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 2 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 6 questions that need to be addressed throughout the report. We recommend 8 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 toward industrialization of the field of pharmacometrics such that a nontechnical audience also understands the role of pharmacometric 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

  6. 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

  7. XPS analysis of humic and fulvic acids

    SciTech Connect

    Desbene, P.L.; Silly, L.; Morizur, J.P.; Delamar, M.

    1986-01-01

    The composition of humic and fulvic acids is examined using X-ray Photoelectron Spectroscopy (XPS). The XPS results are compared to that of elemental analyses. XPS permits an easy detection of the different chemical forms of carbon and sulfur that exist in these complex compounds.

  8. Amino Acid Metabolism Disorders

    MedlinePlus

    ... defects & other health conditions > Amino acid metabolism disorders Amino acid metabolism disorders E-mail to a friend Please ... baby’s newborn screening may include testing for certain amino acid metabolism disorders. These are rare health conditions that ...

  9. Carbolic acid poisoning

    MedlinePlus

    Phenol poisoning; Phenylic acid poisoning; Hydroxybenzene poisoning; Phenic acid poisoning; Benzenol poisoning ... Below are symptoms of carbolic acid poisoning in different parts of the ... urine Decreased urine output No urine output EYES, EARS, ...

  10. Azelaic Acid Topical

    MedlinePlus

    Azelaic acid gel is used to clear the bumps, lesions, and swelling caused by rosacea (a skin disease that ... redness, flushing, and pimples on the face). Azelaic acid cream is used to treat acne. Azelaic acid ...

  11. 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 ...

  12. 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 ...

  13. Acid Lipase Disease

    MedlinePlus

    ... Awards Enhancing Diversity Find People About NINDS NINDS Acid Lipase Disease Information Page Synonym(s): Cholesterol Ester Storage ... Trials Related NINDS Publications and Information What is Acid Lipase Disease ? Acid lipase disease or deficiency occurs ...

  14. 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

  15. 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.

  16. 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.

  17. 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.

  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. Palmitic Acid and Health: Introduction.

    PubMed

    Agostoni, Carlo; Moreno, Luis; Shamir, Raanan

    2016-09-01

    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.

  20. [Technological advances in single-cell genomic analyses].

    PubMed

    Pan, Xing-Hua; Zhu, Hai-Ying; Marjani, Sadie L

    2011-01-01

    The technological progress of the genomics has transformed life science research. The main objectives of genomics are sequencing of new genomes and genome-wide identification of the function and the interaction of genes and their products. The recently developed second generation or next generation sequencing platforms and DNA microarray technology are immensely important and powerful tools for functional genomic analyses. However, their application is limited by the requirement of sufficient amounts of high quality nucleic acid samples. Therefore, when only a single cell or a very small number of cells are available or are preferred, the whole genomic sequencing or functional genomic objectives cannot be achieved conventionally and require a robust amplification method. This review highlights DNA amplification technologies and summarizes the strategies currently utilized for whole genome sequencing of a single cell, with specific focus on studies investigating microorganisms; An outline for targeted re-sequencing enabling the analysis of larger genomes is also provided. Furthermore, the review presents the emerging functional genomic applications using next-generation sequencing or microarray analysis to examine genome-wide transcriptional profile, chromatin modification and other types of protein-DNA binding profile, and CpG methylation mapping in a single cell or a very low quantity of cells. The nature of these technologies and their prospects are also addressed.

  1. Trichloroethylene exposure. Biological monitoring by breath and urine analyses.

    PubMed Central

    Droz, P O; Fernández, J G

    1978-01-01

    A mathematical model developed previously has been used to study some aspects of biological monitoring of exposure to trichloroethylene (TRI) by the analysis of this solvent in alveolar air or of its metabolites, trichloroethanol (TCE) and trichloroacetic acid (TCA), in urine. Assuming that a biological control must be representative of the time-weighted average concentration (TWA), it was found that sampling for TRI and TCE analyses must be carried out the morning after the exposure being considered. On the other hand, for a TCA analysis, the timing of urine sampling is not a determinant factor. Theortical limit concentrations have been set up for these biological indicators, but it is shown that their application must be restricted to exposures which are quantitatively reproducible from one day to the next. In all other cases, it appears that this monitoring method can lead to errors in the estimated exposure concentrations. A tentative method of biological monitoring is therefore proposed. It is based on the analysis of TCE in the urine or TRI in the alveolar air before and after the exposure being monitored. TCA is not considered to be sensitive enough to variations in the inspired concentration to be used as an indicator of a single exposure risk. PMID:629887

  2. Growth curve analyses in selected duck lines.

    PubMed

    Maruyama, K; Vinyard, B; Akbar, M K; Shafer, D J; Turk, C M

    2001-12-01

    1. Growth patterns of male ducks from 4 lines (lines A, B, C and D) selected for market weight were analysed and compared to growth patterns of ducks in the respective line 7 generations earlier. Growth curves were analysed using procedures derived from the Weibull sigmoidal function and the linear-linear relative growth rate model and simple allometry. 2. The ducks were fed ad libitum under 24-h lighting throughout the experiment. At weekly intervals from the time of hatch through 70 d of age, 16 ducks from each line were killed to determine body, carcase, breast-muscle, leg and thigh-muscle, and abdominal fat weights. 3. Line A was the heaviest line, followed by line B, line C and line D. However, body weight, carcase weight and breast-muscle weight at 49 d of age were not significantly different between lines A and B. After 7 generations of selection, the breast-muscle yield was increased to >19% and the abdominal fat percent was reduced to <1.4% in all lines. 4. The Weibull growth curve analysis of body weight showed an increase in the asymptotes during selection, while the age of the inflection point remained constant in all lines (21.3 to 26.0 d). For breast-muscle growth, ducks reached the inflection point 12.8 to 14.3 d later than for body weight. Between line A and line B, asymptotes for body weight, asymptotes for breast-muscle weight and allometric growth coefficients of breast muscle and leg and thigh muscles from 14 to 49 d were not significantly different. 5. The relative growth rate model discriminated body and breast-muscle growth patterns of line A and line B. The initial decline in the relative body growth rate was less and the time to reach the transition was longer in line A than line B. On the other hand, the initial decline in the relative breast-muscle growth rate was greater in line A than line B. PMID:11811908

  3. 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

  4. 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

  5. Applications of Parallel Processing in Configuration Analyses

    NASA Technical Reports Server (NTRS)

    Sundaram, Ppchuraman; Hager, James O.; Biedron, Robert T.

    1999-01-01

    The paper presents the recent progress made towards developing an efficient and user-friendly parallel environment for routine analysis of large CFD problems. The coarse-grain parallel version of the CFL3D Euler/Navier-Stokes analysis code, CFL3Dhp, has been ported onto most available parallel platforms. The CFL3Dhp solution accuracy on these parallel platforms has been verified with the CFL3D sequential analyses. User-friendly pre- and post-processing tools that enable a seamless transfer from sequential to parallel processing have been written. Static load balancing tool for CFL3Dhp analysis has also been implemented for achieving good parallel efficiency. For large problems, load balancing efficiency as high as 95% can be achieved even when large number of processors are used. Linear scalability of the CFL3Dhp code with increasing number of processors has also been shown using a large installed transonic nozzle boattail analysis. To highlight the fast turn-around time of parallel processing, the TCA full configuration in sideslip Navier-Stokes drag polar at supersonic cruise has been obtained in a day. CFL3Dhp is currently being used as a production analysis tool.

  6. DNA microarray analyses in higher plants.

    PubMed

    Galbraith, David W

    2006-01-01

    DNA microarrays were originally devised and described as a convenient technology for the global analysis of plant gene expression. Over the past decade, their use has expanded enormously to cover all kingdoms of living organisms. At the same time, the scope of applications of microarrays has increased beyond expression analyses, with plant genomics playing a leadership role in the on-going development of this technology. As the field has matured, the rate-limiting step has moved from that of the technical process of data generation to that of data analysis. We currently face major problems in dealing with the accumulating datasets, not simply with respect to how to archive, access, and process the huge amounts of data that have been and are being produced, but also in determining the relative quality of the different datasets. A major recognized concern is the appropriate use of statistical design in microarray experiments, without which the datasets are rendered useless. A vigorous area of current research involves the development of novel statistical tools specifically for microarray experiments. This article describes, in a necessarily selective manner, the types of platforms currently employed in microarray research and provides an overview of recent activities using these platforms in plant biology.

  7. 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

  8. Analyse de plomb dans les peintures

    NASA Astrophysics Data System (ADS)

    Broll, N.; Frezouls, J.-M.

    2002-07-01

    The analysis of lead in paints was previously used for the characterisation of pigments. In this way, the analysis is able to specify the century of the painting of a work of art. Recently this technique was also used to determine the toxicity of lead paints in building. This paper compared the result of several X-ray fluorescence spectrometer, either wave length/energy dispersion laboratory apparatus or X-ray microtube/radioactive source portable equipment's. L'analyse du plomb dans les peintures a jusqu'à présent été appliquée essentiellement pour caractériser les pigments lors de leur fabrication et pour identifier des rouvres d'art. Récemment cette technique est également utilisée pour déterminer la toxicité des peintures au plomb dans les bâtiments. Nous avons comparé les performances de plusieurs spectromètres de fluorescence X, soit de laboratoire à dispersion en longueur d'onde ou à dispersion en énergie (avec tube à rayonsX), soit portable avec source radioactive ou tube à rayons X.

  9. 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.

  10. 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

  11. Isolation and Analyses of Axonal Ribonucleoprotein Complexes

    PubMed Central

    Doron-Mandel, Ella; Alber, Stefanie; Oses, Juan A.; Medzihradszky, Katalin F.; Burlingame, Alma L.; Fainzilber, Mike; Twiss, Jeffery L.; Lee, Seung Joon

    2016-01-01

    Cytoskeleton-dependent RNA transport and local translation in axons are gaining increased attention as key processes in the maintenance and functioning of neurons. Specific axonal transcripts have been found to play roles in many aspects of axonal physiology including axon guidance, axon survival, axon to soma communication, injury response and regeneration. This axonal transcriptome requires long-range transport that is achieved by motor proteins carrying transcripts as messenger ribonucleoprotein (mRNP) complexes along microtubules. Other than transport, the mRNP complex plays a major role in the generation, maintenance and regulation of the axonal transcriptome. Identification of axonal RNA binding proteins (RBPs) and analyses of the dynamics of their mRNPs are of high interest to the field. Here we describe methods for the study of interactions between RNA and proteins in axons. First, we describe a protocol for identifying binding proteins for an RNA of interest by using RNA affinity chromatography. Subsequently, we discuss immunoprecipitation (IP) methods allowing the dissection of protein- RNA and protein-protein interactions in mRNPs under various physiological conditions. PMID:26794529

  12. 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.

  13. 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?

  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. Biomechanical analyses of rising from a chair.

    PubMed

    Schultz, A B; Alexander, N B; Ashton-Miller, J A

    1992-12-01

    Quantification of the biomechanical factors that underlie the inability to rise from a chair can help explain why this disability occurs and can aid in the design of chairs and of therapeutic intervention programs. Experimental data collected earlier from 17 young adult and two groups of elderly subjects, 23 healthy and 11 impaired, rising from a standard chair under controlled conditions were analyzed using a planar biomechanical model. The joint torque strength requirements and the location of the floor reaction force at liftoff from the seat in the different groups and under several conditions were calculated. Analyses were also made of how body configurations and the use of hand force affect these joint torques and reaction locations. In all three groups, the required torques at liftoff were modest compared to literature data on voluntary strengths. Among the three groups rising with the use of hands, at the time of liftoff from the seat, the impaired old subjects, on an average, placed the reaction force the most anterior, the healthy old subjects placed it intermediately and the young subjects placed it the least anterior, within the foot support area. Moreover, the results suggest that, at liftoff, all subjects placed more importance on locating the floor reaction force to achieve acceptable postural stability than on diminishing the magnitudes of the needed joint muscle strengths.

  17. 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.

  18. 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.

  19. Verification against perturbed analyses and observations

    NASA Astrophysics Data System (ADS)

    Bowler, N. E.; Cullen, M. J. P.; Piccolo, C.

    2015-07-01

    It has long been known that verification of a forecast against the sequence of analyses used to produce those forecasts can under-estimate the magnitude of forecast errors. Here we show that under certain conditions the verification of a short-range forecast against a perturbed analysis coming from an ensemble data assimilation scheme can give the same root-mean-square error as verification against the truth. This means that a perturbed analysis can be used as a reliable proxy for the truth. However, the conditions required for this result to hold are rather restrictive: the analysis must be optimal, the ensemble spread must be equal to the error in the mean, the ensemble size must be large and the forecast being verified must be the background forecast used in the data assimilation. Although these criteria are unlikely to be met exactly it becomes clear that for most cases verification against a perturbed analysis gives better results than verification against an unperturbed analysis. We demonstrate the application of these results in a idealised model framework and a numerical weather prediction context. In deriving this result we recall that an optimal (Kalman) analysis is one for which the analysis increments are uncorrelated with the analysis errors.

  20. Reproducibility of neuroimaging analyses across operating systems

    PubMed Central

    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. PMID:25964757

  1. 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

  2. Transportation systems analyses. Volume 1: Executive summary

    NASA Astrophysics Data System (ADS)

    1992-11-01

    The principal objective is to accomplish a systems engineering assessment of the nation's space transportation infrastructure. This analysis addresses the necessary elements to perform crew delivery and return, cargo transfer, cargo delivery and return, payload servicing, and the exploration of the Moon and Mars. Specific elements analyzed, but not limited to, include: the Space Exploration Initiative (SEI), the National Launch System (NLS), the current expendable launch vehicle (ELV) fleet, ground facilities, the Space Station Freedom (SSF), and other civil, military and commercial payloads. The performance of this study entails maintaining a broad perspective on the large number of transportation elements that could potentially comprise the U.S. space infrastructure over the next several decades. To perform this systems evaluation, top-level trade studies are conducted to enhance our understanding of the relationship between elements of the infrastructure. This broad 'infrastructure-level perspective' permits the identification of preferred infrastructures. Sensitivity analyses are performed to assure the credibility and usefulness of study results. Conceptual studies of transportation elements contribute to the systems approach by identifying elements (such as ETO node and transfer/excursion vehicles) needed in current and planned transportation systems. These studies are also a mechanism to integrate the results of relevant parallel studies.

  3. Bayesian network learning for natural hazard analyses

    NASA Astrophysics Data System (ADS)

    Vogel, K.; Riggelsen, C.; Korup, O.; Scherbaum, F.

    2014-09-01

    Modern natural hazards research requires dealing with several uncertainties that arise from limited process knowledge, measurement errors, censored and incomplete observations, and the intrinsic randomness of the governing processes. Nevertheless, deterministic analyses are still widely used in quantitative hazard assessments despite the pitfall of misestimating the hazard and any ensuing risks. In this paper we show that Bayesian networks offer a flexible framework for capturing and expressing a broad range of uncertainties encountered in natural hazard assessments. Although Bayesian networks are well studied in theory, their application to real-world data is far from straightforward, and requires specific tailoring and adaptation of existing algorithms. We offer suggestions as how to tackle frequently arising problems in this context and mainly concentrate on the handling of continuous variables, incomplete data sets, and the interaction of both. By way of three case studies from earthquake, flood, and landslide research, we demonstrate the method of data-driven Bayesian network learning, and showcase the flexibility, applicability, and benefits of this approach. Our results offer fresh and partly counterintuitive insights into well-studied multivariate problems of earthquake-induced ground motion prediction, accurate flood damage quantification, and spatially explicit landslide prediction at the regional scale. In particular, we highlight how Bayesian networks help to express information flow and independence assumptions between candidate predictors. Such knowledge is pivotal in providing scientists and decision makers with well-informed strategies for selecting adequate predictor variables for quantitative natural hazard assessments.

  4. 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.

  5. Local spin analyses using density functional theory

    NASA Astrophysics Data System (ADS)

    Abate, Bayileyegn; Peralta, Juan

    Local spin analysis is a valuable technique in computational investigations magnetic interactions on mono- and polynuclear transition metal complexes, which play vital roles in catalysis, molecular magnetism, artificial photosynthesis, and several other commercially important materials. The relative size and complex electronic structure of transition metal complexes often prohibits the use of multi-determinant approaches, and hence, practical calculations are often limited to single-determinant methods. Density functional theory (DFT) has become one of the most successful and widely used computational tools for the electronic structure study of complex chemical systems; transition metal complexes in particular. Within the DFT formalism, a more flexible and complete theoretical modeling of transition metal complexes can be achieved by considering noncollinear spins, in which the spin density is 'allowed to' adopt noncollinear structures in stead of being constrained to align parallel/antiparallel to a universal axis of magnetization. In this meeting, I will present local spin analyses results obtained using different DFT functionals. Local projection operators are used to decompose the expectation value of the total spin operator; first introduced by Clark and Davidson.

  6. Molecular Genetic Characterization of Terreic Acid Pathway in Aspergillus terreus

    DOE PAGES

    Guo, Chun-Jun; Sun, Wei-wen; Bruno, Kenneth S.; Wang, Clay C.

    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.

  7. GLC of amino acids - A survey of contamination.

    NASA Technical Reports Server (NTRS)

    Rash, J. J.; Gehrke, C. W.; Kuo, K. C.; Kvenvolden, K. A.; Stalling, D. L.; Zumwalt, R. W.

    1972-01-01

    Analyses of biological substances and geochemical samples, of both terrestrial and extraterrestrial origin, are reported for amino acids at the 1-10 nanogram per gram level achieved by gas-liquid and ion-exchange chromatographic methods. These studies have shown that nanogram quantities of amino acids, present in water extracts of geochemical samples or in other samples of low amino acid concentration, can be successfully determined only if the researcher is well aware of the possible sources of contamination.

  8. 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.

  9. Molecular and structural analyses of a novel temperature stress-induced lipocalin from wheat and Arabidopsis.

    PubMed

    Frenette Charron, Jean Benoit; Breton, Ghislain; Badawi, Mohamed; Sarhan, Fathey

    2002-04-24

    Two cDNAs corresponding to a novel lipocalin were identified from wheat and Arabidopsis. The two cDNAs designated Tatil for Triticum aestivum L. temperature-induced lipocalin and Attil for Arabidopsis thaliana temperature-induced lipocalin encode polypeptides of 190 and 186 amino acids respectively. Structure analyses indicated the presence of the three structurally conserved regions that characterize lipocalins. Sequence analyses revealed that this novel class of plant lipocalin shares homology with three evolutionarily related lipocalins: the mammalian apolipoprotein D (ApoD), the bacterial lipocalin and the insect Lazarillo. The comparison of the putative tertiary structures of both the human ApoD and the wheat TaTIL suggest that the two proteins differ in membrane attachment and ligand interaction. Northern analyses demonstrated that Tatil and Attil transcripts are upregulated during cold acclimation and heat-shock treatment. The putative functions of this novel class of plant lipocalins during temperature stresses are discussed.

  10. Phytanic acid alpha-oxidase deficiency (Refsum disease) presenting in infancy.

    PubMed

    Herbert, M A; Clayton, P T

    1994-01-01

    This report describes a patient with high serum phytanic acid concentration due to phytanic acid alpha-oxidase deficiency (classical Refsum disease). He presented unusually early, hypotonia and developmental delay being apparent by 7 months. A generalized peroxisomal disorder (so-called 'infantile Refsum disease') was excluded by analyses of pristanic acid, very long-chain fatty acids, bile acids and plasmalogen synthesis. The early presentation raises the possibility of in utero exposure to phytanate.

  11. 13C-DEPLETED MICROBIAL LIPIDS INDICATE SEASONAL METHANOTROPHIC ACTIVITY IN SHALLOW ESTUARINE SEDIMENTS

    EPA Science Inventory

    Compound specific isotope analysis was combined with phospholipid fatty acid (PLFA) analysis to identify methanotrophic activity in members of the sedimentary microbial community in the Altamaha and Savannah River estuaries in Georgia. 13C-depleted PLFAs indicate methane utilizat...

  12. 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.

  13. 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

  14. 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

  15. Phylogenomic analyses and improved resolution of Cetartiodactyla.

    PubMed

    Zhou, Xuming; Xu, Shixia; Yang, Yunxia; Zhou, Kaiya; Yang, Guang

    2011-11-01

    The remarkable antiquity, diversity, and significance in the ecology and evolution of Cetartiodactyla have inspired numerous attempts to resolve their phylogenetic relationships. However, previous analyses based on limited samples of nuclear genes or mitochondrial DNA sequences have generated results that were either inconsistent with one another, weakly supported, or highly sensitive to analytical conditions. Here, we present strongly supported results based upon over 1.4 Mb of an aligned DNA sequence matrix from 110 single-copy nuclear protein-coding genes of 21 Cetartiodactyla species, which represent major Cetartiodactyla lineages, and three species of Perissodactyla and Carnivora as outgroups. Phylogenetic analysis of this newly developed genomic sequence data using a codon-based model and recently developed models of the rate autocorrelation resolved the phylogenetic relationships of the major cetartiodactylan lineages and of those lineages with a high degree of confidence. Cetacea was found to nest within Artiodactyla as the sister group of Hippopotamidae, and Tylopoda was corroborated as the sole base clade of Cetartiodactyla. Within Cetacea, the monophyletic status of Odontoceti relative to Mysticeti, the basal position of Physeteroidea in Odontoceti, the non-monophyly of the river dolphins, and the sister relationship between Delphinidae and Monodontidae+Phocoenidae were strongly supported. In particular, the groups of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins) were validated as unnatural groups. Additionally, a very narrow time frame of ∼3 My (million years) was found for the rapid diversification of delphinids in the late Miocene, which made it difficult to resolve the phylogenetic relationships within the Delphinidae, especially for previous studies with limited data sets. The present study provides a statistically well-supported phylogenetic framework of Cetartiodactyla, which represents an important step toward ending some of

  16. 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).

  17. 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

  18. 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.

  19. 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.

  20. Integrated Genomic Analyses in Bronchopulmonary Dysplasia

    PubMed Central

    Ambalavanan, Namasivayam; Cotten, C. Michael; Page, Grier P.; Carlo, Waldemar A.; Murray, Jeffrey C.; Bhattacharya, Soumyaroop; Mariani, Thomas J.; Cuna, Alain C.; Faye-Petersen, Ona M.; Kelly, David; Higgins, Rosemary D.

    2014-01-01

    Objective To identify single nucleotide polymorphisms (SNPs) and pathways associated with bronchopulmonary dysplasia (BPD) because O2 requirement at 36 weeks’ post-menstrual age risk is strongly influenced by heritable factors. Study design A genome-wide scan was conducted on 1.2 million genotyped SNPs, and an additional 7 million imputed SNPs, using a DNA repository of extremely low birth weight infants. Genome-wide association and gene set analysis was performed for BPD or death, severe BPD or death, and severe BPD in survivors. Specific targets were validated using gene expression in BPD lung tissue and in mouse models. Results Of 751 infants analyzed, 428 developed BPD or died. No SNPs achieved genome-wide significance (p<10−8) although multiple SNPs in adenosine deaminase (ADARB2), CD44, and other genes were just below p<10−6. Of approximately 8000 pathways, 75 were significant at False Discovery Rate (FDR) <0.1 and p<0.001 for BPD/death, 95 for severe BPD/death, and 90 for severe BPD in survivors. The pathway with lowest FDR was miR-219 targets (p=1.41E-08, FDR 9.5E-05) for BPD/death and Phosphorous Oxygen Lyase Activity (includes adenylate and guanylate cyclases) for both severe BPD/death (p=5.68E-08, FDR 0.00019) and severe BPD in survivors (p=3.91E-08, FDR 0.00013). Gene expression analysis confirmed significantly increased miR-219 and CD44 in BPD. Conclusions Pathway analyses confirmed involvement of known pathways of lung development and repair (CD44, Phosphorus Oxygen Lyase Activity) and indicated novel molecules and pathways (ADARB2, Targets of miR-219) involved in genetic predisposition to BPD. PMID:25449221