WorldWideScience

Sample records for gene content estimation

  1. Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes.

    Directory of Open Access Journals (Sweden)

    Yubo Hou

    Full Text Available The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log(10-transformed protein-coding gene number (Y' versus log(10-transformed genome size (X', genome size in kbp were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y' = ln(-46.200+22.678X', whereas non-eukaryotes a linear model, Y' = 0.045+0.977X', both with high significance (p0.91. Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%-1% compared to higher and relatively stable percentages in prokaryotes and viruses (97%-47%. The eukaryotic regression models project that the smallest dinoflagellate genome (3x10(6 kbp contains 38,188 protein-coding (40,086 total genes and the largest (245x10(6 kbp 87,688 protein-coding (92,013 total genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.

  2. Identification and expression analysis of glucosinolate biosynthetic genes and estimation of glucosinolate contents in edible organs of Brassica oleracea subspecies.

    Science.gov (United States)

    Yi, Go-Eun; Robin, Arif Hasan Khan; Yang, Kiwoung; Park, Jong-In; Kang, Jong-Goo; Yang, Tae-Jin; Nou, Ill-Sup

    2015-07-20

    Glucosinolates are anti-carcinogenic, anti-oxidative biochemical compounds that defend plants from insect and microbial attack. Glucosinolates are abundant in all cruciferous crops, including all vegetable and oilseed Brassica species. Here, we studied the expression of glucosinolate biosynthesis genes and determined glucosinolate contents in the edible organs of a total of 12 genotypes of Brassica oleracea: three genotypes each from cabbage, kale, kohlrabi and cauliflower subspecies. Among the 81 genes analyzed by RT-PCR, 19 are transcription factor-related, two different sets of 25 genes are involved in aliphatic and indolic biosynthesis pathways and the rest are breakdown-related. The expression of glucosinolate-related genes in the stems of kohlrabi was remarkably different compared to leaves of cabbage and kale and florets of cauliflower as only eight genes out of 81 were expressed in the stem tissues of kohlrabi. In the stem tissue of kohlrabi, only one aliphatic transcription factor-related gene, Bol036286 (MYB28) and one indolic transcription factor-related gene, Bol030761 (MYB51), were expressed. The results indicated the expression of all genes is not essential for glucosinolate biosynthesis. Using HPLC analysis, a total of 16 different types of glucosinolates were identified in four subspecies, nine of them were aliphatic, four of them were indolic and one was aromatic. Cauliflower florets measured the highest number of 14 glucosinolates. Among the aliphatic glucosinolates, only gluconapin was found in the florets of cauliflower. Glucoiberverin and glucobrassicanapin contents were the highest in the stems of kohlrabi. The indolic methoxyglucobrassicin and aromatic gluconasturtiin accounted for the highest content in the florets of cauliflower. A further detailed investigation and analyses is required to discern the precise roles of each of the genes for aliphatic and indolic glucosinolate biosynthesis in the edible organs.

  3. Identification and Expression Analysis of Glucosinolate Biosynthetic Genes and Estimation of Glucosinolate Contents in Edible Organs of Brassica oleracea Subspecies

    Directory of Open Access Journals (Sweden)

    Go-Eun Yi

    2015-07-01

    Full Text Available Glucosinolates are anti-carcinogenic, anti-oxidative biochemical compounds that defend plants from insect and microbial attack. Glucosinolates are abundant in all cruciferous crops, including all vegetable and oilseed Brassica species. Here, we studied the expression of glucosinolate biosynthesis genes and determined glucosinolate contents in the edible organs of a total of 12 genotypes of Brassica oleracea: three genotypes each from cabbage, kale, kohlrabi and cauliflower subspecies. Among the 81 genes analyzed by RT-PCR, 19 are transcription factor-related, two different sets of 25 genes are involved in aliphatic and indolic biosynthesis pathways and the rest are breakdown-related. The expression of glucosinolate-related genes in the stems of kohlrabi was remarkably different compared to leaves of cabbage and kale and florets of cauliflower as only eight genes out of 81 were expressed in the stem tissues of kohlrabi. In the stem tissue of kohlrabi, only one aliphatic transcription factor-related gene, Bol036286 (MYB28 and one indolic transcription factor-related gene, Bol030761 (MYB51, were expressed. The results indicated the expression of all genes is not essential for glucosinolate biosynthesis. Using HPLC analysis, a total of 16 different types of glucosinolates were identified in four subspecies, nine of them were aliphatic, four of them were indolic and one was aromatic. Cauliflower florets measured the highest number of 14 glucosinolates. Among the aliphatic glucosinolates, only gluconapin was found in the florets of cauliflower. Glucoiberverin and glucobrassicanapin contents were the highest in the stems of kohlrabi. The indolic methoxyglucobrassicin and aromatic gluconasturtiin accounted for the highest content in the florets of cauliflower. A further detailed investigation and analyses is required to discern the precise roles of each of the genes for aliphatic and indolic glucosinolate biosynthesis in the edible organs.

  4. Content validity and its estimation

    Directory of Open Access Journals (Sweden)

    Yaghmale F

    2003-04-01

    Full Text Available Background: Measuring content validity of instruments are important. This type of validity can help to ensure construct validity and give confidence to the readers and researchers about instruments. content validity refers to the degree that the instrument covers the content that it is supposed to measure. For content validity two judgments are necessary: the measurable extent of each item for defining the traits and the set of items that represents all aspects of the traits. Purpose: To develop a content valid scale for assessing experience with computer usage. Methods: First a review of 2 volumes of International Journal of Nursing Studies, was conducted with onlyI article out of 13 which documented content validity did so by a 4-point content validity index (CV! and the judgment of 3 experts. Then a scale with 38 items was developed. The experts were asked to rate each item based on relevance, clarity, simplicity and ambiguity on the four-point scale. Content Validity Index (CVI for each item was determined. Result: Of 38 items, those with CVIover 0.75 remained and the rest were discarded reSulting to 25-item scale. Conclusion: Although documenting content validity of an instrument may seem expensive in terms of time and human resources, its importance warrants greater attention when a valid assessment instrument is to be developed. Keywords: Content Validity, Measuring Content Validity

  5. Estimation of areal soil water content through microwave remote sensing

    NARCIS (Netherlands)

    Oevelen, van P.J.

    2000-01-01

    In this thesis the use of microwave remote sensing to estimate soil water content is investigated. A general framework is described which is applicable to both passive and active microwave remote sensing of soil water content. The various steps necessary to estimate areal soil water content

  6. Optical Method for Estimating the Chlorophyll Contents in Plant Leaves.

    Science.gov (United States)

    Pérez-Patricio, Madaín; Camas-Anzueto, Jorge Luis; Sanchez-Alegría, Avisaí; Aguilar-González, Abiel; Gutiérrez-Miceli, Federico; Escobar-Gómez, Elías; Voisin, Yvon; Rios-Rojas, Carlos; Grajales-Coutiño, Ruben

    2018-02-22

    This work introduces a new vision-based approach for estimating chlorophyll contents in a plant leaf using reflectance and transmittance as base parameters. Images of the top and underside of the leaf are captured. To estimate the base parameters (reflectance/transmittance), a novel optical arrangement is proposed. The chlorophyll content is then estimated by using linear regression where the inputs are the reflectance and transmittance of the leaf. Performance of the proposed method for chlorophyll content estimation was compared with a spectrophotometer and a Soil Plant Analysis Development (SPAD) meter. Chlorophyll content estimation was realized for Lactuca sativa L., Azadirachta indica , Canavalia ensiforme , and Lycopersicon esculentum . Experimental results showed that-in terms of accuracy and processing speed-the proposed algorithm outperformed many of the previous vision-based approach methods that have used SPAD as a reference device. On the other hand, the accuracy reached is 91% for crops such as Azadirachta indica , where the chlorophyll value was obtained using the spectrophotometer. Additionally, it was possible to achieve an estimation of the chlorophyll content in the leaf every 200 ms with a low-cost camera and a simple optical arrangement. This non-destructive method increased accuracy in the chlorophyll content estimation by using an optical arrangement that yielded both the reflectance and transmittance information, while the required hardware is cheap.

  7. Optical Method for Estimating the Chlorophyll Contents in Plant Leaves

    Directory of Open Access Journals (Sweden)

    Madaín Pérez-Patricio

    2018-02-01

    Full Text Available This work introduces a new vision-based approach for estimating chlorophyll contents in a plant leaf using reflectance and transmittance as base parameters. Images of the top and underside of the leaf are captured. To estimate the base parameters (reflectance/transmittance, a novel optical arrangement is proposed. The chlorophyll content is then estimated by using linear regression where the inputs are the reflectance and transmittance of the leaf. Performance of the proposed method for chlorophyll content estimation was compared with a spectrophotometer and a Soil Plant Analysis Development (SPAD meter. Chlorophyll content estimation was realized for Lactuca sativa L., Azadirachta indica, Canavalia ensiforme, and Lycopersicon esculentum. Experimental results showed that—in terms of accuracy and processing speed—the proposed algorithm outperformed many of the previous vision-based approach methods that have used SPAD as a reference device. On the other hand, the accuracy reached is 91% for crops such as Azadirachta indica, where the chlorophyll value was obtained using the spectrophotometer. Additionally, it was possible to achieve an estimation of the chlorophyll content in the leaf every 200 ms with a low-cost camera and a simple optical arrangement. This non-destructive method increased accuracy in the chlorophyll content estimation by using an optical arrangement that yielded both the reflectance and transmittance information, while the required hardware is cheap.

  8. Pedotransfer functions to estimate soil water content at field capacity ...

    Indian Academy of Sciences (India)

    Priyabrata Santra

    2018-03-27

    Mar 27, 2018 ... of the global population (Millennium Ecosystem. Assessment 2005). Likewise, there is a .... Therefore, the main objective of this study was to develop PTFs for arid soils of India to estimate soil water content at FC and PWP.

  9. Estimation of Moisture Content in Coal in Coal Mills

    DEFF Research Database (Denmark)

    Odgaard, Peter Fogh; Mataji, B.

    the moisture content of the coal is proposed based on a simple dynamic energy model of a coal mill, which pulverizes and dries the coal before it is burned in the boiler. An optimal unknown input observer is designed to estimate the moisture content based on an energy balance model. The designed moisture...

  10. Estimation of Moisture Content in Coal in Coal Mills

    DEFF Research Database (Denmark)

    Odgaard, Peter Fogh; Mataji, Babak

    2006-01-01

    the moisture content of the coal is proposed based on a simple dynamic energy model of a coal mill, which pulverizes and dries the coal before it is burned in the boiler. An optimal unknown input observer is designed to estimate the moisture content based on an energy balance model. The designed moisture...

  11. Synaptotagmin gene content of the sequenced genomes

    Directory of Open Access Journals (Sweden)

    Craxton Molly

    2004-07-01

    Full Text Available Abstract Background Synaptotagmins exist as a large gene family in mammals. There is much interest in the function of certain family members which act crucially in the regulated synaptic vesicle exocytosis required for efficient neurotransmission. Knowledge of the functions of other family members is relatively poor and the presence of Synaptotagmin genes in plants indicates a role for the family as a whole which is wider than neurotransmission. Identification of the Synaptotagmin genes within completely sequenced genomes can provide the entire Synaptotagmin gene complement of each sequenced organism. Defining the detailed structures of all the Synaptotagmin genes and their encoded products can provide a useful resource for functional studies and a deeper understanding of the evolution of the gene family. The current rapid increase in the number of sequenced genomes from different branches of the tree of life, together with the public deposition of evolutionarily diverse transcript sequences make such studies worthwhile. Results I have compiled a detailed list of the Synaptotagmin genes of Caenorhabditis, Anopheles, Drosophila, Ciona, Danio, Fugu, Mus, Homo, Arabidopsis and Oryza by examining genomic and transcript sequences from public sequence databases together with some transcript sequences obtained by cDNA library screening and RT-PCR. I have compared all of the genes and investigated the relationship between plant Synaptotagmins and their non-Synaptotagmin counterparts. Conclusions I have identified and compared 98 Synaptotagmin genes from 10 sequenced genomes. Detailed comparison of transcript sequences reveals abundant and complex variation in Synaptotagmin gene expression and indicates the presence of Synaptotagmin genes in all animals and land plants. Amino acid sequence comparisons indicate patterns of conservation and diversity in function. Phylogenetic analysis shows the origin of Synaptotagmins in multicellular eukaryotes and their

  12. Problems of estimation of water content history of loesses

    International Nuclear Information System (INIS)

    Rendell, H.M.

    1983-01-01

    The estimation of 'mean water content' is a major source of error in the TL dating of many sediments. The engineering behaviour of loesses can be used, under certain circumstances, to interfer their content history. The construction of 'stress history' for particular loesses is therefore proposed in order to establish the critical conditions of moisture and applied stress (overburden) at which irreversible structural change occurs. A programme of field and laboratory tests should enable more precise estimates of water content history to be made. (author)

  13. Pathogenicity island mobility and gene content.

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Kelly Porter

    2013-10-01

    Key goals towards national biosecurity include methods for analyzing pathogens, predicting their emergence, and developing countermeasures. These goals are served by studying bacterial genes that promote pathogenicity and the pathogenicity islands that mobilize them. Cyberinfrastructure promoting an island database advances this field and enables deeper bioinformatic analysis that may identify novel pathogenicity genes. New automated methods and rich visualizations were developed for identifying pathogenicity islands, based on the principle that islands occur sporadically among closely related strains. The chromosomally-ordered pan-genome organizes all genes from a clade of strains; gaps in this visualization indicate islands, and decorations of the gene matrix facilitate exploration of island gene functions. A %E2%80%9Clearned phyloblocks%E2%80%9D method was developed for automated island identification, that trains on the phylogenetic patterns of islands identified by other methods. Learned phyloblocks better defined termini of previously identified islands in multidrug-resistant Klebsiella pneumoniae ATCC BAA-2146, and found its only antibiotic resistance island.

  14. Content Adaptive True Motion Estimator for H.264 Video Compression

    Directory of Open Access Journals (Sweden)

    P. Kulla

    2007-12-01

    Full Text Available Content adaptive true motion estimator for H.264 video coding is a fast block-based matching estimator with implemented multi-stage approach to estimate motion fields between two image frames. It considers the theory of 3D scene objects projection into 2D image plane for selection of motion vector candidates from the higher stages. The stages of the algorithm and its hierarchy are defined upon motion estimation reliability measurement (image blocks including two different directions of spatial gradient, blocks with one dominant spatial gradient and blocks including minimal spatial gradient. Parameters of the image classification into stages are set adaptively upon image structure. Due to search strategy are the estimated motion fields more corresponding to a true motion in an image sequence as in the case of conventional motion estimation algorithms that use fixed sets of motion vector candidates from tight neighborhood.

  15. Method to Estimate the Dissolved Air Content in Hydraulic Fluid

    Science.gov (United States)

    Hauser, Daniel M.

    2011-01-01

    In order to verify the air content in hydraulic fluid, an instrument was needed to measure the dissolved air content before the fluid was loaded into the system. The instrument also needed to measure the dissolved air content in situ and in real time during the de-aeration process. The current methods used to measure the dissolved air content require the fluid to be drawn from the hydraulic system, and additional offline laboratory processing time is involved. During laboratory processing, there is a potential for contamination to occur, especially when subsaturated fluid is to be analyzed. A new method measures the amount of dissolved air in hydraulic fluid through the use of a dissolved oxygen meter. The device measures the dissolved air content through an in situ, real-time process that requires no additional offline laboratory processing time. The method utilizes an instrument that measures the partial pressure of oxygen in the hydraulic fluid. By using a standardized calculation procedure that relates the oxygen partial pressure to the volume of dissolved air in solution, the dissolved air content is estimated. The technique employs luminescent quenching technology to determine the partial pressure of oxygen in the hydraulic fluid. An estimated Henry s law coefficient for oxygen and nitrogen in hydraulic fluid is calculated using a standard method to estimate the solubility of gases in lubricants. The amount of dissolved oxygen in the hydraulic fluid is estimated using the Henry s solubility coefficient and the measured partial pressure of oxygen in solution. The amount of dissolved nitrogen that is in solution is estimated by assuming that the ratio of dissolved nitrogen to dissolved oxygen is equal to the ratio of the gas solubility of nitrogen to oxygen at atmospheric pressure and temperature. The technique was performed at atmospheric pressure and room temperature. The technique could be theoretically carried out at higher pressures and elevated

  16. Field, laboratory and estimated soil-water content limits

    African Journals Online (AJOL)

    2005-01-21

    Jan 21, 2005 ... silt (0.002 to 0.05 mm) percentage to estimate the soil-water content at a given soil-water .... ar and br are the intercept and slope values of the regres- .... tions use the particle size classification of the South African Soil.

  17. Estimating chlorophyll content from Eucalyptus dunnii leaves by reflectance values

    Directory of Open Access Journals (Sweden)

    João Alexandre Lopes Dranski

    2016-06-01

    Full Text Available This study aimed to estimate photosynthetic pigments contents from leaves of Eucalyptus dunni Maiden based on values of reflectance spectra of red, green and blue colors obtained with a digital color analyzer. We collected fifty leaves from the lower third of the crown of twenty trees including young as well as mature leaves. From each leaf an area of 14 cm2 of the leaf blade was cut in which we measured reflectance values on the red, green and blue spectra with a portable digital colorimeter, obtained relative index of chlorophyll with a SPAD – 502 and determined the content of the chlorophyll a, b, and a + b by classic method of solvent extraction. We submitted the data to multiple linear regression and nonlinear analysis at 5% of error probability. It was evaluated the occurrence of multicollinearity. The negative exponential model resulted in good fit when data from red spectrum was used for chlorophyll a, green spectrum for chlorophyll b and a + b, making possible correlation coefficients between the estimated values and the extracted above 0.85. Except for the chlorophyll a content, the accuracy in estimates of photosynthetic pigments were higher than estimated by the chlorophyll meter, even with linearity between methods. Therefore, it is possible to estimate photosynthetic pigments on E. dunni leaves through values of red and green wavelengths from a digital color analyser.

  18. Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life.

    Science.gov (United States)

    Kannan, Lavanya; Li, Hua; Rubinstein, Boris; Mushegian, Arcady

    2013-12-19

    The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes and the record of orthologous relationships between their genes to infer the gene content of LUCA, the Last Universal Common Ancestor of all currently living cellular organisms. The crucial parameter, the ratio of gene losses and gene gains, was estimated from the data and was higher in models that take account of the number of in-paralogs in genomes than in models that treat gene presences and absences as a binary trait. While the numbers of genes that are placed confidently into LUCA are similar in the ML methods and in previously published methods that use various parsimony-based approaches, the identities of genes themselves are different. Most of the models of either kind treat the genes found in many existing genomes in a similar way, assigning to them high probabilities of being ancestral ("high ancestrality"). The ML models are more likely than others to assign high ancestrality to the genes that are relatively rare in the present-day genomes.

  19. Estimation of Total Body Fat from Potassium-40 Content

    International Nuclear Information System (INIS)

    Taha Mohamed Taha Ahmed, T.M.T.

    2010-01-01

    This paper concerns on estimation of total body fat from potassium 40 content using total body counting technique. The work performed using fast scan whole body counter. Calibration of that system for K-40 was carried out under assumption that uniformity distribution of radioactivity of potassium was distributed in 10 polyethylene bottles phantom. Different body sizes were represented by 2, 4, 6, 8 and 10 polyethylene bottles; each bottle has a volume of 0.04 m3. The counting efficiency for each body size was determined. Lean body weight (LBW) was calculated for ten males and ten females using appropriate mathematical equation. Total Body Potassium, TBK for the same selected group was measured using whole body counter. A mathematical relationship between lean body weight and potassium content was deduced .Fat contents for some individuals were calculated and weight/height ratio was indicated for fatness.

  20. Sensitivity of probabilistic MCO water content estimates to key assumptions

    International Nuclear Information System (INIS)

    DUNCAN, D.R.

    1999-01-01

    Sensitivity of probabilistic multi-canister overpack (MCO) water content estimates to key assumptions is evaluated with emphasis on the largest non-cladding film-contributors, water borne by particulates adhering to damage sites, and water borne by canister particulate. Calculations considered different choices of damage state degree of independence, different choices of percentile for reference high inputs, three types of input probability density function (pdfs): triangular, log-normal, and Weibull, and the number of scrap baskets in an MCO

  1. Peak flood estimation using gene expression programming

    Science.gov (United States)

    Zorn, Conrad R.; Shamseldin, Asaad Y.

    2015-12-01

    As a case study for the Auckland Region of New Zealand, this paper investigates the potential use of gene-expression programming (GEP) in predicting specific return period events in comparison to the established and widely used Regional Flood Estimation (RFE) method. Initially calibrated to 14 gauged sites, the GEP derived model was further validated to 10 and 100 year flood events with a relative errors of 29% and 18%, respectively. This is compared to the RFE method providing 48% and 44% errors for the same flood events. While the effectiveness of GEP in predicting specific return period events is made apparent, it is argued that the derived equations should be used in conjunction with those existing methodologies rather than as a replacement.

  2. A systematic methodology to estimate added sugar content of foods.

    Science.gov (United States)

    Louie, J C Y; Moshtaghian, H; Boylan, S; Flood, V M; Rangan, A M; Barclay, A W; Brand-Miller, J C; Gill, T P

    2015-02-01

    The effect of added sugar on health is a topical area of research. However, there is currently no analytical or other method to easily distinguish between added sugars and naturally occurring sugars in foods. This study aimed to develop a systematic methodology to estimate added sugar values on the basis of analytical data and ingredients of foods. A 10-step, stepwise protocol was developed, starting with objective measures (six steps) and followed by more subjective estimation (four steps) if insufficient objective data are available. The method developed was applied to an Australian food composition database (AUSNUT2007) as an example. Out of the 3874 foods available in AUSNUT2007, 2977 foods (77%) were assigned an estimated value on the basis of objective measures (steps 1-6), and 897 (23%) were assigned a subjectively estimated value (steps 7-10). Repeatability analysis showed good repeatability for estimated values in this method. We propose that this method can be considered as a standardised approach for the estimation of added sugar content of foods to improve cross-study comparison.

  3. Gene effects and combining abilities for oil content in sunflower

    Directory of Open Access Journals (Sweden)

    Jocković Milan

    2014-01-01

    Full Text Available Considering the worldwide importance of sunflower oil, objective of this study was to evaluate gene effects and combining abilities of six sunflower open pollinated varieties. Varieties were crossed according to incomplete diallel method and produced fifteen F1 progenies. Comparing the mean values of F1 progenies to parents mean in most cases superdominance was expressed as a mode of inheritance. Nonetheless, dominance of better parent and partial dominance of better parent were also recorded as a mode of inheritance. GCA/SCA ratio indicated greater importance of non-additive genetic component in oil content expression. The genetic variance analysis showed that dominant component was more important and dominant genes prevailed compared to recessive genes for oil content in sunflower.

  4. ESTIMATION OF MELANIN CONTENT IN IRIS OF HUMAN EYE

    Directory of Open Access Journals (Sweden)

    E. A. Genina

    2008-12-01

    Full Text Available Based on the experimental data obtained in vivo from digital analysis of color images of human irises, the mean melanin content in human eye irises has been estimated. For registration of color images the digital camera Olympus C-5060 has been used. The images have been obtained from irises of healthy volunteers as well as from irises of patients with open-angle glaucoma. The computer program has been developed for digital analysis of the images. The result has been useful for development of novel methods and optimization of already existing ones for non-invasive glaucoma diagnostics.

  5. Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

    Science.gov (United States)

    2013-01-01

    Background The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. Results We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes and the record of orthologous relationships between their genes to infer the gene content of LUCA, the Last Universal Common Ancestor of all currently living cellular organisms. The crucial parameter, the ratio of gene losses and gene gains, was estimated from the data and was higher in models that take account of the number of in-paralogs in genomes than in models that treat gene presences and absences as a binary trait. Conclusion While the numbers of genes that are placed confidently into LUCA are similar in the ML methods and in previously published methods that use various parsimony-based approaches, the identities of genes themselves are different. Most of the models of either kind treat the genes found in many existing genomes in a similar way, assigning to them high probabilities of being ancestral (“high ancestrality”). The ML models are more likely than others to assign high ancestrality to the genes that are relatively rare in the present-day genomes. Reviewers This article was reviewed by Martijn A Huynen, Toni Gabaldón and Fyodor Kondrashov. PMID:24354654

  6. Water content estimated from point scale to plot scale

    Science.gov (United States)

    Akyurek, Z.; Binley, A. M.; Demir, G.; Abgarmi, B.

    2017-12-01

    Soil moisture controls the portioning of rainfall into infiltration and runoff. Here we investigate measurements of soil moisture using a range of techniques spanning different spatial scales. In order to understand soil water content in a test basin, 512 km2 in area, in the south of Turkey, a Cosmic Ray CRS200B soil moisture probe was installed at elevation of 1459 m and an ML3 ThetaProbe (CS 616) soil moisture sensor was established at 5cm depth used to get continuous soil moisture. Neutron count measurements were corrected for the changes in atmospheric pressure, atmospheric water vapour and intensity of incoming neutron flux. The calibration of the volumetric soil moisture was performed, from the laboratory analysis, the bulk density varies between 1.719 (g/cm3) -1.390 (g/cm3), and the dominant soil texture is silty clay loam and silt loamThe water content reflectometer was calibrated for soil-specific conditions and soil moisture estimates were also corrected with respect to soil temperature. In order to characterize the subsurface, soil electrical resistivity tomography was used. Wenner and Schlumberger array geometries were used with electrode spacing varied from 1m- 5 m along 40 m and 200 m profiles. From the inversions of ERT data it is apparent that within 50 m distance from the CRS200B, the soil is moderately resistive to a depth of 2m and more conductive at greater depths. At greater distances from the CRS200B, the ERT results indicate more resistive soils. In addition to the ERT surveys, ground penetrating radar surveys using a common mid-point configuration was used with 200MHz antennas. The volumetric soil moisture obtained from GPR appears to overestimate those based on TDR observations. The values obtained from CS616 (at a point scale) and CRS200B (at a mesoscale) are compared with the values obtained at a plot scale. For the field study dates (20-22.06.2017) the volumetric moisture content obtained from CS616 were 25.14%, 25.22% and 25

  7. Estimates of Leaf Relative Water Content from Optical Polarization Measurements

    Science.gov (United States)

    Dahlgren, R. P.; Vanderbilt, V. C.; Daughtry, C. S. T.

    2017-12-01

    Remotely sensing the water status of plant canopies remains a long term goal of remote sensing research. Existing approaches to remotely sensing canopy water status, such as the Crop Water Stress Index (CWSI) and the Equivalent Water Thickness (EWT), have limitations. The CWSI, based upon remotely sensing canopy radiant temperature in the thermal infrared spectral region, does not work well in humid regions, requires estimates of the vapor pressure deficit near the canopy during the remote sensing over-flight and, once stomata close, provides little information regarding the canopy water status. The EWT is based upon the physics of water-light interaction in the 900-2000nm spectral region, not plant physiology. Our goal, development of a remote sensing technique for estimating plant water status based upon measurements in the VIS/NIR spectral region, would potentially provide remote sensing access to plant dehydration physiology - to the cellular photochemistry and structural changes associated with water deficits in leaves. In this research, we used optical, crossed polarization filters to measure the VIS/NIR light reflected from the leaf interior, R, as well as the leaf transmittance, T, for 78 corn (Zea mays) and soybean (Glycine max) leaves having relative water contents (RWC) between 0.60 and 0.98. Our results show that as RWC decreases R increases while T decreases. Our results tie R and T changes in the VIS/NIR to leaf physiological changes - linking the light scattered out of the drying leaf interior to its relative water content and to changes in leaf cellular structure and pigments. Our results suggest remotely sensing the physiological water status of a single leaf - and perhaps of a plant canopy - might be possible in the future.

  8. Estimation of Anthocyanin Content of Berries by NIR Method

    International Nuclear Information System (INIS)

    Zsivanovits, G.; Ludneva, D.; Iliev, A.

    2010-01-01

    Anthocyanin contents of fruits were estimated by VIS spectrophotometer and compared with spectra measured by NIR spectrophotometer (600-1100 nm step 10 nm). The aim was to find a relationship between NIR method and traditional spectrophotometric method. The testing protocol, using NIR, is easier, faster and non-destructive. NIR spectra were prepared in pairs, reflectance and transmittance. A modular spectrocomputer, realized on the basis of a monochromator and peripherals Bentham Instruments Ltd (GB) and a photometric camera created at Canning Research Institute, were used. An important feature of this camera is the possibility offered for a simultaneous measurement of both transmittance and reflectance with geometry patterns T0/180 and R0/45. The collected spectra were analyzed by CAMO Unscrambler 9.1 software, with PCA, PLS, PCR methods. Based on the analyzed spectra quality and quantity sensitive calibrations were prepared. The results showed that the NIR method allows measuring of the total anthocyanin content in fresh berry fruits or processed products without destroying them.

  9. [Estimation of vegetation canopy water content using Hyperion hyperspectral data].

    Science.gov (United States)

    Song, Xiao-Ning; Ma, Jian-Wei; Li, Xiao-Tao; Leng, Pei; Zhou, Fang-Cheng; Li, Shuang

    2013-10-01

    Vegetation canopy water content (VCWC) has widespread utility in agriculture, ecology and hydrology. Based on the PROSAIL model, a novel model for quantitative inversion of vegetation canopy water content using Hyperion hyperspectral data was explored. Firstly, characteristics of vegetation canopy reflection were investigated with the PROSAIL radiative transfer model, and it was showed that the first derivative at the right slope (980 - 1 070 nm) of the 970 nm water absorption feature (D98-1 070) was closely related to VCWC, and determination coefficient reached to 0.96. Then, bands 983, 993, 1 003, 1 013, 1 023, 1 033, 1 043, 1 053 and 1 063 nm of Hyperion data were selected to calculate D980-1 070, and VCWC was estimated using the proposed method. Finally, the retrieval result was verified using field measured data in Yingke oasis of the Heihe basin. It indicated that the mean relative error was 12.5%, RMSE was within 0.1 kg x m(-2) and the proposed model was practical and reliable. This study provides a more efficient way for obtaining VCWC of large area.

  10. Can we estimate bacterial growth rates from ribosomal RNA content?

    Energy Technology Data Exchange (ETDEWEB)

    Kemp, P.F.

    1995-12-31

    Several studies have demonstrated a strong relationship between the quantity of RNA in bacterial cells and their growth rate under laboratory conditions. It may be possible to use this relationship to provide information on the activity of natural bacterial communities, and in particular on growth rate. However, if this approach is to provide reliably interpretable information, the relationship between RNA content and growth rate must be well-understood. In particular, a requisite of such applications is that the relationship must be universal among bacteria, or alternately that the relationship can be determined and measured for specific bacterial taxa. The RNA-growth rate relationship has not been used to evaluate bacterial growth in field studies, although RNA content has been measured in single cells and in bulk extracts of field samples taken from coastal environments. These measurements have been treated as probable indicators of bacterial activity, but have not yet been interpreted as estimators of growth rate. The primary obstacle to such interpretations is a lack of information on biological and environmental factors that affect the RNA-growth rate relationship. In this paper, the available data on the RNA-growth rate relationship in bacteria will be reviewed, including hypotheses regarding the regulation of RNA synthesis and degradation as a function of growth rate and environmental factors; i.e. the basic mechanisms for maintaining RNA content in proportion to growth rate. An assessment of the published laboratory and field data, the current status of this research area, and some of the remaining questions will be presented.

  11. Genetic evaluation with major genes and polygenic inheritance when some animals are not genotyped using gene content multiple-trait BLUP.

    Science.gov (United States)

    Legarra, Andrés; Vitezica, Zulma G

    2015-11-17

    In pedigreed populations with a major gene segregating for a quantitative trait, it is not clear how to use pedigree, genotype and phenotype information when some individuals are not genotyped. We propose to consider gene content at the major gene as a second trait correlated to the quantitative trait, in a gene content multiple-trait best linear unbiased prediction (GCMTBLUP) method. The genetic covariance between the trait and gene content at the major gene is a function of the substitution effect of the gene. This genetic covariance can be written in a multiple-trait form that accommodates any pattern of missing values for either genotype or phenotype data. Effects of major gene alleles and the genetic covariance between genotype at the major gene and the phenotype can be estimated using standard EM-REML or Gibbs sampling. Prediction of breeding values with genotypes at the major gene can use multiple-trait BLUP software. Major genes with more than two alleles can be considered by including negative covariances between gene contents at each different allele. We simulated two scenarios: a selected and an unselected trait with heritabilities of 0.05 and 0.5, respectively. In both cases, the major gene explained half the genetic variation. Competing methods used imputed gene contents derived by the method of Gengler et al. or by iterative peeling. Imputed gene contents, in contrast to GCMTBLUP, do not consider information on the quantitative trait for genotype prediction. GCMTBLUP gave unbiased estimates of the gene effect, in contrast to the other methods, with less bias and better or equal accuracy of prediction. GCMTBLUP improved estimation of genotypes in non-genotyped individuals, in particular if these individuals had own phenotype records and the trait had a high heritability. Ignoring the major gene in genetic evaluation led to serious biases and decreased prediction accuracy. CGMTBLUP is the best linear predictor of additive genetic merit including

  12. Correlating Information Contents of Gene Ontology Terms to Infer Semantic Similarity of Gene Products

    Directory of Open Access Journals (Sweden)

    Mingxin Gan

    2014-01-01

    Full Text Available Successful applications of the gene ontology to the inference of functional relationships between gene products in recent years have raised the need for computational methods to automatically calculate semantic similarity between gene products based on semantic similarity of gene ontology terms. Nevertheless, existing methods, though having been widely used in a variety of applications, may significantly overestimate semantic similarity between genes that are actually not functionally related, thereby yielding misleading results in applications. To overcome this limitation, we propose to represent a gene product as a vector that is composed of information contents of gene ontology terms annotated for the gene product, and we suggest calculating similarity between two gene products as the relatedness of their corresponding vectors using three measures: Pearson’s correlation coefficient, cosine similarity, and the Jaccard index. We focus on the biological process domain of the gene ontology and annotations of yeast proteins to study the effectiveness of the proposed measures. Results show that semantic similarity scores calculated using the proposed measures are more consistent with known biological knowledge than those derived using a list of existing methods, suggesting the effectiveness of our method in characterizing functional relationships between gene products.

  13. Iron Content Affects Lipogenic Gene Expression in the Muscle of Nelore Beef Cattle.

    Directory of Open Access Journals (Sweden)

    Wellison Jarles da Silva Diniz

    Full Text Available Iron (Fe is an essential mineral for metabolism and plays a central role in a range of biochemical processes. Therefore, this study aimed to identify differentially expressed (DE genes and metabolic pathways in Longissimus dorsi (LD muscle from cattle with divergent iron content, as well as to investigate the likely role of these DE genes in biological processes underlying beef quality parameters. Samples for RNA extraction for sequencing and iron, copper, manganese, and zinc determination were collected from LD muscles at slaughter. Eight Nelore steers, with extreme genomic estimated breeding values for iron content (Fe-GEBV, were selected from a reference population of 373 animals. From the 49 annotated DE genes (FDR<0.05 found between the two groups, 18 were up-regulated and 31 down-regulated for the animals in the low Fe-GEBV group. The functional enrichment analyses identified several biological processes, such as lipid transport and metabolism, and cell growth. Lipid metabolism was the main pathway observed in the analysis of metabolic and canonical signaling pathways for the genes identified as DE, including the genes FASN, FABP4, and THRSP, which are functional candidates for beef quality, suggesting reduced lipogenic activities with lower iron content. Our results indicate metabolic pathways that are partially influenced by iron, contributing to a better understanding of its participation in skeletal muscle physiology.

  14. Multiscale Bayesian neural networks for soil water content estimation

    Science.gov (United States)

    Jana, Raghavendra B.; Mohanty, Binayak P.; Springer, Everett P.

    2008-08-01

    Artificial neural networks (ANN) have been used for some time now to estimate soil hydraulic parameters from other available or more easily measurable soil properties. However, most such uses of ANNs as pedotransfer functions (PTFs) have been at matching spatial scales (1:1) of inputs and outputs. This approach assumes that the outputs are only required at the same scale as the input data. Unfortunately, this is rarely true. Different hydrologic, hydroclimatic, and contaminant transport models require soil hydraulic parameter data at different spatial scales, depending upon their grid sizes. While conventional (deterministic) ANNs have been traditionally used in these studies, the use of Bayesian training of ANNs is a more recent development. In this paper, we develop a Bayesian framework to derive soil water retention function including its uncertainty at the point or local scale using PTFs trained with coarser-scale Soil Survey Geographic (SSURGO)-based soil data. The approach includes an ANN trained with Bayesian techniques as a PTF tool with training and validation data collected across spatial extents (scales) in two different regions in the United States. The two study areas include the Las Cruces Trench site in the Rio Grande basin of New Mexico, and the Southern Great Plains 1997 (SGP97) hydrology experimental region in Oklahoma. Each region-specific Bayesian ANN is trained using soil texture and bulk density data from the SSURGO database (scale 1:24,000), and predictions of the soil water contents at different pressure heads with point scale data (1:1) inputs are made. The resulting outputs are corrected for bias using both linear and nonlinear correction techniques. The results show good agreement between the soil water content values measured at the point scale and those predicted by the Bayesian ANN-based PTFs for both the study sites. Overall, Bayesian ANNs coupled with nonlinear bias correction are found to be very suitable tools for deriving soil

  15. Estimation of trace metal contents in locally-baked breads

    International Nuclear Information System (INIS)

    Khalid, N.; Rehman, S.

    2013-01-01

    In order to establish base line levels, estimation of some essential trace metals (Cu, Fe, Mn and Zn) has been conducted in four brands of fifteen locally baked breads of Rawalpindi /Islamabad area employing Atomic Absorption Spectrophotometry (AAS). The samples were digested in a mixture of nitric acid and perchloric acid and the analysis was done with air-acetylene flame. The reliability of the procedure employed was verify by analyzing Standard Reference Material, i.e., wheat flour (NBS-SRM-1567) for its Cu, Fe, Mn and Zn contents which were in good agreement with the certified values. The results revealed that brown breads contained higher amount of Fe 177.3 micro g g/sup -1/and Zn 19.27 micro g g/sup -1/while levels of Cu 21.90 micro g g/-sup 1/was found higher in the samples of plain bread. The determined metal concentrations in the bread samples were compared with the reported values for other countries. The effect of kneading/baking/slicing processes on the concentration levels of these metals was also studied. The daily intake of these metals through this source was calculated and compared with the recommended dietary allowance. (author)

  16. Estimation of bitumen and clay content in fine tailings

    International Nuclear Information System (INIS)

    Motta Cabrera, S.C.; Bryan, J.; Kantzas, A.

    2007-01-01

    Fine tailings are the components of tailings ponds and the by-product of the oil sand extraction process, consisting mostly of water with small amounts of bitumen, sand, silts and clays. Because of the large volumes of tailings, an important environmental and production process issue involves the reduction of the remaining bitumen in the tailings stream. This paper presented the results of a study that used low field nuclear magnetic resonance (NMR) in order to estimate the bitumen, clay and water content of synthetic tailings samples. NMR is a non-destructive technique that is utilized to determine compositions of oil and brine emulsions and the viscosity of heavy oil and bitumen as well as in reservoir characterization, measuring properties such as permeability, porosity, mobile and immobile fluids, and fluid saturations. The study prepared and tested numerous samples with variable water, bitumen, sand and clay concentrations in the NMR tool under ambient conditions. Two qualities of water and bitumen were used to prepare the synthetic samples. Each type of water and bitumen was analyzed as a single substance and in a mixture with the typical solids found in tailings composition. These included kaolinite, illite, sodium montmorillonite and sand. These synthetic samples were analyzed using different mixing configurations, as a function of time and in two different NMR tools. It was concluded that NMR is a potential application for on-line determination of tailings streams composition. 18 refs., 3 tabs., 17 figs

  17. Sequence composition and gene content of the short arm of rye (Secale cereale chromosome 1.

    Directory of Open Access Journals (Sweden)

    Silvia Fluch

    Full Text Available BACKGROUND: The purpose of the study is to elucidate the sequence composition of the short arm of rye chromosome 1 (Secale cereale with special focus on its gene content, because this portion of the rye genome is an integrated part of several hundreds of bread wheat varieties worldwide. METHODOLOGY/PRINCIPAL FINDINGS: Multiple Displacement Amplification of 1RS DNA, obtained from flow sorted 1RS chromosomes, using 1RS ditelosomic wheat-rye addition line, and subsequent Roche 454FLX sequencing of this DNA yielded 195,313,589 bp sequence information. This quantity of sequence information resulted in 0.43× sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%. A detailed analysis revealed that more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions. Repetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3% being the most abundant. More than four thousand simple sequence repeat (SSR sites mostly located in gene related sequence reads were identified for possible marker development. The existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads. Synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of Brachypodium distachyon chromosome 2. Comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice. CONCLUSIONS: The present study revealed the gene content and potential gene functions on this chromosome arm and demonstrated numerous sequence elements like SSRs and gene-related sequences, which can be utilised for future research as well as in breeding of wheat and rye.

  18. A Sensitive Measurement for Estimating Impressions of Image-Contents

    Science.gov (United States)

    Sato, Mie; Matouge, Shingo; Mori, Toshifumi; Suzuki, Noboru; Kasuga, Masao

    We have investigated Kansei Content that appeals maker's intention to viewer's kansei. An SD method is a very good way to evaluate subjective impression of image-contents. However, because the SD method is performed after subjects view the image-contents, it is difficult to examine impression of detailed scenes of the image-contents in real time. To measure viewer's impression of the image-contents in real time, we have developed a Taikan sensor. With the Taikan sensor, we investigate relations among the image-contents, the grip strength and the body temperature. We also explore the interface of the Taikan sensor to use it easily. In our experiment, a horror movie is used that largely affects emotion of the subjects. Our results show that there is a possibility that the grip strength increases when the subjects view a strained scene and that it is easy to use the Taikan sensor without its circle base that is originally installed.

  19. Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased.

    Science.gov (United States)

    Xi, Zhenxiang; Liu, Liang; Davis, Charles C

    2015-11-01

    The development and application of coalescent methods are undergoing rapid changes. One little explored area that bears on the application of gene-tree-based coalescent methods to species tree estimation is gene informativeness. Here, we investigate the accuracy of these coalescent methods when genes have minimal phylogenetic information, including the implementation of the multilocus bootstrap approach. Using simulated DNA sequences, we demonstrate that genes with minimal phylogenetic information can produce unreliable gene trees (i.e., high error in gene tree estimation), which may in turn reduce the accuracy of species tree estimation using gene-tree-based coalescent methods. We demonstrate that this problem can be alleviated by sampling more genes, as is commonly done in large-scale phylogenomic analyses. This applies even when these genes are minimally informative. If gene tree estimation is biased, however, gene-tree-based coalescent analyses will produce inconsistent results, which cannot be remedied by increasing the number of genes. In this case, it is not the gene-tree-based coalescent methods that are flawed, but rather the input data (i.e., estimated gene trees). Along these lines, the commonly used program PhyML has a tendency to infer one particular bifurcating topology even though it is best represented as a polytomy. We additionally corroborate these findings by analyzing the 183-locus mammal data set assembled by McCormack et al. (2012) using ultra-conserved elements (UCEs) and flanking DNA. Lastly, we demonstrate that when employing the multilocus bootstrap approach on this 183-locus data set, there is no strong conflict between species trees estimated from concatenation and gene-tree-based coalescent analyses, as has been previously suggested by Gatesy and Springer (2014). Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Silybin content and overexpression of chalcone synthase genes in Silybum marianum L. plants under abiotic elicitation.

    Science.gov (United States)

    El-Garhy, Hoda A S; Khattab, Salah; Moustafa, Mahmoud M A; Abou Ali, Rania; Abdel Azeiz, Ahmed Z; Elhalwagi, Abeer; El Sherif, Fadia

    2016-11-01

    Silymarin, a Silybum marianum seed extract containing a mixture of flavonolignans including silybin, is being used as an antihepatotoxic therapy for liver diseases. In this study, the enhancing effect of gamma irradiation on plant growth parameters of S. marianum under salt stress was investigated. The effect of gamma irradiation, either as a single elicitor or coupled with salinity, on chalcone synthase (CHS) gene expression and silybin A + B yield was also evaluated. The silybin A + B content in S. marianum fruits was estimated by liquid chromatography-mass spectrometry (LC-MS/MS). An increase in silybin content was accompanied by up-regulation of the CHS1, CHS2 and CHS3 genes, which are involved in the silybin biosynthetic pathway. The highest silybin A + B production (0.77 g/100 g plant DW) and transcript levels of the three studied genes (100.2-, 91.9-, and 24.3-fold increase, respectively) were obtained with 100GY gamma irradiation and 4000 ppm salty water. The CHS2 and CHS3 genes were partially sequenced and submitted to the NCBI database under the accession numbers KT252908.1 and KT252909.1, respectively. Developing new approaches to stimulate silybin biosynthetic pathways could be a useful tool to potentiate the use of plants as renewable resources of medicinal compounds. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  1. Photosynthetic bark: use of chlorophyll absorption continuum index to estimate Boswellia papyrifera bark chlorophyll content

    NARCIS (Netherlands)

    Girma, A.; Skidmore, A.K.; Bie, de C.A.J.M.; Bongers, F.; Schlerf, M.

    2013-01-01

    Quantification of chlorophyll content provides useful insight into the physiological performance of plants. Several leaf chlorophyll estimation techniques, using hyperspectral instruments, are available. However, to our knowledge, a non-destructive bark chlorophyll estimation technique is not

  2. Photosynthetic bark : use of chlorophyll absorption continuum index to estimate Boswellia papyrifera bark chlorophyll content

    NARCIS (Netherlands)

    Girma Gebrekidan, A.; Skidmore, A.K.; de Bie, C.A.J.M.; Bongers, Frans; Schlerf, Martin; Schlerf, M.

    2013-01-01

    Quantification of chlorophyll content provides useful insight into the physiological performance of plants. Several leaf chlorophyll estimation techniques, using hyperspectral instruments, are available. However, to our knowledge, a non-destructive bark chlorophyll estimation technique is not

  3. Pedotransfer functions to estimate soil water content at field capacity ...

    Indian Academy of Sciences (India)

    20

    Soil water retention, Dry lands, Western India, Pedotransfer functions, Soil moisture calculator. 1. 2. 3. 4 ..... samples although it is known that structure and macro-porosity of the sample affect water retention (Unger ..... and OC content has positive influence on water retention whereas interaction of clay and OC has negative ...

  4. Gene duplication and divergence affecting drug content in Cannabis sativa.

    Science.gov (United States)

    Weiblen, George D; Wenger, Jonathan P; Craft, Kathleen J; ElSohly, Mahmoud A; Mehmedic, Zlatko; Treiber, Erin L; Marks, M David

    2015-12-01

    Cannabis sativa is an economically important source of durable fibers, nutritious seeds, and psychoactive drugs but few economic plants are so poorly understood genetically. Marijuana and hemp were crossed to evaluate competing models of cannabinoid inheritance and to explain the predominance of tetrahydrocannabinolic acid (THCA) in marijuana compared with cannabidiolic acid (CBDA) in hemp. Individuals in the resulting F2 population were assessed for differential expression of cannabinoid synthase genes and were used in linkage mapping. Genetic markers associated with divergent cannabinoid phenotypes were identified. Although phenotypic segregation and a major quantitative trait locus (QTL) for the THCA/CBDA ratio were consistent with a simple model of codominant alleles at a single locus, the diversity of THCA and CBDA synthase sequences observed in the mapping population, the position of enzyme coding loci on the map, and patterns of expression suggest multiple linked loci. Phylogenetic analysis further suggests a history of duplication and divergence affecting drug content. Marijuana is distinguished from hemp by a nonfunctional CBDA synthase that appears to have been positively selected to enhance psychoactivity. An unlinked QTL for cannabinoid quantity may also have played a role in the recent escalation of drug potency. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  5. Effective Laboratory Method of Chromite Content Estimation in Reclaimed Sands

    Directory of Open Access Journals (Sweden)

    Ignaszak Z.

    2016-09-01

    Full Text Available The paper presents an original method of measuring the actual chromite content in the circulating moulding sand of foundry. This type of material is applied for production of moulds. This is the case of foundry which most frequently perform heavy casting in which for the construction of chemical hardening mould is used, both the quartz sand and chromite sand. After the dry reclamation of used moulding sand, both types of sands are mixed in various ratios resulting that in reclaimed sand silos, the layers of varying content of chromite in mixture are observed. For chromite recuperation from the circulating moulding sand there are applied the appropriate installations equipped with separate elements generating locally strong magnetic field. The knowledge of the current ratio of chromite and quartz sand allows to optimize the settings of installation and control of the separation efficiency. The arduous and time-consuming method of determining the content of chromite using bromoform liquid requires operational powers and precautions during using this toxic liquid. It was developed and tested the new, uncomplicated gravimetric laboratory method using powerful permanent magnets (neodymium. The method is used in the production conditions of casting for current inspection of chromite quantity in used sand in reclamation plant.

  6. Pedotransfer functions to estimate soil water content at field capacity ...

    Indian Academy of Sciences (India)

    20

    available scarce water resources in dry land agriculture, but direct measurement thereof for multiple locations in the field is not always feasible. Therefore, pedotransfer functions (PTFs) were developed to estimate soil water retention at FC and PWP for dryland soils of India. A soil database available for Arid Western India ...

  7. Estimation of U content in coffee samples by fission-track counting

    International Nuclear Information System (INIS)

    Sharma, P.K.; Lal, N.; Nagpaul, K.K.

    1985-01-01

    Because coffee is consumed in large quantities by humans, the authors undertook the study of the uranium content of coffee as a continuation of earlier work to estimate the U content of foodstuffs. Since literature on this subject is scarce, they decided to use the well-established fission-track-counting technique to determine the U content of coffee

  8. Components of variance involved in estimating soil water content and water content change using a neutron moisture meter

    International Nuclear Information System (INIS)

    Sinclair, D.F.; Williams, J.

    1979-01-01

    There have been significant developments in the design and use of neutron moisture meters since Hewlett et al.(1964) investigated the sources of variance when using this instrument to estimate soil moisture. There appears to be little in the literature, however, which updates these findings. This paper aims to isolate the components of variance when moisture content and moisture change are estimated using the neutron scattering method with current technology and methods

  9. Mercury content in Chilean fish and estimated intake levels.

    Science.gov (United States)

    Cortes, Sandra; Fortt, Antonia

    2007-09-01

    The intake of fish products is a major public health concern due to possible methyl mercury exposure, which is especially toxic to the human nervous system. This pilot study (n = 46) was designed to determine mercury concentrations in fish products for national consumption (Chilean jack mackerel, hake, Chilean mussel, tuna) and for export (salmon, Patagonian toothfish, swordfish, southern hake), and to estimate the exposure of the general population. The fish products were collected from markets in Talcahuano, Puerto Montt and Santiago. Samples were analyzed at the National Environmental Center by cold vapor atomic absorption spectrophotometry. Mercury levels in swordfish and one canned tuna sample exceeded levels prescribed by national and international standards. The remaining two export products (Patagonian toothfish, also known as Chilean sea bass, and salmon) complied with international limits, which are more demanding than Chilean regulations. Theoretical estimates of mercury intake varied from 0.08 to 3.8 microg kg(-1) bw day(-1) for high fish consumers, exceeding the provisional tolerable intake for tuna, Chilean seabass, Chilean jack mackerel and swordfish. This group appears to be at the greatest risk from mercury contamination among the Chilean population.

  10. [Vegetation index estimation by chlorophyll content of grassland based on spectral analysis].

    Science.gov (United States)

    Xiao, Han; Chen, Xiu-Wan; Yang, Zhen-Yu; Li, Huai-Yu; Zhu, Han

    2014-11-01

    Comparing the methods of existing remote sensing research on the estimation of chlorophyll content, the present paper confirms that the vegetation index is one of the most practical and popular research methods. In recent years, the increasingly serious problem of grassland degradation. This paper, firstly, analyzes the measured reflectance spectral curve and its first derivative curve in the grasslands of Songpan, Sichuan and Gongger, Inner Mongolia, conducts correlation analysis between these two spectral curves and chlorophyll content, and finds out the regulation between REP (red edge position) and grassland chlorophyll content, that is, the higher the chlorophyll content is, the higher the REIP (red-edge inflection point) value would be. Then, this paper constructs GCI (grassland chlorophyll index) and selects the most suitable band for retrieval. Finally, this paper calculates the GCI by the use of satellite hyperspectral image, conducts the verification and accuracy analysis of the calculation results compared with chlorophyll content data collected from field of twice experiments. The result shows that for grassland chlorophyll content, GCI has stronger sensitivity than other indices of chlorophyll, and has higher estimation accuracy. GCI is the first proposed to estimate the grassland chlorophyll content, and has wide application potential for the remote sensing retrieval of grassland chlorophyll content. In addition, the grassland chlorophyll content estimation method based on remote sensing retrieval in this paper provides new research ideas for other vegetation biochemical parameters' estimation, vegetation growth status' evaluation and grassland ecological environment change's monitoring.

  11. [Estimation of forest canopy chlorophyll content based on PROSPECT and SAIL models].

    Science.gov (United States)

    Yang, Xi-guang; Fan, Wen-yi; Yu, Ying

    2010-11-01

    The forest canopy chlorophyll content directly reflects the health and stress of forest. The accurate estimation of the forest canopy chlorophyll content is a significant foundation for researching forest ecosystem cycle models. In the present paper, the inversion of the forest canopy chlorophyll content was based on PROSPECT and SAIL models from the physical mechanism angle. First, leaf spectrum and canopy spectrum were simulated by PROSPECT and SAIL models respectively. And leaf chlorophyll content look-up-table was established for leaf chlorophyll content retrieval. Then leaf chlorophyll content was converted into canopy chlorophyll content by Leaf Area Index (LAD). Finally, canopy chlorophyll content was estimated from Hyperion image. The results indicated that the main effect bands of chlorophyll content were 400-900 nm, the simulation of leaf and canopy spectrum by PROSPECT and SAIL models fit better with the measured spectrum with 7.06% and 16.49% relative error respectively, the RMSE of LAI inversion was 0. 542 6 and the forest canopy chlorophyll content was estimated better by PROSPECT and SAIL models with precision = 77.02%.

  12. Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

    OpenAIRE

    Kannan, Lavanya; Li, Hua; Rubinstein, Boris; Mushegian, Arcady

    2013-01-01

    Background The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. Results We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes...

  13. Remote Sensing of Vegetation Nitrogen Content for Spatially Explicit Carbon and Water Cycle Estimation

    Science.gov (United States)

    Zhang, Y. L.; Miller, J. R.; Chen, J. M.

    2009-05-01

    Foliage nitrogen concentration is a determinant of photosynthetic capacity of leaves, thereby an important input to ecological models for estimating terrestrial carbon and water budgets. Recently, spectrally continuous airborne hyperspectral remote sensing imagery has proven to be useful for retrieving an important related parameter, total chlorophyll content at both leaf and canopy scales. Thus remote sensing of vegetation biochemical parameters has promising potential for improving the prediction of global carbon and water balance patterns. In this research, we explored the feasibility of estimating leaf nitrogen content using hyperspectral remote sensing data for spatially explicit estimation of carbon and water budgets. Multi-year measurements of leaf biochemical contents of seven major boreal forest species were carried out in northeastern Ontario, Canada. The variation of leaf chlorophyll and nitrogen content in response to various growth conditions, and the relationship between them,were investigated. Despite differences in plant type (deciduous and evergreen), leaf age, stand growth conditions and developmental stages, leaf nitrogen content was strongly correlated with leaf chlorophyll content on a mass basis during the active growing season (r2=0.78). With this general correlation, leaf nitrogen content was estimated from leaf chlorophyll content at an accuracy of RMSE=2.2 mg/g, equivalent to 20.5% of the average measured leaf nitrogen content. Based on this correlation and a hyperspectral remote sensing algorithm for leaf chlorophyll content retrieval, the spatial variation of leaf nitrogen content was inferred from the airborne hyperspectral remote sensing imagery acquired by Compact Airborne Spectrographic Imager (CASI). A process-based ecological model Boreal Ecosystem Productivity Simulator (BEPS) was used for estimating terrestrial carbon and water budgets. In contrast to the scenario with leaf nitrogen content assigned as a constant value without

  14. Estimation of deuterium content in organic compounds by mass spectrometric methods

    International Nuclear Information System (INIS)

    Dave, S.M.; Goomer, N.C.

    1979-01-01

    Many organic sompounds are finding increasing importance in heavy water enrichment programme. New methods based on quantitative chemical conversion have been developed and standardized in for estimating deuterium contents of the exchanging organic molecules by mass spectrometry. The methods have been selected in such a way that the deuterium contents of both exchangeable as well as total hydrogens in the molecule can be conveniently estimated. (auth.)

  15. Energy content estimation by collegians for portion standardized foods frequently consumed in Korea.

    Science.gov (United States)

    Kim, Jin; Lee, Hee Jung; Lee, Hyun Jung; Lee, Sun Ha; Yun, Jee-Young; Choi, Mi-Kyeong; Kim, Mi-Hyun

    2014-01-01

    The purpose of this study is to estimate Korean collegians' knowledge of energy content in the standard portion size of foods frequently consumed in Korea and to investigate the differences in knowledge between gender groups. A total of 600 collegians participated in this study. Participants' knowledge was assessed based on their estimation on the energy content of 30 selected food items with their actual-size photo images. Standard portion size of food was based on 2010 Korean Dietary Reference Intakes, and the percentage of participants who accurately estimated (that is, within 20% of the true value) the energy content of the standard portion size was calculated for each food item. The food for which the most participants provided the accurate estimation was ramyun (instant noodles) (67.7%), followed by cooked rice (57.8%). The proportion of students who overestimated the energy content was highest for vegetables (68.8%) and beverages (68.1%). The proportion of students who underestimated the energy content was highest for grains and starches (42.0%) and fruits (37.1%). Female students were more likely to check energy content of foods that they consumed than male students. From these results, it was concluded that the knowledge on food energy content was poor among collegians, with some gender difference. Therefore, in the future, nutrition education programs should give greater attention to improving knowledge on calorie content and to helping them apply this knowledge in order to develop effective dietary plans.

  16. Estimation of the oxalate content of foods and daily oxalate intake

    Science.gov (United States)

    Holmes, R. P.; Kennedy, M.

    2000-01-01

    BACKGROUND: The amount of oxalate ingested may be an important risk factor in the development of idiopathic calcium oxalate nephrolithiasis. Reliable food tables listing the oxalate content of foods are currently not available. The aim of this research was to develop an accurate and reliable method to measure the food content of oxalate. METHODS: Capillary electrophoresis (CE) and ion chromatography (IC) were compared as direct techniques for the estimation of the oxalate content of foods. Foods were thoroughly homogenized in acid, heat extracted, and clarified by centrifugation and filtration before dilution in water for analysis. Five individuals consuming self-selected diets maintained food records for three days to determine their mean daily oxalate intakes. RESULTS: Both techniques were capable of adequately measuring the oxalate in foods with a significant oxalate content. With foods of very low oxalate content (choice over IC for estimating the oxalate content of foods with a medium (>10 mg/100 g) to high oxalate content due to a faster analysis time and lower running costs, whereas IC may be better suited for the analysis of foods with a low oxalate content. Accurate estimates of the oxalate content of foods should permit the role of dietary oxalate in urinary oxalate excretion and stone formation to be clarified. Other factors, apart from the amount of oxalate ingested, appear to exert a major influence over the amount of oxalate excreted in the urine.

  17. Estimation of canopy carotenoid content of winter wheat using multi-angle hyperspectral data

    Science.gov (United States)

    Kong, Weiping; Huang, Wenjiang; Liu, Jiangui; Chen, Pengfei; Qin, Qiming; Ye, Huichun; Peng, Dailiang; Dong, Yingying; Mortimer, A. Hugh

    2017-11-01

    Precise estimation of carotenoid (Car) content in crops, using remote sensing data, could be helpful for agricultural resources management. Conventional methods for Car content estimation were mostly based on reflectance data acquired from nadir direction. However, reflectance acquired at this direction is highly influenced by canopy structure and soil background reflectance. Off-nadir observation is less impacted, and multi-angle viewing data are proven to contain additional information rarely exploited for crop Car content estimation. The objective of this study was to explore the potential of multi-angle observation data for winter wheat canopy Car content estimation. Canopy spectral reflectance was measured from nadir as well as from a series of off-nadir directions during different growing stages of winter wheat, with concurrent canopy Car content measurements. Correlation analyses were performed between Car content and the original and continuum removed spectral reflectance. Spectral features and previously published indices were derived from data obtained at different viewing angles and were tested for Car content estimation. Results showed that spectral features and indices obtained from backscattering directions between 20° and 40° view zenith angle had a stronger correlation with Car content than that from the nadir direction, and the strongest correlation was observed from about 30° backscattering direction. Spectral absorption depth at 500 nm derived from spectral data obtained from 30° backscattering direction was found to reduce the difference induced by plant cultivars greatly. It was the most suitable for winter wheat canopy Car estimation, with a coefficient of determination 0.79 and a root mean square error of 19.03 mg/m2. This work indicates the importance of taking viewing geometry effect into account when using spectral features/indices and provides new insight in the application of multi-angle remote sensing for the estimation of crop

  18. Consumers' estimation of calorie content at fast food restaurants: cross sectional observational study.

    Science.gov (United States)

    Block, Jason P; Condon, Suzanne K; Kleinman, Ken; Mullen, Jewel; Linakis, Stephanie; Rifas-Shiman, Sheryl; Gillman, Matthew W

    2013-05-23

    To investigate estimation of calorie (energy) content of meals from fast food restaurants in adults, adolescents, and school age children. Cross sectional study of repeated visits to fast food restaurant chains. 89 fast food restaurants in four cities in New England, United States: McDonald's, Burger King, Subway, Wendy's, KFC, Dunkin' Donuts. 1877 adults and 330 school age children visiting restaurants at dinnertime (evening meal) in 2010 and 2011; 1178 adolescents visiting restaurants after school or at lunchtime in 2010 and 2011. Estimated calorie content of purchased meals. Among adults, adolescents, and school age children, the mean actual calorie content of meals was 836 calories (SD 465), 756 calories (SD 455), and 733 calories (SD 359), respectively. A calorie is equivalent to 4.18 kJ. Compared with the actual figures, participants underestimated calorie content by means of 175 calories (95% confidence interval 145 to 205), 259 calories (227 to 291), and 175 calories (108 to 242), respectively. In multivariable linear regression models, underestimation of calorie content increased substantially as the actual meal calorie content increased. Adults and adolescents eating at Subway estimated 20% and 25% lower calorie content than McDonald's diners (relative change 0.80, 95% confidence interval 0.66 to 0.96; 0.75, 0.57 to 0.99). People eating at fast food restaurants underestimate the calorie content of meals, especially large meals. Education of consumers through calorie menu labeling and other outreach efforts might reduce the large degree of underestimation.

  19. Bias in estimating food consumption of fish from stomach-content analysis

    DEFF Research Database (Denmark)

    Rindorf, Anna; Lewy, Peter

    2004-01-01

    This study presents an analysis of the bias introduced by using simplified methods to calculate food intake of fish from stomach contents. Three sources of bias were considered: (1) the effect of estimating consumption based on a limited number of stomach samples, (2) the effect of using average......, a serious positive bias was introduced by estimating food intake from the contents of pooled stomach samples. An expression is given that can be used to correct analytically for this bias. A new method, which takes into account the distribution and evacuation of individual prey types as well as the effect...... of other food in the stomach on evacuation, is suggested for estimating the intake of separate prey types. Simplifying the estimation by ignoring these factors biased estimates of consumption of individual prey types by up to 150% in a data example....

  20. Estimating the fuel moisture content to control the reciprocating grate furnace firing wet woody biomass

    International Nuclear Information System (INIS)

    Striūgas, N.; Vorotinskienė, L.; Paulauskas, R.; Navakas, R.; Džiugys, A.; Narbutas, L.

    2017-01-01

    Highlights: • Combustion of biomass with varying moisture content might lead to unstable operation of a furnace. • Method for automatic control of a furnace fired with wet biomass was developed. • Fuel moisture is estimated by cost-effective indirect method for predictive control. • Fuel moisture estimation methods and furnace control algorithm were validated in an industrial boiler. - Abstract: In small countries like Lithuania with a widespread district heating system, 5–10 MW moving grate biomass furnaces equipped with water boilers and condensing economisers are widely used. Such systems are designed for firing biomass fuels; however, varying fuel moisture, mostly in the range from 30% to 60%, complicates the automated operation. Without manual adjustment of the grate motion mode and other parameters, unstable operation or even extinction of the furnace is possible. To ensure stable furnace operation with moist fuel, the indirect method to estimate the fuel moisture content was developed based on the heat balance of the flue gas condensing economiser. The developed method was implemented into the automatic control unit of the furnace to estimate the moisture content in the feedstock and predictively adjust the furnace parameters for optimal fuel combustion. The indirect method based on the economiser heat balance was experimentally validated in a 6 MW grate-fired furnace fuelled by biomass with moisture contents of 37, 46, 50, 54 and 60%. The analysis shows that the estimated and manually measured values of the fuel moisture content do not differ by more than 3%. This deviation indicates that the indirect fuel moisture calculation method is sufficiently precise and the calculated moisture content varies proportionally to changes in the thermal capacity of the economiser. By smoothing the data using sliding weighted averaging, the oscillations of the fuel moisture content were identified.

  1. Historical Tank Content Estimate for the Northwest Quandrant of the Hanford 200 East Area

    International Nuclear Information System (INIS)

    Brevick, C.H.; Gaddis, L.A.; Pickett, W.W.

    1994-06-01

    Historical Tank Content Estimate of the Northeast Quadrant provides historical evaluations on a tank by tank basis of the radioactive mixed wastes stored in the underground single-shell tanks of the Hanford 200 East area. This report summaries historical information such at waste history, temperature, tank integrity, inventory estimates and tank level history on a tank by tank basis. Tank Farm aerial photos and in-tank photos of each tank are provided. A brief description of instrumentation methods used for waste tank surveillance, along with the components of the data management effort, such as waste status and Transaction Record Summary, Tank Layering Model, Defined Waste Types, and Inventory Estimates to generate these tank content estimates are also given in this report

  2. Historical Tank Content Estimate for the Northwest Quandrant of the Hanford 200 East Area

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.; Gaddis, L.A.; Pickett, W.W.

    1994-06-01

    Historical Tank Content Estimate of the Northeast Quadrant provides historical evaluations on a tank by tank basis of the radioactive mixed wastes stored in the underground single-shell tanks of the Hanford 200 East area. This report summaries historical information such at waste history, temperature, tank integrity, inventory estimates and tank level history on a tank by tank basis. Tank Farm aerial photos and in-tank photos of each tank are provided. A brief description of instrumentation methods used for waste tank surveillance, along with the components of the data management effort, such as waste status and Transaction Record Summary, Tank Layering Model, Defined Waste Types, and Inventory Estimates to generate these tank content estimates are also given in this report.

  3. Supporting document for the Southeast Quadrant historical tank content estimate report for SY-tank farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Gaddis, L.A.; Consort, S.D.

    1995-01-01

    Historical Tank Content Estimate of the Southeast Quadrant provides historical evaluations on a tank by tank basis of the radioactive mixed wastes stored in the underground double-shell tanks of the Hanford 200 East and West Areas. This report summarizes historical information such as waste history, temperature profiles, psychrometric data, tank integrity, inventory estimates and tank level history on a tank by tank basis. Tank Farm aerial photos and in-tank photos of each tank are provided. A brief description of instrumentation methods used for waste tank surveillance are included. Components of the data management effort, such as Waste Status and Transaction Record Summary, Tank Layer Model, Supernatant Mixing Model, Defined Waste Types, and Inventory Estimates which generate these tank content estimates, are also given in this report

  4. Estimation of hydraulic conductivity on clay content in soil determined from resistivity data

    Energy Technology Data Exchange (ETDEWEB)

    Shevnin, Vladimir; Delgado-Rodriguez, Omar; Mousatov, Aleksandr [Mexican Petroleum Institute, Mexico, D.F. (Mexico); Ryjov, Albert [Moscow State Geological Prospecting Academy, Geophysical Faculty, Moscow (Russian Federation)

    2006-07-15

    The influence of clay content in sandy and clayey soils on hydraulic conductivity (filtration coefficient) is considered. A review of published experimental data on the relationship of hydraulic conductivity with soil lithology and grain size, as dependent on clay content is presented. Theoretical calculations include clay content. Experimental and calculated data agree, and several approximation formulas for filtration coefficient vs clay content are presented. Clay content in soil is estimated from electric resistivity data obtained from 2D VES interpretation. A two-step method is proposed, the first step including clay content calculating from soil resistivity and groundwater salinity, and the second step including filtration coefficient estimating from clay content. Two applications are presented. [Spanish] El contenido de arcilla en suelos areno-arcillosos influye sobre la permeabilidad hidraulica (coeficiente de filtracion). Se presenta una revision de datos experimentales publicados que relacionan el coeficiente de filtracion con el tipo litologico del suelo y el tamano de las particulas. A partir de calculos teoricos, se modifican las conocidas formulas que relacionan el coeficiente de filtracion con el contenido de arcilla. Se estima el contenido de arcilla a partir de los datos interpretados por el metodo SEV, y se propone un procedimiento para la estimacion del coeficiente de filtracion: (a) calculo del contenido de arcilla a partir de la resistividad del suelo y de la salinidad del agua subterranea, (b) estimacion del coeficiente de filtracion a partir del contenido de arcilla. Se presentan algunos ejemplos de la aplicacion de esta metodologia.

  5. Genome-wide association study identifies candidate genes for starch content regulation in maize kernels

    Directory of Open Access Journals (Sweden)

    Na Liu

    2016-07-01

    Full Text Available Kernel starch content is an important trait in maize (Zea mays L. as it accounts for 65% to 75% of the dry kernel weight and positively correlates with seed yield. A number of starch synthesis-related genes have been identified in maize in recent years. However, many loci underlying variation in starch content among maize inbred lines still remain to be identified. The current study is a genome-wide association study that used a set of 263 maize inbred lines. In this panel, the average kernel starch content was 66.99%, ranging from 60.60% to 71.58% over the three study years. These inbred lines were genotyped with the SNP50 BeadChip maize array, which is comprised of 56,110 evenly spaced, random SNPs. Population structure was controlled by a mixed linear model (MLM as implemented in the software package TASSEL. After the statistical analyses, four SNPs were identified as significantly associated with starch content (P ≤ 0.0001, among which one each are located on chromosomes 1 and 5 and two are on chromosome 2. Furthermore, 77 candidate genes associated with starch synthesis were found within the 100-kb intervals containing these four QTLs, and four highly associated genes were within 20-kb intervals of the associated SNPs. Among the four genes, Glucose-1-phosphate adenylyltransferase (APS1; Gene ID GRMZM2G163437 is known as an important regulator of kernel starch content. The identified SNPs, QTLs, and candidate genes may not only be readily used for germplasm improvement by marker-assisted selection in breeding, but can also elucidate the genetic basis of starch content. Further studies on these identified candidate genes may help determine the molecular mechanisms regulating kernel starch content in maize and other important cereal crops.

  6. Consumers’ estimation of calorie content at fast food restaurants: cross sectional observational study

    Science.gov (United States)

    Condon, Suzanne K; Kleinman, Ken; Mullen, Jewel; Linakis, Stephanie; Rifas-Shiman, Sheryl; Gillman, Matthew W

    2013-01-01

    Objective To investigate estimation of calorie (energy) content of meals from fast food restaurants in adults, adolescents, and school age children. Design Cross sectional study of repeated visits to fast food restaurant chains. Setting 89 fast food restaurants in four cities in New England, United States: McDonald’s, Burger King, Subway, Wendy’s, KFC, Dunkin’ Donuts. Participants 1877 adults and 330 school age children visiting restaurants at dinnertime (evening meal) in 2010 and 2011; 1178 adolescents visiting restaurants after school or at lunchtime in 2010 and 2011. Main outcome measure Estimated calorie content of purchased meals. Results Among adults, adolescents, and school age children, the mean actual calorie content of meals was 836 calories (SD 465), 756 calories (SD 455), and 733 calories (SD 359), respectively. A calorie is equivalent to 4.18 kJ. Compared with the actual figures, participants underestimated calorie content by means of 175 calories (95% confidence interval 145 to 205), 259 calories (227 to 291), and 175 calories (108 to 242), respectively. In multivariable linear regression models, underestimation of calorie content increased substantially as the actual meal calorie content increased. Adults and adolescents eating at Subway estimated 20% and 25% lower calorie content than McDonald’s diners (relative change 0.80, 95% confidence interval 0.66 to 0.96; 0.75, 0.57 to 0.99). Conclusions People eating at fast food restaurants underestimate the calorie content of meals, especially large meals. Education of consumers through calorie menu labeling and other outreach efforts might reduce the large degree of underestimation. PMID:23704170

  7. Leaf Chlorophyll Content Estimation of Winter Wheat Based on Visible and Near-Infrared Sensors.

    Science.gov (United States)

    Zhang, Jianfeng; Han, Wenting; Huang, Lvwen; Zhang, Zhiyong; Ma, Yimian; Hu, Yamin

    2016-03-25

    The leaf chlorophyll content is one of the most important factors for the growth of winter wheat. Visual and near-infrared sensors are a quick and non-destructive testing technology for the estimation of crop leaf chlorophyll content. In this paper, a new approach is developed for leaf chlorophyll content estimation of winter wheat based on visible and near-infrared sensors. First, the sliding window smoothing (SWS) was integrated with the multiplicative scatter correction (MSC) or the standard normal variable transformation (SNV) to preprocess the reflectance spectra images of wheat leaves. Then, a model for the relationship between the leaf relative chlorophyll content and the reflectance spectra was developed using the partial least squares (PLS) and the back propagation neural network. A total of 300 samples from areas surrounding Yangling, China, were used for the experimental studies. The samples of visible and near-infrared spectroscopy at the wavelength of 450,900 nm were preprocessed using SWS, MSC and SNV. The experimental results indicate that the preprocessing using SWS and SNV and then modeling using PLS can achieve the most accurate estimation, with the correlation coefficient at 0.8492 and the root mean square error at 1.7216. Thus, the proposed approach can be widely used for winter wheat chlorophyll content analysis.

  8. Supporting document for the historical tank content estimate for AN-tank farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.; Stroup, J.L.; Funk, J.W., Fluor Daniel Hanford

    1997-03-06

    This Supporting Document provides historical in-depth characterization information on AN-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the Southeast Quadrant of the Hanford 200 Areas.

  9. Supporting document for the historical tank content estimate for AY-tank farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C H; Stroup, J L; Funk, J. W.

    1997-03-12

    This Supporting Document provides historical in-depth characterization information on AY-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the Southeast Quadrant of the Hanford 200 Areas.

  10. Supporting document for the historical tank content estimate for AW-tank farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H., Stroup, J.L.; Funk, J.W., Fluor Daniel Hanford

    1997-03-06

    This Supporting Document provides historical in-depth characterization information on AW-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the Southeast Quadrant of the Hanford 200 Areas.

  11. Supporting document for the historical tank content estimate for the S-tank farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H., Fluor Daniel Hanford

    1997-02-25

    This Supporting Document provides historical in-depth characterization information on S-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the Southwest Quadrant of the Hanford 200 West Area.

  12. Supporting document for the historical tank content estimate for AP-tank farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.; Stroup, J.L.; Funk, J.W., Fluor Daniel Hanford

    1997-03-06

    This Supporting Document provides historical in-depth characterization information on AP-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the Southeast Quadrant of the Hanford 200 Areas.

  13. Supporting document for the historical tank content estimate for the SX-tank farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H., Fluor Daniel Hanford

    1997-02-25

    This Supporting Document provides historical in-depth characterization information on SX-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the Southwest Quadrant of the Hanford 200 West Area.

  14. Supporting document for the historical tank content estimate for BY-Tank farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.

    1996-06-28

    This Supporting Document provides historical in-depth characterization information on BY-Tank Farm, such as historical waste transfer and level data, tank physical information,temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the northeast quadrant of the Hanford 200 East Area.

  15. Supporting document for the SW Quadrant Historical Tank Content Estimate for U-Tank Farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Gaddis, L.A.; Johnson, E.D.

    1994-06-01

    This Supporting Document provides historical characterization information gathered on U-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature data, sampling data, and drywell and liquid observation well data for Historical Tank Content Estimate of the SW Quadrant at the Hanford 200 West Area

  16. Supporting Document for the SW Quadrant Historical Tank Content Estimate for SX-Tank Farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Gaddis, L.A.; Johnson, E.D.

    1994-06-01

    This Supporting Document provides historical characterization information gathered on SX-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature data, sampling data, and drywell and liquid observation well data for Historical Tank Content Estimate of the SW Quadrant at the Hanford 200 West Area

  17. Supporting document for the historical tank content estimate for BY-Tank farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Newell, R.L.; Funk, J.W.

    1996-01-01

    This Supporting Document provides historical in-depth characterization information on BY-Tank Farm, such as historical waste transfer and level data, tank physical information,temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the northeast quadrant of the Hanford 200 East Area

  18. Supporting document for the historical tank content estimate for AP-tank farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Stroup, J.L.; Funk, J.W.

    1997-01-01

    This Supporting Document provides historical in-depth characterization information on AP-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the Southeast Quadrant of the Hanford 200 Areas

  19. Supporting document for the historical tank content estimate for BX-tank farm

    International Nuclear Information System (INIS)

    Brevick, C.H.

    1996-01-01

    This Supporting Document provides historical in-depth characterization information on BX-Tank Farm, such as historical waste transfer and level data, tank physical information,temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the northeast quadrant of the Hanford 200 East Area

  20. Supporting document for the historical tank content estimate for A-Tank farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Newell, R.L.; Funk, J.W.

    1996-01-01

    This Supporting Document provides historical in-depth characterization information on A-Tank Farm, such as historical waste transfer and level data, tank physical information,temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the northeast quadrant of the Hanford 200 East Area

  1. Supporting document for the historical tank content estimate for AW-tank farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Stroup, J.L.; Funk, J.W.

    1997-01-01

    This Supporting Document provides historical in-depth characterization information on AW-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature plots, liquid observation well plots, chemical analyte and radionuclide inventories for the Historical Tank Content Estimate Report for the Southeast Quadrant of the Hanford 200 Areas

  2. Historical tank content estimate for the northwest quadrant of the Hanford 200 west area

    International Nuclear Information System (INIS)

    Brevick, C.H.; Stroup, J.L.; Funk, J.W.

    1997-01-01

    The Historical Tank Content Estimate for the Quadrant provides historical information on a tank-by-tank basis of the radioactive mixed wastes stored in the underground single-shell tanks for the Hanford 200 West Area. This report summarized historical information such as waste history, level history, temperature history, riser configuration, tank integrity, and inventory estimates on a tank-by-tank basis. Tank farm aerial photographs and interior tank montages are also provided for each tank. A description of the development of data for the document of the inventory estimates provided by Los Alamos National Laboratory are also given in this report

  3. So many genes, so little time: A practical approach to divergence-time estimation in the genomic era.

    Science.gov (United States)

    Smith, Stephen A; Brown, Joseph W; Walker, Joseph F

    2018-01-01

    Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. "Gene shopping", wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated

  4. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

    Directory of Open Access Journals (Sweden)

    Laurence D Hurst

    2015-12-01

    Full Text Available X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE and data from the Functional Annotation of the Mammalian Genome (FANTOM5 project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds, as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased

  5. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    KAUST Repository

    Hurst, Laurence D.

    2015-12-18

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression

  6. Remote estimation of nitrogen and chlorophyll contents in maize at leaf and canopy levels

    Science.gov (United States)

    Schlemmer, M.; Gitelson, A.; Schepers, J.; Ferguson, R.; Peng, Y.; Shanahan, J.; Rundquist, D.

    2013-12-01

    Leaf and canopy nitrogen (N) status relates strongly to leaf and canopy chlorophyll (Chl) content. Remote sensing is a tool that has the potential to assess N content at leaf, plant, field, regional and global scales. In this study, remote sensing techniques were applied to estimate N and Chl contents of irrigated maize (Zea mays L.) fertilized at five N rates. Leaf N and Chl contents were determined using the red-edge chlorophyll index with R2 of 0.74 and 0.94, respectively. Results showed that at the canopy level, Chl and N contents can be accurately retrieved using green and red-edge Chl indices using near infrared (780-800 nm) and either green (540-560 nm) or red-edge (730-750 nm) spectral bands. Spectral bands that were found optimal for Chl and N estimations coincide well with the red-edge band of the MSI sensor onboard the near future Sentinel-2 satellite. The coefficient of determination for the relationships between the red-edge chlorophyll index, simulated in Sentinel-2 bands, and Chl and N content was 0.90 and 0.87, respectively.

  7. Estimation of active pharmaceutical ingredients content using locally weighted partial least squares and statistical wavelength selection.

    Science.gov (United States)

    Kim, Sanghong; Kano, Manabu; Nakagawa, Hiroshi; Hasebe, Shinji

    2011-12-15

    Development of quality estimation models using near infrared spectroscopy (NIRS) and multivariate analysis has been accelerated as a process analytical technology (PAT) tool in the pharmaceutical industry. Although linear regression methods such as partial least squares (PLS) are widely used, they cannot always achieve high estimation accuracy because physical and chemical properties of a measuring object have a complex effect on NIR spectra. In this research, locally weighted PLS (LW-PLS) which utilizes a newly defined similarity between samples is proposed to estimate active pharmaceutical ingredient (API) content in granules for tableting. In addition, a statistical wavelength selection method which quantifies the effect of API content and other factors on NIR spectra is proposed. LW-PLS and the proposed wavelength selection method were applied to real process data provided by Daiichi Sankyo Co., Ltd., and the estimation accuracy was improved by 38.6% in root mean square error of prediction (RMSEP) compared to the conventional PLS using wavelengths selected on the basis of variable importance on the projection (VIP). The results clearly show that the proposed calibration modeling technique is useful for API content estimation and is superior to the conventional one. Copyright © 2011 Elsevier B.V. All rights reserved.

  8. Evaluating the potential of housekeeping genes, rRNAs, snRNAs, microRNAs and circRNAs as reference genes for the estimation of PMI.

    Science.gov (United States)

    Tu, Chunyan; Du, Tieshuai; Shao, Chengchen; Liu, Zengjia; Li, Liliang; Shen, Yiwen

    2018-04-24

    The precise estimation of postmortem interval (PMI) is a critical step in death investigation of forensic cases. Detecting the degradation of RNA in tissues by real time quantitative polymerase chain reaction (RT-qPCR) technology provides a new theoretical basis for estimation of PMI. However, most commonly used reference genes degrade over time, while previous studies seldom consider this when selecting suitable reference genes for the estimation of PMI. Studies have shown microRNAs (miRNAs) are very stable and circular RNAs (circRNAs) have recently emerged as a novel class of RNAs with high stability. We aimed to evaluate the stability of the two kinds of RNAs and normal reference genes using geNorm and NormFinder algorithms to identify tissue-specific reference genes for PMI estimation. The content of candidate RNAs from mouse heart, liver and skeletal muscle tissues were dynamically examined in 8 consecutive days after death. Among the 11 candidate genes (β-actin, Gapdh, Rps18, 5S, 18S, U6, miR-133a, miR-122, circ-AFF1, LC-Ogdh and LC-LRP6), the following genes showed prioritized stability: miR-122, miR-133a and 18S in heart tissues; LC-Ogdh, circ-AFF1 and miR-122 in liver tissues; and miR-133a, circ-AFF1 and LC-LRP6 in skeletal muscle tissues. Our results suggested that miRNAs and circRNAs were more stable as reference genes than other kinds of RNAs regarding PMI estimation. The appropriate internal control genes were not completely the same across tissue types.

  9. MR-based water content estimation in cartilage: design and validation of a method

    DEFF Research Database (Denmark)

    Shiguetomi Medina, Juan Manuel; Kristiansen, Maja Sophie; Ringgaard, Steffen

    Purpose: Design and validation of an MR-based method that allows the calculation of the water content in cartilage tissue. Methods and Materials: Cartilage tissue T1 map based water content MR sequences were used on a 37 Celsius degree stable system. The T1 map intensity signal was analyzed on 6...... cartilage samples from living animals (pig) and on 8 gelatin samples which water content was already known. For the data analysis a T1 intensity signal map software analyzer used. Finally, the method was validated after measuring and comparing 3 more cartilage samples in a living animal (pig). The obtained...... map based water content sequences can provide information that, after being analyzed using a T1-map analysis software, can be interpreted as the water contained inside a cartilage tissue. The amount of water estimated using this method was similar to the one obtained at the dry-freeze procedure...

  10. MoisturEC: an R application for geostatistical estimation of moisture content from electrical conductivity data

    Science.gov (United States)

    Terry, N.; Day-Lewis, F. D.; Werkema, D. D.; Lane, J. W., Jr.

    2017-12-01

    Soil moisture is a critical parameter for agriculture, water supply, and management of landfills. Whereas direct data (as from TDR or soil moisture probes) provide localized point scale information, it is often more desirable to produce 2D and/or 3D estimates of soil moisture from noninvasive measurements. To this end, geophysical methods for indirectly assessing soil moisture have great potential, yet are limited in terms of quantitative interpretation due to uncertainty in petrophysical transformations and inherent limitations in resolution. Simple tools to produce soil moisture estimates from geophysical data are lacking. We present a new standalone program, MoisturEC, for estimating moisture content distributions from electrical conductivity data. The program uses an indicator kriging method within a geostatistical framework to incorporate hard data (as from moisture probes) and soft data (as from electrical resistivity imaging or electromagnetic induction) to produce estimates of moisture content and uncertainty. The program features data visualization and output options as well as a module for calibrating electrical conductivity with moisture content to improve estimates. The user-friendly program is written in R - a widely used, cross-platform, open source programming language that lends itself to further development and customization. We demonstrate use of the program with a numerical experiment as well as a controlled field irrigation experiment. Results produced from the combined geostatistical framework of MoisturEC show improved estimates of moisture content compared to those generated from individual datasets. This application provides a convenient and efficient means for integrating various data types and has broad utility to soil moisture monitoring in landfills, agriculture, and other problems.

  11. Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

    Directory of Open Access Journals (Sweden)

    Puji eLestari

    2013-06-01

    Full Text Available Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both chromosomes. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22 are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.

  12. Analyzing Multiple-Probe Microarray: Estimation and Application of Gene Expression Indexes

    KAUST Repository

    Maadooliat, Mehdi

    2012-07-26

    Gene expression index estimation is an essential step in analyzing multiple probe microarray data. Various modeling methods have been proposed in this area. Amidst all, a popular method proposed in Li and Wong (2001) is based on a multiplicative model, which is similar to the additive model discussed in Irizarry et al. (2003a) at the logarithm scale. Along this line, Hu et al. (2006) proposed data transformation to improve expression index estimation based on an ad hoc entropy criteria and naive grid search approach. In this work, we re-examined this problem using a new profile likelihood-based transformation estimation approach that is more statistically elegant and computationally efficient. We demonstrate the applicability of the proposed method using a benchmark Affymetrix U95A spiked-in experiment. Moreover, We introduced a new multivariate expression index and used the empirical study to shows its promise in terms of improving model fitting and power of detecting differential expression over the commonly used univariate expression index. As the other important content of the work, we discussed two generally encountered practical issues in application of gene expression index: normalization and summary statistic used for detecting differential expression. Our empirical study shows somewhat different findings from the MAQC project (MAQC, 2006).

  13. Application of short-wave infrared (SWIR) spectroscopy in quantitative estimation of clay mineral contents

    International Nuclear Information System (INIS)

    You, Jinfeng; Xing, Lixin; Pan, Jun; Meng, Tao; Liang, Liheng

    2014-01-01

    Clay minerals are significant constituents of soil which are necessary for life. This paper studied three types of clay minerals, kaolinite, illite, and montmorillonite, for they are not only the most common soil forming materials, but also important indicators of soil expansion and shrinkage potential. These clay minerals showed diagnostic absorption bands resulting from vibrations of hydroxyl groups and structural water molecules in the SWIR wavelength region. The short-wave infrared reflectance spectra of the soil was obtained from a Portable Near Infrared Spectrometer (PNIS, spectrum range: 1300∼2500 nm, interval: 2 nm). Due to the simplicity, quickness, and the non-destructiveness analysis, SWIR spectroscopy has been widely used in geological prospecting, chemical engineering and many other fields. The aim of this study was to use multiple linear regression (MLR) and partial least squares (PLS) regression to establish the optimizing quantitative estimation models of the kaolinite, illite and montmorillonite contents from soil reflectance spectra. Here, the soil reflectance spectra mainly refers to the spectral reflectivity of soil (SRS) corresponding to the absorption-band position (AP) of kaolinite, illite, and montmorillonite representative spectra from USGS spectral library, the SRS corresponding to the AP of soil spectral and soil overall spectrum reflectance values. The optimal estimation models of three kinds of clay mineral contents showed that the retrieval accuracy was satisfactory (Kaolinite content: a Root Mean Square Error of Calibration (RMSEC) of 1.671 with a coefficient of determination (R 2 ) of 0.791; Illite content: a RMSEC of 1.126 with a R 2 of 0.616; Montmorillonite content: a RMSEC of 1.814 with a R 2 of 0.707). Thus, the reflectance spectra of soil obtained form PNIS could be used for quantitative estimation of kaolinite, illite and montmorillonite contents in soil

  14. A Key Gene, PLIN1, Can Affect Porcine Intramuscular Fat Content Based on Transcriptome Analysis

    Directory of Open Access Journals (Sweden)

    Bojiang Li

    2018-04-01

    Full Text Available Intramuscular fat (IMF content is an important indicator for meat quality evaluation. However, the key genes and molecular regulatory mechanisms affecting IMF deposition remain unclear. In the present study, we identified 75 differentially expressed genes (DEGs between the higher (H and lower (L IMF content of pigs using transcriptome analysis, of which 27 were upregulated and 48 were downregulated. Notably, Kyoto Encyclopedia of Genes and Genomes (KEGG enrichment analysis indicated that the DEG perilipin-1 (PLIN1 was significantly enriched in the fat metabolism-related peroxisome proliferator-activated receptor (PPAR signaling pathway. Furthermore, we determined the expression patterns and functional role of porcine PLIN1. Our results indicate that PLIN1 was highly expressed in porcine adipose tissue, and its expression level was significantly higher in the H IMF content group when compared with the L IMF content group, and expression was increased during adipocyte differentiation. Additionally, our results confirm that PLIN1 knockdown decreases the triglyceride (TG level and lipid droplet (LD size in porcine adipocytes. Overall, our data identify novel candidate genes affecting IMF content and provide new insight into PLIN1 in porcine IMF deposition and adipocyte differentiation.

  15. A Key Gene, PLIN1, Can Affect Porcine Intramuscular Fat Content Based on Transcriptome Analysis.

    Science.gov (United States)

    Li, Bojiang; Weng, Qiannan; Dong, Chao; Zhang, Zengkai; Li, Rongyang; Liu, Jingge; Jiang, Aiwen; Li, Qifa; Jia, Chao; Wu, Wangjun; Liu, Honglin

    2018-04-04

    Intramuscular fat (IMF) content is an important indicator for meat quality evaluation. However, the key genes and molecular regulatory mechanisms affecting IMF deposition remain unclear. In the present study, we identified 75 differentially expressed genes (DEGs) between the higher (H) and lower (L) IMF content of pigs using transcriptome analysis, of which 27 were upregulated and 48 were downregulated. Notably, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that the DEG perilipin-1 ( PLIN1 ) was significantly enriched in the fat metabolism-related peroxisome proliferator-activated receptor (PPAR) signaling pathway. Furthermore, we determined the expression patterns and functional role of porcine PLIN1. Our results indicate that PLIN1 was highly expressed in porcine adipose tissue, and its expression level was significantly higher in the H IMF content group when compared with the L IMF content group, and expression was increased during adipocyte differentiation. Additionally, our results confirm that PLIN1 knockdown decreases the triglyceride (TG) level and lipid droplet (LD) size in porcine adipocytes. Overall, our data identify novel candidate genes affecting IMF content and provide new insight into PLIN1 in porcine IMF deposition and adipocyte differentiation.

  16. Estimating chlorophyll content of spartina alterniflora at leaf level using hyper-spectral data

    Science.gov (United States)

    Wang, Jiapeng; Shi, Runhe; Liu, Pudong; Zhang, Chao; Chen, Maosi

    2017-09-01

    Spartina alterniflora, one of most successful invasive species in the world, was firstly introduced to China in 1979 to accelerate sedimentation and land formation via so-called "ecological engineering", and it is now widely distributed in coastal saltmarshes in China. A key question is how to retrieve chlorophyll content to reflect growth status, which has important implication of potential invasiveness. In this work, an estimation model of chlorophyll content of S. alterniflora was developed based on hyper-spectral data in the Dongtan Wetland, Yangtze Estuary, China. The spectral reflectance of S. alterniflora leaves and their corresponding chlorophyll contents were measured, and then the correlation analysis and regression (i.e., linear, logarithmic, quadratic, power and exponential regression) method were established. The spectral reflectance was transformed and the feature parameters (i.e., "san bian", "lv feng" and "hong gu") were extracted to retrieve the chlorophyll content of S. alterniflora . The results showed that these parameters had a large correlation coefficient with chlorophyll content. On the basis of the correlation coefficient, mathematical models were established, and the models of power and exponential based on SDb had the least RMSE and larger R2 , which had a good performance regarding the inversion of chlorophyll content of S. alterniflora.

  17. Estimate of Leaf Chlorophyll and Nitrogen Content in Asian Pear (Pyrus serotina Rehd. by CCM-200

    Directory of Open Access Journals (Sweden)

    Mostafa GHASEMI

    2011-03-01

    Full Text Available In many cases evaluation of chlorophyll and nitrogen content in plants need to destructive methods, more time and organic solvents. Application of chlorophyll meters save time and resources. The aim of this study was estimating of chlorophyll and nitrogen content in Asian pear leaves using non-destructive method and rapid quantification of chlorophyll by chlorophyll content meter (CCM-200. This study was conducted on 8 years old Asian pear trees during June 2008 in Tehran, Iran. To develop our regression model, the chlorophyll meter data were correlated with extracted chlorophyll and nitrogen content data obtained from DMSO and Kejeldal methods, respectively. The results showed that, there was positive and linear correlation between CCM-200 data and chlorophyll a (R�=0.7183, chlorophyll b (R�=0.8523, total chlorophyll (R�=0.90, and total nitrogen content (R�=0.76 in Asian pear leaves. Thus, it can be concluded that, CCM-200 can be used in order to predict both chlorophyll and nitrogen content in Asian pear leaves.

  18. Determination of the carbon content of domestic farm produces to estimate offsite C-14 ingestion dose

    International Nuclear Information System (INIS)

    Jung, Y. G.; Kim, M. J.; Lee, G. B.

    2003-01-01

    The carbon content of grains, leafy and root vegetables, and fruits which the Koreans usually eat were calculated to use in the estimation of offsite C-14 ingestion dose. With the data of food intake per day in the Report on 1998 national health and nutrition survey- dietary intake survey, 5 age-group integrate d intake of the 4 farm produce groups were extracted for food items and the amount. Intake percentage in each food group were taken as food weighing factor for the foods. Carbon content was calculated using protein, fat, and carbohydrate content of the foods, and multiplied by the corresponding food weighing factor to derive the content of the food groups. The calculated carbon content of grains, leafy and root vegetables, and fruits were 39.%, 4.2%, 8.0%, and 5.9% respectively. Grains and fruits were not much different from ODCM for carbon content, but vegetables were higher by 0.7%∼4.5%

  19. Joint estimation and contention-resolution protocol for wireless random access

    DEFF Research Database (Denmark)

    Stefanovic, Cedomir; Trillingsgaard, Kasper Fløe; Kiilerich Pratas, Nuno

    2013-01-01

    We propose a contention-based random-access protocol, designed for wireless networks where the number of users is not a priori known. The protocol operates in rounds divided into equal-duration slots, performing at the same time estimation of the number of users and resolution of their transmissi......We propose a contention-based random-access protocol, designed for wireless networks where the number of users is not a priori known. The protocol operates in rounds divided into equal-duration slots, performing at the same time estimation of the number of users and resolution...... successive interference cancellation which, coupled with the use of the optimized access probabilities, enables throughputs that are substantially higher than the traditional slotted ALOHA-like protocols. The key feature of the proposed protocol is that the round durations are not a priori set...

  20. Empirical model to estimate the thermal conductivity of granite with various water contents

    International Nuclear Information System (INIS)

    Cho, Win Jin; Kwon, Sang Ki; Lee, Jae Owan

    2010-01-01

    To obtain the input data for the design and long-term performance assessment of a high-level waste repository, the thermal conductivities of several granite rocks which were taken from the rock cores from the declined borehole were measured. The thermal conductivities of granite were measured under the different conditions of water content to investigate the effects of the water content on the thermal conductivity. A simple empirical correlation was proposed to predict the thermal conductivity of granite as a function of effective porosity and water content which can be measured with relative ease while neglecting the possible effects of mineralogy, structure and anisotropy. The correlation could predict the thermal conductivity of granite with the effective porosity below 2.7% from the KURT site with an estimated error below 10%.

  1. Consumers’ estimation of calorie content at fast food restaurants: cross sectional observational study

    OpenAIRE

    Block, Jason Perry; Condon, Suzanne K; Kleinman, Ken Paul; Mullen, Jewel; Linakis, Stephanie; Rifas-Shiman, Sheryl Lynn; Gillman, Matthew William

    2013-01-01

    Objective: To investigate estimation of calorie (energy) content of meals from fast food restaurants in adults, adolescents, and school age children. Design: Cross sectional study of repeated visits to fast food restaurant chains. Setting: 89 fast food restaurants in four cities in New England, United States: McDonald’s, Burger King, Subway, Wendy’s, KFC, Dunkin’ Donuts. Participants: 1877 adults and 330 school age children visiting restaurants at dinnertime (evening meal) in 2010 and 2011; 1...

  2. Soil sail content estimation in the yellow river delta with satellite hyperspectral data

    Science.gov (United States)

    Weng, Yongling; Gong, Peng; Zhu, Zhi-Liang

    2008-01-01

    Soil salinization is one of the most common land degradation processes and is a severe environmental hazard. The primary objective of this study is to investigate the potential of predicting salt content in soils with hyperspectral data acquired with EO-1 Hyperion. Both partial least-squares regression (PLSR) and conventional multiple linear regression (MLR), such as stepwise regression (SWR), were tested as the prediction model. PLSR is commonly used to overcome the problem caused by high-dimensional and correlated predictors. Chemical analysis of 95 samples collected from the top layer of soils in the Yellow River delta area shows that salt content was high on average, and the dominant chemicals in the saline soil were NaCl and MgCl2. Multivariate models were established between soil contents and hyperspectral data. Our results indicate that the PLSR technique with laboratory spectral data has a strong prediction capacity. Spectral bands at 1487-1527, 1971-1991, 2032-2092, and 2163-2355 nm possessed large absolute values of regression coefficients, with the largest coefficient at 2203 nm. We obtained a root mean squared error (RMSE) for calibration (with 61 samples) of RMSEC = 0.753 (R2 = 0.893) and a root mean squared error for validation (with 30 samples) of RMSEV = 0.574. The prediction model was applied on a pixel-by-pixel basis to a Hyperion reflectance image to yield a quantitative surface distribution map of soil salt content. The result was validated successfully from 38 sampling points. We obtained an RMSE estimate of 1.037 (R2 = 0.784) for the soil salt content map derived by the PLSR model. The salinity map derived from the SWR model shows that the predicted value is higher than the true value. These results demonstrate that the PLSR method is a more suitable technique than stepwise regression for quantitative estimation of soil salt content in a large area. ?? 2008 CASI.

  3. [Research on Oil Sands Spectral Characteristics and Oil Content by Remote Sensing Estimation].

    Science.gov (United States)

    You, Jin-feng; Xing, Li-xin; Pan, Jun; Shan, Xuan-long; Liang, Li-heng; Fan, Rui-xue

    2015-04-01

    Visible and near infrared spectroscopy is a proven technology to be widely used in identification and exploration of hydrocarbon energy sources with high spectral resolution for detail diagnostic absorption characteristics of hydrocarbon groups. The most prominent regions for hydrocarbon absorption bands are 1,740-1,780, 2,300-2,340 and 2,340-2,360 nm by the reflectance of oil sands samples. These spectral ranges are dominated by various C-H overlapping overtones and combination bands. Meanwhile, there is relatively weak even or no absorption characteristics in the region from 1,700 to 1,730 nm in the spectra of oil sands samples with low bitumen content. With the increase in oil content, in the spectral range of 1,700-1,730 nm the obvious hydrocarbon absorption begins to appear. The bitumen content is the critical parameter for oil sands reserves estimation. The absorption depth was used to depict the response intensity of the absorption bands controlled by first-order overtones and combinations of the various C-H stretching and bending fundamentals. According to the Pearson and partial correlation relationships of oil content and absorption depth dominated by hydrocarbon groups in 1,740-1,780, 2,300-2,340 and 2,340-2,360 nm wavelength range, the scheme of association mode was established between the intensity of spectral response and bitumen content, and then unary linear regression(ULR) and partial least squares regression (PLSR) methods were employed to model the equation between absorption depth attributed to various C-H bond and bitumen content. There were two calibration equations in which ULR method was employed to model the relationship between absorption depth near 2,350 nm region and bitumen content and PLSR method was developed to model the relationship between absorption depth of 1,758, 2,310, 2,350 nm regions and oil content. It turned out that the calibration models had good predictive ability and high robustness and they could provide the scientific

  4. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    NARCIS (Netherlands)

    Hurst, Laurence D; Ghanbarian, Avazeh T; Forrest, Alistair R R; Huminiecki, Lukasz; Clevers, J.C.; van de Wetering, M.L.

    2015-01-01

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally

  5. Advances in estimation methods of vegetation water content based on optical remote sensing techniques

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Quantitative estimation of vegetation water content(VWC) using optical remote sensing techniques is helpful in forest fire as-sessment,agricultural drought monitoring and crop yield estimation.This paper reviews the research advances of VWC retrieval using spectral reflectance,spectral water index and radiative transfer model(RTM) methods.It also evaluates the reli-ability of VWC estimation using spectral water index from the observation data and the RTM.Focusing on two main definitions of VWC-the fuel moisture content(FMC) and the equivalent water thickness(EWT),the retrieval accuracies of FMC and EWT using vegetation water indices are analyzed.Moreover,the measured information and the dataset are used to estimate VWC,the results show there are significant correlations among three kinds of vegetation water indices(i.e.,WSI,NDⅡ,NDWI1640,WI/NDVI) and canopy FMC of winter wheat(n=45).Finally,the future development directions of VWC detection based on optical remote sensing techniques are also summarized.

  6. Estimating water content in an active landfill with the aid of GPR

    Energy Technology Data Exchange (ETDEWEB)

    Yochim, April, E-mail: ayochim@regionofwaterloo.ca [Region of Waterloo Waste Management Division, 925 Erb Street West, Waterloo, ON N2J 3Z4 (Canada); Zytner, Richard G., E-mail: rzytner@uoguelph.ca [School of Engineering, University of Guelph, Guelph, ON N1G 2W1 (Canada); McBean, Edward A., E-mail: emcbean@uoguelph.ca [School of Engineering, University of Guelph, Guelph, ON N1G 2W1 (Canada); Endres, Anthony L., E-mail: alendres@sciborg.uwaterloo.ca [Dept. of Earth and Environmental Sciences, University of Waterloo, Waterloo, ON N2L 3G1 (Canada)

    2013-10-15

    Highlights: • Limited information in the literature on the use of GPR to measure in situ water content in a landfill. • Developed GPR method allows measurement of in situ water content in a landfill. • Developed GPR method is appealing to waste management professionals operating landfills. - Abstract: Landfill gas (LFG) receives a great deal of attention due to both negative and positive environmental impacts, global warming and a green energy source, respectively. However, predicting the quantity of LFG generated at a given landfill, whether active or closed is difficult due to the heterogeneities present in waste, and the lack of accurate in situ waste parameters like water content. Accordingly, ground penetrating radar (GPR) was evaluated as a tool for estimating in situ water content. Due to the large degree of subsurface heterogeneity and the electrically conductive clay cap covering landfills, both of which affect the transmission of the electromagnetic pulses, there is much scepticism concerning the use of GPR to quantify in situ water content within a municipal landfill. Two landfills were studied. The first landfill was used to develop the measurement protocols, while the second landfill provided a means of confirming these protocols. GPR measurements were initially completed using the surface GPR approach, but the lack of success led to the use of borehole (BH) GPR. Both zero offset profiling (ZOP) and multiple offset gathers (MOG) modes were tried, with the results indicating that BH GPR using the ZOP mode is the most simple and efficient method to measure in situ water content. The best results were obtained at a separation distance of 2 m, where higher the water content, smaller the effective separation distance. However, an increase in water content did appear to increase the accuracy of the GPR measurements. For the effective separation distance of 2 m at both landfills, the difference between GPR and lab measured water contents were reasonable

  7. Estimating water content in an active landfill with the aid of GPR

    International Nuclear Information System (INIS)

    Yochim, April; Zytner, Richard G.; McBean, Edward A.; Endres, Anthony L.

    2013-01-01

    Highlights: • Limited information in the literature on the use of GPR to measure in situ water content in a landfill. • Developed GPR method allows measurement of in situ water content in a landfill. • Developed GPR method is appealing to waste management professionals operating landfills. - Abstract: Landfill gas (LFG) receives a great deal of attention due to both negative and positive environmental impacts, global warming and a green energy source, respectively. However, predicting the quantity of LFG generated at a given landfill, whether active or closed is difficult due to the heterogeneities present in waste, and the lack of accurate in situ waste parameters like water content. Accordingly, ground penetrating radar (GPR) was evaluated as a tool for estimating in situ water content. Due to the large degree of subsurface heterogeneity and the electrically conductive clay cap covering landfills, both of which affect the transmission of the electromagnetic pulses, there is much scepticism concerning the use of GPR to quantify in situ water content within a municipal landfill. Two landfills were studied. The first landfill was used to develop the measurement protocols, while the second landfill provided a means of confirming these protocols. GPR measurements were initially completed using the surface GPR approach, but the lack of success led to the use of borehole (BH) GPR. Both zero offset profiling (ZOP) and multiple offset gathers (MOG) modes were tried, with the results indicating that BH GPR using the ZOP mode is the most simple and efficient method to measure in situ water content. The best results were obtained at a separation distance of 2 m, where higher the water content, smaller the effective separation distance. However, an increase in water content did appear to increase the accuracy of the GPR measurements. For the effective separation distance of 2 m at both landfills, the difference between GPR and lab measured water contents were reasonable

  8. Content

    DEFF Research Database (Denmark)

    Keiding, Tina Bering

    secondary levels. In subject matter didactics, the question of content is more developed, but it is still mostly confined to teaching on lower levels. As for higher education didactics, discussions on selection of content are almost non-existent on the programmatic level. Nevertheless, teachers are forced...... curriculum, in higher education, and to generate analytical categories and criteria for selection of content, which can be used for systematic didactical reflection. The larger project also concerns reflection on and clarification of the concept of content, including the relation between content at the level......Aim, content and methods are fundamental categories of both theoretical and practical general didactics. A quick glance in recent pedagogical literature on higher education, however, reveals a strong preoccupation with methods, i.e. how teaching should be organized socially (Biggs & Tang, 2007...

  9. QUANTITATIVE ESTIMATION OF VOLUMETRIC ICE CONTENT IN FROZEN GROUND BY DIPOLE ELECTROMAGNETIC PROFILING METHOD

    Directory of Open Access Journals (Sweden)

    L. G. Neradovskiy

    2018-01-01

    Full Text Available Volumetric estimation of the ice content in frozen soils is known as one of the main problems in the engineering geocryology and the permafrost geophysics. A new way to use the known method of dipole electromagnetic profiling for the quantitative estimation of the volumetric ice content in frozen soils is discussed. Investigations of foundation of the railroad in Yakutia (i.e. in the permafrost zone were used as an example for this new approach. Unlike the conventional way, in which the permafrost is investigated by its resistivity and constructing of geo-electrical cross-sections, the new approach is aimed at the study of the dynamics of the process of attenuation in the layer of annual heat cycle in the field of high-frequency vertical magnetic dipole. This task is simplified if not all the characteristics of the polarization ellipse are measured but the only one which is the vertical component of the dipole field and can be the most easily measured. Collected data of the measurements were used to analyze the computational errors of the average values of the volumetric ice content from the amplitude attenuation of the vertical component of the dipole field. Note that the volumetric ice content is very important for construction. It is shown that usually the relative error of computation of this characteristic of a frozen soil does not exceed 20% if the works are performed by the above procedure using the key-site methodology. This level of accuracy meets requirements of the design-and-survey works for quick, inexpensive, and environmentally friendly zoning of built-up remote and sparsely populated territories of the Russian permafrost zone according to a category of a degree of the ice content in frozen foundations of engineering constructions.

  10. Evaluation of Acid Digestion Procedures to Estimate Mineral Contents in Materials from Animal Trials

    Directory of Open Access Journals (Sweden)

    M. N. N. Palma

    2015-11-01

    Full Text Available Rigorously standardized laboratory protocols are essential for meaningful comparison of data from multiple sites. Considering that interactions of minerals with organic matrices may vary depending on the material nature, there could be peculiar demands for each material with respect to digestion procedure. Acid digestion procedures were evaluated using different nitric to perchloric acid ratios and one- or two-step digestion to estimate the concentration of calcium, phosphorus, magnesium, and zinc in samples of carcass, bone, excreta, concentrate, forage, and feces. Six procedures were evaluated: ratio of nitric to perchloric acid at 2:1, 3:1, and 4:1 v/v in a one- or two-step digestion. There were no direct or interaction effects (p>0.01 of nitric to perchloric acid ratio or number of digestion steps on magnesium and zinc contents. Calcium and phosphorus contents presented a significant (p0.01 calcium or phosphorus contents in carcass, excreta, concentrate, forage, and feces. Number of digestion steps did not affect mineral content (p>0.01. Estimated concentration of calcium, phosphorus, magnesium, and zinc in carcass, excreta, concentrated, forage, and feces samples can be performed using digestion solution of nitric to perchloric acid 4:1 v/v in a one-step digestion. However, samples of bones demand a stronger digestion solution to analyze the mineral contents, which is represented by an increased proportion of perchloric acid, being recommended a digestion solution of nitric to perchloric acid 2:1 v/v in a one-step digestion.

  11. A candidate-gene association study for berry colour and anthocyanin content in Vitis vinifera L.

    Directory of Open Access Journals (Sweden)

    Silvana Cardoso

    Full Text Available Anthocyanin content is a trait of major interest in Vitis vinifera L. These compounds affect grape and wine quality, and have beneficial effects on human health. A candidate-gene approach was used to identify genetic variants associated with anthocyanin content in grape berries. A total of 445 polymorphisms were identified in 5 genes encoding transcription factors and 10 genes involved in either the biosynthetic pathway or transport of anthocyanins. A total of 124 SNPs were selected to examine association with a wide range of phenotypes based on RP-HPLC analysis and visual characterization. The phenotypes were total skin anthocyanin (TSA concentration but also specific types of anthocyanins and relative abundance. The visual assessment was based on OIV (Organisation Internationale de la Vigne et du Vin descriptors for berry and skin colour. The genes encoding the transcription factors MYB11, MYBCC and MYC(B were significantly associated with TSA concentration. UFGT and MRP were associated with several different types of anthocyanins. Skin and pulp colour were associated with nine genes (MYB11, MYBCC, MYC(B, UFGT, MRP, DFR, LDOX, CHI and GST. Pulp colour was associated with a similar group of 11 genes (MYB11, MYBCC, MYC(B, MYC(A, UFGT, MRP, GST, DFR, LDOX, CHI and CHS(A. Statistical interactions were observed between SNPs within the transcription factors MYB11, MYBCC and MYC(B. SNPs within LDOX interacted with MYB11 and MYC(B, while SNPs within CHI interacted with MYB11 only. Together, these findings suggest the involvement of these genes in anthocyanin content and on the regulation of anthocyanin biosynthesis. This work forms a benchmark for replication and functional studies.

  12. Estimating the Relative Water Content of Single Leaves from Optical Polarization Measurements

    Science.gov (United States)

    Vanderbilt, Vern; Daughtry, Craig; Dahlgren, Robert

    2016-01-01

    Remotely sensing the water status of plants and the water content of canopies remain long-term goals of remote sensing research. For monitoring canopy water status, existing approaches such as the Crop Water Stress Index and the Equivalent Water Thickness have limitations. The CWSI does not work well in humid regions, requires estimates of the vapor pressure deficit near the canopy during the remote sensing over-flight and, once stomata close, provides little information regarding the canopy water status. The EWI is based upon the physics of water-light interaction, not plant physiology. In this research, we applied optical polarization techniques to monitor the VISNIR light reflected from the leaf interior, R, as well as the leaf transmittance, T, as the relative water content (RWC) of corn (Zea mays) leaves decreased. Our results show that R and T both changed nonlinearly as each leaf dried, R increasing and T decreasing. Our results tie changes in the VISNIR R and T to leaf physiological changes linking the light scattered out of the drying leaf interior to its relative water content and to changes in leaf cellular structure and pigments. Our results suggest remotely sensing the physiological water status of a single leaf and perhaps of a plant canopy might be possible in the future. However, using our approach to estimate the water status of a leaf does not appear possible at present, because our results display too much variability that we do not yet understand.

  13. Estimating rice grain protein contents with SPOT/HRV data acquired at maturing stage

    International Nuclear Information System (INIS)

    Asaka, D.; Shiga, H.

    2003-01-01

    Rice grain protein contents that play an important role in the eating quality of rice can be estimated from leaf color in maturing stage. In order to investigate the distribution of paddy rice grain protein of a wide area, we employed SPOT/HRV data from August to September for successive 4 years, selecting the Naganuma town, Hokkaido as the study area. The relationship between each spectral bands and ground survey data were examined. The result showed that the grain protein contents could be estimated using the normalized difference vegetation index (NDVI) with the absolute root mean square error less than 0.4% under the condition that the time lag between the satellite observation date and the maturing stage was within 20 days. In this period, we would have enough chance to get clear observation data every year under the weather conditions in the study area using the SPOT/HRV sensors that has pointing ability. For major rice varieties cultivated in Hokkaido, the same relationship between NDVI and protein contents was observed. Thus, we conclude that the method proposed in this study is operational in rice production

  14. More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.

    Science.gov (United States)

    Yang, Xing; Xie, Lu; Li, Yixue; Wei, Chaochun

    2009-06-29

    Estimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism. We presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged. By combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future. The list of genomes used in this paper can be found in the supplementary table.

  15. Using LUCAS topsoil database to estimate soil organic carbon content in local spectral libraries

    Science.gov (United States)

    Castaldi, Fabio; van Wesemael, Bas; Chabrillat, Sabine; Chartin, Caroline

    2017-04-01

    The quantification of the soil organic carbon (SOC) content over large areas is mandatory to obtain accurate soil characterization and classification, which can improve site specific management at local or regional scale exploiting the strong relationship between SOC and crop growth. The estimation of the SOC is not only important for agricultural purposes: in recent years, the increasing attention towards global warming highlighted the crucial role of the soil in the global carbon cycle. In this context, soil spectroscopy is a well consolidated and widespread method to estimate soil variables exploiting the interaction between chromophores and electromagnetic radiation. The importance of spectroscopy in soil science is reflected by the increasing number of large soil spectral libraries collected in the world. These large libraries contain soil samples derived from a consistent number of pedological regions and thus from different parent material and soil types; this heterogeneity entails, in turn, a large variability in terms of mineralogical and organic composition. In the light of the huge variability of the spectral responses to SOC content and composition, a rigorous classification process is necessary to subset large spectral libraries and to avoid the calibration of global models failing to predict local variation in SOC content. In this regard, this study proposes a method to subset the European LUCAS topsoil database into soil classes using a clustering analysis based on a large number of soil properties. The LUCAS database was chosen to apply a standardized multivariate calibration approach valid for large areas without the need for extensive field and laboratory work for calibration of local models. Seven soil classes were detected by the clustering analyses and the samples belonging to each class were used to calibrate specific partial least square regression (PLSR) models to estimate SOC content of three local libraries collected in Belgium (Loam belt

  16. [Estimation and Visualization of Nitrogen Content in Citrus Canopy Based on Two Band Vegetation Index (TBVI)].

    Science.gov (United States)

    Wang, Qiao-nan; Ye, Xu-jun; Li, Jin-meng; Xiao, Yu-zhao; He, Yong

    2015-03-01

    Nitrogen is a necessary and important element for the growth and development of fruit orchards. Timely, accurate and nondestructive monitoring of nitrogen status in fruit orchards would help maintain the fruit quality and efficient production of the orchard, and mitigate the pollution of water resources caused by excessive nitrogen fertilization. This study investigated the capability of hyperspectral imagery for estimating and visualizing the nitrogen content in citrus canopy. Hyperspectral images were obtained for leaf samples in laboratory as well as for the whole canopy in the field with ImSpector V10E (Spectral Imaging Ltd., Oulu, Finland). The spectral datas for each leaf sample were represented by the average spectral data extracted from the selected region of interest (ROI) in the hyperspectral images with the aid of ENVI software. The nitrogen content in each leaf sample was measured by the Dumas combustion method with the rapid N cube (Elementar Analytical, Germany). Simple correlation analysis and the two band vegetation index (TBVI) were then used to develop the spectra data-based nitrogen content prediction models. Results obtained through the formula calculation indicated that the model with the two band vegetation index (TBVI) based on the wavelengths 811 and 856 nm achieved the optimal estimation of nitrogen content in citrus leaves (R2 = 0.607 1). Furthermore, the canopy image for the identified TBVI was calculated, and the nitrogen content of the canopy was visualized by incorporating the model into the TBVI image. The tender leaves, middle-aged leaves and elder leaves showed distinct nitrogen status from highto low-levels in the canopy image. The results suggested the potential of hyperspectral imagery for the nondestructive detection and diagnosis of nitrogen status in citrus canopy in real time. Different from previous studies focused on nitrogen content prediction at leaf level, this study succeeded in predicting and visualizing the nutrient

  17. Changes in oil content of transgenic soybeans expressing the yeast SLC1 gene.

    Science.gov (United States)

    Rao, Suryadevara S; Hildebrand, David

    2009-10-01

    The wild type (Wt) and mutant form of yeast (sphingolipid compensation) genes, SLC1 and SLC1-1, have been shown to have lysophosphatidic acid acyltransferase (LPAT) activities (Nageic et al. in J Biol Chem 269:22156-22163, 1993). Expression of these LPAT genes was reported to increase oil content in transgenic Arabidopsis and Brassica napus. It is of interest to determine if the TAG content increase would also be seen in soybeans. Therefore, the wild type SLC1 was expressed in soybean somatic embryos under the control of seed specific phaseolin promoter. Some transgenic somatic embryos and in both T2 and T3 transgenic seeds showed higher oil contents. Compared to controls, the average increase in triglyceride values went up by 1.5% in transgenic somatic embryos. A maximum of 3.2% increase in seed oil content was observed in a T3 line. Expression of the yeast Wt LPAT gene did not alter the fatty acid composition of the seed oil.

  18. Genepleio software for effective estimation of gene pleiotropy from protein sequences.

    Science.gov (United States)

    Chen, Wenhai; Chen, Dandan; Zhao, Ming; Zou, Yangyun; Zeng, Yanwu; Gu, Xun

    2015-01-01

    Though pleiotropy, which refers to the phenomenon of a gene affecting multiple traits, has long played a central role in genetics, development, and evolution, estimation of the number of pleiotropy components remains a hard mission to accomplish. In this paper, we report a newly developed software package, Genepleio, to estimate the effective gene pleiotropy from phylogenetic analysis of protein sequences. Since this estimate can be interpreted as the minimum pleiotropy of a gene, it is used to play a role of reference for many empirical pleiotropy measures. This work would facilitate our understanding of how gene pleiotropy affects the pattern of genotype-phenotype map and the consequence of organismal evolution.

  19. Estimation of Trace Elements (Iodine and Iron Content in Breast Milk

    Directory of Open Access Journals (Sweden)

    N.A. Belykh

    2013-08-01

    Full Text Available The estimation of iodine and iron content in breast milk (n = 88 has been carried out. The study shows that the concentration of iodine and iron in breast milk of the women did not correspond to the physiological needs of an infant. It has been demonstrated that the use of iron-containing vitamin-mineral supplements during lactation has no significant effect on the level of iron in breast milk. The iodine content in breast milk depends on the iodine subsidies. It is shown that the level of micronutrients in breast milk is not affected by the presence of gestational maternal anemia and goiter, due date and place of residence of the family. It is concluded that a statistically significant impact on the level of iodine in the breast milk of combined iodine prophylaxis (acceptance by the mother during lactation drugs potassium iodide (200 mg/day due to the use of iodized salt.

  20. Natural Variation in Synthesis and Catabolism Genes Influences Dhurrin Content in Sorghum

    Directory of Open Access Journals (Sweden)

    Chad M. Hayes

    2015-07-01

    Full Text Available Cyanogenic glucosides are natural compounds found in more than 1000 species of angiosperms that produce HCN and are deemed undesirable for agricultural use. However, these compounds are important components of the primary defensive mechanisms of many plant species. One of the best-studied cyanogenic glucosides is dhurrin [(--hydroxymandelonitrile-β--glucopyranoside], which is produced primarily in sorghum [ (L. Moench]. The biochemical basis for dhurrin metabolism is well established; however, little information is available on its genetic control. Here, we dissect the genetic control of leaf dhurrin content through a genome-wide association study (GWAS using a panel of 700 diverse converted sorghum lines (conversion panel previously subjected to pre-breeding and selected for short stature (∼1 m in height and photoperiod insensitivity. The conversion panel was grown for 2 yr in three environments. Wide variation for leaf dhurrin content was found in the sorghum conversion panel, with the Caudatum group exhibiting the highest dhurrin content and the Guinea group showing the lowest dhurrin content. A GWAS using a mixed linear model revealed significant associations (a false discovery rate [FDR] < 0.05 close to both UGT 185B1 in the canonical biosynthetic gene cluster on chromosome 1 and close to the catabolic dhurrinase loci on chromosome 8. Dhurrin content was associated consistently with biosynthetic genes in the two N-fertilized environments, while dhurrin content was associated with catabolic loci in the environment without supplemental N. These results suggest that genes for both biosynthesis and catabolism are important in determining natural variation for leaf dhurrin in sorghum in different environments.

  1. Assessing the gene content of the megagenome: sugar pine (Pinus lambertiana)

    Science.gov (United States)

    Daniel Gonzalez-Ibeas; Pedro J. Martinez-Garcia; Randi A. Famula; Annette Deflino-Mix; Kristian A. Stevens; Carol A. Loopstra; Charles H. Landley; David B. Neale; Jill L. Wegryzn

    2016-01-01

    Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana...

  2. Historical tank content estimate for the southeast quadrant of the Hanford 200 Areas

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-06-01

    This document provides historical evaluations of the radioactive and mixed waste stored in the Hanford site underground double-shell tanks. A Historical Tank Content Estimate has been developed by reviewing the process histories, waste transfer data, and available physical and chemical characterization data from various Department of Energy and Department of Defense contractors. The historical data will supplement information that is currently being gathered from core sampling. Historical waste transfer and level data, tank physical information, temperature data, and sampling data have been compiled for this report and supporting documents.

  3. Historical tank content estimate for the southeast quadrant of the Hanford 200 Areas

    International Nuclear Information System (INIS)

    1995-06-01

    This document provides historical evaluations of the radioactive and mixed waste stored in the Hanford site underground double-shell tanks. A Historical Tank Content Estimate has been developed by reviewing the process histories, waste transfer data, and available physical and chemical characterization data from various Department of Energy and Department of Defense contractors. The historical data will supplement information that is currently being gathered from core sampling. Historical waste transfer and level data, tank physical information, temperature data, and sampling data have been compiled for this report and supporting documents

  4. Using Sentinel-1 and Landsat 8 satellite images to estimate surface soil moisture content.

    Science.gov (United States)

    Mexis, Philippos-Dimitrios; Alexakis, Dimitrios D.; Daliakopoulos, Ioannis N.; Tsanis, Ioannis K.

    2016-04-01

    Nowadays, the potential for more accurate assessment of Soil Moisture (SM) content exploiting Earth Observation (EO) technology, by exploring the use of synergistic approaches among a variety of EO instruments has emerged. This study is the first to investigate the potential of Synthetic Aperture Radar (SAR) (Sentinel-1) and optical (Landsat 8) images in combination with ground measurements to estimate volumetric SM content in support of water management and agricultural practices. SAR and optical data are downloaded and corrected in terms of atmospheric, geometric and radiometric corrections. SAR images are also corrected in terms of roughness and vegetation with the synergistic use of Oh and Topp models using a dataset consisting of backscattering coefficients and corresponding direct measurements of ground parameters (moisture, roughness). Following, various vegetation indices (NDVI, SAVI, MSAVI, EVI, etc.) are estimated to record diachronically the vegetation regime within the study area and as auxiliary data in the final modeling. Furthermore, thermal images from optical data are corrected and incorporated to the overall approach. The basic principle of Thermal InfraRed (TIR) method is that Land Surface Temperature (LST) is sensitive to surface SM content due to its impact on surface heating process (heat capacity and thermal conductivity) under bare soil or sparse vegetation cover conditions. Ground truth data are collected from a Time-domain reflectometer (TRD) gauge network established in western Crete, Greece, during 2015. Sophisticated algorithms based on Artificial Neural Networks (ANNs) and Multiple Linear Regression (MLR) approaches are used to explore the statistical relationship between backscattering measurements and SM content. Results highlight the potential of SAR and optical satellite images to contribute to effective SM content detection in support of water resources management and precision agriculture. Keywords: Sentinel-1, Landsat 8, Soil

  5. Estimation of black carbon content for biomass burning aerosols from multi-channel Raman lidar data

    Science.gov (United States)

    Talianu, Camelia; Marmureanu, Luminita; Nicolae, Doina

    2015-04-01

    Biomass burning due to natural processes (forest fires) or anthropical activities (agriculture, thermal power stations, domestic heating) is an important source of aerosols with a high content of carbon components (black carbon and organic carbon). Multi-channel Raman lidars provide information on the spectral dependence of the backscatter and extinction coefficients, embedding information on the black carbon content. Aerosols with a high content of black carbon have large extinction coefficients and small backscatter coefficients (strong absorption), while aerosols with high content of organic carbon have large backscatter coefficients (weak absorption). This paper presents a method based on radiative calculations to estimate the black carbon content of biomass burning aerosols from 3b+2a+1d lidar signals. Data is collected at Magurele, Romania, at the cross-road of air masses coming from Ukraine, Russia and Greece, where burning events are frequent during both cold and hot seasons. Aerosols are transported in the free troposphere, generally in the 2-4 km altitude range, and reaches the lidar location after 2-3 days. Optical data are collected between 2011-2012 by a multi-channel Raman lidar and follows the quality assurance program of EARLINET. Radiative calculations are made with libRadTran, an open source radiative model developed by ESA. Validation of the retrievals is made by comparison to a co-located C-ToF Aerosol Mass Spectrometer. Keywords: Lidar, aerosols, biomass burning, radiative model, black carbon Acknowledgment: This work has been supported by grants of the Romanian National Authority for Scientific Research, Programme for Research- Space Technology and Advanced Research - STAR, project no. 39/2012 - SIAFIM, and by Romanian Partnerships in priority areas PNII implemented with MEN-UEFISCDI support, project no. 309/2014 - MOBBE

  6. Study on Hyperspectral Characteristics and Estimation Model of Soil Mercury Content

    Science.gov (United States)

    Liu, Jinbao; Dong, Zhenyu; Sun, Zenghui; Ma, Hongchao; Shi, Lei

    2017-12-01

    In this study, the mercury content of 44 soil samples in Guan Zhong area of Shaanxi Province was used as the data source, and the reflectance spectrum of soil was obtained by ASD Field Spec HR (350-2500 nm) Comparing the reflection characteristics of different contents and the effect of different pre-treatment methods on the establishment of soil heavy metal spectral inversion model. The first order differential, second order differential and reflectance logarithmic transformations were carried out after the pre-treatment of NOR, MSC and SNV, and the sensitive bands of reflectance and mercury content in different mathematical transformations were selected. A hyperspectral estimation model is established by regression method. The results of chemical analysis show that there is a serious Hg pollution in the study area. The results show that: (1) the reflectivity decreases with the increase of mercury content, and the sensitive regions of mercury are located at 392 ~ 455nm, 923nm ~ 1040nm and 1806nm ~ 1969nm. (2) The combination of NOR, MSC and SNV transformations combined with differential transformations can improve the information of heavy metal elements in the soil, and the combination of high correlation band can improve the stability and prediction ability of the model. (3) The partial least squares regression model based on the logarithm of the original reflectance is better and the precision is higher, Rc2 = 0.9912, RMSEC = 0.665; Rv2 = 0.9506, RMSEP = 1.93, which can achieve the mercury content in this region Quick forecast.

  7. COMPARISSON OF DIFFERENT IN VIVO ESTIMATORS OF BODY FAT AND MUSCLE CONTENT IN ADULT CREOLE GOATS

    Directory of Open Access Journals (Sweden)

    Hania Vilar-Martinez

    2009-06-01

    Full Text Available The objective of the present study was to compare the effectiveness of ultrasound measurements (ULT, body condition score (BCS and body mass index (BMI to predict body fat and muscle in goats. Twenty-four adult, ovariectomized, creole goats were fed individually to achieve dissimilar stable body weights (26 to 66 kg. After a six-week period of stabilization BCS was evaluated (average of 4 separate evaluations and BMI calculated (BW/(length x heightx10; average of 2 independent length and height measurements. Fat and muscle coverage over the dorsal (12-13th, lumbar (1st and coxal (1st vertebrae were measured by ultrasound imaging. Animals were slaughtered and visceral fat dissected and weighed. Left half carcass weights were obtained and muscle and fat were dissected and weighed. Left half carcass data were adjusted to whole carcass data. Simple  regression analyses were performed with ULT, BCS and BMI as predictors and visceral (VF, carcass (CF and total fat (TF, and muscle (MU as response variables. Coefficients of variation (CV were calculated for BCS and BMI estimations. ULT measurement of total tissue (fat + muscle coverage over dorsal vertebrae presented the highest predictive value for ULT measurements; thus this measurement is the only reported. Coefficients of determination (R2 for VF, CF and TF were .55, .76 and .68; .78, .82 and .87; .81, .81 and .88 for ULT, BCS and BMI as predictors. R2 for MU were .67, .84 and .76 using ULT, BCS and BMI as predictors. R2 for proportions of VF/BW, CF/BW and TF/BW were .47, .73 and .65; .75, .78 and .88; .74, .71 and .85; when ULT, BCS and BMI were used as predictors. R2 for MS/BW were ≤ .10 using ULT, BCS and BMI as predictors. CV was greater in BCS estimation as compared to BMI estimation (9.7 vs. 3.1 %. BCS and BMI were more accurate in vivo predictors than ULT for body fat content, fat as proportion of BW and body muscle content. ULT, BCS and BMI were completely worthless for predicting

  8. Correlation Lengths for Estimating the Large-Scale Carbon and Heat Content of the Southern Ocean

    Science.gov (United States)

    Mazloff, M. R.; Cornuelle, B. D.; Gille, S. T.; Verdy, A.

    2018-02-01

    The spatial correlation scales of oceanic dissolved inorganic carbon, heat content, and carbon and heat exchanges with the atmosphere are estimated from a realistic numerical simulation of the Southern Ocean. Biases in the model are assessed by comparing the simulated sea surface height and temperature scales to those derived from optimally interpolated satellite measurements. While these products do not resolve all ocean scales, they are representative of the climate scale variability we aim to estimate. Results show that constraining the carbon and heat inventory between 35°S and 70°S on time-scales longer than 90 days requires approximately 100 optimally spaced measurement platforms: approximately one platform every 20° longitude by 6° latitude. Carbon flux has slightly longer zonal scales, and requires a coverage of approximately 30° by 6°. Heat flux has much longer scales, and thus a platform distribution of approximately 90° by 10° would be sufficient. Fluxes, however, have significant subseasonal variability. For all fields, and especially fluxes, sustained measurements in time are required to prevent aliasing of the eddy signals into the longer climate scale signals. Our results imply a minimum of 100 biogeochemical-Argo floats are required to monitor the Southern Ocean carbon and heat content and air-sea exchanges on time-scales longer than 90 days. However, an estimate of formal mapping error using the current Argo array implies that in practice even an array of 600 floats (a nominal float density of about 1 every 7° longitude by 3° latitude) will result in nonnegligible uncertainty in estimating climate signals.

  9. Expression Profiling of Glucosinolate Biosynthetic Genes in Brassica oleracea L. var. capitata Inbred Lines Reveals Their Association with Glucosinolate Content

    Directory of Open Access Journals (Sweden)

    Arif Hasan Khan Robin

    2016-06-01

    Full Text Available Glucosinolates are the biochemical compounds that provide defense to plants against pathogens and herbivores. In this study, the relative expression level of 48 glucosinolate biosynthesis genes was explored in four morphologically-different cabbage inbred lines by qPCR analysis. The content of aliphatic and indolic glucosinolate molecules present in those cabbage lines was also estimated by HPLC analysis. The possible association between glucosinolate accumulation and related gene expression level was explored by principal component analysis (PCA. The genotype-dependent variation in the relative expression level of different aliphatic and indolic glucosinolate biosynthesis genes is the novel result of this study. A total of eight different types of glucosinolates, including five aliphatic and three indolic glucosinolates, was detected in four cabbage lines. Three inbred lines BN3383, BN4059 and BN4072 had no glucoraphanin, sinigrin and gluconapin detected, but the inbred line BN3273 had these three aliphatic glucosinolate compounds. PCA revealed that a higher expression level of ST5b genes and lower expression of GSL-OH was associated with the accumulation of these three aliphatic glucosinolate compounds. PCA further revealed that comparatively higher accumulation of neoglucobrassicin in the inbred line, BN4072, was associated with a high level of expression of MYB34 (Bol017062 and CYP81F1 genes. The Dof1 and IQD1 genes probably trans-activated the genes related to biosynthesis of glucoerucin and methoxyglucobrassicin for their comparatively higher accumulation in the BN4059 and BN4072 lines compared to the other two lines, BN3273 and BN3383. A comparatively higher progoitrin level in BN3273 was probably associated with the higher expression level of the GSL-OH gene. The cabbage inbred line BN3383 accounted for the significantly higher relative expression level for the 12 genes out of 48, but this line had comparatively lower total

  10. INFLUENCE OF GENETIC POLYMORPHISM IN FABP3 AND LEPR GENES ON INTRAMUSCULAR FAT CONTENT IN PIG CARCASSES

    Directory of Open Access Journals (Sweden)

    Kristina Budimir

    2014-06-01

    Full Text Available Intensive production conditions, selection directed to increase the percentage of muscle tissue in carcasses and consumer demand have led to a reduction of intramuscular fat content in pig carcasses. Intramuscular fat is a factor affecting the flavor, juiciness and tenderness of pork meat. FABP protein family causes the differences in the content of intramuscular fat in different pig breeds. FABP3 and LEPR gene are candidate genes for intramuscular fat content and their polymorphisms explain the variability that can occur in different pig breeds. The aim of this paper is to demonstrate the influence of genes on different intramuscular fat content in pig carcasses due to pigs genotype.

  11. Informing Estimates of Program Effects for Studies of Mathematics Professional Development Using Teacher Content Knowledge Outcomes.

    Science.gov (United States)

    Phelps, Geoffrey; Kelcey, Benjamin; Jones, Nathan; Liu, Shuangshuang

    2016-10-03

    Mathematics professional development is widely offered, typically with the goal of improving teachers' content knowledge, the quality of teaching, and ultimately students' achievement. Recently, new assessments focused on mathematical knowledge for teaching (MKT) have been developed to assist in the evaluation and improvement of mathematics professional development. This study presents empirical estimates of average program change in MKT and its variation with the goal of supporting the design of experimental trials that are adequately powered to detect a specified program effect. The study drew on a large database representing five different assessments of MKT and collectively 326 professional development programs and 9,365 teachers. Results from cross-classified hierarchical growth models found that standardized average change estimates across the five assessments ranged from a low of 0.16 standard deviations (SDs) to a high of 0.26 SDs. Power analyses using the estimated pre- and posttest change estimates indicated that hundreds of teachers are needed to detect changes in knowledge at the lower end of the distribution. Even studies powered to detect effects at the higher end of the distribution will require substantial resources to conduct rigorous experimental trials. Empirical benchmarks that describe average program change and its variation provide a useful preliminary resource for interpreting the relative magnitude of effect sizes associated with professional development programs and for designing adequately powered trials. © The Author(s) 2016.

  12. A candidate gene-based association study of tocopherol content and composition in rapeseed (Brassica napus

    Directory of Open Access Journals (Sweden)

    Steffi eFritsche

    2012-06-01

    Full Text Available Rapeseed (Brassica napus L. is the most important oil crop of temperate climates. Rapeseed oil contains tocopherols, also known as vitamin E, which is an indispensable nutrient for humans and animals due to its antioxidant and radical scavenging abilities. Moreover, tocopherols are also important for the oxidative stability of vegetable oils. Therefore, seed oil with increased tocopherol content or altered tocopherol composition is a target for breeding. We investigated the role of nucleotide variations within candidate genes from the tocopherol biosynthesis pathway. Field trials were carried out with 229 accessions from a worldwide B. napus collection which was divided into two panels of 96 and 133 accessions. Seed tocopherol content and composition were measured by HPLC. High heritabilities were found for both traits, ranging from 0.62 to 0.94. We identified polymorphisms by sequencing selected regions of the tocopherol genes from the 96 accession panel. Subsequently, we determined the population structure (Q and relative kinship (K as detected by genotyping with genome-wide distributed SSR markers. Association studies were performed using two models, the structure-based GLM+Q and the PK mixed model. Between 26 and 12 polymorphisms within two genes (BnaX.VTE3.a, BnaA.PDS1.c were significantly associated with tocopherol traits. The SNPs explained up to 16.93 % of the genetic variance for tocopherol composition and up to 10.48 % for total tocopherol content. Based on the sequence information we designed CAPS markers for genotyping the 133 accessions from the 2nd panel. Significant associations with various tocopherol traits confirmed the results from the first experiment. We demonstrate that the polymorphisms within the tocopherol genes clearly impact tocopherol content and composition in B. napus seeds. We suggest that these nucleotide variations may be used as selectable markers for breeding rapeseed with enhanced tocopherol quality.

  13. Development of transgenic Brassica juncea lines for reduced seed sinapine content by perturbing phenylpropanoid pathway genes.

    Directory of Open Access Journals (Sweden)

    Sachin Kajla

    Full Text Available Sinapine is a major anti-nutritive compound that accumulates in the seeds of Brassica species. When ingested, sinapine imparts gritty flavuor in meat and milk of animals and fishy odor to eggs of brown egg layers, thereby compromising the potential use of the valuable protein rich seed meal. Sinapine content in Brassica juncea germplasm ranges from 6.7 to 15.1 mg/g of dry seed weight (DSW which is significantly higher than the prescribed permissible level of 3.0 mg/g of DSW. Due to limited natural genetic variability, conventional plant breeding approach for reducing the sinapine content has largely been unsuccessful. Hence, transgenic approach for gene silencing was adopted by targeting two genes-SGT and SCT, encoding enzymes UDP- glucose: sinapate glucosyltransferase and sinapoylglucose: choline sinapoyltransferase, respectively, involved in the final two steps of sinapine biosynthetic pathway. These two genes were isolated from B. juncea and eight silencing constructs were developed using three different RNA silencing approaches viz. antisense RNA, RNAi and artificial microRNA. Transgenics in B. juncea were developed following Agrobacterium-mediated transformation. From a total of 1232 independent T0 transgenic events obtained using eight silencing constructs, 25 homozygous lines showing single gene inheritance were identified in the T2 generation. Reduction of seed sinapine content in these lines ranged from 15.8% to 67.2%; the line with maximum reduction had sinapine content of 3.79 mg/g of DSW. The study also revealed that RNAi method was more efficient than the other two methods used in this study.

  14. Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-08

    With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

  15. Supporting document for the historical tank content estimate for S tank farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Gaddis, L.A.; Walsh, A.C.

    1994-06-01

    This document provides historical evaluations of the radioactive mixed wastes stored in the Hanford Site 200 West Area underground single-shell tanks (SSTs). A Historical Tank Content Estimate has been developed by reviewing the process histories, waste transfer data, and available physical and chemical characterization data from various Department of Energy (DOE) and Department of Defense (DOD) contractors. The historical data will supplement information gathered from in-tank core sampling activities that are currently underway. A tank history review that is accompanied by current characterization data creates a complete and reliable inventory estimate. Additionally, historical review of the tanks may reveal anomalies or unusual contents that are critical to characterization and post characterization activities. Complete and accurate tank waste characterizations are critical first steps for DOE and Westinghouse Hanford Company safety programs, waste pretreatment, and waste retrieval activities. The scope of this document is limited to all the SSTs in the S Tank Farm of the southwest quadrant of the 200 West Area. Nine appendices compile data on: tank level histories; temperature graphs; surface level graphs; drywell graphs; riser configuration and tank cross section; sampling data; tank photographs; unknown tank transfers; and tank layering comparison. 113 refs

  16. Supporting document for the historical tank content estimate for A Tank Farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Gaddis, L.A.; Walsh, A.C.

    1994-06-01

    This document provides historical evaluations of the radioactive mixed wastes stored in the Hanford Site 200-East Area underground single-shell tanks (SSTs). A Historical Tank Content Estimate has been developed by reviewing the process histories, waste transfer data, and available physical and chemical characterization data from various Department of Energy (DOE) and Department of Defense (DOD) contractors. The historical data will supplement information gathered from in-tank core sampling activities that are currently underway. A tank history review that is accompanied by current characterization data creates a complete and reliable inventory estimate. Additionally, historical review of the tanks may reveal anomalies or unusual contents that are critical to characterization and post characterization activities. Complete and accurate tank waste characterizations are critical first steps for DOE and Westinghouse Hanford Company safety programs, waste pretreatment, and waste retrieval activities. The scope of this document is limited to the SSTs in the A Tank Farm of the northeast quadrant of the 200 East Area. Nine appendices compile data on: tank level histories; temperature graphs; surface level graphs; drywell graphs; riser configuration and tank cross section; sampling data; tank photographs; unknown tank transfers; and tank layering comparison. 113 refs

  17. Supporting document for the historical tank content estimate for S tank farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.; Gaddis, L.A.; Walsh, A.C.

    1994-06-01

    This document provides historical evaluations of the radioactive mixed wastes stored in the Hanford Site 200 West Area underground single-shell tanks (SSTs). A Historical Tank Content Estimate has been developed by reviewing the process histories, waste transfer data, and available physical and chemical characterization data from various Department of Energy (DOE) and Department of Defense (DOD) contractors. The historical data will supplement information gathered from in-tank core sampling activities that are currently underway. A tank history review that is accompanied by current characterization data creates a complete and reliable inventory estimate. Additionally, historical review of the tanks may reveal anomalies or unusual contents that are critical to characterization and post characterization activities. Complete and accurate tank waste characterizations are critical first steps for DOE and Westinghouse Hanford Company safety programs, waste pretreatment, and waste retrieval activities. The scope of this document is limited to all the SSTs in the S Tank Farm of the southwest quadrant of the 200 West Area. Nine appendices compile data on: tank level histories; temperature graphs; surface level graphs; drywell graphs; riser configuration and tank cross section; sampling data; tank photographs; unknown tank transfers; and tank layering comparison. 113 refs.

  18. Supporting document for the historical tank content estimate for A Tank Farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.; Gaddis, L.A.; Walsh, A.C.

    1994-06-01

    This document provides historical evaluations of the radioactive mixed wastes stored in the Hanford Site 200-East Area underground single-shell tanks (SSTs). A Historical Tank Content Estimate has been developed by reviewing the process histories, waste transfer data, and available physical and chemical characterization data from various Department of Energy (DOE) and Department of Defense (DOD) contractors. The historical data will supplement information gathered from in-tank core sampling activities that are currently underway. A tank history review that is accompanied by current characterization data creates a complete and reliable inventory estimate. Additionally, historical review of the tanks may reveal anomalies or unusual contents that are critical to characterization and post characterization activities. Complete and accurate tank waste characterizations are critical first steps for DOE and Westinghouse Hanford Company safety programs, waste pretreatment, and waste retrieval activities. The scope of this document is limited to the SSTs in the A Tank Farm of the northeast quadrant of the 200 East Area. Nine appendices compile data on: tank level histories; temperature graphs; surface level graphs; drywell graphs; riser configuration and tank cross section; sampling data; tank photographs; unknown tank transfers; and tank layering comparison. 113 refs.

  19. Supporting document for the historical tank content estimate for B Tank Farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Gaddis, L.A.; Johnson, E.D.

    1994-06-01

    This document provides historical evaluations of the radioactive mixed wastes stored in the Hanford Site 200-East Area underground single-shell tanks (SSTs). A Historical Tank Content Estimate has been developed by reviewing the process histories, waste transfer data, and available physical and chemical characterization data from various Department of Energy (DOE) and Department of Defense (DOD) contractors. The historical data will supplement information gathered from in-tank core sampling activities that are currently underway. A tank history review that is accompanied by current characterization data creates a complete and reliable inventory estimate. Additionally, historical review of the tanks may reveal anomalies or unusual contents that are critical to characterization and post characterization activities. Complete and accurate tank waste characterizations are critical first steps for DOE and Westinghouse Hanford Company safety programs, waste pretreatment, and waste retrieval activities. The scope of this document is limited to the SSTs in the B Tank Farm of the northeast quadrant of the 200 East Area. Nine appendices compile data on: tank level histories; temperature graphs; surface level graphs; drywell graphs; riser configuration and tank cross section; sampling data; tank photographs; unknown tank transfers; and tank layering comparison. 113 refs

  20. A modified elliptical formula to estimate kidney collagen content in a model of chronic kidney disease.

    Science.gov (United States)

    Nieto, Jake A; Zhu, Janice; Duan, Bin; Li, Jingsong; Zhou, Ping; Paka, Latha; Yamin, Michael A; Goldberg, Itzhak D; Narayan, Prakash

    2018-01-01

    The extent of scarring or renal interstitial collagen deposition in chronic kidney disease (CKD) can only be ascertained by highly invasive, painful and sometimes risky, tissue biopsy. Interestingly, while CKD-related abnormalities in kidney size can often be visualized using ultrasound, not only does the ellipsoid formula used today underestimate true renal size, but the calculated renal size does not inform tubulointerstitial collagen content. We used coronal kidney sections from healthy mice and mice with kidney disease to develop a new formula for estimating renal parenchymal area. While treating the kidney as an ellipse with the major axis (a) the polar distance, this technique involves extending the minor axis (b) into the renal pelvis to obtain a new minor axis, be. The calculated renal parenchymal area is remarkably similar to the true or measured area. Biochemically determined kidney collagen content revealed a strong and positive correlation with the calculated renal parenchymal area. Picrosirius red staining for tubulointerstitial collagen also correlated with calculated renal parenchymal area. The extent of renal scarring, i.e. kidney interstitial collagen content, can now be computed by making just two axial measurements which can easily be accomplished via noninvasive imaging of this organ.

  1. Evaluating the capabilities of vegetation spectral indices on chlorophyll content estimation at Sentinel-2 spectral resolutions

    Science.gov (United States)

    Sun, Qi; Jiao, Quanjun; Dai, Huayang

    2018-03-01

    Chlorophyll is an important pigment in green plants for photosynthesis and obtaining the energy for growth and development. The rapid, nondestructive and accurate estimation of chlorophyll content is significant for understanding the crops growth, monitoring the disease and insect, and assessing the yield of crops. Sentinel-2 equipped with the Multi-Spectral Instrument (MSI), which will provide images with high spatial, spectral and temporal resolution. It covers the VNIR/SWIR spectral region in 13 bands and incorporates two new spectral bands in the red-edge region and a spatial resolution of 20nm, which can be used to derive vegetation indices using red-edge bands. In this paper, we will focus on assessing the potential of vegetation spectral indices for retrieving chlorophyll content from Sentinel-2 at different angles. Subsequently, we used in-situ spectral data and Sentinel-2 data to test the relationship between VIs and chlorophyll content. The REP, MTCI, CIred-edge, CIgreen, Macc01, TCARI/OSAVI [705,750], NDRE1 and NDRE2 were calculated. NDRE2 index displays a strongly similar result for hyperspectral and simulated Sentinel-2 spectral bands (R2 =0.53, R2 =0.51, for hyperspectral and Sentinel-2, respectively). At different observation angles, NDRE2 has the smallest difference in performance (R2 = 0.51, R2 =0.64, at 0° and 15° , respectively).

  2. Estimation of glandular content rate and statistical analysis of the influence of age group and compressed breast thickness on the estimated value

    International Nuclear Information System (INIS)

    Ohmori, Naoki; Ashida, Kenji; Fujita, Osamu

    2003-01-01

    Because the glandular content rate is an important factor in evaluating breast cancer detection and average glandular dose, it is important in mammography research to estimate and analyze this rate. The purpose of this study was to obtain a formula for statistical estimation of the glandular content rate, to clarify statistically the influence of age group and compressed breast thickness (CBT) on estimating the glandular content rate, and to show statistically the general relation between glandular content rate and the factors of age and CBT. The subjects were 740 Japanese women aged 20-91 years (mean±SD: 48.3±12.8 years) who had undergone mammography. In our study, the glandular content rate was statistically estimated from age group, mAs-value, and CBT when subjects underwent mammography, from a phantom simulation, and from MR images of the breast. In addition, multivariate analysis was carried to examine statistically the influence of age group and CBT on glandular content rate. The mean glandular content rate as estimated by age group was as follows: 35.6% for those in their 20s, 33.4% in the 30s, 27.5% in the 40s, 23.8% in the 50s, and 21.8% in those 60 and over. The rate for the subjects as a whole was 27.1%. This study indicated that overestimation occurred if the estimated value of the glandular content rate was not corrected in the 3D-measurement by MRI. In addition, this study showed that the statistical influence on glandular content rate was significantly larger for CBT than age. (author)

  3. Using interpolation to estimate system uncertainty in gene expression experiments.

    Directory of Open Access Journals (Sweden)

    Lee J Falin

    Full Text Available The widespread use of high-throughput experimental assays designed to measure the entire complement of a cell's genes or gene products has led to vast stores of data that are extremely plentiful in terms of the number of items they can measure in a single sample, yet often sparse in the number of samples per experiment due to their high cost. This often leads to datasets where the number of treatment levels or time points sampled is limited, or where there are very small numbers of technical and/or biological replicates. Here we introduce a novel algorithm to quantify the uncertainty in the unmeasured intervals between biological measurements taken across a set of quantitative treatments. The algorithm provides a probabilistic distribution of possible gene expression values within unmeasured intervals, based on a plausible biological constraint. We show how quantification of this uncertainty can be used to guide researchers in further data collection by identifying which samples would likely add the most information to the system under study. Although the context for developing the algorithm was gene expression measurements taken over a time series, the approach can be readily applied to any set of quantitative systems biology measurements taken following quantitative (i.e. non-categorical treatments. In principle, the method could also be applied to combinations of treatments, in which case it could greatly simplify the task of exploring the large combinatorial space of future possible measurements.

  4. Information content of slug tests for estimating hydraulic properties in realistic, high-conductivity aquifer scenarios

    Science.gov (United States)

    Cardiff, Michael; Barrash, Warren; Thoma, Michael; Malama, Bwalya

    2011-06-01

    SummaryA recently developed unified model for partially-penetrating slug tests in unconfined aquifers ( Malama et al., in press) provides a semi-analytical solution for aquifer response at the wellbore in the presence of inertial effects and wellbore skin, and is able to model the full range of responses from overdamped/monotonic to underdamped/oscillatory. While the model provides a unifying framework for realistically analyzing slug tests in aquifers (with the ultimate goal of determining aquifer properties such as hydraulic conductivity K and specific storage Ss), it is currently unclear whether parameters of this model can be well-identified without significant prior information and, thus, what degree of information content can be expected from such slug tests. In this paper, we examine the information content of slug tests in realistic field scenarios with respect to estimating aquifer properties, through analysis of both numerical experiments and field datasets. First, through numerical experiments using Markov Chain Monte Carlo methods for gauging parameter uncertainty and identifiability, we find that: (1) as noted by previous researchers, estimation of aquifer storage parameters using slug test data is highly unreliable and subject to significant uncertainty; (2) joint estimation of aquifer and skin parameters contributes to significant uncertainty in both unless prior knowledge is available; and (3) similarly, without prior information joint estimation of both aquifer radial and vertical conductivity may be unreliable. These results have significant implications for the types of information that must be collected prior to slug test analysis in order to obtain reliable aquifer parameter estimates. For example, plausible estimates of aquifer anisotropy ratios and bounds on wellbore skin K should be obtained, if possible, a priori. Secondly, through analysis of field data - consisting of over 2500 records from partially-penetrating slug tests in a

  5. Soil Moisture Content Estimation Based on Sentinel-1 and Auxiliary Earth Observation Products. A Hydrological Approach.

    Science.gov (United States)

    Alexakis, Dimitrios D; Mexis, Filippos-Dimitrios K; Vozinaki, Anthi-Eirini K; Daliakopoulos, Ioannis N; Tsanis, Ioannis K

    2017-06-21

    A methodology for elaborating multi-temporal Sentinel-1 and Landsat 8 satellite images for estimating topsoil Soil Moisture Content (SMC) to support hydrological simulation studies is proposed. After pre-processing the remote sensing data, backscattering coefficient, Normalized Difference Vegetation Index (NDVI), thermal infrared temperature and incidence angle parameters are assessed for their potential to infer ground measurements of SMC, collected at the top 5 cm. A non-linear approach using Artificial Neural Networks (ANNs) is tested. The methodology is applied in Western Crete, Greece, where a SMC gauge network was deployed during 2015. The performance of the proposed algorithm is evaluated using leave-one-out cross validation and sensitivity analysis. ANNs prove to be the most efficient in SMC estimation yielding R² values between 0.7 and 0.9. The proposed methodology is used to support a hydrological simulation with the HEC-HMS model, applied at the Keramianos basin which is ungauged for SMC. Results and model sensitivity highlight the contribution of combining Sentinel-1 SAR and Landsat 8 images for improving SMC estimates and supporting hydrological studies.

  6. Increasing the amylose content of durum wheat through silencing of the SBEIIa genes

    Directory of Open Access Journals (Sweden)

    Masci Stefania

    2010-07-01

    Full Text Available Abstract Background High amylose starch has attracted particular interest because of its correlation with the amount of Resistant Starch (RS in food. RS plays a role similar to fibre with beneficial effects for human health, providing protection from several diseases such as colon cancer, diabetes, obesity, osteoporosis and cardiovascular diseases. Amylose content can be modified by a targeted manipulation of the starch biosynthetic pathway. In particular, the inactivation of the enzymes involved in amylopectin synthesis can lead to the increase of amylose content. In this work, genes encoding starch branching enzymes of class II (SBEIIa were silenced using the RNA interference (RNAi technique in two cultivars of durum wheat, using two different methods of transformation (biolistic and Agrobacterium. Expression of RNAi transcripts was targeted to the seed endosperm using a tissue-specific promoter. Results Amylose content was markedly increased in the durum wheat transgenic lines exhibiting SBEIIa gene silencing. Moreover the starch granules in these lines were deformed, possessing an irregular and deflated shape and being smaller than those present in the untransformed controls. Two novel granule bound proteins, identified by SDS-PAGE in SBEIIa RNAi lines, were investigated by mass spectrometry and shown to have strong homologies to the waxy proteins. RVA analysis showed new pasting properties associated with high amylose lines in comparison with untransformed controls. Finally, pleiotropic effects on other starch genes were found by semi-quantitative and Real-Time reverse transcription-polymerase chain reaction (RT-PCR. Conclusion We have found that the silencing of SBEIIa genes in durum wheat causes obvious alterations in granule morphology and starch composition, leading to high amylose wheat. Results obtained with two different methods of transformation and in two durum wheat cultivars were comparable.

  7. The use of double laser pulses for the atomic-emission spectral estimation of uranium content in biological samples

    International Nuclear Information System (INIS)

    Patapovich, M.P.; Umreiko, D.S.; Zajogin, A.P.; Buloichik, J.I.

    2012-01-01

    This paper is aimed at the development of the techniques for estimation of the uranium content in biological objects (hair) using the atomic-emission laser analysis with a sufficient accuracy and high processing rate. (authors)

  8. In-line estimation of sulfur and nitrogen contents during hydrotreating of middle distillates

    Directory of Open Access Journals (Sweden)

    M. E. Pacheco

    2009-12-01

    Full Text Available The main objective of this work is analyzing whether it is possible to develop an empirical correlation for in-line estimation of the sulfur and nitrogen contents of the middle distillates Hydrotreating (HDT products for control purposes. Correlations are based only on readily available in-line information of specific gravity variation between feedstock and products, without considering any piece of information about the kinetic behavior of the catalyst. Experimental data were obtained in pilot plants under operating conditions that are representative of refinery operations. Results indicate that the removal of nitrogen and sulfur compounds during middle distillates HDT can be monitored in-line in real time, based on the available measurements of specific gravity. This allows for development and implementation of advanced in-line procedures for monitoring and control of the HDT process in real time.

  9. The impact of intragenic CpG content on gene expression.

    Science.gov (United States)

    Bauer, Asli Petra; Leikam, Doris; Krinner, Simone; Notka, Frank; Ludwig, Christine; Längst, Gernot; Wagner, Ralf

    2010-07-01

    The development of vaccine components or recombinant therapeutics critically depends on sustained expression of the corresponding transgene. This study aimed to determine the contribution of intragenic CpG content to expression efficiency in transiently and stably transfected mammalian cells. Based upon a humanized version of green fluorescent protein (GFP) containing 60 CpGs within its coding sequence, a CpG-depleted variant of the GFP reporter was established by carefully modulating the codon usage. Interestingly, GFP reporter activity and detectable protein amounts in stably transfected CHO and 293 cells were significantly decreased upon CpG depletion and independent from promoter usage (CMV, EF1 alpha). The reduction in protein expression associated with CpG depletion was likewise observed for other unrelated reporter genes and was clearly reflected by a decline in mRNA copy numbers rather than translational efficiency. Moreover, decreased mRNA levels were neither due to nuclear export restrictions nor alternative splicing or mRNA instability. Rather, the intragenic CpG content influenced de novo transcriptional activity thus implying a common transcription-based mechanism of gene regulation via CpGs. Increased high CpG transcription correlated with changed nucleosomal positions in vitro albeit histone density at the two genes did not change in vivo as monitored by ChIP.

  10. Genome-wide scans for delineation of candidate genes regulating seed-protein content in chickpea

    Directory of Open Access Journals (Sweden)

    Hari Deo eUpadhyaya

    2016-03-01

    Full Text Available Identification of potential genes/alleles governing complex seed-protein content (SPC trait is essential in marker-assisted breeding for quality trait improvement of chickpea. Henceforth, the present study utilized an integrated genomics-assisted breeding strategy encompassing trait association analysis, selective genotyping in traditional bi-parental mapping population and differential expression profiling for the first-time to understand the complex genetic architecture of quantitative SPC trait in chickpea. For GWAS (genome-wide association study, high-throughput genotyping information of 16376 genome-based SNPs (single nucleotide polymorphism discovered from a structured population of 336 sequenced desi and kabuli accessions [with 150-200 kb LD (linkage disequilibrium decay] was utilized. This led to identification of seven most effective genomic loci (genes associated [10 to 20% with 41% combined PVE (phenotypic variation explained] with SPC trait in chickpea. Regardless of the diverse desi and kabuli genetic backgrounds, a comparable level of association potential of the identified seven genomic loci with SPC trait was observed. Five SPC-associated genes were validated successfully in parental accessions and homozygous individuals of an intra-specific desi RIL (recombinant inbred line mapping population (ICC 12299 x ICC 4958 by selective genotyping. The seed-specific expression, including differential up-regulation (> 4-fold of six SPC-associated genes particularly in accessions, parents and homozygous individuals of the aforementioned mapping population with high level of contrasting seed-protein content (21-22% was evident. Collectively, the integrated genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in six potential candidate genes regulating SPC trait in chickpea. Of these, a non-synonymous SNP allele-carrying zinc finger transcription factor gene exhibiting strong association with SPC trait

  11. Rapid Estimation of Tocopherol Content in Linseed and Sunflower Oils-Reactivity and Assay.

    Science.gov (United States)

    Prevc, Tjaša; Levart, Alenka; Cigić, Irena Kralj; Salobir, Janez; Ulrih, Nataša Poklar; Cigić, Blaž

    2015-08-13

    The reactivity of tocopherols with 2,2-diphenyl-1-picrylhydrazyl (DPPH) was studied in model systems in order to establish a method for quantifying vitamin E in plant oils. The method was optimized with respect to solvent composition of the assay medium, which has a large influence on the course of reaction of tocopherols with DPPH. The rate of reaction of α-tocopherol with DPPH is higher than that of γ-tocopherol in both protic and aprotic solvents. In ethyl acetate, routinely applied for the analysis of antioxidant potential (AOP) of plant oils, reactions of tocopherols with DPPH are slower and concentration of tocopherols in the assay has a large influence on their molar reactivity. In 2-propanol, however, two electrons are exchanged for both α- and γ-tocopherols, independent of their concentration. 2-propanol is not toxic and is fully compatible with polypropylene labware. The chromatographically determined content of tocopherols and their molar reactivity in the DPPH assay reveal that only tocopherols contribute to the AOP of sunflower oil, whereas the contribution of tocopherols to the AOP of linseed oil is 75%. The DPPH assay in 2-propanol can be applied for rapid and cheap estimation of vitamin E content in plant oils where tocopherols are major antioxidants.

  12. Rapid Estimation of Tocopherol Content in Linseed and Sunflower Oils-Reactivity and Assay

    Directory of Open Access Journals (Sweden)

    Tjaša Prevc

    2015-08-01

    Full Text Available The reactivity of tocopherols with 2,2-diphenyl-1-picrylhydrazyl (DPPH was studied in model systems in order to establish a method for quantifying vitamin E in plant oils. The method was optimized with respect to solvent composition of the assay medium, which has a large influence on the course of reaction of tocopherols with DPPH. The rate of reaction of α-tocopherol with DPPH is higher than that of γ-tocopherol in both protic and aprotic solvents. In ethyl acetate, routinely applied for the analysis of antioxidant potential (AOP of plant oils, reactions of tocopherols with DPPH are slower and concentration of tocopherols in the assay has a large influence on their molar reactivity. In 2-propanol, however, two electrons are exchanged for both α- and γ-tocopherols, independent of their concentration. 2-propanol is not toxic and is fully compatible with polypropylene labware. The chromatographically determined content of tocopherols and their molar reactivity in the DPPH assay reveal that only tocopherols contribute to the AOP of sunflower oil, whereas the contribution of tocopherols to the AOP of linseed oil is 75%. The DPPH assay in 2-propanol can be applied for rapid and cheap estimation of vitamin E content in plant oils where tocopherols are major antioxidants.

  13. Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming.

    Science.gov (United States)

    Lyubetsky, Vassily; Gershgorin, Roman; Gorbunov, Konstantin

    2017-12-06

    Chromosome structure is a very limited model of the genome including the information about its chromosomes such as their linear or circular organization, the order of genes on them, and the DNA strand encoding a gene. Gene lengths, nucleotide composition, and intergenic regions are ignored. Although highly incomplete, such structure can be used in many cases, e.g., to reconstruct phylogeny and evolutionary events, to identify gene synteny, regulatory elements and promoters (considering highly conserved elements), etc. Three problems are considered; all assume unequal gene content and the presence of gene paralogs. The distance problem is to determine the minimum number of operations required to transform one chromosome structure into another and the corresponding transformation itself including the identification of paralogs in two structures. We use the DCJ model which is one of the most studied combinatorial rearrangement models. Double-, sesqui-, and single-operations as well as deletion and insertion of a chromosome region are considered in the model; the single ones comprise cut and join. In the reconstruction problem, a phylogenetic tree with chromosome structures in the leaves is given. It is necessary to assign the structures to inner nodes of the tree to minimize the sum of distances between terminal structures of each edge and to identify the mutual paralogs in a fairly large set of structures. A linear algorithm is known for the distance problem without paralogs, while the presence of paralogs makes it NP-hard. If paralogs are allowed but the insertion and deletion operations are missing (and special constraints are imposed), the reduction of the distance problem to integer linear programming is known. Apparently, the reconstruction problem is NP-hard even in the absence of paralogs. The problem of contigs is to find the optimal arrangements for each given set of contigs, which also includes the mutual identification of paralogs. We proved that these

  14. A framework for scalable parameter estimation of gene circuit models using structural information

    KAUST Repository

    Kuwahara, Hiroyuki

    2013-06-21

    Motivation: Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Results: Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. The Author 2013.

  15. A framework for scalable parameter estimation of gene circuit models using structural information

    KAUST Repository

    Kuwahara, Hiroyuki; Fan, Ming; Wang, Suojin; Gao, Xin

    2013-01-01

    Motivation: Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Results: Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. The Author 2013.

  16. A framework for scalable parameter estimation of gene circuit models using structural information.

    Science.gov (United States)

    Kuwahara, Hiroyuki; Fan, Ming; Wang, Suojin; Gao, Xin

    2013-07-01

    Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. http://sfb.kaust.edu.sa/Pages/Software.aspx. Supplementary data are available at Bioinformatics online.

  17. Acrylamide content in cigarette mainstream smoke and estimation of exposure to acrylamide from tobacco smoke in Poland

    Directory of Open Access Journals (Sweden)

    Hanna Mojska

    2016-07-01

    Our results demonstrate that tobacco smoke is a significant source of acrylamide and total exposure to acrylamide in the population of smokers, on average, is higher by more than 50% in comparison with non-smokers. Our estimation of exposure to acrylamide from tobacco smoke is the first estimation taking into account the actual determined acrylamide content in the cigarettes available on the market.

  18. Gene expression during blow fly development: improving the precision of age estimates in forensic entomology.

    Science.gov (United States)

    Tarone, Aaron M; Foran, David R

    2011-01-01

    Forensic entomologists use size and developmental stage to estimate blow fly age, and from those, a postmortem interval. Since such estimates are generally accurate but often lack precision, particularly in the older developmental stages, alternative aging methods would be advantageous. Presented here is a means of incorporating developmentally regulated gene expression levels into traditional stage and size data, with a goal of more precisely estimating developmental age of immature Lucilia sericata. Generalized additive models of development showed improved statistical support compared to models that did not include gene expression data, resulting in an increase in estimate precision, especially for postfeeding third instars and pupae. The models were then used to make blind estimates of development for 86 immature L. sericata raised on rat carcasses. Overall, inclusion of gene expression data resulted in increased precision in aging blow flies. © 2010 American Academy of Forensic Sciences.

  19. Optimizing cationic and neutral lipids for efficient gene delivery at high serum content.

    Science.gov (United States)

    Chan, Chia-Ling; Ewert, Kai K; Majzoub, Ramsey N; Hwu, Yeu-Kuang; Liang, Keng S; Leal, Cecília; Safinya, Cyrus R

    2014-01-01

    Cationic liposome (CL)-DNA complexes are promising gene delivery vectors with potential application in gene therapy. A key challenge in creating CL-DNA complexes for application is that their transfection efficiency (TE) is adversely affected by serum. In particular, little is known about the effects of a high serum content on TE, even though this may provide design guidelines for application in vivo. We prepared CL-DNA complexes in which we varied the neutral lipid [1,2-dioleoyl-sn-glycerophosphatidylcholine, glycerol-monooleate (GMO), cholesterol], the headgroup charge and chemical structure of the cationic lipid, and the ratio of neutral to cationic lipid; we then measured the TE of these complexes as a function of serum content and assessed their cytotoxicity. We tested selected formulations in two human cancer cell lines (M21/melanoma and PC-3/prostate cancer). In the absence of serum, all CL-DNA complexes of custom-synthesized multivalent lipids show high TE. Certain combinations of multivalent lipids and neutral lipids, such as MVL5(5+)/GMO-DNA complexes or complexes based on the dendritic-headgroup lipid TMVLG3(8+) exhibited high TE both in the absence and presence of serum. Although their TE still dropped to a small extent in the presence of serum, it reached or surpassed that of benchmark commercial transfection reagents, particularly at a high serum content. Two-component vectors (one multivalent cationic lipid and one neutral lipid) can rival or surpass benchmark reagents at low and high serum contents (up to 50%, v/v). We propose guidelines for optimizing the serum resistance of CL-DNA complexes based on a given cationic lipid. Copyright © 2014 John Wiley & Sons, Ltd.

  20. Survival of Antibiotic Resistant Bacteria and Horizontal Gene Transfer Control Antibiotic Resistance Gene Content in Anaerobic Digesters.

    Science.gov (United States)

    Miller, Jennifer H; Novak, John T; Knocke, William R; Pruden, Amy

    2016-01-01

    Understanding fate of antibiotic resistant bacteria (ARB) vs. their antibiotic resistance genes (ARGs) during wastewater sludge treatment is critical in order to reduce the spread of antibiotic resistance through process optimization. Here, we spiked high concentrations of tetracycline-resistant bacteria, isolated from mesophilic (Iso M1-1-a Pseudomonas sp.) and thermophilic (Iso T10-a Bacillus sp.) anaerobic digested sludge, into batch digesters and monitored their fate by plate counts and quantitative polymerase chain reaction (QPCR) of their corresponding tetracycline ARGs. In batch studies, spiked ARB plate counts returned to baseline (thermophilic) or 1-log above baseline (mesophilic) while levels of the ARG present in the spiked isolate [tet(G)] remained high in mesophilic batch reactors. To compare results under semi-continuous flow conditions with natural influent variation, tet(O), tet(W), and sul1 ARGs, along with the intI1 integrase gene, were monitored over a 9-month period in the raw feed sludge and effluent sludge of lab-scale thermophilic and mesophilic anaerobic digesters. sul1 and intI1 in mesophilic and thermophilic digesters correlated positively (Spearman rho = 0.457-0.829, P < 0.05) with the raw feed sludge. There was no correlation in tet(O) or tet(W) ratios in raw sludge and mesophilic digested sludge or thermophilic digested sludge (Spearman rho = 0.130-0.486, P = 0.075-0.612). However, in the thermophilic digester, the tet(O) and tet(W) ratios remained consistently low over the entire monitoring period. We conclude that the influent sludge microbial composition can influence the ARG content of a digester, apparently as a result of differential survival or death of ARBs or horizontal gene transfer of genes between raw sludge ARBs and the digester microbial community. Notably, mesophilic digestion was more susceptible to ARG intrusion than thermophilic digestion, which may be attributed to a higher rate of ARB survival and/or horizontal gene

  1. FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets.

    Science.gov (United States)

    Tiys, Evgeny S; Ivanisenko, Timofey V; Demenkov, Pavel S; Ivanisenko, Vladimir A

    2018-02-09

    Estimation of functional connectivity in gene sets derived from genome-wide or other biological experiments is one of the essential tasks of bioinformatics. A promising approach for solving this problem is to compare gene networks built using experimental gene sets with random networks. One of the resources that make such an analysis possible is CrossTalkZ, which uses the FunCoup database. However, existing methods, including CrossTalkZ, do not take into account individual types of interactions, such as protein/protein interactions, expression regulation, transport regulation, catalytic reactions, etc., but rather work with generalized types characterizing the existence of any connection between network members. We developed the online tool FunGeneNet, which utilizes the ANDSystem and STRING to reconstruct gene networks using experimental gene sets and to estimate their difference from random networks. To compare the reconstructed networks with random ones, the node permutation algorithm implemented in CrossTalkZ was taken as a basis. To study the FunGeneNet applicability, the functional connectivity analysis of networks constructed for gene sets involved in the Gene Ontology biological processes was conducted. We showed that the method sensitivity exceeds 0.8 at a specificity of 0.95. We found that the significance level of the difference between gene networks of biological processes and random networks is determined by the type of connections considered between objects. At the same time, the highest reliability is achieved for the generalized form of connections that takes into account all the individual types of connections. By taking examples of the thyroid cancer networks and the apoptosis network, it is demonstrated that key participants in these processes are involved in the interactions of those types by which these networks differ from random ones. FunGeneNet is a web tool aimed at proving the functionality of networks in a wide range of sizes of

  2. Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips

    NARCIS (Netherlands)

    van Ruissen, Fred; Ruijter, Jan M.; Schaaf, Gerben J.; Asgharnegad, Lida; Zwijnenburg, Danny A.; Kool, Marcel; Baas, Frank

    2005-01-01

    Background: Serial Analysis of Gene Expression ( SAGE) and microarrays have found awidespread application, but much ambiguity exists regarding the evaluation of these technologies. Cross-platform utilization of gene expression data from the SAGE and microarray technology could reduce the need for

  3. Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality

    Directory of Open Access Journals (Sweden)

    Marthey Sylvain

    2011-02-01

    Full Text Available Abstract Background The processing ability of poultry meat is highly related to its ultimate pH, the latter being mainly determined by the amount of glycogen in the muscle at death. The genetic determinism of glycogen and related meat quality traits has been established in the chicken but the molecular mechanisms involved in variations in these traits remain to be fully described. In this study, Chicken Genome Arrays (20 K were used to compare muscle gene expression profiles of chickens from Fat (F and Lean (L lines that exhibited high and low muscle glycogen content, respectively, and of individuals exhibiting extremely high (G+ or low (G- muscle glycogen content originating from the F2 cross between the Fat and Lean lines. Real-time RT-PCR was subsequently performed to validate the differential expression of genes either selected from the microarray analysis or whose function in regulating glycogen metabolism was well known. Results Among the genes found to be expressed in chicken P. major muscle, 197 and 254 transcripts appeared to be differentially expressed on microarrays for the F vs. L and the G+ vs. G- comparisons, respectively. Some involved particularly in lipid and carbohydrate metabolism were selected for further validation studies by real-time RT-PCR. We confirmed that, as in mammals, the down-regulation of CEBPB and RGS2 coincides with a decrease in peripheral adiposity in the chicken, but these genes are also suggested to affect muscle glycogen turnover through their role in the cAMP-dependent signalling pathway. Several other genes were suggested to have roles in the regulation of glycogen storage in chicken muscle. PDK4 may act as a glycogen sensor in muscle, UGDH may compete for glycogen synthesis by using UDP-glucose for glucoronidation, and PRKAB1, PRKAG2, and PHKD may impact on glycogen turnover in muscle, through AMP-activated signalling pathways. Conclusions This study is the first stage in the understanding of molecular

  4. Genepleio Software for Effective Estimation of Gene Pleiotropy from Protein Sequences

    Directory of Open Access Journals (Sweden)

    Wenhai Chen

    2015-01-01

    Full Text Available Though pleiotropy, which refers to the phenomenon of a gene affecting multiple traits, has long played a central role in genetics, development, and evolution, estimation of the number of pleiotropy components remains a hard mission to accomplish. In this paper, we report a newly developed software package, Genepleio, to estimate the effective gene pleiotropy from phylogenetic analysis of protein sequences. Since this estimate can be interpreted as the minimum pleiotropy of a gene, it is used to play a role of reference for many empirical pleiotropy measures. This work would facilitate our understanding of how gene pleiotropy affects the pattern of genotype-phenotype map and the consequence of organismal evolution.

  5. Retinoid X receptor gene expression and protein content in tissues of the rock shell Thais clavigera

    Energy Technology Data Exchange (ETDEWEB)

    Horiguchi, Toshihiro [Research Center for Environmental Risk, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 (Japan)], E-mail: thorigu@nies.go.jp; Nishikawa, Tomohiro [Research Center for Environmental Risk, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 (Japan); Ohta, Yasuhiko [Department of Veterinary Science, Faculty of Agriculture, Tottori University, 4-101 Koyamacho-Minami, Tottori 680-8553 (Japan); Shiraishi, Hiroaki; Morita, Masatoshi [Research Center for Environmental Risk, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 (Japan)

    2007-10-15

    To elucidate the role of retinoid X receptor (RXR) in the development of imposex caused by organotin compounds in gastropod molluscs, we investigated RXR gene expression and RXR protein content in various tissues of male and female wild rock shells (Thais clavigera). Quantitative real-time polymerase chain reaction, Western blotting, and immunohistochemistry with a commercial antibody against human RXR {alpha} revealed that RXR gene expression was significantly higher in the penises of males and imposex-exhibiting females than in the penis-forming areas of normal females (P < 0.01 and P < 0.05, respectively). Western blotting demonstrated that the antibody could detect rock shell RXR and showed that the male penis had the highest content of RXR protein among the analyzed tissues of males and normal females. Immunohistochemical staining revealed nuclear localization of RXR protein in the epithelial and smooth muscle cells of the vas deferens and in the interstitial or connective tissues and epidermis of the penis in males and imposex-exhibiting females. RXR could be involved in the mechanism of induction of male-type genitalia (penis and vas deferens) by organotin compounds in female rock shells.

  6. Biased Gene Conversion and GC-Content Evolution in the Coding Sequences of Reptiles and Vertebrates

    Science.gov (United States)

    Figuet, Emeric; Ballenghien, Marion; Romiguier, Jonathan; Galtier, Nicolas

    2015-01-01

    Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins. PMID:25527834

  7. Studies on tender wheatgrass: estimation of elemental content, bioaccessibility of essential elements and antioxidant activity

    International Nuclear Information System (INIS)

    Reddy, A.V.R.; Acharya, R.; Nair, A.G.C.; Kulkarni, S.D.; Rajurkar, N.S.

    2008-08-01

    Tender wheatgrass is being consumed by human beings in juice form or as it is due to its antioxidant potential and medicinal value. Systematic studies were carried out to (i) estimate elemental profiles as a function of growth period and conditions, bioaccessibility of different elements and the antioxidant potential of the tender wheatgrass, (ii) determine the optimum growth period for obtaining maximum benefit and (iii) examine the possible correlation between antioxidant potential and mineral content. Wheatgrass was grown in four different conditions namely (i) tap water, (ii) tap water with nutrients, (iii) soil and tap water and (iv) soil with nutrient solution. The studies were carried out on the wheatgrass of 5-20 days old. For comparison with laboratory grown wheatgrass, a set of commercially available wheatgrass tablets and wheat seeds were also studied. Instrumental neutron activation analysis (INAA) was used for concentration determination of elements in the wheatgrass, wheat seeds and wheatgrass tablets. A total of 15 elements like Na, K, Ca, Mg, Mn, Br, Fe and Zn were determined in the samples of shoots and roots of tender wheatgrass. A comparison with the recommended dietary allowance (RDA) of different essential elements with that in tender wheatgrass revealed that wheatgrass is a good source of minerals for health benefits rather than a food supplement. Bioaccessible fractions of various elements were estimated by a chemical NAA method by subjecting the samples to in vitro gastric and gastro-intestinal digestion followed by NAA. The bioaccessibility concentrations by both the measurements were in the range of 9-60%. It was found that bioaccessibility of the elements studied was the highest from fresh wheatgrass and the lowest from wheat seeds. Accuracy of the NAA method was evaluated by analyzing two biological reference materials, SRM 1573a (Tomato leaves) from NIST, USA and ICHTJ CTA-vtl-2 (Tobacco leaves) from INCT, Poland. The antioxidant

  8. Contents

    Directory of Open Access Journals (Sweden)

    Editor IJRED

    2012-11-01

    Full Text Available International Journal of Renewable Energy Development www.ijred.com Volume 1             Number 3            October 2012                ISSN 2252- 4940   CONTENTS OF ARTICLES page Design and Economic Analysis of a Photovoltaic System: A Case Study 65-73 C.O.C. Oko , E.O. Diemuodeke, N.F. Omunakwe, and E. Nnamdi     Development of Formaldehyde Adsorption using Modified Activated Carbon – A Review 75-80 W.D.P Rengga , M. Sudibandriyo and M. Nasikin     Process Optimization for Ethyl Ester Production in Fixed Bed Reactor Using Calcium Oxide Impregnated Palm Shell Activated Carbon (CaO/PSAC 81-86 A. Buasri , B. Ksapabutr, M. Panapoy and N. Chaiyut     Wind Resource Assessment in Abadan Airport in Iran 87-97 Mojtaba Nedaei       The Energy Processing by Power Electronics and its Impact on Power Quality 99-105 J. E. Rocha and B. W. D. C. Sanchez       First Aspect of Conventional Power System Assessment for High Wind Power Plants Penetration 107-113 A. Merzic , M. Music, and M. Rascic   Experimental Study on the Production of Karanja Oil Methyl Ester and Its Effect on Diesel Engine 115-122 N. Shrivastava,  , S.N. Varma and M. Pandey  

  9. An Artificial Neural Network for Movement Pattern Analysis to Estimate Blood Alcohol Content Level.

    Science.gov (United States)

    Gharani, Pedram; Suffoletto, Brian; Chung, Tammy; Karimi, Hassan A

    2017-12-13

    Impairments in gait occur after alcohol consumption, and, if detected in real-time, could guide the delivery of "just-in-time" injury prevention interventions. We aimed to identify the salient features of gait that could be used for estimating blood alcohol content (BAC) level in a typical drinking environment. We recruited 10 young adults with a history of heavy drinking to test our research app. During four consecutive Fridays and Saturdays, every hour from 8 p.m. to 12 a.m., they were prompted to use the app to report alcohol consumption and complete a 5-step straight-line walking task, during which 3-axis acceleration and angular velocity data was sampled at a frequency of 100 Hz. BAC for each subject was calculated. From sensor signals, 24 features were calculated using a sliding window technique, including energy, mean, and standard deviation. Using an artificial neural network (ANN), we performed regression analysis to define a model determining association between gait features and BACs. Part (70%) of the data was then used as a training dataset, and the results tested and validated using the rest of the samples. We evaluated different training algorithms for the neural network and the result showed that a Bayesian regularization neural network (BRNN) was the most efficient and accurate. Analyses support the use of the tandem gait task paired with our approach to reliably estimate BAC based on gait features. Results from this work could be useful in designing effective prevention interventions to reduce risky behaviors during periods of alcohol consumption.

  10. An Artificial Neural Network for Movement Pattern Analysis to Estimate Blood Alcohol Content Level

    Directory of Open Access Journals (Sweden)

    Pedram Gharani

    2017-12-01

    Full Text Available Impairments in gait occur after alcohol consumption, and, if detected in real-time, could guide the delivery of “just-in-time” injury prevention interventions. We aimed to identify the salient features of gait that could be used for estimating blood alcohol content (BAC level in a typical drinking environment. We recruited 10 young adults with a history of heavy drinking to test our research app. During four consecutive Fridays and Saturdays, every hour from 8 p.m. to 12 a.m., they were prompted to use the app to report alcohol consumption and complete a 5-step straight-line walking task, during which 3-axis acceleration and angular velocity data was sampled at a frequency of 100 Hz. BAC for each subject was calculated. From sensor signals, 24 features were calculated using a sliding window technique, including energy, mean, and standard deviation. Using an artificial neural network (ANN, we performed regression analysis to define a model determining association between gait features and BACs. Part (70% of the data was then used as a training dataset, and the results tested and validated using the rest of the samples. We evaluated different training algorithms for the neural network and the result showed that a Bayesian regularization neural network (BRNN was the most efficient and accurate. Analyses support the use of the tandem gait task paired with our approach to reliably estimate BAC based on gait features. Results from this work could be useful in designing effective prevention interventions to reduce risky behaviors during periods of alcohol consumption.

  11. Associations of heart and adipocyte fatty acid-binding protein gene expression with intramuscular fat content in pigs

    NARCIS (Netherlands)

    Gerbens, F.; Verburg, F.J.; Moerkerk, van H.T.; Engel, B.; Buist, W.; Veerkamp, J.H.; Pas, te M.F.

    2001-01-01

    Intramuscular fat content is a major determinant of meat quality in pigs. Previously, polymorphisms in the adipocyte and heart fatty acid-binding protein genes, A-FABP and H-FABP, have been significantly associated with genetic variation of intramuscular fat content in a Duroc pig population.

  12. Associations of heart and adipocyte fatty acid-binding protein gene expression with intramuscular fat content in pigs.

    NARCIS (Netherlands)

    Gerbens, F.; Verburg, F.J.; Moerkerk, H.T.B. van; Engel, B.; Buist, W.; Veerkamp, J.H.; Pas, M.F. te

    2001-01-01

    Intramuscular fat content is a major determinant of meat quality in pigs. Previously, polymorphisms in the adipocyte and heart fatty acid-binding protein genes, A-FABP and H-FABP, have been significantly associated with genetic variation of intramuscular fat content in a Duroc pig population.

  13. Supporting document for the historical tank content estimate for SY-tank farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.

    1997-08-12

    The purpose of this historical characterization document is to present the synthesized summaries of the historical records concerning the physical characteristics, radiological, and chemical composition of mixed wastes stored in underground double-shell tanks and the physical condition of these tanks. The double-shell tanks are located on the United States Department of Energy`s Hanford Site, approximately 25 miles northwest or Richland, Washington. The document will be used to assist in characterizing the waste in the tanks in conjunction with the current program of sampling and analyzing the tank wastes. Los Alamos National Laboratory (LANL) developed computer models that used the historical data to attempt to characterize the wastes and to generate estimates of each tank`s inventory. A historical review of the tanks may reveal anomalies or unusual contents that could be critical to characterization and post characterization activities. This document was developed by reviewing the operating plant process histories, waste transfer data, and available physical and chemical data from numerous resources. These resources were generated by numerous contractors from 1945 to the present. Waste characterization, the process of describing the character or quality of a waste, is required by Federal law (Resource Conservation and Recovery Act [RCRA]) and state law (Washington Administrative Code [WAC] 173-303, Dangerous Waste Regulations). Characterizing the waste is necessary to determine methods to safely retrieve, transport, and/or treat the wastes.

  14. Estimation of the parameter of satisfaction with services in tourism: content analysis of online customer reviews

    Directory of Open Access Journals (Sweden)

    Kapilevich Leonid

    2016-01-01

    Full Text Available To increase the competitiveness the hotels have to satisfy their guests’ requirements, anticipate their wishes and offer new services; this is quite problematic for the hotel business. The paper considers the opportunities of employing online guest reviews to reveal the hotel ratings and attributes, significant for guests. The implementation of this research method is specified by the quality of information obtained via the internet; it is published on a voluntary basis, statements are initiated by users; moreover, consumers estimate the services and offers, having certain emotional importance for them; it allows segmenting the factors according to the level of their emotional significance. This segmentation is of utmost importance since the principal aim of the researches devoted to the assessment of the level of consumers’ satisfaction is to reveal the indicators of company activities from the position of customers’ priorities and emotional evaluations. The content analysis discovers the indicators, significant for the beach hotels customers. 90 hotels were grouped according to 16 categories. The results display that the guests responses can be used for investigating the importance of hotel attributes and determining the peculiarities of various hotel customers groups. The obtained results can be used for service package improvement and for hotel description in advertisement and reservation systems.

  15. Supporting document for the historical tank content estimate for SY-tank farm

    International Nuclear Information System (INIS)

    Brevick, C.H.

    1997-01-01

    The purpose of this historical characterization document is to present the synthesized summaries of the historical records concerning the physical characteristics, radiological, and chemical composition of mixed wastes stored in underground double-shell tanks and the physical condition of these tanks. The double-shell tanks are located on the United States Department of Energy's Hanford Site, approximately 25 miles northwest or Richland, Washington. The document will be used to assist in characterizing the waste in the tanks in conjunction with the current program of sampling and analyzing the tank wastes. Los Alamos National Laboratory (LANL) developed computer models that used the historical data to attempt to characterize the wastes and to generate estimates of each tank's inventory. A historical review of the tanks may reveal anomalies or unusual contents that could be critical to characterization and post characterization activities. This document was developed by reviewing the operating plant process histories, waste transfer data, and available physical and chemical data from numerous resources. These resources were generated by numerous contractors from 1945 to the present. Waste characterization, the process of describing the character or quality of a waste, is required by Federal law (Resource Conservation and Recovery Act CRA and state law (Washington Administrative Code AC 173-303, Dangerous Waste Regulations). Characterizing the waste is necessary to determine methods to safely retrieve, transport, and/or treat the wastes

  16. Off-Nadir Hyperspectral Sensing for Estimation of Vertical Profile of Leaf Chlorophyll Content within Wheat Canopies.

    Science.gov (United States)

    Kong, Weiping; Huang, Wenjiang; Casa, Raffaele; Zhou, Xianfeng; Ye, Huichun; Dong, Yingying

    2017-11-23

    Monitoring the vertical profile of leaf chlorophyll (Chl) content within winter wheat canopies is of significant importance for revealing the real nutritional status of the crop. Information on the vertical profile of Chl content is not accessible to nadir-viewing remote or proximal sensing. Off-nadir or multi-angle sensing would provide effective means to detect leaf Chl content in different vertical layers. However, adequate information on the selection of sensitive spectral bands and spectral index formulas for vertical leaf Chl content estimation is not yet available. In this study, all possible two-band and three-band combinations over spectral bands in normalized difference vegetation index (NDVI)-, simple ratio (SR)- and chlorophyll index (CI)-like types of indices at different viewing angles were calculated and assessed for their capability of estimating leaf Chl for three vertical layers of wheat canopies. The vertical profiles of Chl showed top-down declining trends and the patterns of band combinations sensitive to leaf Chl content varied among different vertical layers. Results indicated that the combinations of green band (520 nm) with NIR bands were efficient in estimating upper leaf Chl content, whereas the red edge (695 nm) paired with NIR bands were dominant in quantifying leaf Chl in the lower layers. Correlations between published spectral indices and all NDVI-, SR- and CI-like types of indices and vertical distribution of Chl content showed that reflectance measured from 50°, 30° and 20° backscattering viewing angles were the most promising to obtain information on leaf Chl in the upper-, middle-, and bottom-layer, respectively. Three types of optimized spectral indices improved the accuracy for vertical leaf Chl content estimation. The optimized three-band CI-like index performed the best in the estimation of vertical distribution of leaf Chl content, with R² of 0.84-0.69, and RMSE of 5.37-5.56 µg/cm² from the top to the bottom layers

  17. Validity of estimating the organic carbon content of basin sediment using color measurements

    International Nuclear Information System (INIS)

    Sasaki, Toshinori; Sugai, Toshihiko; Ogami, Takashi; Yanagida, Makoto; Yasue, Ken-ichi

    2010-01-01

    Psychometric lightness (L* value) measured by a colorimeter offers a rapid means of obtaining the organic carbon content of sediment. We measured peat and lacustrine sediments covering the past 300 ka - 106 samples for L* value and 197 samples for organic carbon content. L* values are highly correlated with organic carbon contents. Therefore, L* values are a convenient alternative to measuring organic carbon contents. (author)

  18. An Improved Fuzzy Based Missing Value Estimation in DNA Microarray Validated by Gene Ranking

    Directory of Open Access Journals (Sweden)

    Sujay Saha

    2016-01-01

    Full Text Available Most of the gene expression data analysis algorithms require the entire gene expression matrix without any missing values. Hence, it is necessary to devise methods which would impute missing data values accurately. There exist a number of imputation algorithms to estimate those missing values. This work starts with a microarray dataset containing multiple missing values. We first apply the modified version of the fuzzy theory based existing method LRFDVImpute to impute multiple missing values of time series gene expression data and then validate the result of imputation by genetic algorithm (GA based gene ranking methodology along with some regular statistical validation techniques, like RMSE method. Gene ranking, as far as our knowledge, has not been used yet to validate the result of missing value estimation. Firstly, the proposed method has been tested on the very popular Spellman dataset and results show that error margins have been drastically reduced compared to some previous works, which indirectly validates the statistical significance of the proposed method. Then it has been applied on four other 2-class benchmark datasets, like Colorectal Cancer tumours dataset (GDS4382, Breast Cancer dataset (GSE349-350, Prostate Cancer dataset, and DLBCL-FL (Leukaemia for both missing value estimation and ranking the genes, and the results show that the proposed method can reach 100% classification accuracy with very few dominant genes, which indirectly validates the biological significance of the proposed method.

  19. Metagenomic analysis revealed highly diverse microbial arsenic metabolism genes in paddy soils with low-arsenic contents

    International Nuclear Information System (INIS)

    Xiao, Ke-Qing; Li, Li-Guan; Ma, Li-Ping; Zhang, Si-Yu; Bao, Peng; Zhang, Tong; Zhu, Yong-Guan

    2016-01-01

    Microbe-mediated arsenic (As) metabolism plays a critical role in global As cycle, and As metabolism involves different types of genes encoding proteins facilitating its biotransformation and transportation processes. Here, we used metagenomic analysis based on high-throughput sequencing and constructed As metabolism protein databases to analyze As metabolism genes in five paddy soils with low-As contents. The results showed that highly diverse As metabolism genes were present in these paddy soils, with varied abundances and distribution for different types and subtypes of these genes. Arsenate reduction genes (ars) dominated in all soil samples, and significant correlation existed between the abundance of arr (arsenate respiration), aio (arsenite oxidation), and arsM (arsenite methylation) genes, indicating the co-existence and close-relation of different As resistance systems of microbes in wetland environments similar to these paddy soils after long-term evolution. Among all soil parameters, pH was an important factor controlling the distribution of As metabolism gene in five paddy soils (p = 0.018). To the best of our knowledge, this is the first study using high-throughput sequencing and metagenomics approach in characterizing As metabolism genes in the five paddy soil, showing their great potential in As biotransformation, and therefore in mitigating arsenic risk to humans. - Highlights: • Use metagenomics to analyze As metabolism genes in paddy soils with low-As content. • These genes were ubiquitous, abundant, and associated with diverse microbes. • pH as an important factor controlling their distribution in paddy soil. • Imply combinational effect of evolution and selection on As metabolism genes. - Metagenomics was used to analyze As metabolism genes in paddy soils with low-As contents. These genes were ubiquitous, abundant, and associated with diverse microbes.

  20. An Integrated Field and Hyperspectral Remote Sensing Method for the Estimation of Pigments Content of Stipa Purpurea in Shenzha, Tibet

    Directory of Open Access Journals (Sweden)

    Bo Kong

    2017-01-01

    Full Text Available Stipa purpurea is the representative type of alpine grassland in Tibet and the surviving and development material for herdsmen. This paper takes Shenzha County as the research area. Based on the analysis of typical hyperspectral variables sensitive to chlorophyll content of Stipa purpurea, 10 spectral variables with significant correlation with chlorophyll were extracted. The estimation model of chlorophyll was established. The photosynthetic pigment contents in the Shenzha area were calculated by using HJ-1A remote sensing images. The results show that (1 there are significant correlations between chlorophyll content and spectral variables; in particular, the coefficient of Chlb in Stipa purpurea with RVI is the largest (0.728; (2 10 variables are correlated with chlorophyll, and the order of correlation is Chlb > Chla > Chls; (3 for the estimation of Chla, the EVI is the best variable. RVI, NDVI, and VI2 are suitable for Chlb; RVI and NDVI are also suitable for the estimation of Chls; (4 the mean estimated content of Chla in Stipa bungeana is about 4.88 times that of Chlb, while Cars is slightly more than Chlb; (5 the distribution of Chla is opposite to Chlb and Chls content in water area.

  1. Transcriptional profiles of hybrid Eucalyptus genotypes with contrasting lignin content reveal that monolignol biosynthesis-related genes regulate wood composition

    Directory of Open Access Journals (Sweden)

    Tomotaka eShinya

    2016-04-01

    Full Text Available Eucalyptus species constitutes the most widely planted hardwood trees in temperate and subtropical regions. In this study, we compared the transcript levels of genes involved in lignocellulose formation such as cellulose, hemicellulose and lignin biosynthesis in two selected three-year old hybrid Eucalyptus (Eucalyptus urophylla x E. grandis genotypes (AM063 and AM380 that have different lignin content. AM063 and AM380 had 20.2 and 35.5% of Klason lignin content and 59.0% and 48.2%, -cellulose contents, respectively. We investigated the correlation between wood properties and transcript levels of wood formation-related genes using RNA-seq with total RNAs extracted from developing xylem tissues at a breast height. Transcript levels of cell wall construction genes such as cellulose synthase (CesA and sucrose synthase (SUSY were almost the same in both genotypes. However, AM063 exhibited higher transcript levels of UDP-glucose pyrophosphorylase (UGP and xyloglucan endotransglucoxylase (XTH than those in AM380. Most monolignol biosynthesis- related isozyme genes showed higher transcript levels in AM380. These results indicate monolignol biosynthesis-related genes may regulate wood composition in Eucalyptus. Flavonoids contents were also observed at much higher levels in AM380 as a result of the elevated transcript levels of common phenylpropanoid pathway genes, phenylalanine ammonium lyase (PAL, cinnamate-4-hydroxylase (C4H and 4-coumarate-CoA ligase (4CL. Secondary plant cell wall formation is regulated by many transcription factors. We analyzed genes encoding NAC, WRKY, AP2/ERF and KNOX transcription factors and found higher transcript levels of these genes in AM380. We also observed increased transcription of some MYB and LIM domain transcription factors in AM380 compared to AM063. All these results show that genes related to monolignol biosynthesis may regulate the wood composition and help maintain the ratio of cellulose and lignin contents

  2. A Flow Cytometry Protocol to Estimate DNA Content in the Yellowtail Tetra Astyanax altiparanae

    Directory of Open Access Journals (Sweden)

    Pedro L. P. Xavier

    2017-09-01

    Full Text Available The production of triploid yellowtail tetra Astyanax altiparanae is a key factor to obtain permanently sterile individuals by chromosome set manipulation. Flow cytometric analysis is the main tool for confirmation of the resultant triploids individuals, but very few protocols are specific for A. altiparanae species. The current study has developed a protocol to estimate DNA content in this species. Furthermore, a protocol for long-term storage of dorsal fins used for flow cytometry analysis was established. The combination of five solutions with three detergents (Nonidet P-40 Substitute, Tween 20, and Triton X-100 at 0.1, 0.2, and 0.4% concentration was evaluated. Using the best solution from this first experiment, the addition of trypsin (0.125, 0.25, and 0.5% and sucrose (74 mM and the effects of increased concentrations of the detergents at 0.6 and 1.2% concentration were also evaluated. After adjustment of the protocol for flow cytometry, preservation of somatic tissue or isolated nuclei was also evaluated by freezing (at −20°C and fixation in saturated NaCl solution, acetic methanol (1:3, ethanol, and formalin at 10% for 30 or 60 days of storage at 25°C. Flow cytometry analysis in yellowtail tetra species was optimized using the following conditions: lysis solution: 9.53 mM MgCl2.7H20; 47.67 mM KCl; 15 mM Tris; 74 mM sucrose, 0.6% Triton X-100, pH 8.0; staining solution: Dulbecco's PBS with DAPI 1 μg mL−1; preservation procedure: somatic cells (dorsal fin samples frozen at −20°C. Using this protocol, samples may be stored up to 60 days with good accuracy for flow cytometry analysis.

  3. Estimation of Moisture Content & Metal Ions in White Flowers of Bougainvillea spectabilis and Purple Flowers of Bougainvillea glabra in Pakistan

    OpenAIRE

    *S. A. Rashid; F. S. Rehmani; 1M. Arman; M. Ibrahim; 2S. Shafique

    2011-01-01

    Bougainvillea consists of 18 shrubby species, growing in different parts of Pakistan and is being used as Anti-ulcer, Anti-diarrheal, Anti-microbial, Anti- diabetic, Amylase Inhibition and as for low blood pressure but none of the studies on Bougainvillea focused on the estimation of metal ion concentration. The focus of the present study was to estimation of moisture content and comparative analysis of trace metal ions in white flowers of Bougainvillea spectabilis Willd and Purple flowers of...

  4. Error Analysis of Clay-Rock Water Content Estimation with Broadband High-Frequency Electromagnetic Sensors—Air Gap Effect

    Directory of Open Access Journals (Sweden)

    Thierry Bore

    2016-04-01

    Full Text Available Broadband electromagnetic frequency or time domain sensor techniques present high potential for quantitative water content monitoring in porous media. Prior to in situ application, the impact of the relationship between the broadband electromagnetic properties of the porous material (clay-rock and the water content on the frequency or time domain sensor response is required. For this purpose, dielectric properties of intact clay rock samples experimental determined in the frequency range from 1 MHz to 10 GHz were used as input data in 3-D numerical frequency domain finite element field calculations to model the one port broadband frequency or time domain transfer function for a three rods based sensor embedded in the clay-rock. The sensor response in terms of the reflection factor was analyzed in time domain with classical travel time analysis in combination with an empirical model according to Topp equation, as well as the theoretical Lichtenecker and Rother model (LRM to estimate the volumetric water content. The mixture equation considering the appropriate porosity of the investigated material provide a practical and efficient approach for water content estimation based on classical travel time analysis with the onset-method. The inflection method is not recommended for water content estimation in electrical dispersive and absorptive material. Moreover, the results clearly indicate that effects due to coupling of the sensor to the material cannot be neglected. Coupling problems caused by an air gap lead to dramatic effects on water content estimation, even for submillimeter gaps. Thus, the quantitative determination of the in situ water content requires careful sensor installation in order to reach a perfect probe clay rock coupling.

  5. Error Analysis of Clay-Rock Water Content Estimation with Broadband High-Frequency Electromagnetic Sensors—Air Gap Effect

    Science.gov (United States)

    Bore, Thierry; Wagner, Norman; Delepine Lesoille, Sylvie; Taillade, Frederic; Six, Gonzague; Daout, Franck; Placko, Dominique

    2016-01-01

    Broadband electromagnetic frequency or time domain sensor techniques present high potential for quantitative water content monitoring in porous media. Prior to in situ application, the impact of the relationship between the broadband electromagnetic properties of the porous material (clay-rock) and the water content on the frequency or time domain sensor response is required. For this purpose, dielectric properties of intact clay rock samples experimental determined in the frequency range from 1 MHz to 10 GHz were used as input data in 3-D numerical frequency domain finite element field calculations to model the one port broadband frequency or time domain transfer function for a three rods based sensor embedded in the clay-rock. The sensor response in terms of the reflection factor was analyzed in time domain with classical travel time analysis in combination with an empirical model according to Topp equation, as well as the theoretical Lichtenecker and Rother model (LRM) to estimate the volumetric water content. The mixture equation considering the appropriate porosity of the investigated material provide a practical and efficient approach for water content estimation based on classical travel time analysis with the onset-method. The inflection method is not recommended for water content estimation in electrical dispersive and absorptive material. Moreover, the results clearly indicate that effects due to coupling of the sensor to the material cannot be neglected. Coupling problems caused by an air gap lead to dramatic effects on water content estimation, even for submillimeter gaps. Thus, the quantitative determination of the in situ water content requires careful sensor installation in order to reach a perfect probe clay rock coupling. PMID:27096865

  6. Error Analysis of Clay-Rock Water Content Estimation with Broadband High-Frequency Electromagnetic Sensors--Air Gap Effect.

    Science.gov (United States)

    Bore, Thierry; Wagner, Norman; Lesoille, Sylvie Delepine; Taillade, Frederic; Six, Gonzague; Daout, Franck; Placko, Dominique

    2016-04-18

    Broadband electromagnetic frequency or time domain sensor techniques present high potential for quantitative water content monitoring in porous media. Prior to in situ application, the impact of the relationship between the broadband electromagnetic properties of the porous material (clay-rock) and the water content on the frequency or time domain sensor response is required. For this purpose, dielectric properties of intact clay rock samples experimental determined in the frequency range from 1 MHz to 10 GHz were used as input data in 3-D numerical frequency domain finite element field calculations to model the one port broadband frequency or time domain transfer function for a three rods based sensor embedded in the clay-rock. The sensor response in terms of the reflection factor was analyzed in time domain with classical travel time analysis in combination with an empirical model according to Topp equation, as well as the theoretical Lichtenecker and Rother model (LRM) to estimate the volumetric water content. The mixture equation considering the appropriate porosity of the investigated material provide a practical and efficient approach for water content estimation based on classical travel time analysis with the onset-method. The inflection method is not recommended for water content estimation in electrical dispersive and absorptive material. Moreover, the results clearly indicate that effects due to coupling of the sensor to the material cannot be neglected. Coupling problems caused by an air gap lead to dramatic effects on water content estimation, even for submillimeter gaps. Thus, the quantitative determination of the in situ water content requires careful sensor installation in order to reach a perfect probe clay rock coupling.

  7. Coupled Land Surface-Subsurface Hydrogeophysical Inverse Modeling to Estimate Soil Organic Carbon Content in an Arctic Tundra

    Science.gov (United States)

    Tran, A. P.; Dafflon, B.; Hubbard, S.

    2017-12-01

    Soil organic carbon (SOC) is crucial for predicting carbon climate feedbacks in the vulnerable organic-rich Arctic region. However, it is challenging to achieve this property due to the general limitations of conventional core sampling and analysis methods. In this study, we develop an inversion scheme that uses single or multiple datasets, including soil liquid water content, temperature and ERT data, to estimate the vertical profile of SOC content. Our approach relies on the fact that SOC content strongly influences soil hydrological-thermal parameters, and therefore, indirectly controls the spatiotemporal dynamics of soil liquid water content, temperature and their correlated electrical resistivity. The scheme includes several advantages. First, this is the first time SOC content is estimated by using a coupled hydrogeophysical inversion. Second, by using the Community Land Model, we can account for the land surface dynamics (evapotranspiration, snow accumulation and melting) and ice/liquid phase transition. Third, we combine a deterministic and an adaptive Markov chain Monte Carlo optimization algorithm to better estimate the posterior distributions of desired model parameters. Finally, the simulated subsurface variables are explicitly linked to soil electrical resistivity via petrophysical and geophysical models. We validate the developed scheme using synthetic experiments. The results show that compared to inversion of single dataset, joint inversion of these datasets significantly reduces parameter uncertainty. The joint inversion approach is able to estimate SOC content within the shallow active layer with high reliability. Next, we apply the scheme to estimate OC content along an intensive ERT transect in Barrow, Alaska using multiple datasets acquired in the 2013-2015 period. The preliminary results show a good agreement between modeled and measured soil temperature, thaw layer thickness and electrical resistivity. The accuracy of estimated SOC content

  8. QTL for phytosterol and sinapate ester content in Brassica napus L. collocate with the two erucic acid genes

    Science.gov (United States)

    Amar, Samija; Ecke, Wolfgang; Becker, Heiko C.

    2008-01-01

    Improving oil and protein quality for food and feed purposes is an important goal in rapeseed (Brassica napus L.) breeding programs. Rapeseed contains phytosterols, used to enrich food products, and sinapate esters, which are limiting the utilization of rapeseed proteins in the feed industry. Increasing the phytosterol content of oil and lowering sinapate ester content of meal could increase the value of the oilseed rape crop. The objective of the present study was to identify quantitative trait loci (QTL) for phytosterol and sinapate ester content in a winter rapeseed population of 148 doubled haploid lines, previously found to have a large variation for these two traits. This population also segregated for the two erucic acid genes. A close negative correlation was found between erucic acid and phytosterol content (Spearman’s rank correlation, rs = −0.80**). For total phytosterol content, three QTL were detected, explaining 60% of the genetic variance. The two QTL with the strongest additive effects were mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. For sinapate ester content four QTL were detected, explaining 53% of the genetic variance. Again, a close negative correlation was found between erucic acid and sinapate ester content (rs = −0.66**) and the QTL with the strongest additive effects mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. The results suggests, that there is a pleiotropic effect of the two erucic acid genes on phytosterol and sinapate ester content; the effect of the alleles for low erucic acid content is to increase phytosterol and sinapate ester content. Possible reasons for this are discussed based on known biosynthetic pathways. Electronic supplementary material The online version of this article (doi:10.1007/s00122-008-0734-2) contains supplementary material, which is available to authorized users. PMID:18335203

  9. Ocular gene transfer in the spotlight: implications of newspaper content for clinical communications.

    Science.gov (United States)

    Benjaminy, Shelly; Bubela, Tania

    2014-07-16

    Ocular gene transfer clinical trials are raising hopes for blindness treatments and attracting media attention. News media provide an accessible health information source for patients and the public, but are often criticized for overemphasizing benefits and underplaying risks of novel biomedical interventions. Overly optimistic portrayals of unproven interventions may influence public and patient expectations; the latter may cause patients to downplay risks and over-emphasize benefits, with implications for informed consent for clinical trials. We analyze the news media communications landscape about ocular gene transfer and make recommendations for improving communications between clinicians and potential trial participants in light of media coverage. We analyzed leading newspaper articles about ocular gene transfer (1990-2012) from United States (n = 55), Canada (n = 26), and United Kingdom (n = 77) from Factiva and Canadian Newsstand databases using pre-defined coding categories. We evaluated the content of newspaper articles about ocular gene transfer for hereditary retinopathies, exploring representations of framing techniques, research design, risks/benefits, and translational timelines. The dominant frame in 61% of stories was a celebration of progress, followed by human-interest in 30% of stories. Missing from the positive frames were explanations of research design; articles conflated clinical research with treatment. Conflicts-of-interest and funding sources were similarly omitted. Attention was directed to the benefits of gene transfer, while risks were only reported in 43% of articles. A range of visual outcomes was described from slowing vision loss to cure, but the latter was the most frequently represented even though it is clinically infeasible. Despite the prominence of visual benefit portrayals, 87% of the articles failed to provide timelines for the commencement of clinical trials or for clinical implementation. Our analysis confirms

  10. Characterization of a novel xylanase gene from rumen content of Hu sheep.

    Science.gov (United States)

    Wang, Qian; Luo, Yang; He, Bo; Jiang, Lin-Shu; Liu, Jian-Xin; Wang, Jia-Kun

    2015-12-01

    A novel xylanase gene, xyn-lxy, was cloned from a metagenomic fosmid library, which was previously constructed from the rumen contents of Hu sheep and was functionally characterized in Escherichia coli. The open reading frame was composed of 1923 bp and encoded for 640 amino acids, including a catalytic domain of glycosyl hydrolase family 10 and carbohydrate-binding module 9. The gene showed 97 % identity with uncultured bacterium Contig1552 but low similarity with xylanases from known cellulolytic-degrading microorganisms in the rumen. The recombinant XYN-LXY showed a specific activity of 664.7 U mg(-1). The optimal temperature and pH of the enzyme were 50 °C and 6.0, respectively. Specifically, XYN-LXY was exclusively activated by Mn(2+) among all of the cations and reducing agents tested in this study. An enzymatic hydrolysis assay revealed that XYN-LXY degraded birchwood xylan into xylooligosaccharide with a low degree of polymerization. After incubation for 4 h, the concentration of the dominant product, xylobiose, was 2.297 ± 0.175 mg ml(-1) (74.07 % of total product) followed by xylose with a concentration of 0.656 ± 0.010 mg ml(-1) (21.14 % of total product). The XYN-LXY exhibited deep degradation effects on the xylan substrate, which were rarely observed with endo-xylanase, making it a promising candidate for industrial application, especially in biofuel production.

  11. Changes in Oleic Acid Content of Transgenic Soybeans by Antisense RNA Mediated Posttranscriptional Gene Silencing

    Directory of Open Access Journals (Sweden)

    Ling Zhang

    2014-01-01

    Full Text Available The Delta-12 oleate desaturase gene (FAD2-1, which converts oleic acid into linoleic acid, is the key enzyme determining the fatty acid composition of seed oil. In this study, we inhibited the expression of endogenous Delta-12 oleate desaturase GmFad2-1b gene by using antisense RNA in soybean Williams 82. By employing the soybean cotyledonary-node method, a part of the cDNA of soybean GmFad2-1b 801 bp was cloned for the construction of a pCAMBIA3300 vector under the soybean seed promoter BCSP. Leaf painting, LibertyLink strip, PCR, Southern blot, qRT-PCR, and fatty acid analysis were used to detect the insertion and expression of GmFad2-1b in the transgenic soybean lines. The results indicate that the metabolically engineered plants exhibited a significant increase in oleic acid (up to 51.71% and a reduction in palmitic acid (to <3% in their seed oil content. No structural differences were observed between the fatty acids of the transgenic and the nontransgenic oil extracts.

  12. Estimation of the deoxynivalenol and moisture contents of bulk wheat grain samples by FT-NIR spectroscopy

    Science.gov (United States)

    Deoxynivalenol (DON) levels in harvested grain samples are used to evaluate the Fusarium head blight (FHB) resistance of wheat cultivars and breeding lines. Fourier transform near-infrared (FT-NIR) calibrations were developed to estimate the DON and moisture content (MC) of bulk wheat grain samples ...

  13. Estimation of leaf water content from far infrared (2.5-14µm) spectra using continuous wavelet analysis

    NARCIS (Netherlands)

    Ullah, S.; Skidmore, A.K.; Naeem, M.; Schlerf, M.

    2012-01-01

    The objective of this study was to estimate leaf water content based on continuous wavelet analysis from the far infrared (2.5 - 14.0 μm) spectra. The entire dataset comprised of 394 far infrared spectra which were divided into calibration (262 spectra) and validation (132 spectra) subsets. The far

  14. Comparison of leaf color chart observations with digital photographs and spectral measurements for estimating maize leaf chlorophyll content

    Science.gov (United States)

    Crop nitrogen management is important world-wide, as much for small fields as it is for large operations. Developed as a non-destructive aid for estimating nitrogen content in rice crops, leaf color charts (LCC) are a numbered series of plastic panels that range from yellowgreen to dark green. By vi...

  15. Supporting document for the north east quadrant historical tank content estimate report for AX-tank farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Gaddis, L.A.; Walsh, A.C.

    1994-06-01

    This Supporting Document provides historical in-depth characterization information gathered in AX-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature data, sampling data, and drywell and liquid observation well data for Historical Tank Content Estimate Report of the NE Quadrant and the Hanford 200 East Areas

  16. Supporting document for the north east quadrant historical tank content estimate report for C-Tank Farm

    International Nuclear Information System (INIS)

    Brevick, C.H.; Gaddis, L.A.; Walsh, A.C.

    1994-06-01

    This Supporting Document provides historical in-depth characterization information gathered on C-Tank Farm, such as historical waste transfer and level data, tank physical information, temperature data, sampling data, and drywell and liquid observation well data for Historical Tank Content Estimate Report of the NE Quadrant and the Hanford 200 East Areas

  17. A comparison of two methods for estimating conifer live foliar moisture content

    Science.gov (United States)

    W. Matt Jolly; Ann M. Hadlow

    2012-01-01

    Foliar moisture content is an important factor regulating how wildland fires ignite in and spread through live fuels but moisture content determination methods are rarely standardised between studies. One such difference lies between the uses of rapid moisture analysers or drying ovens. Both of these methods are commonly used in live fuel research but they have never...

  18. Relationship between single nucleotide polymorphism of glycogen synthase gene of Pacific oyster Crassostrea gigas and its glycogen content

    Science.gov (United States)

    Liu, Siwei; Li, Qi; Yu, Hong; Kong, Lingfeng

    2017-02-01

    Glycogen is important not only for the energy supplementary of oysters, but also for human consumption. High glycogen content can improve the stress survival of oyster. A key enzyme in glycogenesis is glycogen synthase that is encoded by glycogen synthase gene GYS. In this study, the relationship between single nucleotide polymorphisms (SNPs) in coding regions of Crassostrea gigas GYS (Cg-GYS) and individual glycogen content was investigated with 321 individuals from five full-sib families. Single-strand conformation polymorphism (SSCP) procedure was combined with sequencing to confirm individual SNP genotypes of Cg-GYS. Least-square analysis of variance was performed to assess the relationship of variation in glycogen content of C. gigas with single SNP genotype and SNP haplotype. As a consequence, six SNPs were found in coding regions to be significantly associated with glycogen content ( P glycogen content ( P glycogen content and provided molecular biological information for the selective breeding of good quality traits of C. gigas.

  19. SiGN-SSM: open source parallel software for estimating gene networks with state space models.

    Science.gov (United States)

    Tamada, Yoshinori; Yamaguchi, Rui; Imoto, Seiya; Hirose, Osamu; Yoshida, Ryo; Nagasaki, Masao; Miyano, Satoru

    2011-04-15

    SiGN-SSM is an open-source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by a statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles. SiGN-SSM is distributed under GNU Affero General Public Licence (GNU AGPL) version 3 and can be downloaded at http://sign.hgc.jp/signssm/. The pre-compiled binaries for some architectures are available in addition to the source code. The pre-installed binaries are also available on the Human Genome Center supercomputer system. The online manual and the supplementary information of SiGN-SSM is available on our web site. tamada@ims.u-tokyo.ac.jp.

  20. Direct Estimate of Cocoa Powder Content in Cakes by Colorimetry and Photoacoustic Spectroscopy

    Science.gov (United States)

    Dóka, O.; Bicanic, D.; Kulcsár, R.

    2014-12-01

    Cocoa is a very important ingredient in the food industry and largely consumed worldwide. In this investigation, colorimetry and photoacoustic spectroscopy were used to directly assess the content of cocoa powder in cakes; both methods provided satisfactory results. The calibration curve was constructed using a series of home-made cakes containing varying amount of cocoa powder. Then, at a later stage, the same calibration curve was used to quantify the cocoa content of several commercially available cakes. For self-made cakes, the relationship between the PAS signal and the content of cocoa powder was linear while a quadratic dependence was obtained for the colorimetric index (brightness) and total color difference ().

  1. Sampling procedure in a willow plantation for estimation of moisture content

    DEFF Research Database (Denmark)

    Nielsen, Henrik Kofoed; Lærke, Poul Erik; Liu, Na

    2015-01-01

    Heating value and fuel quality of wood is closely connected to moisture content. In this work the variation of moisture content (MC) of short rotation coppice (SRC) willow shoots is described for five clones during one harvesting season. Subsequently an appropriate sampling procedure minimising...... labour costs and sampling uncertainty is proposed, where the MC of a single stem section with the length of 10–50 cm corresponds to the mean shoot moisture content (MSMC) with a bias of maximum 11 g kg−1. This bias can be reduced by selecting the stem section according to the particular clone...

  2. Validation of differential gene expression algorithms: Application comparing fold-change estimation to hypothesis testing

    Directory of Open Access Journals (Sweden)

    Bickel David R

    2010-01-01

    Full Text Available Abstract Background Sustained research on the problem of determining which genes are differentially expressed on the basis of microarray data has yielded a plethora of statistical algorithms, each justified by theory, simulation, or ad hoc validation and yet differing in practical results from equally justified algorithms. Recently, a concordance method that measures agreement among gene lists have been introduced to assess various aspects of differential gene expression detection. This method has the advantage of basing its assessment solely on the results of real data analyses, but as it requires examining gene lists of given sizes, it may be unstable. Results Two methodologies for assessing predictive error are described: a cross-validation method and a posterior predictive method. As a nonparametric method of estimating prediction error from observed expression levels, cross validation provides an empirical approach to assessing algorithms for detecting differential gene expression that is fully justified for large numbers of biological replicates. Because it leverages the knowledge that only a small portion of genes are differentially expressed, the posterior predictive method is expected to provide more reliable estimates of algorithm performance, allaying concerns about limited biological replication. In practice, the posterior predictive method can assess when its approximations are valid and when they are inaccurate. Under conditions in which its approximations are valid, it corroborates the results of cross validation. Both comparison methodologies are applicable to both single-channel and dual-channel microarrays. For the data sets considered, estimating prediction error by cross validation demonstrates that empirical Bayes methods based on hierarchical models tend to outperform algorithms based on selecting genes by their fold changes or by non-hierarchical model-selection criteria. (The latter two approaches have comparable

  3. Food photography II: use of food photographs for estimating portion size and the nutrient content of meals.

    Science.gov (United States)

    Nelson, M; Atkinson, M; Darbyshire, S

    1996-07-01

    The aim of the present study was to determine the errors in the conceptualization of portion size using photographs. Male and female volunteers aged 18-90 years (n 136) from a wide variety of social and occupational backgrounds completed 602 assessments of portion size in relation to food photographs. Subjects served themselves between four and six foods at one meal (breakfast, lunch or dinner). Portion sizes were weighed by the investigators at the time of serving, and any waste was weighed at the end of the meal. Within 5 min of the end of the meal, subjects were shown photographs depicting each of the foods just consumed. For each food there were eight photographs showing portion sizes in equal increments from the 5th to the 95th centile of the distribution of portion weights observed in The Dietary and Nutritional Survey of British Adults (Gregory et al. 1990). Subjects were asked to indicate on a visual analogue scale the size of the portion consumed in relation to the eight photographs. The nutrient contents of meals were estimated from food composition tables. There were large variations in the estimation of portion sizes from photographs. Butter and margarine portion sizes tended to be substantially overestimated. In general, small portion sizes tended to be overestimated, and large portion sizes underestimated. Older subjects overestimated portion size more often than younger subjects. Excluding butter and margarine, the nutrient content of meals based on estimated portion sizes was on average within +/- 7% of the nutrient content based on the amounts consumed, except for vitamin C (21% overestimate), and for subjects over 65 years (15-20% overestimate for energy and fat). In subjects whose BMI was less than 25 kg/m2, the energy and fat contents of meals calculated from food composition tables and based on estimated portion size (excluding butter and margarine) were 5-10% greater than the nutrient content calculated using actual portion size, but for those

  4. MR-based Water Content Estimation in Cartilage: Design and Validation of a Method

    DEFF Research Database (Denmark)

    Shiguetomi Medina, Juan Manuel; Kristiansen, Maja Sofie; Ringgaard, Steffen

    2012-01-01

    Objective Design and validation of an MR-based method that allows the calculation of the water content in cartilage tissue. Material and Methods We modified and adapted to cartilage tissue T1 map based water content MR sequences commonly used in the neurology field. Using a 37 Celsius degree stable...... was costumed and programmed. Finally, we validated the method after measuring and comparing 3 more cartilage samples in a living animal (pig). The obtained data was analyzed and the water content calculated. Then, the same samples were freeze-dried (this technique allows to take out all the water that a tissue...... contains) and we measured the water they contained. Results We could reproduce twice the 37 Celsius degree system and could perform the measurements in a similar way. We found that the MR T1 map based water content sequences can provide information that, after being analyzed with a special software, can...

  5. Required Accuracy of Structural Constraints in the Inversion of Electrical Resistivity Data for Improved Water Content Estimation

    Science.gov (United States)

    Heinze, T.; Budler, J.; Weigand, M.; Kemna, A.

    2017-12-01

    Water content distribution in the ground is essential for hazard analysis during monitoring of landslide prone hills. Geophysical methods like electrical resistivity tomography (ERT) can be utilized to determine the spatial distribution of water content using established soil physical relationships between bulk electrical resistivity and water content. However, often more dominant electrical contrasts due to lithological structures outplay these hydraulic signatures and blur the results in the inversion process. Additionally, the inversion of ERT data requires further constraints. In the standard Occam inversion method, a smoothness constraint is used, assuming that soil properties change softly in space. While this applies in many scenarios, sharp lithological layers with strongly divergent hydrological parameters, as often found in landslide prone hillslopes, are typically badly resolved by standard ERT. We use a structurally constrained ERT inversion approach for improving water content estimation in landslide prone hills by including a-priori information about lithological layers. The smoothness constraint is reduced along layer boundaries identified using seismic data. This approach significantly improves water content estimations, because in landslide prone hills often a layer of rather high hydraulic conductivity is followed by a hydraulic barrier like clay-rich soil, causing higher pore pressures. One saturated layer and one almost drained layer typically result also in a sharp contrast in electrical resistivity, assuming that surface conductivity of the soil does not change in similar order. Using synthetic data, we study the influence of uncertainties in the a-priori information on the inverted resistivity and estimated water content distribution. We find a similar behavior over a broad range of models and depths. Based on our simulation results, we provide best-practice recommendations for field applications and suggest important tests to obtain reliable

  6. Breeding bread wheat cultivars for high protein content by transfer of protein genes from Triticum dicoccoides

    International Nuclear Information System (INIS)

    Grama, A.; Gerechter-Amitai, Z.K.; Blum, A.; Rubenthaler, G.L.

    1984-01-01

    Triticum dicoccoides sel. G-25, a selection of wild emmer with a protein content of 20.5% and a kernel weight of 31.5 mg, was used as the donor of protein genes. Since this selection is highly resistant to stripe rust, the object of the crossing programme was to transfer this resistance, together with the high protein potential, to durum and bread wheat cultivars susceptible to the disease. In the tetraploid lines obtained from the T. dicoccoides/T. durum cross, the protein values ranged from 17 to 22%. These lines had resistance to stripe rust from the wild emmer and to stem rust from the durum. After two further crosses between these tetraploid lines and T. aestivum cultivars, several lines were selected which combined good yield, high protein level and resistance to rust diseases. These lines attained protein levels of 14 to 19% in the whole grain and 14 to 17% in the flour, combined with yields of 4.5 to 6.0 t/ha. They had also inherited resistance to stem rust, and in some instances also to leaf rust, from the cultivated wheat parental lines. (author)

  7. Estimating intrinsic and extrinsic noise from single-cell gene expression measurements

    Science.gov (United States)

    Fu, Audrey Qiuyan; Pachter, Lior

    2017-01-01

    Gene expression is stochastic and displays variation (“noise”) both within and between cells. Intracellular (intrinsic) variance can be distinguished from extracellular (extrinsic) variance by applying the law of total variance to data from two-reporter assays that probe expression of identically regulated gene pairs in single cells. We examine established formulas [Elowitz, M. B., A. J. Levine, E. D. Siggia and P. S. Swain (2002): “Stochastic gene expression in a single cell,” Science, 297, 1183–1186.] for the estimation of intrinsic and extrinsic noise and provide interpretations of them in terms of a hierarchical model. This allows us to derive alternative estimators that minimize bias or mean squared error. We provide a geometric interpretation of these results that clarifies the interpretation in [Elowitz, M. B., A. J. Levine, E. D. Siggia and P. S. Swain (2002): “Stochastic gene expression in a single cell,” Science, 297, 1183–1186.]. We also demonstrate through simulation and re-analysis of published data that the distribution assumptions underlying the hierarchical model have to be satisfied for the estimators to produce sensible results, which highlights the importance of normalization. PMID:27875323

  8. Artificial Neural Networks and Gene Expression Programing based age estimation using facial features

    Directory of Open Access Journals (Sweden)

    Baddrud Z. Laskar

    2015-10-01

    Full Text Available This work is about estimating human age automatically through analysis of facial images. It has got a lot of real-world applications. Due to prompt advances in the fields of machine vision, facial image processing, and computer graphics, automatic age estimation via faces in computer is one of the dominant topics these days. This is due to widespread real-world applications, in areas of biometrics, security, surveillance, control, forensic art, entertainment, online customer management and support, along with cosmetology. As it is difficult to estimate the exact age, this system is to estimate a certain range of ages. Four sets of classifications have been used to differentiate a person’s data into one of the different age groups. The uniqueness about this study is the usage of two technologies i.e., Artificial Neural Networks (ANN and Gene Expression Programing (GEP to estimate the age and then compare the results. New methodologies like Gene Expression Programing (GEP have been explored here and significant results were found. The dataset has been developed to provide more efficient results by superior preprocessing methods. This proposed approach has been developed, tested and trained using both the methods. A public data set was used to test the system, FG-NET. The quality of the proposed system for age estimation using facial features is shown by broad experiments on the available database of FG-NET.

  9. A comparative review of estimates of the proportion unchanged genes and the false discovery rate

    Directory of Open Access Journals (Sweden)

    Broberg Per

    2005-08-01

    Full Text Available Abstract Background In the analysis of microarray data one generally produces a vector of p-values that for each gene give the likelihood of obtaining equally strong evidence of change by pure chance. The distribution of these p-values is a mixture of two components corresponding to the changed genes and the unchanged ones. The focus of this article is how to estimate the proportion unchanged and the false discovery rate (FDR and how to make inferences based on these concepts. Six published methods for estimating the proportion unchanged genes are reviewed, two alternatives are presented, and all are tested on both simulated and real data. All estimates but one make do without any parametric assumptions concerning the distributions of the p-values. Furthermore, the estimation and use of the FDR and the closely related q-value is illustrated with examples. Five published estimates of the FDR and one new are presented and tested. Implementations in R code are available. Results A simulation model based on the distribution of real microarray data plus two real data sets were used to assess the methods. The proposed alternative methods for estimating the proportion unchanged fared very well, and gave evidence of low bias and very low variance. Different methods perform well depending upon whether there are few or many regulated genes. Furthermore, the methods for estimating FDR showed a varying performance, and were sometimes misleading. The new method had a very low error. Conclusion The concept of the q-value or false discovery rate is useful in practical research, despite some theoretical and practical shortcomings. However, it seems possible to challenge the performance of the published methods, and there is likely scope for further developing the estimates of the FDR. The new methods provide the scientist with more options to choose a suitable method for any particular experiment. The article advocates the use of the conjoint information

  10. Estimating the relative water content of leaves in a cotton canopy

    Science.gov (United States)

    Vanderbilt, Vern; Daughtry, Craig; Kupinski, Meredith; Bradley, Christine; French, Andrew; Bronson, Kevin; Chipman, Russell; Dahlgren, Robert

    2017-08-01

    Remotely sensing plant canopy water status remains a long term goal of remote sensing research. Established approaches to estimating canopy water status — the Crop Water Stress Index, the Water Deficit Index and the Equivalent Water Thickness — involve measurements in the thermal or reflective infrared. Here we report plant water status estimates based upon analysis of polarized visible imagery of a cotton canopy measured by ground Multi-Spectral Polarization Imager (MSPI). Such estimators potentially provide access to the plant hydrological photochemistry that manifests scattering and absorption effects in the visible spectral region.

  11. Effect of method of deduplication on estimation of differential gene expression using RNA-seq

    Directory of Open Access Journals (Sweden)

    Anna V. Klepikova

    2017-03-01

    Full Text Available Background RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. Results To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI. We also analyzed the influence of sequencing layout (single read or paired end and read length. We found that deduplication without MI greatly affects estimated expression values; this effect is the most pronounced for highly expressed genes. Conclusion The use of unique molecular identifiers greatly improves accuracy of RNA-seq analysis, especially for highly expressed genes. We developed a set of scripts that enable handling of MI and their incorporation into RNA-seq analysis pipelines. Deduplication without MI affects results of differential gene expression analysis, producing a high proportion of false negative results. The absence of duplicate read removal is biased towards false positives. In those cases where using MI is not possible, we recommend using paired-end sequencing layout.

  12. Two-pass imputation algorithm for missing value estimation in gene expression time series.

    Science.gov (United States)

    Tsiporkova, Elena; Boeva, Veselka

    2007-10-01

    Gene expression microarray experiments frequently generate datasets with multiple values missing. However, most of the analysis, mining, and classification methods for gene expression data require a complete matrix of gene array values. Therefore, the accurate estimation of missing values in such datasets has been recognized as an important issue, and several imputation algorithms have already been proposed to the biological community. Most of these approaches, however, are not particularly suitable for time series expression profiles. In view of this, we propose a novel imputation algorithm, which is specially suited for the estimation of missing values in gene expression time series data. The algorithm utilizes Dynamic Time Warping (DTW) distance in order to measure the similarity between time expression profiles, and subsequently selects for each gene expression profile with missing values a dedicated set of candidate profiles for estimation. Three different DTW-based imputation (DTWimpute) algorithms have been considered: position-wise, neighborhood-wise, and two-pass imputation. These have initially been prototyped in Perl, and their accuracy has been evaluated on yeast expression time series data using several different parameter settings. The experiments have shown that the two-pass algorithm consistently outperforms, in particular for datasets with a higher level of missing entries, the neighborhood-wise and the position-wise algorithms. The performance of the two-pass DTWimpute algorithm has further been benchmarked against the weighted K-Nearest Neighbors algorithm, which is widely used in the biological community; the former algorithm has appeared superior to the latter one. Motivated by these findings, indicating clearly the added value of the DTW techniques for missing value estimation in time series data, we have built an optimized C++ implementation of the two-pass DTWimpute algorithm. The software also provides for a choice between three different

  13. Estimation of active pharmaceutical ingredients content using locally weighted partial least squares and statistical wavelength selection.

    OpenAIRE

    Kim, Sanghong; Kano, Manabu; Nakagawa, Hiroshi; Hasebe, Shinji

    2011-01-01

    Development of quality estimation models using near infrared spectroscopy (NIRS) and multivariate analysis has been accelerated as a process analytical technology (PAT) tool in the pharmaceutical industry. Although linear regression methods such as partial least squares (PLS) are widely used, they cannot always achieve high estimation accuracy because physical and chemical properties of a measuring object have a complex effect on NIR spectra. In this research, locally weighted PLS (LW-PLS) wh...

  14. In vitro anthelmintic activity of Barleria buxifolia on Indian adult earthworms and estimation of total flavonoid content

    Directory of Open Access Journals (Sweden)

    Purna A. Chander

    2014-02-01

    Full Text Available Objective: To study the anthelmintic activity of Barleria buxifolia leaf and to estimate the total flavonoid content. Methods: The aqueous and ethanolic leaf extracts were prepared and these were analyzed for total flavonoid content by aluminium chloride colorimetric method and Pheretima posthuma was used for anthelmintic activity by using the different concentrations (10, 20, 40, 80 and 100 mg/mL. Results: All the investigational extracts showed an anthelmintic activity at concentration of 10 mg/mL. The ethanolic extract of 100 mg/mL has produced an significant effect (P<0.001 when compared to aqueous extract. The total flavonoid content was found to be 5.67 mg QE/100 g. Conclusions: From the above study, the leaf extract has shown a good anthelmintic activity.

  15. Direct estimate of cocoa powder content in cakes by colorimetry and photoacoustic spectroscopy

    NARCIS (Netherlands)

    Doka, O.; Bicanic, D.D.; Kulcsar, R.

    2014-01-01

    Cocoa is a very important ingredient in the food industry and largely consumed worldwide. In this investigation, colorimetry and photoacoustic spectroscopy were used to directly assess the content of cocoa powder in cakes; both methods provided satisfactory results. The calibration curve was

  16. Evaluation of surface nuclear magnetic resonance-estimated subsurface water content

    International Nuclear Information System (INIS)

    Mueller-Petke, M; Dlugosch, R; Yaramanci, U

    2011-01-01

    The technique of nuclear magnetic resonance (NMR) has found widespread use in geophysical applications for determining rock properties (e.g. porosity and permeability) and state variables (e.g. water content) or to distinguish between oil and water. NMR measurements are most commonly made in the laboratory and in boreholes. The technique of surface NMR (or magnetic resonance sounding (MRS)) also takes advantage of the NMR phenomenon, but by measuring subsurface rock properties from the surface using large coils of some tens of meters and reaching depths as much as 150 m. We give here a brief review of the current state of the art of forward modeling and inversion techniques. In laboratory NMR a calibration is used to convert measured signal amplitudes into water content. Surface NMR-measured amplitudes cannot be converted by a simple calibration. The water content is derived by comparing a measured amplitude with an amplitude calculated for a given subsurface water content model as input for a forward modeling that must account for all relevant physics. A convenient option to check whether the measured signals are reliable or the forward modeling accounts for all effects is to make measurements in a well-defined environment. Therefore, measurements on top of a frozen lake were made with the latest-generation surface NMR instruments. We found the measured amplitudes to be in agreement with the calculated amplitudes for a model of 100 % water content. Assuming then both the forward modeling and the measurement to be correct, the uncertainty of the model is calculated with only a few per cent based on the measurement uncertainty.

  17. Reduced intracellular c-di-GMP content increases expression of quorum sensing-regulated genes in Pseudomonas aeruginosa

    DEFF Research Database (Denmark)

    Chua, Song Lin; Liu, Yang; Li, Yingying

    2017-01-01

    Cyclic-di-GMP (c-di-GMP) is an intracellular secondary messenger which controls the biofilm life cycle in many bacterial species. High intracellular c-di-GMP content enhances biofilm formation via the reduction of motility and production of biofilm matrix, while low c-di-GMP content in biofilm...... cells leads to increased motility and biofilm dispersal. While the effect of high c-di-GMP levels on bacterial lifestyles is well studied, the physiology of cells at low c-di-GMP levels remains unclear. Here, we showed that Pseudomonas aeruginosa cells with high and low intracellular c-di-GMP contents...... possessed distinct transcriptome profiles. There were 535 genes being upregulated and 432 genes downregulated in cells with low c-di-GMP, as compared to cells with high c-di-GMP. Interestingly, both rhl and pqs quorum-sensing (QS) operons were expressed at higher levels in cells with low intracellular c-di-GMP...

  18. Variation in faecal water content may confound estimates of gastro-intestinal parasite intensity in wild African herbivores.

    Science.gov (United States)

    Turner, W C; Cizauskas, C A; Getz, W M

    2010-03-01

    Estimates of parasite intensity within host populations are essential for many studies of host-parasite relationships. Here we evaluated the seasonal, age- and sex-related variability in faecal water content for two wild ungulate species, springbok (Antidorcas marsupialis) and plains zebra (Equus quagga). We then assessed whether or not faecal water content biased conclusions regarding differences in strongyle infection rates by season, age or sex. There was evidence of significant variation in faecal water content by season and age for both species, and by sex in springbok. Analyses of faecal egg counts demonstrated that sex was a near-significant factor in explaining variation in strongyle parasite infection rates in zebra (P = 0.055) and springbok (P = 0.052) using wet-weight faecal samples. However, once these intensity estimates were re-scaled by the percent of dry matter in the faeces, sex was no longer a significant factor (zebra, P = 0.268; springbok, P = 0.234). These results demonstrate that variation in faecal water content may confound analyses and could produce spurious conclusions, as was the case with host sex as a factor in the analysis. We thus recommend that researchers assess whether water variation could be a confounding factor when designing and performing research using faecal indices of parasite intensity.

  19. Estimating alcohol content of traditional brew in Western Kenya using culturally relevant methods: the case for cost over volume.

    Science.gov (United States)

    Papas, Rebecca K; Sidle, John E; Wamalwa, Emmanuel S; Okumu, Thomas O; Bryant, Kendall L; Goulet, Joseph L; Maisto, Stephen A; Braithwaite, R Scott; Justice, Amy C

    2010-08-01

    Traditional homemade brew is believed to represent the highest proportion of alcohol use in sub-Saharan Africa. In Eldoret, Kenya, two types of brew are common: chang'aa, spirits, and busaa, maize beer. Local residents refer to the amount of brew consumed by the amount of money spent, suggesting a culturally relevant estimation method. The purposes of this study were to analyze ethanol content of chang'aa and busaa; and to compare two methods of alcohol estimation: use by cost, and use by volume, the latter the current international standard. Laboratory results showed mean ethanol content was 34% (SD = 14%) for chang'aa and 4% (SD = 1%) for busaa. Standard drink unit equivalents for chang'aa and busaa, respectively, were 2 and 1.3 (US) and 3.5 and 2.3 (Great Britain). Using a computational approach, both methods demonstrated comparable results. We conclude that cost estimation of alcohol content is more culturally relevant and does not differ in accuracy from the international standard.

  20. Empirical observations offer improved estimates of forest floor carbon content across in the United States

    Science.gov (United States)

    Perry, C. H.; Domke, G. M.; Walters, B. F.; Smith, J. E.; Woodall, C. W.

    2014-12-01

    The Forest Inventory and Analysis (FIA) program of the United States Forest Service reports official estimates of national forest floor carbon (FFC) stocks and stock change to national and international parties, the US Environmental Protection Agency (USEPA) and the United Nations Framework Convention on Climate Change (UNFCCC), respectively. These estimates of national FFC stocks are derived from plot-level predictions of FFC density. We suspect the models used to predict plot-level FFC density are less than ideal for several reasons: (a) they are based upon local studies that may not reflect FFC dynamics at the national scale, (b) they are relatively insensitive to climate change, and (c) they reduce the natural variability of the data leading to misplaced confidence in the estimates. However, FIA has measured forest floor attributes since 2001 on a systematic 1/16th subset of a nation-wide array of inventory plots (7 800 of 125 000 plots). Here we address the efficacy of replacing plot-level model predictions with empirical observations of FFC density while assessing the impact of imputing FFC density values to the full plot network on national stock estimates. First, using an equivalence testing framework, we found model predictions of FFC density to differ significantly from the observations in all regions and forest types; the mean difference across all plots was 21 percent (1.81 Mg·ha-1). Furthermore, the model predictions were biased towards the lower end of extant FFC density observations, underestimating it while greatly truncating the range relative to the observations. Second, the optimal imputation approach (k-Nearest Neighbor, k-NN) resulted in values that were equivalent to observations of FFC density across a range of simulated missingness and maintained the high variability seen in the observations. We used the k-NN approach to impute FFC density values to the 94 percent of FIA inventory plots without soil measurements. Third, using the imputed

  1. Assessing terpene content variability of whitebark pine in order to estimate representative sample size

    Directory of Open Access Journals (Sweden)

    Stefanović Milena

    2013-01-01

    Full Text Available In studies of population variability, particular attention has to be paid to the selection of a representative sample. The aim of this study was to assess the size of the new representative sample on the basis of the variability of chemical content of the initial sample on the example of a whitebark pine population. Statistical analysis included the content of 19 characteristics (terpene hydrocarbons and their derivates of the initial sample of 10 elements (trees. It was determined that the new sample should contain 20 trees so that the mean value calculated from it represents a basic set with a probability higher than 95 %. Determination of the lower limit of the representative sample size that guarantees a satisfactory reliability of generalization proved to be very important in order to achieve cost efficiency of the research. [Projekat Ministarstva nauke Republike Srbije, br. OI-173011, br. TR-37002 i br. III-43007

  2. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.

    Science.gov (United States)

    Gordon, Sean P; Contreras-Moreira, Bruno; Woods, Daniel P; Des Marais, David L; Burgess, Diane; Shu, Shengqiang; Stritt, Christoph; Roulin, Anne C; Schackwitz, Wendy; Tyler, Ludmila; Martin, Joel; Lipzen, Anna; Dochy, Niklas; Phillips, Jeremy; Barry, Kerrie; Geuten, Koen; Budak, Hikmet; Juenger, Thomas E; Amasino, Richard; Caicedo, Ana L; Goodstein, David; Davidson, Patrick; Mur, Luis A J; Figueroa, Melania; Freeling, Michael; Catalan, Pilar; Vogel, John P

    2017-12-19

    While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.

  3. Estimation of water content in the leaves of fruit trees using infra-red images

    International Nuclear Information System (INIS)

    Muramatsu, N.; Hiraoka, K.

    2006-01-01

    A method was developed to evaluate water contents of fruit trees using infra-red photography. The irrigation of potted satsuma mandarin trees and grapevines was suppressed to induce water stress. During the drought treatment the leaf edges of basal parts of the shoots of grapevines became necrotic and the area of necrosis extended as the duration of stress increased. Necrosis was clearly distinguished from the viable areas on infra-red images. In satsuma mandarin, an abscission layer formed at the basal part of the petiole, then the leaves fell. Thus, detailed analysis was indispensable for detecting of the leaf water content. After obtaining infra-red images of satsuma mandarin leaves with or without water stress, a background treatment (subtraction of the background image) was performed on the images, then the average brightness of the leaf was determined using image analyzing software (Image Pro-plus). Coefficient correlation between the water status index using the infra-red camera and water content determined from dry weight and fresh weight of leaves was significant (r = 0.917 for adaxial surface data and r = 0.880 for abaxial surface data). These data indicate that infra-red photography is useful for detecting the degree of plant water stress

  4. Systematized water content calculation in cartilage using T1-mapping MR estimations: design and validation of a mathematical model.

    Science.gov (United States)

    Shiguetomi-Medina, J M; Ramirez-Gl, J L; Stødkilde-Jørgensen, H; Møller-Madsen, B

    2017-09-01

    Up to 80 % of cartilage is water; the rest is collagen fibers and proteoglycans. Magnetic resonance (MR) T1-weighted measurements can be employed to calculate the water content of a tissue using T1 mapping. In this study, a method that translates T1 values into water content data was tested statistically. To develop a predictive equation, T1 values were obtained for tissue-mimicking gelatin samples. 1.5 T MRI was performed using inverse angle phase and an inverse sequence at 37 (±0.5) °C. Regions of interest were manually delineated and the mean T1 value was estimated in arbitrary units. Data were collected and modeled using linear regression. To validate the method, articular cartilage from six healthy pigs was used. The experiment was conducted in accordance with the Danish Animal Experiment Committee. Double measurements were performed for each animal. Ex vivo, all water in the tissue was extracted by lyophilization, thus allowing the volume of water to be measured. This was then compared with the predicted water content via Lin's concordance correlation coefficient at the 95 % confidence level. The mathematical model was highly significant when compared to a null model (p < 0.0001). 97.3 % of the variation in water content can be explained by absolute T1 values. Percentage water content could be predicted as 0.476 + (T1 value) × 0.000193 × 100 %. We found that there was 98 % concordance between the actual and predicted water contents. The results of this study demonstrate that MR data can be used to predict percentage water contents of cartilage samples. 3 (case-control study).

  5. Estimation of feeding patterns for piscivorous fish using individual prey data from stomach contents

    DEFF Research Database (Denmark)

    Berg, Casper Willestofte; Temming, Axel

    2011-01-01

    The problem of estimating temporal feeding patterns using stomach data is considered, where the time of ingestion for each prey item can be predicted through a gastric evacuation model. The arrival of prey is modelled as a nonhomogeneous Poisson process with known periodic intensity. A maximum...

  6. MoisturEC: A New R Program for Moisture Content Estimation from Electrical Conductivity Data.

    Science.gov (United States)

    Terry, Neil; Day-Lewis, Frederick D; Werkema, Dale; Lane, John W

    2018-03-06

    Noninvasive geophysical estimation of soil moisture has potential to improve understanding of flow in the unsaturated zone for problems involving agricultural management, aquifer recharge, and optimization of landfill design and operations. In principle, several geophysical techniques (e.g., electrical resistivity, electromagnetic induction, and nuclear magnetic resonance) offer insight into soil moisture, but data-analysis tools are needed to "translate" geophysical results into estimates of soil moisture, consistent with (1) the uncertainty of this translation and (2) direct measurements of moisture. Although geostatistical frameworks exist for this purpose, straightforward and user-friendly tools are required to fully capitalize on the potential of geophysical information for soil-moisture estimation. Here, we present MoisturEC, a simple R program with a graphical user interface to convert measurements or images of electrical conductivity (EC) to soil moisture. Input includes EC values, point moisture estimates, and definition of either Archie parameters (based on experimental or literature values) or empirical data of moisture vs. EC. The program produces two- and three-dimensional images of moisture based on available EC and direct measurements of moisture, interpolating between measurement locations using a Tikhonov regularization approach. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

  7. MoisturEC: a new R program for moisture content estimation from electrical conductivity data

    Science.gov (United States)

    Terry, Neil; Day-Lewis, Frederick D.; Werkema, Dale D.; Lane, John W.

    2018-01-01

    Noninvasive geophysical estimation of soil moisture has potential to improve understanding of flow in the unsaturated zone for problems involving agricultural management, aquifer recharge, and optimization of landfill design and operations. In principle, several geophysical techniques (e.g., electrical resistivity, electromagnetic induction, and nuclear magnetic resonance) offer insight into soil moisture, but data‐analysis tools are needed to “translate” geophysical results into estimates of soil moisture, consistent with (1) the uncertainty of this translation and (2) direct measurements of moisture. Although geostatistical frameworks exist for this purpose, straightforward and user‐friendly tools are required to fully capitalize on the potential of geophysical information for soil‐moisture estimation. Here, we present MoisturEC, a simple R program with a graphical user interface to convert measurements or images of electrical conductivity (EC) to soil moisture. Input includes EC values, point moisture estimates, and definition of either Archie parameters (based on experimental or literature values) or empirical data of moisture vs. EC. The program produces two‐ and three‐dimensional images of moisture based on available EC and direct measurements of moisture, interpolating between measurement locations using a Tikhonov regularization approach.

  8. Parameter estimation and determinability analysis applied to Drosophila gap gene circuits

    Directory of Open Access Journals (Sweden)

    Jaeger Johannes

    2008-09-01

    Full Text Available Abstract Background Mathematical modeling of real-life processes often requires the estimation of unknown parameters. Once the parameters are found by means of optimization, it is important to assess the quality of the parameter estimates, especially if parameter values are used to draw biological conclusions from the model. Results In this paper we describe how the quality of parameter estimates can be analyzed. We apply our methodology to assess parameter determinability for gene circuit models of the gap gene network in early Drosophila embryos. Conclusion Our analysis shows that none of the parameters of the considered model can be determined individually with reasonable accuracy due to correlations between parameters. Therefore, the model cannot be used as a tool to infer quantitative regulatory weights. On the other hand, our results show that it is still possible to draw reliable qualitative conclusions on the regulatory topology of the gene network. Moreover, it improves previous analyses of the same model by allowing us to identify those interactions for which qualitative conclusions are reliable, and those for which they are ambiguous.

  9. The complete mitochondrial genome of Setaria digitata (Nematoda: Filarioidea): Mitochondrial gene content, arrangement and composition compared with other nematodes.

    Science.gov (United States)

    Yatawara, Lalani; Wickramasinghe, Susiji; Rajapakse, R P V J; Agatsuma, Takeshi

    2010-09-01

    In the present study, we determined the complete mitochondrial (mt) genome sequence (13,839bp) of parasitic nematode Setaria digitata and its structure and organization compared with Onchocerca volvulus, Dirofilaria immitis and Brugia malayi. The mt genome of S. digitata is slightly larger than the mt genomes of other filarial nematodes. S. digitata mt genome contains 36 genes (12 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs) that are typically found in metazoans. This genome contains a high A+T (75.1%) content and low G+C content (24.9%). The mt gene order for S. digitata is the same as those for O. volvulus, D. immitis and B. malayi but it is distinctly different from other nematodes compared. The start codons inferred in the mt genome of S. digitata are TTT, ATT, TTG, ATG, GTT and ATA. Interestingly, the initiation codon TTT is unique to S. digitata mt genome and four protein-coding genes use this codon as a translation initiation codon. Five protein-coding genes use TAG as a stop codon whereas three genes use TAA and four genes use T as a termination codon. Out of 64 possible codons, only 57 are used for mitochondrial protein-coding genes of S. digitata. T-rich codons such as TTT (18.9%), GTT (7.9%), TTG (7.8%), TAT (7%), ATT (5.7%), TCT (4.8%) and TTA (4.1%) are used more frequently. This pattern of codon usage reflects the strong bias for T in the mt genome of S. digitata. In conclusion, the present investigation provides new molecular data for future studies of the comparative mitochondrial genomics and systematic of parasitic nematodes of socio-economic importance. 2010 Elsevier B.V. All rights reserved.

  10. Fusion of Electroencephalogram dynamics and musical contents for estimating emotional responses in music listening

    Directory of Open Access Journals (Sweden)

    Yuan-Pin eLin

    2014-05-01

    Full Text Available Electroencephalography (EEG-based emotion classification during music listening has gained increasing attention nowadays due to its promise of potential applications such as musical affective brain-computer interface (ABCI, neuromarketing, music therapy, and implicit multimedia tagging and triggering. However, music is an ecologically valid and complex stimulus that conveys certain emotions to listeners through compositions of musical elements. Using solely EEG signals to distinguish emotions remained challenging. This study aimed to assess the applicability of a multimodal approach by leveraging the EEG dynamics and acoustic characteristics of musical contents for the classification of emotional valence and arousal. To this end, this study adopted machine-learning methods to systematically elucidate the roles of the EEG and music modalities in the emotion modeling. The empirical results suggested that when whole-head EEG signals were available, the inclusion of musical contents did not improve the classification performance. The obtained performance of 74~76% using solely EEG modality was statistically comparable to that using the multimodality approach. However, if EEG dynamics were only available from a small set of electrodes (likely the case in real-life applications, the music modality would play a complementary role and augment the EEG results from around 61% to 67% in valence classification and from around 58% to 67% in arousal classification. The musical timbre appeared to replace less-discriminative EEG features and led to improvements in both valence and arousal classification, whereas musical loudness was contributed specifically to the arousal classification. The present study not only provided principles for constructing an EEG-based multimodal approach, but also revealed the fundamental insights into the interplay of the brain activity and musical contents in emotion modeling.

  11. Fusion of electroencephalographic dynamics and musical contents for estimating emotional responses in music listening.

    Science.gov (United States)

    Lin, Yuan-Pin; Yang, Yi-Hsuan; Jung, Tzyy-Ping

    2014-01-01

    Electroencephalography (EEG)-based emotion classification during music listening has gained increasing attention nowadays due to its promise of potential applications such as musical affective brain-computer interface (ABCI), neuromarketing, music therapy, and implicit multimedia tagging and triggering. However, music is an ecologically valid and complex stimulus that conveys certain emotions to listeners through compositions of musical elements. Using solely EEG signals to distinguish emotions remained challenging. This study aimed to assess the applicability of a multimodal approach by leveraging the EEG dynamics and acoustic characteristics of musical contents for the classification of emotional valence and arousal. To this end, this study adopted machine-learning methods to systematically elucidate the roles of the EEG and music modalities in the emotion modeling. The empirical results suggested that when whole-head EEG signals were available, the inclusion of musical contents did not improve the classification performance. The obtained performance of 74~76% using solely EEG modality was statistically comparable to that using the multimodality approach. However, if EEG dynamics were only available from a small set of electrodes (likely the case in real-life applications), the music modality would play a complementary role and augment the EEG results from around 61-67% in valence classification and from around 58-67% in arousal classification. The musical timber appeared to replace less-discriminative EEG features and led to improvements in both valence and arousal classification, whereas musical loudness was contributed specifically to the arousal classification. The present study not only provided principles for constructing an EEG-based multimodal approach, but also revealed the fundamental insights into the interplay of the brain activity and musical contents in emotion modeling.

  12. Analysis of iodine content in seaweed by GC-ECD and estimation of iodine intake

    Directory of Open Access Journals (Sweden)

    Tai Sheng Yeh

    2014-06-01

    Full Text Available Edible seaweed products have been consumed in many Asian countries. Edible seaweeds accumulate iodine from seawater, and are therefore a good dietary source of iodine. An adequate consumption of seaweed can eliminate iodine deficiency disorders, but excessive iodine intake is not good for health. The recommended dietary reference intake of 0.15 mg/d and 0.14 mg/d for iodine has been established in the United States and Taiwan, respectively. In this study, 30 samples of seaweed were surveyed for iodine content. The samples included 10 nori (Porphyra, 10 wakame (Undaria, and 10 kombu (Laminaria products. The iodine in seaweed was derivatized with 3-pentanone and detected by gas chromatography-electron capture detector (GC-ECD. The method detection limit was 0.5 mg/kg. The iodine content surveyed for nori was 29.3–45.8 mg/kg, for wakame 93.9–185.1 mg/kg, and for kombu 241–4921 mg/kg. Kombu has the highest average iodine content 2523.5 mg/kg, followed by wakame (139.7 mg/kg and nori (36.9 mg/kg. The GC-ECD method developed in this study is a low-cost alternative to inductively coupled plasma-optical emission spectroscopy for iodine detection in seaweeds. The iodine intake from seaweed in the current survey was calculated and compared with the iodine dietary reference intake of Taiwan. The risk and benefit of seaweed consumption is also discussed.

  13. Stability estimation of autoregulated genes under Michaelis-Menten-type kinetics

    Science.gov (United States)

    Arani, Babak M. S.; Mahmoudi, Mahdi; Lahti, Leo; González, Javier; Wit, Ernst C.

    2018-06-01

    Feedback loops are typical motifs appearing in gene regulatory networks. In some well-studied model organisms, including Escherichia coli, autoregulated genes, i.e., genes that activate or repress themselves through their protein products, are the only feedback interactions. For these types of interactions, the Michaelis-Menten (MM) formulation is a suitable and widely used approach, which always leads to stable steady-state solutions representative of homeostatic regulation. However, in many other biological phenomena, such as cell differentiation, cancer progression, and catastrophes in ecosystems, one might expect to observe bistable switchlike dynamics in the case of strong positive autoregulation. To capture this complex behavior we use the generalized family of MM kinetic models. We give a full analysis regarding the stability of autoregulated genes. We show that the autoregulation mechanism has the capability to exhibit diverse cellular dynamics including hysteresis, a typical characteristic of bistable systems, as well as irreversible transitions between bistable states. We also introduce a statistical framework to estimate the kinetics parameters and probability of different stability regimes given observational data. Empirical data for the autoregulated gene SCO3217 in the SOS system in Streptomyces coelicolor are analyzed. The coupling of a statistical framework and the mathematical model can give further insight into understanding the evolutionary mechanisms toward different cell fates in various systems.

  14. Estimation of Spruce Needle-Leaf Chlorophyll Content Based on DART and PARAS Canopy Reflectance Models

    Czech Academy of Sciences Publication Activity Database

    Yáñez-Rausell, L.; Malenovský, Z.; Rautiainen, M.; Clevers, J G P W.; Lukeš, Petr; Hanuš, Jan; Schaepman, M. E.

    2015-01-01

    Roč. 8, č. 4 (2015), s. 1534-1544 ISSN 1939-1404 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0073 Institutional support: RVO:67179843 Keywords : Chlorophyll a plus b estimation * CHRIS-PROBA * coniferous forest * continuum removal * discrete anisotropic radiative transfer model (DART) * needle-leaf * Norway spruce * optical indices * PARAS * PROSPECT * radiative transfer * recollision probability Subject RIV: EH - Ecology, Behaviour Impact factor: 2.145, year: 2015

  15. Improving water content estimation on landslide-prone hillslopes using structurally-constrained inversion of electrical resistivity data

    Science.gov (United States)

    Heinze, Thomas; Möhring, Simon; Budler, Jasmin; Weigand, Maximilian; Kemna, Andreas

    2017-04-01

    Rainfall-triggered landslides are a latent danger in almost any place of the world. Due to climate change heavy rainfalls might occur more often, increasing the risk of landslides. With pore pressure as mechanical trigger, knowledge of water content distribution in the ground is essential for hazard analysis during monitoring of potentially dangerous rainfall events. Geophysical methods like electrical resistivity tomography (ERT) can be utilized to determine the spatial distribution of water content using established soil physical relationships between bulk electrical resistivity and water content. However, often more dominant electrical contrasts due to lithological structures outplay these hydraulic signatures and blur the results in the inversion process. Additionally, the inversion of ERT data requires further constraints. In the standard Occam inversion method, a smoothness constraint is used, assuming that soil properties change softly in space. This applies in many scenarios, as for example during infiltration of water without a clear saturation front. Sharp lithological layers with strongly divergent hydrological parameters, as often found in landslide prone hillslopes, on the other hand, are typically badly resolved by standard ERT. We use a structurally constrained ERT inversion approach for improving water content estimation in landslide prone hills by including a-priori information about lithological layers. Here the standard smoothness constraint is reduced along layer boundaries identified using seismic data or other additional sources. This approach significantly improves water content estimations, because in landslide prone hills often a layer of rather high hydraulic conductivity is followed by a hydraulic barrier like clay-rich soil, causing higher pore pressures. One saturated layer and one almost drained layer typically result also in a sharp contrast in electrical resistivity, assuming that surface conductivity of the soil does not change in

  16. VOLUME ESTIMATION, DRY WEIGHT, OIL CONTENT AND QUANTITY OF FENCEPOSTS OF CANDEIA (Eremanthus erythropappus (DC MacLeish

    Directory of Open Access Journals (Sweden)

    José Roberto Soares Scolforo

    2004-06-01

    Full Text Available This research aimed at studying the behavior of volume, dry weight, oil content and fence post quantity per diametric class of candeia; to define its stack factor, with and without diametric class control; and to determine equations for estimating the main stem and branches volume, dry weight and oil content of the hole tree, trunk, branches and leaves and fencepost quantity. Data were obtained from a forest inventory carried out in a native candeia forest located in Aiuruoca county, Minas Gerais state - Brazil. Tree volume was calculated through the Huber formula and oil extraction methods employed were “the solvent method” and “vapor hauling method”. For estimation volume, dry weight, oil content and fencepost number the traditional double entry models were used. The oil weight in 1 cubic meter of wood of small dimensions, trees between 5 and 10cm, is around 6 kilos, while the oil content of the largest trees, between 40 and 45cm, is around 11 kilos. The same tendency is observed for the wood volume, without bark, and in the volume of piled up wood, although in these last situations the magnitude of quantities are different. The oil content of candeia trees present the following behavior: in the stem and branches up to 3cm of diameter with bark, it varies from 1,02% to 1,37%, respectively to plants with diameter between 5 and 10cm and between 40 and 45cm; in the branches with less than 3cm of diameter with bark, it varies from 0,33% to 0,65%,respectively, to plants between 5 and 10cm and between 40 and 45cm of diameter; in the leaves it varies from 0,28% to 0,77%, respectively, for plants between 5-10cm and between 40-45cm of diameter. The average stack factor is 1.9087 and diminishes as diameter classes increases. The best model for estimating oil content, dry weight, fence post quantity and volume is the logarithmic form of Schumacher-Hall model.

  17. Application of tristimulus colorimetry to estimate the carotenoids content in ultrafrozen orange juices.

    Science.gov (United States)

    Meléndez-Martínez, Antonio J; Vicario, Isabel M; Heredia, Francisco J

    2003-12-03

    Tristimulus Colorimetry was applied to characterize the color of Valencia late orange juices. Color measurements were made against white background and black background. The profile of the main carotenoids related to the color of the juices was determined by HPLC. Significant correlations (p < 0.05) between b*, Cab* and h(ab) and the content of beta-cryptoxanthin, lutein + zeaxanthin and beta-carotene were found. The correlations between the color parameters L*, a*, b*, Cab* and h(ab) and the carotenoids content were also explored by partial least squares. The results obtained have shown that it is possible to obtain equations, by means of multiple regression models, which allow the determination of the individual carotenoid levels from the CIELAB color parameters, with R2 values always over 0.9. In this sense, equations have been proposed to calculate the retinol equivalents (1 RE = 1 microgram retinol = 12 micrograms beta-carotene = 24 micrograms alpha-carotene = 24 micrograms beta-cryptoxanthin) of the orange juice analyzed as a function of the color parameters calculated from measurement made against white and black backgrounds. The average RE per liter of juice obtained by HPLC was 51.07 +/- 18.89, whereas employing these equations, average RE values obtained were 51.16 +/- 1.36 and 51.21 +/- 1.70 for white background and black background, respectively.

  18. An Advanced Radiative Transfer and Neural Network Scheme and Evaluation for Estimating Water Vapor Content from MODIS Data

    Directory of Open Access Journals (Sweden)

    Kebiao Mao

    2017-07-01

    Full Text Available This work made an improvement upon and a further evaluation of previous work for estimating water vapor content from near-infrared around 1 μm from MODIS data. The accuracy of RM-NN is determined by the complicated relationship of the geophysical parameters. An advanced scheme is proposed for building different training databases for different seasons in different regions to reduce the complexity. The training database includes three parts. The first part is a simulation database by MODTRAN for different weather conditions, which is made as a basic database; the second part is reliable field measurement data in observation stations; and the third part is the MYD05_L2 product on clear days, which is produced by the standard product algorithm for water vapor content. The comparative analyses based on simulation data indicate that maximum accuracy of single condition could be improved by about 34% relative to the “all conditions” results. Two study regions in China and America are selected as test areas, and the evaluation shows that the mean and the standard deviation of estimation error are about 0.08 g cm−2 and 0.09 g cm−2, respectively. All the analysis indicates that the advanced scheme can improve the retrieval accuracy of water vapor content, which can make full use of the advantages of previous methods.

  19. Quantifying The Relative Importance Of Phylogeny And Environmental Preferences As Drivers Of Gene Content In Prokaryotic Microorganisms

    Directory of Open Access Journals (Sweden)

    Javier eTamames

    2016-03-01

    Full Text Available Two complementary forces shape microbial genomes: vertical inheritance of genes by phylogenetic descent, and acquisition of new genes related to adaptation to particular habitats and lifestyles. Quantification of the relative importance of each driving force proved difficult. We determined the contribution of each factor, and identified particular genes or biochemical/cellular processes linked to environmental preferences (i.e., propensity of a taxon to live in particular habitats. Three types of data were confronted: [i] complete genomes, which provide gene content of different taxa; [ii] phylogenetic information, via alignment of 16S rRNA sequences, which allowed determination of the distance between taxa, and [iii] distribution of species in environments via 16S rRNA sampling experiments, reflecting environmental preferences of different taxa. The combination of these three datasets made it possible to describe and quantify the relationships among them. We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations. Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing. These genes are likely important for adaptation of bacteria to particular conditions or habitats, such as carbohydrate or glycan metabolism genes being linked to host-associated environments.

  20. Carotenoid content and root color of cultivated carrot: a candidate-gene association study using an original broad unstructured population.

    Directory of Open Access Journals (Sweden)

    Matthieu Jourdan

    Full Text Available Accumulated in large amounts in carrot, carotenoids are an important product quality attribute and therefore a major breeding trait. However, the knowledge of carotenoid accumulation genetic control in this root vegetable is still limited. In order to identify the genetic variants linked to this character, we performed an association mapping study with a candidate gene approach. We developed an original unstructured population with a broad genetic basis to avoid the pitfall of false positive detection due to population stratification. We genotyped 109 SNPs located in 17 candidate genes – mostly carotenoid biosynthesis genes – on 380 individuals, and tested the association with carotenoid contents and color components. Total carotenoids and β-carotene contents were significantly associated with genes zeaxanthin epoxydase (ZEP, phytoene desaturase (PDS and carotenoid isomerase (CRTISO while α-carotene was associated with CRTISO and plastid terminal oxidase (PTOX genes. Color components were associated most significantly with ZEP. Our results suggest the involvement of the couple PDS/PTOX and ZEP in carotenoid accumulation, as the result of the metabolic and catabolic activities respectively. This study brings new insights in the understanding of the carotenoid pathway in non-photosynthetic organs.

  1. Joint estimation of vertical total electron content (VTEC) and satellite differential code biases (SDCBs) using low-cost receivers

    Science.gov (United States)

    Zhang, Baocheng; Teunissen, Peter J. G.; Yuan, Yunbin; Zhang, Hongxing; Li, Min

    2018-04-01

    Vertical total electron content (VTEC) parameters estimated using global navigation satellite system (GNSS) data are of great interest for ionosphere sensing. Satellite differential code biases (SDCBs) account for one source of error which, if left uncorrected, can deteriorate performance of positioning, timing and other applications. The customary approach to estimate VTEC along with SDCBs from dual-frequency GNSS data, hereinafter referred to as DF approach, consists of two sequential steps. The first step seeks to retrieve ionospheric observables through the carrier-to-code leveling technique. This observable, related to the slant total electron content (STEC) along the satellite-receiver line-of-sight, is biased also by the SDCBs and the receiver differential code biases (RDCBs). By means of thin-layer ionospheric model, in the second step one is able to isolate the VTEC, the SDCBs and the RDCBs from the ionospheric observables. In this work, we present a single-frequency (SF) approach, enabling the joint estimation of VTEC and SDCBs using low-cost receivers; this approach is also based on two steps and it differs from the DF approach only in the first step, where we turn to the precise point positioning technique to retrieve from the single-frequency GNSS data the ionospheric observables, interpreted as the combination of the STEC, the SDCBs and the biased receiver clocks at the pivot epoch. Our numerical analyses clarify how SF approach performs when being applied to GPS L1 data collected by a single receiver under both calm and disturbed ionospheric conditions. The daily time series of zenith VTEC estimates has an accuracy ranging from a few tenths of a TEC unit (TECU) to approximately 2 TECU. For 73-96% of GPS satellites in view, the daily estimates of SDCBs do not deviate, in absolute value, more than 1 ns from their ground truth values published by the Centre for Orbit Determination in Europe.

  2. Concentration-dependent sedimentation properties of ferritin: implications for estimation of iron contents of serum ferritins

    International Nuclear Information System (INIS)

    Niitsu, Y.; Adachi, C.; Takahashi, F.; Goto, Y.; Kohgo, Y.; Urushizaki, I.; Listowsky, I.

    1985-01-01

    Serum ferritins from various sources sedimented at lower densities than tissue ferritins in sucrose gradient centrifugation systems. The sedimentation patterns of ferritins, however, were shown to be dependent on the concentration of the protein; as the concentration decreased the protein appeared to sediment at lower densities. Thus, at the low concentration levels usually used for analysis of serum ferritin, tissue ferritins also sedimented in the same lower density regions. Iron labeling experiments indicated that the sedimentation changes upon dilution were not due to release of iron or was there any indication that the protein dissociated into subunits. The anomalous sedimentation behavior of serum ferritin should therefore not be interpreted in terms of its iron content. The disclosure that serum ferritins may have full complements of iron is counter to the prevalent view that serum ferritins are low iron forms and has potential implications with regard to the sources and possible function of this protein in the circulation

  3. Nitrite and Nitrate Content in Meat Products and Estimated Intake in Denmark From 1998 to 2006

    DEFF Research Database (Denmark)

    Leth, Torben; Fagt, Sisse; Nielsen, S.

    2008-01-01

    The content of nitrite and nitrate in cured meat products has been monitored in Denmark seven times between 1995 and 2006. The maximum permitted added amounts of sodium nitrite in Denmark (60 mg kg(-1) for most products up to 150 mg kg(-1) for special products) have not been exceeded, except...... period with levels varying between 6 and 20 mg sodium nitrite kg(-1) with sausages, meat for open sandwiches and salami-type sausages being the greatest contributors. The mean intake of sodium nitrate was around 1 mg day(-1), which is very low compared with the total intake of 61 mg day(-1). The mean...... group, only very few persons were responsible for the high intake. The conversion of nitrate to nitrite in the saliva and the degradation of nitrite during production and storage must also be considered when evaluating the intake of nitrite....

  4. A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family

    Science.gov (United States)

    Houston, Kelly; Burton, Rachel A.; Sznajder, Beata; Rafalski, Antoni J.; Dhugga, Kanwarpal S.; Mather, Diane E.; Taylor, Jillian; Steffenson, Brian J.; Waugh, Robbie; Fincher, Geoffrey B.

    2015-01-01

    Cellulose is a fundamentally important component of cell walls of higher plants. It provides a scaffold that allows the development and growth of the plant to occur in an ordered fashion. Cellulose also provides mechanical strength, which is crucial for both normal development and to enable the plant to withstand both abiotic and biotic stresses. We quantified the cellulose concentration in the culm of 288 two – rowed and 288 six – rowed spring type barley accessions that were part of the USDA funded barley Coordinated Agricultural Project (CAP) program in the USA. When the population structure of these accessions was analysed we identified six distinct populations, four of which we considered to be comprised of a sufficient number of accessions to be suitable for genome-wide association studies (GWAS). These lines had been genotyped with 3072 SNPs so we combined the trait and genetic data to carry out GWAS. The analysis allowed us to identify regions of the genome containing significant associations between molecular markers and cellulose concentration data, including one region cross-validated in multiple populations. To identify candidate genes we assembled the gene content of these regions and used these to query a comprehensive RNA-seq based gene expression atlas. This provided us with gene annotations and associated expression data across multiple tissues, which allowed us to formulate a supported list of candidate genes that regulate cellulose biosynthesis. Several regions identified by our analysis contain genes that are co-expressed with CELLULOSE SYNTHASE A (HvCesA) across a range of tissues and developmental stages. These genes are involved in both primary and secondary cell wall development. In addition, genes that have been previously linked with cellulose synthesis by biochemical methods, such as HvCOBRA, a gene of unknown function, were also associated with cellulose levels in the association panel. Our analyses provide new insights into the

  5. The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome

    DEFF Research Database (Denmark)

    Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R R

    2015-01-01

    that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues...... abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed...

  6. Fat and carbohydrate content in the diet induces drastic changes in gene expression in young Göttingen minipigs

    DEFF Research Database (Denmark)

    Mentzel, Caroline M.Junker; Figueiredo Cardoso, Tainã; Haagensen, Annika Maria Juul

    2017-01-01

    In human health, there is interest in developing specific diets to reduce body weight. These studies are mainly focused on phenotypic changes induced in blood measurements, i.e., triglycerides, HDL, LDL, and insulin, and on physical changes, i.e., body weight and BMI. To evaluate the biological i....... The new knowledge gained in this study could potentially be of value for considering direct modulation of gene expression by nutrient content in the diet....

  7. Estimating the Energy Content of Wastewater Using Combustion Calorimetry and Different Drying Processes

    Energy Technology Data Exchange (ETDEWEB)

    Korth, Benjamin; Maskow, Thomas; Günther, Susanne; Harnisch, Falk, E-mail: falk.harnisch@ufz.de [Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig (Germany)

    2017-09-19

    The energy content of wastewater is routinely assessed by chemical oxygen demand (COD) measurements that only provide an incomplete picture and the data fundament of other energy parameters remains scarce. The volumetric heat of combustion (Δ{sub C}H) of raw wastewater from a municipal wastewater treatment plant (WWTP) was assessed using oven drying method (Δ{sub C}H{sub vol} = −6.8 ± 4.3 kJ L{sup −1}, n = 20) and freeze drying method (Δ{sub C}H{sub vol} = −20.2 ± 9.7 kJ L{sup −1}, n = 6) illustrating the substantial loss during the oven drying approach. Normalizing Δ{sub C}H to COD of raw wastewater yielded −6.2 ± 3.5 kJ gCOD{sup −1} for oven-dried samples (n = 14) and −13.0 ± 1.6 kJ gCOD{sup −1} for freeze-dried samples (n = 3). A subsequent correlation analysis with further chemical wastewater parameters revealed a dependency of Δ{sub C}H{sub vol} on COD, total organic carbon (TOC), C:N ratio, and total sulfur content. To verify these correlations, wastewater of a second WWTP was sampled and analyzed. Only COD and TOC were in accordance with the data set from the first WWTP representing potential predictors for the chemical energy stored in wastewater for comparable WWTPs. Unfortunately, during the most practical method (oven drying), a certain loss of volatile compounds is inevitable so that the derived Δ{sub C}H{sub vol} systematically underestimates the total energetic potential of wastewater. Nevertheless, this work expands the, so far, little data fundament on the energy resource wastewater and implies the requirement for further long-term studies on different sites and different wastewater types with a highly standardized sample treatment protocol.

  8. StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.

    Science.gov (United States)

    Stavrovskaya, Elena D; Niranjan, Tejasvi; Fertig, Elana J; Wheelan, Sarah J; Favorov, Alexander V; Mironov, Andrey A

    2017-10-15

    Genomics features with similar genome-wide distributions are generally hypothesized to be functionally related, for example, colocalization of histones and transcription start sites indicate chromatin regulation of transcription factor activity. Therefore, statistical algorithms to perform spatial, genome-wide correlation among genomic features are required. Here, we propose a method, StereoGene, that rapidly estimates genome-wide correlation among pairs of genomic features. These features may represent high-throughput data mapped to reference genome or sets of genomic annotations in that reference genome. StereoGene enables correlation of continuous data directly, avoiding the data binarization and subsequent data loss. Correlations are computed among neighboring genomic positions using kernel correlation. Representing the correlation as a function of the genome position, StereoGene outputs the local correlation track as part of the analysis. StereoGene also accounts for confounders such as input DNA by partial correlation. We apply our method to numerous comparisons of ChIP-Seq datasets from the Human Epigenome Atlas and FANTOM CAGE to demonstrate its wide applicability. We observe the changes in the correlation between epigenomic features across developmental trajectories of several tissue types consistent with known biology and find a novel spatial correlation of CAGE clusters with donor splice sites and with poly(A) sites. These analyses provide examples for the broad applicability of StereoGene for regulatory genomics. The StereoGene C ++ source code, program documentation, Galaxy integration scripts and examples are available from the project homepage http://stereogene.bioinf.fbb.msu.ru/. favorov@sensi.org. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  9. Environmental cues induce changes of steviol glycosides contents and transcription of corresponding biosynthetic genes in Stevia rebaudiana.

    Science.gov (United States)

    Yang, Yongheng; Huang, Suzhen; Han, Yulin; Yuan, Haiyan; Gu, Chunsun; Wang, Zhongwei

    2015-01-01

    Plant growth and secondary metabolism are commonly regulated by external cues such as light, temperature and water availability. In this study, the influences of low and high temperatures, dehydration, photoperiods, and different growing stages on the changes of steviol glycosides (SGs) contents and transcription levels of fifteen genes involved in SGs biosynthesis of Stevia rebaudiana Bertoni were examined using HPLC and RT-PCR. The observations showed that the transcript levels of all the fifteen genes were maximum under 25 °C treatment, and the transcription of SrDXS, SrDXR, SrMCT, SrCMK, SrMDS, SrHDS, SrHDR, SrIDI, SrGGDPS, SrCPPS1, SrUGT85C2 and SrUGT76G1 were restrained both in low temperature (15 °C) and high temperature (35 °C). Most genes in SGs biosynthesis pathway exhibited down-regulation in dehydration. To elucidate the effect of photoperiods, the plants were treated by different simulated photoperiods (8 L/16 D, 1 0L/14 D, 14 L/10 D and 16 L/8 D), but no significant transcription changes were observed. In the study of growing stages, there were evident changes of SGs contents, and the transcript levels of all the fifteen genes were minimal in fast growing period, and exhibited evident increase both in flower-bud appearing stage and flowering stage. The obtained results strongly suggest that the effect of environmental cues on steviol glycosides contents and transcription of corresponding biosynthetic genes in S. rebaudiana is significant. It is worth to study deeply. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  10. Preflow stresses in Martian rampart ejecta blankets - A means of estimating the water content

    Science.gov (United States)

    Woronow, A.

    1981-01-01

    Measurements of extents of rampart ejecta deposits as a function of the size of the parent craters support models which, for craters larger than about 6 km diameter, constrain ejecta blankets to all have a similar maximum thickness regardless of the crater size. These volatile-rich ejecta blankets may have failed under their own weights, then flowed radially outward. Assuming this to be so, some of the physicomechanical properties of the ejecta deposits at the time of their emplacement can then be determined. Finite-element studies of the stress magnitudes, distributions, and directions in hypothetical Martian rampart ejecta blankets reveal that the material most likely failed when the shear stresses were less than 500 kPa and the angle of internal friction was between 26 and 36 deg. These figures imply that the ejecta has a water content between 16 and 72%. Whether the upper limit or the lower limit is more appropriate depends on the mode of failure which one presumes: namely, viscous flow of plastic deformation.

  11. Use of the Budyko Framework to Estimate the Virtual Water Content in Shijiazhuang Plain, North China

    Science.gov (United States)

    Zhang, E.; Yin, X.

    2017-12-01

    One of the most challenging steps in implementing analysis of virtual water content (VWC) of agricultural crops is how to properly assess the volume of consumptive water use (CWU) for crop production. In practice, CWU is considered equivalent to the crop evapotranspiration (ETc). Following the crop coefficient method, ETc can be calculated under standard or non-standard conditions by multiplying the reference evapotranspiration (ET0) by one or a few coefficients. However, when current crop growing conditions deviate from standard conditions, accurately determining the coefficients under non-standard conditions remains to be a complicated process and requires lots of field experimental data. Based on regional surface water-energy balance, this research integrates the Budyko framework into the traditional crop coefficient approach to simplify the coefficients determination. This new method enables us to assess the volume of agricultural VWC only based on some hydrometeorological data and agricultural statistic data in regional scale. To demonstrate the new method, we apply it to the Shijiazhuang Plain, which is an agricultural irrigation area in the North China Plain. The VWC of winter wheat and summer maize is calculated and we further subdivide VWC into blue and green water components. Compared with previous studies in this study area, VWC calculated by the Budyko-based crop coefficient approach uses less data and agrees well with some of the previous research. It shows that this new method may serve as a more convenient tool for assessing VWC.

  12. Selenium content in selected foods from the Greek market and estimation of the daily intake

    International Nuclear Information System (INIS)

    Pappa, Eleni C.; Pappas, Athanasios C.; Surai, Peter F.

    2006-01-01

    The total selenium content of foods purchased from the North West part of Greece was determined using hydride generation atomic fluorescence spectroscopy. The results of this study were within the range from other countries. The overall mean average of selenium concentration of the foods examined, in decreasing order, was found in sesame seeds (783.1 ng g -1 ), fish (246 ng g -1 ), legumes (162.5 ng g -1 ), eggs (123 ng g -1 ), bread (91.9 ng g -1 ), meat (71.7 ng g -1 ), cheese (69.8 ng g -1 ), yoghurt (23.6 ng g -1 ), nuts (19.6 ng g -1 ), milk (15.4 ng g -1 ), vegetables (6.5 ng g -1 ) and fruits (3.4 ng g -1 ). Considering the average daily individual consumption of these foods by Greeks, the average daily dietary intake of selenium supplied by this source is 39.3 μg per capita

  13. Selenium content in selected foods from the Greek market and estimation of the daily intake

    Energy Technology Data Exchange (ETDEWEB)

    Pappa, Eleni C. [National Agricultural Research Foundation, Dairy Research Institute, Katsikas 45221, Ioannina (Greece)]. E-mail: instgala@otenet.gr; Pappas, Athanasios C. [Avian Science Research Centre, Animal Health Group, SAC, Auchincruive, Ayr KA6 5HW (United Kingdom); Surai, Peter F. [Avian Science Research Centre, Animal Health Group, SAC, Auchincruive, Ayr KA6 5HW (United Kingdom); Division of Environmental and Evolutionary Biology, University of Glasgow, Glasgow, G12 8QQ, Scotland (United Kingdom)

    2006-12-15

    The total selenium content of foods purchased from the North West part of Greece was determined using hydride generation atomic fluorescence spectroscopy. The results of this study were within the range from other countries. The overall mean average of selenium concentration of the foods examined, in decreasing order, was found in sesame seeds (783.1 ng g{sup -1}), fish (246 ng g{sup -1}), legumes (162.5 ng g{sup -1}), eggs (123 ng g{sup -1}), bread (91.9 ng g{sup -1}), meat (71.7 ng g{sup -1}), cheese (69.8 ng g{sup -1}), yoghurt (23.6 ng g{sup -1}), nuts (19.6 ng g{sup -1}), milk (15.4 ng g{sup -1}), vegetables (6.5 ng g{sup -1}) and fruits (3.4 ng g{sup -1}). Considering the average daily individual consumption of these foods by Greeks, the average daily dietary intake of selenium supplied by this source is 39.3 {mu}g per capita.

  14. Chromoplasts ultrastructure and estimated carotene content in root secondary phloem of different carrot varieties.

    Science.gov (United States)

    Kim, Ji Eun; Rensing, Kim H; Douglas, Carl J; Cheng, Kimberly M

    2010-02-01

    There have been few studies on quantifying carotenoid accumulation in carrots, and none have taken the comparative approach. The abundance and distribution of carotenes in carrot roots of three varieties, white, orange, and high carotene mass (HCM) were compared using light and transmission electron microscopy (TEM). Light microscopy has indicated that, in all three varieties, carotenes were most abundant in the secondary phloem and this area was selected for further TEM analysis. While carotenes were extracted during the fixation process for TEM, the high-pressure freezing technique we employed preserved the spaces (CS) left behind by the extracted carotene crystals. Chromoplasts from the HCM variety contained significantly (P chromoplasts from the orange variety. Chromoplasts from the white variety had few or no CS. There was no significant difference between the HCM and orange varieties in the number of chromoplasts per unit area, but the white variety had significantly (P chromoplasts than the other two varieties. A large number of starch-filled amyloplasts was observed in secondary phloem of the white variety but these were not found in the other two varieties. The results from this comparative approach clearly define the subcellular localization of carotenoids in carrot roots and suggest that while the HCM genotype was selectively bred for increased carotene content, this selection did not lead to increased numbers of carotene-containing chromoplasts but rather greater accumulation of carotene per chromoplast. Furthermore, the results confirm that roots of the white carrot variety retain residual amounts of carotene.

  15. Selenium content in wheat and estimation of the selenium daily intake in different regions of Algeria

    International Nuclear Information System (INIS)

    Beladel, B.; Nedjimi, B.; Mansouri, A.; Tahtat, D.; Belamri, M.; Tchanchane, A.; Khelfaoui, F.; Benamar, M.E.A.

    2013-01-01

    In this work, we have measured the selenium content in wheat produced locally in eight different regions of Algeria from east to west, and we have established the annual consumption of selenium for five socio-professional categories. Instrumental neutron activation analysis is used. The selenium levels in wheat samples varied from 21 (Tiaret) to 153 μg/kg (Khroub), with a mean value about 52 μg/kg. The mean of selenium daily consumption from ingestion of wheat per person in the eight regions varied from 32 to 52 μg/day which is close to the minimal FAO recommendation. - Highlights: ► Cereals and cereal products represent a staple food in Algeria. ► The objective of this study is to determine the Se intake in wheat produced locally. ► The concentration of Se in the wheat reflects the level of the Se in regional soils. ► The mean of Se daily consumption is close to the minimal WHO/FAO recommendation.

  16. Agrobacterium rhizogenes rolB gene affects photosynthesis and chlorophyll content in transgenic tomato (Solanum lycopersicum L.) plants.

    Science.gov (United States)

    Bettini, Priscilla P; Marvasi, Massimiliano; Fani, Fabiola; Lazzara, Luigi; Cosi, Elena; Melani, Lorenzo; Mauro, Maria Luisa

    2016-10-01

    Insertion of Agrobacterium rhizogenes rolB gene into plant genome affects plant development, hormone balance and defence. However, beside the current research, the overall transcriptional response and gene expression of rolB as a modulator in plant is unknown. Transformed rolB tomato plant (Solanum lycopersicum L.) cultivar Tondino has been used to investigate the differential expression profile. Tomato is a well-known model organism both at the genetic and molecular level, and one of the most important commercial food crops in the world. Through the construction and characterization of a cDNA subtracted library, we have investigated the differential gene expression between transgenic clones of rolB and control tomato and have evaluated genes specifically transcribed in transgenic rolB plants. Among the selected genes, five genes encoding for chlorophyll a/b binding protein, carbonic anhydrase, cytochrome b 6 /f complex Fe-S subunit, potassium efflux antiporter 3, and chloroplast small heat-shock protein, all involved in chloroplast function, were identified. Measurement of photosynthesis efficiency by the level of three different photosynthetic parameters (F v /F m , rETR, NPQ) showed rolB significant increase in non-photochemical quenching and a, b chlorophyll content. Our results point to highlight the role of rolB on plant fitness by improving photosynthesis. Copyright © 2016 Elsevier GmbH. All rights reserved.

  17. Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus

    Directory of Open Access Journals (Sweden)

    Zhitao Niu

    2017-11-01

    Full Text Available The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces—selection, mutational biases, and GC-biased gene conversion (gBGC—on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1 consistent GC content evolution trends and mutational biases in single-copy (SC and inverted repeats (IRs regions; and (2 that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus.

  18. Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus

    Science.gov (United States)

    Niu, Zhitao; Xue, Qingyun; Wang, Hui; Xie, Xuezhu; Zhu, Shuying; Liu, Wei; Ding, Xiaoyu

    2017-01-01

    The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces—selection, mutational biases, and GC-biased gene conversion (gBGC)—on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1) consistent GC content evolution trends and mutational biases in single-copy (SC) and inverted repeats (IRs) regions; and (2) that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus. PMID:29099062

  19. Experimental dehydration of natural obsidian and estimation of DH2O at low water contents

    Science.gov (United States)

    Jambon, A.; Zhang, Y.; Stolper, E. M.

    1992-01-01

    Water diffusion experiments were carried out by dehydrating rhyolitic obsidian from Valles Caldera (New Mexico, USA) at 510-980 degrees C. The starting glass wafers contained approximately 0.114 wt% total water, lower than any glasses previously investigated for water diffusion. Weight loss due to dehydration was measured as a function of experiment duration, which permits determination of mean bulk water diffusivity, mean Dw. These diffusivities are in the range of 2.6 to 18 X 10(-14) m2/s and can be fit with the following Arrhenius equation: ln mean Dw (m2/s) = -(25.10 +/- 1.29) - (46,480 +/- 11,400) (J/mol) / RT, except for two replicate runs at 510 degrees C which give mean Dw values much lower than that defined by the above equation. When interpreted according to a model of water speciation in which molecular H2O is the diffusing species with concentration-independent diffusivity while OH units do not contribute to the transport but react to provide H2O, the data (except for the 510 degrees C data) are in agreement with extrapolation from previous results and hence extend the previous data base and provide a test of the applicability of the model to very low water contents. Mean bulk water diffusivities are about two orders of magnitude less than molecular H2O diffusivities because the fraction of molecular H2O out of total water is very small at 0.114 wt% total water and less. The 510 degrees C experimental results can be interpreted as due to slow kinetics of OH to H2O interconversion at low temperatures.

  20. Estimating the carbohydrate content of various forms of tobacco by phenol-sulfuric acid method.

    Science.gov (United States)

    Jain, Vardhaman Mulchand; Karibasappa, Gundabaktha Nagappa; Dodamani, Arun Suresh; Mali, Gaurao Vasant

    2017-01-01

    Due to consumption of various forms of tobacco in large amounts by Indian population, it has become a cause of concern for major oral diseases. In 2008, the WHO named tobacco as the world's single greatest cause of preventable death. It is also known that certain amount of carbohydrates are incorporated in processed tobacco to make it acceptable for consumption. Thus, its role in oral diseases becomes an important question at this point of time. Through this study, it is attempted to find out the carbohydrate content of various forms of tobacco by phenol-sulfuric acid method. Tobacco products selected for the study were Nandi hookah tambakhu (A), photo brand budhaa Punjabi snuff (B), Miraj (C), Gai-chhap tambakhu (D), Hanuman-chhap Pandharpuri tambakhu (E), and Hathi-chhap Bidi (F). The samples were decoded and transported to laboratory and tested at various concentrations by phenol-sulfuric acid method followed by ultraviolet spectrophotometry to determine their absorbance. The present study showed Hathi-chhap bidi/sample F had a maximum absorbance (1.995) at 10 μg/ml which is a smoking form of tobacco followed by rest all smokeless forms of tobacco, i.e. sample C (0.452), sample B (0.253), sample D (0.077), sample E (-0.018), and sample A (-0.127), respectively. As the concentration of tobacco sample increases, their absorbance increases which in turn is suggestive of increase in its carbohydrate concentration. Carbohydrates in the form of sugars, either inherently present or added in it during manufacturing can serve as a risk factor for higher incidence of dental caries.

  1. The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae: structural comparative analysis, gene content and microsatellite detection

    Directory of Open Access Journals (Sweden)

    Andrew W. Gichira

    2017-01-01

    Full Text Available Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp, with a pair of Inverted Repeats (IR 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp and a small single copy (SSC, 18,696. H. abyssinica’s chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

  2. The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection.

    Science.gov (United States)

    Gichira, Andrew W; Li, Zhizhong; Saina, Josphat K; Long, Zhicheng; Hu, Guangwan; Gituru, Robert W; Wang, Qingfeng; Chen, Jinming

    2017-01-01

    Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica 's chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene ( infA ) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica . A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

  3. Growth process in an elephant tusk: Age estimations based on temporal variations in bomb-radiocarbon content

    Energy Technology Data Exchange (ETDEWEB)

    Nakamura, Toshio, E-mail: nakamura@nendai.nagoya-u.ac.jp [Center for Chronological Research, Nagoya University, Chikusa, Nagoya, Aichi 464-8602 (Japan); Koike, Hiroko [Kyushu University Museum, Kyushu University, Hakozaki, Fukuoka, Fukuoka 814-0180 (Japan); Aizawa, Jun; Okuno, Mitsuru [Department of Earth System Science, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, Fukuoka 814-0180 (Japan)

    2015-10-15

    In this study, {sup 14}C analysis by accelerator mass spectrometry (AMS) was applied to age estimation based on temporal variations in bomb-produced-{sup 14}C contents of a full elephant tusk registered at Kyushu University. The tusk measured 175 cm long and 13.8 cm in diameter at the root. Thirty tusk-fragment samples were used for {sup 14}C analysis with AMS to estimate the formation ages of different positions according to catalogued global {sup 14}C contents (F{sup 14}C). The F{sup 14}C value of the tip of the tusk suggested that the elephant was born around 1980, while that of the root suggested death around 1994, a lifespan of at least 14 years, rather shorter period than the average lifetime of an elephant (ca. 80 years). In addition, the F{sup 14}C values of fragments collected along a cross-sectional line suggested that the outer part of the tusk formed first with inner parts being deposited gradually with growth.

  4. Growth process in an elephant tusk: Age estimations based on temporal variations in bomb-radiocarbon content

    International Nuclear Information System (INIS)

    Nakamura, Toshio; Koike, Hiroko; Aizawa, Jun; Okuno, Mitsuru

    2015-01-01

    In this study, "1"4C analysis by accelerator mass spectrometry (AMS) was applied to age estimation based on temporal variations in bomb-produced-"1"4C contents of a full elephant tusk registered at Kyushu University. The tusk measured 175 cm long and 13.8 cm in diameter at the root. Thirty tusk-fragment samples were used for "1"4C analysis with AMS to estimate the formation ages of different positions according to catalogued global "1"4C contents (F"1"4C). The F"1"4C value of the tip of the tusk suggested that the elephant was born around 1980, while that of the root suggested death around 1994, a lifespan of at least 14 years, rather shorter period than the average lifetime of an elephant (ca. 80 years). In addition, the F"1"4C values of fragments collected along a cross-sectional line suggested that the outer part of the tusk formed first with inner parts being deposited gradually with growth.

  5. Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression

    Science.gov (United States)

    McDonald, Bradon R.; Takasuka, Taichi E.; Wendt-Pienkowski, Evelyn; Doering, Drew T.; Raffa, Kenneth F.; Fox, Brian G.; Currie, Cameron R.

    2016-01-01

    The evolution of cellulose degradation was a defining event in the history of life. Without efficient decomposition and recycling, dead plant biomass would quickly accumulate and become inaccessible to terrestrial food webs and the global carbon cycle. On land, the primary drivers of plant biomass deconstruction are fungi and bacteria in the soil or associated with herbivorous eukaryotes. While the ecological importance of plant-decomposing microbes is well established, little is known about the distribution or evolution of cellulolytic activity in any bacterial genus. Here we show that in Streptomyces, a genus of Actinobacteria abundant in soil and symbiotic niches, the ability to rapidly degrade cellulose is largely restricted to two clades of host-associated strains and is not a conserved characteristic of the Streptomyces genus or host-associated strains. Our comparative genomics identify that while plant biomass degrading genes (CAZy) are widespread in Streptomyces, key enzyme families are enriched in highly cellulolytic strains. Transcriptomic analyses demonstrate that cellulolytic strains express a suite of multi-domain CAZy enzymes that are coregulated by the CebR transcriptional regulator. Using targeted gene deletions, we verify the importance of a highly expressed cellulase (GH6 family cellobiohydrolase) and the CebR transcriptional repressor to the cellulolytic phenotype. Evolutionary analyses identify complex genomic modifications that drive plant biomass deconstruction in Streptomyces, including acquisition and selective retention of CAZy genes and transcriptional regulators. Our results suggest that host-associated niches have selected some symbiotic Streptomyces for increased cellulose degrading activity and that symbiotic bacteria are a rich biochemical and enzymatic resource for biotechnology. PMID:27276034

  6. Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina

    DEFF Research Database (Denmark)

    Arvas, Mikko; Kivioja, Teemu; Mitchell, Alex

    2007-01-01

    Saccharomycotina are slightly better characterised and predicted to encode mainly enzymes. The genes specific to Saccharomycotina are enriched in transcription and mitochondrion related functions. Especially mitochondrial ribosomal proteins seem to have diverged from those of Pezizomycotina. In addition, we...

  7. The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.; Banks, Jo Ann; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Bowman, John L.; Gribskov, Michael; dePamphilis, Claude; Albert, Victor A.; Aono, Naoki; Aoyama, Tsuyoshi; Ambrose, Barbara A.; Ashton, Neil W.; Axtell, Michael J.; Barker, Elizabeth; Barker, Michael S.; Bennetzen, Jeffrey L.; Bonawitz, Nicholas D.; Chapple, Clint; Cheng, Chaoyang; Correa, Luiz Gustavo Guedes; Dacre, Michael; DeBarry, Jeremy; Dreyer, Ingo; Elias, Marek; Engstrom, Eric M.; Estelle, Mark; Feng, Liang; Finet, Cedric; Floyd, Sandra K.; Frommer, Wolf B.; Fujita, Tomomichi; Gramzow, Lydia; Gutensohn, Michael; Harholt, Jesper; Hattori, Mitsuru; Heyl, Alexander; Hirai, Tadayoshi; Hiwatashi, Yuji; Ishikawa, Masaki; Iwata, Mineko; Karol, Kenneth G.; Koehler, Barbara; Kolukisaoglu, Uener; Kubo, Minoru; Kurata, Tetsuya; Lalonde, Sylvie; Li, Kejie; Li, Ying; Litt, Amy; Lyons, Eric; Manning, Gerard; Maruyama, Takeshi; Michael, Todd P.; Mikami, Koji; Miyazaki, Saori; Morinaga, Shin-ichi; Murata, Takashi; Mueller-Roeber, Bernd; Nelson, David R.; Obara, Mari; Oguri, Yasuko; Olmstead, Richard G.; Onodera, Naoko; Petersen, Bent Larsen; Pils, Birgit; Prigge, Michael; Rensing, Stefan A.; Riano-Pachon, Diego Mauricio; Roberts, Alison W.; Sato, Yoshikatsu; Scheller, Henrik Vibe; Schulz, Burkhard; Schulz, Christian; Shakirov, Eugene V.; Shibagaki, Nakako; Shinohara, Naoki; Shippen, Dorothy E.; Sorensen, Iben; Sotooka, Ryo; Sugimoto, Nagisa; Sugita, Mamoru; Sumikawa, Naomi; Tanurdzic, Milos; Theilsen, Gunter; Ulvskov, Peter; Wakazuki, Sachiko; Weng, Jing-Ke; Willats, William W.G.T.; Wipf, Daniel; Wolf, Paul G.; Yang, Lixing; Zimmer, Andreas D.; Zhu, Qihui; Mitros, Therese; Hellsten, Uffe; Loque, Dominique; Otillar, Robert; Salamov, Asaf; Schmutz, Jeremy; Shapiro, Harris; Lindquist, Erika; Lucas, Susan; Rokhsar, Daniel

    2011-04-28

    We report the genome sequence of the nonseed vascular plant, Selaginella moellendorffii, and by comparative genomics identify genes that likely played important roles in the early evolution of vascular plants and their subsequent evolution

  8. Estimation of the near surface soil water content during evaporation using air-launched ground-penetrating radar

    KAUST Repository

    Moghadas, Davood

    2014-01-01

    Evaporation is an important process in the global water cycle and its variation affects the near sur-face soil water content, which is crucial for surface hydrology and climate modelling. Soil evaporation rate is often characterized by two distinct phases, namely, the energy limited phase (stage-I) and the soil hydraulic limited period (stage-II). In this paper, a laboratory experiment was conducted using a sand box filled with fine sand, which was subject to evaporation for a period of twenty three days. The setup was equipped with a weighting system to record automatically the weight of the sand box with a constant time-step. Furthermore, time-lapse air-launched ground penetrating radar (GPR) measurements were performed to monitor the evaporation process. The GPR model involves a full-waveform frequency-domain solution of Maxwell\\'s equations for wave propagation in three-dimensional multilayered media. The accuracy of the full-waveform GPR forward modelling with respect to three different petrophysical models was investigated. Moreover, full-waveform inversion of the GPR data was used to estimate the quantitative information, such as near surface soil water content. The two stages of evaporation can be clearly observed in the radargram, which indicates qualitatively that enough information is contained in the GPR data. The full-waveform GPR inversion allows for accurate estimation of the near surface soil water content during extended evaporation phases, when a wide frequency range of GPR (0.8-5.0 GHz) is taken into account. In addition, the results indicate that the CRIM model may constitute a relevant alternative in solving the frequency-dependency issue for full waveform GPR modelling.

  9. GENE ACTION AND HERITABILITY ESTIMATES OF QUANTITATIVE CHARACTERS AMONG LINES DERIVED FROM VARIETAL CROSSES OF SOYBEAN

    Directory of Open Access Journals (Sweden)

    Lukman Hakim

    2017-09-01

    Full Text Available The knowledge of genetic action, heritability and genetic variability is useful and permits plant breeder to design efficient breeding strategies in soybean.  The objectives of this study were to determine gene action, genetic variability, heritability and genetic advance of quantitative characters that could be realized through selection of segregation progenies. The F1 population and F2 progenies of six crosses among five soybean varieties were evaluated at Muneng Experimental Station, East Java during the dry season of 2014.  The lines were planted in a randomized block design with four replications.  The seeds of each F1 and F2 progenies and parents were planted in four rows of 3 m long, 40 cm x 20 cm plant spacing, one plant per hill. The result showed that pod number per plant, seed yield, plant yield and harvest index were found to be predominantly controlled by additive gene effects.  Seed size was also controlled by additive gene effects, with small seed dominant to large seed size.  Plant height was found to be controlled by both additive and nonadditive gene effects.  Similarly, days to maturity was due mainly to additive and nonadditive gene effects, with earliness dominant to lateness.  Days to maturity had the highest heritability estimates of 49.3%, followed by seed size (47.0%, harvest index (45.8%, and pod number per plant (45.5%.  Therefore, they could be used in the selection of a high yielding soybean genotype in the F3 generation. 

  10. Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study

    KAUST Repository

    Fan, M.; Kuwahara, Hiroyuki; Wang, X.; Wang, S.; Gao, Xin

    2015-01-01

    Parameter estimation is a challenging computational problemin the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter esti- mation

  11. Field estimation of soil water content. A practical guide to methods, instrumentation and sensor technology

    International Nuclear Information System (INIS)

    2008-01-01

    During a period of five years, an international group of soil water instrumentation experts were contracted by the International Atomic Energy Agency to carry out a range of comparative assessments of soil water sensing methods under laboratory and field conditions. The detailed results of those studies are published elsewhere. Most of the devices examined worked well some of the time, but most also performed poorly in some circumstances. The group was also aware that the choice of a water measurement technology is often made for economic, convenience and other reasons, and that there was a need to be able to obtain the best results from any device used. The choice of a technology is sometimes not made by the ultimate user, or even if it is, the main constraint may be financial rather than technical. Thus, this guide is presented in a way that allows the user to obtain the best performance from any instrument, while also providing guidance as to which instruments perform best under given circumstances. That said, this expert group of the IAEA reached several important conclusions: (1) the field calibrated neutron moisture meter (NMM) remains the most accurate and precise method for soil profile water content determination in the field, and is the only indirect method capable of providing accurate soil water balance data for studies of crop water use, water use efficiency, irrigation efficiency and irrigation water use efficiency, with a minimum number of access tubes; (2) those electromagnetic sensors known as capacitance sensors exhibit much more variability in the field than either the NMM or direct soil water measurements, and they are not recommended for soil water balance studies for this reason (impractically large numbers of access tubes and sensors are required) and because they are rendered inaccurate by changes in soil bulk electrical conductivity (including temperature effects) that often occur in irrigated soils, particularly those containing

  12. Heterosis in rice seedlings: its relationship to gibberellin content and expression of gibberellin metabolism and signaling genes.

    Science.gov (United States)

    Ma, Qian; Hedden, Peter; Zhang, Qifa

    2011-08-01

    Despite the accumulation of data on the genetic and molecular understanding of heterosis, there is little information on the regulation of heterosis at the physiological level. In this study, we performed a quantitative analysis of endogenous gibberellin (GA) content and expression profiling of the GA metabolism and signaling genes to investigate the possible relationship between GA signaling and heterosis for seedling development in rice (Oryza sativa). The materials used were an incomplete diallele set of 3 × 3 crosses and the six parents. In the growing shoots of the seedlings at 20 d after sowing, significant positive correlations between the contents of some GA species and performance and heterosis based on shoot dry mass were detected. Expression analyses of GA-related genes by real-time reverse transcription-polymerase chain reaction revealed that 13 out of the 16 GA-related genes examined exhibited significant differential expression among the F1 hybrid and its parents, acting predominantly in the modes of overdominance and positive dominance. Expression levels of nine genes in the hybrids displayed significant positive correlations with the heterosis of shoot dry mass. These results imply that GAs play a positive role in the regulation of heterosis for rice seedling development. In shoots plus root axes of 4-d-old germinating seeds that had undergone the deetiolation, mimicking normal germination in soil, the axis dry mass was positively correlated with the content of GA₂₉ but negatively correlated with that of GA₁₉. Our findings provide supporting evidence for GAs playing an important regulatory role in heterosis for rice seedling development.

  13. Cloning and characterization of three squalene epoxidase genes in panax vietnamensis var. fuscidicus, a rare medical plant with high content of ocotillot-type ginsenosides

    International Nuclear Information System (INIS)

    Ma, C.H.; Jiang, N.H.; Chen, J.W.; Zhang, G.H.

    2016-01-01

    Panax vietnamensis var. fuscidiscus, is a new variety of Panax. vietnamensis, which was first found in Jinping County, the southern part of Yunnan Province, China. It is also one of the most prized medicinal plants used in traditional ethnic minority medicine systems. This species contains higher content of ocotillol-type saponin, especially majonoside R2, which make this plant particularly suitable for identification of the SE genes responsible for the biosynthesis of ginsenosides. Three cDNAs encoding SE were cloned from P. vietnamensis var. fuscidiscus, and their molecular characterizations were investigated. The tissue-specific expression patterns of the three SE genes were analyzed by RT-qPCR. The transcription levels of these genes in Methyl jasmonate (MeJA)-treated leaves of P. vietnamensis var. fuscidiscus were also estimated by RT-qPCR. PvfSE, PvfSE2 and PvfSE3 differed in predicted membrane-spanning helices. Phylogenetic analysis grouped these SE into three different clades. The three PvfSE isoforms were all most highly expressed in leaves. Moreover, they exhibited different response patterns under MeJA induction. The three PvfSE isoforms may play different roles in sterol or ginsenoside biosynthesis in this herb This report is the first attempt to clone and expression analysis of SE from P. vietnamensis var. fuscidiscus and provides a new foundation for further understanding the role of SE in the biosynthesis of ginsenosides. (author)

  14. Hyperspectral Estimation of the Chlorophyll Content in Short-Term and Long-Term Restorations of Mangrove in Quanzhou Bay Estuary, China

    Directory of Open Access Journals (Sweden)

    Zhiguo Dou

    2018-04-01

    Full Text Available The chlorophyll content can indicate the general health of vegetation, and can be estimated from hyperspectral data. The aim of this study is to estimate the chlorophyll content of mangroves at different stages of restoration in a coastal wetland in Quanzhou, China, using proximal hyperspectral remote sensing techniques. We determine the hyperspectral reflectance of leaves from two mangrove species, Kandelia candel and Aegiceras corniculatum, from short-term and long-term restoration areas with a portable spectroradiometer. We also measure the leaf chlorophyll content (SPAD value. We use partial-least-squares stepwise regression to determine the relationships between the spectral reflectance and the chlorophyll content of the leaves, and establish two models, a full-wave-band spectrum model and a red-edge position regression model, to estimate the chlorophyll content of the mangroves. The coefficients of determination for the red-edge position model and the full-wave-band model exceed 0.72 and 0.82, respectively. The inverted chlorophyll contents are estimated more accurately for the long-term restoration mangroves than for the short-term restoration mangroves. Our results indicate that hyperspectral data can be used to estimate the chlorophyll content of mangroves at different stages of restoration, and could possibly be adapted to estimate biochemical constituents in leaves.

  15. Genome-Wide Association Study Reveals Novel Genes Associated with Culm Cellulose Content in Bread Wheat (Triticum aestivum, L.

    Directory of Open Access Journals (Sweden)

    Simerjeet Kaur

    2017-11-01

    Full Text Available Plant cell wall formation is a complex, coordinated and developmentally regulated process. Cellulose is the most dominant constituent of plant cell walls. Because of its paracrystalline structure, cellulose is the main determinant of mechanical strength of plant tissues. As the most abundant polysaccharide on earth, it is also the focus of cellulosic biofuel industry. To reduce culm lodging in wheat and for improved ethanol production, delineation of the variation for stem cellulose content could prove useful. We present results on the analysis of the stem cellulose content of 288 diverse wheat accessions and its genome-wide association study (GWAS. Cellulose concentration ranged from 35 to 52% (w/w. Cellulose content was normally distributed in the accessions around a mean and median of 45% (w/w. Genome-wide marker-trait association study using 21,073 SNPs helped identify nine SNPs that were associated (p < 1E-05 with cellulose content. Four strongly associated (p < 8.17E-05 SNP markers were linked to wheat unigenes, which included β-tubulin, Auxin-induced protein 5NG4, and a putative transmembrane protein of unknown function. These genes may be directly or indirectly involved in the formation of cellulose in wheat culms. GWAS results from this study have the potential for genetic manipulation of cellulose content in bread wheat and other small grain cereals to enhance culm strength and improve biofuel production.

  16. Improving the estimation of celiac disease sibling risk by non-HLA genes.

    Directory of Open Access Journals (Sweden)

    Valentina Izzo

    Full Text Available Celiac Disease (CD is a polygenic trait, and HLA genes explain less than half of the genetic variation. Through large GWAs more than 40 associated non-HLA genes were identified, but they give a small contribution to the heritability of the disease. The aim of this study is to improve the estimate of the CD risk in siblings, by adding to HLA a small set of non-HLA genes. One-hundred fifty-seven Italian families with a confirmed CD case and at least one other sib and both parents were recruited. Among 249 sibs, 29 developed CD in a 6 year follow-up period. All individuals were typed for HLA and 10 SNPs in non-HLA genes: CCR1/CCR3 (rs6441961, IL12A/SCHIP1 and IL12A (rs17810546 and rs9811792, TAGAP (rs1738074, RGS1 (rs2816316, LPP (rs1464510, OLIG3 (rs2327832, REL (rs842647, IL2/IL21 (rs6822844, SH2B3 (rs3184504. Three associated SNPs (in LPP, REL, and RGS1 genes were identified through the Transmission Disequilibrium Test and a Bayesian approach was used to assign a score (BS to each detected HLA+SNPs genotype combination. We then classified CD sibs as at low or at high risk if their BS was respectively < or ≥ median BS value within each HLA risk group. A larger number (72% of CD sibs showed a BS ≥ the median value and had a more than two fold higher OR than CD sibs with a BS value < the median (O.R = 2.53, p = 0.047. Our HLA+SNPs genotype classification, showed both a higher predictive negative value (95% vs 91% and diagnostic sensitivity (79% vs 45% than the HLA only. In conclusion, the estimate of the CD risk by HLA+SNPs approach, even if not applicable to prevention, could be a precious tool to improve the prediction of the disease in a cohort of first degree relatives, particularly in the low HLA risk groups.

  17. Mitochondrial content is central to nuclear gene expression: Profound implications for human health.

    Science.gov (United States)

    Muir, Rebecca; Diot, Alan; Poulton, Joanna

    2016-02-01

    We review a recent paper in Genome Research by Guantes et al. showing that nuclear gene expression is influenced by the bioenergetic status of the mitochondria. The amount of energy that mitochondria make available for gene expression varies considerably. It depends on: the energetic demands of the tissue; the mitochondrial DNA (mtDNA) mutant load; the number of mitochondria; stressors present in the cell. Hence, when failing mitochondria place the cell in energy crisis there are major effects on gene expression affecting the risk of degenerative diseases, cancer and ageing. In 2015 the UK parliament approved a change in the regulation of IVF techniques, allowing "Mitochondrial replacement therapy" to become a reproductive choice for women at risk of transmitting mitochondrial disease to their children. This is the first time that this technique will be available. Therefore understanding the interaction between mitochondria and the nucleus has never been more important. © 2015 The Authors. BioEssays Published by WILEY Periodicals, Inc.

  18. Iron Supply Affects Anthocyanin Content and Related Gene Expression in Berries of Vitis vinifera cv. Cabernet Sauvignon.

    Science.gov (United States)

    Shi, Pengbao; Li, Bing; Chen, Haiju; Song, Changzheng; Meng, Jiangfei; Xi, Zhumei; Zhang, Zhenwen

    2017-02-14

    Anthocyanins are important compounds for red grape and red wine quality, and can be influenced by supply of nutrients such as nitrogen, phosphorus, potassium, zinc, and iron. The present work aims to gain a better understanding of the effect of iron supply on anthocyanins concentration in grape berries. To this end, own-rooted four-year-old Cabernet Sauvignon grapevines ( Vitis vinifera ) were fertigated every three days with 0, 23, 46, 92, and 184 μM iron (Fe) from ferric ethylenediamine di ( o -hydroxyphenylacetic) acid (Fe-EDDHA) in a complete nutrient solution. Fe deficiency or excess generally led to higher concentrations of titratable acidity and skin/berry ratio, and to lower reducing sugar content, sugar/acid ratio, pH, berry weight, and concentration of anthocyanins. Most of the individual anthocyanins detected in this study, except cyanidin-3- O -glucoside, delphinidin-3- O -glucoside, and cyanidin-3- O -(6- O -coumaryl)-glucoside, in moderate Fe treatment (46 μM) grapes were significantly higher than those of other treatments. Genes encoding chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), leucoanthocyanidin dioxygenase (LDOX), and anthocyanin O -methyltransferase (AOMT) exhibited higher transcript levels in berries from plants cultivated with 46 μM Fe compared to the ones cultivated with other Fe concentrations. We suggest that grape sugar content, anthocyanins content, and transcriptions of genes involved in anthocyanin biosynthesis were correlated with Fe supply concentrations.

  19. Iron Supply Affects Anthocyanin Content and Related Gene Expression in Berries of Vitis vinifera cv. Cabernet Sauvignon

    Directory of Open Access Journals (Sweden)

    Pengbao Shi

    2017-02-01

    Full Text Available Anthocyanins are important compounds for red grape and red wine quality, and can be influenced by supply of nutrients such as nitrogen, phosphorus, potassium, zinc, and iron. The present work aims to gain a better understanding of the effect of iron supply on anthocyanins concentration in grape berries. To this end, own-rooted four-year-old Cabernet Sauvignon grapevines (Vitis vinifera were fertigated every three days with 0, 23, 46, 92, and 184 μM iron (Fe from ferric ethylenediamine di (o-hydroxyphenylacetic acid (Fe-EDDHA in a complete nutrient solution. Fe deficiency or excess generally led to higher concentrations of titratable acidity and skin/berry ratio, and to lower reducing sugar content, sugar/acid ratio, pH, berry weight, and concentration of anthocyanins. Most of the individual anthocyanins detected in this study, except cyanidin-3-O-glucoside, delphinidin-3-O-glucoside, and cyanidin-3-O-(6-O-coumaryl-glucoside, in moderate Fe treatment (46 μM grapes were significantly higher than those of other treatments. Genes encoding chalcone isomerase (CHI, flavanone 3-hydroxylase (F3H, leucoanthocyanidin dioxygenase (LDOX, and anthocyanin O-methyltransferase (AOMT exhibited higher transcript levels in berries from plants cultivated with 46 μM Fe compared to the ones cultivated with other Fe concentrations. We suggest that grape sugar content, anthocyanins content, and transcriptions of genes involved in anthocyanin biosynthesis were correlated with Fe supply concentrations.

  20. Estimation of lead, cadmium and nickel content by means of Atomic Absorption Spectroscopy in dry fruit bodies of some macromycetes growing in Poland. II.

    Directory of Open Access Journals (Sweden)

    Jan Grzybek

    2014-08-01

    Full Text Available The content of lead, cadmium, and nickel in dry fruit bodies of 34 species of macromyoetes collected in Poland from 72 natural babitats by means of Atomic Absorption Spectroscopy (AAS was estimated.

  1. Genetic variation of γ-tocopherol methyltransferase gene contributes to elevated α-tocopherol content in soybean seeds.

    Science.gov (United States)

    Dwiyanti, Maria S; Yamada, Tetsuya; Sato, Masako; Abe, Jun; Kitamura, Keisuke

    2011-11-07

    Improvement of α-tocopherol content is an important breeding aim to increase the nutritional value of crops. Several efforts have been conducted to improve the α-tocopherol content in soybean [Glycine max (L.) Merr.] through transgenic technology by overexpressing genes related to α-tocopherol biosynthesis or through changes to crop management practices. Varieties with high α-tocopherol content have been identified in soybean germplasms. The heritability of this trait has been characterized in a cross between high α-tocopherol variety Keszthelyi Aproszemu Sarga (KAS) and low α-tocopherol variety Ichihime. In this study, the genetic mechanism of the high α-tocopherol content trait of KAS was elucidated. Through QTL analysis and fine mapping in populations from a cross between KAS and a Japanese variety Ichihime, we identified γ-TMT3, which encodes γ-tocopherol methyltransferase, as a candidate gene responsible for high α-tocopherol concentration in KAS. Several nucleotide polymorphisms including two nonsynonymous mutations were found in the coding region of γ-TMT3 between Ichihime and KAS, but none of which was responsible for the difference in α-tocopherol concentration. Therefore, we focused on transcriptional regulation of γ-TMT3 in developing seeds and leaves. An F5 line that was heterozygous for the region containing γ-TMT3 was self-pollinated. From among the progeny, plants that were homozygous at the γ-TMT3 locus were chosen for further evaluation. The expression level of γ-TMT3 was higher both in developing seeds and leaves of plants homozygous for the γ-TMT3 allele from KAS. The higher expression level was closely correlated with high α-tocopherol content in developing seeds. We generated transgenic Arabidopsis plants harboring GUS gene under the control of γ-TMT3 promoter from KAS or Ichihime. The GUS activity assay showed that the activity of γ-TMT3 promoter from KAS was higher than that of Ichihime. The genetic variation in γ-TMT3

  2. Genetic variation of γ-tocopherol methyltransferase gene contributes to elevated α-tocopherol content in soybean seeds

    Directory of Open Access Journals (Sweden)

    Abe Jun

    2011-11-01

    Full Text Available Abstract Background Improvement of α-tocopherol content is an important breeding aim to increase the nutritional value of crops. Several efforts have been conducted to improve the α-tocopherol content in soybean [Glycine max (L. Merr.] through transgenic technology by overexpressing genes related to α-tocopherol biosynthesis or through changes to crop management practices. Varieties with high α-tocopherol content have been identified in soybean germplasms. The heritability of this trait has been characterized in a cross between high α-tocopherol variety Keszthelyi Aproszemu Sarga (KAS and low α-tocopherol variety Ichihime. In this study, the genetic mechanism of the high α-tocopherol content trait of KAS was elucidated. Results Through QTL analysis and fine mapping in populations from a cross between KAS and a Japanese variety Ichihime, we identified γ-TMT3, which encodes γ-tocopherol methyltransferase, as a candidate gene responsible for high α-tocopherol concentration in KAS. Several nucleotide polymorphisms including two nonsynonymous mutations were found in the coding region of γ-TMT3 between Ichihime and KAS, but none of which was responsible for the difference in α-tocopherol concentration. Therefore, we focused on transcriptional regulation of γ-TMT3 in developing seeds and leaves. An F5 line that was heterozygous for the region containing γ-TMT3 was self-pollinated. From among the progeny, plants that were homozygous at the γ-TMT3 locus were chosen for further evaluation. The expression level of γ-TMT3 was higher both in developing seeds and leaves of plants homozygous for the γ-TMT3 allele from KAS. The higher expression level was closely correlated with high α-tocopherol content in developing seeds. We generated transgenic Arabidopsis plants harboring GUS gene under the control of γ-TMT3 promoter from KAS or Ichihime. The GUS activity assay showed that the activity of γ-TMT3 promoter from KAS was higher than that of

  3. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    KAUST Repository

    Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R. R.; Huminiecki, Lukasz

    2015-01-01

    to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia

  4. Estimating Demand and Cross-Price Elasticity for Very Low Nicotine Content (VLNC) Cigarettes Using a Simulated Demand Task.

    Science.gov (United States)

    Tucker, Megan R; Laugesen, Murray; Grace, Randolph C

    2017-03-03

    Very Low Nicotine Content (VLNC) cigarettes might be useful as part of a tobacco control strategy, but relatively little is known about their acceptability as substitutes for regular cigarettes. We compared subjective effects and demand for regular cigarettes and Very Low Nicotine Content (VLNC) cigarettes, and estimated cross-price elasticity for VLNC cigarettes, using simulated demand tasks. 40 New Zealand smokers sampled a VLNC cigarette and completed Cigarette Purchase Tasks to indicate their demand for regular cigarettes and VLNC cigarettes at a range of prices, and a cross-price task indicating how many regular cigarettes and VLNC cigarettes they would purchase at 0.5x, 1x, and 2x the current market price for regular cigarettes, assuming the price of VLNC cigarettes remained constant. They also rated the subjective effects of the VLNC cigarette and their usual-brand regular cigarettes. Cross-price elasticity for VLNC cigarettes was estimated as 0.24 and was significantly positive, indicating that VLNC cigarettes are partially substitutable for regular cigarettes. VLNC cigarettes were rated as less satisfying and psychologically rewarding than regular cigarettes, but this was unrelated to demand or substitutability. VLNC cigarettes are potentially substitutable for regular cigarettes. Their availability may reduce tobacco consumption, nicotine intake and addiction; making it easier for smokers to quit. VLNC cigarettes share the behavioural and sensory components of smoking whilst delivering negligible levels of nicotine. Although smokers rated VLNCs as less satisfying than regular cigarettes, smokers said they would increase their consumption of VLNCs as the price of regular cigarettes increased, if VLNCs were available at a lower price. This suggests that VLNCs are partially substitutable for regular cigarettes. VLNCs can be part of an effective tobacco control strategy, by reducing nicotine dependence and improving health and financial outcomes for smokers

  5. Identification and characterization of calcium transporter gene family in finger millet in relation to grain calcium content.

    Science.gov (United States)

    Singh, Uma M; Metwal, Mamta; Singh, Manoj; Taj, Gohar; Kumar, Anil

    2015-07-15

    Calcium (Ca) is an essential mineral for proper growth and development of plants as well as animals. In plants including cereals, calcium is deposited in seed during its development which is mediated by specialized Ca transporters. Common cereal seeds contain very low amounts of Ca while the finger millet (Eleusine coracana) contains exceptionally high amounts of Ca in seed. In order to understand the role of Ca transporters in grain Ca accumulation, developing seed transcriptome of two finger millet genotypes (GP-1, low Ca and GP-45 high Ca) differing in seed Ca content was sequenced using Illumina paired-end sequencing technology and members of Ca transporter gene family were identified. Out of 109,218 and 120,130 contigs, 86 and 81 contigs encoding Ca transporters were identified in GP-1 and GP-45, respectively. After removal of redundant sequences, a total of 19 sequences were confirmed as Ca transporter genes, which includes 11 Ca(2+) ATPases, 07 Ca(2+)/cation exchangers and 01 Ca(2+) channel. The differential expressions of all genes were analyzed from transcriptome data and it was observed that 9 and 3 genes were highly expressed in GP-45 and GP-1 genotypes respectively. Validation of transcriptome expression data of selected Ca transporter genes was performed on different stages of developing spikes of both genotypes grown under different concentrations of exogenous Ca. In both genotypes, significant correlation was observed between the expression of these genes, especially EcCaX3, and on the amount of Ca accumulated in seed. The positive correlation of seed mass with the amount of Ca concentration was also observed. The efficient Ca transport property and responsiveness of EcCAX3 towards exogenous Ca could be utilized in future biofortification program. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Variation in relative water content, proline accumulation and stress gene expression in two cowpea landraces under drought.

    Science.gov (United States)

    Zegaoui, Zahia; Planchais, Séverine; Cabassa, Cécile; Djebbar, Reda; Abrous Belbachir, Ouzna; Carol, Pierre

    2017-11-01

    Many landraces of cowpea [Vigna unguiculata (L.) Walp.] are adapted to particular geographical and climatic conditions. Here we describe two landraces grown respectively in arid and temperate areas of Algeria and assess their physiological and molecular responses to drought stress. As expected, when deprived of water cowpea plants lose water over time with a gradual reduction in transpiration rate. The landraces differed in their relative water content (RWC) and whole plant transpiration rate. The landrace from Menia, an arid area, retained more water in adult leaves. Both landraces responded to drought stress at the molecular level by increasing expression of stress-related genes in aerial parts, including proline metabolism genes. Expression of gene(s) encoding proline synthesis enzyme P5CS was up regulated and gene expression of ProDH, a proline catabolism enzyme, was down regulated. Relatively low amounts of proline accumulated in adult leaves with slight differences between the two landraces. During drought stress the most apical part of plants stayed relatively turgid with a high RWC compared to distal parts that wilted. Expression of key stress genes was higher and more proline accumulated at the apex than in distal leaves indicating that cowpea has a non-uniform stress response at the whole plant level. Our study reveals a developmental control of water stress through preferential proline accumulation in the upper tier of the cowpea plant. We also conclude that cowpea landraces display physiological adaptations to water stress suited to the arid and temperate climates in which they are cultivated. Copyright © 2017 Elsevier GmbH. All rights reserved.

  7. High GC Content Cas9-Mediated Genome-Editing and Biosynthetic Gene Cluster Activation in Saccharopolyspora erythraea.

    Science.gov (United States)

    Liu, Yong; Wei, Wen-Ping; Ye, Bang-Ce

    2018-05-18

    The overexpression of bacterial secondary metabolite biosynthetic enzymes is the basis for industrial overproducing strains. Genome editing tools can be used to further improve gene expression and yield. Saccharopolyspora erythraea produces erythromycin, which has extensive clinical applications. In this study, the CRISPR-Cas9 system was used to edit genes in the S. erythraea genome. A temperature-sensitive plasmid containing the PermE promoter, to drive Cas9 expression, and the Pj23119 and PkasO promoters, to drive sgRNAs, was designed. Erythromycin esterase, encoded by S. erythraea SACE_1765, inactivates erythromycin by hydrolyzing the macrolactone ring. Sequencing and qRT-PCR confirmed that reporter genes were successfully inserted into the SACE_1765 gene. Deletion of SACE_1765 in a high-producing strain resulted in a 12.7% increase in erythromycin levels. Subsequent PermE- egfp knock-in at the SACE_0712 locus resulted in an 80.3% increase in erythromycin production compared with that of wild type. Further investigation showed that PermE promoter knock-in activated the erythromycin biosynthetic gene clusters at the SACE_0712 locus. Additionally, deletion of indA (SACE_1229) using dual sgRNA targeting without markers increased the editing efficiency to 65%. In summary, we have successfully applied Cas9-based genome editing to a bacterial strain, S. erythraea, with a high GC content. This system has potential application for both genome-editing and biosynthetic gene cluster activation in Actinobacteria.

  8. Influence of pre-exercise muscle glycogen content on exercise-induced transcriptional regulation of metabolic genes

    DEFF Research Database (Denmark)

    Pilegaard, Henriette; Keller, Charlotte; Steensberg, Adam

    2002-01-01

    Transcription of metabolic genes is transiently induced during recovery from exercise in skeletal muscle of humans. To determine whether pre-exercise muscle glycogen content influences the magnitude and/or duration of this adaptive response, six male subjects performed one-legged cycling exercise...... to lower muscle glycogen content in one leg and then, the following day, completed 2.5 h low intensity two-legged cycling exercise. Nuclei and mRNA were isolated from biopsies obtained from the vastus lateralis muscle of the control and reduced glycogen (pre-exercise glycogen = 609 +/- 47 and 337 +/- 33...... mmol kg(-1) dry weight, respectively) legs before and after 0, 2 and 5 h of recovery. Exercise induced a significant (P glycogen leg only. Although PDK4...

  9. RETRIEVAL OF AEROSOL MICROPHYSICAL PROPERTIES BASED ON THE OPTIMAL ESTIMATION METHOD: INFORMATION CONTENT ANALYSIS FOR SATELLITE POLARIMETRIC REMOTE SENSING MEASUREMENTS

    Directory of Open Access Journals (Sweden)

    W. Z. Hou

    2018-04-01

    Full Text Available This paper evaluates the information content for the retrieval of key aerosol microphysical and surface properties for multispectral single-viewing satellite polarimetric measurements cantered at 410, 443, 555, 670, 865, 1610 and 2250 nm over bright land. To conduct the information content analysis, the synthetic data are simulated by the Unified Linearized Vector Radiative Transfer Model (UNLVTM with the intensity and polarization together over bare soil surface for various scenarios. Following the optimal estimation theory, a principal component analysis method is employed to reconstruct the multispectral surface reflectance from 410 nm to 2250 nm, and then integrated with a linear one-parametric BPDF model to represent the contribution of polarized surface reflectance, thus further to decouple the surface-atmosphere contribution from the TOA measurements. Focusing on two different aerosol models with the aerosol optical depth equal to 0.8 at 550 nm, the total DFS and DFS component of each retrieval aerosol and surface parameter are analysed. The DFS results show that the key aerosol microphysical properties, such as the fine- and coarse-mode columnar volume concentration, the effective radius and the real part of complex refractive index at 550 nm, could be well retrieved with the surface parameters simultaneously over bare soil surface type. The findings of this study can provide the guidance to the inversion algorithm development over bright surface land by taking full use of the single-viewing satellite polarimetric measurements.

  10. Retrieval of Aerosol Microphysical Properties Based on the Optimal Estimation Method: Information Content Analysis for Satellite Polarimetric Remote Sensing Measurements

    Science.gov (United States)

    Hou, W. Z.; Li, Z. Q.; Zheng, F. X.; Qie, L. L.

    2018-04-01

    This paper evaluates the information content for the retrieval of key aerosol microphysical and surface properties for multispectral single-viewing satellite polarimetric measurements cantered at 410, 443, 555, 670, 865, 1610 and 2250 nm over bright land. To conduct the information content analysis, the synthetic data are simulated by the Unified Linearized Vector Radiative Transfer Model (UNLVTM) with the intensity and polarization together over bare soil surface for various scenarios. Following the optimal estimation theory, a principal component analysis method is employed to reconstruct the multispectral surface reflectance from 410 nm to 2250 nm, and then integrated with a linear one-parametric BPDF model to represent the contribution of polarized surface reflectance, thus further to decouple the surface-atmosphere contribution from the TOA measurements. Focusing on two different aerosol models with the aerosol optical depth equal to 0.8 at 550 nm, the total DFS and DFS component of each retrieval aerosol and surface parameter are analysed. The DFS results show that the key aerosol microphysical properties, such as the fine- and coarse-mode columnar volume concentration, the effective radius and the real part of complex refractive index at 550 nm, could be well retrieved with the surface parameters simultaneously over bare soil surface type. The findings of this study can provide the guidance to the inversion algorithm development over bright surface land by taking full use of the single-viewing satellite polarimetric measurements.

  11. DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.

    Science.gov (United States)

    Mazandu, Gaston K; Mulder, Nicola J

    2013-09-25

    The use of Gene Ontology (GO) data in protein analyses have largely contributed to the improved outcomes of these analyses. Several GO semantic similarity measures have been proposed in recent years and provide tools that allow the integration of biological knowledge embedded in the GO structure into different biological analyses. There is a need for a unified tool that provides the scientific community with the opportunity to explore these different GO similarity measure approaches and their biological applications. We have developed DaGO-Fun, an online tool available at http://web.cbio.uct.ac.za/ITGOM, which incorporates many different GO similarity measures for exploring, analyzing and comparing GO terms and proteins within the context of GO. It uses GO data and UniProt proteins with their GO annotations as provided by the Gene Ontology Annotation (GOA) project to precompute GO term information content (IC), enabling rapid response to user queries. The DaGO-Fun online tool presents the advantage of integrating all the relevant IC-based GO similarity measures, including topology- and annotation-based approaches to facilitate effective exploration of these measures, thus enabling users to choose the most relevant approach for their application. Furthermore, this tool includes several biological applications related to GO semantic similarity scores, including the retrieval of genes based on their GO annotations, the clustering of functionally related genes within a set, and term enrichment analysis.

  12. Estimation of carotenoid content at the canopy scale using the carotenoid triangle ratio index from in situ and simulated hyperspectral data

    Science.gov (United States)

    Kong, Weiping; Huang, Wenjiang; Zhou, Xianfeng; Song, Xiaoyu; Casa, Raffaele

    2016-04-01

    Precise estimation of carotenoids (Car) content in plants, from remotely sensed data, is challenging due to their small proportion in the overall total pigment content and to the overlapping of spectral absorption features with chlorophyll (Chl) in the blue region of the spectrum. The use of narrow band vegetation indices (VIs) obtained from hyperspectral data has been considered an effective way to estimate Car content. However, VIs have proved to lack sensitivity to low or high Car content in a number of studies. In this study, the carotenoid triangle ratio index (CTRI), derived from the existing modified triangular vegetation index and a single band reflectance at 531 nm, was proposed and employed to estimate Car canopy content. We tested the potential of three categories of hyperspectral indices earlier proposed for Car, Chl, Car/Chl ratio estimation, and the new CTRI index, for Car canopy content assessment in winter wheat and corn. Spectral reflectance representing plant canopies were simulated using the PROSPECT and SAIL radiative transfer model, with the aim of analyzing saturation effects of these indices, as well as Chl effects on the relationship between spectral indices and Car content. The result showed that the majority of the spectral indices tested, saturated with the increase of Car canopy content above 28 to 64 μg/cm2. Conversely, the CTRI index was more robust and was linearly and highly sensitive to Car content in winter wheat and corn datasets, with coefficients of determination of 0.92 and 0.75, respectively. The corresponding root mean square error of prediction were 6.01 and 9.70 μg/cm2, respectively. Furthermore, the CTRI index did not show a saturation effect and was not greatly influenced by changes of Chl values, outperforming all the other indices tested. Estimation of Car canopy content using the CTRI index provides an insight into diagnosing plant physiological status and environmental stress.

  13. Pedotransfer functions to estimate soil water content at field capacity and permanent wilting point in hot Arid Western India

    Science.gov (United States)

    Santra, Priyabrata; Kumar, Mahesh; Kumawat, R. N.; Painuli, D. K.; Hati, K. M.; Heuvelink, G. B. M.; Batjes, N. H.

    2018-04-01

    Characterization of soil water retention, e.g., water content at field capacity (FC) and permanent wilting point (PWP) over a landscape plays a key role in efficient utilization of available scarce water resources in dry land agriculture; however, direct measurement thereof for multiple locations in the field is not always feasible. Therefore, pedotransfer functions (PTFs) were developed to estimate soil water retention at FC and PWP for dryland soils of India. A soil database available for Arid Western India ( N=370) was used to develop PTFs. The developed PTFs were tested in two independent datasets from arid regions of India ( N=36) and an arid region of USA ( N=1789). While testing these PTFs using independent data from India, root mean square error (RMSE) was found to be 2.65 and 1.08 for FC and PWP, respectively, whereas for most of the tested `established' PTFs, the RMSE was >3.41 and >1.15, respectively. Performance of the developed PTFs from the independent dataset from USA was comparable with estimates derived from `established' PTFs. For wide applicability of the developed PTFs, a user-friendly soil moisture calculator was developed. The PTFs developed in this study may be quite useful to farmers for scheduling irrigation water as per soil type.

  14. Experimental estimation of mutation rates in a wheat population with a gene genealogy approach.

    Science.gov (United States)

    Raquin, Anne-Laure; Depaulis, Frantz; Lambert, Amaury; Galic, Nathalie; Brabant, Philippe; Goldringer, Isabelle

    2008-08-01

    Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. Estimates of the mutation rates are therefore necessary when characterizing diversity in populations. As a complement to the classical experimental designs, we propose to use experimental populations, where the initial state is entirely known and some intermediate states have been thoroughly surveyed, thus providing a short timescale estimation together with a large number of cumulated meioses. In this article, we derived four original gene genealogy-based methods to assess mutation rates with limited bias due to relevant model assumptions incorporating the initial state, the number of new alleles, and the genetic effective population size. We studied the evolution of genetic diversity at 21 microsatellite markers, after 15 generations in an experimental wheat population. Compared to the parents, 23 new alleles were found in generation 15 at 9 of the 21 loci studied. We provide evidence that they arose by mutation. Corresponding estimates of the mutation rates ranged from 0 to 4.97 x 10(-3) per generation (i.e., year). Sequences of several alleles revealed that length polymorphism was only due to variation in the core of the microsatellite. Among different microsatellite characteristics, both the motif repeat number and an independent estimation of the Nei diversity were correlated with the novel diversity. Despite a reduced genetic effective size, global diversity at microsatellite markers increased in this population, suggesting that microsatellite diversity should be used with caution as an indicator in biodiversity conservation issues.

  15. Dualism of gene GC content and CpG pattern in regard to expression in the human genome: magnitude versus breadth.

    Science.gov (United States)

    Vinogradov, Alexander E

    2005-12-01

    In this article, I show that, in the human genome, the GC content in genes (but not the CpG island in the promoter) is related to the maximum level of gene expression among tissues, whereas the promoter CpG island and gene CpG level are more strongly related to the breadth of expression among tissues. The relevance of gene GC content to expression cannot be a consequence (i.e. a byproduct) of transcription because it does not correlate with expression in the germline. The variation of GC content and CpG level can determine the characteristics of gene expression in a synergistic interplay with transcription-factor-binding sites (mediated by chromatin condensation).

  16. Estimating the Population Impact of a New Pediatric Influenza Vaccination Program in England Using Social Media Content.

    Science.gov (United States)

    Wagner, Moritz; Lampos, Vasileios; Yom-Tov, Elad; Pebody, Richard; Cox, Ingemar J

    2017-12-21

    The rollout of a new childhood live attenuated influenza vaccine program was launched in England in 2013, which consisted of a national campaign for all 2 and 3 year olds and several pilot locations offering the vaccine to primary school-age children (4-11 years of age) during the influenza season. The 2014/2015 influenza season saw the national program extended to include additional pilot regions, some of which offered the vaccine to secondary school children (11-13 years of age) as well. We utilized social media content to obtain a complementary assessment of the population impact of the programs that were launched in England during the 2013/2014 and 2014/2015 flu seasons. The overall community-wide impact on transmission in pilot areas was estimated for the different age groups that were targeted for vaccination. A previously developed statistical framework was applied, which consisted of a nonlinear regression model that was trained to infer influenza-like illness (ILI) rates from Twitter posts originating in pilot (school-age vaccinated) and control (unvaccinated) areas. The control areas were then used to estimate ILI rates in pilot areas, had the intervention not taken place. These predictions were compared with their corresponding Twitter-based ILI estimates. Results suggest a reduction in ILI rates of 14% (1-25%) and 17% (2-30%) across all ages in only the primary school-age vaccine pilot areas during the 2013/2014 and 2014/2015 influenza seasons, respectively. No significant impact was observed in areas where two age cohorts of secondary school children were vaccinated. These findings corroborate independent assessments from traditional surveillance data, thereby supporting the ongoing rollout of the program to primary school-age children and providing evidence of the value of social media content as an additional syndromic surveillance tool. ©Moritz Wagner, Vasileios Lampos, Elad Yom-Tov, Richard Pebody, Ingemar J Cox. Originally published in the

  17. Towards Estimating Water Stress through Leaf and Canopy Water Content Derived from Optical and Thermal Hyperspectral Data

    Science.gov (United States)

    Corbin, Amie; Timmermans, Joris; van der Tol, Christiaan; Verhoef, Wout

    2015-04-01

    A competition for available (drinkable) water has arisen. This competition originated due to increasing global population and the respective needs of this population. The water demand for human consumption and irrigation of food producing crops and biofuel related vegetation, has led to early indication of drought as a key issue in many studies. However, while drought monitoring systems might provide some reasonable predictions, at the time of visible symptoms of plant stress, a plant may already be critically affected. Consequently, pre-symptomatic non-destructive monitoring of plants is needed. In many studies of plant stress, this is performed by examining internal plant physiology through existing remote sensing techniques, with varying applications. However, a uniform remote sensing method for identifying early plant stress under drought conditions is still developing. In some instances, observations of vegetation water content are used to assess the impact of soil water deficit on the health of a plant or canopy. When considering water content as an indicator of water stress in a plant, this comments not only on the condition of the plant itself, but also provides indicators of photosynthetic activity and the susceptibility to drought. Several indices of canopy health currently exists (NDVI, DVI, SAVI, etc.) using optical and near infrared reflectance bands. However, these are considered inadequate for vegetation health investigations because such semi-empirical models result in less accuracy for canopy measurements. In response, a large amount of research has been conducted to estimate canopy health directly from considering the full spectral behaviour. In these studies , the canopy reflectance has been coupled to leaf parameters, by using coupling leaf radiative transfer models (RTM), such as PROSPECT, to a canopy RTM such as SAIL. The major shortcomings of these researches is that they have been conducted primarily for optical remote sensing. Recently

  18. Characterization of resistance to tetracyclines and aminoglycosides of sheep mastitis pathogens: study of the effect of gene content on resistance.

    Science.gov (United States)

    Lollai, S A; Ziccheddu, M; Duprè, I; Piras, D

    2016-10-01

    Mastitis causes economic losses and antimicrobials are frequently used for mastitis treatment. Antimicrobial resistance surveys are still rare in the ovine field and characterization of strains is important in order to acquire information about resistance and for optimization of therapy. Bacterial pathogens recovered in milk samples from mastitis-affected ewes were characterized for resistance to tetracyclines and aminoglycosides, members of which are frequently used antimicrobials in small ruminants. A total of 185 strains of staphylococci, streptococci, and enterococci, common mastitis pathogens, were tested for minimal inhibitory concentration (MIC) to tetracycline, doxycycline, minocycline, gentamicin, kanamycin, streptomycin, and for resistance genes by PCR. Effects of different tet genes arrangements on MICs were also investigated. Staphylococci expressed the lowest MIC for tetracycline and tet(K) was the most common gene recovered; tet(M) and tet(O) were also found. Gene content was shown to influence the tetracycline MIC values. Enterococci and streptococci showed higher MICs to tetracyclines and nonsusceptible strains always harboured at least one ribosomal protection gene (MIC above 8 μg ml(-1) ). Streptococci often harboured two or more tet determinants. As regards the resistance to aminoglycosides, staphylococci showed the lowest gentamicin and kanamycin median MIC along with streptomycin high level resistant (HLR) strains (MIC >1024 μg ml(-1) ) all harbouring str gene. The resistance determinant aac(6')-Ie-aph(2″)-Ia was present in few strains. Streptococci were basically nonsusceptible to aminoglycosides but neither HLR isolates nor resistance genes were detected. Enterococci revealed the highest MICs for gentamicin; two str harbouring isolates were shown to be HLR to streptomycin. Evidence was obtained for the circulation of antimicrobial-resistant strains and genes in sheep dairy farming. Tetracycline MIC of 64 μg ml(-1) and high

  19. Cow excrements enhance the occurrence of tetracycline resistance genes in soil regardless of their oxytetracycline content

    Czech Academy of Sciences Publication Activity Database

    Kyselková, Martina; Jirout, Jiří; Chroňáková, Alica; Vrchotová, Naděžda; Bradley, R.; Schmitt, H.; Elhottová, Dana

    2013-01-01

    Roč. 93, č. 10 (2013), s. 2413-2418 ISSN 0045-6535 R&D Projects: GA ČR GAP504/10/2077; GA MŠk(CZ) EE2.3.30.0032; GA MŠk(CZ) ED1.1.00/02.0073 Grant - others:OECD(FR) JA00054767 Institutional support: RVO:60077344 ; RVO:67179843 Keywords : cattle excrement * environmental risk assessment * manured soil * oxytetracycline * tetracycline resistance * tetracycline resistance gene Subject RIV: EE - Microbiology, Virology Impact factor: 3.499, year: 2013

  20. The effect of adipocyte and heart fatty acid-binding protein genes on intramuscular fat and backfat content in Meishan crossbred pigs

    NARCIS (Netherlands)

    Gerbens, F.; Koning, de D.J.; Harders, F.L.; Meuwissen, T.H.E.; Groenen, M.A.M.; Veerkamp, R.L.; Arendonk, van J.A.M.; Pas, te M.F.W.

    2000-01-01

    Effects of genetic variation in porcine adipocyte and heart fatty acid-binding protein genes, A-FABP and H-FABP, respectively, on intramuscular fat (IMF) content and backfat thickness (BFT) were examined in F2 crossbreds of Meishan and Western pigs. The involvement of each FABP gene in IMF accretion

  1. Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.

    Science.gov (United States)

    Kadam, Anagha; Janto, Benjamin; Eutsey, Rory; Earl, Joshua P; Powell, Evan; Dahlgren, Margaret E; Hu, Fen Z; Ehrlich, Garth D; Hiller, N Luisa

    2015-02-02

    There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome. Copyright © 2015 John Wiley & Sons, Inc.

  2. The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes

    Science.gov (United States)

    Pantano, Lorena; Jodar, Meritxell; Bak, Mads; Ballescà, Josep Lluís; Tommerup, Niels; Oliva, Rafael; Vavouri, Tanya

    2015-01-01

    At the end of mammalian sperm development, sperm cells expel most of their cytoplasm and dispose of the majority of their RNA. Yet, hundreds of RNA molecules remain in mature sperm. The biological significance of the vast majority of these molecules is unclear. To better understand the processes that generate sperm small RNAs and what roles they may have, we sequenced and characterized the small RNA content of sperm samples from two human fertile individuals. We detected 182 microRNAs, some of which are highly abundant. The most abundant microRNA in sperm is miR-1246 with predicted targets among sperm-specific genes. The most abundant class of small noncoding RNAs in sperm are PIWI-interacting RNAs (piRNAs). Surprisingly, we found that human sperm cells contain piRNAs processed from pseudogenes. Clusters of piRNAs from human testes contain pseudogenes transcribed in the antisense strand and processed into small RNAs. Several human protein-coding genes contain antisense predicted targets of pseudogene-derived piRNAs in the male germline and these piRNAs are still found in mature sperm. Our study provides the most extensive data set and annotation of human sperm small RNAs to date and is a resource for further functional studies on the roles of sperm small RNAs. In addition, we propose that some of the pseudogene-derived human piRNAs may regulate expression of their parent gene in the male germline. PMID:25904136

  3. Multisite Thrombus Imaging and Fibrin Content Estimation With a Single Whole-Body PET Scan in Rats.

    Science.gov (United States)

    Blasi, Francesco; Oliveira, Bruno L; Rietz, Tyson A; Rotile, Nicholas J; Naha, Pratap C; Cormode, David P; Izquierdo-Garcia, David; Catana, Ciprian; Caravan, Peter

    2015-10-01

    Thrombosis is a leading cause of morbidity and mortality worldwide. Current diagnostic strategies rely on imaging modalities that are specific for distinct vascular territories, but a thrombus-specific whole-body imaging approach is still missing. Moreover, imaging techniques to assess thrombus composition are underdeveloped, although therapeutic strategies may benefit from such technology. Therefore, our goal was to test whether positron emission tomography (PET) with the fibrin-binding probe (64)Cu-FBP8 allows multisite thrombus detection and fibrin content estimation. Thrombosis was induced in Sprague-Dawley rats (n=32) by ferric chloride application on both carotid artery and femoral vein. (64)Cu-FBP8-PET/CT imaging was performed 1, 3, or 7 days after thrombosis to detect thrombus location and to evaluate age-dependent changes in target uptake. Ex vivo biodistribution, autoradiography, and histopathology were performed to validate imaging results. Arterial and venous thrombi were localized on fused PET/CT images with high accuracy (97.6%; 95% confidence interval, 92-100). A single whole-body PET/MR imaging session was sufficient to reveal the location of both arterial and venous thrombi after (64)Cu-FBP8 administration. PET imaging showed that probe uptake was greater in younger clots than in older ones for both arterial and venous thrombosis (P<0.0001). Quantitative histopathology revealed an age-dependent reduction of thrombus fibrin content (P<0.001), consistent with PET results. Biodistribution and autoradiography further confirmed the imaging findings. We demonstrated that (64)Cu-FBP8-PET is a feasible approach for whole-body thrombus detection and that molecular imaging of fibrin can provide, noninvasively, insight into clot composition. © 2015 American Heart Association, Inc.

  4. Dead fuel moisture estimation with MSG-SEVIRI data. Retrieval of meteorological data for the calculation of the equilibrium moisture content

    DEFF Research Database (Denmark)

    Nieto Solana, Hector; Sandholt, Inge; Aguado, Inmaculada

    2010-01-01

    In this study we propose to use remote sensing data to estimate hourly meteorological data and then assess the moisture content of dead fuels. Three different models to estimate the equilibrium moisture content (EMC) were applied together with remotely sensed retrieved air temperature and relative...... humidity. The input data were acquired by the Spinning Enhanced Visible and Infrared Imager (SEVIRI) sensor, on board the Meteosat Second Generation (MSG) satellite, from which air temperature and relative humidity were estimated every 15 min. Air temperature estimations are based on the Temperature-Vegetation...... Index (TVX) algorithm. This algorithm exploits the inverse linear relationship between the land surface temperature and the vegetation fractional cover. This relationship was evaluated in a spatial window where the meteorological forcing is assumed to be constant. To estimate the vapour pressure...

  5. The Peanut (Arachis hypogaea L. Gene AhLPAT2 Increases the Lipid Content of Transgenic Arabidopsis Seeds.

    Directory of Open Access Journals (Sweden)

    Silong Chen

    Full Text Available Lysophosphatidic acid acyltransferase (LPAT, which converts lysophosphatidic acid (LPA to phosphatidic acid (PA, catalyzes the addition of fatty acyl moieties to the sn-2 position of the LPA glycerol backbone in triacylglycerol (TAG biosynthesis. We recently reported the cloning and temporal-spatial expression of a peanut (Arachis hypogaea AhLPAT2gene, showing that an increase in AhLPAT2 transcript levels was closely correlated with an increase in seed oil levels. However, the function of the enzyme encoded by the AhLPAT2 gene remains unclear. Here, we report that AhLPAT2 transcript levels were consistently higher in the seeds of a high-oil cultivar than in those of a low-oil cultivar across different seed developmental stages. Seed-specific overexpression of AhLPAT2 in Arabidopsis results in a higher percentage of oil in the seeds and greater-than-average seed weight in the transgenic plants compared with the wild-type plants, leading to a significant increase in total oil yield per plant. The total fatty acid (FA content and the proportion of unsaturated FAs also increased. In the developing siliques of AhLPAT2-overexpressing plants, the expression levels of genes encoding crucial enzymes involved in de novo FA synthesis, acetyl-CoA subunit (AtBCCP2 and acyl carrier protein 1 (AtACP1 were elevated. AhLPAT2 overexpression also promoted the expression of several key genes related to TAG assembly, sucrose metabolism, and glycolysis. These results demonstrate that the expression of AhLPAT2 plays an important role in glycerolipid production in peanuts.

  6. Citrate content of bone for time since death estimation: results from burials with different physical characteristics and known PMI.

    Science.gov (United States)

    Kanz, Fabian; Reiter, Christian; Risser, Daniele U

    2014-05-01

    A recently introduced method to determine the postmortem interval (PMI) based on quantification of the citrate content in bone was applied on the temporal bones and femora of 20 individuals buried in wooden coffins (WO) and body bags (BB), respectively. Concerning known vs. calculated PMI, a significant difference between the temporal and the femur bone samples of the same individuals was observed in the BB group (p = 0.012). In contrast, differences were insignificant for the WO group (p = 0.400). Moreover, similar levels of underestimation of PMIs resulted from the analysis of the femora for both burial groups (p = 0.247). Also, there was consistently less citrate preserved in the flat temporal bones as compared to the femora, indicating that the cortical layer of the long bones should be preferentially employed for citrate-based PMI estimations. The results call for additional research on subsurface-buried and surface-deposited remains to enhance the accuracy of the published PMI equation. © 2014 American Academy of Forensic Sciences.

  7. A polymorphism in the stearoyl-CoA desaturase gene promoter influences monounsaturated fatty acid content of Duroc × Iberian hams

    Energy Technology Data Exchange (ETDEWEB)

    Henriquez-Rodriguez, E.; Tor, M.; Pena, R.N.; Estany, J.

    2015-07-01

    Data on 74 dry-cured hams from Duroc × Iberian pigs were used to examine whether the tag polymorphism AY487830:g.2228T>C in the promoter region of the stearoyl-CoA desaturase [SCD] gene affect fat desaturation and monounsaturated fatty acid (MUFA) as previously described in purebred Duroc hams. Samples were taken from sliced trays of dry-cured hams marketed as Jamón Ibérico de cebo, which were randomly purchased from the same supplier in different stores of the same supermarket chain. Genomic DNA was isolated from each sample to genotype for SCD and gender. Also, a sample of two slices was used to determine fat content and fatty acid (FA) composition by gas chromatography. The effect of the genotype (TT and CT) and gender (barrows and gilts) was estimated under a Bayesian setting. Results showed that the SCD polymorphism was associated to fat composition but not to fat content, with TT hams showing increased C18:1n-7, C18:1n-9, C20:1n-9 and MUFA (probability between 0.92-0.98) and decreased C18:2n-6, C20:4n-6 and polyunsaturated FA (PUFA) (probability between 0.91-0.99) as compared to the CT. As a result, the TT hams had more MUFA (0.95%) and a higher MUFA/PUFA ratio (0.43) than the CT. Barrows had more saturated FA (SFA) and less PUFA than gilts. No differences in MUFA content were found between genders. The SCD polymorphism had a greater impact on MUFA than using hams from barrows instead of gilts. It is concluded that the SCD polymorphism is a good tool to increase MUFA and MUFA/PUFA ratio in Duroc crossbred dry-cured hams. (Author)

  8. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

    DEFF Research Database (Denmark)

    Kaas, Rolf Sommer; Rundsten, Carsten Friis; Ussery, David

    2012-01-01

    Background Escherichia coli exists in commensal and pathogenic forms. By measuring the variation of individual genes across more than a hundred sequenced genomes, gene variation can be studied in detail, including the number of mutations found for any given gene. This knowledge will be useful...... for creating better phylogenies, for determination of molecular clocks and for improved typing techniques. Results We find 3,051 gene clusters/families present in at least 95% of the genomes and 1,702 gene clusters present in 100% of the genomes. The former 'soft core' of about 3,000 gene families is perhaps...... more biologically relevant, especially considering that many of these genome sequences are draft quality. The E. coli pan-genome for this set of isolates contains 16,373 gene clusters. A core-gene tree, based on alignment and a pan-genome tree based on gene presence/absence, maps the relatedness...

  9. Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing.

    Science.gov (United States)

    Zuo, Yu; Xie, Wenfang; Pang, Yue; Li, Tiesong; Li, Qingwei; Li, Yingying

    2017-01-01

    The composition of the bacterial communities in the hindgut contents of Lampetrs japonica was surveyed by Illumina MiSeq of the 16S rRNA gene. An average of 32385 optimized reads was obtained from three samples. The rarefaction curve based on the operational taxonomic units tended to approach the asymptote. The rank abundance curve representing the species richness and evenness was calculated. The composition of microbe in six classification levels was also analyzed. Top 20 members in genera level were displayed as the classification tree. The abundance of microorganisms in different individuals was displayed as the pie charts at the branch nodes in the classification tree. The differences of top 50 genera in abundance between individuals of lamprey are displayed as a heatmap. The pairwise comparison of bacterial taxa abundance revealed that there are no significant differences of gut microbiota between three individuals of lamprey at a given rarefied depth. Also, the gut microbiota derived from L. japonica displays little similarity with other aquatic organism of Vertebrata after UPGMA analysis. The metabolic function of the bacterial communities was predicted through KEGG analysis. This study represents the first analysis of the bacterial community composition in the gut content of L. japonica. The investigation of the gut microbiota associated with L. japonica will broaden our understanding of this unique organism.

  10. Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Yu Zuo

    Full Text Available The composition of the bacterial communities in the hindgut contents of Lampetrs japonica was surveyed by Illumina MiSeq of the 16S rRNA gene. An average of 32385 optimized reads was obtained from three samples. The rarefaction curve based on the operational taxonomic units tended to approach the asymptote. The rank abundance curve representing the species richness and evenness was calculated. The composition of microbe in six classification levels was also analyzed. Top 20 members in genera level were displayed as the classification tree. The abundance of microorganisms in different individuals was displayed as the pie charts at the branch nodes in the classification tree. The differences of top 50 genera in abundance between individuals of lamprey are displayed as a heatmap. The pairwise comparison of bacterial taxa abundance revealed that there are no significant differences of gut microbiota between three individuals of lamprey at a given rarefied depth. Also, the gut microbiota derived from L. japonica displays little similarity with other aquatic organism of Vertebrata after UPGMA analysis. The metabolic function of the bacterial communities was predicted through KEGG analysis. This study represents the first analysis of the bacterial community composition in the gut content of L. japonica. The investigation of the gut microbiota associated with L. japonica will broaden our understanding of this unique organism.

  11. WAVELENGTH SELECTION OF HYPERSPECTRAL LIDAR BASED ON FEATURE WEIGHTING FOR ESTIMATION OF LEAF NITROGEN CONTENT IN RICE

    Directory of Open Access Journals (Sweden)

    L. Du

    2016-06-01

    Full Text Available Hyperspectral LiDAR (HSL is a novel tool in the field of active remote sensing, which has been widely used in many domains because of its advantageous ability of spectrum-gained. Especially in the precise monitoring of nitrogen in green plants, the HSL plays a dispensable role. The exiting HSL system used for nitrogen status monitoring has a multi-channel detector, which can improve the spectral resolution and receiving range, but maybe result in data redundancy, difficulty in system integration and high cost as well. Thus, it is necessary and urgent to pick out the nitrogen-sensitive feature wavelengths among the spectral range. The present study, aiming at solving this problem, assigns a feature weighting to each centre wavelength of HSL system by using matrix coefficient analysis and divergence threshold. The feature weighting is a criterion to amend the centre wavelength of the detector to accommodate different purpose, especially the estimation of leaf nitrogen content (LNC in rice. By this way, the wavelengths high-correlated to the LNC can be ranked in a descending order, which are used to estimate rice LNC sequentially. In this paper, a HSL system which works based on a wide spectrum emission and a 32-channel detector is conducted to collect the reflectance spectra of rice leaf. These spectra collected by HSL cover a range of 538 nm – 910 nm with a resolution of 12 nm. These 32 wavelengths are strong absorbed by chlorophyll in green plant among this range. The relationship between the rice LNC and reflectance-based spectra is modeled using partial least squares (PLS and support vector machines (SVMs based on calibration and validation datasets respectively. The results indicate that I wavelength selection method of HSL based on feature weighting is effective to choose the nitrogen-sensitive wavelengths, which can also be co-adapted with the hardware of HSL system friendly. II The chosen wavelength has a high correlation with rice LNC

  12. In vivo measurements background estimation of low energy trough the anthropometric parameters correlation and with the potassium body content

    International Nuclear Information System (INIS)

    Sousa, Wanderson O.; Dantas, Ana Leticia A.; Dantas, Bernardo M.

    2002-01-01

    The occupational monitoring of individuals with potential risk of incorporation of radionuclides such as Am-241, U-238, U-235 and Ra-226 by inhalation in workplaces where particulates in suspension can be present, is frequently performed by in vivo measurements of the lungs. The activity calculation involves a comparison of the acquired spectrum with a reference spectrum. The accuracy of the background prediction is critical when the expected activities are close to the minimum detection limit. This is the case of occupational monitoring where most of the activities observed are bellow or very close the detection limit. The use of a inappropriate reference spectrum can lead to false-positive or false-negative results. The variability of potassium content among individuals in one of the major factors in the fluctuation of the count rate in the low energy region of the spectrum. This contribution is associated with the Compton effect due to the interaction of 1461 keV photons emitted by K-40. In order to verify the correlation between the background count rate in the various regions of interest of the low energy spectra with the potassium mass in the body it was designed an experimental procedure consisting of measuring a thoracic phantom containing known amounts of potassium. The strong correlation observed motivated the continuity of this work which consisted in the analysis of real low energy in vivo spectra with the aim of verifying the correlation between anthropometric parameters (sex, age, weight and height) and the count rates in the region of K-40 with the count rates in the low energy regions of interest. The results obtained show a significant correlation between the selected parameters with the count rate of the background. This allows a more reliable estimation of activity of low energy radionuclides in individuals monitored through in vivo measurements. The occupational monitoring. (author)

  13. Hunger and thirst numeric rating scales are not valid estimates for gastric content volumes: a prospective investigation in healthy children.

    Science.gov (United States)

    Buehrer, Sabin; Hanke, Ursula; Klaghofer, Richard; Fruehauf, Melanie; Weiss, Markus; Schmitz, Achim

    2014-03-01

    A rating scale for thirst and hunger was evaluated as a noninvasive, simple and commonly available tool to estimate preanesthetic gastric volume, a surrogate parameter for the risk of perioperative pulmonary aspiration, in healthy volunteer school age children. Numeric scales with scores from 0 to 10 combined with smileys to rate thirst and hunger were analyzed and compared with residual gastric volumes as measured by magnetic resonance imaging and fasting times in three settings: before and for 2 h after drinking clear fluid (group A, 7 ml/kg), before and for 4 vs 6 h after a light breakfast followed by clear fluid (7 ml/kg) after 2 vs 4 h (crossover, group B), and before and for 1 h after drinking clear fluid (crossover, group C, 7 vs 3 ml/kg). In 30 children aged 6.4-12.8 (median 9.8) years, participating on 1-5 (median two) study days, 496 sets of scores and gastric volumes were determined. Large inter- and intra-individual variations were seen at baseline and in response to fluid and food intake. Significant correlations were found between hunger and thirst ratings in all groups, with children generally being more hungry than thirsty. Correlations between scores and duration of fasting or gastric residual volumes were poor to moderate. Receiver operating characteristic (ROC) analysis revealed that thirst and hunger rating scales cannot predict gastric content. Hunger and thirst scores vary considerably inter- and intra-individually and cannot predict gastric volume, nor do they correlate with fasting times in school age children. © 2013 John Wiley & Sons Ltd.

  14. Estimating and Up-Scaling Fuel Moisture and Leaf Dry Matter Content of a Temperate Humid Forest Using Multi Resolution Remote Sensing Data

    Directory of Open Access Journals (Sweden)

    Hamed Adab

    2016-11-01

    Full Text Available Vegetation moisture and dry matter content are important indicators in predicting the behavior of fire and it is widely used in fire spread models. In this study, leaf fuel moisture content such as Live Fuel Moisture Content (LFMC, Leaf Relative Water Content (RWC, Dead Fuel Moisture Content (DFMC, and Leaf Dry Matter Content (LDMC (hereinafter known as moisture content indices (MCI were calculated in the field for different forest species at 32 sites in a temperate humid forest (Zaringol forest located in northeastern Iran. These data and several relevant vegetation-biophysical indices and atmospheric variables calculated using Landsat 7 Enhanced Thematic Mapper Plus (ETM+ data with moderate spatial resolution (30 m were used to estimate MCI of the Zaringol forest using Artificial Neural Network (ANN and Multiple Linear Regression (MLR methods. The prediction of MCI using ANN showed that ETM+ predicted MCI slightly better (Mean Absolute Percentage Error (MAPE of 6%–12% than MLR (MAPE between 8% and 17%. Once satisfactory results in estimating MCI were obtained by using ANN from ETM+ data, these data were then upscaled to estimate MCI using MODIS data for daily monitoring of leaf water and leaf dry matter content at 500 m spatial resolution. For MODIS derived LFMC, LDMC, RWC, and DLMC, the ANN produced a MAPE between 11% and 29% for the indices compared to MLR which produced an MAPE of 14%–33%. In conclusion, we suggest that upscaling is necessary for solving the scale discrepancy problems between the indicators and low spatial resolution MODIS data. The scaling up of MCI could be used for pre-fire alert system and thereby can detect fire prone areas in near real time for fire-fighting operations.

  15. Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study.

    Science.gov (United States)

    Fan, Ming; Kuwahara, Hiroyuki; Wang, Xiaolei; Wang, Suojin; Gao, Xin

    2015-11-01

    Parameter estimation is a challenging computational problem in the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter estimation of gene circuit models from such time-series mRNA data has become an important method for quantitatively dissecting the regulation of gene expression. By focusing on the modeling of gene circuits, we examine here the performance of three types of state-of-the-art parameter estimation methods: population-based methods, online methods and model-decomposition-based methods. Our results show that certain population-based methods are able to generate high-quality parameter solutions. The performance of these methods, however, is heavily dependent on the size of the parameter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, online methods and model decomposition-based methods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fast methods with local search as a subsequent refinement procedure can substantially increase the quality of their parameter estimates to the level on par with the best solution obtained from the population-based methods while maintaining high computational speed. These suggest that such hybrid methods can be a promising alternative to the more commonly used population-based methods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatory mechanisms makes the size of the parameter search space vastly large. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  16. Over-expression of a tobacco nitrate reductase gene in wheat (Triticum aestivum L. increases seed protein content and weight without augmenting nitrogen supplying.

    Directory of Open Access Journals (Sweden)

    Xiao-Qiang Zhao

    Full Text Available Heavy nitrogen (N application to gain higher yield of wheat (Triticum aestivum L. resulted in increased production cost and environment pollution. How to diminish the N supply without losing yield and/or quality remains a challenge. To meet the challenge, we integrated and expressed a tobacco nitrate reductase gene (NR in transgenic wheat. The 35S-NR gene was transferred into two winter cultivars, "Nongda146" and "Jimai6358", by Agrobacterium-mediation. Over-expression of the transgene remarkably enhanced T1 foliar NR activity and significantly augmented T2 seed protein content and 1000-grain weight in 63.8% and 68.1% of T1 offspring (total 67 individuals analyzed, respectively. Our results suggest that constitutive expression of foreign nitrate reductase gene(s in wheat might improve nitrogen use efficiency and thus make it possible to increase seed protein content and weight without augmenting N supplying.

  17. Over-expression of a tobacco nitrate reductase gene in wheat (Triticum aestivum L.) increases seed protein content and weight without augmenting nitrogen supplying.

    Science.gov (United States)

    Zhao, Xiao-Qiang; Nie, Xuan-Li; Xiao, Xing-Guo

    2013-01-01

    Heavy nitrogen (N) application to gain higher yield of wheat (Triticum aestivum L.) resulted in increased production cost and environment pollution. How to diminish the N supply without losing yield and/or quality remains a challenge. To meet the challenge, we integrated and expressed a tobacco nitrate reductase gene (NR) in transgenic wheat. The 35S-NR gene was transferred into two winter cultivars, "Nongda146" and "Jimai6358", by Agrobacterium-mediation. Over-expression of the transgene remarkably enhanced T1 foliar NR activity and significantly augmented T2 seed protein content and 1000-grain weight in 63.8% and 68.1% of T1 offspring (total 67 individuals analyzed), respectively. Our results suggest that constitutive expression of foreign nitrate reductase gene(s) in wheat might improve nitrogen use efficiency and thus make it possible to increase seed protein content and weight without augmenting N supplying.

  18. Methodologies on estimating the energy requirements for maintenance and determining the net energy contents of feed ingredients in swine: a review of recent work.

    Science.gov (United States)

    Li, Zhongchao; Liu, Hu; Li, Yakui; Lv, Zhiqian; Liu, Ling; Lai, Changhua; Wang, Junjun; Wang, Fenglai; Li, Defa; Zhang, Shuai

    2018-01-01

    In the past two decades, a considerable amount of research has focused on the determination of the digestible (DE) and metabolizable energy (ME) contents of feed ingredients fed to swine. Compared with the DE and ME systems, the net energy (NE) system is assumed to be the most accurate estimate of the energy actually available to the animal. However, published data pertaining to the measured NE content of ingredients fed to growing pigs are limited. Therefore, the Feed Data Group at the Ministry of Agricultural Feed Industry Centre (MAFIC) located at China Agricultural University has evaluated the NE content of many ingredients using indirect calorimetry. The present review summarizes the NE research works conducted at MAFIC and compares these results with those from other research groups on methodological aspect. These research projects mainly focus on estimating the energy requirements for maintenance and its impact on the determination, prediction, and validation of the NE content of several ingredients fed to swine. The estimation of maintenance energy is affected by methodology, growth stage, and previous feeding level. The fasting heat production method and the curvilinear regression method were used in MAFIC to estimate the NE requirement for maintenance. The NE contents of different feedstuffs were determined using indirect calorimetry through standard experimental procedure in MAFIC. Previously generated NE equations can also be used to predict NE in situations where calorimeters are not available. Although popular, the caloric efficiency is not a generally accepted method to validate the energy content of individual feedstuffs. In the future, more accurate and dynamic NE prediction equations aiming at specific ingredients should be established, and more practical validation approaches need to be developed.

  19. Enrichment of provitamin A content in wheat (Triticum aestivum L.) by introduction of the bacterial carotenoid biosynthetic genes CrtB and CrtI.

    Science.gov (United States)

    Wang, Cheng; Zeng, Jian; Li, Yin; Hu, Wei; Chen, Ling; Miao, Yingjie; Deng, Pengyi; Yuan, Cuihong; Ma, Cheng; Chen, Xi; Zang, Mingli; Wang, Qiong; Li, Kexiu; Chang, Junli; Wang, Yuesheng; Yang, Guangxiao; He, Guangyuan

    2014-06-01

    Carotenoid content is a primary determinant of wheat nutritional value and affects its end-use quality. Wheat grains contain very low carotenoid levels and trace amounts of provitamin A content. In order to enrich the carotenoid content in wheat grains, the bacterial phytoene synthase gene (CrtB) and carotene desaturase gene (CrtI) were transformed into the common wheat cultivar Bobwhite. Expression of CrtB or CrtI alone slightly increased the carotenoid content in the grains of transgenic wheat, while co-expression of both genes resulted in a darker red/yellow grain phenotype, accompanied by a total carotenoid content increase of approximately 8-fold achieving 4.76 μg g(-1) of seed dry weight, a β-carotene increase of 65-fold to 3.21 μg g(-1) of seed dry weight, and a provitamin A content (sum of α-carotene, β-carotene, and β-cryptoxanthin) increase of 76-fold to 3.82 μg g(-1) of seed dry weight. The high provitamin A content in the transgenic wheat was stably inherited over four generations. Quantitative PCR analysis revealed that enhancement of provitamin A content in transgenic wheat was also a result of the highly coordinated regulation of endogenous carotenoid biosynthetic genes, suggesting a metabolic feedback regulation in the wheat carotenoid biosynthetic pathway. These transgenic wheat lines are not only valuable for breeding wheat varieties with nutritional benefits for human health but also for understanding the mechanism regulating carotenoid biosynthesis in wheat endosperm. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  20. Normalization and gene p-value estimation: issues in microarray data processing.

    Science.gov (United States)

    Fundel, Katrin; Küffner, Robert; Aigner, Thomas; Zimmer, Ralf

    2008-05-28

    Numerous methods exist for basic processing, e.g. normalization, of microarray gene expression data. These methods have an important effect on the final analysis outcome. Therefore, it is crucial to select methods appropriate for a given dataset in order to assure the validity and reliability of expression data analysis. Furthermore, biological interpretation requires expression values for genes, which are often represented by several spots or probe sets on a microarray. How to best integrate spot/probe set values into gene values has so far been a somewhat neglected problem. We present a case study comparing different between-array normalization methods with respect to the identification of differentially expressed genes. Our results show that it is feasible and necessary to use prior knowledge on gene expression measurements to select an adequate normalization method for the given data. Furthermore, we provide evidence that combining spot/probe set p-values into gene p-values for detecting differentially expressed genes has advantages compared to combining expression values for spots/probe sets into gene expression values. The comparison of different methods suggests to use Stouffer's method for this purpose. The study has been conducted on gene expression experiments investigating human joint cartilage samples of osteoarthritis related groups: a cDNA microarray (83 samples, four groups) and an Affymetrix (26 samples, two groups) data set. The apparently straight forward steps of gene expression data analysis, e.g. between-array normalization and detection of differentially regulated genes, can be accomplished by numerous different methods. We analyzed multiple methods and the possible effects and thereby demonstrate the importance of the single decisions taken during data processing. We give guidelines for evaluating normalization outcomes. An overview of these effects via appropriate measures and plots compared to prior knowledge is essential for the biological

  1. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.

    Science.gov (United States)

    Han, Mira V; Thomas, Gregg W C; Lugo-Martinez, Jose; Hahn, Matthew W

    2013-08-01

    Current sequencing methods produce large amounts of data, but genome assemblies constructed from these data are often fragmented and incomplete. Incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. This means that methods attempting to estimate rates of gene duplication and loss often will be misled by such errors and that rates of gene family evolution will be consistently overestimated. Here, we present a method that takes these errors into account, allowing one to accurately infer rates of gene gain and loss among genomes even with low assembly and annotation quality. The method is implemented in the newest version of the software package CAFE, along with several other novel features. We demonstrate the accuracy of the method with extensive simulations and reanalyze several previously published data sets. Our results show that errors in genome annotation do lead to higher inferred rates of gene gain and loss but that CAFE 3 sufficiently accounts for these errors to provide accurate estimates of important evolutionary parameters.

  2. Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study

    KAUST Repository

    Fan, M.

    2015-03-29

    Parameter estimation is a challenging computational problemin the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter esti- mation of gene circuitmodels fromsuch time-series mRNA data has become an importantmethod for quantitatively dissecting the regulation of gene expression. By focusing on themodeling of gene circuits, we examine here the perform- ance of three types of state-of-the-art parameter estimation methods: population-basedmethods, onlinemethods and model-decomposition-basedmethods. Our results show that certain population-basedmethods are able to generate high- quality parameter solutions. The performance of thesemethods, however, is heavily dependent on the size of the param- eter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, onlinemethods andmodel decomposition-basedmethods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fastmethods with local search as a subsequent refinement procedure can substantially increase the qual- ity of their parameter estimates to the level on par with the best solution obtained fromthe population-basedmethods whilemaintaining high computational speed. These suggest that such hybridmethods can be a promising alternative to themore commonly used population-basedmethods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatorymechanismsmakes the size of the parameter search space vastly large. © The Author 2015. Published by Oxford University Press.

  3. Comparison of protoporphyrin IX content and related gene expression in the tissues of chickens laying brown-shelled eggs.

    Science.gov (United States)

    Li, Guangqi; Chen, Sirui; Duan, Zhongyi; Qu, Lujiang; Xu, Guiyun; Yang, Ning

    2013-12-01

    Protoporphyrin IX (PpIX), an immediate precursor of heme, is the main pigment resulting in the brown coloration of eggshell. The brownness and uniformity of the eggshell are important marketing considerations. In this study, 9 chickens laying darker brown shelled eggs and 9 chickens laying lighter brown shelled eggs were selected from 464 individually caged layers in a Rhode Island Red pureline. The PpIX contents were measured with a Microplate Reader at the wavelength of 412 nm and were compared in different tissues of the 2 groups. Although no significant difference in serum, bile, and excreta was found between the 2 groups, PpIX content in the shell gland and eggshell of the darker group was higher than in those of the lighter group, suggesting that PpIX was synthesized in the shell gland. We further determined the expression levels of 8 genes encoding enzymes involved in the heme synthesis and transport in the liver and shell gland at 6 h postoviposition by quantitative PCR. The results showed that expression of aminolevulinic acid synthase-1 (ALAS1) was higher in the liver of hens laying darker brown shelled eggs, whereas in the shell gland the expression levels of ALAS1, coproporphyrinogen oxidase (CPOX), ATP-binding cassette family members ABCB7 and ABCG2, and receptor for feline leukemia virus, subgroup C (FLVCR) were significantly higher in the hens laying darker brown shelled eggs. Our results demonstrated that hens laying darker brown shelled eggs could deposit more PpIX onto the eggshell and the brownness of the eggshell was dependent on the total quantity of PpIX in the eggshell. More heme was synthesized in the liver and shell gland of hens laying darker brown shelled eggs than those of hens laying lighter brown shelled eggs. High expression level of ABCG2 might facilitate the accumulation of PpIX in the shell gland.

  4. Overexpressing Exogenous 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS Genes Increases Fecundity and Auxin Content of Transgenic Arabidopsis Plants

    Directory of Open Access Journals (Sweden)

    Jia Fang

    2018-02-01

    Full Text Available Transgenic glyphosate-tolerant plants overproducing EPSPS (5-enolpyruvylshikimate-3-phosphate synthase may exhibit enhanced fitness in glyphosate-free environments. If so, introgression of transgenes overexpressing EPSPS into wild relative species may lead to increased competitiveness of crop-wild hybrids, resulting in unpredicted environmental impact. Assessing fitness effects of transgenes overexpressing EPSPS in a model plant species can help address this question, while elucidating how overproducing EPSPS affects the fitness-related traits of plants. We produced segregating T2 and T3Arabidopsis thaliana lineages with or without a transgene overexpressing EPSPS isolated from rice or Agrobacterium (CP4. For each of the three transgenes, we compared glyphosate tolerance, some fitness-related traits, and auxin (indole-3-acetic acid content in transgene-present, transgene-absent, empty vector (EV, and parental lineages in a common-garden experiment. We detected substantially increased glyphosate tolerance in T2 plants of transgene-present lineages that overproduced EPSPS. We also documented significant increases in fecundity, which was associated with increased auxin content in T3 transgene-present lineages containing rice EPSPS genes, compared with their segregating transgene-absent lineages, EV, and parental controls. Our results from Arabidopsis with nine transgenic events provide a strong support to the hypothesis that transgenic plants overproducing EPSPS can benefit from a fecundity advantage in glyphosate-free environments. Stimulated biosynthesis of auxin, an important plant growth hormone, by overproducing EPSPS may play a role in enhanced fecundity of the transgenic Arabidopsis plants. The obtained knowledge is useful for assessing environmental impact caused by introgression of transgenes overproducing EPSPS from any GE crop into populations of its wild relatives.

  5. Overexpressing Exogenous 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS) Genes Increases Fecundity and Auxin Content of Transgenic Arabidopsis Plants.

    Science.gov (United States)

    Fang, Jia; Nan, Peng; Gu, Zongying; Ge, Xiaochun; Feng, Yu-Qi; Lu, Bao-Rong

    2018-01-01

    Transgenic glyphosate-tolerant plants overproducing EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) may exhibit enhanced fitness in glyphosate-free environments. If so, introgression of transgenes overexpressing EPSPS into wild relative species may lead to increased competitiveness of crop-wild hybrids, resulting in unpredicted environmental impact. Assessing fitness effects of transgenes overexpressing EPSPS in a model plant species can help address this question, while elucidating how overproducing EPSPS affects the fitness-related traits of plants. We produced segregating T 2 and T 3 Arabidopsis thaliana lineages with or without a transgene overexpressing EPSPS isolated from rice or Agrobacterium ( CP4 ). For each of the three transgenes, we compared glyphosate tolerance, some fitness-related traits, and auxin (indole-3-acetic acid) content in transgene-present, transgene-absent, empty vector (EV), and parental lineages in a common-garden experiment. We detected substantially increased glyphosate tolerance in T 2 plants of transgene-present lineages that overproduced EPSPS. We also documented significant increases in fecundity, which was associated with increased auxin content in T 3 transgene-present lineages containing rice EPSPS genes, compared with their segregating transgene-absent lineages, EV, and parental controls. Our results from Arabidopsis with nine transgenic events provide a strong support to the hypothesis that transgenic plants overproducing EPSPS can benefit from a fecundity advantage in glyphosate-free environments. Stimulated biosynthesis of auxin, an important plant growth hormone, by overproducing EPSPS may play a role in enhanced fecundity of the transgenic Arabidopsis plants. The obtained knowledge is useful for assessing environmental impact caused by introgression of transgenes overproducing EPSPS from any GE crop into populations of its wild relatives.

  6. Regulation of FA and TAG biosynthesis pathway genes in endosperms and embryos of high and low oil content genotypes of Jatropha curcas L.

    Science.gov (United States)

    Sood, Archit; Chauhan, Rajinder Singh

    2015-09-01

    The rising demand for biofuels has raised concerns about selecting alternate and promising renewable energy crops which do not compete with food supply. Jatropha (Jatropha curcas L.), a non-edible energy crop of the family euphorbiaceae, has the potential of providing biodiesel feedstock due to the presence of high proportion of unsaturated fatty acids (75%) in seed oil which is mainly accumulated in endosperm and embryo. The molecular basis of seed oil biosynthesis machinery has been studied in J. curcas, however, what genetic differences contribute to differential oil biosynthesis and accumulation in genotypes varying for oil content is poorly understood. We investigated expression profile of 18 FA and TAG biosynthetic pathway genes in different developmental stages of embryo and endosperm from high (42%) and low (30%) oil content genotypes grown at two geographical locations. Most of the genes showed relatively higher expression in endosperms of high oil content genotype, whereas no significant difference was observed in endosperms versus embryos of low oil content genotype. The promoter regions of key genes from FA and TAG biosynthetic pathways as well as other genes implicated in oil accumulation were analyzed for regulatory elements and transcription factors specific to oil or lipid accumulation in plants such as Dof, CBF (LEC1), SORLIP, GATA and Skn-1_motif etc. Identification of key genes from oil biosynthesis and regulatory elements specific to oil deposition will be useful not only in dissecting the molecular basis of high oil content but also improving seed oil content through transgenic or molecular breeding approaches. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  7. Estimating immunoregulatory gene networks in human herpesvirus type 6-infected T cells

    International Nuclear Information System (INIS)

    Takaku, Tomoiku; Ohyashiki, Junko H.; Zhang, Yu; Ohyashiki, Kazuma

    2005-01-01

    The immune response to viral infection involves complex network of dynamic gene and protein interactions. We present here the dynamic gene network of the host immune response during human herpesvirus type 6 (HHV-6) infection in an adult T-cell leukemia cell line. Using a pathway-focused oligonucleotide DNA microarray, we found a possible association between chemokine genes regulating Th1/Th2 balance and genes regulating T-cell proliferation during HHV-6B infection. Gene network analysis using an integrated comprehensive workbench, VoyaGene, revealed that a gene encoding a TEC-family kinase, ITK, might be a putative modulator in the host immune response against HHV-6B infection. We conclude that Th2-dominated inflammatory reaction in host cells may play an important role in HHV-6B-infected T cells, thereby suggesting the possibility that ITK might be a therapeutic target in diseases related to dysregulation of Th1/Th2 balance. This study describes a novel approach to find genes related with the complex host-virus interaction using microarray data employing the Bayesian statistical framework

  8. Coupled land surface-subsurface hydrogeophysical inverse modeling to estimate soil organic carbon content and explore associated hydrological and thermal dynamics in the Arctic tundra

    Science.gov (United States)

    Phuong Tran, Anh; Dafflon, Baptiste; Hubbard, Susan S.

    2017-09-01

    Quantitative characterization of soil organic carbon (OC) content is essential due to its significant impacts on surface-subsurface hydrological-thermal processes and microbial decomposition of OC, which both in turn are important for predicting carbon-climate feedbacks. While such quantification is particularly important in the vulnerable organic-rich Arctic region, it is challenging to achieve due to the general limitations of conventional core sampling and analysis methods, and to the extremely dynamic nature of hydrological-thermal processes associated with annual freeze-thaw events. In this study, we develop and test an inversion scheme that can flexibly use single or multiple datasets - including soil liquid water content, temperature and electrical resistivity tomography (ERT) data - to estimate the vertical distribution of OC content. Our approach relies on the fact that OC content strongly influences soil hydrological-thermal parameters and, therefore, indirectly controls the spatiotemporal dynamics of soil liquid water content, temperature and their correlated electrical resistivity. We employ the Community Land Model to simulate nonisothermal surface-subsurface hydrological dynamics from the bedrock to the top of canopy, with consideration of land surface processes (e.g., solar radiation balance, evapotranspiration, snow accumulation and melting) and ice-liquid water phase transitions. For inversion, we combine a deterministic and an adaptive Markov chain Monte Carlo (MCMC) optimization algorithm to estimate a posteriori distributions of desired model parameters. For hydrological-thermal-to-geophysical variable transformation, the simulated subsurface temperature, liquid water content and ice content are explicitly linked to soil electrical resistivity via petrophysical and geophysical models. We validate the developed scheme using different numerical experiments and evaluate the influence of measurement errors and benefit of joint inversion on the

  9. Coupled land surface–subsurface hydrogeophysical inverse modeling to estimate soil organic carbon content and explore associated hydrological and thermal dynamics in the Arctic tundra

    Directory of Open Access Journals (Sweden)

    A. P. Tran

    2017-09-01

    Full Text Available Quantitative characterization of soil organic carbon (OC content is essential due to its significant impacts on surface–subsurface hydrological–thermal processes and microbial decomposition of OC, which both in turn are important for predicting carbon–climate feedbacks. While such quantification is particularly important in the vulnerable organic-rich Arctic region, it is challenging to achieve due to the general limitations of conventional core sampling and analysis methods, and to the extremely dynamic nature of hydrological–thermal processes associated with annual freeze–thaw events. In this study, we develop and test an inversion scheme that can flexibly use single or multiple datasets – including soil liquid water content, temperature and electrical resistivity tomography (ERT data – to estimate the vertical distribution of OC content. Our approach relies on the fact that OC content strongly influences soil hydrological–thermal parameters and, therefore, indirectly controls the spatiotemporal dynamics of soil liquid water content, temperature and their correlated electrical resistivity. We employ the Community Land Model to simulate nonisothermal surface–subsurface hydrological dynamics from the bedrock to the top of canopy, with consideration of land surface processes (e.g., solar radiation balance, evapotranspiration, snow accumulation and melting and ice–liquid water phase transitions. For inversion, we combine a deterministic and an adaptive Markov chain Monte Carlo (MCMC optimization algorithm to estimate a posteriori distributions of desired model parameters. For hydrological–thermal-to-geophysical variable transformation, the simulated subsurface temperature, liquid water content and ice content are explicitly linked to soil electrical resistivity via petrophysical and geophysical models. We validate the developed scheme using different numerical experiments and evaluate the influence of measurement errors and

  10. Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.).

    Science.gov (United States)

    Campbell, Raymond; Pont, Simon D A; Morris, Jenny A; McKenzie, Gaynor; Sharma, Sanjeev Kumar; Hedley, Pete E; Ramsay, Gavin; Bryan, Glenn J; Taylor, Mark A

    2014-09-01

    Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9. The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient 'genetical genomics' analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.

  11. Overexpression of Arachis hypogaea AREB1 Gene Enhances Drought Tolerance by Modulating ROS Scavenging and Maintaining Endogenous ABA Content

    Directory of Open Access Journals (Sweden)

    Ling Li

    2013-06-01

    Full Text Available AhAREB1 (Arachis hypogaea Abscisic-acid Response Element Binding Protein 1 is a member of the basic domain leucine zipper (bZIP-type transcription factor in peanut. Previously, we found that expression of AhAREB1 was specifically induced by abscisic acid (ABA, dehydration and drought. To understand the drought defense mechanism regulated by AhAREB1, transgenic Arabidopsis overexpressing AhAREB1 was conducted in wild-type (WT, and a complementation experiment was employed to ABA non-sensitivity mutant abi5 (abscisic acid-insensitive 5. Constitutive expression of AhAREB1 confers water stress tolerance and is highly sensitive to exogenous ABA. Microarray and further real-time PCR analysis revealed that drought stress, reactive oxygen species (ROS scavenging, ABA synthesis/metabolism-related genes and others were regulated in transgenic Arabidopsis overexpressing AhAREB1. Accordingly, low level of ROS, but higher ABA content was detected in the transgenic Arabidopsis plants’ overexpression of AhAREB1. Taken together, it was concluded that AhAREB1 modulates ROS accumulation and endogenous ABA level to improve drought tolerance in transgenic Arabidopsis.

  12. Estimation of the radionuclide content and radionuclide behaviour and the state of the wild nature in the Chernobyl' PNN region

    International Nuclear Information System (INIS)

    Martoshov, V.Z.; Smirnov, E.G.; Suvorova, L.N.; Tarasova, O.V.; Bogatova, L.V.; Torkhova, N.Yu.

    1992-01-01

    As a result radioactive isotope decay an isotope relation in the threw-out radioactive substance changes and to 1991 year is such that: strontium-90, ruthenium-106, Cs-137, cerium-144, plutonium-238,-239,-240; americium-231. Next years the dose commitments will be formed from Sr-90, Cs-137, Pu-239, Am-241. In soils of the thirty kilometer zone the content of the watersoluble Cs-137 do not change with time (0.1-1.0% from the radionuclide content in the soil. The watersoluble form content of Sr-90 is above, than of CS-137, 0.2-1.8%). Six-year investigations in the thirty kilometer, zone show that the Cs-137 concentration in the animal organisms is not changed. In relation to the previous trophic level Cs-137 accumulates in organisms of amphibians, reptiles and predatory mammals and don't in the herbivorous animal organism

  13. Estimate of the melanin content in human hairs by the inverse Monte-Carlo method using a system for digital image analysis

    International Nuclear Information System (INIS)

    Bashkatov, A N; Genina, Elina A; Kochubei, V I; Tuchin, Valerii V

    2006-01-01

    Based on the digital image analysis and inverse Monte-Carlo method, the proximate analysis method is deve-loped and the optical properties of hairs of different types are estimated in three spectral ranges corresponding to three colour components. The scattering and absorption properties of hairs are separated for the first time by using the inverse Monte-Carlo method. The content of different types of melanin in hairs is estimated from the absorption coefficient. It is shown that the dominating type of melanin in dark hairs is eumelanin, whereas in light hairs pheomelanin dominates. (special issue devoted to multiple radiation scattering in random media)

  14. Expression of phytoene synthase1 and carotene desaturase crtI genes result in an increase in the total carotenoids content in transgenic elite wheat (Triticum aestivum L.).

    Science.gov (United States)

    Cong, Ling; Wang, Cheng; Chen, Ling; Liu, Huijuan; Yang, Guangxiao; He, Guangyuan

    2009-09-23

    Dietary micronutrient deficiencies, such as the lack of vitamin A, are a major source of morbidity and mortality worldwide. Carotenoids in food can function as provitamin A in humans, while grains of Chinese elite wheat cultivars generally have low carotenoid contents. To increase the carotenoid contents in common wheat endosperm, transgenic wheat has been generated by expressing the maize y1 gene encoding phytoene synthase driven by a endosperm-specific 1Dx5 promoter in the elite wheat (Triticum aestivum L.) variety EM12, together with the bacterial phytoene desaturase crtI gene from Erwinia uredovora under the constitutive CaMV 35S promoter control. A clear increase of the carotenoid content was detected in the endosperms of transgenic wheat that visually showed a light yellow color. The total carotenoids content was increased up to 10.8-fold as compared with the nontransgenic EM12 cultivar. To test whether the variability of total carotenoid content in different transgenic lines was due to differences in the transgene copy number or expression pattern, Southern hybridization and semiquantitative reverse transcriptase polymerase chain reaction analyses were curried out. The results showed that transgene copy numbers and transcript levels did not associate well with carotenoid contents. The expression patterns of endogenous carotenoid genes, such as the phytoene synthases and carotene desaturases, were also investigated in wild-type and transgenic wheat lines. No significant changes in expression levels of these genes were detected in the transgenic endosperms, indicating that the increase in carotenoid transgenic wheat endosperms resulted from the expression of transgenes.

  15. Intraspecies differences in cold hardiness, carbohydrate content and β-amylase gene expression of Vaccinium corymbosum during cold acclimation and deacclimation.

    Science.gov (United States)

    Lee, Jun Hyung; Yu, Duk Jun; Kim, Su Jin; Choi, Doil; Lee, Hee Jae

    2012-12-01

    Changes in cold hardiness, carbohydrate content and β-amylase gene expression were monitored in the shoots of the highbush blueberry (Vaccinium corymbosum L.) cultivars 'Sharpblue' and 'Jersey' during cold acclimation (CA) and deacclimation (DA). The seasonal patterns were similar in both cultivars, but the levels of cold hardiness determined by electrolyte leakage analysis were significantly different; 'Jersey' was hardier than 'Sharpblue'. Cold hardiness was closely related to total soluble sugar content (r = -0.98** and -0.99** for 'Sharpblue' and 'Jersey', respectively). In 'Jersey', more soluble sugars accumulated during CA. Of the detected soluble sugars, glucose, fructose and raffinose contents were significantly associated with cold hardiness in both cultivars. Sucrose was abundant in both cultivars, and stachyose content changed significantly during CA and DA. However, they were not associated with cold hardiness. A sharp decrease in starch contents in the middle of CA coincided with β-amylase gene (VcBMY) expression, indicating the conversion of starch into soluble sugars. During CA, VcBMY was expressed up to twofold higher in 'Jersey' than in 'Sharpblue'. These results suggest that intraspecies differences in the cold hardiness of highbush blueberries are associated with total soluble sugar content, which is driven partly by differential expression of VcBMY.

  16. Estimating genetic effect sizes under joint disease-endophenotype models in presence of gene-environment interactions

    Directory of Open Access Journals (Sweden)

    Alexandre eBureau

    2015-07-01

    Full Text Available Effects of genetic variants on the risk of complex diseases estimated from association studies are typically small. Nonetheless, variants may have important effects in presence of specific levels of environmental exposures, and when a trait related to the disease (endophenotype is either normal or impaired. We propose polytomous and transition models to represent the relationship between disease, endophenotype, genotype and environmental exposure in family studies. Model coefficients were estimated using generalized estimating equations and were used to derive gene-environment interaction effects and genotype effects at specific levels of exposure. In a simulation study, estimates of the effect of a genetic variant were substantially higher when both an endophenotype and an environmental exposure modifying the variant effect were taken into account, particularly under transition models, compared to the alternative of ignoring the endophenotype. Illustration of the proposed modeling with the metabolic syndrome, abdominal obesity, physical activity and polymorphisms in the NOX3 gene in the Quebec Family Study revealed that the positive association of the A allele of rs1375713 with the metabolic syndrome at high levels of physical activity was only detectable in subjects without abdominal obesity, illustrating the importance of taking into account the abdominal obesity endophenotype in this analysis.

  17. Estimating respiration of roots in soil: interactions with soil CO2, soil temperature and soil water content

    NARCIS (Netherlands)

    Bouma, T.J.; Nielsen, K.F.; Eissenstat, D.M.; Lynch, J.P.

    1997-01-01

    Little information is available on the variability of the dynamics of the actual and observed root respiration rate in relation to abiotic factors. In this study, we describe I) interactions between soil CO2 concentration, temperature, soil water content and root respiration, and II) the effect of

  18. Pedotransfer functions to estimate soil water content at field capacity and permanent wilting point in hot arid western India

    NARCIS (Netherlands)

    Santra, P.; Kumar, M.; Kumawat, R.N.; Painuli, D.K.; Hati, K.M.; Heuvelink, G.B.M.; Batjes, N.H.

    2018-01-01

    Characterization of soil water retention, e.g., water content at field capacity (FC) and permanent wilting point (PWP) over a landscape plays a key role in efficient utilization of available scarce water resources in dry land agriculture; however, direct measurement thereof for multiple locations in

  19. Flow cytometric and microscopic analysis of the effect of tannic acid on plant nuclei and estimation of DNA content

    Czech Academy of Sciences Publication Activity Database

    Loureiro, J.; Rodriguez, E.; Doležel, Jaroslav; Santos, C.

    2006-01-01

    Roč. 98, - (2006), s. 515-527 ISSN 0305-7364 R&D Projects: GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : genome size * flow cytometry * nuclear DNA content Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.448, year: 2006

  20. Integrating multiple vegetation indices via an artificial neural network model for estimating the leaf chlorophyll content of Spartina alterniflora under interspecies competition.

    Science.gov (United States)

    Liu, Pudong; Shi, Runhe; Zhang, Chao; Zeng, Yuyan; Wang, Jiapeng; Tao, Zhu; Gao, Wei

    2017-10-31

    The invasive species Spartina alterniflora and native species Phragmites australis display a significant co-occurrence zonation pattern and this co-exist region exerts most competitive situations between these two species, competing for the limited space, directly influencing the co-exist distribution in the future. However, these two species have different growth ratios in this area, which increase the difficulty to detect the distribution situation directly by remote sensing. As chlorophyll content is a key indicator of plant growth and physiological status, the objective of this study was to reduce the effect of interspecies competition when estimating Cab content; we evaluated 79 published representative indices to determine the optimal indices for estimating the chlorophyll a and b (Cab) content. After performing a sensitivity analysis for all 79 spectral indices, five spectral indices were selected and integrated using an artificial neural network (ANN) to estimate the Cab content of different competition ratios: the Gitelson ratio green index, the transformed chlorophyll absorption ratio index/optimized soil-adjusted vegetation index, the modified normalized difference vegetation index, the chlorophyll fluorescence index, and the Vogelmann chlorophyll index. The ANN method yielded better results (R 2  = 0.7110 and RMSE = 8.3829 μg cm -2 ) on average than the best single spectral index (R 2  = 0.6319 and RMSE = 9.3535 μg cm -2 ), representing an increase of 10.78% in R 2 and a decrease of 10.38% in RMSE. Our results indicated that integrating multiple vegetation indices with an ANN can alleviate the impact of interspecies competition and achieve higher estimation accuracy than the traditional approach using a single index.

  1. Plasticity and innovation of regulatory mechanisms underlying seed oil content mediated by duplicated genes in the palaeopolyploid soybean.

    Science.gov (United States)

    Zhang, Dajian; Zhao, Meixia; Li, Shuai; Sun, Lianjun; Wang, Weidong; Cai, Chunmei; Dierking, Emily C; Ma, Jianxin

    2017-06-01

    Many plants have undergone whole genome duplication (WGD). However, how regulatory networks underlying a particular trait are reshaped in polyploids has not been experimentally investigated. Here we show that the regulatory pathways modulating seed oil content, which involve WRINKLED1 (WRI1), LEAFY COTYLEDON1 (LEC1), and LEC2 in Arabidopsis, have been modified in the palaeopolyploid soybean. Such modifications include functional reduction of GmWRI1b of the GmWRI1a/GmWRI1b homoeologous pair relevant to WRI1, complementary non-allelic dosage effects of the GmLEC1a/GmLEC1b homoeologous pair relevant to LEC1, pseudogenization of the singleton GmLEC2 relevant to LEC2, and the rise of the LEC2-like function of GmABI3b, contrasting to its homoeolog GmABI3a, which maintains the ABSCISIC ACID INSENSITIVE 3 (ABI3)-like function in modulating seed maturation and dormancy. The function of GmABI3b in modulating seed oil biosynthesis was fulfilled by direct binding to a RY (CATGCA) cis-regulatory element in the GmWRI1a promoter, which was absent in the GmWRI1b promoter, resulting in reduction of the GmWRI1b expression. Nevertheless, the three regulators each exhibited similar intensities of purifying selection to their respective duplicates since these pairs were formed by a WGD event that is proposed to have occurred approximately 13 million years ago (mya), suggesting that the differentiation in spatiotemporal expression between the duplicated genes is more likely to be the outcome of neutral variation in regulatory sequences. This study thus exemplifies the plasticity, dynamics, and novelty of regulatory networks mediated by WGD. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  2. A Hybrid One-Way ANOVA Approach for the Robust and Efficient Estimation of Differential Gene Expression with Multiple Patterns.

    Directory of Open Access Journals (Sweden)

    Mohammad Manir Hossain Mollah

    Full Text Available Identifying genes that are differentially expressed (DE between two or more conditions with multiple patterns of expression is one of the primary objectives of gene expression data analysis. Several statistical approaches, including one-way analysis of variance (ANOVA, are used to identify DE genes. However, most of these methods provide misleading results for two or more conditions with multiple patterns of expression in the presence of outlying genes. In this paper, an attempt is made to develop a hybrid one-way ANOVA approach that unifies the robustness and efficiency of estimation using the minimum β-divergence method to overcome some problems that arise in the existing robust methods for both small- and large-sample cases with multiple patterns of expression.The proposed method relies on a β-weight function, which produces values between 0 and 1. The β-weight function with β = 0.2 is used as a measure of outlier detection. It assigns smaller weights (≥ 0 to outlying expressions and larger weights (≤ 1 to typical expressions. The distribution of the β-weights is used to calculate the cut-off point, which is compared to the observed β-weight of an expression to determine whether that gene expression is an outlier. This weight function plays a key role in unifying the robustness and efficiency of estimation in one-way ANOVA.Analyses of simulated gene expression profiles revealed that all eight methods (ANOVA, SAM, LIMMA, EBarrays, eLNN, KW, robust BetaEB and proposed perform almost identically for m = 2 conditions in the absence of outliers. However, the robust BetaEB method and the proposed method exhibited considerably better performance than the other six methods in the presence of outliers. In this case, the BetaEB method exhibited slightly better performance than the proposed method for the small-sample cases, but the the proposed method exhibited much better performance than the BetaEB method for both the small- and large

  3. Non-Invasive Methodology to Estimate Polyphenol Content in Extra Virgin Olive Oil Based on Stepwise Multilinear Regression.

    Science.gov (United States)

    Martínez Gila, Diego Manuel; Cano Marchal, Pablo; Gómez Ortega, Juan; Gámez García, Javier

    2018-03-25

    Normally the olive oil quality is assessed by chemical analysis according to international standards. These norms define chemical and organoleptic markers, and depending on the markers, the olive oil can be labelled as lampante, virgin, or extra virgin olive oil (EVOO), the last being an indicator of top quality. The polyphenol content is related to EVOO organoleptic features, and different scientific works have studied the positive influence that these compounds have on human health. The works carried out in this paper are focused on studying relations between the polyphenol content in olive oil samples and its spectral response in the near infrared spectra. In this context, several acquisition parameters have been assessed to optimize the measurement process within the virgin olive oil production process. The best regression model reached a mean error value of 156.14 mg/kg in leave one out cross validation, and the higher regression coefficient was 0.81 through holdout validation.

  4. Estimating the population impact of a new pediatric influenza vaccination program in England using social media content

    DEFF Research Database (Denmark)

    Wagner, Moritz; Lampos, Vasileios; Yom-Tov, Elad

    2017-01-01

    the influenza season. The 2014/2015 influenza season saw the national program extended to include additional pilot regions, some of which offered the vaccine to secondary school children (11-13 years of age) as well. Objective: We utilized social media content to obtain a complementary assessment......-age children and providing evidence of the value of social media content as an additional syndromic surveillance tool.......Background: The rollout of a new childhood live attenuated influenza vaccine program was launched in England in 2013, which consisted of a national campaign for all 2 and 3 year olds and several pilot locations offering the vaccine to primary school-age children (4-11 years of age) during...

  5. Non-Invasive Methodology to Estimate Polyphenol Content in Extra Virgin Olive Oil Based on Stepwise Multilinear Regression

    Directory of Open Access Journals (Sweden)

    Diego Manuel Martínez Gila

    2018-03-01

    Full Text Available Normally the olive oil quality is assessed by chemical analysis according to international standards. These norms define chemical and organoleptic markers, and depending on the markers, the olive oil can be labelled as lampante, virgin, or extra virgin olive oil (EVOO, the last being an indicator of top quality. The polyphenol content is related to EVOO organoleptic features, and different scientific works have studied the positive influence that these compounds have on human health. The works carried out in this paper are focused on studying relations between the polyphenol content in olive oil samples and its spectral response in the near infrared spectra. In this context, several acquisition parameters have been assessed to optimize the measurement process within the virgin olive oil production process. The best regression model reached a mean error value of 156.14 mg/kg in leave one out cross validation, and the higher regression coefficient was 0.81 through holdout validation.

  6. An index for estimating the potential impact on the environment of the pollutant content in aquatic populations

    Directory of Open Access Journals (Sweden)

    Oscar RAVERA

    2008-02-01

    Full Text Available The so-called "Concentration factor" (C.F. should express a direct positive relationship between the concentration of a pollutant (e.g. metals, radioisotopes in an organism and the concentration of the same pollutant in the water. While this index is very useful in some cases, it cannot give any information on the influence of the biota on its environment, an important topic in research on biogeochemical cycles. A new index (the Influence index has consequently been developed to quantify the potential influence of the pollutant content in the population biomass on the habitat in which the population lives. The value of this index is calculated as the ratio between the pollutant content in the population biomass per sediment surface unit (e.g. m2 and the concentration of the same pollutant in the water, and is expressed as water volume with the same pollutant concentration as in the water of the population habitat. The value increases with the increase of the pollutant content in the population biomass and the decrease of the pollutant concentration in the water. As an example, some applications of the index to heavy metal contaminations of a freshwater mussel (Unio pictorum mancus population are described.

  7. Correlation of the A-FABP Gene Polymorphism and mRNA Expression with Intramuscular Fat Content in Three-Yellow Chicken and Hetian-Black Chicken.

    Science.gov (United States)

    Wang, Yong; Chen, Hongwei; Han, Diangang; Chen, Ying; Muhatai, Gemingguli; Kurban, Tursunjan; Xing, Jinming; He, Jianzhong

    2017-01-02

    The adipocyte-type fatty acid-binding protein (A-FABP) is considered a candidate gene for fat metabolism; thus, it affects fat deposition in chickens. The present study was designed to examine the polymorphism and mRNA abundance of the A-FABP gene with intramuscular fat (IMF) in the pectoralis muscles (PM) and leg muscles (LM) of Three-yellow Chicken (TYC) and Hetian-black Chicken (HTBC). In total, 60 TYCs and 60 HTBCs were sacrificed using exsanguination at market age. The IMF contents of the PM and LM in the HTBC were significantly higher than those in the TYC. Three genotypes of the A-FABP gene first exon, AA, AB, and BB, were examined by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP), and a C51 T mutational site, which is a silent substitution mutation, was revealed. The IMF contents of the AA genotype in the PM of the HTBC were significantly higher than those in the AB genotype; thus, the C51 T mutable site is a gene marker for selecting a higher IMF content in the PM of the HTBC. The relative expression of the A-FABP mRNA in the LM of the HTBC, which was measured by quantitative real-time PCR, was significantly higher than in the TYC. A significantly positive association was detected between A-FABP expression with the IMF contents of the PM and LM of both the TYC and the HTBC. These results provide basic data that might be helpful to further research the role of the A-FABP gene in fat deposition and fatty acid metabolism in chickens.

  8. A shortest-path graph kernel for estimating gene product semantic similarity

    Directory of Open Access Journals (Sweden)

    Alvarez Marco A

    2011-07-01

    Full Text Available Abstract Background Existing methods for calculating semantic similarity between gene products using the Gene Ontology (GO often rely on external resources, which are not part of the ontology. Consequently, changes in these external resources like biased term distribution caused by shifting of hot research topics, will affect the calculation of semantic similarity. One way to avoid this problem is to use semantic methods that are "intrinsic" to the ontology, i.e. independent of external knowledge. Results We present a shortest-path graph kernel (spgk method that relies exclusively on the GO and its structure. In spgk, a gene product is represented by an induced subgraph of the GO, which consists of all the GO terms annotating it. Then a shortest-path graph kernel is used to compute the similarity between two graphs. In a comprehensive evaluation using a benchmark dataset, spgk compares favorably with other methods that depend on external resources. Compared with simUI, a method that is also intrinsic to GO, spgk achieves slightly better results on the benchmark dataset. Statistical tests show that the improvement is significant when the resolution and EC similarity correlation coefficient are used to measure the performance, but is insignificant when the Pfam similarity correlation coefficient is used. Conclusions Spgk uses a graph kernel method in polynomial time to exploit the structure of the GO to calculate semantic similarity between gene products. It provides an alternative to both methods that use external resources and "intrinsic" methods with comparable performance.

  9. Estimation of Soil Moisture Content from the Spectral Reflectance of Bare Soils in the 0.4–2.5 µm Domain

    Directory of Open Access Journals (Sweden)

    Sophie Fabre

    2015-02-01

    Full Text Available This work aims to compare the performance of new methods to estimate the Soil Moisture Content (SMC of bare soils from their spectral signatures in the reflective domain (0.4–2.5 µm in comparison with widely used spectral indices like Normalized Soil Moisture Index (NSMI and Water Index SOIL (WISOIL. Indeed, these reference spectral indices use wavelengths located in the water vapour absorption bands and their performance are thus very sensitive to the quality of the atmospheric compensation. To reduce these limitations, two new spectral indices are proposed which wavelengths are defined using the determination matrix tool by taking into account the atmospheric transmission: Normalized Index of Nswir domain for Smc estimatiOn from Linear correlation (NINSOL and Normalized Index of Nswir domain for Smc estimatiOn from Non linear correlation (NINSON. These spectral indices are completed by two new methods based on the global shape of the soil spectral signatures. These methods are the Inverse Soil semi-Empirical Reflectance model (ISER, using the inversion of an existing empirical soil model simulating the soil spectral reflectance according to soil moisture content for a given soil class, and the convex envelope model, linking the area between the envelope and the spectral signature to the SMC. All these methods are compared using a reference database built with 32 soil samples and composed of 190 spectral signatures with five or six soil moisture contents. Half of the database is used for the calibration stage and the remaining to evaluate the performance of the SMC estimation methods. The results show that the four new methods lead to similar or better performance than the one obtained by the reference indices. The RMSE is ranging from 3.8% to 6.2% and the coefficient of determination R2 varies between 0.74 and 0.91 with the best performance obtained with the ISER model. In a second step, simulated spectral radiances at the sensor level are

  10. Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells.

    Science.gov (United States)

    Tokunaga, Masahiro; Kokubu, Chikara; Maeda, Yusuke; Sese, Jun; Horie, Kyoji; Sugimoto, Nakaba; Kinoshita, Taroh; Yusa, Kosuke; Takeda, Junji

    2014-11-24

    Genome-wide saturation mutagenesis and subsequent phenotype-driven screening has been central to a comprehensive understanding of complex biological processes in classical model organisms such as flies, nematodes, and plants. The degree of "saturation" (i.e., the fraction of possible target genes identified) has been shown to be a critical parameter in determining all relevant genes involved in a biological function, without prior knowledge of their products. In mammalian model systems, however, the relatively large scale and labor intensity of experiments have hampered the achievement of actual saturation mutagenesis, especially for recessive traits that require biallelic mutations to manifest detectable phenotypes. By exploiting the recently established haploid mouse embryonic stem cells (ESCs), we present an implementation of almost complete saturation mutagenesis in a mammalian system. The haploid ESCs were mutagenized with the chemical mutagen N-ethyl-N-nitrosourea (ENU) and processed for the screening of mutants defective in various steps of the glycosylphosphatidylinositol-anchor biosynthetic pathway. The resulting 114 independent mutant clones were characterized by a functional complementation assay, and were shown to be defective in any of 20 genes among all 22 known genes essential for this well-characterized pathway. Ten mutants were further validated by whole-exome sequencing. The predominant generation of single-nucleotide substitutions by ENU resulted in a gene mutation rate proportional to the length of the coding sequence, which facilitated the experimental design of saturation mutagenesis screening with the aid of computational simulation. Our study enables mammalian saturation mutagenesis to become a realistic proposition. Computational simulation, combined with a pilot mutagenesis experiment, could serve as a tool for the estimation of the number of genes essential for biological processes such as drug target pathways when a positive selection of

  11. Rapid estimation of the organic sulphur content of kerogens, coals and asphaltenes by pyrolysis-gas chromatography

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Eglinton, T.I.; Kohnen, M.E.L.; Leeuw, J.W. de

    1990-01-01

    A pyrolysis-gas Chromatographic (py-g.c.) method for estimation of the Sorg/C ratio in kerogens and other forms of sedimentary macromolecular organic matter is described. The method is based upon flash pyrolysis at 610 °C for 10s and areal integration of the FID peaks attributed to

  12. Estimating the content of clover and grass in the sward using a consumer camera and image processing

    DEFF Research Database (Denmark)

    Mortensen, Anders Krogh; Karstoft, Henrik; Søegaard, Karen

    the dry matter ratio of clover and grass in clover grass fields from sparse close up images. First, the light conditions is determined, which is used for selecting model parameters to estimate the coverage of both clover and grass. Next, the clover and grass coverage are transformed to give the dry matter...

  13. Estimation of the Level of Cognitive Development of a Preschool Child Using the System of Situations with Mathematical Contents

    Science.gov (United States)

    Gorev, Pavel M.; Bichurina, Svetlana Y.; Yakupova, Rufiya M.; Khairova, Irina V.

    2016-01-01

    Cognitive development of personality can be considered as one of the key directions of preschool education presented in the world practice, where preschool programs are educational ones, and preschool education is the first level of the general education. Thereby the purpose of the research is to create a model of reliable estimation of cognitive…

  14. Systematized Water content Calculation in Cartilage Using T1-mapping MR Estimations. Design of a Mathematical Model

    DEFF Research Database (Denmark)

    Shiguetomi Medina, Juan Manuel; Ramirez Garcia-Luna, Jose Luis; Rahbek, Ole

    .5 Tesla by calculating absolute T1 values in real maps through inverse angle phase inverse sequence recuperation (11 inversion times, from 200 to 2200 msec) at 37(±0.5) °C. Regions of interest were manually delineated and the mean T1 value was estimated using a T1-map analysis software. The collected data...

  15. Study on the Correlation between Gene Expression and Enzyme Activity of Seven Key Enzymes and Ginsenoside Content in Ginseng in Over Time in Ji'an, China.

    Science.gov (United States)

    Yin, Juxin; Zhang, Daihui; Zhuang, Jianjian; Huang, Yi; Mu, Ying; Lv, Shaowu

    2017-12-11

    Panax ginseng is a traditional medicine. Fresh ginseng is one of the most important industries related to ginseng development, and fresh ginseng of varying ages has different medicinal properties. Previous research has not systematically reported the correlation between changes in key enzyme activity with changes in ginsenoside content in fresh ginseng over time. In this study, for the first time, we use ginseng samples of varying ages in Ji'an and systematically reported the changes in the activity of seven key enzymes (HMGR, FPS, SS, SE, DS, CYP450, and GT). We investigated the content of ginsenoside and gene expression of these key enzymes. Ginsenoside content was measured using HPLC. HPLC, GC-MS, and LC-MS were combined to measure the enzyme activity of the key enzymes. Quantitative PCR was used in the investigation of gene expression. By analyzing the correlation between the enzyme activity and the transcription level of the key enzymes with ginsenoside content, we found that DS and GT enzyme activities are significantly correlated with the ginsenoside content in different ages of ginseng. Our findings might provide a new strategy to discriminate between ginseng of different years. Meanwhile, this research provides important information for the in-depth study of ginsenoside biosynthesis.

  16. Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Fei Gao

    Full Text Available The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. A total of 188,623 optimized reads and 15,527 operational taxonomic units (OTUs were obtained from the ten gut contents samples and four surface sediment samples. The sequences in the sediments, foregut contents, and hindgut contents were assigned to 38.0±4.7, 31.2±6.2 and 27.8±6.5 phyla, respectively. The bacterial richness and Shannon diversity index were both higher in the ambient sediments than in the gut contents. Proteobacteria was the predominant phylum in both the gut contents and sediment samples. The predominant classes in the foregut, hindgut, and ambient sediment were Holophagae and Gammaproteobacteria, Deltaproteobacteria and Gammaproteobacteria, and Gammaproteobacteria and Deltaproteobacteria, respectively. The potential probiotics, including sequences related to Bacillus, lactic acid bacteria (Lactobacillus, Lactococcus, and Streptococcus and Pseudomonas were detected in the gut of A. japonicus. Principle component analysis and heatmap figure showed that the foregut, hindgut, and ambient sediment respectively harbored different characteristic bacterial communities. Selective feeding of A. japonicus may be the primary source of the different bacterial communities between the foregut contents and ambient sediments.

  17. Relative Estimation of Water Content for Flat-Type Inductive-Based Oil Palm Fruit Maturity Sensor

    Directory of Open Access Journals (Sweden)

    Norhisam Misron

    2016-12-01

    Full Text Available The paper aims to study the sensor that identifies the maturity of oil palm fruit bunches by using a flat-type inductive concept based on a resonant frequency technique. Conventionally, a human grader is used to inspect the ripeness of the oil palm fresh fruit bunch (FFB which can be inconsistent and inaccurate. There are various new methods that are proposed with the intention to grade the ripeness of the oil palm FFB, but none has taken the inductive concept. In this study, the resonance frequency of the air coil is investigated. Samples of oil palm FFB are tested with frequencies ranging from 20 Hz to 10 MHz and the results obtained show a linear relationship between the graph of the resonance frequency (MHz against time (Weeks. It is observed that the resonance frequencies obtained for Week 10 (pre-mature and Week 18 (mature are around 8.5 MHz and 9.8 MHz, respectively. These results are compared with the percentage of the moisture content. Hence, the inductive method of the oil palm fruit maturity sensor can be used to detect the change in water content for ripeness detection of the oil palm FFB.

  18. Comparison of invasive and non-invasive electromagnetic methods in soil water content estimation of a dike model

    International Nuclear Information System (INIS)

    Preko, Kwasi; Scheuermann, Alexander; Wilhelm, Helmut

    2009-01-01

    Water infiltration through a dike model under controlled flooding and drainage conditions was investigated using the gravimetric soil water sampling technique and electromagnetic techniques, in particular ground penetrating radar (GPR) applied in different forms, time domain reflectometry with intelligent microelements (TRIME-TDR) and spatial-time domain reflectometry (S-TDR). The experiments were conducted on the model in two phases. In the first phase, the model was flooded with varying water levels between 0 and 1.25 m above the waterproof base of the model. In the second phase, the characteristics of the temporal water content changes were investigated over a period of 65 days as the flood water drained off from the 1.25 m level. The dike model was constructed with soil of the texture class loamy sand. The aim of the experiment was to investigate whether GPR-based invasive and non-invasive methods were able to quantitatively observe and correctly monitor temporal changes in the volumetric water content (VWC) within embankment dams. The VWC values from the various techniques corresponded very well, especially with low VWC values. A comparison with the VWC of gravimetric soil water sampling showed a satisfactory reproducibility. Characteristic discrepancies were recorded with higher values of the VWC. Under saturated conditions only the invasive methods were able to produce reasonable values of the VWC. After the release of the highest flood level, the drainage phase could be characterized by two invasive methods based on the TDR and GPR techniques

  19. Studies on meat color, myoglobin content, enzyme activities, and genes associated with oxidative potential of pigs slaughtered at different growth stages

    Science.gov (United States)

    Yu, Qin Ping; Feng, Ding Yuan; Xiao, Juan; Wu, Fan; He, Xiao Jun; Xia, Min Hao; Dong, Tao; Liu, Yi Hua; Tan, Hui Ze; Zou, Shi Geng; Zheng, Tao; Ou, Xian Hua; Zuo, Jian Jun

    2017-01-01

    Objective This experiment investigated meat color, myoglobin content, enzyme activities, and expression of genes associated with oxidative potential of pigs slaughtered at different growth stages. Methods Sixty 4-week-old Duroc×Landrace×Yorkshire pigs were assigned to 6 replicate groups, each containing 10 pigs. One pig from each group was sacrificed at day 35, 63, 98, and 161 to isolate longissimus dorsi and triceps muscles. Results Meat color scores were higher in pigs at 35 d than those at 63 d and 98 d (pMeat color scores were correlated to the proportion of oxymyoglobin (r = 0.59, pmeat color, myoglobin content, enzyme activities, and genes associated with oxidative potential varied at different stages. PMID:28728400

  20. Relationship of ultrasonic shear wave velocity with oncogene and tumor suppressor gene expression in primary liver cancer lesions as well as angiogenesis factor contents

    Directory of Open Access Journals (Sweden)

    Xing Yin1

    2017-06-01

    Full Text Available Objective: To discuss the relationship of ultrasonic shear wave velocity (SWV with oncogene and tumor suppressor gene expression in primary liver cancer lesions as well as angiogenesis factor contents. Methods: 100 patients with primary liver cancer who underwent surgical treatment in our hospital between March 2014 and September 2016 were collected as observation group, and 50 healthy subjects who received physical examination in our hospital during the same period were collected as normal control group. The ultrasonic SWV levels of two groups of subjects were measured before the operation, and the observation groups were further divided into high SWV group and low SWV group, 50 cases in each group. Intraoperative tumor tissue samples were kept and fluorescence quantitative PCR was used to determine the mRNA expression of oncogenes and tumor suppressor genes. Enzymelinked immunosorbent assay was used to determine serum contents of angiogenesis factors in observation group before operation. Results: Hepatic ultrasonic SWV level in observation group was significantly higher than that in normal control group; proto-oncogene CK, Ki67, Gly-3, Survivin and Pokemon mRNA expression in tumor tissue of high SWV group were higher than those of low SWV group while tumor suppressor genes Tg737, p16, p27, PTEN and runx3 mRNA expression were lower than those of low SWV group; serum angiogenesis factors VEGF, MMP-9 and IGF-1R contents were higher than those in low SWV group. Conclusion: The hepatic ultrasonic SWV level increases in patients with primary liver cancer, and the SWV level is directly correlated with oncogene and tumor suppressor gene expression as well as angiogenesis factor contents.

  1. Analyzing Multiple-Probe Microarray: Estimation and Application of Gene Expression Indexes

    KAUST Repository

    Maadooliat, Mehdi; Huang, Jianhua Z.; Hu, Jianhua

    2012-01-01

    model, which is similar to the additive model discussed in Irizarry et al. (2003a) at the logarithm scale. Along this line, Hu et al. (2006) proposed data transformation to improve expression index estimation based on an ad hoc entropy criteria and naive

  2. Dominance effects estimation of TLR4 and CACNA2D1 genes for ...

    Indian Academy of Sciences (India)

    Samples were genotyped for four SNP-single genotypes and their associations with production traits (breeding values forprotein and fat yield, and protein and fat percentage) were estimated by applying logistic regression analyses. Calculation of contrast between both homozygous and heterozygous genotypes permitted ...

  3. Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle

    Science.gov (United States)

    Selection on important genetic markers can improve estimates of additive and dominance association effects. A composite population of beef cattle was selected for intermediate frequencies of myostatin (GDF8) F94L and µ-calpain (CAPN1) polymorphisms. Important additive associations of the GDF8 locu...

  4. Effects of Increasing Doses of UV-B on Main Phenolic Acids Content, Antioxidant Activity and Estimated Biomass in Lavandin (Lavandula x intermedia).

    Science.gov (United States)

    Usano-Alemany, Jaime; Panjai, Lachinee

    2015-07-01

    Lavandin is a well-known aromatic plant cultivated mainly for its valuable essential oil. Nonetheless, little attention has been paid so far to the quantification of other natural products such as polyphenols. Accordingly, we examined the effect of increasing doses of UV-B radiation on the main phenolic content, antioxidant activity and estimated biomass of one year old lavandin pots compared with pots grown outdoors. Significantly higher total phenolic content and concentration of main polyphenols have been found in outdoor plants. Rosmarinic acid has been described as the major phenolic compound in methanolic extracts (max. 25.9 ± 9.7 mg/g(-1) DW). Furthermore, we found that increasing doses of UV-B promote the plant growth of this species as well as the accumulation of phenolic compounds although with less antioxidant capacity in scavenging DPPH radicals. On the other hand, our results showed a remarkable variability among individual plants regarding the content of major phenolic acids. The application of UV-B doses during plant growth could be a method to promote biomass in this species along with the promotion of higher content of valuable secondary metabolites.

  5. Estimating the Prevalence of Potential Enteropathogenic Escherichia coli and Intimin Gene Diversity in a Human Community by Monitoring Sanitary Sewage

    Science.gov (United States)

    Yang, Kun; Pagaling, Eulyn

    2014-01-01

    Presently, the understanding of bacterial enteric diseases in the community and their virulence factors relies almost exclusively on clinical disease reporting and examination of clinical pathogen isolates. This study aimed to investigate the feasibility of an alternative approach that monitors potential enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) prevalence and intimin gene (eae) diversity in a community by directly quantifying and characterizing target virulence genes in the sanitary sewage. The quantitative PCR (qPCR) quantification of the eae, stx1, and stx2 genes in sanitary sewage samples collected over a 13-month period detected eae in all 13 monthly sewage samples at significantly higher abundance (93 to 7,240 calibrator cell equivalents [CCE]/100 ml) than stx1 and stx2, which were detected sporadically. The prevalence level of potential EPEC in the sanitary sewage was estimated by calculating the ratio of eae to uidA, which averaged 1.0% (σ = 0.4%) over the 13-month period. Cloning and sequencing of the eae gene directly from the sewage samples covered the majority of the eae diversity in the sewage and detected 17 unique eae alleles belonging to 14 subtypes. Among them, eae-β2 was identified to be the most prevalent subtype in the sewage, with the highest detection frequency in the clone libraries (41.2%) and within the different sampling months (85.7%). Additionally, sewage and environmental E. coli isolates were also obtained and used to determine the detection frequencies of the virulence genes as well as eae genetic diversity for comparison. PMID:24141131

  6. Estimating the chlorophyll content in the waters of Guanabara Bay from the LANDSAT multispectral scanning digital data

    Science.gov (United States)

    Dejesusparada, N. (Principal Investigator); Bentancurt, J. J. V.; Herz, B. R.; Molion, L. B.

    1980-01-01

    Detection of water quality in Guanabara Bay using multispectral scanning digital data taken from LANDSAT satellites was examined. To test these processes, an empirical (statistical) approach was choosen to observe the degree of relationship between LANDSAT data and the in situ data taken simultaneously. The linear and nonlinear regression analyses were taken from among those developed by INPE in 1978. Results indicate that the major regression was in the number six MSS band, atmospheric effects, which indicated a correction coefficient of 0.99 and an average error of 6.59 micrograms liter. This error was similar to that obtained in the laboratory. The chlorophyll content was between 0 and 100 micrograms/liter, as taken from the MSS of LANDSAT.

  7. Estimation of total phenolic content, cytotoxicity and in-vitro antioxidant activity of stem bark of Moringa oleifera

    Directory of Open Access Journals (Sweden)

    Kumbhare MR

    2012-04-01

    Full Text Available Objective: To assess the phytochemical constituents, total phenolic content, cytotoxicity and invitro antioxidant activity of stem bark extracts of Moringa oleifera (M. oleifera (Moringaceae. Methods: Brine shrimp lethality (BSL bioassay was used to investigate the cytotoxic effects. DPPH and nitric oxide radical scavenging activity was used to demonstrate antioxidant activity. Results: Phytochemical analysis revealed the presence of tannins, flavonoids, steroids and alkaloids. The LC 50 values were obtained for extracts as 850 毺 g/mL for petroleum ether extract, 800 毺 g/mL for chloroform extract and 900 毺 g/mL for methanol extract. The total phenolic content of the methanolic extract was 50.72% w/w, equivalent to gallic acid. Petroleum ether, chloroform and methanolic extracts of M. oleifera and standard ascorbic acid were found to be scavenger of DPPH radical with an IC 50 of 124.75, 112.08, 54.34 and 13.86 毺 g/mL, respectively. Methanolic extract was found to be good scavenger of DPPH radical. Petroleum ether, chloroform, ethyl acetate soluble fraction of methanolic extracts of M. oleifera and ascorbic acid were found to be scavenger of nitric oxide radical with an IC 50 of 93.32, 65.12, 54.83 and 12.59 毺 g/mL, respectively. Ethyl acetate soluble fraction was found to be good scavenger of nitric oxide radical. Conclusions: It can be concluded that the crude extracts of M. oleifera is a potential source of natural antioxidants, and this justifies its uses in folkloric medicines.

  8. ESTIMATION OF HYDRAULIC CONDUCTIVITY AND CONTENT OF FINES FROM EXPERIMENTAL LAWS THAT CORELATE HYDRAULIC AND ELECTRIC PARAMETERS

    Directory of Open Access Journals (Sweden)

    Héctor José Peinado-Guevara

    2010-09-01

    Full Text Available Hydraulic conductivity is a basic element in the advancement of knowledge of a geological environment in both the flow and transport processes of pollutants for conservation projects, managementand environmental management and also for the development of public policies for protection of ecosystems, among others. The aim of this paper is to obtain the hydraulic conductivity (K and the finescontent (C of saturated granular half using two empirical laws. One correlates the electrical conductivity of saturated granular media σo and water saturated σw which depends on the formation factor(F, cation exchange capacity (CEC and the fines content in the saturated soil. Using data obtained from materials of 18 samples from 6 wells the relationships between F-C and CEC-C were obtained,so the equation reduces to a σo function in terms of σw and C, with a correlation coefficient of R = 0.97. A second experimental law is the one that results from the experimental relationship between K and C,being 1.4054 K 0.1804.C with a correlation coefficient of R = 0.96. From both experimental expressions relationships between K and C, a and C,and C are created so from every pair knowing one of them you get to know the other one. Under the scheme outlined electrical conductivity sections for the saturated medium and fines content are obtained,finding that the groundwater in the study area consists of a thin top layer and beneath it there is a predominantly sandy environment.

  9. Soil water stress affects both cuticular wax content and cuticle-related gene expression in young saplings of maritime pine (Pinus pinaster Ait).

    Science.gov (United States)

    Le Provost, Grégoire; Domergue, Frédéric; Lalanne, Céline; Ramos Campos, Patricio; Grosbois, Antoine; Bert, Didier; Meredieu, Céline; Danjon, Frédéric; Plomion, Christophe; Gion, Jean-Marc

    2013-07-01

    The cuticle is a hydrophobic barrier located at the aerial surface of all terrestrial plants. Recent studies performed on model plants, such as Arabidopsis thaliana, have suggested that the cuticle may be involved in drought stress adaptation, preventing non-stomatal water loss. Although forest trees will face more intense drought stresses (in duration and intensity) with global warming, very few studies on the role of the cuticle in drought stress adaptation in these long-lived organisms have been so far reported. This aspect was investigated in a conifer, maritime pine (Pinus pinaster Ait.), in a factorial design with two genetic units (two half-sib families with different growth rates) and two treatments (irrigated vs non-irrigated), in field conditions. Saplings were grown in an open-sided greenhouse and half were irrigated three times per week for two growing seasons. Needles were sampled three times per year for cuticular wax (composition and content) and transcriptome (of 11 genes involved in cuticle biosynthesis) analysis. Non-irrigated saplings (i) had a higher cuticular wax content than irrigated saplings and (ii) overexpressed most of the genes studied. Both these trends were more marked in the faster growing family. The higher cuticular wax content observed in the non-irrigated treatment associated with strong modifications in products from the decarbonylation pathway suggest that cuticular wax may be involved in drought stress adaptation in maritime pine. This study provides also a set of promising candidate genes for future forward genetic studies in conifers.

  10. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

    Science.gov (United States)

    Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S. T.; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C. J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-Horn, Elizabeth A.; Green, Jack E.; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J. P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H. L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen

    2014-01-01

    Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific

  11. Effects of Sorghum [Sorghum bicolor (L. Moench] Crude Extracts on Starch Digestibility, Estimated Glycemic Index (EGI, and Resistant Starch (RS Contents of Porridges

    Directory of Open Access Journals (Sweden)

    Dilek Lemlioglu-Austin

    2012-09-01

    Full Text Available Bran extracts (70% aqueous acetone of specialty sorghum varieties (tannin, black, and black with tannin were used to investigate the effects of sorghum phenolic compounds on starch digestibility, Estimated Glycemic Index (EGI, and Resistant Starch (RS of porridges made with normal corn starch, enzyme resistant high amylose corn starch, and ground whole sorghum flours. Porridges were cooked with bran extracts in a Rapid Visco-analyser (RVA. The cooking trials indicated that bran extracts of phenolic-rich sorghum varieties significantly reduced EGI, and increased RS contents of porridges. Thus, there could be potential health benefits associated with the incorporation of phenolic-rich sorghum bran extracts into foods to slow starch digestion and increase RS content.

  12. Determinations of 90Sr, 137Cs, 226Ra, 228Ra, 210Pb, 210Po contents in chinese diet and estimations of internal doses due to these radionuclides

    International Nuclear Information System (INIS)

    Zhu Hongda; Wang Shouliang; Meng Wei; Wang Daoping; Zheng Xiujun; Liu Qingfen; Liu Peng

    1993-01-01

    As a part of Chinese Total Diet Survey taken place in 1990, the authors report the determined results on 90 Sr, 137 Cs, 226 Ra, 228 Ra, 210 Pb and 210 Pb and 210 Po contents in various foods of Chinese total diet. Based on obtained dietary composition and the determined contents, the Annual Intakes (AI) and Committed Dose Equivalents (CDE) for the public by ingestion were estimated. It is shown that the total CDE for 6 radionuclides is about 0.24 mSv/a. The food categories and nuclides whose relative contributions to the total are dominant were vegetables, aquatic products and cereal, and 210 Pb, 210 Po, 228 Ra, respectively. The results have updated the data from 1982 survey and have complemented important information for water consumption. The regional difference of dietary compositions and resultant internal doses are discussed as well

  13. Genomic GC-content affects the accuracy of 16S rRNA gene sequencing bsed microbial profiling due to PCR bias

    DEFF Research Database (Denmark)

    Laursen, Martin F.; Dalgaard, Marlene Danner; Bahl, Martin Iain

    2017-01-01

    Profiling of microbial community composition is frequently performed by partial 16S rRNA gene sequencing on benchtop platforms following PCR amplification of specific hypervariable regions within this gene. Accuracy and reproducibility of this strategy are two key parameters to consider, which may...... be influenced during all processes from sample collection and storage, through DNA extraction and PCR based library preparation to the final sequencing. In order to evaluate both the reproducibility and accuracy of 16S rRNA gene based microbial profiling using the Ion Torrent PGM platform, we prepared libraries...... be explained partly by premature read truncation, but to larger degree their genomic GC-content, which correlated negatively with the observed relative abundances, suggesting a PCR bias against GC-rich species during library preparation. Increasing the initial denaturation time during the PCR amplification...

  14. Estimation of cis-9, trans-11 conjugated linoleic acid content in UK foods and assessment of dietary intake in a cohort of healthy adults.

    Science.gov (United States)

    Mushtaq, Sohail; Heather Mangiapane, E; Hunter, Kirsty A

    2010-05-01

    Dietary conjugated linoleic acid (CLA) from ruminant-derived foods may be potentially beneficial to health. The quantity of cis-9, trans-11 CLA and trans-10, cis-12 CLA in a range of UK foodstuffs (112 foods) was determined using triple-column silver ion HPLC. The cis-9, trans-11 CLA content ranged from 1.9 mg/g lipid (mild Cheddar) to 7.3 mg/g lipid (processed cheese) in cheeses, from 0.9 mg/g lipid (ice cream) to 3.7 mg/g lipid (double cream) in non-cheese dairy products, and from 2.9 mg/g lipid (Swedish meatballs) to 6.0 mg/g lipid (minced lamb) in meat products. cis-9, trans-11 CLA concentrations for chocolate and sweets ranged from 0.1 mg/g lipid (hot chocolate) to 4.8 mg/g lipid (buttermint). The trans-10, cis-12 CLA isomer was undetected or negligible in the food samples examined. To provide information about dietary cis-9, trans-11 CLA intakes in the UK, a study was performed to estimate the daily intake of CLA in a cohort of eighteen healthy volunteers (nine female and nine male; aged 21-60 years; mean BMI = 24.0 kg/m2 (sd 2.2)) with a 7-d weighed food record. This information combined with the CLA isomer contents of UK foodstuffs was used to estimate the daily intake of the cohort. The mean daily intake of cis-9, trans-11 CLA was estimated to be 97.5 (sd 73.3) mg/d. Due to its potential health benefits, it is important to determine the CLA content of food and dietary intake as these data will be useful in determining the role of CLA in health and disease.

  15. Use of supermarket receipts to estimate energy and fat content of food purchased by lean and overweight families.

    Science.gov (United States)

    Ransley, J K; Donnelly, J K; Botham, H; Khara, T N; Greenwood, D C; Cade, J E

    2003-10-01

    The aim of this study was to compare the energy and fat content of food purchased for home consumption by households comprising mainly overweight individuals (OH), with those comprising mainly lean individuals (LH). 214 supermarket shoppers and their household were recruited from a Tesco supermarket in Leeds (UK). Households collected supermarket receipts and completed a shopping diary for 28-days, and each member of the household completed a 4-day food record. OH purchased food higher in fat (38% total energy from fat) than LH, (34.9%: p=0.001) and they purchased more energy and fat per adult equivalent, per day than LH (10.05 MJ compared to 9.15 MJ: p=0.01 and 103 g compared to 86 g:p=0.001). Households were 15% more likely to be classified as OH for each additional MJ of energy purchased per person, per day, after adjusting for number of children, household size, age, sex and social class. It was concluded that food purchasing behaviour may be linked to the prevalence of obesity in households who shop at supermarkets.

  16. A Killer Immunoglobulin - Like Receptor Gene - Content Haplotype and A Cognate Human Leukocyte Antigen Ligand are Associated with Autism

    OpenAIRE

    Torres, Anthony; Westover, Jonna; Benson, Michael; Johnson, Randall; Dykes, Annelise

    2016-01-01

    The killing activity of natural killer cells is largely regulated by the binding of class I human leukocyte antigen cognate ligands to killer cell immunoglobulin - like receptor proteins. The killer cell immunoglobulin - like receptor gene - complex contains genes that activate and others that inhibit the killing state of natural killer cells depending on the binding of specific human leukocyte antigen cognate ligands. It has been suggested in previous publications that activating human leuko...

  17. Method for estimating the atmospheric content of sub-micrometer aerosol using direct-sun photometric data

    Science.gov (United States)

    Stefan, S.; Filip, L.

    2009-04-01

    It is well known that the aerosol generated by human activity falls in the sub-micrometer rage [1]. The rapid increase of such emissions led to massive accumulations in the planetary boundary layer. Aerosol pollutants influence the quality of life on the Earth in at least two ways: by direct physiological effects following their penetration into living organisms and by the indirect implications on the overall energy balance of the Earth-atmosphere system. For these reasons monitoring the sub-micrometer aerosol on a global scale, become a stringent necessity in protecting the environment. The sun-photometry proved a very efficient way for such monitoring activities, mainly when vast networks of instruments (like AERONET [2]) are used. The size distribution of aerosols is currently a product of AERONET obtained through an inversion algorithm of sky-photometry data [3, 4]. Alternatively, various methods of investigating the aerosol size distribution have been developed through the use of direct-sun photometric data, with the advantages of simpler computation algorithms and a more convenient use [5, 6]. Our research aims to formulate a new simpler way to retrieve aerosol fine and coarse mode volume concentrations, as well as dimensional information, from direct-sun data. As in other works from the literature [3-6], the main hypothesis is that of a bi-modal shape of the size distribution of aerosols that can be reproduced rather satisfactorily by a linear combination of two lognormal functions. Essentially, the method followed in this paper relies on aerosol size information retrieval through fitting theoretical computations to measured aerosol optical depth (AOD) and related data. To this purpose, the experimental spectral dependence of AOD is interpolated and differentiated numerically to obtain the Ǻngström parameter. The reduced (i.e. normalized to the corresponding columnar volumetric content) contributions of the fine and coarse modes to the AOD have also been

  18. Heterosis in Rice Seedlings: Its Relationship to Gibberellin Content and Expression of Gibberellin Metabolism and Signaling Genes1[W][OA

    Science.gov (United States)

    Ma (马谦), Qian; Hedden, Peter; Zhang (张启发), Qifa

    2011-01-01

    Despite the accumulation of data on the genetic and molecular understanding of heterosis, there is little information on the regulation of heterosis at the physiological level. In this study, we performed a quantitative analysis of endogenous gibberellin (GA) content and expression profiling of the GA metabolism and signaling genes to investigate the possible relationship between GA signaling and heterosis for seedling development in rice (Oryza sativa). The materials used were an incomplete diallele set of 3 × 3 crosses and the six parents. In the growing shoots of the seedlings at 20 d after sowing, significant positive correlations between the contents of some GA species and performance and heterosis based on shoot dry mass were detected. Expression analyses of GA-related genes by real-time reverse transcription-polymerase chain reaction revealed that 13 out of the 16 GA-related genes examined exhibited significant differential expression among the F1 hybrid and its parents, acting predominantly in the modes of overdominance and positive dominance. Expression levels of nine genes in the hybrids displayed significant positive correlations with the heterosis of shoot dry mass. These results imply that GAs play a positive role in the regulation of heterosis for rice seedling development. In shoots plus root axes of 4-d-old germinating seeds that had undergone the deetiolation, mimicking normal germination in soil, the axis dry mass was positively correlated with the content of GA29 but negatively correlated with that of GA19. Our findings provide supporting evidence for GAs playing an important regulatory role in heterosis for rice seedling development. PMID:21693671

  19. Differential Contribution of Endoplasmic Reticulum and Chloroplast ω-3 Fatty Acid Desaturase Genes to the Linolenic Acid Content of Olive (Olea europaea) Fruit.

    Science.gov (United States)

    Hernández, M Luisa; Sicardo, M Dolores; Martínez-Rivas, José M

    2016-01-01

    Linolenic acid is a polyunsaturated fatty acid present in plant lipids, which plays key roles in plant metabolism as a structural component of storage and membrane lipids, and as a precursor of signaling molecules. The synthesis of linolenic acid is catalyzed by two different ω-3 fatty acid desaturases, which correspond to microsomal- (FAD3) and chloroplast- (FAD7 and FAD8) localized enzymes. We have investigated the specific contribution of each enzyme to the linolenic acid content in olive fruit. With that aim, we isolated two different cDNA clones encoding two ω-3 fatty acid desaturases from olive (Olea europaea cv. Picual). Sequence analysis indicates that they code for microsomal (OepFAD3B) and chloroplast (OepFAD7-2) ω-3 fatty acid desaturase enzymes, different from the previously characterized OekFAD3A and OekFAD7-1 genes. Functional expression in yeast of the corresponding OepFAD3A and OepFAD3B cDNAs confirmed that they encode microsomal ω-3 fatty acid desaturases. The linolenic acid content and transcript levels of olive FAD3 and FAD7 genes were measured in different tissues of Picual and Arbequina cultivars, including mesocarp and seed during development and ripening of olive fruit. Gene expression and lipid analysis indicate that FAD3A is the gene mainly responsible for the linolenic acid present in the seed, while FAD7-1 and FAD7-2 contribute mostly to the linolenic acid present in the mesocarp and, therefore, in the olive oil. These results also indicate the relevance of lipid trafficking between the endoplasmic reticulum and chloroplast in determining the linolenic acid content of membrane and storage lipids in oil-accumulating photosynthetic tissues. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  20. Comparing BMD-derived genotoxic potency estimations across variants of the transgenic rodent gene mutation assay.

    Science.gov (United States)

    Wills, John W; Johnson, George E; Battaion, Hannah L; Slob, Wout; White, Paul A

    2017-12-01

    There is growing interest in quantitative analysis of in vivo genetic toxicity dose-response data, and use of point-of-departure (PoD) metrics such as the benchmark dose (BMD) for human health risk assessment (HHRA). Currently, multiple transgenic rodent (TGR) assay variants, employing different rodent strains and reporter transgenes, are used for the assessment of chemically-induced genotoxic effects in vivo. However, regulatory issues arise when different PoD values (e.g., lower BMD confidence intervals or BMDLs) are obtained for the same compound across different TGR assay variants. This study therefore employed the BMD approach to examine the ability of different TGR variants to yield comparable genotoxic potency estimates. Review of over 2000 dose-response datasets identified suitably-matched dose-response data for three compounds (ethyl methanesulfonate or EMS, N-ethyl-N-nitrosourea or ENU, and dimethylnitrosamine or DMN) across four commonly-used murine TGR variants (Muta™Mouse lacZ, Muta™Mouse cII, gpt delta and BigBlue® lacI). Dose-response analyses provided no conclusive evidence that TGR variant choice significantly influences the derived genotoxic potency estimate. This conclusion was reliant upon taking into account the importance of comparing BMD confidence intervals as opposed to directly comparing PoD values (e.g., comparing BMDLs). Comparisons with earlier works suggested that with respect to potency determination, tissue choice is potentially more important than choice of TGR assay variant. Scoring multiple tissues selected on the basis of supporting toxicokinetic information is therefore recommended. Finally, we used typical within-group variances to estimate preliminary endpoint-specific benchmark response (BMR) values across several TGR variants/tissues. We discuss why such values are required for routine use of genetic toxicity PoDs for HHRA. Environ. Mol. Mutagen. 58:632-643, 2017. © 2017 Her Majesty the Queen in Right of Canada

  1. Dissecting a QTL into Candidate Genes Highlighted the Key Role of Pectinesterases in Regulating the Ascorbic Acid Content in Tomato Fruit

    Directory of Open Access Journals (Sweden)

    Valentino Ruggieri

    2015-07-01

    Full Text Available Tomato ( is a crucial component of the human diet because of its high nutritional value and the antioxidant content of its fruit. As a member of the Solanaceae family, it is considered a model species for genomic studies in this family, especially since its genome has been completely sequenced. Among genomic resources available, introgression lines represent a valuable tool to mine the genetic diversity present in wild species. One introgression line, IL12-4, was previously selected for high ascorbic acid (AsA content, and a transcriptomic analysis indicated the involvement of genes controlling pectin degradation in AsA accumulation. In this study the integration of data from different “omics” platforms has been exploited to identify candidate genes that increase AsA belonging to the wild region 12-4. Thirty-two genes potentially involved in pathways controlling AsA levels were analyzed with bioinformatic tools. Two hundred-fifty nonsynonymous polymorphisms were detected in their coding regions, and 11.6% revealed deleterious effects on predicted protein function. To reduce the number of genes that had to be functionally validated, introgression sublines of the region 12–4 were selected using species-specific polymorphic markers between the two species. Four sublines were obtained and we demonstrated that a subregion of around 1 Mbp includes 12 candidate genes potentially involved in AsA accumulation. Among these, only five exhibited structural deleterious variants, and one of the 12 was differentially expressed between the two species. We have highlighted the role of three polymorphic pectinesterases and inhibitors of pectinesterases that merit further investigation.

  2. The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes

    DEFF Research Database (Denmark)

    Pantano, Lorena; Jodar, Meritxell; Bak, Mads

    2015-01-01

    -specific genes. The most abundant class of small noncoding RNAs in sperm are PIWI-interacting RNAs (piRNAs). Surprisingly, we found that human sperm cells contain piRNAs processed from pseudogenes. Clusters of piRNAs from human testes contain pseudogenes transcribed in the antisense strand and processed...... into small RNAs. Several human protein-coding genes contain antisense predicted targets of pseudogene-derived piRNAs in the male germline and these piRNAs are still found in mature sperm. Our study provides the most extensive data set and annotation of human sperm small RNAs to date and is a resource...... for further functional studies on the roles of sperm small RNAs. In addition, we propose that some of the pseudogene-derived human piRNAs may regulate expression of their parent gene in the male germline....

  3. Development of FT-NIR Models for the Simultaneous Estimation of Chlorophyll and Nitrogen Content in Fresh Apple (Malus Domestica Leaves

    Directory of Open Access Journals (Sweden)

    Elena Tamburini

    2015-01-01

    Full Text Available Agricultural practices determine the level of food production and, to great extent, the state of the global environment. During the last decades, the indiscriminate recourse to fertilizers as well as the nitrogen losses from land application have been recognized as serious issues of modern agriculture, globally contributing to nitrate pollution. The development of a reliable Near-Infra-Red Spectroscopy (NIRS-based method, for the simultaneous monitoring of nitrogen and chlorophyll in fresh apple (Malus domestica leaves, was investigated on a set of 133 samples, with the aim of estimating the nutritional and physiological status of trees, in real time, cheaply and non-destructively. By means of a FT (Fourier Transform-NIR instrument, Partial Least Squares (PLS regression models were developed, spanning a concentration range of 0.577%–0.817% for the total Kjeldahl nitrogen (TKN content (R2 = 0.983; SEC = 0.012; SEP = 0.028, and of 1.534–2.372 mg/g for the total chlorophyll content (R2 = 0.941; SEC = 0.132; SEP = 0.162. Chlorophyll-a and chlorophyll-b contents were also evaluated (R2 = 0.913; SEC = 0.076; SEP = 0.101 and R2 = 0.899; SEC = 0.059; SEP = 0.101, respectively. All calibration models were validated by means of 47 independent samples. The NIR approach allows a rapid evaluation of the nitrogen and chlorophyll contents, and may represent a useful tool for determining nutritional and physiological status of plants, in order to allow a correction of nutrition programs during the season.

  4. Fluid inclusion from drill hole DW-5, Hohi geothermal area, Japan: Evidence of boiling and procedure for estimating CO2 content

    Science.gov (United States)

    Sasada, M.; Roedder, E.; Belkin, H.E.

    1986-01-01

    Fluid inclusion studies have been used to derive a model for fluid evolution in the Hohi geothermal area, Japan. Six types of fluid inclusions are found in quartz obtained from the drill core of DW-5 hole. They are: (I) primary liquid-rich with evidence of boiling; (II) primary liquid-rich without evidence of boiling; (III) primary vapor-rich (assumed to have been formed by boiling); (IV) secondary liquid-rich with evidence of boiling; (V) secondary liquid-rich without evidence of boiling; (VI) secondary vapor-rich (assumed to have been formed by boiling). Homogenization temperatures (Th) range between 196 and 347??C and the final melting point of ice (Tm) between -0.2 and -4.3??C. The CO2 content was estimated semiquantitatively to be between 0 and 0.39 wt. % based on the bubble behavior on crushing. NaCl equivalent solid solute salinity of fluid inclusions was determined as being between 0 and 6.8 wt. % after minor correction for CO2 content. Fluid inclusions in quartz provide a record of geothermal activity of early boiling and later cooling. The CO2 contents and homogenization temperatures of fluid inclusions with evidence of boiling generally increase with depth; these changes, and NaCl equivalent solid solute salinity of the fluid can be explained by an adiabatic boiling model for a CO2-bearing low-salinity fluid. Some high-salinity inclusions without CO2 are presumed to have formed by a local boiling process due to a temperature increase or a pressure decrease. The liquid-rich primary and secondary inclusions without evidence of boiling formed during the cooling process. The salinity and CO2 content of these inclusions are lower than those in the boiling fluid at the early stage, probably as a result of admixture with groundwater. ?? 1986.

  5. Estimation of the shelf life of canned marinated hearts of artichoke (Cynara scolymus L. and the content of omega 3 and omega 6

    Directory of Open Access Journals (Sweden)

    Carmen Rojas Padilla

    2010-12-01

    Full Text Available In this study we estimated shelf life of canned marinated hearts of artichoke (Cynara scolymus L. which had the major sensory preference in color and flavor evaluated by a semi trained panel conformed by 15 judges. Also omega 3 and omega 6 content was determined (28.69 g/100g y 43.26 g/100g of fat respectively which are within the limit approved by the World Health Organization. It was done the estimation of the shelf life by accelerated testing, the samples were incubated at 37ºC, 49ºC and 55ºC, evaluating the kinetic of deterioration of the fat in function of the peroxide index that followed a reaction of order zero. The temperature effect was evaluated with the equation of Arrhenius, and the activation energy was 96115.6 J/mol. At a storage temperature of 20 ºC, the estimation of shelf life was 892 days.

  6. Gene expression programming approach for the estimation of moisture ratio in herbal plants drying with vacuum heat pump dryer

    Science.gov (United States)

    Dikmen, Erkan; Ayaz, Mahir; Gül, Doğan; Şahin, Arzu Şencan

    2017-07-01

    The determination of drying behavior of herbal plants is a complex process. In this study, gene expression programming (GEP) model was used to determine drying behavior of herbal plants as fresh sweet basil, parsley and dill leaves. Time and drying temperatures are input parameters for the estimation of moisture ratio of herbal plants. The results of the GEP model are compared with experimental drying data. The statistical values as mean absolute percentage error, root-mean-squared error and R-square are used to calculate the difference between values predicted by the GEP model and the values actually observed from the experimental study. It was found that the results of the GEP model and experimental study are in moderately well agreement. The results have shown that the GEP model can be considered as an efficient modelling technique for the prediction of moisture ratio of herbal plants.

  7. Allelic variation of the inducible costimulator (ICOS) gene: detection of polymorphisms, analysis of the promoter region, and extended haplotype estimation

    DEFF Research Database (Denmark)

    Andersen, A.D.H.; Lange, Marianne; Lillevang, S.T.

    2003-01-01

    The human chromosome region 2q33 including the three costimulatory molecules CD28, CTLA-4 and ICOS, has been subject to much attention due to its linkage to a number of autoimmune diseases. The search for the causal relationship of this linkage has revealed several polymorphisms, but no variations...... in the amino acid sequences except for one polymorphism in, the leader sequence of CTLA-4. In the present study, we examined the ICOS gene of an unrelated group of healthy donors from the Danish population. We were able to report 16 intronic SNP, one intronic G-insert and two repeat regions in intron 4......, consistent with the [T](n) and the [GT](n) regions reported in a Japanese study. Putative haplotypes for the established SNP and repeat polymorphisms have been estimated by computational analysis. Sequencing of similar to3500 by of the upstream region of ICOS revealed an additional eight SNP of which two...

  8. Bloom's syndrome. VI. The disorder in Israel and an estimation of the gene frequency in the Ashkenazim.

    Science.gov (United States)

    German, J; Bloom, D; Passarge, E; Fried, K; Goodman, R M; Katzenellenbogen, I; Laron, Z; Legum, C; Levin, S; Wahrman

    1977-01-01

    An effort was made to identify all individuals with Bloom's syndrome living in Israel between September 1971 and September 1972. Each of the eight individuals located were Jewish and could readily be classified Ashkenazic. The frequency of the Bloom's syndrome gene in Ashkenazim was estimated to be .0042 (minimum), implying a heterozygote frequency greater than 1 in 120. A striking distortion of the sex ratio (M/F = 7.0) may have been due to underascertainment of affected females. One of the affected individuals ascertained during the survey subsequently has died from cancer, which is in keeping with the recognized cancer proneness of this condition. Four of the affected have married, but no conception is known to have occurred, which suggests that sub- or infertility is a feature of the syndrome. PMID:930922

  9. Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes.

    Science.gov (United States)

    Carpenter, Margaret A; Shaw, Martin; Cooper, Rebecca D; Frew, Tonya J; Butler, Ruth C; Murray, Sarah R; Moya, Leire; Coyne, Clarice J; Timmerman-Vaughan, Gail M

    2017-08-01

    Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea. To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. Variation in the percent amylose composition of extracted seed starch and (amylopectin) chain length distribution, one measure of starch structure, were characterized for these lines. Association mapping was undertaken to identify polymorphisms associated with the variation in starch chain length distribution and percent amylose, using a mixed linear model that incorporated population structure and kinship. Associations were found for polymorphisms in seven candidate genes plus Mendel's r locus (which conditions the round versus wrinkled seed phenotype). The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways. The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding.

  10. Effects of heat stress on the endogenous contents of hormones and related gene expression in developing axillary tubes of potato

    Science.gov (United States)

    Potatoes are a cool season crop and optimum tuber initiation, development, yield, and quality require growing temperatures between 15 -20°C. At temperatures above 30°C, tuber initiation is delayed or prevented and developing tubers exhibit decreased starch content, increased malformation, chain-tube...

  11. Nanocarrier-mediated foliar zinc fertilization influences expression of metal homeostasis related genes in flag leaves and enhances gluten content in durum wheat.

    Science.gov (United States)

    Deshpande, Paresh; Dapkekar, Ashwin; Oak, Manoj; Paknikar, Kishore; Rajwade, Jyutika

    2018-01-01

    Wheat is the staple food for most of the world's population; however, it is a poor source of zinc. Foliar fertilization of zinc via zinc loaded chitosan nanocarriers (Zn-CNP) post-anthesis has proved to be a promising approach for grain zinc enhancement in durum wheat as evidenced in our earlier study. However, the molecular mechanism of uptake of zinc via Zn-CNP remains unclear. Foliar application of Zn-CNP was performed at post anthesis stages in two durum wheat cultivars (MACS 3125 and UC1114, containing the Gpc-B1 gene), and expression levels of several metal-related genes were analyzed during early senescence. Zn-CNP application indeed caused changes in gene expression as revealed by qPCR data on representative genes involved in metal homeostasis, phloem transporters, and leaf senescence. Furthermore, zinc-regulated transporters and iron (Fe)-regulated transporter-like protein (ZIP) family [ZIP1, ZIP7, ZIP15], CA (carbonic anhydrase), and DMAS (2'-deoxymugineic acid synthase) in flag leaves exhibited significant correlation with zinc content in the seeds. The analysis of grain endosperm proteins showed enhancement of gamma gliadins while other gluten subunits decreased. Gene expression within ZIP family members varied with the type of cultivar mostly attributed to the Gpc-B1, concentration of external zinc ions as well as the type of tissue analyzed. Correlation analysis revealed the involvement of the selected genes in zinc enhancement. At the molecular level, uptake of zinc via Zn-CNP nanocarrier was comparable to the uptake of zinc via common zinc fertilizers i.e. ZnSO4.

  12. Nanocarrier-mediated foliar zinc fertilization influences expression of metal homeostasis related genes in flag leaves and enhances gluten content in durum wheat.

    Directory of Open Access Journals (Sweden)

    Paresh Deshpande

    Full Text Available Wheat is the staple food for most of the world's population; however, it is a poor source of zinc. Foliar fertilization of zinc via zinc loaded chitosan nanocarriers (Zn-CNP post-anthesis has proved to be a promising approach for grain zinc enhancement in durum wheat as evidenced in our earlier study. However, the molecular mechanism of uptake of zinc via Zn-CNP remains unclear.Foliar application of Zn-CNP was performed at post anthesis stages in two durum wheat cultivars (MACS 3125 and UC1114, containing the Gpc-B1 gene, and expression levels of several metal-related genes were analyzed during early senescence. Zn-CNP application indeed caused changes in gene expression as revealed by qPCR data on representative genes involved in metal homeostasis, phloem transporters, and leaf senescence. Furthermore, zinc-regulated transporters and iron (Fe-regulated transporter-like protein (ZIP family [ZIP1, ZIP7, ZIP15], CA (carbonic anhydrase, and DMAS (2'-deoxymugineic acid synthase in flag leaves exhibited significant correlation with zinc content in the seeds. The analysis of grain endosperm proteins showed enhancement of gamma gliadins while other gluten subunits decreased. Gene expression within ZIP family members varied with the type of cultivar mostly attributed to the Gpc-B1, concentration of external zinc ions as well as the type of tissue analyzed. Correlation analysis revealed the involvement of the selected genes in zinc enhancement.At the molecular level, uptake of zinc via Zn-CNP nanocarrier was comparable to the uptake of zinc via common zinc fertilizers i.e. ZnSO4.

  13. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  14. Low-temperature conditioning of "seed" cloves enhances the expression of phenolic metabolism related genes and anthocyanin content in 'Coreano' garlic (Allium sativum) during plant development.

    Science.gov (United States)

    Dufoo-Hurtado, Miguel D; Zavala-Gutiérrez, Karla G; Cao, Cong-Mei; Cisneros-Zevallos, Luis; Guevara-González, Ramón G; Torres-Pacheco, Irineo; Vázquez-Barrios, M Estela; Rivera-Pastrana, Dulce M; Mercado-Silva, Edmundo M

    2013-11-06

    Low-temperature conditioning of garlic "seed" cloves accelerated the development of the crop cycle, decreased plant growth, and increased the synthesis of phenolic compounds and anthocyanins in the outer scale leaves of the bulbs at harvest time, leading to 3-fold content increase compared with those conditioned at room temperature. Cold conditioning of "seed" cloves also altered the anthocyanin profile during bulb development and at harvest. Two new anthocyanins are reported for the first time in garlic. The high phenolics and anthocyanin contents in bulbs of plants generated from "seed" cloves conditioned at 5 °C for 5 weeks were preceded by overexpression of some putative genes of the phenolic metabolism [6-fold for phenylalanine ammonia lyase (PAL)] and anthocyanin synthesis [1-fold for UDP-sugar:flavonoid 3-O-glycosyltransferase (UFGT)] compared with those conditioned at room temperature.

  15. SNP in Chalcone Synthase gene is associated with variation of 6-gingerol content in contrasting landraces of Zingiber officinale.Roscoe.

    Science.gov (United States)

    Ghosh, Subhabrata; Mandi, Swati Sen

    2015-07-25

    Zingiber officinale, medicinally the most important species within Zingiber genus, contains 6-gingerol as the active principle. This compound obtained from rhizomes of Z.officinale, has immense medicinal importance and is used in various herbal drug formulations. Our record of variation in content of this active principle, viz. 6-gingerol, in land races of this drug plant collected from different locations correlated with our Gene expression studies exhibiting high Chalcone Synthase gene (Chalcone Synthase is the rate limiting enzyme of 6-gingerol biosynthesis pathway) expression in high 6-gingerol containing landraces than in the low 6-gingerol containing landraces. Sequencing of Chalcone Synthase cDNA and subsequent multiple sequence alignment revealed seven SNPs between these contrasting genotypes. Converting this nucleotide sequence to amino acid sequence, alteration of two amino acids becomes evident; one amino acid change (asparagine to serine at position 336) is associated with base change (A→G) and another change (serine to leucine at position 142) is associated with the base change (C→T). Since asparagine at position 336 is one of the critical amino acids of the catalytic triad of Chalcone Synthase enzyme, responsible for substrate binding, our study suggests that landraces with a specific amino acid change viz. Asparagine (found in high 6-gingerol containing landraces) to serine causes low 6-gingerol content. This is probably due to a weak enzyme substrate association caused by the absence of asparagine in the catalytic triad. Detailed study of this finding could also help to understand molecular mechanism associated with variation in 6-gingerol content in Z.officinale genotypes and thereby strategies for developing elite genotypes containing high 6-gingerol content. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. SNPs in genes functional in starch-sugar interconversion associate with natural variation of tuber starch and sugar content of potato (Solanum tuberosum L.).

    Science.gov (United States)

    Schreiber, Lena; Nader-Nieto, Anna Camila; Schönhals, Elske Maria; Walkemeier, Birgit; Gebhardt, Christiane

    2014-07-31

    Starch accumulation and breakdown are vital processes in plant storage organs such as seeds, roots, and tubers. In tubers of potato (Solanum tuberosum L.) a small fraction of starch is converted into the reducing sugars glucose and fructose. Reducing sugars accumulate in response to cold temperatures. Even small quantities of reducing sugars affect negatively the quality of processed products such as chips and French fries. Tuber starch and sugar content are inversely correlated complex traits that are controlled by multiple genetic and environmental factors. Based on in silico annotation of the potato genome sequence, 123 loci are involved in starch-sugar interconversion, approximately half of which have been previously cloned and characterized. By means of candidate gene association mapping, we identified single-nucleotide polymorphisms (SNPs) in eight genes known to have key functions in starch-sugar interconversion, which were diagnostic for increased tuber starch and/or decreased sugar content and vice versa. Most positive or negative effects of SNPs on tuber-reducing sugar content were reproducible in two different collections of potato cultivars. The diagnostic SNP markers are useful for breeding applications. An allele of the plastidic starch phosphorylase PHO1a associated with increased tuber starch content was cloned as full-length cDNA and characterized. The PHO1a-HA allele has several amino acid changes, one of which is unique among all known starch/glycogen phosphorylases. This mutation might cause reduced enzyme activity due to impaired formation of the active dimers, thereby limiting starch breakdown. Copyright © 2014 Schreiber et al.

  17. The Phytoene synthase gene family of apple (Malus x domestica) and its role in controlling fruit carotenoid content.

    Science.gov (United States)

    Ampomah-Dwamena, Charles; Driedonks, Nicky; Lewis, David; Shumskaya, Maria; Chen, Xiuyin; Wurtzel, Eleanore T; Espley, Richard V; Allan, Andrew C

    2015-07-28

    Carotenoid compounds play essential roles in plants such as protecting the photosynthetic apparatus and in hormone signalling. Coloured carotenoids provide yellow, orange and red colour to plant tissues, as well as offering nutritional benefit to humans and animals. The enzyme phytoene synthase (PSY) catalyses the first committed step of the carotenoid biosynthetic pathway and has been associated with control of pathway flux. We characterised four PSY genes found in the apple genome to further understand their involvement in fruit carotenoid accumulation. The apple PSY gene family, containing six members, was predicted to have three functional members, PSY1, PSY2, and PSY4, based on translation of the predicted gene sequences and/or corresponding cDNAs. However, only PSY1 and PSY2 showed activity in a complementation assay. Protein localisation experiments revealed differential localization of the PSY proteins in chloroplasts; PSY1 and PSY2 localized to the thylakoid membranes, while PSY4 localized to plastoglobuli. Transcript levels in 'Granny Smith' and 'Royal Gala' apple cultivars showed PSY2 was most highly expressed in fruit and other vegetative tissues. We tested the transient activation of the apple PSY1 and PSY2 promoters and identified potential and differential regulation by AP2/ERF transcription factors, which suggested that the PSY genes are controlled by different transcriptional mechanisms. The first committed carotenoid pathway step in apple is controlled by MdPSY1 and MdPSY2, while MdPSY4 play little or no role in this respect. This has implications for apple breeding programmes where carotenoid enhancement is a target and would allow co-segregation with phenotypes to be tested during the development of new cultivars.

  18. Effects of 24-epibrassinolide and green light on plastid gene transcription and cytokinin content of barley leaves

    Czech Academy of Sciences Publication Activity Database

    Efimova, N.V.; Vaňková, Radomíra; Kusnetsov, V.; Litvinovskaya, R. P.; Zlobin, Y.L.; Dobrev, Petre; Vedenicheva, N.P.; Savchuk, A. L.; Karnachuk, R. A.; Kudryakova, N.V.; Kuznetsov, V. D.

    2017-01-01

    Roč. 120, APR (2017), s. 32-40 ISSN 0039-128X Institutional support: RVO:61389030 Keywords : lupinus-luteus cotyledons * arabidopsis-thaliana * de-etiolation * abscisic-acid * brassinosteroid biosynthesis * plant development * hormonal balance * mutant * expression * growth * Brassinosteroids * Cytokinin * Gene expression * Green light * Hordeum vulgare * Transcription Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 2.282, year: 2016

  19. Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility

    Czech Academy of Sciences Publication Activity Database

    Sloan, D.B.; Müller, Karel; McCauley, D.; Taylor, D.R.; Štorchová, Helena

    2012-01-01

    Roč. 196, č. 4 (2012), s. 1228-1239 ISSN 0028-646X R&D Projects: GA ČR GA521/09/0261; GA MŠk(CZ) LC06004; GA MŠk ME09035 Institutional research plan: CEZ:AV0Z50380511 Keywords : cytoplasmic male sterility (CMS) * gynodioecy * intracellular gene transfer Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.736, year: 2012

  20. Regulatory polymorphisms in the bovine Ankyrin 1 gene promoter are associated with tenderness and intra-muscular fat content

    LENUS (Irish Health Repository)

    Aslan, Ozlem

    2010-12-15

    Abstract Background Recent QTL and gene expression studies have highlighted ankyrins as positional and functional candidate genes for meat quality. Our objective was to characterise the promoter region of the bovine ankyrin 1 gene and to test polymorphisms for association with sensory and technological meat quality measures. Results Seven novel promoter SNPs were identified in a 1.11 kb region of the ankyrin 1 promoter in Angus, Charolais and Limousin bulls (n = 15 per breed) as well as 141 crossbred beef animals for which meat quality data was available. Eighteen haplotypes were inferred with significant breed variation in haplotype frequencies. The five most frequent SNPs and the four most frequent haplotypes were subsequently tested for association with sensory and technological measures of meat quality in the crossbred population. SNP1, SNP3 and SNP4 (which were subsequently designated regulatory SNPs) and SNP5 were associated with traits that contribute to sensorial and technological measurements of tenderness and texture; Haplotype 1 and haplotype 4 were oppositely correlated with traits contributing to tenderness (P < 0.05). While no single SNP was associated with intramuscular fat (IMF), a clear association with increased IMF and juiciness was observed for haplotype 2. Conclusion The conclusion from this study is that alleles defining haplotypes 2 and 4 could usefully contribute to marker SNP panels used to select individuals with improved IMF\\/juiciness or tenderness in a genome-assisted selection framework.

  1. Regulatory polymorphisms in the bovine Ankyrin 1 gene promoter are associated with tenderness and intramuscular fat content

    Directory of Open Access Journals (Sweden)

    Sweeney Torres

    2010-12-01

    Full Text Available Abstract Background Recent QTL and gene expression studies have highlighted ankyrins as positional and functional candidate genes for meat quality. Our objective was to characterise the promoter region of the bovine ankyrin 1 gene and to test polymorphisms for association with sensory and technological meat quality measures. Results Seven novel promoter SNPs were identified in a 1.11 kb region of the ankyrin 1 promoter in Angus, Charolais and Limousin bulls (n = 15 per breed as well as 141 crossbred beef animals for which meat quality data was available. Eighteen haplotypes were inferred with significant breed variation in haplotype frequencies. The five most frequent SNPs and the four most frequent haplotypes were subsequently tested for association with sensory and technological measures of meat quality in the crossbred population. SNP1, SNP3 and SNP4 (which were subsequently designated regulatory SNPs and SNP5 were associated with traits that contribute to sensorial and technological measurements of tenderness and texture; Haplotype 1 and haplotype 4 were oppositely correlated with traits contributing to tenderness (P Conclusion The conclusion from this study is that alleles defining haplotypes 2 and 4 could usefully contribute to marker SNP panels used to select individuals with improved IMF/juiciness or tenderness in a genome-assisted selection framework.

  2. Retrieval of ice cloud properties using an optimal estimation algorithm and MODIS infrared observations. Part I: Forward model, error analysis, and information content

    Science.gov (United States)

    Wang, Chenxi; Platnick, Steven; Zhang, Zhibo; Meyer, Kerry; Yang, Ping

    2018-01-01

    An optimal estimation (OE) retrieval method is developed to infer three ice cloud properties simultaneously: optical thickness (τ), effective radius (reff), and cloud-top height (h). This method is based on a fast radiative transfer (RT) model and infrared (IR) observations from the MODerate resolution Imaging Spectroradiometer (MODIS). This study conducts thorough error and information content analyses to understand the error propagation and performance of retrievals from various MODIS band combinations under different cloud/atmosphere states. Specifically, the algorithm takes into account four error sources: measurement uncertainty, fast RT model uncertainty, uncertainties in ancillary datasets (e.g., atmospheric state), and assumed ice crystal habit uncertainties. It is found that the ancillary and ice crystal habit error sources dominate the MODIS IR retrieval uncertainty and cannot be ignored. The information content analysis shows that, for a given ice cloud, the use of four MODIS IR observations is sufficient to retrieve the three cloud properties. However, the selection of MODIS IR bands that provide the most information and their order of importance varies with both the ice cloud properties and the ambient atmospheric and the surface states. As a result, this study suggests the inclusion of all MODIS IR bands in practice since little a priori information is available. PMID:29707470

  3. Retrieval of Ice Cloud Properties Using an Optimal Estimation Algorithm and MODIS Infrared Observations. Part I: Forward Model, Error Analysis, and Information Content

    Science.gov (United States)

    Wang, Chenxi; Platnick, Steven; Zhang, Zhibo; Meyer, Kerry; Yang, Ping

    2016-01-01

    An optimal estimation (OE) retrieval method is developed to infer three ice cloud properties simultaneously: optical thickness (tau), effective radius (r(sub eff)), and cloud top height (h). This method is based on a fast radiative transfer (RT) model and infrared (IR) observations from the MODerate resolution Imaging Spectroradiometer (MODIS). This study conducts thorough error and information content analyses to understand the error propagation and performance of retrievals from various MODIS band combinations under different cloud/atmosphere states. Specifically, the algorithm takes into account four error sources: measurement uncertainty, fast RT model uncertainty, uncertainties in ancillary data sets (e.g., atmospheric state), and assumed ice crystal habit uncertainties. It is found that the ancillary and ice crystal habit error sources dominate the MODIS IR retrieval uncertainty and cannot be ignored. The information content analysis shows that for a given ice cloud, the use of four MODIS IR observations is sufficient to retrieve the three cloud properties. However, the selection of MODIS IR bands that provide the most information and their order of importance varies with both the ice cloud properties and the ambient atmospheric and the surface states. As a result, this study suggests the inclusion of all MODIS IR bands in practice since little a priori information is available.

  4. [Mesothelioma in construction workers: risk estimate, lung content of asbestos fibres, claims for compensation for occupational disease in the Veneto Region mesothelioma register].

    Science.gov (United States)

    Merler, E; Bressan, Vittoria; Somigliana, Anna

    2009-01-01

    Work in the construction industry is causing the highest number of mesotheliomas among the residents of the Veneto Region (north-east Italy, 4,5 million inhabitants). To sum up the results on occurrence, asbestos exposure, lung fibre content analyses, and compensation for occupational disease. Case identification and asbestos exposure classification: active search of mesotheliomas that were diagnosed via histological or cytological examinations occurring between 1987 and 2006; a probability of asbestos exposure was attributed to each case, following interviews with the subjects or their relatives and collection of data on the jobs held over their lifetime. Risk estimate among construction workers: the ratio between cases and person-years, the latter derived from the number of construction workers reported by censuses. Lung content of asbestos fibres: examination of lung specimens by Scanning Electron Microscope to determine number and type of fibres. Claims for compensation and compensation awarded: data obtained from the National Institute for Insurance against Occupational Diseases available for the period 1999-2006. of 952 mesothelioma cases classified as due to asbestos exposure, 251 were assigned to work in the construction industry (21 of which due to domestic of environmental exposures), which gives a rate of 4.1 (95% CI 3.6-4.8) x 10(5) x year among construction workers. The asbestos fibre content detected in the lungs of 11 construction workers showed a mean of 1.7 x 10(6) fibres/g dry tissue (range 350,000-3 million) for fibres > 1 micro, almost exclusively due to amphibole fibres. 62% of the claims for compensation were granted but the percentage fell to less than 40% when claims were submitted by a relative, after the death of the subject. The prevalence of mesothelioma occurring among construction workers is high and is associated with asbestos exposure; the risk is underestimated by the subjects and their relatives. All mesotheliomas occurring among

  5. Analysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes.

    Science.gov (United States)

    Mondal, Sunil Kanti; Kundu, Sudip; Das, Rabindranath; Roy, Sujit

    2016-08-01

    Bacteria and archaea have evolved with the ability to fix atmospheric dinitrogen in the form of ammonia, catalyzed by the nitrogenase enzyme complex which comprises three structural genes nifK, nifD and nifH. The nifK and nifD encodes for the beta and alpha subunits, respectively, of component 1, while nifH encodes for component 2 of nitrogenase. Phylogeny based on nifDHK have indicated that Cyanobacteria is closer to Proteobacteria alpha and gamma but not supported by the tree based on 16SrRNA. The evolutionary ancestor for the different trees was also different. The GC1 and GC2% analysis showed more consistency than GC3% which appeared to below for Firmicutes, Cyanobacteria and Euarchaeota while highest in Proteobacteria beta and clearly showed the proportional effect on the codon usage with a few exceptions. Few genes from Firmicutes, Euryarchaeota, Proteobacteria alpha and delta were found under mutational pressure. These nif genes with low and high GC3% from different classes of organisms showed similar expected number of codons. Distribution of the genes and codons, based on codon usage demonstrated opposite pattern for different orientation of mirror plane when compared with each other. Overall our results provide a comprehensive analysis on the evolutionary relationship of the three structural nif genes, nifK, nifD and nifH, respectively, in the context of codon usage bias, GC content relationship and amino acid composition of the encoded proteins and exploration of crucial statistical method for the analysis of positive data with non-constant variance to identify the shape factors of codon adaptation index.

  6. Increase of anthraquinone content in Rubia cordifolia cells transformed by native and constitutively active forms of the AtCPK1 gene.

    Science.gov (United States)

    Shkryl, Yury N; Veremeichik, G N; Makhazen, D S; Silantieva, S A; Mishchenko, N P; Vasileva, E A; Fedoreyev, S A; Bulgakov, V P

    2016-09-01

    Overexpression of both native and mutant forms of AtCPK1 in Rubia cordifolia cells increased anthraquinone production and transcript abundance of the RcIPPI, RcOSBL, RcOSBS , and RcICS genes to different extents. Calcium-dependent protein kinases (CDPKs) are involved in various cell processes and are regulated by a calcium signal system. CDPKs also function in plant defense against stress factors such as pathogens, temperature, and salinity. In this study, we compared the effect of heterologous expression of two forms of the Arabidopsis AtCPK1 gene, native and constitutively active (Ca(2+)-independent), on anthraquinone production in transgenic Rubia cordifolia cells. Significant qualitative and quantitative differences were found in the content of anthraquinone derivatives in control and AtCPK1-transgenic calli. Expression of the AtCPK1 gene increased anthraquinone production by 3 and 12 times for native and constitutively active forms, respectively, compared with control cells. In addition, we identified and quantified the expression of genes encoding key enzymes of the anthraquinone biosynthesis pathway, including isochorismate synthase (ICS), o-succinylbenzoate synthase (OSBS), o-succinylbenzoate ligase (OSBL), and isopentenyl diphosphate isomerase (IPPi). In all AtCPK1-transgenic cell lines, expression of ICS, OSBS, OSBL, and IPPi increased considerably at 14-15 days of subculture and decreased at the end of cultivation (30 days). The results suggest that both native and constitutively active AtCPK1 forms induced anthraquinone accumulation at the logarithmic growth stage via enhancement of expression of genes involved in the metabolism of anthraquinones or their regulatory mechanisms.

  7. Isolation of the human anionic glutathione S-transferase cDNA and the relation of its gene expression to estrogen-receptor content in primary breast cancer

    International Nuclear Information System (INIS)

    Moscow, J.A.; Townsend, A.J.; Goldsmith, M.E.; Whang-Peng, J.; Vickers, P.J.; Poisson, R.; Legault-Poisson, S.; Myers, C.E.; Cowan, K.H.

    1988-01-01

    The development of multidrug resistance in MCF7 human breast cancer cells is associated with overexpression of P-glycoprotein, changes in activities of several detoxication enzymes, and loss of hormone sensitivity and estrogen receptors (ERs). The authors have cloned the cDNA for one of the drug-detoxifying enzymes overexpressed in multidrug-resistant MCF7 cells (Adr R MCF7), the anionic isozyme of glutathione S-transferase (GSTπ). Hybridization with this GSTπ cDNA, GSTπ-1, demonstrated that increased GSTπ activity in Adr R MCF7 cells is associated with overexpression but not with amplification of the gene. They mapped the GSTπ gene to human chromosome 11q13 by in situ hybridization. Since multidrug resistance and GSTπ overexpression are associated with the loss of ERs in Adr R MCF7 cells, they examined several other breast cancer cell lines that were not selected for drug resistance. In each of these cell lines they found an inverse association between GSTπ expression and ER content. They also examined RNA from 21 primary breast cancers and found a similar association between GSTπ expression and ER content in vivo. The finding of similar patterns of expression of a drug-detoxifying enzyme and of ERs in vitro as well as in vivo suggests that ER-negative breast cancer cells may have greater protection against antineoplastic agents conferred by GSTπ than ER-positive tumors

  8. Effects of methyl jasmonate, on stevioside and rebaudioside A content and expression of the ent-Kaurenoic acid 13-hydroxylase gene in Stevia rebaudiana Bert. in vitro

    Directory of Open Access Journals (Sweden)

    Mehrdad Behmanesh

    2014-08-01

    Full Text Available Glycosides are a form of secondary metabolites that consist variety compounds and in some cases can play a role in primary metabolism. Steviol is lipophilic skeleton of Stevioside and Rebaudioside A, two main glycosides of Stevia rebuadiana. Steviol glycosides which are synthesized in S.rebaudiana have important medical and nutritional values as high intensity natural sweeteners. Steviol is synthesized from Kaurenoic acid in chloroplastic Terpenoid pathway that mediated by Kaurenoic acid 13-hydroxylase. In this study, HPLC method and RT-PCR were performed for quantification of glycosides and gene expression (ent-Kaurenoic acid 13-hydroxylase respectively. Methyl jasmonate treatment (at 20 micromolar in vitro induced glycoside biosynthesis significantly (P≤0.05 whereas higher concentration of Methyl jasmonate (100 µM caused a decrease in glycoside production and growth. The most glycoside content of the plant was three days after treatment. Also Methyl jasmonate treatment caused an increase in ent-Kaurenoic 13-hydroxylase gene expression from 6 hours to 48 hours (after treatment Results showed that biosynthesis of Stevia glycosides was probably a defense mechanism against pathogens and herbivore insects. Also we found that different concentrations of Methyl jasmonate, alter the ratio between glycosides rather than the increase in glycoside contents.

  9. Relative transcription of Listeria monocytogenes virulence genes in liver pâtés with varying NaCl content

    DEFF Research Database (Denmark)

    Olesen, Inger; Thorsen, Line; Jespersen, Lene

    2010-01-01

    three liver pâtés with reduced NaCl content of which one also has been supplied with organic acids (Ca-acetate and Ca-lactate). The three strains (EGD-e: reference strain; O57: more NaCl sensitive; 6896: more NaCl tolerant) were selected out of twelve strains based on their growth in BHI broth adjusted......B for both O57 and 6896 were significantly higher when the strains were grown in BHI compared to the standard liver pâté. Reducing the NaCl content of the standard liver pâté did not change relative transcription levels of prfA, inlA, sigB or clpC (except for prfA in O57 and sigB in 6896). However......, the presence of Ca-acetate and Ca-lactate induced relative transcription of the stress response gene, clpC, for all three strains. This study demonstrates that relative microbial gene transcription can be measured in complex food matrices and points to the need for designing experimental set-ups in real food...

  10. Effect of foliar application of salicylic acid, hydrogen peroxide and a xyloglucan oligosaccharide on capsiate content and gene expression associatedwith capsinoids synthesis in Capsicum annuum L.

    Science.gov (United States)

    Zunun-Perez, A Y; Guevara-Figueroa, T; Jimenez-Garcia, S N; Feregrino-Perez, A A; Gautier, F; Guevara-Gonzalez, R G

    2017-06-01

    Capsinoids are non-pungent analogues of capsaicinoids in pepper (Capsicum spp). The absence of pungency, in addition to their biological activities similar to that of capsaicinoids such as anti-inflammatory, antimicrobial, and antioxidant properties, makes capsinoids an excellent option for increasing use in human and animal nutrition, as well as health and pharmaceutical industries. There are only few sources of pepper producing capsinoids, and one of them (accession 509-45-1), Capsicum annuum L., is a potential source for increasing capsinoids content using strategies as controlled elicitation during plant production in the greenhouse. In this research we evaluated the effect of weekly and one-day-before-harvest foliar applications of hydrogen peroxide, salicylic acid and a xyloglucan oligosaccharide on the concentration of capsiate in fruits of this pepper accession, as well as the gene expression of phenylalanine ammonia-lyase (pal), putative aminotransferase (pamt), capsaicin synthase (at3) and β-keto acyl synthase (kas). Results showed that the two tested concentrations of H2O2 significantly increased capsiate content and gene expression associated with capsaicinoids (pamt, at3 and kas) and the phenylpropanoids (pal) pathways. Plant yield was not affected using this induction strategy. Our results indicated that the pre-harvest and weekly application of hydrogen peroxide and xyloglucan oligosaccharide improved production of capsiate in C. annuum L.

  11. A comparative study of natural 40K content estimated through whole body counting and dietary intake around Narora Atomic Power Station

    International Nuclear Information System (INIS)

    Gautam, Y.P.; Dube, B.; Hegde, A.G.

    2005-01-01

    773 radiation workers at NAPS, aged 20 to 59 years, were monitored using Shadow Shield Whole Body Counting System having NaI (Tl) crystal coupled with NETS-3 1 K Multi Channel Analyser (MCA) to determine the 40 K activity in the body and assess internal dose due to naturally occurring 40 K. The data have been segregated to make analyses for vegetarian and non-vegetarian. The average annual dose from 40 K for the subjects is evaluated as 156.4 ± 36.1 mSv. Natural 40 K content in 463 environmental samples collected from Narora environ estimated using NaI(Tl) well type detector coupled with 1 K NETS-3 Multichannel analyser (MCA). Assessment of daily intake of natural 40 K has been estimated from average daily intake of dietary items and the associated 40 K activity. It works out to be 67.17 ± 16.28 Bq/d and that obtained through analysis of complete meal samples was 73.22 ± 9.78 Bq/ d. The average annual dose to a member of public of this region due to natural 40 K through ingestion route works out to be 152.12 ± 36.83 mSv/year. (author)

  12. Estimation of local spectrum content of cervical cancer-related features via two dimensional method of geometric restriction in frequency domain

    International Nuclear Information System (INIS)

    Van Raad, V.

    2004-01-01

    Digital colposcopy is an emerging new technology, which can be used as adjunct to the conventional Pap test for staging of cervical cancer and it can improve the diagnostic accuracy of the test. Computer aided diagnosis (CAD) in digital colposcopy has as a goal to segment and outline abnormal areas on the cervix, one of which is an important anatomical landmark on the ectocervix - the transformation zone (TZ). In this paper we proposed a new method for estimation of the local spectrum features of cervical cancer in vivo. We used a 2D method to estimate the energy of the local frequency bands, using a geometric restriction (GR). In the current work we reported up to 12 dB difference between the local power spectral density content of the region of interest (ROI) and (ROI) C for the mid-frequency band. We devised a method to present pseudo-color visual maps of the cervical images, useful for CAD and successful ROI segmentation. (author)

  13. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.

    Directory of Open Access Journals (Sweden)

    Leila do Nascimento Vieira

    Full Text Available BACKGROUND: Podocarpus lambertii (Podocarpaceae is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. METHODOLOGY/PRINCIPAL FINDINGS: The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR. It contains 118 unique genes and one duplicated tRNA (trnN-GUU, which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi and Araucariaceae (Agathis dammara. Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. CONCLUSION: The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of

  14. Improved estimation of leaf area index and leaf chlorophyll content of a potato crop using multi-angle spectral data - potential of unmanned aerial vehicle imagery

    Science.gov (United States)

    Roosjen, Peter P. J.; Brede, Benjamin; Suomalainen, Juha M.; Bartholomeus, Harm M.; Kooistra, Lammert; Clevers, Jan G. P. W.

    2018-04-01

    In addition to single-angle reflectance data, multi-angular observations can be used as an additional information source for the retrieval of properties of an observed target surface. In this paper, we studied the potential of multi-angular reflectance data for the improvement of leaf area index (LAI) and leaf chlorophyll content (LCC) estimation by numerical inversion of the PROSAIL model. The potential for improvement of LAI and LCC was evaluated for both measured data and simulated data. The measured data was collected on 19 July 2016 by a frame-camera mounted on an unmanned aerial vehicle (UAV) over a potato field, where eight experimental plots of 30 × 30 m were designed with different fertilization levels. Dozens of viewing angles, covering the hemisphere up to around 30° from nadir, were obtained by a large forward and sideways overlap of collected images. Simultaneously to the UAV flight, in situ measurements of LAI and LCC were performed. Inversion of the PROSAIL model was done based on nadir data and based on multi-angular data collected by the UAV. Inversion based on the multi-angular data performed slightly better than inversion based on nadir data, indicated by the decrease in RMSE from 0.70 to 0.65 m2/m2 for the estimation of LAI, and from 17.35 to 17.29 μg/cm2 for the estimation of LCC, when nadir data were used and when multi-angular data were used, respectively. In addition to inversions based on measured data, we simulated several datasets at different multi-angular configurations and compared the accuracy of the inversions of these datasets with the inversion based on data simulated at nadir position. In general, the results based on simulated (synthetic) data indicated that when more viewing angles, more well distributed viewing angles, and viewing angles up to larger zenith angles were available for inversion, the most accurate estimations were obtained. Interestingly, when using spectra simulated at multi-angular sampling configurations as

  15. Estimating leaf functional traits by inversion of PROSPECT: Assessing leaf dry matter content and specific leaf area in mixed mountainous forest

    Science.gov (United States)

    Ali, Abebe Mohammed; Darvishzadeh, Roshanak; Skidmore, Andrew K.; Duren, Iris van; Heiden, Uta; Heurich, Marco

    2016-03-01

    Assessments of ecosystem functioning rely heavily on quantification of vegetation properties. The search is on for methods that produce reliable and accurate baseline information on plant functional traits. In this study, the inversion of the PROSPECT radiative transfer model was used to estimate two functional leaf traits: leaf dry matter content (LDMC) and specific leaf area (SLA). Inversion of PROSPECT usually aims at quantifying its direct input parameters. This is the first time the technique has been used to indirectly model LDMC and SLA. Biophysical parameters of 137 leaf samples were measured in July 2013 in the Bavarian Forest National Park, Germany. Spectra of the leaf samples were measured using an ASD FieldSpec3 equipped with an integrating sphere. PROSPECT was inverted using a look-up table (LUT) approach. The LUTs were generated with and without using prior information. The effect of incorporating prior information on the retrieval accuracy was studied before and after stratifying the samples into broadleaf and conifer categories. The estimated values were evaluated using R2 and normalized root mean square error (nRMSE). Among the retrieved variables the lowest nRMSE (0.0899) was observed for LDMC. For both traits higher R2 values (0.83 for LDMC and 0.89 for SLA) were discovered in the pooled samples. The use of prior information improved accuracy of the retrieved traits. The strong correlation between the estimated traits and the NIR/SWIR region of the electromagnetic spectrum suggests that these leaf traits could be assessed at canopy level by using remotely sensed data.

  16. First study of correlation between oleic acid content and SAD gene polymorphism in olive oil samples through statistical and bayesian modeling analyses.

    Science.gov (United States)

    Ben Ayed, Rayda; Ennouri, Karim; Ercişli, Sezai; Ben Hlima, Hajer; Hanana, Mohsen; Smaoui, Slim; Rebai, Ahmed; Moreau, Fabienne

    2018-04-10

    Virgin olive oil is appreciated for its particular aroma and taste and is recognized worldwide for its nutritional value and health benefits. The olive oil contains a vast range of healthy compounds such as monounsaturated free fatty acids, especially, oleic acid. The SAD.1 polymorphism localized in the Stearoyl-acyl carrier protein desaturase gene (SAD) was genotyped and showed that it is associated with the oleic acid composition of olive oil samples. However, the effect of polymorphisms in fatty acid-related genes on olive oil monounsaturated and saturated fatty acids distribution in the Tunisian olive oil varieties is not understood. Seventeen Tunisian olive-tree varieties were selected for fatty acid content analysis by gas chromatography. The association of SAD.1 genotypes with the fatty acids composition was studied by statistical and Bayesian modeling analyses. Fatty acid content analysis showed interestingly that some Tunisian virgin olive oil varieties could be classified as a functional food and nutraceuticals due to their particular richness in oleic acid. In fact, the TT-SAD.1 genotype was found to be associated with a higher proportion of mono-unsaturated fatty acids (MUFA), mainly oleic acid (C18:1) (r = - 0.79, p SAD.1 association with the oleic acid composition of olive oil was identified among the studied varieties. This correlation fluctuated between studied varieties, which might elucidate variability in lipidic composition among them and therefore reflecting genetic diversity through differences in gene expression and biochemical pathways. SAD locus would represent an excellent marker for identifying interesting amongst virgin olive oil lipidic composition.

  17. Novel [NiFe]- and [FeFe]-hydrogenase gene transcripts indicative of active facultative aerobes and obligate anaerobes in earthworm gut contents.

    Science.gov (United States)

    Schmidt, Oliver; Wüst, Pia K; Hellmuth, Susanne; Borst, Katharina; Horn, Marcus A; Drake, Harold L

    2011-09-01

    The concomitant occurrence of molecular hydrogen (H(2)) and organic acids along the alimentary canal of the earthworm is indicative of ongoing fermentation during gut passage. Fermentative H(2) production is catalyzed by [FeFe]-hydrogenases and group 4 [NiFe]-hydrogenases in obligate anaerobes (e.g., Clostridiales) and facultative aerobes (e.g., Enterobacteriaceae), respectively, functional groups that might respond differently to contrasting redox conditions. Thus, the objectives of this study were to assess the redox potentials of the alimentary canal of Lumbricus terrestris and analyze the hydrogenase transcript diversities of H(2) producers in glucose-supplemented gut content microcosms. Although redox potentials in the core of the alimentary canal were variable on an individual worm basis, average redox potentials were similar. The lowest redox potentials occurred in the foregut and midgut regions, averaging 40 and 110 mV, respectively. Correlation plots between hydrogenase amino acid sequences and 16S rRNA gene sequences indicated that closely related hydrogenases belonged to closely related taxa, whereas distantly related hydrogenases did not necessarily belong to distantly related taxa. Of 178 [FeFe]-hydrogenase gene transcripts, 177 clustered in 12 Clostridiales-affiliated operational taxonomic units, the majority of which were indicative of heretofore unknown hydrogenases. Of 86 group 4 [NiFe]-hydrogenase gene transcripts, 79% and 21% were affiliated with organisms in the Enterobacteriaceae and Aeromonadaceae, respectively. The collective results (i) suggest that fermenters must cope with variable and moderately oxidative redox conditions along the alimentary canal, (ii) demonstrate that heretofore undetected hydrogenases are present in the earthworm gut, and (iii) corroborate previous findings implicating Clostridiaceae and Enterobacteriaceae as active fermentative taxa in earthworm gut content.

  18. Studies on meat color, myoglobin content, enzyme activities, and genes associated with oxidative potential of pigs slaughtered at different growth stages

    Directory of Open Access Journals (Sweden)

    Qin Ping Yu

    2017-12-01

    Full Text Available Objective This experiment investigated meat color, myoglobin content, enzyme activities, and expression of genes associated with oxidative potential of pigs slaughtered at different growth stages. Methods Sixty 4-week-old Duroc×Landrace×Yorkshire pigs were assigned to 6 replicate groups, each containing 10 pigs. One pig from each group was sacrificed at day 35, 63, 98, and 161 to isolate longissimus dorsi and triceps muscles. Results Meat color scores were higher in pigs at 35 d than those at 63 d and 98 d (p<0.05, and those at 98 d were lower than those at 161 d (p<0.05. The total myoglobin was higher on 161 d compared with those at 63 d and 98 d (p<0.05. Increase in the proportions of metmyoglobin and deoxymyoglobin and a decrease in oxymyoglobin were observed between days 35 and 161 (p<0.05. Meat color scores were correlated to the proportion of oxymyoglobin (r = 0.59, p<0.01, and negatively correlated with deoxymyoglobin and metmyoglobin content (r = −0.48 and −0.62, p<0.05. Malate dehydrogenase (MDH activity at 35 d and 98 d was higher than that at 161 d (p<0.05. The highest lactate dehydrogenase/MDH ratio was achieved at 161 d (p<0.05. Calcineurin mRNA expression decreased at 35 d compared to that at 63 d and 98 d (p<0.05. Myocyte enhancer factor 2 mRNA results indicated a higher expression at 161 d than that at 63 d and 98 d (p<0.05. Conclusion Porcine meat color, myoglobin content, enzyme activities, and genes associated with oxidative potential varied at different stages.

  19. Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction.

    Science.gov (United States)

    Wu, Chen; Twort, Victoria G; Crowhurst, Ross N; Newcomb, Richard D; Buckley, Thomas R

    2017-11-16

    Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the

  20. A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle.

    Directory of Open Access Journals (Sweden)

    Junwu Ma

    2014-10-01

    Full Text Available Glycolytic potential (GP in skeletal muscle is economically important in the pig industry because of its effect on pork processing yield. We have previously mapped a major quantitative trait loci (QTL for GP on chromosome 3 in a White Duroc × Erhualian F2 intercross. We herein performed a systems genetic analysis to identify the causal variant underlying the phenotype QTL (pQTL. We first conducted genome-wide association analyses in the F2 intercross and an F19 Sutai pig population. The QTL was then refined to an 180-kb interval based on the 2-LOD drop method. We then performed expression QTL (eQTL mapping using muscle transcriptome data from 497 F2 animals. Within the QTL interval, only one gene (PHKG1 has a cis-eQTL that was colocolizated with pQTL peaked at the same SNP. The PHKG1 gene encodes a catalytic subunit of the phosphorylase kinase (PhK, which functions in the cascade activation of glycogen breakdown. Deep sequencing of PHKG1 revealed a point mutation (C>A in a splice acceptor site of intron 9, resulting in a 32-bp deletion in the open reading frame and generating a premature stop codon. The aberrant transcript induces nonsense-mediated decay, leading to lower protein level and weaker enzymatic activity in affected animals. The mutation causes an increase of 43% in GP and a decrease of>20% in water-holding capacity of pork. These effects were consistent across the F2 and Sutai populations, as well as Duroc × (Landrace × Yorkshire hybrid pigs. The unfavorable allele exists predominantly in Duroc-derived pigs. The findings provide new insights into understanding risk factors affecting glucose metabolism, and would greatly contribute to the genetic improvement of meat quality in Duroc related pigs.

  1. A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle.

    Science.gov (United States)

    Ma, Junwu; Yang, Jie; Zhou, Lisheng; Ren, Jun; Liu, Xianxian; Zhang, Hui; Yang, Bin; Zhang, Zhiyan; Ma, Huanban; Xie, Xianhua; Xing, Yuyun; Guo, Yuanmei; Huang, Lusheng

    2014-10-01

    Glycolytic potential (GP) in skeletal muscle is economically important in the pig industry because of its effect on pork processing yield. We have previously mapped a major quantitative trait loci (QTL) for GP on chromosome 3 in a White Duroc × Erhualian F2 intercross. We herein performed a systems genetic analysis to identify the causal variant underlying the phenotype QTL (pQTL). We first conducted genome-wide association analyses in the F2 intercross and an F19 Sutai pig population. The QTL was then refined to an 180-kb interval based on the 2-LOD drop method. We then performed expression QTL (eQTL) mapping using muscle transcriptome data from 497 F2 animals. Within the QTL interval, only one gene (PHKG1) has a cis-eQTL that was colocolizated with pQTL peaked at the same SNP. The PHKG1 gene encodes a catalytic subunit of the phosphorylase kinase (PhK), which functions in the cascade activation of glycogen breakdown. Deep sequencing of PHKG1 revealed a point mutation (C>A) in a splice acceptor site of intron 9, resulting in a 32-bp deletion in the open reading frame and generating a premature stop codon. The aberrant transcript induces nonsense-mediated decay, leading to lower protein level and weaker enzymatic activity in affected animals. The mutation causes an increase of 43% in GP and a decrease of>20% in water-holding capacity of pork. These effects were consistent across the F2 and Sutai populations, as well as Duroc × (Landrace × Yorkshire) hybrid pigs. The unfavorable allele exists predominantly in Duroc-derived pigs. The findings provide new insights into understanding risk factors affecting glucose metabolism, and would greatly contribute to the genetic improvement of meat quality in Duroc related pigs.

  2. Effect of insertion of Bt gene in corn and different fumonisin content on growth performance of weaned piglets

    Directory of Open Access Journals (Sweden)

    Filippo Rossi

    2011-04-01

    Full Text Available The objective of this study was to compare the effect of Bt corn and isogenic corn on the growth of weaned piglets. One hundred twenty-eight weaned piglets weighing 8.8 ±1.27 kg live weight were randomly assigned to 4 groups of 32 animals each (16 castrated males and 16 females. Bt corn (line MON810 and isogenic corn were produced at two farms located in the Lodi and Venezia provinces (northern Italy. Bt corn had the same chemical composition as the isogenic corn but a lower content of fumonisin B1 (FB1. The experimental period (35 days was divided into two phases: 0-14 d and 15-35 d. There was no significant difference in average daily gain (ADG among groups during the first feeding phase. Compared to animals fed isogenic corn, the piglets fed Bt maize gained more weight during the second feeding phase (Bt: 464.1 g/d, isogenic: 429.1 g/d; P < 0.05. Also, the ADG over the entire trial was higher in piglets fed Bt corn versus piglets fed isogenic corn (Bt: 396.4 g/d, isogenic: 374.1 g/d; P < 0.05. The ADG of the whole period decreased linearly (P<0.05 with respect to FB1 content of diet. Final weight was higher in piglets fed the diet containing Bt corn (Bt: 22.68 kg, isogenic: 21.83 kg; P < 0.05. No differences in feed intake and in the feed:gain ratio were observed, however a linear response between FB1 and feed:gain ratio in first 14 days of the experiment was detected.

  3. Near real-time estimation of ionosphere vertical total electron content from GNSS satellites using B-splines in a Kalman filter

    Science.gov (United States)

    Erdogan, Eren; Schmidt, Michael; Seitz, Florian; Durmaz, Murat

    2017-02-01

    Although the number of terrestrial global navigation satellite system (GNSS) receivers supported by the International GNSS Service (IGS) is rapidly growing, the worldwide rather inhomogeneously distributed observation sites do not allow the generation of high-resolution global ionosphere products. Conversely, with the regionally enormous increase in highly precise GNSS data, the demands on (near) real-time ionosphere products, necessary in many applications such as navigation, are growing very fast. Consequently, many analysis centers accepted the responsibility of generating such products. In this regard, the primary objective of our work is to develop a near real-time processing framework for the estimation of the vertical total electron content (VTEC) of the ionosphere using proper models that are capable of a global representation adapted to the real data distribution. The global VTEC representation developed in this work is based on a series expansion in terms of compactly supported B-spline functions, which allow for an appropriate handling of the heterogeneous data distribution, including data gaps. The corresponding series coefficients and additional parameters such as differential code biases of the GNSS satellites and receivers constitute the set of unknown parameters. The Kalman filter (KF), as a popular recursive estimator, allows processing of the data immediately after acquisition and paves the way of sequential (near) real-time estimation of the unknown parameters. To exploit the advantages of the chosen data representation and the estimation procedure, the B-spline model is incorporated into the KF under the consideration of necessary constraints. Based on a preprocessing strategy, the developed approach utilizes hourly batches of GPS and GLONASS observations provided by the IGS data centers with a latency of 1 h in its current realization. Two methods for validation of the results are performed, namely the self consistency analysis and a comparison

  4. Copy Number Variation of Cytokinin Oxidase Gene Tackx4 Associated with Grain Weight and Chlorophyll Content of Flag Leaf in Common Wheat.

    Science.gov (United States)

    Chang, Cheng; Lu, Jie; Zhang, Hai-Ping; Ma, Chuan-Xi; Sun, Genlou

    2015-01-01

    As the main pigment in photosynthesis, chlorophyll significantly affects grain filling and grain weight of crop. Cytokinin (CTK) can effectively increase chlorophyll content and chloroplast stability, but it is irreversibly inactivated by cytokinin oxidase (CKX). In this study, therefore, twenty-four pairs of primers were designed to identify variations of wheat CKX (Tackx) genes associated with flag leaf chlorophyll content after anthesis, as well as grain weight in 169 recombinant inbred lines (RIL) derived from Triticum aestivum Jing 411 × Hongmangchun 21. Results indicated variation of Tackx4, identified by primer pair T19-20, was proven to significantly associate with chlorophyll content and grain weight in the RIL population. Here, two Tackx4 patterns were identified: one with two co-segregated fragments (Tackx4-1/Tackx4-2) containing 618 bp and 620 bp in size (as in Jing 411), and another with no PCR product. The two genotypes were designated as genotype-A and genotype-B, respectively. Grain weight and leaf chlorophyll content at 5~15 days after anthesis (DAA) were significantly higher in genotype-A lines than those in genotype-B lines. Mapping analysis indicated Tackx4 was closely linked to Xwmc169 on chromosome 3AL, as well as co-segregated with a major quantitative trait locus (QTL) for both grain weight and chlorophyll content of flag leaf at 5~15 DAA. This QTL explained 8.9~22.3% phenotypic variations of the two traits across four cropping seasons. Among 102 wheat varieties, a third genotype of Tackx4 was found and designated as genotype-C, also having two co-segregated fragments, Tackx4-2 and Tackx4-3 (615bp). The sequences of three fragments, Tackx4-1, Tackx4-2, and Tackx4-3, showed high identity (>98%). Therefore, these fragments could be considered as different copies at Tackx4 locus on chromosome 3AL. The effect of copy number variation (CNV) of Tackx4 was further validated. In general, genotype-A contains both significantly higher grain weight

  5. Apparent polyploidization after gamma irradiation: pitfalls in the use of quantitative polymerase chain reaction (qPCR) for the estimation of mitochondrial and nuclear DNA gene copy numbers.

    Science.gov (United States)

    Kam, Winnie W Y; Lake, Vanessa; Banos, Connie; Davies, Justin; Banati, Richard

    2013-05-30

    Quantitative polymerase chain reaction (qPCR) has been widely used to quantify changes in gene copy numbers after radiation exposure. Here, we show that gamma irradiation ranging from 10 to 100 Gy of cells and cell-free DNA samples significantly affects the measured qPCR yield, due to radiation-induced fragmentation of the DNA template and, therefore, introduces errors into the estimation of gene copy numbers. The radiation-induced DNA fragmentation and, thus, measured qPCR yield varies with temperature not only in living cells, but also in isolated DNA irradiated under cell-free conditions. In summary, the variability in measured qPCR yield from irradiated samples introduces a significant error into the estimation of both mitochondrial and nuclear gene copy numbers and may give spurious evidence for polyploidization.

  6. 16S rRNA gene-based association study identified microbial taxa associated with pork intramuscular fat content in feces and cecum lumen.

    Science.gov (United States)

    Fang, Shaoming; Xiong, Xingwei; Su, Ying; Huang, Lusheng; Chen, Congying

    2017-07-19

    Intramuscular fat (IMF) that deposits among muscle fibers or within muscle cells is an important meat quality trait in pigs. Previous studies observed the effects of dietary nutrients and additives on improving the pork IMF. Gut microbiome plays an important role in host metabolism and energy harvest. Whether gut microbiota exerts effect on IMF remains unknown. In this study, we investigated the microbial community structure of 500 samples from porcine cecum and feces using high-throughput 16S rRNA gene sequencing. We found that phylogenetic composition and potential function capacity of microbiome varied between two types of samples. Bacteria wide association study identified 119 OTUs significantly associated with IMF in the two types of samples (FDR microbiome associated with IMF might be caused by the IMF-associated microbial taxa. This study firstly evaluated the contribution of gut microbiome to porcine IMF content. The results presented a potential capacity for improving IMF through modulating gut microbiota.

  7. Estimation of genetic variability and selection response for clutch length in dwarf brown-egg layers carrying or not the naked neck gene

    Directory of Open Access Journals (Sweden)

    Tixier-Boichard Michèle

    2003-03-01

    Full Text Available Abstract In order to investigate the possibility of using the dwarf gene for egg production, two dwarf brown-egg laying lines were selected for 16 generations on average clutch length; one line (L1 was normally feathered and the other (L2 was homozygous for the naked neck gene NA. A control line from the same base population, dwarf and segregating for the NA gene, was maintained during the selection experiment under random mating. The average clutch length was normalized using a Box-Cox transformation. Genetic variability and selection response were estimated either with the mixed model methodology, or with the classical methods for calculating genetic gain, as the deviation from the control line, and the realized heritability, as the ratio of the selection response on cumulative selection differentials. Heritability of average clutch length was estimated to be 0.42 ± 0.02, with a multiple trait animal model, whereas the estimates of the realized heritability were lower, being 0.28 and 0.22 in lines L1 and L2, respectively. REML estimates of heritability were found to decline with generations of selection, suggesting a departure from the infinitesimal model, either because a limited number of genes was involved, or their frequencies were changed. The yearly genetic gains in average clutch length, after normalization, were estimated to be 0.37 ± 0.02 and 0.33 ± 0.04 with the classical methods, 0.46 ± 0.02 and 0.43 ± 0.01 with animal model methodology, for lines L1 and L2 respectively, which represented about 30% of the genetic standard deviation on the transformed scale. Selection response appeared to be faster in line L2, homozygous for the NA gene, but the final cumulated selection response for clutch length was not different between the L1 and L2 lines at generation 16.

  8. Seasonal changes in antifreeze protein gene transcription and water content of beetle Microdera punctipennis (Coleoptera, Tenebrionidae) from Gurbantonggut desert in Central Asia.

    Science.gov (United States)

    Hou, F; Ma, J; Liu, X; Wang, Y; Liu, X N; Zhang, F C

    2010-01-01

    Desert beetle Microdera punctipennis (Coleoptera: Tenebriondae) is a special species in Gurbantonggut Desert in Central Asia. To investigate the possible strategy it employs for cold survival, seasonal changes in supercooling point (SCP), body water content, haemolymph osmolality and antifreeze protein gene (Mpafp) expression were measured over 13 months. Our results show SCPs in M. punctipennis adults changed from -8.0°C in summer to -18.7°C in winter. During winter, adults endured modest water loss; total water decreased from 65.4 percent in summer to 55.9% in winter. Mpafp mRNAs level increased by 13.1 fold from summer to early winter, and haemolymph osmolality increased accordingly from 550 mOsm to 1486 mOsm. Correlation coefficient of Mpafp mRNAs level and SCP indicates that Mpafp mRNA explained 65.3 percent of the variation in SCPs. The correlation between Mpafp mRNA level and total water reflected an indirect influence of antifreeze protein on water content via reducing SCP.

  9. The enhancement of tolerance to salt and cold stresses by modifying the redox state and salicylic acid content via the cytosolic malate dehydrogenase gene in transgenic apple plants.

    Science.gov (United States)

    Wang, Qing-Jie; Sun, Hong; Dong, Qing-Long; Sun, Tian-Yu; Jin, Zhong-Xin; Hao, Yu-Jin; Yao, Yu-Xin

    2016-10-01

    In this study, we characterized the role of an apple cytosolic malate dehydrogenase gene (MdcyMDH) in the tolerance to salt and cold stresses and investigated its regulation mechanism in stress tolerance. The MdcyMDH transcript was induced by mild cold and salt treatments, and MdcyMDH-overexpressing apple plants possessed improved cold and salt tolerance compared to wild-type (WT) plants. A digital gene expression tag profiling analysis revealed that MdcyMDH overexpression largely altered some biological processes, including hormone signal transduction, photosynthesis, citrate cycle and oxidation-reduction. Further experiments verified that MdcyMDH overexpression modified the mitochondrial and chloroplast metabolisms and elevated the level of reducing power, primarily caused by increased ascorbate and glutathione, as well as the increased ratios of ascorbate/dehydroascorbate and glutathione/glutathione disulphide, under normal and especially stress conditions. Concurrently, the transgenic plants produced a high H2 O2 content, but a low O2·- production rate was observed compared to the WT plants. On the other hand, the transgenic plants accumulated more free and total salicylic acid (SA) than the WT plants under normal and stress conditions. Taken together, MdcyMDH conferred the transgenic apple plants a higher stress tolerance by producing more reductive redox states and increasing the SA level; MdcyMDH could serve as a target gene to genetically engineer salt- and cold-tolerant trees. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  10. Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae).

    Science.gov (United States)

    Knowles, Lacey L; Klimov, Pavel B

    2011-11-01

    With the increased availability of multilocus sequence data, the lack of concordance of gene trees estimated for independent loci has focused attention on both the biological processes producing the discord and the methodologies used to estimate phylogenetic relationships. What has emerged is a suite of new analytical tools for phylogenetic inference--species tree approaches. In contrast to traditional phylogenetic methods that are stymied by the idiosyncrasies of gene trees, approaches for estimating species trees explicitly take into account the cause of discord among loci and, in the process, provides a direct estimate of phylogenetic history (i.e. the history of species divergence, not divergence of specific loci). We illustrate the utility of species tree estimates with an analysis of a diverse group of feather mites, the pinnatus species group (genus Proctophyllodes). Discord among four sequenced nuclear loci is consistent with theoretical expectations, given the short time separating speciation events (as evident by short internodes relative to terminal branch lengths in the trees). Nevertheless, many of the relationships are well resolved in a Bayesian estimate of the species tree; the analysis also highlights ambiguous aspects of the phylogeny that require additional loci. The broad utility of species tree approaches is discussed, and specifically, their application to groups with high speciation rates--a history of diversification with particular prevalence in host/parasite systems where species interactions can drive rapid diversification.

  11. Comparison of Gene Expression Programming with neuro-fuzzy and neural network computing techniques in estimating daily incoming solar radiation in the Basque Country (Northern Spain)

    International Nuclear Information System (INIS)

    Landeras, Gorka; López, José Javier; Kisi, Ozgur; Shiri, Jalal

    2012-01-01

    Highlights: ► Solar radiation estimation based on Gene Expression Programming is unexplored. ► This approach is evaluated for the first time in this study. ► Other artificial intelligence models (ANN and ANFIS) are also included in the study. ► New alternatives for solar radiation estimation based on temperatures are provided. - Abstract: Surface incoming solar radiation is a key variable for many agricultural, meteorological and solar energy conversion related applications. In absence of the required meteorological sensors for the detection of global solar radiation it is necessary to estimate this variable. Temperature based modeling procedures are reported in this study for estimating daily incoming solar radiation by using Gene Expression Programming (GEP) for the first time, and other artificial intelligence models such as Artificial Neural Networks (ANNs), and Adaptive Neuro-Fuzzy Inference System (ANFIS). A comparison was also made among these techniques and traditional temperature based global solar radiation estimation equations. Root mean square error (RMSE), mean absolute error (MAE) RMSE-based skill score (SS RMSE ), MAE-based skill score (SS MAE ) and r 2 criterion of Nash and Sutcliffe criteria were used to assess the models’ performances. An ANN (a four-input multilayer perceptron with 10 neurons in the hidden layer) presented the best performance among the studied models (2.93 MJ m −2 d −1 of RMSE). The ability of GEP approach to model global solar radiation based on daily atmospheric variables was found to be satisfactory.

  12. Development of the spectrometric imaging apparatus of laser induced fluorescence from plants and estimation of chlorophyll contents of rice leaves; Laser reiki keiko sokutei sochi no kaihatsu to inehanai no chlorophyll ganryo no suitei

    Energy Technology Data Exchange (ETDEWEB)

    Nakaya, K.; Shoji, K.; Hanyu, H.

    1999-05-01

    Photosynthetic activity of plants is an important factor to assess the micrometeorological effect of plant canopy or to estimate the influence of circumstances such as water stress. Light illumination induces fluorescence from a leaf or suspension of chloroplasts. The red chlorophyll fluorescence had been used to determine the process of the electron transportation in photosynthetic reaction. The fluorescence source other than chlorophyll is not announced sufficiently, but is supposed to be useful to determine the contents of the substance corresponding to physiological response of plants. We developed a fluorescence imaging apparatus to observe spectrum and distribution of laser induced fluorescence from a leaf. Pulsed UV-laser (Nd:YAG) induced blue-green fluorescence and red chlorophyll fluorescence from a green leaf. The pulse modulated measuring light and CCD with image-intensifier (ICCD) enable to detect the fluorescence from plants under illumination. The laser induced fluorescence (LIF) spectra were investigated to estimate the chlorophyll contents in leaves of rice. During the greening course of dark grown etiolated rice leaves, chlorophyll contents were determined using the extraction of leaves and steady state LIF spectra were measured. As a result, the ratio of fluorescent intensity between blue-green and red peaks (F460/F740 and F510/F740) decreased in proportion to alteration of chlorophyll contents respectively. These fluorescence intensity ratios perform more precise estimation of higher chlorophyll contents of leaves than reported red chlorophyll fluorescence intensity ratio (F690/E740). (author)

  13. Estimating risks and relative risks in case-base studies under the assumptions of gene-environment independence and Hardy-Weinberg equilibrium.

    Directory of Open Access Journals (Sweden)

    Tina Tsz-Ting Chui

    Full Text Available Many diseases result from the interactions between genes and the environment. An efficient method has been proposed for a case-control study to estimate the genetic and environmental main effects and their interactions, which exploits the assumptions of gene-environment independence and Hardy-Weinberg equilibrium. To estimate the absolute and relative risks, one needs to resort to an alternative design: the case-base study. In this paper, the authors show how to analyze a case-base study under the above dual assumptions. This approach is based on a conditional logistic regression of case-counterfactual controls matched data. It can be easily fitted with readily available statistical packages. When the dual assumptions are met, the method is approximately unbiased and has adequate coverage probabilities for confidence intervals. It also results in smaller variances and shorter confidence intervals as compared with a previous method for a case-base study which imposes neither assumption.

  14. Estimating Risks and Relative Risks in Case-Base Studies under the Assumptions of Gene-Environment Independence and Hardy-Weinberg Equilibrium

    Science.gov (United States)

    Chui, Tina Tsz-Ting; Lee, Wen-Chung

    2014-01-01

    Many diseases result from the interactions between genes and the environment. An efficient method has been proposed for a case-control study to estimate the genetic and environmental main effects and their interactions, which exploits the assumptions of gene-environment independence and Hardy-Weinberg equilibrium. To estimate the absolute and relative risks, one needs to resort to an alternative design: the case-base study. In this paper, the authors show how to analyze a case-base study under the above dual assumptions. This approach is based on a conditional logistic regression of case-counterfactual controls matched data. It can be easily fitted with readily available statistical packages. When the dual assumptions are met, the method is approximately unbiased and has adequate coverage probabilities for confidence intervals. It also results in smaller variances and shorter confidence intervals as compared with a previous method for a case-base study which imposes neither assumption. PMID:25137392

  15. Intermittent Fasting Promotes Fat Loss With Lean Mass Retention, Increased Hypothalamic Norepinephrine Content, and Increased Neuropeptide Y Gene Expression in Diet-Induced Obese Male Mice.

    Science.gov (United States)

    Gotthardt, Juliet D; Verpeut, Jessica L; Yeomans, Bryn L; Yang, Jennifer A; Yasrebi, Ali; Roepke, Troy A; Bello, Nicholas T

    2016-02-01

    Clinical studies indicate alternate-day, intermittent fasting (IMF) protocols result in meaningful weight loss in obese individuals. To further understand the mechanisms sustaining weight loss by IMF, we investigated the metabolic and neural alterations of IMF in obese mice. Male C57/BL6 mice were fed a high-fat diet (HFD; 45% fat) ad libitum for 8 weeks to promote an obese phenotype. Mice were divided into four groups and either maintained on ad libitum HFD, received alternate-day access to HFD (IMF-HFD), and switched to ad libitum low-fat diet (LFD; 10% fat) or received IMF of LFD (IMF-LFD). After 4 weeks, IMF-HFD (∼13%) and IMF-LFD (∼18%) had significantly lower body weights than the HFD. Body fat was also lower (∼40%-52%) in all diet interventions. Lean mass was increased in the IMF-LFD (∼12%-13%) compared with the HFD and IMF-HFD groups. Oral glucose tolerance area under the curve was lower in the IMF-HFD (∼50%), whereas the insulin tolerance area under the curve was reduced in all diet interventions (∼22%-42%). HPLC measurements of hypothalamic tissue homogenates indicated higher (∼55%-60%) norepinephrine (NE) content in the anterior regions of the medial hypothalamus of IMF compared with the ad libitum-fed groups, whereas NE content was higher (∼19%-32%) in posterior regions in the IMF-LFD group only. Relative gene expression of Npy in the arcuate nucleus was increased (∼65%-75%) in IMF groups. Our novel findings indicate that intermittent fasting produces alterations in hypothalamic NE and neuropeptide Y, suggesting the counterregulatory processes of short-term weight loss are associated with an IMF dietary strategy.

  16. Over-expression of Arabidopsis thaliana SFD1/GLY1, the gene encoding plastid localized glycerol-3-phosphate dehydrogenase, increases plastidic lipid content in transgenic rice plants.

    Science.gov (United States)

    Singh, Vijayata; Singh, Praveen Kumar; Siddiqui, Adnan; Singh, Subaran; Banday, Zeeshan Zahoor; Nandi, Ashis Kumar

    2016-03-01

    Lipids are the major constituents of all membranous structures in plants. Plants possess two pathways for lipid biosynthesis: the prokaryotic pathway (i.e., plastidic pathway) and the eukaryotic pathway (i.e., endoplasmic-reticulum (ER) pathway). Whereas some plants synthesize galactolipids from diacylglycerol assembled in the plastid, others, including rice, derive their galactolipids from diacylglycerols assembled by the eukaryotic pathway. Arabidopsis thaliana glycerol-3-phosphate dehydrogenase (G3pDH), coded by SUPPRESSOR OF FATTY ACID DESATURASE 1 (SFD1; alias GLY1) gene, catalyzes the formation of glycerol 3-phosphate (G3p), the backbone of many membrane lipids. Here SFD1 was introduced to rice as a transgene. Arabidopsis SFD1 localizes in rice plastids and its over-expression increases plastidic membrane lipid content in transgenic rice plants without any major impact on ER lipids. The results suggest that over-expression of plastidic G3pDH enhances biosynthesis of plastid-localized lipids in rice. Lipid composition in the transgenic plants is consistent with increased phosphatidylglycerol synthesis in the plastid and increased galactolipid synthesis from diacylglycerol produced via the ER pathway. The transgenic plants show a higher photosynthetic assimilation rate, suggesting a possible application of this finding in crop improvement.

  17. Estimation of free acid content in lanthanide salt solution used for pH-potentiometric determination of their stability constants with organic ligands

    International Nuclear Information System (INIS)

    Zheltvaj, I.I.; Tishchenko, M.A.

    1985-01-01

    To improve the pH-potentiometric method for determining complex stability constants the possibility of alkalimetric titration of a free acid in the lanthanide perchlorate solution after binding metal ions by disodium salt of ethylene-diamine-tetraacetic acid is studied. The stability constants were determined from the difference between the total acid content after complexon addition and doubled metal cation content in the solution which has been preliminarily determined by the complexonometric method. It is shown that the alkaline (NaOH) equivalent quantities spent for free acid titration either in the absence or presence of the complexon is different. With increase of free acid content in the solution the difference in determinations with complexon and without it is somewhat reduced. Thus, the use of complexon contributes to a higher accuracy in determining the free acid, and in the first place in case of minor contents

  18. To what extent is blood a reasonable surrogate for brain in gene expression studies: estimation from mouse hippocampus and spleen

    Directory of Open Access Journals (Sweden)

    Matthew N Davies

    2009-10-01

    Full Text Available Microarrays are designed to measure genome-wide differences in gene expression. In cases where a tissue is not accessible for analysis (e.g. human brain, it is of interest to determine whether a second, accessible tissue could be used as a surrogate for transcription profiling. Surrogacy has applications in the study of behavioural and neurodegenerative disorders. Comparison between hippocampus and spleen mRNA obtained from a mouse recombinant inbred panel indicates a high degree of correlation between the tissues for genes that display a high heritability of expression level. This correlation is not limited to apparent expression differences caused by sequence polymorphisms in the target sequences and includes both cis and trans genetic effects. A tissue such as blood could therefore give surrogate information on expression in brain for a subset of genes, in particular those co-expressed between the two tissues, which have heritably varying expression.

  19. Microwave remote sensing of temporal variations of brightness temperature and near-surface soil water content during a watershed-scale field experiment, and its application to the estimation of soil physical properties

    International Nuclear Information System (INIS)

    Mattikalli, N.M.; Engman, E.T.; Jackson, T.J.; Ahuja, L.R.

    1998-01-01

    Passive microwave airborne remote sensing was employed to collect daily brightness temperature (T(B)) and near-surface (0-5 cm depth) soil water content (referred to as 'soil water content') data during June 10-18, 1992, in the Little Washita watershed, Oklahoma. A comparison of multitemporal data with the soils data revealed a direct correlation between changes in T(B) and soil water content, and soil texture. Regression relationships were developed for the ratio of percent sand to percent clay (RSC) and effective saturated hydraulic conductivity (K(sat)) in terms of T(B) and soil water content change. Validation of results indicated that both RSC and K(sat) can be estimated with adequate accuracy. The relationships are valid for the region with small variation of soil organic matter content, soils with fewer macropores, and limiting experimental conditions. However, the findings have potential to employ microwave remote sensing for obtaining quick estimates of soil properties over large areas

  20. Estimation of content of anti-TB drugs supplied at centres of the Revised National TB Control Programme in Tamil Nadu, India.

    Science.gov (United States)

    Ramachandran, Geetha; Chandrasekaran, Vedachalam; Hemanth Kumar, Agibothu Kupparam; Dewan, Puneet; Swaminathan, Soumya; Thomas, Aleyamma

    2013-09-01

    To determine the content of certain antituberculosis (TB) drugs supplied at TB treatment centres of the Revised National TB Control Programme (RNTCP) in the state of Tamil Nadu, India. Eight districts across the state were selected, and the following drugs were collected from five settings (District TB centre, TB unit, designated microscopy centres, DOT providers) in each district: rifampicin (150 and 450 mg), isoniazid (300 mg), pyrazinamide (500 and 750 mg), ethambutol (400 and 600 mg), ethionamide (250 mg), levofloxacin (500 mg) and cycloserine (250 mg). A maximum of 10 tablets/capsules were collected from each setting. The drugs were coded prior to analysis. All drugs were assayed by validated spectrophotometric methods. The acceptable limits for drug content were taken as 90-110% of the stated content. More than 90% of tablets of rifampicin 450 mg, isoniazid 300 mg, pyrazinamide 500 and 750 mg, ethambutol 400 and 600 mg and ethionamide 250 mg were within acceptable limits. Eighty per cent of rifampicin 150 mg, 21% of cycloserine 250 mg and 87% of levofloxacin 500 mg were within acceptable limits. The mean cycloserine content was below the acceptable limit in all districts, the mean drug content being 200 mg (range: 108-245 mg). This systematic study showed that the stated drug content of cycloserine was not reached in all districts. Deterioration of cycloserine could be minimised by storing the drug in refrigerators. The geographical location of the districts had no influence on the drug content. © 2013 John Wiley & Sons Ltd.

  1. Efficacy of flagellin gene typing for epidemiological studies of Campylobacter jejuni in poultry estimated by comparison with macrorestriction profiling

    DEFF Research Database (Denmark)

    Petersen, L.; On, S.L.W.

    2000-01-01

    isolates were obtained. The PCR-Fla type of one isolate changed spontaneously after five subcultures, illustrating the relative plasticity of the gene locus. Comparison of MRPs within and between Fla-types support the view that some PCR-Fla types may be conserved within clonal lines. It is concluded...

  2. Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes.

    Science.gov (United States)

    Steppan, Scott; Adkins, Ronald; Anderson, Joel

    2004-08-01

    The muroid rodents are the largest superfamily of mammals, containing nearly one third of all mammal species. We report on a phylogenetic study comprising 53 genera sequenced for four nuclear genes, GHR, BRCA1, RAG1, and c-myc, totaling up to 6400 nucleotides. Most relationships among the subfamilies are resolved. All four genes yield nearly identical phylogenies, differing only in five key regions, four of which may represent particularly rapid radiations. Support is very strong for a fundamental division of the mole rats of the subfamilies Spalacinae and Rhizomyinae from all other muroids. Among the other "core" muroids, a rapid radiation led to at least four distinct lineages: Asian Calomyscus, an African clade of at least four endemic subfamilies, including the diverse Nesomyinae of Madagascar, a hamster clade with maximum diversity in the New World, and an Old World clade including gerbils and the diverse Old World mice and rats (Murinae). The Deomyinae, recently removed from the Murinae, is well supported as the sister group to the gerbils (Gerbillinae). Four key regions appear to represent rapid radiations and, despite a large amount of sequence data, remain poorly resolved: the base of the "core" muroids, among the five cricetid (hamster) subfamilies, within a large clade of Sigmodontinae endemic to South America, and among major geographic lineages of Old World Murinae. Because of the detailed taxon sampling within the Murinae, we are able to refine the fossil calibration of a rate-smoothed molecular clock and apply this clock to date key events in muroid evolution. We calculate rate differences among the gene regions and relate those differences to relative contribution of each gene to the support for various nodes. The among-gene variance in support is greatest for the shortest branches. We present a revised classification for this largest but most unsettled mammalian superfamily.

  3. What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast.

    Directory of Open Access Journals (Sweden)

    Artémis Llamosi

    2016-02-01

    Full Text Available Significant cell-to-cell heterogeneity is ubiquitously observed in isogenic cell populations. Consequently, parameters of models of intracellular processes, usually fitted to population-averaged data, should rather be fitted to individual cells to obtain a population of models of similar but non-identical individuals. Here, we propose a quantitative modeling framework that attributes specific parameter values to single cells for a standard model of gene expression. We combine high quality single-cell measurements of the response of yeast cells to repeated hyperosmotic shocks and state-of-the-art statistical inference approaches for mixed-effects models to infer multidimensional parameter distributions describing the population, and then derive specific parameters for individual cells. The analysis of single-cell parameters shows that single-cell identity (e.g. gene expression dynamics, cell size, growth rate, mother-daughter relationships is, at least partially, captured by the parameter values of gene expression models (e.g. rates of transcription, translation and degradation. Our approach shows how to use the rich information contained into longitudinal single-cell data to infer parameters that can faithfully represent single-cell identity.

  4. ESTIMATION OF MEASUREMENT UNCERTAINTY IN THE DETERMINATION OF Fe CONTENT IN POWDERED TONIC FOOD DRINK USING GRAPHITE FURNACE ATOMIC ABSORPTION SPECTROMETRY

    Directory of Open Access Journals (Sweden)

    Harry Budiman

    2010-06-01

    Full Text Available The evaluation of uncertainty measurement in the determination of Fe content in powdered tonic food drink using graphite furnace atomic absorption spectrometry was carried out. The specification of measurand, source of uncertainty, standard uncertainty, combined uncertainty and expanded uncertainty from this measurement were evaluated and accounted. The measurement result showed that the Fe content in powdered tonic food drink sample was 569.32 µg/5g, with the expanded uncertainty measurement ± 178.20 µg/5g (coverage factor, k = 2, at confidende level 95%. The calibration curve gave the major contribution to the uncertainty of the final results.   Keywords: uncertainty, powdered tonic food drink, iron (Fe, graphite furnace AAS

  5. Fact versus artifact: Avoiding erroneous estimates of sulfated glycosaminoglycan content using the dimethylmethylene blue colorimetric assay for tissue-engineered constructs

    Directory of Open Access Journals (Sweden)

    CH Zheng

    2015-04-01

    Full Text Available The 1,9-dimethylmethylene blue (DMMB assay is widely used to quantify sulfated glycosaminoglycan (sGAG contents of engineered tissues, culture media, tissue samples and bodily fluids, but the assay is subject to interference from polyanions such as hyaluronic acid (HA, DNA and RNA. We examined whether specific combinations of dye pH and absorbance wavelength could minimize non-sGAG artifacts without compromising DMMB assay sensitivity. HA and DNA solutions generated substantial signal at pH 3 but not at pH 1.5. Reducing dye pH did not significantly alter sGAG measurements for normal cartilage and meniscus tissues, but eliminated anomalously high apparent sGAG contents for enzymatically isolated chondrocytes, adipose-derived stem cell (ADSC-agarose constructs and ADSC pellets. In a cartilage tissue-engineering case study, pH 3 dye indicated high apparent sGAG readings throughout culture in both basal and chondrogenic media, with a marked decline between day 14 and 21 for chondrogenic constructs. The pH 1.5 dye, however, indicated minimal sGAG accumulation in basal medium and stable sGAG content throughout culture in chondrogenic medium. As it is often difficult to know a priori whether all groups in a study will have sGAG contents high enough to overwhelm artifacts, we recommend modifying the standard DMMB assay to reduce the risk of spurious findings in tissue engineering and clinical research. Specifically, we recommend shifting to a pH 1.5 DMMB dye and basing quantification on the absorbance difference between 525 nm (µ peak and 595 nm (β peak to compensate for the moderate loss of sensitivity associated with reducing the dye pH.

  6. ESTIMATION OF pH, TOTAL ACID AND ETHANOL CONTENT OF COMMERCIALLY AVAILABLE ALCOHOL-CONTAINING MOUTHWASHES AND ITS EFFECT ON SALIVARY pH

    OpenAIRE

    Rafi Shaik; Sharath Pocha Reddy; Sameeulla Shaik; Sarah Emerald Sheela Nemalladinne; Dandu Sivasai Prasad Reddy; Kotu Nagavenkata Sai Praveen

    2017-01-01

    BACKGROUND Use of mouthwash has become widespread as a part of routine oral hygiene. Mouthwashes may have deleterious effects on oral tissues because of its low pH, high acid content and use of ethanol as an antiseptic agent. MATERIALS AND METHODS A cross-sectional experimental study was conducted among 48 undergraduate dental students. Eight commercially available alcohol-containing mouthwashes, which are available in Indian market were selected for which the pH, total acid an...

  7. Estimation of the Influence of Operational Factors on the Oxygen Content of the Turbine Condensate at the Outlet from the Condenser of Steam Turbine

    Directory of Open Access Journals (Sweden)

    Shempelev A. G.

    2017-08-01

    Full Text Available The aim of the article is to analyze the influence of different factors on the oxygen content in the condensate using the example of the condenser of the steam turbine unit T-110/120-130. For the first time, the authors of the article analyze in details how the basic parameters of the condenser's operation (the condenser heat load, the flow and temperature of the cooling water, the air inflow in the condenser, the condition of the heat exchange surface influence the oxygen content of the condensate. The authors come to the conclusion that with standard air inflow in the vacuum system, the equilibrium oxygen content, which corresponds to the norms in the condensate at the condenser outlet, is only possible in its operation modes when the steam flow to the condenser is more than 50% of the nominal flow and cooling water temperatures are equal to or greater than calculated for this type of condenser. The conclusions are confirmed by the experimental material. The results of the research are the basis for the development of measures aimed to increase the deaerating capacity of condensers depending on specific operating conditions.

  8. A continuous in vitro method for estimation of the bioavailability of minerals and trace elements in foods : application to breads varying in phytic acid content

    NARCIS (Netherlands)

    Wolters, M.G.E.; Schreuder, H.A.W.; Heuvel, G. van den; Lonkhuijsen, H.J. van; Hermus, R.J.J.; Voragen, A.G.J.

    1993-01-01

    A continuous in vitro method for the estimation of the bioavailability of minerals and trace elements is presented. This in vitro method is believed to be more representative of in vivo physiological conditions than in vitro methods based on equilibrium dialysis, because dialysable components are

  9. Content and in-vitro accessibility of pro-vitamin A carotenoids from Sri Lankan cooked non-leafy vegetables and their estimated contribution to vitamin A requirement.

    Science.gov (United States)

    Priyadarshani, A M B; Chandrika, U G

    2007-12-01

    Vitamin A deficiency is a public health problem in Sri Lanka, which affects especially pre-school children. Carrots (Daucus carota), pumpkins (Cucurbita maxima), squashes (Cucurbita moschata) and sweet potatoes (Ipomoea batatas) of orange, yellow-fleshed varieties are good sources of provitamin A carotenoids, but have not been studied in Sri Lanka in terms of the food as eaten. The content of carotenoids in each preparation method and the in-vitro accessibility of beta-carotene and alpha-carotene were determined by high-performance liquid chromatography. The in-vitro method simulates the conditions in the human intestinal tract. The mean contents in dry weight (DW) in different carrot preparations ranged from 406.7 to 456.3, from 183.7 to 213.5 and from 29.0 to 39.6 microg/g for beta-carotene, alpha-carotene and lutein, respectively. The content of carotenoids in different pumpkin preparations varied from 282.1 to 294.4 microg/g DW for beta-carotene, from 155.6 to 157.7 microg/g DW for alpha-carotene and from 218.0 to 228.2 microg/g DW for lutein. The squashes preparation had 44.6 and 40.0 microg/g DW for beta-carotene and alpha-carotene, respectively, and in sweet potatoes beta-carotene ranged from 204.3 to 210.3 microg/g DW. The results showed that the contribution to the recommended daily allowance is greater when these vegetables are prepared as a curry with coconut milk. The percentage contribution to recommended daily allowance from each vegetable cooked with coconut milk was 46.7, 21.8, 1.2 and 10.8 for carrots, pumpkins, squashes and sweet potatoes, respectively.

  10. Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2

    NARCIS (Netherlands)

    Charlebois, R.; Confalonieri, F.; Curtis, B.; Doolittle, W.F.; Duguet, M.; Erauso, G.; Faguy, D.; Gaasterland, T.; Garrett, R.A.; Gordon, P.; Kozera, C.; Medina, N.; Oost, van der J.; Peng, X.; Ragan, M.; She, Q.; Singh, R.K.

    2000-01-01

    The sequence of a 281-kbp contig from the crenarchaeote Sulfolobus solfataricus P2 was determined and analysed. Notable features in this region include 29 ribosomal protein genes, 12 tRNA genes (four of which contain archaeal-type introns), operons encoding enzymes of histidine biosynthesis,

  11. Examining the information content of time-lapse crosshole GPR data collected under different infiltration conditions to estimate unsaturated soil hydraulic properties

    DEFF Research Database (Denmark)

    Scholer, M.; Irving, J.; Zibar, Majken Caroline Looms

    2013-01-01

    Time-lapse geophysical data acquired during transient hydrological experiments are being increasingly employed to estimate subsurface hydraulic properties at the field scale. In particular, crosshole ground-penetrating radar (GPR) data, collected while water infiltrates into the subsurface either...... by natural or artificial means, have been demonstrated in a number of studies to contain valuable information concerning the hydraulic properties of the unsaturated zone. Previous work in this domain has considered a variety of infiltration conditions and different amounts of time-lapse GPR data...... of time-lapse zero-offset-profile (ZOP) GPR traveltime data, collected under three different infiltration conditions, for the estimation of van Genuchten–Mualem (VGM) parameters in a layered subsurface medium. Specifically, we systematically analyze synthetic and field GPR data acquired under natural...

  12. Serve Size and Estimated Energy and Protein Contents of Meals Prepared by ‘Meals on Wheels’ South Australia Inc.: Findings from a Meal Audit Study

    Science.gov (United States)

    Arjuna, Tony; Miller, Michelle; Soenen, Stijn; Chapman, Ian; Visvanathan, Renuka; Luscombe-Marsh, Natalie D

    2018-01-01

    An audit of ‘standard’ (STD) and ‘energy and protein fortified’ (HEHP) meals from Meals on Wheels (MOW) South Australia’s summer menu was conducted to evaluate the consistency, and serve size and nutrient contents, of their menu items. Twenty soups, 20 mains and 20 desserts from each of the STD and HEHP menus were prepared at the MOW South Australia’s kitchen and delivered to three ‘sham(dummy)-clients’ over a 5-week period. Each meal component was weighed in triplicate, to the nearest gram, the variation within the serve weight was calculated, and the overall energy and protein content of each meal was determined using FoodWorks (Xyris Software, Highgate Hill, Queensland, Australia). On average, the variability for soups and mains was ≤6% and for desserts was ≤10% and although the measured serve sizes of the MOW meals were consistently smaller than prescribed serve size, the differences were minor. As a percentage of recommended daily intakes (RDIs) for adults aged over 60 years, we calculated that the STD meals contained 21–39% for energy and 42–63% for protein while the HEHP meals contained 29–55% for energy and 46–69% for protein. These findings demonstrate that MOW meals currently meet the voluntary meal guidelines for energy and protein. PMID:29461476

  13. Serve Size and Estimated Energy and Protein Contents of Meals Prepared by 'Meals on Wheels' South Australia Inc.: Findings from a Meal Audit Study.

    Science.gov (United States)

    Arjuna, Tony; Miller, Michelle; Soenen, Stijn; Chapman, Ian; Visvanathan, Renuka; Luscombe-Marsh, Natalie D

    2018-02-20

    An audit of 'standard' (STD) and 'energy and protein fortified' (HEHP) meals from Meals on Wheels (MOW) South Australia's summer menu was conducted to evaluate the consistency, and serve size and nutrient contents, of their menu items. Twenty soups, 20 mains and 20 desserts from each of the STD and HEHP menus were prepared at the MOW South Australia's kitchen and delivered to three 'sham(dummy)-clients' over a 5-week period. Each meal component was weighed in triplicate, to the nearest gram, the variation within the serve weight was calculated, and the overall energy and protein content of each meal was determined using FoodWorks (Xyris Software, Highgate Hill, Queensland, Australia). On average, the variability for soups and mains was ≤6% and for desserts was ≤10% and although the measured serve sizes of the MOW meals were consistently smaller than prescribed serve size, the differences were minor. As a percentage of recommended daily intakes (RDIs) for adults aged over 60 years, we calculated that the STD meals contained 21-39% for energy and 42-63% for protein while the HEHP meals contained 29-55% for energy and 46-69% for protein. These findings demonstrate that MOW meals currently meet the voluntary meal guidelines for energy and protein.

  14. Serve Size and Estimated Energy and Protein Contents of Meals Prepared by ‘Meals on Wheels’ South Australia Inc.: Findings from a Meal Audit Study

    Directory of Open Access Journals (Sweden)

    Tony Arjuna

    2018-02-01

    Full Text Available An audit of ‘standard’ (STD and ‘energy and protein fortified’ (HEHP meals from Meals on Wheels (MOW South Australia’s summer menu was conducted to evaluate the consistency, and serve size and nutrient contents, of their menu items. Twenty soups, 20 mains and 20 desserts from each of the STD and HEHP menus were prepared at the MOW South Australia’s kitchen and delivered to three ‘sham(dummy-clients’ over a 5-week period. Each meal component was weighed in triplicate, to the nearest gram, the variation within the serve weight was calculated, and the overall energy and protein content of each meal was determined using FoodWorks (Xyris Software, Highgate Hill, Queensland, Australia. On average, the variability for soups and mains was ≤6% and for desserts was ≤10% and although the measured serve sizes of the MOW meals were consistently smaller than prescribed serve size, the differences were minor. As a percentage of recommended daily intakes (RDIs for adults aged over 60 years, we calculated that the STD meals contained 21–39% for energy and 42–63% for protein while the HEHP meals contained 29–55% for energy and 46–69% for protein. These findings demonstrate that MOW meals currently meet the voluntary meal guidelines for energy and protein.

  15. Estimation of DMFT, Salivary Streptococcus Mutans Count, Flow Rate, Ph, and Salivary Total Calcium Content in Pregnant and Non-Pregnant Women: A Prospective Study.

    Science.gov (United States)

    Kamate, Wasim Ismail; Vibhute, Nupura Aniket; Baad, Rajendra Krishna

    2017-04-01

    Pregnancy, a period from conception till birth, causes changes in the functioning of the human body as a whole and specifically in the oral cavity that may favour the emergence of dental caries. Many studies have shown pregnant women at increased risk for dental caries, however, specific salivary caries risk factors and the particular period of pregnancy at heightened risk for dental caries are yet to be explored and give a scope of further research in this area. The aim of the present study was to assess the severity of dental caries in pregnant women compared to non-pregnant women by evaluating parameters like Decayed, Missing, Filled Teeth (DMFT) index, salivary Streptococcus mutans count, flow rate, pH and total calcium content. A total of 50 first time pregnant women in the first trimester were followed during their second trimester, third trimester and postpartum period for the evaluation of DMFT by World Health Organization (WHO) scoring criteria, salivary flow rate by drooling method, salivary pH by pH meter, salivary total calcium content by bioassay test kit and salivary Streptococcus mutans count by semiautomatic counting of colonies grown on Mitis Salivarius (MS) agar supplemented by 0.2U/ml of bacitracin and 10% sucrose. The observations of pregnant women were then compared with same parameters evaluated in the 50 non-pregnant women. Paired t-test and Wilcoxon sign rank test were performed to assess the association between the study parameters. Evaluation of different caries risk factors between pregnant and non-pregnant women clearly showed that pregnant women were at a higher risk for dental caries. Comparison of caries risk parameters during the three trimesters and postpartum period showed that the salivary Streptococcus mutans count had significantly increased in the second trimester , third trimester and postpartum period while the mean pH and mean salivary total calcium content decreased in the third trimester and postpartum period. These

  16. Estimation of DMFT, Salivary Streptococcus Mutans Count, Flow Rate, Ph, and Salivary Total Calcium Content in Pregnant and Non-Pregnant Women: A Prospective Study

    Science.gov (United States)

    Vibhute, Nupura Aniket; Baad, Rajendra Krishna

    2017-01-01

    Introduction Pregnancy, a period from conception till birth, causes changes in the functioning of the human body as a whole and specifically in the oral cavity that may favour the emergence of dental caries. Many studies have shown pregnant women at increased risk for dental caries, however, specific salivary caries risk factors and the particular period of pregnancy at heightened risk for dental caries are yet to be explored and give a scope of further research in this area. Aim The aim of the present study was to assess the severity of dental caries in pregnant women compared to non-pregnant women by evaluating parameters like Decayed, Missing, Filled Teeth (DMFT) index, salivary Streptococcus mutans count, flow rate, pH and total calcium content. Materials and Methods A total of 50 first time pregnant women in the first trimester were followed during their second trimester, third trimester and postpartum period for the evaluation of DMFT by World Health Organization (WHO) scoring criteria, salivary flow rate by drooling method, salivary pH by pH meter, salivary total calcium content by bioassay test kit and salivary Streptococcus mutans count by semiautomatic counting of colonies grown on Mitis Salivarius (MS) agar supplemented by 0.2U/ml of bacitracin and 10% sucrose. The observations of pregnant women were then compared with same parameters evaluated in the 50 non-pregnant women. Paired t-test and Wilcoxon sign rank test were performed to assess the association between the study parameters. Results Evaluation of different caries risk factors between pregnant and non-pregnant women clearly showed that pregnant women were at a higher risk for dental caries. Comparison of caries risk parameters during the three trimesters and postpartum period showed that the salivary Streptococcus mutans count had significantly increased in the second trimester, third trimester and postpartum period while the mean pH and mean salivary total calcium content decreased in the third

  17. Estimation of salivary flow rate, pH, buffer capacity, calcium, total protein content and total antioxidant capacity in relation to dental caries severity, age and gender.

    Science.gov (United States)

    Pandey, Pallavi; Reddy, N Venugopal; Rao, V Arun Prasad; Saxena, Aditya; Chaudhary, C P

    2015-03-01

    The aim of the study was to evaluate salivary flow rate, pH, buffering capacity, calcium, total protein content and total antioxidant capacity in relation to dental caries, age and gender. The study population consisted of 120 healthy children aged 7-15 years that was further divided into two groups: 7-10 years and 11-15 years. In this 60 children with DMFS/dfs = 0 and 60 children with DMFS/dfs ≥5 were included. The subjects were divided into two groups; Group A: Children with DMFS/dfs = 0 (caries-free) Group B: Children with DMFS/dfs ≥5 (caries active). Unstimulated saliva samples were collected from all groups. Flow rates were determined, and samples analyzed for pH, buffer capacity, calcium, total protein and total antioxidant status. Salivary antioxidant activity is measured with spectrophotometer by an adaptation of 2,2'-azino-di-(3-ethylbenzthiazoline-6-sulphonate) assays. The mean difference of the two groups; caries-free and caries active were proved to be statistically significant (P salivary calcium, total protein and total antioxidant level for both the sexes in the age group 7-10 years and for the age 11-15 years the mean difference of the two groups were proved to be statistically significant (P salivary calcium level for both the sexes. Salivary total protein and total antioxidant level were proved to be statistically significant for male children only. In general, total protein and total antioxidants in saliva were increased with caries activity. Calcium content of saliva was found to be more in caries-free group and increased with age.

  18. The estimation of daily intake and organ content of Cs, I, Sr, Th and U in Indian population: Application to the study of their biokinetics

    International Nuclear Information System (INIS)

    Dang, H.S.; Jaiswal, D.D.; Pullat, V.R.; Parameswaran, M.; Krishnamony, S.

    1998-01-01

    The analytical methods involving both instrumental and radiochemical neutron activation techniques (INAA and RNAA) are being standardised for the determination of the elements Cs, I, Sr, Th and U in various kinds of biological samples. The sampling method proposed to be adopted for the estimation of the daily dietary intake, of the above elements is described. Also reported in this paper are the preliminary results on the concentrations of these elements in the food ingredients which form important components of the diet of Indian population. (author)

  19. Determinations of [sup 90]Sr, [sup 137]Cs, [sup 226]Ra, [sup 228]Ra, [sup 210]Pb, [sup 210]Po contents in chinese diet and estimations of internal doses due to these radionuclides

    Energy Technology Data Exchange (ETDEWEB)

    Hongda, Zhu; Shouliang, Wang; Wei, Meng; Daoping, Wang; Xiujun, Zheng; Qingfen, Liu; Peng, Liu [Chinese Academy of Medical Sciences, Tianjin, TJ (China). Inst. of Radiomedicine

    1993-03-01

    As a part of Chinese Total Diet Survey taken place in 1990, the authors report the determined results on [sup 90]Sr, [sup 137]Cs, [sup 226]Ra, [sup 228]Ra, [sup 210]Pb and [sup 210]Pb and [sup 210]Po contents in various foods of Chinese total diet. Based on obtained dietary composition and the determined contents, the Annual Intakes (AI) and Committed Dose Equivalents (CDE) for the public by ingestion were estimated. It is shown that the total CDE for 6 radionuclides is about 0.24 mSv/a. The food categories and nuclides whose relative contributions to the total are dominant were vegetables, aquatic products and cereal, and [sup 210]Pb, [sup 210]Po, [sup 228]Ra, respectively. The results have updated the data from 1982 survey and have complemented important information for water consumption. The regional difference of dietary compositions and resultant internal doses are discussed as well.

  20. In silico analysis and expression profiling of miRNAs targeting genes of steviol glycosides biosynthetic pathway and their relationship with steviol glycosides content in different tissues of Stevia rebaudiana.

    Science.gov (United States)

    Saifi, Monica; Nasrullah, Nazima; Ahmad, Malik Mobeen; Ali, Athar; Khan, Jawaid A; Abdin, M Z

    2015-09-01

    miRNAs are emerging as potential regulators of the gene expression. Their proven promising role in regulating biosynthetic pathways related gene networks may hold the key to understand the genetic regulation of these pathways which may assist in selection and manipulation to get high performing plant genotypes with better secondary metabolites yields and increased biomass. miRNAs associated with genes of steviol glycosides biosynthetic pathway, however, have not been identified so far. In this study miRNAs targeting genes of steviol glycosides biosynthetic pathway were identified for the first time whose precursors were potentially generated from ESTs and nucleotide sequences of Stevia rebaudiana. Thereafter, stem-loop coupled real time PCR based expressions of these miRNAs in different tissues of Stevia rebaudiana were investigated and their relationship pattern was analysed with the expression levels of their target mRNAs as well as steviol glycoside contents. All the miRNAs investigated showed differential expressions in all the three tissues studied, viz. leaves, flowers and stems. Out of the eleven miRNAs validated, the expression levels of nine miRNAs (miR319a, miR319b, miR319c, miR319d, miR319e, miR319f, miR319h, miRstv_7, miRstv_9) were found to be inversely related, while expression levels of the two, i.e. miR319g and miRstv_11 on the contrary, showed direct relation with the expression levels of their target mRNAs and steviol glycoside contents in the leaves, flowers and stems. This study provides a platform for better understanding of the steviol glycosides biosynthetic pathway and these miRNAs can further be employed to manipulate the biosynthesis of these metabolites to enhance their contents and yield in S. rebaudiana. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  1. Field reconnaissance and estimation of petroleum hydrocarbon and heavy metal contents of soils affected by the Ebocha-8 oil spillage in Niger Delta, Nigeria.

    Science.gov (United States)

    Osuji, Leo C; Onojake, Chukunedum M

    2006-04-01

    Field reconnaissance of the Ebocha-8 oil spill-affected site at Obiobi/Obrikom in the Niger Delta region of Nigeria was carried out to assess the extent of damage to the terrestrial ecosystem and delimit the epicenter of oil spillage. Following three successive reconnaissance surveys, the area to be sampled was delimited (200 x 200 m2), and soil samples were collected using the grid method from three replicate quadrats at two depths, surface (0-15 cm) and subsurface (15-30 cm). A geographically similar area located 50 m adjacent to the oil-polluted area was used as a reference (control) site. Total hydrocarbon content (THC) and heavy metal concentrations were later determined in the laboratory by extraction and spetrophotemetric techniques. Generally, the THC of soils at surface and subsurface depths of the oil-polluted plots was 2.06 x 10(4) +/- 4.97 x 10(3) mg/kg and 1.67 x 10(3) +/- 3.61 x 10(2) mg/kg soil, respectively, (no overlap in standard errors at 95% confidence limit) while concentrations of heavy metals(Pb, Cd, V, Cu and Ni) were enhanced, especially at the surface. The high levels of THC and heavy metals may predispose the site, which hitherto served as arable agricultural land, to impaired fertility and possible conflagration. When concentrations of heavy metals reach the levels obtained in this study, they may become toxic to plants or possibly bio-accumulate, thus leading to toxic reactions along the food chain. While the spilled-oil may have contributed to the enhanced levels of the metals in the affected soils, physico-chemical properties of the soils, mobility of metals, and the intense rainfall and flooding that preceded the period of study may have also contributed in part to their enhanced concentrations. The presence of high hydrocarbon content may cause oxygen deprivation, which may result in the death of soil fauna by asphyxiation. There is, therefore, an urgent need to clear the affected site of these excess hydrocarbon deposits so as to

  2. Use of 5-Bromodeoxyuridine and irradiation for the estimation of the myoblast and myocyte content of primary rat heart cell cultures

    International Nuclear Information System (INIS)

    Masse, M.J.O.; Harary, I.

    1980-01-01

    A method for killing dividing cells was adapted for the elimination of dividing heart muscle cells (myoblasts) in cultures. We have used this method to demonstrate their presence and to estimate their number as well as the number of nondividing heart muscle cells (myocytes) in the neo-natal rat heart. Cells were cultivated in BUdR (5-bromodeoxyuridine) 10 -4 M for 3 days and then irradiated with long uv light. The selective elimination of dividing cells led to a loss of myosin Ca 2+ -activated ATPase in the cultures. The percent of ATPase left after irradiation was 32% of the control in cultures derived from 1-day postnatal rats and 48% in cultures from 4-day postnatal rats. This reflects an in vivo shift of myoblasts to myocytes in the muscle cell population as the rat ages

  3. Evaluation of content and estimation of daily intake of cadmium and lead in several varieties of potatoes (Solanum tuberosum L.) cultivated in the Canary Islands (Spain).

    Science.gov (United States)

    Luis, G; Rubio, C; González-Weller, D; Gutiérrez, A J; Revert, C; Hardisson, A

    2014-04-01

    Monitoring the metal content in foods such as potatoes is an important aspect of food safety and regulation. Samples of nine varieties of potatoes (73 samples of local potatoes and 77 samples of imported potatoes) were randomly obtained from supermarkets, farmers markets, and farmer plots in Tenerife (Canary Islands, Spain). The edible portion (pulp) was the only part considered for analysis because Spaniards traditionally eat only peeled potatoes. Cadmium (Cd) and lead (Pb) were determined using graphite furnace atomic absorption spectrometry. Cd concentrations ranged from 0.006 mg/kg in the Cara and Negra varieties to 0.019 mg/kg in the Bonita variety, and Pb concentrations ranged from 0.007 mg/kg in the Up-to-date variety to 0.023 mg/kg in the Recara variety. The mean concentrations of Cd (0.01 mg/kg) and Pb (0.014 mg/kg) were below the limits established by European regulations for potatoes (0.1 mg/kg of wet weight for each metal). Based on a mean consumption of 143.2 g of potato per pe