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.

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    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

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    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.

  3. Gene-centric content management system.

    Science.gov (United States)

    Poverennaya, Ekaterina V; Bogolubova, Nadezhda A; Bylko, Nikolay N; Ponomarenko, Elena A; Lisitsa, Andrey V; Archakov, Alexander I

    2014-01-01

    The Human Proteome Project (HPP) was started two years ago and the international consortia have elaborated a number of informational resources to harbor the HPP data. Selected informational resources are currently used to elaborate the HPP baseline metrics, which were introduced to estimate future contribution of HPP to the knowledge domain. We developed a Web-based tool Gene-centric Content Management System (GenoCMS) for comparing public resources to proprietary results by using the representation of proteins as color-coded catalog. Within our CMS, the features of protein-coding genes are uploaded from the public domain and then appended by additional features derived from original experimental workflows. We describe the heat-map/traffic light representation of our proteomic experiments as the background of data taken from NeXtProt, MS/MS repositories, the Human Protein Atlas and the RNAseqAtlas. The system presented at www.kb18.ru comprises a collaborative knowledge base for annotating the gene sets and disseminating these annotations through the Web. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.

  4. Sugarcane genes associated with sucrose content

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    Vincentz Michel GA

    2009-03-01

    Full Text Available Abstract Background - Sucrose content is a highly desirable trait in sugarcane as the worldwide demand for cost-effective biofuels surges. Sugarcane cultivars differ in their capacity to accumulate sucrose and breeding programs routinely perform crosses to identify genotypes able to produce more sucrose. Sucrose content in the mature internodes reach around 20% of the culms dry weight. Genotypes in the populations reflect their genetic program and may display contrasting growth, development, and physiology, all of which affect carbohydrate metabolism. Few studies have profiled gene expression related to sugarcane's sugar content. The identification of signal transduction components and transcription factors that might regulate sugar accumulation is highly desirable if we are to improve this characteristic of sugarcane plants. Results - We have evaluated thirty genotypes that have different Brix (sugar levels and identified genes differentially expressed in internodes using cDNA microarrays. These genes were compared to existing gene expression data for sugarcane plants subjected to diverse stress and hormone treatments. The comparisons revealed a strong overlap between the drought and sucrose-content datasets and a limited overlap with ABA signaling. Genes associated with sucrose content were extensively validated by qRT-PCR, which highlighted several protein kinases and transcription factors that are likely to be regulators of sucrose accumulation. The data also indicate that aquaporins, as well as lignin biosynthesis and cell wall metabolism genes, are strongly related to sucrose accumulation. Moreover, sucrose-associated genes were shown to be directly responsive to short term sucrose stimuli, confirming their role in sugar-related pathways. Conclusion - Gene expression analysis of sugarcane populations contrasting for sucrose content indicated a possible overlap with drought and cell wall metabolism processes and suggested signaling and

  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 are disc

  6. Estimating potato leaf chlorophyll content using ratio vegetation indices

    NARCIS (Netherlands)

    Kooistra, Lammert; Clevers, Jan G.P.W.

    2016-01-01

    Chlorophyll content at leaf level is an important variable because of its crucial role in photosynthesis and in understanding plant functioning. In this study, we tested the hypothesis that the ratio of a vegetation index (VI) for estimating canopy chlorophyll content (CCC) and one for estimating le

  7. 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...

  8. 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...

  9. 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

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

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    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.

  11. [Hyperspectral estimation models of chlorophyll content in apple leaves].

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    Liang, Shuang; Zhao, Geng-xing; Zhu, Xi-cun

    2012-05-01

    The present study chose the apple orchard of Shandong Agricultural University as the study area to explore the method of apple leaf chlorophyll content estimation by hyperspectral analysis technology. Through analyzing the characteristics of apple leaves' hyperspectral curve, transforming the original spectral into first derivative, red edge position and leaf chlorophyll index (LCI) respectively, and making the correlation analysis and regression analysis of these variables with the chlorophyll content to establish the estimation models and test to select the high fitting precision models. Results showed that the fitting precision of the estimation model with variable of LCI and the estimation model with variable of the first derivative in the band of 521 and 523 nm was the highest. The coefficients of determination R2 were 0.845 and 0.839, the root mean square errors RMSE were 2.961 and 2.719, and the relative errors RE% were 4.71% and 4.70%, respectively. Therefore LCI and the first derivative are the important index for apple leaf chlorophyll content estimation. The models have positive significance to guide the production of apple cultivation.

  12. Synaptotagmin gene content of the sequenced genomes

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    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

  13. Estimation of the diagnostic accuracy of the invA-gene-based PCR technique and a bacteriological culture for the detection of Salmonella spp. in caecal content from slaughtered pigs using Bayesian analysis.

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    Mainar-Jaime, R C; Atashparvar, N; Chirino-Trejo, M

    2008-01-01

    The goal of this study was to estimate the accuracy of the invA-gene-based polymerase chain reaction (PCR) and a culture technique based on pre-enrichment with buffered peptone water, three selective enrichment media (selenite, tetrathionate and Rappaport-Vassiliadis broths) and four selective, solid media (Xylose-Lysine-Tergitol-4, Salmonella/Shigella, Hekton-Enteric and MacConkey), for the detection of Salmonella organisms from caecal samples from slaughter pigs. For this purpose a latent-class (Bayesian) approach was used. Two hundred and three slaughtered pigs were used after grouping them into two groups of 96 and 107 animals. Sensitivity (Se) was estimated to be 56% (95% probability interval 40, 76) for culture and 91% (81, 97) for PCR. The specificity (Sp) of the PCR was 88% (80, 95) while the Sp of the culture had been considered 100% in the statistical analysis as all culture-positive samples were confirmed by serotyping. PCR Se was not affected by the Salmonella serotypes present in the samples analysed. Accordingly, a minimum of 25.5% of the pigs was estimated to harbour Salmonella organisms in their faeces. It was concluded that bacteriology on caecal samples alone was a poor diagnostic method, and that the PCR method could be considered a cost-effective alternative to culture in Salmonella monitoring programmes. However, given the moderate Sp of this molecular technique, PCR-positive samples should be further confirmed through bacteriology.

  14. 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.

  15. A Content-Based Search Algorithm for Motion Estimation

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The basic search algorithm toimplement Motion Estimation (ME) in the H. 263 encoder is a full search.It is simple but time-consuming. Traditional search algorithms are fast, but may cause a fall in image quality or an increase in bit-rate in low bit-rate applications. A fast search algorithm for ME with consideration on image content is proposed in this paper. Experiments show that the proposed algorithm can offer up to 70 percent savings in execution time with almost no sacrifice in PSNR and bit-rate, compared with the full search.

  16. Estimation of Anthocyanin Content of Berries by NIR Method

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    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.

  17. 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.

  18. Estimation of correction coefficients for measured coal bed methane contents

    Institute of Scientific and Technical Information of China (English)

    Lei Bo; Fu Xuehai; Zhou Baoyan; Shen Jian; Zou Mingjun; Feng Qing

    2012-01-01

    Improving the accuracy and precision of coal bed methane (CBM) estimates requires correction of older data from older coal exploration surveys to newer standards.Three methods,the depth gradient method,the contour aerial weight method,and the well-point aerial weight method,were used to estimate the correction coefficient required to predict CBM gas content from coal exploration data.The data from the Nos.3 and 15 coal seams provided the coal exploration data while the CBM exploration stages within the X1 well block located in the southern part of the Qinshui Basin provided the data obtained using newer standards.The results show the correction coefficients obtained from the two aerial weight methods are similar in value but lower than the one obtained from the depth gradient method.The three methods provide similar results for the Nos.3 and 15 seams in that the correction factor is lower for the former seam.The results from the depth gradient method taken together with the coal seam burial depth and the coal rank suggest that variations in the correction factor increase linearly along with coal seam burial depth and coal rank.The correlation obtained can be applied to exploration and the evaluation of coal bed gas resources located in coalfields.

  19. Concordance analysis between estimation methods of milk fatty acid content.

    Science.gov (United States)

    Rodriguez, Mary Ana Petersen; Petrini, Juliana; Ferreira, Evandro Maia; Mourão, Luciana Regina Mangeti Barreto; Salvian, Mayara; Cassoli, Laerte Dagher; Pires, Alexandre Vaz; Machado, Paulo Fernando; Mourão, Gerson Barreto

    2014-08-01

    Considering the milk fatty acid influence on human health, the aim of this study was to compare gas chromatography (GC) and Fourier transform infrared (FTIR) spectroscopy for the determination of these compounds. Fatty acid content (g/100g of fat) were obtained by both methods and compared through Pearson's correlation, linear Bayesian regression, and the Bland-Altman method. Despite the high correlations between the measurements (r=0.60-0.92), the regression coefficient values indicated higher measures for palmitic acid, oleic acid, unsaturated and monounsaturated fatty acids and lower values for stearic acid, saturated and polyunsaturated fatty acids estimated by GC in comparison to FTIR results. This inequality was confirmed in the Bland-Altman test, with an average bias varying from -8.65 to 6.91g/100g of fat. However, the inclusion of 94% of the samples into the concordance limits suggested that the variability of the differences between the methods was constant throughout the range of measurement. Therefore, despite the inequality between the estimates, the methods displayed the same pattern of milk fat composition, allowing similar conclusions about the milk samples under evaluation.

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

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    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.

  1. Improved estimates of ocean heat content from 1960 to 2015.

    Science.gov (United States)

    Cheng, Lijing; Trenberth, Kevin E; Fasullo, John; Boyer, Tim; Abraham, John; Zhu, Jiang

    2017-03-01

    Earth's energy imbalance (EEI) drives the ongoing global warming and can best be assessed across the historical record (that is, since 1960) from ocean heat content (OHC) changes. An accurate assessment of OHC is a challenge, mainly because of insufficient and irregular data coverage. We provide updated OHC estimates with the goal of minimizing associated sampling error. We performed a subsample test, in which subsets of data during the data-rich Argo era are colocated with locations of earlier ocean observations, to quantify this error. Our results provide a new OHC estimate with an unbiased mean sampling error and with variability on decadal and multidecadal time scales (signal) that can be reliably distinguished from sampling error (noise) with signal-to-noise ratios higher than 3. The inferred integrated EEI is greater than that reported in previous assessments and is consistent with a reconstruction of the radiative imbalance at the top of atmosphere starting in 1985. We found that changes in OHC are relatively small before about 1980; since then, OHC has increased fairly steadily and, since 1990, has increasingly involved deeper layers of the ocean. In addition, OHC changes in six major oceans are reliable on decadal time scales. All ocean basins examined have experienced significant warming since 1998, with the greatest warming in the southern oceans, the tropical/subtropical Pacific Ocean, and the tropical/subtropical Atlantic Ocean. This new look at OHC and EEI changes over time provides greater confidence than previously possible, and the data sets produced are a valuable resource for further study.

  2. Genome Variability and Gene Content in Chordopoxviruses: Dependence on Microsatellites

    Science.gov (United States)

    Hatcher, Eneida L.; Wang, Chunlin; Lefkowitz, Elliot J.

    2015-01-01

    To investigate gene loss in poxviruses belonging to the Chordopoxvirinae subfamily, we assessed the gene content of representative members of the subfamily, and determined whether individual genes present in each genome were intact, truncated, or fragmented. When nonintact genes were identified, the early stop mutations (ESMs) leading to gene truncation or fragmentation were analyzed. Of all the ESMs present in these poxvirus genomes, over 65% co-localized with microsatellites—simple sequence nucleotide repeats. On average, microsatellites comprise 24% of the nucleotide sequence of these poxvirus genomes. These simple repeats have been shown to exhibit high rates of variation, and represent a target for poxvirus protein variation, gene truncation, and reductive evolution. PMID:25912716

  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. Snow water content estimation from measured snow temperature

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The vertical temperature profiles of snow and sea ice have been measured in the Arctic during the 2nd Chinese National Arctic Research Expedition in 2003 (CHINARE2003). The high-resolution temperature profile in snow is solved by one-dimensional heat transfer equation. The effective heat diffusivity, internal heat sources are identified. The internal heat source refers to the penetrated solar radiation which usually warms the lower part of the snow layer in summer. By temperature gradient analysis, the zero level can be clarified quantitatively as the boundary of the dry and wet snow. According to the in situ time series of vertical temperature profile, the time series of water content in snow is obtained based on an evaluation method of snow water content associated with the snow and ice physical parameters. The relationship of snow water content and snow temperature and temporal-spatial distribution of snow water content are presented

  5. Fast Estimation of Dietary Fiber Content in Apple

    OpenAIRE

    Le Gall, Sophie; Even, Sonia; Lahaye, Marc

    2016-01-01

    Dietary fibers (DF) are one of the nutritional benefits of fleshy fruit consumption that is becoming a quality criterion for genetic selection by breeders. However, the AOAC total DF content determination is not readily amenable for screening large fruit collections. A new screening method of DF content in an apple collection based on the automated preparation of cell wall material as an alcohol-insoluble residue (AIR) is proposed. The yield of AIR from 27 apple genotypes was compared with DF...

  6. 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 availa

  7. KIR gene content in amerindians indicates influence of demographic factors.

    Directory of Open Access Journals (Sweden)

    Danillo Gardenal Augusto

    Full Text Available Although the KIR gene content polymorphism has been studied worldwide, only a few isolated or Amerindian populations have been analyzed. This extremely diverse gene family codifies receptors that are expressed mainly in NK cells and bind HLA class I molecules. KIR-HLA combinations have been associated to several diseases and population studies are important to comprehend their evolution and their role in immunity. Here we analyzed, by PCR-SSP (specific sequencing priming, 327 individuals from four isolated groups of two of the most important Brazilian Amerindian populations: Kaingang and Guarani. The pattern of KIR diversity among these and other ten Amerindian populations disclosed a wide range of variation for both KIR haplotypes and gene frequencies, indicating that demographic factors, such as bottleneck and founder effects, were the most important evolutionary factors in shaping the KIR polymorphism in these populations.

  8. Estimation of rice leaf nitrogen contents based on hyperspectral LIDAR

    Science.gov (United States)

    Du, Lin; Gong, Wei; Shi, Shuo; Yang, Jian; Sun, Jia; Zhu, Bo; Song, Shalei

    2016-02-01

    Precision agriculture has become a global research hotspot in recent years. Thus, a technique for rapidly monitoring a farmland in a large scale and for accurately monitoring the growing status of crops needs to be established. In this paper, a novel technique, i.e., hyperspectral LIDAR (HL) which worked based on wide spectrum emission and a 32-channel detector was introduced, and its potential in vegetation detection was then evaluated. These spectra collected by HL were used to classify and derive the nitrogen contents of rice under four different nitrogen content levels with support vector machine (SVM) regression. Meanwhile the wavelength selection and channel correction method for achieving high spectral resolution were discussed briefly. The analysis results show that: (1) the reflectance intensity of the selected characteristic wavelengths of HL system has high correlation with different nitrogen contents levels of rice. (2) By increasing the number of wavelengths in calculation, the classification accuracy is greatly improved (from 54% with 4 wavelengths to 83% with 32 wavelengths) and so the regression coefficient r2 is (from 0.51 with 4 wavelengths to 0.75 with 32 wavelengths). (3) Support vector machine (SVM) is a useful regression method for rice leaf nitrogen contents retrieval. These analysis results can help farmers to make fertilization strategies more accurately. The receiving channels and characteristic wavelengths of HL system can be flexibly selected according to different requirements and thus this system will be applied in other fields, such as geologic exploration and environmental monitoring.

  9. NAM-1gene polymorphism and grain protein content in Hordeum.

    Science.gov (United States)

    Jamar, Catherine; Loffet, Francois; Frettinger, Patrick; Ramsay, Luke; Fauconnier, Marie-Laure; du Jardin, Patrick

    2010-04-15

    Grain protein content (GPC) is a key quality factor for malting and brewing process. In wheat, a QTL explaining a large part of GPC variation was identified, which co-localizes with a gene encoding a NAC transcription factor (TtNAM-B1). NAC transcription factors influence GPC by their role in the regulation of senescence and in protein remobilization. An orthologous gene was discovered on barley chromosome 6H where a GPC QTL was mapped. In this study, we identify allelic variation of the NAM-1 gene for three species of Hordeum representing wild and cultivated barley and we investigate the possible link with GPC. Three haplotypes were identified, one corresponds to the sequences of 11 European varieties representing H. vulgare, one corresponds to the sequence found in H. spontaneum and one represents the sequence of H. bulbosum. Three SNPs were identified between H. spontaneum sequence and H. vulgare sequence. One of the H. bulbosum polymorphisms leads to the introduction of a stop codon and a non-functional protein. Differences in GPC between the 11 varieties were found but no polymorphism in the NAM-1 gene was observed, suggesting that differences in expression of the HvNAM-1 gene or other genes should play a role in GPC regulation. Nevertheless based on published values for GPC of H. bulbosum and H. spontaneum compared to GPC measured here in H. vulgare, the non-functional protein is associated with the lower GPC, suggesting that loss of functionality of the NAM-1 gene in Hordeum is related to lower GPC. Moreover H. spontaneum GPC seems to be higher than H. vulgare GPC, suggesting also that allelic variation of the functional NAM-1 gene could be associated with GPC variation within the genus Hordeum. Copyright 2009 Elsevier GmbH. All rights reserved.

  10. Identification of genes related to intramuscular fat content of pig using genome-wide association study.

    Science.gov (United States)

    Won, Sohyoung; Jung, Jaehoon; Park, Eungwoo; Kim, H B

    2017-06-27

    The aim of this study is to identify SNPs and genes related to pig IMF and estimate the heritability of IMF. Genome-wide association study (GWAS) on 704 inbred Berkshires was performed for intramuscular fat content (IMF). To consider the inbreeding among samples, associations of the SNPs with IMF were tested as random effects in a mixed linear model using the genetic relationship matrix by GEMMA. Significant genes were compared with reported pig IMF QTL regions and functional classification of the identified genes were also performed. Heritability of IMF was estimated by GCTA tool. Total 365 SNPs were found to be significant from a cutoff of p-value IMF QTL regions. BMPER, FOXO1, EDAR, RNF149, CD40, PTPN1, SOX9, MYC, MIF were related to mitogen-activated protein kinase (MAPK) pathway which regulates the differentiation to adipocytes. These genes and the genes mapped on QTLs could be the candidate genes affecting IMF. Heritability of IMF was estimated as 0.52, which was relatively high, suggesting that a considerable portion of the total variance of IMF is explained by the SNP information. Our results can contribute to breeding pig with better IMF and therefore, producing pork with better sensory qualities.

  11. Leaf Relative Water Content Estimated from Leaf Reflectance and Transmittance

    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. In the research we report here, we used optical polarization techniques to monitor the 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 change nonlinearly. The result show that the nonlinearities cancel in the ratio R/T, which appears linearly related to RWC for RWC less than 90%. The results suggest that potentially leaf water status and perhaps even canopy water status could be monitored starting from leaf and canopy optical measurements.

  12. Radiometric estimation of water vapor content over Brazil

    Science.gov (United States)

    Karmakar, P. K.; Maiti, M.; Sett, S.; Angelis, C. F.; Machado, L. A. T.

    2011-11-01

    A multi-channel microwave radiometre (make: Radiometrics Corporation) is installed at Instituto Nacional de Pesquisas Espaciais-INPE, Brazil (22°S). The radiometric output of two channels of the radiometer in the form of brightness temperature at 23.834 GHz and 30 GHz, initially, were used to find out the ambient water vapor content and the non-precipitable cloud liquid water content. The necessary algorithm was developed for the purpose. The best results were obtained using the hinge frequency 23.834 GHz and 30 GHz pair having an r.m.s. error of only 2.64. The same methodology was then adopted exploiting 23.034 GHz and 30 GHz pair. In that case the r.m.s. error was 3.42. These results were then compared with those obtained over Kolkata (22°N), India, by using 22.234 GHz and 31.4 GHz radiometric data. This work conclusively suggests the use of a frequency should not be at the water vapor resonance line. Instead, while measuring the vapor content for separation of vapor and cloud liquid, one of them should be a few GHz left or right from the resonance line i.e., at 23.834 GHz and the other one should be around 30 GHz.

  13. 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.

  14. Sensible heat balance estimates of transient soil ice contents for freezing and thawing conditions

    Science.gov (United States)

    Soil ice content is an important component for winter soil hydrology. The sensible heat balance (SHB) method using measurements from heat pulse probes (HPP) is a possible way to determine transient soil ice content. In a previous study, in situ soil ice contents estimates with the SHB method were in...

  15. Estimating Liquid And Gas Contents In A Tank

    Science.gov (United States)

    Walter, Richard T.; Van Buskirk, Paul; Weber, William; Froebel, Richard

    1991-01-01

    General approach to estimation of amounts of liquid and gas in tank based on measurements of pressure perturbations and temperatures and use of thermodynamic relationships among pressures, temperatures, and volumes. Although approach approximate and indirect, advantageous where such direct and precise methods as observation of stationary liquid/gas interface in gravitational field cannot be used. Used in presence or absence of gravitation or acceleration, and regardless of numbers, shapes, and movements of liquid/gas interfaces in tank. Also useful where liquid stationary but too hazardous to permit direct observation. Implemented in variety of ways, depending on type of liquid and conditions of operation and design of tank system.

  16. Non-destructive estimation of foliar carotenoid content of tree species using merged vegetation indices.

    Science.gov (United States)

    Fassnacht, Fabian E; Stenzel, Stefanie; Gitelson, Anatoly A

    2015-03-15

    Leaf pigment content is an important indicator of plant status and can serve to assess the vigor and photosynthetic activity of plants. The application of spectral information gathered from laboratory, field and remote sensing-based spectrometers to non-destructively assess total chlorophyll (Chl) content of higher plants has been demonstrated in earlier studies. However, the precise estimation of carotenoid (Car) content with non-destructive spectral measurements has so far not reached accuracies comparable to the results obtained for Chl content. Here, we examined the potential of a recently developed angular vegetation index (AVI) to estimate total foliar Car content of three tree species. Based on an iterative search of all possible band combinations, we identified a best candidate AVIcar. The identified index showed quite close but essentially not linear relation with Car contents of the examined species with increasing sensitivity to high Car content and a lack of sensitivity to low Car content for which earlier proposed vegetation indices (VI) performed better. To make use of the advantages of both VI types, we developed a simple merging procedure, which combined the AVIcar with two earlier proposed carotenoid indices. The merged indices had close linear relationship with total Car content and outperformed all other examined indices. The merged indices were able to accurately estimate total Car content with a percental root mean square error (%RMSE) of 8.12% and a coefficient of determination of 0.88. Our findings were confirmed by simulations using the radiative transfer model PROSPECT-5. For simulated data, the merged indices again showed a quasi linear relationship with Car content. This strengthens the assumption that the proposed merged indices have a general ability to accurately estimate foliar Car content. Further examination of the proposed merged indices to estimate foliar Car content of other plant species is desirable to prove the general

  17. 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.

  18. 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.

  19. Correlating information contents of gene ontology terms to infer semantic similarity of gene products.

    Science.gov (United States)

    Gan, Mingxin

    2014-01-01

    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.

  20. Exploring the shallow end; estimating information content in transcriptomics studies

    Directory of Open Access Journals (Sweden)

    Daniel J Kliebenstein

    2012-09-01

    Full Text Available Transcriptomics is a major platform to study organismal biology. The advent of new parallel sequencing technologies has opened up a new avenue of transcriptomics with ever deeper and deeper sequencing to identify and quantify each and every transcript in a sample. However, this may not be the best usage of the parallel sequencing technology for all transcriptomics experiments. I utilized the Shannon Entropy approach to estimate the information contained within a transcriptomics experiment and tested the ability of shallow RNAseq to capture the majority of this information. This analysis showed that it was possible to capture nearly all of the network or genomic information present in a variety of transcriptomics experiments using a subset of the most abundant 5000 transcripts or less within any given sample. Thus, it appears that it should be possible and affordable to conduct large scale factorial analysis with a high degree of replication using parallel sequencing technologies.

  1. [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.

  2. Efficient algorithms for reconstructing gene content by co-evolution

    Directory of Open Access Journals (Sweden)

    Tuller Tamir

    2011-10-01

    Full Text Available Abstract Background In a previous study we demonstrated that co-evolutionary information can be utilized for improving the accuracy of ancestral gene content reconstruction. To this end, we defined a new computational problem, the Ancestral Co-Evolutionary (ACE problem, and developed algorithms for solving it. Results In the current paper we generalize our previous study in various ways. First, we describe new efficient computational approaches for solving the ACE problem. The new approaches are based on reductions to classical methods such as linear programming relaxation, quadratic programming, and min-cut. Second, we report new computational hardness results related to the ACE, including practical cases where it can be solved in polynomial time. Third, we generalize the ACE problem and demonstrate how our approach can be used for inferring parts of the genomes of non-ancestral organisms. To this end, we describe a heuristic for finding the portion of the genome ('dominant set’ that can be used to reconstruct the rest of the genome with the lowest error rate. This heuristic utilizes both evolutionary information and co-evolutionary information. We implemented these algorithms on a large input of the ACE problem (95 unicellular organisms, 4,873 protein families, and 10, 576 of co-evolutionary relations, demonstrating that some of these algorithms can outperform the algorithm used in our previous study. In addition, we show that based on our approach a ’dominant set’ cab be used reconstruct a major fraction of a genome (up to 79% with relatively low error-rate (e.g. 0.11. We find that the ’dominant set’ tends to include metabolic and regulatory genes, with high evolutionary rate, and low protein abundance and number of protein-protein interactions. Conclusions The ACE problem can be efficiently extended for inferring the genomes of organisms that exist today. In addition, it may be solved in polynomial time in many practical cases

  3. [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%.

  4. 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

  5. Maximum likelihood for genome phylogeny on gene content.

    Science.gov (United States)

    Zhang, Hongmei; Gu, Xun

    2004-01-01

    With the rapid growth of entire genome data, reconstructing the phylogenetic relationship among different genomes has become a hot topic in comparative genomics. Maximum likelihood approach is one of the various approaches, and has been very successful. However, there is no reported study for any applications in the genome tree-making mainly due to the lack of an analytical form of a probability model and/or the complicated calculation burden. In this paper we studied the mathematical structure of the stochastic model of genome evolution, and then developed a simplified likelihood function for observing a specific phylogenetic pattern under four genome situation using gene content information. We use the maximum likelihood approach to identify phylogenetic trees. Simulation results indicate that the proposed method works well and can identify trees with a high correction rate. Real data application provides satisfied results. The approach developed in this paper can serve as the basis for reconstructing phylogenies of more than four genomes.

  6. Finding Clocks in Genes: A Bayesian Approach to Estimate Periodicity

    Directory of Open Access Journals (Sweden)

    Yan Ren

    2016-01-01

    Full Text Available Identification of rhythmic gene expression from metabolic cycles to circadian rhythms is crucial for understanding the gene regulatory networks and functions of these biological processes. Recently, two algorithms, JTK_CYCLE and ARSER, have been developed to estimate periodicity of rhythmic gene expression. JTK_CYCLE performs well for long or less noisy time series, while ARSER performs well for detecting a single rhythmic category. However, observing gene expression at high temporal resolution is not always feasible, and many scientists are interested in exploring both ultradian and circadian rhythmic categories simultaneously. In this paper, a new algorithm, named autoregressive Bayesian spectral regression (ABSR, is proposed. It estimates the period of time-course experimental data and classifies gene expression profiles into multiple rhythmic categories simultaneously. Through the simulation studies, it is shown that ABSR substantially improves the accuracy of periodicity estimation and clustering of rhythmic categories as compared to JTK_CYCLE and ARSER for the data with low temporal resolution. Moreover, ABSR is insensitive to rhythmic patterns. This new scheme is applied to existing time-course mouse liver data to estimate period of rhythms and classify the genes into ultradian, circadian, and arrhythmic categories. It is observed that 49.2% of the circadian profiles detected by JTK_CYCLE with 1-hour resolution are also detected by ABSR with only 4-hour resolution.

  7. 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).

  8. 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.

  9. The ACACA gene is a potential candidate gene for fat content in sheep milk.

    Science.gov (United States)

    Moioli, B; Scatà, M C; De Matteis, G; Annicchiarico, G; Catillo, G; Napolitano, F

    2013-08-01

    No major gene has yet been reported in sheep that explains the variation of milk fat content. The coding region of the acetyl-CoA carboxylase alpha (ACACA) gene, which plays an important role in de novo fatty acid synthesis, had been investigated, but no non-synonymous mutations have been reported. In this study, the genomic regions encoding the three promoters of the ACACA gene were directly sequenced in 264 sheep of three different breeds, and 10 SNPs were identified. Allele frequencies of most SNPs significantly differed (P = 0.05-0.0001) between breeds. The SNPs that potentially altered either gene regulatory elements or putative binding sites of transcription factors were made evident through in silico analysis. The association analysis with milk traits, performed for one SNP of PIII (GenBank AJ292286, g.1330G>T), showed a significant allelic substitution effect (+0.33%, P sheep milk.

  10. Ionospheric Slant Total Electron Content Analysis Using Global Positioning System Based Estimation

    Science.gov (United States)

    Sparks, Lawrence C. (Inventor); Mannucci, Anthony J. (Inventor); Komjathy, Attila (Inventor)

    2017-01-01

    A method, system, apparatus, and computer program product provide the ability to analyze ionospheric slant total electron content (TEC) using global navigation satellite systems (GNSS)-based estimation. Slant TEC is estimated for a given set of raypath geometries by fitting historical GNSS data to a specified delay model. The accuracy of the specified delay model is estimated by computing delay estimate residuals and plotting a behavior of the delay estimate residuals. An ionospheric threat model is computed based on the specified delay model. Ionospheric grid delays (IGDs) and grid ionospheric vertical errors (GIVEs) are computed based on the ionospheric threat model.

  11. The effect of missing marker genotypes on the accuracy of gene-assisted breeding value estimation: a comparison of methods.

    Science.gov (United States)

    Mulder, H A; Meuwissen, T H E; Calus, M P L; Veerkamp, R F

    2010-01-01

    In livestock populations, missing genotypes on a large proportion of the animals is a major problem when implementing gene-assisted breeding value estimation for genes with known effect. The objective of this study was to compare different methods to deal with missing genotypes on accuracy of gene-assisted breeding value estimation for identified bi-allelic genes using Monte Carlo simulation. A nested full-sib half-sib structure was simulated with a mixed inheritance model with one bi-allelic quantitative trait loci (QTL) and a polygenic effect due to infinite number of polygenes. The effect of the QTL was included in gene-assisted BLUP either by random regression on predicted gene content, i.e. the number of positive alleles, or including haplotype effects in the model with an inverse IBD matrix to account for identity-by-descent relationships between haplotypes using linkage analysis information (IBD-LA). The inverse IBD matrix was constructed using segregation indicator probabilities obtained from multiple marker iterative peeling. Gene contents for unknown genotypes were predicted using either multiple marker iterative peeling or mixed model methodology. For both methods, gene-assisted breeding value estimation increased accuracies of total estimated breeding value (EBV) with 0% to 22% for genotyped animals in comparison to conventional breeding value estimation. For animals that were not genotyped, the increase in accuracy was much lower (0% to 5%), but still substantial when the heritability was 0.1 and when the QTL explained at least 15% of the genetic variance. Regression on predicted gene content yielded higher accuracies than IBD-LA. Allele substitution effects were, however, overestimated, especially when only sires and males in the last generation were genotyped. For juveniles without phenotypic records and traits measured only on females, the superiority of regression on gene content over IBD-LA was larger than when all animals had phenotypes. Missing

  12. Accuracy of soil water content estimates from gamma radiation monitoring data

    Science.gov (United States)

    Mao, Jie; Huisman, Johan Alexander; Reemt Bogena, Heye; Vereecken, Harry

    2016-04-01

    Terrestrial gamma radiation is known to be sensitive to soil water content, and could be promising for soil water content determination because of the availability of continental-scale gamma radiation monitoring networks. However, the accuracy of soil water content estimates that can be obtained from this type of data is currently unknown. Therefore, the aim of this study is to assess the accuracy of soil water content estimates from measured time series of gamma radiation. For this, four gamma radiation monitoring stations were each equipped with four soil water content sensors at 5 and 15 cm depth to provide reference soil water content measurements. The contributions of terrestrial radiation and secondary cosmic radiation were separated from the total amount of measured gamma radiation by assuming that the long-term contribution of secondary cosmic radiation was constant, and that variations were related to changes in air pressure and incoming neutrons. In addition, precipitation effects related to atmospheric washout of radon progenies to the ground that cause an increase of gamma radiation were considered by excluding time periods with precipitation and time periods less than three hours after precipitation. The estimated terrestrial gamma radiation was related to soil water content using an exponential function with two fit parameters. For daily soil water content estimates, the goodness of fit ranged from R2= 0.21 to 0.48 and the RMSE ranged from 0.048 to 0.117 m3m-3. The accuracy of the soil water content estimates improved considerably when a weekly resolution was used (RMSE ranged from 0.029 to 0.084 m3m-3). Overall, these results indicate that gamma radiation monitoring data can be used to obtain useful soil water content information. The remaining differences between measured and estimated soil water content can at least partly be explained by the fact that the terrestrial gamma radiation is strongly determined by the upper few centimeters of the soil

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

    DEFF Research Database (Denmark)

    Rindorf, Anna; Lewy, Peter

    2004-01-01

    , 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......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...... 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....

  14. 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.

  15. Non-destructive estimation of foliar chlorophyll and carotenoid contents: Focus on informative spectral bands

    Science.gov (United States)

    Kira, Oz; Linker, Raphael; Gitelson, Anatoly

    2015-06-01

    Leaf pigment content provides valuable insight into the productivity, physiological and phenological status of vegetation. Measurement of spectral reflectance offers a fast, nondestructive method for pigment estimation. A number of methods were used previously for estimation of leaf pigment content, however, spectral bands employed varied widely among the models and data used. Our objective was to find informative spectral bands in three types of models, vegetation indices (VI), neural network (NN) and partial least squares (PLS) regression, for estimating leaf chlorophyll (Chl) and carotenoids (Car) contents of three unrelated tree species and to assess the accuracy of the models using a minimal number of bands. The bands selected by PLS, NN and VIs were in close agreement and did not depend on the data used. The results of the uninformative variable elimination PLS approach, where the reliability parameter was used as an indicator of the information contained in the spectral bands, confirmed the bands selected by the VIs, NN, and PLS models. All three types of models were able to accurately estimate Chl content with coefficient of variation below 12% for all three species with VI showing the best performance. NN and PLS using reflectance in four spectral bands were able to estimate accurately Car content with coefficient of variation below 14%. The quantitative framework presented here offers a new way of estimating foliar pigment content not requiring model re-parameterization for different species. The approach was tested using the spectral bands of the future Sentinel-2 satellite and the results of these simulations showed that accurate pigment estimation from satellite would be possible.

  16. EDGAR 2.0: an enhanced software platform for comparative gene content analyses.

    Science.gov (United States)

    Blom, Jochen; Kreis, Julian; Spänig, Sebastian; Juhre, Tobias; Bertelli, Claire; Ernst, Corinna; Goesmann, Alexander

    2016-07-01

    The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on the comparison of closely related genomes. By utilizing comparative approaches on gene level it is possible to gain insights into the core genes which represent the set of shared features for a set of organisms under study. Vice versa singleton genes can be identified to elucidate the specific properties of an individual genome. Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics. Over the last years, the software has been continuously improved and a large number of new analysis features have been added. For the new version, EDGAR 2.0, the gene orthology estimation approach was newly designed and completely re-implemented. Among other new features, EDGAR 2.0 provides extended phylogenetic analysis features like AAI (Average Amino Acid Identity) and ANI (Average Nucleotide Identity) matrices, genome set size statistics and modernized visualizations like interactive synteny plots or Venn diagrams. Thereby, the software supports a quick and user-friendly survey of evolutionary relationships between microbial genomes and simplifies the process of obtaining new biological insights into their differential gene content. All features are offered to the scientific community via a web-based and therefore platform-independent user interface, which allows easy browsing of precomputed datasets. The web server is accessible at http://edgar.computational.bio.

  17. 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...... contents derived from pooled stomach samples rather than individual stomachs, and (3) the effect of ignoring biological factors that affect the evacuation of prey. Estimating consumption from only two stomach samples yielded results close to the actual intake rate in a simulation study. In contrast to this......, 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...

  18. Estimated glycemic index and dietary fiber content of cookies elaborated with extruded wheat bran.

    Science.gov (United States)

    Reyes-Pérez, Faviola; Salazar-García, María Guadalupe; Romero-Baranzini, Ana Lourdes; Islas-Rubio, Alma Rosa; Ramírez-Wong, Benjamín

    2013-03-01

    The increasing demand for high-fiber products has favored the design of numerous bakery products rich in fiber such as bread, cookies, and cakes. The objective of this study was to evaluate the dietary fiber and estimated glycemic index of cookies containing extruded wheat bran. Wheat bran was subjected to extrusion process under three temperature profiles: TP1;(60, 75, 85 and 100 °C), TP2;(60, 80, 100 and 120 °C), and TP3;(60, 80, 110 and 140 °C) and three moisture contents: (15, 23, and 31 %). Cookies were elaborated using extruded wheat bran (30 %), separated into two fractions (coarse and fine). The dietary fiber content of cookies elaborated with extruded wheat bran was higher than the controls; C0 (100 % wheat flour) and C1 (30 % of no extruded bran coarse fraction) and C2 (30 % of no extruded bran fine fraction). The higher values of dietary fiber were observed on cookies from treatments 5 (TP1, 31 % moisture content and coarse fraction) and 11 (TP2, 31 % moisture content and coarse fraction). The estimated glycemic index of cookies ranged from 68.54 to 80.16. The dietary fiber content of cookies was increased and the lowest glycemic index corresponded to the cookies elaborated with extruded wheat bran. Cookie made with the treatment 11 had a better dietary fiber content and lower estimated glycemic index.

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

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.; Gaddis, L.A.; Consort, S.D. [Westinghouse Hanford Co., Richland, WA (United States)

    1995-12-31

    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.

  20. 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.

  1. 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.

  2. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-03-14

    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 Areas. 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.

  4. Historical tank content estimate for the northwest quadrant ofthe Hanford 200 west area

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-03-06

    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 Labo1368ratory are also given in this report.

  5. 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.

  6. Radar vegetation indices for estimating the vegetation water content of rice and soybean

    Science.gov (United States)

    Vegetation water content (VWC) is an important biophysical parameter and has a significant role in the retrieval of soil moisture using microwave remote sensing. In this study, the Radar Vegetation Index (RVI) was evaluated for estimating VWC. Analysis utilized a data set obtained using a ground-bas...

  7. 19 CFR 144.12 - Contents of entry summary; estimated duties.

    Science.gov (United States)

    2010-04-01

    ..., Customs Form 7501, shall show the value, classification, and rate of duty as approved by the port director... 19 Customs Duties 2 2010-04-01 2010-04-01 false Contents of entry summary; estimated duties. 144.12 Section 144.12 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND...

  8. 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.

  9. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.

    1996-06-28

    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.

  11. 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.

  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 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.

    1996-06-28

    This Supporting Document provides historical in-depth characterization information on B-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 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.

  16. Supporting document for the historical tank content estimate for C-tank farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.

    1996-06-28

    This Supporting Document provides historical in-depth characterization information on C-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.

  17. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.

    1996-06-28

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H., Westinghouse Hanford

    1996-06-28

    This Supporting Document provides historical in-depth characterization information on AX-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. 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...

  1. Supporting document for the historical tank content estimate of U-tank fram

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H., Fluor Daniel Hanford

    1997-02-26

    This Supporting Document provides historical in-depth characterization information on U-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.

  2. AOAC SMPR 2015.009: Estimation of total phenolic content using Folin-C Assay

    Science.gov (United States)

    This AOAC Standard Method Performance Requirements (SMPR) is for estimation of total soluble phenolic content in dietary supplement raw materials and finished products using the Folin-C assay for comparison within same matrices. SMPRs describe the minimum recommended performance characteristics to b...

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. [Study on estimation of deserts soil total phosphorus content from thermal-infrared emissivity].

    Science.gov (United States)

    Hou, Yan-jun; Tiyip, Tashpolat; Zhang, Fei; Sawut, Mamat; Nurmemet, Ilyas

    2015-02-01

    Soil phosphorus provides nutrient elements for plants, is one of important parameters for evaluating soil quality. The traditional method for soil total phosphorus content (STPC) measurement is not effective and time-consuming. However, remote sensing (RS) enables us to determine STPC in a fast and efficient way. Studies on the estimation of STPC in near-infrared spectroscopy have been developed by scholars, but model accuracy is still poor due to the low absorption coefficient and unclear absorption peak of soil phosphorus in near-infrared. In order to solve the deficiency which thermal-infrared emissivity estimate desert soil total phosphorus content, and could improve precision of estimation deserts soil total phosphorus. In this paper, characteristics of soil thermal-infrared emissivity are analyzed on the basis of laboratory processing and spectral measurement of deserts soil samples from the eastern Junggar Basin. Furthermore, thermal-infrared emissivity based RS models for STPC estimation are established and accuracy assessed. Results show that: when STPC is higher than 0.200 g x kg(-1), the thermal-infrared emissivity increases with the increase of STPC on the wavelength between 8.00 microm and 13 microm, and the emissivity is more sensitive to STPC on the wavelength between 9.00 and 9.6 microm; the estimate mode based on multiple stepwise regression was could not to estimate deserts soil total phosphorus content from thermal-infrared emissivity because the estimation effects of them were poor. The estimation accuracy of model based on partial least squares regression is higher than the model based on multiple stepwise regression. However, the accuracy of second-order differential estimation model based on partial least square regression is higher than based on multiple stepwise regression; The first differential of continuous remove estimation model based on partial least squares regression is the best model with R2 of correction and verification are up to

  5. Application of the Electrical Resistivity Tomography to the stone content estimation

    Science.gov (United States)

    Xie, Y.; Chanzy, André; Courdier, Florence; Mariotte, Nicolas; Rachedi, Sabrina

    2009-04-01

    Electrical Resistivity of the soil is regarded as a proxy for many soil properties as structure, moisture content or bedrock depth. The stone content is important for the trees as a large number of stones in the soil restrict the volume of soil that is available for roots to uptake water and nutrients. The potential of ERT for estimating the stone content is evaluated by regarding the stony soil as a two-exponent mixture with stones, which are less conductive, suspend in a conductive matrix. The resistivity of the two components was obtained separately by 2-electrode and 4-electrode methods. On the basis of the resistivity of the soils and the stones, the stone size effect on the effective resistivity was addressed using numerical modeling by Windows based resistivity modeling program RES2DINV and RES3DINV. The effective resistivity at different stone content was calculated by inverting the simulated potential which reproduces a linear panel experiment. The results demonstrate that stone size effect is not very significant. Field measurements were carried out at Mt-Ventoux and l'Issole, located in south of France in the Provence Region. The sites stand in Karstic terrain with soils having high and variable stone content and lying on a bed rock which can be found very close to the surface. Pits were dug and their stone content (volumetric fraction) was estimated. There is an apparent relation between the effective resistivity values extracted from the ERT inversion results and the stone content, the tendency are in good agreement with theoretical results. However, exceptions are found with relatively higher stone content and lower ER value, it can be explained by 3D effect from soil characteristics surrounding the pit. An error assessment in stone content is given according to the resistivity contrast between phases (stones and soil) and the variability in electric resistivity within each phase.

  6. Evaluation of acid digestion techniques to estimate chromium contents in cattle feces

    Directory of Open Access Journals (Sweden)

    Gabriel Cipriano Rocha

    2015-01-01

    Full Text Available The objective of this work was to evaluate the accuracy of digestion techniques using nitric and perchloric acid at the ratios of 2:1, 3:1, and 4:1 v v-1, in one- or two-step digestion, to estimate chromium contents in cattle feces, using sodium molybdate as a catalyst. Fecal standards containing known chromium contents (0, 2, 4, 6, 8, and 10 g kg-1 were produced from feces of five animals. The chromium content in cattle feces is accurately estimated using digestion techniques based on nitric and perchloric acids, at a 3:1 v v-1 ratio, in one-step digestion, with sodium molybdate as a catalyst.

  7. Sensitivity and uncertainty analysis of estimated soil hydraulic parameters for simulating soil water content

    Science.gov (United States)

    Gupta, Manika; Garg, Naveen Kumar; Srivastava, Prashant K.

    2014-05-01

    The sensitivity and uncertainty analysis has been carried out for the scalar parameters (soil hydraulic parameters (SHPs)), which govern the simulation of soil water content in the unsaturated soil zone. The study involves field experiments, which were conducted in real field conditions for wheat crop in Roorkee, India under irrigated conditions. Soil samples were taken for the soil profile of 60 cm depth at an interval of 15 cm in the experimental field to determine soil water retention curves (SWRCs). These experimentally determined SWRCs were used to estimate the SHPs by least square optimization under constrained conditions. Sensitivity of the SHPs estimated by various pedotransfer functions (PTFs), that relate various easily measurable soil properties like soil texture, bulk density and organic carbon content, is compared with lab derived parameters to simulate respective soil water retention curves. Sensitivity analysis was carried out using the monte carlo simulations and the one factor at a time approach. The different sets of SHPs, along with experimentally determined saturated permeability, are then used as input parameters in physically based, root water uptake model to ascertain the uncertainties in simulating soil water content. The generalised likelihood uncertainty estimation procedure (GLUE) was subsequently used to estimate the uncertainty bounds (UB) on the model predictions. It was found that the experimentally obtained SHPs were able to simulate the soil water contents with efficiencies of 70-80% at all the depths for the three irrigation treatments. The SHPs obtained from the PTFs, performed with varying uncertainties in simulating the soil water contents. Keywords: Sensitivity analysis, Uncertainty estimation, Pedotransfer functions, Soil hydraulic parameters, Hydrological modelling

  8. Underestimating the Alcohol Content of a Glass of Wine: The Implications for Estimates of Mortality Risk

    Science.gov (United States)

    Britton, Annie; O’Neill, Darragh; Bell, Steven

    2016-01-01

    Aims Increases in glass sizes and wine strength over the last 25 years in the UK are likely to have led to an underestimation of alcohol intake in population studies. We explore whether this probable misclassification affects the association between average alcohol intake and risk of mortality from all causes, cardiovascular disease and cancer. Methods Self-reported alcohol consumption in 1997–1999 among 7010 men and women in the Whitehall II cohort of British civil servants was linked to the risk of mortality until mid-2015. A conversion factor of 8 g of alcohol per wine glass (1 unit) was compared with a conversion of 16 g per wine glass (2 units). Results When applying a higher alcohol content conversion for wine consumption, the proportion of heavy/very heavy drinkers increased from 28% to 41% for men and 15% to 28% for women. There was a significantly increased risk of very heavy drinking compared with moderate drinking for deaths from all causes and cancer before and after change in wine conversion; however, the hazard ratios were reduced when a higher wine conversion was used. Conclusions In this population-based study, assuming higher alcohol content in wine glasses changed the estimates of mortality risk. We propose that investigator-led cohorts need to revisit conversion factors based on more accurate estimates of alcohol content in wine glasses. Prospectively, researchers need to collect more detailed information on alcohol including serving sizes and strength. Short summary The alcohol content in a wine glass is likely to be underestimated in population surveys as wine strength and serving size have increased in recent years. We demonstrate that in a large cohort study, this underestimation affects estimates of mortality risk. Investigator-led cohorts need to revisit conversion factors based on more accurate estimates of alcohol content in wine glasses. PMID:27261472

  9. [Chromium content in foods and dietary intake estimation in the Northwest of Mexico].

    Science.gov (United States)

    Grijalva Haro, M I; Ballesteros Vázquez, M N; Cabrera Pacheco, R M

    2001-03-01

    Chromium is an indispensable nutrient for the carbohydrates and lipids metabolism. In this study the chromium content in the twenty main foods of the diet from Northwestern Mexico was determined, as well as the daily mean intake which was estimated based on the food intake basket of this region. Chromium content was analyzed by atomic absorption spectrophotometry using the graphite furnace technique and previous digestion of foods in microwave oven. The chromium mean intake was estimated considering the chromium daily mean intake for person per day and the chromium content of the foods analyzed in this study. The range chromium content in the foods analyzed was between 0.0004 and 0.1641 microgram/g dry weight. White cheese showed the highest chromium content followed by pasta soup, wheat tortilla, bread and meat. The main foods chromium contributors in the diet were: wheat tortilla (20%), white cheese (11%), corn tortilla (11%), pasta soup (10%), milk (10%), meat (9%) and white bread (8%). The daily chromium intake was 30.43 +/- 1.6 micrograms/d. Chromium values obtained in the food analyzed are considered low. Moreover, chromium intake obtained from the diet is not enough to meet the safety and adequate daily chromium intake. Therefore, the population from the Northwestern Mexico has a suboptimal dietary chromium intake.

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

    Science.gov (United States)

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

    2014-03-01

    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 (R2) of 0.791; Illite content: a RMSEC of 1.126 with a R2 of 0.616; Montmorillonite content: a RMSEC of 1.814 with a R2 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.

  11. Query cost estimation through remote system contention states analysis over the Internet

    OpenAIRE

    Liu, Weiru; Liao, Z; Hong, Jun

    2004-01-01

    Query processing over the Internet involving autonomous data sources is a major task in data integration. It requires the estimated costs of possible queries in order to select the best one that has the minimum cost. In this context, the cost of a query is affected by three factors: network congestion, server contention state, and complexity of the query. In this paper, we study the effects of both the network congestion and server contention state on the cost of a query. We refer to these tw...

  12. Estimation of chlorophyll contents in leaves and canopy of steppe vegetation using hyperspectral measurements

    Science.gov (United States)

    Wei, Dandan; Xiao, Chenchao; Zhang, Zhenhua; Wei, Hongyan; Shang, Kun

    2016-04-01

    As an important part of the Eurasian Steppe, the temperate typical steppe in Inner Mongolia is highly representative of the Eurasian vegetation. Compared to multispectral remote sensing, hyperspectral remote sensing is more sensitive in monitoring some characteristics of vegetation. However, the research on the typical temperate steppe in Inner Mongolia is still not perfect, so we selected three sampling zones with different dominant species on the typical steppe in Xilinhot of Inner Mongolia. We collected spectrum of leaves and canopy separately to estimate content of chlorophyll of steppe vegetation. In addition, we compared and analyzed the advantage and feasibility of different estimation methods in estimating chlorophyll contents of meadows which have different dominant species through cross validation. The conclusions drawn in this research are as follows: Due to significant discontinuity, maximum first derivative method and Lagrange interpolation method are not suitable for estimation of chlorophyll of typical steppe. Compared with other methods, the red edge position calculated with four points linear interpolation obviously migrates to long wave direction. Inverted Gaussian model and four points linear interpolation both show low sensitivity for Stipa grandis steppe zone (with Stipa grandis as dominant species) where chlorophyll concentration is low and there is saturation phenomenon and weak stability (obvious variation of R2) for Leymus chinensis steppe (with Leymus chinensis as dominant species) where chlorophyll concentration is high, so they are also not the best choice. Linear extrapolation and polynomial fitting show certain saturation for high concentration of chlorophyll and also high correlation coefficient for both leaves and canopy, so they are suitable for estimation of chlorophyll concentration of leaves and canopy on the steppe. The different methods of extracting red edge are better at estimating chlorophyll of leaves than canopy and the

  13. 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.

  14. GC-HS Method Development for the Estimation of Benzene Content in Lovastatin

    Directory of Open Access Journals (Sweden)

    Patel D

    2013-05-01

    Full Text Available A simple, fast and accurate method has been developed for the estimation of benzene content inLovastatin by Gas Chromatography. The analysis was carried out on Perkin Elmer Clarus 600 GC-HSChromatograph. The column used was DB-624 30m X 0.32 mm X 1.8 μm fused silica analytical column(6% cyanopropylphenyl 94 % dimethylpolysiloxane as a stationary phase.The detector used wasFID detector.

  15. 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

    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...... 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...... 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:The 37 Celsius degree system and the analysis can be reproduced in a similar way. MR T1...

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

    Science.gov (United States)

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

    2013-10-01

    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 2m, 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 2m at both landfills, the difference between GPR and lab measured water contents were reasonable at 33.9% for the drier landfill and 18.1% for the wetter landfill. Infiltration experiments also showed the potential to measure small increases in water content.

  17. Application of Wenner Configuration to Estimate Soil Water Content in Pine Plantations on Sandy Land

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    To estimate the mean value of surface soil water content rapidly, accurately, and nonintrusively, field investigations on soil electrical resistivity (SER) with the Yokogawa 324400 earth resistivity meter and the surface (0-150 cm) soil water content (SWC) with time domain reflectometry (TDR), together with the abiotic factors including soil texture, structure,and salinity concentrations were conducted in the Mongolian pine (Pinus sylvestris var. mongolica) plantations on a sandy land. The measurement of SER was based on the 4-probe Wenner configuration method. Relationships between the values of SWC and SER were obtained based on analysis of the abiotic factors of the research site, which play a key role in affecting the soil electrical resistivity. Results indicate that the SER meter could be used to estimate the mean value of SWC in the Mongolian pine plantations on the sandy land during the growing seasons. The bulky nature of the equipment simplified the cumbersome measurements of soil water content with the general methods. It must be noted that the Wenner configuration method could only provide the mean values of the SWC, and the soil texture, structure,temperature, and solute concentrations influenced the SER and further affected the estimation of the SWC by the SER meter. Therefore, the results of this study could be applied on a sandy land during the growing seasons only. However,the SWC of other soil types also may be obtained according to the individual soil types using the procedures of this study.

  18. An Evaluation of Total Solar Reflectance and Spectral Band Ratioing Techniques for Estimating Soil Water Content

    Science.gov (United States)

    Reginato, R. J.; Vedder, J. F.; Idso, S. B.; Jackson, R. D.; Blanchard, M. B.; Goettelman, R.

    1977-01-01

    For several days in March of 1975, reflected solar radiation measurements were obtained from smooth and rough surfaces of wet, drying, and continually dry Avondale loam at Phoenix, Arizona, with pyranometers located 50 cm above the ground surface and a multispectral scanner flown at a 300-m height. The simple summation of the different band radiances measured by the multispectral scanner proved equally as good as the pyranometer data for estimating surface soil water content if the multispectral scanner data were standardized with respect to the intensity of incoming solar radiation or the reflected radiance from a reference surface, such as the continually dry soil. Without this means of standardization, multispectral scanner data are most useful in a spectral band ratioing context. Our results indicated that, for the bands used, no significant information on soil water content could be obtained by band ratioing. Thus the variability in soil water content should insignificantly affect soil-type discrimination based on identification of type-specific spectral signatures. Therefore remote sensing, conducted in the 0.4- to 1.0-micron wavelength region of the solar spectrum, would seem to be much More suited to identifying crop and soil types than to estimating of soil water content.

  19. 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.

  20. 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.

  1. Experimental design for parameter estimation of gene regulatory networks.

    Directory of Open Access Journals (Sweden)

    Bernhard Steiert

    Full Text Available Systems biology aims for building quantitative models to address unresolved issues in molecular biology. In order to describe the behavior of biological cells adequately, gene regulatory networks (GRNs are intensively investigated. As the validity of models built for GRNs depends crucially on the kinetic rates, various methods have been developed to estimate these parameters from experimental data. For this purpose, it is favorable to choose the experimental conditions yielding maximal information. However, existing experimental design principles often rely on unfulfilled mathematical assumptions or become computationally demanding with growing model complexity. To solve this problem, we combined advanced methods for parameter and uncertainty estimation with experimental design considerations. As a showcase, we optimized three simulated GRNs in one of the challenges from the Dialogue for Reverse Engineering Assessment and Methods (DREAM. This article presents our approach, which was awarded the best performing procedure at the DREAM6 Estimation of Model Parameters challenge. For fast and reliable parameter estimation, local deterministic optimization of the likelihood was applied. We analyzed identifiability and precision of the estimates by calculating the profile likelihood. Furthermore, the profiles provided a way to uncover a selection of most informative experiments, from which the optimal one was chosen using additional criteria at every step of the design process. In conclusion, we provide a strategy for optimal experimental design and show its successful application on three highly nonlinear dynamic models. Although presented in the context of the GRNs to be inferred for the DREAM6 challenge, the approach is generic and applicable to most types of quantitative models in systems biology and other disciplines.

  2. Using GPS Interferometric Reflectometry to estimate soil moisture and vegetation water content fluctuations

    Science.gov (United States)

    Chew, C. C.; Small, E. E.; Larson, K. M.; Braun, J. J.; Shreve, C. M.

    2010-12-01

    High-precision GPS receivers can be used to estimate fluctuations in near surface soil moisture, snow and vegetation water content. This approach, referred to as GPS-Interferometric Reflectometry (GPS-IR), relates precise changes in the geometry of reflected GPS signals to observe soil moisture and snow while simultaneously using signal attenuation and diffuse scattering to infer changes in vegetative state. Previous remote sensing research has shown that microwave signals (e.g., L-band) are optimal for measuring hydrologic variables, such as soil moisture, and because GPS satellites transmit similar signals, they can be useful for sensing water in the environment. In addition, standard GPS antenna configurations that are used in NSF's Plate Boundary Observatory network yield sensing footprints of ~1000 m2. Given this sensitivity, hundreds of GPS receivers that exist in the U.S. could be used to provide near-real time estimates of soil moisture and vegetation water content for satellite validation, drought monitoring and related studies. A significant obstacle to using L-band (or similar) signals for remote sensing is differentiating the effects of soil moisture and vegetation on the retrieval of hydrologic variables. This same challenge exists when using GPS-IR data. We have established nine research sites with identical GPS and hydrologic infrastructure to study this problem. These sites span a wide range of soil, vegetation, and climate types. In addition to daily GPS and hourly soil moisture data, we have collected weekly vegetation water content samples at all sites. Our data demonstrate that soil moisture fluctuations can be estimated from GPS-IR records when vegetation water content is low (moisture and vegetation signals and quantifying errors in our retrieval algorithm.

  3. Progresses in Researches of the Application of Low-Amylose Content Rice Gene for Breeding

    Institute of Scientific and Technical Information of China (English)

    ZHU Chang-lan; SHEN Wen-biao; ZHAI Hu-qu; WAN Jian-min

    2004-01-01

    Amylose content is a key determinant of eating quality of rice. With the characteristics of fluffy texture, glossy appearance when cooked, remaining soft when cooled and excellent puffing ability, the low-amylose rice with amylose content 5-15% could be served as not only cooked rice directly, but also good material for convenience, mixed rice and puffing foods.Current status on characterization, inheritance, molecular mechanism and breeding of lowamylose content rice was reviewed in this paper, strategy of related researches in the era of glymics was mainly discussed furthermore. The future research should focus on screening and enhancing the germplasm, further elucidating the molecular mechanism on mutation of low amylose content, utilizing the genes independent of Wx on low-amylose content rice breeding program, and developing high quality functional rice cultivars for special usage through pyramiding low amylose gene and other special quality genes.

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

    Science.gov (United States)

    Palma, M N N; Rocha, G C; Valadares Filho, S C; Detmann, E

    2015-11-01

    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.

  5. In situ hyperspectral data analysis for pigment content estimation of rice leaves

    Institute of Scientific and Technical Information of China (English)

    程乾; 黄敬峰; 王秀珍; 王人潮

    2003-01-01

    Analyses of the correlation between hyperspectral reflectance and pigment content including chlorephyll-a, chlorephyll-b and carotenoid of leaves in different sites of rice were reported in this paper. The hyperspectral reflectance of late rice during the whole growing season was measured using a Spectroradiometer with spectral range of 350 - 1050 nm and resolution of 3 nm. The chlorophyll-a, chlorephyll-b and carotenoid contents in rice leaves in rice fields to which different levels of nitrogen were applied were measured. The chlorephyll-a content of upper leaves was well correlated with the spectral variables. However, the correlation between both chlorephyll-b and careteniod and the spectral variables was far from that of chlorophyll-a. The potential of hyperspectral reflectance measurement for estimating chlorophyll-a of upper leaves was evaluated using univariate correlation and multivariate regression analysis methods with different types of predictors. This study showed that the most suitable estimated model of chlorephyll-a of upper leaves was obtained by using some hyperspectral variables such as SDr , SDb and their integration.

  6. In situ hyperspectral data analysis for pigment content estimation of rice leaves

    Institute of Scientific and Technical Information of China (English)

    程乾; 黄敬峰; 王秀珍; 王人潮

    2003-01-01

    Analyses of the correlation between hyperspectral reflectance and pigment content including chlorophyll-a, chlorophyll-b and carotenoid of leaves in different sites of rice were reported in this paper. The hyperspectral reflectance of late rice during the whole growing season was measured using a Spectroradiometer with spectral range of 350-1050 nm and resolution of 3 nm. The chlorophyll-a, chlorophyll-b and carotenoid contents in rice leaves in rice fields to which different levels of nitrogen were applied were measured. The chlorophyll-a content of upper leaves was well correlated with the spectral variables. However, the correlation between both chlorophyll-b and caroteniod and the spectral variables was far from that of chlorophyll-a. The potential of hyperspectral reflectance measurement for estimating chlorophyll-a of upper leaves was evaluated using univariate correlation and multivariate regression analysis methods with different types of predictors. This study showed that the most suitable estimated model of chlorophyll-a of upper leaves was obtained by using some hyperspectral variables such as SDr, SDb and their integration.

  7. NEAR INFRARED SPECTROSCOPY FOR ESTIMATING SUGARCANE BAGASSE CONTENT IN MEDIUM DENSITY FIBERBOARD

    Directory of Open Access Journals (Sweden)

    Ugo Leandro Belini

    2011-04-01

    Full Text Available Medium density fiberboard (MDF is an engineered wood product formed by breaking down selected lignin-cellulosic material residuals into fibers, combining it with wax and a resin binder, and then forming panels by applying high temperature and pressure. Because the raw material in the industrial process is ever-changing, the panel industry requires methods for monitoring the composition of their products. The aim of this study was to estimate the ratio of sugarcane (SC bagasse to Eucalyptus wood in MDF panels using near infrared (NIR spectroscopy. Principal component analysis (PCA and partial least square (PLS regressions were performed. MDF panels having different bagasse contents were easily distinguished from each other by the PCA of their NIR spectra with clearly different patterns of response. The PLS-R models for SC content of these MDF samples presented a strong coefficient of determination (0.96 between the NIR-predicted and Lab-determined values and a low standard error of prediction (~1.5% in the cross-validations. A key role of resins (adhesives, cellulose, and lignin for such PLS-R calibrations was shown. PLS-DA model correctly classified ninety-four percent of MDF samples by cross-validations and ninety-eight percent of the panels by independent test set. These NIR-based models can be useful to quickly estimate sugarcane bagasse vs. Eucalyptus wood content ratio in unknown MDF samples and to verify the quality of these engineered wood products in an online process.

  8. Branched Chain Fatty Acid (BCFA) Content of Foods and Estimated Intake in the United States

    Science.gov (United States)

    Bae, SangEun; Lawrence, Peter; Wang, Dong Hao

    2015-01-01

    Branched chain fatty acids (BCFA) are bioactive food components that constitute about 2% of fatty acids in cow’s milk fat. Little systematic information on the BCFA content of other foods is available to estimate dietary intakes. We report BCFA distribution and content of fresh and processed foods representing the major foods of Americans and estimate BCFA intake. BCFA are primarily components of dairy and ruminant foods, and were absent from chicken, pork, and salmon. Dairy and beef delivered most of the 500 mg per day mean intake; in comparison, intake of the widely studied long chain polyunsaturates eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) is estimated to average 100 mg per day. Common adjustments in diet can double BCFA daily intake. The fermented foods sauerkraut and miso had appreciable fractions of BCFA but overall are low fat foods providing very small amounts in the diet, and other fermented foods did not contain BCFA as might have been expected from microbial exposure. These data support the quantitative importance of BCFA delivered primarily from dairy and beef and highlight the need for research into their health effects. PMID:24830474

  9. Satellite-scale Estimates of the "b Parameter" Relating Vegetation Water Content and SMOS Optical Thickness

    Science.gov (United States)

    Patton, J. C.; Hornbuckle, B. K.

    2013-12-01

    Microwave radiation emitted by Earth's land surface is primarily determined by soil moisture and vegetation. One of the effects of vegetation on surface microwave emissions is often termed the "vegetation optical thickness" or "vegetation opacity" and is often abbreviated as tau. Retrievals of soil moisture from microwave radiometer measurements requires knowledge of tau. The Soil Moisture and Ocean Salinity (SMOS) satellite measures microwave radiation at multiple incidence angles, enabling the simultaneous retrieval of soil moisture and tau. Other soil moisture satellites, such as the upcoming Soil Moisture Active Passive (SMAP) satellite, only measure at single incidence angles and may need auxiliary sources of tau data in order to retrieve soil moisture. One proposed method for estimating tau for these satellites is by relating reflectance data, e.g. the normalized difference vegetation index, to vegetation water content (VWC), then relating VWC to tau. VWC and tau can be related through the b parameter, i.e. tau = b x VWC. Values of b for different land cover types have been estimated from tower (~1 m) and airplane (~10-100 m) data, but have not been measured at the satellite scale (~10 km). Estimating b at the satellite scale from measurements at smaller scales is difficult because the effective value of b in a satellite pixel may not be well represented by linear weighted average based on the fraction of each land cover type in the pixel. However, by relating county crop yields, estimated by the USDA National Agricultural Statistics Service, to measurements of SMOS tau, and by using certain allometric relationships, such as the ratio of water to dry matter and the harvest index of crops, we can estimate b at the satellite scale. We have used this method to estimate b for each Iowa county for the years 2010-2012. Initial results suggest that b may change year to year; our current estimates for b in Iowa range from 0.065 in 2010 to 0.100 in 2012. These

  10. Remote estimation of canopy nitrogen content in winter wheat using airborne hyperspectral reflectance measurements

    Science.gov (United States)

    Zhou, Xianfeng; Huang, Wenjiang; Kong, Weiping; Ye, Huichun; Luo, Juhua; Chen, Pengfei

    2016-11-01

    Timely and accurate assessment of canopy nitrogen content (CNC) provides valuable insight into rapid and real-time nitrogen status monitoring in crops. A semi-empirical approach based on spectral index was extensively used for nitrogen content estimation. However, in many cases, due to specific vegetation types or local conditions, the applicability and robustness of established spectral indices for nitrogen retrieval were limited. The objective of this study was to investigate the optimal spectral index for winter wheat (Triticum aestivum L.) CNC estimation using Pushbroom Hyperspectral Imager (PHI) airborne hyperspectral data. Data collected from two different field experiments that were conducted during the major growth stages of winter wheat in 2002 and 2003 were used. Our results showed that a significant linear relationship existed between nitrogen and chlorophyll content at the canopy level, and it was not affected by cultivars, growing conditions and nutritional status of winter wheat. Nevertheless, it varied with growth stages. Periods around heading stage mainly worsened the relationship and CNC estimation, and CNC assessment for growth stages before and after heading could improve CNC retrieval accuracy to some extent. CNC assessment with PHI airborne hyperspectra suggested that spectral indices based on red-edge band including narrowband and broadband CIred-edge, NDVI-like and ND705 showed convincing results in CNC retrieval. NDVI-like and ND705 were sensitive to detect CNC changes less than 5 g/m2, narrowband and broadband CIred-edge were sensitive to a wide range of CNC variations. Further evaluation of CNC retrieval using field measured hyperspectra indicated that NDVI-like was robust and exhibited the highest accuracy in CNC assessment, and spectral indices (CIred-edge and CIgreen) that established on narrow or broad bands showed no obvious difference in CNC assessment. Overall, our study suggested that NDVI-like was the optimal indicator for winter

  11. 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.

  12. 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

  13. Estimating the Relative Water Content of Leaves in a Cotton Canopy

    Science.gov (United States)

    Vanderbilt, Vern; Daughtry, Craig; Kupinski, Meredith; French, Andrew; Chipman, Russell; Dahlgren, Robert

    2017-01-01

    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.Twice during one day, +- 3 hours from solar noon, we collected polarized imagery and relative water content data on a cotton test plot located at the Arid Land Agricultural Research Center, United States Department of Agriculture, Maricopa, AZ. The test plot, a small portion of a large cotton field, contained stressed plants ready for irrigation. The evening prior to data collection we irrigated several rows of plants within the test plot. Thus, ground MSPI imagery from both morning and afternoon included cotton plants with a range of water statuses. Data analysis includes classifying the polarized imagery into sunlit reflecting, sunlit transmitting, shaded foliage and bare soil. We estimate the leaf surface reflection and interior reflection based upon the per pixel polarization and sunview directions. We compare our cotton results with our prior polarization results for corn and soybean leaves measured in the lab and corn leaves measured in the field.

  14. 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.

  15. 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.

  16. Monthly variation in the fat content of anchovy (Engraulis japonicus) in the Yellow Sea: implications for acoustic abundance estimation

    Institute of Scientific and Technical Information of China (English)

    ZHANG Bo; ZHAO Xianyong; DAI Fangqun

    2011-01-01

    Anchovy is a key species in the Yellow Sea ecosystem. An accurate estimate of anchovy abundance is vital for the management of the anchovy stock and measurement of the ecosystem response to changes in anchovy abundance. However, the acoustic fish abundance estimate may be biased by 30%-40% if the fat-content induced target strength variation is not taken into account. We measured the monthly variation in the fat content of anchovy (Engraulis japonicus) in the Yellow Sea, and evaluated the potential effect of variation in fat content on the acoustic assessment of anchovy abundance. The fat content of anchovy varied seasonally, with two maxima and two minima in a year. The highest fat content (14.75%) was measured in the pre-spawning period in May, and the lowest fat content (2.48%) was measured during the post-spawning period in October. Fat content appeared to correlate with water content,but not body size. Assuming that the target strength is decreased by 0.2dB for every 1% increase in fat content, the seasonal difference in the target strength of anchovy may be as high as 2.45 dB. Given this,the acoustic abundance estimate may be biased by between 43% and 76%. Our results highlight the need for more information on the changes in fat content of fishes whose abundance is estimated by acoustic surveys.

  17. 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).

  18. Cytogenetic characterization of olive flounder Paralichthys olivaceus: DNA content, karyotype, AgNORs and location of major ribosomal genes

    Institute of Scientific and Technical Information of China (English)

    WANG Xubo; ZHANG Quanqi; CHEN Yanjie; QI Jie; WANG Zhigang; WANG Xinglian

    2009-01-01

    A cytogenetic analysis of Paralichthys olivaceus was carried out using the flow cytometry method for DNA content, silver staining for the nucleolus organizer region (AgNORs) identification and one-color fluorescence in situ hybridization (FISH) for chromosomal mapping of major ribosomal genes. Nuclear DNA content was estimated by flow cytometry method using Gallus domesticus erythrocytes as the internal reference standard. The C-value of this species was (0.737±0.024) pg, and the DNA contents of each chromosome were estimated to be 16.51 Mb to 39.50 Mb after paired according to the average relative length. The FISH probe was made by PCR amplification of a DNA fragment containing internal transcribed spacers ITS1 between 18S and 5.8S ribosomal RNA gene, and labeled by PCR incorporation of bio-16-dUTP. FISH signals and AgNORs were both located on the secondary constrictions of chromosome 1. These results will provide a better understanding of the cytogenetic information of this species and would help for further research of the karyotype evolution in the order Pleuronectiformes.

  19. Estimating the vertical profiles of cloud water content in warm rain clouds

    Science.gov (United States)

    Li, Rui; Guo, Jingchao; Fu, Yufei; Min, Qinlong; Wang, Yu; Gao, Xiaoming; Dong, Xue

    2017-04-01

    The cloud water content (CWC) in rainy clouds is a crucial parameter to determine the onset and the growth rate of precipitation, and to quantify the associated latent heating rate. No direct retrieval of CWC in rainy cloud from satellite observations is reported due to the difficulties of separating cloud particles from precipitation sized particles. However, based on multiple cloud simulations from the Weather and Research Forecasting (WRF) model, we have found that the CWC profile in warm rains can be well determined by three macro-physical cloud properties of cloud water path (CWP), cloud top height (CTH), and cloud bottom height (CBH). The CBH can be estimated using CWP, CTH and near surface rain rate. We proposed an algorithm with a lookup table for estimating the CWC profile using CWP, CTH and near surface rain rate as inputs. The performance of this algorithm was tested with WRF model simulations and a real drizzle case observed by the CloudSat satellite. Testing verified that the algorithm can retrieve the vertical distribution of CWC correctly with few errors at different spatiotemporal scales. In addition, the algorithm is not confined to particular microphysics schemes and is valid for multiple cloud systems in different areas over the world. This algorithm is expected to improve current knowledge of cloud water content in rainy clouds.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. 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.

  2. Supporting document for the historical tank content estimate for BY 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 BY Tank Farm of the northeast quadrant of the 200 East Area. Nine appendices contain 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.

  3. 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.

  4. Estimating the soil organic carbon content for European NUTS2 regions based on LUCAS data collection.

    Science.gov (United States)

    Panagos, Panos; Ballabio, Cristiano; Yigini, Yusuf; Dunbar, Martha B

    2013-01-01

    Under the European Union Thematic Strategy for Soil Protection, the European Commission Directorate-General for the Environment and the European Environmental Agency (EEA) identified a decline in soil organic carbon and soil losses by erosion as priorities for the collection of policy relevant soil data at European scale. Moreover, the estimation of soil organic carbon content is of crucial importance for soil protection and for climate change mitigation strategies. Soil organic carbon is one of the attributes of the recently developed LUCAS soil database. The request for data on soil organic carbon and other soil attributes arose from an on-going debate about efforts to establish harmonized datasets for all EU countries with data on soil threats in order to support modeling activities and display variations in these soil conditions across Europe. In 2009, the European Commission's Joint Research Centre conducted the LUCAS soil survey, sampling ca. 20,000 points across 23 EU member states. This article describes the results obtained from analyzing the soil organic carbon data in the LUCAS soil database. The collected data were compared with the modeled European topsoil organic carbon content data developed at the JRC. The best fitted comparison was performed at NUTS2 level and showed underestimation of modeled data in southern Europe and overestimation in the new central eastern member states. There is a good correlation in certain regions for countries such as the United Kingdom, Slovenia, Italy, Ireland, and France. Here we assess the feasibility of producing comparable estimates of the soil organic carbon content at NUTS2 regional level for the European Union (EU27) and draw a comparison with existing modeled data. In addition to the data analysis, we suggest how the modeled data can be improved in future updates with better calibration of the model.

  5. Overexpression of UDP-glucose pyrophosphorylase gene could increase cellulose content in Jute (Corchorus capsularis L.).

    Science.gov (United States)

    Zhang, Gaoyang; Qi, Jianmin; Xu, Jiantang; Niu, Xiaoping; Zhang, Yujia; Tao, Aifen; Zhang, Liwu; Fang, Pingping; Lin, Lihui

    2013-12-13

    In this study, the full-length cDNA of the UDP-glucose pyrophosphorylase gene was isolated from jute by homologous cloning (primers were designed according to the sequence of UGPase gene of other plants) and modified RACE techniques; the cloned gene was designated CcUGPase. Using bioinformatic analysis, the gene was identified as a member of the UGPase gene family. Real-time PCR analysis revealed differential spatial and temporal expression of the CcUGPase gene, with the highest expression levels at 40 and 120d. PCR and Southern hybridization results indicate that the gene was integrated into the jute genome. Overexpression of CcUGPase gene in jute revealed increased height and cellulose content compared with control lines, although the lignin content remained unchanged. The results indicate that the jute UGPase gene participates in cellulose biosynthesis. These data provide an important basis for the application of the CcUGPase gene in the improvement of jute fiber quality. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Using measured soil water contents to estimate evapotranspiration and root water uptake profiles - a comparative study

    Science.gov (United States)

    Guderle, M.; Hildebrandt, A.

    2015-01-01

    Understanding the role of plants in soil water relations, and thus ecosystem functioning, requires information about root water uptake. We evaluated four different complex water balance methods to estimate sink term patterns and evapotranspiration directly from soil moisture measurements. We tested four methods. The first two take the difference between two measurement intervals as evapotranspiration, thus neglecting vertical flow. The third uses regression on the soil water content time series and differences between day and night to account for vertical flow. The fourth accounts for vertical flow using a numerical model and iteratively solves for the sink term. None of these methods requires any a priori information of root distribution parameters or evapotranspiration, which is an advantage compared to common root water uptake models. To test the methods, a synthetic experiment with numerical simulations for a grassland ecosystem was conducted. Additionally, the time series were perturbed to simulate common sensor errors, like those due to measurement precision and inaccurate sensor calibration. We tested each method for a range of measurement frequencies and applied performance criteria to evaluate the suitability of each method. In general, we show that methods accounting for vertical flow predict evapotranspiration and the sink term distribution more accurately than the simpler approaches. Under consideration of possible measurement uncertainties, the method based on regression and differentiating between day and night cycles leads to the best and most robust estimation of sink term patterns. It is thus an alternative to more complex inverse numerical methods. This study demonstrates that highly resolved (temporally and spatially) soil water content measurements may be used to estimate the sink term profiles when the appropriate approach is used.

  7. 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.

  8. QTLs and candidate genes for desiccation and abscisic acid content in maize kernels

    Directory of Open Access Journals (Sweden)

    Charcosset Alain

    2010-01-01

    Full Text Available Abstract Background Kernel moisture at harvest is an important trait since a low value is required to prevent unexpected early germination and ensure seed preservation. It is also well known that early germination occurs in viviparous mutants, which are impaired in abscisic acid (ABA biosynthesis. To provide some insight into the genetic determinism of kernel desiccation in maize, quantitative trait loci (QTLs were detected for traits related to kernel moisture and ABA content in both embryo and endosperm during kernel desiccation. In parallel, the expression and mapping of genes involved in kernel desiccation and ABA biosynthesis, were examined to detect candidate genes. Results The use of an intermated recombinant inbred line population allowed for precise QTL mapping. For 29 traits examined in an unreplicated time course trial of days after pollination, a total of 78 QTLs were detected, 43 being related to kernel desiccation, 15 to kernel weight and 20 to ABA content. Multi QTL models explained 35 to 50% of the phenotypic variation for traits related to water status, indicating a large genetic control amenable to breeding. Ten of the 20 loci controlling ABA content colocated with previously detected QTLs controlling water status and ABA content in water stressed leaves. Mapping of candidate genes associated with kernel desiccation and ABA biosynthesis revealed several colocations between genes with putative functions and QTLs. Parallel investigation via RT-PCR experiments showed that the expression patterns of the ABA-responsive Rab17 and Rab28 genes as well as the late embryogenesis abundant Emb5 and aquaporin genes were related to desiccation rate and parental allele effect. Database searches led to the identification and mapping of two zeaxanthin epoxidase (ZEP and five novel 9-cis-epoxycarotenoid dioxygenase (NCED related genes, both gene families being involved in ABA biosynthesis. The expression of these genes appeared independent in

  9. 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

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

    Science.gov (United States)

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

    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 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

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

    Science.gov (United States)

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

    2015-12-01

    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 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

  12. 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

  13. Nondestructive Estimation of Moisture Content, pH and Soluble Solid Contents in Intact Tomatoes Using Hyperspectral Imaging

    OpenAIRE

    Anisur Rahman; Lalit Mohan Kandpal; Santosh Lohumi; Kim, Moon S.; Hoonsoo Lee; Changyeun Mo; Byoung-Kwan Cho

    2017-01-01

    The objective of this study was to develop a nondestructive method to evaluate chemical components such as moisture content (MC), pH, and soluble solid content (SSC) in intact tomatoes by using hyperspectral imaging in the range of 1000–1550 nm. The mean spectra of the 95 matured tomato samples were extracted from the hyperspectral images, and multivariate calibration models were built by using partial least squares (PLS) regression with different preprocessing spectra. The results showed tha...

  14. QTL analysis and candidate gene mapping for the polyphenol content in cider apple.

    Science.gov (United States)

    Verdu, Cindy F; Guyot, Sylvain; Childebrand, Nicolas; Bahut, Muriel; Celton, Jean-Marc; Gaillard, Sylvain; Lasserre-Zuber, Pauline; Troggio, Michela; Guilet, David; Laurens, François

    2014-01-01

    Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.

  15. QTL analysis and candidate gene mapping for the polyphenol content in cider apple.

    Directory of Open Access Journals (Sweden)

    Cindy F Verdu

    Full Text Available Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.

  16. Radial basis network analysis of color parameters to estimate lycopene content on tomato fruits.

    Science.gov (United States)

    Fernández-Ruiz, Virginia; Torrecilla, José S; Cámara, Montaña; Mata, Ma Cortes Sánchez; Shoemaker, Charles

    2010-11-15

    With the purpose of estimating the lycopene concentration in tomato food samples, in an non-destructive way, several types of linear models of color parameters have been tested using individual values of L*, a* and b* values, (a*/b*), (a*(2)/b*(2)) and chroma parameters from tomato juice and fresh tomato fruits obtained with two different apparatus (Minolta CR-200b triestimulus colorimeter and HunterLab LabScan XE). Lycopene concentrations of fresh tomato and tomato juice (used as an input) were analyzed by UV-Vis spectroscopy. For all linear methods applied, the best one to estimate the lycopene concentration in tomato was the L*, a* and b* values of tomato juice measured with Hunter colorimeters (adjusted correlation coefficient, R(a)(2)>0.86 and mean prediction error, MPEcolor parameters (L*, a* and b*) designated as "Lab case", and secondly individually by the (a*/b*), (a*(2)/b*(2)) and chroma parameters. The lycopene concentration estimations were carried out with the lowest MPE and highest R(a)(2) values possible. In order to test the reliability of the non-linear models, external validation process was also performed. From the testing of the all non-linear models applied, the RBEF Lab case model was the best to estimate lycopene content from color parameters (L*, a* and b*) using Minolta or Hunter equipments (MPE lower than 0.009 and R(a)(2) higher than 0.997). This was a simple non-destructive method for predicting lycopene concentration in tomato fruits and tomato juice, which was reproducible and accurate enough to substitute chemical extraction determinations, and may be a useful tool for tomato industry.

  17. Content

    DEFF Research Database (Denmark)

    Keiding, Tina Bering

    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......; Race, 2001; Ramsden, 2003). This trend appears closely related to the ‘from-teaching-to-learning’ movement, which has had a strong influence on pedagogy since the early nineties (Keiding, 2007; Terhart, 2003). Another interpretation of the current interest in methodology can be derived from...... for selection of content (Klafki, 1985, 2000; Myhre, 1961; Nielsen, 2006). These attempts all share one feature, which is that criteria for selection of content appear very general and often, more or less explicitly, deal with teaching at the first Bologna-cycle; i.e. schooling at the primary and lower...

  18. X-Ray Methods to Estimate Breast Density Content in Breast Tissue

    Science.gov (United States)

    Maraghechi, Borna

    This work focuses on analyzing x-ray methods to estimate the fat and fibroglandular contents in breast biopsies and in breasts. The knowledge of fat in the biopsies could aid in their wide-angle x-ray scatter analyses. A higher mammographic density (fibrous content) in breasts is an indicator of higher cancer risk. Simulations for 5 mm thick breast biopsies composed of fibrous, cancer, and fat and for 4.2 cm thick breast fat/fibrous phantoms were done. Data from experimental studies using plastic biopsies were analyzed. The 5 mm diameter 5 mm thick plastic samples consisted of layers of polycarbonate (lexan), polymethyl methacrylate (PMMA-lucite) and polyethylene (polyet). In terms of the total linear attenuation coefficients, lexan ≡ fibrous, lucite ≡ cancer and polyet ≡ fat. The detectors were of two types, photon counting (CdTe) and energy integrating (CCD). For biopsies, three photon counting methods were performed to estimate the fat (polyet) using simulation and experimental data, respectively. The two basis function method that assumed the biopsies were composed of two materials, fat and a 50:50 mixture of fibrous (lexan) and cancer (lucite) appears to be the most promising method. Discrepancies were observed between the results obtained via simulation and experiment. Potential causes are the spectrum and the attenuation coefficient values used for simulations. An energy integrating method was compared to the two basis function method using experimental and simulation data. A slight advantage was observed for photon counting whereas both detectors gave similar results for the 4.2 cm thick breast phantom simulations. The percentage of fibrous within a 9 cm diameter circular phantom of fibrous/fat tissue was estimated via a fan beam geometry simulation. Both methods yielded good results. Computed tomography (CT) images of the circular phantom were obtained using both detector types. The radon transforms were estimated via four energy integrating

  19. Development and evaluation of a rapid strategy to determine enterotoxin gene content in Staphylococcus aureus.

    Science.gov (United States)

    Fischer, Adrien; Francois, Patrice; Holtfreter, Silva; Broeker, Barbara; Schrenzel, Jacques

    2009-05-01

    Enterotoxins of S. aureus are important molecules displaying superantigenic properties. To date no less than 18 enterotoxins have been identified in S. aureus and their role has been documented in very diverse diseases. Using available nucleotide sequence information, we developed a rapid and automated PCR-based approach to evaluate enterotoxin content in S aureus. We studied a collection of S. aureus strains previously analyzed for enterotoxins gene content and report a perfect correlation between simplex and multiplex PCR assays for the presence of all enterotoxin genes described so far. The determination of enterotoxin content relies on 4 multiplex PCR tubes whose amplification products are resolved by a rapid microcapillary electrophoresis. Automated analysis of the PCR profiles evaluates for the presence of the 18 enterotoxin genes in less than 3 h and at moderate cost. Finally, the use of enterotoxin gene content for genotyping purpose was compared to multi-locus variable number of tandem repeat assay and spa genotyping. Analysis revealed an important homogeneity of the genetic backgrounds for strains harboring the egc cluster as well as a large diversity for strains harboring other enterotoxins but lacking the egc cluster. A combined genotyping method that includes rapid enterotoxin content determination appears informative for various epidemiological survey purposes.

  20. Kernel Density Feature Points Estimator for Content-Based Image Retrieval

    CERN Document Server

    Zuva, Tranos; Ojo, Sunday O; Ngwira, Seleman M

    2012-01-01

    Research is taking place to find effective algorithms for content-based image representation and description. There is a substantial amount of algorithms available that use visual features (color, shape, texture). Shape feature has attracted much attention from researchers that there are many shape representation and description algorithms in literature. These shape image representation and description algorithms are usually not application independent or robust, making them undesirable for generic shape description. This paper presents an object shape representation using Kernel Density Feature Points Estimator (KDFPE). In this method, the density of feature points within defined rings around the centroid of the image is obtained. The KDFPE is then applied to the vector of the image. KDFPE is invariant to translation, scale and rotation. This method of image representation shows improved retrieval rate when compared to Density Histogram Feature Points (DHFP) method. Analytic analysis is done to justify our m...

  1. 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.

  2. 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.

  3. On-line topical importance estimation: an effective focused crawling algorithm combining link and content analysis

    Institute of Scientific and Technical Information of China (English)

    Can WANG; Zi-yu GUAN; Chun CHEN; Jia-jun BU; Jun-feng WANG; Huai-zhong LIN

    2009-01-01

    Focused crawling is an important technique for topical resource discovery on the Web. The key issue in focusedcrawling is to prioritize uncrawled uniform resource locators (URLs) in the frontier to focus the crawling on relevant pages.Traditional focused crawlers mainly rely on content analysis. Link-based techniques are not effectively exploited despite their usefulness. In this paper, we propose a new frontier prioritizing algorithm, namely the on-line topical importance estimation (OTIE) algorithm. OTIE combines link-and content-based analysis to evaluate the priority of an uncrawled URL in the frontier. We performed real crawling experiments over 30 topics selected from the Open Directory Project (ODP) and compared harvest rate and target recall of the four crawling algorithms: breadth-first, link-context-prediction, on-line page importance computation (OPlC) and our OTIE. Experimental results showed that OTIE significantly outperforms the other three algorithms on the average target recall while maintaining an acceptable harvest rate. Moreover, OTIE is much faster than the traditional focused crawling algorithm.

  4. Estimation of PCB content in agricultural soils associated with long-term fertilization with organic waste.

    Science.gov (United States)

    Antolín-Rodríguez, Juan M; Sánchez-Báscones, Mercedes; Martín-Ramos, Pablo; Bravo-Sánchez, Carmen T; Martín-Gil, Jesús

    2016-06-01

    Polychlorinated biphenyl (PCB) pollution related to the use of organic waste as fertilizers in agricultural soils is a cause of major concern. In the study presented herein, PCB concentration was studied through a field trial conducted in two agricultural soils in the province of Palencia (Spain) over a 4-year period, assessing the impact of irrigation and of different types of organic waste materials. The amounts of organic waste added to the soil were calculated according to the nitrogen needs of the crop, and the concentration of PCBs was determined before and after the application of the organic waste. The resulting persistence of the total PCB content in the agricultural soils, compared with the PCB concentration in the original soils, ranged from 27% to 90%, with the lowest value corresponding to irrigated soils treated with municipal solid waste compost (MSWC) and the highest value to non-irrigated soils treated with composted sewage sludge (CSS). An estimate of the PCB content in agricultural soils after the application of organic waste materials until year 2050 was obtained, resulting in a value below 5 ng·g(-1), considered a background value for soils in sites far away from potential pollution sources.

  5. Validation of Brix refractometer to estimate colostrum immunoglobulin G content and composition in the sow.

    Science.gov (United States)

    Hasan, S M K; Junnikkala, S; Valros, A; Peltoniemi, O; Oliviero, C

    2016-10-01

    Colostrum is an essential source of immunoglobulin G (IgG) for neonate piglets. However, colostrum IgG content and nutritional composition can vary considerably among sows due to age, parity, feeding regime and immunological background. Currently, there is no practical way to obtain information about colostrum IgG concentration at herd level. We evaluated sows' colostrum IgG content on-farm using a Brix refractometer and its performance was compared with that of an IgG ELISA. In addition, nutritional compositions of the colostrum samples were analyzed using Fourier transform IR spectroscopy. Colostrum samples (5 to 6 ml) (n=153) were obtained within 0 to 3 h of farrowing. However, to obtain a 24 h IgG profile for 11 sows, colostrum samples were collected at 0, 2, 4, 6, 8, 10, 16 and 24 h after farrowing. A 0.3 ml of freshly drawn colostrum sample was used for the on-farm measurement of Brix percentages using a digital refractometer shortly after collection. The remaining fractions of the samples were frozen and submitted to laboratory analysis for total IgG, using a commercially available pig IgG ELISA kit. For nutritional composition analysis, a 35 ml colostrum sample (n=34) was obtained immediately after birth of first piglet from the first three pairs of frontal teats. Colostrum concentrations of IgG averaged 52.03±30.70 mg/ml (mean±SEM) at 0 to 3 h after farrowing. Concentration of IgG decreased on average by 50% during the 1st day of lactation (P30%. Colostrum IgG concentration is highly variable among sows, Brix measurement of a sows' fresh colostrum is an inexpensive, rapid and satisfactorily accurate method of estimating IgG concentration, providing indication of differentiation between good and poor IgG content of colostrum.

  6. Novel Approach for Estimating Nitrogen Content in Paddy Fields Using Low Altitude Remote Sensing System

    Science.gov (United States)

    Saberioon, M. M.; Gholizadeh, A.

    2016-06-01

    Concerns over the use of nitrogen have been increasing due to the high cost of fertilizers and environmental pollutions caused by excess nitrogen application in agricultural fields. Several methods are available to assess the amount of nitrogen in crops, however, they are expensive, time-consuming, inaccurate, and/or require specialists to operate the tools. Researcher recently suggested remote sensing and specifically Low Altitude Remote Sensing (LARS) system of chlorophyll content in crop canopies as a low-cost alternative to estimate plant nitrogen status. The main objective of this study was to develop and test a new Vegetation Index (VI) to determine the status of nitrogen and chlorophyll content in rice leaf by analysing and considering all Visible (Vis) bands. Besides, capability of introduced VI has compared with all known VIs in both Vis and Near Infrared (NIR) bands in canopy scale. To develop the VI, images from 6-pannel leaf colour chart were acquired using Basler Scout scA640-70fc under light-emitting diode lighting, in which principal component analysis was used to retain the lower order principal component to develop a new index called IPCA. A conventional digital camera mounted to an Unmanned Aerial Vehicle (UAV) was also used to acquire images over the rice canopy in Vis bands. Simultaneously, Tetracam agriculture digital camera was employed to acquire rice canopy image in Vis-NIR bands. The results indicated that the proposed index at canopy (r = 0.78) scale could be used as a sensor to determine the status of chlorophyll content consequently for monitoring nitrogen in rice plant through different growth stages. Moreover, results confirmed that a lowcost LARS system would be suited for high spatial and temporal resolution images and data analysis for proper assessment of key nutrients in crop farming in a fast, inexpensive and non-destructive way.

  7. Estimating spatial variations in soil water content from electrical conductivity surveys across semiarid Mediterranean agrosystems

    Science.gov (United States)

    Mekki, Insaf; Jaiez, Zeineb; Jacob, Frédéric

    2014-05-01

    Soil water content (SWC) is an important driver for number of soil, water and energy fluxes at different temporal and spatial scales. The non-invasive electromagnetic induction sensor, such as EM38, that measures the soil apparent electrical conductivity (ECa), has been widely used to infer spatial and temporal patterns of soil properties. The objective of this study has been to explore the opportunity for estimating and mapping the soil water content (SWC) based on in-situ data collected in different fields and during dry and wet soil conditions in a hilly landscape. The experiment was carried out during two campaigns under dry and wet conditions to represent the major soil association, land use and topographic attributes at the cultivated semiarid Mediterranean Lebna catchment, northeastern Tunisia. The temporal evolution of SWC is a dry-wet-dry pattern. Gravimetric soil water content sampling and ECa measured with EM38 (Geonics Ltd., Ontario, Canada) surveys have been performed simultaneously. ECa measurements, geo-referenced with GPS, were collected raising the EM38 to sample at various depths of the soil. The EM38 was placed in both horizontal and vertical dipole modes on a PVC stand 150 cm above the soil surface. The number of investigated points varied between n=70 in February to n=38 in October 2012. Results showed that different SWC related to the soil spatial variability and lead to differences in ECa averaged values and a substantial changes in the ECa as SWC changed. The relationship between SWC an ECa in a separate vertical and horizontal mode using all possible sets of surveys was tested with linear regression. The correlation coefficient between ECa and SWC for the horizontal mode was lower than the vertical mode. Coefficients of determination of linear regressions between SWC in 0-100 cm soil depth and ECa in the vertical mode were, r²=0.74, in February 2013, r²=0.52 in October 2012. The lowest correlations were found in horizontal mode when SWC

  8. 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

    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, functional...

  9. 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; Clevers, JC; Huminiecki, Lukasz

    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

  10. ESTIMATION OF TOTAL POLYPHENOLIC CONTENT IN AQUEOUS AND METHANOLIC EXTRACTS FROM THE BARK OF ACACIA NILOTICA

    Directory of Open Access Journals (Sweden)

    Mayank Tenguria et al

    2012-09-01

    Full Text Available Plant polyphenols have been studied largely because of the possibility that they might underlie the protective effects afforded by fruit and vegetable intake against cancer and other chronic diseases. The objective of the present study is to estimate the total polyphenolic content in aqueous and methanolic extract prepared from the bark of Acacia nilotica plant species. Acacia nilotica (L. Willd. ex Del commonly known as babul, kikar or Indian gum Arabic tree, has been recognized worldwide as a multipurpose tree. Mostly it occurs as an isolated tree and rarely found in patches to a limited extent in forests and has been widely planted on farms throughout the plains of the Indian subcontinent. The bark, root, gum, leaves and flowers have found use for skin diseases, diarrhoea, dysentery, cough, diabetes, eczema, wound healing, burning sensation and as an astringent, demulcent, anti-asthmatic. For present work the bark of well identified A. nilotica (L plant for the extraction of phytochemicals was done from the village Khargawali (Hoshangabad district. 20-20 grams of the fine powdered sample were subjected to soxhlet extraction with 200 ml distilled water and 40% methanol separately at 70oC and 50oC respectively, for 24 hours and concentrated. The percentage yield so obtained was 35 and 32.5% respectively. The extracts were then subjected for preliminary phytochemical screening of alkaloids, tannins, terpenoids, saponins, flavonoids and glycosides the results of which refers to data given in this article. The total phenolic content of the extracts was determined using the Folin-Ciocalteu method with suitable modification. When compared with the gallic acid standard curve the aqueous extract of 0.01 mg/ml dilution contains 0.323 mg/ml approx of total polyphenol content and that of the methanolic extract of the same concentration shows 0.422 mg/ml approx concentration of TPC. Thus from the present study it can be concluded that the aqueous and

  11. Nondestructive Estimation of Moisture Content, pH and Soluble Solid Contents in Intact Tomatoes Using Hyperspectral Imaging

    Directory of Open Access Journals (Sweden)

    Anisur Rahman

    2017-01-01

    Full Text Available The objective of this study was to develop a nondestructive method to evaluate chemical components such as moisture content (MC, pH, and soluble solid content (SSC in intact tomatoes by using hyperspectral imaging in the range of 1000–1550 nm. The mean spectra of the 95 matured tomato samples were extracted from the hyperspectral images, and multivariate calibration models were built by using partial least squares (PLS regression with different preprocessing spectra. The results showed that the regression model developed by PLS regression based on Savitzky–Golay (S–G first-derivative preprocessed spectra resulted in better performance for MC, pH, and the smoothing preprocessed spectra-based model resulted in better performance for SSC in intact tomatoes compared to models developed by other preprocessing methods, with correlation coefficients (rpred of 0.81, 0.69, and 0.74 with root mean square error of prediction (RMSEP of 0.63%, 0.06, and 0.33% Brix respectively. The full wavelengths were used to create chemical images by applying regression coefficients resulting from the best PLS regression model. These results obtained from this study clearly revealed that hyperspectral imaging, together with suitable analysis model, is a promising technology for the nondestructive prediction of chemical components in intact tomatoes.

  12. 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.

  13. CONTENTS

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    The Development and Evolution of the Idea of the Mandate of Heaven in the Zhou Dynasty The changes in the idea of Mandate of Heaven during the Shang and Zhou dynasties are of great significance in the course of the development of traditional Chinese culture. The quickening and awakening of the humanistic spirit was not the entire content of the Zhou idea of Mandate of Heaven. In the process of annihilating the Shang dynasty and setting up their state, the Zhou propagated the idea of the Mandate of Heaven out of practical needs. Their idea of the Mandate of Heaven was not very different from that of the Shang. From the Western Zhou on, the Zhou idea of Mandate of Heaven by no means developed in a linear way along a rational track. The intermingling of rationality and irrationality and of awakening and non-awakening remained the overall state of the Zhou intellectual superstructure after their "spiritual awakening".

  14. QTLs and analysis of the candidate gene for amylose, protein, and moisture content in rice (Oryza sativa L.).

    Science.gov (United States)

    Bruno, Ester; Choi, Yun-Sik; Chung, Il Kyung; Kim, Kyung-Min

    2017-05-01

    In this study, we determined using NIRS the heritability percentage of amylose, protein, and moisture content in polished and unpolished rice in a CNDH population derived from a cross between Cheongcheong and Nagdong rice varieties. The results revealed a higher heritability percentage for the amylose content and compromised heritability for protein and moisture contents. We also conducted QTL analysis of rice for these major components and identified their chromosomal locations on a physical map. We found a total of four QTLs affecting the amylose, protein, and moisture contents of grain on chromosome 7. We constructed physical maps of seven DNA markers responsible for amylose content, six responsible for protein content, and three responsible for moisture content. Furthermore, we classified these genes according to their functions and found 17 genes (over 77%) to be involved in secondary metabolite synthesis, two genes (about 9%), each related to cell function and abiotic stress, and one gene (about 5%) involved in redox signaling.

  15. 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.

  16. Milk Collection in the Rat Using Capillary Tubes and Estimation of Milk Fat Content by Creamatocrit.

    Science.gov (United States)

    Paul, Heather A; Hallam, Megan C; Reimer, Raylene A

    2015-12-16

    Milk, as the sole source of nutrition for the newborn mammal, provides the necessary nutrients and energy for offspring growth and development. It also contains a vast number of bioactive compounds that greatly affect the development of the neonate. The analysis of milk components will help elucidate key factors that link maternal metabolism and health with offspring growth and development. The laboratory rat represents a popular model organism for maternal studies, and rat milk can be used to examine the effect of various maternal physiological, nutritional, and pharmacological interventions on milk components, which may then impact offspring health. Here a simple method of manually collecting milk from the lactating rat that can be performed by a single investigator, does not require specialized vacuum or suction equipment, and provides sufficient milk for subsequent downstream analysis is described. A method for estimating the fat content of milk by measuring the percentage of cream within the milk sample, known as the creamatocrit, is also presented. These methods can ultimately be used to increase insight into maternal-child health and to elucidate maternal factors that are involved in proper growth and development of offspring.

  17. 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.

  18. A new model for estimating subsurface ice content based on combined electrical and seismic data sets

    Directory of Open Access Journals (Sweden)

    C. Hauck

    2011-06-01

    Full Text Available Detailed knowledge of the material properties and internal structures of frozen ground is one of the prerequisites in many permafrost studies. In the absence of direct evidence, such as in-situ borehole measurements, geophysical methods are an increasingly interesting option for obtaining subsurface information on various spatial and temporal scales. The indirect nature of geophysical soundings requires a relation between the measured variables (e.g. electrical resistivity, seismic velocity and the actual subsurface constituents (rock, water, air, ice. In this work, we present a model which provides estimates of the volumetric fractions of these four constituents from tomographic electrical and seismic images. The model is tested using geophysical data sets from two rock glaciers in the Swiss Alps, where ground truth information in form of borehole data is available. First results confirm the applicability of the so-called 4-phase model, which allows to quantify the contributions of ice-, water- and air within permafrost areas as well as detecting solid bedrock. Apart from a similarly thick active layer with enhanced air content for both rock glaciers, the two case studies revealed a heterogeneous distribution of ice and unfrozen water within Muragl rock glacier, where bedrock was detected at depths of 20–25 m, but a comparatively homogeneous ice body with only minor heterogeneities within Murtèl rock glacier.

  19. Analysing global food waste problem: pinpointing the facts and estimating the energy content

    Science.gov (United States)

    Melikoglu, Mehmet; Lin, Carol; Webb, Colin

    2013-06-01

    Food waste is a global problem. Each year food worth billions of dollars is wasted by the developed economies of the world. When food is wasted, the problem does not end at that point. More than 95% of the food waste ends at landfill sites, where converted into methane, carbon dioxide and other greenhouse gasses by anaerobic digestion. The impact of food waste to climate change is catastrophic. Food waste problem tends to increase in next 25 years due to economic and population growth mainly in Asian countries. In addition, when food wastes buried at landfill sites their energy content is lost. Although food waste is a huge problem, its global size and extent has recently become a hot topic in the academic community. This paper summarises the size of the global food waste problem together with the estimation of the amount of energy lost when food wastes dumped at landfill sites. Calculations in this study also revealed that energy lost at landfill sites equals to 43% of the delivered energy used for the preparation of foods in the US, 37% of the hydroelectric power generation of Japan, and more than 100% of the current annual renewable energy demand of UK industries.

  20. [Relationship Between Molecular Marker of Western Main Pig H-FABP Gene and IMF Content.].

    Science.gov (United States)

    Pang, Wei-Jun; Sun, Shi-Duo; Li, Ying; Chen, Guo-Dong; Yang, Gong-She

    2005-05-01

    By using 265 pigs from eight breeds including Duroc,Landrace,Large White,Neijiang,Rongchang,Hanjiang Black,Hanzhong White,Bamei and wild ones, the genetic variations of 5'-upstream region from and the second intron in porcine H-FABP gene were checked by PCR-RFLP molecular marker with HinfI, Hae III and MspI,and effect of H-FABP gene on IMF content was then analyzed by least square analysis.The results showed as follows:(1) 8 pig breeds and wild pig had polymorphism at Hinf I-RFLP site. In above detected breeds,large white,Bamei pig, Hanjiang Black,Hanzhong White pig breeds and wild pig presented low polymorphism while other breeds have mediate polymorphism;(2)Among the tested breeds only 4 Chinese local pig breeds had no polymorphism at the Hae III-RFLP and Msp I-RFLP sites,but Duroc,Landrace,Largewhite, Hanzhong White pig breeds and wild pig had polymorphism. Wild pig at the Hae III-RFLP , Landrace,Largewhite and wild pig at the Hae III-RFLP and Msp I-RFLP sites were low polymorphism,others were mediate polymorphism;(3) H-FABP gene increased IMF content significantly(p0.05). Genetic effect of H-FABP gene on IMF content were HH>Hh>hh,DD.

  1. Fuel moisture content estimation: a land-surface modelling approach applied to African savannas

    Science.gov (United States)

    Ghent, D.; Spessa, A.; Kaduk, J.; Balzter, H.

    2009-04-01

    Despite the importance of fire to the global climate system, in terms of emissions from biomass burning, ecosystem structure and function, and changes to surface albedo, current land-surface models do not adequately estimate key variables affecting fire ignition and propagation. Fuel moisture content (FMC) is considered one of the most important of these variables (Chuvieco et al., 2004). Biophysical models, with appropriate plant functional type parameterisations, are the most viable option to adequately predict FMC over continental scales at high temporal resolution. However, the complexity of plant-water interactions, and the variability associated with short-term climate changes, means it is one of the most difficult fire variables to quantify and predict. Our work attempts to resolve this issue using a combination of satellite data and biophysical modelling applied to Africa. The approach we take is to represent live FMC as a surface dryness index; expressed as the ratio between the Normalised Difference Vegetation Index (NDVI) and land-surface temperature (LST). It has been argued in previous studies (Sandholt et al., 2002; Snyder et al., 2006), that this ratio displays a statistically stronger correlation to FMC than either of the variables, considered separately. In this study, simulated FMC is constrained through the assimilation of remotely sensed LST and NDVI data into the land-surface model JULES (Joint-UK Land Environment Simulator). Previous modelling studies of fire activity in Africa savannas, such as Lehsten et al. (2008), have reported significant levels of uncertainty associated with the simulations. This uncertainty is important because African savannas are among some of the most frequently burnt ecosystems and are a major source of greenhouse trace gases and aerosol emissions (Scholes et al., 1996). Furthermore, regional climate model studies indicate that many parts of the African savannas will experience drier and warmer conditions in future

  2. Triterpenoid saponin content and the expression level of some related genes in calli of Centella asiatica.

    Science.gov (United States)

    Mangas, Susana; Moyano, Elisabeth; Osuna, Lidia; Cusido, Rosa M; Bonfill, Mercedes; Palazón, Javier

    2008-10-01

    Centella asiatica has been extensively studied but there has been no report to date that relates gene expression and centelloside production in non-differentiated tissues. We have determined the content of the four principal triterpenoid bioactive compounds of C. asiatica (asiaticoside, madecassoside, asiatic acid and madecassic acid) in calli grown in different media and checked the expression level of some of the genes in the centelloside biosynthetic pathway. The results when compared with data from in vitro plant cultures showed a significantly lower expression of the gene encoding beta-amyrin synthase in calli, which is consistent with the observed lower production of centellosides (less than 900 microg/g DW), while in the plants the production was around 1.5-2 mg/g DW. Moreover, we find an efficient housekeeping gene for this plant. The biosynthesis of phytosterols is also discussed.

  3. High-Content Analysis of CRISPR-Cas9 Gene-Edited Human Embryonic Stem Cells

    Directory of Open Access Journals (Sweden)

    Jared Carlson-Stevermer

    2016-01-01

    Full Text Available CRISPR-Cas9 gene editing of human cells and tissues holds much promise to advance medicine and biology, but standard editing methods require weeks to months of reagent preparation and selection where much or all of the initial edited samples are destroyed during analysis. ArrayEdit, a simple approach utilizing surface-modified multiwell plates containing one-pot transcribed single-guide RNAs, separates thousands of edited cell populations for automated, live, high-content imaging and analysis. The approach lowers the time and cost of gene editing and produces edited human embryonic stem cells at high efficiencies. Edited genes can be expressed in both pluripotent stem cells and differentiated cells. This preclinical platform adds important capabilities to observe editing and selection in situ within complex structures generated by human cells, ultimately enabling optical and other molecular perturbations in the editing workflow that could refine the specificity and versatility of gene editing.

  4. High-Content Analysis of CRISPR-Cas9 Gene-Edited Human Embryonic Stem Cells.

    Science.gov (United States)

    Carlson-Stevermer, Jared; Goedland, Madelyn; Steyer, Benjamin; Movaghar, Arezoo; Lou, Meng; Kohlenberg, Lucille; Prestil, Ryan; Saha, Krishanu

    2016-01-12

    CRISPR-Cas9 gene editing of human cells and tissues holds much promise to advance medicine and biology, but standard editing methods require weeks to months of reagent preparation and selection where much or all of the initial edited samples are destroyed during analysis. ArrayEdit, a simple approach utilizing surface-modified multiwell plates containing one-pot transcribed single-guide RNAs, separates thousands of edited cell populations for automated, live, high-content imaging and analysis. The approach lowers the time and cost of gene editing and produces edited human embryonic stem cells at high efficiencies. Edited genes can be expressed in both pluripotent stem cells and differentiated cells. This preclinical platform adds important capabilities to observe editing and selection in situ within complex structures generated by human cells, ultimately enabling optical and other molecular perturbations in the editing workflow that could refine the specificity and versatility of gene editing.

  5. 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.

  6. Grouping miRNAs of similar functions via weighted information content of gene ontology.

    Science.gov (United States)

    Lan, Chaowang; Chen, Qingfeng; Li, Jinyan

    2016-12-22

    Regulation mechanisms between miRNAs and genes are complicated. To accomplish a biological function, a miRNA may regulate multiple target genes, and similarly a target gene may be regulated by multiple miRNAs. Wet-lab knowledge of co-regulating miRNAs is limited. This work introduces a computational method to group miRNAs of similar functions to identify co-regulating miRNAsfrom a similarity matrix of miRNAs. We define a novel information content of gene ontology (GO) to measure similarity between two sets of GO graphs corresponding to the two sets of target genes of two miRNAs. This between-graph similarity is then transferred as a functional similarity between the two miRNAs. Our definition of the information content is based on the size of a GO term's descendants, but adjusted by a weight derived from its depth level and the GO relationships at its path to the root node or to the most informative common ancestor (MICA). Further, a self-tuning technique and the eigenvalues of the normalized Laplacian matrix are applied to determine the optimal parameters for the spectral clustering of the similarity matrix of the miRNAs. Experimental results demonstrate that our method has better clustering performance than the existing edge-based, node-based or hybrid methods. Our method has also demonstrated a novel usefulness for the function annotation of new miRNAs, as reported in the detailed case studies.

  7. 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  

  8. Comparison of estimates of body fat content in childhood-onset systemic lupus erythematosus.

    Science.gov (United States)

    Sinicato, N A; Peres, F A; de Oliveira Peliçari, K; de Oliveira Santos, A; Ramos, C D; Marini, R; Appenzeller, S

    2017-04-01

    Objective We aimed to compare estimates of body fat content with respect to their ability to predict the percentage of body fat, confirmed by dual-energy X-ray absorptiometry scans in childhood-onset systemic lupus erythematosus. Methods We included 64 consecutive childhood-onset systemic lupus erythematosus patients and 64 healthy age and sex-matched controls in a cross-sectional study. Anthropometric data, body mass index and body adiposity index were calculated for all subjects. Childhood-onset systemic lupus erythematosus patients were further assessed for clinical and laboratory childhood-onset systemic lupus erythematosus manifestations and fat mass, lean mass and percentage of body fat evaluated by dual-energy X-ray absorptiometry. Results Elevated waist/hip ratio was observed in childhood-onset systemic lupus erythematosus patients when compared to controls ( p systemic lupus erythematosus patients and controls. Using dual-energy X-ray absorptiometry as gold standard we observed that all indirect estimates of body fat were correlated with whole body fat mass. We observed a correlation between height and cumulative corticosteroid dose adjusted by weight ( r = 0.429, p = 0.005) in childhood-onset systemic lupus erythematosus. On whole body analysis we observed a correlation between lean mass and ACR Damage Index scores ( r = -0.395; p = 0.019); percentage of body fat and adjusted Systemic Lupus Erythematosus Disease Activity Index ( r = 0.402; p = 0.008), disease duration ( r = -0.370; p = 0.012). On trunk analysis we observed a correlation between lean mass and ACR Damage Index ( r = -0.319; p = 0.042); percentage of body fat with adjusted Systemic Lupus Erythematosus Disease Activity Index ( r = 0.402; p = 0.005), disease duration ( r = -0.408; p = 0.005). Conclusions This is the first study analyzing body adiposity index in childhood-onset systemic lupus erythematosus patients. We observed that all

  9. 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; Arman, M; Ibrahim, M; Shafique, S.

    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...

  10. Robustness to divergence time underestimation when inferring species trees from estimated gene trees.

    Science.gov (United States)

    DeGiorgio, Michael; Degnan, James H

    2014-01-01

    To infer species trees from gene trees estimated from phylogenomic data sets, tractable methods are needed that can handle dozens to hundreds of loci. We examine several computationally efficient approaches-MP-EST, STAR, STEAC, STELLS, and STEM-for inferring species trees from gene trees estimated using maximum likelihood (ML) and Bayesian approaches. Among the methods examined, we found that topology-based methods often performed better using ML gene trees and methods employing coalescent times typically performed better using Bayesian gene trees, with MP-EST, STAR, STEAC, and STELLS outperforming STEM under most conditions. We examine why the STEM tree (also called GLASS or Maximum Tree) is less accurate on estimated gene trees by comparing estimated and true coalescence times, performing species tree inference using simulations, and analyzing a great ape data set keeping track of false positive and false negative rates for inferred clades. We find that although true coalescence times are more ancient than speciation times under the multispecies coalescent model, estimated coalescence times are often more recent than speciation times. This underestimation can lead to increased bias and lack of resolution with increased sampling (either alleles or loci) when gene trees are estimated with ML. The problem appears to be less severe using Bayesian gene-tree estimates.

  11. 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.

  12. 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

  13. Genetic variability of lactoferrin content estimated by mid-infrared spectrometry in bovine milk.

    Science.gov (United States)

    Soyeurt, H; Colinet, F G; Arnould, V M-R; Dardenne, P; Bertozzi, C; Renaville, R; Portetelle, D; Gengler, N

    2007-09-01

    The effects of lactoferrin (LF) on the immune system have already been shown by many studies. Unfortunately, the current methods used to measure LF levels in milk do not permit the study of the genetic variability of lactoferrin or the performance of routine genetic evaluations. The first aim of this research was to derive a calibration equation permitting the prediction of LF in milk by mid-infrared spectrometry (MIR). The calibration with partial least squares on 69 samples showed a ratio of standard error of cross-validation to standard deviation equal to 1.98. Based on this value, the calibration equation was used to establish an LF indicator trait (predicted LF; pLF) on a large number of milk samples (n = 7,690). A subsequent study of its variability was conducted, which confirmed that stage of lactation and lactation number influence the overall pLF level. Small differences in mean pLF among 7 dairy breeds were also observed. The pLF content of Jersey milk was significantly higher than that in Holstein milk. Therefore, the choice of breed could change the expected LF level. Heritability estimated for pLF was 19.7%. The genetic and phenotypic correlations between somatic cell score and pLF were 0.04 and 0.26, respectively. As somatic cell score increases in presence of mastitis, this observation seems to indicate that pLF, or a function of observed pLF, compared with expected LF might have potential as an indicator of mastitis. The negative genetic correlation (-0.36) between milk yield and pLF could indicate an undesirable effect of selection for high milk production on the overall LF level.

  14. Morphology and LPS content for the estimation of marine bacterioplankton biomass in the Ionian Sea

    Directory of Open Access Journals (Sweden)

    Rosabruna La Ferla

    2004-03-01

    Full Text Available The abundance, morphotypes and biomass of the bacterial assemblages were investigated in the Ionian Sea by using two different methods: the epifluorescent microscopy technique for enumerating and sizing bacterial cells, and the determination of bacterial lipopolysaccharides (LPS. Five bacterial morphotypes were distinguished: cocci, rods, coccobacilli, vibrios and spirillae. The proportions of cocci were higher than those of other morphotypes at every depth, ranging from 39% to 73%. Both rod-shaped bacteria and coccobacilli were homogenously distributed in the water column, while the proportions of vibrios were rather variable. Spirillae occurred only in surface samples and disappeared below 100 m. The two methodologies were compared: LPS concentrations showed a highly significant correlation with the bacterial numbers (P< 0.01; n= 88; r= 0.68, but not with biovolumes, and different ratios between LPS concentrations and bacterial volumes were recorded for the photic and aphotic zones (3.11 ± 1.35 and 0.96 ± 0.37 ng LPS per µm3 respectively. LPS-derived cell carbon content on average was 23 fg C cell-1, similar to the C amount derived by mean cell biovolume (19 fg C cell-1 and the biomass from two highly correlated methods (P< 0.01; n= 95; r= 0.59. Our results confirm that the widely used factor of 20 fg C cell-1 (Lee and Furhman, 1987 should be plausible for studying the biomass of the natural microbial populations in the study area. Nevertheless, the wide variability of the cell size classes, also along the whole water columns, questions the applicability of a constant conversion factor for all the marine ecosystems. Consequently, locally derived biomass estimates of bacteria are essential in order to obtain an accurate evaluation of the bacterial role in biogeochemical cycles.

  15. [Estimating total nitrogen content in wetland vegetation based on measured reflectance spectra].

    Science.gov (United States)

    Liu, Ke; Zhao, Wen-ji; Guo, Xiao-yu; Wang, Yi-hong; Sun, Yong-hua; Miao, Qian

    2012-02-01

    More and more urban wetlands have been supplied with reclaimed water. And monitoring the growth condition of large-area wetland vegetation is playing a very important role in wetland restoration and reconstruction. Recently, remote sensing technology has become an important tool for vegetation growth monitoring. The South Wetland in the Olympic Park, a typical wetland using reused water, was selected as the research area. The leaf reflectance spectra and were acquired for the main wetland plants reed (Phragmites australis) and cattail (Typha angustifolia) with an ASD FieldSpec 3 spectrometer (350 2 500 nm). The total nitrogen (TN) content of leaf samples was determined by Kjeldahl method subsequently. The research established univariate models involving simple ratio spectral index (SR) model and normalized difference spectral index (ND) model, as well as multivariate models including stepwise multiple linear regression (SMLR) model and partial least squares regression (PLSR) model. Moreover, the accuracy of all the models was tested through cross-validated coefficient of determination (R2(CV)) and cross-validated root mean square error (RMSE(CV)). The results showed that (1) comparing different types of wetland plants, the accuracy of all established prediction models using Phragmites australis reflectance spectra was higher than that using Typha angustifolia reflectance spectra. (2) compared with univariate techniques, multivariate regressions improved the estimation of TN concentration in leaves. (3) among the various investigated models, the accuracy of PLSR model was the highest (R2(CV) = 0.80, RMSE(CV) = 0.24). PLSR provided the most useful explorative tool for unraveling the relationship between spectral reflectance and TN consistence of leaves. The result would not only provide a scientific basis for remote sensing retrieval of biochemical variables of wetland vegetation, but also provide a strong scientific basis for the monitoring and management of urban

  16. 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.

  17. 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.

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

    Science.gov (United States)

    Mojska, Hanna; Gielecińska, Iwona; Cendrowski, Andrzej

    2016-09-01

    Acrylamide is a "probably human carcinogen" monomer that can form in heated starchy food as a result of a reaction between asparagine and reducing sugars via Maillard reaction. The main source of acrylamide in human diet are potato products, cereal products and coffee. Tobacco smoke may be another significant source of exposure to acrylamide. The aim of our study was to determine acrylamide content in cigarettes available on the Polish market and to estimate the exposure to acrylamide originating from tobacco smoke in smokers in Poland. The material was cigarettes of the top five brands bought in Poland and tobacco from non-smoked cigarettes. Acrylamide content in cigarettes mainstream smoke was determined by LC-MS/MS. Exposure assessment was carried out using analytical data of acrylamide content in cigarettes and the mean quantity of cigarettes smoked daily by smokers in Poland, assuming body weight at 70 kg. The mean content of acrylamide was 679.3 ng/cigarette (range: 455.0 - 822.5 ng/cigarette). The content of acrylamide was evidenced to correlate positively with total particulate matter (TPM) content in cigarettes. The estimated average exposure to acrylamide from tobacco smoke in adult smokers in Poland is 0.17 μg/kg b.w./day. 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.

  19. 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

  20. Differential expression of carotenoid biosynthetic pathway genes in two contrasting tomato genotypes for lycopene content

    Indian Academy of Sciences (India)

    Shilpa Pandurangaiah; Kundapura V Ravishankar; Kodthalu S Shivashankar; Avverahally T Sadashiva; Kavitha Pillakenchappa; Sunil Kumar Narayanan

    2016-06-01

    Tomato (Solanum lycopersicum L.) is one of the model plants to study the carotenoid biosynthesis. In the present study, the fruit carotenoid content were quantified at different developmental stages for two contrasting genotypes viz. IIHR-249-1and IIHR-2866 by UPLC. Lycopene content was high in IIHR-249-1(19.45 mg/100g fresh weight) compared to IIHR-2866 ((1.88 mg/100g fresh weight) at the ripe stage. qPCR was performed for genes that are involved in the carotenoid biosynthetic pathway to study the difference in lycopene content in fruits of both the genotypes. The expression of Phytoene Synthase (PSY) increased by 36 fold and Phytoene desaturase (PDS) increased by 14fold from immature green stage to ripe stage in IIHR-249-1. The expression of Chloroplast lycopene β cyclase (LCY-B) and Chromoplast lycopene β cyclase (CYC-B) decreased gradually from the initial stage to the ripe stage in IIHR-249-1. IIHR 249-1 showed 3 and 1.8 fold decrease in gene expression for Chloroplast lycopene β cyclase ((LCY-B) and Chromoplast lycopene β cyclase (CYC-B) .The F2 hybrids derived from IIHR-249-1 and IIHR-2866 were analyzed at the ripe stage for lycopene content. The gene expression of Chloroplast lycopene β cyclase (LCY-B) and Chromoplast lycopene β cyclase (CYC-B) in high and low lycopene lines from F2 progenies also showed the decrease in transcript levels of both the genes in high lycopene F2 lines. We wish to suggest that the differential expression of Lycopene β -cyclases can be used in marker assisted breeding.

  1. 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.

  2. 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

    wide comparison of protein coding gene content of Saccharomycotina and Pezizomycotina, which include industrially important yeasts and filamentous fungi, respectively. RESULTS: Our analysis shows that based on genome redundancy, the traditional model organisms Saccharomyces cerevisiae and Neurospora......BACKGROUND: Several dozen fungi encompassing traditional model organisms, industrial production organisms and human and plant pathogens have been sequenced recently and their particular genomic features analysed in detail. In addition comparative genomics has been used to analyse specific sub...

  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. 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 ...

  5. 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...

  6. Supporting document for the North East Quandrant Historical Tank Content Estimate Report for BX-Tank Farm

    Energy Technology Data Exchange (ETDEWEB)

    Brevick, C.H.

    1994-06-01

    This supporting document provides historical in-depth characterization information gathered on BX-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 Quandrant and the Hanford 200 East Areas.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  9. 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.

  10. Evaluation of Radar Vegetation Indices for Vegetation Water Content Estimation Using Data from a Ground-Based SMAP Simulator

    Science.gov (United States)

    Srivastava, Prashant K.; O'Neill, Peggy; Cosh, Michael; Lang, Roger; Joseph, Alicia

    2015-01-01

    Vegetation water content (VWC) is an important component of microwave soil moisture retrieval algorithms. This paper aims to estimate VWC using L band active and passive radar/radiometer datasets obtained from a NASA ground-based Soil Moisture Active Passive (SMAP) simulator known as ComRAD (Combined Radar/Radiometer). Several approaches to derive vegetation information from radar and radiometer data such as HH, HV, VV, Microwave Polarization Difference Index (MPDI), HH/VV ratio, HV/(HH+VV), HV/(HH+HV+VV) and Radar Vegetation Index (RVI) are tested for VWC estimation through a generalized linear model (GLM). The overall analysis indicates that HV radar backscattering could be used for VWC content estimation with highest performance followed by HH, VV, MPDI, RVI, and other ratios.

  11. Estimation of the Total Atmospheric Water Vapor Content and Land Surface Temperature Based on AATSR Thermal Data

    Directory of Open Access Journals (Sweden)

    Rong Liu

    2008-03-01

    Full Text Available The total atmospheric water vapor content (TAWV and land surfacetemperature (LST play important roles in meteorology, hydrology, ecology and some otherdisciplines. In this paper, the ENVISAT/AATSR (The Advanced Along-Track ScanningRadiometer thermal data are used to estimate the TAWV and LST over the Loess Plateauin China by using a practical split window algorithm. The distribution of the TAWV isaccord with that of the MODIS TAWV products, which indicates that the estimation of thetotal atmospheric water vapor content is reliable. Validations of the LST by comparingwith the ground measurements indicate that the maximum absolute derivation, themaximum relative error and the average relative error is 4.0K, 11.8% and 5.0%respectively, which shows that the retrievals are believable; this algorithm can provide anew way to estimate the LST from AATSR data.

  12. 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...

  13. On the use of surface neutron-gamma gauges to estimate soil water content

    Energy Technology Data Exchange (ETDEWEB)

    Tominaga, T.T.; Cassaro, F.A.M.; Reichardt, K. E-mail: klaus@cena.usp.br; Bacchi, O.O.S.; Oliveira, J.C.M.; Timm, L.C

    2002-09-01

    Surface neutron-gamma gauges are handy instruments to measure soil water contents and bulk densities of surface layers. Although available for some decades, their optimal use is still not well established. This study is a contribution to improve their use, mainly in relation to calibration, and of the effect of soil dry bulk density on soil water content measurements.

  14. Estimation of protein content in the plasma of young chickens by a refractometric method.

    Science.gov (United States)

    Morgan, G W; Thaxton, P; Edens, F W

    1975-07-01

    This study was conducted to evaluate a refractometric method for determination of protein content of chicken plasma. Comparison of the results obtained with the refractometric and the Lowry methods indicated that refractometry, when used with due caution in a typical laboratory situation, provided a simple, fast, inexpensive and valid method for determining the protein content of plasma from young chickens.

  15. 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.

  16. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L. Wilczek

    Directory of Open Access Journals (Sweden)

    Sommanas Warunee

    2009-11-01

    Full Text Available Abstract Background Mungbean is an important economical crop in Asia. However, genomic research has lagged behind other crop species due to the lack of polymorphic DNA markers found in this crop. The objective of this work is to develop and characterize microsatellite or simple sequence repeat (SSR markers from genome shotgun sequencing of mungbean. Result We have generated and characterized a total of 470,024 genome shotgun sequences covering 100.5 Mb of the mungbean (Vigna radiata (L. Wilczek genome using 454 sequencing technology. We identified 1,493 SSR motifs that could be used as potential molecular markers. Among 192 tested primer pairs in 17 mungbean accessions, 60 loci revealed polymorphism with polymorphic information content (PIC values ranging from 0.0555 to 0.6907 with an average of 0.2594. Majority of microsatellite markers were transferable in Vigna species, whereas transferability rates were only 22.90% and 24.43% in Phaseolus vulgaris and Glycine max, respectively. We also used 16 SSR loci to evaluate phylogenetic relationship of 35 genotypes of the Asian Vigna group. The genome survey sequences were further analyzed to search for gene content. The evidence suggested 1,542 gene fragments have been sequence tagged, that fell within intersected existing gene models and shared sequence homology with other proteins in the database. Furthermore, potential microRNAs that could regulate developmental stages and environmental responses were discovered from this dataset. Conclusion In this report, we provided evidence of generating remarkable levels of diverse microsatellite markers and gene content from high throughput genome shotgun sequencing of the mungbean genomic DNA. The markers could be used in germplasm analysis, accessing genetic diversity and linkage mapping of mungbean.

  17. Exploiting genomics resources to identify candidate genes underlying antioxidants content in tomato fruit

    Directory of Open Access Journals (Sweden)

    Roberta eCalafiore

    2016-04-01

    Full Text Available The tomato is a model species for fleshy fruit development and ripening, as well as for genomics studies of others Solanaceae. Many genetic and genomics resources, including databases for sequencing, transcriptomics and metabolomics data, have been developed and are today available. The purpose of the present work was to uncover new genes and/or alleles that determine ascorbic acid and carotenoids accumulation, by exploiting one Solanum pennellii introgression lines (IL7-3 harboring quantitative trait loci (QTL that increase the content of these metabolite in the fruit. The higher ascorbic acid and carotenoids content in IL7-3 was confirmed at three fruit developmental stages. The tomato genome reference sequence and the recently released S. pennellii genome sequence were investigated to identify candidate genes that might control ascorbic acid and carotenoids accumulation. First of all, a refinement of the wild region borders in the IL7-3 was achieved by analyzing CAPS markers designed in our laboratory. Afterwards, six candidate genes associated to ascorbic acid and one with carotenoids metabolism were identified exploring the annotation and the Gene Ontology terms of genes included in the region. Variants between the sequence of the wild and the cultivated alleles of these genes were investigated for their functional relevance and their potential effects on the protein sequences were predicted. Transcriptional levels of candidate genes in the introgression region were extracted from RNA-Seq data available for the entire S. pennellii introgression lines collection and verified by Real-Time qPCR. Finally, seven IL7-3 sub-lines were genotyped using 28 species-specific markers and then were evaluated for metabolites content. These analyses evidenced a significant decrease in transcript abundance for one 9-cis-epoxycarotenoid dioxygenase and one L-ascorbate oxidase homolog, whose role in the accumulation of carotenoids and ascorbic acid is

  18. Development of Simple Functional Markers for Low Glutelin Content Gene 1 (Lgc1) in Rice (Oryza sativa)

    Institute of Scientific and Technical Information of China (English)

    CHEN Tao; TIAN Meng-xiang; ZHANG Ya-dong; ZHU Zhen; ZHAO Ling; ZHAO Qing-yong; LIN Jing; ZHOU Li-hui; WANG Cai-lin

    2010-01-01

    Rice with low glutelin content is suitable as functional food for patients affected by kidney failure. Low glutelin- content gene Lgc1 in rice has a 3.5-kb deletion between two highly similar glutelin genes GluB4 and GluB5, which locates on the short arm of chromosome 2. To improve the selection efficiency in low glutelin-content rice breeding, two molecular markers designated as InDel-Lgc1-1 and InDel-Lgc1-2 were developed to detect the low glutelin-content gene Lgc1. A double PCR detection indicated that combined use of the two markers could easily distinguish the genotypes of Lgc1 from different rice varieties. Therefore, as a simple and low-cost technique, the molecular marker could be widely used to identify different varieties with Lgc1 gene and applied in marker-assisted selection of low glutelin-content rice.

  19. 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.

  20. 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.

  1. LINE X TESTER ANALYSIS IN COMBINING ABILITIES ESTIMATION OF SUNFLOWER OIL CONTENT

    Directory of Open Access Journals (Sweden)

    Ivica Liović

    2012-12-01

    Full Text Available Results of line x tester analysis for 15 sunflower genotypes of the Agricultural Institute Osijek are presented in this paper. Three A lines (cms and three Rf testers with different oil content level (low, medium, high in all combinations (nine crosses were crossed in 2010. In 2011, the lines, testers and their crosses were sown in field trials at two locations (Karanac and Osijek. The oil content was determined after harvesting, whereas line x tester analysis was conducted based on the obtained results. Variance of lines and testers, which refers to the general combining ability (GCA was much higher than the variance of line x tester, related to specific combining ability (SCA. It showed on dominant role of the additive component of genetic variance in the inheritance of oil content. Statistically significant differences were not determined between the GCA and SCA effects. The highest values of GCA for oil content had line 2 (medium oil content and tester 6 (high oil content at both locations. The largest contribution for oil content had lines (57.81 and 51.28 % followed by testers (28.88 and 26.27 % and the lowest accounts for interaction (13.31 and 22.45 % at both locations (Karanac and Osijek.

  2. Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of sphaeropleales (chlorophyta).

    Science.gov (United States)

    Fučíková, Karolina; Lewis, Paul O; González-Halphen, Diego; Lewis, Louise A

    2014-08-08

    The majority of our knowledge about mitochondrial genomes of Viridiplantae comes from land plants, but much less is known about their green algal relatives. In the green algal order Sphaeropleales (Chlorophyta), only one representative mitochondrial genome is currently available-that of Acutodesmus obliquus. Our study adds nine completely sequenced and three partially sequenced mitochondrial genomes spanning the phylogenetic diversity of Sphaeropleales. We show not only a size range of 25-53 kb and variation in intron content (0-11) and gene order but also conservation of 13 core respiratory genes and fragmented ribosomal RNA genes. We also report an unusual case of gene arrangement convergence in Neochloris aquatica, where the two rns fragments were secondarily placed in close proximity. Finally, we report the unprecedented usage of UCG as stop codon in Pseudomuriella schumacherensis. In addition, phylogenetic analyses of the mitochondrial protein-coding genes yield a fully resolved, well-supported phylogeny, showing promise for addressing systematic challenges in green algae. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. 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 ().

  4. Alterations in seed development gene expression affect size and oil content of Arabidopsis seeds.

    Science.gov (United States)

    Fatihi, Abdelhak; Zbierzak, Anna Maria; Dörmann, Peter

    2013-10-01

    Seed endosperm development in Arabidopsis (Arabidopsis thaliana) is under control of the polycomb group complex, which includes Fertilization Independent Endosperm (FIE). The polycomb group complex regulates downstream factors, e.g. Pheres1 (PHE1), by genomic imprinting. In heterozygous fie mutants, an endosperm develops in ovules carrying a maternal fie allele without fertilization, finally leading to abortion. Another endosperm development pathway depends on MINISEED3 (a WRKY10 transcription factor) and HAIKU2 (a leucine-rich repeat kinase). While the role of seed development genes in the embryo and endosperm establishment has been studied in detail, their impact on metabolism and oil accumulation remained unclear. Analysis of oil, protein, and sucrose accumulation in mutants and overexpression plants of the four seed development genes revealed that (1) seeds carrying a maternal fie allele accumulate low oil with an altered composition of triacylglycerol molecular species; (2) homozygous mutant seeds of phe1, mini3, and iku2, which are smaller, accumulate less oil and slightly less protein, and starch, which accumulates early during seed development, remains elevated in mutant seeds; (3) embryo-specific overexpression of FIE, PHE1, and MINI3 has no influence on seed size and weight, nor on oil, protein, or sucrose content; and (4) overexpression of IKU2 results in seeds with increased size and weight, and oil content of overexpressed IKU2 seeds is increased by 35%. Thus, IKU2 overexpression represents a novel strategy for the genetic manipulation of the oil content in seeds.

  5. Effect of metallothionein 2A gene polymorphism on allele-specific gene expression and metal content in prostate cancer

    Energy Technology Data Exchange (ETDEWEB)

    Krześlak, Anna; Forma, Ewa [Department of Cytobiochemistry, University of Łódź, Pomorska 141/143, 90-236 Łódź (Poland); Chwatko, Grażyna [Department of Environmental Chemistry, University of Łódź, Pomorska 163, 90-236 Łódź (Poland); Jóźwiak, Paweł; Szymczyk, Agnieszka [Department of Cytobiochemistry, University of Łódź, Pomorska 141/143, 90-236 Łódź (Poland); Wilkosz, Jacek; Różański, Waldemar [2nd Department of Urology, Medical University of Łódź, Pabianicka 62, 93-513 Łódź (Poland); Bryś, Magdalena, E-mail: zreg@biol.uni.lodz.pl [Department of Cytobiochemistry, University of Łódź, Pomorska 141/143, 90-236 Łódź (Poland)

    2013-05-01

    Metallothioneins (MTs) are highly conserved, small molecular weight, cysteine rich proteins. The major physiological functions of metallothioneins include homeostasis of essential metals Zn and Cu and protection against cytotoxicity of heavy metals. The aim of this study was to determine whether there is an association between the − 5 A/G single nucleotide polymorphism (SNP; rs28366003) in core promoter region and expression of metallothionein 2A (MT2A) gene and metal concentration in prostate cancer tissues. MT2A polymorphism was determined by the polymerase chain reaction–restriction fragment length polymorphism technique (PCR–RFLP) using 412 prostate cancer tissue samples. MT2A gene expression analysis was performed by real-time RT-PCR method. A significant association between rs28366003 genotype and MT2A expression level was found. The average mRNA level was found to be lower among minor allele carriers (the risk allele) than average expression among homozygotes for the major allele. Metal levels were analyzed by flamed atomic absorption spectrometer system. Highly statistically significant associations were detected between the SNP and Cd, Zn, Cu and Pb levels. The results of Spearman's rank correlation showed that the expressions of MT2A and Cu, Pb and Ni concentrations were negatively correlated. On the basis of the results obtained in this study, we suggest that SNP polymorphism may affect the MT2A gene expression in prostate and this is associated with some metal accumulation. - Highlights: • MT2A gene expression and metal content in prostate cancer tissues • Association between SNP (rs28366003) and expression of MT2A • Significant associations between the SNP and Cd, Zn, Cu and Pb levels • Negative correlation between MT2A gene expression and Cu, Pb and Ni levels.

  6. [Estimating nonstructural carbon content of tree crown considering its spatial variability: A case study on Juglans mandshurica and Ulmus japonica].

    Science.gov (United States)

    Cheng, Fang-yan; Wang, Chuan-kuan

    2015-08-01

    Using Juglans mandshurica and Ulmus japonica as test materials, we examined the variability in nonstructural carbohydrates (NSC) concentrations in the branches with different basal diameters with a branch analysis method and explored potential errors in estimating the crown-scale NSC content introduced from various sampling protocols. The results showed that organs significantly influenced the crown NSC concentrations for both species. The mean concentrations of the sum of soluble sugars and starch (TNC) of the leaves, new twigs, old branches, and dead branches were 17.6%, 12.6%, 5.7% and 2.9%, respectively. Most of the NSC concentrations in leaves and new twigs varied insignificantly with basal diameter, age, length and height of the branch. However, the NSC concentration in old branches increased significantly with decreasing the basal diameter, age and length of the branch, and with increasing the relative height of the branch. Among the branch traits, basal diameter was the best predictor for the NSC concentration of the old branch (the R2 between 0.87 and 0.95). The mean TNC contents of leaves, new branches, and old branches for the two species accounted for 28%, 2% and 70% of the crown TNC content, respectively. Considering the effect of the spatial variability in the estimation of NSC content, we recommend the sampling protocol that applies the NSC concentration of new twigs and old branches with a diameter of 3 cm to up-scale the crown NSC content as a simple and practical method.

  7. 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...... 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:The 37 Celsius degree system and the analysis can be reproduced in a similar way. MR T1...

  8. Rapid and accurate estimation of blood saturation, melanin content, and epidermis thickness from spectral diffuse reflectance.

    OpenAIRE

    2010-01-01

    We present a method to determine chromophore concentrations, blood saturation, and epidermal thickness of human skin from diffuse reflectance spectra. Human skin was approximated as a plane-parallel slab of variable thickness supported by a semi-infinite layer corresponding to the epidermis and dermis, respectively. The absorption coefficient was modeled as a function of melanin content for the epidermis and blood content and oxygen saturation for the dermis. The scattering coefficient and re...

  9. The Entropy Estimation of the Physics’ Course Content on the Basis of Intradisciplinary Connections’ Information Model

    Science.gov (United States)

    Tatyana, Gnitetskaya

    2016-08-01

    In this paper the information model of intradisciplinary connections and semantic structures method are described. The information parameters, which we use in information model, are introduced. The question we would like to answer in this paper is - how to optimize the Physics Course’ content. As an example, the differences between entropy values in the contents of physics lecture with one topic but different logics of explanations are showed.

  10. GA3 content in young and mature antheridia of Chara tomentosa estimated by capillary electrophoresis

    OpenAIRE

    Dariusz Stępiński; Andrzej Kaźmierczak

    2011-01-01

    The content of gibberellic acid (GA3) in male sex organs of Chara tomentosa L. was estimated using capillary electrophoresis. Young antheridia contained 0.25 μg GA3 while mature ones 0.48 μg per antheridium. Although there are significant differences in GA3 content in antheridia between C. vulgaris and C. tomentosa, these values calculated per one spe...

  11. Univariate and Default Standard Unit Biases in Estimation of Body Weight and Caloric Content

    Science.gov (United States)

    Geier, Andrew B.; Rozin, Paul

    2009-01-01

    College students estimated the weight of adult women from either photographs or a live presentation by a set of models and estimated the calories in 1 of 2 actual meals. The 2 meals had the same items, but 1 had larger portion sizes than the other. The results suggest: (a) Judgments are biased toward transforming the example in question to the…

  12. Identification of Nucleotide-Level Changes Impacting Gene Content and Genome Evolution in Orthopoxviruses

    Science.gov (United States)

    Hatcher, Eneida L.; Hendrickson, Robert Curtis

    2014-01-01

    ABSTRACT Poxviruses are composed of large double-stranded DNA (dsDNA) genomes coding for several hundred genes whose variation has supported virus adaptation to a wide variety of hosts over their long evolutionary history. Comparative genomics has suggested that the Orthopoxvirus genus in particular has undergone reductive evolution, with the most recent common ancestor likely possessing a gene complement consisting of all genes present in any existing modern-day orthopoxvirus species, similar to the current Cowpox virus species. As orthopoxviruses adapt to new environments, the selection pressure on individual genes may be altered, driving sequence divergence and possible loss of function. This is evidenced by accumulation of mutations and loss of protein-coding open reading frames (ORFs) that progress from individual missense mutations to gene truncation through the introduction of early stop mutations (ESMs), gene fragmentation, and in some cases, a total loss of the ORF. In this study, we have constructed a whole-genome alignment for representative isolates from each Orthopoxvirus species and used it to identify the nucleotide-level changes that have led to gene content variation. By identifying the changes that have led to ESMs, we were able to determine that short indels were the major cause of gene truncations and that the genome length is inversely proportional to the number of ESMs present. We also identified the number and types of protein functional motifs still present in truncated genes to assess their functional significance. IMPORTANCE This work contributes to our understanding of reductive evolution in poxviruses by identifying genomic remnants such as single nucleotide polymorphisms (SNPs) and indels left behind by evolutionary processes. Our comprehensive analysis of the genomic changes leading to gene truncation and fragmentation was able to detect some of the remnants of these evolutionary processes still present in orthopoxvirus genomes and

  13. Optimizing Cationic and Neutral Lipids for Efficient Gene Delivery at High Serum Content

    Science.gov (United States)

    Majzoub, Ramsey N.; Hwu, Yeu-kuang; Liang, Keng S.; Leal, Cecília; Safinya, Cyrus R.

    2014-01-01

    Background Cationic liposome (CL)-DNA complexes are promising gene delivery vectors with potential applications in gene therapy. A key challenge in creating CL-DNA complexes for applications is that their transfection efficiency (TE) is adversely affected by serum. In particular, little is known about the effects of high serum contents on TE even though this may provide design guidelines for applications in vivo. Methods We prepared CL-DNA complexes in which we varied the neutral lipid (DOPC, 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). Results 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, in particular at high serum content. Conclusions 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 suggest guidelines for optimizing the serum resistance of CL-DNA complexes based on a given cationic lipid. PMID:24753287

  14. County-based estimates of nitrogen and phosphorus content of animal manure in the United States for 1982, 1987, and 1992.

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This data set contains county estimates of nitrogen and phosphorus content of animal wastes produced annually for the years 1982, 1987, and 1992. The estimates are...

  15. Comparing direct vs. indirect estimates of gene flow within a population of a scattered tree species.

    Science.gov (United States)

    Oddou-Muratorio, Sylvie; Klein, Etienne K

    2008-06-01

    The comparison between historical estimates of gene flow, using variance in allelic frequencies, and contemporary estimates of gene flow, using parentage assignment, is expected to provide insights into ecological and evolutionary processes at work within and among populations. Genetic variation at six microsatellite loci was used to quantify genetic structure in the insect-pollinated, animal-dispersed, low-density tree Sorbus torminalis L. Crantz, and to derive historical estimates of gene flow. The neighbourhood size and root-mean-squared dispersal distance inferred from seedling genotypes (N(b) = 70 individuals, sigma(e) = 417 m) were similar to those inferred from adult genotypes (N(b) = 114 individuals, sigma(e) = 472 m). We also used parentage analyses and a neighbourhood model approach after an evaluation of the statistical properties of this method on simulated data. From our data, we estimated even contributions of seed- and pollen-mediated dispersal to the genetic composition of established seedlings, with both fat-tailed pollen and seed dispersal kernels, and slightly higher mean distance of pollen dispersal (248 m) as compared to seed dispersal (135 m). The resulting contemporary estimate of gene dispersal distance (sigma(c) = 211 m) was approximately twofold smaller than the historical estimates. Besides different assumptions and statistical nuances of both approaches, this discrepancy is likely to reflect a recent restriction in the scale of gene flow which requires manager's attention in a context of increasing forest fragmentation.

  16. 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.

  17. Estimating exotic gene flow into native pine stands: zygotic vs. gametic components.

    Science.gov (United States)

    Unger, G M; Vendramin, G G; Robledo-Arnuncio, J J

    2014-11-01

    Monitoring contemporary gene flow from widespread exotic plantations is becoming an important problem in forest conservation genetics. In plants, where both seed and pollen disperse, three components of exotic gene flow with potentially unequal consequences should be, but have not been, explicitly distinguished: zygotic, male gametic and female gametic. Building on a previous model for estimating contemporary rates of zygotic and male gametic gene flow among plant populations, we present here an approach that additionally estimates the third (female gametic) gene flow component, based on a combination of uni- and biparentally inherited markers. Using this method and a combined set of chloroplast and nuclear microsatellites, we estimate gene flow rates from exotic plantations into two Iberian relict stands of maritime pine (Pinus pinaster) and Scots pine (Pinus sylvestris). Results show neither zygotic nor female gametic gene flow but moderate (6-8%) male gametic introgression for both species, implying significant dispersal of pollen, but not of seeds, from exotic plantations into native stands shortly after introduced trees reached reproductive maturity. Numerical simulation results suggest that the model yields reasonably accurate estimates for our empirical data sets, especially for larger samples. We discuss conservation management implications of observed levels of exposure to nonlocal genes and identify research needs to determine potentially associated hazards. Our approach should be useful for plant ecologists and ecosystem managers interested in the vectors of contemporary genetic connectivity among discrete plant populations.

  18. A method for canopy water content estimation for highly vegetated surfaces-shortwave infrared perpendicular water stress index

    Institute of Scientific and Technical Information of China (English)

    GHULAM; Abduwasit; LI; Zhao-Liang; QIN; QiMing; TONG; QingXi; WANG; JiHua; KASIMU; Alimujiang; ZHU; Lin

    2007-01-01

    In this paper, a new method for canopy water content (FMC) estimation for highly vegetated surfaces- shortwave infrared perpendicular water stress index (SPSI) is developed using NIR, SWIR wavelengths of Enhanced Thematic Mapper Plus (ETM+) on the basis of spectral features and distribution of surface targets with different water conditions in NIR-SWIR spectral space. The developed method is further explored with radiative transfer simulations using PROSPECT, Lillesaeter, SailH and 6S. It is evident from the results of validation derived from satellite synchronous field measurements that SPSI is highly correlated with FMC, coefficient of determination (R squared) and root mean square error are 0.79 and 26.41%. The paper concludes that SPSI has a potential in vegetation water content estimation in terms of FMC.

  19. Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss.

    Science.gov (United States)

    Zamani-Dahaj, Seyed Alireza; Okasha, Mohamed; Kosakowski, Jakub; Higgs, Paul G

    2016-07-01

    We analyze patterns of gene presence and absence in a maximum likelihood framework with rate parameters for gene gain and loss. Standard methods allow independent gains and losses in different parts of a tree. While losses of the same gene are likely to be frequent, multiple gains need to be considered carefully. A gene gain could occur by horizontal transfer or by origin of a gene within the lineage being studied. If a gene is gained more than once, then at least one of these gains must be a horizontal transfer. A key parameter is the ratio of gain to loss rates, a/v We consider the limiting case known as the infinitely many genes model, where a/v tends to zero and a gene cannot be gained more than once. The infinitely many genes model is used as a null model in comparison to models that allow multiple gains. Using genome data from cyanobacteria and archaea, it is found that the likelihood is significantly improved by allowing for multiple gains, but the average a/v is very small. The fraction of genes whose presence/absence pattern is best explained by multiple gains is only 15% in the cyanobacteria and 20% and 39% in two data sets of archaea. The distribution of rates of gene loss is very broad, which explains why many genes follow a treelike pattern of vertical inheritance, despite the presence of a significant minority of genes that undergo horizontal transfer. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. Gene frequencies and admixture estimates in four Mexican urban centers.

    Science.gov (United States)

    Lisker, R; Ramirez, E; Briceño, R P; Granados, J; Babinsky, V

    1990-12-01

    We studied 202 individuals from the city of Leon in Guanajuato state, 228 from Merida, Yucatan, 220 from Oaxaca, Oaxaca, and 257 from Saltillo, Coahuila, to learn the distribution of the ABO, MN, Rh, and Duffy blood groups, serum haptoglobin, albumin, and factor Bf types, and red cell hemoglobin and glucose-6-phosphate dehydrogenase types. With the gene frequencies obtained, we performed admixture measurements with a maximum likelihood method, obtaining a trihybrid model for black, Indian, and white ancestry with the following proportions: 0.084, 0.513, and 0.403 in Leon: 0.059, 0.512, and 0.429 in Merida; 0.018, 0.676, and 0.306 in Oaxaca; and 0.073, 0.547, and 0.380 in Saltillo. The general pattern has high Indian ancestry followed by white and black ancestry. This pattern is congruent with most other studies performed in Mexico, including the east coast, where Indian ancestry predominates despite a clear increase in the black contribution.

  1. Combining Hierarchical and Associative Gene Ontology Relations with Textual Evidence in Estimating Gene and Gene Product Similarity

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Riensche, Roderick M.; Beagley, Nathaniel; Baddeley, Bob L.; Tratz, Stephen C.; Gregory, Michelle L.

    2007-03-01

    Gene and gene product similarity is a fundamental diagnostic measure in analyzing biological data and constructing predictive models for functional genomics. With the rising influence of the Gene Ontology, two complementary approaches have emerged where the similarity between two genes or gene products is obtained by comparing Gene Ontology (GO) annotations associated with the genes or gene products. One approach captures GO-based similarity in terms of hierarchical relations within each gene subontology. The other approach identifies GO-based similarity in terms of associative relations across the three gene subontologies. We propose a novel methodology where the two approaches can be merged with ensuing benefits in coverage and accuracy, and demonstrate that further improvements can be obtained by integrating textual evidence extracted from relevant biomedical literature.

  2. 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

    system (the closest to the body temperature) we measured, using the modified MR sequences, the T1 map intensity signal 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...... 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...

  3. 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

    system (the closest to the body temperature) we measured, using the modified MR sequences, the T1 map intensity signal 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...... 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...

  4. [Quantitative estimation of CaO content in surface rocks using hyperspectral thermal infrared emissivity].

    Science.gov (United States)

    Zhang, Li-Fu; Zhang, Xue-Wen; Huang, Zhao-Qiang; Yang, Hang; Zhang, Fei-Zhou

    2011-11-01

    The objective of the present paper is to study the quantitative relationship between the CaO content and the thermal infrared emissivity spectra. The surface spectral emissivity of 23 solid rocks samples were measured in the field and the first derivative of the spectral emissivity was also calculated. Multiple linear regression (MLR), principal component analysis (PCR) and partial least squares regression (PLSR) were modeled and the regression results were compared. The results show that there is a good relationship between CaO content and thermal emissivity spectra features; emissivities become lower when CaO content increases in the 10.3-13 mm region; the first derivative spectra have a better predictive ability compared to the original emissivity spectra.

  5. Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation

    Directory of Open Access Journals (Sweden)

    Natarajan Sripriya

    2004-02-01

    Full Text Available Abstract Background Gene microarray technology provides the ability to study the regulation of thousands of genes simultaneously, but its potential is limited without an estimate of the statistical significance of the observed changes in gene expression. Due to the large number of genes being tested and the comparatively small number of array replicates (e.g., N = 3, standard statistical methods such as the Student's t-test fail to produce reliable results. Two other statistical approaches commonly used to improve significance estimates are a penalized t-test and a Z-test using intensity-dependent variance estimates. Results The performance of these approaches is compared using a dataset of 23 replicates, and a new implementation of the Z-test is introduced that pools together variance estimates of genes with similar minimum intensity. Significance estimates based on 3 replicate arrays are calculated using each statistical technique, and their accuracy is evaluated by comparing them to a reliable estimate based on the remaining 20 replicates. The reproducibility of each test statistic is evaluated by applying it to multiple, independent sets of 3 replicate arrays. Two implementations of a Z-test using intensity-dependent variance produce more reproducible results than two implementations of a penalized t-test. Furthermore, the minimum intensity-based Z-statistic demonstrates higher accuracy and higher or equal precision than all other statistical techniques tested. Conclusion An intensity-based variance estimation technique provides one simple, effective approach that can improve p-value estimates for differentially regulated genes derived from replicated microarray datasets. Implementations of the Z-test algorithms are available at http://vessels.bwh.harvard.edu/software/papers/bmcg2004.

  6. 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.

  7. 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

    2014-12-19

    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.

  8. Estimation of moisture and oil content of in-shell nuts with a capacitance sensor using discrete wavelet analysis

    Science.gov (United States)

    Kandala, Chari V.; Sundaram, Jaya; Govindarajan, K. N.; Butts, Chris L.; Subbiah, Jeyam

    2009-03-01

    Moisture and oil contents are important quality factors often measured and monitored in the processing and storage of food products such as corn and peanuts. For estimating these parameters for peanuts nondestructively a parallel-plate capacitance sensor was used in conjunction with an impedance analyzer. Impedance, phase angle and dissipation factor were measured for the parallel-plate system, holding the in-shell peanut samples between its plates, at frequencies ranging between 1MHz and 30 MHz in intervals of 0.5 MHz. The acquired signals were analyzed with discrete wavelet analysis. The signals were decomposed to 6 levels using Daubechies mother wavelet. The decomposition coefficients of the sixth level were passed onto a stepwise variable selection routine to select significant variables. A linear regression was developed using only the significant variables to predict the moisture and oil content of peanut pods (inshell peanuts) from the impedance measurements. The wavelet analysis yielded similar R2 values with fewer variables as compared to multiple linear and partial least squares regressions. The estimated values were found to be in good agreement with the standard values for the samples tested. Ability to estimate the moisture and oil contents in peanuts without shelling them will be of considerable help to the peanut industry.

  9. 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.

  10. 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.

  11. Estimation of chlorophyll content of Phragmites australis based on PROSPECT and DART models in the saltmarsh of Yangtze Estuary

    Science.gov (United States)

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

    2016-09-01

    Phragmites australis is a native dominant specie in the Yangtze Estuary, which plays a key role in the structure and function of wetland ecosystem. One key question is how to estimate the Chlorophyll content quickly and effectively at large scales, which could be used to reflect the growth condition and calculate the vegetation productivity. The aim of this work was to estimate Chlorophyll content of P. australis based on the PROSPECT and DART (Discrete Anisotropic Radiative Transfer) model. A total of 6 widely used Vegetation indices (VIs) were chosen (i.e., Normalized Difference Vegetation Index (NDVI), Structure Insensitive Pigment Index (SIPI), Colouration Index (COI), Simple Ratio Index (SR), Cater Index (CAI), and Red-edge Position Linear Interpolation (REP_Li)) and calculated, and then the relationship between VIs and Cab were analyzed. Results showed that COI and SIPI were sensitive to the leaf chlorophyll content as the chlorophyll content changes at the leaf scale. Meanwhile, no obvious saturation phenomenon was observed for these two indices compared to other indices.

  12. Estimation of growth rate of Skeletonema costatum based on relative expression amount of PCNA gene

    Institute of Scientific and Technical Information of China (English)

    HE Shanying; YU Zhigang

    2008-01-01

    Partial sequence of Skeletonema costatum proliferating cell nuclear antigen (PCNA) gene was obtained by reverse transcriptase PCR(RT-PCR) and 3' rapid amplification of cDNA ends (3'-RACE) techniques.Based on the obtained PCNA and cytochrome b gene(Cyt b gene) sequences,a real-time fluorescent quantitative PCR (FQ-PCR) method was developed to detect the expres-sion S.costatum PCNA gene,and this method was applied to study the relationship between the growth rate of S.costatum and the average expression amount of PCNA gene in a single cell.The expression amount of PCNA gene had large variation in cells col-lected at different culture phases,and the trend was well consistent with the growth rate,which suggested that the expression amount of PCNA gene correlated well with the cell division,and the PCNA could be a promising indicator for the S.costatum cell proliferation.Furthermore,using the PCNA gene as the objective gene and the Cyt b gene as the house-keeping gene,a new method for estimating the in situ growth rate of S.costatum was established by analysis of the relative expression quantity (REQ) of the PCNA gene.

  13. Research on the Estimation Model of Soil Moisture Content Based on the Characteristics of Thermal Infrared Data

    Institute of Scientific and Technical Information of China (English)

    Jun; XU; Jianjun; JIANG

    2013-01-01

    With the portable Fourier Transform Infrared Spectroscopy (FTIR), the reflectance spectra of soil samples with different moisture content are measured in laboratory for expounding the characteristic of radiation in the thermal infrared part of the spectrum with different soil moisture content. A model of estimating the moisture content in soil is attempted to make based on Moisture Diagnostic Index (MDI). In general,the spectral characteristic of soil emissivity in laboratory includes the following aspects.Firstly,in the region of 8.0-9.5 μm,along with the increase of soil moisture content,the emissivity of soil increases to varying degrees. The spectral curves are parallel relatively and have a tendency to become horizontal and the absorbed characteristic of reststrahlen is also weakened relatively with the increase of soil moisture in this region.Secondly,in the region of 11.0-14.0 μm,the emissivity of soil has a tendency of increasing.There is an absorption value near about 12.7 μm. As the soil moisture content increases,the depth of absorption also increases. This phenomenon may be caused by soil moisture absorption. Methods as derivative, difference and standardized ratio transformation may weaken the background noise effectively to the spectrum data. Especially using the ratio of the emissivity to the average of 8-14 μm may obviously enhance the correlation between soil moisture and soil emissivity. According to the result of correlation analysis, the 8.237 μm is regarded as the best detecting band for soil moisture content. Moreover,based on the Moisture Diagnostic Index ( MDI) in the 8.194-8.279 μm, the logarithmic model of estimating soil moisture is made.

  14. 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

  15. Use of Water Content Reflectometers in Bioinfiltration/Bioretention to Measure Water Movement and Estimate Evapotranspiration

    Science.gov (United States)

    Most bioinfiltration/bioretention models assume runoff is evenly distributed across the surface area and after the engineered fill media is no longer saturated, the volumetric water content (VWC) is constant throughout the media profile and at field capacity. Four to nine water ...

  16. 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 constru

  17. Derivation of an equation to estimate marrow content of bovine cervical vertebrae.

    Science.gov (United States)

    Gebault, R A; Field, R A; Means, W J; Russell, W C

    1998-08-01

    Marrow content of bovine cervical vertebrae from Choice- and Select-grade carcasses weighing 294 to 343 kg was determined so that a method to monitor the amount of marrow in meat from advanced meat/bone separation machinery and recovery (AMR) systems could be developed. The marrow determination requires cleaning and then ashing bones. Because a large difference in ash content of bone and bone marrow exists and because cartilage content of cervical vertebrae in Choice and Select beef is relatively constant, it was possible to derive the following equation: Weight of marrow = [weight of cartilage (% ash in cartilage - % ash in bone) + % ash in bone (total weight) - (total ash)]/[(% ash in bone - % ash in marrow)]. Constants for ash in fresh bone, marrow, and cartilage were 58.51, .57, and 2.14% with SD of 2.23, .15, and .30%, respectively. A cartilage content of 9.5% along with cervical vertebrae weight and total ash weight were also used to calculate 33.9% marrow in cervical vertebrae. Means for marrow pressed or centrifuged from bovine cervical vertebrae were lower than those obtained from the equation. Therefore, pressing and centrifuging left some marrow in spongy bone. Our ashing method for determining the amount of marrow in whole cervical vertebrae should be useful for determining marrow remaining in cervical vertebrae of bone cakes from AMR systems. Percentage ash in pressed bones is higher and the calculated marrow content is lower when pressed bones are compared to cervical vertebrae that are not pressed. The amount of marrow in whole cervical vertebrae minus the amount left in cervical vertebrae from bone cakes equals the amount in meat from AMR systems.

  18. Changes of trehalose content and expression of relative genes during the bioethanol fermentation by Saccharomyces cerevisiae.

    Science.gov (United States)

    Yi, Chenfeng; Wang, Fenglian; Dong, Shijun; Li, Hao

    2016-10-01

    Traditionally, trehalose is considered as a protectant to improve the ethanol tolerance of Saccharomyces cerevisiae. In this study, to clarify the changes and roles of trehalose during the bioethanol fermentation, trehalose content and expression of related genes at lag, exponential, and stationary phases (i.e., 2, 8, and 16 h of batch fermentation process) were determined. Although yeast cells at exponential and stationary phase had higher trehalose content than cells at lag phase (P 0.05). Moreover, expression of the trehalose degradation-related genes NTH1 and NTH2 decreased at exponential phase in comparison with that at lag phase; compared with cells at lag phase, cells at stationary phase had higher expression of TPS1, ATH1, NTH1, and NTH2 but lower expression of TPS2. During the lag-exponential phase transition, downregulation of NTH1 and NTH2 promoted accumulation of trehalose, and to some extent, trehalose might confer ethanol tolerance to S. cerevisiae before stationary phase. During the exponential-stationary phase transition, upregulation of TPS1 contributed to accumulation of trehalose, and Tps1 protein might be indispensable in yeast cells to withstand ethanol stress at the stationary phase. Moreover, trehalose would be degraded to supply carbon source at stationary phase.

  19. 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.

  20. Chordate Hox and ParaHox gene clusters differ dramatically in their repetitive element content.

    Science.gov (United States)

    Osborne, Peter W; Ferrier, David E K

    2010-02-01

    The ParaHox and Hox gene clusters control aspects of animal anterior-posterior development and are related as paralogous evolutionary sisters. Despite this relationship, it is not clear if the clusters operate in similar ways, with similar constraints. To compare clusters, we examined the transposable-element (TE) content of amphioxus and mammalian ParaHox and Hox clusters. Chordate Hox clusters are known to be largely devoid of TEs, possibly due to gene regulation and constraints on clustering in these animals. Here, we describe several novel amphioxus TEs and show that the amphioxus ParaHox cluster is a hotspot for TE insertion. TE contents of mammalian ParaHox loci are at background levels, in stark contrast to chordate Hox clusters. This marks a significant difference between Hox and ParaHox clusters. The presence of so many potentially disruptive elements implies selection constrains these ParaHox clusters as they have not dispersed despite 500 My of evolution for each lineage.

  1. Estimating the extent of horizontal gene transfer in metagenomic sequences

    Directory of Open Access Journals (Sweden)

    Moya Andrés

    2008-03-01

    Full Text Available Abstract Background Although the extent of horizontal gene transfer (HGT in complete genomes has been widely studied, its influence in the evolution of natural communities of prokaryotes remains unknown. The availability of metagenomic sequences allows us to address the study of global patterns of prokaryotic evolution in samples from natural communities. However, the methods that have been commonly used for the study of HGT are not suitable for metagenomic samples. Therefore it is important to develop new methods or to adapt existing ones to be used with metagenomic sequences. Results We have created two different methods that are suitable for the study of HGT in metagenomic samples. The methods are based on phylogenetic and DNA compositional approaches, and have allowed us to assess the extent of possible HGT events in metagenomes for the first time. The methods are shown to be compatible and quite precise, although they probably underestimate the number of possible events. Our results show that the phylogenetic method detects HGT in between 0.8% and 1.5% of the sequences, while DNA compositional methods identify putative HGT in between 2% and 8% of the sequences. These ranges are very similar to these found in complete genomes by related approaches. Both methods act with a different sensitivity since they probably target HGT events of different ages: the compositional method mostly identifies recent transfers, while the phylogenetic is more suitable for the detections of older events. Nevertheless, the study of the number of HGT events in metagenomic sequences from different communities shows a consistent trend for both methods: the lower amount is found for the sequences of the Sargasso Sea metagenome, while the higher quantity is found in the whale fall metagenome from the bottom of the ocean. The significance of these observations is discussed. Conclusion The computational approaches that are used to find possible HGT events in complete

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

    Directory of Open Access Journals (Sweden)

    Ussery David

    2007-09-01

    Full Text Available Abstract Background Several dozen fungi encompassing traditional model organisms, industrial production organisms and human and plant pathogens have been sequenced recently and their particular genomic features analysed in detail. In addition comparative genomics has been used to analyse specific sub groups of fungi. Notably, analysis of the phylum Saccharomycotina has revealed major events of evolution such as the recent genome duplication and subsequent gene loss. However, little has been done to gain a comprehensive comparative view to the fungal kingdom. We have carried out a computational genome wide comparison of protein coding gene content of Saccharomycotina and Pezizomycotina, which include industrially important yeasts and filamentous fungi, respectively. Results Our analysis shows that based on genome redundancy, the traditional model organisms Saccharomyces cerevisiae and Neurospora crassa are exceptional among fungi. This can be explained by the recent genome duplication in S. cerevisiae and the repeat induced point mutation mechanism in N. crassa. Interestingly in Pezizomycotina a subset of protein families related to plant biomass degradation and secondary metabolism are the only ones showing signs of recent expansion. In addition, Pezizomycotina have a wealth of phylum specific poorly characterised genes with a wide variety of predicted functions. These genes are well conserved in Pezizomycotina, but show no signs of recent expansion. The genes found in all fungi except 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 highlight several individual gene families with interesting phylogenetic distributions. Conclusion Our analysis predicts that all Pezizomycotina unlike

  3. A hierarchical statistical model for estimating population properties of quantitative genes

    Directory of Open Access Journals (Sweden)

    Wu Rongling

    2002-06-01

    Full Text Available Abstract Background Earlier methods for detecting major genes responsible for a quantitative trait rely critically upon a well-structured pedigree in which the segregation pattern of genes exactly follow Mendelian inheritance laws. However, for many outcrossing species, such pedigrees are not available and genes also display population properties. Results In this paper, a hierarchical statistical model is proposed to monitor the existence of a major gene based on its segregation and transmission across two successive generations. The model is implemented with an EM algorithm to provide maximum likelihood estimates for genetic parameters of the major locus. This new method is successfully applied to identify an additive gene having a large effect on stem height growth of aspen trees. The estimates of population genetic parameters for this major gene can be generalized to the original breeding population from which the parents were sampled. A simulation study is presented to evaluate finite sample properties of the model. Conclusions A hierarchical model was derived for detecting major genes affecting a quantitative trait based on progeny tests of outcrossing species. The new model takes into account the population genetic properties of genes and is expected to enhance the accuracy, precision and power of gene detection.

  4. Origin of worldwide cultivated barley revealed by NAM-1 gene and grain protein content

    Directory of Open Access Journals (Sweden)

    Yonggang eWang

    2015-09-01

    Full Text Available The origin, evolution and distribution of cultivated barley provides powerful insights into the historic origin and early spread of agrarian culture. Here, population-based genetic diversity and phylogenetic analyses were performed to determine the evolution and origin of barley and how domestication and subsequent introgression have affected the genetic diversity and changes in cultivated barley on a worldwide scale. A set of worldwide cultivated and wild barleys from Asia and Tibet of China were analyzed using the sequences for NAM-1 gene and gene-associated traits-GPC (grain protein content. Our results showed Tibetan wild barley distinctly diverged from Near Eastern barley, and confirmed that Tibet is one of the origin and domestication centers for cultivated barley, and in turn supported a polyphyletic origin of domesticated barley. Comparison of haplotype composition among geographic regions revealed gene flow between Eastern and Western barley populations, suggesting that the Silk Road might have played a crucial role in the spread of genes. The GPC in the 118 cultivated and 93 wild barley accessions ranged from 6.73% to 12.35% with a mean of 9.43%. Overall, wild barley had higher averaged GPC (10.44% than cultivated barley. Two unique haplotypes (Hap2 and Hap7 caused by a base mutations (at position 544 in the coding region of the NAM-1 gene might have a significant impact on the GPC. SNPs and haplotypes of NAM-1 associated with GPC in barley could provide a useful method for screening GPC in barley germplasm. The Tibetan wild accessions with lower GPC could be useful for malt barley breeding

  5. Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

    Science.gov (United States)

    Kembel, Steven W.; Wu, Martin; Eisen, Jonathan A.; Green, Jessica L.

    2012-01-01

    The abundance of different SSU rRNA (“16S”) gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly – from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data. PMID:23133348

  6. Information content-based gene ontology semantic similarity approaches: toward a unified framework theory.

    Science.gov (United States)

    Mazandu, Gaston K; Mulder, Nicola J

    2013-01-01

    Several approaches have been proposed for computing term information content (IC) and semantic similarity scores within the gene ontology (GO) directed acyclic graph (DAG). These approaches contributed to improving protein analyses at the functional level. Considering the recent proliferation of these approaches, a unified theory in a well-defined mathematical framework is necessary in order to provide a theoretical basis for validating these approaches. We review the existing IC-based ontological similarity approaches developed in the context of biomedical and bioinformatics fields to propose a general framework and unified description of all these measures. We have conducted an experimental evaluation to assess the impact of IC approaches, different normalization models, and correction factors on the performance of a functional similarity metric. Results reveal that considering only parents or only children of terms when assessing information content or semantic similarity scores negatively impacts the approach under consideration. This study produces a unified framework for current and future GO semantic similarity measures and provides theoretical basics for comparing different approaches. The experimental evaluation of different approaches based on different term information content models paves the way towards a solution to the issue of scoring a term's specificity in the GO DAG.

  7. Information Content-Based Gene Ontology Semantic Similarity Approaches: Toward a Unified Framework Theory

    Science.gov (United States)

    Mazandu, Gaston K.; Mulder, Nicola J.

    2013-01-01

    Several approaches have been proposed for computing term information content (IC) and semantic similarity scores within the gene ontology (GO) directed acyclic graph (DAG). These approaches contributed to improving protein analyses at the functional level. Considering the recent proliferation of these approaches, a unified theory in a well-defined mathematical framework is necessary in order to provide a theoretical basis for validating these approaches. We review the existing IC-based ontological similarity approaches developed in the context of biomedical and bioinformatics fields to propose a general framework and unified description of all these measures. We have conducted an experimental evaluation to assess the impact of IC approaches, different normalization models, and correction factors on the performance of a functional similarity metric. Results reveal that considering only parents or only children of terms when assessing information content or semantic similarity scores negatively impacts the approach under consideration. This study produces a unified framework for current and future GO semantic similarity measures and provides theoretical basics for comparing different approaches. The experimental evaluation of different approaches based on different term information content models paves the way towards a solution to the issue of scoring a term's specificity in the GO DAG. PMID:24078912

  8. 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.

  9. 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

  10. Estimates of nuclear DNA content in 98 species of brown algae (Phaeophyta)

    OpenAIRE

    Phillips, Naomi; Kapraun, Donald F.; Gómez Garreta, Amelia; Ribera Siguan, M. Antonia; Rull, Jorde L.; Salvador Soler, Noemi; Lewis, Raymond; Kawai, Hiroshi

    2011-01-01

    Background and aims Brown algae are critical components of marine ecosystems around the world. However, the genome of only one species of the class has so far been sequenced. This contrasts with numerous sequences available for model organisms such as higher plants, flies or worms. The present communication expands our coverage of DNA content information to 98 species of brown algae with a view to facilitating further genomic investigations of the class. Methodology The DNA-localizing fluoroc...

  11. 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...

  12. Regression techniques for estimating soil organic carbon contents from VIS/NIR reflectance spectra

    Science.gov (United States)

    Schwanghart, W.; Jarmer, T.; Bayer, A.; Hoffmann, U.; Hunziker, M.; Kuhn, N. J.; Ehlers, M.

    2012-04-01

    Soil reflectance spectroscopy is regarded as a promising approach to efficiently obtain densely sampled soil organic carbon (SOC) estimates at various spatial scales. The estimates are usually based on a statistical modeling approach since physical models are mostly not applicable owing to the manifold influences on soil spectra by different soil constituents and properties. Different multivariate statistical methods exist to estimate SOC concentrations in soil samples using visible and near infra-red (VIS/NIR) reflectance spectra. All these techniques face the challenge of generating accurate predictive models with a disproportionate large number of variables compared to the number of observations in such datasets, and in addition highly correlated independent variables. This often results in overfitting and may at the same time reduce the predictive power of such models. In this study, we conduct a rigorous assessment of the predictive ability of different regression techniques (stepwise regression, robust regression with feature selection, lasso, ridge regression, elastic net, principal component (PC) regression, partial least squares (PLS) regression). We apply datasets from different environments to include a wide variety of soils and to investigate the effects of different SOC variances and concentrations on model performance. Our hypothesis is that the predictive ability of regression techniques can be significantly improved by using more advanced techniques such as PLS regression. We discuss our findings with respect to the applicability of SOC estimation from VIS/NIR reflectance spectra in different environments.

  13. Toward the Estimation of Surface Soil Moisture Content Using Geostationary Satellite Data over Sparsely Vegetated Area

    Directory of Open Access Journals (Sweden)

    Pei Leng

    2015-04-01

    Full Text Available Based on a novel bare surface soil moisture (SSM retrieval model developed from the synergistic use of the diurnal cycles of land surface temperature (LST and net surface shortwave radiation (NSSR (Leng et al. 2014. “Bare Surface Soil Moisture Retrieval from the Synergistic Use of Optical and Thermal Infrared Data”. International Journal of Remote Sensing 35: 988–1003., this paper mainly investigated the model’s capability to estimate SSM using geostationary satellite observations over vegetated area. Results from the simulated data primarily indicated that the previous bare SSM retrieval model is capable of estimating SSM in the low vegetation cover condition with fractional vegetation cover (FVC ranging from 0 to 0.3. In total, the simulated data from the Common Land Model (CoLM on 151 cloud-free days at three FLUXNET sites that with different climate patterns were used to describe SSM estimates with different underlying surfaces. The results showed a strong correlation between the estimated SSM and the simulated values, with a mean Root Mean Square Error (RMSE of 0.028 m3·m−3 and a coefficient of determination (R2 of 0.869. Moreover, diurnal cycles of LST and NSSR derived from the Meteosat Second Generation (MSG satellite data on 59 cloud-free days were utilized to estimate SSM in the REMEDHUS soil moisture network (Spain. In particular, determination of the model coefficients synchronously using satellite observations and SSM measurements was explored in detail in the cases where meteorological data were not available. A preliminary validation was implemented to verify the MSG pixel average SSM in the REMEDHUS area with the average SSM calculated from the site measurements. The results revealed a significant R2 of 0.595 and an RMSE of 0.021 m3·m−3.

  14. Inverse modeling of soil water content to estimate the hydraulic properties of a shallow soil and the associated weathered bedrock

    Science.gov (United States)

    Le Bourgeois, O.; Bouvier, C.; Brunet, P.; Ayral, P.-A.

    2016-10-01

    Modeling soil water flow requires the knowledge of numerous parameters associated to the water content and the soil hydraulic properties. Direct estimations of those parameters in laboratory require expensive equipment and the obtained parameters are generally not representative at the field scale because of the limitation of core sample size. Indirect methods such as inverse modeling are known to get efficient estimations and are easier to set up and process for large-scale studies. In this study, we investigated the capacity of an inverse modeling procedure to estimate the soil and the bedrock hydrodynamic properties only from in situ soil water content measurements at multiple depths under natural conditions. Multi-objective parameter optimization was performed using the HYDRUS-1D software and an external optimization procedure based on the NSGA-II algorithm. In a midslope shallow soil, water content was monitored at 3 depths, 20, 40, and 60 cm during 12 intense rainfall events, whose amounts ranged between 50 and 250 mm and duration between 1 and 5 days. The vertical profile was considered as 2 layers of soils above a third layer representing the weathered schist rock. This deep layer acted as a deep boundary condition, which features the bedrock permeability and water storage. Each layer was described trough the 6 parameters of the Mualem-van Genuchten formulation. The calibrated parameters appeared to have very low uncertainty while allowing a good modelisation of the observed water content variations. The calibrated saturated water content was close to the laboratory porosity measurements while the saturated hydraulic conductivity showed that the soil was highly permeable, as measured in the field. The inverse modeling approach allowed an estimation of the hydraulic properties of the bedrock layer where no measurement was available. The bedrock layer was found to have a low saturated hydraulic conductivity (model failed sometimes to reproduce the saturation

  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. 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.

  18. 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.

  19. 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.

  20. Estimating chlorophyll content and bathymetry of Lake Tahoe using AVIRIS data

    Science.gov (United States)

    Hamilton, Michael K.; Davis, Curtiss O.; Rhea, W. J.; Pilorz, Stuart H.; Carder, Kendall L.

    1993-01-01

    Data on chlorophyll content and bathymetry of Lake Tahoe obtained on August 9, 1990 by the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) are compared to concurrent in situ surface and in-water measurements. Measured parameters included profiles of percent transmission of monochromatic light, stimulated chlorophyll fluorescence, photosynthetically available radiation, spectral upwelling and downwelling irradiance, and upwelling radiance. Several analyses were performed illustrating the utility of the AVIRIS over a dark water scene. Image-derived chlorophyll concentration compared extremely well with that measured with bottle samples. A bathymetry map of the shallow parts of the lake was constructed which compares favorably with published lake soundings.

  1. Use of microwave digestion for estimation of heavy metal content of soils in a geochemical survey.

    Science.gov (United States)

    McGrath, D

    1998-07-01

    A procedure for the rapid and safe analysis of soils with widely differing organic matter contents has been investigated and validated. Surface soils, totalling 295 and sampled on a grid basis, representing 22% of the land-base of the Republic of Ireland, have been analysed for cadmium, chromium, copper, nickel, lead and zinc. Soil concentrations of cadmium, chromium, lead and nickel exhibit patterns of regionalised elevation. Implications of this elevation are considered in relation to sewage sludge application to land, future requirement for baseline surveys and concerns over concentrations in food products.

  2. Medical image segmentation to estimate HER2 gene status in breast cancer

    Science.gov (United States)

    Palacios-Navarro, Guillermo; Acirón-Pomar, José Manuel; Vilchez-Sorribas, Enrique; Zambrano, Eddie Galarza

    2016-02-01

    This work deals with the estimation of HER2 Gene status in breast tumour images treated with in situ hybridization techniques (ISH). We propose a simple algorithm to obtain the amplification factor of HER2 gene. The obtained results are very close to those obtained by specialists in a manual way. The developed algorithm is based on colour image segmentation and has been included in a software application tool for breast tumour analysis. The developed tool focus on the estimation of the seriousness of tumours, facilitating the work of pathologists and contributing to a better diagnosis.

  3. ROBUST HYPERPARAMETER ESTIMATION PROTECTS AGAINST HYPERVARIABLE GENES AND IMPROVES POWER TO DETECT DIFFERENTIAL EXPRESSION

    Science.gov (United States)

    Phipson, Belinda; Lee, Stanley; Majewski, Ian J.; Alexander, Warren S.; Smyth, Gordon K.

    2017-01-01

    One of the most common analysis tasks in genomic research is to identify genes that are differentially expressed (DE) between experimental conditions. Empirical Bayes (EB) statistical tests using moderated genewise variances have been very effective for this purpose, especially when the number of biological replicate samples is small. The EB procedures can however be heavily influenced by a small number of genes with very large or very small variances. This article improves the differential expression tests by robustifying the hyperparameter estimation procedure. The robust procedure has the effect of decreasing the informativeness of the prior distribution for outlier genes while increasing its informativeness for other genes. This effect has the double benefit of reducing the chance that hypervariable genes will be spuriously identified as DE while increasing statistical power for the main body of genes. The robust EB algorithm is fast and numerically stable. The procedure allows exact small-sample null distributions for the test statistics and reduces exactly to the original EB procedure when no outlier genes are present. Simulations show that the robustified tests have similar performance to the original tests in the absence of outlier genes but have greater power and robustness when outliers are present. The article includes case studies for which the robust method correctly identifies and downweights genes associated with hidden covariates and detects more genes likely to be scientifically relevant to the experimental conditions. The new procedure is implemented in the limma software package freely available from the Bioconductor repository.

  4. The clustering of galaxies as a function of their photometrically-estimated atomic gas content

    CERN Document Server

    Li, Cheng; Fu, Jian; Wang, Jing; Catinella, Barbara; Fabello, Silvia; Schiminovich, David; Zhang, Wei

    2012-01-01

    We introduce a new photometric estimator of the HI mass fraction (M_HI/M_*) in local galaxies, which is a linear combination of four parameters: stellar mass, stellar surface mass density, NUV-r colour, and g-i colour gradient. It is calibrated using samples of nearby galaxies (0.025estimates even for HI-rich galaxies. We apply this estimator to a sample of ~24,000 galaxies from the SDSS/DR7 in the same redshift range. We then bin these galaxies by stellar mass and HI mass fraction and compute projected two point cross-correlation functions with respect to a reference galaxy sample. Results are compared with predictions from current semi-analytic models of galaxy formation. The agreement is good for galaxies with stellar masses larger than 10^10 M_sun, but not for lower mass systems. We then extend the analysis by studying the bias of HI-poor or HI-rich galaxies with respect to galaxie...

  5. 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.

  6. Indirect Estimates of the Total Gas Content of SDSS-IV/MaNGA Galaxies from Optical Emission Lines

    Science.gov (United States)

    Tremonti, Christina A.; Pace, Zachary; Andrews, Brett; Law, David R.; Li, Cheng; Martinsson, Thomas; Masters, Karen; Stark, David; Sanchez, Sebastian; Storchi-Bergmann, Thaisa; MaNGA Team

    2016-01-01

    To understand galaxy evolution it is critical to obtain a census of both the stellar and gaseous contents of galaxies. The SDSS-IV MaNGA survey will deliver exquisite stellar mass maps of ~10,000 nearby galaxies. However, radio surveys capable of providing matched resolution gas data for a large fraction of the MaNGA sample are a decade or more away. We are therefore exploring a new technique for obtaining maps of the total gas content directly from the MaNGA data. Following the method outlined in Brinchmann et al. 2013, we use the dust optical depth and the nebular metallicity measured from optical emission lines to estimate the total gas surface density in individual spaxels. We combine this with estimates of the stellar mass in each spaxel to produce spatially resolved estimates of the gas mass fraction. We compare trends in the global gas mass fraction with stellar mass and NUV-r color to those found in the literature. We explore how the radial gas mass fraction gradients of MaNGA galaxies correlate with other properties such as total stellar mass, specific star formation rate (SFR/M*), concentration, and environment.

  7. Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution.

    Science.gov (United States)

    Sun, Yanxia; Moore, Michael J; Zhang, Shoujun; Soltis, Pamela S; Soltis, Douglas E; Zhao, Tingting; Meng, Aiping; Li, Xiaodong; Li, Jianqiang; Wang, Hengchang

    2016-03-01

    The grade of early-diverging eudicots includes five major lineages: Ranunculales, Trochodendrales, Buxales, Proteales and Sabiaceae. To examine the evolution of plastome structure in early-diverging eudicots, we determined the complete plastome sequences of eight previously unsequenced early-diverging eudicot taxa, Pachysandra terminalis (Buxaceae), Meliosma aff. cuneifolia (Sabiaceae), Sabia yunnanensis (Sabiaceae), Epimedium sagittatum (Berberidaceae), Euptelea pleiosperma (Eupteleaceae), Akebia trifoliata (Lardizabalaceae), Stephania japonica (Menispermaceae) and Papaver somniferum (Papaveraceae), and compared them to previously published plastomes of the early-diverging eudicots Buxus, Tetracentron, Trochodendron, Nelumbo, Platanus, Nandina, Megaleranthis, Ranunculus, Mahonia and Macadamia. All of the newly sequenced plastomes share the same 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes, except for that of Epimedium, in which infA is pseudogenized and clpP is highly divergent and possibly a pseudogene. The boundaries of the plastid Inverted Repeat (IR) were found to vary significantly across early-diverging eudicots; IRs ranged from 24.3 to 36.4kb in length and contained from 18 to 33 genes. Based on gene content, the IR was classified into six types, with shifts among types characterized by high levels of homoplasy. Reconstruction of ancestral IR gene content suggested that 18 genes were likely present in the IR region of the ancestor of eudicots. Maximum likelihood phylogenetic analysis of a 79-gene, 97-taxon data set that included all available early-diverging eudicots and representative sampling of remaining angiosperm diversity largely agreed with previous estimates of early-diverging eudicot relationships, but resolved Trochodendrales rather than Buxales as sister to Gunneridae, albeit with relatively weak bootstrap support, conflicting with what has been found for these three clades in most previous analyses. In addition, Proteales was

  8. 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

  9. Recent transient tracer distributions in the Fram Strait: estimation of anthropogenic carbon content and transport

    Directory of Open Access Journals (Sweden)

    T. Stöven

    2015-09-01

    Full Text Available The storage of anthropogenic carbon in the ocean's interior is an important process which modulates the increasing carbon dioxide concentrations in the atmosphere. The polar regions are expected to be net sinks for anthropogenic carbon. Transport estimates of dissolved inorganic carbon and the anthropogenic offset can thus provide information about the magnitude of the corresponding storage processes. Here we present a transient tracer, dissolved inorganic carbon (DIC and total alkalinity (TA data set along 78°50′ N sampled in the Fram Strait in 2012. A theory on tracer relationships is introduced which allows for an application of the Inverse Gaussian – Transit Time Distribution (IG-TTD at high latitudes and the estimation of anthropogenic carbon concentrations. Current velocity measurements along the same section were used to estimate the net flux of DIC and anthropogenic carbon through the Fram Strait. The new theory explains the differences between the theoretical (IG-TTD based tracer age relationship and the specific tracer age relationship of the field data by saturation effects during water mass formation and/or the deliberate release experiment of SF6 in the Greenland Sea in 1996 rather than by different mixing or ventilation processes. Based on this assumption, a maximum SF6 excess of 0.5–0.8 fmol kg−1 was determined in the Fram Strait at intermediate depths (500–1600 m. The anthropogenic carbon concentrations are 50–55 μmol kg−1 in the Atlantic Water/Recirculating Atlantic Water, 40–45 μmol kg−1 in the Polar Surface Water/warm Polar Surface Water and between 10–35 μmol kg−1 in the deeper water layers, with lowest concentrations in the bottom layer. The net DIC and anthropogenic carbon fluxes through the Fram Strait indicate a balanced exchange between the Arctic Ocean and the North Atlantic, although with high uncertainties.

  10. Recent transient tracer distributions in the Fram Strait: estimation of anthropogenic carbon content and transport

    Science.gov (United States)

    Stöven, T.; Tanhua, T.; Hoppema, M.; von Appen, W.-J.

    2015-09-01

    The storage of anthropogenic carbon in the ocean's interior is an important process which modulates the increasing carbon dioxide concentrations in the atmosphere. The polar regions are expected to be net sinks for anthropogenic carbon. Transport estimates of dissolved inorganic carbon and the anthropogenic offset can thus provide information about the magnitude of the corresponding storage processes. Here we present a transient tracer, dissolved inorganic carbon (DIC) and total alkalinity (TA) data set along 78°50' N sampled in the Fram Strait in 2012. A theory on tracer relationships is introduced which allows for an application of the Inverse Gaussian - Transit Time Distribution (IG-TTD) at high latitudes and the estimation of anthropogenic carbon concentrations. Current velocity measurements along the same section were used to estimate the net flux of DIC and anthropogenic carbon through the Fram Strait. The new theory explains the differences between the theoretical (IG-TTD based) tracer age relationship and the specific tracer age relationship of the field data by saturation effects during water mass formation and/or the deliberate release experiment of SF6 in the Greenland Sea in 1996 rather than by different mixing or ventilation processes. Based on this assumption, a maximum SF6 excess of 0.5-0.8 fmol kg-1 was determined in the Fram Strait at intermediate depths (500-1600 m). The anthropogenic carbon concentrations are 50-55 μmol kg-1 in the Atlantic Water/Recirculating Atlantic Water, 40-45 μmol kg-1 in the Polar Surface Water/warm Polar Surface Water and between 10-35 μmol kg-1 in the deeper water layers, with lowest concentrations in the bottom layer. The net DIC and anthropogenic carbon fluxes through the Fram Strait indicate a balanced exchange between the Arctic Ocean and the North Atlantic, although with high uncertainties.

  11. CT scan range estimation using multiple body parts detection: let PACS learn the CT image content.

    Science.gov (United States)

    Wang, Chunliang; Lundström, Claes

    2016-02-01

    The aim of this study was to develop an efficient CT scan range estimation method that is based on the analysis of image data itself instead of metadata analysis. This makes it possible to quantitatively compare the scan range of two studies. In our study, 3D stacks are first projected to 2D coronal images via a ray casting-like process. Trained 2D body part classifiers are then used to recognize different body parts in the projected image. The detected candidate regions go into a structure grouping process to eliminate false-positive detections. Finally, the scale and position of the patient relative to the projected figure are estimated based on the detected body parts via a structural voting. The start and end lines of the CT scan are projected to a standard human figure. The position readout is normalized so that the bottom of the feet represents 0.0, and the top of the head is 1.0. Classifiers for 18 body parts were trained using 184 CT scans. The final application was tested on 136 randomly selected heterogeneous CT scans. Ground truth was generated by asking two human observers to mark the start and end positions of each scan on the standard human figure. When compared with the human observers, the mean absolute error of the proposed method is 1.2% (max: 3.5%) and 1.6% (max: 5.4%) for the start and end positions, respectively. We proposed a scan range estimation method using multiple body parts detection and relative structure position analysis. In our preliminary tests, the proposed method delivered promising results.

  12. Assessing the performance of different model-based techniques to estimate water content in the upper soil layer

    Science.gov (United States)

    Negm, Amro; Capodici, Fulvio; Ciraolo, Giuseppe; Maltese, Antonino; Minacapilli, Mario; Provenzano, Giuseppe; Rallo, Giovanni

    2016-04-01

    The knowledge of soil water content (SWC) of the upper soil layer is important for most hydrological processes occurring over vegetated areas and under dry climate. Because direct field measurements of SWC are difficult, the use of different type of sensors and model-based approaches have been proposed and extensively used during the last decade. The main objective of this work is to assess the performance of two models estimating SWC of the upper soil layer: the transient line heat source method and the physically based Hydrus-1D model. The models' performance is assessed using field measurements acquired through a Time Domain Reflectometer (TDR). The experiment was carried out on an olive orchard located near the town of Castelvetrano (South-West of Sicily - latitude 37.6429°, longitude 12.8471°). The temporal dynamic of topsoil water content was investigated in two samplers, under wet and dry conditions. The samplers were opened at the upper boundary and inserted into the soil to ensure the continuity of the soil surface. A K2D Pro sensor allowed to measure the soil thermal properties allowing to estimate soil thermal inertia and then SWC. The physically based Hydrus-1D model was also used to estimate SWC of both samples. Hourly records of soil water contents, acquired by a TDR100 probe, were used to validate both the considered models. The comparison between SWCs simulated by Hydrus-1D and the corresponding values measured by the TDR method evidenced a good agreement. Similarly, even SWCs derived from the thermal diffusion model resulted fairly close to those measured with the TDR.

  13. Sequence Similarity of Clostridium difficile Strains by Analysis of Conserved Genes and Genome Content Is Reflected by Their Ribotype Affiliation

    Science.gov (United States)

    Kurka, Hedwig; Ehrenreich, Armin; Ludwig, Wolfgang; Monot, Marc; Rupnik, Maja; Barbut, Frederic; Indra, Alexander; Dupuy, Bruno; Liebl, Wolfgang

    2014-01-01

    PCR-ribotyping is a broadly used method for the classification of isolates of Clostridium difficile, an emerging intestinal pathogen, causing infections with increased disease severity and incidence in several European and North American countries. We have now carried out clustering analysis with selected genes of numerous C. difficile strains as well as gene content comparisons of their genomes in order to broaden our view of the relatedness of strains assigned to different ribotypes. We analyzed the genomic content of 48 C. difficile strains representing 21 different ribotypes. The calculation of distance matrix-based dendrograms using the neighbor joining method for 14 conserved genes (standard phylogenetic marker genes) from the genomes of the C. difficile strains demonstrated that the genes from strains with the same ribotype generally clustered together. Further, certain ribotypes always clustered together and formed ribotype groups, i.e. ribotypes 078, 033 and 126, as well as ribotypes 002 and 017, indicating their relatedness. Comparisons of the gene contents of the genomes of ribotypes that clustered according to the conserved gene analysis revealed that the number of common genes of the ribotypes belonging to each of these three ribotype groups were very similar for the 078/033/126 group (at most 69 specific genes between the different strains with the same ribotype) but less similar for the 002/017 group (86 genes difference). It appears that the ribotype is indicative not only of a specific pattern of the amplified 16S–23S rRNA intergenic spacer but also reflects specific differences in the nucleotide sequences of the conserved genes studied here. It can be anticipated that the sequence deviations of more genes of C. difficile strains are correlated with their PCR-ribotype. In conclusion, the results of this study corroborate and extend the concept of clonal C. difficile lineages, which correlate with ribotypes affiliation. PMID:24482682

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

    Directory of Open Access Journals (Sweden)

    *S. A. Rashid

    2011-12-01

    Full Text Available 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 Bougainvillea glabra Choisy. The metal ions concentration either essential or non essential, critically affect the biological system of the human body. Here are many factors including the different types of pollution-fertilizer, insecticides, pesticides and other forms of air and water pollution etc.- that effect directly on metal ion concentration in Bougainvillea and indirectly in biological system if used traditionally as medicine.

  15. 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.

  16. 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

  17. A reliable and accurate portable device for rapid quantitative estimation of iodine content in different types of edible salt

    Directory of Open Access Journals (Sweden)

    Kapil Yadav

    2015-01-01

    Full Text Available Background: Continuous monitoring of salt iodization to ensure the success of the Universal Salt Iodization (USI program can be significantly strengthened by the use of a simple, safe, and rapid method of salt iodine estimation. This study assessed the validity of a new portable device, iCheck Iodine developed by the BioAnalyt GmbH to estimate the iodine content in salt. Materials and Methods: Validation of the device was conducted in the laboratory of the South Asia regional office of the International Council for Control of Iodine Deficiency Disorders (ICCIDD. The validity of the device was assessed using device specific indicators, comparison of iCheck Iodine device with the iodometric titration, and comparison between iodine estimation using 1 g and 10 g salt by iCheck Iodine using 116 salt samples procured from various small-, medium-, and large-scale salt processors across India. Results: The intra- and interassay imprecision for 10 parts per million (ppm, 30 ppm, and 50 ppm concentrations of iodized salt were 2.8%, 6.1%, and 3.1%, and 2.4%, 2.2%, and 2.1%, respectively. Interoperator imprecision was 6.2%, 6.3%, and 4.6% for the salt with iodine concentrations of 10 ppm, 30 ppm, and 50 ppm respectively. The correlation coefficient between measurements by the two methods was 0.934 and the correlation coefficient between measurements using 1 g of iodized salt and 10 g of iodized salt by the iCheck Iodine device was 0.983. Conclusions: The iCheck Iodine device is reliable and provides a valid method for the quantitative estimation of the iodine content of iodized salt fortified with potassium iodate in the field setting and in different types of salt.

  18. Colorimetric method for the estimation of total limonoid aglycones and glucoside contents in citrus juices.

    Science.gov (United States)

    Breksa, Andrew P; Ibarra, Phil

    2007-06-27

    A method for estimating the total limonoid aglycone and glucoside concentrations in Citrus samples in terms of limonin and limonin glucoside equivalents is presented. The method consists of extraction followed by colorimetric quantification. The colorimetric quantification was based on the formation of red to orange colored derivatives resulting from the treatment of limonin, limonin glucoside, or a fruit extract with 4-(dimethylamino)benzaldehyde (DMAB) in the presence of perchloric and acetic acids. Absorbance maxima for the limonin and limonin glucoside derivatives were found to be 470 and 503 nm, respectively. The influence of DMAB concentration, reaction time, and solvent composition on color development and sensitivity were investigated and optimal assay conditions established. With a microplate format under these conditions, the limits of detection and quantification were determined to be 0.25 and 0.50 microg/mL for limonin and 0.50 and 1.0 microg/mL for limonin glucoside.

  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. 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.

  1. Optical scattering coefficient estimated by optical coherence tomography correlates with collagen content in ovarian tissue

    Science.gov (United States)

    Yang, Yi; Wang, Tianheng; Biswal, Nrusingh C.; Wang, Xiaohong; Sanders, Melinda; Brewer, Molly; Zhu, Quing

    2011-09-01

    Optical scattering coefficient from ex vivo unfixed normal and malignant ovarian tissue was quantitatively extracted by fitting optical coherence tomography (OCT) A-line signals to a single scattering model. 1097 average A-line measurements at a wavelength of 1310 nm were performed at 108 sites obtained from 18 ovaries. The average scattering coefficient obtained from the normal tissue group consisted of 833 measurements from 88 sites was 2.41 mm-1 (+/-0.59), while the average coefficient obtained from the malignant tissue group consisted of 264 measurements from 20 sites was 1.55 mm-1 (+/-0.46). The malignant ovarian tissue showed significant lower scattering than the normal group (p collagen within OCT imaging depth was analyzed from the tissue histological section stained with Sirius Red. The average collagen area fraction (CAF) obtained from the normal tissue group was 48.4% (+/-12.3%), while the average CAF obtained from the malignant tissue group was 11.4% (+/-4.7%). A statistical significance of the collagen content was found between the two groups (p < 0.001). These results demonstrated that quantitative measurements of optical scattering coefficient from OCT images could be a potential powerful method for ovarian cancer detection.

  2. 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.

  3. VALIDATED HPTLC METHOD FOR ESTIMATION OF CURCUMIN CONTENT IN DIETARY SUPPLEMENT FORMULATION

    Directory of Open Access Journals (Sweden)

    V.A. Kekre et al

    2012-10-01

    Full Text Available The simple, accurate and precise HPTLC method was developed for quantification of curcumin content in dietary supplement formulation. In this method, individual curcuminoids (curcumin, demethoxy curcumin and bisdemethoxy curcumin with piperine were resolved using mobile phase n-hexane: ethyl acetate: methanol: formic acid (8: 2: 1: 2-3 drops v/v on a plate precoated with silica gel 60 F254 and quantified densitometrically in absorbance mode at 421 nm. The Rf value of curcumin was found to be 0.29. Linearity for curcumin was established between concentration range of 100-180 ng/spot with correlation coefficient of 0.999. The method was further validated as per ICH guidelines. The LOD and LOQ values for curcumin were found to be 27.3 ng and 82.7 ng respectively. The results of percent recovery and repeatability studies with standard deviation (≤2%, concluded that the developed method was accurate and precise and can be used for routine analysis of curcumin in dietary supplement formulations.

  4. 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

    for a few samples back in 2002. The intake, mean and intake distribution of sodium nitrite have been calculated from 1998 to 2006 with data from the Danish dietary survey conducted in 2000-02 on Danes from four to 75 years of age. The amounts used by industry have been relatively stable through the whole......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...

  5. A codon substitution model that incorporates the effect of the GC contents, the gene density and the density of CpG islands of human chromosomes

    Directory of Open Access Journals (Sweden)

    Misawa Kazuharu

    2011-08-01

    Full Text Available Abstract Background Developing a model for codon substitutions is essential for the analyses of protein sequences. Recent studies on the mutation rates in the non-coding regions have shown that CpG mutation rates in the human genome are negatively correlated to the local GC content and to the densities of functional elements. This study aimed at understanding the effect of genomic features, namely, GC content, gene density, and frequency of CpG islands, on the rates of codon substitution in human chromosomes. Results Codon substitution rates of CpG to TpG mutations, TpG to CpG mutations, and non-CpG transitions and transversions in humans were estimated by comparing the coding regions of thousands of human and chimpanzee genes and inferring their ancestral sequences by using macaque genes as the outgroup. Since the genomic features are depending on each other, partial regression coefficients of these features were obtained. Conclusion The substitution rates of codons depend on gene densities of the chromosomes. Transcription-associated mutation is one such pressure. On the basis of these results, a model of codon substitutions that incorporates the effect of genomic features on codon substitution in human chromosomes was developed.

  6. Evidence that Natural Selection is the Primary Cause of the Guanine-cytosine Content Variation in Rice Genes

    Institute of Scientific and Technical Information of China (English)

    Xiaoli Shi; Xiyin Wang; Zhe Li; Qihui Zhu; Ji Yang; Song Ge; Jingchu Luo

    2007-01-01

    Cereal genes are classified into two distinct classes according to the guanine-cytosine (GC) content at the third codon sites (GC3). Natural selection and mutation bias have been proposed to affect the GC content. However, there has been controversy about the cause of GC variation. Here, we characterized the GC content of 1 092 paralogs and other single-copy genes in the duplicated chromosomal regions of the rice genome (ssp. indica) and classified the paralogs into GC3-rich and GC3-poor groups. By referring to out-group sequences from Arabidopsis and maize, we confirmed that the average synonymous substitution rate of the GC3-rich genes is significantly lower than that of the GC3-poor genes. Furthermore,we explored the other possible factors corresponding to the GC variation including the length of coding sequences, the number of exons in each gene, the number of genes in each family, the location of genes on chromosomes and the protein functions. Consequently, we propose that natural selection rather than mutation bias was the primary cause of the GC variation.

  7. Estimation of the metabolizable energy content of meat and bone meal for swine.

    Science.gov (United States)

    Olukosi, O A; Adeola, O

    2009-08-01

    Experiments were conducted to determine apparent ME (AME) and apparent nitrogen-corrected ME (AME(n)) of 21 meat and bone meal (MBM) samples and to develop regression equations for predicting energy value of MBM. One hundred ninety-eight 32-kg of BW barrows were used for the study. The 22 treatments consisted of 1 corn-soybean meal reference diet and 21 test diets in which 21 MBM samples replaced 100 g/kg of corn and soybean meal such that the ratio of corn and soybean meal was the same in the reference and test diets. The DE, AME, and AME(n) of the MBM samples were determined by the difference method in a metabolism study consisting of 5-d adjustment and 5 d of total collection of feces and urine. On a DM basis, GE of MBM ranged from 3,895 to 5,193 kcal/kg, CP ranged from 491 to 641 g/kg, and ash ranged from 142 to 338 g/kg. The AME of the MBM samples ranged from 2,320 to 3,872 kcal/kg, whereas AME(n) ranged from 2,212 to 3,767 kcal/kg. None of the proximate compositions explained >50% of the variation in energy content of the MBM. Fat was positively correlated with GE, DE, AME, and AME(n) (r MBM. Crude protein:fat and GE:fat were negatively correlated with DE, AME, and AME(n) of the MBM (r ranged from -0.17 to -0.39), but fat:ash had the greatest positive correlation with AME and AME(n) compared with other ratios tested. When the data from 1 MBM sample that was an outlier were removed from the analysis, R(2) was 0.42 for AME and AME(n). The 4 variables that produced the best prediction equation for AME and AME(n) were GE, CP, P, and ash. The prediction equation for AME using these variables was AME = 13,587 - (1.25 x GE, kcal/kg) - (3.51 x CP, g/kg) + (30.4 x P, g/kg) - (16.4 x Ash, g/kg), and for AME(n), the equation was AME(n) = 13,547 - (1.25 x GE, kcal/kg) - (3.59 x CP, g/kg) + (31.0 x P, g/kg) - (16.5 x Ash, g/kg). It was concluded from this study that MBM is a good energy source for pigs and that, although other extrinsic factors may contribute to the

  8. The correlation coefficient of GC content of the genome-wide genes is positively correlated with animal evolutionary relationships.

    Science.gov (United States)

    Du, Hongli; Hu, Haofu; Meng, Yuhuan; Zheng, Weihao; Ling, Fei; Wang, Jufang; Zhang, Xiquan; Nie, Qinghua; Wang, Xiaoning

    2010-09-24

    In this study, we present a new method for evaluating animal evolutionary relationships. We used the GC% levels of genome-wide genes to determine the correlation between the GC% content and evolutionary relationship. The correlation coefficients of the GC% content of the orthologous genes of the paired animal species were calculated for a total of 21 species, and the evolutionary branching dates of these 21 species were derived from fossil records. The correlation coefficient of the GC% content of the orthologous genes of the species pair under study served as an indicator of their evolutionary relationship. Moreover, there was a decreasing linear relationship between the correlation coefficient and evolutionary branching date (R(2)=0.930).

  9. 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.

  10. Remote Estimation of Leaf and Canopy Water Content in Winter Wheat with Different Vertical Distribution of Water-Related Properties

    Directory of Open Access Journals (Sweden)

    Shishi Liu

    2015-04-01

    Full Text Available This study analyzed the vertical distribution of gravimetric water content (GWC, relative water content (RWC, and equivalent water thickness (EWT in winter wheat during heading and early ripening stages, and evaluated the position of leaf number at which Vegetation Indexes (VIs can best retrieve canopy water-related properties of winter wheat. Results demonstrated that the vertical distribution of these properties followed a near-bell-shaped curve with the highest values at the intermediate leaf position. GWC of the top three or four leaves during the heading stage and the top two or three leaves during the early ripening stage can represent the GWC of the whole canopy, but the RWC and EWT of the whole canopy should be calculated based on the top four leaves. At leaf level, the analysis demonstrated strong relationships between EWT and VIs for the top leaf layer, but for GWCD, GWCF, and RWC, the strongest relationships with VIs were found in the intermediate leaf layers. At canopy level, VIs provided the most accurate estimation of GWCfor the top three or four leaves. Water absorption-based VIs could estimate canopy EWT of winter wheat for the top four leaves, but the suitable bands sensitive to water absorptions should be carefully selected for the studied species.

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

    Science.gov (United States)

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

    2015-10-01

    In this study, 14C analysis by accelerator mass spectrometry (AMS) was applied to age estimation based on temporal variations in bomb-produced-14C 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 14C analysis with AMS to estimate the formation ages of different positions according to catalogued global 14C contents (F14C). The F14C 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 F14C 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.

  12. 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.

  13. Genetic polymorphisms of the AMPD1 gene and their correlations with IMP contents in Fast Partridge and Lingshan chickens.

    Science.gov (United States)

    Hu, Jin; Yu, Ping; Ding, Xiaoling; Xu, Minglong; Guo, Baoping; Xu, Yinxue

    2015-12-15

    The object of this study was to evaluate associations between the adenosine monophosphate deaminase 1 (AMPD1) gene polymorphisms and inosine monophosphate acid (IMP) contents of chicken to provide a molecular marker for breeding. Three single nucleotide polymorphisms (SNPs), g.4064G/A, g.5573A/G and g.6805G/A were detected in exons IV, VI, and VIII of the AMPD1 gene in Fast Partridge and Lingshan chickens, respectively. All were purine conversion and caused no alteration in amino acid sequence. Statistical analysis revealed that Lingshan chicken with the homozygous genotype AA at position 4064 and 6805 had a significantly greater IMP content than those with the GG genotype (Pchicken with the genotype GG at position 6805 had a significantly greater IMP content compared with those with the AA genotype (Pchickens. The results in our study suggest that SNP 6805A/G can be used as a possible candidate marker of IMP content of chicken.

  14. Estimating Galactic gas content using different tracers: Compatibility of results, dark gas, and unidentified TeV sources

    CERN Document Server

    Pedaletti, Giovanna; Torres, Diego F; Natale, Giovanni

    2014-01-01

    A large fraction of Galactic very-high energy (VHE; E$\\gtrsim$100 GeV) $\\gamma$-ray sources is cataloged as unidentified. In this work we explore the possibility that these unidentified sources are located in ambients particularly rich in material content unaccounted by traditional tracers. In a scenario where the VHE emission is due to the interaction of the accelerated particles with a target mass, a large mass of untraced material could be substantially contributing to the VHE emission from these regions. Here, we use three tracers for the commonly explored components: intensity of the $^\\textrm{12}$CO(1$\\rightarrow$0) line to trace the molecular material, HI hyperfine transition at 21cm to trace atomic hydrogen, and dust emission to trace the total hydrogen content. We show that the estimates of material content from these three tracers are compatible if the uncertainty on the respective conversion factors is taken into account. No additional gas component is found in these regions. However, a simple mass...

  15. Estimation of the intramuscular fat content of m. longissimus thoracis in crossbred beef cattle based on live animal measurements.

    Science.gov (United States)

    Nogalski, Zenon; Pogorzelska-Przybyłek, Paulina; Białobrzewski, Ireneusz; Modzelewska-Kapituła, Monika; Sobczuk-Szul, Monika; Purwin, Cezary

    2017-03-01

    The objective of this study was to determine the usefulness of live animal measurements in estimating the intramuscular fat (IMF) content of m. longissimus thoracis (MLT) in beef cattle. Live animal measurements were performed in young crossbred bulls (96) and steers (59), the offspring of Holstein-Friesian (HF) cows and beef bulls (Limousin, Hereford and Charolais), at the end of the fattening period. The content of intramuscular fat was determined in samples from MLT by chemical analyses. A prediction model was developed by stepwise regression. In the validation model, the values of R(2)=0.74, RMSE=0.37% were determined. The results indicate that selected biometric (chest width, chest girth) ultrasound measurements (thickness of subcutaneous rump and back fat) and selected blood parameters (triglycerides) can be used to predict IMF content with satisfactory precision and accuracy. The analyzed parameters could constitute a valuable tool in the process of selecting beef quality traits and determining the slaughter value of young beef cattle. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. 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.

  17. 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.

  18. Powerful regulatory systems and post-transcriptional gene silencing resist increases in cellulose content in cell walls of barley

    OpenAIRE

    Tan, Hwei-Ting; Shirley, Neil J; Singh, Rohan R; Henderson, Marilyn; Dhugga, Kanwarpal S; Mayo, Gwenda M; Fincher, Geoffrey B.; Burton, Rachel A.

    2015-01-01

    Background The ability to increase cellulose content and improve the stem strength of cereals could have beneficial applications in stem lodging and producing crops with higher cellulose content for biofuel feedstocks. Here, such potential is explored in the commercially important crop barley through the manipulation of cellulose synthase genes (CesA). Results Barley plants transformed with primary cell wall (PCW) and secondary cell wall (SCW) barley cellulose synthase (HvCesA) cDNAs driven b...

  19. Induced mutations in the starch branching enzyme II (SBEII) genes increase amylose and resistant starch content in durum wheat.

    Science.gov (United States)

    Hazard, Brittany; Zhang, Xiaoqin; Colasuonno, Pasqualina; Uauy, Cristobal; Beckles, Diane M; Dubcovsky, Jorge

    2012-01-01

    Starch is the largest component of the wheat (Triticum aestivum L.) grain and consists of approximately 70-80% amylopectin and 20-30% amylose. Amylopectin is a highly-branched, readily digested polysaccharide, whereas amylose has few branches and forms complexes that resist digestion and mimic dietary fiber (resistant starch). Down-regulation of the starch branching enzyme II (SBEII) gene by RNA interference (RNAi) was previously shown to increase amylose content in both hexaploid and tetraploid wheat. We generated ethyl methane sulphonate (EMS) mutants for the SBEIIa-A and SBEIIa-B homoeologs in the tetraploid durum wheat variety Kronos (T. turgidum ssp. durum L.). Single-gene mutants showed non-significant increases in amylose and resistant starch content, but a double mutant combining a SBEIIa-A knock-out mutation with a SBEIIa-B splice-site mutation showed a 22% increase in amylose content (P<0.0001) and a 115% increase in resistant starch content (P<0.0001). In addition, we obtained mutants for the A and B genome copies of the paralogous SBEIIb gene, mapped them 1-2 cM from SBEIIa, and generated double SBEIIa-SBEIIb mutants to study the effect of the SBEIIb gene in the absence of SBEIIa. These mutants are available to those interested in increasing amylose content and resistant starch in durum wheat.

  20. [Estimation of organic matter content of north fluvo-aquic soil based on the coupling model of wavelet transform and partial least squares].

    Science.gov (United States)

    Wang, Yan-Cang; Yang, Gui-Jun; Zhu, Jin-Shan; Gu, Xiao-He; Xu, Peng; Liao, Qin-Hong

    2014-07-01

    For improving the estimation accuracy of soil organic matter content of the north fluvo-aquic soil, wavelet transform technology is introduced. The soil samples were collected from Tongzhou district and Shunyi district in Beijing city. And the data source is from soil hyperspectral data obtained under laboratory condition. First, discrete wavelet transform efficiently decomposes hyperspectral into approximate coefficients and detail coefficients. Then, the correlation between approximate coefficients, detail coefficients and organic matter content was analyzed, and the sensitive bands of the organic matter were screened. Finally, models were established to estimate the soil organic content by using the partial least squares regression (PLSR). Results show that the NIR bands made more contributions than the visible band in estimating organic matter content models; the ability of approximate coefficients to estimate organic matter content is better than that of detail coefficients; The estimation precision of the detail coefficients fir soil organic matter content decreases with the spectral resolution being lower; Compared with the commonly used three types of soil spectral reflectance transforms, the wavelet transform can improve the estimation ability of soil spectral fir organic content; The accuracy of the best model established by the approximate coefficients or detail coefficients is higher, and the coefficient of determination (R2) and the root mean square error (RMSE) of the best model for approximate coefficients are 0.722 and 0.221, respectively. The R2 and RMSE of the best model for detail coefficients are 0.670 and 0.255, respectively.

  1. A “GC-rich” method for mammalian gene expression:A dominant role of non-coding DNA GC content in the regulation of mammalian gene expression

    Institute of Scientific and Technical Information of China (English)

    Gilbert; Rishton; Matthew; (Mizhou); HUI

    2010-01-01

    High mammalian gene expression was obtained for more than twenty different proteins in different cell types by just a few laboratory scale stable gene transfections for each protein.The stable expression vectors were constructed by inserting a naturally-occurring 1.006 kb or a synthetic 0.733 kb DNA fragment(including intron) of extremely GC-rich at the 5’ or/and 3’ flanking regions of these protein genes or their gene promoters.This experiment is the first experimental evidence showing that a non-coding extremely GC-rich DNA fragment is a super "chromatin opening element" and plays an important role in mammalian gene expression.This experiment has further indicated that chromatin-based regulation of mammalian gene expression is at least partially embedded in DNA primary structure,namely DNA GC-content.

  2. Using measured soil water contents to estimate evapotranspiration and root water uptake profiles – a comparative study

    Directory of Open Access Journals (Sweden)

    M. Guderle

    2014-09-01

    Full Text Available Understanding the role of plants for soil water relations, and thus for ecosystem functioning, requires information about root water uptake. We evaluated four different complex water balance methods to estimate sink term patterns and evapotranspiration directly from soil moisture measurements. We tested four methods: the first two take the difference between two measurement intervals as evapotranspiration, thus neglecting vertical flow. The third uses regression on the soil water content time series and differences between day and night to account for vertical flow. The fourth accounts for vertical flow using a numerical model and iteratively solves for the sink term. Neither of those methods requires any a priori information of root distribution parameters or evapotranspiration, which is the advantage, compared to common root water uptake models. To test the methods, a synthetic experiment with numerical simulations for a grassland ecosystem was conducted. Additionally, the time series were perturbed to simulate common sensor errors, like those due to measurement precision and inaccurate sensor calibration. We tested each method for a range of measurement frequencies and applied performance criteria to evaluate the suitability of each method. In general, we show that methods accounting for vertical flow predict evapotranspiration and the sink term distribution more accurately than the simpler approaches. Under consideration of possible measurement uncertainties, the method based on regression and differentiating between day and night cycles leads to the best and most robust estimation of sink term patterns. It is thus an alternative to more complex inverse numerical methods. This study demonstrates that highly resolved (temporal and spatial soil water content measurements may be used to estimate the sink term profiles when the appropriate approach is used.

  3. 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

  4. Seasonal variation in vegetation water content estimated from proximal sensing and MODIS time series in a Mediterranean Fluxnet site

    Directory of Open Access Journals (Sweden)

    G. Mendiguren

    2015-04-01

    Full Text Available This study evaluates three different metrics of vegetation water content estimated from proximal sensing and MODIS satellite imagery: Fuel Moisture Content (FMC, Equivalent Water Thickness (EWT and Canopy Water Content (CWC. Dry matter (Dm and Leaf area Index (LAI were also analyzed in order to connect FMC with EWT and EWT with CWC, respectively. This research took place in a Fluxnet site located in Mediterranean wooded grassland (dehesa ecosystem in Las Majadas del Tietar (Spain. Results indicated that FMC and EWT showed lower spatial variation than CWC. The spatial variation within the MODIS pixel was not as critical as its temporal trend, so to capture better the variability, fewer plots should be sampled but more times. Due to the high seasonal Dm variability, a constant annual value would not work to predict EWT from FMC. Relative root mean square error (RRMSE evaluated the performance of nine spectral indices to compute each variable. VARI provided the worst results in all cases. For proximal sensing, GEMI worked best for both FMC (RRMSE = 34.5% and EWT (RRMSE = 27.43% while NDII and GVMI performed best for CWC (RRMSE =30.27% and 31.58% respectively. For MODIS data, results were a bit better with EVI as the best predictor for FMC (RRMSE = 33.81% and CWC (RRMSE = 27.56% and GEMI for EWT (RRMSE = 24.6%. To explain these differences, proximal sensing measures only grasslands at nadir view angle, but MODIS includes also trees, their shades, and other artifacts at up to 20° view angle. CWC was better predicted than the other two water content variables, probably because CWC depends on LAI, which is highly correlated to the spectral indices. Finally, these empirical methods outperformed FMC and CWC products based on radiative transfer model inversion.

  5. 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.

  6. 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.

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

    Science.gov (United States)

    Chesnokov, Mikhail S.; Lazarevich, Natalia L.; Penin, Aleksey A.

    2017-01-01

    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. PMID:28321364

  8. 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 polymorphism on the glycogen content and provided molecular biological information for the selective breeding of good quality traits of C. gigas.

  9. Parentage versus two-generation analyses for estimating pollen-mediated gene flow in plant populations.

    Science.gov (United States)

    Burczyk, Jaroslaw; Koralewski, Tomasz E

    2005-07-01

    Assessment of contemporary pollen-mediated gene flow in plants is important for various aspects of plant population biology, genetic conservation and breeding. Here, through simulations we compare the two alternative approaches for measuring pollen-mediated gene flow: (i) the NEIGHBORHOOD model--a representative of parentage analyses, and (ii) the recently developed TWOGENER analysis of pollen pool structure. We investigate their properties in estimating the effective number of pollen parents (N(ep)) and the mean pollen dispersal distance (delta). We demonstrate that both methods provide very congruent estimates of N(ep) and delta, when the methods' assumptions considering the shape of pollen dispersal curve and the mating system follow those used in data simulations, although the NEIGHBORHOOD model exhibits generally lower variances of the estimates. The violations of the assumptions, especially increased selfing or long-distance pollen dispersal, affect the two methods to a different degree; however, they are still capable to provide comparable estimates of N(ep). The NEIGHBORHOOD model inherently allows to estimate both self-fertilization and outcrossing due to the long-distance pollen dispersal; however, the TWOGENER method is particularly sensitive to inflated selfing levels, which in turn may confound and suppress the effects of distant pollen movement. As a solution we demonstrate that in case of TWOGENER it is possible to extract the fraction of intraclass correlation that results from outcrossing only, which seems to be very relevant for measuring pollen-mediated gene flow. The two approaches differ in estimation precision and experimental efforts but they seem to be complementary depending on the main research focus and type of a population studied.

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

    OpenAIRE

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

    2010-01-01

    Udgivelsesdato: 2010 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 whi...

  11. Estimation of the ash and sulphur contents of coal using kriging method; Kriging yontemi ile komur kul ve kukurt iceriklerinin tahmini

    Energy Technology Data Exchange (ETDEWEB)

    Yalcin, E.; Saydam, S.; Kose, H.

    1996-12-31

    Prediction of ash and sulphur content of coal used in coal fired power plants is important for the precautions to be taken to prevent environmental pollution. In this study, the ash and sulphur content of coal from the Collolar Coal Area were estimated using the Kriging method at different block dimensions. The effect of block dimensions on the estimations was determined. 6 refs., 5 figs., 4 tabs.

  12. Variance Components and Genetic Parameters Estimated for Fat and Protein Content in Individual Months of Lactation: The Case of Tsigai Sheep.

    Science.gov (United States)

    Oravcová, Marta

    2016-02-01

    The objective of this study was to assess variance components and genetic parameters for fat and protein content in Tsigai sheep using multivariate animal models in which fat and protein content in individual months of lactation were treated as different traits, and univariate models in which fat and protein content were treated as repeated measures of the same traits. Test day measurements were taken between the second and the seventh month of lactation. The fixed effects were lactation number, litter size and days in milk. The random effects were animal genetic effect and permanent environmental effect of ewe. The effect of flock-year-month of test day measurement was fitted either as a fixed (FYM) or random (fym) effect. Heritabilities for fat content were estimated between 0.06 and 0.17 (FYM fitted) and between 0.06 and 0.11 (fym fitted). Heritabilities for protein content were estimated between 0.15 and 0.23 (FYM fitted) and between 0.10 and 0.18 (fym fitted). For fat content, variance ratios of permanent environmental effect of ewe were estimated between 0.04 and 0.11 (FYM fitted) and between 0.02 and 0.06 (fym fitted). For protein content, variance ratios of permanent environmental effect of ewe were estimated between 0.13 and 0.20 (FYM fitted) and between 0.08 and 0.12 (fym fitted). The proportion of phenotypic variance explained by fym effect ranged from 0.39 to 0.43 for fat content and from 0.25 to 0.36 for protein content. Genetic correlations between individual months of lactation ranged from 0.74 to 0.99 (fat content) and from 0.64 to 0.99 (protein content). Fat content heritabilities estimated with univariate animal models roughly corresponded with heritability estimates from multivariate models: 0.13 (FYM fitted) and 0.07 (fym fitted). Protein content heritabilities estimated with univariate animal models also corresponded with heritability estimates from multivariate models: 0.18 (FYM fitted) and 0.13 (fym fitted).

  13. Light affects ascorbate content and ascorbate-related gene expression in tomato leaves more than in fruits.

    Science.gov (United States)

    Massot, Capucine; Stevens, Rebecca; Génard, Michel; Longuenesse, Jean-Jacques; Gautier, Hélène

    2012-01-01

    Little is known about the light regulation of vitamin C synthesis in fruits. In contrast, previous studies in leaves revealed that VTC2 (coding for GDP-L: -galactose phosphorylase) was one of the key genes up-regulated by light in leaves. Our objective was to determine how the expression of ascorbate (AsA) synthesis genes in tomato (Solanum lycopersicum) was modified according to light irradiance in both leaves and fruits. Seven days of shading strongly decreased total ascorbate (reduced and oxidized form) content in leaves (50%) and to a lesser extent in fruits (10%). Among the last six steps of AsA biosynthesis, only two genes, VTC2 and GPP1 (one of the two unigenes coding for L: -galactose-1-P phosphatase in tomato), were down-regulated by long-term shading in red ripe fruits, compared to seven genes regulated in leaves. This underlines that light affects AsA-related gene expression more in leaves than in ripening fruits. Moreover, this study reveals strong daily changes in transcript levels of enzymes of the AsA biosynthetic pathway in leaves (11 of the 12 studied genes showed significant changes in their expression pattern). Among those genes, we found that diurnal variation in transcript levels of VTC2 and GME1 correlated to leaf AsA content measured 8 h later. This study provides a new hypothesis on the role of GME1 in addition to VTC2 in light-regulated AsA biosynthesis.

  14. 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...

  15. Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

    Science.gov (United States)

    Zeng, Liping; Zhang, Qiang; Sun, Renran; Kong, Hongzhi; Zhang, Ning; Ma, Hong

    2014-01-01

    Angiosperms are the most successful plants and support human livelihood and ecosystems. Angiosperm phylogeny is the foundation of studies of gene function and phenotypic evolution, divergence time estimation and biogeography. The relationship of the five divergent groups of the Mesangiospermae (~99.95% of extant angiosperms) remains uncertain, with multiple hypotheses reported in the literature. Here transcriptome data sets are obtained from 26 species lacking sequenced genomes, representing each of the five groups: eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae. Phylogenetic analyses using 59 carefully selected low-copy nuclear genes resulted in highly supported relationships: sisterhood of eudicots and a clade containing Chloranthaceae and Ceratophyllaceae, with magnoliids being the next sister group, followed by monocots. Our topology allows a re-examination of the evolutionary patterns of 110 morphological characters. The molecular clock estimates of Mesangiospermae diversification during the late to middle Jurassic correspond well to the origins of some insects, which may have been a factor facilitating early angiosperm radiation. PMID:25249442

  16. 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.

  17. Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed.

    Science.gov (United States)

    Wüst, Pia K; Nacke, Heiko; Kaiser, Kristin; Marhan, Sven; Sikorski, Johannes; Kandeler, Ellen; Daniel, Rolf; Overmann, Jörg

    2016-05-01

    Modern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actino bacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  18. Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed

    Science.gov (United States)

    Wüst, Pia K.; Nacke, Heiko; Kaiser, Kristin; Marhan, Sven; Sikorski, Johannes; Kandeler, Ellen; Daniel, Rolf

    2016-01-01

    Modern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actinobacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms. PMID:26896137

  19. Expression of flavonoid biosynthesis genes vis-à-vis rutin content variation in different growth stages of Fagopyrum species.

    Science.gov (United States)

    Gupta, Nidhi; Sharma, Sunil K; Rana, Jai C; Chauhan, Rajinder S

    2011-11-15

    Buckwheat is one of the field crops with the highest concentration of rutin, an important flavonoid of medicinal value. Two species of buckwheat, Fagopyrum esculentum and Fagopyrum tataricum, are the major sources of rutin. Seeds of latter contain 40-50× higher rutin compared to the former. The physiological and molecular bases of rutin content variation between Fagopyrum species are not known. The current study investigated the differences in rutin content in seeds and in other tissues and growth stages of two Fagopyrum species, and also correlated those differences with the expression of flavonoid pathway genes. The analysis of rutin content dynamics at different growth stages, S1-S9 (from seed germination to mature seed formation) of Fagopyrum species revealed that rutin content was higher during seedling stages of F. tataricum (3.5 to 4.6-fold) compared to F. esculentum and then increased exponentially from stages S3 to S6 (different leaf maturing stages and inflorescence) of F. esculentum, whereas it fluctuated in F. tataricum. The rutin content was highest in the inflorescence stage (S6) of both species, with a relatively higher biosynthesis and accumulation during post-flowering stages of F. tataricum compared to F. esculentum. The expression of flavonoid pathway genes, through qRT-PCR, in different growth stages vis-à-vis rutin content variation showed differential expression for four genes, PAL, CHS, CHI and FLS with the amounts of transcripts relatively higher in F. tataricum compared to F. esculentum, thereby, correlating these genes with the biosynthesis and accumulation of rutin. The expression of PAL was highest, 7.69 and 8.96-fold in Stages 2 (seedling stage) and 9 (fully developed seeds) of F. tataricum compared to F. esculentum, respectively. The expression of the CHS gene correlated with the rutin content because it was highest in the flowers (S6) and fully developed seeds (S9) of both Fagopyrum species, with relatively higher transcript amounts

  20. Spatially Explicit Estimation of Clay and Organic Carbon Content in Agricultural Soils Using Multi-Annual Imaging Spectroscopy Data

    Directory of Open Access Journals (Sweden)

    Heike Gerighausen

    2012-01-01

    Full Text Available Information on soil clay and organic carbon content on a regional to local scale is vital for a multitude of reasons such as soil conservation, precision agriculture, and possibly also in the context of global environmental change. The objective of this study was to evaluate the potential of multi-annual hyperspectral images acquired with the HyMap sensor (450–2480 nm during three flight campaigns in 2004, 2005, and 2008 for the prediction of clay and organic carbon content on croplands by means of partial least squares regression (PLSR. Supplementary, laboratory reflectance measurements were acquired under standardized conditions. Laboratory spectroscopy yielded prediction errors between 19.48 and 35.55 g kg−1 for clay and 1.92 and 2.46 g kg−1 for organic carbon. Estimation errors with HyMap image spectra ranged from 15.99 to 23.39 g kg−1 for clay and 1.61 to 2.13 g kg−1 for organic carbon. A comparison of parameter predictions from different years confirmed the predictive ability of the models. BRDF effects increased model errors in the overlap of neighboring flight strips up to 3 times, but an appropriated preprocessing method can mitigate these negative influences. Using multi-annual image data, soil parameter maps could be successively complemented. They are exemplarily shown providing field specific information on prediction accuracy and image data source.

  1. 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.

  2. 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.

  3. Conservation of gene order and content in the circular chromosomes of 'Candidatus Liberibacter asiaticus' and other Rhizobiales.

    Directory of Open Access Journals (Sweden)

    L David Kuykendall

    Full Text Available 'Ca. Liberibacter asiaticus,' an insect-vectored, obligate intracellular bacterium associated with citrus-greening disease, also called "HLB," is a member of the Rhizobiales along with nitrogen-fixing microsymbionts Sinorhizobium meliloti and Bradyrhizobium japonicum, plant pathogen Agrobacterium tumefaciens and facultative intracellular mammalian pathogen Bartonella henselae. Comparative analyses of their circular chromosomes identified 514 orthologous genes shared among all five species. Shared among all five species are 50 identical blocks of microsyntenous orthologous genes (MOGs, containing a total of 283 genes. While retaining highly conserved genomic blocks of microsynteny, divergent evolution, horizontal gene transfer and niche specialization have disrupted macrosynteny among the five circular chromosomes compared. Highly conserved microsyntenous gene clusters help define the Rhizobiales, an order previously defined by 16S RNA gene similarity and herein represented by the three families: Bartonellaceae, Bradyrhizobiaceae and Rhizobiaceae. Genes without orthologs in the other four species help define individual species. The circular chromosomes of each of the five Rhizobiales species examined had genes lacking orthologs in the other four species. For example, 63 proteins are encoded by genes of 'Ca. Liberibacter asiaticus' not shared with other members of the Rhizobiales. Of these 63 proteins, 17 have predicted functions related to DNA replication or RNA transcription, and some of these may have roles related to low genomic GC content. An additional 17 proteins have predicted functions relevant to cellular processes, particularly modifications of the cell surface. Seventeen unshared proteins have specific metabolic functions including a pathway to synthesize cholesterol encoded by a seven-gene operon. The remaining 12 proteins encoded by 'Ca. Liberibacter asiaticus' genes not shared with other Rhizobiales are of bacteriophage origin. 'Ca

  4. Nonparametric Estimates of Gene × Environment Interaction Using Local Structural Equation Modeling

    Science.gov (United States)

    Briley, Daniel A.; Harden, K. Paige; Bates, Timothy C.; Tucker-Drob, Elliot M.

    2017-01-01

    Gene × Environment (G×E) interaction studies test the hypothesis that the strength of genetic influence varies across environmental contexts. Existing latent variable methods for estimating G×E interactions in twin and family data specify parametric (typically linear) functions for the interaction effect. An improper functional form may obscure the underlying shape of the interaction effect and may lead to failures to detect a significant interaction. In this article, we introduce a novel approach to the behavior genetic toolkit, local structural equation modeling (LOSEM). LOSEM is a highly flexible nonparametric approach for estimating latent interaction effects across the range of a measured moderator. This approach opens up the ability to detect and visualize new forms of G×E interaction. We illustrate the approach by using LOSEM to estimate gene × socioeconomic status (SES) interactions for six cognitive phenotypes. Rather than continuously and monotonically varying effects as has been assumed in conventional parametric approaches, LOSEM indicated substantial nonlinear shifts in genetic variance for several phenotypes. The operating characteristics of LOSEM were interrogated through simulation studies where the functional form of the interaction effect was known. LOSEM provides a conservative estimate of G×E interaction with sufficient power to detect statistically significant G×E signal with moderate sample size. We offer recommendations for the application of LOSEM and provide scripts for implementing these biometric models in Mplus and in OpenMx under R. PMID:26318287

  5. Effects of 24-epibrassinolide and green light on plastid gene transcription and cytokinin content of barley leaves.

    Science.gov (United States)

    Efimova, Marina V; Vankova, Radomira; Kusnetsov, Victor V; Litvinovskaya, Raisa P; Zlobin, Ilya E; Dobrev, Petre; Vedenicheva, Nina P; Savchuk, Alina L; Karnachuk, Raisa A; Kudryakova, Natalia V; Kuznetsov, Vladimir V

    2017-04-01

    In order to evaluate whether brassinosteroids (BS) and green light regulate the transcription of plastid genes in a cross-talk with cytokinins (CKs), transcription rates of 12 plastid genes (ndhF, rrn23, rpoB, psaA, psaB, rrn16, psbA, psbD, psbK, rbcL, atpB, and trnE/trnY) as well as the accumulation of transcripts of some photoreceptors (PHYA, CRY2, CRY1A, and CRY1B) and signaling (SERK and CAS) genes were followed in detached etiolated barley leaves exposed to darkness, green or white light ±1μm 24-epibrassinolide (EBL). EBL in the dark was shown to up-regulate the transcription of 12 plastid genes, while green light activated 10 genes and the EBL combined with the green light affected the transcription of only two genes (psaB and rpoB). Green light inhibited the expression of photoreceptor genes, except for CRY1A. Under the green light, EBL practically did not affect the expression of CRY1A, CAS and SERK genes, but it reduced the influence of white light on the accumulation of CAS, CRY1A, CRY1B, and SERK gene transcripts. The total content of BS in the dark and under white light remained largely unchanged, while under green light the total content of BRs (brassinolide, castasterone, and 6-deoxocastasterone) and HBRs (28-homobrassinolide, 28-homocastasterone, and 6-deoxo-28-homocastasterone) increased. The EBL-dependent up-regulation of plastome transcription in the dark was accompanied by a significant decrease in CK deactivation by O-glucosylation. However, no significant effect on the content of active CKs was detected. EBL combined with green light moderately increased the contents of trans-zeatin and isopentenyladenine, but had a negative effect on cis-zeatin. The most significant promotive effect of EBL on active CK bases was observed in white light. The data obtained suggest the involvement of CKs in the BS- and light-dependent transcription regulation of plastid genes. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Improving Estimates of Root-zone Soil Water Content Using Soil Hydrologic Properties and Remotely Sensed Soil Moisture

    Science.gov (United States)

    Baldwin, D. C.; Miller, D. A.; Singha, K.; Davis, K. J.; Smithwick, E. A.

    2013-12-01

    Newly defined relationships between remotely sensed soil moisture and soil hydraulic parameters were used to develop fine-scale (100 m) maps of root-zone soil moisture (RZSM) content at the regional scale on a daily time-step. There are several key outcomes from our research: (1) the first multi-layer regional dataset of soil hydraulic parameters developed from gSSURGO data for hydrologic modeling efforts in the Chequemegon Ecosystem Atmospheric Study (ChEAS) region, (2) the operation and calibration of a new model for estimating soil moisture flow through the root-zone at eddy covariance towers across the U.S. using remotely sensed active and passive soil moisture products, and (3) region-wide maps of estimated root-zone soil moisture content. The project links soil geophysical analytical approaches (pedotransfer functions) to new applications in remote sensing of soil moisture that detect surface moisture (~5 cm depth). We answer two key questions in soil moisture observation and prediction: (1) How do soil hydrologic properties of U.S. soil types quantitatively relate to surface-to-subsurface water loss? And (2) Does incorporation of fine-scale soil hydrologic parameters with remotely sensed soil moisture data provide improved hindcasts of in situ RZSM content? The project meets several critical research needs in estimation of soil moisture from remote sensing. First, soil moisture is known to vary spatially with soil texture and soil hydraulic properties that do not align well with the spatial resolution of current remote sensing products of soil moisture (~ 50 km2). To address this, we leveraged new advances in gridded soil parameter information (gSSURGO) together with existing remotely sensed estimates of surface soil moisture into a newly emerging semi-empirical modeling approach called SMAR (Soil Moisture Analytical Relationship). The SMAR model was calibrated and cross-validated using existing soil moisture data from a portion of AMERIFLUX tower sites and

  7. Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

    Directory of Open Access Journals (Sweden)

    Liswi Saif W

    2009-05-01

    Full Text Available Abstract Background The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies. Results Sequences from ultraviolet-sensitive (UVRh, blue-sensitive (BRh, and long-wavelength sensitive (LWRh opsins,EF-1α and COI were obtained from 27 taxa representing the five major butterfly families (5535 bp total. Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus (15.3–35.6 Mya was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis (4.7–13.6 Mya, and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene (13.5–26.1 Mya. Our family-level results are congruent with

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

    Science.gov (United States)

    Pilegaard, Henriette; Keller, Charlotte; Steensberg, Adam; Helge, Jørn Wulff; Pedersen, Bente Klarlund; Saltin, Bengt; Neufer, P Darrell

    2002-05-15

    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 6-fold) than in the control (< 3-fold) trial. Induction of PDK4 and UCP3 mRNA in response to exercise was also significantly higher in the low glycogen (11.4- and 3.5-fold, respectively) than in the control (5.0- and 1.7-fold, respectively) trial. These data indicate that low muscle glycogen content enhances the transcriptional activation of some metabolic genes in response to exercise, raising the possibility that signalling mechanisms sensitive to glycogen content and/or FFA availability may be linked to the transcriptional control of exercise-responsive genes.

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

    Science.gov (United States)

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

    2016-04-01

    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.

  10. Identification of differentially expressed genes in longissimus muscle of pigs with high and low intramuscular fat content using RNA sequencing.

    Science.gov (United States)

    Lim, K S; Lee, K T; Park, J E; Chung, W H; Jang, G W; Choi, B H; Hong, K C; Kim, T H

    2017-04-01

    Intramuscular fat (IMF) content in pork is an important element of consumer preference and is positively correlated with meat quality, including tenderness and juiciness. With advances in RNA sequencing technologies, transcriptome-related differences can be associated with specific traits in animals. The objective of this study was to investigate differentially expressed genes (DEGs) closely related to IMF content in porcine longissimus muscle using RNA sequencing. A total of 107 Berkshire pigs were used for IMF content measurements, and significant differences between extremely high (H, n = 3) and low (L, n = 3) IMF content groups were found (P change ≥2). Functional analyses with DEGs revealed that lipid metabolism (SCD and FASN) was one of the significant biological processes related to IMF content determination. In addition, we found that DEGs related to muscle regeneration (MYOG and VEGFA) and extracellular matrix (COL1A1, COL1A2, COL5A1, COL14A1 and COL15A1) were changed among individuals with extreme IMF contents. These results will aid in understanding the regulation of IMF content in pigs.

  11. Transgenic Leucaena leucocephala expressing the Rhizobium gene pydA encoding a meta-cleavage dioxygenase shows reduced mimosine content.

    Science.gov (United States)

    Jube, Sandro L R; Borthakur, Dulal

    2010-04-01

    The use of the tree-legume Leucaena leucocephala (leucaena), which contains high levels of proteins in its foliage, is limited due to the presence of the toxic free amino acid mimosine. The goal of this research was to develop transgenic leucaena with reduced mimosine content. Two genes, pydA and pydB, encoding a meta-cleavage dioxygenase (EC 1.13.11.2) and a pyruvate hydrolase (EC 3.7.1.6), respectively, from the mimosine-degrading leucaena symbiont Rhizobium sp. strain TAL1145, were used to transform leucaena. These bacterial genes were sequence-optimized for expression in leucaena and cloned into the plant binary vector pCAMBIA3201 for Agrobacterium tumefaciens-mediated transformation. Using immature zygotic embryos as the start explant material, six pydA and three pydB transgenic lines were developed. The presence and expression of the bacterial genes in the transgenic lines were verified by PCR, reverse transcriptase PCR, and Southern analyses. HPLC analyses of the transgenic plants determined that the mimosine contents of the pydA-expressing lines were reduced up to 22.5% in comparison to the wild-type. No significant reduction in mimosine content was observed in the pydB-expressing lines. This is the first example of using a gene from a bacterial symbiont to reduce the toxicity of a tree-legume.

  12. Variable Autosomal and X Divergence Near and Far from Genes Affects Estimates of Male Mutation Bias in Great Apes.

    Science.gov (United States)

    Narang, Pooja; Wilson Sayres, Melissa A

    2016-12-31

    Male mutation bias, when more mutations are passed on via the male germline than via the female germline, is observed across mammals. One common way to infer the magnitude of male mutation bias, α, is to compare levels of neutral sequence divergence between genomic regions that spend different amounts of time in the male and female germline. For great apes, including human, we show that estimates of divergence are reduced in putatively unconstrained regions near genes relative to unconstrained regions far from genes. Divergence increases with increasing distance from genes on both the X chromosome and autosomes, but increases faster on the X chromosome than autosomes. As a result, ratios of X/A divergence increase with increasing distance from genes and corresponding estimates of male mutation bias are significantly higher in intergenic regions near genes versus far from genes. Future studies in other species will need to carefully consider the effect that genomic location will have on estimates of male mutation bias.

  13. DNA G+C content of the third codon position and codon usage biases of human genes.

    Science.gov (United States)

    Sueoka, N; Kawanishi, Y

    2000-12-30

    The human genome, as in other eukaryotes, has a wide heterogeneity in the DNA base composition. The evolutionary basis for this heterogeneity has been unknown. A previous study of the human genome (846 genes analyzed) has shown that, in the major range of the G+C content in the third codon position (0.25-0.75), biases from the Parity Rule 2 (PR2) among the synonymous codons of the four-codon amino acids are similar except in the highest G+C range (Sueoka, N., 1999. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position. Gene 238, 53-58.). PR2 is an intra-strand rule where A=T and G=C are expected when there are no biases between the two complementary strands of DNA in mutation and selection rates (substitution rates). In this study, 14,026 human genes were analyzed. In addition, the third codon positions of two-codon amino acids were analyzed. New results show the following: (a) The G+C contents of the third codon position of human genes are scattered in the G+C range of 0.22-0.96 in the third codon position. (b) The PR2 biases are similar in the range of 0.25-0.75, whereas, in the high G+C range (0.75-0.96; 13% of the genes), the PR2-bias fingerprints are different from those of the major range. (c) Unlike the PR2 biases, the G+C contents of the third codon position for both four-codon and two-codon amino acids are all correlated almost perfectly with the G+C content of the third codon position over the total G+C ranges. These results support the notion that the directional mutation pressure, rather than the directional selection pressure, is mainly responsible for the heterogeneity of the G+C content of the third codon position.

  14. 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...

  15. 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.

  16. Assessing HYDRUS-2D model to estimate soil water contents and olive tree transpiration fluxes under different water distribution systems

    Science.gov (United States)

    Autovino, Dario; Negm, Amro; Rallo, Giovanni; Provenzano, Giuseppe

    2016-04-01

    In Mediterranean countries characterized by limited water resources for agricultural and societal sectors, irrigation management plays a major role to improve water use efficiency at farm scale, mainly where irrigation systems are correctly designed to guarantee a suitable application efficiency and the uniform water distribution throughout the field. In the last two decades, physically-based agro-hydrological models have been developed to simulate mass and energy exchange processes in the soil-plant-atmosphere (SPA) system. Mechanistic models like HYDRUS 2D/3D (Šimunek et al., 2011) have been proposed to simulate all the components of water balance, including actual crop transpiration fluxes estimated according to a soil potential-dependent sink term. Even though the suitability of these models to simulate the temporal dynamics of soil and crop water status has been reported in the literature for different horticultural crops, a few researches have been considering arboreal crops where the higher gradients of root water uptake are the combination between the localized irrigation supply and the three dimensional root system distribution. The main objective of the paper was to assess the performance of HYDRUS-2D model to evaluate soil water contents and transpiration fluxes of an olive orchard irrigated with two different water distribution systems. Experiments were carried out in Castelvetrano (Sicily) during irrigation seasons 2011 and 2012, in a commercial farm specialized in the production of table olives (Olea europaea L., var. Nocellara del Belice), representing the typical variety of the surrounding area. During the first season, irrigation water was provided by a single lateral placed along the plant row with four emitters per plant (ordinary irrigation), whereas during the second season a grid of emitters laid on the soil was installed in order to irrigate the whole soil surface around the selected trees. The model performance was assessed based on the

  17. Onsite and online FT-NIR spectroscopy for the estimation of total nitrogen and moisture content in poultry manure.

    Science.gov (United States)

    Tamburini, E; Castaldelli, G; Ferrari, G; Marchetti, M G; Pedrini, P; Aschonitis, V G

    2015-01-01

    The nitrogen and moisture of manure are highly variable parameters and depend on animal type, husbandry techniques, environmental conditions and storage time. The precision in manure dose estimation for crops fertilization depends on the total nitrogen and moisture content just before its incorporation in the field. The aim of the study is to develop a Fourier Transform Near Infrared (FT-NIR) spectroscopy method to determine the total Kjeldhal nitrogen (TKN%) and moisture (M%) of different types of poultry manure prior to land application. Samples covering a wide range of poultry types and different husbandry conditions were obtained from farms of North-Eastern Italy in order to develop the method. The method was calibrated (R(2) = 0.94 for TKN%, R(2) = 0.99 for M%) and validated (R(2) = 0.82 for TKN%, R(2) = 0.95 for M%) in the laboratory. An external validation was also performed in situ with independent samples, of similar origin to the previous data set, which were collected just before application in the field. Spectra acquisitions for these samples were carried out using the same instrumentation which was placed in a special vehicle for monitoring campaigns. The results showed satisfactory prediction accuracy (R(2) = 0.82 for TKN%, R(2) = 0.93 for M%). Finally, an additional analysis was performed to discriminate the different types of poultry effluents. The TKN and M measurements in the disposal areas indicated that current agronomic practices lead to more than double poultry manure oversupply. The proposed FT-NIR methodology aims to improve the current fertilization management and environmental protection by providing fast and precise estimations of poultry manure doses prior to land application.

  18. Evaluation of Sentinel-2 Red-Edge Bands for Empirical Estimation of Green LAI and Chlorophyll Content

    Directory of Open Access Journals (Sweden)

    José Moreno

    2011-07-01

    Full Text Available ESA’s upcoming satellite Sentinel-2 will provide Earth images of high spatial, spectral and temporal resolution and aims to ensure continuity for Landsat and SPOT observations. In comparison to the latter sensors, Sentinel-2 incorporates three new spectral bands in the red-edge region, which are centered at 705, 740 and 783 nm. This study addresses the importance of these new bands for the retrieval and monitoring of two important biophysical parameters: green leaf area index (LAI and chlorophyll content (Ch. With data from several ESA field campaigns over agricultural sites (SPARC, AgriSAR, CEFLES2 we have evaluated the efficacy of two empirical methods that specifically make use of the new Sentinel-2 bands. First, it was shown that LAI can be derived from a generic normalized difference index (NDI using hyperspectral data, with 674 nm with 712 nm as best performing bands. These bands are positioned closely to the Sentinel-2 B4 (665 nm and the new red-edge B5 (705 nm band. The method has been applied to simulated Sentinel-2 data. The resulting green LAI map was validated against field data of various crop types, thereby spanning a LAI between 0 and 6, and yielded a RMSE of 0.6. Second, the recently developed “Normalized Area Over reflectance Curve” (NAOC, an index that derives Ch from hyperspectral data, was studied on its compatibility with simulated Sentinel-2 data. This index integrates the reflectance curve between 643 and 795 nm, thereby including the new Sentinel-2 bands in the red-edge region. We found that these new bands significantly improve the accuracy of Ch estimation. Both methods emphasize the importance of red-edge bands for operational estimation of biophysical parameters from Sentinel-2.

  19. Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms

    Science.gov (United States)

    Tamames, Javier; Sánchez, Pablo D.; Nikel, Pablo I.; Pedrós-Alió, Carlos

    2016-01-01

    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. PMID:27065987

  20. 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.

  1. The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr.

    Science.gov (United States)

    Carlini, D B; Chen, Y; Stephan, W

    2001-01-01

    To gain insights into the relationship between codon bias, mRNA secondary structure, third-codon position nucleotide distribution, and gene expression, we predicted secondary structures in two related drosophilid genes, Adh and Adhr, which differ in degree of codon bias and level of gene expression. Individual structural elements (helices) were inferred using the comparative method. For each gene, four types of randomization simulations were performed to maintain/remove codon bias and/or to maintain or alter third-codon position nucleotide composition (N3). In the weakly expressed, weakly biased gene Adhr, the potential for secondary structure formation was found to be much stronger than in the highly expressed, highly biased gene Adh. This is consistent with the observation of approximately equal G and C percentages in Adhr ( approximately 31% across species), whereas in Adh the N3 distribution is shifted toward C (42% across species). Perturbing the N3 distribution to approximately equal amounts of A, G, C, and T increases the potential for secondary structure formation in Adh, but decreases it in Adhr. On the other hand, simulations that reduce codon bias without changing N3 content indicate that codon bias per se has only a weak effect on the formation of secondary structures. These results suggest that, for these two drosophilid genes, secondary structure is a relatively independent, negative regulator of gene expression. Whereas the degree of codon bias is positively correlated with level of gene expression, strong individual secondary structural elements may be selected for to retard mRNA translation and to decrease gene expression. PMID:11606539

  2. Power Estimation for Gene-Longevity Association Analysis Using Concordant Twins

    DEFF Research Database (Denmark)

    Tan, Qihua; Zhao, Jing Hua; Kruse, Torben A

    2014-01-01

    Statistical power is one of the major concerns in genetic association studies. Related individuals such as twins are valuable samples for genetic studies because of their genetic relatedness. Phenotype similarity in twin pairs provides evidence of genetic control over the phenotype variation...... in a population. The genetic association study on human longevity, a complex trait that is under control of both genetic and environmental factors, has been confronted by the small sample sizes of longevity subjects which limit statistical power. Twin pairs concordant for longevity have increased probability...... for carrying beneficial genes and thus are useful samples for gene-longevity association analysis. We conducted a computer simulation to estimate the power of association study using longevity concordant twin pairs. We observed remarkable power increases in using singletons from longevity concordant twin pairs...

  3. Bayesian Hierarchical Model for Estimating Gene Expression Intensity Using Multiple Scanned Microarrays

    Directory of Open Access Journals (Sweden)

    Auvinen Petri

    2008-01-01

    Full Text Available We propose a method for improving the quality of signal from DNA microarrays by using several scans at varying scanner sen-sitivities. A Bayesian latent intensity model is introduced for the analysis of such data. The method improves the accuracy at which expressions can be measured in all ranges and extends the dynamic range of measured gene expression at the high end. Our method is generic and can be applied to data from any organism, for imaging with any scanner that allows varying the laser power, and for extraction with any image analysis software. Results from a self-self hybridization data set illustrate an improved precision in the estimation of the expression of genes compared to what can be achieved by applying standard methods and using only a single scan.

  4. Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology.

    Directory of Open Access Journals (Sweden)

    David A Ball

    Full Text Available The use of microfluidics in live cell imaging allows the acquisition of dense time-series from individual cells that can be perturbed through computer-controlled changes of growth medium. Systems and synthetic biologists frequently perform gene expression studies that require changes in growth conditions to characterize the stability of switches, the transfer function of a genetic device, or the oscillations of gene networks. It is rarely possible to know a priori at what times the various changes should be made, and the success of the experiment is unknown until all of the image processing is completed well after the completion of the experiment. This results in wasted time and resources, due to the need to repeat the experiment to fine-tune the imaging parameters. To overcome this limitation, we have developed an adaptive imaging platform called GenoSIGHT that processes images as they are recorded, and uses the resulting data to make real-time adjustments to experimental conditions. We have validated this closed-loop control of the experiment using galactose-inducible expression of the yellow fluorescent protein Venus in Saccharomyces cerevisiae. We show that adaptive imaging improves the reproducibility of gene expression data resulting in more accurate estimates of gene network parameters while increasing productivity ten-fold.

  5. Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology.

    Science.gov (United States)

    Ball, David A; Lux, Matthew W; Adames, Neil R; Peccoud, Jean

    2014-01-01

    The use of microfluidics in live cell imaging allows the acquisition of dense time-series from individual cells that can be perturbed through computer-controlled changes of growth medium. Systems and synthetic biologists frequently perform gene expression studies that require changes in growth conditions to characterize the stability of switches, the transfer function of a genetic device, or the oscillations of gene networks. It is rarely possible to know a priori at what times the various changes should be made, and the success of the experiment is unknown until all of the image processing is completed well after the completion of the experiment. This results in wasted time and resources, due to the need to repeat the experiment to fine-tune the imaging parameters. To overcome this limitation, we have developed an adaptive imaging platform called GenoSIGHT that processes images as they are recorded, and uses the resulting data to make real-time adjustments to experimental conditions. We have validated this closed-loop control of the experiment using galactose-inducible expression of the yellow fluorescent protein Venus in Saccharomyces cerevisiae. We show that adaptive imaging improves the reproducibility of gene expression data resulting in more accurate estimates of gene network parameters while increasing productivity ten-fold.

  6. Estimation of total phenolic content, in-vitro antioxidant and anti-inflammatory activity of flowers of Moringa oleifera

    Institute of Scientific and Technical Information of China (English)

    Fatma Alhakmani; Sokindra Kumar; Shah Alam Khan

    2013-01-01

    Objective: To evaluate and compare the antioxidant potential and anti-inflammatory activity of ethanolic extract of flowers of Moringa oleifera (M. oleifera) grown in Oman. Methods: Flowers of M. oleifera were collected in the month of December 2012 and identified by a botanist. Alcoholic extract of the dry pulverized flowers of M. oleifera were obtained by cold maceration method. The ethanolic flower extract was subjected to preliminary phytochemical screening as the reported methods. Folin-Ciocalteu reagent was used to estimate total phenolic content. DPPH was used to determine in-vitro antioxidant activity and anti-inflammatory activity of flowers was investigated by protein denaturation method. Results:Phytochemical analysis of extract showed presence of major classes of phytochemicals such as tannins, alkaloids, flavonoids, cardiac glycosides etc. M. oleifera flowers were found to contain 19.31 mg/g of gallic acid equivalent of total phenolics in dry extract but exhibited moderate antioxidant activity. The anti-inflammatory activity of plant extract was significant and comparable with the standard drug diclofenac sodium. Conclusions:The results of our study suggest that flowers of M. oleifera possess potent anti-inflammatory activity and are also a good source of natural antioxidants. Further study is needed to identify the chemical compounds responsible for their anti-inflammatory activity.

  7. Comparison of temporal fluctuations in the total electron content estimates from EISCAT and GPS along the same line of sight

    Directory of Open Access Journals (Sweden)

    B. Forte

    2013-04-01

    Full Text Available The impact of space weather events on satellite-based technologies (e.g. satellite navigation and precise positioning is typically quantified on the basis of the total electron content (TEC and temporal fluctuations associated with it. GNSS (global navigation satellite systems TEC measurements are integrated over a long distance and thus may include contributions from different regions of the ionised atmosphere which may prevent the resolution of the mechanisms ultimately responsible for given observations. The purpose of the experiment presented here was to compare TEC estimates from EISCAT and GPS measurements. The EISCAT measurements were obtained along the same line of sight of a given GPS satellite observed from Tromsø. The present analyses focussed on the comparison of temporal fluctuations in the TEC between aligned GPS and EISCAT measurements. A reasonably good agreement was found between temporal fluctuations in TEC observed by EISCAT and those observed by a co-located GPS ionospheric monitor along the same line of sight, indicating a contribution from structures at E and F altitudes mainly to the total TEC in the presence of ionisation enhancements possibly caused by particle precipitation in the nighttime sector. The experiment suggests the great potential in the measurements to be performed by the future EISCAT_3D system, limited only in the localised geographic region to be covered.

  8. 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.

  9. ASSOCIATIONS BETWEEN POLYMORPHISM OF GROWTH HORMONE GENE WITH MILK PRODUCTION, FAT AND PROTEIN CONTENT IN FRIESIAN HOLSTEIN CATTLE

    Directory of Open Access Journals (Sweden)

    T. Hartatik

    2016-02-01

    Full Text Available The aim of the research was to determine the associations between polymorphism of the bovine growth hormone (GH gene (Leu/Val and milk production of Friesian Holstein Cattle. A total of 62 cows which consist of two Friesian Holstein cattle groups (from New Zealand=19 heads and Australia=43 heads were used for the research. We performed the Polymerase Chain Reaction and followed by Restriction Fragment Length Polymorphism using AluI restriction enzyme. The genotype was observed base on the target gene GH 211 bp in the part of intron 4 and exon 5 of growth hormone gene. The frequencies of genotypes LL were found higher than genotype LV in both groups. Friesian Holstein cattle from New Zealand showed the genotype LL and LV as 84% and 16%, respectively. Friesian Holstein cattle from Australia show the genotype LL and LV as 79% and 21%, respectively. The association between Leu/Val polymorphism on milk production, fat and protein content in both groups did not show the significant effect. Base on two groups of the origin of cattle, the result showed the significant different on fat and protein content of milk. Fat and protein contents of milk were higher in breed of FH imported from Australia compared to those in breed of FH imported from New Zailand.

  10. 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.

  11. 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

    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...

  12. 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 b6/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 (Fv/Fm, 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.

  13. Structural analysis of the wheat genes encoding NADH-dependent glutamine-2-oxoglutarate amidotransferases and correlation with grain protein content.

    Directory of Open Access Journals (Sweden)

    Domenica Nigro

    Full Text Available BACKGROUND: Nitrogen uptake and the efficient absorption and metabolism of nitrogen are essential elements in attempts to breed improved cereal cultivars for grain or silage production. One of the enzymes related to nitrogen metabolism is glutamine-2-oxoglutarate amidotransferase (GOGAT. Together with glutamine synthetase (GS, GOGAT maintains the flow of nitrogen from NH4 (+ into glutamine and glutamate, which are then used for several aminotransferase reactions during amino acid synthesis. RESULTS: The aim of the present work was to identify and analyse the structure of wheat NADH-GOGAT genomic sequences, and study the expression in two durum wheat cultivars characterized by low and high kernel protein content. The genomic sequences of the three homoeologous A, B and D NADH-GOGAT genes were obtained for hexaploid Triticum aestivum and the tetraploid A and B genes of Triticum turgidum ssp. durum. Analysis of the gene sequences indicates that all wheat NADH-GOGAT genes are composed of 22 exons and 21 introns. The three hexaploid wheat homoeologous genes have high conservation of sequence except intron 13 which shows differences in both length and sequence. A comparative analysis of sequences among di- and mono-cotyledonous plants shows both regions of high conservation and of divergence. qRT-PCR performed with the two durum wheat cvs Svevo and Ciccio (characterized by high and low protein content, respectively indicates different expression levels of the two NADH-GOGAT-3A and NADH-GOGAT-3B genes. CONCLUSION: The three hexaploid wheat homoeologous NADH-GOGAT gene sequences are highly conserved - consistent with the key metabolic role of this gene. However, the dicot and monocot amino acid sequences show distinctive patterns, particularly in the transit peptide, the exon 16-17 junction, and the C-terminus. The lack of conservation in the transit peptide may indicate subcellular differences between the two plant divisions - while the sequence

  14. 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

    and validate the vapour pressure models. Finally air temperature and vapour pressure were combined to calculate the EMC for dead fuels and the transfer of errors of these estimates have been assessed with ground meteorological data for three different EMC models. Promising results were obtained, with mean......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......-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...

  15. 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.

  16. 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.

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

    Science.gov (United States)

    Saina, Josphat K.; Long, Zhicheng; Hu, Guangwan; Gituru, Robert W.

    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.

  18. The effect of missing marker genotypes on the accuracy of gene-assisted breeding value estimation: a comparison of methods

    NARCIS (Netherlands)

    Mulder, H.A.; Meuwissen, T.H.E.; Calus, M.P.L.; Veerkamp, R.F.

    2010-01-01

    In livestock populations, missing genotypes on a large proportion of the animals is a major problem when implementing geneassisted breeding value estimation for genes with known effect. The objective of this study was to compare different methods to deal with missing genotypes on accuracy of gene-as

  19. Wavelength Selection of Hyperspectral LIDAR Based on Feature Weighting for Estimation of Leaf Nitrogen Content in Rice

    Science.gov (United States)

    Du, Lin; Shi, Shuo; Gong, Wei; Yang, Jian; Sun, Jia; Mao, Feiyue

    2016-06-01

    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 which can be

  20. [Analysis of allelic content of genes responsible for baking properties in allocytoplasmic wheat hybrids].

    Science.gov (United States)

    Klimushina, M V; Divashuk, M G; Mukhammed, T A K; Semenov, O G; Karlov, G I

    2013-05-01

    A collection comprised of allocytoplasmic hybrids of mild wheat (ACPH) was screened for the allelic state of genes responsible for baking properties (high-molecular glutenins, puroindolines, and Waxy). The possibility of the introgression of the Waxy gene of T. timopheevii into the mild wheat genome was demonstrated in several ACPH samples using the set of molecular markers. Allelic gene variants responsible for the baking properties were revealed for 22 ACPH samples, which make it possible to detect the most challenging samples for both molecular-genetic research and applied science.

  1. The ectopic expression of the wheat Puroindoline genes increase germ size and seed oil content in transgenic corn.

    Science.gov (United States)

    Zhang, Jinrui; Martin, John M; Beecher, Brian; Lu, Chaofu; Hannah, L Curtis; Wall, Michael L; Altosaar, Illimar; Giroux, Michael J

    2010-11-01

    Plant oil content and composition improvement is a major goal of plant breeding and biotechnology. The Puroindoline a and b (PINA and PINB) proteins together control whether wheat seeds are soft or hard textured and share a similar structure to that of plant non-specific lipid-transfer proteins. Here we transformed corn (Zea mays L.) with the wheat (Triticum aestivum L.) puroindoline genes (Pina and Pinb) to assess their effects upon seed oil content and quality. Pina and Pinb coding sequences were introduced into corn under the control of a corn Ubiquitin promoter. Three Pina/Pinb expression positive transgenic events were evaluated over two growing seasons. The results showed that Pin expression increased germ size significantly without negatively impacting seed size. Germ yield increased 33.8% while total seed oil content was increased by 25.23%. Seed oil content increases were primarily the result of increased germ size. This work indicates that higher oil content corn hybrids having increased food or feed value could be produced via puroindoline expression.

  2. Distribution of Genes and Repetitive Elements in the Diabrotica virgifera virgifera Genome Estimated Using BAC Sequencing

    Directory of Open Access Journals (Sweden)

    Brad S. Coates

    2012-01-01

    Full Text Available Feeding damage caused by the western corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with 104±34.5 kb inserts was created, which has an ~4.56X genome coverage based upon a 2.58 Gb (2.80 pg flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17 Mb of data (~0.05% genome coverage and indicated ~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs. Sequencing genes within BAC full inserts demonstrated that TE densities are high within intergenic and intron regions and contribute to the increased gene size. Comparison of homologous genome regions cloned within different BAC clones indicated that TE movement may cause haplotype variation within the inbred strain. The data presented here indicate that the D. virgifera virgifera genome is large in size and contains a high proportion of repetitive sequence. These BAC sequencing methods that are applicable for characterization of genomes prior to sequencing may likely be valuable resources for genome annotation as well as scaffolding.

  3. PCR-based diversity estimates of artificial and environmental 18S rRNA gene libraries.

    Science.gov (United States)

    Potvin, Marianne; Lovejoy, Connie

    2009-01-01

    Environmental clone libraries constructed using small subunit ribosomal RNA (rRNA) or other gene-specific primers have become the standard molecular approach for identifying microorganisms directly from their environment. This technique includes an initial polymerase chain reaction (PCR) amplification step of a phylogenetically useful marker gene using universal primers. Although it is acknowledged that such primers introduce biases, there have been few studies if any to date systematically examining such bias in eukaryotic microbes. We investigated some implications of such bias by constructing clone libraries using several universal primer pairs targeting rRNA genes. Firstly, we constructed artificial libraries using a known mix of small cultured pelagic arctic algae with representatives from five major lineages and secondly we investigated environmental samples using several primer pairs. No primer pair retrieved all of the original algae in the artificial clone libraries and all showed a favorable bias toward the dinoflagellate Polarella glacialis and a bias against the prasinophyte Micromonas and a pennate diatom. Several other species were retrieved by only one primer pair tested. Despite this, sequences from nine environmental libraries were diverse and contained representatives from all major eukaryotic clades expected in marine samples. Further, libraries from the same sample grouped together using Bray-Curtis clustering, irrespective of primer pairs. We conclude that environmental PCR-based techniques are sufficient to compare samples, but the total diversity will probably always be underestimated and relative abundance estimates should be treated with caution.

  4. Statin-Induced Increases in Atrophy Gene Expression Occur Independently of Changes in PGC1α Protein and Mitochondrial Content.

    Directory of Open Access Journals (Sweden)

    Craig A Goodman

    Full Text Available One serious side effect of statin drugs is skeletal muscle myopathy. Although the mechanism(s responsible for statin myopathy remains to be fully determined, an increase in muscle atrophy gene expression and changes in mitochondrial content and/or function have been proposed to play a role. In this study, we examined the relationship between statin-induced expression of muscle atrophy genes, regulators of mitochondrial biogenesis, and markers of mitochondrial content in slow- (ST and fast-twitch (FT rat skeletal muscles. Male Sprague Dawley rats were treated with simvastatin (60 or 80 mg·kg(-1·day(-1 or vehicle control via oral gavage for 14 days. In the absence of overt muscle damage, simvastatin treatment induced an increase in atrogin-1, MuRF1 and myostatin mRNA expression; however, these were not associated with changes in peroxisome proliferator gamma co-activator 1 alpha (PGC-1α protein or markers of mitochondrial content. Simvastatin did, however, increase neuronal nitric oxide synthase (nNOS, endothelial NOS (eNOS and AMPK α-subunit protein expression, and tended to increase total NOS activity, in FT but not ST muscles. Furthermore, simvastatin induced a decrease in β-hydroxyacyl CoA dehydrogenase (β-HAD activity only in FT muscles. These findings suggest that the statin-induced activation of muscle atrophy genes occurs independent of changes in PGC-1α protein and mitochondrial content. Moreover, muscle-specific increases in NOS expression and possibly NO production, and decreases in fatty acid oxidation, could contribute to the previously reported development of overt statin-induced muscle damage in FT muscles.

  5. Difference in capsaicinoid biosynthesis gene expression in the pericarp reveals elevation of capsaicinoid contents in chili peppers (Capsicum chinense).

    Science.gov (United States)

    Tanaka, Yoshiyuki; Nakashima, Fumihiro; Kirii, Erasmus; Goto, Tanjuro; Yoshida, Yuichi; Yasuba, Ken-Ichiro

    2017-02-01

    This research reveals that the up-regulated expression of multiple capsaicinoid biosynthetic genes in pericarp tissue leads to the elevation of total capsaicinoid content in chili pepper fruit. Capsaicinoids are health-functional compounds that are produced uniquely in chili pepper fruits. A high capsaicinoid level is one of the major parameters determining the commercial quality and health-promoting properties of chili peppers. To investigate the mechanisms responsible for its high contents, we compared an extremely pungent cultivar 'Trinidad Moruga Scorpion Yellow' (MY) with other cultivars of different pungency levels (Fushimi-amanaga, Takanotsume, Red Habanero). Capsaicinoid concentrations were markedly higher in MY fruit (23.9 mg/g DW) than in other pungent cultivars including 'Red Habanero' (HB) fruit (14.3 mg/g DW). Comparative analysis of MY and HB reveals that both cultivars accumulated similar capsaicinoid concentrations in the placental septum, with that in the HB pericarp (1.8 mg/g DW) being markedly lower than that in the placental septum (69.1 mg/g DW). The capsaicinoid concentration in HB fruit is dependent on the placental septum, as reported in other accessions. Therefore, even though placental septum tissue contains high capsaicinoid concentrations, those in the pericarp and seeds attenuated its total content. In contrast, the MY pericarp exhibited a markedly higher concentration (23.2 mg/g DW). A qRT-PCR analysis revealed that multiple capsaicinoid biosynthetic pathway genes (Pun1, pAMT, KAS, and BCAT) were strongly up-regulated in placental septum of pungent cultivars. The genes were expressed exclusively in the MY pericarp, but were barely detected in the pericarps of other pungent cultivars. Collectively, the present study indicates that the up-regulated expression of these genes not only in placental septum but also in pericarp plays an important role in driving capsaicinoid accumulation in the whole fruit.

  6. 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

  7. Parallel mutual information estimation for inferring gene regulatory networks on GPUs

    Directory of Open Access Journals (Sweden)

    Liu Weiguo

    2011-06-01

    Full Text Available Abstract Background Mutual information is a measure of similarity between two variables. It has been widely used in various application domains including computational biology, machine learning, statistics, image processing, and financial computing. Previously used simple histogram based mutual information estimators lack the precision in quality compared to kernel based methods. The recently introduced B-spline function based mutual information estimation method is competitive to the kernel based methods in terms of quality but at a lower computational complexity. Results We present a new approach to accelerate the B-spline function based mutual information estimation algorithm with commodity graphics hardware. To derive an efficient mapping onto this type of architecture, we have used the Compute Unified Device Architecture (CUDA programming model to design and implement a new parallel algorithm. Our implementation, called CUDA-MI, can achieve speedups of up to 82 using double precision on a single GPU compared to a multi-threaded implementation on a quad-core CPU for large microarray datasets. We have used the results obtained by CUDA-MI to infer gene regulatory networks (GRNs from microarray data. The comparisons to existing methods including ARACNE and TINGe show that CUDA-MI produces GRNs of higher quality in less time. Conclusions CUDA-MI is publicly available open-source software, written in CUDA and C++ programming languages. It obtains significant speedup over sequential multi-threaded implementation by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs.

  8. Transcriptional Analysis of Stearoyl-Acyl Carrier Protein Desaturase Genes from Olive (Olea europaea) in Relation to the Oleic Acid Content of the Virgin Olive Oil.

    Science.gov (United States)

    Parvini, Farshid; Sicardo, M Dolores; Hosseini-Mazinani, Mehdi; Martinez-Rivas, Jose M; Hernandez, M Luisa

    2016-10-02

    The specific contribution of different stearoyl-ACP desaturase (SAD) genes to the oleic acid content in olive (Olea europaea) fruit has been studied. Towards that end, we isolated three distinct cDNA clones encoding three SAD isoforms from olive (cv. Picual), as revealed by sequence analysis. The expression levels of olive SAD genes were determined in different tissues from Picual and Arbequina cultivars, including developing mesocarp and seed, together with the unsaturated fatty acid content. Lipid and gene expression analysis indicate that OeSAD2 seems to be the main gene contributing to the oleic acid content of the olive fruit and, therefore, of the virgin olive oil. This conclusion was confirmed when the study was extended to Hojiblanca, Picudo and Manzanilla cultivars. Furthermore, our data indicate that the olive microsomal oleate desaturase gene OeFAD2-2, but not OeSAD2, is responsible for the linoleic acid content in the virgin olive oil.

  9. Pyrogenic Carbon in soils: a literature-based inventory and a global estimation of its content in soil organic carbon and stocks

    Directory of Open Access Journals (Sweden)

    Moritz Reisser

    2016-08-01

    Full Text Available Pyrogenic carbon (PyC is considered one of the most stable components in soil and can represent more than 30% of total soil organic carbon (SOC. However, few estimates of global PyC stock or distribution exist and thus PyC is not included in any global carbon cycle models, despite its potential major relevance for the soil pool. To obtain a global picture, we reviewed the literature for published PyC content in SOC data. We generated the first PyC database including more than 560 measurements from 55 studies. Despite limitations due to heterogeneous distribution of the studied locations and gaps in the database, we were able to produce a worldwide PyC inventory. We found that global PyC represent on average 13.7% of the SOC and can be even up to 60%, making it one of the largest groups of identifiable compounds in soil, together with polysaccharides. We observed a consistent range of PyC content in SOC, despite the diverse methods of quantification. We tested the PyC content against different environmental explanatory variables: fire and land use (fire characteristics, land use, net primary productivity, climate (temperature, precipitation, climatic zones, altitude and pedogenic properties (clay content, pH, SOC content. Surprisingly, soil properties explain PyC content the most. Soils with clay content higher than 50% contain significantly more PyC (> 30% of the SOC than with clay content lower than 5% (< 6% of the SOC. Alkaline soils contain at least 50% more PyC than acidic soils. Furthermore, climatic conditions, represented by climatic zone or mean temperature or precipitation, correlate significantly with the PyC content. By contrast, fire characteristics could only explain PyC content, if site-specific information was available. Datasets derived from remote sensing did not explain the PyC content.To show the potential of this database, we used it in combination with other global datasets to create a global worldwide PyC content and a

  10. Pyrogenic Carbon in soils: a literature-based inventory and a global estimation of its content in soil organic carbon and stocks

    Science.gov (United States)

    Reisser, Moritz; Purves, Ross; Schmidt, Michael W. I.; Abiven, Samuel

    2016-08-01

    Pyrogenic carbon (PyC) is considered one of the most stable components in soil and can represent more than 30% of total soil organic carbon (SOC). However, few estimates of global PyC stock or distribution exist and thus PyC is not included in any global carbon cycle models, despite its potential major relevance for the soil pool. To obtain a global picture, we reviewed the literature for published PyC content in SOC data. We generated the first PyC database including more than 560 measurements from 55 studies. Despite limitations due to heterogeneous distribution of the studied locations and gaps in the database, we were able to produce a worldwide PyC inventory. We found that global PyC represent on average 13.7% of the SOC and can be even up to 60%, making it one of the largest groups of identifiable compounds in soil, together with polysaccharides. We observed a consistent range of PyC content in SOC, despite the diverse methods of quantification. We tested the PyC content against different environmental explanatory variables: fire and land use (fire characteristics, land use, net primary productivity), climate (temperature, precipitation, climatic zones, altitude) and pedogenic properties (clay content, pH, SOC content). Surprisingly, soil properties explain PyC content the most. Soils with clay content higher than 50% contain significantly more PyC (> 30% of the SOC) than with clay content lower than 5% (Alkaline soils contain at least 50% more PyC than acidic soils. Furthermore, climatic conditions, represented by climatic zone or mean temperature or precipitation, correlate significantly with the PyC content. By contrast, fire characteristics could only explain PyC content, if site-specific information was available. Datasets derived from remote sensing did not explain the PyC content. To show the potential of this database, we used it in combination with other global datasets to create a global worldwide PyC content and a stock estimation, which resulted

  11. A review of satellite-based methods of estimating live fuel moisture content for fire danger assessment: moving towards operational products

    Science.gov (United States)

    One of the primary variables affecting ignition and spread of wildfire is fuel moisture content (FMC), which is the ratio of water mass to dry mass in living and dead plant material. Because dead FMC may be estimated from available weather data, remote sensing is needed to monitor the spatial distr...

  12. Quantitative in vivo CT arthrography of the human osteoarthritic knee to estimate cartilage sulphated glycosaminoglycan content : correlation with ex-vivo reference standards

    NARCIS (Netherlands)

    van Tiel, J; Siebelt, M; Reijman, M; Bos, P.K.; Waarsing, J H; Zuurmond, A-M; Nasserinejad, K; van Osch, G J V M; Verhaar, J A N; Krestin, G P; Weinans, H; Oei, E H G

    OBJECTIVE: Recently, computed tomography arthrography (CTa) was introduced as quantitative imaging biomarker to estimate cartilage sulphated glycosaminoglycan (sGAG) content in human cadaveric knees. Our aim was to assess the correlation between in vivo CTa in human osteoarthritis (OA) knees and ex

  13. Quantitative in vivo CT arthrography of the human osteoarthritic knee to estimate cartilage sulphated glycosaminoglycan content: correlation with ex-vivo reference standards

    NARCIS (Netherlands)

    Tiel, J. van; Siebelt, M.; Reijman, M.; Bos, P.K.; Waarsing, J.H.; Zuurmond, A.M.; Nasserinejad, K.; Osch, G.J.V.M. van; Verhaar, J.A.N.; Krestin, G.P.; Weinans, H.; Oei, E.H.G.

    2016-01-01

    Objective. Recently, computed tomography arthrography (CTa) was introduced as quantitative imaging biomarker to estimate cartilage sulphated glycosaminoglycan (sGAG) content in human cadaveric knees. Our aim was to assess the correlation between in vivo CTa in human osteoarthritis (OA) knees and ex

  14. Massively convergent evolution for ribosomal protein gene content in plastid and mitochondrial genomes.

    Science.gov (United States)

    Maier, Uwe-G; Zauner, Stefan; Woehle, Christian; Bolte, Kathrin; Hempel, Franziska; Allen, John F; Martin, William F

    2013-01-01

    Plastid and mitochondrial genomes have undergone parallel evolution to encode the same functional set of genes. These encode conserved protein components of the electron transport chain in their respective bioenergetic membranes and genes for the ribosomes that express them. This highly convergent aspect of organelle genome evolution is partly explained by the redox regulation hypothesis, which predicts a separate plastid or mitochondrial location for genes encoding bioenergetic membrane proteins of either photosynthesis or respiration. Here we show that convergence in organelle genome evolution is far stronger than previously recognized, because the same set of genes for ribosomal proteins is independently retained by both plastid and mitochondrial genomes. A hitherto unrecognized selective pressure retains genes for the same ribosomal proteins in both organelles. On the Escherichia coli ribosome assembly map, the retained proteins are implicated in 30S and 50S ribosomal subunit assembly and initial rRNA binding. We suggest that ribosomal assembly imposes functional constraints that govern the retention of ribosomal protein coding genes in organelles. These constraints are subordinate to redox regulation for electron transport chain components, which anchor the ribosome to the organelle genome in the first place. As organelle genomes undergo reduction, the rRNAs also become smaller. Below size thresholds of approximately 1,300 nucleotides (16S rRNA) and 2,100 nucleotides (26S rRNA), all ribosomal protein coding genes are lost from organelles, while electron transport chain components remain organelle encoded as long as the organelles use redox chemistry to generate a proton motive force.

  15. 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.

  16. Alterations in Seed Development Gene Expression Affect Size and Oil Content of Arabidopsis Seeds1[C][W][OPEN

    Science.gov (United States)

    Fatihi, Abdelhak; Zbierzak, Anna Maria; Dörmann, Peter

    2013-01-01

    Seed endosperm development in Arabidopsis (Arabidopsis thaliana) is under control of the polycomb group complex, which includes Fertilization Independent Endosperm (FIE). The polycomb group complex regulates downstream factors, e.g. Pheres1 (PHE1), by genomic imprinting. In heterozygous fie mutants, an endosperm develops in ovules carrying a maternal fie allele without fertilization, finally leading to abortion. Another endosperm development pathway depends on MINISEED3 (a WRKY10 transcription factor) and HAIKU2 (a leucine-rich repeat kinase). While the role of seed development genes in the embryo and endosperm establishment has been studied in detail, their impact on metabolism and oil accumulation remained unclear. Analysis of oil, protein, and sucrose accumulation in mutants and overexpression plants of the four seed development genes revealed that (1) seeds carrying a maternal fie allele accumulate low oil with an altered composition of triacylglycerol molecular species; (2) homozygous mutant seeds of phe1, mini3, and iku2, which are smaller, accumulate less oil and slightly less protein, and starch, which accumulates early during seed development, remains elevated in mutant seeds; (3) embryo-specific overexpression of FIE, PHE1, and MINI3 has no influence on seed size and weight, nor on oil, protein, or sucrose content; and (4) overexpression of IKU2 results in seeds with increased size and weight, and oil content of overexpressed IKU2 seeds is increased by 35%. Thus, IKU2 overexpression represents a novel strategy for the genetic manipulation of the oil content in seeds. PMID:24014578

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

    Directory of Open Access Journals (Sweden)

    Adam J Book

    2016-06-01

    Full Text Available 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.

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

    Science.gov (United States)

    Book, Adam J; Lewin, Gina R; McDonald, Bradon R; Takasuka, Taichi E; Wendt-Pienkowski, Evelyn; Doering, Drew T; Suh, Steven; Raffa, Kenneth F; Fox, Brian G; Currie, Cameron R

    2016-06-01

    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.

  19. 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.

  20. Timing of gene expression from different genetic systems in shaping leucine and isoleucine contents of rapeseed (Brassica napus L.) meal

    Indian Academy of Sciences (India)

    Guo Lin Chen; Jian Guo Wu; Murali-Tottekkaad Variath; Chun Hai Shi

    2011-12-01

    Experiments were conducted on rapeseed (Brassica napus L.) using a diallel design with nine parents: Youcai 601, Double 20-4, Huashuang 3, Gaoyou 605, Zhongyou 821, Eyouchangjia, Zhong R-888, Tower and Zheshuang 72. The seed developmental process was divided into five stages, namely initial (days 1–15 after flowering), early (days 16–22 after flowering), middle (days 23–29), late (days 30–36), and maturing (days 37–43) developmental stages. The variation of dynamic genetic effects for leucine and isoleucine contents of rapeseed meal was analysed at five developmental stages, across different environments using the genetic models with time-dependent measures. The results from unconditional and conditional analyses indicated that the expression of diploid embryo, cytoplasmic and diploid maternal plant genes were important for leucine and isoleucine contents at different developmental stages of rapeseed, particularly at the initial and early developmental stages. Among different genetic systems, nutrition quality traits were mainly controlled by the accumulative or net maternal main effects and their GE interaction effects, except at maturity when the net diploid embryo effects were larger. The expression of genes was affected by the environmental conditions on 15, 22, 29 or 36 days after flowering, but was more stable at mature stage. For the isoleucine content the narrow-sense heritabilities on 15, 22, 29, 36, and 43 days after flowering were 43.0, 65.7, 60.1, 65.5 and 78.2%, respectively, while for the leucine content the corresponding narrow-sense heritabilities were relatively smaller. The interaction heritabilities were more important than the general heritabilities at the first three developmental times. The improvement for isoleucine content could be achieved by selection based on the higher narrow-sense heritabilities. Various genetic systems exhibited genetic correlations among the developmental times or leucine and isoleucine contents. A

  1. Estimation of Moisture Content of Forest Canopy and Floor from SAR Data Part I: Volume Scattering Case

    Science.gov (United States)

    Moghaddam, M.; Saatchi, S.

    1996-01-01

    To understand and predict the functioning of forest biomes, their interaction with the atmosphere, and their growth rates, the knowledge of moisture content of their canopy and the floor soil is essential. The synthetic aperture radar on airborne and spaceborne platforms has proven to be a flexible tool for measuring electromagnetic back- scattering properties of vegetation related to their moisture content.

  2. 48 CFR 52.223-9 - Estimate of Percentage of Recovered Material Content for EPA-Designated Items.

    Science.gov (United States)

    2010-10-01

    ... recovered material content for EPA-designated item(s) delivered and/or used in contract performance... responsible for the performance of this contract and hereby certify that the percentage of recovered material content for EPA-designated items met the applicable contract specifications or other...

  3. Proteomic Analysis of the Marine Cyanobacterium Synechococcus WH8102 and Implications for Estimates of the Cellular Iron Content

    Science.gov (United States)

    Saito, M. A.; Bertrand, E. M.; Bulygin, V.; Moran, D.; Waterbury, J. B.

    2008-12-01

    The proteome of the marine cyanobacterium Synechococcus WH8102 was analyzed by nanospray liquid chromatography mass spectrometry (nLC-MS) with two major goals: to provide a first examination of the relative abundance of the most abundant proteins in this important microbe and to provide the necessary mass spectra for future quantification of biogeochemically significant proteins. Analyses of 37 nLC-MS runs of whole cell tryptic digestions and SDS-PAGE gel separated tryptic digestions resulted in a total of 636 proteins identified, 376 identified with two or more tryptic peptides. The identifications used the Sequest algorithm with stringent data filters on 54003 observed peptides, 3066 of which were unique, with a false positive rate of 2.2%. These measured proteins represent ~ 25.2% (14.8% with >= 2 peptides) of the open reading frames (ORFs) in the genome, similar to or higher than the percentage found in other cyanobacterial proteome studies thus far. The relative abundance of the more abundant proteins in the proteome was examined using the exponentially modified protein abundance index from a single nLC-MS run that identified 372 proteins (14.7% of the ORFs) from 7743 observed peptides (1224 unique peptides). Estimates of the relative abundance showed the photosynthesis and respiration category contributing approximately 32% of the total detected protein, hypothetical proteins contributing about 16%, and translation about 12%. Of biogeochemical interest, multiple types of nitrogen assimilation systems were observed to be simultaneously expressed as proteins, only 5 of the 21 B12 biosynthesis proteins were identified likely due to low abundance, and the metalloproteins metallothionein and nickel superoxide dismutase were relatively abundant. In contrast to previous predictions of a high photosystem I: photosystem II ratio of approximately 3 in the cyanobacteria and a resultant high cellular iron content, the ratio of the average relative abundances of all

  4. UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation.

    Directory of Open Access Journals (Sweden)

    Shaun D Jackman

    Full Text Available When working on an ongoing genome sequencing and assembly project, it is rather inconvenient when gene identifiers change from one build of the assembly to the next. The gene labelling system described here, UniqTag, addresses this common challenge. UniqTag assigns a unique identifier to each gene that is a representative k-mer, a string of length k, selected from the sequence of that gene. Unlike serial numbers, these identifiers are stable between different assemblies and annotations of the same data without requiring that previous annotations be lifted over by sequence alignment. We assign UniqTag identifiers to ten builds of the Ensembl human genome spanning eight years to demonstrate this stability. The implementation of UniqTag in Ruby and an R package are available at https://github.com/sjackman/uniqtag sjackman/uniqtag. The R package is also available from CRAN: install.packages ("uniqtag". Supplementary material and code to reproduce it is available at https://github.com/sjackman/uniqtag-paper.

  5. UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation

    Science.gov (United States)

    Jackman, Shaun D.; Bohlmann, Joerg; Birol, İnanç

    2015-01-01

    When working on an ongoing genome sequencing and assembly project, it is rather inconvenient when gene identifiers change from one build of the assembly to the next. The gene labelling system described here, UniqTag, addresses this common challenge. UniqTag assigns a unique identifier to each gene that is a representative k-mer, a string of length k, selected from the sequence of that gene. Unlike serial numbers, these identifiers are stable between different assemblies and annotations of the same data without requiring that previous annotations be lifted over by sequence alignment. We assign UniqTag identifiers to ten builds of the Ensembl human genome spanning eight years to demonstrate this stability. The implementation of UniqTag in Ruby and an R package are available at https://github.com/sjackman/uniqtag sjackman/uniqtag. The R package is also available from CRAN: install.packages ("uniqtag"). Supplementary material and code to reproduce it is available at https://github.com/sjackman/uniqtag-paper. PMID:26020645

  6. Correlation between Pr1 and Pr2 gene content and virulence in Metarhizium anisopliae strains.

    Science.gov (United States)

    Rosas-García, Ninfa M; Avalos-de-León, Osvaldo; Villegas-Mendoza, Jesús M; Mireles-Martínez, Maribel; Barboza-Corona, J E; Castañeda-Ramírez, J C

    2014-11-28

    Metarhizium anisopliae is a widely studied model to understand the virulence factors that participate in pathogenicity. Proteases such as subtilisin-like enzymes (Pr1) and trypsin-like enzymes (Pr2) are considered important factors for insect cuticle degradation. In four M. anisopliae strains (798, 6342, 6345, and 6347), the presence of pr1 and pr2 genes, as well as the enzymatic activity of these genes, was correlated with their virulence against two different insect pests. The 11 pr1 genes (A, B, C, D, E, F, G, H, I, J, and K) and pr2 gene were found in all strains. The activity of individual Pr1 and Pr2 proteases exhibited variation in time (24, 48, 72, and 96 h) and in the presence or absence of chitin as the inductor. The highest Pr1 enzymatic activity was shown by strain 798 at 48 h with chitin. The highest Pr2 enzymatic activity was exhibited by the 6342 and 6347 strains, both grown with chitin at 24 and 48 h, respectively. Highest mortality on S. exigua was caused by strain 6342 at 48 h, and strains 6342, 6345, and 6347 caused the highest mortality 7 days later. Mortality on Prosapia reached 30% without variation. The presence of subtilisin and trypsin genes and the activity of these proteases in M. anisopliae strains cannot be associated with the virulence against the two insect pests. Probably, subtilisin and trypsin enzyme production is not a vital factor for pathogenicity, but its contribution is important to the pathogenicity process.

  7. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    Directory of Open Access Journals (Sweden)

    Ramy Karam Aziz

    2015-05-01

    Full Text Available Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. We propose adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.

  8. Estimating the biodegradation of pesticide in soils by monitoring pesticide-degrading gene expression.

    Science.gov (United States)

    Monard, Cécile; Martin-Laurent, Fabrice; Lima, Oscar; Devers-Lamrani, Marion; Binet, Françoise

    2013-04-01

    Assessing in situ microbial abilities of soils to degrade pesticides is of great interest giving insight in soil filtering capability, which is a key ecosystem function limiting pollution of groundwater. Quantification of pesticide-degrading gene expression by reverse transcription quantitative PCR (RT-qPCR) was tested as a suitable indicator to monitor pesticide biodegradation performances in soil. RNA extraction protocol was optimized to enhance the yield and quality of RNA recovered from soil samples to perform RT-qPCR assays. As a model, the activity of atrazine-degrading communities was monitored using RT-qPCRs to estimate the level of expression of atzD in five agricultural soils showing different atrazine mineralization abilities. Interestingly, the relative abundance of atzD mRNA copy numbers was positively correlated to the maximum rate and to the maximal amount of atrazine mineralized. Our findings indicate that the quantification of pesticide-degrading gene expression may be suitable to assess biodegradation performance in soil and monitor natural attenuation of pesticide.

  9. 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.

  10. 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

  11. Effects of Rosiglitazone and Metformin on Liver Fat Content, Hepatic Insulin Resistance, Insulin Clearance, and Gene Expression in Adipose Tissue in Patients With Type 2 Diabetes

    National Research Council Canada - National Science Library

    Mirja Tiikkainen; Anna-Maija Häkkinen; Elena Korsheninnikova; Tuulikki Nyman; Sari Mäkimattila; Hannele Yki-Järvinen

    2004-01-01

    Effects of Rosiglitazone and Metformin on Liver Fat Content, Hepatic Insulin Resistance, Insulin Clearance, and Gene Expression in Adipose Tissue in Patients With Type 2 Diabetes Mirja Tiikkainen 1 , Anna-Maija...

  12. Variants of the melanocortin 1 receptor gene (MC1R) and P gene would be effective for estimating the population origin of an individual.

    Science.gov (United States)

    Masui, Sosuke; Nakatome, Masato; Matoba, Ryoji

    2009-04-01

    The population origin of an individual is often required to be determined from specimens left at a crime scene for estimating a suspect and individual identity. The melanocortin 1 receptor gene (MC1R) and P gene are associated with human pigmentation. Although there have been several reports that these genes are highly polymorphic in human populations, it is unclear if the allele variants can be used to estimate the population origin of an individual. We aimed to estimate the ethnic origin of a particular individual by using single nucleotide polymorphisms (SNPs). Four SNPs (MC1R gene: R163Q and P gene: IVS5+1001, IVS13+113 and H615R) were genotyped in 394 volunteers from 4 ethnically defined populations using a PCR-based assay. The results revealed that the allele variants were present with high frequency in Asian populations but were low in European and African populations. On the basis of these results, we defined a specific combination of a genotype (R163Q) and a diplotype group (IVS5+1001, IVS13+113 and H615R). This study indicates that the specific combination of a genotype and a diplotype group would be effective for estimating the population origin of an individual from a list of population groups.

  13. SEMI-BLIND SOURCE SEPARATION FOR ESTIMATION OF CLAY CONTENT OVER SEMI-VEGETATED AREAS, FROM VNIR/SWIR HYPERSPECTRAL AIRBORNE DATA

    Directory of Open Access Journals (Sweden)

    W. Ouerghemmi

    2015-08-01

    Full Text Available The applicability of Visible, Near-Infrared and Short Wave Infrared (VNIR/SWIR hyperspectral imagery for soil property mapping decreases when surfaces are partially covered by vegetation. The objective of this research was to develop and evaluate a methodology based on the “double-extraction” technique, for clay content estimation over semi-vegetated surfaces using VNIR/SWIR hyperspectral airborne data. The “double-extraction” technique initially proposed by Ouerghemmi et al. (2011 consists of 1 an extraction of a soil reflectance spectrum ssoil from semi-vegetated spectra using a Blind Source Separation technique, and 2 an extraction of clay content from the soil reflectance spectrum ssoil, using a multivariate regression method. In this paper, the Source Separation approach is Semi-Blind thanks to the integration of field knowledge in Source Separation model. And the multivariate regression method is a partial least squares regression (PLSR model. This study employed VNIR/SWIR HyMap airborne data acquired in a French Mediterranean region over an area of 24 km2. Our results showed that our methodology based on the “double-extraction” technique is accurate for clay content estimation when applied to pixels under a specific Cellulose Absorption Index threshold. Finally the clay content can be estimated over around 70% of the semi-vegetated pixels of our study area, which may offer an extension of soil properties mapping, at the moment restricted to bare soils.

  14. 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.

  15. Estimating chlorophyll content and photochemical yield of photosystem II (ΦPSII) using solar-induced chlorophyll fluorescence measurements at different growing stages of attached leaves.

    Science.gov (United States)

    Tubuxin, Bayaer; Rahimzadeh-Bajgiran, Parinaz; Ginnan, Yusaku; Hosoi, Fumiki; Omasa, Kenji

    2015-09-01

    This paper illustrates the possibility of measuring chlorophyll (Chl) content and Chl fluorescence parameters by the solar-induced Chl fluorescence (SIF) method using the Fraunhofer line depth (FLD) principle, and compares the results with the standard measurement methods. A high-spectral resolution HR2000+ and an ordinary USB4000 spectrometer were used to measure leaf reflectance under solar and artificial light, respectively, to estimate Chl fluorescence. Using leaves of Capsicum annuum cv. 'Sven' (paprika), the relationships between the Chl content and the steady-state Chl fluorescence near oxygen absorption bands of O2B (686nm) and O2A (760nm), measured under artificial and solar light at different growing stages of leaves, were evaluated. The Chl fluorescence yields of ΦF 686nm/ΦF 760nm ratios obtained from both methods correlated well with the Chl content (steady-state solar light: R(2) = 0.73; artificial light: R(2) = 0.94). The SIF method was less accurate for Chl content estimation when Chl content was high. The steady-state solar-induced Chl fluorescence yield ratio correlated very well with the artificial-light-induced one (R(2) = 0.84). A new methodology is then presented to estimate photochemical yield of photosystem II (ΦPSII) from the SIF measurements, which was verified against the standard Chl fluorescence measurement method (pulse-amplitude modulated method). The high coefficient of determination (R(2) = 0.74) between the ΦPSII of the two methods shows that photosynthesis process parameters can be successfully estimated using the presented methodology.

  16. Prototypical Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

    OpenAIRE

    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 orthologue...

  17. [Hyper spectral estimation method for soil alkali hydrolysable nitrogen content based on discrete wavelet transform and genetic algorithm in combining with partial least squares DWT-GA-PLS)].

    Science.gov (United States)

    Chen, Hong-Yan; Zhao, Geng-Xing; Li, Xi-Can; Wang, Xiang-Feng; Li, Yu-Ling

    2013-11-01

    Taking the Qihe County in Shandong Province of East China as the study area, soil samples were collected from the field, and based on the hyperspectral reflectance measurement of the soil samples and the transformation with the first deviation, the spectra were denoised and compressed by discrete wavelet transform (DWT), the variables for the soil alkali hydrolysable nitrogen quantitative estimation models were selected by genetic algorithms (GA), and the estimation models for the soil alkali hydrolysable nitrogen content were built by using partial least squares (PLS) regression. The discrete wavelet transform and genetic algorithm in combining with partial least squares (DWT-GA-PLS) could not only compress the spectrum variables and reduce the model variables, but also improve the quantitative estimation accuracy of soil alkali hydrolysable nitrogen content. Based on the 1-2 levels low frequency coefficients of discrete wavelet transform, and under the condition of large scale decrement of spectrum variables, the calibration models could achieve the higher or the same prediction accuracy as the soil full spectra. The model based on the second level low frequency coefficients had the highest precision, with the model predicting R2 being 0.85, the RMSE being 8.11 mg x kg(-1), and RPD being 2.53, indicating the effectiveness of DWT-GA-PLS method in estimating soil alkali hydrolysable nitrogen content.

  18. Rice Crop Field Monitoring System with Radio Controlled Helicopter Based Near Infrared Cameras Through Nitrogen Content Estimation and Its Distribution Monitoring

    Directory of Open Access Journals (Sweden)

    Kohei Arai

    2013-03-01

    Full Text Available Rice crop field monitoring system with radio controlled helicopter based near infrared cameras is proposed together with nitrogen content estimation method for monitoring its distribution in the field in concern. Through experiments at the Saga Prefectural Agricultural Research Institute: SPARI, it is found that the proposed system works well for monitoring nitrogen content in the rice crop which indicates quality of the rice crop and its distribution in the field in concern. Therefore, it becomes available to maintain the rice crop fields in terms of quality control.

  19. 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

  20. [Application study of the thermal infrared emissivity spectra in the estimation of salt content of saline soil].

    Science.gov (United States)

    Xia, Jun; Tashpolat, Tiyip; Mamat, Sawut; Zhang, Fei; Han, Gui-Hong

    2012-11-01

    Studying of soil salinization is of great significance for agricultural production in arid area oasis, thermal infrared remote sensing technology provides a new technology and method in this field. Authors used Fourier transform infrared spectrometer to measure the oasis saline soil in field, employed iterative spectrally smooth temperature/emissivity separation algorithm (ISSTES) to separate temperature and emissivity, and acquired the thermal infrared emissivity data of the saline soil. Through researching the emissivity spectral feature of saline soil, and concluded that soil emissivity will reduce with the increasing of salt content from 8 to 13 microm, so emissivity spectra is more sensitive to salt factor from 8 to 9.5 microm. Then, analyzed the correlation between original emissivity spectra and its first derivative, second derivative and normalized ratio with salt content, the result showed that they have a negative correlation relationship between soil emissivity and salt content, and the correlation between emissivity first derivative and salt content is highest, reach to 0.724 2, the corresponding bands are from 8.370 745-8.390 880 microm. Finally, established the quadratic function regression model, its determination coefficient is 0.741 4, and root mean square error is 0.235 5, the result explained that the approach of using thermal infrared emissivity to retrieve the salt content of saline soil is feasible.

  1. [Estimating total nitrogen content in reclaimed water based on hyperspectral reflectance information from emergent plants: a case study of Mencheng Lake Wetland Park in Beijing, China].

    Science.gov (United States)

    Liu, Hui; Gong, Zhao-ning; Zhao, Wen-ji

    2014-12-01

    Hyperspectral reflectance information is a crucial method to detect total nitrogen content in plant leaves, meanwhile, vegetation nitrogen content has a strong relationship with nitrogen in water. Taking Mencheng Lake Wetland Park supplied with reclaimed water as study area, the vegetation hyperspectral data (Phragmites australis and Typha angustifolia), and the content of total nitrogen in water were detected to investigate the feasibility of estimating total nitrogen content in reclaimed water based on hyperspectral reflectance information from emergent plants. We established simple linear regression model, stepwise multiple linear regression model and partial least square regression model based on four hyperspectral indices (spectral indices, normalized difference indices, trilateral parameters, absorption feature parameters), respectively. The accuracy of these models was coefficient of determination (R2) and root mean square error (RMSE). The results showed that stepwise multiple linear regression model and partial least square regression model predicted more accurately than simple linear regression model, and the accuracy of prediction models based on P. australis reflectance spectra was higher than those on T. angustifolia. Partial least square regression model was the most useful explorative tool for unraveling the relationship between spectral reflectance of P. australis and total nitrogen content in water with R2 of 0.854 and RMSE of 0.647. 500-700 nm was the best band range for detecting water total nitrogen content. The reflectance ratio of green peak and red valley could be effectively predicted by the absorption feature parameters.

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

    Directory of Open Access Journals (Sweden)

    Eliana Henriquez-Rodriguez

    2015-12-01

    Full Text Available 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.

  3. Development of a Method to Estimate Moisture Diffusivity as a Function of Local Moisture Content for the Numerical Simulation of Food Drying Process

    Science.gov (United States)

    Vongchanh, Kinnaleth; Kudo, Kazuhiko; Konishi, Yasuyuki; Ariyadi, Suwono; Halim, Abdurrachim

    A method to estimate the moisture diffusivity (Dm) of fish-sausage is given as a function of local moisture content. The correlation of the moisture diffusivity is determined by matching the time history of the numerically estimated average moisture content and that obtained from an experiment. The simulation is based on a semi-two dimensional heat and mass transfer analysis with shrinkage and variable thermal properties. The data of the sausage's properties and its shrinkage during the course of drying are obtained from the experiment. The drying air conditions are 50±2oC of temperature and 0.67±0.02 m/s of velocity with 5.1-6.2% of RH. The size of the specimen is approximately 70, 100 and 10 mm of width, length and thickness, respectively. The calculated result of the drying curve using obtained Dm, local gives an error less than ±1.5%.

  4. Estimation of lunar titanium content: Based on absorption features of Chang’E-1 interference imaging spectrometer (ⅡM)

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Two linear regression models based on absorption features extracted from CE-1 IIM image data are presented to discuss the relationship between absorption features and titanium content. We computed five absorption parameters (Full Wave at Half Maximum (FWHM), absorption position, absorption area, absorption depth and absorption asymmetry) of the spectra collected at Apollo 17 landing sites to build two regression models, one with FWHM and the other without FWHM due to the low relation coefficient between FWHM and Ti content. Finally Ti content measured from Apollo 17 samples and Apollo 16 samples was used to test the accuracy. The results show that the predicted values of the model with FWHM have many singular values and the result of model without FWHM is more stable. The two models are relatively accurate for high-Ti districts, while seem inexact and disable for low-Ti districts.

  5. The gene pat-2, which induces natural parthenocarpy, alters the gibberellin content in unpollinated tomato ovaries.

    Science.gov (United States)

    Fos, M; Nuez, F; García-Martínez, J L

    2000-02-01

    We investigated the role of gibberellins (GAs) in the effect of pat-2, a recessive mutation that induces facultative parthenocarpic fruit development in tomato (Lycopersicon esculentum Mill.) using near-isogenic lines with two different genetic backgrounds. Unpollinated wild-type Madrigal (MA/wt) and Cuarenteno (CU/wt) ovaries degenerated, but GA(3) application induced parthenocarpic fruit growth. On the contrary, parthenocarpic growth of MA/pat-2 and CU/pat-2 fruits, which occurs in the absence of pollination and hormone application, was not affected by GA(3). Pollinated MA/wt and parthenocarpic MA/pat-2 ovary development was negated by paclobutrazol, and this inhibitory effect was counteracted by GA(3). The main GAs of the early-13-hydroxylation pathway (GA(1), GA(3), GA(8), GA(19), GA(20), GA(29), GA(44), GA(53), and, tentatively, GA(81)) and two GAs of the non-13-hydroxylation pathway (GA(9) and GA(34)) were identified in MA/wt ovaries by gas chromatography-selected ion monitoring. GAs were quantified in unpollinated ovaries at flower bud, pre-anthesis, and anthesis. In unpollinated MA/pat-2 and CU/pat-2 ovaries, the GA(20) content was much higher (up to 160 times higher) and the GA(19) content was lower than in the corresponding non-parthenocarpic ovaries. The application of an inhibitor of 2-oxoglutarate-dependent dioxygenases suggested that GA(20) is not active per se. The pat-2 mutation may increase GA 20-oxidase activity in unpollinated ovaries, leading to a higher synthesis of GA(20), the precursor of an active GA.

  6. The complete mitochondrial genome of Neobenedenia melleni (Platyhelminthes: Monogenea): mitochondrial gene content, arrangement and composition compared with two Benedenia species.

    Science.gov (United States)

    Zhang, Juan; Wu, Xiangyun; Li, Yanwei; Zhao, Mengwei; Xie, Mingquan; Li, Anxing

    2014-10-01

    The complete mitochondrial (mt) genome sequences of Neobenedenia melleni were determined and compared with those of Benedenia seriolae and B. hoshinai. This circular genome comprises 13,270 bp and includes all 36 typical mt genes found in flatworms. Total AT content of N. melleni is 75.9 %. ATG is the most common start codon, while nad4L is initiated by GTG. All protein-coding genes are predicted to terminate with TAG and TAA. N. melleni has the trnR with a TCG anticodon, which is the same to B. seriolae but different from B. hoshinai (ACG). The mt gene arrangement of N. melleni is similar to that of B. seriolae and B. hoshinai with the exception of three translocations (trnF, trnT and trnG). The overlapped region between nad4L and nad4 was found in the N. melleni mt genome, which was also reported for the published Gyrodactylus species, but it was not found in those of B. seriolae and B. hoshinai, which are non-coding regions instead. The present study provides useful molecular characters for species or strain identification and systematic studies of this parasite.

  7. 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

  8. Elemental partitioning and isotopic fractionation of Zn between metal and silicate and geochemical estimation of the S content of the Earth's core

    Science.gov (United States)

    Mahan, Brandon; Siebert, Julien; Pringle, Emily A.; Moynier, Frédéric

    2017-01-01

    Zinc metal-silicate fractionation provides experimental access to the conditions of core formation and Zn has been used to estimate the S contents of the Earth's core and of the bulk Earth, assuming that they share similar volatility and that Zn was not partitioned into the Earth's core. Therefore, Zn provides both direct and indirect information into the origin and eventual fate of volatile and siderophile elements on Earth. However, the partitioning of Zn between metal and silicate - as well as the associated isotopic fractionation - is not well known. We have conducted a suite of partitioning experiments to characterize Zn elemental partitioning and isotopic fractionation between metal and silicate as a function of time, temperature, and composition. Experiments were conducted at 2 GPa and temperatures from 1473 K to 2273 K in a piston cylinder apparatus, with run durations from 5 to 240 min for four distinct starting materials. Chemical and isotopic equilibrium is achieved within 10 min of experimental outset. Zinc metal-silicate isotopic fractionation displays no resolvable dependence on temperature, composition, or oxygen fugacity within the data set. Therefore, the Zn isotopic composition of silicate phases can be used as a proxy for bulk telluric bodies. Partitioning results from this study and data from literature were used to robustly parameterize Zn metal-silicate partitioning as a function of temperature, pressure, and redox state. Using this parametric characterization and viable formation conditions, we have estimated a range of Zn contents in the cores of iron meteorite parent bodies (i.e. iron meteorites) of ∼0.1-150 ppm, in good agreement with natural observations. We have also calculated the first geochemical estimates for the Zn contents of the Earth's core and of the bulk Earth, at 242 ± 107 ppm and 114 ± 34 ppm (respectively), that consider the slightly siderophile behavior of Zn. These estimates of the Zn contents of the Earth's core and

  9. Development of flow cytometric protocol for nuclear DNA content estimation and determination of chromosome number in Pongamia pinnata L., a valuable biodiesel plant.

    Science.gov (United States)

    Ramesh, Aadi Moolam; Basak, Supriyo; Choudhury, Rimjhim Roy; Rangan, Latha

    2014-01-01

    The potentiality of Pongamia pinnata L. as a sustainable source of feedstock for the biodiesel industry is dependent on an extensive knowledge of the genome structure of the plant. Flow cytometry, with propidium iodide (PI) as the DNA stain, was used to estimate the nuclear DNA content of P. pinnata, with respect to Zea mays 'CE-777' as standard. The internal and pseudo-internal standardization was followed on account of the inhibitory effect of secondary compounds on PI intercalation. The antioxidants (PVP-40 and β-mercaptoethanol) were added to the nuclear isolation buffer for the reduction of inhibitory effect of P. pinnata cytosol. Nuclear DNA content estimation was done for P. pinnata leaves from different altitudes (37-117 m height from sea level) of Assam. Flow cytometry analysis indicated that the nuclear DNA content of P. pinnata is 2.66 pg with predicted 1C value of 1,300 Mb using Z. mays as standard. Coefficient of variation in flow cytometric analysis was within the limit of 5 % indicating that the results were reliable. Somatic chromosome numbers were counted from root-tip cells and was found to be 2n = 22 corresponding to the diploid level (x = 11). A decreasing trend in the nuclear DNA content was observed for the species of different altitudes.

  10. Effect of the exclusion of crustal ions (Ca2+, Mg 2+, and K+) in estimating water content of PM2.5 at polluted and clean areas

    Science.gov (United States)

    Lee, Hyung-Min; Kim, Yong Pyo

    2011-09-01

    Effect of the exclusion of crustal ions (Ca2+, Mg2+, and K+) in estimating water content of PM2.5 is investigated using a gas/aerosol equilibrium model, SCAPE 2 (Simulating Composition of Atmospheric Particles at Equilibrium 2), (Kim et al., 1993; Kim and Seinfeld, 1995; Meng et al., 1998), for the particles collected at polluted city, Seoul, and clean background offshore, Gosan, Korea. Measurement data show higher concentration of all inorganic species at Seoul, up to 5 times higher in average equivalent concentration especially for volatile species. At both sites there were sufficient equivalent fractions of t-NH3 (total ammonia = NH3+NH4+ to neutralize acidic species such as t-H2SO4 (total sulfuric acid = H2SO4+SO42-), t-HNO3 (total nitric acid = HNO3+NO3-) and t-HCl (total hydrochloric acid = HCl+Cl-). t-NH3 and t-HNO3 were higher at Seoul while t-H2SO4 was higher at Gosan. With respect to the estimated water content differences between with and without crustal ions, all the samples are classified into 3 cases; increased, decreased, and constant water content. We identified that change in inorganic composition contributes to increase of water content for aqueous aerosols. And those inorganic compositions vary differently according to ambient atmospheric composition. Meanwhile, aerosol phase shifting from the aqueous to solid phase is the main contributor to decrease of water content and binary salt composition change in the solid phase appears as no change of water content.

  11. Use of Water Content Reflectometers in Bioinfiltration/Bioretention to Measure Water Movement and Estimate Evapotranspiration - abstract

    Science.gov (United States)

    Most bioinfiltration/bioretention models assume runoff is evenly distributed across the surface area and after the engineered fill media is no longer saturated, the volumetric water content (VWC) is constant throughout the media profile and at field capacity. Four to nine water ...

  12. 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

  13. The impact of vertical measurement depth on the information content of soil moisture for latent heat flux estimation

    Science.gov (United States)

    Using ground-based soil moisture and latent/sensible heat fluxes observations acquired from the Ameriflux Network, we calculate the mutual information (MI) content between multiple soil moisture variables and evaporative fraction (EF) to examine the existence of information in vertically-integrated ...

  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

    Background Water is present in all human body. Healthy tissues encompass an intricate balance of water inside cells and extracellular matrix. Disease can cause this relation to be altered. It has been published that MR technology is able to measure water content, but no quantitative method has be...

  15. In vitro and In vivo Antioxidant Evaluation and Estimation of Total Phenolic, Flavonoidal Content of Mimosa pudica L

    Science.gov (United States)

    Patro, Ganesh; Bhattamisra, Subrat Kumar; Mohanty, Bijay Kumar; Sahoo, Himanshu Bhusan

    2016-01-01

    Objective: Mimosa pudica Linn. (Mimosaceae) is traditionally used as a folk medicine to treat various ailments including convulsions, alopecia, diarrhea, dysentery, insomnia, tumor, wound healing, snake bite, etc., Here, the study was aimed to evaluate the antioxidant potential of M. pudica leaves extract against 2, 2-diphenyl-1-picrylhydrazyl (DPPH) (in vitro) and its modulatory effect on rat brain enzymes. Materials and Methods: Total phenolic, flavonoid contents, and in vitro antioxidant potential against DPPH radical were evaluated from various extracts of M. pudica leaves. In addition, ethyl acetate extract of Mimosa pudica leaves (EAMP) in doses of 100, 200, and 400 mg/kg/day were administered orally for 7 consecutive days to albino rats and evaluated for the oxidative stress markers as thiobarbituric acid reactive substances (TBARS), superoxide dismutase (SOD), catalase (CAT), and glutathione (GSH) from rat brain homogenate. Results: The ethyl acetate extract showed the highest total phenolic content and total flavonoid content among other extracts of M. pudica leaves. The percentage inhibition and IC50 value of all the extracts were followed dose-dependency and found significant (P pudica exhibits both in vitro antioxidant activity against DPPH and in vivo antioxidant activity by modulating brain enzymes in the rat. This could be further correlated with its potential to neuroprotective activity due to the presence of flavonoids and phenolic contents in the extract. SUMMARY Total phenolic, flavonoid contents and in-vitro antioxidant potential were evaluated from various extracts of M. pudica leaves. Again, in-vivo antioxidant evaluation from brain homogenate on oxidative stress markers as TBARS, SOD, CAT and GSH from rat was investigated. Our findings revealed that M. pudica possesses both in-vitro and in-vivo antioxidant activity due to presence of phenolics and flavonoids. PMID:26941532

  16. In vitro and In vivo Antioxidant Evaluation and Estimation of Total Phenolic, Flavonoidal Content of Mimosa pudica L.

    Science.gov (United States)

    Patro, Ganesh; Bhattamisra, Subrat Kumar; Mohanty, Bijay Kumar; Sahoo, Himanshu Bhusan

    2016-01-01

    Mimosa pudica Linn. (Mimosaceae) is traditionally used as a folk medicine to treat various ailments including convulsions, alopecia, diarrhea, dysentery, insomnia, tumor, wound healing, snake bite, etc., Here, the study was aimed to evaluate the antioxidant potential of M. pudica leaves extract against 2, 2-diphenyl-1-picrylhydrazyl (DPPH) (in vitro) and its modulatory effect on rat brain enzymes. Total phenolic, flavonoid contents, and in vitro antioxidant potential against DPPH radical were evaluated from various extracts of M. pudica leaves. In addition, ethyl acetate extract of Mimosa pudica leaves (EAMP) in doses of 100, 200, and 400 mg/kg/day were administered orally for 7 consecutive days to albino rats and evaluated for the oxidative stress markers as thiobarbituric acid reactive substances (TBARS), superoxide dismutase (SOD), catalase (CAT), and glutathione (GSH) from rat brain homogenate. The ethyl acetate extract showed the highest total phenolic content and total flavonoid content among other extracts of M. pudica leaves. The percentage inhibition and IC50 value of all the extracts were followed dose-dependency and found significant (P pudica exhibits both in vitro antioxidant activity against DPPH and in vivo antioxidant activity by modulating brain enzymes in the rat. This could be further correlated with its potential to neuroprotective activity due to the presence of flavonoids and phenolic contents in the extract. Total phenolic, flavonoid contents and in-vitro antioxidant potential were evaluated from various extracts of M. pudica leaves. Again, in-vivo antioxidant evaluation from brain homogenate on oxidative stress markers as TBARS, SOD, CAT and GSH from rat was investigated. Our findings revealed that M. pudica possesses both in-vitro and in-vivo antioxidant activity due to presence of phenolics and flavonoids.

  17. 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.

  18. Estimation of Heterosis, Combining ability and Gene action in Pigeonpea [Cajanus cajan (L. Millsp.

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    Yamanura,, *Lokesha R., Dharmaraj, P.S., Muniswamy, S. and Diwan, J.R.

    2014-06-01

    Full Text Available Eight cytoplasmic-genetic male sterile lines with A2 (Cajanus scarabaeoides and A4 (Cajanus cajanifolius cytoplasm were crossed with 10 testers in a line × tester design. Resultant 80 experimental hybrids were evaluated along with parents and check (Maruti in lattice design with two replications. Combining ability analysis evinced predominance of non-additive gene effects for 10 characters indicating relevance of heterosis breeding for improving yield attributes. The gca effects of parents revealed that ICPA-2078, GT-308A, PKV-TATA, ARCCV-2 and GPHR-08-11 were good general combiners for seed yield and its direct components. The estimates of sca effects revealed that nine experimental hybrids had significant, desirable and positive sca effects for seed yield. The cross combination ICPA-2092 x VIPUL, ICPA-2078 x BSMR-856 and ICPA-2078 x ARCCV-2 were good specific combiners for number of secondary branches, number of pods per plant, seed yield per plant. These parental combinations are being used for exploitation of hybrid vigour.

  19. Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks.

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    Ricardo de Matos Simoes

    Full Text Available The inference of gene regulatory networks from gene expression data is a difficult problem because the performance of the inference algorithms depends on a multitude of different factors. In this paper we study two of these. First, we investigate the influence of discrete mutual information (MI estimators on the global and local network inference performance of the C3NET algorithm. More precisely, we study 4 different MI estimators (Empirical, Miller-Madow, Shrink and Schürmann-Grassberger in combination with 3 discretization methods (equal frequency, equal width and global equal width discretization. We observe the best global and local inference performance of C3NET for the Miller-Madow estimator with an equal width discretization. Second, our numerical analysis can be considered as a systems approach because we simulate gene expression data from an underlying gene regulatory network, instead of making a distributional assumption to sample thereof. We demonstrate that despite the popularity of the latter approach, which is the traditional way of studying MI estimators, this is in fact not supported by simulated and biological expression data because of their heterogeneity. Hence, our study provides guidance for an efficient design of a simulation study in the context of network inference, supporting a systems approach.

  20. Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks.

    Science.gov (United States)

    de Matos Simoes, Ricardo; Emmert-Streib, Frank

    2011-01-01

    The inference of gene regulatory networks from gene expression data is a difficult problem because the performance of the inference algorithms depends on a multitude of different factors. In this paper we study two of these. First, we investigate the influence of discrete mutual information (MI) estimators on the global and local network inference performance of the C3NET algorithm. More precisely, we study 4 different MI estimators (Empirical, Miller-Madow, Shrink and Schürmann-Grassberger) in combination with 3 discretization methods (equal frequency, equal width and global equal width discretization). We observe the best global and local inference performance of C3NET for the Miller-Madow estimator with an equal width discretization. Second, our numerical analysis can be considered as a systems approach because we simulate gene expression data from an underlying gene regulatory network, instead of making a distributional assumption to sample thereof. We demonstrate that despite the popularity of the latter approach, which is the traditional way of studying MI estimators, this is in fact not supported by simulated and biological expression data because of their heterogeneity. Hence, our study provides guidance for an efficient design of a simulation study in the context of network inference, supporting a systems approach.

  1. The Beta-Binomial Distribution for Estimating the Number of False Rejections in Microarray Gene Expression Studies.

    Science.gov (United States)

    Hunt, Daniel L; Cheng, Cheng; Pounds, Stanley

    2009-03-15

    In differential expression analysis of microarray data, it is common to assume independence among null hypotheses (and thus gene expression levels). The independence assumption implies that the number of false rejections V follows a binomial distribution and leads to an estimator of the empirical false discovery rate (eFDR). The number of false rejections V is modeled with the beta-binomial distribution. An estimator of the beta-binomial false discovery rate (bbFDR) is then derived. This approach accounts for how the correlation among non-differentially expressed genes influences the distribution of V. Permutations are used to generate the observed values for V under the null hypotheses and a beta-binomial distribution is fit to the values of V. The bbFDR estimator is compared to the eFDR estimator in simulation studies of correlated non-differentially expressed genes and is found to outperform the eFDR for certain scenarios. As an example, this method is also used to perform an analysis that compares the gene expression of soft tissue sarcoma samples to normal tissue samples.

  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

    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......-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...... 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...

  3. 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

  4. In vitro and In vivo Antioxidant evaluation and estimation of total phenolic, flavonoidal content of Mimosa pudica L

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    Ganesh Patro

    2016-01-01

    Full Text Available Objective: Mimosa pudica Linn. (Mimosaceae is traditionally used as a folk medicine to treat various ailments including convulsions, alopecia, diarrhea, dysentery, insomnia, tumor, wound healing, snake bite, etc., Here, the study was aimed to evaluate the antioxidant potential of M. pudica leaves extract against 2, 2-diphenyl-1-picrylhydrazyl (DPPH (in vitro and its modulatory effect on rat brain enzymes. Materials and Methods: Total phenolic, flavonoid contents, and in vitro antioxidant potential against DPPH radical were evaluated from various extracts of M. pudica leaves. In addition, ethyl acetate extract of Mimosa pudica leaves (EAMP in doses of 100, 200, and 400 mg/kg/day were administered orally for 7 consecutive days to albino rats and evaluated for the oxidative stress markers as thiobarbituric acid reactive substances (TBARS, superoxide dismutase (SOD, catalase (CAT, and glutathione (GSH from rat brain homogenate. Results: The ethyl acetate extract showed the highest total phenolic content and total flavonoid content among other extracts of M. pudica leaves. The percentage inhibition and IC 50 value of all the extracts were followed dose-dependency and found significant (P < 0.01 as compared to standard (ascorbic acid. The oxidative stress markers as SOD, CAT, and GSH were increased significantly (P < 0.01 at 200 and 400 mg/kg of EAMP treated animals and decreased significantly the TBARS level at 400 mg/kg of EAMP as compared to control group. Conclusion: These results revealed that the ethyl acetate extract of M. pudica exhibits both in vitro antioxidant activity against DPPH and in vivo antioxidant activity by modulating brain enzymes in the rat. This could be further correlated with its potential to neuroprotective activity due to the presence of flavonoids and phenolic contents in the extract.

  5. Estimating dispersal and gene flow in the neotropical freshwater turtle Hydromedusa maximiliani (Chelidae by combining ecological and genetic methods

    Directory of Open Access Journals (Sweden)

    Souza Franco L.

    2002-01-01

    Full Text Available Hydromedusa maximiliani is a vulnerable neotropical freshwater turtle endemic to mountainous regions of the Atlantic rainforest in southeastern Brazil. Random amplified polymorphic DNA (RAPD was used to estimate the gene flow and dispersal for individuals inhabiting rivers and streams within a drainage. Nine primers generated 27 scoreable bands, of which 9 (33% were polymorphic and produced 12 RAPD phenotypes. The gene flow estimates (Nm among turtles inhabiting different rivers and streams were variable, ranging from 0.09 to 3.00 (mean: 0.60. For some loci, the rates of gene flow could offset population differentiation (Nm > 1, whereas for others random genetic drift could result in population divergence (Nm < 1. Since the genetic variation of this turtle seems to be structured according to the natural hierarchical system of rivers and streams within drainages, management programs involving translocations between different regions across the geographical range of H. maximiliani should be viewed with caution.

  6. Down-regulation of glycosyltransferase 8D genes in Populus trichocarpa caused reduced mechanical strength and xylan content in wood.

    Science.gov (United States)

    Li, Quanzi; Min, Douyong; Wang, Jack Peng-Yu; Peszlen, Ilona; Horvath, Laszlo; Horvath, Balazs; Nishimura, Yufuko; Jameel, Hasan; Chang, Hou-Min; Chiang, Vincent L

    2011-02-01

    Members of glycosyltransferase protein families GT8, GT43 and GT47 are implicated in the biosynthesis of xylan in the secondary cell walls of Arabidopsis. The Arabidopsis mutant irx8 has a 60% reduction in xylan. However, over-expression of an ortholog of Arabidopsis IRX8, poplar PoGT8D, in Arabidopsis irx8 mutant could not restore xylan synthesis. The functions of tree GT8D genes remain unclear. We identified two GT8 gene homologs, PtrGT8D1 and PtrGT8D2, in Populus trichocarpa. They are the only two GT8D members and are abundantly and specifically expressed in the differentiating xylem of P. trichocarpa. PtrGT8D1 transcript abundance was >7 times that of PtrGT8D2. To elucidate the genetic function of GT8D in P. trichocarpa, the expression of PtrGT8D1 and PtrGT8D2 was simultaneously knocked down through RNAi. Four transgenic lines had 85-94% reduction in transcripts of PtrGT8D1 and PtrGT8D2, resulting in 29-36% reduction in stem wood xylan content. Xylan reduction had essentially no effect on cellulose quantity but caused an 11-25% increase in lignin. These transgenics exhibit a brittle wood phenotype, accompanied by increased vessel diameter and thinner fiber cell walls in stem xylem. Stem modulus of elasticity and modulus of rupture were reduced by 17-29% and 16-23%, respectively, and were positively correlated with xylan content but negatively correlated with lignin quantity. These results suggest that PtrGT8Ds play key roles in xylan biosynthesis in wood. Xylan may be a more important factor than lignin affecting the stiffness and fracture strength of wood.

  7. 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...

  8. 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...

  9. 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…

  10. Comparative Genomics of cpn60-Defined Enterococcus hirae Ecotypes and Relationship of Gene Content Differences to Competitive Fitness.

    Science.gov (United States)

    Katyal, Isha; Chaban, Bonnie; Hill, Janet E

    2016-11-01

    Natural microbial communities undergo selection-driven succession with changes in environmental conditions and available nutrients. In a previous study of the pig faecal Enterococcus community, we demonstrated that cpn60 universal target (UT) sequences could resolve phenotypically and genotypically distinct ecotypes of Enterococcus spp. that emerged over time in the faecal microbiome of growing pigs. In this study, we characterized genomic diversity in the identified Enterococcus hirae ecotypes in order to define further the nature and degree of genome content differences between taxa resolved by cpn60 UT sequences. Genome sequences for six representative isolates (two from each of three ecotypes) were compared. Differences in phosphotransferase systems and amino acid metabolism pathways for glutamine, proline and selenocysteine were observed. Differences in the lac family phosphotransferase system corresponded to lactose utilization phenotypes of the isolates. Competitive fitness of the E. hirae ecotypes was evaluated by in vitro growth competition assays in pig faecal extract medium. Isolates from E. hirae-1 and E. hirae-2 ecotypes were able to out-compete isolates from the E. hirae-3 ecotype, consistent with the relatively low abundance of E. hirae-3 relative to E. hirae-1 and E. hirae-2 previously observed in the pig faecal microbiome, and with observed differences between the ecotypes in gene content related to biosynthetic capacity. Results of this study provide a genomic basis for the definition of ecotypes within E. hirae and confirm the utility of the cpn60 UT sequence for high-resolution profiling of complex microbial communities.

  11. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position.

    Science.gov (United States)

    Sueoka, N

    1999-09-30

    The genome of higher eukaryotes consists of genes having a widely heterogeneous base composition at the third codon position. Ubiquitous variability of the DNA base composition has the following two aspects: intragenomic heterogeneity of the G+C content and the amino-acid-specific translation-coupled biases from the Parity Rule 2 (PR2). PR2 is an intrastrand rule where A = T and G = C are expected if there is no bias in mutation and selection between the two complementary strands of DNA. To examine whether or not the biases from PR2 are responsible for the wide heterogeneity of the DNA G+C content in human, the third codon position of 846 human genes was analyzed. Genes were separated into six groups according to their G+C content of the third codon position, and each group was examined for the translation-coupled PR2 biases in the nucleotide composition of the third codon position for two- and four-codon amino acids. The results show that genes in the different G+C content groups have similar PR2 biases, indicating that the intragenomic heterogeneity of the G+C content is not correlated with translation-coupled biases from the PR2. Therefore, the heterogeneity of the G+C content is likely to be determined by some other mechanism (e.g. locally variable directional mutation pressures) than amino-acid-specific selections for the codon preference.

  12. Using seed purity data to estimate an average pollen mediated gene flow from crops to wild relatives.

    Science.gov (United States)

    Lavigne, C; Klein, E K; Couvet, D

    2002-01-01

    Gene flow from crops to wild related species has been recently under focus in risk-assessment studies of the ecological consequences of growing transgenic crops. However, experimental studies addressing this question are usually temporally or spatially limited. Indirect population-structure approaches can provide more global estimates of gene flow, but their assumptions appear inappropriate in an agricultural context. In an attempt to help the committees providing advice on the release of transgenic crops, we present a new method to estimate the quantity of genes migrating from crops to populations of related wild plants by way of pollen dispersal. This method provides an average estimate at a landscape level. Its originality is based on the measure of the inverse gene flow, i.e. gene flow from the wild plants to the crop. Such gene flow results in an observed level of impurities from wild plants in crop seeds. This level of impurity is usually known by the seed producers and, in any case, its measure is easier than a direct screen of wild populations because crop seeds are abundant and their genetic profile is known. By assuming that wild and cultivated plants have a similar individual pollen dispersal function, we infer the level of pollen-mediated gene flow from a crop to the surrounding wild populations from this observed level of impurity. We present an example for sugar beet data. Results suggest that under conditions of seed production in France (isolation distance of 1,000 m) wild beets produce high numbers of seeds fathered by cultivated plants.

  13. Where genes meet environment-integrating the role of gut luminal contents, immunity and pancreas in type 1 diabetes.

    Science.gov (United States)

    Scott, Fraser W; Pound, Lynley D; Patrick, Christopher; Eberhard, Chandra E; Crookshank, Jennifer A

    2017-01-01

    The rise in new cases of type 1 diabetes (T1D) in genetically susceptible individuals over the past half century has been attributed to numerous environmental "triggers" or promoters such as enteroviruses, diet, and most recently, gut bacteria. No single cause has been identified in humans, likely because there are several pathways by which one can develop T1D. There is renewed attention to the role of the gut and its immune system in T1D pathogenesis based largely on recent animal studies demonstrating that altering the gut microbiota affects diabetes incidence. Although T1D patients display dysbiosis in the gut microbiome, it is unclear whether this is cause or effect. The heart of this question involves several moving parts including numerous risk genes, diet, viruses, gut microbiota, timing, and loss of immune tolerance to β-cells. Most clinical trials have addressed only one aspect of this puzzle using some form of immune suppression, without much success. The key location where our genes meet and deal with the environment is the gastrointestinal tract. The influence of all of its major contents, including microbes, diet, and immune system, must be understood as part of the integrative biology of T1D before we can develop durable means of preventing, treating, or curing this disease. In the present review, we expand our previous gut-centric model based on recent developments in the field. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. [CDS cloning and relationship between intramuscular fat content and mRNA expression of PID1 gene in pig].

    Science.gov (United States)

    Qian, Yuan; Zeng, Yong-Qing; Du, Jin-Fang; Cui, Jing-Xiang; Li, Hua; Chen, Qi-Mei; Song, Yi-Ping; Chen, Wei

    2010-11-01

    To explore the relationship between the expression of PID1 gene and fat deposition, we cloned CDS of PID1 from porcine fat and muscle tissues by RT-PCR using degenerate primers, and investigated expression of this gene in various tissues (i.e., liver, backfat, and muscle tissues) of different breeds (i.e., Yorkshire, Laiwu, and Lulai Black) by real-time fluorescence quantitative PCR. The results showed that 654 bp CDS of porcine PID1 was obtained by sequencing and was 93.88%, 66.94% and 88.07% identical to those of the human, rat, and Bos taurus, respectively. The expression of PID1 mRNA in various tissues and breeds, on the whole, tended to be liver > fat > muscle and Laiwu > Lulai Black > Yorkshire, respectively. For different breeds, PID1 mRNA abundance in liver had significant difference (P 0.05). For the three groups of Laiwu pigs with high (LWH), intermediate (LWI), and low IMF content (LWL), PID1 mRNA level was higher in liver tissue of LWH than that of LWL significantly (P PID1 mRNA abundance was not correlated with IMF in these three tissues of Laiwu breed, but it was positively correlated with IMF in the tissues of these three breeds (P PID1 may be related to fat deposition.

  15. 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

    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...

  16. Estimating and mapping chlorophyll content for a heterogeneous grassland: Comparing prediction power of a suite of vegetation indices across scales between years

    Science.gov (United States)

    Tong, Alexander; He, Yuhong

    2017-04-01

    This study investigates the performance of existing vegetation indices for retrieving chlorophyll content for a semi-arid mixed grass prairie ecosystem across scales using in situ data collected in 2012 and 2013. A 144 published broadband (21) and narrowband (123) vegetation indices are evaluated to estimate chlorophyll content. Results indicate that narrowband indices utilize reflectance data from one or more wavelengths in the red-edge region (∼690-750 nm) perform better. Broadband indices are found to be as effective as narrowband indices for chlorophyll content estimation at both leaf and canopy scales. The empirical relationships are generally stronger at the canopy than the leaf scale, attributable to the fact that leaf samples are collected during the peak growing season when chlorophyll in plant species are uniform. SPOT-5 and CASI-550 derived chlorophyll maps result in map accuracies of 63.56% and 78.88% respectively. The assessment of vegetation chlorophylls at the canopy level, especially using remote sensing imagery is important for providing information pertaining to ecosystem health such as the physiological status, productivity, or phenology of vegetation.

  17. Estimation of soil water repellency of different particle size fractions in relation with carbon content by different methods.

    Science.gov (United States)

    Rodríguez-Alleres, María; de Blas, Esther; Benito, Elena

    2007-05-25

    The water repellency of soils with different texture under different types of plant cover was determined by applying the WDPT and MED methods to both whole samples and the following size fractions: 2-1, 1-0.5, 0.5-0.25, 0.25-0.05 and water repellency in the finest fraction (<0.05 mm) as a result of its higher organic carbon content. On the other hand, all fractions in the forest soils, which were extremely water repellent, contributed to the overall repellency; in any case, the MED test revealed that the finest fraction was strongly repellent in the forest soils as well.

  18. Heavy metal content in edible salts in Isfahan and estimation of their daily intake via salt consumption

    Directory of Open Access Journals (Sweden)

    Hajar Pourgheysari

    2012-01-01

    Conclusions: There was a significant difference between the heavy metal concentrations and their guideline values. Estimation of the health risk due to heavy metals was not possible as PTWI showed total intake of a metal by total food consumption during a week. Therefore, it was important to assess the public health risks arising from the presence of these toxic contaminants in the foods consumed by the population of Iran.

  19. Organ- and Growing Stage-Specific Expression of Solanesol Biosynthesis Genes in Nicotiana tabacum Reveals Their Association with Solanesol Content

    Directory of Open Access Journals (Sweden)

    Ning Yan

    2016-11-01

    Full Text Available Solanesol is a noncyclic terpene alcohol that is composed of nine isoprene units and mainly accumulates in solanaceous plants, especially tobacco (Nicotiana tabacum L.. In the present study, RNA-seq analyses of tobacco leaves, stems, and roots were used to identify putative solanesol biosynthesis genes. Six 1-deoxy-d-xylulose 5-phosphate synthase (DXS, two 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR, two 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase (IspD, four 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase (IspE, two 2-C-methyl-d-erythritol 2,4-cyclo-diphosphate synthase (IspF, four 1-hydroxy-2-methyl-2-(E-butenyl 4-diphosphate synthase (IspG, two 1-hydroxy-2-methyl-2-(E-butenyl 4-diphosphate reductase (IspH, six isopentenyl diphosphate isomerase (IPI, and two solanesyl diphosphate synthase (SPS candidate genes were identified in the solanesol biosynthetic pathway. Furthermore, the two N. tabacum SPS proteins (NtSPS1 and NtSPS2, which possessed two conserved aspartate-rich DDxxD domains, were highly homologous with SPS enzymes from other solanaceous plant species. In addition, the solanesol contents of three organs and of leaves from four growing stages of tobacco plants corresponded with the distribution of chlorophyll. Our findings provide a comprehensive evaluation of the correlation between the expression of different biosynthesis genes and the accumulation of solanesol, thus providing valuable insight into the regulation of solanesol biosynthesis in tobacco.

  20. Coastal soil clay content estimation using reflectance spectroscopy%反射光谱估算滨海土壤黏粒含量

    Institute of Scientific and Technical Information of China (English)

    焦彩霞; 郑光辉; 赏刚; 孙东敏

    2016-01-01

    Clay content is an important soil property that affects the structure, nutrient supply and other characteristics of soils. Variations in clay content can indicate the degree of soil development or soil age. In traditional chemical analyses of soil properties, the extractant interacts in the solution and at the solution-particle interface, thus altering the equilibrium between the soil solid and solution phases. Soil reflectance spectroscopy has been developed as an effective alternative method of measuring soil properties primarily because it requires minimal sample preparation and it is fast, cost-effective, non-destructive and non-hazardous to the soil. In recent decades, research on the use of reflectance spectroscopy in soil science has achieved rapid advances. Reflectance spectroscopy can be successfully applied to estimate the soil clay content. However, the mechanisms of soil clay content estimation using reflectance spectroscopy are not very clear. The goals of this study were to identify the bands within the range of 360-2490 nm that can be used to estimate the clay content and explore the mechanisms of the clay content estimation using reflectance spectroscopy. A total of 150 coastal soil samples were collected. The soil reflectance spectra were measured in a dark room using a FieldSpec 3 portable spectrometer. Raw spectral data were pre-processed by smoothing (R) and then by first derivative (FD), continuum removal (CR) or reciprocal transformation (DS). Calibration (75 soil samples) and validation datasets (75 soil samples) were obtained from 1,000 random selections of the data. Stepwise multiple linear regression (SMLR) and partial least squares regression (PLSR) were performed to estimate the soil clay content and to further identify the bands useful for modeling this parameter. The results indicated that the SMLR analysis of CR and R spectra and the PLSR analysis of R and FD spectra were characterized by good calibration and validation accuracies

  1. Seed-Specific Expression of a Lysine-Rich Protein Gene, GhLRP, from Cotton Significantly Increases the Lysine Content in Maize Seeds

    Directory of Open Access Journals (Sweden)

    Jing Yue

    2014-03-01

    Full Text Available Maize seed storage proteins are a major source of human and livestock consumption. However, these proteins have poor nutritional value, because they are deficient in lysine and tryptophan. Much research has been done to elevate the lysine content by reducing zein content or regulating the activities of key enzymes in lysine metabolism. Using the naturally lysine-rich protein genes, sb401 and SBgLR, from potato, we previously increased the lysine and protein contents of maize seeds. Here, we examined another natural lysine-rich protein gene, GhLRP, from cotton, which increased the lysine content of transgenic maize seeds at levels varying from 16.2% to 65.0% relative to the wild-type. The total protein content was not distinctly different, except in the six transgenic lines. The lipid and starch levels did not differ substantially in Gossypium hirsutum L. lysine-rich protein (GhLRP transgenic kernels when compared to wild-type. The agronomic characteristics of all the transgenic maize were also normal. GhLRP is a high-lysine protein candidate gene for increasing the lysine content of maize. This study provided a valuable model system for improving maize lysine content.

  2. Seed-specific expression of a lysine-rich protein gene, GhLRP, from cotton significantly increases the lysine content in maize seeds.

    Science.gov (United States)

    Yue, Jing; Li, Cong; Zhao, Qian; Zhu, Dengyun; Yu, Jingjuan

    2014-03-27

    Maize seed storage proteins are a major source of human and livestock consumption. However, these proteins have poor nutritional value, because they are deficient in lysine and tryptophan. Much research has been done to elevate the lysine content by reducing zein content or regulating the activities of key enzymes in lysine metabolism. Using the naturally lysine-rich protein genes, sb401 and SBgLR, from potato, we previously increased the lysine and protein contents of maize seeds. Here, we examined another natural lysine-rich protein gene, GhLRP, from cotton, which increased the lysine content of transgenic maize seeds at levels varying from 16.2% to 65.0% relative to the wild-type. The total protein content was not distinctly different, except in the six transgenic lines. The lipid and starch levels did not differ substantially in Gossypium hirsutum L. lysine-rich protein (GhLRP) transgenic kernels when compared to wild-type. The agronomic characteristics of all the transgenic maize were also normal. GhLRP is a high-lysine protein candidate gene for increasing the lysine content of maize. This study provided a valuable model system for improving maize lysine content.

  3. On the influence of the diurnal variations of aerosol content to estimate direct aerosol radiative forcing using MODIS data

    Science.gov (United States)

    Xu, Hui; Guo, Jianping; Ceamanos, Xavier; Roujean, Jean-Louis; Min, Min; Carrer, Dominique

    2016-09-01

    Long-term measurements of aerosol optical depth (AOD) from the Aerosol Robotic Network (AERONET) located in Beijing reveal a strong diurnal cycle of aerosol load staged by seasonal patterns. Such pronounced variability is matter of importance in respect to the estimation of daily averaged direct aerosol radiative forcing (DARF). Polar-orbiting satellites could only offer a daily revisit, which turns in fact to be even much less in case of frequent cloudiness. Indeed, this places a severe limit to properly capture the diurnal variations of AOD and thus estimate daily DARF. Bearing this in mind, the objective of the present study is however to evaluate the impact of AOD diurnal variations for conducting quantitative assessment of DARF using Moderate Resolution Imaging Spectroradiometer (MODIS) AOD data over Beijing. We provide assessments of DARF with two different assumptions about diurnal AOD variability: taking the observed hourly-averaged AOD cycle into account and assuming constant MODIS (including Terra and Aqua) AOD value throughout the daytime. Due to the AOD diurnal variability, the absolute differences in annual daily mean DARFs, if the constant MODIS/Terra (MODIS/Aqua) AOD value is used instead of accounting for the observed hourly-averaged daily variability, is 1.2 (1.3) Wm-2 at the top of the atmosphere, 27.5 (30.6) Wm-2 at the surface, and 26.4 (29.3) Wm-2 in the atmosphere, respectively. During the summertime, the impact of the diurnal AOD variability on seasonal daily mean DARF estimates using MODIS Terra (Aqua) data can reach up to 2.2 (3.9) Wm-2 at the top of the atmosphere, 43.7 (72.7) Wm-2 at the surface, and 41.4 (68.8) Wm-2 in the atmosphere, respectively. Overall, the diurnal variation in AOD tends to cause large bias in the estimated DARF on both seasonal and annual scales. In summertime, the higher the surface albedo, the stronger impact on DARF at the top of the atmosphere caused by dust and biomass burning (continental) aerosol. This

  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. 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.

  6. Effects of sorghum [Sorghum bicolor (L.) Moench] crude extracts on starch digestibility, Estimated Glycemic Index (EGI), and Resistant Starch (Rs) contents of porridges.

    Science.gov (United States)

    Lemlioglu-Austin, Dilek; Turner, Nancy D; McDonough, Cassandra M; Rooney, Lloyd W

    2012-09-17

    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.

  7. 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.

  8. 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.

  9. Does physical activity in adolescence have site-specific and sex-specific benefits on young adult bone size, content, and estimated strength?

    Science.gov (United States)

    Duckham, Rachel L; Baxter-Jones, Adam D G; Johnston, James D; Vatanparast, Hassanali; Cooper, David; Kontulainen, Saija

    2014-02-01

    The long-term benefits of habitual physical activity during adolescence on adult bone structure and strength are poorly understood. We investigated whether physically active adolescents had greater bone size, density, content, and estimated bone strength in young adulthood when compared to their peers who were inactive during adolescence. Peripheral quantitative computed tomography (pQCT) was used to measure the tibia and radius of 122 (73 females) participants (age mean ± SD, 29.3 ± 2.3 years) of the Saskatchewan Pediatric Bone Mineral Accrual Study (PBMAS). Total bone area (ToA), cortical density (CoD), cortical area (CoA), cortical content (CoC), and estimated bone strength in torsion (SSIp ) and muscle area (MuA) were measured at the diaphyses (66% tibia and 65% radius). Total density (ToD), trabecular density (TrD), trabecular content (TrC), and estimated bone strength in compression (BSIc ) were measured at the distal ends (4%). Participants were grouped by their adolescent physical activity (PA) levels (inactive, average, and active) based on mean PA Z-scores obtained from serial questionnaire assessments completed during adolescence. We compared adult bone outcomes across adolescent PA groups in each sex using analysis of covariance followed by post hoc pairwise comparisons with Bonferroni adjustments. When adjusted for adult height, MuA, and PA, adult males who were more physically active than their peers in adolescence had 13% greater adjusted torsional bone strength (SSIp , p adolescence had 10% larger adjusted CoA (p adolescence seemed to persist into young adulthood, with greater ToA and SSIp in males, and greater CoA, CoC, and TrC in females.

  10. 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.

  11. 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.

  12. ESTIMATION OF pH, TOTAL ACID AND ETHANOL CONTENT OF COMMERCIALLY AVAILABLE ALCOHOL-CONTAINING MOUTHWASHES AND ITS EFFECT ON SALIVARY pH

    Directory of Open Access Journals (Sweden)

    Rafi Shaik

    2017-07-01

    Full Text Available 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 and ethanol content was estimated. 48 subjects were randomly divided into 8 groups. Unstimulated salivary samples were collected before rinsing, then subjects were asked to rinse with 10 mL mouthwash for 60 seconds and salivary samples were collected immediately after rinsing. Salivary pH before and after rinsing was estimated using digital pH meter. RESULTS Listerine original mouthwash was found to have lowest pH (3.84 and highest acid content (26.8%. High alcohol content was seen in Listerine fresh burst mouthwash (26%. Mean salivary pH before and after rinsing showed a significant difference among all the groups with highest mean salivary pH difference for Listerine fresh burst mouthwash (1.21. Post-hoc Turkey’s analysis to compare the change in mean salivary pH between study groups showed a significant difference between Listerine original, Listerine fresh burst and Listerine cool mint mouthwash with other mouthwashes. CONCLUSION There was a significant reduction in salivary pH after rinsing with low pH, high acid and high alcohol-containing mouthwashes.

  13. 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.

  14. 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.

  15. Relation of fat-mass and obesity-associated gene polymorphism to fat mass content and body mass index in obese children.

    Science.gov (United States)

    Pyrzak, Beata; Wisniewska, Alicja; Majcher, Anna; Tysarowski, Andrzej; Demkow, Urszula

    2013-01-01

    Fat mass content, fat distribution, and fat-mass and obesity associated (FTO) gene have been reported among a broad spectrum of genetic variation connected with body weight. The aim of our study was to investigate whether the T/A rs9939609 polymorphism of the FTO gene may influence obesity and metabolic indices in children. A 160 children were examined (136 obese and 24 non-obese). The anthropometric measurements and calculations included: height, weight, waist and hip circumference, sum of the thickness of 3 and 10 skin folds, % of fat content, % FAT- BIA , % LBM-BIA. BMI, SDS of BMI, WHR, and WHtR. Fasting plasma total cholesterol (TC), HDL and LDL-cholesterol, triglycerides (TG), oral glucose tolerance test (OGTT), and HOMA-IR were analyzed and the blood pressure were measured. The rs9939609 polymorphism of FTO gene was genotyped by allele-specific real-time polymerase chain- reaction (RT-PCR). We found that the mean concentrations of TC, TG, LDLC, and HOMA-IR were significantly higher, and HDL was lower in the obese than in non-obese children. The presence of TT, but not AA alleles, related to the percentage of fat content, BMI, and z-score of BMI. None of the other anthropometric indices did differ between the children with gene polymorphism and wild homozygous. In conclusion, rs9939609 polymorphism in the fat-mass and obesity-associated gene is associated with BMI and the percent of fat content in children.

  16. Effect of fluorescence characteristics and different algorithms on the estimation of leaf nitrogen content based on laser-induced fluorescence lidar in paddy rice.

    Science.gov (United States)

    Yang, Jian; Sun, Jia; Du, Lin; Chen, Biwu; Zhang, Zhenbing; Shi, Shuo; Gong, Wei

    2017-02-20

    Paddy rice is one of the most significant food sources and an important part of the ecosystem. Thus, accurate monitoring of paddy rice growth is highly necessary. Leaf nitrogen content (LNC) serves as a crucial indicator of growth status of paddy rice and determines the dose of nitrogen (N) fertilizer to be used. This study aims to compare the predictive ability of the fluorescence spectra excited by different excitation wavelengths (EWs) combined with traditional multivariate analysis algorithms, such as principal component analysis (PCA), back-propagation neural network (BPNN), and support vector machine (SVM), for estimating paddy rice LNC from the leaf level with three different fluorescence characteristics as input variables. Then, six estimation models were proposed. Compared with the five other models, PCA-BPNN was the most suitable model for the estimation of LNC by improving R2 and reducing RMSE and RE. For 355, 460 and 556 nm EWs, R2 was 0.89, 0.80 and 0.88, respectively. Experimental results demonstrated that the fluorescence spectra excited by 355 and 556 nm EWs were superior to those excited by 460 nm for the estimation of LNC with different models. BPNN algorithm combined with PCA may provide a helpful exploratory and predictive tool for fluorescence spectra excited by appropriate EW based on practical application requirements for monitoring the N status of crops.

  17. Feasibility analysis of using inverse modeling for estimating field-scale evapotranspiration in maize and soybean fields from soil water content monitoring networks

    Science.gov (United States)

    Foolad, Foad; Franz, Trenton E.; Wang, Tiejun; Gibson, Justin; Kilic, Ayse; Allen, Richard G.; Suyker, Andrew

    2017-03-01

    In this study, the feasibility of using inverse vadose zone modeling for estimating field-scale actual evapotranspiration (ETa) was explored at a long-term agricultural monitoring site in eastern Nebraska. Data from both point-scale soil water content (SWC) sensors and the area-average technique of cosmic-ray neutron probes were evaluated against independent ETa estimates from a co-located eddy covariance tower. While this methodology has been successfully used for estimates of groundwater recharge, it was essential to assess the performance of other components of the water balance such as ETa. In light of recent evaluations of land surface models (LSMs), independent estimates of hydrologic state variables and fluxes are critically needed benchmarks. The results here indicate reasonable estimates of daily and annual ETa from the point sensors, but with highly varied soil hydraulic function parameterizations due to local soil texture variability. The results of multiple soil hydraulic parameterizations leading to equally good ETa estimates is consistent with the hydrological principle of equifinality. While this study focused on one particular site, the framework can be easily applied to other SWC monitoring networks across the globe. The value-added products of groundwater recharge and ETa flux from the SWC monitoring networks will provide additional and more robust benchmarks for the validation of LSM that continues to improve their forecast skill. In addition, the value-added products of groundwater recharge and ETa often have more direct impacts on societal decision-making than SWC alone. Water flux impacts human decision-making from policies on the long-term management of groundwater resources (recharge), to yield forecasts (ETa), and to optimal irrigation scheduling (ETa). Illustrating the societal benefits of SWC monitoring is critical to insure the continued operation and expansion of these public datasets.

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

    Directory of Open Access Journals (Sweden)

    Kaas Rolf S

    2012-10-01

    Full Text Available Abstract 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 of the 186 sequenced E. coli genomes. The core-gene tree displays high confidence and divides the E. coli strains into the observed MLST type clades and also separates defined phylotypes. Conclusion The results of comparing a large and diverse E. coli dataset support the theory that reliable and good resolution phylogenies can be inferred from the core-genome. The results further suggest that the resolution at the isolate level may, subsequently be improved by targeting more variable genes. The use of whole genome sequencing will make it possible to eliminate, or at least reduce, the need for several typing steps used in traditional epidemiology.

  19. Application Fourier transform near infrared spectrometer in rapid estimation of soluble solids content of intact citrus fruits

    Institute of Scientific and Technical Information of China (English)

    LU Hui-shan; XU Hui-rong; YING Yi-bin; FU Xia-ping; YU Hai-yan; TIAN Hai-qing

    2006-01-01

    Nondestructive method of measuring soluble solids content (SSC) of citrus fruits was developed using Fourier transform near infrared reflectance (FT-NIR) measurements collected through optics fiber. The models describing the relationship between SSC and the NIR spectra of citrus fruits were developed and evaluated. Different spectra correction algorithms (standard normal variate (SNV), multiplicative signal correction (MSC)) were used in this study. The relationship between laboratory SSC and FT-NIR spectra of citrus fruits was analyzed via principle component regression (PCR) and partial least squares (PLS) regression method. Models based on the different spectral ranges were compared in this research. The first derivative and second derivative were applied to all spectra to reduce the effects of sample size, light scattering, instrument noise, etc. Different baseline correction methods were applied to improve the spectral data quality. Among them the second derivative method after baseline correction produced best noise removing capability and yielded optimal calibration models. A total of 170 NIR spectra were acquired; 135 NIR spectra were used to develop the calibration model; the remaining spectra were used to validate the model. The developed PLS model describing the relationship between SSC and NIR reflectance spectra could predict SSC of 35 samples with correlation coefficient of 0.995 and RMSEP of 0.79°Brix.

  20. The ascorbic acid content of tomato fruits is associated with the expression of genes involved in pectin degradation

    Directory of Open Access Journals (Sweden)

    Di Matteo Antonio

    2010-08-01

    Full Text Available Abstract Background High levels of ascorbic acid (AsA in tomato fruits provide health benefits for humans and also play an important role in several aspects of plant life. Although AsA metabolism has been characterized in detail, the genetic mechanisms controlling AsA accumulation in tomatoes are poorly understood. The transcriptional control of AsA levels in fruits can be investigated by combining the advanced genetic and genomic resources currently available for tomato. A comparative transcriptomic analysis of fruit tissues was carried out on an introgression line containing a QTL promoting AsA accumulation in the fruit, using a parental cultivar with lower AsA levels as a reference. Results Introgression line IL 12-4 (S. pennellii in a S. lycopersicum background was selected for transcriptomic analysis because it maintained differences in AsA levels compared to the parental genotypes M82 and S. pennellii over three consecutive trials. Comparative microarray analysis of IL 12-4 and M82 fruits over a 2-year period allowed 253 differentially-expressed genes to be identified, suggesting that AsA accumulation in IL 12-4 may be caused by a combination of increased metabolic flux and reduced utilization of AsA. In particular, the upregulation of a pectinesterase and two polygalacturonases suggests that AsA accumulation in IL12-4 fruit is mainly achieved by increasing flux through the L-galactonic acid pathway, which is driven by pectin degradation and may be triggered by ethylene. Conclusions Based on functional annotation, gene ontology classification and hierarchical clustering, a subset of the 253 differentially-expressed transcripts was used to develop a model to explain the higher AsA content in IL 12-4 fruits in terms of metabolic flux, precursor availability, demand for antioxidants, abundance of reactive oxygen species and ethylene signaling.

  1. Revisiting the diffusion approximation to estimate evolutionary rates of gene family diversification.

    Science.gov (United States)

    Gjini, Erida; Haydon, Daniel T; David Barry, J; Cobbold, Christina A

    2014-01-21

    Genetic diversity in multigene families is shaped by multiple processes, including gene conversion and point mutation. Because multi-gene families are involved in crucial traits of organisms, quantifying the rates of their genetic diversification is important. With increasing availability of genomic data, there is a growing need for quantitative approaches that integrate the molecular evolution of gene families with their higher-scale function. In this study, we integrate a stochastic simulation framework with population genetics theory, namely the diffusion approximation, to investigate the dynamics of genetic diversification in a gene family. Duplicated genes can diverge and encode new functions as a result of point mutation, and become more similar through gene conversion. To model the evolution of pairwise identity in a multigene family, we first consider all conversion and mutation events in a discrete manner, keeping track of their details and times of occurrence; second we consider only the infinitesimal effect of these processes on pairwise identity accounting for random sampling of genes and positions. The purely stochastic approach is closer to biological reality and is based on many explicit parameters, such as conversion tract length and family size, but is more challenging analytically. The population genetics approach is an approximation accounting implicitly for point mutation and gene conversion, only in terms of per-site average probabilities. Comparison of these two approaches across a range of parameter combinations reveals that they are not entirely equivalent, but that for certain relevant regimes they do match. As an application of this modelling framework, we consider the distribution of nucleotide identity among VSG genes of African trypanosomes, representing the most prominent example of a multi-gene family mediating parasite antigenic variation and within-host immune evasion. © 2013 Published by Elsevier Ltd. All rights reserved.

  2. 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.

  3. Evaluation of Modeling Schemes to Estimate Evapotranspiration and Root Zone Soil Water Content over Vineyard using a Scintillometer and Remotely Sensed Surface Energy Balance

    Science.gov (United States)

    Geli, H. M. E.; Gonzalez-Piqueras, J.; Isidro, C., Sr.

    2016-12-01

    Actual crop evapotranspiration (ETa) and root zone soil water content (SMC) are key operational variable to monitor water consumption and water stress condition for improve vineyard grapes productivity and quality. This analysis, evaluates the estimation of ETa and SMC based on two modeling approaches. The first approach is a hybrid model that couples a thermal-based two source energy balance (TSEB) model (Norman et al. 1995) and water balance model to estimate the two variable (Geli 2012). The second approach is based on Large Aperture Scintillometer (LAS)-based estimates of sensible heat flux. The LAS-based estimates of sensible heat fluxes were used to calculate latent heat flux as the residual of surface energy balance equation on hourly basis which was converted to daily ETa. The calculated ETa from the scintillometer was then couple with the water balance approach to provide updated ETa_LAS and SMC_LAS. Both estimates of ETa and SMC based on LAS (i.e. ETa_LAS and SMC_LAS) and TSEB (ETa_TSEB and SMC_TSEB) were compared with ground-based observation from eddy covariance and soil water content measurements at multiple depths. The study site is an irrigated vineyard located in Central Spain Primary with heterogeneous surface conditions in term of irrigation practices and the ground based observation over the vineyard were collected during the summer of 2007. Preliminary results of the inter-comparison of the two approaches suggests relatively good between both modeling approaches and ground-based observations with RMSE lower than 1.2 mm/day for ETa and lower than 20% for SMC. References Norman, J. M., Kustas, W. P., & Humes, K. S. (1995). A two-source approach for estimating soil and vegetation energy fluxes in observations of directional radiometric surface temperature. Agricultural and Forest Meteorology, 77, 263293. Geli, Hatim M. E. (2012). Modeling spatial surface energy fluxes of agricultural and riparian vegetation using remote sensing, Ph. D. dissertation

  4. Application of near-infrared reflectance spectroscopy for the estimation of protein and L-canavanine contents in seeds of one-flowered vetch (Vicia articulate Hornem.)

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez Vioque, R.; Rodriguez Conde, M. F.; Mozos Pascual, M. de los

    2009-07-01

    In this work it has been evaluated the effectiveness of near-infrared reflectance spectroscopy (NIRS) for the estimation of two constituents affecting the nutritional quality of the seeds of one-flowered vetch (Vicia articulate Hornem.): protein and L-canavanine, a toxic non-protein amino acid. The NIRS calibrations showed good statistics with coefficients of multiple determination (R{sup 2}) of 0.97 for total protein and 0.95 for L-canavanine. The developed equations were further used to estimate the contents of protein and L-canavanine of a set of unknown samples (external validation). The equation for total protein was able to predict with an accuracy similar to that of the reference method showing a correlation (r{sup 2}) between the reference and predicted values of 0.95. In the case of L-canavanine, r{sup 2} was only 0.72 and the equation was only effective to discriminate samples into groups of low, medium and high contents. (Author) 20 refs.

  5. 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 de