The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes

Background  

High quality annotation of the genes and transposable elements in complex genomes requires a human-curated integration of multiple sources of computational evidence. These evidences include results from a diversity of ab initio prediction programs as well as homology-based searches. Most of these programs operate on a single contiguous sequence at a time, and the results are generated in a diverse array of readable formats that must be translated to a standardized file format. These translated results must then be concatenated into a single source, and then presented in an integrated form for human curation.     

Chemical and physical changes in milk protein concentrate (MPC80) powder during storage

The solubility and chemical changes due to the Maillard reaction were investigated in milk protein concentrate powder containing 80% protein (MPC80) during storage at temperatures and relative humidities in the ranges of 25-40 °C and 44-84%, respectively. The Maillard reaction was studied by measuring furosine (a product of lactosylated protein after digestion with acid) and free hydroxymethylfurfural (HMF) contents by HPLC and L*, a*, b* values with a color-meter. Furosine, free HMF, and browning in MPC80 increased during storage, whereas the solubility decreased. The correlation between the Maillard reaction and solubility loss was explored in modified MPC80 to which glucose was added to enhance the rate of the Maillard reaction. More furosine and brown pigments were observed in the glucose-containing MPC80 than in MPC80 with added lactose. The opposite trend occurred for solubility, suggesting that the Maillard reaction may be a cause of solubility loss in MPC powder.     

土壤持水特性参数与土壤质地尺度关系的联合多重分形分析

Soil water-retention characteristics at measurement scales are generally different from those at application scales, and there is scale disparity between them and soil physical properties. The relationships between two water-retention parameters, the scaling parameter related to the inverse of the air-entry pressure (αvG, cm-1) and the curve shape factor related to soil pore-size distribution (n) of the van Genuchten water-retention equation, and soil texture (sand, silt, and clay contents) were examined at multiple scales. One hundred twenty-eight undisturbed soil samples were collected from a 640-m transect located in Fuxin, China. Soil water-retention curves were measured and the van Genuchten parameters were obtained by curve fitting. The relationships between the two parameters and soil texture at the observed scale and at multiple scales were evaluated using Pearson correlation and joint multifractal analyses, respectively. The results of Pearson correlation analysis showed that the parameter αvG was significantly correlated with sand, silt, and clay contents at the observed scale. Joint multifractal analyses, however, indicated that the parameter αvG was not correlated with silt and sand contents at multiple scales. The parameter n was positively correlated with clay content at multiple scales. Sand content was significantly correlated with the parameter n at the observed scale but not at multiple scales. Clay contents were strongly correlated to both water-retention parameters because clay content was relatively low in the soil studied, indicating that water retention was dominated by clay content in the field of this study at all scales. These suggested that multiple-scale analyses were necessary to fully grasp the spatial variability of soil water-retention characteristics.     

Determination of chlorate and chlorite and mutagenicity of seafood treated with aqueous chlorine dioxide.

The use of chlorine dioxide (ClO(2)) as a potential substitute for aqueous chlorine to improve the quality of seafood products has not been approved by regulatory agencies due to health concerns related to the production of chlorite (ClO(2)(-)) and chlorate (ClO(3)(-)) as well as possible mutagenic/carcinogenic reaction products. Cubes of Atlantic salmon (Salmo salar) and red grouper (Epinephelus morio) were treated with 20 or 200 ppm aqueous chlorine or ClO(2) solutions for 5 min, and extracts of the treated fish cubes and test solutions were checked for mutagenicity using the Ames Salmonella/microsome assay. No mutagenic activity was detected in the treated fish samples or test solutions with ClO(2). Only the sample treated with 200 ppm chlorine showed weak mutagenic activity toward S. typhimurium TA 100. No chlorite residue was detected in sea scallops, mahi-mahi, or shrimp treated with ClO(2) at 3.9-34.9 ppm. However, low levels of chlorate residues were detected in some of the treated samples. In most cases, the increase in chlorate in treated seafood was time- and dose-related.     

Distribution and Phytoavailability of Lead in a Soil Contaminated with Lead Shot

Water, Air, &; Soil Pollution - This paper presents a study of Pb contamination of soil at a clay target shooting facility in Canterbury, New Zealand. The spatial distribution of Pb...     

DETERMINATION OF 14C IN SOIL BY A GEL SUSPENSION METHOD

Radioactivity in soils labelled with ¹⁴C was determined by suspending the finely ground soil in a thixotropic gel, dispersing it by ultrasonics and counting the dispersion in a liquid scintillation spectrometer. The relationship between the weight of sample and counting efficiency was found to be almost linear. Using 30 mg soil, the counting efficiency is 50 per cent and ¹⁴C may be determined with an average coefficient of variation of 1.5 per cent to within 5 per cent of the value determined by oxidative procedures.     

Stability of monoterpenes encapsulated in gum Arabic by spray-drying

Microencapsulation using spray-drying was tested with gum arabic and monoterpenes as wall and core materials, respectively. Citral, linalool, beta-myrcene, limonene, and beta-pinene were used at concentrations of 10, 20, and 30% with respect to the wall material. The greatest percentages of retention occurred at a concentration of 10%. Linalool and citral presented the greatest losses with increase in concentration. The hydrocarbons used were the most retained. Of the hydrocarbons, beta-pinene was better retained in the capsules than limonene, and beta-myrcene was the least retained of all. The capsules presented similar external morphologies, with no apparent cracks or porosity and an average size varying between 15.7 and 23.2 microm. The stability of the capsules to temperature was monitored for 33 days. The degradation products of the monoterpenes were evaluated. The results indicated a greater stability of the capsules containing beta-pinene and citral than of those containing linalool and beta-myrcene presenting the lowest retentions.     

Degradation of lignin in wheat straw during growth of the oyster mushroom (Pleurotus ostreatus) using off-line thermochemolysis with tetramethylammonium hydroxide and solid-state (13)C NMR.

The oyster mushroom (Pleurotus ostreatus) is widely cultivated on wheat straw (Triticum aestivum); however, there is a need to better understand the relationship between the chemical composition of the compost and mushroom growth. Wheat straw was degraded over a period of 63 days by P. ostreatus during which time it was sampled at weekly intervals. Off-line thermochemolysis with tetramethylammonium hydroxide and solid-state (13)C NMR were then used in the molecular characterization of the undegraded wheat straw and the degraded samples. The degraded wheat straw samples had a lower proportion of syringyl- to guaiacyl-derived moieties and cinnamyl- to guaiacyl-derived moieties than the undegraded control. There were increases in both guaiacyl and syringyl acid to aldehyde ratios with composting time, which showed that side-chain oxidation has been mediated by P. ostreatus. The (13)C NMR spectra confirmed the increase in carboxyl content but indicated that the overall lignin and methoxyl contents remained relatively constant, although some nonsystematic variations were observed. The spectra also showed a decrease in amorphous noncellulosic polysaccharides in relation to the crystalline cellulose upon degradation.     

Plant growth-rate dependence of detrital carbon storage in ecosystems

Detrital carbon accumulation accounts for most of an ecosystem's capacity to store organic carbon because the carbon contained as plant detritus exceeds that stored in living plants by about threefold. A comparative analysis of the mass and turnover of detrital carbon in ecosystems demonstrates that these properties are strongly related to the turnover rate of the dominant primary producers and are poorly related to ecosystem primary production. These results contribute to an understanding of the factors that control carbon storage in ecosystems and the role of carbon storage in the global carbon budget.     

New method for detecting cellular transforming genes

Tumor induction in athymic nude mice can be used to detect dominant transforming genes in cellular DNA. Mouse NIH 3T3 cells freshly transfected with either cloned Moloney sarcoma proviral DNA or cellular DNA's derived from virally transformed cells induced tumors when injected into athymic nu/nu mice. Tumors were also induced by cells transfected with DNA from two tumor-derived and one chemically transformed human cell lines. The mouse tumors induced by human cell line DNA's contained human DNA sequences, and DNA derived from these tumors was capable of inducing both tumors and foci on subsequent transfection. Tumor induction in nude mice represents a useful new method for the detection and selection of cells transformed by cellular oncogenes.