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Abdelrahman, H. M., Olk, D. C., Dinnes, D., Ventrella, D., Miano, T., & Cocozza, C. (2016). Occurrence and abundance of carbohydrates and amino compounds in sequentially extracted labile soil organic matter fractions. Journal of Soils and Sediments, 16(10), 2375–2384.
Abstract: Purpose The study aimed to describe the carbohydrates and amino compounds content in soil, the light fraction (LF), the >53 μm particulate organic matter (POM), and the mobile humic acid (MHA) fraction and to find out whether the carbohydrates and amino compounds can be used to explain the origin of SOM fractions. Materials and methods Soil samples were collected from two agricultural fields managed under organic farming in southern Italy. The LF, the POM, and the MHA were sequentially extracted from each soil sample then characterized. Seven neutral sugars and 19 amino compounds (amino acids and amino sugars) were determined in each soil sample and its correspondent fractions. Results and discussion The MHA contained less carbohydrate than the LF or the POM but its carbohydrates, although dominated by arabinose, were relatively with larger microbial contribution as revealed by the mannose/xylose ratio. The amino compounds were generally less in the LF or the POM than in the MHA, while the fungal (aspartic and serine) and bacterial (alanine and glycine) amino acids were larger in the MHA than in the LF or the POM, underlining the microbial contribution to the MHA. Results from both sites indicated that total carbohydrates content decreased moving from the LF (younger fraction) to the MHA (older fraction), which seems to follow a decomposition continuum of organic matter in the soil-plant system. Conclusions The study showed that the MHA is a labile humified fraction of soil C due to its content of carbohydrates and concluded that the content of carbohydrates and amino compounds in the LF, the POM and the MHA can depict the nature of these fractions and their cycling pattern and response to land management.
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Van Oijen, M., & Höglind, M. (2016). Toward a Bayesian procedure for using process-based models in plant breeding, with application to ideotype design. Euphytica, 207(3), 627–643.
Abstract: Process-based grassland models (PBMs) simulate growth and development of vegetation over time. The models tend to have a large number of parameters that represent properties of the plants. To simulate different cultivars of the same species, different parameter values are required. Parameter differences may be interpreted as genetic variation for plant traits. Despite this natural connection between PBMs and plant genetics, there are only few examples of successful use of PBMs in plant breeding. Here we present a new procedure by which PBMs can help design ideotypes, i.e. virtual cultivars that optimally combine properties of existing cultivars. Ideotypes constitute selection targets for breeding. The procedure consists of four steps: (1) Bayesian calibration of model parameters using data from cultivar trials, (2) Estimating genetic variation for parameters from the combination of cultivar-specific calibrated parameter distributions, (3) Identifying parameter combinations that meet breeding objectives, (4) Translating model results to practice, i.e. interpreting parameters in terms of practical selection criteria. We show an application of the procedure to timothy (Phleum pratense L.) as grown in different regions of Norway.
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Brylińska, M., Sobkowiak, S., Stefańczyk, E., & Śliwka, J. (2016). Potato cultivation system affects population structure of Phytophthora infestans. Fungal Ecology, 20, 132–143.
Abstract: Phytophthora infestans is one of the most destructive potato pathogens. Many factors influence the population structure of P. infestans, including migration, climate and type of potato cultivation. Here, we analyse 365 P. infestans isolates collected from three regions of Poland over three years. We determined mating type, mitochondrial haplotype, resistance to metalaxyl, virulence and polymorphism at 14 simple sequence repeat (SSR) loci. Analysis of SSR markers showed high genetic diversity associated with this population. Model-based structure analysis grouped 299 unique genotypes into four main clusters. The P. infestans isolates collected from the Mlochow region, which has the most intensive level of potato cultivation, formed a distinct cluster, indicating a strong effect of the cultivation system on pathogen population structure. Three clusters contained isolates with frequent presence of three alleles at one locus, which may affect their capacity for sexual reproduction and preserve groups of fit genotypes that propagate asexually. (C) 2016 Elsevier Ltd and The British Mycological Society.
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Vitali, A., Lana, E., Amadori, M., Bernabucci, U., Nardone, A., & Lacetera, N. (2014). Analysis of factors associated with mortality of heavy slaughter pigs during transport and lairage. J. Anim. Sci., 92(11), 5134–5141.
Abstract: The study was based on data collected during 5 yr (2003-2007) and was aimed at assessing the effects of the month, slaughter house of destination (differing for stocking density, openings, brightness, and cooling device types), length of the journey, and temperature-humidity index (THI) on mortality of heavy slaughter pigs (approximately 160 kg live weight) during transport and lairage. Data were obtained from 24,098 journeys and 3,676,153 pigs transported from 1,618 farms to 3 slaughter houses. Individual shipments were the unit of observation. The terms dead on arrival (DOA) and dead in pen (DIP) refer to pigs that died during transport and in lairage at the abattoir before slaughtering, respectively. These 2 variables were assessed as the dependent counts in separate univariate Poisson regressions. The independent variables assessed univariately in each set of regressions were month of shipment, slaughter house of destination, time traveled, and each combination of the month with the time traveled. Two separate piecewise regressions were done. One used DOA counts within THI levels over pigs transported as a dependent ratio and the second used DIP counts within THI levels over pigs from a transport kept in lairage as a dependent ratio. The THI was the sole independent variable in each case. The month with the greatest frequency of deaths was July with a risk ratio of 1.22 (confidence interval: 1.06-1.36; P < 0.05) and 1.27 (confidence interval: 1.06-1.51; P < 0.05) for DOA and DIP, respectively. The lower mortality risk ratios for DOA and DIP were recorded for January and March (P < 0.05). The aggregated data of the summer (June, July, and August) versus non-summer (January, March, September, and November) months showed a greater risk of pigs dying during the hot season when considering both transport and lairage (P < 0.05). The mortality risk ratio of DIP was lower at the slaughter house with the lowest stocking density (0.64 m(2)/100 kg live weight), large open windows on the roof and sidewalls, low brightness (40 lx) lights, and high-pressure sprinklers as cooling devices. The mortality risk ratio of DOA increased significantly for journeys longer than 2 h, whereas no relationship was found between length of transport and DIP. The piecewise analysis pointed out that 78.5 and 73.6 THI were the thresholds above which the mortality rate increased significantly for DOA and DIP, respectively. These results may help the pig industry to improve the welfare of heavy slaughter pigs during transport and lairage.
Keywords: Abattoirs/*statistics & numerical data; Animals; *Data Interpretation, Statistical; Humidity/adverse effects; Light/adverse effects; *Mortality; Retrospective Studies; Seasons; Swine/*physiology; Temperature; Time Factors; Transportation/*statistics & numerical data; lairage; mortality; pigs; temperature-humidity index; transport
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Van Oosten, M. J., Sharkhuu, A., Batelli, G., Bressan, R. A., & Maggio, A. (2013). The Arabidopsis thaliana mutant air1 implicates SOS3 in the regulation of anthocyanins under salt stress. Plant Mol. Biol., 83(4-5), 405–415.
Abstract: The accumulation of anthocyanins in plants exposed to salt stress has been largely documented. However, the functional link and regulatory components underlying the biosynthesis of these molecules during exposure to stress are largely unknown. In a screen of second site suppressors of the salt overly sensitive3-1 (sos3-1) mutant, we isolated the anthocyanin-impaired-response-1 (air1) mutant. air1 is unable to accumulate anthocyanins under salt stress, a key phenotype of sos3-1 under high NaCl levels (120 mM). The air1 mutant showed a defect in anthocyanin production in response to salt stress but not to other stresses such as high light, low phosphorous, high temperature or drought stress. This specificity indicated that air1 mutation did not affect anthocyanin biosynthesis but rather its regulation in response to salt stress. Analysis of this mutant revealed a T-DNA insertion at the first exon of an Arabidopsis thaliana gene encoding for a basic region-leucine zipper transcription factor. air1 mutants displayed higher survival rates compared to wild-type in oxidative stress conditions, and presented an altered expression of anthocyanin biosynthetic genes such as F3H, F3’H and LDOX in salt stress conditions. The results presented here indicate that AIR1 is involved in the regulation of various steps of the flavonoid and anthocyanin accumulation pathways and is itself regulated by the salt-stress response signalling machinery. The discovery and characterization of AIR1 opens avenues to dissect the connections between abiotic stress and accumulation of antioxidants in the form of flavonoids and anthocyanins.
Keywords: Anthocyanins/analysis/*metabolism; Arabidopsis/drug effects/*genetics/physiology/radiation effects; Arabidopsis Proteins/*genetics/metabolism; Basic-Leucine Zipper Transcription Factors/*genetics/metabolism; Flavonoids/metabolism; *Gene Expression Regulation, Plant; Light; Mutagenesis, Insertional; Phenotype; Plant Roots/drug effects/genetics/physiology/radiation effects; Plant Shoots/drug effects/genetics/physiology/radiation effects; Real-Time Polymerase Chain Reaction; Sodium Chloride/pharmacology; Stress, Physiological
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