Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes     

Kalodimos CG  Biris N  Bonvin AM  Levandoski MM  Guennuegues M  Boelens R  Kaptein R 《Science (New York, N.Y.)》2004,305(5682):386-389

Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding domain with nonspecific DNA. The same set of residues can switch roles from a purely electrostatic interaction with the DNA backbone in the nonspecific complex to a highly specific binding mode with the base pairs of the cognate operator sequence. The protein-DNA interface of the nonspecific complex is flexible on biologically relevant time scales that may assist in the rapid and efficient finding of the target site.  相似文献   

Effects of crop density and tillage system on grain yield and N uptake from soil and atmosphere of sole and intercropped pea and oat   总被引：1，自引：0，他引：1  

Angelika Neumann  Knut Schmidtke  Rolf Rauber 《Field Crops Research》2007,100(2-3):285-293

Pea (Pisum sativum L.) and oat (Avena sativa L.) were grown as sole and mixed crops in various densities under two different tillage systems on a loess soil near Göttingen/Germany in a 2-year field experiment (2002/2003). In the conventional tillage system a mouldboard plough (CT) was used and in the minimum tillage system a rotary harrow (MT) was employed. The effect of crop density and tillage system on the grain dry matter and grain N yields, N₂ fixation and soil N uptake were determined to address the following questions: (i) which mixture compositions exhibit the highest grain yields compared to the sole crops, (ii) which mixture compositions also fix a high level of N₂ and leave low levels of residual inorganic soil N after harvest, and (iii) whether the intercrop advantage is influenced by the tillage system. For (i) the result in 2002 showed that the highest grain yields of both sole cropped pea and oat and intercropped pea and oat were achieved at the highest densities. In 2003, when the inorganic soil N content was higher and weather conditions were warmer and drier, grain yields were significantly higher than in 2002, but sole as well as intercropped pea and oat gave their highest grain yields at lower densities. For both years and tillage systems, the highest intercrop advantages were achieved in mixtures with densities above the optimal sole crop densities. The result for (ii) was that a distinctly higher proportion of nitrogen was derived from the atmosphere (Ndfa) by intercropped pea than by sole cropped pea. However, the uptake of soil N by intercropped pea and oat was not reduced in comparison with that of sole cropped oat as the decrease in the uptake of N from the soil by oat at lower oat densities in the mixture was compensated for by the soil N uptake of pea. Additionally, the N_min-N content of the soil following the mixtures and sole cropped oat did not differ, especially in the deeper soil layers because oat in mixture was forced to take up more soil N from deeper layers. Therefore, the risk of soil N losses through leaching after mixtures was lower compared to sole cropped pea. The tillage system (iii) had no significant influence on grain yield and soil N uptake, but N₂ fixation and the competitive ability of intercropped pea were higher under CT than with MT. An additional result was that intercropping led to a significantly increased grain N content of both pea and oat compared to the sole crops. The increase in grain N content from sole to intercrop was from 3.30 to 3.42% for pea and from 1.73 to 1.96% for oat as a mean for both years and tillage systems. The present study confirms that growing pea and oat as intercrops highlights potential economic and environmental benefits which still need to be understood in more detail in order to exploit intercropping to a greater extent.  相似文献   

Nitrogen mineralization from mature bio‐waste compost in vineyard soils. III Simulation of soil mineral‐nitrogen dynamics     

Claas Nendel  Kurt‐Christian Kersebaum  Rolf Nieder  Roland Kubiak 《植物养料与土壤学杂志》2007,170(5):598-607

A model for nitrogen (N) dynamics in compost‐amended vineyard soils was tested for its predictive power. A soil–mineral N data set from a 3‐year field study on four different vineyard sites was used for model evaluation. The soils were treated with mature bio‐waste compost (30 and 50 Mg ha^–1 fresh matter, respectively). The model calculated soil mineral‐N contents at all sites with an overall mean bias error of –2.2 kg N ha^–1 for layers of 0.1 m thickness and an overall mean absolute error of 7.4 kg N ha^–1 layer^–1. Modeling efficiencies for the simulations of the respective treatments ranged from –0.05 to 0.41, and Willmott's Index of Agreement showed values of between 0.41 and 0.81. Acceptable model predictions as defined by the observed variability of mineral‐N contents in the respective soils ranged from 40% to 72%. A strong increase in soil mineral‐N concentration following the compost application at all sites could not be reproduced with the model, thereby reducing the prediction accuracy significantly. The model performance confirms that previously derived N‐mineralization parameters are suitable to describe the N release from soil‐applied mature bio‐waste compost under the environmental conditions of vineyards in Germany.  相似文献   

Delayed harvest of reed canary grass translocates more nutrients in rhizomes     

Dr Shaojun Xiong  Staffan Landström  Rolf Olsson 《Acta Agriculturae Scandinavica, Section B - Plant Soil Science》2013,63(4):306-316

Abstract

Two field experiments, one in large plots and the other in small framed plots, were conducted in Umeå, northern Sweden. The objectives were (1) to examine the seasonal patterns of rhizome growth and nutrient dynamics of the energy crop reed canary grass (Phalaris arundinacea L.) in ley I and II, and (2) to evaluate the roles of soil type (mineral vs. organic), fertilisation level (0, 50, and 100 kg N ha^?1s), and season/harvest time (Oct-96, May-97, and Aug-97) on the rhizome growth and nutrient dynamics by means of a factorially designed experiment. The general pattern of rhizome growth was that biomass was low in June during initiation of shoot growth, but increased steadily during the growing season, reached a peak in late autumn, and remained high until next spring. The N and P accumulation in rhizomes followed a similar pattern. During ley years I and II, reed canary grass rhizome growth was less dependent on soil type, and more dependent on fertilisation and season, with fertilisation being the most important predictor of growth. The season/harvest time, followed by soil type, was the most important factor for both concentrations and therefore total uptake of N, P, and K in rhizomes. Soil type affected N content in rhizomes significantly, and also interacted with season and enhanced the effect on N, P, and K content in rhizomes. The seasonal dynamics of the nutrient content in rhizomes indicate a remobilisation of the nutrients from rhizomes to the regrowth of shoots and roots in spring and relocation/storage from aboveground shoots to rhizomes during late summer and autumn. The results of this study suggest that delaying the harvest to later than October would result in considerably more energy and nutrient resources being translocated from aboveground shoots to rhizomes for growth in the next season.  相似文献   

APS8, a Polymeric Alkylpyridinium Salt Blocks α7 nAChR and Induces Apoptosis in Non-Small Cell Lung Carcinoma     

Ana Zovko  Kristina Viktorsson  Rolf Lewensohn  Katja Kolo?a  Metka Filipi?  Hong Xing  William R. Kem  Laura Paleari  Tom Turk 《Marine drugs》2013,11(7):2574-2594

Naturally occurring 3-alkylpyridinium polymers (poly-APS) from the marine sponge Reniera sarai, consisting of monomers containing polar pyridinium and nonpolar alkyl chain moieties, have been demonstrated to exert a wide range of biological activities, including a selective cytotoxicity against non-small cell lung cancer (NSCLC) cells. APS8, an analog of poly-APS with defined alkyl chain length and molecular size, non-competitively inhibits α7 nicotinic acetylcholine receptors (nAChRs) at nanomolar concentrations that are too low to be acetylcholinesterase (AChE) inhibitory or generally cytotoxic. In the present study we show that APS8 inhibits NSCLC tumor cell growth and activates apoptotic pathways. APS8 was not toxic for normal lung fibroblasts. Furthermore, in NSCLC cells, APS8 reduced the adverse anti-apoptotic, proliferative effects of nicotine. Our results suggest that APS8 or similar compounds might be considered as lead compounds to develop antitumor therapeutic agents for at least certain types of lung cancer.  相似文献   

PRODUCT DEVELOPMENT IN AQUACULTURE: DEDUCING PRODUCT FORM FROM PRODUCT CLASS INFORMATION     

Tor Korneliussen  Stig Ingebrigtsen  Rolf Volden 《Aquaculture Economics & Management (Blackwell Science)》2013,17(3):213-221

Marketing scholars argue that product development should begin by examining the needs and wants of consumers, but what should product developers do when consumers are not able to express their needs and wants for a new product? To overcome this problem, we propose and test a model using consumers' product class information to deduce preferences for a product form. It is shown that this application can help firms get a handle on the problem of consumers not being able to articulate their needs and wants for a new product.  相似文献   

Genotypes and phenotypes of an <Emphasis Type="Italic">ex situ</Emphasis><Emphasis Type="Italic">Vitis vinifera</Emphasis> ssp. <Emphasis Type="Italic">sylvestris</Emphasis> (Gmel.) Beger germplasm collection from the Upper Rhine Valley     

Susanne Barth  Astrid Forneck  Fabienne Verzeletti  Rolf Blaich  Fritz Schumann 《Genetic Resources and Crop Evolution》2009,56(8):1171-1181

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Influence of fertilization, mulch color, early forcing, fruit order, planting date, shading, growing Environment, and genotype on the contents of selected phenolics in strawberry (Fragaria x ananassa Duch.) fruits     

Anttonen MJ  Hoppula KI  Nestby R  Verheul MJ  Karjalainen RO 《Journal of agricultural and food chemistry》2006,54(7):2614-2620

The influence of agricultural practices (fertilization, mulch color, early forcing, and planting date), environment (light and growing area), cultivar, and fruit order on the selected phenolic content and antioxidant activity in strawberry (Fragaria x ananassa Duch.) fruits was studied. Three different levels of fertilization were given to plants in the fertilization experiment. The lowest fertilization level increased the contents of flavonols and ellagic acid from 19 to 57%. Between cultivars, up to 4-fold differences were found in the flavonol content, and it also varied according to growing environment. Planting date in glasshouse production was important for the phenolic content, and a statistically significant interaction was found between planting date and fruit order. Fruit order caused at highest 1.5-2.0-fold differences in the contents of phenolics. Interestingly, compared with other phenolics, anthocyanins were affected differently by many factors. Thus, the findings show that minor cultivation changes can increase the content of phenolics, especially in under-glass production where conditions can be easily manipulated.  相似文献   

GOAnnotator: linking protein GO annotations to evidence text     

Francisco M Couto  Mário J Silva  Vivian Lee  Emily Dimmer  Evelyn Camon  Rolf Apweiler  Harald Kirsch  Dietrich Rebholz-Schuhmann 《Journal of Biomedical Discovery and Collaboration》2006,1(1):19

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Association mapping of quality traits in potato (Solanum tuberosum L.)   总被引：3，自引：1，他引：2  

Björn B. D’hoop  Maria João Paulo  Rolf A. Mank  Herman J. van Eck  Fred A. van Eeuwijk 《Euphytica》2008,161(1-2):47-60

In this paper, we describe the assessment of linkage disequilibrium and its decay in a collection of potato cultivars. In addition, we report on a simple regression based association mapping approach and its results to quality traits in potato. We selected 221 tetraploid potato cultivars and progenitor lines, representing the global diversity in potato, with emphasis on genetic variation for agro-morphological and quality traits. Phenotypic data for these agro-morphological and quality traits were obtained from recent trials performed by five breeding companies. The collection was genotyped with 250 AFLP^® markers from five primer combinations. The genetic position of a subset of the markers could be inferred from an ultra dense potato map. Decay of linkage disequilibrium was estimated by calculating the squared correlation between pairs of markers using marker band intensities. Marker-trait associations were investigated by fitting single marker regression models for phenotypic traits on marker band intensities with and without correction for population structure. The paper illustrates the potential of association mapping in tetraploid potato, because existing phenotypic data, a modest number of AFLP markers, and a relatively simple statistical analysis, allowed identifying interesting associations.  相似文献