Docking of Antizyme to Ornithine Decarboxylase and Antizyme Inhibitor using Experimental Mutant and Double-Mutant Cycle Data

Antizyme (Az) is a highly conserved key regulatory protein bearing a major role in regulating polyamine levels in the cell. It has the ability to bind and inhibit ornithine decarboxylase (ODC), targeting it for degradation. Az inhibitor (AzI) impairs the activity of Az. In this study, we mapped the binding sites of ODC and AzI on Az using Ala scan mutagenesis and generated models of the two complexes by constrained computational docking. In order to scan a large number of mutants in a short time, we developed a workflow combining high-throughput mutagenesis, small-scale parallel partial purification of His-tagged proteins and their immobilization on a tris-nitrilotriacetic-acid-coated surface plasmon resonance chip. This combination of techniques resulted in a significant reduction in time for production and measurement of large numbers of mutant proteins. The data-driven docking results suggest that both proteins occupy the same binding site on Az, with Az binding within a large groove in AzI and ODC. However, single-mutant data provide information concerning the location of the binding sites only, not on their relative orientations. Therefore, we generated a large number of double-mutant cycles between residues on Az and ODC and used the resulting interaction energies to restrict docking. The model of the complex is well defined and accounts for the mutant data generated here, and previously determined biochemical data for this system. Insights on the structure and function of the complexes, as well as general aspects of the method, are discussed.     

Solanum Tuber-bearing Species Resistance Behavior Against Nacobbus aberrans

Naccobus aberrans is a major pest of the potato crop in the Andean regions of Argentina, Bolivia, and Perú. It is endemic in northwest Argentina and is also found in lowlands. The resistance of eleven Andean potato landraces and three accessions of the wild tuber-bearing species Solanum acaule, S. infundibuliforme, and S. megistacrolobum were evaluated against a population of N. aberrans from Coctaca, Jujuy province, while Solanum tuberosum ssp. tuberosum 'Spunta', 'Kennebec', and 'Frital INTA' were evaluated against a population from the southeast of Buenos Aires province. The presence, the number of galls, and the number of individuals were recorded. In addition, a reproduction factor was calculated and races were determined. Results showed that the N. aberrans population from Coctaca corresponded to race 2 and the population from the lowlands belonged to the sugar beet group. Landrace Azul, one genotype of S. megistacrolobum, and two genotypes of S. acaule showed resistance towards the race from Coctaca while no infection was recorded in potato cultivars with the Naccobus race from the lowland area.     

Evaluation of the sustainability of contrasted pig farming systems: breeding programmes

The sustainability of breeding activities in 15 pig farming systems in five European countries was evaluated. One conventional and two differentiated systems per country were studied. The Conventional systems were the standard systems in their countries. The differentiated systems were of three categories: Adapted Conventional with focus on animal welfare, meat quality or environment (five systems); Traditional with local breeds in small-scale production (three systems) and Organic (two systems). Data were collected with a questionnaire from nine breeding organisations providing animals and semen to the studied farming systems and from, on average, five farmers per farming system. The sustainability assessment of breeding activities was performed in four dimensions. The first dimension described whether the market for the product was well defined, and whether the breeding goal reflected the farming system and the farmers’ demands. The second dimension described recording and selection procedures, together with genetic change in traits that were important in the system. The third dimension described genetic variation, both within and between pig breeds. The fourth dimension described the management of the breeding organisation, including communication, transparency, and technical and human resources. The results show substantial differences in the sustainability of breeding activities, both between farming systems within the same category and between different categories of farming systems. The breeding activities are assessed to be more sustainable for conventional systems than for differentiated systems in three of the four dimensions. In most differentiated farming systems, breeding goals are not related to the system, as these systems use the same genetic material as conventional systems. The breeds used in Traditional farming systems are important for genetic biodiversity, but the small scale of these systems renders them vulnerable. It is hoped that, by reflecting on different aspects of sustainability, this study will encourage sustainable developments in pig production.     

红树林植物露兜树营养成分分析

本文对红树林植物露兜树的营养成分进行了分析,结果表明,露兜树中含有多种营养成分,丰富的矿质元素和维生素及其β-胡萝卜素。露兜树中至少含有17种氨基酸。旨在为开发利用植物资源提供科学依据。     

伊犁地区野生毛牛蒡和牛蒡的种群分布、生态和群落特性的研究

在充分踏察的基础上,选择具有代表性的样地,接线路调查法和样地调查法得出野生毛牛蒡和牛蒡种群的分布格局在伊犁地区总体上呈随机分布,占86．7％的调查样地;小范围内也有群聚分布的,占13．3％的调查样地;分布于喜光、低海拔、对土壤适应性高、生活力强等是牛蒡和毛牛蒡的生态习性;常与各类草本为伍,与菊科、禾本科、唇形科、藜科、蓼科、蒺藜科等常见科的植物均能共生于同一环境,是牛蒡和毛牛蒡的群落学特性;植被类型和人为因素是影响它们分布的环境因素。     

A stochastic bio-economic pig farm model to assess the impact of innovations on farm performance

Recently developed innovations may improve the economic and environmental sustainability of pig production systems. Generic models are needed to assess the impact of innovations on farm performance. Here we developed a stochastic bio-economic farm model for a typical farrow-to-finish pig farm to assess the impact of innovations on private and social profits. The model accounts for emissions of greenhouse gases from feed production and manure by using the shadow price of CO₂, and for stochasticity of economic and biological parameters. The model was applied to assess the impact of using locally produced alternative feed sources (i.e. co-products) in the diets of finishing pigs on private and social profits of a typical Brazilian farrow-to-finish pig farm. Three cases were defined: a reference case (with a standard corn–soybean meal-based finishing diet), a macaúba case (with a macaúba kernel cake-based finishing diet) and a co-products case (with a co-products-based finishing diet). Pigs were assumed to be fed to equal net energy intakes in the three cases. Social profits are 34% to 38% lower than private profits in the three cases. Private and social profits are about 11% and 14% higher for the macaúba case than the reference case, whereas they are 3% and 7% lower for the co-products case, respectively. Environmental costs are higher under the alternative cases than the reference case suggesting that other benefits (e.g. costs and land use) should be considered to utilize co-products. The CV of farm profits is between 75% and 87% in the three cases following from the volatility of prices over time and variations in biological parameters between fattening pigs.     

Nonmuscle Myosin-Dependent Synthesis of Type I Collagen

Type I collagen, synthesized in all tissues as the heterotrimer of two α1(I) polypeptides and one α2(I) polypeptide, is the most abundant protein in the human body. Here we show that intact nonmuscle myosin filaments are required for the synthesis of heterotrimeric type I collagen. Conserved 5′ stem-loop in collagen α1(I) and α2(I) mRNAs binds the RNA-binding protein LARP6. LARP6 interacts with nonmuscle myosin through its C-terminal domain and associates collagen mRNAs with the filaments. Dissociation of nonmuscle myosin filaments results in secretion of collagen α1(I) homotrimer, diminished intracellular colocalization of collagen α1(I) and α2(I) polypeptides (required for folding of the heterotrimer), and their increased intracellular degradation. Inhibition of the motor function of myosin has similar collagen-specific effects, while disruption of actin filaments has a general effect on protein secretion. Nonmuscle myosin copurifies with polysomes, and there is a subset of polysomes involved in myosin-dependent translation of collagen mRNAs. These results indicate that association of collagen mRNAs with nonmuscle myosin filaments is necessary to coordinately synthesize collagen α1(I) and α2(I) polypeptides. We postulate that LARP6/myosin-dependent mechanism regulates the synthesis of heterotrimeric type I collagen by coordinating the translation of collagen mRNAs.     

Extracellular matrix changes in knee joint cartilage following bone-active drug treatment

Certain drugs or treatments that are known to affect bone quality or integrity might have side effects on the extracellular matrix of articular cartilage. We investigated the effects of vitamin D and calcium deficiency, estrogen deficiency, and hypercortisolism alone or in combination with bisphosphonates or sodium fluoride in an animal model, viz., the Göttingen miniature pig (n=29). The articular cartilage from knee joints was analyzed for its content of glycosaminoglycans (GAGs, as macromolecules responsible for the elasticity of articular cartilage) by a spectrometric method with dimethylene blue chloride. In cryo- or paraffin sections, alkaline phosphatase (AP, as an enzyme indicating mineralization or reorganization of articular cartilage matrix) was localized by enzyme histochemistry, and positive cells were counted, whereas differently sulfated GAGs were stained histochemically. A significant decrease in GAG content was measured in ovariectomized and long-term glucocorticoid-treated animals compared with untreated animals. In the glucocorticoid/sodium fluoride group, GAGs were significantly diminished, and significantly fewer AP-positive chondrocytes were counted compared with the control. GAG content was slightly higher, and significantly more AP-positive chondrocytes were counted in short-term glucocorticoid-treated animals then in the control group. GAGs, as part of proteoglycans, are responsible for the water-storage capacity that gives articular cartilage its unique property of elasticity. Thus, ovariectomy and long-term glucocorticoid therapy, especially when combined with sodium fluoride, have detrimental effects on this tissue.This work was in part supported by Deutsche Forschungsgemeinschaft (DFG) project no. Schr 430/5–1, 5–2 and G 1289/1–1, 1–2