RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

We describe RosettaRemodel, a generalized framework for flexible protein design that provides a versatile and convenient interface to the Rosetta modeling suite. RosettaRemodel employs a unified interface, called a blueprint, which allows detailed control over many aspects of flexible backbone protein design calculations. RosettaRemodel allows the construction and elaboration of customized protocols for a wide range of design problems ranging from loop insertion and deletion, disulfide engineering, domain assembly, loop remodeling, motif grafting, symmetrical units, to de novo structure modeling

The relevance of nanoscale biological fragments for ice nucleation in clouds

Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles

Community compensation in the context of Carbon Capture and Storage: Current debates and practices

Societal opposition has the potential to slow down the implementation of Carbon Capture and Storage (CCS). One of the difficulties is that the perceived benefits associated with a CCS facility for local communities tend to be low compared to its perceived burdens. As is the case for other low carbon technologies, community compensation (or community benefits) has been suggested as a way to restore this perceived imbalance. A diverse literature has looked into the role of community compensation across various land uses and research fields. Synthesis is limited, while at the same time, the provision of community compensation in practice is moving from an ad hoc to a more institutionalized approach. Therefore, it is important to take stock of the literature. This paper provides a review of the community compensation literature in the form of four debates, drawing together environmental social science research on different low carbon technologies (e.g. CCS, renewable energy). In addition, current practices in community compensation for four European countries are discussed. The two parts of this paper are brought together in a set of lessons for the provision of community compensation for future CCS projects; in turn, suggestions for further research are made to address remaining knowledge gaps

Evaluation of a High Throughput Starch Analysis Optimised for Wood

Starch is the most important long-term reserve in trees, and the analysis of starch is therefore useful source of physiological information. Currently published protocols for wood starch analysis impose several limitations, such as long procedures and a neutralization step. The high-throughput standard protocols for starch analysis in food and feed represent a valuable alternative. However, they have not been optimised or tested with woody samples. These have particular chemical and structural characteristics, including the presence of interfering secondary metabolites, low reactivity of starch, and low starch content. In this study, a standard method for starch analysis used for food and feed (AOAC standard method 996.11) was optimised to improve precision and accuracy for the analysis of starch in wood. Key modifications were introduced in the digestion conditions and in the glucose assay. The optimised protocol was then evaluated through 430 starch analyses of standards at known starch content, matrix polysaccharides, and wood collected from three organs (roots, twigs, mature wood) of four species (coniferous and flowering plants). The optimised protocol proved to be remarkably precise and accurate (3%), suitable for a high throughput routine analysis (35 samples a day) of specimens with a starch content between 40 mg and 21 µg. Samples may include lignified organs of coniferous and flowering plants and non-lignified organs, such as leaves, fruits and rhizomes

High accumulation of soluble sugars in deep supercooling Japanese white birch xylem parenchyma cells.

• Seasonal changes in the accumulation of soluble sugars in extracellular freezing cortical parenchyma cells and deep supercooling xylem parenchyma cells in Japanese white birch (Betula platyphylla var. japonica) were compared to identify the effects of soluble sugars on the mechanism of deep supercooling, which keeps the liquid state of water in cells under extremely low temperatures for long periods. • Soluble sugars in both tissues were analyzed by high-performance liquid chromatography (HPLC), and the concentrations of sugars in cells were estimated by histological observation of occupancy rates of parenchyma cells in each tissue. Relative and equilibrium melting points of parenchyma cells were measured by differential thermal analysis and cryoscanning electron microscopy, respectively. • In both xylem and cortical parenchyma cells, amounts of sucrose, raffinose and stachyose increased in winter, but amounts of fructose and glucose exhibited little change throughout the entire year. In addition, no sugars were found to be specific for either tissue. Combined results of HPLC analyses, histological observation and melting point analyses confirmed that the concentration of sugars was much higher in xylem cells than in cortical cells. • It is thought that the higher concentration of soluble sugars in xylem cells may contribute to facilitation of deep supercooling in xylem cells by depressing the nucleation temperature