Ethical considerations in fish research

Fishes are used in a wide range of scientific studies, from conservation research with potential benefits to the species used to biomedical research with potential human benefits. Fish research can take place in both laboratories and field environments and methods used represent a continuum from non-invasive observations, handling, through to experimental manipulation. While some countries have legislation or guidance regarding the use of fish in research, many do not and there exists a diversity of scientific opinions on the sentience of fish and how we determine welfare. Nevertheless, there is a growing pressure on the scientific community to take more responsibility for the animals they work with through maximising the benefits of their research to humans or animals while minimising welfare or survival costs to their study animals. In this review, we focus primarily on the refinement of common methods used in fish research based on emerging knowledge with the aim of improving the welfare of fish used in scientific studies. We consider the use of anaesthetics and analgesics and how we mark individuals for identification purposes. We highlight the main ethical concerns facing researchers in both laboratory and field environments and identify areas that need urgent future research. We hope that this review will help inform those who wish to refine their ethical practices and stimulate thought among fish researchers for further avenues of refinement. Improved ethics and welfare of fishes will inevitably lead to increased scientific rigour and is in the best interests of both fishes and scientists.     

Benchmarking of structure refinement methods for protein complex models

Protein structure docking is the process in which the quaternary structure of a protein complex is predicted from individual tertiary structures of the protein subunits. Protein docking is typically performed in two main steps. The subunits are first docked while keeping them rigid to form the complex, which is then followed by structure refinement. Structure refinement is crucial for a practical use of computational protein docking models, as it is aimed for correcting conformations of interacting residues and atoms at the interface. Here, we benchmarked the performance of eight existing protein structure refinement methods in refinement of protein complex models. We show that the fraction of native contacts between subunits is by far the most straightforward metric to improve. However, backbone dependent metrics, based on the Root Mean Square Deviation proved more difficult to improve via refinement.     

Sn‐Alloy Foil Electrode with Mechanical Prelithiation: Full‐Cell Performance up to 200 Cycles

Self‐supporting Sn foil is a promising high‐volumetric‐capacity anode for lithium ion batteries (LIBs), but it suffers from low initial Coulombic efficiency (ICE). Here, mechanical prelithiation is adopted to improve ICE, and it is found that Sn foils with coarser grains are prone to cause electrode damage. To mitigate damage and prepare thinner lithiated electrodes, 3Ag0.5Cu96.5Sn foil is used that has more refined grains (5–10 µm) instead of Sn (50–100 µm), where the abundant grain boundaries (GBs) offer more sliding systems to release stress and reduce deep fractures. Thus, the thickness of Li_x3Ag0.5Cu96.5Sn can be reduced to 50 µm, compared to 100 µm Li_xSn. When the foils contact open air, the Sn‐Li‐O(H) products are more stable than Li‐O(H), thus Li_x3Ag0.5Cu96.5Sn shows outstanding air stability. The as‐prepared 50 µm foil anode achieves stable 200 cycles in LiFePO₄//Li_x3Ag0.5Cu96.5Sn full cell (≈2.65 mAh cm^?2) and the capacity retention is 95%. Even at 5C, the capacity of Li_x3Ag0.5Cu96.5Sn is still up to ≈1.8 mAh cm^?2. The cycle life of NCM523//Li_x3Ag0.5Cu96.5Sn full cell exceeds that of NCM523//Li. Furthermore, 70 µm Li_x3Ag0.5Cu96.5Sn is used as double‐sided anode for a 3 cm × 2.8 cm pouch cell and its actual volumetric capacity density is 674 mAh cm^?3 after 50 cycles.     

Li[Ni0.9Co0.09W0.01]O2: A New Type of Layered Oxide Cathode with High Cycling Stability

Substituting W for Al in the Ni‐rich cathode Li[Ni_0.885Co_0.10Al_0.015]O₂ (NCA89) produces Li[Ni_0.9Co_0.09W_0.01]O₂ (NCW90) with markedly reduced primary particle size. Particle size refinement considerably improves the cathode's cycling stability such that the NCW90 cathode retains 92% of its initial capacity after 1000 cycles (compared to 63% for NCA89), while the cathode produces a high initial discharge capacity of 231.2 mAh g^?1 (at 0.1 C). Thus, the proposed NCW90 can deliver high energy density and a long battery lifetime simultaneously, unlike other Ni‐rich layered oxide cathodes. This unprecedented cycling stability is mainly attributed to a series of interparticular microfractures that absorb the anisotropic lattice strain caused by a deleterious phase transition near the charge end, thereby improving the cathode's resistance to fracture. Microcrack suppression preserves the mechanical integrity of the cathode particles during cycling and protects the particle interior from detrimental electrolyte attack. The proposed NCW90 cathode provides an improved material from which a new series of Ni‐rich layered cathode can be developed for next‐generation electric vehicles.     

Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics

The most successful protein structure prediction methods to date have been template‐based modeling (TBM) or homology modeling, which predicts protein structure based on experimental structures. These high accuracy predictions sometimes retain structural errors due to incorrect templates or a lack of accurate templates in the case of low sequence similarity, making these structures inadequate in drug‐design studies or molecular dynamics simulations. We have developed a new physics based approach to the protein refinement problem by mimicking the mechanism of chaperons that rehabilitate misfolded proteins. The template structure is unfolded by selectively (targeted) pulling on different portions of the protein using the geometric based technique FRODA, and then refolded using hierarchically restrained replica exchange molecular dynamics simulations (hr‐REMD). FRODA unfolding is used to create a diverse set of topologies for surveying near native‐like structures from a template and to provide a set of persistent contacts to be employed during re‐folding. We have tested our approach on 13 previous CASP targets and observed that this method of folding an ensemble of partially unfolded structures, through the hierarchical addition of contact restraints (that is, first local and then nonlocal interactions), leads to a refolding of the structure along with refinement in most cases (12/13). Although this approach yields refined models through advancement in sampling, the task of blind selection of the best refined models still needs to be solved. Overall, the method can be useful for improved sampling for low resolution models where certain of the portions of the structure are incorrectly modeled. Proteins 2015; 83:2279–2292. © 2015 Wiley Periodicals, Inc.     

基于模板的蛋白质结构预测

基于模板的蛋白结构预测和不依赖模板的蛋白结构预测是计算预测蛋白质三维结构的两种方法,前者由于具有快速和较高准确性的优点,而得到了广泛的应用.基于模板的结构预测是通过寻找与目标蛋白序列相似并且有实验测定的结构作为模板,进而构建目标序列的结构模型的方法.文章详细综述了基于模板的结构预测方法的步骤、关键环节,并对影响结构预测...     

Electrostatic properties deduced from refined structures of NADH-cytochrome b5 reductase and the other flavin-dependent reductases: Pyridine nucleotide-binding and interaction with an electron-transfer partner

Electrostatic properties on the protein surface were examined on the basis of the crystal structure of NADH-cytochrome b₅ reductase refined to a crystallographic R factor of 0.223 at 2.1 Å resolution and of the other three flavin-dependent reductases. A structural comparison of NADH-cytochrome b₅ reductase with the other flavin-dependent reductases, ferredoxin-NADP⁺ reductase, phthalate dioxygenase reductase, and nitrate reductase, showed that the α/β structure is the common motif for binding pyridine nucleotide. Although the amino acid residues associated with pyridine nucleotide-binding are not conserved, the electrostatic properties and the location of the pyridine nucleotide-binding pockets of NADH-requiring reductases were similar to each other. The electrostatic potential of the surface near the flavin-protruding side (dimethylbenzene end of the flavin ring) of NADH-cytochrome b₅ reductase was positive over a wide area while that of the surface near the heme-binding site of cytochrome b₅ was negative. This implied that the flavin-protruding side of NADH-cytochrome b₅ reductase is suitable for interacting with its electron-transfer partner, cytochrome b₅. This positive potential area is conserved among four flavin-dependent reductases. A comparison of the electron-transfer partners of four flavin-dependent reductases showed that there are significant differences in the distribution of electrostatic potential between inter-molecular and inter-domain electron-transfer reactions. © 1996 Wiley-Liss, Inc.     

The structure of rubredoxin from Desulfovibrio desulfuricans strain 27774 at 1.5 A resolution

The structure of a small rubredoxin from the bacterium Desulfovibrio desulfuricans has been determined and refined at 1.5 A resolution. The hairpin loop containing seven residues in other rubredoxins is missing in this 45 residue molecule, and once that fact was determined by amino acid sequencing studies, refinement progressed smoothly to an R value of 0.093 for all reflections from 5 to 1.5 A resolution. Nearly all of the water molecules in the well-ordered triclinic unit cell have been added to the crystallographic model. As in the other refined rubredoxin models, the Fe-S4 complex is slightly distorted from ideal tetrahedral coordination.     

姜黄色素及其提制方法

来源于姜科姜黄属植物姜黄根茎的姜黄是国内外食品行业允许使用的重要天然色素之一,具有重要的开发利用价值。姜黄素的主要提取方法可分为有机溶剂提取法和水提取法;精制方法主要包括专一性溶剂法、酸碱法、酶水解法和柱层析法等。文中对各种方法进行了简要介绍和评述。