Potential Application of Turnip Oil (Raphanus sativus L.) for Biodiesel Production: Physical–Chemical Properties of Neat Oil, Biofuels and their Blends with Ultra-Low Sulphur Diesel (ULSD)

Turnip oil (TO; Raphanus sativus L.) produces seeds that contain around 26 wt% of inedible base stock that are suitable as a potential feedstock for biodiesel production. A turnip oil methyl ester (TME) was prepared from acid-catalyzed pretreated TO in an effort to evaluate important fuel properties of turnip oil-based biodiesel, such as kinematic viscosity, cloud point, pour point (PP), cold filter plugging point, acid value, oxidative stability and lubricity. A comparison was made with soybean oil methyl esters (SME) as per biodiesel fuel standards such as ASTM D6751 and EN 14214. TME was characterized using FTIR, HPLC and ¹H NMR. Except PP property, SME displays superior fuel properties compared to TME. Blends (B5 and B20) of TME in ultra-low sulphur diesel fuel (ULSD) were also assessed for the aforesaid fuel properties and compared to an analogous set of blends of soybean oil methyl ester in ULSD as per petro diesel fuel standards such as ASTM D975 and D7467. TME B5 blends in ULSD displayed improved PP property in comparison to neat ULSD and blends of SME in ULSD. It was demonstrated that the B5 and B20 blends of TME in ULSD had acceptable fuel properties as per ASTM D975 (for B5 blend) and ASTM D7467 (for B20 blend). In summary, turnip oil has potential as an alternative, non-food feedstock for biodiesel production.     

Rational design of the survivin/CDK4 complex by combining protein–protein docking and molecular dynamics simulations

Survivin, the smallest inhibitor of apoptosis protein (IAP), is a valid target for cancer research. It mediates both the apoptosis pathway and the cell cycle and has been proposed to form a complex with the cyclin-dependent kinase protein CDK4. The resulting complex transports CDK4 from the cytosol to the nucleus, where CDK4 participates in cell division. Survivin has been recognized as a node protein that interacts with several partners; disruption of the formed complexes can lead to new anticancer compounds. We propose a rational model of the survivin/CDK4 complex that fulfills the experimental evidence and that can be used for structure-based design of inhibitors modifying its interface recognition. In particular, the suggested complex involves the alpha helical domain of survivin and resembles the mode of binding of survivin in the survivin/borealin X-ray structure. The proposed model has been obtained by combining protein–protein docking, fractal-based shape complementarity, electrostatics studies and extensive molecular dynamics simulations.

Cu3P Binary Phosphide: Synthesis via a Wet Mechanochemical Method and Electrochemical Behavior as Negative Electrode Material for Lithium‐Ion Batteries

Mechanochemical synthesis of Cu₃P in the presence of n‐dodecane results in a material with a secondary particle size distribution of 10 μm, secondary particles which consist of homogeneously agglomerated 20 nm primary particles. The electrochemical performance of Cu₃P with lithium is influenced by the reaction depth, in other words by the lower potential cut‐off. During the electrochemical reaction, the displacement of copper by lithium from the Cu₃P structure until the formation of Li₃P and Cu deteriorates the capacity retention. Improved performance was obtained when the charge potential was limited to 0.50 V (vs. Li/Li⁺) and the formation of the Li_xCu_3‐xP phase (0 ≤ × ≤ 2). In this case, when the potential is limited to 0.5 V, the capacity is stable for more than 50 cycles. Acceptable electrochemical performances in Li‐ion cells within the voltage range 0.50–2.0 V (vs. Li/Li⁺) were shown when Cu₃P was used as an anode and Li_1.2(Ni_0.13Mn_0.54Co_0.13)O₂ and LiNi_0.5Mn_1.5O₄ as positive electrode materials.     

Effects of post-thaw incubation on motility,acrosomal integrity and in vitro fertilizing capacity of boar spermatozoa cryopreserved in 0.5 and 5 ml straws

The effect of post-thaw incubation (0 vs. 5 h at 15 °C) and straw size (5 vs. 0.5 ml) on motility, acrosomal integrity and in vitro fertilizing (IVF) capacity of cryopreserved boar spermatozoa was studied. In samples assessed immediately after thawing, no differences were found between the two straw sizes. After 5 h post-thaw incubation, all parameters, except polyspermy, decreased and, spermatozoa packaged in 5 ml straws showed better functional and IVF parameters than these in 0.5 ml straws.     

Road-associated edge effects in Amazonia change termite community composition by modifying environmental conditions

Roads and road-building are among the most important environmental impacts on forests near urban areas, but their effects on ecosystem processes and species distributions remain poorly known. Termites are the primary decomposer organisms in tropical forests and their spatial distribution is strongly affected by vegetation and soil structure. We studied the impacts of road construction on termite community structure in an Amazonian forest fragment near Manaus, Brazil. One leading question was whether the fragment under study was large enough to maintain the termite species pool present in nearby continuous forests. We also asked how soil moisture and canopy openness varied with proximity to roads, and whether these changes were associated with changes in termite species richness and composition in the fragment. While the forest fragment had a termite composition very similar to that of continuous forests, roads caused important changes in soil moisture and canopy openness, especially when close to forest edges. At distances of up to 81 m from roads, changes in soil moisture were significantly related to changes in termite species composition, but there was no correlation between canopy openness and species richness or composition. These results suggest that fragmentation caused by roads impacts termites in a different and less damaging manner than fragmentation caused by other kinds of degradation, and that even fragments bisected by roads can support very diverse communities and even undescribed taxa of termites. We conclude that a buffer zone should be established for conservation purposes in the reserves surrounded by roads.     

Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field

We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native -sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting.     

Two strings to the systems biology bow: co-extracting the metabolome and proteome of yeast

Experimental samples are valuable and can represent a significant investment in time and resources. It is highly desirable at times to obtain as much information as possible from a single sample. This is especially relevant for systems biology approaches in which several ‘omics platforms are studied simultaneously. Unfortunately, each platform has a particular extraction methodology which increases sample number and sample volume requirements when multiple ‘omics are analyzed. We evaluated the integration of a yeast extraction method; specifically we explored whether fractions from a single metabolite extraction could be apportioned to multiple downstream ‘omics analytical platforms. In addition, we examined how variations to a chloroform/methanol yeast metabolite extraction regime influence metabolite recoveries. We show that protein suitable for proteomic analysis can be recovered from a metabolite extraction and that recovery of lipids, while reproducible, are not wholly quantitative. Higher quenching solution temperatures (?30 °C) can be used without significant leakage of intracellular metabolites when lower fermentation temperatures (20 °C) are employed. However, extended residence time in quenching solution, in combination with vigorous washing of quenched cell pellets, leads to extensive leakage of intracellular metabolites. Finally, there is minimal difference in metabolite amounts obtained when metabolite extractions are performed at 4 °C compared to extractions at ?20 °C. The evaluated extraction method delivers material suitable for metabolomic and proteomic analyses from the same sample preparation.