Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants

The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X‐ray crystallographic structure of higher plant PsbQ residues S14‐Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this “missing link”, we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N‐terminal residues 1–45 the solution structure deviates significantly from the X‐ray crystallographic one, while the four‐helix bundle core found previously is confirmed. A short α‐helix is observed in the solution structure at the location where a β‐strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N‐terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β‐strand are found. Proteins 2015; 83:1677–1686. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

Roles of dominant understory Sasa bamboo in carbon and nitrogen dynamics following canopy tree removal in a cool‐temperate forest in northern Japan

To clarify the role of dense understory vegetation in the stand structure, and in carbon (C) and nitrogen (N) dynamics of forest ecosystems with various conditions of overstory trees, we: (i) quantified the above‐ and below‐ground biomasses of understory dwarf bamboo (Sasa senanensis) at the old canopy‐gap area and the closed‐canopy area and compared the stand‐level biomasses of S. senanensis with that of overstory trees; (ii) determined the N leaching, soil respiration rates, fine‐root dynamics, plant area index (PAI) of S. senanensis, and soil temperature and moisture at the tree‐cut patches (cut) and the intact closed‐canopy patches (control). The biomass of S. senanensis in the canopy‐gap area was twice that at the closed‐canopy area. It equated to 12% of total biomass above ground but 41% below ground in the stand. The concentrations of NO₃^? and NH₄⁺ in the soil solution and soil respiration rates did not significantly change between cut and control plots, indicating that gap creation did not affect the C or N dynamics in the soil. Root‐length density and PAI of S. senanensis were significantly greater at the cut plots, suggesting the promotion of S. senanensis growth following tree cutting. The levels of soil temperature and soil moisture were not changed following tree cutting. These results show that S. senanensis is a key component species in this cool‐temperate forest ecosystem and plays significant roles in mitigating the loss of N and C from the soil following tree cutting by increasing its leaf and root biomass and stabilizing the soil environment.     

Influence of parameter values on the oscillation sensitivities of two p53–Mdm2 models

Biomolecular networks that present oscillatory behavior are ubiquitous in nature. While some design principles for robust oscillations have been identified, it is not well understood how these oscillations are affected when the kinetic parameters are constantly changing or are not precisely known, as often occurs in cellular environments. Many models of diverse complexity level, for systems such as circadian rhythms, cell cycle or the p53 network, have been proposed. Here we assess the influence of hundreds of different parameter sets on the sensitivities of two configurations of a well-known oscillatory system, the p53 core network. We show that, for both models and all parameter sets, the parameter related to the p53 positive feedback, i.e. self-promotion, is the only one that presents sizeable sensitivities on extrema, periods and delay. Moreover, varying the parameter set values to change the dynamical characteristics of the response is more restricted in the simple model, whereas the complex model shows greater tunability. These results highlight the importance of the presence of specific network patterns, in addition to the role of parameter values, when we want to characterize oscillatory biochemical systems.

Electronic supplementary material

The online version of this article (doi:10.1007/s11693-015-9173-y) contains supplementary material, which is available to authorized users.     

Enhancing Phytoremediation Potential of Pennisetum clandestinum Hochst in Cadmium-Contaminated Soil Using Smoke-Water and Smoke-Isolated Karrikinolide

The use of plant growth regulators (PGRs) and biostimulants to enhance phytoextraction is gaining popularity in phytoremediation technology. This study investigated the stimulatory effects of smoke-water (SW), a smoke-derived compound karrikinolide (KAR₁) and other known plant growth regulators (PGRs) [gibberellic acid (GA₃), kinetin (Kin) and indole-3-butyric acid (IBA)] to enhance the phytoextraction potential of Pennisetum clandestinum. Pennisetum clandestinum seedlings were grown for 10 weeks in vermiculite using Hoagland's nutrient solution and were treated with cadmium (Cd) (2, 5, and 10 mg L^?1) and SW, KAR₁ and PGRs. KAR₁ exhibited positive effects on shoot and root dry weight (140 and 137 mg respectively) at the highest concentration of Cd (10 mg L^?1) compared to all the other treatments. KAR₁ and SW treatments used in the present study significantly improved the phytoextraction potential of P. clandestinum (602 and 575 mg kg^?1 respectively) compared to the other tested PGRs. This is the first report on the use of SW and KAR₁ to enhance phytoremediation potential in P. clandestinum. Further studies are needed to elucidate the exact mechanisms of smoke constituents involved in phytoextraction potential of plant species.     

Depositing Fullerenes in Swollen Polymer Layers via Sequential Processing of Organic Solar Cells

Polymer solar cells are conventionally processed by coating a multicomponent mixture containing polymer, fullerene, solvent, and cosolvent. The photovoltaic performance strongly depends on the nanoscale morphology of the blend, which is largely determined by the precise nature of the solvent composition and drying conditions. Here, an alternative processing route is investigated in which the two active layer components are deposited sequentially via spin coating or doctor blading. Spin coating the fullerene from o‐dichlorobenzene on top of the polymer provides virtually identical morphologies and photovoltaic performance. Using blade coating, the influence of the second‐layer solvent for the fullerene derivative is investigated in further detail. Different aromatic solvents are compared regarding swelling of the polymer layer, fullerene solubility, and evaporation rate. It is found that while swelling of the polymer by the second‐layer solvent is a necessity for sequential processing, the solubility of the fullerene derivative in this solvent has the strongest influence on solar cell performance. Homogeneous layers in which a sufficient amount of fullerene can infiltrate the polymer film can only be achieved when solvents are used that have a very high solubility for the fullerene and swell the polymer layer.     

Comparative Study of Effects of Terminal Non‐Alkyl Aromatic and Alkyl Groups on Small‐Molecule Solar Cell Performance

Small‐molecule donors for solar cells are usually end‐capped with π‐systems or aliphatic chains extending the π‐conjugation of the molecules's backbone. Compared with alkyl terminals, π‐systems can form π?π arrangements, for example, with an aligning spherical fullerene π‐system. To study the effects of two kinds of terminals on the solar cell performance, the non‐alkyl, branched aromatic and electron‐donating diphenylamine (DPA) and the aliphatic n‐butyl (n‐Bu) unit are selected as end‐capping groups on a diketopyrrolo­pyrrole‐based linear backbone, affording two new solution‐processable small‐molecule donors. Photovoltaic data indicate that by changing the end‐function from n‐Bu to DPA, the photocurrent significantly increases from 8.35 to 15.64 mA cm^?2 and the efficiency from 3.2 to 5.8%. Characterization of absorption, morphology, recombination, and carrier transportation clearly demonstrates that the higher photocurrent can be attributed to a higher density of the mobile carriers (i.e., free holes, in this case). The DPA end‐functions enhance the light‐harvesting capacity, improve the charge dissociation, and reduce the recombination loss, all of which lead to more carriers being collected by the electrode. This work demonstrates that the choice of end‐function along the molecular backbone is as important to improve the cell performance as the light‐harvesting backbone and the side‐chains.     

一类带时滞竞争模型的周期解

研究了来源于水生种群植化相克的模型,提出了带时滞的半线性抛物系统．用上下解方法讨论了抛物方程组周期解存在性的原理,利用特征函数构造所提出抛物系统的上解,给出了正周期解存在的充分条件．     

具性别和阶段结构的非自治二种群捕食者-食饵系统研究

讨论了一类食饵具有性别结构,捕食者具有阶段结构的非自治捕食者．食饵系统,运用Liapunov函数方法,得到了该系统一致持续生存的充分条件．对于该模型的周期系统,在适当条件下,存在唯一、全局渐近稳定的周期解．对更具普遍意义的概周期现象,也得出了概周期正解唯一存在且全局渐近稳定的充分条件．