富γ-氨基丁酸水稻种质筛选及与子粒性状相关性分析

利用高效液相色谱法,测定了108份水稻种质资源材料子粒中的γ-氨基丁酸含量,分析了不同种质资源材料间γ-氨基丁酸含量差异及与子粒性状的相关性,以γ-氨基丁酸含量差异较大的高粱稻-1与宁农黑粳配制杂交组合,测定亲本、杂交F1及216个F2子粒中的γ-氨基丁酸含量,分析其含量与相对胚重和子粒性状的相关性及变异系数,估算各性状的广义遗传力。结果表明:108份种质资源材料子粒中的γ-氨基丁酸含量变异范围为2.39~12.03 mg/100g,,平均含量为6.30±1.99 mg/100g,变异系数为31.59%;不同水稻种质资源材料子粒中的γ-氨基丁酸含量与粒厚、千粒重呈极显著的负相关;杂交F1子粒γ-氨基丁酸含量为8.39±0.11 mg/100g,介于双亲之间;F2单株子粒中的γ-氨基丁酸含量总体呈偏正态分布,且出现明显的超亲现象,说明水稻子粒中的γ-氨基丁酸含量是由多基因控制的数量性状遗传;杂交F2子粒中的γ-氨基丁酸含量与相对胚重呈极显著的正相关,与粒厚、千粒重呈极显著的负相关,与粒长呈显著的负相关;F2单株子粒中的γ-氨基丁酸含量、粒厚和千粒重的广义遗传力相对较高,分别为98.12%、91.99%、96.37%,在育种中对这些性状可进行早期选择。     

Collective Fluctuations in the Dynamics of Adaptation and Other Traveling Waves

The dynamics of adaptation are difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from random genetic drift arising in a vanguard of particularly fit individuals of the population. Several approaches have been developed to analyze the crucial role of genetic drift on the expected dynamics of adaptation, including the mean fitness of the entire population, or the fate of newly arising beneficial deleterious mutations. However, little is known about how genetic drift causes fluctuations to emerge on the population level, where it becomes palpable as variations in the adaptation speed and the fitness distribution. Yet these phenomena control the decay of genetic diversity and variability in evolution experiments and are key to a truly predictive understanding of evolutionary processes. Here, we show that correlations induced by these emergent fluctuations can be computed at any arbitrary order by a suitable choice of a dynamical constraint. The resulting linear equations exhibit fluctuation-induced terms that amplify short-distance correlations and suppress long-distance ones. These terms, which are in general not small, control the decay of genetic diversity and, for wave-tip dominated (“pulled”) waves, lead to anticorrelations between the tip of the wave and the lagging bulk of the population. While it is natural to consider the process of adaptation as a branching random walk in fitness space subject to a constraint (due to finite resources), we show that other traveling wave phenomena in ecology and evolution likewise fall into this class of constrained branching random walks. Our methods, therefore, provide a systematic approach toward analyzing fluctuations in a wide range of population biological processes, such as adaptation, genetic meltdown, species invasions, or epidemics.     

Azadirachtin(A) distinctively modulates subdomain 2 of actin – novel mechanism to induce depolymerization revealed by molecular dynamics study

Azadirachtin(A) (AZA), a potential insecticide from neem, binds to actin and induces depolymerization in Drosophila. AZA binds to the pocket same as that of Latrunculin A (LAT), but LAT inhibits actin polymerization by stiffening the actin structure and affects the ADP–ATP exchange. The mechanism by which AZA induces actin depolymerization is not clearly understood. Therefore, different computational experiments were conducted to delineate the precise mechanism of AZA-induced actin depolymerization. Molecular dynamics studies showed that AZA strongly interacted with subdomain 2 and destabilized the interactions between subdomain 2 of one actin and subdomains 1 and 4 of the adjacent actin, causing the separation of actin subunits. The separation was observed between subdomain 3 of subunit n and subdomain 4 of subunit n + 2. However, the specific triggering point for the separation of the subunits was the destabilization of direct interactions between subdomain 2 of subunit n (Arg39, Val45, Gly46 and Arg62) and subdomain 4 of subunit n + 2 (Asp286, Ile287, Asp288, Ile289, Asp244 and Lys291). These results reveal a unique mechanism of an actin filament modulator that induces depolymerization. This mechanism of AZA can be used to design similar molecules against mammalian actins for cancer therapy.     

Development of a grand canonical-kinetic Monte Carlo scheme for simulation of mixtures

A rejection-free methodology-based kinetic Monte Carlo (kMC) method has been developed in the grand canonical ensemble to simulate fluid mixtures. It comprises two different moves: entropic displacement of a selected molecule (based on the Rosenbluth algorithm) in the volume space of the system, and exchange of molecules with the surroundings (insertion or deletion). These two moves are made sequentially with M displacement moves followed by one exchange. The displacement moves are treated as sub-NVT sequences within a grand canonical ensemble. The procedure for deletion or insertion of a molecule is either, based on the Rosenbluth algorithm, or on a direct comparison, in which the average activity of one component is compared with its specified activity. The components are chosen either with equal probability or with a probability proportional to their density. The implementation of rejection-free kMC is much simpler than the Metropolis importance sampling MC procedure, which requires three different types of move, all of which must be tested for acceptance or rejection. The new scheme has been evaluated by applying it to fluid argon and to an equimolar mixture of methane, ethane and propane.     

A comparative study on fluorescent cholesterol analogs as versatile cellular reporters

Cholesterol (Chol) is a crucial component of cellular membranes, but knowledge of its intracellular dynamics is scarce. Thus, it is of utmost interest to develop tools for visualization of Chol organization and dynamics in cells and tissues. For this purpose, many studies make use of fluorescently labeled Chol analogs. Unfortunately, the introduction of the label may influence the characteristics of the analog, such as its localization, interaction, and trafficking in cells; hence, it is important to get knowledge of such bias. In this report, we compared different fluorescent lipid analogs for their performance in cellular assays: 1) plasma membrane incorporation, specifically the preference for more ordered membrane environments in phase-separated giant unilamellar vesicles and giant plasma membrane vesicles; 2) cellular trafficking, specifically subcellular localization in Niemann-Pick type C disease cells; and 3) applicability in fluorescence correlation spectroscopy (FCS)-based and super-resolution stimulated emission depletion-FCS-based measurements of membrane diffusion dynamics. The analogs exhibited strong differences, with some indicating positive performance in the membrane-based experiments and others in the intracellular trafficking assay. However, none showed positive performance in all assays. Our results constitute a concise guide for the careful use of fluorescent Chol analogs in visualizing cellular Chol dynamics.     

Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase

Cytochrome c Oxidase (CcO) reduces O₂, the terminal electron acceptor, to water in the aerobic, respiratory electron transport chain. The energy released by O₂ reductions is stored by removing eight protons from the high pH, N-side, of the membrane with four used for chemistry in the active site and four pumped to the low pH, P-side. The proton transfers must occur along controllable proton pathways that prevent energy dissipating movement towards the N-side. The CcO N-side has well established D- and K-channels to deliver protons to the protein interior. The P-side has a buried core of hydrogen-bonded protonatable residues designated the Proton Loading Site cluster (PLS cluster) and many protonatable residues on the P-side surface, providing no obvious unique exit. Hydrogen bond pathways were identified in Molecular Dynamics (MD) trajectories of Rb. sphaeroides CcO prepared in the P_R state with the heme a₃ propionate and Glu286 in different protonation states. Grand Canonical Monte Carlo sampling of water locations, polar proton positions and residue protonation states in trajectory snapshots identify a limited number of water mediated, proton paths from PLS cluster to the surface via a (P-exit) cluster of residues. Key P-exit residues include His93, Ser168, Thr100 and Asn96. The hydrogen bonds between PLS cluster and P-exit clusters are mediated by a water wire in a cavity centered near Thr100, whose hydration can be interrupted by a hydrophobic pair, Leu255B (near Cu_A) and Ile99. Connections between the D channel and PLS via Glu286 are controlled by a second, variably hydrated cavity.

太原汾河蓄水区浮游植物细胞密度及其与营养元素的关系

水体营养元素是影响水体生态系统的重要因素,决定着水体中不同的浮游生物群落结构,也是评价水质和水体营养状态的重要指标。对太原汾河蓄水区9个样点浮游植物和各项水环境及营养元素进行了调查与分析,调查期间发现(1)该流域蓝藻和绿藻为主要优势类群,即构成了以蓝-绿藻门为主要的浮游群落。平水期与丰水期优势种均以蓝藻门的微小色球藻(Chroococcus minutus)、微小平裂藻(Merismopedia tenuissima)、小颤藻(Oscillatoria tenuis)、铜绿微囊藻(Microcystis aeruginosa)为主,其丰度分别占平水期和丰水期藻细胞总数的42.95%和59.24%。叶绿素a含量随地理位置变化明显,中下游显著高于上游。(2)太原汾河蓄水区水质均达到富营养状态。由于太原汾河蓄水区沿途的生活垃圾、污水的不合理排放,导致汾河中总氮、总磷等指标偏高,最终导致整个水体处于轻度富营养状态或中度富营养状态。(3)叶绿素a含量与水温、总氮、总磷呈显著正相关,与有机物含量呈极显著正相关,总磷的影响最为明显,说明磷可能是该地区浮游植物生长的限制因子。     

漓江河岸带枫杨群落主要木本植物种间联结与相关分析

种间联结能够反映植物群落中物种间的关系和群落的稳定程度,对植被的恢复与重建、生物多样性保护等具有重要的意义和价值。为了解漓江河岸带枫杨群落的种间联结特征,基于2×2联列表,通过方差比率(VR)、χ~2检验、Pearson相关系数、Spearman秩相关系数检验及PCA排序等,对枫杨群落主要木本植物种间关联性进行定量分析和生态种组划分。结果表明:(1)乔木层、灌木层以及乔木和灌木层的总体种间关联性均呈不显著正联结,表明枫杨群落处于较稳定的阶段;(2)χ~2检验结果显示,绝大多数种对呈不显著关联,说明群落各种对间关联较弱,各物种间呈独立分布格局;(3)Pearson相关检验和Spearman秩相关检验发现各层次的显著率均较低,种间相关性不显著的种对占绝大部分,种间相关性不强;(4)χ~2检验、Pearson相关系数检验和Spearman秩相关系数检验结果虽具有一致性,但也存在一定的差异,Spearman秩相关系数检验更具灵敏性,结合3种方法使用效果更佳;(5)根据PCA排序和种间联结关系,将20个主要物种划分为4个生态种组。