Population genomics from pool sequencing

Next generation sequencing of pooled samples is an effective approach for studies of variability and differentiation in populations. In this paper we provide a comprehensive set of estimators of the most common statistics in population genetics based on the frequency spectrum, namely the Watterson estimator , nucleotide pairwise diversity Π, Tajima's D, Fu and Li's D and F, Fay and Wu's H, McDonald‐Kreitman and HKA tests and , corrected for sequencing errors and ascertainment bias. In a simulation study, we show that pool and individual θ estimates are highly correlated and discuss how the performance of the statistics vary with read depth and sample size in different evolutionary scenarios. As an application, we reanalyse sequences from Drosophila mauritiana and from an evolution experiment in Drosophila melanogaster. These methods are useful for population genetic projects with limited budget, study of communities of individuals that are hard to isolate, or autopolyploid species.     

Genes versus environment: geography and phylogenetic relationships shape the chemical profiles of stingless bees on a global scale

Chemical compounds are highly important in the ecology of animals. In social insects, compounds on the body surface represent a particularly interesting trait, because they comprise different compound classes that are involved in different functions, such as communication, recognition and protection, all of which can be differentially affected by evolutionary processes. Here, we investigate the widely unknown and possibly antagonistic influence of phylogenetic and environmental factors on the composition of the cuticular chemistry of tropical stingless bees. We chose stingless bees because some species are unique in expressing not only self-produced compounds, but also compounds that are taken up from the environment. By relating the cuticular chemistry of 40 bee species from all over the world to their molecular phylogeny and geographical occurrence, we found that distribution patterns of different groups of compounds were differentially affected by genetic relatedness and biogeography. The ability to acquire environmental compounds was, for example, highly correlated with the bees'' phylogeny and predominated in evolutionarily derived species. Owing to the presence of environmentally derived compounds, those species further expressed a higher chemical and thus functional diversity. In Old World species, chemical similarity of both environmentally derived and self-produced compounds was particularly high among sympatric species, even when they were less related to each other than to allopatric species, revealing a strong environmental effect even on largely genetically determined compounds. Thus, our findings do not only reveal an unexpectedly strong influence of the environment on the cuticular chemistry of stingless bees, but also demonstrate that even within one morphological trait (an insect''s cuticular profile), different components (compound classes) can be differentially affected by different drivers (relatedness and biogeography), depending on the functional context.     

猴头菌多糖不同脱色方法的研究

为选择最适于猴头菌多糖的脱色方法,本论文先比较了活性炭吸附法、化学脱色法、大孔树脂法等三种常用的脱色方法对猴头菌多糖的脱色效果及脱色前后免疫活性的变化,发现大孔树脂法更适合于猴头菌多糖的脱色,接着对十种不同类型的大孔树脂进行了筛选,通过脱色前后脱色率、多糖保留率及体外免疫活性的比较,最后发现大孔弱碱性阴离子树脂D315最适合用于猴头菌粗多糖的脱色.     

Characterization and immobilization on nickel-chelated Sepharose of a glutamate decarboxylase A from Lactobacillus brevis BH2 and its application for production of GABA

A gene encoding glutamate decarboxylase A (GadA) from Lactobacillus brevis BH2 was expressed in a His-tagged form in Escherichia coli cells, and recombinant protein exists as a homodimer consisting of identical subunits of 53?kDa. GadA was absolutely dependent on the ammonium sulfate concentration for catalytic activity and secondary structure formation. GadA was immobilized on the metal affinity resin with an immobilization yield of 95.8%. The pH optima of the immobilized enzyme were identical with those of the free enzyme. However, the optimum temperature for immobilized enzyme was 5?°C higher than that for the free enzyme. The immobilized GadA retained its relative activity of 41% after 30 reuses of reaction within 30?days and exhibited a half-life of 19 cycles within 19?days. A packed-bed bioreactor with immobilized GadA showed a maximum yield of 97.8% GABA from 50?mM l-glutamate in a flow-through system under conditions of pH 4.0 and 55?°C.     

Statistical optimization of critical medium components for lipase production from Yarrowia lipolytica (MTCC 35)

Statistical optimization is an effective technique for the investigation of complex processes with minimal number of experimental runs. In this study, statistical approach was used to study the optimization of media components for lipase production from Yarrowia lipolytica MTCC 35. Mahua cake, glucose, MnCl₂ and KH₂PO₄ were screened to be the most significant variables among the nine medium variables that were tested to determine influence on lipase production by Plackett–Burman design. Central Composite Design was used for further optimization of these screened variables for enhanced lipase production. The determination coefficient (R²) value of 0.922 showed that the regression models adequately explain the data variation and represent the actual relationships between the variables and response. The optimum values of investigated variables for the maximum lipase production were 6.0% Mahua cake, 2.0% glucose, 0.2% MnCl₂ and 0.2% KH₂PO₄. The maximum lipase production (9.40 U mL^?1) was obtained under optimal condition.     

Combining Nature‐Inspired,Graphene‐Wrapped Flexible Electrodes with Nanocomposite Polymer Electrolyte for Asymmetric Capacitive Energy Storage

Two kinds of free‐standing electrodes, reduced graphene oxide (rGO)‐wrapped Fe‐doped MnO₂ composite (G‐MFO) and rGO‐wrapped hierarchical porous carbon microspheres composite (G‐HPC) are fabricated using a frozen lake‐inspired, bubble‐assistance method. This configuration fully enables utilization of the synergistic effects from both components, endowing the materials to be excellent electrodes for flexible and lightweight electrochemical capacitors. Moreover, a nonaqueous HPC‐doped gel polymer electrolyte (GPE‐HPC) is employed to broad voltage window and improve heat resistance. A fabricated asymmetric supercapacitor based on G‐MFO cathode and G‐HPC anode with GPE‐HPC electrolyte achieves superior flexibility and reliability, enhanced energy/power density, and outstanding cycling stability. The ability to power light‐emitting diodes also indicates the feasibility for practical use. Therefore, it is believed that this novel design may hold great promise for future flexible electronic devices.     

Diurnal patterns in Scots pine stem oleoresin pressure in a boreal forest

Coniferous tree stems contain large amounts of oleoresin under positive pressure in the resin ducts. Studies in North‐American pines indicated that the stem oleoresin exudation pressure (OEP) correlates negatively with transpiration rate and soil water content. However, it is not known how the OEP changes affect the emissions of volatile vapours from the trees. We measured the OEP, xylem diameter changes indicating changes in xylem water potential and monoterpene emissions under field conditions in mature Scots pine (Pinus sylvestris L.) trees in southern Finland. Contrary to earlier reports, the diurnal OEP changes were positively correlated with temperature and transpiration rate. OEP was lowest at the top part of the stem, where water potentials were also more negative, and often closely linked to ambient temperature and stem monoterpene emissions. However, occasionally OEP was affected by sudden changes in vapour pressure deficit (VPD), indicating the importance of xylem water potential on OEP as well. We conclude that the oleoresin storage pools in tree stems are in a dynamic relationship with ambient temperature and xylem water potential, and that the canopy monoterpene emission rates may therefore be also regulated by whole tree processes and not only by the conditions prevailing in the upper canopy.     

Foraging success under uncertainty: search tradeoffs and optimal space use

Understanding the structural complexity and the main drivers of animal search behaviour is pivotal to foraging ecology. Yet, the role of uncertainty as a generative mechanism of movement patterns is poorly understood. Novel insights from search theory suggest that organisms should collect and assess new information from the environment by producing complex exploratory strategies. Based on an extension of the first passage time theory, and using simple equations and simulations, we unveil the elementary heuristics behind search behaviour. In particular, we show that normal diffusion is not enough for determining optimal exploratory behaviour but anomalous diffusion is required. Searching organisms go through two critical sequential phases (approach and detection) and experience fundamental search tradeoffs that may limit their encounter rates. Using experimental data, we show that biological search includes elements not fully considered in contemporary physical search theory. In particular, the need to consider search movement as a non‐stationary process that brings the organism from one informational state to another. For example, the transition from remaining in an area to departing from it may occur through an exploratory state where cognitive search is challenged. Therefore, a more comprehensive view of foraging ecology requires including current perspectives about movement under uncertainty.     

大孔树脂固定化磷脂酶D

磷脂酶D(PhospholipaseD,EC3.1.4.4,PLD)是催化磷酸酯键水解和碱基交换反应的一类酶的总称.利用PLD的转碱基作用是目前催化合成磷脂酰丝氨酸(PS)的最佳途径.本实验以5种大孔树脂为载体固定化磷脂酶D(PLD)进行了研究.以酶回收率为主要指标,选择了最佳载体和优化了固定化条件.结果表明:非极性阳离子交换树脂H103是最佳固定化载体;其最优固定化条件:加酶液量1.2 mL,固定时间80 min,pH 6.0柠檬酸-柠檬酸钠的缓冲液浓度为10 mmol/L.最佳固定化条件下,固定化之后的PLD比游离PLD酶活提高了三倍.     

Identification and Quantitative Determination of Resin Acids from Corsican Pinus pinaster Aiton Oleoresin Using 13C‐NMR Spectroscopy

Twenty‐three resin samples have been obtained by tapping from individual Pinus pinaster adult trees grown in Corsica and submitted to acido‐basic partition. Identification and quantitative determination of resin acids has been carried out using ¹³C‐NMR spectroscopy following a method developed by our group. The main components were dehydroabietic acid (up to 37.6 %), levopimaric acid (up to 35.5 %) and abietic acid (up to 24.7 %). A lignan, pinoresinol, has been identified in some samples. Within the 23 compositions, submitted to k‐means analysis and Principal Component Analysis, two clusters have been perfectly differentiated, whose compositions were dominated by dehydroabietic acid (Group I, M=23.5 %, SD=6.3) and levopimaric acid (Group II, M=21.2 %; SD=6.2), respectively. Both compositions have been observed in the three locations of harvest.