Asymptotic Distributions of Coalescence Times and Ancestral Lineage Numbers for Populations with Temporally Varying Size

The distributions of coalescence times and ancestral lineage numbers play an essential role in coalescent modeling and ancestral inference. Both exact distributions of coalescence times and ancestral lineage numbers are expressed as the sum of alternating series, and the terms in the series become numerically intractable for large samples. More computationally attractive are their asymptotic distributions, which were derived in Griffiths (1984) for populations with constant size. In this article, we derive the asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. For a sample of size n, denote by T_m the mth coalescent time, when m + 1 lineages coalesce into m lineages, and A_n(t) the number of ancestral lineages at time t back from the current generation. Similar to the results in Griffiths (1984), the number of ancestral lineages, A_n(t), and the coalescence times, T_m, are asymptotically normal, with the mean and variance of these distributions depending on the population size function, N(t). At the very early stage of the coalescent, when t → 0, the number of coalesced lineages n − A_n(t) follows a Poisson distribution, and as m → n, n(n ? 1)T_m/2N(0) follows a gamma distribution. We demonstrate the accuracy of the asymptotic approximations by comparing to both exact distributions and coalescent simulations. Several applications of the theoretical results are also shown: deriving statistics related to the properties of gene genealogies, such as the time to the most recent common ancestor (TMRCA) and the total branch length (TBL) of the genealogy, and deriving the allele frequency spectrum for large genealogies. With the advent of genomic-level sequencing data for large samples, the asymptotic distributions are expected to have wide applications in theoretical and methodological development for population genetic inference.     

Gross primary productivity of phytoplankton and planktonic respiration in inland floodplain wetlands of southeast Australia: habitat-dependent patterns and regulating processes

Gross primary productivity (GPP) of phytoplankton and planktonic respiration (PR) (i.e., planktonic metabolism) are critical pathways for carbon transformation in many aquatic ecosystems. In inland floodplain wetlands with variable inundation regimes, quantitative measurements of GPP and PR are rare and their relationships with wetland environmental conditions are largely unknown. We measured PR and the GPP of phytoplankton using light and dark biological oxygen demand bottles in open waters of channel and non-channel floodplain habitats of inland floodplain wetlands of southeast Australia that had been inundated by environmental water. Overall, GPP varied from 3.7 to 405.5 mg C m^?3 h^?1 (mean ± standard error: 89.4 ± 9.2 mg C m^?3 h^?1, n = 81), PR from 1.5 to 251.6 mg C m^?3 h^?1 (43.2 ± 5.6 mg C m^?3 h^?1, n = 81), and GPP/PR from 0.2 to 15.6 (3.0 ± 0.3, n = 81). In terms of wetland environmental conditions, total nitrogen (TN) ranged from 682.0 to 14,700.0 mg m^?3 (mean ± standard error: 2,643.0 ± 241.6 mg m^?3, n = 81), total phosphorus (TP) from 48.0 to 1,405.0 mg m^?3 (316.8 ± 31.4 mg m^?3, n = 81), and dissolved organic carbon (DOC) from 1.9 to 46.3 g m^?3 (22.0 ± 1.6 g m^?3, n = 81). Using ordinary least-squares multiple regression analyses, the rates of GPP and PR, and their ratio (GPP/PR) were modeled as a function of TN, TP, and DOC that had been measured concomitantly. The “best” models predicted GPP and GPP/PR ratio in channel habitats as a function of DOC; and GPP, PR, and GPP/PR in non-channel floodplain habitats as a function of TN and/or TP. The models explained between 46 and 74 % of the variance in channel habitats and between 17 and 87 % of the variance in non-channel floodplain habitats. Net autotrophy (mean GPP/PR 3.0) of planktonic metabolism in our work supports the prevailing view that wetlands are a net sink for carbon dioxide. We propose a nutrient-DOC framework, combined with hydrological and geomorphological delineations, to better predict and understand the planktonic metabolism in inland floodplain wetlands.     

The Site Frequency Spectrum for General Coalescents

General genealogical processes such as Λ- and Ξ-coalescents, which respectively model multiple and simultaneous mergers, have important applications in studying marine species, strong positive selection, recurrent selective sweeps, strong bottlenecks, large sample sizes, and so on. Recently, there has been significant progress in developing useful inference tools for such general models. In particular, inference methods based on the site frequency spectrum (SFS) have received noticeable attention. Here, we derive a new formula for the expected SFS for general Λ- and Ξ-coalescents, which leads to an efficient algorithm. For time-homogeneous coalescents, the runtime of our algorithm for computing the expected SFS is O(n²),  where n is the sample size. This is a factor of n² faster than the state-of-the-art method. Furthermore, in contrast to existing methods, our method generalizes to time-inhomogeneous Λ- and Ξ-coalescents with measures that factorize as Λ(dx)/ζ(t) and Ξ(dx)/ζ(t),  respectively, where ζ denotes a strictly positive function of time. The runtime of our algorithm in this setting is O(n³). We also obtain general theoretical results for the identifiability of the Λ measure when ζ is a constant function, as well as for the identifiability of the function ζ under a fixed Ξ measure.     

Carbon Dioxide and Methane Fluxes From Tree Stems,Coarse Woody Debris,and Soils in an Upland Temperate Forest

Forest soils and canopies are major components of ecosystem CO₂ and CH₄ fluxes. In contrast, less is known about coarse woody debris and living tree stems, both of which function as active surfaces for CO₂ and CH₄ fluxes. We measured CO₂ and CH₄ fluxes from soils, coarse woody debris, and tree stems over the growing season in an upland temperate forest. Soils were CO₂ sources (4.58 ± 2.46 µmol m^?2 s^?1, mean ± 1 SD) and net sinks of CH₄ (?2.17 ± 1.60 nmol m^?2 s^?1). Coarse woody debris was a CO₂ source (4.23 ± 3.42 µmol m^?2 s^?1) and net CH₄ sink, but with large uncertainty (?0.27 ± 1.04 nmol m^?2 s^?1) and with substantial differences depending on wood decay status. Stems were CO₂ sources (1.93 ± 1.63 µmol m^?2 s^?1), but also net CH₄ sources (up to 0.98 nmol m^?2 s^?1), with a mean of 0.11 ± 0.21 nmol m^?2 s^?1 and significant differences depending on tree species. Stems of N. sylvatica, F. grandifolia, and L. tulipifera consistently emitted CH₄, whereas stems of A. rubrum, B. lenta, and Q. spp. were intermittent sources. Coarse woody debris and stems accounted for 35% of total measured CO₂ fluxes, whereas CH₄ emissions from living stems offset net soil and CWD CH₄ uptake by 3.5%. Our results demonstrate the importance of CH₄ emissions from living stems in upland forests and the need to consider multiple forest components to understand and interpret ecosystem CO₂ and CH₄ dynamics.     

Sperm competition games: Sperm size (mass) and number under raffle and displacement, and the evolution of P2

We examine models for evolution of sperm size (i.e. mass m) and number (s) under three mechanisms of sperm competition at low ‘risk’ levels: (i) raffle with no constraint on space available for competing sperm, (ii) direct displacement mainly by seminal fluid, and (iii) direct displacement mainly by sperm mass. Increasing sperm mass increases a sperm's ‘competitive weight’ against rival sperm through a diminishing returns function, r(m). ESS total ejaculate expenditure (the product m^?s^?) increases in all three models with sperm competition risk, q. If r(m), or ratio r′(m)/r(m), is independent of ESS sperm numbers, ESS sperm mass remains constant, and the sperm mass/number ratio (m^?/s^?) therefore decreases with risk. Dependency of sperm mass on risk can arise if r(m) depends on competing sperm density (sperm number / space available for sperm competition). Such dependencies generate complex relationships between sperm mass and number with risk, depending both on the mechanism and how sperm density affects r(m). While numbers always increase with risk, mass can either increase or decrease, but m^?/s^? typically decreases with risk unless sperm density strongly influences r(m). Where there is no extrinsic loading due to mating order, ESS paternity of the second (i.e. last) male to mate (P₂) under displacement always exceeds 0.5, and increases with risk (in the raffle P₂=0.5). Caution is needed when seeking evidence for a sperm size-number trade off. Although size and number trade-off independently against effort spent on acquiring matings, their product, m^?s^?, is invariant or fixed at a given risk level, effectively generating a size-number trade off. However, unless controlled for the effects of risk, the relation between m^? and s^? can be either positive or negative (a positive relation is usually taken as evidence against a size-number trade off).     

Promising properties of a formate dehydrogenase from a methanol-assimilating yeast Ogataea parapolymorpha DL-1 in His-tagged form

The cDNA gene coding for formate dehydrogenase (FDH) from Ogataea parapolymorpha DL-1 was cloned and expressed in Escherichia coli. The recombinant enzyme was purified by nickel affinity chromatography and was characterized as a homodimer composed of two identical subunits with approximately 40 kDa in each monomer. The enzyme showed wide pH optimum of catalytic activity from pH 6.0 to 7.0. It had relatively high optimum temperature at 65 °C and retained 93, 88, 83, and 71 % of its initial activity after 4 h of exposure at 40, 50, 55, and 60 °C, respectively, suggesting that this enzyme had promising thermal stability. In addition, the enzyme was characterized to have significant tolerance ability to organic solvents such as dimethyl sulfoxide, n-butanol, and n-hexane. The Michaelis–Menten constant (K _m), turnover number (k _cat), and catalytic efficiency (k _cat/K _m) values of the enzyme for the substrate sodium formate were estimated to be 0.82 mM, 2.32 s^?1, and 2.83 mM^?1 s^?1, respectively. The K _m for NAD⁺ was 83 μM. Due to its wide pH optimum, promising thermostability, and high organic solvent tolerance, O. parapolymorpha FDH may be a good NADH regeneration catalyst candidate.     

Photosynthetic refixing of CO2 is responsible for the apparent disparity between mitochondrial respiration in the light and in the dark

The net photosynthetic rate (P _N), the sample room CO₂ concentration (CO₂S) and the intercellular CO₂ concentration (C _i) in response to PAR, of C₃ (wheat and bean) and C₄ (maize and three-colored amaranth) plants were measured. Results showed that photorespiration (R _p) of wheat and bean could not occur at 2 % O₂. At 2 % O₂ and 0 μmol mol^?1 CO₂, P _N can be used to estimate the rate of mitochondrial respiration in the light (R _d). The R _d decreased with increasing PAR, and ranged between 3.20 and 2.09 μmol CO₂ m^?2 s^?1 in wheat. The trend was similar for bean (between 2.95 and 1.70 μmol CO₂ m^?2 s^?1), maize (between 2.27 and 0.62 μmol CO₂ m^?2 s^?1) and three-colored amaranth (between 1.37 and 0.49 μmol CO₂ m^?2 s^?1). The widely observed phenomenon of R _d being lower than R _n can be attributed to refixation, rather than light inhibition. For all plants tested, CO₂ recovery rates increased with increasing light intensity from 32 to 55 % (wheat), 29 to 59 % (bean), 54 to 87 % (maize) and 72 to 90 % (three-colored amaranth) at 50 and 2,000 μmol m^?2 s^?1, respectively.     

Preconditioning 2D Integer Data for Fast Convex Hull Computations

In order to accelerate computing the convex hull on a set of n points, a heuristic procedure is often applied to reduce the number of points to a set of s points, s ≤ n, which also contains the same hull. We present an algorithm to precondition 2D data with integer coordinates bounded by a box of size p × q before building a 2D convex hull, with three distinct advantages. First, we prove that under the condition min(p, q) ≤ n the algorithm executes in time within O(n); second, no explicit sorting of data is required; and third, the reduced set of s points forms a simple polygonal chain and thus can be directly pipelined into an O(n) time convex hull algorithm. This paper empirically evaluates and quantifies the speed up gained by preconditioning a set of points by a method based on the proposed algorithm before using common convex hull algorithms to build the final hull. A speedup factor of at least four is consistently found from experiments on various datasets when the condition min(p, q) ≤ n holds; the smaller the ratio min(p, q)/n is in the dataset, the greater the speedup factor achieved.     

Confounding Effects of Soil Moisture on the Relationship Between Ecosystem Respiration and Soil Temperature in Switchgrass

Understanding the response of ecosystem respiration (ER) to major environmental drivers is critical for estimating carbon sequestration and large-scale modeling research. Temperature effect on ER is modified by other environmental factors, mainly soil moisture, and such information is lacking for switchgrass (Panicum virgatum L.) ecosystems. The objective of this study was to examine seasonal variation in ER and its relationship with soil temperature (T _s) and moisture in a switchgrass field. ER from the nighttime net ecosystem CO₂ exchange measurements by eddy covariance system during the 2011 and 2012 growing seasons was analyzed. Nighttime ER ranged from about 2 (early growing season) to as high as 13 μmol m^?2 s^?1 (peak growing period) and showed a clear seasonality, with low rates during warm (>30 °C) and dry periods (<0.20 m³ m^?3 of soil water content). No single temperature or moisture function described variability in ER on the seasonal scale. However, an exponential temperature–respiration function explained over 50 % of seasonal variation in ER at adequate soil moisture (>0.20 m³ m^?3), indicating that soil moisture <0.20 m³ m^?3 started to limit ER. Due to the limitation of soil–atmosphere gas exchange, ER rates declined markedly in wet soil conditions (>0.35 m³ m^?3) as well. Consequently, both dry and wet conditions lowered temperature sensitivity of respiration (Q ₁₀). Stronger ER–T _s relationships were observed at higher soil moisture levels. These results demonstrate that soil moisture greatly influences the dynamics of ER and its relationship with T _s in drought prone switchgrass ecosystems.     

Fed-Batch Cultivation of Arthrospira platensis Using Carbon Dioxide from Alcoholic Fermentation and Urea as Carbon and Nitrogen Sources

To reduce CO₂ emissions from alcoholic fermentation, Arthrospira platensis was cultivated in tubular photobioreactor using either urea or nitrate as nitrogen sources at different light intensities (60 μmol m^?2 s^?1?≤?I?≤?240 μmol m^?2 s^?1). The type of carbon source (pure CO₂ or CO₂ from fermentation) did not show any appreciable influence on the main cultivation parameters, whereas substitution of nitrate for urea increased the nitrogen-to-cell conversion factor (Y _X/N ), and the maximum cell concentration (X _m ) and productivity (P _X ) increased with I. As a result, the best performance using gaseous emissions from alcoholic fermentation (X _m ?=?2,960?±?35 g m^?3, P _X ?=?425?±?5.9 g m^?3 day^?1 and Y _X/N ?=?15?±?0.2 g g^?1) was obtained at I?=?120 μmol m^?2 s^?1 using urea as nitrogen source. The results obtained in this work demonstrate that the combined use of effluents rich in urea and carbon dioxide could be exploited in large-scale cyanobacteria cultivations to reduce not only the production costs of these photosynthetic microorganisms but also the environmental impact associated to the release of greenhouse emissions.     

Electronic fine structure calculation of metal complexes with three-open-shell <Emphasis Type="Italic">s</Emphasis>, <Emphasis Type="Italic">d,and p</Emphasis> configurations

The ligand field density functional theory (LFDFT) algorithm is extended to treat the electronic structure and properties of systems with three-open-shell electron configurations, exemplified in this work by the calculation of the core and semi-core 1s, 2s, and 3s one-electron excitations in compounds containing transition metal ions. The work presents a model to non-empirically resolve the multiplet energy levels arising from the three-open-shell systems of non-equivalent ns, 3d, and 4p electrons and to calculate the oscillator strengths corresponding to the electric-dipole 3d ^m  → ns ¹3d ^m 4p ¹ transitions, with n = 1, 2, 3 and m = 0, 1, 2, …, 10 involved in the s electron excitation process. Using the concept of ligand field, the Slater-Condon integrals, the spin-orbit coupling constants, and the parameters of the ligand field potential are determined from density functional theory (DFT). Therefore, a theoretical procedure using LFDFT is established illustrating the spectroscopic details at the atomic scale that can be valuable in the analysis and characterization of the electronic spectra obtained from X-ray absorption fine structure or electron energy loss spectroscopies.     

Cloning, Expression, and Enzymatic Characterization of Isocitrate Dehydrogenase from Helicobacter pylori

Isocitrate dehydrogenase (IDH) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate with NAD(P) as a cofactor in the tricarboxylic acid cycle. As a housekeeping protein in Helicobacter pylori, IDH was considered as a possible candidate for serological diagnostics and detection. Here, we identified a new icd gene encoding IDH from H. pylori strain SS1. The recombinant H. pylori isocitrate dehydrogenase (HpIDH) was cloned, expressed, and purified in E. coli system. The enzymatic characterization of HpIDH demonstrates its activity with k _cat of 87 s^?1, K _m of 124 μM and k _cat/K _m of 7 × 10⁵ M^?1s^?1 toward isocitrate, k _cat of 80 s^?1, K _m of 176 μM and k _cat/K _m of 4.5 × 10⁵ M^?1s^?1 toward NADP. The optimum pH of the enzyme activity is around 9.0, and the optimum temperature is around 50 °C. This current work is expected to help better understand the features of HpIDH and provide useful information for H. pylori serological diagnostics and detection.     

Ecosystem respiration derived from 222Rn measurements on Rishiri Island, Japan

We evaluated the nighttime CO₂ flux (ecosystem respiration) on Rishiri Island, located at the northern tip of Hokkaido, Japan, from 2009 to 2011, by using the relationship between atmospheric ²²²Rn and CO₂ concentrations. The annual mean CO₂ flux was 1.8 μmol m^?2 s^?1, with a maximum monthly mean in July (4.6 ± 2.6 μmol m^?2 s^?1) and a broad minimum from December to March (0.33 ± 0.29 μmol m^?2 s^?1). The annual mean was comparable to fluxes at the JapanFlux sites in northern Japan. During the season of snow cover (mid-December to early April), the CO₂ flux was low (0.45 ± 0.43 μmol m^?2 s^?1). Total annual respiration was estimated at 679 ± 174 g cm^?2, about 8 % of which occurred during the season of snow cover.     

Response of chlorophyll d-containing cyanobacterium Acaryochloris marina to UV and visible irradiations

We have previously investigated the response mechanisms of photosystem II complexes from spinach to strong UV and visible irradiations (Wei et al J Photochem Photobiol B 104:118–125, 2011). In this work, we extend our study to the effects of strong light on the unusual cyanobacterium Acaryochloris marina, which is able to use chlorophyll d (Chl d) to harvest solar energy at a longer wavelength (740 nm). We found that ultraviolet (UV) or high level of visible and near-far red light is harmful to A. marina. Treatment with strong white light (1,200 μmol quanta m^?2 s^?1) caused a parallel decrease in PSII oxygen evolution of intact cells and in extracted pigments Chl d, zeaxanthin, and α-carotene analyzed by high-performance liquid chromatography, with severe loss after 6 h. When cells were irradiated with 700 nm of light (100 μmol quanta m^?2 s^?1) there was also bleaching of Chl d and loss of photosynthetic activity. Interestingly, UVB radiation (138 μmol quanta m^?2 s^?1) caused a loss of photosynthetic activity without reduction in Chl d. Excess absorption of light by Chl d (visible or 700 nm) causes a reduction in photosynthesis and loss of pigments in light harvesting and photoprotection, likely by photoinhibition and inactivation of photosystem II, while inhibition of photosynthesis by UVB radiation may occur by release of Mn ion(s) in Mn₄CaO₅ center in photosystem II.     

Highly active β-xylosidases of glycoside hydrolase family 43 operating on natural and artificial substrates

The hemicellulose xylan constitutes a major portion of plant biomass, a renewable feedstock available for conversion to biofuels and other bioproducts. β-xylosidase operates in the deconstruction of the polysaccharide to fermentable sugars. Glycoside hydrolase family 43 is recognized as a source of highly active β-xylosidases, some of which could have practical applications. The biochemical details of four GH43 β-xylosidases (those from Alkaliphilus metalliredigens QYMF, Bacillus pumilus, Bacillus subtilis subsp. subtilis str. 168, and Lactobacillus brevis ATCC 367) are examined here. Sedimentation equilibrium experiments indicate that the quaternary states of three of the enzymes are mixtures of monomers and homodimers (B. pumilus) or mixtures of homodimers and homotetramers (B. subtilis and L. brevis). k _cat and k _cat/K _m values of the four enzymes are higher for xylobiose than for xylotriose, suggesting that the enzyme active sites comprise two subsites, as has been demonstrated by the X-ray structures of other GH43 β-xylosidases. The K _i values for d-glucose (83.3–357 mM) and d-xylose (15.6–70.0 mM) of the four enzymes are moderately high. The four enzymes display good temperature (K _t ^0.5?～?45 °C) and pH stabilities (>4.6 to <10.3). At pH 6.0 and 25 °C, the enzyme from L. brevis ATCC 367 displays the highest reported k _cat and k _cat/K _m on natural substrates xylobiose (407 s^?1, 138 s^?1?mM^?1), xylotriose (235 s^?1, 80.8 s^?1?mM^?1), and xylotetraose (146 s^?1, 32.6 s^?1?mM^?1).     

2-Methylisoborneol production characteristics of <Emphasis Type="Italic">Pseudanabaena</Emphasis> sp. FACHB 1277 isolated from Xionghe Reservoir,China

The cyanobacterium Pseudanabaena sp. FACHB 1277, a 2-methylisoborneol (2-MIB) producer isolated from Xionghe Reservoir, was identified by molecular biological methods based on the 16S rDNA sequence. Pseudanabaena sp. FACHB 1277 is a planktonic freshwater species with relatively high 2-MIB per cell density value (7.76?×?10^?6 ng cell^?1) and specific growth rate (0.25?±?0.01 d^?1). The effects of temperature and light intensity on 2-MIB production of Pseudanabaena sp. FACHB 1277 were investigated. Of the six temperatures tested, 10, 15, 20, 25, 30, and 35 °C, the maximum total 2-MIB per cell density and minimum cell density were observed at 10 °C, while the total 2-MIB and dissolved 2-MIB (including extracellular and dissolved intracellular 2-MIB) increased with increasing temperature. Among the six tested light intensities (10, 25, 40, 55, 70, and 85 μmol photons m^?2 s^?1), the minimum total 2-MIB per cell density and maximum cell density were observed at 25 μmol photons m^?2 s^?1. The total 2-MIB and extracellular 2-MIB increased with light intensity increasing from 10 to 40 μmol photons m^?2 s^?1, while no significant increase was observed when the light intensity was higher than 40 μmol photons m^?2 s^?1. The maximum intracellular 2-MIB (including dissolved and bound) occurred at 25 μmol photons m^?2 s^?1. The present study indicates that increasing temperature could favor the conversion of bound intracellular to dissolved 2-MIB, while increasing light intensity stimulates the release of dissolved intracellular 2-MIB into the environment.     

Enhancement of phenylpropanoid enzymes and lignin in Phalaenopsis orchid and their influence on plant acclimatisation at different levels of photosynthetic photon flux

Effects of three levels of photosynthetic photon flux (PPF: 60, 160 and 300 μmol m⁻²s⁻¹) were investigated in one-month-old Phalaenopsis plantlets acclimatised ex vitro. Optimal growth, chlorophyll and carotenoid concentations, and a high carotenoid:chlorophyll a ratio were obtained at 160 μmol m⁻²s⁻¹, while net CO₂ assimilation (A), stomatal conductance (g), transpiration rate (E) and leaf temperature peaked at 300 μmol m⁻²s⁻¹, indicating the ability of the plants to grow ex vitro. Adverse effects of the highest PPF were reflected in loss of chlorophyll, biomass, non-protein thiol and cysteine, but increased proline. After acclimatisation, glucose-6-phosphate dehydrogenase, shikimate dehydrogenase, phenylalanine ammonia-lyase (PAL) and cinnamyl alcohol dehydrogenase (CAD) increased, as did lignin. Peroxidases (POD), which play an important role in lignin synthesis, were induced in acclimatised plants. Polyphenol oxidase (PPO) and β-glucosidase (β-GS) activities increased to a maximum in acclimatised plants at 300 μmol m⁻²s⁻¹. A positive correlation between PAL, CAD activity and lignin concentration was observed, especially at 160 and 300 μmol m⁻²s⁻¹. The study concludes that enhancement of lignin biosynthesis probably not only adds rigidity to plant cell walls but also induces defence against radiation stress. A PPF of 160 μmol m⁻²s⁻¹was suitable for acclimatisation when plants were transferred from in vitro conditions.     

Different responses of photosystem I and photosystem II in three tropical oilseed crops exposed to chilling stress and subsequent recovery

Key message

Different responses of photosystem I and II to chilling.

Abstract

Tropical crops are sensitive to chilling stress, but the underlying physiological mechanisms are unclear. We investigated the maximum quantum yield of PSII (F _v/F _m), the maximum photo-oxidizable P700 (P _m), the energy distribution in PSII, and the redox state of P700 in leaves of seedlings of three promising oilseed crops originating from tropical regions, Plukenetia volubilis, Jatropha curcas and Ricinus communis, during chilling treatment and subsequent recovery under a photon flux density of 450 μmol m^?2 s^?1. Our results showed that F _v/F _m decreased progressively and significantly to about 44.7, 62.2 and 77.0 % of the control after chilling treatment for 3 days in P. volubilis, J. curcas and R. communis, respectively, mainly due to the decrease in F _m (maximum fluorescence of PSII). After recovery under 18 °C for 6 days, F _v/F _m recovered to 81.4 and 94.9 % of the control in J. curcas and R. communis, but only to 26.3 % in P. volubilis. Under chilling stress and subsequent recovery, P _m remained stable in J. curcas and R. communis, whereas it decreased slightly in P. volubilis. These results indicated that PSII was more sensitive to chilling stress than PSI under moderate light for all three species, and that P. volubilis was the most susceptible. Cyclic electron flow around PSI and effective quantum yield of photosystem II [Y _(CEF)/Y _(II)] ratio were stimulated much more in J. curcas and R. communis compared with that in P. volubilis under chilling conditions, resulting in more severe injury as indicated by higher accumulation of hydrogen peroxide and malondialdehyde. There was a significantly negative relationship between F _v/F _m and Y _(CEF)/Y _(II), suggesting that stimulation of Y _(CEF)/Y _(II) plays a pivotal role in protecting PSI and PSII from photoinhibition caused by chilling stress.     

GH52 xylosidase from Geobacillus stearothermophilus: characterization and introduction of xylanase activity by site-directed mutagenesis of Tyr509

A xylosidase gene, gsxyn, was cloned from the deep-sea thermophilic Geobacillus stearothermophilus, which consisted of 2,118 bp and encoded a protein of 705 amino acids with a calculated molecular mass of 79.8 kDa. The GSxyn of glycoside hydrolase family 52 (GH52) displayed its maximum activity at 70 °C and pH 5.5. The K _m and k _cat values of GSxyn for ρNPX were 0.48 mM and 36.64 s^?1, respectively. Interestingly, a new exo-xylanase activity was introduced into GSxyn by mutating the tyrosine509 into glutamic acid, whereas the resultant enzyme variant, Y509E, retained the xylosidase activity. The optimum xylanase activity of theY509E mutant displayed at pH 6.5 and 50 °C, and retained approximately 45 % of its maximal activity at 55 °C, pH 6.5 for 60 min. The K _m and k _cat values of the xylanase activity of Y509E mutant for beechwood xylan were 5.10 mg/ml and 22.53 s^?1, respectively. The optimum xylosidase activity of theY509E mutant displayed at pH 5.5 and 60 °C. The K _m and k _cat values of the xylosidase activity of Y509E mutant for ρNPX were 0.51 mM and 22.53 s^?1, respectively. This report demonstrated that GH52 xylosidase has provided a platform for generating bifunctional enzymes for industrially significant and complex substrates, such as plant cell wall.     

Optimization of heterologous expression of the phytase (PPHY) of Pichia anomala in P. pastoris and its applicability in fractionating allergenic glycinin from soy protein

The phytase (PPHY) of Pichia anomala has the requisite properties of thermostability and acidstability, broad substrate spectrum, and protease insensitivity, which make it a suitable candidate as a feed and food additive. The 1,389-bp PPHY gene was amplified from P. anomala genomic DNA, cloned in pPICZαA, and expressed extracellularly in P. pastoris X33. Three copies of PPHY have been detected integrated into the chromosomal DNA of the recombinant P. pastoris. The size exclusion chromatography followed by electrophoresis of the pure rPPHY confirmed that this is a homohexameric glycoprotein of ~420 kDa with a 24.3 % portion as N-linked glycans. The temperature and pH optima of rPPHY are 60 °C and 4.0, similar to the endogenous enzyme. The kinetic characteristics K _m, V _max, K _cat, and K _cat/K _m of rPPHY are 0.2 ± 0.03 mM, 78.2 ± 1.43 nmol mg^?1 s^?1, 65,655 ± 10.92 s^?1, and 328.3 ± 3.12 μM^?1 s^?1, respectively. The optimization of medium components led to a 21.8-fold improvement in rPPHY production over the endogenous yeast. The rPPHY titer attained in shake flasks could also be sustained in the laboratory fermenter. The rPPHY accounts for 57.1 % of the total secreted protein into the medium. The enzyme has been found useful in fractionating allergenic protein glycinin from soya protein besides dephytinization.