Environmental Fluctuations and Level of Density-Compensation Strongly Affects the Probability of Fixation and Fixation Times

The probability of, and time to, fixation of a mutation in a population has traditionally been studied by the classic Wright–Fisher model where population size is constant. Recent theoretical expansions have covered fluctuating populations in various ways but have not incorporated models of how the environment fluctuates in combination with different levels of density-compensation affecting fecundity. We tested the hypothesis that the probability of, and time to, fixation of neutral, advantageous and deleterious mutations is dependent on how the environment fluctuates over time, and on the level of density-compensation. We found that fixation probabilities and times were dependent on the pattern of autocorrelation of carrying capacity over time and interacted with density-compensation. The pattern found was most pronounced at small population sizes. The patterns differed greatly depending on whether the mutation was neutral, advantageous, or disadvantageous. The results indicate that the degree of mismatch between carrying capacity and population size is a key factor, rather than population size per se, and that effective population sizes can be very low also when the census population size is far above the carrying capacity. This study highlights the need for explicit population dynamic models and models for environmental fluctuations for the understanding of the dynamics of genes in populations.     

Optimization of in vitro multiple shoot clump induction and plantlet regeneration of Kentucky bluegrass (Poa pratensis)

An efficient protocol for Kentucky bluegrass (Poa pratensis L.) in vitro culture was established using shoot apices of seedlings as explants. The optimal procedure of this protocol for majority of the genotypes was that meristematic cell clumps and small calluses were firstly induced from the bases of explants on initial culture medium supplemented with 0.9 μM 2,4-d and 8.9 μM 6-BA for 20 d, then were separated and transferred to shoot clumps induction medium containing 8.9 μM 6-BA for the formation of multiple shoot clumps. The percentage of multiple shoot clumps and numbers of shoots per clump were deeply related with the combinations of different plant growth regulators, duration of initial culture, the intensity of illumination and genotypes. Histological observation of the induced explants revealed that the meristematic cell clumps were produced from repeated division of the cortical cells and original meristematic primodium cells of explants, and the multiple shoots were formed via organogenesis pathway in the meristematic cell regions of cultures on shoot clumps induction medium. In this study, plantlets were efficiently regenerated on large scale from seven cultivars of Kentucky bluegrass. Hence the meristematic cell clumps and small calluses in this protocol could be considered good targets for genetic transformation of Kentucky bluegrass.     

Modeling and Estimation of Kinetic Parameters and Replicative Fitness of HIV-1 from Flow-Cytometry-Based Growth Competition Experiments

Growth competition assays have been developed to quantify the relative fitness of HIV-1 mutants. In this article, we develop mathematical models to describe viral/cellular dynamic interactions in the assay system from which the competitive fitness indices or parameters are defined. In our previous HIV-viral fitness experiments, the concentration of uninfected target cells was assumed to be constant (Wu et al. 2006). But this may not be true in some experiments. In addition, dual infection may frequently occur in viral fitness experiments and may not be ignorable. Here, we relax these two assumptions and extend our earlier viral fitness model (Wu et al. 2006). The resulting models then become nonlinear ODE systems for which closed-form solutions are not achievable. In the new model, the viral relative fitness is a function of time since it depends on the target cell concentration. First, we studied the structure identifiability of the nonlinear ODE models. The identifiability analysis showed that all parameters in the proposed models are identifiable from the flow-cytometry-based experimental data that we collected. We then employed a global optimization approach (the differential evolution algorithm) to directly estimate the kinetic parameters as well as the relative fitness index in the nonlinear ODE models using nonlinear least square regression based on the experimental data. Practical identifiability was investigated via Monte Carlo simulations.     

EPR and ENDOR studies of Fe(II) hemoproteins reduced and oxidized at 77 K

γ-irradiation of frozen solutions of Fe(II) hemoproteins at 77 K generates both electron paramagnetic resonance (EPR) active singly reduced and oxidized heme centers trapped in the conformation of the Fe(II) precursors. The reduction products of pentacoordinate (S = 2) Fe(II) globins, peroxidases and cytochrome P450cam show EPR and electron–nuclear double resonance (ENDOR) spectra characteristic of (3d ⁷) Fe(I) species. In addition, cryoreduced Fe(II) α-chains of hemoglobin and myoglobin exhibit an S = 3/2 spin state produced by antiferromagnetic coupling between a porphyrin anion radical and pentacoordinate (S = 2) Fe(II). The spectra of cryoreduced forms of Fe(II) hemoglobin α-chains and deoxymyoglobin reveal that the Fe(II) precursors adopt multiple conformational substates. Reduction of hexacoordinate Fe(II) cytochrome c and cytochrome b ₅ as well as carboxy complexes of deoxyglobins produces only Fe(II) porphyrin π-anion radical species. The low-valent hemoprotein intermediates produced by cryoreduction convert to the Fe(II) states at T > 200 K. Cryogenerated Fe(III) cytochrome c and cytochrome b ₅ have spectra similar to these for the resting Fe(III) states, whereas the spectra of the products of cryooxidation of pentacoordinate Fe(II) globins and peroxidases are different. Cryooxidation of CO–Fe(II) globins generates Fe(III) hemes with quantum-mechanically admixed S = 3/2, 5/2 ground states. The trapped Fe(III) species relax to the equilibrium ferric states upon annealing at T > 190 K. Both cryooxidized and reduced centers provide very sensitive EPR/ENDOR structure probes of the EPR-silent Fe(II) state. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Biosorption of Cd(II) and Pb(II) onto brown seaweed, Lobophora variegata (Lamouroux): kinetic and equilibrium studies

The present work deals with the biosorption performance of raw and chemically modified biomass of the brown seaweed Lobophora variegata for removal of Cd(II) and Pb(II) from aqueous solution. The biosorption capacity was significantly altered by pH of the solution delineating that the higher the pH, the higher the Cd(II) and Pb(II) removal. Kinetic and isotherm experiments were carried out at the optimal pH 5.0. The metal removal rates were conspicuously rapid wherein 90% of the total sorption occurred within 90 min. Biomass treated with CaCl₂ demonstrated the highest potential for the sorption of the metal ions with the maximum uptake capacities i.e. 1.71 and 1.79 mmol g⁻¹ for Cd(II) and Pb(II), respectively. Kinetic data were satisfactorily manifested by a pseudo-second order chemical sorption process. The process mechanism consisting of both surface adsorption and pore diffusion was found to be complex. The sorption data have been analyzed and fitted to sorption isotherm of the Freundlich, Langmuir, and Redlich–Peterson models. The regression coefficient for both Langmuir and Redlich–Peterson isotherms were higher than those secured for Freundlich isotherm implying that the biosorption system is possibly monolayer coverage of the L. variegata surface by the cadmium and lead ions. FT-IR studies revealed that Cd(II) and Pb(II) binding to L. variegata occurred primarily through biomass carboxyl groups accompanied by momentous interactions of the biomass amino and amide groups. In this study, we have observed that L. variegata had maximum biosorption capacity for Cd(II) and Pb(II) reported so far for any marine algae. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Rediscovery and phylogenetic placement of Olpidiopsis gillii (de Wildeman) Friedmann,a holocarpic oomycete parasitoid of freshwater diatoms

The genus Olpidiopsis of the Oomycota includes several species that are aquatic parasites and hyperparasites. Despite their widespread occurrence and potential ecological importance, only a handful of these species has been subjected to phylogenetic investigations, so far. Most species have not been observed and reported for several decades. In the current study, the freshwater diatom parasite Olpidiopsis gillii (de Wild.) Friedmann was rediscovered from the river Main in Germany and investigated for its phylogenetic placement using nuclear small ribosomal subunit (SSU) sequences. The absence of a zoospore diplanetism is a characteristic of the genus Olpidiopsis, which is in contrast to the diplanetism observed in species of Ectrogella. The phylogenetic reconstruction revealed that Olpidiopsis gillii is a basal lineage within the oomycetes, grouping together with the recently-described marine diatom parasite Olpidiopsis drebesii with high support, and loosely associated with Olpidiopsis species parasitising red algae. However, as there are no sequence data available for the type species of both Olpidiopsis and Ectrogella the taxonomic assignment of these simple holocarpic parasites of algae and diatoms remains fraught with uncertainty.     

Anatomy and morphology of photinia (Photinia × fraseri Dress) in vitro plants inoculated with rhizobacteria

Photinia × fraseri Dress (photinia) is a woody plant with high ornamental value. The anatomy and morphology of micropropagated photinia inoculated with the plant growth-promoting rhizobacteria Azospirillum brasilense and Azotobacter chroococcum, in combination with pulses of 49.2 μM indole-3-butyric acid during rhizogenesis, were characterized using light and electron microscopy. Leaves of inoculated in vitro plants showed better development than those subjected to auxin control only. All inoculated treatments, independent of the bacterial strain used, had leaves with two layers of palisade parenchyma, a thick cuticle and linear unicellular trichomes. There was no proliferation of undifferentiated tissue in any treatment and the plants showed shoot–root vascular connections. Ex vitro leaves and in vitro plants inoculated with Azospirillum brasilense Cd and Azotobacter chroococcum 42 had large stomata with elliptic aperture radially surrounded by small stomata on the abaxial foliar surface. In addition, plants of these treatments had a large root hair zone over the root surface. Bacteria were only observed on surfaces of root hairs. The results suggest that the structural changes induced by bacterial inoculation of photinia in vitro plants could lead to better adaptation to ex vitro conditions after transplanting.     

Patterns and rates of erosion in dead Porites across the Great Barrier Reef (Australia) after 2 years and 4 years of exposure

Rates and agents of erosion were investigated experimentally at six sites located along a cross shelf transect from the northern Queensland coast out into the Coral Sea. Rates of internal and external erosion of coral blocks, and accretion by coralline algae were measured after 2 years and 4 years of exposure. Blocks were cut from live colonies of Porites sp., which were collected from the outer barrier reef in north Queensland. They were then washed, dried, measured, weighed and attached to grids that were firmly attached to dead coral substrate at depths of 7–10 m. Significant differences in all three parameters were found within and among sites, and rates increased with increasing duration of exposure. Inshore sites were characterized by low rates of external erosion compared to offshore sites. Agents responsible for internal erosion differed among sites, with boring sponges being most abundant on the two inshore reefs, and molluscs most abundant at the offshore sites. Deposit-feeding polychaetes were more abundant at the two inshore sites, while filter and surface deposit feeders were more common at the offshore sites. Net erosion rates varied among sites (1.090±0.499 to 7.846±3.218 kg m²), and the relative importance of the components of erosion changed markedly along the cross-shelf transect.     

Detachment-accelerated ripening and senescence of strawberry (Fragaria × ananassa Duch. cv. Akihime) fruit and the regulation role of multiple phytohormones

To study the detachment stress on the ripeness of strawberry fruit, physiological characteristics of strawberry fruit on and off plant during ripeness and senescence processes were investigated. The results indicated that the ripeness of strawberry fruit upon detachment was accelerated, in terms of firmness, soluble solid content and especially color development. The color of fruit off plant changed rapidly from white to full red in 1–2 days. The respiratory rate in fruit off plant was strengthened, higher than that on plant. Abscisic acid level and ethylene production in fruit off plant were also higher than those on plant and auxin degradation was exacerbated by detachment. Expression levels of FaMYB1, FabHLH3 and FaTTG1 were generally reduced with phenotypes of redder color and more anthocyanin accumulation in fruit off plant. Results also suggested that the detachment initially stimulated ethylene and abscisic acid production and auxin degradation, which modulated ripening-related gene expression and at last enhanced fruit pigmentation.     

Isolation and characterization of fourteen microsatellites from a tree peony (Paeonia suffruticosa)

Tree peonies are well known garden flowers and very important medicinal plants with some 1,000 cultivars. Most of the cultivars are believed to be of hybrid origin and their wild parents are suffering from severe depopulation. To rejuvenate the traditional cultivars and assess the genetic diversity of the critically endangered wild species for conservation purpose, it is crucial to use suitable molecular markers. In this study, we isolated 14 polymorphic microsatellite loci from an enriched genomic library. These loci were verified by re-cloning and re-sequencing and their characteristics were tested with 20 individuals. On average there are 5.5 alleles per locus, and mean values of observed heterozygosity and expected heterozygosity are 0.41 and 0.67, respectively.     

Isolation and characterization of polymorphic microsatellite loci in Castanopsis chinensis Hance (Fagaceae)

Twelve novel microsatellite loci were isolated and characterized from enriched genomic libraries of Castanopsis chinensis. Four previously reported microsatellites from Castanopsis cuspidata were cross-amplified in C. chinensis. Forty-two sample trees from a wild population were tested for polymorphism using a set of the 16 polymorphic microsatellites. The average allele number of these microsatellites was 4.6 per locus, ranging from 2 to 7. The ranges of observed and expected heterozygosity were 0.262–1.000 and 0.238–0.818, respectively. Significant deviations from Hardy–Weinberg equilibrium were detected at five loci and no linkage disequilibrium was observed.     

Serological identification and molecular characterization of B (A) 02 subtype in patients and blood donors from Eastern China

This study was designed to identify the rare?type?ABO?blood?groups, B(A) 02, from Eastern China. Three samples with discordant serological results during routine blood type identification and four samples from one sample’ family were selected. All of them were detected by serological method. The exon 6 and 7 of the ABO genes were amplified by PCR and sequenced. They were typed as AsubB by serology and as BO by genotype. In AsubB samples, nt 700C>G mutation was detected in B gene, which was previously defined as B(A)02 alleles. In these seven samples, six showed B(A)02/O01 and one showed B(A)02/O02.B(A)02 allele was found to be more common in this study than B(A)04 which is considered to be more frequent than B(A)02. The careful identification of rare blood types is important for the safety of clinical blood transfusion.     

Normal and superconducting state specific heat of Mg1 − xAlxB2 (0 < x < 0.2)

A theoretical analysis of specific heat C(T) behaviour of the Mg_1 ? xAl_xB₂ (0 < x < 0.2) in the temperature domain 0 ≤ T ≤ 300 K is presented. Calculations of C(T) have been made within the two-component scheme: one is the phonon and the other is the electronic contribution. Phonon specific heat is well estimated from the Debye and Einstein temperature for Mg_1 ? xAl_xB₂ obtained following an overlap repulsive potential. The interatomic potential of this model includes contributions from the long-range Coulomb attraction and the short-range overlap repulsion and the van der Waals attraction. The fermion constituent as the electronic specific heat is deduced using a suitable trial function above and below T_c. At the critical temperature, the discontinuity in specific heat is higher than that of other samples and the transition is sharper than for most samples. The theoretical results from boson and fermion terms are then compared with the experimental results.     

Haploid plants from anther cultures of poplar (Populus × beijingensis)

Homozygous genotypes are valuable for genetic and genomic studies in higher plants. However, obtaining homozygous perennial woody plants using conventional breeding techniques is currently a challenge due to a long juvenile period, high heterozygosity, and substantial inbreeding depression. In vitro androgenesis has been used to develop haploid and doubled haploid plants. In the present study, we report the regeneration of haploid lines of poplar (Populus × beijingensis) via anther culture. Anthers at the uninucleate stage were induced to produce callus using three basic media. Two auxins (naphthalene acetic acid [NAA] and 2,4-dichloro-phenoxyacetic acid [2,4-D]), and two cytokinin (kinetin [KT] and 6-benzyladenine [BA]) were tested to explore the influence of plant growth regulators on callus response. H medium (Bourgin and Nitsch 1967) supplemented with 1.0 mg/L NAA and 1.0 mg/L KT induced the highest rate of callus formation. When callus obtained from anthers were subcultured in MS medium containing 1.0 mg/L BA and 0.2 mg/L NAA, followed by transfer to half-strength MS medium supplemented with indole-3-butyric acid (0.2–0.5 mg/L), the formation of regenerated plantlets increased dramatically. Inclusion of gibberellic acid (0.02–0.2 mg/L) in addition to a combination of BA (0.6 mg/L)-NAA (0.2 mg/L) in the culture medium resulted in enhanced frequency of shoot development, as well as greater internode elongation. Ploidy analysis of 580 regenerated plants, using both flow cytometry and chromosome counting, revealed 10.3 % haploid and 1.0 % triploid plantlets. The remaining plantlets were all diploid.     

In vitro response of encapsulated and non-encapsulated somatic embryos of Kinnow mandarin (Citrus nobilis Lour × C. deliciosa Tenora)

The aim of present investigation was to study the effect of storage conditions on percentage germination of encapsulated and non-encapsulated somatic embryos of Kinnow mandarin (Citrus nobilis Lour × C. deliciosa Tenora). Different batches of encapsulated and non-encapsulated embryos were preserved at room temperature, 4°C, in liquid nitrogen as such and by embedding in liquid paraffin. In the encapsulated somatic embryos stored at room temperature in sealed Petri plates, percentage of germination was 24.99%, but 5.55% in non-encapsulated embryos after 3 days of storage. Encapsulated embryos stored in vials containing liquid paraffin at room temperature were germinated at 18.05% after 60 days of storage, while it was 13.88% in non-encapsulated embryos after 45 days of storage. Encapsulated somatic embryos stored at 4°C in sealed Petri plates remained viable for up to 75 days with 6.94% germination, whereas non-encapsulated embryos remained viable for up to 45 days with 24.99% germination. Encapsulated embryos stored at 4°C in vials filled with paraffin germinated at 11.11% after 120 days of storage, but 5.55% in non-encapsulated embryos after 90 days of storage. Encapsulated and non-encapsulated embryos stored in liquid nitrogen showed 58.33 and 51.38% survival, respectively, after 7 months of storage. The plantlets developed from these embryos were transplanted after acclimatization and are growing normal.     

Physiological responses of wheat and barley to Russian wheat aphid, Diuraphis noxia (Mordvilko) and bird cherry-oat aphid, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)

Although aphids are among the most injurious of all agronomic insect pests, much remains unknown about how their feeding alters plant physiology. Two experiments were conducted to examine the physiological responses of wheat, Triticum aestivum L. and barley, Hordeum vulgare L. to injury by Diuraphis noxia (Mordvilko) and Rhopalosiphum padi (L.) (Hemiptera: Aphididae). Gas-exchange parameters, chlorophyll fluorescence, and chlorophyll content were examined at 3, 6, and 9 days post-infestation on control and aphid (D. noxia and R. padi) infested treatments. In general, chlorophyll content and chlorophyll fluorescence parameters (non-variable minimal fluorescence, maximal fluorescence, and variable fluorescence) were not significantly affected by either aphid species. Photochemical and non-photochemical quenching coefficients were significantly impacted by both aphid species, suggesting that aphid feeding may influence the photoprotective xanthophyll cycle altering the thylakoid membrane pH gradient. Feeding by both aphid species resulted in an increase in electron transport rate, but at different time periods. Wheat plants infested with D. noxia had accelerated declines in photosynthetic capacity when compared to R. padi-infested and control plants. These plants exhibited decreased values for A_max, which was accompanied by decreased values for V_cmax and J_max Neither aphid species negatively affected the photosynthetic capacity of the barley plants until day 9. At this time, aphid-infested plants had decreased values for A_max which was accompanied by decreased values in J_max. Although R. padi feeding does not typically result in visual damage symptoms as previously demonstrated, clearly this aphid does have an impact on the gas-exchange and chlorophyll fluorescence of its host plants. Handling editor: Heikki Hokkanen     

Growth kinetics of 1–2 mm and 3–4 mm colonies of Nostoc sphaeroides (Cyanophyta) in outdoor culture

Nostoc sphaeroides Kützing was cultivated in paddlewheel-driven raceway ponds and the growth kinetics of 1-2 mm and 3-4 mm colonies of N. sphaeroides was studied. The biomass productivities in 2.5 m(2) raceway ponds inoculated with 1-2 mm and 3-4 mm colonies were 5.2 and 0.25 g dry wt m(-2) d(-1), respectively. Furthermore, differently sized colonies showed different relative water content, total soluble carbohydrates, chlorophyll a content and density of filaments. This is the first report on mass culture of N. sphaeroides under outdoor conditions.