Population size structure,growth, arm number and damage in the sea star Archaster angulatus Müller and Troschel, 1842 (Echinodermata: Asteroidea)

Monthly sampling for the sea star Archaster angulatus revealed at least four cohorts with linear growth in the 0+ and 1+ year groups to about 26 months after which growth slows and conforms to the von Bertalanffy model of growth. The appearance of small individuals (arm radius (R) < 20 mm) from March to May is consistent with the discrete December/January spawning period. Sea stars attain R of 38.7 mm at one year, 73.7 mm at two years and maturity occurs in the second year. The 3+ year and 4+ year cohorts were difficult to detect reliably, but sample number peaks at 90–94 mm and 105–107 mm in January of both 2010 and 2011 are indicative of size at three and four years. Two methods of estimating von Bertalanffy growth parameters both yielded estimates of 127 mm for L_inf and k values of 0.41 and 0.49. Comparison of size at age estimates from growth models and cohort analysis suggested the actual value of k after maturity lies between 0.35 and 0.45. Four-armed (1.48%), six-armed (1.26%) and seven-armed (0.11%) individuals were present in the population and arm damage, thought to have resulted from sublethal predation was observed in 13.8% of sea stars.     

Simulation of protein diffusion: a sensitive probe of protein–solvent interactions

Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein–water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius (R_S), which was derived from the diffusion coefficient and the viscosity. R_S was compared to the geometric radius (R_G) of CALB, which was derived from the protein density. R_S and R_G differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein–water system sufficiently, and using the complete production run for the determination of the diffusion coefficient.     

Excluded volume of hard cylinders of variable aspect ratio

In this article, we report expressions for the excluded volume, v _ex and second virial coefficient, B ₂, of hard cylinders as a function of their aspect ratio (𝒜 = L/D), where L and D are the length and diameter of the cylinder, respectively. These expressions are valid for aspect ratio values within the interval 0.001 < 𝒜 < 100, that covers from thin plates to long rods and reproduce Monte Carlo (MC) simulation values. We compare these results with Onsager's predictions and with reported values of hard bodies of similar geometry, as cut spheres (CS), hard spherocylinders (HSC) and linear tangent hard sphere chains (LTHSC). Simulation values for v _ex were obtained with an overlap algorithm that is also presented in detail. The obtained results can be applied in theoretical and computer simulation studies of discotic liquid crystals.     

Thermal and chemical denaturation of Colocasia esculenta tuber agglutinin from α2β2 to unfolded state

The major tuber storage protein of Colocasia esculenta, is a monocot mannose-binding, widely used dietary lectin, containing two polypeptides of 12.0 and 12.4 kDa. By both gel filtration and dynamic light scattering at pH 7.2, the lectin has a α₂β₂ form of apparent molecular mass of 48.2 kDa and a hydrodynamic radius of 6.1 ± .2 nm; however, at pH 3, it migrates as αβ and has a reduced hydrodynamic radius of 4.6 ± .3 nm. Our circular dichroism spectroscopy studies show that the lectin retains approximately 100% of its secondary structure between pH 2–8, going down to ~90% for extreme acidic/alkaline conditions. The fluorescence emission maxima of 346 to 350 nm for pH 4 to 10 show that the tryptophan residues are relatively exposed. The unfolding is a simple two-state process, N₄ ? 4U, as seen in our denaturation scan profiles. These denaturation profiles, monitored separately by fluorescence, far-UV CD, and near-UV CD, are completely super imposable. Analyses of these profiles provide an estimate of several thermodynamic parameters at each guanidinium chloride concentration, including the melting temperature T_g, which is 346.9 K in 0 M, but lowers to 321.8 K in 3.6 M. Dimeric and tetrameric interfaces observed in the crystal structure for the same protein are used to rationalize solution data in some detail.     

Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains

A Monte Carlo analysis is presented which establishes a relationship between the rotational diffusion coefficients and the flexibility (persistence length, P) of short, wormlike chains. The results of this analysis are presented in terms of experimentally observable quantities; namely, the rotational relaxation times for the field-free decay of optical anisotropy. The pertinent theoretical quantity is R, defined as the ratio of the longest rotational relaxation time of a wormlike chain to the transverse rotational relaxation time of a rigid cylinder having the same axial length (L) and segmental volume. R, so defined, is essentially independent of the axial ratio of the cylinder for any value of L/P within the range of validity of the present analysis (axial ratio > 20; 0.1 < L/P < 5). It is pointed out that P can be determined with reasonable accuracy even in the absence of a precise knowledge of the local hydrodynamic radius of the chain.     

A mechanobiological investigation of platelets

Understanding mechanotransduction pathways leading to thrombosis will require progressive steps, including determination of the mechanical behavior of the platelet membrane in response to applied loads. The platelet membrane deformation capacity, as quantified by membrane progression into a borosilicate glass micropipette of defined internal diameter, was probed in murine platelets using a controlled range of negative pressure (0–7 cm H₂O). Based on our observations that the platelet portion outside the micropipette was mostly spherical and that the platelet volume did not change upon aspiration, a novel continuum mechanics-based model of the platelet micropipette aspiration experiment was created, and a new hyperelastic isotropic material model including membrane residual tension was proposed for the platelet membrane. Murine platelet membranes maintained an average linear deformation behavior: L _p/R _p = 146,100p _i × R _p + 19.923, where L _p is the platelet length aspirated in the micropipette (m), R _p is micropipette radius (m) and p _i is the aspiration pressure (Pa). The theoretical model was used to generate material constants for the murine platelet membrane that allowed for an accurate simulation of the micropipette aspiration experiments. From published results, another set of material constants was established for the human platelet membrane. Limited cases of platelet lysis upon aspiration were analyzed using the theoretical model to determine preliminary membrane tension strength values.     

Genealogy with seasonality,the basic reproduction number,and the influenza pandemic

The basic reproduction number R ₀ has been used in population biology, especially in epidemiology, for several decades. But a suitable definition in the case of models with periodic coefficients was given only in recent years. The definition involves the spectral radius of an integral operator. As in the study of structured epidemic models in a constant environment, there is a need to emphasize the biological meaning of this spectral radius. In this paper we show that R ₀ for periodic models is still an asymptotic per generation growth rate. We also emphasize the difference between this theoretical R ₀ for periodic models and the “reproduction number” obtained by fitting an exponential to the beginning of an epidemic curve. This difference has been overlooked in recent studies of the H1N1 influenza pandemic.     

Conformation of the high molecular weight form ofDunaliella salina phosphofructokinase in solution by means of small-angle X-ray diffraction and viscosity measurements

Summary The intrinsic viscosity of phosphofructokinase fromDunaliella salina in different states of aggregation was determined. The instrinsic viscosity [], of the biologically active tetramer, with a molecular weight of 320,000, was found to be 6.5 ml·g^–1 at 4°C. Moreover, for the inactive dimer, with a molecular weight of 160,000, a value of []=8.0 ml·g^–1 was determined. The high molecular weight aggregate of phosphofructokinase fromDunaliella salina, that shows little activity, has an intrinsic viscosity of 23.2 ml·g^–1, which is significantly higher than that found for the active tetramer and the inactive dimer.Small angle X-ray scattering experiments in solution of this high molecular from of phosphofructokinase fromDunaliella salina reveal a radius of gyration of the cross section ofR _c=49.0 Å at an ionic strength of 0.15 M and_pH 7.2. Furthermore, a comparison of the values obtained for the tetramer and the radius of gyration (R _g=52.9 Å) with those of typical spherical proteins (3–4 ml·g^–1) shows that the values of [] andR _g are significantly larger for the high molecular weight form of phosphofructokinase than for the spherical proteins. The high intrinsic viscosity of the polymeric form of phosphofructokinase suggests an end-to-end aggregation consisting of monomeric units with heights,h=80–90 Å, and a cylindrical diameter of approximately 140.0 Å, resulting in a long rod of a total length of 1,800 Å and a molecular weight of two million. On the basis of the experimentally observedR _c and [] values, using a prolate ellipsoid of revolution as a model, the hydrodynamic volume and the hydration, the axial ratio could be determined to be 12. The native tetrameric form contains 0.4 g H₂O/g protein, whereas the higher aggregate structure corresponds to a hydration of 0.60 g H₂O/g protein.     

Using severity factor as a parameter to optimize krill treatment under subcritical water conditions

The aim of this study was to optimize the conditions for subcritical water treatment of krill, as expressed with a single parameter: the severity factor (log R₀). Raw krill was treated under subcritical water conditions at various log R₀ values (1.54–3.75) by varying the treatment temperatures (120–180 °C) and times (0–10 min) in two different sizes of batch-type vessel (10 and 117 mL). The log R₀ value could efficiently describe changes in various properties of the obtained liquid extracts and solid residues. The most desirable shrimp-like flavor intensity and highest sensory preference were obtained for log R₀ values of 2.75–3.01. The results also proved that severity factor can be used as a single parameter to control subcritical water treatment conditions in differently sized batch-type vessels to produce shrimp-like flavor extract and residue from krill.     

Approximation of the Basic Reproduction Number <Emphasis Type="Italic">R</Emphasis><Subscript>0</Subscript> for Vector-Borne Diseases with a Periodic Vector Population

The main purpose of this paper is to give an approximate formula involving two terms for the basic reproduction number R ₀ of a vector-borne disease when the vector population has small seasonal fluctuations of the form p(t) = p ₀ (1+ε cos (ωt − φ)) with ε ≪ 1. The first term is similar to the case of a constant vector population p but with p replaced by the average vector population p ₀. The maximum correction due to the second term is (ε²/8)% and always tends to decrease R ₀. The basic reproduction number R ₀ is defined through the spectral radius of a linear integral operator. Four numerical methods for the computation of R ₀ are compared using as example a model for the 2005/2006 chikungunya epidemic in La Réunion. The approximate formula and the numerical methods can be used for many other epidemic models with seasonality. MSC 92D30 ⋅ 45C05 ⋅ 47A55     

Landscape discontinuities influence the population structure of Acer opalus ssp. obtusatum Waldst. & Kit. ex Willdenow

The major goal of landscape genetics is to understand how landscape structure genetic variation in natural populations. We investigated molecular diversity in Acer opalus subsp. obtusatum sampled from 95 sites using 14 nuclear microsatellite loci. The average number of alleles per nuclear microsatellite locus differed among sampling sites; the number was high (4.9 alleles) in populations from the Basilicata and Molise regions, where heterozygosity was also high (0.679, Molise; 0.669, Basilicata). Differentiation between sites was often low (mean F_ST = 0.220), indicating few genetic differences between most sites. There was a clear excess of homozygotes (mean H_o = 0.450, mean H_e = 0.513) and a relatively high F_IS (mean = 0.451), suggesting a consistent level of inbreeding in many A. opalus subsp. obtusatum populations. There was a significant pattern of isolation by distance across the study area (Mantel test; R² = 0.0662, P < 0.001). Two assignment methods (Structure and Geneland) produced some similarities in their definitions of population structure, especially for populations from the Campania and Tuscany regions. These two important genetic discontinuities were not associated with any physical barriers.     

Physiological and cellular responses to fluoride stress in tea (<Emphasis Type="Italic">Camellia sinensis</Emphasis>) leaves

Tea (Camellia sinensis (L.) O. Kuntze) hyper-accumulates fluoride (F), mainly in the leaves. To understand how tea copes with the stress caused by F, we tracked photosynthesis, antioxidant defense, and cell ultrastructure under different F concentrations (0–50 mg L^?1). High F (≥5 mg L^?1) caused decreases in photosynthetic and chlorophyll fluorescence parameters. Activated oxygen metabolism was altered by F, as manifested in increasing lipid peroxidation, electrolyte leakage (EL), and accumulation of H₂O₂. The activities of ascorbate peroxidase (APX, EC 1.11.1.1) and catalase (CAT, EC 1.11.1.6) increased at 0–5 mg L^?1 F, but sharply decreased less than 10–50 mg L^?1 F. The activity of manganese superoxide dismutase (Mn-SOD, EC 1.15.1.1) decreased with increasing F concentration. Expression of genes encoding antioxidant enzymes were in accordance with their measured activities. The results suggest that the antioxidant enzymes in the tea plant can eliminate reactive oxygen species (ROS) at <5 mg L^?1 F, but not at 20–50 mg L^?1 F. High F increased the number of epidermal hairs on tea leaves and decreased the stomatal aperture, reducing water loss. The leaf cellular structure appeared normal under 1–50 mg L^?1 F, although starch grains in chloroplast increased with increasing F. Proline and betaine play important roles in osmotic regulation in tea plant tolerating F stress. ROS scavenging and greater number of epidermal hairs are likely parts of the tea plant F-tolerance mechanism.     

Light scattering and viscosity study of heat aggregation of insulin

Aggregation behavior and hydrodynamic parameters of insulin have been determined from static and dynamic light scattering experiments and intrinsic viscosity measurements carried out at pH 4.0, 7.5, and 9.0 in the temperature range 20–40°C in aqueous solutions. The protein aggregated extensively at elevated temperatures in the acidic solutions. Intermolecular interactions were found to be attractive and to increase with temperature. The measured intrinsic viscosity [η], diffusion coefficient D₀, molecular weight M, and radius of gyration R_g exhibited the universal behavior: M[η] = (2.4 ± 02) × 10⁻²⁷ (R_e,η/R_e,D)³(D_0η/T)⁻³ and (D₀√n)₋₁ ≃ (√6 πη₀ζβ/k_BT) [1 + 0.201)(v/β³)√n], where n is the number of segments in the polypeptide. The effective hydrodynamic radii deduced from [η], (R_e, η) and the same deduced from D₀, (R_e,D) showed a constant ratio, (R_e,η/R_e,D = 1.1 ± 0.1). R_e,D/R_g = ξ was found to be (0.76 ± 0.07). From the known solvent viscosity η₀, the segment length β was deduced to be (10 ± 1) Å. The excluded volume was deduced to be (5 Å)³ regardless of pH. The Flory-Huggins interaction parameter was found to be χ = 0.45 ± 0.04, independent of pH and temperature. © 1998 John Wiley & Sons, Inc. Biopoly 45: 1–8, 1998     

Response of soil surface CO2 flux in a boreal forest to ecosystem warming

Soil surface carbon dioxide (CO₂) flux (R_S) was measured for 2 years at the Boreal Soil and Air Warming Experiment site near Thompson, MB, Canada. The experimental design was a complete random block design that consisted of four replicate blocks, with each block containing a 15 m × 15 m control and heated plot. Black spruce [Picea mariana (Mill.) BSP] was the overstory species and Epilobium angustifolium was the dominant understory. Soil temperature was maintained (～5 °C) above the control soil temperature using electric cables inside water filled polyethylene tubing for each heated plot. Air inside a 7.3‐m‐diameter chamber, centered in the soil warming plot, contained approximately nine black spruce trees was heated ～5 °C above control ambient air temperature allowing for the testing of soil‐only warming and soil+air warming. Soil surface CO₂ flux (R_S) was positively correlated (P < 0.0001) to soil temperature at 10 cm depth. Soil surface CO₂ flux (R_S) was 24% greater in the soil‐only warming than the control in 2004, but was only 11% greater in 2005, while R_S in the soil+air warming treatments was 31% less than the control in 2004 and 23% less in 2005. Live fine root mass (< 2 mm diameter) was less in the heated than control treatments in 2004 and statistically less (P < 0.01) in 2005. Similar root mass between the two heated treatments suggests that different heating methods (soil‐only vs. soil+air warming) can affect the rate of decomposition.     

Comparison of the structure of ribosomal 5S RNA from E. coli and from rat liver using X-ray scattering and dynamic light scattering

The structures of eukaryotic ribosomal 5S RNA from rat liver and of prokaryotic 5S RNA from E. coli (A-conformer) have been investigated by scattering methods. For both molecules, a molar mass of 44,500±4,000 was determined from small angle X-ray scattering as well as from dynamic light scattering. The shape parameters of the two rRNAs, volume V _c, surface O _c, radius of gyration R _s, maximum dimension of the molecule L, thickness D, and cross section radius of gyration R _sq, agree within the experimental error limits. The mean values are V _c=57±3 nm³, O _c=165±10 nm², R _s=3.37±0.05 nm, L=10.8±0.7 nm, D=1.57±0.07 nm, R _sa=0.92±0.01 nm.Identical structures for the E. coli 5S rRNA and the rat liver 5S rRNA at a resolution of 1 nm can be deduced from this agreement and from the comparison of experimental X-ray scattering curves and of experimental electron distance distribution function. The flat shape model derived for prokaryotic and eukaryotic 5S rRNA shows a compact region and two protruding arms. Double helical stems are eleven-fold helices with a mean base pair distance of 0.28 nm. Combining the shape information obtained from X-ray scattering with the information about the frictional behaviour of the molecules, deduced from the diffusion coefficients D _20,w ⁰ =(5.9±0.2)·10^-7 cm²s^-1 and (6.2±0.2)·10^-7 cm²s^-1 for rat liver 5S rRNA and E. coli 5S rRNA, respectively, a solvation shell of about 0.3 nm thickness around both molecules is determined. This structural similarity and the consensus secondary structure pattern derived from comparative sequence analyses suggest that all 5S rRNAs may indeed have conserved essentially the same type of folding of their polynucleotide strands during evolution, despite having very different sequences.     

The beneficial effect of repaglinide on in vitro maturation and development ability of immature mouse oocytes

Repaglinide is a hypoglycemic drug, causing depolarization of the cell membrane, opening the voltage-gated calcium channels, and then increasing intracellular calcium in the pancreatic B cells by inhibition of the K-ATP-sensitive channels. Oocyte in vitro maturation (IVM) is influenced by different factors such as calcium signaling. In this study, we examined the effects of repaglinide on in vitro maturation and fertilization ability of mouse oocyte. Immature oocytes were isolated from female Naval Medical Research Institute mice which are 6–8 wk old mechanically and then cultured in 30 μl droplets of T6 medium with different concentrations of repaglinide. The control group did not receive repaglinide (R₀). Treatment groups received different concentrations (5, 10, and 100 nM and 1 and 10 μM) of repaglinide (R₁, R₂, R₃, R₄, and R₅, respectively). Oocyte in vitro maturation rate was assessed after 24 h. In vitro fertilization was performed using metaphase II oocytes obtained from R₀ and R₄ treatments. Embryo cleavage rate was calculated at 48 h post-IVF. Chi-square test was used for evaluating difference between control and treatment groups (p < 0.05). Oocyte maturation rate after 24 h in treatment groups R₂, R₃, R₄, and R₅ was significantly higher than that in the control (p < 0.05). Supplementation of medium with 1 μM of repaglinide (R₄) during IVM significantly improved outcome of embryo cleavage rate than control at 48 h post-IVF (p < 0.05). In conclusion, repaglinide can be considered as an effective agent for in vitro oocyte maturation and embryo cleavage.     

Phytoremediation of Bisphenol A and Total Dissolved Solids by the Mangrove Plant,Bruguiera Gymnorhiza

Bruguiera gymnorhiza, an evergreen mangrove tree, is tolerant of bisphenol A (BPA) and has potential BPA removal capability. BPA is highly toxic to plants at high concentrations, wherein they exhibit damaged symptoms such as chlorosis, necrosis, and wilting. The LD₅₀ of BPA toxicity for this plant was statistically estimated to be 39.97 mg L^–1. B. gymnorhiza can reduce COD from 15408 ± 246 to 49 ± 30 mg L^–1 by (approximately 99% reduction of the initial value) and can reduce content to levels below the industrial effluent standard of Thailand (<120 mg L^–1) within 48 days. This plant can completely remove BPA from the solution within 51 days of treatment. Polysaccharides and organic acids were found in the solution and were caused by plant response to the toxicity of BPA. In addition, B. gymnorrhiza can also reduce total dissolved solids (TDS) and salinity in real wastewater. Therefore, B. gymnorrhiza has potential for removal of BPA and TDS in contaminated in wastewater.     

Statistics of branching and hairpin helices for the dAT copolymer

At low temperatures a single strand of dAT copolymer tends to form a double helix with a loop at one end (hairpin). At slightly higher temperatures a branched structure (consisting of many hairpins connected by coiled regions) appears. The equilibrium properties of this branched structure are studied here by a propagator method. In particular the radius of gyration R_G is calculated; under typical conditions, R_G is expected to show a minimum at a temperature slightly below melting, in agreement with viscosity measurements. The present calculation is restricted to rather sharp transitions, for which the size of each helical region is large, even at the melting point. Then, in a rather broad range of molecular weights, M, R_G is proportional to M^1/4(as in the Zimm-Stockmayer theory of simple branched polymers).     

Filipin and its interaction with cholesterol in aqueous media studied using static and dynamic light scattering

Aggregation of filipin in aqueous medium and filipin-induced changes in cholesterol micelles have been studied using intensity and dynamic light scattering. The dependencies of filipin aggregate dimensions on concentration, solvent, and temperature were studied, and revealed that the aggregates do not have a well-defined geometry, i.e., a critical micelle concentration cannot be detected and stable structures are not formed. The aggregates are of size R_g ≈ 110 nm and R_h ≈ 63 nm, referring to the radius of gyration and hydrodynamic radius, respectively. In the concentration range studied (1 μM < C < 30 μM), a low molecular weight species (monomer/dimer) is always present together with the aggregates. In ethanol/ water mixtures, large (R_g ≈ 500 nm), narrow distribution aggregates are formed in the water volume fraction range 0.45 < Φ_H2_O < 0.65. Aggregation also occurs on changing the temperature; In the range 7–37°C, smaller aggregates (10–30 nm) form and the process is only partially reversible. No pronounced effect of filipin on the structure of the cholesterol micelles was observed (a small increase in R_g and R_h is noted). These results rule out any “specificity” for the filipin interactions with cholesterol, which has been considered a key event in the filipin biochemical mode of action. A reevaluatiori Of this question is suggested and some alternatives are advanced. © 1994 John Wiley & Sons, Inc.