Evaluation of a proposed surface colonization equation usingThermothrix thiopara as a model organism

The colonization equation shown below was evaluated usingThermothrix thiopara as a model organism. $$N = (A/\mu )e^{\mu t} - A/\mu $$ where: N=number of cells on surface (cells field^?1); A = attachment rate (cells field^?1 h^?1); M=specific growth rate (h^?1); t=incubation period (h). Previous studies of microbial surface colonization consider attachment and growth independently. However, the proposed colonization equation integrates the effects of simultaneous attachment and growth. Using this equation, the specific growth rate ofT. thiopara was found to be 0.38±0.3 h^?1 during in situ colonization. Estimates ofμ were independent of incubation period after 4 h (2 generations). Shorter incubations were inadequate to produce sufficient microcolonies for accurate determination of specific growth rate. Empirical data for the time course of colonization fell within the 95% confidence interval of predicted values. The attachment rate, although assumed to be constant, was found to continuously increase with time. This increase may have been an artifact due to the continuous deposition of travertine on the surface, or may indicate the need for a function to replace A in the colonization equation. Using the exponential growth equation, the progeny of cells that attach during incubation are considered to be progeny of cells that attach initially. This erroneously inflated the growth rate by 55%.     

Derivation of a growth rate equation describing microbial surface colonization

A surface growth rate equation is derived which describes simultaneous growth and attachment during microbial surface colonization. The equation simplifies determination of attachment and growth rate, and does not require a computer program for solution. This rate equation gives the specific growth rate (Μ) as a function of the number of cells on the surface (N), the incubation period (t), and the number of colonies (C_i) containing either one cell, two cells, four cells, etc, as shown below. $$\mu = \frac{{\ln (\frac{N}{{C_i }} + 1)}}{t}$$ The attachment rate (A) is given by the following relationship: $$A = \mu C_i $$ The proposed colonization kinetics are compared with exponential growth kinetics using 3-dimensional computer plots. Colonization kinetics diverged most from exponential kinetics when the growth rate was low or the attachment rate was high. Using these kinetics, it is possible to isolate the effects of growth and attachment on microbial surface colonization.     

Continuous cultivation of Lactobacillus brevis NCL912 for production of gamma-aminobutyric acid

A continuous cultivation method for Lactobacillus brevis NCL912 to synthesize gamma-aminobutyric acid was developed in this work. Different dilution rates were evaluated for obtaining steady state in continuous cultivation. The results showed that steady state could be achieved at dilution rates from 0.08 to 0.12 h^?1. The highest gamma-aminobutyric acid productivity (5.11 g L^?1?h^?1) was obtained at dilution rate of 0.09 h^?1. The kinetic models were established for continuous gamma-aminobutyric acid production by using the Monod equation for microbial growth, and the Luedeking–Piret equation for product formation. The microbial growth and product formation can be described by equations $ \mu = {{{0.1234{C_S}}} \left/ {{\left( {0.9338+{C_S}} \right)}} \right.} $ and $ {Q_P}=6.86\,\mathrm{g}\,{{\mathrm{g}}^{-1 }}\mathrm{cell}\,{{\mathrm{h}}^{-1 }} $ , respectively. The production of gamma-aminobutyric acid by L. brevis NCL912 was non-growth-associated.     

Bi-ionic flows through a single homogeneous membrane

The form of the equations for bi-ionic flows through a cation-exchanger membrane is investigated. Simple algebraic flow equations are given by a first-order expansion of an integral of the Nernst-Planck d.e.'s calculated under the assumption of local electroneutrality. Donnan equilibrium is used to find the ionic partition at the membrane-solution interfaces. Using standard techniques it is found that the cation flow equations can be put into the form $$J_i = \lambda (C_i^I C_j^{II} - C_i^{II} C_j^I ) + \frac{{\tau _i }}{F}I,i \ne j = 1,2,$$ where, however, λ and τ _i are functions of the mean concentrations across the membrane. Thus it is shown that the osmotic force Δπ _si=2 RT(C _i ^I -C _i ^II ) cannot be the driving force in the bi-ionic flow equations as might be expected in a generalization of the Kedem-Katchalsky equation for a single salt.     

Kinetic models of coupling between H+ and Na+-translocation and ATP synthesis/hydrolysis by F0F1-ATPases: Can a cell utilize both\Delta \bar \mu _{H^ + } and\Delta \bar \mu _{Na^ + } for ATP synthesis underin vivo conditions using the same enzyme?

Kinetic models of the F₀F₁-ATPase able to transport H⁺ or/and Na⁺ ions are proposed. It is assumed that (i) H⁺ and Na⁺ compete for the same binding sites, (ii) ion translocation through F₀ is coupled to the rate-limiting step of the F₁-catalyzed reaction. The main characteristics of the dependences of ATP synthesis and hydrolysis rates on Δφ, ΔpH, and ΔpNa are predicted for various versions of the coupling model. The mechanism of the switchover from \(\Delta \bar \mu _{H^ + } \) -dependent synthesis to the \(\Delta \bar \mu _{Na^ + } \) -dependent one is demonstrated. It is shown that even with a drastic drop in \(\Delta \bar \mu _{H^ + } \) , ATP hydrolysis by the proton mode of catalysis can be effectively inhibited by Δφ and ΔpNa. The results obtained strongly support the possibility that the same F₀F₁-ATPase in bacterial cells can utilize both \(\Delta \bar \mu _{H^ + } \) and \(\Delta \bar \mu _{Na^ + } \) for ATP synthesis underin vivo conditions.     

Growth of Wolinella succinogenes with polysulphide as terminal acceptor of phosphorylative electron transport

Polysulphide was formed according to reaction (1), when tetrathionate was (1) $${\text{S}}_4 {\text{O}}_6^{2 - } + {\text{HS}}^ - \to 2{\text{S}}_2 {\text{O}}_3^{2 - } + {\text{S(O)}} + {\text{H}}^ + $$ added to an anaerobic buffer (pH 8.5) containing excess sulphide. S(O) denotes the zero oxidation state sulphur in the polysulphide mixture S _infn ^sup2- . The addition of formate to the polysulphide solution in the presence of Wolinella succinogenes caused the reduction of polysulphide according to reaction (2). The bacteria grew in a medium containing formate and sulphide, (2) $${\text{HCO}}_2^ - + {\text{S(O)}} + {\text{H}}2{\text{O}} \to {\text{HCO}}_3^ - + {\text{HS}}^ - + {\text{H}}^ + $$ when tetrathionate was continuously added. The cell density increased proportional to reaction (3) which represents the sum of reactions (1) and (3) $${\text{HCO}}_2^ - + {\text{S}}_{\text{4}} {\text{O}}_6^{2 - } + {\text{H}}2{\text{O}} \to {\text{HCO}}_3^ - + 2{\text{S}}_{\text{2}} {\text{O}}_3^{2 - } + 2{\text{H}}^ + $$ (2). The cell yield per mol formate was nearly the same as during growth on formate and elemental sulphur, while the velocity of growth was greater. The specific activities of polysulphide reduction by formate measured with bacteria grown with tetrathionate or with elemental sulphur were consistent with the growth parameters. The results suggest that W. succinogenes grow at the expense of formate oxidation by polysulphide and that polysulphide is an intermediate during growth on formate and elemental sulphur.     

Stochastic population growth in spatially heterogeneous environments

Classical ecological theory predicts that environmental stochasticity increases extinction risk by reducing the average per-capita growth rate of populations. For sedentary populations in a spatially homogeneous yet temporally variable environment, a simple model of population growth is a stochastic differential equation dZ _t = μ Z _t dt + σ Z _t dW _t , t ≥ 0, where the conditional law of Z _t+Δt ? Z _t given Z _t = z has mean and variance approximately z μΔt and z ² σ ²Δt when the time increment Δt is small. The long-term stochastic growth rate ${\lim_{t \to \infty} t^{-1}\log Z_t}$ for such a population equals ${\mu -\frac{\sigma^2}{2}}$ . Most populations, however, experience spatial as well as temporal variability. To understand the interactive effects of environmental stochasticity, spatial heterogeneity, and dispersal on population growth, we study an analogous model ${{\bf X}_t = (X_t^1, \ldots, X_t^n)}$ , t ≥ 0, for the population abundances in n patches: the conditional law of X _t+Δt given X _t = x is such that the conditional mean of ${X_{t+\Delta t}^i - X_t^i}$ is approximately ${[x^i \mu_i + \sum_j (x^j D_{ji} - x^i D_{ij})] \Delta t}$ where μ _i is the per capita growth rate in the ith patch and D _ij is the dispersal rate from the ith patch to the jth patch, and the conditional covariance of ${X_{t+\Delta t}^i - X_t^i}$ and ${X_{t + \Delta t}^j - X_t^j}$ is approximately x ⁱ x ^j σ _ij Δt for some covariance matrix Σ = (σ _ij ). We show for such a spatially extended population that if ${S_t = X_t^1 + \cdots + X_t^n}$ denotes the total population abundance, then Y _t = X _t /S _t , the vector of patch proportions, converges in law to a random vector Y _∞ as ${t \to \infty}$ , and the stochastic growth rate ${\lim_{t \to \infty} t^{-1}\log S_t}$ equals the space-time average per-capita growth rate ${\sum_i \mu_i \mathbb{E}[Y_\infty^i]}$ experienced by the population minus half of the space-time average temporal variation ${\mathbb{E}[\sum_{i,j}\sigma_{ij}Y_\infty^i Y_\infty^j]}$ experienced by the population. Using this characterization of the stochastic growth rate, we derive an explicit expression for the stochastic growth rate for populations living in two patches, determine which choices of the dispersal matrix D produce the maximal stochastic growth rate for a freely dispersing population, derive an analytic approximation of the stochastic growth rate for dispersal limited populations, and use group theoretic techniques to approximate the stochastic growth rate for populations living in multi-scale landscapes (e.g. insects on plants in meadows on islands). Our results provide fundamental insights into “ideal free” movement in the face of uncertainty, the persistence of coupled sink populations, the evolution of dispersal rates, and the single large or several small (SLOSS) debate in conservation biology. For example, our analysis implies that even in the absence of density-dependent feedbacks, ideal-free dispersers occupy multiple patches in spatially heterogeneous environments provided environmental fluctuations are sufficiently strong and sufficiently weakly correlated across space. In contrast, for diffusively dispersing populations living in similar environments, intermediate dispersal rates maximize their stochastic growth rate.     

Whole-cell hydroxylation of n-octane by Escherichia coli strains expressing the CYP153A6 operon

CYP153A6 is a well-studied terminal alkane hydroxylase which has previously been expressed in Pseudomonas putida and Escherichia coli by using the pCom8 plasmid. In this study, CYP153A6 was successfully expressed in E. coli BL21(DE3) by cloning the complete operon from Mycobacterium sp. HXN-1500, also encoding the ferredoxin reductase and ferredoxin, into pET28b(+). LB medium with IPTG as well as auto-induction medium was used to express the proteins under the T7 promoter. A maximum concentration of 1.85?μM of active CYP153A6 was obtained when using auto-induction medium, while with IPTG induction of LB cultures, the P450 concentration peaked at 0.6–0.8?μM. Since more biomass was produced in auto-induction medium, the specific P450 content was often almost the same, 0.5–1.0?μmol P450 g _DCW ^?1 , for both methods. Analytical scale whole-cell biotransformations of n-octane were conducted with resting cells, and it was found that high P450 content in biomass did not necessarily result in high octanol production. Whole cells from LB cultures induced with IPTG gave higher specific and volumetric octanol formation rates than biomass from auto-induction medium. A maximum of 8.7?g octanol L _BRM ^?1 was obtained within 24?h (0.34?g L _BRM ^?1 ?h^?1) with IPTG-induced cells containing only 0.20?μmol P450 g _DCW ^?1 , when glucose (22?g L _BRM ^?1 ) was added for cofactor regeneration.     

A numerical experiment on the determination of kinetic rate constants in the presence of diffusion

Two chemicals,A andB, are allowed to diffuse together and a reaction described by $$A + B\mathop \rightleftharpoons \limits_{K_{ - 1} }^{K_1 } C$$ is allowed to proceed. This system is described mathematically by a system of partial differential equations. A numerical procedure is presented to find the rate constants ofK ₁ andK _?1. A systematic analysis of the effects of errors is also presented.     

Kinetics study of pyridine biodegradation by a novel bacterial strain,Rhizobium sp. NJUST18

Biodegradation of pyridine by a novel bacterial strain, Rhizobium sp. NJUST18, was studied in batch experiments over a wide concentration range (from 100 to 1,000 mg l^?1). Pyridine inhibited both growth of Rhizobium sp. NJUST18 and biodegradation of pyridine. The Haldane model could be fitted to the growth kinetics data well with the kinetic constants μ* = 0.1473 h^?1, K _s = 793.97 mg l^?1, K _i = 268.60 mg l^?1 and S _m = 461.80 mg l^?1. The true μ _max, calculated from μ*, was found to be 0.0332 h^?1. Yield coefficient Y _X/S depended on S _i and reached a maximum of 0.51 g g^?1 at S _i of 600 mg l^?1. V _max was calculated by fitting the pyridine consumption data with the Gompertz model. V _max increased with initial pyridine concentration up to 14.809 mg l^?1 h^?1. The q _S values, calculated from $V_{ \hbox{max} }$ , were fitted with the Haldane equation, yielding q _Smax = 0.1212 g g^?1 h^?1 and q* = 0.3874 g g^?1 h^?1 at S _m′ = 507.83 mg l^?1, K _s′ = 558.03 mg l^?1, and K _i′ = 462.15 mg l^?1. Inhibition constants for growth and degradation rate value were in the same range. Compared with other pyridine degraders, μ _max and S _m obtained for Rhizobium sp. NJUST18 were relatively high. High K _i and K _i′ values and extremely high K _s and K _s′ values indicated that NJUST18 was able to grow on pyridine within a wide concentration range, especially at relatively high concentrations.     

Chemical characterization of the O-specific chain of Sphaerotilus natans ATCC 13338 lipopolysaccharide

The chemical structure of the O-specific chain of the Sphaerotilus natans lipopolysaccharide was established. The isolated polysaccharide moiety contained neutral sugars (rhamnose, glucose, and l-glycero-d-manno-heptose), 3-deoxy-d-manno-octulosonic acid (Kdo), phosphate and ethanolamine. Alditol acetate and methylation analyses showed that the O-specific chain contained linear pentasaccharide repeating units, composed of four units of rhamnose, substituted at 3-position, and one unit of glucose, substituted at 4-position. Oxidation by chromium trioxide showed that all sugars were α-linked. The structure proposed for the O-specific chain has been confirmed by periodate oxidation, and by ¹H-and ¹³C-NMR spectroscopic studies for the original and the Smith-degraded PS moiety. The O-specific unit of the S. natans LPS has the following structure: $$\begin{gathered} [ \to 4) - Glup - (1\xrightarrow{a}3) - Rhap - (1\xrightarrow{a}3) - Rhap - \hfill \\ - (1\xrightarrow{a}3) - Rhap - (1\xrightarrow{a}3) - Rhap - (1]_n \xrightarrow{a} \hfill \\ \end{gathered} $$      

Age structure, growth and mortality estimates of an endemic Ptychobarbus dipogon (Regan, 1905) (Cyprinidae: Schizothoracinae) in the Lhasa River, Tibet

Ptychobarbus dipogon is an endemic fish in the Yarlung Tsangpo River, but its biology is poorly known. We sampled 582 specimens (total length, TL, between 70.6 and 593.0 mm) from April 2004 to August 2006 in the Lhasa River, Tibet. We estimated ages based on the counts of alternating opaque and translucent zones (annuli) in thin transverse sections of lapilli otoliths. Ages ranged from 1⁺ to 23⁺ years for males and 1⁺ to 44⁺ for females. The observed 44⁺ years was the oldest reported for schizothoracine fishes. Females attained a larger size than males. The TL–weight relationship was W?=?7.12?×?10^?6 TL ^3.006 for combined sexes. The growth parameters fitted von Bertalanffy growth functions were $L_\infty = 598.66\,{\text{mm}}$ , k?=?0.0898 year^?1, t ₀?=??0.7261 year and $W_\infty = 1585.38\;{\text{g}}$ for females and $L_\infty = 494.23{\text{ mm}}$ , k?=?0.1197 year^?1, t ₀?=??0.7296 year and $W_\infty = 904.88{\text{ g}}$ for males. The longevities of 32.7 year for females and 24.3 year for males were similar to the observed ages. Using an empirical model we estimated the instantaneous rate of total mortality (Z) at 0.28 per year in the lower reaches. Z in the upper and middle stocks was close to the M because of unexploited or lightly exploited stock. Protracted longevity, slow growth, low natural mortality and large body size were typical characteristics of P. dipogon. The current declining trend of P. dipogon could be prevented by altering fishing regulations.     

Photosynthesis in Pineapple (Ananas comosus comosus [L.] Merr) Measured Using PAM (Pulse Amplitude Modulation) Fluorometry

PAM (Pulse Amplitude Modulation) fluorometer techniques directly measure the light reactions of photosynthesis that are otherwise difficult to estimate in CAM (Crassulacean Acid metabolism) plants such as pineapple (Ananas comosus comosus cv. Phuket). PAM machines calculate photosynthesis as the Electron Transport Rate (ETR) through PSII (4 electrons per O₂ produced) as mol m^?2 s^?1. P vs. E curves fitted the waiting-in-line function (an equation of the form $ {\hbox{ETR}} = \left( {{\hbox{ET}}{{\hbox{R}}_{{ \max }}} \times {\hbox{E}}/{{\hbox{E}}_{\rm{opt}}}} \right).{{\hbox{e}}^{{1} - {\rm{E}}/{\rm{Eopt}}}} $ ) allowing half-saturating and optimal irradiances (E_opt) to be estimated. Effective Quantum Yield (Y_max), Electron Transport Rate (ETR_max) and the Non-Photochemical Quenching parameter, NPQ_max all vary on a diurnal cycle but the parameter qN_max does not show a systematic variation over a diurnal period. Phuket pineapple is a “sun plant” with Optimum Irradiance (E_opt) from 755 to 1,130 μmol m^?2 s^?1 (400–700 nm) PAR but photosynthetic capacity is very low in the late afternoon even though light conditions are favourable for rapid photosynthesis. Total CO₂ fixed nocturnally as C4-dicarboxylic acids by leaves of the Phuket pineapple was only ≈0.14 gC m^?2 d^?1 (0.012 mol C m^?2 d^?1). Titratable acid of leaves was depleted about 3 pm (15:00) and shows a classical CAM diurnal cycle. The Phuket pineapple variety only stored enough CO₂ as C4 acids to account for only about 2.5% of photosynthesis (P_g) estimated using the PAM machine (≈5.6 gC m^?2 d^?1). Phuket pineapples are classifiable as CAM-Cycling plants but nocturnal fixation of CO₂ is so low compared to the more familiar Smooth Cayenne variety that it probably recycles only a small proportion of the respiratory CO₂ produced in leaves at night and so even CAM-cycling is only of minor importance to the carbon economy of the plant. Unlike the Smooth Cayenne pineapple variety, which fixes large amounts of CO₂ nocturnally, the Phuket pineapple is for practical purposes a C3 plant.     

Effects of negative air ions on oxygen uptake kinetics,recovery and performance in exercise: a randomized,double-blinded study

Limited research has suggested that acute exposure to negatively charged ions may enhance cardio-respiratory function, aerobic metabolism and recovery following exercise. To test the physiological effects of negatively charged air ions, 14 trained males (age: 32?±?7 years; \( \overset{\cdotp }{V}{\mathrm{O}}_{2 \max } \) : 57?±?7 mL min^?1 kg^?1) were exposed for 20 min to either a high-concentration of air ions (ION: 220?±?30?×?10³ ions cm^?3) or normal room conditions (PLA: 0.1?±?0.06?×?10³ ions cm^?3) in an ionization chamber in a double-blinded, randomized order, prior to performing: (1) a bout of severe-intensity cycling exercise for determining the time constant of the phase II \( \overset{\cdotp }{V}{\mathrm{O}}_2 \) response (τ) and the magnitude of the \( \overset{\cdotp }{V}{\mathrm{O}}_2 \) slow component (SC); and (2) a 30-s Wingate test that was preceded by three 30-s Wingate tests to measure plasma [adrenaline] (ADR), [nor-adrenaline] (N-ADR) and blood [lactate] (B_Lac) over 20 min during recovery in the ionization chamber. There was no difference between ION and PLA for the phase II \( \overset{\cdotp }{V}{\mathrm{O}}_2 \) τ (32?±?14 s vs. 32?±?14 s; P?=?0.7) or \( \overset{\cdotp }{V}{\mathrm{O}}_2 \) SC (404?±?214 mL vs 482?±?217 mL; P?=?0.17). No differences between ION and PLA were observed at any time-point for ADR, N-ADR and B_Lac as well as on peak and mean power output during the Wingate tests (all P?>?0.05). A high-concentration of negatively charged air ions had no effect on aerobic metabolism during severe-intensity exercise or on performance or the recovery of the adrenergic and metabolic responses after repeated-sprint exercise in trained athletes.     

Estimation of viscosity from passage time of liquids flowing through a microchannel array

Recently, a microchannel flow analyzer (MC-FAN) has been used to study the flow properties of blood. However, the correlation between blood passage time measured by use of the MC-FAN and hemorheology has not been clarified. In this study, a simple model is proposed for estimation of liquid viscosity from the passage time t _p of liquids. The t _p data for physiological saline were well represented by the model. According to the model, the viscosity of Newtonian fluids was estimated reasonably well from the t _p data. For blood samples, although the viscosity $ \eta_{\text{mc}} $ estimated from t _p was shown to be smaller than the viscosity $ \eta_{{450{\text{s}}^{ - 1} }} $ measured by use of a rotatory viscometer at a shear rate of 450 s^?1, $ \eta_{\text{mc}} $ was correlated with $ \eta_{{450{\text{s}}^{ - 1} }} $ . An empirical equation for estimation of $ \eta_{{450{\text{s}}^{ - 1} }} $ from $ \eta_{\text{mc}} $ of blood samples is proposed.     

Theory of antigen-antibody induced particulate aggreagation—I. General assumptions and basic theory

A theory of antigen-antibody induced particulate aggregation is developed by investigating the stability of model systems of particles. Conditions for the formation of large aggregates are derived by imposing the requirement that at equilibrium a statistically significant number of redundant bonds would occur in a reduced monomer-dimer model system. A relationship is obtained which predicts the fractional agglutination in the reduced dimer system as a function of the antigen, antibody and particulate concentrations: $$\frac{g}{{2f c_0 (1 - g)^{2^ - } }} = \frac{{s_1 }}{r} + \frac{{s_1 s_2 }}{{2!r^2 }} + ... + \frac{{s_1 s_2 ...s_j }}{{j!r^j }},$$ wherec ₀ is the initial concentration of monomer,f is a proximity factor,g is the fractional agglutination,s _i is the average rate of formation of theith bond from an (i?1)th bound dimer, andr is the average rate of dissociation of a single antibody-antigen bond.