A mechanistic model for gas–liquid mass transfer prediction in a rocking disposable bioreactor

Rocking disposable bioreactors are a newer approach to smaller-scale cell growth that use a cyclic rocking motion to induce mixing and oxygen transfer from the headspace gas into the liquid. Compared with traditional stirred-tank and pneumatic bioreactors, rocking bioreactors operate in a very different physical mode and in this study the oxygen transfer pathways are reassessed to develop a fundamental mass transfer (k_La) model that is compared with experimental data. The model combines two mechanisms, namely surface aeration and oxygenation via a breaking wave with air entrainment, borrowing concepts from ocean wave models. Experimental data for across the range of possible operating conditions (rocking speed, angle, and liquid volume) confirms the validity of the modeling approach, with most predictions falling within ±20% of the experimental values. At low speeds (up to 20 rpm) the surface aeration mechanism is shown to be dominant with a of around 3.5 hr⁻¹, while at high speeds (40 rpm) and angles the breaking wave mechanism contributes up to 91% of the overall (65 hr⁻¹). This model provides an improved fundamental basis for understanding gas–liquid mass transfer for the operation, scale-up, and potential design improvements for rocking bioreactors.     

RISK OF POPULATION EXTINCTION FROM FIXATION OF NEW DELETERIOUS MUTATIONS

The fixation of new deleterious mutations is analyzed for a randomly mating population of constant size with no environmental or demographic stochasticity. Mildly deleterious mutations are far more important in causing loss of fitness and eventual extinction than are lethal and semilethal mutations in populations with effective sizes, N_e, larger than a few individuals. If all mildly deleterious mutations have the same selection coefficient, s against heterozygotes and 2s against homozygotes, the mean time to extinction, , is asymptotically proportional to for 4N_es > 1. Nearly neutral mutations pose the greatest risk of extinction for stable populations, because the magnitude of selection coefficient that minimizes is about ? = 0.4/N_e. The influence of variance in selection coefficients among mutations is analyzed assuming a gamma distribution of s, with mean and variance . The mean time to extinction increases with variance in selection coefficients if is near ?, but can decrease greatly if is much larger than ?. For a given coefficient of variation of , the mean time to extinction is asymptotically proportional to for . When s is exponentially distributed, (c = 1) is asymptotically proportional to . These results in conjunction with data on the rate and magnitude of mildly deleterious mutations in Drosophila melanogaster indicate that even moderately large populations, with effective sizes on the order of N_e = 10³, may incur a substantial risk of extinction from the fixation of new mutations.     

Estimation of Trichoderma QM 9414 biomass and growth rate by indirect means

Trichoderma QM 9414 was aerobically grown on glucose as the sole carbon and energy sources in a chemostat culture. The specific rates of glucose consumption (Q_G), oxygen consumption (Q), and carbon dioxide production (Q) at the steady state were measured to estimate the growth and maintenance requirements. From the results it was estimated that 2 mol adenosine triphosphate (ATP) were produced when1 mol NADH was oxidized through the respiratory chain of this microorganism. The true growth yield for ATP (Y_ATP) and specific ATP consumption rate for maintenance (Q) calculated with this value were 0.0106 g dry cell/mmol ATP and 5.2 mmol ATP/g dry cell/hr, respectively. Using the relationships between specific growth rate (μ) and (Q) and between μ and Q_G obtained from chemostat-culture data, cell and glucose concentration histories were estimated from the carbon dioxide production rate during the batch culture. The estimated cell concentrations agreed with the experimentally measured values. Glucose concentration were slightly overestimated.     

Using kinetics and modeling to predict denitrification fluxes in elemental-sulfur-based biofilms

Elemental sulfur (S⁰) can serve as an electron donor for water and wastewater denitrification, but few researchers have addressed the kinetics of S ⁰–based reduction of nitrate (NO ₃ ⁻), nitrite (NO ₂ ⁻), and nitrous oxide (N ₂O). In addition, S ⁰-based denitrifying biofilms are counter-diffusional. This is because the electron donor (S ⁰) is supplied from the biofilm attachment surface while the acceptor, for example, NO ₃ ⁻, is supplied from the bulk liquid. No existing mathematical model for S ⁰-based denitrification considers this behavior. In this study, batch tests were used to determine the kinetic parameters for the reduction of NO ₃ ⁻, NO ₂ ⁻, and N ₂O. Additionally, a biofilm model was developed to explore the effects of counter-diffusion on overall fluxes, that is, the mass of NO ₃ ⁻ or NO ₂ ⁻ removed per unit biofilm support area per unit time. The maximum specific substrate utilization rates () for NO ₃ ⁻, NO ₂ ⁻, and N ₂O were 3.54, 1.98, and 6.28 g N g COD ⁻¹·d ⁻¹, respectively. The maximum specific growth rates () were 0.71, 1.21, and 1.67 d ⁻¹ for NO ₃ ⁻ to NO ₂ ⁻, NO ₂ ⁻ to N ₂O, and N ₂O to N ₂, respectively. Results suggest that the observed NO ₂ ⁻ accumulation during S ⁰-based denitrification results from a low for NO ₂ ⁻ relative to that for NO ₃ ⁻. The high for N ₂O, relative to that for NO ₃ ⁻ and NO ₂ ⁻, suggest that little N ₂O accumulation occurs during denitrification. A counter-diffusional biofilm model was used to predict trends for NO ₃ ⁻ fluxes, and confirmed NO ₂ ⁻ accumulation in S ⁰-based denitrification biofilms. It also explains the observed detrimental effects of biofilm thickness on denitrification fluxes. This study allows a more accurate prediction of NO ₃ ⁻, NO ₂ ⁻, and N ₂O transformations in S ⁰-based denitrification.     

MATERNAL INHERITANCE AND ITS EFFECT ON ADAPTIVE EVOLUTION: A QUANTITATIVE GENETIC ANALYSIS OF MATERNAL EFFECTS IN A NATURAL PLANT POPULATION

A mother can influence a trait in her offspring both by the genes she transmits (Mendelian inheritance) and by maternal attributes that directly affect that trait in her offspring (maternal inheritance). Maternal inheritance can alter the direction, rate, and duration of adaptive evolution from standard Mendelian models and its impact on adaptive evolution is virtually unexplored in natural populations. In a hierarchical quantitative genetic analysis to determine the magnitude and structure of maternal inheritance in the winter annual plant, Collinsia verna, I consider three potential models of inheritance. These range from a standard Mendelian model estimating only direct (i.e., Mendelian) additive and environmental variance components to a maternal inheritance model estimating six additive and environmental variance components: direct additive and environmental variances; maternal additive and environmental variances; and the direct-maternal additive () and environmental covariances. The structure of maternal inheritance differs among the 10 traits considered at four stages in the life cycle. Early in the life cycle, seed weight and embryo weight display substantial , a negative , and a positive . Subsequently, cotyledon diameter displays and of roughly the same magnitude and negative . For fall rosettes, leaf number and length are best described by a Mendelian model. In the spring, leaf length displays maternal inheritance with significant and and a negative . All maternally inherited traits show significant negative . Predicted response to selection under maternal inheritance depends on and as well as . Negative results in predicted responses in the opposite direction to selection for seed weight and embryo weight and predicted responses near zero for all subsequent maternally inherited traits. Maternal inheritance persists through the life cycle of this annual plant for a number of size-related traits and will alter the direction and rate of evolutionary response in this population.     

THE MAINTENANCE OF POLYGENIC VARIATION IN FINITE POPULATIONS

Models of the maintenance of genetic variance in a polygenic trait have usually assumed that population size is infinite and that selection is weak. Consequently, they will overestimate the amount of variation maintained in finite populations. I derive approximations for the equilibrium genetic variance, in finite populations under weak stabilizing selection for triallelic loci and for an infinite “rare alleles” model. These are compared to results for neutral characters, to the “Gaussian allelic” model, and to Wright's approximation for a biallelic locus under arbitrary selection pressures. For a variety of parameter values, the three-allele, Gaussian, and Wrightian approximations all converge on the neutral model when population size is small. As expected, far less equilibrium genetic variance can be maintained if effective population size, N, is on the order of a few hundred than if N is infinite. All of the models predict that comparisons among populations with N less than about 10⁴ should show substantial differences in . While it is easier to maintain absolute when alleles interact to yield dominance or overdominance for fitness, less additivity also makes more susceptible to differences in N. I argue that experimental data do not seem to reflect the predicted degree of relationship between N and . This calls into question the ability of mutation-selection balance or simple balancing selection to explain observed . The dependence of on N could be used to test the adequacy of mutation-selection balance models.     

A new proposal for measurement of the adjusted mean crowding through consideration of size variability in habitat units

The mean crowding has previously been measured under the assumption that all quadrats or habitat units have the same size, even though the actual habitat units such as seeds or leaves are generally variable in size. A new index, ‘adjusted mean crowding’, which is adjusted for this variability can be given as where Q is the total number of habitat units in the whole area, x_j the number of individuals in the jth habitat unit, and a_j is defined as the ‘relative size’ of the jth habitat unit, i.e. a_y=y_y/(∑y_j/Q) where y_j is the actually measured size of the jth habitat unit. It is expected that and for the uniform distribution and the random distribution ‘per unit size’, respectively. The comparison between and regressions ( analysis) for the egg distribution pattern of Callosobruchus chinensis or C. maculatus proved that the regression is biased by a positive correlation between the egg number per seed and seed size rather than by a density-dependent change in the ovipositional behavior.     

Performance of a pilot-scale packed bed reactor for perchlorate reduction using a sulfur oxidizing bacterial consortium

A novel sulfur‐utilizing perchlorate reducing bacterial consortium successfully treated perchlorate (ClO) in prior batch and bench‐scale packed bed reactor (PBR) studies. This study examined the scale up of this process for treatment of water from a ClO and RDX contaminated aquifer in Cape Cod Massachusetts. A pilot‐scale upflow PBR (～250‐L) was constructed with elemental sulfur and crushed oyster shell packing media. The reactor was inoculated with sulfur oxidizing ClO reducing cultures enriched from a wastewater seed. Sodium sulfite provided a good method of dissolved oxygen removal in batch cultures, but was found to promote the growth of bacteria that carry out sulfur disproportionation and sulfate reduction, which inhibited ClO reduction in the pilot system. After terminating sulfite addition, the PBR successfully removed 96% of the influent ClO in the groundwater at an empty bed contact time (EBCT) of 12 h (effluent ClO of 4.2 µg L^?1). Simultaneous ClO and NO reduction was observed in the lower half of the reactor before reactions shifted to sulfur disproportionation and sulfate reduction. Analyses of water quality profiles were supported by molecular analysis, which showed distinct groupings of ClO and NO degrading organisms at the inlet of the PBR, while sulfur disproportionation was the primary biological process occurring in the top potion of the reactor. Biotechnol. Bioeng. 2012; 109:637–646. © 2011 Wiley Periodicals, Inc.     

THE EFFECT OF SOFT SELECTION ON THE VARIABILITY OF A QUANTITATIVE TRAIT

The equilibrium phenotypic variance of a normally distributed quantitative character P under soft selection is studied. This character is assumed to undergo Gaussian stabilizing selection W(p, x) = exp[–(p – x)²/2w²]. The environmentally determined optimum (x) is a normal variable with variance s². A stable equilibrium with is found, so that increases both with increasing environmental heterogeneity and with increasing local intensity of stabilizing selection. It is shown that both genetic and environmental components of the variance are selected until this equilibrium is reached. Habitat selection, supposed to be normal (with variance H²) around the optimum, also increases the value. Nevertheless, relatively intense local stabilizing selection (w < s) and accurate habitat choice (H < s) are required for the initial spread and the evolutionary stability of this habitat selection.     

Derepressive effect of NH on hydrogen production by deleting the glnA1 gene in Rhodobacter sphaeroides

Purple non‐sulfur (PNS) bacteria produce hydrogen by photofermentation of organic acids in wastewater. However, NH in wastewater may inhibit hydrogen synthesis by repressing the expression and activity of nitrogenase, the enzyme catalyzing hydrogen production in PNS bacteria. In this study, the Rhodobacter sphaeroides 6016 glnA gene encoding glutamine synthetase (GS) was knocked out by homologous recombination, and the effects on hydrogen production and nitrogenase activity were examined. Using 3 mM glutamine as the nitrogen source, hydrogen production (1,245–1,588 mL hydrogen/L culture) and nitrogenase activity were detected in the mutant in the presence of relatively high NH concentrations (15–40 mM), whereas neither was detected in the wild‐type strain under the same conditions. Further analysis indicated that high NH concentrations greatly inhibited the expression of nifA and nitrogenase gene in the wild‐type strain but not in the glnA1^? mutant. These observations suggest that GS is essential to NH repression of nitrogenase and that deletion of glnA1 results in the complete derepression of nitrogenase by preventing NH assimilation in vivo, thus relieving the inhibition of nifA and nitrogenase gene expression. Knocking out glnA1 therefore provides an efficient approach to removing the inhibitory effects of ammonium ions in R. sphaeroides and possibly in other hydrogen‐producing PNS bacteria. Biotechnol. Bioeng. 2010;106: 564–572. © 2010 Wiley Periodicals, Inc.     

Tiller population dynamics of reciprocally transplanted Eriophorum vaginatum L. ecotypes in a changing climate

Moist tussock tundra, dominated by the sedge Eriophorum vaginatum L., covers approximately 3.36 × 10⁸ km² of arctic surface area along with large amounts of subarctic land area. Eriophorum vaginatum exhibits ecotypic differentiation along latitudinal gradients in Alaska. While ecotypic differentiation may be beneficial during periods of climate stability, it may be detrimental as climate changes, causing adaptational lag. Following harvest of a 30-year reciprocal transplant experiment, age-specific demographic data on E. vaginatum tillers were collected to parameterize a Leslie matrix. Yellow Taxi analysis, based on Tukey's Jackknife, was used to determine mean pseudovalues of tiller population growth rate () for four source populations of E. vaginatum tussocks that were transplanted to each of three gardens along a latitudinal gradient. Source populations responded differentially along the latitudinal gradient. Survival and daughter tiller production influenced differences seen at the mid-latitude garden, and the overall tiller population performance was generally improved by northward transplanting relative to southward transplanting. A comparison of home-source and away-source within the same transplant garden indicates no home-site advantage. Although populations were still growing when transplanted to home-sites ( = 1.056), tiller population growth rate increased as ΔGDD became more negative relative to the home site (i.e., as tussocks were transplanted north). These results imply that populations are affected by climate gradients in a manner consistent with adaptational lag. This study documenting the response of high-latitude ecotypes to climate gradients may be an indication of the possible future effects of climate shift in more southern latitudes.     

Fed batch culture of Saccharomyces cerevisiae: A perspective of computer control to enhance the productivity in baker's yeast cultivation

A means to avoid the glucose effect in the production of baker's yeast from glucose and/or molasses in a fed batch culture by controlling the feed rate of fresh medium with an ad hoc measurement of the respiratory quotient, RQ, is presented. The feed rate is changed stepwise here such that the value of RQ ranges from 1.0 to 1.2 throughout the cultivation. Thus far, the specific growth rate based on the total cell mass and the growth yield obtained throughout are 0.24 hr^?1 and 0.55 g cell/g glucose. Prior to the experimental run mentioned above, equations to predetermine the feed rate and concentration of glucose in the feed are derived from the mass balance of limiting substrates (glucose). Since values of either RQ or I (Q x, oxygen consumption rate with respect to the total cell mass in the fermenter) can be measured quite easily and reliably, computer control of the fermentation in light of this information is discussed.     

Studies on ventilation of culture broths. I. Behavior of CO2 in model systems

The rate of dissolution and dehydration of CO₂ in a liquid model system was investigated. Components in the model system established the main conditions which may exist, in the extracellular space of a microbiological culture liquid. The charge in voltage of a glass electrode was measured which indicated the formation of H⁺ ions in the H₂CO₃ ? HCO H⁺ reaction. The rate of CO₂ hydration increased with the increase of temperature from 0 to 40°C. Likewise the equilibrium of the reaction was shifted towards the forward reaction. Similar results were observed when the tip velocity of the impeller was increased. Data suggest that agitation promotes the dissolution of CO₂ in the culture liquid through the reduction of gas-liquid film resistance in the diffusion of this gas. The rate of hydration of CO₂ into the bulk of the liquid was independent of pCO₂ above the surface of the liquid but depended on pCO₂ in the gas bubble within the liquid. The concentration of HCO was, furthermore, influenced by the buffer components, buffer capacity, and the viscosity of the system. Since pCO₂ and the HCO concentration in the extracellular space depend on both physical and chemical factors, the ventilation of a culture liquid necessitates both exhaust of CO₂ from the gas bubbles of the culture broth and shift of the H₂CO₃ ? HCO + H⁺ reaction towards the backward direction.     

Application of the\mathop m\limits^* - m method to the analysis of spatial patterns by changing the quadrat sizemethod to the analysis of spatial patterns by changing the quadrat size

A method for the analysis of spatial pattern using quadrats of different sizes is developed on the basis of the relationship of mean crowding () to mean density (m). The -on-m regression obtained by successive changes in quadrat size in a single population (unit-size relation) shows a characteristic pattern according to the type of distribution. By aid of the ρ-index proposed here, we can distinguish the random, aggregated and uniform distributions of the basic components (individual or group of individuals). The ρ serves as an index of spatial correlation between neighbouring quadrats, and it also provides information on the approximate area occupied by clump (colony), distribution pattern of individuals within clumps, and possibly the distribution pattern of clumps themselves. Even in a specified type of distribution, the unit-size relation is not necessarily identical with the relation for a series of populations at a particular quadrat size (series relation). The changes in the series relationship with successive changes of quadrat sizes are also considered for some basic patterns of distributions. The combined use of the unit-size and the series relations for a set of populations of the species under study may provide a satisfactory picture of the spatial pattern characteristic of the species. Application of the method is illustrated by using distribution data of several species of animals and plants. The advantage of the present method over other methods are discussed, and the formulae for determining the optimum quadrat unit in sampling surveys are given.     

Characterization of a biofilm membrane reactor and its prospects for fine chemical synthesis

Biofilms are known to be robust biocatalysts. Conventionally, they have been mainly applied for wastewater treatment, however recent reports about their employment for chemical synthesis are increasingly attracting attention. Engineered Pseudomonas sp. strain VLB120ΔC biofilm growing in a tubular membrane reactor was utilized for the continuous production of (S)‐styrene oxide. A biofilm specific morphotype appeared in the effluent during cultivation, accounting for 60–80% of the total biofilm irrespective of inoculation conditions but with similar specific activities as the original morphotype. Mass transfer of the substrate styrene and the product styrene oxide was found to be dependent on the flow rate but was not limiting the epoxidation rate. Oxygen was identified as one of the main parameters influencing the biotransformation rate. Productivity was linearly dependent on the specific membrane area and on the tube wall thickness. On average volumetric productivities of 24 g L day^?1 with a maximum of 70 g L day^?1 and biomass concentrations of 45 g_BDW L have been achieved over long continuous process periods (≥50 days) without reactor downtimes. Biotechnol. Bioeng. 2010. 105: 705–717. © 2009 Wiley Periodicals, Inc.     

Inorganic carbon sources and biomass regulation in intensive microalgal cultures

Three freshwater and one marine algal species were grown under inorganic carbon limitation in laboratory continuous cultures. Comparisons were made between HCO₃^? alkalinity and bubbled CO₂ as carbon sources. HCO₃^? alkalinity was an excellent source of inorganic carbon below specific pH levels, but chemical precipitation at high pH placed an upper limit on productivity that was far lower than potential light-limiting levels. With bubbled CO₂ it was possible to achieve light limitation. The main factor controlling productivity was the mass flux of inorganic carbon added to the culture, which is the product of gas flow rate and influent P level. Small bubbles were more efficient than large bubbles at low gas flow rates and P levels, but led to froth flotation of algal cells and concomitant reductions in productivity at high bubble rates. At 1% CO₂ productivity was still dependent on mass fluxes of added carbon, but was independent of bubble size. At high bubble rates with 1% CO₂ narcosis was evident. Maximum yields occurred at intermediate dilution rates when inorganic carbon was supplied via bubbled gas.     

HEMOGLOBIN POLYMORPHISMS IN DEER MICE (PEROMYSCUS MANICULATUS): PHYSIOLOGY OF BETA-GLOBIN VARIANTS AND ALPHA-GLOBIN RECOMBINANTS

Wild populations of deer mice (Peromyscus maniculatus) contain hemoglobin polymorphisms at both alpha-globin (Hba, Hbc) and beta-globin (Hbd) loci. Population gene frequencies of beta-globin variants (d⁰ and d¹ haplotypes) are not correlated with altitude, whereas a¹c¹ alpha-globin haplotypes are fixed in low-altitude populations, and a⁰c⁰ haplotypes reach near fixation at high altitudes. We examined the effects of alpha- and beta-globin variants on blood oxygen affinity and on aerobic performance, measured as maximum oxygen consumption (). Exercise and cold exposure were used to elicit . Experiments were performed at low (340 m) and high (3,800 m) altitude to include the range of oxygen partial pressures encountered by wild deer mice. Beta-globin variants had little effect on blood oxygen affinity or . Oxygen-dissociation curves from a⁰c⁰ and a¹c¹ homozygotes and heterozygotes had similar shapes, but the P₅₀ of a⁰c⁰ homozygotes was significantly lower than that of other genotypes. Mice carrying a¹c¹/a¹c¹ genotypes had the highest at low altitude, but mice with a⁰c⁰/a⁰c⁰ genotypes had the highest at high altitude. Mice carrying rare recombinant alpha-globin haplotypes (a⁰c¹) had lower than nonrecombinant genotypes as a whole but in most cases were not significantly different from nonrecombinant heterozygotes (a⁰c⁰/a¹c¹). We conclude that genetic adaptation to different altitudes was important in the evolution of deer mouse alpha-globin polymorphisms and in the maintenance of linkage disequilibrium in the alpha-globin loci but was not a significant factor in the evolution of beta-globin polymorphisms.     

Differential responses of two wetland graminoids to high ammonium at different pH values

Enhanced soil ammonium () concentrations in wetlands often lead to graminoid dominance, but species composition is highly variable. Although is readily taken up as a nutrient, several wetland species are known to be sensitive to high concentrations or even suffer toxicity, particularly at low soil pH. More knowledge about differential graminoid responses to high availability in relation to soil pH can help to better understand vegetation changes. The responses of two wetland graminoids, Juncus acutiflorus and Carex disticha, to high (2 mmol·l^?1) versus control (20 μmol·l^?1) concentrations were tested in a controlled hydroponic set up, at two pH values (4 and 6). A high concentration did not change total biomass for these species at either pH, but increased C allocation to shoots and increased P uptake, leading to K and Ca limitation, depending on pH treatment. More than 50% of N taken up by C. disticha was invested in N‐rich amino acids with decreasing C:N ratio, but only 10% for J. acutiflorus. Although both species appeared to be well adapted to high loadings in the short term, C. disticha showed higher classic detoxifying responses that are early warning indicators for decreased tolerance in the long term. In general, the efficient aboveground biomass allocation, P uptake and N detoxification explain the competitive strength of wetland graminoids at the expense of overall biodiversity at high loading. In addition, differential responses to enhanced affect interspecific competition among graminoids and lead to a shift in vegetation composition.     

Minireview: demystifying microbial reaction energetics

The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of the standard Gibbs energy () define the direction and energy yield of a reaction; they do not. is one part of the actual Gibbs energy of a reaction (ΔG_r ), with a second part accounting for deviations from the standard composition. It is also frequently assumed that applies only to 25 °C and 1 bar; it does not. is a function of temperature and pressure. Here, we review how to determine ΔG_r as a function of temperature, pressure and chemical composition for microbial catabolic reactions, including a discussion of the effects of ionic strength on ΔG_r and highlighting the large effects when multi-valent ions are part of the reaction. We also calculate ΔG_r for five example catabolisms at specific environmental conditions: aerobic respiration of glucose in freshwater, anaerobic respiration of acetate in marine sediment, hydrogenotrophic methanogenesis in a laboratory batch reactor, anaerobic ammonia oxidation in a wastewater reactor and aerobic pyrite oxidation in acid mine drainage. These examples serve as templates to determine the energy yields of other catabolic reactions at environmentally relevant conditions.