Thermodynamic analysis of growth of Methanobacterium thermoautotrophicum

Growth of Methanobacterium thermoautotrophicum, an anaerobic archaebacterium using methanogenesis as the catabolic pathway, is characterized by large heat production rates, up to 13 W g⁻¹, and low biomass yields, in the order of 0.02 C‐mol mol⁻¹ H₂ consumed. These values, indicating a possibly “inefficient” growth mechanism, warrant a thermodynamic analysis to obtain a better understanding of the growth process. The growth‐associated heat production (Δ_rH) and the growth‐associated Gibbs energy dissipation per mol biomass formed (Δ_rG) were −3730 kJ C‐mol⁻¹ and −802 kJ C‐mol⁻¹, respectively. The Gibbs energy change found in this study is indeed unusually high as compared to aerobic methylotrophes, but not untypical for methanogens grown on CO₂. It explains the low biomass yield. Based on the information available on the energetic metabolism and on an ATP balance, the biomass yield can be predicted to be approximately in the range of the experimentally determined value. The fact that the exothermicity exceeds vastly even the Gibbs energy change can be explained by a dramatic entropy decrease of the catabolic reaction. Microbial growth characterized by entropy reduction and correspondingly by unusually large heat production may be called entropy‐retarded growth. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 64: 74–81, 1999.     

天然碱泥分离用生物絮凝剂产生菌的分离与鉴定

通过多点采样,多次反复筛选,从蔬菜土地壤中筛选出一株具有高絮凝活性的细菌,细菌生长过程中可产生具有絮凝作用的胞外分泌物,经实验对内蒙天然碱碱泥具有强絮凝作用。通过对菌株的个体形态特征,菌落形态特征,运动性进行观察;同时对其接触酶,氧化酶等生理生化指标进行了测试,最终确定为产气肠杆菌（Enterobacter aerogenes)。该菌株可以利用单糖尤其是葡萄糖产酸,并可利用果糖产酸,兼性厌氧。     

Comparison of growth and maintenance parameters for cellulase biosynthesis by Trichoderma reesei-C5 with some published data

Growth and maintenance parameters μ_max, K_s, m, and Y_m for cellulase biosynthesis on lactose by T. reesei-C5 were estimated and compared with published data on other soluble substrates and mutant strains of T. reesei in continuous culture. Growth was favored at higher feed lactose but cellulase productivities did not increase proportionally, suggesting that a degree of inhibition and/or catabolic repression within the strain is possible. The estimated values of growth kinetics and maintenance parameters varied little but were within a reasonable range of published data on other soluble substrates and mutant strains of T. reesei in continuous cultures.     

Effect of oxygen tension, salinity, temperature and organic matter concentration on the growth and nitrifying activity of an estuarine strain of Nitrosomonas

Abstract The effects of O₂ tension, temperature, salt concentration and organic matter concentration on the growth and nitrifying activity of Nitrosomonas N₃ isolated from Tay Estuary sediments have been investigated. Chemostat-grown cultures were able to grow and nitrify at dissolved O₂ concentrations as low as 0.1 mg O₂· 1⁻¹ (cell population densities were 15% of those obtained in fully aerated cultures). This bacterium was sensitive to reduced temperatures as chemostat-grown cultures washed out at growth temperatures below 15°C, at dilution rates > 0.025 · h⁻¹. Batch-grown cultures of Nitrosomonas N₃ were used to study the effects of NaCl and complex organic matter concentration on nitrifying activity. Maximum rates of NH⁺₄ oxidation were recorded at NaCl concentrations of 1% w/v, whilst tryptone soya broth (TSB), nutrient broth (NB), yeast extract broth (YEB) and peptone were inhibitory at concentrations > 10 mg · 1⁻¹.     

Glucoamylase production in continuous cultures of Aspergillus niger with special emphasis on growth parameters

Maltose-limited continuous culture of Aspergillus niger was carried out with potassium nitrate to investigate growth and glucoamylase formation characteristics. Glucoamylase production was dependent on the specific growth rate. The maximal amount of glucoamylase (units/l and U/g dry weight) was obtained at =0.08h–1, and the maximum specific rate of production (units/g/dry weight per hour) was at =0.2h–1. The maintenance coefficients (ms and mATP) were higher than for some other fungi. Maximal growth yields on substrate, oxygen and ATP (Yxsm, YxO2m and Yxam) were very efficient (high) and the value of Yxam, which cannot exceed the theoretical maximal value, is obtained when a P/O ratio of 1:1 is assumed. This indicates that biomass formation is energetically inexpensive and most of the expended energy has to be invested in the process of glucoamylase excretion.     

A Bayesian analysis of the effect of selection for growth rate on growth curves in rabbits

Gompertz growth curves were fitted to the data of 137 rabbits from control (C) and selected (S) lines. The animals came from a synthetic rabbit line selected for an increased growth rate. The embryos from generations 3 and 4 were frozen and thawed to be contemporary of rabbits born in generation 10. Group C was the offspring of generations 3 and 4, and group S was the contemporary offspring of generation 10. The animals were weighed individually twice a week during the first four weeks of life, and once a week thereafter, until 20 weeks of age. Subsequently, the males were weighed weekly until 40 weeks of age. The random samples of the posterior distributions of the growth curve parameters were drawn by using Markov Chain Monte Carlo (MCMC) methods. As a consequence of selection, the selected animals were heavier than the C animals throughout the entire growth curve. Adult body weight, estimated as a parameter of the Gompertz curve, was 7% higher in the selected line. The other parameters of the Gompertz curve were scarcely affected by selection. When selected and control growth curves are represented in a metabolic scale, all differences disappear.     

Theoretical analysis of intrinsic reaction kinetics and the behavior of immobilized enzymes system for steady-state conditions

Mathematical modeling of immobilized enzymes under different kinetics mechanism viz. simple Michaelis–Menten, uncompetitive substrate inhibition, total competitive product inhibition, total non-competitive product inhibition and reversible Michaelis–Menten reaction are discussed. These five kinetic models are based on reaction diffusion equations containing non-linear terms related to Michaelis–Menten kinetics of the enzymatic reaction. Modified Adomian decomposition method is employed to derive the general analytical expressions of substrate and product concentration for all these five mechanisms for all possible values of the parameters Φ_S (Thiele modulus for substrate), Φ_P (Thiele modulus for product) and α (dimensionless inhibition degree). Also we have presented the general analytical expressions for the mean integrated effectiveness factor for all values of parameters. Analytical results are compared with the numerical results and also with the limiting case results, which are found to be good in agreement.     

A chemostat culture as a tool for the improvement of a recombinant E. coli strain over-producing penicillin G acylase

The recombinant strain RE3(pKA18) of Escherichia coli constitutively overproduces penicillin G acylase (PGA) from plasmid-borne gene pga. The host strain RE3 bears the same pga gene on its chromosome, the expression of which is controlled by the natural mechanism of induction with phenylacetic acid (PA). To evaluate the maximum biosynthetic capacity for PGA, induction of the chromosomal pga by PA was studied in a culture of the recombinant strain. PGA production by batch cultures of RE3(pKA18) and RE3 showed a different response to the addition of PA to the medium: while an addition of PA induces PGA in a culture of strain RE3 as expected, in recombinant cells it lowers the specific activity of PGA and a large amount of PGA is released into the culture medium. To improve the PGA production, the strain RE3(pKA18) was cultured in a carbon-limited chemostat and subjected to selection pressure in a medium supplemented with phenylacetic acid amide (PAA). Phenylacetic acid amide served as a source of nitrogen, an inducer of PGA and a factor exerting positive selection pressure on the maintenance of the recombinant plasmid. After 130 generations of growth in the presence of the inducer, no recombinant strain with constitutive expression of the chromosomal gene pga was detected in the prevailing P(+) subpopulation in the chemostat. Shake-flask experiments with the parent recombinant strain RE3(pKA18), host strain RE3, chemostat evolvant ERE3(epKA18), the cured host ERE3 alone, and its derivative after retransformation with ancestral plasmid ERE3(pKA18) showed that inactivation of the plasmid-borne pga by a frame-shift mutation (plasmid epKA18) occurred in the plasmid-bearing subpopulation accumulated in the chemostat. Marked adaptive changes evolved in the host ERE3 during a 130 generation culture: (1) the specific growth rate of the host increased by 30% in a medium without PA, (2) the copy number of plasmids pKA18 and epKA18 in the host cultured in PA-free medium dropped by about 40%, and (3) the leakage of PGA from the cell in the presence of PA found in strain RE3(pKA18) was not observed in strain ERE3(pKA18). This new recombinant strain with modified traits was constructed by means of retransformation of the evolved host ERE3 with ancestral plasmid pKA18.     

A unified stoichiometric model for oxidative and oxidoreductive growth of yeasts

Yeasts degrade glucose through different metabolic pathways, where the choice of the pathway is dependent on the nature of the limitation in the various substrates. When oxygen is limiting in addition to glucose, yeasts often grow according to a mixture of oxidative and reductive metabolism. Oxygen may be limiting either by supply or by inherent biological restrictions such as the respiratory bottleneck in Saccharomyces cerevisiae or by both. A unified model incorporating both supply and biological limitations is proposed for the quantitative prediction of growth rates, consumption and production rates, as well as key metabolite concentrations during mixed oxidoreductive metabolism occuring as a result of such oxygen limitations. This simple unstructured model can be applied to different yeast strains while at the same time requiring a minimum number of measured parameters. "Estimators" are utilized in order to predict the presence of supply-side or biological limitations. The values of these estimators also characterize the relative importance of oxidative to total metabolism. Results from the aerobic and oxygen-limited chemostat cultures were used to corroborate the model predictions. During these experiments, the heat released by the yeast cultures was also monitored on-line. The model correctly predicted the overall stoichiometry, steady-state concentrations, and rates including heat dissipation rates measured in the various situations of oxygen limitations. Direct continuous measurements such as heat can be used in conjunction with the unified model for on-line proces control. (c) 1992 John Wiley & Sons, Inc.     

Drosophila growth cones: A genetically tractable platform for the analysis of axonal growth dynamics

The formation of neuronal networks, during development and regeneration, requires outgrowth of axons along reproducible paths toward their appropriate postsynaptic target cells. Axonal extension occurs at growth cones (GCs) at the tips of axons. GC advance and navigation requires the activity of their cytoskeletal networks, comprising filamentous actin (F‐actin) in lamellipodia and filopodia as well as dynamic microtubules (MTs) emanating from bundles of the axonal core. The molecular mechanisms governing these two cytoskeletal networks, their cross‐talk, and their response to extracellular signaling cues are only partially understood, hindering our conceptual understanding of how regulated changes in GC behavior are controlled. Here, we introduce Drosophila GCs as a suitable model to address these mechanisms. Morphological and cytoskeletal readouts of Drosophila GCs are similar to those of other models, including mammals, as demonstrated here for MT and F‐actin dynamics, axonal growth rates, filopodial structure and motility, organizational principles of MT networks, and subcellular marker localization. Therefore, we expect fundamental insights gained in Drosophila to be translatable into vertebrate biology. The advantage of the Drosophila model over others is its enormous amenability to combinatorial genetics as a powerful strategy to address the complexity of regulatory networks governing axonal growth. Thus, using pharmacological and genetic manipulations, we demonstrate a role of the actin cytoskeleton in a specific form of MT organization (loop formation), known to regulate GC pausing behavior. We demonstrate these events to be mediated by the actin‐MT linking factor Short stop, thus identifying an essential molecular player in this context. © 2009 Wiley Periodicals, Inc. Develop Neurobiol 2010     

Advantages of continuous over batch reactors for the kinetic analysis of enzymes inhibited by an unknown substrate impurity

A new experimental technique, employing a continuous stirred-tank reactor, for studying enzyme kinetics in the presence of inhibitor-contaminated substrate is described. The proposed method is simulated mathematically for competitive, uncompetitive, and mixed-type noncompetitive inhibition. The step-by-step experimental procedure is described, as is the necessary data analysis for determining the kinetic parameters. Differences in system response for enzyme inhibition by excess substrate and by an impurity are illustrated, and a stability analysis of the system is performed.     

A method for the quantitative analysis of nerve growth in vitro

Summary A method is described for the quantitative analysis of the nerve-growth-promoting activity of biological molecules in tissue culture. The criteria used for the evaluation of this activity is based on the neurite length as well as the total number of neurites produced by the explant of whole dorsal root ganglia from 12-d-old chick embryos. A nerve growth index (NGI) is given to each ganglion during each of a 5-d culture period. The NGI is defined as the product of average neurite length in millimeters and the total number of neurites. We report that with increasing concentrations of fetal bovine serum, there was a proportional increase in NGI due to increased neurite density while the neurite length was not greatly affected. The NGI of several proteins with known nerve growth promoting activity, namely nerve growth factor, insulin, transferrin, and fibronectin were investigated for their activity and compared with that of fetal bovine serum. This work was supported in part by grant GM-10374 from the National Institutes of Health, Bethesda, MD.     

Bacterial growth rate and growth pouch nodulation profile differences as possible ways of Bradyrhizobium japonicum strain screening for low P soils

This work studied the effects of P fertilization on nodulation of field-grown soybean by two Bradyrhizobium strains (SMGS₁ and THA₇), and checked if differences between strains were consistent with bacterial growth and growth pouch nodulation ability in response to P availability. In the field, nodule dry weight and nitrogen fixation activity of inoculated soybean were studied on typical acid soils of Thaïland at the flowering (R₁) stage and at the end of grain filling. Grain yield, growth and phosphorus content were recorded. The bradyrhizobial strains were cultivated in culture medium, and growth parameters recorded. Nodulation patterns were observed during growth pouch experiments: infective root cells were inoculated with strains cultivated at two P concentrations in their culture media, namely 1 M and 1 mM. Ten days after inoculation, the position of each nodule was measured relative to the root tip (RT) mark, expressed relative to the smallest emerging root hairs-RT distance in the nodulation frequency profile, and the consistency of responses was tested. In the field, on P deficient soils, dry weight of nodules was higher with Bradyrhizobium japonicum strain SMGS₁ than with strain THA₇. P supply increased the number and dry weight of nodules for both strains, with a higher dry weight response for THA₇ than for SMGS₁. It also had a positive effect on tissue phosphorus status and grain yield at R₈ stage. In growth media, significant differences were recorded between strains under P-limiting conditions: The growth rate was higher for strain SMGS₁, as well as the maximal number of bacterial cells supported. With growth pouch, inoculating plants with bacteria grown in P-deficient medium resulted in a less intense nodulation of roots by THA₇, and with nodules appearing earlier on roots than in the case of SMGS₁. At 1 mM P, there was no significant difference between strains. Thus, strain THA₇ is more affected by P deficiency than strain SMGS₁. Although P was not supplied in the same way in the soil and in the growth pouch experiments, this consistency of behaviour between work scales indicates that phosphorus availability is a key component for a successful inoculation. Furthermore, the study of bacterial growth rates and nodulation profile represents an interesting step for bacterial screening for low P soils. [-11pt]     

一类微生物连续培养竞争模型的定性分析

研究一类微生物连续培养竞争模型的解的结构,分析了平衡点的稳定性及平衡点附近极限环存在唯一性,证明系统存在正向不变集。     

A Bayesian approach for the analysis of panel-count data with dependent termination

We consider modeling and Bayesian analysis for panel-count data when the termination time for each subject may depend on its history of the recurrent events. We propose a fully specified semiparametric model for the joint distribution of the recurrent events and the termination time. For this model, we provide a natural motivation, derive several novel properties, and develop a Bayesian analysis based on a Markov chain Monte Carlo algorithm. Comparisons are made to other existing models and methods for panel-count data. We demonstrate the usefulness of our new models and methodologies through the reanalysis of a data set from a clinical trial.     

Production of recombinant h-AT III with mammalian cell cultures using capillary electrophoresis for product monitoring

The importance of mammalian cell cultures for biotechnological production processes is steadily increasing, despite the high demands of these organisms on their culture conditions. Efforts towards a more efficient bioprocess generally concentrate on maximizing the culture's life time, the cell number, and the product concentration. Here recombinant BHK 21 c13 cells are used to produce rh-AT III, an anticoagulant of high therapeutic value. The influence of the process mode (batch, repeated batch, continuous perfusion) and the process temperature (30°C vs. 37°C) on the above mentioned parameters is investigated. It is possible to increase the length of the culture from 140 h (batch) to more than 500 h (continuous perfusion culture), while concomitantly increasing the cell density from 0.72 10⁶/ml (batch) to 2.27 10⁶/ml (repeated batch) and 2.87 10⁶/ml (continuous perfusion culture). The accumulation of toxic metabolites, such as lactate, can be curtailed by reducing the bioreactor temperature from 37°C to 30°C during the later part of the exponential growth phase. Fast and reliable product monitoring became essential during process optimization. Capillary zone electrophoresis (CZE) in uncoated fused silica capillaries was studied for that purpose and compared to the standard ELISA. Under optimized conditions an AT III quantification could be done within 2 min with CZE. The detection limit was 5 g/ml. A relative standard deviation of less than 0.9% was calculated. The detection limit could be lowered by one order of magnitude by using a two dimensional system, where an liquid chromatographic (LC) system is coupled to the CZE. Concomitantly the resolution is improved. The two-dimensional analysis required 5 min. Membrane adsorbers (MA) were used as stationary phase in the LC-system, to allow the application of high flow rates (5–10 ml/min). The correlation between the LC-CZE analysis and the standard AT III-ELISA was excellent, with r²: 0.965. Using the assay for at line product monitoring, it is shown, that the process temperature is of no consequence for the productivity whereas the process mode strongly influences this parameter.     

Isolation by genetic and physiological characteristics of a fuel-ethanol fermentative Saccharomyces cerevisiae strain with potential for genetic manipulation

Fuel ethanol fermentation process is a complex environment with an intensive succession of yeast strains. The population stability depends on the use of a well-adapted strain that can fit to a particular industrial plant. This stability helps to keep high level of ethanol yield and it is absolutely required when intending to use recombinant strains. Yeast strains have been previously isolated from different distilleries in Northeast Brazil and clustered in genetic strains by PCR-fingerprinting. In this report we present the isolation and selection of a novel Saccharomyces cerevisiae strain by its high dominance in the yeast population. The new strain, JP1 strain, presented practically the same fermentative capacity and stress tolerance like the most used commercial strains, with advantages of being highly adapted to different industrial units in Northeast Brazil that used sugar cane juice as substrate. Moreover, it presented higher transformation efficiency that pointed out its potential for genetic manipulations. The importance of this strain selection programme for ethanol production is discussed.     

Performance,carcass traits and serum metabolomic profile of Nellore males with different genetic potential for post-weaning growth

The BW has been largely used as a selection criterion in genetic selection programmes; however, increases in BW can affect animal metabolism and metabolites. The knowledge of how genetic potential for growth affects the metabolites can give a footprint of growth metabolism. This research aimed to evaluate the effect of genetic potential for post-weaning growth (GG) on performance, carcass traits and serum metabolome of non-castrated Nellore males during the finishing phase. Forty-eight Nellore non-castrated males, with divergent potential for post-weaning growth, were selected and divided into two groups: high potential for post-weaning growth (HG; n = 24) and low potential for post-weaning growth (LG; n = 24). Animals were kept and fed for 90 days where performance and ultrasound carcass traits were evaluated. Blood samples were collected at the beginning and end of feeding period to analyse serum metabolites concentration. The hot carcass weight and dressing percentage were recorded at slaughter. The feedlot performance and carcass traits were not affected by genetic potential. The HG animals had a lower glucose (P = 0.039), glutamate (P = 0.038), glutamine (P = 0.004), greater betaine (P = 0.039) and pyruvate (P = 0.039) compared to the LG group at the beginning of feedlot. In addition, higher creatine phosphate concentrations were observed at the beginning of feeding period, compared to final, for both groups (P = 0.039). In conclusion, the genetic potential for post-weaning growth does not affect performance and carcass traits during the finishing period. Differences in metabolite concentrations can be better found at the beginning of feedlot, providing a footprint of growth metabolism, but similar metabolite concentration at the end of finishing period.     

Impact of developmental variance on behavior of models for insect populations II. Models for populations with density dependent restrictions on growth

The impact of variation in developmental times on behavior of models for insect populations is investigated with special reference to models which include various types of intraspecific competition. At low densities, increases in developmental variation led to decreases in reproductive rate. At high densities, increases in developmental variation led to increases in reproductive rate. There was little change in the relationship between developmental variance and generation time as density increased.     

脂肪酶产生菌Aspergillus sp. FS132产酶条件的初步优化及其18S rRNA基因序列的比较分析

从新疆火焰山口土样中分离的一株脂肪酶产生菌FS132,菌落形态表明为霉菌。对其产酶条件的初步优化表明,产酶的最适培养时间为45h,培养基最适初始pH 7.0,最适培养温度36℃,最适摇瓶空气量25mL/250mL锥形瓶。为进一步鉴定该菌株,克隆测定了该菌18S rRNA基因序列。并对其进行系统进化树分析,结果表明该菌与已报道的Aspergillus tamarii具有最紧密亲缘关系。