Incubation experiments on nitrogen mineralization in loess and sandy soils

Summary In aerobic incubation experiments, nitrogen mineralization was investigated in agricultural loess and sandy soils. Fresh, fieldmoist samples were used for incubation. Using an optimization procedure the N-mineralization was split into two nitrogen fractions: A resistant, slowly decomposable organic N-fraction (index rpm) and a fast decomposable N-fraction (index dpm).Loess- and sandy soils showed similar mean reaction coefficients for N-mineralization. The results also indicated that the amount of mineralizable nitrogen in the resistant N-fraction depended directly on clay content.Soil sampling at different times during crop growing period gave different mineralization amounts and courses.Effect of added plant residues on N-mineralization, was also studied by incubation. Variation of type and quantity of added residues changed the net N-mineralization in a characteristic way: Sugar beet leaves, added in minced form, caused an increase in mineralization; while straw caused a temporary immobilization, followed by remineralization.Incubation experiments on undisturbed soil columns showed nearly linear mineralization with time.This paper was presented in part at the 1983 Congress of the German Soil Science Society held at Trier.     

N-mineralization in Löss-Parabrownearthes: Incubation experiments

Summary Nitrogen mineralization in Löss-Parabrownearthes was studied in long-term incubation experiments at different temperatures. Results obtained were used to optimize the parameters of a first-order kinetic model for N-mineralization of these soils: average reaction coefficients obtained by incubationat 35°C are 0.00737±0.00081 per day for the old organic material, and 0.25±0.07 per day for the fresh organic material.The mineralizable nitrogen of the fresh organic material at the beginning of march amounts to about 90±20 kg N/(ha*30 cm), independent of the kind of preceding crop. Temperature dependence of mineralization was estimated roughly. Attempts to simplify the procedure of evaluation of these parameters are described.Aqualfs and Udalfs according to the 7th approximation.     

A continuous optimization approach for inferring parameters in mathematical models of regulatory networks

Background

The advances of systems biology have raised a large number of sophisticated mathematical models for describing the dynamic property of complex biological systems. One of the major steps in developing mathematical models is to estimate unknown parameters of the model based on experimentally measured quantities. However, experimental conditions limit the amount of data that is available for mathematical modelling. The number of unknown parameters in mathematical models may be larger than the number of observation data. The imbalance between the number of experimental data and number of unknown parameters makes reverse-engineering problems particularly challenging.

Results

To address the issue of inadequate experimental data, we propose a continuous optimization approach for making reliable inference of model parameters. This approach first uses a spline interpolation to generate continuous functions of system dynamics as well as the first and second order derivatives of continuous functions. The expanded dataset is the basis to infer unknown model parameters using various continuous optimization criteria, including the error of simulation only, error of both simulation and the first derivative, or error of simulation as well as the first and second derivatives. We use three case studies to demonstrate the accuracy and reliability of the proposed new approach. Compared with the corresponding discrete criteria using experimental data at the measurement time points only, numerical results of the ERK kinase activation module show that the continuous absolute-error criteria using both function and high order derivatives generate estimates with better accuracy. This result is also supported by the second and third case studies for the G1/S transition network and the MAP kinase pathway, respectively. This suggests that the continuous absolute-error criteria lead to more accurate estimates than the corresponding discrete criteria. We also study the robustness property of these three models to examine the reliability of estimates. Simulation results show that the models with estimated parameters using continuous fitness functions have better robustness properties than those using the corresponding discrete fitness functions.

Conclusions

The inference studies and robustness analysis suggest that the proposed continuous optimization criteria are effective and robust for estimating unknown parameters in mathematical models.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-256) contains supplementary material, which is available to authorized users.     

Ammonium uptake and mineralization in prairie streams: chamber incubation and short-term nutrient addition experiments

1. We used two separate approaches to estimate ambient ammonium cycling in the north and south branches of Kings Creek, a prairie stream. Chamber experiments were conducted to determine ammonium uptake and mineralization rates associated with epilithic biofilms and filamentous algae collected from the streams. A series of short-term whole-stream ammonium addition experiments were also conducted to estimate the rate of uptake at ambient stream concentrations, based on the relationship between ammonium concentrations and uptake rates.
2. Chamber experiments were scaled up to whole-stream levels, resulting in ambient gross uptake estimates of 0.08  μ g⁻² s⁻¹ for the north branch and 0.16  μ g⁻² s⁻¹ for the south branch. The substrata-specific estimates of mineralization were higher than uptake in both streams.
3. Substrata-specific measurements indicated that ammonium uptake is higher in riffle habitats than in pools habitats. The results of the short-term ammonium addition experiments support these findings.
4. Short-term ammonium addition experiments show that uptake rates saturate with increasing ammonium concentrations. The observed saturation of uptake rates is consistent with a Michaelis–Menten relationship.
5. Scaled estimates of uptake from the chamber experiments were similar to estimates of ambient ammonium uptake based on the whole-stream experiments, and were comparable with previous estimates of ammonium uptake and mineralization made by using stable isotope tracer methods in Kings Creek.     

马克斯克鲁维酵母菌菊粉酶的异源表达及低聚果糖制备工艺优化

【目的】低聚果糖是新型的食品和保健品原料,具有广阔的市场需求。以菊粉酶水解菊粉制备低聚果糖的酶法工艺是先进的绿色制造。本研究旨在获得高产的菊粉酶菌株及以菊粉为原料酶法制备低聚果糖的优化工艺。【方法】采用基因工程手段克隆马克斯克鲁维酵母菌(Kluyveromyces marxianus)的菊粉酶基因,实现其在毕赤酵母中的高效表达;测定菊粉酶在不同p H、温度、金属离子和底物浓度等条件下的酶活变化趋势,获得最佳的反应参数;通过高效液相色谱法检测水解产物,获得不同酶量水解产物各组分分布。【结果】菊粉酶工程菌株在10 L发酵罐中的产菊粉酶活达1 570 U/m L、蛋白质含量为2.75 g/L发酵液;菊粉酶最适反应参数为:在体积为1 L的反应体系中,p H 5.0、反应温度50°C、含0.2 mmol/L Mg2+以及菊粉浓度为8%。在该条件下,酶量为10 U时菊粉被完全水解。水解产物中单糖和二糖含量仅为9.25%,而低聚果糖(C3-C8)含量为90.75%,且C3-C5低聚果糖含量高达72.92%。【结论】克隆了K.marxianus菊粉酶基因并实现了高效表达,获得了水解菊粉制备低聚果糖的最佳工艺条件。为菊粉酶的大量生产及低聚果糖的酶法制备奠定了良好的基础。     

Effect of copper activity on carbon and nitrogen mineralization in field-aged copper-enriched soils

Summary Nitrogen and C mineralization were investigated in five soils which had received anthropogenic Cu inputs many years ago, and compared to control soils. Copper activity was used to assess the active or toxic form of Cu; the activity of Cu in the soils ranged from approximately 10^–10 to 10^–7 M. No effect of the Cu was observed on the mineralization rates, indicating that either the Cu levels were not toxic or that microbial adaptation to Cu inputs had occurred at the sites. The ion activity product ((Cu)(OH)²) is suggested as a possible indicator of plant available Cu.     

Prediction of nitrogen availability and rice yield in lowland soils: Nitrogen mineralization parameters

Field experiments were conducted under flooded soil conditions using Maahas clay amended with urea and rice straw-sesbania mixtures during the wet and dry seasons. Parallel laboratory incubation tests were done. The objectives were 1) to determine N mineralization patterns and establish the relationship between mineralization parameters and either N availability or grain yield, and 2) to correlate the results of organic N mineralization studies in the laboratory with data from field experiments. The N mineralization patterns of flooded soils in the laboratory followed a logistic function. In laboratory studies, mineralization potential was positively correlated with extractable soil NH₄ ⁺-N at the end of the incubation period (cumulative available N). Likewise, mineralization potential calculated from laboratory studies was positively correlated with N uptake and grain yield from field studies. Extractable (NH₄ ⁺+NO₃ ^–)-N in the field correlated positively with extractable NH₄ ⁺-N in the laboratory. The extractable NH₄ ⁺-N from laboratory incubations at 14 days after transplanting, panicle initiation, and maturity was also highly and positively correlated with grain yield from field experiments.     

Determination of human arterial wall parameters from clinical data

This study suggests a method to compute the material parameters for arteries in vivo from clinically registered pressure-radius signals. The artery is modelled as a hyperelastic, incompressible, thin-walled cylinder and the membrane stresses are computed using a strain energy. The material parameters are determined in a minimisation process by tuning the membrane stress to the stress obtained by enforcing global equilibrium. In addition to the mechanical model, the study also suggests a preconditioning of the pressure-radius signal. The preconditioning computes an average pressure-radius cycle from all consecutive cycles in the registration and removes, or reduces, undesirable disturbances. The effect is a robust parameter identification that gives a unique solution. The proposed method is tested on clinical data from three human abdominal aortas and the results show that the material parameters from the proposed method do not differ significantly (p < 0.01) from the corresponding parameters obtained by averaging the result from consecutive cycles.     

Effects of management practices on annual net N-mineralization in a restored prairie and maize agroecosystems

Nitrogen (N) mineralization is a spatially variable and difficult component of the N cycle to quantify accurately under field conditions. Net N-mineralization was compared by direct measurement, indirect estimate, and laboratory incubation for a restored tallgrass prairie and for deficiently and optimally N-fertilized, no-tillage (NT) and chisel-plowed (CP) maize (Zea mays L.) agroecosystems on Plano silt loam soil (fine-silty, mixed, superactive, mesic Typic Argiudoll) in Wisconsin, USA. Four years of in-situ field measurements using an incubated-soil-core/ion-exchange-resin-bag technique showed that land use significantly affected net N-mineralization. Net N-mineralization was consistently smaller in the restored prairie than in the maize agroecosystems and typically larger in the CP than in the NT maize agroecosystems. Three independent methods for indirectly estimating annual net N-mineralization (i.e., N budget residual, deficiently N-fertilized plant N uptake, and profile-scaled in-situ field measurements) were relatively consistent at capturing land-use and tillage effects on net N-mineralization. Laboratory incubation and periodic leaching of Fall-sampled soils demonstrated that both mineralized N and labile C were co-limiting factors influencing N-mineralization in agricultural soils and generally supported field measurements by showing a significant difference in net N-mineralization with and without added fertilizer-N.     

EUF-N fractions in different soils during a vegetation period in pot and field experiments

Summary Mobilization of soil-borne N, N fertilization and N removal by crops influence EUF-NO₃-N contents as well as EUF-N_org contents in the course of a vegetation period. N mobilization alone (no N fertilization) increases the EUF-N_org contents only temporarily (mainly in May and July), while in December they are almost the same as in March (Table 1). The EUF-NO₃ contents, on the contrary, increase during the vegetation period, so that an increment in NO₃ is registered in unplanted pots in December. This increment is larger the higher the EUF-N_org contents are in March (Table 2).N fertilization increases the contents of both EUF-N_org and EUF-NO₃, so that there is an increment in EUF-N_org as well as EUF-NO₃ in December (Table 2). This finding also applies to field experiments under fallow (Figs. 4 and 5). However, in contrast to the pot experiment, the EUF-N contents in the field experiment were only temporarily increased by N mobilization alone. This means that N immobilization had taken place which had not been observed in the pot experiment under stable moisture conditions (Fig. 4 and Table 1).A close correlation between hot-water-soluble N contents and EUF-N_org is found only under uniform management conditions (uniform N-fertilizer rates). Depending on the time of sampling different regression equations are, however, obtained because of changes in EUF-N_org due to N mobilization, whereas the hot-water-soluble N contents hardly show any variations during the vegetation period (Fig. 6 and Table 3).     

Simulation of nitrogen mineralization and transport in loess-parabrownearthes: Plot experiments

Summary In order to simulate the Nmin distributions in field plot experiments, a first order kinetic model for mineralization is combined with a transport model described earlier in this journal. Comparison of simulated and experimental figures shows satisfying agreement. The main advantages of these models are: i. only few and easy to measure input data are required and ii. both model equations, for mineralization and transport of Nmin, are simple to solve rendering short computing times even using a microcomputer.Aqualfs and Udalfs, according to the 7th approximation     

Determination of critical K concentrations in sap from individual leaves or from whole plants using K-interruption experiments

Summary A new method is described for estimating critical K concentrations from K interruption experiments using only 2 treatments. Frequent measurements are made of the growth and K concentration of plants subjected to either continued or interrupted K supply and the data used to define the relation between relative yield and K concentration for the K-deficient plants. Critical concentrations are estimated from the results using a mathematical model of plant growth to interpolate over the critical concentration region of the curve. The method has the advantage that the critical concentrations are determined at the exact time that growth is affected. The method was tested using data from previously published experiments with lettuce in which the concentrations of K were measured in sap from both the total shoot and from individual leaf petioles. The model accurately predicted the form of the relationship between relative yield and K concentration for the total shoot and for young expanding leaves, but consistently deviated from the data for recently matured ones. Average estimates of critical concentration ranged fromca. 18 to 34 mmoll⁻¹ in the young leaves and from 48 to 67 mmoll⁻¹ in the mature ones when Na salts were present or absent respectively. The values for total shoot sap were similar to those for mature leaves. The critical concentrations for young expanding leaves were virtually identical to the minimum believed to be needed for the maintenance of important biochemical processes in individual cells, and suggests that a single critical K concentration for plant sap might apply to a wide range of crops provided an actively growing part of the plant is sampled.     

Estimating the availability of nutrients from processed swine lagoon solids through incubation studies

Potential environmental hazards from the excess accumulation of swine (Sus scrofa domesticus) manure in eastern North Carolina and new state guidelines on treatment alternatives have necessitated the reevaluation of best management practices for disposal of swine waste (manure and effluent) as a fertilizer source on local crop land. Creation of a value-added product is one viable means of utilizing and economically redistributing the nutrients in swine manure. Incubation studies using four agricultural soils from eastern North Carolina were conducted with pelletized processed swine lagoon solids (PSLS) (1.7% N, 2.5% P, 0.12% Cu and 0.18% Zn) composed of dewatered swine lagoon sludge plus rock flour. The PSLS was added at three application rates (0, 200, 400 mg N kg⁻¹ soil) and incubated for 16 weeks at 25°C. The soil was sampled at 0, 1, 2, 4, 8, 12, and 16 weeks and analyzed for NO₃–N, NH₄–N and Mehlich III-extractable P, Zn, and Cu. High concentrations of NH₄–N and low concentrations of NO₃–N were present in the soils shortly after addition of PSLS. After the second week, extractable NH₄–N dropped to <4 mg kg⁻¹, while the soil concentration of NO₃–N increased rapidly. The amount of NO₃–N generated reached 90% of its final value after the fourth week. Across the four soils, 24–35% of the added N, 15–50% of the added P, 20–50% of the added Zn and 15–20% of the added Cu was extractable after 8 weeks. The PSLS is an excellent source of P, but may require additional N if used as a fertilizer source for most row crops.     

Distributions of oxygen,nutrient, and metabolic waste concentrations in multicellular spheroids and their dependence on spheroid parameters

The distribution of oxygen, nutrients and metabolic wastes in multicellular tumor spheroids and its dependence on the parameters characterizing the spheroid (i.e., spheroid geometry, diffusivity, and consumption/ production rates of biological substances) have been investigated by a theoretical analysis: 1. Parameter dependence is qualitatively demonstrated and visualized. 2. Reduction of the number of variables by specific coordinate transformations made it possible to generate nomograms from which concentration distributions for any choice of parameter values may easily be obtained. In particular, these nomograms may also be used for estimating concentration profiles of metabolic waste products, e.g. of lactate, which are expected to accumulate in the tumor spheroids. 3. An additional set of nomograms is given which is more convenient for determining time courses of these concentrations during spheroid growth. 4. A quantitative sensitivity analysis of parameter dependencies is performed to identify those parameters upon which a concentration of interest depends most critically in a given experimental situation. Offprint requests to: W Mueller-Klieser     

High turnover of fungal hyphae in incubation experiments

Soil biological studies are often conducted on sieved soils without the presence of plants. However, soil fungi build delicate mycelial networks, often symbiotically associated with plant roots (mycorrhizal fungi). We hypothesized that as a result of sieving and incubating without plants, the total fungal biomass decreases. To test this, we conducted three incubation experiments. We expected total and arbuscular mycorrhizal (AM) fungal biomass to be higher in less fertilized soils than in fertilized soils, and thus to decrease more during incubation. Indeed, we found that fungal biomass decreased rapidly in the less fertilized soils. A shift towards thicker hyphae occurred, and the fraction of septate hyphae increased. However, analyses of phospholipid fatty acids (PLFAs) and neutral lipid fatty acids could not clarify which fungal groups were decreasing. We propose that in our soils, there was a fraction of fungal biomass that was sensitive to fertilization and disturbance (sieving, followed by incubation without plants) with a very high turnover (possibly composed of fine hyphae of AM and saprotrophic fungi), and a fraction that was much less vulnerable with a low turnover (composed of saprotrophic fungi and runner hyphae of AMF). Furthermore, PLFAs might not be as sensitive in detecting changes in fungal biomass as previously thought.     

Leaching of nitrogen from subtropical soils as affected by nitrification potential and base cations

A soil column method was used to determine the effect of nitrification on leaching of nitrate and ammonium from three acid subtropical soils after application of ammonium bicarbonate. Three soils, designated QF, GB and SU, derived from Quaternary red earth, granite and tertiary red sandstone, were collected from forest land, brush land and upland field, ranged in nitrification potential and cation exchange capacity. The results indicated that nitrate leaching increased with the soil nitrification potential. The soils with higher nitrification potential had a higher nitrate peak concentration and required a shorter time to reach it. In soils QF and GB with low cation exchange capacity, and a low content of exchangeable base cations, there were not sufficient base cations to accompany the nitrate leached with the result that ammonium and hydrogen ions were leached from the soil, and pH changes occurred in different layers of the soil column.     

Estimating the kernel parameters of premises-based stochastic models of farmed animal infectious disease epidemics using limited, incomplete, or ongoing data

Three different estimators are presented for the types of parameters present in mathematical models of animal epidemics. The estimators make use of the data collected during an epidemic, which may be limited, incomplete, or under collection on an ongoing basis. When data are being collected on an ongoing basis, the estimated parameters can be used to evaluate putative control strategies. These estimators were tested using simulated epidemics based on a spatial, discrete-time, gravity-type, stochastic mathematical model containing two parameters. Target epidemics were simulated with the model and the three estimators were implemented using various combinations of collected data to independently determine the two parameters.     

Circadian clock effects on cellular proliferation: Insights from theory and experiments

Oscillations of the cellular circadian clock have emerged as an important regulator of many physiological processes, both in health and in disease. One such process, cellular proliferation, is being increasingly recognized to be affected by the circadian clock. Here, we review how a combination of experimental and theoretical work has furthered our understanding of the way circadian clocks couple to the cell cycle and play a role in tissue homeostasis and cancer. Finally, we discuss recently introduced methods for modeling coupling of clocks based on techniques from survival analysis and machine learning and highlight their potential importance for future studies.     

A method for the estimation of gene flow parameters from a population structure caused by restricted gene flow and genetic drift

Summary A method has been developed which enables the estimation of the plant gene flow parameters _p (pollen dispersal), _s (seed dispersal) and t (outcrossing rate) from a selection-free continuously structured population in equilibrium. The method uses Wright's F-coefficients and introduces a new F-function which describes the genetic similarity as a function of the spatial distance. The method has been elaborated for wind pollinated plant species but can be modified for insect pollination and for animal species. In practice allozymes will provide for the necessary neutral genetic variation. The more loci used and the more intermediate the gene frequencies, the more reliable the results. For the estimation of _p and t together (when the outcrossing rate is not known) at least two chromosomally unlinked loci are required. The method for estimating _s depends on whether the plant species is annual or perennial. The mechanism of selfing has been analysed by the explanation of the value of t by three components: population density (d), pollen flow (_p) and relative fertilization potential of own pollen (Z). The concepts of neighbourhood size and isolation by distance, developed by Wright, who used a single gene flow parameter , have been extended to the situation which is realistic for seed plants, using all three parameters _p, _s and t. When _p is large with respect to _s, _s largely determines the value of the neighbourhood size, whereas _p is the most dominating factor in isolation by distance. The use of local effective population size and mean gene transport per generation instead of neighbourhood size and neighbourhood area, respectively, is proposed to avoid confusion. Computer simulations have been carried out to check the validity and the reliability of the method. Populations of 200 plants, using two or three loci with intermediate allele frequencies, gave good results in the calculation of _p with known value of t and of _s and N_e. With unknown t, especially with lower values of t, larger populations of at least 1,000 plants are necessary to obtain reasonably accurate results for _p and mean gene transport per generation M.Grassland Species Research Group Publication No. 81