Anton J. B. van Boxtel

d-Xylose concentration-dependent hydrolase expression profiles and the function of CreA and XlnR in Aspergillus niger.

ABSTRACT Aspergillus niger is an important organism for the production of industrial enzymes such as hemicellulases and pectinases. The xylan-backbone monomer, d-xylose, is an inducing substance for the coordinate expression of a large number of polysaccharide-degrading enzymes. In this study, the responses of 22 genes to low (1 mM) and high (50 mM) d-xylose concentrations were investigated. These 22 genes encode enzymes that function as xylan backbone-degrading enzymes, accessory enzymes, cellulose-degrading enzymes, or enzymes involved in the pentose catabolic pathway in A. niger. Notably, genes encoding enzymes that have a similar function (e.g., xylan backbone degradation) respond in a similar manner to different concentrations of d-xylose. Although low d-xylose concentrations provoke the greatest change in transcript levels, in particular, for hemicellulase-encoding genes, transcript formation in the presence of high concentrations of d-xylose was also observed. Interestingly, a high d-xylose concentration is favorable for certain groups of genes. Furthermore, the repressing influence of CreA on the transcription and transcript levels of a subset of these genes was observed regardless of whether a low or high concentration of d-xylose was used. Interestingly, the decrease in transcript levels of certain genes on high d-xylose concentrations is not reflected by the transcript level of their activator, XlnR. Regardless of the d-xylose concentration applied and whether CreA was functional, xlnR was constitutively expressed at a low level.

Modeling and analysis of the dynamic behavior of the XlnR regulon in Aspergillus niger.

BackgroundIn this paper the dynamics of the transcription-translation system for XlnR regulon in Aspergillus niger is modeled. The model is based on Hill regulation functions and uses ordinary differential equations. The network response to a trigger of D-xylose is considered and stability analysis is performed. The activating, repressive feedback, and the combined effect of the two feedbacks on the network behavior are analyzed.ResultsSimulation and systems analysis showed significant influence of activating and repressing feedback on metabolite expression profiles. The dynamics of the D-xylose input function has an important effect on the profiles of the individual metabolite concentrations. Variation of the time delay in the feedback loop has no significant effect on the pattern of the response. The stability and existence of oscillatory behavior depends on which proteins are involved in the feedback loop.ConclusionsThe dynamics in the regulation properties of the network are dictated mainly by the transcription and translation degradation rate parameters, and by the D-xylose consumption profile. This holds true with and without feedback in the network. Feedback was found to significantly influence the expression dynamics of genes and proteins. Feedback increases the metabolite abundance, changes the steady state values, alters the time trajectories and affects the response oscillatory behavior and stability conditions. The modeling approach provides insight into network behavioral dynamics particularly for small-sized networks. The analysis of the network dynamics has provided useful information for experimental design for future in vitro experimental work.

Online automatic tuning and control for fed-batch cultivation

Performance of controllers applied in biotechnological production is often below expectation. Online automatic tuning has the capability to improve control performance by adjusting control parameters. This work presents automatic tuning approaches for model reference specific growth rate control during fed-batch cultivation. The approaches are direct methods that use the error between observed specific growth rate and its set point; systematic perturbations of the cultivation are not necessary. Two automatic tuning methods proved to be efficient, in which the adaptation rate is based on a combination of the error, squared error and integral error. These methods are relatively simple and robust against disturbances, parameter uncertainties, and initialization errors. Application of the specific growth rate controller yields a stable system. The controller and automatic tuning methods are qualified by simulations and laboratory experiments with Bordetella pertussis.

Evaluation of Design Strategies for Time Course Experiments in Genetic Networks: Case Study of the XlnR Regulon in Aspergillus niger

One of the challenges in genetic network reconstruction is finding experimental designs that maximize the information content in a data set. In this paper, the information value of mRNA transcription time course experiments was used to compare experimental designs. The study concerns the dynamic response of genes in the XlnR regulon of Aspergillus niger, with the goal to find the best moment in time to administer an extra pulse of inducing D-xylose. Low and high D-xylose pulses were used to perturb the XlnR regulon. Evaluation of the experimental methods was based on simulation of the regulon. Models that govern the regulation of the target genes in this regulon were used for the simulations. Parameter sensitivity analysis, the Fisher Information Matrix (FIM) and the modified E-criterion were used to assess the design performances. The results show that the best time to give a second D-xylose pulse is when the D-xylose concentration from the first pulse has not yet completely faded away. Due to the presence of a repression effect the strength of the second pulse must be optimized, rather than maximized. The results suggest that the modified E-criterion is a better metric than the sum of integrals of absolute sensitivity for comparing alternative designs.

The physics of tissue formation with mesenchymal stem cells

Cells react to various forms of physical phenomena that promote and maintain the formation of tissues. The best example of this are cells of musculoskeletal origin, such as mesenchymal stem cells (MSCs), which consistently proliferate or differentiate under cues from hydrostatic pressure, diffusive mass transport, shear stress, surface chemistry, mechanotransduction, and molecular kinetics. To date, no other cell type shows greater receptiveness to macroscopic and microscopic cues, highlighting the acute sensitivity of MSCs and the importance of physical principles in tissue homeostasis. In this review, we describe the literature that has shown how physical phenomena govern MSCs biology and provide insight into the mechanisms and strategies that can spur new biotechnological applications with tissue biology.

Scaling-up vaccine production : implementation aspects of a biomass growth observer and controller

This study considers two aspects of the implementation of a biomass growth observer and specific growth rate controller in scale-up from small- to pilot-scale bioreactors towards a feasible bulk production process for whole-cell vaccine against whooping cough. The first is the calculation of the oxygen uptake rate, the starting point for online monitoring and control of biomass growth, taking into account the dynamics in the gas-phase. Mixing effects and delays are caused by amongst others the headspace and tubing to the analyzer. These gas phase dynamics are modelled using knowledge of the system in order to reconstruct oxygen consumption. The second aspect is to evaluate performance of the monitoring and control system with the required modifications of the oxygen consumption calculation on pilot-scale. In pilot-scale fed-batch cultivation good monitoring and control performance is obtained enabling a doubled concentration of bulk vaccine compared to standard batch production.

Supporting data of spatiotemporal proliferation of human stromal cells adjusts to nutrient availability and leads to stanniocalcin-1 expression in vitro and in vivo

This data article contains seven figures and two tables supporting the research article entitled: spatiotemporal proliferation of human stromal cells adjusts to nutrient availability and leads to stanniocalcin-1 expression in vitro and in vivo[1]. The data explain the culture of stromal cells in vitro in three culture systems: discs, scaffolds and scaffolds in a perfusion bioreactor system. Also, quantification of extracellular matrix components (ECM) in vitro and staining of ECM components in vivo can be found here. Finally the quantification of blood vessels dimensions from CD31 signals and representative histograms of stanniocalcin-1 fluorescent signals in negative controls and experimental conditions in vivo are presented.

Moisture Dependent Diffusion and Shrinkage in Yam during Drying

Abstract Crank’s analytical approximations for Fick’s diffusion equation were used to investigate the effect of moisture dependent sample thickness and diffusivity on the behavior of yam (Dioscoreaceae rotundata) cubicles during drying processes. Drying and shrinkage experiments were separately conducted at temperatures of 30, 40 and 50 °C in a cabinet drier. The comparative study of moisture dependent shrinkage and moisture dependent diffusivity justifies the interdependence of diffusivity and shrinkage due to water loss during drying. The behavior for yam is best explained by a combination of fractal moisture dependent shrinkage and moisture dependent diffusion, describing both the drying and rate curves better with good prediction of the high moisture regions. This assertion was reached as a result of low mean square error, standard error, percentage relative deviation, Akaike’s Information Criterion and high coefficient of determination. The results may indicate a varying mobility of water in food matrix of different moisture content in the multilayer and monolayer regimes.

Evaluation of design strategies for time course experiments in genetic networks: the XlnR regulon in Aspergillus niger

One of the challenges in the reconstruction of genetic network is to find experimental designs that maximize the information content in the data. In this work the information value of time course experiments (TCEs) is used to rank experimental designs. The study concerns the dynamic response of genes in the XlnR regulon of Aspergillus niger, whereby it was the goal to find the best moment to administer an extra pulse of inducing D-xylose. Low and high trigger concentrations are considered. The models that govern the regulation of the target genes in this regulon are used for simulation. Parameter sensitivity analysis, Fisher Information Matrix (FIM) and the E-modified criterion are used for the design performance assessment. The results show that the best time to give a second pulse of a low concentration trigger of D-xylose is when the D-xylose concentration from the first pulse is not yet completed reduced. Secondly, pulses with high trigger concentrations were simulated, parameter sensitivities computed, and the experimental designs evaluated. Overall, after the first pulse of 1 mM D-xylose, using a second pulse of 5 (or 10) mM D-xylose yields the best experimental design - leading to improved parameter estimates.