A novel lake-zoning framework for large lakes based on numerical modelling

Because of the high spatial heterogeneity of the ecosystem properties of large lakes, the characterisation of lake zones is particularly helpful for designing zone-specific strategies for water management practices. In this study, we developed a lake-zoning framework by investigating the lateral dispersion of inflow pollutants through dye-tracking experiments in a case study of a large shallow lake (Lake Chaohu) in China. A two-dimensional hydrodynamic and mass transport model was used to quantify the impacts of inflow rivers on this lake. Results from 2012 to 2014 showed that the lake zoning results were more stable at the annual scale than at the seasonal scale, implying that the seasonal scale is not suitable for the establishment of lake zones. A driving factor analysis showed that inflow discharge was a more critical factor determining lake zones than wind conditions. In contrast to previous lake zoning methods, the proposed framework implements lake zoning quantitatively through hydrodynamic modelling.     

Denitrification and a numerical modelling approach for shallow waters

A numerical model (`DiffDeni') has been developed to describe the disappearance of nitrate from the water column of 10–200 cm deep waters. The disappearance is caused by bacterial denitrification in the sediments. The model employs the molecular diffusion constant, an acceleration factor describing eddy diffusion, and three bacterial growth constants, viz. the inoculum size, the maximum growth rate and the half saturation constant for the hyperbolic process. The values of these system-constants were varied over a wide range. The curves obtained were compared with the curves for well-defined situations, viz. in which diffusion takes place without any or with a complete, immediate reaction. These cases have analytical solutions, and were simulated closely by the model `DiffDeni', though this model is based on different assumptions. It is shown that, when the bacterial growth rate is above a critical value, a negative exponential curve describes the nitrate disappearance well. On the other hand, a more complicated negative exponential equation can be used to describe the first phase of this denitrification in which bacterial activity is low and nitrate behaves as a conservative compound. The change-over period from phase 1 (no reaction) to phase 2 (complete, immediate reaction) which may vary between <1 and 50 days cannot be described analytically (mathematically correctly). The influence of temperature on denitrification is assessed and it is shown that both bacterial activity and diffusion may influence the denitrification rate.     

A novel microstructural approach in tendon viscoelastic modelling at the fibrillar level

Novel applications in rehabilitation, surgery and tissue engineering require the knowledge of the mechanical behaviour of the tissues at microstructural level. The aim of this work is to investigate the viscoelastic properties of the tendon from the interaction of its biological constituents in the fibrillar network. Traction, relaxation and creep in-vitro tests have been performed on porcine flexor digital tendons. A viscoelastic constitutive equation at finite deformation is presented. The fibrillar deformation modes are described through a network of adaptive links between collagen type I and decorin. The theoretical predictions fit accurately the experimental data. The results of the model demonstrate the mechanical importance of glycosaminoglycan chains of decorin for the differential recruitment and the activation of fibrillar collagen.     

A numerical approach to ion channel modelling using whole-cell voltage-clamp recordings and a genetic algorithm

The activity of trans-membrane proteins such as ion channels is the essence of neuronal transmission. The currently most accurate method for determining ion channel kinetic mechanisms is single-channel recording and analysis. Yet, the limitations and complexities in interpreting single-channel recordings discourage many physiologists from using them. Here we show that a genetic search algorithm in combination with a gradient descent algorithm can be used to fit whole-cell voltage-clamp data to kinetic models with a high degree of accuracy. Previously, ion channel stimulation traces were analyzed one at a time, the results of these analyses being combined to produce a picture of channel kinetics. Here the entire set of traces from all stimulation protocols are analysed simultaneously. The algorithm was initially tested on simulated current traces produced by several Hodgkin-Huxley–like and Markov chain models of voltage-gated potassium and sodium channels. Currents were also produced by simulating levels of noise expected from actual patch recordings. Finally, the algorithm was used for finding the kinetic parameters of several voltage-gated sodium and potassium channels models by matching its results to data recorded from layer 5 pyramidal neurons of the rat cortex in the nucleated outside-out patch configuration. The minimization scheme gives electrophysiologists a tool for reproducing and simulating voltage-gated ion channel kinetics at the cellular level.     

A trait-based approach for modelling microbial litter decomposition

Trait-based models are an emerging tool in ecology with the potential to link community dynamics, environmental responses and ecosystem processes. These models represent complex communities by defining taxa with trait combinations derived from prior distributions that may be constrained by trade-offs. Herein I develop a model that links microbial community composition with physiological and enzymatic traits to predict litter decomposition rates. This approach allows for trade-offs among traits that represent alternative microbial strategies for resource acquisition. The model predicts that optimal strategies depend on the level of enzyme production in the whole community, which determines resource availability and decomposition rates. There is also evidence for facilitation and competition among microbial taxa that co-occur on decomposing litter. These interactions vary with community investment in extracellular enzyme production and the magnitude of trade-offs affecting enzyme biochemical traits. The model accounted for 69% of the variation in decomposition rates of 15 Hawaiian litter types and up to 26% of the variation in enzyme activities. By explicitly representing diversity, trait-based models can predict ecosystem processes based on functional trait distributions in a community. The model developed herein illustrates that traits influencing microbial enzyme production are some of the key controls on litter decomposition rates.     

A hybrid representation approach for modelling complex dynamic bioprocesses

This paper considers the use of hybrid models to represent the dynamic behaviour of biotechnological processes. Each hybrid model consists of a set of non linear differential equations and a neural model. The set of differential equations attempts to describe as much as possible the phenomenology of the process whereas neural networks model predict some key parameters that are an essential part of the phenomenological model. The neural model is obtained indirectly, that is, using the prediction errors of one or more state variables to adjust its weights instead of successive presentations of input-output data of the neural network. This approach allows to use actual measurements to derive a suitable neural model that not only represents the variation of some key parameters but it is also able to partly include dynamic behaviour unaccounted for by the phenomenological model. The approach is described in detail using three test cases: (1) the fermentation of glucose to gluconic acid by the micro-organism Pseudomonas ovalis, (2) the growth of filamentous fungi in a solid state fermenter, and (3) the propagation of filamentous fungi growing on a 2-D solid substrate. Results for the three applications clearly demon- strate that using a hybrid model is a viable alternative for modelling complex biotechnological bioprocesses.     

A novel dialysis procedure for the crystallization of proteins

Various dialysis methods are commonly employed for the crystallization of proteins. Typical procedures include the use of dialysis bags, dialysis buttons or Zeppezauer microdiffusion cells. The general principle involved is that the protein solution is gradually brought to a point of supersaturation by imposing a gradient of ionic strength or organic solvent concentration across the wall of the dialysis membrane. However, in some cases, the imposition of this gradient across the dialysis membrane can result in the formation of a large number of crystal nucleation sites, thereby giving rise to a reduction in the maximum size of the crystals which can be obtained. A novel 'double-dialysis' procedure which incorporates a second dialysis membrane, thus reducing the rate of equilibration in the crystallization experiment, has been developed in our laboratory. The system has been employed successfully on the delta toxin of Staphylococcus aureus resulting in a useful increase in crystal size. A more quantitative analysis of the technique has been carried out on rat liver malic enzyme. The results of a limited series of crystallization trials with this protein have shown that employment of the 'double-dialysis' technique allows a fine control of the rate of crystal nucleation and therefore provides a mechanism for the controlled growth of large crystals.     

A novel chromatographic procedure for purification of bacterial plasmids

A new, rapid procedure for purifying bacterial plasmids with high recovery is described. The sequence of operations consists essentially of treatment with alkali, ribonuclease, and proteinase K, followed by chisam extraction and gel filtration on Sephacryl S-1000, and finally a precipitation step using isopropanol at room temperature. The method gives rather good yields of plasmid DNA of high purity, and lends itself to scaling up.     

A novel surgical procedure for bridging of massive bone defects

BACKGROUND: Bony defects arising from tumor resection or debridement after infection, non-union or trauma present a challenging problem to orthopedic surgeons, as well as patients due to compliance issues. Current treatment options are time intensive, require more than one operation and are associated with high rate of complications. For this reason, we developed a new surgical procedure to bridge a massive long bone defect. METHODS: To bridge the gap, an in situ periosteal sleeve is elevated circumferentially off of healthy diaphyseal bone adjacent to the bone defect. Then, the adjacent bone is osteotomized and the transport segment is moved along an intramedullary nail, out of the periosteal sleeve and into the original diaphyseal defect, where it is docked. Vascularity is maintained through retention of the soft tissue attachments to the in situ periosteal sleeve. In addition, periosteal osteogenesis can be augmented through utilization of cancellous bone graft or in situ cortical bone adherent to the periosteal sleeve. RESULTS: The proposed procedure is novel in that it exploits the osteogenic potential of the periosteum by replacing the defect arising from resection of tissue out of a pathological area with a defect in a healthy area of tissue, through transport of the adjacent bone segment. Furthermore, the proposed procedure has several advantages over the current standard of care including ease of implementation, rapid patient mobilization, and no need for specialized implants (intramedullary nails are standard inventory for surgical oncology and trauma departments) or costly orthobiologics. CONCLUSIONS: The proposed procedure offers a viable and potentially preferable alternative to the current standard treatment modalities, particularly in areas of the world where few surgeons are trained for procedures such as distraction osteogenesis (e.g. the Ilizarov procedure) as well as areas of the world where surgeons have little access to expensive, complex devices and orthobiologics.     

A micromechanical procedure for modelling the anisotropic mechanical properties of brain white matter

This paper proposes a micromechanics algorithm utilising the finite element method (FEM) for the analysis of heterogeneous matter. The characterisation procedure takes the material properties of the constituents, axons and extracellular matrix (ECM) as input data. The material properties of both the axons and the matrix are assumed to have linear viscoelastic behaviour with a perfect bonding between them. The results of the modelling have been validated with experimental data with material white input from brainstem by considering the morphology of brainstem in which most axons are oriented in longitudinal direction in the form of a uniaxial fibrous composite material. The method is then employed to examine the undulations of axons within different subregions of white matter and to study the impact due to axon/matrix volume fractions. For such purposes, different unit cells composed of wavy geometries and with various volume factions have been exposed to the six possible loading scenarios. The results will clearly demonstrate the undulation and axon volume fraction impacts. In this respect, undulation affects the material stiffness heavily in the axon longitudinal direction, whereas the axons' volume fraction has a much greater impact on the mechanical properties of the white matter in general. Also the results show that the created stresses and strains in the axons and matrix under loading will be impacted by undulation change. With increase in undulation the matrix suffers higher stresses when subjected to tension, whereas axons suffer higher stresses in shear. The axons always exhibit higher stresses whereas the matrix exhibits higher strains. The evaluated time-dependent local stress and strain concentrations within a repeating unit cell of the material model are indicative of the mechanical behaviour of the white tissue under different loading scenarios.     

A novel procedure for protein extraction from formalin-fixed paraffin-embedded tissues

Most of the archived pathological specimens in hospitals are kept as formalin-fixed paraffin-embedded tissues (FFPE) for long-term preservation. Up to now, these samples are only used for immunohistochemistry in a clinical routine as it is difficult to recover intact protein from these FFPE tissues. Here, we report a novel, short time-consuming and cost-effective method to extract full-length, non-degraded proteins from FFPE tissues. This procedure is combined with an effective and non-toxic deparaffinisation process and an extraction method based on antigen-retrieval, high concentration of SDS and high temperature. We have obtained enough intact protein to be detected by Western blotting analysis. This technique will allow utilising these stored FFPE tissues in several applications for protein analysis helping to advance the translational studies in cancer and other diseases.     

A novel procedure for separating small peptides on polyacrylamide gels

A simple and fast procedure that allows the separation of small(1–3 kDa) peptides on glycine-SDS gels is described. Peptideswere separated by glycine-SDS/PAGE as a result of in situ complexation of peptide/SDS during electrophoretic migration and visualized by Coomassie blue staining. The data presented here shows the separation of small peptides of different isoelectric points, sizes, and hydrophobicity on polyacrylamidemini gels. Ten different peptides have been tested with this method. The data suggest the dependence of SDS/peptide complex formation and migration due to the number of basic amino acid residues, length of peptide and the hydrophobicity/hydrophilicity ratio.     

A novel procedure for separating small peptides on polyacrylamide gels

Summary A simple and fast procedure that allows the separation of small (1–3 kDa) peptides on glycine-SDS gels is described. Peptides were separated by glycine-SDS/PAGE as a result ofin situ complexation of peptide/SDS during electrophoretic migration and visualized by Coomassie blue staining. The data presented here shows the separation of small peptides of different isoelectric points, sizes, and hydrophobicity on polyacrylamide mini gels. Ten different peptides have been tested with this method. The data suggest the dependence of SDS/peptide complex formation and migration due to the number of basic amino acid residues, length of peptide and the hydrophobicity/hydrophilicity ratio.     

A modelling approach towards epidermal homoeostasis control

In order to grasp the features arising from cellular discreteness and individuality, in large parts of cell tissue modelling agent-based models are favoured. The subclass of off-lattice models allows for a physical motivation of the intercellular interaction rules. We apply an improved version of a previously introduced off-lattice agent-based model to the steady-state flow equilibrium of skin. The dynamics of cells is determined by conservative and drag forces, supplemented with delta-correlated random forces. Cellular adjacency is detected by a weighted Delaunay triangulation. The cell cycle time of keratinocytes is controlled by a diffusible substance provided by the dermis. Its concentration is calculated from a diffusion equation with time-dependent boundary conditions and varying diffusion coefficients. The dynamics of a nutrient is also taken into account by a reaction-diffusion equation. It turns out that the analysed control mechanism suffices to explain several characteristics of epidermal homoeostasis formation. In addition, we examine the question of how in silico melanoma with decreased basal adhesion manage to persist within the steady-state flow equilibrium of the skin. Interestingly, even for melanocyte cell cycle times being substantially shorter than for keratinocytes, tiny stochastic effects can lead to completely different outcomes. The results demonstrate that the understanding of initial states of tumour growth can profit significantly from the application of off-lattice agent-based models in computer simulations.