Mathematical modelling as a tool for management in eutrophication control of shallow lakes

The eutrophication model Delwaq-Bloom-Switch is developed to be a functional tool for water management. Therefore it includes nutrients, algal biomass and composition as well as water transparency. A module describing the interaction between water and bottom gives the model the flexibility to deal with measures, such as a decrease of the external phosphorus loading and flushing with water differing in composition from the lake water. This paper focuses on the functional aspects of the model, the results of an application on Lake Veluwe, The Netherlands, and the implications for water management.With one set of coefficients DBS reproduces the most important characteristics of Lake Veluwe for a period of two years before measures (reduction of the external loading and flushing during the winter months) and eight years after the measures. The phosphorus concentration decreased and became growth limiting for algae instead of nitrogen and light. Both in measurements and modelling results, the algal composition changed from blue-green algae dominance to green algae and diatom dominance. Lake Veluwe had a relatively short transient phase after reduction of external loading, because high nitrate concentrations in the flushing water inhibited a long period with high phosphorus releases from the bottom.Model calculations were carried out to investigate the effects of fish stock management and optimization of flushing. Both measures are promising.     

Developing a cyclin blueprint as a tool for mapping the cell cycle in GS-NS0

The cell cycle is at the center of growth, productivity, and death of mammalian cell cultures. There exists a need to identify and quantify major landmarks in the cell cycle of industrially relevant mammalian cell lines and its association with productivity; central for designing productivity optimization strategies. Herein, we studied the expression of three cyclins, under both perturbed and unperturbed growth, by flow cytometry in batch cultures of GS-NS0. The perturbed systems involved two different DNA synthesis inhibitors, thymidine and dimethyl sulfoxide (DMSO). This approach enables the establishment of characteristic cyclin profiles, timings, and thresholds. In particular, two G₁ class cyclins (D1 and E1), and one G₂ cyclin (B1) were investigated. Cyclin B1 showed a clear cell cycle phase-specific expression increasing during G₂ phase where it was approximately 40% higher when compared to G₁ phase. Similarly, cyclin E1 showed a clear pattern being expressed approximately 10% higher in G₁ compared to G₂ phase and decreased through S phase. Cyclin D1 expression was fairly invariable throughout the cell cycle phases. The observed patterns provide a blueprint of the cell line's cell cycle, which can be used for the development of biologically accurate and experimentally validated distributed cell cycle models.     

Neural networks as a tool for control and management of a biological reactor for treating hydrogen sulphide

Based on an experimental database consisting of 194 daily cases, artificial neural networks were used to model the removal efficiency of a biofilter for treating hydrogen sulphide (H₂S). In this work, the removal efficiency of the reactor was considered as a function of the changes in the air flow and concentration of H₂S entering the biofilter. In order to obtain true representative values, the removal efficiencies (outputs) were measured 24 h after each input was changed. A MLP (multilayer perceptron 2-2-1) model with two input variables (unit flow and concentration of the contaminant fed into the biofilter) rendered good prediction values with a determination coefficient of 0.92 for the removal efficiency within the range studied. This means that the MLP model can explain 92% of the overall variability detected in the biofilter corresponding to a wide range of operating conditions.     

In vitro fertilization as a tool for investigating sexual reproduction of angiosperms

In vitro fertilization (IVF) of isolated male and female gametes of flowering plants was first accomplished in the last decade. Successful isolation of male and female gametes, and culturing of in vitro zygotes to form new plants, is a prelude to the use of IVF for research into the cellular and molecular control of fertilization in higher plants and its application as a tool in biotechnology. Genes unique to male and female gametes and zygotes of higher plants, although currently incompletely characterized, are expected to permit direct molecular dissection of fertilization. By applying IVF and microculture to zygotes and endosperm obtained by both in vivo and in vitro methods, newly activated fusion products may be observed and manipulated in media where they are directly accessible to the techniques of molecular cell biology. IVF and zygote culture may also offer potential for creating new hybrid plants by fusing isolated gametes from different species to produce unique zygotes and ultimately plants that would be impossible to obtain using typical crossing techniques. Transformation and regeneration frequencies using IVF may also be high enough to avoid the necessity of adding controversial antibiotic and herbicide resistant genes to screen transformed products. This review describes advances using IVF in plant sexual reproduction and discusses its potential in the genetic improvement of flowering plants.     

Chemical inhibitors: a tool for plant cell cycle studies

Synchrony provides a large number of cells at defined points of the cell cycle. Highly synchronised cells are powerful and effective tools for molecular analyses and for studying the biochemical events of the cell cycle in plants. Usually, plant cell suspensions can be synchronised by chemical agents, which arrest the cell cycle by acting on the driving forces of the cell cycle engine such as cyclin-dependent kinase activity, enzymes involved in DNA synthesis or proteolysis of cell cycle regulators or by acting on the cell cycle apparatus (mitotic spindle). The specificity, reversibility and efficiency of each type of cell cycle inhibitor are described and related to their mode of action.     

Alloxan-induced luminol luminescence as a tool for investigating mechanisms of radical-mediated diabetogenicity.

It is not clear whether the muscle wasting commonly observed in hyperthyroidism is due to alteration in the rate of protein synthesis or degradation. The effect of experimental hyperthyroidism on skeletal-muscle proteolysis in the rat was studied by measuring alanine and tyrosine release from isolated skeletal muscles in vitro and 3-methyl-histidine excretion in vivo. Alanine release from the isolated epitrochlaris-muscle preparation was increased as soon as 24h after a 25 microgram dose of L-tri-iodothyronine in vivo. Conversely, alanine release from muscles of hypothyroid rats was decreased, but restored by L-tri-iodothyronine supplementation before death. Furthermore, 3-methylhistidine excretion was increased in hyperthyroid rats throughout an 18-day treatment period. The increased amino acid release from isolated muscles and the increased 3-methylhistidine excretion in vivo strongly suggests that hyperthyroidism increases skeletal-muscle proteolysis. Furthermore, the thyroid-hormone concentration may be an important factor in regulating muscle proteolysis.     

Electronic structure calculations as a tool for investigating acyl migrations in ester saponins

The possibility of acyl migrations in ester saponins from Maesa lanceolata was investigated by molecular mechanics and electronic structure calculations carried out on the major constituent maesasaponin IV3 (3beta-O-[[alpha-L-rhamnopyranosyl-(1-->2)-[beta-D-galactopyranosyl-(1-->3)]-[beta-D-galactopyranosyl-(1-->2)]-beta-D-gluco-pyranuronyl]-21beta-angeloyloxy-22alpha-propanoyloxy-13beta,28-oxido-olean-16alpha, 28alpha-diol). It was confirmed that acyl migrations could occur in rings D and E of maesasaponins.     

Additive partitioning as a tool for investigating the flora diversity in oceanic archipelagos

This paper introduces the integration of additive partitioning with species—area relationships to island biogeography in order to address the question “How are the pteridophyte and spermatophyte native and endemic flora of different oceanic archipelagos partitioned across islands?”.Species richness data of all endemic species and all native species of pteridophytes and spermatophytes were obtained for the Azores, Canaries and Cape Verde in the Atlantic Ocean and Galápagos, Hawaii and Marquesas in the Pacific Ocean. Additive partitioning of species diversity was used to quantify how much of the total diversity of an oceanic archipelago flora (γ-diversity) is due to (i) the mean species richness of the flora of each island (α-diversity), (ii) the variability in species richness of the floras across islands (β_Nestedness) and (iii) the complementarity in species composition of the floras of different islands (β_Replacement). The analysis was separately performed for the native and endemic pteridophyte and spermatophyte floras.The diversity partitioning of the six archipelagos showed large differences in how the flora of each archipelago is partitioned among the α, β_Nestedness and β_Replacement components, for pteridophytes and spermatophytes and for all endemic species and all native species. The α-diversity was more important for all native species than for endemic species and more important for pteridophytes than for spermatophytes, with the Azores showing outstanding high values of α-diversity. The β_Nestedness was higher for pteridophytes than for spermatophytes and higher for endemic species than for all native species in both pteridophytes and spermatophytes. The values of β_Replacement suggested that: (i) the spermatophyte native flora is more differentiated across islands than the pteridophyte native flora and (ii) the pteridophyte endemic flora and, especially, the spermatophyte endemic flora are more differentiated across islands than the corresponding native flora. An outstanding value of β_Replacement for endemic and all native spermatophytes was found in Hawaii, confirming the biogeographical island differentiation in this archipelago.     

siRNA as a tool for investigating organogenesis: The pitfalls and the promises

Removing the function of a specific gene from a developing organ, by making a ‘knockout’ mouse, is a powerful method for analyzing the molecular pathways that control organogenesis. The technique is expensive, though, in terms of time and money, and complex strategies for producing conditional knockouts are needed for genes that are essential for early development of the embryo, for which an unconditional knockout would be lethal before the organ of interest begins to form. Small interfering RNAs (siRNAs) offer a method of knocking down the expression of specific genes with no need for genomic manipulation. Almost as soon as they had been discovered, siRNAs began to be used to explore the molecular biology of mammalian cells in conventional, two-dimensional culture. They have now also been applied successfully, by several groups, to knock down specific genes in various organ rudiments developing in organ culture. This article reviews the basic technique of siRNA-mediated gene knockdown and how it is being applied to organ culture. It also reviews some of the current problems and challenges in the field, and the ways in which these problems are likely to be overcome.Key words: siRNA, RNAi, organ culture, organogenesis, organ development, 3D culture     

Regulated proteolysis as a force to control the cell cycle

In this issue of Structure, Rood and colleagues report that substrate architecture is a key factor in promoting the complete and processive degradation of the Caulobacter cell cycle regulator PdeA by the protease ClpXP. This investigation highlights the important role that the adaptor protein CpdR serves in regulating presentation of PdeA to ClpXP.     

Evolution of networks and sequences in eukaryotic cell cycle control

The molecular networks regulating the G1-S transition in budding yeast and mammals are strikingly similar in network structure. However, many of the individual proteins performing similar network roles appear to have unrelated amino acid sequences, suggesting either extremely rapid sequence evolution, or true polyphyly of proteins carrying out identical network roles. A yeast/mammal comparison suggests that network topology, and its associated dynamic properties, rather than regulatory proteins themselves may be the most important elements conserved through evolution. However, recent deep phylogenetic studies show that fungal and animal lineages are relatively closely related in the opisthokont branch of eukaryotes. The presence in plants of cell cycle regulators such as Rb, E2F and cyclins A and D, that appear lost in yeast, suggests cell cycle control in the last common ancestor of the eukaryotes was implemented with this set of regulatory proteins. Forward genetics in non-opisthokonts, such as plants or their green algal relatives, will provide direct information on cell cycle control in these organisms, and may elucidate the potentially more complex cell cycle control network of the last common eukaryotic ancestor.     

Flow cytometric analysis of the cell cycle: Mathematical modeling and biological interpretation

Estimation of the repartition of asynchronous cells in the cell cycle can be explained by two hypotheses: the cells are supposed to be distributed into three groups: cells with a 2c DNA content (G0/1 phase), cells with a 4c DNA content (G2 + M phase) and cells with a DNA content ranging from 2c to 4c (S phase); there is a linear relationship between the amount of fluorescence emitted by the fluorescent probe which reveals the DNA and the DNA content. According to these hypotheses, the cell cycle can be represented by the following equation: [formula: see text] All the solutions for this equation are approximations. Non parametric methods (or graphical methods: rectangle, peak reflect) only use one or two phase(s) of the cell cycle, the remaining phase(s) being estimated by exclusion. In parametric methods (Dean & Jett, Baisch II, Fried), the DNAT(x) distribution is supposed to be known and is composed of two gaussians (representative of G0/1 and G2 + M) and a P(x,y) function representative of S phase. Despite the generality, these models are not applicable to all sample types, particularly heterogeneous cell populations with various DNA content. In addition, the cell cycle is dependent on several regulation points (transition from quiescence to proliferation, DNA synthesis initiation, mitosis induction) and biological perturbations can also lead to cytokinesis perturbations. Before the emergence of flow cytometry, the current view of cell cycle resided in the assessment of cell proliferation (increase in cell number) or the kinetic of molecules incorporation (DNA precursors).(ABSTRACT TRUNCATED AT 250 WORDS)     

neuroConstruct: a tool for modeling networks of neurons in 3D space

Conductance-based neuronal network models can help us understand how synaptic and cellular mechanisms underlie brain function. However, these complex models are difficult to develop and are inaccessible to most neuroscientists. Moreover, even the most biologically realistic network models disregard many 3D anatomical features of the brain. Here, we describe a new software application, neuroConstruct, that facilitates the creation, visualization, and analysis of networks of multicompartmental neurons in 3D space. A graphical user interface allows model generation and modification without programming. Models within neuroConstruct are based on new simulator-independent NeuroML standards, allowing automatic generation of code for NEURON or GENESIS simulators. neuroConstruct was tested by reproducing published models and its simulator independence verified by comparing the same model on two simulators. We show how more anatomically realistic network models can be created and their properties compared with experimental measurements by extending a published 1D cerebellar granule cell layer model to 3D.     

Mathematical modeling as a tool to investigate the design and operation of the zymotis packed-bed bioreactor for solid-state fermentation

Zymotis bioreactors for solid-state fermentation (SSF) are packed-bed bioreactors with internal cooling plates. This design has potential to overcome the problem of heat removal, which is one of the main challenges in SSF. In ordinary packed-bed bioreactors, which lack internal plates, large axial temperature gradients arise, leading to poor microbial growth in the end of the bed near the air outlet. The Zymotis design is suitable for SSF processes in which the substrate bed must be maintained static, but little is known about how to design and operate Zymotis bioreactors. We use a two-dimensional heat transfer model, describing the growth of Aspergillus niger on a starchy substrate, to provide guidelines for the optimum design and operation of Zymotis bioreactors. As for ordinary packed-beds, the superficial velocity of the process air is a key variable. However, the Zymotis design introduces other important variables, namely, the spacing between the internal cooling plates and the temperature of the cooling water. High productivities can be achieved at large scale, but only if small spacings between the cooling plates are used, and if the cooling water temperature is varied during the fermentation in response to bed temperatures.     

Photochemistry as a tool in investigating ionic channels: Photoaffinity probes

TPMP is a noncompetitive inhibitor of the nicotinic acetycholine receptor which blocks agonist-induced ion flux by directly interacting with the receptor's ion channel. By activation with UV light it can be made to react covalently with its binding site in the receptor protein. Here a method is described to perform this photolabeling with a time resolution comparable to the physiological event of channel opening and closing. By this technique structural transitions within the receptor can be visualized and transient conformational states can be labeled covalently and irreversibly.     

Functional magnetic resonance imaging as a tool for investigating human cortical motor function.

Non-invasive functional magnetic resonance imaging (fMRI) mapping techniques sensitive to the local changes of blood flow, blood volume, and blood oxygenation which accompany neuronal activation have been widely used over the last few years to investigate the functional organization of human cortical motor systems, and specifically of the primary motor cortex. Validation studies have demonstrated a good correspondence between quantitative and topographic aspects of data acquired by fMRI and positron emission tomography. The spatial and temporal resolution affordable by fMRI has allowed to achieve new important information on the distributed representation of hand movements in multiple functional modules, and on the intensity and spatial extent of neural activation in the contralateral and ipsilateral primary motor cortex in relation to parametric and nonparametric aspects of movement and to the degree of handedness. Neural populations with different functional characteristics have been identified in anatomically defined regions, and the temporal aspects of the activation during voluntary movement tracked in different components of the motor system. Finally, this technique has proved useful to deepen our understanding of the neural basis of motor imagery, demonstrating increased activity in the primary motor cortex during mental representation of sequential finger movements.