Drosophila: a "model" model system to study neurodegeneration

The fruit fly, Drosophila melanogaster, is a powerful model genetic organism that has been used since the turn of the previous century in the study of complex biological problems. In the last decade, numerous researchers have focused their attention on understanding neurodegenerative diseases by utilizing this model system. Numerous Drosophila mutants have been isolated that profoundly affect neural viability and integrity of the nervous system with age. Additionally, many transgenic strains have been developed as models of human disease conditions. We review the existing Drosophila neurodegenerative mutants and transgenic disease models, and discuss the role of the fruit fly in therapeutic development for neurodegenerative diseases.     

The NADPH oxidase complex of phagocytic leukocytes: a biochemical and cytochemical view

The NADPH oxidase complex catalyzes the formation of superoxide (O₂ ^–) in phagocytic leukocytes. This paper reviews recent advances in our understanding of this enzyme system. Recent studies have defined conditions for reconstitution of this enzymatic activity with purified proteins in a cell-free system. The role of the individual proteins that make up the active complex, their regulation and the effects of mutations in these proteins are discussed. While these studies represent major achievements, it is clear from cytochemical investigations that additional levels of complexity exist in the modulation of the NADPH oxidase complex in vivo. A major role for cytochemical analysis in understanding the cell biological aspects of the generation of reactive oxygen species is discussed.Portions of this review were presented at the 36th Symposium of the Society for Histochemistry, 21 September 1994, Heidelberg, Germany     

Growth and ligninolytic system production dynamics of the Phanerochaete chrysosporium fungus A modelling and optimization approach

The well-documented ability to degrade lignin and a variety of complex chemicals showed by the white-rot fungus Phanerochaete chrysosporium has made it the subject of many studies in areas of environmental concern, including pulp bioleaching and bioremediation technologies. However, until now, most of the work in this field has been focused on the ligninolytic sub-system but, due to the great complexity of the involved processes, less progress has been made in understanding the biochemical regulatory structure that could explain growth dynamics, the substrate utilization and the ligninolytic system production itself. In this work we want to tackle this problem from the perspectives and approaches of systems biology, which have been shown to be effective in the case of complex systems. We will use a top-down approach to the construction of this model aiming to identify the cellular sub-systems that play a major role in the whole process. We have investigated growth dynamics, substrate consumption and lignin peroxidase production of the P. chrysosporium wild type under a set of definite culture conditions. Based on data gathered from different authors and in our own experimental determinations, we built a model using a GMA power-law representation, which was used as platform to make predictive simulations. Thereby, we could assess the consistency of some current assumptions about the regulatory structure of the overall process. The model parameters were estimated from a time series experimental measurements by means of an algorithm previously adapted and optimized for power-law models. The model was subsequently checked for quality by comparing its predictions with the experimental behavior observed in new, different experimental settings and through perturbation analysis aimed to test the robustness of the model. Hence, the model showed to be able to predict the dynamics of two critical variables such as biomass and lignin peroxidase activity when in conditions of nutrient deprivation and after pulses of veratryl alcohol. Moreover, it successfully predicts the evolution of the variables during both, the active growth phase and after the deprivation shock. The close agreement between the predicted and observed behavior and the advanced understanding of its kinetic structure and regulatory features provides the necessary background for the design of a biotechnological set-up designed for the continuous production of the ligninolityc system and its optimization.     

<Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> as an experimental tool for the study of complex neurological diseases: Parkinson’s disease,Alzheimer’s disease and autism spectrum disorder

The nematode Caenorhabditis elegans has a very well-defined and genetically tractable nervous system which offers an effective model to explore basic mechanistic pathways that might be underpin complex human neurological diseases. Here, the role C. elegans is playing in understanding two neurodegenerative conditions, Parkinson’s and Alzheimer’s disease (AD), and a complex neurological condition, autism, is used as an exemplar of the utility of this model system. C. elegans is an imperfect model of Parkinson’s disease because it lacks orthologues of the human disease-related genes PARK1 and LRRK2 which are linked to the autosomal dominant form of this disease. Despite this fact, the nematode is a good model because it allows transgenic expression of these human genes and the study of the impact on dopaminergic neurons in several genetic backgrounds and environmental conditions. For AD, C. elegans has orthologues of the amyloid precursor protein and both human presenilins, PS1 and PS2. In addition, many of the neurotoxic properties linked with Aβ amyloid and tau peptides can be studied in the nematode. Autism spectrum disorder is a complex neurodevelopmental disorder characterised by impairments in human social interaction, difficulties in communication, and restrictive and repetitive behaviours. Establishing C. elegans as a model for this complex behavioural disorder is difficult; however, abnormalities in neuronal synaptic communication are implicated in the aetiology of the disorder. Numerous studies have associated autism with mutations in several genes involved in excitatory and inhibitory synapses in the mammalian brain, including neuroligin, neurexin and shank, for which there are C. elegans orthologues. Thus, several molecular pathways and behavioural phenotypes in C. elegans have been related to autism. In general, the nematode offers a series of advantages that combined with knowledge from other animal models and human research, provides a powerful complementary experimental approach for understanding the molecular mechanisms and underlying aetiology of complex neurological diseases.     

Control of tissue homeostasis,tumorigenesis, and degeneration by coupled bidirectional bistable switches

The Hippo-YAP/TAZ signaling pathway plays a critical role in tissue homeostasis, tumorigenesis, and degeneration disorders. The regulation of YAP/TAZ levels is controlled by a complex regulatory network, where several feedback loops have been identified. However, it remains elusive how these feedback loops contain the YAP/TAZ levels and maintain the system in a healthy physiological state or trap the system in pathological conditions. Here, a mathematical model was developed to represent the YAP/TAZ regulatory network. Through theoretical analyses, three distinct states that designate the one physiological and two pathological outcomes were found. The transition from the physiological state to the two pathological states is mechanistically controlled by coupled bidirectional bistable switches, which are robust to parametric variation and stochastic fluctuations at the molecular level. This work provides a mechanistic understanding of the regulation and dysregulation of YAP/TAZ levels in tissue state transitions.     

Catalytic Coupling of Oxidative Phosphorylation,ATP Demand,and Reactive Oxygen Species Generation

Competing models of mitochondrial energy metabolism in the heart are highly disputed. In addition, the mechanisms of reactive oxygen species (ROS) production and scavenging are not well understood. To deepen our understanding of these processes, a computer model was developed to integrate the biophysical processes of oxidative phosphorylation and ROS generation. The model was calibrated with experimental data obtained from isolated rat heart mitochondria subjected to physiological conditions and workloads. Model simulations show that changes in the quinone pool redox state are responsible for the apparent inorganic phosphate activation of complex III. Model simulations predict that complex III is responsible for more ROS production during physiological working conditions relative to complex I. However, this relationship is reversed under pathological conditions. Finally, model analysis reveals how a highly reduced quinone pool caused by elevated levels of succinate is likely responsible for the burst of ROS seen during reperfusion after ischemia.     

SNARE proteins and schizophrenia: linking synaptic and neurodevelopmental hypotheses

Much of the focus of neurobiological research into schizophrenia is based on the concept that disrupted synaptic connectivity underlies the pathology of the disorder. Disruption of synaptic connectivity is proposed to be a consequence of both disrupted synaptic transmission in adulthood and abnormalities in the processes controlling synaptic connectivity during development of the central nervous system. This synaptic hypothesis fits with neurodevelopmental models of schizophrenia and our understanding of the mechanisms of antipsychotic medication. This conceptual model has fostered efforts to define the exact synaptic pathology further. Synaptic proteins are obvious candidates for such studies, and the integral role of the SNARE complex, and SNARE-associated proteins, in synaptic transmission will ensure that it is the focus of much of this research. Significant new insights into the role of this complex are arising from new mouse models of human disease. Here the evidence from both animal and human clinical studies showing that the SNARE complex has a key role to play in the aetiology and pathogenesis of schizophrenia is discussed.     

Molecular machines in archaeal DNA replication

The archaeal DNA replication apparatus is a simplified version of that of eukaryotes and has attracted attention as a tractable model system for the orthologous, but significantly more complex eukaryal machinery. A variety of archaeal model organisms have been investigated with strong emphasis on structural and biochemical analyses of replication-associated proteins. In this review we will describe recent advances in understanding the properties of the replicative helicase, the MCM complex, and the role of the sliding clamp, PCNA, in mediating a range of protein-DNA transactions. Although both complexes form ring shaped assemblies, they play very distinct roles at the leading and trailing edges of the replication fork machinery respectively.     

Hierarchical semantic composition of biosimulation models using bond graphs

Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model development and simulation. Nevertheless, existing computational models in biology and physiology are often not modular and therefore difficult to assemble into larger models. Even when this is possible, the resulting model may not be useful due to inconsistencies either with the laws of physics or the physiological behaviour of the system. Here, we propose a general methodology for composing models, combining the energy-based bond graph approach with semantics-based annotations. This approach improves model composition and ensures that a composite model is physically plausible. As an example, we demonstrate this approach to automated model composition using a model of human arterial circulation. The major benefit is that modellers can spend more time on understanding the behaviour of complex biological and physiological systems and less time wrangling with model composition.     

Up-regulation of MCM3 Relates to Neuronal Apoptosis After Traumatic Brain Injury in Adult Rats

Minichromosome maintenance complex component 3, one of the minichromosome maintenance proteins, functions as a part of pre-replication complex to initiate DNA replication in eukaryotes. Minichromosome maintenance complex component 3 (MCM3) was mainly implied in cell proliferation and tumorigenesis. In addition, MCM3 might play an important role in neuronal apoptosis. However, the functions of MCM3 in central nervous system are still with limited acquaintance. In this study, we performed a traumatic brain injury (TBI) model in adult rats. Western blot and immunohistochemistry staining showed up-regulation of MCM3 in the peritrauma brain cortex. The expression patterns of active caspase-3 and Bax, Bcl-2 were parallel with that of MCM3. Immunofluorescent staining and terminal deoxynucleotidyl transferase-mediated biotinylated-dUTP nick-end labeling suggested that MCM3 was involved in neuronal apoptosis. In conclusion, our data indicated that MCM3 might play an important role in neuronal apoptosis following TBI. Further understanding of these insights could serve as the basis for broadening the therapeutic scope against TBI.     

Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis

Mathematical modeling is required for understanding the complex behavior of large signal transduction networks. Previous attempts to model signal transduction pathways were often limited to small systems or based on qualitative data only. Here, we developed a mathematical modeling framework for understanding the complex signaling behavior of CD95(APO-1/Fas)-mediated apoptosis. Defects in the regulation of apoptosis result in serious diseases such as cancer, autoimmunity, and neurodegeneration. During the last decade many of the molecular mechanisms of apoptosis signaling have been examined and elucidated. A systemic understanding of apoptosis is, however, still missing. To address the complexity of apoptotic signaling we subdivided this system into subsystems of different information qualities. A new approach for sensitivity analysis within the mathematical model was key for the identification of critical system parameters and two essential system properties: modularity and robustness. Our model describes the regulation of apoptosis on a systems level and resolves the important question of a threshold mechanism for the regulation of apoptosis.     

The role of phasins in the morphogenesis of poly(3-hydroxybutyrate) granules

Recent developments in the understanding of the structure of polyhydroxyalkanoate, PHA, granules in bacteria are documented in the literature and point to the role of structural proteins, phasins, in granule formation and stabilization. We have previously conceived a computer program which successfully simulates granule formation in vitro, in the absence of phasins. Now we are extending the computer model to a more complex system, including phasins, to quantify their anticipated effect on the granule properties. The simulation enabled us to propose real experiments to test the validity of the model and provide a framework for a better understanding of PHA granule formation in vivo.     

Conventional and newly developed bioheat transport models in vascularized tissues: A review

Heat transfer in a biological system is a complex process and its analysis is difficult. Heterogeneous vascular architecture, blood flow in the complex network of arteries and veins, varying metabolic heat generation rates and dependence of tissue properties on its physiological condition contribute to this complexity. The understanding of heat transfer in human body is important for better insight of thermoregulatory mechanism and physiological conditions. Its understanding is also important for accurate prediction of thermal transport and temperature distribution during biomedical applications. During the last three decades, many attempts have been made by researchers to model the complex thermal behavior of the human body. These models, viz., blood perfusion, countercurrent, thermal phase-lag, porous-media, perturbation, radiation, etc. have their corresponding strengths and limitations. Along with their biomedical applications, this article reviews various contextual issues associated with these models. After brief discussion of early bioheat models, the newly developed bioheat models are discussed in detail. Dependence of these models on biological properties, viz., thermophysical and optical properties are also discussed.     

Requirement of a Tha4-conserved transmembrane glutamate in thylakoid Tat translocase assembly revealed by biochemical complementation

The thylakoid Tat system employs three membrane components and the pH gradient to transport folded proteins. The translocase is signal-assembled, i.e. a receptor complex containing cpTatC and Hcf106 binds the precursor protein, and upon membrane energization, Tha4 is recruited to the precursor-receptor complex to effect translocation. We developed a two-step complementation assay to examine the implied central role of Tha4 in translocation. The first step results in the inactivation of endogenous Tha4 with specific antibodies. The second step involves integrating exogenous Tha4 and presenting the system with precursor protein. We verified this approach by confirming the results obtained recently with the Escherichia coli Tha4 ortholog TatA, i.e. that the carboxyl terminus is dispensable and the amphipathic helix essential for transport. We then investigated a conserved Tha4 transmembrane glutamate in detail. Substitution of glutamate 10 with alanine, glutamine, and even aspartate largely eliminated the ability of Tha4 to complement transport, whereas a conservative substitution elsewhere in the transmembrane domain was without effect. Chemical cross-linking assays showed that the mutated Tha4s failed to be recruited to the receptor complex under transport conditions, indicating a role for the transmembrane glutamate in translocase assembly. This assay promises an avenue into understanding the role of Tha4 in both the assembly and translocation steps of the Tat translocase.     

Electron paramagnetic resonance of nitrosylprotoheme dimethyl ester complexes with imidazole derivatives as model systems for nitrosylhemoproteins.

For the purpose of understanding the electron paramagnetic resonance (epr) spectral change of nitrosylhemoproteins under various conditions, the epr spectra for the model system have been analyzed. The model system consists of the nitrogen oxide complex of the iron(II) protoporphyrin IX dimethyl ester and various imidazole derivatives (three hindered and six unhindered imidazole derivatives). The results of the analysis indicate the existence of two molecular species in the model system, which differ in structure of the FeNO unit. These observations were compared with those for the nitrosylhemoproteins.     

A quantitative genetics and ecological model system: understanding the aliphatic glucosinolate biosynthetic network via QTLs

Plants’ sessile nature has led them to develop chemical defenses, secondary metabolites, to directly cope with environmental changes rather than escape to more favorable sites. The diversity and fluctuation in biological stresses faced by a plant have generated extraordinary genetic diversity controlling the synthesis and regulation of secondary metabolites that is only now being explored. The glucosinolate secondary metabolites, amino acid derived thioglucosides specific to the order Capparales, is a model system for understanding the molecular basis of complex quantitative traits and their potential ecological role. This review focuses on the extensive progress being made towards understanding the complete molecular basis underlying the glucosinolate genetic diversity at both biosynthetic and regulatory loci. This has identified a highly interactive genetic network whereby biosynthetic loci have additional functions as regulatory loci and laid the foundation for glucosinolates to be a model system for understanding quantitative traits in a broader context.     

Quorum sensing in Pseudomonas aeruginosa biofilms

In nature, the bulk of bacterial biomass is believed to exist as an adherent community of cells called a biofilm. Pseudomonas aeruginosa has become a model organism for studying this mode of growth. Over the past decade, significant strides have been made towards understanding biofilm development in P. aeruginosa and we now have a clearer picture of the mechanisms involved. Available evidence suggests that construction of these sessile communities proceeds by many different pathways, rather than a specific programme of biofilm development. A cell-to-cell communication mechanism known as quorum sensing (QS) has been found to play a role in P. aeruginosa biofilm formation. Because both QS and biofilms are impacted by the surrounding environment, understanding the full involvement of cell-to-cell signalling in establishing these complex communities represents a challenge. Nevertheless, under set conditions, several links between QS and biofilm formation have been recognized, which is the focus of this review. A role for antibiotics as alternative QS signalling molecules influencing biofilm development is also discussed.     

Methodology for protein-ligand binding studies: application to a model for drug resistance, the HIV/FIV protease system.

A protocol for the rapid energetic analysis of protein-ligand complexes has been developed. This protocol involves the generation of protein-ligand complex ensembles followed by an analysis of the binding free energy components. We apply this methodology toward understanding the origin of binding specificity within the human immunodeficiency virus/feline immunodeficiency virus (HIV/FIV) protease system, a model system for drug resistance studies. A distinct difference in the internal strain of an inhibitor within each protein environment clearly favors the HIV protease complex, as observed experimentally. Our analysis also predicts that residues within the S2-S3 pockets of the FIV protease active site are responsible for this strain. Close examination of the active site residue contributions to interaction energy and desolvation energy identifies specific amino acids that may also play a role in determining the binding preferences of these two enzymes. Proteins 1999;36:318-331.     

Computational fluid dynamics modeling of mass transfer behavior in a bioreactor for hairy root culture. I. Model development and experimental validation

A two-dimensional axisymmetric computational fluid dynamics (CFD) model based on a porous media model and a discrete population balance model was established to investigate the hydrodynamics and mass transfer behavior in an airlift bioreactor for hairy root culture.During the hairy root culture of Echinacea purpurea, liquid and gas velocity, gas holdup, mass transfer rate, as well as oxygen concentration distribution in the airlift bioreactor were simulated by this CFD model. Simulative results indicated that liquid flow and turbulence played a dominant role in oxygen mass transfer in the growth domain of the hairy root culture. The dissolved oxygen concentration in the hairy root clump increased from the bottom to the top of the bioreactor cultured with the hairy roots, which was verified by the experimental detection of dissolved oxygen concentration in the hairy root clump. This methodology provided insight understanding on the complex system of hairy root culture and will help to eventually guide the bioreactor design and process intensification of large-scale hairy root culture.