Synthesis, biological activity, and preliminary pharmacokinetic evaluation of analogues of a phosphosulfomannan angiogenesis inhibitor (PI-88)

The phosphosulfomannan 1 (PI-88) is a mixture of highly sulfated oligosaccharides that is currently undergoing clinical evaluation in cancer patients. As well as it's anticancer properties, 1 displays a number of other interesting biological activities. A series of analogues of 1 were synthesized with a single carbon (pentasaccharide) backbone to facilitate structural characterization and interpretation of biological results. In a fashion similar to 1, all compounds were able to inhibit heparanase and to bind tightly to the proangiogenic growth factors FGF-1, FGF-2, and VEGF. The compounds also inhibited the infection of cells and cell-to-cell spread of herpes simplex virus (HSV-1). Preliminary pharmacokinetic data indicated that the compounds displayed different pharmacokinetic behavior compared with 1. Of particular note was the n-octyl derivative, which was cleared 3 times less rapidly than 1 and may provide increased systemic exposure.

A mathematical model of integrin-mediated haptotactic cell migration

Haptotactic cell migration, a directed response to gradients of cell—extracellular matrix adhesion, is an important process in a number of biological phenomena such as wound healing and tumour cell invasion. Previously, mathematical models of haptotaxis have been developed on the premise that cells migrate in response to gradients in the density of the extracellular matrix. In this paper, we develop a novel mathematical model of haptotaxis which includes the adhesion receptors known as integrins and a description of their functional activation, local recruitment and protrusion as part of lamellipodia. Through the inclusion of integrins, the modelled cell matter is able to respond to a true gradient of cell–matrix adhesion, represented by functionally active integrins. We also show that previous matrix-mediated models are in fact a subset of the novel integrin-mediated models, characterised by specific choices of diffusion and haptotaxis coefficients in their model equations. Numerical solutions suggest the existence of travelling waves of cell migration that are confirmed via a phase plane analysis of a simplified model.

A Mixture model with random-effects components for clustering correlated gene-expression profiles

Motivation: The clustering of gene profiles across some experimental conditions of interest contributes significantly to the elucidation of unknown gene function, the validation of gene discoveries and the interpretation of biological processes. However, this clustering problem is not straightforward as the profiles of the genes are not all independently distributed and the expression levels may have been obtained from an experimental design involving replicated arrays. Ignoring the dependence between the gene profiles and the structure of the replicated data can result in important sources of variability in the experiments being overlooked in the analysis, with the consequent possibility of misleading inferences being made. We propose a random-effects model that provides a unified approach to the clustering of genes with correlated expression levels measured in a wide variety of experimental situations. Our model is an extension of the normal mixture model to account for the correlations between the gene profiles and to enable covariate information to be incorporated into the clustering process. Hence the model is applicable to longitudinal studies with or without replication, for example, time-course experiments by using time as a covariate, and to cross-sectional experiments by using categorical covariates to represent the different experimental classes. Results: We show that our random-effects model can be fitted by maximum likelihood via the EM algorithm for which the E(expectation) and M(maximization) steps can be implemented in closed form. Hence our model can be fitted deterministically without the need for time-consuming Monte Carlo approximations. The effectiveness of our model-based procedure for the clustering of correlated gene profiles is demonstrated on three real datasets, representing typical microarray experimental designs, covering time-course, repeated-measurement and cross-sectional data. In these examples, relevant clusters of the genes are obtained, which are supported by existing gene-function annotation. A synthetic dataset is considered too.

Applicability of experience from laboratory reactors with biological phosphorus removal in full-scale plants

Enhanced biological phosphorus removal (EBPR) has been used at many wastewater treatment plants all over the world for many years. In this study a full-scale sludge with good EBPR was tested with P-release batch tests and combined FISH/MAR (fluorescence in situ hybridisation and microautoradiography). Proposed models of PAOs and GAOs (polyphosphate- and glycogen-accumulating organisms) and microbial methods suggested from studies of laboratory reactors were found to be applicable also on sludge from full-scale plants. Dependency of pH and the uptake of both acetate and propionate were studied and used for calculations for verifying the models and results from microbial methods. All rates found from the batch tests with acetate were higher than in the batch tests with propionate, which was explained by the finding that only those parts of the bacterial community that were able to take up acetate anaerobically were able to take up propionate anaerobically.

Biogenesis of caveolae: a structural model for caveolin-induced domain formation

Caveolae are striking morphological features of the plasma membrane of mammalian cells. Caveolins, the major proteins of caveolae, play a crucial role in the formation of these invaginations of the plasma membrane; however, the precise mechanisms involved are only just starting to be unravelled. Recent studies suggest that caveolae are stable structures first generated in the Golgi complex. Their formation and exit from the Golgi complex is associated with caveolin oligomerisation, acquisition of detergent insolubility, and association with cholesterol. Modelling of caveolin-membrane interactions together with in vitro studies of caveolin peptides are providing new insights into how caveolin-lipid interactions could generate the unique architecture of the caveolar domain.

Competition between polyphosphate and glycogen accumulating organisms in enhanced biological phosphorus removal systems with acetate and propionate as carbon sources

Enhanced biological phosphorus removal (EBPR) is a widely used process for achieving phosphorus removal from wastewater. A potential reason for EBPR failure is the undesirable growth of glycogen accumulating organisms (GAOs), which can compete for carbon sources with the bacterial group responsible for phosphorus removal from wastewater: the polyphosphate accumulating organisms (PAOs). This study investigates the impact of carbon source on EBPR performance and the competition between PAOs and GAOs. Two sequencing batch reactors (SBRs) were operated during a 4-6 month period and fed with a media containing acetate or propionate, respectively, as the sole carbon source. It was found that the acetate fed SBR rarely achieved a high level of phosphorus removal, and that a large portion of the microbial community was comprised of Candidatus Competibacter phosphatis, a known GAO. The propionate fed SBR, however, achieved stable phosphorus removal throughout the study, apart from one brief disturbance. The bacterial community of the propionate fed SBR was dominated by Candidatus Accumulibacter phosphatis, a known PAO, and did not contain Competibacter In a separate experiment, another SBR was seeded with a mixture of PAOs and a group of alphaproteobacterial GAOs, both enriched with propionate as the sole carbon source. Stable EBPR was achieved and the PAO population increased while the GAOs appeared to be out-competed. The results of this paper suggest that propionate may provide PAOs with a selective advantage over GAOs in the PAO-GAO competition, particularly through the minimisation of Competibacter Propionate may be a more suitable substrate than acetate for enhancing phosphorus removal in EBPR systems. (c) 2005 Elsevier B.V. All rights reserved.

Modelling biological processes under anaerobic conditions through integrating titrimetric and off-gas measurements - applied to EBPR systems

An innovative method for modelling biological processes under anaerobic conditions is presented and discussed. The method is based on titrimetric and off-gas measurements. Titrimetric data is recorded as the addition rate of hydroxyl ions or protons that is required to maintain pH in a bioreactor at a constant level. An off-gas analysis arrangement measures, among other things, the transfer rate of carbon dioxide. The integration of these signals results in a continuous signal which is solely related to the biological reactions. When coupled with a mathematical model of the biological reactions, the signal allows a detailed characterisation of these reactions, which would otherwise be difficult to achieve. Two applications of the method to the enhanced biological phosphorus removal processes are presented and discussed to demonstrate the principle and effectiveness of the method.

Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence

Topological measures of large-scale complex networks are applied to a specific artificial regulatory network model created through a whole genome duplication and divergence mechanism. This class of networks share topological features with natural transcriptional regulatory networks. Specifically, these networks display scale-free and small-world topology and possess subgraph distributions similar to those of natural networks. Thus, the topologies inherent in natural networks may be in part due to their method of creation rather than being exclusively shaped by subsequent evolution under selection. The evolvability of the dynamics of these networks is also examined by evolving networks in simulation to obtain three simple types of output dynamics. The networks obtained from this process show a wide variety of topologies and numbers of genes indicating that it is relatively easy to evolve these classes of dynamics in this model. (c) 2006 Elsevier Ireland Ltd. All rights reserved.

Optimization of integrated chemical-biological degradation of a reactive azo dye using response surface methodology

The integrated chemical-biological degradation combining advanced oxidation by UV/H2O2 followed by aerobic biodegradation was used to degrade C.I. Reactive Azo Red 195A, commonly used in the textile industry in Australia. An experimental design based on the response surface method was applied to evaluate the interactive effects of influencing factors (UV irradiation time, initial hydrogen peroxide dosage and recirculation ratio of the system) on decolourisation efficiency and optimizing the operating conditions of the treatment process. The effects were determined by the measurement of dye concentration and soluble chemical oxygen demand (S-COD). The results showed that the dye and S-COD removal were affected by all factors individually and interactively. Maximal colour degradation performance was predicted, and experimentally validated, with no recirculation, 30 min UV irradiation and 500 mg H2O2/L. The model predictions for colour removal, based on a three-factor/five-level Box-Wilson central composite design and the response surface method analysis, were found to be very close to additional experimental results obtained under near optimal conditions. This demonstrates the benefits of this approach in achieving good predictions while minimising the number of experiments required. (c) 2006 Elsevier B.V. All rights reserved.

Physiological and haematological findings and clinical observations in a model of acute systemic anaphylaxis in Dirofilaria immitis-sensitised cats

Objective This study aims to understand the pathophysiology of anaphylaxis in Dirofflaria immitis-sensitised cats by analysing objective physiological and haematological measurements after challenge. Design Nineteen healthy D immitis-naive cats were sensitised using weekly injections of aluminium hydroxide-adjuvanted D immitis antigen, administered subcutaneously over 6 weeks. After sensitisation, cats (n = 16) were anaesthetised and challenged with intravenous D immitis antigen. A control group (n = 3) was sham-challenged using intravenous sterile 0.9% saline. Systolic blood pressure (measured non-invasively/indirectly), respiratory rate, degree of dyspnoea, blood 0, saturation, expired CO2, and heart rate and were measured immediately before and at 10 to 15 min intervals after challenge until terminal apnoea occurred or euthanasia at 140 mins post-challenge. Blood was collected for complete blood count immediately before and at 10, 20 and 35 mins after challenge. Clinical observations were recorded as they occurred. Results Antigen-challenged cats were divided into two groups: acute (apnoea occurred within 25 mins of challenge) and subacute (breathing at 25 mins after challenge). In both groups, the degree of dyspnoea increased and blood O-2 saturation and blood pressure decreased. Respiratory rate increased in the subacute group. Expired CO2 decreased in both Ag-challenged and control groups. Haematocrit increased in the subacute group. Neutrophil count decreased in the acute group and platelet count decreased in the subacute group. Eosinophil count decreased in the subacute and control groups. Sustained dyspnoea and gastrointestinal signs were the most common clinical manifestations of anaphylaxis in the antigen-challenged cats. Conclusions Intravenous challenge with D immitis antigen in sensitised cats results in dyspnoea, hypoxaemia and systemic hypotension accompanied by haemoconcentration.

Polyethism and comparability of termite choice assays in a model system using Microcerotermes turneri (Termitidae : Termitinae): Implications for standardised testing techniques

Traditional measures of termite food preference assess consequences of foraging behavior such as wood consumption, aggregation and/or termite survivorship. Although studies have been done to investigate the specifics of foraging behavior this is not generally integrated into choice assay experiments. Here choice assays were conducted with small isolated (orphaned) groups of workers and compared with choice assays involving foragers from whole nests (non-orphaned) in the laboratory. Aggregation to two different wood types was used as a measure of preference. Specific worker caste and instars participating in initial exploration were compared between assay methods, with samples of termites taken from nest carton material and sites where termites were feeding. Aggregation results differ between choice assay techniques. Castes and instars responsible for initial exploration, as determined in whole nest trials, were not commonly found exploring in isolated group trials, nor were they numerous in termites taken from active feeding sites. Consequently the use of small groups of M. turneri worker termites extracted from active feeding sites may not be appropriate for use in choice assays.

Predicting population dynamics of weed biological control agents: science or gazing into crystal balls?

Various factors can influence the population dynamics of phytophages post introduction, of which climate is fundamental. Here we present an approach, using a mechanistic modelling package (CLIMEX), that at least enables one to make predictions of likely dynamics based on climate alone. As biological control programs will have minimal funding for basic work (particularly on population dynamics), we show how predictions can be made using a species geographical distribution, relative abundance across its range, seasonal phenology and laboratory rearing data. Many of these data sets are more likely to be available than long-term population data, and some can be incorporated into the exploratory phase of a biocontrol program. Although models are likely to be more robust the more information is available, useful models can be developed using information on species distribution alone. The fitted model estimates a species average response to climate, and can be used to predict likely geographical distribution if introduced, where the agent is likely to be more abundant (i.e. good locations) and more importantly for interpretation of release success, the likely variation in abundance over time due to intra- and inter-year climate variability. The latter will be useful in predicting both the seasonal and long-term impacts of the potential biocontrol agent on the target weed. We believe this tool may not only aid in the agent selection process, but also in the design of release strategies, and for interpretation of post-introduction dynamics and impacts. More importantly we are making testable predictions. If biological control is to become more of a science making and testing such hypothesis will be a key component.

The DVD animal model of schizophrenia: Effects of low maternal vitamin D on brain dopamine

Background: We have previously shown that the offspring of vitamin D3 depleted rats have enlarged ventricles and altered neurotrophin profiles (reduced NGF and GDNF). These findings enhance the biological plausibility that low prenatal vitamin D may be a risk factor for schizophrenia. Our recent behavioural studies have found that adult rats with developmental vitamin D deficiency (DVD) have a subtle increase in baseline locomotor activity and a heightened response to dopamine (DA) antagonists. The aim of this study was to investigate brain DA neurochemistry in the DVD model. Methods: We examined cerebrums and striatal tissue from neonates and a variety of brain tissues from the remaining littermates at adulthood. DA, DOPAC, HVA, serotonin and 5HIAA were analysed by HPLC. Single point comparisons for DA1, DA2 and NMDA receptors were also assessed in these tissues. Results: Significant increases in DA and HVA were found in brains from DVD deplete neonates (P=0.01). However, DA and its metabolites were not increased in either the neonate or adult striatum, however there was a trend towards increased DA and its metabolites in the accumbens (P=0.1). Receptor densities were unaffected by prenatal vitamin D levels. Conclusions: Although the effect of maternal diet appears to increase DA production and turnover in neonatal brain, this does not persist into adulthood. Thus other factors must underlie the increased locomotor activity noted in these animals. Future experiments will concentrate on monitoring accumbens and striatal DA release and turnover using microdialysis in pharmacologically challenged behavioural paradigms. References: Eyles D, Brown J; Mackay-Sim A, McGrath J, Feron F. (2003) Vitamin D3 and brain development. Neuroscience 118 (3) 641–653. Burne T, McGrath J, Eyles D, Mackay-Sim A. Behavioural characterization of vitamin D receptor knockout mice. (2005) Behavioural Brain Res: 157 299–308.

What does the animal model teach us about the effects of physical activity on growing bone?

Experiments to design physical activity programs that optimize their osteogenic potential are difficult to accomplish in humans. The aim of this article is to review the contributions that animal studies have made to knowledge of the loading conditions that are osteogenic to the skeleton during growth, as well as to consider to what extent animal studies fail to provide valid models of physical activity and skeletal maturation. Controlled loading studies demonstrate that static loads are ineffective, and that bone formation is threshold driven and dependent on strain rate, amplitude, and duration of loading. Only a few loading cycles per session are required, and distributed bouts are more osteogenic than sessions of long duration. Finally, animal models fail to inform us of the most appropriate ways to account for the variations in biological maturation that occur in our studies of children and adolescents, requiring the use of techniques for studying human growth and development.