Some novel techniques of parameter estimation for the dynamical models in biological systems

Inverse problems based on using experimental data to estimate unknown parameters of a system often arise in biological and chaotic systems. In this paper, we consider parameter estimation in systems biology involving linear and non-linear complex dynamical models, including the Michaelis–Menten enzyme kinetic system, a dynamical model of competence induction in Bacillus subtilis bacteria and a model of feedback bypass in B. subtilis bacteria. We propose some novel techniques for inverse problems. Firstly, we establish an approximation of a non-linear differential algebraic equation that corresponds to the given biological systems. Secondly, we use the Picard contraction mapping, collage methods and numerical integration techniques to convert the parameter estimation into a minimization problem of the parameters. We propose two optimization techniques: a grid approximation method and a modified hybrid Nelder–Mead simplex search and particle swarm optimization (MH-NMSS-PSO) for non-linear parameter estimation. The two techniques are used for parameter estimation in a model of competence induction in B. subtilis bacteria with noisy data. The MH-NMSS-PSO scheme is applied to a dynamical model of competence induction in B. subtilis bacteria based on experimental data and the model for feedback bypass. Numerical results demonstrate the effectiveness of our approach.

A Krylov-based finite state projection algorithm for solving the chemical master equation arising in the discrete modelling of biological systems

Biochemical reactions underlying genetic regulation are often modelled as a continuous-time, discrete-state, Markov process, and the evolution of the associated probability density is described by the so-called chemical master equation (CME). However the CME is typically difficult to solve, since the state-space involved can be very large or even countably infinite. Recently a finite state projection method (FSP) that truncates the state-space was suggested and shown to be effective in an example of a model of the Pap-pili epigenetic switch. However in this example, both the model and the final time at which the solution was computed, were relatively small. Presented here is a Krylov FSP algorithm based on a combination of state-space truncation and inexact matrix-vector product routines. This allows larger-scale models to be studied and solutions for larger final times to be computed in a realistic execution time. Additionally the new method computes the solution at intermediate times at virtually no extra cost, since it is derived from Krylov-type methods for computing matrix exponentials. For the purpose of comparison the new algorithm is applied to the model of the Pap-pili epigenetic switch, where the original FSP was first demonstrated. Also the method is applied to a more sophisticated model of regulated transcription. Numerical results indicate that the new approach is significantly faster and extendable to larger biological models.

A software tool for simulating spatial separation and kinetics in biological membranes

Self-segregation and compartimentalisation are observed experimentally to occur spontaneously on live membranes as well as reconstructed model membranes. It is believed that many of these processes are caused or supported by anomalous diffusive behaviours of biomolecules on membranes due to the complex and heterogeneous nature of these environments. These phenomena are on the one hand of great interest in biology, since they may be an important way for biological systems to selectively localize receptors, regulate signaling or modulate kinetics; and on the other, they provide an inspiration for engineering designs that mimick natural systems. We present an interactive software package we are developing for the purpose of simulating such processes numerically using a fundamental Monte Carlo approach. This program includes the ability to simulate kinetics and mass transport in the presence of either mobile or immobile obstacles and other relevant structures such as liquid-ordered lipid microdomains. We also present preliminary simulation results regarding the selective spatial localization and chemical kinetics modulating power of immobile obstacles on the membrane, obtained using the program.

Biological and environmental determinants

- describe the complex web of determinants as part of broad causal pathways that affect health - identify and discuss the range of physical, biological and environmental determinants that impact on health - suggest why it is important to the practice of public health that you understand how determinants contribute to health - understand the complexity of health and illness and the multifaceted role of health determinants - relate determinants of health to public health activity and realise the need for multisectoral action and multiple approaches when working to improve health

Mammalian phylogeny

Living mammals can be divided into three subclasses (monotremes, marsupials and placentals) and within these, about 27 orders. Final resolution of the relationships between the orders is only now being achieved with the increased availability of deoxyribonucleic acid (DNA) sequences. Highlights include the deep division of placental mammals into African (Afrotheria), South American (Xenarthra) and northern hemisphere (Boreoeutheria) super-orders, and the finding that the once considered primitive ‘Insectivora’ and ‘Edentata’ clades, in fact, have members distributed widely among these super-orders. Another surprise finding from DNA studies has been that whale origins lie among the even-toed ungulates (Artiodactyla). Our order, Primates is most closely related to the flying lemurs and next, the tree shrews. With the mammal phylogeny becoming well resolved, it is increasingly being used as a framework for inferring evolutionary and ecological processes, such as adaptive radiation.

Biological responses of human bone marrow mesenchymal stem cells to Sr-M-Si (M = Zn, Mg) silicate bioceramics

Strontium (Sr), Zinc (Zn), magnesium (Mg), and silicon (Si) are reported to be essential trace elements for the growth and mineralization of bone. We speculated that the combination of these bioactive elements in bioceramics may be effective to regulate the osteogenic property of boneforming cells. In this study, two Sr-containing silicate bioceramics, Sr2ZnSi2O7 (SZS) and Sr2MgSi2O7 (SMS), were prepared. The biological response of human bone marrow mesenchymal stem cells (BMSCs) to the two bioceramics (in the forms of powders and dense ceramic bulks) was systematically studied. In powder form, the effect of powder extracts on the viability and alkaline phosphatase (ALP) activity of BMSCs was investigated. In ceramic disc form, both direct and indirect coculture of BMSCs with ceramic discs were used to investigate their biological response, including attachment, proliferation, ALP activity, and bone-related genes expression. Beta-tricalcium phosphate (b-TCP) and akermanite (Ca2MgSi2O7, CMS) were used as control materials. The results showed that the Sr, Zn, and Si (or Sr, Mg, and Si)-containing ionic products from SZS and SMS powders enhanced ALP activity of BMSCs, compared to those from b-TCP. Both SZS and SMS ceramic discs supported the growth of BMSCs, and most importantly, significantly enhanced the ALP activity and bone-related genes expression of BMSCs as compared to b-TCP. The results suggest that the specific combination of bioactive ions (Sr, Zn, Si, e.g.) in bioceramics is a viable way to improve the biological performance of biomaterials, and the form of materials and surface properties were nonnegligible factors to influence cell response.

Offsetting greenhouse gas emissions through biological carbon sequestration in North Eastern Australia

The Kyoto Protocol recognises trees as a sink of carbon and a valid means to offset greenhouse gas emissions and meet internationally agreed emissions targets. This study details biological carbon sequestration rates for common plantation species Araucaria cunninghamii (hoop pine), Eucalyptus cloeziana, Eucalyptus argophloia, Pinus elliottii and Pinus caribaea var hondurensis and individual land areas required in north-eastern Australia to offset greenhouse gas emissions of 1000tCO 2e. The 3PG simulation model was used to predict above and below-ground estimates of biomass carbon for a range of soil productivity conditions for six representative locations in agricultural regions of north-eastern Australia. The total area required to offset 1000tCO 2e ranges from 1ha of E. cloeziana under high productivity conditions in coastal North Queensland to 45ha of hoop pine in low productivity conditions of inland Central Queensland. These areas must remain planted for a minimum of 30years to meet the offset of 1000tCO 2e.

The spatial distribution of rodent damage in Australian macadamia (Macadamia integrifolia) orchards

The Black Rat (Rattus rattus), a global pest within the macadamia production industry, causes up to 30% crop damage in Australian orchards. During early stages of production in Australia, research demonstrated the importance of non crop adjacent habitats as significant in affecting the patterns of crop damage seen throughout orchards. Where once rodent damage was limited to the outside edges of orchard blocks, growers are now reporting finding crop damage throughout entire orchards. This study therefore aims to explore the spatial patterns of rodent distribution and damage now occurring in Australian macadamia orchards. We show that rodent damage and rodent distribution in these newer production regions differ from that shown in previous Australian research. Previous Australian research has shown damage patterns which were associated with the edges of orchard blocks however this study demonstrates a more widespread damage distribution. In the current study there is no relationship between rodent damage and the orchard edge. Arboreal rodent nests were identified within these newer orchard systems, suggesting rodents are residing within the tree component of the orchard system and not dependent on adjacent non-crop habitat for shelter. Results from this study confirm that rodents have modified their nesting and foraging behaviour in newer orchards systems in Australia. We suggest that this is a response of increased and prolonged availability of macadamia nuts in newer production regions enabling populations to be maintained throughout the year. Management strategies will require modification if control is to be achieved.

Modelling resilience in a water supply system : contrasting conditions of drought and flood

This paper presents an approach to modelling the resilience of a generic (potable) water supply system. The system is contextualized as a meta-system consisting of three subsystems to represent the natural catchment, the water treatment plant and the water distribution infrastructure for urban use. An abstract mathematical model of the meta-system is disaggregated progressively to form a cascade of equations forming a relational matrix of models. This allows the investigation of commonly implicit relationships between various operational components within the meta system, the in-depth understanding of specific system components and influential factors and the incorporation of explicit disturbances to explore system behaviour. Consequently, this will facilitate long-term decision making to achieve sustainable solutions for issues such as, meeting a growing demand or managing supply-side influences in the meta-system under diverse water availability regimes. This approach is based on the hypothesis that the means to achieve resilient supply of water may be better managed by modelling the effects of changes at specific levels that have a direct or in some cases indirect impact on higher-order outcomes. Additionally, the proposed strategy allows the definition of approaches to combine disparate data sets to synthesise previously missing or incomplete higher-order information, a scientifically robust means to define and carry out meta-analyses using knowledge from diverse yet relatable disciplines relevant to different levels of the system and for enhancing the understanding of dependencies and inter-dependencies of variable factors at various levels across the meta-system. The proposed concept introduces an approach for modelling a complex infrastructure system as a meta system which consists of a combination of bio-ecological, technical and socio-technical subsystems.

Viable chimaeric viruses confirm the biological importance of sequence specific maize streak virus movement protein and coat protein interactions

Background. A variety of interactions between up to three different movement proteins (MPs), the coat protein (CP) and genomic DNA mediate the inter- and intra-cellular movement of geminiviruses in the genus Begomovirus. Although movement of viruses in the genus Mastrevirus is less well characterized, direct interactions between a single MP and the CP of these viruses is also clearly involved in both intra- and intercellular trafficking of virus genomic DNA. However, it is currently unknown how specific these MP-CP interactions are, nor how disruption of these interactions might impact on virus viability. Results. Using chimaeric genomes of two strains of Maize streak virus (MSV) we adopted a genetic approach to investigate the gross biological effects of interfering with interactions between virus MP and CP homologues derived from genetically distinct MSV isolates. MP and CP genes were reciprocally exchanged, individually and in pairs, between maize (MSV-Kom)- and Setaria sp. (MSV-Set)-adapted isolates sharing 78% genome-wide sequence identity. All chimaeras were infectious in Zea mays c.v. Jubilee and were characterized in terms of symptomatology and infection efficiency. Compared with their parental viruses, all the chimaeras were attenuated in symptom severity, infection efficiency, and the rate at which symptoms appeared. The exchange of individual MP and CP genes resulted in lower infection efficiency and reduced symptom severity in comparison with exchanges of matched MP-CP pairs. Conclusion. Specific interactions between the mastrevirus MP and CP genes themselves and/or their expression products are important determinants of infection efficiency, rate of symptom development and symptom severity. © 2008 van der Walt et al; licensee BioMed Central Ltd.

Coal seam gas waters - their geochemical signature and potential environmental implications

Coal Seam Gas (CSG) is a form of natural gas (mainly methane) sorbed in underground coal beds. To mine this gas, wells are drilled directly into an underground coal seam and groundwater (CSG water) is pumped out to the surface. This lowers the downhole piezometric pressure and enables gas desporption from the coal matrix. In the United States, this gas has been extracted commercially since the 1980s. The economic success of US CSG projects has inspired exploration and development in Australia and New Zealand. In Australia, Queensland’s Bowen and Surat basins have been the subject of increased CSG development over the last decade. CSG growth in other Australian basins has not matured to the same level but exploration and development are taking place at an accelerated pace in the Sydney Basin (Illawarra and the Hunter Valley, NSW) and in the Gunnedah Basin. Similarly, CSG exploration in New Zealand has focused in the Waikato region (Maramarua and Huntly), in the West Coast region (Buller, Reefton, and Greymouth), and in Southland (Kaitangata, Mataura, and Ohai). Figure 1 shows a Shcoeller diagram with CSG samples from selected basins in Australia, New Zealand, and the USA. CSG water from all of these basins exhibit the same geochemical signature – low calcium, low magnesium, high bicarbonate, low sulphate and, sometimes, high chloride. This water quality is a direct result of specific biological and geological processes that have taken part in the formation of CSG. In general, these processes include the weathering of rocks (carbonates, dolomite, and halite), cation exchange with clays (responsible for enhanced sodium and depleted calcium and magnesium), and biogenic processes (accounting for the presence of high bicarbonate concentrations). The salinity of CSG waters tends to be brackish (TDS < 30000 mg/l) with a fairly neutral pH. These particular characteristics need to be taken into consideration when assessing water management and disposal alternatives. Environmental issues associated with CSG water disposal have been prominent in developed basins such as the Powder River Basin (PRB) in the United States. When disposed on the land or used for irrigation, water having a high dissolved salts content may reduce water availability to crops thus affecting crop yield. In addition, the high sodium, low calcium and low magnesium concentrations increase the potential to disperse soils and significantly reduce the water infiltration rate. Therefore, CSG waters need to be properly characterised, treated, and disposed to safeguard the environment without compromising other natural resources.

A micro-level indexing model for assessing urban ecosystem sustainability

Purpose – As a consequence of rapid urbanisation and globalisation, cities have become the engines of population and economic growth. Hence, natural resources in and around the cities have been exposed to externalities of urban development processes. This paper introduces a new sustainability assessment approach that is tested in a pilot study. The paper aims to assist policy-makers and planners investigating the impacts of development on environmental systems, and produce effective policies for sustainable urban development. Design/methodology/approach – The paper introduces an indicator-based indexing model entitled “Indexing Model for the Assessment of Sustainable Urban Ecosystems” (ASSURE). The ASSURE indexing model produces a set of micro-level environmental sustainability indices that is aimed to be used in the evaluation and monitoring of the interaction between human activities and urban ecosystems. The model is an innovative approach designed to assess the resilience of ecosystems towards impacts of current development plans and the results serve as a guide for policymakers to take actions towards achieving sustainability. Findings – The indexing model has been tested in a pilot case study within the Gold Coast City, Queensland, Australia. This paper presents the methodology of the model and outlines the preliminary findings of the pilot study. The paper concludes with a discussion on the findings and recommendations put forward for future development and implementation of the model. Originality/value – Presently, there is a few sustainability indices developed to measure the sustainability at local, regional, national and international levels. However, due to challenges in data collection difficulties and availability of local data, there is no effective assessment model at the microlevel that the assessment of urban ecosystem sustainability accurately. The model introduced in this paper fills this gap by focusing on parcel-scale and benchmarking the environmental performance in micro-level.

Automatic particle picking of biological molecules imaged by electron microscopy

One of the next great challenges of cell biology is the determination of the enormous number of protein structures encoded in genomes. In recent years, advances in electron cryo-microscopy and high-resolution single particle analysis have developed to the point where they now provide a methodology for high resolution structure determination. Using this approach, images of randomly oriented single particles are aligned computationally to reconstruct 3-D structures of proteins and even whole viruses. One of the limiting factors in obtaining high-resolution reconstructions is obtaining a large enough representative dataset ($>100,000$ particles). Traditionally particles have been manually picked which is an extremely labour intensive process. The problem is made especially difficult by the low signal-to-noise ratio of the images. This paper describes the development of automatic particle picking software, which has been tested with both negatively stained and cryo-electron micrographs. This algorithm has been shown to be capable of selecting most of the particles, with few false positives. Further work will involve extending the software to detect differently shaped and oriented particles.