ScrumPy: metabolic modelling with Python

ScrumPy is a software package used for the definition and analysis of metabolic models. It is written using the Python programming language that is also used as a user interface. ScrumPy has features for both kinetic and structural modelling, but the emphasis is on structural modelling and those features of most relevance to analysis of large (genome-scale) models. The aim is at describing ScrumPy's functionality to readers with some knowledge of metabolic modelling, but implementation, programming and other computational details are omitted. ScrumPy is released under the Gnu Public Licence, and available for download from http://mudshark.brookes.ac.uk/ ScrumPy.     

Sucrose Mobilisation in Sugarcane Stalk Induced by Heterotrophic Axillary Bud Growth

A theoretical high-yield sugarcane biofactory can be idealised as containing culm tissue that functions as a secondary source tissue rather than a sink. To investigate this potential process, heterotrophic axillary bud outgrowth from sugarcane (Saccharum spp. hybrids) setts was used as a model system to demonstrate that sucrose is a mobilisable carbon source. The outgrowth and subsequent biomass accumulation of axillary buds from two-eye setts of mature sugarcane stalks grown in the dark was used to measure carbon mobilisation from sett internode pith tissue. After 42 days growth 99.0 ± 0.72% of sett internode pith sucrose was depleted and 2.66 ± 0.16 g of new tissue accumulated. Comparison with a control treatment in which axillary buds were excised at day zero demonstrated that carbon mobilisation was driven by the accumulation of new biomass. Profiling of soluble carbohydrates (viz. sucrose, glucose and fructose), starch, total soluble protein, total amino nitrogen, free amino acids and total insoluble material showed that the sucrose stored in the sett internode pith was the only available carbon source of sufficient size at day zero for the observed biomass accumulation. Other metabolites mobilised were glucose, fructose and some amino acids, notably isoleucine and leucine that were depleted in shoot treatment setts at day 42.     

Early Exposure to Ethylene Modifies Shoot Development and Increases Sucrose Accumulation Rate in Sugarcane

Sugarcane varieties (Saccharum spp. hybrids) that accumulate high levels of sucrose at the start of the harvest season are of considerable commercial interest. Our understanding of the factors that contribute to early sucrose accumulation in these varieties is limited. In this study we used the plant hormone ethylene to investigate the relationship between growth and early sucrose accumulation in sugarcane. The sugarcane variety KQ228 was exposed to a low concentration of the ethylene-forming compound 2-chloroethylphosphonic acid (CEPA) for a prolonged duration commencing from shoot emergence. The changes in sucrose accumulation and plant growth were investigated. Results from two glasshouse experiments revealed that the CEPA-treated plants accumulated a significantly higher amount of sucrose in their primary culm 2 and 3½ months post-germination. The treated plants had taller primary culms with many smaller internodes, smaller leaves, and a higher photosynthetic rate. Despite producing smaller internodes, treated culms were comparable in fresh weight and volume to the controls due to the compensating effect of faster internode formation. We identified three factors that may have contributed to the early accumulation of more sucrose in the treated culm: (1) the specific leaf area of young leaves was greater indicating efficient diversion of photoassimilate to sink tissue, (2) internode formation was initiated earlier, and (3) internodes continued to form at a faster rate. Consequently, a greater proportion of the internodes in the treated sugarcane matured earlier and began filling with sucrose sooner. The higher reducing sugar level in the apical region of the culm probably contributed to faster internode development. This coincided with elevated vacuolar and cell wall acid invertase gene expression that increased sucrose turnover in the vacuole and increased apoplastic uptake of reducing sugars. These findings extend our understanding of how some sugarcane varieties can naturally accumulate a high level of sucrose early in the season.     

A reference business process for ecological niche modelling

Ecological niche modelling combines species occurrence points with environmental raster layers in order to obtain models for describing the probabilistic distribution of species. The process to generate an ecological niche model is complex. It requires dealing with a large amount of data, use of different software packages for data conversion, for model generation and for different types of processing and analyses, among other functionalities. A software platform that integrates all requirements under a single and seamless interface would be very helpful for users. Furthermore, since biodiversity modelling is constantly evolving, new requirements are constantly being added in terms of functions, algorithms and data formats. This evolution must be accompanied by any software intended to be used in this area. In this scenario, a Service-Oriented Architecture (SOA) is an appropriate choice for designing such systems. According to SOA best practices and methodologies, the design of a reference business process must be performed prior to the architecture definition. The purpose is to understand the complexities of the process (business process in this context refers to the ecological niche modelling problem) and to design an architecture able to offer a comprehensive solution, called a reference architecture, that can be further detailed when implementing specific systems. This paper presents a reference business process for ecological niche modelling, as part of a major work focused on the definition of a reference architecture based on SOA concepts that will be used to evolve the openModeller software package for species modelling. The basic steps that are performed while developing a model are described, highlighting important aspects, based on the knowledge of modelling experts. In order to illustrate the steps defined for the process, an experiment was developed, modelling the distribution of Ouratea spectabilis (Mart.) Engl. (Ochnaceae) using openModeller. As a consequence of the knowledge gained with this work, many desirable improvements on the modelling software packages have been identified and are presented. Also, a discussion on the potential for large-scale experimentation in ecological niche modelling is provided, highlighting opportunities for research. The results obtained are very important for those involved in the development of modelling tools and systems, for requirement analysis and to provide insight on new features and trends for this category of systems. They can also be very helpful for beginners in modelling research, who can use the process and the experiment example as a guide to this complex activity.     

Changes in the sugarcane metabolome with stem development. Are they related to sucrose accumulation?

Sucrose content increases with internode development down the stem of sugarcane. In an attempt to determine which other changes in metabolites may be linked to sucrose accumulation gas chromatography-mass spectrometry was used to obtain metabolic profiles from methanol/water extracts of four samples of different age down the stem of cultivar Q117. Extracts were derivatized with either N-methyl-N-(trimethylsilyl) trifluoracetamide (TMS) or N-methyl N-(tert-butyldimethylsilyl) trifluoroacetamide (TBS) separately in order to increase the number of metabolites that could be detected. This resulted in the measurement of 121 and 71 metabolites from the TMS and TBS derivatization, respectively. Fifty-five metabolites were identified using commercial and publicly available libraries. Statistical analysis of the metabolite profiles resulted in clustering of tissue types. Particular metabolites were correlated with the level of sucrose accumulation, which as expected increased down the stem. Metabolites, such as tricarboxylic acid cycle intermediates and amino acids, were more abundant in the M2 sample (meristem to internode 2) that was actively growing and decreased in an apparently coordinated developmentally programmed manner in more mature internodes down the stem. However, other metabolites such as trehalose and raffinose showed positive correlations with sucrose concentration. Here we discuss the technique used to measure metabolites in sugarcane and the changes in metabolite abundance down the sugarcane stem.     

Evidence for the uptake of sucrose intact into sugarcane internodes

Application of [¹⁴C]fructosyl sucrose was used to determine whether sucrose cleavage was necessary for sucrose uptake by sugarcane (Saccharum spp.) internode tissue. Although approximately 25% of ¹⁴C in the apoplast was present as fructose, indicating some sucrose cleavage, less than 15% of the label was randomized in the sucrose that remained in the tissue after a 30 minute osmoticum rinse. This is insufficient to support cleavage and resynthesis as the sole sucrose transport scheme. The lack of randomization of label between the glucose and fructose moieties of the sucrose molecule was taken as presumptive evidence that sucrose does not have to be cleaved prior to uptake by parenchyma cells in sugarcane internode tissue.     

W3-SWEET: Carbohydrate Modeling By Internet

The software tool SWEET accessible through Internet is described which rapidly converts the commonly used sequence information of complex carbohydrates directly into a preliminary but reliable 3D model. The basic idea is to link preconstructed 3D molecular templates of monosaccharides in a specific way of binding as defined in the sequence information. In a subsequent step a fast routine to explore the conformational space for each glycosidic linkage has been implemented. Systematic rotations around the glycosidic linkages are performed, calculating the van der Waals interactions for each step of rotation. The user interaction is supported by an input spreadsheet consisting of a grid of sugar symbol and connection type cells. Several ways to visualise and to output the generated structures and related information are implemented. Since interactivity is an absolute prerequisite for each WWW application, the limitations of the approach are discussed in detail. SWEET will open modelling techniques to a broader range of users, especially for those who do not have access to the required hard- and software equipment.     

Sucrose accumulation in sugarcane: a potential target for crop improvement

Sugarcane is a highly productive crop plant with the capacity of storing large amounts of sucrose. Sucrose accumulation in the stem of sugarcane has been studied extensively. The initial recognition and characterization of the enzymes involved in sucrose synthesis and cleavage led to the widely accepted models of how sucrose accumulation occurs in the storage tissue. New insights were gained into the physiological role of individual enzyme activities in the process of sucrose accumulation in sugarcane. Studies on cell cultures and on isolated cell fragments initially supported and strengthened these models, but more recent research has revealed their weaknesses. A dynamic model of rapid cycling of sucrose and turnover of sucrose between vacuole, metabolic and apoplastic compartments explains much of the data, but the details of how the cycling is regulated needs to be explored. Genomic research into sucrose metabolism has been based on the premise that cataloging genes expressed in association with the stalk development would ultimately lead to the identification of genes controlling the accumulation of sucrose. Considerable progress has been made in understanding and manipulating the sugarcane genome using biotechnological and cell biology approaches. Thus, the greater understanding of physiology of sucrose accumulation and the sugarcane genome will play a significant role in the future sugarcane improvement programs and will offer new opportunities to develop it as a new-generation industrial crop.     

Kinetic model of sucrose accumulation in maturing sugarcane culm tissue

Biochemically, it is not completely understood why or how commercial varieties of sugarcane (Saccharum officinarum) are able to accumulate sucrose in high concentrations. Such concentrations are obtained despite the presence of sucrose synthesis/breakdown cycles (futile cycling) in the culm of the storage parenchyma. Given the complexity of the process, kinetic modelling may help to elucidate the factors governing sucrose accumulation or direct the design of experimental optimisation strategies. This paper describes the extension of an existing model of sucrose accumulation (Rohwer, J.M., Botha, F.C., 2001. Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 358, 437-445) to account for isoforms of sucrose synthase and fructokinase, carbon partitioning towards fibre formation, and the glycolytic enzymes phosphofructokinase (PFK), pyrophosphate-dependent PFK and aldolase. Moreover, by including data on the maximal activity of the enzymes as measured in different internodes, a growth model was constructed that describes the metabolic behaviour as sugarcane parenchymal tissue matures from internodes 3-10. While there was some discrepancy between modelled and experimentally determined steady-state sucrose concentrations in the cytoplasm, steady-state fluxes showed a better fit. The model supports a hypothesis of vacuolar sucrose accumulation against a concentration gradient. A detailed metabolic control analysis of sucrose synthase showed that each isoform has a unique control profile. Fructose uptake by the cell and sucrose uptake by the vacuole had a negative control on the futile cycling of sucrose and a positive control on sucrose accumulation, while the control profile for neutral invertase was reversed. When the activities of these three enzymes were changed from their reference values, the effects on futile cycling and sucrose accumulation were amplified. The model can be run online at the JWS Online database (http://jjj.biochem.sun.ac.za/database/uys).     

Population modeling for a captive squirrel monkey colony

Population modeling for a squirrel monkey colony breeding in a captive laboratory environment was approached with the use of two different mathematical modeling techniques. Deterministic modeling was used initially on a spreadsheet to estimate future census figures for animals in various age/sex classes. Historical data were taken as input parameters for the model, combined with harvesting policies to calculate future population figures in the colony. This was followed by a more sophisticated stochastic model that is capable of accommodating random variations in biological phenomena, as well as smoothing out measurement errors. Point estimates (means) for input parameters used in the deterministic model are replaced by probability distributions fitted into historical data from colony records. With the use of Crystal Ball (Decisioneering, Inc., Denver, CO) software, user-selected distributions are embedded in appropriate cells in the spreadsheet model. A Monte Carlo simulation scheme running within the spreadsheet draws (on each cycle) random values for input parameters from the distribution embedded in each relevant cell, and thus generates output values for forecast variables. After several thousand runs, a distribution is formed at the output end representing estimates for population figures (forecast variables) in the form of probability distributions. Such distributions provide the decision-maker with a mathematical habitat for statistical analysis in a stochastic setting. In addition to providing standard statistical measures (e.g., mean, variance, and range) that describe the location and shape of the distribution, this approach offers the potential for investigating crucial issues such as conditions surrounding the plausibility of extinction.     

Software for quantitation and visualization of expression array data

Software is described that facilitates the analysis of phosphoimages from large array hybridizations. The Macintosh PowerPC-compatible application and its manual are available at no charge from http:?people.bu.edu/strehlow. The software is compatible with both custom formats and array filters from three commercial manufacturers. It allows the rapid quantitation of every spot on images of hybridizations to large arrays. The user drags grids of squares over the spots on the image to define the coordinates of each spot, then aligns and edits the position of the grid. The software then corrects the positions as necessary and quantitates up to 27,000 spots per image. It stores the numerical values for each signal in a format called the fingerprint file. Fingerprint files can be directly averaged or compared, allowing the user to find mean values or differences in data from independent hybridization experiments. Data can be recalled from the fingerprint file and can be output in a variety of spreadsheet formats with several options for background correction. Finally, the software offers an output format that allows the convenient visualization of data points using animated, three-dimensional graphs.     

Sugarcane Internode Composition During Crop Development

Sugarcane sugar and bagasse can be utilized for the production of ethanol or other biofuels. A better understanding of the changes in composition with development along the stalk and with crop development will maximize the usage of sugarcane for this purpose. Two experiments were designed to elucidate internode composition changes during the growing season. In experiment 1, an internode of stalks of 5 modern cultivars were marked at the start of elongation, and then sampled every 1 to 2?weeks from July until October. Sugars were extracted and assayed, and a sequential detergent method was used to estimate hemicellulose, cellulose, and lignin contents. In experiment 2, internodes 1, 3, 5, 7, 9, and 11 down the stalk were sampled in late July (grand growth) and late September (ripening). Internode length, fresh weight, dry weight, water content, and sugar contents were determined as well as cell wall composition. Both experiments were repeated in 2?years. As internodes elongated, total sugar increased, and hemicellulose decreased as a proportion of neutral detergent fiber, while cellulose and lignin increased. After elongation, sucrose and lignin increased, and cellulose content decreased with internode age. The variability in cell wall composition among the five cultivars suggests that selection for desirable composition may be possible. In Experiment 2, hemicellulose contents were lower, and lignin and ash contents were higher at ripening than during grand growth. Delaying sugarcane harvest to maximize sucrose content may decrease bagasse suitability for cellulosic ethanol production because of the increased lignin content.     

Carbon allocation to the insoluble fraction,respiration and triose-phosphate cycling in the sugarcane culm

The changes in carbon allocation to non-sucrose metabolic pathways were investigated in developing internodes of sugarcane. Radiolabelling studies were done on internode 3, 6 and 9 tissues, representing three stages of increasing maturity. Carbon partitioning into sucrose increased from 34% of total ¹⁴C uptake in internode 3, to 66% in internodes 9. In immature tissue, the protein and fibre components were the dominant competing sinks with sucrose for incoming carbon, to which 14 and 16% of carbon was allocated. Increased carbon allocation to sucrose with tissue maturity coincided with a decrease in partitioning to fibre and total respiration. Between internodes 3 and 9 carbon allocation to total respiration decreased by 9%, and to fibre by 14%. Carbon cycling between the triose- and hexose phosphate pools was evident in all internodes. More than 90% of carbon entering triose-phosphates was returned to hexose in internode 3 tissue, and this flux decreased with tissue maturity.     

Molecular modelling and simulations in cancer research

The complexity of cancer and the vast amount of experimental data available have made computer-aided approaches necessary. Biomolecular modelling techniques are becoming increasingly easier to use, whereas hardware and software are becoming better and cheaper. Cross-talk between theoretical and experimental scientists dealing with cancer-research from a molecular approach, however, is still uncommon. This is in contrast to other fields, such as amyloid-related diseases, where molecular modelling studies are widely acknowledged. The aim of this review paper is therefore to expose some of the more common approaches in molecular modelling to cancer scientists in simple terms, illustrating success stories while also revealing the limitations of computational studies at the molecular level.     

甘蔗种质资源自然条件下耐寒性评价

为了解广西农业科学院甘蔗研究所种质资源圃(南宁)保存的400份甘蔗种质材料的耐寒性表现,在2008年初低温灾害的自然条件下,以蔗茎节间受害指数和节间生长点受害指数为基础,通过系统聚类方法将参试材料分为不同耐寒性表现类群。结果表明,2008年初的低温灾害属于阴雨霜冻类型,400份甘蔗种质材料可分为5个耐寒性表现类群,耐寒性强的材料有226份(56.50%),耐寒性较强的材料有103份(26.75%),耐寒性一般的材料有53份(13.25%),耐寒性较差的材料有7份(1.75%),耐寒性差的材料有7份(1.75%)。可构建甘蔗耐寒性指数(CTI):CTI=0.3×节间受害指数+0.7×节间生长点受害指数。节间生长点对低温伤害的敏感性高于蔗茎节间组织,建议作为耐寒性评价的重要指标之一;甘蔗耐寒性指数可以用于评价阴雨霜冻灾害下甘蔗种质材料的耐寒性。     

Metabolic Changes Associated with the Sink-Source Transition During Sprouting of the Axillary Buds on the Sugarcane Culm

Sucrose, glucose and fructose concentrations, and sucrolytic enzyme activities were measured in the developing shoots and internodes of sprouting sugarcane setts (Saccharum spp, variety N19). The most striking change during the sink-source transition of the internode and germination of the axillary bud is a more than five-fold induction of cell wall invertase in the germinating bud. In contrast, soluble acid invertase is the main sucrose hydrolytic activity induced in the internodal tissue. A cycle of breakdown and synthesis of sucrose was evident in both the internodes and the shoots. During shoot establishment, the sucrose content decreased and the hexose content increased in the internodal tissues while both sucrose and hexoses continuously accumulated in the shoots. Over the sprouting period internode, dry mass was reduced by 25 and 30 % in plants incubated in a dark/light cycle or total darkness, respectively. Sucrose accounted for 90 % of the dry mass loss. The most significant changes in SuSy activity are in the synthesis direction in the shoots resulting in a decrease in the breakdown/synthesis ratio. In contrast the SuSy activity in the internodal tissue decrease and more so in the synthesis activity resulting in an increase in the breakdown to synthesis ratio.     

Sampling and sensitivity analyses tools (SaSAT) for computational modelling

SaSAT (Sampling and Sensitivity Analysis Tools) is a user-friendly software package for applying uncertainty and sensitivity analyses to mathematical and computational models of arbitrary complexity and context. The toolbox is built in Matlab^®, a numerical mathematical software package, and utilises algorithms contained in the Matlab^® Statistics Toolbox. However, Matlab^® is not required to use SaSAT as the software package is provided as an executable file with all the necessary supplementary files. The SaSAT package is also designed to work seamlessly with Microsoft Excel but no functionality is forfeited if that software is not available. A comprehensive suite of tools is provided to enable the following tasks to be easily performed: efficient and equitable sampling of parameter space by various methodologies; calculation of correlation coefficients; regression analysis; factor prioritisation; and graphical output of results, including response surfaces, tornado plots, and scatterplots. Use of SaSAT is exemplified by application to a simple epidemic model. To our knowledge, a number of the methods available in SaSAT for performing sensitivity analyses have not previously been used in epidemiological modelling and their usefulness in this context is demonstrated.     

Systems biology and metabolic modelling unveils limitations to polyhydroxybutyrate accumulation in sugarcane leaves; lessons for C4 engineering

In planta production of the bioplastic polyhydroxybutyrate (PHB) is one important way in which plant biotechnology can address environmental problems and emerging issues related to peak oil. However, high biomass C₄ plants such as maize, switch grass and sugarcane develop adverse phenotypes including stunting, chlorosis and reduced biomass as PHB levels in leaves increase. In this study, we explore limitations to PHB accumulation in sugarcane chloroplasts using a systems biology approach, coupled with a metabolic model of C₄ photosynthesis. Decreased assimilation was evident in high PHB‐producing sugarcane plants, which also showed a dramatic decrease in sucrose and starch content of leaves. A subtle decrease in the C/N ratio was found which was not associated with a decrease in total protein content. An increase in amino acids used for nitrogen recapture was also observed. Based on the accumulation of substrates of ATP‐dependent reactions, we hypothesized ATP starvation in bundle sheath chloroplasts. This was supported by mRNA differential expression patterns. The disruption in ATP supply in bundle sheath cells appears to be linked to the physical presence of the PHB polymer which may disrupt photosynthesis by scattering photosynthetically active radiation and/or physically disrupting thylakoid membranes.     

Downregulation of pyrophosphate: d-fructose-6-phosphate 1-phosphotransferase activity in sugarcane culms enhances sucrose accumulation due to elevated hexose-phosphate levels

Analyses of transgenic sugarcane clones with 45–95% reduced cytosolic pyrophosphate: d-fructose-6-phosphate 1-phosphotransferase (PFP, EC 2.7.1.90) activity displayed no visual phenotypical change, but significant changes were evident in in vivo metabolite levels and fluxes during internode development. In three independent transgenic lines, sucrose concentrations increased between three- and sixfold in immature internodes, compared to the levels in the wildtype control. There was an eightfold increase in the hexose-phosphate:triose-phosphate ratio in immature internodes, a significant restriction in the triose phosphate to hexose phosphate cycle and significant increase in sucrose cycling as monitored by ¹³C nuclear magnetic resonance. This suggests that an increase in the hexose-phosphate concentrations resulting from a restriction in the conversion of hexose phosphates to triose phosphates drive sucrose synthesis in the young internodes. These effects became less pronounced as the tissue matured. Decreased expression of PFP also resulted in an increase of the ATP/ADP and UTP/UDP ratios, and an increase of the total uridine nucleotide and, at a later stage, the total adenine nucleotide pool, revealing strong interactions between PPi metabolism and general energy metabolism. Finally, decreased PFP leads to a reduction of PPi levels in older internodes indicating that in these developmental stages PFP acts in the gluconeogenic direction. The lowered PPi levels might also contribute to the absence of increases in sucrose contents in the more mature tissues of transgenic sugarcane with reduced PFP activity.