FAME, the Flux Analysis and Modeling Environment

Background

The creation and modification of genome-scale metabolic models is a task that requires specialized software tools. While these are available, subsequently running or visualizing a model often relies on disjoint code, which adds additional actions to the analysis routine and, in our experience, renders these applications suboptimal for routine use by (systems) biologists.

Results

The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps. FAME is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities. It comes with a comprehensive manual and a quick-start tutorial, and can be accessed online at http://f-a-m-e.org/.

Conclusions

With FAME, we present the community with an open source, user-friendly, web-based "one stop shop" for stoichiometric modeling. We expect the application will be of substantial use to investigators and educators alike.     

Nonaccidental properties underlie shape recognition in Mammalian and nonmammalian vision

An infinite number of 2D patterns on the retina can correspond to a single 3D object. How do visual systems resolve this ill-posed problem and recognize objects from only a few 2D retinal projections in varied exposure conditions? Theories of object recognition rely on the nonaccidental statistics of edge properties, mainly symmetry, collinearity, curvilinearity, and cotermination. These statistics are determined by the image-formation process (i.e., the 2D retinal projection of a 3D object ); their existence under a range of viewpoints enables viewpoint-invariant recognition. An important question in behavioral biology is whether the visual systems of nonmammalian animals have also evolved biases to utilize nonaccidental statistics . Here, we trained humans and pigeons to recognize four shapes. With the Bubbles technique, we determined which stimulus properties both species used to recognize the shapes. Both humans and pigeons used cotermination, the most diagnostic nonaccidental property of real-world objects, despite evidence from a model computer observer that cotermination was not the most diagnostic pictorial information in this particular task. This result reveals that a nonmammalian visual system that is different anatomically from the human visual system is also biased to recognize objects from nonaccidental statistics.     

Developmental regulation of protein kinase A expression and activity in Schistosoma mansoni

cAMP-dependent protein kinases (PKAs) are the main transducers of cAMP signalling in eukaryotic cells. Recently we reported the identification and characterisation of a PKA catalytic subunit (SmPKA-C) in Schistosoma mansoni that is required for adult schistosome viability in vitro. To gain further insights into the role of SmPKA-C in biological processes during the schistosome life cycle, we undertook a quantitative analysis of SmPKA-C mRNA expression in different life cycle stages. Our data shows that SmPKA-C mRNA expression is developmentally regulated, with the highest levels of expression in cercariae and adult female worms. To evaluate the biological role of SmPKA-C in these developmental stages, cercariae and adult worms were treated with various concentrations of PKA inhibitors. Treatment of cercariae with H-89 or PKI 14-22 amide resulted in loss of viability suggesting that, as in adults, PKA is an essential enzyme activity in this infectious larval stage. In adult worms, in vitro exposure to sub-lethal concentrations of H-89 or PKI 14-22 amide resulted in inhibition of egg production in a dose-dependent manner. Furthermore, using a murine model of schistosome infection where S. mansoni fecundity is impaired, we show that reduced rates of egg production in vivo correlate with significant reductions in SmPKA-C mRNA expression and PKA activity. Finally, restoration of parasite egg production in vivo also resulted in normalisation of SmPKA-C mRNA expression and PKA activity. Taken together, our data suggest that PKA signalling is required for cercarial viability and may play a specific role in the reproductive activity of adult worms.     

A water-centred framework to assess the effects of salinity on the growth and yield of wheat and barley

We conducted a field experiment in two alpine meadows to investigate the short-term effects of nitrogen enrichment and plant litter biomass on plant species richness, the percent cover of functional groups, soil microbial biomass, and enzyme activity in two alpine meadow communities. The addition of nitrogen fertilizer to experimental plots over two growing seasons increased plant production, as indicated by increases in both the living plant biomass and litter biomass in the Kobresia humilis meadow community. In contrast, fertilization had no significant effect on the amounts of living biomass and litter biomass in the K. tibetica meadow. The litter treatment results indicate that litter removal significantly increased the living biomass and decreased the litter biomass in the K. humilis meadow; however, litter-removal and litter-intact treatments had no impact on the amounts of living biomass and litter biomass in the K. tibetica meadow. Litter production depended on the degree of grass cover and was also influenced by nitrogen enrichment. The increase in plant biomass reflects a strong positive effect of nitrogen enrichment and litter removal on grasses in the K. humilis meadow. Neither fertilization nor litter removal had any impact on the grass biomass in the K. tibetica meadow. Sedge biomass was not significantly affected by either nutrient enrichment or litter removal in either alpine meadow community. The plant species richness decreased in the K. humilis meadow following nitrogen addition. In the K. humilis meadow, microbial biomass C increased significantly in response to the nitrogen enrichment and litter removal treatments. Enzyme activities differed depending on the enzyme and the different alpine meadow communities; in general, enzyme activities were higher in the upper soil layers (0–10 cm and 10–20 cm) than in the lower soil layers (20–40 cm). The amounts of living plant biomass and plant litter biomass in response to the different treatments of the two alpine meadow communities affected the soil microbial biomass C, soil organic C, and soil fertility. These results suggest that the original soil conditions, plant community composition, and community productivity are very important in regulating plant community productivity and microbial biomass and activity.     

Pyric Herbivory and the Nexus Between Forage,Fire and Native and Introduced Large Grazing Herbivores in Australian Tropical Savannas

Earth’s tropical savannas typically support high biomass of diverse grazing herbivores that depend on a highly fluctuating resource: high-quality forage. An annual wet–dry cycle, fire and herbivory combine to influence forage quality and availability throughout the year. In the savannas of northern Australia, a depauperate suite of large native (marsupial) herbivores (wallaroos [Osphranter spp.] and the agile wallaby [Notamacropus agilis]) compete for resources with non-native large herbivores introduced in the late nineteenth century, particularly bovines (feral and managed cattle [Bos spp.] and feral water buffalo [Bubalus bubalis]) that now dominate the landscape. Anecdotal reports of recent population declines of large macropods and negative impacts of bovines highlight the need to better understand the complex relationship between forage, fire and abundance of native and introduced large herbivores. The pyric herbivory conceptual model, which posits complex feedbacks between fire and herbivory and was developed outside Australia, predicts that native and introduced large herbivores will both respond positively to post-fire forage production in Australian savannas where they co-occur. We used grazing exclosures, forage biomass and nutrient analyses and motion-sensor camera-trapping to evaluate the overall robustness of the pyric herbivory model in the Australian context, specifically whether forage quantity and quality are impacted by herbivory, season and fire activity, and which forage attributes most influence large grazing herbivore abundance. Forage quantity, as measured by live, dead and total herbaceous biomass and proportion of biomass alive, was higher inside herbivore exclosures, even at relatively low densities of herbivores. Forage quality, as measured by fibre content, was not affected by herbivory, however, crude protein content of live herbaceous biomass was greater outside herbivore exclosures. Recent fire was an important predictor of all measures of forage quantity and quality. Recent fire occurrence decreased overall quantity (biomass) but increased quality (decreased fibre content and increased crude protein content); late dry season fires resulted in forage with the highest crude protein content. The predictions of the pyric herbivory conceptual model are consistent with observations of the feeding behaviour of introduced bovines and some large macropods in northern Australian savannas, lending support to the global generality of pyric herbivory in fire-prone grassy biomes.

     

Seasonal water availability predicts the relative abundance of C3 and C4 grasses in Australia

Aim Numerous studies have examined the climatic factors that influence the abundance of C₄ species within the grass flora (C₄ relative species richness) in various regions throughout the world, but very few have examined the relative abundance of C₄ vs. C₃ grasses (C₄ relative abundance). We sought to determine the climatic factors that influence C₄ relative abundance throughout Australia. Location Australia (including Tasmania). Methods We measured C₄ relative abundance at 168 locations and measured δ¹³C (the abundance of ¹³C relative to ¹²C) of the bone collagen of 779 kangaroos collected throughout Australia, as bone collagen δ¹³C was assumed to be proportional to the relative abundance of C₄ grasses in the diet. Results Both C₄ relative abundance and kangaroo bone collagen δ¹³C were found to have a strong positive relationship with seasonal water availability, i.e. the distribution of rainfall in the C₄ vs. C₃ growing seasons (76% and 69% of deviance explained, respectively). There was clear evidence that seasonal water availability was a better predictor of both C₄ relative abundance and bone collagen δ¹³C than other climate variables such as mean annual temperature and January daily minimum temperature. However, seasonal water availability appeared to be a relatively poor predictor of C₄ relative species richness, which was most closely related to January daily minimum temperature (90% of deviance explained). Main conclusions Our results highlight the relatively poor relationship between C₄ relative abundance and C₄ relative species richness, and suggest that these two variables may be related to different climatic factors. They also suggest that caution is required when using C₄ relative species richness to infer the relative biomass and productivity of C₄ grasses on a global scale.     

The rate of oxygen utilization by cells

The discovery of oxygen is considered by some to be the most important scientific discovery of all time—from both physical-chemical/astrophysics and biology/evolution viewpoints. One of the major developments during evolution is the ability to capture dioxygen in the environment and deliver it to each cell in the multicellular, complex mammalian body—on demand, i.e., just in time. Humans use oxygen to extract approximately 2550 calories (10.4 MJ) from food to meet daily energy requirements. This combustion requires about 22 mol of dioxygen per day, or 2.5 × 10^− 4 mol s^− 1. This is an average rate of oxygen utilization of 2.5 × 10^− 18 mol cell^− 1 s^− 1, i.e., 2.5 amol cell^− 1 s^− 1. Cells have a wide range of oxygen utilization, depending on cell type, function, and biological status. Measured rates of oxygen utilization by mammalian cells in culture range from < 1 to > 350 amol cell^− 1 s^− 1. There is a loose positive linear correlation of the rate of oxygen consumption by mammalian cells in culture with cell volume and cell protein. The use of oxygen by cells and tissues is an essential aspect of the basic redox biology of cells and tissues. This type of quantitative information is fundamental to investigations in quantitative redox biology, especially redox systems biology.     

Clathrin- and AP-2-binding sites in HIP1 uncover a general assembly role for endocytic accessory proteins

Clathrin-mediated endocytosis is a major pathway for the internalization of macromolecules into the cytoplasm of eukaryotic cells. The principle coat components, clathrin and the AP-2 adaptor complex, assemble a polyhedral lattice at plasma membrane bud sites with the aid of several endocytic accessory proteins. Here, we show that huntingtin-interacting protein 1 (HIP1), a binding partner of huntingtin, copurifies with brain clathrin-coated vesicles and associates directly with both AP-2 and clathrin. The discrete interaction sequences within HIP1 that facilitate binding are analogous to motifs present in other accessory proteins, including AP180, amphiphysin, and epsin. Bound to a phosphoinositide-containing membrane surface via an epsin N-terminal homology (ENTH) domain, HIP1 associates with AP-2 to provide coincident clathrin-binding sites that together efficiently recruit clathrin to the bilayer. Our data implicate HIP1 in endocytosis, and the similar modular architecture and function of HIP1, epsin, and AP180 suggest a common role in lipid-regulated clathrin lattice biogenesis.     

Translocation of S100A1(1) calcium binding protein during heart surgery

Myocardial ischemia during cardiopulmonary bypass terminated by reperfusion generally leads to different degrees of damage of the cardiomyocytes induced by transient cytosolic Ca(2+) overload. Recently, much attention has been paid to the role of heart-specific Ca(2+)-binding proteins in the pathogenesis of myocardial ischemia-reperfusion injury. S100A1 is a heart-specific EF-hand Ca(2+)-binding protein that is directly involved in a variety of Ca(2+)-mediated functions in myocytes. The aim of our study was to investigate the localization and translocation of S100A1 in the human heart under normal (baseline) conditions and after prolonged ischemia and reperfusion of the myocardium. Our data suggest that S100A1 is directly involved in the transient perioperative myocardial damage caused by ischemia during open heart surgery in humans. Given its role in the contractile function of muscle cells, this S100 protein could be an important "intracellular link" in ischemia-reperfusion injury of the heart.     

Species Survival in Fragmented Landscapes: Where to From Here?

We summarise the contributions of empiricists, modellers, and practitioners in this issue of Biodiversity and Conservation, and highlight the most important areas for future research on species survival in fragmented landscapes. Under the theme uncertainty in research and management, we highlight five areas for future research. First, we know little about the effects of density dependence on the viability of metapopulations, a requirement for fragmented landscapes. Second, successful early attempts suggest that it is worth developing more rigorous calibration methods for population viability analysis with spatially explicit, individual-based models. In particular, the balance between model complexity, ease of calibration, and precision, needs to be addressed. Third, we need to improve methods to discriminate between models, including alternatives to time-series approaches. Fourth, when our ability to reduce model uncertainty is weak, we need to incorporate this uncertainty in population viability analysis. Fifth, population viability analysis and decision analysis can be integrated to make uncertainty an explicit part of the decision process. An important future direction is extending the decision framework to adaptive management. Under the theme tools for quantifying risk and predicting species sensitivity to fragmentation, we highlight three areas for future research. First, we need to develop tools to support comparative approaches to population viability analysis. Second, population modelling can be used to find rules of thumb to support conservation decisions when very little is known about a species. Rules of thumb need to be extended to the problem of managing for multiple species. Third, species traits might be useful for predicting sensitivity but predictions could be further refined by considering the relative importance of population processes at different scales. Under the theme tools for reassembling fragmented landscapes, we consider the focal species approach, and highlight aspects of the approach that require more rigorous testing. Finally, we highlight two important areas for future research not presented in the previous themes or papers in this volume. First, we need to incorporate the deterministic effects of habitat modification into the modelling framework of population viability analysis. Second, an avenue of research that remains largely unexplored is the combination of landscape-scale experiments and population modelling, especially using data from existing fragmentation experiments and from experiments designed to test the effects of defragmenting landscapes.