Different modelling tools of aquatic ecosystems: A proposal for a unified approach

Over the last few decades, several modelling tools have been developed for the simulation of hydrodynamic and biogeochemical processes in aquatic ecosystems. Until late 70's, coupling hydrodynamic models to biogeochemical models was not common and today, problems linked to the different scales of interest remain. The time scale of hydrodynamic phenomena in coastal zone (minutes to hours) is much lower than that of biogeochemistry (few days). Over the last years, there has been an increasing tendency to couple hydrodynamic and biogeochemical models in a clear recognition of the importance of incorporating in one model the feedbacks between physical, chemical and biological processes. However, different modelling teams tend to adopt different modelling tools, with the result that benchmarking exercises are sometimes difficult to achieve in projects involving several institutions. Therefore, the objectives of this paper are to provide a quick overview of available modelling approaches for hydrodynamic and biogeochemical modelling, to help people choose among the diversity of available models, as a function of their particular needs, and to propose a unified approach to allow modellers to share software code, based on the object oriented programming potentiality. This approach is based on having object dynamic link libraries that may be linked to different model shells. Each object represents different processes and respective variables, e.g. hydrodynamic, phytoplankton and zooplankton objects. Some simple rules are proposed to link available objects to programs written in different source codes.     

Preparation of substituted anilines from nitro compounds by using supported gold catalysts

A protocol for the chemoselective hydrogenation of nitro compounds to the corresponding anilines by means of supported gold catalysts is described. Nitro groups on different compounds--containing double bonds, carbonyl, nitrile or amide groups--have been successfully hydrogenated on supported gold nanoparticles (Au/TiO2 and Au/Fe2O3), using a batch reactor under H2 pressure. Unlike other noble metals, gold shows high chemoselectivity towards reduction of the nitro group, at near-complete conversion of the substrate. The total time to carry out this protocol strongly depends on the reaction step, which is a function of the activity of the catalyst and the nature of the substrate.     

Tellurite-induced oxidative stress leads to cell death of murine hepatocarcinoma cells

Data regarding tellurium (Te) toxicity are scarce. Studies on its metabolism, performed mainly in bacteria, underline a major role of reactive oxygen species (ROS). We investigated whether tellurite undergoes redox cycling leading to ROS formation and cancer cell death. The murine hepatocarcinoma Transplantable Liver Tumor (TLT) cells were challenged with tellurite either in the presence or in the absence of different compounds as N-acetylcysteine (NAC), 3-methyladenine, BAPTA-AM, and catalase. NAC inhibition of tellurite-mediated toxicity suggested a major role of oxidative stress. Tellurite also decreased both glutathione (GSH) and ATP content by 57 and 80%, respectively. In the presence of NAC however, the levels of such markers were almost fully restored. Tellurite-mediated ROS generation was assessed both by using the fluorescent, oxidation-sensitive probe dichlorodihydrofluorescein diacetate (DCHF-DA) and electron spin resonance (ESR) spectroscopy to detect hydroxyl radical formation. Cell death occurs by a caspase-independent mechanism, as shown by the lack of caspase-3 activity and no cleavage of poly(ADP-ribose)polymerase (PARP). The presence of γ-H2AX suggests tellurite-induced DNA strand breaking, NAC being unable to counteract it. Although the calcium chelator BAPTA-AM did show no effect, the rapid phosphorylation of eIF2α suggests that, in addition to oxidative stress, an endoplasmic reticulum (ER) stress may be involved in the mechanisms leading to cell death by tellurite.     

Transcriptomics throughout the life cycle of Leishmania infantum: High down-regulation rate in the amastigote stage

Leishmania infantum is the causative agent of zoonotic visceral leishmaniasis in the Mediterranean Basin. The promastigote and amastigote stages alternate in the life cycle of the parasite, developing inside the sand-fly gut and inside mammalian phagocytic cells, respectively. High-throughput genomic and proteomic analyses have not focused their attention on promastigote development, although partial approaches have been made in Leishmania major and Leishmania braziliensis. For this reason we have studied the expression modulation of an etiological agent of visceral leishmaniasis throughout the life cycle, which has been performed by means of complete genomic microarrays. In the context of constitutive genome expression in Leishmania spp. described elsewhere and confirmed here (5.7%), we found a down-regulation rate of 68% in the amastigote stage, which has been contrasted by binomial tests and includes the down-regulation of genes involved in translation and ribosome biogenesis. These findings are consistent with the hypothesis of pre-adaptation of the parasite to intracellular survival at this stage.     

Distinct mechanisms control human naive and antigen-experienced CD8+ T lymphocyte proliferation

Human Ag-specific CD8(+) T lymphocytes are heterogeneous and include functionally distinct populations. In this study, we report that at least two distinct mechanisms control the expansion of circulating naive, memory, and effector CD8(+) T lymphocytes when exposed to mitogen or Ag stimulation. The first one leads to apoptosis and occurs shortly after in vitro stimulation. Susceptibility to cell death is prominent among primed T cell subsets, and it is inversely correlated with the size of the ex vivo Bcl-2(high) population within these subsets. Importantly, the Bcl-2(high) phenotype is associated to the proportion of responsive CD8(+) T cells, independently of their differentiation stage. The second one depends on the expression of newly synthesized cyclin-dependent kinase inhibitor p16(INK4a) that occurs in a significant fraction of T cells that had been actively cycling, leading to their cell cycle arrest upon stimulation. Strikingly, accumulation of p16(INK4a) protein preferentially occurs in naive as opposed to primed derived T lymphocytes and is not related to apoptosis. Significant levels of p16 are readily detectable in a small number of ex vivo CD8(+) T cells. Our observations reveal that activation-induced p16 expression represents an alternative process to apoptosis, limiting the proliferation potential of activated naive derived T lymphocytes.     

COPASI--a COmplex PAthway SImulator

MOTIVATION: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods. RESULTS: Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features. We discuss numerical issues with these features; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation. AVAILABILITY: The complete software is available in binary (executable) for MS Windows, OS X, Linux (Intel) and Sun Solaris (SPARC), as well as the full source code under an open source license from http://www.copasi.org.