Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism

Kinetic models of metabolism require detailed knowledge of kinetic parameters. However, due to measurement errors or lack of data this knowledge is often uncertain. The model of glycolysis in the parasitic protozoan Trypanosoma brucei is a particularly well analysed example of a quantitative metabolic model, but so far it has been studied with a fixed set of parameters only. Here we evaluate the effect of parameter uncertainty. In order to define probability distributions for each parameter, information about the experimental sources and confidence intervals for all parameters were collected. We created a wiki-based website dedicated to the detailed documentation of this information: the SilicoTryp wiki (http://silicotryp.ibls.gla.ac.uk/wiki/Glycolysis). Using information collected in the wiki, we then assigned probability distributions to all parameters of the model. This allowed us to sample sets of alternative models, accurately representing our degree of uncertainty. Some properties of the model, such as the repartition of the glycolytic flux between the glycerol and pyruvate producing branches, are robust to these uncertainties. However, our analysis also allowed us to identify fragilities of the model leading to the accumulation of 3-phosphoglycerate and/or pyruvate. The analysis of the control coefficients revealed the importance of taking into account the uncertainties about the parameters, as the ranking of the reactions can be greatly affected. This work will now form the basis for a comprehensive Bayesian analysis and extension of the model considering alternative topologies.     

Spontaneous cyclic embryonic movements in humans and guinea pigs

Motility assessment before birth can be used to evaluate the integrity of the nervous system. Sideways bending (SB) of head and/or rump, the earliest embryonic motility in both humans and guinea pigs, can be visualized sonographically. We know from other species that early embryonic motility is cyclic. This study explores the distribution of SB-to-SB intervals in human and guinea pig embryos before the appearance of more complex movements such as general movements. We hypothesized that the activity in both species is cyclic. We made 15-min sonographic recordings of SBs between 5 weeks and 0 days (5wk0d) and 7wk0d conceptional age (CA) in 18 human embryos of uncomplicated IVF pregnancies (term 38 weeks) and in 20 guinea pig embryos between 3wk4d and 4wk0d CA (term 9 weeks). SB-to-SB interval durations were categorized as long (≥10 s) or short (<10 s) intervals. For human embryos, the median values for long and short intervals were 61 s (range, 10-165 s) and 3 s (range, 1-9 s) respectively; for guinea pigs 38 s (range, 10-288 s) and 5 s (range, 1-9 s), respectively. During development, the duration of long intervals decreased while the number of short intervals increased for both species. The earliest embryonic motility in the human and guinea pig is performed cyclically with distinct developmental milestones. The resemblance of their interval development offers promising possibilities to use the guinea pig as a noninvasive animal model of external influences on motor and neural development.     

Phosphite-derivatized ruthenium-carbohydrate complexes in the catalytic hydration of nitriles. short communication

The synthesis of metal complexes with bioligands is one option to introduce chirally defined ligands to catalysts. Herein, the hydration of nitriles to the corresponding carboxamides by use of ruthenium(II) complexes is described, which were obtained by attaching derivatives of the 3,5,6-bicyclophosphite-alpha-D-glucofuranoside ligand.     

Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domain

Iron-sulfur proteins play indispensable roles in a broad range of biochemical processes. The biogenesis of iron-sulfur proteins is a complex process that has become a subject of extensive research. The final step of iron-sulfur protein assembly involves transfer of an iron-sulfur cluster from a cluster-donor to a cluster-acceptor protein. This process is facilitated by a specialized chaperone system, which consists of a molecular chaperone from the Hsc70 family and a co-chaperone of the J-domain family. The 3.0 A crystal structure of a human mitochondrial J-type co-chaperone HscB revealed an L-shaped protein that resembles Escherichia coli HscB. The important difference between the two homologs is the presence of an auxiliary metal-binding domain at the N terminus of human HscB that coordinates a metal via the tetracysteine consensus motif CWXCX(9-13)FCXXCXXXQ. The domain is found in HscB homologs from animals and plants as well as in magnetotactic bacteria. The metal-binding site of the domain is structurally similar to that of rubredoxin and several zinc finger proteins containing rubredoxin-like knuckles. The normal mode analysis of HscB revealed that this L-shaped protein preferentially undergoes a scissors-like motion that correlates well with the conformational changes of human HscB observed in the crystals.     

Substance P and secretoneurin in vitreous aspirates of patients with various vitreoretinal diseases

By means of highly sensitive radioimmunoassays, the levels of substance P (SP) and secretoneurin (SN) were detected in vitreous aspirates of patients with macular holes which served as controls, in patients with nonproliferative diabetic retinopathy (DR), active proliferative diabetic retinopathy (active PDR), inactive PDR, rhegmatogenous retinal detachment and proliferative vitreoretinopathy (PVR). Furthermore, SN-like immunoreactivities were characterized by reversed phase-HPLC. The concentration of SN was more than 20-fold higher in macular holes when compared with SP and reversed phase HPLC revealed evidence that the vitreous levels of SN represent authentic SN. SN was significantly decreased in patients with nonproliferative DR, active PDR and inactive PDR by more than 70% which seems to result from a reduced expression and/or secretion from the cilary epithelium and a reduced release from the retina both due to diabetes mellitus. By contrast SP was increased in rhegmatogenous retinal detachment most obviously due to an enhanced outflow of the peptide through retinal breaks. Despite their proangiogenic activities, SP and SN are unlikely to be involved in the pathogenesis of neovascularizations in DR because of their unchanged and reduced levels, respectively, but the low levels of both peptides may facilitate the regression of vasoproliferations following laser photocoagulation.     

Worldwide invasion of vector mosquitoes: present European distribution and challenges for Spain

An Asiatic mosquito species, Aedes albopictus, began to spread worldwide in the 1970s thanks to marine transport of tires and other goods, leading to colonization of many areas of the world. This species is a vector of major human diseases such as Dengue, Yellow Fever and the West Nile virus. In Europe, it was established in Albania and Italy and has been detected in other countries such as France; no records exist for Spain as yet. Colonization by Aedes albopictus is a major public health concern considering that the West Nile virus and several other viruses are known to circulate sporadically in the Mediterranean. Additionally, the parent species Aedes aegypti was the vector causing severe outbreaks of Dengue and Yellow Fever two centuries ago. Although Ae. aegypti was also introduced, it was eradicated from Spain. Both mosquitoes shared habitat types, diseases transmitted and many bionomic data. This article contains a review of the present Ae. albopictusdistribution range worldwide and discusses the likelihood of an establishment in Spain in view of climatological and geographical data. This revised version was published online in July 2006 with corrections to the Cover Date.     

Comparing and evaluating process-based ecosystem model predictions of carbon and water fluxes in major European forest biomes

Process‐based models can be classified into: (a) terrestrial biogeochemical models (TBMs), which simulate fluxes of carbon, water and nitrogen coupled within terrestrial ecosystems, and (b) dynamic global vegetation models (DGVMs), which further couple these processes interactively with changes in slow ecosystem processes depending on resource competition, establishment, growth and mortality of different vegetation types. In this study, four models – RHESSys, GOTILWA+, LPJ‐GUESS and ORCHIDEE – representing both modelling approaches were compared and evaluated against benchmarks provided by eddy‐covariance measurements of carbon and water fluxes at 15 forest sites within the EUROFLUX project. Overall, model‐measurement agreement varied greatly among sites. Both modelling approaches have somewhat different strengths, but there was no model among those tested that universally performed well on the two variables evaluated. Small biases and errors suggest that ORCHIDEE and GOTILWA+ performed better in simulating carbon fluxes while LPJ‐GUESS and RHESSys did a better job in simulating water fluxes. In general, the models can be considered as useful tools for studies of climate change impacts on carbon and water cycling in forests. However, the various sources of variation among models simulations and between models simulations and observed data described in this study place some constraints on the results and to some extent reduce their reliability. For example, at most sites in the Mediterranean region all models generally performed poorly most likely because of problems in the representation of water stress effects on both carbon uptake by photosynthesis and carbon release by heterotrophic respiration (R_h). The use of flux data as a means of assessing key processes in models of this type is an important approach to improving model performance. Our results show that the models have value but that further model development is necessary with regard to the representation of the some of the key ecosystem processes.