Roberto Marangoni

ELDONET – European Light Dosimeter Network. Hardware and Software

Abstract A three-channel dosimeter has been developed to measure solar radiation in the UV-B (280–315 nm), UV-A (315–400 nm) and PAR (400–700 nm) wavelength bands. A total of 31 instruments have been installed in Europe from Abisko in Northern Sweden to Gran Canaria, covering most light-climate zones. In addition, instruments are installed in India, Africa, New Zealand and South America. Seven of the instruments have been installed under water (each in conjunction with a terrestrial instrument), and two instruments are located in high mountain locations (Zugspitze, Germany and Sierra Nevada, Spain). The instruments use an integrating Ulbricht sphere and silicon photodiodes in combination with custom-made filters. All instruments are carefully calibrated to ensure a high standard of quality control and documentation. The software records all data (three light channels, external and internal temperature and depth for the underwater instruments) at 1 min intervals, displays them on a PC, stores the data on disk and transmits the data to the central server in Pisa (http://power.ib.pi.cnr.it:80/eldonet), where all available data can be seen in graphical form and downloaded as ASCII files.

VICE: a VIrtual CEll

We report on the specification and analysis of VICE, a hypothetical cell with a genome as basic as possible. We used an enhanced version of the π-calculus and a prototype running it to study the behaviour of VICE. The results of our experimentation in silico confirm that our virtual cell “survives” in an optimal environment and shows a behaviour similar to that of real prokaryotes.

A Semantic Web for bioinformatics: goals, tools, systems, applications

Network Tools and Applications in Biology (NETTAB) [1] is a series of workshops focused on the most promising and innovative Information and Communication Technologies (ICT) tools and to their usefulness in Bioinformatics. These workshops aim at introducing participants to innovative network standards and technologies that are being applied to the biology field. To this end, each year a special emphasis is given to a focus theme. Workshops also include special sessions devoted both to the general theme of the series of workshops, i.e. “Network Tools and Applications in Biology”, and to further topics selected by local organizers. Biological data integration issues were already discussed in previous editions of this series of workshops, including topics such as “CORBA and XML: towards a bioinformatics integrated network environment” (NETTAB 2001) [2], “Agents in Bioinformatics” (NETTAB 2002) [3], “Workflows management: new abilities for the biological information overflow” (NETTAB 2005) [4] and “Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics” (NETTAB 2006) [5,6]. The Seventh NETTAB workshop was held at the Computer Science Department of the University of Pisa, on June 12-15, 2007, having “A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications” as focus theme. Adjunct themes were “Algorithms in bioinformatics” and “Formal Methods for Systems Biology”. This BMC Bioinformatics Supplement includes the best papers and posters – representing all the themes - from works presented at the workshop.

Characterization of the emergent properties of a synthetic quasi-cellular system.

BackgroundThe process of solutes entrapment during liposomes formation is interesting for the investigation of the relationship between the formation of compartments and the distribution of molecules inside them; a relevant issue in the studies of the origin of life. Theoretically, when no interactions are supposed among the chemical species to be entrapped, the entrapment is described by a standard Poisson process. But very recent experimental findings show that, for small liposomes (100 nm diameter), the distribution of entrapped molecules is best described by a power-law function. This is of a great importance, as the two random processes give rise to two completely different scenarios. Here we present an in silico stochastic simulation of the encapsulation of a cell-free molecular translation system (the PURE system), obtained following two different entrapment models: a pure Poisson process, and a power-law. The protein synthesis inside the liposomes has been studied in both cases, with the aim to highlight experimental observables that could be measured to assess which model gives a better representation of the real process.ResultsFirstly, a minimal model for in vitro protein synthesis, based on the PURE system molecular composition, has been formalized. Then, we have designed a reliable experimental simulation where stochastic factors affect the reaction course inside the compartment. To this end, 24 solutes, which represent the PURE system components, have been stochastically distributed among vesicles by following either a Poisson or a power-law distribution. The course of the protein synthesis within each vesicle has been consequently calculated, as a function of vesicle size. Our study can predict translation yield in a population of small liposomes down to the attoliter (10-18 L) range. Our results show that the efficiency of protein synthesis peaks at approximately 3·10-16 L (840 nm diam.) with a Poisson distribution of solutes, while a relative optimum is found at around 10-17 L (275 nm diam.) for the power-law statistics.ConclusionsOur simulation clearly shows that the wet-lab measurement of an effective protein synthesis at smaller volumes than 10-17 L would rule out, according to our models, a Poisson distribution of solutes.

Effects of UV-B irradiation on the motility and photo motility of the marine ciliate Fabrea salina

Abstract Fabrea salina is a motile ciliate marine protozoan that belongs to the order Heterotrichida, and which exhibits photomotile reactions. We report here the results of a study on motility and phototaxis of F. salina exposed to artificial UV irradiation. The UV-A radiation component does not induce any alteration in the motile or photomotile behavior; UV-B radiation causes a significant increase in cell speed, even after short exposure times, and totally inhibits the phototactic reaction after 60 min of irradiation. The speed increase is transient, whereas the phototactic reaction is irreversibly damaged. Fluorescence measurements indicate that there is no apparent damage to one of the potential candidates for photoreception in F. salina, i.e. a hypericin-like pigment. Phototactic sensitivity curves show that a higher fluence rate is required to obtain a half-maximum response in UV-B-treated samples compared with the rate required for the controls, while the saturation level of the phototactic response is definitely lower in UV-irradiated samples. These results suggest that UV-B irradiation may damage cell structures, such as membrane channels, and may also alter important functions, such as photosensory transduction.

ELDONET – European Light Dosimeter Network: Structure and functions of the ELDONET server

The European Light Dosimeter Network (ELDONET) project has been designed with the purpose of establishing an efficient system to monitor solar radiation in Europe, in as many as possible locations. This paper describes the structure of the server that collects and processes the data acquired by the different stations belonging to the network, and makes them freely available on the Internet to the scientific community. The server is able to receive data either via FTP from the Internet or via modem and to process them looking for errors or inconsistencies. Moreover, it automatically generates graphs, Web-pages and FTP archives. The server has been active for some years in testing mode and is now fully operative.

A computational approach to the functional screening of genomes

Comparative genomics usually involves managing the functional aspects of genomes, by simply comparing gene-by-gene functions. Following this approach, Mushegian and Koonin proposed a hypothetical minimal genome, Minimal Gene Set (MGS), aiming for a possible oldest ancestor genome. They obtained MGS by comparing the genomes of two simple bacteria and eliminating duplicated or functionally identical genes. The authors raised the fundamental question of whether a hypothetical organism possessing MGS is able to live or not. We attacked this viability problem specifying in silico the metabolic pathways of the MGS-based prokaryote. We then performed a dynamic simulation of cellular metabolic activities in order to check whether the MGS-prokaryote reaches some equilibrium state and produces the necessary biomass. We assumed these two conditions to be necessary for a living organism. Our simulations clearly show that the MGS does not express an organism that is able to live. We then iteratively proceeded with functional replacements in order to obtain a genome composition that gives rise to equilibrium. We ruled out 76 of the original 254 genes in the MGS, because they resulted in duplication from a functional point of view. We also added seven genes not present in the MGS. These genes encode for enzymes involved in critical nodes of the metabolic network. These modifications led to a genome composed of 187 elements expressing a virtually living organism, Virtual Cell (ViCe), that exhibits homeostatic capabilities and produces biomass. Moreover, the steady-state distribution of the concentrations of virtual metabolites that resulted was similar to that experimentally measured in bacteria. We conclude then that ViCe is able to “live in silico.”

Odorant-binding proteins and olfactory coding in the solitary bee Osmia cornuta

Solitary bees are major pollinators but their chemical communication system has been poorly studied. We investigated olfactory coding in Osmia cornuta from two perspectives, chemical and biochemical. We identified (E)-geranyl acetone and 2-hexyl-1,3-dioxolane, specifically secreted by females and males, respectively. A transcriptome analysis of antennae revealed 48 ORs (olfactory receptors), six OBPs (odorant-binding proteins), five CSPs (chemosensory proteins), and a single SNMP (sensory neuron membrane protein). The numbers of ORs and OBPs are much lower than in the honeybee, in particular, C-minus OBPs are lacking in the antennae of O. cornuta. We have expressed all six OBPs of O. cornuta and studied their binding specificities. The best ligands are common terpene plant odorants and both volatiles produced by the bee and identified in this work.

A method for prediction of accessible sites on an mRNA sequence for target selection of hammerhead ribozymes.

Hammerhead ribozymes are short RNA molecules endowed with endoribonucleolytic activity. Their use as molecular tools for specific inhibition of gene translation is affected by many factors including the target accessibility. A method for the prediction of accessible target sites for hammerhead ribozymes within a given RNA sequence is described. This method maps all putative NUH cleavage sites (N = A, C, G, U and H = A, C, U) and picks out short flanking regions as the binding domain for the corresponding ribozyme. The probabilistic level of unfolding, accessibility score (AS), is then calculated for each target region on the basis of a comparison of all folding structures obtained for the target RNA and arranged according to the Boltzmanns distribution. At the end, a series of imposed limits gives the best target sequences endowed with highly probable accessibility and with a potentially active catalytic structure of the hammerhead sequence. A successive experimental approach to verify the effective accessibility of selected targets was used. For that, antisense oligonucleotides addressed to the coding region of bcl2 mRNA were synthesized and administered to the MCF7 human cell line. The inhibition of gene expression, as measured by western analysis of the BCL2 protein, demonstrated that all target sites selected on the basis of their putative accessibility were actually sensitive to antisense treatments while the inaccessible ones were not. The application of this target discovery method to ribozyme design is proposed in order to satisfy a crucial condition.

On representing biological systems through multiset rewriting

We model qualitative and quantitative aspects of metabolic pathways by using a stochastic version of Multiset Rewriting (SMSR). They offer a natural way of describing both the static and the dynamic aspects of metabolic pathways. We argue that, due to its simple conceptual model, SMSR may be conveniently used as an intermediate language where many higher level specification languages may be compiled (e.g., as in the security protocol example). As a first step, we show also how SMSR may be used to simulate Stochastic Petri Nets for describing metabolic pathways.