Solid-phase microextraction (SPME) analysis of six Italian populations of Ephedra nebrodensis Tineo ex Guss. subsp. nebrodensis

Headspace solid-phase microextraction (HS-SPME) coupled with GC/FID and GC/MS was applied for the first time in the analysis of the volatile fraction of an Ephedra species. Notably, six Italian populations (Marche, Abruzzo, and Sardinia) of Ephedra nebrodensis subsp. nebrodensis, covering almost the entire Italian area, were investigated to examine the chemical variability and to support the taxonomy of the species. A fiber screening with polymethylsiloxane (PDMS), Carboxen(TM) /polymethylsiloxane (CAR/PDMS), and polymethylsiloxane/divinylbenzene (PDMS/DVB) coatings, together with an optimization of the extraction conditions were carried out before analysis of the six populations. A total of 119 volatiles were identified in the headspace of different samples, accounting for 63.35-100.00% of the total volatiles. A great variability was found in the qualitative composition of different samples, since only 18 components were in common among all populations. The headspace composition was dominated by sesquiterpene hydrocarbons (52.30-88.32%), with β-maaliene (traces-7.49%), β-patchoulene (traces-1.29%), β-panasinsene (traces-6.85%), α-isocomene (traces-31.25%), α-trans-bergamotene (traces-6.95%), alloaromadendrene (traces-33.20%), α-acoradiene (traces-9.41%), and γ-muurolene (0.61-16.33%) being the most abundant constituents. Noteworthy is the occurrence in a sample of two major unknown sesquiterpenes, one hydrocarbon (24.49%, RI: 1396) and one oxygenated compound (10.37%, RI: 1591), whose mass spectra were reported for the first time. Multivariate chemometric techniques, such as cluster analysis (CA) and principal component analysis (PCA), were used to characterize the samples according to the geographical origin.     

Cytogenetic effects of hycanthone in the rat

Hycanthone methanesulfonate (HCT), a new drug used for the treatment of schistosomiasis, was examined for its ability to produce chromosomal abnormalities in rat bone marrow cells. Rats were given intraperitoneal injections of HCT at 40, 80, or 100 mg/kg and were killed at 6, 24, or 48 h. All levels produced a significant increase cells with abnormalities at all three time periods. There was a significant linear relationship between arithmetic dose and the proportion of cells affected. Based on two of the three experiments peformed, assuming the same slope holds in the vicinity of 0, the upper 95% confidence limits on the expected risk at level of 0.5] mg/kg would be a 0.055% increase in affected cells above control values.     

In search of noise-induced bimodality

Many biological studies are carried out on large populations of cells, often in order to obtain enough material to make measurements. However, we now know that noise is endemic in biological systems and this results in cell-to-cell variability in what appears to be a population of identical cells. Although often neglected, this noise can have a dramatic effect on system responses to environmental cues with significant and often counter-intuitive biological outcomes. A recent study in BMC Systems Biology provides an example of this, documenting a bimodal distribution of activated extracellular signal-regulated kinase in a population of cells exposed to epidermal growth factor and demonstrating that the observed bimodality of the response is induced purely by noise.See research article: http://www.biomedcentral.com/1752-0509/6/109     

The SBW-MATLAB interface

SUMMARY: The SBW-MATLAB Interface allows MATLAB users to take advantage of the wide variety of tools available through SBW, the Systems Biology Workbench (Sauro et al. (2003) OMICS, 7, 355-372). It also enables MATLAB users to themselves create SBW-enabled tools which can be freely distributed.     

Effects of ozone exposure or fungal pathogen on white lupin leaves as determined by imaging of chlorophyll a fluorescence.

Chlorophyll fluorescence has been used routinely to investigate photosynthetic activity in plants subjected to both biotic and abiotic stresses. The aim of this work was to compare the perturbations in photosynthesis induced by ozone and by a pathogen. By using a conventional fluorometer a similar response pattern was observed in inoculated and O(3)-fumigated leaves. The application of chlorophyll fluorescence imaging provided further detailed information on the spatial-temporal heterogeneity of the response of white lupin leaves to fungal pathogen or to ozone fumigation. In particular, 48 h after artificial inoculation with the necrotrophic fungal pathogen Pleiochaeta setosa, the leaves showed a remarkable alteration in PSII operating efficiency (Phi(PSII)), which affected the whole surface. Afterwards, the infection site was surrounded by a ring of increased photosynthetic activity. The response of ozonated leaves was quite different. The reduction in Phi(PSII) was already evident 24h after fumigation; moreover, a distinct heterogeneity of the fluorescence yield was observed and the major veins displayed a lowered Phi(PSII).     

Enzyme-enzyme interactions and control analysis. 1. The case of non-additivity: monomer-oligomer associations

Two usual assumptions of the treatment of metabolism are: (a) the rates of isolated enzyme reactions are additive, i.e., that rate is proportional to enzyme concentration; (b) in a system, the rates of individual enzyme reactions are not influenced by interactions with other enzymes, i.e. that they are acting independently, except by being coupled through shared metabolites. On this basis, control analysis has established theorems and experimental methods for studying the distribution of control. These assumptions are not universally true and it is shown that the theorems can be modified to take account of such deviations. This is achieved by defining additional elasticity coefficients, designated by the symbol pi, which quantify the effects of homologous and heterologous enzyme interactions. Here we show that for the case of non-proportionality of rate with enzyme concentration, (pi ii not equal to 1), the summation theorems are given by (Formula: see text). The example of monomer-oligomer equilibria is used to illustrate non-additive behaviour and experimental methods for their study are suggested.     

Bifurcation discovery tool

MOTIVATION: Biochemical networks often yield interesting behavior such as switching, oscillation and chaotic dynamics. This article describes a tool that is capable of searching for bifurcation points in arbitrary ODE-based reaction networks by directing the user to regions in the parameter space, where such interesting dynamical behavior can be observed. RESULTS: We have implemented a genetic algorithm that searches for Hopf bifurcations, turning points and bistable switches. The software is implemented as a Systems Biology Workbench (SBW) enabled module and accepts the standard SBML model format. The interface permits a user to choose the parameters to be searched, admissible parameter ranges, and the nature of the bifurcation to be sought. The tool will return the parameter values for the model for which the particular behavior is observed. AVAILABILITY: The software, tutorial manual and test models are available for download at the following website: http:/www.sys-bio.org/ under the bifurcation link. The software is an open source and licensed under BSD.     

Inhibitory Effects of 1-Deazaadenosine Analogues on HIV Replication and Adenosine Deaminase

Abstract

A series of 2′,3′-dideoxy-N⁶-(cyclo)alkyl-1-deazaadenosine derivatives were synthesized starting from 2,6-dichloro-1-deazapurine (9). The new nucleosides proved to be good inhibitors of HIV-1 replication, the most active being the 2′,3′-dideoxy-2-chloro-N⁶-cycloctyl-1-deazaadenosine (14h, ED₅₀ = 0.4 μ).     

Computational tools for metabolic engineering

A great variety of software applications are now employed in the metabolic engineering field. These applications have been created to support a wide range of experimental and analysis techniques. Computational tools are utilized throughout the metabolic engineering workflow to extract and interpret relevant information from large data sets, to present complex models in a more manageable form, and to propose efficient network design strategies. In this review, we present a number of tools that can assist in modifying and understanding cellular metabolic networks. The review covers seven areas of relevance to metabolic engineers. These include metabolic reconstruction efforts, network visualization, nucleic acid and protein engineering, metabolic flux analysis, pathway prospecting, post-structural network analysis and culture optimization. The list of available tools is extensive and we can only highlight a small, representative portion of the tools from each area.