Initial characterization of the human central proteome

Background  

On the basis of large proteomics datasets measured from seven human cell lines we consider their intersection as an approximation of the human central proteome, which is the set of proteins ubiquitously expressed in all human cells. Composition and properties of the central proteome are investigated through bioinformatics analyses.     

Induction of larval metamorphosis of the coral Acropora millepora by tetrabromopyrrole isolated from a Pseudoalteromonas bacterium

The induction of larval attachment and metamorphosis of benthic marine invertebrates is widely considered to rely on habitat specific cues. While microbial biofilms on marine hard substrates have received considerable attention as specific signals for a wide and phylogenetically diverse array of marine invertebrates, the presumed chemical settlement signals produced by the bacteria have to date not been characterized. Here we isolated and fully characterized the first chemical signal from bacteria that induced larval metamorphosis of acroporid coral larvae (Acropora millepora). The metamorphic cue was identified as tetrabromopyrrole (TBP) in four bacterial Pseudoalteromonas strains among a culture library of 225 isolates obtained from the crustose coralline algae Neogoniolithon fosliei and Hydrolithon onkodes. Coral planulae transformed into fully developed polyps within 6 h, but only a small proportion of these polyps attached to the substratum. The biofilm cell density of the four bacterial strains had no influence on the ratio of attached vs. non-attached polyps. Larval bioassays with ethanolic extracts of the bacterial isolates, as well as synthetic TBP resulted in consistent responses of coral planulae to various doses of TBP. The lowest bacterial density of one of the Pseudoalteromonas strains which induced metamorphosis was 7,000 cells mm(-2) in laboratory assays, which is on the order of 0.1-1% of the total numbers of bacteria typically found on such surfaces. These results, in which an actual cue from bacteria has been characterized for the first time, contribute significantly towards understanding the complex process of acroporid coral larval settlement mediated through epibiotic microbial biofilms on crustose coralline algae.     

PTR-ToF-MS and data mining methods: a new tool for fruit metabolomics

Proton Transfer Reaction-Mass Spectrometry (PTR-MS) in its recently developed implementation based on a time-of-flight mass spectrometer (PTR-ToF-MS) has been evaluated as a possible tool for rapid non-destructive investigation of the volatile compounds present in the metabolome of apple cultivars and clones. Clone characterization is a cutting-edge problem in technical management and royalty application, not only for apple, aiming at unveiling real properties which differentiate the mutated individuals. We show that PTR-ToF-MS coupled with multivariate and data mining methods may successfully be employed to obtain accurate varietal and clonal apple fingerprint. In particular, we studied the VOC emission profile of five different clones belonging to three well known apple cultivars, such as ??Fuji??, ??Golden Delicious?? and ??Gala??. In all three cases it was possible to set classification models which can distinguish all cultivars and some of the clones considered in this study. Furthermore, in the case of ??Gala?? we also identified estragole and hexyl 2-methyl butanoate contributing to such clone characterization. Beside its applied relevance, no data on the volatile profiling of apple clones are available so far, our study indicates the general viability of a metabolomic approach for volatile compounds in fruit based on rapid PTR-ToF-MS fingerprinting.     

Planktonic bacteria and fungi are selectively eliminated by exposure to marine macroalgae in close proximity

To test whether macroalgae affect microbial colonizers in close proximity in a phylum-specific fashion, the community richness of planktonic bacteria and fungi was analyzed with selective oligonucleotide probes targeting the Cytophaga/Flavobacterium/Bacteroides (CFB), Alphaproteobacteria and Roseobacter group and the ITS1 region of marine fungi. Naturally occuring planktonic microorganisms were incubated in the presence of macroalgae or in seawater previously conditioned with macroalgal metabolites. The red algae Ceramium rubrum and Mastocarpus stellatus as well as seawater conditioned with these algae reduced the community composition of bacteria to a greater extent than the brown alga Laminaria digitata, indicating that metabolites differed among macroalgae or that the susceptibility of planktonic bacteria towards alga-derived antimicrobials correlated with their phylogenetic affiliation. The most affected phylotypes belonged to the CFB and the Roseobacter clade. The planktonic fungal community was only affected in the presence of macroalgae and not in algal-conditioned water, but with a specificity different from that observed for bacteria. The macroalgae L. digitata and M. stellatus exhibited more pronounced antifungal effects than C. rubrum. This study demonstrates macroalgal defenses against epiphytic microorganisms based on natural delivery mechanisms of allelochemicals utilizing a culture-independent approach, thus minimizing the ecological bias inherent to culture-dependent studies based on few microbial isolates.     

The Morphostatic Limit for a Model of Skeletal Pattern Formation in the Vertebrate Limb

A recently proposed mathematical model of a “core” set of cellular and molecular interactions present in the developing vertebrate limb was shown to exhibit pattern-forming instabilities and limb skeleton-like patterns under certain restrictive conditions, suggesting that it may authentically represent the underlying embryonic process (Hentschel et al., Proc. R. Soc. B 271, 1713–1722, 2004). The model, an eight-equation system of partial differential equations, incorporates the behavior of mesenchymal cells as “reactors,” both participating in the generation of morphogen patterns and changing their state and position in response to them. The full system, which has smooth solutions that exist globally in time, is nonetheless highly complex and difficult to handle analytically or numerically. According to a recent classification of developmental mechanisms (Salazar-Ciudad et al., Development 130, 2027–2037, 2003), the limb model of Hentschel et al. is “morphodynamic,” since differentiation of new cell types occurs simultaneously with cell rearrangement. This contrasts with “morphostatic” mechanisms, in which cell identity becomes established independently of cell rearrangement. Under the hypothesis that development of some vertebrate limbs employs the core mechanism in a morphostatic fashion, we derive in an analytically rigorous fashion a pair of equations representing the spatiotemporal evolution of the morphogen fields under the assumption that cell differentiation relaxes faster than the evolution of the overall cell density (i.e., the morphostatic limit of the full system). This simple reaction–diffusion system is unique in having been derived analytically from a substantially more complex system involving multiple morphogens, extracellular matrix deposition, haptotaxis, and cell translocation. We identify regions in the parameter space of the reduced system where Turing-type pattern formation is possible, which we refer to as its “Turing space.” Obtained values of the parameters are used in numerical simulations of the reduced system, using a new Galerkin finite element method, in tissue domains with nonstandard geometry. The reduced system exhibits patterns of spots and stripes like those seen in developing limbs, indicating its potential utility in hybrid continuum-discrete stochastic modeling of limb development. Lastly, we discuss the possible role in limb evolution of selection for increasingly morphostatic developmental mechanisms.     

On-line monitoring of microbial volatile metabolites by proton transfer reaction-mass spectrometry

A method for analysis of volatile organic compounds (VOCs) from microbial cultures was established using proton transfer reaction-mass spectrometry (PTR-MS). A newly developed sampling system was coupled to a PTR-MS instrument to allow on-line monitoring of VOCs in the dynamic headspaces of microbial cultures. The novel PTR-MS method was evaluated for four reference organisms: Escherichia coli, Shigella flexneri, Salmonella enterica, and Candida tropicalis. Headspace VOCs in sampling bottles containing actively growing cultures and uninoculated culture medium controls were sequentially analyzed by PTR-MS. Characteristic marker ions were found for certain microbial cultures: C. tropicalis could be identified by several unique markers compared with the other three organisms, and E. coli and S. enterica were distinguishable from each other and from S. flexneri by specific marker ions, demonstrating the potential of this method to differentiate between even closely related microorganisms. Although the temporal profiles of some VOCs were similar to the growth dynamics of the microbial cultures, most VOCs showed a different temporal profile, characterized by constant or decreasing VOC levels or by single or multiple peaks over 24 h of incubation. These findings strongly indicate that the temporal evolution of VOC emissions during growth must be considered if characterization or differentiation based on microbial VOC emissions is attempted. Our study may help to establish the analysis of VOCs by on-line PTR-MS as a routine method in microbiology and as a tool for monitoring environmental and biotechnological processes.