Role of the EGF +61A>G polymorphism in melanoma pathogenesis: an experience on a large series of Italian cases and controls

<p>Abstract</p> <p>Background</p> <p>A single nucleotide polymorphism (61A>G) in the epidermal growth factor (<it>EGF</it>) gene has been implicated in both melanoma pathogenesis and increased melanoma risk. To further evaluate this association, we conducted a case-control study in a clinic-based Italian population.</p> <p>Methods</p> <p>Individuals with less than 10 (N = 127) or more than 100 (N = 128) benign nevi, and patients with cutaneous melanoma (N = 418) were investigated for the <it>EGF </it>+61A>G polymorphism, using an automated sequencing approach.</p> <p>Results</p> <p>Overall, no difference in <it>EGF </it>genotype frequencies was observed among subjects with different number of nevi as well as when non-melanoma healthy controls were compared with the melanoma patients. However, a heterogeneous distribution of the frequencies of the G/G genotype was detected among cases and controls originating from North Italy (21.1 and 18.3%, respectively) vs. those from South Italy (12.6 and 17.1%, respectively).</p> <p>Conclusion</p> <p>Our findings further suggest that <it>EGF </it>+61A>G polymorphism may have a limited impact on predisposition and/or pathogenesis of melanoma and its prevalence may vary in different populations.</p

Phylogenetic organization of bacterial activity.

Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism\u27s ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.The ISME Journal advance online publication, 4 March 2016; doi:10.1038/ismej.2016.28

Secondary Metabolites of Marine Microbes: From Natural Products Chemistry to Chemical Ecology

Marine natural products (MNPs) exhibit a wide range of pharmaceutically relevant bioactivities, including antibiotic, antiviral, anticancer, or anti-inflammatory properties. Besides marine macroorganisms such as sponges, algae, or corals, specifically marine bacteria and fungi have shown to produce novel secondary metabolites (SMs) with unique and diverse chemical structures that may hold the key for the development of novel drugs or drug leads. Apart from highlighting their potential benefit to humankind, this review is focusing on the manifold functions of SMs in the marine ecosystem. For example, potent MNPs have the ability to exile predators and competing organisms, act as attractants for mating purposes, or serve as dye for the expulsion or attraction of other organisms. A large compilation of literature on the role of MNPs in marine ecology is available, and several reviews evaluated the function of MNPs for the aforementioned topics. Therefore, we focused the second part of this review on the importance of bioactive compounds from crustose coralline algae (CCA) and their role during coral settlement, a topic that has received less attention. It has been shown that certain SMs derived from CCA and their associated bacteria are able to induce attachment and/or metamorphosis of many benthic invertebrate larvae, including globally threatened reef-building scleractinian corals. This review provides an overview on bioactivities of MNPs from marine microbes and their potential use in medicine as well as on the latest findings of the chemical ecology and settlement process of scleractinian corals and other invertebrate larvae

Elemental stoichiometry of fungi and bacteria strains from grassland leaf litter

In most terrestrial environments, our knowledge of the elemental composition and stoichiometry of microorganisms stems from indirect whole community analyses. In contrast, we have little direct knowledge of the elemental composition of specific microorganisms and the variation between and within Fungi and Bacteria. To address this issue, we isolated and identified the elemental content of 87 strains of Fungi and Bacteria isolated from grassland leaf litter. The isolated strains were affiliated with a broad range of diversity including Ascomycota and Basidiomycota for Fungi, and Proteobacteria, Bacteroidetes, and Actinobacteria for Bacteria. The C:P and C:N but not N:P ratios were significantly higher in Fungi than in Bacteria. Extensive strain variation in elemental composition was partly linked to phylogeny and growth rate. Across all strains, the geometric mean C:N:P was 88:15:1. This overall ratio was significantly higher than reported for other leaf litter and terrestrial whole communities but closer to the canonical Redfield ratio characterizing marine microorganisms. This result warrants further investigation into the discrepancy between whole community and isolated strain elemental ratios. © 2014 Elsevier Ltd

Elemental stoichiometry of fungi and bacteria strains from grassland leaf litter

In most terrestrial environments, our knowledge of the elemental composition and stoichiometry of microorganisms stems from indirect whole community analyses. In contrast, we have little direct knowledge of the elemental composition of specific microorganisms and the variation between and within Fungi and Bacteria. To address this issue, we isolated and identified the elemental content of 87 strains of Fungi and Bacteria isolated from grassland leaf litter. The isolated strains were affiliated with a broad range of diversity including Ascomycota and Basidiomycota for Fungi, and Proteobacteria, Bacteroidetes, and Actinobacteria for Bacteria. The C:P and C:N but not N:P ratios were significantly higher in Fungi than in Bacteria. Extensive strain variation in elemental composition was partly linked to phylogeny and growth rate. Across all strains, the geometric mean C:N:P was 88:15:1. This overall ratio was significantly higher than reported for other leaf litter and terrestrial whole communities but closer to the canonical Redfield ratio characterizing marine microorganisms. This result warrants further investigation into the discrepancy between whole community and isolated strain elemental ratios. © 2014 Elsevier Ltd

Temporal variation overshadows the response of leaf litter microbial communities to simulated global change

Bacteria and fungi drive the decomposition of dead plant biomass (litter), an important step in the terrestrial carbon cycle. Here we investigate the sensitivity of litter microbial communities to simulated global change (drought and nitrogen addition) in a California annual grassland. Using 16S and 28S rDNA amplicon pyrosequencing, we quantify the response of the bacterial and fungal communities to the treatments and compare these results to background, temporal (seasonal and interannual) variability of the communities. We found that the drought and nitrogen treatments both had significant effects on microbial community composition, explaining 2-6% of total compositional variation. However, microbial composition was even more strongly influenced by seasonal and annual variation (explaining 14-39%). The response of microbial composition to drought varied by season, while the effect of the nitrogen addition treatment was constant through time. These compositional responses were similar in magnitude to those seen in microbial enzyme activities and the surrounding plant community, but did not correspond to a consistent effect on leaf litter decomposition rate. Overall, these patterns indicate that, in this ecosystem, temporal variability in the composition of leaf litter microorganisms largely surpasses that expected in a short-term global change experiment. Thus, as for plant communities, future microbial communities will likely be determined by the interplay between rapid, local background variability and slower, global changes

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge

Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki’s Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition