1.ChainRank, a chain prioritisation method for contextualisation of biological networks.
Tényi Á1,2, de Atauri P3,4, Gomez-Cabrero D5, Cano I6,7, Clarke K8, Falciani F9, Cascante M10,11, Roca J12,13, Maier D14. BMC Bioinformatics. 2016 Jan 5;17:17. doi: 10.1186/s12859-015-0864-x.
BACKGROUND: Advances in high throughput technologies and growth of biomedical knowledge have contributed to an exponential increase in associative data. These data can be represented in the form of complex networks of biological associations, which are suitable for systems analyses. However, these networks usually lack both, context specificity in time and space as well as the distinctive borders, which are usually assigned in the classical pathway view of molecular events (e.g. signal transduction). This complexity and high interconnectedness call for automated techniques that can identify smaller targeted subnetworks specific to a given research context (e.g. a disease scenario).
2.Indicators and Methods to Understand Past Environments from ExoMars Rover Drills.
Kereszturi A1, Bradak B2,3, Chatzitheodoridis E4, Ujvari G2. Orig Life Evol Biosph. 2016 Mar 31. [Epub ahead of print]
Great advances are expected during the analysis of drilled material acquired from 2 m depth by ExoMars rover, supported by the comparison to local context, and the joint use of different instruments. Textural information might be less detailed relatively to what is usually obtained at outcrops during classical geological field work on the Earth, partly because of the lack of optical imaging of the borehole wall and also because the collected samples are crushed. However sub-mm scale layering and some other sedimentary features might be identified in the borehole wall observations, or in the collected sample prior to crushing, and also at nearby outcrops. The candidate landing sites provide different targets and focus for research: Oxia Planum requires analysis of phyllosilicates and OH content, at Mawrth Vallis the layering of various phyllosilicates and the role of shallow-subsurface leaching should be emphasized. At Aram Dorsum the particle size and fluvial sedimentary features will be interesting.
3.Activated prostaglandin D2 receptors on macrophages enhance neutrophil recruitment into the lung.
Jandl K1, Stacher E2, Bálint Z3, Sturm EM1, Maric J1, Peinhaupt M1, Luschnig P1, Aringer I4, Fauland A5, Konya V6, Dahlen SE7, Wheelock CE5, Kratky D8, Olschewski A3, Marsche G1, Schuligoi R1, Heinemann A9. J Allergy Clin Immunol. 2016 Mar;137(3):833-43. doi: 10.1016/j.jaci.2015.11.012. Epub 2016 Jan 12.
BACKGROUND: Prostaglandin (PG) D2 is an early-phase mediator in inflammation, but its action and the roles of the 2 D-type prostanoid receptors (DPs) DP1 and DP2 (also called chemoattractant receptor-homologous molecule expressed on TH2 cells) in regulating macrophages have not been elucidated to date.
4.Laboratory evolution of microbial interactions in bacterial biofilms.
Martin M1, Hölscher T1, Dragoš A1, Cooper VS2, Kovács ÁT3. J Bacteriol. 2016 Apr 4. pii: JB.01018-15. [Epub ahead of print]
Microbial adaptation is conspicuous in essentially every environment but the mechanisms of adaptive evolution are poorly understood. Studying evolution in the laboratory under controlled conditions can be a tractable approach, particularly when new, discernible phenotypes evolve rapidly. This is especially the case in the spatially structured environments of biofilms, which promote the occurrence and stability of new, heritable phenotypes. Further, diversity in biofilms can give rise to nascent social interactions among coexisting mutants and enable the study of the emerging field of sociomicrobiology. Here, we review findings from laboratory evolution experiments with eitherPseudomonas fluorescensorBurkholderia cenocepaciain spatially structured environments that promote biofilm formation. In both systems, ecotypes with overlapping niches evolve and produce competitive or facilitative interactions that lead to novel community attributes, demonstrating the parallelism of adaptive processes captured in the lab.