Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map

Parkinson's disease (PD) is a major neurodegenerative chronic disease, most likely caused by a complex interplay of genetic and environmental factors. Information on various aspects of PD pathogenesis is rapidly increasing and needs to be efficiently organized, so that the resulting data is available for exploration and analysis. Here we introduce a computationally tractable, comprehensive molecular interaction map of PD. This map integrates pathways implicated in PD pathogenesis such as synaptic and mitochondrial dysfunction, impaired protein degradation, alpha-synuclein pathobiology and neuroinflammation. We also present bioinformatics tools for the analysis, enrichment and annotation of the map, allowing the research community to open new avenues in PD research. The PD map is accessible at http://minerva.uni.lu/pd_map.     

Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

The genus Tenacibaculum, a member of the family Flavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogen Tenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the species T. maritimum constitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoring Tenacibaculum infections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related to T. dicentrarchi, a recently described species.     

Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans

let-7 microRNA (miRNA) regulates heterochronic genes in developmental timing of the nematode Caenorhabditis elegans. Binding of miRNA to messenger RNA (mRNA) and structural features of the complex are crucial for gene silencing. We herein present the NMR solution structure of a model mimicking the interaction of let-7 miRNA with its complementary site (LCS 2) in the 3′ untranslated region (3′-UTR) of the lin-41 mRNA. A structural study was performed by NMR spectroscopy using NOE restraints, torsion angle restraints and residual dipolar couplings. The 33-nt RNA construct folds into a stem–loop structure that features two stem regions which are separated by an asymmetric internal loop. One of the stems comprises a GU wobble base pair, which does not alter its overall A-form RNA conformation. The asymmetric internal loop adopts a single, well-defined structure in which three uracils form a base triple, while two adenines form a base pair. The 3D structure of the construct gives insight into the structural aspects of interactions between let-7 miRNA and lin-41 mRNA.     

Rainfall reduction impacts rhizosphere biogeochemistry in eucalypts grown in a deep Ferralsol in Brazil

Plant and Soil - Comparing root functioning under contrasting rainfall regimes can help assessing the capacity of plant species to cope with more intense and frequent drought predicted under...     

Observations of a distinctive morphotype of killer whale (Orcinus orca), type D, from subantarctic waters

Studies have shown that killer whale (Orcinus orca) communities in high latitudes regularly comprise assemblages of sympatric ‘ecotypes’—forms that differ in morphology, behavior, and prey preferences. Although they can appear superficially similar, recent genetic evidence suggests that breeding is assortative among ecotypes within individual communities, and species-level divergences are inferred in some cases. Here, we provide information on a recently recognized ‘type D’ killer whale based on photographs of a 1955 mass stranding in New Zealand and our own six at-sea sightings since 2004. It is the most distinctive-looking form of killer whale that we know of, immediately recognizable by its extremely small white eye patch. Its geographic range appears to be circumglobal in subantarctic waters between latitudes 40°S and 60°S. School sizes are relatively large (mean 17.6; range 9–35; n = 7), and although nothing is known about the type D diet, it is suspected to include fish because groups have been photographed around longline vessels where they reportedly depredate Patagonian toothfish (Dissostichus eleginoides).     

Photoprotection and xanthophyll‐cycle activity in three marine diatoms1

Light is one of the most important factors affecting marine phytoplankton growth, and its variability in time and space strongly influences algal performance and success. The hypothesis tested in this work is that the activity of the xanthophyll cycle and the development of nonphotochemical quenching could be considered a functional trait of algal diversity. If this hypothesis is true, a relationship must exist between fast‐activated pigment variations linked to photoprotective behavior and the ecology of the species. This assumption was tested on three diatoms: Skeletonema marinoi Sarno et Zingone, Thalassiosira rotula Meunier, and Chaetoceros socialis Lauder. These three diatoms occupy different ecological niches. Strains of these diatoms were subjected to five changes in irradiance. Xanthophyll‐cycle activity, quantum yield of fluorescence, and electron transport rate were the main parameters determined. There were marked interspecific differences in xanthophyll‐cycle activity, and these differences were dependent on the light history of the cells. Chaetoceros socialis responded efficiently to changing irradiance, which might relate to its dominance during the spring bloom in some coastal areas. In contrast, T. rotula responded with a slower photoprotection activation, which seems to reflect its more offshore ecological distribution. The photoresponse of S. marinoi (a late‐winter coastal species blooming in the Adriatic Sea) was light‐history dependent, becoming photoinhibited under high light when acclimated to low light, but capable of reaching a high photoprotection level when acclimated to moderate light. Our hypothesis on the photoprotection capacity as a functional trait in microalgae seems to be validated given the results of this study.     

The basement membrane microenvironment directs the normalization and survival of bioengineered human skin equivalents.

Epithelial-mesenchymal interactions promote the morphogenesis and homeostasis of human skin. However, the role of the basement membrane (BM) during this process is not well-understood. To directly study how BM proteins influence epidermal differentiation, survival and growth, we developed novel 3D human skin equivalents (HSEs). These tissues were generated by growing keratinocytes at an air-liquid interface on polycarbonate membranes coated with individual matrix proteins (Type I Collagen, Type IV Collagen or fibronectin) that were placed on contracted Type I Collagen gels populated with dermal fibroblasts. We found that only keratinocytes grown on membranes coated with the BM protein Type IV Collagen showed optimal tissue architecture that was similar to control tissues grown on de-epidermalized dermis (AlloDerm) that contained intact BM. In contrast, tissues grown on proteins not found in BM, such as fibronectin and Type I Collagen, demonstrated aberrant tissue architecture that was linked to a significant elevation in apoptosis and lower levels of proliferation of basal keratinocytes. While all tissues demonstrated a normalized, linear pattern of deposition of laminin 5, tissues grown on Type IV Collagen showed elevated expression of alpha6 integrin, Type IV Collagen and Type VII Collagen, suggesting induction of BM organization. Keratinocyte differentiation (Keratin 1 and filaggrin) was not dependent on the presence of BM proteins. Thus, Type IV Collagen acts as a critical microenvironmental factor in the BM that is needed to sustain keratinocyte growth and survival and to optimize epithelial architecture.     

A complete collection of single‐gene deletion mutants of Acinetobacter baylyi ADP1

We have constructed a collection of single‐gene deletion mutants for all dispensable genes of the soil bacterium Acinetobacter baylyi ADP1. A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. This essentiality data set is 88% consistent with the Escherichia coli data set inferred from the Keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as essential in Pseudomonas aeruginosa are also essential in ADP1. Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2‐3 butanediol, glucose, etc.). This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches.