A grey future for Europe: Sciurus carolinensis is replacing native red squirrels in Italy

Introduced mammals can cause extinction of native species due to replacement competition, disease, predation or hybridization. We studied the colonization of Piedmont (NW-Italy) by American grey squirrel (Sciurus carolinensis) and its effect on the native red squirrel (Sciurus vulgaris). Presence/absence data (2 × 2 km²), of both species were (re)constructed using questionnaires, literature, existing databases, unpublished information, and direct monitoring with hair-tubes. In 1970 red squirrels were still widespread and greys were restricted to forests near the introduction site. By 1990, grey squirrels had increased their range to 220 km², which coincided with the disappearance of native squirrels from 33 squares inside this range. The invasive species continued its spread occupying an area of 2,016 km² in 2010; within this area red squirrels went extinct in 88 squares. Overall, from 1970 to 2010 red squirrel went extinct in 62 % of 2 × 2 km² (ca. 1,689 km²), and were replaced by grey squirrels. The spread of the alien species was slow in the first 20 years, but doubled in the successive two decades. Nevertheless spread was slower than in Ireland and England. Grey squirrel adapt to climate and habitats in both North and South Europe, causing extinction of the native red squirrel. A EU LIFE co-funded project with the aim to control the grey squirrel in North Italy and recent trade-restrictions and trade-ban are a first step in reducing the risk of grey squirrels invading other countries, but their effectiveness will have to be evaluated.     

Bioinformatics role of the WGCNA analysis and co-expression network identifies of prognostic marker in lung cancer

Lung cancer is the most talked about cancer in the world. It is also one of the cancers that currently has a high mortality rate. The aim of our research is to find more effective therapeutic targets and prognostic markers for human lung cancer. First, we download gene expression data from the GEO database. We performed weighted co-expression network analysis on the selected genes, we then constructed scale-free networks and topological overlap matrices, and performed correlation modular analysis with the cancer group. We screened the 200 genes with the highest correlation in the cyan module for functional enrichment analysis and protein interaction network construction, found that most of them focused on cell division, tumor necrosis factor-mediated signaling pathways, cellular redox homeostasis, reactive oxygen species biosynthesis, and other processes, and were related to the cell cycle, apoptosis, HIF-1 signaling pathway, p53 signaling pathway, NF-κB signaling pathway, and several cancer disease pathways are involved. Finally, we used the GEPIA website data to perform survival analysis on some of the genes with GS > 0.6 in the cyan module. CBX3, AHCY, MRPL12, TPGB, TUBG1, KIF11, LRRC59, MRPL17, TMEM106B, ZWINT, TRIP13, and HMMR was identified as an important prognostic factor for lung cancer patients. In summary, we identified 12 mRNAs associated with lung cancer prognosis. Our study contributes to a deeper understanding of the molecular mechanisms of lung cancer and provides new insights into drug use and prognosis.     

Three‐dimensional microscale modelling of CO2 transport and light propagation in tomato leaves enlightens photosynthesis

We present a combined three‐dimensional (3‐D) model of light propagation, CO₂ diffusion and photosynthesis in tomato (Solanum lycopersicum L.) leaves. The model incorporates a geometrical representation of the actual leaf microstructure that we obtained with synchrotron radiation X‐ray laminography, and was evaluated using measurements of gas exchange and leaf optical properties. The combination of the 3‐D microstructure of leaf tissue and chloroplast movement induced by changes in light intensity affects the simulated CO₂ transport within the leaf. The model predicts extensive reassimilation of CO₂ produced by respiration and photorespiration. Simulations also suggest that carbonic anhydrase could enhance photosynthesis at low CO₂ levels but had little impact on photosynthesis at high CO₂ levels. The model confirms that scaling of photosynthetic capacity with absorbed light would improve efficiency of CO₂ fixation in the leaf, especially at low light intensity.     

Range of the Greater Flamingo, Phoenicopterus roseus , metapopulation in the Mediterranean: new insights from Turkey

Metapopulation conservation should rely on a flyway approach aiming at assessing the spatial range of metapopulations by estimating the level of exchanges among local populations. In the western Mediterranean, Greater Flamingos have been shown to constitute a metapopulation with natal and breeding dispersal among colonies. In this paper, we examine whether this metapopulation reaches Turkey using a band-resighting study. Our results are the first evidence of natal and breeding dispersal from the western Mediterranean to Turkey, and suggest that the Gediz Delta, one of the two Turkish breeding colonies, can play a significant role in the recruitment of flamingos from the western Mediterranean. In 2003 and 2004, breeders of western Mediterranean origin accounted for more than 1.2 and 1.9% of the estimated breeding population of the Gediz Delta, respectively. Our observations also indicate that the western Mediterranean and Southwest Asia may constitute two sets of populations, which overlap in Turkey. Finally, the resightings of flamingos banded in Turkey show that post-fledging dispersal from Turkey reaches both the eastern and western Mediterranean wetlands. Future data on the natal and breeding dispersal of flamingos born in Turkey could clarify further the connection between Turkey and the western Mediterranean metapopulation.     

Microbial co-occurrence relationships in the human microbiome

The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the dental plaque) are more likely to co-occur in complementary niches. This approach thus serves to open new opportunities for future targeted mechanistic studies of the microbial ecology of the human microbiome.