Gene flow at major transitional areas in sea bass (Dicentrarchus labrax) and the possible emergence of a hybrid swarm

The population genetic structure of sea bass (Dicentrarchus labrax) along a transect from the Atlantic Ocean (AO) to the Eastern Mediterranean (EM) Sea differs from that of most other marine taxa in this area. Three populations (AO, Western Mediterranean [WM], EM) are recognized today, which were originally two allopatric populations. How two ancestral genetic units have evolved into three distinct units has not been addressed yet. Therefore, to investigate mechanisms that lead to the emergence of the central WM population, its current status, and its connectivity with the two parental populations, we applied 20 nuclear loci that were either gene associated or gene independent. Results confirmed the existence of three distinct gene pools, with higher differentiation at two transitional areas, the Almeria‐Oran Front (AOF) and of the Siculo‐Tunisian Strait (STS), than within any population. Significant linkage disequilibrium and heterozygote excess indicated that the STS is probably another tension zone, as already described for the AOF. Neutrality tests fail to reveal marker loci that could be driven by selection within or among metapopulations, except for locus DLA0068. Collectively, results support that the central WM population arose by trapping two tensions zones at distinct geographic locations of limited connectivity. Population assignment further revealed that WM individuals were more introgressed than individuals from the other two metapopulations. This suggests that this population might result from hybrid swarming, and was or is still seeded by genes received through the filter of each tension zone.     

Biodegradation by activated sludge and toxicity of tetracycline into a semi-industrial membrane bioreactor

Much attention has been devoted recently to the fate of pharmaceutically active compounds such as tetracycline antibiotics in soil and water. Tetracycline (TC) biodegradability by activated sludge derived from membrane bioreactor (MBR) treating swine wastewater via CO₂-evolution was evaluated by means of modified Sturm test, which was also used to evaluate its toxicity on carbon degradation. The impact of tetracycline on a semi-industrial MBR process was also examined and confronted to lab-scale experiments. After tetracycline injection in the pilot, no disturbance was detected on the elimination of organic matters and ammonium (nitrification), reaching after injection 88% and 99% respectively; only denitrification was slightly affected. Confirming the ruggedness and the superiority of membrane bioreactors over conventional bioreactors, no toxicity was observed at the considered level of TC in the pilot (20 mg TOC L⁻¹), while at lab-scale sodium benzoate biodegradation was completely inhibited from 10 mg TOC L⁻¹ TC. The origin of the activated sludge showed a significant impact on the performances, since the ultimate biodegradation was in the range −50% to −53% for TC concentrations in the range 10–20 mg TOC L⁻¹ with conventional bioreactor sludge and increased to 18% for 40 mg TOC L⁻¹ of TC with activated sludge derived from the MBR pilot. This confirmed the higher resistance of activated sludge arising from membrane bioreactor.     

flowCore: a Bioconductor package for high throughput flow cytometry

Background  

Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or drug discovery settings. However, data management and data analysis methods have not advanced sufficiently far from the initial small-scale studies to support modeling in the presence of multiple covariates.     

Visualizing HIV-1 Assembly

The assembly of an HIV-1 particle is a complex, multistep process involving several viral and cellular proteins, RNAs and lipids. While many macroscopic and fixed-cell microscopic techniques have provided important insights into the structure of HIV-1 particles and the mechanisms by which they assemble, analysis of individual particles and their assembly in living cells offers the potential of surmounting many of the limitations inherent in other approaches. In this review, we discuss how the recent application of live-cell microscopic imaging techniques has increased our understanding of the process of HIV-1 particle assembly. In particular, we focus on recent studies that have employed total internal reflection fluorescence microscopy and other single-virion imaging techniques in live cells. These approaches have illuminated the dynamics of Gag protein assembly, viral RNA packaging and ESCRT (endosomal sorting complex required for transport) protein recruitment at the level of individual viral particles. Overall, the particular advantages of individual particle imaging in living cells have yielded findings that would have been difficult or impossible to obtain using macroscopic or fixed-cell microscopic techniques.     

Correction to: Imaging plant responses to water deficit using electrical resistivity tomography

Plant and Soil - Soil microorganisms play an important role in biogeochemical cycles in terrestrial ecosystems. Increasing nitrogen (N) and phosphorus (P) deposition are likely to regulate...     

Microbial Communities Inhabiting a Rare Earth Element Enriched Birnessite-Type Manganese Deposit in the Ytterby Mine,Sweden

The dominant initial phase formed during microbially mediated manganese oxidation is a poorly crystalline birnessite-type phyllomanganate. The occurrence of manganese deposits containing this mineral is of interest for increased understanding of microbial involvement in the manganese cycle. A culture independent molecular approach is used as a first step to investigate the role of microorganisms in forming rare earth element enriched birnessite-type manganese oxides, associated with water bearing rock fractures in a tunnel of the Ytterby mine, Sweden. 16S rRNA gene results show that the chemotrophic bacterial communities are diverse and include a high percentage of uncultured unclassified bacteria while archaeal diversity is low with Thaumarchaeota almost exclusively dominating the population. Ytterby clones are frequently most similar to clones isolated from subsurface environments, low temperature milieus and/or settings rich in metals. Overall, bacteria are dominant compared to archaea. Both bacterial and archaeal abundances are up to four orders of magnitude higher in manganese samples than in fracture water. Potential players in the manganese cycling are mainly found within the ferromanganese genera Hyphomicrobium and Pedomicrobium, and a group of Bacteroidetes sequences that cluster within an uncultured novel genus most closely related to the Terrimonas. This study strongly suggest that the production of the YBS deposit is microbially mediated.