Density-dependence across dispersal stages in a hermaphrodite land snail: insights from discrete choice models

Dispersal movements, i.e. movements leading to gene flow, are key behaviours with important, but only partially understood, consequences for the dynamics and evolution of populations. In particular, density-dependent dispersal has been widely described, yet how it is determined by the interaction with individual traits, and whether density effects differ between the three steps of dispersal (departure, transience, and settlement), remains largely unknown. Using a semi-natural landscape, we studied dispersal choices of Cornu aspersum land snails, a species in which negative effects of crowding are well documented, and analysed them using dispersal discrete choice models, a new method allowing the analysis of dispersal decisions by explicitly considering the characteristics of all available alternatives and their interaction with individual traits. Subadults were more dispersive than adults, confirming existing results. In addition, departure and settlement were both density dependent: snails avoided crowded patches at both ends of the dispersal process, and subadults were more reluctant to settle into crowded patches than adults. Moreover, we found support for carry-over effects of release density on subsequent settlement decisions: snails from crowded contexts were more sensitive to density in their subsequent immigration choices. The fact that settlement decisions were informed indicates that costs of prospecting are not as important as previously thought in snails, and/or that snails use alternative ways to collect information, such as indirect social information (e.g. trail following). The observed density-dependent dispersal dynamics may play an important role in the ability of C. aspersum to successfully colonise frequently human-disturbed habitats around the world.     

Rapid label‐free quantitative analysis of the E. coli BL21(DE3) inner membrane proteome

Biological membranes define cells and cellular compartments and are essential in regulating bidirectional flow of chemicals and signals. Characterizing their protein content therefore is required to determine their function, nevertheless, the comprehensive determination of membrane‐embedded sub‐proteomes remains challenging. Here, we experimentally characterized the inner membrane proteome (IMP) of the model organism E. coli BL21(DE3). We took advantage of the recent extensive re‐annotation of the theoretical E. coli IMP regarding the sub‐cellular localization of all its proteins. Using surface proteolysis of IMVs with variable chemical treatments followed by nanoLC‐MS/MS analysis, we experimentally identified ～45% of the expressed IMP in wild type E. coli BL21(DE3) with 242 proteins reported here for the first time. Using modified label‐free approaches we quantified 220 IM proteins. Finally, we compared protein levels between wild type cells and those over‐synthesizing the membrane‐embedded translocation channel SecYEG proteins. We propose that this proteomics pipeline will be generally applicable to the determination of IMP from other bacteria.     

Spermidine triggering effect to the signal transduction through the AtoS–AtoC/Az two-component system in Escherichia coli

Recent analysis revealed that, in Escherichia coli the AtoS–AtoC/Az two-component system (TCS) and its target atoDAEB operon regulate the biosynthesis of short-chain poly-(R)-3-hydroxybutyrate (cPHB) biosynthesis, a biopolymer with many physiological roles, upon acetoacetate-mediated induction. We report here that spermidine further enhanced this effect, in E. coli that overproduces both components of the AtoS–AtoC/Az TCS, without altering their protein levels. However, bacteria that overproduce either AtoS or AtoC did not display this phenotype. The extrachromosomal introduction of AtoS–AtoC/Az in an E. coli ΔatoSC strain restored cPHB biosynthesis to the level of the atoSC⁺ cells, in the presence of the polyamine. Lack of enhanced cPHB production was observed in cells overproducing the TCS that did not have the atoDAEB operon. Spermidine attained the cPHB enhancement through the AtoC/Az response regulator phosphorylation, since atoC phosphorylation site mutants, which overproduce AtoS, accumulated less amounts of cPHB, compared to their wild-type counterparts. Exogenous addition of N⁸-acetyl-spermidine resulted in elevated amounts of cPHB but at lower levels than those attained upon spermidine addition. Furthermore, AtoS–AtoC/Az altered the intracellular distribution of cPHB according to the inducer recognized by the TCS. Overall, AtoS–AtoC/Az TCS was induced by spermidine to regulate both the biosynthesis and the intracellular distribution of cPHB in E. coli.     

The use of an oil absorber as a strategy to overcome starvation periods in degrading 1,2-dichloroethane in waste gas

This work investigates the use of an oil absorber as an operational strategy in vapor phase bioreactors exposed to starvation periods, during the treatment of inhibitory pollutants. After being exposed to 1,2-dichloroethane (DCE) starvation periods, the response and stability of a combined oil-absorber-bioscrubber (OAB) system was compared to that of a bioscrubber only (BO) system. In the BO system, after a 5.2 days starvation period, the DCE removal efficiency was reduced to 12%, and 6 days were needed to recover the initial removal efficiency when the DCE feed resumed. The total organic discharged (TOD(DCE)) was 16,500 g(DCE) m(bioscrubber) (-3) after the DCE starvation. Biomass analysis performed using fluorescence in situ hybridisation (FISH) showed that the microbial activity was significantly reduced during the starvation period and that 5 days were needed to recover the initial activity, after the re-introduction of DCE. In contrast, the performance of the OAB system was stable during 5.2 days of DCE starvation. The DCE removal efficiency was not affected when the DCE feed resumed and the TOD(DCE) was significantly reduced to 2,850 g(DCE) m(bioscrubber) (-3). During starvation, the activity of the microbial culture in the OAB system showed a substantially lower decrease than in the BO system and recovered almost immediately the initial activity after the re-introduction of DCE. Additionally, a mathematical model describing the performance of the OAB system was developed. The results of this study show that the OAB system can effectively sustain the biological treatment of waste gas during starvation periods of inhibitory pollutants.     

Molecular modeling and functional analysis of the AtoS-AtoC two-component signal transduction system of Escherichia coli

The AtoS-AtoC two-component signal transduction system positively regulates the expression of the atoDAEB operon in Escherichia coli. Upon acetoacetate induction, AtoS sensor kinase autophosphorylates and subsequently phosphorylates, thereby activating, the response regulator AtoC. In a previous work we have shown that AtoC is phosphorylated at both aspartate 55 and histidine73. In this study, based on known three-dimensional structures of other two component regulatory systems, we modeled the 3D-structure of the receiver domain of AtoC in complex with the putative dimerization/autophosphorylation domain of the AtoS sensor kinase. The produced structural model indicated that aspartate 55, but not histidine 73, of AtoC is in close proximity to the conserved, putative phosphate-donor, histidine (H398) of AtoS suggesting that aspartate 55 may be directly involved in the AtoS-AtoC phosphate transfer. Subsequent biochemical studies with purified recombinant proteins showed that AtoC mutants with alterations of aspartate 55, but not histidine 73, were unable to participate in the AtoS-AtoC phosphate transfer in support of the modeling prediction. In addition, these AtoC mutants displayed reduced DNA-dependent ATPase activity, although their ability to bind their target DNA sequences in a sequence-specific manner was found to be unaltered.     

Dry reagent dipstick test combined with 23S rRNA PCR for molecular diagnosis of bacterial infection in arthroplasty

Periprosthetic joint infections present a challenging problem in orthopaedics. Conventional methods for detection of arthroplasty infections rely on bacterial culture of synovial fluid aspirates. During recent years, however, molecular tests that are based on DNA amplification by the polymerase chain reaction (PCR), followed by electrophoretic analysis of the products, have been introduced. We report a simple and inexpensive assay that allows visual detection and confirmation of the PCR-amplified sequences by hybridization within minutes. The assay is performed in a dry reagent dipstick format (strip) and does not require special instrumentation. Universal primers are used for PCR of the 23S ribosomal RNA (rRNA) gene. The biotinylated amplification product is hybridized with dA-tailed probes that are specific for six pathogens commonly involved in periprosthetic joint infections. The mixture is applied to the strip, which is then immersed in the appropriate buffer. The buffer migrates along the strip by capillary action and rehydrates gold nanoparticles with oligo(dT) strands attached to their surface. The nanoparticles bind to the target DNA through hybridization, and the hybrids are captured by immobilized streptavidin at the test zone of the strip, producing a characteristic red line. Unbound nanoparticles are captured by immobilized oligo(dT) strands at the control zone of the strip, generating a second line. The dipstick test was applied to the detection of Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Enterococcus faesium, and Haemophilus influenza. Twelve samples of synovial fluids from patients were analyzed for the detection and identification of the infection caused by the six pathogens. The results were compared with bacterial cultures.     

Isolation of a bacterial consortium able to degrade the fungicide thiabendazole: the key role of a Sphingomonas phylotype

Thiabendazole (TBZ) is a fungicide used in fruit-packaging plants. Its application leads to the production of wastewaters requiring detoxification. In the absence of efficient treatment methods, biological depuration of these effluents could be a viable alternative. However, nothing is known regarding the microbial degradation of the recalcitrant and toxic to aquatics TBZ. We report the isolation, via enrichment cultures from a polluted soil, of the first bacterial consortium able to rapidly degrade TBZ and use it as a carbon source. Repeated efforts using various culture-dependent approaches failed to isolate TBZ-degrading bacteria in axenic cultures. Denaturating gradient gel electrophoresis (DGGE) and cloning showed that the consortium was composed of α-, β- and γ-Proteobacteria. Culture-independent methods including antibiotics-driven selection with DNA/RNA-DGGE, q-PCR and stable isotope probing (SIP)-DGGE identified a Sphingomonas phylotype (B13) as the key degrading member. Cross-feeding studies with structurally related chemicals showed that ring substituents of the benzimidazole moiety (thiazole or furan rings) favoured the cleavage of the imidazole moiety. LC-MS/MS analysis verified that TBZ degradation proceeds via cleavage of the imidazole moiety releasing thiazole-4-carboxamidine, which was not further transformed, and the benzoyl moiety, possibly as catechol, which was eventually consumed by the bacterial consortium as suggested by SIP-DGGE.

     

The Effect of Fused 12-Membered Nickel Metallacrowns on DNA and their Antibacterial Activity

The synthesis, characterization and the biological study of a series of Ni(ll)₂(carboxylato)₂ [12- MC_{Ni(II)N(shi)2(pko)2}-4][12-MC_{Ni(ii)N(sh03(pko)}-4] (CH₃OH)₃(H₃O) fused 12-membered metallacrowns with 10 metal ions and commercial available herbicides or anti-inflammatory drugs as carboxylato ligands are reported. All the compounds have a mixed ligand composition with salicylhydroxamic acid and di-2-pyridylketonoxime as chelate agents. The compounds construct metallacrown cores {[12-MC_{Ni(n)N(sj02(pko)2}-4][12-MC_{Ni(ll)N(shO3(pko)}-4]}²⁺ following the pattern [-Ni-O-N-]₄. The neutral decanuclear [Ni(II)(A)]₂[12-MC_{Ni(II)N(shi)2(pko)2}-4][12-MC_{Ni(II)N(pko)3(pko)}-4] fused metallacrown, consists of two [12-MC_{M(ox)N(ligand)}-4] units the {Ni(ll)(A)[12-MC_{Ni(II)N(shi)2(pko)2}-4]} and {Ni(II)(A)[12-MC_{Ni(II)N(shi)3(pko)}-4]} with 1⁺ and 1^- charge, respectively. Each metallacrown unit has four ring Ni(II) ions and one additional encapsulated Ni(II) ion in planar arrangement. The anionic unit is bonded with cationic one creating binuclear moieties. The herbicide or antiiflammatory carboxylato ligands are bridging the central octahedral nickel atom with a ring metal ion in a bindetate fashion. The effect on DNA and their antibacterial activity was examined. The changes in the mobility can be attributed to the altered structures of the pDNA treated with Ni(II) complexes. Evaluating the data of the antibacterial activity of the compounds tested, we can conclude that nickel complexes present strong antibacterial activity.