ALBERT

Description: R-type bacteriocins are contractile phage tail-like structures that are bactericidal towards related bacterial species. The C-terminal region of the phage tail fiber protein determines target-binding specificity. The mutualistic bacteria Xenorhabdus nematophila and X. bovienii produce R-type bacteriocins (xenorhabdicins) that are selectively active against different Xenorhabdus species. We analyzed the P2-type remnant prophage clusters in draft sequences of nine strains of X. bovienii . The C-terminal tail fiber region in each of the respective strains was unique and consisted of mosaics of modular units. The region between the main tail fiber gene ( xbpH1 ) and the sheath gene ( xbpS1 ) contained a variable number of modules encoding tail fiber fragments. DNA inversion and module exchange between strains was involved in generating tail fiber diversity. Xenorhabdicin-enriched fractions from three different X. bovienii strains isolated from the same nematode species displayed distinct activities against each other. In one set of strains, the strain that produced highly active xenorhabdicin was able to eliminate a sensitive strain. In contrast, xenorhabdicin activity was not a determining factor in the competitive fitness of a second set of strains. These findings suggest that related strains of X. bovienii use xenorhabdicin and additional antagonistic molecules to compete against each other.

Description: Anabaena PCC7120 has two annotated toxin–antitoxin systems: MazEF and HicAB. Overexpression of either of the toxins severely inhibited the growth of Escherichia coli BL21(p lysS )(DE3). Of the two Anabaena toxins, MazF exhibited higher toxicity than HicA as evidenced by (i) 100-fold lower viability upon overexpression of MazF compared to HicA; (ii) complete loss of cell viability within 1 h of induction of MazF expression, as against 〉10 3 colony forming units mL –1 in case of HicA; (iii) inability to maintain the MazF overexpressing plasmid in E. coli cells; and (iv) neutralisation of the toxin was effective at the molar ratio of 1:1.9 for MazF:MazE and 13:1 for HicA:HicB, indicating higher antitoxin requirement for neutralisation of MazF. The growth inhibitory effect of MazF was found to be higher in lag phase cultures compared to mid-logarithmic phase cultures of E. coli , while the reverse was true for HicA. The results suggest possible distinct roles for MazEF and HicAB systems of Anabaena .

Description: Animal-associated microbiotas form complex communities, which play crucial functions for their host, including susceptibility to infections. Despite increasing attention to bats as reservoirs of zoonotic pathogens, their microbiota is poorly documented, especially for samples potentially implicated in pathogen transmission such as urine and saliva. Here, using low-biomass individual samples, we examined the composition and structure of bacterial communities excreted by insectivorous bats, focusing on three body habitats (saliva, urine and faeces). We show that niche specialisation occurs as bacterial community composition was distinct across body habitats with the majority of phylotypes being body habitat specific. Our results suggest that urine harbours more diverse bacterial communities than saliva and faeces and reveal potentially zoonotic bacteria such as Leptospira , Rickettsia , Bartonella and Coxiella in all body habitats. Our study emphasised that, in addition to the traditional use of gut-associated samples such as faeces, both urine and saliva are also of interest because of their diverse microbiota and the potential transmission of pathogenic bacteria. Our results represent a critical baseline for future studies investigating the interactions between microbiota and infection dynamics in bats.

Description: By introducing two types of zenith troposphere delay (ZTD) products in precise point positioning (PPP), we developed the ZTD-corrected PPP and the ZTD-constrained PPP, both of them reduced the PPP convergence time. Both enhanced PPP methods are examined by global empirical ZTD models and regional ZTD corrections. For global ZTD models, we verified that ZTD-corrected PPP will deviate the positioning results, while ZTD-constrained PPP could produce unbiased estimations. Therefore, the latter is utilized to study the performance of global ZTD models (ITG, GPT2w, GZTD and UNB3m). After numerous experiments, we found that the performance of ZTD models was positively related to the real ZTD accuracy, and we proposed a universal tropospheric stochastic model 2SQR(9rms) which denotes double the square of nine times ZTD rms, to constrain ZTD in PPP. The proposed model subsequently was validated by real-time static and kinematic ZTD-constrained PPP on the premise that the ZTD rms on every station was known. Compared with traditional PPP, in static PPP, the number of improved stations is increased by 15.5 per cent (ITG), 14.4 per cent (GPT2w), 11.1 per cent (GZTD) and 8.3 per cent (UNB3m). For kinematic PPP, PPP constrained by ITG model still had the best performance, the number of improved stations is increased by 14.4 per cent, after 30 min of initialization time, 13.4 cm east, 13.4 cm north and 11.7 cm up positioning accuracy was obtained, compared with 15.3 cm east, 15.3 cm north and 14.3 cm up accuracy by traditional PPP. In addition, experiments using regional ZTD corrections to enhance real-time PPP showed that both ZTD-corrected PPP and ZTD-constrained PPP can notably reduce the convergence time on the vertical component (within 15 cm).

Description: Commodity-equity return co-movements rose dramatically during the Great Recession. This development took place following what has been dubbed the "financialization" of commodity markets. We first document changes since 1995 in the relative importance of financial institutions’ activity in agricultural futures markets. We then use a structural vector autoregression (VAR) model to ascertain the role of that activity in explaining correlations between weekly grain, livestock, and equity returns from 1995–2015. We provide robust evidence that, accounting for shocks that are idiosyncratic to agricultural markets, world business cycle shocks have a substantial and long-lasting impact on the latter’s co-movements with financial markets. In contrast, changes in the intensity of financial speculation have an impact on cross-market return linkages that is shorter-lived and not statistically significant in all model specifications.

Description: We study fluctuations in the degree-2 zonal spherical harmonic coefficient of the Earth's gravity potential, C 20 , over the period 2003–2015. This coefficient is related to the Earth's oblateness and studying its temporal variations, C 20 , can be used to monitor large-scale mass movements between high and low latitude regions. We examine C 20 inferred from six different sources, including satellite laser ranging (SLR), GRACE and global geophysical fluids models. We further include estimates that we derive from measured variations in the length-of-day (LOD), from the inversion of global crustal displacements as measured by GPS, as well as from the combination of GRACE and the output of an ocean model as described by Sun et al. We apply a sequence of trend and seasonal moving average filters to the different time-series in order to decompose them into an interannual, a seasonal and an intraseasonal component. We then perform a comparison analysis for each component, and we further estimate the noise level contained in the different series using an extended version of the three-cornered-hat method. For the seasonal component, we generally obtain a very good agreement between the different sources, and except for the LOD-derived series, we find that over 90 per cent of the variance in the seasonal components can be explained by the sum of an annual and semiannual oscillation of constant amplitudes and phases, indicating that the seasonal pattern is stable over the considered time period. High consistency between the different estimates is also observed for the intraseasonal component, except for the solution from GRACE, which is known to be affected by a strong tide-like alias with a period of about 161 d. Estimated interannual components from the different sources are generally in agreement with each other, although estimates from GRACE and LOD present some discrepancies. Slight deviations are further observed for the estimate from the geophysical models, likely to be related to the omission of polar ice and groundwater changes in the model combination we use. On the other hand, these processes do not seem to play an important role at seasonal and shorter timescales, as the sum of modelled atmospheric, oceanic and hydrological effects effectively explains the observed C 20 variations at those scales. We generally obtain very good results for the solution from SLR, and we confirm that this well-established technique accurately tracks changes in C 20 . Good agreement is further observed for the estimate from the GPS inversion, showing that this indirect method is successful in capturing fluctuations in C 20 on scales ranging from intra- to interannual. Obtaining accurate estimates from LOD, however, remains a challenging task and more reliable models of atmospheric wind fields are needed in order to obtain high-quality C 20 , in particular at the seasonal scale. The combination of GRACE data and the output of an ocean model appears to be a promising approach, particularly since corresponding C 20 is not affected by tide-like aliases, and generally gives better results than the solution from GRACE, which still seems to be of rather poor quality.

Description: Many toxic insecticides used worldwide as well as some chemical warfare agents are phosphotriester derivatives. Therefore, detoxification of organophosphorus compounds has become the subject of many studies and in particular bioremediation, based on the phosphotriesterase catalysed hydrolysis of these compounds, has shown to be an effective and ecological methodology. In order to identify new bacterial phosphotriesterases, a simple and sensitive fluorimetric screening method on solid media was employed that allowed the selection of six strains with phosphotriesterase activity. Since pH and temperature are important parameters for bioremediation of contaminated soils and waters, the influence of these variables on the rate of the enzymatic hydrolysis was assessed. This study afforded notable results, being the most remarkable one the increased activity exhibited by Nocardia asteroides and Streptomyces setonii strains at 50°C, 7 and 30 times higher than at 30°C, respectively. Compared with the results obtained with Brevundimonas diminuta , whose activity is usually considered as reference, an increase of 26 and 75 times is observed, respectively.

Description: Neonicotinoids are neurotoxic systemic insecticides used in plant protection worldwide. Unfortunately, application of neonicotinoids affects both beneficial and target insects indiscriminately. Being water soluble and persistent, these pesticides are capable of disrupting both food chains and biogeochemical cycles. This review focuses on the biodegradation of neonicotinoids in soil and water systems by the bacterial community. Several bacterial strains have been isolated and identified as capable of transforming neonicotinoids in the presence of an additional carbon source. Environmental parameters have been established for accelerated transformation in some of these strains. Studies have also indicated that enhanced biotransformation of these pesticides can be accomplished by mixed microbial populations under optimised environmental conditions. Substantial research into the identification of neonicotinoid-mineralising bacterial strains and identification of the genes and enzymes responsible for neonicotinoid degradation is still required to complete the understanding of microbial biodegradation pathways, and advance bioremediation efforts.

Description: We consider a new approach to both the forward and inverse problems in post-seismic deformation. We present a method for forward modelling post-seismic deformation in a self-gravitating, heterogeneous and compressible earth with a variety of linear and nonlinear rheologies. We further demonstrate how the adjoint method can be applied to the inverse problem both to invert for rheological structure and to calculate the sensitivity of a given surface measurement to changes in rheology or time-dependence of the source. Both the forward and inverse aspects are illustrated with several numerical examples implemented in a spherically symmetric earth model.

Description: This study aimed to evaluate the survival and gene expression of Vibrio harveyi under starvation conditions. The microcosms V. harveyi were incubated in sterilized seawater for 4 weeks at room temperature. Overall, the cell numeration declined rapidly about 10 3 CFU/ml during starvation, with a tiny rebound at day 21. Scanning electron microscopy revealed that rod-shaped cells became sphere with a rippled cell surface. By polymerase chain reaction (PCR) assay, nine genes, named lux R, tox R, vhh B, fla A, top A, fur , rpo S, mre B and fts Z, were detected in the non-starved cells. In the starved cells, the expression levels of the detected genes declined substantially ranging from 0.005-fold to 0.028-fold compared to the non-starved cells performed by reverse transcription quantitative real-time PCR with 16S rRNA as the internal control. In the recovering cells, the expression levels of the detected genes, except lux R and mre B, were upregulated dramatically compared to the wild, especially top A (23.720-fold), fur (39.400-fold) and tox R (9.837-fold), validating that the expressions of both the metabolism and virulence genes were important for growth and survival of V. harveyi. The results may shed a new light on understanding of stress adaptation in bacteria.