Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates

Glutamate synthase (GltS) is a complex iron-sulfur flavoprotein that catalyzes the reductive transfer of L-glutamine amide group to the C2 carbon of 2-oxoglutarate yielding two molecules of L-glutamate. Molecular dynamics calculations in explicit solvent were carried out to gain insight into the conformational flexibility of GltS and into the role played by the enzyme substrates in regulating the catalytic cycle. We have modelled the free (unliganded) form of Azospirillum brasilense GltS alpha subunit and the structure of the reduced enzyme in complex with the L-glutamine and 2-oxoglutarate substrates starting from the crystallographically determined coordinates of the GltS alpha subunit in complex with L-methionine sulphone and 2-oxoglutarate. The present 4-ns molecular dynamics calculations reveal that the GltS glutaminase site may exist in a catalytically inactive conformation unable to bind glutamine, and in a catalytically competent conformation, which is stabilized by the glutamine substrate. Substrates binding also induce (1) closure of the loop formed by residues 263-271 with partial shielding of the glutaminase site from solvent, and (2) widening of the ammonia tunnel entrance at the glutaminase end to allow for ammonia diffusion toward the synthase site. The Q-loop of glutamate synthase, which acts as an active site lid in other amidotransferases, seems to maintain an open conformation. Finally, binding of L-methionine sulfone, a glutamine analog that mimics the tetrahedral transient species occurring during its hydrolysis, causes a coordinated rigid-body motion of segments of the glutaminase domain that results in the inactive conformation observed in the crystal structure of GltS alpha subunit.     

Creating a mutant luciferase resistant to HPV chemical inhibition by random mutagenesis and colony-level screening.

Firefly luciferase covers a wide range of applications. One common usage of the bioluminescence assay is the measurement of intracellular concentration of adenosine triphosphate (ATP) for cell viability. However, inhibition of the enzyme reaction by chemicals in the assay has so far limited the application of luciferase for high production volume (HPV) chemical testing. The objective of this research was to obtain a mutant luciferase with increased stability to inhibition by HPV chemicals, yet retaining specific activity comparable to, or better than, wild-type luciferase. The enzymatic properties of the wild-type luciferase were improved by random mutagenesis and colony-level screening. In this paper, the detailed process of creating mutant luciferases for testing the toxicity of HPV chemicals is described. As a result, two mutant luciferases were created, with different degrees of improved tolerance to inhibition by chloroform and other HPV chemicals.     

Interplay between FGFR2b‐induced autophagy and phagocytosis: role of PLCγ‐mediated signalling

Signalling of the epithelial splicing variant of the fibroblast growth factor receptor 2 (FGFR2b) induces both autophagy and phagocytosis in human keratinocytes. Here, we investigated, in the cell model of HaCaT keratinocytes, whether the two processes might be related and the possible involvement of PLCγ signalling. Using fluorescence and electron microscopy, we demonstrated that the FGFR2b‐induced phagocytosis and autophagy involve converging autophagosomal and phagosomal compartments. Moreover, the forced expression of FGFR2b signalling mutants and the use of specific inhibitors of FGFR2b substrates showed that the receptor‐triggered autophagy requires PLCγ signalling, which in turn activates JNK1 via PKCδ. Finally, we found that in primary human keratinocytes derived from light or dark pigmented skin and expressing different levels of FGFR2b, the rate of phagocytosis and autophagy and the convergence of the two intracellular pathways are dependent on the level of receptor expression, suggesting that FGFR2b signalling would control in vivo the number of melanosomes in keratinocytes, determining skin pigmentation.     

Accounting for inventory data and methodological choice uncertainty in a comparative life cycle assessment: the case of integrated multi-trophic aquaculture in an offshore Mediterranean enterprise

Purpose

Integrated multi-trophic aquaculture (IMTA), growing different species in the same space, is a technology that may help manage the environmental impacts of coastal aquaculture. Nutrient discharges to seawater from monoculture aquaculture are conceptually minimized in IMTA, while expanding the farm economic base. In this study, we investigate the environmental trade-offs for a small-to-medium enterprise (SME) considering a shift from monoculture towards IMTA production of marine fish.

Methods

A comparative life cycle assessment (LCA), including uncertainty analysis, was implemented for an aquaculture SME in Italy. Quantification and simultaneous propagation of uncertainty of inventory data and uncertainty due to the choice of allocation method were combined with dependent sampling to account for relative uncertainties and statistical testing and interpretation to understand the uncertainty analysis results. Monte Carlo simulations were used as a propagation method. The environmental impacts per kilo of fish produced in monoculture and in IMTA were compared. Twelve impact categories were considered. The comparison is first made excluding uncertainty (deterministic LCA) and then accounting for uncertainties.

Results and discussion

Deterministic LCA results evidence marginal differences between the impacts of IMTA and monoculture fish production. IMTA performs better on all impacts studied. However, statistical testing and interpretation of the uncertainty analysis results showed that only mean impacts for climate change are significantly different for both productive systems, favoring IMTA. For the case study, technical variables such as scales of production of the species from different trophic levels, their integration (space and time), and the choice of species determine the trade-offs. Also, LCA methodological choices such as that for an allocation method and the treatment of relative uncertainties were determinant in the comparison of environmental trade-offs.

Conclusions

The case study showed that environmental trade-offs between monoculture and IMTA fish production depend on technical variables and methodological choices. The combination of statistical methods to quantify, propagate, and interpret uncertainty was successfully tested. This approach supports more robust environmental trade-off assessments between alternatives in LCAs with uncertainty analysis by adding information on the significance of results. It was difficult to establish whether IMTA does bring benefits given the scales of production in the case study. We recommend that the methodology defined here is applied to fully industrialized IMTA systems or bay-scale environments, to provide more robust conclusions about the environmental benefits of this aquaculture type in Europe.

     

Sodium orthovanadate associated with pharmacological doses of ascorbate causes an increased generation of ROS in tumor cells that inhibits proliferation and triggers apoptosis

Pharmacological doses of ascorbate were evaluated for its ability to potentiate the toxicity of sodium orthovanadate (Na₃VO₄) in tumor cells. Cytotoxicity, inhibition of cell proliferation, generation of ROS and DNA fragmentation were assessed in T24 cells. Na₃VO₄ was cytotoxic against T24 cells (EC₅₀ = 5.8 μM at 24 h), but in the presence of ascorbate (100 μM) the EC₅₀ fell to 3.3 μM. Na₃VO₄ plus ascorbate caused a strong inhibition of cell proliferation (up to 20%) and increased the generation of ROS (4-fold). Na₃VO₄ did not directly cleave plasmid DNA, at this aspect no synergism was found occurring between Na₃VO₄ and ascorbate once the resulting action of the combination was no greater than that of both substances administered separately. Cells from Ehrlich ascites carcinoma-bearing mice were used to determine the activity of antioxidant enzymes, the extent of the oxidative damage and the type of cell death. Na₃VO₄ alone, or combined with ascorbate, increased catalase activity, but only Na₃VO₄ plus ascorbate increased superoxide dismutase activity (up to 4-fold). Oxidative damage on proteins and lipids was higher due to the treatment done with Na₃VO₄ plus ascorbate (2–3-fold). Ascorbate potentiated apoptosis in tumor cells from mice treated with Na₃VO₄. The results indicate that pharmacological doses of ascorbate enhance the generation of ROS induced by Na₃VO₄ in tumor cells causing inhibition of proliferation and apoptosis. Apoptosis induced by orthovanadate and ascorbate is closer related to inhibition on Bcl-xL and activation of Bax. Our data apparently rule out a mechanism of cell demise p53-dependent or related to Cdk2 impairment.     

Phylogenetic affinities of Phobetinus to other pirate spider genera (Araneae: Mimetidae) as indicated by spinning field morphology

Spinnerets from Phobetinus sagittifer and an undescribed Phobetinus species were examined by scanning electron microscopy to gain a better understanding of this genus' relationships to other genera in the family Mimetidae. Consistent with placement of Phobetinus in Mimetinae, females possessed two synapomorphies of this subfamily; enlarged cylindrical silk gland spigots with domed shafts and a single cylindrical spigot per posterior lateral spinneret (PLS). Spinning field features overall suggest Phobetinus is most closely related to Mimetus, followed by Australomimetus, then Ero. A possible synapomorphy of a clade including Mimetus and Phobetinus is a pair of modified piriform silk gland spigots on each anterior lateral spinneret of adult males located adjacent to the secondary major ampullate silk gland tartipore. These spigots were present in P. sagittifer; however, similarly positioned spigots in the undescribed species were not obviously modified (i.e., wider or with larger openings relative to the other piriform spigots). Close affinity to Mimetus was also indicated by tartipore-accommodated PLS aciniform silk glands in both Phobetinus species. These have been consistently observed in Mimetus, but not in Australomimetus or Ero. Somatic and genitalic drawings of P. sagittifer are provided to aid identification and similarities are noted between male pedipalps of Mimetus and Phobetinus.     

Metformin Attenuates the Exacerbation of the Allergic Eosinophilic Inflammation in High Fat-Diet-Induced Obesity in Mice

A positive relationship between obesity and asthma has been well documented. The AMP-activated protein kinase (AMPK) activator metformin reverses obesity-associated insulin resistance (IR) and inhibits different types of inflammatory responses. This study aimed to evaluate the effects of metformin on the exacerbation of allergic eosinophilic inflammation in obese mice. Male C57BL6/J mice were fed for 10 weeks with high-fat diet (HFD) to induce obesity. The cell infiltration and inflammatory markers in bronchoalveolar lavage (BAL) fluid and lung tissue were evaluated at 48 h after ovalbumin (OVA) challenge. HFD obese mice displayed peripheral IR that was fully reversed by metformin (300 mg/kg/day, two weeks). OVA-challenge resulted in higher influx of total cell and eosinophils in lung tissue of obese mice compared with lean group. As opposed, the cell number in BAL fluid of obese mice was reduced compared with lean group. Metformin significantly reduced the tissue eosinophil infiltration and prevented the reduction of cell counts in BAL fluid. In obese mice, greater levels of eotaxin, TNF-α and NOx, together with increased iNOS protein expression were observed, all of which were normalized by metformin. In addition, metformin nearly abrogated the binding of NF-κB subunit p65 to the iNOS promoter gene in lung tissue of obese mice. Lower levels of phosphorylated AMPK and its downstream target acetyl CoA carboxylase (ACC) were found in lung tissue of obese mice, which were restored by metformin. In separate experiments, the selective iNOS inhibitor aminoguanidine (20 mg/kg, 3 weeks) and the anti-TNF-α mAb (2 mg/kg) significantly attenuated the aggravation of eosinophilic inflammation in obese mice. In conclusion, metformin inhibits the TNF-α-induced inflammatory signaling and NF-κB-mediated iNOS expression in lung tissue of obese mice. Metformin may be a good pharmacological strategy to control the asthma exacerbation in obese individuals.     

Identification of Novel Vaccine Candidates against Multidrug-Resistant Acinetobacter baumannii

Acinetobacter baumannii is an emerging opportunistic bacterium associated with nosocomial infections in intensive care units. The alarming increase in infections caused by A. baumannii is strongly associated with enhanced resistance to antibiotics, in particular carbapenems. This, together with the lack of a licensed vaccine, has translated into significant economic, logistic and health impacts to health care facilities. In this study, we combined reverse vaccinology and proteomics to identify surface-exposed and secreted antigens from A. baumannii. Using in silico prediction tools and comparative genome analysis in combination with in vitro proteomic approaches, we identified 42 antigens that could be used as potential vaccine targets. Considering the paucity of effective antibiotics available to treat multidrug-resistant A. baumannii infections, these vaccine targets may serve as a framework for the development of a broadly protective multi-component vaccine, an outcome that would have a major impact on the burden of A. baumannii infections in intensive care units across the globe.