Zika Virus Growth in Human Kidney Cells Is Restricted by an Elevated Glucose Level

Mosquito-borne Zika virus (ZIKV) became a real threat to human health due to the lack of vaccine and effective antiviral treatment. The virus has recently been responsible for a global outbreak leading to millions of infected cases. ZIKV complications were highlighted in adults with Guillain–Barré syndrome and in newborns with increasing numbers of congenital disorders ranging from mild developmental delays to fatal conditions. The ability of ZIKV to establish a long-term infection in diverse organs including the kidneys has been recently documented but the consequences of such a viral infection are still debated. Our study aimed to determine whether the efficiency of ZIKV growth in kidney cells relates to glucose concentration. Human kidney HK-2 cells were infected with different ZIKV strains in presence of normal and high glucose concentrations. Virological assays showed a decrease in viral replication without modifying entry steps (viral binding, internalization, fusion) under high glucose conditions. This decrease replication was associated with a lower virus progeny and increased cell viability when compared to ZIKV-infected HK-2 cells in normal glucose concentration. In conclusion, we showed for the first time that an elevated glucose level influences ZIKV replication level with an effect on kidney cell survival.     

Alteration of the Route to Menaquinone towards Isochorismate-Derived Metabolites

Chorismate and isochorismate constitute branch-point intermediates in the biosynthesis of many aromatic metabolites in microorganisms and plants. To obtain unnatural compounds, we modified the route to menaquinone in Escherichia coli. We propose a model for the binding of isochorismate to the active site of MenD ((1R,2S, 5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxycyclohex-3-ene-1-carboxylate (SEPHCHC) synthase) that explains the outcome of the native reaction with α-ketoglutarate. We have rationally designed variants of MenD for the conversion of several isochorismate analogues. The double-variant Asn117Arg–Leu478Thr preferentially converts (5S,6S)-5,6-dihydroxycyclohexa-1,3-diene-1-carboxylate (2,3-trans-CHD), the hydrolysis product of isochorismate, with a >70-fold higher ratio than that for the wild type. The single-variant Arg107Ile uses (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate (2,3-trans-CHA) as substrate with >6-fold conversion compared to wild-type MenD. The novel compounds have been made accessible in vivo (up to 5.3 g L⁻¹). Unexpectedly, as the identified residues such as Arg107 are highly conserved (>94 %), some of the designed variations can be found in wild-type SEPHCHC synthases from other bacteria (Arg107Lys, 0.3 %). This raises the question for the possible natural occurrence of as yet unexplored branches of the shikimate pathway.     

Quantitative pharmacophore models with inductive logic programming

Three-dimensional models, or pharmacophores, describing Euclidean constraints on the location on small molecules of functional groups (like hydrophobic groups, hydrogen acceptors and donors, etc.), are often used in drug design to describe the medicinal activity of potential drugs (or ‘ligands’). This medicinal activity is produced by interaction of the functional groups on the ligand with a binding site on a target protein. In identifying structure-activity relations of this kind there are three principal issues: (1) It is often difficult to “align” the ligands in order to identify common structural properties that may be responsible for activity; (2) Ligands in solution can adopt different shapes (or `conformations’) arising from torsional rotations about bonds. The 3-D molecular substructure is typically sought on one or more low-energy conformers; and (3) Pharmacophore models must, ideally, predict medicinal activity on some quantitative scale. It has been shown that the logical representation adopted by Inductive Logic Programming (ILP) naturally resolves many of the difficulties associated with the alignment and multi-conformation issues. However, the predictions of models constructed by ILP have hitherto only been nominal, predicting medicinal activity to be present or absent. In this paper, we investigate the construction of two kinds of quantitative pharmacophoric models with ILP: (a) Models that predict the probability that a ligand is “active”; and (b) Models that predict the actual medicinal activity of a ligand. Quantitative predictions are obtained by the utilising the following statistical procedures as background knowledge: logistic regression and naive Bayes, for probability prediction; linear and kernel regression, for activity prediction. The multi-conformation issue and, more generally, the relational representation used by ILP results in some special difficulties in the use of any statistical procedure. We present the principal issues and some solutions. Specifically, using data on the inhibition of the protease Thermolysin, we demonstrate that it is possible for an ILP program to construct good quantitative structure-activity models. We also comment on the relationship of this work to other recent developments in statistical relational learning. Editors: Tamás Horváth and Akihiro Yamamoto     

A shell for cooperating expert systems

Abstract: This paper describes a shell for cooperating expert systems that has been developed at the University of Porto. The main goal of this shell is two-fold: to generate a community of cooperative knowledge-based systems and to develop several special reasoning techniques which can be used under a distributed and cooperative paradigm. UPShell is able to convert a set of generated intelligent systems (ISs) into a community of cooperative ISs. In this first version it is already possible to generate different intelligent systems which are able to run 'simultaneously' as separate Unix processes and, using a message-passing mechanism, to communicate among themselves. They can be set to pursue an overall goal in a cooperative way. Moreover, several tasks can be given to each IS to be solved simultaneously, and the IS can switch from task to task according to dynamic priorities reflecting the urgency attached to the specific sub-tasks that emerge. The shell described here may also be used to test, within a distributed environment, some time-bounded reasoning techniques that are presently being developed. The paper has three main parts: a general overview of the UPShell (Section 1); a tutorial explaining, by means of examples, how to use the package (Section 2); and, finally, some considerations on the reasoning techniques used and future improvements (Sections 3–5).     

Performance evaluation of a water/silicone oil two‐phase partitioning bioreactor using Rhodococcus erythropolis T902.1 to remove volatile organic compounds from gaseous effluents

BACKGROUND: In the framework of biological processes used for waste gas treatment, the impact of the inoculum size on the start‐up performance needs to be better evaluated. Moreover, only a few studies have investigated the behaviour of elimination capacity and biomass viability in a two‐phase partitioning bioreactor (TPPB) used for waste gas treatment. Lastly, the impact of ethanol as a co‐substrate remains misunderstood. RESULTS: Firstly, no benefit of inoculation with a high cellular density (>1.5 g L^?1) was observed in terms of start‐up performance. Secondly, the TPPB was monitored for 38 days to characterise its behaviour under several operational conditions. The removal efficiency remained above 63% for an inlet concentration of 7 g isopropylbenzene (IPB) m^?3 and at some time points reached 92% during an intermittent loading phase (10 h day^?1), corresponding to a mean elimination capacity of 4 × 10^?3 g L^?1 min^?1 (240 g m^?3 h^?1) for a mean IPB inlet load of 6.19 × 10^?3 g L^?1 min^?1 (390 g m^?3 h^?1). Under continuous IPB loading, the performance of the TPPB declined, but the period of biomass acclimatisation to this operational condition was shorter than 5 days. The biomass grew to approximately 10 g L^?1 but the cellular viability changed greatly during the experiment, suggesting an endorespiration phenomenon in the bioreactor. It was also shown that simultaneous degradation of IPB and ethanol occurred, suggesting that ethanol improves the biodegradation process without causing oxygen depletion. CONCLUSION: A water/silicone oil TPPB with ethanol as co‐substrate allowed the removal of a high inlet load of IPB during an experiment lasting 38 days. Copyright © 2008 Society of Chemical Industry     

Organic matter release in low temperature thermal treatment of biological sludge for reduction of excess sludge production.

Thermal treatment applied in association with a biological system allows for a significant reduction in excess sludge production (approximately 50%). In general, heat treatment is described as a sludge disintegration technique. This paper offers a thorough study on the impact of heat treatment, at temperatures below 100 degrees C, on the solubilisation of the sludge COD and its biodegradability. Discontinuous heating experiments were performed on activated and digested sludge. At all temperatures tested the released COD for digested sludge was systematically higher than that for activated sludge (15 and 40%, respectively, at 95 degrees C for 40 min of contact time). For the first 30 min, a 1st order kinetic, with respect to the residual COD, was systematically found. In the range of 40-95 degrees C, digested sludge had a lower activation energy than activated sludge (26 kcal/mol compared to 70-160 kcal/mol). COD solubilisation is thus more positively influenced by temperature in the case of activated sludge. This may be due to the significant difference in the ratio of protein/carbohydrate in digested and activated sludge (1-5 and 0.2-0.7, respectively). The increase in the COD/TKN ratio in the solubilised fraction after thermal treatment of activated sludge suggests a preferential solubilisation of proteins over carbohydrates. Respirometric tests performed on the solubilised COD showed that whatever the sludge origin, only 40-50% of released COD is biodegradable at a conventional hydraulic retention time (i.e., 24 h). Hence, heat treatment would act more through organic matter solubilisation rather than by a biodegradability increase.