A Bacterial Toxin Inhibits DNA Replication Elongation through a Direct Interaction with the β Sliding Clamp

Toxin-antitoxin (TA) systems are ubiquitous on bacterial chromosomes, yet the mechanisms regulating their activity and the molecular targets of toxins remain incompletely defined. Here, we identify SocAB, an atypical TA system in Caulobacter crescentus. Unlike canonical TA systems, the toxin SocB is unstable and constitutively degraded by the protease ClpXP; this degradation requires the antitoxin, SocA, as a proteolytic adaptor. We find that the toxin, SocB, blocks replication elongation through an interaction with the sliding clamp, driving replication fork collapse. Mutations that suppress SocB toxicity map to either the hydrophobic cleft on the clamp that binds DNA polymerase III or a clamp-binding motif in SocB. Our findings suggest that SocB disrupts replication by outcompeting other clamp-binding proteins. Collectively, our results expand the diversity of mechanisms employed by TA systems to regulate toxin activity and inhibit bacterial growth, and they suggest that inhibiting clamp function may be a generalizable antibacterial strategy.Howard Hughes Medical Institute (Summer Medical Fellowship)National Science Foundation (U.S.). Graduate Research Fellowship ProgramNational Institutes of Health (U.S.) (R01GM082899

Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam

Background: Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions: Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development

Histological Evaluation of the Biocompatibility of Polyurea Crosslinked Silica Aerogel Implants in a Rat Model: A Pilot Study

Background: Aerogels are a versatile group of nanostructured/nanoporous materials with physical and chemical properties that can be adjusted to suit the application of interest. In terms of biomedical applications, aerogels are particularly suitable for implants such as membranes, tissue growth scaffolds, and nerve regeneration and guidance inserts. The mesoporous nature of aerogels can also be used for diffusion based release of drugs that are loaded during the drying stage of the material. From the variety of aerogels polyurea crosslinked silica aerogels have the most potential for future biomedical applications and are explored here. Methodology: This study assessed the short and long term biocompatibility of polyurea crosslinked silica aerogel implants in a Sprague-Dawley rat model. Implants were inserted at two different locations a) subcutaneously (SC), at the dorsum and b) intramuscularly (IM), between the gluteus maximus and biceps femoris of the left hind extremity. Nearby muscle and other internal organs were evaluated histologically for inflammation, tissue damage, fibrosis and movement (travel) of implant. Conclusion/Significance: In general polyurea crosslinked silica aerogel (PCSA) was well tolerated as a subcutaneous and an intramuscular implant in the Sprague-Dawley rat with a maximum incubation time of twenty months. In some cases a thin fibrous capsule surrounded the aerogel implant and was interpreted as a normal response to foreign material. No noticeable toxicity was found in the tissues surrounding the implants nor in distant organs. Comparison was made with control rats without any implants inserted, and animals with suture material present. No obvious or noticeable changes were sustained by the implants at either location. Careful necropsy and tissue histology showed age-related changes only. An effective sterilization technique for PCSA implants as well as staining and sectioning protocol has been established. These studies further support the notion that silica-based aerogels could be useful as biomaterials. © 2012 Sabri et al

Transport Phenomena and Structuring in Shear Flow of Suspensions near Solid Walls

In this paper we apply the lattice-Boltzmann method and an extension to particle suspensions as introduced by Ladd et al. to study transport phenomena and structuring effects of particles suspended in a fluid near sheared solid walls. We find that a particle free region arises near walls, which has a width depending on the shear rate and the particle concentration. The wall causes the formation of parallel particle layers at low concentrations, where the number of particles per layer decreases with increasing distance to the wall.Comment: 14 pages, 14 figure

Load Shedding in Microgrids with Dual Neural Networks and AHP Algorithm

This paper proposes a new load shedding method based on the application of a Dual Neural Network (NN). The combination of a Back-Propagation Neural Network (BPNN) and of Particle Swarm Optimization (PSO) aims to quickly predict and propose a load shedding strategy when a fault occurs in the microgrid (MG) system. The PSO algorithm has the ability to search and compare multiple points, so the proposed NN training method helps determine the link weights faster and stronger. As a result, the proposed method saves training time and achieves higher accuracy. The Analytic Hierarchy Process (AHP) algorithm is applied to rank the loads based on their importance factor. The results of the ratings of the loads serve as a basis for constructing the load shedding strategies of a NN combined with the PSO algorithm (ANN-PSO). The proposed load shedding method is tested on an IEEE 25-bus 8-generator MG power system. The simulation results show that the frequency recovery of the power system is positive. The proposed neural network adapts well to the simulated data of the system and achieves high performance in fault prediction

The novel method to reduce the silica content in lignin recovered from black liquor originating from rice straw

Difficulties in the production of lignin from rice straw because of high silica content in the recovered lignin reduce its recovery yield and applications as bio-fuel and aromatic chemicals. Therefore, the objective of this study is to develop a novel method to reduce the silica content in lignin from rice straw more effectively and selectively. The method is established by monitoring the precipitation behavior as well as the chemical structure of precipitate by single-stage acidification at different pH values of black liquor collected from the alkaline treatment of rice straw. The result illustrates the significant influence of pH on the physical and chemical properties of the precipitate and the supernatant. The simple two-step acidification of the black liquor at pilot-scale by sulfuric acid 20w/v% is applied to recover lignin at pH 9 and pH 3 and gives a percentage of silica removal as high as 94.38%. Following the developed process, the high-quality lignin could be produced from abundant rice straw at the industrial-scale