PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction

Peptidoglycan recognition proteins (PGRPs) are ubiquitous among animals and play pivotal functions in insect immunity. Non-catalytic PGRPs are involved in the activation of immune pathways by binding to the peptidoglycan (PGN), whereas amidase PGRPs are capable of cleaving the PGN into non-immunogenic compounds. Drosophila PGRP-LB belongs to the amidase PGRPs and downregulates the immune deficiency (IMD) pathway by cleaving meso-2,6-diaminopimelic (meso-DAP or DAP)-type PGN. While the recognition process is well analyzed for the non-catalytic PGRPs, little is known about the enzymatic mechanism for the amidase PGRPs, despite their essential function in immune homeostasis. Here, we analyzed the specific activity of different isoforms of Drosophila PGRP-LB towards various PGN substrates to understand their specificity and role in Drosophila immunity. We show that these isoforms have similar activity towards the different compounds. To analyze the mechanism of the amidase activity, we performed site directed mutagenesis and solved the X-ray structures of wild-type Drosophila PGRP-LB and its mutants, with one of these structures presenting a protein complexed with the tracheal cytotoxin (TCT), a muropeptide derived from the PGN. Only the Y78F mutation abolished the PGN cleavage while other mutations reduced the activity solely. Together, our findings suggest the dynamic role of the residue Y78 in the amidase mechanism by nucleophilic attack through a water molecule to the carbonyl group of the amide function destabilized by Zn²⁺.     

Automatic computation of pebble roundness using digital imagery and discrete geometry

The shape of sedimentary particles is an important property, from which geographical hypotheses related to abrasion, distance of transport, river behavior, etc. can be formulated. In this paper, we use digital image analysis, especially discrete geometry, to automatically compute some shape parameters such as roundness, i.e. a measure of how much the corners and edges of a particle have been worn away.In contrast to previous work in which traditional digital images analysis techniques, such as Fourier transform, are used, we opted for a discrete geometry approach that allowed us to implement Wadell's original index, which is known to be more accurate, but more time consuming to implement in the field.Our implementation of Wadell's original index is highly correlated (92%) with the roundness classes of Krumbein's chart, used as a ground-truth. In addition, we show that other geometrical parameters, which are easier to compute, can be used to provide good approximations of roundness.We also used our shape parameters to study a set of pebbles digital images taken from the Progo basin river network (Indonesia). The results we obtained are in agreement with previous work and open new possibilities for geomorphologists thanks to automatic computation.     

Flux-Conservative Hermite Methods for Simulation of Nonlinear Conservation Laws

A new class of Hermite methods for solving nonlinear conservation laws is presented. While preserving the high order spatial accuracy for smooth solutions in the existing Hermite methods, the new methods come with better stability properties. Artificial viscosity in the form of the entropy viscosity method is added to capture shocks.     

Cu-assisted induced atomic-level bivalent Fe confined on N-doped carbon concave dodecahedrons for acid oxygen reduction electrocatalysis

Atomically dispersed transition metals anchored on N-doped carbon have been successfully developed as promising electrocatalysts for acidic oxygen reduction reaction (ORR). Nonetheless, how to introduce and construct single-atomic active sites is still a big challenge. Herein, a novel concave dodecahedron catalyst of N-doped carbon (FeCuNC) with well confined atomically dispersed bivalent Fe sites was facilely developed via a Cu-assisted induced strategy. The obtained catalyst delivered outstanding ORR performance in 0.5 M H₂SO₄ media with a half-wave potential (E_1/2) of 0.82 V (vs reversible hydrogen electrode, RHE), stemming from the highly active bivalent Fe-N_x sites with sufficient exposure and accessibility guaranteed by the high specific surface area and curved surface. This work provides a simple but efficient metal-assisted induced strategy to tune the configurations of atomically dispersed active sites as well as microscopy structures of carbon matrix to develop promising PGM-free catalysts for proton exchange membrane fuel cell (PEMFC) applications.     

Understanding of the annealing temperature impact on ion implanted bifacial n‐type solar cells to reach 20.3% efficiency

Ion implantation has the advantage of being a unidirectional doping technique. Unlike gaseous diffusion, this characteristic highlights strong possibilities to simplify solar cell process flows. The use of ion implantation doping for n‐type PERT bifacial solar cells is a promising process, but mainly if it goes with a unique co‐annealing step to activate both dopants and to grow a SiO₂ passivation layer. To develop this process and our SONIA cells, we studied the impact of the annealing temperature and that of the passivation layers on the electrical quality of the implanted B‐emitter and P‐BSF. A high annealing temperature (above 1000 °C) was necessary to fully activate the boron atoms and to anneal the implantation damages. Low J_0BSF (BSF contribution to the saturation current density) of 180 fA/cm² was reached at this high temperature with the best SiO₂ passivation layer. An average efficiency of 19.7% was reached using this simplified process flow (“co‐anneal process”) on large area (239 cm²) Cz solar cells. The efficiency was limited by a low FF, probably due to contaminations by metallization pastes. Improved performances were achieved in the case of a “separated anneals” process where the P‐BSF is activated at a lower temperature range. An average efficiency of 20.2% was obtained in this case, with a 20.3% certified cell. Copyright © 2014 John Wiley & Sons, Ltd.     

Comparison of ionic liquid,acid and alkali pretreatments for sugarcane bagasse enzymatic saccharification

BACKGROUND: Much attention has been given to applying ionic liquids (ILs) as an alternative pretreatment method for lignocellulosic biomass. This study aims to select the most suitable type of IL for pretreating sugarcane bagasse (SCB). The potential of ILs for pretreatment was evaluated and compared with conventional pretreatment media, acids and alkalis. The performance of the pretreatment media was evaluated based on the amount of reducing sugar produced from enzymatic saccharification, the energy requirement, and changes in the chemical structure and crystallinity index of the pretreated bagasse. RESULTS: 1‐ethyl‐3‐methylimidazolium acetate [EMIM]oAc was selected as the most suitable IL for SCB pretreatment. The optimum yields of reducing sugar obtained from [EMIM]oAc‐, alkali‐, and acid‐pretreated SCB were 69.5%, 92.8% and 41.3%, respectively. Although a lower yield of reducing sugar was obtained, [EMIM]oAc pretreatment required the least energy to pretreat 1 kg of SCB. Moreover, the percentage of SCB loss during [EMIM]oAc pretreatment was the lowest. [EMIM]oAc‐pretreated SCB also had the lowest crystallinity index (CI) with the most amorphous structure. CONCLUSION: [EMIM]oAc appears to be another option for pretreating SCB, and other issues such as the recyclability of [EMIM]oAc is worth investigating. Copyright © 2011 Society of Chemical Industry     

Measure of circularity for parts of digital boundaries and its fast computation

This paper focuses on the design of an effective method that computes the measure of circularity of a part of a digital boundary. An existing circularity measure of a set of discrete points, which is used in computational metrology, is extended to the case of parts of digital boundaries. From a single digital boundary, two sets of points are extracted so that the circularity measure computed from these sets is representative of the circularity of the digital boundary. Therefore, the computation consists of two steps. First, the inner and outer sets of points are extracted from the input part of a digital boundary using digital geometry tools. Next, the circularity measure of these sets is computed using classical tools of computational geometry. It is proved that the algorithm is linear in time in the case of convex parts thanks to the specificity of digital data, and is in O(nlogn) otherwise. Experiments done on synthetic and real images illustrate the interest of the properties of the circularity measure.     

Carbon nanotubes for interconnects in future integrated circuits: The challenge of the density

A CVD process with a high density of CNTs has been developed on doped silicon material thanks to plasma pre-treatment of the catalyst. With this process small diameter double and triple wall CNTs with an average diameter of 3.8 nm have been grown. The density of the best materials on blanket substrate is larger than 10¹² cm^? 2. These materials have been successfully integrated in via holes with a diameter ranging between 1 µm and 0.3 µm with an equivalent density. In 140 nm hole diameter large 70 nm bundle formations have been observed. In these bundles a density of CNT walls close to 10¹³ cm^? 2 has been estimated.     

P2X7 Receptors and TMEM16 Channels Are Functionally Coupled with Implications for Macropore Formation and Current Facilitation

P2X7 receptors (P2X7) are cationic channels involved in many diseases. Following their activation by extracellular ATP, distinct signaling pathways are triggered, which lead to various physiological responses such as the secretion of pro-inflammatory cytokines or the modulation of cell death. P2X7 also exhibit unique behaviors, such as “macropore” formation, which corresponds to enhanced large molecule cell membrane permeability and current facilitation, which is caused by prolonged activation. These two phenomena have often been confounded but, thus far, no clear mechanisms have been resolved. Here, by combining different approaches including whole-cell and single-channel recordings, pharmacological and biochemical assays, CRISPR/Cas9 technology and cell imaging, we provide evidence that current facilitation and macropore formation involve functional complexes comprised of P2X7 and TMEM16, a family of Ca²⁺-activated ion channel/scramblases. We found that current facilitation results in an increase of functional complex-embedded P2X7 open probability, a result that is recapitulated by plasma membrane cholesterol depletion. We further show that macropore formation entails two distinct large molecule permeation components, one of which requires functional complexes featuring TMEM16F subtype, the other likely being direct permeation through the P2X7 pore itself. Such functional complexes can be considered to represent a regulatory hub that may orchestrate distinct P2X7 functionalities.