Crystal structure of human METTL6, the m3C methyltransferase

In tRNA, the epigenetic m3C modification at position 32 in the anticodon loop is highly conserved in eukaryotes, which maintains the folding and basepairing functions of the anticodon. However, the responsible enzymes METTL2 and METTL6 were identified only in recent years. The loss of human METTL6 (hMETTL6) affects the translational process and proteostasis in cells, while in mESCs cells, it leads to defective pluripotency potential. Despite its important functions, the catalytic mechanism of the C32 methylation by this enzyme is poorly understood. Here we present the 1.9 Å high-resolution crystal structure of hMETTL6 bound by SAH. The key residues interacting with the ligand were identified and their roles were confirmed by ITC. We generated a docking model for the hMETTL6-SAH-CMP ternary complex. Interestingly, the CMP molecule binds into a cavity in a positive patch with the base ring pointing to the inside, suggesting a flipped-base mechanism for methylation. We further generated a model for the quaternary complex with tRNASer as a component, which reasonably explained the biochemical behaviors of hMETTL6. Taken together, our crystallographic and biochemical studies provide important insight into the molecular recognition mechanism by METTL6 and may aid in the METTL-based rational drug design in the future.

PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides

The cell wall of the human bacterial pathogen Group A Streptococcus (GAS) consists of peptidoglycan decorated with the Lancefield group A carbohydrate (GAC). GAC is a promising target for the development of GAS vaccines. In this study, employing chemical, compositional, and NMR methods, we show that GAC is attached to peptidoglycan via glucosamine 1-phosphate. This structural feature makes the GAC-peptidoglycan linkage highly sensitive to cleavage by nitrous acid and resistant to mild acid conditions. Using this characteristic of the GAS cell wall, we identify PplD as a protein required for deacetylation of linkage N-acetylglucosamine (GlcNAc). X-ray structural analysis indicates that PplD performs catalysis via a modified acid/base mechanism. Genetic surveys in silico together with functional analysis indicate that PplD homologs deacetylate the polysaccharide linkage in many streptococcal species. We further demonstrate that introduction of positive charges to the cell wall by GlcNAc deacetylation protects GAS against host cationic antimicrobial proteins.

Reduced Chemical Kinetic Reaction Mechanism for Dimethyl Ether-Air Combustion

Development and validation of a new reduced dimethyl ether-air (DME) reaction mechanism is presented. The mechanism was developed using a modular approach that has previously been applied to several alkane and alkene fuels, and the present work pioneers the use of the modular methodology, with its underlying H/C1/O base mechanism, on an oxygenated fuel. The development methodology uses a well-characterized H/C1/O base mechanism coupled to a reduced set of fuel and intermediate product submechanisms. The mechanism for DME presented in this work includes 30 species and 69 irreversible reactions. When used in combustion simulation the mechanism accurately reproduced key combustion characteristics and the small size enables use in computationally demanding Large Eddy Simulations (LES) and Direct Numerical Simulations (DNS). It has been developed to accurately predict, among other parameters, laminar burning velocity and ignition delay times, including the negative temperature regime. The evaluation of the mechanism and comparison to experimental data and several detailed and reduced mechanisms covers a wide range of conditions with respect to temperature, pressure and fuel-to-air ratio. There is good agreement with experimental data and the detailed reference mechanisms at all investigated conditions. The mechanism uses fewer reactions than any previously presented DME-air mechanism, without losing in predictability.

An Overview of CMOS Photodetectors Utilizing Current-Assistance for Swift and Efficient Photo-Carrier Detection

This review paper presents an assortment of research on a family of photodetectors which use the same base mechanism, current assistance, for the operation. Current assistance is used to create a drift field in the semiconductor, more specifically silicon, in order to improve the bandwidth and the quantum efficiency. Based on the detector and application, the drift field can be static or modulated. Applications include 3D imaging (both direct and indirect time-of-flight), optical receivers and fluorescence lifetime imaging. This work discusses the current-assistance principle, the various photodetectors using this principle and a comparison is made with other state-of-the-art photodetectors used for the same application.

Identification and Expression Profiling Analysis of the Cation/Ca2+ Exchanger (CCX) Gene Family: Overexpression of SlCCX1-LIKE Regulates the Leaf Senescence in Tomato Flowering Phase

Cation gradients in plant cellular compartments are maintained by the synergistic actions of various ion exchangers, pumps, and channels. Cation/Ca2+ exchanger (CCX) is one of the clades of the Ca2+/cation antiporter super family. Here, five SlCCX genes were identified in tomato. Sequence analysis indicated that SlCCXs have the conserved motifs as the CCX domain. Analysis of the expression level of each member of tomato CCX gene family under cation (Mg2+, Mn2+, Na+, and Ca2+) treatment was determined by qRT-PCR. Tomato CCX demonstrated different degrees of responding to cation treatment. Changes in SlCCX1-LIKE expression was induced by Mg2+ and Mn2+ treatment. Analysis of the expression of SlCCX genes in different tissues demonstrated that constitutive high expression of a few genes, including SlCCX1-LIKE and SlCCX5, indicated their role in tomato organ growth and development. Overexpression of SlCCX1-LIKE dramatically induced leaf senescence. Transcriptome analysis showed that genes related to ROS and several IAA signaling pathways were significantly downregulated, whereas ETH and ABA signaling pathway-related genes were upregulated in overexpression of SlCCX1-LIKE (OE-SlCCX1-LIKE) plants, compared with the wild type (WT). Moreover, overexpression of SlCCX1-LIKE plants accumulated more ROS content but less Mg2+ content. Collectively, the findings of this study provide insights into the base mechanism through which CCXs regulate leaf senescence in tomato.

In Situ IR Studies on the Mechanism of Dimethyl Carbonate Synthesis from Methanol and Carbon Dioxide

The synthesis of dimethyl carbonate (DMC) from methanol and Carbon dioxide (CO2) has been investigated over 5% Rh/Al2O3 catalyst. Diffuse Reflectance Infrared Fourier Transfer Spectroscopy (DRIFTS) was used to probe the reaction adsorbates which showed that activation of methanol and CO2 involves generation of intermediate methoxy species and formate ingredients, participating in elementary steps of DMC formation. Formation of DMC involves parallel routes comprising interaction of the OH group of Al2O3 through an acid/base mechanism and formate pathway with participation of metal sites. DMC in acid/base pathway is formed via methoxy species to form methoxy carbonate (CH3O)CO2 (active adsorbate), which then reacts with the methyl species to form DMC. The pathway involving metal Rh sites generates an additional elementary step for the involvement of CO2 in the reaction through active formate species. The synergy of parallel pathways determines the performance of the 5% Rh/Al2O3 catalyst. Further improvement of catalyst performance should be based on such a feature of the reaction mechanism.

Gcn5-Related N-Acetyltransferases (GNATs) With a Catalytic Serine Residue Can Play Ping-Pong Too

Enzymes in the Gcn5-related N-acetyltransferase (GNAT) superfamily are widespread and critically involved in multiple cellular processes ranging from antibiotic resistance to histone modification. While acetyl transfer is the most widely catalyzed reaction, recent studies have revealed that these enzymes are also capable of performing succinylation, condensation, decarboxylation, and methylcarbamoylation reactions. The canonical chemical mechanism attributed to GNATs is a general acid/base mechanism; however, mounting evidence has cast doubt on the applicability of this mechanism to all GNATs. This study shows that the Pseudomonas aeruginosa PA3944 enzyme uses a nucleophilic serine residue and a hybrid ping-pong mechanism for catalysis instead of a general acid/base mechanism. To simplify this enzyme’s kinetic characterization, we synthesized a polymyxin B substrate analog and performed molecular docking experiments. We performed site-directed mutagenesis of key active site residues (S148 and E102) and determined the structure of the E102A mutant. We found that the serine residue is essential for catalysis toward the synthetic substrate analog and polymyxin B, but the glutamate residue is more likely important for substrate recognition or stabilization. Our results challenge the current paradigm of GNAT mechanisms and show that this common enzyme scaffold utilizes different active site residues to accomplish a diversity of catalytic reactions.

Synthesis, Characterization and Anticancer Activity of (5,1-Substituted)-3-(indoline-4-(thiophene-2-yl-methylene)-2-(p-tolyl)-2-methylene)-4,3-dihydro-1H-imidazole-5-one Derivatives

The synthesis of novel imidazole-5-one derivatives (5a-j) was allowed in a conventional method by way of Erlenmeyer and Schiff base mechanism. Compound 2a was synthesized by Erlenmeyer reaction of N-(4-methoxy benzoyl)glycine with 2-thiophene-carboxaldehyde in the presence of acetic anhydride and anhydrous sodium acetate. Finally, it undergoes dehydration reaction with Schiff bases of isatin derivatives (4a-j) to yield final compounds 5a-j. The organic potentials of the newly synthesized imidazole-5-one derivatives have been evaluated for their in vitro anticancer activity by MTT assay method. It against MCF-7 cells as comparison with doxorubicin popular drug. The synthesized compounds 5e, 5f and 5j exhibited excellent anticancer activity against MCF-7 cell lines.

Capturing the Effects of NOx and SOx Impurities on Oxy-Combustion Under Supercritical CO2 Conditions for Coal-Derived Syngas and Natural Gas Mixtures

Direct fired supercritical carbon dioxide cycles are one of the most promising power generation method in terms of their efficiency and environmental friendliness. Two most important challenges in implementing these cycles are the high pressure (300 bar) and high CO2 dilution (>80 %) in the combustor. The design and development of supercritical oxy-combustors for natural gas requires accurate reaction kinetic models to predict the combustion outcomes. The presence of small amount of impurities in natural gas and other feed streams to oxy-combustors makes these predictions even more complex. During oxy-combustion, trace amounts of nitrogen present in the oxidizer is converted to NOx and gets into the combustion chamber along with the recirculated CO2. Similarly, natural gas can contain trace amount of ammonia and sulfurous impurities which gets converted to NOx and SOx and gets back into the combustion chamber with recirculated CO2. In this work, a reaction model is developed for predicting the effect of impurities like NOx and SOx on supercritical methane combustion. The base mechanism used in this work is GRI 3.0. H2S combustion chemistry is obtained from Bongartz et al. while NOx chemistry is from Konnov et al. The reaction model is then optimized for a pressure range of 30–300 bar using high pressure shock tube data from literature. It is then validated with data obtained from literature for methane combustion, H2S oxidation and NOx effects on ignition delay. The effect of impurities on CH4 combustion up to 16 atm is validated using NOx doped methane studies obtained from literature. In order to validate the model for high pressure conditions, experiments are conducted in a high pressure (∼100 bar) shock tube facility at UCF for natural gas identical mixtures with N2O as impurity. Current results show that there is significant change in ignition delay with the presence of impurities. A comparison is made with experimental data using the developed model and predictions are found to be in good agreement. The model developed was used to study the effect of impurities on CO formation from sCO2 combustor. It was found that NOx helps in reducing CO formation while presence of H2S results in formation of more CO. The reaction mechanism developed herein can also be used as a base mechanism to develop reduced mechanism for use in CFD simulations.

Probing the Effects of NOx and SOx Impurities on Oxy-Fuel Combustion in Supercritical CO2: Shock Tube Experiments and Chemical Kinetic Modeling

The direct-fired supercritical carbon dioxide cycles are one of the most promising power generation methods in terms of their efficiency and environmental friendliness. Two important challenges in implementing these cycles are the high pressure (300 bar) and high CO2 dilution (>80%) in the combustor. The design and development of supercritical oxy-combustors for natural gas require accurate reaction kinetic models to predict the combustion outcomes. The presence of a small amount of impurities in natural gas and other feed streams to oxy-combustors makes these predictions even more complex. During oxy-combustion, trace amounts of nitrogen present in the oxidizer is converted to NOx and gets into the combustion chamber along with the recirculated CO2. Similarly, natural gas can contain a trace amount of ammonia and sulfurous impurities that get converted to NOx and SOx and get back into the combustion chamber with recirculated CO2. In this work, a reaction model is developed for predicting the effect of impurities such as NOx and SOx on supercritical methane combustion. The base mechanism used in this work is GRI Mech 3.0. H2S combustion chemistry is obtained from Bongartz et al. while NOx chemistry is from Konnov. The reaction model is then optimized for a pressure range of 30–300 bar using high-pressure shock tube data from the literature. It is then validated with data obtained from the literature for methane combustion, H2S oxidation, and NOx effects on ignition delay. The effect of impurities on CH4 combustion up to 16 atm is validated using NOx-doped methane studies obtained from the literature. In order to validate the model for high-pressure conditions, experiments are conducted at the UCF shock tube facility using natural gas identical mixtures with N2O as an impurity at ∼100 bar. Current results show that there is a significant change in ignition delay with the presence of impurities. A comparison is made with experimental data using the developed model and predictions are found to be in good agreement. The model developed was used to study the effect of impurities on CO formation from sCO2 combustors. It was found that NOx helps in reducing CO formation while the presence of H2S results in the formation of more CO. The reaction mechanism developed herein can also be used as a base mechanism to develop reduced mechanisms for use in CFD simulations.