A deep learning model for predicting blastocyst formation from cleavage-stage human embryos using time-lapse images.

Efficient prediction of blastocyst formation from early-stage human embryos is imperative for improving the success rates of assisted reproductive technology (ART). Clinics transfer embryos at the blastocyst stage on Day-5 but Day-3 embryo transfer offers the advantage of a shorter culture duration, which reduces exposure to laboratory conditions, potentially enhancing embryonic development within a more conducive uterine environment and improving the likelihood of successful pregnancies. In this paper, we present a novel ResNet-GRU deep-learning model to predict blastocyst formation at 72 HPI.

Computational analysis of the effect of Gly100Ala mutation on the thermostability of SazCA.

Maintaining the protein stability upon mutation is a challenging task in protein engineering. In the present computational study, we induced a single point Gly100Ala mutation in SazCA and examined the factors governing the stability and flexibility of the mutated form, and compared it to that of the wildtype using molecular dynamics simulations. We observed higher structural stability and lesser residual mobility in the mutated SazCA.

Enzyme-substrate interactions in orotate-mimetic OPRT inhibitor complexes: a QM/MM analysis.

Orotate phosphoribosyltransferase (OPRT) catalyses the reversible phosphoribosyl transfer from α-D-5-phosphoribosyl-1-pyrophosphate (PRPP) to orotic acid (OA) to yield orotidine 5'-monophosphate (OMP) during the synthesis of nucleotides. Numerous studies have reported the inhibition of this reaction as a strategy to check diseases like tuberculosis, malaria and cancer. Insight into the inhibition of this reaction is, therefore, of urgent interest.

Efficient proton shuttle makes SazCA an excellent CO hydration enzyme.

The fastest member of the carbonic anhydrase family catalysing the reversible hydration of carbon dioxide to bicarbonate ions has been recently reported to be SazCA. While thermostable, this enzyme shows exceptional activity at 353 K for the reaction. This study explores the molecular basis for the exceptional activity of SazCA, in contrast to SspCA, probed using molecular dynamics simulations.

Biomimetic CO hydration activity of boronic acids.

Inspired by the recent experimental reports on boron containing compounds to be active and biomimetic for carbon capture, we report the mechanistic details of CO2 hydration activities of boronic acids using density functional theory calculations. Four boronic acids were analyzed, viz., [3-methyl-6-(1H-pyrazol-1-yl)phenyl]boronic acid, 3-aminophenylboronic acid, 2,6-dibromophenylboronic acid and 2,6-bis(trifluoromethyl)phenylboronic acid.

Structural and thermodynamic analysis of factors governing the stability and thermal folding/unfolding of SazCA.

Molecular basis of protein stability at different temperatures is a fundamental problem in protein science that is substantially far from being accurately and quantitatively solved as it requires an explicit knowledge of the temperature dependence of folding free energy of amino acid residues. In the present study, we attempted to gain insights into the thermodynamic stability of SazCA and its implications on protein folding/unfolding. We report molecular dynamics simulations of water solvated SazCA in a temperature range of 293-393 K to study the relationship between the thermostability and flexibility.

Molecular dynamics simulations identify the regions of compromised thermostability in SazCA.

The present study examined the structure and dynamics of the most active and thermostable carbonic anhydrase, SazCA, probed using molecular dynamics simulations. The molecular system was described by widely used biological force-fields (AMBER, CHARMM22, CHARMM36, and OPLS-AA) in conjunction with TIP3P water model. The comparison of molecular dynamics simulation results suggested AMBER to be a suitable choice to describe the structure and dynamics of SazCA.

On the ligand-free palladium cluster catalysed Suzuki-Miyaura reaction.

C-C cross coupling reactions have been widely used for developing synthesis protocols for pharmaceuticals and agricultural products in the past few decades. Of all the reported C-C cross coupling reactions, the Suzuki-Miyaura reaction is preferred because of its mild reaction conditions, the commercial availability of associated reagents and the ease of removal of boron containing by-products. Recently, Corma and co-workers [Leyva-Perez et al.

On interaction of arginine, cysteine and guanine with a nano-TiO cluster.

Nanoscopic properties of TiO augmented with its physicochemical properties and biocompatibility make it a material interest in the biomedical field. Efficient methods to design of such materials require a thorough understanding of associated nano-bio interfaces. In the present study, density functional theory calculations were performed to study the interactions of arginine, cysteine and guanine with a nano-TiO cluster.

On the stability of hydroxyl groups on substituted titania.

The present study reports the stability of hydroxyl groups involving the surface coordinated oxygens of Pd,C,N-doped, and Pd/C and Pd/N-codoped anatase TiO, probed using DFT calculations. Two unique surface planes, (001) and (100), were chosen for the analysis of the stability of hydroxyl groups and their activities were studied by net oxygen activation analysis. The hydroxyl group formation energies ranged between -6.

Dry reforming activity due to ionic Ru in LaRuO: the role of specific carbonates.

Dry reforming of methane was carried out over LaRuO (x = 0.005, 0.01).

QM/MM analysis of effect of divalent metal ions on OPRT action.

The role of Mg cofactor in orotate phosphoribosyltransferase (OPRT) catalyzed synthesis of orotidine monophosphate (OMP) from phosphoribosyl pyrophosphate (PRPP) and orotate (OA) in substrate binding and the influence of the identity of the divalent metal ion on the reaction mechanism were addressed in this study using quantum mechanics/molecular mechanics framework. Energetics of migration and binding of different substrate complexes in the active site cavity was established. A quantitative analysis of various processes indicated the reaction pathway to consist of complexation of Mg with PRPP, migration of Mg-PRPP and OA towards the active site, binding of OA to OPRT, and binding of Mg-PRPP complex to OA-OPRT complex.

QM/MM reveals the sequence of substrate binding during OPRT action.

Computational investigation of orotate phosphoribosyltransferase (OPRT) action, an enzymatic reaction between phosphoribosyl pyrophosphate (PRPP) and orotic acid (OA) to yield orotidine 5'-monophosphate (OMP), was carried out. Insights into the pathways of the substrate attack step of the reaction were developed under the quantum mechanics/molecular mechanics framework with S. cerevisiae strain as the representative enzyme bearer.

Computational insights into crystal plane dependence of thermal activity of anion (C and N)-substituted titania.

Geometry optimizations of anion (C and N) doped anatase TiO were carried out by using DFT+U calculations. Various anion vacancy sites were examined to study the synergistic effects of anion doping accompanied with anion vacancy formation on lattice oxygen activation. Two non-identical crystal planes (0 0 1) and (1 0 0) were chosen for C and N substitutions.

Highly Active Tungsten Oxide Nanoplate Electrocatalysts for the Hydrogen Evolution Reaction in Acidic and Near Neutral Electrolytes.

An efficient, cost-effective, and earth-abundant catalyst that could drive the production of hydrogen from water without or with little external energy is the ultimate goal toward hydrogen economy. Herein, nanoplates of tungsten oxide and its hydrates (WO·HO) as promising electrocatalysts for the hydrogen evolution reaction (HER) are reported. The square-shaped and stacked WO·HO nanoplates are synthesized at room temperature under air in ethanol only, making it as a promising green synthesis strategy.

Adsorption of C gases over CeO-based catalysts: synergism of cationic sites and anionic vacancies.

The synthesis of novel and efficient catalysts for acetylene hydrogenation exhibiting high selectivity towards ethylene is important due to the presence of selective acetylene hydrogenation reaction in petrochemical processing. Since adsorption of C gases constitutes the primary step in catalytic hydrogenation and governs the selectivity of the catalysts, we have explored the C-adsorption potential of reducible CeO-based systems. The adsorption of C-gases over CeO-based materials was assessed using experimental in situ spectroscopic techniques and in silico theoretical studies based on density functional theory.

Enhancing the performance of single-chambered microbial fuel cell using manganese/palladium and zirconium/palladium composite cathode catalysts.

Application of ZrO, MnO, palladium, palladium-substituted-zirconium oxide (ZrPdO) and palladium-substituted-manganese oxide (MnPdO) cathode catalysts in a single-chambered microbial fuel cell (MFC) was explored. The highest power generation (1.28W/m) was achieved in MFC with MnPdO catalyst, which was higher than that with MnO (0.

Mechanistic insights into biomimetic carbonic anhydrase action catalyzed by doped carbon nanotubes and graphene.

Electronic structural analyses of hydrogen terminated metal doped carbon nanotube/graphene (M-CNT/Gr, MN-CNT/Gr, M = Ru/Rh) and ruthenium cluster decorated carbon nanotube/graphene (Ru-CNT/Gr) were carried out for examining the biomimetic catalytic activity towards CO hydration reaction. The carbonic anhydrase action was followed for the reaction of CO with HO resulting in a bicarbonate ion and a proton. All the catalysts were found to be active for CO hydration and the mechanism proved them to be biomimetic.

Computational Design of New Heterofullerene-Based Biomimetic α-Carbonic Anhydrase Analogues.

The biomimetic CO hydration activity of Ru/Rh-doped fullerenes was revealed by using density functional theory calculations. The mechanism of CO hydration on the proposed heterofullerenes followed the mechanistic action of α-carbonic anhydrases, and consisted of the adsorption and deprotonation of H O, CO interaction with hydroxyl groups, CO bending, and proton transfer to give the HCO-3 product. Free-energy landscapes for the reaction showed the catalysts to be active for the reaction.

On origin and evolution of carbonic anhydrase isozymes: A phylogenetic analysis from whole-enzyme to active site.

Genetic evolution of carbonic anhydrase enzyme provides an interesting instance of functional similarity in spite of structural diversity of the members of a given family of enzymes. Phylogenetic analysis of α-, β- and γ-carbonic anhydrase was carried out to determine the evolutionary relationships among various members of the family with the enzyme marking its presence in a wide range of cellular and chromosomal locations. The presence of more than one class of enzymes in a particular organism was revealed by phylogenetic time tree.

Enhanced bioavailability and bioefficacy of an amorphous solid dispersion of curcumin.

Curcumin has been shown to have a wide variety of biological activities for various human diseases including inflammation, diabetes and cancer. However, the poor oral bioavailability of curcumin poses a significant pharmacological barrier to its use therapeutically and/or as a functional food. Here we report the evaluation of the bioavailability and bio-efficacy of curcumin as an amorphous solid dispersion (ASD) in a matrix consisting of hydroxypropyl methyl cellulose (HPMC), lecithin and isomalt using hot melt extrusion for application in food products.

Development and validation of LC-MS/MS method for the estimation of β-hydroxy-β-methylbutyrate in rat plasma and its application to pharmacokinetic studies.

A simple, sensitive and specific high-performance liquid chromatography mass spectrometry (LC-MS/MS) method was developed and validated for the quantification of β-hydroxy-β-methyl butyrate (HMB) in small volumes of rat plasma using warfarin as an internal standard (IS). The API-4000 LC-MS/MS was operated under the multiple reaction-monitoring mode using the electrospray ionization technique. A simple liquid-liquid extraction process was used to extract HMB and IS from rat plasma.

New insights into selective heterogeneous nucleation of metal nanoparticles on oxides by microwave-assisted reduction: rapid synthesis of high-activity supported catalysts.

Microwave-based methods are widely employed to synthesize metal nanoparticles on various substrates. However, the detailed mechanism of formation of such hybrids has not been addressed. In this paper, we describe the thermodynamic and kinetic aspects of reduction of metal salts by ethylene glycol under microwave heating conditions.

Rapid synthesis of ultrahigh adsorption capacity zirconia by a solution combustion technique.

Tetragonal ZrO(2) was synthesized by the solution combustion technique using glycine as the fuel. The compound was characterized by X-ray diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy, infrared spectroscopy, and BET surface area analysis. The ability of this compound to adsorb dyes was investigated, and the compound had a higher adsorption capacity than commercially activated carbon.

Noble metal ionic sites for catalytic hydrogen combustion: spectroscopic insights.

A catalytic hydrogen combustion reaction was carried out over noble metal catalysts substituted in ZrO(2) and TiO(2) in ionic form. The catalysts were synthesized by the solution combustion technique. The compounds showed high activity and CO tolerance for the reaction.