The complex of methyltransferase-like proteins 3 and 14 (METTL3-14) is the major enzyme that deposits N6-methyladenosine (m6A) modifications on messenger RNA (mRNA) in humans. METTL3-14 plays key roles in various biological processes through its methyltransferase (MTase) activity. However, little is known about its substrate recognition and methyl transfer mechanism from its cofactor and methyl donor S-adenosylmethionine (SAM). Here, we study the MTase mechanism of METTL3-14 by a combined experimental and multiscale simulation approach using bisubstrate analogues (BAs), conjugates of a SAM-like moiety connected to the N6-atom of adenosine. Molecular dynamics simulations based on crystal structures of METTL3-14 with BAs suggest that the Y406 side chain of METTL3 is involved in the recruitment of adenosine and release of m6A. A crystal structure with a BA representing the transition state of methyl transfer shows a direct involvement of the METTL3 side chains E481 and K513 in adenosine binding which is supported by mutational analysis. Quantum mechanics/molecular mechanics (QM/MM) free energy calculations indicate that methyl transfer occurs without prior deprotonation of adenosine-N6. Furthermore, the QM/MM calculations provide further support for the role of electrostatic contributions of E481 and K513 to catalysis. The multidisciplinary approach used here sheds light on the (co)substrate binding mechanism, catalytic step, and (co)product release, and suggests that the latter step is rate-limiting for METTL3. The atomistic information on the substrate binding and methyl transfer reaction of METTL3 can be useful for understanding the mechanisms of other RNA MTases and for the design of transition state analogues as their inhibitors.

MIL-53(Al) is a metal-organic framework (MOF) with unique properties, including structural flexibility, thermal stability, and luminescence. Its ability to adsorb volatile organic compounds (VOCs) and water vapor makes it a promising platform for sensing applications. This study investigated the adsorption mechanism of MIL-53(Al) with different VOCs, including ketones, alcohols, aromatics, and water molecules, focusing on structural transformations due to pore size variation and photoluminescence properties. The reported results assess MIL-53(Al) selectivity towards different VOCs and provide insights into their fundamental properties and potential applications in sensing.

The wide array of structures and characteristics found in ZnO-based nanostructures offers them a versatile range of uses. Over the past decade, significant attention has been drawn to the possible applications of these materials in the biomedical field, owing to their distinctive electronic, optical, catalytic, and antimicrobial attributes, alongside their exceptional biocompatibility and surface chemistry. With environmental degradation and an aging population contributing to escalating healthcare needs and costs, particularly in developing nations, there's a growing demand for more effective and affordable biomedical devices with innovative functionalities. This review delves into particular essential facets of different synthetic approaches (chemical and green) that contribute to the production of effective multifunctional nano-ZnO particles for biomedical applications. Outlining the conjugation of ZnO nanoparticles highlights the enhancement of biomedical capacity while lowering toxicity. Additionally, recent progress in the study of ZnO-based nano-biomaterials tailored for biomedical purposes is explored, including biosensing, bioimaging, tissue regeneration, drug delivery, as well as vaccines and immunotherapy. The final section focuses on nano-ZnO particles' toxicity mechanism with special emphasis to their neurotoxic potential, as well as the primary toxicity pathways, providing an overall review of the up-to-date development and future perspectives of nano-ZnO particles in the biomedicine field.

Metal-organic frameworks and supramolecular metal-organic frameworks (SMOFs) exhibit great potential for a broad range of applications taking advantage of the high surface area and pore sizes and tunable chemistry. In particular, metalloporphyrin-based MOFs and SMOFs are becoming of great importance in many fields due to the bioessential functions of these macrocycles that are being mimicked. On the other hand, during the last years, proton-conducting materials have aroused much interest, and those presenting high conductivity values are potential candidates to play a key role in some solid-state electrochemical devices such as batteries and fuel cells. In this way, using metalloporphyrins as building units we have obtained a new crystalline material with formula [H(bipy)]2[(MnTPPS)(H2O)2]·2bipy·14H2O, where bipy is 4,4'-bipyidine and TPPS4- is the meso-tetra(4-sulfonatephenyl) porphyrin. The crystal structure shows a zig-zag water chain along the [100] direction located between the sulfonate groups of the porphyrin. Taking into account those structural features, the compound was tested for proton conduction by complex electrochemical impedance spectroscopy (EIS). The as-obtained conductivity is 1 × 10-2 S·cm-1 at 40 °C and 98% relative humidity, which is a remarkably high value.

The determination of thyroid hormones has practical clinical significance for the diagnosis of hyperthyroidism and hypothyroidism diseases. Considering this aspect, a wide range of analytical methods for the detection of analytes, including immunoassay, chemiluminescence, mass spectroscopy and high-performance liquid chromatography, among others, has been developed. This type of analysis provides feasible results. Nevertheless, it requires qualified staff, special facilities and is time-consuming. For this reason, this paper relies on the fabrication of an electrochemical device developed with inkjet printing technology for the free detection of Thyroxine (T4). To manufacture our electrochemical device, several aspects were considered from the use of materials that amplify electrical signals, to finding a supramolecular scaffold that possess affinity towards the target analyte and the need of preconcentrating the analyte on the electrode's surface. For this task, printed devices were modified with a hybrid nanomaterial consisting of reduced graphene oxide (rGO) tuned with Au nanoparticles (Au-NPs) and an entrapment agent and different thiolated cyclodextrins (x-CD-SH) as carrying agents. Analytes were preconcentrated via supramolecular chemistry due to the formation of an inclusion complex between the cyclodextrin and hormones. Morphological and electrochemical characterization of the final device was carried out to ensure the proper workability of the electrode, achieving excellent response, sensitivity and limit of detection (LOD).

The modern global trend toward sustainable processes that meet the requirements of "green chemistry" provides new opportunities for the broad application of highly active, selective, and specific enzymatic reactions. However, the effective application of enzymes in industrial processes requires the development of systems for the remote regulation of their activity triggered by external physical stimuli, one of which is a low-frequency magnetic field (LFMF). Magnetic nanoparticles (MNPs) transform the energy of an LFMF into mechanical forces and deformations applied to enzyme molecules on the surfaces of MNPs. Here, we demonstrate the up- and down-regulation of two biotechnologically important enzymes, yeast alcohol dehydrogenase (YADH) and soybean formate dehydrogenase (FDH), in aggregates with gold-covered magnetic nanoparticles (GCMNPs) triggered by an LFMF. Two types of aggregates, "dimeric" (with the enzyme attached to several GCMNPs simultaneously), with YADH or FDH, and "monomeric" (the enzyme attached to only one GCMNP), with FDH, were synthesized. Depending on the aggregate type ("dimeric" or "monomeric"), LFMF treatment led to a decrease (down-regulation) or an increase (up-regulation) in enzyme activity. For "dimeric" aggregates, we observed 67 ± 9% and 47 ± 7% decreases in enzyme activity under LFMF exposure for YADH and FDH, respectively. Moreover, in the case of YADH, varying the enzyme or the cross-linking agent concentration led to different magnitudes of the LFMF effect, which was more significant at lower enzyme and higher cross-linking agent concentrations. Different responses to LFMF exposure depending on cofactor presence were also demonstrated. This effect might result from a varying cofactor binding efficiency to enzymes. For the "monomeric" aggregates with FDH, the LFMF treatment caused a significant increase in enzyme activity; the magnitude of this effect depended on the cofactor type: we observed up to 40% enzyme up-regulation in the case of NADP+, while almost no effect was observed in the case of NAD+.

In the last decade, silicon-based quantum dots (SiQDs) have attracted the attention of researchers due to their unique properties for which they are used in medical applications and in vivo imaging. Detection of cytotoxic effects in vivo is essential for understanding the mechanisms of toxicity, a mandatory step before their administration to human subjects. In this context, we aimed to evaluate the in vivo hepatic and renal acute toxicity of SiQDs obtained by laser ablation. The nanoparticles were administrated at different doses (0, 1, 10, and 100 mg of QDs/kg of body weight) by intravenous injection into the caudal vein of Swiss mice. After 1, 6, 24, and 72 h, the animals were euthanatized, and liver and kidney tissues were used in further toxicity tests. The time- and dose-dependent effects of SiQDs on the antioxidant defense system of mice liver and kidney were investigated by quantifying the activity of antioxidant enzymes (catalase, superoxide dismutase, glutathione peroxidase, glutathione reductase, and glutathione S-transferase) in correlation with the morphological changes and inflammatory status in the liver and kidneys. The results showed a decrease in the activities of antioxidant enzymes and histopathological changes, except for superoxide dismutase, in which no significant changes were registered compared with the control. Furthermore, the immunohistochemical expression of TNF-α was significant at doses over 10 mg of QDs/kg of body weight and were still evident at 72 h after administration. Our results showed that doses under 10 mg of SiQDs/kg of b.w. did not induce hepatic and renal toxicity, providing useful information for further clinical trials.

The global increase in multidrug-resistant bacteria poses a challenge to public health and requires the development of new antibacterial materials. In this study, we examined the bactericidal properties of mesoporous silica-coated silver nanoparticles, varying the core sizes (ca. 28 nm and 51 nm). We also investigated gold nanoparticles (ca. 26 nm) coated with mesoporous silica as possible inert metal cores. To investigate the modification of antimicrobial activity after the surface charge change, we used silver nanoparticles with a silver core of 28 nm coated with a mesoporous shell (ca. 16 nm) and functionalized with a terminal amine group. Furthermore, we developed a facile method to create mesoporous silica-coated silver nanoparticles (Ag@mSiO2) doped films using polyurethane (IROGRAN®) as a polymer matrix via solution casting. The antibacterial effects of silver nanoparticles with different core sizes were analyzed against Gram-negative and Gram-positive bacteria relevant to the healthcare and food industry. The results demonstrated that gold nanoparticles were inert, while silver nanoparticles exhibited antibacterial effects against Gram-negative (Escherichia coli and Salmonella enterica subsp. enterica serovar Choleraesuis) and Gram-positive (Bacillus cereus) strains. In particular, the larger Ag@mSiO2 nanoparticles showed a minimum inhibitory concentration (MIC) and a minimum bactericidal concentration (MBC) of 18 µg/mL in the Salmonella strain. Furthermore, upon terminal amine functionalization, reversing the surface charge to positive values, there was a significant increase in the antibacterial activity of the NPs compared to their negative counterparts. Finally, the antimicrobial properties of the nanoparticle-doped polyurethane films revealed a substantial improvement in antibacterial efficacy. This study provides valuable information on the potential of mesoporous silica-coated silver nanoparticles and their applications in fighting multidrug-resistant bacteria, especially in the healthcare and food industries.

Molten slag has different properties depending on its composition. The relationship between its composition, structure, and properties has been the focus of attention in industrial manufacturing processes. This review describes the atomistic scale mechanisms by which oxides of different compositions affect the properties and structure of slag, and depicts the current state of research in the atomic simulation of molten slag. At present, the research on the macroscopic properties of molten slag mainly focuses on viscosity, free-running temperature, melting point, and desulphurization capacity. Regulating the composition has become the most direct and effective way to control slag properties. Analysis of the microevolution mechanism is the fundamental way to grasp the macroscopic properties. The microstructural evolution mechanism, especially at the atomic and nanoscale of molten slag, is reviewed from three aspects: basic oxides, acidic oxides, and amphoteric oxides. The evolution of macroscopic properties is analyzed in depth through the evolution of the atomic structure. Resolution of the macroscopic properties of molten slag by the atomic structure plays a crucial role in the development of fundamental theories of physicochemistry.

The initial electrical characteristics and bias stabilities of thin-film transistors (TFTs) are vital factors regarding the practical use of electronic devices. In this study, the dependence of positive bias stress (PBS) instability on an initial threshold voltage (VTH) and its origin were analyzed by understanding the roles of slow and fast traps in solution-processed oxide TFTs. To control the initial VTH of oxide TFTs, the indium oxide (InOx) semiconductor was doped with aluminum (Al), which functioned as a carrier suppressor. The concentration of oxygen vacancies decreased as the Al doping concentration increased, causing a positive VTH shift in the InOx TFTs. The VTH shift (∆VTH) caused by PBS increased exponentially when VTH was increased, and a distinct tendency was observed as the gate bias stress increased due to a high vertical electric field in the oxide dielectric. In addition, the recovery behavior was analyzed to reveal the influence of fast and slow traps on ∆VTH by PBS. Results revealed that the effect of the slow trap increased as the VTH moved in the positive direction; this occured because the main electron trap location moved away from the interface as the Fermi level approached the conduction band minimum. Understanding the correlation between VTH and PBS instability can contribute to optimizing the fabrication of oxide TFT-based circuits for electronic applications.

Regioselective C6 and C2,C3 carboxylated cellulose nanofibrils (CNFs) have been robustly generated from dissolving pulp, a readily available source of unmodified cellulose, via stoichiometrically optimized 2,2,6,6-tetramethylpyperidine-1-oxyl (TEMPO)-mediated and sequential sodium periodate-sodium chlorite (PC) oxidation coupled with high-speed blending. Both regioselectively optimized carboxylated CNF series possess the widest ranges of comparable charges (0.72-1.48 mmol/g for T-CNFs vs. 0.72-1.10 mmol/g for PC-CNFs), but similar ranges of thickness (1.3-2.4 nm for T-CNF, 1.8-2.7 nm PC-CNF), widths (4.6-6.6 nm T-CNF, 5.5-5.9 nm PC-CNF), and lengths (254-481 nm T-CNF, 247-442 nm PC-CNF). TEMPO-mediated oxidation is milder and one-pot, thus more time and process efficient, whereas the sequential periodate-chlorite oxidation produces C2,C3 dialdehyde intermediates that are amenable to further chemical functionalization or post-reactions. These two well-characterized regioselectively carboxylated CNF series represent coherent cellulose nanomaterial models from a single woody source and have served as references for their safety study toward the development of a safer-by-design substance evaluation tool.

Polyphosphate exhibits a unique post-translational modification-like function, known as histidine polyphosphate modification (HPM), marked by a robust non-covalent interaction with histidine repeat proteins. Here, we present a protocol for detecting HPM of human proteins via maltose-binding protein-tagged expression in E. coli. We describe steps for detecting HPM by observing electrophoretic mobility shifts on NuPAGE gels followed by western blot. We then detail procedures for analyzing the influence of ionic strength and pH on HPM. For complete details on the use and execution of this protocol, please refer to Neville et al.1.

Drosophila intestinal tumors show an extended cellular heterogeneity. We devise a protocol to assess tumor cell heterogeneity by employing nuclear size measurement and immunofluorescence-based cell lineage analysis. We describe steps for intestinal dissection, staining, and imaging, followed by detailed procedures for nuclear size analysis. This approach detects overall heterogeneity across the entire tumor cell population and deviations within specific cell populations. The procedure is also applicable for analyzing the heterogeneity of wild-type intestinal cells in various contexts. For complete details on the use and execution of this protocol, please refer to Pranoto et al.1.

A novel class of protein misfolding characterized by either the formation of non-native noncovalent lasso entanglements in the misfolded structure or loss of native entanglements has been predicted to exist and found circumstantial support through biochemical assays and limited-proteolysis mass spectrometry data. Here, we examine whether it is possible to design small molecule compounds that can bind to specific folding intermediates and thereby avoid these misfolded states in computer simulations under idealized conditions (perfect drug-binding specificity, zero promiscuity, and a smooth energy landscape). Studying two proteins, type III chloramphenicol acetyltransferase (CAT-III) and D-alanyl-D-alanine ligase B (DDLB), that were previously suggested to form soluble misfolded states through a mechanism involving a failure-to-form of native entanglements, we explore two different drug design strategies using coarse-grained structure-based models. The first strategy, in which the native entanglement is stabilized by drug binding, failed to decrease misfolding because it formed an alternative entanglement at a nearby region. The second strategy, in which a small molecule was designed to bind to a non-native tertiary structure and thereby destabilize the native entanglement, succeeded in decreasing misfolding and increasing the native state population. This strategy worked because destabilizing the entanglement loop provided more time for the threading segment to position itself correctly to be wrapped by the loop to form the native entanglement. Further, we computationally identified several FDA-approved drugs with the potential to bind these intermediate states and rescue misfolding in these proteins. This study suggests it is possible for small molecule drugs to prevent protein misfolding of this type.

The phlebotomine sandfly, Lutzomyia longipalpis, a major vector of the Leishmania parasite, uses terpene pheromones to attract conspecifics for mating. Examination of the L. longipalpis genome revealed a putative terpene synthase (TPS), which-upon heterologous expression in, and purification from, Escherichia coli-yielded a functional enzyme. The TPS, termed LlTPS, converted geranyl diphosphate (GPP) into a mixture of monoterpenes with low efficiency, of which β-ocimene was the major product. (E,E)-farnesyl diphosphate (FPP) principally produced small amounts of (E)-β-farnesene, while (Z,E)- and (Z,Z)-FPP yielded a mixture of bisabolene isomers. None of these mono- and sesquiterpenes are known volatiles of L. longipalpis. Notably, however, when provided with (E,E,E)-geranylgeranyl diphosphate (GGPP), LlTPS gave sobralene as its major product. This diterpene pheromone is released by certain chemotypes of L. longipalpis, in particular those found in the Ceará state of Brazil. Minor diterpene components were also seen as products of the enzyme that matched those seen in a sandfly pheromone extract.

Global atmospheric methane concentrations rose by 10 to 15 ppb/y in the 1980s before abruptly slowing to 2 to 8 ppb/y in the early 1990s. This period in the 1990s is known as the "methane slowdown" and has been attributed in part to the collapse of the former Soviet Union (USSR) in December 1991, which may have decreased the methane emissions from oil and gas operations. Here, we develop a methane plume detection system based on probabilistic deep learning and human-labeled training data. We use this method to detect methane plumes from Landsat 5 satellite observations over Turkmenistan from 1986 to 2011. We focus on Turkmenistan because economic data suggest it could account for half of the decline in oil and gas emissions from the former USSR. We find an increase in both the frequency of methane plume detections and the magnitude of methane emissions following the collapse of the USSR. We estimate a national loss rate from oil and gas infrastructure in Turkmenistan of more than 10% at times, which suggests the socioeconomic turmoil led to a lack of oversight and widespread infrastructure failure in the oil and gas sector. Our finding of increased oil and gas methane emissions from Turkmenistan following the USSR's collapse casts doubt on the long-standing hypothesis regarding the methane slowdown, begging the question: "what drove the 1992 methane slowdown?"

PEX5, the peroxisomal protein shuttling receptor, binds newly synthesized proteins in the cytosol and transports them to the organelle. During its stay at the peroxisomal protein translocon, PEX5 is monoubiquitinated at its cysteine 11 residue, a mandatory modification for its subsequent ATP-dependent extraction back into the cytosol. The reason why a cysteine and not a lysine residue is the ubiquitin acceptor is unknown. Using an established rat liver-based cell-free in vitro system, we found that, in contrast to wild-type PEX5, a PEX5 protein possessing a lysine at position 11 is polyubiquitinated at the peroxisomal membrane, a modification that negatively interferes with the extraction process. Wild-type PEX5 cannot retain a polyubiquitin chain because ubiquitination at cysteine 11 is a reversible reaction, with the E2-mediated deubiquitination step presenting faster kinetics than PEX5 polyubiquitination. We propose that the reversible nonconventional ubiquitination of PEX5 ensures that neither the peroxisomal protein translocon becomes obstructed with polyubiquitinated PEX5 nor is PEX5 targeted for proteasomal degradation.

Melanoma incidence is on the rise in East Asia, yet studies of the molecular landscape are lacking in this population. We examined patients with melanoma who underwent next-generation sequencing (NGS) at a single tertiary center in South Korea, focusing on patients harboring NRAS or RAF alterations who received belvarafenib, a pan-RAF dimer inhibitor, through the Expanded Access Program (EAP).

The combination of granulocyte-colony stimulating factor (G-CSF) and plerixafor is one of the approaches for hematopoietic stem cell mobilization in patients with multiple myeloma (MM), non-Hodgkin's lymphoma (NHL), and Hodgkin's lymphoma (HL). This systematic review and meta-analysis aimed to determine the ability of G-CSF + plerixafor to mobilize peripheral blood (PB) CD34+ cells and examine its safety profile.

Anomalous transport of topological semimetals has generated significant interest for applications in optoelectronics, nanoscale devices, and interconnects. Understanding the origin of novel transport is crucial to engineering the desired material properties, yet their orders of magnitude higher transport than single-particle mobilities remain unexplained. This work demonstrates the dramatic mobility enhancements result from phonons primarily returning momentum to electrons due to phonon-electron dominating over phonon-phonon scattering. Proving this idea, proposed by Peierls in 1932, requires tuning electron and phonon dispersions without changing symmetry, topology, or disorder. This is achieved by combining de Haas - van Alphen (dHvA), electron transport, Raman scattering, and first-principles calculations in the topological semimetals MX2 (M = Nb, Ta and X = Ge, Si). Replacing Ge with Si brings the transport mobilities from an order magnitude larger than single particle ones to nearly balanced. This occurs without changing the crystal structure or topology and with small differences in disorder or Fermi surface. Simultaneously, Raman scattering and first-principles calculations establish phonon-electron dominated scattering only in the MGe2 compounds. Thus, this study proves that phonon-drag is crucial to the transport properties of topological semimetals and provides insight to engineer these materials further.