MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction.

MOTIVATION: Constructing a phylogenetic tree requires calculating the evolutionary distance between samples or species via large-scale resequencing data, a process that is both time-consuming and computationally demanding. Striking the right balance between accuracy and efficiency is a significant challenge. RESULTS: To address this, we introduce a new algorithm, MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction. AVAILABILITY AND IMPLEMENTATION: MIKE is publicly available on Github at https://github.com/Argonum-Clever2/mike.git.

Single Atom Ru Doped Ni2P/Fe3P Heterostructure for Boosting Hydrogen Evolution for Water Splitting.

Modulating the chemical composition and structure has been considered as one of the most promising strategies for developing high-efficient water splitting catalysts. Here, a single-atom Ru doped Ni2P/Fe3P catalyst is synthesized by introducing the dispersed Ru atoms to adjust Ni2P/Fe3P heterostructure. Single atom Ru provides effective hydrogen evolution reaction (HER) active sites for boosting catalytic activities. The catalyst with only 0.2 wt.% content of Ru exhibits an overpotential of 19.3 mV at 10 mA cm-2, which is obviously lower than 146.1 mV of Ni2P/Fe3P. Notably, an alkaline overall water electrolyzer based on Ru-Ni2P/Fe3P catalysts achieves a cell voltage of 1.47 V and operates over 600 h at 10 mA cm-2, which is superior to that of benchmark RuO2//Pt/C (1.61 V). The theoretical calculations further confirm that Ru single atom doping can effectively optimize the hydrogen/water adsorption free energy of the active site and therefore improve the HER activity of heterostructure. This work provides a valuable reference to design high-activity and durability catalyst for water splitting through the double modulation of interface-effect and atomic doping.

GLUT1 promotes cell proliferation via binds and stabilizes phosphorylated EGFR in lung adenocarcinoma.

BACKGROUND: While previous studies have primarily focused on Glucose transporter type 1 (GLUT1) related glucose metabolism signaling, we aim to discover if GLUT1 promotes tumor progression through a non-metabolic pathway. METHODS: The RNA-seq and microarray data were comprehensively analyzed to evaluate the significance of GLUT1 expression in lung adenocarcinoma (LUAD). The cell proliferation, colony formation, invasion, and migration were used to test GLUT1 's oncogenic function. Co-immunoprecipitation and mass spectrum (MS) were used to uncover potential GLUT1 interacting proteins. RNA-seq, DIA-MS, western blot, and qRT-PCR to probe the change of gene and cell signaling pathways. RESULTS: We found that GLUT1 is highly expressed in LUAD, and higher expression is related to poor patient survival. GLUT1 knockdown caused a decrease in cell proliferation, colony formation, migration, invasion, and induced apoptosis in LUAD cells. Mechanistically, GLUT1 directly interacted with phosphor-epidermal growth factor receptor (p-EGFR) and prevented EGFR protein degradation via ubiquitin-mediated proteolysis. The GLUT1 inhibitor WZB117 can increase the sensitivity of LUAD cells to EGFR-tyrosine kinase inhibitors (TKIs) Gefitinib. CONCLUSIONS: GLUT1 expression is higher in LUAD and plays an oncogenic role in lung cancer progression. Combining GLUT1 inhibitors and EGFR-TKIs could be a potential therapeutic option for LUAD treatment.

Accelerated Wound Healing by Electrospun Multifunctional Fibers with Self-Powered Performance.

Wound healing has been a persistent clinical challenge for a long time. Electrical stimulation is an effective therapy with the potential to accelerate wound healing. In this work, the self-powered electrospun nanofiber membranes (triples) were constructed as multifunctional wound dressings with electrical stimulation and biochemical capabilities. Triple was composed of a hydrolyzable inner layer with antiseptic and hemostatic chitosan, a hydrophilic core layer loaded with conductive AgNWs, and a hydrophobic outer layer fabricated by self-powered PVDF. Triple exhibited presentable wettability and acceptable moisture permeability. Electrical performance tests indicated that triple can transmit electrical signals formed by the piezoelectric effect to the wound. High antibacterial activities were observed for triple against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa, with inhibition rates of 96.52, 98.63, and 97.26%, respectively. In vitro cell assays demonstrated that triple cells showed satisfactory proliferation and mobility. A whole blood clotting test showed that triple can enhance hemostasis. The innovative self-powered multifunctional fibers presented in this work offer a promising approach to addressing complications and expediting the promotion of chronic wound healing.

Remarkable Toughening of Plastic with Monodispersed Nano-CaCO3: From Theoretical Predictions to Experimental Validation.

The structure-property relationship of poly(vinyl chloride) (PVC)/CaCO3 nanocomposites is investigated by all-atom molecular dynamics (MD) simulations. MD simulation results indicate that the dispersity of nanofillers, interfacial bonding, and chain mobility are imperative factors to improve the mechanical performance of nanocomposites, especially toughness. The tensile behavior and dissipated work of the PVC/CaCO3 model demonstrate that 12 wt % CaCO3 modified with oleate anion and dodecylbenzenesulfonate can impart high toughness to PVC due to its good dispersion, favorable interface interaction, and weak migration of PVC chains. Under the guidance of MD simulation, we experimentally prepared a transparent PVC/CaCO3 nanocomposite with good mechanical properties by in situ polymerization of monodispersed CaCO3 in vinyl chloride monomers. Interestingly, experimental tests indicate that the optimum toughness of a nanocomposite (a 368% increase in the elongation at break and 204% improvement of the impact strength) can be indeed realized by adding 12 wt % CaCO3 modified with oleic acid and dodecylbenzenesulfonic acid, which is remarkably consistent with the MD simulation prediction. In short, this work provides a proof-of-concept of using MD simulation to guide the experimental synthesis of PVC/CaCO3 nanocomposites, which can be considered as an example to develop other functional nanocomposites.

Carbene-Catalyzed Atroposelective Construction of Chiral Diaryl Ethers.

Atropoisomeric chemotypes of diaryl ethers-related scaffolds are prevalent in naturally active compounds. Nevertheless, there remains considerable research to be carried out on the catalytic asymmetric synthesis of these axially chiral molecules. In this instance, we disclose an N-heterocyclic carbene (NHC)-catalyzed synthesis of axially chiral diaryl ethers via atroposelective esterification of dialdehyde-containing diaryl ethers. NHC desymmetrization produces axially chiral diaryl ether atropisomers with high yields and enantioselectivities in moderate circumstances. Chiral diaryl ether compounds may be precursors for highly functionalized diaryl ethers with bioactivity and chiral ligands for asymmetric catalysis.

Creating a functional single-chromosome yeast.

Eukaryotic genomes are generally organized in multiple chromosomes. Here we have created a functional single-chromosome yeast from a Saccharomyces cerevisiae haploid cell containing sixteen linear chromosomes, by successive end-to-end chromosome fusions and centromere deletions. The fusion of sixteen native linear chromosomes into a single chromosome results in marked changes to the global three-dimensional structure of the chromosome due to the loss of all centromere-associated inter-chromosomal interactions, most telomere-associated inter-chromosomal interactions and 67.4% of intra-chromosomal interactions. However, the single-chromosome and wild-type yeast cells have nearly identical transcriptome and similar phenome profiles. The giant single chromosome can support cell life, although this strain shows reduced growth across environments, competitiveness, gamete production and viability. This synthetic biology study demonstrates an approach to exploration of eukaryote evolution with respect to chromosome structure and function.

LncRNA BBOX1-AS1 targets miR-361-3p/COL1A1 axis to drive the progression of oesophageal carcinoma.

BACKGROUND: Oesophageal carcinoma (EC) is one of the types of prevalent malignant cancer in the globe. Many researchers reported the vital role played by long-coding RNAs in EC. In the current research, we investigated the mechanisms of the action of lncRNA BBOX1-AS1 in EC progression. METHODS: In EC tissues and EC cells, the expression levels of miR-361-3p along with COL1A1 and BBOX1-AS1 were detected through RT-qPCR or western blotting. MiR-361-3p interactions with BBOX1-AS1 or COL1A1 were verified through Luciferase reporter and RIP tests. Loss of function combined with caspase-3 activity, CCK-8 and Transwell assays was performed to investigate cell apoptosis, proliferation and migration, respectively. Knockdown of BBOX1-AS1 was used for evaluating BBOX1-AS1 effects on tumour development in vivo. RESULTS: BBOX1-AS1 was remarkably elevated in EC tissues and cells. In addition, the silencing of BBOX1-AS1 attenuated the cell viability, cell migration and enhanced cell apoptosis of EC, as well as suppressed EC tumour formation in vivo. Moreover, BBOX1-AS1 was found to be a sponge of miR-361-3p, which downregulated miR-361-3p expression. MiR-361-3p inhibitor rescued the anti-tumour effect of BBOX1-AS1 knockdown on the progression of EC. Furthermore, we discovered that miR-361-3p specially bound to COL1A1 3'UTR and downregulated COL1A1 and COL1A1 reduction declined the promoting effect of silencing miR-361-3p on EC cell malignant phenotypes. CONCLUSION: BBOX1-AS1 facilitated the EC development and malignancy via miR-361-3p/COL1A1 axis, indicating BBOX1-AS1 could be a novel therapy target for the diagnostic of EC.

Iridium-Catalyzed Asymmetric Allylic Substitution Reaction of 4-Hydroxypyran-2-one.

Pyranones have raised great concerns owing to their considerable applications in a variety of sectors. However, the development of direct asymmetric allylation of 4-hydroxypyran-2-ones is still restricted. Herein, we present an effective iridium-catalyzed asymmetric functionalization technique for the synthesis of 4-hydroxypyran-2-one derivatives over direct and efficient catalytic asymmetric Friedel-Crafts-type allylation by using allyl alcohols. The allylation products could be obtained with good to high yields (up to 96%) and excellent enantioselectivities (>99% ee). Therefore, the disclosed technique provides a new asymmetric synthetic strategy to explore pyranone derivatives in depth, thus providing an interesting approach for global application and further utilization in organic synthesis and pharmaceutical chemistry.

A Dynamic Kinetic Resolution Approach to Axially Chiral Diaryl Ethers by Catalytic Atroposelective Transfer Hydrogenation.

Diaryl ethers are widespread in biologically active compounds, ligands and catalysts. It is known that the diaryl ether skeleton may exhibit atropisomerism when both aryl rings are unsymmetrically substituted with bulky groups. Despite recent advances, only very few catalytic asymmetric methods have been developed to construct such axially chiral compounds. We describe herein a dynamic kinetic resolution approach to axially chiral diaryl ethers via a Brønsted acid catalyzed atroposelective transfer hydrogenation (ATH) reaction of dicarbaldehydes with anilines. The desired diaryl ethers could be obtained in moderate to good chemical yields (up to 79 %) and high enantioselectivities (up to 95 % ee) under standard reaction conditions. Such structural motifs are interesting precursors for further transformations and may have potential applications in the synthesis of chiral ligands or catalysts.

PtCuRu Nanoflowers with Ru-Rich Edge for Efficient Fuel-Cell Electrocatalysis.

Enhancing the catalytic activity of Pt-based alloy by a rational structural design is the key to addressing the sluggish kinetics of direct alcohol fuel cells. Herein, a facile one-pot method is reported to synthesize PtCuRu nanoflowers (NFs). The synergetic effect among Pt, Cu, and Ru can lower the d-band center of Pt, regulate the morphology, generate Ru-rich edge, and allow the exposure of more high index facets. The optimized Pt0.68 Cu0.18 Ru0.14 NFs exhibit outstanding electrocatalytic performances and excellent anti-poisoning abilities. The specific activities for the methanol oxidation reaction (MOR) (7.65 mA cm-2 ) and ethanol oxidation reaction (EOR) (7.90 mA cm-2 ) are 6.0 and 7.1 times higher than commercial Pt/C, respectively. The CO stripping experiment and the chronoamperometric (5000 s) demonstrate the superior anti-poisoning property and durability performance. Density functional theory calculations confirm that high metallization degree leads to the decrease of d-band center, the promotion of oxidation of CO, and improvement of the inherent activity and anti-poisoning ability. A Ru-rich edge exposes abundant high index facets to accelerate the reaction kinetics of rate-determining steps by decreasing the energy barrier for forming *HCOOH (MOR) and CC bond breaking (EOR).

N-Doped MoS2 Nanoflowers for Efficient Cr(VI) Removal.

The removal of Cr(VI) has attracted extensive attention since it causes serious harm to public health. Herein, we report a two-step method to synthesize N-doped MoS2 nanoflowers (NFs) with controllable sizes, which are first utilized for Cr(VI) removal and display outstanding removal performance. The N-MoS2 NFs with an average size of 40 nm (N-MoS2 NFs-40 nm) can rapidly remove Cr(VI) in 15 min under optimal conditions. The maximum adsorption capacity of N-MoS2 NFs-40 nm can reach 787.41 mg·g-1, which is significantly larger than that of N-MoS2 NFs-150 and -400 nm (314.46 and 229.88 mg·g-1). Meanwhile, N-MoS2 NFs-400 nm have a higher maximum adsorption capacity than pure MoS2 NFs-400 nm (172.12 mg·g-1). In this adsorption/reduction process, N-MoS2 NFs have abundant adsorption sites due to a high surface area. N doping can generate more sulfur vacancy defects in the MoS2 NF structure to accelerate electron transfer and enhance the reduction of Cr(VI) to low-toxicity Cr(III). This study provides a facile approach to fabricating N-MoS2 nanoflowers and demonstrates their superior removal ability for Cr(VI).

Versatilely Manipulating the Mechanical Properties of Polymer Nanocomposites by Incorporating Porous Fillers: A Molecular Dynamics Simulation Study.

Polymer nanocomposites (PNCs) have been attracting myriad scientific and technological attention due to their promising mechanical and functional properties. However, there remains a need for an efficient method that can further strengthen the mechanical performance of PNCs. Here, we propose a strategy to design and fabricate novel PNCs by incorporating porous fillers (PFs) such as metal-organic frameworks with ultrahigh specific surface areas and tunable nanospaces to polymer matrices via coarse-grained molecular dynamics simulations. Three important parameters─the polymer chain stiffness (k), the interaction strength between the PF center and the end functional groups of polymer chains (εcenter end), and the PF weight fraction (w)─are systematically examined. First, attributed to the penetration of polymer chains into PFs at a strong εcenter end, the dimension of polymer chains such as the radius of gyration and the end-to-end distance increases greatly as a function of k compared to the case of the neat polymer system. The penetration of polymer chains is validated by characterizing the radial distribution function between end functional groups and filler centers, as well as the visualization of the snapshots. Also, the dispersion state of PFs tends to be good because of the chain penetration. Then, the glass transition temperature ratio of PNCs to that of the neat systems exhibits a maximum in the case of k = 5ε, indicating that the strongest interlocking between polymer chains and PFs occurs at intermediate chain stiffness. The polymer chain dynamics of PNCs decreases to a plateau at k = 5ε and then becomes stable, and the relative mobility to that of the neat system as well presents the same variation trend. Furthermore, the mechanical property under uniaxial deformation is thoroughly studied, and intermediates k, εcenter end, and w can bring about the best mechanical property. This is because of the robust penetration and interaction, which is confirmed by calculating the stress of every component of PNCs with and without end functional groups and PF centers as well as the nonbonded interaction energy change between different components. Finally, the optimal condition (k = 5.36ε, εcenter end = 5.29ε, and w = 6.54%) to design the PNC with superior mechanical behavior is predicted by Gaussian process regression, an active machine learning (ML) method. Overall, incorporating PFs greatly enhances the entanglements and interactions between polymer chains and nanofillers and brings effective mechanical reinforcements with lower filler weight fractions. We anticipate that this will provide new routes to the design of mechanically reinforced PNCs.

Unveiling the high-activity origin of single-atom iron catalysts for oxygen reduction reaction.

It is still a grand challenge to develop a highly efficient nonprecious-metal electrocatalyst to replace the Pt-based catalysts for oxygen reduction reaction (ORR). Here, we propose a surfactant-assisted method to synthesize single-atom iron catalysts (SA-Fe/NG). The half-wave potential of SA-Fe/NG is only 30 mV less than 20% Pt/C in acidic medium, while it is 30 mV superior to 20% Pt/C in alkaline medium. Moreover, SA-Fe/NG shows extremely high stability with only 12 mV and 15 mV negative shifts after 5,000 cycles in acidic and alkaline media, respectively. Impressively, the SA-Fe/NG-based acidic proton exchange membrane fuel cell (PEMFC) exhibits a high power density of 823 mW cm-2 Combining experimental results and density-functional theory (DFT) calculations, we further reveal that the origin of high-ORR activity of SA-Fe/NG is from the Fe-pyrrolic-N species, because such molecular incorporation is the key, leading to the active site increase in an order of magnitude which successfully clarifies the bottleneck puzzle of why a small amount of iron in the SA-Fe catalysts can exhibit extremely superior ORR activity.

Mechanical and Self-Healing Behavior of Matrix-Free Polymer Nanocomposites Constructed via Grafted Graphene Nanosheets.

Through molecular dynamics (MD) simulation, the structure and mechanical properties of matrix-free polymer nanocomposites (PNCs) constructed via polymer-grafted graphene nanosheets are studied. The dispersion of graphene sheets is characterized by the radial distribution function (RDF) between graphene sheets. We observe that a longer polymer chain length Lg leads to a relatively better dispersion state attributed to the formation of a better brick-mud structure, effectively screening the van der Waals interactions between sheets. By tuning the interaction strength εend-end between end functional groups of grafted chains, we construct physical networks with various robustness characterized by the formation of the fractal clusters at high εend-end values. The effects of εend-end and Lg on the mechanical properties are examined, and the enhancement of the stress-strain behavior is observed with the increase of εend-end and Lg. Structural evolution during deformation is quantified by calculating the orientation of the graphene sheets and their distribution, the stress decomposition, and the size of the clusters formed between end groups and their distribution. Then, we briefly study the effects of time and temperature on the self-healing behavior of these unique PNCs in the rubbery state. Lastly, the self-healing kinetics is quantitatively analyzed. In general, this work can provide some rational guidelines to design and fabricate matrix-free PNCs with both excellent mechanical and self-healing properties.

Ketone-Directed Cobalt(III)-Catalyzed Regioselective C2 Amidation of Indoles.

An efficient cobalt(III)-catalyzed method for the direct C-H amidation of unprotected indoles for 2-amino indole scaffold construction has been developed. With dioxazolone as the amidating reagent, a variety of 2-amino indole derivatives were achieved in moderate to excellent yields using an organic acid as the additive and a ketone as the directing group.

Pd-Catalyzed Dearomative Asymmetric Allylic Alkylation of Naphthols with Alkoxyallenes.

A Pd-catalyzed linear selective intermolecular asymmetric dearomative allylic alkylation reaction of naphthols with alkoxyallenes under mild reaction conditions is reported. The transformation is successfully promoted by Pd2(dba)3 and the chiral Trost ligand and provides a general atom-efficient protocol to obtain various ß-naphthalenones bearing an all carbon quaternary stereogenic center in good yields and chemo- and stereoselectivities.

Surfactant-Free Aqueous Dispersions of Shape- and Size-Controlled Zirconia Colloidal Nanocrystal Clusters with Enhanced Photocatalytic Activity.

Colloidal nanocrystal clusters (CNCs) are formed by clustering nanocrystals into secondary structures, which represent a new class of materials and have attracted considerable attention, owing to their unique collective properties and novel functionalities achieved from the ensembles in addition to the properties of each individual subunit. Here, we design a simple route to prepare aqueous dispersions of highly stable ZrO2 CNCs with tunable shape and size without modification. ZrO2 CNCs are composed of many ZrO2 nanocrystals each with a size of about 7 nm and possess a mesoporous structure. Both cube-like and star-like shapes of CNCs can be achieved by using different alkaline sources, while the size of CNCs can be adjusted by changing the hydrothermal time. The as-prepared aqueous dispersions of ZrO2 CNCs display an enhanced photocatalytic activity in the degradation of rhodamine B (RhB), compared with ZrO2 nanodispersions. More interestingly, star-like ZrO2 CNCs show better photocatalytic degradation properties than those of cube-like counterparts and even commercial P25. Furthermore, ZrO2 CNCs are easily recycled and can be used for the degradation of a range of dye systems.

Palladium-Catalyzed Allylic Substitution Reaction of Benzothiazolylacetamide with Allylic Alcohols in Water.

An efficient tetrakis(triphenylphosphine)palladium- and Brønsted acid catalyzed allylic substitution reaction of benzothiazolylacetamide with allylic alcohols in water has been developed, and the corresponding allylated products were afforded in good to excellent (up to 99%) yields with high regioselectivities. This straightforward protocol exhibits good functional group tolerance and scalability.

Synthesis of Transparent Aqueous ZrO2 Nanodispersion with a Controllable Crystalline Phase without Modification for a High-Refractive-Index Nanocomposite Film.

The controllable synthesis of metal oxide nanoparticles is of fundamental and technological interest. In this article, highly transparent aqueous nanodispersion of ZrO2 with controllable crystalline phase, high concentration, and long-term stability was facilely prepared without any modification via the reaction of inexpensive inorganic zirconium salt and sodium hydroxide in water under an acid surrounding, combined with hydrothermal treatment. The as-prepared transparent nanodispersion had an average particle size of 7 nm, a high stability of 18 months, and a high solid content of 35 wt %. ZrO2 nanocrystals could be readily dispersed in many solvents with high polarity including ethanol, dimethyl sulfoxide, acetic acid, ethylene glycol, and N, N-dimethylformamide, forming stable transparent nanodispersions. Furthermore, highly transparent polyvinyl alcohol/ZrO2 nanocomposite films with high refractive index were successfully prepared with a simple solution mixing route. The refractive index could be tuned from 1.528 to 1.754 (@ 589 nm) by changing the mass fraction (0-80 wt %) of ZrO2 in transparent nanocomposite films.