Dynamic landscape and evolution of m6A methylation in human.

m6A is a prevalent internal modification in mRNAs and has been linked to the diverse effects on mRNA fate. To explore the landscape and evolution of human m6A, we generated 27 m6A methylomes across major adult tissues. These data reveal dynamic m6A methylation across tissue types, uncover both broadly or tissue-specifically methylated sites, and identify an unexpected enrichment of m6A methylation at non-canonical cleavage sites. A comparison of fetal and adult m6A methylomes reveals that m6A preferentially occupies CDS regions in fetal tissues. Moreover, the m6A sub-motifs vary between fetal and adult tissues or across tissue types. From the evolutionary perspective, we uncover that the selection pressure on m6A sites varies and depends on their genic locations. Unexpectedly, we found that ∼40% of the 3'UTR m6A sites are under negative selection, which is higher than the evolutionary constraint on miRNA binding sites, and much higher than that on A-to-I RNA modification. Moreover, the recently gained m6A sites in human populations are clearly under positive selection and associated with traits or diseases. Our work provides a resource of human m6A profile for future studies of m6A functions, and suggests a role of m6A modification in human evolutionary adaptation and disease susceptibility.

Edges of graphene and carbon nanotubes with high catalytic performance for the oxygen reduction reaction.

We invented a practical and simple wet-grinding method to break conventional graphene sheets and CNTs for the production of new graphene/CNTs with adequate edge density (about 25 000 atoms per graphene-fragment of about 1 µm2 in size) and no detectable changes in intrinsic defects, extrinsic impurities, and even surface-area. Measurements using the standard cyclic voltammetry, rotating disk electrode and rotating ring-disk electrode techniques all confirm that such mildly fragmented graphene, as well as carbon-nanotubes treated similarly using this wet-grinding method, can facilitate the fast 4-electron oxygen reduction reaction (ORR) pathway. Our first-principles computational studies of the ORR on graphene, as well as the relevant known data in the literature, support an intriguing proposition that the ORR can be speeded up simply by increasing the edge-density of graphene. The adsorption of O2 involving both oxygen atoms, which causes O-O elongation, is best facilitated at the edge of graphene, facilitating a multi-step 4-electron ORR process.

Construction of multileveled and oriented micro/nano channels in Mg doped hydroxyapitite bioceramics and their effect on mimicking mechanical property of cortical bone and biological performance of cancellous bone.

Drawing on the structure and components of natural bone, this study developed Mg-doped hydroxyapatite (Mg-HA) bioceramics, characterized by multileveled and oriented micro/nano channels. These channels play a critical role in ensuring both mechanical and biological properties, making bioceramics suitable for various bone defects, particularly those bearing loads. Bioceramics feature uniformly distributed nanogrooves along the microchannels. The compressive strength or fracture toughness of the Mg-HA bioceramics with micro/nano channels formed by single carbon nanotube/carbon fiber (CNT/CF) (Mg-HA(05-CNT/CF)) are comparable to those of cortical bone, attributed to a combination of strengthened compact walls and microchannels, along with a toughening mechanism involving crack pinning and deflection at nanogroove intersections. The introduction of uniform nanogrooves also enhanced the porosity by 35.4 %, while maintaining high permeability owing to the capillary action in the oriented channels. This leads to superior degradation properties, protein adsorption, and in vivo osteogenesis compared with bioceramics with only microchannels. Mg-HA(05-CNT/CF) exhibited not only high strength and toughness comparable to cortical bone, but also permeability similar to cancellous bone, enhanced cell activity, and excellent osteogenic properties. This study presents a novel approach to address the global challenge of applying HA-based bioceramics to load-bearing bone defects, potentially revolutionizing their application in tissue engineering.

Potential Load-Bearing Bone Substitution Material: Carbon-Fiber-Reinforced Magnesium-Doped Hydroxyapatite Composites with Excellent Mechanical Performance and Tailored Biological Properties.

A potential load-bearing bone substitution and repair material, that is, carbon fiber (CF)-reinforced magnesium-doped hydroxyapatite (CF/Mg-HAs) composites with excellent mechanical performance and tailored biological properties, was constructed via the hydrothermal method and spark plasma sintering. A high-resolution transmission electron microscopy (TEM) was employed to characterize the nanostructure of magnesium-doped hydroxyapatite (Mg-HA). TEM images showed that the doping of Mg-induced distortions and dislocations in the hydroxyapatite lattice, resulting in decreased crystallinity and enhanced dissolution. Compressive strengths of 10% magnesium-doped hydroxyapatite (1Mg-HAs) and CF-reinforced 1Mg-HAs (CF/1Mg-HAs) were within the range of that of cortical bone. Compared with 1Mg-HAs, the fracture toughness of CF/1Mg-HAs increased by approximately 38%. The bioactivity, biocompatibility, and osteogenic induction properties of Mg-HAs and CF/Mg-HAs composites were evaluated in vitro using simulated body fluid (SBF) immersion, cell culture, osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs), and expression of genes associated with osteogenesis. When Mg-HAs were immersed in SBF, Mg2+ continued to release for up to 21 days. Mg-HAs demonstrated a satisfactory ability to induce apatite formation in comparison with HAs. The cell proliferation and morphology on CF/1Mg-HAs were similar to those of 1Mg-HAs, suggesting that adding CF had no adverse effect on cellular activity. The expression levels of osteogenesis-related genes [osteocalcin (OPN), osteopontin (OCN), and runt-related transcription factor 2 (Runx2)] on 1Mg-HAs were significantly higher at days 3 and 7 than those on HAs and 0.5Mg-HAs groups. This finding suggests that a certain amount of Mg doping had beneficial influences in the different stages of osteogenic differentiation and could induce osteogenic differentiation of BMSCs. The new bone volume to total volume ratio of implanted 1Mg-HAs (30.9% ± 4.1%) and CF/1Mg-HAs (25.4% ± 5.4%) was remarkably higher than that of HAs (21.6% ± 3.9%). 1Mg-HAs and CF/1Mg-HAs tailored an ideal effect of new bone information and implant osseointegration. The excellent mechanical performance and tailored biological properties of CF/Mg-HAs were attributed to nano Mg-doped HA, CF reinforcing, refined microstructure, and controlled composition.

Developmental mRNA m5C landscape and regulatory innovations of massive m5C modification of maternal mRNAs in animals.

m5C is one of the longest-known RNA modifications, however, its developmental dynamics, functions, and evolution in mRNAs remain largely unknown. Here, we generate quantitative mRNA m5C maps at different stages of development in 6 vertebrate and invertebrate species and find convergent and unexpected massive methylation of maternal mRNAs mediated by NSUN2 and NSUN6. Using Drosophila as a model, we reveal that embryos lacking maternal mRNA m5C undergo cell cycle delays and fail to timely initiate maternal-to-zygotic transition, implying the functional importance of maternal mRNA m5C. From invertebrates to the lineage leading to humans, two waves of m5C regulatory innovations are observed: higher animals gain cis-directed NSUN2-mediated m5C sites at the 5' end of the mRNAs, accompanied by the emergence of more structured 5'UTR regions; humans gain thousands of trans-directed NSUN6-mediated m5C sites enriched in genes regulating the mitotic cell cycle. Collectively, our studies highlight the existence and regulatory innovations of a mechanism of early embryonic development and provide key resources for elucidating the role of mRNA m5C in biology and disease.

Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals.

mRNA m5C, which has recently been implicated in the regulation of mRNA mobility, metabolism and translation, plays important regulatory roles in various biological events. Two types of m5C sites are found in mRNAs. Type I m5C sites, which contain a downstream G-rich triplet motif and are computationally predicted to be located at the 5' end of putative hairpin structures, are methylated by NSUN2. Type II m5C sites contain a downstream UCCA motif and are computationally predicted to be located in the loops of putative hairpin structures. However, their biogenesis remains unknown. Here we identified NSUN6, a methyltransferase that is known to methylate C72 of tRNAThr and tRNACys, as an mRNA methyltransferase that targets Type II m5C sites. Combining the RNA secondary structure prediction, miCLIP, and results from a high-throughput mutagenesis analysis, we determined the RNA sequence and structural features governing the specificity of NSUN6-mediated mRNA methylation. Integrating these features into an NSUN6-RNA structural model, we identified an NSUN6 variant that largely loses tRNA methylation but retains mRNA methylation ability. Finally, we revealed a weak negative correlation between m5C methylation and translation efficiency. Our findings uncover that mRNA m5C is tightly controlled by an elaborate two-enzyme system, and the protein-RNA structure analysis strategy established may be applied to other RNA modification writers to distinguish the functions of different RNA substrates of a writer protein.

irCLASH reveals RNA substrates recognized by human ADARs.

Adenosine deaminases acting on RNA (ADARs) convert adenosines to inosines in double-stranded RNA (dsRNA) in animals. Despite their importance, ADAR RNA substrates have not been mapped extensively in vivo. Here we develop irCLASH to map RNA substrates recognized by human ADARs and uncover features that determine their binding affinity and editing efficiency. We also observe a dominance of long-range interactions within ADAR substrates and analyze differences between ADAR1 and ADAR2 editing substrates. Moreover, we unexpectedly discovered that ADAR proteins bind dsRNA substrates tandemly in vivo, each with a 50-bp footprint. Using RNA duplexes recognized by ADARs as readout of pre-messenger RNA structures, we reveal distinct higher-order architectures between pre-messenger RNAs and mRNAs. Our transcriptome-wide atlas of ADAR substrates and the features governing RNA editing observed in our study will assist in the rational design of guide RNAs for ADAR-mediated RNA base editing.

Sintering Behavior and Mechanical Properties of Mullite Fibers/Hydroxyapatite Ceramic.

The effect of fiber content and sintering temperature on sintering behavior and mechanical properties of mullite fibers/hydroxyapatite composites was studied. The composites were fabricated by hydrothermal synthesis and pressureless sintering. The amount of fibers was varied from 5 wt % to 15 wt % through hydrothermal synthesis, mullite fibers and hydroxyapatite composite powders were subsequently sintered at temperatures of 1150, 1250, and 1350 °C. The composites presented a more perturbed structure by increasing fiber content. Moreover, the composites experienced pore coalescence and exhibited a dense microstructure at elevated temperature. X-ray diffraction indicated that the composites underwent various chemical reactions and generated silicate glasses. The generation of silicate glasses increased the driving force of particle rearrangement and decreased the number of pores, which promoted densification of the composites. Densification typically leads to increased hardness and bending strength. The study proposes a densification mechanism and opens new insights into the sintering properties of these materials.

Improved dispersion of SiC whisker in nano hydroxyapatite and effect of atmospheres on sintering of the SiC whisker reinforced nano hydroxyapatite composites.

In order to improve the mechanical properties of nano hydroxyapatite (HA), silicon carbide whisker (SiCw) with excellent mechanical and biological properties was used as the reinforcement for SiC whisker reinforced nano hydroxyapatite (SiCw/HA) composites. Hydrothermal synthesis method was adopted to prepare the uniformly dispersed SiCw and HA composite powders, and SiCw/HA composites were fabricated by pressureless sintering. The interfacial bonding state and mechanical properties of SiCw/HA composites in different sintering atmospheres (air and N2) were systematically investigated. The results show that the uniformity of the composite powders decreases with the increase of SiCw content, and the cross-section of SiCw/HA composites gradually changes from glossy and smooth to rough and undulate. When the content of SiCw is 15 wt%, the maximum bending strength and fracture toughness of the composites sintered in air atmosphere (HAW15) are 40.85 MPa and 1.82 MPa·m1/2 respectively, which are higher than those of pure HA. Compared with those of the SiCw/HA composites sintered in N2 atmosphere, the bending strength and fracture toughness of the HAW15 composites are increased by 154.2% and 10.3%, respectively. Moreover, Simulated body fluid (SBF) and in vitro cell behavior tests indicate that the SiCw/HA composites still have excellent bioactivity. The possible strengthening and toughening mechanisms of SiCw/HA composites are that the dispersion of SiCw in HA matrix is improved by hydrothermal process, and the interfacial bonding property is enhanced because of the reaction fusion on interface of SiCw/HA composites during sintering in air atmosphere. The adoption of hydrothermal process improves the dispersion uniformity of SiCw in HA matrix. When sintering in air atmosphere, the interfacial bonding property of SiCw/HA composite is enhanced via the reaction fusion (SiO2 is formed by the oxidation of SiCw). Both of them lead to the increase of strength and toughness of the composites. This study would provide additional insights into the feasibility of SiCw/HA composites as load-bearing implant materials in orthopedic applications.

Design and fabrication of carbon fibers with needle-like nano-HA coating to reinforce granular nano-HA composites.

Carbon fibers (CFs) with needle-like nano-hydroxyapatite (nHA) coating were first used as reinforcing materials named nHA-CFs to improve the mechanical properties of pure HA. A powder mixture containing nHA-CFs and granular nano-HA (gHA) was directly sintered by hot pressing at appropriate sintering pressure and temperature. A three-phase nHA-CFs/gHA composite was designed, fabricated, and used as an artificial bone. Results show that the bending strengths of the nHA-CFs/gHA composite are approximately 41.1% and 59.2% higher than those of CFs/gHA composite and pure HA, respectively. The possible reinforcing mechanism of nHA-CFs in the composite is also proposed at the end. When nHA-CFs are applied for preparation of nHA-CFs/gHA composites, the internal stress on its phase boundary with gHA matrix generated during cooling of sintered is significantly reduced due to the presence of the nHA coatings. It infers that nHA coatings on CFs might act as a bridge to control the forming of interfacial gaps between the gHA matrix and the CFs effectively. Our work provides additional insights into the feasibility of nHA-CFs/gHA composites as load-bearing implant materials in clinical applications.

Controllable preparation of a nano-hydroxyapatite coating on carbon fibers by electrochemical deposition and chemical treatment.

A nano-hydroxyapatite (HA) coating with appropriate thickness and morphology similar to that of human bone tissue was directly prepared onto the surfaces of carbon fibers (CFs). A mixed solution of nitric acid, hydrochloric acid, sulfuric acid, and hydrogen peroxide (NHSH) was used in the preparation process. The coating was fabricated by combining NHSH treatment and electrochemical deposition (ECD). NHSH treatment is easy to operate, produces rapid reaction, and highly effective. This method was first used to induce the nucleation and growth of HA crystals on the CF surfaces. Numerous O-containing functional groups, such as hydroxyl (-OH) and carboxyl (-COOH) groups, were grafted onto the CF surfaces by NHSH treatment (NHSH-CFs); as such, the amounts of these groups on the functionalized CFs increased by nearly 8- and 12-fold, respectively, compared with those on untreated CFs. After treatment, the NHSH-CFs not only acquired larger specific surface areas but retained surfaces free from serious corrosion or breakage. Hence, NHSH-CFs are ideal depositional substrates of HA coating during ECD. ECD was successfully used to prepare a nano-rod-like HA coating on the NHSH-CF surfaces. The elemental composition, structure, and morphology of the HA coating were effectively controlled by adjusting various technological parameters, such as the current density, deposition time, and temperature. The average central diameter of HA crystals and the coating density increased with increasing deposition time. The average central diameter of most HA crystals on the NHSH-CFs varied from approximately 60 nm to 210 nm as the deposition time increased from 60 min to 180 min. Further studies on a possible deposition mechanism revealed that numerous O-containing functional groups on the NHSH-CF surfaces could associate with electrolyte ions (Ca(2+)) to form special chemical bonds. These bonds can induce HA coating deposition and improve the interfacial bonding strength between the HA coating and NHCH-CFs. The results of this study and the proposed preparation of uniform and dense nano-HA coating provide theoretical and practical guidance for future investigations of active HA coatings on fiber materials for medical products and implants. This work also lays the foundation for the wider use of HA-coated CFs/HA composite implants in clinical application.

The effect of magnetic field on electrochemically deposited calcium phosphate/collagen coatings.

Nanostructured calcium phosphate/collagen (CaP/COL) coatings were deposited on the carbon/carbon (C/C) composites through electrochemical deposition (ECD) under magnetic field. The effect of magnetic fields with different orientations on the morphology and composition was investigated. Both the morphology and composition of the coatings could be altered by superimposed magnetic field. Under zero magnetic field and magnetic field, three-dimensional network structure consisting of collagen fibers and CaP were formed on the C/C substrate. The applied magnetic field in the electric field helped to form nanostructured and plate-like CaP on collagen fibers. For the ECD under magnetic field, the Ca/P molar ratio of the coatings was lower than the one under B=0. This may be contributed to the decreased electrical resistance or the increased electrical conductivity of electrolyte solutions under magnetic field. The nanosized CaP/COL coatings exhibited the similar morphology to the human bone and could present excellent cell bioactivity and osteoblast functions.