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5-Formylcytidine (f5C) is one type of post-transcriptional RNA modification, which is known at the wobble position of tRNA in mitochondria and essential for mitochondrial protein synthesis. Here, we show a method to detect f5C modifications in RNA and a transcriptome-wide f5C mapping technique, named f5C-seq. It is developed based on the treatment of pyridine borane, which can reduce f5C to 5,6-dihydrouracil, thus inducing C-to-T transition in f5C sites during PCR to achieve single-base resolution detection. More than 1000 f5C sites were identified after mapping in Saccharomyces cerevisiae by f5C-seq. Moreover, codon composition demonstrated a preference for f5C within wobble sites in mRNA, suggesting the potential role in regulation of translation. These findings expand the scope of the understanding of cytosine modifications in mRNA.

Deamination of cytosine and dUMP misincorporation have been found to be capable of producing uracil in the genome. This study presents the AI-seq (artificial incorporation modified nucleobase for sequencing), a “base substitution”, which not only is capable of profiling uracil at single-nucleotide resolution and showing its centromeric enrichment but could also reveal that the identified uracil sites are derived from cytosine deamination. All the results indicate the potential biological significance of uracil as the epigenetic modification., An artificial incorporation modified nucleobase strategy was developed to profile genome-wide deoxyuridine at single-base resolution by a “base substitution” strategy.

Amyotrophic lateral sclerosis (ALS) was initially thought to be associated with oxidative stress when it was first linked to mutant superoxide dismutase 1 (SOD1). The subsequent discovery of ALS-linked genes functioning in RNA processing and proteostasis raised the question of how different biological pathways converge to cause the disease. Both familial and sporadic ALS are characterized by the aggregation of the essential DNA- and RNA-binding protein TDP-43, suggesting a central role in ALS etiology. Here we report that TDP-43 aggregation in neuronal cells of mouse and human origin causes sensitivity to oxidative stress. Aggregated TDP-43 sequesters specific microRNAs (miRNAs) and proteins, leading to increased levels of some proteins while functionally depleting others. Many of those functionally perturbed gene products are nuclear-genome-encoded mitochondrial proteins, and their dysregulation causes a global mitochondrial imbalance that augments oxidative stress. We propose that this stress-aggregation cycle may underlie ALS onset and progression.

5-Formylcytidine (f

Adsorption and dissociation of H2O on monolayer MoS2 surface doped with B/Si explored by first principle calculations coupled with climb image nudged elastic band method. The impurity B/Si atoms are more likely to occupy sulfur atom lattice positions with lower formation energies, which results in the breaking of surface chemically inertness of the MoS2 (001) plane. Free H2O molecules can be adsorbed on doped surfaces with lower adsorption energies, and form chemical bonds between oxygen and impurity atoms. Adsorbed H2O can be separated into OH radical and hydrogen adatom with a lower dissociation energy barrier on these doped systems (including impurity B/Si single doped, B and Si co-doped). Furthermore, the adsorbed OH radical can be further dissociated into oxygen and hydrogen adatoms on the surface of B and Si co-doped MoS2. Our theoretical study suggests that substrate of monolayer MoS2 doped with impurity B, Si may be a potential alternative choice for hydrogen evolution reaction.

Porous silica SBA-15 was synthesized using triblock copolymer P123 as structure template and tetraethyl orthosilicate (TEOS, C8H20O4Si) as silicon source. The pore structure was adjusted by using swelling agent 1,3,5-trimethylbenzene (TMB). Small angle X-ray scattering (SAXS) and high resolution transmission electron microscopy (HRTEM) indicate that the pore morphology changes in three stages with increasing TMB/P123 ratio. In the first stage (TMB/P123 τ 3 and τ 4, which are due to o-Ps annihilation in micropores and mesopores, respectively. It was found that the mesopores are open pores and the micropores are closed pores. With the increase of TMB ratio, the number and size of micropores show nearly no change, but the mesopore size increases gradually with increasing TMB/P123 ratio up to 0.5, which are in agreement with the results of the N2 adsorption/desorption measurements. However after the pores evolves into mesoporous foam, the pore size obtained from o-Ps lifetime is less than that of N2 adsorption/desorption measurements.

Sex reversal, representing extraordinary sexual plasticity during the life cycle, not only triggers reproduction in animals but also affects reproductive and endocrine system-related diseases and cancers in humans. Sex reversal has been broadly reported in animals, however, an integrated resource hub of sex reversal information is still lacking. Here, we constructed a comprehensive database named ASER by integrating sex reversal-related data of 18 species from Teleostei to Mammals. We systematically collected 40,018 published papers and mined the Sex Reversal-associated Genes (SRGs), including their regulatory networks, from 1,611 core papers. We annotated homologous genes and computed conservation scores for whole genomes across the 18 species. Furthermore, we collected 206 available RNA-seq data and investigated the expression dynamics of SRGs during sex reversal or sex determination processes. In addition, we manually annotated 551 ISH images of SRGs from the literature and described their spatial expression in the gonads. Collectively, ASER provides a unique and integrated resource for researchers to query and reuse organized data to explore the mechanisms and applications of SRGs in animal breeding and human health. The ASER database is publicly available at http://aser.ihb.ac.cn/.

m6A RNA modification is implicated in multiple cellular responses. However, its function in the innate immune cells is poorly understood. Here, we identified major m6A “writers” as the top candidate genes regulating macrophage activation by LPS in an RNA binding protein focused CRISPR screening. We have confirmed that Mettl3-deficient macrophages exhibited reduced TNF-α production upon LPS stimulation in vitro. Consistently, Mettl3flox/flox;Lyzm-Cre mice displayed increased susceptibility to bacterial infection and showed faster tumor growth. Mechanistically, the transcripts of the Irakm gene encoding a negative regulator of TLR4 signaling were highly decorated by m6A modification. METTL3 deficiency led to the loss of m6A modification on Irakm mRNA and slowed down its degradation, resulting in a higher level of IRAKM, which ultimately suppressed TLR signaling–mediated macrophage activation. Our findings demonstrate a previously unknown role for METTL3-mediated m6A modification in innate immune responses and implicate the m6A machinery as a potential cancer immunotherapy target.

Sex reversal, representing an extraordinary sexual plasticity during the life cycle, not only triggers reproduction in animals but also affects reproductive and endocrine system-related diseases and cancers in humans. Sex reversal has been broadly reported in animals, however, an integrated resource hub of sex reversal information is still lacking. Here, we constructed a comprehensive database named ASER (Animal Sex Reversal) by integrating sex reversal-related data of 18 species from teleostei to mammals. We systematically collected 40,018 published papers and mined the sex reversal-associated genes (SRGs), including their regulatory networks, from 1611 core papers. We annotated homologous genes and computed conservation scores for whole genomes across the 18 species. Furthermore, we collected available RNA-seq datasets and investigated the expression dynamics of SRGs during sex reversal or sex determination processes. In addition, we manually annotated 550 in situ hybridization (ISH), fluorescencein situhybridization (FISH), and immunohistochemistry (IHC) images of SRGs from the literature and described their spatial expression in the gonads. Collectively, ASER provides a unique and integrated resource for researchers to query and reuse organized data to explore the mechanisms and applications of SRGs in animal breeding and human health. The ASER database is publicly available at http://aser.ihb.ac.cn/.

CRISPR screening identifies RNA m6A modification as negative regulator of TLR signaling pathway for proper innate immune response., m6A RNA modification is implicated in multiple cellular responses. However, its function in the innate immune cells is poorly understood. Here, we identified major m6A “writers” as the top candidate genes regulating macrophage activation by LPS in an RNA binding protein focused CRISPR screening. We have confirmed that Mettl3-deficient macrophages exhibited reduced TNF-α production upon LPS stimulation in vitro. Consistently, Mettl3flox/flox;Lyzm-Cre mice displayed increased susceptibility to bacterial infection and showed faster tumor growth. Mechanistically, the transcripts of the Irakm gene encoding a negative regulator of TLR4 signaling were highly decorated by m6A modification. METTL3 deficiency led to the loss of m6A modification on Irakm mRNA and slowed down its degradation, resulting in a higher level of IRAKM, which ultimately suppressed TLR signaling–mediated macrophage activation. Our findings demonstrate a previously unknown role for METTL3-mediated m6A modification in innate immune responses and implicate the m6A machinery as a potential cancer immunotherapy target.

Summary Chemical modifications to nucleobases have a great influence on various cellular processes, by making gene regulation more complex, thus indicating their profound impact on aspects of heredity, growth, and disease. Here, we provide the first genome-wide map of 5-formyluracil (5fU) in living tissues and evaluate the potential roles for 5fU in genomics. We show that an azido derivative of (2-benzimidazolyl)acetonitrile has high selectivity for enriching 5fU-containing genomic DNA. The results have demonstrated the feasibility of using this method to determine the genome-wide distribution of 5fU. Intriguingly, most 5fU sites were found in intergenic regions and introns. Also, distribution of 5fU in human thyroid carcinoma tissues is positively correlated with binding sites of POLR2A protein, which indicates that 5fU may distributed around POLR2A-binding sites., Graphical Abstract, Highlights • The derivative of (2-benzimidazolyl)acetonitrile (azi-BIAN) can selectivity label 5fU • Azi-BIAN can selectively label and pull down 5fU in the genome for NGS • The first genome-wide map of 5fU in mammalian genomic DNA • 5fU is highly enriched at intergenic regions and introns, Chemistry; Genetics; Molecular Genetics

MicroRNAs (miRNAs) are well known to target 3' untranslated regions (3' UTRs) in mRNAs, thereby silencing gene expression at the post-transcriptional level. Multiple reports have also indicated the ability of miRNAs to target protein-coding sequences (CDS); however, miRNAs have been generally believed to function through similar mechanisms regardless of the locations of their sites of action. Here, we report a class of miRNA-recognition elements (MREs) that function exclusively in CDS regions. Through functional and mechanistic characterization of these 'unusual' MREs, we demonstrate that CDS-targeted miRNAs require extensive base-pairing at the 3' side rather than the 5' seed; cause gene silencing in an Argonaute-dependent but GW182-independent manner; and repress translation by inducing transient ribosome stalling instead of mRNA destabilization. These findings reveal distinct mechanisms and functional consequences of miRNAs that target CDS versus the 3' UTR and suggest that CDS-targeted miRNAs may use a translational quality-control-related mechanism to regulate translation in mammalian cells.

High purity $$\hbox {In}_2\hbox {O}_3$$ nanopowders were subjected to different thermal treatments to investigate the role of defects on the lattice thermal conductivity. The powders were first treated by spark plasma sintering (SPS) at $$700\,^{\circ}\hbox {C}$$ and annealed in air between 700 and $$1300\,^{\circ}\hbox {C}$$ . X-ray diffraction measurements show that the samples are single phase, and the diffraction peaks become sharper with increasing of annealing temperature, indicating improvement in crystallinity and increase in grain size. The $$\hbox {In}_2\hbox {O}_3$$ nanopowders were also treated by SPS sintering at different temperatures without subsequent annealing. On the contrary, the average grain size of $$\hbox {In}_2\hbox {O}_3$$ treated by SPS has no obvious change with the increase in sintering temperatures. Positron annihilation measurements reveal large amounts of monovacancies and vacancy clusters in the $$\hbox {In}_2\hbox {O}_3$$ nanocrystals. The monovacancies gradually recover and the vacancy clusters transform into smaller vacancies with increasing annealing or sintering temperatures. The lattice thermal conductivity increases with the increase in annealing or sintering temperature, which shows close correlation with the recovery of vacancy defects after heat treatment. This gives us strong evidence that vacancy defects play an important role on the suppression of lattice thermal conductivity in nanostructured thermoelectric materials.

Due to the ultrawide bandgap (4.9 eV), high carrier mobility (300 cm2V−1s−1), and high thermal stability, β−Ga2O3 can be a potential candidate for high-temperature thermoelectric materials. However, the intrinsically high thermal conductivity may hinder its application for thermoelectric conversion. In this work, porous β−Ga2O3 was prepared by the solvothermal method together with spark plasma sintering technology. Positron lifetime measurement and N2 adsorption confirm the introduction of pores by adding sucrose in the sample preparation. The sucrose-derived β−Ga2O3 sintered at a relatively low temperature of 600 °C remains highly porous, which results in an extremely low thermal conductivity of 0.45 W m−1K−1 at room temperature, and it further decreases to 0.29 W m−1K−1 at 600 °C. This is the lowest thermal conductivity for β−Ga2O3 reported so far. Our work provides an avenue to reduce the thermal conductivity for β−Ga2O3 and is believed to be widely applicable to many other thermoelectric materials.

The stability of various defects in monolayer MoS 2 , as well as their interactions with free O 2 molecules were investigated by density functional theory (DFT) calculations coupled with the nudged elastic band (NEB) method. The defects including S vacancy (monosulfur and disulfue vacancies), antisite defect (Mo S ) and external Mo atom can exist steadily in monolayer MoS 2 , and introduce defect levels in these defective systems, which breaks the surface chemical inertness and significantly enhances the adsorption capacity for free O 2 . The adsorption energy calculations and electronic properties analysis suggest that there is a strong interaction between O 2 molecule and defective system. The adsorbed O 2 on the defective surface can dissociate with a lower activation energy barrier, which produce two active oxygen atoms. Especially, two Mo atoms can occupy one Mo lattice site, and adsorbed O 2 on the top of the Mo atom can then dissociate directly with the lowest activation energy barrier. Hence, our work may provide useful information to design MoS 2 -based gas sensor or catalysts.

Ship detection plays an important role in remote-sensing image processing. In this article, we propose a multi-layer sparse coding model-based ship detection (MSCMSD) method, integrating bottom-up and top-down mechanisms, for ship detection with high-resolution remote-sensing images. The multi-layer sparse coding model was designed to reveal the way how information is processed by human visual system. It is adopted in MSCMSD to detect candidate regions containing ships before any further processing. To detect ships from candidate regions, an omnidirectional solution is also proposed for deformable parts model-based ship detection. As demonstrated in the experiments, MSCMSD can detect ships from optical remote-sensing images with a higher accuracy than other state-of-the-art algorithms.

Co $$^+$$ ions with multiple energies from 50 to 380 keV were implanted into ZnO single crystals up to a total dose of $$1.25\times 10^{17}\,\hbox {cm}^2$$ . The implanted samples were annealed in open air for 30 min between 200 and 1100 $$^{\circ }$$ C. All the samples before and after implantation and annealing were characterized by X-ray diffraction (XRD), Raman scattering and positron annihilation measurements. XRD and Raman scattering measurements indicate that Co implantation induces severe lattice damage, and after annealing the damage recovers gradually. No Co clusters or Co-related second phase was observed in the implanted samples. Doppler broadening of positron annihilation radiation measurements using a slow positron beam reveals a large number of vacancy clusters introduced by Co implantation. After annealing up to 1000 $$^{\circ }$$ C, almost all the defects induced by implantation are removed. The implanted samples show clear ferromagnetism measured at 5 K. It shows very slight decrease after annealing at 700 $$^{\circ }$$ C and becomes much weaker after annealing at 1000 $$^{\circ }$$ C. The origin of ferromagnetism is most probably due to substitution of Co $$^+$$ ions at Zn lattice sites. However, it is apparent that the decrease in magnetization after annealing is consistent with the vacancy recovery process, indicating that the ferromagnetism in Co-implanted ZnO is mediated by defects such as Zn vacancy (V $$_{Zn}$$ ) or vacancy clusters. First principles calculations also support that Zn-related monovacancies and vacancy clusters can enhance the ferromagnetism in Co-doped ZnO.

Simultaneous fluorogenic switch-on detection and single-base resolution analysis of 5fC through yielding an intramolecular cyclization nucleobase has been presented., 5-Formylcytosine (5fC), which plays an important role in epigenetic functions, has received widespread attention in many related fields. Here, we demonstrate a new design for both the fluorogenic switch-on detection and single-base resolution analysis of 5fC through selectively reacting a reagent with 5fC to yield an intramolecular cyclization nucleobase. The generated product, bearing a similar benzothiazole-iminocoumarin scaffold, is highly fluorescent and enables us to qualitatively and quantitatively detect 5fC moieties in γ-irradiated calf thymus DNA. Additionally, losing the exocyclic 4-amino group in 5fC causes the incorporation of dATP through base pairing with the generated nucleobase during polymerase extension, which helped us to analyze the 5fC sites in both single- and double-stranded oligonucleotides. Our Sanger and Illumina sequencing results show great potential in single-base resolution analysis of 5fC. It is hopeful that a similar design may be used for more detection targets.

The interaction of O2 with doped monolayer MoS2 and the effect of hydrogenation are studied by first-principles calculations coupled with the CI-NEB method. Surface chemically inertness of the MoS2 (001) plane can be broken by doping with Co, Ni and Cu atoms. Impurity levels are induced around the Fermi level and lead to the decrease of band gap, which is beneficial to the adsorption of O2 molecule. The activated oxygen atoms are produced through a dissociation reaction. The introduction of hydrogen atoms into the surface of doped MoS2 system presents favorable effect for O2 adsorption and dissociation. More impurity levels appear in the hydrogenated MoS2-Co/Ni system, and more electrons are localized at 3d orbital of Co/Ni atom, these systems all present excellent adsorption capacity. Hydrogenation reaction occurs by a hydrogen adatom smoothly migrating to the adsorbed O2 with the formation of OOH radical. The elongated OO bond of OOH radical can be dissociated with a lower activation energy barrier, producing an OH radical and activated oxygen atom. Our theoretical studies suggest that the doped monolayer MoS2 system is effective for capturing O2 molecule, and the hydrogenation is found to facilitate adsorption and dissociation of O2 molecule. Keywords: MoS2, Interaction, First principles, Hydrogenation

Malvaceae is a family of flowering plants containing many economically important plant species including cotton, cacao and durian. Recently, the genomes of several Malvaceae species have been decoded, and many omics data were generated for individual species. However, no integrative database of multiple species, enabling users to jointly compare and analyse relevant data, is available for Malvaceae. Thus, we developed a user-friendly database named MaGenDB (http://magen.whu.edu.cn) as a functional genomics hub for the plant community. We collected the genomes of 13 Malvaceae species, and comprehensively annotated genes from different perspectives including functional RNA/protein element, gene ontology, KEGG orthology, and gene family. We processed 374 sets of diverse omics data with the ENCODE pipelines and integrated them into a customised genome browser, and designed multiple dynamic charts to present gene/RNA/protein-level knowledge such as dynamic expression profiles and functional elements. We also implemented a smart search system for efficiently mining genes. In addition, we constructed a functional comparison system to help comparative analysis between genes on multiple features in one species or across closely related species. This database and associated tools will allow users to quickly retrieve large-scale functional information for biological discovery.

A sol-gel process was used to synthesize gel precursors of CaCu 3 Ti 4 O 12 (CCTO) ceramics. The XRD patterns show that a considerable amount of CCTO phase has been formed after the gels were calcined at 800 °C and 900 °C and after the sintering process for the samples all the second phases have disappeared. The SEM images display that the microstructure morphology is obviously affected by synthesizing temperatures. The grain size increases with the increasing sintering temperature and some melt Cu-rich phase appears at grain boundaries of the sample sintered at 1100 °C. Positron annihilation lifetime and Doppler broadening spectra results indicate that the concentration of Cu 2+ vacancies increases with the increase of sintering temperature and the defect species remains the same. High defect concentration of samples sintered at1070 °C and 1100 °C leads to poor stability of permittivity and large dielectric loss values at low frequencies and poor nonlinear behavior. The results of impedance spectroscopy support well the views.

Adsorption of small gas molecules (O2, NO, NO2 and NH3) on transition-metal Cu atom embedded monolayer MoS2 was investigated by first-principles calculations based on the density-functional theory (DFT). The embedded Cu atom is strongly constrained on the sulfur vacancy of monolayer MoS2 with a high diffusion barrier. The stable adsorption geometry, charge transfer and electronic structures of these gas molecules on monolayer MoS2 embedded with transition-metal Cu atom are discussed in detail. It is found that the monolayer MoS2 with embedded Cu atom can effectively capture these gas molecules with high adsorption energy. The NH3 molecule acts as electron donor after adsorption, which is different from the other gas molecules (O2, NO, and NO2). The results suggest that MoS2-Cu system may be promising for future applications in gas molecules sensing and catalysis, which is similar to those of the transition-metal embedded graphene.

Positron lifetime and Doppler broadening of positron annihilation radiation were measured as a function of time to study the irradiation effect by 22Na positron source in fine powdered alumina. The γ-Al2O3 samples were put in a vacuum chamber with a pressure of about 10−6 Torr and were cooled down to 10 K by a closed-cycle helium gas refrigerator. The irradiation of γ-Al2O3 samples by positron source was taken for a duration of about two days immediately after the sample was cooled down. After that, the sample was subjected to a warm up process from 10 K to 300 K with a step of 10 K. Positron lifetime and Doppler broadening spectra were measured simultaneously during these processes. Two long lifetime components corresponding to ortho-positronium annihilation were observed. A significant shortening of these long lifetime components and a large increase in S parameter is observed during irradiation. It is supposed that positron source irradiation creates a large number of paramagnetic centers on the surface of the γ-Al2O3 grains, which induce spin conversion quenching of positronium. The irradiation induced paramagnetic centers are unstable above 70 K and are nearly annealed out when the temperature rises to 190 K. After warming up of the sample to room temperature, the positron lifetime spectrum is identical to that before irradiation. It was also found that after irradiation, a medium long lifetime component of about 5 ns appears, of which the intensity increases with increasing irradiation time. This may be originated from the formation of the surface o-Ps state. This surface o-Ps state is also inhibited at elevated temperatures. Our results indicate that positronium is a very sensitive probe for the surface defects in porous materials.

Mesoporous silica with ordered pore structure was synthesized at various temperatures using TEOS as the silica source and P123 as the template. Both small angle X-ray scattering (SAXS) and high resolution transition electron microscopy (HRTEM) measurements verify the ordered pore structure of the synthesized SiO 2 . With synthesis temperature increasing, the pore structure has slight damage at 130 °C, while it shows ordered structure again at 150 °C. When the synthesis temperature increases to 180 °C, the ordered pore structure is severely destructed. The change of pore structure is further confirmed by scanning electron microscopy (SEM) measurements. Positron lifetime measurements reveal four lifetime components in the synthesized mesoporous SiO 2 , and the two long lifetimes τ 3 and τ 4 correspond to the annihilation of o-Ps in the micropores and large pores of the material, respectively. The longest lifetime τ 4 tends to increase slightly with increasing synthesis temperature. However, its intensity I 4 shows an overall decrease with exception at 150 °C. At the synthesis temperature of 180 °C, the intensity I 4 decreases drastically to about 17.5%. This indicates variation of the size and fraction of pores with increasing synthesis temperature, and the pore structure is seriously destructed at 180 °C. By comparing with the N 2 adsorption–desorption measurements, it was found that the Goworek's model is more suitable for the size estimation of cylindrical pores from the o-Ps lifetime, while Dull's and Ito's model is appropriate for the rectangular and spherical pores, respectively.

CaCu3Ti4O12 (CCTO) ceramics were prepared by the sol–gel process and sintered by the spark plasma sintering (SPS) process at different temperatures. The SPS process temperature has an important effect on the microtopography of CCTO ceramics. The results of EDS and positron annihilation spectroscopy indicate that Cu2+ diffuses from the inside to the surface of grains during the sintering process at high temperature. The permittivity (er) of CCTO ceramics at the corresponding frequencies increases with increasing SPS temperature. However, the frequency stability of er over the frequency range 40–106 Hz wanes gradually. The CCTO ceramics sintered at 900°Cand 950 °C present very low dielectric loss values(about 0.02) near 10 kHz. The change in er and tanδ for CCTO ceramics can be explained by the internal barrier layer capacitance (IBLC) model and AC (alternating current) impedance spectra. The results of I–V nonlinear characteristics for CCTO ceramics make clear that the potential barrier height has a positive effect on the value of nonlinear coefficient.

Annihilation of positronium (Ps) in static magnetic fields is investigated by positron annihilation lifetime (PAL) and Doppler broadening (DB) measurements of γ-Al2O3 nanopowder. The properties of four eigenstates of Ps atoms ( | 1,1 ⟩ , | 1 , − 1 ⟩ , | + ⟩ (long-lived eigenstate mixed from | 1,0 ⟩ and | 0,0 ⟩ due to Zeeman effect), and | − ⟩ (short-lived eigenstate mixed from | 1,0 ⟩ and | 0,0 ⟩ due to Zeeman effect)) were revealed from PAL and DB results. Thereafter, with magnetic field increasing from 0.105 to 0.760 T, clear and regular variation of Ps annihilation parameters are observed: (1) The mean lifetime of the three long-lived Ps states ( | 1,1 ⟩ , | 1 , − 1 ⟩ , and | + ⟩ ) shows clear quenching effect; (2) The formation probability of each Ps eigenstate ( | 1,1 ⟩ , | 1 , − 1 ⟩ , | + ⟩ , and | − ⟩ ) keeps unchanged; (3) The intensity of the narrow component (derived from multi-Gaussian fitting) of DB spectrum exhibits a gradual increase which is in good agreement with the theoretical calculation from PAL results (2γ decay of | + ⟩ and | − ⟩ states, and pick-off quenching of long-lived Ps states); (4) The intensity of the low energy region of DB spectrum is diminished by the decrease of 3γ decay of | + ⟩ state. The quantitative correlations between magnetic field and o-Ps annihilation parameters will be helpful for the further understanding of complex Ps quenching effects, such as the effect mixed from orhto-para spin conversion and magnetic quenching.

RNA sequencing has greatly facilitated gene expression studies but is weak in studying temporal RNA dynamics; this issue can be addressed by analyzing nascent RNAs. A famous method for nascent RNA analysis is metabolic labeling with noncanonic nucleoside followed by affinity purification, however, purification processes can always introduce biases into data analysis. Here, a chemical method for nascent RNA sequencing that avoids affinity purification based on acrylonitrile‐mediated uridine‐to‐cytidine (U‐to‐C) conversion (AMUC‐seq) via 4‐thiouridine (s4U) cyanoethylation is presented. This method converts s4U base‐pairing with guanine through the nucleophilic addition of s4U to acrylonitrile. The high reaction efficiency permits AMUC‐seq directly and efficiently to recover nascent RNA information from total RNAs. AMUC‐seq is validated by being used to detect mRNA half‐lives and investigating the direct gene targets of a G‐quadruplex stabilizer, which can be regarded as potential anticancer drug, in human cells. Thousands of direct gene targets of this drug are verified (these genes are significantly enriched in cancer such as SRC and HRAS). AMUC‐seq also confirms G‐quadruplex stabilization that impacts RNA polyadenylation. These results show AMUC‐seq is qualified for the study of temporal RNA dynamics, and it can be a promising strategy to study the therapeutic mechanism of transcription‐modulating drugs., 4‐thiouridine (s4U) cyanoethylation converts in the nascent RNA to cytidine in a base‐pairing manner, representing a promising strategy for enrichment‐free nascent RNA detection that further benefits transcriptome‐wide analysis of temporal RNA dynamics.

5-Hydroxymethylcytosine (5hmC) is known as one of the vital players in nuclear reprogramming and the process of active DNA demethylation., 5-Hydroxymethylcytosine (5hmC) is known as one of the vital players in nuclear reprogramming and the process of active DNA demethylation. Although the development of whole-genome sequencing methods for modified cytosine bases has burgeoned, the easily operated gene-specific loci detection of 5hmC has rarely been reported. Herein, we present a single-base resolution approach, i.e., chemical-assisted mismatch sequencing (CAM-Seq), which, when combined with traditional oxidation and chemical labeling mediation, can be used for mapping 5hmC at base resolution. We employ chemical oxidation to transform 5hmC to 5-formylcytosine (5fC), followed by chemical labeling to induce C-to-T base changes owing to the fact that the loss of the exocyclic 4-amino group of labeled 5fC leads to C to T conversion and subsequent pairing with adenosine (A) in PCR. The feasibility of CAM-Seq is demonstrated in different synthetic oligonucleotide models as well as in part of the genome of 5hmC-rich mouse embryonic stem cells (mESCs). Moreover, the gene fragment containing 5hmC can be easily biotinylated after oxidation, showing high enrichment efficiency. Our method has the potential capability to map 5hmC in genomic DNA and thus will contribute to promoting the understanding of the epigenetic modification of 5hmC.

Innovative detection techniques to achieve precise m6A distribution within mammalian transcriptome can advance our understanding of its biological functions. We specifically introduced the atom-specific replacement of oxygen with progressively larger atoms (sulfur and selenium) at 4-position of deoxythymidine triphosphate to weaken its ability to base pair with m6A, while maintaining A-T* base pair virtually the same as the natural one. 4SedTTP turned out to be an outstanding candidate that endowed m6A with a specific signature of RT truncation, thereby making this “RT-silent” modification detectable with the assistance of m6A demethylase FTO through next-generation sequencing. This antibody-independent, 4SedTTP-involved and FTO-assisted strategy is applicable in m6A identification, even for two closely gathered m6A sites, within an unknown region at single-nucleotide resolution.

Thermoelectric Zn4Sb3 prepared by spark plasma sintering (SPS) method has been studied by X-ray diffraction (XRD) and positron annihilation spectroscopy. A reversible structural transformation between β-Zn4Sb3 and ZnSb was confirmed by XRD measurements. It was found that the as-milled powder is composed of the pure β-Zn4Sb3 phase, but after SPS, one side of the sintered sample changes to the ZnSb phase. Upon annealing at 300 °C, the ZnSb phase converts back to β-Zn4Sb3 phase. During these phase transition processes, Zn migration driven by direct current and Zn diffusion activated by annealing play important roles. Another interesting finding is that excess Zn can suppress the decomposition of β-Zn4Sb3 into ZnSb and Zn. Positron annihilation lifetime measurements confirm that the diffusion of Zn introduces large amounts of vacancy clusters in the ZnSb-side, and most of them are recovered when the ZnSb phase converts back to β-Zn4Sb3 due to the migration of Zn driven by annealing. The positron lifetime results further show the acceleration of Zn migration at about 150 °C. The existence of Zn vacancies is also observed in the β-Zn4Sb3 structure.

Clathrate Ba 6 Ge 25 is prepared by melt method and spark plasma sintering. Structural transition below room temperature is studied by positron annihilation and X-ray diffraction measurements. There is a pronounced transition in the temperature range of 200–250 K which might be involved with the movement of Ba atoms in Ge cages and result in disordered structure. This transition is further confirmed by the theoretical calculation of positron annihilation states. Thus our results confirm the structural models proposed by Carrillo-Cabrera et al. (2005). The measured specific heat capacity, electric resistivity and magnetic susceptibility all show anomalous transition in the same temperature range, indicating that the movement of Ba atoms in the cage has influence on the thermal, electric as well as magnetic properties of Ba 6 Ge 25 .

In this paper, we present the study of local molecular motions in poly (methyl methacrylate) (PMMA) below glass transition temperature by measuring the ortho-positronium (o-Ps) intensity. Two series of experiments were performed: (1) the PMMA sample was irradiated by 22 Na positron source with elongated time at room temperature, 225 K and 16 K, respectively, and positron lifetime spectra were measured as a function of irradiation time and (2) Positron lifetime and Doppler broadening spectra were measured as a function of temperature from 16 to 350 K after positron irradiation at 16 K for more than 350 h. While the o-Ps lifetime always shows no change with elapsed time, decrease and increase of o-Ps intensity I 3 are observed at 225 K and 16 K, which are interpreted as the result of positron irradiation-induced free radicals and trapped electrons, respectively. With temperature increasing from 16 K, there is a continuous drop of I 3 beginning at around 100 K. This is due to some local group movements such as the ester and main chain methyl group rotations, which lead to the detrapping of accumulated electrons. These local motions do not need additional free volume, so we observed no change of the o-Ps lifetime. Some other structural relaxations such as β-relaxation are also observed and discussed.

Commercial Al–Mg alloy AA5083 was severely deformed with thickness reduction from 50 mm to 1 mm by hot rolling plus cold rolling. Isochronal annealing studies of this heavily deformed Al–Mg alloy were investigated by positron annihilation and Vickers microhardness as well as X-ray diffraction measurements. Positrons are almost fully trapped at dislocations in the as deformed sample. This suggests that deformation introduces large amounts of dislocations. The Vickers microhardness also increases from 71 Hv to 155 Hv after deformation. Most of the deformation induced dislocations are annealed out at 250 °C. At the same time, the microhardness also decreases to about 90 Hv after annealing at 200–250 °C and remain stable after further annealing up to 500 °C. This indicates that hardening of the AA5083 alloy is primarily due to dislocations. Dislocation-solute interaction may be also responsible for the strengthening of hardness.

CoO/Al 2 O 3 catalysts were prepared by wet impregnation method with CoO contents ranging from 0 wt% to 24 wt%. X-ray diffraction and X-ray photoelectron spectroscopy measurements suggest formation of CoO after calcined in N 2 . Quantitative X-ray diffraction analysis indicates monolayer dispersion capacity of CoO in CoO/Al 2 O 3 catalysts to be about 3 wt%. Positron annihilation lifetime and coincidence Doppler broadening measurements were performed to study the dispersion state of CoO on Al 2 O 3 . The positron lifetime measurements reveal two long lifetime components τ 3 and τ 4 , which correspond to ortho -positronium annihilation lifetime in microvoids and large pores, respectively. It was found that the positronium atom is very sensitive to the dispersion state of CoO on Al 2 O 3 . The presence of CoO significantly decreases both the lifetime and the intensity of τ 4 . Detailed analysis of the coincidence Doppler broadening measurements suggests that with the CoO content lower than the monolayer dispersion, spin conversion reaction of positronium is induced by CoO. When the cobalt content is higher than the monolayer dispersion capacity, inhibition of positronium formation becomes the dominate effect.

Spermiogenesis is a highly orchestrated developmental process during which chromatin condensation decouples transcription from translation. Spermiogenic mRNAs are transcribed earlier and stored in a translationally inert state until needed for translation; however, it remains largely unclear how such repressed mRNAs become activated during spermiogenesis. We previously reported that the MIWI/piRNA machinery is responsible for mRNA elimination during late spermiogenesis in preparation for spermatozoa production. Here we unexpectedly discover that the same machinery is also responsible for activating translation of a subset of spermiogenic mRNAs to coordinate with morphological transformation into spermatozoa. Such action requires specific base-pairing interactions of piRNAs with target mRNAs in their 3′ UTRs, which activates translation through coupling with cis-acting AU-rich elements to nucleate the formation of a MIWI/piRNA/eIF3f/HuR super-complex in a developmental stage-specific manner. These findings reveal a critical role of the piRNA system in translation activation, which we show is functionally required for spermatid development.

Two mesoporous In 2 O 3 were prepared with different pore size by using KIT-6 template synthesized at temperature of 50 ° C and 100 ∘ C (designated as 50 ° C– In 2 O 3 and 100 ∘ C– In 2 O 3 ), respectively. Small angle X-ray scattering and transmission electron microscope measurements all confirm ordered pore structure in the synthesized In 2 O 3 . N 2 adsorption/desorption analysis indicates that the pore size in these two In 2 O 3 is about 11.06 nm and 8.737 nm, respectively. Positron lifetime measurements suggest existence of both micropores and mesopores in the porous In 2 O 3 samples, and the mesopore size in 100 ∘ C– In 2 O 3 is smaller than that in 50 ∘ C– In 2 O 3 . The porosity of 50 ° C– In 2 O 3 and 100 ∘ C– In 2 O 3 is about 44% and 40%, respectively. Comparing with the bulk In 2 O 3 obtained by SPS sintering of the commercial In 2 O 3 nanopowders at high temperature of 900 ∘ C, the thermal conductivity of porous In 2 O 3 decreases by more than an order of magnitude. For the 100 ∘ C– In 2 O 3 , the thermal conductivity is as low as 0.58 W m − 1 K − 1 at room temperature of 25 ∘ C, which is below the amorphous limit. On the other hand, the electrical conductivity of the porous In 2 O 3 is deteriorated by the pore structure, but it is partially compensated by the increase of Seebeck coefficient. The overall ZT factor increases to higher than 0.08 at 300 ∘ C for 50 ∘ C– In 2 O 3 , which is almost three times that of the bulk In 2 O 3 .

In this study, polycrystalline SnSe was synthesized via a rapid, cost-effective, and large-scale synthesis route. The obtained SnSe powders were pressed into pellets via spark plasma sintering (SPS) at different temperatures. Powder X-ray diffraction (XRD) and field-emission scanning electron microscopy (FESEM) were used to characterize the crystal structures and morphology of the SnSe samples. The XRD results indicate that the orientation factors increase monotonously with the increase of sintering temperature. The FESEM images show that sintering temperatures have no obvious influence on the particle size. Positron annihilation measurements indicate that vacancy defects exist in all the sintered SnSe samples, and they recover gradually with increasing sintering temperatures. These vacancy defects are responsible for the lower lattice thermal conductivity in samples sintered at lower temperatures. The electrical conductivity, power factor, thermal conductivity, and figure of merit ZT show nearly the same variation trend, which increases initially with the increasing sintering temperature up to 550 °C then decreases with further increase of the sintering temperature, which is possibly due to slight oxidation of SnSe. A maximum ZT value of ∼0.47 at 430 °C was achieved for the 550 °C sintered sample, which is higher than those reported for undoped polycrystalline SnSe around this temperature. Thus, we provide a simple, energy-saving, and effective method to synthesize polycrystalline SnSe in large quantities, and SPS is an effective method to optimize thermoelectric performance.

Li-doped ZnO polycrystals with Li2CO3 concentration between 0 and 15 at.% have been prepared using a solid state reaction method. After annealing of the mixed samples at 1200 °C, Li2CO3 completely decomposed to Li2O and the lattice parameters a/c first increase with Li2CO3 concentration up to 5 at.%, and then decrease with increasing Li2CO3 concentration. This indicates that Li atoms prefer interstitial sites at low concentration and substitute Zn sites when Li concentration is beyond a certain threshold. Positron annihilation measurements were performed for undoped ZnO and Li2CO3-doped ZnO with 15 at.% samples as a function of annealing temperature. A high concentration of vacancy defects is observed in the undoped and as-prepared Li2CO3-doped samples, and they are fully removed after annealing at 1200 °C. The average positron lifetimes of all Li2CO3-doped samples after annealing at 1200 °C are the same, suggesting that Li doping has little effect on the positron lifetime in ZnO. This might be due to the invisibility of positron to Lii or LiiLiZn complex, which is further confirmed by theoretical calculation.

NiO/ γ -Al 2 O 3 catalysts with NiO content of 9 wt% and 24 wt% were prepared by solid state reaction method. They are annealed in air at temperatures from 100 °C to 1000 °C. Positron lifetime spectra were measured to study the microstructure variation during annealing process. Four positron lifetime components were resolved with two long lifetime τ 3 and τ 4 , which can be attributed to the ortho-positronium lifetime in microvoids and large pores, respectively. It was found that the longest lifetime τ 4 is rather sensitive to the chemical environment of the large pores. The NiO active centers in the catalysts cause decrease of both τ 4 and its intensity I 4 , which is due to the spin-conversion of positronium induced by NiO. However, after heating the catalysts above 600 °C, abnormal increase of the lifetime τ 4 is observed. This is due to the formation of NiAl 2 O 4 spinel from the reaction of NiO and γ -Al 2 O 3 . The generated NiAl 2 O 4 weakens the spin-conversion effect of positronium, thus leads to the increase of o-Ps lifetime τ 4 . Formation of NiAl 2 O 4 is further confirmed by both X-ray diffraction and X-ray photoelectron spectroscopy measurements.

The pore structure of NiO/γ-Al 2 O 3 catalysts is characterized by positron lifetime and Doppler broadening measurements. A very long lifetime τ 4 of 92 ns is resolved from the positron lifetime spectrum measured for pure Al 2 O 3 , which could be attributed to the ortho-positronium (o-Ps) lifetime in large pores. It was also found that the fitted lifetime τ 4 and its corresponding intensity I 4 obtained from the lifetime spectra both decrease with narrowing energy window of the stop channel in the fast–fast coincidence lifetime measurement system. This suggests that the ultra long lifetime is primarily due to the self annihilation of o-Ps which emits three gamma-rays. Such 3γ annihilation is further evidenced by measuring the Doppler broadening of annihilation gamma rays in coincidence with the prompt gamma rays (1.28 MeV) emitted from the 22 Na positron source. In NiO/γ-Al 2 O 3 catalysts both the lifetime τ 4 and its intensity I 4 decreases with increasing NiO content (from 3 wt% to 40 wt%), which indicates decreasing of the number of 3γ events. The 3γ annihilation parameter analyzed from the coincidence Doppler broadening spectrum shows consistent decrease with increasing NiO content.