The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation.

Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.

Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction.

Pan-genomic open reading frames (ORFs) potentially carry protein-coding gene or coding variant information in a population. In this study, we suggest that pan-genomic ORFs are promising to be utilized in estimation of heritability and genomic prediction. A Saccharomyces cerevisiae dataset with whole-genome SNPs, pan-genomic ORFs, and the copy numbers of those ORFs is used to test the effectiveness of ORF data as a predictor in three prediction models for 35 traits. Our results show that the ORF-based heritability can capture more genetic effects than SNP-based heritability for all traits. Compared to SNP-based genomic prediction (GBLUP), pan-genomic ORF-based genomic prediction (OBLUP) is distinctly more accurate for all traits, and the predictive abilities on average are more than doubled across all traits. For four traits, the copy number of ORF-based prediction(CBLUP) is more accurate than OBLUP. When using different numbers of isolates in training sets in ORF-based prediction, the predictive abilities for all traits increased as more isolates are added in the training sets, suggesting that with very large training sets the prediction accuracy will be in the range of the square root of the heritability. We conclude that pan-genomic ORFs have the potential to be a supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction.

Lateral layered semiconductor multijunctions for novel electronic devices.

Layered semiconductors, represented by transition metal dichalcogenides, have attached extensive attention due to their unique and tunable electrical and optical properties. In particular, lateral layered semiconductor multijunctions, including homojunctions, heterojunctions, hybrid junctions and superlattices, present a totally new degree of freedom in research on electronic devices beyond traditional materials and their structures, providing unique opportunities for the development of new structures and operation principle-based high performance devices. However, the advances in this field are limited by the precise synthesis of high-quality junctions and greatly hampered by ambiguous device performance limits. Herein, we review the recent key breakthroughs in the design, synthesis, electronic structure and property modulation of lateral semiconductor multijunctions and focus on their application-specific devices. Specifically, the synthesis methods based on different principles, such as chemical and external source-induced methods, are introduced stepwise for the controllable fabrication of semiconductor multijunctions as the basics of device application. Subsequently, their structure and property modulation are discussed, including control of their electronic structure, exciton dynamics and optical properties before the fabrication of lateral layered semiconductor multijunction devices. Precise property control will potentially result in outstanding device performances, including high-quality diodes and FETs, scalable logic and analog circuits, highly efficient optoelectronic devices, and unique electrochemical devices. Lastly, we focus on several of the most essential but unresolved debates in this field, such as the true advantages of few-layer vs. monolayer multijunctions, how sharp the interface should be for specific functional devices, and the superiority of lateral multijunctions over vertical multijunctions, highlighting the next-phase strategy to enhance the performance potential of lateral multijunction devices.

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced-representation sequencing data.

Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity (ROH) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reduced-representation sequencing method. After imputation and quality control, 60 850 high-confidence SNPs were retained for ROH detection. A simulation was performed to explore the reliability of ROH detection with imputed data. Different ROH-related variables were compared between imputed and non-missing genotypes used in ROH detection. Furthermore, ROH islands were evaluated and annotated to find genes influenced by inbreeding in these pigs. The simulation results showed that imputed data with 0.7 as the average missing genotype rate and three heterozygotes allowed in a sliding window have comparable ROH detected compared with data with no missing genotypes. Compared with Western pig breeds, Chinese pigs had more autosomes covered by ROH longer than 5 Mb, indicating higher inbreeding in Chinese pigs in recent times. Genes related to reproduction, immunity, meat quality and adaptability in Chinese pigs and several genes related to growth speed and immunity in Western pigs were observed in short ROH islands. The reproduction-related gene PRM1 was found to be located in the most frequent long ROH island in Chinese pigs, which might explain the decreasing fertility in Chinese pig breeds.

ZnO nanorod/porous silicon nanowire hybrid structures as highly-sensitive NO2 gas sensors at room temperature.

ZnO nanorod/porous silicon nanowire (ZnO/PSiNW) hybrids with three different structures as highly sensitive NO2 gas sensors were obtained. PSiNWs were first synthesized by metal-assisted chemical etching, and then seeded in three different ways. After that ZnO nanorods were grown on the seeded surface of PSiNWs using a hydrothermal procedure. ZnO/PSiNW hybrids showed excellent gas sensing performance for various NO2 concentrations (5-50 ppm) at room temperature, and the electrical resistance change rate reached as high as 35.1% when responding to 50 ppm NO2. The distinct enhancement was mainly attributed to the faster carrier transportation after combination, the increase in gas sensing areas and the oxygen vacancy (VO) concentration. Moreover, the p-type gas sensing behavior was explained by the gas sensing mechanism and the effect of VO concentration on gas sensing properties was also discussed concerning the photoluminescence (PL) spectra performance.

Detection of selection signatures of population-specific genomic regions selected during domestication process in Jinhua pigs.

Chinese pigs have been undergoing both natural and artificial selection for thousands of years. Jinhua pigs are of great importance, as they can be a valuable model for exploring the genetic mechanisms linked to meat quality and other traits such as disease resistance, reproduction and production. The purpose of this study was to identify distinctive footprints of selection between Jinhua pigs and other breeds utilizing genome-wide SNP data. Genotyping by genome reducing and sequencing was implemented in order to perform cross-population extended haplotype homozygosity to reveal strong signatures of selection for those economically important traits. This work was performed at a 2% genome level, which comprised 152 006 SNPs genotyped in a total of 517 individuals. Population-specific footprints of selective sweeps were searched for in the genome of Jinhua pigs using six native breeds and three European breeds as reference groups. Several candidate genes associated with meat quality, health and reproduction, such as GH1, CRHR2, TRAF4 and CCK, were found to be overlapping with the significantly positive outliers. Additionally, the results revealed that some genomic regions associated with meat quality, immune response and reproduction in Jinhua pigs have evolved directionally under domestication and subsequent selections. The identified genes and biological pathways in Jinhua pigs showed different selection patterns in comparison with the Chinese and European breeds.

Enhanced field-emission of silver nanoparticle-graphene oxide decorated ZnO nanowire arrays.

This work presents a new method to improve the field emission (FE) properties of semiconductors decorated with low-cost graphene oxide (GO) nanosheets and trace amounts of noble metal. The Ag/GO/ZnO composite emitter exhibited efficient FE properties with a low turn-on field of 1.4 V µm(-1) and a high field enhancement factor of 7018. The excellent FE properties of the Ag/GO/ZnO composite can be attributed to the tunneling effect of electrons through the heterojunction. The FE properties of the Ag/GO/ZnO composite are slightly better than those of the Ag/ZnO composite which forms an energy well that collects electrons on interfaces when an electric field is applied. This behavior is associated with heterostructures that offer more contact points and protrusions between ZnO nanowire arrays (NWAs) and Ag/GO, which leads to easier electron transfer. High-resolution transmission electron microscopy (HRTEM) and X-ray photoelectron spectroscopy (XPS) were employed to characterise the connection and evolution of the ZnO NWAs and Ag/GO composites.

Enhanced photoelectrochemical properties of TiO2 nanorod arrays decorated with CdS nanoparticles.

TiO2 nanorod arrays (TiO2 NRAs) sensitized with CdS nanoparticles were fabricated via successive ion layer adsorption and reaction (SILAR), and TiO2 NRAs were obtained by oxidizing Ti NRAs obtained through oblique angle deposition. The TiO2 NRAs decorated with CdS nanoparticles exhibited excellent photoelectrochemical and photocatalytic properties under visible light, and the one decorated with 20 SILAR cycles CdS nanoparticles shows the best performance. This can be attributed to the enhanced separation of electrons and holes by forming heterojunctions of CdS nanoparticles and TiO2 NRAs. This provides a promising way to fabricate the material for solar energy conversion and wastewater degradation.

Unveiling Shared Immune Responses in Porcine Alveolar Macrophages during ASFV and PRRSV Infection Using Single-Cell RNA-seq.

African swine fever virus (ASFV) and porcine reproductive and respiratory syndrome virus (PRRSV) infections lead to severe respiratory diseases in pigs, resulting in significant economic losses for the global swine industry. While numerous studies have focused on specific gene functions or pathway activities during infection, an investigation of shared immune responses in porcine alveolar macrophages (PAMs) after ASFV and PRRSV infections was lacking. In this study, we conducted a comparison using two single-cell transcriptomic datasets generated from PAMs under ASFV and PRRSV infection. Pattern recognition receptors (PRRs) RIG-I (DDX58), MDA5 (IFIH1), and LGP2 (DHX58) were identified as particularly recognizing ASFV and PRRSV, triggering cellular defense responses, including the upregulation of four cytokine families (CCL, CXCL, IL, and TNF) and the induction of pyroptosis. Through weighted gene co-expression network analysis and protein-protein interaction analysis, we identified thirteen gene and protein interactions shared by both scRNA-seq analyses, suggesting the ability to inhibit both ASFV and PRRSV viral replication. We discovered six proteins (PARP12, PARP14, HERC5, DDX60, RSAD2, and MNDA) in PAMs as inhibitors of ASFV and PRRSV replication. Collectively, our findings showed detailed characterizations of the immune responses in PAMs during ASFV and PRRSV infections, which may facilitate the treatments of these viral diseases.

Emerging probing perspective of two-dimensional materials physics: terahertz emission spectroscopy.

Terahertz (THz) emission spectroscopy (TES) has emerged as a highly effective and versatile technique for investigating the photoelectric properties of diverse materials and nonlinear physical processes in the past few decades. Concurrently, research on two-dimensional (2D) materials has experienced substantial growth due to their atomically thin structures, exceptional mechanical and optoelectronic properties, and the potential for applications in flexible electronics, sensing, and nanoelectronics. Specifically, these materials offer advantages such as tunable bandgap, high carrier mobility, wideband optical absorption, and relatively short carrier lifetime. By applying TES to investigate the 2D materials, their interfaces and heterostructures, rich information about the interplay among photons, charges, phonons and spins can be unfolded, which provides fundamental understanding for future applications. Thus it is timely to review the nonlinear processes underlying THz emission in 2D materials including optical rectification, photon-drag, high-order harmonic generation and spin-to-charge conversion, showcasing the rich diversity of the TES employed to unravel the complex nature of these materials. Typical applications based on THz emissions, such as THz lasers, ultrafast imaging and biosensors, are also discussed. Step further, we analyzed the unique advantages of spintronic terahertz emitters and the future technological advancements in the development of new THz generation mechanisms leading to advanced THz sources characterized by wide bandwidth, high power and integration, suitable for industrial and commercial applications. The continuous advancement and integration of TES with the study of 2D materials and heterostructures promise to revolutionize research in different areas, including basic materials physics, novel optoelectronic devices, and chips for post-Moore's era.

Optofluidic crystallithography for directed growth of single-crystalline halide perovskites.

Crystallization is a fundamental phenomenon which describes how the atomic building blocks such as atoms and molecules are arranged into ordered or quasi-ordered structure and form solid-state materials. While numerous studies have focused on the nucleation behavior, the precise and spatiotemporal control of growth kinetics, which dictates the defect density, the micromorphology, as well as the properties of the grown materials, remains elusive so far. Herein, we propose an optical strategy, termed optofluidic crystallithography (OCL), to solve this fundamental problem. Taking halide perovskites as an example, we use a laser beam to manipulate the molecular motion in the native precursor environment and create inhomogeneous spatial distribution of the molecular species. Harnessing the coordinated effect of laser-controlled local supersaturation and interfacial energy, we precisely steer the ionic reaction at the growth interface and directly print arbitrary single crystals of halide perovskites of high surface quality, crystallinity, and uniformity at a high printing speed of 102 µm s-1. The OCL technique can be potentially extended to the fabrication of single-crystal structures beyond halide perovskites, once crystallization can be triggered under the laser-directed local supersaturation.

Indirect to direct band gap transition in ultra-thin silicon films.

Free standing silicon layers undergo a transition from indirect to direct band gap semiconductor, which predicts a new possible way in silicon band gap engineering. The thickness and crystal orientation of the exposed surface are crucial. Our simulations reveal that the (100) films with thickness of ∼1.05 nm and (110) films with thickness of ∼1.14 nm could maintain the direct band gap structure. However, the (111) films always show indirect band gap structure even if the monolayer is constructed. The electron states density calculations were also carried out and the transition of the band gap structure is considered to be determined by the quantum confinement and surface termination conditions. The momentum matrix element calculations were also carried out, approving the effective direct band gap transitions for these ultra-thin films.

MoO x thin films deposited by magnetron sputtering as an anode for aqueous micro-supercapacitors.

In order to examine the potential application of non-stoichiometric molybdenum oxide as anode materials for aqueous micro-supercapacitors, conductive MoO x films (2 ⩽ x ⩽ 2.3) deposited via RF magnetron sputtering at different temperatures were systematically studied for composition, structure and electrochemical properties in an aqueous solution of Li2SO4. The MoO x (x ≈ 2.3) film deposited at 150 °C exhibited a higher areal capacitance (31 mF cm-2 measured at 5 mV s-1), best rate capability and excellent stability at potentials below -0.1 V versus saturated calomel electrode, compared to the films deposited at room temperature and at higher temperatures. These superior properties were attributed to the multi-valence composition and mixed-phase microstructure, i.e., the coexistence of MoO2 nanocrystals and amorphous MoO x (2.3 < x ⩽ 3). A mechanism combining Mo(IV) oxidation/reduction on the hydrated MoO2 grain surfaces and cation intercalation/extrusion is proposed to illustrate the pseudo-capacitive process.

Utilizing Variants Identified with Multiple Genome-Wide Association Study Methods Optimizes Genomic Selection for Growth Traits in Pigs.

Improving the prediction accuracies of economically important traits in genomic selection (GS) is a main objective for researchers and breeders in the livestock industry. This study aims at utilizing potentially functional SNPs and QTLs identified with various genome-wide association study (GWAS) models in GS of pig growth traits. We used three well-established GWAS methods, including the mixed linear model, Bayesian model and meta-analysis, as well as 60K SNP-chip and whole genome sequence (WGS) data from 1734 Yorkshire and 1123 Landrace pigs to detect SNPs related to four growth traits: average daily gain, backfat thickness, body weight and birth weight. A total of 1485 significant loci and 24 candidate genes which are involved in skeletal muscle development, fatty deposition, lipid metabolism and insulin resistance were identified. Compared with using all SNP-chip data, GS with the pre-selected functional SNPs in the standard genomic best linear unbiased prediction (GBLUP), and a two-kernel based GBLUP model yielded average gains in accuracy by 4 to 46% (from 0.19 ± 0.07 to 0.56 ± 0.07) and 5 to 27% (from 0.16 ± 0.06 to 0.57 ± 0.05) for the four traits, respectively, suggesting that the prioritization of preselected functional markers in GS models had the potential to improve prediction accuracies for certain traits in livestock breeding.

Electric-field control of reversible electronic and magnetic transitions in two-dimensional oxide monolayer magnets.

Atomically thin oxide magnetic materials are highly desirable due to the promising potential to integrate two-dimensional (2D) magnets into next-generation spintronics. Therefore, 2D oxide magnetism is expected to be effectively tuned by the magnetic and electrical fields, holding prospective for future low-dissipation electronic devices. However, the electric-field control of 2D oxide monolayer magnetism has rarely been reported. Here, we present the realization of 2D monolayer magnetism in oxide (SrRuO3)1/(SrTiO3)N (N = 1, 3) superlattices that shows an efficient and reversible phase transition through electric-field controlled proton (H+) evolution. By using ionic liquid gating to modulate the proton concentration in (SrRuO3)1/(SrTiO3)1 superlattice, an electric-field induced metal-insulator transition was observed, along with gradually suppressed magnetic ordering and modulated magnetic anisotropy. Theoretical analysis reveals that proton intercalation plays a crucial role in both electronic and magnetic phase transitions. Strikingly, SrTiO3 layers can act as a proton sieve, which have a significant influence on proton evolution. Our work stimulates the tuning functionality of 2D oxide monolayer magnetism by voltage control, providing potential for future energy-efficient electronics.

3D printing of inorganic nanomaterials by photochemically bonding colloidal nanocrystals.

3D printing of inorganic materials with nanoscale resolution offers a different materials processing pathway to explore devices with emergent functionalities. However, existing technologies typically involve photocurable resins that reduce material purity and degrade properties. We develop a general strategy for laser direct printing of inorganic nanomaterials, as exemplified by more than 10 semiconductors, metal oxides, metals, and their mixtures. Colloidal nanocrystals are used as building blocks and photochemically bonded through their native ligands. Without resins, this bonding process produces arbitrary three-dimensional (3D) structures with a large inorganic mass fraction (~90%) and high mechanical strength. The printed materials preserve the intrinsic properties of constituent nanocrystals and create structure-dictated functionalities, such as the broadband chiroptical responses with an anisotropic factor of ~0.24 for semiconducting cadmium chalcogenide nanohelical arrays.

Study of the Oxidation Behavior of Fine-Grained Graphite ET-10 by Combining X-ray µCT with Mercury Porosimetry.

By combining X-ray micro-computed tomography with mercury porosimetry, the evolution of the oxygen supply, porous structure, mass loss and oxidized compositions were investigated to characterize the oxidation behavior of fine-grained graphite ET-10, regarding the geometry of the specimen and its oxidation temperature. Here, the porous structure and the gas flows out of and into the porous structure were comprehensively compared for two kinds of specimens-large pure graphite (D = H = 25.4 mm), oxidized at a test facility based on ASTM D7542, and small partially SiC-coated graphite (D ≈ 1 mm and H = 1.95 mm), oxidized in the bottom section of a U-type tube. The fine grains and large geometry resulted in small pores and long flow distances, which exhausted the oxygen in the small stream to the interior of the specimen, making its oxidation deviate from the kinetics-controlled regime. In addition, the well-known three-regime theory was reasonably reinterpreted regarding the oxidation of different compositions, binders and fillers. The kinetics-controlled uniform oxidation mainly oxidizing binders is restricted by their limited contents, while the rate of surface-dominated oxidation increases continuously via the consumption of more fillers. Furthermore, we proposed a new design for the test facility used for the oxidation experiment, wherein a partially shielded millimeter specimen can be oxidized in the long straight bottom section of a U-tube, and this will be discussed further in related future studies.

3D nanoprinting of semiconductor quantum dots by photoexcitation-induced chemical bonding.

Three-dimensional (3D) laser nanoprinting allows maskless manufacturing of diverse nanostructures with nanoscale resolution. However, 3D manufacturing of inorganic nanostructures typically requires nanomaterial-polymer composites and is limited by a photopolymerization mechanism, resulting in a reduction of material purity and degradation of intrinsic properties. We developed a polymerization-independent, laser direct writing technique called photoexcitation-induced chemical bonding. Without any additives, the holes excited inside semiconductor quantum dots are transferred to the nanocrystal surface and improve their chemical reactivity, leading to interparticle chemical bonding. As a proof of concept, we printed arbitrary 3D quantum dot architectures at a resolution beyond the diffraction limit. Our strategy will enable the manufacturing of free-form quantum dot optoelectronic devices such as light-emitting devices or photodetectors.

Rapid detection of polychlorinated biphenyls at trace levels in real environmental samples by surface-enhanced Raman scattering.

Detection of trace levels of persistent pollutants in the environment is difficult but significant. Organic pollutant homologues, due to their similar physical and chemical properties, are even more difficult to distinguish, especially in trace amounts. We report here a simple method to detect polychlorinated biphenyls (PCBs) in soil and distilled spirit samples by the surface-enhanced Raman scattering technique using Ag nanorod arrays as substrates. By this method, polychlorinated biphenyls can be detected to a concentration of 5 µg/g in dry soil samples within 1 minute. Furthermore, based on simulation and understanding of the Raman characteristics of PCBs, we recognized homologues of tetrachlorobiphenyl by using the surface-enhance Raman scattering method even in trace amounts in acetone solutions, and their characteristic Raman peaks still can be distinguished at a concentration of 10(-6) mol/L. This study provides a fast, simple and sensitive method for the detection and recognition of organic pollutants such as polychlorinated biphenyls.

Contrastive analysis of the Raman spectra of polychlorinated benzene: hexachlorobenzene and benzene.

Detection of persistent pollutants such as polychlorinated benzene in environment in trace amounts is challenging, but important. It is more difficult to distinguish homologues and isomers of organic pollutantd when present in trace amounts because of their similar physical and chemical properties. In this work we simulate the Raman spectra of hexachlorobenzene and benzene, and figure out the vibration mode of each main peak. The effect on the Raman spectrum of changing substituents from H to Cl is analyzed to reveal the relations between the Raman spectra of homologues and isomers of polychlorinated benzene, which should be helpful for distinguishing one kind of polychlorinated benzene from its homologues and isomers by surface enhanced Raman scattering.