Structure Analysis Research Articles

When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications.

Third-generation sequencing technology has found widespread application in the genomic, transcriptomic, and epigenetic research of both human and livestock genetics. This technology offers significant advantages in the sequencing of complex genomic regions, the identification of intricate structural variations, and the production of high-quality genomes. Its attributes, including long sequencing reads, obviation of PCR amplification, and direct determination of DNA/RNA, contribute to its efficacy. This review presents a comprehensive overview of third-generation sequencing technologies, exemplified by single-molecule real-time sequencing (SMRT) and Oxford Nanopore Technology (ONT). Emphasizing the research advancements in livestock genomics, the review delves into genome assembly, structural variation detection, transcriptome sequencing, and epigenetic investigations enabled by third-generation sequencing. A comprehensive analysis is conducted on the application and potential challenges of third-generation sequencing technology for genome detection in livestock. Beyond providing valuable insights into genome structure analysis and the identification of rare genes in livestock, the review ventures into an exploration of the genetic mechanisms underpinning exemplary traits. This review not only contributes to our understanding of the genomic landscape in livestock but also provides fresh perspectives for the advancement of research in this domain.

Structure and Photophysics of N-Tolanyl-phenochalcogenazines and their Radical Cations.

The study focuses on the structural and photophysical characteristics of neutral and oxidized forms of N-tolanyl-phenochalcogenazines PZX-tolan with X=O, S, Se, and Te. X-ray crystal structure analyses show a pseudo-equatorial (pe) structure of the tolan substituent in the O, S, and Se dyads, while the Te dyad possesses a pseudo-axial (pa) structure. DFT calculations suggest the pe structure for O and S, and the pa structure for Se and Te as stable forms. Steady-state and femtosecond-time resolved optical spectroscopy in toluene solution indicate that the O and S dyads emit from a CT state, whereas the Se and Te dyads emit from a tolan-localized state. The T1 state is tolan-localized in all cases, showing phosphorescence at 77 K. The heavy atom effect of chalcogens induces intersystem crossing from S1 to Tx, resulting in a decreasing S1 lifetime from 2.1 ns to 0.42 ps. The T1 states possess potential for singlet oxygen sensitization with a high quantum yield (ca. 40 %) for the O, S, and Se dyads. Radical cations exhibit spin density primarily localized at the heterocycle. EPR measurements and quasirelativistic DFT calculations reveal a very strong g-tensor anisotropy, supporting the pe structure for the S and Se derivatives.

Whole-genome comparison of two same-genotype macrolide-resistant Bordetella pertussis isolates collected in Japan.

The emergence of macrolide-resistant Bordetella pertussis (MRBP) is a significant problem because it reduces treatment options for pertussis and exacerbates the severity and spread of the disease. MRBP has been widely prevalent in mainland China since the 2010s and has been sporadically detected in other Asian countries. In Japan, two MRBP clinical strains were first isolated in Tokyo and Osaka between June and July 2018. The isolates BP616 in Osaka and BP625 in Tokyo harbored the same virulence-associated allelic genes (including ptxP1, ptxA1, prn1, fim3A, and fhaB3) and MT195 genotype and exhibited similar antimicrobial susceptibility profiles. However, despite their simultaneous occurrence, a distinguishable epidemiological link between these isolates could not be established. To gain further insight into the genetic relationship between these isolates in this study, we performed whole-genome analyses. Phylogenetic analysis based on genome-wide single-nucleotide polymorphisms revealed that the isolates belonged to one of the three clades of Chinese MRBP isolates, but there were 11 single-nucleotide polymorphism differences between BP616 and BP625. Genome structure analysis revealed two large inversions (202 and 523 kbp) and one small transposition (3.8 kbp) between the genomes. These findings indicate that the two Japanese MRBP isolates are closely related to Chinese MRBP isolates but are genomically distinct, suggesting that they were introduced into Japan from mainland China through different transmission routes.

ISKIN: Integrated application of machine learning and Mondrian conformal prediction to detect skin sensitizers in cosmetic raw materials

AbstractAnimal experiments traditionally identify sensitizers in cosmetic materials. However, with growing concerns over animal ethics and bans on such experiments globally, alternative methods like machine learning are gaining prominence for their efficiency and cost‐effectiveness. In this study, to develop a robust sensitizer detector model, we first constructed benchmark data sets using data from previous studies and a public database, then 589 sensitizers and 831 nonsensitizers were collected. In addition, a graph‐based autoencoder and Mondrian conformal prediction (MCP) were combined to build a robust sensitizer detector, iSKIN. In the independent test set, the Matthews correlation coefficient (MCC) and the area under the receiver operating characteristic curve (ROCAUC) values of the iSKIN model without MCP were 0.472 and 0.804, respectively, which are higher than those of the three baseline models. When setting the significance level in MCP at 0.7, the MCC and ROCAUC values of iSKIN could achieve 0.753 and 0.927, respectively. Regrouping experiments proved that the MCP method is robust in the improvement of model performance. Through key structure analysis, seven key substructures in sensitizers were identified to guide cosmetic material design. Notably, long chains with halogen atoms and phenyl groups with two chlorine atoms at ortho‐positions were potential sensitizers. Finally, a user‐friendly web tool (http://www.iskin.work/) of the iSKIN model was deployed to be used by other researchers. In summary, the proposed iSKIN model has achieved state‐of‐the‐art performance so far, which can contribute to the safety evaluation of cosmetic raw materials and provide a reference for the chemical structure design of these materials.

Structure analysis and universal approximation of IT2 TS FLC using NT algorithm

The analytical structure plays an important role in system design and stability analysis of FLC. Structure analysis of traditional IT2 TS FLCs using Zadeh min operator and KM algorithm requires multiple IC dividing, which results in complex calculation and cumbersome parameter adjustment. This article proposes a new IT2 TS FLC by adopting product-type operator and NT algorithm. The proposed controller has such advantages: 1)use product-type operator to skip the partitioning in fuzzy inference process;2) use NT algorithm to avoid determining switching points and sorting rule consequents in type-reduction process. Then, the controller is proved to be universal approximator and sufficient condition is deduced. Finally, we derive the analytical structure of the controller by substituting the parameters, and study the relationship between the uncertainty parameter θ and the analytical structure when the rule consequents are symmetric or asymmetric. Both the computational costs during operation and the computational workload for structural analysis can be reduced significantly by using the new FLC.

The Crystal Structure and Physicochemical Properties of New Complexes Containing a CuII-LnIII-CuII Core

Three new cationic complexes, [Cu4Tb2(H2L)4(NO3)4(H2O)3](NO3)2·5.5H2O·2MeOH (1), [Cu4Ho2(H2L)4(NO3)4(H2O)3](NO3)2·7.5H2O (2), and [Cu4Er2(H2 L)4(NO3)4(H2O)3](NO3)2·7H2O·3MeOH (3), were synthesized and studied using elemental and TG/DTG/DSC analyses, single-crystal X-ray diffraction, and magnetic measurements. The structure analysis showed that 1–3 crystallize as (NO3)-bridged compounds and that the lanthanide(III) ion acts as a joint connecting two [CuH2L] coordination units. In each heterotrinuclear unit, an asymmetry in the degree of planarity of the bridging CuO2Ln fragments is observed. The CuII ions are five- and six-coordinate, with distorted square pyramidal and octahedral geometry, respectively, whereas the LnIII ions are nine-coordinate. The solvates 1–3 are stable at room temperature, and their desolvation process is consistent with the loss of water and/or methanol molecules. The temperature dependence of the magnetic susceptibility and the field-dependent magnetization indicate the weak ferromagnetic interaction between the paramagnetic centers CuII and TbIII/HoIII 1 and 2.

SeqCorr-EUNet: A sequence correction dual-flow network for segmentation and quantification of anterior segment OCT image

The accurate segmentation of AS-OCT images is a prerequisite for the morphological details analysis of anterior segment structure and the extraction of clinical biological parameters, which play an essential role in the diagnosis, evaluation, and preoperative prognosis management of many ophthalmic diseases. Manually marking the boundaries of the anterior segment tissue is time-consuming and error-prone, with inherent speckle noise, various artifacts, and some low-quality scanned images further increasing the difficulty of the segmentation task. In this work, we propose a novel model called SeqCorr-EUNet with a dual-flow architecture based on convolutional gated recursive sequence correction for semantic segmentation and quantification of AS-OCT images. An EfficientNet encoder is employed to enhance the intra-slice features extraction ability of semantic segmentation flow. The sequence correction flow based on ConvGRU is introduced to extract inter-slice features from consecutive adjacent slices. Spatio-temporal information is fused to correct the morphological details of pre-segmentation results. And the channel attention gate is inserted into the skip-connection between encoder and decoder to enrich the contextual information and suppress the noise of irrelevant regions. Based on the segmentation results of the anterior segment structures, we achieved automatic extraction of essential clinical parameters, 3D reconstruction of the anterior chamber structure, and measurement of anterior chamber volume. The proposed SeqCorr-EUNet has been evaluated on the public AS-OCT dataset. The experimental results show that our method is competitive compared with the existing methods and significantly improves the segmentation and quantification performance of low-quality imaging structures in AS-OCT images.

Wind Analysis of PEB and Conventional Steel structure with constant span to rise Ratio

Wind Analysis of PEB and Conventional Steel structure with constant span to rise Ratio

Design of a new cantilevered cylindrical traveling wave ultrasonic motor

In this paper, a composite excitation method is used to optimize the design of an existing cantilevered cylindrical ultrasonic motor to avoid vibration interference. Modal and transient simulation analysis of the stator structure was carried out by the finite element method. Optimized stator structure is simpler than the original motor. Simulation analysis results show that the circumferential amplitude is increased by more than 35% with 55.7% reduction in ceramic usage.

Formation Mechanism of Environmentally Persistent Free Radicals on Alkaline Earth Oxide Surfaces.

The formation of environmentally persistent free radicals (EPFRs) is usually related to transition-metal oxides in particulate matter (PM). However, recent studies suggest that alkaline-earth-metal oxides (AEMOs) in PM also influence EPFRs formation, but the exact mechanism remains unclear. Here, density functional theory calculations were performed to investigate the formation mechanism of EPFRs by C6H5OH on AEMO (MgO, CaO, and BaO) surfaces and compare it with that on transition-metal oxide (ZnO and CuO) surfaces. Results indicate that EPFRs can be rapidly formed on AEMOs by dissociative adsorption of C6H5OH, accompanied by electrons transfer. As the alkalinity of AEMOs increases, both adsorption energy and the number of electron transfers gradually increase. Also, the stability of the formed EPFRs is mainly attributed to the electrostatic and van der Waals interactions between the phenoxy radical and surfaces. Notably, the formation mechanism of EPFRs on AEMOs is similar to that on ZnO but differs from that on CuO, as suggested through geometric structure and charge distribution analyses. This study not only elucidates the formation mechanisms of EPFRs on AEMOs but also provides theoretical insights into addressing EPFRs pollution.

A novel magnetic actuated ultra-clean poppet valve and its dynamic characteristics analysis

The liquid delivery in the semiconductor process is highly protected against leakage and contamination. To avoid the dynamic sealing points in valves, a novel ultra-clean poppet valve driven by permanent magnets is proposed. To reduce the risk of instability due to the lack of a fixed connection structure, static and dynamic characteristic analyses of the valve poppet needs to be carried out. However, the conventional theoretical model of poppet vibration generally focuses on the vibration in axial direction, which lacks consideration of the vibration in lateral direction. Therefore, a new theoretical model for analyzing the vibration characteristics in both axial and lateral directions is proposed. The displacement of poppet and flow response of the valve are predicted. Based on the experimental system of non-contacting displacement measurement, the accuracy of the model is verified. Furthermore, the influence of parameters on the stability is revealed through theoretical calculation, which provides a reference for the design of magnetic actuated valve.

Genome-wide identification and expression analysis of autophagy-related genes (ATG) in Gossypium spp. reveals their crucial role in stress tolerance

Autophagy is an evolutionarily conserved process mediated by AuTophaGy (ATG) genes, in which cellular components are degraded and recycled within vacuoles or lysosome. Yeast ATG was extensively studied; their homologs are reported in plants including Arabidopsis. However, they have not been reported in cotton. In the present study, the ATG cascade genes were studied in four Gossypium species, namely G. hirsutum, G. arboreum, G. herbaceum, and G. raimondii. A total of 40 GhirATG, 33 GaATG, 34 GherbATG, and 25 GrATG genes were identified in these species. These ATG sequences exhibited conserved ATG domains and other overlapping domains, including Ras, Pkinase, Snf7, WD40, Glyco_hydro_17, and bZIP_1, and were named based on their phylogenetic relationships with Arabidopsis ATGs. A phylogenetic analysis revealed evolutionary relationships among ATG genes among these species, as well as significant sub-clades indicating patterns of gene retention. Based on synonymous and non-synonymous substitutions, cotton groups diverged at different times from Arabidopsis. Gene structure analysis and chromosome localization showed exon-intron patterns and locations. Expression analysis of ATGs in different tissues during development and under stress conditions indicated their functional specificity. The ATG8 subclass genes were significantly expressed under abiotic stress conditions, indicating their role in stress response. In addition, qRT-PCR analysis of selected 12 GhirATGs in leaves treated with stress elicitors, MeJA, SA, NaCl, and PEG for varying time intervals showed a pattern of their significant upregulation. The findings contribute to our understanding of autophagy-related processes in cotton, including their potential role in stress response and development.

Atomic ordered doping leads to enhanced sensitivity of phosgene gas detection in graphene nanoribbon: a quantum DFT approach

We explore a novel sensor for detection of phosgene gas by graphene derivatives such as pristine and doped graphene nanoribbons via first principles calculations. The interaction of phosgene molecule with various edge and center doped configurations of boron, phosphorus and boron-phosphorus co-doped armchair graphene nanoribbon (AGNR) and zigzag graphene nanoribbon (ZGNR) is investigated through density functional theory (DFT). P-doped systems showcase chemisorption, displaying enhanced sensitivity to phosgene detection as reflected by a more negative adsorption energy values, accompanied by a prominent charge transfer due to the doping. Regardless of nanoribbon geometry, the binding energies of P-doped systems exhibit notable uniformity within the range of −8.01 eV to −8.49 eV, however the adsorption energies in ZGNR are significantly lower than those observed in AGNR. Due to much higher(lower) electron-donating (accepting) capacity of phosphorous(boron) atoms in comparison to ‘C’ atom, substitutional doping with ‘P’ or ‘B’ atoms in AGNR has signifiant impact on the structural, electronic and adsorption properties of the nanoribbons. We observe that phosphorus doped configurations (edge/center) effectively interact with phosgene molecule with higher adsorption that corresponds to the chemisorption phenomenon. The strongest adsorption energy (−8.83 eV) is obtained for P doped configurations, followed by that for B+P co-doped AGNR (−4.23 eV). These results suggest significantly stronger adsorption of phosgene gas on P doped AGNR than on any other systems reported so far. Band structure analysis estimates that by phosphorus doping, changes in the band gap is significant and it also shows prominent changes in the band structures. Isosurface electronic charge density plots identify that the transfer of charge takes place from graphene system to phosgene molecule. Thus, significant variation in adsorption and electronic properties of P doped AGNR reveal that these geometries immensely promote the detection of phosgene gas, and may be considered as promising chemical sensor for phosgene removal.

Genome-wide identification, gene expression and haplotype analysis of the rhomboid-like gene family in wheat (Triticum aestivum L.).

The rhomboid-like (RBL) gene encodes serine protease, which plays an important role in the response to cell development and diverse stresses. However, genome-wide identification, expression profiles, and haplotype analysis of the RBL family genes have not been performed in wheat (Triticum aestivum L.). This study investigated the phylogeny and diversity of the RBL family genes in the wheat genome through various approaches, including gene structure analysis, evolutionary relationship analysis, promoter cis-acting element analysis, expression pattern analysis, and haplotype analysis. The 41 TaRBL genes were identified and divided into five subfamilies in the wheat genome. RBL family genes were expanded through segmented duplication and purification selection. The cis-element analysis revealed their involvement in various stress responses and plant development. The results of RNA-seq and quantitative real-time-PCR showed that TaRBL genes displayed higher expression levels in developing spike/grain and were differentially regulated under polyethylene glycol, NaCl, and abscisic acid treatments, indicating their roles in grain development and abiotic stress response. A kompetitive allele-specific PCR molecular marker was developed to confirm the single nucleotide polymorphism of TaRBL14a gene in 263 wheat accessions. We found that the elite haplotype TaRBL14a-Hap2 showed a significantly higher 1000-grain weight than TaRBL14a-Hap11 in at least three environments, and the TaRBL14a-Hap2 was positively selected in wheat breeding. The findings will provide a good insight into the evolutionary and functional characteristics of the TaRBL genes family in wheat and lay the foundation for future exploration of the regulatory mechanisms of TaRBL genes in plant growth and development, as well as their response to abiotic stresses.

Role of Edge Reconstruction in the Synthesis of Few-Layer Black Phosphorene.

Recent advancements in preparing few-layer black phosphorene (BP) are hindered by edge reconstruction challenges. Our previous studies have revealed the factors contributing to the difficulty of growing few-layer BP. In this study, we have successfully identified three reconstructed edges in bi- and multilayer BP through a combination of the crystal structure analysis by particle swarm optimization (CALYPSO) global structure search and density functional theory (DFT). Notably, the reconstruction between adjacent layers proves more beneficial than self-passivation or maintaining pristine edges. Among the reconstructed edges, the reconstructed ZZ edge is the most stable, regardless of the number of layers. Calculated electronic band structures reveal a significant transition in the electronic properties of black phosphorus nanoribbons (BPNRs), changing from metallic to semiconducting. This insight not only enhances the understanding of the fundamental properties of BP but also provides valuable theoretical guidance for the experimental growth of BPNRs or black phosphorus nanowires (BPNWs).

Geographical and temporal distribution of multidrug-resistant Salmonella Infantis in Europe and the Americas.

Recently emerged S. Infantis strains carrying resistance to several commonly used antimicrobials have been reported from different parts of the globe, causing human cases of salmonellosis and with occurrence reported predominantly in broiler chickens. Here, we performed phylogenetic and genetic clustering analyses to describe the population structure of 417 S. Infantis originating from multiple European countries and the Americas collected between 1985 and 2019. Of these, 171 were collected from 56 distinct premises located in England and Wales (E/W) between 2009 and 2019, including isolates linked to incursions of multidrug-resistant (MDR) strains from Europe associated with imported poultry meat. The analysis facilitated the comparison of isolates from different E/W sources with isolates originating from other countries. There was a high degree of congruency between the outputs of different types of population structure analyses revealing that the E/W and central European (Germany, Hungary, and Poland) isolates formed several disparate groups, which were distinct from the cluster relating to the United States (USA) and Ecuador/Peru, but that isolates from Brazil were closely related to the E/W and the central European isolates. Nearly half of the analysed strains/genomes (194/417) harboured the IncFIB(pN55391) replicon typical of the "parasitic" pESI-like megaplasmid found in diverse strains of S. Infantis. The isolates that contained the IncFIB(pN55391) replicon clustered together, despite originating from different parts of the globe. This outcome was corroborated by the time-measured phylogeny, which indicated that the initial acquisition of IncFIB(pN55391) likely occurred in Europe in the late 1980s, with a single introduction of IncFIB(pN55391)-carrying S. Infantis to the Americas several years later. Most of the antimicrobial resistance (AMR) genes were identified in isolates that harboured one or more different plasmids, but based on the short-read assemblies, only a minority of the resistance genes found in these isolates were identified as being associated with the detected plasmids, whereas the hybrid assemblies comprising the short and long reads demonstrated that the majority of the identified AMR genes were associated with IncFIB(pN55391) and other detected plasmid replicon types. This finding underlies the importance of applying appropriate methodologies to investigate associations of AMR genes with bacterial plasmids.

Designable Synthesis of Layered Silicates and Tunable Interlayer Expanded to Zeolites.

Layered zeolitic silicates and corresponding interlayer-expanded porous materials exhibit attractive application potential in wide fields. Nonetheless, designable synthesis and structure analysis of layered silicates remain challenging. Herein, two kinds of layered silicates are synthesized using different di-quaternary ammonium-type organic structure-directing agents (OSDAs). Their crystal structures are analyzed and verified by 3D electron diffraction (3D ED) and high-resolution TEM imaging. The suitable configurations of OSDA can lead to desirable interlayer states. Additionally, two new zeolite structures both with 12-membered ring (MR) channels intersected by 8 MR channels and larger interlayer spaces are constructed from layered silicate precursors by interlayer silylation. The new zeolitic material exhibits potential application in adsorption of organic pollution and catalytic reaction. This study is expected to develop versatile ways for the design and synthesis of layered silicates even zeolites and provide references in characterizing layered materials and zeolites as well.

Exploring the Impact of Different Milling Parameters of Fe/SiO2 Composites on Their Structural and Magnetic Properties.

This research focuses on the production process of soft magnetic composites in the form of 3D bulk compacts made from insulated powder particles using different milling parameters, aiming to enhance their magnetic properties and to study an innovative method of the powder surface "smoothing" technique. A structure analysis using scanning electron microscopy (SEM), EDS, and optical microscopy is also included. We found out that the samples made by the innovative method have lower density values. This can be caused by a more consistent SiO2 insulation layer on highly pure iron powder particles. A correlation between the mechanical smoothing method and better insulation of powder particles can help to provide eco-friendlier solutions for the preparation of soft magnetic composites, such as less usage of reagents and more consistent coverage of powder particles with lower final insulation thickness. The magnetic properties of these compacts are evaluated by coercive field, permeability, and loss measurements. The particle-level smoothing technique in some cases can reduce the value of coercivity up to 20%. For some samples, the ball-to-powder ratio has a bigger impact on magnetic properties than surface treatment, which can be caused by an increased amount of insulation in the SMC compacts.

High dielectric permittivity and relaxation-induced dielectric pulsing effect-like in [1,3-bis(1-methylimidazolium)propane][Pb2I6] crystal

Herein, a new hybrid, [1,3-bis(1-methylimidazolium)propane][Pb2I6] (1), was synthesized and thoroughly characterized using microanalysis, thermogravimetric analysis (TG), differential scanning calorimetry (DSC), and powdered X-ray diffraction (PXRD) techniques. The crystal structure of 1 reveals one-dimensional face-sharing PbI6 octahedral chains composed of Pb2+ and I− ions, with the disordered 1,3-bis(1-methylimidazolium)propane dications positioned between these inorganic chains. Remarkably, 1 exhibits high dielectric permittivity (∼200) across a wide temperature range of 123–423 K. Moreover, it demonstrates a relaxation-induced dielectric pulsing effect-like, characterized by a broad and temperature-independent dielectric anomaly peak around 263 K in ε'−T plots. The mechanisms responsible for the high dielectric permittivity and the origin of the relaxation-induced dielectric pulsing effect-like are further discussed through a comprehensive analysis of the variable-temperature crystal structure.

Metagenome-Based Analysis of the Microbial Community Structure and Drug-Resistance Characteristics of Livestock Feces in Anhui Province, China.

We analyzed metagenome data of feces from sows at different physiological periods reared on large-scale farms in Anhui Province, China, to provide a better understanding of the microbial diversity of the sow intestinal microbiome and the structure of antibiotic-resistance genes (ARGs) and virulence genes it carries. Species annotation of the metagenome showed that in the porcine intestinal microbiome, bacteria were dominant, representing >97% of the microorganisms at each physiological period. Firmicutes and Proteobacteria dominated the bacterial community. In the porcine gut microbiome, the viral component accounted for an average of 0.65%, and the species annotation results indicated that most viruses were phages. In addition, we analyzed the microbiome for ARGs and virulence genes. Multidrug-like, MLS-like, and tetracycline-like ARGs were most abundant in all samples. Evaluation of the resistance mechanisms indicated that antibiotic inactivation was the main mechanism of action in the samples. It is noteworthy that there was a significant positive correlation between ARGs and the total microbiome. Moreover, comparative analysis with the Virulence Factor Database showed that adhesion virulence factors were most abundant.