Host combats porcine reproductive and respiratory syndrome virus infection at non-coding RNAs level.

Porcine reproductive and respiratory syndrome virus (PRRSV) poses a significant threat to the global swine industry. The emergence of new, highly virulent strains has precipitated recurrent outbreaks worldwide, underscoring the ongoing battle between host and virus. Thus, there is an imperative to formulate a more comprehensive and effective disease control strategy. Studies have shown that host non-coding RNA (ncRNA) is an important regulator of host - virus interactions in PRRSV infection. Hence, a thorough comprehension of the roles played by ncRNAs in PRRSV infection can augment our understanding of the pathogenic mechanisms underlying PRRSV infection. This review focuses on elucidating contemporary insights into the roles of host microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in PRRSV infection, providing both theoretical foundations and fresh perspectives for ongoing research into the mechanisms driving PRRSV infection and its pathogenesis.

Consensus Clustering Analysis Identifies Ferroptosis-Related Patient Clusters and Predictive Signature Construction Based on Ferroptosis-Related Genes in Ischemic Cardiomyopathy.

Background: Ischemic cardiomyopathy (ICM) significantly contributes to global disease burden, while the role of ferroptosis in ICM remains underexplored. Methods: We identified differentially expressed ferroptosis-related genes (DEFRGs) by analyzing the GSE57338 dataset and cross-referencing with FerrDb. Consensus clustering was then used to identify ferroptosis-associated clusters within the ICM samples. A ferroptosis-specific predictive signature was developed using the least absolute shrinkage and selection operator (LASSO) method and validated with the GSE5406 dataset. Additionally, quantitative real-time PCR (qRT-PCR) experiments were performed to validate the 11 feature genes in a rat ICM model. Results: We identified 15 DEFRGs in GSE57338, which distinguished two patient clusters with distinct ferroptosis gene expression, pathway enrichment profiles, and metabolic characteristics. All DEFRGs were upregulated in cluster 2. Potential therapeutic targets were also identified for different ICM patient clusters. The 11-gene predictive signature (TXNRD1, STEAP3, STAT3, SCL2A1, PLIN2, NQO1, NNMT, IL33, ENPP2, ARRDC3, ALOX5) showed robust predictive power in both training and validation sets. High-risk patients exhibited increased infiltration of CD8+ T cells, CD4+ naïve T cells, M0/M1 macrophages, and resting mast cells, along with significant enrichment in epithelial mesenchymal transition and interferon responses. Low-risk patients had higher infiltration of regulatory T cells and monocytes. Results of qPCR analysis confirmed the bioinformatic analysis, validating the expression of the 11 feature genes in the rat ICM model. Conclusion: We identified two ferroptosis-related clusters in ICM patients and developed a predictive signature based on ferroptosis-related genes. Our findings highlight the importance of ferroptosis in ICM and offer new insights for its diagnosis and treatment.

Effect of Alloying on Microstructure and Mechanical Properties of AlCoCrFeNi2.1 Eutectic High-Entropy Alloy.

In order to explore the effect of alloying on the microstructures and mechanical properties of AlCoCrFeNi2.1 eutectic high-entropy alloys (EHEAs), 0.1, 0.2, and 0.3 at.% V, Mo, and B were added to the AlCoCrFeNi2.1 alloy in this work. The effects of the elements and contents on the phase composition, microstructures, mechanical properties, and fracture mechanism were investigated. The results showed that the crystal structures of the AlCoCrFeNi2.1 EHEAs remained unchanged, and the alloys were still composed of FCC and BCC structures, whose content varied with the addition of alloying elements. After alloying, the aggregation of Co, Cr, Al, and Ni elements remained unchanged, and the V and Mo were distributed in both dendritic and interdendritic phases. The tensile strengths of the alloys all exceeded 1000 MPa when the V and Mo elements were added, and the Mo0.2 alloy had the highest tensile strength, of 1346.3 MPa, and fracture elongation, of 24.6%. The alloys with the addition of V and Mo elements showed a mixed ductile and brittle fracture, while the B-containing alloy presented a cleavage fracture. The fracture mechanism of Mo0.2 alloy is mainly crack propagation in the BCC lamellae, and the FCC dendritic lamellae exhibit the characteristics of plastic deformation.

The OsNAC41-RoLe1-OsAGAP module promotes root development and drought resistance in upland rice.

Drought is a major environmental stress limiting crop yields worldwide. Upland rice (Oryza sativa) has evolved complex genetic mechanisms for adaptative growth under drought stress. However, few genetic variants that mediate drought resistance in upland rice have been identified, and little is known about the evolution of this trait during rice domestication. In this study, using a genome-wide association study we identified ROOT LENGTH 1 (RoLe1) that controls rice root length and drought resistance. We found that a G-to-T polymorphism in the RoLe1 promoter causes increased binding of the transcription factor OsNAC41 and thereby enhanced expression of RoLe1. We further showed that RoLe1 interacts with OsAGAP, an ARF-GTPase activating protein involved in auxin-dependent root development, and interferes with its function to modulate root development. Interestingly, RoLe1 could enhance crop yield by increasing the seed-setting rate under moderate drought conditions. Genomic evolutionary analysis revealed that a newly arisen favorable allelic variant, proRoLe1-526T, originated from the midwest Asia and was retained in upland rice during domestication. Collectively, our study identifies an OsNAC41-RoLe1-OsAGAP module that promotes upland rice root development and drought resistance, providing promising genetic targets for molecular breeding of drought-resistant rice varieties.

Engineering Carrier Density and Effective Mass of Plasmonic TiN Films by Tailoring Nitrogen Vacancies.

The introduction of nitrogen vacancies has been shown to be an effective way to tune the plasmonic properties of refractory titanium nitrides. However, its underlying mechanism remains debated due to the lack of high-quality single-crystalline samples and a deep understanding of electronic properties. Here, a series of epitaxial titanium nitride films with varying nitrogen vacancy concentrations (TiNx) were synthesized. Spectroscopic ellipsometry measurements revealed that the plasmon energy could be tuned from 2.64 eV in stoichiometric TiN to 3.38 eV in substoichiometric TiNx. Our comprehensive analysis of electrical and plasmonic properties showed that both the increased electronic states around the Fermi level and the decreased carrier effective mass due to the modified electronic band structures are responsible for tuning the plasmonic properties of TiNx. Our findings offer a deeper understanding of the tunable plasmonic properties in epitaxial TiNx films and are beneficial for the development of nitride plasmonic devices.

Natural variation in the Tn1a promoter regulates tillering in rice.

Rice tillering is an important agronomic trait that influences plant architecture and ultimately affects yield. This can be genetically improved by mining favourable variations in genes associated with tillering. Based on a previous study on dynamic tiller number, we cloned the gene Tiller number 1a (Tn1a), which encodes a membrane-localised protein containing the C2 domain that negatively regulates tillering in rice. A 272 bp insertion/deletion at 387 bp upstream of the start codon in the Tn1a promoter confers a differential transcriptional response and results in a change in tiller number. Moreover, the TCP family transcription factors Tb2 and TCP21 repress the Tn1a promoter activity by binding to the TCP recognition site within the 272 bp indel. In addition, we identified that Tn1a may affect the intracellular K+ content by interacting with a cation-chloride cotransporter (OsCCC1), thereby affecting the expression of downstream tillering-related genes. The Tn1a+272 bp allele, associated with high tillering, might have been preferably preserved in rice varieties in potassium-poor regions during domestication. The discovery of Tn1a is of great significance for further elucidating the genetic basis of tillering characteristics in rice and provides a new and favourable allele for promoting the geographic adaptation of rice to soil potassium.

Porcine granulosa cell transcriptomic analyses reveal the differential regulation of lncRNAs and mRNAs in response to all-trans retinoic acid in vitro.

Objective: The active metabolite of vitamin A, all-trans retinoic acid (ATRA), is involved in the proliferation and differentiation of granulosa cells, and promotes the follicular development, oocyte maturation, and ovulation in mammals. This study aims to investigate the ATRA induced potential long noncoding RNAs (lncRNAs) that regulate the expression of genes associated with granulosa cell proliferation and follicular development. Methods: The lncRNA and mRNA profiles of porcine granulosa cells from ATRA treatment and control group in vitro were constructed through RNA sequencing. Meanwhile, the sequencing data were verified using quantitative polymerase chain reaction (qPCR). Results: A total of 86 differentially expressed lncRNAs and 128 differentially expressed genes (DEGs) were detected in granulosa cells after ATRA treatment. The qRT-PCR results were consistent with the RNA-seq data. Functional annotation analysis revealed that the DEGs were remarkably enriched in ovary function and reproduction which contained FoxO, Hippo, Oocyte meiosis, mTOR signaling pathway, as well as several pathways associated with hormone regulation like Oxytocin signaling pathway and Steroid hormone biosynthesis. Moreover, an interaction network of lncRNAs and their cis-target DEGs was constructed, and 7 differentially expressed lncRNAs and 6 cis-target DEGs were enriched in ovarian steroidogenesis and reproduction. Conclusion: These findings expand the lncRNA catalogue and provide a basis for further studies on the mechanism of ATRA-mediated lncRNA regulation of follicular development in pigs.

Health Impacts of Fine Particulate Matter Shift Due to Urbanization in China.

Rapid urbanization and industrialization have resulted in diverse anthropogenic activities and emissions between urban and non-urban regions, leading to varying levels of exposure to air pollutants and associated health risks. However, endeavors to mitigate air pollution and health benefits have displayed considerable heterogeneity across different regions. Therefore, comprehending the changes in air pollutant concentrations and health impacts within an urbanization context is imperative for promoting environmental equity. This paper uses gross domestic product (GDP)- and population-weighted methods to distinguish anthropogenic emissions from urban and non-urban areas in China and quantified their contributions to fine particulate matter (PM2.5) using the Community Multiscale Air Quality (CMAQ) model in 2010 and 2019. Anthropogenic emissions from urban and non-urban (outside urban) regions decreased by 26 and 44% from 2010 to 2019, respectively, resulting in 31 and 28% reductions of PM2.5 in China. PM2.5-related premature mortality attributed to non-urban and urban anthropogenic emission decreases by 8%. Non-urban anthropogenic activities are the main contributor to PM2.5 (56% in 2010 and 2019) and its associated premature mortality (59%), which also predominantly affects non-urban premature mortality (37-42% in 2010-2019). Population changes increase the proportion of premature mortality in urban populations (7-19%) from 2010 to 2019. This study emphasizes the shift of affected populations due to urbanization and population changes.

Flexible Sono-Piezo Patch for Functional Sweat Gland Repair through Endogenous Microenvironmental Remodeling.

Remodeling the endogenous regenerative microenvironment in wounds is crucial for achieving scarless, functional tissue regeneration, especially the functional recovery of skin appendages such as sweat glands in burn patients. However, current approaches mostly rely on the use of exogenous materials or chemicals to stimulate cell proliferation and migration, while the remodeling of a pro-regenerative microenvironment remains challenging. Herein, we developed a flexible sono-piezo patch (fSPP) that aims to create an endogenous regenerative microenvironment to promote the repair of sweat glands in burn wounds. This patch, composed of multifunctional fibers with embedded piezoelectric nanoparticles, utilized low-intensity pulsed ultrasound (LIPUS) to activate electrical stimulation of the target tissue, resulting in enhanced pro-regenerative behaviors of niche tissues and cells, including peripheral nerves, fibroblasts, and vasculatures. We further demonstrated the effective wound healing and regeneration of functional sweat glands in burn injuries solely through such physical stimulation. This noninvasive and drug-free therapeutic approach holds significant potential for the clinical treatment of burn injuries.

Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants.

CD8+ T cell immunity, mediated by human leukocyte antigen (HLA) and T cell receptor (TCR), plays a critical role in conferring immune memory and protection against viral pathogens. The emergence of SARS-CoV-2 variants poses a serious challenge to the efficacy of current vaccines. Whereas numerous SARS-CoV-2 mutations associated with immune escape from CD8+ T cells have been documented, the molecular effects of most mutations on epitope-specific TCR recognition remain largely unexplored. Here, we studied an HLA-A24-restricted NYN epitope (Spike448-456) that elicits broad CD8+ T cell responses in COVID-19 patients characterized by a common TCR repertoire. Four natural mutations, N450K, L452Q, L452R, and Y453F, arose within the NYN epitope and have been transmitted in certain viral lineages. Our findings indicate that these mutations have minimal impact on the epitope's presentation by cell surface HLA, yet they diminish the affinities of their respective peptide-HLA complexes (pHLAs) for NYN peptide-specific TCRs, particularly L452R and Y453F. Furthermore, we determined the crystal structure of HLA-A24 loaded with the Y453F peptide (NYNYLFRLF), and subsequently a ternary structure of the public TCRNYN-I complexed to the original NYN-HLA-A24 (NYNYLYRLF). Our structural analysis unveiled that despite competent presentation by HLA, the mutant Y453F peptide failed to establish a stable TCR-pHLA ternary complex due to reduced peptide: TCR contacts. This study supports the idea that cellular immunity restriction is an important driving force behind viral evolution.

SARS-CoV-2 replication and drug discovery.

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to wreak havoc across the globe. This sudden and deadly pandemic emphasizes the necessity for anti-viral drug development that can be rapidly administered to reduce morbidity, mortality, and virus propagation. Thus, lacking efficient anti-COVID-19 treatment, and especially given the lengthy drug development process as well as the critical death tool that has been associated with SARS-CoV-2 since its outbreak, drug repurposing (or repositioning) constitutes so far, the ideal and ready-to-go best approach in mitigating viral spread, containing the infection, and reducing the COVID-19-associated death rate. Indeed, based on the molecular similarity approach of SARS-CoV-2 with previous coronaviruses (CoVs), repurposed drugs have been reported to hamper SARS-CoV-2 replication. Therefore, understanding the inhibition mechanisms of viral replication by repurposed anti-viral drugs and chemicals known to block CoV and SARS-CoV-2 multiplication is crucial, and it opens the way for particular treatment options and COVID-19 therapeutics. In this review, we highlighted molecular basics underlying drug-repurposing strategies against SARS-CoV-2. Notably, we discussed inhibition mechanisms of viral replication, involving and including inhibition of SARS-CoV-2 proteases (3C-like protease, 3CLpro or Papain-like protease, PLpro) by protease inhibitors such as Carmofur, Ebselen, and GRL017, polymerases (RNA-dependent RNA-polymerase, RdRp) by drugs like Suramin, Remdesivir, or Favipiravir, and proteins/peptides inhibiting virus-cell fusion and host cell replication pathways, such as Disulfiram, GC376, and Molnupiravir. When applicable, comparisons with SARS-CoV inhibitors approved for clinical use were made to provide further insights to understand molecular basics in inhibiting SARS-CoV-2 replication and draw conclusions for future drug discovery research.

Influence of Epoxy Resin Interlayer Interfaces on Electrical Tree Growth and Breakdown Characteristics.

The solid-solid insulation interface structure is a typical interface in extra-high-voltage power equipment, in which the multilayer epoxy resin material is a key component in the insulation structure of the power equipment, and the study of its interface characteristics is the most important. In this paper, epoxy-epoxy cross-linking interface specimens were prepared through experiments, and the degree of cross-linking between the interfaces was analyzed by changing the ratio of the curing agent and adding hydroxyl-terminated liquid nitrile rubber (HTBN) particles; it can be concluded that there exists a weak cross-linking reaction between the interfaces. The electrical tree measurement and alternating current (AC) breakdown test platform were set up, and three different cases of no interface, the electric field direction parallel to the interface, and the electric field direction perpendicular to the interface were tested, through which it was concluded that the existence of the interface inhibited the development of the electrical tree. For the three different cases of AC breakdown tested, it was concluded that the presence of an interface enhances the AC breakdown strength when the electric field direction is parallel to the interface and decreases the AC breakdown strength when the electric field direction is perpendicular to the interface through the interface, affecting the charge transport.

Transcriptome analysis of Vero cells infected with attenuated vaccine strain CDV-QN-1.

To better understand the interaction between attenuated vaccines and host antiviral responses, we used bioinformatics and public transcriptomics data to analyze the immune response mechanisms of host cells after canine distemper virus (CDV) infection in Vero cells and screened for potential key effector factors. In this study, CDV-QN-1 infect with Vero cells at an MOI of 0.5, and total RNA was extracted from the cells 24 h later and reverse transcribed into cDNA. Transcriptome high-throughput sequencing perform using Illumina. The results showed that 438 differentially expressed genes were screened, of which 409 were significantly up-regulated and 29 were significantly down-regulated. Eight differentially expressed genes were randomly selected for RT-qPCR validation, and the change trend was consistent with the transcriptomics data. GO and KEGG analysis of differentially expressed genes revealed that most of the differentially expressed genes in CDV-QN-1 infection in the early stage were related to immune response and antiviral activity. The enriched signaling pathways mainly included the interaction between cytokines and cytokine receptors, the NF-kappa B signaling pathway, the Toll-like receptor signaling pathway, and the NOD-like receptor signaling pathway. This study provides a foundation for further exploring the pathogenesis of CDV and the innate immune response of host cells in the early stage of infection.

QTL detection and candidate gene identification of qCTB1 for cold tolerance in the Yunnan plateau landrace rice.

Cold stress is one of the main abiotic stresses that affects rice growth and production worldwide. Dissection of the genetic basis is important for genetic improvement of cold tolerance in rice. In this study, a new source of cold-tolerant accession from the Yunnan plateau, Lijiangxiaoheigu, was used as the donor parent and crossed with a cold-sensitive cultivar, Deyou17, to develop recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis for cold tolerance at the early seedling and booting stages in rice. In total, three QTLs for cold tolerance at the early seedling stage on chromosomes 2 and 7, and four QTLs at the booting stage on chromosomes 1, 3, 5, and 7, were identified. Haplotype and linear regression analyses showed that QTL pyramiding based on the additive effect of these favorable loci has good potential for cold tolerance breeding. Effect assessment in the RIL and BC3F3 populations demonstrated that qCTB1 had a stable effect on cold tolerance at the booting stage in the genetic segregation populations. Under different cold stress conditions, qCTB1 was fine-mapped to a 341-kb interval between markers M3 and M4. Through the combination of parental sequence comparison, candidate gene-based association analysis, and tissue and cold-induced expression analyses, eight important candidate genes for qCTB1 were identified. This study will provide genetic resources for molecular breeding and gene cloning to improve cold tolerance in rice. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01488-3.

Monovalent, bivalent and biparatopic nanobodies targeting S1 protein of porcine epidemic diarrhea virus efficiently neutralized the virus infectivity.

BACKGROUND: Porcine epidemic diarrhea virus (PEDV) is a highly contagious coronavirus that causes severe diarrhea and death in neonatal piglets, which has brought huge economic losses to the pork industry worldwide since its first discovery in the early 1970s in Europe. Passive immunization with neutralizing antibodies against PEDV is an effective prevention measure. To date, there are no effective therapeutic drugs to treat the PEDV infection. RESULTS: We conducted a screening of specific nanobodies against the S1 protein from a phage display library obtained from immunized alpacas. Through competitive binding to antigenic epitopes, we selected instead of chose nanobodies with high affinity and constructed a multivalent tandem. These nanobodies were shown to inhibit PEDV infectivity by the neutralization assay. The antiviral capacity of nanobody was found to display a dose-dependent pattern, as demonstrated by IFA, TCID50, and qRT-PCR analyses. Notably, biparatopic nanobody SF-B exhibited superior antiviral activity. Nanobodies exhibited low cytotoxicity and high stability even under harsh temperature and pH conditions, demonstrating their potential practical applicability to animals. CONCLUSIONS: Nanobodies exhibit remarkable biological properties and antiviral effects, rendering them a promising candidate for the development of anti-PEDV drugs.

Association of blood trihalomethane concentrations with diabetes mellitus in older adults in the US: a cross-sectional study of NHANES 2013-2018.

Background: Previous studies have demonstrated that there is a correlation between trihalomethanes and disease progression, such as allergic diseases. As we know, only few studies focused on the relationship between trihalomethanes and metabolic diseases, such as diabetes mellitus. Objective: The aim of this study was to further explore the associations between blood trihalomethane concentrations and diabetes mellitus in older adults in the US. Methods: Data were collected from the National Health and Nutrition Examination Study (NHANES) database in the survey cycle during 2013 to 2018, including 2,511 older adults in the US whose blood trihalomethane concentrations were measured, involving chloroform (TCM) and brominated trihalomethanes (Br-THMs). Br-THMs include bromodichloromethane (BDCM), dibromochloromethane (DBCM), and bromoform (TBM). Meanwhile, the concentration of total trihalomethanes (TTHMs) was also measured later. A multivariate logistic regression and restricted cubic spline were used to examine the relationship between blood THMs and diabetes mellitus. Meanwhile, we performed a subgroup analysis, which aims to explore the stability of this relationship in different subgroups. In order to further consider the impact of various disinfection by-products on diabetes, we also used weighted quantile sum (WQS). To explore the correlation in trihalomethanes, we plot a correlation heatmap. Results: Adjusting for potential confounders, we found that there was a significant negative association between chloroform and diabetes mellitus [Model 1 (adjusted for covariates including age, sex, and race, OR = 0.71; 95% CI: 0.50-1.02; p = 0.068; p for trend = 0.094); Model 2 (adjusted for all covariates, OR = 0.68; 95% CI: 0.48-0.96; p = 0.029; p for trend = 0.061)]. In the bromodichloromethane, we reached a conclusion that is similar to TCM [Model 1 (adjusted for covariates including age, sex, and race, OR = 0.54; 95% CI: 0.35-0.82; p = 0.005; p for trend = 0.002); Model 2 (adjusted for all covariates, OR = 0.54; 95% CI: 0.35-0.82; p = 0.003; p for trend = 0.002)]. Meanwhile, the restricted cubic spline curve also further confirms this result (p overall = 0.0027; p overall< 0.001). Based on the analysis in the subgroups, we found that the value p for interaction in the majority of subgroups is higher than 0.1. Trihalomethanes and diabetes were inversely associated, and in the WQS, chloroform and bromodichloromethane were found to be the major contributors to this relationship. In the correlation analysis, we found that most trihalomethanes have a weak correlation, except for TBM and TCM with a strong correlation. Conclusion: Our results in this study showed that blood chloroform, bromodichloromethane concentrations, and diabetes mellitus in older adults in the US are negatively correlated, suggesting that chloroform and bromodichloromethane can be protective factors for diabetes.

Genome-wide Mapping of Topoisomerase Binding Sites Suggests Topoisomerase 3α (TOP3A) as a Reader of Transcription-Replication Conflicts (TRC).

Both transcription and replication can take place simultaneously on the same DNA template, potentially leading to transcription-replication conflicts (TRCs) and topological problems. Here we asked which topoisomerase(s) is/are the best candidate(s) for sensing TRC. Genome-wide topoisomerase binding sites were mapped in parallel for all the nuclear topoisomerases (TOP1, TOP2A, TOP2B, TOP3A and TOP3B). To increase the signal to noise ratio (SNR), we used ectopic expression of those topoisomerases in H293 cells followed by a modified CUT&Tag method. Although each topoisomerase showed distinct binding patterns, all topoisomerase binding signals positively correlated with gene transcription. TOP3A binding signals were suppressed by DNA replication inhibition. This was also observed but to a lesser extent for TOP2A and TOP2B. Hence, we propose the involvement of TOP3A in sensing both head-on TRCs (HO-TRCs) and co-directional TRCs (CD-TRCs). In which case, the TOP3A signals appear concentrated within the promoters and first 20 kb regions of the 5' -end of genes, suggesting the prevalence of TRCs and the recruitment of TOP3A in the 5'-regions of transcribed and replicated genes.