Generation of an infectious cDNA clone for NADC30-like PRRSV.

The porcine reproductive and respiratory syndrome virus (PRRSV) is a highly significant infectious disease that poses a substantial threat to the global pig industry. In recent years, the NADC30-like strain has gradually emerged as prevalent in China, causing a profound impact on the country's pig farming industry. Therefore, it is important to conduct an in-depth study on the characteristics and gene functions of the NADC30-like strain. An infectious cDNA clone is an indispensable tool for investigating the functions of viral genes. In this current study, we successfully isolated a NADC30-like strain and constructed its full-length infectious cDNA clone. The utilization of this clone will facilitate our investigation into the viral replication, pathogenesis, and immune response associated with the PRRSV NADC30-like strain.

Performance evaluation and clinical application of the UA-5600 automatic dry chemistry urine analyzer in renal diseases.

Background: Urine testing as a routine screening programme, abnormal test results can be suggestive to clinicians but can sometimes be overlooked, and the establishment of a diagnostic model can better assist clinicians in identifying potential problems. BLD (blood), LEU (leukocyte), PRO (protein) and GLU (glucose) are the four most important parameters in urine testing, and the accuracy of their results is a key concern for clinicians, so it is essential to verify the accuracy of their results. In this study, we evaluated the analytical and clinical performance of Mindray's automatic urine dry chemistry analyzer, the UA-5600 (Hereinafter referred to as the (UA-5600), and the test strips configured with the instrument, and developed a machine-learning (ML) model for kidney disease screening from the results of 11 parameters output from the UA-5600 with the aim of detecting abnormal urine test results. Methods: Urine samples from outpatients and inpatients at The First Affiliated Hospital of Sun Yat-sen University were collected from August to September 2022 to evaluate the performance of the Mindray UA-5600 dry chemistry analyzer and test strips. The evaluation of the UA-5600 and its test strips focused on the agreement of the urine BLD and LEU readings with the RBC (red blood cell) and WBC (white blood cell) counts obtained by the Mindray EH-2090 urine formed element analyzer. We also compared the PRO and GLU readings with the results of the Mindray BS-2800M biochemistry analyzer. Urine samples from outpatients and inpatients were retrospectively analysed and grouped according to LIS diagnosis. Additionally, eight ML models for kidney disease screening were developed using 11 parameters measured by the UA-5600. And the model was validated by the validation set. Results: The UA-5600 had an 89.55% concordance rate for BLD and a 91.04% concordance rate for LEU compared to the EH-2090 analyzer. When benchmarked against the BS-2800M, the concordance rates for PRO and GLU were 94.14% and 95.20%, respectively. A total of 1,691 samples were used for the construction of the ML models, of which 346 patients (135 males and 211 females, age range: 18 to 98 years) diagnosed with renal disease, and 1,345 patients (397 males and 948 females, age range: 18 to 92 years) with non-renal disease diagnosed with other conditions. Notably, the Naïve Bayes (NB) model, which was built from the UA-5600 parameters, demonstrated superior predictive capabilities for renal disease, with an area under the receiver operating characteristic curve of 0.9470, a sensitivity of 0.7767, and a specificity of 0.9457. Conclusions: The Mindray UA-5600 demonstrates robust detection abilities for both BLD and LEU, and its results for PRO and GLU align closely with those obtained from the chemistry analyzer. The NB model has a good screening ability and shows promise as an effective screening tool.

The N-glycosylation at positions 652 and 661 of viral spike protein negatively modulates porcine deltacoronavirus entry.

N-glycosylation is a highly conserved glycan modification that plays crucial roles in various physiological processes, including protein folding, trafficking, and signal transduction. Porcine deltacoronavirus (PDCoV) poses a newly emerging threat to the global porcine industry. The spike protein of PDCoV exhibits a high level of N-glycosylation; however, its role in viral infection remains poorly understood. In this study, we applied a lentivirus-based entry reporter system to investigate the role of N-glycosylation on the viral spike protein during PDCoV entry stage. Our findings demonstrate that N-glycosylation at positions 652 and 661 of the viral spike protein significantly reduces the infectivity of PDCoV pseudotyped virus. Overall, our results unveil a novel function of N-glycosylation in PDCoV infection, highlighting its potential for facilitating the development of antiviral strategies.

Enhancing antitumor efficacy of oncolytic virus M1 via albendazole-sustained CD8+ T cell activation.

The immune response plays a crucial role in the functionality of oncolytic viruses. In this study, Albendazole, an antihelminthic drug known to modulate the immune checkpoint PD-L1, was combined with the oncolytic virus M1 (OVM1) to treat mice with either prostate cancer (RM-1) or glioma (GL261) tumors. This combination therapy enhanced anti-tumor effects in immunocompetent mice, but not in immunodeficient ones, without increasing OVM1 replication. Instead, it led to an increase in the number of CD8+ T cells within the tumor, downregulated the expression of PD1 on CD8+ T cells, and upregulated activation markers such as Ki67, CD44, and CD69 and the secretion of cytotoxic factors including interferon (IFN)-γ, granzyme B, and tumor necrosis factor (TNF)-α. Consistently, it enhanced the in vitro tumor-killing activity of lymphocytes from tumor-draining lymph nodes or spleens. The synergistic effect of Albendazole on OVM1 was abolished by depleting CD8+ T cells, suggesting a CD8+ T cell-dependent mechanism. In addition, Albendazole and OVM1 therapy increased CTLA4 expression in the spleen, and the addition of CTLA4 antibodies further enhanced the anti-tumor efficacy in vivo. In summary, Albendazole can act synergistically with oncolytic viruses via CD8+ T cell activation, and the Albendazole/OVM1 combination can overcome resistance to CTLA4-based immune checkpoint blockade therapy.

Genome editing of pseudorabies virus in the CRISPR/Cas9 era: a mini-review.

Pseudorabies virus (PRV) is an important swine virus that has a significant impact on the global swine industry. PRV is a member of the herpesvirus family, specifically the alphaherpesvirus subfamily, and has been extensively utilized as a prototype herpesvirus. Notably, recent studies have reported that PRV sporadically spills over into humans. The PRV genome is approximately 150 kb in size and is difficult to manipulate at the genomic level. The development of clustered regularly interspaced short palindromic repeat-associated protein (CRISPR/Cas9) technology has revolutionized PRV genome editing. CRISPR/Cas9 has been widely used in the construction of reporter viruses, knock-out/knock-in of genes of interest, single virus tracking and antiviral strategies. Most importantly, for vaccine development, virulence gene knockout PRV vaccine candidates can be obtained within 2 weeks using CRISPR/Cas9. In this mini-review, we provide a concise overview of the application of CRISPR/Cas9 in PRV research and mainly share our experience with methods for efficiently editing the PRV genome. Through this review, we hope to give researchers better insight into the genome editing of pseudorabies virus.

Identification of the receptor of oncolytic virus M1 as a therapeutic predictor for multiple solid tumors.

Over the last decade, oncolytic virus (OV) therapy has shown its promising potential in tumor treatment. The fact that not every patient can benefit from it highlights the importance for defining biomarkers that help predict patients' responses. As particular self-amplifying biotherapeutics, the anti-tumor effects of OVs are highly dependent on the host factors for viral infection and replication. By using weighted gene co-expression network analysis (WGCNA), we found matrix remodeling associated 8 (MXRA8) is positively correlated with the oncolysis induced by oncolytic virus M1 (OVM). Consistently, MXRA8 promotes the oncolytic efficacy of OVM in vitro and in vivo. Moreover, the interaction of MXRA8 and OVM studied by single-particle cryo-electron microscopy (cryo-EM) showed that MXRA8 directly binds to this virus. Therefore, MXRA8 acts as the entry receptor of OVM. Pan-cancer analysis showed that MXRA8 is abundant in most solid tumors and is highly expressed in tumor tissues compared with adjacent normal ones. Further study in cancer cell lines and patient-derived tumor tissues revealed that the tumor selectivity of OVM is predominantly determined by a combinational effect of the cell membrane receptor MXRA8 and the intracellular factor, zinc-finger antiviral protein (ZAP). Taken together, our study may provide a novel dual-biomarker for precision medicine in OVM therapy.

Fos Facilitates Gallid Alpha-Herpesvirus 1 Infection by Transcriptional Control of Host Metabolic Genes and Viral Immediate Early Gene.

Gallid alpha-herpesvirus 1, also known as avian infectious laryngotracheitis virus (ILTV), continues to cause huge economic losses to the poultry industry worldwide. Similar to that of other herpesvirus-encoded proteins, the expression of viral genes encoded by ILTV is regulated by a cascade, and the underlying regulatory mechanism remains largely unclear. The viral immediate-early (IE) gene ICP4 plays a prominent role in the initiation of the transcription of early and late genes during ILTV replication. In this study, we identified AP-1 as the key regulator of the transcription of ILTV genes by bioinformatics analysis of genome-wide transcriptome data. Subsequent functional studies of the key members of the AP-1 family revealed that Fos, but not Jun, regulates ILTV infection through AP-1 since knockdown of Fos, but not Jun, by gene silencing significantly reduced ICP4 transcription and subsequent viral genome replication and virion production. Using several approaches, we identified ICP4 as a bona fide target gene of Fos that regulated Fos and has Fos response elements within its promoter. Neither the physical binding of Jun to the promoter of ICP4 nor the transcriptional activity of Jun was observed. In addition, knockdown of Fos reduced the transcription of MDH1 and ATP5A1, genes encoding two host rate-limiting enzymes essential for the production of the TCA intermediates OAA and ATP. The biological significance of the transcriptional regulation of MDH1 and ATP5A1 by Fos in ILTV infection was supported by the fact that anaplerosis of OAA and ATP rescued both ICP4 transcription and virion production in infected cells under when Fos was silenced. Our study identified the transcription factor Fos as a key regulator of ILTV infection through its transcription factor function on both the virus and host sides, improving the current understanding of both avian herpesvirus-host interactions and the roles of AP-1 in viral infection.

Global exploration of the metabolic requirements of gallid alphaherpesvirus 1.

Although therapeutics targeting viral metabolic processes have been considered as promising strategies to treat herpesvirus infection, the metabolic requirements of gallid alphaherpesvirus 1 (ILTV), which is economically important to the poultry industry worldwide, remain largely unknown. Using the ILTV-susceptible but nonpermissive chicken cell line DF-1 and the ILTV-permissive chicken cell line LMH as models, the present study explored the metabolic requirements of ILTV by global transcriptome analysis and metabolome assays of ILTV infected cell lines in combination with a set of functional validations. The extensive metabolic exploration demonstrated that ILTV infection tended to promote a metabolic shift from glycolysis to fatty acid (FA) and nucleotide biosynthesis and utilizes glutamine independently of glutaminolysis, without significant general effect on the TCA cycle. In addition, different metabolic pathways were found to be required for distinct stages of ILTV replication. Glucose and glutamine were required for the transcription of viral immediate early gene ICP4 and subsequent steps of viral replication. However, FA synthesis was essential for assembly but not required for other upstream steps of ILTV replication. Moreover, the metabolic requirements of ILTV infection revealed in chicken cell lines were further validated in chicken primary cells isolated from chicken embryo kidneys and chicken embryo livers. The present study, to the best of our knowledge, provides the first global metabolic profile of animal herpesviruses and illustrates the main characteristics of the metabolic program of ILTV.

Two Phenotype-Differentiated Acinetobacter baumannii Mutants That Survived in a Meropenem Selection Display Large Differences in Their Transcription Profiles.

37662RM1 and 37662RM2 are two phenotypically different, carbapenem-resistant mutants of Acinetobacter baumannii 37662 isolate following selection with meropenem (MEM) at sub-inhibitory concentrations. 37662RM2 lacks capsule synthesis and shows dramatically increased biofilm formation, while 37662RM1 shows merely impaired capsule synthesis. Here we report that 37662RM1 and RM2 have transcription profiles that are different from those of their starting strain, 37662WT. There were far more differentially expressed genes in 37662RM2 than in 37662RM1. The capsule polysaccharide (CPS) synthesis-required genes (itrA2, gtr5, psaA, psaB, psaC, psaD, psaE, psaF, kpsS2, wzx, wzy, wza, wzb, and wzc) showed reduced transcription levels in 37662RM2, which may at least partially explain the loss of capsule synthesis. The csu operon genes responsible for pili assembly and their regulator genes bfmR-bfmS were over-expressed in 37662RM2. This result together with the established critical roles of these genes in biofilm formation provide solid evidence that up-regulation of csu and bfmR-bfmS should be considered responsible for the enhanced biofilm formation in 37662RM2. ISAba1 was found to insert into the intergenic region between the csu operon and the acrR gene and should be responsible for the significant up-regulation of acrR, which was proposed to be associated with biofilm formation. Genome sequencing revealed that the ISAba1 upstream bla OXA- 508 (a new member of bla OXA- 51-like) and acrR were duplicated, suggesting a replicative transposition event. Altogether, the phenotype divergence driven by MEM selection mainly occurs at the RNA level and the transposition of ISAba1 plays an important role in modulating gene expression to adapt to the environment.

Gallid Herpesvirus 1 Initiates Apoptosis in Uninfected Cells through Paracrine Repression of p53.

Apoptosis is a common innate defense mechanism of host cells against viral infection and is therefore suppressed by many viruses, including herpes simplex virus (HSV), via various strategies. A recent in vivo study reported the apoptosis of remote uninfected cells during Gallid herpesvirus 1 (GaHV-1) infection, yet little is known about this previously unknown aspect of herpesvirus-host interactions. The aim of the present study was to investigate the apoptosis of uninfected host cells during GaHV-1 infection. The present study used in vitro and in ovo models, which avoided potential interference by host antiviral immunity, and demonstrated that this GaHV-1-host interaction is independent of host immune responses and important for both the pathological effect of viral infection and early viral dissemination from the primary infection site to distant tissues. Further, we revealed that GaHV-1 infection triggers this process in a paracrine-regulated manner. Using genome-wide transcriptome analyses in combination with a set of functional studies, we found that this paracrine-regulated effect requires the repression of p53 activity in uninfected cells. In contrast, the activation of p53 not only prevented the apoptosis of remote uninfected cells and subsequent pathological damage induced by GaHV-1 infection but also delayed viral dissemination significantly. Moreover, p53 activation repressed viral replication both in vitro and in ovo, suggesting that dual cell-intrinsic mechanisms underlie the suppression of GaHV-1 infection by p53 activation. This study uncovers the mechanism underlying the herpesvirus-triggered apoptosis of remote host cells and extends our understanding of both herpesvirus-host interactions and the roles of p53 in viral infection.IMPORTANCE It is well accepted that herpesviruses suppress the apoptosis of host cells via various strategies to ensure sustained viral replication during infection. However, a recent in vivo study reported the apoptosis of remote uninfected cells during GaHV-1 infection. The mechanism and the biological meaning of this unexpected herpesvirus-host interaction are unclear. This study uncovers the mechanisms of herpesvirus-triggered apoptosis in uninfected cells and may also contribute to a mechanistic illustration of paracrine-regulated apoptosis induced by other viruses in uninfected host cells.

Experimental Study of Anisotropic Stress/Strain Relationships of Aortic and Pulmonary Artery Homografts and Synthetic Vascular Grafts.

Homografts and synthetic grafts are used in surgery for congenital heart disease (CHD). Determining these materials' mechanical properties will aid in understanding tissue behavior when subjected to abnormal CHD hemodynamics. Homograft tissue samples from anterior/posterior aspects, of ascending/descending aorta (AA, DA), innominate artery (IA), left subclavian artery (LScA), left common carotid artery (LCCA), main/left/right pulmonary artery (MPA, LPA, RPA), and synthetic vascular grafts, were obtained in three orientations: circumferential, diagonal (45 deg relative to circumferential direction), and longitudinal. Samples were subjected to uniaxial tensile testing (UTT). True strain-Cauchy stress curves were individually fitted for each orientation to calibrate Fung model. Then, they were used to calibrate anisotropic Holzapfel-Gasser model (R2 > 0.95). Most samples demonstrated a nonlinear hyperelastic strain-stress response to UTT. Stiffness (measured by tangent modulus at different strains) in all orientations were compared and shown as contour plots. For each vessel segment at all strain levels, stiffness was not significantly different among aspects and orientations. For synthetic grafts, stiffness was significantly different among orientations (p < 0.042). Aorta is significantly stiffer than pulmonary artery at 10% strain, comparing all orientations, aspects, and regions (p = 0.0001). Synthetic grafts are significantly stiffer than aortic and pulmonary homografts at all strain levels (p < 0.046). Aortic, pulmonary artery, and synthetic grafts exhibit hyperelastic biomechanical behavior with anisotropic effect. Differences in mechanical properties among vascular grafts may affect native tissue behavior and ventricular/arterial mechanical coupling, and increase the risk of deformation due to abnormal CHD hemodynamics.

Controlled fragmentation of multimaterial fibres and films via polymer cold-drawing.

Polymer cold-drawing is a process in which tensile stress reduces the diameter of a drawn fibre (or thickness of a drawn film) and orients the polymeric chains. Cold-drawing has long been used in industrial applications, including the production of flexible fibres with high tensile strength such as polyester and nylon. However, cold-drawing of a composite structure has been less studied. Here we show that in a multimaterial fibre composed of a brittle core embedded in a ductile polymer cladding, cold-drawing results in a surprising phenomenon: controllable and sequential fragmentation of the core to produce uniformly sized rods along metres of fibre, rather than the expected random or chaotic fragmentation. These embedded structures arise from mechanical-geometric instabilities associated with 'neck' propagation. Embedded, structured multimaterial threads with complex transverse geometry are thus fragmented into a periodic train of rods held stationary in the polymer cladding. These rods can then be easily extracted via selective dissolution of the cladding, or can self-heal by thermal restoration to re-form the brittle thread. Our method is also applicable to composites with flat rather than cylindrical geometries, in which case cold-drawing leads to the break-up of an embedded or coated brittle film into narrow parallel strips that are aligned normally to the drawing axis. A range of materials was explored to establish the universality of this effect, including silicon, germanium, gold, glasses, silk, polystyrene, biodegradable polymers and ice. We observe, and verify through nonlinear finite-element simulations, a linear relationship between the smallest transverse scale and the longitudinal break-up period. These results may lead to the development of dynamical and thermoreversible camouflaging via a nanoscale Venetian-blind effect, and the fabrication of large-area structured surfaces that facilitate high-sensitivity bio-detection.

Evolutionary expansion of nematode-specific glycine-rich secreted peptides.

Genome-wide comparisons across 10 species from algae Guillardia theta to mammal human indicated that Caenorhabditis elegans and Caenorhabditis briggsae were highly enriched for glycine-rich secreted peptides (GRSPs) (110 GRSPs in C. elegans and 93 in C. briggsae) in this study. Chromosomal mapping showed that most GRSPs were clustered on the two nematode genomes [103 (93.64%) in C. elegans and 82 (88.17%) in C. briggsae], which could be divided into 18 cluster units in C. elegans and 13 in C. briggsae, respectively. Except for four C. elegans GRSPs clusters without matching clusters in C. briggsae, all other GRSPs clusters had paired synteny block between the two nematode genomes. Analyzing transcriptome datasets quantified by microarray indicated extensive genome-wide co-expression of GRSPs clusters after C. elegans infections. Highly homologous coding sequences and conserved exon-intron structures indicated that GRSPs tight clusters were likely derived from local DNA duplications. Phylogenetic conservation of synteny blocks between their genomes, co-expression of GRSPs clusters after C. elegans infections, and strong purifying selections of coding sequences may indicate evolutionary constraints acting on C. elegans to guarantee that C. elegans could mount rapid systematic responses to infections by co-expression, co-regulation, and co-functionality of GRSPs clusters.