Cell-surface d-glucuronyl C5-epimerase binds to porcine deltacoronavirus spike protein facilitating viral entry.

Porcine deltacoronavirus (PDCoV) is an emerging swine enteric coronavirus with zoonotic potential. The coronavirus spike (S) glycoprotein, especially the S1 subunit, mediates viral entry by binding to cellular receptors. However, the functional receptor of PDCoV remains poorly understood. In this study, we used the soluble PDCoV S1 protein as bait to capture the S1-binding cellular transmembrane proteins in combined immunoprecipitation and mass spectrometry analyses. A single guide RNA screen identified d-glucuronyl C5-epimerase (GLCE), a heparan sulfate-modifying enzyme, as a proviral host factor for PDCoV infection. GLCE knockout significantly inhibited the attachment and internalization stages of PDCoV infection. We also demonstrated the interaction between GLCE and PDCoV S with coimmunoprecipitation in both an overexpression system and PDCoV-infected cells. GLCE could be localized to the cell membrane, and an anti-GLCE antibody suppressed PDCoV infection. Although GLCE expression alone did not render nonpermissive cells susceptible to PDCoV infection, GLCE promoted the binding of PDCoV S to porcine amino peptidase N (pAPN), acting synergistically with pAPN to enhance PDCoV infection. In conclusion, our results demonstrate that GLCE is a novel cell-surface factor facilitating PDCoV entry and provide new insights into PDCoV infection. IMPORTANCE: The identification of viral receptors is of great significance, potentially extending our understanding of viral infection and pathogenesis. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus with the potential for cross-species transmission. However, the receptors or coreceptors of PDCoV are still poorly understood. The present study confirms that d-glucuronyl C5-epimerase (GLCE) is a positive regulator of PDCoV infection, promoting viral attachment and internalization. The anti-GLCE antibody suppressed PDCoV infection. Mechanically, GLCE interacts with PDCoV S and promotes the binding of PDCoV S to porcine amino peptidase N (pAPN), acting synergistically with pAPN to enhance PDCoV infection. This work identifies GLCE as a novel cell-surface factor facilitating PDCoV entry and paves the way for further insights into the mechanisms of PDCoV infection.

Cleavage of HDAC6 to dampen its antiviral activity by nsp5 is a common strategy of swine enteric coronaviruses.

HDAC6, a structurally and functionally unique member of the histone deacetylase (HDAC) family, is an important host factor that restricts viral infection. The broad-spectrum antiviral activity of HDAC6 makes it a potent antiviral agent. Previously, we found that HDAC6 functions to antagonize porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus with zoonotic potential. However, the final outcome is typically a productive infection that materializes as cells succumb to viral infection, indicating that the virus has evolved sophisticated mechanisms to combat the antiviral effect of HDAC6. Here, we demonstrate that PDCoV nonstructural protein 5 (nsp5) can cleave HDAC6 at glutamine 519 (Q519), and cleavage of HDAC6 was also detected in the context of PDCoV infection. More importantly, the anti-PDCoV activity of HDAC6 was damaged by nsp5 cleavage. Mechanistically, the cleaved HDAC6 fragments (amino acids 1-519 and 520-1159) lost the ability to degrade PDCoV nsp8 due to their impaired deacetylase activity. Furthermore, nsp5-mediated cleavage impaired the ability of HDAC6 to activate RIG-I-mediated interferon responses. We also tested three other swine enteric coronaviruses (transmissible gastroenteritis virus, porcine epidemic diarrhea virus, and swine acute diarrhea syndrome-coronavirus) and found that all these coronaviruses have adopted similar mechanisms to cleave HDAC6 in both an overexpression system and virus-infected cells, suggesting that cleavage of HDAC6 is a common strategy utilized by swine enteric coronaviruses to antagonize the host's antiviral capacity. Together, these data illustrate how swine enteric coronaviruses antagonize the antiviral function of HDAC6 to maintain their infection, providing new insights to the interaction between virus and host.IMPORTANCEViral infections and host defenses are in constant opposition. Once viruses combat or evade host restriction, productive infection is achieved. HDAC6 is a broad-spectrum antiviral protein that has been demonstrated to inhibit many viruses, including porcine deltacoronavirus (PDCoV). However, whether HDAC6 is reciprocally targeted and disabled by viruses remains unclear. In this study, we used PDCoV as a model and found that HDAC6 is targeted and cleaved by nsp5, a viral 3C-like protease. The cleaved HDAC6 loses its deacetylase activity as well as its ability to degrade viral proteins and activate interferon responses. Furthermore, this cleavage mechanism is shared among other swine enteric coronaviruses. These findings shed light on the intricate interplay between viruses and HDAC6, highlighting the strategies employed by viruses to evade host antiviral defenses.

The APC/CTAD1-WIDE LEAF 1-NARROW LEAF 1 pathway controls leaf width in rice.

Leaf morphology is one of the most important features of the ideal plant architecture. However, the genetic and molecular mechanisms controlling this feature in crops remain largely unknown. Here, we characterized the rice (Oryza sativa) wide leaf 1 (wl1) mutant, which has wider leaves than the wild-type due to more vascular bundles and greater distance between small vascular bundles. WL1 encodes a Cys-2/His-2-type zinc finger protein that interacts with Tillering and Dwarf 1 (TAD1), a co-activator of the anaphase-promoting complex/cyclosome (APC/C) (a multi-subunit E3 ligase). The APC/CTAD1 complex degrades WL1 via the ubiquitin-26S proteasome degradation pathway. Loss-of-function of TAD1 resulted in plants with narrow leaves due to reduced vascular bundle numbers and distance between the small vascular bundles. Interestingly, we found that WL1 negatively regulated the expression of a narrow leaf gene, NARROW LEAF 1 (NAL1), by recruiting the co-repressor TOPLESS-RELATED PROTEIN and directly binding to the NAL1 regulatory region to inhibit its expression by reducing the chromatin histone acetylation. Furthermore, biochemical and genetic analyses revealed that TAD1, WL1, and NAL1 operated in a common pathway to control the leaf width. Our study establishes an important framework for understanding the APC/CTAD1-WL1-NAL1 pathway-mediated control of leaf width in rice, and provides insights for improving crop plant architecture.

Porcine deltacoronavirus accessory protein NS6 harnesses VPS35-mediated retrograde trafficking to facilitate efficient viral infection.

IMPORTANCE: Retrograde transport has been reported to be closely associated with normal cellular biological processes and viral replication. As an emerging enteropathogenic coronavirus with zoonotic potential, porcine deltacoronavirus (PDCoV) has attracted considerable attention. However, whether retrograde transport is associated with PDCoV infection remains unclear. Our present study demonstrates that retromer protein VPS35 acts as a critical host factor that is required for PDCoV infection. Mechanically, VPS35 interacts with PDCoV NS6, mediating the retrograde transport of NS6 from endosomes to the Golgi and preventing it from lysosomal degradation. Recombinant PDCoVs with an NS6 deletion display resistance to VPS35 deficiency. Our work reveals a novel evasion mechanism of PDCoV that involves the manipulation of the retrograde transport pathway by VPS35, providing new insight into the mechanism of PDCoV infection.

Mapping and candidate gene analysis of QTLs for grain shape in a rice chromosome segment substitution line Z485 and breeding of SSSLs.

Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including qGL12, qGW12, and qRLW12, were identified through the F2 population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of qGL12 for grain length and qGW12 for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design. Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01480-x.

Determinants of health poverty vulnerability in rural areas of Western China in the post-poverty relief era: an analysis based on the Anderson behavioral model.

BACKGROUND: Although China has eliminated absolute poverty, the effects of sickness still pose a threat to the prospect of returning to poverty in western rural areas. However, poverty governance extends beyond solving absolute poverty, and should enhance the family's ability to resist risks, proactively identify the existence of risks, and facilitate preventive measures to reduce the probability of falling into poverty again. This study aimed to assess the health poverty vulnerability of rural households in western China and decompose its determinants. METHODS: Based on survey data from 2022, the three-stage feasible generalized least squares method was used to calculate the health poverty vulnerability index. Then, Anderson's health behavior theory model was extended to analyse various influencing factors using binary logistic regression, and the contribution of each influencing factor was decomposed using the Shapley index. Finally, Tobit regression and the censored least absolute deviations estimation (clad) method were used to test the model's robustness. RESULTS: A total of 5455 families in the rural Ningxia region of western China were included in the study. The health poverty vulnerability index of the sample population in 2022 was 0.3000 ± 0.2223, and families with vulnerability ≥0.5 accounted for 16.9% of the sample population. From the Anderson behavioral model, the three models including propensity, enabling, and demand factors had the best fit, and the AIC and BIC values were the smallest. The Shapley decomposition showed that the dimensions of the propensity factor, number of residents, age and educational level of the household head, and dependency ratio were the most important factors influencing vulnerability to health poverty. Tobit regression and the clad method proved the reliability of the constructed model through a robustness test. CONCLUSION: Rural areas still face the risk of becoming poor or falling into poverty owing to residents' health problems. Health poverty alleviation should gradually change from a focus on treatment to prevention, and formulate a set of accurate and efficient intervention policies from a forward-looking perspective to consolidate the results of health poverty alleviation and prevent widescale poverty return.

Genome-Wide CRISPR/Cas9 Screen Reveals a Role for SLC35A1 in the Adsorption of Porcine Deltacoronavirus.

Porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus, not only causes diarrhea in piglets but also possesses the potential to infect humans. To better understand host-virus genetic dependencies and find potential therapeutic targets for PDCoV, we used a porcine single-guide RNA (sgRNA) lentivirus library to screen host factors related to PDCoV infection in LLC-PK1 cells. The solute carrier family 35 member A1 (SLC35A1), a key molecule in the sialic acid (SA) synthesis pathway, was identified as a host factor required for PDCoV infection. A knockout of SLC35A1 caused decreases in the amounts of cell surface sialic acid (SA) and viral adsorption; meanwhile, trypsin promoted the use of SA in PDCoV infection. By constructing and assessing a series of recombinant PDCoV strains with the deletion or mutation of possible critical domain or amino acid residues for SA binding in the S1 N-terminal domain, we found that S T182 might be a PDCoV SA-binding site. However, the double knockout of SLC35A1 and amino peptidase N (APN) could not block PDCoV infection completely. Additionally, we found that different swine enteric coronaviruses, including transmissible gastroenteritis coronavirus, porcine epidemic diarrhea virus, and swine acute diarrhea syndrome coronavirus, are differentially dependent on SA. Overall, our study uncovered a collection of host factors that can be exploited as drug targets against PDCoV infection and deepened our understanding of the relationship between PDCoV and SA. IMPORTANCE Identifying the host factors required for replication will be helpful to uncover the pathogenesis mechanisms and develop antivirals against the emerging coronavirus porcine deltacoronavirus (PDCoV). Herein, we performed a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 knockout screen, the results of which revealed that the solute carrier family 35 member A1 (SLC35A1) is a host factor required for PDCoV infection that acts by regulating cell surface sialic acid (SA). We also identified the T182 site in the N-terminal domain of PDCoV S1 subunit as being associated with the SA-binding site and found that trypsin promotes the use of cell surface SA by PDCoV. Furthermore, different swine enteric coronaviruses use SLC35A1 differently for infection. This is the first study to screen host factors required for PDCoV replication using a genome-wide CRISPR-Cas9 functional knockout, thereby providing clues for developing antiviral drugs against PDCoV infection.

Design, synthesis, and anti-triple negative breast cancer activity of novel Toosendanin derivatives.

Toosendanin (TSN) is a natural anti-cancer compound that is isolated from the traditional Chinese herbal Melia toosendan Sieb et Zucc. However, the research effect of TSN in the treatment of Triple negative breast cancer (TNBC) is still far from ideal. In this work, we investigated TSN and its derivatives in terms of their actions against MDA-MB-231 and HCC1806 TNBC cell lines. The results indicated that TSN and its derivative 11 showed excellent antitumor activity. Preliminary mechanistic studies showed that both compounds TSN and 11 induced S-phase arrest and G2/M phase cell number decrease in HCC1806 cells. Also, TSN and 11 significantly reduced the protein level of the well-known cancer suppressor gene p53, reduced the phosphorylation of AKT and ERK, and also induced the accumulation of phosphorylated p38 and p21.

Development of actein derivatives as potent anti-triple negative breast cancer agents.

Actein is a natural triterpenoid glycoside, isolated from the rhizomes of Cimicifuga foetida, which have been demonstrated to be potential in the treatment of breast cancer previously. Herein, we described the design and synthesis of a series of actein derivatives as anti-triple negative breast cancer (TNBC) inhibitors. Of which, the most promising derivative 27 exhibited significant inhibitory activity against human TNBC cell lines HCC1806 and MDA-MB-231, with IC50 values of 2.78 and 9.11 µM, respectively. Structure-activity relationships of actein derivatives were also discussed. Moreover, preliminary mechanism investigation revealed that 27 significantly inhibited cancer cell proliferation via cell cycle arrest at S phase. In addition, western blot analysis showed that the activation of MAPK signaling pathway might contribute to derivative 27 induced cell death. Overall, these results indicate that 27 has the potential to be developed as a lead compound and compounds with the actein scaffold are a promising novel class of inhibitors to treat TNBC.

Ethnic and geographic variations in multiple chronic conditions among community-dwelling older people in Xinjiang: a cross-sectional study.

BACKGROUND: Multiple chronic conditions (MCC) refer to the presence of two or more chronic diseases. The incidence of MCC is higher in older people, and increases with age. Studies have shown an association between MCC and increased adverse outcome, as well as the higher mortality, decline of physical function, and poor quality of life in older populations. Herein, for the first time we provide the data of ethnic and geographic variations in the prevalence of MCC among community-dwelling older people in Xinjiang, China. METHODS: A multilevel random sampling method was employed to perform an epidemiological survey in community-dwelling older adults in southern, northern, and eastern Xinjiang between January 2019 to December 2019. In total, 87,000 participants volunteered, with a response rate of 96.67%; 490 participants with incomplete data were excluded and data from 86,510 participants were analyzed. RESULTS: Our analysis demonstrated that hypertension (51.5%), obesity (27.0%), diabetes (16.9%), heart disease (8.2%), and anxiety/depression (4.5%) were the five main chronic diseases in Xinjiang. The prevalence of MCC in the population surveyed was 33.4% (95%CI, 33.1-33.7). The prevalence in females was 36.6% (95%CI, 36.1-37), which was higher than that in male (30%,95%CI, 29.5-30.4). The prevalence of MCC in older people aged 60-69, 70-79, 80-89, and ≥ 90 years was 32.7% (95%CI, 32.2-33.3), 34.3% (95%CI, 33.9-34.7), 32.5% (95% CI, 31.7-33.3), and 25.9% (95% CI, 23.5-28.3) respectively. As far as the ethnic group was concerned, the prevalence of MCC in Uygur, Han, Kazak, Hui, and Mongolian was 31.3% (95%CI, 30.9-31.7), 34.4% (95%CI, 33.9-35), 40.4% (95%CI, 39.1-41.8), 40.8% (95%CI, 38.9-42.7), 44.4% (95%CI, 38.1-50.6), respectively. The prevalence of MCC was 32.8% (95%CI, 32.1-33.5), 31.7% (95%CI, 31.2-32.1), 36.0% (95%CI, 35.3-36.7) and 39.2% (95%CI, 38.1-40.3) among uneducated, educated for 1-6, 7-9, and more than 10 years. After adjusting for age, sex, smoking, alcohol consumption, and education by level, the binary logistic analysis showed that, compared with eastern Xinjiang, the risk of MCC in the southern area was increased (odds ratio [OR], 1.418; 95% confidence interval [CI], 1.367-1.471), and it was relatively higher in northern Xinjiang (OR, 2.021; 95% CI, 1.944-2.102). Compared with Uygur, Han, Kazakh, Hui and Mongolian had an increased risk of MCC, which was (OR, 1.075; 95% CI, 1.040-1.111), (OR, 1.414; 95% CI, 1.332-1.501), (OR, 1.515; 95% CI, 1.396-1.644), (OR, 1.566; 95% CI, 1.216-2.017), respectively. CONCLUSIONS: There are ethnic and geographic variations in multiple chronic conditions among community-dwelling older people in Xinjiang. The older adults living in northern and southern Xinjiang and Han, Kazakh, Mongolian and Hui older adults have a higher risk of MCC.

Chemical Synthesis Enables the Configurational Determination of Myristriol, a Highly Oxygenated Phenylpropanoid from Myristica fragrans Houtt.

A new phenylpropanoid, myristriol (1), along with 11 known ones were isolated from the seed kernel of Myristica fragrans Houtt. Their chemical structures were clearly elucidated by extensive spectroscopic analysis. In which, the relative configuration of 1 was finally determined as erythro-1 by comparison the NMR data of two synthetic erythro- and threo-diastereoisomers with that of natural 1.

Estimating the effects of policies on infertility prevalence worldwide.

BACKGROUND: Infertility has troubled millions of people worldwide while always being an ignored issue. The high cost of treatment or lack of services placed a barrier to the alleviation of infertility status. Governments play a significant role to promote infertility-related policies for better access to infertility services and comprehensive supports for infertile people. METHODS: Data of infertility status indicators and infertility-related policies in ten representative countries were collected. An infertility-related policy system was established, then classification and quantification were processed according to specific criteria, and different policy implementation patterns were identified. The effectiveness of specific infertility-related policy and various patterns on infertility prevalence relief between 1990 and 2017 were evaluated via generalized linear models and analyses of covariance for the first time. RESULTS: Economic support policies would be less prioritized compared with social security policies, while economic support policy had a significant positive role in the decline of female infertility prevalence (ß = -2·16, p = 0·042). In detail, insurance coverage and economic reward policies were crucial (ß = -3·31, p = 0·031; ß = -4·10, p = 0·025) with adjusted with covariates. The effect of economic support-oriented pattern was relatively better than other patterns for both male and female infertility prevalence relief. Nevertheless, the effectiveness of gradual-promotion pattern seemed preferable for male infertility prevalence relief while was similar with simultaneous-promotion pattern for females. CONCLUSIONS: Our data-driven analysis revealed that insurance coverage and economic reward policies played the pivotal role in moderation of female infertility status. Economic support-oriented pattern and gradual-promotion pattern were preferable when promoting infertility-related policies.

LF1 regulates the lateral organs polarity development in rice.

The patterning of adaxial-abaxial tissues plays a vital role in the morphology of lateral organs, which is maintained by antagonism between the genes that specify adaxial and abaxial tissue identity. The homeo-domain leucine zipper class III (HD-ZIP III) family genes regulate adaxial identity; however, little information is known about the physical interactions or transcriptionally regulated downstream genes of HD-ZIP III. In this study, we identified a dominant rice mutant, lateral floret 1 (lf1), which has defects in lateral organ polarity. LF1 encodes the HD-ZIP III transcription factor, which expressed in the adaxial area of lateral organs. LF1 can activate directly the expression of LITTLE ZIPPER family gene OsZPR4 and HD-ZIP II family gene OsHOX1, and OsZPR4 and OsHOX1 respectively interact with LF1 to form a heterodimer to repress the transcriptional activity of LF1. LF1 influences indole-3-acetic acid (IAA) content by directly regulating the expression of OsYUCCA6. Therefore, LF1 forms negative feedback loops between OsZPR4 and OsHOX1 to affect IAA content, leading to the regulation of lateral organs polarity development. These results reveal the cross-talk among HD-ZIP III, LITTLE ZIPPER, and HD-ZIP II proteins and provide new insights into the molecular mechanisms underlying the polarity development of lateral organs.

Aerobic Copper-Catalyzed Intramolecular Cascade Oxidative Isomerization/[4+4] Cyclization of 2,2'-Disubstituted Stilbenes.

An aerobic copper-catalyzed cascade oxidative isomerization/[4+4] cyclization of 2,2'-disubstituted stilbenes is described. Under the mild CuCl/DBED/air catalytic system, various 5,10-heteroatom-containing tetrahydroindeno[2,1-a]indenes were efficiently prepared through the difunctionalizations of alkenes in a highly atom economic manner. Mechanistic investigations suggested the bicyclic product was likely formed through a sequence of rapid single-electron oxidation/[4+4] cyclization from 2,2'-disubstituted stilbene. The antarafacial manner of the thermally allowed [4+4] cyclization was further proven by series of control experiments and density functional theory calculations. Our findings provide an important addition to the aerobic copper-catalyzed oxidative cyclization.

Replicative capacity of four porcine enteric coronaviruses in LLC-PK1 cells.

Enteric coronaviruses (CoVs) are major pathogens that cause diarrhea in piglets. To date, four porcine enteric CoVs have been identified: transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and HKU2-like porcine enteric alphacoronavirus (PEAV). In this study, we investigated the replicative capacity of these four enteric CoVs in LLC-PK1 cells, a porcine kidney cell line. The results showed that LLC-PK1 cells are susceptible to all four enteric CoVs, particularly to TGEV and PDCoV infections, indicating that LLC-PK1 cells can be applied to porcine enteric CoV research in vitro, particularly for coinfection studies.

Bifidobacterium bifidum SAM-VI Riboswitch Conformation Change Requires Peripheral Helix Formation.

The Bifidobacterium bifidum SAM-VI riboswitch undergoes dynamic conformational changes that modulate downstream gene expression. Traditional structural methods such as crystallography capture the bound conformation at high resolution, and additional efforts would reveal details from the dynamic transition. Here, we revealed a transcription-dependent conformation model for Bifidobacterium bifidum SAM-VI riboswitch. In this study, we combine small-angle X-ray scattering, chemical probing, and isothermal titration calorimetry to unveil the ligand-binding properties and conformational changes of the Bifidobacterium bifidum SAM-VI riboswitch and its variants. Our results suggest that the SAM-VI riboswitch contains a pre-organized ligand-binding pocket and stabilizes into the bound conformation upon binding to SAM. Whether the P1 stem formed and variations in length critically influence the conformational dynamics of the SAM-VI riboswitch. Our study provides the basis for artificially engineering the riboswitch by manipulating its peripheral sequences without modifying the SAM-binding core.

Effects of lactic acid bacteria on rearing water bacterial community in Eriocheir sinensis culture.

The Chinese mitten crab (CMC, Eriocheir sinensi) culture in ponds is a unique aquaculture system. Probiotics are commonly used in the maintenance of the health of pond-cultured CMCs. However, the effects of probiotics on the bacterial community of CMC-culturing water remain unclear. This study utilized 16S rRNA gene amplicon sequencing to assess changes in the bacterial community composition, diversity, assembly, and co-occurrence patterns in CMC-culturing water following probiotic application. The results indicate that the α-diversity of the bacterial community in CMC-culturing water varied with time following probiotic application. The addition of probiotics to the water resulted in an increase in the occurrence of new operational taxonomic units (OTUs). The bacterial community assembly in the CMC-culturing water was shaped by a balance between deterministic and stochastic processes, while commercial probiotics enhanced the proportion of heterogeneous selection. In addition, including OTU2953 (Burkholderiaceae) and OTU3005 (Lactobacillaceae), from the commercial probiotics served as keystone species in the bacterial network of CMC-culturing water. Overall, probiotic application had a significant impact on the bacterial ecology of CMC-culturing water.

Comprehensive application of AI algorithms with TCR NGS data for glioma diagnosis.

T-cell receptor (TCR) detection can examine the extent of T-cell immune responses. Therefore, the article analyzed characteristic data of glioma obtained by DNA-based TCR high-throughput sequencing, to predict the disease with fewer biomarkers and higher accuracy. We downloaded data online and obtained six TCR-related diversity indices to establish a multidimensional classification system. By comparing actual presence of the 602 correlated sequences, we obtained two-dimensional and multidimensional datasets. Multiple classification methods were utilized for both datasets with the classification accuracy of multidimensional data slightly less to two-dimensional datasets. This study reduced the TCR ß sequences through feature selection methods like RFECV (Recursive Feature Elimination with Cross-Validation). Consequently, using only the presence of these three sequences, the classification AUC value of 96.67% can be achieved. The combination of the three correlated TCR clones obtained at a source data threshold of 0.1 is: CASSLGGNTEAFF_TRBV12_TRBJ1-1, CASSYSDTGELFF_TRBV6_TRBJ2-2, and CASSLTGNTEAFF_TRBV12_TRBJ1-1. At 0.001, the combination is: CASSLGETQYF_TRBV12_TRBJ2-5, CASSLGGNQPQHF_TRBV12_TRBJ1-5, and CASSLSGNTIYF_TRBV12_TRBJ1-3. This method can serve as a potential diagnostic and therapeutic tool, facilitating diagnosis and treatment of glioma and other cancers.

Exosomes mediate the antibody-resistant intercellular transmission of porcine epidemic diarrhea virus.

Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic enteric coronavirus that causes severe enteritis and lethal watery diarrhea in suckling piglets, leading to tremendous economic losses. Exosomes have been reported to participate in intercellular communication by the transportation of a variety of biological materials, including RNAs, lipids, and proteins. However, PEDV transmission routes have not yet been fully elucidated, and whether exosomes function in PEDV transmission remains unclear. In this study, we extracted and purified exosomes from PEDV-infected Vero cells using a stringent isolation method with a combination of chemical precipitation, ultracentrifugation, and incubation with CD63-labeled magnetic beads. We found that exosomes from PEDV-infected Vero cells contain viral genomic RNA and viral nucleocapsid protein. Furthermore, we demonstrated that the purified exosomes from PEDV-infected cells are capable of transmitting the virus to both PEDV-susceptible and non-susceptible cells. Importantly, exosome-mediated PEDV infection was resistant to neutralization by PEDV-specific neutralizing antibodies that potently neutralized free PEDV. Our study reveals a potential immune evasion mechanism utilized by PEDV and provides new insight into the transmission and infection of this important pathogen.

Porcine deltacoronavirus uses heparan sulfate as an attachment receptor.

Porcine deltacoronavirus (PDCoV) is a newly emerging swine enteropathogenic coronavirus with extensive tissue tropism and cross-species transmission potential. Heparan sulfate (HS) is a complex polysaccharide ubiquitously expressed on cell surfaces and the extracellular matrix and acts as an attachment factor for many viruses. However, whether PDCoV uses HS as an attachment receptor is unclear. In this study, we found that treatment with heparin sodium or heparinase Ⅱ significantly inhibited PDCoV binding and infection among LLC-PK1 and IPI-2I cells. Attenuation of HS sulfuration by sodium chlorate also impeded PDCoV binding and infection. Moreover, we demonstrated that HS functioned independently of amino peptidase N (APN), a functional PDCoV receptor, in PDCoV infection. Molecular docking revealed that the S1 subunit of the PDCoV spike protein might be a putative region for HS binding. Taken together, these results firstly confirmed that HS is an attachment receptor for PDCoV infection, providing new insight into better understanding the mechanisms of PDCoV-host interactions.