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.

First report of leaf blight caused by Nigrospora hainanensis on Euonymus japonicus in China.

Euonymus japonicus Thunb., belonging to the family Celastreace and native to East Asia, is a widely cultivated evergreen ornamental woody plant with important ecological and economic values. In May 2023, serious leaf blight of E. japonicus occurred in the campus green space at Guiyang University, Guizhou Province, China (26°55'85"N, 106°78'04"E). Early symptom appeared as small, circular light brown spots on the edges or tips of the leaves. Then, the spot developed visible necrosis, initially light brown to dark brown halos with clear margins. Subsequently, severely infected leaves appear totally wilt, and significantly decrease their ornamental values. In a 0.07-ha field, the disease incidence reached to 40-55%. To identify the pathogen, ten typical symptomatic E. japonicus leaves were collected. They were initially immersed in 75% ethanol for 3 min, and by sodium hypochlorite (4% NaClO) solution for 45 s, and ultimately rinsed with sterile distilled water (dH2O) five times for not less than 1 min each time, then, placed the leaves on potato dextrose agar (PDA) medium and cultured for 5 days at 25°C in constant temperature incubator. Cultures were purified to yield eight isolates. Early colonies are white and regularly rounded, gradually turning dark brown to black with fluffy mycelium. Conidia were single celled, smooth, black, spherical or ellipsoidal. The conidia size of the representative strain, GY-2 and GY-3, was averagely 12.3-17.3 µm × 10.8-17 µm (n = 50). The conidiogenous cells were monoblastic, hyaline, globose or ampulliform. Morphology-based identification revealed the strain as Nigrospora spp. (Wang et al., 2017). For further confirmation, PCR of GY-2 and GY-3 DNA was performed with the primers ITS1/ITS4 (White et al., 1990), Bt2a-F/Bt2b-R (Glass and Don-aldson 1995), and TEF1-728F/TEF1-986R (Carbone and Kohn 1999). Sequences of the ITS region, TUB and TEF1 genes from the strain GY-2 and GY-3 were deposited in GenBank. (GY-2: OR999377, PP112221 and PP150467; GY-3: PP406871, PP421045 and PP421046, respectively). BLAST analysis showed GY-2 100%, 100%, and 98.36%; GY-3 99.43%, 98.21% and 100% (ITS region, TEF1, and TUB) identity to N. hainanensis sequences (accession numbers. NR_153480.1, KY019415.1, and KY019464.1; KX986094.1, OP611475.1, and KY019597.1). Additionally, tandem sequences of ITS, TUB and TEF1 constructed by MEGA 7.0 confimed the homology through the phylogenetic tree. Pathogenicity tests were conducted on healthy plants grown, each 5 mm diameter of active growing mycelium plug of isolate GY-2 was attached to 15 leaves from five healthy 2-year-old E. japonicu plants. The same number of leaves in the control group were treated with non-inoculated plugs only. All the plants were incubated at 25°C and 75% relative humidity with a 16-h/8-h photoperiod. After 10 days, no symptoms appeared on the leaves of the control group. In contrast, symptomatic blight appeared on all leaves inoculated with GY-2. Pathogenicity tests were performed five times. Pure strains were re-isolated from diseased leaves and, confirmed to be N. hainanensis based on the above methods. Recently, Nigrospora oryzae was reported as causal agent of leaf spots on Euonymus japonicus in China (Xu et al., 2023). To our knowledge, this study is the first report of N. hainanensis causing leaf blight on E. japonicu. Identification of the etiological agent may provide assistance for sustainable management in the future.

NLRP inflammasomes in health and disease.

NLRP inflammasomes are a group of cytosolic multiprotein oligomer pattern recognition receptors (PRRs) involved in the recognition of pathogen-associated molecular patterns (PAMPs) and danger-associated molecular patterns (DAMPs) produced by infected cells. They regulate innate immunity by triggering a protective inflammatory response. However, despite their protective role, aberrant NLPR inflammasome activation and gain-of-function mutations in NLRP sensor proteins are involved in occurrence and enhancement of non-communicating autoimmune, auto-inflammatory, and neurodegenerative diseases. In the last few years, significant advances have been achieved in the understanding of the NLRP inflammasome physiological functions and their molecular mechanisms of activation, as well as therapeutics that target NLRP inflammasome activity in inflammatory diseases. Here, we provide the latest research progress on NLRP inflammasomes, including NLRP1, CARD8, NLRP3, NLRP6, NLRP7, NLRP2, NLRP9, NLRP10, and NLRP12 regarding their structural and assembling features, signaling transduction and molecular activation mechanisms. Importantly, we highlight the mechanisms associated with NLRP inflammasome dysregulation involved in numerous human auto-inflammatory, autoimmune, and neurodegenerative diseases. Overall, we summarize the latest discoveries in NLRP biology, their forming inflammasomes, and their role in health and diseases, and provide therapeutic strategies and perspectives for future studies about NLRP inflammasomes.

Identification, Characterization, Cloning, and Cross-Reactivity of Zan b 2, a Novel Pepper Allergen of 11S Legumin.

Protein from Sichuan peppers can elicit mild to severe allergic reactions. However, little is known about their allergenic proteins. We aimed to isolate, identify, clone, and characterize Sichuan pepper allergens and to determine its allergenicity and cross-reactivities. Sichuan pepper seed proteins were extracted and then analyzed by SDS-PAGE. Western blotting was performed with sera from Sichuan pepper-allergic individuals. Proteins of interest were purified using hydrophobic interaction chromatography and gel filtration and further analyzed by analytical ultracentrifugation, circular dichroism spectroscopy, and mass spectrometry (MS). Their coding region was amplified in the genome. IgE reactivity and cross-reactivity of allergens were evaluated by dot blot, enzyme-linked immunosorbent assay (ELISA), and competitive ELISA. Western blot showed IgE binding to a 55 kDa protein. This protein was homologous to the citrus proteins and has high stability and a sheet structure. Four DNA sequences were cloned. Six patients' sera (60%) showed specific IgE reactivity to this purified 11S protein, which was proved to have cross-reactivation with extracts of cashew nuts, pistachios, and citrus seeds. A novel allergen in Sichuan pepper seeds, Zan b 2, which belongs to the 11S globulin family, was isolated and identified. Its cross-reactivity with cashew nuts, pistachios, and citrus seeds was demonstrated.

The CARD8 T60 variant associates with NLRP1 and negatively regulates its activation.

The NLRP1 inflammasome functions as canonical cytosolic sensor in response to intracellular infections and is implicated in auto-inflammatory diseases. But the regulation and signal transduction mechanisms of NLRP1 are incompletely understood. Here, we show that the T60 variant of CARD8, but not the canonical T48 isoform, negatively regulates the NLRP1 inflammasome activation by directly interacting with the receptor molecule NLRP1 and inhibiting inflammasome assembly. Furthermore, our results suggest that different ASC preference in three types of inflammasomes, namely the ASC-indispensable NLRP1 inflammasome, ASC-dispensable mNLRP1b inflammasome and ASC-independent CARD8 inflammasome, is mainly caused by the CARD domain, not the UPA subdomain. Based on the systematic site-directed mutagenesis and structural analysis, we find that signal transduction of the NLRP1 inflammasome relies on multiple interaction surfaces at its CARD domain. Finally, our results partly explain how mutations in NLRP1 lead to its constitutive activation in auto-inflammatory diseases. In conclusion, our study not only reveals how CARD8 downregulates the NLRP1 inflammasome activation, but also provides insights into the assembly mechanisms of CARD-containing inflammasomes.

Associations between carotid atherosclerotic plaque characteristics determined by magnetic resonance imaging and improvement of cognition in patients undergoing carotid endarterectomy.

Background: To determine the predictive value of carotid plaque characteristics for the improvement of cognition in patients with moderate-to-severe carotid stenosis after carotid endarterectomy (CEA), using vessel wall magnetic resonance imaging (MRI). Methods: This was a prospective cohort study. Patients with unilateral, moderate-to-severe carotid stenosis referred to the Peking University Third Hospital for CEA were prospectively recruited and underwent carotid vessel wall MRI within 1 week before CEA. We performed Montreal Cognitive Assessment (MoCA) within 1 week before and 3-4 days after CEA. The morphological and compositional characteristics of carotid plaques on MRI were evaluated. Improvement of cognition was defined as >10% increase of the total MoCA score after CEA compared with baseline. Carotid plaque characteristics were compared between patients with and without cognitive improvement. Results: In total, 105 patients (91 males; mean age, 65.5±8.4 years) were included. The volume {48.0 [interquartile range (IQR), 21.0 to 91.6] vs. 16.3 (IQR, 8.1 to 53.1) mm3; P=0.005} and cumulative slice [4.0 (IQR, 3.0 to 7.0) vs. 3.0 (IQR, 2.0 to 5.0); P=0.019] of carotid calcification, and maximum percentage of calcification area [13.1% (IQR, 6.0% to 19.8%) vs. 6.2% (IQR, 3.7% to 10.8%); P=0.004] were significantly smaller in participants with cognitive improvement compared to those without. Univariate logistic regression analysis showed that volume [odds ratio (OR) =0.994; 95% confidence interval (CI): 0.989 to 1.000; P=0.043] and cumulative slice (OR =0.823; 95% CI: 0.698 to 0.970; P=0.020) of carotid calcification, and maximum percentage of calcification area (OR =0.949; 95% CI: 0.909 to 0.991; P=0.018) were significantly correlated with cognitive improvement. After adjusting for confounding factors, these associations remained statistically or marginally significant (volume: OR =0.994; 95% CI: 0.988 to 1.000; P=0.057; maximum percentage of calcification area: OR =0.937; 95% CI: 0.890 to 0.987; P=0.014; and cumulative slice: OR =0.791; 95% CI: 0.646 to 0.967; P=0.022). No significant associations were found between other plaque characteristics and cognitive improvement (all P>0.05). Conclusions: More than half of the participants with unilateral, moderate-to-severe carotid atherosclerotic stenosis had cognitive improvement. The size of calcification might be an effective indicator of cognitive improvement after CEA.

Comparing Symptomatic and Asymptomatic Carotid Artery Atherosclerosis in Patients With Bilateral Carotid Vulnerable Plaques Using Magnetic Resonance Imaging.

We compared plaque characteristics between symptomatic and asymptomatic sides in patients with bilateral carotid vulnerable plaques using magnetic resonance imaging (MRI). Participants (n = 67; mean age: 65.8 ± 7.7 years, 61 males) with bilateral carotid vulnerable plaques were included. Vulnerable plaques were characterized by intraplaque hemorrhage (IPH), large lipid-rich necrotic core (LRNC), or fibrous cap rupture (FCR) on MRI. Symptomatic vulnerable plaques showed greater plaque burden, LRNC volume (median: 221.4 vs 134.8 mm3, P = .003), IPH volume (median: 32.2 vs 22.5 mm3, P = .030), maximum percentage (Max%) LRNC (median: 51.3% vs 41.8%, P = .002), Max%IPH (median: 13.4% vs 9.5%, P = .022), cumulative slices of LRNC (median: 10 vs 8, P = .005), and more juxtaluminal IPH and/or thrombus (29.9% vs 6.0%, P = .001) and FCR (37.3% vs 16.4%, P = .007) than asymptomatic ones. After adjusting for plaque burden, differences in juxtaluminal IPH and/or thrombus (odds ratio [OR]: 5.49, 95% CI: 1.61-18.75, P = .007) and FCR (OR: 2.90, 95% CI: 1.16-7.24, P = .022) between bilateral sides remained statistically significant. For patients with bilateral carotid vulnerable plaques, symptomatic plaques had greater burden, more juxtaluminal IPH and/or thrombus, and FCR compared with asymptomatic ones. The differences in juxtaluminal IPH and/or thrombus and FCR between bilateral sides were independent of plaque burden.

Experimental and numerical analysis of non-contact magnetic detecting signal of girth welds on steel pipelines.

The quality of the girth welds on pipelines is a critical point regarding the safe operation. Non-contact pipeline magnetic detection (NPMD) is a non-destructive detection technology based on the metal magnetic memory (MMM) method. However, present studies mostly focus on the qualitative analysis of girth welds instead of accurate quantitative analysis of the stress status. Here, many hydraulic tests in sealed pipelines are performed to investigate the magnetic signal under different internal pressures and detection heights. A numerical model of magnetic signal is established and verified by the experimental results. The results show the characteristics of the signal that the y component has sinusoidal fluctuations when the x and z component reach the extreme values. A new parameter Kvs is proposed to comprehensively reflect the stress status of the girth welds. It is founded that the residual strength ratio (RSR) reduces from 0.97 to 0.83 when the Kvs max increases from 7500 to 13500 nT/m The magnetic signals decay exponentially in the second order when the detection height varies within 0.1-1.0 m. This study provides a theoretical and experimental basis for identifying the stress status of the girth welds on pipelines.

Profiling CD8+ T cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants.

Cellular immunity is important in determining the disease severity of COVID-19 patients. However, current understanding of SARS-CoV-2 epitopes mediating cellular immunity is limited. Here we apply T-Scan, a recently developed method, to identify CD8+ T cell epitopes from COVID-19 patients of four major HLA-A alleles. Several identified epitopes are conserved across human coronaviruses, which might mediate pre-existing cellular immunity to SARS-CoV-2. In addition, we identify and validate four epitopes that were mutated in the newly circulating variants, including the Delta variant. The mutations significantly reduce T cell responses to the epitope peptides in convalescent and vaccinated samples. We further determine the crystal structure of HLA-A∗02:01/HLA-A∗24:02 in complex with the epitope KIA_S/NYN_S, respectively, which reveals the importance of K417 and L452 of the spike protein for binding to HLA. Our data suggest that evading cellular immunity might contribute to the increased transmissibility and disease severity associated with the new SARS-CoV-2 variants.

Geometrical characteristics associated with atherosclerotic disease in the basilar artery: a magnetic resonance vessel wall imaging study.

BACKGROUND: Vascular geometry may play an important role in the development of atherosclerosis. This study aimed to investigate the relationships between the geometrical characteristics of basilar artery (BA) and the presence, burden, and distribution of BA plaques using magnetic resonance vessel wall imaging. METHODS: Patients with cerebrovascular symptoms in the posterior circulation were recruited and underwent magnetic resonance imaging. The BA's geometrical characteristics, including actual length, straightened length, tortuosity, lateral basilar artery-vertebral artery (VA) angle, lateral mid-BA angle, and BA convexity, were measured. The presence of plaques, stenosis, and plaque burden, including mean and maximal wall thickness, were evaluated. The BA's cross-sectional vessel wall was divided into 4 quadrants: dorsal, ventral, right, and left quadrant. The distribution of BA plaques was analyzed. RESULTS: Of 344 recruited patients (mean age: 68.1±11.1 years; 200 males), 100 (29.1%) had BA plaques. Patients with BA plaques had higher tortuosity of the BA (13.6±9.0 vs. 9.7±7.7, P<0.001) compared to those without BA plaques. Multivariate regression analysis showed that tortuosity of the BA was associated with the presence of BA plaques (OR, 1.641; 95% CI, 1.232 to 2.186; P=0.001) and mean wall thickness (ß, 0.045; 95% CI, 0.008 to 0.081; P=0.017). The plaque distribution in the left wall and right wall of BA was more frequent in patients with right (P=0.006) and left (P<0.001) convex BA, respectively. CONCLUSIONS: The BA's geometrical characteristics, particularly tortuosity and convexity, are independently associated with the presence, burden, and distribution of plaques in the BA.

What Drives Patients Affected by Depression to Share in Online Depression Communities? A Social Capital Perspective.

Online depression communities give people additional opportunities to share their experiences and exchange social support to care for themselves in fighting against depression. We aimed to explore what drives patients to share in online depression communities. We used three dimensions of social capital (structural, relational, and cognitive) to explain their sharing behaviors. We further proposed that five factors (social interaction ties, a sense of shared identity, trust, expertise, and a sense of shared values) will have significant, positive effects on sharing behaviors and that there are differences among patients who have spent different lengths of time participating in online depression communities. We then chose a popular online depression community in China as our data source and obtained a dataset consisting of 31,440 posts from 197 members. Then, we employed panel data regression analyses to test all six hypotheses. The results revealed that all five factors had significant, positive effects (p < 0.01) on patients' sharing behaviors, and the effects were significantly different across groups. Our empirical results help designers and managers of online depression communities take specific measures to facilitate community members' access to social capital resources. Meanwhile, our results have implications for existing health management and e-health literature.

The beta oscillation conditions in a simplified basal ganglia network.

Parkinson's disease is a type of motor dysfunction disease that is induced mainly by abnormal interactions between the subthalamic nucleus (STN) and globus pallidus (GP) neurons. Periodic oscillatory activities with frequencies of 13-30 Hz are the main physiological characteristics of Parkinson's disease. In this paper, we built a class of STN-GP networks to explore beta oscillation conditions. A theoretical formula was obtained for generating oscillations without internal GP connections. Based on this formula, we studied the effects of cortex inputs, striatum inputs, coupling weights and delays on oscillation conditions, and the theoretical results are in good agreement with the numerical results. The onset mechanism can be explained by the model, and the internal GP connection has little effect on oscillations. Finally, we compared oscillation conditions with those in previous studies and found that the delays and coupling weights required for generating oscillations may decrease as the number of nuclei increases. We hope that the results obtained will inspire future theoretical and experimental studies.

Phytosterol content and the campesterol:sitosterol ratio influence cotton fiber development: role of phytosterols in cell elongation.

Phytosterols play an important role in plant growth and development, including cell division, cell elongation, embryogenesis, cellulose biosynthesis, and cell wall formation. Cotton fiber, which undergoes synchronous cell elongation and a large amount of cellulose synthesis, is an ideal model for the study of plant cell elongation and cell wall biogenesis. The role of phytosterols in fiber growth was investigated by treating the fibers with tridemorph, a sterol biosynthetic inhibitor. The inhibition of phytosterol biosynthesis resulted in an apparent suppression of fiber elongation in vitro or in planta. The determination of phytosterol quantity indicated that sitosterol and campesterol were the major phytosterols in cotton fibers; moreover, higher concentrations of these phytosterols were observed during the period of rapid elongation of fibers. Furthermore, the decrease and increase in campesterol:sitosterol ratio was associated with the increase and decease in speed of elongation, respectively, during the elongation stage. The increase in the ratio was associated with the transition from cell elongation to secondary cell wall synthesis. In addition, a number of phytosterol biosynthetic genes were down-regulated in the short fibers of ligon lintless-1 mutant, compared to its near-isogenic wild-type TM-1. These results demonstrated that phytosterols play a crucial role in cotton fiber development, and particularly in fiber elongation.

Health-related hot topic detection in online communities using text clustering.

Recently, health-related social media services, especially online health communities, have rapidly emerged. Patients with various health conditions participate in online health communities to share their experiences and exchange healthcare knowledge. Exploring hot topics in online health communities helps us better understand patients' needs and interest in health-related knowledge. However, the statistical topic analysis employed in previous studies is becoming impractical for processing the rapidly increasing amount of online data. Automatic topic detection based on document clustering is an alternative approach for extracting health-related hot topics in online communities. In addition to the keyword-based features used in traditional text clustering, we integrate medical domain-specific features to represent the messages posted in online health communities. Three disease discussion boards, including boards devoted to lung cancer, breast cancer and diabetes, from an online health community are used to test the effectiveness of topic detection. Experiment results demonstrate that health-related hot topics primarily include symptoms, examinations, drugs, procedures and complications. Further analysis reveals that there also exist some significant differences among the hot topics discussed on different types of disease discussion boards.