Enhancing humoral and mucosal immune response of PED vaccine candidate by fusing S1 protein to nanoparticle multimerization.

Porcine epidemic diarrhea virus (PEDV) is a highly infectious pathogen with a high mortality rate, which poses a serious threat to newborn piglets. A rapid, safe and effective vaccine is necessary for protecting pigs from PED infection. Nanoparticles have become molecular scaffolds for displaying soluble antigens due to their unique physical and chemical properties. Here, a vaccine candidate was based on the display of PEDV S1 protein on a mi3 nanoparticle platform using SpyTag/SpyCatcher technology. The size, zeta potential and microstructure of the S1-mi3 NPs were investigated, and their effects on the uptake of antigen-presenting cells (APCs) and maturation of dendritic cells (DCs) were analyzed. Mice were immunized via muscular and intranasal administrations, and the levels of humoral, cellular and mucosal immune responses were analyzed. As a result, S1 proteins were surface-displayed on NPs successfully, which self-assembled into nanoparticles composed of 60 subunits and showed superior safety and stability. In addition, mi3 NPs promoted antigen internalization and dendritic cell (DCs) maturation. In the mouse model, S1-mi3 NPs significantly increased the PEDV-specific antibody including serum IgG, secretory IgA (SIgA) and neutralizing antibodies (NAb). Furthermore, S1-mi3 NPs elicited more CD3+CD4+ and CD3+CD8+ T cell and cellular immune-related cytokines (IFN-γ and IL-4) compared to monomeric S1. In particular, it can induce an effective germinal center-specific (GC) B cell response, which is closely related to the production of neutralizing antibodies. Overall, S1-mi3 NPs are a promising subunit vaccine candidate against PEDV, and this self-assembly NPs also provide an attractive platform for improving vaccine efficacy against emerging pathogens.

Double-layered N-S1 protein nanoparticle immunization elicits robust cellular immune and broad antibody responses against SARS-CoV-2.

BACKGROUND: The COVID-19 pandemic is a persistent global threat to public health. As for the emerging variants of SARS-CoV-2, it is necessary to develop vaccines that can induce broader immune responses, particularly vaccines with weak cellular immunity. METHODS: In this study, we generated a double-layered N-S1 protein nanoparticle (N-S1 PNp) that was formed by desolvating N protein into a protein nanoparticle as the core and crosslinking S1 protein onto the core surface against SARS-CoV-2. RESULTS: Vaccination with N-S1 PNp elicited robust humoral and vigorous cellular immune responses specific to SARS-CoV-2 in mice. Compared to soluble protein groups, the N-S1 PNp induced a higher level of humoral response, as evidenced by the ability of S1-specific antibodies to block hACE2 receptor binding and neutralize pseudovirus. Critically, N-S1 PNp induced Th1-biased, long-lasting, and cross-neutralizing antibodies, which neutralized the variants of SARS-CoV-2 with minimal loss of activity. N-S1 PNp induced strong responses of CD4+ and CD8+ T cells, mDCs, Tfh cells, and GCs B cells in spleens. CONCLUSIONS: These results demonstrate that N-S1 PNp vaccination is a practical approach for promoting protection, which has the potential to counteract the waning immune responses against SARS-CoV-2 variants and confer broad efficacy against future new variants. This study provides a new idea for the design of next-generation SARS-CoV-2 vaccines based on the B and T cells response coordination.

Estimate of the C-Cl photoionization cross section and absolute photoionization cross sections of chlorinated organic compounds.

Chlorinated organic compounds are prominently used for industrial production, but their vapors and emission byproducts can cause detrimental effects to human health and the environment. To accurately quantify organochlorine compounds, the absolute photoionization cross section of tetrachloroethylene, chlorobenzene, 1,2-dichlorobenzene, and chloroacetone are measured using multiplexed synchrotron photoionization mass spectrometry at the Advanced Light Source at Lawrence Berkeley National Laboratory. These measurements allow for the estimation of the C-Cl photoionization cross section, increasing quantification accuracy of chlorinated emissions for kinetic modeling and pollutant mitigation. CBS-QB3 calculations of adiabatic ionization energies and thermochemical appearance energies are also presented and agree well with the experimental results.

An optimized denoising method for ICESat-2 photon-counting data considering heterogeneous density and weak connectivity.

The Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) can obtain underwater elevation due to its strong penetration ability. However, the photons recorded by ICESat-2 include a large amount of noise that needs to be removed. Although density-based clustering methods can finish signal photon extraction, heterogeneous density and weak connectivity in photon data distribution impede their denoising performance, especially for sparse signals in deep water and drastic topographic change areas. In this paper, a novel fused denoising method based on the local outlier factor and inverse distance metric is proposed to overcome the above problems. The local outlier factor and inverse distance metric are calculated based on K-nearest neighbors (KNNs), taking into account not only the difference in density but also the directional uniformity of the data distribution. Using six trajectories under various seabed topographies, the proposed method is compared with state-of-the-art ICESat-2 photon denoising algorithms and official ATL03 results. The results indicate that the overall accuracy of the proposed method can surpass 96%, and the proposed method maintains higher recall but also has a lower false positive rate. Compared with the results of other methods, the proposed method can better adopt areas with abrupt topographic changes and deep water. The extracted signal strips are more unbroken and continuous. This study can contribute to pioneering a new perspective for ICESat-2 photon-counting data denoising research that is limited to using only density-based algorithms.

Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands.

Cordia subcordata trees or shrubs, belonging to the Boraginaceae family, have strong resistance and have adapted to their habitat on a tropical coral island in China, but the lack of genome information regarding its genetic background is unclear. In this study, the genome was assembled using both short/long whole genome sequencing reads and Hi-C reads. The assembled genome was 475.3 Mb, with 468.7 Mb (99.22%) of the sequences assembled into 16 chromosomes. Repeat sequences accounted for 54.41% of the assembled genome. A total of 26,615 genes were predicted, and 25,730 genes were functionally annotated using different annotation databases. Based on its genome and the other 17 species, phylogenetic analysis using 336 single-copy genes obtained from ortholog analysis showed that C. subcordata was a sister to Coffea eugenioides, and the divergence time was estimated to be 77 MYA between the two species. Gene family evolution analysis indicated that the significantly expanded gene families were functionally related to chemical defenses against diseases. These results can provide a reference to a deeper understanding of the genetic background of C. subcordata and can be helpful in exploring its adaptation mechanism on tropical coral islands in the future.

Ni/Mn-Complex-Tethered Tetranuclear Polyoxovanadates: Crystal Structure and Inhibitory Activity on Human Hepatocellular Carcinoma (HepG-2).

Polyoxometalates (POMs) exhibit unique structural characteristics and excellent physical and chemical properties, which have attracted significant attention from scholars in the fields of anticancer research and chemotherapy. Herein, we successfully synthesized and structurally characterized two novel polyoxovanadates (POVs), denoted as POVs-1 and POVs-2, where [M(1-vIM)4]2[VV4O12]·H2O (M: NiII and MnII, 1-vinylimidazole abbreviated as 1-vIM) serve as ligands. The two POVs are isomeric and consist of fundamental structural units, each comprising one [V4O12]4- cluster, two [M(1-vIM)4]2+ cations, and one water molecule. Subsequently, we evaluated the cell viability of human hepatocellular carcinoma (HepG-2) cells treated with the synthesized POVs using the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazoliumbromide) assay. And the changes in cell nucleus morphology, mitochondrial membrane potential (Δψm), and reactive oxygen species levels in HepG-2 exposed to POVs were monitored using specific fluorescent staining techniques. Both hybrid POVs showed potent inhibitory activities, induing apoptosis in HepG-2 cells along with significant mitochondria dysfunction and a burst of reactive oxygen species. Notably, the inhibitory effects of POVs-2 were more pronounced than those of POVs-1, which is primarily attributed to the different transition metal ions present. These findings underscore the intricate relationship between the metal components, structural characteristics, and the observed antitumor activities in HepG-2 cells.

Development and characterization of monoclonal antibody against the critical loop structure of african swine fever virus P72 protein.

African swine fever (ASF) is a highly infectious and lethal viral disease caused by the African swine fever virus (ASFV). The four prominent loop structures on the surface of the primary structural protein P72 are considered to be key protective epitopes. In this study, the four critical loops (ER1-4) of the ASFV p72 protein were individually fused to hepatitis B virus core particles (HBc) and self-assembled into nanoparticles to preserve the natural conformation of the loop structure and enhance its immunogenicity. Then, four recombinant proteins were obtained in E. coli expression system and monoclonal antibodies (mAbs) were developed and characterized. All 10 mAbs obtained were able to react with P72 protein and ASFV with potencies up to 1:204 800. Amino acids 250-274, 279-299 and 507-517 of the P72 protein were identified as linear epitopes and highly conserved. The mAb 4G8 showed the highest inhibition rate of 84% against ASFV positive sera. Importantly, neutralization experiments illustrated that mAb 4G8 has a 67% inhibition rate, indicating that its corresponding epitopes are potential candidates for ASFV vaccine. In conclusion, highly immunogenic nanoparticles of the ASFV P72 key loop were constructed to induce the production of highly effective mAbs and clarify their epitope information for the diagnosis and prevention of ASFV.

Microstructures and Mechanical Properties of a Nanostructured Al-Zn-Mg-Cu-Zr-Sc Alloy under Natural Aging.

Nanocrystalline (NC) structure can lead to the considerable strengthening of metals and alloys. Obtaining appropriate comprehensive mechanical properties is always the goal of metallic materials. Here, a nanostructured Al-Zn-Mg-Cu-Zr-Sc alloy was successfully processed by high-pressure torsion (HPT) followed by natural aging. The microstructures and mechanical properties of the naturally aged HPT alloy were analyzed. The results show that the naturally aged HPT alloy primarily consists of nanoscale grains (~98.8 nm), nano-sized precipitates (20-28 nm in size), and dislocations (1.16 × 1015 m-2), and exhibits a high tensile strength of 851 ± 6 MPa and appropriate elongation of 6.8 ± 0.2%. In addition, the multiple strengthening modes that were activated and contributed to the yield strength of the alloy were evaluated according to grain refinement strengthening, precipitation strengthening, and dislocation strengthening, and it is shown that grain refinement strengthening and precipitation strengthening are the main strengthening mechanisms. The results of this study provide an effective pathway for achieving the optimal strength-ductility match of materials and guiding the subsequent annealing treatment.

Satellite-derived bathymetry integrating spatial and spectral information of multispectral images.

As a significant and cost-effective method of obtaining shallow seabed topography, satellite derived bathymetry (SDB) can acquire a wide range of shallow sea depth by integrating a small quantity of in-situ water depth data. This method is a beneficial addition to traditional bathymetric topography. The seafloor's spatial heterogeneity leads to inaccuracies in bathymetric inversion, which reduces bathymetric accuracy. By utilizing multispectral data with multidimensional features, an SDB approach incorporating spectral and spatial information of multispectral images is proposed in this study. In order to effectively increase the accuracy of bathymetry inversion throughout the entire area, first the random forest with spatial coordinates is established to control bathymetry spatial variation on a large scale. Next, the Kriging algorithm is used to interpolate bathymetry residuals, and the interpolation results are used to adjust bathymetry spatial variation on a small scale. The data from three shallow water sites are experimentally processed to validate the method. Compared with other established bathymetric inversion techniques, the experimental results show that the method effectively reduces the error in bathymetry estimation caused by spatial heterogeneity of the seabed, producing high-precision inversion bathymetry with a root mean square error of 0.78 to 1.36 meters.

Celastrol inhibits store operated calcium entry and suppresses psoriasis.

Introduction: Psoriasis is an inflammatory autoimmune skin disease that is hard to cure and prone to relapse. Currently available global immunosuppressive agents for psoriasis may cause severe side effects, thus it is crucial to identify new therapeutic reagents and druggable signaling pathways for psoriasis. Methods: To check the effects of SOCE inhibitors on psoriasis, we used animal models, biochemical approaches, together with various imaging techniques, including calcium, confocal and FRET imaging. Results and discussion: Store operated calcium (Ca2+) entry (SOCE), mediated by STIM1 and Orai1, is crucial for the function of keratinocytes and immune cells, the two major players in psoriasis. Here we showed that a natural compound celastrol is a novel SOCE inhibitor, and it ameliorated the skin lesion and reduced PASI scores in imiquimod-induced psoriasis-like mice. Celastrol dose- and time-dependently inhibited SOCE in HEK cells and HaCaT cells, a keratinocyte cell line. Mechanistically, celastrol inhibited SOCE via its actions both on STIM1 and Orai1. It inhibited Ca2+ entry through constitutively-active Orai1 mutants independent of STIM1. Rather than blocking the conformational switch and oligomerization of STIM1 during SOCE activation, celastrol diminished the transition from oligomerized STIM1 into aggregates, thus locking STIM1 in a partially active state. As a result, it abolished the functional coupling between STIM1 and Orai1, diminishing SOCE signals. Overall, our findings identified a new SOCE inhibitor celastrol that suppresses psoriasis, suggesting that SOCE pathway may serve as a new druggable target for treating psoriasis.

Spy&IAC enables specific capture of SpyTagged proteins for rapid assembly of plug-and-display nanoparticle vaccines.

From modular vaccine production to protein assembly on nanoparticles, the SpyCatcher/SpyTag system provides a convenient plug-and-display procedure. Here, we established a general-purpose immunoaffinity chromatography (IAC) method for SpyTagged proteins (Spy&IAC). SpyTags are displayed on the surface of nanoparticles to induce high-affinity monoclonal antibodies, allowing the specific capture of the target protein. Taking the key core antigenic regions of two coronaviruses that are currently more threatened in the field of human and animal diseases, the nucleocapsid (N) protein of SARS-CoV-2 and the COE protein of porcine epidemic diarrhea virus (PEDV) as model proteins, a purification model with SpyTag at the N-terminal or C-terminal expressed in E. coli or mammalian cells was constructed. After the efficient elution of Spy&IAC, the final yield of several proteins is about 3.5-15 mg/L culture, and the protein purity is above 90 %. Purification also preserves the assembly function and immunogenicity of the protein to support subsequent modular assembly and immunization programs. This strategy provides a general tool for the efficient purification of SpyTagged proteins from different expression sources and different tag positions, enabling the production of modular vaccines at lower cost and in a shorter time, which will prepare the public health field for potential pandemic threats.

Quantifying the Knowledge in a DNN to Explain Knowledge Distillation for Classification.

Compared to traditional learning from scratch, knowledge distillation sometimes makes the DNN achieve superior performance. In this paper, we provide a new perspective to explain the success of knowledge distillation based on the information theory, i.e., quantifying knowledge points encoded in intermediate layers of a DNN for classification. To this end, we consider the signal processing in a DNN as a layer-wise process of discarding information. A knowledge point is referred to as an input unit, the information of which is discarded much less than that of other input units. Thus, we propose three hypotheses for knowledge distillation based on the quantification of knowledge points. 1. The DNN learning from knowledge distillation encodes more knowledge points than the DNN learning from scratch. 2. Knowledge distillation makes the DNN more likely to learn different knowledge points simultaneously. In comparison, the DNN learning from scratch tends to encode various knowledge points sequentially. 3. The DNN learning from knowledge distillation is often more stably optimized than the DNN learning from scratch. To verify the above hypotheses, we design three types of metrics with annotations of foreground objects to analyze feature representations of the DNN, i.e., the quantity and the quality of knowledge points, the learning speed of different knowledge points, and the stability of optimization directions. In experiments, we diagnosed various DNNs on different classification tasks, including image classification, 3D point cloud classification, binary sentiment classification, and question answering, which verified the above hypotheses.

Development and characterization of monoclonal antibodies against the extracellular domain of African swine fever virus structural protein, CD2v.

African swine fever virus (ASFV), a DNA double-stranded virus with high infectivity and mortality, causing a devastating blow to the pig industry and the world economy. The CD2v protein is an essential immunoprotective protein of ASFV. In this study, we expressed the extracellular region of the CD2v protein in the 293F expression system to achieve proper glycosylation. Monoclonal antibodies (mAbs) were prepared by immunizing mice with the recombinant CD2v protein. Eventually, four mAbs that target the extracellular region of the ASFV CD2v protein were obtained. All four mAbs responded well to the ASFV HLJ/18 strain and recognized the same linear epitope, 154SILE157. The specific shortest amino acid sequence of this epitope has been accurately identified for the first time. Meaningfully, the 154SILE157 epitope was highly conformed in the ASFV Chinese epidemic strain and Georgia2008/1 strains according to the analysis of the conservation and have a fair protective effect. These findings contribute to further understanding of the protein function of CD2v and provide potential support for the development of diagnostic tools and vaccines for ASFV.

One-Step Synthesis of 3D Pore-Structured Adsorbent by Cross-Linked PEI and Graphene Oxide Sheets and Its Application in CO2 Adsorption.

In this study, a one-step method of polyethylenimine (PEI) cross-linking graphene oxide (GO) was used to prepare a 3D pore-structured adsorbent with abundant amine groups for chemisorption of CO2. The cross-linking of PEI with GO sheets and the vacuum freeze-drying step are the keys to the formation of the 3D pore structure. The results of characterization analysis revealed that the as-prepared adsorbent had a 3D porous structure rich in amine groups. Besides, the adsorption/desorption test showed that the prepared adsorbent has excellent and stable adsorption performance, and the maximum CO2 adsorption capacity is 2.18 mmol/g at 343 K and 10 vol % CO2. Moreover, the adsorption kinetics analysis indicated that the adsorption process was dominated by homogeneous adsorption, and the adsorbent had a strong affinity with CO2. Finally, the correlation analysis shows that the kinetic constants obtained by the Avrami model simulation can be effectively used for the actual CO2 adsorption process design.

Dual Antimelanogenic Effect of Nicotinamide-Stabilized Phloretin Nanocrystals in Larval Zebrafish.

Melanin is a kind of dark insoluble pigment that can cause pigmentation and free-radical clearance, inducing melasma, freckles, and chloasma, affecting the quality of life of patients. Due to poor water solubility and low safety, the absorption of poorly water-soluble drugs is limited by the hinderance of a skin barrier. Therefore, it is necessary to develop new, safe, and highly efficient drugs to improve their transdermal absorption efficiency and thus to inhibit the production of melanin. To address these issues, we developed a new nicotinamide (NIC)-stabilized phloretin nanocrystals (PHL-NCs). First, NC technology significantly increased the solubility of PHL. The in vitro release results indicated that at 6 h, the dissolution of the PHL-NIC-NCs was 101.39% ± 2.40% and of the PHL-NCs was 84.92% ± 4.30%, while that of the physical mixture of the two drugs was only 64.43% ± 0.02%. Second, NIC acted not only as a stabilizer to enlarge the storage time of PHL-NIC-NCs (improved to 10-day in vitro stability) but also as a melanin transfer inhibitor to inhibit melanin production. Finally, we verified the melanin inhibition effect of PHL-NIC-NCs evaluated by the zebrafish model. It showed that 0.38 mM/L PHL-NIC-NCs have a lower tyrosinase activity at 62.97% ± 0.52% and have less melanin at 36.57% ± 0.44%. The inhibition effect of PHL-NCs and PHL-NIC-NCs was stronger compared to the positive control arbutin. In conclusion, the combination of NIC and PHL achieves better inhibition of tyrosinase and inhibition of melanin production through synergism. This will provide a direction to the subsequent development of melanin-inhibiting drugs and the combined use of pharmaceutical agents.

Synthesis, Characterization and Application of Amine-Functionalized Hierarchically Micro-Mesoporous Silicon Composites for CO2 Capture in Flue Gas.

An efficient CO2 adsorbent with a hierarchically micro-mesoporous structure and a large number of amine groups was fabricated by a two-step synthesis technique. Its structural properties, surface groups, thermal stability and CO2 adsorption performance were fully investigated. The analysis results show that the prepared CO2 adsorbent has a specific hierarchically micro-mesoporous structure and highly uniformly dispersed amine groups that are favorable for the adsorption of CO2. At the same time, the CO2 adsorption capacity of the prepared adsorbent can reach a maximum of 3.32 mmol-CO2/g-adsorbent in the actual flue gas temperature range of 303-343 K. In addition, the kinetic analysis results indicate that both the adsorption process and the desorption process have rapid adsorption/desorption rates. Finally, the fitting of the CO2 adsorption/desorption experimental data by Avrami's fractional kinetic model shows that the CO2 adsorption rate is mainly controlled by the intra-particle diffusion rate, and the temperature has little effect on the adsorption rate.

Translation initiation site of mRNA is selected through dynamic interaction with the ribosome.

Initiation of protein synthesis from the correct start codon of messenger RNA (mRNA) is crucial to translation fidelity. In bacteria, the start codon is usually preceded by a 4- to 6-mer adenosine/guanosine-rich Shine­Dalgarno (SD) sequence. Both the SD sequence and the start codon comprise the core ribosome-binding site (RBS), to which the 30S ribosomal subunit binds to initiate translation. How the rather short and degenerate information inside the RBS can be correctly accommodated by the ribosome is not well understood. Here, we used single-molecule techniques to tackle this long-standing issue. We found that the 30S subunit initially binds to mRNA through the SD sequence, whereas the downstream RBS undergoes dynamic motions, especially when it forms structures. The mRNA is either dissociated or stabilized by initiation factors, such as initiation factor 3 (IF3). The initiator transfer RNA (tRNA) further helps the 30S subunit accommodate mRNA and unwind up to 3 base pairs of the RBS structure. Meanwhile, the formed complex of the 30S subunit with structured mRNA is not stable and tends to disassociate. IF3 promotes dissociation by dismissing the bound initiator tRNA. Thus, initiation factors may accelerate the dynamic assembly­disassembly process of 30S­mRNA complexes such that the correct RBS can be preferentially selected. Our study provides insights into how the bacterial ribosome identifies a typical translation initiation site from mRNA.

Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry.

The dual-specificity tyrosine phosphorylation-regulated kinase DYRK2 has emerged as a critical regulator of cellular processes. We took a chemical biology approach to gain further insights into its function. We developed C17, a potent small-molecule DYRK2 inhibitor, through multiple rounds of structure-based optimization guided by several co-crystallized structures. C17 displayed an effect on DYRK2 at a single-digit nanomolar IC50 and showed outstanding selectivity for the human kinome containing 467 other human kinases. Using C17 as a chemical probe, we further performed quantitative phosphoproteomic assays and identified several novel DYRK2 targets, including eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) and stromal interaction molecule 1 (STIM1). DYRK2 phosphorylated 4E-BP1 at multiple sites, and the combined treatment of C17 with AKT and MEK inhibitors showed synergistic 4E-BP1 phosphorylation suppression. The phosphorylation of STIM1 by DYRK2 substantially increased the interaction of STIM1 with the ORAI1 channel, and C17 impeded the store-operated calcium entry process. These studies collectively further expand our understanding of DYRK2 and provide a valuable tool to pinpoint its biological function.

Development and characterization of recombinant ASFV CD2v protein nanoparticle-induced monoclonal antibody.

African swine fever (ASF) caused by African swine fever virus (ASFV) is becoming a serious threat to the swine industry worldwide. CD2v is a key pathogenic factor of ASFV and the protective antigen with low immunogenicity, whereas viral protein-based nanoparticles have advantages of precise assembly and high immunogenicity. In this study, the CD2v protein fused with Norovirus (NoV) P particle assembled into nanoparticle for improved immunogenicity. Then, CD2v protein nanoparticle and monomer CD2v protein were expressed in HEK293F cells. The former induced higher levels of antibodies, and thus highly potent monoclonal antibodies (mAbs) were generated and characterized. The highest antibody titration of mAb 10A3 reached 1:2048000, and mAb 2E9 had the highest inhibition percent of 84% when competed with ASFV positive serum. Meanwhile, all mAbs reacted specifically with the denatured CD2v protein, and the linear epitope with the location of amino acids 28th to 51st of CD2v extracellular domain sequence was identified. In summary, this study produced a highly immunogenic CD2v protein and generated high-titer mAbs, the precise location of linear epitope on the CD2v was further determined. These findings may provide a powerful help for etiology and serological detection of ASFV.