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.

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.

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.

Global fitness landscapes of the Shine-Dalgarno sequence.

Shine-Dalgarno sequences (SD) in prokaryotic mRNA facilitate protein translation by pairing with rRNA in ribosomes. Although conventionally defined as AG-rich motifs, recent genomic surveys reveal great sequence diversity, questioning how SD functions. Here, we determined the molecular fitness (i.e., translation efficiency) of 49 synthetic 9-nt SD genotypes in three distinct mRNA contexts in Escherichia coli We uncovered generic principles governing the SD fitness landscapes: (1) Guanine contents, rather than canonical SD motifs, best predict the fitness of both synthetic and endogenous SD; (2) the genotype-fitness correlation of SD promotes its evolvability by steadily supplying beneficial mutations across fitness landscapes; and (3) the frequency and magnitude of deleterious mutations increase with background fitness, and adjacent nucleotides in SD show stronger epistasis. Epistasis results from disruption of the continuous base pairing between SD and rRNA. This "chain-breaking" epistasis creates sinkholes in SD fitness landscapes and may profoundly impact the evolution and function of prokaryotic translation initiation and other RNA-mediated processes. Collectively, our work yields functional insights into the SD sequence variation in prokaryotic genomes, identifies a simple design principle to guide bioengineering and bioinformatic analysis of SD, and illuminates the fundamentals of fitness landscapes and molecular evolution.

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.

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.

Formation of frameshift-stimulating RNA pseudoknots is facilitated by remodeling of their folding intermediates.

Programmed -1 ribosomal frameshifting is an essential regulation mechanism of translation in viruses and bacteria. It is stimulated by mRNA structures inside the coding region. As the structure is unfolded repeatedly by consecutive translating ribosomes, whether it can refold properly each time is important in performing its function. By using single-molecule approaches and molecular dynamics simulations, we found that a frameshift-stimulating RNA pseudoknot folds sequentially through its upstream stem S1 and downstream stem S2. In this pathway, S2 folds from the downstream side and tends to be trapped in intermediates. By masking the last few nucleotides to mimic their gradual emergence from translating ribosomes, S2 can be directed to fold from the upstream region. The results show that the intermediates are greatly suppressed, suggesting that mRNA refolding may be modulated by ribosomes. Moreover, masking the first few nucleotides of S1 favors the folding from S2 and yields native pseudoknots, which are stable enough to retrieve the masked nucleotides. We hypothesize that translating ribosomes can remodel an intermediate mRNA structure into a stable conformation, which may in turn stimulate backward slippage of the ribosome. This supports an interactive model of ribosomal frameshifting and gives an insightful account addressing previous experimental observations.

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.

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.

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.

Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot.

Frameshifting is an essential process that regulates protein synthesis in many viruses. The ribosome may slip backward when encountering a frameshift motif on the messenger RNA, which usually contains a pseudoknot structure involving tertiary base pair interactions. Due to the lack of detailed molecular explanations, previous studies investigating which features of the pseudoknot are important to stimulate frameshifting have presented diverse conclusions. Here we constructed a bimolecular pseudoknot to dissect the interior tertiary base pairs and used single-molecule approaches to assess the structure targeted by ribosomes. We found that the first ribosome target stem was resistant to unwinding when the neighboring loop was confined along the stem; such constrained conformation was dependent on the presence of consecutive adenosines in this loop. Mutations that disrupted the distal base triples abolished all remaining tertiary base pairs. Changes in frameshifting efficiency correlated with the stem unwinding resistance. Our results demonstrate that various tertiary base pairs are coordinated inside a highly efficient frameshift-stimulating RNA pseudoknot and suggest a mechanism by which mechanical resistance of the pseudoknot may persistently act on translocating ribosomes.

[The Research on Reinspection Problems in Supervisory Sampling Inspection for Medical Devices].

Supervisory sampling inspection is one of the administrative supervision measures for medical devices. As the reinspection work affects the final conclusion of sampling inspection, inappropriate overturn during the reinspection has already impaired the impartiality and authority of the supervisory inspection work. By the statistics of survey materials, this article analyzes the reasons for requesting reinspection and making overturns, and proposes a scheme for eliminating the interference factors such as the understanding divergences and the defects of standards, the inspection capacity and the issues of sampled devices, etc. To enhance the authoritative of reinspection, this article also proposes principals of evasion, precedence, arbitration and assessment, and the improvement of the reinspection workflow in order to make the reinspection work more appropriate, more efficient and more impartial.

Polyphosphide anion-mediated simultaneous P, Au co-alloying with Pd for anti-poisoning formic acid oxidation.

An innovative polyphosphide route is developed to synthesize a series of P-doped PdAu ternary alloys. The alloying of P and Au optimizes the electronic structure and reduces the back-donation of d electrons to CO. Meanwhile, the generation of CO is largely inhibited by the highly selective direct pathway arising from the synergistic electron/ligand effect of Au and P, leading to a remarkable anti-poisoning capability for formic acid oxidation.

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.

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.

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.

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.

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.

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.