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The low-energy mutual neutralization (MN) reactions Na+ + H- → Na(nl) + H have been studied by employing the full quantum-mechanical molecular-orbital close-coupling (QMOCC) method over a wide energy range of 10-3 to 103 eV/u. Total and state-selective cross sections have been investigated and compared with the available theoretical and experimental data, and the state-selective rate coefficients for the temperature range of 100-10000 K have been obtained. In the present work, all the necessary highly excited state are included, and the influence of rotational couplings and 10 active electrons are considered. It is found that in the energy below 10 eV/u, the Na(4s) state is the most dominant exit state with a contribution of approximately 78% to the branch fraction, which is in best agreement with the experimental data. For energies above 10 eV/u, the MN total cross section is larger than those obtained in other theoretical calculations and shows a slow decreasing trend because the main exit states change, when the energy is above 100 eV/u, the dominant exit state becomes the Na(3p) state, while the Na(4s) state becomes the third most important exit state.

We present a net-shaped DNA nanostructure (called “DNA Net” herein) design strategy for selective recognition and high-affinity capture of the intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers releases fluorescent signal upon virus binding that is easily read by a hand-held fluorimeter for a rapid (in 10 mins), simple (mix- and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive (∼ $1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1×103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms.

Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species

CS molecule, which plays a key role in atmospheric and astrophysical circumstances, has drawn great attention for long time. Owing to its large state density, the detailed information of the electronic structure of CS is still lacking. In this work, the high-level MRCI+Q method is used to compute the potential energy curves, dipole moments and transition dipole moments of singlet and triplet states correlated with the lowest dissociation limit of CS, based on which high accurate vibration–rotation levels and spectroscopic constants of bound states are evaluated. The opacity of CS relevant to atmospheric circumstance is computed at a pressure of 100 atms for different temperatures. With the increase of temperature, band systems from different transitions mingle with each other, and band boundaries become blurred, which are originated from the increased population on vibrational excited states and electronic excited states at high temperature.

BNAbs of VH1-69 germline origin from a Chinese patient recognize the V3 glycan supersite via a disulfide-locked long HCDR3 loop., An oligomannose patch around the V3 base of HIV-1 envelope glycoprotein (Env) is recognized by multiple classes of broadly neutralizing antibodies (bNAbs). Here, we investigated the bNAb response to the V3 glycan supersite in an HIV-1–infected Chinese donor by Env-specific single B cell sorting, structural and functional studies, and longitudinal analysis of antibody and virus repertoires. Monoclonal antibodies 438-B11 and 438-D5 were isolated that potently neutralize HIV-1 with moderate breadth, are encoded by the VH1-69 germline gene, and have a disulfide-linked long HCDR3 loop. Crystal structures of Env-bound and unbound antibodies revealed heavy chain–mediated recognition of the glycan supersite with a unique angle of approach and a critical role of the intra-HCDR3 disulfide. The mechanism of viral escape was examined via single-genome amplification/sequencing and glycan mutations around the N332 supersite. Our findings further emphasize the V3 glycan supersite as a prominent target for Env-based vaccine design.

An HCV vaccine strategy displays optimized E2 cores on nanoparticles for eliciting a cross-neutralizing B cell response., Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 are responsible for cell entry, with E2 being the major target of neutralizing antibodies (NAbs). Here, we present a comprehensive strategy for B cell–based HCV vaccine development through E2 optimization and nanoparticle display. We redesigned variable region 2 in a truncated form (tVR2) on E2 cores derived from genotypes 1a and 6a, resulting in improved stability and antigenicity. Crystal structures of three optimized E2 cores with human cross-genotype NAbs (AR3s) revealed how the modified tVR2 stabilizes E2 without altering key neutralizing epitopes. We then displayed these E2 cores on 24- and 60-meric nanoparticles and achieved substantial yield and purity, as well as enhanced antigenicity. In mice, these nanoparticles elicited more effective NAb responses than soluble E2 cores. Next-generation sequencing (NGS) defined distinct B cell patterns associated with nanoparticle-induced antibody responses, which target the conserved neutralizing epitopes on E2 and cross-neutralize HCV genotypes.

Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 are critical for cell entry with E2 being the major target of neutralizing antibodies (NAbs). Here, we present a comprehensive strategy for B cell-based HCV vaccine development through E2 optimization and nanoparticle display. We redesigned variable region 2 in a truncated form (tVR2) on E2 cores derived from genotypes 1a and 6a, resulting in improved stability and antigenicity. Crystal structures of three optimized E2 cores with human cross-genotype NAbs (AR3s) revealed how the modified tVR2 stabilizes E2 without altering key neutralizing epitopes. We then displayed these E2 cores on 24- and 60-meric nanoparticles and achieved high yield, high purity, and enhanced antigenicity. In mice, these nanoparticles elicited more effective NAb responses than soluble E2 cores. Next-generation sequencing (NGS) defined distinct B-cell patterns associated with nanoparticle-induced antibody responses, which cross-neutralized HCV by targeting the conserved neutralizing epitopes on E2.One Sentence SummaryAn HCV vaccine strategy is presented that displays redesigned E2 cores on nanoparticles as vaccine candidates for eliciting a broadly neutralizing B-cell response.

SUMMARYOvercoming envelope metastability is crucial to trimer-based HIV-1 vaccine design. Here, we present a coherent vaccine strategy by minimizing metastability. For ten strains across five clades, we demonstrate that gp41 ectodomain (gp41ECTO) is the main source of envelope metastability by replacing wild-type gp41ECTOwith BG505 gp41ECTOof the uncleaved prefusion-optimized (UFO) design. These gp41ECTO-swapped trimers can be produced in CHO cells with high yield and high purity. Crystal structure of a gp41ECTO-swapped trimer elucidates how a neutralization-resistant tier 3 virus evades antibody recognition of the V2 apex. UFO trimers of transmitted/founder (T/F) viruses and UFO trimers containing a consensus-based ancestral gp41ECTOsuggest an evolutionary root of the metastability. Gp41ECTO-stabilized trimers can be readily displayed on 24- and 60-meric nanoparticles, with incorporation of additional T cell help illustrated for a hyperstable 60-mer. In mice and rabbits, gp140 nanoparticles induced more effective tier 2 neutralizing antibody response than trimers with statistical significance.HIGHLIGHTSgp41 is the main source of HIV-1 envelope metastabilityBG505 gp41 of the UFO design stabilizes gp140 trimers of diverse subtypesgp41 stabilization facilitates gp140 nanoparticle assembly and improves productionNanoparticles elicit tier 2 neutralizing antibodies more effectively than trimers

Electron-capture and excitation processes in He+ +H collisions have been studied by using the full quantum-mechanical molecular orbital close-coupling (QMOCC) and the two-center atomic orbital close-coupling (TC-AOCC) methods in the energy ranges 10-2–5 keV/u and 0.1–100 keV/u, respectively. The spin-selected state-selective cross sections for these processes in the He+ +H collision system are reported for the first time. The spin-averaged total electron capture and excitation cross sections, as well as the emission cross section for Balmer α radiation, are compared with the results of available experimental and previous theoretical results in the overlapping energy ranges.

Broadly neutralizing antibodies (bNAbs) have provided valuable insights into the humoral immune response to HIV-1. While rationally designed epitope scaffolds and well-folded gp140 trimers have been proposed as vaccine antigens, a comparative understanding of their antibody responses has not yet been established. In this study, we probed antibody responses to the N332 supersite and the membrane-proximal external region (MPER) in the context of heterologous protein scaffolds and native-like gp140 trimers. Ferritin nanoparticles and fragment crystallizable (Fc) regions were utilized as multivalent carriers to display scaffold antigens with grafted N332 and MPER epitopes, respectively. Trimeric scaffolds were also identified to stabilize the MPER-containing BG505 gp140.681 trimer in a native-like conformation. Following structural and antigenic evaluation, a subset of scaffold and trimer antigens was selected for immunization in BALB/c mice. Serum binding revealed distinct patterns of antibody responses to these two bNAb targets presented in different structural contexts. For example, the N332 nanoparticles elicited glycan epitope-specific antibody responses that could also recognize the native trimer, while a scaffolded BG505 gp140.681 trimer generated a stronger and more rapid antibody response to the trimer apex than its parent gp140.664 trimer. Furthermore, next-generation sequencing (NGS) of mouse splenic B cells revealed expansion of antibody lineages with long heavy-chain complementarity-determining region 3 (HCDR3) loops upon activation by MPER scaffolds, in contrast to the steady repertoires primed by N332 nanoparticles and a soluble gp140.664 trimer. These findings will facilitate the future development of a coherent vaccination strategy that combines both epitope-focused and trimer-based approaches., IMPORTANCE Both epitope-focused and trimer-based strategies are currently being explored in HIV-1 vaccine development, which aims to elicit broadly neutralizing antibodies (bNAbs) targeting conserved epitopes on the viral envelope (Env). However, little is known about the differences in antibody response to these bNAb targets presented by foreign scaffolds and native Env. In this study, a systematic effort was undertaken to design multivalent epitope scaffolds and soluble gp140.681 trimers with a complete antigenic surface, and to comparatively analyze the antibody responses elicited by these antigens to the N332 supersite and MPER in a mouse model. This study will inform both epitope-focused and trimer-based vaccine design and will facilitate integration of the two vaccine strategies.

Aims. Electron capture in collisions of highly charged O6+ions with ground-state hydrogen atoms is a very important process in solar wind X-ray studies.Methods. In the present study, the full quantum-mechanical molecular-orbital close-coupling method is employed to study electron capture reactions in collisions of O6+ion with ground-state atomic hydrogen in the energy region from 10−4keV u−1to 5 keV u−1. The ab initio multi-reference single- and double-excitation configuration interaction (MRD-CI) method is used to calculate the potential and coupling data used in the QMOCC calculations.Results. Total and state-selective cross sections for the dominant and subdominant reaction channels are calculated and compared with the available experimental and theoretical data. The branching ratios for Lithium-like O5+excited ions are used to calculate the contribution of cascade radiative transitions fromn = 5 levels to the population of 4l states. From the calculated cross sections, reaction rate coefficients are obtained for temperatures between 1000 and 1 × 109K and compared with other calculations.

Aims. The radiative charge transfer and association processes in Li − + H collisions are studied in the 10 -10 −10 eV center-of-mass energy range. Methods. we carried out total and ν -resolved state-selective cross sections have been carried out by using the fully quantum, optical potential, and semiclassical methods. Results. In the energy region below ~ 0.8 eV, the radiative association process is the dominant decay channel, while radiative charge transfer dominates at higher energies. Rich resonance structures are observed in the cross sections of both processes in the 0.1−1.5 eV energy range; These structures are associated with the quasi-bound states below the top of the centrifugal barrier of the effective potential in the entrance channel for specific vibrational and angular momentum states. It is found that with the increase of collision energy, the resonances occur for higher angular momentum states and lower vibrational states. Besides the cross sections for the studied processes we also present their reaction rate coefficients in the 10 -6 –10 6 K temperature range.