Neutral Base Research Articles

Nitro rotation tuned dissociative electron attachment upon targeted radiosensitizer 4-substituted Z bases.

In this work, a set of new potential radiation sensitizers (4-substituted Z-bases: 4XZ, X = F, Cl, Br, and I) are designed based on the artificial 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (Z), which can selectively bind to breast cancer cells. The calculated electron affinities in water solution show that the halogenated Z-bases are efficient electron acceptors which possess significant electron-withdrawing characters following the order of 4XZ > Z ≫ U. To ensure the effective electron attachment induced dissociation, we constructed the energy profiles related to the X-C bond cleavage of neutral and anionic bases. The results show that the X-C bond becomes relatively weak after the electron attachment. In particular, the electron induced dehalogenations of (4BrZ)- and (4IZ)- are low-barrier and exothermic, which support a high radiosensitivity. Furthermore, we characterized the vibrational excitation effect on the dissociative electron attachment, which demonstrates that the charge distribution can be regulated by the rotation-induced structural distortion accompanied by the electron localization on the nitro group. Also examined is the influence of base pairing on the dehalogenation, which is not only conducive to the electron-driven dissociation but is also beneficial to the stabilization of related products. The current study suggests 4BrZ and 4IZ can be regarded as potential targeted radiosensitizers with possible applications in reducing the side effects in radiotherapy.

PH-regulated interaction modes between cyanidin-3-glucoside and phenylboronic acid-modified alginate

Stabilizing mechanisms through covalent and non-covalent interactions have been studied along the years for color stabilization of anthocyanin dyes. In this work, the chemical functionalization of a natural and biocompatible marine-based polysaccharide (alginic acid) with 3-aminophenylboronic acid via carbodiimide coupling chemistry was carried out in order to create a bifunctional material for pH-dependent selective interaction with colored cyanidin-3-glucoside chemical species. The interaction studies were performed by UV–Vis, 1H, and 11B NMR spectroscopy. Overall, the apparent acidic and hydration constants are more stabilized in the presence of phenylboronic acid-modified alginate. For more acidic pH values the red cationic flavylium cation of cyanidin-3-glucoside mainly interacts through non-covalent electrostatic interactions with the carboxylate groups of the biopolymer derivative with association constant around 0.5 mM−1 while at higher pH values boronate-catechol covalent bonds are favored, promoting the stabilization of the colored neutral and anionic quinoidal bases of anthocyanins instead of colorless hemiketal and chalcones.

Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain.

Antibodies that potently neutralize SARS-CoV-2 target mainly the receptor-binding domain or the N-terminal domain (NTD). Over a dozen potently neutralizing NTD-directed antibodies have been studied structurally, and all target a single antigenic supersite in NTD (site 1). Here, we report the cryo-EM structure of a potent NTD-directed neutralizing antibody 5-7, which recognizes a site distinct from other potently neutralizing antibodies, inserting a binding loop into an exposed hydrophobic pocket between the two sheets of the NTD β sandwich. Interestingly, this pocket was previously identified as the binding site for hydrophobic molecules, including heme metabolites, but we observe that their presence does not substantially impede 5-7 recognition. Mirroring its distinctive binding, antibody 5-7 retains neutralization potency with many variants of concern (VOCs). Overall, we reveal that a hydrophobic pocket in NTD proposed for immune evasion can be used by the immune system for recognition.

Development of a label-free plasmonic gold nanoparticles aggregates sensor on the basis of charge neutralization for the detection of zearalenone

Mycotoxin contamination of corn has been considered a serious problem because it can accumulate in different organs or tissues via ingestion or skin contact and cause several health problems in humans. We have constructed a label-free, colorimetric, and fluorescence dual-channel sensing platform for the detection of zearalenone. Here, we demonstrate that plasmonic gold nanoparticles aggregates could be rapidly formed on the basis of charge neutralization by positively charged SYBR Green I. The sensing platform allowed quantitative detection as low as 0.89 μg kg−1 and visual detection as low as 2.5 μg kg−1. The charge neutralization strategy eliminates a major source of instability in conventional gold nanoparticles colorimetric measurements and paves the way for accurate, label-free bioanalysis.

A whole-institution approach towards sustainability: a crucial aspect of higher education’s individual and collective engagement with the SDGs and beyond

PurposeHigher education and its leadership are not yet using their potential impact for a sustainable future. This paper aims to focus on UN developments and the long history of university involvement in sustainability might create more interest and understanding that sustainably oriented universities are actually possible and a much stronger role for higher education is needed when nations are discussing their future.Design/methodology/approachLiterature review with a focus on international treaties and declarations on the UN level and international university networks, literature review of the background and potential of the whole-institution approach and the need/suggestions for further research, also to measure advancement.FindingsHistory shows a strong engagement of higher education with sustainability from its beginnings. There have been strong calls/offers from within university networks to take a crucial role in moving towards sustainable development that involves more than teaching about sustainability. The international community calls for higher education to be involved in policymaking rather than simply implementation, have been limited and the full potential of higher education institutions using all opportunities such as being living labs for sustainability has not as yet been realized. Currently, calls for engagement are often still limited to training and providing research when scientific evidence is wanted.Research limitations/implicationsLiterature review focused on UN level treaties/declarations English- and German-language review national developments limited to samples of members of the Sustainable Development Goal (SDG) 4 subcluster in the Higher Education and Research for Sustainable Development (HESD) Global Cluster by the International Association of Universities (IAU).Practical implicationsGuidance for university leaders and other stakeholders to become aware of and consider a whole-institution approach. Practitioner relevance as countries is encouraged to embed UN recommendations, treaties and declarations. Defining opportunities for further research. Presenting the HESD Cluster by the IAU as a sample for new approaches of higher education to interact with the SDGs.Social implicationsStrengthening the role of higher education in the pursuit of a better future would focus on science and research as a neutral basis for decision-making and policy development. Sustainability embedded in all streams of university can help universities to be a practical example of the possibilities of sustainability at work.Originality/valueComposition of authors with UN background and involvement. Focus on UN treaties/declarations and guidance for academics and practitioners in leadership on adopted UN and other international documents. Summarizing the background of the whole-institution approach as a genuine development over time but including limitations and implications for future roles for higher education leadership. IAU SDG 4 Subcluster is unique in its own approach and with its connections to a global network of higher education institutions and UNESCO.

Auxiliary interfaces support the evolution of specific toxin-antitoxin pairing.

Toxin-antitoxin (TA) systems are a large family of genes implicated in the regulation of bacterial growth and its arrest in response to attacks. These systems encode nonsecreted toxins and antitoxins that specifically pair, even when present in several paralogous copies per genome. Salmonella enterica serovar Typhimurium contains three paralogous TacAT systems that block bacterial translation. We determined the crystal structures of the three TacAT complexes to understand the structural basis of specific TA neutralization and the evolution of such specific pairing. In the present study, we show that alteration of a discrete structural add-on element on the toxin drives specific recognition by their cognate antitoxin underpinning insulation of the three pairs. Similar to other TA families, the region supporting TA-specific pairing is key to neutralization. Our work reveals that additional TA interfaces beside the main neutralization interface increase the safe space for evolution of pairing specificity.

Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail.

Understanding the molecular basis for immune recognition of SARS-CoV-2 spike (S) glycoprotein antigenic sites will inform development of improved therapeutics. We determined the structures of two human monoclonal antibodies AZD8895 and AZD1061, which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor binding domain (RBD) of SARS-CoV-2, in order to define the genetic and structural basis of neutralization. AZD8895 forms an “aromatic cage” at the heavy/light chain interface using germline-encoded residues in complementarity determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals. AZD1061 has an unusually long LCDR1, and HCDR3 make interactions with the opposite face of the RBD from that of AZD8895. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the crucial binding residues of both antibodies and identified positions of concern with regards to virus escape from antibody-mediated neutralization. Both AZD8895 and AZD1061 have strong neutralizing activity against SARS-CoV-2 and variants of concern with antigenic substitutions in the RBD. We conclude that germline-encoded antibody features enable recognition of the SARS-CoV-2 spike RBD and demonstrate the utility of the cocktail AZD7442 in neutralizing emerging variant viruses.

Unusual photophysical properties of fluorescent cytosine analogues utilized in real-time detecting i-motif DNA: A theoretical study

In this work, we report a theoretical study on the optical properties of a set of fluorescent cytosine analogues as indicators to examine the structural changes during the four-stranded intercalated motif (i-motif) formation. Herein, the neutral bases, protonated monomers and hemiprotonated base pairs corresponding to different stages of the forming process are considered. The calculated results reveal that the modified cytosine analogues show red-shifted absorption and bright fluorescence emission arisen from the increased π-conjugation characters. Especially, the 1,3-diaza-2-oxophenoxazine (tCO) possesses high fluorescence intensity, large Stokes shift and distinct wavelengths for all considered configurations (445 nm for neutral base, 546 nm for protonated monomer and 509 nm for hemiprotonated base pair), in which the tCO becomes potential candidate for application in detecting i-motif structure. Besides, the fluorescence quenching induced by the proton transfer is observed depending on base pairing, which is another efficient optical probe during the i-motif formation. Also examined are the effects of binding to deoxyribose, which can red-shift the fluorescence emissions and enhance fluorescence intensities for both monomers and base pair.

Neutralization of the anthrax toxin by antibody-mediated stapling of its membrane-penetrating loop.

Anthrax infection is associated with severe illness and high mortality. Protective antigen (PA) is the central component of the anthrax toxin, which is one of two major virulence factors of Bacillus anthracis, the causative agent of anthrax disease. Upon endocytosis, PA opens a pore in the membranes of endosomes, through which the cytotoxic enzymes of the toxin are extruded. The PA pore is formed by a cooperative conformational change in which the membrane-penetrating loops of PA associate, forming a hydrophobic rim that pierces the membrane. Due to its crucial role in anthrax progression, PA is an important target for monoclonal antibody-based therapy. cAb29 is a highly effective neutralizing antibody against PA. Here, the cryo-EM structure of PA in complex with the Fab portion of cAb29 was determined. It was found that cAb29 neutralizes the toxin by clamping the membrane-penetrating loop of PA to the static surface-exposed loop of the D3 domain of the same subunit, thereby preventing pore formation. These results provide the structural basis for the antibody-based neutralization of PA and bring into focus the membrane-penetrating loop of PA as a target for the development of better anti-anthrax vaccines.

Drivers of the peaking and decoupling between CO2 emissions and economic growth around 2030 in China.

Reaching the peak of carbon dioxide emissions is the basis and premise of carbon neutrality. In this paper, the factor decomposition model was used to analyze the influencing factors and effects of carbon dioxide emissions. Causal chain model of elastic decoupling was established. The historical decoupling state between carbon dioxide emissions and economic growth and the decoupling effect of its influencing factors were analyzed. The prediction model of carbon dioxide emissions was used to explore the change trend of China's carbon dioxide emissions and its peak in the short and medium term in the future. The elastic decoupling trend between carbon dioxide emissions and economic growth was predicted. The results show that economic growth is the main force driving carbon dioxide emissions. Both energy intensity and energy consumption structure have a strong inhibiting effect on carbon dioxide emissions except for a few years, but the former has a more significant inhibiting effect than the latter. In general, the elastic decoupling between carbon dioxide emissions and economic growth has experienced a state from weak decoupling to growth linkage and then to weak decoupling. And this weak decoupling trend will continue to increase in the short and medium term. During the 14th Five-year and 15th Five-year period, if the average annual economic growth rate will be maintained at 4.61 to 5.85%, energy intensity will be reduced by 16.14 to 18.37%, and the proportion of non-fossil energy in the energy consumption structure at the end of the 14th, 15th, and 16th Five-Year Plan period will be around 19.9%, 23.2%, and 26.1%, respectively, and then the intensity of carbon dioxide emissions will continue to decline. It is expected to reach the peak of carbon dioxide emissions between 10,453 and 10,690 billion tons from 2025 to 2027. And the earlier the peak time is, the smaller the peak is, which would provide valuable time for carbon neutrality and room to reduce carbon dioxide emissions in the medium and long term.

Solid-phase synthesis of protonated nitrogen-containing heterocyclic compounds with the boron cluster anions starting from [Eu(H2O)9]2[B10Cl10]3: Synthesis, structure, and thermal properties of (НL)2[B10Cl10] (L = 7-amino-4-methylcoumarin or 1-ethyl-2-(4-methoxyphenyl) azobenzimidazole)

The paper proposes a new method for the synthesis of salts of a perchlorinated derivative of the decahydro-closo-decaborate anion with neutral N-containing organic bases L1 and L2 starting from previously prepared europium precursor [Eu(H2O)9]2[B10Cl10]3. Compound [Eu(H2O)9]2[B10Cl10]3 was first synthesized and characterized by elemental analysis, X-ray powder diffraction, IR spectroscopy and its thermal properties were studied by TGA. The protonation of organic bases L was carried out in the solid phase in the presence of precursor [Eu(H2O)9]2[B10Cl10]3. For comparison, the reaction was carried out in solution: in the CH3CN/CF3COOH system and in an aqueous solution of (H3O)2[B10Cl10] with pronounced acidic properties. The influence of reaction conditions on the composition and structure of the final products was analyzed. Salts of the composition (НL)2[B10Cl10] (L is 1-ethyl-2-(4-methoxyphenyl)azobenzimidazole (L1) and 7-amino-4-methylcoumarin (L2)) and (HL2)(H9O4) [B10Cl10] were synthesized and characterized by X-ray diffraction. The thermal properties of the obtained salts and ligand L1 (C16H16N4O) were studied in air in the temperature range 20–600°С.

Crypto-punditry and the media neutrality crisis

ABSTRACT This article describes the corrosive practice of “crypto-punditry,” whereby subjective analysis is smuggled into media coverage under the guise of objective reporting. In search of a neutral basis for analyzing events, journalists latch onto public opinion. However, this opinion is rarely expressed directly. Instead, reporters engage in speculative assessment about what public opinion might be. Unfortunately, in an effort to shield themselves from charges of bias, journalists have triggered a counterproductive autoimmune practice which targets precisely those elements of descriptive reporting that give it strength: fairness, accountability, public interest. To make this argument, I first develop a theory of crypto-punditry and outline its effects. I then use content analysis to show that this practice has become far more common in political reporting over the past decade. I conclude by using the 2016 US presidential election as a case study to illustrate its effects.

Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge during the global pandemic and may facilitate escape from current antibody therapies and vaccine protection. Here we showed that the South African variant B.1.351 was the most resistant to current monoclonal antibodies and convalescent plasma from coronavirus disease 2019 (COVID-19)-infected individuals, followed by the Brazilian variant P.1 and the United Kingdom variant B.1.1.7. This resistance hierarchy corresponded with Y144del and 242–244del mutations in the N-terminal domain and K417N/T, E484K, and N501Y mutations in the receptor-binding domain (RBD) of SARS-CoV-2. Crystal structure analysis of the B.1.351 triple mutant (417N-484K-501Y) RBD complexed with the monoclonal antibody P2C-1F11 revealed the molecular basis for antibody neutralization and escape. B.1.351 and P.1 also acquired the ability to use mouse and mink ACE2 receptors for entry. Our results demonstrate major antigenic shifts and potential broadening of the host range for B.1.351 and P.1 variants, which poses serious challenges to current antibody therapies and vaccine protection.

Technocracy and the Tragedy of EU Governance

In a historical perspective, technocracy, emphasising bureaucratic and technical expertise in political, social and economic areas, is a double edge sword: on the one side, it guaranteed the condition for international cooperation post-WW II, providing as an ideologically neutral basis the condition for governance in a politically bitter international climate. On the other hand, it indicates the tragedy of increasing delegitimization of EU governance, causing the alienation of political willing from the peo-ple that is (mis-)used by populists present-day and their slogan ‘back to the people’. Technocracy is theoretically symbolised through the functionalism of EU integration, politically manifest in the re-definition of democracy from “input”- to “output”-orientation by e.g. Fritz Scharpf. The tragedy of EU politics being trapped in technocratic governance as condition of the possibility and calamity of coop-eration at the same time is analytically at the heart to understand contemporary approaches of EU (dis-)integration and identity. However, in both understanding alienation and (populist) opposition to the EU integration processes as systemic phenomena, deeply seeded in the structure of the EU and of EU policy studies themselves, as well as in suggesting a triangular democratic process to rectify the EU’s birth deficit, the paper significantly goes beyond current policy studies (e.g. on EU dis-integration) and their non-normative stance. These studies are still anchored in the epistemological commitments of neo-functionalism that need finally to be overcome as they tend to ignore the human factor and agency in politics.

Cost-efficiency analysis of conversion from reference pegfilgrastim to its biosimilar (pegfilgrastim-jmdb) and expanded access to food and transportation support for Medicare/Medicaid patients within the CMS Oncology Care Model.

e18837 Background: The CMS Oncology Care Model (OCM) aims to improve quality of care and health outcomes in cancer centers at the same or lower cost. We performed cost-efficiency analyses of converting selected cancer patients (pts) from reference pegfilgrastim (PFG) to its biosimilar (PFG-jmdb); and simulated re-allocating savings to provide nutrition and transportation support to CMS beneficiaries within OCM. Methods: Incidence rates for breast, ovarian, lung, colorectal cancers and non-Hodgkin lymphoma were extracted from SEER, further stratified by age <65 (commercial insurance) or >65 (Medicare) adjusted for Medicare/Medicaid mix. Chemotherapy (CTX) rates were matched to tumor type; of these 19.4% were assumed to require PFG prophylaxis (PPX). Two models compared respectively prefilled syringe (PFS) and on-body injector (OBI) reference PFG to PFS PFG-jmdb. Cost inputs included Average Sales Price (ASP) 3Q20 for Medicare and National Average Drug Acquisition Cost (NADAC, estimated by wholesale acquisition cost (WAC)-3.9%) for Medicaid pts plus medication administration. Cost savings across various biosimilar conversion rates for CTX cycles 1-6 were translated into $100 units of healthy food or medical transportation. Results: In 2020, biosimilar conversion for the estimated 31,210 Medicare and 1,722 Medicaid pts in the 5 tumor types needing PFG PPX yielded savings of up to ̃$19M (Medicare) and ̃$20M (Medicaid). These savings could have provided a monthly $100 food or transportation check to at least 24,716 Medicare or 33,630 Medicaid pts for 6 months. Conclusions: Savings from biosimilar conversion can be re-allocated on a budget neutral basis to food and transportation support to pts with such needs. This achieves the dual OCM aim of reducing drug budgets while enhancing patient-centric support services.[Table: see text]

Structural basis for broad coronavirus neutralization.

Three highly pathogenic β-coronaviruses have crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. To evaluate the possibility of identifying antibodies with broad neutralizing activity, we isolated a monoclonal antibody, termed B6, that cross-reacts with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses. B6 broadly neutralizes entry of pseudotyped viruses from lineages A and C, but not from lineage B, and the latter includes SARS-CoV and SARS-CoV-2. Cryo-EM, X-ray crystallography and membrane fusion assays reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery. The data indicate that antibody binding sterically interferes with the spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages, along with a proof of concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-β-coronavirus vaccine.

Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19.

SummaryIndividuals with the 2019 coronavirus disease (COVID-19) show varying severity of the disease, ranging from asymptomatic to requiring intensive care. Although monoclonal antibodies specific to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been identified, we still lack an understanding of the overall landscape of B cell receptor (BCR) repertoires in individuals with COVID-19. We use high-throughput sequencing of bulk and plasma B cells collected at multiple time points during infection to characterize signatures of the B cell response to SARS-CoV-2 in 19 individuals. Using principled statistical approaches, we associate differential features of BCRs with different disease severity. We identify 38 significantly expanded clonal lineages shared among individuals as candidates for responses specific to SARS-CoV-2. Using single-cell sequencing, we verify the reactivity of BCRs shared among individuals to SARS-CoV-2 epitopes. Moreover, we identify the natural emergence of a BCR with cross-reactivity to SARS-CoV-1 and SARS-CoV-2 in some individuals. Our results provide insights important for development of rational therapies and vaccines against COVID-19.

Structural basis of tetanus toxin neutralization by native human monoclonal antibodies.

Four potent native human monoclonal antibodies (mAbs) targeting distinct epitopes on tetanus toxin (TeNT) are isolated with neutralization potency ranging from approximately 17mg to 6mg each that are equivalent to 250 IU of human anti-TeNT immunoglobulin. TT0170 binds fragment B, and TT0069 and TT0155 bind fragment AB. mAb TT0067 binds fragment C and blocks the binding of TeNT to gangliosides. The co-crystal structure of TT0067 with fragment C of TeNT at a 2.0-Å resolution demonstrates that mAb TT0067 directly occupies the W pocket of one of the receptor binding sites on TeNT, resulting in blocking the binding of TeNT to ganglioside on the surface of host cells. This study reveals at the atomic level the mechanism of action by the TeNT neutralizing antibody. The key neutralization epitope on the fragment C of TeNT identified in our work provides the critical information for the development of fragment C of TeNT as a better and safer tetanus vaccine.

Intervention Strategies for Seasonal and Emerging Respiratory Viruses with Drugs and Vaccines Targeting Viral Surface Glycoproteins.

Vaccines and therapeutics targeting viral surface glycoproteins are a major component of disease prevention for respiratory viral diseases. Over the years, vaccines have proven to be the most successful intervention for preventing disease. Technological advances in vaccine platforms that focus on viral surface glycoproteins have provided solutions for current and emerging pathogens like SARS-CoV-2, and our understanding of the structural basis for antibody neutralization is guiding the selection of other vaccine targets for respiratory viruses like RSV. This review discusses the role of viral surface glycoproteins in disease intervention approaches.

Characterization of a highly neutralizing single monoclonal antibody to botulinum neurotoxin type A.

Compared to conventional antisera strategies, monoclonal antibodies (mAbs) represent an alternative and safer way to treat botulism, a fatal flaccid paralysis due to botulinum neurotoxins (BoNTs). In addition, mAbs offer the advantage to be produced in a reproducible manner. We previously identified a unique and potent mouse mAb (TA12) targeting BoNT/A1 with high affinity and neutralizing activity. In this study, we characterized the molecular basis of TA12 neutralization by combining Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) with site-directed mutagenesis and functional studies. We found that TA12 recognizes a conformational epitope located at the interface between the HCN and HCC subdomains of the BoNT/A1 receptor-binding domain (HC ). The TA12-binding interface shares common structural features with the ciA-C2 VHH epitope and lies on the face opposite recognized by ciA-C2- and the CR1/CR2-neutralizing mAbs. The single substitution of N1006 was sufficient to affect TA12 binding to HC confirming the position of the epitope. We further uncovered that the TA12 epitope overlaps with the BoNT/A1-binding site for both the neuronal cell surface receptor synaptic vesicle glycoprotein 2 isoform C (SV2C) and the GT1b ganglioside. Hence, TA12 potently blocks the entry of BoNT/A1 into neurons by interfering simultaneously with the binding of SV2C and to a lower extent GT1b. Our study reveals the unique neutralization mechanism of TA12 and emphasizes on the potential of using single mAbs for the treatment of botulism type A.