SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape.

The 501Y.V2 variants of SARS-CoV-2 containing multiple mutations in spike are now dominant in South Africa and are rapidly spreading to other countries. Here, experiments with 18 pseudotyped viruses showed that the 501Y.V2 variants do not confer increased infectivity in multiple cell types except for murine ACE2-overexpressing cells, where a substantial increase in infectivity was observed. Notably, the susceptibility of the 501Y.V2 variants to 12 of 17 neutralizing monoclonal antibodies was substantially diminished, and the neutralization ability of the sera from convalescent patients and immunized mice was also reduced for these variants. The neutralization resistance was mainly caused by E484K and N501Y mutations in the receptor-binding domain of spike. The enhanced infectivity in murine ACE2-overexpressing cells suggests the possibility of spillover of the 501Y.V2 variants to mice. Moreover, the neutralization resistance we detected for the 501Y.V2 variants suggests the potential for compromised efficacy of monoclonal antibodies and vaccines.

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity.

The spike protein of SARS-CoV-2 has been undergoing mutations and is highly glycosylated. It is critically important to investigate the biological significance of these mutations. Here, we investigated 80 variants and 26 glycosylation site modifications for the infectivity and reactivity to a panel of neutralizing antibodies and sera from convalescent patients. D614G, along with several variants containing both D614G and another amino acid change, were significantly more infectious. Most variants with amino acid change at receptor binding domain were less infectious, but variants including A475V, L452R, V483A, and F490L became resistant to some neutralizing antibodies. Moreover, the majority of glycosylation deletions were less infectious, whereas deletion of both N331 and N343 glycosylation drastically reduced infectivity, revealing the importance of glycosylation for viral infectivity. Interestingly, N234Q was markedly resistant to neutralizing antibodies, whereas N165Q became more sensitive. These findings could be of value in the development of vaccine and therapeutic antibodies.

Experimental Direct Quantum Fidelity Learning via a Data-Driven Approach.

Fidelity estimation is an important technique for evaluating prepared quantum states in noisy quantum devices. A recent theoretical work proposed a frugal approach called neural quantum fidelity estimation (NQFE) [X. Zhang et al., Phys. Rev. Lett. 127, 130503 (2021).PRLTAO0031-900710.1103/PhysRevLett.127.130503]. While this requires a much smaller number of measurement operators than full quantum state tomography, it uses a weight-based floating measurement strategy that predetermines the top global Pauli operators that contribute the most to the fidelity and uses discrete fidelity intervals as predictions. In this Letter, we develop a measurement-fixed NQFE based on a transformer model which requires less measurement cost and can output continuous estimates of fidelity. Here we further experimentally apply the NQFE in a realistic situation using a nuclear spin quantum processor. We prepare the ground states of local Hamiltonians and arbitrary states and investigate how to estimate their fidelity with reference states, and we compare the fidelity estimation strategy with our and the original NQFE to conventional tomography. It is shown that NQFE can estimate the fidelity with comparable accuracy to the tomography approach. In the future, NQFE will become an important tool for benchmarking quantum states ahead of the advent of well-trusted fault-tolerant quantum computers.

The establishment of a multiplex fluorescent polymerase chain reaction coupled with capillary electrophoresis analysis technology enables the simultaneous detection of 16 genotypes of human papillomavirus.

BACKGROUND: The detection and accurate genotyping of human papillomavirus (HPV) infection is critical for preventing and effectively treating cervical cancer. METHODS: A multiplex fluorescent polymerase chain reaction (PCR) coupled with a capillary electrophoresis method was developed for the simultaneous detection of the 16 most prevalent HPV genotypes. Twenty-five pairs of primers were ultimately selected to ensure that both E and L regions of nine HPV genotypes, as well as the E regions of seven HPV genotypes could be accurately amplified. RESULTS: This method enables the simultaneous detection and differentiation of 16 HPV genotypes in a single closed-tube reaction, accurately distinguishing products with molecular weight differences >1 bp through capillary electrophoresis. This method demonstrated exceptional accuracy, specificity, and repeatability with a detection limit of 10 copies/µL for all 16 HPV genotypes. Furthermore, 152 cervical swab specimens were obtained to compare the disparities between this approach and Cobas 4800 HPV detection method. The concordance rate and κ value were 90.1% and 0.802, respectively, indicating a high level of agreement. The established detection method was successfully applied to cervical swab specimens for determining HPV genotypes across all levels of cervical lesions, HPV52, 56, 16, and 59 were found to be most prevalent with infection rates of 10.8%, 9.1%, 6.5%, and 6.2%, respectively. CONCLUSIONS: This study has successfully established a detection method capable of simultaneously identifying 16 HPV genotypes. This approach can be further applied to HPV vaccine research and surveillance, with the potential for broad applications.

Spatiotemporal cytoskeleton organizations determine morphogenesis of multicellular trichomes in tomato.

Plant trichomes originate from epidermal cell, forming protective structure from abiotic and biotic stresses. Different from the unicellular trichome in Arabidopsis, tomato trichomes are multicellular structure and can be classified into seven different types based on cell number, shape and the presence of glandular cells. Despite the importance of tomato trichomes in insect resistance, our understanding of the tomato trichome morphogenesis remains elusive. In this study, we quantitatively analyzed morphological traits of trichomes in tomato and further performed live imaging of cytoskeletons in stably transformed lines with actin and microtubule markers. At different developmental stages, two types of cytoskeletons exhibited distinct patterns in different trichome cells, ranging from transverse, spiral to longitudinal. This gradual transition of actin filament angle from basal to top cells could correlate with the spatial expansion mode in different cells. Further genetic screen for aberrant trichome morphology led to the discovery of a number of independent mutations in SCAR/WAVE and ARP2/3 complex, which resulted in actin bundling and distorted trichomes. Disruption of microtubules caused isotropic expansion while abolished actin filaments entirely inhibited axial extension of trichomes, indicating that microtubules and actin filaments may control distinct aspects of trichome cell expansion. Our results shed light on the roles of cytoskeletons in the formation of multicellular structure of tomato trichomes.

Magnetic metal-organic frameworks as adsorbents for the detection of azo pigments in food matrices.

Azo pigments with azo functional groups (-NN-) are commonly used in foods. Through rational design, here we report synthesis of a novel magnetic metal-organic framework (MOF-545) and the use of Fe3O4@MOF-545 for the selective separation of azo pigments from beverages. We find that Fe3O4@MOF-545 exhibits excellent adsorption/removal capacities for new coccine (NC, 459 mg g-1) and lemon yellow (LY, 476 mg g-1) individually. The results indicated that the adsorption capacities of Fe3O4@MOF-545 were 5 times higher than reported previously. The large surface area (120.4 m2/g) and the suitable pore size (1.6 nm) of Fe3O4@MOF-545 provided multiple accessible channels for azo pigment adsorption. The adsorption kinetics, stability, recovery, and reusability of Fe3O4@MOF-545 were all reported. The recoveries ranged from 92.9 to 104.5%, reflecting the capacity of MOF-545 to efficiently separate NC and LY. Fe3O4@MOF-545 is suitable for azo pigment determination and separation in food matrices.

Development of an automated, high-throughput SARS-CoV-2 neutralization assay based on a pseudotyped virus using a vesicular stomatitis virus (VSV) vector.

ABSTRACTThe global outbreak of COVID-19 has caused a severe threat to human health; therefore, simple, high-throughput neutralization assays are desirable for developing vaccines and drugs against COVID-19. In this study, a high-titre SARS-CoV-2 pseudovirus was successfully packaged by truncating the C-terminus of the SARS-CoV-2 spike protein by 21 amino acids and infecting 293 T cells that had been stably transfected with the angiotensin-converting enzyme 2 (ACE2) receptor and furin (named AF cells), to establish a simple, high-throughput, and automated 384-well plate neutralization assay. The method was optimized for cell amount, virus inoculation, incubation time, and detection time. The automated assay showed good sensitivity, accuracy, reproducibility, Z' factor, and a good correlation with the live virus neutralization assay. The high-throughput approach would make it available for the SARS-CoV-2 neutralization test in large-scale clinical trials and seroepidemiological surveys which would aid the accelerated vaccine development and evaluation.

[One-step rapid enrichment and detection of malachite green in aquaculture water based on metal-organic framework hydrogel].

Malachite green is a triphenylmethane compound, which has a good effect on disease prevention and control in the breeding of aquatic products, but it is a prohibited drug because it is detrimental to human health. Owing to the low content of target malachite green and complex components in the actual sample, simultaneously achieving good enrichment, high sensitivity, convenience, and rapidity detecting is difficult. Metal-organic framework (MOF) has a multidimensional network structure, good stability, and large specific surface area, and has broad application prospects in adsorption. However, the small particle size of MOF materials and the difficulty of recycling hinder their development. The hydrogel has a three-dimensional network structure that can encapsulate the MOF nanomaterials in the network, enhancing adsorption performance and facilitating separation from the adsorbed solution. In this study, MOF materials were prepared, and hydrogel doped with MOF nanomaterials (polyacrylamide-sodium alginate/metal-organic framework, PAAM-SA/MOF) was used to investigate the adsorption of malachite green in aquaculture water. The transmission electron microscopy was used to characterize MOF nanomaterials, scanning electron microscopy was used to examine the morphology and structure of the hydrogels before and after adsorption of malachite green, representing the successful synthesis of adsorbent materials with excellent properties. The mechanical properties of the hydrogels were investigated using a tensile testing machine, with a maximum tensile strain of up to 300%, without breaking and failing to remove when separated from the solution to be tested. The pore size of PAAM-SA/MOF hydrogel is considerably smaller than that of PAAM-SA, which is beneficial to increase the specific surface area of the adsorbent and thus improve the adsorption performance. A series of optimizations were performed on the adsorption conditions of the hydrogel adsorbent and the optimized conditions were obtained as follows: the amount of adsorbent used was 0.1 g, adsorption time was 5 h, the pH of malachite green solution was 9, the adsorption temperature was 40 ℃, and the initial concentration of malachite green solution was 100 mg/L. Under these conditions the adsorption efficiency could reach up to 97%. Furthermore, the adsorbed malachite green was eluted with organic solvents of various polarities, and the highest desorption efficiency was achieved when acetonitrile with higher polarity was used as the eluent. Simultaneously, the eluent volume was optimized, with 2 mL acetonitrile added to the malachite green-enriched hydrogel adsorbent to achieve the highest desorption efficiency of 99%. The enriched sample was separated using a Dionex Bonded Silica Products C18 column (50 mm×2.1 mm, 3 µm), and eluted with an ammonium acetate-acetonitrile solvent system. The results showed that the limit of detection (LOD, S/N=3) was 0.083 µg/L, the limit of quantification (LOQ, S/N=10) was 0.25 µg/L, and the spiked recoveries of malachite green at high, medium, and low levels were 84.8%-118.1% with the relative standard deviations less than 5.1%. The pretreatment is simplified using this approach and combines the respective advantages of MOF and hydrogel to enable one-step enrichment of malachite green in aquaculture water. The additional MOF material can exert good adsorption in the hydrogel system, which solves the problem of low recovery of traditional MOF materials caused by tiny particle size, facilitating direct extraction after adsorption, and also solves the problem of low adsorption efficiency of pure hydrogel, improving the overall adsorption efficiency and recyclability. The actual sample test shows that the new hydrogel adsorption material can be used to extract and detect trace malachite green in aquaculture water. It is a novel, fast and convenient pretreatment approach with great potential in food detection.

pH-responsive magnetic artificial melanin with tunable aggregation-induced stronger magnetism for rapid remediation of plastic fragments.

The global occurrence of plastic fragment pollutants in water resources has raised concerns about food safety, drinking water security, and long-term ecological impacts worldwide. The different chemical nature, the persistence, and the smaller size make micro-plastics accumulators for toxins that pose a potential threat to human health. Generally, the smaller the size of the plastic fragments is, the more difficult it is to remove them from the aquatic environment. Methods to remove plastics from water or other media are highly needed. Here, we develop core-shell superparamagnetic melanin nanoparticles, which can put magnetism on nano-/micro-plastics within 30 s and then rapidly remove them from water by applying an external magnetic field. The shell material (artificial nano-melanin) provides simultaneously attractive electrostatic, hydrophobic interaction, and van der Waals' forces to attract nano-/micro-plastics, which plays a key role in the rapid remediation of the plastic fragments. With this principle applied to a simple method, the average removal efficiency achieves 89.3%. We show a method for high-throughput remediation of various micro-plastics with simple materials and processes, which have the potential for rapid, green, and large-scale remediation in the future.

Immunogenicity and safety of two novel human papillomavirus 4- and 9-valent vaccines in Chinese women aged 20-45 years: A randomized, blinded, controlled with Gardasil (type 6/11/16/18), phase III non-inferiority clinical trial.

BACKGROUND: Human papillomavirus (HPV) infections were the main cause of anogenital cancers and warts. HPV 6/11/16/18 vaccines provide protection against the high-risk types of HPV responsible for 70% of cervical cancers and 90% of genital warts. This randomized, blinded, non-inferiority phase III trial was to determine whether immunogenicity and tolerability would be non-inferior among women after receiving two novel 4- and 9-valent HPV vaccines (4vHPV, HPV 6/11/16/18; 9vHPV, HPV 6/11/16/18/31/33/45/52/58) compared with those receiving Gardasil 4 (4-valent). METHODS: 1680 females between 20 and 45 years were randomized in a 2:1:1 ratio to 20-26, 27-35, or 36-45 y groups. Subjects then equally assigned to receive 4vHPV, 9vHPV or Gardasil 4 (control) vaccine at months 0, 2, and 6. End points included non-inferiority of HPV-6/11/16/18 antibodies for 4vHPV versus control, and 9vHPV versus control and safety. The immunogenicity non-inferiority was pre-defined as the lower bound of 95% confidence interval (CI) of seroconversion rate (SCR) difference > -10% and the lower bound of 95% CI of geometric mean antibody titer (GMT) ratio > 0.5. RESULTS: Among the three vaccine groups, more than 99% of the participants seroconverted to all 4 HPV types. The pre-specified statistical non-inferiority criterion for the immunogenicity hypothesis was met: all the lower bounds of 95% CIs on SCR differences exceeded -10% for each vaccine HPV type and the corresponding lower bounds of 95% CIs for GMT ratios > 0.5. Across vaccination groups, the most common vaccination reaction were injection-site adverse events (AEs), including pain, swelling, and redness. General and serious AEs were similar in the three groups. There were no deaths. CONCLUSIONS: This study demonstrated that the novel 4- and 9-valent HPV vaccination was highly immunogenic and generally well tolerated, both of which were non-inferior to Gardasil 4 in immunogenicity and safety.

Mutation of SlARC6 leads to tissue-specific defects in chloroplast development in tomato.

The proliferation and development of chloroplasts are important for maintaining the normal chloroplast population in plant tissues. Most studies have focused on chloroplast maintenance in leaves. In this study, we identified a spontaneous mutation in a tomato mutant named suffulta (su), in which the stems appeared albinic while the leaves remained normal. Map-based cloning showed that Su encodes a DnaJ heat shock protein that is a homolog of the Arabidopsis gene AtARC6, which is involved in chloroplast division. Knockdown and knockout of SlARC6 in wild-type tomato inhibit chloroplast division, indicating the conserved function of SlARC6. In su mutants, most mesophyll cells contain only one or two giant chloroplasts, while no chloroplasts are visible in 60% of stem cells, resulting in the albinic phenotype. Compared with mature tissues, the meristem of su mutants suggested that chloroplasts could partially divide in meristematic cells, suggesting the existence of an alternative mechanism in those dividing cells. Interestingly, the adaxial petiole cells of su mutants contain more chloroplasts than the abaxial cells. In addition, prolonged lighting can partially rescue the albinic phenotypes in su mutants, implying that light may promote SlACR6-independent chloroplast development. Our results verify the role of SlACR6 in chloroplast division in tomato and uncover the tissue-specific regulation of chloroplast development.

Functional comparison of SARS-CoV-2 with closely related pangolin and bat coronaviruses.

The origin and intermediate host for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is yet to be determined. Coronaviruses found to be closely related to SARS-CoV-2 include RaTG13 derived from bat and two clusters (PCoV-GD and PCoV-GX) of coronaviruses identified in pangolin. Here, we studied the infectivity and antigenicity patterns of SARS-CoV-2 and the three related coronaviruses. Compared with the other three viruses, RaTG13 showed almost no infectivity to a variety of cell lines. The two pangolin coronaviruses and SARS-CoV-2 showed similar infectious activity. However, in SARS-CoV-2-susceptible cell lines, the pangolin coronaviruses presented even higher infectivity. The striking difference between the SARS-CoV-2 and pangolin coronaviruses is that the latter can infect porcine cells, which could be partially attributed to an amino acid difference at the position of 498 of the spike protein. The infection by SARS-CoV-2 was mainly mediated by Furin and TMPRSS2, while PCoV-GD and PCoV-GX mainly depend on Cathepsin L. Extensive cross-neutralization was found between SARS-CoV-2 and PCoV-GD. However, almost no cross-neutralization was observed between PCoV-GX and SARS-CoV-2 or PCoV-GD. More attention should be paid to pangolin coronaviruses and to investigate the possibility of these coronaviruses spreading across species to become zoonoses among pigs or humans.

Quantification of SARS-CoV-2 neutralizing antibody by a pseudotyped virus-based assay.

Pseudotyped viruses are useful virological tools because of their safety and versatility. On the basis of a vesicular stomatitis virus (VSV) pseudotyped virus production system, we developed a pseudotyped virus-based neutralization assay against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in biosafety level 2 facilities. Compared with the binding antibody test, the neutralization assay could discriminate the protective agents from the antibody family. This protocol includes production and titration of the SARS-CoV-2 S pseudotyped virus and the neutralization assay based on it. Various types of samples targeting virus attachment and entry could be evaluated for their potency, including serum samples derived from animals and humans, monoclonal antibodies and fusion inhibitors (peptides or small molecules). If the pseudotyped virus stock has been prepared in advance, it will take 2 days to get the potency data for the candidate samples. Experience in handling cells is needed before implementing this protocol.

Establishment and validation of a pseudovirus neutralization assay for SARS-CoV-2.

Pseudoviruses are useful virological tools because of their safety and versatility, especially for emerging and re-emerging viruses. Due to its high pathogenicity and infectivity and the lack of effective vaccines and therapeutics, live SARS-CoV-2 has to be handled under biosafety level 3 conditions, which has hindered the development of vaccines and therapeutics. Based on a VSV pseudovirus production system, a pseudovirus-based neutralization assay has been developed for evaluating neutralizing antibodies against SARS-CoV-2 in biosafety level 2 facilities. The key parameters for this assay were optimized, including cell types, cell numbers, virus inoculum. When tested against the SARS-CoV-2 pseudovirus, SARS-CoV-2 convalescent patient sera showed high neutralizing potency, which underscore its potential as therapeutics. The limit of detection for this assay was determined as 22.1 and 43.2 for human and mouse serum samples respectively using a panel of 120 negative samples. The cutoff values were set as 30 and 50 for human and mouse serum samples, respectively. This assay showed relatively low coefficient of variations with 15.9% and 16.2% for the intra- and inter-assay analyses respectively. Taken together, we established a robust pseudovirus-based neutralization assay for SARS-CoV-2 and are glad to share pseudoviruses and related protocols with the developers of vaccines or therapeutics to fight against this lethal virus.

Spatial Expression and Functional Analysis of Casparian Strip Regulatory Genes in Endodermis Reveals the Conserved Mechanism in Tomato.

Casparian strip (CS) is an impregnation of endodermal cell wall, forming an apoplastic diffusion barrier which forces the symplastic and selective transport of nutrients across endodermis. This extracellular structure can be found in the roots of all higher plants and is thought to provide the protection of vascular tissues. In Arabidopsis, a genetic toolbox regulating the formation of Casparian strips has emerged recently. However, Arabidopsis has the stereotypical root which is much simpler than most other plant species. To understand the Casparian strip formation in a more complex root system, we examined CS regulatory pathways in tomato. Our results reveal a spatiotemporally conserved expression pattern of most essential components of CS machinery in tomato. Further functional analyses verify the role of homologous CS genes in the Casparian strip formation in tomato, indicating the functional conservation of CS regulatory cascade in tomato.

Building information modelling review with potential applications in tunnel engineering of China.

Building information modelling (BIM) can be applied to tunnel engineering to address a number of problems, including complex structure, extensive design, long construction cycle and increased security risks. To promote the development of tunnel engineering in China, this paper combines actual cases, including the Xingu mountain tunnel and the Shigu Mountain tunnel, to systematically analyse BIM applications in tunnel engineering in China. The results indicate that BIM technology in tunnel engineering is currently mainly applied during the design stage rather than during construction and operation stages. The application of BIM technology in tunnel engineering covers many problems, such as a lack of standards, incompatibility of different software, disorganized management, complex combination with GIS (Geographic Information System), low utilization rate and poor awareness. In this study, through summary of related research results and engineering cases, suggestions are introduced and an outlook for the BIM application in tunnel engineering in China is presented, which provides guidance for design optimization, construction standards and later operation maintenance.