Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD.

Neutralizing antibodies (NAbs) hold great promise for clinical interventions against SARS-CoV-2 variants of concern (VOCs). Understanding NAb epitope-dependent antiviral mechanisms is crucial for developing vaccines and therapeutics against VOCs. Here we characterized two potent NAbs, EH3 and EH8, isolated from an unvaccinated pediatric patient with exceptional plasma neutralization activity. EH3 and EH8 cross-neutralize the early VOCs and mediate strong Fc-dependent effector activity in vitro. Structural analyses of EH3 and EH8 in complex with the receptor-binding domain (RBD) revealed the molecular determinants of the epitope-driven protection and VOC evasion. While EH3 represents the prevalent IGHV3-53 NAb whose epitope substantially overlaps with the ACE2 binding site, EH8 recognizes a narrow epitope exposed in both RBD-up and RBD-down conformations. When tested in vivo, a single-dose prophylactic administration of EH3 fully protected stringent K18-hACE2 mice from lethal challenge with Delta VOC. Our study demonstrates that protective NAbs responses converge in pediatric and adult SARS-CoV-2 patients.

Development of matrix certified reference material for accurate determination of docosahexaenoic acid in milk powder.

A novel matrix certified reference material (CRM) of docosahexaenoic acid in milk powder [GBW (E) 100641] was first developed. The CRM candidates was prepared by adding appropriate levels of docosahexaenoic acid to cow's milk, then powder sprayed, lyophilized, mixed, dispensed and sterilized. An optimized acetylchloride-methanol method was proposed and used for the characterization. The CRM characterization was carried out in six laboratories in accordance with ISO Guide 35 requirements. The certified value of CRM was 0.69 mg/g with an uncertainty of 0.08 mg/g (k = 2). The CRM was sufficiently homogeneous between and within bottles and stable up to 6 month at -20℃ and 7 days below 50 â„ƒ. The uncertainty was evaluated by combing the contributions from characterization, homogeneity and stability. Thus, the CRM can be used for quality control and method validation to ensure the accurate and reliable measurements of docosahexaenoic acid in milk for quality monitoring.

An approach to assessing ecological quality status due to microalgae bloom using biofilm-dwelling protozoa based on biological trait analysis.

Functional diversity/distinctness measure based trait has been proved to be a robust indicator to summarize the description of community structures and to assess water quality in different types of aquatic environment. In this study, for identifying the shielding effect of microalgae against protozoan grazing, a nine-day survey was conducted by exposing protozoan communities to a series of concentration gradients (100 (control), 104, 105, 106 and 107 cells ml-1) of two microalgae, respectively. Our results showed clear resistance of two test microalgae against protozoan grazing in five treatments. The functional distinctness measures commonly represented a decreasing trend along the gradient of concentrations of both microalgae. Ellipse tests based on the paired functional distinctness indices revealed that community functioning represented an uptrend departure from the expected pattern with the concentrations of both microalgae increase. Therefore, we suggest that the functional distinctness measures might be a reliable approach to detect the ecological effect of microalgae against protozoan grazing.

Seasonal variability in biological trait pattern of biofilm-dwelling protozoa in colonization surveys for marine bioassessment.

Biological trait analysis (BTA) has been proved to be a powerful tool to evaluate marine water quality. The species trait distributions of biofilm-dwelling protozoa were studied in a coastal region of the Yellow Sea, northern China, during a four-season cycle. The BTA demonstrated that: (1) the protozoa showed a significant seasonal variability in biological trait pattern during the colonization process across four seasons; (2) the colonization dynamics in species trait distribution followed different temporal models; (3) the functional dynamics in spring and summer were significantly different from those in autumn and winter (P < 0.05); and (4) functional diversity showed lower values in spring and summer than in autumn and winter. These findings suggest that BTA is subject to a high seasonal variability during colonization surveys when protozoa are used as bioindicators of marine water quality.

Seasonal variation in biological trait distribution of periphytic protozoa in coastal ecosystem: A baseline study for marine bioassessment.

To reveal the seasonal variability in biological trait distribution for monitoring surveys based on periphytic protozoa, a baseline survey was carried out in a coastal region of Yellow Sea, northern China. A total of 40 slide samples were collected in a four season cycle after an exposure time period of 14 days. The results demonstrated that: (1) the community-weighted means (CWM) of algivores with large and medium sizes were high in spring and summer, while bacterivores with small size were high in autumn and winter; (2) there was a significant seasonal variation in the protozoan community functions, especially from spring/summer to autumn and winter; and (3) functional diversity indices generally peaked in spring or summer. Thus, there was a significant seasonal variation in protozoan community functions and this approach may be used to determine an optimal sampling strategy for monitoring programs in marine ecosystems.

[Use of Iron-modified Calcite as an Active Capping Material to Control Phosphorus Release from Sediments in Surface Water Bodies].

The use of calcite (CA) as an active capping material has high potential for controlling the release of phosphorus (P) from sediments, but its efficiency still needs to be enhanced. To address this issue, an iron-modified CA (Fe-CA) was prepared, the removal performance of phosphate from aqueous solution by Fe-CA was studied, and the efficiency of the use of Fe-CA as an active capping material to prevent the liberation of P from sediments was investigated. The results showed that Fe-CA exhibited much higher phosphate removal ability than CA. The phosphate removal efficiency of Fe-CA increased with an increase in the Fe-CA dosage. Increasing the initial phosphate concentration gave rise to an increase in the amount of phosphate removed by Fe-CA, and the maximum amount of phosphate removed by Fe-CZ reached 3.09 mg·g-1. Sediment capping with Fe-CA could effectively control the release of soluble reactive P (SRP) from the sediment into the overlying water, leading to a very low concentration of SRP in the overlying water. Additionally, the Fe-CA capping also resulted in the transformation of a small amount of redox-sensitive P (BD-P) and metal-oxide-bound P (NaOH-rP) in sediments to residual P (Res-P), leading to a slight increase in the stability of P in the sediment. The overwhelming majority (90.8%) of P bound by the Fe-CA capping layer existed in the form of NaOH-rP, calcium-bound P (HCl-P), and Res-P, which are relatively very stable. Furthermore, the percentage of bioavailable P (BAP) as a proportion of total extractable P in the P-bound Fe-CA capping layer was very low, and the bound P was re-released with difficulty into the water column for algae growth. Compared to CA capping, the efficiency for the control of sedimentary P release into the overlying water by Fe-CA capping was much higher, and the stability of P bound by the Fe-CA capping layer was also higher. The results of this work indicate that Fe-CA is a very promising active capping material for the interception of the release of P from sediments into the overlying water.

[Regulating Effect and Mechanism of Calcite/Chlorapatite Mixture Addition on Transformation and Transport of Phosphorus in Sediments].

Understanding the effect of calcite and chlorapatite mixture (CA/ClAP) addition on the mobilization of phosphorus (P) in sediments is crucial to the application of CA/ClAP as an amendment material to control the release of P from sediments. To address this issue, batch experiments were conducted to investigate the removal performance of phosphate by CA/ClAP, and sediment incubation experiments were carried out to study the effect of CA/ClAP addition on the mobilization of P in sediments. The results showed that the removal ability of phosphate by CA/ClAP was much higher than those by calcite and chlorapatite, and the kinetics data of phosphate removal by CA/ClAP followed a pseudo-second-order kinetics model. Increasing calcite and chlorapatite dosages would be favorable for the removal of phosphate by CA/ClAP, and coexisting Ca2+ enhanced the phosphate removal. CA/ClAP addition not only reduced the concentration of soluble reactive P (SRP) in the overlying water, but also decreased the concentration of SRP in the pore water. The addition of CA/ClAP in sediments caused an increase in the content of P in the sediments, but the increased P mainly existed in the form of calcium-bound P (HCl-P), which was difficult to be re-released into the water column under anoxic and common pH (5-9) conditions. The reduction of SRP in the pore water after the addition of CA/ClAP played an important role in the prevention of sedimentary P liberation into the overlying water by the CA/ClAP amendment. The results of this work indicate that CA/ClAP can be used as an amendment material for interception of the release of P from sediments into overlying water.

Colonization dynamics of protozoan communities in marine bioassessment surveys using two modified sampling systems.

Colonization dynamics of protozoan communities were investigated at a depth of 1 m in the coastal waters of the Yellow Sea, northern China from May to June 2019, using modified glass slide (mGS) and modified polyurethane foam unit (mPFU) systems. The colonization process and growth curves of protozoa were well fitted to the MacArthur-Wilson and logistic models in both systems, respectively. However, they showed significant differences in both colonization dynamics and biodiversity/functional parameters between the mGS and mPFU systems. The H' (species diversity), the G (colonization rate), and Amax (maximum abundance) were higher, while the value of T90% (the time for reaching 90% equilibrium species number) was lower in the mGS system than those in the mPFU system. Multivariate analyses demonstrated that protozoa showed different models of colonization dynamics in both systems. The results suggest that the mGS system might be more effective than the mPFU system in marine bioassessment surveys.

[Adsorption of Phosphate on Mg/Fe Layered Double Hydroxides (Mg/Fe-LDH) and Use of Mg/Fe-LDH as an Amendment for Controlling Phosphorus Release from Sediments].

We determine the efficiency and mechanism of Mg/Fe layered double hydroxides (Mg/Fe-LDH) addition for the control of phosphorus (P) release from sediments by studying the adsorption behavior and mechanism of phosphate from an aqueous solution on Mg/Fe-LDH. The impact of Mg/Fe-LDH addition on the mobilization of P in sediments as well as the adsorptive removal of phosphate by sediments is investigated, and the stabilization of P bound by Mg/Fe-LDH is also evaluated. Results showed that the kinetics data of phosphate adsorption onto Mg/Fe-LDH fitted better with the Elovich kinetics model than with the pseudo-first-order and pseudo-second-order kinetics models, and that the Freundlich and Dubinin-Radushkevich models were more suitable for describing the adsorption isotherm behavior of phosphate on Mg/Fe-LDH than the Langmuir model. Phosphate adsorption possessed a wide effective pH range of 4-10. Coexisting Ca2+ and Mg2+ enhanced phosphate adsorption onto Mg/Fe-LDH, while coexisting Na+, K+, and Cl- had negligible impacts on the phosphate adsorption. The presence of SO42- and HCO3- in aqueous solution inhibited the adsorption of phosphate on Mg/Fe-LDH. The phosphate adsorption mechanisms were deduced to be anion exchange, electrostatic attraction, ligand exchange and inner-sphere complex formation. The addition of Mg/Fe-LDH into sediments not only greatly reduced the concentration of reactive soluble P (SRP) in the overlying water, but also significantly decreased the level of SRP in the pore water. In addition, Mg/Fe-LDH addition also increased the adsorption capacity for the sediments, and the phosphate adsorption ability for the Mg/Fe-LDH-amended sediments increased with increased amendment dosage. Almost half of the phosphate bound by Mg/Fe-LDH existed in the form of relatively stable P, i.e., metal oxide-bound P (NaOH-rP), which was difficult to release back into the water column under normal pH and anoxic conditions. Nearly half of the phosphate bound by Mg/Fe-LDH existed in the form of easily released P, i.e., NH4Cl extractable P (NH4Cl-P) and redox-sensitive P (BD-P), which had a high risk of re-releasing into the water column. We conclude that it is very necessary for Mg/Fe-LDH to be recycled from the sediments after the application of Mg/Fe-LDH as an amendment to control sedimentary P liberation.

Molecularly imprinted electrochemical sensor based on polypyrrole/dopamine@graphene incorporated with surface molecularly imprinted polymers thin film for recognition of olaquindox.

In this paper, an advanced molecularly imprinted electrochemical sensor (MIECS) based on electropolymerized olaquindox (OLA) surface molecularly imprinted polymer thin film on a modified glassy carbon electrode (GCE) was developed for the detection of OLA. It was fabricated by coating dopamine@graphene (DGr) on GCE, then electropolymerizing pyrrole (Py) and molecularly imprinted polymers (MIPs). Graphene (Gr) was introduced for improving conductivity and sensitivity. Dopamine (DA) was used for dispersion and adhesion of Gr. Polypyrrole (PPy) could fix DGr and enhance the current response evidently. The established sensor could selectively recognize OLA but not the analogs of OLA. Some essential parameters controlling the performance of the developed sensor were investigated and optimized. Under optimal conditions, the linear relationship between the current intensity and OLA concentration was obtained from 50 nmol L-1 to 500 nmol L-1 with a limit of detection (LOD) of 7.5 nmol L-1. Analytical results of OLA based on the developed MIECS for fish and feedstuffs showed a good agreement with the results based on high performance liquid chromatography (HPLC).

In-situ graft-crosslinked gold nanoparticles with high-density surface defects and coated with a polytaurine membrane for the voltammetric determination of dopamine.

Well-dispersed and graft-crosslinked gold nanoparticles (AuNPs) were synthesized by the reduction of tetrachloroaurate with hydrazine at room temperature. The AuNPs possess a high density of surface defects which is due to grafting of n-octanoic acid to polyvinylpyrrolidone. The physical and chemical properties of the resulting AuNPs were characterized by UV-vis, XRD, TEM/HRTEM, SAED, and XPS, respectively. The modified AuNPs were placed on a glassy carbon electrode (GCE) in an electropolymerized taurine layer to obtain a sensitive, selective, stable and rapid electrochemical dopamine sensor. The peak current, typically measured at 0.17 V (vs. SCE), increases linearly in the 1.0 to 120 µM dopamine concentration range, and the limit of detection (at S/N = 3) is 0.16 µM with a sensitivity of 2.94 µA·µM-1·cm-2. The sensor was successfully applied to the determination of dopamine in injections and spiked serum samples. The recoveries from spiked serum samples range from 97.5 to 102.4%, with RSDs ranging between 2.8 and 3.4%. Graphical abstract Schematic representation of a glassy carbon electrode modified with in-situ graft-crosslinked gold nanoparticles combined with an electropolymerized polytaurine membrane. The sensor exhibits excellent features towards dopamine determination.

A molecularly imprinted electrochemiluminescence sensor based on upconversion nanoparticles enhanced by electrodeposited rGO for selective and ultrasensitive detection of clenbuterol.

A simple, efficient and sensitive molecularly imprinted electrochemiluminescence sensor (MIECLS) based on reduced graphene oxide (rGO) and upconversion nanoparticles (UCNPs) was developed for determination of clenbuterol (CLB). In this study, rGO generated by electrodeposition of graphene oxide not only acted as carrier for immobilizing UCNPs, but also had a significant impact in boosting electrochemiluminescence (ECL) response of UCNPs thanks to its high conductivity, superior electron transport rate and large specific surface area. UCNPs as an advanced ECL emitter possessed wonderful ECL performance. Furthermore, the introduction of molecularly imprinted polymers (MIP) endowed the ECL sensor a new character of specifically identifying analyte CLB. Under the optimal experimental conditions, the ECL signal was proportional to the logarithm of CLB concentration in the range of 10nM to 100µM with a low detection limit of 6.3nM. The proposed MIECLS combining the advantages of UCNPs-ECL and MIP exhibited good sensitivity, desirable selectivity and favorable stability, indicating enormous potential in the future of food safety detection.

Molecular analysis of human solute carrier SLC26 anion transporter disease-causing mutations using 3-dimensional homology modeling.

The availability of the first crystal structure of a bacterial member (SLC26Dg) of the solute carrier SLC26 family of anion transporters has allowed us to create 3-dimensional models of all 10 human members (SLC26A1-A11, A10 being a pseudogene) of these membrane proteins using the Phyre2 bioinformatic tool. The homology modeling predicted that the SLC26 human proteins, like the SLC26Dg template, all consist of 14 transmembrane segments (TM) arranged in a 7+7 inverted topology with the amino-termini of two half-helices (TM3 and 10) facing each other in the centre of the protein to create the anion-binding site, linked to a C-terminal cytosolic sulfate transporter anti-sigma factor antagonist (STAS) domain. A plethora of human diseases are associated with mutations in the genes encoding human SLC26 transporters, including chondrodysplasias with varying severity in SLC26A2 (~50 mutations, 27 point mutations), congenital chloride-losing diarrhea in SLC26A3 (~70 mutations, 31 point mutations) and Pendred Syndrome or deafness autosomal recessive type 4 in SLC26A4 (~500 mutations, 203 point mutations). We have localized all of these point mutations in the 3-dimensional structures of the respective SLC26A2, A3 and A4 proteins and systematically analyzed their effect on protein structure. While most disease-causing mutations may cause folding defects resulting in impaired trafficking of these membrane glycoproteins from the endoplasmic reticulum to the cell surface - as demonstrated in a number of functional expression studies - the modeling also revealed that a number of pathogenic mutations are localized to the anion-binding site, which may directly affect transport function.

Structural biology of solute carrier (SLC) membrane transport proteins.

The human solute carriers (SLCs) comprise over 400 different transporters, organized into 65 families ( http://slc.bioparadigms.org/ ) based on their sequence homology and transport function. SLCs are responsible for transporting extraordinarily diverse solutes across biological membranes, including inorganic ions, amino acids, lipids, sugars, neurotransmitters and drugs. Most of these membrane proteins function as coupled symporters (co-transporters) utilizing downhill ion (H+ or Na+) gradients as the driving force for the transport of substrate against its concentration gradient into cells. Other members work as antiporters (exchangers) that typically contain a single substrate-binding site with an alternating access mode of transport, while a few members exhibit channel-like properties. Dysfunction of SLCs is correlated with numerous human diseases and therefore they are potential therapeutic drug targets. In this review, we identified all of the SLC crystal structures that have been determined, most of which are from prokaryotic species. We further sorted all the SLC structures into four main groups with different protein folds and further discuss the well-characterized MFS (major facilitator superfamily) and LeuT (leucine transporter) folds. This review provides a systematic analysis of the structure, molecular basis of substrate recognition and mechanism of action in different SLC family members.

Effect of SLC26 anion transporter disease-causing mutations on the stability of the homologous STAS domain of E. coli DauA (YchM).

The human solute carrier 26 (SLC26) family of anion transporters consists of ten members that are found in various organs in the body including the stomach, intestine, kidney, thyroid and ear where they transport anions including bicarbonate, chloride and sulfate, typically in an exchange mode. Mutations in these genes cause a plethora of diseases such as diastrophic dysplasia affecting sulfate uptake into chondrocytes (SLC26A2), congenital chloride-losing diarrhoea (SLC26A3) affecting chloride secretion in the intestine and Pendred's syndrome (SLC26A4) resulting in hearing loss. To understand how these mutations affect the structures of the SLC26 membrane proteins and their ability to function properly, 12 human disease-causing mutants from SLC26A2, SLC26A3 and SLC26A4 were introduced into the equivalent sites of the sulfate transporter anti-sigma factor antagonist (STAS) domain of a bacterial homologue SLC26 protein DauA (YchM). Biophysical analyses including size-exclusion chromatography, circular dichroism (CD), differential scanning fluorimetry (DSF) and tryptophan fluorescence revealed that most mutations caused protein instability and aggregation. The mutation A463K, equivalent to N558K in human SLC26A4, which is located within α-helix 1 of the DauA STAS domain, stabilized the protein. CD measurements showed that most disease-related mutants had a mildly reduced helix content, but were more sensitive to thermal denaturation. Fluorescence spectroscopy showed that the mutants had more open structures and were more readily denatured by urea, whereas DSF indicated more labile folds. Overall, we conclude that the disease-associated mutations destabilized the STAS domain resulting in an increased propensity to misfold and aggregate.

A Call for Systematic Research on Solute Carriers.

Solute carrier (SLC) membrane transport proteins control essential physiological functions, including nutrient uptake, ion transport, and waste removal. SLCs interact with several important drugs, and a quarter of the more than 400 SLC genes are associated with human diseases. Yet, compared to other gene families of similar stature, SLCs are relatively understudied. The time is right for a systematic attack on SLC structure, specificity, and function, taking into account kinship and expression, as well as the dependencies that arise from the common metabolic space.

Highly sensitive graphene-Pt nanocomposites amperometric biosensor and its application in living cell H2O2 detection.

A sensitive hydrogen peroxide (H2O2) sensor was constructed based on graphene-Pt (RGO-Pt) nanocomposites and used to measure the release of H2O2 from living cells. The graphene and Pt nanoparticles (Pt NPs) were modified on glassy carbon electrode (GCE) by the physical adsorption and electrodeposition of K2PtCl6 solution, respectively. Through characterization by scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS), it was observed that the electrodeposited Pt NPs were densely covered and well distributed on the entire graphene surface. Electrochemical study demonstrates that the RGO-Pt nanocomposites modified glassy carbon electrode exhibited a high peak current and low overpotential toward the reduction of H2O2. The relevant detection limit of H2O2 is ∼0.2 µM with a wide linear range from 0.5 µM to 3.475 mM, displaying a much higher sensitivity (459 ± 3 mA M(-1) cm(-2), n = 5) than that of Pt nanoparticles or graphene modified electrode. This novel biosensor can measure the H2O2 release from living cells because of its low detection limit, wide linear range, and higher sensitivity.

Tip-to-tip interaction in the crystal packing of PACSIN 2 is important in regulating tubulation activity.

The F-BAR domain containing proteins PACSINs are cytoplasmic phosphoproteins involved in various membrane deformations, such as actin reorganization, vesicle transport and microtubule movement. Our previous study shows that all PACSINs are composed of crescent shaped dimers with two wedge loops, and the wedge loop-mediated lateral interaction between neighboring dimers is important for protein packing and tubulation activity. Here, from the crystal packing of PACSIN 2, we observed a tight tip-to-tip interaction, in addition to the wedge loop-mediated lateral interaction. With this tip-to-tip interaction, the whole packing of PACSIN 2 shows a spiral-like assembly with a central hole from the top view. Elimination of this tip-to-tip connection inhibited the tubulation function of PACSIN 2, indicating that tip-to-tip interaction plays an important role in membrane deformation activity. Together with our previous study, we proposed a packing model for the assembly of PACSIN 2 on membrane, where the proteins are connected by tip-to-tip and wedge loop-mediated lateral interactions on the surface of membrane to generate various diameter tubules.

Rigidity of wedge loop in PACSIN 3 protein is a key factor in dictating diameters of tubules.

BAR (Bin/amphiphysin/Rvs) domain-containing proteins participate in cellular membrane remodeling. The F-BAR proteins normally generate low curvature tubules. However, in the PACSIN subfamily, the F-BAR domain from PACSIN 1 and 2 can induce both high and low curvature tubules. We found that unlike PACSIN 1 and 2, PACSIN 3 could only induce low curvature tubules. To elucidate the key factors that dictate the tubule curvature, crystal structures of all three PACSIN F-BAR domains were determined. A novel type of lateral interaction mediated by a wedge loop is observed between the F-BAR neighboring dimers. Comparisons of the structures of PACSIN 3 with PACSIN 1 and 2 indicate that the wedge loop of PACSIN 3 is more rigid, which influences the lateral interactions between assembled dimers. We further identified the residues that affect the rigidity of the loop by mutagenesis and determined the structures of two PACSIN 3 wedge loop mutants. Our results suggest that the rigidity-mediated conformations of the wedge loop correlate well with the various crystal packing modes and membrane tubulations. Thus, the rigidity of the wedge loop is a key factor in dictating tubule diameters.

Inkjet printing of nanoporous gold electrode arrays on cellulose membranes for high-sensitive paper-like electrochemical oxygen sensors using ionic liquid electrolytes.

A simple approach to the mass production of nanoporous gold electrode arrays on cellulose membranes for electrochemical sensing of oxygen using ionic liquid (IL) electrolytes was established. The approach, combining the inkjet printing of gold nanoparticle (GNP) patterns with the self-catalytic growth of these patterns into conducting layers, can fabricate hundreds of self-designed gold arrays on cellulose membranes within several hours using an inexpensive inkjet printer. The resulting paper-based gold electrode arrays (PGEAs) had several unique properties as thin-film sensor platforms, including good conductivity, excellent flexibility, high integration, and low cost. The porous nature of PGEAs also allowed the addition of electrolytes from the back cellulose membrane side and controllably produced large three-phase electrolyte/electrode/gas interfaces at the front electrode side. A novel paper-based solid-state electrochemical oxygen (O(2)) sensor was therefore developed using an IL electrolyte, 1-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF(6)). The sensor looked like a piece of paper but possessed high sensitivity for O(2) in a linear range from 0.054 to 0.177 v/v %, along with a low detection limit of 0.0075% and a short response time of less than 10 s, foreseeing its promising applications in developing cost-effective and environment-friendly paper-based electrochemical gas sensors.