Background Coronavirus disease 2019 (COVID-19) has become a public health emergency. The widely used reverse transcription–polymerase chain reaction (RT-PCR) method has limitations for clinical diagnosis and treatment. Methods A total of 323 samples from 76 COVID-19–confirmed patients were analyzed by droplet digital PCR (ddPCR) and RT-PCR based 2 target genes (ORF1ab and N). Nasal swabs, throat swabs, sputum, blood, and urine were collected. Clinical and imaging data were obtained for clinical staging. Results In 95 samples that tested positive by both methods, the cycle threshold (Ct) of RT-PCR was highly correlated with the copy number of ddPCR (ORF1ab gene, R2 = 0.83; N gene, R2 = 0.87). Four (4/161) negative and 41 (41/67) single-gene positive samples tested by RT-PCR were positive according to ddPCR with viral loads ranging from 11.1 to 123.2 copies/test. The viral load of respiratory samples was then compared and the average viral load in sputum (17 429 ± 6920 copies/test) was found to be significantly higher than in throat swabs (2552 ± 1965 copies/test, P < .001) and nasal swabs (651 ± 501 copies/test, P < .001). Furthermore, the viral loads in the early and progressive stages were significantly higher than that in the recovery stage (46 800 ± 17 272 vs 1252 ± 1027, P < .001) analyzed by sputum samples. Conclusions Quantitative monitoring of viral load in lower respiratory tract samples helps to evaluate disease progression, especially in cases of low viral load.

Acid-sensing ion channels (ASICs) have long been considered as extracellular proton (H(+))-gated cation channels, and peripheral ASIC3 channels seem to be a natural sensor of acidic pain. Here, we report the identification of a nonproton sensor on ASIC3. We show first that 2-guanidine-4-methylquinazoline (GMQ) causes persistent ASIC3 channel activation at the normal pH. Using GMQ as a probe and combining mutagenesis and covalent modification analysis, we then uncovered a ligand sensor lined by residues around E423 and E79 of the extracellular "palm" domain of the ASIC3 channel that is crucial for activation by nonproton activators. Furthermore, we show that GMQ activates sensory neurons and causes pain-related behaviors in an ASIC3-dependent manner, indicating the functional significance of ASIC activation by nonproton ligands. Thus, natural ligands beyond protons may activate ASICs under physiological and pathological conditions through the nonproton ligand sensor, serving for channel activation independent of abrupt and marked acidosis.

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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 COVID-19-infected individuals, followed by the Brazilian variant P.1 and the UK 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 structural analysis of B.1.351 triple mutant (417N-484K-501Y) RBD complexed with 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 receptor for entry. Our results demonstrate major antigenic shifts and potential broadening of the host range for B.1.351 and P.1 variants, which pose serious challenges to our current antibody therapies and vaccine protection.

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ATP-binding cassette (ABC) transporters, composed of importers and exporters, form one of the biggest protein superfamilies that transport a variety of substrates across the membrane, powered by ATP hydrolysis. Most ABC transporters are composed of two transmembrane domains and two cytoplasmic nucleotide-binding domains. Also, importers from prokaryotes usually have extra solute-binding proteins in the periplasm that are responsible for the binding of substrates. Structures of importers have been reported that suggested a two-state model for the transport mechanism. Energy-coupling factor (ECF) transporters belong to a new class of ATP-binding cassette importers. Each ECF transporter comprises an energy-coupling module consisting of a transmembrane T protein (EcfT), two nucleotide-binding proteins (EcfA and EcfA'), and another transmembrane substrate-specific binding S protein (EcfS). Despite the similarities with ABC transporters, ECF transporters have different organizational and functional properties. The lack of solute-binding proteins in ECF transporters differentiates them clearly from the canonical ABC importers. Previously reported structures of the EcfS proteins RibU and ThiT clearly demonstrated the binding site of substrate riboflavin and thiamine, respectively. However, the organization of the four different components and the transport mechanism of ECF transporters remain unknown. Here we present the structure of an intact folate ECF transporter from Lactobacillus brevis at a resolution of 3 Å. This structure was captured in an inward-facing, nucleotide-free conformation with no bound substrate. The folate-binding protein FolT is nearly parallel to the membrane and is bound almost entirely by EcfT, which adopts an L shape and connects to EcfA and EcfA' through two coupling helices. Two conserved XRX motifs from the coupling helices of EcfT have a vital role in energy coupling by docking into EcfA-EcfA'. We propose a transport model that involves a substantial conformational change of FolT.

This paper reconstructs the evolutionary history of the Pearl River delta over the last 9000 years and investigates land—sea interaction in a large deltaic complex which formed under the influence of Asian monsoon climate. Specifically, this research examines the delta evolution in the context of three driving mechanisms: (1) rising sea level that influences the available accommodation space, (2) fluvial discharge as influenced by monsoon climate and (3) human activities that alter sedimentation within the deltaic system. Results reveal that the formation of deltaic sequences was initiated as a consequence of rapid sea-level rise between 9000 and 7000 cal. yr BP. The rate of sea-level rise slowed down markedly around 7000 cal. yr BP and sedimentation switched from transgressive to regressive. Initially, both the progradation of the delta plains near the apex and aggradation of delta front sedimentation in the central and lower parts of the receiving basin were fast owing to strong monsoonal-driven runoff. The progradation rate gradually slowed down between 6800 and 2000 cal. yr BP as monsoonal-driven runoff weakened. Rapid shoreline advances during the last 2000 years were the result of significantly increased human activities, a practice that trapped sediments in the encircled tidal flats along the front of delta plains. The evolutionary history of the Pearl River delta demonstrates the interplay between the three driving mechanisms.

Abstract. We assess the relative contributions of different sources of organic matter, marine vs. terrestrial, to oxygen consumption in an emerging hypoxic zone in the lower Pearl River Estuary (PRE), a large eutrophic estuary located in Southern China. Our cruise, conducted in July 2014, consisted of two legs before and after the passing of Typhoon Rammasun, which completely de-stratified the water column. The stratification recovered rapidly, within 1 day after the typhoon. We observed algal blooms in the upper layer of the water column and hypoxia underneath in bottom water during both legs. Repeat sampling at the initial hypoxic station showed severe oxygen depletion down to 30 µmol kg −1 before the typhoon and a clear drawdown of dissolved oxygen after the typhoon. Based on a three endmember mixing model and the mass balance of dissolved inorganic carbon and its isotopic composition, the δ 13 C of organic carbon remineralized in the hypoxic zone was −23.2 ± 1.1 ‰. We estimated that 65 ± 16 % of the oxygen-consuming organic matter was derived from marine sources, and the rest (35 ± 16 %) was derived from the continent. In contrast to a recently studied hypoxic zone in the East China Sea off the Changjiang Estuary where marine organic matter dominated oxygen consumption, here terrestrial organic matter significantly contributed to the formation and maintenance of hypoxia. How varying amounts of these organic matter sources drive oxygen consumption has important implications for better understanding hypoxia and its mitigation in bottom waters.