Since its outbreak in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread with high transmission efficiency across the world, putting health care as well as economic systems under pressure. During the course of the pandemic, the originally identified SARS-CoV-2 variant has been multiple times replaced by various mutant versions, which showed enhanced fitness due to increased infection and transmission rates. In order to find an explanation for why SARS-CoV-2 and its emerging mutated versions showed enhanced transmission efficiency compared with SARS-CoV (2002), an enhanced binding affinity of the spike protein to human angiotensin converting enzyme 2 (hACE2) has been proposed by crystal structure analysis and was identified in cell culture models. Kinetic analysis of the interaction of various spike protein constructs with hACE2 was considered to be best described by a Langmuir-based 11 stoichiometric interaction. However, we demonstrate in this report that the SARS-CoV-2 spike proteon kinetic. However, we demonstrate here that there is a secondary state binding step that may be essential for novel VOCs in order to further increase their infectivity. These findings are important for quantitatively understanding the infection process of SARS-CoV-2 and characterization of emerging SARS-CoV-2 variants of spike proteins. Thus, they provide a tool for predicting the potential infectivity of the respective viral variants based on secondary rate transition and secondary complex stability.Effective strategies to eliminate human immunodeficiency virus type 1 (HIV-1) reservoirs are likely to require more thorough characterizations of proviruses that persist on antiretroviral therapy (ART). The rarity of infected CD4+ T-cells and related technical challenges have limited the characterization of integrated proviruses. Current approaches using next-generation sequencing can be inefficient and limited sequencing depth can make it difficult to link proviral sequences to their respective integration sites. Here, we report on an efficient method by which HIV-1 proviruses and their sites of integration are amplified and sequenced. Across five HIV-1-positive individuals on clinically effective ART, a median of 41.2% (n = 88 of 209) of amplifications yielded near-full-length proviruses and their 5′-host-virus junctions containing a median of 430 bp (range, 18 to 1,363 bp) of flanking host sequence. Unexpectedly, 29.5% (n = 26 of 88) of the sequenced proviruses had structural asymmetries between the 5′ ands and genetic structures, and the need for efficient amplification and sequencing of the provirus and its integration site. Here, we describe a novel, integrated, two-step method (individual proviral sequencing assay [IPSA]) that amplifies the host-virus junction and the full-length provirus except for the last 69 bp of the 3′ long terminal repeat (LTR). Using this method, we identified the integration sites of proviruses, including those that are sequence intact and replication competent or defective. Importantly, this new method identified previously unreported asymmetries between LTRs that have implications for how proviruses are detected and quantified. Fludarabine solubility dmso The IPSA method reported is unaffected by LTR asymmetries, permitting a more accurate and comprehensive characterization of the proviral landscape.Recombinant forms of adeno-associated virus (rAAV) are vectors of choice in the development of treatments for a number of genetic dispositions. Greater understanding of AAV’s molecular virology is needed to underpin needed improvements in efficiency and specificity. Recent advances have included identification of a near-universal entry receptor, AAVR, and structures detected by cryo-electron microscopy (EM) single particle analysis (SPA) that revealed, at high resolution, only the domains of AAVR most tightly bound to AAV. Here, cryogenic electron tomography (cryo-ET) is applied to reveal the neighboring domains of the flexible receptor. For AAV5, where the PKD1 domain is bound strongly, PKD2 is seen in three configurations extending away from the virus. AAV2 binds tightly to the PKD2 domain at a distinct site, and cryo-ET now reveals four configurations of PKD1, all different from that seen in AAV5. The AAV2 receptor complex also shows unmodeled features on the inner surface that appear to be an equilibrium despite measurable dependence of AAV2 transduction on both domains.Microbial life in glacier-fed streams (GFSs) is dominated by benthic biofilms which fulfill critical ecosystem processes. However, it remains unclear how the bacterial communities of these biofilms assemble in stream ecosystems characterized by rapid turnover of benthic habitats and high suspended sediment loads. Using16S rRNA gene amplicon sequence data collected from 54 GFSs across the Himalayas, European Alps, and Scandinavian Mountains, we found that benthic biofilms harbor bacterial communities that are distinct from the bacterial assemblages suspended in the streamwater. Our data showed a decrease in species richness in the benthic biofilms compared to the bacterial cells putatively free-living in the water. The benthic biofilms also differed from the suspended water fractions in terms of community composition. Differential abundance analyses highlighted bacterial families that were specific to the benthic biofilms and the suspended assemblages. Notably, source-sink models suggested that the benthic biolection is the underlying process to this differentiation. This is unexpected given that bacterial cells that are freely living or attached to the abundant sediment particles suspended in the water continuously mix with the benthic biofilms. The latter colonize loose sediments that are subject to high turnover owing to the forces of the water flow. Our research unravels the existence of a microbiome specific to benthic biofilms in glacier-fed streams, now under major threats due to global warming.Dehalococcoides mccartyi strains harboring vinyl chloride (VC) reductive dehalogenase (RDase) genes are keystone bacteria for VC detoxification in groundwater aquifers, and bioremediation monitoring regimens focus on D. mccartyi biomarkers. We isolated a novel anaerobic bacterium, „Candidatus Dehalogenimonas etheniformans“ strain GP, capable of respiratory dechlorination of VC to ethene. This bacterium couples formate and hydrogen (H2) oxidation to the reduction of trichloro-ethene (TCE), all dichloroethene (DCE) isomers, and VC with acetate as the carbon source. Cultures that received formate and H2 consumed the two electron donors concomitantly at similar rates. A 16S rRNA gene-targeted quantitative PCR (qPCR) assay measured growth yields of (1.2 ± 0.2) × 108 and (1.9 ± 0.2) × 108 cells per μmol of VC dechlorinated in cultures with H2 or formate as electron donor, respectively. About 1.5-fold higher cell numbers were measured with qPCR targeting cerA, a single-copy gene encoding a putative VC RDase. A VC derized the first non-Dehalococcoides bacterium, „Candidatus Dehalogenimonas etheniformans“ strain GP, capable of metabolic reductive dechlorination of TCE, all DCE isomers, and VC to environmentally benign ethene. In addition to hydrogen, the new isolate utilizes formate as electron donor for reductive dechlorination, providing opportunities for more effective electron donor delivery to the contaminated subsurface. The discovery that a broader microbial diversity can achieve detoxification of toxic chlorinated ethenes in anoxic aquifers illustrates the potential of naturally occurring microbes for biotechnological applications.

Air pollution disparities by socioeconomic status (SES) are well documented for the United States, with most literature indicating an inverse relationship (i.e., higher concentrations for lower-SES populations). Few studies exist for China, a country accounting for 26% of global premature deaths from ambient air pollution.

Our objective was to test the relationship between ambient air pollution exposures and SES in China.

We combined estimated year 2015 annual-average ambient levels of nitrogen dioxide (

NO

2

) and fine particulate matter [PM

≤

2.5

μ

m

in aerodynamic diameter (

PM

2.5

)] with national demographic information. Pollution estimates were derived from a national empirical model for China at

1

-km

spatial resolution; demogrur study provides the most comprehensive picture to date of ambient air pollution disparities in China; the results differ dramatically from results and from theories to explain conditions in the United States. https//doi.org/10.1289/EHP9872.

Multiple analyses here reveal that in China, ambient NO2 and PM2.5 concentrations are higher for high-SES than for low-SES individuals; these results are robust to multiple sensitivity analyses. Our findings are consistent with the idea that in China’s current industrialization and urbanization stage, economic development is correlated with both SES and air pollution. To our knowledge, our study provides the most comprehensive picture to date of ambient air pollution disparities in China; the results differ dramatically from results and from theories to explain conditions in the United States. https//doi.org/10.1289/EHP9872.

The effects of an alternative bleaching method on the total phenolic content (TPC) and antioxidant activity (AA) of yerba mate extracts were evaluated. Traditional bleaching (‚zapeco‘) was compared with submerging the leaves in water followed by a hot air oven-drying process. Seven different approaches, i.e. linear model (LM), response surface model (RSM), Mamdani, Larsen, adaptive neuro-fuzzy inference system (ANFIS) with the product (Prod) and the minimum (Min) operators, and ANFIS with automatically membership functions (Auto), were employed to compare the TPC of yerba mate extracts based on drying temperature and AA assays.

The results showed that if leaves were bleached followed by drying at higher temperatures, we obtained higher AA and TPC values. For submerging bleaching treatment, RSM model delivered the best accuracy measures with a mean absolute error (MAE), average absolute percentage error (MAPE), and mean squared error (MSE) of 0.128, 0.006, and 0.028, respectively. The ANFIS Auto model was the best for traditional bleaching treatment, with MAE, MAPE, and MSE of 0.490, 0.013, and 0.612, respectively.

The results suggest a second-order linear relation between drying temperature, AA assays to TPC, and a high level of relation complexity of drying temperature, AA assays, and TPC. The evaluated soft-computing approaches have the excellent ability to estimate TPC from bleached leaves. © 2022 Society of Chemical Industry.

The results suggest a second-order linear relation between drying temperature, AA assays to TPC, and a high level of relation complexity of drying temperature, AA assays, and TPC. The evaluated soft-computing approaches have the excellent ability to estimate TPC from bleached leaves. © 2022 Society of Chemical Industry.