The programmed death-1 (PD-1) and its ligand PD-L1 (B7-H1) signaling pathway has been the focus of much enthusiasm in the fields of tumor immunology and oncology with recent FDA approval of the ...anti-PD-1 antibodies pembrolizumab and nivolumab and the anti-PD-L1 antibodies durvalumab, atezolimuab, and avelumab. These therapies, referred to here as PD-L1/PD-1 checkpoint blockade therapies, are designed to block the interaction between PD-L1, expressed by tumor cells, and PD-1, expressed by tumor-infiltrating CD8
T cells, leading to enhanced antitumor CD8
T cell responses and tumor regression. The influence of PD-L1 expressed by tumor cells on antitumor CD8
T cell responses is well characterized, but the impact of PD-L1 expressed by immune cells has not been well defined for antitumor CD8
T cell responses. Although PD-L1 expression by tumor cells has been used as a biomarker in selection of patients for PD-L1/PD-1 checkpoint blockade therapies, patients whose tumor cells lack PD-L1 expression often respond positively to PD-L1/PD-1 checkpoint blockade therapies. This suggests that PD-L1 expressed by non-malignant cells may also contribute to antitumor immunity. Here, we review the functions of PD-L1 expressed by immune cells in the context of CD8
T cell priming, contraction, and differentiation into memory populations, as well as the role of PD-L1 expressed by tumor cells in regulating antitumor CD8
T cell responses.
This critical review presents the key factors that control the occurrence of natural elements from the uranium- and thorium-decay series, also known as naturally occurring radioactive materials ...(NORM), including uranium, radium, radon, lead, polonium, and their isotopes in groundwater resources. Given their toxicity and radiation, elevated levels of these nuclides in drinking water pose human health risks, and therefore understanding the occurrence, sources, and factors that control the mobilization of these nuclides from aquifer rocks is critical for better groundwater management and human health protection. The concentrations of these nuclides in groundwater are a function of the groundwater residence time relative to the decay rates of the nuclides, as well as the net balance between nuclides mobilization (dissolution, desorption, recoil) and retention (adsorption, precipitation). This paper explores the factors that control this balance, including the relationships between the elemental chemistry (e.g., solubility and speciation), lithological and hydrogeological factors, groundwater geochemistry (e.g., redox state, pH, ionic strength, ion-pairs availability), and their combined effects and interactions. The various chemical properties of each of the nuclides results in different likelihoods for co-occurrence. For example, the primordial 238U, 222Rn, and, in cases of high colloid concentrations also 210Po, are all more likely to be found in oxic groundwater. In contrast, in reducing aquifers, Ra nuclides, 210Pb, and in absence of high colloid concentrations, 210Po, are more mobile and frequently occur in groundwater. In highly permeable sandstone aquifers that lack sufficient adsorption sites, Ra is often enriched, even in low salinity and oxic groundwater. This paper also highlights the isotope distributions, including those of relatively long-lived nuclides (238U/235U) with abundances that depend on geochemical conditions (e.g., fractionation induced from redox processes), as well as shorter-lived nuclides (234U/238U, 228Ra/226Ra, 224Ra/228Ra, 210Pb/222Rn, 210Po/210Pb) that are strongly influenced by physical (recoil), lithological, and geochemical factors. Special attention is paid in evaluating the ability to use these isotope variations to elucidate the sources of these nuclides in groundwater, mechanisms of their mobilization from the rock matrix (e.g., recoil, ion-exchange), and retention into secondary mineral phases and ion-exchange sites.
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•Differential occurrence of naturally occurring U, Ra, Rn, Po, and Pb nuclides in groundwater resources.•The balance between mobilization and retention from and into aquifer rocks controls nuclides occurrence in groundwater.•Aquifer lithology, hydrogeology, and groundwater geochemistry are the major factors that control nuclides distribution.•Distinction between nuclides mobilization associated with chemical and physical (recoil) processes.•Isotope ratios can be used to delineate mechanisms and sources of nuclides mobilization from aquifer rocks.
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern ...of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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•A SARS-CoV-2 variant with Spike G614 has replaced D614 as the dominant pandemic form•The consistent increase of G614 at regional levels may indicate a fitness advantage•G614 is associated with lower RT PCR Cts, suggestive of higher viral loads in patients•The G614 variant grows to higher titers as pseudotyped virions
Korber et al. present evidence that there are now more SARS-CoV-2 viruses circulating in the human population globally that have the G614 form of the Spike protein versus the D614 form that was originally identified from the first human cases in Wuhan, China. Follow-up studies show that patients infected with G614 shed more viral nucleic acid compared with those with D614, and G614-bearing viruses show significantly higher infectious titers in vitro than their D614 counterparts.
Amide N-methylation is important for the activity and permeability of bioactive compounds but can be challenging to perform selectively. The broad-spectrum antimicrobial natural products thiolutin ...and holomycin differ only by an N-methyl group at the endocyclic amide of thiolutin, but only thiolutin exhibits antifungal activity. The enzyme responsible for amide N-methylation in thiolutin biosynthesis has remained elusive. Here, we identified and characterized the amide N-methyltransferase DtpM that is encoded >400 kb outside of the thiolutin gene cluster. DtpM catalyzes efficient conversion of holomycin to thiolutin, exhibits broad substrate scope toward dithiolopyrrolones, and has high thermal stability. In addition, sequence similarity network analysis suggests DtpM is more closely related to phenol O-methyltransferases than some amide methyltransferases. This study expands the limited examples of amide N-methyltransferases and may facilitate chemoenzymatic synthesis of diverse dithiolopyrrolone compounds as potential therapeutics.
Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and ...organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.
G protein-coupled receptors (GPCRs) are the largest class of cell surface drug targets. Advances in stabilization of GPCR:transducer complexes, together with improvements in cryoelectron microscopy ...(cryo-EM) have recently been applied to structure-assisted drug design for GPCR agonists. Nonetheless, limitations in the commercial application of these approaches, including the use of nanobody 35 (Nb35) to aid complex stabilization and the high cost of 300 kV imaging, have restricted broad application of cryo-EM in drug discovery. Here, using the PF 06882961-bound GLP-1R as exemplar, we validated the formation of stable complexes with a modified Gs protein in the absence of Nb35. In parallel, we compare 200 versus 300 kV image acquisition using a Falcon 4 or K3 direct electron detector. Moreover, the 200 kV Glacios-Falcon 4 yielded a 3.2 Å map with clear density for bound drug and multiple structurally ordered waters. Our work paves the way for broader commercial application of cryo-EM for GPCR drug discovery.
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•High-resolution imaging of GPCRs using non-proprietary technologies•3.2 Å structure of a GPCR using a 200 kV microscope•Imaging of small-molecule agonist class B GPCR with no stabilizing nanobodies
Traditionally, G protein-coupled receptors (GPCRs) need to be biochemically stabilized to be studied by cryo-EM. We show that it is possible to obtain high-quality 3D reconstructions without the need for a stabilizing nanobody. We also show that excellent imaging results can be obtained on both 200 and 300 kV microscopes.
Abstract
Background
There is no proven antiviral or immunomodulatory therapy for coronavirus disease 2019 (COVID-19). The disease progression associated with the proinflammatory host response ...prompted us to examine the role of early corticosteroid therapy in patients with moderate to severe COVID-19.
Methods
We conducted a single pretest, single posttest quasi-experiment in a multicenter health system in Michigan from 12 March to 27 March 2020. Adult patients with confirmed moderate to severe COVID were included. A protocol was implemented on 20 March 2020 using early, short-course, methylprednisolone 0.5 to 1 mg/kg/day divided in 2 intravenous doses for 3 days. Outcomes of standard of care (SOC) and early corticosteroid groups were evaluated, with a primary composite endpoint of escalation of care from ward to intensive care unit (ICU), new requirement for mechanical ventilation, and mortality. All patients had at least 14 days of follow-up.
Results
We analyzed 213 eligible subjects, 81 (38%) and 132 (62%) in SOC and early corticosteroid groups, respectively. The composite endpoint occurred at a significantly lower rate in the early corticosteroid group (34.9% vs 54.3%, P = .005). This treatment effect was observed within each individual component of the composite endpoint. Significant reduction in median hospital length of stay was also observed in the early corticosteroid group (5 vs 8 days, P < .001). Multivariate regression analysis demonstrated an independent reduction in the composite endpoint at 14-days controlling for other factors (adjusted odds ratio: 0.41; 95% confidence interval, .22 – .77).
Conclusions
An early short course of methylprednisolone in patients with moderate to severe COVID-19 reduced escalation of care and improved clinical outcomes.
Clinical Trials Registration
NCT04374071.
In this multicenter quasi-experimental study of 213 patients, we demonstrate early short course of methylprednisolone in moderate to severe COVID-19 patients reduced the composite endpoint of escalation of care from ward to Intensive Care Unit, new requirement for mechanical ventilation, and mortality.
Cryo‐electron microscopy (cryo‐EM) can now be used to determine high‐resolution structural information on a diverse range of biological specimens. Recent advances have been driven primarily by ...developments in microscopes and detectors, and through advances in image‐processing software. However, for many single‐particle cryo‐EM projects, major bottlenecks currently remain at the sample‐preparation stage; obtaining cryo‐EM grids of sufficient quality for high‐resolution single‐particle analysis can require the careful optimization of many variables. Common hurdles to overcome include problems associated with the sample itself (buffer components, labile complexes), sample distribution (obtaining the correct concentration, affinity for the support film), preferred orientation, and poor reproducibility of the grid‐making process within and between batches. This review outlines a number of methodologies used within the electron‐microscopy community to address these challenges, providing a range of approaches which may aid in obtaining optimal grids for high‐resolution data collection.
This paper describes different approaches that cryo‐EM users can take to improve the quality of their sample distribution and ice for high‐resolution single‐particle cryo‐EM.
It is increasingly being recognised that the interplay between commensal and pathogenic bacteria can dictate the outcome of infection. Consequently, there is a need to understand how commensals ...interact with their human host and influence pathogen behaviour at epithelial surfaces. Neisseria meningitidis, a leading cause of sepsis and meningitis, exclusively colonises the human nasopharynx and shares this niche with several other Neisseria species, including the commensal Neisseria cinerea. Here, we demonstrate that during adhesion to human epithelial cells N. cinerea co-localises with molecules that are also recruited by the meningococcus, and show that, similar to N. meningitidis, N. cinerea forms dynamic microcolonies on the cell surface in a Type four pilus (Tfp) dependent manner. Finally, we demonstrate that N. cinerea colocalises with N. meningitidis on the epithelial cell surface, limits the size and motility of meningococcal microcolonies, and impairs the effective colonisation of epithelial cells by the pathogen. Our data establish that commensal Neisseria can mimic and affect the behaviour of a pathogen on epithelial cell surfaces.
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