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Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. Here, we structurally aligned the diverse RNR family by the conserved catalytic barrel to reconstruct the first large-scale phylogeny consisting of 6779 sequences that unites all extant classes of the RNR family and performed evo-velocity analysis to independently validate our evolutionary model. With a robust phylogeny in-hand, we uncovered a novel, phylogenetically distinct clade that is placed as ancestral to the classes I and II RNRs, which we have termed clade Ø. We employed small-angle X-ray scattering (SAXS), cryogenicelectron microscopy (cryo-EM), and AlphaFold2 to investigate a member of this clade from Synechococcus phage S-CBP4 and report the most minimal RNR architecture to-date. Based on our analyses, we propose an evolutionary model of diversification in the RNR family and delineate how our phylogeny can be used as a roadmap for targeted future study [ABSTRACT FROM AUTHOR]

The article focuses on the prosecution of corrupt foreign officials in the U.S. courts. Although U.S. prosecutions can only reach a handful of the most notorious corruption cases in transition countries, high-profile crimes are some of the most damaging to the rule of law because they reinforce the low costs of flouting the law. Using U.S. courts to indirectly enforce a developing country's own laws would not supplant local enforcement' but would instead ensure that prominent officials do not escape punishment while the local judiciary develops.

This article describes an Alberta Heritage Foundation for Medical Research (AHFMR) initiative to enhance the review process for its training awards using a new tool based on the ProGrid® decision-assist software. Changes that the AHFMR made are analyzed, as is the manner in which the review system was developed and refined, the initial assessment of the value added for applicants, reviewers, and the funding decision-maker, and the implications of this approach for the future. Implementation of the new tool resulted in a number of modifications to the AHFMR's review process in the areas of definition, rationality, fairness, timeliness, and responsiveness. The new process also provides the foundation with increased capacity for performance measurement and program evaluation. [ABSTRACT FROM AUTHOR]

Endothelial colony forming cell (ECFC)-derived exosomes protect mice against ischemic kidney injury, via transfer of microRNA-(miR)-486-5p. Mechanisms mediating exosome recruitment to tissues are unclear. We hypothesized that ECFC exosomes target ischemic kidneys, involving interaction between exosomal CXC chemokine receptor type 4 (CXCR4) and stromal cell-derived factor (SDF)-1α. Ischemia-reperfusion was induced in mice by bilateral renal vascular clamp, with intravenous infusion of exosomes at reperfusion. Optical imaging determined exosome biodistribution, and miR-486-5p was measured by real-time PCR. Human umbilical vein endothelial cells (HUVECs) were cultured to study the CXCR4/SDF-1α interaction. Targeting of administered exosomes to ischemic kidneys was detected 30 min and 4 hrs after reperfusion. Exosomes increased miR-486-5p levels only in kidneys, within proximal tubules, glomeruli, and endothelial cells. Uptake of fluorescently-labeled exosomes into HUVECs, and exosomal transfer of miR-486-5p were enhanced by hypoxia, effects blocked by neutralizing antibody to SDF-1α or by the CXCR4 inhibitor plerixafor. Infusion of ECFC exosomes prevented ischemic kidney injury in vivo, an effect that was not observed when exosomes were pre-incubated with plerixafor. These data indicate that ECFC exosomes selectively target the kidneys after ischemic injury, with rapid cellular transfer of miR486-5p. Targeting of exosomes may involve interaction of CXCR4 with endothelial cell SDF-1α. [ABSTRACT FROM AUTHOR]

The ongoing COVID-19 pandemic has had great societal and health consequences. Despite the availability of vaccines, infection rates remain high due to immune evasive Omicron sublineages. Broad-spectrum antivirals are needed to safeguard against emerging variants and future pandemics. We used messenger RNA (mRNA) display under a reprogrammed genetic code to find a spike-targeting macrocyclic peptide that inhibits SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) Wuhan strain infection and pseudoviruses containing spike proteins of SARS-CoV-2 variants or related sarbecoviruses. Structural and bioinformatic analyses reveal a conserved binding pocket between the receptor-binding domain, N-terminal domain, and S2 region, distal to the angiotensin-converting enzyme 2 receptor-interaction site. Our data reveal a hitherto unexplored site of vulnerability in sarbecoviruses that peptides and potentially other drug-like molecules can target. [ABSTRACT FROM AUTHOR]

Viral mutations are an emerging concern in reducing SARS-CoV-2 vaccination efficacy. Second-generation vaccines will need to elicit neutralizing antibodies against sites that are evolutionarily conserved across the sarbecovirus subgenus. Here, we immunized mice containing a human antibody repertoire with diverse sarbecovirus receptor-binding domains (RBDs) to identify antibodies targeting conserved sites of vulnerability. Antibodies with broad reactivity against diverse clade B RBDs targeting the conserved class 4 epitope, with recurring IGHV/IGKV pairs, were readily elicited but were non-neutralizing. However, rare class 4 antibodies binding this conserved RBD supersite showed potent neutralization of SARS-CoV-2 and all variants of concern. Structural analysis revealed that the neutralizing ability of cross-reactive antibodies was reserved only for those with an elongated CDRH3 that extends the antiparallel beta-sheet RBD core and orients the antibody light chain to obstruct ACE2-RBD interactions. These results identify a structurally defined pathway for vaccine strategies eliciting escape-resistant SARS-CoV-2 neutralizing antibodies. [Display omitted] • Immunization with diverse sarbecorvirus RBDs induces cross-reactive antibodies • Cross-reactive antibodies use recurrent IGHV/IGKVs that mainly bind the class 4 epitope • Diverse sarbecovirus RBD responses vary in the dominance of class 4 epitope antibodies • Neutralizing class 4 antibodies are rare and extend the RBD beta-sheet main chain Viral mutations are an emerging concern in reducing SARS-CoV-2 vaccination efficacy. Burnett et al. immunized humanized mice with different diverse sarbecovirus RBDs to elicit antibodies targeting conserved sites. Non-neutralizing cross-reactive antibodies targeting the conserved class 4 epitope were readily elicited. Neutralizing ability was reserved only for antibodies binding this conserved supersite through an elongated CDRH3 that obstructed ACE2-RBD interactions. [ABSTRACT FROM AUTHOR]

Public health interventions guided by clustering of HIV-1 molecular sequences may be impacted by choices of analytical approaches. We identified commonly-used clustering analytical approaches, applied them to 1886 HIV-1 Rhode Island sequences from 2004–2018, and compared concordance in identifying molecular HIV-1 clusters within and between approaches. We used strict (topological support ≥ 0.95; distance 0.015 substitutions/site) and relaxed (topological support 0.80–0.95; distance 0.030–0.045 substitutions/site) thresholds to reflect different epidemiological scenarios. We found that clustering differed by method and threshold and depended more on distance than topological support thresholds. Clustering concordance analyses demonstrated some differences across analytical approaches, with RAxML having the highest (91%) mean summary percent concordance when strict thresholds were applied, and three (RAxML-, FastTree regular bootstrap- and IQ-Tree regular bootstrap-based) analytical approaches having the highest (86%) mean summary percent concordance when relaxed thresholds were applied. We conclude that different analytical approaches can yield diverse HIV-1 clustering outcomes and may need to be differentially used in diverse public health scenarios. Recognizing the variability and limitations of commonly-used methods in cluster identification is important for guiding clustering-triggered interventions to disrupt new transmissions and end the HIV epidemic. [ABSTRACT FROM AUTHOR]