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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]

In addition to its value in the study of molecular evolution, ancestral sequence reconstruction (ASR) has emerged as a useful methodology for engineering proteins with enhanced properties. Proteins generated by ASR often exhibit unique or improved activity, stability, and/or promiscuity, all of which are properties that are valued by protein engineers. Comparison between extant proteins and evolutionary intermediates generated by ASR also allows protein engineers to identify substitutions that have contributed to functional innovation or diversification within protein families. As ASR becomes more widely adopted as a protein engineering approach, it is important to understand the applications, limitations, and recent developments of this technique. This review highlights recent exemplifications of ASR, as well as technical aspects of the reconstruction process that are relevant to protein engineering. [Display omitted] • Proteins produced by ancestral sequence reconstruction (ASR) often exhibit high activity, stability, and evolvability. • ASR studies guide engineering by highlighting function-shifting substitutions. • ASR emphasizes fundamental drivers of, and constraints to, functional innovation. • Recent developments in ASR are making it more accessible to protein engineers. [ABSTRACT FROM AUTHOR]

Nutritional status can affect surgical patients in terms of stress response, healing time, and outcomes. Several abnormalities are known to have a high prevalence in the general population such as vitamin D deficiency (VDD) and subclinical hypothyroidism. We hypothesized that there will be elevated rates of nutritional deficiencies in preoperative patients which may adversely affect postoperative outcomes following pediatric otolaryngology surgery. IRB approval was obtained for a cross-sectional cohort study. Consecutive patients underwent nutritional evaluation when being scheduled for surgery including TSH, albumin and vitamin D. Demographic data, supplementation, and early complication rates were collected. 125 patients were included in the final cohort with adequate demographic distribution. Based on anthropometric data, 12% of our cohort was found to be undernourished, and 40% of our cohort with elevated BMI. However, there was no relationship found between Z-scores and complications. VDD was noted in 83/125 (66.4%) patients. Our cohort had increased rates of VDD in patients with elevated BMI and African American ethnicity. Thyroid hormone abnormalities were present in 12 patients. Mean serum albumin level was 4.29 in our cohort all within normal range. We did find increased risk of postoperative complications in patients with previously diagnosed comorbidities. (p=0.006). There is no current recommendation or consensus for nutritional assessment in preoperative pediatric patients. Our study did not show statistically significant correlation with z-scores, low vitamin D levels with supplementation, albumin, or TSH to postoperative complications. However, our patient cohort had higher than average rates of VDD compared to the many studies of the general pediatric population and significant negative correlation between vitamin D levels and z-scores. By early preoperative identification of VDD and supplementation with calciferol, we found no significant difference in complication rates in patients based on their initial vitamin D status. We suggest screening preoperative patients using z-score calculations and vitamin D levels based on individual patient risk factors including atrisk patient populations such as African American children, and obese children. [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]

• Designing genetically encoded fluorescence-based analyte biosensors is not trivial. • Many current design efforts take a nature-inspired, modular approach. • Individual sensor components can be engineered separately for desired properties. • Screening of large variant libraries is often required to optimize biosensors. Biosensors that selectively report on the presence of specific small molecule analytes have applications in many fields of research, medicine and biotechnology. Here, we review recent advances and emerging approaches in the design and optimisation of genetically encoded fluorescence-based small molecule biosensors. We discuss how natural sensory proteins can be exploited to produce novel biosensors and the strategies for optimizing ligand specificity and fluorescence readout. Finally, we provide insight into high-throughput sensor optimisation and discuss the challenges that are faced when designing novel biosensors. [ABSTRACT FROM AUTHOR]

Engineered proteins, especially enzymes, are now commonly used in many industries owing to their catalytic power, specific binding of ligands, and properties as materials and food additives. As the number of potential uses for engineered proteins has increased, the interest in engineering or designing proteins to have greater stability, activity and specificity has increased in turn. With any rational engineering or design pursuit, the success of these endeavours relies on our fundamental understanding of the systems themselves; in the case of proteins, their structure-dynamics-function relationships. Proteins are most commonly rationally engineered by targeting the residues that we understand to be functionally important, such as enzyme active sites or ligand-binding sites. This means that the majority of the protein, i.e. regions remote from the active- or ligand-binding site, is often ignored. However, there is a growing body of literature that reports on, and rationalises, the successful engineering of proteins at remote sites. This minireview will discuss the current state of the art in protein engineering, with a particular focus on engineering regions that are remote from active- or ligand-binding sites. As the use of protein technologies expands, exploiting the potential improvements made possible through modifying remote regions will become vital if we are to realise the full potential of protein engineering and design. [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]

Female sex protects against development of acute kidney injury (AKI). While sex hormones may be involved in protection, the role of differential gene expression is unknown. We conducted gene profiling in male and female mice with or without kidney ischemia-reperfusion injury (IRI). Mice underwent bilateral renal pedicle clamping (30 min), and tissues were collected 24 h after reperfusion. RNA-sequencing (RNA-Seq) was performed on proximal tubules (PTs) and kidney endothelial cells. Female mice were resistant to ischemic injury compared with males, determined by plasma creatinine and neutrophil gelatinase-associated lipocalin (NGAL), histologic scores, neutrophil infiltration, and extent of apoptosis. Sham mice had sex-specific gene disparities in PT and endothelium, and male mice showed profound gene dysregulation with ischemia-reperfusion compared with females. After ischemia PTs from females exhibited smaller increases compared with males in injury-associated genes lipocalin-2 (Lcn2), hepatitis A virus cellular receptor 1 (Havcr1), and keratin 18 (Krt18), and no up-regulation of SRY-Box transcription factor 9 (Sox9) or keratin 20 (Krt20). Endothelial up-regulation of adhesion molecules and cytokines/chemokines occurred in males, but not females. Up-regulated genes in male ischemic PTs were linked to tumor necrosis factor (TNF) and Toll-like receptor (TLR) pathways, while female ischemic PTs showed up-regulated genes in pathways related to transport. The data highlight sex-specific gene expression differences in male and female PTs and endothelium before and after ischemic injury that may underlie disparities in susceptibility to AKI. [ABSTRACT FROM AUTHOR]

Great efforts are devoted to end the HIV epidemic as it continues to have profound public health consequences in the United States and throughout the world, and new interventions and strategies are continuously needed. The use of HIV sequence data to infer transmission networks holds much promise to direct public heath interventions where they are most needed. As these new methods are being implemented, evaluating their benefits is essential. In this paper, we recognize challenges associated with such evaluation, and make the case that overcoming these challenges is key to the use of HIV sequence data in routine public health actions to disrupt HIV transmission networks. [ABSTRACT FROM AUTHOR]

Great efforts are devoted to end the HIV epidemic as it continues to have profound public health consequences in the United States and throughout the world, and new interventions and strategies are continuously needed. The use of HIV sequence data to infer transmission networks holds much promise to direct public heath interventions where they are most needed. As these new methods are being implemented, evaluating their benefits is essential. In this paper, we recognize challenges associated with such evaluation, and make the case that overcoming these challenges is key to the use of HIV sequence data in routine public health actions to disrupt HIV transmission networks. [ABSTRACT FROM AUTHOR]

A methodology to screen additives in lead-acid batteries is critical. We developed a three-electrode system that can rapidly check the dynamic charge acceptance (DCA) and hydrogen evolution of electrodes. The electrode with 2% MXene and 0.2% carbon black shows a better DCA, which indicates its great potential in the start–stop technology. [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]

Many political scientists maintain that public policies diffuse across states and that proximate states, in particular, influence one another's policy activities. Using state-funded merit aid for college as its case, this article takes a new approach to the study of the diffusion phenomenon, leaving behind conventional techniques used by generations of innovation/diffusion scholars, and asks policy makers themselves to what they attribute state policy adoption. The authors' findings suggest that merit aid programs diffuse as a function of competition among neighboring states not only for students but also for revenue and ideas. Close policy communities and personal contacts among state policy makers and agency staff also condition policy adoption by spreading information about, and assessments of, educational innovations. [ABSTRACT FROM AUTHOR]

Background: One approach to increasing the reach of syringe programs in rural areas could be through provision of syringes at community pharmacies. This study evaluated relationships between state-specific syringe policies, pharmacy, and pharmacist characteristics and pharmacists' nonprescription syringe dispensing behaviors in a 3- state Appalachian region at high risk for HIV and HCV transmission.Methods: We conducted a telephone census of community pharmacies in the Appalachian counties of North Carolina, Tennessee, and Virginia from April-June 2018. Behaviors studied included having ever sold syringes without a prescription, quantity of individuals to whom nonprescription syringes were dispensed in the past 30 days, having ever denied a request for nonprescription syringes, and past 30-day denial of nonprescription syringe requests. Behavioral intention and perceptions of legality were elicited.Results: A response rate of 52.3 % was achieved (N = 391). North Carolina pharmacists reported increased past 30-day dispensing, less denial of nonprescription syringe requests, and decreased justification for syringe dispensing (proof of medical need) as compared to Tennessee and Virginia pharmacists. Behavioral intention to dispense did not vary by state but did vary by political affiliation. Perceptions of syringe dispensing legality in NC were significantly different from those in TN and VA.Conclusions: Significant differences in pharmacists' perceptions and behaviors were noted across state lines with North Carolina pharmacists reporting more engagement in syringe dispensing as compared to pharmacists in Tennessee and Virginia. Policy allowing pharmacists to dispense syringes to people who inject drugs appears to foster some but not all pharmacist engagement in this harm reduction intervention. [ABSTRACT FROM AUTHOR]

Presents a study which determined the effectiveness of postal prompts to general practitioners and patients on the quality of primary care after coronary heart disease surgery. Principal and secondary outcome measures; Result and discussion; Conclusion.

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]