Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex.

SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated and transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryoelectron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template product in complex with two molecules of the nsp13 helicase. The Nidovirales order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12 thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapy development.

Using a Function-First "Scout Fragment"-Based Approach to Develop Allosteric Covalent Inhibitors of Conformationally Dynamic Helicase Mechanoenzymes.

Helicases, classified into six superfamilies, are mechanoenzymes that utilize energy derived from ATP hydrolysis to remodel DNA and RNA substrates. These enzymes have key roles in diverse cellular processes, such as translation, ribosome assembly, and genome maintenance. Helicases with essential functions in certain cancer cells have been identified, and helicases expressed by many viruses are required for their pathogenicity. Therefore, helicases are important targets for chemical probes and therapeutics. However, it has been very challenging to develop chemical inhibitors for helicases, enzymes with high conformational dynamics. We envisioned that electrophilic "scout fragments", which have been used in chemical proteomic studies, could be leveraged to develop covalent inhibitors of helicases. We adopted a function-first approach, combining enzymatic assays with enantiomeric probe pairs and mass spectrometry, to develop a covalent inhibitor that selectively targets an allosteric site in SARS-CoV-2 nsp13, a superfamily-1 helicase. Further, we demonstrate that scout fragments inhibit the activity of two human superfamily-2 helicases, BLM and WRN, involved in genome maintenance. Together, our findings suggest an approach to discover covalent inhibitor starting points and druggable allosteric sites in conformationally dynamic mechanoenzymes.

The relationship between the force applied and perceived by the surgeon during ureteral access sheath placement: ex-vivo experimental model.

PURPOSE: To define a peak force of insertion (PFOI) threshold for ureteral damage during ureteral access sheath (UAS) placement on an experimental ureteral orifice model. METHODS: A specially designed water tank using 2 laparoscopic 5 mm ports and 2 different size (10 Fr and 8 Fr) sealing cap adaptors (SCA) as ureteral orifices was used to perform the test. A 10-12 Fr UAS was fixed to a load cell and the force of insertion (FOI) was continuously recorded with a digital force gauge.13 experts in the field of endourology who participated performed 3 UAS insertions. The FOI was recorded initially with 10 Fr followed by 8 Fr SCA. On the final insertion, the orifice was obstructed, leaving a 5 cm length to insert the UAS. The experts were asked to "Stop at the point they anticipate ureteral damage, and they would not proceed in real life". RESULTS: Using 10 Fr SCA the PFOI was 2.12 ± 0.58 Newton (N) (range:1.48-3.48) while 8 Fr SCA showed a PFOI 5.76 ± 0.96 N (range:4.05-7.35). Six of the experts, said they would stop proceeding when they reached above 5.1 N. Three experts had PFOI < 5.1 N and the other 4 stated they would go with PFOIs of 5.88, 6.16, 6.69 and 7.35 N when using SCA of 8 Fr.The highest load they would stop proceeding had a PFOI of 6.09 ± 1.87 N (range: 2.53-10.74). CONCLUSION: The PFOI threshold for ureteral damage inserting UAS of the experts is variable. Although FOI is a subjective perception, experience suggests that ureteral injury may occur at an average of 6.05 N perceived by surgeons' tactile feedback. In-vivo measurement of UAS PFOI may confirm a threshold.

The copper chaperone CCS facilitates copper binding to MEK1/2 to promote kinase activation.

Normal physiology relies on the precise coordination of intracellular signaling pathways that respond to nutrient availability to balance cell growth and cell death. The canonical mitogen-activated protein kinase pathway consists of the RAF-MEK-ERK signaling cascade and represents one of the most well-defined axes within eukaryotic cells to promote cell proliferation, which underscores its frequent mutational activation in human cancers. Our recent studies illuminated a function for the redox-active micronutrient copper (Cu) as an intracellular mediator of signaling by connecting Cu to the amplitude of mitogen-activated protein kinase signaling via a direct interaction between Cu and the kinases MEK1 and MEK2. Given the large quantities of molecules such as glutathione and metallothionein that limit cellular toxicity from free Cu ions, evolutionarily conserved Cu chaperones facilitate efficient delivery of Cu to cuproenzymes. Thus, a dedicated cellular delivery mechanism of Cu to MEK1/2 likely exists. Using surface plasmon resonance and proximity-dependent biotin ligase studies, we report here that the Cu chaperone for superoxide dismutase (CCS) selectively bound to and facilitated Cu transfer to MEK1. Mutants of CCS that disrupt Cu(I) acquisition and exchange or a CCS small-molecule inhibitor were used and resulted in reduced Cu-stimulated MEK1 kinase activity. Our findings indicate that the Cu chaperone CCS provides fidelity within a complex biological system to achieve appropriate installation of Cu within the MEK1 kinase active site that in turn modulates kinase activity and supports the development of novel MEK1/2 inhibitors that target the Cu structural interface or blunt dedicated Cu delivery mechanisms via CCS.

Force-dependent stimulation of RNA unwinding by SARS-CoV-2 nsp13 helicase.

The superfamily 1 helicase nonstructural protein 13 (nsp13) is required for SARS-CoV-2 replication. The mechanism and regulation of nsp13 has not been explored at the single-molecule level. Specifically, force-dependent unwinding experiments have yet to be performed for any coronavirus helicase. Here, using optical tweezers, we find that nsp13 unwinding frequency, processivity, and velocity increase substantially when a destabilizing force is applied to the RNA substrate. These results, along with bulk assays, depict nsp13 as an intrinsically weak helicase that can be activated >50-fold by piconewton forces. Such force-dependent behavior contrasts the known behavior of other viral monomeric helicases, such as hepatitis C virus NS3, and instead draws stronger parallels to ring-shaped helicases. Our findings suggest that mechanoregulation, which may be provided by a directly bound RNA-dependent RNA polymerase, enables on-demand helicase activity on the relevant polynucleotide substrate during viral replication.

Improving the benefits of HIV testing and referrals in large household surveys through active linkages to care: lessons and recommendations from the Namibia population-based HIV impact assessment (NAMPHIA), 2017.

In household-based surveys that include rapid HIV testing services (HTS), passive referral systems that give HIV-positive participants information about how and where to access ART but minimal follow-up support from survey staff may result in suboptimal linkage. In the 2017 Namibia Population-based HIV Impact Assessment (NAMPHIA), we piloted a system of active linkage to care and ART (ALCART) that utilized the infrastructure of existing community-based partner organizations (CBPOs). All HIV-positive participants age 15-64 years not on ART were given standard passive referrals to ART plus the option to participate in ALCART. Cases were assigned to CBPOs in participants' localities. Healthcare workers from the CBPO's contacted cases and facilitated their linkage to facility-based ART. A total of 510 participants were eligible and consented to ALCART. The majority were new diagnoses (80.8%), while the remainder were previously diagnosed but not on ART (19.2%). Of the 510, 473 (92.7%) were successfully linked into care. Of these, all but one initiated ART. Our ALCART system used existing CBPOs and contributed to >90% linkage-to-care and >99% ART-initiation among linked participants in a large, nationally-representative survey. This approach can be used to improve the potential benefits of HTS in other large population-based surveys.

Identification and Characterization of a B-Raf Kinase α-Helix Critical for the Activity of MEK Kinase in MAPK Signaling.

In the MAPK pathway, an oncogenic V600E mutation in B-Raf kinase causes the enzyme to be constitutively active, leading to aberrantly high phosphorylation levels of its downstream effectors, MEK and ERK kinases. The V600E mutation in B-Raf accounts for more than half of all melanomas and ∼3% of all cancers, and many drugs target the ATP binding site of the enzyme for its inhibition. Because B-Raf can develop resistance against these drugs and such drugs can induce paradoxical activation, drugs that target allosteric sites are needed. To identify other potential drug targets, we generated and kinetically characterized an active form of B-RafV600E expressed using a bacterial expression system. In doing so, we identified an α-helix on B-Raf, found at the B-Raf-MEK interface, that is critical for their interaction and the oncogenic activity of B-RafV600E. We assessed the binding between B-Raf mutants and MEK using pull downs and biolayer interferometry and assessed phosphorylation levels of MEK in vitro and in cells as well as its downstream target ERK to show that mutating certain residues on this α-helix is detrimental to binding and downstream activity. Our results suggest that this B-Raf α-helix binding site on MEK could be a site to target for drug development to treat B-RafV600E-induced melanomas.

Ratiometric SERS detection of polycyclic aromatic hydrocarbons assisted by ß-cyclodextrin-modified gold nanoparticles.

A surface-enhanced Raman scattering (SERS) method is described for the determination of trace polycyclic aromatic hydrocarbons (PAHs) in the environment efficiently and economically. Detection sensitivity is improved by modifying gold nanoparticles (AuNPs) with 4-mercaptophenylboronic acid (4-MPBA) conjugated to ß-cyclodextrin (ß-CD) as a new method for ratiometric determination of PAHs in solution. Pyrene (with a Raman band at 580 cm-1) and anthracene (750 cm-1) were used as the model analytes, while 4-MPBA (1570 cm-1) was used as the internal reference to normalize the SERS signals. The intensity ratios of pyrene/4-MPBA increase linearly in the 2 to 10 nM pyrene concentration range, and the intensity ratios of anthracene/4-MPBA increase linearly in the 10 to 100 nM anthracene concentration range. The detection limits are 0.4 nM for pyrene and 4.4 nM for anthracene. This method was applied to the determination of the two analytes in soil sample extracts and the recoveries of pyrene (at levels of 236 ng∙g-1 and 170 ng∙g-1) and anthracene (334 ng∙g-1 and 510 ng∙g-1) agreed well with the results from GC-MS analyses. The good recovery rates (101.8% and 102.5% for pyrene and 106.4% and 101.7% for anthracene) confirmed the reliability of the method. Graphical abstract Schematic illustration of SERS signal enhancement of pyrene, as an example of polycyclic aromatic hydrocarbons, by ß-cyclodextrin modified gold nanoparticles.

Mechanism of BRAF Activation through Biochemical Characterization of the Recombinant Full-Length Protein.

BRAF kinase plays an important role in mitogen-activated protein kinase (MAPK) signaling and harbors activating mutations in about half of melanomas and in a smaller percentage in many other cancers. Despite its importance, few in vitro studies have been performed to characterize the biochemical properties of full-length BRAF. Herein, a strategy to generate an active, intact form of BRAF protein suitable for in vitro enzyme kinetics is described. It is shown that purified, intact BRAF protein autophosphorylates the kinase activation loop and this can be enhanced by binding the MEK protein substrate through an allosteric mechanism. These studies provide in vitro evidence that BRAF selectively binds to active RAS and that the BRAF/CRAF heterodimer is the most active form, relative to their respective homodimers. Full-length BRAF analysis with small-molecule BRAF inhibitors shows that two drugs, dabrafenib and vemurafenib, can modestly enhance kinase activity of BRAF at low concentration. Taken together, this characterization of intact BRAF contributes to a framework for understanding its role in cell signaling.

Modelling the UNAIDS 90-90-90 treatment cascade for gay, bisexual and other men who have sex with men in South Africa: using the findings of a data triangulation process to map a way forward.

A data triangulation exercise was carried out between 2013 and 2015 to assess the HIV epidemic and response among gay, bisexual and other men who have sex with men (GBMSM) in South Africa. We used the findings to assess progress in achieving the UNAIDS 90-90-90 goals for GBMSM in the country. Three scenarios were developed using different GBMSM population factors (2.0, 3.5 and 5.0% of males aged ≥15) to estimate the population size, HIV prevalence of 13.2-49.5%, and 68% of GBMSM knowing their status. Due to data gaps, general population data were used as estimates of GBMSM on antiretroviral therapy (ART) and virologically suppressed (25.7 and 84.0%, respectively). The biggest gap is access to ART. To address the data gap we recommend developing data collection tools, indicators, and further quantification of HIV cascades. Targeted testing, linkage to services and scaled-up prevention interventions (including pre-exposure prophylaxis) are also required.

Update of the ICUD-SIU consultation on stone technology behind ureteroscopy.

INTRODUCTION: Ureteroscopy is now the most frequent treatment used around the world for stone disease. Technological advancement, efficiency, safety, and minimally invasiveness of this procedure are some of the reasons for this change of trend. MATERIALS AND METHODS: In this review of the literature, a search of the PubMed database was conducted to identify articles related to ureteroscopy and accessories. The committee assigned by the International Consultation on Urological Disease reviewed all the data and produced a consensus statement relating to the ureteroscopy and all the particularities around this procedure. CONCLUSION: This manuscript provides literatures and recommendations for endourologists to keep them informed in regard to the preoperative, intraoperative, and postoperative consideration in regard of a ureteroscopy.

Case Study - Case Studies in Cystinuria.

The diagnosis and treatment of patients with rare inherited metabolic disorders associated with recurrent and often obstructive kidney stones are important to the prevention of chronic kidney disease or end stage renal disease. Two case studies in this article describe the diagnosis and management of cystinuria, the most common rare kidney stone disorder.

Estimating the Prevalence and Predictors of Incorrect Condom Use Among Sexually Active Adults in Kenya: Results From a Nationally Representative Survey.

BACKGROUND: Condom use continues to be an important primary prevention tool to reduce the acquisition and transmission of HIV and other sexually transmitted infections. However, incorrect use of condoms can reduce their effectiveness. METHODS: Using data from a 2012 nationally representative cross-sectional household survey conducted in Kenya, we analyzed a subpopulation of sexually active adults and estimated the percent that used condoms incorrectly during sex, and the type of condom errors. We used multivariable logistic regression to determine variables to be independently associated with incorrect condom use. RESULTS: Among 13,720 adolescents and adults, 8014 were sexually active in the previous 3 months (60.3%; 95% confidence interval [CI], 59.0-61.7). Among those who used a condom with a sex partner, 20% (95% CI, 17.4-22.6) experienced at least one instance of incorrect condom use in the previous 3 months. Of incorrect condom users, condom breakage or leakage was the most common error (52%; 95% CI, 44.5-59.6). Factors found to be associated with incorrect condom use were multiple sexual partnerships in the past 12 months (2 partners: adjusted odds ratio [aOR], 1.5; 95% CI, 1.0-2.0; P = 0.03; ≥3: aOR, 2.3; 95% CI, 1.5-3.5; P < 0.01) and reporting symptoms of a sexually transmitted infection (aOR, 2.8; 95% CI, 1.8-4.3; P < 0.01). CONCLUSIONS: Incorrect condom use is frequent among sexually active Kenyans and this may translate into substantial HIV transmission. Further understanding of the dynamics of condom use and misuse, in the broader context of other prevention strategies, will aid program planners in the delivery of appropriate interventions aimed at limiting such errors.

HIV Serodisclosure and Sexual Behavior During International Travel.

When traveling internationally, HIV serodisclosure and knowledge of partners' serostatus were hampered by the lack of a common language. Condomless anal intercourse was less likely to occur in partnerships where HIV serostatus was not disclosed or known. Taken together, these observations suggest that language barriers may affect sexual decision making.

Gay and bisexual men engage in fewer risky sexual behaviors while traveling internationally: a cross-sectional study in San Francisco.

BACKGROUND: International travel poses potential challenges to HIV prevention. A number of studies have observed an association between travel and behavioural disinhibition. In the present study, we assessed differences in sexual behaviour while travelling internationally and within the USA, compared with being in the home environment. METHODS: A probability-based sample of men who have sex with men (MSM) from the San Francisco Bay Area who had travelled internationally in the previous 12 months was recruited through an adapted respondent-driven sampling methodology (N=501). Participants completed interviewer-administered, computer-assisted surveys. RESULTS: Detailed partner-by-partner behavioural data by destination type were collected on 2925 sexual partnerships: 1028 while travelling internationally, 665 while travelling within the USA and 1232 while staying in the San Francisco Bay Area. The proportion of partnerships during international travel that involved unprotected anal intercourse (UAI) was lower compared with during domestic travel and staying locally. International travel was associated with decreased odds of receptive UAI (AOR=0.65, p=0.02) compared with staying locally and there was a trend towards decreased odds of insertive UAI (AOR=0.70, p=0.07). CONCLUSIONS: MSM engaged in proportionately fewer sexual activities which present a high HIV transmission risk when travelling internationally, namely unprotected receptive and insertive anal intercourse and particularly with HIV serodiscordant partners. The lower sexual risk-taking during international travel was robust to controlling for many factors, including self-reported HIV serostatus, age, relationship status and type of partnership. These findings suggest that when travelling internationally, MSM may experience behavioural disinhibition to a lesser extent than had been described previously.

The Post-Ureteroscopic Lesion Scale (PULS): a multicenter video-based evaluation of inter-rater reliability.

PURPOSE: The Post-Ureteroscopic Lesion Scale (PULS) offers a simple grading system for the description of ureteral lesions after ureteroscopy. In this article, we present the results of a video-based multicenter evaluation of the inter-rater reliability of clinically important PULS grades 0-3. METHODS: Video sequences at the end of ureteroscopy (final passage) were recorded for 100 consecutive patients at a single institution and assessed by experienced urologists (n = 20) and senior residents (n = 17) at 19 international centers. The cohort included only patients with lesions grades 0-3 (with grades 2 and 3 subsumed as 2 + since distinction is defined by an extravasation of contrast medium in fluoroscopy). The gradings were evaluated for inter-rater reliability and in terms of simplicity, validity, comprehensibility, reproducibility, and usefulness. RESULTS: Overall, inter-rater reliability was high (Kendall's W = 0.69, p < 0.001) and was comparable between specialists (Kendall's W = 0.69, p < 0.001) and residents (Kendall's W = 0.71, p < 0.001). The matched ratings showed grade 0 in 43.0 % of patients and grades 1 or 2 + in 44.0 and 13.0 % of patients, respectively. Results of the questionnaires indicated a high degree of acceptance, with an overall rating of 1.76 (1.64-1.93 for different items, scale 1-6). CONCLUSIONS: Inter-rater reliability of the endoscopically assessable PULS was high among urologists with different levels of experience in different countries worldwide. The validated PULS system may be used for standardized reporting of ureteral lesions/injuries after ureteroscopy. In addition, PULS will enable more selective standardization of indications for postoperative DJ stenting based on the randomized controlled trials.

Opioid and Antimicrobial Prescription Patterns During Emergency Medicine Encounters Among Uninsured Patients.

The purpose of this study was to characterize opioid and antimicrobial prescribing among uninsured patients seeking emergency medical care and to build predictive machine learning models. Uninsured patients were less likely to receive an opioid medication, more likely to receive non-opioid alternatives, and less likely to receive an antimicrobial prescription. The most impactful contributing factors were housing status, comorbidities, and recidivism.

Immune checkpoint inhibitors in high-grade upper tract urothelial carcinoma: Paradigm shift emphasizing organ preservation.

Objective: The aim was to evaluate the role of immune check point inhibitors (ICIs) in patients with high-grade upper tract urothelial carcinoma (UTUC) who are managed endoscopically when nephroureterectomy (NU) is not feasible, such as in patients who are either not candidates for NU or decline extirpative surgery. Methods: All patients diagnosed with high-grade UTUC and managed endoscopically between January 1996 and August 2022 were included in the study. Subsequently, patients were categorised based on their use of ICIs into group 1 (patients who did not receive ICIs) and group 2 (patients who received ICIs). Survival outcomes were assessed using Kaplan-Meier analysis, while a multivariable regression model was employed to analyse the impact of clinical characteristics on survival. Results: A total of 29 patients were enrolled, with 14 in group 1 and 15 in group 2. Both groups exhibited similar demographic and disease characteristics, including multifocality, laterality and initial tumour size. The median follow-up period was 29.2 months. Notably, group 2 demonstrated significantly enhanced overall and metastasis-free survival rates compared to group 1. At 47.8 months, the overall survival rate was 0% (all patients died) in group 1, whereas it was 85.7% in group 2. Similarly, the metastasis-free survival rate was 0% (all patients had metastatic disease) in group 1 at 40.6 months, whereas it reached 78.0% in group 2. The multivariable analysis indicated a correlation between ICI usage and improved survival outcomes, with a hazard ratio of 0.002. Conclusion: Utilisation of adjuvant ICIs in the setting of endoscopically treated patients with high-grade UTUC is associated with significantly improved survival rates. ICIs should be considered in this patient population, however, more studies with larger sample size are warranted.