Molecular dynamics investigation of DNA fragments bound to the anti-HIV protein SAMHD1 reveals alterations in allosteric communications.

The sterile alpha motif and histidine-aspartate domain-containing protein 1 (or SAMHD1), a human dNTP-triphosphohydrolase, contributes to HIV-1 restriction in select terminally differentiated cells of the immune system. While the prevailing hypothesis is that the catalytically active form of the protein is an allosterically triggered tetramer, whose HIV-1 restriction properties are attributed to its dNTP - triphosphohydrolase activity, it is also known to bind to ssRNA and ssDNA oligomers. A complete picture of the structure-function relationship of the enzyme is still elusive and the function corresponding to its nucleic acid binding ability is debated. In this in silico study, we investigate the stability, preference and allosteric effects of DNA oligomers bound to SAMHD1. In particular, we compare the binding of DNA and RNA oligomers of the same sequence and also consider the binding of DNA fragments with phosphorothioate bonds in the backbone. The results are compared with the canonical form with the monomers connected by GTP/dATP crossbridges. The simulations indicate that SAMHD1 dimers preferably bind to DNA and RNA oligomers compared to GTP/dATP. However, allosteric communication channels are altered in the nucleic acid acid bound complexes compared to the canonical form. All results are consistent with the hypothesis that the DNA bound form of the protein correspond to an unproductive off-pathway state where the protein is sequestered and not available for dNTP hydrolysis.

The design and validation of a low-cost trans perineal (TP) prostate biopsy simulator for training: improving trainees' confidence and cognitive targeting skills.

PURPOSE: The aim of this research was to create a novel and low-cost TP prostate biopsy simulator that has face, content and construct validity with high educational value. METHODS: This research developed a trans perineal prostate (TP) biopsy simulator using 3D-printed moulds and tissue-mimicking materials. Important regions (anterior, mid, and posterior zones) were coded with different colours. Ultrasound visible abnormal lesions were embedded in the prostate phantom. Expert and novice participants in TP biopsies were recruited. Essential skills were identified through the consensus of six experts. These skills were assessed through tasks performed by participants. This included the accuracy and timing of systematic and target biopsies. Immediate feedback was determined by the colour of the biopsy cores taken. A survey was distributed to evaluate its realism and educational value. RESULTS: The material cost of one simulator was £7.50. This simulator was proven to have face, content, and construct validity. There was a significant difference (p = 0.02) in the accuracy of systematic biopsies between both experts and novices. Significant difference was also observed (p = 0.01), in accurately identifying target lesion on ultrasound between both groups. Participants rated the overall realism of the simulator 4.57/5 (range 3-5). 100% of the experts agreed that introducing this simulator to training will be beneficial. 85.7% of the participants strongly agree that the simulator improved their confidence in TP biopsies. CONCLUSION: There is value in integrating this proof-of-concept TP prostate biopsy simulator into training. It has highly rated educational value and has face, content, and construct validity.

Single vs replicate Real-Time PCR SARS-CoV-2 testing: Lessons learned for effective pandemic management.

Coronavirus Disease 19 (COVID-19) caused by the SARS-CoV-2 virus remains a global pandemic having a serious impact on national economies and healthcare infrastructure. Accurate infection detection protocols are key to policy guidance and decision making. In this pilot study, we compared single versus replicate PCR testing for effective and accurate SARS-CoV-2 infection detection. One-Step Real-Time RT-PCR was employed for the detection of SARS-CoV-2 RNA isolated from individual nasopharyngeal swabs. A total of 10,014 swabs, sampled from the general public (hospital admissions, A&E, elective surgeries, cancer patients, care home residents and healthcare staff), were tested using standard replicate testing. Our analysis demonstrates that approximately 19% of SARS-CoV-2 infected individuals would have been reported as false negative if single sample Real-Time PCR testing was used. Therefore, two replicate tests can substantially decrease the risk of false negative reporting and reduce hospital and community infection rates. As the number of variants of concern increases, we believe that replicate testing is an essential consideration for effective SARS-CoV-2 infection detection and prevention of further outbreaks. A strategic approach limiting the number of missed infections is crucial in controlling the rise of new SARS-CoV-2 variants as well as the management of future pandemics.

Dimeric Hold States of Anti-HIV Protein SAMHD1 are Redox Tunable.

The sterile α motif and histidine-aspartate domain-containing protein 1 (or SAMHD1) is a human protein that restricts HIV-1 in select terminally differentiated cells of the immune system by acting as a triphosphohydrolase, lowering dNTP pools. The functionally active form of the protein has been reported to be a tetramer where adjacent monomers are linked by GTP-Mg+2-dNTP cross-bridges, although some studies have also suggested the existence of a dimeric form of this protein. In this in silico study, we have investigated the stability of SAMHD1 dimeric "hold states" as well as the role of intrachain disulfide bonds. We have found that dimeric-GTP bound SAMHD1 can exist as a viable meso-stable hold state with extensive motion in the C-terminal domain, which is quenched upon tetramer assembly. The redox switch comprised of residues C341, C350, and C522 was found to be linked to changes in the allosteric site, suggesting a mechanism for initiating tetramer disassembly. The disulfide state of the protein dimer (C341-S-S-C350 vs C341-S-S-C522) also plays a role in driving affinities for the allosteric dATP molecules. In sum, our results suggest a model wherein dimeric SAMHD1 exists as a "hold state" in the cytosol, ready to be activated by dATP concentrations, where the "tunability" of this activation is further regulated by the redox state of the enzyme.