Feasibility of virtual reality based training for optimising COVID-19 case handling in Uganda.

BACKGROUND: Epidemics and pandemics are causing high morbidity and mortality on a still-evolving scale exemplified by the COVID-19 pandemic. Infection prevention and control (IPC) training for frontline health workers is thus essential. However, classroom or hospital ward-based training portends an infection risk due to the in-person interaction of participants. We explored the use of Virtual Reality (VR) simulations for frontline health worker training since it trains participants without exposing them to infections that would arise from in-person training. It does away with the requirement for expensive personal protective equipment (PPE) that has been in acute shortage and improves learning, retention, and recall. This represents the first attempt in deploying VR-based pedagogy in a Ugandan medical education context. METHODS: We used animated VR-based simulations of bedside and ward-based training scenarios for frontline health workers. The training covered the donning and doffing of PPE, case management of COVID-19 infected individuals, and hand hygiene. It used VR headsets to actualize an immersive experience, via a hybrid of fully-interactive VR and 360° videos. The level of knowledge acquisition between individuals trained using this method was compared to similar cohorts previously trained in a classroom setting. That evaluation was supplemented by a qualitative assessment based on feedback from participants about their experience. RESULTS: The effort resulted in a COVID-19 IPC curriculum adapted into VR, corresponding VR content, and a pioneer cohort of VR trained frontline health workers. The formalized comparison with classroom-trained cohorts showed relatively better outcomes by way of skills acquired, speed of learning, and rates of information retention (P-value = 4.0e-09). In the qualitative assessment, 90% of the participants rated the method as very good, 58.1% strongly agreed that the activities met the course objectives, and 97.7% strongly indicated willingness to refer the course to colleagues. CONCLUSION: VR-based COVID-19 IPC training is feasible, effective and achieves enhanced learning while protecting participants from infections within a pandemic setting in Uganda. It is a delivery medium transferable to the contexts of other highly infectious diseases.

A G-protein-coupled chemoattractant receptor recognizes lipopolysaccharide for bacterial phagocytosis.

Phagocytes locate microorganisms via chemotaxis and then consume them using phagocytosis. Dictyostelium amoebas are stereotypical phagocytes that prey on diverse bacteria using both processes. However, as typical phagocytic receptors, such as complement receptors or Fcγ receptors, have not been found in Dictyostelium, it remains mysterious how these cells recognize bacteria. Here, we show that a single G-protein-coupled receptor (GPCR), folic acid receptor 1 (fAR1), simultaneously recognizes the chemoattractant folate and the phagocytic cue lipopolysaccharide (LPS), a major component of bacterial surfaces. Cells lacking fAR1 or its cognate G-proteins are defective in chemotaxis toward folate and phagocytosis of Klebsiella aerogenes. Computational simulations combined with experiments show that responses associated with chemotaxis can also promote engulfment of particles coated with chemoattractants. Finally, the extracellular Venus-Flytrap (VFT) domain of fAR1 acts as the binding site for both folate and LPS. Thus, fAR1 represents a new member of the pattern recognition receptors (PRRs) and mediates signaling from both bacterial surfaces and diffusible chemoattractants to reorganize actin for chemotaxis and phagocytosis.

Regioisomerization of Antimalarial Drug WR99210 Explains the Inactivity of a Commercial Stock.

WR99210, a former antimalarial drug candidate now widely used for the selection of Plasmodium transfectants, selectively targets the parasite's dihydrofolate reductase thymidine synthase bifunctional enzyme (DHFR-TS) but not human DHFR, which is not fused with TS. Accordingly, WR99210 and plasmids expressing the human dhfr gene have become valued tools for the genetic modification of parasites in the laboratory. Concerns over the ineffectiveness of WR99210 from some sources encouraged us to investigate the biological and chemical differences of supplies from two different companies (compounds 1 and 2). Compound 1 proved effective at low nanomolar concentrations against Plasmodium falciparum parasites, whereas compound 2 was ineffective, even at micromolar concentrations. Intact and fragmented mass spectra indicated identical molecular formulae of the unprotonated (free base) structures of compounds 1 and 2; however, the compounds displayed differences by thin-layer chromatography, reverse-phase high-performance liquid chromatography, and UV-visible spectroscopy, indicating important isomeric differences. Structural evaluations by 1H, 13C, and 15N nuclear magnetic resonance spectroscopy confirmed compound 1 as WR99210 and compound 2 as a dihydrotriazine regioisomer. Induced fit computational docking models showed that compound 1 binds tightly and specifically in the P. falciparum DHFR active site, whereas compound 2 fits poorly to the active site in loose and varied orientations. Stocks and concentrates of WR99210 should be monitored for the presence of regioisomer 2, particularly when they are not supplied as the hydrochloride salt or are exposed to basic conditions that may promote rearrangement. Absorption spectroscopy can serve for assays of the unrearranged and rearranged triazines.

Novel signal transducer and activator of transcription 1 mutation disrupts small ubiquitin-related modifier conjugation causing gain of function.

BACKGROUND: Sumoylation is a posttranslational reversible modification of cellular proteins through the conjugation of small ubiquitin-related modifier (SUMO) and comprises an important regulator of protein function. OBJECTIVE: We sought to characterize the molecular mechanism of a novel mutation at the SUMO motif on signal transducer and activator of transcription 1 (STAT1). METHODS: STAT1 sequencing and functional characterization were performed in transfection experiments by using immunoblotting and immunoprecipitation in STAT1-deficient cell lines. Transcriptional response and target gene activation were also investigated in PBMCs. RESULTS: We identified a novel STAT1 mutation (c.2114A>T, p.E705V) within the SUMO motif (702IKTE705) in a patient with disseminated Rhodococcus species infection, Norwegian scabies, chronic mucocutaneous candidiasis, hypothyroidism, and esophageal squamous cell carcinoma. The mutation is located in the tail segment and is predicted to disrupt STAT1 sumoylation. Immunoprecipitation experiments performed in transfected cells confirmed absent STAT1 sumoylation for E705V, whereas it was present in wild-type (WT) STAT1 cells, as well as the loss-of-function mutants L706S and Y701C. Furthermore, stimulation with IFN-γ led to enhanced STAT1 phosphorylation, enhanced transcriptional activity, and target gene expression in the E705V-transfected compared with WT-transfected cells. Computer modeling of WT and mutant STAT1 molecules showed variations in the accessibility of the phosphorylation site Y701, which corresponded to the loss-of-function and gain-of-function variants. CONCLUSION: This is the first report of a mutation in the STAT1 sumoylation motif associated with clinical disease. These data reinforce sumoylation as a key posttranslational regulatory modification of STAT1 and identify a novel mechanism for gain-of-function STAT1 disease in human subjects.

DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides.

Antimicrobial peptides (AMPs) are anti-infectives that may represent a novel and untapped class of biotherapeutics. Increasing interest in AMPs means that new peptides (natural and synthetic) are discovered faster than ever before. We describe herein a new version of the Database of Antimicrobial Activity and Structure of Peptides (DBAASPv.2, which is freely accessible at http://dbaasp.org). This iteration of the database reports chemical structures and empirically-determined activities (MICs, IC50, etc.) against more than 4200 specific target microbes for more than 2000 ribosomal, 80 non-ribosomal and 5700 synthetic peptides. Of these, the vast majority are monomeric, but nearly 200 of these peptides are found as homo- or heterodimers. More than 6100 of the peptides are linear, but about 515 are cyclic and more than 1300 have other intra-chain covalent bonds. More than half of the entries in the database were added after the resource was initially described, which reflects the recent sharp uptick of interest in AMPs. New features of DBAASPv.2 include: (i) user-friendly utilities and reporting functions, (ii) a 'Ranking Search' function to query the database by target species and return a ranked list of peptides with activity against that target and (iii) structural descriptions of the peptides derived from empirical data or calculated by molecular dynamics (MD) simulations. The three-dimensional structural data are critical components for understanding structure-activity relationships and for design of new antimicrobial drugs. We created more than 300 high-throughput MD simulations specifically for inclusion in DBAASP. The resulting structures are described in the database by novel trajectory analysis plots and movies. Another 200+ DBAASP entries have links to the Protein DataBank. All of the structures are easily visualized directly in the web browser.

Structural and functional comparisons of salivary α-glucosidases from the mosquito vectors Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus.

Mosquito vectors of medical importance both blood and sugar feed, and their saliva contains bioactive molecules that aid in both processes. Although it has been shown that the salivary glands of several mosquito species exhibit α-glucosidase activities, the specific enzymes responsible for sugar digestion remain understudied. We therefore expressed and purified three recombinant salivary α-glucosidases from the mosquito vectors Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus and compared their functions and structures. We found that all three enzymes were expressed in the salivary glands of their respective vectors and were secreted into the saliva. The proteins, as well as mosquito salivary gland extracts, exhibited α-glucosidase activity, and the recombinant enzymes displayed preference for sucrose compared to p-nitrophenyl-α-D-glucopyranoside. Finally, we solved the crystal structure of the Ae. aegypti α-glucosidase bound to two calcium ions at a 2.3 Ångstrom resolution. Molecular docking suggested that the Ae. aegypti α-glucosidase preferred di- or polysaccharides compared to monosaccharides, consistent with enzymatic activity assays. Comparing structural models between the three species revealed a high degree of similarity, suggesting similar functional properties. We conclude that the α-glucosidases studied herein are important enzymes for sugar digestion in three mosquito species.

Human ESCRT-I and ALIX function as scaffolding helical filaments in vivo.

The Endosomal Sorting Complex Required for Transport (ESCRT) is an evolutionarily conserved machinery that performs reverse-topology membrane scission in cells universally required from cytokinesis to budding of enveloped viruses. Upstream acting ESCRT-I and ALIX control these events and link recruitment of viral and cellular partners to late-acting ESCRT-III CHMP4 through incompletely understood mechanisms. Using structure-function analyses combined with super-resolution imaging, we show that ESCRT-I and ALIX function as distinct helical filaments in vivo . Together, they are essential for optimal structural scaffolding of HIV-1 nascent virions, the retention of viral and human genomes through defined functional interfaces, and recruitment of CHMP4 that itself assembles into corkscrew-like filaments intertwined with ESCRT-I or ALIX helices. Disruption of filament assembly or their conformationally clustered RNA binding interfaces in human cells impaired membrane abscission, resulted in major structural instability and leaked nucleic acid from nascent virions and nuclear envelopes. Thus, ESCRT-I and ALIX function as helical filaments in vivo and serve as both nucleic acid-dependent structural scaffolds as well as ESCRT-III assembly templates. Significance statement: When cellular membranes are dissolved or breached, ESCRT is rapidly deployed to repair membranes to restore the integrity of intracellular compartments. Membrane sealing is ensured by ESCRT-III filaments assembled on the inner face of membrane; a mechanism termed inverse topology membrane scission. This mechanism, initiated by ESCRT-I and ALIX, is universally necessary for cytokinesis, wound repair, budding of enveloped viruses, and more. We show ESCRT-I and ALIX individually oligomerize into helical filaments that cluster newly discovered nucleic acid-binding interfaces and scaffold-in genomes within nascent virions and nuclear envelopes. These oligomers additionally appear to serve as ideal templates for ESCRT-III polymerization, as helical filaments of CHMP4B were found intertwined ESCRT-I or ALIX filaments in vivo . Similarly, corkscrew-like filaments of ALIX are also interwoven with ESCRT-I, supporting a model of inverse topology membrane scission that is synergistically reinforced by inward double filament scaffolding.

African Centers of Excellence in Bioinformatics and Data Intensive Science: Building Capacity for Enhancing Data Intensive Infectious Diseases Research in Africa.

Africa faces both a disproportionate burden of infectious diseases coupled with unmet needs in bioinformatics and data science capabilities which impacts the ability of African biomedical researchers to vigorously pursue research and partner with institutions in other countries. The African Centers of Excellence in Bioinformatics and Data Intensive Science are collaborating with African academic institutions, industry partners, the Foundation for the National Institutes of Health (FNIH) and the National Institute of Allergy and Infectious Diseases (NIAID) at the National Institutes of Health (NIH) in a public-private partnership to address these challenges through enhancing computational infrastructure, fostering the development of advanced bioinformatics and data science skills among local researchers and students and providing innovative emerging technologies for infectious diseases research.

The structures of two salivary proteins from the West Nile vector Culex quinquefasciatus reveal a beta-trefoil fold with putative sugar binding properties.

Female mosquitoes require blood meals for egg development. The saliva of blood feeding arthropods contains biochemically active molecules, whose anti-hemostatic and anti-inflammatory properties facilitate blood feeding on vertebrate hosts. While transcriptomics has presented new opportunities to investigate the diversity of salivary proteins from hematophagous arthropods, many of these proteins remain functionally undescribed. Previous transcriptomic analysis of female salivary glands from Culex quinquefasciatus, an important vector of parasitic and viral infections, uncovered a 12-member family of putatively secreted proteins of unknown function, named the Cysteine and Tryptophan-Rich (CWRC) proteins. Here, we present advances in the characterization of two C. quinquefasciatus CWRC family members, CqDVP-2 and CqDVP-4, including their enrichment in female salivary glands, their specific localization within salivary gland tissues, evidence that these proteins are secreted into the saliva, and their native crystal structures, at 2.3 â€‹Å and 1.87 â€‹Å, respectively. The ß-trefoil fold common to CqDVP-2 and CqDVP-4 is similar to carbohydrate-binding proteins, including the B subunit of the AB toxin, ricin, from the castor bean Ricinus communis. Further, we used a glycan array approach, which identifies carbohydrate ligands associated with inflammatory processes and signal transduction. Glycan array 300 testing identified 100 carbohydrate moieties with positive binding to CqDVP-2, and 77 glycans with positive binding to CqDVP-4. The glycan with the highest relative fluorescence intensities, which exhibited binding to both CqDVP-2 and CqDVP-4, was used for molecular docking experiments. We hypothesize that these proteins bind to carbohydrates on the surface of cells important to host immunology. Given that saliva is deposited into the skin during a mosquito bite, and acts as the vehicle for arbovirus inoculation, understanding the role of these proteins in pathogen transmission is of critical importance. This work presents the first solved crystal structures of C. quinquefasciatus salivary proteins with unknown function. These two molecules are the second and third structures reported from salivary proteins from C. quinquefasciatus, an important, yet understudied disease vector.

Feasibility of Virtual Reality based Training for Optimising COVID-19 Case Handling in Uganda.

Background Epidemics and pandemics are causing high morbidity and mortality on a still-evolving scale exemplified by the COVID-19 pandemic. Infection prevention and control (IPC) training for frontline health workers is thus essential. However, classroom or hospital ward based training portends an infection risk due to the in-person interaction of participants. We explored the use of Virtual Reality (VR) simulations for frontline health worker training since it trains participants without exposing them to infections that would arise from in-person training. It does away with the requirement for expensive Personal Protective Equipment (PPE) that has been in acute shortage and improves learning, retention and recall. This represents the first attempt in deploying VR-based pedagogy in a Ugandan medical education context. Methods We used animated VR-based simulations of bedside and ward-based training scenarios for frontline health workers. The training covered the wearing and stripping of PPE, case management of COVID-19 infected individuals and hand hygiene. It used VR headsets and Graphics Processing Units (GPUs) to actualize an immersive experience, via a hybrid of VR renditions and 360degrees videos. We then compared the level of knowledge acquisition between individuals trained using this method to comparable cohorts previously trained in a classroom setting. That evaluation was supplemented by a qualitative assessment based on feedback from participants about their experience. Results The effort resulted into a well-designed COVID-19 IPC VR curriculum, equivalent VR content and a pioneer cohort of trained frontline health workers. The formalized comparison with classroom-trained cohorts showed relatively better outcomes by way of skills acquired, speed of learning and rates of information retention ( P-value =4.0e-09) - suggesting the effectiveness and feasibility of VR as a medium of medical training. Additionally, in the qualitative assessment 90% of the participants rated the method as very good, 58.1% strongly agreed that the activities met the course objectives, and 97.7 % strongly indicated willingness to refer the course to colleagues. Conclusion VR-based COVID-19 IPC training is feasible, effective and achieves enhanced learning while protecting participants from infections within a pandemic context in Uganda. It is a delivery medium transferable to the contexts of other highly infectious diseases.

Virtual screening for R-groups, including predicted pIC50 contributions, within large structural databases, using Topomer CoMFA.

Multiple R-groups (monovalent fragments) are implicitly accessible within most of the molecular structures that populate large structural databases. R-group searching would desirably consider pIC50 contribution forecasts as well as ligand similarities or docking scores. However, R-group searching, with or without pIC50 forecasts, is currently not practical. The most prevalent and reliable source of pIC50 predictions, existing 3D-QSAR approaches, is also difficult and somewhat subjective. Yet in 25 of 25 trials on data sets on which a field-based 3D-QSAR treatment had already succeeded, substitution of objective (canonically generated) topomer poses for the original structure-guided manual alignments produced acceptable 3D-QSAR models, on average having almost equivalent statistical quality to the published models, and with negligible effort. Their overall pIC50 prediction error is 0.805, calculated as the average over these 25 topomer CoMFA models in the standard deviations of pIC50 predictions, derived from the 1109 possible "leave-out-one-R-group" (LOORG) pIC50 contributions. (This novel LOORG protocol provides a more realistic and stringent test of prediction accuracy than the customary "leave-out-one-compound" LOO approach.) The associated average predictive r(2) of 0.495 indicates a pIC50 prediction accuracy roughly halfway between perfect and useless. To assess the ability of topomer-CoMFA based virtual screening to identify "highly active" R-groups, a Receiver Operating Curve (ROC) approach was adopted. Using, as the binary criterion for a "highly active" R-group, a predicted pIC50 greater than the top 25% of the observed pIC50 range, the ROC area averaged across the 25 topomer CoMFA models is 0.729. Conventionally interpreted, the odds that a "highly active" R-group will indeed confer such a high pIC50 are 0.729/(1-0.729) or almost 3 to 1. To confirm that virtual screening within large collections of realized structures would provide a useful quantity and variety of R-group suggestions, combining shape similarity with the "highly active" pIC50, the 50 searches provided by these 25 models were applied to 2.2 million structurally distinct R-group candidates among 2.0 million structures within a ZINC database, identifying an average of 5705 R-groups per search, with the highest predicted pIC50 combination averaging 1.6 log units greater than the highest reported pIC50s.