Structural and functional studies of the phage Sf6 terminase small subunit reveal a DNA-spooling device facilitated by structural plasticity

In many DNA viruses, genome packaging is initiated by the small subunit of the packaging terminase, which specifically binds to the packaging signal on viral DNA and directs assembly of the terminase holoenzyme. We have experimentally mapped the DNA-interacting region on Shigella virus Sf6 terminase small subunit gp1, which occupies extended surface areas encircling the gp1 octamer, indicating that DNA wraps around gp1 through extensive contacts. High resolution structures reveal large-scale motions of the gp1 DNA-binding domain mediated by the curved helix formed by residues 54-81 and an intermolecular salt bridge formed by residues Arg67 and Glu73, indicating remarkable structural plasticity underlying multivalent, pleomorphic gp1:DNA interactions. These results provide spatial restraints for protein:DNA interactions, which enable construction of a three-dimensional pseudo-atomic model for a DNA-packaging initiation complex assembled from the terminase small subunit and the packaging region on viral DNA. Our results suggest that gp1 functions as a DNA-spooling device, which may transform DNA into a specific architecture appropriate for interaction with and cleavage by the terminase large subunit prior to DNA translocation into viral procapsid. This may represent a common mechanism for the initiation step of DNA packaging in tailed dsDNA bacterial viruses

The Structure of the Herpes Simplex Virus DNA-Packaging Terminase pUL15 Nuclease Domain Suggests an Evolutionary Lineage among Eukaryotic and Prokaryotic Viruses

This is the publisher's version, also available electronically from http://jvi.asm.org/content/87/12/7140Herpes simplex virus 1 (HSV-1), the prototypic member of herpesviruses, employs a virally encoded molecular machine called terminase to package the viral double-stranded DNA (dsDNA) genome into a preformed protein shell. The terminase contains a large subunit that is thought to cleave concatemeric viral DNA during the packaging initiation and completion of each packaging cycle and supply energy to the packaging process via ATP hydrolysis. We have determined the X-ray structure of the C-terminal domain of the terminase large-subunit pUL15 (pUL15C) from HSV-1. The structure shows a fold resembling those of bacteriophage terminases, RNase H, integrases, DNA polymerases, and topoisomerases, with an active site clustered with acidic residues. Docking analysis reveals a DNA-binding surface surrounded by flexible loops, indicating considerable conformational changes upon DNA binding. In vitro assay shows that pUL15C possesses non-sequence-specific, Mg2+-dependent nuclease activity. These results suggest that pUL15 uses an RNase H-like, metal ion-mediated catalysis mechanism for cleavage of viral concatemeric DNA. The structure reveals extra structural elements in addition to the RNase H-like fold core and variations in local architecture of the nuclease active site, which are conserved in herpesvirus terminases and bear great similarity to the phage T4 gp17 but are distinct from podovirus and siphovirus orthologs and cellular RNase H, delineating a new evolutionary lineage among a large family of eukaryotic viruses and simple and complex prokaryotic viruses

Highlighting a Digital Platform to Assess Young People Needs: Reaching and Engaging Adolescents and Young Adults for Care Continuum in Health Project (REACH)

Young people (YP), defined as individuals aged between 10 and 24 years, are a vulnerable population. Leveraging digital platforms to reach YP is essential in identifying protective and risk behaviors among this population. The objectives of this study were to (1) examine the user-inclusive development process of a theory-based digital platform to reach YP, (2) describe aspects of the digital application prototype, and (3) provide preliminary findings from the utilization of the app. We present the five-step design process for building the app. The app, known as the REACH-AYA survey, consisted of 98 closed-ended questions with built-in skip-logic algorithms and took approximately 7 min to complete. The survey questions centered on behavioral, lifestyle, and psychosocial factors, which were adopted from different validated instruments, thereby addressing 10 different domains. During the pilot phase, participants utilized the app, critiqued its features, and provided iterative feedback. We used respondent-driven sampling to recruit participants in Nairobi, Kenya, the leading county in high-speed data connectivity. Once recruited, each participant completed the survey and later sent it to their peers until the desired sample size was achieved. The REACH-AYA app prototype was guided and developed by the design thinking approach with an initial pilot sample of 33 YP for pre-testing. The end-user pre-testing assessed for functionality, time, and adaptability. The app was then launched initially through social media, reaching 1101 YP, with approximately eighty percent (n = 887) having completed the survey by the close of the study. The majority of the participants were male (59%), and approximately (69%) of the participants were aged between 15 and 24 years. This is one of the few studies that demonstrate user-centric methodologies of app development and real-life application in identifying protective and risk factors for the wellbeing of YP. Methodologies and lessons learned from this research may benefit other disciplines using digital technology to reach YP or other difficult-to-reach populations

Highlighting a Digital Platform to Assess Young People Needs: Reaching and Engaging Adolescents and Young Adults for Care Continuum in Health Project (REACH)

Young people (YP), defined as individuals aged between 10 and 24 years, are a vulnerable population. Leveraging digital platforms to reach YP is essential in identifying protective and risk behaviors among this population. The objectives of this study were to (1) examine the user-inclusive development process of a theory-based digital platform to reach YP, (2) describe aspects of the digital application prototype, and (3) provide preliminary findings from the utilization of the app. We present the five-step design process for building the app. The app, known as the REACH-AYA survey, consisted of 98 closed-ended questions with built-in skip-logic algorithms and took approximately 7 min to complete. The survey questions centered on behavioral, lifestyle, and psychosocial factors, which were adopted from different validated instruments, thereby addressing 10 different domains. During the pilot phase, participants utilized the app, critiqued its features, and provided iterative feedback. We used respondent-driven sampling to recruit participants in Nairobi, Kenya, the leading county in high-speed data connectivity. Once recruited, each participant completed the survey and later sent it to their peers until the desired sample size was achieved. The REACH-AYA app prototype was guided and developed by the design thinking approach with an initial pilot sample of 33 YP for pre-testing. The end-user pre-testing assessed for functionality, time, and adaptability. The app was then launched initially through social media, reaching 1101 YP, with approximately eighty percent (n = 887) having completed the survey by the close of the study. The majority of the participants were male (59%), and approximately (69%) of the participants were aged between 15 and 24 years. This is one of the few studies that demonstrate user-centric methodologies of app development and real-life application in identifying protective and risk factors for the wellbeing of YP. Methodologies and lessons learned from this research may benefit other disciplines using digital technology to reach YP or other difficult-to-reach populations

Neonatal, Infant, and Child Mortality among Women Exposed to Intimate Partner Violence in East Africa: A Multi-Country Analysis

© 2020 The Author(s). Background: Most neonatal, infant, and child deaths occur in low- and middle-income countries (LMICs), where incidence of intimate partner violence (IPV) is highest in the world. Despite these facts, research regarding whether the two are associated is limited. The main objective was to examine associations between IPV amongst East African women and risk of death among their neonates, infants, and children, as well as related variables. Methods: Analysis was conducted on data drawn from the Demographic and Health Surveys (DHS) conducted by ICF Macro/MEASURE DHS in five East African countries: Burundi, Kenya, Rwanda, Tanzania, and Uganda. The analytical sample included 11,512 women of reproductive age (15-49 years). The outcome variables, described by proportions and frequencies, were the presence or absence of neonatal, infant, and under-five mortality. Our variable of interest, intimate partner violence, was a composite variable of physical, sexual, and emotional abuse; chi-square tests were used to analyze its relationship with categorical variables. Adjusted odds ratios (aOR) were also used in linking sexual autonomy to independent variables. Results: Children born to women who experienced IPV were significantly more likely to die as newborns (aOR = 1.3, 95% confidence interval [CI]: 1.4-2.2) and infants (aOR = 1.9, 95% CI: 1.6-2.2), and they were more likely to die by the age of five (aOR = 1.5, 95% CI: 1.01-1.55). Socioeconomic indicators including area of residence, wealth index, age of mother/husband, religion, level of education, employment status, and mass media usage were also significantly associated with IPV. After regression modelling, mothers who were currently using contraceptives were determined less likely to have their children die as newborns (aOR = 0.5, 95% CI: 0.3-0-7), as infants (aOR = 0.5, 95% CI: 0.3-06), and by age five (aOR = 0.4, 95% CI: 02-0.6). Conclusion: Understanding IPV as a risk indicator for neonatal, infant, and child deaths can help in determining appropriate interventions. IPV against women should be considered an urgent priority within programs and policies aimed at maximizing survival of infants and children in East Africa and the wellbeing and safety of their mothers

A field bioassay for assessing ivermectin bio-efficacy in wild malaria vectors

Abstract Background Ivermectin (IVM) mass drug administration is a candidate complementary malaria vector control tool. Ingestion of blood from IVM treated hosts results in reduced survival in mosquitoes. Estimating bio-efficacy of IVM on wild-caught mosquitoes requires they ingest the drug in a blood meal either through a membrane or direct feeding on a treated host. The latter, has ethical implications, and the former results in low feeding rates. Therefore, there is a need to develop a safe and effective method for IVM bio-efficacy monitoring in wild mosquitoes. Methods Insectary-reared Anopheles gambiae s.s. were exposed to four IVM doses: 85, 64, 43, 21 ng/ml, and control group (0 ng/ml) in three different solutions: (i) blood, (ii) 10% glucose, (iii) four ratios (1:1, 1:2, 1:4, 1:8) of blood in 10% glucose, and fed through filter paper. Wild-caught An. gambiae s.l. were exposed to 85, 43 and 21 ng/ml IVM in blood and 1:4 ratio of blood-10% glucose mixture. Survival was monitored for 28 days and a pool of mosquitoes from each cohort sacrificed immediately after feeding and weighed to determine mean weight of each meal type. Results When administered in glucose solution, mosquitocidal effect of IVM was not comparable to the observed effects when similar concentrations were administered in blood. Equal concentrations of IVM administered in blood resulted in pronounced reductions in mosquito survival compared to glucose solution only. However, by adding small amounts of blood to glucose solution, mosquito mortality rates increased resulting in similar effects to what was observed during blood feeding. Conclusion Bio-efficacy of ivermectin is strongly dependent on mode of drug delivery to the mosquito and likely influenced by digestive processes. The assay developed in this study is a good candidate for field-based bio-efficacy monitoring: wild mosquitoes readily feed on the solution, the assay can be standardized using pre-selected concentrations and by not involving treated blood hosts (human or animal) variation in individual pharmacokinetic profiles as well as ethical issues are bypassed. Meal volumes did not explain the difference in the lethality of IVM across the different meal types necessitating further research on the underlying mechanisms

Data release: targeted systematic literature search for tick and tick-borne pathogen distributions in six countries in sub-Saharan Africa from 1901 to 2020

Abstract Background Surveillance data documenting tick and tick-borne disease (TBD) prevalence is needed to develop risk assessments and implement control strategies. Despite extensive research in Africa, there is no standardized, comprehensive review. Methods Here we tackle this knowledge gap, by producing a comprehensive review of research articles on ticks and TBD between 1901 and 2020 in Chad, Djibouti, Ethiopia, Kenya, Tanzania, and Uganda. Over 8356 English language articles were recovered. Our search strategy included 19 related MeSH terms. Articles were reviewed, and 331 met inclusion criteria. Articles containing mappable data were compiled into a standardized data schema, georeferenced, and uploaded to VectorMap. Results Tick and pathogen matrixes were created, providing information on vector distributions and tick–pathogen associations within the six selected African countries. Conclusions These results provide a digital, mappable database of current and historical tick and TBD distributions across six countries in Africa, which can inform specific risk modeling, determine surveillance gaps, and guide future surveillance priorities. Graphical Abstrac

Applying an evolutionary mismatch framework to understand disease susceptibility.

Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of lifestyle diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be mismatched and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit genotype by environment (GxE) interactions, with different health effects in ancestral versus modern environments. To identify such loci, we advocate for combining genomic tools in partnership with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the matched to mismatched spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures