Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints

Dengue viruses (DENV) cause debilitating and potentially life-threatening acute disease throughout the tropical world. While drug development efforts are underway, there are concerns that resistant strains will emerge rapidly. Indeed, antiviral drugs that target even conserved regions in other RNA viruses lose efficacy over time as the virus mutates. Here, we sought to determine if there are regions in the DENV genome that are not only evolutionarily conserved but genetically constrained in their ability to mutate and could hence serve as better antiviral targets. High-throughput sequencing of DENV-1 genome directly from twelve, paired dengue patients’ sera and then passaging these sera into the two primary mosquito vectors showed consistent and distinct sequence changes during infection. In particular, two residues in the NS5 protein coding sequence appear to be specifically acquired during infection in Ae. aegypti but not Ae. albopictus. Importantly, we identified a region within the NS3 protein coding sequence that is refractory to mutation during human and mosquito infection. Collectively, these findings provide fresh insights into antiviral targets and could serve as an approach to defining evolutionarily constrained regions for therapeutic targeting in other RNA viruses.     

Identification of MicroRNAs and Transcript Targets in Camelina sativa by Deep Sequencing and Computational Methods

Camelina sativa is an annual oilseed crop that is under intensive development for renewable resources of biofuels and industrial oils. MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play key roles in diverse plant biological processes. Here, we conducted deep sequencing on small RNA libraries prepared from camelina leaves, flower buds and two stages of developing seeds corresponding to initial and peak storage products accumulation. Computational analyses identified 207 known miRNAs belonging to 63 families, as well as 5 novel miRNAs. These miRNAs, especially members of the miRNA families, varied greatly in different tissues and developmental stages. The predicted miRNA target genes are involved in a broad range of physiological functions including lipid metabolism. This report is the first step toward elucidating roles of miRNAs in C. sativa and will provide additional tools to improve this oilseed crop for biofuels and biomaterials.     

Influenza Seasonality in the Tropics and Subtropics – When to Vaccinate?

BackgroundThe timing of the biannual WHO influenza vaccine composition selection and production cycle has been historically directed to the influenza seasonality patterns in the temperate regions of the northern and southern hemispheres. Influenza activity, however, is poorly understood in the tropics with multiple peaks and identifiable year-round activity. The evidence-base needed to take informed decisions on vaccination timing and vaccine formulation is often lacking for the tropics and subtropics. This paper aims to assess influenza seasonality in the tropics and subtropics. It explores geographical grouping of countries into vaccination zones based on optimal timing of influenza vaccination.MethodsInfluenza seasonality was assessed by different analytic approaches (weekly proportion of positive cases, time series analysis, etc.) using FluNet and national surveillance data. In case of discordance in the seasonality assessment, consensus was built through discussions with in-country experts. Countries with similar onset periods of their primary influenza season were grouped into geographical zones.ResultsThe number and period of peak activity was ascertained for 70 of the 138 countries in the tropics and subtropics. Thirty-seven countries had one and seventeen countries had two distinct peaks. Countries near the equator had secondary peaks or even identifiable year-round activity. The main influenza season in most of South America and Asia started between April and June. The start of the main season varied widely in Africa (October and December in northern Africa, April and June in Southern Africa and a mixed pattern in tropical Africa). Eight “influenza vaccination zones” (two each in America and Asia, and four in Africa and Middle East) were defined with recommendations for vaccination timing and vaccine formulation. The main limitation of our study is that FluNet and national surveillance data may lack the granularity to detect sub-national variability in seasonality patterns.ConclusionDistinct influenza seasonality patterns, though complex, could be ascertained for most countries in the tropics and subtropics using national surveillance data. It may be possible to group countries into zones based on similar recommendations for vaccine timing and formulation.     

A DNA vaccine against chikungunya virus is protective in mice and induces neutralizing antibodies in mice and nonhuman primates

Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus indigenous to tropical Africa and Asia. Acute illness is characterized by fever, arthralgias, conjunctivitis, rash, and sometimes arthritis. Relatively little is known about the antigenic targets for immunity, and no licensed vaccines or therapeutics are currently available for the pathogen. While the Aedes aegypti mosquito is its primary vector, recent evidence suggests that other carriers can transmit CHIKV thus raising concerns about its spread outside of natural endemic areas to new countries including the U.S. and Europe. Considering the potential for pandemic spread, understanding the development of immunity is paramount to the development of effective counter measures against CHIKV. In this study, we isolated a new CHIKV virus from an acutely infected human patient and developed a defined viral challenge stock in mice that allowed us to study viral pathogenesis and develop a viral neutralization assay. We then constructed a synthetic DNA vaccine delivered by in vivo electroporation (EP) that expresses a component of the CHIKV envelope glycoprotein and used this model to evaluate its efficacy. Vaccination induced robust antigen-specific cellular and humoral immune responses, which individually were capable of providing protection against CHIKV challenge in mice. Furthermore, vaccine studies in rhesus macaques demonstrated induction of nAb responses, which mimicked those induced in convalescent human patient sera. These data suggest a protective role for nAb against CHIKV disease and support further study of envelope-based CHIKV DNA vaccines.     

The Two-Photon Reversible Reaction of the Bistable Jumping Spider Rhodopsin-1

Bistable opsins are photopigments expressed in both invertebrates and vertebrates. These light-sensitive G-protein-coupled receptors undergo a reversible reaction upon illumination. A first photon initiates the cis to trans isomerization of the retinal chromophore—attached to the protein through a protonated Schiff base—and a series of transition states that eventually results in the formation of the thermally stable and active Meta state. Excitation by a second photon reverts this process to recover the original ground state. On the other hand, monostable opsins (e.g., bovine rhodopsin) lose their chromophore during the decay of the Meta II state (i.e., they bleach). Spectroscopic studies on the molecular details of the two-photon cycle in bistable opsins are limited. Here, we describe the successful expression and purification of recombinant rhodopsin-1 from the jumping spider Hasarius adansoni (JSR1). In its natural configuration, spectroscopic characterization of JSR1 is hampered by the similar absorption spectra in the visible spectrum of the inactive and active states. We solved this issue by separating their absorption spectra by replacing the endogenous 11-cis retinal chromophore with the blue-shifted 9-cis JSiR1. With this system, we used time-resolved ultraviolet-visible spectroscopy after pulsed laser excitation to obtain kinetic details of the rise and decay of the photocycle intermediates. We also used resonance Raman spectroscopy to elucidate structural changes of the retinal chromophore upon illumination. Our data clearly indicate that the protonated Schiff base is stable throughout the entire photoreaction. We additionally show that the accompanying conformational changes in the protein are different from those of monostable rhodopsin, as recorded by light-induced FTIR difference spectroscopy. Thus, we envisage JSR1 as becoming a model system for future studies on the reaction mechanisms of bistable opsins, e.g., by time-resolved x-ray crystallography.     

Molecular Evolution of PvMSP3α Block II in Plasmodium vivax from Diverse Geographic Origins

Block II of Plasmodium vivax merozoite surface protein 3α (PvMSP3α) is conserved and has been proposed as a potential candidate for a malaria vaccine. The present study aimed to compare sequence diversity in PvMSP3a block II at a local microgeographic scale in a village as well as from larger geographic regions (countries and worldwide). Blood samples were collected from asymptomatic carriers of P. vivax in a village at the western border of Thailand and PvMSP3α was amplified and sequenced. For population genetic analysis, 237 PvMSP3α block II sequences from eleven P. vivax endemic countries were analyzed. PvMSP3α sequences from 20 village-level samples revealed two length variant types with one type containing a large deletion in block I. In contrast, block II was relatively conserved; especially, some non-synonymous mutations were extensively shared among 11 parasite populations. However, the majority of the low-frequency synonymous variations were population specific. The conserved pattern of nucleotide diversity in block II sequences was probably due to functional/structural constraints, which were further supported by the tests of neutrality. Notably, a small region in block II that encodes a predicted B cell epitope was highly polymorphic and showed signs of balancing selection, signifying that this region might be influenced by the immune selection and may serve as a starting point for designing multi-antigen/stage epitope based vaccines against this parasite.     

Measuring Health-Related Quality of Life in Strabismus: A Modification of the Adult Strabismus-20 (AS-20) Questionnaire Using Rasch Analysis

PurposeTo evaluate the psychometric properties of the Adult Strabismus-20 (AS-20)- a health-related quality of life (HRQoL) questionnaire in adults with strabismus, and if flawed, to revise the AS-20 and its subscales creating valid measurement scales.Methods584 adults (meanage, 27.5 years) with strabismus were recruited from an outpatient clinic at a South Indian tertiary eye care centre and were administered the AS-20 questionnaire.The AS-20 was translated and back translated into two Indian languages. The AS-20 and its two 10-item subscales – ‘psychosocial’ and ‘function’were assessed separately for fit to the Rasch model, including an assessment of the rating scale, unidimensionality (by principal components analysis), measurement precision by person separation reliability, PSR, targeting, and differential item functioning (DIF; notable > 1.0 logits).ResultsResponse categories were not used as intended, thereby, required re-organization and reducing their number from 5 to 3. The AS-20 had adequate measurement precision (PSR = 0.87) but lacked unidimensionality; however, deletion of the six multi-dimensionality causing items and an additional three misfitting items resulted in 11-item unidimensional questionnaire (AS-11). Two items failed to satisfy the model expectations in the ‘psychosocial’ subscale and were deleted – resulting in an 8-item unidimensional scale with adequate PSR (0.81) and targeting (0.23 logits). One item misfit in the ‘function’ subscale and was deleted—resulting in a 9 item Rasch-revised unidimensional subscale with acceptable PSR (0.80) and targeting (0.97 logits).None of the items displayed notable DIF by age, gender and level of education.ConclusionsThe AS-11 and its two Rasch-revised subscales – 8-item psychosocial and 9-item function subscale may be more appropriate than the original AS-20 and its two 10-item subscales for use as unidimensional measures of HRQoL in adults with strabismus in India. Further work is required to establish the validity of the revised rating scale.     

A Cohort Study of Morbidity,Mortality and Health Seeking Behavior following Rural Health Center Visits by Children under 12 in Southwestern Uganda

Background

Children discharged from hospitals in developing countries are at high risk of morbidity and mortality. However, few data describe these outcomes among children seen and discharged from rural outpatient centers.

Objective

The objective of this exploratory study was to identify predictors of immediate and follow-up morbidity and mortality among children visiting a rural health center in Uganda.

Methods

Subjects 0–12 years of age seeking care with a caregiver were consecutively enrolled from a single rural health center in Southwestern Uganda. Baseline variables were collected by research nurses and outcomes of referral, admission or death were recorded (immediate events). Death, hospital admission and health seeking occurring during the 30 days following the clinic visit were also determined (follow-up events). Univariate logistic regression was performed to identify baseline variables associated with immediate outcome and follow-up outcomes.

Results

Over the four-month recruitment period 717 subjects were enrolled. There were 85 (11.9%) immediate events (10.1% were admitted, 2.2% were referred, none died). Forty-seven (7.8%) events occurred within 30 days after the visit (7.3% sought care from a health provider, 1.5% were admitted and 0.5% died). Variables associated with immediate events included living more than 30 minutes from the health center, age older than 5 years, having received an antimalarial prior to the visit, having seen a community health worker prior to the visit, elevated respiratory rate or temperature, and depressed weight-for-age z score or decreased oxygen saturation. These variables were not associated with follow-up events.

Conclusions

Sick-child visits at a rural health center in South Western Uganda were associated with rates of mortality and subsequent admission of less than 2% in the period following the sick child visits. Other types of health seeking behavior occurred in approximately 7% of subjects during this same period. Several variables were associated with immediate events but there were no reliable predictors of follow-up events, possibly due to low statistical power.     

Affected Kindred Analysis of Human X Chromosome Exomes to Identify Novel X-Linked Intellectual Disability Genes

X-linked Intellectual Disability (XLID) is a group of genetically heterogeneous disorders caused by mutations in genes on the X chromosome. Deleterious mutations in ~10% of X chromosome genes are implicated in causing XLID disorders in ~50% of known and suspected XLID families. The remaining XLID genes are expected to be rare and even private to individual families. To systematically identify these XLID genes, we sequenced the X chromosome exome (X-exome) in 56 well-established XLID families (a single affected male from 30 families and two affected males from 26 families) using an Agilent SureSelect X-exome kit and the Illumina HiSeq 2000 platform. To enrich for disease-causing mutations, we first utilized variant filters based on dbSNP, the male-restricted portions of the 1000 Genomes Project, or the Exome Variant Server datasets. However, these databases present limitations as automatic filters for enrichment of XLID genes. We therefore developed and optimized a strategy that uses a cohort of affected male kindred pairs and an additional small cohort of affected unrelated males to enrich for potentially pathological variants and to remove neutral variants. This strategy, which we refer to as Affected Kindred/Cross-Cohort Analysis, achieves a substantial enrichment for potentially pathological variants in known XLID genes compared to variant filters from public reference databases, and it has identified novel XLID candidate genes. We conclude that Affected Kindred/Cross-Cohort Analysis can effectively enrich for disease-causing genes in rare, Mendelian disorders, and that public reference databases can be used effectively, but cautiously, as automatic filters for X-linked disorders.