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.     

Are Female Sex Workers Able to Negotiate Condom Use with Male Clients? The Case of Mobile FSWs in Four High HIV Prevalence States of India

Introduction

Condom promotion among female sex workers (FSWs) is a key intervention in India’s National AIDS Control Program. However, there is limited understanding of how FSWs negotiate condom use with male clients, particularly in the context of their mobility for sex work. The objective of this study is to examine the factors associated with the mobile FSWs’ ability to refuse unsafe sex and successfully negotiate condom use with unwilling male clients.

Methods

Data for 5498 mobile FSWs from a cross-sectional survey conducted in 22 districts of four states in southern India were analyzed. Questions assessed FSWs’ ability to refuse clients unprotected sex, convince unwilling clients for condom use and negotiate condom use in a new location. Logistic regression models were constructed to examine the association between socio-demographics, economic vulnerability, sex work practice, and program exposure and condom negotiation ability.

Results

A majority of FSWs (60%) reported the ability to refuse clients for unprotected sex, but less than one-fifth reported the ability to successfully convince an unwilling client to use a condom or to negotiate condom use in a new site. Younger and older mobile FSWs compared to those who were in the middle age group, those with longer sex work experience, with an income source other than sex work, with program exposure and who purchased condoms for use, reported the ability to refuse unprotected sex, to successfully negotiate condom use with unwilling clients and to do so at new sites.

Conclusion

FSWs need to be empowered to not only refuse unprotected sex but also to be able to motivate and convince unwilling clients for condom use, including those in new locations. In addition to focusing on condom promotion, interventions must address the factors that impact FSWs’ ability to negotiate condom use.     

Role of Community Group Exposure in Reducing Sexually Transmitted Infection-Related Risk among Female Sex Workers in India

Background

Empowering female sex workers (FSWs) to address structural barriers and forming community groups (CGs) through community mobilization are seen as essential components of HIV prevention programs in India. Taking the membership of a CG as an exposure intervention, we hypothesized whether participation in a CG lead to reduced sexually transmitted infections (STIs) and increased treatment-seeking behavior among FSWs in three selected states of India — Andhra Pradesh, Maharashtra and Tamil Nadu.

Methods and Findings

The propensity score matching (PSM) approach examined the effect of CG membership, as against no membership, on STI-related risk, described as selected outcome measures — presence of any STI, self-reported STI symptoms, and treatment-seeking behavior among FSWs. A cross sectional bio-behavioral survey was administered in 2009–2010 and covered 7,806 FSWs through two-stage probability-based conventional and time location cluster sampling in 23 administrative districts of Andhra Pradesh, Maharashtra and Tamil Nadu. Only 2,939 FSWs were reported to be members of a CG and among them 4.5% had any STIs. A majority of FSWs were aged above 24 years (86.4%), had ever been married (73%), operated from a public place for solicitation (81.5%), and had ever received HIV test results (75.6%). The average effect of CG exposure was reduction in STI prevalence by 4%, while self-reported STI symptom treatment-seeking behavior increased by 13.7%.

Conclusion

FSWs who were exposed to a CG were at a substantially lower risk of STIs than those who were unexposed. The FSWs exposed to a CG had a higher chance of seeking STI treatment from public and private health facilities. Collectivization related challenges must be overcome to provide access to tailored STI prevention and care services.     

Comparative proteomics of dehydration response in the rice nucleus: New insights into the molecular basis of genotype‐specific adaptation

Dehydration is the most crucial environmental factor that considerably reduces the crop harvest index, and thus has become a concern for global agriculture. To better understand the role of nuclear proteins in water‐deficit condition, a nuclear proteome was developed from a dehydration‐sensitive rice cultivar IR‐64 followed by its comparison with that of a dehydration‐tolerant c.v. Rasi. The 2DE protein profiling of c.v. IR‐64 coupled with MS/MS analysis led to the identification of 93 dehydration‐responsive proteins (DRPs). Among those identified proteins, 78 were predicted to be destined to the nucleus, accounting for more than 80% of the dataset. While the detected number of protein spots in c.v. IR‐64 was higher when compared with that of Rasi, the number of DRPs was found to be less. Fifty‐seven percent of the DRPs were found to be common to both sensitive and tolerant cultivars, indicating significant differences between the two nuclear proteomes. Further, we constructed a functional association network of the DRPs of c.v. IR‐64, which suggests that a significant number of the proteins are capable of interacting with each other. The combination of nuclear proteome and interactome analyses would elucidate stress‐responsive signaling and the molecular basis of dehydration tolerance in plants.     

GiRaF: robust, computational identification of influenza reassortments via graph mining

Reassortments in the influenza virus--a process where strains exchange genetic segments--have been implicated in two out of three pandemics of the 20th century as well as the 2009 H1N1 outbreak. While advances in sequencing have led to an explosion in the number of whole-genome sequences that are available, an understanding of the rate and distribution of reassortments and their role in viral evolution is still lacking. An important factor in this is the paucity of automated tools for confident identification of reassortments from sequence data due to the challenges of analyzing large, uncertain viral phylogenies. We describe here a novel computational method, called GiRaF (Graph-incompatibility-based Reassortment Finder), that robustly identifies reassortments in a fully automated fashion while accounting for uncertainties in the inferred phylogenies. The algorithms behind GiRaF search large collections of Markov chain Monte Carlo (MCMC)-sampled trees for groups of incompatible splits using a fast biclique enumeration algorithm coupled with several statistical tests to identify sets of taxa with differential phylogenetic placement. GiRaF correctly finds known reassortments in human, avian, and swine influenza populations, including the evolutionary events that led to the recent 'swine flu' outbreak. GiRaF also identifies several previously unreported reassortments via whole-genome studies to catalog events in H5N1 and swine influenza isolates.     

Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis

Sequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants. We report an effective Illumina sequencing strategy utilizing pooled samples with novel quality (Srfim) and filtering (SERVIC ⁴ E) algorithms. We sequenced 24 exons in two cohorts of 480 samples each, identifying 47 coding variants, including 30 present once per cohort. Validation by Sanger sequencing revealed an excellent combination of sensitivity and specificity for variant detection in pooled samples of both cohorts as compared to publicly available algorithms.     

Identification of haplotypes in promoter of prolactin gene and their effect on egg production and quality traits in layer chicken

Expression of prolactin hormone is a crucial event in regulating egg production in chickens for which promoter plays the vital role in expressing the prolactin gene. The objective of the present study was to identify haplotypes in the prolactin promoter and their effects on egg production and egg quality traits in White Leghorn chicken. Single stranded conformation polymorphism followed by sequencing was conducted to explore polymorphism at 561 bp promoter of prolactin gene. The effect of haplotype combinations on egg production and quality traits were estimated following general linear model technique. The expression of prolactin by different haplogroups was quantified by qPCR. Total 28 haplotypes were found in White Leghorn chicken of which h1 haplotype possessed the highest frequency of 0.46 and h8, h14, h16, h25, h26, and h28 haplotypes had the lowest frequency (0.1%). The egg production up to 52 and 64 weeks of age were found to be significantly (p < 0.05) associated with haplotype combinations where the highest 52-w (52 weeks) egg production was found in animals with h1/h22 combination and the lowest production was observed in the birds with h1/h2 haplogroup. The haplotype combinations had the significant effect (p < 0.05) on Haugh Unit, yolk index and albumen weight at 40 weeks of age; Haugh Unit and albumen weight at 52 weeks of age and Haugh unit, yolk weight and yolk percentage at 64 weeks of age. The prolactin expression in h1/h22 birds was found to be the lowest and in h1/h5 birds to be the highest. The prolactin expression showed significant effect on 52-w egg production and albumin weight at 52 weeks age. In conclusion, it may be stated that the prolactin promoter was highly polymorphic and had the significant association with egg production and quality traits in White Leghorn chicken.     

Occurrence and colonization of nematophagous fungi in different substrates,agricultural soils and root galls

Seventeen species of nematophagous fungi were recorded, three species were endoparasitic and fourteen species were predacious fungi. Among the predacious fungi Arthrobotrys oligospora, Dactylaria brochopaga and Monacrosporium eudermatum were very frequent, whereas others were recorded at lower frequency. Twelve species of nematophagous fungi from compost as well as cow dung manure, 15 species from leaf litter and only eight species from agricultural soils were recorded. In general, substrate colonization by nematophagous fungi was higher in leaf litter, compost and cow dung manure. The agricultural soil amended with FYM (farm yard manure) recorded nine species of nematophagous fungi while unamended soil recorded only seven species. Thirteen species of nematophagous fungi were recorded from soils under banyan tree. Of all these fungi unidentified net-forming fungus, M. eudermatum, A. cladodes, D. brochopaga, S. hadra, A. oligospora and A. dactyloides had higher percentage of soil colonization. In soil collected under pipal tree only eight species were recorded, of which A. oligospora, A. cladode and an unidentified fungus were more predominant as their percentage colonized in soil samples was higher. Few studies have examined root galls as a substratum for colonization of nematophagous fungi. Of all the root gall samples, okra root galls recorded maximum colonization by predacious fungi. Maximum percentage of root gall colonization was recorded for M. eudermatum followed by A. oligospora and M. ellipsosporum. M. eudermatum was also most predominant colonizer of balsam, brinjal and rice root galls.     

Pediatric in-Hospital Death from Infectious Disease in Uganda: Derivation of Clinical Prediction Models

Background

Pediatric hospital mortality from infectious diseases in resource constrained countries remains unacceptably high. Improved methods of risk-stratification can assist in referral decision making and resource allocation. The purpose of this study was to create prediction models for in-hospital mortality among children admitted with suspected infectious diseases.

Methods

This two-site prospective observational study enrolled children between 6 months and 5 years admitted with a proven or suspected infection. Baseline clinical and laboratory variables were collected on enrolled children. The primary outcome was death during admission. Stepwise logistic regression minimizing Akaike’s information criterion was used to identify the most promising multivariate models. The final model was chosen based on parsimony.

Results

1307 children were enrolled consecutively, and 65 (5%) of whom died during their admission. Malaria, pneumonia and gastroenteritis were diagnosed in 50%, 31% and 8% of children, respectively. The primary model included an abnormal Blantyre coma scale, HIV and weight-for-age z-score. This model had an area under the curve (AUC) of 0.85 (95% CI, 0.80–0.89) with a sensitivity and specificity of 83% and 76%, respectively. The positive and negative predictive values were 15% and 99%, respectively. Two alternate models with similar performance characteristics were developed withholding HIV and weight-for-age z-score, for use when these variables are not available.

Conclusions

Risk stratification of children admitted with infectious diseases can be calculated based on several easily measured variables. Risk stratification at admission can be used for allocation of scarce human and physical resources and to guide referral among children admitted to lower level health facilities.