Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite’s biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.

PurposeTo evaluate prevalence and associated factors for myopia in high school students in Beijing.MethodsGrade 10 and 11 high school students were randomly selected from nine randomly selected districts of Beijing. The students underwent non-cylcoplegic auto-refractometry and an interview.ResultsOut of 4798 eligible students, 4677 (93.4%) students (mean age:16.9±0.7years;range:16–18 years) participated. Mean refractive error of right eyes and left eyes was −2.78±2.29 diopters and −2.59±2.50 diopters, respectively. Prevalence of myopia (defined as ≤ −1.00 diopters in the worse eye) was 80.7% (95% Confidence Interval (CI): 79.6–81.8%). Out of 3773 students with myopia, 1525 (40.4%) wore glasses daily. In multiple logistic regression analysis, a higher prevalence of myopia was associated with female sex (odds ratio (OR) = 1.31;95%CI:1.11–1.55), Han ethnicity (OR = 1.64;95%CI:1.28–2.11), attending key schools (OR = 1.48;95%CI:1.24,1.77), higher family income (OR = 1.37;95%CI:1.09–1.71), longer time spent for near work (OR = 1.43;95%CI:1.06–1.93), shorter near work distance (OR = 1.87;95%CI:1.55–2.26), lower frequency of active rest during studying (OR = 1.40;95%CI:1.16–1.70), and parental myopia (OR = 2.28;95%CI:1.80–2.87). The interaction between distance from near work and time spent for near work was statistically (P = 0.03) significant. In multiple logistic regression analysis, higher prevalence of high myopia (≤-6.0 diopters) was associated with studying in key schools (OR = 1.38;95%CI:1.05,1.81), lower frequency of active rest during studying (OR = 1.40;95%CI:1.09,1.79), and a higher number of myopic parents (OR = 2.66;95%CI:2.08,3.40).ConclusionsA prevalence of about 80% for myopia and a prevalence of about 10% for high myopia in students aged 16 to 18 years and attending classes of grade 10 and 11 in a Chinese metropolitan region is another example of the high prevalence of moderate and high myopia in metropolitan areas of China. With this young myopic generation getting older, myopia as cause for visual impairment and blindness may further increase in importance. Future studies may address whether active rests during studying with looking into the distance are preventive against myopia development or progression.

Abbreviations: aa, amino acid(s); Ab, antibody; AMA1, apical membrane antigen 1; GST, Glutathione S transferase; PBS, phosphate-buffered saline; PCR, polymerase chain reaction; RON, rhoptry neck protein. AbstractErythrocyte invasion is an essential step in the establishment of host infection by malaria parasites, and is a major target of intervention strategies that attempt to control the disease.Recent proteome analysis of the closely-related apicomplexan parasite, Toxoplasma gondii, falciparum, suggesting that co-operative function of the rhoptry and microneme proteins is a common mechanism in apicomplexan parasites during host cell invasion. PfRON2 possesses a region displaying homology with the rhoptry body protein PfRhopH1/Clag, a component of the RhopH complex. However, here we present co-immunoprecipitation studies which suggest that PfRON2 is not a component of the RhopH complex and has an independent role. Nucleotide polymorphism analysis suggested that PfRON2 was under diversifying selective pressure. This evidence suggests that RON2 appears to have a fundamental role in host cell invasion by apicomplexan parasites, and is a potential target for malaria intervention strategies.

PurposeTo assess factors associated with myopia in school children in rural and urban parts of Greater Beijing.MethodsThe Beijing Pedriatic Eye Study was a population-based cross-sectional study, in which one school of each level (primary, junior high, senior high) was randomly selected from nine randomly selected districts out of 18 districts of Greater Beijing. The children underwent non-cylcoplegic refractometry and their parents an interview.ResultsOf 16,771 eligible students, 15,066 (89.8%) children (7,769 (51.6%) girls) participated, with 8,860 (58.8%) participants living in the rural region. Mean age was 13.2±3.4 years (range:7–18 years). In multivariate analysis, prevalence of myopia (defined as ≤−1.00 diopters) was associated with higher age (Odds ratio(OR):1.37; 95% confidence interval(CI):1.35,1.39), female gender (OR:1.35;95%CI:1.25,1.47), key school type (OR:0.77;95%CI: 0.70,0.85), higher family income (OR:1.04;95%CI:1.01,1.07), parental myopia (OR:1.46;95%CI:1.40,1.53), dim reading illumination (OR:0.93;95%CI: 0.88,0.98), longer daily studying duration (OR:1.10;95%CI:1.06,1.15), shorter duration of watching television (or computer) (OR:0.93;95%CI:0.89,0.97), higher self-reported protein intake (OR:0.94;95%CI:0.90,0.99), feeling well about life and status (OR:0.93;95%CI:0.89,0.98), and feeling tired or dizzy (OR:0.94;95%CI:0.91,0.97). Prevalence of high myopia (defined as ≤−6.00 diopters) was associated with higher age (OR:1.43;95%CI:1.38, 1.48), key school type (OR:0.61;95%CI:0.49,0.74), family income (OR:1.07;95%CI:1.02,1.13), parental myopia (OR:1.65;95%CI:1.54,1.76), dim reading illumination (OR:0.86;95%CI:0.77,0.96), less rest during studying (OR:1.18;95%CI:1.10,1.27), feeling well about life and studying (OR:0.88;95%CI: 0.81,0.96) and feeling dizzy or tired (OR:0.93;95%CI:0.87,0.99). Prevalence of high myopia (defined as ≤−8.00 diopters) was significantly associated with higher age (OR:1.39;95%CI:1.31,1.48;), key school type (OR:0.61;95%CI:0.42,0.88) and parental myopia (OR:1.87;95%CI:1.66,2.12).ConclusionsMyopia in school children in Greater Beijing was associated with higher age, female gender, school type, parental myopia, higher socioeconomic background, dim reading illumination, longer daily studying duration, less rest during study, shorter duration of watching television (or computer), higher self-reported protein intake, feeling well about life and status, and feeling tired and dizzy.

The diploid strawberry Fragaria vesca serves as an ideal model plant for cultivated strawberry ( Fragaria × ananassa , 8 x ) and the Rosaceae family. The F. vesca genome was initially published in 2011 using older technologies. Recently, a new and greatly improved F. vesca genome, designated V4, was published. However, the number of annotated genes is remarkably reduced in V4 (28,588 genes) compared to the prior annotations (32,831 to 33,673 genes). Additionally, the annotation of V4 (v4.0.a1) implements a new nomenclature for gene IDs (FvH4_XgXXXXX), rather than the previous nomenclature (geneXXXXX). Hence, further improvement of the V4 genome annotation and assigning gene expression levels under the new gene IDs with existing transcriptome data are necessary to facilitate the utility of this high-quality F. vesca genome V4. Here, we built a new and improved annotation, v4.0.a2, for F. vesca genome V4. The new annotation has a total of 34,007 gene models with 98.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCOs). In this v4.0.a2 annotation, gene models of 8,342 existing genes are modified, 9,029 new genes are added, and 10,176 genes possess alternatively spliced isoforms with an average of 1.90 transcripts per locus. Transcription factors/regulators and protein kinases are globally identified. Interestingly, the transcription factor family FAr-red-impaired Response 1 ( FAR1 ) contains 82 genes in v4.0.a2 but only two members in v4.0.a1. Additionally, the expression levels of all genes in the new annotation across a total of 46 different tissues and stages are provided. Finally, miRNAs and their targets are reanalyzed and presented. Altogether, this work provides an updated genome annotation of the F. vesca V4 genome as well as a comprehensive gene expression atlas with the new gene ID nomenclature, which will greatly facilitate gene functional studies in strawberry and other evolutionarily related plant species.