Deep Whole-Genome Sequencing of 100 Southeast Asian Malays

Whole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30× coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (<5%) markers, a larger number of individuals might have to be whole-genome sequenced so that the accuracy currently afforded by the 1KGP can be achieved. The SSMP data are expected to be the benchmark for evaluating the value of deep population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies.     

Investigating the association between OPA1 polymorphisms and glaucoma: comparison between normal tension and high tension primary open angle glaucoma

OPA1, the gene responsible for autosomal dominant optic atrophy, represents a good candidate gene for glaucoma, as there are similarities in the clinical phenotype and OPA1 is expressed in the optic nerve. Single nucleotide polymorphisms on intervening sequence (IVS) 8 of the OPA1gene (genotype IVS8+4 C/T;+32T/C) were recently found to be strongly associated with normal tension glaucoma (NTG). In order to investigate whether this association exists in patients with high-tension glaucoma (HTG), 90 well-characterized HTG patients were examined for the presence of these OPA1polymorphisms by PCR amplification followed by bi-directional sequencing. Five out of 90 HTG subjects (5.6%; 95% CI 1.8-12.5) were found to carry the OPA1 genotype IVS 8+4 C/T; +32 T/C, compared with 32/163 (19.6%; 95% CI 13.8-26.6) NTG subjects [chi(2)=9.2, P=0.002, OR 4.1 (95% CI 1.6-11.1)], and 7/186 (3.8%; 95% CI 1.5-7.6) control subjects [chi(2)=0.47, P=0.49, OR 1.5 (95% CI 0.5-4.9)]. These results indicate that unlike NTG, the OPA1 genotype IVS8+4 C/T,+32T/C is not significantly associated with high-tension primary open angle glaucoma, and suggest genetic heterogeneity between the conditions.     

Diversity and abundance of nematode-trapping fungi from decaying litter in terrestrial, freshwater and mangrove habitats

Nematode-trapping fungi are ubiquitous in terrestrial habitats in dung, soils, litter and woody debris and they also occur in freshwater, but only one species has been found in marine habitats. The purpose of this study was therefore to investigate whether nematode-trapping fungi occurred in mangrove habitats. To achieve this we assessed the diversity of nematode-trapping fungi on decaying litter from mangroves, freshwater and terrestrial habitats (22 sites) in Hong Kong. Composite samples (n = 1,320) of decaying litter (wood and leaves) were examined and a total of 31 species of nematode-trapping fungi belonging to four genera, Arthrobotrys, Monacrosporium, and Dactylella were recorded. Twenty-nine species reported in this study are new records for Hong Kong and 16 species are new records from mangrove habitats worldwide. Nematode trapping fungi are therefore present in marine environments. Commonly encountered taxa were Arthrobotrys oligospora and Monacrosporium thaumasium which are abundant in all habitats. A. oligospora, M. thaumasium and Arthrobotrys musiformis were frequent (F > 10%). Twenty-six species were rare (0.16–9.32%). Species richness and diversity was higher in terrestrial than in freshwater and mangrove habitats (ANOVA, P < 0.001). A higher mean diversity was observed on decaying leaves as compared to decaying wood in all habitats (P < 0.001). Based on Shannon diversity index, it was also observed that taxa characterized by adhesive nets were more frequent in all habitats. This can be explained by the fact that these taxa may have a better competitive saprotrophic ability which would allow them to compete favourably in nutrient limited environments. Abiotic factors that could be linked to differences in species diversity between decaying wood and leaves are also discussed.     

Aggregation of Lepidostomatidae in small mesh size litter-bags: implication to the leaf litter decomposition process

Invertebrate colonization during leaf litter decomposition was studied at the 2nd order of Yanase River, Iruma city, Saitama, Japan from November 13, 2002 to May 20, 2003. Two different mesh sizes (1 and 5 mm) of litter-bags were used to evaluate the decomposition of leaf litter of Sakura (Prunus lannesiana), bags were placed equally in riffle (water flow velocity: 0.2–0.6 m s⁻¹) and pool (water flow velocity: 0.04–0.06 m s⁻¹). Mass loss and invertebrates in the litter-bags were monitored at interval between 1 and 3 weeks, and the invertebrates were classified based on their functional feeding group. Among the invertebrates found inside the litter-bags, the case-bearing shredder Lepidostomatidae was the most dominant invertebrates and they were the early colonizer that appeared about 3 months after the litter-bags immersion. In absence or low number of leaf-shredders, the decomposition rates in 1 and 5 mm litter mesh bags followed the exponential (or first-order) decay kinetic (R ²: 0.72–0.92). However, the presence of a large number of leaf-shredders in 1 mm litter-bags caused an acceleration of decomposition process; that even resulted faster mass loss than the loss from the 5 mm mesh bags placed in riffle area (0.030 day⁻¹ vs. 0.011 day⁻¹). Our results shows the importance of using different mesh sizes of litter-bags in decomposition study, which is applicable to the experiment in lotic or lentic ecosystem. Using smaller mesh size of litter-bags can provide information on how significant the effect of detritus feeders on the decomposition process, while the bigger mesh size can represent better the natural decomposition process when a large number detritus feeders is present in the smaller mesh size of litter-bags.     

Are C-Reactive Protein Associated Genetic Variants Associated with Serum Levels and Retinal Markers of Microvascular Pathology in Asian Populations from Singapore?

Introduction

C-reactive protein (CRP) levels are associated with cardiovascular disease and systemic inflammation. We assessed whether CRP-associated loci were associated with serum CRP and retinal markers of microvascular disease, in Asian populations.

Methods

Genome-wide association analysis (GWAS) for serum CRP was performed in East-Asian Chinese (N = 2,434) and Malays (N = 2,542) and South-Asian Indians (N = 2,538) from Singapore. Leveraging on GWAS data, we assessed, in silico, association levels among the Singaporean datasets for 22 recently identified CRP-associated loci. At loci where directional inconsistencies were observed, quantification of inter-ethnic linkage disequilibrium (LD) difference was determined. Next, we assessed association for a variant at CRP and retinal vessel traits [central retinal artery equivalent (CRAE) and central retinal vein equivalent (CRVE)] in a total of 24,132 subjects of East-Asian, South-Asian and European ancestry.

Results

Serum CRP was associated with SNPs in/near APOE, CRP, HNF1A and LEPR (p-values ≤4.7×10⁻⁸) after meta-analysis of Singaporean populations. Using a candidate-SNP approach, we further replicated SNPs at 4 additional loci that had been recently identified to be associated with serum CRP (IL6R, GCKR, IL6 and IL1F10) (p-values ≤0.009), in the Singaporean datasets. SNPs from these 8 loci explained 4.05% of variance in serum CRP. Two SNPs (rs2847281 and rs6901250) were detected to be significant (p-value ≤0.036) but with opposite effect directions in the Singaporean populations as compared to original European studies. At these loci we did not detect significant inter-population LD differences. We further did not observe a significant association between CRP variant and CRVE or CRAE levels after meta-analysis of all Singaporean and European datasets (p-value >0.058).

Conclusions

Common variants associated with serum CRP, first detected in primarily European studies, are also associated with CRP levels in East-Asian and South-Asian populations. We did not find a causal link between CRP and retinal measures of microvascular disease.     

Whole-Genome Sequencing of Aspergillus terreus Species Complex

Mycopathologia - Aspergillus terreus species complex is an opportunistic fungal pathogen increasingly implicated in invasive infection, as well as chronic respiratory disease. Currently, an...     

Malaria Burden and Artemisinin Resistance in the Mobile and Migrant Population on the Thai–Myanmar Border, 1999–2011: An Observational Study

Background

The Shoklo Malaria Research Unit has been working on the Thai–Myanmar border for 25 y providing early diagnosis and treatment (EDT) of malaria. Transmission of Plasmodium falciparum has declined, but resistance to artesunate has emerged. We expanded malaria activities through EDT and evaluated the impact over a 12-y period.

Methods and Findings

Between 1 October 1999 and 30 September 2011, the Shoklo Malaria Research Unit increased the number of cross-border (Myanmar side) health facilities from two to 11 and recorded the number of malaria consultations. Changes in malaria incidence were estimated from a cohort of pregnant women, and prevalence from cross-sectional surveys. In vivo and in vitro antimalarial drug efficacy were monitored. Over this period, the number of malaria cases detected increased initially, but then declined rapidly. In children under 5 y, the percentage of consultations due to malaria declined from 78% (95% CI 76–80) (1,048/1,344 consultations) to 7% (95% CI 6.2–7.1) (767/11,542 consultations), p<0.001. The ratio of P. falciparum/P. vivax declined from 1.4 (95% CI 1.3–1.4) to 0.7 (95% CI 0.7–0.8). The case fatality rate was low (39/75,126; 0.05% [95% CI 0.04–0.07]). The incidence of malaria declined from 1.1 to 0.1 episodes per pregnant women-year. The cumulative proportion of P. falciparum decreased significantly from 24.3% (95% CI 21.0–28.0) (143/588 pregnant women) to 3.4% (95% CI 2.8–4.3) (76/2,207 pregnant women), p<0.001. The in vivo efficacy of mefloquine-artesunate declined steadily, with a sharp drop in 2011 (day-42 PCR-adjusted cure rate 42% [95% CI 20–62]). The proportion of patients still slide positive for malaria at day 3 rose from 0% in 2000 to reach 28% (95% CI 13–45) (8/29 patients) in 2011.

Conclusions

Despite the emergence of resistance to artesunate in P. falciparum, the strategy of EDT with artemisinin-based combination treatments has been associated with a reduction in malaria in the migrant population living on the Thai–Myanmar border. Although limited by its observational nature, this study provides useful data on malaria burden in a strategically crucial geographical area. Alternative fixed combination treatments are needed urgently to replace the failing first-line regimen of mefloquine and artesunate. Please see later in the article for the Editors'' Summary     

A miRNA involved in phosphate-starvation response in Arabidopsis

Although microRNAs (miRNAs) have been documented to regulate development in plants and animals , the function of miRNAs in physiology is unclear. miR399 has multiple target sites in the 5' untranslated region (UTR) of a gene encoding a putative ubiquitin-conjugating enzyme (UBC) in Arabidopsis thaliana. We report here that miR399 was highly induced, whereas the target UBC mRNA was reduced by low-phosphate (Pi) stress. In transgenic plants with constitutive expression of miR399, UBC mRNA accumulation was suppressed even under high Pi. The expression of transgene UBC mRNA with 5' UTR miR399 target sites, but not the one without 5' UTR, was reduced under low-Pi condition. Furthermore, transgenic Arabidopsis plants with constitutive expression of miR399 accumulated more Pi than the wild-type, and transgenic plants expressing the UBC mRNA without 5' UTR (miRNA-deregulated) showed less inhibition of primary root growth and less induction of a Pi transporter gene by low-Pi stress than those of wild-type plants. We conclude that miR399 downregulates UBC mRNA accumulation by targeting the 5' UTR, and this regulation is important for plant responses to Pi starvation. The results suggest that miRNAs have functional roles for plants to cope with fluctuations in mineral-nutrient availability in the soil.     

Monohydroxycarotenoids from diphenylamine-inhibited cultures of Rhodospirillum rubrum

The monohydroxycarotenoids formed by diphenylamine-inhibited cultures of Rhodospirillum rubrum have been investigated. Nine have been isolated and identified as 1-hydroxy-1,2-dihydrophytofluene (1), 1-Hydroxy-1,2,7′,8′,11′,12′-hexahydrolycopene (2), chloroxanthin (3), 1-methoxy-1′-hydroxy-1,2,1′,2′-tetrahydrophytofluene (4a), 1′-hydroxy-3,4,1′,2′,11′,12′-hexahydrospheroidene (5, 1′-hydroxy-3,4,1′,2′-tetrahydrospheroidene (6, 1′-hydroxy 1′,2′-dihydrospheroidene (7), rhodovibrin (8a) and monodeme thylated spirilloxanthin (9). 4a, 5 and 6 are novel carotenoids, and a definite structure has been assigned to 2 for the first time; the structure of 1 has been amended. The possible role of these carotenoids in spirilloxanthin biosynthesis is discussed.