Unlocking Short Read Sequencing for Metagenomics

Background

Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved.

Methodology/Principal Findings

We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.

Conclusions/Significance

This strategy is broadly applicable to sequencing applications that benefit from low-cost high-throughput sequencing, but require longer read lengths. We demonstrate that our approach enables metagenomic analyses using the Illumina Genome Analyzer, with low error rates, and at a fraction of the cost of pyrosequencing.     

Phylogenetic variation and polymorphism at the Toll-like receptor 4 locus (TLR4)

Background  

Differences in responses to bacterial surface lipopolysaccharides (LPSs) are apparent between and within mammalian species. It has been shown in mice that resistance to LPS is caused by defects in the Toll-like receptor 4 gene (Tlr4), the product of which is thought to bind LPS and mediate LPS signal transduction in immune system cells.     

Patterns of sugar feeding and host plant preferences in adult males of An. gambiae (Diptera: Culicidae)

Sugar feeding by male mosquitoes is critical for their success in mating competition . However, the facets of sugar source finding under natural conditions remain unknown. Here, evidence obtained in Western Burkina Faso indicated that the distribution of An. gambiae s.s. (M and S molecular forms) males across different peri‐domestic habitats is dependent on the availability of potential sugar sources from which they obtain more favorable sites for feeding or resting. Among field‐collected anophelines, a higher proportion of specimens containing fructose were found on flowering Mangifera indica (Anacardiaceae), Dolonix regia (Fabaceae), Thevetia neriifolia (Apocynaceae), Senna siamea, and Cassia sieberiana (both Fabaceae) compared to that recorded on other nearby plants, suggesting that some plants are favored for use as a sugar source over others. Y‐tube olfactometer assays with newly‐emerged An. gambiae s.s. exposed to odors from individual plants and some combinations thereof showed that males use odor cues to guide their preference. The number of sugar‐positive males was variable in a no‐choice cage assay, consistent with the olfactory response patterns towards corresponding odor stimuli. T hese experiments provide the first evidence both in field and laboratory conditions for previously unstudied interactions between males of An. gambiae and natural sugar sources.     

Historical overview and geographical distribution of neglected tropical diseases amenable to preventive chemotherapy in the Republic of the Congo: A systematic review

BackgroundNeglected Tropical Diseases amenable to Preventive Chemotherapy (PC-NTDs) affect the poorest populations around the world, especially in Africa. Scientific information on the distribution and level of endemicity of these diseases in the Republic of the Congo (RoC) is scarce in the published literature. We sought to collect all available epidemiological data on PC-NTDs in the RoC to document the historical and current situation and identify challenges in reaching the elimination of NTDs.MethodsWe searched Medline and Horizon databases for studies published until to July 4^th, 2019, on onchocerciasis, lymphatic filariasis, soil-transmitted helminth infections, schistosomiasis, and trachoma in the RoC. Unpublished reports were also reviewed. We included all epidemiological studies containing community data and excluded case reports. Location, prevalence data, and dates of the studies were extracted.Principal findingsWe identified 933 records, of which 56 met the inclusion criteria. The articles published before 1960 mainly concerned onchocerciasis and schistosomiasis. Despite a low number over the studied period, since 2005 there has been a steady increase in the number of publications. Most of the studies were cross-sectional and conducted in the general population. Trachoma is endemic in the Sangha and Likouala departments (prevalence of trachomatous inflammation-follicular > 5% in some villages), and further mapping is essential to properly assess the burden of this disease in the country. While the prevalence of soil-transmitted helminths is still high (over 20%) in a large part of Congo, cases of lymphatic filariasis (based on Wuchereria bancrofti antigenaemia and/or microfilaraemia) and onchocerciasis are becoming rare and very focused. To achieve the elimination of PC-NTDs, further intervention is required.ConclusionsExcept for trachoma, whose epidemiological situation should be better evaluated, PC-NTDs are endemic in the RoC, and actions to control them have been taken by health authorities. To eliminate PC-NTDs, which are still present in some locations, new mapping surveys are needed, and increased investment in scientific research should be encouraged in the country.     

Evolutionary insight from whole-genome sequencing of experimentally evolved microbes

Experimental evolution (EE) combined with whole‐genome sequencing (WGS) has become a compelling approach to study the fundamental mechanisms and processes that drive evolution. Most EE‐WGS studies published to date have used microbes, owing to their ease of propagation and manipulation in the laboratory and relatively small genome sizes. These experiments are particularly suited to answer long‐standing questions such as: How many mutations underlie adaptive evolution, and how are they distributed across the genome and through time? Are there general rules or principles governing which genes contribute to adaptation, and are certain kinds of genes more likely to be targets than others? How common is epistasis among adaptive mutations, and what does this reveal about the variety of genetic routes to adaptation? How common is parallel evolution, where the same mutations evolve repeatedly and independently in response to similar selective pressures? Here, we summarize the significant findings of this body of work, identify important emerging trends and propose promising directions for future research. We also outline an example of a computational pipeline for use in EE‐WGS studies, based on freely available bioinformatics tools.     

Role of environmental factors in autoantibody production - importance of a detailed analysis in a small cohort

In the previous issue of Arthritis Research & Therapy, Muro and colleagues reported a detailed epidemiologic analysis in central Japan on one of the new myositis-specific autoantibodies to MDA-5 (melanoma differentiation-associated gene 5), which is associated with clinically amyopathic dermatomyositis accompanying interstitial lung disease. The increasing prevalence of anti-MDA-5, higher prevalence in small rural towns, and geographical clustering in two areas along the Kiso River suggest a role of environmental factors associated with rural communities or the river/water system or both. A detailed analysis of a small cohort may offer clues, which is ignored in multi-center studies, to the pathogenesis of systemic rheumatic diseases and autoantibody production.     

Cyclooxygenase inhibition with acetylsalicylic acid unmasks a role for prostacyclin in erythropoietin-induced hypertension in uremic rats

We previously reported that thromboxane (TX)A2 synthesis and receptor blockade prevented recombinant human erythropoietin (rhEPO)-induced hypertension in chronic renal failure rats. The present study was designed to investigate the effect of a cyclooxygenase inhibitor, acetylsalicylic acid (ASA), on blood pressure, renal function, and the concentration of eicosano?ds and endothelin-1 (ET-1) in vascular and renal tissues of rhEPO-treated or rhEPO-untreated uremic rats. Renal failure was induced by a 2-stage 5/6 renal mass ablation. Rats were divided into 4 groups: vehicle, rhEPO (100 U/kg, s.c., 3 times per week), ASA (100 mg x kg(-1) x day(-1), and rhEPO + ASA; all animals were administered drugs for 3 weeks. The TXA2- and prostacyclin (PGI2)-stable metabolites (TXB2 and 6-keto-PGF1alpha, respectively), as well as ET-1, were measured in renal cortex and either the thoracic aorta or mesenteric arterial bed. The uremic rats developed anemia, uremia, and hypertension. They also exhibited a significant increase in vascular and renal TXB2 (p < 0.01) and 6-keto-PGF1alpha (p < 0.01) concentrations. rhEPO therapy corrected the anemia but aggravated hypertension (p < 0.05). TXB2 and ET-1 tissue levels further increased (p < 0.05) whereas 6-keto-PGF1alpha was unchanged in rhEPO-treated rats compared with uremic rats receiving the vehicle. ASA therapy did not prevent the increase in systolic blood pressure nor the progression of renal disease in rhEPO-treated or rhEPO-untreated uremic rats, but suppressed both TXB2 and 6-keto-PGF1alpha tissue concentrations (p < 0.05). ASA had no effect on vascular and renal ET-1 levels. Cyclooxygenase inhibition had no effect on rhEPO-induced hypertension owing, in part, to simultaneous inhibition of both TXA2 and its vasodilatory counterpart PGI2 synthesis, whereas the vascular ET-1 overproduction was maintained. These results stress the importance of preserving PGI2 production when treating rhEPO-induced hypertension under uremic conditions.     

A New Entodiniomorphid Ciliate,Troglocorys cava n. g., n. sp., from the Wild Eastern Chimpanzee (Pan troglodytes schweinfurthii) from Uganda

ABSTRACT. Troglocorys cava n. g., n. sp. is described from the feces of wild eastern chimpanzee, Pan troglodytes schweinfurthii, in Uganda. This new species has a spherical body with a frontal lobe, a long vestibulum, a cytoproct located at the posterior dorsal side of the body, an ovoid macronucleus, a contractile vacuole near the cytoproct, and a large concavity on the left surface of the body. Buccal ciliature is non‐retractable and consists of three ciliary zones: an adoral zone surrounding the vestibular opening, a dorso‐adoral zone extending transversely at the basis of the frontal lobe, and a vestibular zone longitudinally extending in a gently spiral curve to line the surface of the vestibulum. Two non‐retractable somatic ciliary zones comprise arches over the body surface: a short dorsal ciliary arch extending transversely at the basis of the frontal lobe and a wide C‐shaped left ciliary arch in the left concavity. Because of the presence of three ciliary zones in the non‐retractable buccal ciliature, the present genus might be a member of the family Blepharocorythidae, but the large left concavity and the C‐shaped left ciliary arch are unique, such structures have never been described from other blepharocorythids.