Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

BACKGROUND: Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB. METHODS: Parasite DNA with high (>95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8-12 mers as primers. These primers were selected on the basis of their differential frequency of binding the desired (P. falciparum DNA) and contaminating (human) genomes. RESULTS: Using sWGA method, clinical samples from 156 malaria patients, including 120 paired samples for head-to-head comparison of DBS and leucodepleted VB were sequenced. Greater than 18-fold enrichment of P. falciparum DNA was achieved from DBS extracts. The parasitaemia threshold to achieve >5× coverage for 50% of the genome was 0.03% (40 parasites per 200 white blood cells). Over 99% SNP concordance between VB and DBS samples was achieved after excluding missing calls. CONCLUSION: The sWGA methods described here provide a reliable and scalable way of generating P. falciparum genome sequence data from DBS samples. The current data indicate that it will be possible to get good quality sequence on most if not all drug resistance loci from the majority of symptomatic malaria patients. This technique overcomes a major limiting factor in P. falciparum genome sequencing from field samples, and paves the way for large-scale epidemiological applications

Adaptive Out-Orientations with Applications

We give simple algorithms for maintaining edge-orientations of a fully-dynamic graph, such that the out-degree of each vertex is bounded. On one hand, we show how to orient the edges such that the out-degree of each vertex is proportional to the arboricity $\alpha$ of the graph, in a worst-case update time of $O(\log^2 n \log \alpha)$. On the other hand, motivated by applications in dynamic maximal matching, we obtain a different trade-off, namely the improved worst case update time of $O(\log n \log \alpha)$ for the problem of maintaining an edge-orientation with at most $O(\alpha + \log n)$ out-edges per vertex. Since our algorithms have update times with worst-case guarantees, the number of changes to the solution (i.e. the recourse) is naturally limited. Our algorithms make choices based entirely on local information, which makes them automatically adaptive to the current arboricity of the graph. In other words, they are arboricity-oblivious, while they are arboricity-sensitive. This both simplifies and improves upon previous work, by having fewer assumptions or better asymptotic guarantees. As a consequence, one obtains an algorithm with improved efficiency for maintaining a $(1+\varepsilon)$ approximation of the maximum subgraph density, and an algorithm for dynamic maximal matching whose worst-case update time is guaranteed to be upper bounded by $O(\alpha + \log n\log \alpha)$, where $\alpha$ is the arboricity at the time of the update

Retarding Field Integrated Fluorescence and Electron Microscope

The authors present the application of a retarding field between the electron objective lens and sample in an integrated fluorescence and electron microscope. The retarding field enhances signal collection and signal strength in the electron microscope. This is beneficial for samples prepared for integrated fluorescence and electron microscopy as the amount of staining material added to enhance electron microscopy signal is typically lower compared to conventional samples in order to preserve fluorescence. We demonstrate signal enhancement through the applied retarding field for both 80-nm post-embedding immunolabeled sections and 100-nm in-resin preserved fluorescence sections. Moreover, we show that tuning the electron landing energy particularly improves imaging conditions for ultra-thin (50 nm) sections, where optimization of both retarding field and interaction volume contribute to the signal improvement. Finally, we show that our integrated retarding field setup allows landing energies down to a few electron volts with 0.3 eV dispersion, which opens new prospects for assessing electron beam induced damage by in situ quantification of the observed bleaching of the fluorescence following irradiation

The relationship between size and longevity of the malaria vector Anopheles gambiae (s.s.) depends on the larval environment

Abstract Background Understanding the variation in vector-borne disease transmission intensity across time and space relies on a thorough understanding of the impact of environmental factors on vectorial capacity traits of mosquito populations. This is driven primarily by variation in larval development and growth, with carryover effects influencing adult traits such as longevity and adult body size. The relationship between body size and longevity strongly affects the evolution of life histories and the epidemiology of vector-borne diseases. This relationship ranges from positive to negative but the reasons for this variability are not clear. Both traits depend on a number of environmental factors, but primarily on temperature as well as availability of nutritional resources. We therefore asked how the larval environment of the mosquito Anopheles gambiae Giles (sensu stricto) (Diptera: Culicidae) affects the relationship between body size and longevity. Methods We reared the larvae of An. gambiae individually at three temperatures (21, 25 and 29 °C) and two food levels (the standard and 50% of our laboratory diet) and measured adult size and longevity. We estimated the direct and indirect (via adult size) effects of food and temperature on longevity with a piecewise structural equation model (SEM). Results We confirmed the direct effects of food and temperature during larval development on body size, as wing length decreased with increasing temperature and decreasing food levels. While the overall relationship between size and longevity was weak, we measured striking differences among environments. At 25 °C there was no clear relationship between size and longevity; at 29 °C the association was negative with standard food but positive with low food; whereas at 21 °C it was positive with standard food but negative with low food. Conclusions The larval environment influences the adult’s fitness in complex ways with larger mosquitoes living longer in some environments but not in others. This confirmed our hypothesis that the relationship between size and longevity is not limited to a positive correlation. A better understanding of this relationship and its mechanisms may improve the modelling of the transmission of vector borne diseases, the evolution of life history traits, and the influence of vector control

Environmental flows in support of sustainable intensification of agriculture in the Letaba River Basin, South Africa

This study evaluates the socioecological consequences of the potential trade-offs between maintaining environmental flows (e-flows) and providing water for sustainable subsistence agriculture and livelihoods to the vulnerable human communities living along the lower Great Letaba River in South Africa. Implementation of e-flows is now generally recognized as an essential part of water resources management as they are designed to ensure that sufficient water is retained in a river to protect river ecosystems and all the beneficiaries of services that arise from those ecosystems. Understanding the relationship between e-flows and the use of water for small-scale agriculture is important for the management of trade-offs. The Letaba River Basin and it's tributary, the Great/Groot Letaba, are located in the eastern part of the Limpopo province in South Africa. This is one of the most important river basins in the region supporting both large-scale commercial and small-scale farmers. The river sustains many vulnerable human communities who depend on the ecosystem services provided by the river. Yet, the water resources of the Letaba River are heavily overutilized due to expanding developments, including upstream dams with associated offtakes mostly for irrigation. The findings of the study indicate that irrigation water demand from subsistence agriculture in the Great Letaba Basin amounted to around 2 million cubic meters annually with median demand not exceeding 300,000 cubic meters per month. This means that irrigation water demand from smallholder agriculture only amounts to about one-tenth of the estimated e-flow requirement. However, small-scale farmers contend with an increasing crop water gap which limits irrigated agriculture, especially during the dry season. Given the need to sustainably maintain e-flows for ecological purposes, crop water gaps are only likely to increase and compromise the sustainability of irrigated agriculture. With active upstream supplementation of river flows from dams to maintain both environmental and livelihoods-oriented river flows, the crop water gap can be fully eliminated. This supplementation is not assured due to competing uses

Protecting biodiversity in British Columbia: Recommendations for developing species at risk legislation

British Columbia has the greatest biological diversity of any province or territory in Canada. Yet increasing numbers of species in British Columbia are threatened with extinction. The current patchwork of provincial laws and regulations has not effectively prevented species declines. Recently, the Provincial Government has committed to enacting an endangered species law. Drawing upon our scientific and legal expertise, we offer recommendations for key features of endangered species legislation that build upon strengths and avoid weaknesses observed elsewhere. We recommend striking an independent Oversight Committee to provide recommendations about listing species, organize Recovery Teams, and monitor the efficacy of actions taken. Recovery Teams would evaluate and prioritize potential actions for individual species or groups of species that face common threats or live in a common area, based on best available evidence (including natural and social science and Indigenous Knowledge). Our recommendations focus on implementing an adaptive approach, with ongoing and transparent monitoring and reporting, to reduce delays between determining when a species is at risk and taking effective actions to save it. We urge lawmakers to include this strong evidentiary basis for species recovery as they tackle the scientific and socioeconomic challenges of building an effective species at risk Act

Protecting biodiversity in British Columbia: Recommendations for developing species at risk legislation

British Columbia has the greatest biological diversity of any province or territory in Canada. Yet increasing numbers of species in British Columbia are threatened with extinction. The current patchwork of provincial laws and regulations has not effectively prevented species declines. Recently, the Provincial Government has committed to enacting an endangered species law. Drawing upon our scientific and legal expertise, we offer recommendations for key features of endangered species legislation that build upon strengths and avoid weaknesses observed elsewhere. We recommend striking an independent Oversight Committee to provide recommendations about listing species, organize Recovery Teams, and monitor the efficacy of actions taken. Recovery Teams would evaluate and prioritize potential actions for individual species or groups of species that face common threats or live in a common area, based on best available evidence (including natural and social science and Indigenous Knowledge). Our recommendations focus on implementing an adaptive approach, with ongoing and transparent monitoring and reporting, to reduce delays between determining when a species is at risk and taking effective actions to save it. We urge lawmakers to include this strong evidentiary basis for species recovery as they tackle the scientific and socioeconomic challenges of building an effective species at risk Act

Prevalence of DHP Toxicity and Detection of \u3cem\u3eS. jonesii\u3c/em\u3e in Ruminants Consuming \u3cem\u3eLeucaena leucocephala\u3c/em\u3e in Eastern Indonesia

Leucaena leucocephala (leucaena) is a productive forage tree legume widely used in eastern Indonesia. While highly nutritious, it possesses the toxin mimosine which adversely affects animal production. In ruminants, mimosine is readily converted to the two isomers of dihydroxypyridine (3,4-DHP and 2,3-DHP) known to cause goitre, suppress appetite, and cause severe mineral deficiencies. These adverse symptoms may be partially responsible for the reluctance of some farmers to feed leucaena. A bacterium capable of complete degradation of DHP, Synergistes jonesii, originally discovered in Hawaii in goats consuming leucaena (Jones and Megarrity 1986), was later found in Indonesia which led to the assumption that all Indonesian ruminants were protected from leucaena toxicity even on 100% leucaena diets. The objective of this study, conducted during October-November 2011, was to confirm this hypothesis via an extensive survey of the toxicity status of ruminants consuming leucaena in eastern Indonesia

Anomalous excitonic phase diagram in band-gap-tuned Ta2Ni(Se,S)5

During a band-gap-tuned semimetal-to-semiconductor transition, Coulomb attraction between electrons and holes can cause spontaneously formed excitons near the zero-band-gap point, or the Lifshitz transition point. This has become an important route to realize bulk excitonic insulators -- an insulating ground state distinct from single-particle band insulators. How this route manifests from weak to strong coupling is not clear. In this work, using angle-resolved photoemission spectroscopy (ARPES) and high-resolution synchrotron x-ray diffraction (XRD), we investigate the broken symmetry state across the semimetal-to-semiconductor transition in a leading bulk excitonic insulator candidate system Ta2Ni(Se,S)5. A broken symmetry phase is found to be continuously suppressed from the semimetal side to the semiconductor side, contradicting the anticipated maximal excitonic instability around the Lifshitz transition. Bolstered by first-principles and model calculations, we find strong interband electron-phonon coupling to play a crucial role in the enhanced symmetry breaking on the semimetal side of the phase diagram. Our results not only provide insight into the longstanding debate of the nature of intertwined orders in Ta2NiSe5, but also establish a basis for exploring band-gap-tuned structural and electronic instabilities in strongly coupled systems.Comment: 27 pages, 4 + 9 figure