Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).     

Ethnopharmacological practices by livestock farmers in Uganda: Survey experiences from Mpigi and Gulu districts

Background

There is continued reliance on conventional veterinary drugs including anthelmintics, to some of which resistance has developed. Loss of indigenous technical knowledge (ITK) from societies affects the opportunities for utilization of ethnopharmacological practices unless properly documented. This study was conducted to identify common traditional practices using medicinal plants against helminthosis and other livestock diseases in Mpigi and Gulu districts of Uganda.

Methods

Seven focus group discussions with ten farmers per group plus 18 key informant interviews were held in each district from August to November 2011. Ranking was used to quantify disease burdens and to identify priority livestock and breeds. Samples of each plant were submitted to Makerere University herbarium for identification and documentation. The local name, relative availability and International Union for Conservation of Nature (IUCN) status were recorded.

Results

Seventy six farmers in Mpigi and 74 in Gulu were interviewed. Theileriosis and helminthosis were the most common disease conditions in cattle and goats, respectively. Forty plant species within 34 genera from 22 botanical families were identified, with 20 of these used against helminthosis. Other plants treated wounds and ecto-parasites, theileriosis, retained placenta and bovine ephemeral fever. Non-plant practices (7) and plants cited were used in combination depending on availability. Males older than 40 years had most ethnopharmacological knowledge. Most plants (75%, n?=?40) were common, but 10 were rare. IUCN status was not evaluated for 95% of these plants. Conventional and traditional drug use in Gulu and Mpigi districts was different (χ²?=?24; p?<?0.001). The scientific, English, Luganda and Acholi names of all plants and their availability within the communities are documented herein.

Conclusion

This is the first detailed livestock-related ethnopharmacological study in Gulu district. Farmers in Uganda are still using a variety of practices to treat livestock ailments. Scientific validation and evaluation of conservation status are urgently needed to ensure future availability and knowledge about these plant resources.     

Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Productivity, 15N dynamics and water use efficiency in low‐ and high‐input switchgrass systems

Sustainable and environmentally benign switchgrass production systems need to be developed for switchgrass to become a large‐scale dedicated energy crop. An experiment was conducted in California from 2009 to 2011 to determine the sustainability of low‐ and high‐input irrigated switchgrass systems as a function of yield, irrigation requirement, crop N removal, N translocation from aboveground (AG) to belowground (BG) biomass during senescence, and fertilizer ¹⁵N recovery (FNR) in the AG and BG biomass (0–300 cm), and soil (0–300 cm). The low‐input system consisted of a single‐harvest (mid‐fall) irrigated until flowering (early summer), while the high‐input system consisted of a two‐harvest system (early summer and mid‐fall) irrigated throughout the growing season. Three N fertilization rates (0, 100, and 200 kg N ha^?1 yr^?1) were applied as subtreatments in a single application in the spring of each year. A single pulse of ¹⁵N enriched fertilizer was applied in the first year of the study to micro‐plots within the 100 kg N ha^?1 subplots. Average yields across years under optimal N rates (100 and 200 kg ha^?1 yr^?1 for low‐ and high‐input systems, respectively) were 20.7 and 24.8 Mg ha^?1. However, the low input (372 ha mm) required 47% less irrigation than the high‐input system (705 ha mm) and achieved higher irrigation use efficiency. In addition, the low‐input system had 46% lower crop N removal, 53% higher N stored in BG biomass, and a positive N balance, presumably due to 49% of ¹⁵N translocation from AG to BG biomass during senescence. Furthermore, at the end of 3 years, the low‐input system had lower fertilizer ¹⁵N removed by harvest (26%) and higher FNR remaining in the system in BG biomass plus soil (31%) than the high‐input system (45% and 21%, respectively). Based on these findings, low‐input systems are more sustainable than high‐input systems in irrigated Mediterranean climates.