The Mn4Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser

The structure of photosystem II and the catalytic intermediate states of the Mn₄CaO₅ cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.     

Mechanical control of the endothelial barrier

The integrity of the endothelial barrier is controlled by the combined action of chemical and mechanical signaling systems. Permeability-regulating factors signal through small GTPases to regulate the architecture of the cytoskeleton and this has a strong impact on the morphology and stability of VE-cadherin-based cell–cell junctions. The details of how structural and mechanical properties of the actin cytoskeleton influence cell–cell adhesion and how this impacts the dynamic regulation of the endothelial barrier, are beginning to be elucidated. In this review, we discuss the physical and regulatory interactions between the VE-cadherin complex and the actomysoin cytoskeleton, as they are the main determinants of cell–cell adhesion and the mechanical architecture of the cytoskeleton. We discuss, based on recent in vitro data, how a balance between Linear Adherens Junctions, paralleled by cortical actin bundles and Focal Adherens Junctions, connected to radial action bundles, determines endothelial barrier function. We discuss how small GTPases control this balance by regulating the spatial organization and mechanics of actomyosin. We propose a hypothetical model of how biochemical and mechanical signals cooperate locally, at the actomyosin–adhesion interface to open and re-seal the barrier in a rapid and controlled manner.     

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.