Eliasen Bengtsson (weaponbengal66)

We present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.The majority of the area contaminated by the Fukushima Daiichi Nuclear Power Plant accident is covered with forests. We developed a dataset for radiocaesium (137Cs) in trees, soil, and mushrooms measured at numerous forest sites. The 137Cs activity concentration and inventory data reported in scientific journal papers written in English and Japanese, governmental reports, and governmental monitoring data on the web were collated. The ancillary information describing the forest stands were also collated, and further environmental information (e.g. climate) was derived from the other databases using longitude and latitude coordinates of the sampling locations. The database contains 8593, 4105, and 3189 entries of activity concentration data for trees, soil, and mushrooms, and 471 and 3521 entries of inventory data for trees and soil, respectively, which were collected from 2011 to 2017, and covers the entire Fukushima prefecture. The data can be used to document and understand the spatio-temporal dynamics of radiocaesium in the affected region and to aid the development and validation of models of radiocaesium dynamics in contaminated forests.In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram-positive bacteria contain a transcription factor HelD that is able to remove and recycle stalled complexes, but it was not known how it performed this function. Here, using single particle cryo-electron microscopy, we have determined the structures of Bacillus subtilis RNA polymerase (RNAP) elongation and HelD complexes, enabling analysis of the conformational changes that occur in RNAP driven by HelD interaction. HelD has a 2-armed structure which penetrates deep into the primary and secondary channels of RNA polymerase. Eliglustat in vivo One arm removes nucleic acids from the active site, and the other induces a large conformational change in the primary channel leading to removal and recycling of the stalled polymerase, representing a novel mechanism for recycling transcription complexes in bacteria.Sexual reproduction is almost ubiquitous among extant eukaryotes. As most asexual lineages are short-lived, abandoning sex is commonly regarded as an evolutionary dead end. Still, putative anciently asexual lineages challenge this view. One of the most striking examples are bdelloid rotifers, microscopic freshwater invertebrates believed to have completely abandoned sexual reproduction tens of Myr ago. Here, we compare whole genomes of 11 wild-caught individuals of the bdelloid rotifer Adineta vaga and present evidence that some patterns in its genetic variation are incompatible with strict clonality and lack of genetic exchange. These patterns include genotype proportions close to Hardy-Weinberg expectations within loci, lack of linkage disequilibrium between distant loci, incongruent hap