POPSEQ Anchoring and ordering contig assemblies from next generation sequencing data by population sequencing

Mascher M. POPSEQ Anchoring and ordering contig assemblies from next generation sequencing data by population sequencing. Bielefeld: Universität Bielefeld; 2014

From Smokes to Smokestacks: Lessons from Tobacco for the Future of Climate Change Liability

In this article, we imagine a future Canada (circa 2030) wherein the world has managed to avoid the worst climate change but nevertheless has begun to experience considerable warming. Governments of all levels, but especially provincial ones, are incurring unprecedented costs to mitigate the effects of climate change and to adapt to new and uncertain climatic regimes. We then consider how legislatures might respond to these challenges. In our view, the answer may lie in the unprecedented story of tobacco liability, and especially the promulgation in the late 1990s of provincial legislation specifically designed to enable provinces to recover the public healthcare costs of tobacco-related disease. Although comparisons between the tobacco industry and the fossil-fuel industry are increasingly common, this article is the first to consider the legally-relevant differences and similarities between these two contexts in detail. It also sets out the main elements of a potential Climate Change Damages and Adaptation Costs Recovery Act. As will be seen, the design of such legislation engages several complex legal issues, implicating not only tort doctrine but also questions of legislative competence and private international law. Nevertheless, our initial assessment is that such legislation is both likely and feasible. Our analysis focuses primarily on Canadian law but should also be relevant to other jurisdictions that are increasingly grappling with the costs of climate change mitigation and adaptation

Maize Source Leaf Adaptation to Nitrogen Deficiency Affects Not Only Nitrogen and Carbon Metabolism But Also Control of Phosphate Homeostasis

Schlueter U, Mascher M, Colmsee C, et al. Maize Source Leaf Adaptation to Nitrogen Deficiency Affects Not Only Nitrogen and Carbon Metabolism But Also Control of Phosphate Homeostasis. Plant Physiology. 2012;160(3):1384-1406.Crop plant development is strongly dependent on the availability of nitrogen (N) in the soil and the efficiency of N utilization for biomass production and yield. However, knowledge about molecular responses to N deprivation derives mainly from the study of model species. In this article, the metabolic adaptation of source leaves to low N was analyzed in maize (Zea mays) seedlings by parallel measurements of transcriptome and metabolome profiling. Inbred lines A188 and B73 were cultivated under sufficient (15 mM) or limiting (0.15 mM) nitrate supply for up to 30 d. Limited availability of N caused strong shifts in the metabolite profile of leaves. The transcriptome was less affected by the N stress but showed strong genotype-and age-dependent patterns. N starvation initiated the selective down-regulation of processes involved in nitrate reduction and amino acid assimilation; ammonium assimilation-related transcripts, on the other hand, were not influenced. Carbon assimilation-related transcripts were characterized by high transcriptional coordination and general down-regulation under low-N conditions. N deprivation caused a slight accumulation of starch but also directed increased amounts of carbohydrates into the cell wall and secondary metabolites. The decrease in N availability also resulted in accumulation of phosphate and strong down-regulation of genes usually involved in phosphate starvation response, underlining the great importance of phosphate homeostasis control under stress conditions

BARLEX – the Barley Draft Genome Explorer

Colmsee C, Beier S, Himmelbach A, et al. BARLEX – the Barley Draft Genome Explorer. Molecular Plant. 2015;8(6):964-966

Insulation and wiring specificity of BceR-like response regulators and their target promoters in <i>Bacillus subtilis</i>

BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities

Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’

We have established a high-quality, chromosome-level genome assembly for the hexaploid common wheat cultivar ‘Fielder’, an American, soft, white, pastry-type wheat released in 1974 and known for its amenability to Agrobacterium tumefaciens-mediated transformation and genome editing. Accurate, long-read sequences were obtained using PacBio circular consensus sequencing with the HiFi approach. Sequence reads from 16 SMRT cells assembled using the hifiasm assembler produced assemblies with N50 greater than 20 Mb. We used the Omni-C chromosome conformation capture technique to order contigs into chromosome-level assemblies, resulting in 21 pseudomolecules with a cumulative size of 14.7 and 0.3 Gb of unanchored contigs. Mapping of published short reads from a transgenic wheat plant with an edited seed-dormancy gene, TaQsd1, identified four positions of transgene insertion into wheat chromosomes. Detection of guide RNA sequences in pseudomolecules provided candidates for off-target mutation induction. These results demonstrate the efficiency of chromosome-scale assembly using PacBio HiFi reads and their application in wheat genome-editing studies