Bielefeld University

About: Bielefeld University is a education organization based out in Bielefeld, Nordrhein-Westfalen, Germany. It is known for research contribution in the topics: Population & Quantum chromodynamics. The organization has 10123 authors who have published 26576 publications receiving 728250 citations. The organization is also known as: University of Bielefeld & UNIVERSITAET BIELEFELD.

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Abstract: Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

Abstract: High-throughput sequencing for transcript profiling in plants has revealed that alternative splicing (AS) affects a much higher proportion of the transcriptome than was previously assumed. AS is involved in most plant processes and is particularly prevalent in plants exposed to environmental stress. The identification of mutations in predicted splicing factors and spliceosomal proteins that affect cell fate, the circadian clock, plant defense, and tolerance/sensitivity to abiotic stress all point to a fundamental role of splicing/AS in plant growth, development, and responses to external cues. Splicing factors affect the AS of multiple downstream target genes, thereby transferring signals to alter gene expression via splicing factor/AS networks. The last two to three years have seen an ever-increasing number of examples of functional AS. At a time when the identification of AS in individual genes and at a global level is exploding, this review aims to bring together such examples to illustrate the extent and importance of AS, which are not always obvious from individual publications. It also aims to ensure that plant scientists are aware that AS is likely to occur in the genes that they study and that dynamic changes in AS and its consequences need to be considered routinely.

Plant tolerance to drought and salinity: stress regulating transcription factors and their functional significance in the cellular transcriptional network.

Abstract: Understanding the responses of plants to the major environmental stressors drought and salt is an important topic for the biotechnological application of functional mechanisms of stress adaptation. Here, we review recent discoveries on regulatory systems that link sensing and signaling of these environmental cues focusing on the integrative function of transcription activators. Key components that control and modulate stress adaptive pathways include transcription factors (TFs) ranging from bZIP, AP2/ERF, and MYB proteins to general TFs. Recent studies indicate that molecular dynamics as specific homodimerizations and heterodimerizations as well as modular flexibility and posttranslational modifications determine the functional specificity of TFs in environmental adaptation. Function of central regulators as NAC, WRKY, and zinc finger proteins may be modulated by mechanisms as small RNA (miRNA)-mediated posttranscriptional silencing and reactive oxygen species signaling. In addition to the key function of hub factors of stress tolerance within hierarchical regulatory networks, epigenetic processes as DNA methylation and posttranslational modifications of histones highly influence the efficiency of stress-induced gene expression. Comprehensive elucidation of dynamic coordination of drought and salt responsive TFs in interacting pathways and their specific integration in the cellular network of stress adaptation will provide new opportunities for the engineering of plant tolerance to these environmental stressors.

Template-based question answering over RDF data

Abstract: As an increasing amount of RDF data is published as Linked Data, intuitive ways of accessing this data become more and more important. Question answering approaches have been proposed as a good compromise between intuitiveness and expressivity. Most question answering systems translate questions into triples which are matched against the RDF data to retrieve an answer, typically relying on some similarity metric. However, in many cases, triples do not represent a faithful representation of the semantic structure of the natural language question, with the result that more expressive queries can not be answered. To circumvent this problem, we present a novel approach that relies on a parse of the question to produce a SPARQL template that directly mirrors the internal structure of the question. This template is then instantiated using statistical entity identification and predicate detection. We show that this approach is competitive and discuss cases of questions that can be answered with our approach but not with competing approaches.