An activation domain of plasmid R1 TraI protein delineates stages of gene transfer initiation

Bacterial conjugation is a form of type IV secretion that transports protein and DNA to recipient cells. Specific bacteriophage exploit the conjugative pili and cell envelope spanning protein machinery of these systems to invade bacterial cells. Infection by phage R17 requires F-like pili and coupling protein TraD, which gates the cytoplasmic entrance of the secretion channel. Here we investigate the role of TraD in R17 nucleoprotein uptake and find parallels to secretion mechanisms. The relaxosome of IncFII plasmid R1 is required. A ternary complex of plasmid oriT, TraD and a novel activation domain within the N-terminal 992 residues of TraI contributes a key mechanism involving relaxase-associated properties of TraI, protein interaction and the TraD ATPase. Helicase-associated activities of TraI are dispensable. These findings distinguish for the first time specific protein domains and complexes that process extracellular signals into distinct activation stages in the type IV initiation pathway. The study also provided insights into the evolutionary interplay of phage and the plasmids they exploit. Related plasmid F adapted to R17 independently of TraI. It follows that selection for phage resistance drives not only variation in TraA pilins but diversifies TraD and its binding partners in a plasmid-specific manner

Toward a New Science of Information

The concept of information has become a crucial topic in several emerging scientific disciplines, as well as in organizations, in companies and in everyday life. Hence it is legitimate to speak of the so-called information society; but a scientific understanding of the Information Age has not had time to develop. Following this evolution we face the need of a new transdisciplinary understanding of information, encompassing many academic disciplines and new fields of interest. Therefore a Science of Information is required. The goal of this paper is to discuss the aims, the scope, and the tools of a Science of Information. Furthermore we describe the new Science of Information Institute (SOII), which will be established as an international and transdisciplinary organization that takes into consideration a larger perspective of information

What was web 2.0? Versions as the dominant mode of internet history

This paper explores Web 2.0 as the marker of a discourse about the nature and purpose of the internet in the recent past. It focuses on how Web 2.0 introduced to our thinking about the internet a discourse of versions. Such a discourse enables the telling of a ‘history’ of the internet which involves a complex interweaving of past, present and future, as represented by the additional versions which the introduction of Web 2.0 enabled. The paper concludes that the discourse of versions embodied in Web 2.0 obscures as much as it reveals, and suggests a new project based on investigations of the everyday memories of the internet by which individual users create their own histories of online technology

Fine-scale genetic structure and marginal processes in an expanding population of Biscutella laevigata L. (Brassicaceae).

Evolutionary processes acting at the expanding margins of a species' range are still poorly understood. Genetic drift is considered prevalent in marginal populations, and the maintenance of genetic diversity during recolonization might seem puzzling. To investigate such processes, a fine-scale investigation of 219 individuals was performed within a population of Biscutella laevigata (Brassicaceae), located at the leading edge of its range. The survey used amplified fragment length polymorphisms (AFLPs). As commonly reported across the whole species distribution range, individual density and genetic diversity decreased along the local axis of recolonization of this expanding population, highlighting the enduring effect of the historical colonization on present-day diversity. The self-incompatibility system of the plant may have prevented local inbreeding in newly found patches and sustained genetic diversity by ensuring gene flow from established populations. Within the more continuously populated region, spatial analysis of genetic structure revealed restricted gene flow among individuals. The distribution of genotypes formed a mosaic of relatively homogenous patches within the continuous population. This pattern could be explained by a history of expansion by long-distance dispersal followed by fine-scale diffusion (that is, a stratified dispersal combination). The secondary contact among expanding patches apparently led to admixture among differentiated genotypes where they met (that is, a reshuffling effect). This type of dynamics could explain the maintenance of genetic diversity during recolonization

Non-invasive and high-throughput interrogation of exon-specific isoform expression.

Expression of exon-specific isoforms from alternatively spliced mRNA is a fundamental mechanism that substantially expands the proteome of a cell. However, conventional methods to assess alternative splicing are either consumptive and work-intensive or do not quantify isoform expression longitudinally at the protein level. Here, we therefore developed an exon-specific isoform expression reporter system (EXSISERS), which non-invasively reports the translation of exon-containing isoforms of endogenous genes by scarlessly excising reporter proteins from the nascent polypeptide chain through highly efficient, intein-mediated protein splicing. We applied EXSISERS to quantify the inclusion of the disease-associated exon 10 in microtubule-associated protein tau (MAPT) in patient-derived induced pluripotent stem cells and screened Cas13-based RNA-targeting effectors for isoform specificity. We also coupled cell survival to the inclusion of exon 18b of FOXP1, which is involved in maintaining pluripotency of embryonic stem cells, and confirmed that MBNL1 is a dominant factor for exon 18b exclusion. EXSISERS enables non-disruptive and multimodal monitoring of exon-specific isoform expression with high sensitivity and cellular resolution, and empowers high-throughput screening of exon-specific therapeutic interventions

Demographic population structure and fungal associations of plants colonizing High Arctic glacier forelands, Petuniabukta, Svalbard

The development of vegetation in Arctic glacier forelands has been described as unidirectional, non-replacement succession characterized by the gradual establishment of species typical for mature tundra with no species turnover. Our study focused on two early colonizers of High Arctic glacier forelands: Saxifraga oppositifolia (Saxifragaceae) and Braya purpurascens (Brassicaceae). While the first species is a common generalist also found in mature old growth tundra communities, the second specializes on disturbed substrate. The demographic population structures of the two study species were investigated along four glacier forelands in Petuniabukta, north Billefjorden, in central Spitsbergen, Svalbard. Young plants of both species occurred exclusively on young substrate, implying that soil conditions are favourable for establishment only before soil crusts develop. We show that while S. oppositifolia persists from pioneer successional stages and is characterized by increased size and flowering, B. purpurascens specializes on disturbed young substrate and does not follow the typical unidirectional, non-replacement succession pattern. Plants at two of the forelands were examined for the presence of root-associated fungi. Fungal genus Olpidium (Fungus incertae sedis) was found along a whole successional gradient in one of the forelands