Single-molecule analysis of Mss116-mediated group II intron folding

DEAD-box helicases are conserved enzymes involved in nearly all aspects of RNA metabolism, but their mechanisms of action remain unclear. Here, we investigated the mechanism of the DEAD-box protein Mss116 on its natural substrate, the group II intron ai5γ. Group II introns are structurally complex catalytic RNAs considered evolutionarily related to the eukaryotic spliceosome, and an interesting paradigm for large RNA folding. We used single-molecule fluorescence to monitor the effect of Mss116 on folding dynamics of a minimal active construct, ai5γ-D135. The data show that Mss116 stimulates dynamic sampling between states along the folding pathway, an effect previously observed only with high Mg(2+) concentrations. Furthermore, the data indicate that Mss116 promotes folding through discrete ATP-independent and ATP-dependent steps. We propose that Mss116 stimulates group II intron folding through a multi-step process that involves electrostatic stabilization of early intermediates and ATP hydrolysis during the final stages of native state assembly.     

Epistemology and Logistics: A Critical Overview

Epistemology is about acquiring knowledge and understanding. Building on the concept of epistemology, described and elaborated on, the focus of this paper is on philosophical reflection on the methodological underpinnings of logistics. A conceptual framework is outlined to analyze methodological assumptions underlying a scientific inquiry. Use of the framework is demonstrated by presenting and analyzing earlier works from within the area of logistics. Based on these analyses, it is concluded that logistics from an epistemological point of view is under change and in motion. Formerly, logistics was building heavily on objectivist methodological suppositions and positivist theory of knowledge was dominating. Although the positivist tradition still has a strong position in the area, it cannot be neglected that new logistics epistemologies are emerging and evolving, bringing new scientific approaches to logistics. It is argued that the new perspectives are closer to a more interpretive conception of social theory and subjectivist methodological suppositions. However, it is also argued that there are still theoretical perspectives on organizations, notably streams of complexity theories, not yet being adopted within the area of logistics. Such theories could, if adopted, change logistics organizations in the future. Neglecting to challenge the epistemology, of a discipline may result in an obsolete paradigm. The idea behind the paper is, therefore, that by challenging the underpinning meta theoretical assumptions, and by reflecting upon them, a more holistic and multidisciplinary approach to logistics improvement will be achieved.