Kulturelle Muster im Bodenverständnis

2016 gründete die Internationale Bodenkundliche Union (IUSS) eine neue Arbeitsgruppe zum Thema "Cultural Patterns of Soil Understanding". Denn wie Böden wahrgenommen, verstanden und behandelt werden, ist auch ein kulturhistorisches und kulturpsychologisches Produkt. Auch die Wissenschaften und ihre verschiedenen Schulen sind Teil von Kulturen und somit in ihren Fragen, Herangehensweisen und Interpretationsansätzen kulturell geprägt. – Und welche Art von „Bodenkommunikation“ im gesellschaftlichen und politischen Raum welche Wirkung zeitigt, hängt auch stark davon ab, mit welchen Worten und Bildern in der Öffentlichkeit über „Boden“ gesprochen wird und welche Deutungsrahmen das vermittelt. Weil aber dieser allgemeine Befund nicht genügt, brauchen wir Erkenntnisfortschritte zu kulturellen Mustern im Bodenverständnis, die nur auf inter- und transdisziplinären Wegen zu gewinnen sind. Wichtige Bereiche, wo Querschnittsthemen und kulturelle Muster des Bodenverständnisses gefunden werden können, sind zum Beispiel: 1) Die Geschichte der wissenschaftlichen Bodenkunde im soziokulturellen Kontext. 2) Die Agrar- und Agrarkulturgeschichte weltweit. 3) Verschiedene kulturelle Konzepte von Naturräumen wie z.B. englisch „land“, französisch „terroir“, brasilianisch „território“, andin „Pachamama“ oder deutsch „Heimat“. 4) Die Darstellung und Symbolik des Bodens in der Kunstgeschichte; die Darstellung und Symbolik des Bodens in heutiger Aktionskunst zwecks Förderung des Bodenbewusstseins. 5) Ansätze und Erfahrungen der „Bodenbildung“ in verschiedenen Sprachräumen und Kulturarealen und mit verschiedenen Altersgruppen und Bildungsvoraussetzungen. 6) Religiöse Traditionen und individuelle Spiritualität als Erfahrungsräume und Deutungsvoraussetzungen für Naturbeziehung einschließlich der Kultivierung des Erdreiches. 7) Tiefen- und kulturpsychologische Analysen zu archetypischen Mustern in der Naturbeziehung und speziell auch im Bodenverständnis. In diesem Vortrag werden Beispiele zu kulturellen Mustern im Bodenverständnis vorgebracht. Damit soll dieses Thema verstärkt in die Aktivitäten der Kommission VIII „Boden in Bildung und Gesellschaft“ der DBG eingebracht werden. Und weil auch eine internationale (und interkulturelle) Bearbeitung dieser Fragen Sinn macht, sollten auch Möglichkeiten einer fruchtbaren Zusammenarbeit mit der genannten, vom Autor geleiteten IUSS-Arbeitsgruppe sowie allgemein der Division 4 der IUSS („Boden und Gesellschaft“) geprüft werden

Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis

MicroRNAs (miRNAs) are endogenously produced ∼21-nt riboregulators that associate with Argonaute (Ago) proteins to direct mRNA cleavage or repress the translation of complementary RNAs. Capturing the molecular mechanisms of miRNA interacting with its target will not only reinforce the understanding of underlying RNA interference but also fuel the design of more effective small-interfering RNA strands. To address this, in the present work the RNA-bound (Ago-miRNA, Ago-miRNA-target) and RNA-free Ago forms were analyzed by performing both molecular dynamics simulations and thermodynamic analysis. Based on the principal component analysis results of the simulation trajectories as well as the correlation analysis in fluctuations of residues, we discover that: 1) three important (PAZ, Mid and PIWI) domains exist in Argonaute which define the global dynamics of the protein; 2) the interdomain correlated movements are so crucial for the interaction of Ago-RNAs that they not only facilitate the relaxation of the interactions between residues surrounding the RNA binding channel but also induce certain conformational changes; and 3) it is just these conformational changes that expand the cavity of the active site and open putative pathways for both the substrate uptake and product release. In addition, by thermodynamic analysis we also discover that for both the guide RNA 5′-end recognition and the facilitated site-specific cleavage of the target, the presence of two metal ions (of Mg2+) plays a predominant role, and this conclusion is consistent with the observed enzyme catalytic cleavage activity in the ternary complex (Ago-miRNA-mRNA). Our results find that it is the set of arginine amino acids concentrated in the nucleotide-binding channel in Ago, instead of the conventionally-deemed seed base-paring, that makes greater contributions in stabilizing the binding of the nucleic acids to Ago

Improved siRNA/shRNA Functionality by Mismatched Duplex

siRNA (small interfering RNA) and shRNA (small hairpin RNA) are powerful and commonly used tools in biomedical research. Currently, siRNAs are generally designed as two 21 nt strands of RNA that include a 19 nt completely complementary part and a 2 nt overhang. However, since the si/shRNAs use the endogenous miRNA machinery for gene silencing and the miRNAs are generally 22 nt in length and contain multiple internal mismatches, we tested if the functionality can be increased by designing the si/shRNAs to mimic a miRNA structure. We systematically investigated the effect of single or multiple mismatches introduced in the passenger strand at different positions on siRNA functionality. Mismatches at certain positions could significantly increase the functionality of siRNAs and also, in some cases decreased the unwanted passenger strand functionality. The same strategy could also be used to design shRNAs. Finally, we showed that both si and miRNA structured oligos (siRNA with or without mismatches in the passenger strand) can repress targets in all individual Ago containing cells, suggesting that the Ago proteins do not differentiate between si/miRNA-based structure for silencing activity

Effects of local mRNA structure on posttranscriptional gene silencing

Antisense oligodeoxynucleotides (AONs) and short interfering RNAs (siRNAs) effect posttranscriptional gene silencing (PTGS) by hybridizing to an mRNA and then directing its cleavage. To understand the constraints that mRNA structure imposes on AON- vs. siRNA-mediated PTGS, AON- and siRNA-mediated cleavage of defined mRNA structures was monitored in Drosophila embryo whole-cell lysates. We observed that AON-directed cleavage was ≈3-fold faster than cleavage with a siRNA directed to the same target site. Furthermore, and unexpectedly, AON-mediated cleavage was found to be much less fastidious with respect to target sequence accessibility, as measured by the presence of unpaired nucleotides, than a corresponding siRNA. Nonetheless, in vivo, siRNAs silenced their mRNA target at least 2-fold more efficiently than the corresponding AON. These seemingly contradictory results suggested that additional, as yet undefined factors play an important role in regulating PTGS efficiency in vivo. We used a well defined RNA-binding protein, αCP, and its corresponding high-affinity RNA-binding site to explore this hypothesis. We found that prebound αCP effectively blocked AON-mediated cleavage of the RNA-binding site compared with cleavage of the site in the absence of αCP. We conclude that higher-order structures formed by RNA and bound proteins play an important role in determining the efficiency of AON-directed PTGS. We hypothesize that strategies aimed at removing RNA-binding proteins might significantly improve AON-mediated PTGS in vivo