TY  - INPR
A1  - Lendlein, Andreas
A1  - Neffe, Axel T.
A1  - Jerome, Christine
T1  - Advanced functional polymers for medicine
T2  - Advanced healthcare materials
Y1  - 2014
U6  - https://doi.org/10.1002/adhm.201400718
SN  - 2192-2640
SN  - 2192-2659
VL  - 3
IS  - 12
SP  - 1939
EP  - 1940
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Kind, Barbara
A1  - Muster, Britta
A1  - Staroske, Wolfgang
A1  - Herce, Henry D.
A1  - Sachse, Rene
A1  - Rapp, Alexander
A1  - Schmidt, Franziska
A1  - Koss, Sarah
A1  - Cardoso, M. Cristina
A1  - Lee-Kirsch, Min Ae
T1  - Altered spatio-temporal dynamics of RNase H2 complex assembly at replication and repair sites in Aicardi-Goutieres syndrome
JF  - Human molecular genetics
N2  - Ribonuclease H2 plays an essential role for genome stability as it removes ribonucleotides misincorporated into genomic DNA by replicative polymerases and resolves RNA/DNA hybrids. Biallelic mutations in the genes encoding the three RNase H2 subunits cause Aicardi-Goutieres syndrome (AGS), an early-onset inflammatory encephalopathy that phenotypically overlaps with the autoimmune disorder systemic lupus erythematosus. Here we studied the intracellular dynamics of RNase H2 in living cells during DNA replication and in response to DNA damage using confocal time-lapse imaging and fluorescence cross-correlation spectroscopy. We demonstrate that the RNase H2 complex is assembled in the cytosol and imported into the nucleus in an RNase H2B-dependent manner. RNase H2 is not only recruited to DNA replication foci, but also to sites of PCNA-dependent DNA repair. By fluorescence recovery after photobleaching, we demonstrate a high mobility and fast exchange of RNase H2 at sites of DNA repair and replication. We provide evidence that recruitment of RNase H2 is not only PCNA-dependent, mediated by an interaction of the B subunit with PCNA, but also PCNA-independent mediated via the catalytic domain of the A subunit. We found that AGS-associated mutations alter complex formation, recruitment efficiency and exchange kinetics at sites of DNA replication and repair suggesting that impaired ribonucleotide removal contributes to AGS pathogenesis.
Y1  - 2014
U6  - https://doi.org/10.1093/hmg/ddu319
SN  - 0964-6906
SN  - 1460-2083
VL  - 23
IS  - 22
SP  - 5950
EP  - 5960
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Lecourieux, Fatma
A1  - Kappel, Christian
A1  - Lecourieux, David
A1  - Serrano, Alejandra
A1  - Torres, Elizabeth
A1  - Arce-Johnson, Patricio
A1  - Delrot, Serge
T1  - An update on sugar transport and signalling in grapevine
JF  - Journal of experimental botany
N2  - In addition to their role as a source of reduced carbon, sugars may directly or indirectly control a wide range of activities in plant cells, through transcriptional and post-translational regulation. This control has been studied in detail using Arabidopsis thaliana, where genetic analysis offers many possibilities. Much less is known about perennial woody species. For several years, various aspects of sugar sensing and signalling have been investigated in the grape (Vitis vinifera L.) berry, an organ that accumulates high concentrations of hexoses in the vacuoles of flesh cells. Here we review various aspects of this topic: the molecular basis of sugar transport and its regulation by sugars in grapevine; the functional analysis of several sugar-induced genes; the effects of some biotic and abiotic stresses on the sugar content of the berry; and finally the effects of exogenous sugar supply on the ripening process in field conditions. A picture of complex feedback and multiprocess regulation emerges from these data.
KW  - Fruit biology
KW  - grapevine
KW  - signalling
KW  - stress
KW  - sugar
KW  - transport
Y1  - 2014
U6  - https://doi.org/10.1093/jxb/ert394
SN  - 0022-0957
SN  - 1460-2431
VL  - 65
IS  - 3
SP  - 821
EP  - 832
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - THES
A1  - Girbig, Dorothee
T1  - Analysing concerted criteria for local dynamic properties of metabolic systems
T1  - Die Analyse koordinierter Kriterien für lokale dynamische Eigenschaften metabolischer Systeme
N2  - Metabolic systems tend to exhibit steady states that can be measured in terms of their concentrations and fluxes. These measurements can be regarded as a phenotypic representation of all the complex interactions and regulatory mechanisms taking place in the underlying metabolic network. Such interactions determine the system's response to external perturbations and are responsible, for example, for its asymptotic stability or for oscillatory trajectories around the steady state. However, determining these perturbation responses in the absence of fully specified kinetic models remains an important challenge of computational systems biology. Structural kinetic modeling (SKM) is a framework to analyse whether a metabolic steady state remains stable under perturbation, without requiring detailed knowledge about individual rate equations. It provides a parameterised representation of the system's Jacobian matrix in which the model parameters encode information about the enzyme-metabolite interactions. Stability criteria can be derived by generating a large number of structural kinetic models (SK-models) with randomly sampled parameter sets and evaluating the resulting Jacobian matrices. The parameter space can be analysed statistically in order to detect network positions that contribute significantly to the perturbation response. Because the sampled parameters are equivalent to the elasticities used in metabolic control analysis (MCA), the results are easy to interpret biologically. In this project, the SKM framework was extended by several novel methodological improvements. These improvements were evaluated in a simulation study using a set of small example pathways with simple Michaelis Menten rate laws. Afterwards, a detailed analysis of the dynamic properties of the neuronal TCA cycle was performed in order to demonstrate how the new insights obtained in this work could be used for the study of complex metabolic systems. The first improvement was achieved by examining the biological feasibility of the elasticity combinations created during Monte Carlo sampling. Using a set of small example systems, the findings showed that the majority of sampled SK-models would yield negative kinetic parameters if they were translated back into kinetic models. To overcome this problem, a simple criterion was formulated that mitigates such infeasible models and the application of this criterion changed the conclusions of the SKM experiment. The second improvement of this work was the application of supervised machine-learning approaches in order to analyse SKM experiments. So far, SKM experiments have focused on the detection of individual enzymes to identify single reactions important for maintaining the stability or oscillatory trajectories. In this work, this approach was extended by demonstrating how SKM enables the detection of ensembles of enzymes or metabolites that act together in an orchestrated manner to coordinate the pathways response to perturbations. In doing so, stable and unstable states served as class labels, and classifiers were trained to detect elasticity regions associated with stability and instability. Classification was performed using decision trees and relevance vector machines (RVMs). The decision trees produced good classification accuracy in terms of model bias and generalizability. RVMs outperformed decision trees when applied to small models, but encountered severe problems when applied to larger systems because of their high runtime requirements. The decision tree rulesets were analysed statistically and individually in order to explore the role of individual enzymes or metabolites in controlling the system's trajectories around steady states. The third improvement of this work was the establishment of a relationship between the SKM framework and the related field of MCA. In particular, it was shown how the sampled elasticities could be converted to flux control coefficients, which were then investigated for their predictive information content in classifier training. After evaluation on the small example pathways, the methodology was used to study two steady states of the neuronal TCA cycle with respect to their intrinsic mechanisms responsible for stability or instability. The findings showed that several elasticities were jointly coordinated to control stability and that the main source for potential instabilities were mutations in the enzyme alpha-ketoglutarate dehydrogenase.
N2  - Metabolische Systeme neigen zur Ausbildung von Fließgleichgewichten, deren Konzentrationen und Reaktionsflüsse experimentell charakterisierbar sind. Derartige Messungen bieten eine phänotypische Repräsentation der zahlreichen Interaktionen und regulatorischen Mechanismen des zugrundeliegenden metabolischen Netzwerks. Diese Interaktionen bestimmen die Reaktion des Systems auf externe Perturbationen, wie z.B. dessen asymptotische Stabilität und Oszillationen. Die Charakterisierung solcher Eigenschaften ist jedoch schwierig, wenn kein entsprechendes kinetisches Modell mit allen Ratengleichungen und kinetischen Parametern für das untersuchte System zur Verfügung steht. Die strukturelle kinetische Modellierung (SKM) ermöglicht die Untersuchung dynamischer Eigenschaften wie Stabilität oder Oszillationen, ohne die Ratengleichungen und zugehörigen Parameter im Detail zu kennen. Statt dessen liefert sie eine parametrisierte Repräsentation der Jacobimatrix, in welcher die einzelnen Parameter Informationen über die Sättigung der Enzyme des Systems mit ihren Substraten kodieren. Die Parameter entsprechen dabei den Elastizitäten aus der metabolischen Kontrollanalyse, was ihre biologische Interpretation vereinfacht. Stabilitätskriterien werden durch Monte Carlo Verfahren hergeleitet, wobei zunächst eine große Anzahl struktureller kinetische Modelle (SK-Modelle) mit zufällig gezogenen Parametermengen generiert, und anschließend die resultierenden Jacobimatrizen evaluiert werden. Im Anschluss kann der Parameterraum statistisch analysiert werden, um Enzyme und Metabolite mit signifikantem Einfluss auf die Stabilität zu detektieren. In der vorliegenden Arbeit wurde das bisherige SKM-Verfahren durch neue methodische Verbesserungen erweitert. Diese Verbesserungen wurden anhand einer Simulationsstudie evaluiert, welche auf kleinen Beispielsystemen mit einfachen Michaelis Menten Kinetiken basierte. Im Anschluss wurden sie für eine detaillierte Analyse der dynamischen Eigenschaften des Zitratzyklus verwendet. Die erste Erweiterung der bestehenden Methodik wurde durch Untersuchung der biologischen Machbarkeit der zufällig erzeugten Elastizitäten erreicht. Es konnte gezeigt werden, dass die Mehrheit der zufällig erzeugten SK-Modelle zu negativen Michaeliskonstanten führt. Um dieses Problem anzugehen, wurde ein einfaches Kriterium formuliert, welches das Auftreten solcher biologisch unrealistischer SK-Modelle verhindert. Es konnte gezeigt werden, dass die Anwendung des Kriteriums die Ergebnisse von SKM Experimenten stark beeinflussen kann. Der zweite Beitrag bezog sich auf die Analyse von SKM-Experimenten mit Hilfe überwachter maschineller Lernverfahren. Bisherige SKM-Studien konzentrierten sich meist auf die Detektion individueller Elastizitäten, um einzelne Reaktionen mit Einfluss auf das Stabilitäts- oder oszillatorische Verhalten zu identifizieren. In dieser Arbeit wurde demonstriert, wie SKM Experimente im Hinblick auf multivariate Muster analysiert werden können, um Elastizitäten zu entdecken, die gemeinsam auf orchestrierte und koordinierte Weise die Eigenschaften des Systems bestimmen. Sowohl Entscheidungsbäume als auch Relevanzvektormaschinen (RVMs) wurden als Klassifikatoren eingesetzt. Während Entscheidungsbäume im allgemeinen gute Klassifikationsergebnisse lieferten, scheiterten RVMs an ihren großen Laufzeitbedürfnissen bei Anwendung auf ein komplexes System wie den Zitratzyklus. Hergeleitete Entscheidungsbaumregeln wurden sowohl statistisch als auch individuell analysiert, um die Koordination von Enzymen und Metaboliten in der Kontrolle von Trajektorien des Systems zu untersuchen. Der dritte Beitrag, welcher in dieser Arbeit vorgestellt wurde, war die Etablierung der Beziehung zwischen SKM und der metabolischer Kontrollanalyse. Insbesondere wurde gezeigt, wie die zufällig generierten Elastizitäten in Flusskontrollkoeffizienten umgewandelt werden. Diese wurden im Anschluss bezüglich ihres Informationsgehaltes zum Klassifikationstraining untersucht. Nach der Evaluierung anhand einiger kleiner Beispielsysteme wurde die neue Methodik auf die Studie zweier Fließgleichgewichte des neuronalen Zitratzyklus angewandt, um intrinsische Mechanismen für Stabilität oder Instabilität zu finden. Die Ergebnisse identifizierten Mutationen im Enzym alpha-ketoglutarate dehydrogenase als wahrscheinlichste Quelle füur Instabilitäten.
KW  - Systembiologie
KW  - mathematische Modellierung
KW  - systems biology
KW  - mathematical modeling
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-72017
ER  - 
TY  - JOUR
A1  - Kuekenshoener, Tim
A1  - Hagemann, Urs B.
A1  - Wohlwend, Daniel
A1  - Raeuber, Christina
A1  - Baumann, Tobias
A1  - Keller, Sandro
A1  - Einsle, Oliver
A1  - Mueller, Kristian M.
A1  - Arndt, Katja Maren
T1  - Analysis of Selected and Designed Chimeric D- and L-alpha-Helix Assemblies
JF  - Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences
N2  - D-Peptides have been attributed pharmacological advantages over regular L-peptides, yet design rules are largely unknown. Based on a designed coiled coil-like D/L heterotetramer, named L-Base/D-Acid, we generated a library offering alternative residues for interaction with the D-peptide. Phage display selection yielded one predominant peptide, named HelixA, that differed at 13 positions from the scaffold helix. In addition to the observed D-/L-heterotetramers, ratio-dependent intermediate states were detected by isothermal titration calorimetry. Importantly, the formation of the selected HelixA/D-Acid bundle passes through fewer intermediate states than L-Base/D-Acid. Back mutation of HelixA core residues to L-Base (HelixLL) revealed that the residues at e/g-positions are responsible for the different intermediates. Furthermore, a Val-core variant (PeptideVV) was completely devoid of binding D-Acid, whereas an Ile-core helix (HelixII) interacted with D-Acid in a significantly more specific complex than L-Base.
Y1  - 2014
U6  - https://doi.org/10.1021/bm5006883
SN  - 1525-7797
SN  - 1526-4602
VL  - 15
IS  - 9
SP  - 3296
EP  - 3305
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Brust, Henrike
A1  - Lehmann, Tanja
A1  - Fettke, Jörg
T1  - Analysis of the functional interaction of arabidopsis starch synthase and branching enzyme isoforms reveals that the cooperative action of SSI and BEs results in glucans with polymodal chain length distribution similar to amylopectin
JF  - PLoS one
N2  - Starch synthase (SS) and branching enzyme (BE) establish the two glycosidic linkages existing in starch. Both enzymes exist as several isoforms. Enzymes derived from several species were studied extensively both in vivo and in vitro over the last years, however, analyses of a functional interaction of SS and BE isoforms are missing so far. Here, we present data from in vitro studies including both interaction of leaf derived and heterologously expressed SS and BE isoforms. We found that SSI activity in native PAGE without addition of glucans was dependent on at least one of the two BE isoforms active in Arabidopsis leaves. This interaction is most likely not based on a physical association of the enzymes, as demonstrated by immunodetection and native PAGE mobility analysis of SSI, BE2, and BE3. The glucans formed by the action of SSI/BEs were analysed using leaf protein extracts from wild type and be single mutants (Atbe2 and Atbe3 mutant lines) and by different combinations of recombinant proteins. Chain length distribution (CLD) patterns of the formed glucans were irrespective of SSI and BE isoforms origin and still independent of assay conditions. Furthermore, we show that all SS isoforms (SSI-SSIV) were able to interact with BEs and form branched glucans. However, only SSI/BEs generated a polymodal distribution of glucans which was similar to CLD pattern detected in amylopectin of Arabidopsis leaf starch. We discuss the impact of the SSI/BEs interplay for the CLD pattern of amylopectin.
Y1  - 2014
U6  - https://doi.org/10.1371/journal.pone.0102364
SN  - 1932-6203
VL  - 9
IS  - 7
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Horn, Susanne
A1  - Prost, Stefan
A1  - Stiller, Mathias
A1  - Makowiecki, Daniel
A1  - Kuznetsova, Tatiana
A1  - Benecke, Norbert
A1  - Pucher, Erich
A1  - Hufthammer, Anne K.
A1  - Schouwenburg, Charles
A1  - Shapiro, Beth
A1  - Hofreiter, Michael
T1  - Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe
JF  - Molecular ecology
N2  - After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.
KW  - Conservation Biology
KW  - Phylogeography
KW  - Conservation Genetics
KW  - Population Genetics - Empirical
Y1  - 2014
U6  - https://doi.org/10.1111/mec.12691
SN  - 0962-1083
SN  - 1365-294X
VL  - 23
IS  - 7
SP  - 1717
EP  - 1729
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Roder, Phillip
A1  - Hille, Carsten
T1  - ANG-2 for quantitative Na+ determination in living cells by time-resolved fluorescence microscopy
JF  - Photochemical & photobiological sciences
N2  - Sodium ions (Na+) play an important role in a plethora of cellular processes, which are complex and partly still unexplored. For the investigation of these processes and quantification of intracellular Na+ concentrations ([Na+](i)), two-photon coupled fluorescence lifetime imaging microscopy (2P-FLIM) was performed in the salivary glands of the cockroach Periplaneta americana. For this, the novel Na+-sensitive fluorescent dye Asante NaTRIUM Green-2 (ANG-2) was evaluated, both in vitro and in situ. In this context, absorption coefficients, fluorescence quantum yields and 2P action cross-sections were determined for the first time. ANG-2 was 2P-excitable over a broad spectral range and displayed fluorescence in the visible spectral range. Although the fluorescence decay behaviour of ANG-2 was triexponential in vitro, its analysis indicates a Na+-sensitivity appropriate for recordings in living cells. The Na+-sensitivity was reduced in situ, but the biexponential fluorescence decay behaviour could be successfully analysed in terms of quantitative [Na+](i) recordings. Thus, physiological 2P-FLIM measurements revealed a dopamine-induced [Na+](i) rise in cockroach salivary gland cells, which was dependent on a Na+-K+-2Cl-cotransporter (NKCC) activity. It was concluded that ANG-2 is a promising new sodium indicator applicable for diverse biological systems.
Y1  - 2014
U6  - https://doi.org/10.1039/c4pp00061g
SN  - 1474-905X
SN  - 1474-9092
VL  - 13
IS  - 12
SP  - 1699
EP  - 1710
PB  - Royal Society of Chemistry
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Radchuk, Viktoriia
A1  - Johst, Karin
A1  - Groeneveld, Jürgen
A1  - Turlure, Camille
A1  - Grimm, Volker
A1  - Schtickzelle, Nicolas
T1  - Appropriate resolution in time and model structure for population viability analysis: Insights from a butterfly metapopulation
JF  - : an international journal
N2  - The importance of a careful choice of the appropriate scale for studying ecological phenomena has been stressed repeatedly. However, issues of spatial scale in metapopulation dynamics received much more attention compared to temporal scale. Moreover, multiple calls were made to carefully choose the appropriate model structure for Population Viability Analysis (PVA). We assessed the effect of using coarser resolution in time and model structure on population dynamics. For this purpose, we compared outcomes of two PVA models differing in their time step: daily individual-based model (dIBM) and yearly stage-based model (ySBM), loaded with empirical data on a well-known metapopulation of the butterfly Boloria eunomia. Both models included the same environmental drivers of population dynamics that were previously identified as being the most important for this species. Under temperature change scenarios, both models yielded the same qualitative scenario ranking, but they quite substantially differed quantitatively with dIBM being more pessimistic in absolute viability measures. We showed that these differences stemmed from inter-individual heterogeneity in dIBM allowing for phenological shifts of individual appearance. We conclude that a finer temporal resolution and an individual-based model structure allow capturing the essential mechanisms necessary to go beyond mere PVA scenario ranking. We encourage researchers to carefully chose the temporal resolution and structure of their model aiming at (1) depicting the processes important for (meta)population dynamics of the species and (2) implementing the environmental change scenarios expected for their study system in the future, using the temporal resolution at which such changes are predicted to operate.
KW  - Temporal grain
KW  - Model complexity
KW  - Model comparison
KW  - Population dynamics
KW  - Individual-based model
KW  - Stage-based model
Y1  - 2014
U6  - https://doi.org/10.1016/j.biocon.2013.12.004
SN  - 0006-3207
SN  - 1873-2917
VL  - 169
SP  - 345
EP  - 354
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Stief, Anna
A1  - Altmann, Simone
A1  - Hoffmann, Karen
A1  - Pant, Bikram Datt
A1  - Scheible, Wolf-Rüdiger
A1  - Bäurle, Isabel
T1  - Arabidopsis miR156 regulates tolerance to recurring environmental stress through SPL transcription factors
JF  - The plant cell
N2  - Plants are sessile organisms that gauge stressful conditions to ensure survival and reproductive success. While plants in nature often encounter chronic or recurring stressful conditions, the strategies to cope with those are poorly understood. Here, we demonstrate the involvement of ARGONAUTE1 and the microRNA pathway in the adaptation to recurring heat stress (HS memory) at the physiological and molecular level. We show that miR156 isoforms are highly induced after HS and are functionally important for HS memory. miR156 promotes sustained expression of HS-responsive genes and is critical only after HS, demonstrating that the effects of modulating miR156 on HS memory do not reflect preexisting developmental alterations. miR156 targets SPL transcription factor genes that are master regulators of developmental transitions. SPL genes are posttranscriptionally downregulated by miR156 after HS, and this is critical for HS memory. Altogether, the miR156-SPL module mediates the response to recurring HS in Arabidopsis thaliana and thus may serve to integrate stress responses with development.
Y1  - 2014
U6  - https://doi.org/10.1105/tpc.114.123851
SN  - 1040-4651
SN  - 1532-298X
VL  - 26
IS  - 4
SP  - 1792
EP  - 1807
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  -