@phdthesis{Schwuchow2019,
  author    = {Schwuchow, Viola},
  title     = {Charakterisierung der periplasmatischen Aldehyd-Oxidoreduktase (PaoABC) aus Escherichia coli},
  school      = {Universit{\"a}t Potsdam},
  pages     = {119},
  year      = {2019},
  abstract  = {Im Mittelpunkt dieser Arbeit standen Analysen zur Charakterisierung der periplasmatischen Aldehyd Oxidoreduktase aus E. coli. Kinetische Untersuchungen mit Ferricyanid als Elektronenakzeptor unter anaeroben Bedingungen zeigten f{\"u}r dieses Enzym eine h{\"o}here Aktivit{\"a}t als unter aeroben Bedingungen. Die getroffene Hypothese, dass PaoABC f{\"a}hig ist Elektronen an molekularen Sauerstoff weiter zu geben, konnte best{\"a}tigt werden. F{\"u}r den Umsatz aromatischer Aldehyde mit molekularem Sauerstoff wurde ein Optimum von pH 6,0 ermittelt. Dies steht im Gegensatz zur Reaktion mit Ferricyanid, mit welchem ein pH-Optimum von 4,0 gezeigt wurde. Die Reaktion von PaoABC mit molekularem Sauerstoff generiert zwar Wasserstoffperoxid, die Produktion von Superoxid konnte dagegen nicht beobachtet werden. Dass aerobe Bedingungen einen Einfluss auf das Ausl{\"o}sen der Expression von PaoABC haben, wurde in dieser Arbeit ebenfalls ermittelt. Im Zusammenhang mit der Produktion von ROS durch PaoABC wurde die Funktion eines k{\"u}rzlich in Elektronentransfer-Distanz zum FAD identifizierten [4Fe4S]-Clusters untersucht. Ein Austausch der f{\"u}r die Bindung des Clusters zust{\"a}ndigen Cysteine f{\"u}hrte zur Instabilit{\"a}t der Proteinvarianten, weswegen f{\"u}r diese keine weiteren Untersuchungen erfolgten. Daher wird zumindest ein struktur-stabilisierender Einfluss des [4Fe4S]-Clusters angenommen. Zur weiteren Untersuchung der Funktion dieses Clusters, wurde ein zwischen FAD und [4Fe4S]-Cluster lokalisiertes Arginin gegen ein Alanin ausgetauscht. Diese Proteinvariante zeigte eine reduzierte Geschwindigkeit der Reaktion gegen{\"u}ber dem Wildtyp. Die Bildung von Superoxid konnte auch hier nicht beobachtet werden. Die Vermutung, dass dieser Cluster einen elektronen-sammelnden Mechanismus unterst{\"u}tzt, welcher die Radikalbildung verhindert, kann trotz allem nicht ausgeschlossen werden. Da im Umkreis des Arginins weitere geladene und aromatische Aminos{\"a}uren lokalisiert sind, k{\"o}nnen diese den notwendigen Elektronentransfer {\"u}bernehmen. Neben der Ermittlung eines physiologischen Elektronenakzeptors und dessen Einfluss auf die Expression von PaoABC zeigt diese Arbeit auch, dass die Chaperone PaoD und MocA w{\"a}hrend der Reifung des MCD-Kofaktor eine gemeinsame Bindung an PaoABC realisieren. Es konnte im aktiven Zentrum von PaoABC ein Arginin beschrieben werden, welches auf Grund der engen Nachbarschaft zum MCD-Kofaktor und zum Glutamat (PaoABC-EC692) am Prozess der Substratbindung beteiligt ist. Im Zusammenhang mit dem Austausch dieses Arginins gegen ein Histidin oder ein Lysin wurden die Enzymspezifit{\"a}t und der Einfluss physiologischer Bedingungen, wie pH und Ionenst{\"a}rke, auf die Reaktion des Enzyms untersucht. Gegen{\"u}ber dem Wildtyp zeigten die Varianten mit molekularem Sauerstoff eine geringere Affinit{\"a}t zum Substrat aber auch eine h{\"o}here Geschwindigkeit der Reaktion. Vor allem f{\"u}r die Histidin-Variante konnte im gesamten pH-Bereich ein instabiles Verhalten bestimmt werden. Der Grund daf{\"u}r wurde durch das L{\"o}sen der Struktur der Histidin-Variante beschreiben. Durch den Austausch der Aminos{\"a}uren entf{\"a}llt die stabilisierende Wirkung der delokalisierten Elektronen des Arginins und es kommt zu einer Konformations{\"a}nderung im aktiven Zentrum. Neben der Reaktion von PaoABC mit einer Vielzahl aromatischer Aldehyde konnte auch der Umsatz von Salicylaldehyd zu Salicyls{\"a}ure durch PaoABC in einer Farbreaktion bestimmt werden. Durch Ausschluss von molekularem Sauerstoff als terminaler Elektronenakzeptor, in einer enzym-gekoppelten Reaktion, erfolgte ein Elektronentransport auf Ferrocencarboxyls{\"a}ure. Die Kombination aus beiden Methoden erm{\"o}glichte eine Verwendung von Ferrocen-Derivaten zur Generierung einer enzym-gekoppelten Reaktion mit PaoABC. Die Untersuchungen zu PaoABC zeigen, dass die Vielfalt der durch das Enzym katalysierten Rektionen weitere M{\"o}glichkeiten der enzymatischen Bestimmung biokatalytischer Prozesse bietet.},
  language  = {de}
}
@article{CoduttiBenteFaivreetal.2019,
  author    = {Codutti, Agnese and Bente, Klaas and Faivre, Damien and Klumpp, Stefan},
  title     = {Chemotaxis in external fields: Simulations for active magnetic biological matter},
  series = {PLoS Computational Biology : a new community journal},
  volume    = {15},
  journal   = {PLoS Computational Biology : a new community journal},
  number    = {12},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1553-734X},
  doi       = {10.1371/journal.pcbi.1007548},
  pages     = {26},
  year      = {2019},
  abstract  = {The movement of microswimmers is often described by active Brownian particle models. Here we introduce a variant of these models with several internal states of the swimmer to describe stochastic strategies for directional swimming such as run and tumble or run and reverse that are used by microorganisms for chemotaxis. The model includes a mechanism to generate a directional bias for chemotaxis and interactions with external fields (e.g., gravity, magnetic field, fluid flow) that impose forces or torques on the swimmer. We show how this modified model can be applied to various scenarios: First, the run and tumble motion of E. coli is used to establish a paradigm for chemotaxis and investigate how it is affected by external forces. Then, we study magneto-aerotaxis in magnetotactic bacteria, which is biased not only by an oxygen gradient towards a preferred concentration, but also by magnetic fields, which exert a torque on an intracellular chain of magnets. We study the competition of magnetic alignment with active reorientation and show that the magnetic orientation can improve chemotaxis and thereby provide an advantage to the bacteria, even at rather large inclination angles of the magnetic field relative to the oxygen gradient, a case reminiscent of what is expected for the bacteria at or close to the equator. The highest gain in chemotactic velocity is obtained for run and tumble with a magnetic field parallel to the gradient, but in general a mechanism for reverse motion is necessary to swim against the magnetic field and a run and reverse strategy is more advantageous in the presence of a magnetic torque. This finding is consistent with observations that the dominant mode of directional changes in magnetotactic bacteria is reversal rather than tumbles. Moreover, it provides guidance for the design of future magnetic biohybrid swimmers. Author summary In this paper, we propose a modified Active Brownian particle model to describe bacterial swimming behavior under the influence of external forces and torques, in particular of a magnetic torque. This type of interaction is particularly important for magnetic biohybrids (i.e. motile bacteria coupled to a synthetic magnetic component) and for magnetotactic bacteria (i.e. bacteria with a natural intracellular magnetic chain), which perform chemotaxis to swim along chemical gradients, but are also directed by an external magnetic field. The model allows us to investigate the benefits and disadvantages of such coupling between two different directionality mechanisms. In particular we show that the magnetic torque can speed chemotaxis up in some conditions, while it can hinder it in other cases. In addition to an understanding of the swimming strategies of naturally magnetotactic organisms, the results may guide the design of future biomedical devices.},
  language  = {en}
}
@article{PlikkEngelsLuotoetal.2019,
  author    = {Plikk, Anna and Engels, Stefan and Luoto, Tomi P. and Nazarova, Larisa B. and Salonen, J. Sakari and Helmens, Karin F.},
  title     = {Chironomid-based temperature reconstruction for the Eemian Interglacial (MIS 5e) at Sokli, northeast Finland},
  series = {Journal of paleolimnology},
  volume    = {61},
  journal   = {Journal of paleolimnology},
  number    = {3},
  publisher = {Springer Science},
  address   = {Dordrecht},
  issn      = {0921-2728},
  doi       = {10.1007/s10933-018-00064-y},
  pages     = {355 -- 371},
  year      = {2019},
  abstract  = {The Last Interglacial (Eemian, MIS 5e) can be considered a test-bed for climate dynamics under a warmer-than-present climate. In this study we present a chironomid record from the high latitude Sokli site (N Finland), where a long continuous sediment sequence from the last interglacial has been preserved from glacial erosion. The chironomid-analysis shows a diverse fauna, with dominance of warm-water indicators and shifts in assemblage composition that can be attributed to temperature, lake depth, productivity and habitat availability. Quantitative mean July paleotemperature estimates based on the chironomid data indicate overall mean July air temperatures up to 1 degrees C warmer than present. Two cooling events can be discerned, the Tunturi event, dated to about 127.5kaBP, in the lower part of the sequence, and the Varrio event, dated to about 119kaBP, associated with the beginning of a cooling trend in the upper part of the record. Warm conditions already at the onset of the interglacial contrast with a recent chironomid-based last interglacial temperature reconstruction from Denmark, which suggests a late onset of Eemian warming. The relatively small increase in inferred temperatures compared to present day temperatures at Sokli differs from other high latitude Eemian sites, and likely reflects the influence of the Atlantic Meridional Overturning Circulation in maintaining already elevated temperatures in Fennoscandia during interglacials.},
  language  = {en}
}
@article{ZimmermannHarmsEppetal.2019,
  author    = {Zimmermann, Heike Hildegard and Harms, Lars and Epp, Laura Saskia and Mewes, Nick and Bernhardt, Nadine and Kruse, Stefan and Stoof-Leichsenring, Kathleen Rosemarie and Pestryakova, Luidmila Agafyevna and Wieczorek, Mareike and Trense, Daronja and Herzschuh, Ulrike},
  title     = {Chloroplast and mitochondrial genetic variation of larches at the Siberian tundrataiga ecotone revealed by de novo assembly},
  series = {PLoS one},
  volume    = {14},
  journal   = {PLoS one},
  number    = {7},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0216966},
  pages     = {21},
  year      = {2019},
  abstract  = {Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/ L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.},
  language  = {en}
}
@article{AngeleskaNikoloski2019,
  author    = {Angeleska, Angela and Nikoloski, Zoran},
  title     = {Coherent network partitions},
  series = {Discrete applied mathematics},
  volume    = {266},
  journal   = {Discrete applied mathematics},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0166-218X},
  doi       = {10.1016/j.dam.2019.02.048},
  pages     = {283 -- 290},
  year      = {2019},
  abstract  = {Graph clustering is widely applied in the analysis of cellular networks reconstructed from large-scale data or obtained from experimental evidence. Here we introduce a new type of graph clustering based on the concept of coherent partition. A coherent partition of a graph G is a partition of the vertices of G that yields only disconnected subgraphs in the complement of G. The coherence number of G is then the size of the smallest edge cut inducing a coherent partition. A coherent partition of G is optimal if the size of the inducing edge cut is the coherence number of G. Given a graph G, we study coherent partitions and the coherence number in connection to (bi)clique partitions and the (bi)clique cover number. We show that the problem of finding the coherence number is NP-hard, but is of polynomial time complexity for trees. We also discuss the relation between coherent partitions and prominent graph clustering quality measures.},
  language  = {en}
}
@article{BhuvaneshMachatschekLysyakovaetal.2019,
  author    = {Bhuvanesh, Thanga and Machatschek, Rainhard Gabriel and Lysyakova, Liudmila and Kratz, Karl and Schulz, Burkhard and Ma, Nan and Lendlein, Andreas},
  title     = {Collagen type-IV Langmuir and Langmuir-Schafer layers as model biointerfaces to direct stem cell adhesion},
  series = {Biomedical materials : materials for tissue engineering and regenerative medicine},
  volume    = {14},
  journal   = {Biomedical materials : materials for tissue engineering and regenerative medicine},
  number    = {2},
  publisher = {Inst. of Physics Publ.},
  address   = {Bristol},
  issn      = {1748-6041},
  doi       = {10.1088/1748-605X/aaf464},
  pages     = {17},
  year      = {2019},
  abstract  = {In biomaterial development, the design of material surfaces that mimic the extra-cellular matrix (ECM) in order to achieve favorable cellular instruction is rather challenging. Collagen-type IV (Col-IV), the major scaffolding component of Basement Membranes (BM), a specialized ECM with multiple biological functions, has the propensity to form networks by self-assembly and supports adhesion of cells such as endothelial cells or stem cells. The preparation of biomimetic Col-IV network-like layers to direct cell responses is difficult. We hypothesize that the morphology of the layer, and especially the density of the available adhesion sites, regulates the cellular adhesion to the layer. The Langmuir monolayer technique allows for preparation of thin layers with precisely controlled packing density at the air-water (A-W) interface. Transferring these layers onto cell culture substrates using the Langmuir-Schafer (LS) technique should therefore provide a pathway for preparation of BM mimicking layers with controlled cell adherence properties. In situ characterization using ellipsometry and polarization modulation-infrared reflection absorption spectroscopy of Col-IV layer during compression at the A-W interface reveal that there is linear increase of surface molecule concentration with negligible orientational changes up to a surface pressure of 25 mN m(-1). Smooth and homogeneous Col-IV network-like layers are successfully transferred by LS method at 15 mN m(-1) onto poly(ethylene terephthalate) (PET), which is a common substrate for cell culture. In contrast, the organization of Col-IV on PET prepared by the traditionally employed solution deposition method results in rather inhomogeneous layers with the appearance of aggregates and multilayers. Progressive increase in the number of early adherent mesenchymal stem cells (MSCs) after 24 h by controlling the areal Col-IV density by LS transfer at 10, 15 and 20 mN m(-1) on PET is shown. The LS method offers the possibility to control protein characteristics on biomaterial surfaces such as molecular density and thereby, modulate cell responses.},
  language  = {en}
}
@article{NaseriBehrendRieperetal.2019,
  author    = {Naseri, Gita and Behrend, Jessica and Rieper, Lisa and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors},
  series = {Nature Communications},
  volume    = {10},
  journal   = {Nature Communications},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-019-10224-x},
  pages     = {18},
  year      = {2019},
  abstract  = {Balanced expression of multiple genes is central for establishing new biosynthetic pathways or multiprotein cellular complexes. Methods for efficient combinatorial assembly of regulatory sequences (promoters) and protein coding sequences are therefore highly wanted. Here, we report a high-throughput cloning method, called COMPASS for COMbinatorial Pathway ASSembly, for the balanced expression of multiple genes in Saccharomyces cerevisiae. COMPASS employs orthogonal, plant-derived artificial transcription factors (ATFs) and homologous recombination-based cloning for the generation of thousands of individual DNA constructs in parallel. The method relies on a positive selection of correctly assembled pathway variants from both, in vivo and in vitro cloning procedures. To decrease the turnaround time in genomic engineering, COMPASS is equipped with multi-locus CRISPR/Cas9-mediated modification capacity. We demonstrate the application of COMPASS by generating cell libraries producing n-carotene and co-producing p-ionone and biosensor-responsive naringenin. COMPASS will have many applications in synthetic biology projects that require gene expression balancing.},
  language  = {en}
}
@article{KahlLenhardJoshi2019,
  author    = {Kahl, Sandra M. and Lenhard, Michael and Joshi, Jasmin Radha},
  title     = {Compensatory mechanisms to climate change in the widely distributed species Silene vulgaris},
  series = {The journal of ecology},
  volume    = {107},
  journal   = {The journal of ecology},
  number    = {4},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0022-0477},
  doi       = {10.1111/1365-2745.13133},
  pages     = {1918 -- 1930},
  year      = {2019},
  abstract  = {The adaptation of plants to future climatic conditions is crucial for their survival. Not surprisingly, phenotypic responses to climate change have already been observed in many plant populations. These responses may be due to evolutionary adaptive changes or phenotypic plasticity. Especially plant species with a wide geographic range are either expected to show genetic differentiation in response to differing climate conditions or to have a high phenotypic plasticity. We investigated phenotypic responses and plasticity as an estimate of the adaptive potential in the widespread species Silene vulgaris. In a greenhouse experiment, 25 European populations covering a geographic range from the Canary Islands to Sweden were exposed to three experimental precipitation and two temperature regimes mimicking a possible climate-change scenario for central Europe. We hypothesized that southern populations have a better performance under high temperature and drought conditions, as they are already adapted to a comparable environment. We found that our treatments significantly influenced the plants, but did not reveal a latitudinal difference in response to climate treatments for most plant traits. Only flower number showed a stronger plasticity in northern European populations (e.g. Swedish populations) where numbers decreased more drastically with increased temperature and decreased precipitation treatment. Synthesis. The significant treatment response in Silene vulgaris, independent of population origin - except for the number of flowers produced - suggests a high degree of universal phenotypic plasticity in this widely distributed species. This reflects the likely adaptation strategy of the species and forms the basis for a successful survival strategy during upcoming climatic changes. However, as flower number, a strongly fitness-related trait, decreased more strongly in northern populations under a climate-change scenario, there might be limits to adaptation even in this widespread, plastic species.},
  language  = {en}
}
@article{KuekenNikoloski2019,
  author    = {K{\"u}ken, Anika and Nikoloski, Zoran},
  title     = {Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {179},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  number    = {3},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.18.01273},
  pages     = {894 -- 906},
  year      = {2019},
  abstract  = {Successfully designed and implemented plant-specific synthetic metabolic pathways hold promise to increase crop yield and nutritional value. Advances in synthetic biology have already demonstrated the capacity to design artificial biological pathways whose behavior can be predicted and controlled in microbial systems. However, the transfer of these advances to model plants and crops faces the lack of characterization of plant cellular pathways and increased complexity due to compartmentalization and multicellularity. Modern computational developments provide the means to test the feasibility of plant synthetic metabolic pathways despite gaps in the accumulated knowledge of plant metabolism. Here, we provide a succinct systematic review of optimization-based and retrobiosynthesis approaches that can be used to design and in silico test synthetic metabolic pathways in large-scale plant context-specific metabolic models. In addition, by surveying the existing case studies, we highlight the challenges that these approaches face when applied to plants. Emphasis is placed on understanding the effect that metabolic designs can have on native metabolism, particularly with respect to metabolite concentrations and thermodynamics of biochemical reactions. In addition, we discuss the computational developments that may help to transform the identified challenges into opportunities for plant synthetic biology.},
  language  = {en}
}
@article{SowemimoKnoxBrownBorcherdsetal.2019,
  author    = {Sowemimo, Oluwakemi T. and Knox-Brown, Patrick and Borcherds, Wade and Rindfleisch, Tobias and Thalhammer, Anja and Daughdrill, Gary W.},
  title     = {Conserved Glycines Control Disorder and Function in the Cold-Regulated Protein, COR15A},
  series = {Biomolecules},
  volume    = {9},
  journal   = {Biomolecules},
  number    = {3},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2218-273X},
  doi       = {10.3390/biom9030084},
  pages     = {17},
  year      = {2019},
  abstract  = {Cold-regulated (COR) 15A is an intrinsically disordered protein (IDP) from Arabidopsis thaliana important for freezing tolerance. During freezing-induced cellular dehydration, COR15A transitions from a disordered to mostly alpha-helical structure. We tested whether mutations that increase the helicity of COR15A also increase its protective function. Conserved glycine residues were identified and mutated to alanine. Nuclear magnetic resonance (NMR) spectroscopy was used to identify residue-specific changes in helicity for wildtype (WT) COR15A and the mutants. Circular dichroism (CD) spectroscopy was used to monitor the coil-helix transition in response to increasing concentrations of trifluoroethanol (TFE) and ethylene glycol. The impact of the COR15A mutants on the stability of model membranes during a freeze-thaw cycle was investigated by fluorescence spectroscopy. The results of these experiments showed the mutants had a higher content of alpha-helical structure and the increased alpha-helicity improved membrane stabilization during freezing. Comparison of the TFE- and ethylene glycol-induced coil-helix transitions support our conclusion that increasing the transient helicity of COR15A in aqueous solution increases its ability to stabilize membranes during freezing. Altogether, our results suggest the conserved glycine residues are important for maintaining the disordered structure of COR15A but are also compatible with the formation of alpha-helical structure during freezing induced dehydration.},
  language  = {en}
}
@phdthesis{Schirmer2019,
  author    = {Schirmer, Annika},
  title     = {Consistent individual differences in movement-related behaviour as equalising and/or stabilising mechanisms for species coexistence},
  school      = {Universit{\"a}t Potsdam},
  pages     = {154},
  year      = {2019},
  abstract  = {The facilitation of species coexistence has been a central theme in ecological research for years, highlighting two key aspects: ecological niches and competition between species. According to the competitive exclusion principle, the overlap of species niches predicts the amount of shared resources and therefore competition between species, determining their ability to coexist. Only if niches of two species are sufficiently different, thus niche overlap is low, competition within species is higher than competition between species and stable coexistence is possible. Thereby, differences in species mean traits are focused on and conspecific individuals are assumed to be interchangeable. This approach might be outdated since behaviour, as a key aspect mediating niche differentiation between species, is individual based. Individuals from one species consistently differ across time and situations in their behavioural traits. Causes and consequences of consistent behavioural differences have been thoroughly investigated stimulating their recent incorporation into ecological interactions and niche theory. Spatial components have so far been largely overlooked, although animal movement is strongly connected to several aspects of ecological niches and interactions between individuals. Furthermore, numerous movement aspects haven been proven to be crucially influenced by consistent individual differences. Considering spatial parameters could therefore crucially broaden our understanding of how individual niches are formed and ecological interactions are shaped. Furthermore, extending established concepts on species interactions by an individual component could provide new insights into how species coexistence is facilitated and local biodiversity is maintained. The main aim of this thesis was to test whether consistent inter-individual differences can facilitate the coexistence of ecological similar species. Therefore, the effects of consistent inter-individual differences on the spatial behaviour of two rodent species, the bank vole (Myodes glareolus) and the striped field mouse (Apodemus agrarius), were investigated and put in the context of: (i) individual spatial niches, (ii) interactions between species, and (iii) the importance of different levels of behavioural variation within species for their interactions. Consistent differences of study animals in boldness and exploration were quantified with the same tests in all presented studies and always combined with observations of movement and space use via automated VHF radio telemetry. Consequently, results are comparable throughout the thesis and the methods provide a common denominator for all chapters. The first two chapters are based on observations of free-ranging rodents in natural populations, while chapter III represents an experimental approach under semi-natural conditions. Chapter I focusses on the effect of consistent differences in boldness and exploration on movement and space use of bank voles and their contribution to individual spatial niche separation. Results show boldness to be the dominating predictor for spatial parameters in bank voles. Irrespective of sex, bolder individuals had larger home ranges, moved longer distances, had less spatial interactions with conspecifics and occupied different microhabitats compared to shy individuals. The same boldness-dependent spatial patterns could be observed in striped field mice which is reported in chapter II. Therefore, both study species showed individual spatial niche occupation. Chapter II builds on findings from the first chapter, investigating the effect of boldness driven individual spatial niche occupation on the interactions between species. Irrespective of species and sex, bolder individuals had more interspecific spatial interactions, but less intraspecific interactions, compared to shy individuals. Due to individual niches occupation the competitive environment individuals experience is not random. Interactions are restricted to individuals of similar behavioural type with presumably similar competitive ability, which could balance differences on the species level and support coexistence. In chapter III the experimental populations were either comprised of only shy or only bold bank voles, while striped field mice varied, creating either a shy- or bold-biased competitive community. Irrespective of behavioural type, striped field mice had more intraspecific interactions in bold-biased competitive communities. Only in a shy-biased competitive community, bolder striped field mice had less interspecific interactions compared to shy individuals. Bank voles showed no difference in intra- or interspecific interactions between populations. Chapter III highlights, that not only consistent inter-individual differences per se are important for interactions within and between species, but also the amount of behavioural variation within coexisting species. Overall, this thesis highlights the importance of considering consistent inter-individual differences in a spatial context and their connection to individual spatial niche occupation, as well as the resulting effects on interactions within and between species. Individual differences are discussed in the context of similarity of individuals, individual and species niche width, and individual and species niche overlap. Thereby, this thesis makes one step further from the existing research on individual niches towards integrating consistent inter-individual differences into the larger framework of species coexistence.},
  language  = {en}
}
@article{GuenthelDonisKirillinetal.2019,
  author    = {G{\"u}nthel, Marco and Donis, Daphne and Kirillin, Georgiy and Ionescu, Danny and Bizic, Mina and McGinnis, Daniel F. and Grossart, Hans-Peter and Tang, Kam W.},
  title     = {Contribution of oxic methane production to surface methane emission in lakes and its global importance},
  series = {Nature Communications},
  volume    = {10},
  journal   = {Nature Communications},
  publisher = {Nature Publishing Group UK},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-019-13320-0},
  pages     = {10},
  year      = {2019},
  abstract  = {Recent discovery of oxic methane production in sea and lake waters, as well as wetlands, demands re-thinking of the global methane cycle and re-assessment of the contribution of oxic waters to atmospheric methane emission. Here we analysed system-wide sources and sinks of surface-water methane in a temperate lake. Using a mass balance analysis, we show that internal methane production in well-oxygenated surface water is an important source for surface-water methane during the stratified period. Combining our results and literature reports, oxic methane contribution to emission follows a predictive function of littoral sediment area and surface mixed layer volume. The contribution of oxic methane source(s) is predicted to increase with lake size, accounting for the majority (>50\%) of surface methane emission for lakes with surface areas >1 km(2).},
  language  = {en}
}
@phdthesis{Wozniak2019,
  author    = {Wozniak, Natalia Joanna},
  title     = {Convergent evolution of the selfing syndrome in the genus Capsella},
  school      = {Universit{\"a}t Potsdam},
  pages     = {229},
  year      = {2019},
  language  = {en}
}
@misc{LeproNagelKlumppetal.2019,
  author    = {Lepro, Valentino and Nagel, Oliver and Klumpp, Stefan and Lipowsky, Reinhard and Beta, Carsten},
  title     = {Cooperative Transport by Amoeboid Cells},
  series = {Biophysical journal},
  volume    = {116},
  journal   = {Biophysical journal},
  number    = {3},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2018.11.682},
  pages     = {122A -- 122A},
  year      = {2019},
  language  = {en}
}
@article{TangBackhausRiemannetal.2019,
  author    = {Tang, Kam W. and Backhaus, Liv and Riemann, Lasse and Koski, Marja and Grossart, Hans-Peter and Munk, Peter and Nielsen, Torkel Gissel},
  title     = {Copepod carcasses in the subtropical convergence zone of the Sargasso Sea},
  series = {Journal of plankton research},
  volume    = {41},
  journal   = {Journal of plankton research},
  number    = {4},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0142-7873},
  doi       = {10.1093/plankt/fbz038},
  pages     = {549 -- 560},
  year      = {2019},
  abstract  = {The oligotrophic subtropical gyre covers a vast area of the Atlantic Ocean. Decades of time-series monitoring have generated detailed temporal information about zooplankton species and abundances at fixed locations within the gyre, but their live/dead status is often omitted, especially in the dynamic subtropical convergence zone (STCZ) where the water column stratification pattern can change considerably across the front as warm and cold water masses converge. We conducted a detailed survey in the North Atlantic STCZ and showed that over 85\% of the copepods were typically concentrated in the upper 200 m. Copepod carcasses were present in all samples and their proportional numerical abundances increased with depth, reaching up to 91\% at 300-400 m. Overall, 14-19\% of the copepods within the upper 200 m were carcasses. Shipboard experiments showed that during carcass decomposition, microbial respiration increased, and the bacterial community associated with the carcasses diverged from that in the ambient water. Combining field and experimental data, we estimated that decomposing copepod carcasses constitute a negligible oxygen sink in the STCZ, but sinking carcasses may represent an overlooked portion of the passive carbon sinking flux and should be incorporated in future studies of carbon flux in this area.},
  language  = {en}
}
@article{MazzaDammhahnEccardetal.2019,
  author    = {Mazza, Valeria and Dammhahn, Melanie and Eccard, Jana and Palme, Rupert and Zaccaroni, Marco and Jacob, Jens},
  title     = {Coping with style: individual differences in responses to environmental variation},
  series = {Behavioral ecology and sociobiology},
  volume    = {73},
  journal   = {Behavioral ecology and sociobiology},
  number    = {10},
  publisher = {Springer},
  address   = {New York},
  issn      = {0340-5443},
  doi       = {10.1007/s00265-019-2760-2},
  pages     = {11},
  year      = {2019},
  abstract  = {Between-individual differences in coping with stress encompass neurophysiological, cognitive and behavioural reactions. The coping style model proposes two alternative response patterns to challenges that integrate these types of reactions. The "proactive strategy" combines a general fight-or-flight response and inflexibility in learning with a relatively low HPA (hypothalamic-pituitary-adrenal) response. The "reactive strategy" includes risk aversion, flexibility in learning and an enhanced HPA response. Although numerous studies have investigated the possible covariance of cognitive, behavioural and physiological responses, findings are still mixed. In the present study, we tested the predictions of the coping style model in an unselected population of bank voles (Myodes glareolus) (N = 70). We measured the voles' boldness, activity, speed and flexibility in learning and faecal corticosterone metabolite levels under three conditions (holding in indoor cages, in outdoor enclosures and during open field test). Individuals were moderately consistent in their HPA response across situations. Proactive voles had significantly lower corticosterone levels than reactive conspecifics in indoor and outdoor conditions. However, we could not find any co-variation between cognitive and behavioural traits and corticosterone levels in the open field test. Our results partially support the original coping style model but suggest a more complex relationship between cognitive, behavioural and endocrine responses than was initially proposed.},
  language  = {en}
}
@article{delaCruzMachensMesserschmidtetal.2019,
  author    = {de la Cruz, Jorge Gonzalez and Machens, Fabian and Messerschmidt, Katrin and Bar-Even, Arren},
  title     = {Core Catalysis of the Reductive Glycine Pathway Demonstrated in Yeast},
  series = {ACS synthetic biology},
  volume    = {8},
  journal   = {ACS synthetic biology},
  number    = {5},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {2161-5063},
  doi       = {10.1021/acssynbio.8b00464},
  pages     = {911 -- 917},
  year      = {2019},
  abstract  = {One-carbon (C1) compounds are attractive microbial feedstocks as they can be efficiently produced from widely available resources. Formate, in particular, represents a promising growth substrate, as it can be generated from electrochemical reduction of CO2 and fed to microorganisms in a soluble form. We previously identified the synthetic reductive glycine pathway as the most efficient route for aerobic growth on formate. We further demonstrated pathway activity in Escherichia coli after expression of both native and foreign genes. Here, we explore whether the reductive glycine pathway could be established in a model microorganism using only native enzymes. We used the yeast Saccharomyces cerevisiae as host and show that overexpression of only endogenous enzymes enables glycine biosynthesis from formate and CO2 in a strain that is otherwise auxotrophic for glycine. We find the pathway to be highly active in this host, where 0.125 mM formate is sufficient to support growth. Notably, the formate-dependent growth rate of the engineered S. cerevisiae strain remained roughly constant over a very wide range of formate concentrations, 1-500 mM, indicating both high affinity for formate use and high tolerance toward elevated concentration of this C1 feedstock. Our results, as well the availability of endogenous NAD-dependent formate dehydrogenase, indicate that yeast might be an especially suitable host for engineering growth on formate.},
  language  = {en}
}
@article{FrombachUnbehauenKurniasihetal.2019,
  author    = {Frombach, Janna and Unbehauen, Michael and Kurniasih, Indah N. and Schumacher, Fabian and Volz, Pierre and Hadam, Sabrina and Rancan, Fiorenza and Blume-Peytavi, Ulrike and Kleuser, Burkhard and Haag, Rainer and Alexiev, Ulrike and Vogt, Annika},
  title     = {Core-multishell nanocarriers enhance drug penetration and reach keratinocytes and antigen-presenting cells in intact human skin},
  series = {Journal of controlled release},
  volume    = {299},
  journal   = {Journal of controlled release},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0168-3659},
  doi       = {10.1016/j.jconrel.2019.02.028},
  pages     = {138 -- 148},
  year      = {2019},
  abstract  = {In reconstructed skin and diffusion cell studies, core-multishell nanocarriers (CMS-NC) showed great potential for drug delivery across the skin barrier. Herein, we investigated penetration, release of dexamethasone (DXM), in excised full-thickness human skin with special focus on hair follicles (HF). Four hours and 16 h after topical application of clinically relevant dosages of 10 mu g DXM/cm(2) skin encapsulated in CMS-NC (12 nm diameter, 5.8\% loading), presence of DXM in the tissue as assessed by fluorescence microscopy of anti-DXM-stained tissue sections as well as ELISA and HPLC-MS/MS in tissue extracts was enhanced compared to standard LAW-creme but lower compared to DXM aqueous/alcoholic solution. Such enhanced penetration compared to conventional cremes offers high potential for topical therapies, as recurrent applications of corticosteroid solutions face limitations with regard to tolerability and fast drainage. The findings encourage more detailed investigations on where and how the nanocarrier and drug dissociate within the skin and what other factors, e.g. thermodynamic activity, influence the penetration of this formulations. Microscopic studies on the spatial distribution within the skin revealed accumulation in HF and furrows accompanied by limited cellular uptake assessed by flow cytometry (up to 9\% of total epidermal cells). FLIM clearly visualized the presence of CMS-NC in the viable epidermis and dermis. When exposed in situ a fraction of up to 25\% CD1a(+) cells were found within the epidermal CMS-NC+ population compared to approximately 3\% CD1a(+)/CMS-NC+ cells after in vitro exposure in short-term cultures of epidermal cell suspensions. The latter reflects the natural percentage of Langerhans cells (LC) in epidermis suspensions and indicated that CMS-NC were not preferentially internalized by one cell type. The increased CMS-NC+ LC proportion after exposure within the tissue is in accordance with the strategic suprabasal LC-localization. More specifically we postulate that the extensive dendrite meshwork, their position around HF orifices and their capacity to modulate tight junctions facilitated a preferential uptake of CMS-NC by LC within the skin. This newly identified aspect of CMS-NC penetration underlines the potential of CMS-NC for dermatotherapy and encourages further investigations of CMS-NC for the delivery of other molecule classes for which intracellular delivery is even more crucial.},
  language  = {en}
}
@misc{HorreoBreedveldLindtkeetal.2019,
  author    = {Horreo, J. L. and Breedveld, Merel Cathelijne and Lindtke, D. and Heulin, B. and Surget-Groba, Yann and Fitze, Patrick S.},
  title     = {Correction: Genetic introgression among differentiated clades is lower among clades exhibiting different parity modes. - (Heredity. - 123, (2019) pg 264)},
  series = {Heredity},
  volume    = {123},
  journal   = {Heredity},
  number    = {2},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {0018-067X},
  doi       = {10.1038/s41437-019-0223-1},
  pages     = {285 -- 285},
  year      = {2019},
  abstract  = {The original version of this Article contained an error in the spelling of the author Y. Surget-Groba, which was incorrectly given as J. Surget-Groba. This has now been corrected in both the PDF and HTML versions of the Article.},
  language  = {en}
}
@misc{NumbergerDreierVullioudetal.2019,
  author    = {Numberger, Daniela and Dreier, Carola and Vullioud, Colin and Gabriel, Guelsah and Greenwood, Alex D. and Grossart, Hans-Peter},
  title     = {Correction: Recovery of influenza A viruses from lake water and sediments by experimental inoculation (vol 14, e0216880, 2019)},
  series = {PLoS one},
  volume    = {14},
  journal   = {PLoS one},
  number    = {6},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0218882},
  pages     = {1},
  year      = {2019},
  language  = {en}
}
@misc{HoeferDiLellaDahmanietal.2019,
  author    = {H{\"o}fer, Chris Tina and Di Lella, Santiago and Dahmani, Ismail and Jungnick, Nadine and Bordag, Natalie and Bobone, Sara and Huan, Q. and Keller, S. and Herrmann, A. and Chiantia, Salvatore},
  title     = {Corrigendum to: Structural determinants of the interaction between influenza A virus matrix protein M1 and lipid membranes (Biochimica et Biophysica Acta (BBA) - Biomembranes. - 1861, (2019), pg 1123-1134)},
  series = {Biochimica et biophysica acta : Biomembranes},
  volume    = {1861},
  journal   = {Biochimica et biophysica acta : Biomembranes},
  number    = {10},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0005-2736},
  doi       = {10.1016/j.bbamem.2019.07.002},
  pages     = {1},
  year      = {2019},
  language  = {en}
}
@article{RaatzvanVelzenGaedke2019,
  author    = {Raatz, Michael and van Velzen, Ellen and Gaedke, Ursula},
  title     = {Co-adaptation impacts the robustness of predator-prey dynamics against perturbations},
  series = {Ecology and Evolution},
  volume    = {9},
  journal   = {Ecology and Evolution},
  number    = {7},
  publisher = {John Wiley \& Sons},
  address   = {Hoboken, NJ},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.5006},
  pages     = {3823 -- 3836},
  year      = {2019},
  abstract  = {Global change threatens the maintenance of ecosystem functions that are shaped by the persistence and dynamics of populations. It has been shown that the persistence of species increases if they possess larger trait adaptability. Here, we investigate whether trait adaptability also affects the robustness of population dynamics of interacting species and thereby shapes the reliability of ecosystem functions that are driven by these dynamics. We model co-adaptation in a predator-prey system as changes to predator offense and prey defense due to evolution or phenotypic plasticity. We investigate how trait adaptation affects the robustness of population dynamics against press perturbations to environmental parameters and against pulse perturbations targeting species abundances and their trait values. Robustness of population dynamics is characterized by resilience, elasticity, and resistance. In addition to employing established measures for resilience and elasticity against pulse perturbations (extinction probability and return time), we propose the warping distance as a new measure for resistance against press perturbations, which compares the shapes and amplitudes of pre- and post-perturbation population dynamics. As expected, we find that the robustness of population dynamics depends on the speed of adaptation, but in nontrivial ways. Elasticity increases with speed of adaptation as the system returns more rapidly to the pre-perturbation state. Resilience, in turn, is enhanced by intermediate speeds of adaptation, as here trait adaptation dampens biomass oscillations. The resistance of population dynamics strongly depends on the target of the press perturbation, preventing a simple relationship with the adaptation speed. In general, we find that low robustness often coincides with high amplitudes of population dynamics. Hence, amplitudes may indicate the robustness against perturbations also in other natural systems with similar dynamics. Our findings show that besides counteracting extinctions, trait adaptation indeed strongly affects the robustness of population dynamics against press and pulse perturbations.},
  language  = {en}
}
@article{SchwarzLossowKoppetal.2019,
  author    = {Schwarz, Maria and Lossow, Kristina and Kopp, Johannes Florian and Schwerdtle, Tanja and Kipp, Anna Patricia},
  title     = {Crosstalk of Nrf2 with the Trace Elements Selenium, Iron, Zinc, and Copper},
  series = {Nutrients},
  volume    = {11},
  journal   = {Nutrients},
  number    = {9},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2072-6643},
  doi       = {10.3390/nu11092112},
  pages     = {18},
  year      = {2019},
  abstract  = {Trace elements, like Cu, Zn, Fe, or Se, are important for the proper functioning of antioxidant enzymes. However, in excessive amounts, they can also act as pro-oxidants. Accordingly, trace elements influence redox-modulated signaling pathways, such as the Nrf2 pathway. Vice versa, Nrf2 target genes belong to the group of transport and metal binding proteins. In order to investigate whether Nrf2 directly regulates the systemic trace element status, we used mice to study the effect of a constitutive, whole-body Nrf2 knockout on the systemic status of Cu, Zn, Fe, and Se. As the loss of selenoproteins under Se-deprived conditions has been described to further enhance Nrf2 activity, we additionally analyzed the combination of Nrf2 knockout with feeding diets that provide either suboptimal, adequate, or supplemented amounts of Se. Experiments revealed that the Nrf2 knockout partially affected the trace element concentrations of Cu, Zn, Fe, or Se in the intestine, liver, and/or plasma. However, aside from Fe, the other three trace elements were only marginally modulated in an Nrf2-dependent manner. Selenium deficiency mainly resulted in increased plasma Zn levels. One putative mediator could be the metal regulatory transcription factor 1, which was up-regulated with an increasing Se supply and downregulated in Se-supplemented Nrf2 knockout mice.},
  language  = {en}
}
@misc{JaricHegerMonzonetal.2019,
  author    = {Jaric, Ivan and Heger, Tina and Monzon, Federico Castro and Jeschke, Jonathan M. and Kowarik, Ingo and McConkey, Kim R. and Pysek, Petr and Sagouis, Alban and Essl, Franz},
  title     = {Crypticity in Biological Invasions},
  series = {Trends in Ecology \& Evolution},
  volume    = {34},
  journal   = {Trends in Ecology \& Evolution},
  number    = {4},
  publisher = {Elsevier},
  address   = {London},
  issn      = {0169-5347},
  doi       = {10.1016/j.tree.2018.12.008},
  pages     = {291 -- 302},
  year      = {2019},
  abstract  = {Ecological effects of alien species can be dramatic, but management and prevention of negative impacts are often hindered by crypticity of the species or their ecological functions. Ecological functions can change dramatically over time, or manifest after long periods of an innocuous presence. Such cryptic processes may lead to an underestimation of long-term impacts and constrain management effectiveness. Here, we present a conceptual framework of crypticity in biological invasions. We identify the underlying mechanisms, provide evidence of their importance, and illustrate this phenomenon with case studies. This framework has potential to improve the recognition of the full risks and impacts of invasive species.},
  language  = {en}
}
@article{JoseClementeMorenoOmranianSaezetal.2019,
  author    = {Jose Clemente-Moreno, Maria and Omranian, Nooshin and Saez, Patricia and Maria Figueroa, Carlos and Del-Saz, Nestor and Elso, Mhartyn and Poblete, Leticia and Orf, Isabel and Cuadros-Inostroza, Alvaro and Cavieres, Lohengrin and Bravo, Leon and Fernie, Alisdair R. and Ribas-Carbo, Miquel and Flexas, Jaume and Nikoloski, Zoran and Brotman, Yariv and Gago, Jorge},
  title     = {Cytochrome respiration pathway and sulphur metabolism sustain stress tolerance to low temperature in the Antarctic species Colobanthus quitensis},
  series = {New phytologist : international journal of plant science},
  volume    = {225},
  journal   = {New phytologist : international journal of plant science},
  number    = {2},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0028-646X},
  doi       = {10.1111/nph.16167},
  pages     = {754 -- 768},
  year      = {2019},
  abstract  = {Understanding the strategies employed by plant species that live in extreme environments offers the possibility to discover stress tolerance mechanisms. We studied the physiological, antioxidant and metabolic responses to three temperature conditions (4, 15, and 23 degrees C) of Colobanthus quitensis (CQ), one of the only two native vascular species in Antarctica. We also employed Dianthus chinensis (DC), to assess the effects of the treatments in a non-Antarctic species from the same family. Using fused LASSO modelling, we associated physiological and biochemical antioxidant responses with primary metabolism. This approach allowed us to highlight the metabolic pathways driving the response specific to CQ. Low temperature imposed dramatic reductions in photosynthesis (up to 88\%) but not in respiration (sustaining rates of 3.0-4.2 mu mol CO2 m(-2) s(-1)) in CQ, and no change in the physiological stress parameters was found. Its notable antioxidant capacity and mitochondrial cytochrome respiratory activity (20 and two times higher than DC, respectively), which ensure ATP production even at low temperature, was significantly associated with sulphur-containing metabolites and polyamines. Our findings potentially open new biotechnological opportunities regarding the role of antioxidant compounds and respiratory mechanisms associated with sulphur metabolism in stress tolerance strategies to low temperature.},
  language  = {en}
}
@phdthesis{Gupta2019,
  author    = {Gupta, Saurabh},
  title     = {Deciphering stress acclimation mechanisms in plants with extreme abiotic stress tolerence using genomics approaches},
  school      = {Universit{\"a}t Potsdam},
  pages     = {161},
  year      = {2019},
  language  = {en}
}
@article{KluthStadionGottmannetal.2019,
  author    = {Kluth, Oliver and Stadion, Mandy and Gottmann, Pascal and Aga-Barfknecht, Heja and J{\"a}hnert, Markus and Scherneck, Stephan and Vogel, Heike and Krus, Ulrika and Seelig, Anett and Ling, Charlotte and Gerdes, Jantje and Sch{\"u}rmann, Annette},
  title     = {Decreased expression of cilia genes in pancreatic islets as a risk factor for type 2 diabetes in mice and humans},
  series = {Cell reports},
  volume    = {26},
  journal   = {Cell reports},
  number    = {11},
  publisher = {Cell Press},
  address   = {Maryland Heights},
  issn      = {2211-1247},
  doi       = {10.1016/j.celrep.2019.02.056},
  pages     = {3027 -- 3036},
  year      = {2019},
  abstract  = {An insufficient adaptive beta-cell compensation is a hallmark of type 2 diabetes (T2D). Primary cilia function as versatile sensory antennae regulating various cellular processes, but their role on compensatory beta-cell replication has not been examined. Here, we identify a significant enrichment of downregulated, cilia-annotated genes in pancreatic islets of diabetes-prone NZO mice as compared with diabetes-resistant B6-ob/ob mice. Among 327 differentially expressed mouse cilia genes, 81 human orthologs are also affected in islets of diabetic donors. Islets of nondiabetic mice and humans show a substantial overlap of upregulated cilia genes that are linked to cell-cycle progression. The shRNA-mediated suppression of KIF3A, essential for ciliogenesis, impairs division of MINE beta cells as well as in dispersed primary mouse and human islet cells, as shown by decreased BrdU incorporation. These findings demonstrate the substantial role of cilia-gene regulation on islet function and T2D risk.},
  language  = {en}
}
@article{DengZouWangetal.2019,
  author    = {Deng, Zijun and Zou, Jie and Wang, Weiwei and Nie, Yan and Tung, Wing-Tai and Ma, Nan and Lendlein, Andreas},
  title     = {Dedifferentiation of mature adipocytes with periodic exposure to cold},
  series = {Clinical hemorheology and microcirculation : blood flow and vessels},
  volume    = {71},
  journal   = {Clinical hemorheology and microcirculation : blood flow and vessels},
  number    = {4},
  publisher = {IOS Press},
  address   = {Amsterdam},
  issn      = {1386-0291},
  doi       = {10.3233/CH-199005},
  pages     = {415 -- 424},
  year      = {2019},
  abstract  = {Lipid-containing adipocytes can dedifferentiate into fibroblast-like cells under appropriate culture conditions, which are known as dedifferentiated fat (DFAT) cells. However, the relative low dedifferentiation efficiency with the established protocols limit their widespread applications. In this study, we found that adipocyte dedifferentiation could be promoted via periodic exposure to cold (10 degrees C) in vitro. The lipid droplets in mature adipocytes were reduced by culturing the cells in periodic cooling/heating cycles (10-37 degrees C) for one week. The periodic temperature change led to the down-regulation of the adipogenic genes (FABP4, Leptin) and up-regulation of the mitochondrial uncoupling related genes (UCP1, PGC-1 alpha, and PRDM16). In addition, the enhanced expression of the cell proliferation marker Ki67 was observed in the dedifferentiated fibroblast-like cells after periodic exposure to cold, as compared to the cells cultured in 37 degrees C. Our in vitro model provides a simple and effective approach to promote lipolysis and can be used to improve the dedifferentiation efficiency of adipocytes towards multipotent DFAT cells.},
  language  = {en}
}
@article{ThomasCarvalhoHaileetal.2019,
  author    = {Thomas, Jessica E. and Carvalho, Gary R. and Haile, James and Rawlence, Nicolas J. and Martin, Michael D. and Ho, Simon Y. W. and Sigfusson, Arnor P. and Josefsson, Vigfus A. and Frederiksen, Morten and Linnebjerg, Jannie F. and Castruita, Jose A. Samaniego and Niemann, Jonas and Sinding, Mikkel-Holger S. and Sandoval-Velasco, Marcela and Soares, Andre E. R. and Lacy, Robert and Barilaro, Christina and Best, Juila and Brandis, Dirk and Cavallo, Chiara and Elorza, Mikelo and Garrett, Kimball L. and Groot, Maaike and Johansson, Friederike and Lifjeld, Jan T. and Nilson, Goran and Serjeanston, Dale and Sweet, Paul and Fuller, Errol and Hufthammer, Anne Karin and Meldgaard, Morten and Fjeldsa, Jon and Shapiro, Beth and Hofreiter, Michael and Stewart, John R. and Gilbert, M. Thomas P. and Knapp, Michael},
  title     = {Demographic reconstruction from ancient DNA supports rapid extinction of the great auk},
  series = {eLife},
  volume    = {8},
  journal   = {eLife},
  publisher = {eLife Sciences Publications},
  address   = {Cambridge},
  issn      = {2050-084X},
  doi       = {10.7554/eLife.47509},
  pages     = {35},
  year      = {2019},
  abstract  = {The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.},
  language  = {en}
}
@article{RancanVolkmannGiulbudagianetal.2019,
  author    = {Rancan, Fiorenza and Volkmann, Hildburg and Giulbudagian, Michael and Schumacher, Fabian and Stanko, Jessica Isolde and Kleuser, Burkhard and Blume-Peytavi, Ulrike and Calderon, Marcelo and Vogt, Annika},
  title     = {Dermal Delivery of the High-Molecular-Weight Drug Tacrolimus by Means of Polyglycerol-Based Nanogels},
  series = {Pharmaceutics : Molecular Diversity Preservation International},
  volume    = {11},
  journal   = {Pharmaceutics : Molecular Diversity Preservation International},
  number    = {8},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1999-4923},
  doi       = {10.3390/pharmaceutics11080394},
  pages     = {14},
  year      = {2019},
  abstract  = {Polyglycerol-based thermoresponsive nanogels (tNGs) have been shown to have excellent skin hydration properties and to be valuable delivery systems for sustained release of drugs into skin. In this study, we compared the skin penetration of tacrolimus formulated in tNGs with a commercial 0.1\% tacrolimus ointment. The penetration of the drug was investigated in ex vivo abdominal and breast skin, while different methods for skin barrier disruption were investigated to improve skin permeability or simulate inflammatory conditions with compromised skin barrier. The amount of penetrated tacrolimus was measured in skin extracts by liquid chromatography tandem-mass spectrometry (LC-MS/MS), whereas the inflammatory markers IL-6 and IL-8 were detected by enzyme-linked immunosorbent assay (ELISA). Higher amounts of tacrolimus penetrated in breast as compared to abdominal skin or in barrier-disrupted as compared to intact skin, confirming that the stratum corneum is the main barrier for tacrolimus skin penetration. The anti-proliferative effect of the penetrated drug was measured in skin tissue/Jurkat cells co-cultures. Interestingly, tNGs exhibited similar anti-proliferative effects as the 0.1\% tacrolimus ointment. We conclude that polyglycerol-based nanogels represent an interesting alternative to paraffin-based formulations for the treatment of inflammatory skin conditions.},
  language  = {en}
}
@article{BrechunZhenJaikaranetal.2019,
  author    = {Brechun, Katherine E. and Zhen, Danlin and Jaikaran, Anna and Borisenko, Vitali and Kumauchi, Masato and Hoff, Wouter D. and Arndt, Katja Maren and Woolley, Andrew G},
  title     = {Detection of Incorporation of p-Coumaric Acid into Photoactive Yellow Protein Variants in Vivo},
  series = {Biochemistry},
  volume    = {58},
  journal   = {Biochemistry},
  number    = {23},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {0006-2960},
  doi       = {10.1021/acs.biochem.9b00279},
  pages     = {2682 -- 2694},
  year      = {2019},
  abstract  = {We report the design and characterization of photoactive yellow protein (PYP)-blue fluorescent protein (mTagBFP) fusion constructs that permit the direct assay of reconstitution and function of the PYP domain. These constructs allow for in vivo testing of co-expression systems for enzymatic production of the p-coumaric acid-based PYP chromophore, via the action of tyrosine ammonia lyase and p-coumaroyl-CoA ligase (pCL or 4CL). We find that different 4CL enzymes can function to reconstitute PYP, including 4CL from Arabidopsis thaliana that can produce similar to 100\% holo-PYP protein under optimal conditions. mTagBFP fusion constructs additionally enable rapid analysis of effects of mutations on PYP photocycles. We use this mTagBFP fusion strategy to demonstrate in vivo reconstitution of several PYP-based optogenetic tools in Escherichia coli via a biosynthesized chromophore, an important step for the use of these optogenetic tools in vivo in diverse hosts.},
  language  = {en}
}
@phdthesis{Luzarowski2019,
  author    = {Luzarowski, Marcin},
  title     = {Development and application of biochemical approaches for characterisation of the protein-protein-metabolite interactome in model organisms' A. thaliana and S. cerevisiae},
  school      = {Universit{\"a}t Potsdam},
  pages     = {123},
  year      = {2019},
  language  = {en}
}
@article{ChenLiZhangetal.2019,
  author    = {Chen, Shun-Gang and Li, Ji and Zhang, Fan and Xiao, Bo and Hu, Jia-Ming and Cui, Yin-Qiu and Hofreiter, Michael and Hou, Xin-Dong and Sheng, Gui-Lian and Lai, Xu-Long and Yuan, Jun-Xia},
  title     = {Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China},
  series = {Mitochondrial DNA Part A},
  volume    = {30},
  journal   = {Mitochondrial DNA Part A},
  number    = {7},
  publisher = {Routledge, Taylor \& Francis Group},
  address   = {Abingdon},
  issn      = {2470-1394},
  doi       = {10.1080/24701394.2019.1659250},
  pages     = {786 -- 793},
  year      = {2019},
  abstract  = {Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95\% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis a slow increase in female effective population size of C. bactrianus from 5000 years ago, which to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.},
  language  = {en}
}
@article{HassanWollenberger2019,
  author    = {Hassan, Rabeay Y. A. and Wollenberger, Ulla},
  title     = {Direct determination of bacterial cell viability using carbon nanotubes modified screen-printed electrodes},
  series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis},
  volume    = {31},
  journal   = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis},
  number    = {6},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1040-0397},
  doi       = {10.1002/elan.201900047},
  pages     = {1112 -- 1117},
  year      = {2019},
  abstract  = {For the early detection of bacterial infection, there is a need for rapid, sensitive, and label-free assays. Thus, in this study, nanostrucured microbial electrochemical platform is designed to monitor the viability and cell growth of S. aureus. Using multi-walled carbon nanotube modified screen-printed electrodes (MWCNTs/SPE), the cyclic voltammetric measurements showed only one irreversible oxidation peak at 600 mV vs Ag/AgCl that accounts for the viable and metabolically active bacterial cells. The assay was optimized and the secreted metabolites, in the extracellular matrix, were directly detected. The peak current showed a positive correlation with viable cell numbers ranging from OD600 nm of 0.1 to 1.1, indicating that the activity of live cells can be quantified. Consequently, responses of viable and non-viable cells of S. aureus to the effects of antibiotic and respiratory chain inhibitors were determined. Thus, the proposed nanostructure-based bacterial sensor provides a reasonable and reliable way for real-time monitoring of live-dead cell functions, and antibacterial profiling.},
  language  = {en}
}
@phdthesis{PerlazaJimenez2019,
  author    = {Perlaza-Jimenez, Laura},
  title     = {Discerning functional associations and relationships between molecules in Arabidopsis thaliana using genome-wide correlated mutations},
  school      = {Universit{\"a}t Potsdam},
  pages     = {118},
  year      = {2019},
  language  = {en}
}
@article{KruseGerdesKathetal.2019,
  author    = {Kruse, Stefan and Gerdes, Alexander and Kath, Nadja J. and Epp, Laura Saskia and Stoof-Leichsenring, Kathleen Rosemarie and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {Dispersal distances and migration rates at the arctic treeline in Siberia - a genetic and simulation-based study},
  series = {Biogeosciences},
  volume    = {16},
  journal   = {Biogeosciences},
  number    = {6},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1726-4170},
  doi       = {10.5194/bg-16-1211-2019},
  pages     = {1211 -- 1224},
  year      = {2019},
  abstract  = {A strong temperature increase in the Arctic is expected to lead to latitudinal treeline shift. This tundra-taiga turnover would cause a positive vegetation-climate feedback due to albedo decrease. However, reliable estimates of tree migration rates are currently lacking due to the complex processes involved in forest establishment, which depend strongly on seed dispersal. We aim to fill this gap using LAVESI, an individual-based and spatially explicit Larix vegetation simulator. LAVESI was designed to simulate plots within homogeneous forests. Here, we improve the implementation of the seed dispersal function via field-based investigations. We inferred the effective seed dispersal distances of a typical open-forest stand on the southern Taymyr Peninsula (northern central Siberia) from genetic parentage analysis using eight nuclear microsatellite markers. The parentage analysis gives effective seed dispersal distances (median similar to 10 m) close to the seed parents. A comparison between simulated and observed effective seed dispersal distances reveals an overestimation of recruits close to the releasing tree and a shorter dispersal distance generally. We thus adapted our model and used the newly parameterised version to simulate south-to-north transects; a slow-moving treeline front was revealed. The colonisation of the tundra areas was assisted by occasional long-distance seed dispersal events beyond the treeline area. The treeline (similar to 1 tree ha(-1)) advanced by similar to 1.6 m yr(-1), whereas the forest line (similar to 100 trees ha(-1)) advanced by only similar to 0.6 m yr(-1). We conclude that the treeline in northern central Siberia currently lags behind the current strong warming and will continue to lag in the near future.},
  language  = {en}
}
@phdthesis{Tong2019,
  author    = {Tong, Hao},
  title     = {Dissection of genetic architecture of intermediate phenotypes and predictions in plants},
  school      = {Universit{\"a}t Potsdam},
  pages     = {127},
  year      = {2019},
  abstract  = {Determining the relationship between genotype and phenotype is the key to understand the plasticity and robustness of phenotypes in nature. While the directly observable plant phenotypes (e.g. agronomic, yield and stress resistance traits) have been well-investigated, there is still a lack in our knowledge about the genetic basis of intermediate phenotypes, such as metabolic phenotypes. Dissecting the links between genotype and phenotype depends on suitable statistical models. The state-of-the-art models are developed for directly observable phenotypes, regardless the characteristics of intermediate phenotypes. This thesis aims to fill the gaps in understanding genetic architecture of intermediate phenotypes, and how they tie to composite traits, namely plant growth. The metabolite levels and reaction fluxes, as two aspects of metabolic phenotypes, are shaped by the interrelated chemical reactions formed in genome-scale metabolic network. Here, I attempt to answer the question: Can the knowledge of underlying genome-scale metabolic network improve the model performance for prediction of metabolic phenotypes and associated plant growth? To this end, two projects are investigated in this thesis. Firstly, we propose an approach that couples genomic selection with genome-scale metabolic network and metabolic profiles in Arabidopsis thaliana to predict growth. This project is the first integration of genomic data with fluxes predicted based on constraint-based modeling framework and data on biomass composition. We demonstrate that our approach leads to a considerable increase of prediction accuracy in comparison to the state-of-the-art methods in both within and across environment predictions. Therefore, our work paves the way for combining knowledge on metabolic mechanisms in the statistical approach underlying genomic selection to increase the efficiency of future plant breeding approaches. Secondly, we investigate how reliable is genomic selection for metabolite levels, and which single nucleotide polymorphisms (SNPs), obtained from different neighborhoods of a given metabolic network, contribute most to the accuracy of prediction. The results show that the local structure of first and second neighborhoods are not sufficient for predicting the genetic basis of metabolite levels in Zea mays. Furthermore, we find that the enzymatic SNPs can capture most the genetic variance and the contribution of non-enzymatic SNPs is in fact small. To comprehensively understand the genetic architecture of metabolic phenotypes, I extend my study to a local Arabidopsis thaliana population and their hybrids. We analyze the genetic architecture in primary and secondary metabolism as well as in growth. In comparison to primary metabolites, compounds from secondary metabolism were more variable and show more non-additive inheritance patterns which could be attributed to epistasis. Therefore, our study demonstrates that heterozygosity in local Arabidopsis thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism. The studies in this thesis improve the knowledge of genetic architecture of metabolic phenotypes in both inbreed and hybrid population. The approaches I proposed to integrate genome-scale metabolic network with genomic data provide the opportunity to obtain mechanistic insights about the determinants of agronomically important polygenic traits.},
  language  = {en}
}
@article{TangSullivanHongetal.2019,
  author    = {Tang, Alan T. and Sullivan, Katie Rose and Hong, Courtney C. and Goddard, Lauren M. and Mahadevan, Aparna and Ren, Aileen and Pardo, Heidy and Peiper, Amy and Griffin, Erin and Tanes, Ceylan and Mattei, Lisa M. and Yang, Jisheng and Li, Li and Mericko-Ishizuka, Patricia and Shen, Le and Hobson, Nicholas and Girard, Romuald and Lightle, Rhonda and Moore, Thomas and Shenkar, Robert and Polster, Sean P. and Roedel, Claudia Jasmin and Li, Ning and Zhu, Qin and Whitehead, Kevin J. and Zheng, Xiangjian and Akers, Amy and Morrison, Leslie and Kim, Helen and Bittinger, Kyle and Lengner, Christopher J. and Schwaninger, Markus and Velcich, Anna and Augenlicht, Leonard and Abdelilah-Seyfried, Salim and Min, Wang and Marchuk, Douglas A. and Awad, Issam A. and Kahn, Mark L.},
  title     = {Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation},
  series = {Science Translational Medicine},
  volume    = {11},
  journal   = {Science Translational Medicine},
  number    = {520},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {1946-6234},
  doi       = {10.1126/scitranslmed.aaw3521},
  pages     = {14},
  year      = {2019},
  abstract  = {Cerebral cavernous malformation (CCM) is a genetic, cerebrovascular disease. Familial CCM is caused by genetic mutations in KRIT1, CCM2, or PDCD10. Disease onset is earlier and more severe in individuals with PDCD10 mutations. Recent studies have shown that lesions arise from excess mitogen-activated protein kinase kinase kinase 3 (MEKK3) signaling downstream of Toll-like receptor 4 (TLR4) stimulation by lipopolysaccharide derived from the gut microbiome. These findings suggest a gut-brain CCM disease axis but fail to define it or explain the poor prognosis of patients with PDCD10 mutations. Here, we demonstrate that the gut barrier is a primary determinant of CCM disease course, independent of microbiome configuration, that explains the increased severity of CCM disease associated with PDCD10 deficiency. Chemical disruption of the gut barrier with dextran sulfate sodium augments CCM formation in a mouse model, as does genetic loss of Pdcd10, but not Krit1, in gut epithelial cells. Loss of gut epithelial Pdcd10 results in disruption of the colonic mucosal barrier. Accordingly, loss of Mucin-2 or exposure to dietary emulsifiers that reduce the mucus barrier increases CCM burden analogous to loss of Pdcd10 in the gut epithelium. Last, we show that treatment with dexamethasone potently inhibits CCM formation in mice because of the combined effect of action at both brain endothelial cells and gut epithelial cells. These studies define a gut-brain disease axis in an experimental model of CCM in which a single gene is required for two critical components: gut epithelial function and brain endothelial signaling.},
  language  = {en}
}
@article{RadchukKramerSchadtFickeletal.2019,
  author    = {Radchuk, Viktoriia and Kramer-Schadt, Stephanie and Fickel, J{\"o}rns and Wilting, Andreas},
  title     = {Distributions of mammals in Southeast Asia: The role of the legacy of climate and species body mass},
  series = {Journal of biogeography},
  volume    = {46},
  journal   = {Journal of biogeography},
  number    = {10},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0305-0270},
  doi       = {10.1111/jbi.13675},
  pages     = {2350 -- 2362},
  year      = {2019},
  abstract  = {Aim Current species distributions are shaped by present and past biotic and abiotic factors. Here, we assessed whether abiotic factors (habitat availability) in combination with past connectivity and a biotic factor (body mass) can explain the unique distribution pattern of Southeast Asian mammals, which are separated by the enigmatic biogeographic transition zone, the Isthmus of Kra (IoK), for which no strong geophysical barrier exists. Location Southeast Asia. Taxon Mammals. Methods We projected habitat suitability for 125 mammal species using climate data for the present period and for two historic periods: mid-Holocene (6 ka) and last glacial maximum (LGM 21 ka). Next, we employed a phylogenetic linear model to assess how present species distributions were affected by the suitability of areas in these different periods, habitat connectivity during LGM and species body mass. Results Our results show that cooler climate during LGM provided suitable habitat south of IoK for species presently distributed north of IoK (in mainland Indochina). However, the potentially suitable habitat for these Indochinese species did not stretch very far southwards onto the exposed Sunda Shelf. Instead, we found that the emerged landmasses connecting Borneo and Sumatra provided suitable habitat for forest dependent Sundaic species. We show that for species whose current distribution ranges are mainly located in Indochina, the area of the distribution range that is located south of IoK is explained by the suitability of habitat in the past and present in combination with the species body mass. Main conclusions We demonstrate that a strong geophysical barrier may not be necessary for maintaining a biogeographic transition zone for mammals, but that instead a combination of abiotic and biotic factors may suffice.},
  language  = {en}
}
@article{MediniFarhatAlRawietal.2019,
  author    = {Medini, Wided and Farhat, Nejia and Al-Rawi, Shadha and Mahto, Harendra and Qasim, Hadeel and Ben-Halima, Emna and Bessrour, Mouna and Chibani, Farhat and Abdelly, Chedly and Fettke, J{\"o}rg and Rabhi, Mokded},
  title     = {Do carbohydrate metabolism and partitioning contribute to the higher salt tolerance of Hordeum marinum compared to Hordeum vulgare?},
  series = {Acta Physiologiae Plantarum},
  volume    = {41},
  journal   = {Acta Physiologiae Plantarum},
  number    = {12},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {0137-5881},
  doi       = {10.1007/s11738-019-2983-x},
  pages     = {12},
  year      = {2019},
  abstract  = {The aim of the present work was to check whether carbohydrate metabolism and partitioning contribute to the higher salt tolerance of the facultative halophyte Hordeum marinum compared to the glycophyte Hordeum vulgare. Seedlings with the same size from the two species were hydroponically grown at 0 (control), 150, and 300 mM NaCl for 3 weeks. H. marinum maintained higher relative growth rate, which was concomitant with a higher aptitude to maintain better shoot tissue hydration and membrane integrity under saline conditions compared to H. vulgare. Gas exchanges were reduced in the two species under saline conditions, but an increase in their water use efficiency was recorded. H. marinum exhibited an increase in leaf soluble sugar concentrations under saline conditions together with an enhancement in the transglucosidase DPE2 (EC 2.4.1.25) activity at 300 mM NaCl. However, H. vulgare showed a high increase in starch phosphorylase (EC 2.4.1.1) activity under saline conditions together with a decrease in leaf glucose and starch concentrations at 300 mM NaCl. In roots, both species accumulated glucose and fructose at 150 mM NaCl, but H. marinum exhibited a marked decrease in soluble sugar concentrations and an increase in starch concentration at 300 mM NaCl. Our data constitute an initiation to the involvement of carbohydrate metabolism and partitioning in salt responses of barley species and further work is necessary to elucidate how their flexibility confers higher tolerance to H. marinum compared to H. vulgare.},
  language  = {en}
}
@article{SchoepkeHeinzePaetzigetal.2019,
  author    = {Sch{\"o}pke, Benito and Heinze, Johannes and P{\"a}tzig, Marlene and Heinken, Thilo},
  title     = {Do dispersal traits of wetland plant species explain tolerance against isolation effects in naturally fragmented habitats?},
  series = {Plant ecology : an international journal},
  volume    = {220},
  journal   = {Plant ecology : an international journal},
  number    = {9},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1385-0237},
  doi       = {10.1007/s11258-019-00955-8},
  pages     = {801 -- 815},
  year      = {2019},
  abstract  = {The effects of habitat fragmentation and isolation on plant species richness have been verified for a wide range of anthropogenically fragmented habitats, but there is currently little information about their effects in naturally small and isolated habitats. We tested whether habitat area, heterogeneity, and isolation affect the richness of wetland vascular plant species in kettle holes, i.e., small glacially created wetlands, in an agricultural landscape of 1 km(2) in NE Germany. We compared fragmentation effects with those of forest fragments in the same landscape window. Since wetland and forest species might differ in their tolerance to isolation, and because isolation effects on plant species may be trait dependent, we asked which key life history traits might foster differences in isolation tolerance between wetland and forest plants. We recorded the flora and vegetation types in 83 isolated sites that contained 81 kettle holes and 25 forest fragments. Overall, the number of wetland species increased with increasing area and heterogeneity, i.e., the number of vegetation types, while area was not a surrogate for heterogeneity in these naturally fragmented systems. Isolation did not influence the number of wetland species but decreased the number of forest species. We also found that seeds of wetland species were on average lighter, more persistent and better adapted to epizoochory, e.g., by waterfowl, than seeds of forest species. Therefore, we suggest that wetland species are more tolerant to isolation than forest species due to their higher dispersal potential in space and time, which may counterbalance the negative effects of isolation.},
  language  = {en}
}
@article{RossbergGaedkeKratina2019,
  author    = {Rossberg, Axel G. and Gaedke, Ursula and Kratina, Pavel},
  title     = {Dome patterns in pelagic size spectra reveal strong trophic cascades},
  series = {Nature Communications},
  volume    = {10},
  journal   = {Nature Communications},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-019-12289-0},
  pages     = {11},
  year      = {2019},
  abstract  = {In ecological communities, especially the pelagic zones of aquatic ecosystems, certain bodysize ranges are often over-represented compared to others. Community size spectra, the distributions of community biomass over the logarithmic body-mass axis, tend to exhibit regularly spaced local maxima, called "domes", separated by steep troughs. Contrasting established theory, we explain these dome patterns as manifestations of top-down trophic cascades along aquatic food chains. Compiling high quality size-spectrum data and comparing these with a size-spectrum model introduced in this study, we test this theory and develop a detailed picture of the mechanisms by which bottom-up and top-down effects interact to generate dome patterns. Results imply that strong top-down trophic cascades are common in freshwater communities, much more than hitherto demonstrated, and may arise in nutrient rich marine systems as well. Transferring insights from the general theory of nonlinear pattern formation to domes patterns, we provide new interpretations of past lake-manipulation experiments.},
  language  = {en}
}
@article{EsslDawsonKreftetal.2019,
  author    = {Essl, Franz and Dawson, Wayne and Kreft, Holger and Pergl, Jan and Pysek, Petr and van Kleunen, Mark and Weigelt, Patrick and Mang, Thomas and Dullinger, Stefan and Lenzner, Bernd and Moser, Dietmar and Maurel, Noelie and Seebens, Hanno and Stein, Anke and Weber, Ewald and Chatelain, Cyrille and Inderjit, and Genovesi, Piero and Kartesz, John and Morozova, Olga and Nishino, Misako and Nowak, Pauline M. and Pagad, Shyama and Shu, Wen-sheng and Winter, Marten},
  title     = {Drivers of the relative richness of naturalized and invasive plant species on Earth},
  series = {AoB PLANTS},
  volume    = {11},
  journal   = {AoB PLANTS},
  number    = {5},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {2041-2851},
  doi       = {10.1093/aobpla/plz051},
  pages     = {13},
  year      = {2019},
  abstract  = {Biological invasions are a defining feature of the Anthropocene, but the factors that determine the spatially uneven distribution of alien plant species are still poorly understood. Here, we present the first global analysis of the effects of biogeographic factors, the physical environment and socio-economy on the richness of naturalized and invasive alien plants. We used generalized linear mixed-effects models and variation partitioning to disentangle the relative importance of individual factors, and, more broadly, of biogeography, physical environment and socio-economy. As measures of the magnitude of permanent anthropogenic additions to the regional species pool and of species with negative environmental impacts, we calculated the relative richness of naturalized (= RRN) and invasive (= RRI) alien plant species numbers adjusted for the number of native species in 838 terrestrial regions. Socio-economic factors (per-capita gross domestic product (GDP), population density, proportion of agricultural land) were more important in explaining RRI (similar to 50 \% of the explained variation) than RRN (similar to 40 \%). Warm-temperate and (sub)tropical regions have higher RRN than tropical or cooler regions. We found that socio-economic pressures are more relevant for invasive than for naturalized species richness. The expectation that the southern hemisphere is more invaded than the northern hemisphere was confirmed only for RRN on islands, but not for mainland regions nor for RRI. On average, islands have similar to 6-fold RRN, and >3-fold RRI compared to mainland regions. Eighty-two islands (=26 \% of all islands) harbour more naturalized alien than native plants. Our findings challenge the widely held expectation that socio-economic pressures are more relevant for plant naturalization than for invasive plants. To meet international biodiversity targets and halt the detrimental consequences of plant invasions, it is essential to disrupt the connection between socio-economic development and plant invasions by improving pathway management, early detection and rapid response.},
  language  = {en}
}
@article{YanChenSchumacheretal.2019,
  author    = {Yan, Wenhao and Chen, Dijun and Schumacher, Julia and Durantini, Diego and Engelhorn, Julia and Chen, Ming and Carles, Cristel C. and Kaufmann, Kerstin},
  title     = {Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis},
  series = {Nature Communications},
  volume    = {10},
  journal   = {Nature Communications},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-019-09513-2},
  pages     = {16},
  year      = {2019},
  abstract  = {Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase. hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers.},
  language  = {en}
}
@article{SchwarzerJoshi2019,
  author    = {Schwarzer, Christian and Joshi, Jasmin Radha},
  title     = {Ecotypic differentiation, hybridization and clonality facilitate the persistence of a cold-adapted sedge in European bogs},
  series = {Biological journal of the Linnean Society : a journal of evolution},
  volume    = {128},
  journal   = {Biological journal of the Linnean Society : a journal of evolution},
  number    = {4},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0024-4066},
  doi       = {10.1093/biolinnean/blz141},
  pages     = {909 -- 925},
  year      = {2019},
  abstract  = {Recent research has shown that many cold-adapted species survived the last glacial maximum (LGM) in northern refugia. Whether this evolutionary history has had consequences for their genetic diversity and adaptive potential remains unknown. We sampled 14 populations of Carex limosa, a sedge specialized to bog ecosystems, along a latitudinal gradient from its Scandinavian core to the southern lowland range-margin in Germany. Using microsatellite and experimental common-garden data, we evaluated the impacts of global climate change along this gradient and assessed the conservation status of the southern marginal populations. Microsatellite data revealed two highly distinct genetic groups and hybrid individuals. In our common-garden experiment, the two groups showed divergent responses to increased nitrogen/phosphorus (N/P) availability, suggesting ecotypic differentiation. Each group formed genetically uniform populations at both northern and southern sampling areas. Mixed populations occurred throughout our sampling area, an area that was entirely glaciated during the LGM. The fragmented distribution implies allopatric divergence at geographically separated refugia that putatively differed in N/P availability. Molecular data and an observed low hybrid fecundity indicate the importance of clonal reproduction for hybrid populations. At the southern range-margin, however, all populations showed effects of clonality, lowered fecundity and low competitiveness, suggesting abiotic and biotic constraints to population persistence.},
  language  = {en}
}
@article{KielarXinXuetal.2019,
  author    = {Kielar, Charlotte and Xin, Yang and Xu, Xiaodan and Zhu, Siqi and Gorin, Nelli and Grundmeier, Guido and M{\"o}ser, Christin and Smith, David M. and Keller, Adrian},
  title     = {Effect of staple age on DNA origami nanostructure assembly and stability},
  series = {Molecules},
  volume    = {24},
  journal   = {Molecules},
  number    = {14},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1420-3049},
  doi       = {10.3390/molecules24142577},
  pages     = {12},
  year      = {2019},
  abstract  = {DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at -20 degrees C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.},
  language  = {en}
}
@article{KolmakovaGladyshevFonvielleetal.2019,
  author    = {Kolmakova, Olesya V. and Gladyshev, Michail I. and Fonvielle, Jeremy Andre and Ganzert, Lars and Hornick, Thomas and Grossart, Hans-Peter},
  title     = {Effects of zooplankton carcasses degradation on freshwater bacterial community composition and implications for carbon cycling},
  series = {Environmental microbiology},
  volume    = {21},
  journal   = {Environmental microbiology},
  number    = {1},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1462-2912},
  doi       = {10.1111/1462-2920.14418},
  pages     = {34 -- 49},
  year      = {2019},
  abstract  = {Non-predatory mortality of zooplankton provides an abundant, yet, little studied source of high quality labile organic matter (LOM) in aquatic ecosystems. Using laboratory microcosms, we followed the decomposition of organic carbon of fresh C-13-labelled Daphnia carcasses by natural bacterioplankton. The experimental setup comprised blank microcosms, that is, artificial lake water without any organic matter additions (B), and microcosms either amended with natural humic matter (H), fresh Daphnia carcasses (D) or both, that is, humic matter and Daphnia carcasses (HD). Most of the carcass carbon was consumed and respired by the bacterial community within 15 days of incubation. A shift in the bacterial community composition shaped by labile carcass carbon and by humic matter was observed. Nevertheless, we did not observe a quantitative change in humic matter degradation by heterotrophic bacteria in the presence of LOM derived from carcasses. However, carcasses were the main factor driving the bacterial community composition suggesting that the presence of large quantities of dead zooplankton might affect the carbon cycling in aquatic ecosystems. Our results imply that organic matter derived from zooplankton carcasses is efficiently remineralized by a highly specific bacterial community, but does not interfere with the bacterial turnover of more refractory humic matter.},
  language  = {en}
}
@article{OzcelikayKurbanogluZhangetal.2019,
  author    = {Ozcelikay, Goksu and Kurbanoglu, Sevinc and Zhang, Xiaorong and S{\"o}z, {\c{C}}ağla Kosak and Wollenberger, Ulla and Ozkan, Sibel A. and Yarman, Aysu and Scheller, Frieder W.},
  title     = {Electrochemical MIP Sensor for Butyrylcholinesterase},
  series = {Polymers},
  volume    = {11},
  journal   = {Polymers},
  number    = {12},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4360},
  doi       = {10.3390/polym11121970},
  pages     = {11},
  year      = {2019},
  abstract  = {Molecularly imprinted polymers (MIPs) mimic the binding sites of antibodies by substituting the amino acid-scaffold of proteins by synthetic polymers. In this work, the first MIP for the recognition of the diagnostically relevant enzyme butyrylcholinesterase (BuChE) is presented. The MIP was prepared using electropolymerization of the functional monomer o-phenylenediamine and was deposited as a thin film on a glassy carbon electrode by oxidative potentiodynamic polymerization. Rebinding and removal of the template were detected by cyclic voltammetry using ferricyanide as a redox marker. Furthermore, the enzymatic activity of BuChE rebound to the MIP was measured via the anodic oxidation of thiocholine, the reaction product of butyrylthiocholine. The response was linear between 50 pM and 2 nM concentrations of BuChE with a detection limit of 14.7 pM. In addition to the high sensitivity for BuChE, the sensor responded towards pseudo-irreversible inhibitors in the lower mM range.},
  language  = {en}
}
@phdthesis{Zhang2019,
  author    = {Zhang, Xiaorong},
  title     = {Electrosynthesis and characterization of molecularly imprinted polymers for peptides and proteins},
  school      = {Universit{\"a}t Potsdam},
  pages     = {116},
  year      = {2019},
  language  = {en}
}
@article{RomeroMujalliJeltschTiedemann2019,
  author    = {Romero-Mujalli, Daniel and Jeltsch, Florian and Tiedemann, Ralph},
  title     = {Elevated mutation rates are unlikely to evolve in sexual species, not even under rapid environmental change},
  series = {BMC Evolutionary Biology},
  volume    = {19},
  journal   = {BMC Evolutionary Biology},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2148},
  doi       = {10.1186/s12862-019-1494-0},
  pages     = {9},
  year      = {2019},
  abstract  = {Background Organisms are expected to respond to changing environmental conditions through local adaptation, range shift or local extinction. The process of local adaptation can occur by genetic changes or phenotypic plasticity, and becomes especially relevant when dispersal abilities or possibilities are somehow constrained. For genetic changes to occur, mutations are the ultimate source of variation and the mutation rate in terms of a mutator locus can be subject to evolutionary change. Recent findings suggest that the evolution of the mutation rate in a sexual species can advance invasion speed and promote adaptation to novel environmental conditions. Following this idea, this work uses an individual-based model approach to investigate if the mutation rate can also evolve in a sexual species experiencing different conditions of directional climate change, under different scenarios of colored stochastic environmental noise, probability of recombination and of beneficial mutations. The color of the noise mimicked investigating the evolutionary dynamics of the mutation rate in different habitats. Results The results suggest that the mutation rate in a sexual species experiencing directional climate change scenarios can evolve and reach relatively high values mainly under conditions of complete linkage of the mutator locus and the adaptation locus. In contrast, when they are unlinked, the mutation rate can slightly increase only under scenarios where at least 50\% of arising mutations are beneficial and the rate of environmental change is relatively fast. This result is robust under different scenarios of stochastic environmental noise, which supports the observation of no systematic variation in the mutation rate among organisms experiencing different habitats. Conclusions Given that 50\% beneficial mutations may be an unrealistic assumption, and that recombination is ubiquitous in sexual species, the evolution of an elevated mutation rate in a sexual species experiencing directional climate change might be rather unlikely. Furthermore, when the percentage of beneficial mutations and the population size are small, sexual species (especially multicellular ones) producing few offspring may be expected to react to changing environments not by adaptive genetic change, but mainly through plasticity. Without the ability for a plastic response, such species may become - at least locally - extinct.},
  language  = {en}
}
@article{SignorePaijmansHofreiteretal.2019,
  author    = {Signore, Anthony V. and Paijmans, Johanna L. A. and Hofreiter, Michael and Fago, Angela and Weber, Roy E. and Springer, Mark S. and Campbell, Kevin L.},
  title     = {Emergence of a chimeric globin pseudogene and increased Hemoglobin Oxygen Affinity Underlie the evolution of aquatic specializations in Sirenia},
  series = {Molecular biology and evolution},
  volume    = {36},
  journal   = {Molecular biology and evolution},
  number    = {6},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0737-4038},
  doi       = {10.1093/molbev/msz044},
  pages     = {1134 -- 1147},
  year      = {2019},
  abstract  = {As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller's sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb-O2 affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb-O2 affinity in (sub)Arctic Steller's sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.},
  language  = {en}
}
@article{LopezdeGuerenuBastianWessigetal.2019,
  author    = {L{\´o}pez de Guere{\~n}u, Anna and Bastian, Philipp and Wessig, Pablo and John, Leonard and Kumke, Michael Uwe},
  title     = {Energy Transfer between Tm-Doped Upconverting Nanoparticles and a Small Organic Dye with Large Stokes Shift},
  series = {Biosensors : open access journal},
  volume    = {9},
  journal   = {Biosensors : open access journal},
  number    = {1},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2079-6374},
  doi       = {10.3390/bios9010009},
  pages     = {17},
  year      = {2019},
  abstract  = {Lanthanide-doped upconverting nanoparticles (UCNP) are being extensively studied for bioapplications due to their unique photoluminescence properties and low toxicity. Interest in RET applications involving UCNP is also increasing, but due to factors such as large sizes, ion emission distributions within the particles, and complicated energy transfer processes within the UCNP, there are still many questions to be answered. In this study, four types of core and core-shell NaYF4-based UCNP co-doped with Yb3+ and Tm3+ as sensitizer and activator, respectively, were investigated as donors for the Methyl 5-(8-decanoylbenzo[1,2-d:4,5-d ']bis([1,3]dioxole)-4-yl)-5-oxopentanoate (DBD-6) dye. The possibility of resonance energy transfer (RET) between UCNP and the DBD-6 attached to their surface was demonstrated based on the comparison of luminescence intensities, band ratios, and decay kinetics. The architecture of UCNP influenced both the luminescence properties and the energy transfer to the dye: UCNP with an inert shell were the brightest, but their RET efficiency was the lowest (17\%). Nanoparticles with Tm3+ only in the shell have revealed the highest RET efficiencies (up to 51\%) despite the compromised luminescence due to surface quenching.},
  language  = {en}
}
@phdthesis{Yishai2019,
  author    = {Yishai, Oren},
  title     = {Engineering the reductive glycine pathway in Escherichia coli},
  school      = {Universit{\"a}t Potsdam},
  pages     = {86},
  year      = {2019},
  language  = {en}
}
@article{LozadaGobilardStangPirhoferWalzletal.2019,
  author    = {Lozada Gobilard, Sissi Donna and Stang, Susanne and Pirhofer-Walzl, Karin and Kalettka, Thomas and Heinken, Thilo and Schr{\"o}der, Boris and Eccard, Jana and Jasmin Radha, Jasmin},
  title     = {Environmental filtering predicts plant-community trait distribution and diversity},
  series = {Ecology and Evolution},
  journal   = {Ecology and Evolution},
  publisher = {John Wiley \& Sons, Inc.},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.4883},
  pages     = {13},
  year      = {2019},
  abstract  = {Meta-communities of habitat islands may be essential to maintain biodiversity in anthropogenic landscapes allowing rescue effects in local habitat patches. To understand the species-assembly mechanisms and dynamics of such ecosystems, it is important to test how local plant-community diversity and composition is affected by spatial isolation and hence by dispersal limitation and local environmental conditions acting as filters for local species sorting. We used a system of 46 small wetlands (kettle holes)—natural small-scale freshwater habitats rarely considered in nature conservation policies—embedded in an intensively managed agricultural matrix in northern Germany. We compared two types of kettle holes with distinct topographies (flatsloped, ephemeral, frequently plowed kettle holes vs. steep-sloped, more permanent ones) and determined 254 vascular plant species within these ecosystems, as well as plant functional traits and nearest neighbor distances to other kettle holes. Differences in alpha and beta diversity between steep permanent compared with ephemeral flat kettle holes were mainly explained by species sorting and niche processes and mass effect processes in ephemeral flat kettle holes. The plant-community composition as well as the community trait distribution in terms of life span, breeding system, dispersal ability, and longevity of seed banks significantly differed between the two habitat types. Flat ephemeral kettle holes held a higher percentage of non-perennial plants with a more persistent seed bank, less obligate outbreeders and more species with seed dispersal abilities via animal vectors compared with steep-sloped, more permanent kettle holes that had a higher percentage of wind-dispersed species. In the flat kettle holes, plant-species richness was negatively correlated with the degree of isolation, whereas no such pattern was found for the permanent kettle holes. Synthesis: Environment acts as filter shaping plant diversity (alpha and beta) and plant-community trait distribution between steep permanent compared with ephemeral flat kettle holes supporting species sorting and niche mechanisms as expected, but we identified a mass effect in ephemeral kettle holes only. Flat ephemeral kettle holes can be regarded as meta-ecosystems that strongly depend on seed dispersal and recruitment from a seed bank, whereas neighboring permanent kettle holes have a more stable local species diversity.},
  language  = {en}
}
@article{SchlaegelSignerHerdeetal.2019,
  author    = {Schl{\"a}gel, Ulrike E. and Signer, Johannes and Herde, Antje and Eden, Sophie and Jeltsch, Florian and Eccard, Jana and Dammhahn, Melanie},
  title     = {Estimating interactions between individuals from concurrent animal movements},
  series = {Methods in ecology and evolution : an official journal of the British Ecological Society},
  volume    = {10},
  journal   = {Methods in ecology and evolution : an official journal of the British Ecological Society},
  number    = {8},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2041-210X},
  doi       = {10.1111/2041-210X.13235},
  pages     = {1234 -- 1245},
  year      = {2019},
  abstract  = {Animal movements arise from complex interactions of individuals with their environment, including both conspecific and heterospecific individuals. Animals may be attracted to each other for mating, social foraging, or information gain, or may keep at a distance from others to avoid aggressive encounters related to, e.g., interference competition, territoriality, or predation. With modern tracking technology, more datasets are emerging that allow to investigate fine-scale interactions between free-ranging individuals from movement data, however, few methods exist to disentangle fine-scale behavioural responses of interacting individuals when these are highly individual-specific. In a framework of step-selection functions, we related movements decisions of individuals to dynamic occurrence distributions of other individuals obtained through kriging of their movement paths. Using simulated data, we tested the method's ability to identify various combinations of attraction, avoidance, and neutrality between individuals, including asymmetric (i.e. non-mutual) behaviours. Additionally, we analysed radio-telemetry data from concurrently tracked small rodents (bank vole, Myodes glareolus) to test whether our method could detect biologically plausible behaviours. We found that our method was able to successfully detect and distinguish between fine-scale interactions (attraction, avoidance, neutrality), even when these were asymmetric between individuals. The method worked best when confounding factors were taken into account in the step-selection function. However, even when failing to do so (e.g. due to missing information), interactions could be reasonably identified. In bank voles, responses depended strongly on the sexes of the involved individuals and matched expectations. Our approach can be combined with conventional uses of step-selection functions to tease apart the various drivers of movement, e.g. the influence of the physical and the social environment. In addition, the method is particularly useful in studying interactions when responses are highly individual-specific, i.e. vary between and towards different individuals, making our method suitable for both single-species and multi-species analyses (e.g. in the context of predation or competition).},
  language  = {en}
}
@article{RosenbaumRaatzWeithoffetal.2019,
  author    = {Rosenbaum, Benjamin and Raatz, Michael and Weithoff, Guntram and Fussmann, Gregor F. and Gaedke, Ursula},
  title     = {Estimating parameters from multiple time series of population dynamics using bayesian inference},
  series = {Frontiers in ecology and evolution},
  volume    = {6},
  journal   = {Frontiers in ecology and evolution},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {2296-701X},
  doi       = {10.3389/fevo.2018.00234},
  pages     = {14},
  year      = {2019},
  abstract  = {Empirical time series of interacting entities, e.g., species abundances, are highly useful to study ecological mechanisms. Mathematical models are valuable tools to further elucidate those mechanisms and underlying processes. However, obtaining an agreement between model predictions and experimental observations remains a demanding task. As models always abstract from reality one parameter often summarizes several properties. Parameter measurements are performed in additional experiments independent of the ones delivering the time series. Transferring these parameter values to different settings may result in incorrect parametrizations. On top of that, the properties of organisms and thus the respective parameter values may vary considerably. These issues limit the use of a priori model parametrizations. In this study, we present a method suited for a direct estimation of model parameters and their variability from experimental time series data. We combine numerical simulations of a continuous-time dynamical population model with Bayesian inference, using a hierarchical framework that allows for variability of individual parameters. The method is applied to a comprehensive set of time series from a laboratory predator-prey system that features both steady states and cyclic population dynamics. Our model predictions are able to reproduce both steady states and cyclic dynamics of the data. Additionally to the direct estimates of the parameter values, the Bayesian approach also provides their uncertainties. We found that fitting cyclic population dynamics, which contain more information on the process rates than steady states, yields more precise parameter estimates. We detected significant variability among parameters of different time series and identified the variation in the maximum growth rate of the prey as a source for the transition from steady states to cyclic dynamics. By lending more flexibility to the model, our approach facilitates parametrizations and shows more easily which patterns in time series can be explained also by simple models. Applying Bayesian inference and dynamical population models in conjunction may help to quantify the profound variability in organismal properties in nature.},
  language  = {en}
}
@article{LundgreenJaspersTravingetal.2019,
  author    = {Lundgreen, Regitze B. C. and Jaspers, Cornelia and Traving, Sachia J. and Ayala, Daniel J. and Lombard, Fabien and Grossart, Hans-Peter and Nielsen, Torkel G. and Munk, Peter and Riemann, Lasse},
  title     = {Eukaryotic and cyanobacterial communities associated with marine snow particles in the oligotrophic Sargasso Sea},
  series = {Scientific reports},
  volume    = {9},
  journal   = {Scientific reports},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-019-45146-7},
  pages     = {12},
  year      = {2019},
  abstract  = {Marine snow aggregates represent heterogeneous agglomerates of dead and living organic matter. Composition is decisive for their sinking rates, and thereby for carbon flux to the deep sea. For oligotrophic oceans, information on aggregate composition is particularly sparse. To address this, the taxonomic composition of aggregates collected from the subtropical and oligotrophic Sargasso Sea (Atlantic Ocean) was characterized by 16S and 18S rRNA gene sequencing. Taxonomy assignment was aided by a collection of the contemporary plankton community consisting of 75 morphologically and genetically identified plankton specimens. The diverse rRNA gene reads of marine snow aggregates, not considering Trichodesmium puffs, were dominated by copepods (52\%), cnidarians (21\%), radiolarians (11\%), and alveolates (8\%), with sporadic contributions by cyanobacteria, suggesting a different aggregate composition than in eutrophic regions. Composition linked significantly with sampling location but not to any measured environmental parameters or plankton biomass composition. Nevertheless, indicator and network analyses identified key roles of a few rare taxa. This points to complex regulation of aggregate composition, conceivably affected by the environment and plankton characteristics. The extent to which this has implications for particle densities, and consequently for sinking rates and carbon sequestration in oligotrophic waters, needs further interrogation.},
  language  = {en}
}
@article{VonRaabStraubeRausBazosetal.2019,
  author    = {Von Raab-Straube, Eckhard and Raus, Thomas and Bazos, Ioannis and Cornec, J. P. and De Belair, Gerard. and Dimitrakopoulos, P. G. and El Mokni, Ridha and Fateryga, Alexander V. and Fateryga, Valentina V. and Fridlender, Alain and Gil, Jaime and Grigorenko, V. N. and Hand, Ralf and Kovalchuk, A. and Mastrogianni, A. and Otto, R. and R{\"a}tzel, Stefan and Raus, Th. and Ristow, Michael and Salas Pascual, M. and Strid, Arne and Svirin, S. A. and Tsiripidis, Ioannis. and Uhlich, Holger and Vela, Errol and Verloove, Filip and Vidakis, K. and Yena, Andriy Vasylyovych and Yevseyenkov, P. E. and Zeddam, A.},
  title     = {Euro plus Med-Checklist Notulae, 11},
  series = {Willdenowia},
  volume    = {49},
  journal   = {Willdenowia},
  number    = {3},
  publisher = {Botanischer Garten \& botanisches Museum Berlin-Dahlem},
  address   = {Berlin},
  issn      = {0511-9618},
  doi       = {10.3372/wi.49.49312},
  pages     = {421 -- 445},
  year      = {2019},
  abstract  = {This is the eleventh of a series of miscellaneous contributions, by various authors, where hitherto unpublished data relevant to both the Med-Checklist and the Euro+Med (or Sisyphus) projects are presented. This instalment deals with the families Anacardiaceae, Asparagaceae (incl. Hyacinthaceae), Bignoniaceae, Cactaceae, Compositae, Cruciferae, Cyperaceae, Ericaceae, Gramineae, Labiatae, Leguminosae, Orobanchaceae, Polygonaceae, Rosaceae, Solanaceae and Staphyleaceae. It includes new country and area records and taxonomic and distributional considerations for taxa in Bidens, Campsis, Centaurea, Cyperus, Drymocallis, Engem, Hoffmannseggia, Hypopitys, Lavandula, Lithraea, Melilotus, Nicotiana, Olimarabidopsis, Opuntia, Orobanche, Phelipanche, Phragmites, Rumex, Salvia, Schinus, Staphylea, and a new combination in Drimia.},
  language  = {en}
}
@article{SmithDupontMcCarthyetal.2019,
  author    = {Smith, Sarah R. and Dupont, Chris L. and McCarthy, James K. and Broddrick, Jared T. and Obornik, Miroslav and Horak, Ales and F{\"u}ssy, Zolt{\´a}n and Cihlar, Jaromir and Kleessen, Sabrina and Zheng, Hong and McCrow, John P. and Hixson, Kim K. and Araujo, Wagner L. and Nunes-Nesi, Adriano and Fernie, Alisdair R. and Nikoloski, Zoran and Palsson, Bernhard O. and Allen, Andrew E.},
  title     = {Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom},
  series = {Nature Communications},
  volume    = {10},
  journal   = {Nature Communications},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-019-12407-y},
  pages     = {14},
  year      = {2019},
  abstract  = {Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa.},
  language  = {en}
}
@misc{SowemimoBorcherdsKnoxBrownetal.2019,
  author    = {Sowemimo, Oluwakemi and Borcherds, Wade and Knox-Brown, Patrick and Rindfleisch, Tobias and Thalhammer, Anja and Daughdrill, Gary},
  title     = {Evolution of Transient Helicity and Disorder in Late Embryogenesis Abundant Protein COR15A},
  series = {Biophysical journal},
  volume    = {116},
  journal   = {Biophysical journal},
  number    = {3},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2018.11.2553},
  pages     = {473A -- 473A},
  year      = {2019},
  abstract  = {Cold regulated protein 15A (COR15A) is a nuclear encoded, intrinsically disordered protein that is found in Arabidopsis thaliana. It belongs to the Late Embryogenesis Abundant (LEA) family of proteins and is responsible for increased freezing tolerance in plants. COR15A is intrinsically disordered in dilute solutions and adopts a helical structure upon dehydration or in the presence of co-solutes such as TFE and ethylene glycol. This helical structure is thought to be important for protecting plants from dehydration induced by freezing. Multiple protein sequence alignments revealed the presence of several conserved glycine residues that we hypothesize keeps COR15A from becoming helical in dilute solutions. Using AGADIR, the change in helical content of COR15A when these conserved glycine residues were mutated to alanine residues was predicted. Based on the predictions, glycine to alanine mutants were made at position 68, and 54,68,81, and 84. Labeled samples of wildtype COR15A and mutant proteins were purified and NMR experiments were performed to examine any structural changes induced by the mutations. To test the effects of dehydration on the structure of COR15A, trifluoroethanol, an alcohol based co solvent that is proposed to induce/stabilize helical structure in peptides was added to the NMR samples, and the results of the experiment showed an increase in helical content, compared to the samples without TFE. To test the functional differences between wild type and the mutants, liposome leakage assays were performed. The results from these assays suggest the more helical mutants may augment membrane stability.},
  language  = {en}
}
@article{WeissSchalowJeltschetal.2019,
  author    = {Weiss, Lina and Schalow, Linda and Jeltsch, Florian and Geissler, Katja},
  title     = {Experimental evidence for root competition effects on community evenness in one of two phytometer species},
  series = {Journal of plant ecology},
  volume    = {12},
  journal   = {Journal of plant ecology},
  number    = {2},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1752-9921},
  doi       = {10.1093/jpe/rty021},
  pages     = {281 -- 291},
  year      = {2019},
  abstract  = {Aims Plant-plant interactions, being positive or negative, are recognized to be key factors in structuring plant communities. However, it is thought that root competition may be less important than shoot competition due to greater size symmetry belowground. Because direct experimental tests on the importance of root competition are scarce, we aim at elucidating whether root competition may have direct or indirect effects on community structure. Indirect effects may occur by altering the overall size asymmetry of competition through root-shoot competitive interactions. Methods We used a phytometer approach to examine the effects of root, shoot and total competition intensity and importance on evenness of experimental plant communities. Thereby two different phytometer species, Festuca brevipila and Dianthus carthusianorum, were grown in small communities of six grassland species over three levels of light and water availability, interacting with neighbouring shoots, roots, both or not at all. Important Findings We found variation in community evenness to be best explained if root and shoot (but not total) competition were considered. However, the effects were species specific: in Dianthus communities increasing root competition increased plant community evenness, while in Festuca communities shoot competition was the driving force of this evenness response. Competition intensities were influenced by environmental conditions in Dianthus, but not in Festuca phytometer plants. While we found no evidence for root-shoot interactions for neither phytometer species root competition in Dianthus communities led to increased allocation to shoots, thereby increasing the potential ability to perform in size-asymmetric competition for light. Our experiment demonstrates the potential role of root competition in structuring plant communities.},
  language  = {en}
}
@article{HerppichMartinToetzkeetal.2019,
  author    = {Herppich, Werner B. and Martin, Craig E. and T{\"o}tzke, Christian and Manke, Ingo and Kardjilov, Nikolay},
  title     = {External water transport is more important than vascular transport in the extreme atmospheric epiphyte Tillandsia usneoides (Spanish moss)},
  series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology},
  volume    = {42},
  journal   = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology},
  number    = {5},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0140-7791},
  doi       = {10.1111/pce.13496},
  pages     = {1645 -- 1656},
  year      = {2019},
  abstract  = {Most epiphytic bromeliads, especially those in the genus Tillandsia, lack functional roots and rely on the absorption of water and nutrients by large, multicellular trichomes on the epidermal surfaces of leaves and stems. Another important function of these structures is the spread of water over the epidermal surface by capillary action between trichome "wings" and epidermal surface. Although critical for the ultimate absorption by these plants, understanding of this function of trichomes is primarily based on light microscope observations. To better understand this phenomenon, the distribution of water was followed by its attenuation of cold neutrons following application of H2O to the cut end of Tillandsia usneoides shoots. Experiments confirmed the spread of added water on the external surfaces of this "atmospheric" epiphyte. In a morphologically and physiologically similar plant lacking epidermal trichomes, water added to the cut end of a shoot clearly moved via its internal xylem and not on its epidermis. Thus, in T. usneoides, water moves primarily by capillarity among the overlapping trichomes forming a dense indumentum on shoot surfaces, while internal vascular water movement is less likely. T. usneoides, occupying xeric microhabitats, benefits from reduction of water losses by low-shoot xylem hydraulic conductivities.},
  language  = {en}
}
@misc{DasGuptaRoeschHochreinetal.2019,
  author    = {Das Gupta, Mainak and Roesch, Florian and Hochrein, Lena and Machens, Fabian and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {Facilitating Genome Engineering Through RNP-mediated Precise Gene Targeting},
  series = {In Vitro Cellular \& Developmental Biology - Plant},
  volume    = {55},
  journal   = {In Vitro Cellular \& Developmental Biology - Plant},
  number    = {4},
  publisher = {Springer},
  address   = {New York},
  issn      = {1054-5476},
  pages     = {481 -- 481},
  year      = {2019},
  language  = {en}
}
@article{KoussoroplisSchaelickeRaatzetal.2019,
  author    = {Koussoroplis, Apostolos-Manuel and Sch{\"a}licke, Svenja and Raatz, Michael and Bach, Moritz and Wacker, Alexander},
  title     = {Feeding in the frequency domain},
  series = {Ecology letters},
  volume    = {22},
  journal   = {Ecology letters},
  number    = {7},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1461-023X},
  doi       = {10.1111/ele.13267},
  pages     = {1104 -- 1114},
  year      = {2019},
  abstract  = {Theory predicts that resource variability hinders consumer performance. How this effect depends on the temporal structure of resource fluctuations encountered by individuals remains poorly understood. Combining modelling and growth experiments with Daphnia magna, we decompose the complexity of resource fluctuations and test the effect of resource variance, supply peak timing (i.e. phase) and co-limiting resource covariance along a gradient from high to low frequencies reflecting fine- to coarse-grained environments. Our results show that resource storage can buffer growth at high frequencies, but yields a sensitivity of growth to resource peak timing at lower ones. When two resources covary, negative covariance causes stronger growth depression at low frequencies. However, negative covariance might be beneficial at intermediate frequencies, an effect that can be explained by digestive acclimation. Our study provides a mechanistic basis for understanding how alterations of the environmental grain size affect consumers experiencing variable nutritional quality in nature.},
  language  = {en}
}
@article{HausmannZoschkeWolffetal.2019,
  author    = {Hausmann, Christian and Zoschke, Christian and Wolff, Christopher and Darvin, Maxim E. and Sochorova, Michaela and Kovacik, Andrej and Wanjiku, Barbara and Schumacher, Fabian and Tigges, Julia and Kleuser, Burkhard and Lademann, Juergen and Fritsche, Ellen and Vavrova, Katerina and Ma, Nan and Schaefer-Korting, Monika},
  title     = {Fibroblast origin shapes tissue homeostasis, epidermal differentiation, and drug uptake},
  series = {Scientific reports},
  volume    = {9},
  journal   = {Scientific reports},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-019-39770-6},
  pages     = {10},
  year      = {2019},
  abstract  = {Preclinical studies frequently lack predictive value for human conditions. Human cell-based disease models that reflect patient heterogeneity may reduce the high failure rates of preclinical research. Herein, we investigated the impact of primary cell age and body region on skin homeostasis, epidermal differentiation, and drug uptake. Fibroblasts derived from the breast skin of female 20- to 30-yearolds or 60- to 70-year-olds and fibroblasts from juvenile foreskin (<10 years old) were compared in cell monolayers and in reconstructed human skin (RHS). RHS containing aged fibroblasts differed from its juvenile and adult counterparts, especially in terms of the dermal extracellular matrix composition and interleukin-6 levels. The site from which the fibroblasts were derived appeared to alter fibroblast-keratinocyte crosstalk by affecting, among other things, the levels of granulocyte-macrophage colony-stimulating factor. Consequently, the epidermal expression of filaggrin and e-cadherin was increased in RHS containing breast skin fibroblasts, as were lipid levels in the stratum corneum. In conclusion, the region of the body from which fibroblasts are derived appears to affect the epidermal differentiation of RHS, while the age of the fibroblast donors determines the expression of proteins involved in wound healing. Emulating patient heterogeneity in preclinical studies might improve the treatment of age-related skin conditions.},
  language  = {en}
}
@article{SchaelickeSobischMartinCreuzburgetal.2019,
  author    = {Sch{\"a}licke, Svenja and Sobisch, Lydia-Yasmin and Martin-Creuzburg, Dominik and Wacker, Alexander},
  title     = {Food quantity-quality co-limitation},
  series = {Freshwater biology},
  volume    = {64},
  journal   = {Freshwater biology},
  number    = {5},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0046-5070},
  doi       = {10.1111/fwb.13272},
  pages     = {903 -- 912},
  year      = {2019},
  abstract  = {Food quantity and quality are highly variable in natural systems. Therefore, their interplay and the associated effects on consumer population growth are important for predator-prey interactions and community dynamics. Experiments in which consumers were exposed to elemental nutrient limitations along food quantity gradients suggest that food quality effects on consumer performance are relevant only at high food quantities. However, elemental nutrients act differently on physiological processes than biochemical nutrients. So far, the interactive effects of food quantity and biochemical compounds on consumer performance have been insufficiently studied. We studied interactive effects of food quantity and biochemical food quality on population growth, including fecundity and survival, of the freshwater rotifer Brachionus calyciflorus. We hypothesised that these life history traits are differently affected by the availability of biochemical nutrients and that food quality effects gain importance with increasing food quantity. In a first experiment, we established food quantity and quality gradients by providing rotifers with different concentrations of a low-quality food, the sterol-free cyanobacterium Synechococcus elongatus, supplemented with increasing amounts of cholesterol. In a second experiment, food quantity and quality gradients were established by providing different proportions of two prey species differing in biochemical food quality, i.e. S.elongatus and the lipid-rich alga Nannochloropsis limnetica, at different total food concentrations. We found that the effects of cholesterol supplementation on population growth increased with increasing food quantity. This interactive effect on population growth was mainly due to food quality effects on fecundity, as effects on survival remained constant along the food quantity gradient. In contrast, when feeding on the mixed algal diet, the food quality effect associated with increasing the proportion of the high-quality alga did not change along the food quantity gradient. The data on survival and fecundity demonstrate the missing interactive effect of food quantity and quality on population growth, as both traits were oppositely affected. Survival was affected by food quality primarily at low food quantity, whereas food quality effects on fecundity were stronger at high food quantity. Our results highlight the significance of essential biochemicals in mediating the interactive effects of food quantity and quality on population growth. The interplay between food quantity and biochemical food quality limitation seems to influence resource allocation patterns in order to optimise survival or reproduction, which may strongly affect population dynamics in variable environments. As opposed to exploring the function of a single nutrient via supplementation, using algae mixtures allowed us to assess food quality effects on consumer performance in a more natural context by taking potential interactive effects of multiple co-limiting nutrients into account.},
  language  = {en}
}
@article{RundHeylmannSeiwertetal.2019,
  author    = {Rund, Katharina M. and Heylmann, Daniel and Seiwert, Nina and Wecklein, Sabine and Oger, Camille and Galano, Jean-Marie and Durand, Thierry and Chen, Rongjun and G{\"u}ler, Faikah and Fahrer, J{\"o}rg and Bornhorst, Julia and Schebb, Nils Helge},
  title     = {Formation of trans-epoxy fatty acids correlates with formation of isoprostanes and could serve as biomarker of oxidative stress},
  series = {Prostaglandins \& Other Lipid Mediators},
  volume    = {144},
  journal   = {Prostaglandins \& Other Lipid Mediators},
  publisher = {Elsevier},
  address   = {New York},
  issn      = {1098-8823},
  doi       = {10.1016/j.prostaglandins.2019.04.004},
  pages     = {10},
  year      = {2019},
  abstract  = {In mammals, epoxy-polyunsaturated fatty acids (epoxy-PUFA) are enzymatically formed from naturally occurring all-cis PUFA by cytochrome P450 monooxygenases leading to the generation of cis-epoxy-PUFA (mixture of R,S- and S,R-enantiomers). In addition, also non-enzymatic chemical peroxidation gives rise to epoxy-PUFA leading to both, cis- and trans-epoxy-PUFA (mixture of R,R- and S,S-enantiomers). Here, we investigated for the first time trans-epoxy-PUFA and the trans/cis-epoxy-PUFA ratio as potential new biomarker of lipid peroxidation. Their formation was analyzed in correlation with the formation of isoprostanes (IsoP), which are commonly used as biomarkers of oxidative stress. Five oxidative stress models were investigated including incubations of three human cell lines as well as the in vivo model Caenorhabditis elegans with tert-butyl hydroperoxide (t-BOOH) and analysis of murine kidney tissue after renal ischemia reperfusion injury (IRI). A comprehensive set of IsoP and epoxy-PUFA derived from biologically relevant PUFA (ARA, EPA and DHA) was simultaneously quantified by LC-ESI(-)-MS/MS. Following renal IRI only a moderate increase in the kidney levels of IsoP and no relevant change in the trans/cis-epoxy-PUFA ratio was observed. In all investigated cell lines (HCT-116, HepG2 and Caki-2) as well as C. elegans a dose dependent increase of both, IsoP and the trans/cis-epoxy-PUFA ratio in response to the applied t-BOOH was observed. The different cell lines showed a distinct time dependent pattern consistent for both classes of autoxidatively formed oxylipins. Clear and highly significant correlations of the trans/cisepoxy-PUFA ratios with the IsoP levels were found in all investigated cell lines and C. elegans. Based on this, we suggest the trans/cis-epoxy-PUFA ratio as potential new biomarker of oxidative stress, which warrants further investigation.},
  language  = {en}
}
@article{ColomaGaedkeSivonenetal.2019,
  author    = {Coloma, Sebastian and Gaedke, Ursula and Sivonen, Kaarina and Hiltunen, Teppo},
  title     = {Frequency of virus-resistant hosts determines experimental community dynamics},
  series = {Ecology : a publication of the Ecological Society of America},
  volume    = {100},
  journal   = {Ecology : a publication of the Ecological Society of America},
  number    = {1},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0012-9658},
  doi       = {10.1002/ecy.2554},
  pages     = {10},
  year      = {2019},
  abstract  = {Parasites, such as bacterial viruses (phages), can have large effects on host populations both at the ecological and evolutionary levels. In the case of cyanobacteria, phages can reduce primary production and infected hosts release intracellular nutrients influencing planktonic food web structure, community dynamics, and biogeochemical cycles. Cyanophages may be of great importance in aquatic food webs during large cyanobacterial blooms unless the host population becomes resistant to phage infection. The consequences on plankton community dynamics of the evolution of phage resistance in bloom forming cyanobacterial populations are still poorly studied. Here, we examined the effect of different frequencies of a phage-resistant genotype within a filamentous nitrogen-fixing Nodularia spumigena population on an experimental plankton community. Three Nodularia populations with different initial frequencies (0\%, 5\%, and 50\%) of phage-resistant genotypes were inoculated in separate treatments with the phage 2AV2, the green alga Chlorella vulgaris, and the rotifer Brachionus plicatilis, which formed the experimental plankton community subjected to either nitrogen-limited or nitrogen-rich conditions. We found that the frequency of the phage-resistant Nodularia genotype determined experimental community dynamics. Cyanobacterial populations with a high frequency (50\%) of the phage-resistant genotype dominated the cultures despite the presence of phages, retaining most of the intracellular nitrogen in the plankton community. In contrast, populations with low frequencies (0\% and 5\%) of the phage-resistant genotype were lysed and reduced to extinction by the phage, transferring the intracellular nitrogen held by Nodularia to Chlorella and rotifers, and allowing Chlorella to dominate the communities and rotifers to survive. This study shows that even though phages represent minuscule biomass, they can have key effects on community composition and eco-evolutionary feedbacks in plankton communities.},
  language  = {en}
}
@phdthesis{Dammhahn2019,
  author    = {Dammhahn, Melanie},
  title     = {From individual variation to community structure : paterns, determinants and consequences of within- and between-species variation in behaviour, life-history and ecology},
  school      = {Universit{\"a}t Potsdam},
  pages     = {431},
  year      = {2019},
  language  = {en}
}
@phdthesis{Devkar2019,
  author    = {Devkar, Vikas Suresh},
  title     = {Functional characterization of NAC transcription factors ATAF1 and SITAF1 in growth and abiotic stress tolerance in tomato},
  school      = {Universit{\"a}t Potsdam},
  year      = {2019},
  language  = {en}
}
@article{DondapatiLuebberdingZemellaetal.2019,
  author    = {Dondapati, Srujan Kumar and L{\"u}bberding, Henning and Zemella, Anne and Thoring, Lena and W{\"u}stenhagen, Doreen Anja and Kubick, Stefan},
  title     = {Functional Reconstitution of Membrane Proteins Derived From Eukaryotic Cell-Free Systems},
  series = {Frontiers in pharmacology},
  volume    = {10},
  journal   = {Frontiers in pharmacology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1663-9812},
  doi       = {10.3389/fphar.2019.00917},
  pages     = {9},
  year      = {2019},
  abstract  = {Cell-free protein synthesis (CFPS) based on eukaryotic Sf21 lysate is gaining interest among researchers due to its ability to handle the synthesis of complex human membrane proteins (MPs). Additionally Sf21 cell-free systems contain endogenous microsomal vesicles originally derived from the endoplasmic reticulum (ER). After CFPS, MPs will be translocated into the microsomal vesicles membranes present in the lysates. Thus microsomal membranes offer a natural environment for de novo synthesized MPs. Despite the advantage of synthesizing complex MPs with post translational modifications directly into the microsomal membranes without any additional solubilization supplements, batch based Sf21 cell-free synthesis suffers from low yields. The bottleneck for MPs in particular after the synthesis and incorporation into the microsomal membranes is to analyze their functionality. Apart from low yields of the synthesized MPs with batch based cell-free synthesis, the challenges arise in the form of cytoskeleton elements and peripheral endogenous proteins surrounding the microsomes which may impede the functional analysis of the synthesized proteins. So careful sample processing after the synthesis is particularly important for developing the appropriate functional assays. Here we demonstrate how MPs (native and batch synthesized) from ER derived microsomes can be processed for functional analysis by electrophysiology and radioactive uptake assay methods. Treatment of the microsomal membranes either with a sucrose washing step in the case of human serotonin transporter (hSERT) and sarco/endoplasmic reticulum Ca2+/ATPase (SERCA) pump or with mild detergents followed by the preparation of proteoliposomes in the case of the human voltage dependent anionic channel (hVDAC1) helps to analyze the functional properties of MPs.},
  language  = {en}
}
@article{GrimmSeyfarthMihoubHenle2019,
  author    = {Grimm-Seyfarth, Annegret and Mihoub, Jean-Baptiste and Henle, Klaus},
  title     = {Functional traits determine the different effects of prey, predators, and climatic extremes on desert reptiles},
  series = {Ecosphere : the magazine of the International Ecology University},
  volume    = {10},
  journal   = {Ecosphere : the magazine of the International Ecology University},
  number    = {9},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2150-8925},
  doi       = {10.1002/ecs2.2865},
  pages     = {17},
  year      = {2019},
  abstract  = {Terrestrial reptiles are particularly vulnerable to climate change. Their highest density and diversity can be found in hot drylands, ecosystems which demonstrate extreme climatic conditions. However, reptiles are not isolated systems but part of a large species assemblage with many trophic dependencies. While direct relations among climatic conditions, invertebrates, vegetation, or reptiles have already been explored, to our knowledge, species' responses to direct and indirect pathways of multiple climatic and biotic factors and their interactions have rarely been examined comprehensively. We investigated direct and indirect effects of climatic and biotic parameters on the individual (body condition) and population level (occupancy) of eight abundant lizard species with different functional traits in an arid Australian lizard community using a 30-yr multi-trophic monitoring study. We used structural equation modeling to disentangle single and interactive effects. We then assessed whether species could be grouped into functional groups according to their functional traits and their responses to different parameters. We found that lizard species differed strongly in how they responded to climatic and biotic factors. However, the factors to which they responded seemed to be determined by their functional traits. While responses on body condition were determined by habitat, activity time, and prey, responses on occupancy were determined by habitat specialization, body size, and longevity. Our findings highlight the importance of indirect pathways through climatic and biotic interactions, which should be included into predictive models to increase accuracy when predicting species' responses to climate change. Since one might never obtain all mechanistic pathways at the species level, we propose an approach of identifying relevant species traits that help grouping species into functional groups at different ecological levels, which could then be used for predictive modeling.},
  language  = {en}
}
@misc{GrossartVandenWyngaertKagamietal.2019,
  author    = {Grossart, Hans-Peter and Van den Wyngaert, Silke and Kagami, Maiko and Wurzbacher, Christian and Cunliffe, Michael and Rojas-Jimenz, Keilor},
  title     = {Fungi in aquatic ecosystems},
  series = {Nature reviews. Microbiology},
  volume    = {17},
  journal   = {Nature reviews. Microbiology},
  number    = {6},
  publisher = {Nature Publ. Group},
  address   = {Basingstoke},
  issn      = {1740-1526},
  doi       = {10.1038/s41579-019-0175-8},
  pages     = {339 -- 354},
  year      = {2019},
  abstract  = {Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.},
  language  = {en}
}
@misc{DietrichJacobsZhengetal.2019,
  author    = {Dietrich, Stefan and Jacobs, Simone and Zheng, Ju-Sheng and Meidtner, Karina and Schwingshackl, Lukas and Schulze, Matthias Bernd},
  title     = {Gene-lifestyle interaction on risk of type 2 diabetes},
  series = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
  volume    = {20},
  journal   = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
  number    = {11},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1467-7881},
  doi       = {10.1111/obr.12921},
  pages     = {1557 -- 1571},
  year      = {2019},
  abstract  = {The pathophysiological influence of gene-lifestyle interactions on the risk to develop type 2 diabetes (T2D) is currently under intensive research. This systematic review summarizes the evidence for gene-lifestyle interactions regarding T2D incidence. MEDLINE, EMBASE, and Web of Science were systematically searched until 31 January 2019 to identify publication with (a) prospective study design; (b) T2D incidence; (c) gene-diet, gene-physical activity, and gene-weight loss intervention interaction; and (d) population who are healthy or prediabetic. Of 66 eligible publications, 28 reported significant interactions. A variety of different genetic variants and dietary factors were studied. Variants at TCF7L2 were most frequently investigated and showed interactions with fiber and whole grain on T2D incidence. Further gene-diet interactions were reported for, eg, a western dietary pattern with a T2D-GRS, fat and carbohydrate with IRS1 rs2943641, and heme iron with variants of HFE. Physical activity showed interaction with HNF1B, IRS1, PPAR gamma, ADRA2B, SLC2A2, and ABCC8 variants and weight loss interventions with ENPP1, PPAR gamma, ADIPOR2, ADRA2B, TNF alpha, and LIPC variants. However, most findings represent single study findings obtained in European ethnicities. Although some interactions have been reported, their conclusiveness is still low, as most findings were not yet replicated across multiple study populations.},
  language  = {en}
}
@article{HorreoBreedveldLindtkeetal.2019,
  author    = {Horreo, J. L. and Breedveld, Merel Cathelijne and Lindtke, D. and Heulin, B. and Surget-Groba, Yann and Fitze, Patrick S.},
  title     = {Genetic introgression among differentiated clades is lower among clades exhibiting different parity modes},
  series = {Heredity},
  volume    = {123},
  journal   = {Heredity},
  number    = {2},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {0018-067X},
  doi       = {10.1038/s41437-019-0201-7},
  pages     = {264 -- 272},
  year      = {2019},
  abstract  = {Mechanisms leading to sympatric speciation are diverse and may build up reproductive isolation. Reproductive isolation among differentiated clades may exist due to genetic incompatibilities, sexual selection, differences in parity mode, reduced post-zygotic survival or reproductive success of hybrids. Here, we test whether differences in parity mode lead to reproductive isolation by investigating introgression in Zootoca vivipara, a lizard species exhibiting oviparous and viviparous reproduction. We measured introgression in transects spanning different viviparous clades, different oviparous subclades, transects containing oviparous and viviparous clades, and transects within the same subclade (control transects). Introgression in transects spanning oviparous and viviparous clades was one order of magnitude smaller than transects spanning the same reproductive mode and no statistical differences existed between transects spanning the same reproductive mode and control transects. Among types of transects, no significant differences existed in genetic and geographic distances, nor number of detected alleles. Moreover, hybrids were detected in all types of transects, showing that parity mode alone does not necessarily lead to complete reproductive isolation, which suggests that reinforcement may play an important role. The evolution of different parity modes together with reinforcement may thus promote reproductive isolation and rapid speciation, potentially explaining why only six of the almost 40,000 vertebrates belonging to groups consisting of viviparous and oviparous species exhibit bimodal reproduction.},
  language  = {en}
}
@article{EinumFossenParryetal.2019,
  author    = {Einum, Sigurd and Fossen, Erlend I. F. and Parry, Victor and Pelabon, Christophe},
  title     = {Genetic variation in metabolic rate and correlations with other energy budget components and life history in Daphnia magna},
  series = {Evolutionary Biology},
  volume    = {46},
  journal   = {Evolutionary Biology},
  number    = {2},
  publisher = {Springer},
  address   = {New York},
  issn      = {0071-3260},
  doi       = {10.1007/s11692-019-09473-x},
  pages     = {170 -- 178},
  year      = {2019},
  abstract  = {Much is known about the genetic variance in certain components of metabolism, most notably resting and maximum metabolic rate. This is in stark contrast to the lack of information on genetic variance in the metabolic rate of individuals that feed and express routine activity, and how this rate correlates with other components of the energy budget or life history traits. Here we quantify genetic variance in metabolic rate (MR) under such conditions, as well as food consumption, juvenile somatic growth rate and age at maturation under ad lib food availability in a set of 10 clones of Daphnia magna from a natural population. Broad sense evolvabilities (0.16 0.56\%) were on the same order of magnitude as those typically observed for physiological and life history traits, and suggest that all these traits have the potential to evolve within this population. We did not find support for the previously hypothesized positive genetic correlation between metabolic rate and growth rate. Rather, the patterns of genetic correlations suggest that genetic variance in food consumption is the single most influential trait shaping somatic growth rate, but that additional variance in growth can be explained by considering the joint effect of consumption and MR. The genetic variance in consumption and MR also translated into genetic variance in age at maturation, creating a direct link between these energy budget components and a life history trait with strong fitness effects. Moreover, a weak positive correlation between MR and food consumption suggests the presence of substantial amounts of independent genetic control of these traits, consistent with results obtained using genomic approaches.},
  language  = {en}
}
@article{DongGuptaSieversetal.2019,
  author    = {Dong, Yanni and Gupta, Saurabh and Sievers, Rixta and Wargent, Jason J. and Wheeler, David and Putterill, Joanna and Macknight, Richard and Gechev, Tsanko S. and M{\"u}ller-R{\"o}ber, Bernd and Dijkwel, Paul P.},
  title     = {Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals environment},
  series = {BMC genomics},
  volume    = {20},
  journal   = {BMC genomics},
  number    = {1},
  publisher = {BMC},
  address   = {London},
  issn      = {1471-2164},
  doi       = {10.1186/s12864-019-6084-4},
  pages     = {14},
  year      = {2019},
  abstract  = {BackgroundPachycladon cheesemanii is a close relative of Arabidopsis thaliana and is an allotetraploid perennial herb which is widespread in the South Island of New Zealand. It grows at altitudes of up to 1000m where it is subject to relatively high levels of ultraviolet (UV)-B radiation. To gain first insights into how Pachycladon copes with UV-B stress, we sequenced its genome and compared the UV-B tolerance of two Pachycladon accessions with those of two A. thaliana accessions from different altitudes.ResultsA high-quality draft genome of P. cheesemanii was assembled with a high percentage of conserved single-copy plant orthologs. Synteny analysis with genomes from other species of the Brassicaceae family found a close phylogenetic relationship of P. cheesemanii with Boechera stricta from Brassicaceae lineage I. While UV-B radiation caused a greater growth reduction in the A. thaliana accessions than in the P. cheesemanii accessions, growth was not reduced in one P. cheesemanii accession. The homologues of A. thaliana UV-B radiation response genes were duplicated in P. cheesemanii, and an expression analysis of those genes indicated that the tolerance mechanism in P. cheesemanii appears to differ from that in A. thaliana.ConclusionAlthough the P. cheesemanii genome shows close similarity with that of A. thaliana, it appears to have evolved novel strategies allowing the plant to tolerate relatively high UV-B radiation.},
  language  = {en}
}
@article{GuptaDongDijkweletal.2019,
  author    = {Gupta, Saurabh and Dong, Yanni and Dijkwel, Paul P. and M{\"u}ller-R{\"o}ber, Bernd and Gechev, Tsanko S.},
  title     = {Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation},
  series = {International Journal of Molecular Sciences},
  volume    = {20},
  journal   = {International Journal of Molecular Sciences},
  number    = {12},
  publisher = {Molecular Diversity Preservation International},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms20123101},
  pages     = {22},
  year      = {2019},
  abstract  = {Abiotic stress is one of the major threats to plant crop yield and productivity. When plants are exposed to stress, production of reactive oxygen species (ROS) increases, which could lead to extensive cellular damage and hence crop loss. During evolution, plants have acquired antioxidant defense systems which can not only detoxify ROS but also adjust ROS levels required for proper cell signaling. Ascorbate peroxidase (APX), glutathione peroxidase (GPX), catalase (CAT) and superoxide dismutase (SOD) are crucial enzymes involved in ROS detoxification. In this study, 40 putative APX, 28 GPX, 16 CAT, and 41 SOD genes were identified from genomes of the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, and the mesophile Selaginella moellendorffi. Phylogenetic analyses classified the APX, GPX, and SOD proteins into five clades each, and CAT proteins into three clades. Using co-expression network analysis, various regulatory modules were discovered, mainly involving glutathione, that likely work together to maintain ROS homeostasis upon desiccation stress in resurrection species. These regulatory modules also support the existence of species-specific ROS detoxification systems. The results suggest molecular pathways that regulate ROS in resurrection species and the role of APX, GPX, CAT and SOD genes in resurrection species during stress.},
  language  = {en}
}
@article{NumbergerRiedelMcEwenetal.2019,
  author    = {Numberger, Daniela and Riedel, Thomas and McEwen, Gayle and N{\"u}bel, Ulrich and Frentrup, Martinique and Schober, Isabel and Bunk, Boyke and Spr{\"o}er, Cathrin and Overmann, J{\"o}rg and Grossart, Hans-Peter and Greenwood, Alex D.},
  title     = {Genomic analysis of three Clostridioides difficile isolates from urban water sources},
  series = {Anaerobe},
  volume    = {56},
  journal   = {Anaerobe},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {1075-9964},
  doi       = {10.1016/j.anaerobe.2019.01.002},
  pages     = {22 -- 26},
  year      = {2019},
  abstract  = {We investigated inflow of a wastewater treatment plant and sediment of an urban lake for the presence of Clostridioides difficile by cultivation and PCR. Among seven colonies we sequenced the complete genomes of three: two non-toxigenic isolates from wastewater and one toxigenic isolate from the urban lake. For all obtained isolates, a close genomic relationship with human-derived isolates was observed. (C) 2019 Elsevier Ltd. All rights reserved.},
  language  = {en}
}
@article{JeltschGrimmReegetal.2019,
  author    = {Jeltsch, Florian and Grimm, Volker and Reeg, Jette and Schl{\"a}gel, Ulrike E.},
  title     = {Give chance a chance},
  series = {Ecosphere},
  volume    = {10},
  journal   = {Ecosphere},
  number    = {5},
  publisher = {ESA},
  address   = {Ithaca, NY},
  issn      = {2150-8925},
  doi       = {10.1002/ecs2.2700},
  pages     = {19},
  year      = {2019},
  abstract  = {A large part of biodiversity theory is driven by the basic question of what allows species to coexist in spite of a confined number of niches. A substantial theoretical background to this question is provided by modern coexistence theory (MCT), which rests on mathematical approaches of invasion analysis to categorize underlying mechanisms into factors that reduce either niche overlap (stabilizing mechanisms) or the average fitness differences of species (equalizing mechanisms). While MCT has inspired biodiversity theory in the search for these underlying mechanisms, we feel that the strong focus on coexistence causes a bias toward the most abundant species and neglects the plethora of species that are less abundant and often show high local turnover. Given the more stochastic nature of their occurrence, we advocate a complementary cross-level approach that links individuals, small populations, and communities and explicitly takes into account (1) a more complete inclusion of environmental and demographic stochasticity affecting small populations, (2) intraspecific trait variation and behavioral plasticity, and (3) local heterogeneities, interactions, and feedbacks. Focusing on mechanisms that drive the temporary coviability of species rather than infinite coexistence, we suggest a new approach that could be dubbed coviability analysis (CVA). From a modeling perspective, CVA builds on the merged approaches of individual-based modeling and population viability analysis but extends them to the community level. From an empirical viewpoint, CVA calls for a stronger integration of spatiotemporal data on variability and noise, changing drivers, and interactions at the level of individuals. The resulting large volumes of data from multiple sources could be strongly supported by novel techniques tailored to the discovery of complex patterns in high-dimensional data. By complementing MCT through a stronger focus on the coviability of less common species, this approach can help make modern biodiversity theory more comprehensive, predictive, and relevant for applications.},
  language  = {en}
}
@article{PoradaTammRaggioetal.2019,
  author    = {Porada, Philipp and Tamm, Alexandra and Raggio, Jose and Yafang, Cheng and Kleidon, Axel and P{\"o}schl, Ulrich and Weber, Bettina},
  title     = {Global NO and HONO emissions of biological soil crusts estimated by a process-based non-vascular vegetation model},
  series = {Biogeosciences},
  volume    = {16},
  journal   = {Biogeosciences},
  publisher = {Copernicus Publ.},
  address   = {G{\"o}ttingen},
  issn      = {1726-4170},
  doi       = {10.5194/bg-16-2003-2019},
  pages     = {2003 -- 2031},
  year      = {2019},
  abstract  = {The reactive trace gases nitric oxide (NO) and nitrous acid (HONO) are crucial for chemical processes in the atmosphere, including the formation of ozone and OH radicals, oxidation of pollutants, and atmospheric self-cleaning. Recently, empirical studies have shown that biological soil crusts are able to emit large amounts of NO and HONO, and they may therefore play an important role in the global budget of these trace gases. However, the upscaling of local estimates to the global scale is subject to large uncertainties, due to unknown spatial distribution of crust types and their dynamic metabolic activity. Here, we perform an alternative estimate of global NO and HONO emissions by biological soil crusts, using a process-based modelling approach to these organisms, combined with global data sets of climate and land cover. We thereby consider that NO and HONO are emitted in strongly different proportions, depending on the type of crust and their dynamic activity, and we provide a first estimate of the global distribution of four different crust types. Based on this, we estimate global total values of 1.04 Tg yr⁻¹ NO-N and 0.69 Tg yr⁻¹ HONO-N released by biological soil crusts. This corresponds to around 20\% of global emissions of these trace gases from natural ecosystems. Due to the low number of observations on NO and HONO emissions suitable to validate the model, our estimates are still relatively uncertain. However, they are consistent with the amount estimated by the empirical approach, which confirms that biological soil crusts are likely to have a strong impact on global atmospheric chemistry via emissions of NO and HONO.},
  language  = {en}
}
@article{TiegsCostelloIskenetal.2019,
  author    = {Tiegs, Scott D. and Costello, David M. and Isken, Mark W. and Woodward, Guy and McIntyre, Peter B. and Gessner, Mark O. and Chauvet, Eric and Griffiths, Natalie A. and Flecker, Alex S. and Acuna, Vicenc and Albarino, Ricardo and Allen, Daniel C. and Alonso, Cecilia and Andino, Patricio and Arango, Clay and Aroviita, Jukka and Barbosa, Marcus V. M. and Barmuta, Leon A. and Baxter, Colden V. and Bell, Thomas D. C. and Bellinger, Brent and Boyero, Luz and Brown, Lee E. and Bruder, Andreas and Bruesewitz, Denise A. and Burdon, Francis J. and Callisto, Marcos and Canhoto, Cristina and Capps, Krista A. and Castillo, Maria M. and Clapcott, Joanne and Colas, Fanny and Colon-Gaud, Checo and Cornut, Julien and Crespo-Perez, Veronica and Cross, Wyatt F. and Culp, Joseph M. and Danger, Michael and Dangles, Olivier and de Eyto, Elvira and Derry, Alison M. and Diaz Villanueva, Veronica and Douglas, Michael M. and Elosegi, Arturo and Encalada, Andrea C. and Entrekin, Sally and Espinosa, Rodrigo and Ethaiya, Diana and Ferreira, Veronica and Ferriol, Carmen and Flanagan, Kyla M. and Fleituch, Tadeusz and Shah, Jennifer J. Follstad and Frainer, Andre and Friberg, Nikolai and Frost, Paul C. and Garcia, Erica A. and Lago, Liliana Garcia and Garcia Soto, Pavel Ernesto and Ghate, Sudeep and Giling, Darren P. and Gilmer, Alan and Goncalves, Jose Francisco and Gonzales, Rosario Karina and Graca, Manuel A. S. and Grace, Mike and Grossart, Hans-Peter and Guerold, Francois and Gulis, Vlad and Hepp, Luiz U. and Higgins, Scott and Hishi, Takuo and Huddart, Joseph and Hudson, John and Imberger, Samantha and Iniguez-Armijos, Carlos and Iwata, Tomoya and Janetski, David J. and Jennings, Eleanor and Kirkwood, Andrea E. and Koning, Aaron A. and Kosten, Sarian and Kuehn, Kevin A. and Laudon, Hjalmar and Leavitt, Peter R. and Lemes da Silva, Aurea L. and Leroux, Shawn J. and Leroy, Carri J. and Lisi, Peter J. and MacKenzie, Richard and Marcarelli, Amy M. and Masese, Frank O. and Mckie, Brendan G. and Oliveira Medeiros, Adriana and Meissner, Kristian and Milisa, Marko and Mishra, Shailendra and Miyake, Yo and Moerke, Ashley and Mombrikotb, Shorok and Mooney, Rob and Moulton, Tim and Muotka, Timo and Negishi, Junjiro N. and Neres-Lima, Vinicius and Nieminen, Mika L. and Nimptsch, Jorge and Ondruch, Jakub and Paavola, Riku and Pardo, Isabel and Patrick, Christopher J. and Peeters, Edwin T. H. M. and Pozo, Jesus and Pringle, Catherine and Prussian, Aaron and Quenta, Estefania and Quesada, Antonio and Reid, Brian and Richardson, John S. and Rigosi, Anna and Rincon, Jose and Risnoveanu, Geta and Robinson, Christopher T. and Rodriguez-Gallego, Lorena and Royer, Todd V. and Rusak, James A. and Santamans, Anna C. and Selmeczy, Geza B. and Simiyu, Gelas and Skuja, Agnija and Smykla, Jerzy and Sridhar, Kandikere R. and Sponseller, Ryan and Stoler, Aaron and Swan, Christopher M. and Szlag, David and Teixeira-de Mello, Franco and Tonkin, Jonathan D. and Uusheimo, Sari and Veach, Allison M. and Vilbaste, Sirje and Vought, Lena B. M. and Wang, Chiao-Ping and Webster, Jackson R. and Wilson, Paul B. and Woelfl, Stefan and Xenopoulos, Marguerite A. and Yates, Adam G. and Yoshimura, Chihiro and Yule, Catherine M. and Zhang, Yixin X. and Zwart, Jacob A.},
  title     = {Global patterns and drivers of ecosystem functioning in rivers and riparian zones},
  series = {Science Advances},
  volume    = {5},
  journal   = {Science Advances},
  number    = {1},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {2375-2548},
  doi       = {10.1126/sciadv.aav0486},
  pages     = {8},
  year      = {2019},
  abstract  = {River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.},
  language  = {en}
}
@article{VehKorupWalz2019,
  author    = {Veh, Georg and Korup, Oliver and Walz, Ariane},
  title     = {Hazard from Himalayan glacier lake outburst floods},
  series = {Proceedings of the National Academy of Sciences of the United States of America : PNAS},
  volume    = {117},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America : PNAS},
  number    = {2},
  publisher = {National Academy of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1914898117},
  pages     = {907 -- 912},
  year      = {2019},
  abstract  = {Sustained glacier melt in the Himalayas has gradually spawned more than 5,000 glacier lakes that are dammed by potentially unstable moraines. When such dams break, glacier lake outburst floods (GLOFs) can cause catastrophic societal and geomorphic impacts. We present a robust probabilistic estimate of average GLOFs return periods in the Himalayan region, drawing on 5.4 billion simulations. We find that the 100-y outburst flood has an average volume of 33.5(+3.7)/(-3.7) x 10(6) m(3) (posterior mean and 95\% highest density interval [HDI]) with a peak discharge of 15,600(+2.000)/(-1,800) m(3).S-1. Our estimated GLOF hazard is tied to the rate of historic lake outbursts and the number of present lakes, which both are highest in the Eastern Himalayas. There, the estimated 100-y GLOF discharge (similar to 14,500 m(3).s(-1)) is more than 3 times that of the adjacent Nyainqentanglha Mountains, and at least an order of magnitude higher than in the Hindu Kush, Karakoram, and Western Himalayas. The GLOF hazard may increase in these regions that currently have large glaciers, but few lakes, if future projected ice loss generates more unstable moraine-dammed lakes than we recognize today. Flood peaks from GLOFs mostly attenuate within Himalayan headwaters, but can rival monsoon-fed discharges in major rivers hundreds to thousands of kilometers downstream. Projections of future hazard from meteorological floods need to account for the extreme runoffs during lake outbursts, given the increasing trends in population, infrastructure, and hydropower projects in Himalayan headwaters.},
  language  = {en}
}
@article{Wardelmann2019,
  author    = {Wardelmann, Kristina},
  title     = {Hormonal regulation of neuronal mitochondrial unfolded protein response and its impact on metabolism},
  pages     = {108},
  year      = {2019},
  abstract  = {The hypothalamus is the main brain area of central regulation of whole body metabolism through impacting food intake and energy expenditure. For the complex regulation, high amounts of energy are needed and mainly provided by mitochondria. Hence, mitochondrial function is crucial for cell homeostasis and modulates central insulin sensitivity. Thus, mitochondrial dysfunction is associated with insulin resistance in the brain and therefore is involved in the pathogenesis of type-2 diabetes (T2D). Mitochondrial health and protein homeostasis is propagated by mitochondrial stress responses like e.g. mitochondrial unfolded protein response (UPRmt). Therefore, studies regarding the regulation of mitochondrial homeostasis are crucial for understanding its effects on the central nervous system (CNS) for the progression of metabolic and nutrition-dependent disorders. One main aim of this thesis was to investigate the metabolic regulation of mitochondrial stress responsiveness in the hypothalamus. The observed results showed that functional ERK-dependent insulin signaling is needed for regulation of mitochondrial stress response (MSR) genes and positively impacted the metabolism by controlling mitochondrial proteostasis without affecting mitochondrial biogenesis. To further explore the role of MSR genes for brain cell homeostasis and its consequences for the metabolism, one of the key players - the mitochondrial chaperone heat shock protein 10 (Hsp10) - was studied in detail. Hsp10 expression was decreased in insulin-resistant, hyperglycemic db/db mice brains along with increased protein oxidation. Leptin, another key hormone in regulating metabolism, was able to induce Hsp10 in neurons. Appropriately, lentiviral-mediated knock down (KD) of Hsp10 introduced into hypothalamic CLU-183 cells induced mitochondrial dysfunction, altered mitochondrial dynamics and increased contact sites between mitochondria and endoplasmic reticulum (ER). In addition, Hsp10 KD caused cellular insulin resistance along with increasing oxidative stress specifically in mitochondrial fraction. Interestingly, acute Hsp10 KD in the arcuate nucleus of the hypothalamus in C57BL/6N male mice did not change body weight or food intake, but it increased plasma leptin concentrations suggesting an effect on global leptin signaling. It increased hepatic markers of gluconeogenesis and hepatic insulin resistance along with features of low-grade inflammation. Long-term studies of hypothalamic Hsp10 KD mice revealed unaltered systemic insulin sensitivity. The demonstrated increase in markers of hepatic gluconeogenesis of acute Hsp10 KD was still exhibited after 13 weeks, but insulin resistance in the liver was no longer observed. In conclusion, hypothalamic insulin action regulates MSR and ensures proper mitochondrial function which positively affects metabolism. In addition, hypothalamic Hsp10 acts as a modulator of both insulin and leptin signaling and is identified as pivotal for the regulation of central mitochondrial function as well as insulin sensitivity in the brain and it impacts liver function. It may present a regulator of brain-liver crosstalk influencing hepatic gluconeogenesis and insulin sensitivity through a novel regulatory signaling mechanism.},
  language  = {en}
}
@article{RaatzBacchiPirhoferWalzletal.2019,
  author    = {Raatz, Larissa and Bacchi, Nina and Pirhofer Walzl, Karin and Glemnitz, Michael and M{\"u}ller, Marina E. H. and Jasmin Radha, Jasmin and Scherber, Christoph},
  title     = {How much do we really lose?},
  series = {Ecology and Evolution},
  volume    = {9},
  journal   = {Ecology and Evolution},
  number    = {13},
  publisher = {John Wiley \& Sons},
  address   = {S.I.},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.5370},
  pages     = {7838 -- 7848},
  year      = {2019},
  abstract  = {Natural landscape elements (NLEs) in agricultural landscapes contribute to biodiversity and ecosystem services, but are also regarded as an obstacle for large-scale agricultural production. However, the effects of NLEs on crop yield have rarely been measured. Here, we investigated how different bordering structures, such as agricultural roads, field-to-field borders, forests, hedgerows, and kettle holes, influence agricultural yields. We hypothesized that (a) yield values at field borders differ from mid-field yields and that (b) the extent of this change in yields depends on the bordering structure. We measured winter wheat yields along transects with log-scaled distances from the border into the agricultural field within two intensively managed agricultural landscapes in Germany (2014 near G{\"o}ttingen, and 2015-2017 in the Uckermark). We observed a yield loss adjacent to every investigated bordering structure of 11\%-38\% in comparison with mid-field yields. However, depending on the bordering structure, this yield loss disappeared at different distances. While the proximity of kettle holes did not affect yields more than neighboring agricultural fields, woody landscape elements had strong effects on winter wheat yields. Notably, 95\% of mid-field yields could already be reached at a distance of 11.3 m from a kettle hole and at a distance of 17.8 m from hedgerows as well as forest borders. Our findings suggest that yield losses are especially relevant directly adjacent to woody landscape elements, but not adjacent to in-field water bodies. This highlights the potential to simultaneously counteract yield losses close to the field border and enhance biodiversity by combining different NLEs in agricultural landscapes such as creating strips of extensive grassland vegetation between woody landscape elements and agricultural fields. In conclusion, our results can be used to quantify ecocompensations to find optimal solutions for the delivery of productive and regulative ecosystem services in heterogeneous agricultural landscapes.},
  language  = {en}
}
@article{RaatzBacchiWalzletal.2019,
  author    = {Raatz, Larissa and Bacchi, Nina and Walzl, Karin Pirhofer and Glemnitz, Michael and M{\"u}ller, Marina E. H. and Jasmin Radha, Jasmin and Scherber, Christoph},
  title     = {How much do we really lose?},
  series = {Ecology and evolution},
  volume    = {9},
  journal   = {Ecology and evolution},
  number    = {13},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.5370},
  pages     = {7838 -- 7848},
  year      = {2019},
  abstract  = {Natural landscape elements (NLEs) in agricultural landscapes contribute to biodiversity and ecosystem services, but are also regarded as an obstacle for large-scale agricultural production. However, the effects of NLEs on crop yield have rarely been measured. Here, we investigated how different bordering structures, such as agricultural roads, field-to-field borders, forests, hedgerows, and kettle holes, influence agricultural yields. We hypothesized that (a) yield values at field borders differ from mid-field yields and that (b) the extent of this change in yields depends on the bordering structure. We measured winter wheat yields along transects with log-scaled distances from the border into the agricultural field within two intensively managed agricultural landscapes in Germany (2014 near Gottingen, and 2015-2017 in the Uckermark). We observed a yield loss adjacent to every investigated bordering structure of 11\%-38\% in comparison with mid-field yields. However, depending on the bordering structure, this yield loss disappeared at different distances. While the proximity of kettle holes did not affect yields more than neighboring agricultural fields, woody landscape elements had strong effects on winter wheat yields. Notably, 95\% of mid-field yields could already be reached at a distance of 11.3 m from a kettle hole and at a distance of 17.8 m from hedgerows as well as forest borders. Our findings suggest that yield losses are especially relevant directly adjacent to woody landscape elements, but not adjacent to in-field water bodies. This highlights the potential to simultaneously counteract yield losses close to the field border and enhance biodiversity by combining different NLEs in agricultural landscapes such as creating strips of extensive grassland vegetation between woody landscape elements and agricultural fields. In conclusion, our results can be used to quantify ecocompensations to find optimal solutions for the delivery of productive and regulative ecosystem services in heterogeneous agricultural landscapes.},
  language  = {en}
}
@article{MotaEsmaeeliMoghaddamTabalvandaniCoelhoetal.2019,
  author    = {Mota, Cristiano and Esmaeeli Moghaddam Tabalvandani, Mariam and Coelho, Catarina and Santos-Silva, Teresa and Wolff, Martin and Foti, Alessandro and Leimk{\"u}hler, Silke and Romao, Maria Joao},
  title     = {Human aldehyde oxidase (hAOX1)},
  series = {FEBS Open Bio},
  volume    = {9},
  journal   = {FEBS Open Bio},
  number    = {5},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2211-5463},
  doi       = {10.1002/2211-5463.12617},
  pages     = {925 -- 934},
  year      = {2019},
  abstract  = {Human aldehyde oxidase (hAOX1) is a molybdenum enzyme with high toxicological importance, but its physiological role is still unknown. hAOX1 metabolizes different classes of xenobiotics and is one of the main drug-metabolizing enzymes in the liver, along with cytochrome P450. hAOX1 oxidizes and inactivates a large number of drug molecules and has been responsible for the failure of several phase I clinical trials. The interindividual variability of drug-metabolizing enzymes caused by single nucleotide polymorphisms (SNPs) is highly relevant in pharmaceutical treatments. In this study, we present the crystal structure of the inactive variant G1269R, revealing the first structure of a molybdenum cofactor (Moco)-free form of hAOX1. These data allowed to model, for the first time, the flexible Gate 1 that controls access to the active site. Furthermore, we inspected the thermostability of wild-type hAOX1 and hAOX1 with various SNPs (L438V, R1231H, G1269R or S1271L) by CD spectroscopy and ThermoFAD, revealing that amino acid exchanges close to the Moco site can impact protein stability up to 10 degrees C. These results correlated with biochemical and structural data and enhance our understanding of hAOX1 and the effect of SNPs in the gene encoding this enzyme in the human population. EnzymesAldehyde oxidase (); xanthine dehydrogenase (); xanthine oxidase (). DatabasesStructural data are available in the Protein Data Bank under the accession number .},
  language  = {en}
}
@article{NunesNesiAlseekhdeOliveiraSilvaetal.2019,
  author    = {Nunes-Nesi, Adriano and Alseekh, Saleh and de Oliveira Silva, Franklin Magnum and Omranian, Nooshin and Lichtenstein, Gabriel and Mirnezhad, Mohammad and Romero Gonzalez, Roman R. and Sabio y Garcia, Julia and Conte, Mariana and Leiss, Kirsten A. and Klinkhamer, Peter Gerardus Leonardus and Nikoloski, Zoran and Carrari, Fernando and Fernie, Alisdair R.},
  title     = {Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds},
  series = {Metabolomics},
  volume    = {15},
  journal   = {Metabolomics},
  number    = {46},
  publisher = {Springer},
  address   = {New York},
  issn      = {1573-3882},
  doi       = {10.1007/s11306-019-1503-8},
  pages     = {13},
  year      = {2019},
  abstract  = {IntroductionTo date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism.ObjectiveThis study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues.MethodsThe analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses.ResultsChanges in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism.ConclusionsOverall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.},
  language  = {en}
}
@article{WitzelAbuRishaAlbersetal.2019,
  author    = {Witzel, Katja and Abu Risha, Marua and Albers, Philip and B{\"o}rnke, Frederik and Hanschen, Franziska S.},
  title     = {Identification and Characterization of Three Epithiospecifier Protein Isoforms in Brassica oleracea},
  series = {Frontiers in plant science},
  volume    = {10},
  journal   = {Frontiers in plant science},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2019.01552},
  pages     = {14},
  year      = {2019},
  abstract  = {Glucosinolates present in Brassicaceae play a major role in herbivory defense. Upon tissue disruption, glucosinolates come into contact with myrosinase, which initiates their breakdown to biologically active compounds. Among these, the formation of epithionitriles is triggered by the presence of epithiospecifier protein (ESP) and a terminal double bond in the glucosinolate side chain. One ESP gene is characterized in the model plant Arabidopsis thaliana (AtESP; At1g54040.2). However, Brassica species underwent genome triplication since their divergence from the Arabidopsis lineage. This indicates the presence of multiple ESP isoforms in Brassica crops that are currently poorly characterized. We identified three B. oleracea ESPs, specifically BoESP1 (LOC106296341), BoESP2 (LOC106306810), and BoESP3 (LOC106325105) based on in silico genome analysis. Transcript and protein abundance were assessed in shoots and roots of four B. oleracea vegetables, namely broccoli, kohlrabi, white, and red cabbage, because these genotypes showed a differential pattern for the formation of glucosinolate hydrolysis products as well for their ESP activity. BoESP1 and BoESP2 were expressed mainly in shoots, while BoESP3 was abundant in roots. Biochemical characterization of heterologous expressed BoESP isoforms revealed different substrate specificities towards seven glucosinolates: all isoforms showed epithiospecifier activity on alkenyl glucosinolates, but not on non-alkenyl glucosinolates. The pH-value differently affected BoESP activity: while BoESP1 and BoESP2 activities were optimal at pH 6-7, BoESP3 activity remained relatively stable from pH 4 to 7. In order test their potential for the in vivo modification of glucosinolate breakdown, the three isoforms were expressed in A. thaliana Hi-0, which lacks AtESP expression, and analyzed for the effect on their respective hydrolysis products. The BoESPs altered the hydrolysis of allyl glucosinolate in the A. thaliana transformants to release 1-cyano-2,3-epithiopropane and reduced formation of the corresponding 3-butenenitrile and allyl isothiocyanate. Plants expressing BoESP2 showed the highest percentage of released epithionitriles. Given these results, we propose a model for isoform-specific roles of B. oleracea ESPs in glucosinolate breakdown.},
  language  = {en}
}
@article{TannerLichtenbergKraag2019,
  author    = {Tanner, Norman and Lichtenberg-Kraag, Birgit},
  title     = {Identification and Quantification of Single and Multi-Adulteration of Beeswax by FTIR-ATR Spectroscopy},
  series = {European journal of lipid science and technology},
  volume    = {121},
  journal   = {European journal of lipid science and technology},
  number    = {12},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1438-7697},
  doi       = {10.1002/ejlt.201900245},
  pages     = {10},
  year      = {2019},
  abstract  = {Marketing of adulterated beeswax foundation has recently become a major economic problem for beekeepers. Paraffin contamination leads to collapse of combs, and stearic acid has a negative influence on the development of bee brood. The quality of beeswax for beekeeping has not been standardized in EU regulations. Recently, it was shown that attenuated total reflectance Fourier-transform infrared spectroscopy (FTIR-ATR) can be used to determine beeswax adulteration. Differences in the IR spectra of authentic beeswax can be identified and calculated through comparison with authentic beeswax. In this study, the method is further validated by employing a high number of samples of authentic beeswax from different origins. Low quantification and detection limits are achieved for paraffin, stearic acid, tallow, carnauba wax, and candelilla wax. Furthermore, the FTIR-ATR analytical conditions are verified by analyzing 358 samples of commercial and beekeeper-produced beeswax foundations. Multi-adulterated samples with as many as five different additives in beeswax mixtures are identified with the same accuracy as single substances. Additionally, the spectra of a further 14 different natural and synthetic waxes and hardened fats are analyzed and are compared with beeswax. Finally, a spectral library is established that can be used for further studies. Practical Applications: FTIR-ATR is a fast and cost-efficient tool in beeswax analysis for accurately monitoring a high sample volume. Analysis of 358 beeswax foundations showed an adulteration of 21.8\% of the samples with paraffin, stearic acid, tallow, and combinations. Based on the results of this study, it is possible to detect beeswax adulteration of less than 3\% of these adulterants and their combinations by FTIR-ATR spectroscopy. This method can be used for monitoring beeswax foundations to identify adulterated materials, exclude these materials from the recycling process, and produce high-quality beeswax, which is essential for bee health.},
  language  = {en}
}
@article{MalinovaKoesslerOrawetzetal.2019,
  author    = {Malinova, Irina and K{\"o}ssler, Stella and Orawetz, Tom and Matthes, Ulrike and Orzechowski, Slawomir and Koch, Anke and Fettke, J{\"o}rg},
  title     = {Identification of two Arabidopsis thaliana plasma membrane transporters able to transport glucose 1-phosphate},
  series = {Plant \& cell physiology},
  volume    = {61},
  journal   = {Plant \& cell physiology},
  number    = {2},
  publisher = {Oxford University Press},
  address   = {Oxford},
  issn      = {0032-0781},
  doi       = {10.1093/pcp/pcz206},
  pages     = {381 -- 392},
  year      = {2019},
  abstract  = {Primary carbohydrate metabolism in plants includes several sugar and sugar-derivative transport processes. Over recent years, evidences have shown that in starch-related transport processes, in addition to glucose 6-phosphate, maltose, glucose and triose-phosphates, glucose 1-phosphate also plays a role and thereby increases the possible fluxes of sugar metabolites in planta. In this study, we report the characterization of two highly similar transporters, At1g34020 and At4g09810, in Arabidopsis thaliana, which allow the import of glucose 1-phosphate through the plasma membrane. Both transporters were expressed in yeast and were biochemically analyzed to reveal an antiport of glucose 1-phosphate/phosphate. Furthermore, we showed that the apoplast of Arabidopsis leaves contained glucose 1-phosphate and that the corresponding mutant of these transporters had higher glucose 1-phosphate amounts in the apoplast and alterations in starch and starch-related metabolism.},
  language  = {en}
}
@article{ReschkeDuffusSchrapersetal.2019,
  author    = {Reschke, Stefan and Duffus, Benjamin R. and Schrapers, Peer and Mebs, Stefan and Teutloff, Christian and Dau, Holger and Haumann, Michael and Leimk{\"u}hler, Silke},
  title     = {Identification of YdhV as the First Molybdoenzyme Binding a Bis-Mo-MPT Cofactor in Escherichia coli},
  series = {Biochemistry},
  volume    = {58},
  journal   = {Biochemistry},
  number    = {17},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {0006-2960},
  doi       = {10.1021/acs.biochem.9b00078},
  pages     = {2228 -- 2242},
  year      = {2019},
  abstract  = {The oxidoreductase YdhV in Escherichia coli has been predicted to belong to the family of molybdenum/tungsten cofactor (Moco/Wco)-containing enzymes. In this study, we characterized the YdhV protein in detail, which shares amino acid sequence homology with a tungsten-containing benzoyl-CoA reductase binding the bis-W-MPT (for metal-binding pterin) cofactor. The cofactor was identified to be of a bis-Mo-MPT type with no guanine nucleotides present, which represents a form of Moco that has not been found previously in any molybdoenzyme. Our studies showed that YdhV has a preference for bis-Mo-MPT over bis-W-MPT to be inserted into the enzyme. In-depth characterization of YdhV by X-ray absorption and electron paramagnetic resonance spectroscopies revealed that the bis-Mo-MPT cofactor in YdhV is redox active. The bis-Mo-MPT and bis-W-MPT cofactors include metal centers that bind the four sulfurs from the two dithiolene groups in addition to a cysteine and likely a sulfido ligand. The unexpected presence of a bis-Mo-MPT cofactor opens an additional route for cofactor biosynthesis in E. coli and expands the canon of the structurally highly versatile molybdenum and tungsten cofactors.},
  language  = {en}
}
@article{FritzeCostantiniFickeletal.2019,
  author    = {Fritze, Marcus and Costantini, David and Fickel, J{\"o}rns and Wehner, Dana and Czirjak, Gsbor A. and Voigt, Christian Claus},
  title     = {Immune response of hibernating European bats to a fungal challenge},
  series = {Biology open},
  volume    = {8},
  journal   = {Biology open},
  number    = {10},
  publisher = {Company biologists ltd},
  address   = {Cambridge},
  issn      = {2046-6390},
  doi       = {10.1242/bio.046078},
  pages     = {10},
  year      = {2019},
  abstract  = {Immunological responses of hibernating mammals are suppressed at low body temperatures, a possible explanation for the devastating effect of the white-nose syndrome on hibernating North American bats. However, European bats seem to cope well with the fungal causative agent of the disease. To better understand the immune response of hibernating bats, especially against fungal pathogens, we challenged European greater mouse-eared bats (Myotis myotis) by inoculating the fungal antigen zymosan. We monitored torpor patterns, immune gene expressions, different aspects of the acute phase response and plasma oxidative status markers, and compared them with sham-injected control animals at 30 min, 48 h and 96 h after inoculation. Torpor patterns, body temperatures, body masses, white blood cell counts, expression of immune genes, reactive oxygen metabolites and non-enzymatic antioxidant capacity did not differ between groups during the experiment. However, zymosan injected bats had significantly higher levels of haptoglobin than the control animals. Our results indicate that hibernating greater mouse-eared bats mount an inflammatory response to a fungal challenge, with only mild to negligible consequences for the energy budget of hibernation. Our study gives a first hint that hibernating European bats may have evolved a hibernation-adjusted immune response in order to balance the trade-off between competent pathogen elimination and a prudent energy-saving regime.},
  language  = {en}
}
@article{MehrenWuertzKozakSaueretal.2019,
  author    = {Mehren, Christoph and Wuertz-Kozak, Karin and Sauer, Daniel and Hitzl, Wolfgang and Pehlivanoglu, Tuna and Heider, Franziska},
  title     = {Implant Design and the Anchoring Mechanism Influence the Incidence of Heterotopic Ossification in Cervical Total Disc Replacement at 2-year Follow-up},
  series = {Spine},
  volume    = {44},
  journal   = {Spine},
  number    = {21},
  publisher = {Lippincott Williams \& Wilkins},
  address   = {Philadelphia},
  issn      = {0362-2436},
  doi       = {10.1097/BRS.0000000000003098},
  pages     = {1471 -- 1480},
  year      = {2019},
  abstract  = {Study Design. A nonrandomized, prospective, and single-center clinical trial. Objective. The aim of this study was to determine whether the prosthesis design, and especially changes in the primary anchoring mechanism between the keel-based ProDisc C and the spike-based ProDisc Vivo, affects the frequency of heterotopic ossification (HO) formation over time. Summary of Background Data. The occurrence of motion-restricting HO as well as underlying risk factors has so far been a widely discussed, but not well understand phenomenon. The anchoring mechanism and the opening of the anterior cortex may be possible causes of this unwanted complication. Methods. Forty consecutive patients treated with the ProDisc C and 42 consecutive patients treated with the ProDisc Vivo were compared with respect to radiological and clinical outcome, with 2 years of follow-up. Clinical outcome scores included the Neck Disability Index (NDI), Visual Analogue Scale (VAS), and arm and neck pain self-assessment questionnaires. Radiological outcomes included the segmental lordosis and range of motion (ROM) of the index-segment as well as the occurrence of HO. Results. The clinical outcome parameters improved in both groups significantly. [ProDisc C: VAS arm and neck pain from 6.3 and 6.2 preoperatively to 0.7 and 1.3; NDI from 23.0 to 3.7; ProDisc Vivo: VAS arm and neck pain from 6.3 and 4.9 to 1.4 and 1.6, NDI from 34.1 to 8.7; 2-year follow-up (FU)]. The ProDisc Vivo cohort demonstrated a significantly lower incidence of HO than the ProDisc C group at 1-year FU (P = 0.0005) and 2-year FU (P = 0.005). Specifically, high-grade HO occurred in 9\% versus 31\%. Conclusion. These findings demonstrate that prosthesis designs that allow primary anchoring without violation of the cortical surface help to reduce the incidence of severe ossification, possibly affecting the functionality and mobility of the artificial disc device over of time.},
  language  = {en}
}
@phdthesis{Gottmann2019,
  author    = {Gottmann, Pascal},
  title     = {In silico Analyse zur Kl{\"a}rung der Beteiligung von micro-RNAs, die in QTL lokalisiert sind, an den metabolischen Erkrankungen Adipositas und Typ-2-Diabetes mit Hilfe von Mausmodellen},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XIII, 106},
  year      = {2019},
  language  = {de}
}
@misc{BrauneLatourReinthaleretal.2019,
  author    = {Braune, Steffen and Latour, Robert A. and Reinthaler, Markus and Landmesser, Ulf and Lendlein, Andreas and Jung, Friedrich},
  title     = {In Vitro Thrombogenicity Testing of Biomaterials},
  series = {Advanced healthcare materials},
  volume    = {8},
  journal   = {Advanced healthcare materials},
  number    = {21},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2192-2640},
  doi       = {10.1002/adhm.201900527},
  pages     = {17},
  year      = {2019},
  abstract  = {The short- and long-term thrombogenicity of implant materials is still unpredictable, which is a significant challenge for the treatment of cardiovascular diseases. A knowledge-based approach for implementing biofunctions in materials requires a detailed understanding of the medical device in the biological system. In particular, the interplay between material and blood components/cells as well as standardized and commonly acknowledged in vitro test methods allowing a reproducible categorization of the material thrombogenicity requires further attention. Here, the status of in vitro thrombogenicity testing methods for biomaterials is reviewed, particularly taking in view the preparation of test materials and references, the selection and characterization of donors and blood samples, the prerequisites for reproducible approaches and applied test systems. Recent joint approaches in finding common standards for a reproducible testing are summarized and perspectives for a more disease oriented in vitro thrombogenicity testing are discussed.},
  language  = {en}
}
@article{HeslopWinkelAnthonyetal.2019,
  author    = {Heslop, J. K. and Winkel, Matthias and Anthony, K. M. Walter and Spencer, R. G. M. and Podgorski, D. C. and Zito, P. and Kholodov, A. and Zhang, M. and Liebner, Susanne},
  title     = {Increasing organic carbon biolability with depth in yedoma permafrost},
  series = {Journal of geophysical research : Biogeosciences},
  volume    = {124},
  journal   = {Journal of geophysical research : Biogeosciences},
  number    = {7},
  publisher = {American Geophysical Union},
  address   = {Washington},
  issn      = {2169-8953},
  doi       = {10.1029/2018JG004712},
  pages     = {2021 -- 2038},
  year      = {2019},
  abstract  = {Permafrost thaw subjects previously frozen organic carbon (OC) to microbial decomposition, generating the greenhouse gases (GHG) carbon dioxide (CO2) and methane (CH4) and fueling a positive climate feedback. Over one quarter of permafrost OC is stored in deep, ice-rich Pleistocene-aged yedoma permafrost deposits. We used a combination of anaerobic incubations, microbial sequencing, and ultrahigh-resolution mass spectrometry to show yedoma OC biolability increases with depth along a 12-m yedoma profile. In incubations at 3 degrees C and 13 degrees C, GHG production per unit OC at 12-versus 1.3-m depth was 4.6 and 20.5 times greater, respectively. Bacterial diversity decreased with depth and we detected methanogens at all our sampled depths, suggesting that in situ microbial communities are equipped to metabolize thawed OC into CH4. We concurrently observed an increase in the relative abundance of reduced, saturated OC compounds, which corresponded to high proportions of C mineralization and positively correlated with anaerobic GHG production potentials and higher proportions of OC being mineralized as CH4. Taking into account the higher global warming potential (GWP) of CH4 compared to CO2, thawed yedoma sediments in our study had 2 times higher GWP at 12-versus 9.0-m depth at 3 degrees C and 15 times higher GWP at 13 degrees C. Considering that yedoma is vulnerable to processes that thaw deep OC, our findings imply that it is important to account for this increasing GHG production and GWP with depth to better understand the disproportionate impact of yedoma on the magnitude of the permafrost carbon feedback.},
  language  = {en}
}
@article{SchirmerHerdeEccardetal.2019,
  author    = {Schirmer, Annika and Herde, Antje and Eccard, Jana and Dammhahn, Melanie},
  title     = {Individuals in space: personality-dependent space use, movement and microhabitat use facilitate individual spatial niche specialization},
  series = {Oecologia},
  volume    = {189},
  journal   = {Oecologia},
  number    = {3},
  publisher = {Springer},
  address   = {New York},
  issn      = {0029-8549},
  doi       = {10.1007/s00442-019-04365-5},
  pages     = {647 -- 660},
  year      = {2019},
  abstract  = {Personality-dependent space use and movement might be crucially influencing ecological interactions, giving way to individual niche specialization. This new approach challenges classical niche theory with potentially great ecological consequences, but so far has only scarce empirical support. Here, we investigated if and how consistent inter-individual differences in behavior predict space use and movement patterns in free-ranging bank voles (Myodes glareolus) and thereby contribute to individual niche specialization. Individuals were captured and marked from three different subpopulations in North-East Germany. Inter-individual differences in boldness and exploration were quantified via repeated standardized tests directly in the field after capture. Subsequently, space use and movement patterns of a representative sample of the behavioral variation (n=21 individuals) were monitored via automated VHF telemetry for a period of four days, yielding on average 384 locations per individual. Bolder individuals occupied larger home ranges and core areas (estimated via kernel density analyses), moved longer distances, spatially overlapped with fewer conspecifics and preferred different microhabitats based on vegetation cover compared to shyer individuals. We found evidence for personality-dependent space use, movement, and occupation of individual spatial niches in bank voles. Thus, besides dietary niche specialization also spatial dimensions of ecological niches vary among individuals within populations, which may have important consequences for ecological interactions within- and between species.},
  language  = {en}
}
@phdthesis{Scherer2019,
  author    = {Scherer, Philipp C{\´e}dric},
  title     = {Infection on the move},
  school      = {Universit{\"a}t Potsdam},
  pages     = {x, 107, XXXVIII},
  year      = {2019},
  abstract  = {Movement plays a major role in shaping population densities and contact rates among individuals, two factors that are particularly relevant for disease outbreaks. Although any differences in movement behaviour due to individual characteristics of the host and heterogeneity in landscape structure are likely to have considerable consequences for disease dynamics, these mechanisms are neglected in most epidemiological studies. Therefore, developing a general understanding how the interaction of movement behaviour and spatial heterogeneity shapes host densities, contact rates and ultimately pathogen spread is a key question in ecological and epidemiological research. In my thesis, I address this gap using both theoretical and empirical modelling approaches. In the theoretical part of my thesis, I investigated bottom-up effects of individual movement behaviour and landscape structure on host density, contact rates, and ultimately disease dynamics. I extended an established agent-based model that simulates ecological and epidemiological key processes to incorporate explicit movement of host individuals and landscape complexity. Neutral landscape models are a powerful basis for spatially-explicit modelling studies to imitate the complex characteristics of natural landscapes. In chapter 2, the first study of my thesis, I introduce two complementary R packages, NLMR and landscapetools, that I have co-developed to simplify the workflow of simulation and customization of such landscapes. To demonstrate the use of the packages I present a case study using the spatially explicit eco-epidemiological model and show that landscape complexity per se increases the probability of disease persistence. By using simple rules to simulate explicit host movement, I highlight in chapter 3 how disease dynamics are affected by population-level properties emerging from different movement rules leading to differences in the realized movement distance, spatiotemporal host density, and heterogeneity in transmission rates. As a consequence, mechanistic movement decisions based on the underlying landscape or conspecific competition led to considerably higher probabilities than phenomenological random walk approaches due directed movement leading to spatiotemporal differences in host densities. The results of these two chapters highlight the need to explicitly consider spatial heterogeneity and host movement behaviour when theoretical approaches are used to assess control measures to prevent outbreaks or eradicate diseases. In the empirical part of my thesis (chapter 4), I focus on the spatiotemporal dynamics of Classical Swine Fever in a wild boar population by analysing epidemiological data that was collected during an outbreak in Northern Germany persisting for eight years. I show that infection risk exhibits different seasonal patterns on the individual and the regional level. These patterns on the one hand show a higher infection risk in autumn and winter that may arise due to onset of mating behaviour and hunting intensity, which result in increased movement ranges. On the other hand, the increased infection risk of piglets, especially during the birth season, indicates the importance of new susceptible host individuals for local pathogen spread. The findings of this chapter underline the importance of different spatial and temporal scales to understand different components of pathogen spread that can have important implications for disease management. Taken together, the complementary use of theoretical and empirical modelling in my thesis highlights that our inferences about disease dynamics depend heavily on the spatial and temporal resolution used and how the inclusion of explicit mechanisms underlying hosts movement are modelled. My findings are an important step towards the incorporation of spatial heterogeneity and a mechanism-based perspective in eco-epidemiological approaches. This will ultimately lead to an enhanced understanding of the feedbacks of contact rates on pathogen spread and disease persistence that are of paramount importance to improve predictive models at the interface of ecology and epidemiology.},
  language  = {en}
}
@article{LangaryNikoloski2019,
  author    = {Langary, Damoun and Nikoloski, Zoran},
  title     = {Inference of chemical reaction networks based on concentration profiles using an optimization framework},
  series = {Chaos : an interdisciplinary journal of nonlinear science},
  volume    = {29},
  journal   = {Chaos : an interdisciplinary journal of nonlinear science},
  number    = {11},
  publisher = {American Institute of Physics},
  address   = {Melville},
  issn      = {1054-1500},
  doi       = {10.1063/1.5120598},
  pages     = {12},
  year      = {2019},
  abstract  = {Understanding the structure of reaction networks along with the underlying kinetics that lead to particular concentration readouts of the participating components is the first step toward optimization and control of (bio-)chemical processes. Yet, solutions to the problem of inferring the structure of reaction networks, i.e., characterizing the stoichiometry of the participating reactions provided concentration profiles of the participating components, remain elusive. Here, we present an approach to infer the stoichiometric subspace of a chemical reaction network from steady-state concentration data profiles obtained from a continuous isothermal reactor. The subsequent problem of finding reactions consistent with the observed subspace is cast as a series of mixed-integer linear programs whose solution generates potential reaction vectors together with a measure of their likelihood. We demonstrate the efficiency and applicability of the proposed approach using data obtained from synthetic reaction networks and from a well-established biological model for the Calvin-Benson cycle. Furthermore, we investigate the effect of missing information, in the form of unmeasured species or insufficient diversity within the data set, on the ability to accurately reconstruct the network reactions. The proposed framework is, in principle, applicable to many other reaction systems, thus providing future extensions to understanding reaction networks guiding chemical reactors and complex biological mixtures. (C) 2019 Author(s).},
  language  = {en}
}