@article{DeLombaerdeVerheyenPerringetal.2018, author = {De Lombaerde, Emiel and Verheyen, Kris and Perring, Michael P. and Bernhardt-Roemermann, Markus and Van Calster, Hans and Brunet, Jorg and Chudomelova, Marketa and Decocq, Guillaume and Diekmann, Martin and Durak, Tomasz and Hedl, Radim and Heinken, Thilo and Hommel, Patrick and Jaroszewicz, Bogdan and Kopecky, Martin and Lenoir, Jonathan and Macek, Martin and M{\´a}liš, František and Mitchell, Fraser J. G. and Naaf, Tobias and Newman, Miles and Petř{\´i}k, Petr and Reczyńska, Kamila and Schmidt, Wolfgang and Swierkosz, Krzysztof and Vild, Ondrej and Wulf, Monika and Baetena, Lander}, title = {Responses of competitive understorey species to spatial environmental gradients inaccurately explain temporal changes}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {30}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, publisher = {Elsevier GMBH}, address = {M{\"u}nchen}, issn = {1439-1791}, doi = {10.1016/j.baae.2018.05.013}, pages = {52 -- 64}, year = {2018}, abstract = {Understorey plant communities play a key role in the functioning of forest ecosystems. Under favourable environmental conditions, competitive understorey species may develop high abundances and influence important ecosystem processes such as tree regeneration. Thus, understanding and predicting the response of competitive understorey species as a function of changing environmental conditions is important for forest managers. In the absence of sufficient temporal data to quantify actual vegetation changes, space-for-time (SFT) substitution is often used, i.e. studies that use environmental gradients across space to infer vegetation responses to environmental change over time. Here we assess the validity of such SFT approaches and analysed 36 resurvey studies from ancient forests with low levels of recent disturbances across temperate Europe to assess how six competitive understorey plant species respond to gradients of overstorey cover, soil conditions, atmospheric N deposition and climatic conditions over space and time. The combination of historical and contemporary surveys allows (i) to test if observed contemporary patterns across space are consistent at the time of the historical survey, and, crucially, (ii) to assess whether changes in abundance over time given recorded environmental change match expectations from patterns recorded along environmental gradients in space. We found consistent spatial relationships at the two periods: local variation in soil variables and overstorey cover were the best predictors of individual species' cover while interregional variation in coarse-scale variables, i.e. N deposition and climate, was less important. However, we found that our SFT approach could not accurately explain the large variation in abundance changes over time. We thus recommend to be cautious when using SFT substitution to infer species responses to temporal changes.}, language = {en} } @article{MuhlRoelkeZoharyetal.2018, author = {Muhl, Rika M. W. and Roelke, Daniel L. and Zohary, Tamar and Moustaka-Gouni, Maria and Sommer, Ulrich and Borics, Gabor and Gaedke, Ursula and Withrow, Frances G. and Bhattacharyya, Joydeb}, title = {Resisting annihilation}, series = {Ecology letters}, volume = {21}, journal = {Ecology letters}, number = {9}, publisher = {Wiley}, address = {Hoboken}, issn = {1461-023X}, doi = {10.1111/ele.13109}, pages = {1390 -- 1400}, year = {2018}, abstract = {Allelopathic species can alter biodiversity. Using simulated assemblages that are characterised by neutrality, lumpy coexistence and intransitivity, we explore relationships between within-assemblage competitive dissimilarities and resistance to allelopathic species. An emergent behaviour from our models is that assemblages are more resistant to allelopathy when members strongly compete exploitatively (high competitive power). We found that neutral assemblages were the most vulnerable to allelopathic species, followed by lumpy and then by intransitive assemblages. We find support for our modeling in real-world time-series data from eight lakes of varied morphometry and trophic state. Our analysis of this data shows that a lake's history of allelopathic phytoplankton species biovolume density and dominance is related to the number of species clusters occurring in the plankton assemblages of those lakes, an emergent trend similar to that of our modeling. We suggest that an assemblage's competitive power determines its allelopathy resistance.}, language = {en} } @article{KlauschiesCoutinhoGaedke2018, author = {Klauschies, Toni and Coutinho, Renato Mendes and Gaedke, Ursula}, title = {A beta distribution-based moment closure enhances the reliability of trait-based aggregate models for natural populations and communities}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {381}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2018.02.001}, pages = {46 -- 77}, year = {2018}, abstract = {Ecological communities are complex adaptive systems that exhibit remarkable feedbacks between their biomass and trait dynamics. Trait-based aggregate models cope with this complexity by focusing on the temporal development of the community's aggregate properties such as its total biomass, mean trait and trait variance. They are based on particular assumptions about the shape of the underlying trait distribution, which is commonly assumed to be normal. However, ecologically important traits are usually restricted to a finite range, and empirical trait distributions are often skewed or multimodal. As a result, normal distribution-based aggregate models may fail to adequately represent the biomass and trait dynamics of natural communities. We resolve this mismatch by developing a new moment closure approach assuming the trait values to be beta-distributed. We show that the beta distribution captures important shape properties of both observed and simulated trait distributions, which cannot be captured by a Gaussian. We further demonstrate that a beta distribution-based moment closure can strongly enhance the reliability of trait-based aggregate models. We compare the biomass, mean trait and variance dynamics of a full trait distribution (FD) model to the ones of beta (BA) and normal (NA) distribution-based aggregate models, under different selection regimes. This way, we demonstrate under which general conditions (stabilizing, fluctuating or disruptive selection) different aggregate models are reliable tools. All three models predicted very similar biomass and trait dynamics under stabilizing selection yielding unimodal trait distributions with small standing trait variation. We also obtained an almost perfect match between the results of the FD and BA models under fluctuating selection, promoting skewed trait distributions and ongoing oscillations in the biomass and trait dynamics. In contrast, the NA model showed unrealistic trait dynamics and exhibited different alternative stable states, and thus a high sensitivity to initial conditions under fluctuating selection. Under disruptive selection, both aggregate models failed to reproduce the results of the FD model with the mean trait values remaining within their ecologically feasible ranges in the BA model but not in the NA model. Overall, a beta distribution-based moment closure strongly improved the realism of trait-based aggregate models.}, language = {en} } @article{OprzeskaZingrebeMeyerRoloffetal.2018, author = {Oprzeska-Zingrebe, Ewa Anna and Meyer, Susann and Roloff, Alexander and Kunte, Hans-J{\"o}rg and Smiatek, Jens}, title = {Influence of compatible solute ectoine on distinct DNA structures}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {20}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {40}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c8cp03543a}, pages = {25861 -- 25874}, year = {2018}, abstract = {In nature, the cellular environment of DNA includes not only water and ions, but also other components and co-solutes, which can exert both stabilizing and destabilizing effects on particular oligonucleotide conformations. Among them, ectoine, known as an important osmoprotectant organic co-solute in a broad range of pharmaceutical products, turns out to be of particular relevance. In this article, we study the influence of ectoine on a short single-stranded DNA fragment and on double-stranded helical B-DNA in aqueous solution by means of atomistic molecular dynamics (MD) simulations in combination with molecular theories of solution. Our results demonstrate a conformation-dependent binding behavior of ectoine, which favors the unfolded state of DNA by a combination of electrostatic and dispersion interactions. In conjunction with the Kirkwood-Buff theory, we introduce a simple framework to compute the influence of ectoine on the DNA melting temperature. Our findings reveal a significant linear decrease of the melting temperature with increasing ectoine concentration, which is found to be in qualitative agreement with results from denaturation experiments. The outcomes of our computer simulations provide a detailed mechanistic rationale for the surprising destabilizing influence of ectoine on distinct DNA structures.}, language = {en} } @misc{RandallJuengelRimannetal.2018, author = {Randall, Matthew J. and J{\"u}ngel, Astrid and Rimann, Markus and Wuertz-Kozak, Karin}, title = {Advances in the biofabrication of 3D Skin in vitro}, series = {Frontiers in Bioengineeringand Biotechnology}, volume = {6}, journal = {Frontiers in Bioengineeringand Biotechnology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {2296-4185}, doi = {10.3389/fbioe.2018.00154}, pages = {12}, year = {2018}, abstract = {The relevance for in vitro three-dimensional (3D) tissue culture of skin has been present for almost a century. From using skin biopsies in organ culture, to vascularized organotypic full-thickness reconstructed human skin equivalents, in vitro tissue regeneration of 3D skin has reached a golden era. However, the reconstruction of 3D skin still has room to grow and develop. The need for reproducible methodology, physiological structures and tissue architecture, and perfusable vasculature are only recently becoming a reality, though the addition of more complex structures such as glands and tactile corpuscles require advanced technologies. In this review, we will discuss the current methodology for biofabrication of 3D skin models and highlight the advantages and disadvantages of the existing systems as well as emphasize how new techniques can aid in the production of a truly physiologically relevant skin construct for preclinical innovation.}, language = {en} } @article{JetzschmannYarmanRustametal.2018, author = {Jetzschmann, Katharina J. and Yarman, Aysu and Rustam, L. and Kielb, P. and Urlacher, V. B. and Fischer, A. and Weidinger, I. M. and Wollenberger, Ulla and Scheller, Frieder W.}, title = {Molecular LEGO by domain-imprinting of cytochrome P450 BM3}, series = {Colloids and surfaces : an international journal devoted to fundamental and applied research on colloid and interfacial phenomena in relation to systems of biological origin ; B, Biointerfaces}, volume = {164}, journal = {Colloids and surfaces : an international journal devoted to fundamental and applied research on colloid and interfacial phenomena in relation to systems of biological origin ; B, Biointerfaces}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0927-7765}, doi = {10.1016/j.colsurfb.2018.01.047}, pages = {240 -- 246}, year = {2018}, abstract = {Hypothesis: Electrosynthesis of the MIP nano-film after binding of the separated domains or holocytochrome BM3 via an engineered anchor should result in domain-specific cavities in the polymer layer. Experiments: Both the two domains and the holo P450 BM3 have been bound prior polymer deposition via a N-terminal engineered his6-anchor to the electrode surface. Each step of MIP preparation was characterized by cyclic voltammetry of the redox-marker ferricyanide. Rebinding after template removal was evaluated by quantifying the suppression of the diffusive permeability of the signal for ferricyanide and by the NADH-dependent reduction of cytochrome c by the reductase domain (BMR). Findings: The working hypothesis is verified by the discrimination of the two domains by the respective MIPs: The holoenzyme P450 BM3 was ca. 5.5 times more effectively recognized by the film imprinted with the oxidase domain (BMO) as compared to the BMR-MIP or the non-imprinted polymer (NIP). Obviously, a cavity is formed during the imprinting process around the hiss-tag-anchored BMR which cannot accommodate the broader BMO or the P450 BM3. The affinity of the MIP towards P450 BM3 is comparable with that to the monomer in solution. The hiss-tagged P450 BM3 binds (30 percent) stronger which shows the additive effect of the interaction with the MIP and the binding to the electrode.}, language = {en} } @article{PerringBernhardtRoemermannBaetenetal.2018, author = {Perring, Michael P. and Bernhardt-Roemermann, Markus and Baeten, Lander and Midolo, Gabriele and Blondeel, Haben and Depauw, Leen and Landuyt, Dries and Maes, Sybryn L. and De Lombaerde, Emiel and Caron, Maria Mercedes and Vellend, Mark and Brunet, Joerg and Chudomelova, Marketa and Decocq, Guillaume and Diekmann, Martin and Dirnboeck, Thomas and Doerfler, Inken and Durak, Tomasz and De Frenne, Pieter and Gilliam, Frank S. and Hedl, Radim and Heinken, Thilo and Hommel, Patrick and Jaroszewicz, Bogdan and Kirby, Keith J. and Kopecky, Martin and Lenoir, Jonathan and Li, Daijiang and Malis, Frantisek and Mitchell, Fraser J. G. and Naaf, Tobias and Newman, Miles and Petrik, Petr and Reczynska, Kamila and Schmidt, Wolfgang and Standovar, Tibor and Swierkosz, Krzysztof and Van Calster, Hans and Vild, Ondrej and Wagner, Eva Rosa and Wulf, Monika and Verheyen, Kris}, title = {Global environmental change effects on plant community composition trajectories depend upon management legacies}, series = {Global change biology}, volume = {24}, journal = {Global change biology}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {1354-1013}, doi = {10.1111/gcb.14030}, pages = {1722 -- 1740}, year = {2018}, abstract = {The contemporary state of functional traits and species richness in plant communities depends on legacy effects of past disturbances. Whether temporal responses of community properties to current environmental changes are altered by such legacies is, however, unknown. We expect global environmental changes to interact with land-use legacies given different community trajectories initiated by prior management, and subsequent responses to altered resources and conditions. We tested this expectation for species richness and functional traits using 1814 survey-resurvey plot pairs of understorey communities from 40 European temperate forest datasets, syntheses of management transitions since the year 1800, and a trait database. We also examined how plant community indicators of resources and conditions changed in response to management legacies and environmental change. Community trajectories were clearly influenced by interactions between management legacies from over 200 years ago and environmental change. Importantly, higher rates of nitrogen deposition led to increased species richness and plant height in forests managed less intensively in 1800 (i.e., high forests), and to decreases in forests with a more intensive historical management in 1800 (i.e., coppiced forests). There was evidence that these declines in community variables in formerly coppiced forests were ameliorated by increased rates of temperature change between surveys. Responses were generally apparent regardless of sites' contemporary management classifications, although sometimes the management transition itself, rather than historic or contemporary management types, better explained understorey responses. Main effects of environmental change were rare, although higher rates of precipitation change increased plant height, accompanied by increases in fertility indicator values. Analysis of indicator values suggested the importance of directly characterising resources and conditions to better understand legacy and environmental change effects. Accounting for legacies of past disturbance can reconcile contradictory literature results and appears crucial to anticipating future responses to global environmental change.}, language = {en} } @article{KellerKunzeBommeretal.2018, author = {Keller, Sebastian and Kunze, Cindy and Bommer, Martin and Paetz, Christian and Menezes, Riya C. and Svatos, Ales and Dobbek, Holger and Schubert, Torsten}, title = {Selective Utilization of Benzimidazolyl-Norcobamides as Cofactors by the Tetrachloroethene Reductive Dehalogenase of Sulfurospirillum multivorans}, series = {Journal of bacteriology}, volume = {200}, journal = {Journal of bacteriology}, number = {8}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {0021-9193}, doi = {10.1128/JB.00584-17}, pages = {14}, year = {2018}, abstract = {The organohalide-respiring bacterium Sulfurospirillum multivorans produces a unique cobamide, namely, norpseudo-B-12, which serves as cofactor of the tetrachloroethene (PCE) reductive dehalogenase (PceA). As previously reported, a replacement of the adeninyl moiety, the lower base of the cofactor, by exogenously applied 5,6-dimethylbenzimidazole led to inactive PceA. To explore the general effect of benzimidazoles on the PCE metabolism, the susceptibility of the organism for guided biosynthesis of various singly substituted benzimidazolyl-norcobamides was investigated, and their use as cofactor by PceA was analyzed. Exogenously applied 5-methylbenzimidazole (5-MeBza), 5-hydroxybenzimidazole (5-OHBza), and 5-methoxybenzimidazole (5-OMeBza) were found to be efficiently incorporated as lower bases into norcobamides (NCbas). Structural analysis of the NCbas by nuclear magnetic resonance spectroscopy uncovered a regioselectivity in the utilization of these precursors for NCba biosynthesis. When 5-MeBza was added, a mixture of 5-MeBza-norcobamide and 6-MeBza-norcobamide was formed, and the PceA enzyme activity was affected. In the presence of 5-OHBza, almost exclusively 6-OHBza-norcobamide was produced, while in the presence of 5-OMeBza, predominantly 5-OMeBza-norcobamide was detected. Both NCbas were incorporated into PceA, and no negative effect on the PceA activity was observed. In crystal structures of PceA, both NCbas were bound in the base-off mode with the 6-OHBza and 5-OMeBza lower bases accommodated by the same solvent-exposed hydrophilic pocket that harbors the adenine as the lower base of authentic norpseudo-B-12. In this study, a selective production of different norcobamide isomers containing singly substituted benzimidazoles as lower bases is shown, and unique structural insights into their utilization as co-factors by a cobamide-containing enzyme are provided. IMPORTANCE Guided biosynthesis of norcobamides containing singly substituted benzimidazoles as lower bases by the organohalide-respiring epsilonproteobacterium Sulfurospirillum multivorans is reported. An unprecedented specificity in the formation of norcobamide isomers containing hydroxylated or methoxylated benzimidazoles was observed that implicated a strict regioselectivity of the norcobamide biosynthesis in the organism. In contrast to 5,6-dimethylbenzimidazolyl-norcobamide, the incorporation of singly substituted benzimidazolyl-norcobamides as a cofactor into the tetrachloroethene reductive dehalogenase was not impaired. The enzyme was found to be functional with different isomers and not limited to the use of adeninyl-norcobamide. Structural analysis of the enzyme equipped with either adeninyl-or benzimidazolyl-norcobamide cofactors visualized for the first time structurally different cobamides bound in base-off conformation to the cofactor-binding site of a cobamide-containing enzyme.}, language = {en} } @article{HilongaOtienoGhorbanietal.2018, author = {Hilonga, S. and Otieno, Joseph N. and Ghorbani, Abdolbaset and Pereus, D. and Kocyan, Alexander and de Boer, H.}, title = {Trade of wild-harvested medicinal plant species in local markets of Tanzania and its implications for conservation}, series = {South African journal of botany : an international interdisciplinary journal for botanical sciences}, volume = {122}, journal = {South African journal of botany : an international interdisciplinary journal for botanical sciences}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0254-6299}, doi = {10.1016/j.sajb.2018.08.012}, pages = {214 -- 224}, year = {2018}, abstract = {In Tanzania, about 10\% of the reported 12,000 species of higher plants are estimated to be used as medicine for treating different human health problems. Most of the medicinal plants are collected from wild populations, but their trade and quantities are not properly recorded. Monitoring of trade in wild-harvested medicinal plants is challenging asmostmaterials are traded in various processed forms and most vendors practice informal trade. Yet, monitoring is important for conservation and sustainability. This study aims to assess the trade of wild-harvested medicinal plant species in local markets of Tanzania and its implications for conservation. Semi-structured interviews were used to record frequency, volume of trade and uses of wild-harvested medicinal plants in Arusha, Dodoma, Mbeya, Morogoro and Mwanza regions. Relative frequency of citation and informant consensus factor were calculated for each species and mentioned use category. Forty vendors were interviewed, and 400 out of 522 collected market samples were identified to 162 species from herbarium-deposited collections. Plant parts with the largest volume of trade were roots (3818 kg), bark (1163 kg) and leaves (492 kg). The most frequently traded species were Zanthoxylum chalybaeum Engl., Albizia anthelmintica Brongn., Zanha africana (Radlk.) Exell, Warburgia stuhlmannii and Vachellia nilotica (L.) P.J.H. Hurter \& Mabb. The most popular medicinal plants in the markets are connected to local health problems including malaria, libido disorders or infertility. The high diversity of commercialized plants used for medicinal issues mainly relies on wild stock for local consumption and international trade, and this has significant implications for conservation concerns. (C) 2018 SAAB. Published by Elsevier B.V. All rights reserved.}, language = {en} } @article{PereusOtienoGhorbanietal.2018, author = {Pereus, D. and Otieno, J. N. and Ghorbani, Abdolbaset and Kocyan, Alexander and Hilonga, S. and de Boer, H. J.}, title = {Diversity of Hypoxis species used in ethnomedicine in Tanzania}, series = {South African journal of botany : an international interdisciplinary journal for botanical sciences}, volume = {122}, journal = {South African journal of botany : an international interdisciplinary journal for botanical sciences}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0254-6299}, doi = {10.1016/j.sajb.2018.03.004}, pages = {336 -- 341}, year = {2018}, abstract = {The corms of different Hypoxis species (Hypoxidaceae) are used for the treatment and management of a variety of human ailments and disorders in African traditional medicine. However, the used corms are morphologically similar and it is not known whether this has resulted in different species being harvested, prescribed and sold as the same species. Ethnomedicinal information regarding its use in Tanzania is scanty and the available ethnobotanical information about the plants is mostly from various studies done outside Tanzania. The objective of the study was to document the diverse uses of Hypoxis in Tanzania and study what species are used and whether preferences exist for specific species. Focus group discussions and in depth interviews with informants were done in 15 regions of Tanzania to document local uses of Hypoxis species and collect vouchers for identification. Traditional practitioners use Hypoxis to manage a variety of human illness in Tanzania, and appear to use different species indiscriminately for medicine, socio-cultural applications and for food. Medicinal uses include treatment of benign prostate hypertrophy, cancer, diabetes, gout, headache, HIV/AIDS, infertility, ringworms, stomachache, and urinary tract infections. In Tanzania, different Hypoxis species are used indiscriminately for a range of sociocultural and medicinal purposes. The reported medicinal uses could aid testing and evaluation of traditional herbal medicine and more research is needed to test their pharmacological effects. (C) 2018 SAAB. Published by Elsevier B.V. All rights reserved.}, language = {en} } @article{PratHajnyGrunewaldetal.2018, author = {Prat, Tomas and Hajny, Jakub and Grunewald, Wim and Vasileva, Mina and Molnar, Gergely and Tejos, Ricardo and Schmid, Markus and Sauer, Michael and Friml, Jiř{\´i}}, title = {WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity}, series = {PLoS Genetics : a peer-reviewed, open-access journal}, volume = {14}, journal = {PLoS Genetics : a peer-reviewed, open-access journal}, number = {1}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1007177}, pages = {18}, year = {2018}, abstract = {Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17-and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain-and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development.}, language = {en} } @article{LuReichetzederPrehnetal.2018, author = {Lu, Yong-Ping and Reichetzeder, Christoph and Prehn, Cornelia and von Websky, Karoline and Slowinski, Torsten and Chen, You-Peng and Yin, Liang-Hong and Kleuser, Burkhard and Yang, Xue-Song and Adamski, Jerzy and Hocher, Berthold}, title = {Fetal serum metabolites are independently associated with Gestational diabetes mellitus}, series = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, volume = {45}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, number = {2}, publisher = {Karger}, address = {Basel}, issn = {1015-8987}, doi = {10.1159/000487119}, pages = {625 -- 638}, year = {2018}, abstract = {Background/Aims: Gestational diabetes (GDM) might be associated with alterations in the metabolomic profile of affected mothers and their offspring. Until now, there is a paucity of studies that investigated both, the maternal and the fetal serum metabolome in the setting of GDM. Mounting evidence suggests that the fetus is not just passively affected by gestational disease but might play an active role in it. Metabolomic studies performed in maternal blood and fetal cord blood could help to better discern distinct fetal from maternal disease interactions. Methods: At the time of birth, serum samples from mothers and newborns (cord blood samples) were collected and screened for 163 metabolites utilizing tandem mass spectrometry. The cohort consisted of 412 mother/child pairs, including 31 cases of maternal GDM. Results: An initial non-adjusted analysis showed that eight metabolites in the maternal blood and 54 metabolites in the cord blood were associated with GDM. After Benjamini-Hochberg (BH) procedure and adjustment for confounding factors for GDM, fetal phosphatidylcholine acyl-alkyl C 32:1 and proline still showed an independent association with GDM. Conclusions: This study found metabolites in cord blood which were associated with GDM, even after adjustment for established risk factors of GDM. To the best of our knowledge, this is the first study demonstrating an independent association between fetal serum metabolites and maternal GDM. Our findings might suggest a potential effect of the fetal metabolome on maternal GDM. (c) 2018 The Author(s) Published by S. Karger AG, Basel}, language = {en} } @article{GeigerKocyan2018, author = {Geiger, Daniel L. and Kocyan, Alexander}, title = {Studies on Oberonia 3. Aberrant flowers and other floral modifications in the orchid genus Oberonia}, series = {Nordic Journal of botany}, volume = {36}, journal = {Nordic Journal of botany}, number = {1-2}, publisher = {Wiley}, address = {Hoboken}, issn = {0107-055X}, doi = {10.1111/njb.01699}, pages = {8}, year = {2018}, abstract = {Orchid flowers are amongst the most conspicuous attractions that plants have generated over evolutionary epochs. However, organ homology in particular of androecium and gynoecium of orchid flowers have been, and are still, the subject of long-term discussion. Studies of aberrant - teratologic - flowers have traditionally helped to clarify organ identity in orchids. We here present for the first time teratological flowers within the florally smallest and inconspicuous orchid genus Oberonia and illustrate them by light and scanning electron microscopy. Pseudopeloria with half of a lateral petal transformed into a lip was found in O. costeriana J.J.Sm. and O. mucronata (D.Don) Ormerod \& Seidenf. A supernumerary lip is known from O. mucronata. Oberonia rufilabris Lindl. is documented with multiple aberrations: triple gynostemium and a total of 10 tepals, twin flowers, and duplicate lips. We interpret these aberrations in light of known floral developmental and organ identity information.}, language = {en} } @article{TejosRodriguezFurlanAdamowskietal.2018, author = {Tejos, Ricardo and Rodriguez-Furlan, Cecilia and Adamowski, Maciej and Sauer, Michael and Norambuena, Lorena and Friml, Jiri}, title = {PATELLINS are regulators of auxin-mediated PIN1 relocation and plant development in Arabidopsis thaliana}, series = {Journal of cell science}, volume = {131}, journal = {Journal of cell science}, number = {2}, publisher = {Company of Biologists Limited}, address = {Cambridge}, issn = {0021-9533}, doi = {10.1242/jcs.204198}, pages = {10}, year = {2018}, abstract = {Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We used a microarray-based approach to find regulators of the auxin-induced PIN relocation in Arabidopsis thaliana root, and identified a subset of a family of phosphatidylinositol transfer proteins (PITPs), the PATELLINs (PATLs). Here, we show that PATLs are expressed in partially overlapping cell types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests that PATLs play a redundant and crucial role in polarity and patterning in Arabidopsis.}, language = {en} } @article{LukanMachensColletal.2018, author = {Lukan, Tjaša and Machens, Fabian and Coll, Anna and Baebler, Špela and Messerschmidt, Katrin and Gruden, Kristina}, title = {Plant X-tender}, series = {PLOS ONE}, volume = {13}, journal = {PLOS ONE}, number = {1}, publisher = {Public Library of Science}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0190526}, pages = {19}, year = {2018}, abstract = {Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster introduction of synthetic biology into plant science.}, language = {en} } @article{OezerScheffler2018, author = {{\"O}zer, Aydan and Scheffler, Christiane}, title = {Affinity to host population stimulates physical growth in adult offspring of Turkish migrants in Germany}, series = {Journal of biological and clinical anthropology}, volume = {74}, journal = {Journal of biological and clinical anthropology}, number = {5}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/anthranz/2018/0825}, pages = {359 -- 364}, year = {2018}, abstract = {Because of political conflicts and climate change, migration will be increased worldwide and integration in host societies is a challenge also for migrants. We hypothesize that migrants, who take up the challenge in a new social environment are taller than migrants who do not pose this challenge. We analyze by a questionnaire possible social, nutritional and ethnic influencing factors to body height (BH) of adult offspring of Turkish migrants (n = 82, 39 males) aged from 18 to 34 years (mean age 24.6 years). The results of multiple regression (downward selection) show that the more a male adult offspring of Turkish migrants feels like belonging to the Turkish culture, the smaller he is (95\% CI, -3.79, -0.323). Further, the more a male adult offspring of Turkish migrants feels like belonging to the German culture, the taller he is (95\% CI, -0.152, 1.738). We discussed it comparable to primates taking up their challenge in dominance, where as a result their body size increase is associated with higher IGF-1 level. IGF-1 is associated with emotional belonging and has a fundamental role in the regulation of metabolism and growth of the human body. With all pilot characteristics of our study results show that the successful challenge of integration in a new society is strongly associated with the emotional integration and identification in the sense of a personal sense of belonging to society. We discuss taller BH as a signal of social growth adjustment. In this sense, a secular trend of BH adaptation of migrants to hosts is a sign of integration.}, language = {en} } @article{BentsGrothSatake2018, author = {Bents, Dominik and Groth, Detlef and Satake, Takashi}, title = {The secular trend and network effects on height of male Japanese students from 1955 to 2015}, series = {Journal of biological and clinical anthropology}, volume = {74}, journal = {Journal of biological and clinical anthropology}, number = {5}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/anthranz/2018/0838}, pages = {423 -- 429}, year = {2018}, abstract = {Introduction: Body height is influenced by biological factors such as genetics, nutrition and health, but also by the social network, and environmental and economical factors. During centuries, the Japanese society has developed on islands. This setting provides ideal natural conditions for studying the influence of social networks on human height. Material and methods: We investigated body height of male Japanese students aged 17.5 years obtained in 47 prefectures, from the Japanese school health survey of the years 1955, 1975, 1995, and 2015. Results: Japanese students increased in height from 163.23 cm in 1955 to 170.84 cm in 1995, with no further increase thereafter (170.63 cm in 2015). Students living in neighboring prefectures were similar in height. The correlation of height between neighboring prefectures ranged between r = 0.79 and r = 0.49 among first degree neighbors, between r = 0.49 and r = 0.21 among second degree neighbors and dropped to insignificance among third degree neighbors indicating psychosocial effects of the community on body height. Tall stature and short stature prefectures did not remain tall or short throughout history. Autocorrelations of height within the same prefectures decreased from the 20 years periods of 1955-1975, 1975-1995 and 1995-2015 (r = 0.52, r = 0.61, r = 0.63, respectively) to the 40 years periods of 1955-1995 and 1975-2015 (r = 0.49, r = 0.52), down to the 60 years period of 1955-2015 (r = 0.27), indicating significant volatility of height. Conclusion: Body height of 17.5 years old Japanese students increased since 1955. Body height depended on height of the neighboring prefecture, but was volatile with decreasing autocorrelation during a period of 60 years.}, language = {en} } @article{LiuGroth2018, author = {Liu, Yuk-Chien and Groth, Detlef}, title = {Body height, social dominance and the political climate}, series = {Journal of biological and clinical anthropology}, volume = {74}, journal = {Journal of biological and clinical anthropology}, number = {5}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/anthranz/2018/0855}, pages = {445 -- 450}, year = {2018}, abstract = {Background: The association between stature and social dominance is known. Dominance within social groups and current politics are related issues. We therefore aimed to compare estimates of the opinion of a population about their current political issues, with physical growth. Material and methods: We used data on the 2012 and the 2014 elections for the Japanese House of Representatives and the percent proportion of votes of the 47 prefectures of Japan, and regional data on body height of 17.5 year old men and women. Information on capita income, possession of mobile phones, urban/rural population ratio, and age distribution were added to capture socioeconomic factors. Four political parties were present in most of the 47 prefectures: the Liberal Democratic Party (LDP), the Democratic Party of Japan (DPJ), the New Komeito Party (Kom) that is known for their social network community, and the Japanese Communist Party (JCP). Results: A dense network of associations exists between height, age distribution, per capita income, number of smartphones, and voting results. Male and female body height was inversely related with the proportion of votes for New Komeito Party. Average stature decreases by one mm per percent votes for this political party. Medium strong positive associations were found for male body height and voting results of the DPJ and for female body height with the JCP election results. Conclusion: In modern Japan, popular preferences for conservative political structures coincide with shorter stature.}, language = {en} } @article{TischewDierschkeSchwabeetal.2018, author = {Tischew, Sabine and Dierschke, Hartmut and Schwabe, Angelika and Garve, Eckhard and Heinken, Thilo and Holzel, Norbert and Bergmeier, Erwin and Remy, Dominique and Haerdtle, Werner}, title = {Pflanzengesellschaft des Jahres 2019: Die Glatthaferwiese}, series = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, journal = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, number = {38}, publisher = {Floristisch-Soziologische Arbeitsgemeinschaft}, address = {G{\"o}ttingen}, issn = {0722-494X}, doi = {10.14471/2018.38.011}, pages = {287 -- 295}, year = {2018}, abstract = {Um Themen des Schutzes von Pflanzengemeinschaften wirksamer in der breiten {\"O}ffentlichkeit zu kommunizieren wird der Vorstand der „Floristisch-Soziologischen Arbeitsgemeinschaft (FlorSoz)" ab 2019 eine „Pflanzengesellschaft des Jahres" ausrufen. Damit sollen politische und administrative Entscheidungs- und Umsetzungsprozesse zur Erhaltung der Vielfalt von {\"O}kosystemen und Pflanzengesellschaften in Deutschlands gezielt unterst{\"u}tzt werden. F{\"u}r das Jahr 2019 wurde die Glatthaferwiese ausgew{\"a}hlt. Sie z{\"a}hlt aktuell zu den durch Artenverarmung und Fl{\"a}chenr{\"u}ckgang besonders bedrohten Pflanzengesellschaften Deutschlands. Es sind deshalb dringend Maßnahmen zum Schutz und zur Wiederherstellung notwendig. Dieser Artikel gibt einen kurzen {\"U}berblick zur naturschutzfachlichen Bedeutung von Glatthaferwiesen und deren {\"O}kosystemleistungen sowie zur floristisch-soziologischen Erforschung, zu Ursachen ihres R{\"u}ckgangs und zu geeigneten Gegenmaßnahmen.}, language = {de} } @article{ZhaoXiaWuetal.2018, author = {Zhao, Liming and Xia, Yan and Wu, Xiao-Yuan and Schippers, Jos H. M. and Jing, Hai-Chun}, title = {Phenotypic analysis and molecular markers of leaf senescence}, series = {Plant Senescence: Methods and Protocols}, volume = {1744}, journal = {Plant Senescence: Methods and Protocols}, publisher = {Humana Press Inc.}, address = {Totowa}, isbn = {978-1-4939-7672-0}, issn = {1064-3745}, doi = {10.1007/978-1-4939-7672-0_3}, pages = {35 -- 48}, year = {2018}, abstract = {The process of leaf senescence consists of the final stage of leaf development. It has evolved as a mechanism to degrade macromolecules and micronutrients and remobilize them to other developing parts of the plant; hence it plays a central role for the survival of plants and crop production. During senescence, a range of physiological, morphological, cellular, and molecular events occur, which are generally referred to as the senescence syndrome that includes several hallmarks such as visible yellowing, loss of chlorophyll and water content, increase of ion leakage and cell death, deformation of chloroplast and cell structure, as well as the upregulation of thousands of so-called senescence-associated genes (SAGs) and downregulation of photosynthesis-associated genes (PAGs). This chapter is devoted to methods characterizing the onset and progression of leaf senescence at the morphological, physiological, cellular, and molecular levels. Leaf senescence normally progresses in an age-dependent manner but is also induced prematurely by a variety of environmental stresses in plants. Focused on the hallmarks of the senescence syndrome, a series of protocols is described to asses quantitatively the senescence process caused by developmental cues or environmental perturbations. We first briefly describe the senescence process, the events associated with the senescence syndrome, and the theories and methods to phenotype senescence. Detailed protocols for monitoring senescence in planta and in vitro, using the whole plant and the detached leaf, respectively, are presented. For convenience, most of the protocols use the model plant species Arabidopsis and rice, but they can be easily extended to other plants.}, language = {en} } @article{SolovyevPrakashBhatiaetal.2018, author = {Solovyev, Nikolay and Prakash, N. Tejo and Bhatia, Poonam and Prakash, Ranjana and Drobyshev, Evgenii J. and Michalke, Bernhard}, title = {Selenium-rich mushrooms cultivation on a wheat straw substrate from seleniferous area in Punjab, India}, series = {Journal of trace elements in medicine and biology}, volume = {50}, journal = {Journal of trace elements in medicine and biology}, publisher = {Elsevier}, address = {Jena}, issn = {0946-672X}, doi = {10.1016/j.jtemb.2018.07.027}, pages = {362 -- 366}, year = {2018}, abstract = {Intensive rice-wheat cultivation cycle in Northern belt of India in general and in the State of Punjab in particular results in large volumes of straw and other post-harvest residue annually. The agricultural area, bordering the districts of Nawanshahr and Hoshiarpur, is popularly known as the seleniferous belt of India. The agri-residues, generated in seleniferous region of this state, are observed to contain significantly high concentration of selenium (Se). The present study was aimed to evaluate the Se uptake by different mushroom species: Pleurotus sajorcaju, Pleurotus ostreatus, Pleurotus citrinopileatus, Agaricus bisporus, and Volvariella volvacea, cultivated on Se-rich wheat and paddy straw from the seleniferous region. Wheat (Pleurotus species and A. bisporus) and paddy straw (V. volvacea) was inoculated with the mycelium spawn and left for 7-20 days, depending on the species, to grow. Control mushrooms were grown analogously using the agricultural residues from non-seleniferous area of the State of Punjab. All fruiting bodies were collected and analyzed in triplicate. Se was quantified using inductively coupled plasma sector field mass spectrometry. The Se accumulation was high in all species under study, being the highest in A. bisporus (1396 mu g/g vs. 46.8 mu g/g in controls - dry weight) and V. volvacea (231 mu g/g vs. 3.77 mu g/g - dry weight). The observed biological efficiency and total yield for all mushroom species showed good and unaltered productivity in Se-rich conditions, if compared to the controls. The Se-rich mushrooms can be prospective Se-supplements sourcing and biofortified foods, providing readily bioavailable and accessible Se for the diets deficient of this biologically essential element.}, language = {en} } @article{PerillonvandeWeyerPaezoltetal.2018, author = {Perillon, Cecile and van de Weyer, Klaus and P{\"a}zolt, Jens and Kasprzak, Peter and Hilt, Sabine}, title = {Changes in submerged macrophyte colonization in shallow areas of an oligo-mesotrophic lake and the potential role of groundwater}, series = {Limnologica : ecology and management of inland waters}, volume = {68}, journal = {Limnologica : ecology and management of inland waters}, publisher = {Elsevier}, address = {Jena}, issn = {0075-9511}, doi = {10.1016/j.limno.2017.03.002}, pages = {168 -- 176}, year = {2018}, abstract = {Groundwater influx can significantly contribute to nutrient budgets of lakes and its influence is strongest in shallow littoral areas. In oligo-or mesotrophic systems, additional nutrient supply by groundwater influx may affect benthic primary producers and their interactions. Potential changes can be expected in community composition, biomass, stoichiometry and interactions between submerged macrophytes and epiphyton.}, language = {en} } @article{KoloraWeigertSaffarietal.2018, author = {Kolora, Sree Rohit Raj and Weigert, Anne and Saffari, Amin and Kehr, Stephanie and Walter Costa, Maria Beatriz and Spr{\"o}er, Cathrin and Indrischek, Henrike and Chintalapati, Manjusha and Lohse, Konrad and Doose, Gero and Overmann, J{\"o}rg and Bunk, Boyke and Bleidorn, Christoph and Grimm-Seyfarth, Annegret and Henle, Klaus and Nowick, Katja and Faria, Rui and Stadler, Peter F. and Schlegel, Martin}, title = {Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation}, series = {GigaScience}, volume = {8}, journal = {GigaScience}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {2047-217X}, doi = {10.1093/gigascience/giy160}, pages = {15}, year = {2018}, abstract = {Background Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. Findings Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. Conclusion The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.}, language = {en} } @article{VannesteValdesVerheyenetal.2018, author = {Vanneste, Thomas and Valdes, Alicia and Verheyen, Kris and Perring, Michael P. and Bernhardt-Roemermann, Markus and Andrieu, Emilie and Brunet, Jorg and Cousins, Sara A. O. and Deconchat, Marc and De Smedt, Pallieter and Diekmann, Martin and Ehrmann, Steffen and Heinken, Thilo and Hermy, Martin and Kolb, Annette and Lenoir, Jonathan and Liira, Jaan and Naaf, Tobias and Paal, Taavi and Wulf, Monika and Decocq, Guillaume and De Frenne, Pieter}, title = {Functional trait variation of forest understorey plant communities across Europe}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {34}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, publisher = {Elsevier GmbH}, address = {M{\"u}nchen}, issn = {1439-1791}, doi = {10.1016/j.baae.2018.09.004}, pages = {1 -- 14}, year = {2018}, abstract = {Global environmental changes are expected to alter the functional characteristics of understorey herb-layer communities, potentially affecting forest ecosystem functioning. However, little is known about what drives the variability of functional traits in forest understories. Here, we assessed the role of different environmental drivers in shaping the functional trait distribution of understorey herbs in fragmented forests across three spatial scales. We focused on 708 small, deciduous forest patches located in 16 agricultural landscape windows, spanning a 2500-km macroclimatic gradient across the temperate forest biome in Europe. We estimated the relative effect of patch-scale, landscape-scale and macroclimatic variables on the community mean and variation of plant height, specific leaf area and seed mass. Macroclimatic variables (monthly temperature and precipitation extremes) explained the largest proportion of variation in community trait means (on average 77\% of the explained variation). In contrast, patch-scale factors dominated in explaining community trait variation (on average 68\% of the explained variation). Notably, patch age, size and internal heterogeneity had a positive effect on the community-level variability. Landscape-scale variables explained only a minor part of the variation in both trait distribution properties. The variation explained by shared combinations of the variable groups was generally negligible. These findings highlight the importance of considering multiple spatial scales in predictions of environmental-change effects on the functionality of forest understories. We propose that forest management sustainability could benefit from conserving larger, historically continuous and internally heterogeneous forest patches to maximise ecosystem service diversity in rural landscapes. (C) 2018 Gesellschaft fur Okologie. Published by Elsevier GmbH. All rights reserved.}, language = {en} } @article{ZhivkovaKieckerLangeretal.2018, author = {Zhivkova, Veselina and Kiecker, Felix and Langer, Peter and Eberle, J{\"u}rgen}, title = {Crucial role of reactive oxygen species (ROS) for the proapoptotic effects of indirubin derivative DKP-073 in melanoma cells}, series = {Molecular carcinogenesis}, volume = {58}, journal = {Molecular carcinogenesis}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {0899-1987}, doi = {10.1002/mc.22924}, pages = {258 -- 269}, year = {2018}, abstract = {Melanoma represents a prime example demonstrating the success of targeted therapy in cancer. Nevertheless, it remained a deadly disease until now, and the identification of new, independent strategies as well as the understanding of their molecular mechanisms may help to finally overcome the high mortality. Both indirubins and TNF-related apoptosis-inducing ligand (TRAIL) represent promising candidates. Here, the indirubin derivative DKP-073 is shown to trigger apoptosis in melanoma cells, which is enhanced by the combination with TRAIL and is accompanied by complete loss of cell viability. Addressing the signaling cascade, characteristic molecular steps were identified as caspase-3 activation, downregulation of XIAP, upregulation of p53 and TRAIL receptor 2, loss of mitochondrial membrane potential, and STAT-3 dephosphorylation. The decisive step, however, turned out to be the early production of ROS already at 1 h. This was proven by antioxidant pretreatment, which completely abolished apoptosis induction and loss of cell viability as well as abrogated all signaling effects listed above. Thus, ROS appeared as upstream of all proapoptotic signaling. The data indicate a dominant role of ROS in apoptosis regulation, and the new pathway may expose a possible Achilles heel of melanoma.}, language = {en} } @article{BurschelDecovicNuberetal.2018, author = {Burschel, Sabrina and Decovic, Doris Kreuzer and Nuber, Franziska and Stiller, Marie and Hofmann, Maud and Zupok, Arkadiusz and Siemiatkowska, Beata and Gorka, Michal Jakub and Leimk{\"u}hler, Silke and Friedrich, Thorsten}, title = {Iron-sulfur cluster carrier proteins involved in the assembly of Escherichia coli NADH}, series = {Molecular microbiology}, volume = {111}, journal = {Molecular microbiology}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {0950-382X}, doi = {10.1111/mmi.14137}, pages = {31 -- 45}, year = {2018}, abstract = {The NADH:ubiquinone oxidoreductase (respiratory complex I) is the main entry point for electrons into the Escherichia coli aerobic respiratory chain. With its sophisticated setup of 13 different subunits and 10 cofactors, it is anticipated that various chaperones are needed for its proper maturation. However, very little is known about the assembly of E. coli complex I, especially concerning the incorporation of the iron-sulfur clusters. To identify iron-sulfur cluster carrier proteins possibly involved in the process, we generated knockout strains of NfuA, BolA, YajL, Mrp, GrxD and IbaG that have been reported either to be involved in the maturation of mitochondrial complex I or to exert influence on the clusters of bacterial complex. We determined the NADH and succinate oxidase activities of membranes from the mutant strains to monitor the specificity of the individual mutations for complex I. The deletion of NfuA, BolA and Mrp led to a decreased stability and partially disturbed assembly of the complex as determined by sucrose gradient centrifugation and native PAGE. EPR spectroscopy of cytoplasmic membranes revealed that the BolA deletion results in the loss of the binuclear Fe/S cluster N1b.}, language = {en} } @article{PancraceIshidaBriandetal.2018, author = {Pancrace, Claire and Ishida, Keishi and Briand, Enora and Pichi, Douglas Gatte and Weiz, Annika R. and Guljarmow, Arthur and Scalvenzi, Thibault and Sassoon, Nathalie and Hertweck, Christian and Dittmann, Elke and Gugger, Muriel}, title = {Unique Biosynthetic Pathway in Bloom-Forming Cyanobacterial Genus Microcystis Jointly Assembles Cytotoxic Aeruginoguanidines and Microguanidines}, series = {ACS chemical biology}, volume = {14}, journal = {ACS chemical biology}, number = {1}, publisher = {American Chemical Society}, address = {Washington}, issn = {1554-8929}, doi = {10.1021/acschembio.8b00918}, pages = {67 -- 75}, year = {2018}, abstract = {The cyanobacterial genus Microcystis is known to produce an elaborate array of structurally unique and biologically active natural products, including hazardous cyanotoxins. Cytotoxic aeruginoguanidines represent a yet unexplored family of peptides featuring a trisubstituted benzene unit and farnesylated arginine derivatives. In this study, we aimed at assigning these compounds to a biosynthetic gene cluster by utilizing biosynthetic attributes deduced from public genomes of Microcystis and the sporadic distribution of the metabolite in axenic strains of the Pasteur Culture Collection of Cyanobacteria. By integrating genome mining with untargeted metabolomics using liquid chromatography with mass spectrometry, we linked aeruginoguanidine (AGD) to a nonribosomal peptide synthetase gene cluster and coassigned a significantly smaller product to this pathway, microguanidine (MGD), previously only reported from two Microcystis blooms. Further, a new intermediate class of compounds named microguanidine amides was uncovered, thereby further enlarging this compound family. The comparison of structurally divergent AGDs and MGDs reveals an outstanding versatility of this biosynthetic pathway and provides insights into the assembly of the two compound subfamilies. Strikingly, aeruginoguanidines and microguanidines were found to be as widespread as the hepatotoxic microcystins, but the occurrence of both toxin families appeared to be mutually exclusive.}, language = {en} } @article{MittlerBlasiusGaedkeetal.2018, author = {Mittler, Udo and Blasius, Bernd and Gaedke, Ursula and Ryabov, Alexey B.}, title = {Length-volume relationship of lake phytoplankton}, series = {Limnology and Oceanography: Methods}, volume = {17}, journal = {Limnology and Oceanography: Methods}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1541-5856}, doi = {10.1002/lom3.10296}, pages = {58 -- 68}, year = {2018}, abstract = {The shapes of phytoplankton units (unicellular organisms and colonies) are extremely diverse, and no unique relationship exists between their volume, V, and longest linear dimension, L. However, an approximate scaling between these parameters can be found because the shape variations within each size class are constrained by cell physiology, grazing pressure, and optimality of resource acquisition. To determine this scaling and to test for its seasonal and interannual variation under changing environmental conditions, we performed weighted regression analysis of time-dependent length-volume relations of the phytoplankton community in large deep Lake Constance from 1979 to 1999. We show that despite a large variability in species composition, the V(L) relationship can be approximated as a power law, V similar to L-alpha, with a scaling exponent alpha = 3 for small cells (L < 25 mu m) and alpha = 1.7 if the fitting is performed over the entire length range, including individual cells and colonies. The best description is provided by a transitional power function describing a regime change from a scaling exponent of 3 for small cells to an exponent of 0.4 in the range of large phytoplankton. Testing different weighted fitting approaches we show that remarkably the best prediction of the total community biovolume from measurements of L and cell density is obtained when the regression is weighted with the squares of species abundances. Our approach should also be applicable to other systems and allows converting phytoplankton length distributions (e.g., obtained with automatic monitoring such as flow cytometry) into distributions of biovolume and biovolume-related phytoplankton traits.}, language = {en} } @article{vanVelzenThieserBerendonketal.2018, author = {van Velzen, Ellen and Thieser, Tamara and Berendonk, Thomas U. and Weitere, Markus and Gaedke, Ursula}, title = {Inducible defense destabilizes predator-prey dynamics}, series = {Oikos}, volume = {127}, journal = {Oikos}, number = {11}, publisher = {Wiley}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.04868}, pages = {1551 -- 1562}, year = {2018}, abstract = {Phenotypic plasticity in prey can have a dramatic impact on predator-prey dynamics, e.g. by inducible defense against temporally varying levels of predation. Previous work has overwhelmingly shown that this effect is stabilizing: inducible defenses dampen the amplitudes of population oscillations or eliminate them altogether. However, such studies have neglected scenarios where being protected against one predator increases vulnerability to another (incompatible defense). Here we develop a model for such a scenario, using two distinct prey phenotypes and two predator species. Each prey phenotype is defended against one of the predators, and vulnerable to the other. In strong contrast with previous studies on the dynamic effects of plasticity involving a single predator, we find that increasing the level of plasticity consistently destabilizes the system, as measured by the amplitude of oscillations and the coefficients of variation of both total prey and total predator biomasses. We explain this unexpected and seemingly counterintuitive result by showing that plasticity causes synchronization between the two prey phenotypes (and, through this, between the predators), thus increasing the temporal variability in biomass dynamics. These results challenge the common view that plasticity should always have a stabilizing effect on biomass dynamics: adding a single predator-prey interaction to an established model structure gives rise to a system where different mechanisms may be at play, leading to dramatically different outcomes.}, language = {en} } @article{vanKleunenEsslPergletal.2018, author = {van Kleunen, Mark and Essl, Franz and Pergl, Jan and Brundu, Giuseppe and Carboni, Marta and Dullinger, Stefan and Early, Regan and Gonzalez-Moreno, Pablo and Groom, Quentin J. M. and Hulme, Philip E. and Kueffer, Christoph and K{\"u}hn, Ingolf and Maguas, Cristina and Maurel, Noelie and Novoa, Ana and Parepa, Madalin and Pysek, Petr and Seebens, Hanno and Tanner, Rob and Touza, Julia and Verbrugge, Laura and Weber, Ewald and Dawson, Wayne and Kreft, Holger and Weigelt, Patrick and Winter, Marten and Klonner, Guenther and Talluto, Matthew V. and Dehnen-Schmutz, Katharina}, title = {The changing role of ornamental horticulture in alien plant invasions}, series = {Biological reviews}, volume = {93}, journal = {Biological reviews}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {1464-7931}, doi = {10.1111/brv.12402}, pages = {1421 -- 1437}, year = {2018}, abstract = {The number of alien plants escaping from cultivation into native ecosystems is increasing steadily. We provide an overview of the historical, contemporary and potential future roles of ornamental horticulture in plant invasions. We show that currently at least 75\% and 93\% of the global naturalised alien flora is grown in domestic and botanical gardens, respectively. Species grown in gardens also have a larger naturalised range than those that are not. After the Middle Ages, particularly in the 18th and 19th centuries, a global trade network in plants emerged. Since then, cultivated alien species also started to appear in the wild more frequently than non-cultivated aliens globally, particularly during the 19th century. Horticulture still plays a prominent role in current plant introduction, and the monetary value of live-plant imports in different parts of the world is steadily increasing. Historically, botanical gardens - an important component of horticulture - played a major role in displaying, cultivating and distributing new plant discoveries. While the role of botanical gardens in the horticultural supply chain has declined, they are still a significant link, with one-third of institutions involved in retail-plant sales and horticultural research. However, botanical gardens have also become more dependent on commercial nurseries as plant sources, particularly in North America. Plants selected for ornamental purposes are not a random selection of the global flora, and some of the plant characteristics promoted through horticulture, such as fast growth, also promote invasion. Efforts to breed non-invasive plant cultivars are still rare. Socio-economical, technological, and environmental changes will lead to novel patterns of plant introductions and invasion opportunities for the species that are already cultivated. We describe the role that horticulture could play in mediating these changes. We identify current research challenges, and call for more research efforts on the past and current role of horticulture in plant invasions. This is required to develop science-based regulatory frameworks to prevent further plant invasions.}, language = {en} } @article{BeermannWestburyHofreiteretal.2018, author = {Beermann, Jan and Westbury, Michael V. and Hofreiter, Michael and Hilgers, Leon and Deister, Fabian and Neumann, Hermann and Raupach, Michael J.}, title = {Cryptic species in a well-known habitat}, series = {Scientific reports}, volume = {8}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-018-25225-x}, pages = {26}, year = {2018}, abstract = {Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.}, language = {en} } @article{KnebelNeebZahnetal.2018, author = {Knebel, Constanze and Neeb, Jannika and Zahn, Elisabeth and Schmidt, Flavia and Carazo, Alejandro and Holas, Ondej and Pavek, Petr and P{\"u}schel, Gerhard Paul and Zanger, Ulrich M. and S{\"u}ssmuth, Roderich and Lampen, Alfonso and Marx-Stoelting, Philip and Braeuning, Albert}, title = {Unexpected Effects of Propiconazole, Tebuconazole, and Their Mixture on the Receptors CAR and PXR in Human Liver Cells}, series = {Toxicological sciences}, volume = {163}, journal = {Toxicological sciences}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1096-6080}, doi = {10.1093/toxsci/kfy026}, pages = {170 -- 181}, year = {2018}, abstract = {Analyzing mixture toxicity requires an in-depth understanding of the mechanisms of action of its individual components. Substances with the same target organ, same toxic effect and same mode of action (MoA) are believed to cause additive effects, whereas substances with different MoAs are assumed to act independently. Here, we tested 2 triazole fungicides, propiconazole, and tebuconazole (Te), for individual and combined effects on liver toxicity-related endpoints. Both triazoles are proposed to belong to the same cumulative assessment group and are therefore thought to display similar and additive behavior. Our data show that Te is an antagonist of the constitutive androstane receptor (CAR) in rats and humans, while propiconazole is an agonist of this receptor. Both substances activate the pregnane X-receptor (PXR) and further induce mRNA expression of CYP3A4. CYP3A4 enzyme activity, however, is inhibited by propiconazole. For common targets of PXR and CAR, the activation of PXR by Te overrides CAR inhibition. In summary, propiconazole and Te affect different hepatotoxicity-relevant cellular targets and, depending on the individual endpoint analyzed, act via similar or dissimilar mechanisms. The use of molecular data based on research in human cell systems extends the picture to refine cumulative assessment group grouping and substantially contributes to the understanding of mixture effects of chemicals in biological systems.}, language = {en} } @article{MummGodinaKozieletal.2018, author = {Mumm, Rebekka and Godina, Elena and Koziel, Slawomir and Musalek, Martin and Sedlak, Petr and Wittwer-Backofen, Ursula and Hess, Volker and Dasgupta, Parasmani and Henneberg, Maciej and Scheffler, Christiane}, title = {External skeletal robusticity of children and adolescents}, series = {Journal of biological and clinical anthropology}, volume = {74}, journal = {Journal of biological and clinical anthropology}, number = {5}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/anthranz/2018/0826}, pages = {383 -- 391}, year = {2018}, abstract = {Background: In our modern world, the way of life in nutritional and activity behaviour has changed. As a consequence, parallel trends of an epidemic of overweight and a decline in external skeletal robusticity are observed in children and adolescents. Aim: We aim to develop reference centiles for external skeletal robusticity of European girls and boys aged 0 to 18 years using the Frame Index as an indicator and identify population specific age-related patterns. Methods: We analysed cross-sectional \& longitudinal data on body height and elbow breadth of boys and girls from Europe (0-18 years, n = 41.679), India (7-18 years, n = 3.297) and South Africa (3-18 years, n = 4.346). As an indicator of external skeletal robusticity Frame Index after Frisancho (1990) was used. We developed centiles for boys and girls using the LMS-method and its extension. Results: Boys have greater external skeletal robusticity than girls. Whereas in girls Frame Index decreases continuously during growth, an increase of Frame Index from 12 to 16 years in European boys can be observed. Indian and South African boys are almost similar in Frame Index to European boys. In girls, the pattern is slightly different. Whereas South African girls are similar to European girls, Indian girls show a lesser external skeletal robusticity. Conclusion: Accurate references for external skeletal robusticity are needed to evaluate if skeletal development is adequate per age. They should be used to monitor effects of changes in way of life and physical activity levels in children and adolescents to avoid negative health outcomes like osteoporosis and arthrosis.}, language = {en} } @phdthesis{deVera2018, author = {de Vera, Jean-Pierre Paul}, title = {The relevance of ecophysiology in astrobiology and planetary research}, school = {Universit{\"a}t Potsdam}, pages = {219}, year = {2018}, abstract = {Eco-physiological processes are expressing the interaction of organisms within an environmental context of their habitat and their degree of adaptation, level of resistance as well as the limits of life in a changing environment. The present study focuses on observations achieved by methods used in this scientific discipline of "Ecophysiology" and to enlarge the scientific context in a broader range of understanding with universal character. The present eco-physiological work is building the basis for classifying and exploring the degree of habitability of another planet like Mars by a bio-driven experimentally approach. It offers also new ways of identifying key-molecules which are playing a specific role in physiological processes of tested organisms to serve as well as potential biosignatures in future space exploration missions with the goal to search for life. This has important implications for the new emerging scientific field of Astrobiology. Astrobiology addresses the study of the origin, evolution, distribution and future of life in the universe. The three fundamental questions which are hidden behind this definition are: how does life begin and evolve? Is there life beyond Earth and, if so, how can we detect it? What is the future of life on Earth and in the universe? It means that this multidisciplinary field encompasses the search for habitable environments in our Solar System and habitable planets outside our Solar System. It comprises the search for the evidence of prebiotic chemistry and life on Mars and other bodies in our Solar System like the icy moons of the Jovian and Saturnian system, laboratory and field research into the origins and early evolution of life on Earth, and studies of the potential for life to adapt to challenges on Earth and in space. For this purpose an integrated research strategy was applied, which connects field research, laboratory research allowing planetary simulation experiments with investigation enterprises performed in space (particularly performed in the low Earth Orbit.}, language = {en} } @misc{CisekTokarzKontenisetal.2018, author = {Cisek, Richard and Tokarz, Danielle and Kontenis, Lukas and Barzda, Virginijus and Steup, Martin}, title = {Polarimetric second harmonic generation microscopy}, series = {Starch-Starke}, volume = {70}, journal = {Starch-Starke}, number = {1-2}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0038-9056}, doi = {10.1002/star.201700031}, pages = {15}, year = {2018}, abstract = {Second harmonic generation (SHG) is a nonlinear optical process that inherently generates signal in non-centrosymmetric materials, such as starch granules, and therefore can be used for label-free imaging. Both intensity and polarization of SHG are determined by material properties that are characterized by the nonlinear susceptibility tensor, ((2)). Examination of the tensor is performed for each focal volume of the image by measuring the outgoing polarization state of the SHG signal for a set of incoming laser beam polarizations. Mapping of nonlinear properties expressed as the susceptibility ratio reveals structural features including the organization of crystalline material within a single starch granule, and the distribution of structural properties in a population of granules. Isolated granules, as well as in situ starch, can be analyzed using polarimetric SHG microscopy. Due to the fast sample preparation and short imaging times, polarimetric SHG microscopy allows for a quick assessment of starch structure and permits rapid feedback for bioengineering applications. This article presents the basics of SHG theory and microscopy applications for starch-containing materials. Quantification of ultrastructural features within individual starch granules is described. New results obtained by polarization resolved SHG microscopy of starch granules are presented for various maize genotypes revealing heterogeneity within a single starch particle and between various granules.}, language = {en} } @article{GrzesiukSpijkermanLachmannetal.2018, author = {Grzesiuk, Malgorzata and Spijkerman, Elly and Lachmann, Sabrina C. and Wacker, Alexander}, title = {Environmental concentrations of pharmaceuticals directly affect phytoplankton and effects propagate through trophic interactions}, series = {Ecotoxicology and Environmental Safety}, volume = {156}, journal = {Ecotoxicology and Environmental Safety}, publisher = {Elsevier}, address = {San Diego}, issn = {0147-6513}, doi = {10.1016/j.ecoenv.2018.03.019}, pages = {271 -- 278}, year = {2018}, abstract = {Pharmaceuticals are found in freshwater ecosystems where even low concentrations in the range of ng L-1 may affect aquatic organisms. In the current study, we investigated the effects of chronic exposure to three pharmaceuticals on two microalgae, a potential modulation of the effects by additional inorganic phosphorus (Pi) limitation, and a potential propagation of the pharmaceuticals' effect across a trophic interaction. The latter considers that pharmaceuticals are bioaccumulated by algae, potentially metabolized into more (or less) toxic derivates and consequently consumed by zooplankton. We cultured Acutodesmus obliquus and Nannochloropsis limnetica in Pi-replete and Pi-limited medium contaminated with one of three commonly human used pharmaceuticals: fluoxetine, ibuprofen, and propranolol. Secondly, we tested to what extent first level consumers (Daphnia magna) were affected when fed with pharmaceutical-grown algae. Chronic exposure, covering 30 generations, led to (i) decreased cell numbers of A. obliquus in the presence of fluoxetine (under Pi-replete conditions) (ii) increased carotenoid to chlorophyll ratios in N. limnetica (under Pi-limited conditions), and (iii) increased photosynthetic yields in A. obliquus (in both Pi-conditions). In addition, ibuprofen affected both algae and their consumer: Feeding ibuprofen-contaminated algae to Pi-stressed D. magna improved their survival. We demonstrate, that even very low concentrations of pharmaceuticals present in freshwater ecosystems can significantly affect aquatic organisms when chronically exposed. Our study indicates that pharmaceutical effects can cross trophic levels and travel up the food chain.}, language = {en} } @article{SpijkermanBehrendFachetal.2018, author = {Spijkerman, Elly and Behrend, Hella and Fach, Bettina and Gaedke, Ursula}, title = {Decreased phosphorus incorporation explains the negative effect of high iron concentrations in the green microalga Chlamydomonas acidophila}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {626}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2018.01.188}, pages = {1342 -- 1349}, year = {2018}, abstract = {The green microalga Chlamydomonas acidophila is an important primary producer in very acidic lakes (pH 2.0-3.5), characterized by high concentrations of ferric iron (up to 1 g total Fe L-1) and low rates of primary production. It was previously suggested that these high iron concentrations result in high iron accumulation and inhibit photosynthesis in C. acidophila. To test this, the alga was grown in sterilized lake water and in medium with varying total iron concentrations under limiting and sufficient inorganic phosphorus (Pi) supply, because Pi is an important growth limiting nutrient in acidic waters. Photosynthesis and growth of C. acidophila as measured over 5 days were largely unaffected by high total iron concentrations and only decreased if free ionic Fe3+ concentrations exceeded 100 mg Fe3+ L-1. Although C. acidophila was relatively rich in iron (up to 5 mmol Fe: mol C), we found no evidence of iron toxicity. In contrast, a concentration of 260 mg total Fe L-1 (i.e. 15 mg free ionic Fe3+ L-1), which is common in many acidic lakes, reduced Pi-incorporation by 50\% and will result in Pi-limited photosynthesis. The resulting Pi-limitation present at high iron and Pi concentrations was illustrated by elevated maximum Pi-uptake rates. No direct toxic effects of high iron were found, but unfavourable chemical Pi-speciation reduced growth of the acidophile alga.}, language = {en} } @misc{UhligGehreKammereretal.2018, author = {Uhlig, Katja and Gehre, Christian P. and Kammerer, Sarah and K{\"u}pper, Jan-Heiner and Coleman, Charles Dominic and P{\"u}schel, Gerhard Paul and Duschl, Claus}, title = {Real-time monitoring of oxygen consumption of hepatocytes in a microbioreactor}, series = {Toxicology letters}, volume = {295}, journal = {Toxicology letters}, publisher = {Elsevier}, address = {Clare}, issn = {0378-4274}, doi = {10.1016/j.toxlet.2018.06.652}, pages = {S115 -- S115}, year = {2018}, language = {en} } @phdthesis{Bibi2018, author = {Bibi, Faysal}, title = {Paleoecology and evolution in the Afro-Arabian neogene}, school = {Universit{\"a}t Potsdam}, year = {2018}, abstract = {This cumulative habilitation thesis presents new work on the systematics, paleoecology, and evolution of antelopes and other large mammals, focusing mainly on the late Miocene to Pleistocene terrestrial fossil record of Africa and Arabia. The studies included here range from descriptions of new species to broad-scale analyses of diversification and community evolution in large mammals over millions of years. A uniting theme is the evolution, across both temporal and spatial scales, of the environments and faunas that characterize modern African savannas today. One conclusion of this work is that macroevolutionary changes in large mammals are best characterized at regional (subcontinental to continental) and long-term temporal scales. General views of evolution developed on records that are too restricted in spatial and temporal extent are likely to ascribe too much influence to local or short-lived events. While this distinction in the scale of analysis and interpretation may seem trivial, it is challenging to implement given the geographically and temporally uneven nature of the fossil record, and the difficulties of synthesizing spatially and temporally dispersed datasets. This work attempts to do just that, bringing together primary fossil discoveries from eastern Africa to Arabia, from the Miocene to the Pleistocene, and across a wide range of (mainly large mammal) taxa. The end result is support for hypotheses stressing the impact of both climatic and biotic factors on long-term faunal change, and a more geographically integrated view of evolution in the African fossil record.}, language = {en} } @phdthesis{Lawas2018, author = {Lawas, Lovely Mae F.}, title = {Molecular characterization of rice exposed to heat and drought stress at flowering and early grain filling}, pages = {VII, 150}, year = {2018}, language = {en} } @phdthesis{Stoessel2018, author = {St{\"o}ßel, Daniel}, title = {Biomarker Discovery in Multiple Sclerosis and Parkinson's disease}, school = {Universit{\"a}t Potsdam}, pages = {135}, year = {2018}, abstract = {Neuroinflammatory and neurodegenerative diseases such as Parkinson's (PD) and multiple sclerosis (MS) often result in a severe impairment of the patient´s quality of life. Effective therapies for the treatment are currently not available, which results in a high socio-economic burden. Due to the heterogeneity of the disease subtypes, stratification is particularly difficult in the early phase of the disease and is mainly based on clinical parameters such as neurophysiological tests and central nervous imaging. Due to good accessibility and stability, blood and cerebrospinal fluid metabolite markers could serve as surrogates for neurodegenerative processes. This can lead to an improved mechanistic understanding of these diseases and further be used as "treatment response" biomarkers in preclinical and clinical development programs. Therefore, plasma and CSF metabolite profiles will be identified that allow differentiation of PD from healthy controls, association of PD with dementia (PDD) and differentiation of PD subtypes such as akinetic rigid and tremor dominant PD patients. In addition, plasma metabolites for the diagnosis of primary progressive MS (PPMS) should be investigated and tested for their specificity to relapsing-remitting MS (RRMS) and their development during PPMS progression. By applying untargeted high-resolution metabolomics of PD patient samples and in using random forest and partial least square machine learning algorithms, this study identified 20 plasma metabolites and 14 CSF metabolite biomarkers. These differentiate against healthy individuals with an AUC of 0.8 and 0.9 in PD, respectively. We also identify ten PDD specific serum metabolites, which differentiate against healthy individuals and PD patients without dementia with an AUC of 1.0, respectively. Furthermore, 23 akinetic-rigid specific plasma markers were identified, which differentiate against tremor-dominant PD patients with an AUC of 0.94 and against healthy individuals with an AUC of 0.98. These findings also suggest more severe disease pathology in the akinetic-rigid PD than in tremor dominant PD. In the analysis of MS patient samples a partial least square analysis yielded predictive models for the classification of PPMS and resulted in 20 PPMS specific metabolites. In another MS study unknown changes in human metabolism were identified after administration of the multiple sclerosis drug dimethylfumarate, which is used for the treatment of RRMS. These results allow to describe and understand the hitherto completely unknown mechanism of action of this new drug and to use these findings for the further development of new drugs and targets against RRMS. In conclusion, these results have the potential for improved diagnosis of these diseases and improvement of mechanistic understandings, as multiple deregulated pathways were identified. Moreover, novel Dimethylfumarate targets can be used to aid drug development and treatment efficiency. Overall, metabolite profiling in combination with machine learning identified as a promising approach for biomarker discovery and mode of action elucidation.}, language = {en} } @article{MalinovaMahtoBrandtetal.2018, author = {Malinova, Irina and Mahto, Harendra and Brandt, Felix and AL-Rawi, Shadha and Qasim, Hadeel and Brust, Henrike and Hejazi, Mahdi and Fettke, J{\"o}rg}, title = {EARLY STARVATION1 specifically affects the phosphorylation action of starch-related dikinases}, series = {The plant journal}, volume = {95}, journal = {The plant journal}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.13937}, pages = {126 -- 137}, year = {2018}, abstract = {Starch phosphorylation by starch-related dikinases glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD) is a key step in starch degradation. Little information is known about the precise structure of the glucan substrate utilized by the dikinases and about the mechanisms by which these structures may be influenced. A 50-kDa starch-binding protein named EARLY STARVATION1 (ESV1) was analyzed regarding its impact on starch phosphorylation. In various invitro assays, the influences of the recombinant protein ESV1 on the actions of GWD and PWD on the surfaces of native starch granules were analyzed. In addition, we included starches from various sources as well as truncated forms of GWD. ESV1 preferentially binds to highly ordered, -glucans, such as starch and crystalline maltodextrins. Furthermore, ESV1 specifically influences the action of GWD and PWD at the starch granule surface. Starch phosphorylation by GWD is decreased in the presence of ESV1, whereas the action of PWD increases in the presence of ESV1. The unique alterations observed in starch phosphorylation by the two dikinases are discussed in regard to altered glucan structures at the starch granule surface.}, language = {en} } @article{LisowskaRoedelManetetal.2018, author = {Lisowska, Justyna and R{\"o}del, Claudia Jasmin and Manet, Sandra and Miroshnikova, Yekaterina A. and Boyault, Cyril and Planus, Emmanuelle and De Mets, Richard and Lee, Hsiao-Hui and Destaing, Olivier and Mertani, Hichem and Boulday, Gwenola and Tournier-Lasserve, Elisabeth and Balland, Martial and Abdelilah-Seyfried, Salim and Albiges-Rizo, Corinne and Faurobert, Eva}, title = {The CCM1-CCM2 complex controls complementary functions of ROCK1 and ROCK2 that are required for endothelial integrity}, series = {Journal of cell science}, volume = {131}, journal = {Journal of cell science}, number = {15}, publisher = {Company biologists LTD}, address = {Cambridge}, issn = {0021-9533}, doi = {10.1242/jcs.216093}, pages = {15}, year = {2018}, abstract = {Endothelial integrity relies on a mechanical crosstalk between intercellular and cell-matrix interactions. This crosstalk is compromised in hemorrhagic vascular lesions of patients carrying loss-of-function mutations in cerebral cavernous malformation (CCM) genes. RhoA/ROCK-dependent cytoskeletal remodeling is central to the disease, as it causes unbalanced cell adhesion towards increased cell-extracellular matrix adhesions and destabilized cell-cell junctions. This study reveals that CCM proteins directly orchestrate ROCK1 and ROCK2 complementary roles on the mechanics of the endothelium. CCM proteins act as a scaffold, promoting ROCK2 interactions with VE-cadherin and limiting ROCK1 kinase activity. Loss of CCM1 (also known as KRIT1) produces excessive ROCK1-dependent actin stress fibers and destabilizes intercellular junctions. Silencing of ROCK1 but not ROCK2 restores the adhesive and mechanical homeostasis of CCM1 and CCM2-depleted endothelial monolayers, and rescues the cardiovascular defects of ccm1 mutant zebrafish embryos. Conversely, knocking down Rock2 but not Rock1 in wild-type zebrafish embryos generates defects reminiscent of the ccm1 mutant phenotypes. Our study uncovers the role of the CCM1-CCM2 complex in controlling ROCK1 and ROCK2 to preserve endothelial integrity and drive heart morphogenesis. Moreover, it solely identifies the ROCK1 isoform as a potential therapeutic target for the CCM disease.}, language = {en} } @article{DonatLourencoPaolinietal.2018, author = {Donat, Stefan and Lourenco, Marta Sofia Rocha and Paolini, Alessio and Otten, Cecile and Renz, Marc and Abdelilah-Seyfried, Salim}, title = {Heg1 and Ccm1/2 proteins control endocardial mechanosensitivity during zebrafish valvulogenesis}, series = {eLife}, volume = {7}, journal = {eLife}, publisher = {eLife Sciences Publications}, address = {Cambridge}, issn = {2050-084X}, doi = {10.7554/eLife.28939}, pages = {22}, year = {2018}, abstract = {Endothelial cells respond to different levels of fluid shear stress through adaptations of their mechanosensitivity. Currently, we lack a good understanding of how this contributes to sculpting of the cardiovascular system. Cerebral cavernous malformation (CCM) is an inherited vascular disease that occurs when a second somatic mutation causes a loss of CCM1/KRIT1, CCM2, or CCM3 proteins. Here, we demonstrate that zebrafish Krit1 regulates the formation of cardiac valves. Expression of heg1, which encodes a binding partner of Krit1, is positively regulated by blood-flow. In turn, Heg1 stabilizes levels of Krit1 protein, and both Heg1 and Krit1 dampen expression levels of klf2a, a major mechanosensitive gene. Conversely, loss of Krit1 results in increased expression of klf2a and notch1b throughout the endocardium and prevents cardiac valve leaflet formation. Hence, the correct balance of blood-flow-dependent induction and Krit1 protein mediated repression of klf2a and notch1b ultimately shapes cardiac valve leaflet morphology.}, language = {en} } @article{OlmerEngelsUsmanetal.2018, author = {Olmer, Ruth and Engels, Lena and Usman, Abdulai and Menke, Sandra and Malik, Muhammad Nasir Hayat and Pessler, Frank and Goehring, Gudrun and Bornhorst, Dorothee and Bolten, Svenja and Abdelilah-Seyfried, Salim and Scheper, Thomas and Kempf, Henning and Zweigerdt, Robert and Martin, Ulrich}, title = {Differentiation of Human Pluripotent Stem Cells into Functional Endothelial Cells in Scalable Suspension Culture}, series = {Stem Cell Reports}, volume = {10}, journal = {Stem Cell Reports}, number = {5}, publisher = {Springer}, address = {New York}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2018.03.017}, pages = {16}, year = {2018}, abstract = {Endothelial cells (ECs) are involved in a variety of cellular responses. As multifunctional components of vascular structures, endothelial (progenitor) cells have been utilized in cellular therapies and are required as an important cellular component of engineered tissue constructs and in vitro disease models. Although primary ECs from different sources are readily isolated and expanded, cell quantity and quality in terms of functionality and karyotype stability is limited. ECs derived from human induced pluripotent stem cells (hiPSCs) represent an alternative and potentially superior cell source, but traditional culture approaches and 2D differentiation protocols hardly allow for production of large cell numbers. Aiming at the production of ECs, we have developed a robust approach for efficient endothelial differentiation of hiPSCs in scalable suspension culture. The established protocol results in relevant numbers of ECs for regenerative approaches and industrial applications that show in vitro proliferation capacity and a high degree of chromosomal stability.}, language = {en} } @misc{PaoliniAbdelilahSeyfried2018, author = {Paolini, Alessio and Abdelilah-Seyfried, Salim}, title = {The mechanobiology of zebrafish cardiac valve leaflet formation}, series = {Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature}, volume = {55}, journal = {Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature}, publisher = {Elsevier}, address = {London}, issn = {0955-0674}, doi = {10.1016/j.ceb.2018.05.007}, pages = {52 -- 58}, year = {2018}, abstract = {Over a lifetime, rhythmic contractions of the heart provide a continuous flow of blood throughout the body. An essential morphogenetic process during cardiac development which ensures unidirectional blood flow is the formation of cardiac valves. These structures are largely composed of extracellular matrix and of endocardial cells, a specialized population of endothelial cells that line the interior of the heart and that are subjected to changing hemodynamic forces. Recent studies have significantly expanded our understanding of this morphogenetic process. They highlight the importance of the mechanobiology of cardiac valve formation and show how biophysical forces due to blood flow drive biochemical and electrical signaling required for the differentiation of cells to produce cardiac valves.}, language = {en} } @article{HilgersHartmannHofreiteretal.2018, author = {Hilgers, Leon and Hartmann, Stefanie and Hofreiter, Michael and von Rintelen, Thomas}, title = {Novel Genes, Ancient Genes, and Gene Co-Option Contributed o the Genetic Basis of the Radula, a Molluscan Innovation}, series = {Molecular biology and evolution}, volume = {35}, journal = {Molecular biology and evolution}, number = {7}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msy052}, pages = {1638 -- 1652}, year = {2018}, abstract = {The radula is the central foraging organ and apomorphy of the Mollusca. However, in contrast to other innovations, including the mollusk shell, genetic underpinnings of radula formation remain virtually unknown. Here, we present the first radula formative tissue transcriptome using the viviparous freshwater snail Tylomelania sarasinorum and compare it to foot tissue and the shell-building mantle of the same species. We combine differential expression, functional enrichment, and phylostratigraphic analyses to identify both specific and shared genetic underpinnings of the three tissues as well as their dominant functions and evolutionary origins. Gene expression of radula formative tissue is very distinct, but nevertheless more similar to mantle than to foot. Generally, the genetic bases of both radula and shell formation were shaped by novel orchestration of preexisting genes and continuous evolution of novel genes. A significantly increased proportion of radula-specific genes originated since the origin of stem-mollusks, indicating that novel genes were especially important for radula evolution. Genes with radula-specific expression in our study are frequently also expressed during the formation of other lophotrochozoan hard structures, like chaetae (hes1, arx), spicules (gbx), and shells of mollusks (gbx, heph) and brachiopods (heph), suggesting gene co-option for hard structure formation. Finally, a Lophotrochozoa-specific chitin synthase with a myosin motor domain (CS-MD), which is expressed during mollusk and brachiopod shell formation, had radula-specific expression in our study. CS-MD potentially facilitated the construction of complex chitinous structures and points at the potential of molecular novelties to promote the evolution of different morphological innovations.}, language = {en} } @article{PaijmansBarlowFoersteretal.2018, author = {Paijmans, Johanna L. A. and Barlow, Axel and F{\"o}rster, Daniel W. and Henneberger, Kirstin and Meyer, Matthias and Nickel, Birgit and Nagel, Doris and Wors{\o}e Havm{\o}ller, Rasmus and Baryshnikov, Gennady F. and Joger, Ulrich and Rosendahl, Wilfried and Hofreiter, Michael}, title = {Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations}, series = {BMC Evolutionary Biology}, volume = {18}, journal = {BMC Evolutionary Biology}, number = {156}, publisher = {BioMed Central und Springer}, address = {London, Berlin und Heidelberg}, issn = {1471-2148}, doi = {10.1186/s12862-018-1268-0}, pages = {12}, year = {2018}, abstract = {Background Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.}, language = {en} } @article{TaronLellBarlowetal.2018, author = {Taron, Ulrike H. and Lell, Moritz and Barlow, Axel and Paijmans, Johanna L. A.}, title = {Testing of Alignment Parameters for Ancient Samples}, series = {Genes}, volume = {9}, journal = {Genes}, number = {3}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes9030157}, pages = {1 -- 12}, year = {2018}, abstract = {High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present 'TAPAS', (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.}, language = {en} } @article{TaronLellBarlowetal.2018, author = {Taron, Ulrike H. and Lell, Moritz and Barlow, Axel and Paijmans, Johanna L. A.}, title = {Testing of Alignment Parameters for Ancient Samples}, series = {Genese}, volume = {9}, journal = {Genese}, number = {3}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes9030157}, pages = {12}, year = {2018}, abstract = {High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present 'TAPAS', (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.}, language = {en} }