@misc{deVeraAlawiBackhausetal.2019, author = {de Vera, Jean-Pierre Paul and Alawi, Mashal and Backhaus, Theresa and Baque, Mickael and Billi, Daniela and Boettger, Ute and Berger, Thomas and Bohmeier, Maria and Cockell, Charles and Demets, Rene and de la Torre Noetzel, Rosa and Edwards, Howell and Elsaesser, Andreas and Fagliarone, Claudia and Fiedler, Annelie and Foing, Bernard and Foucher, Frederic and Fritz, J{\"o}rg and Hanke, Franziska and Herzog, Thomas and Horneck, Gerda and H{\"u}bers, Heinz-Wilhelm and Huwe, Bj{\"o}rn and Joshi, Jasmin Radha and Kozyrovska, Natalia and Kruchten, Martha and Lasch, Peter and Lee, Natuschka and Leuko, Stefan and Leya, Thomas and Lorek, Andreas and Martinez-Frias, Jesus and Meessen, Joachim and Moritz, Sophie and Moeller, Ralf and Olsson-Francis, Karen and Onofri, Silvano and Ott, Sieglinde and Pacelli, Claudia and Podolich, Olga and Rabbow, Elke and Reitz, G{\"u}nther and Rettberg, Petra and Reva, Oleg and Rothschild, Lynn and Garcia Sancho, Leo and Schulze-Makuch, Dirk and Selbmann, Laura and Serrano, Paloma and Szewzyk, Ulrich and Verseux, Cyprien and Wadsworth, Jennifer and Wagner, Dirk and Westall, Frances and Wolter, David and Zucconi, Laura}, title = {Limits of life and the habitability of Mars}, series = {Astrobiology}, volume = {19}, journal = {Astrobiology}, number = {2}, publisher = {Liebert}, address = {New Rochelle}, issn = {1531-1074}, doi = {10.1089/ast.2018.1897}, pages = {145 -- 157}, year = {2019}, abstract = {BIOMEX (BIOlogy and Mars EXperiment) is an ESA/Roscosmos space exposure experiment housed within the exposure facility EXPOSE-R2 outside the Zvezda module on the International Space Station (ISS). The design of the multiuser facility supports-among others-the BIOMEX investigations into the stability and level of degradation of space-exposed biosignatures such as pigments, secondary metabolites, and cell surfaces in contact with a terrestrial and Mars analog mineral environment. In parallel, analysis on the viability of the investigated organisms has provided relevant data for evaluation of the habitability of Mars, for the limits of life, and for the likelihood of an interplanetary transfer of life (theory of lithopanspermia). In this project, lichens, archaea, bacteria, cyanobacteria, snow/permafrost algae, meristematic black fungi, and bryophytes from alpine and polar habitats were embedded, grown, and cultured on a mixture of martian and lunar regolith analogs or other terrestrial minerals. The organisms and regolith analogs and terrestrial mineral mixtures were then exposed to space and to simulated Mars-like conditions by way of the EXPOSE-R2 facility. In this special issue, we present the first set of data obtained in reference to our investigation into the habitability of Mars and limits of life. This project was initiated and implemented by the BIOMEX group, an international and interdisciplinary consortium of 30 institutes in 12 countries on 3 continents. Preflight tests for sample selection, results from ground-based simulation experiments, and the space experiments themselves are presented and include a complete overview of the scientific processes required for this space experiment and postflight analysis. The presented BIOMEX concept could be scaled up to future exposure experiments on the Moon and will serve as a pretest in low Earth orbit.}, language = {en} } @article{delaCruzMachensMesserschmidtetal.2019, author = {de la Cruz, Jorge Gonzalez and Machens, Fabian and Messerschmidt, Katrin and Bar-Even, Arren}, title = {Core Catalysis of the Reductive Glycine Pathway Demonstrated in Yeast}, series = {ACS synthetic biology}, volume = {8}, journal = {ACS synthetic biology}, number = {5}, publisher = {American Chemical Society}, address = {Washington}, issn = {2161-5063}, doi = {10.1021/acssynbio.8b00464}, pages = {911 -- 917}, year = {2019}, abstract = {One-carbon (C1) compounds are attractive microbial feedstocks as they can be efficiently produced from widely available resources. Formate, in particular, represents a promising growth substrate, as it can be generated from electrochemical reduction of CO2 and fed to microorganisms in a soluble form. We previously identified the synthetic reductive glycine pathway as the most efficient route for aerobic growth on formate. We further demonstrated pathway activity in Escherichia coli after expression of both native and foreign genes. Here, we explore whether the reductive glycine pathway could be established in a model microorganism using only native enzymes. We used the yeast Saccharomyces cerevisiae as host and show that overexpression of only endogenous enzymes enables glycine biosynthesis from formate and CO2 in a strain that is otherwise auxotrophic for glycine. We find the pathway to be highly active in this host, where 0.125 mM formate is sufficient to support growth. Notably, the formate-dependent growth rate of the engineered S. cerevisiae strain remained roughly constant over a very wide range of formate concentrations, 1-500 mM, indicating both high affinity for formate use and high tolerance toward elevated concentration of this C1 feedstock. Our results, as well the availability of endogenous NAD-dependent formate dehydrogenase, indicate that yeast might be an especially suitable host for engineering growth on formate.}, language = {en} } @article{DeCahsanWestburyDrewsetal.2019, author = {De Cahsan, Binia and Westbury, Michael V. and Drews, Hauke and Tiedemann, Ralph}, title = {The complete mitochondrial genome of a European fire-bellied toad (Bombina bombina) from Germany}, series = {Mitochondrial DNA Part B}, volume = {4}, journal = {Mitochondrial DNA Part B}, number = {1}, publisher = {Taylor \& Francis Group}, address = {London}, issn = {2380-2359}, doi = {10.1080/23802359.2018.1547143}, pages = {498 -- 500}, year = {2019}, abstract = {The European fire-bellied toad, Bombina bombina, is a small aquatic toad belonging to the family Bombinatoridae. The species is native to the lowlands of Central and Eastern Europe, where population numbers have been in decline in recent past decades. Here, we present the first complete mitochondrial genome of the endangered European fire-bellied toad from Northern Germany recovered using iterative mapping. Phylogenetic analyses including other representatives of the Bombinatoridae placed our German specimen as sister to a Polish B. bombina sequence with high support. This finding is congruent with the postulated Pleistocene history of the species. Our complete mitochondrial genome represents an important resource for further population analysis of the European fire-bellied toad, especially those found within Germany.}, language = {en} } @misc{DeCahsanWestburyDrewsetal.2019, author = {De Cahsan, Binia and Westbury, Michael V. and Drews, Hauke and Tiedemann, Ralph}, title = {The complete mitochondrial genome of a European fire-bellied toad (Bombina bombina) from Germany}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {532}, issn = {1866-8372}, doi = {10.25932/publishup-42322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-423222}, pages = {3}, year = {2019}, abstract = {The European fire-bellied toad, Bombina bombina, is a small aquatic toad belonging to the family Bombinatoridae. The species is native to the lowlands of Central and Eastern Europe, where population numbers have been in decline in recent past decades. Here, we present the first complete mitochondrial genome of the endangered European fire-bellied toad from Northern Germany recovered using iterative mapping. Phylogenetic analyses including other representatives of the Bombinatoridae placed our German specimen as sister to a Polish B. bombina sequence with high support. This finding is congruent with the postulated Pleistocene history of the species. Our complete mitochondrial genome represents an important resource for further population analysis of the European fire-bellied toad, especially those found within Germany.}, language = {en} } @misc{DasGuptaRoeschHochreinetal.2019, author = {Das Gupta, Mainak and Roesch, Florian and Hochrein, Lena and Machens, Fabian and M{\"u}ller-R{\"o}ber, Bernd}, title = {Facilitating Genome Engineering Through RNP-mediated Precise Gene Targeting}, series = {In Vitro Cellular \& Developmental Biology - Plant}, volume = {55}, journal = {In Vitro Cellular \& Developmental Biology - Plant}, number = {4}, publisher = {Springer}, address = {New York}, issn = {1054-5476}, pages = {481 -- 481}, year = {2019}, language = {en} } @phdthesis{Dammhahn2019, author = {Dammhahn, Melanie}, title = {From individual variation to community structure : paterns, determinants and consequences of within- and between-species variation in behaviour, life-history and ecology}, school = {Universit{\"a}t Potsdam}, pages = {431}, year = {2019}, language = {en} } @misc{DahmaniLudwigChiantia2019, author = {Dahmani, Ismail and Ludwig, Kai and Chiantia, Salvatore}, title = {Influenza A matrix protein M1 induces lipid membrane deformation via protein multimerization}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {768}, issn = {1866-8372}, doi = {10.25932/publishup-43868}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438689}, pages = {16}, year = {2019}, abstract = {The matrix protein M1 of the Influenza A virus (IAV) is supposed to mediate viral assembly and budding at the plasma membrane (PM) of infected cells. In order for a new viral particle to form, the PM lipid bilayer has to bend into a vesicle toward the extracellular side. Studies in cellular models have proposed that different viral proteins might be responsible for inducing membrane curvature in this context (including M1), but a clear consensus has not been reached. In the present study, we use a combination of fluorescence microscopy, cryogenic transmission electron microscopy (cryo-TEM), cryo-electron tomography (cryo-ET) and scanning fluorescence correlation spectroscopy (sFCS) to investigate M1-induced membrane deformation in biophysical models of the PM. Our results indicate that M1 is indeed able to cause membrane curvature in lipid bilayers containing negatively charged lipids, in the absence of other viral components. Furthermore, we prove that protein binding is not sufficient to induce membrane restructuring. Rather, it appears that stable M1-M1 interactions and multimer formation are required in order to alter the bilayer three-dimensional structure, through the formation of a protein scaffold. Finally, our results suggest that, in a physiological context,M1-induced membrane deformation might be modulated by the initial bilayer curvature and the lateral organization of membrane components (i.e. the presence of lipid domains).}, language = {en} } @article{DahmaniLudwigChiantia2019, author = {Dahmani, Ismail and Ludwig, Kai and Chiantia, Salvatore}, title = {Influenza A matrix protein M1 induces lipid membrane deformation via protein multimerization}, series = {Bioscience Reports}, volume = {39}, journal = {Bioscience Reports}, number = {8}, publisher = {Portland Press}, address = {Colchester}, issn = {0144-8463}, doi = {10.1042/BSR20191024}, pages = {16}, year = {2019}, abstract = {The matrix protein M1 of the Influenza A virus (IAV) is supposed to mediate viral assembly and budding at the plasma membrane (PM) of infected cells. In order for a new viral particle to form, the PM lipid bilayer has to bend into a vesicle toward the extracellular side. Studies in cellular models have proposed that different viral proteins might be responsible for inducing membrane curvature in this context (including M1), but a clear consensus has not been reached. In the present study, we use a combination of fluorescence microscopy, cryogenic transmission electron microscopy (cryo-TEM), cryo-electron tomography (cryo-ET) and scanning fluorescence correlation spectroscopy (sFCS) to investigate M1-induced membrane deformation in biophysical models of the PM. Our results indicate that M1 is indeed able to cause membrane curvature in lipid bilayers containing negatively charged lipids, in the absence of other viral components. Furthermore, we prove that protein binding is not sufficient to induce membrane restructuring. Rather, it appears that stable M1-M1 interactions and multimer formation are required in order to alter the bilayer three-dimensional structure, through the formation of a protein scaffold. Finally, our results suggest that, in a physiological context,M1-induced membrane deformation might be modulated by the initial bilayer curvature and the lateral organization of membrane components (i.e. the presence of lipid domains).}, language = {en} } @article{CoramanDietzHempeletal.2019, author = {Coraman, Emrah and Dietz, Christian and Hempel, Elisabeth and Ghazaryan, Astghik and Levin, Eran and Presetnik, Primoz and Zagmajster, Maja and Mayer, Frieder}, title = {Reticulate evolutionary history of a Western Palaearctic Bat Complex explained by multiple mtDNA introgressions in secondary contacts}, series = {Journal of biogeography}, volume = {46}, journal = {Journal of biogeography}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {0305-0270}, doi = {10.1111/jbi.13509}, pages = {343 -- 354}, year = {2019}, abstract = {Aim There is an increasing evidence showing that species within various taxonomic groups have reticulate evolutionary histories with several cases of introgression events. Investigating the phylogeography of species complexes can provide insight into these introgressions, and when and where these hybridizations occurred. In this study, we investigate the biogeography of a widely distributed Western Palaearctic bat species complex, namely Myotis nattereri sensu lato. This complex exhibits high genetic diversity and in its western distribution range is composed of deeply diverged genetical lineages. However, little is known about the genetic structure of the eastern populations. We also infer the conservation and taxonomical implications of the identified genetic divergences. Taxon Myotis nattereri sensu lato including M. schaubi. Location Western Palaearctic. Methods We analysed 161 specimens collected from 67 locations and sequenced one mitochondrial and four nuclear DNA markers, and combined these with the available GenBank sequences. We used haplotype networks, PCA, t-SNE and Bayesian clustering algorithms to investigate the population structure and Bayesian trees to infer the phylogenetic relationship of the lineages. Results We identified deeply divergent genetical lineages. In some cases, nuclear and mitochondrial markers were discordant, which we interpret are caused by hybridization between lineages. We identified three such introgression events. These introgressions occurred when spatially separated lineages came into contact after range expansions. Based on the genetic distinction of the identified lineages, we suggest a revision in the taxonomy of this species group with two possible new species: M. hoveli and M. tschuliensis. Main conclusions Our findings suggest that the M. nattereri complex has a reticulate evolutionary history with multiple cases of hybridizations between some of the identified lineages.}, language = {en} } @article{CookLiCaietal.2019, author = {Cook, Katherine V. and Li, Chuang and Cai, Haiyuan and Krumholz, Lee R. and Hambright, K. David and Paerl, Hans W. and Steffen, Morgan M. and Wilson, Alan E. and Burford, Michele A. and Grossart, Hans-Peter and Hamilton, David P. and Jiang, Helong and Sukenik, Assaf and Latour, Delphine and Meyer, Elisabeth I. and Padisak, Judit and Qin, Boqiang and Zamor, Richard M. and Zhu, Guangwei}, title = {The global Microcystis interactome}, series = {Limnology and oceanography}, volume = {65}, journal = {Limnology and oceanography}, publisher = {Wiley}, address = {Hoboken}, issn = {0024-3590}, doi = {10.1002/lno.11361}, pages = {S194 -- S207}, year = {2019}, abstract = {Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280 degrees longitudinal and 90 degrees latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole-community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.}, language = {en} } @article{ColomaGaedkeSivonenetal.2019, author = {Coloma, Sebastian and Gaedke, Ursula and Sivonen, Kaarina and Hiltunen, Teppo}, title = {Frequency of virus-resistant hosts determines experimental community dynamics}, series = {Ecology : a publication of the Ecological Society of America}, volume = {100}, journal = {Ecology : a publication of the Ecological Society of America}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {0012-9658}, doi = {10.1002/ecy.2554}, pages = {10}, year = {2019}, abstract = {Parasites, such as bacterial viruses (phages), can have large effects on host populations both at the ecological and evolutionary levels. In the case of cyanobacteria, phages can reduce primary production and infected hosts release intracellular nutrients influencing planktonic food web structure, community dynamics, and biogeochemical cycles. Cyanophages may be of great importance in aquatic food webs during large cyanobacterial blooms unless the host population becomes resistant to phage infection. The consequences on plankton community dynamics of the evolution of phage resistance in bloom forming cyanobacterial populations are still poorly studied. Here, we examined the effect of different frequencies of a phage-resistant genotype within a filamentous nitrogen-fixing Nodularia spumigena population on an experimental plankton community. Three Nodularia populations with different initial frequencies (0\%, 5\%, and 50\%) of phage-resistant genotypes were inoculated in separate treatments with the phage 2AV2, the green alga Chlorella vulgaris, and the rotifer Brachionus plicatilis, which formed the experimental plankton community subjected to either nitrogen-limited or nitrogen-rich conditions. We found that the frequency of the phage-resistant Nodularia genotype determined experimental community dynamics. Cyanobacterial populations with a high frequency (50\%) of the phage-resistant genotype dominated the cultures despite the presence of phages, retaining most of the intracellular nitrogen in the plankton community. In contrast, populations with low frequencies (0\% and 5\%) of the phage-resistant genotype were lysed and reduced to extinction by the phage, transferring the intracellular nitrogen held by Nodularia to Chlorella and rotifers, and allowing Chlorella to dominate the communities and rotifers to survive. This study shows that even though phages represent minuscule biomass, they can have key effects on community composition and eco-evolutionary feedbacks in plankton communities.}, language = {en} } @article{ColangeliSchlaegelOberteggeretal.2019, author = {Colangeli, Pierluigi and Schl{\"a}gel, Ulrike E. and Obertegger, Ulrike and Petermann, Jana S. and Tiedemann, Ralph and Weithoff, Guntram}, title = {Negative phototactic response to UVR in three cosmopolitan rotifers: a video analysis approach}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {844}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-018-3801-y}, pages = {43 -- 54}, year = {2019}, language = {en} } @article{ChenLiZhangetal.2019, author = {Chen, Shun-Gang and Li, Ji and Zhang, Fan and Xiao, Bo and Hu, Jia-Ming and Cui, Yin-Qiu and Hofreiter, Michael and Hou, Xin-Dong and Sheng, Gui-Lian and Lai, Xu-Long and Yuan, Jun-Xia}, title = {Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China}, series = {Mitochondrial DNA Part A}, volume = {30}, journal = {Mitochondrial DNA Part A}, number = {7}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {2470-1394}, doi = {10.1080/24701394.2019.1659250}, pages = {786 -- 793}, year = {2019}, abstract = {Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95\% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis a slow increase in female effective population size of C. bactrianus from 5000 years ago, which to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.}, language = {en} } @article{ChaturvediMehrotraKumarietal.2019, author = {Chaturvedi, Neha and Mehrotra, Bagish and Kumari, Sangeeta and Gupta, Saurabh and Subramanya, Hosahalli and Saberwal, Gayatri}, title = {Some data quality issues at ClinicalTrials.gov}, series = {Trials}, volume = {20}, journal = {Trials}, publisher = {BMC}, address = {London}, issn = {1745-6215}, doi = {10.1186/s13063-019-3408-2}, pages = {8}, year = {2019}, language = {en} } @article{ChapmanLantOhashietal.2019, author = {Chapman, Eric M. and Lant, Benjamin and Ohashi, Yota and Yu, Bin and Schertzberg, Michael and Go, Christopher and Dogra, Deepika and Koskimaki, Janne and Girard, Romuald and Li, Yan and Fraser, Andrew G. and Awad, Issam A. and Abdelilah-Seyfried, Salim and Gingras, Anne-Claude and Derry, William Brent}, title = {A conserved CCM complex promotes apoptosis non-autonomously by regulating zinc homeostasis}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-09829-z}, pages = {15}, year = {2019}, abstract = {Apoptotic death of cells damaged by genotoxic stress requires regulatory input from surrounding tissues. The C. elegans scaffold protein KRI-1, ortholog of mammalian KRIT1/CCM1, permits DNA damage-induced apoptosis of cells in the germline by an unknown cell non-autonomous mechanism. We reveal that KRI-1 exists in a complex with CCM-2 in the intestine to negatively regulate the ERK-5/MAPK pathway. This allows the KLF-3 transcription factor to facilitate expression of the SLC39 zinc transporter gene zipt-2.3, which functions to sequester zinc in the intestine. Ablation of KRI-1 results in reduced zinc sequestration in the intestine, inhibition of IR-induced MPK-1/ERK1 activation, and apoptosis in the germline. Zinc localization is also perturbed in the vasculature of krit1(-/-) zebrafish, and SLC39 zinc transporters are mis-expressed in Cerebral Cavernous Malformations (CCM) patient tissues. This study provides new insights into the regulation of apoptosis by cross-tissue communication, and suggests a link between zinc localization and CCM disease.}, language = {en} } @misc{CeulemansGaedkeKlauschiesetal.2019, author = {Ceulemans, Ruben and Gaedke, Ursula and Klauschies, Toni and Guill, Christian}, title = {The effects of functional diversity on biomass production, variability, and resilience of ecosystem functions in a tritrophic system}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {744}, issn = {1866-8372}, doi = {10.25932/publishup-43543}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435439}, pages = {16}, year = {2019}, abstract = {Diverse communities can adjust their trait composition to altered environmental conditions, which may strongly influence their dynamics. Previous studies of trait-based models mainly considered only one or two trophic levels, whereas most natural system are at least tritrophic. Therefore, we investigated how the addition of trait variation to each trophic level influences population and community dynamics in a tritrophic model. Examining the phase relationships between species of adjacent trophic levels informs about the strength of top-down or bottom-up control in non-steadystate situations. Phase relationships within a trophic level highlight compensatory dynamical patterns between functionally different species, which are responsible for dampening the community temporal variability. Furthermore, even without trait variation, our tritrophic model always exhibits regions with two alternative states with either weak or strong nutrient exploitation, and correspondingly low or high biomass production at the top level. However, adding trait variation increased the basin of attraction of the high-production state, and decreased the likelihood of a critical transition from the high- to the lowproduction state with no apparent early warning signals. Hence, our study shows that trait variation enhances resource use efficiency, production, stability, and resilience of entire food webs.}, language = {en} } @article{CeulemansGaedkeKlauschiesetal.2019, author = {Ceulemans, Ruben and Gaedke, Ursula and Klauschies, Toni and Guill, Christian}, title = {The effects of functional diversity on biomass production, variability, and resilience of ecosystem functions in a tritrophic system}, series = {Scientific Reports}, volume = {9}, journal = {Scientific Reports}, publisher = {Macmillan Publishers Limited}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-43974-1}, pages = {16}, year = {2019}, abstract = {Diverse communities can adjust their trait composition to altered environmental conditions, which may strongly influence their dynamics. Previous studies of trait-based models mainly considered only one or two trophic levels, whereas most natural system are at least tritrophic. Therefore, we investigated how the addition of trait variation to each trophic level influences population and community dynamics in a tritrophic model. Examining the phase relationships between species of adjacent trophic levels informs about the strength of top-down or bottom-up control in non-steadystate situations. Phase relationships within a trophic level highlight compensatory dynamical patterns between functionally different species, which are responsible for dampening the community temporal variability. Furthermore, even without trait variation, our tritrophic model always exhibits regions with two alternative states with either weak or strong nutrient exploitation, and correspondingly low or high biomass production at the top level. However, adding trait variation increased the basin of attraction of the high-production state, and decreased the likelihood of a critical transition from the high- to the lowproduction state with no apparent early warning signals. Hence, our study shows that trait variation enhances resource use efficiency, production, stability, and resilience of entire food webs.}, language = {en} } @article{CastanoMartinezSchumacherSchumacheretal.2019, author = {Casta{\~n}o Mart{\´i}nez, Mar{\´i}a Teresa and Schumacher, Fabian and Schumacher, Silke and Kochlik, Bastian Max and Weber, Daniela and Grune, Tilman and Biemann, Ronald and McCann, Adrian and Abraham, Klaus and Weikert, Cornelia and Kleuse, Burkhard and Sch{\"u}rmann, Annette and Laeger, Thomas}, title = {Methionine restriction prevents onset of type 2 diabetes in NZO mice}, series = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, volume = {33}, journal = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, number = {6}, publisher = {Federation of American Societies for Experimental Biology}, address = {Bethesda}, issn = {0892-6638}, doi = {10.1096/fj.201900150R}, pages = {7092 -- 7102}, year = {2019}, abstract = {Dietary methionine restriction (MR) is well known to reduce body weight by increasing energy expenditure (EE) and insulin sensitivity. An elevated concentration of circulating fibroblast growth factor 21 (FGF21) has been implicated as a potential underlying mechanism. The aims of our study were to test whether dietary MR in the context of a high-fat regimen protects against type 2 diabetes in mice and to investigate whether vegan and vegetarian diets, which have naturally low methionine levels, modulate circulating FGF21 in humans. New Zealand obese (NZO) mice, a model for polygenic obesity and type 2 diabetes, were placed on isocaloric high-fat diets (protein, 16 kcal\%; carbohydrate, 52 kcal\%; fat, 32 kcal\%) that provided methionine at control (Con; 0.86\% methionine) or low levels (0.17\%) for 9 wk. Markers of glucose homeostasis and insulin sensitivity were analyzed. Among humans, low methionine intake and circulating FGF21 levels were investigated by comparing a vegan and a vegetarian diet to an omnivore diet and evaluating the effect of a short-term vegetarian diet on FGF21 induction. In comparison with the Con group, MR led to elevated plasma FGF21 levels and prevented the onset of hyperglycemia in NZO mice. MR-fed mice exhibited increased insulin sensitivity, higher plasma adiponectin levels, increased EE, and up-regulated expression of thermogenic genes in subcutaneous white adipose tissue. Food intake and fat mass did not change. Plasma FGF21 levels were markedly higher in vegan humans compared with omnivores, and circulating FGF21 levels increased significantly in omnivores after 4 d on a vegetarian diet. These data suggest that MR induces FGF21 and protects NZO mice from high-fat diet-induced glucose intolerance and type 2 diabetes. The normoglycemic phenotype in vegans and vegetarians may be caused by induced FGF21. MR akin to vegan and vegetarian diets in humans may offer metabolic benefits via increased circulating levels of FGF21 and merits further investigation.-Castano-Martinez, T., Schumacher, F., Schumacher, S., Kochlik, B., Weber, D., Grune, T., Biemann, R., McCann, A., Abraham, K., Weikert, C., Kleuser, B., Schurmann, A., Laeger, T. Methionine restriction prevents onset of type 2 diabetes in NZO mice.}, language = {en} } @phdthesis{Canitz2019, author = {Canitz, Julia}, title = {Genome and karyotype evolution underlying speciation and diversification of electric organ discharges in African weakly electric fish (Campylomormyrus, Mormyridae, Teleostei)}, school = {Universit{\"a}t Potsdam}, pages = {111}, year = {2019}, abstract = {The African weakly electric fish genus Campylomormyrus is a well-investigated fish group of the species-rich family Mormyridae. They are able to generate species-specific electric organ discharges (EODs) which vary in their waveform characteristics including polarity, phase umber and duration. In mormyrid species EODs are used for communication, species discrimination and mate recognition, and it is thought hat they serve as pre-zygotic isolation mechanism driving sympatric speciation by promoting assortative mating. The EOD diversification, its volutionary effects and the link to species divergence have been examined histologically, behaviorally, and genetically. Molecular analyses are a major tool to identify species and their phenotypic traits by studying the underlying genes. The genetic variability between species further provides information from which evolutionary processes, such as speciation, can be deduced. Hence, the ultimate aim of this study is the investigation of genetic variability within the African weakly electric fish genus Campylomormyrus to better understand their sympatric speciation and comprehend their evolutionary drivers. In order to extend the current knowledge and gain more insights into its species history, karyological and genomic approaches are being pursued considering species differences. Previous studies have shown that species with different EOD duration have specific gene expression patterns and single nucleotide polymorphisms (SNPs). As EODs play a crucial role during the evolution of Campylomormyrus species, the identification of its underlying genes may suggest how the EOD diversity evolved and whether this trait is based on a complex network of genetic processes or is regulated by only a few genes. The results obtained in this study suggest that genes with non-synonymous SNPs, which are exclusive to C. tshokwe with an elongated EOD, have frequent functions ssociated with tissue morphogenesis and transcriptional regulation. Therefore, it is proposed that these processes likely co-determine EOD characteristics of Campylomormyrus species. Furthermore, genome-wide analyses confirm the genetic difference among most Campylomormyrus species. In contrast, the same analyses reveal genetic similarity among individuals of the alces-complex showing different EOD waveforms. It is therefore hypothesized that the low genetic variability and high EOD diversity represents incipient sympatric speciation. The karyological description of a Campylomormyrus species provides crucial information about chromosome number and shapes. Its diploid chromosome number of 2n=48 supports the conservation of this trait within Mormyridae. Differences have been detected in the number of bi-armed chromosomes which is unusually high compared to other mormyrid species. This high amount can be due to chromosome rearrangements which could cause genetic incompatibility and reproductive isolation. Hence an alternative hypothesis regarding processes which cause sympatric speciation is that chromosome differences are involved in the speciation process of Campylomormyrus by acting as postzygotic isolation mechanism. In summary, the karyological and genomic investigations conducted in this study contributed to the increase of knowledge about Campylomormyrus species, to the solution of some existing ambiguities like phylogenetic relationships and to the raising of new hypothesis explaining the sympatric speciation of those African weakly electric fish. This study provides a basis for future genomic research to obtain a complete picture for causes and results of evolutionary processes in Campylomormyrus.}, language = {en} } @article{BoertleinSchumacherKleuseretal.2019, author = {B{\"o}rtlein, Charlene and Schumacher, Fabian and Kleuser, Burkhard and D{\"o}lken, Lars and Avota, Elita}, title = {Role of Neutral Sphingomyelinase-2 (NSM 2) in the Control of T Cell Plasma Membrane Lipid Composition and Cholesterol Homeostasis}, series = {Frontiers in cell and developmental biology}, volume = {7}, journal = {Frontiers in cell and developmental biology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {2296-634X}, doi = {10.3389/fcell.2019.00226}, pages = {16}, year = {2019}, abstract = {The activity of neutral sphingomyelinase-2 (NSM2) to catalyze the conversion of sphingomyelin (SM) to ceramide and phosphocholine at the cytosolic leaflet of plasma membrane (PM) is important in T cell receptor (TCR) signaling. We recently identified PKC zeta as a major NSM2 downstream effector which regulates microtubular polarization. It remained, however, unclear to what extent NSM2 activity affected overall composition of PM lipids and downstream effector lipids in antigen stimulated T cells. Here, we provide a detailed lipidomics analyses on PM fractions isolated from TCR stimulated wild type and NSM2 deficient (Delta NSM) Jurkat T cells. This revealed that in addition to that of sphingolipids, NSM2 depletion also affected concentrations of many other lipids. In particular, NSM2 ablation resulted in increase of lyso-phosphatidylcholine (LPC) and lyso-phosphatidylethanolamine (LPE) which both govern PM biophysical properties. Crucially, TCR dependent upregulation of the important T cell signaling lipid diacylglycerol (DAG), which is fundamental for activation of conventional and novel PKCs, was abolished in Delta NSM cells. Moreover, NSM2 activity was found to play an important role in PM cholesterol transport to the endoplasmic reticulum (ER) and production of cholesteryl esters (CE) there. Most importantly, CE accumulation was essential to sustain human T cell proliferation. Accordingly, inhibition of CE generating enzymes, the cholesterol acetyltransferases ACAT1/SOAT1 and ACAT2/SOAT2, impaired TCR driven expansion of both CD4(+) and CD8(+) T cells. In summary, our study reveals an important role of NSM2 in regulating T cell functions by its multiple effects on PM lipids and cholesterol homeostasis.}, language = {en} } @article{BuschKlausSchaeferetal.2019, author = {Busch, Verena and Klaus, Valentin Helmut and Schaefer, Deborah and Prati, Daniel and Boch, Steffen and M{\"u}ller, J{\"o}rg and Chiste, Melanie and Mody, Karsten and Bl{\"u}thgen, Nico and Fischer, Markus and H{\"o}lzel, Norbert and Kleinebecker, Till}, title = {Will I stay or will I go? Plant species-specific response and tolerance to high land-use intensity in temperate grassland ecosystems}, series = {Journal of vegetation science}, volume = {30}, journal = {Journal of vegetation science}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {1100-9233}, doi = {10.1111/jvs.12749}, pages = {674 -- 686}, year = {2019}, language = {en} } @article{BubnerBuchheitFriedrichetal.2019, author = {Bubner, Ben and Buchheit, Ramona and Friedrich, Frank and Kummer, Volker and Scholler, Markus}, title = {Species identification of European forest pathogens of the genus Milesina (Pucciniales) using urediniospore morphology and molecular barcoding including M. woodwardiana sp. nov.}, series = {MycoKeys}, journal = {MycoKeys}, number = {48}, publisher = {Pensoft Publishers}, address = {Sofia}, issn = {1314-4057}, doi = {10.3897/mycokeys.48.30350}, pages = {1 -- 40}, year = {2019}, abstract = {Species of rust fungi of the genus Milesina (Pucciiastraceae, Pucciniales) are distributed mainly in northern temperate regions. They host-alternate between needles of fir (Abies spp.) and fronds of ferns (species of Polypodiales). Milesina species are distinguished based on host taxonomy and urediniospore morphology. In this study, 12 species of Milesina from Europe were revised. Specimens were examined by light and scanning electron microscopy for urediniospore morphology with a focus on visualising germ pores (number, size and position) and echinulation. In addition, barcode loci (ITS, nad6, 28S) were used for species delimitation and for molecular phylogenetic analyses. Barcodes of 72 Milesina specimens were provided, including 11 of the 12 species. Whereas urediniospore morphology features were sufficient to distinguish all 12 Milesina species except for 2 (M. blechni and M. kriegeriana), ITS sequences separated only 4 of 11 species. Sequencing with 28S and nad6 did not improve species resolution. Phylogenetic analysis, however, revealed four phylogenetic groups within Milesina that also correlate with specific urediniospore characters (germ pore number and position and echinulation). These groups are proposed as new sections within Milesina (sections Milesina, Vogesiacae M. Scholler \& Bubner, sect. nov., Scolopendriorum M. Scholler \& Bubner, sect. nov. and Carpaticae M. Scholler \& Bubner, sect. nov.). In addition, Milesina woodwardiana Buchheit \& M. Scholler, sp. nov. on Woodwardia radicans, a member of the type section Milesina, is newly described. An identification key for European Milesina species, based on urediniospore features, is provided.}, language = {en} } @article{BroekerSinelnikovGustavusetal.2019, author = {Br{\"o}ker, Katharine and Sinelnikov, Evgeny and Gustavus, Dirk and Schumacher, Udo and P{\"o}rtner, Ralf and Hoffmeister, Hans and L{\"u}th, Stefan and Dammermann, Werner}, title = {Mass Production of Highly Active NK Cells for Cancer Immunotherapy in a GMP Conform Perfusion Bioreactor}, series = {Frontiers in Bioengineering and Biotechnology}, volume = {7}, journal = {Frontiers in Bioengineering and Biotechnology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {2296-4185}, doi = {10.3389/fbioe.2019.00194}, pages = {17}, year = {2019}, abstract = {NK cells have emerged as promising candidates for cancer immunotherapy, especially due to their ability to fight circulating tumor cells thereby preventing metastases formation. Hence several studies have been performed to generate and expand highly cytotoxic NK cells ex vivo, e.g., by using specific cytokines to upregulate both their proliferation and surface expression of distinct activating receptors. Apart from an enhanced activity, application of NK cells as immunotherapeutic agent further requires sufficient cell numbers and a high purity. All these parameters depend on a variety of different factors including the starting material, additives like cytokines as well as the culture system. Here we analyzed PBMC-derived NK cells of five anonymized healthy donors expanded under specific conditions in an innovative perfusion bioreactor system with respect to their phenotype, IFN gamma production, and cytotoxicity in vitro. Important features of the meander type bioreactors used here are a directed laminar flow of medium and control of relevant process parameters. Cells are cultivated under "steady state" conditions in perfusion mode. Our data demonstrate that expansion of CD3(+) T cell depleted PBMCs in our standardized system generates massive amounts of highly pure (>85\%) and potent anticancer active NK cells. These cells express a variety of important receptors driving NK cell recruitment, adhesion as well as activation. More specifically, they express the chemokine receptors CXCR3, CXCR4, and CCR7, the adhesion molecules L-selectin, LFA-1, and VLA-4, the activating receptors NKp30, NKp44, NKp46, NKG2D, DNAM1, and CD16 as well as the death ligands TRAIL and Fas-L. Moreover, the generated NK cells show a strong IFN gamma expression upon cultivation with K562 tumor cells and demonstrate a high cytotoxicity toward leukemic as well as solid tumor cell lines in vitro. Altogether, these characteristics promise a high clinical potency of thus produced NK cells awaiting further evaluation.}, language = {en} } @article{BroekerRoskeVallerianietal.2019, author = {Broeker, Nina K. and Roske, Yvette and Valleriani, Angelo and Stephan, Mareike Sophia and Andres, Dorothee and Koetz, Joachim and Heinemann, Udo and Barbirz, Stefanie}, title = {Time-resolved DNA release from an O-antigen-specific Salmonella bacteriophage with a contractile tail}, series = {The journal of biological chemistry}, volume = {294}, journal = {The journal of biological chemistry}, number = {31}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {1083-351X}, doi = {10.1074/jbc.RA119.008133}, pages = {11751 -- 11761}, year = {2019}, abstract = {Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 angstrom resolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an E15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches.}, language = {en} } @misc{BreedveldFolkertsmaEccard2019, author = {Breedveld, Merel Cathelijne and Folkertsma, Remco and Eccard, Jana}, title = {Rodent mothers increase vigilance behaviour when facing infanticide risk}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch- Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch- Naturwissenschaftliche Reihe}, number = {766}, issn = {1866-8372}, doi = {10.25932/publishup-43807}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438074}, pages = {12}, year = {2019}, abstract = {Infanticide, the killing of unrelated young, is widespread and frequently driven by sexual conflict. especially in mammals with exclusive maternal care, infanticide by males is common and females suffer fitness costs. Recognizing infanticide risk and adjusting offspring protection accordingly should therefore be adaptive in female mammals. Using a small mammal (Myodes glareolus) in outdoor enclosures, we investigated whether lactating mothers adjust offspring protection, and potential mate search behaviour, in response to different infanticide risk levels. We presented the scent of the litter's sire or of a stranger male near the female's nest, and observed female nest presence and movement by radiotracking. While both scents simulated a mating opportunity, they represented lower (sire) and higher (stranger) infanticide risk. compared to the sire treatment, females in the stranger treatment left their nest more often, showed increased activity and stayed closer to the nest, suggesting offspring protection from outside the nest through elevated alertness and vigilance. females with larger litters spent more time investigating scents and used more space in the sire but not in the stranger treatment. Thus, current investment size affected odour inspection and resource acquisition under higher risk. Adjusting nest protection and resource acquisition to infanticide risk could allow mothers to elicit appropriate (fitness-saving) counterstrategies, and thus, may be widespread.}, language = {en} } @article{BreedveldFolkertsmaEccard2019, author = {Breedveld, Merel Cathelijne and Folkertsma, Remco and Eccard, Jana}, title = {Rodent mothers increase vigilance behaviour when facing infanticide risk}, series = {Scientific Reports}, volume = {9}, journal = {Scientific Reports}, publisher = {Macmillan Publishers Limited, part of Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-48459-9}, pages = {10}, year = {2019}, abstract = {Infanticide, the killing of unrelated young, is widespread and frequently driven by sexual conflict. especially in mammals with exclusive maternal care, infanticide by males is common and females suffer fitness costs. Recognizing infanticide risk and adjusting offspring protection accordingly should therefore be adaptive in female mammals. Using a small mammal (Myodes glareolus) in outdoor enclosures, we investigated whether lactating mothers adjust offspring protection, and potential mate search behaviour, in response to different infanticide risk levels. We presented the scent of the litter's sire or of a stranger male near the female's nest, and observed female nest presence and movement by radiotracking. While both scents simulated a mating opportunity, they represented lower (sire) and higher (stranger) infanticide risk. compared to the sire treatment, females in the stranger treatment left their nest more often, showed increased activity and stayed closer to the nest, suggesting offspring protection from outside the nest through elevated alertness and vigilance. females with larger litters spent more time investigating scents and used more space in the sire but not in the stranger treatment. Thus, current investment size affected odour inspection and resource acquisition under higher risk. Adjusting nest protection and resource acquisition to infanticide risk could allow mothers to elicit appropriate (fitness-saving) counterstrategies, and thus, may be widespread.}, language = {en} } @article{BrechunZhenJaikaranetal.2019, author = {Brechun, Katherine E. and Zhen, Danlin and Jaikaran, Anna and Borisenko, Vitali and Kumauchi, Masato and Hoff, Wouter D. and Arndt, Katja Maren and Woolley, Andrew G}, title = {Detection of Incorporation of p-Coumaric Acid into Photoactive Yellow Protein Variants in Vivo}, series = {Biochemistry}, volume = {58}, journal = {Biochemistry}, number = {23}, publisher = {American Chemical Society}, address = {Washington}, issn = {0006-2960}, doi = {10.1021/acs.biochem.9b00279}, pages = {2682 -- 2694}, year = {2019}, abstract = {We report the design and characterization of photoactive yellow protein (PYP)-blue fluorescent protein (mTagBFP) fusion constructs that permit the direct assay of reconstitution and function of the PYP domain. These constructs allow for in vivo testing of co-expression systems for enzymatic production of the p-coumaric acid-based PYP chromophore, via the action of tyrosine ammonia lyase and p-coumaroyl-CoA ligase (pCL or 4CL). We find that different 4CL enzymes can function to reconstitute PYP, including 4CL from Arabidopsis thaliana that can produce similar to 100\% holo-PYP protein under optimal conditions. mTagBFP fusion constructs additionally enable rapid analysis of effects of mutations on PYP photocycles. We use this mTagBFP fusion strategy to demonstrate in vivo reconstitution of several PYP-based optogenetic tools in Escherichia coli via a biosynthesized chromophore, an important step for the use of these optogenetic tools in vivo in diverse hosts.}, language = {en} } @phdthesis{Brechun2019, author = {Brechun, Katherine E.}, title = {Development and application of genetic networks for engineering photo-controlled proteins}, doi = {10.25932/publishup-43092}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430924}, school = {Universit{\"a}t Potsdam}, pages = {xxiv, 195}, year = {2019}, abstract = {Light-switchable proteins are being used increasingly to understand and manipulate complex molecular systems. The success of this approach has fueled the development of tailored photo-switchable proteins, to enable targeted molecular events to be studied using light. The development of novel photo-switchable tools has to date largely relied on rational design. Complementing this approach with directed evolution would be expected to facilitate these efforts. Directed evolution, however, has been relatively infrequently used to develop photo-switchable proteins due to the challenge presented by high-throughput evaluation of switchable protein activity. This thesis describes the development of two genetic circuits that can be used to evaluate libraries of switchable proteins, enabling optimization of both the on- and off-states. A screening system is described, which permits detection of DNA-binding activity based on conditional expression of a fluorescent protein. In addition, a tunable selection system is presented, which allows for the targeted selection of protein-protein interactions of a desired affinity range. This thesis additionally describes the development and characterization of a synthetic protein that was designed to investigate chromophore reconstitution in photoactive yellow protein (PYP), a promising scaffold for engineering photo-controlled protein tools.}, language = {en} } @article{BrauneGuetschowBlaut2019, author = {Braune, Annett and G{\"u}tschow, Michael and Blaut, Michael}, title = {An NADH-Dependent Reductase from Eubacterium ramulus Catalyzes the Stereospecific Heteroring Cleavage of Flavanones and Flavanonols}, series = {Applied and environmental microbiology}, volume = {85}, journal = {Applied and environmental microbiology}, number = {19}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {0099-2240}, doi = {10.1128/AEM.01233-19}, pages = {15}, year = {2019}, abstract = {The human intestinal anaerobe Eubacterium ramulus is known for its ability to degrade various dietary flavonoids. In the present study, we demonstrate the cleavage of the heterocyclic C-ring of flavanones and flavanonols by an oxygen-sensitive NADH-dependent reductase, previously described as enoate reductase, from E. ramulus. This flavanone- and flavanonol-cleaving reductase (Fcr) was purified following its heterologous expression in Escherichia coli and further characterized. Fcr cleaved the flavanones naringenin, eriodictyol, liquiritigenin, and homoeriodictyol. Moreover, the flavanonols taxifolin and dihydrokaempferol served as substrates. The catalyzed reactions were stereospecific for the (2R)-enantiomers of the flavanone substrates and for the (25,35)-configured flavanonols. The enantioenrichment of the nonconverted stereoisomers allowed for the determination of hitherto unknown flavanone racemization rates. Fcr formed the corresponding dihydrochalcones and hydroxydihydrochalcones in the course of an unusual reductive cleavage of cyclic ether bonds. Fcr did not convert members of other flavonoid subclasses, including flavones, flavonols, and chalcones, the latter indicating that the reaction does not involve a chalcone intermediate. This view is strongly supported by the observed enantiospecificity of Fcr. Cinnamic acids, which are typical substrates of bacterial enoate reductases, were also not reduced by Fcr. Based on the presence of binding motifs for dinucleotide cofactors and a 4Fe-4S cluster in the amino acid sequence of Fcr, a cofactor-mediated hydride transfer from NADH onto C-2 of the respective substrate is proposed. IMPORTANCE Gut bacteria play a crucial role in the metabolism of dietary flavonoids, thereby contributing to their activation or inactivation after ingestion by the human host. Thus, bacterial activities in the intestine may influence the beneficial health effects of these polyphenolic plant compounds. While an increasing number of flavonoid-converting gut bacterial species have been identified, knowledge of the responsible enzymes is still limited. Here, we characterized Fcr as a key enzyme involved in the conversion of flavonoids of several subclasses by Eubacterium ramulus, a prevalent human gut bacterium. Sequence similarity of this enzyme to hypothetical proteins from other flavonoid-degrading intestinal bacteria in databases suggests a more widespread occurrence of this enzyme. Functional characterization of gene products of human intestinal microbiota enables the assignment of metagenomic sequences to specific bacteria and, more importantly, to certain activities, which is a prerequisite for targeted modulation of gut microbial functionality.}, language = {en} } @article{BornhorstXiaNakajimaetal.2019, author = {Bornhorst, Dorothee and Xia, Peng and Nakajima, Hiroyuki and Dingare, Chaitanya and Herzog, Wiebke and Lecaudey, Virginie and Mochizuki, Naoki and Heisenberg, Carl-Philipp and Yelon, Deborah and Abdelilah-Seyfried, Salim}, title = {Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-12068-x}, pages = {10}, year = {2019}, abstract = {Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed.}, language = {en} } @article{BontrupTaylorFliesseretal.2019, author = {Bontrup, Carolin and Taylor, William R. and Fliesser, Michael and Visscher, Rosa and Green, Tamara and Wippert, Pia-Maria and Zemp, Roland}, title = {Low back pain and its relationship with sitting behaviour among sedentary office workers}, series = {Applied ergonomics : human factors in technology and society}, volume = {81}, journal = {Applied ergonomics : human factors in technology and society}, publisher = {Elsevier}, address = {Oxford}, issn = {0003-6870}, doi = {10.1016/j.apergo.2019.102894}, pages = {8}, year = {2019}, abstract = {The relationships between sedentary lifestyle, sitting behaviour, and low back pain (LBP) remain controversial. In this study, we investigated the relationship between back pain and occupational sitting habits in 64 call-centre employees. A textile pressure mat was used to evaluate and parameterise sitting behaviour over a total of 400 h, while pain questionnaires evaluated acute and chronic LBP. Seventy-five percent of the participants reported some level of either chronic or acute back pain. Individuals with chronic LBP demonstrated a possible trend (t-test not significant) towards more static sitting behaviour compared to their pain-free counterparts. Furthermore, a greater association was found between sitting behaviour and chronic LBP than for acute pain/disability, which is plausibly due to a greater awareness of pain-free sitting positions in individuals with chronic pain compared to those affected by acute pain.}, language = {en} } @article{BoliusWiednerWeithoff2019, author = {Bolius, Sarah and Wiedner, Claudia and Weithoff, Guntram}, title = {Low invasion success of an invasive cyanobacterium in a chlorophyte dominated lake}, series = {Scientific reports}, volume = {9}, journal = {Scientific reports}, publisher = {Macmillan Publishers Limited}, address = {London}, issn = {2045-2322}, pages = {12}, year = {2019}, language = {en} } @misc{BlockDenfeldStockwelletal.2019, author = {Block, Benjamin D. and Denfeld, Blaize A. and Stockwell, Jason D. and Flaim, Giovanna and Grossart, Hans-Peter and Knoll, Lesley B. and Maier, Dominique B. and North, Rebecca L. and Rautio, Milla and Rusak, James A. and Sadro, Steve and Weyhenmeyer, Gesa A. and Bramburger, Andrew J. and Branstrator, Donn K. and Salonen, Kalevi and Hampton, Stephanie E.}, title = {The unique methodological challenges of winter limnology}, series = {Limnology and Oceanography: Methods}, volume = {17}, journal = {Limnology and Oceanography: Methods}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1541-5856}, doi = {10.1002/lom3.10295}, pages = {42 -- 57}, year = {2019}, abstract = {Winter is an important season for many limnological processes, which can range from biogeochemical transformations to ecological interactions. Interest in the structure and function of lake ecosystems under ice is on the rise. Although limnologists working at polar latitudes have a long history of winter work, the required knowledge to successfully sample under winter conditions is not widely available and relatively few limnologists receive formal training. In particular, the deployment and operation of equipment in below 0 degrees C temperatures pose considerable logistical and methodological challenges, as do the safety risks of sampling during the ice-covered period. Here, we consolidate information on winter lake sampling and describe effective methods to measure physical, chemical, and biological variables in and under ice. We describe variation in snow and ice conditions and discuss implications for sampling logistics and safety. We outline commonly encountered methodological challenges and make recommendations for best practices to maximize safety and efficiency when sampling through ice or deploying instruments in ice-covered lakes. Application of such practices over a broad range of ice-covered lakes will contribute to a better understanding of the factors that regulate lakes during winter and how winter conditions affect the subsequent ice-free period.}, language = {en} } @article{BetkeLokstein2019, author = {Betke, Alexander and Lokstein, Heiko}, title = {Two-photon excitation spectroscopy of photosynthetic light-harvesting complexes and pigments}, series = {Faraday discussions}, volume = {216}, journal = {Faraday discussions}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1359-6640}, doi = {10.1039/c8fd00198g}, pages = {494 -- 506}, year = {2019}, abstract = {In addition to (bacterio)chlorophylls, (B)Chls, light-harvesting complexes (LHCs) bind carotenoids, and/or their oxygen derivatives, xanthophylls. Xanthophylls/carotenoids have pivotal functions in LHCs: in stabilization of the structure, as accessory light-harvesting pigments and, probably most importantly, in photoprotection. Xanthophylls are assumed to be involved in the not yet fully understood mechanism of energy-dependent (qE) non-photochemical quenching of Chl fluorescence (NPQ) in higher plants and algae. The so called "xanthophyll cycle" appears to be crucial in this regard. The molecular mechanism(s) of xanthophyll involvement in qE/NPQ have not been established, yet. Moreover, excitation energy transfer (EET) processes involving carotenoids are also difficult to study, due to the fact that transitions between the ground state (S-0, 1(1)A(g)(-)) and the lowest excited singlet state (S-1, 2(1)A(g)(-)) of carotenoids are optically one-photon forbidden ("dark"). Two-photon excitation spectroscopic techniques have been used for more than two decades to study one-photon forbidden states of carotenoids. In the current study, two-photon excitation profiles of LHCII samples containing different xanthophyll complements were measured in the presumed 1(1)A(g)(-) -> 2(1)A(g)(-) (S-0 -> S-1) transition spectral region of the xanthophylls, as well as for isolated chlorophylls a and b in solution. The results indicate that direct two-photon excitation of Chls in this spectral region is dominant over that by xanthophylls. Implications of the results for proposed mechanism(s) of qE/NPQ will be discussed.}, language = {en} } @phdthesis{Behm2019, author = {Behm, Laura Vera Johanna}, title = {Thermoresponsive Zellkultursubstrate f{\"u}r zeitlich-r{\"a}umlich gesteuertes Auswachsen neuronaler Zellen}, doi = {10.25932/publishup-43619}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436196}, school = {Universit{\"a}t Potsdam}, pages = {VII, 105}, year = {2019}, abstract = {Ein wichtiges Ziel der Neurowissenschaften ist das Verst{\"a}ndnis der komplexen und zugleich faszinierenden, hochgeordneten Vernetzung der Neurone im Gehirn, welche neuronalen Prozessen, wie zum Beispiel dem Wahrnehmen oder Lernen wie auch Neuropathologien zu Grunde liegt. F{\"u}r verbesserte neuronale Zellkulturmodelle zur detaillierten Untersuchung dieser Prozesse ist daher die Rekonstruktion von geordneten neuronalen Verbindungen dringend erforderlich. Mit Oberfl{\"a}chenstrukturen aus zellattraktiven und zellabweisenden Beschichtungen k{\"o}nnen neuronale Zellen und ihre Neuriten in vitro strukturiert werden. Zur Kontrolle der neuronalen Verbindungsrichtung muss das Auswachsen der Axone zu benachbarten Zellen dynamisch gesteuert werden, zum Beispiel {\"u}ber eine ver{\"a}nderliche Zug{\"a}nglichkeit der Oberfl{\"a}che. In dieser Arbeit wurde untersucht, ob mit thermoresponsiven Polymeren (TRP) beschichtete Zellkultursubstrate f{\"u}r eine dynamische Kontrolle des Auswachsens neuronaler Zellen geeignet sind. TRP k{\"o}nnen {\"u}ber die Temperatur von einem zellabweisenden in einen zellattraktiven Zustand geschaltet werden, womit die Zug{\"a}nglichkeit der Oberfl{\"a}che f{\"u}r Zellen dynamisch gesteuert werden kann. Die TRP-Beschichtung wurde mikrostrukturiert, um einzelne oder wenige neuronale Zellen zun{\"a}chst auf der Oberfl{\"a}che anzuordnen und das Auswachsen der Zellen und Neuriten {\"u}ber definierte TRP-Bereiche in Abh{\"a}ngigkeit der Temperatur zeitlich und r{\"a}umlich zu kontrollieren. Das Protokoll wurde mit der neuronalen Zelllinie SH-SY5Y etabliert und auf humane induzierte Neurone {\"u}bertragen. Die Anordnung der Zellen konnte bei Kultivierung im zellabweisenden Zustand des TRPs f{\"u}r bis zu 7 Tage aufrecht erhalten werden. Durch Schalten des TRPs in den zellattraktiven Zustand konnte das Auswachsen der Neuriten und Zellen zeitlich und r{\"a}umlich induziert werden. Immunozytochemische F{\"a}rbungen und Patch-Clamp-Ableitungen der Neurone demonstrierten die einfache Anwendbarkeit und Zellkompatibilit{\"a}t der TRP-Substrate. Eine pr{\"a}zisere r{\"a}umliche Kontrolle des Auswachsens der Zellen sollte durch lokales Schalten der TRP-Beschichtung erreicht werden. Daf{\"u}r wurden Mikroheizchips mit Mikroelektroden zur lokalen Jouleschen Erw{\"a}rmung der Substratoberfl{\"a}che entwickelt. Zur Evaluierung der generierten Temperaturprofile wurde eine Temperaturmessmethode entwickelt und die erhobenen Messwerte mit numerisch simulierten Werten abgeglichen. Die Temperaturmessmethode basiert auf einfach zu applizierenden Sol-Gel-Schichten, die den temperatursensitiven Fluoreszenzfarbstoff Rhodamin B enthalten. Sie erm{\"o}glicht oberfl{\"a}chennahe Temperaturmessungen in trockener und w{\"a}ssriger Umgebung mit hoher Orts- und Temperaturaufl{\"o}sung. Numerische Simulationen der Temperaturprofile korrelierten gut mit den experimentellen Daten. Auf dieser Basis konnten Geometrie und Material der Mikroelektroden hinsichtlich einer lokal stark begrenzten Temperierung optimiert werden. Ferner wurden f{\"u}r die Kultvierung der Zellen auf den Mikroheizchips eine Zellkulturkammer und Kontaktboard f{\"u}r die elektrische Kontaktierung der Mikroelektroden geschaffen. Die vorgestellten Ergebnisse demonstrieren erstmalig das enorme Potential thermoresponsiver Zellkultursubstrate f{\"u}r die zeitlich und r{\"a}umlich gesteuerte Formation geordneter neuronaler Verbindungen in vitro. Zuk{\"u}nftig k{\"o}nnte dies detaillierte Studien zur neuronalen Informationsverarbeitung oder zu Neuropathologien an relevanten, humanen Zellmodellen erm{\"o}glichen.}, language = {de} } @article{BeckmannBeckerKadowetal.2019, author = {Beckmann, Nadine and Becker, Katrin Anne and Kadow, Stephanie and Schumacher, Fabian and Kramer, Melanie and Kuehn, Claudine and Schulz-Schaeffer, Walter J. and Edwards, Michael J. and Kleuser, Burkhard and Gulbins, Erich and Carpinteiro, Alexander}, title = {Acid Sphingomyelinase Deficiency Ameliorates Farber Disease}, series = {International journal of molecular sciences}, volume = {20}, journal = {International journal of molecular sciences}, number = {24}, publisher = {MDPI}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms20246253}, pages = {18}, year = {2019}, abstract = {Farber disease is a rare lysosomal storage disorder resulting from acid ceramidase deficiency and subsequent ceramide accumulation. No treatments for Farber disease are clinically available, and affected patients have a severely shortened lifespan. We have recently reported a novel acid ceramidase deficiency model that mirrors the human disease closely. Acid sphingomyelinase is the enzyme that generates ceramide upstream of acid ceramidase in the lysosomes. Using our acid ceramidase deficiency model, we tested if acid sphingomyelinase could be a potential novel therapeutic target for the treatment of Farber disease. A number of functional acid sphingomyelinase inhibitors are clinically available and have been used for decades to treat major depression. Using these as a therapeutic for Farber disease, thus, has the potential to improve central nervous symptoms of the disease as well, something all other treatment options for Farber disease can't achieve so far. As a proof-of-concept study, we first cross-bred acid ceramidase deficient mice with acid sphingomyelinase deficient mice in order to prevent ceramide accumulation. Double-deficient mice had reduced ceramide accumulation, fewer disease manifestations, and prolonged survival. We next targeted acid sphingomyelinase pharmacologically, to test if these findings would translate to a setting with clinical applicability. Surprisingly, the treatment of acid ceramidase deficient mice with the acid sphingomyelinase inhibitor amitriptyline was toxic to acid ceramidase deficient mice and killed them within a few days of treatment. In conclusion, our study provides the first proof-of-concept that acid sphingomyelinase could be a potential new therapeutic target for Farber disease to reduce disease manifestations and prolong survival. However, we also identified previously unknown toxicity of the functional acid sphingomyelinase inhibitor amitriptyline in the context of Farber disease, strongly cautioning against the use of this substance class for Farber disease patients.}, language = {en} } @article{BatsiosIshikawaAnkerholdRothetal.2019, author = {Batsios, Petros and Ishikawa-Ankerhold, Hellen Christina and Roth, Heike and Schleicher, Michael and Wong, Catherine C. L. and M{\"u}ller-Taubenberger, Annette}, title = {Ate1-mediated posttranslational arginylation affects substrate adhesion and cell migration in Dictyostelium discoideum}, series = {Molecular biology of the cell : the official publication of the American Society for Cell Biology}, volume = {30}, journal = {Molecular biology of the cell : the official publication of the American Society for Cell Biology}, number = {4}, publisher = {American Society for Cell Biology}, address = {Bethesda}, issn = {1059-1524}, doi = {10.1091/mbc.E18-02-0132}, pages = {453 -- 466}, year = {2019}, abstract = {The highly conserved enzyme arginyl-tRNA-protein transferase (Ate1) mediates arginylation, a posttranslational modification that is only incompletely understood at its molecular level. To investigate whether arginylation affects actin-dependent processes in a simple model organism, Dictyostelium discoideum, we knocked out the gene encoding Ate1 and characterized the phenotype of ate1-null cells. Visualization of actin cytoskeleton dynamics by live-cell microscopy indicated significant changes in comparison to wild-type cells. Ate1-null cells were almost completely lacking focal actin adhesion sites at the substrate-attached surface and were only weakly adhesive. In two-dimensional chemotaxis assays toward folate or cAMP, the motility of ate1-null cells was increased. However, in three-dimensional chemotaxis involving more confined conditions, the motility of ate1-null cells was significantly reduced. Live-cell imaging showed that GFP-tagged Ate1 rapidly relocates to sites of newly formed actin-rich protrusions. By mass spectrometric analysis, we identified four arginylation sites in the most abundant actin isoform of Dictyostelium, in addition to arginylation sites in other actin isoforms and several actin-binding proteins. In vitro polymerization assays with actin purified from ate1-null cells revealed a diminished polymerization capacity in comparison to wild-type actin. Our data indicate that arginylation plays a crucial role in the regulation of cytoskeletal activities.}, language = {en} } @article{BatsiosGraefKoonceetal.2019, author = {Batsios, Petros and Gr{\"a}f, Ralph and Koonce, Michael P. and Larochelle, Denis A. and Meyer, Irene}, title = {Nuclear envelope organization in Dictyostelium discoideum}, series = {The international journal of developmental biology}, volume = {63}, journal = {The international journal of developmental biology}, number = {8-10}, publisher = {UBC Pr}, address = {Bilbao}, issn = {0214-6282}, doi = {10.1387/ijdb.190184rg}, pages = {509 -- 519}, year = {2019}, abstract = {The nuclear envelope consists of the outer and the inner nuclear membrane, the nuclear lamina and the nuclear pore complexes, which regulate nuclear import and export.The major constituent of the nuclear lamina of Dictyostelium is the lamin NE81. It can form filaments like B-type lamins and it interacts with Sun 1, as well as with the LEM/HeH-family protein Src1. Sun 1 and Src1 are nuclear envelope transmembrane proteins involved in the centrosome-nucleus connection and nuclear envelope stability at the nucleolar regions, respectively. In conjunction with a KASH-domain protein, Sun 1 usually forms a so-called LINC complex.Two proteins with functions reminiscent of KASH-domain proteins at the outer nuclear membrane of Dictyostelium are known; interaptin which serves as an actin connector and the kinesin Kif9 which plays a role in the microtubule-centrosome connector. However, both of these lack the conserved KASH-domain. The link of the centrosome to the nuclear envelope is essential for the insertion of the centrosome into the nuclear envelope and the appropriate spindle formation. Moreover, centrosome insertion is involved in perm eabilization of the mitotic nucleus, which ensures access of tubulin dimers and spindle assembly factors. Our recent progress in identifying key molecular players at the nuclear envelope of Dictyostelium promises further insights into the mechanisms of nuclear envelope dynamics.}, language = {en} } @article{BatistaMorenoRomeroQiuetal.2019, author = {Batista, Rita A. and Moreno-Romero, Jordi and Qiu, Yichun and van Boven, Joram and Santos-Gonzalez, Juan and Figueiredo, Duarte Dionisio and K{\"o}hler, Claudia}, title = {The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons}, series = {eLife}, volume = {8}, journal = {eLife}, publisher = {eLife Sciences Publications}, address = {Cambridge}, issn = {2050-084X}, doi = {10.7554/eLife.50541}, pages = {29}, year = {2019}, abstract = {MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.}, language = {en} } @article{BatistaFigueiredoSantosGonzalezetal.2019, author = {Batista, Rita A. and Figueiredo, Duarte Dionisio and Santos-Gonzalez, Juan and K{\"o}hler, Claudia}, title = {Auxin regulates endosperm cellularization in Arabidopsis}, series = {Genes \& Development}, volume = {33}, journal = {Genes \& Development}, number = {7-8}, publisher = {Cold Spring Harbor Laboratory Press}, address = {Cold Spring Harbor, NY}, issn = {0890-9369}, doi = {10.1101/gad.316554.118}, pages = {466 -- 476}, year = {2019}, abstract = {The endosperm is an ephemeral tissue that nourishes the developing embryo, similar to the placenta in mammals. In most angiosperms, endosperm development starts as a syncytium, in which nuclear divisions are not followed by cytokinesis. The timing of endosperm cellularization largely varies between species, and the event triggering this transition remains unknown. Here we show that increased auxin biosynthesis in the endosperm prevents its cellularization, leading to seed arrest. Auxin-overproducing seeds phenocopy paternal-excess triploid seeds derived from hybridizations of diploid maternal plants with tetraploid fathers. Concurrently, auxin-related genes are strongly overexpressed in triploid seeds, correlating with increased auxin activity. Reducing auxin biosynthesis and signaling reestablishes endosperm cellularization in triploid seeds and restores their viability, highlighting a causal role of increased auxin in preventing endosperm cellularization. We propose that auxin determines the time of endosperm cellularization, and thereby uncovered a central role of auxin in establishing hybridization barriers in plants.}, language = {en} } @misc{BartholomaeusLenhard2019, author = {Bartholom{\"a}us, Lisa and Lenhard, Michael}, title = {Plant Biology: Learning to Love Yourself}, series = {Current biology}, volume = {29}, journal = {Current biology}, number = {14}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2019.06.015}, pages = {R695 -- R697}, year = {2019}, abstract = {In self-incompatible plants the female style rejects self pollen, yet the extent to which the female style in the many self-compatible species can still select between different pollen genotypes and thus bias fertilization success is unclear. A new study identifies the molecular basis for how styles of the self-compatible coyote tobacco bias the fertilization success of pollen genotypes using matching gene expression patterns in a manner analogous to cryptic female choice in animals.}, language = {en} } @article{BarchewitzGuljamowMeissneretal.2019, author = {Barchewitz, Tino and Guljamow, Arthur and Meißner, Sven and Timm, Stefan and Henneberg, Manja and Baumann, Otto and Hagemann, Martin and Dittmann, Elke}, title = {Non-canonical localization of RubisCO under high-light conditions in the toxic cyanobacterium Microcystis aeruginosa PCC7806}, series = {Environmental microbiology}, volume = {21}, journal = {Environmental microbiology}, number = {12}, publisher = {Wiley}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.14837}, pages = {4836 -- 4851}, year = {2019}, abstract = {The frequent production of the hepatotoxin microcystin (MC) and its impact on the lifestyle of bloom-forming cyanobacteria are poorly understood. Here, we report that MC interferes with the assembly and the subcellular localization of RubisCO, in Microcystis aeruginosa PCC7806. Immunofluorescence, electron microscopic and cellular fractionation studies revealed a pronounced heterogeneity in the subcellular localization of RubisCO. At high cell density, RubisCO particles are largely separate from carboxysomes in M. aeruginosa and relocate to the cytoplasmic membrane under high-light conditions. We hypothesize that the binding of MC to RubisCO promotes its membrane association and enables an extreme versatility of the enzyme. Steady-state levels of the RubisCO CO2 fixation product 3-phosphoglycerate are significantly higher in the MC-producing wild type. We also detected noticeable amounts of the RubisCO oxygenase reaction product secreted into the medium that may support the mutual interaction of M. aeruginosa with its heterotrophic microbial community.}, language = {en} } @phdthesis{Baleka2019, author = {Baleka, Sina Isabelle}, title = {Palaeogenetic analyses of extinct Elephantidae from temperate and subtropical climates}, school = {Universit{\"a}t Potsdam}, pages = {xiii, 114}, year = {2019}, language = {en} } @article{AwanSchiebelBoehmetal.2019, author = {Awan, Asad Bashir and Schiebel, Juliane and Boehm, Alexander and Nitschke, Joerg and Sarwar, Yasra and Schierack, Peter and Ali, Aamir}, title = {Association of biofilm formation and cytotoxic potential with multidrug resistance in clinical isolates of pseudomonas aeruginosa}, series = {EXCLI Journal}, volume = {18}, journal = {EXCLI Journal}, publisher = {Leibniz Research Centre for Working Environment and Human Factors}, address = {Dortmund}, issn = {1611-2156}, doi = {10.17179/excli2018-1948}, pages = {79 -- 90}, year = {2019}, abstract = {Multidrug resistant (MDR) Pseudomonas aeruginosa having strong biofilm potential and virulence factors are a serious threat for hospitalized patients having compromised immunity In this study, 34 P. aeruginosa isolates of human origin (17 MDR and 17 non-MDR clinical isolates) were checked for biofilm formation potential in enriched and minimal media. The biofilms were detected using crystal violet method and a modified software package of the automated VideoScan screening method. Cytotoxic potential of the isolates was also investigated on HepG2, LoVo and T24 cell lines using automated VideoScan technology. Pulse field gel electrophoresis revealed 10 PFGE types in MDR and 8 in non-MDR isolates. Although all isolates showed biofilm formation potential, strong biofilm formation was found more in enriched media than in minimal media. Eight MDR isolates showed strong biofilm potential in both enriched and minimal media by both detection methods. Strong direct correlation between crystal violet and VideoScan methods was observed in identifying strong biofilm forming isolates. High cytotoxic effect was observed by 4 isolates in all cell lines used while 6 other isolates showed high cytotoxic effect on T24 cell line only. Strong association of multidrug resistance was found with biofilm formation as strong biofilms were observed significantly higher in MDR isolates (p-value < 0.05) than non-MDR isolates. No significant association of cytotoxic potential with multidrug resistance or biofilm formation was found (p-value > 0.05). The MDR isolates showing significant cytotoxic effects and strong biofilm formation impose a serious threat for hospitalized patients with weak immune system.}, language = {en} } @misc{Arnold2019, author = {Arnold, Patrick}, title = {The origin of morphological integration and modularity in the Mammalian Neck}, series = {Journal of morphology}, volume = {280}, journal = {Journal of morphology}, publisher = {Wiley}, address = {Hoboken}, issn = {0362-2525}, doi = {10.1002/jmor.21003}, pages = {S13 -- S13}, year = {2019}, language = {en} } @article{AngeleskaNikoloski2019, author = {Angeleska, Angela and Nikoloski, Zoran}, title = {Coherent network partitions}, series = {Discrete applied mathematics}, volume = {266}, journal = {Discrete applied mathematics}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0166-218X}, doi = {10.1016/j.dam.2019.02.048}, pages = {283 -- 290}, year = {2019}, abstract = {Graph clustering is widely applied in the analysis of cellular networks reconstructed from large-scale data or obtained from experimental evidence. Here we introduce a new type of graph clustering based on the concept of coherent partition. A coherent partition of a graph G is a partition of the vertices of G that yields only disconnected subgraphs in the complement of G. The coherence number of G is then the size of the smallest edge cut inducing a coherent partition. A coherent partition of G is optimal if the size of the inducing edge cut is the coherence number of G. Given a graph G, we study coherent partitions and the coherence number in connection to (bi)clique partitions and the (bi)clique cover number. We show that the problem of finding the coherence number is NP-hard, but is of polynomial time complexity for trees. We also discuss the relation between coherent partitions and prominent graph clustering quality measures.}, language = {en} } @article{AndresDelgadoErnstGalardiCastillaetal.2019, author = {Andr{\´e}s-Delgado, Laura and Ernst, Alexander and Galardi-Castilla, Mar{\´i}a and Bazaga, David and Peralta, Marina and M{\"u}nch, Juliane and Gonzalez-Rosa, Juan M. and Marques, In{\^e}s and Tessadori, Federico and de la Pompa, Jos{\´e} Luis and Vermot, Julien and Mercader, Nadia}, title = {Actin dynamics and the Bmp pathway drive apical extrusion of proepicardial cells}, series = {Development : Company of Biologists}, volume = {146}, journal = {Development : Company of Biologists}, number = {13}, publisher = {The Company of Biologists Ltd}, address = {Cambridge}, issn = {0950-1991}, doi = {10.1242/dev.174961}, pages = {15}, year = {2019}, abstract = {The epicardium, the outer mesothelial layer enclosing the myocardium, plays key roles in heart development and regeneration. During embryogenesis, the epicardium arises from the proepicardium (PE), a cell cluster that appears in the dorsal pericardium (DP) close to the venous pole of the heart. Little is known about how the PE emerges from the pericardial mesothelium. Using a zebrafish model and a combination of genetic tools, pharmacological agents and quantitative in vivo imaging, we reveal that a coordinated collective movement of DP cells drives PE formation. We found that Bmp signaling and the actomyosin cytoskeleton promote constriction of the DP, which enables PE cells to extrude apically. We provide evidence that cell extrusion, which has been described in the elimination of unfit cells from epithelia and the emergence of hematopoietic stem cells, is also a mechanism for PE cells to exit an organized mesothelium and fulfil their developmental fate to form a new tissue layer, the epicardium.}, language = {en} } @article{AltintasTakidenUteschetal.2019, author = {Altintas, Zeynep and Takiden, Aref and Utesch, Tillmann and Mroginski, Maria A. and Schmid, Bianca and Scheller, Frieder W. and S{\"u}ssmuth, Roderich D.}, title = {Integrated approaches toward high-affinity artificial protein binders obtained via computationally simulated epitopes for protein recognition}, series = {Advanced functional materials}, volume = {29}, journal = {Advanced functional materials}, number = {15}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1616-301X}, doi = {10.1002/adfm.201807332}, pages = {11}, year = {2019}, abstract = {Widely used diagnostic tools make use of antibodies recognizing targeted molecules, but additional techniques are required in order to alleviate the disadvantages of antibodies. Herein, molecular dynamic calculations are performed for the design of high affinity artificial protein binding surfaces for the recognition of neuron specific enolase (NSE), a known cancer biomarker. Computational simulations are employed to identify particularly stabile secondary structure elements. These epitopes are used for the subsequent molecular imprinting, where surface imprinting approach is applied. The molecular imprints generated with the calculated epitopes of greater stability (Cys-Ep1) show better binding properties than those of lower stability (Cys-Ep5). The average binding strength of imprints created with stabile epitopes is found to be around twofold and fourfold higher for the NSE derived peptide and NSE protein, respectively. The recognition of NSE is investigated in a wide concentration range, where high sensitivity (limit of detection (LOD) = 0.5 ng mL(-1)) and affinity (dissociation constant (K-d) = 5.3 x 10(-11)m) are achieved using Cys-Ep1 imprints reflecting the stable structure of the template molecules. This integrated approach employing stability calculations for the identification of stabile epitopes is expected to have a major impact on the future development of high affinity protein capturing binders.}, language = {en} } @article{AlkerSchwerdtleSchomburgetal.2019, author = {Alker, Wiebke and Schwerdtle, Tanja and Schomburg, Lutz and Haase, Hajo}, title = {A Zinpyr-1-based Fluorimetric Microassay for Free Zinc in Human Serum}, series = {International journal of molecular sciences}, volume = {20}, journal = {International journal of molecular sciences}, number = {16}, publisher = {MDPI}, address = {Basel}, issn = {1661-6596}, doi = {10.3390/ijms20164006}, pages = {13}, year = {2019}, abstract = {Zinc is an essential trace element, making it crucial to have a reliable biomarker for evaluating an individual's zinc status. The total serum zinc concentration, which is presently the most commonly used biomarker, is not ideal for this purpose, but a superior alternative is still missing. The free zinc concentration, which describes the fraction of zinc that is only loosely bound and easily exchangeable, has been proposed for this purpose, as it reflects the highly bioavailable part of serum zinc. This report presents a fluorescence-based method for determining the free zinc concentration in human serum samples, using the fluorescent probe Zinpyr-1. The assay has been applied on 154 commercially obtained human serum samples. Measured free zinc concentrations ranged from 0.09 to 0.42 nM with a mean of 0.22 ± 0.05 nM. It did not correlate with age or the total serum concentrations of zinc, manganese, iron or selenium. A negative correlation between the concentration of free zinc and total copper has been seen for sera from females. In addition, the free zinc concentration in sera from females (0.21 ± 0.05 nM) was significantly lower than in males (0.23 ± 0.06 nM). The assay uses a sample volume of less than 10 µL, is rapid and cost-effective and allows us to address questions regarding factors influencing the free serum zinc concentration, its connection with the body's zinc status, and its suitability as a future biomarker for an individual's zinc status.}, language = {en} } @article{AlbersUestuenWitzeletal.2019, author = {Albers, Philip and {\"U}st{\"u}n, Suayib and Witzel, Katja and Kraner, Max Erdmund and B{\"o}rnke, Frederik}, title = {A Remorin from Nicotiana benthamiana Interacts with the Pseudomonas Type-III Effector Protein HopZ1a and is Phosphorylated by the Immune-Related Kinase PBS1}, series = {Molecular Plant-Microbe Interactions}, volume = {32}, journal = {Molecular Plant-Microbe Interactions}, number = {9}, publisher = {Amer phytopathological SOC}, address = {ST Paul}, issn = {0894-0282}, doi = {10.1094/MPMI-04-19-0105-R}, pages = {1229 -- 1242}, year = {2019}, abstract = {The plasma membrane (PM) is at the interface of plant-pathogen interactions and, thus, many bacterial type-III effector (T3E) proteins target membrane-associated processes to interfere with immunity. The Pseudomonas syringae T3E HopZ1a is a host cell PM-localized effector protein that has several immunity-associated host targets but also activates effector-triggered immunity in resistant backgrounds. Although HopZ1a has been shown to interfere with early defense signaling at the PM, no dedicated PM-associated HopZ1a target protein has been identified until now. Here, we show that HopZ1a interacts with the PM-associated remorin protein NbREM4 from Nicotiana benthamiana in several independent assays. NbREM4 relocalizes to membrane nanodomains after treatment with the bacterial elicitor flg22 and transient overexpression of NbREM4 in N. benthamiana induces the expression of a subset of defense-related genes. We can further show that NbREM4 interacts with the immune-related receptor-like cytoplasmic kinase avrPphB-susceptible 1 (PBS1) and is phosphorylated by PBS1 on several residues in vitro. Thus, we conclude that NbREM4 is associated with early defense signaling at the PM. The possible relevance of the HopZ1a-NbREM4 interaction for HopZ1a virulence and avirulence functions is discussed.}, language = {en} } @article{AdemKueteMbavengetal.2019, author = {Adem, Fozia A. and Kuete, Victor and Mbaveng, Armelle T. and Heydenreich, Matthias and Koch, Andreas and Ndakala, Albert and Irungu, Beatrice and Yenesew, Abiy and Efferth, Thomas}, title = {Cytotoxic flavonoids from two Lonchocarpus species}, series = {Natural Product Research}, volume = {33}, journal = {Natural Product Research}, number = {18}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {1478-6419}, doi = {10.1080/14786419.2018.1462179}, pages = {2609 -- 2617}, year = {2019}, abstract = {A new isoflavone, 4′-prenyloxyvigvexin A (1) and a new pterocarpan, (6aR,11aR)-3,8-dimethoxybitucarpin B (2) were isolated from the leaves of Lonchocarpus bussei and the stem bark of Lonchocarpus eriocalyx, respectively. The extract of L. bussei also gave four known isoflavones, maximaisoflavone H, 7,2′-dimethoxy-3′,4′-methylenedioxyisoflavone, 6,7,3′-trimethoxy-4′,5′-methylenedioxyisoflavone, durmillone; a chalcone, 4-hydroxylonchocarpin; a geranylated phenylpropanol, colenemol; and two known pterocarpans, (6aR,11aR)-maackiain and (6aR,11aR)-edunol. (6aR,11aR)-Edunol was also isolated from the stem bark of L. eriocalyx. The structures of the isolated compounds were elucidated by spectroscopy. The cytotoxicity of the compounds was tested by resazurin assay using drug-sensitive and multidrug-resistant cancer cell lines. Significant antiproliferative effects with IC50 values below 10 μM were observed for the isoflavones 6,7,3′-trimethoxy-4′,5′-methylenedioxyisoflavone and durmillone against leukemia CCRF-CEM cells; for the chalcone, 4-hydroxylonchocarpin and durmillone against its resistant counterpart CEM/ADR5000 cells; as well as for durmillone against the resistant breast adenocarcinoma MDA-MB231/BCRP cells and resistant gliobastoma U87MG.ΔEGFR cells.}, language = {en} } @misc{OPUS4-62367, title = {Vielfalt in der Uckermark}, editor = {Berlin-Brandenburgisches Institut f{\"u}r Biodiverst{\"a}tsforschung,}, publisher = {oerding print GmbH}, address = {Braunschweig}, pages = {62}, year = {2019}, language = {de} }