@article{AltmannThimmEssigmannetal.2001, author = {Altmann, Thomas and Thimm, O. and Essigmann, B. and Kloska, Sebastian and Buckhout, Thomas J.}, title = {Response of arabidopsis to iron deficiency stress as revealed by microarray analysis}, year = {2001}, language = {en} } @article{AltmannTaylorKingetal.2003, author = {Altmann, Thomas and Taylor, Janet and King, Ross. D. and Fiehn, Oliver}, title = {Application of metabolomics to plant genotype discrimination using statistics and machine learning}, year = {2003}, language = {en} } @article{AltmannSchmidSoerensenetal.2003, author = {Altmann, Thomas and Schmid, K. J. and S{\"o}rensen, Rossleff T. and Stracke, R. and T{\"o}rjek, Otto and Mitchel-Olds, T. and Weisshaar, Bernd}, title = {Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana}, year = {2003}, language = {en} } @article{AltmannSchlueterMuschaketal.2003, author = {Altmann, Thomas and Schl{\"u}ter, U. and Muschak, M. and Berger, Dieter}, title = {Photosynthetic performance of an Arabidopsis mutant with elevated stomatal density (sdd1-1) under different light regimes}, year = {2003}, language = {en} } @article{AltmannSchlueterKoepkeetal.2002, author = {Altmann, Thomas and Schl{\"u}ter, U. and K{\"o}pke, D. and M{\"u}ssig, Carsten}, title = {Analysis of carbohydrate metabolism of CPD antisense plants and the brassinosteroid-deficient cbb1 mutant}, year = {2002}, language = {en} } @article{AltmannNarang2001, author = {Altmann, Thomas and Narang, R. A.}, title = {Phosphate accquisition heterosis in Arabidopsis thaliana : a morphological and physiological analysis}, year = {2001}, language = {en} } @article{AltmannMuessigFischer2002, author = {Altmann, Thomas and M{\"u}ssig, Carsten and Fischer, Sabine}, title = {Brassinosteroid-regulated gene expression}, year = {2002}, language = {en} } @article{AltmannMuessig2001, author = {Altmann, Thomas and M{\"u}ssig, Carsten}, title = {Brassinosteroid signaling in plants}, year = {2001}, language = {en} } @article{AltmannKossmann2001, author = {Altmann, Thomas and Koßmann, Jens}, title = {Photosynthesis and primary metabolism}, issn = {1360-1385}, year = {2001}, language = {en} } @article{AltmannFiehnKloska2001, author = {Altmann, Thomas and Fiehn, Oliver and Kloska, Sebastian}, title = {Integrated studies on plant biology using multiparallel techniques}, year = {2001}, language = {en} } @article{AltmannColebatchKloskaetal.2002, author = {Altmann, Thomas and Colebatch, G. and Kloska, Sebastian and Trevaskis, B. and Freund, S. and Udvardi, M. K.}, title = {Novel aspects of symbiotic nitrogen fixation uncovered by transcript profiling with cDNA arrays}, year = {2002}, language = {en} } @article{AltmannBrandtKloskaetal.2002, author = {Altmann, Thomas and Brandt, Stephan Peter and Kloska, Sebastian and Kehr, Julia}, title = {Using array hybridization to monitore gene expression at the single cell level}, year = {2002}, language = {en} } @article{AltmannBasseKerschbameretal.2002, author = {Altmann, Thomas and Basse, Christoph W. and Kerschbamer, Christine and Brustmann, Markus and Kahmann, Regine}, title = {Evidence for a Ustilago maydis steroid 5 alpha-reductase by functional expression in Arabidopsis det2-1 mutants}, year = {2002}, language = {en} } @article{Altmann2002, author = {Altmann, Thomas}, title = {Methodik der funktionellen Genomanalyse : wie mit Mikroarrays die Aktivit{\"a}t vieler Gene erfasst wird}, year = {2002}, language = {de} } @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{AlterMeyerPostetal.2015, author = {Alter, S. Elizabeth and Meyer, Matthias and Post, Klaas and Czechowski, Paul and Gravlund, Peter and Gaines, Cork and Rosenbaum, Howard C. and Kaschner, Kristin and Turvey, Samuel T. and van der Plicht, Johannes and Shapiro, Beth and Hofreiter, Michael}, title = {Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100}, series = {Molecular ecology}, volume = {24}, journal = {Molecular ecology}, number = {7}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.13121}, pages = {1510 -- 1522}, year = {2015}, abstract = {Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.}, language = {en} } @article{AlshareefOtterbachAlluetal.2022, author = {Alshareef, Nouf Owdah and Otterbach, Sophie L. and Allu, Annapurna Devi and Woo, Yong H. and de Werk, Tobias and Kamranfar, Iman and M{\"u}ller-R{\"o}ber, Bernd and Tester, Mark and Balazadeh, Salma and Schm{\"o}ckel, Sandra M.}, title = {NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis}, series = {Scientific reports}, volume = {12}, journal = {Scientific reports}, number = {1}, publisher = {Nature Research}, address = {Berlin}, issn = {2045-2322}, doi = {10.1038/s41598-022-14429-x}, pages = {15}, year = {2022}, abstract = {Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. 'Thermomemory' is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/ CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Ara bidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like atafl, anac055 mutants show improved thermomemory, revealing a potential co-control of both NACTFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory.}, language = {en} } @article{AlseekhTohgeWendenbergetal.2015, author = {Alseekh, Saleh and Tohge, Takayuki and Wendenberg, Regina and Scossa, Federico and Omranian, Nooshin and Li, Jie and Kleessen, Sabrina and Giavalisco, Patrick and Pleban, Tzili and M{\"u}ller-R{\"o}ber, Bernd and Zamir, Dani and Nikoloski, Zoran and Fernie, Alisdair R.}, title = {Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato}, series = {The plant cell}, volume = {27}, journal = {The plant cell}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.132266}, pages = {485 -- 512}, year = {2015}, abstract = {A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.}, language = {en} } @phdthesis{Alseekh2015, author = {Alseekh, Saleh}, title = {Identification and mode of inheritance of quantitative trait loci (QTL) for metabolite abundance in tomato}, school = {Universit{\"a}t Potsdam}, pages = {134}, year = {2015}, language = {en} } @article{AlmathenCharruauMohandesanetal.2016, author = {Almathen, Faisal and Charruau, Pauline and Mohandesan, Elmira and Mwacharo, Joram M. and Orozco-terWengel, Pablo and Pitt, Daniel and Abdussamad, Abdussamad M. and Uerpmann, Margarethe and Uerpmann, Hans-Peter and De Cupere, Bea and Magee, Peter and Alnaqeeb, Majed A. and Salim, Bashir and Raziq, Abdul and Dessie, Tadelle and Abdelhadi, Omer M. and Banabazi, Mohammad H. and Al-Eknah, Marzook and Walzer, Chris and Fayer, Bernard and Hofreiter, Michael and Peters, Joris and Hanotte, Olivier and Burger, Pamela A.}, title = {Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1519508113}, pages = {6707 -- 6712}, year = {2016}, abstract = {Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species' range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the "restocking from the wild" hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.}, language = {en} } @article{AlluSojaWuetal.2014, author = {Allu, Annapurna Devi and Soja, Aleksandra Maria and Wu, Anhui and Szymanski, Jedrzej and Balazadeh, Salma}, title = {Salt stress and senescence: identification of cross-talk regulatory components}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {14}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/eru173}, pages = {3993 -- 4008}, year = {2014}, abstract = {Leaf senescence is an active process with a pivotal impact on plant productivity. It results from extensive signalling cross-talk coordinating environmental factors with intrinsic age-related mechanisms. Although many studies have shown that leaf senescence is affected by a range of external parameters, knowledge about the regulatory systems that govern the interplay between developmental programmes and environmental stress is still vague. Salinity is one of the most important environmental stresses that promote leaf senescence and thus affect crop yield. Improving salt tolerance by avoiding or delaying senescence under stress will therefore play an important role in maintaining high agricultural productivity. Experimental evidence suggests that hydrogen peroxide (H2O2) functions as a common signalling molecule in both developmental and salt-induced leaf senescence. In this study, microarray-based gene expression profiling on Arabidopsis thaliana plants subjected to long-term salinity stress to induce leaf senescence was performed, together with co-expression network analysis for H2O2-responsive genes that are mutually up-regulated by salt induced-and developmental leaf senescence. Promoter analysis of tightly co-expressed genes led to the identification of seven cis-regulatory motifs, three of which were known previously, namely CACGTGT and AAGTCAA, which are associated with reactive oxygen species (ROS)-responsive genes, and CCGCGT, described as a stress-responsive regulatory motif, while the others, namely ACGCGGT, AGCMGNC, GMCACGT, and TCSTYGACG were not characterized previously. These motifs are proposed to be novel elements involved in the H2O2-mediated control of gene expression during salinity stress-triggered and developmental senescence, acting through upstream transcription factors that bind to these sites.}, language = {en} } @article{AlluSimancasBalazadehetal.2017, author = {Allu, Annapurna Devi and Simancas, Barbara and Balazadeh, Salma and Munne-Bosch, Sergi}, title = {Defense-Related Transcriptional Reprogramming in Vitamin E-Deficient Arabidopsis Mutants Exposed to Contrasting Phosphate Availability}, series = {Frontiers in plant science}, volume = {8}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2017.01396}, pages = {20}, year = {2017}, abstract = {Vitamin E inhibits the propagation of lipid peroxidation and helps protecting photosystem II from photoinhibition, but little is known about its possible role in plant response to Pi availability. Here, we aimed at examining the effect of vitamin E deficiency in Arabidopsis thaliana vte mutants on phytohormone contents and the expression of transcription factors in plants exposed to contrasting Pi availability. Plants were subjected to two doses of Pi, either unprimed (controls) or previously exposed to low Pi (primed). In the wild type, alpha-tocopherol contents increased significantly in response to repeated periods of low Pi, which was paralleled by increased growth, indicative of a priming effect. This growth-stimulating effect was, however, abolished in vte mutants. Hormonal profiling revealed significant effects of Pi availability, priming and genotype on the contents of jasmonates and salicylates; remarkably, vte mutants showed enhanced accumulation of both hormones under low Pi. Furthermore, expression profiling of 1,880 transcription factors by qRT-PCR revealed a pronounced effect of priming on the transcript levels of 45 transcription factors mainly associated with growth and stress in wild-type plants in response to low Pi availability; while distinct differences in the transcriptional response were detected in vte mutants. We conclude that alpha-tocopherol plays a major role in the response of plants to Pi availability not only by protecting plants from photo-oxidative stress, but also by exerting a control over growth-and defense-related transcriptional reprogramming and hormonal modulation.}, language = {en} } @article{AlluBrotmanXueetal.2016, author = {Allu, Annapurna Devi and Brotman, Yariv and Xue, Gang-Ping and Balazadeh, Salma}, title = {Transcription factor ANAC032 modulates JA/SA signalling in response to Pseudomonas syringae infection}, series = {EMBO reports}, volume = {17}, journal = {EMBO reports}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1469-221X}, doi = {10.15252/embr.201642197}, pages = {1578 -- 1589}, year = {2016}, abstract = {Responses to pathogens, including host transcriptional reprogramming, require partially antagonistic signalling pathways dependent on the phytohormones salicylic (SA) and jasmonic (JA) acids. However, upstream factors modulating the interplay of these pathways are not well characterized. Here, we identify the transcription factor ANAC032 from Arabidopsis thaliana as one such regulator in response to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst). ANAC032 directly represses MYC2 activation upon Pst attack, resulting in blockage of coronatine-mediated stomatal reopening which restricts entry of bacteria into plant tissue. Furthermore, ANAC032 activates SA signalling by repressing NIMIN1, a key negative regulator of SA-dependent defence. Finally, ANAC032 reduces expression of JA-responsive genes, including PDF1.2A. Thus, ANAC032 enhances resistance to Pst by generating an orchestrated transcriptional output towards key SA- and JA-signalling genes coordinated through direct binding of ANAC032 to the MYC2, NIMIN1 and PDF1.2A promoters.}, language = {en} } @article{AllhoffRitterskampRalletal.2015, author = {Allhoff, Korinna Theresa and Ritterskamp, Daniel and Rall, Bj{\"o}rn C. and Drossel, Barbara and Guill, Christian}, title = {Evolutionary food web model based on body masses gives realistic networks with permanent species turnover}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep10955}, pages = {12}, year = {2015}, abstract = {The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the complexity and stability of such food webs, we developed an eco-evolutionary model in which new species emerge as modifications of existing ones and dynamic ecological interactions determine which species are viable. The food-web structure thereby emerges from the dynamical interplay between speciation and trophic interactions. The proposed model is less abstract than earlier evolutionary food web models in the sense that all three evolving traits have a clear biological meaning, namely the average body mass of the individuals, the preferred prey body mass, and the width of their potential prey body mass spectrum. We observed networks with a wide range of sizes and structures and high similarity to natural food webs. The model networks exhibit a continuous species turnover, but massive extinction waves that affect more than 50\% of the network are not observed.}, language = {en} } @article{AllanWeisserFischeretal.2013, author = {Allan, Eric and Weisser, Wolfgang W. and Fischer, Markus and Schulze, Ernst-Detlef and Weigelt, Alexandra and Roscher, Christiane and Baade, Jussi and Barnard, Romain L. and Bessler, Holger and Buchmann, Nina and Ebeling, Anne and Eisenhauer, Nico and Engels, Christof and Fergus, Alexander J. F. and Gleixner, Gerd and Gubsch, Marlen and Halle, Stefan and Klein, Alexandra-Maria and Kertscher, Ilona and Kuu, Annely and Lange, Markus and Le Roux, Xavier and Meyer, Sebastian T. and Migunova, Varvara D. and Milcu, Alexandru and Niklaus, Pascal A. and Oelmann, Yvonne and Pasalic, Esther and Petermann, Jana S. and Poly, Franck and Rottstock, Tanja and Sabais, Alexander C. W. and Scherber, Christoph and Scherer-Lorenzen, Michael and Scheu, Stefan and Steinbeiss, Sibylle and Schwichtenberg, Guido and Temperton, Vicky and Tscharntke, Teja and Voigt, Winfried and Wilcke, Wolfgang and Wirth, Christian and Schmid, Bernhard}, title = {A comparison of the strength of biodiversity effects across multiple functions}, series = {Oecologia}, volume = {173}, journal = {Oecologia}, number = {1}, publisher = {Springer}, address = {New York}, issn = {0029-8549}, doi = {10.1007/s00442-012-2589-0}, pages = {223 -- 237}, year = {2013}, abstract = {In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 \% of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination.}, language = {en} } @article{AllanManningAltetal.2015, author = {Allan, Eric and Manning, Pete and Alt, Fabian and Binkenstein, Julia and Blaser, Stefan and Bl{\"u}thgen, Nico and B{\"o}hm, Stefan and Grassein, Fabrice and H{\"o}lzel, Norbert and Klaus, Valentin H. and Kleinebecker, Till and Morris, E. Kathryn and Oelmann, Yvonne and Prati, Daniel and Renner, Swen C. and Rillig, Matthias C. and Schaefer, Martin and Schloter, Michael and Schmitt, Barbara and Sch{\"o}ning, Ingo and Schrumpf, Marion and Solly, Emily and Sorkau, Elisabeth and Steckel, Juliane and Steffen-Dewenter, Ingolf and Stempfhuber, Barbara and Tschapka, Marco and Weiner, Christiane N. and Weisser, Wolfgang W. and Werner, Michael and Westphal, Catrin and Wilcke, Wolfgang and Fischer, Markus}, title = {Land use intensification alters ecosystem multifunctionality via loss of biodiversity and changes to functional composition}, series = {Ecology letters}, volume = {18}, journal = {Ecology letters}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1461-023X}, doi = {10.1111/ele.12469}, pages = {834 -- 843}, year = {2015}, abstract = {Global change, especially land-use intensification, affects human well-being by impacting the delivery of multiple ecosystem services (multifunctionality). However, whether biodiversity loss is a major component of global change effects on multifunctionality in real-world ecosystems, as in experimental ones, remains unclear. Therefore, we assessed biodiversity, functional composition and 14 ecosystem services on 150 agricultural grasslands differing in land-use intensity. We also introduce five multifunctionality measures in which ecosystem services were weighted according to realistic land-use objectives. We found that indirect land-use effects, i.e. those mediated by biodiversity loss and by changes to functional composition, were as strong as direct effects on average. Their strength varied with land-use objectives and regional context. Biodiversity loss explained indirect effects in a region of intermediate productivity and was most damaging when land-use objectives favoured supporting and cultural services. In contrast, functional composition shifts, towards fast-growing plant species, strongly increased provisioning services in more inherently unproductive grasslands.}, language = {en} } @article{AllanBossdorfDormannetal.2014, author = {Allan, Eric and Bossdorf, Oliver and Dormann, Carsten F. and Prati, Daniel and Gossner, Martin M. and Tscharntke, Teja and Bl{\"u}thgen, Nico and Bellach, Michaela and Birkhofer, Klaus and Boch, Steffen and B{\"o}hm, Stefan and B{\"o}rschig, Carmen and Chatzinotas, Antonis and Christ, Sabina and Daniel, Rolf and Diek{\"o}tter, Tim and Fischer, Christiane and Friedl, Thomas and Glaser, Karin and Hallmann, Christine and Hodac, Ladislav and H{\"o}lzel, Norbert and Jung, Kirsten and Klein, Alexandra-Maria and Klaus, Valentin H. and Kleinebecker, Till and Krauss, Jochen and Lange, Markus and Morris, E. Kathryn and M{\"u}ller, J{\"o}rg and Nacke, Heiko and Pasalic, Esther and Rillig, Matthias C. and Rothenwoehrer, Christoph and Schally, Peter and Scherber, Christoph and Schulze, Waltraud X. and Socher, Stephanie A. and Steckel, Juliane and Steffan-Dewenter, Ingolf and T{\"u}rke, Manfred and Weiner, Christiane N. and Werner, Michael and Westphal, Catrin and Wolters, Volkmar and Wubet, Tesfaye and Gockel, Sonja and Gorke, Martin and Hemp, Andreas and Renner, Swen C. and Sch{\"o}ning, Ingo and Pfeiffer, Simone and K{\"o}nig-Ries, Birgitta and Buscot, Francois and Linsenmair, Karl Eduard and Schulze, Ernst-Detlef and Weisser, Wolfgang W. and Fischer, Markus}, title = {Interannual variation in land-use intensity enhances grassland multidiversity}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {1}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1312213111}, pages = {308 -- 313}, year = {2014}, abstract = {Although temporal heterogeneity is a well-accepted driver of biodiversity, effects of interannual variation in land-use intensity (LUI) have not been addressed yet. Additionally, responses to land use can differ greatly among different organisms; therefore, overall effects of land-use on total local biodiversity are hardly known. To test for effects of LUI (quantified as the combined intensity of fertilization, grazing, and mowing) and interannual variation in LUI (SD in LUI across time), we introduce a unique measure of whole-ecosystem biodiversity, multidiversity. This synthesizes individual diversity measures across up to 49 taxonomic groups of plants, animals, fungi, and bacteria from 150 grasslands. Multidiversity declined with increasing LUI among grasslands, particularly for rarer species and aboveground organisms, whereas common species and belowground groups were less sensitive. However, a high level of interannual variation in LUI increased overall multidiversity at low LUI and was even more beneficial for rarer species because it slowed the rate at which the multidiversity of rare species declined with increasing LUI. In more intensively managed grasslands, the diversity of rarer species was, on average, 18\% of the maximum diversity across all grasslands when LUI was static over time but increased to 31\% of the maximum when LUI changed maximally over time. In addition to decreasing overall LUI, we suggest varying LUI across years as a complementary strategy to promote biodiversity conservation.}, 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} } @phdthesis{Alkatib2012, author = {Alkatib, Sibah}, title = {Further insights into plastid tRNA and reading of the genetic code in Nicotiana tabacum and Analysis of plastid ribosomal proteins in nicotiana tabacum}, address = {Potsdam}, pages = {138 S.}, year = {2012}, language = {en} } @misc{AlirezaeizanjaniWaljorHintscheetal.2017, author = {Alirezaeizanjani, Zahra and Waljor, V. and Hintsche, Marius and Beta, Carsten}, title = {How growth conditions affect bacterial chemotaxis responses}, series = {European biophysics journal : with biophysics letters ; an international journal of biophysics}, volume = {46}, journal = {European biophysics journal : with biophysics letters ; an international journal of biophysics}, publisher = {Springer}, address = {New York}, issn = {0175-7571}, pages = {S281 -- S281}, year = {2017}, language = {en} } @phdthesis{Alirezaeizanjani2020, author = {Alirezaeizanjani, Zahra}, title = {Movement strategies of a multi-mode bacterial swimmer}, doi = {10.25932/publishup-47580}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-475806}, school = {Universit{\"a}t Potsdam}, pages = {xix, 111}, year = {2020}, abstract = {Bacteria are one of the most widespread kinds of microorganisms that play essential roles in many biological and ecological processes. Bacteria live either as independent individuals or in organized communities. At the level of single cells, interactions between bacteria, their neighbors, and the surrounding physical and chemical environment are the foundations of microbial processes. Modern microscopy imaging techniques provide attractive and promising means to study the impact of these interactions on the dynamics of bacteria. The aim of this dissertation is to deepen our understanding four fundamental bacterial processes - single-cell motility, chemotaxis, bacterial interactions with environmental constraints, and their communication with neighbors - through a live cell imaging technique. By exploring these processes, we expanded our knowledge on so far unexplained mechanisms of bacterial interactions. Firstly, we studied the motility of the soil bacterium Pseudomonas putida (P. putida), which swims through flagella propulsion, and has a complex, multi-mode swimming tactic. It was recently reported that P. putida exhibits several distinct swimming modes - the flagella can push and pull the cell body or wrap around it. Using a new combined phase-contrast and fluorescence imaging set-up, the swimming mode (push, pull, or wrapped) of each run phase was automatically recorded, which provided the full swimming statistics of the multi-mode swimmer. Furthermore, the investigation of cell interactions with a solid boundary illustrated an asymmetry for the different swimming modes; in contrast to the push and pull modes, the curvature of runs in wrapped mode was not affected by the solid boundary. This finding suggested that having a multi-mode swimming strategy may provide further versatility to react to environmental constraints. Then we determined how P. putida navigates toward chemoattractants, i.e. its chemotaxis strategies. We found that individual run modes show distinct chemotactic responses in nutrition gradients. In particular, P. putida cells exhibited an asymmetry in their chemotactic responsiveness; the wrapped mode (slow swimming mode) was affected by the chemoattractant, whereas the push mode (fast swimming mode) was not. These results can be seen as a starting point to understand more complex chemotaxis strategies of multi-mode swimmers going beyond the well-known paradigm of Escherichia coli, that exhibits only one swimming mode. Finally we considered the cell dynamics in a dense population. Besides physical interactions with their neighbors, cells communicate their activities and orchestrate their population behaviors via quorum-sensing. Molecules that are secreted to the surrounding by the bacterial cells, act as signals and regulate the cell population behaviour. We studied P. putida's motility in a dense population by exposing the cells to environments with different concentrations of chemical signals. We found that higher amounts of chemical signals in the surrounding influenced the single-cell behaviourr, suggesting that cell-cell communications may also affect the flagellar dynamics. In summary, this dissertation studies the dynamics of a bacterium with a multi-mode swimming tactic and how it is affected by the surrounding environment using microscopy imaging. The detailed description of the bacterial motility in fundamental bacterial processes can provide new insights into the ecology of microorganisms.}, language = {en} } @article{AliRungeDutbayevetal.2016, author = {Ali, Tahir and Runge, Fabian and Dutbayev, Ayan and Schmuker, Angelika and Solovyeva, Irina and Nigrelli, Lisa and Buch, Ann-Katrin and Xia, Xiaojuan and Ploch, Sebastian and Orren, Ouria and Kummer, Volker and Paule, Juraj and Celik, Ali and Vakhrusheva, Ljudmila and Gabrielyan, Ivan and Thines, Marco}, title = {Microthlaspi erraticum (Jord.) T. Ali et Thines has a wide distribution, ranging from the Alps to the Tien Shan}, series = {Flora : morphology, distribution, functional ecology of plants}, volume = {225}, journal = {Flora : morphology, distribution, functional ecology of plants}, publisher = {American Chemical Society}, address = {Jena}, issn = {0367-2530}, doi = {10.1016/j.flora.2016.09.008}, pages = {76 -- 81}, year = {2016}, abstract = {Microthlaspi is a predominantly Eurasian genus which also occurs in the northernmost parts of Africa (Maghreb). The most widespread species of the genus is M. perfoliatum, which can be found from Sweden to Algeria and from Portugal to China. The other species are thought to have much more confined distribution ranges, often covering only a few hundred kilometres. This is also believed for the diploid M. erraticum, which was recently re-appraised as a taxon independent from the tetra- to hexaploid M. perfoliatum. Previously, M. erraticum was believed to be present only in Central Europe, from the East of France to Slovenia. In order to gain a deeper understanding of the ecology, evolution and migration history of Microthlaspi it was the focus of the current study to investigate, if M. erraticum is present in habitats outside Central Europe, but with microclimates similar to Central Europe. It is demonstrated that M. erraticum is much more widespread than previously thought, while other lineages apart from M. perfoliatum s.str. and M. erraticum seem to have restricted distribution ranges. The latter species was observed from the Alps and their foreland, the Balkans, the mountainous areas around the Black Sea, Southern Siberia, as well as the Altai and Tien Shan mountains. This demonstrates a widespread occurrence of this easily-overlooked species. (C) 2016 Elsevier GmbH. All rights reserved.}, language = {en} } @phdthesis{Alhajturki2018, author = {Alhajturki, Dema}, title = {Characterization of altered inflorescence architecture in Arabidopsis thaliana BG-5 x Kro-0 hybrid}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-420934}, school = {Universit{\"a}t Potsdam}, pages = {109}, year = {2018}, abstract = {A reciprocal cross between two A. thaliana accessions, Kro-0 (Krotzenburg, Germany) and BG-5 (Seattle, USA), displays purple rosette leaves and dwarf bushy phenotype in F1 hybrids when grown at 17 °C and a parental-like phenotype when grown at 21 °C. This F1 temperature-dependent-dwarf-bushy phenotype is characterized by reduced growth of the primary stem together with an increased number of branches. The reduced stem growth was the strongest at the first internode. In addition, we found that a temperature switch from 21 °C to 17 °C induced the phenotype only before the formation of the first internode of the stem. Similarly, the F1 dwarf-bushy phenotype could not be reversed when plants were shifted from 17 °C to 21 °C after the first internode was formed. Metabolic analysis showed that the F1 phenotype was associated with a significant upregulation of anthocyanin(s), kaempferol(s), salicylic acid, jasmonic acid and abscisic acid. As it has been previously shown that the dwarf-bushy phenotype is linked to two loci, one on chromosome 2 from Kro-0 and one on chromosome 3 from BG-5, an artificial micro-RNA approach was used to investigate the necessary genes on these intervals. From the results obtained, it was found that two genes, AT2G14120 that encodes for a DYNAMIN RELATED PROTEIN3B and AT2G14100 that encodes a member of the Cytochrome P450 family protein CYP705A13, were necessary for the appearance of the F1 phenotype on chromosome 2. It was also discovered that AT3G61035 that encodes for another cytochrome P450 family protein CYP705A13 and AT3G60840 that encodes for a MICROTUBULE-ASSOCIATED PROTEIN65-4 on chromosome 3 were both necessary for the induction of the F1 phenotype. To prove the causality of these genes, genomic constructs of the Kro-0 candidate genes on chromosome 2 were transferred to BG-5 and genomic constructs of the chromosome 3 candidate genes from BG-5 were transferred to Kro-0. The T1 lines showed that these genes are not sufficient alone to induce the phenotype. In addition to the F1 phenotype, more severe phenotypes were observed in the F2 generations that were grouped into five different phenotypic classes. Whilst seed yield was comparable between F1 hybrids and parental lines, three phenotypic classes in the F2 generation exhibited hybrid breakdown in the form of reproductive failure. This F2 hybrid breakdown was less sensitive to temperature and showed a dose-dependent effect of the loci involved in F1 phenotype. The severest class of hybrid breakdown phenotypes was observed only in the population of backcross with the parent Kro-0, which indicates a stronger contribution of the BG-5 allele when compared to the Kro-0 allele on the hybrid breakdown phenotypes. Overall, the findings of my thesis provide a further understanding of the genetic and metabolic factors underlying altered shoot architecture in hybrid dysfunction.}, language = {en} } @book{AleAghaBoyleBraunetal.2008, author = {Ale-Agha, Nosratollah and Boyle, H. and Braun, Uwe and Butin, H. and Jage, Horst and Kummer, Volker and Shin, H.}, title = {Taxonomy, host range and distribution of some powdery mildew fungi (Erysiphales)}, year = {2008}, abstract = {Oidium pedaliacearum sp. nov. (; O. sesami, nom. inval.) and Podosphaera macrospora comb. et stat. nov. (; Sphaerotheca alpina f. macrospora) are introduced, and the taxonomy and distribution of Erysiphe celosiae is discussed. New host species and new collections of Erysiphe cruciferarum (on Cleome hassleriana), E. flexuosa (on Aesculus hippocastanum), E. hedwigii (on Viburnum carlesii), E. heraclei (on Tinguarra montana), E. cf. macleayae (on Macleaya cordata), E. prunastri (on Prunus cerasifera), E. sedi (on Sedum aff. spectabilis), E. trifolii (on Trigonella caerulea), Golovinomyces cichoracearum (on Argyranthemum pinnatifidum subsp. succulentum), G. cf. hydrophyllacearum (on Nemophila menziesii), G. orontii (on Nolana spp.), G. cf. orontii (on Tiarella cordifolia), Neoerysiphe cumminsiana (on Bidens cf. ferulifolia), Oidium clitoriae (on Clitoria ternatea), O. cf. hortensiae (on Philadelphus coronarius), O. pedilanthi (on Pedilanthus tithymaloides), Oidium (Pseudoidium) sp. (on Utricularia alpina), Podosphaera sp. (on Bergia capensis), Sawadaea bicornis (on Acer platanoides) and S. tulasnei (on Acer ginnala and A. tatarica) are recorded from France, Germany, Greece and Mexico.}, language = {en} } @article{AleAghaBolayBraunetal.2004, author = {Ale-Agha, Nosratollah and Bolay, Adrien and Braun, Uwe and Jage, Horst and Kummer, Volker and Lebeda, Ales and Piatek, Marcin and Shin, Hyeon-Dong and Zimmermannova-Pastircakova, Katarina}, title = {Erysiphe catalpae and E. elevata in Europe}, year = {2004}, language = {en} } @phdthesis{Albus2010, author = {Albus, Christin Anne}, title = {Identifizierung und Charakterisierung neuer Proteine mit Funktionen in der Biogenese des Photosyntheseapparates}, address = {Potsdam}, pages = {149 S. : Ill., graph. Darst.}, year = {2010}, language = {de} } @article{AlbrechtKochLodeetal.2001, author = {Albrecht, Tanja and Koch, Anke and Lode, Anja and Greve, Burkhard and Schneider-Mergener, Jens and Steup, Martin}, title = {Plastidic (Pho1-type) phosphorylase isoforms in potato (Solanum tuberosum L.) plants : expression analysis and immunochemical characterization}, year = {2001}, language = {en} } @article{AlbrechtHaebelKochetal.2004, author = {Albrecht, Tanja and Haebel, Sophie and Koch, Anke and Krause, Ulrike and Eckermann, Nora and Steup, Martin}, title = {Yeast glycogenin (Glg2p) produced in Escherichia coli is simultaneously glucosylated at two vicinal tyrosin residues but results in a reduced bacterial glycogen accumulation}, year = {2004}, abstract = {Saccharomyces cerevisiae possesses two glycogenin isoforms (designated as Glg1p and Glg2p) that both contain a conserved tyrosine residue, Tyr232. However, Glg2p possesses an additional tyrosine residue, Tyr230 and therefore two potential autoglucosylation sites. Glucosylation of Glg2p was studied using both matrix-assisted laser desorption ionization and electrospray quadrupole time of flight mass spectrometry. Glg2p, carrying a C-terminal (His(6)) tag, was produced in Escherichia coli and purified. By tryptic digestion and reversed phase chromatography a peptide (residues 219-246 of the complete Glg2p sequence) was isolated that contained 4-25 glucosyl residues. Following incubation of Glg2p with UDPglucose, more than 36 glucosyl residues were covalently bound to this peptide. Using a combination of cyanogen bromide cleavage of the protein backbone, enzymatic hydrolysis of glycosidic bonds and reversed phase chromatography, mono- and diglucosylated peptides having the sequence PNYGYQSSPAM were generated. MS/MS spectra revealed that glucosyl residues were attached to both Tyr232 and Tyr230 within the same peptide. The formation of the highly glucosylated eukaryotic Glg2p did not favour the bacterial glycogen accumulation. Under various experimental conditions Glg2p-producing cells accumulated approximately 30\% less glycogen than a control transformed with a Glg2p lacking plasmid. The size distribution of the glycogen and extractable activities of several glycogen-related enzymes were essentially unchanged. As revealed by high performance anion exchange chromatography, the intracellular maltooligosaccharide pattern of the bacterial cells expressing the functional eukaryotic transgene was significantly altered. Thus, the eukaryotic glycogenin appears to be incompatible with the bacterial initiation of glycogen biosynthesis}, language = {en} } @article{AlbrechtGrevePuschetal.1998, author = {Albrecht, Tanja and Greve, Burkhard and Pusch, Kerstin and Koßmann, Jens and Buchner, Peter and Wobus, Ulrich and Steup, Martin}, title = {Homo- and Heterodimers of Pho1-Type Phosphorylase Isoforms in Solanum tuberosum L. as Revealed by Sequence- Specific Antibodies}, year = {1998}, language = {en} } @phdthesis{Albrecht1998, author = {Albrecht, Tanja}, title = {Quart{\"a}rstruktur, Funktion und Lokation der Pho 1-Phosphorylasen aus Solanum tuberosum L.}, address = {Potsdam}, pages = {122 S. : graph. Darst.}, year = {1998}, language = {de} } @article{AlbertiGonzalezPaijmansetal.2018, author = {Alberti, Federica and Gonzalez, Javier and Paijmans, Johanna L. A. and Basler, Nikolas and Preick, Michaela and Henneberger, Kirstin and Trinks, Alexandra and Rabeder, Gernot and Conard, Nicholas J. and Muenzel, Susanne C. and Joger, Ulrich and Fritsch, Guido and Hildebrandt, Thomas and Hofreiter, Michael and Barlow, Axel}, title = {Optimized DNA sampling of ancient bones using Computed Tomography scans}, series = {Molecular ecology resources}, volume = {18}, journal = {Molecular ecology resources}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12911}, pages = {1196 -- 1208}, year = {2018}, abstract = {The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99\% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.}, language = {en} } @article{AlbertGrasseinSchurretal.2011, author = {Albert, C{\´e}cile H. and Grassein, Fabrice and Schurr, Frank Martin and Vieilledent, Ghislain and Violle, Cyrille}, title = {When and how should intraspecific variability be considered in trait-based plant ecology?}, series = {Perspectives in plant ecology, evolution and systematics}, volume = {13}, journal = {Perspectives in plant ecology, evolution and systematics}, number = {3}, publisher = {Elsevier}, address = {Jena}, issn = {1433-8319}, doi = {10.1016/j.ppees.2011.04.003}, pages = {217 -- 225}, year = {2011}, abstract = {Trait-based studies have become extremely common in plant ecology. Trait-based approaches often rely on the tacit assumption that intraspecific trait variability (ITV) is negligible compared to interspecific variability, so that species can be characterized by mean trait values. Yet, numerous recent studies have challenged this assumption by showing that ITV significantly affects various ecological processes. Accounting for ITV may thus strengthen trait-based approaches, but measuring trait values on a large number of individuals per species and site is not feasible. Therefore, it is important and timely to synthesize existing knowledge on ITV in order to (1) decide critically when ITV should be considered, and (2) establish methods for incorporating this variability. Here we propose a practical set of rules to identify circumstances under which ITV should be accounted for. We formulate a spatial trait variance partitioning hypothesis to highlight the spatial scales at which ITV cannot be ignored in ecological studies. We then refine a set of four consecutive questions on the research question, the spatial scale, the sampling design, and the type of studied traits, to determine case-by-case if a given study should quantify ITV and test its effects. We review methods for quantifying ITV and develop a step-by-step guideline to design and interpret simulation studies that test for the importance of ITV. Even in the absence of quantitative knowledge on ITV, its effects can be assessed by varying trait values within species within realistic bounds around the known mean values. We finish with a discussion of future requirements to further incorporate ITV within trait-based approaches. This paper thus delineates a general framework to account for ITV and suggests a direction towards a more quantitative trait-based ecology.}, language = {en} } @article{AlbertAuffretCosynsetal.2015, author = {Albert, Aurelie and Auffret, Alistair G. and Cosyns, Eric and Cousins, Sara A. O. and Eichberg, Carsten and Eycott, Amy E. and Heinken, Thilo and Hoffmann, Maurice and Jaroszewicz, Bogdan and Malo, Juan E. and Marell, Anders and Mouissie, Maarten and Pakeman, Robin J. and Picard, Melanie and Plue, Jan and Poschlod, Peter and Provoost, Sam and Schulze, Kiowa Alraune and Baltzinger, Christophe}, title = {Seed dispersal by ungulates as an ecological filter: a trait-based meta-analysis}, series = {Oikos}, volume = {124}, journal = {Oikos}, number = {9}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.02512}, pages = {1109 -- 1120}, year = {2015}, abstract = {Plant communities are often dispersal-limited and zoochory can be an efficient mechanism for plants to colonize new patches of potentially suitable habitat. We predicted that seed dispersal by ungulates acts as an ecological filter - which differentially affects individuals according to their characteristics and shapes species assemblages - and that the filter varies according to the dispersal mechanism (endozoochory, fur-epizoochory and hoof-epizoochory). We conducted two-step individual participant data meta-analyses of 52 studies on plant dispersal by ungulates in fragmented landscapes, comparing eight plant traits and two habitat indicators between dispersed and non-dispersed plants. We found that ungulates dispersed at least 44\% of the available plant species. Moreover, some plant traits and habitat indicators increased the likelihood for plant of being dispersed. Persistent or nitrophilous plant species from open habitats or bearing dry or elongated diaspores were more likely to be dispersed by ungulates, whatever the dispersal mechanism. In addition, endozoochory was more likely for diaspores bearing elongated appendages whereas epizoochory was more likely for diaspores released relatively high in vegetation. Hoof-epizoochory was more likely for light diaspores without hooked appendages. Fur-epizoochory was more likely for diaspores with appendages, particularly elongated or hooked ones. We thus observed a gradient of filtering effect among the three dispersal mechanisms. Endozoochory had an effect of rather weak intensity (impacting six plant characteristics with variations between ungulate-dispersed and non-dispersed plant species mostly below 25\%), whereas hoof-epizoochory had a stronger effect (eight characteristics included five ones with above 75\% variation), and fur-epizoochory an even stronger one (nine characteristics included six ones with above 75\% variation). Our results demonstrate that seed dispersal by ungulates is an ecological filter whose intensity varies according to the dispersal mechanism considered. Ungulates can thus play a key role in plant community dynamics and have implications for plant spatial distribution patterns at multiple scales.}, 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} } @misc{AlbersUestuenWitzeletal.2018, author = {Albers, Philip and Uestuen, Suayib and Witzel, Katja and Bornke, Frederik}, title = {Identification of a novel target of the bacterial effector HopZ1a}, series = {Phytopathology}, volume = {108}, journal = {Phytopathology}, number = {10}, publisher = {American Phytopathological Society}, address = {Saint Paul}, issn = {0031-949X}, pages = {1}, year = {2018}, abstract = {The plant pathogen Pseudomonas syringae is a gram-negative bacterium which infects a wide range of plant species including important crops plants. To suppress plant immunity and cause disease P.syringae injects type-III effector proteins (T3Es) into the plant cell cytosol. In this study, we identified a novel target of the well characterized bacterial T3E HopZ1a. HopZ1a is an acetyltransferase that was shown to disrupt vesicle transport during innate immunity by acetylating tubulin. Using a yeast-two-hybrid screen approach, we identified a REMORIN (REM) protein from tobacco as a novel HopZ1a target. HopZ1a interacts with REM at the plasma membrane (PM) as shown by split-YFP experiments. Interestingly, we found that PBS1, a well-known kinase involved in plant immunity also interacts with REM in pull-down assays, and at the PM as shown by BiFC. Furthermore, we confirmed that REM is phosphorylated by PBS1 in vitro. Overexpression of REM provokes the upregulation of defense genes and leads to disease-like phenotypes pointing to a role of REM in plant immune signaling. Further protein-protein interaction studies reveal novel REM binding partners with a possible role in plant immune signaling. Thus, REM might act as an assembly hub for an immune signaling complex targeted by HopZ1a. Taken together, this is the first report describing that a REM protein is targeted by a bacterial effector. How HopZ1a might mechanistically manipulate the plant immune system through interfering with REM function will be discussed.}, language = {en} } @phdthesis{Albers2018, author = {Albers, Philip}, title = {Funktionelle Charakterisierung des bakteriellen Typ-III Effektorproteins HopZ1a in Nicotiana benthamiana}, school = {Universit{\"a}t Potsdam}, pages = {viii, 134}, year = {2018}, abstract = {Um das Immunsystem der Pflanze zu manipulieren translozieren gram-negative pathogene Bakterien Typ-III Effektorproteine (T3E) {\"u}ber ein Typ-III Sekretionssystem (T3SS) in die pflanzliche Wirtszelle. Dort lokalisieren T3Es in verschiedenen subzellul{\"a}ren Kompartimenten, wo sie Zielproteine modifizieren und so die Infektion beg{\"u}nstigen. HopZ1a, ein T3E des Pflanzenpathogens Pseudomonas syringae pv. syringae, ist eine Acetyltransferase und lokalisiert {\"u}ber ein Myristolierungsmotiv an der Plasmamembran der Wirtszelle. Obwohl gezeigt wurde, dass HopZ1a die fr{\"u}he Signalweiterleitung an der Plasmamembran st{\"o}rt, wurde bisher kein mit der Plasmamembran assoziiertes Zielprotein f{\"u}r diesen T3E identifiziert. Um bisher unbekannte HopZ1a-Zieleproteine zu identifizieren wurde im Vorfeld dieser Arbeit eine Hefe-Zwei-Hybrid-Durchmusterung mit einer cDNA-Bibliothek aus Tabak durchgef{\"u}hrt, wobei ein nicht n{\"a}her charakterisiertes Remorin als Interaktor gefunden wurde. Bei dem Remorin handelt es sich um einen Vertreter der Gruppe 4 der Remorin-Familie, weshalb es in NbREM4 umbenannt wurde. Durch den Einsatz verschiedener Interaktionsstudien konnte demonstriert werden, dass HopZ1a mit NbREM4 in Hefe, in vitro und in planta wechselwirkt. Es wurde ferner deutlich, dass HopZ1a auf spezifische Weise mit dem konservierten C-Terminus von NbREM4 interagiert, das Remorin jedoch in vitro nicht acetyliert. Analysen mittels BiFC haben zudem ergeben, dass NbREM4 in Homodimeren an der Plasmamembran lokalisiert, wo auch die Interaktion mit HopZ1a stattfindet. Eine funktionelle Charakterisierung von NbREM4 ergab, dass das Remorin eine spezifische Rolle im Immunsystem der Pflanze einnimmt. Die transiente Expression in N. benthamiana induziert die Expression von Abwehrgenen sowie einen ver{\"a}nderten Blattph{\"a}notyp. In A. thaliana wird HopZ1a {\"u}ber das Decoy ZED1 und das R-Protein ZAR1 erkannt, was zur Ausl{\"o}sung einer starken Hypersensitiven Antwort (HR von hypersensitive response) f{\"u}hrt. Es konnte im Rahmen dieser Arbeit gezeigt werden, dass ZAR1 in N. benthamiana konserviert ist, NbREM4 jedoch nicht in der ETI als Decoy fungiert. Mit Hilfe einer Hefe-Zwei-Hybrid-Durchmusterung mit NbZAR1 als K{\"o}der konnten zwei Proteine, die Catalase CAT1 und der Protonenpumpeninteraktor PPI1, als Interaktoren von NbZAR1 identifiziert werden, welche m{\"o}glicherweise in der Regulation der HR eine Rolle spielen. Aus Voruntersuchungen war bekannt, dass NbREM4 mit weiteren, nicht n{\"a}her charakterisierten Proteinen aus Tabak interagieren k{\"o}nnte. Eine phylogenetische Einordnung hat gezeigt, dass es sich um die bekannte Immun-Kinase PBS1 sowie zwei E3-Ubiquitin-Ligasen, NbSINA1 und NbSINAL3, handelt. PBS1 interagiert mit NbREM4 an der Plasmamembran und phosphoryliert das Remorin innerhalb des intrinsisch ungeordneten N-Terminus. Mittels Massenspektrometrie konnten die Serine an Position 64 und 65 innerhalb der Aminos{\"a}uresequenz von NbREM4 als PBS1-abh{\"a}ngige Phosphorylierungsstellen identifiziert wurden. NbSINA1 und NbSINAL3 besitzen in vitro Ubiquitinierungsaktivit{\"a}t, bilden Homo- und Heterodimere und interagieren ebenfalls mit dem N-terminalen Teil von NbREM4, wobei sie das Remorin in vitro nicht ubiquitinieren. Aus den in dieser Arbeit gewonnenen Ergebnissen l{\"a}sst sich ableiten, dass der bakterielle T3E HopZ1a gezielt mit dem Tabak-Remorin NbREM4 an der Plasmamembran interagiert und {\"u}ber einen noch unbekannten Mechanismus mit dem Immunsystem der Pflanze interferiert, wobei NbREM4 m{\"o}glicherweise eine Rolle als Adapter- oder Ankerprotein zukommt, {\"u}ber welches HopZ1a mit weiteren Immunkomponenten interagiert. NbREM4 ist Teil eines gr{\"o}ßeren Immunnetzwerkes, zu welchem die bekannte Immun-Kinase PBS1 und zwei E3-Ubiquitin-Ligasen geh{\"o}ren. Mit NbREM4 konnte damit erstmalig ein membranst{\"a}ndiges Protein mit einer Funktion im Immunsystem der Pflanze als Zielprotein von HopZ1a identifiziert werden.}, language = {de} } @phdthesis{ALRawi2020, author = {AL-Rawi, Shadha}, title = {Biochemical studies to determine the role of Early Starvation 1 (ESV1) protein and its homologue Like-Early Starvation 1 (LESV) during starch degradation}, doi = {10.25932/publishup-48395}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-483956}, school = {Universit{\"a}t Potsdam}, pages = {215}, year = {2020}, abstract = {Depending on the biochemical and biotechnical approach, the aim of this work was to understand the mechanism of protein-glucan interactions in regulation and control of starch degradation. Although starch degradation starts with the phosphorylation process, the mechanisms by which this process is controlling and adjusting starch degradation are not yet fully understood. Phosphorylation is a major process performed by the two dikinases enzymes α-glucan, water dikinase (GWD) and phosphoglucan water dikinase (PWD). GWD and PWD enzymes phosphorylate the starch granule surface; thereby stimulate starch degradation by hydrolytic enzymes. Despite these important roles for GWD and PWD, so far the biochemical processes by which these enzymes are able to regulate and adjust the rate of phosphate incorporation into starch during the degradation process haven't been understood. Recently, some proteins were found associated with the starch granule. Two of these proteins are named Early Starvation Protein 1 (ESV1) and its homologue Like-Early Starvation Protein 1 (LESV). It was supposed that both are involved in the control of starch degradation, but their function has not been clearly known until now. To understand how ESV1 and LESV-glucan interactions are regulated and affect the starch breakdown, it was analyzed the influence of ESV1 and LESV proteins on the phosphorylating enzyme GWD and PWD and hydrolysing enzymes ISA, BAM, and AMY. However, the analysis determined the location of LESV and ESV1 in the chloroplast stroma of Arabidopsis. Mass spectrometry data predicted ESV1and LESV proteins as a product of the At1g42430 and At3g55760 genes with a predicted mass of ~50 kDa and ~66 kDa, respectively. The ChloroP program predicted that ESV1 lacks the chloroplast transit peptide, but it predicted the first 56 amino acids N-terminal region as a chloroplast transit peptide for LESV. Usually, the transit peptide is processed during transport of the proteins into plastids. Given that this processing is critical, two forms of each ESV1 and LESV were generated and purified, a full-length form and a truncated form that lacks the transit peptide, namely, (ESV1and tESV1) and (LESV and tLESV), respectively. Both protein forms were included in the analysis assays, but only slight differences in glucan binding and protein action between ESV1 and tESV1 were observed, while no differences in the glucan binding and effect on the GWD and PWD action were observed between LESV and tLESV. The results revealed that the presence of the N-terminal is not massively altering the action of ESV1 or LESV. Therefore, it was only used the ESV1 and tLESV forms data to explain the function of both proteins. However, the analysis of the results revealed that LESV and ESV1 proteins bind strongly at the starch granule surface. Furthermore, not all of both proteins were released after their incubation with starches after washing the granules with 2\% [w/v] SDS indicates to their binding to the deeper layers of the granule surface. Supporting of this finding comes after the binding of both proteins to starches after removing the free glucans chains from the surface by the action of ISA and BAM. Although both proteins are capable of binding to the starch structure, only LESV showed binding to amylose, while in ESV1, binding was not observed. The alteration of glucan structures at the starch granule surface is essential for the incorporation of phosphate into starch granule while the phosphorylation of starch by GWD and PWD increased after removing the free glucan chains by ISA. Furthermore, PWD showed the possibility of starch phosphorylation without prephosphorylation by GWD. Biochemical studies on protein-glucan interactions between LESV or ESV1 with different types of starch showed a potentially important mechanism of regulating and adjusting the phosphorylation process while the binding of LESV and ESV1 leads to altering the glucan structures of starches, hence, render the effect of the action of dikinases enzymes (GWD and PWD) more able to control the rate of starch degradation. Despite the presence of ESV1 which revealed an antagonistic effect on the PWD action as the PWD action was decreased without prephosphorylation by GWD and increased after prephosphorylation by GWD (Chapter 4), PWD showed a significant reduction in its action with or without prephosphorylation by GWD in the presence of ESV1 whether separately or together with LESV (Chapter 5). However, the presence of LESV and ESV1 together revealed the same effect compared to the effect of each one alone on the phosphorylation process, therefore it is difficult to distinguish the specific function between them. However, non-interactions were detected between LESV and ESV1 or between each of them with GWD and PWD or between GWD and PWD indicating the independent work for these proteins. It was also observed that the alteration of the starch structure by LESV and ESV1 plays a role in adjusting starch degradation rates not only by affecting the dikinases but also by affecting some of the hydrolysing enzymes since it was found that the presence of LESV and ESV1leads to the reduction of the action of BAM, but does not abolish it.}, language = {en} } @phdthesis{AlFadel2018, author = {Al Fadel, Frdoos}, title = {Influence of sphingosine 1-phosphate and its receptor modulators on the development of liver fibrosis}, school = {Universit{\"a}t Potsdam}, pages = {156}, year = {2018}, language = {en} } @article{AksuFrascaWollenbergeretal.2011, author = {Aksu, Yilmaz and Frasca, Stefano and Wollenberger, Ursula and Driess, Matthias and Thomas, Arne}, title = {A molecular precursor approach to tunable porous tin-rich indium tin oxide with durable high electrical conductivity for bioelectronic devices}, series = {Chemistry of materials : a publication of the American Chemical Society}, volume = {23}, journal = {Chemistry of materials : a publication of the American Chemical Society}, number = {7}, publisher = {American Chemical Society}, address = {Washington}, issn = {0897-4756}, doi = {10.1021/cm103087p}, pages = {1798 -- 1804}, year = {2011}, abstract = {The preparation of porous, i.e., high surface area electrodes from transparent conducting oxides, is a valuable goal in materials chemistry as such electrodes can enable further development of optoelectronic, electrocatalytic, or bioelectronic devices. In this work the first tin-rich mesoporous indium tin oxide is prepared using the molecular heterobimetallic single-source precursor, indium tin tris-tert-butoxide, together with an appropriate structure-directing template, yielding materials with high surface areas and tailorable pore size. The resulting mesoporous tin-rich ITO films show a high and durable electrical conductivity and transparency, making them interesting materials for hosting electroactive biomolecules such as proteins. In fact, its unique performance in bioelectronic applications has been demonstrated by immobilization of high amounts of cytochrome c into the mesoporous film which undergo redox processes directly with the conductive electrode material.}, language = {en} } @article{AichnerDubbertKieletal.2022, author = {Aichner, Bernhard and Dubbert, David and Kiel, Christine and Kohnert, Katrin and Ogashawara, Igor and Jechow, Andreas and Harpenslager, Sarah-Faye and H{\"o}lker, Franz and Nejstgaard, Jens Christian and Grossart, Hans-Peter and Singer, Gabriel and Wollrab, Sabine and Berger, Stella Angela}, title = {Spatial and seasonal patterns of water isotopes in northeastern German lakes}, series = {Earth system science data : ESSD}, volume = {14}, journal = {Earth system science data : ESSD}, number = {4}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1866-3508}, doi = {10.5194/essd-14-1857-2022}, pages = {1857 -- 1867}, year = {2022}, abstract = {Water stable isotopes (delta O-18 and delta H-2) were analyzed in samples collected in lakes, associated with riverine systems in northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water samples collected at (a) lake shores (sampled in March and July 2020), (b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020), (c) multiple spatially distributed spots in four selected lakes (in September 2020), and (d) the outflow of Muggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40-60 cm below the water surface and directly transferred into a measurement vial, while at buoys a Limnos water sampler was used to obtain samples from 1 m below the surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer, with a measurement uncertainty of < 0.15 parts per thousand (delta O-18) and < 0.0 parts per thousand (delta H-2). The data give information about the vegetation period and the full seasonal isotope amplitude in the sampled lakes and about spatial isotope variability in different branches of the associated riverine systems.}, language = {en} }