@misc{ZupokIobbiNivolMejeanetal.2019, author = {Zupok, Arkadiusz and Iobbi-Nivol, Chantal and Mejean, Vincent and Leimk{\"u}hler, Silke}, title = {The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria}, series = {Metallomics : integrated biometal science}, volume = {11}, journal = {Metallomics : integrated biometal science}, number = {10}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1756-5901}, doi = {10.1039/c9mt00186g}, pages = {1602 -- 1624}, year = {2019}, abstract = {Bacterial molybdoenzymes are key enzymes involved in the global sulphur, nitrogen and carbon cycles. These enzymes require the insertion of the molybdenum cofactor (Moco) into their active sites and are able to catalyse a large range of redox-reactions. Escherichia coli harbours nineteen different molybdoenzymes that require a tight regulation of their synthesis according to substrate availability, oxygen availability and the cellular concentration of molybdenum and iron. The synthesis and assembly of active molybdoenzymes are regulated at the level of transcription of the structural genes and of translation in addition to the genes involved in Moco biosynthesis. The action of global transcriptional regulators like FNR, NarXL/QP, Fur and ArcA and their roles on the expression of these genes is described in detail. In this review we focus on what is known about the molybdenum- and iron-dependent regulation of molybdoenzyme and Moco biosynthesis genes in the model organism E. coli. The gene regulation in E. coli is compared to two other well studied model organisms Rhodobacter capsulatus and Shewanella oneidensis.}, language = {en} } @article{ZupokGorkaSiemiatkowskaetal.2019, author = {Zupok, Arkadiusz and G{\´o}rka, Michał Jakub and Siemiatkowska, Beata and Skirycz, Aleksandra and Leimk{\"u}hler, Silke}, title = {Iron-Dependent Regulation of Molybdenum Cofactor Biosynthesis Genes in Escherichia coli}, series = {Journal of bacteriology}, volume = {201}, journal = {Journal of bacteriology}, number = {17}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {0021-9193}, doi = {10.1128/JB.00382-19}, pages = {15}, year = {2019}, abstract = {Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In recent years it has become obvious that the availability of iron plays an important role in the biosynthesis of Moco. First, the MoaA protein binds two (4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional NFe-4S) cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the L-cysteine desulfurase IscS, which is a shared protein with a main role in the assembly of Fe-S clusters. In this report, we investigated the transcriptional regulation of the moaABCDE operon by focusing on its dependence on cellular iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, our data show that the regulation of the moaABCDE operon at the level of transcription is only marginally influenced by the availability of iron. Nevertheless, intracellular levels of Moco were decreased under iron-limiting conditions, likely based on an inactive MoaA protein in addition to lower levels of the L-cysteine desulfurase IscS, which simultaneously reduces the sulfur availability for Moco production. IMPORTANCE FNR is a very important transcriptional factor that represents the master switch for the expression of target genes in response to anaerobiosis. Among the FNR-regulated operons in Escherichia coli is the moaABCDE operon, involved in Moco biosynthesis. Molybdoenzymes have essential roles in eukaryotic and prokaryotic organisms. In bacteria, molybdoenzymes are crucial for anaerobic respiration using alternative electron acceptors. This work investigates the connection of iron availability to the biosynthesis of Moco and the production of active molybdoenzymes.}, language = {en} } @article{ZimmermannHarmsEppetal.2019, author = {Zimmermann, Heike Hildegard and Harms, Lars and Epp, Laura Saskia and Mewes, Nick and Bernhardt, Nadine and Kruse, Stefan and Stoof-Leichsenring, Kathleen Rosemarie and Pestryakova, Luidmila Agafyevna and Wieczorek, Mareike and Trense, Daronja and Herzschuh, Ulrike}, title = {Chloroplast and mitochondrial genetic variation of larches at the Siberian tundrataiga ecotone revealed by de novo assembly}, series = {PLoS one}, volume = {14}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0216966}, pages = {21}, year = {2019}, abstract = {Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/ L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.}, language = {en} } @article{ZhangRammingHeinkeetal.2019, author = {Zhang, Yunming and Ramming, Anna and Heinke, Lisa and Altschmied, Lothar and Slotkin, R. Keith and Becker, J{\"o}rg D. and Kappel, Christian and Lenhard, Michael}, title = {The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development}, series = {The plant journal}, volume = {99}, journal = {The plant journal}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.14348}, pages = {655 -- 672}, year = {2019}, abstract = {RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence-labelling strategy, we have characterized this defect in more detail using RNA and small-RNA sequencing. In addition to global defects in the expression of pollen-differentiation genes, paps1 null-mutant pollen shows a strong overaccumulation of transposable element (TE) transcripts, yet a depletion of 21- and particularly 24-nucleotide-long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding TEs. Double-mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4, mutations. In particular, the double-mutant of paps1 and rna-dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast.}, language = {en} } @phdthesis{Zhang2019, author = {Zhang, Xiaorong}, title = {Electrosynthesis and characterization of molecularly imprinted polymers for peptides and proteins}, school = {Universit{\"a}t Potsdam}, pages = {116}, year = {2019}, language = {en} } @article{ZhangBramskiTutusetal.2019, author = {Zhang, Shuhao and Bramski, Julia and Tutus, Murat and Pietruszka, J{\"o}rg and B{\"o}ker, Alexander and Reinicke, Stefan}, title = {A Biocatalytically Active Membrane Obtained from Immobilization of 2-Deoxy-D-ribose-5-phosphate Aldolase on a Porous Support}, series = {ACS applied materials \& interfaces}, volume = {11}, journal = {ACS applied materials \& interfaces}, number = {37}, publisher = {American Chemical Society}, address = {Washington}, issn = {1944-8244}, doi = {10.1021/acsami.9b12029}, pages = {34441 -- 34453}, year = {2019}, abstract = {Aldol reactions play an important role in organic synthesis, as they belong to the class of highly beneficial C-C-linking reactions. Aldol-type reactions can be efficiently and stereoselectively catalyzed by the enzyme 2-deoxy-D-ribose-5-phosphate aldolase (DERA) to gain key intermediates for pharmaceuticals such as atorvastatin. The immobilization of DERA would open the opportunity for a continuous operation mode which gives access to an efficient, large-scale production of respective organic intermediates. In this contribution, we synthesize and utilize DERA/polymer conjugates for the generation and fixation of a DERA bearing thin film on a polymeric membrane support. The conjugation strongly increases the tolerance of the enzyme toward the industrial relevant substrate acetaldehyde while UV-cross-linkable groups along the conjugated polymer chains provide the opportunity for covalent binding to the support. First, we provide a thorough characterization of the conjugates followed by immobilization tests on representative, nonporous cycloolefinic copolymer supports. Finally, immobilization on the target supports constituted of polyacrylonitrile (PAN) membranes is performed, and the resulting enzymatically active membranes are implemented in a simple membrane module setup for the first assessment of biocatalytic performance in the continuous operation mode using the combination hexanal/acetaldehyde as the substrate.}, language = {en} } @phdthesis{Zemella2019, author = {Zemella, Anne}, title = {Fluoreszenzmarkierung und Modifizierung von komplexen Proteinen in eukaryotischen zellfreien Systemen durch die Etablierung von orthogonalen tRNA/Aminoacyl-tRNA-Synthetase-Paaren}, doi = {10.25932/publishup-44236}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-442361}, school = {Universit{\"a}t Potsdam}, pages = {XI, 141}, year = {2019}, abstract = {Die funktionelle Charakterisierung von therapeutisch relevanten Proteinen kann bereits durch die Bereitstellung des Zielproteins in ad{\"a}quaten Mengen limitierend sein. Dies trifft besonders auf Membranproteine zu, die aufgrund von zytotoxischen Effekten auf die Produktionszelllinie und der Tendenz Aggregate zu bilden, in niedrigen Ausbeuten an aktivem Protein resultieren k{\"o}nnen. Der lebende Organismus kann durch die Verwendung von translationsaktiven Zelllysaten umgangen werden- die Grundlage der zellfreien Proteinsynthese. Zu Beginn der Arbeit wurde die ATP-abh{\"a}ngige Translation eines Lysates auf der Basis von kultivierten Insektenzellen (Sf21) analysiert. F{\"u}r diesen Zweck wurde ein ATP-bindendes Aptamer eingesetzt, durch welches die Translation der Nanoluziferase reguliert werden konnte. Durch die dargestellte Applizierung von Aptameren, k{\"o}nnten diese zuk{\"u}nftig in zellfreien Systemen f{\"u}r die Visualisierung der Transkription und Translation eingesetzt werden, wodurch zum Beispiel komplexe Prozesse validiert werden k{\"o}nnen. Neben der reinen Proteinherstellung k{\"o}nnen Faktoren wie posttranslationale Modifikationen sowie eine Integration in eine lipidische Membran essentiell f{\"u}r die Funktionalit{\"a}t des Membranproteins sein. Im zweiten Abschnitt konnte, im zellfreien Sf21-System, f{\"u}r den G-Protein-gekoppelten Rezeptor Endothelin B sowohl eine Integration in die endogen vorhandenen Endoplasmatisch Retikulum-basierten Membranstrukturen als auch Glykosylierungen, identifiziert werden. Auf der Grundlage der erfolgreichen Synthese des ET-B-Rezeptors wurden verschiedene Methoden zur Fluoreszenzmarkierung des Adenosin-Rezeptors A2a (Adora2a) angewandt und optimiert. Im dritten Abschnitt wurde der Adora2a mit Hilfe einer vorbeladenen tRNA, welche an eine fluoreszierende Aminos{\"a}ure gekoppelt war, im zellfreien Chinesischen Zwerghamster Ovarien (CHO)-System markiert. Zus{\"a}tzlich konnte durch den Einsatz eines modifizierten tRNA/Aminoacyl-tRNA-Synthetase-Paares eine nicht-kanonische Aminos{\"a}ure an Position eines integrierten Amber-Stopcodon in die Polypeptidkette eingebaut und die funktionelle Gruppe im Anschluss an einen Fluoreszenzfarbstoff gekoppelt werden. Aufgrund des offenen Charakters eignen sich zellfreie Proteinsynthesesysteme besonders f{\"u}r eine Integration von exogenen Komponenten in den Translationsprozess. Mit Hilfe der Fluoreszenzmarkierung wurde eine ligandvermittelte Konformations{\"a}nderung im Adora2a {\"u}ber einen Biolumineszenz-Resonanzenergietransfer detektiert. Durch die Etablierung der Amber-Suppression wurde dar{\"u}ber hinaus das Hormon Erythropoetin pegyliert, wodurch Eigenschaften wie Stabilit{\"a}t und Halbwertszeit des Proteins ver{\"a}ndert wurden. Zu guter Letzt wurde ein neues tRNA/Aminoacyl-tRNA-Synthetase-Paar auf Basis der Methanosarcina mazei Pyrrolysin-Synthetase etabliert, um das Repertoire an nicht-kanonischen Aminos{\"a}uren und den damit verbundenen Kopplungsreaktionen zu erweitern. Zusammenfassend wurden die Potenziale zellfreier Systeme in Bezug auf der Herstellung von komplexen Membranproteinen und der Charakterisierung dieser durch die Einbringung einer positionsspezifischen Fluoreszenzmarkierung verdeutlicht, wodurch neue M{\"o}glichkeiten f{\"u}r die Analyse und Funktionalisierung von komplexen Proteinen geschaffen wurden.}, language = {de} } @article{ZeitlerYeAndreyevaetal.2019, author = {Zeitler, Stefanie and Ye, Lian and Andreyeva, Aksana and Schumacher, Fabian and Monti, Juliana and N{\"u}rnberg, Bernd and Nowak, Gabriel and Kleuser, Burkhard and Reichel, Martin and Fejtova, Anna and Kornhuber, Johannes and Rhein, Cosima and Friedland, Kristina}, title = {Acid sphingomyelinase - a regulator of canonical transient receptor potential channel 6 (TRPC6) activity}, series = {Journal of neurochemistry}, volume = {150}, journal = {Journal of neurochemistry}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {0022-3042}, doi = {10.1111/jnc.14823}, pages = {678 -- 690}, year = {2019}, abstract = {Recent investigations propose the acid sphingomyelinase (ASM)/ceramide system as a novel target for antidepressant action. ASM catalyzes the breakdown of the abundant membrane lipid sphingomyelin to the lipid messenger ceramide. This ASM-induced lipid modification induces a local shift in membrane properties, which influences receptor clustering and downstream signaling. Canonical transient receptor potential channels 6 (TRPC6) are non-selective cation channels located in the cell membrane that play an important role in dendritic growth, synaptic plasticity and cognition in the brain. They can be activated by hyperforin, an ingredient of the herbal remedy St. John's wort for treatment of depression disorders. Because of their role in the context of major depression, we investigated the crosstalk between the ASM/ceramide system and TRPC6 ion channels in a pheochromocytoma cell line 12 neuronal cell model (PC12 rat pheochromocytoma cell line). Ca2+ imaging experiments indicated that hyperforin-induced Ca2+ influx through TRPC6 channels is modulated by ASM activity. While antidepressants, known as functional inhibitors of ASM activity, reduced TRPC6-mediated Ca2+ influx, extracellular application of bacterial sphingomyelinase rebalanced TRPC6 activity in a concentration-related way. This effect was confirmed in whole-cell patch clamp electrophysiology recordings. Lipidomic analyses revealed a decrease in very long chain ceramide/sphingomyelin molar ratio after ASM inhibition, which was connected with changes in the abundance of TRPC6 channels in flotillin-1-positive lipid rafts as visualized by western blotting. Our data provide evidence that the ASM/ceramide system regulates TRPC6 channels likely by controlling their recruitment to specific lipid subdomains and thereby fine-tuning their physical properties.}, language = {en} } @article{YuanHouBarlowetal.2019, author = {Yuan, Jun-Xia and Hou, Xin-Dong and Barlow, Axel and Preick, Michaela and Taron, Ulrike H. and Alberti, Federica and Basler, Nikolas and Deng, Tao and Lai, Xu-Long and Hofreiter, Michael and Sheng, Gui-Lian}, title = {Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China}, series = {PLOS ONE}, volume = {14}, journal = {PLOS ONE}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0216883}, pages = {12}, year = {2019}, abstract = {The extant diversity of horses (family Equidae) represents a small fraction of that occurring over their evolutionary history. One such lost lineage is the subgenus Sussemionus, which is thought to have become extinct during the Middle Pleistocene. However, recent molecular studies and morphological analysis have revealed that one of their representatives, E. ovodovi, did exist in Siberia during the Late Pleistocene. Fossil materials of E. ovodovi have thus far only been found in Russia. In this study, we extracted DNA from three equid fossil specimens excavated from northeastern China dated at 12,770-12,596, 29,525-28,887 and 40,201-38,848 cal. yBP, respectively, and retrieved three near-complete mitochondrial genomes from the specimens. Phylogenetic analyses cluster the Chinese haplotypes together with previously published Russian E. ovodovi, strongly supporting the assignment of these samples to this taxon. The molecular identification of E. ovodovi in northeastern China extends the known geographical range of this fossil species by several thousand kilometers to the east. The estimated coalescence time of all E. ovodovi haplotypes is approximately 199 Kya, with the Chinese haplotypes coalescing approximately 130 Kya. With a radiocarbon age of 12,770-12,596 cal. yBP, the youngest sample in this study represents the first E. ovodovi sample dating to the terminal Pleistocene, moving the extinction date of this species forwards considerably compared to previously documented fossils. Overall, comparison of our three mitochondrial genomes with the two published ones suggests a genetic diversity similar to several extant species of the genus Equus.}, language = {en} } @article{YuWuNowaketal.2019, author = {Yu, Yanjun and Wu, Shenjie and Nowak, Jacqueline and Wang, Guangda and Han, Libo and Feng, Zhidi and Mendrinna, Amelie and Ma, Yinping and Wang, Huan and Zhang, Xiaxia and Tian, Juan and Dong, Li and Nikoloski, Zoran and Persson, Staffan and Kong, Zhaosheng}, title = {Live-cell imaging of the cytoskeleton in elongating cotton fibres}, series = {Nature plants}, volume = {5}, journal = {Nature plants}, number = {5}, publisher = {Nature Publ. Group}, address = {London}, issn = {2055-026X}, doi = {10.1038/s41477-019-0418-8}, pages = {498 -- 504}, year = {2019}, abstract = {Cotton (Gossypium hirsutum) fibres consist of single cells that grow in a highly polarized manner, assumed to be controlled by the cytoskeleton(1-3). However, how the cytoskeletal organization and dynamics underpin fibre development remains unexplored. Moreover, it is unclear whether cotton fibres expand via tip growth or diffuse growth(2-4). We generated stable transgenic cotton plants expressing fluorescent markers of the actin and microtubule cytoskeleton. Live-cell imaging revealed that elongating cotton fibres assemble a cortical filamentous actin network that extends along the cell axis to finally form actin strands with closed loops in the tapered fibre tip. Analyses of F-actin network properties indicate that cotton fibres have a unique actin organization that blends features of both diffuse and tip growth modes. Interestingly, typical actin organization and endosomal vesicle aggregation found in tip-growing cell apices were not observed in fibre tips. Instead, endomembrane compartments were evenly distributed along the elongating fibre cells and moved bi-directionally along the fibre shank to the fibre tip. Moreover, plus-end tracked microtubules transversely encircled elongating fibre shanks, reminiscent of diffusely growing cells. Collectively, our findings indicate that cotton fibres elongate via a unique tip-biased diffuse growth mode.}, language = {en} } @phdthesis{Yishai2019, author = {Yishai, Oren}, title = {Engineering the reductive glycine pathway in Escherichia coli}, school = {Universit{\"a}t Potsdam}, pages = {86}, year = {2019}, language = {en} } @article{YangPerreraSaplaouraetal.2019, author = {Yang, Lei and Perrera, Valentina and Saplaoura, Eleftheria and Apelt, Federico and Bahin, Mathieu and Kramdi, Amira and Olas, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd and Sokolowska, Ewelina and Zhang, Wenna and Li, Runsheng and Pitzalis, Nicolas and Heinlein, Manfred and Zhang, Shoudong and Genovesio, Auguste and Colot, Vincent and Kragler, Friedrich}, title = {m(5)C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants}, series = {Current biology}, volume = {29}, journal = {Current biology}, number = {15}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2019.06.042}, pages = {2465 -- 2476.e5}, year = {2019}, abstract = {In plants, transcripts move to distant body parts to potentially act as systemic signals regulating development and growth. Thousands of messenger RNAs (mRNAs) are transported across graft junctions via the phloem to distinct plant parts. Little is known regarding features, structural motifs, and potential base modifications of transported transcripts and how these may affect their mobility. We identified Arabidopsis thalianam RNAs harboring the modified base 5-methylcytosine (m(5)C) and found that these are significantly enriched in mRNAs previously described as mobile, moving over graft junctions to distinct plant parts. We confirm this finding with graft-mobile methylated mRNAs TRANSLATIONALLY CONTROLLED TUMOR PROTEIN 1 (TCTP1) and HEAT SHOCK COGNATE PROTEIN 70.1 (HSC70.1), whose mRNA transport is diminished in mutants deficient in m(5)C mRNA methylation. Together, our results point toward an essential role of cytosine methylation in systemic mRNA mobility in plants and that TCTP1 mRNA mobility is required for its signaling function.}, language = {en} } @article{YanChenSchumacheretal.2019, author = {Yan, Wenhao and Chen, Dijun and Schumacher, Julia and Durantini, Diego and Engelhorn, Julia and Chen, Ming and Carles, Cristel C. and Kaufmann, Kerstin}, title = {Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-09513-2}, pages = {16}, year = {2019}, abstract = {Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase. hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers.}, language = {en} } @misc{YamamichiKlauschiesMineretal.2019, author = {Yamamichi, Masato and Klauschies, Toni and Miner, Brooks E. and van Velzen, Ellen}, title = {Modelling inducible defences in predator-prey interactions}, series = {Ecology letters}, volume = {22}, journal = {Ecology letters}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {1461-023X}, doi = {10.1111/ele.13183}, pages = {390 -- 404}, year = {2019}, abstract = {Inducible defences against predation are widespread in the natural world, allowing prey to economise on the costs of defence when predation risk varies over time or is spatially structured. Through interspecific interactions, inducible defences have major impacts on ecological dynamics, particularly predator-prey stability and phase lag. Researchers have developed multiple distinct approaches, each reflecting assumptions appropriate for particular ecological communities. Yet, the impact of inducible defences on ecological dynamics can be highly sensitive to the modelling approach used, making the choice of model a critical decision that affects interpretation of the dynamical consequences of inducible defences. Here, we review three existing approaches to modelling inducible defences: Switching Function, Fitness Gradient and Optimal Trait. We assess when and how the dynamical outcomes of these approaches differ from each other, from classic predator-prey dynamics and from commonly observed eco-evolutionary dynamics with evolving, but non-inducible, prey defences. We point out that the Switching Function models tend to stabilise population dynamics, and the Fitness Gradient models should be carefully used, as the difference with evolutionary dynamics is important. We discuss advantages of each approach for applications to ecological systems with particular features, with the goal of providing guidelines for future researchers to build on.}, language = {en} } @article{WuHanRodriguezSillkeetal.2019, author = {Wu, Hao and Han, Yijie and Rodriguez Sillke, Yasmina and Deng, Hongzhang and Siddiqui, Sophiya and Treese, Christoph and Schmidt, Franziska and Friedrich, Marie and Keye, Jacqueline and Wan, Jiajia and Qin, Yue and K{\"u}hl, Anja A. and Qin, Zhihai and Siegmund, Britta and Glauben, Rainer}, title = {Lipid droplet-dependent fatty acid metabolism controls the immune suppressive phenotype of tumor-associated macrophages}, series = {EMBO molecular medicine}, volume = {11}, journal = {EMBO molecular medicine}, number = {11}, publisher = {Wiley}, address = {Hoboken}, issn = {1757-4676}, doi = {10.15252/emmm.201910698}, pages = {17}, year = {2019}, abstract = {Tumor-associated macrophages (TAMs) promote tumor growth and metastasis by suppressing tumor immune surveillance. Herein, we provide evidence that the immunosuppressive phenotype of TAMs is controlled by long-chain fatty acid metabolism, specifically unsaturated fatty acids, here exemplified by oleate. Consequently, en-route enriched lipid droplets were identified as essential organelles, which represent effective targets for chemical inhibitors to block in vitro polarization of TAMs and tumor growth in vivo. In line, analysis of human tumors revealed that myeloid cells infiltrating colon cancer but not gastric cancer tissue indeed accumulate lipid droplets. Mechanistically, our data indicate that oleate-induced polarization of myeloid cells depends on the mammalian target of the rapamycin pathway. Thus, our findings reveal an alternative therapeutic strategy by targeting the pro-tumoral myeloid cells on a metabolic level.}, language = {en} } @phdthesis{Wozniak2019, author = {Wozniak, Natalia Joanna}, title = {Convergent evolution of the selfing syndrome in the genus Capsella}, school = {Universit{\"a}t Potsdam}, pages = {229}, year = {2019}, language = {en} } @article{WitzelAbuRishaAlbersetal.2019, author = {Witzel, Katja and Abu Risha, Marua and Albers, Philip and B{\"o}rnke, Frederik and Hanschen, Franziska S.}, title = {Identification and Characterization of Three Epithiospecifier Protein Isoforms in Brassica oleracea}, series = {Frontiers in plant science}, volume = {10}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2019.01552}, pages = {14}, year = {2019}, abstract = {Glucosinolates present in Brassicaceae play a major role in herbivory defense. Upon tissue disruption, glucosinolates come into contact with myrosinase, which initiates their breakdown to biologically active compounds. Among these, the formation of epithionitriles is triggered by the presence of epithiospecifier protein (ESP) and a terminal double bond in the glucosinolate side chain. One ESP gene is characterized in the model plant Arabidopsis thaliana (AtESP; At1g54040.2). However, Brassica species underwent genome triplication since their divergence from the Arabidopsis lineage. This indicates the presence of multiple ESP isoforms in Brassica crops that are currently poorly characterized. We identified three B. oleracea ESPs, specifically BoESP1 (LOC106296341), BoESP2 (LOC106306810), and BoESP3 (LOC106325105) based on in silico genome analysis. Transcript and protein abundance were assessed in shoots and roots of four B. oleracea vegetables, namely broccoli, kohlrabi, white, and red cabbage, because these genotypes showed a differential pattern for the formation of glucosinolate hydrolysis products as well for their ESP activity. BoESP1 and BoESP2 were expressed mainly in shoots, while BoESP3 was abundant in roots. Biochemical characterization of heterologous expressed BoESP isoforms revealed different substrate specificities towards seven glucosinolates: all isoforms showed epithiospecifier activity on alkenyl glucosinolates, but not on non-alkenyl glucosinolates. The pH-value differently affected BoESP activity: while BoESP1 and BoESP2 activities were optimal at pH 6-7, BoESP3 activity remained relatively stable from pH 4 to 7. In order test their potential for the in vivo modification of glucosinolate breakdown, the three isoforms were expressed in A. thaliana Hi-0, which lacks AtESP expression, and analyzed for the effect on their respective hydrolysis products. The BoESPs altered the hydrolysis of allyl glucosinolate in the A. thaliana transformants to release 1-cyano-2,3-epithiopropane and reduced formation of the corresponding 3-butenenitrile and allyl isothiocyanate. Plants expressing BoESP2 showed the highest percentage of released epithionitriles. Given these results, we propose a model for isoform-specific roles of B. oleracea ESPs in glucosinolate breakdown.}, language = {en} } @article{Wiebke2019, author = {Wiebke, Ullmann}, title = {Warum hat Bayern mehr Feldhasen als Brandenburg?}, series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018}, journal = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018}, publisher = {oerding print GmbH}, address = {Braunschweig}, pages = {46 -- 47}, year = {2019}, language = {de} } @article{WerchmeisterTangXiaoetal.2019, author = {Werchmeister, Rebecka Maria Larsen and Tang, Jing and Xiao, Xinxin and Wollenberger, Ulla and Hjuler, Hans Aage and Ulstrup, Jens and Zhang, Jingdong}, title = {Three-Dimensional Bioelectrodes Utilizing Graphene Based Bioink}, series = {Journal of The Electrochemical Society}, volume = {166}, journal = {Journal of The Electrochemical Society}, number = {16}, publisher = {The Electrochemical Society}, address = {Pennington}, issn = {0013-4651}, doi = {10.1149/2.0261916jes}, pages = {G170 -- G177}, year = {2019}, abstract = {Enzyme immobilization using nanomaterials offers new approaches to enhanced bioelectrochemical performance and is essential for the preparation of bioelectrodes with high reproducibility and low cost. In this report, we describe the development of new three-dimensional (3D) bioelectrodes by immobilizing a "bioink" of glucose oxidase (GOD) in a matrix of reduced graphene oxides (RGOs), polyethylenimine (PEI), and ferrocene carboxylic acid (FcCOOH) on carbon paper (CP). CP with 3D interwoven carbon fibers serves as a solid porous and electronically conducting skeleton, providing large surface areas and space for loading the bioink and diffusion of substrate molecules, respectively. RGO enhances contact between the GOD-matrix and CP, maintaining high conductivity. The composition of the bioink has been systematically optimized. The GOD bioelectrodes show linearly increasing electrocatalytic oxidation current toward glucose concentration up to 48 mM. A hybrid enzymatic biofuel cell equipped with the GOD bioelectrode as a bioanode and a platinum cathode furthermore registers a maximum power density of 5.1 mu W cm(-2) and an open circuit voltage of 0.40 V at 25 degrees C. The new method reported of preparing a bioelectrode by drop-casting the bioink onto the substrate electrode is facile and versatile, with the potential of application also for other enzymatic bioelectrodes.}, language = {en} } @article{WendlerEnenkel2019, author = {Wendler, Petra and Enenkel, Cordula}, title = {Nuclear Transport of Yeast Proteasomes}, series = {Frontiers in molecular biosciences}, volume = {6}, journal = {Frontiers in molecular biosciences}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {2296-889X}, doi = {10.3389/fmolb.2019.00034}, pages = {12}, year = {2019}, abstract = {Proteasomes are key proteases in regulating protein homeostasis. Their holo-enzymes are composed of 40 different subunits which are arranged in a proteolytic core (CP) flanked by one to two regulatory particles (RP). Proteasomal proteolysis is essential for the degradation of proteins which control time-sensitive processes like cell cycle progression and stress response. In dividing yeast and human cells, proteasomes are primarily nuclear suggesting that proteasomal proteolysis is mainly required in the nucleus during cell proliferation. In yeast, which have a closed mitosis, proteasomes are imported into the nucleus as immature precursors via the classical import pathway. During quiescence, the reversible absence of proliferation induced by nutrient depletion or growth factor deprivation, proteasomes move from the nucleus into the cytoplasm. In the cytoplasm of quiescent yeast, proteasomes are dissociated into CP and RP and stored in membrane-less cytoplasmic foci, named proteasome storage granules (PSGs). With the resumption of growth, PSGs clear and mature proteasomes are transported into the nucleus by Blm10, a conserved 240 kDa protein and proteasome-intrinsic import receptor. How proteasomes are exported from the nucleus into the cytoplasm is unknown.}, language = {en} } @article{WeissWulff2019, author = {Weiß, Lina and Wulff, Monika}, title = {Ver{\"a}nderung der Landnutzung in der nord-westlichen Uckermark von 1780 bis heute}, series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018}, journal = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018}, publisher = {oerding print GmbH}, address = {Braunschweig}, pages = {20 -- 21}, year = {2019}, language = {de} } @article{WeissSchalowJeltschetal.2019, author = {Weiss, Lina and Schalow, Linda and Jeltsch, Florian and Geissler, Katja}, title = {Experimental evidence for root competition effects on community evenness in one of two phytometer species}, series = {Journal of plant ecology}, volume = {12}, journal = {Journal of plant ecology}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1752-9921}, doi = {10.1093/jpe/rty021}, pages = {281 -- 291}, year = {2019}, abstract = {Aims Plant-plant interactions, being positive or negative, are recognized to be key factors in structuring plant communities. However, it is thought that root competition may be less important than shoot competition due to greater size symmetry belowground. Because direct experimental tests on the importance of root competition are scarce, we aim at elucidating whether root competition may have direct or indirect effects on community structure. Indirect effects may occur by altering the overall size asymmetry of competition through root-shoot competitive interactions. Methods We used a phytometer approach to examine the effects of root, shoot and total competition intensity and importance on evenness of experimental plant communities. Thereby two different phytometer species, Festuca brevipila and Dianthus carthusianorum, were grown in small communities of six grassland species over three levels of light and water availability, interacting with neighbouring shoots, roots, both or not at all. Important Findings We found variation in community evenness to be best explained if root and shoot (but not total) competition were considered. However, the effects were species specific: in Dianthus communities increasing root competition increased plant community evenness, while in Festuca communities shoot competition was the driving force of this evenness response. Competition intensities were influenced by environmental conditions in Dianthus, but not in Festuca phytometer plants. While we found no evidence for root-shoot interactions for neither phytometer species root competition in Dianthus communities led to increased allocation to shoots, thereby increasing the potential ability to perform in size-asymmetric competition for light. Our experiment demonstrates the potential role of root competition in structuring plant communities.}, language = {en} } @article{VonRaabStraubeRausBazosetal.2019, author = {Von Raab-Straube, Eckhard and Raus, Thomas and Bazos, Ioannis and Cornec, J. P. and De Belair, Gerard. and Dimitrakopoulos, P. G. and El Mokni, Ridha and Fateryga, Alexander V. and Fateryga, Valentina V. and Fridlender, Alain and Gil, Jaime and Grigorenko, V. N. and Hand, Ralf and Kovalchuk, A. and Mastrogianni, A. and Otto, R. and R{\"a}tzel, Stefan and Raus, Th. and Ristow, Michael and Salas Pascual, M. and Strid, Arne and Svirin, S. A. and Tsiripidis, Ioannis. and Uhlich, Holger and Vela, Errol and Verloove, Filip and Vidakis, K. and Yena, Andriy Vasylyovych and Yevseyenkov, P. E. and Zeddam, A.}, title = {Euro plus Med-Checklist Notulae, 11}, series = {Willdenowia}, volume = {49}, journal = {Willdenowia}, number = {3}, publisher = {Botanischer Garten \& botanisches Museum Berlin-Dahlem}, address = {Berlin}, issn = {0511-9618}, doi = {10.3372/wi.49.49312}, pages = {421 -- 445}, year = {2019}, abstract = {This is the eleventh of a series of miscellaneous contributions, by various authors, where hitherto unpublished data relevant to both the Med-Checklist and the Euro+Med (or Sisyphus) projects are presented. This instalment deals with the families Anacardiaceae, Asparagaceae (incl. Hyacinthaceae), Bignoniaceae, Cactaceae, Compositae, Cruciferae, Cyperaceae, Ericaceae, Gramineae, Labiatae, Leguminosae, Orobanchaceae, Polygonaceae, Rosaceae, Solanaceae and Staphyleaceae. It includes new country and area records and taxonomic and distributional considerations for taxa in Bidens, Campsis, Centaurea, Cyperus, Drymocallis, Engem, Hoffmannseggia, Hypopitys, Lavandula, Lithraea, Melilotus, Nicotiana, Olimarabidopsis, Opuntia, Orobanche, Phelipanche, Phragmites, Rumex, Salvia, Schinus, Staphylea, and a new combination in Drimia.}, language = {en} } @article{VeloAntonBoratyńskiFerreiraetal.2019, author = {Velo-Ant{\´o}n, Guillermo and Boratyński, Zbyszek and Ferreira, Clara Mendes and Lima, Vanessa O. and Alves, Paulo C. and Brito, Jos{\´e} C.}, title = {Intraspecific genetic diversity and distribution of North African hedgehogs (Mammalia: Erinaceidae)}, series = {Biological journal of the Linnean Society : a journal of evolution}, volume = {127}, journal = {Biological journal of the Linnean Society : a journal of evolution}, number = {1}, publisher = {Oxford University Press}, address = {Oxford}, issn = {0024-4066}, doi = {10.1093/biolinnean/blz030}, pages = {156 -- 163}, year = {2019}, abstract = {Despite growing efforts to halt biodiversity loss, knowledge of species diversity and distribution is highly geographically biased, leaving some areas unexplored. Taxa distributed in remote, desert areas, such as hedgehogs (Mammalia; Eulipotyphla) in North Africa, are good examples of current knowledge gaps in systematics and biogeography. Here we studied the geographical distribution and intraspecific genetic diversity of hedgehogs in North Africa. Specimens belonging to North African and Eurasian species were analysed with mitochondrial (control region, CR) and nuclear (recombination activating gene 1, RAG1) gene fragments. This revealed a broader geographical distribution of Atelerix algirus in south-western Libya and of Paraechinus aethiopicus along the Atlantic Sahara. High intraspecific genetic differentiation was found in A. algirus and A. albiventris at the mitochondrial level, with nuclear haplotype sharing across their ranges. These findings suggest that biogeographical patterns of hedgehogs in North Africa are more complex than previously suggested, highlighting a need for further investigation in this remote and poorly known area.}, language = {en} } @phdthesis{Vandrich2019, author = {Vandrich, Jasmina}, title = {Metabolic Engineering in Halomonas elongata}, school = {Universit{\"a}t Potsdam}, pages = {80}, year = {2019}, language = {en} } @article{ToulouseSchmuckerMeteschetal.2019, author = {Toulouse, Charlotte Marguerite and Schmucker, Sonja and Metesch, Kristina and Pfannstiel, Jens and Michel, Bernd and Starke, Ines and M{\"o}ller, Heiko Michael and Stefanski, Volker and Steuber, Julia}, title = {Mechanism and impact of catecholamine conversion by Vibrio cholerae}, series = {Biochimica et biophysica acta : Bioenergetics}, volume = {1860}, journal = {Biochimica et biophysica acta : Bioenergetics}, number = {6}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0005-2728}, doi = {10.1016/j.bbabio.2019.04.003}, pages = {478 -- 487}, year = {2019}, abstract = {Bacterial pathogens are influenced by signaling molecules including the catecholamines adrenaline and noradrenaline which are host-derived hormones and neurotransmitters. Adrenaline and noradrenaline modulate growth, motility and virulence of bacteria. We show that adrenaline is converted by the pathogen Vibrio cholerae to adrenochrome in the course of respiration, and demonstrate that superoxide produced by the respiratory, Na+ - translocating NADH:quinone oxidoreductase (NQR) acts as electron acceptor in the oxidative conversion of adrenaline to adrenochrome. Adrenochrome stimulates growth of V. cholerae, and triggers specific responses in V. cholerae and in immune cells. We performed a quantitative proteome analysis of V. cholerae grown in minimal medium with glucose as carbon source without catecholamines, or with adrenaline, noradrenaline or adrenochrome. Significant regulation of proteins participating in iron transport and iron homeostasis, in energy metabolism, and in signaling was observed upon exposure to adrenaline, noradrenaline or adrenochrome. On the host side, adrenochrome inhibited lipopolysaccharide-triggered formation of TNF-alpha by THP-1 monocytes, though to a lesser extent than adrenaline. It is proposed that adrenochrome produced from adrenaline by respiring V. cholerae functions as effector molecule in pathogen-host interaction.}, language = {en} } @phdthesis{Tong2019, author = {Tong, Hao}, title = {Dissection of genetic architecture of intermediate phenotypes and predictions in plants}, school = {Universit{\"a}t Potsdam}, pages = {127}, year = {2019}, abstract = {Determining the relationship between genotype and phenotype is the key to understand the plasticity and robustness of phenotypes in nature. While the directly observable plant phenotypes (e.g. agronomic, yield and stress resistance traits) have been well-investigated, there is still a lack in our knowledge about the genetic basis of intermediate phenotypes, such as metabolic phenotypes. Dissecting the links between genotype and phenotype depends on suitable statistical models. The state-of-the-art models are developed for directly observable phenotypes, regardless the characteristics of intermediate phenotypes. This thesis aims to fill the gaps in understanding genetic architecture of intermediate phenotypes, and how they tie to composite traits, namely plant growth. The metabolite levels and reaction fluxes, as two aspects of metabolic phenotypes, are shaped by the interrelated chemical reactions formed in genome-scale metabolic network. Here, I attempt to answer the question: Can the knowledge of underlying genome-scale metabolic network improve the model performance for prediction of metabolic phenotypes and associated plant growth? To this end, two projects are investigated in this thesis. Firstly, we propose an approach that couples genomic selection with genome-scale metabolic network and metabolic profiles in Arabidopsis thaliana to predict growth. This project is the first integration of genomic data with fluxes predicted based on constraint-based modeling framework and data on biomass composition. We demonstrate that our approach leads to a considerable increase of prediction accuracy in comparison to the state-of-the-art methods in both within and across environment predictions. Therefore, our work paves the way for combining knowledge on metabolic mechanisms in the statistical approach underlying genomic selection to increase the efficiency of future plant breeding approaches. Secondly, we investigate how reliable is genomic selection for metabolite levels, and which single nucleotide polymorphisms (SNPs), obtained from different neighborhoods of a given metabolic network, contribute most to the accuracy of prediction. The results show that the local structure of first and second neighborhoods are not sufficient for predicting the genetic basis of metabolite levels in Zea mays. Furthermore, we find that the enzymatic SNPs can capture most the genetic variance and the contribution of non-enzymatic SNPs is in fact small. To comprehensively understand the genetic architecture of metabolic phenotypes, I extend my study to a local Arabidopsis thaliana population and their hybrids. We analyze the genetic architecture in primary and secondary metabolism as well as in growth. In comparison to primary metabolites, compounds from secondary metabolism were more variable and show more non-additive inheritance patterns which could be attributed to epistasis. Therefore, our study demonstrates that heterozygosity in local Arabidopsis thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism. The studies in this thesis improve the knowledge of genetic architecture of metabolic phenotypes in both inbreed and hybrid population. The approaches I proposed to integrate genome-scale metabolic network with genomic data provide the opportunity to obtain mechanistic insights about the determinants of agronomically important polygenic traits.}, language = {en} } @article{TiegsCostelloIskenetal.2019, author = {Tiegs, Scott D. and Costello, David M. and Isken, Mark W. and Woodward, Guy and McIntyre, Peter B. and Gessner, Mark O. and Chauvet, Eric and Griffiths, Natalie A. and Flecker, Alex S. and Acuna, Vicenc and Albarino, Ricardo and Allen, Daniel C. and Alonso, Cecilia and Andino, Patricio and Arango, Clay and Aroviita, Jukka and Barbosa, Marcus V. M. and Barmuta, Leon A. and Baxter, Colden V. and Bell, Thomas D. C. and Bellinger, Brent and Boyero, Luz and Brown, Lee E. and Bruder, Andreas and Bruesewitz, Denise A. and Burdon, Francis J. and Callisto, Marcos and Canhoto, Cristina and Capps, Krista A. and Castillo, Maria M. and Clapcott, Joanne and Colas, Fanny and Colon-Gaud, Checo and Cornut, Julien and Crespo-Perez, Veronica and Cross, Wyatt F. and Culp, Joseph M. and Danger, Michael and Dangles, Olivier and de Eyto, Elvira and Derry, Alison M. and Diaz Villanueva, Veronica and Douglas, Michael M. and Elosegi, Arturo and Encalada, Andrea C. and Entrekin, Sally and Espinosa, Rodrigo and Ethaiya, Diana and Ferreira, Veronica and Ferriol, Carmen and Flanagan, Kyla M. and Fleituch, Tadeusz and Shah, Jennifer J. Follstad and Frainer, Andre and Friberg, Nikolai and Frost, Paul C. and Garcia, Erica A. and Lago, Liliana Garcia and Garcia Soto, Pavel Ernesto and Ghate, Sudeep and Giling, Darren P. and Gilmer, Alan and Goncalves, Jose Francisco and Gonzales, Rosario Karina and Graca, Manuel A. S. and Grace, Mike and Grossart, Hans-Peter and Guerold, Francois and Gulis, Vlad and Hepp, Luiz U. and Higgins, Scott and Hishi, Takuo and Huddart, Joseph and Hudson, John and Imberger, Samantha and Iniguez-Armijos, Carlos and Iwata, Tomoya and Janetski, David J. and Jennings, Eleanor and Kirkwood, Andrea E. and Koning, Aaron A. and Kosten, Sarian and Kuehn, Kevin A. and Laudon, Hjalmar and Leavitt, Peter R. and Lemes da Silva, Aurea L. and Leroux, Shawn J. and Leroy, Carri J. and Lisi, Peter J. and MacKenzie, Richard and Marcarelli, Amy M. and Masese, Frank O. and Mckie, Brendan G. and Oliveira Medeiros, Adriana and Meissner, Kristian and Milisa, Marko and Mishra, Shailendra and Miyake, Yo and Moerke, Ashley and Mombrikotb, Shorok and Mooney, Rob and Moulton, Tim and Muotka, Timo and Negishi, Junjiro N. and Neres-Lima, Vinicius and Nieminen, Mika L. and Nimptsch, Jorge and Ondruch, Jakub and Paavola, Riku and Pardo, Isabel and Patrick, Christopher J. and Peeters, Edwin T. H. M. and Pozo, Jesus and Pringle, Catherine and Prussian, Aaron and Quenta, Estefania and Quesada, Antonio and Reid, Brian and Richardson, John S. and Rigosi, Anna and Rincon, Jose and Risnoveanu, Geta and Robinson, Christopher T. and Rodriguez-Gallego, Lorena and Royer, Todd V. and Rusak, James A. and Santamans, Anna C. and Selmeczy, Geza B. and Simiyu, Gelas and Skuja, Agnija and Smykla, Jerzy and Sridhar, Kandikere R. and Sponseller, Ryan and Stoler, Aaron and Swan, Christopher M. and Szlag, David and Teixeira-de Mello, Franco and Tonkin, Jonathan D. and Uusheimo, Sari and Veach, Allison M. and Vilbaste, Sirje and Vought, Lena B. M. and Wang, Chiao-Ping and Webster, Jackson R. and Wilson, Paul B. and Woelfl, Stefan and Xenopoulos, Marguerite A. and Yates, Adam G. and Yoshimura, Chihiro and Yule, Catherine M. and Zhang, Yixin X. and Zwart, Jacob A.}, title = {Global patterns and drivers of ecosystem functioning in rivers and riparian zones}, series = {Science Advances}, volume = {5}, journal = {Science Advances}, number = {1}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {2375-2548}, doi = {10.1126/sciadv.aav0486}, pages = {8}, year = {2019}, abstract = {River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.}, language = {en} } @article{ThomasCarvalhoHaileetal.2019, author = {Thomas, Jessica E. and Carvalho, Gary R. and Haile, James and Rawlence, Nicolas J. and Martin, Michael D. and Ho, Simon Y. W. and Sigfusson, Arnor P. and Josefsson, Vigfus A. and Frederiksen, Morten and Linnebjerg, Jannie F. and Castruita, Jose A. Samaniego and Niemann, Jonas and Sinding, Mikkel-Holger S. and Sandoval-Velasco, Marcela and Soares, Andre E. R. and Lacy, Robert and Barilaro, Christina and Best, Juila and Brandis, Dirk and Cavallo, Chiara and Elorza, Mikelo and Garrett, Kimball L. and Groot, Maaike and Johansson, Friederike and Lifjeld, Jan T. and Nilson, Goran and Serjeanston, Dale and Sweet, Paul and Fuller, Errol and Hufthammer, Anne Karin and Meldgaard, Morten and Fjeldsa, Jon and Shapiro, Beth and Hofreiter, Michael and Stewart, John R. and Gilbert, M. Thomas P. and Knapp, Michael}, title = {Demographic reconstruction from ancient DNA supports rapid extinction of the great auk}, series = {eLife}, volume = {8}, journal = {eLife}, publisher = {eLife Sciences Publications}, address = {Cambridge}, issn = {2050-084X}, doi = {10.7554/eLife.47509}, pages = {35}, year = {2019}, abstract = {The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.}, language = {en} } @phdthesis{Thirumalaikumar2019, author = {Thirumalaikumar, Venkatesh P.}, title = {Investigating drought and heat stress regulatory networks in Arabidopsis and tomato}, school = {Universit{\"a}t Potsdam}, pages = {154}, year = {2019}, language = {en} } @article{TeckentrupKramerSchadtJeltsch2019, author = {Teckentrup, Lisa and Kramer-Schadt, Stephanie and Jeltsch, Florian}, title = {The risk of ignoring fear: underestimating the effects of habitat loss and fragmentation on biodiversity}, series = {Landscape ecology}, volume = {34}, journal = {Landscape ecology}, number = {12}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2973}, doi = {10.1007/s10980-019-00922-8}, pages = {2851 -- 2868}, year = {2019}, language = {en} } @phdthesis{Teckentrup2019, author = {Teckentrup, Lisa}, title = {Understanding predator-prey interactions}, doi = {10.25932/publishup-43162}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431624}, school = {Universit{\"a}t Potsdam}, pages = {ix, 133}, year = {2019}, abstract = {Predators can have numerical and behavioral effects on prey animals. While numerical effects are well explored, the impact of behavioral effects is unclear. Furthermore, behavioral effects are generally either analyzed with a focus on single individuals or with a focus on consequences for other trophic levels. Thereby, the impact of fear on the level of prey communities is overlooked, despite potential consequences for conservation and nature management. In order to improve our understanding of predator-prey interactions, an assessment of the consequences of fear in shaping prey community structures is crucial. In this thesis, I evaluated how fear alters prey space use, community structure and composition, focusing on terrestrial mammals. By integrating landscapes of fear in an existing individual-based and spatially-explicit model, I simulated community assembly of prey animals via individual home range formation. The model comprises multiple hierarchical levels from individual home range behavior to patterns of prey community structure and composition. The mechanistic approach of the model allowed for the identification of underlying mechanism driving prey community responses under fear. My results show that fear modified prey space use and community patterns. Under fear, prey animals shifted their home ranges towards safer areas of the landscape. Furthermore, fear decreased the total biomass and the diversity of the prey community and reinforced shifts in community composition towards smaller animals. These effects could be mediated by an increasing availability of refuges in the landscape. Under landscape changes, such as habitat loss and fragmentation, fear intensified negative effects on prey communities. Prey communities in risky environments were subject to a non-proportional diversity loss of up to 30\% if fear was taken into account. Regarding habitat properties, I found that well-connected, large safe patches can reduce the negative consequences of habitat loss and fragmentation on prey communities. Including variation in risk perception between prey animals had consequences on prey space use. Animals with a high risk perception predominantly used safe areas of the landscape, while animals with a low risk perception preferred areas with a high food availability. On the community level, prey diversity was higher in heterogeneous landscapes of fear if individuals varied in their risk perception compared to scenarios in which all individuals had the same risk perception. Overall, my findings give a first, comprehensive assessment of the role of fear in shaping prey communities. The linkage between individual home range behavior and patterns at the community level allows for a mechanistic understanding of the underlying processes. My results underline the importance of the structure of the landscape of fear as a key driver of prey community responses, especially if the habitat is threatened by landscape changes. Furthermore, I show that individual landscapes of fear can improve our understanding of the consequences of trait variation on community structures. Regarding conservation and nature management, my results support calls for modern conservation approaches that go beyond single species and address the protection of biotic interactions.}, language = {en} } @article{Teckentrup2019, author = {Teckentrup, Lisa}, title = {Gefahr an jeder Ecke}, series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018}, journal = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018}, publisher = {oerding print GmbH}, address = {Braunschweig}, pages = {54 -- 55}, year = {2019}, language = {de} } @phdthesis{Taube2019, author = {Taube, Robert}, title = {Characterisations of Fungal Communities in Temperate Lakes}, school = {Universit{\"a}t Potsdam}, pages = {139}, year = {2019}, language = {en} } @article{TarazonaMachatschekSchulzetal.2019, author = {Tarazona, Natalia A. and Machatschek, Rainhard Gabriel and Schulz, Burkhard and Auxiliadora Prieto Jim{\´e}nez, M. and Lendlein, Andreas}, title = {Molecular Insights into the Physical Adsorption of Amphiphilic Protein PhaF onto Copolyester Surfaces}, series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, volume = {20}, journal = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, number = {9}, publisher = {American Chemical Society}, address = {Washington}, issn = {1525-7797}, doi = {10.1021/acs.biomac.9b00069}, pages = {3242 -- 3252}, year = {2019}, abstract = {Phasins are amphiphilic proteins located at the polymer-cytoplasm interface of bacterial polyhydroxyalkanoates (PHA). The immobilization of phasins on biomaterial surfaces is a promising way to enhance the hydrophilicity and supply cell- directing elements in bioinstructing processes. Optimizing the physical adsorption of phasins requires deep insights into molecular processes during polymer-protein interactions to preserve their structural conformation while optimizing surface coverage. Here, the assembly, organization, and stability of phasin PhaF from Pseudomonas putida at interfaces is disclosed. The Langmuir technique, combined with in situ microscopy and spectroscopic methods, revealed that PhaF forms stable and robust monolayers at different temperatures, with an almost flat orientation of its alpha-helix at the air-water interface. PhaF adsorption onto preformed monolayers of poly[(3-R-hydroxyoctanoate)-co-(3-R-hydroxyhexanoate)] (PHOHHx), yields stable mixed layers below pi = similar to 15.7 mN/m. Further insertion induces a molecular reorganization. PHOHHx with strong surface hydrophobicity is a more adequate substrate for PhaF adsorption than the less hydrophobic poly[(rac-lactide)-co-glycolide] (PLGA). The observed orientation of the main axis of the protein in relation to copolyester interfaces ensures the best exposure of the hydrophobic residues, providing a suitable coating strategy for polymer functionalization.}, language = {en} } @article{TarazonaMachatschekLendlein2019, author = {Tarazona, Natalia A. and Machatschek, Rainhard Gabriel and Lendlein, Andreas}, title = {Unraveling the interplay between abiotic hydrolytic degradation and crystallization of bacterial polyesters comprising short and medium side-chain-length Polyhydroxyalkanoates}, series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, volume = {21}, journal = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, number = {2}, publisher = {American Chemical Society}, address = {Washington}, issn = {1525-7797}, doi = {10.1021/acs.biomac.9b01458}, pages = {761 -- 771}, year = {2019}, abstract = {Polyhydroxyalkanoates (PHAs) have attracted attention as degradable (co)polyesters which can be produced by microorganisms with variations in the side chain. This structural variation influences not only the thermomechanical properties of the material but also its degradation behavior. Here, we used Langmuir monolayers at the air-water (A-W) interface as suitable models for evaluating the abiotic degradation of two PHAs with different side-chain lengths and crystallinity. By controlling the polymer state (semi crystalline, amorphous), the packing density, the pH, and the degradation mechanism, we could draw several significant conclusions. (i) The maximum degree of crystallinity for a PHA film to be efficiently degraded up to pH = 12.3 is 40\%. (ii) PHA made of repeating units with shorter side-chain length are more easily hydrolyzed under alkaline conditions. The efficiency of alkaline hydrolysis decreased by about 65\% when the polymer was 40\% crystalline. (iii) In PHA films with a relatively high initial crystallinity, abiotic degradation initiated a chemicrystallization phenomenon, detected as an increase in the storage modulus (E'). This could translate into an increase in brittleness and reduction in the material degradability. Finally, we demonstrate the stability of the measurement system for long-term experiments, which allows degradation conditions for polymers that could closely simulate real-time degradation.}, language = {en} } @article{TannerLichtenbergKraag2019, author = {Tanner, Norman and Lichtenberg-Kraag, Birgit}, title = {Identification and Quantification of Single and Multi-Adulteration of Beeswax by FTIR-ATR Spectroscopy}, series = {European journal of lipid science and technology}, volume = {121}, journal = {European journal of lipid science and technology}, number = {12}, publisher = {Wiley}, address = {Hoboken}, issn = {1438-7697}, doi = {10.1002/ejlt.201900245}, pages = {10}, year = {2019}, abstract = {Marketing of adulterated beeswax foundation has recently become a major economic problem for beekeepers. Paraffin contamination leads to collapse of combs, and stearic acid has a negative influence on the development of bee brood. The quality of beeswax for beekeeping has not been standardized in EU regulations. Recently, it was shown that attenuated total reflectance Fourier-transform infrared spectroscopy (FTIR-ATR) can be used to determine beeswax adulteration. Differences in the IR spectra of authentic beeswax can be identified and calculated through comparison with authentic beeswax. In this study, the method is further validated by employing a high number of samples of authentic beeswax from different origins. Low quantification and detection limits are achieved for paraffin, stearic acid, tallow, carnauba wax, and candelilla wax. Furthermore, the FTIR-ATR analytical conditions are verified by analyzing 358 samples of commercial and beekeeper-produced beeswax foundations. Multi-adulterated samples with as many as five different additives in beeswax mixtures are identified with the same accuracy as single substances. Additionally, the spectra of a further 14 different natural and synthetic waxes and hardened fats are analyzed and are compared with beeswax. Finally, a spectral library is established that can be used for further studies. Practical Applications: FTIR-ATR is a fast and cost-efficient tool in beeswax analysis for accurately monitoring a high sample volume. Analysis of 358 beeswax foundations showed an adulteration of 21.8\% of the samples with paraffin, stearic acid, tallow, and combinations. Based on the results of this study, it is possible to detect beeswax adulteration of less than 3\% of these adulterants and their combinations by FTIR-ATR spectroscopy. This method can be used for monitoring beeswax foundations to identify adulterated materials, exclude these materials from the recycling process, and produce high-quality beeswax, which is essential for bee health.}, language = {en} } @article{TangBackhausRiemannetal.2019, author = {Tang, Kam W. and Backhaus, Liv and Riemann, Lasse and Koski, Marja and Grossart, Hans-Peter and Munk, Peter and Nielsen, Torkel Gissel}, title = {Copepod carcasses in the subtropical convergence zone of the Sargasso Sea}, series = {Journal of plankton research}, volume = {41}, journal = {Journal of plankton research}, number = {4}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0142-7873}, doi = {10.1093/plankt/fbz038}, pages = {549 -- 560}, year = {2019}, abstract = {The oligotrophic subtropical gyre covers a vast area of the Atlantic Ocean. Decades of time-series monitoring have generated detailed temporal information about zooplankton species and abundances at fixed locations within the gyre, but their live/dead status is often omitted, especially in the dynamic subtropical convergence zone (STCZ) where the water column stratification pattern can change considerably across the front as warm and cold water masses converge. We conducted a detailed survey in the North Atlantic STCZ and showed that over 85\% of the copepods were typically concentrated in the upper 200 m. Copepod carcasses were present in all samples and their proportional numerical abundances increased with depth, reaching up to 91\% at 300-400 m. Overall, 14-19\% of the copepods within the upper 200 m were carcasses. Shipboard experiments showed that during carcass decomposition, microbial respiration increased, and the bacterial community associated with the carcasses diverged from that in the ambient water. Combining field and experimental data, we estimated that decomposing copepod carcasses constitute a negligible oxygen sink in the STCZ, but sinking carcasses may represent an overlooked portion of the passive carbon sinking flux and should be incorporated in future studies of carbon flux in this area.}, language = {en} } @article{TangWerchmeisterPredaetal.2019, author = {Tang, Jing and Werchmeister, Rebecka Maria Larsen and Preda, Loredana and Huang, Wei and Zheng, Zhiyong and Leimk{\"u}hler, Silke and Wollenberger, Ulla and Xiao, Xinxin and Engelbrekt, Christian and Ulstrup, Jens and Zhang, Jingdong}, title = {Three-dimensional sulfite oxidase bioanodes based on graphene functionalized carbon paper for sulfite/O-2 biofuel cells}, series = {ACS catalysis}, volume = {9}, journal = {ACS catalysis}, number = {7}, publisher = {American Chemical Society}, address = {Washington}, issn = {2155-5435}, doi = {10.1021/acscatal.9b01715}, pages = {6543 -- 6554}, year = {2019}, abstract = {We have developed a three-dimensional (3D) graphene electrode suitable for the immobilization of human sulfite oxidase (hSO), which catalyzes the electrochemical oxidation of sulfite via direct electron transfer (DET). The electrode is fabricated by drop-casting graphene-polyethylenimine (G-P) composites on carbon papers (CPs) precoated with graphene oxide (GO). The negatively charged hSO can be adsorbed electrostatically on the positively charged matrix (G-P) on CP electrodes coated with GO (CPG), with a proper orientation for accelerated DET. Notably, further electrochemical reduction of G-P on CPG electrodes leads to a 9-fold increase of the saturation catalytic current density (j(m)) for sulfite oxidation reaching 24.4 +/- 0.3 mu A to cm(-2), the highest value among reported DET-based hSO bioelectrodes. The increased electron transfer rate plays a dominating role in the enhancement of direct enzymatic current because of the improved electric contact of hSO with the electrode, The optimized hSO bioelectrode shows a significant catalytic rate (k(cat): 25.6 +/- 0.3 s(-1)) and efficiency (k(cat)/K-m: 0.231 +/- 0.003 s(-1) mu M-1) compared to the reported hSO bioelectrodes. The assembly of the hSO bioanode and a commercial platinum biocathode allows the construction of sulfite/O-2 enzymatic biofuel cells (EBFCs) with flowing fuels. The optimized EBFC displays an open-circuit voltage (OCV) of 0.64 +/- 0.01 V and a maximum power density of 61 +/- 6 mu W cm(-2) (122 +/- 12 mW m(-3)) at 30 degrees C, which exceeds the best reported value by more than 6 times.}, language = {en} } @article{TangSullivanHongetal.2019, author = {Tang, Alan T. and Sullivan, Katie Rose and Hong, Courtney C. and Goddard, Lauren M. and Mahadevan, Aparna and Ren, Aileen and Pardo, Heidy and Peiper, Amy and Griffin, Erin and Tanes, Ceylan and Mattei, Lisa M. and Yang, Jisheng and Li, Li and Mericko-Ishizuka, Patricia and Shen, Le and Hobson, Nicholas and Girard, Romuald and Lightle, Rhonda and Moore, Thomas and Shenkar, Robert and Polster, Sean P. and Roedel, Claudia Jasmin and Li, Ning and Zhu, Qin and Whitehead, Kevin J. and Zheng, Xiangjian and Akers, Amy and Morrison, Leslie and Kim, Helen and Bittinger, Kyle and Lengner, Christopher J. and Schwaninger, Markus and Velcich, Anna and Augenlicht, Leonard and Abdelilah-Seyfried, Salim and Min, Wang and Marchuk, Douglas A. and Awad, Issam A. and Kahn, Mark L.}, title = {Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation}, series = {Science Translational Medicine}, volume = {11}, journal = {Science Translational Medicine}, number = {520}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {1946-6234}, doi = {10.1126/scitranslmed.aaw3521}, pages = {14}, year = {2019}, abstract = {Cerebral cavernous malformation (CCM) is a genetic, cerebrovascular disease. Familial CCM is caused by genetic mutations in KRIT1, CCM2, or PDCD10. Disease onset is earlier and more severe in individuals with PDCD10 mutations. Recent studies have shown that lesions arise from excess mitogen-activated protein kinase kinase kinase 3 (MEKK3) signaling downstream of Toll-like receptor 4 (TLR4) stimulation by lipopolysaccharide derived from the gut microbiome. These findings suggest a gut-brain CCM disease axis but fail to define it or explain the poor prognosis of patients with PDCD10 mutations. Here, we demonstrate that the gut barrier is a primary determinant of CCM disease course, independent of microbiome configuration, that explains the increased severity of CCM disease associated with PDCD10 deficiency. Chemical disruption of the gut barrier with dextran sulfate sodium augments CCM formation in a mouse model, as does genetic loss of Pdcd10, but not Krit1, in gut epithelial cells. Loss of gut epithelial Pdcd10 results in disruption of the colonic mucosal barrier. Accordingly, loss of Mucin-2 or exposure to dietary emulsifiers that reduce the mucus barrier increases CCM burden analogous to loss of Pdcd10 in the gut epithelium. Last, we show that treatment with dexamethasone potently inhibits CCM formation in mice because of the combined effect of action at both brain endothelial cells and gut epithelial cells. These studies define a gut-brain disease axis in an experimental model of CCM in which a single gene is required for two critical components: gut epithelial function and brain endothelial signaling.}, language = {en} } @article{TanabeLeimkuehlerDahl2019, author = {Tanabe, Tomohisa Sebastian and Leimk{\"u}hler, Silke and Dahl, Christiane}, title = {The functional diversity of the prokaryotic sulfur carrier protein TusA}, series = {Advances in microbial physiology}, volume = {75}, journal = {Advances in microbial physiology}, editor = {Poole, RK}, publisher = {Elsevier Acad. Press}, address = {Amsterdam}, isbn = {978-0-12-817715-0}, issn = {0065-2911}, doi = {10.1016/bs.ampbs.2019.07.004}, pages = {233 -- 277}, year = {2019}, abstract = {Persulfide groups participate in a wide array of biochemical pathways and are chemically very versatile. The TusA protein has been identified as a central element supplying and transferring sulfur as persulfide to a number of important biosynthetic pathways, like molybdenum cofactor biosynthesis or thiomodifications in nucleosides of tRNAs. In recent years, it has furthermore become obvious that this protein is indispensable for the oxidation of sulfur compounds in the cytoplasm. Phylogenetic analyses revealed that different TusA protein variants exists in certain organisms, that have evolved to pursue specific roles in cellular pathways. The specific TusA-like proteins thereby cannot replace each other in their specific roles and are rather specific to one sulfur transfer pathway or shared between two pathways. While certain bacteria like Escherichia coli contain several copies of TusA-like proteins, in other bacteria like Allochromatium vinosum a single copy of TusA is present with an essential role for this organism. Here, we give an overview on the multiple roles of the various TusA-like proteins in sulfur transfer pathways in different organisms to shed light on the remaining mysteries of this versatile protein.}, language = {en} } @article{TabaresJimenezZimmermannDietzeetal.2019, author = {Tabares Jimenez, Ximena del Carmen and Zimmermann, Heike Hildegard and Dietze, Elisabeth and Ratzmann, Gregor and Belz, Lukas and Vieth-Hillebrand, Andrea and Dupont, Lydie and Wilkes, Heinz and Mapani, Benjamin and Herzschuh, Ulrike}, title = {Vegetation state changes in the course of shrub encroachment in an African savanna since about 1850 CE and their potential drivers}, series = {Ecology and evolution}, volume = {10}, journal = {Ecology and evolution}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.5955}, pages = {962 -- 979}, year = {2019}, abstract = {Shrub encroachment has far-reaching ecological and economic consequences in many ecosystems worldwide. Yet, compositional changes associated with shrub encroachment are often overlooked despite having important effects on ecosystem functioning. We document the compositional change and potential drivers for a northern Namibian Combretum woodland transitioning into a Terminalia shrubland. We use a multiproxy record (pollen, sedimentary ancient DNA, biomarkers, compound-specific carbon (delta C-13) and deuterium (delta D) isotopes, bulk carbon isotopes (delta(13)Corg), grain size, geochemical properties) from Lake Otjikoto at high taxonomical and temporal resolution. We provide evidence that state changes in semiarid environments may occur on a scale of one century and that transitions between stable states can span around 80 years and are characterized by a unique vegetation composition. We demonstrate that the current grass/woody ratio is exceptional for the last 170 years, as supported by n-alkane distributions and the delta C-13 and delta(13)Corg records. Comparing vegetation records to environmental proxy data and census data, we infer a complex network of global and local drivers of vegetation change. While our delta D record suggests physiological adaptations of woody species to higher atmospheric pCO(2) concentration and drought, our vegetation records reflect the impact of broad-scale logging for the mining industry, and the macrocharcoal record suggests a decrease in fire activity associated with the intensification of farming. Impact of selective grazing is reflected by changes in abundance and taxonomical composition of grasses and by an increase of nonpalatable and trampling-resistant taxa. In addition, grain-size and spore records suggest changes in the erodibility of soils because of reduced grass cover. Synthesis. We conclude that transitions to an encroached savanna state are supported by gradual environmental changes induced by management strategies, which affected the resilience of savanna ecosystems. In addition, feedback mechanisms that reflect the interplay between management legacies and climate change maintain the encroached state.}, language = {en} } @article{StegerKimGanzertetal.2019, author = {Steger, Kristin and Kim, Amy Taeyen and Ganzert, Lars and Grossart, Hans-Peter and Smart, David R.}, title = {Floodplain soil and its bacterial composition are strongly affected by depth}, series = {FEMS microbiology ecology}, volume = {95}, journal = {FEMS microbiology ecology}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0168-6496}, doi = {10.1093/femsec/fiz014}, pages = {11}, year = {2019}, abstract = {We studied bacterial abundance and community structure of five soil cores using high-throughput sequencing of the 16S rRNA gene. Shifts in the soil bacterial composition were more pronounced within a vertical profile than across the landscape. Soil organic carbon (SOC) and nitrogen (N) concentrations decreased exponentially with soil depth and revealed a buried carbon-rich horizon between 0.8 and 1.3 m across all soil cores. This buried horizon was phylogenetically similar to its surrounding subsoils supporting the idea that the type of carbon, not necessarily the amount of carbon was driving the apparent similarities. In contrast to other studies, Nitrospirae was one of our major phyla with relatively high abundances throughout the soil profile except for the surface soil. Although depth is the major driver shaping soil bacterial community structure, positive correlations with SOC and N concentrations, however, were revealed with the bacterial abundance of Acidobacteria, one of the major, and Gemmatimonadetes, one of the minor phyla in our study. Our study showed that bacterial diversity in soils below 2.0 m can be still as high if not higher than in the above laying subsurface soil suggesting that various bacteria throughout the soil profile influence major biogeochemical processes in floodplain soils.}, language = {en} } @article{StaszekKrasuskaOtulakKozieletal.2019, author = {Staszek, Pawel and Krasuska, Urszula and Otulak-Koziel, Katarzyna and Fettke, J{\"o}rg and Gniazdowska, Agnieszka}, title = {Canavanine-Induced Decrease in Nitric Oxide Synthesis Alters Activity of Antioxidant System but Does Not Impact S-Nitrosoglutathione Catabolism in Tomato Roots}, series = {Frontiers in plant science}, volume = {10}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2019.01077}, pages = {18}, year = {2019}, abstract = {Canavanine (CAN) is a nonproteinogenic amino acid synthesized in legumes. In mammalians, as arginine analogue, it is an inhibitor of nitric oxide synthase (NOS) activity. The aim of this study was to investigate the impact of CAN-induced nitric oxide level limitation on the antioxidant system and S-nitrosoglutathione (GSNO) metabolism in roots of tomato seedlings. Treatment with CAN (10 or 50 mu M) for 24-72 h led to restriction in root growth. Arginine-dependent NOS-like activity was almost completely inhibited, demonstrating direct effect of CAN action. CAN increased total antioxidant capacity and the level of sulphydryl groups. Catalase (CAT) and superoxide dismutase (SOD) activity decreased in CAN exposed roots. CAN supplementation resulted in the decrease of transcript levels of genes coding CAT (with the exception of CAT1). Genes coding SOD (except MnSOD and CuSOD) were upregulated by CAN short treatment; prolonged exposition to 50-mu M CAN resulted in downregulation of FeSOD, CuSOD, and SODP-2. Activity of glutathione reductase dropped down after short-term (10-mu M CAN) supplementation, while glutathione peroxidase activity was not affected. Transcript levels of glutathione reductase genes declined in response to CAN. Genes coding glutathione peroxidase were upregulated by 50-mu M CAN, while 10-mu M CAN downregulated GSHPx1. Inhibition of NOS-like activity by CAN resulted in lower GSNO accumulation in root tips. Activity of GSNO reductase was decreased by short-term supplementation with CAN. In contrast, GSNO reductase protein abundance was higher, while transcript levels were slightly altered in roots exposed to CAN. This is the first report on identification of differentially nitrated proteins in response to supplementation with nonproteinogenic amino acid. Among nitrated proteins differentially modified by CAN, seed storage proteins (after short-term CAN treatment) and components of the cellular redox system (after prolonged CAN supplementation) were identified. The findings demonstrate that due to inhibition of NOS-like activity, CAN leads to modification in antioxidant system. Limitation in GSNO level is due to lower nitric oxide formation, while GSNO catabolism is less affected. We demonstrated that monodehydroascorbate reductase, activity of which is inhibited in roots of CAN-treated plants, is the protein preferentially modified by tyrosine nitration.}, language = {en} } @article{SrokaGodunkoRutschmannetal.2019, author = {Sroka, Pavel and Godunko, Roman J. and Rutschmann, Sereina and Angeli, Kamila B. and Salles, Frederico F. and Gattolliat, Jean-Luc}, title = {A new species of Bungona in Turkey (Ephemeroptera, Baetidae)}, series = {Zoosytematics and evolution}, volume = {95}, journal = {Zoosytematics and evolution}, number = {1}, publisher = {Pensoft Publ.}, address = {Sofia}, issn = {1860-0743}, doi = {10.3897/zse.95.29487}, pages = {1 -- 13}, year = {2019}, abstract = {By using an integrative approach, we describe a new species of mayfly, Bungona (Chopralla) pontica sp. n., from Turkey. The discovery of a representative of the tropical mayfly genus Bungona in the Middle East is rather unexpected. The new species shows all the main morphological characters of the subgenus Chopralla, which has its closest related species occurring in southeastern Asia. Barcoding clearly indicated that the new species represents an independent lineage isolated for a very long time from other members of the complex. The claw is equipped with two rows of three or four flattened denticles. This condition is a unique feature of Bungona (Chopralla) pontica sp. n. among West Palaearctic mayfly species. Within the subgenus Chopralla, the species can be identified by the presence of a simple, not bifid right prostheca (also present only in Bungona (Chopralla) liebenauae (Soldan, Braasch \& Muu, 1987)), the shape of the labial palp, and the absence of protuberances on pronotum.}, language = {en} } @article{SperberWelkePetazzietal.2019, author = {Sperber, Hannah Sabeth and Welke, Robert-William and Petazzi, Roberto Arturo and Bergmann, Ronny and Schade, Matthias and Shai, Yechiel and Chiantia, Salvatore and Herrmann, Andreas and Schwarzer, Roland}, title = {Self-association and subcellular localization of Puumala hantavirus envelope proteins}, series = {Scientific reports}, volume = {9}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-018-36879-y}, pages = {15}, year = {2019}, abstract = {Hantavirus assembly and budding are governed by the surface glycoproteins Gn and Gc. In this study, we investigated the glycoproteins of Puumala, the most abundant Hantavirus species in Europe, using fluorescently labeled wild-type constructs and cytoplasmic tail (CT) mutants. We analyzed their intracellular distribution, co-localization and oligomerization, applying comprehensive live, single-cell fluorescence techniques, including confocal microscopy, imaging flow cytometry, anisotropy imaging and Number\&Brightness analysis. We demonstrate that Gc is significantly enriched in the Golgi apparatus in absence of other viral components, while Gn is mainly restricted to the endoplasmic reticulum (ER). Importantly, upon co-expression both glycoproteins were found in the Golgi apparatus. Furthermore, we show that an intact CT of Gc is necessary for efficient Golgi localization, while the CT of Gn influences protein stability. Finally, we found that Gn assembles into higher-order homo-oligomers, mainly dimers and tetramers, in the ER while Gc was present as mixture of monomers and dimers within the Golgi apparatus. Our findings suggest that PUUV Gc is the driving factor of the targeting of Gc and Gn to the Golgi region, while Gn possesses a significantly stronger self-association potential.}, language = {en} } @misc{SowemimoKnoxBrownBorcherdsetal.2019, author = {Sowemimo, Oluwakemi T. and Knox-Brown, Patrick and Borcherds, Wade and Rindfleisch, Tobias and Thalhammer, Anja and Daughdrill, Gary W.}, title = {Conserved glycines control disorder and function in the cold-regulated protein, COR15A}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1089}, issn = {1866-8372}, doi = {10.25932/publishup-47221}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-472217}, pages = {19}, year = {2019}, abstract = {Cold-regulated (COR) 15A is an intrinsically disordered protein (IDP) from Arabidopsis thaliana important for freezing tolerance. During freezing-induced cellular dehydration, COR15A transitions from a disordered to mostly alpha-helical structure. We tested whether mutations that increase the helicity of COR15A also increase its protective function. Conserved glycine residues were identified and mutated to alanine. Nuclear magnetic resonance (NMR) spectroscopy was used to identify residue-specific changes in helicity for wildtype (WT) COR15A and the mutants. Circular dichroism (CD) spectroscopy was used to monitor the coil-helix transition in response to increasing concentrations of trifluoroethanol (TFE) and ethylene glycol. The impact of the COR15A mutants on the stability of model membranes during a freeze-thaw cycle was investigated by fluorescence spectroscopy. The results of these experiments showed the mutants had a higher content of alpha-helical structure and the increased alpha-helicity improved membrane stabilization during freezing. Comparison of the TFE- and ethylene glycol-induced coil-helix transitions support our conclusion that increasing the transient helicity of COR15A in aqueous solution increases its ability to stabilize membranes during freezing. Altogether, our results suggest the conserved glycine residues are important for maintaining the disordered structure of COR15A but are also compatible with the formation of alpha-helical structure during freezing induced dehydration.}, language = {en} } @article{SowemimoKnoxBrownBorcherdsetal.2019, author = {Sowemimo, Oluwakemi T. and Knox-Brown, Patrick and Borcherds, Wade and Rindfleisch, Tobias and Thalhammer, Anja and Daughdrill, Gary W.}, title = {Conserved Glycines Control Disorder and Function in the Cold-Regulated Protein, COR15A}, series = {Biomolecules}, volume = {9}, journal = {Biomolecules}, number = {3}, publisher = {MDPI}, address = {Basel}, issn = {2218-273X}, doi = {10.3390/biom9030084}, pages = {17}, year = {2019}, abstract = {Cold-regulated (COR) 15A is an intrinsically disordered protein (IDP) from Arabidopsis thaliana important for freezing tolerance. During freezing-induced cellular dehydration, COR15A transitions from a disordered to mostly alpha-helical structure. We tested whether mutations that increase the helicity of COR15A also increase its protective function. Conserved glycine residues were identified and mutated to alanine. Nuclear magnetic resonance (NMR) spectroscopy was used to identify residue-specific changes in helicity for wildtype (WT) COR15A and the mutants. Circular dichroism (CD) spectroscopy was used to monitor the coil-helix transition in response to increasing concentrations of trifluoroethanol (TFE) and ethylene glycol. The impact of the COR15A mutants on the stability of model membranes during a freeze-thaw cycle was investigated by fluorescence spectroscopy. The results of these experiments showed the mutants had a higher content of alpha-helical structure and the increased alpha-helicity improved membrane stabilization during freezing. Comparison of the TFE- and ethylene glycol-induced coil-helix transitions support our conclusion that increasing the transient helicity of COR15A in aqueous solution increases its ability to stabilize membranes during freezing. Altogether, our results suggest the conserved glycine residues are important for maintaining the disordered structure of COR15A but are also compatible with the formation of alpha-helical structure during freezing induced dehydration.}, language = {en} } @misc{SowemimoBorcherdsKnoxBrownetal.2019, author = {Sowemimo, Oluwakemi and Borcherds, Wade and Knox-Brown, Patrick and Rindfleisch, Tobias and Thalhammer, Anja and Daughdrill, Gary}, title = {Evolution of Transient Helicity and Disorder in Late Embryogenesis Abundant Protein COR15A}, series = {Biophysical journal}, volume = {116}, journal = {Biophysical journal}, number = {3}, publisher = {Cell Press}, address = {Cambridge}, issn = {0006-3495}, doi = {10.1016/j.bpj.2018.11.2553}, pages = {473A -- 473A}, year = {2019}, abstract = {Cold regulated protein 15A (COR15A) is a nuclear encoded, intrinsically disordered protein that is found in Arabidopsis thaliana. It belongs to the Late Embryogenesis Abundant (LEA) family of proteins and is responsible for increased freezing tolerance in plants. COR15A is intrinsically disordered in dilute solutions and adopts a helical structure upon dehydration or in the presence of co-solutes such as TFE and ethylene glycol. This helical structure is thought to be important for protecting plants from dehydration induced by freezing. Multiple protein sequence alignments revealed the presence of several conserved glycine residues that we hypothesize keeps COR15A from becoming helical in dilute solutions. Using AGADIR, the change in helical content of COR15A when these conserved glycine residues were mutated to alanine residues was predicted. Based on the predictions, glycine to alanine mutants were made at position 68, and 54,68,81, and 84. Labeled samples of wildtype COR15A and mutant proteins were purified and NMR experiments were performed to examine any structural changes induced by the mutations. To test the effects of dehydration on the structure of COR15A, trifluoroethanol, an alcohol based co solvent that is proposed to induce/stabilize helical structure in peptides was added to the NMR samples, and the results of the experiment showed an increase in helical content, compared to the samples without TFE. To test the functional differences between wild type and the mutants, liposome leakage assays were performed. The results from these assays suggest the more helical mutants may augment membrane stability.}, language = {en} } @article{SongLiNowaketal.2019, author = {Song, Yu and Li, Gang and Nowak, Jacqueline and Zhang, Xiaoqing and Xu, Dongbei and Yang, Xiujuan and Huang, Guoqiang and Liang, Wanqi and Yang, Litao and Wang, Canhua and Bulone, Vincent and Nikoloski, Zoran and Hu, Jianping and Persson, Staffan and Zhang, Dabing}, title = {The Rice Actin-Binding Protein RMD Regulates Light-Dependent Shoot Gravitropism}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {181}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.19.00497}, pages = {630 -- 644}, year = {2019}, abstract = {Light and gravity are two key determinants in orientating plant stems for proper growth and development. The organization and dynamics of the actin cytoskeleton are essential for cell biology and critically regulated by actin-binding proteins. However, the role of actin cytoskeleton in shoot negative gravitropism remains controversial. In this work, we report that the actin-binding protein Rice Morphology Determinant (RMD) promotes reorganization of the actin cytoskeleton in rice (Oryza sativa) shoots. The changes in actin organization are associated with the ability of the rice shoots to respond to negative gravitropism. Here, light-grown rmd mutant shoots exhibited agravitropic phenotypes. By contrast, etiolated rmd shoots displayed normal negative shoot gravitropism. Furthermore, we show that RMD maintains an actin configuration that promotes statolith mobility in gravisensing endodermal cells, and for proper auxin distribution in light-grown, but not dark-grown, shoots. RMD gene expression is diurnally controlled and directly repressed by the phytochrome-interacting factor-like protein OsPIL16. Consequently, overexpression of OsPIL16 led to gravisensing and actin patterning defects that phenocopied the rmd mutant. Our findings outline a mechanism that links light signaling and gravity perception for straight shoot growth in rice.}, language = {en} }