@misc{NakamuraClaesGrebeetal.2018, author = {Nakamura, Moritaka and Claes, Andrea R. and Grebe, Tobias and Hermkes, Rebecca and Viotti, Corrado and Ikeda, Yoshihisa and Grebe, Markus}, title = {Auxin and ROP GTPase signaling of polar nuclear migration in root epidermal hair cells}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {992}, issn = {1866-8372}, doi = {10.25932/publishup-44127}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441278}, pages = {378 -- 391}, year = {2018}, abstract = {Polar nuclear migration is crucial during the development of diverse eukaryotes. In plants, root hair growth requires polar nuclear migration into the outgrowing hair. However, knowledge about the dynamics and the regulatory mechanisms underlying nuclear movements in root epidermal cells remains limited. Here, we show that both auxin and Rho-of-Plant (ROP) signaling modulate polar nuclear position at the inner epidermal plasma membrane domain oriented to the cortical cells during cell elongation as well as subsequent polar nuclear movement to the outer domain into the emerging hair bulge in Arabidopsis (Arabidopsis thaliana). Auxin signaling via the nuclear AUXIN RESPONSE FACTOR7 (ARF7)/ARF19 and INDOLE ACETIC ACID7 pathway ensures correct nuclear placement toward the inner membrane domain. Moreover, precise inner nuclear placement relies on SPIKE1 Rho-GEF, SUPERCENTIPEDE1 Rho-GDI, and ACTIN7 (ACT7) function and to a lesser extent on VTI11 vacuolar SNARE activity. Strikingly, the directionality and/or velocity of outer polar nuclear migration into the hair outgrowth along actin strands also are ACT7 dependent, auxin sensitive, and regulated by ROP signaling. Thus, our findings provide a founding framework revealing auxin and ROP signaling of inner polar nuclear position with some contribution by vacuolar morphology and of actin-dependent outer polar nuclear migration in root epidermal hair cells.}, language = {en} } @misc{KunstmannScheidtBuchwaldetal.2018, author = {Kunstmann, Ruth Sonja and Scheidt, Tom and Buchwald, Saskia and Helm, Alexandra and Mulard, Laurence A. and Fruth, Angelika and Barbirz, Stefanie}, title = {Bacteriophage Sf6 Tailspike Protein for Detection of Shigella flexneri Pathogens}, series = {Viruses}, journal = {Viruses}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-417831}, pages = {18}, year = {2018}, abstract = {Bacteriophage research is gaining more importance due to increasing antibiotic resistance. However, for treatment with bacteriophages, diagnostics have to be improved. Bacteriophages carry adhesion proteins, which bind to the bacterial cell surface, for example tailspike proteins (TSP) for specific recognition of bacterial O-antigen polysaccharide. TSP are highly stable proteins and thus might be suitable components for the integration into diagnostic tools. We used the TSP of bacteriophage Sf6 to establish two applications for detecting Shigella flexneri (S. flexneri), a highly contagious pathogen causing dysentery. We found that Sf6TSP not only bound O-antigen of S. flexneri serotype Y, but also the glucosylated O-antigen of serotype 2a. Moreover, mass spectrometry glycan analyses showed that Sf6TSP tolerated various O-acetyl modifications on these O-antigens. We established a microtiter plate-based ELISA like tailspike adsorption assay (ELITA) using a Strep-tag®II modified Sf6TSP. As sensitive screening alternative we produced a fluorescently labeled Sf6TSP via coupling to an environment sensitive dye. Binding of this probe to the S. flexneri O-antigen Y elicited a fluorescence intensity increase of 80\% with an emission maximum in the visible light range. The Sf6TSP probes thus offer a promising route to a highly specific and sensitive bacteriophage TSP-based Shigella detection system.}, language = {en} } @phdthesis{Alhajturki2018, author = {Alhajturki, Dema}, title = {Characterization of altered inflorescence architecture in Arabidopsis thaliana BG-5 x Kro-0 hybrid}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-420934}, school = {Universit{\"a}t Potsdam}, pages = {109}, year = {2018}, abstract = {A reciprocal cross between two A. thaliana accessions, Kro-0 (Krotzenburg, Germany) and BG-5 (Seattle, USA), displays purple rosette leaves and dwarf bushy phenotype in F1 hybrids when grown at 17 °C and a parental-like phenotype when grown at 21 °C. This F1 temperature-dependent-dwarf-bushy phenotype is characterized by reduced growth of the primary stem together with an increased number of branches. The reduced stem growth was the strongest at the first internode. In addition, we found that a temperature switch from 21 °C to 17 °C induced the phenotype only before the formation of the first internode of the stem. Similarly, the F1 dwarf-bushy phenotype could not be reversed when plants were shifted from 17 °C to 21 °C after the first internode was formed. Metabolic analysis showed that the F1 phenotype was associated with a significant upregulation of anthocyanin(s), kaempferol(s), salicylic acid, jasmonic acid and abscisic acid. As it has been previously shown that the dwarf-bushy phenotype is linked to two loci, one on chromosome 2 from Kro-0 and one on chromosome 3 from BG-5, an artificial micro-RNA approach was used to investigate the necessary genes on these intervals. From the results obtained, it was found that two genes, AT2G14120 that encodes for a DYNAMIN RELATED PROTEIN3B and AT2G14100 that encodes a member of the Cytochrome P450 family protein CYP705A13, were necessary for the appearance of the F1 phenotype on chromosome 2. It was also discovered that AT3G61035 that encodes for another cytochrome P450 family protein CYP705A13 and AT3G60840 that encodes for a MICROTUBULE-ASSOCIATED PROTEIN65-4 on chromosome 3 were both necessary for the induction of the F1 phenotype. To prove the causality of these genes, genomic constructs of the Kro-0 candidate genes on chromosome 2 were transferred to BG-5 and genomic constructs of the chromosome 3 candidate genes from BG-5 were transferred to Kro-0. The T1 lines showed that these genes are not sufficient alone to induce the phenotype. In addition to the F1 phenotype, more severe phenotypes were observed in the F2 generations that were grouped into five different phenotypic classes. Whilst seed yield was comparable between F1 hybrids and parental lines, three phenotypic classes in the F2 generation exhibited hybrid breakdown in the form of reproductive failure. This F2 hybrid breakdown was less sensitive to temperature and showed a dose-dependent effect of the loci involved in F1 phenotype. The severest class of hybrid breakdown phenotypes was observed only in the population of backcross with the parent Kro-0, which indicates a stronger contribution of the BG-5 allele when compared to the Kro-0 allele on the hybrid breakdown phenotypes. Overall, the findings of my thesis provide a further understanding of the genetic and metabolic factors underlying altered shoot architecture in hybrid dysfunction.}, language = {en} } @misc{Graef2018, author = {Gr{\"a}f, Ralph}, title = {Comparative biology of centrosomal structures in eukaryotes}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1063}, issn = {1866-8372}, doi = {10.25932/publishup-47229}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-472294}, pages = {11}, year = {2018}, abstract = {The centrosome is not only the largest and most sophisticated protein complex within a eukaryotic cell, in the light of evolution, it is also one of its most ancient organelles. This special issue of "Cells" features representatives of three main, structurally divergent centrosome types, i.e., centriole-containing centrosomes, yeast spindle pole bodies (SPBs), and amoebozoan nucleus-associated bodies (NABs). Here, I discuss their evolution and their key-functions in microtubule organization, mitosis, and cytokinesis. Furthermore, I provide a brief history of centrosome research and highlight recently emerged topics, such as the role of centrioles in ciliogenesis, the relationship of centrosomes and centriolar satellites, the integration of centrosomal structures into the nuclear envelope and the involvement of centrosomal components in non-centrosomal microtubule organization.}, language = {en} } @misc{RaatzvanVelzenGaedke2018, author = {Raatz, Michael and van Velzen, Ellen and Gaedke, Ursula}, title = {Co-adaptation impacts the robustness of predator-prey dynamics against perturbations}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {809}, issn = {1866-8372}, doi = {10.25932/publishup-44248}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-442489}, pages = {16}, year = {2018}, abstract = {Global change threatens the maintenance of ecosystem functions that are shaped by the persistence and dynamics of populations. It has been shown that the persistence of species increases if they possess larger trait adaptability. Here, we investigate whether trait adaptability also affects the robustness of population dynamics of interacting species and thereby shapes the reliability of ecosystem functions that are driven by these dynamics. We model co-adaptation in a predator-prey system as changes to predator offense and prey defense due to evolution or phenotypic plasticity. We investigate how trait adaptation affects the robustness of population dynamics against press perturbations to environmental parameters and against pulse perturbations targeting species abundances and their trait values. Robustness of population dynamics is characterized by resilience, elasticity, and resistance. In addition to employing established measures for resilience and elasticity against pulse perturbations (extinction probability and return time), we propose the warping distance as a new measure for resistance against press perturbations, which compares the shapes and amplitudes of pre- and post-perturbation population dynamics. As expected, we find that the robustness of population dynamics depends on the speed of adaptation, but in nontrivial ways. Elasticity increases with speed of adaptation as the system returns more rapidly to the pre-perturbation state. Resilience, in turn, is enhanced by intermediate speeds of adaptation, as here trait adaptation dampens biomass oscillations. The resistance of population dynamics strongly depends on the target of the press perturbation, preventing a simple relationship with the adaptation speed. In general, we find that low robustness often coincides with high amplitudes of population dynamics. Hence, amplitudes may indicate the robustness against perturbations also in other natural systems with similar dynamics. Our findings show that besides counteracting extinctions, trait adaptation indeed strongly affects the robustness of population dynamics against press and pulse perturbations.}, language = {en} } @misc{BeermannWestburyHofreiteretal.2018, author = {Beermann, Jan and Westbury, Michael V. and Hofreiter, Michael and Hilgers, Leon and Deister, Fabian and Neumann, Hermann and Raupach, Michael J.}, title = {Cryptic species in a well-known habitat}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {1059}, issn = {1866-8372}, doi = {10.25932/publishup-46079}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-460792}, pages = {28}, year = {2018}, abstract = {Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.}, language = {en} } @phdthesis{Schwahn2018, author = {Schwahn, Kevin}, title = {Data driven approaches to infer the regulatory mechanism shaping and constraining levels of metabolites in metabolic networks}, doi = {10.25932/publishup-42324}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-423240}, school = {Universit{\"a}t Potsdam}, pages = {109}, year = {2018}, abstract = {Systems biology aims at investigating biological systems in its entirety by gathering and analyzing large-scale data sets about the underlying components. Computational systems biology approaches use these large-scale data sets to create models at different scales and cellular levels. In addition, it is concerned with generating and testing hypotheses about biological processes. However, such approaches are inevitably leading to computational challenges due to the high dimensionality of the data and the differences in the dimension of data from different cellular layers. This thesis focuses on the investigation and development of computational approaches to analyze metabolite profiles in the context of cellular networks. This leads to determining what aspects of the network functionality are reflected in the metabolite levels. With these methods at hand, this thesis aims to answer three questions: (1) how observability of biological systems is manifested in metabolite profiles and if it can be used for phenotypical comparisons; (2) how to identify couplings of reaction rates from metabolic profiles alone; and (3) which regulatory mechanism that affect metabolite levels can be distinguished by integrating transcriptomics and metabolomics read-outs. I showed that sensor metabolites, identified by an approach from observability theory, are more correlated to each other than non-sensors. The greater correlations between sensor metabolites were detected both with publicly available metabolite profiles and synthetic data simulated from a medium-scale kinetic model. I demonstrated through robustness analysis that correlation was due to the position of the sensor metabolites in the network and persisted irrespectively of the experimental conditions. Sensor metabolites are therefore potential candidates for phenotypical comparisons between conditions through targeted metabolic analysis. Furthermore, I demonstrated that the coupling of metabolic reaction rates can be investigated from a purely data-driven perspective, assuming that metabolic reactions can be described by mass action kinetics. Employing metabolite profiles from domesticated and wild wheat and tomato species, I showed that the process of domestication is associated with a loss of regulatory control on the level of reaction rate coupling. I also found that the same metabolic pathways in Arabidopsis thaliana and Escherichia coli exhibit differences in the number of reaction rate couplings. I designed a novel method for the identification and categorization of transcriptional effects on metabolism by combining data on gene expression and metabolite levels. The approach determines the partial correlation of metabolites with control by the principal components of the transcript levels. The principle components contain the majority of the transcriptomic information allowing to partial out the effect of the transcriptional layer from the metabolite profiles. Depending whether the correlation between metabolites persists upon controlling for the effect of the transcriptional layer, the approach allows us to group metabolite pairs into being associated due to post-transcriptional or transcriptional regulation, respectively. I showed that the classification of metabolite pairs into those that are associated due to transcriptional or post-transcriptional regulation are in agreement with existing literature and findings from a Bayesian inference approach. The approaches developed, implemented, and investigated in this thesis open novel ways to jointly study metabolomics and transcriptomics data as well as to place metabolic profiles in the network context. The results from these approaches have the potential to provide further insights into the regulatory machinery in a biological system.}, language = {en} } @misc{DittmannHeinkenSchmidt2018, author = {Dittmann, Thea and Heinken, Thilo and Schmidt, Marcus}, title = {Die W{\"a}lder von Magdeburgerforth (Fl{\"a}ming, Sachsen-Anhalt)}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1053}, issn = {1866-8372}, doi = {10.25932/publishup-46005}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-460058}, pages = {11 -- 42}, year = {2018}, abstract = {In einem rund 2.200 ha großen Waldgebiet bei Magdeburgerforth (Fl{\"a}ming, Sachsen-Anhalt) wur-den 1948 bis 1950 von Harro Passarge 120 Vegetationsaufnahmen sowie eine Vegetationskartierung erstellt. Das Gebiet zeichnet sich durch eine große Vielfalt an Waldtypen aus den Verb{\"a}nden Agrostio-Quercion petraeae, Alnion glutinosae, Alnion incanae, Carpinion betuli, Dicrano-Pinion und Quercion roboris aus. Daher und weil viele der heute in W{\"a}ldern wirksamen Prozesse (z. B. Stickstoffeintrag, Klimawandel) vor 60 Jahren noch nicht sp{\"u}rbar waren, bietet sich das Gebiet f{\"u}r eine Wiederholungs-untersuchung besonders an. Da die Aufnahmefl{\"a}chen von Passarge nicht punktgenau verortet waren, wurden im Jahr 2014 in einem {\"u}ber die Forstabteilungen und die Vegetationskarte definierten Such-raum immer die der Erstaufnahme {\"a}hnlichsten Waldbest{\"a}nde erfasst. Insgesamt konnten 97 (81 \%) der Aufnahmen wiederholt werden. Vegetationsver{\"a}nderungen werden mithilfe einer NMDS-Ordination, der Gegen{\"u}berstellung von α-Diversit{\"a}t, Zeigerwerten und Waldbindungskategorien f{\"u}r die beiden Aufnahmezeitpunkte sowie {\"u}ber die Identifikation von Gewinner- und Verlierer-Arten analysiert.Auch wenn methodenbedingt bei der Wiederholungsuntersuchung nur die jeweils geringstm{\"o}gliche Vegetationsver{\"a}nderung abgebildet wird, konnten Ergebnisse erzielt werden, die mit denen quasi-permanenter Plots {\"u}bereinstimmen. Die beobachteten allgemeinen Trends (Eutrophierung, Sukzession nach Nutzungswandel, Verlust lichtliebender und magerkeitszeigender Arten, Ausbreitung von stick-stoffliebenden Arten und mesophilen Waldarten, Einwanderung von Neophyten, keine generelle Ab-nahme der Artenzahl) stimmen gut mit den in zahlreichen Studien aus mitteleurop{\"a}ischen W{\"a}ldern festgestellten {\"u}berein. Durch das von nassen bis trockenen sowie von bodensauer-n{\"a}hrstoffarmen bis zu relativ basenreichen B{\"o}den reichende Standortsspektrum innerhalb des Untersuchungsgebietes konnte aber - deutlicher als in den meisten bisherigen Fallstudien - gezeigt werden, dass sich die Resilienz der W{\"a}lder gegen{\"u}ber Vegetationsver{\"a}nderung je nach Ausgangsgesellschaft stark unterscheidet und jeweils unterschiedliche Treiber wirksam sind. Stellario-Carpinetum und Luzulo-Quercetum erwiesen sich als relativ stabil, und auch in den Feuchtw{\"a}ldern des Circaeo-Alnetum gab es trotz eines Arten-wechsels wenig Hinweise auf Umweltver{\"a}nderungen. Dagegen wiesen die W{\"a}lder n{\"a}hrstoffarmer Standorte (Sphagno-Alnetum, Betulo-Quercetum, Dicrano-Pinion) viele Verliererarten und eine starke Eutrophierungstendenz auf. Die in besonderem Maße von historischen Waldnutzungsformen abh{\"a}ngi-gen thermophilen W{\"a}lder und die Flechten-Kiefernw{\"a}lder gingen weitgehend verloren.}, language = {de} } @misc{WeyrichJeschekSchrapersetal.2018, author = {Weyrich, Alexandra and Jeschek, Marie and Schrapers, Katharina T. and Lenz, Dorina and Chung, Tzu Hung and Ruebensam, Kathrin and Yasar, Sermin and Schneemann, Markus and Ortmann, Sylvia and Jewgenow, Katarina and Fickel, J{\"o}rns}, title = {Diet changes alter paternally inherited epigenetic pattern in male Wild guinea pigs}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1065}, issn = {1866-8372}, doi = {10.25932/publishup-46003}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-460031}, pages = {14}, year = {2018}, abstract = {Epigenetic modifications, of which DNA methylation is the most stable, are a mechanism conveying environmental information to subsequent generations via parental germ lines. The paternal contribution to adaptive processes in the offspring might be crucial, but has been widely neglected in comparison to the maternal one. To address the paternal impact on the offspring's adaptability to changes in diet composition, we investigated if low protein diet (LPD) in F0 males caused epigenetic alterations in their subsequently sired sons. We therefore fed F0 male Wild guinea pigs with a diet lowered in protein content (LPD) and investigated DNA methylation in sons sired before and after their father's LPD treatment in both, liver and testis tissues. Our results point to a 'heritable epigenetic response' of the sons to the fathers' dietary change. Because we detected methylation changes also in the testis tissue, they are likely to be transmitted to the F2 generation. Gene-network analyses of differentially methylated genes in liver identified main metabolic pathways indicating a metabolic reprogramming ('metabolic shift'). Epigenetic mechanisms, allowing an immediate and inherited adaptation may thus be important for the survival of species in the context of a persistently changing environment, such as climate change.}, language = {en} } @misc{OlmerEngelsUsmanetal.2018, author = {Olmer, Ruth and Engels, Lena and Usman, Abdulai and Menke, Sandra and Malik, Muhammad Nasir Hayat and Pessler, Frank and G{\"o}hring, Gudrun and Bornhorst, Dorothee and Bolten, Svenja and Abdelilah-Seyfried, Salim and Scheper, Thomas and Kempf, Henning and Zweigerdt, Robert and Martin, Ulrich}, title = {Differentiation of Human Pluripotent Stem Cells into Functional Endothelial Cells in Scalable Suspension Culture}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {5}, issn = {1866-8372}, doi = {10.25932/publishup-42709}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427095}, pages = {18}, year = {2018}, abstract = {Endothelial cells (ECs) are involved in a variety of cellular responses. As multifunctional components of vascular structures, endothelial (progenitor) cells have been utilized in cellular therapies and are required as an important cellular component of engineered tissue constructs and in vitro disease models. Although primary ECs from different sources are readily isolated and expanded, cell quantity and quality in terms of functionality and karyotype stability is limited. ECs derived from human induced pluripotent stem cells (hiPSCs) represent an alternative and potentially superior cell source, but traditional culture approaches and 2D differentiation protocols hardly allow for production of large cell numbers. Aiming at the production of ECs, we have developed a robust approach for efficient endothelial differentiation of hiPSCs in scalable suspension culture. The established protocol results in relevant numbers of ECs for regenerative approaches and industrial applications that show in vitro proliferation capacity and a high degree of chromosomal stability.}, language = {en} }