@phdthesis{Arnold2014, author = {Arnold, Anne}, title = {Modeling photosynthesis and related metabolic processes : from detailed examination to consideration of the metabolic context}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72277}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Mathematical modeling of biological systems is a powerful tool to systematically investigate the functions of biological processes and their relationship with the environment. To obtain accurate and biologically interpretable predictions, a modeling framework has to be devised whose assumptions best approximate the examined scenario and which copes with the trade-off of complexity of the underlying mathematical description: with attention to detail or high coverage. Correspondingly, the system can be examined in detail on a smaller scale or in a simplified manner on a larger scale. In this thesis, the role of photosynthesis and its related biochemical processes in the context of plant metabolism was dissected by employing modeling approaches ranging from kinetic to stoichiometric models. The Calvin-Benson cycle, as primary pathway of carbon fixation in C3 plants, is the initial step for producing starch and sucrose, necessary for plant growth. Based on an integrative analysis for model ranking applied on the largest compendium of (kinetic) models for the Calvin-Benson cycle, those suitable for development of metabolic engineering strategies were identified. Driven by the question why starch rather than sucrose is the predominant transitory carbon storage in higher plants, the metabolic costs for their synthesis were examined. The incorporation of the maintenance costs for the involved enzymes provided a model-based support for the preference of starch as transitory carbon storage, by only exploiting the stoichiometry of synthesis pathways. Many photosynthetic organisms have to cope with processes which compete with carbon fixation, such as photorespiration whose impact on plant metabolism is still controversial. A systematic model-oriented review provided a detailed assessment for the role of this pathway in inhibiting the rate of carbon fixation, bridging carbon and nitrogen metabolism, shaping the C1 metabolism, and influencing redox signal transduction. The demand of understanding photosynthesis in its metabolic context calls for the examination of the related processes of the primary carbon metabolism. To this end, the Arabidopsis core model was assembled via a bottom-up approach. This large-scale model can be used to simulate photoautotrophic biomass production, as an indicator for plant growth, under so-called optimal, carbon-limiting and nitrogen-limiting growth conditions. Finally, the introduced model was employed to investigate the effects of the environment, in particular, nitrogen, carbon and energy sources, on the metabolic behavior. This resulted in a purely stoichiometry-based explanation for the experimental evidence for preferred simultaneous acquisition of nitrogen in both forms, as nitrate and ammonium, for optimal growth in various plant species. The findings presented in this thesis provide new insights into plant system's behavior, further support existing opinions for which mounting experimental evidences arise, and posit novel hypotheses for further directed large-scale experiments.}, language = {en} } @misc{ArnoldBoehlichDallapiazzaetal.2008, author = {Arnold, Rafael and Boehlich, Sabine and Dallapiazza, Michael and Denz, Rebekka and Feinberg, Anat and Gr{\"o}zinger, Elvira and Gr{\"o}zinger, Karl E. and Heni, Clemens and J{\"u}tte, Daniel and J{\"u}tte, Robert and Jurewicz, Grażyna and Kamoshida, Satoko and Kerbel, Arturo and K{\"u}hn-Ludewig, Maria and Nath, Holger and Riemer, Nathanael and R{\"o}sch, Juliane and Rubin, Joel and Saß, Anne-Christin and Ueda, Kazuo}, title = {PaRDeS : Zeitschrift der Vereinigung f{\"u}r J{\"u}dische Studien e.V. = Jiddische Quellen}, number = {14}, editor = {Denz, Rebekka and Dubrau, Alexander and Riemer, Nathanael}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-940793-41-6}, issn = {1862-7684}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-19179}, year = {2008}, abstract = {Wissenschaftliche Artikel: Sabine Boehlich "Nisters Nay-gayst. Der Schriftsteller als Zaddik" Juliane R{\"o}sch „Di berliner hobn nisht gegloybt zeyere oygn". Das jiddischsprachige Theater GOSET und der Regisseur Alexander Granovsky Anne-Christin Saß „Wenn die Nazi-Verbrecher nach Hause kommen" - Dovid Eynhorns Berichte {\"u}ber die nationalsozialistischen Verbrechen im New Yorker Forverts 1940-1945 Rebekka Denz Der „Froyenvinkl" : Die Frauenrubrik in der bundischen Tageszeitung „Naye Folkstsaytung" Nathanael Riemer Some parallels of stories in Glikls of Hameln Zikhroynes Jiddisch aus aller Welt: Holger Nath The First Yiddish Summer Program in Birobidzhan (August 13-August 30, 2007) Satoko Kamoshida A woman and a language: In the case of a Yiddish speaker in Israel Arturo Kerbel "Dear brother! Where from are you coming?" A brief history of the Yiddish language and culture in Mexiko Kazuo Ueda Jiddischforschung in Japan Essay: Elvira Gr{\"o}zinger Die Deutsche Bahn und die Krux mit dem Gedenken Tagungsberichte: "Zwischenr{\"a}ume". J{\"u}disch-christliche Lebenswelten unter venezianischer Herrschaft im sp{\"a}ten Mittelalter und der fr{\"u}hen Neuzeit. Venedig, Deutsches Studienzentrum und Dipartimento di Studi Storici der Universit{\"a}t Ca' Foscari, 5.9.-7.9. 2007. (Daniel J{\"u}tte) "Global Forum for Combating Antisemitism", Israelisches Außenministerium, Jerusalem, 24.-25.2. 2008. (Clemens Heni) Rezensionen: Arno Herzig/Cay Rademacher (Hg.): Die Geschichte der Juden in Deutschland (Robert J{\"u}tte) Georg Bossong: Die Sepharden. Geschichte und Kultur der spanischen Juden (Rafael Arnold) Barbara Staudinger: Die j{\"u}dische Welt und die Wittelsbacher (Daniel J{\"u}tte) Leon Modena: J{\"u}dische Riten, Sitten und Gebr{\"a}uche. Hg., {\"u}bersetzt und kommentiert von Rafael Arnold (Karl E. Gr{\"o}zinger) Kenneth Stow: An Image and Its Interpreters. Continuity in the Catholic-Jewish Encounter (Elvira Gr{\"o}zinger) Aldina Quintana Rodr{\´i}guez: Geograf{\´i}a Ling{\"u}{\´i}stica del Judeoespa{\~n}ol. Estudio sincr{\´o}nico y diacr{\´o}nico (Rafael Arnold) Wolfgang Vogt: Moses Mendelssohns Beschreibung der Wirklichkeit menschlichen Erkennens (Grazyna Jurewicz) Stefan M{\"u}ller-Doohm (Hg.): Adorno-Portraits. Erinnerungen von Zeitgenossen (Michael Dallapiazza) Andrea L{\"o}w: Juden im Getto Litzmannstadt. Lebensbedingungen, Selbstwahrnehmung, Verhalten. Die Chronik des Gettos Lodz/Litzmannstadt. Hg. v. Sascha Feuchert, Erwin Leibfried, J{\"o}rg Riecke (Maria K{\"u}hn-Ludewig) Egl{\`e} Bendikait{\`e}: Sionistinis sajudis Lietuvoje. Litauisches Historisches Institut (Elvira Gr{\"o}zinger) Barbara Staudinger (Hg.): Von Bayern nach Erez Israel. Auf den Spuren j{\"u}discher Volkskunst. From Bavaria to Eretz Israel. Tracing Jewish Folk Art (Anat Feinberg) Hugh Denman (Hg.): Isaac Bashevis Singer: His Work and His World (Elvira Gr{\"o}zinger) Annkatrin Dahm: Der Topos der Juden. Studien zur Geschichte des Antisemitismus im deutschsprachigen Musikschrifttum (Daniel J{\"u}tte) Max Peter Baumann/Tim Becker/Raphael Woebs (Hg.): Musik und Kultur im j{\"u}dischen Leben der Gegenwart (Joel E. Rubin)}, language = {de} } @book{AmbauenArnoldBeckeretal.2021, author = {Ambauen, Ladina and Arnold, Maren and Becker, Christian and Chahrour, Mohamed Chaker and Destanovic, Edis and Fretter, Alexandra and Geißler, Marc and Gr{\"u}nberg, Uwe and Habl, Moritz and Hoffmann, Sandra and Juchler, Ingo and Jurkatis, Lena Christine and Keitel, Bernhard and Losensky, Nikolai and Mrowietz, Christian and Nadol, Dominic and Naumann, Asja and Ockenga, Imke and Pohlandt, Anne and P{\"u}rschel, Tobias and Recktenwald, Michelle and Stephan, Roswitha and Tuchel, Johannes and Weinkamp, Christina and Weiß, Christian and Wiecking, Ole and Wockenfuß, Patricia and Zalitatsch, Nora Lina}, title = {Mildred Harnack und die Rote Kapelle in Berlin}, editor = {Juchler, Ingo}, edition = {2., verbesserte Auflage}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-500-2}, doi = {10.25932/publishup-48176}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-481762}, publisher = {Universit{\"a}t Potsdam}, pages = {170}, year = {2021}, abstract = {Mildred Harnack, geb. Fish, stammte urspr{\"u}nglich aus Milwaukee, Wisconsin. Zusammen mit ihrem Ehemann Arvid Harnack zog sie nach Deutschland und lebte seit 1930 in Berlin. Hier lehrte die Literaturwissenschaftlerin an der Friedrich-Wilhelms-Universit{\"a}t (heute Humboldt-Universit{\"a}t) und am Berliner Abendgymnasium (heute Peter A. Silbermann-Schule). Bereits kurz nach der Macht{\"u}bernahme von Adolf Hitler hatte sich um das Ehepaar Harnack ein Kreis von Freunden gebildet, der gegen die Herrschaft der Nationalsozialisten opponierte. Dazu z{\"a}hlten auch Karl Behrens und Bodo Schl{\"o}singer, die beide Sch{\"u}ler Mildred Harnacks am Berliner Abendgymnasium waren. Mildred Harnack konnte mit Hilfe ihrer Kontakte zur amerikanischen Botschaft ihren Sch{\"u}lern im nationalsozialistischen Deutschland ansonsten nicht zug{\"a}ngliche Informationen besorgen. Aufgrund von Funkkontakten des Freundeskreises zur Sowjetunion wurde die Gruppe von den Nationalsozialisten Rote Kapelle genannt - „rot" bezog sich auf deren linke Haltung und mit „Kapelle" wurden Funker assoziiert, die wie Pianisten in einer Kapelle spielen. Der Berliner Oppositionszirkel umfasste bis zu seiner Zerschlagung durch die Nationalsozialisten etwa 150 Personen verschiedenster Berufsgruppen, unterschiedlicher parteipolitischer Einstellungen und Konfessionen. Die Gruppe verfertigte oppositionelle Flugbl{\"a}tter und lieferte Informationen an die amerikanische Botschaft sowie an die Sowjetunion. Mildred Harnack wurde - wie viele ihrer Mitstreiterinnen und Mitstreiter - nach ihrer Verhaftung vom Reichskriegsgericht zum Tode verurteilt und am 16. Februar 1943 in Pl{\"o}tzensee guillotiniert. In diesem Band stellen Studierende der Universit{\"a}t Potsdam sowie H{\"o}rerinnen und H{\"o}rer der Peter A. Silbermann-Schule (Berlin) nach einem kurzen {\"U}berblick zum Widerstand gegen den Nationalsozialismus in Deutschland das Netzwerk der Roten Kapelle sowie die Biographien von Mildred Harnack und ihren Sch{\"u}lern Karl Behrens und Bodo Schl{\"o}singer vom Berliner Abendgymnasium eindr{\"u}cklich vor.}, language = {de} } @book{AmbauenArnoldBeckeretal.2017, author = {Ambauen, Ladina and Arnold, Maren and Becker, Christian and Chahrour, Mohamed Chaker and Destanovic, Edis and Fretter, Alexandra and Geißler, Marc and Gr{\"u}nberg, Uwe and Habl, Moritz and Hoffmann, Sandra and Juchler, Ingo and Jurkatis, Lena Christine and Keitel, Bernhard and Losensky, Nikolai and Mrowietz, Christian and Nadol, Dominic and Naumann, Asja and Ockenga, Imke and Pohlandt, Anne and P{\"u}rschel, Tobias and Recktenwald, Michelle and Stephan, Roswitha and Tuchel, Johannes and Weinkamp, Christina and Weiß, Christian and Wiecking, Ole and Wockenfuß, Patricia and Zalitatsch, Nora Lina}, title = {Mildred Harnack und die Rote Kapelle in Berlin}, editor = {Juchler, Ingo}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-407-4}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-398166}, publisher = {Universit{\"a}t Potsdam}, pages = {170}, year = {2017}, abstract = {Mildred Harnack, geb. Fish, stammte urspr{\"u}nglich aus Milwaukee, Wisconsin. Zusammen mit ihrem Ehemann Arvid Harnack zog sie nach Deutschland und lebte seit 1930 in Berlin. Hier lehrte die Literaturwissenschaftlerin an der Friedrich-Wilhelms-Universit{\"a}t (heute Humboldt-Universit{\"a}t) und am Berliner Abendgymnasium (heute Peter A. Silbermann-Schule). Bereits kurz nach der Macht{\"u}bernahme von Adolf Hitler hatte sich um das Ehepaar Harnack ein Kreis von Freunden gebildet, der gegen die Herrschaft der Nationalsozialisten opponierte. Dazu z{\"a}hlten auch Karl Behrens und Bodo Schl{\"o}singer, die beide Sch{\"u}ler Mildred Harnacks am Berliner Abendgymnasium waren. Mildred Harnack konnte mit Hilfe ihrer Kontakte zur amerikanischen Botschaft ihren Sch{\"u}lern im nationalsozialistischen Deutschland ansonsten nicht zug{\"a}ngliche Informationen besorgen. Aufgrund von Funkkontakten des Freundeskreises zur Sowjetunion wurde die Gruppe von den Nationalsozialisten Rote Kapelle genannt - „rot" bezog sich auf deren linke Haltung und mit „Kapelle" wurden Funker assoziiert, die wie Pianisten in einer Kapelle spielen. Der Berliner Oppositionszirkel umfasste bis zu seiner Zerschlagung durch die Nationalsozialisten etwa 150 Personen verschiedenster Berufsgruppen, unterschiedlicher parteipolitischer Einstellungen und Konfessionen. Die Gruppe verfertigte oppositionelle Flugbl{\"a}tter und lieferte Informationen an die amerikanische Botschaft sowie an die Sowjetunion. Mildred Harnack wurde - wie viele ihrer Mitstreiterinnen und Mitstreiter - nach ihrer Verhaftung vom Reichskriegsgericht zum Tode verurteilt und am 16. Februar 1943 in Pl{\"o}tzensee guillotiniert. In diesem Band stellen Studierende der Universit{\"a}t Potsdam sowie H{\"o}rerinnen und H{\"o}rer der Peter A. Silbermann-Schule (Berlin) nach einem kurzen {\"U}berblick zum Widerstand gegen den Nationalsozialismus in Deutschland das Netzwerk der Roten Kapelle sowie die Biographien von Mildred Harnack und ihren Sch{\"u}lern Karl Behrens und Bodo Schl{\"o}singer vom Berliner Abendgymnasium eindr{\"u}cklich vor.}, language = {de} } @article{ArnoldNikoloski2014, author = {Arnold, Anne and Nikoloski, Zoran}, title = {In search for an accurate model of the photosynthetic carbon metabolism}, series = {Mathematics and computers in simulation : transactions of IMACS}, volume = {96}, journal = {Mathematics and computers in simulation : transactions of IMACS}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-4754}, doi = {10.1016/j.matcom.2012.03.011}, pages = {171 -- 194}, year = {2014}, abstract = {The photosynthetic carbon metabolism, including the Calvin-Benson cycle, is the primary pathway in C-3-plants, producing starch and sucrose from CO2. Understanding the interplay between regulation and efficiency of this pathway requires the development of mathematical models which would explain the observed dynamics of metabolic transformations. Here, we address this question by casting the existing models of Calvin-Benson cycle and the end-product processes into an analysis framework which not only facilitates the comparison of the different models, but also allows for their ranking with respect to chosen criteria, including stability, sensitivity, robustness and/or compliance with experimental data. The importance of the photosynthetic carbon metabolism for the increase of plant biomass has resulted in many models with various levels of detail. We provide the largest compendium of 15 existing, well-investigated models together with a comprehensive classification as well as a ranking framework to determine the best-performing models for metabolic engineering and planning of in silica experiments. The classification can be additionally used, based on the model structure, as a tool to identify the models which match best the experimental design. The provided ranking is just one alternative to score models and, by changing the weighting factor, this framework also could be applied for selection of other criteria of interest.}, language = {en} } @article{MettlerMuehlhausHemmeetal.2014, author = {Mettler, Tabea and M{\"u}hlhaus, Timo and Hemme, Dorothea and Sch{\"o}ttler, Mark Aurel and Rupprecht, Jens and Idoine, Adam and Veyel, Daniel and Pal, Sunil Kumar and Yaneva-Roder, Liliya and Winck, Flavia Vischi and Sommer, Frederik and Vosloh, Daniel and Seiwert, Bettina and Erban, Alexander and Burgos, Asdrubal and Arvidsson, Samuel Janne and Schoenfelder, Stephanie and Arnold, Anne and Guenther, Manuela and Krause, Ursula and Lohse, Marc and Kopka, Joachim and Nikoloski, Zoran and M{\"u}ller-R{\"o}ber, Bernd and Willmitzer, Lothar and Bock, Ralph and Schroda, Michael and Stitt, Mark}, title = {Systems analysis of the response of photosynthesis, metabolism, and growth to an increase in irradiance in the photosynthetic model organism chlamydomonas reinhardtii}, series = {The plant cell}, volume = {26}, journal = {The plant cell}, number = {6}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.124537}, pages = {2310 -- 2350}, year = {2014}, abstract = {We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.}, language = {en} } @article{GrimbsArnoldKoseskaetal.2011, author = {Grimbs, Sergio and Arnold, Anne and Koseska, Aneta and Kurths, J{\"u}rgen and Selbig, Joachim and Nikoloski, Zoran}, title = {Spatiotemporal dynamics of the Calvin cycle multistationarity and symmetry breaking instabilities}, series = {Biosystems : journal of biological and information processing sciences}, volume = {103}, journal = {Biosystems : journal of biological and information processing sciences}, number = {2}, publisher = {Elsevier}, address = {Oxford}, issn = {0303-2647}, doi = {10.1016/j.biosystems.2010.10.015}, pages = {212 -- 223}, year = {2011}, abstract = {The possibility of controlling the Calvin cycle has paramount implications for increasing the production of biomass. Multistationarity, as a dynamical feature of systems, is the first obvious candidate whose control could find biotechnological applications. Here we set out to resolve the debate on the multistationarity of the Calvin cycle. Unlike the existing simulation-based studies, our approach is based on a sound mathematical framework, chemical reaction network theory and algebraic geometry, which results in provable results for the investigated model of the Calvin cycle in which we embed a hierarchy of realistic kinetic laws. Our theoretical findings demonstrate that there is a possibility for multistationarity resulting from two sources, homogeneous and inhomogeneous instabilities, which partially settle the debate on multistability of the Calvin cycle. In addition, our tractable analytical treatment of the bifurcation parameters can be employed in the design of validation experiments.}, language = {en} } @misc{ArnoldNikoloski2011, author = {Arnold, Anne and Nikoloski, Zoran}, title = {A quantitative comparison of Calvin-Benson cycle models}, series = {Trends in plant science}, volume = {16}, journal = {Trends in plant science}, number = {12}, publisher = {Elsevier}, address = {London}, issn = {1360-1385}, doi = {10.1016/j.tplants.2011.09.004}, pages = {676 -- 683}, year = {2011}, abstract = {The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering.}, language = {en} }