@article{BreuerNowakIvakovetal.2017,
  author    = {Breuer, David and Nowak, Jacqueline and Ivakov, Alexander and Somssich, Marc and Persson, Staffan and Nikoloski, Zoran},
  title     = {System-wide organization of actin cytoskeleton determines organelle transport in hypocotyl plant cells},
  series = {Proceedings of the National Academy of Sciences of the United States of America},
  volume    = {114},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1706711114},
  pages     = {E5741 -- E5749},
  year      = {2017},
  abstract  = {The actin cytoskeleton is an essential intracellular filamentous structure that underpins cellular transport and cytoplasmic streaming in plant cells. However, the system-level properties of actin-based cellular trafficking remain tenuous, largely due to the inability to quantify key features of the actin cytoskeleton. Here, we developed an automated image-based, network-driven framework to accurately segment and quantify actin cytoskeletal structures and Golgi transport. We show that the actin cytoskeleton in both growing and elongated hypocotyl cells has structural properties facilitating efficient transport. Our findings suggest that the erratic movement of Golgi is a stable cellular phenomenon that might optimize distribution efficiency of cell material. Moreover, we demonstrate that Golgi transport in hypocotyl cells can be accurately predicted from the actin network topology alone. Thus, our framework provides quantitative evidence for system-wide coordination of cellular transport in plant cells and can be readily applied to investigate cytoskeletal organization and transport in other organisms.},
  language  = {en}
}
@misc{BreuerNowakIvakovetal.2017,
  author    = {Breuer, David and Nowak, Jacqueline and Ivakov, Alexander and Somssich, Marc and Persson, Staffan and Nikoloski, Zoran},
  title     = {System-wide organization of actin cytoskeleton determines organelle transport in hypocotyl plant cells},
  series = {Proceedings of the National Academy of Sciences of the United States of America},
  volume    = {114},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1712371114},
  pages     = {E6732 -- E6732},
  year      = {2017},
  language  = {en}
}
@article{WangTohgeIvakovetal.2015,
  author    = {Wang, Ting and Tohge, Takayuki and Ivakov, Alexander and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair R. and Mutwil, Marek and Schippers, Jos H. M. and Persson, Staffan},
  title     = {Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {169},
  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.15.00962},
  pages     = {1027 -- +},
  year      = {2015},
  abstract  = {Abiotic stresses, such as salinity, cause global yield loss of all major crop plants. Factors and mechanisms that can aid in plant breeding for salt stress tolerance are therefore of great importance for food and feed production. Here, we identified a MYB-like transcription factor, Salt-Related MYB1 (SRM1), that negatively affects Arabidopsis (Arabidopsis thaliana) seed germination under saline conditions by regulating the levels of the stress hormone abscisic acid (ABA). Accordingly, several ABA biosynthesis and signaling genes act directly downstream of SRM1, including SALT TOLERANT1/NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3, RESPONSIVE TO DESICCATION26, and Arabidopsis NAC DOMAIN CONTAINING PROTEIN19. Furthermore, SRM1 impacts vegetative growth and leaf shape. We show that SRM1 is an important transcriptional regulator that directly targets ABA biosynthesis and signaling-related genes and therefore may be regarded as an important regulator of ABA-mediated salt stress tolerance.},
  language  = {en}
}
@article{FujikuraElsaesserBreuningeretal.2014,
  author    = {Fujikura, Ushio and Elsaesser, Lore and Breuninger, Holger and Sanchez-Rodriguez, Clara and Ivakov, Alexander and Laux, Thomas and Findlay, Kim and Persson, Staffan and Lenhard, Michael},
  title     = {Atkinesin-13A modulates cell-wall synthesis and cell expansion in arabidopsis thaliana via the THESEUS1 pathway},
  series = {PLoS Genetics : a peer-reviewed, open-access journal},
  volume    = {10},
  journal   = {PLoS Genetics : a peer-reviewed, open-access journal},
  number    = {9},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1553-7390},
  doi       = {10.1371/journal.pgen.1004627},
  pages     = {15},
  year      = {2014},
  abstract  = {Growth of plant organs relies on cell proliferation and expansion. While an increasingly detailed picture about the control of cell proliferation is emerging, our knowledge about the control of cell expansion remains more limited. We demonstrate the internal-motor kinesin AtKINESIN-13A (AtKIN13A) limits cell expansion and cell size in Arabidopsis thaliana, ion atkinl3a mutants forming larger petals with larger cells. The homolog, AtKINESIN-13B, also affects cell expansion and double mutants display growth, gametophytic and early embryonic defects, indicating a redundant role of he two genes. AtKIN13A is known to depolymerize microtubules and influence Golgi motility and distribution. Consistent his function, AtKIN13A interacts genetically with ANGUSTIFOLIA, encoding a regulator of Golgi dynamics. Reduced AtIGN13A activity alters cell wall structure as assessed by Fourier-transformed infrared-spectroscopy and triggers signalling he THESEUS1-dependent cell-wall integrity pathway, which in turn promotes the excess cell expansion in the atkinl3a mutant. Thus, our results indicate that the intracellular activity of AtKIN13A regulates cell expansion and wall architecture via THESEUS1, providing a compelling case of interplay between cell wall integrity sensing and expansion.},
  language  = {en}
}
@article{MartinsHejaziFettkeetal.2013,
  author    = {Martins, Marina Camara Mattos and Hejazi, Mahdi and Fettke, J{\"o}rg and Steup, Martin and Feil, Regina and Krause, Ursula and Arrivault, Stephanie and Vosloh, Daniel and Figueroa, Carlos Maria and Ivakov, Alexander and Yadav, Umesh Prasad and Piques, Maria and Metzner, Daniela and Stitt, Mark and Lunn, John Edward},
  title     = {Feedback inhibition of starch degradation in arabidopsis leaves mediated by trehalose 6-phosphate},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {163},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  number    = {3},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.113.226787},
  pages     = {1142 -- 1163},
  year      = {2013},
  abstract  = {Many plants accumulate substantial starch reserves in their leaves during the day and remobilize them at night to provide carbon and energy for maintenance and growth. In this paper, we explore the role of a sugar-signaling metabolite, trehalose-6-phosphate (Tre6P), in regulating the accumulation and turnover of transitory starch in Arabidopsis (Arabidopsis thaliana) leaves. Ethanol-induced overexpression of trehalose-phosphate synthase during the day increased Tre6P levels up to 11-fold. There was a transient increase in the rate of starch accumulation in the middle of the day, but this was not linked to reductive activation of ADP-glucose pyrophosphorylase. A 2- to 3-fold increase in Tre6P during the night led to significant inhibition of starch degradation. Maltose and maltotriose did not accumulate, suggesting that Tre6P affects an early step in the pathway of starch degradation in the chloroplasts. Starch granules isolated from induced plants had a higher orthophosphate content than granules from noninduced control plants, consistent either with disruption of the phosphorylation-dephosphorylation cycle that is essential for efficient starch breakdown or with inhibition of starch hydrolysis by beta-amylase. Nonaqueous fractionation of leaves showed that Tre6P is predominantly located in the cytosol, with estimated in vivo Tre6P concentrations of 4 to 7 mu M in the cytosol, 0.2 to 0.5 mu M in the chloroplasts, and 0.05 mu M in the vacuole. It is proposed that Tre6P is a component in a signaling pathway that mediates the feedback regulation of starch breakdown by sucrose, potentially linking starch turnover to demand for sucrose by growing sink organs at night.},
  language  = {en}
}
@phdthesis{Ivakov2011,
  author    = {Ivakov, Alexander},
  title     = {Metabolic interactions in leaf development in Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-59730},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Das Wachstum und {\"U}berleben von Pflanzen basiert auf der Photosynthese in den Bl{\"a}ttern. Diese beinhaltet die Aufnahme von Kohlenstoffdioxid aus der Atmosph{\"a}re und das simultane Einfangen von Lichtenergie zur Bildung organischer Molek{\"u}le. Diese werden nach dem Eintritt in den Metabolismus in viele andere Komponenten umgewandelt, welche die Grundlage f{\"u}r die Zunahme der Biomasse bilden. Bl{\"a}tter sind Organe, die auf die Fixierung von Kohlenstoffdioxid spezialisiert sind. Die Funktionen der Bl{\"a}tter beinhalten vor allem die Optimierung und Feinregulierung vieler Prozesse, um eine effektive Nutzung von Ressourcen und eine maximale Photosynthese zu gew{\"a}hrleisten. Es ist bekannt, dass sich die Morphologie der Bl{\"a}tter den Wachstumsbedingungen der Pflanze anpasst und eine wichtige Rolle bei der Optimierung der Photosynthese spielt. Trotzdem ist die Regulation dieser Art der Anpassung bisher nicht verstanden. Die allgemeine Zielsetzung dieser vorliegenden Arbeit ist das Verst{\"a}ndnis wie das Wachstum und die Morphologie der Bl{\"a}tter im Modellorganismus Arabidopsis thaliana reguliert werden. Besondere Aufmerksamkeit wurde hierbei der M{\"o}glichkeit geschenkt, dass es interne metabolische Signale in der Pflanze geben k{\"o}nnte, die das Wachstum und die Entwicklung von Bl{\"a}ttern beeinflussen. Um diese Fragestellung zu untersuchen, muss das Wachstum und die Entwicklung von Bl{\"a}ttern oberhalb des Levels des einzelnen Organs und im Kontext der gesamten Pflanze betrachtet werden, weil Bl{\"a}tter nicht eigenst{\"a}ndig wachsen, sondern von Ressourcen und regulatorischen Einfl{\"u}ssen der ganzen Pflanze abh{\"a}ngig sind. Aufgrund der Komplexit{\"a}t dieser Fragestellung wurden drei komplement{\"a}re Ans{\"a}tze durchgef{\"u}hrt. Im ersten und spezifischsten Ansatz wurde untersucht ob eine flussabw{\"a}rts liegende Komponente des Zucker-Signalwegs, Trehalose-6-Phosphat (Tre-6-P), das Blattwachstum und die Blattentwicklung beinflussen kann. Um diese Frage zu beantworten wurden transgene Arabidopsis-Linien mit einem gest{\"o}rten Gehalt von Tre-6-P durch die Expression von bakteriellen Proteinen die in dem metabolismus von trehalose beteiligt sind. Die Pflanzen-Linien wurden unter Standard-Bendingungen in Erde angebaut und ihr Metabolismus und ihre Blattmorphologie untersucht. Diese Experimente f{\"u}hrten auch zu einem unerwarteten Projekt hinsichtlich einer m{\"o}glichen Rolle von Tre-6-P in der Regulation der Stomata. In einem zweiten, allgemeineren Ansatz wurde untersucht, ob {\"A}nderungen im Zucker-Gehalt der Pflanzen die Morphogenese der Bl{\"a}tter als Antwort auf Licht beeinflussen. Dazu wurden eine Reihe von Mutanten, die im Zentralmetabolismus beeintr{\"a}chtigt sind, in derselben Lichtbedingung angezogen und bez{\"u}glich ihrer Blattmorphologie analysiert. In einem dritten noch allgemeineren Ansatz wurde die nat{\"u}rliche Variation von morphologischen Auspr{\"a}gungen der Bl{\"a}tter und Rosette anhand von wilden Arabidopsis {\"O}kotypen untersucht, um zu verstehen wie sich die Blattmorphologie auf die Blattfunktion und das gesamte Pflanzenwachstum auswirkt und wie unterschiedliche Eigenschaften miteinander verkn{\"u}pft sind. Das Verh{\"a}ltnis der Blattanzahl zum Gesamtwachstum der Pflanze und Blattgr{\"o}ße wurde gesondert weiter untersucht durch eine Normalisierung der Blattanzahl auf das Frischgewicht der Rosette, um den Parameter „leafing Intensity" abzusch{\"a}tzen. Leafing Intensity integrierte Blattanzahl, Blattgr{\"o}ße und gesamtes Rosettenwachstum in einer Reihe von Kompromiss-Interaktionen, die in einem Wachstumsvorteil resultieren, wenn Pflanzen weniger, aber gr{\"o}ßere Bl{\"a}tter pro Einheit Biomasse ausbilden. Dies f{\"u}hrte zu einem theoretischen Ansatz in dem ein einfaches allometrisch mathematisches Modell konstruiert wurde, um Blattanzahl, Blattgr{\"o}ße und Pflanzenwachstum im Kontext der gesamten Pflanze Arabidopsis zu verkn{\"u}pfen.},
  language  = {en}
}