@misc{WackervonElert2001,
  author    = {Wacker, Alexander and von Elert, Eric},
  title     = {Polyunsaturated fatty acids : evidence for non-substitutable biochemical resources in Daphnia galeata},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-17587},
  year      = {2001},
  abstract  = {The factors that determine the efficiency of energy transfer in aquatic food webs have been investigated for many decades. The plant-animal interface is the most variable and least predictable of all levels in the food web. In order to study determinants of food quality in a large lake and to test the recently proposed central importance of the long-chained eicosapentaenoic acid (EPA) at the pelagic producer-grazer interface, we tested the importance of polyunsaturated fatty acids (PUFAs) at the pelagic producerconsumer interface by correlating sestonic food parameters with somatic growth rates of a clone of Daphnia galeata. Daphnia growth rates were obtained from standardized laboratory experiments spanning one season with Daphnia feeding on natural seston from Lake Constance, a large pre-alpine lake. Somatic growth rates were fitted to sestonic parameters by using a saturation function. A moderate amount of variation was explained when the model included the elemental parameters carbon (r2 = 0.6) and nitrogen (r2 = 0.71). A tighter fit was obtained when sestonic phosphorus was incorporated (r2 = 0.86). The nonlinear regression with EPA was relatively weak (r2 = 0.77), whereas the highest degree of variance was explained by three C18-PUFAs. The best (r2 = 0.95), and only significant, correlation of Daphnia's growth was found with the C18-PUFA α-linolenic acid (α-LA; C18:3n-3). This correlation was weakest in late August when C:P values increased to 300, suggesting that mineral and PUFA-limitation of Daphnia's growth changed seasonally. Sestonic phosphorus and some PUFAs showed not only tight correlations with growth, but also with sestonic α-LA content. We computed Monte Carlo simulations to test whether the observed effects of α-LA on growth could be accounted for by EPA, phosphorus, or one of the two C18-PUFAs, stearidonic acid (C18:4n-3) and linoleic acid (C18:2n-6). With >99 \% probability, the correlation of growth with α-LA could not be explained by any of these parameters. In order to test for EPA limitation of Daphnia's growth, in parallel with experiments on pure seston, growth was determined on seston supplemented with chemostat-grown, P-limited Stephanodiscus hantzschii, which is rich in EPA. Although supplementation increased the EPA content 80-800x, no significant changes in the nonlinear regression of the growth rates with α-LA were found, indicating that growth of Daphnia on pure seston was not EPA limited. This indicates that the two fatty acids, EPA and α-LA, were not mutually substitutable biochemical resources and points to different physiological functions of these two PUFAs. These results support the PUFA-limitation hypothesis for sestonic C:P < 300 but are contrary to the hypothesis of a general importance of EPA, since no evidence for EPA limitation was found. It is suggested that the resource ratios of EPA and α-LA rather than the absolute concentrations determine which of the two resources is limiting growth.},
  language  = {en}
}
@misc{WackervonElert2002,
  author    = {Wacker, Alexander and von Elert, Eric},
  title     = {Strong influences of larval diet history on subsequent post-settlement growth in the freshwater mollusc Dreissena polymorpha},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-17627},
  year      = {2002},
  abstract  = {Significant seasonal variation in size at settlement has been observed in newly settled larvae of Dreissena polymorpha in Lake Constance. Diet quality, which varies temporally and spatially in freshwater habitats, has been suggested as a significant factor influencing life history and development of freshwater invertebrates. Accordingly, experiments were conducted with field-collected larvae to test the hypothesis that diet quality can determine planktonic larval growth rates, size at settlement and subsequent post-metamorphic growth rates. Larvae were fed one of two diets or starved. One diet was composed of cyanobacterial cells which are deficient in polyunsaturated fatty acids (PUFAs), and the other was a mixed diet rich in PUFAs. Freshly metamorphosed animals from the starvation treatment had a carbon content per individual 70\% lower than that of larvae fed the mixed diet. This apparent exhaustion of larval internal reserves resulted in a 50\% reduction of the postmetamorphic growth rates. Growth was also reduced in animals previously fed the cyanobacterial diet. Hence, low food quantity or low food quality during the larval stage of D. polymorpha lead to irreversible effects for postmetamorphic animals, and is related to inferior competitive abilities.},
  language  = {en}
}
@article{BormkiKnoescheSchneider2003,
  author    = {Bormki, G. and Kn{\"o}sche, Ralf and Schneider, Ingo},
  title     = {Untersuchungen zur N-Mineralisation und -Remobilisierung im Sediment eines extrem flachen Auensees (Schollener See)},
  series = {Brandenburgische Umwelt-Berichte : BUB ; Schriftenreihe der Mathematisch-Naturwissenschaftlichen Fakult{\"a}t der Universit{\"a}t Potsdam},
  volume    = {13},
  journal   = {Brandenburgische Umwelt-Berichte : BUB ; Schriftenreihe der Mathematisch-Naturwissenschaftlichen Fakult{\"a}t der Universit{\"a}t Potsdam},
  issn      = {1434-2375},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-4081},
  pages     = {114 -- 120},
  year      = {2003},
  language  = {de}
}
@article{BurkartWichmannWattenbachetal.2003,
  author    = {Burkart, Michael and Wichmann, Matthias and Wattenbach, Martin and P{\"o}tsch, Joachim},
  title     = {Die Vegetation der unteren Havelaue},
  series = {Brandenburgische Umwelt-Berichte : BUB ; Schriftenreihe der Mathematisch-Naturwissenschaftlichen Fakult{\"a}t der Universit{\"a}t Potsdam},
  volume    = {13},
  journal   = {Brandenburgische Umwelt-Berichte : BUB ; Schriftenreihe der Mathematisch-Naturwissenschaftlichen Fakult{\"a}t der Universit{\"a}t Potsdam},
  issn      = {1434-2375},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-4035},
  pages     = {53 -- 71},
  year      = {2003},
  language  = {de}
}
@phdthesis{Unterstab2005,
  author    = {Unterstab, Gunhild},
  title     = {Charakterisierung der viralen Genprodukte p10 und P des Borna Disease Virus},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6905},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {Das Borna Disease Virus (BDV, Bornavirus) besitzt ein einzelstr{\"a}ngiges RNA-Genom negativer Polarit{\"a}t und ist innerhalb der Ordnung Mononegavirales der Prototyp einer eigenen Virusfamilie, die der Bornaviridae. Eine außergew{\"o}hnliche Eigenschaft des Virus ist seine nukle{\"a}re Transkription und Replikation, eine weitere besteht in seiner F{\"a}higkeit, als neurotropes Virus sowohl in vivo als auch in vitro persistente Infektionen zu etablieren. Die zugrunde liegenden Mechanismen sowohl der Replikation als auch der Persistenz sind derzeit noch unzureichend verstanden, auch deshalb, weil das Virus noch relativ „jung" ist: Erste komplette Sequenzen des RNA-Genoms wurden 1994 publiziert und erst vor einigen Monaten gelang die Generierung rekombinanter Viren auf der Basis klonierter cDNA. Im Mittelpunkt dieser Arbeit standen das p10 Protein und das Phosphoprotein (P), die von der gemeinsamen Transkriptionseinheit II in {\"u}berlappenden Leserahmen kodiert werden. Als im Kern der Wirtszelle replizierendes Virus ist das Bornavirus auf zellul{\"a}re Importmechanismen angewiesen, um den Kernimport aller an der Replikation beteiligten viralen Proteine zu gew{\"a}hrleisten. Das p10 Protein ist ein negativer Regulator der viralen RNA-abh{\"a}ngigen RNA-Polymerase (L). In vitro Importexperimente zeigten, dass p10 {\"u}ber den klassischen Importin alpha/beta abh{\"a}ngigen Kernimportweg in den Nukleus transportiert wird. Dies war unerwartet, da p10 kein vorhersagbares klassisches Kernlokalisierungssignal (NLS) besitzt und weist darauf hin, dass der zellul{\"a}re Importapparat offensichtlich flexibler ist als allgemein angenommen. Die ersten 20 N-terminalen AS vermitteln sowohl Kernimport als auch die Bindung an den Importrezeptor Importin alpha. Durch Di-Alanin-Austauschmutagenese wurden die f{\"u}r diesen Transportprozess essentiellen AS identifiziert und die Bedeutung hydrophober und polarer AS-Reste demonstriert. Die F{\"a}higkeit des Bornavirus, persistente Infektionen zu etablieren, wirft die Frage auf, wie das Virus die zellul{\"a}ren antiviralen Abwehrmechanismen, insbesondere das Typ I Interferon (IFN)-System, unterwandert. Das virale P Protein wurde in dieser Arbeit als potenter Antagonist der IFN-Induktion charakterisiert. Es verhindert die Phosphorylierung des zentralen Transkriptionsfaktors IRF3 durch die zellul{\"a}re Kinase TBK1 und somit dessen Aktivierung. Der Befund, dass P mit TBK1 Komplexe bildet und zudem auch als Substrat f{\"u}r die zellul{\"a}re Kinase fungiert, erlaubt es, erstmalig einen Mechanismus zu postulieren, in dem ein virales Protein (BDV-P) als putatives TBK1-Pseudosubstrat die IRF3-Aktivierung kompetitiv hemmt.},
  subject      = {Interferon <beta->},
  language  = {de}
}
@phdthesis{Schauer2006,
  author    = {Schauer, Nicolas},
  title     = {Quantitative trait loci (QTL) for metabolite accumulation and metabolic regulation : metabolite profiling of interspecific crosses of tomato},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7643},
  school      = {Universit{\"a}t Potsdam},
  year      = {2006},
  abstract  = {The advent of large-scale and high-throughput technologies has recently caused a shift in focus in contemporary biology from decades of reductionism towards a more systemic view. Alongside the availability of genome sequences the exploration of organisms utilizing such approach should give rise to a more comprehensive understanding of complex systems. Domestication and intensive breeding of crop plants has led to a parallel narrowing of their genetic basis. The potential to improve crops by conventional breeding using elite cultivars is therefore rather limited and molecular technologies, such as marker assisted selection (MAS) are currently being exploited to re-introduce allelic variance from wild species. Molecular breeding strategies have mostly focused on the introduction of yield or resistance related traits to date. However given that medical research has highlighted the importance of crop compositional quality in the human diet this research field is rapidly becoming more important. Chemical composition of biological tissues can be efficiently assessed by metabolite profiling techniques, which allow the multivariate detection of metabolites of a given biological sample. Here, a GC/MS metabolite profiling approach has been applied to investigate natural variation of tomatoes with respect to the chemical composition of their fruits. The establishment of a mass spectral and retention index (MSRI) library was a prerequisite for this work in order to establish a framework for the identification of metabolites from a complex mixture. As mass spectral and retention index information is highly important for the metabolomics community this library was made publicly available. Metabolite profiling of tomato wild species revealed large differences in the chemical composition, especially of amino and organic acids, as well as on the sugar composition and secondary metabolites. Intriguingly, the analysis of a set of S. pennellii introgression lines (IL) identified 889 quantitative trait loci of compositional quality and 326 yield-associated traits. These traits are characterized by increases/decreases not only of single metabolites but also of entire metabolic pathways, thus highlighting the potential of this approach in uncovering novel aspects of metabolic regulation. Finally the biosynthetic pathway of the phenylalanine-derived fruit volatiles phenylethanol and phenylacetaldehyde was elucidated via a combination of metabolic profiling of natural variation, stable isotope tracer experiments and reverse genetic experimentation.},
  subject      = {Tomate},
  language  = {en}
}
@inproceedings{KuehlingMaerkerZehe2006,
  author    = {K{\"u}hling, Matthias and M{\"a}rker, Michael and Zehe, Erwin},
  title     = {Musterdynamik und Fernerkundung in der D{\"o}beritzer Heide : [Poster]},
  editor    = {Gzik, Axel and Hochschild, Volker and Schneider, Ingo and Schr{\"o}der, Boris},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7277},
  year      = {2006},
  abstract  = {Mit der politischen Wende in den Staaten des ehemaligen Ostblockes wurde f{\"u}r viele milit{\"a}risch genutzte Fl{\"a}chen ein tiefgreifender Nutzungswandel eingeleitet. Truppen{\"u}bungspl{\"a}tze als stark gest{\"o}rte Bestandteile unserer Kulturlandschaft weisen auf großen Fl{\"a}chen naturschutzfachlich wertvolle Habitatmosaike mit speziellen Lebensgemeinschaften auf. Der Nutzungswandel ist mit einer Ver{\"a}nderung der Vegetationsstrukturen (Sukzession) und weiteren landschafts{\"o}kologischen Prozessen verbunden. Der ehemalige Truppen{\"u}bungsplatz D{\"o}beritz im Norden der Landeshauptstadt Potsdam kann auf eine lange milit{\"a}rische Nutzungsgeschichte verweisen (erste Man{\"o}ver des Soldatenk{\"o}nigs im Jahr 1713). Nach 1992 wurden das NSG D{\"o}beritzer Heide (3.415 ha) und das NSG Ferbitzer Bruch (1.155 ha) ausgewiesen. Als Schutzgebiete nach der Vogelschutzrichtlinie sind sie Bestandteile des koh{\"a}renten Schutzgebietssystems Natura 2000 der europ{\"a}ischen Gemeinschaft. Trotz des Schutzstatus und der milit{\"a}rischen Altlasten unterliegt das Gebiet als gr{\"o}ßte zusammenh{\"a}ngende Naturfl{\"a}che im engeren Verflechtungsraum des Landes Brandenburg einem hohen Nutzungsdruck. <hr> Interdisziplin{\"a}res Zentrum f{\"u}r Musterdynamik und Angewandte Fernerkundung Workshop vom 9. - 10. Februar 2006},
  language  = {de}
}
@phdthesis{Fritz2006,
  author    = {Fritz, Christina},
  title     = {Der Einfluß des prim{\"a}ren Stickstoffstoffwechsels auf den Aminos{\"a}ure- und Sekund{\"a}rstoffwechsel in Nicotiana tabacum L.},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-13322},
  school      = {Universit{\"a}t Potsdam},
  year      = {2006},
  abstract  = {Es ist bekannt, dass {\"A}nderungen im Kohlenstoff- bzw. Stickstoffstaus der Pflanzen zu einer parallelen statt reziproken {\"A}nderung der kohlenstoff- und stickstoffhaltigen Prim{\"a}rmetabolite f{\"u}hren. Unter diesem Gesichtspunkt wurden in der vorliegenden Arbeit der Aminos{\"a}urestoffwechsel und der Sekund{\"a}rstoffwechsel unter reduzierten Stickstoffbedingungen untersucht. Zur Beeinflussung des Stickstoffstoffwechsels wurden nitratmangelern{\"a}hrte Tabakwildtyppflanzen und Genotypen mit unterschiedlich stark reduzierter Nitratreduktase-Aktivit{\"a}t verwendet. Dieses experimentelle System erlaubt zus{\"a}tzlich durch den Vergleich Nitrat defizienter Wildtyppflanzen mit Nitrat akkumulierenden NIA-Transformanten Prozesse zu identifizieren, die durch Nitrat gesteuert werden. Die Analysen der Prim{\"a}r- und Sekund{\"a}rmetabolite wurde in allen Genotypen diurnal durchgef{\"u}hrt, um auch tageszeitlich abh{\"a}ngige Prozesse zu identifizieren. Die Analyse der absoluten Gehalte aller individuellen Aminos{\"a}uren enth{\"u}llte bei den meisten erstaunlich stabile diurnale Muster mit einem Anstieg w{\"a}hrend des Tages und einem Abfall in der Nacht in Wildtyppflanzen gewachsen mit ausreichend Nitrat. Dieses Ergebnis legt die Schlussfolgerung nahe, dass die Biosynthese der Aminos{\"a}uren koordiniert abl{\"a}uft. In Pflanzen mit reduziertem Stickstoffstatus haben diese diurnalen Muster jedoch keinen Bestand. Die Kombination des erzeugten stickstoffbasierten Aminos{\"a}uredatensatz in Kombination mit einem bereits erzeugten Aminos{\"a}uredatensatz unter kohlenstofflimitierten Bedingungen von Matt et al. (2002) f{\"u}hrte durch Hauptkomponentenanalyse (PCA) und Korrelationsanalyse zu dem Ergebnis, dass die Hypothese nach einer koordinierten Aminos{\"a}urebiosynthese nicht allgemeine G{\"u}ltigkeit hat. Die PCA identifizierte Glutamin, Glutamat, Aspartat, Glycin, Pheny-lalanin und Threonin als Faktoren, die den Datens{\"a}tzen ihre charakteristische Eigenschaft und deren Varianz verleihen. Die Korrelationsanalyse zeigte, dass die sehr guten Korrelationen der individuellen Aminos{\"a}uren untereinander in reduzierten Stickstoff- und Kohlenstoffbedingungen sich verschlechtern. Das Verh{\"a}ltnis einer einzelnen Aminos{\"a}ure relativ zu den anderen f{\"u}hrte zur Identifizierung einiger Aminos{\"a}uren, die individuelle Antworten auf Stickstoff- und/oder Kohlenstoffstatus zeigen, und/oder speziell auf Nitrat, Licht und/oder den E-nergiestatus der Thylakoidmembran. Glutamat beispielsweise verh{\"a}lt sich in den meisten Situationen stabil, Phenylalanin dagegen zeigt in jeder physiologischen Situation eine individuelle Antwort. Die Ergebnisse dieser Arbeit f{\"u}hren zu einer Erweiterung der Hypothese einer koordinierten Synthese der Aminos{\"a}uren dahingehend, dass diese nicht generell f{\"u}r alle Aminos{\"a}uren angenommen werden kann. Es gibt einige Aminos{\"a}uren deren, Anteile sich situationsbedingt anpassen. Die Reduktion des Stickstoffstatus in nitratmangelern{\"a}hrten Tabakwildtyppflanzen f{\"u}hrte zu der, nach der „Carbon-Nutrient-Balance" Hypothese erwarteten Verlagerung der kohlenstoffreichen Phenylpropanoide und des stickstoffreichen Nikotins. Die Erh{\"o}hung der Phenylpropanoidgehalte war nicht in der Nitrat akkumulierenden NIA-Transformante zu beobachten und somit konnte Nitrat als regulatorisches Element identifiziert werden. Ein Einfluss der Vorl{\"a}ufermetabolite konnte ausgeschlossen werden, da sowohl nitratmangelern{\"a}hrter Wildtyp als auch die Nitrat akkumulierende NIA-Transformante {\"a}hnliche Gehalte dieser aufwiesen. Genexpressionsanalysen {\"u}ber Mikroarray-Hybridisierung und quantitative RT-PCR zeigten, dass Nitrat durch noch nicht gekl{\"a}rte Mechanismen Einfluss auf die Expression einiger Gene nimmt, die dem Phenylpropanoidstoffwechsels zugeordnet sind. Aus der Arbeit hervorgegangene Ver{\"o}ffentlichungen: Christina Fritz, Natalia Palacios-Rojas, Regina Feil und Mark Stitt (2006) Regulation of Secondary Metabolism by the Carbon-Nitrogen Status in Tobacco: Nitrate Inhibits Large Sectors of Phenylpropanoid Metabolism. Plant Journal 46, 533 - 548 Christina Fritz, Petra Matt, Cathrin M{\"u}ller, Regina Feil und Mark Stitt (2006) Impact of the Carbon-Nitrogen Status on the Amino Acid Profile in Tobacco Source Leaves. Plant, Cell and Environment 29 (11), 2009 - 2111},
  language  = {de}
}
@inproceedings{PoppBlaumDomptailetal.2006,
  author    = {Popp, Alexander and Blaum, Niels and Domptail, Stephanie and Herpel, Nicole and Gr{\"o}ngr{\"o}ft, Alexander and Hoffman, T. T. and J{\"u}rgens, Norbert and Milton, Sue and Nuppenau, Ernst-August and Rossmanith, Eva and Schmidt, Michael and Vogel, Melanie and Vohland, Katrin and Jeltsch, Florian},
  title     = {From satellite imagery to soil-plant interactions},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7302},
  year      = {2006},
  abstract  = {Decisions for the conservation of biodiversity and sustainable management of natural resources are typically related to large scales, i.e. the landscape level. However, understanding and predicting the effects of land use and climate change on scales relevant for decision-making requires to include both, large scale vegetation dynamics and small scale processes, such as soil-plant interactions. Integrating the results of multiple BIOTA subprojects enabled us to include necessary data of soil science, botany, socio-economics and remote sensing into a high resolution, process-based and spatially-explicit model. Using an example from a sustainably-used research farm and a communally used and degraded farming area in semiarid southern Namibia we show the power of simulation models as a tool to integrate processes across disciplines and scales.},
  language  = {en}
}
@inproceedings{RossmanithBlaumKeiletal.2006,
  author    = {Rossmanith, Eva and Blaum, Niels and Keil, Manfred and Langerwisch, F. and Meyer, Jork and Popp, Alexander and Schmidt, Michael and Schultz, Christoph and Schwager, Monika and Vogel, Melanie and Wasiolka, Bernd and Jeltsch, Florian},
  title     = {Scaling up local population dynamics to regional scales},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7320},
  year      = {2006},
  abstract  = {In semi-arid savannas, unsustainable land use can lead to degradation of entire landscapes, e.g. in the form of shrub encroachment. This leads to habitat loss and is assumed to reduce species diversity. In BIOTA phase 1, we investigated the effects of land use on population dynamics on farm scale. In phase 2 we scale up to consider the whole regional landscape consisting of a diverse mosaic of farms with different historic and present land use intensities. This mosaic creates a heterogeneous, dynamic pattern of structural diversity at a large spatial scale. Understanding how the region-wide dynamic land use pattern affects the abundance of animal and plant species requires the integration of processes on large as well as on small spatial scales. In our multidisciplinary approach, we integrate information from remote sensing, genetic and ecological field studies as well as small scale process models in a dynamic region-wide simulation tool. <hr> Interdisziplin{\"a}res Zentrum f{\"u}r Musterdynamik und Angewandte Fernerkundung Workshop vom 9. - 10. Februar 2006.},
  language  = {en}
}
@phdthesis{Hoffmann2007,
  author    = {Hoffmann, Toni},
  title     = {Cloning and characterisation of the HMA3 gene and its promoter from Arabidopsis halleri (L.) O'Kane and Al'Shehbaz and Arabidopsis thaliana (L.) Heynhold},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15259},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Being living systems unable to adjust their location to changing environmental conditions, plants display homeostatic networks that have evolved to maintain transition metal levels in a very narrow concentration range in order to avoid either deficiency or toxicity. Hence, plants possess a broad repertoire of mechanisms for the cellular uptake, compartmentation and efflux, as well as for the chelation of transition metal ions. A small number of plants are hypertolerant to one or a few specific transition metals. Some metal tolerant plants are also able to hyperaccumulate metal ions. The Brassicaceae family member Arabidopis halleri ssp. halleri (L.) O´KANE and AL´SHEHBAZ is a hyperaccumulator of zinc (Zn), and it is closely related to the non-hypertolerant and non-hyperaccumulating model plant Arabidopsis thaliana (L.) HEYNHOLD. The close relationship renders A. halleri a promising emerging model plant for the comparative investigation of the molecular mechanisms behind hypertolerance and hyperaccumulation. Among several potential candidate genes that are probably involved in mediating the zinc-hypertolerant and zinc-hyperaccumulating trait is AhHMA3. The AhHMA3 gene is highly similar to AtHMA3 (AGI number: At4g30120) in A. thaliana, and its encoded protein belongs to the P-type IB ATPase family of integral membrane transporter proteins that transport transition metals. In contrast to the low AtHMA3 transcript levels in A. thaliana, the gene was found to be constitutively highly expressed across different Zn treatments in A. halleri, especially in shoots. In this study, the cloning and characterisation of the HMA3 gene and its promoter from Arabidopsis halleri (L.) O´KANE and AL´SHEHBAZ and Arabidopsis thaliana (L.) HEYNHOLD is described. Heterologously expressed AhHMA3 mediated enhanced tolerance to Zn and to a much lesser degree to cadmium (Cd) but not to cobalt (Co) in metal-sensitive mutant strains of budding yeast. It is demonstrated that the genome of A. halleri contains at least four copies of AhHMA3, AhHMA3-1 to AhHMA3-4. A copy-specific real-time RT-PCR indicated that an AhHMA3-1 related gene copy is the source of the constitutively high transcript level in A. halleri and not a gene copy similar to AhHMA3-2 or AhHMA3-4. In accordance with the enhanced AtHMA3mRNA transcript level in A. thaliana roots, an AtHMA3 promoter-GUS gene construct mediated GUS activity predominantly in the vascular tissues of roots and not in shoots. However, the observed AhHMA3-1 and AhHMA3-2 promoter-mediated GUS activity in A. thaliana or A. halleri plants did not reflect the constitutively high expression of AhHMA3 in shoots of A. halleri. It is suggested that other factors e. g. characteristic sequence inserts within the first intron of AhHMA3-1 might enable a constitutively high expression. Moreover, the unknown promoter of the AhHMA3-3 gene copy could be the source of the constitutively high AhHMA3 transcript levels in A. halleri. In that case, the AhHMA3-3 sequence is predicted to be highly homologous to AhHMA3-1. The lack of solid localisation data for the AhHMA3 protein prevents a clear functional assignment. The provided data suggest several possible functions of the AhHMA3 protein: Like AtHMA2 and AtHMA4 it might be localised to the plasma membrane and could contribute to the efficient translocation of Zn from root to shoot and/or to the cell-to-cell distribution of Zn in the shoot. If localised to the vacuolar membrane, then a role in maintaining a low cytoplasmic zinc concentration by vacuolar zinc sequestration is possible. In addition, AhHMA3 might be involved in the delivery of zinc ions to trichomes and mesophyll leaf cells that are major zinc storage sites in A. halleri.},
  language  = {en}
}
@misc{Koechert2007,
  type      = {Master Thesis},
  author    = {K{\"o}chert, Karl},
  title     = {Development of a method to assess EAAT1 transcription levels in Alzheimer's disease},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15965},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Zur Zeit leiden ca. 24 Millionen Menschen auf der ganzen Welt unter Demenz, Alzheimer macht dabei 50-60\% aller Demenzf{\"a}lle aus. Da der Anteil der Bev{\"o}lkerung, der an Demenz leidet, proportional zum Alter zunimmt und der Anteil {\"a}lterer Menschen in der Gesellschaft von Jahr zu Jahr steigt, wird Alzheimer immer mehr zu einem ernstzunehmenden, gesellschaftlichen Problem. Zum Stand der heutigen Forschung ist es etabliert, dass die Aminos{\"a}ure Glutamat - quantitativ einer der wichtigsten Neurotransmitter im Zentralen Nervensystem (ZNS) - toxische Konzentrationen erreichen kann wenn sie - im Zuge der {\"U}bertragung von Aktionspotentialen - nach ihrer Freisetzung nicht aus dem Synaptischen Spalt entfernt wird. Viele Studien haben gezeigt, dass in der Alzheimerschen Krankheit die Glutamataufnahme beeintr{\"a}chtigt ist, was zu toxischen Konzentrationen von Glutamat und dem daraus folgenden Absterben von Neuronen f{\"u}hrt. Der exitatorische Aminos{\"a}uretransporter 1 (EAAT1) geh{\"o}rt zu der Familie der Na+-abh{\"a}ngigen Glutamattransporter und stellt nach EAAT2 den quantitativ wichtigsten Glutamattransporter im ZNS dar. In diesem Projekt wurde eine bis dahin f{\"u}r den Menschen nicht bekannte EAAT1 Spleißvariante, in der Exon 3 ausgeschnitten wird, nachgewiesen. Diese Variante wurde EAAT1Δ3 genannt und stellt damit mit EAAT1Δ9 die zweite f{\"u}r EAAT1 nachgewiesene Spleißvariante dar. Eine auf real-time RT-PCR basierende Methode wurde entwickelt, um die Transkripte von EAAT1 wildtyp (EAAT1 wt), EAAT1Δ3 und EAAT1Δ9 zu quantifizieren. Proben aus verschiedenen Hirnarealen wurden aus einem Set von Kontrollen und Alzheimerf{\"a}llen bei der Quantifizierung verwendet. Die gew{\"a}hlten Areale sind von der Alzheimerschen Krankheit unterschiedlich stark betroffen. Dies diente als interne Kontrolle f{\"u}r die durchgef{\"u}hrten Experimente und erm{\"o}glichte so die Differenzierung zwischen beobachteten Effekten: Nur Effekte die alleinig in von Alzheimer betroffenen Gehirnarealen auftreten, k{\"o}nnen als spezifisch f{\"u}r die Krankheit angesehen werden. Die Resultate diese Projektes zeigen, dass EAAT1Δ3 in sehr geringer Anzahl transkribiert wird, die nur 0.15\% der EAAT1 wt Transkription entspricht. Dahingegen entspricht das EAAT1 Δ9 Transkript im Durchschnitt 26.6\% des EAAT1 wt Transkripts. Es wurde nachgewiesen, dass die Transkriptionsrate aller EAAT1 Varianten in Alzheimerf{\"a}llen signifikant reduziert ist (P<0.0001). Dies unterst{\"u}tzt die Theorie, dass bei Alzheimerf{\"a}llen die EAAT1 Proteinexpression stark reduziert und der Glutamattransport, der normalerweise durch diesen Transporter gew{\"a}hrleistet wird, stark eingeschr{\"a}nkt ist. Dies wiederum resultiert in toxisch hohen Glutamatkonzentrationen und damit dem Absterben von Neuronen. Die gefundene Reduktion der EAAT1Transkription ist nicht spezifisch f{\"u}r Gehirnareale die von Alzheimer betroffen sind, sondern tritt in selbem Maße in nicht von Alzheimer betroffenen Gehirnarealen auf. Daraus l{\"a}sst sich schließen, dass die Reduktion der EAAT1 Transkription eher ein Resultat eines in der Alzheimerschen Krankheit pr{\"a}senten, grundlegenden Krankheitsmechanismus ist als deren Ursache.},
  language  = {en}
}
@phdthesis{Senger2007,
  author    = {Senger, Toralf},
  title     = {Untersuchungen zur Metallhom{\"o}ostase in Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-13234},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Alle Organismen sind f{\"u}r ihr {\"U}berleben auf Metalle angewiesen. Hierbei gibt es f{\"u}r jedes Metall einen Konzentrationsbereich, der das Optimum zwischen Metallmangel, -bedarf und -toxizit{\"a}t darstellt. Es gilt mittlerweile als erwiesen, dass alle Organismen zur Aufrechterhaltung des Metallgleichgewichts ein komplexes Netzwerk von Proteinen und niedermolekularen Verbindungen entwickelt haben. Die molekularen Komponenten dieses Netzwerks sind nur zu einem Teil bekannt und charakterisiert: In den letzten Jahren wurden einige Proteinfamilien identifiziert, deren Mitglieder Metalle durch Lipidmembranen transportieren. Eine dieser Metalltransporterfamilien ist die Cation Diffusion Facilitator (CDF)-Familie: Alle charakterisierten Mitglieder exportieren Metalle aus dem Zytoplasma - entweder in zellul{\"a}re Kompartimente oder aus der Zelle heraus. Von den zw{\"o}lf Mitgliedern dieser Familie in Arabidopsis thaliana (A. thaliana) - Metall Toleranz Protein (MTP)-1 bis -12 - wurden bisher AtMTP1 und AtMTP3 charakterisiert. In dieser Arbeit wird die Charakterisierung von AtMTP2 beschrieben. Wie die homologen Proteine AtMTP1 und AtMTP3 f{\"u}hrt AtMTP2 zu Zn-Toleranz, wenn es heterolog in Zn-sensitiven Hefemutanten exprimiert wird. Mit AtMTP2 transformierte Hefemutanten zeigten dar{\"u}ber hinaus erh{\"o}hte Co-Toleranz. Expression von chim{\"a}ren AtMTP2/GFP Fusionsproteinen in Hefe, A.thaliana protoplasten und in stabil transformierten A.thalinana Planzenlinien deutet auf Lokalisation of AtMTP2 in Membranen des Endoplasmatischen Retikulums (ER) hin, wenn GFP an den C-Terminus von MTP2 fusioniert wird. Fusion of GFP an den N-Terminus von AtMTP2 f{\"u}hrte zu Lokalisation in der vakuol{\"a}ren Membran, was wahrscheinlichsten auf Fehllokalisierung durch Maskierung eines ER-Retentionsmotivs (XXRR) am N-Terminus von AtMTP2 zur{\"u}ckgeht. Dies legt nahe, dass AtMTP2 die erw{\"a}hnten Metalle in das Endomembransystem der Zelle transportieren kann. Eine gewebespezifische Lokalisierung wurde mit Pflanzen durchgef{\"u}hrt, die das β-Glucuronidase (GUS)-Reporterprotein bzw. chim{\"a}re Fusionsproteine aus EGFP und AtMTP2 unter Kontrolle des nativen pMTP2-Promotors exprimierten. Diese Experimente best{\"a}tigten zum einen, dass der pMTP2-Promotor nur unter Zn-Defizienz aktiv ist. GUS-Aktivit{\"a}t wurde unter diesen Bedingungen in zwei Zonen der Wurzelspitze beobachtet: in den isodiametrischen Zellen der meristematischen Zone und in der beginnenden Wurzelhaarzone. Dar{\"u}ber hinaus konnte gezeigt werden, dass die EGFP-Fusionsproteine unter Kontrolle des nativen pMTP2-Promotors nur in epidermalen Zellen exprimiert werden. F{\"u}r eine homozygote Knockout- Linie, mtp2-S3, konnte bisher kein eindeutiger Ph{\"a}notyp identifiziert werden. Auf Grundlage der bisher durchgef{\"u}hrten Charakterisierung von AtMTP2 erscheinen zwei Modelle der Funktion von AtMTP2 in der Pflanze m{\"o}glich: AtMTP2 k{\"o}nnte essentiell f{\"u}r die Versorgung des ER mit Zn unter Zn-Mangelbedingungen sein. Hierf{\"u}r spricht, dass AtMTP2 in jungen, teilungsaktiven und damit Zn-ben{\"o}tigenden Wurzelzonen exprimiert wird. Die auf die Epidermis beschr{\"a}nkte Lokalisation k{\"o}nnte bei diesem Modell auf die M{\"o}glichkeit der zwischenzellul{\"a}ren Zn-Verteilung innerhalb des ER {\"u}ber Desmotubules hindeuten. Alternativ k{\"o}nnte AtMTP2 eine Funktion bei der Detoxifizierung von Zn unter Zn-Schock Bedingungen haben: Es ist bekannt, dass unter Zn- Mangelbedingungen die Expression der zellul{\"a}ren Zn-Aufnahmesysteme hochreguliert wird. Wenn nun die Zn-Verf{\"u}gbarkeit im Boden z. B durch eine pH-{\"A}nderung innerhalb kurzer Zeit stark ansteigt, besteht die Notwendigkeit der Entgiftung von Zn innerhalb der Zelle, bis der starke Einstrom von Zn ins Zytoplasma durch die Deaktivierung der Zn-Aufnahmesysteme und einer geringeren Expression in der Pflanze gedrosselt ist. Ein {\"a}hnlicher Mechanismus wurde in der B{\"a}ckerhefe S. cerevisae beschrieben, in der dar{\"u}ber hinaus ein Zn-Transporter verst{\"a}rkt exprimiert wird, der Zn durch Transport in die Vakuole entgiften kann. Es ist durchaus m{\"o}glich, dass in Arabidopsis AtMTP2 die Zn-Detoxifizierung unter diesen speziellen Bedingungen durch Zn-Transport in das ER oder die Vakuole vermittelt. Zur Identifikation weiterer Komponenten des Metallhom{\"o}ostasenetzwerks sind verschiedene Ans{\"a}tze denkbar. In dieser Arbeit wurde in Hefe ein heterologer Screen durchgef{\"u}hrt, um Interaktoren f{\"u}r vier Mitglieder der Arabidopsis-CDF-Familie zu identifizieren. Unter den 11 im Hefesystem best{\"a}tigten Kandidaten befindet sich mit AtSPL1 ein AtMTP1-Interaktionskandidat, der m{\"o}glicherweise eine Rolle bei der Cu-,Zn-Hom{\"o}ostase spielt. Als wahrscheinliche AtMTP3-Interaktionskandidaten wurde die c"-Untereinheit der vakuol{\"a}ren H+-ATPase AtVHA identifiziert sowie mit AtNPSN13 ein Protein, das vermutlich eine Rolle bei Fusionen von Vesikeln mit Zielmembranen spielt. Ein anderer Ansatz zur Identifikation neuer Metallhom{\"o}ostasegene ist die vergleichende Elementanalyse von nat{\"u}rlichen oder mutagenisierten Pflanzenpopulationen. Voraussetzung f{\"u}r diesen Ansatz ist die schnelle und genaue Analyse des Elementgehalts von Pflanzen. Eine etablierte Methode zur simultanen Bestimmung von bis zu 65 Elementen in einer Probe ist die Inductively Coupled Plasma Optical Emission Spectrometry (ICP OES). Der limitierende Faktor f{\"u}r einen hohen Probendurchsatz ist die Notwendigkeit, Proben f{\"u}r die Analyse zu verfl{\"u}ssigen. Eine alternative Methode der Probenzuf{\"u}hrung zum Analyseger{\"a}t ist die elektrothermale Verdampfung (ETV) der Probe. Zur weitgehend automatisierten Analyse von Pflanzenmaterial mit minimiertem Arbeitsaufwand wurde eine Methode entwickelt, die auf der Kopplung der ETV mit der ICP OES basiert.},
  language  = {de}
}
@phdthesis{Wagner2007,
  author    = {Wagner, Dirk},
  title     = {Microbial perspectives of the methane cycle in permafrost ecosystems in the Eastern Siberian Arctic : implications for the global methane budget},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15434},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {The Arctic plays a key role in Earth's climate system as global warming is predicted to be most pronounced at high latitudes and because one third of the global carbon pool is stored in ecosystems of the northern latitudes. In order to improve our understanding of the present and future carbon dynamics in climate sensitive permafrost ecosystems, the present study concentrates on investigations of microbial controls of methane fluxes, on the activity and structure of the involved microbial communities, and on their response to changing environmental conditions. For this purpose an integrated research strategy was applied, which connects trace gas flux measurements to soil ecological characterisation of permafrost habitats and molecular ecological analyses of microbial populations. Furthermore, methanogenic archaea isolated from Siberian permafrost have been used as potential keystone organisms for studying and assessing life under extreme living conditions. Long-term studies on methane fluxes were carried out since 1998. These studies revealed considerable seasonal and spatial variations of methane emissions for the different landscape units ranging from 0 to 362 mg m-2 d-1. For the overall balance of methane emissions from the entire delta, the first land cover classification based on Landsat images was performed and applied for an upscaling of the methane flux data sets. The regionally weighted mean daily methane emissions of the Lena Delta (10 mg m-2 d-1) are only one fifth of the values calculated for other Arctic tundra environments. The calculated annual methane emission of the Lena Delta amounts to about 0.03 Tg. The low methane emission rates obtained in this study are the result of the used remotely sensed high-resolution data basis, which provides a more realistic estimation of the real methane emissions on a regional scale. Soil temperature and near soil surface atmospheric turbulence were identified as the driving parameters of methane emissions. A flux model based on these variables explained variations of the methane budget corresponding to continuous processes of microbial methane production and oxidation, and gas diffusion through soil and plants reasonably well. The results show that the Lena Delta contributes significantly to the global methane balance because of its extensive wetland areas. The microbiological investigations showed that permafrost soils are colonized by high numbers of microorganisms. The total biomass is comparable to temperate soil ecosystems. Activities of methanogens and methanotrophs differed significantly in their rates and distribution patterns along both the vertical profiles and the different investigated soils. The methane production rates varied between 0.3 and 38.9 nmol h-1 g-1, while the methane oxidation ranged from 0.2 to 7.0 nmol h-1 g-1. Phylogenetic analyses of methanogenic communities revealed a distinct diversity of methanogens affiliated to Methanomicrobiaceae, Methanosarcinaceae and Methanosaetaceae, which partly form four specific permafrost clusters. The results demonstrate the close relationship between methane fluxes and the fundamental microbiological processes in permafrost soils. The microorganisms do not only survive in their extreme habitat but also can be metabolic active under in situ conditions. It was shown that a slight increase of the temperature can lead to a substantial increase in methanogenic activity within perennially frozen deposits. In case of degradation, this would lead to an extensive expansion of the methane deposits with their subsequent impacts on total methane budget. Further studies on the stress response of methanogenic archaea, especially Methanosarcina SMA-21, isolated from Siberian permafrost, revealed an unexpected resistance of the microorganisms against unfavourable living conditions. A better adaptation to environmental stress was observed at 4 °C compared to 28 °C. For the first time it could be demonstrated that methanogenic archaea from terrestrial permafrost even survived simulated Martian conditions. The results show that permafrost methanogens are more resistant than methanogens from non-permafrost environments under Mars-like climate conditions. Microorganisms comparable to methanogens from terrestrial permafrost can be seen as one of the most likely candidates for life on Mars due to their physiological potential and metabolic specificity.},
  language  = {en}
}
@misc{KoechyBrakenhielm2008,
  author    = {K{\"o}chy, Martin and Br{\aa}kenhielm, Sven},
  title     = {Separation of effects of moderate N deposition from natural change in ground vegetation of forests and bogs},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-16621},
  year      = {2008},
  abstract  = {The effect of moderate rates of nitrogen deposition on ground floor vegetation is poorly predicted by uncontrolled surveys or fertilization experiments using high rates of nitrogen (N) addition. We compared the temporal trends of ground floor vegetation in permanent plots with moderate (7-13 kg ha-1 year-1) and lower bulk N deposition (4-6 kg ha-1 year-1) in southern Sweden during 1982-1998. We examined whether trends differed between growth forms (vascular plants and bryophytes) and vegetation types (three types of coniferous forest, deciduous forest, and bog). Trends of site-standardized cover and richness varied among growth forms, vegetation types, and deposition regions. Cover in spruce forests decreased at the same rate with both moderate and low deposition. In pine forests cover decreased faster with moderate deposition and in bogs cover decreased faster with low deposition. Cover of bryophytes in spruce forests increased at the same rate with both moderate and low deposition. In pine forests cover decreased faster with moderate deposition and in bogs and deciduous forests there was a strong non-linear increase with moderate deposition. The trend of number of vascular plants was constant with moderate and decreased with low deposition. We found no trend in the number of bryophyte species. We propose that the decrease of cover and number with low deposition was related to normal ecosystem development (increased shading), suggesting that N deposition maintained or increased the competitiveness of some species in the moderate-deposition region. Deposition had no consistent negative effect on vegetation suggesting that it is less important than normal successional processes.},
  language  = {en}
}
@phdthesis{Oey2008,
  author    = {Oey, Melanie},
  title     = {Chloroplasts as bioreactors : high-yield production of active bacteriolytic protein antibiotics},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-28950},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {Plants, more precisely their chloroplasts with their bacterial-like expression machinery inherited from their cyanobacterial ancestors, can potentially offer a cheap expression system for proteinaceous pharmaceuticals. This system would be easily scalable and provides appropriate safety due to chloroplasts maternal inheritance. In this work, it was shown that three phage lytic enzymes (Pal, Cpl-1 and PlyGBS) could be successfully expressed at very high levels and with high stability in tobacco chloroplasts. PlyGBS expression reached an amount of foreign protein accumulation (> 70\% TSP) that has never been obtained before. Although the high expression levels of PlyGBS caused a pale green phenotype with retarded growth, presumably due to exhaustion of plastid protein synthesis capacity, development and seed production were not impaired under greenhouse conditions. Since Pal and Cpl-1 showed toxic effects when expressed in E. coli, a special plastid transformation vector (pTox) was constructed to allow DNA amplification in bacteria. The construction of the pTox transformation vector allowing a recombinase-mediated deletion of an E. coli transcription block in the chloroplast, leading to an increase of foreign protein accumulation to up to 40\% of TSP for Pal and 20\% of TSP for Cpl-1. High dose-dependent bactericidal efficiency was shown for all three plant-derived lytic enzymes using their pathogenic target bacteria S. pyogenes and S. pneumoniae. Confirmation of specificity was obtained for the endotoxic proteins Pal and Cpl-1 by application to E. coli cultures. These results establish tobacco chloroplasts as a new cost-efficient and convenient production platform for phage lytic enzymes and address the greatest obstacle for clinical application. The present study is the first report of lysin production in a non-bacterial system. The properties of chloroplast-produced lysins described in this work, their stability, high accumulation rate and biological activity make them highly attractive candidates for future antibiotics.},
  language  = {en}
}
@misc{KoechyMathajJeltschetal.2008,
  author    = {K{\"o}chy, Martin and Mathaj, Martin and Jeltsch, Florian and Malkinson, Dan},
  title     = {Resilience of stocking capacity to changing climate in arid to Mediterranean landscapes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-18720},
  year      = {2008},
  abstract  = {Small livestock is an important resource for rural human populations in dry climates. How strongly will climate change affect the capacity of the rangeland? We used hierarchical modelling to scale quantitatively the growth of shrubs and annual plants, the main food of sheep and goats, to the landscape extent in the eastern Mediterranean region. Without grazing, productivity increased in a sigmoid way with mean annual precipitation. Grazing reduced productivity more strongly the drier the landscape. At a point just under the stocking capacity of the vegetation, productivity declined precipitously with more intense grazing due to a lack of seed production of annuals. We repeated simulations with precipitation patterns projected by two contrasting IPCC scenarios. Compared to results based on historic patterns, productivity and stocking capacity did not differ in most cases. Thus, grazing intensity remains the stronger impact on landscape productivity in this dry region even in the future.},
  language  = {en}
}
@misc{SteinfathGaertnerLisecetal.2009,
  author    = {Steinfath, Matthias and G{\"a}rtner, Tanja and Lisec, Jan and Meyer, Rhonda C. and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim},
  title     = {Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1324},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43111},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431115},
  pages     = {9},
  year      = {2009},
  abstract  = {A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80\% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This proof of concept could be interesting for breeders. The example population exhibits substantial mid-parent biomass heterosis. The results of feature selection could therefore be used to shed light on the origin of heterosis. In this respect, mainly dominance effects were detected.},
  language  = {en}
}
@article{SteinfathGaertnerLisecetal.2009,
  author    = {Steinfath, Matthias and G{\"a}rtner, Tanja and Lisec, Jan and Meyer, Rhonda Christiane and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim},
  title     = {Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers},
  series = {Theoretical and applied genetics : TAG ; international journal of plant breeding research},
  volume    = {120},
  journal   = {Theoretical and applied genetics : TAG ; international journal of plant breeding research},
  publisher = {Springer},
  address   = {Berlin},
  issn      = {0040-5752},
  doi       = {10.1007/s00122-009-1191-2},
  pages     = {239 -- 247},
  year      = {2009},
  abstract  = {A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80\% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This proof of concept could be interesting for breeders. The example population exhibits substantial mid-parent biomass heterosis. The results of feature selection could therefore be used to shed light on the origin of heterosis. In this respect, mainly dominance effects were detected.},
  language  = {en}
}
@phdthesis{Schuette2011,
  author    = {Sch{\"u}tte, Moritz},
  title     = {Evolutionary fingerprints in genome-scale networks},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-57483},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Mathematical modeling of biological phenomena has experienced increasing interest since new high-throughput technologies give access to growing amounts of molecular data. These modeling approaches are especially able to test hypotheses which are not yet experimentally accessible or guide an experimental setup. One particular attempt investigates the evolutionary dynamics responsible for today's composition of organisms. Computer simulations either propose an evolutionary mechanism and thus reproduce a recent finding or rebuild an evolutionary process in order to learn about its mechanism. The quest for evolutionary fingerprints in metabolic and gene-coexpression networks is the central topic of this cumulative thesis based on four published articles. An understanding of the actual origin of life will probably remain an insoluble problem. However, one can argue that after a first simple metabolism has evolved, the further evolution of metabolism occurred in parallel with the evolution of the sequences of the catalyzing enzymes. Indications of such a coevolution can be found when correlating the change in sequence between two enzymes with their distance on the metabolic network which is obtained from the KEGG database. We observe that there exists a small but significant correlation primarily on nearest neighbors. This indicates that enzymes catalyzing subsequent reactions tend to be descended from the same precursor. Since this correlation is relatively small one can at least assume that, if new enzymes are no "genetic children" of the previous enzymes, they certainly be descended from any of the already existing ones. Following this hypothesis, we introduce a model of enzyme-pathway coevolution. By iteratively adding enzymes, this model explores the metabolic network in a manner similar to diffusion. With implementation of an Gillespie-like algorithm we are able to introduce a tunable parameter that controls the weight of sequence similarity when choosing a new enzyme. Furthermore, this method also defines a time difference between successive evolutionary innovations in terms of a new enzyme. Overall, these simulations generate putative time-courses of the evolutionary walk on the metabolic network. By a time-series analysis, we find that the acquisition of new enzymes appears in bursts which are pronounced when the influence of the sequence similarity is higher. This behavior strongly resembles punctuated equilibrium which denotes the observation that new species tend to appear in bursts as well rather than in a gradual manner. Thus, our model helps to establish a better understanding of punctuated equilibrium giving a potential description at molecular level. From the time-courses we also extract a tentative order of new enzymes, metabolites, and even organisms. The consistence of this order with previous findings provides evidence for the validity of our approach. While the sequence of a gene is actually subject to mutations, its expression profile might also indirectly change through the evolutionary events in the cellular interplay. Gene coexpression data is simply accessible by microarray experiments and commonly illustrated using coexpression networks where genes are nodes and get linked once they show a significant coexpression. Since the large number of genes makes an illustration of the entire coexpression network difficult, clustering helps to show the network on a metalevel. Various clustering techniques already exist. However, we introduce a novel one which maintains control of the cluster sizes and thus assures proper visual inspection. An application of the method on Arabidopsis thaliana reveals that genes causing a severe phenotype often show a functional uniqueness in their network vicinity. This leads to 20 genes of so far unknown phenotype which are however suggested to be essential for plant growth. Of these, six indeed provoke such a severe phenotype, shown by mutant analysis. By an inspection of the degree distribution of the A.thaliana coexpression network, we identified two characteristics. The distribution deviates from the frequently observed power-law by a sharp truncation which follows after an over-representation of highly connected nodes. For a better understanding, we developed an evolutionary model which mimics the growth of a coexpression network by gene duplication which underlies a strong selection criterion, and slight mutational changes in the expression profile. Despite the simplicity of our assumption, we can reproduce the observed properties in A.thaliana as well as in E.coli and S.cerevisiae. The over-representation of high-degree nodes could be identified with mutually well connected genes of similar functional families: zinc fingers (PF00096), flagella, and ribosomes respectively. In conclusion, these four manuscripts demonstrate the usefulness of mathematical models and statistical tools as a source of new biological insight. While the clustering approach of gene coexpression data leads to the phenotypic characterization of so far unknown genes and thus supports genome annotation, our model approaches offer explanations for observed properties of the coexpression network and furthermore substantiate punctuated equilibrium as an evolutionary process by a deeper understanding of an underlying molecular mechanism.},
  language  = {en}
}