@article{Kohnen2011, author = {Kohnen, Saskia}, title = {Vernachl{\"a}ssigte Dyslexien}, series = {Spektrum Patholinguistik}, journal = {Spektrum Patholinguistik}, number = {4}, issn = {1869-3822}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-54226}, pages = {75 -- 81}, year = {2011}, language = {de} } @article{MeinuschNeumann2011, author = {Meinusch, Miriam and Neumann, Sandra}, title = {Systematisches Review zur Ermittlung wissenschaftlicher Evidenzen der Dysphagie bei LKGS-Fehlbildungen}, series = {Spektrum Patholinguistik}, journal = {Spektrum Patholinguistik}, number = {4}, issn = {1869-3822}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-54291}, pages = {149 -- 170}, year = {2011}, language = {de} } @article{Tagoe2011, author = {Tagoe, Tanja}, title = {Sprache und Emotion bei Kindern und Jugendlichen mit Williams-Beuren-Syndrom}, series = {Spektrum Patholinguistik}, journal = {Spektrum Patholinguistik}, number = {4}, issn = {1869-3822}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-54367}, pages = {217 -- 236}, year = {2011}, language = {de} } @article{EtzienMachlebLorenz2011, author = {Etzien, Maria and Machleb, Franziska and Lorenz, Antje}, title = {Semantische versus wortform-spezifische Merkmalsanalyse in der Behandlung von Wortabrufst{\"o}rungen bei Aphasie}, series = {Spektrum Patholinguistik}, journal = {Spektrum Patholinguistik}, number = {4}, issn = {1869-3822}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-54337}, pages = {193 -- 197}, year = {2011}, language = {de} } @article{Kentner2011, author = {Kentner, Gerrit}, title = {Rhythmus-Syntax-Interaktion beim Lesen}, series = {Spektrum Patholinguistik}, journal = {Spektrum Patholinguistik}, number = {4}, issn = {1869-3822}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-54234}, pages = {83 -- 93}, year = {2011}, language = {de} } @phdthesis{Wischnewski2011, author = {Wischnewski, Juliane}, title = {Reconstructing climate variability on the Tibetan Plateau : comparing aquatic and terrestrial signals}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-52453}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {Spatial and temporal temperature and moisture patterns across the Tibetan Plateau are very complex. The onset and magnitude of the Holocene climate optimum in the Asian monsoon realm, in particular, is a subject of considerable debate as this time period is often used as an analogue for recent global warming. In the light of contradictory inferences regarding past climate and environmental change on the Tibetan Plateau, I have attempted to explain mismatches in the timing and magnitude of change. Therefore, I analysed the temporal variation of fossil pollen and diatom spectra and the geochemical record from palaeo-ecological records covering different time scales (late Quaternary and the last 200 years) from two core regions in the NE and SE Tibetan Plateau. For interpretation purposes I combined my data with other available palaeo-ecological data to set up corresponding aquatic and terrestrial proxy data sets of two lake pairs and two sets of sites. I focused on the direct comparison of proxies representing lacustrine response to climate signals (e.g., diatoms, ostracods, geochemical record) and proxies representing changes in the terrestrial environment (i.e., terrestrial pollen), in order to asses whether the lake and its catchments respond at similar times and magnitudes to environmental changes. Therefore, I introduced the established numerical technique procrustes rotation as a new approach in palaeoecology to quantitatively compare raw data of any two sedimentary records of interest in order to assess their degree of concordance. Focusing on the late Quaternary, sediment cores from two lakes (Kuhai Lake 35.3°N; 99.2°E; 4150 m asl; and Koucha Lake 34.0°N; 97.2°E; 4540 m asl) on the semi-arid northeastern Tibetan Plateau were analysed to identify post-glacial vegetation and environmental changes, and to investigate the responses of lake ecosystems to such changes. Based on the pollen record, five major vegetation and climate changes could be identified: (1) A shift from alpine desert to alpine steppe indicates a change from cold, dry conditions to warmer and more moist conditions at 14.8 cal. ka BP, (2) alpine steppe with tundra elements points to conditions of higher effective moisture and a stepwise warming climate at 13.6 cal. ka BP, (3) the appearance of high-alpine meadow vegetation indicates a further change towards increased moisture, but with colder temperatures, at 7.0 cal. ka BP, (4) the reoccurrence of alpine steppe with desert elements suggests a return to a significantly colder and drier phase at 6.3 cal. ka BP, and (5) the establishment of alpine steppe-meadow vegetation indicates a change back to relatively moist conditions at 2.2 cal. ka BP. To place the reconstructed climate inferences from the NE Tibetan Plateau into the context of Holocene moisture evolution across the Tibetan Plateau, I applied a five-scale moisture index and average link clustering to all available continuous pollen and non-pollen palaeoclimate records from the Tibetan Plateau, in an attempt to detect coherent regional and temporal patterns of moisture evolution on the Plateau. However, no common temporal or spatial pattern of moisture evolution during the Holocene could be detected, which can be assigned to the complex responses of different proxies to environmental changes in an already very heterogeneous mountain landscape, where minor differences in elevation can result in marked variations in microenvironments. Focusing on the past 200 years, I analysed the sedimentary records (LC6 Lake 29.5°N, 94.3°E, 4132 m asl; and Wuxu Lake 29.9°N, 101.1°E, 3705 m asl) from the southeastern Tibetan Plateau. I found that despite presumed significant temperature increases over that period, pollen and diatom records from the SE Tibetan Plateau reveal only very subtle changes throughout their profiles. The compositional species turnover investigated over the last 200 years appears relatively low in comparison to the species reorganisations during the Holocene. The results indicate that climatically induced ecological thresholds are not yet crossed, but that human activity has an increasing influence, particularly on the terrestrial ecosystem. Forest clearances and reforestation have not caused forest decline in our study area, but a conversion of natural forests to semi-natural secondary forests. The results from the numerical proxy comparison of the two sets of two pairs of Tibetan lakes indicate that the use of different proxies and the work with palaeo-ecological records from different lake types can cause deviant stories of inferred change. Irrespective of the timescale (Holocene or last 200 years) or region (SE or NE Tibetan Plateau) analysed, the agreement in terms of the direction, timing, and magnitude of change between the corresponding terrestrial data sets is generally better than the match between the corresponding lacustrine data sets, suggesting that lacustrine proxies may partly be influenced by in-lake or local catchment processes whereas the terrestrial proxy reflects a more regional climatic signal. The current disaccord on coherent temporal and spatial climate patterns on the Tibetan Plateau can partly be ascribed to the complexity of proxy response and lake systems on the Tibetan Plateau. Therefore, a multi-proxy, multi-site approach is important in order to gain a reliable climate interpretation for the complex mountain landscape of the Tibetan Plateau.}, language = {en} } @article{BethmannScheichBrechmann2011, author = {Bethmann, Anja and Scheich, Henning and Brechmann, Andr{\´e}}, title = {Produktion von Eigennamen}, series = {Spektrum Patholinguistik}, journal = {Spektrum Patholinguistik}, number = {4}, issn = {1869-3822}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-54246}, pages = {95 -- 116}, year = {2011}, language = {de} } @misc{BuschMeissnerPotthoffetal.2011, author = {Busch, Jan Philip and Meißner, Tobias and Potthoff, Annegret and Oswald, Sascha}, title = {Plating of nano zero-valent iron (nZVI) on activated carbon : a fast delivery method of iron for source remediation?}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-53792}, year = {2011}, abstract = {The use of nano zerovalent iron (nZVI) for environmental remediation is a promising new technique for in situ remediation. Due to its high surface area and high reactivity, nZVI is able to dechlorinate organic contaminants and render them harmless. Limited mobility, due to fast aggregation and sedimentation of nZVI, limits the capability for source and plume remediation. Carbo-Iron is a newly developed material consisting of activated carbon particles (d50 = 0,8 µm) that are plated with nZVI particles. These particles combine the mobility of activated carbon and the reactivity of nZVI. This paper presents the first results of the transport experiments.}, language = {en} } @book{OPUS4-5518, title = {Personalmanagement in der brandenburgischen Landesverwaltung}, editor = {Salomon-Hengst, Annette and Kirchner, Steffi and Stumpenhusen, Susanne and Westphal, Volker-Gerd}, publisher = {Universit{\"a}tsverlags Potsdam}, address = {Potsdam}, isbn = {978-3-86956-149-3}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-53846}, publisher = {Universit{\"a}t Potsdam}, pages = {345}, year = {2011}, abstract = {In der brandenburgischen Landesverwaltung und Justiz sollen in den n{\"a}chsten Jahren noch ca. 8.000 Stellen eingespart werden. Gleichzeitig sind die Landesverwaltung und die Justiz an die demografische Entwicklung und die damit verbundenen Aufgabenver{\"a}nderungen anzupassen. Das ressort{\"u}bergreifende Personalmanagement gewinnt hierdurch an Bedeutung. Um den Prozess zu gestalten, hat die Landesregierung eine Besetzungsrichtlinie erlassen und mit den Gewerkschaften einen Tarifvertrag zum Verwaltungsumbau (TV Umbau) abgeschlossen, die in diesem Band ebenso abgedruckt sind, wie die Durchf{\"u}hrungshinweise des Ministeriums des Innern. Dar{\"u}ber hinaus enth{\"a}lt der Band die aktuell geltende Personalbedarfsplanung bis Ende 2015, die Dr. Folke Schneider erl{\"a}utert. In einem Beitrag von Volker-Gerd Westphal wird eine Gesamtschau der Rahmenbedingungen f{\"u}r das Personalmanagement in der brandenburgischen Landesverwaltung und Justiz vorgenommen.}, language = {de} } @misc{BostonHaleVasishthetal.2011, author = {Boston, Marisa Ferrara and Hale, John T. and Vasishth, Shravan and Kliegl, Reinhold}, title = {Parallel processing and sentence comprehension difficulty}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-57159}, year = {2011}, abstract = {Eye fixation durations during normal reading correlate with processing difficulty but the specific cognitive mechanisms reflected in these measures are not well understood. This study finds support in German readers' eyefixations for two distinct difficulty metrics: surprisal, which reflects the change in probabilities across syntactic analyses as new words are integrated, and retrieval, which quantifies comprehension difficulty in terms of working memory constraints. We examine the predictions of both metrics using a family of dependency parsers indexed by an upper limit on the number of candidate syntactic analyses they retain at successive words. Surprisal models all fixation measures and regression probability. By contrast, retrieval does not model any measure in serial processing. As more candidate analyses are considered in parallel at each word, retrieval can account for the same measures as surprisal. This pattern suggests an important role for ranked parallelism in theories of sentence comprehension.}, language = {en} } @phdthesis{Popovic2011, author = {Popovic, Jelena}, title = {Novel lithium iron phosphate materials for lithium-ion batteries}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-54591}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {Conventional energy sources are diminishing and non-renewable, take million years to form and cause environmental degradation. In the 21st century, we have to aim at achieving sustainable, environmentally friendly and cheap energy supply by employing renewable energy technologies associated with portable energy storage devices. Lithium-ion batteries can repeatedly generate clean energy from stored materials and convert reversely electric into chemical energy. The performance of lithium-ion batteries depends intimately on the properties of their materials. Presently used battery electrodes are expensive to be produced; they offer limited energy storage possibility and are unsafe to be used in larger dimensions restraining the diversity of application, especially in hybrid electric vehicles (HEVs) and electric vehicles (EVs). This thesis presents a major progress in the development of LiFePO4 as a cathode material for lithium-ion batteries. Using simple procedure, a completely novel morphology has been synthesized (mesocrystals of LiFePO4) and excellent electrochemical behavior was recorded (nanostructured LiFePO4). The newly developed reactions for synthesis of LiFePO4 are single-step processes and are taking place in an autoclave at significantly lower temperature (200 deg. C) compared to the conventional solid-state method (multi-step and up to 800 deg. C). The use of inexpensive environmentally benign precursors offers a green manufacturing approach for a large scale production. These newly developed experimental procedures can also be extended to other phospho-olivine materials, such as LiCoPO4 and LiMnPO4. The material with the best electrochemical behavior (nanostructured LiFePO4 with carbon coating) was able to delive a stable 94\% of the theoretically known capacity.}, language = {en} } @phdthesis{Robinson2011, author = {Robinson, Alexander}, title = {Modeling the Greenland Ice Sheet response to climate change in the past and future}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-50430}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {The Greenland Ice Sheet (GIS) contains enough water volume to raise global sea level by over 7 meters. It is a relic of past glacial climates that could be strongly affected by a warming world. Several studies have been performed to investigate the sensitivity of the ice sheet to changes in climate, but large uncertainties in its long-term response still exist. In this thesis, a new approach has been developed and applied to modeling the GIS response to climate change. The advantages compared to previous approaches are (i) that it can be applied over a wide range of climatic scenarios (both in the deep past and the future), (ii) that it includes the relevant feedback processes between the climate and the ice sheet and (iii) that it is highly computationally efficient, allowing simulations over very long timescales. The new regional energy-moisture balance model (REMBO) has been developed to model the climate and surface mass balance over Greenland and it represents an improvement compared to conventional approaches in modeling present-day conditions. Furthermore, the evolution of the GIS has been simulated over the last glacial cycle using an ensemble of model versions. The model performance has been validated against field observations of the present-day climate and surface mass balance, as well as paleo information from ice cores. The GIS contribution to sea level rise during the last interglacial is estimated to be between 0.5-4.1 m, consistent with previous estimates. The ensemble of model versions has been constrained to those that are consistent with the data, and a range of valid parameter values has been defined, allowing quantification of the uncertainty and sensitivity of the modeling approach. Using the constrained model ensemble, the sensitivity of the GIS to long-term climate change was investigated. It was found that the GIS exhibits hysteresis behavior (i.e., it is multi-stable under certain conditions), and that a temperature threshold exists above which the ice sheet transitions to an essentially ice-free state. The threshold in the global temperature is estimated to be in the range of 1.3-2.3°C above preindustrial conditions, significantly lower than previously believed. The timescale of total melt scales non-linearly with the overshoot above the temperature threshold, such that a 2°C anomaly causes the ice sheet to melt in ca. 50,000 years, but an anomaly of 6°C will melt the ice sheet in less than 4,000 years. The meltback of the ice sheet was found to become irreversible after a fraction of the ice sheet is already lost - but this level of irreversibility also depends on the temperature anomaly.}, language = {en} } @book{RaithRaaseReinhardt2011, author = {Raith, Michael M. and Raase, Peter and Reinhardt, J{\"u}rgen}, title = {Leitfaden zur D{\"u}nnschliffmikroskopie}, isbn = {978-3-00-036420-4}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-bbdig-252}, publisher = {Universit{\"a}t Potsdam}, pages = {IV, 125}, year = {2011}, language = {de} } @book{RaithRaaseReinhardt2011, author = {Raith, Michael M. and Raase, Peter and Reinhardt, J{\"u}rgen}, title = {Leitfaden zur D{\"u}nnschliffmikroskopie}, isbn = {978-3-00-036420-4}, doi = {10.25932/publishup-59930}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-599301}, publisher = {Universit{\"a}t Potsdam}, pages = {IV, 125}, year = {2011}, language = {de} } @phdthesis{Lauterbach2011, author = {Lauterbach, Stefan}, title = {Lateglacial to Holocene climatic and environmental changes in Europe : multi-proxy studies on lake sediments along a transect from northern Italy to northeastern Poland}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-58157}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {Sediment records of three European lakes were investigated in order to reconstruct the regional climate development during the Lateglacial and Holocene, to investigate the response of local ecosystems to climatic fluctuations and human impact and to relate regional peculiarities of past climate development to climatic changes on a larger spatial scale. The Lake Hańcza (NE Poland) sediment record was studied with a focus on reconstructing the early Holocene climate development and identifying possible differences to Western Europe. Following the initial Holocene climatic improvement, a further climatic improvement occurred between 10 000 and 9000 cal. a BP. Apparently, relatively cold and dry climate conditions persisted in NE Poland during the first ca. 1500 years of the Holocene, most likely due to a specific regional atmospheric circulation pattern. Prevailing anticyclonic circulation linked to a high-pressure cell above the remaining Scandinavian Ice Sheet (SIS) might have blocked the eastward propagation of warm and moist Westerlies and thus attenuated the early Holocene climatic amelioration in this region until the final decay of the SIS, a pattern different from climate development in Western Europe. The Lateglacial sediment record of Lake Mondsee (Upper Austria) was investigated in order to study the regional climate development and the environmental response to rapid climatic fluctuations. While the temperature rise and environmental response at the onset of the Holocene took place quasi-synchronously, major leads and lags in proxy responses characterize the onset of the Lateglacial Interstadial. In particular, the spread of coniferous woodlands and the reduction of detrital flux lagged the initial Lateglacial warming by ca. 500-750 years. Major cooling at the onset of the Younger Dryas took place synchronously with a change in vegetation, while the increase of detrital matter flux was delayed by about 150-300 years. Complex proxy responses are also detected for short-term Lateglacial climatic fluctuations. In summary, periods of abrupt climatic changes are characterized by complex and temporally variable proxy responses, mainly controlled by ecosystem inertia and the environmental preconditions. A second study on the Lake Mondsee sediment record focused on two small-scale climate deteriorations around 8200 and 9100 cal. a BP, which have been triggered by freshwater discharges to the North Atlantic, causing a shutdown of the Atlantic meridional overturning circulation (MOC). Combining microscopic varve counting and AMS 14C dating yielded a precise duration estimate (ca. 150 years) and absolute dating of the 8.2 ka cold event, both being in good agreement with results from other palaeoclimate records. Moreover, a sudden temperature overshoot after the 8.2 ka cold event was identified, also seen in other proxy records around the North Atlantic. This was most likely caused by enhanced resumption of the MOC, which also initiated substantial shifts of oceanic and atmospheric front systems. Although there is also evidence from other proxy records for pronounced recovery of the MOC and atmospheric circulation changes after the 9.1 ka cold event, no temperature overshoot is seen in the Lake Mondsee record, indicating the complex behaviour of the global climate system. The Holocene sediment record of Lake Iseo (northern Italy) was studied to shed light on regional earthquake activity and the influence of climate variability and anthropogenic impact on catchment erosion and detrital flux into the lake. Frequent small-scale detrital layers within the sediments reflect allochthonous sediment supply by extreme surface runoff events. During the early to mid-Holocene, increased detrital flux coincides with periods of cold and wet climate conditions, thus apparently being mainly controlled by climate variability. In contrast, intervals of high detrital flux during the late Holocene partly also correlate with phases of increased human impact, reflecting the complex influences on catchment erosion processes. Five large-scale event layers within the sediments, which are composed of mass-wasting deposits and turbidites, are supposed to have been triggered by strong local earthquakes. While the uppermost of these event layers is assigned to a documented adjacent earthquake in AD 1222, the four other layers are supposed to be related to previously undocumented prehistorical earthquakes.}, language = {en} } @misc{KlieglBates2011, author = {Kliegl, Reinhold and Bates, Douglas}, title = {International Collaboration in Psychology is on the Rise}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-57045}, year = {2011}, abstract = {There has been a substantial increase in the percentage for publications with co-authors located in departments from different countries in 12 major journals of psychology. The results are evidence for a remarkable internationalization of psychological research, starting in the mid 1970s and increasing in rate at the beginning of the 1990s. This growth occurs against a constant number of articles with authors from the same country; it is not due to a concomitant increase in the number of co-authors per article. Thus, international collaboration in psychology is obviously on the rise.}, language = {en} } @book{Ludwig2011, author = {Ludwig, Joachim}, title = {Forschungsbasierte Lehre als Lehre im Format der Forschung}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-49858}, publisher = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {Wissenschaftler sind regelm{\"a}ßig mehr an Forschung interessiert als an Lehre. Dies hat verschiedene Gr{\"u}nde, auf die hier nicht im Einzelnen eingegangen werden soll. Einer dieser Gr{\"u}nde liegt im eigenen Professionsverst{\"a}ndnis als Forscher/in bzw. Wissenschaftler/in begr{\"u}ndet. Im Kern geht es dabei um Entdeckungen, um Innovationen, um die Weiterentwicklung vorhandenen Wissens. Lehre wird dem gegen{\"u}ber als intermedi{\"a}rer Bereich gesehen, in dem vorhandenes Wissen reproduziert wird, der deshalb mehr dem Berufssystem zugeh{\"o}rig ist und weniger dem Wissenschaftssystem (Fangmann 2006, S. 30). Lehre erscheint deshalb als Belastung, die mit Forschung nicht korrespondiert, eher von Forschung abh{\"a}lt, insbesondere wenn Studierende den eigenen Lehrbem{\"u}hungen passiv gegen{\"u}berstehen und der Ertrag der Lehre zweifelhaft erscheint. Im Folgenden soll die Verwandtschaft von Forschung und Lernen dargestellt und auf ihre korrespondierenden Logiken verwiesen werden. Grundlage daf{\"u}r ist ein lerntheoretisches Modell, das Lernen subjekttheoretisch als soziales Handeln konzipiert (Holzkamp 1993), das mit Forschen vergleichbar ist. Forschungsbasierte Lehre wird im Kontext einer subjekttheoretischen Didaktik (Ludwig 2006) als Lehre im Format der Forschung vorgestellt, die Lernen unterst{\"u}tzen kann, weil Lernen dem Forschungsprozess {\"a}hnelt. Typen, Ertr{\"a}ge und Umsetzungsprobleme forschungsbasierter Lehre werden kurz skizziert.}, language = {de} } @article{Peters2011, author = {Peters, Friedrich Ernst}, title = {Formelhaftigkeit, ein Wesenszug des Plattdeutschen}, series = {Digitale Edition : Friedrich Peters}, journal = {Digitale Edition : Friedrich Peters}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-56867}, year = {2011}, abstract = {F. E. Peters stellt in seiner Studie {\"U}berlegungen zur Idiomatik und Phraseologie des Plattdeutschen an, der Muttersprache des Schriftstellers. Er pl{\"a}diert daf{\"u}r, das Plattdeutsche in seiner Besonderheit und unabh{\"a}ngig von Vergleichen mit dem Hochdeutschen zu bewerten und zu w{\"u}rdigen. K{\"u}rze, Pr{\"a}gnanz, Anschaulichkeit und intuitive Treffsicherheit des Plattdeutschen werden hervorgehoben und anhand von Beispielen aus dem Alltag belegt. Peters unterstreicht die sich in dem Bewahren von Formeln ausdr{\"u}ckende „einf{\"a}ltige Sprachfr{\"o}mmigkeit" des Plattdeutschen, f{\"u}r ihn ein Zeichen junger und primitiverer Sprachen, gewissermaßen „Sprach-Marionetten" im Kleistschen Sinn ausgestattet mit der Anmut des Unbewussten.}, language = {de} } @article{Talabardon2011, author = {Talabardon, Susanne}, title = {Expeditionen in die Fremde}, series = {Mobilisierte Kulturen}, journal = {Mobilisierte Kulturen}, number = {1}, issn = {2192-3019}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-57428}, pages = {285 -- 310}, year = {2011}, language = {de} } @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} }