@phdthesis{Montulet2024, author = {Montulet, Orianne}, title = {Functional characterization of putative interactors of the Cellulose Synthase Complex}, school = {Universit{\"a}t Potsdam}, pages = {160}, year = {2024}, language = {en} } @phdthesis{Apodiakou2024, author = {Apodiakou, Anastasia}, title = {Analysis of the regulation of SDI genes, unravelling the role of the SLIM1 transcription factor, and the SNRK3.15 kinase in Arabidopsis under sulfur deprivation}, school = {Universit{\"a}t Potsdam}, pages = {141}, year = {2024}, language = {en} } @phdthesis{Seerangan2023, author = {Seerangan, Kumar}, title = {Actin-based regulation of cell and tissue scale morphologenesis in develpoping leaves}, school = {Universit{\"a}t Potsdam}, pages = {120}, year = {2023}, language = {en} } @article{MarinBeloquiZhangGuoetal.2022, author = {Marin-Beloqui, Jose and Zhang, Guanran and Guo, Junjun and Shaikh, Jordan and Wohrer, Thibaut and Hosseini, Seyed Mehrdad and Sun, Bowen and Shipp, James and Auty, Alexander J. and Chekulaev, Dimitri and Ye, Jun and Chin, Yi-Chun and Sullivan, Michael B. and Mozer, Attila J. and Kim, Ji-Seon and Shoaee, Safa and Clarke, Tracey M.}, title = {Insight into the origin of trapping in polymer/fullerene blends with a systematic alteration of the fullerene to higher adducts}, series = {Journal of physical chemistry C}, volume = {126}, journal = {Journal of physical chemistry C}, number = {5}, publisher = {American Chemical Society}, address = {Washington}, issn = {1932-7447}, doi = {10.1021/acs.jpcc.1c10378}, pages = {2708 -- 2719}, year = {2022}, abstract = {The bimolecular recombination characteristics of conjugated polymer poly[(4,4'-bis(2-ethylhexyl)dithieno[3,2-b:2',3'-d]silole)-2,6-diyl-alt-(2,5-bis 3-tetradecylthiophen-2-y1 thiazolo 5,4-d thiazole)-2,5diy1] (PDTSiTTz) blended with the fullerene series PC60BM, ICMA, ICBA, and ICTA have been investigated using microsecond and femtosecond transient absorption spectroscopy, in conjunction with electroluminescence measurements and ambient photoemission spectroscopy. The non-Langevin polymer PDTSiTTz allows an inspection of intrinsic bimolecular recombination rates uninhibited by diffusion, while the low oscillator strengths of fullerenes allow polymer features to dominate, and we compare our results to those of the well-known polymer Si-PCPDTBT. Using mu s-TAS, we have shown that the trap -limited decay dynamics of the PDTSiTTz polaron becomes progressively slower across the fullerene series, while those of Si-PCPDTBT are invariant. Electroluminescence measurements showed an unusual double peak in pristine PDTSiTTz, attributed to a low energy intragap charge transfer state, likely interchain in nature. Furthermore, while the pristine PDTSiTTz showed a broad, low-intensity density of states, the ICBA and ICTA blends presented a virtually identical DOS to Si-PCPDTBT and its blends. This has been attributed to a shift from a delocalized, interchain highest occupied molecular orbital (HOMO) in the pristine material to a dithienosilole-centered HOMO in the blends, likely a result of the bulky fullerenes increasing interchain separation. This HOMO localization had a side effect of progressively shifting the polymer HOMO to shallower energies, which was correlated with the observed decrease in bimolecular recombination rate and increased "trap" depth. However, since the density of tail states remained the same, this suggests that the traditional viewpoint of "trapping" being dominated by tail states may not encompass the full picture and that the breadth of the DOS may also have a strong influence on bimolecular recombination.}, language = {en} } @article{FlovenzWangHersiretal.2022, author = {Fl{\´o}venz, {\´O}lafur G. and Wang, Rongjiang and Hersir, Gylfi P{\´a}ll and Dahm, Torsten and Hainzl, Sebastian and Vassileva, Magdalena and Drouin, Vincent and Heimann, Sebastian and Isken, Marius Paul and Gudnason, Egill {\´A}. and {\´A}g{\´u}stsson, Kristj{\´a}n and {\´A}g{\´u}stsd{\´o}ttir, Thorbj{\"o}rg and Hor{\´a}lek, Josef and Motagh, Mahdi and Walter, Thomas R. and Rivalta, Eleonora and Jousset, Philippe and Krawczyk, Charlotte M. and Milkereit, Claus}, title = {Cyclical geothermal unrest as a precursor to Iceland's 2021 Fagradalsfjall eruption}, series = {Nature geoscience}, volume = {15}, journal = {Nature geoscience}, number = {5}, publisher = {Nature Research}, address = {Berlin}, issn = {1752-0894}, doi = {10.1038/s41561-022-00930-5}, pages = {397 -- 404}, year = {2022}, abstract = {Understanding and constraining the source of geodetic deformation in volcanic areas is an important component of hazard assessment. Here, we analyse deformation and seismicity for one year before the March 2021 Fagradalsfjall eruption in Iceland. We generate a high-resolution catalogue of 39,500 earthquakes using optical cable recordings and develop a poroelastic model to describe three pre-eruptional uplift and subsidence cycles at the Svartsengi geothermal field, 8 km west of the eruption site. We find the observed deformation is best explained by cyclic intrusions into a permeable aquifer by a fluid injected at 4 km depth below the geothermal field, with a total volume of 0.11 ± 0.05 km3 and a density of 850 ± 350 kg m-3. We therefore suggest that ingression of magmatic CO2 can explain the geodetic, gravity and seismic data, although some contribution of magma cannot be excluded.}, language = {en} } @article{KayaDupontNivetFrielingetal.2022, author = {Kaya, Mustafa Y{\"u}cel and Dupont-Nivet, Guillaume and Frieling, Joost and Fioroni, Chiara and Rohrmann, Alexander and Alt{\i}ner, Sevin{\c{c}} {\"O}zkan and Vardar, Ezgi and Tanyas, Hakan and Mamtimin, Mehmut and Zhaojie, Guo}, title = {The Eurasian epicontinental sea was an important carbon sink during the Palaeocene-Eocene thermal maximum}, series = {Communications earth and environment}, volume = {3}, journal = {Communications earth and environment}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2662-4435}, doi = {10.1038/s43247-022-00451-4}, pages = {10}, year = {2022}, abstract = {The Palaeocene-Eocene Thermal Maximum (ca. 56 million years ago) offers a primary analogue for future global warming and carbon cycle recovery. Yet, where and how massive carbon emissions were mitigated during this climate warming event remains largely unknown. Here we show that organic carbon burial in the vast epicontinental seaways that extended over Eurasia provided a major carbon sink during the Palaeocene-Eocene Thermal Maximum. We coupled new and existing stratigraphic analyses to a detailed paleogeographic framework and using spatiotemporal interpolation calculated ca. 720-1300 Gt organic carbon excess burial, focused in the eastern parts of the Eurasian epicontinental seaways. A much larger amount (2160-3900 Gt C, and when accounting for the increase in inundated shelf area 7400-10300 Gt C) could have been sequestered in similar environments globally. With the disappearance of most epicontinental seas since the Oligocene-Miocene, an effective negative carbon cycle feedback also disappeared making the modern carbon cycle critically dependent on the slower silicate weathering feedback.}, language = {en} } @phdthesis{Hagemann2024, author = {Hagemann, Justus}, title = {On the molecular evolution of sengis (Macroscelidea)}, doi = {10.25932/publishup-64197}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-641975}, school = {Universit{\"a}t Potsdam}, pages = {xiii, 144}, year = {2024}, abstract = {This thesis focuses on the molecular evolution of Macroscelidea, commonly referred to as sengis. Sengis are a mammalian order belonging to the Afrotherians, one of the four major clades of placental mammals. Sengis currently consist of twenty extant species, all of which are endemic to the African continent. They can be separated in two families, the soft-furred sengis (Macroscelididae) and the giant sengis (Rhynchocyonidae). While giant sengis can be exclusively found in forest habitats, the different soft-furred sengi species dwell in a broad range of habitats, from tropical rain-forests to rocky deserts. Our knowledge on the evolutionary history of sengis is largely incomplete. The high level of superficial morphological resemblance among different sengi species (especially the soft-furred sengis) has for example led to misinterpretations of phylogenetic relationships, based on morphological characters. With the rise of DNA based taxonomic inferences, multiple new genera were defined and new species described. Yet, no full taxon molecular phylogeny exists, hampering the answering of basic taxonomic questions. This lack of knowledge can be to some extent attributed to the limited availability of fresh-tissue samples for DNA extraction. The broad African distribution, partly in political unstable regions and low population densities complicate contemporary sampling approaches. Furthermore, the DNA information available usually covers only short stretches of the mitochondrial genome and thus a single genetic locus with limited informational content. Developments in DNA extraction and library protocols nowadays offer the opportunity to access DNA from museum specimens, collected over the past centuries and stored in natural history museums throughout the world. Thus, the difficulties in fresh-sample acquisition for molecular biological studies can be overcome by the application of museomics, the research field which emerged from those laboratory developments. This thesis uses fresh-tissue samples as well as a vast collection museum specimens to investigate multiple aspects about the macroscelidean evolutionary history. Chapter 4 of this thesis focuses on the phylogenetic relationships of all currently known sengi species. By accessing DNA information from museum specimens in combination of fresh tissue samples and publicly available genetic resources it produces the first full taxon molecular phylogeny of sengis. It confirms the monophyly of the genus Elephantulus and discovers multiple deeply divergent lineages within different species, highlighting the need for species specific approaches. The study furthermore focuses on the evolutionary time frame of sengis by evaluating the impact of commonly varied parameters on tree dating. The results of the study show, that the mitochondrial information used in previous studies to temporal calibrate the Macroscelidean phylogeny led to an overestimation of node ages within sengis. Especially soft-furred sengis are thus much younger than previously assumed. The refined knowledge of nodes ages within sengis offer the opportunity to link e.g. speciation events to environmental changes. Chapter 5 focuses on the genus Petrodromus with its single representative Petrodromus tetradactylus. It again exploits the opportunities of museomics and gathers a comprehensive, multi-locus genetic dataset of P. tetradactylus individuals, distributed across most the known range of this species. It reveals multiple deeply divergent lineages within Petrodromus, whereby some could possibly be associated to previously described sub-species, at least one was formerly unknown. It underscores the necessity for a revision of the genus Petrodromus through the integration of both molecular and morphological evidence. The study, furthermore identifies changing forest distributions through climatic oscillations as main factor shaping the genetic structure of Petrodromus. Chapter 6 uses fresh tissue samples to extent the genomic resources of sengis by thirteen new nuclear genomes, of which two were de-novo assembled. An extensive dataset of more than 8000 protein coding one-to-one orthologs allows to further refine and confirm the temporal time frame of sengi evolution found in Chapter 4. This study moreover investigates the role of gene-flow and incomplete lineage sorting (ILS) in sengi evolution. In addition it identifies clade specific genes of possible outstanding evolutionary importance and links them to potential phenotypic traits affected. A closer investigation of olfactory receptor proteins reveals clade specific differences. A comparison of the demographic past of sengis to other small African mammals does not reveal a sengi specific pattern.}, language = {en} } @article{KloseGuillemoteauVignolietal.2023, author = {Klose, Tim and Guillemoteau, Julien and Vignoli, Giulio and Walter, Judith and Herrmann, Andreas and Tronicke, Jens}, title = {Structurally constrained inversion by means of a Minimum Gradient Support regularizer}, series = {Geophysical journal international}, volume = {233}, journal = {Geophysical journal international}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0956-540X}, doi = {10.1093/gji/ggad041}, pages = {1938 -- 1949}, year = {2023}, abstract = {Many geophysical inverse problems are known to be ill-posed and, thus, requiring some kind of regularization in order to provide a unique and stable solution. A possible approach to overcome the inversion ill-posedness consists in constraining the position of the model interfaces. For a grid-based parameterization, such a structurally constrained inversion can be implemented by adopting the usual smooth regularization scheme in which the local weight of the regularization is reduced where an interface is expected. By doing so, sharp contrasts are promoted at interface locations while standard smoothness constraints keep affecting the other regions of the model. In this work, we present a structurally constrained approach and test it on the inversion of frequency-domain electromagnetic induction (FD-EMI) data using a regularization approach based on the Minimum Gradient Support stabilizer, which is capable to promote sharp transitions everywhere in the model, i.e., also in areas where no structural a prioriinformation is available. Using 1D and 2D synthetic data examples, we compare the proposed approach to a structurally constrained smooth inversion as well as to more standard (i.e., not structurally constrained) smooth and sharp inversions. Our results demonstrate that the proposed approach helps in finding a better and more reliable reconstruction of the subsurface electrical conductivity distribution, including its structural characteristics. Furthermore, we demonstrate that it allows to promote sharp parameter variations in areas where no structural information are available. Lastly, we apply our structurally constrained scheme to FD-EMI field data collected at a field site in Eastern Germany to image the thickness of peat deposits along two selected profiles. In this field example, we use collocated constant offset ground-penetrating radar (GPR) data to derive structural a priori information to constrain the inversion of the FD-EMI data. The results of this case study demonstrate the effectiveness and flexibility of the proposed approach.}, language = {en} } @article{CordobaTongBurgosetal.2023, author = {C{\´o}rdoba, Sandra Correa and Tong, Hao and Burgos, Asdrubal and Zhu, Feng and Alseekh, Saleh and Fernie, Alisdair R. and Nikoloski, Zoran}, title = {Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism}, series = {Nature Communications}, volume = {14}, journal = {Nature Communications}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-023-40644-9}, pages = {12}, year = {2023}, abstract = {The use of automated tools to reconstruct lipid metabolic pathways is not warranted in plants. Here, the authors construct Plant Lipid Module for Arabidopsis rosette using constraint-based modeling, demonstrate its integration in other plant metabolic models, and use it to dissect the genetic architecture of lipid metabolism. Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83\%) of single lethal knock-outs and 75\% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40\% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism.}, language = {en} } @article{CescaSuganRudzinskietal.2022, author = {Cesca, Simone and Sugan, Monica and Rudzinski, Lukasz and Vajedian, Sanaz and Niemz, Peter and Plank, Simon and Petersen, Gesa and Deng, Zhiguo and Rivalta, Eleonora and Vuan, Alessandro and Linares, Milton Percy Plasencia and Heimann, Sebastian and Dahm, Torsten}, title = {Massive earthquake swarm driven by magmatic intrusion at the Bransfield Strait, Antarctica}, series = {Communications earth and environment}, volume = {3}, journal = {Communications earth and environment}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2662-4435}, doi = {10.1038/s43247-022-00418-5}, pages = {11}, year = {2022}, abstract = {An earthquake swarm affected the Bransfield Strait, Antarctica, a unique rift basin in transition from intra-arc rifting to ocean spreading. The swarm, counting similar to 85,000 volcano-tectonic earthquakes since August 2020, is located close to the Orca submarine volcano, previously considered inactive. Simultaneously, geodetic data reported up to similar to 11 cm north-westward displacement over King George Island. We use a broad variety of geophysical data and methods to reveal the complex migration of seismicity, accompanying the intrusion of 0.26-0.56 km(3) of magma. Strike-slip earthquakes mark the intrusion at depth, while shallower normal faulting the similar to 20 km long lateral growth of a dike. Seismicity abruptly decreased after a Mw 6.0 earthquake, suggesting the magmatic dike lost pressure with the slipping of a large fault. A seafloor eruption is likely, but not confirmed by sea surface temperature anomalies. The unrest documents episodic magmatic intrusion in the Bransfield Strait, providing unique insights into active continental rifting.}, language = {en} }