@article{AverbeckApioPlathetal.2009, author = {Averbeck, Christiane and Apio, Ann and Plath, Martin and Wronski, Torsten}, title = {Environmental parameters and anthropogenic effects predicting the spatial distribution of wild ungulates in the Akagera savannah ecosystem}, issn = {0141-6707}, doi = {10.1111/j.1365-2028.2009.01076.x}, year = {2009}, abstract = {Savannah areas affected by human activities such as livestock keeping and agriculture are often characterized by shifts in landscape structuring, with a predominance of few(er) habitat types. This is typically accompanied by pronounced changes in the communities of ungulates. The aim of this study was to find out whether shifts in ungulate communities in Lake Mburo National Park (LMNP) are primarily predicted by an alteration in the composition of the preferred habitat types or if more complex interactions between habitat changes and the prevalence of ungulates occur. Monthly road counts were used to establish the number of eleven ungulate species in LMNP and adjacent unprotected Ankole Ranching Scheme. The common duiker (Sylvicapra grimmia campbelliae Gray, 1843) was found in more abundance in disturbed areas, while showing a significant change in habitat use. Common duiker tended to use the vegetation type otherwise used by the bushbuck (Tragelaphus scriptus dama Neumann, 1902). Our results support the claim that the occurrence of ungulates is not only directly affected by the availability of 'suitable' habitats, but behavioural plasticity and competitive exclusion also need to be considered.}, language = {en} } @article{AverbeckApioPlathetal.2010, author = {Averbeck, Christiane and Apio, Ann and Plath, Martin and Wronski, Torsten}, title = {Hunting differentially affects mixed-sex and bachelor-herds in a gregarious ungulate, the impala (Aepyceros melampus: Bovidae)}, issn = {0141-6707}, doi = {10.1111/j.1365-2028.2009.01118.x}, year = {2010}, abstract = {We investigated herd-sizes and herd-compositions of Impala (Aepyceros melampus) inside a protected area [Lake Mburo National Park (LMNP) in western Uganda] and the unprotected adjacent ranchland [the Ankole Ranching Scheme (ARS)]. Impala experience intense hunting and poaching in the study area, and poaching is especially strong on the ARS. We found evidence for changes in overall group-sizes in both mixed-sex and pure bachelor herds between areas in and outside LMNP. Mixed-sex herds strongly decreased in size outside the National Park, but bachelor herds even slightly increased in size. While the group-composition of mixed-sex herds was very similar in areas in and outside LMNP, bachelor herds comprised more yearlings and subadult males on the ARS. Our study suggests that effects of hunting and other human nuisance may differ between herd types: mixed herds probably decrease in size because females are more strongly hunted. Around LMNP, impala are usually hunted using nets and spears, thereby increasing the hunters' chance of being injured. Poachers therefore prefer hornless females (and their calves), as it is less dangerous to handle net-caught females than males. As a result, males are less hunted, but increased vigilance and, therefore, reduced aggression among the members of a bachelor herd, may account for the observed increase in herd sizes and changes in group-compositions.}, language = {en} } @article{AvcilarKucukgozeBartholomaeusVarelaetal.2016, author = {Avcilar-Kucukgoze, Irem and Bartholom{\"a}us, Alexander and Varela, Juan A. Cordero and Kaml, Robert Franz-Xaver and Neubauer, Peter and Budisa, Nediljko and Ignatova, Zoya}, title = {Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli}, series = {Nucleic acids research}, volume = {44}, journal = {Nucleic acids research}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gkw697}, pages = {8324 -- 8334}, year = {2016}, abstract = {Translation is a central cellular process and is optimized for speed and fidelity. The speed of translation of a single codon depends on the concentration of aminoacyl-tRNAs. Here, we used microarray-based approaches to analyze the charging levels of tRNAs in Escherichia coli growing at different growth rates. Strikingly, we observed a non-uniform aminoacylation of tRNAs in complex media. In contrast, in minimal medium, the level of aminoacyl-tRNAs is more uniform and rises to approximately 60\%. Particularly, the charging level of tRNA(Ser), tRNA(Cys), tRNA(Thr) and tRNA(His) is below 50\% in complex medium and their aminoacylation levels mirror the degree that amino acids inhibit growth when individually added to minimal medium. Serine is among the most toxic amino acids for bacteria and tRNAs(Ser) exhibit the lowest charging levels, below 10\%, at high growth rate although intracellular serine concentration is plentiful. As a result some serine codons are among the most slowly translated codons. A large fraction of the serine is most likely degraded by L-serine-deaminase, which competes with the seryl-tRNA-synthetase that charges the tRNAs(Ser). These results indicate that the level of aminoacylation in complex media might be a competition between charging for translation and degradation of amino acids that inhibit growth.}, language = {en} } @phdthesis{AvcilarKucukgoze2016, author = {Avcilar-Kucukgoze, Irem}, title = {Effect of tRNA Aminoacylation and Cellular Resources Allocation on the Dynamics of Translation in Escherichia coli}, school = {Universit{\"a}t Potsdam}, pages = {131}, year = {2016}, language = {en} } @article{AutenriethHartmannLahetal.2018, author = {Autenrieth, Marijke and Hartmann, Stefanie and Lah, Ljerka and Roos, Anna and Dennis, Alice B. and Tiedemann, Ralph}, title = {High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)}, series = {Molecular ecology resources}, volume = {18}, journal = {Molecular ecology resources}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12932}, pages = {1469 -- 1481}, year = {2018}, abstract = {The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50\% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.}, language = {en} } @misc{AutenriethErnstDeavilleetal.2018, author = {Autenrieth, Marijke and Ernst, Anja and Deaville, Rob and Demaret, Fabien and Ijsseldijk, Lonneke L. and Siebert, Ursula and Tiedemann, Ralph}, title = {Putative origin and maternal relatedness of male sperm whales (Physeter macrocephalus) recently stranded in the North Sea}, series = {Mammalian biology = Zeitschrift f{\"u}r S{\"a}ugetierkunde}, volume = {88}, journal = {Mammalian biology = Zeitschrift f{\"u}r S{\"a}ugetierkunde}, publisher = {Elsevier}, address = {M{\"u}nchen}, issn = {1616-5047}, doi = {10.1016/j.mambio.2017.09.003}, pages = {156 -- 160}, year = {2018}, abstract = {The globally distributed sperm whale (Physeter macrocephalus) has a partly matrilineal social structure with predominant male dispersal. At the beginning of 2016, a total of 30 male sperm whales stranded in five different countries bordering the southern North Sea. It has been postulated that these individuals were on a migration route from the north to warmer temperate and tropical waters where females live in social groups. By including samples from four countries (n = 27), this event provided a unique chance to genetically investigate the maternal relatedness and the putative origin of these temporally and spatially co-occuring male sperm whales. To utilize existing genetic resources, we sequenced 422 bp of the mitochondrial control region, a molecular marker for which sperm whale data are readily available from the entire distribution range. Based on four single nucleotide polymorphisms (SNPs) within the mitochondrial control region, five matrilines could be distinguished within the stranded specimens, four of which matched published haplotypes previously described in the Atlantic. Among these male sperm whales, multiple matrilineal lineages co-occur. We analyzed the population differentiation and could show that the genetic diversity of these male sperm whales is comparable to the genetic diversity in sperm whales from the entire Atlantic Ocean. We confirm that within this stranding event, males do not comprise maternally related individuals and apparently include assemblages of individuals from different geographic regions. (c) 2017 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.}, language = {en} } @phdthesis{Autenrieth2020, author = {Autenrieth, Marijke}, title = {Population genomics of two odontocetes in the North Atlantic and adjacent waters}, school = {Universit{\"a}t Potsdam}, pages = {IX, 110}, year = {2020}, abstract = {Due to continuously intensifying human usage of the marine environment worldwide ranging cetaceans face an increasing number of threats. Besides whaling, overfishing and by-catch, new technical developments increase the water and noise pollution, which can negatively affect marine species. Cetaceans are especially prone to these influences, being at the top of the food chain and therefore accumulating toxins and contaminants. Furthermore, they are extremely noise sensitive due to their highly developed hearing sense and echolocation ability. As a result, several cetacean species were brought to extinction during the last century or are now classified as critically endangered. This work focuses on two odontocetes. It applies and compares different molecular methods for inference of population status and adaptation, with implications for conservation. The worldwide distributed sperm whale (Physeter macrocephalus) shows a matrilineal population structure with predominant male dispersal. A recently stranded group of male sperm whales provided a unique opportunity to investigate male grouping for the first time. Based on the mitochondrial control region, I was able to infer that male bachelor groups comprise multiple matrilines, hence derive from different social groups, and that they represent the genetic variability of the entire North Atlantic. The harbor porpoise (Phocoena phocoena) occurs only in the northern hemisphere. By being small and occurring mostly in coastal habitats it is especially prone to human disturbance. Since some subspecies and subpopulations are critically endangered, it is important to generate and provide genetic markers with high resolution to facilitate population assignment and subsequent protection measurements. Here, I provide the first harbour porpoise whole genome, in high quality and including a draft annotation. Using it for mapping ddRAD seq data, I identify genome wide SNPs and, together with a fragment of the mitochondrial control region, inferred the population structure of its North Atlantic distribution range. The Belt Sea harbors a distinct subpopulation oppose to the North Atlantic, with a transition zone in the Kattegat. Within the North Atlantic I could detect subtle genetic differentiation between western (Canada-Iceland) and eastern (North Sea) regions, with support for a German North Sea breading ground around the Isle of Sylt. Further, I was able to detect six outlier loci which show isolation by distance across the investigated sampling areas. In employing different markers, I could show that single maker systems as well as genome wide data can unravel new information about population affinities of odontocetes. Genome wide data can facilitate investigation of adaptations and evolutionary history of the species and its populations. Moreover, they facilitate population genetic investigations, providing a high resolution, and hence allowing for detection of subtle population structuring especially important for highly mobile cetaceans.}, language = {en} } @misc{AugusiakVandenBrinkGrimm2014, author = {Augusiak, Jacqueline and Van den Brink, Paul J. and Grimm, Volker}, title = {Merging validation and evaluation of ecological models to 'evaludation': A review of terminology and a practical approach}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {280}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2013.11.009}, pages = {117 -- 128}, year = {2014}, abstract = {Confusion about model validation is one of the main challenges in using ecological models for decision support, such as the regulation of pesticides. Decision makers need to know whether a model is a sufficiently good representation of its real counterpart and what criteria can be used to answer this question. Unclear terminology is one of the main obstacles to a good understanding of what model validation is, how it works, and what it can deliver. Therefore, we performed a literature review and derived a standard set of terms. 'Validation' was identified as a catch-all term, which is thus useless for any practical purpose. We introduce the term 'evaludation', a fusion of 'evaluation' and 'validation', to describe the entire process of assessing a model's quality and reliability. Considering the iterative nature of model development, the modelling cycle, we identified six essential elements of evaludation: (i) 'data evaluation' for scrutinising the quality of numerical and qualitative data used for model development and testing; (ii) 'conceptual model evaluation' for examining the simplifying assumptions underlying a model's design; (iii) 'implementation verification' for testing the model's implementation in equations and as a computer programme; (iv) 'model output verification' for comparing model output to data and patterns that guided model design and were possibly used for calibration; (v) 'model analysis' for exploring the model's sensitivity to changes in parameters and process formulations to make sure that the mechanistic basis of main behaviours of the model has been well understood; and (vi) 'model output corroboration' for comparing model output to new data and patterns that were not used for model development and parameterisation. Currently, most decision makers require 'validating' a model by testing its predictions with new experiments or data. Despite being desirable, this is neither sufficient nor necessary for a model to be useful for decision support. We believe that the proposed set of terms and its relation to the modelling cycle can help to make quality assessments and reality checks of ecological models more comprehensive and transparent. (C) 2013 Elsevier B.V. All rights reserved.}, language = {en} } @article{AudisioClineSolanoetal.2014, author = {Audisio, Paolo and Cline, Andrew R. and Solano, Emanuela and Mancini, Emiliano and Lamanna, Francesco and Antonini, Gloria and Trizzino, Marco}, title = {A peculiar new genus and species of pollen-beetle (Coleoptera, Nitidulidae) from eastern Africa, with a molecular phylogeny of related Meligethinae}, series = {Systematics and biodiversity}, volume = {12}, journal = {Systematics and biodiversity}, number = {1}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {1477-2000}, doi = {10.1080/14772000.2013.877539}, pages = {77 -- 91}, year = {2014}, language = {en} } @article{AttermeyerTittelAllgaieretal.2015, author = {Attermeyer, Katrin and Tittel, Joerg and Allgaier, Martin and Frindte, Katharina and Wurzbacher, Christian and Hilt, Sabine and Kamjunke, Norbert and Grossart, Hans-Peter}, title = {Effects of Light and Autochthonous Carbon Additions on Microbial Turnover of Allochthonous Organic Carbon and Community Composition}, series = {Microbial ecology}, volume = {69}, journal = {Microbial ecology}, number = {2}, publisher = {Springer}, address = {New York}, issn = {0095-3628}, doi = {10.1007/s00248-014-0549-4}, pages = {361 -- 371}, year = {2015}, abstract = {The fate of allochthonous dissolved organic carbon (DOC) in aquatic systems is primarily controlled by the turnover of heterotrophic bacteria. However, the roles that abiotic and biotic factors such as light and DOC release by aquatic primary producers play in the microbial decomposition of allochthonous DOC is not well understood. We therefore tested if light and autochthonous DOC additions would increase allochthonous DOC decomposition rates and change bacterial growth efficiencies and community composition (BCC). We established continuous growth cultures with different inocula of natural bacterial communities and alder leaf leachates (DOCleaf) with and without light exposure before amendment. Furthermore, we incubated DOCleaf together with autochthonous DOC from lysed phytoplankton cultures (DOCphyto). Our results revealed that pretreatments of DOCleaf with light resulted in a doubling of bacterial growth efficiency (BGE), whereas additions of DOCphyto or combined additions of DOCphyto and light had no effect on BGE. The change in BGE was not accompanied by shifts in the phylogenetic structure of the BCC, but BCC was influenced by the DOC source. Our results highlight that a doubling of BGE is not necessarily accompanied by a shift in BCC and that BCC is more strongly affected by resource properties.}, language = {en} } @article{AttermeyerPremkeHornicketal.2013, author = {Attermeyer, Katrin and Premke, Katrin and Hornick, Thomas and Hilt, Sabine and Grossart, Hans-Peter}, title = {Ecosystem-level studies of terrestrial carbon reveal contrasting bacterial metabolism in different aquatic habitats}, series = {Ecology : a publication of the Ecological Society of America}, volume = {94}, journal = {Ecology : a publication of the Ecological Society of America}, number = {12}, publisher = {Wiley}, address = {Washington}, issn = {0012-9658}, doi = {10.1890/13-0420.1}, pages = {2754 -- 2766}, year = {2013}, abstract = {In aquatic systems, terrestrial dissolved organic matter (t-DOM) is known to stimulate bacterial activities in the water column, but simultaneous effects of autumnal leaf input on water column and sediment microbial dynamics in littoral zones of lakes remain largely unknown. The study's objective was to determine the effects of leaf litter on bacterial metabolism in the littoral water and sediment, and subsequently, the consequences for carbon cycling and food web dynamics. Therefore, in late fall, we simultaneously measured water and sediment bacterial metabolism in the littoral zone of a temperate shallow lake after adding terrestrial particulate organic matter (t-POM), namely, maize leaves. To better evaluate bacterial production (BP) and community respiration (CR) in sediments, we incubated sediment cores with maize leaves of different quality (nonleached and leached) under controlled laboratory conditions. Additionally, to quantify the incorporated leaf carbon into microbial biomass, we determined carbon isotopic ratios of fatty acids from sediment and leaf-associated microbes from a laboratory experiment using C-13-enriched beech leaves. The concentrations of dissolved organic carbon (DOC) increased significantly in the lake after the addition of maize leaves, accompanied by a significant increase in water BP. In contrast, sediment BP declined after an initial peak, showing no positive response to t-POM addition. Sediment BP and CR were also not stimulated by t-POM in the laboratory experiment, either in short-term or in long-term incubations, except for a short increase in CR after 18 hours. However, this increase might have reflected the metabolism of leaf-associated microorganisms. We conclude that the leached t-DOM is actively incorporated into microbial biomass in the water column but that the settling leached t-POM (t-POML) does not enter the food web via sediment bacteria. Consequently, t-POML is either buried in the sediment or introduced into the aquatic food web via microorganisms (bacteria and fungi) directly associated with t-POML and via benthic macroinvertebrates by shredding of t-POML. The latter pathway represents a benthic shortcut which efficiently transfers t-POML to higher trophic levels.}, language = {en} } @article{AttermeyerHornickKayleretal.2014, author = {Attermeyer, Katrin and Hornick, T. and Kayler, Zachary and Bahr, A. and Zwirnmann, E. and Grossart, Hans-Peter and Premke, K.}, title = {Enhanced bacterial decomposition with increasing addition of autochthonous to allochthonous carbon without any effect on bacterial community composition}, series = {Biogeosciences}, volume = {11}, journal = {Biogeosciences}, number = {6}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1726-4170}, doi = {10.5194/bg-11-1479-2014}, pages = {1479 -- 1489}, year = {2014}, abstract = {Dissolved organic carbon (DOC) concentrations - mainly of terrestrial origin - are increasing worldwide in inland waters. Heterotrophic bacteria are the main consumers of DOC and thus determine DOC temporal dynamics and availability for higher trophic levels. Our aim was to study bacterial carbon (C) turnover with respect to DOC quantity and chemical quality using both allochthonous and autochthonous DOC sources. We incubated a natural bacterial community with allochthonous C (C-13-labeled beech leachate) and increased concentrations and pulses (intermittent occurrence of organic matter input) of autochthonous C (phytoplankton lysate). We then determined bacterial C consumption, activities, and community composition together with the C flow through bacteria using stable C isotopes. The chemical analysis of single sources revealed differences in aromaticity and low-and high-molecular-weight substance fractions (LMWS and HMWS, respectively) between allochthonous and autochthonous C sources. Both DOC sources (allochthonous and autochthonous DOC) were metabolized at a high bacterial growth efficiency (BGE) around 50\%. In treatments with mixed sources, rising concentrations of added autochthonous DOC resulted in a further, significant increase in bacterial DOC consumption of up to 68\% when nutrients were not limiting. This rise was accompanied by a decrease in the humic substance (HS) fraction and an increase in bacterial biomass. Changes in DOC concentration and consumption in mixed treatments did not affect bacterial community composition (BCC), but BCC differed in single vs. mixed incubations. Our study highlights that DOC quantity affects bacterial C consumption but not BCC in nutrient-rich aquatic systems. BCC shifted when a mixture of allochthonous and autochthonous C was provided simultaneously to the bacterial community. Our results indicate that chemical quality rather than source of DOC per se (allochthonous vs. autochthonous) determines bacterial DOC turnover.}, language = {en} } @article{AttermeyerGrossartFluryetal.2017, author = {Attermeyer, Katrin and Grossart, Hans-Peter and Flury, Sabine and Premke, Katrin}, title = {Bacterial processes and biogeochemical changes in the water body of kettle holes - mainly driven by autochthonous organic matter?}, series = {Aquatic sciences : research across boundaries}, volume = {79}, journal = {Aquatic sciences : research across boundaries}, publisher = {Springer}, address = {Basel}, issn = {1015-1621}, doi = {10.1007/s00027-017-0528-1}, pages = {675 -- 687}, year = {2017}, abstract = {Kettle holes are small inland waters formed from glacially-created depressions often situated in agricultural landscapes. Due to their high perimeter-to-area ratio facilitating a high aquatic-terrestrial coupling, kettle holes can accumulate high concentrations of organic carbon and nutrients, fueling microbial activities and turnover rates. Thus, they represent hotspots of carbon turnover in the landscape, but their bacterial activities and controlling factors have not been well investigated. Therefore, we aimed to assess the relative importance of various environmental factors on bacterial and biogeochemical processes in the water column of kettle holes and to disentangle their variations. In the water body of ten kettle holes in north-eastern Germany, we measured several physico-chemical and biological parameters such as carbon quantity and quality, as well as bacterial protein production (BP) and community respiration (CR) in spring, early summer and autumn 2014. Particulate organic matter served as an indicator of autochthonous production and represented an important parameter to explain variations in BP and CR. This notion is supported by qualitative absorbance indices of dissolved molecules in water samples and C: N ratios of the sediments, which demonstrate high fractions of autochthonous organic matter (OM) in the studied kettle holes. In contrast, dissolved chemical parameters were less important for bacterial activities although they revealed strong differences throughout the growing season. Pelagic bacterial activities and dynamics might thus be regulated by autochthonous OM in kettle holes implying a control of important biogeochemical processes by internal primary production rather than facilitated exchange with the terrestrial surrounding due to a high perimeter-to-area ratio.}, language = {en} } @phdthesis{Attermeyer2013, author = {Attermeyer, Katrin}, title = {Effects of allochthonous organic carbon on bacterial metabolism and community structure, and consequences for carbon cycling in smal, shallow lakes}, address = {Potsdam}, pages = {182 S.}, year = {2013}, language = {en} } @phdthesis{Athikomrattanakul2011, author = {Athikomrattanakul, Umporn}, title = {Development and characterization of molecularly imprinted polymers as binding elements against nitrofurantoin}, address = {Potsdam}, pages = {97 S.}, year = {2011}, language = {en} } @article{AstMuellerFlehretal.2011, author = {Ast, Sandra and M{\"u}ller, Holger and Flehr, Roman and Klamroth, Tillmann and Walz, Bernd and Holdt, Hans-J{\"u}rgen}, title = {High Na+ and K+-induced fluorescence enhancement of a pi-conjugated phenylaza-18-crown-6-triazol-substituted coumarin fluoroionophore}, series = {Chemical communications}, volume = {47}, journal = {Chemical communications}, number = {16}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1359-7345}, doi = {10.1039/c0cc04370b}, pages = {4685 -- 4687}, year = {2011}, abstract = {The new pi-conjugated 1,2,3-triazol-1,4-diyl fluoroionophore 1 generated via Cu(I) catalyzed [3 + 2] cycloaddition shows high fluorescence enhancement factors (FEF) in the presence of Na+ (FEF = 58) and K+ (FEF = 27) in MeCN and high selectivity towards K+ under simulated physiological conditions (160 mM K+ or Na+, respectively) with a FEF of 2.5 for K+.}, language = {en} } @article{AschenbrennerWalz1998, author = {Aschenbrenner, Stefan and Walz, Bernd}, title = {Pleated septate junctions in leech photoreceptors : ultrastructure, arrangement of septa, gate and fence functions}, year = {1998}, language = {en} } @article{ArvidssonPerezRodriguezMuellerRoeber2011, author = {Arvidsson, Samuel Janne and Perez-Rodriguez, Paulino and M{\"u}ller-R{\"o}ber, Bernd}, title = {A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects}, series = {New phytologist : international journal of plant science}, volume = {191}, journal = {New phytologist : international journal of plant science}, number = {3}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0028-646X}, doi = {10.1111/j.1469-8137.2011.03756.x}, pages = {895 -- 907}, year = {2011}, abstract = {To gain a deeper understanding of the mechanisms behind biomass accumulation, it is important to study plant growth behavior. Manually phenotyping large sets of plants requires important human resources and expertise and is typically not feasible for detection of weak growth phenotypes. Here, we established an automated growth phenotyping pipeline for Arabidopsis thaliana to aid researchers in comparing growth behaviors of different genotypes. The analysis pipeline includes automated image analysis of two-dimensional digital plant images and evaluation of manually annotated information of growth stages. It employs linear mixed-effects models to quantify genotype effects on total rosette area and relative leaf growth rate (RLGR) and ANOVAs to quantify effects on developmental times. Using the system, a single researcher can phenotype up to 7000 plants d(-1). Technical variance is very low (typically < 2\%). We show quantitative results for the growth-impaired starch-excessmutant sex4-3 and the growth-enhancedmutant grf9. We show that recordings of environmental and developmental variables reduce noise levels in the phenotyping datasets significantly and that careful examination of predictor variables (such as d after sowing or germination) is crucial to avoid exaggerations of recorded phenotypes and thus biased conclusions.}, language = {en} } @phdthesis{Arvidsson2010, author = {Arvidsson, Samuel Janne}, title = {Identification of growth-related tonoplast proteins in Arabidopsis thaliana}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-52408}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {In a very simplified view, the plant leaf growth can be reduced to two processes, cell division and cell expansion, accompanied by expansion of their surrounding cell walls. The vacuole, as being the largest compartment of the plant cell, plays a major role in controlling the water balance of the plant. This is achieved by regulating the osmotic pressure, through import and export of solutes over the vacuolar membrane (the tonoplast) and by controlling the water channels, the aquaporins. Together with the control of cell wall relaxation, vacuolar osmotic pressure regulation is thought to play an important role in cell expansion, directly by providing cell volume and indirectly by providing ion and pH homestasis for the cytosoplasm. In this thesis the role of tonoplast protein coding genes in cell expansion in the model plant Arabidopsis thaliana is studied and genes which play a putative role in growth are identified. Since there is, to date, no clearly identified protein localization signal for the tonoplast, there is no possibility to perform genome-wide prediction of proteins localized to this compartment. Thus, a series of recent proteomic studies of the tonoplast were used to compile a list of cross-membrane tonoplast protein coding genes (117 genes), and other growth-related genes from notably the growth regulating factor (GRF) and expansin families were included (26 genes). For these genes a platform for high-throughput reverse transcription quantitative real time polymerase chain reaction (RT-qPCR) was developed by selecting specific primer pairs. To this end, a software tool (called QuantPrime, see http://www.quantprime.de) was developed that automatically designs such primers and tests their specificity in silico against whole transcriptomes and genomes, to avoid cross-hybridizations causing unspecific amplification. The RT-qPCR platform was used in an expression study in order to identify candidate growth related genes. Here, a growth-associative spatio-temporal leaf sampling strategy was used, targeting growing regions at high expansion developmental stages and comparing them to samples taken from non-expanding regions or stages of low expansion. Candidate growth related genes were identified after applying a template-based scoring analysis on the expression data, ranking the genes according to their association with leaf expansion. To analyze the functional involvement of these genes in leaf growth on a macroscopic scale, knockout mutants of the candidate growth related genes were screened for growth phenotypes. To this end, a system for non-invasive automated leaf growth phenotyping was established, based on a commercially available image capture and analysis system. A software package was developed for detailed developmental stage annotation of the images captured with the system, and an analysis pipeline was constructed for automated data pre-processing and statistical testing, including modeling and graph generation, for various growth-related phenotypes. Using this system, 24 knockout mutant lines were analyzed, and significant growth phenotypes were found for five different genes.}, language = {en} } @phdthesis{Artins2023, author = {Artins, Anthony}, title = {Crosstalk between Target Of Rapamycin (TOR) and sugar signaling in Arabidopsis thaliana}, school = {Universit{\"a}t Potsdam}, pages = {125}, year = {2023}, language = {en} } @phdthesis{Arsova2009, author = {Arsova, Borjana}, title = {Functional characterization of two fructokinase-like proteins that potentially integrate metabolic and redox signals to control plastid gene expression}, address = {Potsdam}, pages = {V, 117 S. : Ill., graph. Darst.}, year = {2009}, language = {en} } @phdthesis{Arrivault2005, author = {Arrivault, St{\´e}phanie}, title = {Functional characterization of Arabidopsis thaliana MTP3, a putative metal transport protein of the cation diffusion facilitator (CDF) family}, pages = {VII, 121 Bl. : Ill., graph. Darst.}, year = {2005}, language = {en} } @phdthesis{Arnold2014, author = {Arnold, Stefanie}, title = {Epitop-Kartierung von PBP2A und Identifizierung MRSA-spezifischer immunodominanter Peptidsequenzen}, pages = {XIX, 120}, year = {2014}, language = {de} } @article{ArnoldRutschmann2022, author = {Arnold, Patrick and Rutschmann, Sereina}, title = {UCE sequencing-derived mitogenomes reveal the timing of mitochondrial replacement in Malagasy shrew tenrecs (Afrosoricida, Tenrecidae, Microgale)}, series = {Mammalian biology = Zeitschrift f{\"u}r S{\"a}ugetierkunde}, volume = {102}, journal = {Mammalian biology = Zeitschrift f{\"u}r S{\"a}ugetierkunde}, number = {2}, publisher = {Springer}, address = {Heidelberg}, issn = {1616-5047}, doi = {10.1007/s42991-022-00246-2}, pages = {531 -- 536}, year = {2022}, abstract = {Malagasy shrew tenrecs (Microgale) have increasingly been used to study speciation genetics over the last years. A previous study recently uncovered gene flow between the Shrew-toothed shrew tenrec (M. soricoides) and sympatric southern population of the Pale shrew tenrec (M. fotsifotsy). This gene flow has been suggested to be accompanied by complete mitochondrial replacement in M. fotsifotsy. To explore the temporal framework of this replacement, we assembled mitogenomes from publicly available sequencing data of ultra-conserved elements. We were able to assemble complete and partial mitogenomes for 19 specimens from five species of shrew tenrecs, which represents a multifold increase in mitogenomic resources available for all tenrecs. Phylogenetic inferences and sequence simulations support the close relationship between the mitochondrial lineages of M. soricoides and the southern population of M. fotsifotsy. Based on the nuclear divergence of northern and southern populations of M. fotsifotsy and the mitochondrial divergence between the latter and M. soricoides, there was a mean time window for replacement of similar to 350,000 years. This timeframe implies that the effective size of the ancestral M. fotsifotsy southern population was less 70,000.}, language = {en} } @misc{Arnold2019, author = {Arnold, Patrick}, title = {The origin of morphological integration and modularity in the Mammalian Neck}, series = {Journal of morphology}, volume = {280}, journal = {Journal of morphology}, publisher = {Wiley}, address = {Hoboken}, issn = {0362-2525}, doi = {10.1002/jmor.21003}, pages = {S13 -- S13}, year = {2019}, language = {en} } @article{Arnold2020, author = {Arnold, Patrick}, title = {Evolution of the mammalian neck from developmental, morpho-functional, and paleontological perspectives}, series = {Journal of Mammalian Evolution}, volume = {28}, journal = {Journal of Mammalian Evolution}, number = {2}, publisher = {Springer}, address = {New York}, issn = {1064-7554}, doi = {10.1007/s10914-020-09506-9}, pages = {173 -- 183}, year = {2020}, abstract = {The mammalian neck adopts a variety of postures during daily life and generates numerous head trajectories. Despite its functional diversity, the neck is constrained to seven cervical vertebrae in (almost) all mammals. Given this low number, an unexpectedly high degree of modularity of the mammalian neck has more recently been uncovered. This work aims to review neck modularity in mammals from a developmental, morpho-functional, and paleontological perspective and how high functional diversity evolved in the mammalian neck after the occurrence of meristic limitations. The fixed number of cervical vertebrae and the developmental modularity of the mammalian neck are closely linked to anterior Hox genes expression and strong developmental integration between the neck and other body regions. In addition, basic neck biomechanics promote morpho-functional modularity due to preferred motion axes in the cranio-cervical and cervico-thoracic junction. These developmental and biomechanical determinants result in the characteristic and highly conserved shape variation among the vertebrae that delimits morphological modules. The step-wise acquisition of these unique cervical traits can be traced in the fossil record. The increasing functional specialization of neck modules, however, did not evolve all at once but started much earlier in the upper than in the lower neck. Overall, the strongly conserved modularity in the mammalian neck represents an evolutionary trade-off between the meristic constraints and functional diversity. Although a morpho-functional partition of the neck is common among amniotes, the degree of modularity and the way neck disparity is realized is unique in mammals.}, language = {en} } @article{ArnoldNikoloski2014, author = {Arnold, Anne and Nikoloski, Zoran}, title = {In search for an accurate model of the photosynthetic carbon metabolism}, series = {Mathematics and computers in simulation : transactions of IMACS}, volume = {96}, journal = {Mathematics and computers in simulation : transactions of IMACS}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-4754}, doi = {10.1016/j.matcom.2012.03.011}, pages = {171 -- 194}, year = {2014}, abstract = {The photosynthetic carbon metabolism, including the Calvin-Benson cycle, is the primary pathway in C-3-plants, producing starch and sucrose from CO2. Understanding the interplay between regulation and efficiency of this pathway requires the development of mathematical models which would explain the observed dynamics of metabolic transformations. Here, we address this question by casting the existing models of Calvin-Benson cycle and the end-product processes into an analysis framework which not only facilitates the comparison of the different models, but also allows for their ranking with respect to chosen criteria, including stability, sensitivity, robustness and/or compliance with experimental data. The importance of the photosynthetic carbon metabolism for the increase of plant biomass has resulted in many models with various levels of detail. We provide the largest compendium of 15 existing, well-investigated models together with a comprehensive classification as well as a ranking framework to determine the best-performing models for metabolic engineering and planning of in silica experiments. The classification can be additionally used, based on the model structure, as a tool to identify the models which match best the experimental design. The provided ranking is just one alternative to score models and, by changing the weighting factor, this framework also could be applied for selection of other criteria of interest.}, language = {en} } @misc{ArnoldNikoloski2011, author = {Arnold, Anne and Nikoloski, Zoran}, title = {A quantitative comparison of Calvin-Benson cycle models}, series = {Trends in plant science}, volume = {16}, journal = {Trends in plant science}, number = {12}, publisher = {Elsevier}, address = {London}, issn = {1360-1385}, doi = {10.1016/j.tplants.2011.09.004}, pages = {676 -- 683}, year = {2011}, abstract = {The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering.}, language = {en} } @phdthesis{Arnold2014, author = {Arnold, Anne}, title = {Modeling photosynthesis and related metabolic processes : from detailed examination to consideration of the metabolic context}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72277}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Mathematical modeling of biological systems is a powerful tool to systematically investigate the functions of biological processes and their relationship with the environment. To obtain accurate and biologically interpretable predictions, a modeling framework has to be devised whose assumptions best approximate the examined scenario and which copes with the trade-off of complexity of the underlying mathematical description: with attention to detail or high coverage. Correspondingly, the system can be examined in detail on a smaller scale or in a simplified manner on a larger scale. In this thesis, the role of photosynthesis and its related biochemical processes in the context of plant metabolism was dissected by employing modeling approaches ranging from kinetic to stoichiometric models. The Calvin-Benson cycle, as primary pathway of carbon fixation in C3 plants, is the initial step for producing starch and sucrose, necessary for plant growth. Based on an integrative analysis for model ranking applied on the largest compendium of (kinetic) models for the Calvin-Benson cycle, those suitable for development of metabolic engineering strategies were identified. Driven by the question why starch rather than sucrose is the predominant transitory carbon storage in higher plants, the metabolic costs for their synthesis were examined. The incorporation of the maintenance costs for the involved enzymes provided a model-based support for the preference of starch as transitory carbon storage, by only exploiting the stoichiometry of synthesis pathways. Many photosynthetic organisms have to cope with processes which compete with carbon fixation, such as photorespiration whose impact on plant metabolism is still controversial. A systematic model-oriented review provided a detailed assessment for the role of this pathway in inhibiting the rate of carbon fixation, bridging carbon and nitrogen metabolism, shaping the C1 metabolism, and influencing redox signal transduction. The demand of understanding photosynthesis in its metabolic context calls for the examination of the related processes of the primary carbon metabolism. To this end, the Arabidopsis core model was assembled via a bottom-up approach. This large-scale model can be used to simulate photoautotrophic biomass production, as an indicator for plant growth, under so-called optimal, carbon-limiting and nitrogen-limiting growth conditions. Finally, the introduced model was employed to investigate the effects of the environment, in particular, nitrogen, carbon and energy sources, on the metabolic behavior. This resulted in a purely stoichiometry-based explanation for the experimental evidence for preferred simultaneous acquisition of nitrogen in both forms, as nitrate and ammonium, for optimal growth in various plant species. The findings presented in this thesis provide new insights into plant system's behavior, further support existing opinions for which mounting experimental evidences arise, and posit novel hypotheses for further directed large-scale experiments.}, language = {en} } @misc{ArnisonBibbBierbaumetal.2013, author = {Arnison, Paul G. and Bibb, Mervyn J. and Bierbaum, Gabriele and Bowers, Albert A. and Bugni, Tim S. and Bulaj, Grzegorz and Camarero, Julio A. and Campopiano, Dominic J. and Challis, Gregory L. and Clardy, Jon and Cotter, Paul D. and Craik, David J. and Dawson, Michael and Dittmann-Th{\"u}nemann, Elke and Donadio, Stefano and Dorrestein, Pieter C. and Entian, Karl-Dieter and Fischbach, Michael A. and Garavelli, John S. and Goeransson, Ulf and Gruber, Christian W. and Haft, Daniel H. and Hemscheidt, Thomas K. and Hertweck, Christian and Hill, Colin and Horswill, Alexander R. and Jaspars, Marcel and Kelly, Wendy L. and Klinman, Judith P. and Kuipers, Oscar P. and Link, A. James and Liu, Wen and Marahiel, Mohamed A. and Mitchell, Douglas A. and Moll, Gert N. and Moore, Bradley S. and Mueller, Rolf and Nair, Satish K. and Nes, Ingolf F. and Norris, Gillian E. and Olivera, Baldomero M. and Onaka, Hiroyasu and Patchett, Mark L. and Piel, J{\"o}rn and Reaney, Martin J. T. and Rebuffat, Sylvie and Ross, R. Paul and Sahl, Hans-Georg and Schmidt, Eric W. and Selsted, Michael E. and Severinov, Konstantin and Shen, Ben and Sivonen, Kaarina and Smith, Leif and Stein, Torsten and Suessmuth, Roderich D. and Tagg, John R. and Tang, Gong-Li and Truman, Andrew W. and Vederas, John C. and Walsh, Christopher T. and Walton, Jonathan D. and Wenzel, Silke C. and Willey, Joanne M. and van der Donk, Wilfred A.}, title = {Ribosomally synthesized and post-translationally modified peptide natural products overview and recommendations for a universal nomenclature}, series = {Natural product reports : a journal of current developments in bio-organic chemistry}, volume = {30}, journal = {Natural product reports : a journal of current developments in bio-organic chemistry}, number = {1}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {0265-0568}, doi = {10.1039/c2np20085f}, pages = {108 -- 160}, year = {2013}, abstract = {This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.}, language = {en} } @book{Arndt2010, author = {Arndt, Katja Maren}, title = {Proteine zur Krebstherapie - Zielen, Steuern, Hemmen : Antrittsvorlesung 2010-12-08}, publisher = {Univ.-Bibl.}, address = {Potsdam}, year = {2010}, abstract = {Biotechnologie, Biologie, Protein Engineering, Therapeutische Peptide, Protein Design, Selektionssysteme / biotechnology, biology, protein enginieering, therapeutic peptides, protein design, selection systems}, language = {de} } @phdthesis{ArmaregoMarriott2016, author = {Armarego-Marriott, Tegan}, title = {From dark to light}, school = {Universit{\"a}t Potsdam}, pages = {158}, year = {2016}, language = {en} } @misc{ArltSchwiebsJaptoketal.2014, author = {Arlt, Olga and Schwiebs, Anja and Japtok, Lukasz and Rueger, Katja and Katzy, Elisabeth and Kleuser, Burkhard and Radeke, Heinfried H.}, title = {Sphingosine-1-Phosphate modulates dendritic cell function: focus on non-migratory effects in vitro and in vivo}, series = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, volume = {34}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, number = {1}, publisher = {Karger}, address = {Basel}, issn = {1015-8987}, doi = {10.1159/000362982}, pages = {27 -- 44}, year = {2014}, abstract = {Dendritic cells (DCs) are the cutting edge in innate and adaptive immunity. The major functions of these antigen presenting cells are the capture, endosomal processing and presentation of antigens, providing them an exclusive ability to provoke adaptive immune responses and to induce and control tolerance. Immature DCs capture and process antigens, migrate towards secondary lymphoid organs where they present antigens to naive T cells in a well synchronized sequence of procedures referred to as maturation. Indeed, recent research indicated that sphingolipids are modulators of essential steps in DC homeostasis. It has been recognized that sphingolipids not only modulate the development of DC subtypes from precursor cells but also influence functional activities of DCs such as antigen capture, and cytokine profiling. Thus, it is not astonishing that sphingolipids and sphingolipid metabolism play a substantial role in inflammatory diseases that are modulated by DCs. Here we highlight the function of sphingosine 1-phosphate (S1P) on DC homeostasis and the role of SIP and SW metabolism in inflammatory diseases.}, language = {en} } @phdthesis{Arlt2007, author = {Arlt, Matthias}, title = {Studien zur Initiation, Ausbreitung und {\"U}bertragbarkeit verschiedener Varianten von posttranskriptionellem Transgensilencing anhand molekularer Charakteristika in Arabidopsis thaliana}, address = {Potsdam}, pages = {VIII, 159 S. : graph. Darst.}, year = {2007}, language = {de} } @misc{AriasAndresRojasJimenezGrossart2018, author = {Arias-Andres, Maria and Rojas-Jimenez, Keilor and Grossart, Hans-Peter}, title = {Collateral effects of microplastic pollution on aquatic microorganisms}, series = {Trends in Analytical Chemistry}, volume = {112}, journal = {Trends in Analytical Chemistry}, publisher = {Elsevier}, address = {Oxford}, issn = {0165-9936}, doi = {10.1016/j.trac.2018.11.041}, pages = {234 -- 240}, year = {2018}, abstract = {Microplastics (MP) provide a unique and extensive surface for microbial colonization in aquatic ecosystems. The formation of microorganism-microplastic complexes, such as biofilms, maximizes the degradation of organic matter and horizontal gene transfer. In this context, MP affect the structure and function of microbial communities, which in turn render the physical and chemical fate of MP. This new paradigm generates challenges for microbiology, ecology, and ecotoxicology. Dispersal of MP is concomitant with that of their associated microorganisms and their mobile genetic elements, including antibiotic resistance genes, islands of pathogenicity, and diverse metabolic pathways. Functional changes in aquatic microbiomes can alter carbon metabolism and food webs, with unknown consequences on higher organisms or human microbiomes and hence health. Here, we examine a variety of effects of MP pollution from the microbial ecology perspective, whose repercussions on aquatic ecosystems begin to be unraveled. (C) 2018 Elsevier B.V. All rights reserved.}, language = {en} } @article{AriasAndresKluemperRojasJimenezetal.2018, author = {Arias-Andres, Maria and Kluemper, Uli and Rojas-Jimenez, Keilor and Grossart, Hans-Peter}, title = {Microplastic pollution increases gene exchange in aquatic ecosystems}, series = {Environmental pollution}, volume = {237}, journal = {Environmental pollution}, publisher = {Elsevier}, address = {Oxford}, issn = {0269-7491}, doi = {10.1016/j.envpol.2018.02.058}, pages = {253 -- 261}, year = {2018}, abstract = {Pollution by microplastics in aquatic ecosystems is accumulating at an unprecedented scale, emerging as a new surface for biofilm formation and gene exchange. In this study, we determined the permissiveness of aquatic bacteria towards a model antibiotic resistance plasmid, comparing communities that form biofilms on microplastics vs. those that are free-living. We used an exogenous and red-fluorescent E. coli donor strain to introduce the green-fluorescent broad-host-range plasmid pKJKS which encodes for trimethoprim resistance. We demonstrate an increased frequency of plasmid transfer in bacteria associated with microplastics compared to bacteria that are free-living or in natural aggregates. Moreover, comparison of communities grown on polycarbonate filters showed that increased gene exchange occurs in a broad range of phylogenetically-diverse bacteria. Our results indicate horizontal gene transfer in this habitat could distinctly affect the ecology of aquatic microbial communities on a global scale. The spread of antibiotic resistance through microplastics could also have profound consequences for the evolution of aquatic bacteria and poses a neglected hazard for human health.}, language = {en} } @article{AriasAndresKettnerMikietal.2018, author = {Arias Andr{\´e}s, Mar{\´i}a de Jes{\´u}s and Kettner, Marie Therese and Miki, Takeshi and Grossart, Hans-Peter}, title = {Microplastics: New substrates for heterotrophic activity contribute to altering organic matter cycles in aquatic ecosystems}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {635}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2018.04.199}, pages = {1152 -- 1159}, year = {2018}, abstract = {Heterotrophic microbes with the capability to process considerable amounts of organic matter can colonize microplastic particles (MP) in aquatic ecosystems. Weather colonization of microorganisms on MP will alter ecological niche and functioning of microbial communities remains still unanswered. Therefore, we compared the functional diversity of biofilms on microplastics when incubated in three lakes in northeastern Germany differing in trophy and limnological features. For all lakes, we compared heterotrophic activities of MP biofilms with those of microorganisms in the surrounding water by using Biolog (R) EcoPlates and assessed their oxygen consumption in microcosm assays with and without MP. The present study found that the total biofilm biomass was higher in the oligo-mesotrophic and dystrophic lakes than in the eutrophic lake. In all lakes, functional diversity profiles of MP biofilms consistently differed from those in the surrounding water. However, solely in the oligo-mesotrophic lake MP biofilms had a higher functional richness compared to the ambient water. These results demonstrate that the functionality and hence the ecological role of MP-associated microbial communities are context-dependent, i.e. different environments lead to substantial changes in biomass build up and heterotrophic activities of MP biofilms. We propose that MP surfaces act as new niches for aquatic microorganisms and that the constantly increasing MP pollution has the potential to globally impact carbon dynamics of pelagic environments by altering heterotrophic activities. (C) 2018 Elsevier B.V. All rights reserved.}, language = {en} } @phdthesis{AriasAndres2018, author = {Arias Andr{\´e}s, Mar{\´i}a de Jes{\´u}s}, title = {Microbial gene exchange on microplastic particles}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-417241}, school = {Universit{\"a}t Potsdam}, pages = {94}, year = {2018}, abstract = {Plastic pollution is ubiquitous on the planet since several millions of tons of plastic waste enter aquatic ecosystems each year. Furthermore, the amount of plastic produced is expected to increase exponentially shortly. The heterogeneity of materials, additives and physical characteristics of plastics are typical of these emerging contaminants and affect their environmental fate in marine and freshwaters. Consequently, plastics can be found in the water column, sediments or littoral habitats of all aquatic ecosystems. Most of this plastic debris will fragment as a product of physical, chemical and biological forces, producing particles of small size. These particles (< 5mm) are known as "microplastics" (MP). Given their high surface-to-volume ratio, MP stimulate biofouling and the formation of biofilms in aquatic systems. As a result of their unique structure and composition, the microbial communities in MP biofilms are referred to as the "Plastisphere." While there is increasing data regarding the distinctive composition and structure of the microbial communities that form part of the plastisphere, scarce information exists regarding the activity of microorganisms in MP biofilms. This surface-attached lifestyle is often associated with the increase in horizontal gene transfer (HGT) among bacteria. Therefore, this type of microbial activity represents a relevant function worth to be analyzed in MP biofilms. The horizontal exchange of mobile genetic elements (MGEs) is an essential feature of bacteria. It accounts for the rapid evolution of these prokaryotes and their adaptation to a wide variety of environments. The process of HGT is also crucial for spreading antibiotic resistance and for the evolution of pathogens, as many MGEs are known to contain antibiotic resistance genes (ARGs) and genetic determinants of pathogenicity. In general, the research presented in this Ph.D. thesis focuses on the analysis of HGT and heterotrophic activity in MP biofilms in aquatic ecosystems. The primary objective was to analyze the potential of gene exchange between MP bacterial communities vs. that of the surrounding water, including bacteria from natural aggregates. Moreover, the thesis addressed the potential of MP biofilms for the proliferation of biohazardous bacteria and MGEs from wastewater treatment plants (WWTPs) and associated with antibiotic resistance. Finally, it seeks to prove if the physiological profile of MP biofilms under different limnological conditions is divergent from that of the water communities. Accordingly, the thesis is composed of three independent studies published in peer-reviewed journals. The two laboratory studies were performed using both model and environmental microbial communities. In the field experiment, natural communities from freshwater ecosystems were examined. In Chapter I, the inflow of treated wastewater into a temperate lake was simulated with a concentration gradient of MP particles. The effects of MP on the microbial community structure and the occurrence of integrase 1 (int 1) were followed. The int 1 is a marker associated with mobile genetic elements and known as a proxy for anthropogenic effects on the spread of antimicrobial resistance genes. During the experiment, the abundance of int1 increased in the plastisphere with increasing MP particle concentration, but not in the surrounding water. In addition, the microbial community on MP was more similar to the original wastewater community with increasing microplastic concentrations. Our results show that microplastic particles indeed promote persistence of standard indicators of microbial anthropogenic pollution in natural waters. In Chapter II, the experiments aimed to compare the permissiveness of aquatic bacteria towards model antibiotic resistance plasmid pKJK5, between communities that form biofilms on MP vs. those that are free-living. The frequency of plasmid transfer in bacteria associated with MP was higher when compared to bacteria that are free-living or in natural aggregates. Moreover, comparison increased gene exchange occurred in a broad range of phylogenetically-diverse bacteria. The results indicate a different activity of HGT in MP biofilms, which could affect the ecology of aquatic microbial communities on a global scale and the spread of antibiotic resistance. Finally, in Chapter III, physiological measurements were performed to assess whether microorganisms on MP had a different functional diversity from those in water. General heterotrophic activity such as oxygen consumption was compared in microcosm assays with and without MP, while diversity and richness of heterotrophic activities were calculated by using Biolog® EcoPlates. Three lakes with different nutrient statuses presented differences in MP-associated biomass build up. Functional diversity profiles of MP biofilms in all lakes differed from those of the communities in the surrounding water, but only in the oligo-mesotrophic lake MP biofilms had a higher functional richness compared to the ambient water. The results support that MP surfaces act as new niches for aquatic microorganisms and can affect global carbon dynamics of pelagic environments. Overall, the experimental works presented in Chapters I and II support a scenario where MP pollution affects HGT dynamics among aquatic bacteria. Among the consequences of this alteration is an increase in the mobilization and transfer efficiency of ARGs. Moreover, it supposes that changes in HGT can affect the evolution of bacteria and the processing of organic matter, leading to different catabolic profiles such as demonstrated in Chapter III. The results are discussed in the context of the fate and magnitude of plastic pollution and the importance of HGT for bacterial evolution and the microbial loop, i.e., at the base of aquatic food webs. The thesis supports a relevant role of MP biofilm communities for the changes observed in the aquatic microbiome as a product of intense human intervention.}, language = {en} } @article{ArendZimmerXuetal.2023, author = {Arend, Marius and Zimmer, David and Xu, Rudan and Sommer, Frederik and M{\"u}hlhaus, Timo and Nikoloski, Zoran}, title = {Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale}, series = {Nature Communications}, volume = {14}, journal = {Nature Communications}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-023-40498-1}, pages = {9}, year = {2023}, abstract = {Metabolic engineering of microalgae offers a promising solution for sustainable biofuel production, and rational design of engineering strategies can be improved by employing metabolic models that integrate enzyme turnover numbers. However, the coverage of turnover numbers for Chlamydomonas reinhardtii, a model eukaryotic microalga accessible to metabolic engineering, is 17-fold smaller compared to the heterotrophic cell factory Saccharomyces cerevisiae. Here we generate quantitative protein abundance data of Chlamydomonas covering 2337 to 3708 proteins in various growth conditions to estimate in vivo maximum apparent turnover numbers. Using constrained-based modeling we provide proxies for in vivo turnover numbers of 568 reactions, representing a 10-fold increase over the in vitro data for Chlamydomonas. Integration of the in vivo estimates instead of in vitro values in a metabolic model of Chlamydomonas improved the accuracy of enzyme usage predictions. Our results help in extending the knowledge on uncharacterized enzymes and improve biotechnological applications of Chlamydomonas.}, language = {en} } @article{ArbeiterTegetmeyer2011, author = {Arbeiter, Susanne and Tegetmeyer, Cosima}, title = {Home range and habitat use by aquatic warblers acrocephalus paludicola on their wintering grounds in Northwestern Senegal}, series = {Acta ornithologica}, volume = {46}, journal = {Acta ornithologica}, number = {2}, publisher = {Museum and Institute of Zoology, Polish Academy of Sciences}, address = {Warsaw}, issn = {0001-6454}, doi = {10.3161/000164511X625883}, pages = {117 -- 126}, year = {2011}, abstract = {The Aquatic Warbler Acrocephalus paludicola was once a common breeding bird in mesotrophic fen mires all over Central and Western Europe. In the last century large parts of its habitat have been destroyed by wetland drainage and agricultural intensification. Besides protecting the remaining breeding habitats, it is of great importance to preserve suitable migration stopover habitats and wintering grounds to avert the extinction of the species. We determined home-range size and the use of vegetation associations of Aquatic Warblers on the wintering grounds in a flooded plain north of the Djoudj National Park in Senegal. Individual birds (11) were caught in mist nets and equipped with radio transmitters. Locations were assessed by radiotelemetry and a compositional analysis was conducted to determine which vegetation types were preferred within home ranges. Similar to their behaviour on the breeding grounds, the Aquatic Warblers showed no territorial behaviour in their winter quarters. They used home ranges that averaged 4 ha in size, which they shared with conspecifics and other warblers. The home ranges overlapped 54\% on average, with a maximum of 90\% in an area used by four individuals. The vegetation structure of the wintering habitat is similar to breeding grounds and stopover sites of the species. Preferential vegetation had 80\% to 100\% cover and consisted of 60 to 90 cm high stands of Oryza longistaminata, Scirpus maritimus or Eleocharis mutata. Most birds stayed more often near the edge of open water, probably for foraging. A constant inundation seems essential, because Aquatic Warblers never occurred in desiccated parts of the study site.}, language = {en} } @article{AraujoNunesNesiNikoloskietal.2012, author = {Araujo, Wagner L. and Nunes-Nesi, Adriano and Nikoloski, Zoran and Sweetlove, Lee J. and Fernie, Alisdair R.}, title = {Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues}, series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, volume = {35}, journal = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0140-7791}, doi = {10.1111/j.1365-3040.2011.02332.x}, pages = {1 -- 21}, year = {2012}, abstract = {The tricarboxylic acid (TCA) cycle is a crucial component of respiratory metabolism in both photosynthetic and heterotrophic plant organs. All of the major genes of the tomato TCA cycle have been cloned recently, allowing the generation of a suite of transgenic plants in which the majority of the enzymes in the pathway are progressively decreased. Investigations of these plants have provided an almost complete view of the distribution of control in this important pathway. Our studies suggest that citrate synthase, aconitase, isocitrate dehydrogenase, succinyl CoA ligase, succinate dehydrogenase, fumarase and malate dehydrogenase have control coefficients flux for respiration of -0.4, 0.964, -0.123, 0.0008, 0.289, 0.601 and 1.76, respectively; while 2-oxoglutarate dehydrogenase is estimated to have a control coefficient of 0.786 in potato tubers. These results thus indicate that the control of this pathway is distributed among malate dehydrogenase, aconitase, fumarase, succinate dehydrogenase and 2-oxoglutarate dehydrogenase. The unusual distribution of control estimated here is consistent with specific non-cyclic flux mode and cytosolic bypasses that operate in illuminated leaves. These observations are discussed in the context of known regulatory properties of the enzymes and some illustrative examples of how the pathway responds to environmental change are given.}, language = {en} } @phdthesis{AranaCeballos2006, author = {Arana-Ceballos, Fernando Alberto}, title = {Biochemical and physiological studies of Arabidopsis thaliana Diacylglycerol Kinase 7 (AtDGK7)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-13729}, school = {Universit{\"a}t Potsdam}, year = {2006}, abstract = {A family of diacylglycerol kinases (DGK) phosphorylates the substrate diacylglycerol (DAG) to generate phosphatidic acid (PA) . Both molecules, DAG and PA, are involved in signal transduction pathways. In the model plant Arabidopsis thaliana, seven candidate genes (named AtDGK1 to AtDGK7) code for putative DGK isoforms. Here I report the molecular cloning and characterization of AtDGK7. Biochemical, molecular and physiological experiments of AtDGK7 and their corresponding enzyme are analyzed. Information from Genevestigator says that AtDGK7 gene is expressed in seedlings and adult Arabidopsis plants, especially in flowers. The AtDGK7 gene encodes the smallest functional DGK predicted in higher plants; but also, has an alternative coding sequence containing an extended AtDGK7 open reading frame, confirmed by PCR and submitted to the GenBank database (under the accession number DQ350135). The new cDNA has an extension of 439 nucleotides coding for 118 additional amino acids The former AtDGK7 enzyme has a predicted molecular mass of ~41 kDa and its activity is affected by pH and detergents. The DGK inhibitor R59022 also affects AtDGK7 activity, although at higher concentrations (i.e. IC50 ~380 µM). The AtDGK7 enzyme also shows a Michaelis-Menten type saturation curve for 1,2-DOG. Calculated Km and Vmax were 36 µM 1,2-DOG and 0.18 pmol PA min-1 mg of protein-1, respectively, under the assay conditions. Former protein AtDGK7 are able to phosphorylate different DAG analogs that are typically found in plants. The new deduced AtDGK7 protein harbors the catalytic DGKc and accessory domains DGKa, instead the truncated one as the former AtDGK7 protein (Gomez-Merino et al., 2005).}, language = {en} } @phdthesis{Arabi2015, author = {Arabi, Fayezeh}, title = {Functional characterization of Sulfur Deficiency Induced genes, SDI1 and SDI2, in Arabidopsis thaliana}, school = {Universit{\"a}t Potsdam}, pages = {97}, year = {2015}, language = {en} } @article{ApriyantoTambunan2021, author = {Apriyanto, Ardha and Tambunan, Van Basten}, title = {Draft genome sequence, annotation, and SSR mining data of Elaeidobius kamerunicus Faust., an essential oil palm pollinating weevil}, series = {Data in Brief}, volume = {34}, journal = {Data in Brief}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2352-3409}, doi = {10.1016/j.dib.2021.106745}, pages = {7}, year = {2021}, abstract = {Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) is an essential insect pollinator in oil palm plantations. Recently, researches have been undertaken to improve pollination efficiency using this species. A fundamental understanding of the genes related to this pollinator behavior is necessary to achieve this goal. Here, we present the draft genome sequence, annotation, and simple sequence repeat (SSR) marker data for this pollinator. In total, 34.97 Gb of sequence data from one male individual (monoisolate) were obtained using Illumina short-read platform NextSeq 500. The draft genome assembly was found to be 269.79 Mb and about 59.9\% of completeness based on Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment. Functional gene annotation predicted about 26.566 genes. Also, a total of 281.668 putative SSR markers were identified. This draft genome sequence is a valuable resource for understanding the population genetics, phylogenetics, dispersal patterns, and behavior of this species.}, language = {en} } @article{ApriyantoTambunan2020, author = {Apriyanto, Ardha and Tambunan, Van Basten}, title = {The complete mitochondrial genome of oil palm pollinating weevil, Elaeidobius kamerunicus Faust}, series = {Mitochondrial DNA: Part B}, volume = {5}, journal = {Mitochondrial DNA: Part B}, number = {3}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {2380-2359}, doi = {10.1080/23802359.2020.1823899}, pages = {3450 -- 3452}, year = {2020}, abstract = {Elaeidobius kamerunicusis the most important insect pollinator in oil palm plantations. In this study, the mitochondrial genome (mitogenome) ofE. kamerunicus(17.729 bp), a member of the Curculionidae family, will be reported. The mitogenome consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a putative control region (CR). Phylogenetic analysis based on 13 protein-coding genes (PCGs) using maximum Likelihood (ML) methods indicated thatE. kamerunicusbelongs to the Curculionidae family. This mitochondrial genome provides essential information for understanding genetic populations, phylogenetics, molecular evolution, and other biological applications in this species.}, language = {en} } @article{ApriyantoCompartZimmermannetal.2022, author = {Apriyanto, Ardha and Compart, Julia and Zimmermann, Vincent and Alseekh, Saleh and Fernie, Alisdair R. and Fettke, J{\"o}rg}, title = {Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.)}, series = {Food chemistry}, volume = {393}, journal = {Food chemistry}, publisher = {Elsevier}, address = {New York, NY [u.a.]}, issn = {0308-8146}, doi = {10.1016/j.foodchem.2022.133361}, pages = {11}, year = {2022}, abstract = {Oil palm (Elaeis guineensis Jacq.) is the most productive oil-producing crop per hectare of land. The oil that accumulates in the mesocarp tissue of the fruit is the highest observed among fruit-producing plants. A comparative analysis between high-, medium-, and low-yielding oil palms, particularly during fruit development, revealed unique characteristics. Metabolomics analysis was able to distinguish accumulation patterns defining of the various developmental stages and oil yield. Interestingly, high- and medium-yielding oil palms exhibited substantially increased sucrose levels compared to low-yielding palms. In addition, parameters such as starch granule morphology, granule size, total starch content, and starch chain length distribution (CLD) differed significantly among the oil yield categories with a clear correlation between oil yield and various starch parameters. These results provide new insights into carbohydrate and starch metabolism for biosynthesis of oil palm fruits, indicating that starch and sucrose can be used as novel, easy-to-analyze, and reliable biomarker for oil yield.}, language = {en} } @misc{ApriyantoCompartFettke2022, author = {Apriyanto, Ardha and Compart, Julia and Fettke, J{\"o}rg}, title = {A review of starch, a unique biopolymer - structure, metabolism and in planta modifications}, series = {Plant science : an international journal of experimental plant biology}, volume = {318}, journal = {Plant science : an international journal of experimental plant biology}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0168-9452}, doi = {10.1016/j.plantsci.2022.111223}, pages = {8}, year = {2022}, abstract = {Starch is a complex carbohydrate polymer produced by plants and especially by crops in huge amounts. It consists of amylose and amylopectin, which have alpha-1,4-and alpha-1,6-linked glucose units. Despite this simple chemistry, the entire starch metabolism is complex, containing various (iso)enzymes/proteins. However, whose interplay is still not yet fully understood. Starch is essential for humans and animals as a source of nutrition and energy. Nowadays, starch is also commonly used in non-food industrial sectors for a variety of purposes. However, native starches do not always satisfy the needs of a wide range of (industrial) applications. This review summarizes the structural properties of starch, analytical methods for starch characterization, and in planta starch modifications.}, language = {en} } @article{ApriyantoCompartFettke2023, author = {Apriyanto, Ardha and Compart, Julia and Fettke, J{\"o}rg}, title = {Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield}, series = {Frontiers in plant science}, volume = {14}, journal = {Frontiers in plant science}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2023.1220237}, pages = {13}, year = {2023}, abstract = {The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.}, language = {en} } @article{ApriyantoAjambang2022, author = {Apriyanto, Ardha and Ajambang, Walter}, title = {Transcriptomic dataset for early inflorescence stages of oil palm in response to defoliation stress}, series = {Data in Brief}, volume = {41}, journal = {Data in Brief}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2352-3409}, doi = {10.1016/j.dib.2022.107914}, pages = {6}, year = {2022}, abstract = {Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.}, language = {en} } @phdthesis{Apriyanto2023, author = {Apriyanto, Ardha}, title = {Analysis of starch metabolism in source and sink tissue of plants}, school = {Universit{\"a}t Potsdam}, pages = {166}, year = {2023}, abstract = {Starch is an essential biopolymer produced by plants. Starch can be made inside source tissue (such as leaves) and sink tissue (such as fruits and tubers). Nevertheless, understanding how starch metabolism is regulated in source and sink tissues is fundamental for improving crop production. Despite recent advances in the understanding of starch and its metabolism, there is still a knowledge gap in the source and sink metabolism. Therefore, this study aimed to summarize the state of the art regarding starch structure and metabolism inside plants. In addition, this study aimed to elucidate the regulation of starch metabolism in the source tissue using the leaves of a model organism, Arabidopsis thaliana, and the sink tissue of oil palm (Elaeis guineensis) fruit as a commercial crop. The research regarding the source tissue will focus on the effect of the blockage of starch degradation on the starch parameter in leaves, especially in those of A. thaliana, which lack both disproportionating enzyme 2 (DPE2) and plastidial glucan phosphorylase 1 (PHS1) (dpe2/phs1). The additional elimination of phosphoglucan water dikinase (PWD), starch excess 4 (SEX4), isoamylase 3 (ISA3), and disproportionating enzyme 1 (DPE1) in the dpe2/phs1 mutant background demonstrates the alteration of starch granule number per chloroplast. This study provides insights into the control mechanism of granule number regulation in the chloroplast. The research regarding the sink tissue will emphasize the relationship between starch metabolism and the lipid metabolism pathway in oil palm fruits. This study was conducted to observe the alteration of starch parameters, metabolite abundance, and gene expression during oil palm fruit development with different oil yields. This study shows that starch and sucrose can be used as biomarkers for oil yield in oil palms. In addition, it is revealed that the enzyme isoforms related to starch metabolism influence the oil production in oil palm fruit. Overall, this thesis presents novel information regarding starch metabolism in the source tissue of A.thaliana and the sink tissue of E.guineensis. The results shown in this thesis can be applied to many applications, such as modifying the starch parameter in other plants for specific needs.}, language = {en} }