TY - THES A1 - Arsova, Borjana T1 - Functional characterization of two fructokinase-like proteins that potentially integrate metabolic and redox signals to control plastid gene expression Y1 - 2009 CY - Potsdam ER - TY - THES A1 - Arrivault, Stéphanie T1 - Functional characterization of Arabidopsis thaliana MTP3, a putative metal transport protein of the cation diffusion facilitator (CDF) family Y1 - 2005 ER - TY - THES A1 - Arnold, Stefanie T1 - Epitop-Kartierung von PBP2A und Identifizierung MRSA-spezifischer immunodominanter Peptidsequenzen Y1 - 2014 ER - TY - JOUR A1 - Arnold, Patrick A1 - Rutschmann, Sereina T1 - UCE sequencing-derived mitogenomes reveal the timing of mitochondrial replacement in Malagasy shrew tenrecs (Afrosoricida, Tenrecidae, Microgale) JF - Mammalian biology = Zeitschrift für Säugetierkunde N2 - 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. KW - Microgale KW - Tenrecs KW - Gene flow KW - Mitochondrial replacement KW - Madagascar Y1 - 2022 U6 - https://doi.org/10.1007/s42991-022-00246-2 SN - 1616-5047 SN - 1618-1476 VL - 102 IS - 2 SP - 531 EP - 536 PB - Springer CY - Heidelberg ER - TY - GEN A1 - Arnold, Patrick T1 - The origin of morphological integration and modularity in the Mammalian Neck T2 - Journal of morphology Y1 - 2019 U6 - https://doi.org/10.1002/jmor.21003 SN - 0362-2525 SN - 1097-4687 VL - 280 SP - S13 EP - S13 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Arnold, Patrick T1 - Evolution of the mammalian neck from developmental, morpho-functional, and paleontological perspectives JF - Journal of Mammalian Evolution N2 - 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. KW - cervical spine KW - modularity KW - developmental constraints KW - mammalian body KW - plan KW - neck evolution Y1 - 2020 U6 - https://doi.org/10.1007/s10914-020-09506-9 SN - 1064-7554 SN - 1573-7055 VL - 28 IS - 2 SP - 173 EP - 183 PB - Springer CY - New York ER - TY - JOUR A1 - Arnold, Anne A1 - Nikoloski, Zoran T1 - In search for an accurate model of the photosynthetic carbon metabolism JF - Mathematics and computers in simulation : transactions of IMACS N2 - 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. KW - Calvin-Benson cycle KW - Carbon metabolism KW - Model ranking KW - Differential and algebraic equations Y1 - 2014 U6 - https://doi.org/10.1016/j.matcom.2012.03.011 SN - 0378-4754 SN - 1872-7166 VL - 96 SP - 171 EP - 194 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Arnold, Anne A1 - Nikoloski, Zoran T1 - A quantitative comparison of Calvin-Benson cycle models JF - Trends in plant science N2 - 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. Y1 - 2011 U6 - https://doi.org/10.1016/j.tplants.2011.09.004 SN - 1360-1385 VL - 16 IS - 12 SP - 676 EP - 683 PB - Elsevier CY - London ER - TY - THES A1 - Arnold, Anne T1 - Modeling photosynthesis and related metabolic processes : from detailed examination to consideration of the metabolic context T1 - Modellierung von Photosynthese und damit zusammenhängende metabolische Prozesse : von detaillierter Betrachtung hin zur Erörterung im metabolischen Kontext N2 - 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. N2 - Mathematische Modellierung biologischer Systeme eröffnet die Möglichkeit systematisch die Funktionsweise biologischer Prozesse und ihrer Wechselwirkungen mit der Umgebung zu untersuchen. Um präzise und biologisch relevante Vorhersagen treffen zu können, muss eine Modellierungsstrategie konzipiert werden, deren Annahmen das untersuchte Szenario bestmöglichst widerspiegelt und die dem Trade-off der Komplexität der zugrunde liegenden mathematischen Beschreibung gerecht wird: Detailtreue gegenüber Größe. Dementsprechend kann das System detailliert, in kleinerem Umfang oder in vereinfachter Darstellung im größeren Maßstab untersucht werden. In dieser Arbeit wird mittels verschiedener Modellierungsansätze, wie kinetischen und stöchiometrischen Modellen, die Rolle der Photosynthese und damit zusammenhängender biochemischer Prozesse im Rahmen des Pflanzenstoffwechsels analysiert. Der Calvin-Benson-Zyklus, als primärer Stoffwechselweg der Kohlenstofffixierung in C3-Pflanzen, ist der erste Schritt der Stärke- und Saccharoseproduktion, welche maßgeblich für das Wachstum von Pflanzen sind. Basierend auf einer integrativen Analyse zur Modellklassifizierung wurden aus der größten bekannten Sammlung von (kinetischen) Modellen des Calvin-Benson-Zyklus diejenigen ermittelt, die für die Entwicklung von Metabolic-Engineering-Strategien geeignet sind. Angeregt von der Fragestellung warum Kohlenstoff transitorisch vorwiegend in Form von Stärke anstatt Saccharose gespeichert wird, wurden die metabolischen Kosten beider Syntheseprozesse genauer betrachtet. Die Einbeziehung der Bereitstellungskosten der beteiligten Enzyme stützt die Tatsache, dass bevorzugt Stärke als temporärer Kohlenstoffspeicher dient. Die entprechende Untersuchung erfolgte einzig auf Grundlage der Stöchiometrie der Synthesewege. In vielen photosynthetisch-aktiven Organismen findet zudem Photorespiration statt, die der Kohlenstofffixierung entgegenwirkt. Die genaue Bedeutung der Photorespiration für den Pflanzenmetabolismus ist noch umstritten. Eine detaillierte Einschätzung der Rolle dieses Stoffwechselweges bezüglich der Inhibierung der Kohlenstofffixierungsrate, der Verknüpfung von Kohlenstoff- und Stickstoffmetabolismus, der Ausprägung des C1-Stoffwechsels sowie die Einflussnahme auf die Signaltransduktion wurde in einer modell-basierten, kritischen Analyse vorgenommen. Um die Photosynthese in ihrem metabolischen Kontext verstehen zu können, ist die Betrachtung der angrenzenden Prozesse des primären Kohlenstoffmetabolismus unverzichtbar. Hierzu wurde in einem Bottom-up Ansatz das Arabidopsis core Modell entworfen, mittels dessen die Biomasseproduktion, als Indikator für Pflanzenwachtum, unter photoautotrophen Bedingungen simuliert werden kann. Neben sogenannten optimalen Wachstumsbedingungen kann dieses großangelegte Modell auch kohlenstoff- und stickstofflimitierende Umweltbedingungen simulieren. Abschließend wurde das vorgestellte Modell zur Untersuchung von Umwelteinflüssen auf das Stoffwechselverhalten herangezogen, im speziellen verschiedene Stickstoff-, Kohlenstoff- und Energiequellen. Diese auschließlich auf der Stöchiometrie basierende Analyse bietet eine Erklärung für die bevorzugte, gleichzeitige Aufnahme von Nitrat und Ammonium, wie sie in verschiedenen Spezies für optimales Wachstum experimentell beobachtet wurde. Die Resultate dieser Arbeit liefern neue Einsichten in das Verhalten von pflanzlichen Systemen, stützen existierende Ansichten, für die zunehmend experimentelle Hinweise vorhanden sind, und postulieren neue Hypothesen für weiterführende großangelegte Experimente. KW - stöchiometrische Modellierung KW - kinetische Modellierung KW - metabolische Netzwerke KW - metabolische Kosten KW - Photosynthese KW - stoichiometric modeling KW - kinetic modeling KW - metabolic networks KW - metabolic costs KW - photosynthesis Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-72277 ER - TY - JOUR A1 - Arnison, Paul G. A1 - Bibb, Mervyn J. A1 - Bierbaum, Gabriele A1 - Bowers, Albert A. A1 - Bugni, Tim S. A1 - Bulaj, Grzegorz A1 - Camarero, Julio A. A1 - Campopiano, Dominic J. A1 - Challis, Gregory L. A1 - Clardy, Jon A1 - Cotter, Paul D. A1 - Craik, David J. A1 - Dawson, Michael A1 - Dittmann-Thünemann, Elke A1 - Donadio, Stefano A1 - Dorrestein, Pieter C. A1 - Entian, Karl-Dieter A1 - Fischbach, Michael A. A1 - Garavelli, John S. A1 - Goeransson, Ulf A1 - Gruber, Christian W. A1 - Haft, Daniel H. A1 - Hemscheidt, Thomas K. A1 - Hertweck, Christian A1 - Hill, Colin A1 - Horswill, Alexander R. A1 - Jaspars, Marcel A1 - Kelly, Wendy L. A1 - Klinman, Judith P. A1 - Kuipers, Oscar P. A1 - Link, A. James A1 - Liu, Wen A1 - Marahiel, Mohamed A. A1 - Mitchell, Douglas A. A1 - Moll, Gert N. A1 - Moore, Bradley S. A1 - Mueller, Rolf A1 - Nair, Satish K. A1 - Nes, Ingolf F. A1 - Norris, Gillian E. A1 - Olivera, Baldomero M. A1 - Onaka, Hiroyasu A1 - Patchett, Mark L. A1 - Piel, Jörn A1 - Reaney, Martin J. T. A1 - Rebuffat, Sylvie A1 - Ross, R. Paul A1 - Sahl, Hans-Georg A1 - Schmidt, Eric W. A1 - Selsted, Michael E. A1 - Severinov, Konstantin A1 - Shen, Ben A1 - Sivonen, Kaarina A1 - Smith, Leif A1 - Stein, Torsten A1 - Suessmuth, Roderich D. A1 - Tagg, John R. A1 - Tang, Gong-Li A1 - Truman, Andrew W. A1 - Vederas, John C. A1 - Walsh, Christopher T. A1 - Walton, Jonathan D. A1 - Wenzel, Silke C. A1 - Willey, Joanne M. A1 - van der Donk, Wilfred A. T1 - Ribosomally synthesized and post-translationally modified peptide natural products overview and recommendations for a universal nomenclature JF - Natural product reports : a journal of current developments in bio-organic chemistry N2 - 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. Y1 - 2013 U6 - https://doi.org/10.1039/c2np20085f SN - 0265-0568 VL - 30 IS - 1 SP - 108 EP - 160 PB - Royal Society of Chemistry CY - Cambridge ER - TY - BOOK A1 - Arndt, Katja Maren T1 - Proteine zur Krebstherapie - Zielen, Steuern, Hemmen : Antrittsvorlesung 2010-12-08 N2 - Biotechnologie, Biologie, Protein Engineering, Therapeutische Peptide, Protein Design, Selektionssysteme / biotechnology, biology, protein enginieering, therapeutic peptides, protein design, selection systems Y1 - 2010 UR - http://info.ub.uni-potsdam.de/multimedia/show_multimediafile.php?mediafile_id=239 PB - Univ.-Bibl. CY - Potsdam ER - TY - THES A1 - Armarego-Marriott, Tegan T1 - From dark to light BT - an overexpression and systems biology approach to investigate the development of functional thylakoid membranes Y1 - 2016 ER - TY - JOUR A1 - Arlt, Olga A1 - Schwiebs, Anja A1 - Japtok, Lukasz A1 - Rueger, Katja A1 - Katzy, Elisabeth A1 - Kleuser, Burkhard A1 - Radeke, Heinfried H. T1 - Sphingosine-1-Phosphate modulates dendritic cell function: focus on non-migratory effects in vitro and in vivo JF - Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology N2 - 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. KW - Sphingosine-1-phosphate KW - Dendritic cells KW - Fingolimod KW - IL-12 KW - Inflammation Y1 - 2014 U6 - https://doi.org/10.1159/000362982 SN - 1015-8987 SN - 1421-9778 VL - 34 IS - 1 SP - 27 EP - 44 PB - Karger CY - Basel ER - TY - THES A1 - Arlt, Matthias T1 - Studien zur Initiation, Ausbreitung und Übertragbarkeit verschiedener Varianten von posttranskriptionellem Transgensilencing anhand molekularer Charakteristika in Arabidopsis thaliana Y1 - 2007 CY - Potsdam ER - TY - JOUR A1 - Arias-Andres, Maria A1 - Rojas-Jimenez, Keilor A1 - Grossart, Hans-Peter T1 - Collateral effects of microplastic pollution on aquatic microorganisms BT - An ecological perspective JF - Trends in Analytical Chemistry N2 - 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. KW - Microplastics (MP) KW - Biofilms KW - HGT KW - Microbial ecology KW - Carbon cycling KW - Aquatic ecosystems KW - Health risk assessment Y1 - 2018 U6 - https://doi.org/10.1016/j.trac.2018.11.041 SN - 0165-9936 SN - 1879-3142 VL - 112 SP - 234 EP - 240 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Arias-Andres, Maria A1 - Kluemper, Uli A1 - Rojas-Jimenez, Keilor A1 - Grossart, Hans-Peter T1 - Microplastic pollution increases gene exchange in aquatic ecosystems JF - Environmental pollution N2 - 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. KW - Microplastics KW - Aquatic ecosystems KW - Biofilm KW - Horizontal gene transfer KW - Antibiotic resistance Y1 - 2018 U6 - https://doi.org/10.1016/j.envpol.2018.02.058 SN - 0269-7491 SN - 1873-6424 VL - 237 SP - 253 EP - 261 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Arias Andrés, María de Jesús A1 - Kettner, Marie Therese A1 - Miki, Takeshi A1 - Grossart, Hans-Peter T1 - Microplastics: New substrates for heterotrophic activity contribute to altering organic matter cycles in aquatic ecosystems JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - 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. KW - Microplastics KW - Microorganisms KW - Biofilms KW - Total biomass KW - Heterotrophic activity KW - Functional diversity KW - Multi-functionality index Y1 - 2018 U6 - https://doi.org/10.1016/j.scitotenv.2018.04.199 SN - 0048-9697 SN - 1879-1026 VL - 635 SP - 1152 EP - 1159 PB - Elsevier CY - Amsterdam ER - TY - THES A1 - Arias Andrés, María de Jesús T1 - Microbial gene exchange on microplastic particles T1 - Mikrobieller Gentransfer auf Mikroplastikpartikel N2 - 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. N2 - Die Plastikverschmutzung ist auf dem Planeten allgegenwärtig, da jährlich mehrere Millionen Tonnen Plastikabfall in die aquatische Ökosystemen gelangen. Darüber hinaus wird erwartet, dass die Menge an produziertem Plastik in naher Zukunft exponentiell ansteigen wird. Die Heterogenität der Kunststoffmaterialien, ihrer Additive und physikalischen Eigenschaften ist typisch für diese neu auftretenden Schadstoffe und beeinflusst deren Umweltverhalten in Meeres- und Süßwasser. Als Folge kann Plastik in der Wassersäule, den Sedimenten oder Küstenlebensräumen aller aquatischen Ökosysteme gefunden werden. Die meisten dieser Plastikabfälle fragmentieren durch das Zusammenspiel physikalischer, chemischer und biologischer Kräfte, wodurch kleine Partikel erzeugt werden. Diese Partikel (<5mm) sind auch bekannt als "Mikroplastik" (MP). Aufgrund ihres hohen Oberflächen-Volumen-Verhältnisses stimuliert MP das Biofouling und somit die Bildung von Biofilmen in aquatischen Systemen. Aufgrund ihrer einzigartigen Struktur und Zusammensetzung werden die mikrobiellen Gemeinschaften in MP-Biofilmen als "Plastisphäre" bezeichnet. Während es immer mehr Daten über die spezifische Zusammensetzung und Struktur der mikrobiellen Gemeinschaften – die Teil dieser Plastisphäre sind – gibt, existieren hingegen nur wenige Informationen über die Aktivität von Mikroorganismen in MP-Biofilmen. Dieser Lebensstil des Anheftens und Besiedelns von Oberflächen ist oft mit der Zunahme von horizontalem Gentransfer (HGT) unter Bakterien verknüpft. Diese Art der mikrobiellen Aktivität stellt eine besonders relevante Funktion dar und sollte daher in MP-Biofilmen analysiert werden. Der horizontale Austausch von mobilen genetischen Elementen (MGEs) ist ein wesentliches Merkmal von Bakterien. Er ist verantwortlich für die schnelle Evolution dieser Prokaryoten und ihre Anpassungsfähigkeit an verschiedenste Umweltbedingungen. Der Prozess des HGT ist zudem entscheidend für die Verbreitung von Antibiotikaresistenzen sowie für die Entwicklung von Pathogenen, da viele MGEs bekanntermaßen Antibiotikaresistenzgene (ARGs) und genetische Determinanten für Pathogenität enthalten. Im Allgemeinen konzentriert sich die Forschung in der vorliegenden Dissertation auf die Analyse des HGT und der heterotrophen Aktivität in MP-Biofilmen in aquatischen Ökosystemen. Das Hauptziel besteht darin, das Potenzial des Genaustausches zwischen MP-Bakteriengemeinschaften und dem des umgebenden Wassers, einschließlich der Bakterien in natürlichen Aggregaten, zu analysieren. Darüber hinaus befasst sich diese Doktorarbeit mit dem Potenzial von MP-Biofilmen zur Ausbreitung biologisch gefährlicher Bakterien und MGEs, die aus Kläranlagen stammen und mit Antibiotikaresistenzen assoziiert sind. Schließlich soll bei verschiedenen limnologischen Bedingungen überprüft werden, ob das jeweilige physiologische Profil von MP-Biofilmen von dem der Wassergemeinschaften abweicht. Dementsprechend besteht die Arbeit aus drei unabhängigen Studien, die in Fachzeitschriften veröffentlicht wurden. In den beiden Laborstudien wurden sowohl mikrobielle Modell- als auch Umwelt-Gemeinschaften betrachtet. Im Freilandexperiment wurden schließlich die natürlichen Gemeinschaften aus Süßwasserökosystemen untersucht. In Kapitel I wurde der Zufluss von geklärtem Abwasser mit einem Konzentrationsgradienten von MP-Partikeln in einen See der gemäßigten Klimazone simuliert. Dabei wurden die Effekte von MP auf die mikrobielle Gemeinschaftsstruktur und das Auftreten von Integrase 1 (int 1) verfolgt. Int 1 ist ein Marker, der mit mobilen genetischen Elementen assoziiert ist und zur Abschätzung anthropogener Einflüsse auf die Ausbreitung antimikrobieller Resistenzgene verwendet ist. Während des Experiments erhöhte sich das Vorkommen von Int1 in der Plastisphäre mit zunehmender MP-Partikelkonzentration, jedoch nicht im umgebenden Wasser. Darüber hinaus ähnelte die mikrobielle Gemeinschaft auf MP zunehmend der ursprünglichen Abwassergemeinschaft mit steigender Mikroplastikkonzentration. Unsere Ergebnisse zeigen, dass Mikroplastikpartikel tatsächlich die Persistenz von Standardindikatoren mikrobieller anthropogener Verschmutzung in natürlichen Gewässern fördern. In Kapitel II wurde die Permissivität von aquatischen Bakterien gegen das Modell-Plasmid für Antibiotikaresistenz pKJK5 zwischen Gemeinschaften, die Biofilme auf MP bilden, gegenüber denen, die frei leben, verglichen. Die Häufigkeit des Plasmidtransfers unter den MP-assoziierten Bakterien war höher als unter Bakterien, die frei oder in natürlichen Aggregaten leben. Der verstärkte Genaustausch trat darüber hinaus bei einem breiten Spektrum phylogenetisch diverser Bakterien auf. Die Ergebnisse deuten auf eine unterschiedliche Aktivität von HGT in MP-Biofilmen hin, welche die Ökologie aquatischer mikrobieller Gemeinschaften auf globaler Ebene sowie die Verbreitung von Antibiotikaresistenzen beeinflussen könnten. Schließlich wurden in Kapitel III physiologische Messungen durchgeführt, um festzustellen, ob Mikroorganismen auf MP eine andere funktionelle Diversität aufwiesen als jene im Wasser. Die generelle heterotrophe Aktivität, wie der Sauerstoffverbrauch, wurde in Mikrokosmentests mit und ohne MP verglichen, während die Diversität und Vielfalt heterotropher Aktivitäten mit Hilfe von Biolog® EcoPlates berechnet wurden. Drei Seen mit unterschiedlichen Nährstoffbedingungen wiesen Unterschiede in der Ausprägung der MP-assoziierten Biomasse auf. In allen Seen unterschieden sich die funktionellen Diversitätsprofile der MP-Biofilme von denen der Gemeinschaften im umgebenden Wasser, aber nur die MP-Biofilme des oligo-mesotrophen Sees hatten eine höhere funktionelle Vielfalt im Verglichen zum Umgebungswasser. Die Ergebnisse verdeutlichen, dass MP-Oberflächen als neue Nischen für aquatische Mikroorganismen fungieren und die globale Kohlenstoffdynamik im Pelagial beeinflussen können. Insgesamt unterstützen die in den Kapiteln I und II vorgestellten experimentellen Studien ein Szenario, in dem die Umweltverschmutzung durch MP die HGT-Dynamik zwischen aquatischen Bakterien beeinflusst. Zu den Folgen dieser Veränderung gehört eine Erhöhung der Mobilisierungs- und Übertragungseffizienz von ARGs. Darüber hinaus wird vermutet, dass eine Beeinflussung des HGT die Evolution von Bakterien und die Umsetzung von organischem Material verändern könnte, was zu verschiedenen katabolischen Profilen führt, wie in Kapitel III gezeigt. Die Ergebnisse werden in Zusammenhang mit dem Ausmaß der Plastikverschmutzung sowie der Bedeutung von HGT für die bakterielle Entwicklung und „mikrobielle Schleife“, d. h. an der Basis der aquatischen Nahrungsnetze, diskutiert. Diese Doktorarbeit veranschaulicht die Bedeutung von MP-Biofilmgemeinschaften für die beobachteten Veränderungen des aquatischen Mikrobioms als eine Folge der intensiven anthropogenen Eingriffe. KW - microplastics KW - horizontal gene transfer KW - aquatic ecosystem KW - microorganisms KW - Mikroplastikpartikel KW - horizontaler Gentransfer KW - aquatische Ökosysteme KW - Mikroorganismen Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-417241 ER - TY - JOUR A1 - Arend, Marius A1 - Zimmer, David A1 - Xu, Rudan A1 - Sommer, Frederik A1 - Mühlhaus, Timo A1 - Nikoloski, Zoran T1 - Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale JF - Nature Communications N2 - 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. KW - Computational models KW - Enzymes KW - Proteomics Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-40498-1 SN - 2041-1723 VL - 14 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Arbeiter, Susanne A1 - Tegetmeyer, Cosima T1 - Home range and habitat use by aquatic warblers acrocephalus paludicola on their wintering grounds in Northwestern Senegal JF - Acta ornithologica N2 - 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. KW - Acrocephalus paludicola KW - Djoudj National Park KW - radio telemetry KW - transsaharan migrant KW - vegetation structure Y1 - 2011 U6 - https://doi.org/10.3161/000164511X625883 SN - 0001-6454 VL - 46 IS - 2 SP - 117 EP - 126 PB - Museum and Institute of Zoology, Polish Academy of Sciences CY - Warsaw ER - TY - JOUR A1 - Araujo, Wagner L. A1 - Nunes-Nesi, Adriano A1 - Nikoloski, Zoran A1 - Sweetlove, Lee J. A1 - Fernie, Alisdair R. T1 - Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues JF - Plant, cell & environment : cell physiology, whole-plant physiology, community physiology N2 - 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. KW - metabolic control analysis KW - metabolic regulation KW - respiration KW - Solanum lycopersicum (tomato) KW - TCA cycle Y1 - 2012 U6 - https://doi.org/10.1111/j.1365-3040.2011.02332.x SN - 0140-7791 VL - 35 IS - 1 SP - 1 EP - 21 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Arana-Ceballos, Fernando Alberto T1 - Biochemical and physiological studies of Arabidopsis thaliana Diacylglycerol Kinase 7 (AtDGK7) T1 - Biochemische physiologische Studien an der Arabidopsis thaliana Diazylglyzerol Kinase 7 (AtDGK7) N2 - 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). N2 - Wachstum und Entwicklung sind die Kennzeichen lebender Systeme. Diese Prozesse unterliegen einer strengen Regulation im Organismus. Diacylglycerol (DAG) und Phosphatidsäure (PA) sind wesentliche Elemente in der Signalübertragung in Organismen. In Säugetieren kann DAG auf drei verschiedenen Wegen metabolisiert werden, die Entstehung von PA durch Phosphorylierung der freien Hydroxyl-Gruppe von DAG ist jedoch der am häufigsten vorkommende Stoffwechselweg. Die enzymatische Umsetzung dieser Reaktion wird von der Familie der Diacylglycerol-Kinasen (DGKs) katalysiert. Molekulare und biochemische Untersuchungen konnten die Anwesenheit von DGKs in Drosophila melanogaster, Arabidopsis thaliana und jüngst auch in Dictyostelium discoideum zeigen. In der vorliegenden Arbeit wird die Klonierung und Charakterisierung von AtDGK7 aus Arabidopsis thaliana präsentiert, einem Vertreter des pflanzlichen DGK-Clusters II. Das Transkript von AtDGK7 findet sich in der gesamten Pflanze, jedoch sind die Transkriptmengen in Blüten und jungem Gewebe stark erhöht. Rekombinant hergestelltes AtDGK7 ist katalytisch aktiv und akzeptiert DAG-ähnliche Moleküle mit mindestens einer ungesättigten Fettsäure als bevorzugtes Substrat. AtDGK2, ein weiteres Mitglied der DGK-Familie, und AtDGK7 metabolisieren Substrate, welche in Pflanzen physiologisch relevant sind. Das als DGK-Inhibitor beschriebene Molekül 6-{2-{4-[(4-fluorophenyl)phenylmethylene]-1-piperidinyl}ethyl}-7-methyl-5H-thiazolo(3,2-a)pyrimidine-5-one (R59022) inhibiert bei Konzentrationen von 50-100 µM rekombinant hergestelltes AtDGK2 in vitro. In ähnlichen Konzentrationen eingesetzt modifiziert R59022 das Wurzelwachstum. Dies weist darauf hin, dass DGKs in Entwicklungsprozessen eine Rolle spielen. In in vitro Experimenten wurde AtDGK7 von R59022 allerdings erst in Konzentrationen über 100 µM inhibiert. Ferner wird in der vorliegenden Arbeit die erfolgreiche Klonierung einer cDNA beschrieben, die für AtDGK7 aus A. thaliana kodiert und welche im Vergleich zu der bereits bekannten cDNA um 439 bp länger ist. Expressionsanalysen mit Hilfe eines Promotor-ß-glucuronidase (GUS) Fusions-Produktes zeigten die Aktivität von AtDGK7 in vielen Geweben, vor allem aber in Schließzellen, im Konnektiv-Gewebe der Antheren, sowie besonders in den Spitzen der Seitenwurzeln. Physiologische Untersuchungen unter abiotischem Stress (Verwendung verschiedener Konzentrationen von Stickstoff, Saccharose, Auxin und Inhibitoren von Auxin-Transportern) wurden mit AtDGK7 T-DNA-Insertionslinien sowie mit den Promotor-GUS-Linien durchgeführt. AtDGK7 T-DNA-Insertionslinien zeigten eine starke Inhibierung des Seitenwurzel-Wachstums unter limitierenden Stickstoff- und/oder Saccharose-Konzentrationen. In einigen der T-DNA-Insertionslinien inhibierte die Zugabe eines Inhibitors für Auxin-Transport (TIBA; 2,3,5-triiodobenzoic acid) die Bildung von Haupt- und Seitenwurzeln fast vollständig. Die Inhibition des Wurzelwachstums in den T-DNA-Insertionslinien konnte teilweise durch die Zugabe von 50nM NAA (α-naphtalene acetic acid) revertiert werden. Aus den vorliegenden Ergebnissen wird die Hypothese abgeleitet, dass AtDGK7 im Zusammenspiel mit Auxin in Signaltransduktionsprozessen eine Rolle spielt, welche das Wachstum und die Entwicklung in Pflanzen regulieren. KW - AtDGK gene KW - Diacylglycerol KW - Phosphatidsäure KW - Diacylglycerol-Kinasen KW - Signaltransduktionsprozesse KW - AtDGK genes KW - auxin KW - diacylglycerol KW - phosphatidic acid KW - signaling Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-13729 ER - TY - THES A1 - Arabi, Fayezeh T1 - Functional characterization of Sulfur Deficiency Induced genes, SDI1 and SDI2, in Arabidopsis thaliana Y1 - 2015 ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Tambunan, Van Basten T1 - Draft genome sequence, annotation, and SSR mining data of Elaeidobius kamerunicus Faust., an essential oil palm pollinating weevil JF - Data in Brief N2 - 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. KW - Whole-genome sequencing KW - NGS KW - Simple Sequence Repeat KW - Weevil KW - Curculionidae KW - Oil Palm KW - Pollinator KW - Genomics Y1 - 2021 U6 - https://doi.org/10.1016/j.dib.2021.106745 SN - 2352-3409 VL - 34 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Tambunan, Van Basten T1 - The complete mitochondrial genome of oil palm pollinating weevil, Elaeidobius kamerunicus Faust BT - (Coleoptera : Curculionidae) JF - Mitochondrial DNA: Part B N2 - 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. KW - Mitogenome KW - oil palm KW - pollinator KW - phylogeny KW - weevil Y1 - 2020 U6 - https://doi.org/10.1080/23802359.2020.1823899 SN - 2380-2359 VL - 5 IS - 3 SP - 3450 EP - 3452 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Compart, Julia A1 - Zimmermann, Vincent A1 - Alseekh, Saleh A1 - Fernie, Alisdair R. A1 - Fettke, Jörg T1 - Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.) JF - Food chemistry N2 - 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. KW - carbohydrate KW - mesocarp KW - metabolites KW - oil palm KW - oil yield KW - sucrose; KW - starch Y1 - 2022 U6 - https://doi.org/10.1016/j.foodchem.2022.133361 SN - 0308-8146 SN - 1873-7072 VL - 393 PB - Elsevier CY - New York, NY [u.a.] ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Compart, Julia A1 - Fettke, Jörg T1 - A review of starch, a unique biopolymer - structure, metabolism and in planta modifications JF - Plant science : an international journal of experimental plant biology N2 - 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. KW - starch KW - starch structure KW - starch surface KW - starch modifications; KW - analytics Y1 - 2022 U6 - https://doi.org/10.1016/j.plantsci.2022.111223 SN - 0168-9452 SN - 1873-2259 VL - 318 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Compart, Julia A1 - Fettke, Jörg T1 - Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield JF - Frontiers in plant science N2 - 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. KW - starch KW - oil yield KW - fruit development KW - gene expression KW - RNA-seq KW - and palm KW - oil KW - Elaeis guineensis Jacq Y1 - 2023 U6 - https://doi.org/10.3389/fpls.2023.1220237 SN - 1664-462X VL - 14 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Ajambang, Walter T1 - Transcriptomic dataset for early inflorescence stages of oil palm in response to defoliation stress JF - Data in Brief N2 - 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. KW - Complete defoliation KW - Flower development KW - Leaf axil KW - NGS KW - RNA-seq KW - Sex KW - determination Y1 - 2022 U6 - https://doi.org/10.1016/j.dib.2022.107914 SN - 2352-3409 VL - 41 PB - Elsevier CY - Amsterdam ER - TY - THES A1 - Apriyanto, Ardha T1 - Analysis of starch metabolism in source and sink tissue of plants T1 - Analyse des Stärkestoffwechsels im Source und Sink Gewebe von Pflanzen N2 - 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. N2 - Stärke ist ein unverzichtbares Biopolymer, das von Pflanzen sowohl in den Quellgeweben (sources, z. B. Blätter) als auch in den Senkengeweben (sinks, z. B. Früchten und Knollen) gebildet wird. Daher ist ein profundes Wissen über die Regulation des Stärkestoffwechsel in den source und sink Organen von grundlegender Bedeutung für die Verbesserung der Pflanzenproduktion. Trotz der jüngsten Fortschritte im Verständnis des Stärkestoffwechsels bleiben weiterhin viele Fragen über den detaillierten source und sink Metabolismus offen. Ziel dieser Studie war es daher, den aktuellen Forschungsstand über die Struktur und den Stoffwechsel von Stärke in Pflanzen aufzuzeigen. Darüber hinaus sollte in dieser Studie die Regulierung des Stärkestoffwechsels in den Blättern (source) des Modellorganismus Arabidopsis thaliana und in den Ölpalmfrüchten (sink) von Elaeis guineensis, einer Nutzpflanze, aufgeklärt werden. Die Analyse des source Gewebes konzentrierte sich dabei auf die Auswirkungen auf Stärkeparamter wie beispielsweise die Granulazahl durch die Blockierung des Stärkeabbaus in Blättern. Dazu wurde die Arabidopsis Mutante, der das cytosolische Disproportionating Enzym 2 (DPE2) und die plastidiale Glucanphosphorylase 1 (PHS1) fehlen (dpe2/phs1), untersucht. Ebenfalls wurden Dreifachmutanten im Hintergund von dpe2/phs1, denen Starch excess 4 (SEX4), Isoamylase 3, Phosphoglucan-Wasser-Dikinase (PWD) oder das Disproportionating Enzym 1 (DPE1) fehlen, erzeugt. Die Analyse zeigt, dass die Anzahl der Stärkegranula pro Chloroplast nicht festgelegt ist und während des gesamten Wachstums der Pflanze reguliert wird. Diese Daten liefern ein verbessertes Verständnis über die Komplexität der Kontrollmechanismen der Granulazahlregulation in Chloroplasten. Die Untersuchung des sink Gewebes soll die Beziehung zwischen dem Stärkestoffwechsel und dem Lipidstoffwechselweg in Ölpalmenfrüchten verdeutlichen. Diese Studie wurde durchgeführt, um die Veränderung von Stärkeparametern, die Häufigkeit von Metaboliten und die Genexpression während der Entwicklung von Ölpalmenfrüchten mit unterschiedlichen Ölausbeuten zu erforschen. Die Analyse zeigt, dass sowohl Stärke als auch Saccharose als reliable Biomarker für den Ölertrag von Ölpalmen verwendet werden können. Darüber hinaus konnte bewiesen werden, dass die mit dem Stärkestoffwechsel verbundenen Enzymisoformen die Ölproduktion in Ölpalmenfrüchten beeinflussen. Insgesamt liefert diese Arbeit neue Informationen über den Stärkestoffwechsel im source Gewebe von A.thaliana und im sink von E.guineensis. Die in dieser Arbeit gezeigten Ergebnisse können für viele Anwendungen genutzt werden, z. B. für die Veränderung der Stärkeparameter in anderen Pflanzen für spezifische Bedürfnisse. KW - starch KW - oil palm KW - Arabidopsis thaliana KW - source and sink KW - Arabidopsis thaliana KW - Palmöl KW - Source und Sink KW - Stärke Y1 - 2023 ER - TY - JOUR A1 - Appelhagen, Ingo A1 - Huep, Gunnar A1 - Lu, Gui-Hua A1 - Strompen, Georg A1 - Weisshaar, Bernd A1 - Sagasser, Martin T1 - Weird fingers : functional analysis of WIP domain proteins N2 - WIP proteins form a plant specific subfamily of C2H2 zinc finger (ZF) proteins. In this study, we functionally characterized the WIP domain, which consists of four ZF motifs, and discuss molecular functions for WIP proteins. Mutations in each of the ZFs lead to loss of function of the TT1/WIP1 protein in Arabiopsis thaliana. SV40 type nuclear localisation signals were detected in two of the ZFs and functionally characterized using GFP fusions as well as new mutant alleles identified by TILLING. Promoter swap experiments showed that selected WIP proteins are partially able to take over TT1 function. Activity of the AtBAN promoter, a potential TT1 target, could be increased by the addition of TT1 to the TT2-TT8-TTG1 regulatory complex. Y1 - 2010 UR - http://www.sciencedirect.com/science/journal/00145793 U6 - https://doi.org/10.1016/j.febslet.2010.06.007 SN - 0014-5793 ER - TY - THES A1 - Apodiakou, Anastasia T1 - 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 Y1 - 2024 ER - TY - JOUR A1 - Apio, Ann A1 - Plath, Martin A1 - Wronski, Torsten T1 - Patterns of gastrointestinal parasitic infections in the bushbuck Tragelaphus scriptus from the Queen Elizabeth National Park, Uganda JF - Journal of helminthology N2 - Seasonal, host sex and age-related variations in helminth egg and coccidian oocyst counts were investigated in a naturally infected wild bushbuck (Tragelaphus scriptus) population in Queen Elizabeth National Park, western Uganda from April 2000 to February 2002. The prevalence and mean intensity quantified as the number of eggs and oocysts per gram of faeces were taken as a measure of parasite burdens. Host sex and age-related differences in prevalence values were not found but the overall prevalence of Eimeria sp. was significantly higher during the rainy season, and peak counts were recorded either during or soon after a peak rainfall. A similar trend was observed for Moniezia spp., although the results were marginally not significant. There were also no significant differences in mean intensity values, relative to host sex, age or season. Y1 - 2006 U6 - https://doi.org/10.1076/JOH2006343 SN - 0022-149X VL - 80 IS - 3 SP - 213 EP - 218 PB - Univ. Press CY - Cambridge ER - TY - JOUR A1 - Apio, Ann A1 - Plath, Martin A1 - Wronski, Torsten T1 - Localised defecation sites : a tactic to avoid re-infection by gastro-intestinal tract parasites in bushbuck, Tragelaphus scriptus? N2 - Bushbuck (Tragelaphus scriptus) often deposit faeces at specific localised defecation sites (LDS). We tested whether LDS have a function in the context of parasite avoidance. In a population of bushbuck in Queen Elizabeth National Park, Uganda, seven radio-collared individuals were observed. We recorded feeding behaviour inside and outside LDS. Furthermore, pasture contamination with gastro-intestinal tract parasites inside and outside LDS was examined. There were significant differences between the expected and the observed feeding rates inside LDS, but, contrary to our prediction, the bushbuck increased their feeding rate inside LDS. There was no significant difference in the parasite contamination of pastures inside and outside LDS. We discuss the hypothesis that LDS mainly serve a social function in bushbuck communities, whereas parasite avoidance seems to play a minor or no role Y1 - 2006 UR - http://www.springerlink.com/content/105357 U6 - https://doi.org/10.1007/s10164-005-0166-2 SN - 0289-0771 ER - TY - JOUR A1 - Apio, Ann A1 - Muwanika, Vincent B. A1 - Plath, Martin A1 - Wronski, Torsten T1 - Seasonal variation in reproductive behaviour of bushbuck (Tragelaphus scriptus Pallas, 1766) in an equatorial savannah ecosystem N2 - While several authors suggest that bushbuck (Tragelaphus scriptus Pallas) from tropical areas with an approximately bimodal rainfall pattern breed throughout the year, there is also a report of seasonal breeding in this species. In this study, we provide indirect evidence of seasonality in reproduction by analysing behavioural data (e.g. rates of mixed-sex sightings) in a population of bushbuck inhabiting an equatorial savannah ecosystem in western Uganda. Observation rates of mixed-sex sightings were correlated with rainfall patterns. We suggest that peaks in reproductive behaviour following the wet season may be advantageous if calves are born during the next wet season, when fresh vegetation is available. Y1 - 2009 UR - http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2028 U6 - https://doi.org/10.1111/j.1365-2028.2008.01000.x SN - 0141-6707 ER - TY - JOUR A1 - Apio, Ann A1 - Kabasa, John David A1 - Ketmaier, Valerio A1 - Schroeder, Christoph A1 - Plath, Martin A1 - Tiedemann, Ralph T1 - Female philopatry and male dispersal in a cryptic, bush-dwelling antelope : a combined molecular and behavioural approach N2 - In most mammals, females are philopatric while males disperse in order to avoid inbreeding. We investigated social structure in a solitary ungulate, the bushbuck Tragelaphus sylvaticus in Queen Elizabeth National Park, Uganda by combining behavioural and molecular data. We correlated spatial and social vicinity of individual females with a relatedness score obtained from mitochondrial DNA analysis. Presumed clan members shared the same haplotype, showed more socio-positive interactions and had a common home range. Males had a higher haplotype diversity than females. All this suggests the presence of a matrilineal structure in the study population. Moreover, we tested natal dispersal distances between male and female yearlings and used control region sequences to confirm that females remain in their natal breeding areas whereas males disperse. In microsatellite analysis, males showed a higher genetic variability than females. The impoverished genetic variability of females at both molecular marker sets is consistent with a philopatric and matrilineal structure, while the higher degree of genetic variability of males is congruent with a higher dispersal rate expected in this sex. Evidence even for male long-distance dispersal is brought about by one male carrying a haplotype of a different subspecies, previously not described to occur in this area. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=0952-8369 U6 - https://doi.org/10.1111/j.1469-7998.2009.00654.x SN - 0952-8369 ER - TY - JOUR A1 - Apelt, Federico A1 - Breuer, David A1 - Olas, Justyna Jadwiga A1 - Annunziata, Maria Grazia A1 - Flis, Anna A1 - Nikoloski, Zoran A1 - Kragler, Friedrich A1 - Stitt, Mark T1 - Circadian, Carbon, and Light Control of Expansion Growth and Leaf Movement JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants Y1 - 2017 U6 - https://doi.org/10.1104/pp.17.00503 SN - 0032-0889 SN - 1532-2548 VL - 174 SP - 1949 EP - 1968 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Apelt, Federico A1 - Breuer, David A1 - Nikoloski, Zoran A1 - Stitt, Mark A1 - Kragler, Friedrich T1 - Phytotyping(4D): a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth JF - The plant journal N2 - Integrative studies of plant growth require spatially and temporally resolved information from high-throughput imaging systems. However, analysis and interpretation of conventional two-dimensional images is complicated by the three-dimensional nature of shoot architecture and by changes in leaf position over time, termed hyponasty. To solve this problem, Phytotyping(4D) uses a light-field camera that simultaneously provides a focus image and a depth image, which contains distance information about the object surface. Our automated pipeline segments the focus images, integrates depth information to reconstruct the three-dimensional architecture, and analyses time series to provide information about the relative expansion rate, the timing of leaf appearance, hyponastic movement, and shape for individual leaves and the whole rosette. Phytotyping(4D) was calibrated and validated using discs of known sizes, and plants tilted at various orientations. Information from this analysis was integrated into the pipeline to allow error assessment during routine operation. To illustrate the utility of Phytotyping(4D), we compare diurnal changes in Arabidopsis thaliana wild-type Col-0 and the starchless pgm mutant. Compared to Col-0, pgm showed very low relative expansion rate in the second half of the night, a transiently increased relative expansion rate at the onset of light period, and smaller hyponastic movement including delayed movement after dusk, both at the level of the rosette and individual leaves. Our study introduces light-field camera systems as a tool to accurately measure morphological and growth-related features in plants. Significance Statement Phytotyping(4D) is a non-invasive and accurate imaging system that combines a 3D light-field camera with an automated pipeline, which provides validated measurements of growth, movement, and other morphological features at the rosette and single-leaf level. In a case study in which we investigated the link between starch and growth, we demonstrated that Phytotyping(4D) is a key step towards bridging the gap between phenotypic observations and the rich genetic and metabolic knowledge. KW - plant growth KW - hyponasty KW - 3D imaging KW - light-field camera KW - Arabidopsis thaliana KW - pgm KW - technical advance Y1 - 2015 U6 - https://doi.org/10.1111/tpj.12833 SN - 0960-7412 SN - 1365-313X VL - 82 IS - 4 SP - 693 EP - 706 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Apelt, Federico T1 - Implementation of an imaging-based approach using a 3D light-field camera to analyse plant growth behaviour Y1 - 2015 ER - TY - THES A1 - Apel, Wiebke T1 - Untersuchung und Veränderung der Genexpression und Proteinstabilität in Plastiden höherer Pflanzen Y1 - 2009 CY - Potsdam ER - TY - JOUR A1 - Apanasewicz, Anna A1 - Groth, Detlef A1 - Scheffler, Christiane A1 - Hermanussen, Michael A1 - Piosek, Magdalena A1 - Wychowaniec, Patrycja A1 - Babiszewska, Magdalena A1 - Barbarska, Olga A1 - Ziomkiewicz, Anna T1 - Traumatized women’s infants are bigger than children of mothers without traumas JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger N2 - Life history theory predicts that experiencing stress during the early period of life will result in accelerated growth and earlier maturation. Indeed, animal and some human studies documented a faster pace of growth in the offspring of stressed mothers. Recent advances in epigenetics suggest that the effects of early developmental stress might be passed across the generations. However, evidence for such intergenerational transmission is scarce, at least in humans. Here we report the results of the study investigating the association between childhood trauma in mothers and physical growth in their children during the first months of life. Anthropometric and psychological data were collected from 99 mothers and their exclusively breastfed children at the age of 5 months. The mothers completed the Early Life Stress Questionnaire to assess childhood trauma. The questionnaire includes questions about the most traumatic events that they had experienced before the age of 12 years. Infant growth was evaluated based on the anthropometric measurements of weight, length, and head circumference. Also, to control for the size of maternal investment, the composition of breast milk samples taken at the time of infant anthropometric measurements was investigated. The children of mothers with higher early life stress tended to have higher weight and bigger head circumference. The association between infant anthropometrics and early maternal stress was not affected by breast milk composition, suggesting that the effect of maternal stress on infant growth was independent of the size of maternal investment. Our results demonstrate that early maternal trauma may affect the pace of growth in the offspring and, in consequence, lead to a faster life history strategy. This effect might be explained via changes in offspring epigenetics. KW - maternal trauma KW - early life trauma KW - breastfed infant development KW - POLS Y1 - 2020 U6 - https://doi.org/10.1127/anthranz/2020/1285 SN - 0003-5548 SN - 2363-7099 VL - 77 IS - 5 SP - 359 EP - 374 PB - Schweizerbart science publishers CY - Stuttgart ER - TY - JOUR A1 - Antonietti, Markus A1 - Lopez-Salas, Nieves A1 - Primo, Ana T1 - Adjusting the Structure and Electronic Properties of Carbons for Metal-Free Carbocatalysis of Organic Transformations JF - Advanced materials N2 - Carbon nanomaterials doped with some other lightweight elements were recently described as powerful, heterogeneous, metal-free organocatalysts, adding to their high performance in electrocatalysis. Here, recent observations in traditional catalysis are reviewed, and the underlying reaction mechanisms of the catalyzed organic transformations are explored. In some cases, these are due to specific active functional sites, but more generally the catalytic activity relates to collective properties of the conjugated nanocarbon frameworks and the electron transfer from and to the catalytic centers and substrates. It is shown that the !earnings are tightly related to those of electrocatalysis; i.e., the search for better electrocatalysts also improves chemocatalysis, and vice versa. Carbon-carbon heterojunction effects and some perspectives on future possibilities are discussed at the end. KW - active sites KW - carbocatalysis KW - carbon electrical collective properties KW - metal-free KW - nanocarbon materials Y1 - 2018 U6 - https://doi.org/10.1002/adma.201805719 SN - 0935-9648 SN - 1521-4095 VL - 31 IS - 13 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Ansell, Stephen W. A1 - Stenoien, Hans K. A1 - Grundmann, Michael A1 - Schneider, Harald A1 - Hemp, Andreas A1 - Bauer, N. A1 - Russell, S. J. A1 - Vogel, Johannes C. T1 - Population structure and historical biogeography of European Arabidopsis lyrata N2 - Understanding the natural history of model organisms is important for the effective use of their genomic resourses. Arabidopsis lyrata has emerged as a useful plant for studying ecological and evolutionary genetics, based on its extensive natural variation, sequenced genome and close relationship to A. thaliana. We studied genetic diversity across the entire range of European Arabidopsis lyrata ssp. petraea, in order to explore how population history has influenced population structure. We sampled multiple populations from each region, using nuclear and chloroplast genome markers, and combined population genetic and phylogeographic approaches. Within-population diversity is substantial for nuclear allozyme markers (mean P = 0.610, A(e) = 1.580, H-e = 0.277) and significantly partitioned among populations (F- ST = 0.271). The Northern populations have modestly increased inbreeding (F-IS = 0.163 verses F-IS = 0.093), but retain comparable diversity to central European populations. Bottlenecks are common among central and northern Europe populations, indicating recent demographic history as a dominant factor in structuring the European diversity. Although the genetic structure was detected at all geographic scales, two clear differentiated units covering northern and central European areas (F-CT = 0.155) were identified by Bayesian analysis and supported by regional pairwise F-CT calculations. A highly similar geographic pattern was observed from the distribution of chloroplast haplotypes, with the dominant northern haplotypes absent from central Europe. We conclude A. l. petraea's cold-tolerance and preference for disturbed habitats enabled glacial survival between the alpine and Nordic glaciers in central Europe and an additional cryptic refugium. While German populations are probable peri-glacial leftovers, Eastern Austrian populations have diversity patterns possibly compatible with longer-term survival. Y1 - 2010 UR - http://www.nature.com/hdy/archive/index.html U6 - https://doi.org/10.1038/Hdy.2010.10 SN - 0018-067X ER - TY - JOUR A1 - Angelopoulos, Michael A1 - Overduin, Pier Paul A1 - Westermann, Sebastian A1 - Tronicke, Jens A1 - Strauss, Jens A1 - Schirrmeister, Lutz A1 - Biskaborn, Boris A1 - Liebner, Susanne A1 - Maksimov, Georgii A1 - Grigoriev, Mikhail N. A1 - Grosse, Guido T1 - Thermokarst lake to lagoon transitions in Eastern Siberia BT - do submerged taliks refreeze? JF - Journal of geophysical research : Earth surface N2 - As the Arctic coast erodes, it drains thermokarst lakes, transforming them into lagoons, and, eventually, integrates them into subsea permafrost. Lagoons represent the first stage of a thermokarst lake transition to a marine setting and possibly more saline and colder upper boundary conditions. In this research, borehole data, electrical resistivity surveying, and modeling of heat and salt diffusion were carried out at Polar Fox Lagoon on the Bykovsky Peninsula, Siberia. Polar Fox Lagoon is a seasonally isolated water body connected to Tiksi Bay through a channel, leading to hypersaline waters under the ice cover. The boreholes in the center of the lagoon revealed floating ice and a saline cryotic bed underlain by a saline cryotic talik, a thin ice-bearing permafrost layer, and unfrozen ground. The bathymetry showed that most of the lagoon had bedfast ice in spring. In bedfast ice areas, the electrical resistivity profiles suggested that an unfrozen saline layer was underlain by a thick layer of refrozen talik. The modeling showed that thermokarst lake taliks can refreeze when submerged in saltwater with mean annual bottom water temperatures below or slightly above 0 degrees C. This occurs, because the top-down chemical degradation of newly formed ice-bearing permafrost is slower than the refreezing of the talik. Hence, lagoons may precondition taliks with a layer of ice-bearing permafrost before encroachment by the sea, and this frozen layer may act as a cap on gas migration out of the underlying talik. KW - thermokarst lake KW - talik KW - lagoon KW - subsea permafrost KW - salt diffusion KW - Siberia Y1 - 2020 U6 - https://doi.org/10.1029/2019JF005424 SN - 2169-9003 SN - 2169-9011 VL - 125 IS - 10 PB - American Geophysical Union CY - Washington ER - TY - JOUR A1 - Angeleska, Angela A1 - Omranian, Sara A1 - Nikoloski, Zoran T1 - Coherent network partitions BT - Characterizations with cographs and prime graphs JF - Theoretical computer science : the journal of the EATCS N2 - We continue to study coherent partitions of graphs whereby the vertex set is partitioned into subsets that induce biclique spanned subgraphs. The problem of identifying the minimum number of edges to obtain biclique spanned connected components (CNP), called the coherence number, is NP-hard even on bipartite graphs. Here, we propose a graph transformation geared towards obtaining an O (log n)-approximation algorithm for the CNP on a bipartite graph with n vertices. The transformation is inspired by a new characterization of biclique spanned subgraphs. In addition, we study coherent partitions on prime graphs, and show that finding coherent partitions reduces to the problem of finding coherent partitions in a prime graph. Therefore, these results provide future directions for approximation algorithms for the coherence number of a given graph. KW - Graph partitions KW - Network clustering KW - Cographs KW - Coherent partition KW - Prime graphs Y1 - 2021 U6 - https://doi.org/10.1016/j.tcs.2021.10.002 SN - 0304-3975 VL - 894 SP - 3 EP - 11 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Angeleska, Angela A1 - Nikoloski, Zoran T1 - Coherent network partitions JF - Discrete applied mathematics N2 - Graph clustering is widely applied in the analysis of cellular networks reconstructed from large-scale data or obtained from experimental evidence. Here we introduce a new type of graph clustering based on the concept of coherent partition. A coherent partition of a graph G is a partition of the vertices of G that yields only disconnected subgraphs in the complement of G. The coherence number of G is then the size of the smallest edge cut inducing a coherent partition. A coherent partition of G is optimal if the size of the inducing edge cut is the coherence number of G. Given a graph G, we study coherent partitions and the coherence number in connection to (bi)clique partitions and the (bi)clique cover number. We show that the problem of finding the coherence number is NP-hard, but is of polynomial time complexity for trees. We also discuss the relation between coherent partitions and prominent graph clustering quality measures. KW - Graph partitions KW - Network clustering KW - Coherence number KW - Coherent partition Y1 - 2019 U6 - https://doi.org/10.1016/j.dam.2019.02.048 SN - 0166-218X SN - 1872-6771 VL - 266 SP - 283 EP - 290 PB - Elsevier CY - Amsterdam ER - TY - THES A1 - Aneley, Gedif Mulugeta T1 - Drought tolerance prediction of potato by automatic phenotyping of morphological and physiological traits T1 - Vorhersage von Trockentoleranz in Kartoffel durch automatische Phänotypisierung morphologischer und physiologischer Eigenschaften N2 - Potato is the 4th most important food crop in the world. Especially in tropical and sub-tropical potato production, drought is a yield limiting factor. Potato is sensitive to water stress. Potato yield loss under water stress could be reduced by using tolerant varieties and adjusted agronomic practices. Direct selection for yield under water-stressed conditions requires long selection cycles. Thus, identification of markers for marker-assisted selection may speed up breeding. The objective of this thesis is to identify morphological markers for drought tolerance by continuously monitoring plant growth and canopy temperature with an automatic phenotyping system. The phenotyping was performed in drought-stress experiments that were conducted in population A with 64 genotypes and population B with 21 genotypes in the screenhouse in 2015 and 2016 (population A) and in 2017 and 2018 (population B). Drought tolerance was quantified as deviation of the relative tuber starch yield from the experimental median (DRYM) and parent median (DRYMp). Relative tuber starch yield is starch yield under drought stress relative to the average starch yield of the respective cultivar under control conditions in the same experiment. The specific DRYM value was calculated based on the yield data of the same experiment or the global DRYM that was calculated from yield data derived from data combined over yeas of respective population or across multiple experiments including VALDIS and TROST experiments (2011-2016). Analysis of variance found a significant effect of genotype on DRYM indicating that the tolerance variation required for marker identification was given in both populations. Canopy growth was monitored continuously six times a day over five to ten weeks by a laser scanner system and yielded information on leaf area, plant height and leaf angle for population A and additionally on leaf inclination and light penetration depth for population B. Canopy temperature was measured 48 times a day over six to seven weeks by infrared thermometry in population B. From the continuous IRT surface temperature data set, the canopy temperature for each plant was selected by matching the time stamp of the IRT data with laser scanner data. Mean, maximum, range and growth rate values were calculated from continuous laser scanner measurements of respective canopy parameters. Among the canopy parameters, the maximum and mean values in long-term stress conditions showed better correlation with DRYM values calculated in the same experiment than growth rate and diurnal range values. Therefore, drought tolerance index prediction was done from maximum and mean values of canopy parameters. The tolerance index in specific experiment condition was linearly predicted by simple regression model from different single canopy parameters under long-term stress condition in population A (2016) and population B (2017 and 2018). Among the canopy parameters maximum light penetration depth (2017), mean leaf angle (2017, 2018, and 2016), mean leaf inclination or mean canopy temperature depression (2017 and 2018), maximum plant height (2017) were selected as tolerance predictors. However, no single parameters were sufficient to predict DRYM. Therefore, several independent parameters were integrated in a multiple regression model. In multiple regression model, specific experiment DRYM values in population A was predicted from mean leaf angle (2016). In population B, specific tolerance could be predicted from maximum light penetration depth and mean leaf inclination (2017) and mean leaf inclination (2018) or mean canopy temperature depression and mean leaf angle (2018). In data combined over season of population A, the multiple linear regression model selected maximum plant height and mean leaf angle as tolerance predictor. In Population B, mean leaf inclination was selected as tolerance predictor. However, in population A, the variation explained by the final model was too low. Furthermore, the average tolerances respective to parent median (2011-2018) across FGH plants or all plants (FGH and field) were predicted from maximum plant height (population A) and maximum plant height and mean leaf inclination (population B). Altogether, canopy parameters could be used as markers for drought tolerance. Therefore, water stress breeding in potato could be speed up through using leaf inclination, light penetration depth, plant height and canopy temperature depression as markers for drought tolerance, especially in long-term stress conditions. N2 - Die Kartoffel ist die viertwichtigste Nahrungspflanze der Welt. Besonders in den Tropen und Subtropen ist Trockenheit ein ertragsbegrenzender Faktor für die Kartoffelproduktion. Kartoffeln sind empfindlich gegen Trockenstress. Der Ertragsverlust von Kartoffeln unter Wasserstress könnte durch die Verwendung von toleranten Sorten und angepasste Anbaupraxis verringert werden. Die direkte Selektion für Ertrag unter Trockenstressbedingungen erfordert lange Selektionszyklen. Daher kann die Identifizierung von Markern für marker-assisted Selektion die Züchtung beschleunigen. Das Ziel dieser Arbeit ist es, morphologische Marker für Trockentoleranz mit Hilfe von kontinuierlichen Messungen von Pflanzenwachstum und Bestandstemperatur mittels automatischer Phänotypisierung zu identifizieren. Die Phänotypisierung wurde in Trockenstressexperimenten durchgeführt, welche mit 64 Genotypen aus Population A und 21 Genotypen aus Population B in einem Foliengewächshaus in 2015 und 2016 (Population A) bzw. 2017 und 2018 (Population B) stattgefunden haben. Die Trockentoleranz wurde als Abweichung des relativen Stärkeertrags der Knollen vom experimentellen Median (DRYM) und dem Elternmedian (DRYMp) quantifiziert. Der relative Stärkeertrag ist der Stärkeertrag unter Trockenstress relativ zum mittleren Stärkeertrag der Sorte unter optimaler Bewässerung im gleichen Experiment. Der spezifische DRYM wurde auf der Basis der Ertragsdaten des gleichen Experiments berechnet oder der globale DRYM wurde auf der Basis der Ertragsdaten kombinierter Experimente aus mehreren Jahren für die gleiche Population oder für mehrere Experimente auch aus VALDIS und TROST (2011-2016) berechnet. Die Varianzanalyse zeigte einen signifikanten Effekt des Genotyps auf DRYM, so dass die für die Identifizierung von Markern erforderliche Toleranzvariation in beiden Populationen gegeben war. Die Bestandsentwicklung wurde mit einem Laserscanner-System kontinuierlich sechsmal täglich über fünf bis zehn Wochen gemessen und lieferte Informationen zu Blattfläche, Pflanzenhöhe und Blattwinkel für Population A sowie zusätzlich Blattneigung und Lichteinfalltiefe für Population B. Die Oberflächentemperatur wurde 48mal täglich für sechs bis sieben Wochen mittels Infrarot-Thermometrie in Population B gemessen. Aus dem kontinuierlichen IRT-Oberflächentemperatur-Datensatz wurde die Oberflächentemperatur jeder Pflanze bestimmt, indem die Zeitstempel der IRT-Daten mit denen der Laserscannerdaten abgeglichen wurden. Mittelwert, Maximum, Streubereich (range) und Wachstumsrate wurden für die Bestandsparameter der Laserscannermessungen bestimmt. Unter den Bestandsparametern zeigten die Maxima und Mittelwerte unter Langzeitstress die bessere Korrelation mit dem Toleranzindex DRYM, der aus dem gleichen Experiment berechnet wurde, als die Wachstumsrate und der Streubereich. Die Trockentoleranzprognose wurde daher aus den Maxima und Mittelwerte der Bestandsparameter gemacht. Der Toleranzindex spezifischer Versuche wurde linear mit einem einfachen Regressionsmodell aus verschiedenen einzelnen Bestandparameters unter Langzeitstressbedingungen in Population A (2016) und Population (B) (2017 und 2018) vorhergesagt. Toleranz-Prognoseparameter wurden unter den Bestandparametern maximale Lichteinfalltiefe (2017), mittlerer Blattwinkel (2017, 2018 und 2016), mittlere Blattneigung und mittlere Oberflächentemperatur-Abweichung (2017 und 2018), maximale Pflanzenhöhe (2017) ausgewählt. Kein einzelner Parameter war jedoch ausreichend um DRYM vorherzusagen. Daher wurden mehrere unabhängige Parameter in einem multiplen Regressionsmodell integriert. Im multiplen Regressionsmodel wurde der spezifische Experiment-DRYM in Population A aus dem mittleren Blattwinkel (2016) vorhergesagt. In Population B konnte die spezifische Toleranz aus der maximalen Lichteinfalltiefe, der maximalen Blattneigung (2017) und der mittleren Blattneigung (2018) oder der mittleren Oberflächentemperatur-Abweichung und dem mittleren Blattwinkel (2018) vorhergesagt werden. In Daten aus mehreren Anbauperioden von Population A wählte das multiple lineare Regressionsmodel maximale Pflanzenhöhe und mittleren Blattwinkel als Prognoseparameter für Toleranz aus. In Population B wurde mittlere Blattneigung als Prognoseparameter für Toleranz ausgewählt. In Population A war jedoch die Variation, die durch das Endmodell erklärt wurde, zu niedrig. Die mittlere Toleranz hinsichtlich des Medians der Eltern (2011 – 2018) über alle FGH Pflanzen oder alle Pflanzen (FGH und Feld) wurde ferner aus der maximalen Pflanzenhöhe (Population A) und der maximalen Pflanzenhöhe und mittleren Blattneigung (Population) vorhergesagt. Insgesamt konnten Bestandsparameter als Marker für Trockentoleranz genutzt werden. Dementsprechend könnte Trockenstresszucht in Kartoffeln beschleunigt werden, indem Blattneigung, Lichteinfalltiefe, Pflanzenhöhe und Oberflächentemperatur-Abweichung als Marker für Trockentoleranz, insbesondere unter Langzeitstressbedingungen, genutzt werden. (Übersetzung Karin Köhl, 4.6.2020). KW - Canopy parameters KW - Drought tolerance KW - DRYM KW - Bestandsparameter KW - Trockentoleranz KW - DRYM Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-486836 ER - TY - JOUR A1 - Andrés-Delgado, Laura A1 - Ernst, Alexander A1 - Galardi-Castilla, María A1 - Bazaga, David A1 - Peralta, Marina A1 - Münch, Juliane A1 - Gonzalez-Rosa, Juan M. A1 - Marques, Inês A1 - Tessadori, Federico A1 - de la Pompa, José Luis A1 - Vermot, Julien A1 - Mercader, Nadia T1 - Actin dynamics and the Bmp pathway drive apical extrusion of proepicardial cells JF - Development : Company of Biologists N2 - The epicardium, the outer mesothelial layer enclosing the myocardium, plays key roles in heart development and regeneration. During embryogenesis, the epicardium arises from the proepicardium (PE), a cell cluster that appears in the dorsal pericardium (DP) close to the venous pole of the heart. Little is known about how the PE emerges from the pericardial mesothelium. Using a zebrafish model and a combination of genetic tools, pharmacological agents and quantitative in vivo imaging, we reveal that a coordinated collective movement of DP cells drives PE formation. We found that Bmp signaling and the actomyosin cytoskeleton promote constriction of the DP, which enables PE cells to extrude apically. We provide evidence that cell extrusion, which has been described in the elimination of unfit cells from epithelia and the emergence of hematopoietic stem cells, is also a mechanism for PE cells to exit an organized mesothelium and fulfil their developmental fate to form a new tissue layer, the epicardium. KW - Actomyosin KW - Bmp KW - Cell extrusion KW - Proepicardium KW - Zebrafish KW - Heart development Y1 - 2019 U6 - https://doi.org/10.1242/dev.174961 SN - 0950-1991 SN - 1477-9129 VL - 146 IS - 13 PB - The Company of Biologists Ltd CY - Cambridge ER - TY - JOUR A1 - Andresen, Heiko A1 - Grötzinger, Carsten A1 - Zarse, Kim A1 - Birringer, Marc A1 - Hessenius, Carsten A1 - Kreuzer, Oliver Johannes A1 - Ehrentreich-Förster, Eva A1 - Bier, Frank Fabian T1 - Peptide microarrays with site-specifically immobilized synthetic peptides for antibody diagnostics N2 - Peptide microarrays bear the potential to discover molecular recognition events on protein level, particularly in the field of molecular immunology, in a manner and with an efficiency comparable to the performance of DNA microarrays. We developed a novel peptide microarray platform for the detection of antibodies in liquid samples. The system comprises site-specific solution phase coupling of biotinylated peptides to NeutrAvidin, localized microdispensing of peptide-NeutrAvidin conjugates onto activated glass slides and a fluorescence immuno sandwich assay format for antibody capture and detection. Our work includes synthetic peptides deduced from amino acid sequences of immunodominant linear epitopes, such as the T7 phage capsid protein, Herpes simplex virus glycoprotein D, c-myc protein and three domains of the Human coronavirus 229E polymerase polyprotein. We demonstrate that our method produces peptide arrays with excellent spot morphology which are capable of specific and sensitive detection of monoclonal antibodies from fluid samples. Y1 - 2006 UR - http://www.sciencedirect.com/science/journal/09254005 U6 - https://doi.org/10.1016/j.snb.2005.07.033 SN - 0925-4005 ER - TY - JOUR A1 - Andresen, Heiko A1 - Grotzinger, Carsten A1 - Zarse, Kim A1 - Kreuzer, Oliver Johannes A1 - Ehrentreich-Förster, Eva A1 - Bier, Frank Fabian T1 - Functional peptide microarrays for specific and sensitive antibody diagnostics N2 - Peptide microarrays displaying biologically active small synthetic peptides in a high-density format provide an attractive technology to probe complex samples for the presence and/or function of protein analytes. We present a new approach for manufacturing functional peptide microarrays for molecular immune diagnostics. Our method relies on the efficiency of site-specific solution-phase coupling of biotinylated synthetic peptides to NeutrAvidin (NA) and localized microdispensing of peptide-NA-complexes onto activated glass surfaces. Antibodies are captured in a sandwich manner between surface immobilized peptide probes and fluorescence-labeled secondary antibodies. Our work includes a total of 54 peptides derived from immunodominant linear epitopes of the T7 phage capsid protein, Herpes simplex virus glycoprotein D, c-myc protein, and three domains of the Human coronavirus polymerase polyprotein and their cognate mAbs. By using spacer molecules of different type and length for NA-mediated peptide presentation, we show that the incorporation of a minimum spacer length is imperative for antibody binding, whereas the peptide immobilization direction has only secondary importance for antibody affinity and binding. We further demonstrate that the peptide array is capable of detecting low-picomolar concentrations of mAbs in buffered solutions and diluted human serum with high specificity Y1 - 2006 UR - http://www3.interscience.wiley.com/cgi-bin/jhome/76510741 U6 - https://doi.org/10.1002/pmic.200500343 SN - 1615-9853 ER -