TY - THES A1 - Swart, Corné T1 - Managing protein activity in A. thaliana BT - A proteomic approach to understanding SUMOylation as well as the regulation of carbohydrate metabolism Y1 - 2017 ER - TY - THES A1 - Hochrein, Lena T1 - Development of a new DNA-assembly method and its application for the establishment of a red light-sensing regulation system T1 - Entwicklung einer neuartigen DNS-Assemblierungsmethode und ihre Anwendung für die Etablierung eines Rotlicht-responsiven Regulierungssystems N2 - In der hier vorgelegten Doktorarbeit wurde eine Strategie zur schnellen, einfachen und zuverlässigen Assemblierung von DNS-Fragmenten, genannt AssemblX, entwickelt. Diese kann genutzt werden, um komplexe DNS-Konstrukte, wie beispielsweise komplette Biosynthesewege, aufzubauen. Dies dient der Produktion von technisch oder medizinisch relevanten Produkten in biotechnologisch nutzbaren Organismen. Die Vorteile der Klonierungsstrategie liegen in der Schnelligkeit der Klonierung, der Flexibilität bezüglich des Wirtsorganismus, sowie der hohen Effektivität, die durch gezielte Optimierung erreicht wurde. Die entwickelte Technik erlaubt die nahtlose Assemblierung von Genfragmenten und bietet eine Komplettlösung von der Software-gestützten Planung bis zur Fertigstellung von DNS-Konstrukten, welche die Größe von Mini-Chromosomen erreichen können. Mit Hilfe der oben beschriebenen AssemblX Strategie wurde eine optogenetische Plattform für die Bäckerhefe Saccharomyces cerevisiae etabliert. Diese besteht aus einem Rotlicht-sensitiven Photorezeptor und seinem interagierenden Partner aus Arabidopsis thaliana, welche in lichtabhängiger Weise miteinander agieren. Diese Interaktion wurde genutzt, um zwei Rotlicht-aktivierbare Proteine zu erstellen: Einen Transkriptionsfaktor, der nach Applikation eines Lichtpulses die Produktion eines frei wählbaren Proteins stimuliert, sowie eine Cre Rekombinase, die ebenfalls nach Bestrahlung mit einer bestimmten Wellenlänge die zufallsbasierte Reorganisation bestimmter DNS-Konstrukte ermöglicht. Zusammenfassend wurden damit drei Werkzeuge für die synthetische Biologie etabliert. Diese ermöglichen den Aufbau von komplexen Biosynthesewegen, deren Licht-abhängige Regulation, sowie die zufallsbasierte Rekombination zu Optimierungszwecken. N2 - With Saccharomyces cerevisiae being a commonly used host organism for synthetic biology and biotechnology approaches, the work presented here aims at the development of novel tools to improve and facilitate pathway engineering and heterologous protein production in yeast. Initially, the multi-part assembly strategy AssemblX was established, which allows the fast, user-friendly and highly efficient construction of up to 25 units, e.g. genes, into a single DNA construct. To speed up complex assembly projects, starting from sub-gene fragments and resulting in mini-chromosome sized constructs, AssemblX follows a level-based approach: Level 0 stands for the assembly of genes from multiple sub-gene fragments; Level 1 for the combination of up to five Level 0 units into one Level 1 module; Level 2 for linkages of up to five Level 1 modules into one Level 2 module. This way, all Level 0 and subsequently all Level 1 assemblies can be carried out simultaneously. Individually planned, overlap-based Level 0 assemblies enable scar-free and sequence-independent assemblies of transcriptional units, without limitations in fragment number, size or content. Level 1 and Level 2 assemblies, which are carried out via predefined, computationally optimized homology regions, follow a standardized, highly efficient and PCR-free scheme. AssemblX follows a virtually sequence-independent scheme with no need for time-consuming domestication of assembly parts. To minimize the risk of human error and to facilitate the planning of assembly projects, especially for individually designed Level 0 constructs, the whole AssemblX process is accompanied by a user-friendly webtool. This webtool provides the user with an easy-to-use operating surface and returns a bench-protocol including all cloning steps. The efficiency of the assembly process is further boosted through the implementation of different features, e.g. ccdB counter selection and marker switching/reconstitution. Due to the design of homology regions and vector backbones the user can flexibly choose between various overlap-based cloning methods, enabling cost-efficient assemblies which can be carried out either in E. coli or yeast. Protein production in yeast is additionally supported by a characterized library of 40 constitutive promoters, fully integrated into the AssemblX toolbox. This provides the user with a starting point for protein balancing and pathway engineering. Furthermore, the final assembly cassette can be subcloned into any vector, giving the user the flexibility to transfer the individual construct into any host organism different from yeast. As successful production of heterologous compounds generally requires a precise adjustment of protein levels or even manipulation of the host genome to e.g. inhibit unwanted feedback regulations, the optogenetic transcriptional regulation tool PhiReX was designed. In recent years, light induction was reported to enable easy, reversible, fast, non-toxic and nearly gratuitous regulation, thereby providing manifold advantages compared to conventional chemical inducers. The optogenetic interface established in this study is based on the photoreceptor PhyB and its interacting protein PIF3. Both proteins, derived from Arabidopsis thaliana, dimerize in a red/far-red light-responsive manner. This interaction depends on a chromophore, naturally not available in yeast. By fusing split proteins to both components of the optical dimerizer, active enzymes can be reconstituted in a light-dependent manner. For the construction of the red/far-red light sensing gene expression system PhiReX, a customizable synTALE-DNA binding domain was fused to PhyB, and a VP64 activation domain to PIF3. The synTALE-based transcription factor allows programmable targeting of any desired promoter region. The first, plasmid-based PhiReX version mediates chromophore- and light-dependent expression of the reporter gene, but required further optimization regarding its robustness, basal expression and maximum output. This was achieved by genome-integration of the optical regulator pair, by cloning the reporter cassette on a high-copy plasmid and by additional molecular modifications of the fusion proteins regarding their cellular localization. In combination, this results in a robust and efficient activation of cells over an incubation time of at least 48 h. Finally, to boost the potential of PhiReX for biotechnological applications, yeast was engineered to produce the chromophore. This overcomes the need to supply the expensive and photo-labile compound exogenously. The expression output mediated through PhiReX is comparable to the strong constitutive yeast TDH3 promoter and - in the experiments described here - clearly exceeds the commonly used galactose inducible GAL1 promoter. The fast-developing field of synthetic biology enables the construction of complete synthetic genomes. The upcoming Synthetic Yeast Sc2.0 Project is currently underway to redesign and synthesize the S. cerevisiae genome. As a prerequisite for the so-called “SCRaMbLE” system, all Sc2.0 chromosomes incorporate symmetrical target sites for Cre recombinase (loxPsym sites), enabling rearrangement of the yeast genome after induction of Cre with the toxic hormonal substance beta-estradiol. To overcome the safety concern linked to the use of beta-estradiol, a red light-inducible Cre recombinase, dubbed L-SCRaMbLE, was established in this study. L-SCRaMbLE was demonstrated to allow a time- and chromophore-dependent recombination with reliable off-states when applied to a plasmid containing four genes of the beta-carotene pathway, each flanked with loxPsym sites. When directly compared to the original induction system, L-SCRaMbLE generates a larger variety of recombination events and lower basal activity. In conclusion, L-SCRaMbLE provides a promising and powerful tool for genome rearrangement. The three tools developed in this study provide so far unmatched possibilities to tackle complex synthetic biology projects in yeast by addressing three different stages: fast and reliable biosynthetic pathway assembly; highly specific, orthogonal gene regulation; and tightly controlled synthetic evolution of loxPsym-containing DNA constructs. KW - synthetic biology KW - pathway engineering KW - DNA assembly KW - transcription factor KW - Cre recombinase KW - optogenetics KW - synthetische Biologie KW - Optimierung von Biosynthesewegen KW - DNS Assemblierung KW - Transkriptionsfaktor KW - Cre Rekombinase KW - Optogenetik Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-404441 ER - TY - THES A1 - Kubsch, Bastian T1 - Phase-specific fusion between biomembranes using SNARE mimetics Y1 - 2017 ER - TY - THES A1 - Bajdzienko, Krzysztof T1 - Analysis of Target of Rapamycin (Tor) induced changes of the Arabidopsis thaliana proteome using sub-cellular resolution Y1 - 2017 ER - TY - THES A1 - Heise, Janine T1 - Phylogenetic and physiological characterization of deep-biosphere microorganisms in El’gygytgyn Crater Lake sediments T1 - Phylogenetische und physiologische Charakterisierung der Tiefen Biosphäre in El'gygytgyn Kraterseesedimenten N2 - The existence of diverse and active microbial ecosystems in the deep subsurface – a biosphere that was originally considered devoid of life – was discovered in multiple microbiological studies. However, most of the studies are restricted to marine ecosystems, while our knowledge about the microbial communities in the deep subsurface of lake systems and their potentials to adapt to changing environmental conditions is still fragmentary. This doctoral thesis aims to build up a unique data basis for providing the first detailed high-throughput characterization of the deep biosphere of lacustrine sediments and to emphasize how important it is to differentiate between the living and the dead microbial community in deep biosphere studies. In this thesis, up to 3.6 Ma old sediments (up to 317 m deep) of the El’gygytgyn Crater Lake were examined, which represents the oldest terrestrial climate record of the Arctic. Combining next generation sequencing with detailed geochemical characteristics and other environmental parameters, the microbial community composition was analyzed in regard to changing climatic conditions within the last 3.6 Ma to 1.0 Ma (Pliocene and Pleistocene). DNA from all investigated sediments was successfully extracted and a surprisingly diverse (6,910 OTUs) and abundant microbial community in the El’gygytgyn deep sediments were revealed. The bacterial abundance (10³-10⁶ 16S rRNA copies g⁻¹ sediment) was up to two orders of magnitudes higher than the archaeal abundance (10¹-10⁵) and fluctuates with the Pleistocene glacial/interglacial cyclicality. Interestingly, a strong increase in the microbial diversity with depth was observed (approximately 2.5 times higher diversity in Pliocene sediments compared to Pleistocene sediments). The increase in diversity with depth in the Lake El’gygytgyn is most probably caused by higher sedimentary temperatures towards the deep sediment layers as well as an enhanced temperature-induced intra-lake bioproductivity and higher input of allochthonous organic-rich material during Pliocene climatic conditions. Moreover, the microbial richness parameters follow the general trends of the paleoclimatic parameters, such as the paleo-temperature and paleo-precipitation. The most abundant bacterial representatives in the El’gygytgyn deep biosphere are affiliated with the phyla Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria, which are also commonly distributed in the surrounding permafrost habitats. The predominated taxon was the halotolerant genus Halomonas (in average 60% of the total reads per sample). Additionally, this doctoral thesis focuses on the live/dead differentiation of microbes in cultures and environmental samples. While established methods (e.g., fluorescence in situ hybridization, RNA analyses) are not applicable to the challenging El’gygytgyn sediments, two newer methods were adapted to distinguish between DNA from live cells and free (extracellular, dead) DNA: the propidium monoazide (PMA) treatment and the cell separation adapted for low amounts of DNA. The applicability of the DNA-intercalating dye PMA was successfully evaluated to mask free DNA of different cultures of methanogenic archaea, which play a major role in the global carbon cycle. Moreover, an optimal procedure to simultaneously treat bacteria and archaea was developed using 130 µM PMA and 5 min of photo-activation with blue LED light, which is also applicable on sandy environmental samples with a particle load of ≤ 200 mg mL⁻¹. It was demonstrated that the soil texture has a strong influence on the PMA treatment in particle-rich samples and that in particular silt and clay-rich samples (e.g., El’gygytgyn sediments) lead to an insufficient shielding of free DNA by PMA. Therefore, a cell separation protocol was used to distinguish between DNA from live cells (intracellular DNA) and extracellular DNA in the El’gygytgyn sediments. While comparing these two DNA pools with a total DNA pool extracted with a commercial kit, significant differences in the microbial composition of all three pools (mean distance of relative abundance: 24.1%, mean distance of OTUs: 84.0%) was discovered. In particular, the total DNA pool covers significantly fewer taxa than the cell-separated DNA pools and only inadequately represents the living community. Moreover, individual redundancy analyses revealed that the microbial community of the intra- and extracellular DNA pool are driven by different environmental factors. The living community is mainly influenced by life-dependent parameters (e.g., sedimentary matrix, water availability), while the extracellular DNA is dependent on the biogenic silica content. The different community-shaping parameters and the fact, that a redundancy analysis of the total DNA pool explains significantly less variance of the microbial community, indicate that the total DNA represents a mixture of signals of the live and dead microbial community. This work provides the first fundamental data basis of the diversity and distribution of microbial deep biosphere communities of a lake system over several million years. Moreover, it demonstrates the substantial importance of extracellular DNA in old sediments. These findings may strongly influence future environmental community analyses, where applications of live/dead differentiation avoid incorrect interpretations due to a failed extraction of the living microbial community or an overestimation of the past community diversity in the course of total DNA extraction approaches. N2 - Innerhalb der letzten 20 Jahre wurden diverse und aktive mikrobielle Gemeinschaften in zahlreichen Habitaten der tiefen Biosphäre gefunden, in denen zuvor kein Leben denkbar war. Die mikrobiologischen Untersuchungen beschränken sich dabei meist auf marine Ökosysteme, wohingegen das Wissen über die tiefe Biosphäre von Seesystemen und die Anpassung der Mikroorganismen an sich ändernde klimatische Bedingungen noch sehr eingeschränkt ist. Ziel dieser Arbeit ist es, die mikrobielle Gemeinschaftsstruktur der tiefen Biosphäre des El‘gygytgyn Kratersees in Hinblick auf klimatische Veränderungen der vergangenen 1,0 bis 3,6 Millionen Jahre zu charakterisieren, beeinflussende Umweltparameter zu detektieren und dabei zwischen der lebenden und toten mikrobiellen Gemeinschaft zu differenzieren. Die Seesedimente (43-317 m tief) weisen eine erstaunlich hohe Diversität (6910 OTUs) und Mikrobenfülle (10³-10⁶ bakterielle, 10¹-10⁵ archaeale 16S rRNA Kopien g⁻¹ Sediment) auf, wobei eine 2,5-fach höhere Diversität in den pliozänen Sedimenten im Vergleich zu den jüngeren pleistozänen Sedimenten detektiert werden konnte. Der Diversitätsanstieg mit zunehmendem Sedimentalter (und Tiefe) basiert höchstwahrscheinlich auf die erhöhte temperaturinduzierte Bioaktivität im See und dem erhöhten Eintrag von Organik reichen Material innerhalb des Pliozäns (feucht und warm). Die Unterscheidung zwischen der DNA lebender Mikroben (intrazellulare DNA) und freier DNA (extrazellulare DNA, meist von toten Mikroben) wurde durch die Adaption von zwei Extraktionsmethoden, der Behandlung mit Propidium-Monoazid (PMA) und der Zellseparation, erreicht. Dabei wurde ein PMA-Protokoll (130 µM PMA, 5 Min Lichtaktivierung mit blauen LEDs) zur erfolgreichen Behandlung von Reinkulturen methanogener Archaeen etabliert, das auch für sandige Umweltproben (Partikelbeladung ≤ 200 mg mL⁻¹) nutzbar ist. Für die feinporigeren Seesedimente des El’gygytgyn Kratersees wurden die zellseparierten DNA-Pools der iDNA und eDNA mit dem Gesamt-DNA-Extrakt (kommerzielles Kit) verglichen, wobei die DNA-Pools starke Unterschiede in ihrer Zusammensetzung aufzeigten (24,1% Distanz basierend auf relative Häufigkeiten) und der Gesamt-DNA-Extrakt die lebende mikrobielle Gemeinschaft nur unzureichend widerspiegeln konnte. Individuelle Redundanzanalysen (RDA) zeigten, dass die mikrobielle Gemeinschaft der iDNA von lebensbeeinflussenden Parametern abhängig ist (u.a. Sedimentmatrix, Wasserverfügbarkeit), wohingegen die der eDNA maßgeblich durch den Anteil an biogener Kieselerde (silica) beeinflusst wird. Diese Arbeit stellt die erste umfangreiche Datenbasis der Diversität und Verteilung von Mikroorganismengemeinschaften in der tiefen Biosphäre eines Seesystems über mehrere Millionen Jahre dar. Zusätzlich zeigt die Studie, dass die Lebend/Tot-Unterscheidung, mit dem ein höherer Anteil der Varianz innerhalb der Gemeinschaft durch Umweltparameter erklärt werden kann, im Vergleich zur Gesamt-DNA-Extraktion ein wesentlicher Schritt zur genauen Widerspiegelung der mikrobiellen Gemeinschaft und deren Funktion in der Tiefen Biosphäre ist. KW - Mikrobiologie KW - El`gygytgyn Kratersee KW - Tiefe Biosphäre KW - Diversität KW - microbiology KW - El’gygytgyn Crater Lake KW - diversity KW - deep biosphere Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-403436 ER - TY - THES A1 - Suchoszek, Monika T1 - Characterization of inducible galactolipid biosynthesis mutants in tobacco N2 - Chloroplast membranes have a unique composition characterized by very high contents of the galactolipids, MGDG and DGDG. Many studies on constitutive, galactolipid-deficient mutants revealed conflicting results about potential functions of galactolipids in photosynthetic membranes. Likely, this was caused by pleiotropic effects such as starvation artefacts because of impaired photosynthesis from early developmental stages of the plants onward. Therefore, an ethanol inducible RNAi-approach has been taken to suppress two key enzymes of galactolipid biosynthesis in the chloroplast, MGD1 and DGD1. Plants were allowed to develop fully functional source leaves prior to induction, which then could support plant growth. Then, after the ethanol induction, both young and mature leaves were investigated over time. Our studies revealed similar changes in both MGDG- and DGDG-deficient lines, however young and mature leaves of transgenic lines showed a different response to galactolipid deficiency. While no changes of photosynthetic parameters and minor changes in lipid content were observed in mature leaves of transgenic lines, strong reductions in total chlorophyll content and in the accumulation of all photosynthetic complexes and significant changes in contents of various lipid groups occurred in young leaves. Microscopy studies revealed an appearance of lipid droplets in the cytosol of young leaves in all transgenic lines which correlates with significantly higher levels of TAGs. Since in young leaves the production of membrane lipids is lowered, the excess of fatty acids is used for storage lipids production, resulting in the accumulation of TAGs. Our data indicate that both investigated galactolipids serve as structural lipids since changes in photosynthetic parameters were mainly the result of reduced amounts of all photosynthetic constituents. In response to restricted galactolipid synthesis, thylakoid biogenesis is precisely readjusted to keep the proper stoichiometry and functionality of the photosynthetic apparatus. Ultimately, the data revealed that downregulation of one galactolipid triggers changes not only in chloroplasts but also in the nucleus as shown by downregulation of nuclear encoded subunits of the photosynthetic complexes. KW - galactolipids KW - photosynthesis KW - tobacco Y1 - 2017 ER - TY - THES A1 - Ribeiro Martins, Renata Filipa T1 - Deciphering evolutionary histories of Southeast Asian Ungulates T1 - Entschlüsselung der Evolutionsgeschichte Südostasiatischer Huftiere BT - comparative phylogeography in a biodiversity hotspot BT - vergleichende Phylogeographie in einem Biodiversitaets-Hotspot N2 - Im Verlauf von Jahrmillionen gestalteten evolutionäre Kräfte die Verbreitung und genetische Variabilität von Arten, indem sie die Anpassungsfähigkeit und Überlebenswahrscheinlichkeit dieser Arten beeinflussten. Da Südostasien eine außerordentlich artenreiche Region darstellt, eignet sie sich besonders, um den Einfluss dieser Kräfte zu untersuchen. Historische Klimaveränderungen hatten dramatische Auswirkungen auf die Verfügbarkeit sowie die Verbreitung von Habitaten in Südostasien, weil hierdurch wiederholt das Festland mit sonst isolierten Inseln verbunden wurde. Dies beeinflusste nicht nur, wie Arten in dieser Region verbreitet sind, sondern ermöglichte auch eine zunehmende genetische Variabilität. Zwar ist es bekannt, dass Arten mit ähnlicher Evolutionsgeschichte unterschiedliche phylogeographische Muster aufweisen können. Die zugrundeliegenden Mechanismen sind jedoch nur gering verstanden. Diese Dissertation behandelt die Phylogeographie von drei Gruppen von Huftieren, welche im Süden und Südosten Asiens vorkommen. Dabei war das vornehmliche Ziel, zu verstehen, wie es zur Ausbildung verschiedener Arten sowie zu einer regionalen Verteilung von genetischer Variabilität kam. Hierfür untersuchte ich die mitochondrialen Genome alter Proben. Dadurch war es möglich, Populationen des gesamten Verbreitungsgebietes der jeweiligen Arten zu untersuchen – auch solche Populationen, die heutzutage nicht mehr existieren. Entsprechend der einzelnen Huftiergruppen ist diese Arbeit in drei Kapitel unterteilt: Muntjaks (Muntiacus sp.), Hirsche der Gattung Rusa und asiatische Nashörner. Alle drei Gruppen weisen eine Aufteilung in unterschiedliche Linien auf, was jeweils direkt auf Ereignisse des Pleistozäns zurückgeführt werden kann. Muntjaks sind eine weit verbreitete Art, die in verschiedensten Habitaten vorkommen kann. Ich wies nach, dass es in der Vergangenheit zu genetischem Austausch zwischen Populationen von verschiedenen Inseln des Sundalandes kam. Dies deutet auf die Fähigkeit von Muntjaks hin, sich an die ehemaligen Landbrücken anzupassen. Jedoch zeige ich auch, dass mindestens zwei Hindernisse bei ihrer Verbreitung existierten, wodurch es zu einer Differenzierung von Populationen kam: eine Barriere trennte Populationen des asiatischen Festlands von denen der Sundainseln, die andere isolierte sri-lankische von restlichen Muntjaks. Die zwei untersuchten Rusa-Arten weisen ein anderes Muster auf, was wiederum eine weitere Folge der pleistozänen Landbrücken darstellt. Beide Arten sind ausschließlich monophyletisch. Allerdings gibt es Anzeichen für die Hybridisierung dieser Arten auf Java, was durch eine frühere Ausbreitung des sambar (R. unicolor) gefördert wurde. Aufgrund dessen fand ich zudem, dass all jene Individuen der anderen Art, R. timorensis, die durch den Menschen auf die östlichen Sundainseln gebracht wurden, in Wahrheit Hybride sind. Für den dritten Teil war es mir möglich, Proben von Vertretern ausgestorbener Populationen vom asiatischen Festland des Sumatra- und des Java-Nashorns (Dicerorhinus sumatrensis und Rhinoceros sondaicus) zu analysieren. Die Ergebnisse meiner Arbeit belegen, dass die genetische Vielfalt dieser historischen Populationen bedeutend größer war als die der heutigen Nachkommen. Ihre jeweilige Evolutionsgeschichte korreliert stark mit pleistozänen Prozessen. Außerdem betonen meine Ergebnisse das enorme Ausmaß von verlorener genetischer Diversität dieser stark bedrohten Arten. Jede Art besitzt eine individuelle phylogeographische Geschichte. Ebenso fand ich aber auch allgemeingültige Muster von genetischer Differenzierung in allen Gruppen, welche direkt mit Ereignissen des Pleistozäns assoziiert werden können. Vergleicht man jedoch die einzelnen Ergebnisse der Arten, wird deutlich, dass die gleichen geologischen Prozesse nicht zwangsläufig in gleiche evolutive Ergebnisse resultieren. Einer der Gründe hierfür könnte zum Beispiel die unterschiedliche Durchlässigkeit der entstandenen Landkorridore des Sundaschelfs sein. Die Möglichkeit diese neuen Habitate zu nutzen und somit auch zu passieren steht im direkten Bezug zu den spezifischen ökologischen Bedürfnissen der Arten.Zusammenfassend leisten meine Erkenntnisse einen wichtigen Beitrag, die Evolution und geographische Aufteilung der genetischen Vielfalt in diesem Hotspot an Biodiversität zu verstehen. Obendrein können sie aber auch Auswirkungen auf die Erhaltung und systematische Klassifikation der untersuchten Arten haben. N2 - During the course of millions of years, evolutionary forces have shaped the current distribution of species and their genetic variability, by influencing their phylogeny, adaptability and probability of survival. Southeast Asia is an extraordinary biodiverse region, where past climate events have resulted in dramatic changes in land availability and distribution of vegetation, resulting likewise in periodic connections between isolated islands and the mainland. These events have influenced the way species are distributed throughout this region but, more importantly, they influenced the genesis of genetic diversity. Despite the observation that a shared paleo-history resulted in very diverse species phylogeographic patterns, the mechanisms behind these patterns are still poorly understood. In this thesis, I investigated and contrasted the phylogeography of three groups of ungulate species distributed within South and Southeast Asia, aiming to understand what mechanisms have shaped speciation and geographical distribution of genetic variability. For that purpose, I analysed the mitogenomes of historical samples, in order to account for populations from the entire range of species distributions – including populations that no longer exist. This thesis is organized in three manuscripts, which correspond to the three investigated groups: red muntjacs, Rusa deer and Asian rhinoceros. Red muntjacs are a widely distributed species and occur in very different habitats. We found evidence for gene-flow among populations of different islands, indicative of their ability to utilize the available land corridors. However, we described also the existence of at least two dispersal barriers that created population differentiation within this group; one isolated Sundaic and Mainland populations and the second separated individuals from Sri Lanka. Second, the two Rusa species investigated here revealed another consequence of the historical land connections. While the two species were monophyletic, we found evidence of hybridisation in Java, facilitated by the expansion of the widespread sambar, Rusa unicolor. Consequently, I found that all the individuals of Javan deer, R. timorensis which were transported to the east of Sundaland by humans, to be of hybrid descent. In the last manuscript, we were able to include samples from the extinct mainland populations of both Sumatran and Javan rhinoceros. The results revealed a much higher genetic diversity of the historical populations than ever reported for the contemporaneous survivors. Their evolutionary histories revealed a close relationship to climatic events of the Pleistocene but, more importantly, point out the vast extent of genetic erosion within these two endangered species. The specific phylogeographic history of the species showed some common patters of genetic differentiation that could be directly linked to the climatic and geological changes on the Sunda Shelf during the Pleistocene. However, by contrasting these results I discussed that the same geological events did not always result in similar histories. One obvious example was the different permeability of the land corridors of Sundaland, as the ability of each species to utilize this newly available land was directly related to their specific ecological requirements. Taken together, these results have an important contribution to the general understanding of evolution in this biodiversity hotspot and the main drivers shaping the distribution of genetic diversity, but could also have important consequences for taxonomy and conservation of the three investigated groups. KW - biogeography KW - Southeast Asia KW - ungulates KW - NGS KW - evolutionary history KW - Phylogeographie KW - Südostasien KW - Huftiere KW - Evolutionsgenetik Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-404669 ER - TY - THES A1 - Weiß, Lina T1 - Understanding the emergence and maintenance of biodiversity in grasslands BT - linking individual plant responses to community patterns Y1 - 2017 ER - TY - THES A1 - Kruse, Stefan T1 - Larix treeline dynamics in northern Siberia inferred from population genetics and individual-based modelling Y1 - 2017 ER - TY - THES A1 - Janowski, Marcin Andrzej T1 - Investigating role of the essential GTPase - AtRsgA in the assembly of the small ribosomal subunit in Arabidopsis thaliana chloroplast Y1 - 2017 ER - TY - THES A1 - Belkius, Karolina Dorota T1 - Systems biology approach to investigate the development and degradation of the photosynthetic apparatus during leaf ontogenesis in higher plants Y1 - 2017 ER - TY - THES A1 - Diez Cocero, Mercedes T1 - Analysis of Rubisco - carbonic anhydrase fusions in tobacco as an approach to reduce photorespiration Y1 - 2017 ER - TY - THES A1 - Fichtner, Franziska T1 - The role of Trehalose 6-Phosphate synthase 1 and trehalose 6-phosphate in plant metabolism and development Y1 - 2017 ER - TY - THES A1 - Janowski, Marcin Andrzej T1 - Investigating role of the essential GTPase - AtRsgA in the assembly of the small ribosomal subunit in Arabidopsis thaliana chloroplast N2 - Plastid protein biosynthesis occurs on bacterial-type 70S ribosomes consisting of a large (50S) and a small (30S) subunit. However, since many steps of ribosome biogenesis are not thermodynamically favorable at biological conditions, it requires many assembly factors. One group of assembly factors, circularly permuted GTPases, was implicated in 30S subunit maturation in E. coli, by a protein RsgA. RsgA orthologues are present in bacteria and plastid-containing species and in silico analysis revealed presence of a RsgA-like protein in Arabidopsis thaliana. To functionally characterize the Arabidopsis orthologue, two AtRsgA T-DNA insertion lines were analyzed in this study. The exon line (rsgA-e) led to embryo lethality, while the intron line (rsgA-i) caused severe dwarf, pale green phenotype. Further investigation of rsgA-i mutant line revealed defects in chloroplast biogenesis which led to increased number of chloroplasts, decreased chloroplast size, decreased air space between mesophyll cells and smaller shoot apical meristems, which showed unusual proplastid accumulation. Moreover, rsgA-i plants showed reduction in chlorophyll A and B content, decreased electron transport rate and photosynthetic efficiency. Further analyses revealed that the protein is involved in chloroplast 30S subunit maturation. Interestingly, we observed that while chloroplast-targeted and chloroplast-encoded proteins are generally downregulated in the mutant, a contrasting upregulation of the corresponding transcripts is observed, indicating an elaborate compensatory mechanism. To conclude, the study presented here reveals a ribosome assembly factor and a compensatory mechanism activated during impaired chloroplast function. KW - ribosome assembly KW - GTPase KW - chloro-ribosome KW - translation Y1 - 2017 ER - TY - THES A1 - Diez Cocero, Mercedes T1 - Analysis of Rubisco – carbonic anhydrase fusions in tobacco as an approach to reduce photorespiration N2 - Rubisco catalyses the first step of CO2 assimilation into plant biomass. Despite its crucial role, it is notorious for its low catalytic rate and its tendency to fix O2 instead of CO2, giving rise to a toxic product that needs to be recycled in a process known as photorespiration. Since almost all our food supply relies on Rubisco, even small improvements in its specificity for CO2 could lead to an improvement of photosynthesis and ultimately, crop yield. In this work, we attempted to improve photosynthesis by decreasing photorespiration with an artificial CCM based on a fusion between Rubisco and a carbonic anhydrase (CA). A preliminary set of plants contained fusions between one of two CAs, bCA1 and CAH3, and the N- or C-terminus of RbcL connected by a small flexible linker of 5 amino acids. Subsequently, further fusion proteins were created between RbcL C-terminus and bCA1/CAH3 with linkers of 14, 23, 32, and 41 amino acids. The transplastomic tobacco plants carrying fusions with bCA1 were able to grow autotrophically even with the shortest linkers, albeit at a low rate, and accumulated very low levels of the fusion protein. On the other hand, plants carrying fusions with CAH3 were autotrophic only with the longer linkers. The longest linker permitted nearly wild-type like growth of the plants carrying fusions with CAH3 and increased the levels of fusion protein, but also of smaller degradation products. The fusion of catalytically inactive CAs to RbcL did not cause a different phenotype from the fusions with catalytically active CAs, suggesting that the selected CAs were not active in the fusion with RbcL or their activity did not have an effect on CO2 assimilation. However, fusions to RbcL did not abolish RbcL catalytic activity, as shown by the autotrophic growth, gas exchange and in vitro activity measurements. Furthermore, Rubisco carboxylation rate and specificity for CO2 was not altered in some of the fusion proteins, suggesting that despite the defect in RbcL folding or assembly caused by the fusions, the addition of 60-150 amino acids to RbcL does not affect its catalytic properties. On the contrary, most growth defects of the plants carrying RbcL-CA fusions are related to their reduced Rubisco content, likely caused by impaired RbcL folding or assembly. Finally, we found that fusions with RbcL C-terminus were better tolerated than with the N-terminus, and increasing the length of the linker relieved the growth impairment imposed by the fusion to RbcL. Together, the results of this work constitute considerable relevant findings for future Rubisco engineering. N2 - Rubisco katalysiert den ersten Schritt der CO2-Assimilierung. Trotz seiner bedeutenden Rolle, zeichnet sich Rubisco durch eine niedrige katalytische Geschwindigkeit aus. Außerdem, entsteht bei der Bindung von O2 anstatt CO2 ein toxisches Zwischenprodukt, welches in einem Prozess, genannt Photorespiration, aufbereitet wird. Da fast die gesamte Nahrungsmittelversorgung auf der Aktivität von Rubisco basiert, könnten schon kleine Verbesserungen in der Spezifität für CO2 zu einem großen Effekt in der Photosysntheserate und letztendlich größeren Ernteerträgen führen. In dieser Arbeit wurde versucht die Effizienz der Photosynthese zu verbessern, indem ein künstlicher CO2 konzentrierender Mechanismus aus einer Fusion von RbcL und einer Carboanhydrase (CA) gebildet wird. Als Vorversuch wurden je bCA1 und CAH3 an Rubiscos C- beziehungsweise N-Terminus mittels eines kleinen, flexiblen Linkers aus 5 Aminosäuren fusioniert. Anschließend wurden weitere Fusionsproteine zwischen dem C-Terminus von RbcL und bCA1/CAH3 mittels Linkern von 14, 23, 32 und 41 Aminosäuren Länge in Chloroplasten von Tabak eingebracht. Die entstandenen transplastomischen Pflanzen mit bCA1-Fusionen waren trotz ihres sehr langsamen Wachstums dazu fähig schon bei kurzen Linkern autotroph zu wachsen und geringe Mengen an Fusionsproteinen zu akkumulieren. Pflanzen mit CAH3 Fusionsproteinen hingegen waren nur mit längeren Linkern autotroph, zeigten aber dafür ähnliche Wachstumsraten zum Wildtyp bei Nutzung des längsten Linkers. Außerdem enthielten diese Pflanzen größere Mengen an Fusionsproteinen aber auch eine erhöhte Anreicherung von kleineren Abbauprodukten. Bei den in dieser Arbeit gewählten CA als Fusionsprotein mit RbcL konnte im Vergleich mit katalytisch inaktiven Varianten kein Effekt auf die CO2-Assimilierung gefunden werden. Wie das autotroph Wachstum sowie die Gaswechsel- und in-vitro-Aktivitätsmessungen zeigen, haben die Fusionen allerdings nicht die katalytische Aktivität von Rubisco blockiert. Ebenso verhielt sich die Carboxylierungsrate von Rubisco und deren Spezifität für CO2 unverändert. Dies weist darauf hin, dass trotz Rubiscos Faltungs- oder Assemblierungsdefekten das Anfügen von 60-150 Aminosäure an den C-Terminus von RbcL nicht die katalytische Leistung des Enzyms beeinträchtigt. Im Gegenteil, die Wachstumsdefekte waren durch die geringe Menge an Rubisco begründet, vermutlich verursacht durch Defekte in der Faltung oder Assemblierung von RbcL. Schlussendlich konnten wichtige Erkenntnisse für zukünftige gentechnische Veränderungen von Rubisco gemacht werden: Fusionen mit dem C-Terminus von RbcL wurden besser toleriert als mit dem N-Terminus und längere Linker verringerten die von der Fusion ausgelösten Wachstumsdefekte. KW - Rubisco KW - fusion Y1 - 2017 ER - TY - THES A1 - Tabatabaei, Iman T1 - Development of new selection systems for organellar genome transformation N2 - Plant cells host two important organelles: mitochondria, known as the cell’s ‘powerhouse’, which act by converting oxygen and nutrients into ATP, and plastids, which perform photosynthesis. These organelles contain their own genomes that encode proteins required for gene expression and energy metabolism. Transformation technologies offer great potential for investigating all aspects of the physiology and gene expression of these organelles in vivo. In addition, organelle transformation can be a valuable tool for biotechnology and molecular plant breeding. Plastid transformation systems are well-developed for a few higher plants, however, mitochondrial transformation has so far only been reported for Saccharomyces cerevisiae and the unicellular alga Chlamydomonas reinhardtii. Development of an efficient new selection marker for plastid transformation is important for several reasons, including facilitating supertransformation of the plastid genome for metabolic engineering purposes and for producing multiple knock-outs or site-directed mutagenesis of two unlinked genes. In this work, we developed a novel selection system for Nicotiana tabacum (tobacco) chloroplast transformation with an alternative marker. The marker gene, aac(6′)-Ie/aph(2′′)-Ia, was cloned into different plastid transformation vectors and several candidate aminoglycoside antibiotics were investigated as selection agents. Generally, the efficiency of selection and the transformation efficiency with aac(6′)-Ie/aph(2′′)-Ia as selectable marker in combination with the aminoglycoside antibiotic tobramycin was similarly high as that with the standard marker gene aadA and spectinomycin selection. Furthermore, our new selection system may be useful for the development of plastid transformation for new species, including cereals, the world’s most important food crops, and could also be helpful for the establishment of a selection system for mitochondrial transformation. To date, all attempts to achieve mitochondrial transformation for higher plants have been unsuccessful. A mitochondrial transformation system for higher plants would not only provide a potential for studying mitochondrial physiology but could also provide a method to introduce cytoplasmic male sterility into crops to produce hybrid seeds. Establishing a stable mitochondrial transformation system in higher plants requires several steps including delivery of foreign DNA, stable integration of the foreign sequences into the mitochondrial genome, efficient expression of the transgene, a highly regenerable tissue culture system that allows regeneration of the transformed cells into plants, and finally, a suitable selection system to identify cells with transformed mitochondrial genomes. Among all these requirements, finding a good selection is perhaps the most important obstacle towards the development of a mitochondrial transformation system for higher plants. In this work, two selection systems were tested for mitochondrial transformation: kanamycin as a selection system in combination with the antibiotic-inactivating marker gene nptII, and sulfadiazine as a selection agent that inhibits the folic acid biosynthesis pathway residing in plant mitochondria in combination with the sul gene encoding an enzyme that is insensitive to inhibition by sulfadiazine. Nuclear transformation experiments were considered as proof of the specificity of the sulfadiazine selection system for mitochondria. We showed that an optimized sulfadiazine selection system, with the Sul protein targeted to mitochondria, is much more efficient than the previous sulfadiazine selection system, in which the Sul protein was targeted to the chloroplast. We also showed by systematic experiments that the efficiency of selection and nuclear transformation of the optimized sulfadiazine selection was higher compared to the standard kanamycin selection system. Finally, we also investigated the suitability of this selection system for nuclear transformation of the model alga Chlamydomonas reinhardtii, obtaining promising results. Although we designed several mitochondrial transformation vectors with different expression elements and integration sites in the mitochondrial genome based on the sulfadiazine system, and different tissue culture condition were also considered, we were not able to obtain mitochondrial transformation with this system. Nonetheless, establishing the sul gene as an efficient and specific selection marker for mitochondria addresses one of the major bottlenecks and may pave the way to achieve mitochondrial transformation in higher plants. KW - plastid transformation KW - tobramycin KW - bifunctional enzyme KW - mitochondrial transformation KW - sulfadiazine Y1 - 2017 ER - TY - GEN A1 - Schwarzenberger, Anke A1 - Christjani, Mark A1 - Wacker, Alexander T1 - Longevity of Daphnia and the attenuation of stress responses by melatonin N2 - The widespread occurrence of melatonin in prokaryotes as well as eukaryotes indicates that this indoleamine is considerably old. This high evolutionary age has led to the development of diverse functions of melatonin in different organisms, such as the detoxification of reactive oxygen species and anti-stress effects. In insects, i.e. Drosophila, the addition of melatonin has also been shown to increase the life span of this arthropod, probably by reducing age-related increasing oxidative stress. Although the presence of melatonin was recently found to exist in the ecological and toxicological model organism Daphnia, its function in this cladoceran has thus far not been addressed. Therefore, we challenged Daphnia with three different stressors in order to investigate potential stress-response attenuating effects of melatonin. i) Female and male daphnids were exposed to melatonin in a longevity experiment, ii) Daphnia were confronted with stress signals from the invertebrate predator Chaoborus sp., and iii) Daphnia were grown in high densities, i.e. under crowding-stress conditions. Results In our experiments we were able to show that longevity of daphnids was not affected by melatonin. Therefore, age-related increasing oxidative stress was probably not compensated by added melatonin. However, melatonin significantly attenuated Daphnia’ s response to acute predator stress, i.e. the formation of neckteeth which decrease the ability of the gape-limited predator Chaoborus sp. to handle their prey. In addition, melatonin decreased the extent of crowding-related production of resting eggs of Daphnia. Conclusions Our results confirm the effect of melatonin on inhibition of stress-signal responses of Daphnia. Until now, only a single study demonstrated melatonin effects on behavioral responses due to vertebrate kairomones, whereas we clearly show a more general effect of melatonin: i) on morphological predator defense induced by an invertebrate kairomone and ii) on life history characteristics transmitted by chemical cues from conspecifics. Therefore, we could generally confirm that melatonin plays a role in the attenuation of responses to different stressors in Daphnia. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 405 KW - Daphnia KW - chaoborus kairomone KW - melatonin KW - crowding KW - longevity KW - stress response Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401476 ER - TY - GEN A1 - Zhu, Fangjun A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - Allele-specific expression at the androgen receptor alpha gene in a hybrid unisexual fish, the Amazon molly (Poecilia formosa) N2 - The all-female Amazon molly (Poecilia formosa) is the result of a hybridization of the Atlantic molly (P. mexicana) and the sailfin molly (P. latipinna) approximately 120,000 years ago. As a gynogenetic species, P. formosa needs to copulate with heterospecific males including males from one of its bisexual ancestral species. However, the sperm only triggers embryogenesis of the diploid eggs. The genetic information of the sperm donor typically will not contribute to the next generation of P. formosa. Hence, P. formosa possesses generally one allele from each of its ancestral species at any genetic locus. This raises the question whether both ancestral alleles are equally expressed in P. formosa. Allele-specific expression (ASE) has been previously assessed in various organisms, e.g., human and fish, and ASE was found to be important in the context of phenotypic variability and disease. In this study, we utilized Real-Time PCR techniques to estimate ASE of the androgen receptor alpha (arα) gene in several distinct tissues of Amazon mollies. We found an allelic bias favoring the maternal ancestor (P. mexicana) allele in ovarian tissue. This allelic bias was not observed in the gill or the brain tissue. Sequencing of the promoter regions of both alleles revealed an association between an Indel in a known CpG island and differential expression. Future studies may reveal whether our observed cis-regulatory divergence is caused by an ovary-specific trans-regulatory element, preferentially activating the allele of the maternal ancestor. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 395 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-403875 ER - TY - JOUR A1 - Zhu, Fangjun A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - Allele-specific expression at the androgen receptor alpha gene in a hybrid unisexual fish, the Amazon molly (Poecilia formosa) JF - PLoS one N2 - The all-female Amazon molly (Poecilia formosa) is the result of a hybridization of the Atlantic molly (P. mexicana) and the sailfin molly (P. latipinna) approximately 120,000 years ago. As a gynogenetic species, P. formosa needs to copulate with heterospecific males including males from one of its bisexual ancestral species. However, the sperm only triggers embryogenesis of the diploid eggs. The genetic information of the sperm donor typically will not contribute to the next generation of P. formosa. Hence, P. formosa possesses generally one allele from each of its ancestral species at any genetic locus. This raises the question whether both ancestral alleles are equally expressed in P. formosa. Allele-specific expression (ASE) has been previously assessed in various organisms, e.g., human and fish, and ASE was found to be important in the context of phenotypic variability and disease. In this study, we utilized Real-Time PCR techniques to estimate ASE of the androgen receptor alpha (arα) gene in several distinct tissues of Amazon mollies. We found an allelic bias favoring the maternal ancestor (P. mexicana) allele in ovarian tissue. This allelic bias was not observed in the gill or the brain tissue. Sequencing of the promoter regions of both alleles revealed an association between an Indel in a known CpG island and differential expression. Future studies may reveal whether our observed cis-regulatory divergence is caused by an ovary-specific trans-regulatory element, preferentially activating the allele of the maternal ancestor. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0186411 SN - 1932-6203 VL - 12 IS - 10 SP - 1 EP - 14 PB - PLoS CY - Lawrence, Kan. ER - TY - GEN A1 - Fer, Istem A1 - Tietjen, Britta A1 - Jeltsch, Florian A1 - Wolff, Christian Michael T1 - The influence of El Nino-Southern Oscillation regimes on eastern African vegetation and its future implications under the RCP8.5 warming scenario N2 - The El Nino-Southern Oscillation (ENSO) is the main driver of the interannual variability in eastern African rainfall, with a significant impact on vegetation and agriculture and dire consequences for food and social security. In this study, we identify and quantify the ENSO contribution to the eastern African rainfall variability to forecast future eastern African vegetation response to rainfall variability related to a predicted intensified ENSO. To differentiate the vegetation variability due to ENSO, we removed the ENSO signal from the climate data using empirical orthogonal teleconnection (EOT) analysis. Then, we simulated the ecosystem carbon and water fluxes under the historical climate without components related to ENSO teleconnections. We found ENSO-driven patterns in vegetation response and confirmed that EOT analysis can successfully produce coupled tropical Pacific sea surface temperature-eastern African rainfall teleconnection from observed datasets. We further simulated eastern African vegetation response under future climate change as it is projected by climate models and under future climate change combined with a predicted increased ENSO intensity. Our EOT analysis highlights that climate simulations are still not good at capturing rainfall variability due to ENSO, and as we show here the future vegetation would be different from what is simulated under these climate model outputs lacking accurate ENSO contribution. We simulated considerable differences in eastern African vegetation growth under the influence of an intensified ENSO regime which will bring further environmental stress to a region with a reduced capacity to adapt effects of global climate change and food security. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 394 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-403853 ER - TY - JOUR A1 - Fer, Istem A1 - Tietjen, Britta A1 - Jeltsch, Florian A1 - Wolff, Christian Michael T1 - The influence of El Nino-Southern Oscillation regimes on eastern African vegetation and its future implications under the RCP8.5 warming scenario JF - Biogeosciences N2 - The El Nino-Southern Oscillation (ENSO) is the main driver of the interannual variability in eastern African rainfall, with a significant impact on vegetation and agriculture and dire consequences for food and social security. In this study, we identify and quantify the ENSO contribution to the eastern African rainfall variability to forecast future eastern African vegetation response to rainfall variability related to a predicted intensified ENSO. To differentiate the vegetation variability due to ENSO, we removed the ENSO signal from the climate data using empirical orthogonal teleconnection (EOT) analysis. Then, we simulated the ecosystem carbon and water fluxes under the historical climate without components related to ENSO teleconnections. We found ENSO-driven patterns in vegetation response and confirmed that EOT analysis can successfully produce coupled tropical Pacific sea surface temperature-eastern African rainfall teleconnection from observed datasets. We further simulated eastern African vegetation response under future climate change as it is projected by climate models and under future climate change combined with a predicted increased ENSO intensity. Our EOT analysis highlights that climate simulations are still not good at capturing rainfall variability due to ENSO, and as we show here the future vegetation would be different from what is simulated under these climate model outputs lacking accurate ENSO contribution. We simulated considerable differences in eastern African vegetation growth under the influence of an intensified ENSO regime which will bring further environmental stress to a region with a reduced capacity to adapt effects of global climate change and food security. Y1 - 2017 U6 - https://doi.org/10.5194/bg-14-4355-2017 SN - 1726-4170 SN - 1726-4189 VL - 14 IS - 18 SP - 4355 EP - 4374 PB - Copernicus CY - Katlenburg-Lindau ER - TY - GEN A1 - Machens, Fabian A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Messerschmidt, Katrin T1 - Synthetic Promoters and Transcription Factors for Heterologous Protein Expression in Saccharomyces cerevisiae N2 - Orthogonal systems for heterologous protein expression as well as for the engineering of synthetic gene regulatory circuits in hosts like Saccharomyces cerevisiae depend on synthetic transcription factors (synTFs) and corresponding cis-regulatory binding sites. We have constructed and characterized a set of synTFs based on either transcription activator-like effectors or CRISPR/Cas9, and corresponding small synthetic promoters (synPs) with minimal sequence identity to the host’s endogenous promoters. The resulting collection of functional synTF/synP pairs confers very low background expression under uninduced conditions, while expression output upon induction of the various synTFs covers a wide range and reaches induction factors of up to 400. The broad spectrum of expression strengths that is achieved will be useful for various experimental setups, e.g., the transcriptional balancing of expression levels within heterologous pathways or the construction of artificial regulatory networks. Furthermore, our analyses reveal simple rules that enable the tuning of synTF expression output, thereby allowing easy modification of a given synTF/synP pair. This will make it easier for researchers to construct tailored transcriptional control systems. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 393 KW - JUB1 KW - chimeric transcription factors KW - dead Cas9 KW - gene expression KW - synthetic biology KW - synthetic circuits KW - transcriptional regulation Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-403804 ER - TY - JOUR A1 - Machens, Fabian A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Messerschmidt, Katrin T1 - Synthetic Promoters and Transcription Factors for Heterologous Protein Expression in Saccharomyces cerevisiae JF - Frontiers in Bioengineering and Biotechnology N2 - Orthogonal systems for heterologous protein expression as well as for the engineering of synthetic gene regulatory circuits in hosts like Saccharomyces cerevisiae depend on synthetic transcription factors (synTFs) and corresponding cis-regulatory binding sites. We have constructed and characterized a set of synTFs based on either transcription activator-like effectors or CRISPR/Cas9, and corresponding small synthetic promoters (synPs) with minimal sequence identity to the host’s endogenous promoters. The resulting collection of functional synTF/synP pairs confers very low background expression under uninduced conditions, while expression output upon induction of the various synTFs covers a wide range and reaches induction factors of up to 400. The broad spectrum of expression strengths that is achieved will be useful for various experimental setups, e.g., the transcriptional balancing of expression levels within heterologous pathways or the construction of artificial regulatory networks. Furthermore, our analyses reveal simple rules that enable the tuning of synTF expression output, thereby allowing easy modification of a given synTF/synP pair. This will make it easier for researchers to construct tailored transcriptional control systems. KW - JUB1 KW - synthetic biology KW - transcriptional regulation KW - gene expression KW - synthetic circuits KW - dead Cas9 KW - chimeric transcription factors Y1 - 2017 U6 - https://doi.org/10.3389/fbioe.2017.00063 SN - 2296-4185 VL - 5 SP - 1 EP - 11 PB - Frontiers CY - Lausanne ER - TY - THES A1 - Kunstmann, Ruth Sonja T1 - Design of a high-affinity carbohydrate binding protein T1 - Design eines hoch-affin Kohlenhydrat-bindenden Proteins N2 - Kohlenhydrat-Protein Interaktionen sind in der Natur weitverbreitet. Sie stellen die Grundlage für viele biologische Prozesse dar, wie zum Beispiel Immunantworten, Wundheilung und Infektionsprozesse von pathogenen Viren oder Bakterien mit einem Wirt wie dem Menschen. Neben der Infektion von Menschen können aber auch Bakterien selbst durch so genannte Bakteriophagen infiziert werden, welche für den Menschen ungefährlich sind. Diese Infektion involviert die spezifische Erkennung der pathogenen Bakterien, die Vermehrung der Bakteriophagen und schließlich die Abtötung der Bakterien. Dabei können die Mechanismen der spezifischen Erkennung genutzt werden, pathogene Bakterien auf Lebensmitteln zu detektieren oder die Diagnose von Infektionen zu vereinfachen. Die spezifische Erkennung von Enteritis-erzeugenden Bakterien wie Escherichia coli, Salmonella spp. oder Shigella flexneri durch Bakteriophagen der Familie der Podoviridae erfolgt über die Bindung eines sogenannten tailspike proteins des Bakteriophagen an das aus Kohlenhydraten-bestehende O-Antigen des Lipopolysaccharids von Gram-negativen Bakterien. Das tailspike protein spaltet das O-Antigen um den Bakteriophage an die Oberfläche des Bakteriums zu führen, damit eine Infektion stattfinden kann. Die Affinität des tailspike proteins zum O-Antigen ist dabei sehr niedrig, um nach Spaltung des O-Antigens das Spaltungsprodukt zu lösen und wiederum neues Substrat zu binden. In dieser Arbeit wurde ein tailspike protein des Bakteriophagen Sf6 verwendet (Sf6 TSP), das spezifisch an das O-Antigen von Shigella flexneri Y bindet. Eine inaktive Variante des Sf6 TSP wurde verwendet um einen hoch-affin bindenden Sensor für pathogene Shigella zu entwickeln. Der Shigella-Sensor wurde durch Kopplung von unterschiedlichen Proteinmutanten mit einem fluoreszierendem Molekül erhalten. Dabei zeigte eine dieser Mutanten bei Bindung von Shigella O-Antigen ein Fluoreszenz-Signal im Bereich des sichtbaren Lichts. Molekulardynamische Simulationen wurde anhand der erzeugten Proteinmutanten als Methode zum rationalen Design von hoch-affin Kohlenhydrat-bindenden Proteinen getestet und die resultierenden Affinitätsvorhersagen wurden über Oberflächenplasmonresonanz-Experimente überprüft. Aus weiteren experimentellen und simulierten Daten konnten schließlich Schlussfolgerungen über die Ursprünge von Kohlenhydrat-Protein Interaktionen gezogen werden, die eine Einsicht über den Einfluss von Wasser in diesem Bindungsprozess lieferten. N2 - Carbohydrate-protein interactions are ubiquitous in nature. They provide the initial molecular contacts in many cell-cell processes as for example immune responses, signal transduction, egg fertilization and infection processes of pathogenic viruses and bacteria. Furthermore, bacteria themselves are infected by bacteriophages, viruses which can cause the bacterial lysis, but do not affect other hosts. The infection process of a bacteriophage involves the specific detection and binding of the bacterium, which can be based on a carbohydrate-protein interaction. The mechanism of specific detection of pathogenic bacteria can thereby be useful for the development of bacteria sensors in the food industry or for tools in diagnostics. Bacteriophages of the Podoviridae family use tailspike proteins for the specific detection of enteritis causing bacteria as Escherichia coli, Salmonella spp. or Shigella flexneri. The tailspike protein provides the first contact by binding to the carbohydrate containing O-antigen part of lipopolysaccharide in the Gram-negative cell wall. After binding to O-antigen repeating units, the enzymatic activity of tailspike proteins leads to cleavage of the carbohydrate chains, which enables the bacteriophage to approach the bacterial surface for DNA injection. Tailspike proteins thereby exhibit a relatively low affinity to the oligosaccharide structures of O-antigen due to the necessary binding, cleavage and release cycle, compared for example to antibodies. In this work it was aimed to study the determinants that influence carbohydrate affinity in the extended TSP binding grooves. This is a prerequisite to design a high-affinity tailspike protein based bacteria sensor. For this purpose the tailspike protein of the bacteriophage Sf6 (Sf6 TSP) was used, which specifically binds Shigella flexneri Y O-antigen with two tetrasaccharide repeating units at the intersubunits of the trimeric β-helix protein. The Sf6 TSP endorhamnosidase cleaves the O-antigen, which leads to an octasaccharide as the main product. The binding affinity of inactive Sf6 TSP towards polysaccharide was characterized by fluorescence titration experiments and surface plasmon resonance (SPR). Moreover, cysteine mutations were introduced into the Sf6 TSP binding site for the covalent thiol-coupling of an environment-sensitive fluorescent label to obtain a sensor for Shigella flexneri Y based on TSP-O-antigen recognition. This sensor showed a more than 100 % amplitude increase of a visible light fluorescence upon the binding of a polysaccharide test solution. Improvements of the TSP sensor can be achieved by increasing the tailspike affinity towards the O-antigen. Therefore molecular dynamics simulations evaluating ligand flexibility, hydrogen bond occupancies and water network distributions were used for affinity prediction on the available cysteine mutants of Sf6 TSP. The binding affinities were experimentally analyzed by SPR. This combined computational and experimental set-up for the design of a high-affinity carbohydrate binding protein could successfully distinguish strongly increased and decreased affinities of single amino acid mutants. A thermodynamically and structurally well characterized set of another tailspike protein HK620 TSP with high-affinity mutants was used to evaluate the influence of water molecules on binding affinity. The free enthalpy of HK620 TSP oligosaccharide complex formation thereby either derived from the replacement of a conserved water molecule or by immobilization of two water molecules upon ligand binding. Furthermore, the enthalpic and entropic contributions of water molecules in a hydrophobic binding pocket could be assigned by free energy calculations. The findings in this work can be helpful for the improvement of carbohydrate docking and carbohydrate binding protein engineering algorithms in the future. KW - Kohlenhydrat-Protein Interaction KW - carbohydrate-protein interaction KW - bacterial sensor KW - Bakterien Sensor Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-403458 ER - TY - THES A1 - Bülbül, Selin T1 - Functional characterization of the BBX14 transcription factor from Arabidopsis thaliana Y1 - 2017 ER - TY - GEN A1 - Hoffmann, Stefan A. A1 - Wohltat, Christian A1 - Müller, Kristian M. A1 - Arndt, Katja Maren T1 - A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter N2 - For various experimental applications, microbial cultures at defined, constant densities are highly advantageous over simple batch cultures. Due to high costs, however, devices for continuous culture at freely defined densities still experience limited use. We have developed a small-scale turbidostat for research purposes, which is manufactured from inexpensive components and 3D printed parts. A high degree of spatial system integration and a graphical user interface provide user-friendly operability. The used optical density feedback control allows for constant continuous culture at a wide range of densities and offers to vary culture volume and dilution rates without additional parametrization. Further, a recursive algorithm for on-line growth rate estimation has been implemented. The employed Kalman filtering approach based on a very general state model retains the flexibility of the used control type and can be easily adapted to other bioreactor designs. Within several minutes it can converge to robust, accurate growth rate estimates. This is particularly useful for directed evolution experiments or studies on metabolic challenges, as it allows direct monitoring of the population fitness. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 390 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-403406 ER - TY - JOUR A1 - Hoffmann, Stefan A. A1 - Wohltat, Christian A1 - Müller, Kristian M. A1 - Arndt, Katja Maren T1 - A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter JF - PLoS one N2 - For various experimental applications, microbial cultures at defined, constant densities are highly advantageous over simple batch cultures. Due to high costs, however, devices for continuous culture at freely defined densities still experience limited use. We have developed a small-scale turbidostat for research purposes, which is manufactured from inexpensive components and 3D printed parts. A high degree of spatial system integration and a graphical user interface provide user-friendly operability. The used optical density feedback control allows for constant continuous culture at a wide range of densities and offers to vary culture volume and dilution rates without additional parametrization. Further, a recursive algorithm for on-line growth rate estimation has been implemented. The employed Kalman filtering approach based on a very general state model retains the flexibility of the used control type and can be easily adapted to other bioreactor designs. Within several minutes it can converge to robust, accurate growth rate estimates. This is particularly useful for directed evolution experiments or studies on metabolic challenges, as it allows direct monitoring of the population fitness. Y1 - 2017 U6 - https://doi.org/10.1371/JOURNAL.PONE.0181923 SN - 1932-6203 VL - 12 IS - 7 SP - 1 EP - 15 PB - PLoS CY - Lawrence, Kan. ER - TY - THES A1 - Zimmermann, Heike Hildegard T1 - Vegetation changes and treeline dynamics in northern Siberia since the last interglacial revealed by sedimentary ancient DNA metabarcoding and organelle genome assembly of modern larches Y1 - 2017 ER - TY - GEN A1 - Sammler, Svenja A1 - Ketmaier, Valerio A1 - Havenstein, Katja A1 - Krause, Ulrike A1 - Curio, Eberhard A1 - Tiedemann, Ralph T1 - Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss N2 - Background: The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in similar to 600 base pairs (bp) of the mitochondrial control region I and at 12-19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay), and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant) sister taxa, the Luzon Tarictic Hornbill (P. manillae) from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus) from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Results: Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. Conclusions: We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A. leucocephalus. Because of the low potential for gene flow and population exchange across islands, saving of the remaining birds of almost extinct local populations - be it in the wild or in captivity - is particularly important to preserve the species' genetic potential. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 378 KW - biogeography KW - bucerotidae KW - conservation genetics KW - genetic diversity loss KW - microsatellites KW - mitochondrial control region I KW - Philippine archipelago KW - phylogeography Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401108 ER - TY - THES A1 - Ulbricht-Jones, Elena Sofia T1 - The virescent and narrow leaf phenotype of a plastome-genome-incompatible Oenothera hybrid is associated with the plastid gene accD and fatty acid synthesis Y1 - 2017 ER - TY - THES A1 - Bremer, Anne T1 - Structural and functional characterization of three closely related intrinsically disordered proteins from the model plant Arabidopsiis thaliana Y1 - 2017 ER - TY - THES A1 - Nagel, Rebecca T1 - Genetic and behavioral investigations into African weakly electric fish (Osteoglossomorpha: Mormyridae) speciation Y1 - 2017 ER - TY - THES A1 - Lachmann, Sabrina C. T1 - Ecophysiology matters: Inorganic carbon acquisition in green microalgae related to different nutrient conditions Y1 - 2017 ER - TY - THES A1 - Robaina Estevez, Semidan T1 - Context-specific metabolic predictions T1 - Kontextspezifische metabolische Vorhersagen BT - computational methods and applications BT - Berechnungsmethoden und Anwendungen N2 - All life-sustaining processes are ultimately driven by thousands of biochemical reactions occurring in the cells: the metabolism. These reactions form an intricate network which produces all required chemical compounds, i.e., metabolites, from a set of input molecules. Cells regulate the activity through metabolic reactions in a context-specific way; only reactions that are required in a cellular context, e.g., cell type, developmental stage or environmental condition, are usually active, while the rest remain inactive. The context-specificity of metabolism can be captured by several kinds of experimental data, such as by gene and protein expression or metabolite profiles. In addition, these context-specific data can be assimilated into computational models of metabolism, which then provide context-specific metabolic predictions. This thesis is composed of three individual studies focussing on context-specific experimental data integration into computational models of metabolism. The first study presents an optimization-based method to obtain context-specific metabolic predictions, and offers the advantage of being fully automated, i.e., free of user defined parameters. The second study explores the effects of alternative optimal solutions arising during the generation of context-specific metabolic predictions. These alternative optimal solutions are metabolic model predictions that represent equally well the integrated data, but that can markedly differ. This study proposes algorithms to analyze the space of alternative solutions, as well as some ways to cope with their impact in the predictions. Finally, the third study investigates the metabolic specialization of the guard cells of the plant Arabidopsis thaliana, and compares it with that of a different cell type, the mesophyll cells. To this end, the computational methods developed in this thesis are applied to obtain metabolic predictions specific to guard cell and mesophyll cells. These cell-specific predictions are then compared to explore the differences in metabolic activity between the two cell types. In addition, the effects of alternative optima are taken into consideration when comparing the two cell types. The computational results indicate a major reorganization of the primary metabolism in guard cells. These results are supported by an independent 13C labelling experiment. N2 - Alle lebenserhaltenden Prozesse werden durch tausende biochemische Reaktionen in der Zelle bestimmt, welche den Metabolismus charakterisieren. Diese Reaktionen bilden ein komplexes Netzwerk, welches alle notwendigen chemischen Verbindungen, die sogenannten Metabolite, aus einer bestimmten Menge an Ausgangsmolekülen produziert Zellen regulieren ihren Stoffwechsel kontextspezifisch, dies bedeutet, dass nur Reaktionen die in einem zellulären Kontext, zum Beispiel Zelltyp, Entwicklungsstadium oder verschiedenen Umwelteinflüssen, benötigt werden auch tatsächlich aktiv sind. Die übrigen Reaktionen werden als inaktiv betrachtet. Die Kontextspezifität des Metabolismus kann durch verschiedene experimentelle Daten, wie Gen- und Proteinexpressionen oder Metabolitprofile erfasst werden. Zusätzlich können diese Daten in Computersimulationen des Metabolismus integriert werden, um kontextspezifische (metabolische) Vorhersagen zu treffen. Diese Doktorarbeit besteht aus drei unabhängigen Studien, welche die Integration von kontextspezifischen experimentellen Daten in Computersimulationen des Metabolismus thematisieren. Die erste Studie beschreibt ein Konzept, basierend auf einem mathematischen Optimierungsproblem, welches es erlaubt kontextspezifische, metabolische Vorhersagen zu treffen. Dabei bietet diese vollautomatische Methode den Vorteil vom Nutzer unabhängige Parameter, zu verwenden. Die zweite Studie untersucht den Einfluss von alternativen optimalen Lösungen, welche bei kontextspezifischen metabolischen Vorhersagen generiert werden. Diese alternativen Lösungen stellen metabolische Modellvorhersagen da, welche die integrierten Daten gleichgut wiederspiegeln, sich aber grundlegend voneinander unterscheiden können. Diese Studie zeigt verschiedene Ansätze alternativen Lösungen zu analysieren und ihren Einfluss auf die Vorhersagen zu berücksichtigen. Schlussendlich, untersucht die dritte Studie die metabolische Spezialisierung der Schließzellen in Arabidopsis thaliana und vergleicht diese mit einer weiteren Zellart, den Mesophyllzellen. Zu diesem Zweck wurden die in dieser Doktorarbeit vorgestellten Methoden angewandt um metabolische Vorhersagen speziell für Schließzellen und Mesophyllzellen zu erhalten. Anschließend wurden die zellspezifischen Vorhersagen auf Unterschiede in der metabolischen Aktivität der Zelltypen, unter Berücksichtigung des Effekt von alternativen Optima, untersucht. Die Ergebnisse der Simulationen legen eine grundlegende Neuorganisation des Primärmetabolismus in Schließzellen verglichen mit Mesophyllzellen nahe. Diese Ergebnisse werden durch unabhängige 13C markierungs Experimente bestätigt. KW - systems biology KW - bioinformatics KW - metabolic networks KW - constraint-based modeling KW - data integration KW - Systemsbiologie KW - Bioinformatik KW - Stoffwechselnetze KW - Constraint-basierte Modellierung KW - Datenintegration Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401365 ER - TY - GEN A1 - Herde, Antje A1 - Eccard, Jana T1 - Consistency in boldness, activity and exploration at different stages of life N2 - Background: Animals show consistent individual behavioural patterns over time and over situations. This phenomenon has been referred to as animal personality or behavioural syndromes. Little is known about consistency of animal personalities over entire life times. We investigated the repeatability of behaviour in common voles (Microtus arvalis) at different life stages, with different time intervals, and in different situations. Animals were tested using four behavioural tests in three experimental groups: 1. before and after maturation over three months, 2. twice as adults during one week, and 3. twice as adult animals over three months, which resembles a substantial part of their entire adult life span of several months. Results: Different behaviours were correlated within and between tests and a cluster analysis showed three possible behavioural syndrome-axes, which we name boldness, exploration and activity. Activity and exploration behaviour in all tests was highly repeatable in adult animals tested over one week. In animals tested over maturation, exploration behaviour was consistent whereas activity was not. Voles that were tested as adults with a three-month interval showed the opposite pattern with stable activity but unstable exploration behaviour. Conclusions: The consistency in behaviour over time suggests that common voles do express stable personality over short time. Over longer periods however, behaviour is more flexible and depending on life stage (i.e. tested before/after maturation or as adults) of the tested individual. Level of boldness or activity does not differ between tested groups and maintenance of variation in behavioural traits can therefore not be explained by expected future assets as reported in other studies. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 376 KW - animal personality KW - behavioural type KW - Microtus arvalis KW - common vole KW - plasticity KW - consistency KW - repeatability Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401395 ER - TY - GEN A1 - Kuehnel, Susanne A1 - Kupfer, Alexander T1 - Sperm storage in caecilian amphibians N2 - Background: Female sperm storage has evolved independently multiple times among vertebrates to control reproduction in response to the environment. In internally fertilising amphibians, female salamanders store sperm in cloacal spermathecae, whereas among anurans sperm storage in oviducts is known only in tailed frogs. Facilitated through extensive field sampling following historical observations we tested for sperm storing structures in the female urogenital tract of fossorial, tropical caecilian amphibians. Findings: In the oviparous Ichthyophis cf. kohtaoensis, aggregated sperm were present in a distinct region of the posterior oviduct but not in the cloaca in six out of seven vitellogenic females prior to oviposition. Spermatozoa were found most abundantly between the mucosal folds. In relation to the reproductive status decreased amounts of sperm were present in gravid females compared to pre-ovulatory females. Sperm were absent in females past oviposition. Conclusions: Our findings indicate short-term oviductal sperm storage in the oviparous Ichthyophis cf. kohtaoensis. We assume that in female caecilians exhibiting high levels of parental investment sperm storage has evolved in order to optimally coordinate reproductive events and to increase fitness. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 375 KW - reproduction KW - sperm storage KW - amphibians KW - caecilians Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400987 ER - TY - THES A1 - Hethey, Christoph Philipp T1 - Cell physiology based pharmacodynamic modeling of antimicrobial drug combinations T1 - Zellphysiologie-basierte pharmakodynamische Modellierung von antimikrobiellen Wirkstoffkombinationen N2 - Mathematical models of bacterial growth have been successfully applied to study the relationship between antibiotic drug exposure and the antibacterial effect. Since these models typically lack a representation of cellular processes and cell physiology, the mechanistic integration of drug action is not possible on the cellular level. The cellular mechanisms of drug action, however, are particularly relevant for the prediction, analysis and understanding of interactions between antibiotics. Interactions are also studied experimentally, however, a lacking consent on the experimental protocol hinders direct comparison of results. As a consequence, contradictory classifications as additive, synergistic or antagonistic are reported in literature. In the present thesis we developed a novel mathematical model for bacterial growth that integrates cell-level processes into the population growth level. The scope of the model is to predict bacterial growth under antimicrobial perturbation by multiple antibiotics in vitro. To this end, we combined cell-level data from literature with population growth data for Bacillus subtilis, Escherichia coli and Staphylococcus aureus. The cell-level data described growth-determining characteristics of a reference cell, including the ribosomal concentration and efficiency. The population growth data comprised extensive time-kill curves for clinically relevant antibiotics (tetracycline, chloramphenicol, vancomycin, meropenem, linezolid, including dual combinations). The new cell-level approach allowed for the first time to simultaneously describe single and combined effects of the aforementioned antibiotics for different experimental protocols, in particular different growth phases (lag and exponential phase). Consideration of ribosomal dynamics and persisting sub-populations explained the decreased potency of linezolid on cultures in the lag phase compared to exponential phase cultures. The model captured growth rate dependent killing and auto-inhibition of meropenem and - also for vancomycin exposure - regrowth of the bacterial cultures due to adaptive resistance development. Stochastic interaction surface analysis demonstrated the pronounced antagonism between meropenem and linezolid to be robust against variation in the growth phase and pharmacodynamic endpoint definition, but sensitive to a change in the experimental duration. Furthermore, the developed approach included a detailed representation of the bacterial cell-cycle. We used this representation to describe septation dynamics during the transition of a bacterial culture from the exponential to stationary growth phase. Resulting from a new mechanistic understanding of transition processes, we explained the lag time between the increase in cell number and bacterial biomass during the transition from the lag to exponential growth phase. Furthermore, our model reproduces the increased intracellular RNA mass fraction during long term exposure of bacteria to chloramphenicol. In summary, we contribute a new approach to disentangle the impact of drug effects, assay readout and experimental protocol on antibiotic interactions. In the absence of a consensus on the corresponding experimental protocols, this disentanglement is key to translate information between heterogeneous experiments and also ultimately to the clinical setting. N2 - Der Zusammenhang zwischen antibiotischer Exposition und antibakterieller Wirkung wird derzeitlich erfolgreich mithilfe von mathematischen Bakterienwachstumsmodellen studiert. Üblicherweise ignorieren diese Modelle jedoch die bakterielle Physiologie und Prozesse auf Zellebene. Es folgt, dass das mechanistische Einbinden von Wirkstoffeffekten auf Zellebene nicht möglich ist. Jedoch ist der zelluläre Wirkmechanismus besonders relevant für die Vorhersage, die Analyse und das Verständnis von Antibiotikainteraktionen. Leider gibt es keinen Konsens bezüglich des experimentellen Protokolls, um diese Interaktionen zu untersuchen. Das ist einer der Gründe, warum wir in der Literatur widersprüchliche Klassifizierungen von Antibiotikainteraktionen als additiv, synergistisch oder antagonistisch finden. In der vorliegenden Arbeit entwickelten wir ein neuartiges mathematisches Bakterienwachstumsmodel, welches Prozesse auf Zellebene in das Populationswachstum einbindet. Der Anwendungszweck dieses Models ist die Vorhersage bakteriellen Wachstums unter antimikrobieller Mehrfachexposition in vitro. Um das zu erreichen, kombinierten wir die Zellebene beschreibende Daten aus der Literatur mit Wachstumsdaten für Bacillus subtilis, Escherichia coli und Staphylococcus aureus. Die die Zellebene beschreibenden Daten bezogen sich auf Wachstums-bestimmende Charakteristika einer Referenzzelle, unter anderem auf die ribosomale Konzentration und Effizienz. Die Wachstumsdaten beinhalteten umfangreiche Zeit-Absterbe-Kurven für klinisch relevante Antibiotika (Tetracyclin, Chloramphenicol, Vancomycin, Meropenem, Linezolid) und Zweifachkombinationen aus diesen. Der neue Zellebenen-Ansatz erlaubt es erstmalig, einzelne und kombinierte Effekte der erwähnten Antibiotika für unterschiedliche experimentelle Protokolle gleichzeitig zu beschreiben. Insbesondere beziehen sich diese Unterschiede auf die Wachstumsphasen (Lag oder exponentiellen Phase). Die Berücksichtigung der ribosomalen Konzentration und persistenter Subpopulationen erklärte die verminderte Potenz von Linezolid gegen Kulturen in der Lag Phase im Vergleich zu Kulturen, die sich in der exponentiellen Phase befanden. Das Model erfasst Wachstumsraten-abhängiges Zelltöten und die Selbstinhibierung von Meropenem und - ebenso für Vancomycin - ein Wiederanwachsen der bakteriellen Kulturen aufgrund von adaptiver Resistenzentwicklung. Stochastische Analysen der Interaktionsoberflächen zeigen, dass der ausgeprägte Antagonismus zwischen Meropenem und Linezolid zwar robust gegenüber Variation der Wachstumsphase und der Definition des pharmakodynamischen Endpunktes reagiert, jedoch empfindlich von der Zeitspanne des Experiments beeinflusst wird. Desweiteren enthält der entwickelte Ansatz eine detaillierte Repräsentation des bakteriellen Zellzyklus. Wir nutzten diese Repräsentation, um Septierungsdynamiken während des Übergangs einer bakteriellen Kultur aus der exponentiellen Phase in die stationäre Phase zu beschreiben. Basierend auf einem neugewonnenen mechanistischen Verständnis für diese Übergänge, konnten wir außerdem die zeitliche Verzögerung erklären, die zwischen dem Anstieg der Zellanzahl und der Biomasse während des Übergangs von Lag zu exponentieller Phase auftritt. Außerdem reproduziert unser Modell den erhöhten intrazellulären RNA Massenanteil, der auftritt, wenn Bakterien Chloramphenikol ausgesetzt werden. Zusammenfassend steuern wir einen neuen Ansatz bei, der es erlaubt, die Einflüsse von Wirkstoffeffekten, Endpunktdefinitionen und des experimentellen Protokolls zu entflechten. Da kein Konsens hinsichtlich eines entsprechenden experimentellen Protokolls existiert, ist eine solche Entflechtung der Schlüssel, um Informationen zwischen unterschiedlichen Experimenten - und letztendlich auch in die Klinik - zu transferieren. KW - antibiotic combinations KW - bacterial population growth KW - pharmacodynamics KW - drug drug interactions KW - time-kill curves KW - ribosomal dynamics KW - Antibiotika KW - Wirkstoffinteraktionen KW - Pharmakodynamik KW - mathematische Modellierung KW - mathematical modelling Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401056 ER - TY - GEN A1 - Breuninger, Holger A1 - Lenhard, Michael T1 - Expression of the central growth regulator BIG BROTHER is regulated by multiple cis-elements N2 - Background Much of the organismal variation we observe in nature is due to differences in organ size. The observation that even closely related species can show large, stably inherited differences in organ size indicates a strong genetic component to the control of organ size. Despite recent progress in identifying factors controlling organ growth in plants, our overall understanding of this process remains limited, partly because the individual factors have not yet been connected into larger regulatory pathways or networks. To begin addressing this aim, we have studied the upstream regulation of expression of BIG BROTHER (BB), a central growth-control gene in Arabidopsis thaliana that prevents overgrowth of organs. Final organ size and BB expression levels are tightly correlated, implying the need for precise control of its expression. BB expression mirrors proliferative activity, yet the gene functions to limit proliferation, suggesting that it acts in an incoherent feedforward loop downstream of growth activators to prevent over-proliferation. Results To investigate the upstream regulation of BB we combined a promoter deletion analysis with a phylogenetic footprinting approach. We were able to narrow down important, highly conserved, cis-regulatory elements within the BB promoter. Promoter sequences of other Brassicaceae species were able to partially complement the A. thaliana bb-1 mutant, suggesting that at least within the Brassicaceae family the regulatory pathways are conserved. Conclusions This work underlines the complexity involved in precise quantitative control of gene expression and lays the foundation for identifying important upstream regulators that determine BB expression levels and thus final organ size. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 374 KW - Asymmetric interlaced PCR KW - Organ Groth KW - DNA Elements KW - Arabidopsis KW - Plants KW - Brassicaceae KW - Phylogeny KW - Database KW - Place KW - Size Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400971 ER - TY - GEN A1 - Eccard, Jana A1 - Jokinen, Ilmari A1 - Ylönen, Hannu T1 - Loss of density-dependence and incomplete control by dominant breeders in a territorial species with density outbreaks N2 - Background A territory as a prerequisite for breeding limits the maximum number of breeders in a given area, and thus lowers the proportion of breeders if population size increases. However, some territorially breeding animals can have dramatic density fluctuations and little is known about the change from density-dependent processes to density-independence of breeding during a population increase or an outbreak. We suggest that territoriality, breeding suppression and its break-down can be understood with an incomplete-control model, developed for social breeders and social suppression. Results We studied density dependence in an arvicoline species, the bank vole, known as a territorial breeder with cyclic and non-cyclic density fluctuations and periodically high densities in different parts of its range. Our long-term data base from 38 experimental populations in large enclosures in boreal grassland confirms that breeding rates are density-regulated at moderate densities, probably by social suppression of subordinate potential breeders. We conducted an experiment, were we doubled and tripled this moderate density under otherwise the same conditions and measured space use, mortality, reproduction and faecal stress hormone levels (FGM) of adult females. We found that mortality did not differ among the densities, but the regulation of the breeding rate broke down: at double and triple densities all females were breeding, while at the low density the breeding rate was regulated as observed before. Spatial overlap among females increased with density, while a minimum territory size was maintained. Mean stress hormone levels were higher in double and triple densities than at moderate density. Conclusions At low and moderate densities, breeding suppression by the dominant breeders, But above a density-threshold (similar to a competition point), the dominance of breeders could not be sustained (incomplete control). In our experiment, this point was reached after territories could not shrink any further, while the number of intruders continued to increase with increasing density. Probably suppression becomes too costly for the dominants, and increasing number of other breeders reduces the effectiveness of threats. In wild populations, crossing this threshold would allow for a rapid density increase or population outbreaks, enabling territorial species to escape density-dependency. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 372 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400939 ER - TY - GEN A1 - Sieck, Mungla A1 - Ibisch, Pierre L. A1 - Moloney, Kirk A. A1 - Jeltsch, Florian T1 - Current models broadly neglect specific needs of biodiversity conservation in protected areas under climate change N2 - Background Protected areas are the most common and important instrument for the conservation of biological diversity and are called for under the United Nations' Convention on Biological Diversity. Growing human population densities, intensified land-use, invasive species and increasing habitat fragmentation threaten ecosystems worldwide and protected areas are often the only refuge for endangered species. Climate change is posing an additional threat that may also impact ecosystems currently under protection. Therefore, it is of crucial importance to include the potential impact of climate change when designing future nature conservation strategies and implementing protected area management. This approach would go beyond reactive crisis management and, by necessity, would include anticipatory risk assessments. One avenue for doing so is being provided by simulation models that take advantage of the increase in computing capacity and performance that has occurred over the last two decades. Here we review the literature to determine the state-of-the-art in modeling terrestrial protected areas under climate change, with the aim of evaluating and detecting trends and gaps in the current approaches being employed, as well as to provide a useful overview and guidelines for future research. Results Most studies apply statistical, bioclimatic envelope models and focus primarily on plant species as compared to other taxa. Very few studies utilize a mechanistic, process-based approach and none examine biotic interactions like predation and competition. Important factors like land-use, habitat fragmentation, invasion and dispersal are rarely incorporated, restricting the informative value of the resulting predictions considerably. Conclusion The general impression that emerges is that biodiversity conservation in protected areas could benefit from the application of modern modeling approaches to a greater extent than is currently reflected in the scientific literature. It is particularly true that existing models have been underutilized in testing different management options under climate change. Based on these findings we suggest a strategic framework for more effectively incorporating the impact of climate change in models exploring the effectiveness of protected areas. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 368 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400894 ER - TY - GEN A1 - Sammler, Svenja A1 - Bleidorn, Christoph A1 - Tiedemann, Ralph T1 - Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination N2 - Background: Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle". Results: Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i. e., in every generation. Conclusions: The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 367 KW - d-loop region KW - concerted evolution KW - gene order KW - birds KW - phylogeny KW - heteroplasmy KW - organization KW - duplication KW - vertebrates KW - alignment Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400889 ER - TY - GEN A1 - Dortay, Hakan A1 - Müller-Röber, Bernd T1 - A highly efficient pipeline for protein expression in Leishmania tarentolae using infrared fluorescence protein as marker N2 - Background: Leishmania tarentolae, a unicellular eukaryotic protozoan, has been established as a novel host for recombinant protein production in recent years. Current protocols for protein expression in Leishmania are, however, time consuming and require extensive lab work in order to identify well-expressing cell lines. Here we established an alternative protein expression work-flow that employs recently engineered infrared fluorescence protein (IFP) as a suitable and easy-to-handle reporter protein for recombinant protein expression in Leishmania. As model proteins we tested three proteins from the plant Arabidopsis thaliana, including a NAC and a type-B ARR transcription factor. Results: IFP and IFP fusion proteins were expressed in Leishmania and rapidly detected in cells by deconvolution microscopy and in culture by infrared imaging of 96-well microtiter plates using small cell culture volumes (2 mu L - 100 mu L). Motility, shape and growth of Leishmania cells were not impaired by intracellular accumulation of IFP. In-cell detection of IFP and IFP fusion proteins was straightforward already at the beginning of the expression pipeline and thus allowed early pre-selection of well-expressing Leishmania clones. Furthermore, IFP fusion proteins retained infrared fluorescence after electrophoresis in denaturing SDS-polyacrylamide gels, allowing direct in-gel detection without the need to disassemble cast protein gels. Thus, parameters for scaling up protein production and streamlining purification routes can be easily optimized when employing IFP as reporter. Conclusions: Using IFP as biosensor we devised a protocol for rapid and convenient protein expression in Leishmania tarentolae. Our expression pipeline is superior to previously established methods in that it significantly reduces the hands-on-time and work load required for identifying well-expressing clones, refining protein production parameters and establishing purification protocols. The facile in-cell and in-gel detection tools built on IFP make Leishmania amenable for high-throughput expression of proteins from plant and animal sources. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 366 KW - System KW - Donovani Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400876 ER - TY - THES A1 - Pandey-Pant, Pooja T1 - Comparative transcriptomics and functional genomics during phosphorus limitation in plants Y1 - 2017 ER - TY - GEN A1 - Peng, Lei A1 - Yarman, Aysu A1 - Jetzschmann, Katharina J. A1 - Jeoung, Jae-Hun A1 - Schad, Daniel A1 - Dobbek, Holger A1 - Wollenberger, Ursula A1 - Scheller, Frieder W. T1 - Molecularly imprinted electropolymer for a hexameric heme protein with direct electron transfer and peroxide electrocatalysis N2 - For the first time a molecularly imprinted polymer (MIP) with direct electron transfer (DET) and bioelectrocatalytic activity of the target protein is presented. Thin films of MIPs for the recognition of a hexameric tyrosine-coordinated heme protein (HTHP) have been prepared by electropolymerization of scopoletin after oriented assembly of HTHP on a self-assembled monolayer (SAM) of mercaptoundecanoic acid (MUA) on gold electrodes. Cavities which should resemble the shape and size of HTHP were formed by template removal. Rebinding of the target protein sums up the recognition by non-covalent interactions between the protein and the MIP with the electrostatic attraction of the protein by the SAM. HTHP bound to the MIP exhibits quasi-reversible DET which is reflected by a pair of well pronounced redox peaks in the cyclic voltammograms (CVs) with a formal potential of −184.4 ± 13.7 mV vs. Ag/AgCl (1 M KCl) at pH 8.0 and it was able to catalyze the cathodic reduction of peroxide. At saturation the MIP films show a 12-fold higher electroactive surface concentration of HTHP than the non-imprinted polymer (NIP). T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 362 KW - molecularly imprinted polymers KW - self-assembled monolayer KW - direct electron transfer KW - hydrogen peroxide KW - bioelectrocatalysis Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400627 ER - TY - GEN A1 - Menger, Marcus A1 - Yarman, Aysu A1 - Erdőssy, Júlia A1 - Yildiz, Huseyin Bekir A1 - Gyurcsányi, Róbert E. A1 - Scheller, Frieder W. T1 - MIPs and aptamers for recognition of proteins in biomimetic sensing N2 - Biomimetic binders and catalysts have been generated in order to substitute the biological pendants in separation techniques and bioanalysis. The two major approaches use either "evolution in the test tube" of nucleotides for the preparation of aptamers or total chemical synthesis for molecularly imprinted polymers (MIPs). The reproducible production of aptamers is a clear advantage, whilst the preparation of MIPs typically leads to a population of polymers with different binding sites. The realization of binding sites in the total bulk of the MIPs results in a higher binding capacity, however, on the expense of the accessibility and exchange rate. Furthermore, the readout of the bound analyte is easier for aptamers since the integration of signal generating labels is well established. On the other hand, the overall negative charge of the nucleotides makes aptamers prone to non-specific adsorption of positively charged constituents of the sample and the "biological" degradation of non-modified aptamers and ionic strength-dependent changes of conformation may be challenging in some application. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 357 KW - biomimetic recognition elements KW - aptamers KW - molecularly imprinted polymers KW - chemical sensors KW - aptasensors KW - in vitro selection KW - SELEX Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400496 ER - TY - GEN A1 - Zwickel, Theresa A1 - Kahl, Sandra M. A1 - Klaffke, Horst A1 - Rychlik, Michael A1 - Müller, Marina E. H. T1 - Spotlight on the underdogs BT - an analysis of underrepresented alternaria mycotoxins formed depending on varying substrate, time and temperature conditions N2 - Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 °C, 25 °C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 °C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 353 KW - Alternaria infectoria KW - A. tenuissima KW - mycotoxin profile KW - wheat KW - rice KW - Alternaria toxin sulfates KW - modified Alternaria toxins KW - altertoxins KW - altenuic acid KW - HPLC-MS/MS Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400438 ER - TY - THES A1 - Loiacono, Filomena Vanessa T1 - Transfer of chloroplast RNA editing events between species BT - faithful reconstitution and fateful effects Y1 - 2017 ER - TY - THES A1 - Wu, Si T1 - Exploring the Arabidopsis metabolic landscape by genetic mapping integrated with network analysis Y1 - 2017 ER - TY - THES A1 - Morling, Karoline T1 - Import and decomposition of dissolved organic carbon in pre-dams of drinking water reservoirs T1 - Eintrag und Abbau von gelösten Kohlenstoffen in Vorsperren von Trinkwassertalsperren N2 - Dissolved organic carbon (DOC) depicts a key component in the aquatic carbon cycle as well as for drinking water production from surface waters. DOC concentrations increased in water bodies of the northern hemisphere in the last decades, posing ecological consequences and water quality problems. Within the pelagic zone of lakes and reservoirs, the DOC pool is greatly affected by biological activity as DOC is simultaneously produced and decomposed. This thesis aimed for a conceptual understanding of organic carbon cycling and DOC quality changes under differing hydrological and trophic conditions. Further, the occurrence of aquatic priming was investigated, which has been proposed as a potential process facilitating the microbial decomposition of stable allochthonous DOC within the pelagic zone. To study organic carbon cycling under different hydrological conditions, quantitative and qualitative investigations were carried out in three pre-dams of drinking water reservoirs exhibiting a gradient in DOC concentrations and trophic states. All pre-dams were mainly autotrophic in their epilimnia. Discharge and temperature were identified as the key factors regulating net production and respiration in the upper water layers of the pre-dams. Considerable high autochthonous production was observed during the summer season under higher trophic status and base flow conditions. Up to 30% of the total gained organic carbon was produced within the epilimnia. Consequently, this affected the DOC quality within the pre-dams over the year and enhanced characteristics of algae-derived DOC were observed during base flow in summer. Allochthonous derived DOC dominated at high discharges and oligotrophic conditions when production and respiration were low. These results underline that also small impoundments with typically low water residence times are hotspots of carbon cycling, significantly altering water quality in dependence of discharge conditions, temperature and trophic status. Further, it highlights that these factors need to be considered in future water management as increasing temperatures and altered precipitation patterns are predicted in the context of climate change. Under base flow conditions, heterotrophic bacteria preferentially utilized older DOC components with a conventional radiocarbon age of 195-395 years before present (i.e. before 1950). In contrast, younger carbon components (modern, i.e. produced after 1950) were mineralized following a storm flow event. This highlights that age and recalcitrance of DOC are independent from each other. To assess the ages of the microbially consumed DOC, a simplified method was developed to recover the respired CO2 from heterotrophic bacterioplankton for carbon isotope analyses (13C, 14C). The advantages of the method comprise the operation of replicate incubations at in-situ temperatures using standard laboratory equipment and thus enabling an application in a broad range of conditions. Aquatic priming was investigated in laboratory experiments during the microbial decomposition of two terrestrial DOC substrates (peat water and soil leachate). Thereby, natural phytoplankton served as a source of labile organic matter and the total DOC pool increased throughout the experiments due to exudation and cell lysis of the growing phytoplankton. A priming effect for both terrestrial DOC substrates was revealed via carbon isotope analysis and mixing models. Thereby, priming was more pronounced for the peat water than for the soil leachate. This indicates that the DOC source and the amount of the added labile organic matter might influence the magnitude of a priming effect. Additional analysis via high-resolution mass spectrometry revealed that oxidized, unsaturated compounds were more strongly decomposed under priming (i.e. in phytoplankton presence). Given the observed increase in DOC concentrations during the experiments, it can be concluded that aquatic priming is not easily detectable via net concentration changes alone and could be considered as a qualitative effect. The knowledge gained from this thesis contributes to the understanding of aquatic carbon cycling and demonstrated how DOC dynamics in freshwaters vary with hydrological, seasonal and trophic conditions. It further demonstrated that aquatic priming contributes to the microbial transformation of organic carbon and the observed decay of allochthonous DOC during transport in inland waters. N2 - Gelöster organischer Kohlenstoff (dissolved organic carbon, DOC) bildet nicht nur eine zentrale Komponente des aquatischen Kohlenstoffkreislaufs, sondern auch für die Gewinnung von Trinkwasser aus Oberflächengewässern. In den letzten Jahrzehnten stiegen die DOC-Konzentrationen in Gewässern der nördlichen Hemisphäre an und führen sowohl zu ökologischen Konsequenzen als auch zu Wasserqualitätsproblemen. Die Zusammensetzung des DOC im Pelagial von Seen und Talsperren wird erheblich durch biologische Aktivität beeinflusst, da DOC-Verbindungen gleichzeitig produziert und abgebaut werden. Im Fokus meiner Dissertation standen ein konzeptionelles Verständnis des organischen Kohlenstoffkreislaufs und die damit verbundenen Änderungen in der DOC-Qualität unter verschiedenen hydrologischen und trophischen Bedingungen. Weiterhin wurde das Auftreten eines aquatischen Priming-Effektes untersucht, welcher den mikrobiellen Abbau von stabilem allochthonem DOC im Pelagial fördern könnte. Quantitative und qualitative Untersuchungen wurden unter verschiedenen hydrologischen Bedingungen in drei Vorsperren von Trinkwassertalsperren durchgeführt, die einen Gradienten an DOC-Konzentrationen und Trophie aufwiesen. Alle Vorsperren waren im Epilimnion überwiegend autotroph. Abfluss und Temperatur wurden als Schlüsselfaktoren identifiziert, die Produktion und Respiration in den oberen Wasserschichten der Vorsperren regulieren. Eine vergleichsweise hohe autotrophe Produktion wurde während der Sommer-monate bei hoher Trophie und Basisabfluss beobachtet. Bis zu 30% des gesamten eingetragenen organischen Kohlenstoffes wurde im Epilimnion produziert. Dies beeinflusste die DOC-Qualität in den Vorsperren erheblich und es traten vermehrt Charakteristiken von algenbürtigem DOC unter Basisabfluss in den Sommermonaten auf. Allochthoner DOC dominierte bei hohen Abflüssen und unter oligotrophen Bedingungen, wenn Produktion und Respiration gering waren. Diese Ergebnisse unterstreichen, dass auch kleine Speicherbecken mit typischerweise kurzen Wasser-aufenthaltszeiten „Hotspots“ für Kohlenstoffumsetzung sind und die Wasserqualität signifikant in Abhängigkeit von Abflussbedingungen, Temperatur und Trophie verändern. Diese Faktoren sind auch für zukünftiges Wassermanagement bedeutsam, da steigende Temperaturen und veränderte Niederschläge im Zuge des Klimawandels prognostiziert werden. Unter Basisabfluss verwerteten heterotrophe Bakterien vorrangig ältere DOC-Komponenten mit einem konventionellen Radiokarbonalter von 195-395 Jahren B.P. („before present“, d. h. vor 1950). Im Gegensatz dazu wurden jüngere DOC-Komponenten (modern, d. h. nach 1950 produziert) nach einem Regenwetterzufluss abgebaut. Daraus lässt sich schließen, dass Alter und mikrobielle Verwertbarkeit des DOC voneinander unabhängig sind. Um das Alter des genutzten DOC zu bestimmen, wurde eine vereinfachte Methode entwickelt, die das Auffangen des bakteriell respirierten CO2 und eine anschließende Analyse der Kohlenstoffisotope (13C, 14C) ermöglicht. Die Vorteile der Methode liegen vor allem in der Verwendung von Replikaten, die bei in-situ Temperaturen inkubiert werden können und in der Nutzung von gängiger Laborausstattung. Dies ermöglicht eine Anwendung der Methode unter einer weiten Bandbreite von Bedingungen. Der aquatische Priming-Effekt wurde in Laborexperimenten während des mikrobiellen Abbaus von zwei terrestrischen DOC-Substraten (Moorwasser und Bodeneluat) untersucht. Phytoplankton diente als Quelle für labile organische Substanz und die DOC-Konzentrationen nahmen durch Exudation und Zelllysis des wachsenden Phytoplanktons während des Experimentes zu. Ein Priming-Effekt wurde für beide terrestrischen DOC-Substrate mittels Analyse von Kohlenstoffisotopen und Mischungsmodellen nachgewiesen, wobei der Priming-Effekt für das Moorwasser stärker ausgeprägt war als für das Bodeneluat. Analysen mittels hochauflösender Massenspektrometrie zeigten, dass verstärkt oxidierte und ungesättigte Verbindungen während des Primings (d. h. in Anwesenheit von Phytoplankton) abgebaut wurden. Aus den angestiegenen DOC-Konzentrationen während des Experimentes kann geschlussfolgert werden, dass ein aquatischer Priming-Effekt nicht allein über Konzentrationsänderungen nachweisbar ist und vielmehr als ein qualitativer Effekt betrachtet werden kann. Diese Arbeit trägt zum Verständnis des aquatischen Kohlenstoffkreislaufs bei und zeigt wie DOC-Dynamiken in Süßgewässern mit hydrologischen, saisonalen und trophischen Bedingungen variieren. Weiterhin wurde gezeigt, dass der aquatische Priming-Effekt zu dem mikrobiellen Umsatz von organischem Kohlenstoff und dem beobachteten Abbau von terrestrischen DOC während des Transportes in Binnengewässern beiträgt. KW - organic carbon KW - water reservoir KW - freshwater ecosystems KW - carbon isotopes KW - degradation KW - radiocarbon KW - autotrophy KW - net production KW - organic matter quality KW - high resolution mass spectrometry KW - microbial decomposition KW - organischer Kohlenstoff KW - Talsperre KW - Kohlenstoffisotope KW - Radiokarbon KW - Autotrophie KW - Nettoproduktion KW - organisches Material KW - hochauflösende Massenspektrometrie KW - mikrobieller Abbau KW - gelöster organischer Kohlenstoff Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-399110 ER - TY - THES A1 - Zeng, Ting T1 - Nanoparticles promoted biocatalysis BT - Electrochemical investigation of human sulfite oxidase on nanoparticles modified electrodes Y1 - 2017 ER - TY - THES A1 - Sedaghatmehr, Mastoureh T1 - Unraveling the regulatory mechanisms of heat stress memory in Arabidopsis thaliana Y1 - 2017 ER - TY - GEN A1 - Klose, Sascha Peter A1 - Rolke, Daniel A1 - Baumann, Otto T1 - Morphogenesis of honeybee hypopharyngeal gland during pupal development N2 - Background The hypopharyngeal gland of worker bees contributes to the production of the royal jelly fed to queens and larvae. The gland consists of thousands of two-cell units that are composed of a secretory cell and a duct cell and that are arranged in sets of about 12 around a long collecting duct. Results By fluorescent staining, we have examined the morphogenesis of the hypopharyngeal gland during pupal life, from a saccule lined by a pseudostratified epithelium to the elaborate organ of adult worker bees. The hypopharyngeal gland develops as follows. (1) Cell proliferation occurs during the first day of pupal life in the hypopharyngeal gland primordium. (2) Subsequently, the epithelium becomes organized into rosette-like units of three cells. Two of these will become the secretory cell and the duct cell of the adult secretory units; the third cell contributes only temporarily to the development of the secretory units and is eliminated by apoptosis in the second half of pupal life. (3) The three-cell units of flask-shaped cells undergo complex changes in cell morphology. Thus, by mid-pupal stage, the gland is structurally similar to the adult hypopharyngeal gland. (4) Concomitantly, the prospective secretory cell attains its characteristic subcellular organization by the invagination of a small patch of apical membrane domain, its extension to a tube of about 100 μm in length (termed a canaliculus), and the expansion of the tube to a diameter of about 3 μm. (6) Finally, the canaliculus-associated F-actin system becomes reorganized into rings of bundled actin filaments that are positioned at regular distances along the membrane tube. Conclusions The morphogenesis of the secretory units in the hypopharyngeal gland of the worker bee seems to be based on a developmental program that is conserved, with slight modification, among insects for the production of dermal glands. Elaboration of the secretory cell as a unicellular seamless epithelial tube occurs by invagination of the apical membrane, its extension likely by targeted exocytosis and its expansion, and finally the reorganisation of the membrane-associated F-actin system. Our work is fundamental for future studies of environmental effects on hypopharyngeal gland morphology and development. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 337 KW - Exocrine gland KW - Insect KW - Epithelial tube KW - Organogenesis KW - Cell polarity KW - Actin cytoskeleton KW - Apoptosis KW - Invagination Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-395712 ER - TY - JOUR A1 - Klose, Sascha Peter A1 - Rolke, Daniel A1 - Baumann, Otto T1 - Morphogenesis of honeybee hypopharyngeal gland during pupal development JF - Frontiers in zoology N2 - Background The hypopharyngeal gland of worker bees contributes to the production of the royal jelly fed to queens and larvae. The gland consists of thousands of two-cell units that are composed of a secretory cell and a duct cell and that are arranged in sets of about 12 around a long collecting duct. Results By fluorescent staining, we have examined the morphogenesis of the hypopharyngeal gland during pupal life, from a saccule lined by a pseudostratified epithelium to the elaborate organ of adult worker bees. The hypopharyngeal gland develops as follows. (1) Cell proliferation occurs during the first day of pupal life in the hypopharyngeal gland primordium. (2) Subsequently, the epithelium becomes organized into rosette-like units of three cells. Two of these will become the secretory cell and the duct cell of the adult secretory units; the third cell contributes only temporarily to the development of the secretory units and is eliminated by apoptosis in the second half of pupal life. (3) The three-cell units of flask-shaped cells undergo complex changes in cell morphology. Thus, by mid-pupal stage, the gland is structurally similar to the adult hypopharyngeal gland. (4) Concomitantly, the prospective secretory cell attains its characteristic subcellular organization by the invagination of a small patch of apical membrane domain, its extension to a tube of about 100 μm in length (termed a canaliculus), and the expansion of the tube to a diameter of about 3 μm. (6) Finally, the canaliculus-associated F-actin system becomes reorganized into rings of bundled actin filaments that are positioned at regular distances along the membrane tube. Conclusions The morphogenesis of the secretory units in the hypopharyngeal gland of the worker bee seems to be based on a developmental program that is conserved, with slight modification, among insects for the production of dermal glands. Elaboration of the secretory cell as a unicellular seamless epithelial tube occurs by invagination of the apical membrane, its extension likely by targeted exocytosis and its expansion, and finally the reorganisation of the membrane-associated F-actin system. Our work is fundamental for future studies of environmental effects on hypopharyngeal gland morphology and development. KW - Exocrine gland KW - Insect KW - Epithelial tube KW - Organogenesis KW - Cell polarity KW - Actin cytoskeleton KW - Apoptosis KW - Invagination Y1 - 2017 U6 - https://doi.org/10.1186/s12983-017-0207-z SN - 1742-9994 VL - 14 PB - BioMed Central CY - London ER - TY - GEN A1 - Koussoroplis, Apostolos-Manuel A1 - Schwarzenberger, Anke A1 - Wacker, Alexander T1 - Diet quality determines lipase gene expression and lipase/esterase activity in Daphnia pulex N2 - We studied the short- (12 h) and long-term (144 h) response of Daphnia pulex lipases to quality shifts in diets consisting of different mixtures of the green alga Scenedesmus with the cyanobacterium Synechococcus, two species with contrasting lipid compositions. The lipase/esterase activity in both the gut and the body tissues had fast responses to the diet shift and increased with higher dietary contributions of Synechococcus. When screening the Daphnia genome for TAG lipases, we discovered a large gene-family expansion of these enzymes. We used a subset of eight genes for mRNA expression analyses and distinguished between influences of time and diet on the observed gene expression patterns. We identified five diet-responsive lipases of which three showed a sophisticated short- and long-term pattern of expression in response to small changes in food-quality. Furthermore, the gene expression of one of the lipases was strongly correlated to lipase/esterase activity in the gut suggesting its potentially major role in digestion. These findings demonstrate that the lipid-related enzymatic machinery of D. pulex is finely tuned to diet and might constitute an important mechanism of physiological adaptation in nutritionally complex environments. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 336 KW - Cyanobacteria KW - Digestive enzyme activity KW - Nutritional quality KW - Lipases Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-395661 ER - TY - JOUR A1 - Koussoroplis, Apostolos-Manuel A1 - Schwarzenberger, Anke A1 - Wacker, Alexander T1 - Diet quality determines lipase gene expression and lipase/esterase activity in Daphnia pulex JF - Biology open : BiO N2 - We studied the short- (12 h) and long-term (144 h) response of Daphnia pulex lipases to quality shifts in diets consisting of different mixtures of the green alga Scenedesmus with the cyanobacterium Synechococcus, two species with contrasting lipid compositions. The lipase/esterase activity in both the gut and the body tissues had fast responses to the diet shift and increased with higher dietary contributions of Synechococcus. When screening the Daphnia genome for TAG lipases, we discovered a large gene-family expansion of these enzymes. We used a subset of eight genes for mRNA expression analyses and distinguished between influences of time and diet on the observed gene expression patterns. We identified five diet-responsive lipases of which three showed a sophisticated short- and long-term pattern of expression in response to small changes in food-quality. Furthermore, the gene expression of one of the lipases was strongly correlated to lipase/esterase activity in the gut suggesting its potentially major role in digestion. These findings demonstrate that the lipid-related enzymatic machinery of D. pulex is finely tuned to diet and might constitute an important mechanism of physiological adaptation in nutritionally complex environments. KW - Cyanobacteria KW - Digestive enzyme activity KW - Nutritional quality KW - Lipases Y1 - 2017 U6 - https://doi.org/10.1242/bio.022046 VL - 6 SP - 210 EP - 216 PB - The company of Biologists CY - Cambridge ER - TY - THES A1 - Georgiev, Vasil T1 - Light-induced transformations in biomembranes T1 - Lichtinduzierte Transformationen in Biomembranen N2 - Cellular membranes constantly experience remodeling, as exemplified by morphological changes during endo- and exocytosis. Regulation of membrane morphology is essential for these processes. In this work, we attempt to establish a regulation path based on the use of photoswitches exhibiting conformational changes in model membranes, namely, giant unilamellar vesicles (GUVs). The mechanism of the changes in the GUVs’ morphology caused by isomerization of the photosensitive molecules has been previously explored but still remains elusive. We examine the morphological reshaping of GUVs in the presence of the photoswitch o-tetrafluoroazobenzene (F-azo) and show that the mechanism behind the resulting morphological changes involves both an increase in the membrane area and generation of a positive spontaneous curvature. First, we characterize the partitioning of F-azo in a single-component membrane using both experimental and computational approaches. The partition coefficient calculated from molecular dynamic simulations agrees with experimental data obtained with size-exclusion chromatography. Then, we implement the approach of vesicle electrodeformation in order to assess the increase in the membrane area, which is observed as a result of the conformational change of F-azo. Finally, the local and the effective membrane spontaneous curvatures were estimated from the observed shapes of vesicles exhibiting outward budding. We then extend the application of the F-azo to multicomponent lipid membranes, which exhibit a coexistence of domains in different liquid phases due to a miscibility gap between the lipids. We perform initial experiments to investigate whether F-azo can be employed to modulate the lateral lipid packing and organization. We observe either complete mixing of the domains or the appearing of disordered domains within the domains of more ordered phase. The type of behavior observed in response to the photoisomerization of F-azo was dependent on the used lipid composition. We believe that the findings introduced here will have an impact in understanding and controlling both lipid phase modulation and regulation of the membrane morphology in membrane systems. N2 - Zelluläre Membranen durchlaufen ständige Formveränderungen wie zum Beispiel bei der Endo- und Exozytose. Für diese und andere Prozesse ist eine Regulierung der Membranmorphologie notwendig. In der vorliegenden Arbeit wurden riesen unilamellare Vesikel (giant unilamellar vesicles, GUVs) als Modelmembranen genutzt. Änderungen der Vesikelform wurde durch lichtschaltbare Moleküle (Fotoschalter) erzielt. Dass die Isomerisierung von lichtempfindlichen Molekülen eine Verformung von GUV ermöglichen kann, war bekannt. Jedoch war der zugrunde liegende Mechanismus unklar. In dieser Arbeit wurde zur Untersuchung dieses Mechanismus o-Tetrafluoroazobenzol (F-azo) als Fotoschalter verwendet. Damit konnte gezeigt werden, dass sowohl eine Vergrößerung der Membranfläche als auch das Entstehen einer positiven, spontanen Membrankrümmung den morphologischen Veränderungen zu Grunde liegen. Durch experimentelle und computergestützte Methoden konnte zunächst die Verteilung von F-azo in Membranen, die aus nur einer Komponente bestehen, quantifiziert werden. Der Verteilungskoeffizient aus molekular-dynamik Simulationen stimmte dabei mit den experimentellen Daten aus der Größenausschluss-Chromatographie überein. Im Anschluss bestimmten wir die Änderung der Membranfläche mit Hilfe von GUV-Verformung durch elektrische Felder, und konnten die Veränderung der lokalen und effektiven spontanen Membrankrümmung durch Beobachtung der Vesikelformen abschätzen. Um herauszufinden ob F-azo die laterale Verdichtung und Organisation von Membranlipiden moduliert, weitteten wir die Experimente auf mehr-komponenten Membranen aus. Diese sind durch die Koexistenz von Domänen zweier flüssiger Lipid-Phasen gekennzeichnet. Wir konnten sowohl das Auftreten von Domänen ungeordneter Lipidphasen in geordneten Lipidphasen beobachten, als auch die Entstehung homogener GUVs durch komplette Mischung beider Lipidphasen. Wir konnten zeigen, dass die unterschiedliche Beeinflussung der Domänen durch die Licht-induzierte Isomerisierung von F-azo dabei von der Zusammensetzung der Membranen abhängig ist. Mit den hier beschriebenen Ergebnissen legen wir einen Grundstein, für die lichtinduzierte Kontrolle über Membranenmorphologien sowie für die Foto-Modulation von Lipidphasen. KW - giant unilamellar vesicles KW - morphological changes KW - light KW - photoswitches KW - riesen unilamellare Vesikel KW - morphologischen Veränderungen KW - Licht KW - Fotoschalter Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-395309 ER - TY - GEN A1 - Bareither, Nils A1 - Scheffel, André A1 - Metz, Johannes T1 - Distribution of polyploid plants in the common annual Brachypodium distachyon (s.l.) in Israel is not linearly correlated with aridity N2 - The ecological benefits of polyploidy are intensely debated. Some authors argue that plants with duplicated chromosome sets (polyploids) are more stress-resistant and superior colonizers and may thus outnumber their low ploidy conspecifics in more extreme habitats. Brachypodium distachyon (sensu lato), for example, a common annual grass in Israel and the entire Mediterranean basin, comprises three cytotypes of differing chromosome numbers that were recently proposed as distinct species. It was suggested that increased aridity increases the occurrence of its polyploid cytotype. Here, we tested at two spatial scales whether polyploid plants of B. distachyon s.l. are more frequently found in drier habitats in Israel. We collected a total of 430 specimens (i) along a largescale climatic gradient with 15 thoroughly selected sites (spanning 114–954 mm annual rainfall), and (ii) from corresponding Northern (more mesic) and Southern (more arid) hill slopes to assess the micro-climatic difference between contrasting exposures. Cytotypes were then determined via flow cytometry. Polyploid plants comprised 90% of all specimens and their proportion ranged between 0% and 100% per site. However, this proportion was not correlated with aridity along the large-scale gradient, nor were polyploids more frequently found on Southern exposures. Our results show for both spatial scales that increasing aridity is not the principal driver for the distribution of polyploids in B. distachyon s.l. in Israel. Notably, though, diploid plants were restricted essentially to four intermediate sites, while polyploids dominated the most arid and the most mesic sites. This, to some degree, clustered pattern suggests that the distribution of cytotypes is not entirely random and calls for future studies to assess further potential drivers. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 334 KW - Aridity KW - Brachypodium distachyon KW - Brachypodium hybridum KW - Brachypodium stacei KW - cytotype KW - exposition KW - Israel KW - Mediterranean grass species KW - polyploidization KW - rainfall gradient KW - slope aspect Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-395293 ER - TY - THES A1 - Heim, Olga T1 - Spatiotemporal effects on bat activity above intensively managed farmland N2 - Intakte und widerstandsfähige Ökosysteme sind essenziell für die Aufrechterhaltung optimaler Lebensbedingungen für das Leben auf der Erde. Die Basis für solche Ökosysteme bilden intakte ökologische Wechselwirkungen zwischen einer Vielzahl von Arten. Durch den beispiellosen Verlust der Biodiversität, welcher durch die in der zweiten Hälfte des 20. Jahrhunderts zunehmende Intensivierung der Agrarwirtschaft und die Zerstörung und Fragmentierung von Habitaten hervorgerufen wurde, können ökologische Wechselwirkungen und damit die Funktionsfähigkeit von Agrarökosystemen stark eingeschränkt werden. Um den Rückgang der Biodiversität in Agrarökosystemen abschwächen zu können, müssen wir die ökologischen Wechselwirkungen in Agrarökosystemen besser verstehen. Hierbei spielen Fledermäuse eine besondere Rolle, weil sie verschiedenste ökologische Nischen besetzen und eine Reihe von Ökosystemleistungen erfüllen so wie z.B. die Kontrolle von Schädlingspopulationen in Agrarlandschaften. Überdies trägt die Ordnung der Fledermäuse (Chiroptera) beträchtlich zur globalen Diversität der Säugetiere bei. Obwohl viele Fledermauspopulationen durch die Intensivierung der Agrarwirtschaft dezimiert wurden, ist noch relativ wenig darüber bekannt wie unterschiedliche Fledermausarten die offene Agrarlandschaft nutzen. Dieses Wissen ist jedoch essenziell für den Schutz von Fledermausarten in intensiv bewirtschafteten Agrarlandschaften und dringend notwendig besonders vor dem Hintergrund der vorhergesagten erweiterten Ausweitung der intensiven Agrarwirtschaft. Zusätzlich werden Fledermäuse durch den zuletzt massiven Ausbau von Windkraftanlagen, welche für viele Vogel- und Fledermausarten ein erhöhtes Tötungsrisiko darstellen, bedroht. Das Ziel dieser Dissertation war es deshalb, die Einflüsse ausgewählter raum-zeitlicher Faktoren auf die artspezifische Fledermausaktivität über intensiv genutzten Agrarflächen in einer von Agrarwirtschaft dominierten Landschaft zu untersuchen. Dazu habe ich die Fledermausaktivität mittels passiver akustischer Echoortungsaufnahme in den Jahren 2012 bis 2014 auf insgesamt 113 Untersuchungsflächen in offenen Ackerflächen im Nordosten Brandenburgs erfasst. Die Echoortungsrufe in etwa 27.779 Aufnahmen habe ich manuell bis auf die Art bestimmt und die berechneten artspezifischen Aktivitätsparameter mit Hilfe von komplexen statistischen Verfahren untersucht. Im ersten Kapitel dieser Arbeit, habe ich die berechneten Aktivitätsparameter von ökologisch unterschiedlichen Fledermausgruppen auf saisonale Muster hin untersucht. Dabei war ich besonders an Unterschieden zu den bekannten saisonalen Aktivitätsmustern in naturnahen Habitaten interessiert. Im zweiten Kapitel dieser Arbeit, habe ich den Einfluss von linearen Gehölzstrukturen am Feldrand und von kleinen Wasserflächen (Söllen) innerhalb von Ackerflächen auf die Flug- und Jagdaktivität verschiedener Fledermausarten über diesen Flächen untersucht. Zusätzlich war ich daran interessiert, ob sich etwaige Effekte dieser Landschaftselemente auf die Fledermausaktivität im Laufe des Jahres verändern. Im dritten Kapitel dieser Arbeit war es mein Ziel den Zusammenhang zwischen unterschiedlichen räumlichen und zeitlichen Einflüssen auf die artspezifische Fledermausaktivität über offenen Agrarflächen zu untersuchen. Dabei habe ich meine Untersuchungen auf Faktoren fokussiert, die dafür bekannt sind Fledermausaktivität zu beeinflussen, wie z.B. Faktoren auf kleinräumiger Skala, die mit der Beuteverfügbarkeit zusammenhängen, und verschiedene Landschaftscharakteristika auf großräumiger Skala. Auf der zeitlichen Skala, habe ich mich auf den Einfluss der Saison konzentriert. Zusammenfassend heben die Ergebnisse dieser Arbeit die Wichtigkeit naturnaher Landschaftselemente für die Fledermausaktivität über Agrarflächen hervor. Allerdings war nicht nur die Landschaftsstruktur für die Fledermausaktivität über Ackerflächen ausschlaggebend, sondern auch der Einfluss von interaktiven Effekten zwischen z.B. Landschaftscharakteristika und der lokalen Beuteverfügbarkeit. Ein weiteres Kernergebnis ist die saisonale Variabilität des Einflusses der Landschaftsstruktur auf die Fledermausaktivität. Hierbei hatten bestimmte Landschaftselemente vor allem im Sommer einen großen Einfluss auf die Fledermausaktivität. Das Potenzial der Ökosystemleistung durch spezifische Fledermausarten, welches wiederholt in den unterschiedlichen Kapiteln hervorgehoben wurde, ist ein weiteres Kernergebnis. Da die Fledermausaktivität jedoch stark von der Landschaftsstruktur in der Umgebung abhängt, ist es wichtig diese fledermausfreundlich zu gestalten, um die Ökosystemleistung der Schädlingskontrolle über Agrarflächen nutzen zu können. Schlussendlich trägt diese Arbeit in ihrer Gesamtheit zum bestehenden Wissen über die Fledermausbiologie und -ökologie bei und verdeutlicht die komplexen Wechselwirkungen unterschiedlicher Einflüsse auf mehreren raum-zeitlichen Ebenen. Die Ergebnisse dieser Arbeit können als Basis zur Verbesserung und Entwicklung von Schutzmaßnahmen für Fledermäuse in intensiv genutzten Agrarlandschaften dienen. Da Fledermäuse als gute Bioindikatoren gelten, können effektive Schutzmaßnahmen für Fledermäuse auch zum Schutz anderer Arten beitragen und damit potenziell den weiteren Verlust der Biodiversität in Agrarlandschaften abschwächen. N2 - Biodiversity and intact ecological interactions form the basis for functional and resilient ecosystems that maintain optimal conditions for life on earth. During the second half of the 20th century, especially land-use changes and an intensification of agricultural management caused an unprecedented loss of biodiversity in agroecosystems worldwide. Concerns have been raised that the ongoing loss of biodiversity would ultimately lead to impaired ecological interactions and ecosystem functioning in agricultural landscapes. In order to stop biodiversity loss while producing enough food for a growing world population, we need to gain detailed knowledge on ecological interactions and the functioning of agroecosystems as a whole. Bats (Chiroptera) represent an important component of global biodiversity, occupy a variety of ecological niches and fulfill numerous ecosystem services. Especially in temperate zone agroecosystems, bats were repeatedly reported to contribute to the reduction of pest insects above intensively managed arable fields. However, bat populations have been decimated by the consequence of land-use intensification which led to their legal protection status in the European Union (Council of Europe, 1979). The increasing number of wind turbines on arable fields poses an additional threat to bats as they might get injured or killed when flying too close to wind turbine blades. Although a large amount of land area is covered by arable fields, not much is known about how bats use the intensively managed agricultural landscape. In the present thesis, my general aim was to identify the relevance of factors at different spatiotemporal scales for shaping species-specific bat activity above intensively managed arable fields. Therefore, I repeatedly monitored bat activity above open arable fields in a landscape dominated by agriculture which is located in Northeast Brandenburg, Germany. From 2012 to 2014, I recorded echolocation calls of bats on a total of 113 sites using a passive acoustic approach. I obtained a total of 27,779 recordings, identified the recorded echolocation calls manually to species level and calculated species-specific bat activity measures. Depending on the focus of research, I modeled the obtained species-specific activity measures using generalized linear and additive mixed effect models. In Chapter I, I focused on identifying seasonal patterns in several species-specific activity measures of different functional bat groups. In Chapter II, I investigated small-scale effects of landscape elements, such as hedgerows and forest edges, on the flight and foraging activity of different bat species along the edge-field interface. Additionally, I aimed at identifying whether these effects are influenced by small ponds located within arable field and whether these effects change across seasons. In Chapter III, my aim was to investigate the interaction between factors from different spatiotemporal levels on the flight and foraging activity of bats above arable fields. At the small spatial scale, I focused on prey availability, at a large spatial scale on selected parameters which describe landscape characteristics and at the temporal scale on seasonal effects. The major findings obtained in each chapter can be summarized in the following three points. The first major finding is that not only landscape elements on a small spatial scale, e.g. a hedgerow at the edge of an arable field, but also landscape characteristics on a large spatial scale, e.g. landscape composition, shaped species-specific bat activity above open arable fields. This activity was also strongly influenced by interactions between landscape characteristics and local prey availability. Second, the influence of landscape elements and characteristics on bat activity above arable fields was not constant over time but changed across seasons with the strongest impact during summer as compared to spring and autumn. Third, I found indications of ecosystem service provided by N. noctula and P. nathusii in all three chapters, as especially these bat species were repeatedly found to forage above arable fields. This foraging activity was positively influenced by the proximity to landscape elements at the edge of the arable field but also by the presence of small ponds within the arable field. In light of the obtained findings, I strongly recommend protecting and most importantly recreating semi-natural landscape elements in the agricultural landscape. Furthermore, I strongly recommend against the construction of wind turbines close to these linear woody vegetation edges as bats were found to be active close to these landscape elements. Additionally, the operation times for wind turbines should be down-regulated during the mating and migration period in autumn due to high bat activity above arable fields. Since bats are considered being good bioindicators, effective conservation measures for bats might contribute to the protection of species from other taxa leading to an overall support of biodiversity in agricultural landscapes. In their entirety, the findings in this thesis contribute to the knowledge of different aspects of bat ecology and shed light on the complex interplay between factors from different spatiotemporal levels that shape bat activity above arable fields. Additionally, they can serve as a basis for the improvement and development of conservation measures for bats in agricultural landscapes. KW - European bats KW - Europäische Fledermausarten KW - conventional agriculture KW - konventionelle Landwirtschaft KW - landscape analysis KW - Landschaftsanalyse KW - conservation KW - Naturschutz Y1 - 2017 ER - TY - THES A1 - Knecht, Volker T1 - Modeling Biomolecular Association Y1 - 2017 ER - TY - GEN A1 - Schmidt, Andreas A1 - Rabsch, Wolfgang A1 - Broeker, Nina K. A1 - Barbirz, Stefanie T1 - Bacteriophage tailspike protein based assay to monitor phase variable glucosylations in Salmonella O-antigens N2 - Background Non-typhoid Salmonella Typhimurium (S. Typhimurium) accounts for a high number of registered salmonellosis cases, and O-serotyping is one important tool for monitoring epidemiology and spread of the disease. Moreover, variations in glucosylated O-antigens are related to immunogenicity and spread in the host. However, classical autoagglutination tests combined with the analysis of specific genetic markers cannot always reliably register phase variable glucose modifications expressed on Salmonella O-antigens and additional tools to monitor O-antigen glucosylation phenotypes of S. Typhimurium would be desirable. Results We developed a test for the phase variable O-antigen glucosylation state of S. Typhimurium using the tailspike proteins (TSP) of Salmonella phages 9NA and P22. We used this ELISA like tailspike adsorption (ELITA) assay to analyze a library of 44 Salmonella strains. ELITA was successful in discriminating strains that carried glucose 1-6 linked to the galactose of O-polysaccharide backbone (serotype O1) from non-glucosylated strains. This was shown by O-antigen compositional analyses of the respective strains with mass spectrometry and capillary electrophoresis. The ELITA test worked rapidly in a microtiter plate format and was highly O-antigen specific. Moreover, TSP as probes could also detect glucosylated strains in flow cytometry and distinguish multiphasic cultures differing in their glucosylation state. Conclusions Tailspike proteins contain large binding sites with precisely defined specificities and are therefore promising tools to be included in serotyping procedures as rapid serotyping agents in addition to antibodies. In this study, 9NA and P22TSP as probes could specifically distinguish glucosylation phenotypes of Salmonella on microtiter plate assays and in flow cytometry. This opens the possibility for flow sorting of cell populations for subsequent genetic analyses or for monitoring phase variations during large scale O-antigen preparations necessary for vaccine production. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 313 KW - Bacteriophage KW - Flow cytometry KW - O-antigen KW - O-serotyping KW - Phase variation KW - Salmonella Typhimurium KW - Tailspike protein Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-103769 ER -