@phdthesis{Andresen2007,
  author    = {Andresen, Heiko},
  title     = {Analytische Biochips auf der Basis vollsynthetischer Peptide f{\"u}r die serologische Multiparameterdiagnostik},
  address   = {Potsdam},
  pages     = {XII, 155 S. : Ill., graph. Darst.},
  year      = {2007},
  language  = {de}
}
@article{AndresenvonNickischRosenegkBier2009,
  author    = {Andresen, Dennie and von Nickisch-Rosenegk, Markus and Bier, Frank Fabian},
  title     = {Helicase dependent OnChip-amplification and its use in multiplex pathogen detection},
  issn      = {0009-8981},
  doi       = {10.1016/j.cca.2009.03.021},
  year      = {2009},
  abstract  = {Background: The need for fast, specific and sensitive multiparametric detection methods is an ever growing demand in molecular diagnostics. Here we report on a newly developed method, the helicase dependent Onchip amplification (OnChip-HDA). This approach integrates the analysis and detection in one single reaction thus leading to time and cost savings in multiparametric analysis. Methods: HDA is an isothermal amplification method that is not depending on thermocycling as known from PCR due to the helicases' ability to unwind DNA double-strands. We have combined the HDA with microarray based detection, making it suitable for multiplex detection. As an example we used the Onchip HDA in single and multiplex amplifications for the detection of the two pathogens N. gonorrhoeae and S. aureus directly on surface bound primers. Results: We have successfully shown the OnChip-HDA and applied it for single- and duplex- detection of the pathogens N. gonorrhoeae and S. aureus. Conclusion: We have developed a new method, the OnChip-HDA for the multiplex detection of pathogens. Its simplicity in reaction setup and potential for miniaturization and multiparametric analysis is advantageous for the integration in miniaturized Lab on Chip systems, e.g. needed in point of care diagnostics.},
  language  = {en}
}
@article{AndresenvonNickischRosenegkBier2009,
  author    = {Andresen, Dennie and von Nickisch-Rosenegk, Markus and Bier, Frank Fabian},
  title     = {Helicase-dependent amplification : use in OnChip amplification and potential for point-of-care diagnostics},
  issn      = {1473-7159},
  doi       = {10.1586/erm.09.46},
  year      = {2009},
  abstract  = {Isothermal amplification technologies are emerging on the horizon that could have the potential to pose as alternatives to PCR in terms of sensitivity and ease of use. One of the most recent isothermal technologies is helicase- dependent amplification (HDA). This technology uses the helicase's capability to disrupt the hydrogen bonds of a Watson-Crick base pair in order to separate dsDNA. A denaturation step, as is used in PCR, is no longer required. This gives rise to new, less expensive and less complicated designs for point-of-care devices and 'Lab on Chip' systems. Helicase-dependent OnChip-amplification (OnChip-HDA) is a further step into this direction as it integrates the HDA technology with microarray technology and its power of multiplexing. This special report will give an overview on the HDA and OnChip-HDA technology, and its potential for point-of-care diagnostics.},
  language  = {en}
}
@phdthesis{Andresen2009,
  author    = {Andresen, Dennie},
  title     = {Entwicklung von Microarrays f{\"u}r die Multiparameteranalytik und Etablierung einer Multiplex-OnChip-PCR},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-39462},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {In der molekularen Diagnostik besteht ein Bedarf an schnellen und spezifischen Testsystemen, die entweder f{\"u}r die Labordiagnostik oder in Point of Care-Umgebungen eingesetzt werden k{\"o}nnen. Um dieses Ziel zu erreichen, stehen die Miniaturisierung und Parallelisierung im Mittelpunkt des Forschungsinteresses. Die f{\"u}hrende Methode im Bereich der DNA-Analytik ist derzeit die Realtime-PCR. Dieser Technologie sind hinsichtlich der Multiplexf{\"a}higkeit technologischen H{\"u}rden gesetzt, da derzeit nur eine Analyse von maximal vier Parametern parallel in einem Versuchsansatz erfolgen kann. Microarrays stellen hingegen die ben{\"o}tigten Voraussetzungen zur Verf{\"u}gung, um als Werkzeuge f{\"u}r die Multiparameteranalyse in verschiedensten Anwendungsbereichen zu dienen. Ein Schwerpunkt dieser Arbeit war es, Multiplex-PCRs und diagnostische Microarrays zu entwickeln, die f{\"u}r analytische Fragestellungen eine schnelle und zuverl{\"a}ssige Multiparameteranalytik erm{\"o}glichen, um die bisherigen Einschr{\"a}nkungen aktueller Nachweisverfahren zu vermeiden. Als Anwendungen wurden zum einen ein Nachweissystem f{\"u}r acht relevante Gefl{\"u}gelpathogene zur {\"U}berwachung in der Gefl{\"u}gelzucht, zum anderen ein Nachweissystem zur Identifikation potentiell allergener Lebensmittelinhaltstoffe entwickelt. Neben der Entwicklung geeigneter PCR und Multiplex-PCR-Verfahren sowie spezifischer Microarrays f{\"u}r die Detektion der gesuchten Zielsequenzen stand auch die weiterf{\"u}hrende Integration von DNA-Amplifikation und Microarray-Technologie im Fokus dieser Arbeit. Die OnChip-Amplifikation stellt eine M{\"o}glichkeit dar, um DNA-Analytik und Detektion in einem Reaktionsschritt zu integrieren. Entsprechend wurden die in der Arbeit entwickelten PCR- und Multiplex-PCR-Verfahren zum Nachweis potentieller allergener Lebensmittelinhaltsstoffe f{\"u}r die OnChip-Amplifikation adaptiert und Reaktionsbedingungen getestet, die eine Multiparameteranalyse auf dem Chip erm{\"o}glichen. Die entwickelten OnChip-PCR-Verfahren zeigten eine hohe Spezifit{\"a}t sowohl in Single- als auch in der Multiplex-OnChip-PCR. Eine Sensitivit{\"a}t von 10 Kopien bzw. <10ppm konnte in Single-OnChip-PCRs f{\"u}r den Nachweis allergener Lebensmittelinhaltsstoffe gezeigt werden. In Multiplex-OnChip-PCRs konnten 10-100ppm allergene Verunreinigungen spezifisch in unterschiedlichen Lebensmitteln nachgewiesen werden. Ein weiterer Schritt in Richtung einer m{\"o}glichen Verwendung im Point of Care-Bereich stellt der Einsatz eines isothermalen Amplifikationsverfahrens dar. Vorteil eines solchen Verfahrens ist die M{\"o}glichkeit, auf das ansonsten ben{\"o}tigte Thermocycling zu verzichten. Dies vereinfacht eine Integration der OnChip-Amplifikation in mobile Analyseger{\"a}te oder Lab on Chip-Systeme und qualifiziert das Verfahren f{\"u}r den Einsatz in Point of Care-Umgebungen. In dieser Arbeit wurde eine noch junge isothermale Amplifikationsmethode, die helikase-abh{\"a}ngige Amplifikation (HDA), hinsichtlich ihrer Eignung f{\"u}r die Integration auf einem Microarray getestet. Hierf{\"u}r konnte die bislang erste OnChip-HDA f{\"u}r Einzel- und Duplex-Nachweise von Pathogenen entwickelt werden.},
  language  = {de}
}
@phdthesis{Andres2008,
  author    = {Andres, Janin},
  title     = {Untersuchungen {\"u}ber Regulationsmechanismen der 11beta-Hydroxysteroid Dehydrogenase Typ 1},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33033},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {Die 11beta-HSD1 reguliert intrazellul{\"a}r die Cortisolkonzentration durch Regeneration von Cortison z.B. aus dem Blutkreislauf, zu Cortisol. Daher stellt diese ein wichtiges Element in der Glucocorticoid-vermittelten Genregulation dar. Die 11beta-HSD1 wird ubiquit{\"a}r exprimiert, auf hohem Niveau besonders in Leber, Fettgewebe und glatten Muskelzellen. Insbesondere die Bedeutung der 11beta-HSD1 in Leber und Fettgewebe konnte mehrfach nachgewiesen werden. In der Leber f{\"u}hrte eine erh{\"o}hte Aktivit{\"a}t aufgrund einer {\"U}berexpression in M{\"a}usen zu einer verst{\"a}rkten Gluconeogeneserate. Des Weiteren konnte gezeigt werden, dass eine erh{\"o}hte Expression und erh{\"o}hte Enzymaktivit{\"a}t der 11beta-HSD1 im subkutanen und viszeralen Fettgewebe assoziiert ist mit Fettleibigkeit, Insulinresistenz und Dyslipid{\"a}mie. {\"U}ber die Regulation ist jedoch noch wenig bekannt. Zur Untersuchung der Promotoraktivit{\"a}t wurde der Promotorbereich von -3034 bis +188, vor und nach dem Translations- und Transkriptionsstart, der 11beta-HSD1 kloniert. 8 Promotorfragmente wurden mittels Dual-Luciferase-Assay in humanen HepG2-Zellen sowie undifferenzierten und differenzierten murinen 3T3-L1-Zellen untersucht. Anschließend wurde mittels nicht-radioaktiven EMSA die Bindung des TATA-Binding Proteins (TBP) sowie von CCAAT/Enhancer-Binding-Proteinen (C/EBP) an ausgew{\"a}hlte Promotorregionen analysiert. Nach der Charakterisierung des Promotors wurden spezifische endogene und exogene Regulatoren untersucht. Fetts{\"a}uren modifizieren die Entstehung von Adipositas und Insulinresistenz. Ihre Wirkung wird u.a. PPARgamma-abh{\"a}ngig vermittelt und kann durch das Inkretin (Glucose-dependent insulinotropic Peptide) GIP modifiziert werden. So wurden die Effekte von unterschiedlichen Fetts{\"a}uren, vom PPARgamma Agonisten Rosiglitazon sowie dem Inkretin GIP auf die Expression und Enzymaktivit{\"a}t der 11beta-HSD1 untersucht. Dies wurde in-vitro-, tierexperimentell und in humanen in-vivo-Studien realisiert. Zuletzt wurden 2 Single Nucleotide Polymorphismen (SNP) im Promotorbereich der 11beta-HSD1 in der Zellkultur im Hinblick auf potentielle Funktionalit{\"a}t analysiert sowie die Assoziation mit Diabetes mellitus Typ 2 und K{\"o}rpergewicht in der MeSyBePo-Kohorte bei rund 1.800 Personen untersucht. Die Luciferase-Assays zeigten basal eine zell-spezifische Regulation der 11beta-HSD1, wobei in allen 3 untersuchten Zelltypen die Bindung eines Repressors nachgewiesen werden konnte. Zudem konnte eine m{\"o}gliche Bindung des TBPs sowie von C/EBP-Proteinen an verschiedene Positionen gezeigt werden. Die Transaktivierungsassays mit den C/EBP-Proteinen -alpha, -beta und -delta zeigten eben-falls eine zellspezifische Regulation des 11beta-HSD1-Promotors. Die Aktivit{\"a}t und Expression der 11beta-HSD1 wurde durch die hier untersuchten endogenen und exogenen Faktoren spezifisch modifiziert, was sowohl in-vitro als auch in-vivo in unterschiedlichen Modellsystemen dargestellt werden konnte. Die Charakterisierung der MeSyBePo-Kohorte ergab keine direkten Assoziationen zwischen Polymorphismus und klinischem Ph{\"a}notyp, jedoch Tendenzen f{\"u}r eine erh{\"o}htes K{\"o}rper-gewicht und Typ 2 Diabetes mellitus in Abh{\"a}ngigkeit des Genotyps. Der Promotor der 11beta-HSD1 konnte aufgrund der Daten aus den Luciferaseassays sowie den Daten aus den EMSA-Analysen n{\"a}her charakterisiert werden. Dieser zeigt eine variable und zell-spezifische Regulation. Ein wichtiger Regulator stellen insbesondere in den HepG2-Zellen die C/EBP-Proteine -alpha, -beta und -delta dar. Aus den in-vivo-Studien ergab sich eine Regulation der 11beta-HSD1 durch endogene, exogene und pharmakologische Substanzen, die durch die Zellkulturversuche best{\"a}tigt und n{\"a}her charakterisiert werden konnten.},
  language  = {de}
}
@article{AndresRoskeDoeringetal.2012,
  author    = {Andres, Dorothee and Roske, Yvette and Doering, Carolin and Heinemann, Udo and Seckler, Robert and Barbirz, Stefanie},
  title     = {Tail morphology controls DNA release in two Salmonella phages with one lipopolysaccharide receptor recognition system},
  series = {Molecular microbiology},
  volume    = {83},
  journal   = {Molecular microbiology},
  number    = {6},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0950-382X},
  doi       = {10.1111/j.1365-2958.2012.08006.x},
  pages     = {1244 -- 1253},
  year      = {2012},
  abstract  = {Bacteriophages use specific tail proteins to recognize host cells. It is still not understood to molecular detail how the signal is transmitted over the tail to initiate infection. We have analysed in vitro DNA ejection in long-tailed siphovirus 9NA and short-tailed podovirus P22 upon incubation with Salmonella typhimurium lipopolysaccharide (LPS). We showed for the first time that LPS alone was sufficient to elicit DNA release from a siphovirus in vitro. Crystal structure analysis revealed that both phages use similar tailspike proteins for LPS recognition. Tailspike proteins hydrolyse LPS O antigen to position the phage on the cell surface. Thus we were able to compare in vitro DNA ejection processes from two phages with different morphologies with the same receptor under identical experimental conditions. Siphovirus 9NA ejected its DNA about 30 times faster than podovirus P22. DNA ejection is under control of the conformational opening of the particle and has a similar activation barrier in 9NA and P22. Our data suggest that tail morphology influences the efficiencies of particle opening given an identical initial receptor interaction event.},
  language  = {en}
}
@article{AndresHankeBaxaetal.2010,
  author    = {Andres, Dorothee and Hanke, Christin and Baxa, Ulrich and Seul, Anait and Barbirz, Stefanie and Seckler, Robert},
  title     = {Tailspike interactions with lipopolysaccharide effect DNA ejection from phage P22 particles in vitro},
  issn      = {0021-9258},
  doi       = {10.1074/jbc.M110.169003},
  year      = {2010},
  abstract  = {Initial attachment of bacteriophage P22 to the Salmonella host cell is known to be mediated by interactions between lipopolysaccharide (LPS) and the phage tailspike proteins (TSP), but the events that subsequently lead to DNA injection into the bacterium are unknown. We used the binding of a fluorescent dye and DNA accessibility to DNase and restriction enzymes to analyze DNA ejection from phage particles in vitro. Ejection was specifically triggered by aggregates of purified Salmonella LPS but not by LPS with different O-antigen structure, by lipid A, phospholipids, or soluble O-antigen polysaccharide. This suggests that P22 does not use a secondary receptor at the bacterial outer membrane surface. Using phage particles reconstituted with purified mutant TSP in vitro, we found that the endorhamnosidase activity of TSP degrading the O-antigen polysaccharide was required prior to DNA ejection in vitro and DNA replication in vivo. If, however, LPS was pre-digested with soluble TSP, it was no longer able to trigger DNA ejection, even though it still contained five O-antigen oligosaccharide repeats. Together with known data on the structure of LPS and phage P22, our results suggest a molecular model. In this model, tail-spikes position the phage particles on the outer membrane surface for DNA ejection. They force gp26, the central needle and plug protein of the phage tail machine, through the core oligosaccharide layer and into the hydrophobic portion of the outer membrane, leading to refolding of the gp26 lazo-domain, release of the plug, and ejection of DNA and pilot proteins.},
  language  = {en}
}
@article{AndresGohlkeBroekeretal.2013,
  author    = {Andres, Dorothee and Gohlke, Ulrich and Br{\"o}ker, Nina Kristin and Schulze, Stefan and Rabsch, Wolfgang and Heinemann, Udo and Barbirz, Stefanie and Seckler, Robert},
  title     = {An essential serotype recognition pocket on phage P22 tailspike protein forces Salmonella enterica serovar Paratyphi A O-antigen fragments to bind as nonsolution conformers},
  series = {Glycobiology},
  volume    = {23},
  journal   = {Glycobiology},
  number    = {4},
  publisher = {Oxford Univ. Press},
  address   = {Cary},
  issn      = {0959-6658},
  doi       = {10.1093/glycob/cws224},
  pages     = {486 -- 494},
  year      = {2013},
  abstract  = {Bacteriophage P22 recognizes O-antigen polysaccharides of Salmonella enterica subsp. enterica (S.) with its tailspike protein (TSP). In the serovars S. Typhimurium, S. Enteritidis, and S. Paratyphi A, the tetrasaccharide repeat units of the respective O-antigens consist of an identical main chain trisaccharide but different 3,6-dideoxyhexose substituents. Here, the epimers abequose, tyvelose and paratose determine the specific serotype. P22 TSP recognizes O-antigen octasaccharides in an extended binding site with a single 3,6-dideoxyhexose binding pocket. We have isolated S. Paratyphi A octasaccharides which were not available previously and determined the crystal structure of their complex with P22 TSP. We discuss our data together with crystal structures of complexes with S. Typhimurium and S. Enteritidis octasaccharides determined earlier. Isothermal titration calorimetry showed that S. Paratyphi A octasaccharide binds P22 TSP less tightly, with a difference in binding free energy of similar to 7 kJ mol(-1) at 20 degrees C compared with S. Typhimurium and S. Enteritidis octasaccharides. Individual protein-carbohydrate contacts were probed by amino acid replacements showing that the dideoxyhexose pocket contributes to binding of all three serotypes. However, S. Paratyphi A octasaccharides bind in a conformation with an energetically unfavorable phi/epsilon glycosidic bond angle combination. In contrast, octasaccharides from the other serotypes bind as solution-like conformers. Two water molecules are conserved in all P22 TSP complexes with octasaccharides of different serotypes. They line the dideoxyhexose binding pocket and force the S. Paratyphi A octasaccharides to bind as nonsolution conformers. This emphasizes the role of solvent as part of carbohydrate binding sites.},
  language  = {en}
}
@article{AndresBaxaHankeetal.2010,
  author    = {Andres, Dorothee and Baxa, Ulrich and Hanke, Christin and Seckler, Robert and Barbirz, Stefanie},
  title     = {Carbohydrate binding of Salmonella phage P22 tailspike protein and its role during host cell infection},
  issn      = {0300-5127},
  doi       = {10.1042/Bst0381386},
  year      = {2010},
  abstract  = {TSPs (tailspike proteins) are essential infection organelles of bacteriophage P22. Upon infection, P22TSP binds to and cleaves the O-antigen moiety of the LPS (lipopolysaccharide) of its Salmonella host To elucidate the role of TSP during infection, we have studied binding to oligosaccharides and polysaccharides of Salmonella enteric Typhimurium and Enteritidis in vitro. P22TSP is a trimeric beta-helical protein with a carbohydrate-binding site on each subunit. Octasaccharide O-antigen fragments bind to P22TSP with micromolar dissociation constants. Moreover, P22TSP is an endorhamnosidase and cleaves the host O-antigen. Catalytic residues lie at the periphery of the high-affinity binding site, which enables unproductive binding modes, resulting in slow hydrolysis. However, the role of this hydrolysis function during infection remains unclear. Binding of polysaccharide to P22TSP is of high avidity with slow dissociation rates when compared with oligosaccharides. In vivo, the infection of Salmonella with phage P22 can be completely inhibited by the addition of LPS, indicating that binding of phage to its host via TSP is an essential step for infection.},
  language  = {en}
}
@phdthesis{Andres2012,
  author    = {Andres, Dorothee},
  title     = {Biophysical chemistry of lipopolysaccharide specific bacteriophages},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-59261},
  school      = {Universit{\"a}t Potsdam},
  year      = {2012},
  abstract  = {Carbohydrate recognition is a ubiquitous principle underlying many fundamental biological processes like fertilization, embryogenesis and viral infections. But how carbohydrate specificity and affinity induce a molecular event is not well understood. One of these examples is bacteriophage P22 that binds and infects three distinct Salmonella enterica (S.) hosts. It recognizes and depolymerizes repetitive carbohydrate structures of O antigen in its host´s outer membrane lipopolysaccharide molecule. This is mediated by tailspikes, mainly β helical appendages on phage P22 short non contractile tail apparatus (podovirus). The O antigen of all three Salmonella enterica hosts is built from tetrasaccharide repeating units consisting of an identical main chain with a distinguished 3,6 dideoxyhexose substituent that is crucial for P22 tailspike recognition: tyvelose in S. Enteritidis, abequose in S. Typhimurium and paratose in S. Paratyphi. In the first study the complexes of P22 tailspike with its host's O antigen octasaccharide were characterized. S. Paratyphi octasaccharide binds less tightly (ΔΔG≈7 kJ/mol) to the tailspike than the other two hosts. Crystal structure analysis of P22 tailspike co crystallized with S. Paratyphi octasaccharides revealed different interactions than those observed before in tailspike complexes with S. Enteritidis and S. Typhimurium octasaccharides. These different interactions occur due to a structural rearrangement in the S. Paratyphi octasaccharide. It results in an unfavorable glycosidic bond Φ/Ψ angle combination that also had occurred when the S. Paratyphi octasaccharide conformation was analyzed in an aprotic environment. Contributions of individual protein surface contacts to binding affinity were analyzed showing that conserved structural waters mediate specific recognition of all three different Salmonella host O antigens. Although different O antigen structures possess distinct binding behavior on the tailspike surface, all are recognized and infected by phage P22. Hence, in a second study, binding measurements revealed that multivalent O antigen was able to bind with high avidity to P22 tailspike. Dissociation rates of the polymer were three times slower than for an octasaccharide fragment pointing towards high affinity for O antigen polysaccharide. Furthermore, when phage P22 was incubated with lipopolysaccharide aggregates before plating on S. Typhimurium cells, P22 infectivity became significantly reduced. Therefore, in a third study, the function of carbohydrate recognition on the infection process was characterized. It was shown that large S. Typhimurium lipopolysaccharide aggregates triggered DNA release from the phage capsid in vitro. This provides evidence that phage P22 does not use a second receptor on the Salmonella surface for infection. P22 tailspike binding and cleavage activity modulate DNA egress from the phage capsid. DNA release occurred more slowly when the phage possessed mutant tailspikes with less hydrolytic activity and was not induced if lipopolysaccharides contained tailspike shortened O antigen polymer. Furthermore, the onset of DNA release was delayed by tailspikes with reduced binding affinity. The results suggest a model for P22 infection induced by carbohydrate recognition: tailspikes position the phage on Salmonella enterica and their hydrolytic activity forces a central structural protein of the phage assembly, the plug protein, onto the host´s membrane surface. Upon membrane contact, a conformational change has to occur in the assembly to eject DNA and pilot proteins from the phage to establish infection. Earlier studies had investigated DNA ejection in vitro solely for viruses with long non contractile tails (siphovirus) recognizing protein receptors. Podovirus P22 in this work was therefore the first example for a short tailed phage with an LPS recognition organelle that can trigger DNA ejection in vitro. However, O antigen binding and cleaving tailspikes are widely distributed in the phage biosphere, for example in siphovirus 9NA. Crystal structure analysis of 9NA tailspike revealed a complete similar fold to P22 tailspike although they only share 36 \% sequence identity. Moreover, 9NA tailspike possesses similar enzyme activity towards S. Typhimurium O antigen within conserved amino acids. These are responsible for a DNA ejection process from siphovirus 9NA triggered by lipopolysaccharide aggregates. 9NA expelled its DNA 30 times faster than podovirus P22 although the associated conformational change is controlled with a similar high activation barrier. The difference in DNA ejection velocity mirrors different tail morphologies and their efficiency to translate a carbohydrate recognition signal into action.},
  language  = {en}
}
@article{AndreevRaschkeBiskabornetal.2021,
  author    = {Andreev, Andrei and Raschke, Elena and Biskaborn, Boris and Vyse, Stuart Andrew and Courtin, J{\´e}r{\´e}my and B{\"o}hmer, Thomas and Stoof-Leichsenring, Kathleen R. and Kruse, Stefan and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {Late Pleistocene to Holocene vegetation and climate changes in northwestern Chukotka (Far East Russia) deduced from lakes Ilirney and Rauchuagytgyn pollen records},
  series = {Boreas : an international journal of quaternary research},
  volume    = {50},
  journal   = {Boreas : an international journal of quaternary research},
  number    = {3},
  publisher = {Wiley-Blackwell},
  address   = {Oxford [u.a.]},
  issn      = {0300-9483},
  doi       = {10.1111/bor.12521},
  pages     = {652 -- 670},
  year      = {2021},
  abstract  = {This paper presents two new pollen records and quantitative climate reconstructions from northern Chukotka documenting environmental changes over the last 27.9 ka. Open tundra- and steppe-like habitats dominated between 27.9 and 18.7 cal. ka BP. Betula and Alnus shrubs might have grown in sheltered microhabitats but disappeared after 18.7 cal. ka BP. Although the climate was rather harsh, local herb-dominated communities supported herbivores as is evident by the presence of coprophilous spores in the sediments. The increase in Salix and Cyperaceae similar to 16.1 cal. ka BP suggests climate amelioration. Shrub Betula appeared similar to 15.9 cal. ka BP, and became dominant after similar to 15.52 cal. ka BP, whilst typical steppe communities drastically reduced. Very high presence of Botryococcus in the Lateglacial sediments reflects widespread shallow habitats, probably due to lake level increase. Shrub Alnus became common after similar to 13 cal. ka BP reflecting further climate amelioration. Simultaneously, herb communities gradually decreased in the vegetation reaching a minimum similar to 11.8 cal. ka BP. A gradual decrease of algae remains suggests a reduction of shallow-water habitats. Shrubby and graminoid tundra was dominant similar to 11.8-11.1 cal. ka BP, later Salix stands significantly decreased. The forest-tundra ecotone established in the Early Holocene, shortly after 11.1 cal. ka BP. Low contents of green algae in the Early Holocene sediments likely reflect deeper aquatic conditions. The most favourable climate conditions were between similar to 10.6 and 7 cal. ka BP. Vegetation became similar to the modern after similar to 7 cal. ka BP but Pinus pumila came to the Ilirney area at about 1.2 cal. ka BP. It is important to emphasize that the study area provided refugia for Betula and Alnus during MIS 2. It is also notable that our records do not reflect evidence of Younger Dryas cooling, which is inconsistent with some regional environmental records but in good accordance with some others.},
  language  = {en}
}
@article{AndreevNazarovaLenzetal.2022,
  author    = {Andreev, Andrei and Nazarova, Larisa B. and Lenz, Marlene M. and B{\"o}hmer, Thomas and Syrykh, Ludmila and Wagner, Bernd and Melles, Martin and Pestryakova, Luidmila A. and Herzschuh, Ulrike},
  title     = {Late Quaternary paleoenvironmental reconstructions from sediments of Lake Emanda (Verkhoyansk Mountains, East Siberia)},
  series = {Journal of quaternary science : JQS},
  volume    = {37},
  journal   = {Journal of quaternary science : JQS},
  number    = {5},
  publisher = {Wiley},
  address   = {New York, NY [u.a.]},
  issn      = {0267-8179},
  doi       = {10.1002/jqs.3419},
  pages     = {884 -- 899},
  year      = {2022},
  abstract  = {Continuous pollen and chironomid records from Lake Emanda (65 degrees 17'N, 135 degrees 45'E) provide new insights into the Late Quaternary environmental history of the Yana Highlands (Yakutia). Larch forest with shrubs (alders, pines, birches) dominated during the deposition of the lowermost sediments suggesting its Early Weichselian [Marine Isotope Stage (MIS) 5] age. Pollen- and chironomid-based climate reconstructions suggest July temperatures (T-July) slightly lower than modern. Gradually increasing amounts of herb pollen and cold stenotherm chironomid head capsules reflect cooler and drier environments, probably during the termination of MIS 5. T-July dropped to 8 degrees C. Mostly treeless vegetation is reconstructed during MIS 3. Tundra and steppe communities dominated during MIS 2. Shrubs became common after similar to 14.5 ka BP but herb-dominated habitats remained until the onset of the Holocene. Larch forests with shrub alder and dwarf birch dominated after the Holocene onset, ca. 11.7 ka BP. Decreasing amounts of shrub pollen during the Lateglacial are assigned to the Older Dryas and Younger Dryas with T-July similar to 7.5 degrees C. T-July increased up to 13 degrees C. Shrub stone pine was present after similar to 7.5 ka BP. The vegetation has been similar to modern since ca. 5.8 ka BP. Chironomid diversity and concentration in the sediments increased towards the present day, indicating the development of richer hydrobiological communities in response to the Holocene thermal maximum.},
  language  = {en}
}
@article{AndradeLuCordeiroetal.2022,
  author    = {Andrade, Luis and Lu, Yunlong and Cordeiro, Andre and Costa, Jo{\~a}o M. F. and Wigge, Philip Anthony and Saibo, Nelson J. M. and Jaeger, Katja E.},
  title     = {The evening complex integrates photoperiod signals to control flowering in rice},
  series = {Proceedings of the National Academy of Sciences of the United States of America : PNAS},
  volume    = {119},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America : PNAS},
  number    = {26},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.2122582119},
  pages     = {8},
  year      = {2022},
  abstract  = {Plants use photoperiodism to activate flowering in response to a particular daylength. In rice, flowering is accelerated in short-day conditions, and even a brief exposure to light during the dark period (night-break) is sufficient to delay flowering. Although many of the genes involved in controlling flowering in rice have been uncovered, how the long- and short-day flowering pathways are integrated, and the mechanism of photoperiod perception is not understood. While many of the signaling components controlling photoperiod-activated flowering are conserved between Arabidopsis and rice, flowering in these two systems is activated by opposite photoperiods. Here we establish that photoperiodism in rice is controlled by the evening complex (EC). We show that mutants in the EC genes LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) paralogs abolish rice flowering. We also show that the EC directly binds and suppresses the expression of flowering repressors, including PRR37 and Ghd7. We further demonstrate that light acts via phyB to cause a rapid and sustained posttranslational modification of ELF3-1. Our results suggest a mechanism by which the EC is able to control both long- and short-day flowering pathways.},
  language  = {en}
}
@phdthesis{AndradeLinares2011,
  author    = {Andrade Linares, Diana Roc{\´i}o},
  title     = {Characterization of tomato root-endophytic fungi and analysis of their effects on plant development, on fruit yield and quality and on interaction with the pathogen Verticillium dahliae},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-51375},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Non-mycorrhizal fungal endophytes are able to colonize internally roots without causing visible disease symptoms establishing neutral or mutualistic associations with plants. These fungi known as non-clavicipitaceous endophytes have a broad host range of monocot and eudicot plants and are highly diverse. Some of them promote plant growth and confer increased abiotic-stress tolerance and disease resistance. According to such possible effects on host plants, it was aimed to isolate and to characterize native fungal root endophytes from tomato (Lycopersicon esculentum Mill.) and to analyze their effects on plant development, plant resistance and fruit yield and quality together with the model endophyte Piriformospora indica. Fifty one new fungal strains were isolated from desinfected tomato roots of four different crop sites in Colombia. These isolates were roughly characterized and fourteen potential endophytes were further analyzed concerning their taxonomy, their root colonization capacity and their impact on plant growth. Sequencing of the ITS region from the ribosomal RNA gene cluster and in-depth morphological characterisation revealed that they correspond to different phylogenetic groups among the phylum Ascomycota. Nine different morphotypes were described including six dark septate endophytes (DSE) that did not correspond to the Phialocephala group. Detailed confocal microscopy analysis showed various colonization patterns of the endophytes inside the roots ranging from epidermal penetration to hyphal growth through the cortex. Tomato pot experiments under glass house conditions showed that they differentially affect plant growth depending on colonization time and inoculum concentration. Three new isolates (two unknown fungal endophyte DSE48, DSE49 and one identified as Leptodontidium orchidicola) with neutral or positiv effects were selected and tested in several experiments for their influence on vegetative growth, fruit yield and quality and their ability to diminish the impact of the pathogen Verticillium dahliae on tomato plants. Although plant growth promotion by all three fungi was observed in young plants, vegetative growth parameters were not affected after 22 weeks of cultivation except a reproducible increase of root diameter by the endophyte DSE49. Additionally, L. orchidicola increased biomass and glucose content of tomato fruits, but only at an early date of harvest and at a certain level of root colonization. Concerning bioprotective effects, the endophytes DSE49 and L. orchidicola decreased significantly disease symptoms caused by the pathogen V. dahliae, but only at a low dosis of the pathogen. In order to analyze, if the model root endophytic fungus Piriformospora indica could be suitable for application in production systems, its impact on tomato was evaluated. Similarly to the new fungal isolates, significant differences for vegetative growth parameters were only observable in young plants and, but protection against V. dahliae could be seen in one experiment also at high dosage of the pathogen. As the DSE L. orchidicola, P. indica increased the number and biomass of marketable tomatoes only at the beginning of fruit setting, but this did not lead to a significant higher total yield. If the effects on growth are due to a better nutrition of the plant with mineral element was analyzed in barley in comparison to the arbuscular mycorrhizal fungus Glomus mosseae. While the mycorrhizal fungus increased nitrogen and phosphate uptake of the plant, no such effect was observed for P. indica. In summary this work shows that many different fungal endophytes can be also isolated from roots of crops and, that these isolates can have positive effects on early plant development. This does, however, not lead to an increase in total yield or in improvement of fruit quality of tomatoes under greenhouse conditions.},
  language  = {en}
}
@article{AndorfMeyerSelbigetal.2012,
  author    = {Andorf, Sandra and Meyer, Rhonda C. and Selbig, Joachim and Altmann, Thomas and Repsilber, Dirk},
  title     = {Integration of a systems biological network analysis and QTL results for biomass heterosis in arabidopsis thaliana},
  series = {PLoS one},
  volume    = {7},
  journal   = {PLoS one},
  number    = {11},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0049951},
  pages     = {10},
  year      = {2012},
  abstract  = {To contribute to a further insight into heterosis we applied an integrative analysis to a systems biological network approach and a quantitative genetics analysis towards biomass heterosis in early Arabidopsis thaliana development. The study was performed on the parental accessions C24 and Col-0 and the reciprocal crosses. In an over-representation analysis it was tested if the overlap between the resulting gene lists of the two approaches is significantly larger than expected by chance. Top ranked genes in the results list of the systems biological analysis were significantly over-represented in the heterotic QTL candidate regions for either hybrid as well as regarding mid-parent and best-parent heterosis. This suggests that not only a few but rather several genes that influence biomass heterosis are located within each heterotic QTL region. Furthermore, the overlapping resulting genes of the two integrated approaches were particularly enriched in biomass related pathways. A chromosome-wise over-representation analysis gave rise to the hypothesis that chromosomes number 2 and 4 probably carry a majority of the genes involved in biomass heterosis in the early development of Arabidopsis thaliana.},
  language  = {en}
}
@phdthesis{Andorf2011,
  author    = {Andorf, Sandra},
  title     = {A systems biological approach towards the molecular basis of heterosis in Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-51173},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Heterosis is defined as the superiority in performance of heterozygous genotypes compared to their corresponding genetically different homozygous parents. This phenomenon is already known since the beginning of the last century and it has been widely used in plant breeding, but the underlying genetic and molecular mechanisms are not well understood. In this work, a systems biological approach based on molecular network structures is proposed to contribute to the understanding of heterosis. Hybrids are likely to contain additional regulatory possibilities compared to their homozygous parents and, therefore, they may be able to correctly respond to a higher number of environmental challenges, which leads to a higher adaptability and, thus, the heterosis phenomenon. In the network hypothesis for heterosis, presented in this work, more regulatory interactions are expected in the molecular networks of the hybrids compared to the homozygous parents. Partial correlations were used to assess this difference in the global interaction structure of regulatory networks between the hybrids and the homozygous genotypes. This network hypothesis for heterosis was tested on metabolite profiles as well as gene expression data of the two parental Arabidopsis thaliana accessions C24 and Col-0 and their reciprocal crosses. These plants are known to show a heterosis effect in their biomass phenotype. The hypothesis was confirmed for mid-parent and best-parent heterosis for either hybrid of our experimental metabolite as well as gene expression data. It was shown that this result is influenced by the used cutoffs during the analyses. Too strict filtering resulted in sets of metabolites and genes for which the network hypothesis for heterosis does not hold true for either hybrid regarding mid-parent as well as best-parent heterosis. In an over-representation analysis, the genes that show the largest heterosis effects according to our network hypothesis were compared to genes of heterotic quantitative trait loci (QTL) regions. Separately for either hybrid regarding mid-parent as well as best-parent heterosis, a significantly larger overlap between the resulting gene lists of the two different approaches towards biomass heterosis was detected than expected by chance. This suggests that each heterotic QTL region contains many genes influencing biomass heterosis in the early development of Arabidopsis thaliana. Furthermore, this integrative analysis led to a confinement and an increased confidence in the group of candidate genes for biomass heterosis in Arabidopsis thaliana identified by both approaches.},
  language  = {en}
}
@article{AnderssonScharnweberEkloev2022,
  author    = {Andersson, Matilda L. and Scharnweber, Inga Kristin and Ekl{\"o}v, Peter},
  title     = {The interaction between metabolic rate, habitat choice, and resource use in a polymorphic freshwater species},
  series = {Ecology and evolution},
  volume    = {12},
  journal   = {Ecology and evolution},
  number    = {8},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.9129},
  pages     = {12},
  year      = {2022},
  abstract  = {Resource polymorphism is common across taxa and can result in alternate ecotypes with specific morphologies, feeding modes, and behaviors that increase performance in a specific habitat. This can result in high intraspecific variation in the expression of specific traits and the extent to which these traits are correlated within a single population. Although metabolic rate influences resource acquisition and the overall pace of life of individuals it is not clear how metabolic rate interacts with the larger suite of traits to ultimately determine individual fitness. We examined the relationship between metabolic rates and the major differences (habitat use, morphology, and resource use) between littoral and pelagic ecotypes of European perch (Perca fluviatilis) from a single lake in Central Sweden. Standard metabolic rate (SMR) was significantly higher in pelagic perch but did not correlate with resource use or morphology. Maximum metabolic rate (MMR) was not correlated with any of our explanatory variables or with SMR. Aerobic scope (AS) showed the same pattern as SMR, differing across habitats, but contrary to expectations, was lower in pelagic perch. This study helps to establish a framework for future experiments further exploring the drivers of intraspecific differences in metabolism. In addition, since metabolic rates scale with temperature and determine predator energy requirements, our observed differences in SMR across habitats will help determine ecotype-specific vulnerabilities to climate change and differences in top-down predation pressure across habitats.},
  language  = {en}
}
@article{AndersProchnowSchlaudereretal.2004,
  author    = {Anders, Kenneth and Prochnow, Annette and Schlauderer, Ralf and Wiegleb, Gerhard},
  title     = {Die Szenario-Methode als Instrument der Naturschutzplanung im Offenland},
  isbn      = {3-540-22449-1},
  year      = {2004},
  language  = {de}
}
@article{AndersProchnowFuerstenauetal.2003,
  author    = {Anders, Kenneth and Prochnow, Annette and F{\"u}rstenau, Stefan and Segert, Astrid and Zierke, Irene},
  title     = {Offenlandmanagement durch kontrolliertes Brennen : ein Beitrag aus sozio{\"o}konomischer Perspektive},
  year      = {2003},
  language  = {de}
}
@article{AndersMrzljakWallschlaegeretal.2004,
  author    = {Anders, Kenneth and Mrzljak, Jadranka and Wallschl{\"a}ger, Hans-Dieter and Wiegleb, Gerhard},
  title     = {Handbuch Offenlandmanagement am Beispiel ehemaliger und in Nutzung befindlicher Truppen{\"u}bungspl{\"a}tze},
  publisher = {Springer},
  address   = {Berlin},
  isbn      = {3-540-22449-1},
  pages     = {320 S.},
  year      = {2004},
  language  = {de}
}