@article{EngqvistSchmitzGertzmannetal.2015, author = {Engqvist, Martin K. M. and Schmitz, Jessica and Gertzmann, Anke and Florian, Alexandra and Jaspert, Nils and Arif, Muhammad and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair and Maurino, Veronica G.}, title = {GLYCOLATE OXIDASE3, a Glycolate Oxidase Homolog of Yeast L-Lactate Cytochrome c Oxidoreductase, Supports L-Lactate Oxidation in Roots of Arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.01003}, pages = {1042 -- 1061}, year = {2015}, abstract = {In roots of Arabidopsis (Arabidopsis thaliana), L-lactate is generated by the reduction of pyruvate via L-lactate dehydrogenase, but this enzyme does not efficiently catalyze the reverse reaction. Here, we identify the Arabidopsis glycolate oxidase (GOX) paralogs GOX1, GOX2, and GOX3 as putative L-lactate-metabolizing enzymes based on their homology to CYB2, the L-lactate cytochrome c oxidoreductase from the yeast Saccharomyces cerevisiae. We found that GOX3 uses L-lactate with a similar efficiency to glycolate; in contrast, the photorespiratory isoforms GOX1 and GOX2, which share similar enzymatic properties, use glycolate with much higher efficiencies than L-lactate. The key factor making GOX3 more efficient with L-lactate than GOX1 and GOX2 is a 5- to 10-fold lower Km for the substrate. Consequently, only GOX3 can efficiently metabolize L-lactate at low intracellular concentrations. Isotope tracer experiments as well as substrate toxicity tests using GOX3 loss-of-function and overexpressor plants indicate that L-lactate is metabolized in vivo by GOX3. Moreover, GOX3 rescues the lethal growth phenotype of a yeast strain lacking CYB2, which cannot grow on L-lactate as a sole carbon source. GOX3 is predominantly present in roots and mature to aging leaves but is largely absent from young photosynthetic leaves, indicating that it plays a role predominantly in heterotrophic rather than autotrophic tissues, at least under standard growth conditions. In roots of plants grown under normoxic conditions, loss of function of GOX3 induces metabolic rearrangements that mirror wild-type responses under hypoxia. Thus, we identified GOX3 as the enzyme that metabolizes L-lactate to pyruvate in vivo and hypothesize that it may ensure the sustainment of low levels of L-lactate after its formation under normoxia.}, language = {en} } @article{WangTohgeIvakovetal.2015, author = {Wang, Ting and Tohge, Takayuki and Ivakov, Alexander and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair and Mutwil, Marek and Schippers, Jos H. M. and Persson, Staffan}, title = {Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.00962}, pages = {1027 -- +}, year = {2015}, abstract = {Abiotic stresses, such as salinity, cause global yield loss of all major crop plants. Factors and mechanisms that can aid in plant breeding for salt stress tolerance are therefore of great importance for food and feed production. Here, we identified a MYB-like transcription factor, Salt-Related MYB1 (SRM1), that negatively affects Arabidopsis (Arabidopsis thaliana) seed germination under saline conditions by regulating the levels of the stress hormone abscisic acid (ABA). Accordingly, several ABA biosynthesis and signaling genes act directly downstream of SRM1, including SALT TOLERANT1/NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3, RESPONSIVE TO DESICCATION26, and Arabidopsis NAC DOMAIN CONTAINING PROTEIN19. Furthermore, SRM1 impacts vegetative growth and leaf shape. We show that SRM1 is an important transcriptional regulator that directly targets ABA biosynthesis and signaling-related genes and therefore may be regarded as an important regulator of ABA-mediated salt stress tolerance.}, language = {en} } @article{IonescuBizicIonescuKhalilietal.2015, author = {Ionescu, Danny and Bizic-Ionescu, Mina and Khalili, Arzhang and Malekmohammadi, Reza and Morad, Reza Mohammad and de Beer, Dirk and Grossart, Hans-Peter}, title = {A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep14706}, pages = {12}, year = {2015}, abstract = {Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO2 into aquatic sediments for thousands of years. Budget calculations of the biological carbon pump are heavily based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, which are strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities resembled in-situ communities and greatly differed from those in the closed systems. The active particle-associated community in the flow-through system was stable for days, contrary to hours previously reported for closed incubations. In contrast to enhanced respiration rates, the decrease in photosynthetic rates on particles throughout the incubation was much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes estimated using traditional methods.}, language = {en} } @article{LiCorriganYangetal.2015, author = {Li, Chenhong and Corrigan, Shannon and Yang, Lei and Straube, Nicolas and Harris, Mark and Hofreiter, Michael and White, William T. and Naylor, Gavin J. P.}, title = {DNA capture reveals transoceanic gene flow in endangered river sharks}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {43}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1508735112}, pages = {13302 -- 13307}, year = {2015}, abstract = {For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.}, language = {en} } @article{SonnemannPfestorfJeltschetal.2015, author = {Sonnemann, Ilja and Pfestorf, Hans and Jeltsch, Florian and Wurst, Susanne}, title = {Community-Weighted Mean Plant Traits Predict Small Scale Distribution of Insect Root Herbivore Abundance}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {10}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0141148}, pages = {14}, year = {2015}, abstract = {Small scale distribution of insect root herbivores may promote plant species diversity by creating patches of different herbivore pressure. However, determinants of small scale distribution of insect root herbivores, and impact of land use intensity on their small scale distribution are largely unknown. We sampled insect root herbivores and measured vegetation parameters and soil water content along transects in grasslands of different management intensity in three regions in Germany. We calculated community-weighted mean plant traits to test whether the functional plant community composition determines the small scale distribution of insect root herbivores. To analyze spatial patterns in plant species and trait composition and insect root herbivore abundance we computed Mantel correlograms. Insect root herbivores mainly comprised click beetle (Coleoptera, Elateridae) larvae (43\%) in the investigated grasslands. Total insect root herbivore numbers were positively related to community-weighted mean traits indicating high plant growth rates and biomass (specific leaf area, reproductive-and vegetative plant height), and negatively related to plant traits indicating poor tissue quality (leaf C/N ratio). Generalist Elaterid larvae, when analyzed independently, were also positively related to high plant growth rates and furthermore to root dry mass, but were not related to tissue quality. Insect root herbivore numbers were not related to plant cover, plant species richness and soil water content. Plant species composition and to a lesser extent plant trait composition displayed spatial autocorrelation, which was not influenced by land use intensity. Insect root herbivore abundance was not spatially autocorrelated. We conclude that in semi-natural grasslands with a high share of generalist insect root herbivores, insect root herbivores affiliate with large, fast growing plants, presumably because of availability of high quantities of food. Affiliation of insect root herbivores with large, fast growing plants may counteract dominance of those species, thus promoting plant diversity.}, language = {en} } @article{BergholzJeltschWeissetal.2015, author = {Bergholz, Kolja and Jeltsch, Florian and Weiß, Lina and Pottek, Janine and Geißler, Katja and Ristow, Michael}, title = {Fertilization affects the establishment ability of species differing in seed mass via direct nutrient addition and indirect competition effects}, series = {Oikos}, volume = {124}, journal = {Oikos}, number = {11}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.02193}, pages = {1547 -- 1554}, year = {2015}, abstract = {Fertilization causes species loss and species dominance changes in plant communities worldwide. However, it still remains unclear how fertilization acts upon species functional traits, e.g. seed mass. Seed mass is a key trait of the regeneration strategy of plants, which influences a range of processes during the seedling establishment phase. Fertilization may select upon seed mass, either directly by increased nutrient availability or indirectly by increased competition. Since previous research has mainly analyzed the indirect effects of fertilization, we disentangled the direct and indirect effects to examine how nutrient availability and competition influence the seed mass relationships on four key components during seedling establishment: seedling emergence, time of seedling emergence, seedling survival and seedling growth. We conducted a common garden experiment with 22 dry grassland species with a two-way full factorial design that simulated additional nutrient supply and increased competition. While we found no evidence that fertilization either directly by additional nutrient supply or indirectly by increased competition alters the relationship between seed mass and (time of) seedling emergence, we revealed that large seed mass is beneficial under nutrient-poor conditions (seedlings have greater chances of survival, particularly in nutrient-poor soils) as well as under competition (large-seeded species produced larger seedlings, which suffered less from competition than small-seeded species). Based on these findings, we argue that both factors, i.e. nutrient availability and competition intensity, ought to be considered to understand how fertilization influences seedling establishment and species composition with respect to seed mass in natural communities. We propose a simple conceptual model, in which seed mass in natural communities is determined by competition intensity and nutrient availability. Here, we hypothesize that seed mass shows a U-shaped pattern along gradients of soil fertility, which may explain the contrasting soil fertility-seed mass relationships found in the recent literature.}, language = {en} } @article{GludGrossartLarsenetal.2015, author = {Glud, Ronnie N. and Grossart, Hans-Peter and Larsen, Morten and Tang, Kam W. and Arendt, Kristine E. and Rysgaard, Soren and Thamdrup, Bo and Gissel Nielsen, Torkel}, title = {Copepod carcasses as microbial hot spots for pelagic denitrification}, series = {Limnology and oceanography}, volume = {60}, journal = {Limnology and oceanography}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0024-3590}, doi = {10.1002/lno.10149}, pages = {2026 -- 2036}, year = {2015}, abstract = {Copepods are exposed to a high non-predatory mortality and their decomposing carcasses act as microniches with intensified microbial activity. Sinking carcasses could thereby represent anoxic microenvironment sustaining anaerobic microbial pathways in otherwise oxic water columns. Using non-invasive O-2 imaging, we document that carcasses of Calanus finmarchicus had an anoxic interior even at fully air-saturated ambient O-2 level. The extent of anoxia gradually expanded with decreasing ambient O-2 levels. Concurrent microbial sampling showed the expression of nitrite reductase genes (nirS) in all investigated carcass samples and thereby documented the potential for microbial denitrification in carcasses. The nirS gene was occasionally expressed in live copepods, but not as consistently as in carcasses. Incubations of sinking carcasses in (15)NO3-amended seawater demonstrated denitrification, of which on average 34\%+/- 17\% (n=28) was sustained by nitrification. However, the activity was highly variable and was strongly dependent on the ambient O-2 levels. While denitrification was present even at air-saturation (302 mol L-1), the average carcass specific activity increased several orders of magnitude to approximate to 1 nmol d(-1) at 20\% air-saturation (55 mol O-2 L-1) at an ambient temperature of 7 degrees C. Sinking carcasses of C. finmarchicus therefore represent hotspots of pelagic denitrification, but the quantitative importance as a sink for bioavailable nitrogen is strongly dependent on the ambient O-2 level. The importance of carcass associated denitrification could be highly significant in O-2 depleted environments such as Oxygen Minimum Zones (OMZ).}, language = {en} } @article{ToppingAlroeFarrelletal.2015, author = {Topping, Christopher J. and Alroe, Hugo Fjelsted and Farrell, Katharine N. and Grimm, Volker}, title = {Per Aspera ad Astra: Through Complex Population Modeling to Predictive Theory}, series = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, volume = {186}, journal = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, number = {5}, publisher = {Univ. of Chicago Press}, address = {Chicago}, issn = {0003-0147}, doi = {10.1086/683181}, pages = {669 -- 674}, year = {2015}, abstract = {Population models in ecology are often not good at predictions, even if they are complex and seem to be realistic enough. The reason for this might be that Occam's razor, which is key for minimal models exploring ideas and concepts, has been too uncritically adopted for more realistic models of systems. This can tic models too closely to certain situations, thereby preventing them from predicting the response to new conditions. We therefore advocate a new kind of parsimony to improve the application of Occam's razor. This new parsimony balances two contrasting strategies for avoiding errors in modeling: avoiding inclusion of nonessential factors (false inclusions) and avoiding exclusion of sometimes-important factors (false exclusions). It involves a synthesis of traditional modeling and analysis, used to describe the essentials of mechanistic relationships, with elements that arc included in a model because they have been reported to be or can arguably be assumed to be important under certain conditions. The resulting models should be able to reflect how the internal organization of populations change and thereby generate representations of the novel behavior necessary for complex predictions, including regime shifts.}, language = {en} } @unpublished{JulichGrunerPanditLendlein2015, author = {Julich-Gruner, Konstanze K. and Pandit, Abhay and Lendlein, Andreas}, title = {Advanced Functional Polymers Addressing the Needs of Modern Medicine}, series = {Macromolecular rapid communications}, volume = {36}, journal = {Macromolecular rapid communications}, number = {21}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1022-1336}, doi = {10.1002/marc.201500575}, pages = {1859 -- 1861}, year = {2015}, language = {en} } @article{SeebensEsslDawsonetal.2015, author = {Seebens, Hanno and Essl, Franz and Dawson, Wayne and Fuentes, Nicol and Moser, Dietmar and Pergl, Jan and Pysek, Petr and van Kleunen, Mark and Weber, Ewald and Winter, Marten and Blasius, Bernd}, title = {Global trade will accelerate plant invasions in emerging economies under climate change}, series = {Global change biology}, volume = {21}, journal = {Global change biology}, number = {11}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1354-1013}, doi = {10.1111/gcb.13021}, pages = {4128 -- 4140}, year = {2015}, abstract = {Trade plays a key role in the spread of alien species and has arguably contributed to the recent enormous acceleration of biological invasions, thus homogenizing biotas worldwide. Combining data on 60-year trends of bilateral trade, as well as on biodiversity and climate, we modeled the global spread of plant species among 147 countries. The model results were compared with a recently compiled unique global data set on numbers of naturalized alien vascular plant species representing the most comprehensive collection of naturalized plant distributions currently available. The model identifies major source regions, introduction routes, and hot spots of plant invasions that agree well with observed naturalized plant numbers. In contrast to common knowledge, we show that the 'imperialist dogma,' stating that Europe has been a net exporter of naturalized plants since colonial times, does not hold for the past 60 years, when more naturalized plants were being imported to than exported from Europe. Our results highlight that the current distribution of naturalized plants is best predicted by socioeconomic activities 20 years ago. We took advantage of the observed time lag and used trade developments until recent times to predict naturalized plant trajectories for the next two decades. This shows that particularly strong increases in naturalized plant numbers are expected in the next 20 years for emerging economies in megadiverse regions. The interaction with predicted future climate change will increase invasions in northern temperate countries and reduce them in tropical and (sub) tropical regions, yet not by enough to cancel out the trade-related increase.}, language = {en} } @article{LemkeKolbGraaeetal.2015, author = {Lemke, Isgard H. and Kolb, Annette and Graae, Bente J. and De Frenne, Pieter and Acharya, Kamal P. and Blandino, Cristina and Brunet, Jorg and Chabrerie, Olivier and Cousins, Sara A. O. and Decocq, Guillaume and Heinken, Thilo and Hermy, Martin and Liira, Jaan and Schmucki, Reto and Shevtsova, Anna and Verheyen, Kris and Diekmann, Martin}, title = {Patterns of phenotypic trait variation in two temperate forest herbs along a broad climatic gradient}, series = {Plant ecology : an international journal}, volume = {216}, journal = {Plant ecology : an international journal}, number = {11}, publisher = {Springer}, address = {Dordrecht}, issn = {1385-0237}, doi = {10.1007/s11258-015-0534-0}, pages = {1523 -- 1536}, year = {2015}, abstract = {Phenotypic trait variation plays a major role in the response of plants to global environmental change, particularly in species with low migration capabilities and recruitment success. However, little is known about the variation of functional traits within populations and about differences in this variation on larger spatial scales. In a first approach, we therefore related trait expression to climate and local environmental conditions, studying two temperate forest herbs, Milium effusum and Stachys sylvatica, along a similar to 1800-2500 km latitudinal gradient. Within each of 9-10 regions in six European countries, we collected data from six populations of each species and recorded several variables in each region (temperature, precipitation) and population (light availability, soil parameters). For each plant, we measured height, leaf area, specific leaf area, seed mass and the number of seeds and examined environmental effects on within-population trait variation as well as on trait means. Most importantly, trait variation differed both between and within populations. Species, however, differed in their response. Intrapopulation variation in Milium was consistently positively affected by higher mean temperatures and precipitation as well as by more fertile local soil conditions, suggesting that more productive conditions may select for larger phenotypic variation. In Stachys, particularly light availability positively influenced trait variation, whereas local soil conditions had no consistent effects. Generally, our study emphasises that intra-population variation may differ considerably across larger scales-due to phenotypic plasticity and/or underlying genetic diversity-possibly affecting species response to global environmental change.}, language = {en} } @article{JonesGonzalezFortesConnelletal.2015, author = {Jones, Eppie R. and Gonz{\´a}lez-Fortes, Gloria M. and Connell, Sarah and Siska, Veronika and Eriksson, Anders and Martiniano, Rui and McLaughlin, Russell L. and Llorente, Marcos Gallego and Cassidy, Lara M. and Gamba, Cristina and Meshveliani, Tengiz and Bar-Yosef, Ofer and Mueller, Werner and Belfer-Cohen, Anna and Matskevich, Zinovi and Jakeli, Nino and Higham, Thomas F. G. and Currat, Mathias and Lordkipanidze, David and Hofreiter, Michael and Manica, Andrea and Pinhasi, Ron and Bradley, Daniel G.}, title = {Upper Palaeolithic genomes reveal deep roots of modern Eurasians}, series = {Nature Communications}, volume = {6}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms9912}, pages = {8}, year = {2015}, abstract = {We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers similar to 45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers similar to 25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe similar to 3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.}, language = {en} } @article{LotkowskaTohgeFernieetal.2015, author = {Lotkowska, Magda E. and Tohge, Takayuki and Fernie, Alisdair and Xue, Gang-Ping and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd}, title = {The Arabidopsis Transcription Factor MYB112 Promotes Anthocyanin Formation during Salinity and under High Light Stress}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.00605}, pages = {1862 -- 1880}, year = {2015}, abstract = {MYB transcription factors (TFs) are important regulators of flavonoid biosynthesis in plants. Here, we report MYB112 as a formerly unknown regulator of anthocyanin accumulation in Arabidopsis (Arabidopsis thaliana). Expression profiling after chemically induced overexpression of MYB112 identified 28 up-and 28 down-regulated genes 5 h after inducer treatment, including MYB7 and MYB32, which are both induced. In addition, upon extended induction, MYB112 also positively affects the expression of PRODUCTION OF ANTHOCYANIN PIGMENT1, a key TF of anthocyanin biosynthesis, but acts negatively toward MYB12 and MYB111, which both control flavonol biosynthesis. MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C) CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay and chromatin immunoprecipitation coupled to quantitative polymerase chain reaction, we show that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters, revealing them as direct downstream target genes. We further show that MYB112 expression is up-regulated by salinity and high light stress, environmental parameters that both require the MYB112 TF for anthocyanin accumulation under these stresses. In contrast to several other MYB TFs affecting anthocyanin biosynthesis, MYB112 expression is not controlled by nitrogen limitation or an excess of carbon. Thus, MYB112 constitutes a regulator that promotes anthocyanin accumulation under abiotic stress conditions.}, language = {en} } @article{SbragagliaLamannaMatetal.2015, author = {Sbragaglia, Valerio and Lamanna, Francesco and Mat, Audrey M. and Rotllant, Guiomar and Joly, Silvia and Ketmaier, Valerio and de la Iglesia, Horacio O. and Aguzzi, Jacopo}, title = {Identification, Characterization, and Diel Pattern of Expression of Canonical Clock Genes in Nephrops norvegicus (Crustacea: Decapoda) Eyestalk}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0141893}, pages = {17}, year = {2015}, abstract = {The Norway lobster, Nephrops norvegicus, is a burrowing decapod with a rhythmic burrow emergence (24 h) governed by the circadian system. It is an important resource for European fisheries and its behavior deeply affects its availability. The current knowledge of Nephrops circadian biology is phenomenological as it is currently the case for almost all crustaceans. In attempt to elucidate the putative molecular mechanisms underlying circadian gene regulation in Nephrops, we used a transcriptomics approach on cDNA extracted from the eyestalk, a structure playing a crucial role in controlling behavior of decapods. We studied 14 male lobsters under 12-12 light-darkness blue light cycle. We used the Hiseq 2000 Illumina platform to sequence two eyestalk libraries (under light and darkness conditions) obtaining about 90 millions 100-bp paired-end reads. Trinity was used for the de novo reconstruction of transcriptomes; the size at which half of all assembled bases reside in contigs (N50) was equal to 1796 (light) and 2055 (darkness). We found a list of candidate clock genes and focused our attention on canonical ones: timeless, period, clock and bmal1. The cloning of assembled fragments validated Trinity outputs. The putative Nephrops clock genes showed high levels of identity (blastx on NCBI) with known crustacean clock gene homologs such as Eurydice pulchra (period: 47\%, timeless: 59\%, bmal1: 79\%) and Macrobrachium rosenbergii (clock: 100\%). We also found a vertebrate-like cryptochrome 2. RT-qPCR showed that only timeless had a robust diel pattern of expression. Our data are in accordance with the current knowledge of the crustacean circadian clock, reinforcing the idea that the molecular clockwork of this group shows some differences with the established model in Drosophila melanogaster.}, language = {en} } @article{StanislasHuserBarbosaetal.2015, author = {Stanislas, Thomas and Huser, Anke and Barbosa, Ines C. R. and Kiefer, Christian S. and Brackmann, Klaus and Pietra, Stefano and Gustavsson, Anna and Zourelidou, Melina and Schwechheimer, Claus and Grebe, Markus}, title = {Arabidopsis D6PK is a lipid domain-dependent mediator of root epidermal planar polarity}, series = {Nature plants}, volume = {1}, journal = {Nature plants}, number = {11}, publisher = {Nature Publ. Group}, address = {London}, issn = {2055-026X}, doi = {10.1038/NPLANTS.2015.162}, pages = {9}, year = {2015}, abstract = {Development of diverse multicellular organisms relies on coordination of single-cell polarities within the plane of the tissue layer (planar polarity). Cell polarity often involves plasma membrane heterogeneity generated by accumulation of specific lipids and proteins into membrane subdomains. Coordinated hair positioning along Arabidopsis root epidermal cells provides a planar polarity model in plants, but knowledge about the functions of proteo-lipid domains in planar polarity signalling remains limited. Here we show that Rho-of-plant (ROP) 2 and 6, phosphatidylinositol-4-phosphate 5-kinase 3 (PIP5K3), DYNAMIN-RELATED PROTEIN (DRP) 1A and DRP2B accumulate in a sterol-enriched, polar membrane domain during root hair initiation. DRP1A, DRP2B, PIP5K3 and sterols are required for planar polarity and the AGCVIII kinase D6 PROTEIN KINASE (D6PK) is a modulator of this process. D6PK undergoes phosphatidylinositol-4,5-bisphosphate- and sterol-dependent basal-to-planar polarity switching into the polar, lipid-enriched domain just before hair formation, unravelling lipid-dependent D6PK localization during late planar polarity signalling.}, language = {en} } @article{BordagKlieJuerchottetal.2015, author = {Bordag, Natalie and Klie, Sebastian and J{\"u}rchott, Kathrin and Vierheller, Janine and Schiewe, Hajo and Albrecht, Valerie and Tonn, J{\"o}rg-Christian and Schwartz, Christoph and Schichor, Christian and Selbig, Joachim}, title = {Glucocorticoid (dexamethasone)-induced metabolome changes in healthy males suggest prediction of response and side effects}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep15954}, pages = {12}, year = {2015}, abstract = {Glucocorticoids are indispensable anti-inflammatory and decongestant drugs with high prevalence of use at (similar to)0.9\% of the adult population. Better holistic insights into glucocorticoid-induced changes are crucial for effective use as concurrent medication and management of adverse effects. The profiles of 214 metabolites from plasma of 20 male healthy volunteers were recorded prior to and after ingestion of a single dose of 4 mg dexamethasone (+20 mg pantoprazole). Samples were drawn at three predefined time points per day: seven untreated (day 1 midday - day 3 midday) and four treated (day 3 evening - day 4 evening) per volunteer. Statistical analysis revealed tremendous impact of dexamethasone on the metabolome with 150 of 214 metabolites being significantly deregulated on at least one time point after treatment (ANOVA, Benjamini-Hochberg corrected, q < 0.05). Inter-person variability was high and remained uninfluenced by treatment. The clearly visible circadian rhythm prior to treatment was almost completely suppressed and deregulated by dexamethasone. The results draw a holistic picture of the severe metabolic deregulation induced by single-dose, short-term glucocorticoid application. The observed metabolic changes suggest a potential for early detection of severe side effects, raising hope for personalized early countermeasures increasing quality of life and reducing health care costs.}, language = {en} } @article{NeuschaeferRubeSchraplauScheweetal.2015, author = {Neuschaefer-Rube, Frank and Schraplau, Anne and Schewe, Bettina and Lieske, Stefanie and Kruetzfeldt, Julia-Mignon and Ringel, Sebastian and Henkela, Janin and Birkenfeld, Andreas L. and P{\"u}schel, Gerhard Paul}, title = {Arylhydrocarbon receptor-dependent mIndy (SIc13a5) induction as possible contributor to benzo[a]pyrene-induced lipid accumulation in hepatocytes}, series = {Toxicology}, volume = {337}, journal = {Toxicology}, publisher = {Elsevier}, address = {Clare}, issn = {0300-483X}, doi = {10.1016/j.tox.2015.08.007}, pages = {1 -- 9}, year = {2015}, abstract = {Non-alcoholic fatty liver disease is a growing problem in industrialized and developing countries. Hepatic lipid accumulation is the result of an imbalance between fatty acid uptake, fatty acid de novo synthesis, beta-oxidation and secretion of triglyceride-rich lipoproteins from the hepatocyte. A central regulator of hepatic lipid metabolism is cytosolic citrate that can either be derived from the mitochondrium or be taken up from the blood via the plasma membrane sodium citrate transporter NaCT, the product of the mammalian INDY gene (SLC13A5). mINDY ablation protects against diet-induced steatosis whereas mINDY expression is increased in patients with hepatic steatosis. Diet-induced hepatic steatosis is also enhanced by activation of the arylhyrocarbon receptor (AhR) both in humans and animal models. Therefore, the hypothesis was tested whether the mINDY gene might be a target of the AhR. In accordance with such a hypothesis, the AhR activator benzo[a]pyrene induced the mINDY expression in primary cultures of rat hepatocytes in an AhR-dependent manner. This induction resulted in an increased citrate uptake and citrate incorporation into lipids which probably was further enhanced by the benzo[a]pyrene-dependent induction of key enzymes of fatty acid synthesis. A potential AhR binding site was identified in the mINDY promoter that appears to be conserved in the human promoter. Elimination or mutation of this site largely abolished the activation of the mINDY promoter by benzo[a]pyrene. This study thus identified the mINDY as an AhR target gene. AhR-dependent induction of the mINDY gene might contribute to the development of hepatic steatosis. (C) 2015 Elsevier Ireland Ltd. All rights reserved.}, language = {en} } @article{KopyshevLomadzeFeldmannetal.2015, author = {Kopyshev, Alexey and Lomadze, Nino and Feldmann, David and Genzer, Jan and Santer, Svetlana}, title = {Making polymer brush photosensitive with azobenzene containing surfactants}, series = {Polymer : the international journal for the science and technology of polymers}, volume = {79}, journal = {Polymer : the international journal for the science and technology of polymers}, publisher = {Elsevier}, address = {Oxford}, issn = {0032-3861}, doi = {10.1016/j.polymer.2015.09.023}, pages = {65 -- 72}, year = {2015}, abstract = {We report on rendering polyelectrolyte brushes photosensitive by loading them with azobenzene-containing cationic surfactants. Planar poly( methacrylic acid) (PMAA) brushes are synthesized using the "grafting from" free-radical polymerization scheme followed by exposure to a solution of photosensitive surfactants consisting of positively-charged head groups and hydrophobic tails into which azobenzene moieties are inserted. In this study the length of the hydrophobic methylene spacer connecting the azobenzene and the charged head group ranges from 4 to 10 CH2 groups. Under irradiation with UV light, the photo-isomerization of azobenzene integrated into a surfactant results in a change in size, geometry, dipole moment and free volume of the whole molecule. When the brush loaded with photosensitive surfactants is exposed to irradiation with UV interference patterns, the topography of the brush deforms following the distribution of the light intensity, exhibiting surface relief gratings (SRG). Since SRG formation is accompanied by a local rupturing of polymer chains in areas from which the polymer material is receding, most of the polymer material is removed from the surface during treatment with good solvent, leaving behind characteristic patterns of lines or dots. The azobenzene molecules still integrated within the polymer film can be removed by washing the brush with water. The remaining nano-structured brush can then be re-used for further functionalization. Although the opto-mechanically induced rupturing occurs for all surfactants, larger species do not penetrate deep enough into the brush such that after rupturing a leftover layer of polymer material remains on the substrate. This indicates that rupturing occurs predominantly in regions of high surfactant density.}, language = {en} } @article{FrindteAllgaierGrossartetal.2015, author = {Frindte, Katharina and Allgaier, Martin and Grossart, Hans-Peter and Eckert, Werner}, title = {Microbial response to experimentally controlled redox transitions at the sediment water interface}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0143428}, pages = {17}, year = {2015}, abstract = {The sediment-water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment-water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment-water interface.}, language = {en} } @misc{HixsonSharmaKainzetal.2015, author = {Hixson, Stefanie M. and Sharma, Bhanu and Kainz, Martin J. and Wacker, Alexander and Arts, Michael T.}, title = {Production, distribution, and abundance of long-chain omega-3 polyunsaturated fatty acids: a fundamental dichotomy between freshwater and terrestrial ecosystems}, series = {Environmental reviews = Dossiers environnement}, volume = {23}, journal = {Environmental reviews = Dossiers environnement}, number = {4}, publisher = {NRC Research Press}, address = {Ottawa}, issn = {1208-6053}, doi = {10.1139/er-2015-0029}, pages = {414 -- 424}, year = {2015}, abstract = {Long-chain polyunsaturated fatty acids (LC-PUFA) are critical for the health of aquatic and terrestrial organisms; therefore, understanding the production, distribution, and abundance of these compounds is imperative. Although the dynamics of LC-PUFA production and distribution in aquatic environments has been well documented, a systematic and comprehensive comparison to LC-PUFA in terrestrial environments has not been rigorously investigated. Here we use a data synthesis approach to compare and contrast fatty acid profiles of 369 aquatic and terrestrial organisms. Habitat and trophic level were interacting factors that determined the proportion of individual omega-3 (n-3) or omega-6 (n-6) PUFA in aquatic and terrestrial organisms. Higher total n-3 content compared with n-6 PUFA and a strong prevalence of the n-3 PUFA eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) characterized aquatic versus terrestrial organisms. Conversely, terrestrial organisms had higher linoleic acid (LNA) and alpha-linolenic acid (ALA) contents than aquatic organisms; however, the ratio of ALA: LNA was higher in aquatic organisms. The EPA + DHA content was higher in aquatic animals than terrestrial organisms, and increased from algae to invertebrates to vertebrates in the aquatic environment. An analysis of covariance (ANCOVA) revealed that fatty acid composition was highly dependent on the interaction between habitat and trophic level. We conclude that freshwater ecosystems provide an essential service through the production of n-3 LC-PUFA that are required to maintain the health of terrestrial organisms including humans.}, language = {en} } @unpublished{MuellerRoeber2015, author = {M{\"u}ller-R{\"o}ber, Bernd}, title = {That "crispert" in Plant Cultivation}, series = {Journal f{\"u}r Verbraucherschutz und Lebensmittelsicherheit = Journal of consumer protection and food safety}, volume = {10}, journal = {Journal f{\"u}r Verbraucherschutz und Lebensmittelsicherheit = Journal of consumer protection and food safety}, number = {4}, publisher = {Springer}, address = {Basel}, issn = {1661-5751}, doi = {10.1007/s00003-015-0985-1}, pages = {305 -- 306}, year = {2015}, language = {de} } @article{ElsnerSchiblerHofreiteretal.2015, author = {Elsner, Julia and Schibler, Joerg and Hofreiter, Michael and Schlumbaum, Angela}, title = {Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland}, series = {Archaeological and anthropological sciences}, volume = {7}, journal = {Archaeological and anthropological sciences}, number = {4}, publisher = {Springer}, address = {Heidelberg}, issn = {1866-9557}, doi = {10.1007/s12520-014-0213-4}, pages = {505 -- 515}, year = {2015}, abstract = {Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the-inevitable-heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions.}, language = {en} } @article{PieckHerlemannJuergensetal.2015, author = {Pieck, Angelika and Herlemann, Daniel P. P. and Juergens, Klaus and Grossart, Hans-Peter}, title = {Particle-Associated Differ from Free-Living Bacteria in Surface Waters of the Baltic Sea}, series = {Frontiers in microbiology}, volume = {6}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2015.01297}, pages = {13}, year = {2015}, abstract = {Many studies on bacterial community composition (BCC) do not distinguish between particle associated (PA) and free-living (FL) bacteria or neglect the PA fraction by pre-filtration removing most particles. Although temporal and spatial gradients in environmental variables are known to shape BCC, it remains unclear how and to what extent PA and FL bacterial diversity responds to such environmental changes. To elucidate the BCC of both bacterial fractions related to different environmental settings, we studied surface samples of three Baltic Sea stations (marine, mesohaline, and oligohaline) in two different seasons (summer and fall/winter). Amplicon sequencing of the 16S rRNA gene revealed significant differences in BCC of both bacterial fractions among stations and seasons, with a particularly high number of PA operational taxonomic units (OTUs at genus-level) at the marine station in both seasons. "Shannon and Simpson indices" showed a higher diversity of PA than FL bacteria at the marine station in both seasons and at the oligohaline station in fall/winter. In general, a high fraction of bacterial OTUs was found exclusively in the PA fraction (52\% of total OTUs). These findings indicate that PA bacteria significantly contribute to overall bacterial richness and that they differ from FL bacteria. Therefore, to gain a deeper understanding on diversity and dynamics of aquatic bacteria, PA and FL bacteria should be generally studied independently.}, language = {en} } @unpublished{EnsslinTschoepeBurkartetal.2015, author = {Ensslin, Andreas and Tschoepe, Okka and Burkart, Michael and Joshi, Jasmin Radha}, title = {Fitness decline and adaptation to novel environments in ex situ plant collections: Current knowledge and future perspectives}, series = {: an international journal}, volume = {192}, journal = {: an international journal}, publisher = {Elsevier}, address = {Oxford}, issn = {0006-3207}, doi = {10.1016/j.biocon.2015.10.012}, pages = {394 -- 401}, year = {2015}, abstract = {The conservation of rare plant species as living collections in botanic gardens and arboreta has become an established tool in the battle against worldwide species' extinctions. However, the establishment of ex situ collections with a high conservation value requires a sound understanding of the evolutionary processes that may reduce the suitability of these collections for future reintroductions. Particularly, risks such as fitness decline of cultivated plants over time, trait shifts and loss of adaptation to the original habitat due to changes in selection regimes have rarely been addressed so far. Based on a literature review and results of our own project we show that genetic drift can lead to fitness decline in ex situ cultivated plants, but these drift effects strongly depend on the conditions and cultivation history in the ex situ facility. Furthermore, we provide evidence that shifts in traits such as germination and flowering time, and a decrease in stress tolerance to drought and competition can reduce the conservation value of ex situ collections. These threats associated with ex situ conditions require more attention by researchers, curators and conservationists. We need to increase knowledge on traits that are subject to novel selection pressures in ex situ collections, and to define population sizes that prevent genetic drift. Establishing conservation networks with replicated collections across gardens and balancing the seed contribution of mother plants to the next generation within a collection are suggested as first steps to increase the conservation value of ex situ plant collections. (C) 2015 Elsevier Ltd. All rights reserved.}, language = {en} } @article{MarcusBochDurkaetal.2015, author = {Marcus, Tamar and Boch, Steffen and Durka, Walter and Fischer, Markus and Gossner, Martin M. and M{\"u}ller, J{\"o}rg and Sch{\"o}ning, Ingo and Weisser, Wolfgang W. and Drees, Claudia and Assmann, Thorsten}, title = {Living in Heterogeneous Woodlands - Are Habitat Continuity or Quality Drivers of Genetic Variability in a Flightless Ground Beetle?}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {12}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0144217}, pages = {18}, year = {2015}, abstract = {Although genetic diversity is one of the key components of biodiversity, its drivers are still not fully understood. While it is known that genetic diversity is affected both by environmental parameters as well as habitat history, these factors are not often tested together. Therefore, we analyzed 14 microsatellite loci in Abax parallelepipedus, a flightless, forest dwelling ground beetle, from 88 plots in two study regions in Germany. We modeled the effects of historical and environmental variables on allelic richness, and found for one of the regions, the Schorfheide-Chorin, a significant effect of the depth of the litter layer, which is a main component of habitat quality, and of the sampling effort, which serves as an inverse proxy for local population size. For the other region, the Schwabische Alb, none of the potential drivers showed a significant effect on allelic richness. We conclude that the genetic diversity in our study species is being driven by current local population sizes via environmental variables and not by historical processes in the studied regions. This is also supported by lack of genetic differentiation between local populations sampled from ancient and from recent woodlands. We suggest that the potential effects of former fragmentation and recolonization processes have been mitigated by the large and stable local populations of Abax parallelepipedus in combination with the proximity of the ancient and recent woodlands in the studied landscapes.}, language = {en} } @misc{HermanussenSchefflerGrothetal.2015, author = {Hermanussen, Michael and Scheffler, Christiane and Groth, Detlef and Aßmann, Christian}, title = {Height and skeletal morphology in relation to modern life style}, series = {Journal of physiological anthropology}, volume = {34}, journal = {Journal of physiological anthropology}, publisher = {BioMed Central}, address = {London}, issn = {1880-6805}, doi = {10.1186/s40101-015-0080-4}, pages = {5}, year = {2015}, abstract = {Height and skeletal morphology strongly relate to life style. Parallel to the decrease in physical activity and locomotion, modern people are slimmer in skeletal proportions. In German children and adolescents, elbow breadth and particularly relative pelvic breadth (50th centile of bicristal distance divided by body height) have significantly decreased in recent years. Even more evident than the changes in pelvic morphology are the rapid changes in body height in most modern countries since the end-19th and particularly since the mid-20th century. Modern Japanese mature earlier; the age at take-off (ATO, the age at which the adolescent growth spurt starts) decreases, and they are taller at all ages. Preece-Baines modelling of six national samples of Japanese children and adolescents, surveyed between 1955 and 2000, shows that this gain in height is largely an adolescent trend, whereas height at take-off (HTO) increased by less than 3 cm since 1955; adolescent growth (height gain between ATO and adult age) increased by 6 cm. The effect of globalization on the modern post-war Japanese society ("community effect in height") on adolescent growth is discussed.}, language = {en} } @article{HahnSolomunWellhausenetal.2015, author = {Hahn, Marc Benjamin and Solomun, Tihomir and Wellhausen, Robert and Hermann, Sabrina and Seitz, Harald and Meyer, Susann and Kunte, Hans-J{\"o}rg and Zeman, Johannes and Uhlig, Frank and Smiatek, Jens and Sturm, Heinz}, title = {Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {119}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {49}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.5b09506}, pages = {15212 -- 15220}, year = {2015}, abstract = {Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-S-protein (G5P) to a single-stranded DNA (dT(25)). Due to the very high hygroscopicity of ectoine, it was possible to analyze the highly stable hydration shell by confocal Raman spectroscopy. Corresponding molecular dynamics simulation results revealed a significant change of the water dielectric constant in the presence of a high molar ectoine concentration as compared to pure water. The SPR data showed that the amount of protein bound to DNA decreases in the presence of ectoine, and hence, the protein-DNA dissociation constant increases in a concentration-dependent manner. Concomitantly, the Raman spectra in terms of the amide I region revealed large changes in the protein secondary structure. Our results indicate that ectoine strongly affects the molecular recognition between the protein and the oligonudeotide, which has important consequences for osmotic regulation mechanisms.}, language = {en} } @misc{McKennaLeimkuehlerHerteretal.2015, author = {McKenna, Shane M. and Leimk{\"u}hler, Silke and Herter, Susanne and Turner, Nicholas J. and Carnell, Andrew J.}, title = {Enzyme cascade reactions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-102271}, pages = {3271 -- 3275}, year = {2015}, abstract = {A one-pot tandem enzyme reaction using galactose oxidase M3-5 and aldehyde oxidase PaoABC was used to convert hydroxymethylfurfural (HMF) to the pure bioplastics precursor FDCA in 74\% isolated yield. A range of alcohols was also converted to carboxylic acids in high yield under mild conditions.}, language = {en} } @phdthesis{Kamranfar2015, author = {Kamranfar, Iman}, title = {Functional analysis of gene regulatory networks controlled by stress responsive transcription factors in Arabidopsis thaliana}, school = {Universit{\"a}t Potsdam}, pages = {151}, year = {2015}, language = {en} } @misc{MuinodeBruijnPajoroetal.2015, author = {Mui{\~n}o, Jose M. and de Bruijn, Suzanne and Pajoro, Alice and Geuten, Koen and Vingron, Martin and Angenent, Gerco C. and Kaufmann, Kerstin}, title = {Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-96580}, pages = {1225 -- 1245}, year = {2015}, abstract = {Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon.}, language = {en} } @misc{KappelTrostCzesnicketal.2015, author = {Kappel, Christian and Trost, Gerda and Czesnick, Hj{\"o}rdis and Ramming, Anna and Kolbe, Benjamin and Vi, Song Lang and Bispo, Cl{\´a}udia and Becker, J{\"o}rg D. and de Moor, Cornelia and Lenhard, Michael}, title = {Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-96400}, pages = {1 -- 30}, year = {2015}, abstract = {The poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.}, language = {en} } @article{KappelTrostCzesnicketal.2015, author = {Kappel, Christian and Trost, Gerda and Czesnick, Hj{\"o}rdis and Ramming, Anna and Kolbe, Benjamin and Vi, Son Lang and Bispo, Cl{\´a}udia and Becker, J{\"o}rg D. and de Moor, Cornelia and Lenhard, Michael}, title = {Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana}, series = {PLoS Genetics : a peer-reviewed, open-access journal}, volume = {11}, journal = {PLoS Genetics : a peer-reviewed, open-access journal}, number = {8}, publisher = {Public Library of Science}, address = {San Francisco}, issn = {1553-7390}, doi = {10.1371/journal.pgen.1005474}, pages = {30}, year = {2015}, abstract = {The poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.}, language = {en} } @phdthesis{Sakschewski2015, author = {Sakschewski, Boris}, title = {Impacts of major anthropogenic pressures on the terrestrial biosphere and its resilience to global change}, school = {Universit{\"a}t Potsdam}, pages = {159}, year = {2015}, language = {en} } @article{MuinodeBruijnPajoroetal.2015, author = {Mui{\~n}o, Jose M. and de Bruijn, Suzanne and Pajoro, Alice and Geuten, Koen and Vingron, Martin and Angenent, Gerco C. and Kaufmann, Kerstin}, title = {Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor}, series = {Molecular biology and evolution : MBE}, volume = {33}, journal = {Molecular biology and evolution : MBE}, number = {1}, publisher = {Oxford University Press}, address = {Oxford}, issn = {1537-1719}, doi = {10.1093/molbev/msv210}, year = {2015}, abstract = {lower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon.}, language = {en} } @masterthesis{Kreibich2015, type = {Bachelor Thesis}, author = {Kreibich, Christoph}, title = {Erucas{\"a}ure in Brassica napus L. - ein ph{\"a}notypisches Merkmal im Genetikunterricht und ihr Nachweis mit Hilfe von Papierchromatographie}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93341}, school = {Universit{\"a}t Potsdam}, pages = {II, 35}, year = {2015}, abstract = {Erucic acid is a mono-unsaturated fatty acid that is naturally found in large quantities in seeds of rapeseed (Brassica napus L.) and other Brassica species. Erucic acid represents an important resource in the industry, however, due to its injurious effects on the heart muscle, this fatty acid is considered to be nutritionally harmful. Therefore, new high quality rapeseed cultivars were bred in order to eliminate the content of erucic acid in rapeseed oil at the end of the 20th century. In the breeding process, paper chromatography was used for the distinction between seeds with high and low content of erucic acid. Here, this outdated method was revised and optimized for educational purposes. By means of paper chromatography the qualitative content of erucic acid and four other unsaturated fatty acids was analyzed in rapeseed and linseed. The character 'erucic acid content', determined by two additive genes, can be used as a practical example of a phenotypic marker in school lessons, for instance, in the course 'achievement of plant breeding'. Thus, this qualitative analysis of erucic acid content enables the teacher to connect classical genetics with modern methods of plant genetics.}, language = {de} } @misc{SicardKappelJosephsetal.2015, author = {Sicard, Adrien and Kappel, Christian and Josephs, Emily B. and Wha Lee, Young and Marona, Cindy and Stinchcombe, John R. and Wright, Stephen I. and Lenhard, Michael}, title = {Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93568}, year = {2015}, abstract = {In the Bateson-Dobzhansky-Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles.}, language = {en} } @article{SicardKappelJosephsetal.2015, author = {Sicard, Adrien and Kappel, Christian and Josephs, Emily B. and Wha Lee, Young and Marona, Cindy and Stinchcombe, John R. and Wright, Stephen I. and Lenhard, Michael}, title = {Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella}, series = {Nature Communications}, volume = {6}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms8960}, year = {2015}, abstract = {In the Bateson-Dobzhansky-Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles.}, language = {en} } @misc{ValentePhillimoreEtienne2015, author = {Valente, Luis M. and Phillimore, Albert B. and Etienne, Rampal S.}, title = {Equilibrium and non-equilibrium dynamics simultaneously operate in the Gal{\´a}pagos islands}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93525}, pages = {9}, year = {2015}, abstract = {Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Gal{\´a}pagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Gal{\´a}pagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent-like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non-equilibrium and equilibrium ecological paradigms.}, language = {en} } @article{ValentePhillimoreEtienne2015, author = {Valente, Luis M. and Phillimore, Albert B. and Etienne, Rampal S.}, title = {Equilibrium and non-equilibrium dynamics simultaneously operate in the Gal{\´a}pagos islands}, series = {Ecology letters}, volume = {18}, journal = {Ecology letters}, publisher = {Wiley-Blackwell}, address = {Oxford}, issn = {1461-0248}, doi = {10.1111/ele.12461}, pages = {844 -- 852}, year = {2015}, abstract = {Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Gal{\´a}pagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Gal{\´a}pagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent-like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non-equilibrium and equilibrium ecological paradigms.}, language = {en} } @phdthesis{Laemke2015, author = {L{\"a}mke, J{\"o}rn}, title = {Determining the future in the past}, school = {Universit{\"a}t Potsdam}, pages = {149}, year = {2015}, language = {en} } @phdthesis{Balazadeh2015, author = {Balazadeh, Salma}, title = {New insights into the molecular mechanisms of leaf senescence}, school = {Universit{\"a}t Potsdam}, year = {2015}, language = {en} } @article{Steup2015, author = {Steup, Martin}, title = {Raum und Zahl in der Pflanzenphysiologie}, series = {Raum und Zahl}, journal = {Raum und Zahl}, publisher = {Trafo}, address = {Berlin}, isbn = {978-3-86464-082-7}, pages = {77 -- 109}, year = {2015}, language = {de} } @phdthesis{Paijmans2015, author = {Paijmans, Johanna L. A.}, title = {Application of hybridisation capture to investigate complete mitogenomes from ancient samples}, school = {Universit{\"a}t Potsdam}, pages = {207}, year = {2015}, language = {en} } @phdthesis{Liebrich2015, author = {Liebrich, Marietta}, title = {Einfluss von Prozessoptimierungen auf die mikrobielle Diversit{\"a}t und die Effizienz der Gasbildung in Co-Verg{\"a}rungsanlagen der Abfallwirtschaft}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-91066}, school = {Universit{\"a}t Potsdam}, pages = {VII, 102}, year = {2015}, abstract = {Im Hinblick auf die Problematik der Umweltverschmutzung durch die Nutzung fossiler Brennstoffe ist es n{\"o}tig, eine langfristig stabile und umweltfreundliche Energieversorgung zu gew{\"a}hrleisten. Eine M{\"o}glichkeit, den Energiebedarf CO2-neutral zu decken, ist die Nutzung von Biogas. Hierbei spielt der Einsatz von biogenen Reststoffen, die durch einen hohen Anteil an Kohlenhydraten, Fetten und Proteinen gekennzeichnet sind und daher ein hohes Biogaspotential besitzen, eine wichtige Rolle. Voraussetzung f{\"u}r die Effizienz und Rentabilit{\"a}t solcher Anlagen ist u. a. ein stabiler Gasbildungsprozess. Da bisher noch nicht alle Aspekte der Biogasbildung vollst{\"a}ndig verstanden sind, werden die Anlagen oft nicht optimal ausgelastet, um Prozessst{\"o}rungen wie z. B. {\"U}bers{\"a}uerung zu vermeiden. Um dennoch auftretende Prozessst{\"o}rungen zu beheben, k{\"o}nnen unterschiedliche Maßnahmen durchgef{\"u}hrt werden. Neben der Senkung der Raumbelastung, ist es m{\"o}glich, den pH-Wert durch die Zugabe von Natronlauge oder Calciumoxid anzuheben. In der vorliegenden Arbeit wurden sowohl Prozessst{\"o}rungen als auch Prozessregenerierungen an einer großtechnischen Biogasanlage und in Laborversuchen untersucht. Dabei galt es, neben den physikalischen und chemischen Parametern, die mikrobielle Bioz{\"o}nose mit Hilfe des genetischen Fingerprintings zu charakterisieren und {\"A}nderungen zu detektieren. W{\"a}hrend der Prozessregenerierungen wurden nach der Zugabe von CaO Ver{\"a}nderungen des G{\"a}rrestes beobachtet. Es bildeten sich Pellets, die im Hinblick auf ihre Funktion f{\"u}r die Prozessregenerierung und die Prozessstabilit{\"a}t molekularbiologisch und mikroskopisch untersucht wurden. Es wurde weiterhin der Frage nachgegangen, welche Rolle die Mikroorganismen bei der Entstehung der Pellets spielen. Die vor allem aus Calcium und Fetts{\"a}uren bestehenden Pellets dienten als Aufwuchsfl{\"a}chen f{\"u}r verschiedene Mikroorganismen. Die Bildung von Biofilmen, wie sie auf und in den Pellets nachgewiesen wurde, bot f{\"u}r Mikroorganismen einen Schutz vor negativen Umwelteinfl{\"u}ssen wie z. B. hohe Propions{\"a}urekonzentrationen. Unter diesen g{\"u}nstigen Bedingungen war die Bildung von Biogas auch unter hohen Wasserstoffpartialdr{\"u}cken, die den Abbau von Propions{\"a}ure hemmten, m{\"o}glich. Als Indikator f{\"u}r bessere Lebensbedingungen wurde im Laborversuch ein Methanoculleus receptaculi-verwandter Organismus identifiziert. Dieses methanogene Archaeon wurde im Pellet nachgewiesen, w{\"a}hrend es im G{\"a}rrest erst nach der Prozessregenerierung detektiert wurde. Der Nachweis eines im Vergleich zum umgebenden G{\"a}rrest h{\"o}heren Anteils an Archaeen im Kern der Pellets sowie von Biofilmen/EPS, verschiedenen Phosphatsalzen und schwerl{\"o}slichen Calciumsalzen zeigte, dass sowohl Pr{\"a}zipitation und Adsorption als auch Degradation von LCFA dazu f{\"u}hren, dass deren Konzentration im fl{\"u}ssigen G{\"a}rrest gesenkt wird. Dadurch nimmt die Hemmung auf die Bioz{\"o}nose ab und die Biogasbildungsrate steigt. Daher ist der Abbau der Fetts{\"a}uren auch bei einem niedrigen pH-Wert und unter hohen Wasserstoffpartialdr{\"u}cken m{\"o}glich und der Biogasbildungsprozess ist langfristig stabil. Die Bildung von Pellets unterst{\"u}tzt die Prozessstabilit{\"a}t, sofern diese nicht zu groß werden und dann u. a. die Durchmischung behindern und den Ablauf verstopfen. Nach erfolgreicher Prozessstabilisierung wurden keine Pellets im G{\"a}rrest beobachtet. Der Abbau des organischen Materials wurde sowohl durch die steigende Calciumkonzentration als auch die steigende Gasproduktion angezeigt.}, language = {de} } @phdthesis{Balk2015, author = {Balk, Maria}, title = {3D structured shape-memory hydrogels with enzymatically-induced shape shifting}, school = {Universit{\"a}t Potsdam}, pages = {128}, year = {2015}, language = {en} } @phdthesis{Apelt2015, author = {Apelt, Federico}, title = {Implementation of an imaging-based approach using a 3D light-field camera to analyse plant growth behaviour}, school = {Universit{\"a}t Potsdam}, pages = {227}, year = {2015}, language = {en} } @phdthesis{Ploetner2015, author = {Pl{\"o}tner, Bj{\"o}rn}, title = {F2 hybrid chlorosis in a cross between the Arabidopsis thaliana accessions Shahdara and Lovvik-5}, school = {Universit{\"a}t Potsdam}, pages = {99}, year = {2015}, language = {en} } @phdthesis{Olszewska2015, author = {Olszewska, Agata}, title = {Forming magnetic chain with the help of biological organisms}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-89767}, school = {Universit{\"a}t Potsdam}, pages = {101}, year = {2015}, abstract = {Magnetite nanoparticles and their assembly comprise a new area of development for new technologies. The magnetic particles can interact and assemble in chains or networks. Magnetotactic bacteria are one of the most interesting microorganisms, in which the assembly of nanoparticles occurs. These microorganisms are a heterogeneous group of gram negative prokaryotes, which all show the production of special magnetic organelles called magnetosomes, consisting of a magnetic nanoparticle, either magnetite (Fe3O4) or greigite (Fe3S4), embedded in a membrane. The chain is assembled along an actin-like scaffold made of MamK protein, which makes the magnetosomes to arrange in mechanically stable chains. The chains work as a compass needle in order to allow cells to orient and swim along the magnetic field of the Earth. The formation of magnetosomes is known to be controlled at the molecular level. The physico-chemical conditions of the surrounding environment also influence biomineralization. The work presented in this manuscript aims to understand how such external conditions, in particular the extracellular oxidation reduction potential (ORP) influence magnetite formation in the strain Magnetospirillum magneticum AMB-1. A controlled cultivation of the microorganism was developed in a bioreactor and the formation of magnetosomes was characterized. Different techniques have been applied in order to characterize the amount of iron taken up by the bacteria and in consequence the size of magnetosomes produced at different ORP conditions. By comparison of iron uptake, morphology of bacteria, size and amount of magnetosomes per cell at different ORP, the formation of magnetosomes was inhibited at ORP 0 mV, whereas reduced conditions, ORP - 500 mV facilitate biomineralization process. Self-assembly of magnetosomes occurring in magnetotactic bacteria became an inspiration to learn from nature and to construct nanoparticles assemblies by using the bacteriophage M13 as a template. The M13 bacteriophage is an 800 nm long filament with encapsulated single-stranded DNA that has been recently used as a scaffold for nanoparticle assembly. I constructed two types of assemblies based on bacteriophages and magnetic nanoparticles. A chain - like assembly was first formed where magnetite nanoparticles are attached along the phage filament. A sperm - like construct was also built with a magnetic head and a tail formed by phage filament. The controlled assembly of magnetite nanoparticles on the phage template was possible due to two different mechanism of nanoparticle assembly. The first one was based on the electrostatic interactions between positively charged polyethylenimine coated magnetite nanoparticles and negatively charged phages. The second phage -nanoparticle assembly was achieved by bioengineered recognition sites. A mCherry protein is displayed on the phage and is was used as a linker to a red binding nanobody (RBP) that is fused to the one of the proteins surrounding the magnetite crystal of a magnetosome. Both assemblies were actuated in water by an external magnetic field showing their swimming behavior and potentially enabling further usage of such structures for medical applications. The speed of the phage - nanoparticles assemblies are relatively slow when compared to those of microswimmers previously published. However, only the largest phage-magnetite assemblies could be imaged and it is therefore still unclear how fast these structures can be in their smaller version.}, language = {en} } @phdthesis{Quast2015, author = {Quast, Robert B.}, title = {Synthesis and site-directed modification of membrane proteins using non-canonical amino acids in a cell-free system derived from cultured Spodoptera frugiperda cells}, school = {Universit{\"a}t Potsdam}, pages = {87}, year = {2015}, language = {en} } @phdthesis{Lischke2015, author = {Lischke, Betty}, title = {Food web regulation under different forcing regimes in shallow lakes}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-89149}, school = {Universit{\"a}t Potsdam}, pages = {131}, year = {2015}, abstract = {The standing stock and production of organismal biomass depends strongly on the organisms' biotic environment, which arises from trophic and non-trophic interactions among them. The trophic interactions between the different groups of organisms form the food web of an ecosystem, with the autotrophic and bacterial production at the basis and potentially several levels of consumers on top of the producers. Feeding interactions can regulate communities either by severe grazing pressure or by shortage of resources or prey production, termed top-down and bottom-up control, respectively. The limitations of all communities conglomerate in the food web regulation, which is subject to abiotic and biotic forcing regimes arising from external and internal constraints. This dissertation presents the effects of alterations in two abiotic, external forcing regimes, terrestrial matter input and long-lasting low temperatures in winter. Diverse methodological approaches, a complex ecosystem model study and the analysis of two whole-lake measurements, were performed to investigate effects for the food web regulation and the resulting consequences at the species, community and ecosystem scale. Thus, all types of organisms, autotrophs and heterotrophs, at all trophic levels were investigated to gain a comprehensive overview of the effects of the two mentioned altered forcing regimes. In addition, an extensive evaluation of the trophic interactions and resulting carbon fluxes along the pelagic and benthic food web was performed to display the efficiencies of the trophic energy transfer within the food webs. All studies were conducted in shallow lakes, which is worldwide the most abundant type of lakes. The specific morphology of shallow lakes allows that the benthic production contributes substantially to the whole-lake production. Further, as shallow lakes are often small they are especially sensitive to both, changes in the input of terrestrial organic matter and the atmospheric temperature. Another characteristic of shallow lakes is their appearance in alternative stable states. They are either in a clear-water or turbid state, where macrophytes and phytoplankton dominate, respectively. Both states can stabilize themselves through various mechanisms. These two alternative states and stabilizing mechanisms are integrated in the complex ecosystem model PCLake, which was used to investigate the effects of the enhanced terrestrial particulate organic matter (t-POM) input to lakes. The food web regulation was altered by three distinct pathways: (1) Zoobenthos received more food, increased in biomass which favored benthivorous fish and those reduced the available light due to bioturbation. (2) Zooplankton substituted autochthonous organic matter in their diet by suspended t-POM, thus the autochthonous organic matter remaining in the water reduced its transparency. (3) T-POM suspended into the water and reduced directly the available light. As macrophytes are more light-sensitive than phytoplankton they suffered the most from the lower transparency. Consequently, the resilience of the clear-water state was reduced by enhanced t-POM inputs, which makes the turbid state more likely at a given nutrient concentration. In two subsequent winters long-lasting low temperatures and a concurrent long duration of ice coverage was observed which resulted in low overall adult fish biomasses in the two study lakes - Schulzensee and Gollinsee, characterized by having and not having submerged macrophytes, respectively. Before the partial winterkill of fish Schulzensee allowed for a higher proportion of piscivorous fish than Gollinsee. However, the partial winterkill of fish aligned both communities as piscivorous fish are more sensitive to low oxygen concentrations. Young of the year fish benefitted extremely from the absence of adult fish due to lower predation pressure. Therefore, they could exert a strong top-down control on crustaceans, which restructured the entire zooplankton community leading to low crustacean biomasses and a community composition characterized by copepodites and nauplii. As a result, ciliates were released from top-down control, increased to high biomasses compared to lakes of various trophic states and depths and dominated the zooplankton community. While being very abundant in the study lakes and having the highest weight specific grazing rates among the zooplankton, ciliates exerted potentially a strong top-down control on small phytoplankton and particle-attached bacteria. This resulted in a higher proportion of large phytoplankton compared to other lakes. Additionally, the phytoplankton community was evenly distributed presumably due to the numerous fast growing and highly specific ciliate grazers. Although, the pelagic food web was completely restructured after the subsequent partial winterkills of fish, both lakes were resistant to effects of this forcing regime at the ecosystem scale. The consistently high predation pressure on phytoplankton prevented that Schulzensee switched from the clear-water to the turbid state. Further mechanisms, which potentially stabilized the clear-water state, were allelopathic effects by macrophytes and nutrient limitation in summer. The pelagic autotrophic and bacterial production was an order of magnitude more efficient transferred to animal consumers than the respective benthic production, despite the alterations of the food web structure after the partial winterkill of fish. Thus, the compiled mass-balanced whole-lake food webs suggested that the benthic bacterial and autotrophic production, which exceeded those of the pelagic habitat, was not used by animal consumers. This holds even true if the food quality, additional consumers such as ciliates, benthic protozoa and meiobenthos, the pelagic-benthic link and the potential oxygen limitation of macrobenthos were considered. Therefore, low benthic efficiencies suggest that lakes are primarily pelagic systems at least at the animal consumer level. Overall, this dissertation gives insights into the regulation of organism groups in the pelagic and benthic habitat at each trophic level under two different forcing regimes and displays the efficiency of the carbon transfer in both habitats. The results underline that the alterations of external forcing regimes affect all hierarchical level including the ecosystem.}, language = {en} }