@unpublished{MuellerRoeber2015,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}
}
@phdthesis{Liput2015,
  author    = {Liput, Magdalena},
  title     = {Investigation of the biogenesis and use of ribosomes in Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {158},
  year      = {2015},
  language  = {en}
}
@phdthesis{Borschewski2015,
  author    = {Borschewski, Aljona},
  title     = {Bedeutung der Interaktion von Calcineurin und SORLA f{\"u}r die Regulation des Na⁺,K⁺,2Cl⁻-Kotransporters (NKCC2) in der Niere},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-89205},
  school      = {Universit{\"a}t Potsdam},
  pages     = {II, 86},
  year      = {2015},
  abstract  = {Der Na⁺-K⁺-2Cl⁻-Kotransporter (NKCC2) wird im distalen Nephron der Niere exprimiert. Seine Verteilung umfasst die Epithelien der medull{\"a}ren und kortikalen Teile der dicken aufsteigenden Henle-Schleife (Thick ascending limb, TAL) und die Macula densa. Resorptiver NaCl-Transport {\"u}ber den NKCC2 dient dem renalen Konzentrierungsmechanismus und reguliert systemisch auch Volumenstatus und Blutdruck. Die Aktivit{\"a}t des NKCC2 ist mit der Phosphorylierung seiner N-terminalen Aminos{\"a}urereste Serin 126 und Threonin 96/101 verbunden. Vermittelt wird diese durch die homologen Kinasen SPAK (SPS-related proline/alanine-rich kinase) und OSR1 (Oxidative stress responsive kinase 1), die hierzu ihrerseits phosphoryliert werden m{\"u}ssen. Der regulatorische Kontext dieser Kinasen ist mittlerweile gut charakterisiert. {\"U}ber Mechanismen und Produkte, die den NKCC2 deaktivieren, war hingegen weniger bekannt. Ziel der Arbeit war daher zu untersuchen, welche Wege zur Deaktivierung des Transporters f{\"u}hren. Der intrazellul{\"a}re Sortierungsrezeptor SORLA (Sorting-protein-related receptor with A-type repeats) war zuvor in seiner Bedeutung f{\"u}r das Nephron charakterisiert worden. Ein SORLA-defizientes Mausmodell weist unter anderem eine stark verringerte NKCC2-Phosphorylierung auf. Unter osmotischem Stress k{\"o}nnen SORLA-defiziente M{\"a}use ihren Urin weniger effizient konzentrieren. Meine Resultate zeigen mit hochaufl{\"o}sender Technik, dass SORLA apikal im TAL lokalisiert ist und dass mit NKCC2 eine anteilige Kolokalisation besteht. Unter SORLA Defizienz war die f{\"u}r die NKCC2 Aktivit{\"a}t maßgebliche SPAK/OSR1-Phosphorylierung gegen{\"u}ber dem Wildtyp nicht ver{\"a}ndert. Jedoch war die ebenfalls im TAL exprimierte Phosphatase Calcineurin Aβ (CnAβ) per Western blot um das zweifache gesteigert. Parallel hierzu wurde immunhistochemisch die Kolokalisation von verst{\"a}rktem CnAβ-Signal und NKCC2 best{\"a}tigt. Beide Befunde geben zusammen den Hinweis auf einen Bezug zwischen der reduzierten NKCC2-Phosphorylierung und der gesteigerten Pr{\"a}senz von CnAβ bei SORLA Defizienz. Die parallel induzierte {\"U}berexpression von SORLA in HEK-Zellen zeigte entsprechend eine Halbierung der CnAβ Proteinmenge. SORLA steuert demzufolge sowohl die Abundanz als auch die zellul{\"a}re Verteilung der Phosphatase. Weiterhin ließ sich die Interaktion zwischen CnAβ und SORLA (intrazellul{\"a}re Dom{\"a}ne) mittels Co-Immunpr{\"a}zipitation bzw. GST-pulldown assay nachweisen. Auch die Interaktion zwischen CnAβ und NKCC2 wurde auf diesem Weg belegt. Da allerdings weder SORLA noch NKCC2 ein spezifisches Bindungsmuster f{\"u}r CnAβ aufweisen, sind vermutlich intermedi{\"a}re Adapterproteine bei ihrer Bindung involviert. Die pharmakologische Inhibition von CnAβ mittels Cyclosporin A (CsA; 1 h) f{\"u}hrte bei SORLA Defizienz zur Normalisierung der NKCC2-Phosphorylierung. Entsprechend f{\"u}hrte in vitro die Gabe von CsA bei TAL Zellen zu einer 7-fach gesteigerten NKCC2-Phosphorylierung. Zusammenfassend zeigen die Ergebnisse, dass die Phosphatase CnAβ {\"u}ber ihre Assoziation mit NKCC2 diesen im adluminalen Zellkompartiment deaktivieren kann. Gesteuert wird dieser Vorgang durch die Eigenschaft von SORLA, CnAβ apikal zu reduzieren und damit die adluminale Phosphorylierung und Aktivit{\"a}t von NKCC2 zu unterst{\"u}tzen. Da Calcineurin-Inhibitoren derzeit die Grundlage der immunsupprimierenden Therapie darstellen, haben die Ergebnisse eine klinische Relevanz. Angesichts der Co-Expression von SORLA und CnAβ in verschiedenen anderen Organen k{\"o}nnen die Ergebnisse auch {\"u}ber die Niere hinaus Bedeutung erlangen.},
  language  = {de}
}
@phdthesis{Fuenfgeld2015,
  author    = {F{\"u}nfgeld, Maximilian},
  title     = {Compartmentation of adenine nucleotide metabolism},
  school      = {Universit{\"a}t Potsdam},
  pages     = {113},
  year      = {2015},
  language  = {en}
}
@phdthesis{Herde2015,
  author    = {Herde, Antje},
  title     = {Individual differences and seasonal variation in behaviour},
  school      = {Universit{\"a}t Potsdam},
  pages     = {111},
  year      = {2015},
  language  = {en}
}
@phdthesis{Arabi2015,
  author    = {Arabi, Fayezeh},
  title     = {Functional characterization of Sulfur Deficiency Induced genes, SDI1 and SDI2, in Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {97},
  year      = {2015},
  language  = {en}
}
@misc{LamannaKirschbaumWauricketal.2015,
  author    = {Lamanna, Francesco and Kirschbaum, Frank and Waurick, Isabelle and Dieterich, Christoph and Tiedemann, Ralph},
  title     = {Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae)},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-86997},
  year      = {2015},
  abstract  = {Background African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C.tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ's transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO.},
  language  = {en}
}
@phdthesis{Kabelitz2015,
  author    = {Kabelitz, Tina},
  title     = {Natural and induced variation in the silencing of a Mutator-like transposon from Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {188},
  year      = {2015},
  language  = {en}
}
@phdthesis{Olas2015,
  author    = {Olas, Justyna Jadwiga},
  title     = {Nutrients regulate flowering time},
  school      = {Universit{\"a}t Potsdam},
  pages     = {190},
  year      = {2015},
  language  = {en}
}
@phdthesis{Menke2015,
  author    = {Menke, Sebastian},
  title     = {Investigating the impact of intrinsic and extrinsic factors on gut bacterial communities in Namibian wildlife species using a large-scale next-generation sequencing approach},
  school      = {Universit{\"a}t Potsdam},
  pages     = {109},
  year      = {2015},
  language  = {en}
}
@article{LamannaKirschbaumWauricketal.2015,
  author    = {Lamanna, Francesco and Kirschbaum, Frank and Waurick, Isabelle and Dieterich, Christoph and Tiedemann, Ralph},
  title     = {Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae)},
  series = {BMC Genomics},
  volume    = {16},
  journal   = {BMC Genomics},
  number    = {668},
  publisher = {Biomed Central},
  address   = {London},
  issn      = {1471-2164},
  doi       = {10.1186/s12864-015-1858-9},
  year      = {2015},
  abstract  = {Background African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C.tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ's transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO.},
  language  = {en}
}
@phdthesis{Lamanna2015,
  author    = {Lamanna, Francesco},
  title     = {Adaptive radiation and speciation in African weakly-electric fish},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-80097},
  school      = {Universit{\"a}t Potsdam},
  pages     = {114},
  year      = {2015},
  abstract  = {The rise of evolutionary novelties is one of the major drivers of evolutionary diversification. African weakly-electric fishes (Teleostei, Mormyridae) have undergone an outstanding adaptive radiation, putatively owing to their ability to communicate through species-specific Electric Organ Discharges (EODs) produced by a novel, muscle-derived electric organ. Indeed, such EODs might have acted as effective pre-zygotic isolation mechanisms, hence favoring ecological speciation in this group of fishes. Despite the evolutionary importance of this organ, genetic investigations regarding its origin and function have remained limited. The ultimate aim of this study is to better understand the genetic basis of EOD production by exploring the transcriptomic profiles of the electric organ and of its ancestral counterpart, the skeletal muscle, in the genus Campylomormyrus. After having established a set of reference transcriptomes using "Next-Generation Sequencing" (NGS) technologies, I performed in silico analyses of differential expression, in order to identify sets of genes that might be responsible for the functional differences observed between these two kinds of tissues. The results of such analyses indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ; ii) the metabolic activity of the electric organ might be specialized towards the production and turnover of membrane structures; iii) several ion channels are highly expressed in the electric organ in order to increase excitability, and iv) several myogenic factors might be down-regulated by transcription repressors in the EO. A secondary task of this study is to improve the genus level phylogeny of Campylomormyrus by applying new methods of inference based on the multispecies coalescent model, in order to reduce the conflict among gene trees and to reconstruct a phylogenetic tree as closest as possible to the actual species-tree. By using 1 mitochondrial and 4 nuclear markers, I was able to resolve the phylogenetic relationships among most of the currently described Campylomormyrus species. Additionally, I applied several coalescent-based species delimitation methods, in order to test the hypothesis that putatively cryptic species, which are distinguishable only from their EOD, belong to independently evolving lineages. The results of this analysis were additionally validated by investigating patterns of diversification at 16 microsatellite loci. The results suggest the presence of a new, yet undescribed species of Campylomormyrus.},
  language  = {en}
}
@phdthesis{Weits2015,
  author    = {Weits, Daniel},
  title     = {Regulation of the molecular response to low oxygen in plants},
  school      = {Universit{\"a}t Potsdam},
  pages     = {113},
  year      = {2015},
  language  = {en}
}
@phdthesis{Thieme2015,
  author    = {Thieme, Christoph J.},
  title     = {Sequence and structure determinants of microRNA maturation and the elucidation of RNA transport in plants},
  school      = {Universit{\"a}t Potsdam},
  pages     = {137},
  year      = {2015},
  language  = {en}
}
@phdthesis{Heyneke2015,
  author    = {Heyneke, Elmien},
  title     = {The role of the calcineurin B-like interacting protein kinase, CIPK14 in regulating plant nutrient metabolism},
  school      = {Universit{\"a}t Potsdam},
  pages     = {135},
  year      = {2015},
  language  = {en}
}
@phdthesis{Shivanand2015,
  author    = {Shivanand, Lathe Rahul},
  title     = {DUF1068 protein family members are involved in cell wall formation in Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {393},
  year      = {2015},
  language  = {en}
}
@misc{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},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-84432},
  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{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 = {Public Library of Science},
  address   = {Lawrence},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0141893},
  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}
}
@phdthesis{Timofeeva2015,
  author    = {Timofeeva, Nadezda},
  title     = {Effect of ions and amino-acid sequence on collagen structure},
  school      = {Universit{\"a}t Potsdam},
  pages     = {121},
  year      = {2015},
  language  = {en}
}
@phdthesis{Swiadek2015,
  author    = {Swiadek, Magdalena Agnieszka},
  title     = {Hybrid necrosis in local populations of Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {109},
  year      = {2015},
  language  = {en}
}
@phdthesis{Grune2015,
  author    = {Grune, Jana},
  title     = {Effects of a novel non-steroidal mineralocorticoid receptor antagonist on cardiac hypertrophy},
  school      = {Universit{\"a}t Potsdam},
  pages     = {98},
  year      = {2015},
  language  = {en}
}