@phdthesis{Kloss2016, author = {Kloß, Lena}, title = {The link between genetic diversity and species diversity}, school = {Universit{\"a}t Potsdam}, pages = {109}, year = {2016}, language = {en} } @phdthesis{Hoffmann2016, author = {Hoffmann, Stefan}, title = {In vivo Selection of Switchable DNA-Binding Proteins}, school = {Universit{\"a}t Potsdam}, pages = {97}, year = {2016}, language = {en} } @phdthesis{Zhang2016, author = {Zhang, Youjun}, title = {Investigation of the TCA cycle and glycolytic metabolons and their physiological impacts in plants}, school = {Universit{\"a}t Potsdam}, pages = {175}, year = {2016}, language = {en} } @phdthesis{Loewenberg2016, author = {L{\"o}wenberg, Candy}, title = {Shape-memory effect of gelatin-based hydrogels}, school = {Universit{\"a}t Potsdam}, pages = {122}, year = {2016}, language = {en} } @phdthesis{Klauschies2016, author = {Klauschies, Toni}, title = {Revealing causes and consequences of functional diversity using trait-based models}, school = {Universit{\"a}t Potsdam}, pages = {231}, year = {2016}, language = {en} } @phdthesis{Stief2016, author = {Stief, Anna}, title = {Genetics and ecology of plant heat stress memory}, school = {Universit{\"a}t Potsdam}, pages = {175}, year = {2016}, language = {en} } @phdthesis{Beltran2016, author = {Beltran, Juan Camilo Moreno}, title = {Characterization of the Clp protease complex and identification of putative substrates in N. tabacum}, school = {Universit{\"a}t Potsdam}, year = {2016}, language = {en} } @article{ZhuSchluppTiedemann2016, author = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph}, title = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, number = {6}, publisher = {PLoS}, address = {Lawrence, Kan.}, issn = {1932-6203}, doi = {10.1371/JOURNAL.PONE.0156209}, pages = {19}, year = {2016}, abstract = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.}, language = {en} } @article{BatsiosRenBaumannetal.2016, author = {Batsios, Petros and Ren, Xiang and Baumann, Otto and Larochelle, Denis A. and Gr{\"a}f, Ralph}, title = {Src1 is a Protein of the Inner Nuclear Membrane Interacting with the Dictyostelium Lamin NE81}, series = {Cells}, volume = {5}, journal = {Cells}, number = {1}, publisher = {MDPI}, address = {Basel}, issn = {2073-4409}, doi = {10.3390/cells5010013}, year = {2016}, abstract = {The nuclear envelope (NE) consists of the outer and inner nuclear membrane (INM), whereby the latter is bound to the nuclear lamina. Src1 is a Dictyostelium homologue of the helix-extension-helix family of proteins, which also includes the human lamin-binding protein MAN1. Both endogenous Src1 and GFP-Src1 are localized to the NE during the entire cell cycle. Immuno-electron microscopy and light microscopy after differential detergent treatment indicated that Src1 resides in the INM. FRAP experiments with GFP-Src1 cells suggested that at least a fraction of the protein could be stably engaged in forming the nuclear lamina together with the Dictyostelium lamin NE81. Both a BioID proximity assay and mis-localization of soluble, truncated mRFP-Src1 at cytosolic clusters consisting of an intentionally mis-localized mutant of GFP-NE81 confirmed an interaction of Src1 and NE81. Expression GFP-Src11-646, a fragment C-terminally truncated after the first transmembrane domain, disrupted interaction of nuclear membranes with the nuclear lamina, as cells formed protrusions of the NE that were dependent on cytoskeletal pulling forces. Protrusions were dependent on intact microtubules but not actin filaments. Our results indicate that Src1 is required for integrity of the NE and highlight Dictyostelium as a promising model for the evolution of nuclear architecture.}, 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} } @phdthesis{Orf2016, author = {Orf, Isabel}, title = {Photorespiratory metabolism in the cyanobacterial model Synechocystis sp. strain PCC 6803}, school = {Universit{\"a}t Potsdam}, pages = {90}, year = {2016}, 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{Reinecke2016, author = {Reinecke, Antje Adriana}, title = {Impact of protein structure on the mechanics and assembly of mytilus byssal threads}, school = {Universit{\"a}t Potsdam}, pages = {101}, year = {2016}, 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} } @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} } @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{ShahnejatBushehri2016, author = {Shahnejat-Bushehri, Sara}, title = {Unravelling the role of the Arabidopsis NAC transcription factor JUNGBRUNNEN1 (JUB1) for the regulation of growth and stress responses}, school = {Universit{\"a}t Potsdam}, pages = {155}, year = {2016}, 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} } @article{KlauschiesVasseurGaedke2016, author = {Klauschies, Toni and Vasseur, David A. and Gaedke, Ursula}, title = {Trait adaptation promotes species coexistence in diverse predator and prey communities}, series = {Ecology and evolution}, journal = {Ecology and evolution}, publisher = {John Wiley \& Sons, Inc.}, issn = {2045-7758}, doi = {10.1002/ece3.2172}, pages = {19}, year = {2016}, abstract = {Species can adjust their traits in response to selection which may strongly influence species coexistence. Nevertheless, current theory mainly assumes distinct and time-invariant trait values. We examined the combined effects of the range and the speed of trait adaptation on species coexistence using an innovative multispecies predator-prey model. It allows for temporal trait changes of all predator and prey species and thus simultaneous coadaptation within and among trophic levels. We show that very small or slow trait adaptation did not facilitate coexistence because the stabilizing niche differences were not sufficient to offset the fitness differences. In contrast, sufficiently large and fast trait adaptation jointly promoted stable or neutrally stable species coexistence. Continuous trait adjustments in response to selection enabled a temporally variable convergence and divergence of species traits; that is, species became temporally more similar (neutral theory) or dissimilar (niche theory) depending on the selection pressure, resulting over time in a balance between niche differences stabilizing coexistence and fitness differences promoting competitive exclusion. Furthermore, coadaptation allowed prey and predator species to cluster into different functional groups. This equalized the fitness of similar species while maintaining sufficient niche differences among functionally different species delaying or preventing competitive exclusion. In contrast to pre- vious studies, the emergent feedback between biomass and trait dynamics enabled supersaturated coexistence for a broad range of potential trait adaptation and parameters. We conclude that accounting for trait adaptation may explain stable and supersaturated species coexistence for a broad range of environmental conditions in natural systems when the absence of such adaptive changes would preclude it. Small trait changes, coincident with those that may occur within many natural populations, greatly enlarged the number of coexisting species.}, language = {en} } @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{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{Bartholomaeus2016, author = {Bartholom{\"a}us, Alexander}, title = {Analyzing Transcriptional and Translational Control in E. coli using Deep-Seq Data}, school = {Universit{\"a}t Potsdam}, pages = {179}, year = {2016}, 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} } @article{YanChenKaufmann2016, author = {Yan, Wenhao and Chen, Dijun and Kaufmann, Kerstin}, title = {Efficient multiplex mutagenesis by RNA-guided Cas9 and its use in the characterization of regulatory elements in the AGAMOUS gene}, series = {Plant methods}, volume = {12}, journal = {Plant methods}, publisher = {BioMed Central}, address = {London}, issn = {1746-4811}, doi = {10.1186/s13007-016-0125-7}, pages = {1 -- 9}, year = {2016}, abstract = {Background The efficiency of multiplex editing in plants by the RNA-guided Cas9 system is limited by efficient introduction of its components into the genome and by their activity. The possibility of introducing large fragment deletions by RNA-guided Cas9 tool provides the potential to study the function of any DNA region of interest in its 'endogenous' environment. Results Here, an RNA-guided Cas9 system was optimized to enable efficient multiplex editing in Arabidopsis thaliana. We demonstrate the flexibility of our system for knockout of multiple genes, and to generate heritable large-fragment deletions in the genome. As a proof of concept, the function of part of the second intron of the flower development gene AGAMOUS in Arabidopsis was studied by generating a Cas9-free mutant plant line in which part of this intron was removed from the genome. Further analysis revealed that deletion of this intron fragment results 40 \% decrease of AGAMOUS gene expression without changing the splicing of the gene which indicates that this regulatory region functions as an activator of AGAMOUS gene expression. Conclusions Our modified RNA-guided Cas9 system offers a versatile tool for the functional dissection of coding and non-coding DNA sequences in plants.}, 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} } @article{WackerPiephoHarwoodetal.2016, author = {Wacker, Alexander and Piepho, Maike and Harwood, John L. and Guschina, Irina A. and Arts, Michael T.}, title = {Light-Induced Changes in Fatty Acid Profiles of Specific Lipid Classes in Several Freshwater Phytoplankton Species}, series = {Frontiers in plant science : FPLS}, volume = {7}, journal = {Frontiers in plant science : FPLS}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2016.00264}, pages = {1 -- 13}, year = {2016}, abstract = {We tested the influence of two light intensities [40 and 300 μmol PAR / (m2s)] on the fatty acid composition of three distinct lipid classes in four freshwater phytoplankton species. We chose species of different taxonomic classes in order to detect potentially similar reaction characteristics that might also be present in natural phytoplankton communities. From samples of the bacillariophyte Asterionella formosa, the chrysophyte Chromulina sp., the cryptophyte Cryptomonas ovata and the zygnematophyte Cosmarium botrytis we first separated glycolipids (monogalactosyldiacylglycerol, digalactosyldiacylglycerol, and sulfoquinovosyldiacylglycerol), phospholipids (phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and phosphatidylserine) as well as non-polar lipids (triacylglycerols), before analyzing the fatty acid composition of each lipid class. High variation in the fatty acid composition existed among different species. Individual fatty acid compositions differed in their reaction to changing light intensities in the four species. Although no generalizations could be made for species across taxonomic classes, individual species showed clear but small responses in their ecologically-relevant omega-3 and omega-6 polyunsaturated fatty acids (PUFA) in terms of proportions and of per tissue carbon quotas. Knowledge on how lipids like fatty acids change with environmental or culture conditions is of great interest in ecological food web studies, aquaculture, and biotechnology, since algal lipids are the most important sources of omega-3 long-chain PUFA for aquatic and terrestrial consumers, including humans.}, 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{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{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} } @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{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} } @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} } @phdthesis{Krishnamoorthy2015, author = {Krishnamoorthy, Praveen}, title = {Regulatory roles of Ptdlns(4,5)P2 in trafficking of the cellulose synthase complex and identification of distinct plasma membrane localisation patterns of Arabidopsis PiP5-kinases}, school = {Universit{\"a}t Potsdam}, pages = {133}, year = {2015}, language = {en} } @phdthesis{Pfestorf2015, author = {Pfestorf, Hans}, title = {Land use intensity and insect root herbivores}, school = {Universit{\"a}t Potsdam}, pages = {161}, year = {2015}, language = {en} } @phdthesis{Lieske2015, author = {Lieske, Stefanie}, title = {Regulaton des mIndy-Gens durch Interleukin-6, Oncostatin M und Glucagon und die physiologischen Konsequenzen im Lipidstoffwechsel prim{\"a}rer Hepatozyten}, school = {Universit{\"a}t Potsdam}, pages = {178}, year = {2015}, language = {de} } @phdthesis{Zupok2015, author = {Zupok, Arkadiusz}, title = {The psbB-operon is a major locus for plastome-genome incompatibility in Oenothera}, school = {Universit{\"a}t Potsdam}, pages = {108}, year = {2015}, language = {en} }